fabio-0.1.3/0000755000175000017500000000000012233272207013357 5ustar jeromejerome00000000000000fabio-0.1.3/fabio.egg-info/0000755000175000017500000000000012233272207016131 5ustar jeromejerome00000000000000fabio-0.1.3/fabio.egg-info/SOURCES.txt0000644000175000017500000002654112233272206020024 0ustar jeromejerome00000000000000MANIFEST.in README.txt setup.py stdeb.cfg doc/Makefile doc/make.bat doc/html/.buildinfo doc/html/Changelog.html doc/html/INSTALL.html doc/html/genindex.html doc/html/getting_started.html doc/html/index.html doc/html/objects.inv doc/html/py-modindex.html doc/html/search.html doc/html/searchindex.js doc/html/_modules/index.html doc/html/_modules/fabio/GEimage.html doc/html/_modules/fabio/HiPiCimage.html doc/html/_modules/fabio/OXDimage.html doc/html/_modules/fabio/TiffIO.html doc/html/_modules/fabio/adscimage.html doc/html/_modules/fabio/binaryimage.html doc/html/_modules/fabio/bruker100image.html doc/html/_modules/fabio/brukerimage.html doc/html/_modules/fabio/cbfimage.html doc/html/_modules/fabio/compression.html doc/html/_modules/fabio/converters.html doc/html/_modules/fabio/datIO.html doc/html/_modules/fabio/dm3image.html doc/html/_modules/fabio/edfimage.html doc/html/_modules/fabio/fabioimage.html doc/html/_modules/fabio/fabioutils.html doc/html/_modules/fabio/file_series.html doc/html/_modules/fabio/fit2dmaskimage.html doc/html/_modules/fabio/fit2dspreadsheetimage.html doc/html/_modules/fabio/kcdimage.html doc/html/_modules/fabio/mar345image.html doc/html/_modules/fabio/marccdimage.html doc/html/_modules/fabio/openimage.html doc/html/_modules/fabio/pilatusimage.html doc/html/_modules/fabio/pnmimage.html doc/html/_modules/fabio/readbytestream.html doc/html/_modules/fabio/tifimage.html doc/html/_modules/fabio/xsdimage.html doc/html/_sources/Changelog.txt doc/html/_sources/INSTALL.txt doc/html/_sources/getting_started.txt doc/html/_sources/index.txt doc/html/_sources/api/fabio.txt doc/html/_sources/api/modules.txt 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epydoc/toc-fabio.dm3image-module.html epydoc/toc-fabio.edfimage-module.html epydoc/toc-fabio.fabioimage-module.html epydoc/toc-fabio.fabioutils-module.html epydoc/toc-fabio.file_series-module.html epydoc/toc-fabio.fit2dmaskimage-module.html epydoc/toc-fabio.fit2dspreadsheetimage-module.html epydoc/toc-fabio.kcdimage-module.html epydoc/toc-fabio.mar345_IO-module.html epydoc/toc-fabio.mar345image-module.html epydoc/toc-fabio.marccdimage-module.html epydoc/toc-fabio.mytest-module.html epydoc/toc-fabio.openimage-module.html epydoc/toc-fabio.pilatusimage-module.html epydoc/toc-fabio.pnmimage-module.html epydoc/toc-fabio.readbytestream-module.html epydoc/toc-fabio.tifimage-module.html epydoc/toc-fabio.xsdimage-module.html epydoc/toc.html fabio-src/GEimage.py fabio-src/GEimage_old.py fabio-src/HiPiCimage.py fabio-src/OXDimage.py fabio-src/TiffIO.py fabio-src/__init__.py fabio-src/adscimage.py fabio-src/binaryimage.py fabio-src/bruker100image.py fabio-src/brukerimage.py fabio-src/cbfimage.py fabio-src/compression.py fabio-src/converters.py fabio-src/datIO.py fabio-src/dm3image.py fabio-src/edfimage.py fabio-src/fabioimage.py fabio-src/fabioutils.py fabio-src/file_series.py fabio-src/fit2dmaskimage.py fabio-src/fit2dspreadsheetimage.py fabio-src/kcdimage.py fabio-src/mar345image.py fabio-src/marccdimage.py fabio-src/openimage.py fabio-src/pilatusimage.py fabio-src/pnmimage.py fabio-src/readbytestream.py fabio-src/templateimage.py fabio-src/tifimage.py fabio-src/xsdimage.py pylint/.pylintrc pylint/GEimage.py.lint pylint/GEimage_old.py.lint pylint/HiPiCimage.py.lint pylint/OXDimage.py.lint pylint/TiffIO.py.lint pylint/__init__.py.lint pylint/adscimage.py.lint pylint/benchheader.py.lint pylint/binaryimage.py.lint pylint/bruker100image.py.lint pylint/brukerimage.py.lint pylint/cbfimage.py.lint pylint/compression.py.lint pylint/converters.py.lint pylint/datIO.py.lint pylint/dm3image.py.lint pylint/edfimage.py.lint pylint/fabian_mar_header.py.lint pylint/fabioimage.py.lint pylint/fabioutils.py.lint pylint/file_series.py.lint pylint/fit2dmaskimage.py.lint pylint/fit2dspreadsheetimage.py.lint pylint/kcdimage.py.lint pylint/lintem.py pylint/mar345image.py.lint pylint/marccdimage.py.lint pylint/oldtifimage.py.lint pylint/openimage.py.lint pylint/pilatusimage.py.lint pylint/pnmimage.py.lint pylint/profile_compressed.py.lint pylint/readbytestream.py.lint pylint/templateimage.py.lint pylint/testGEimage.py.lint pylint/testOXDimage.py.lint pylint/testXSDimage.py.lint pylint/test_all.py.lint pylint/test_all_images.py.lint pylint/test_file_series.py.lint pylint/test_filename_steps.py.lint pylint/test_flat_binary.py.lint pylint/testadscimage.py.lint pylint/testbrukerimage.py.lint pylint/testcbfimage.py.lint pylint/testcompression.py.lint pylint/testedfimage.py.lint pylint/testfabioimage.py.lint pylint/testfilenames.py.lint pylint/testfit2dmaskimage.py.lint pylint/testheadernotsingleton.py.lint pylint/testkcdimage.py.lint pylint/testmar345image.py.lint pylint/testmccdimage.py.lint pylint/testopenheader.py.lint pylint/testopenimage.py.lint pylint/testtifgz.py.lint pylint/testtifimage.py.lint pylint/tifimage.py.lint pylint/utilstest.py.lint pylint/xsdimage.py.lint src/byte_offset.c src/byte_offset.pyx src/ccp4_pack.c src/ccp4_pack.h src/cf_io.pyx src/cf_iomodule.c src/columnfile.c src/columnfile.h src/mar345_IO.c src/mar345_IO.pyx src/stdint.h test/__init__.py test/benchheader.py test/profile_compressed.py test/testGEimage.py test/testOXDimage.py test/testXSDimage.py test/test_all.py test/test_all_images.py test/test_file_series.py test/test_filename_steps.py test/test_flat_binary.py test/testadscimage.py test/testbrukerimage.py test/testcbfimage.py test/testcompression.py test/testedfimage.py test/testfabioimage.py test/testfilenames.py test/testfit2dmaskimage.py test/testheadernotsingleton.py test/testkcdimage.py test/testmar345image.py test/testmccdimage.py test/testopenheader.py test/testopenimage.py test/testtifgz.py test/testtifimage.py test/utilstest.py test/profile/benchheader.py test/profile/profile_compressed.pyfabio-0.1.3/setup.cfg0000644000175000017500000000007312233272207015200 0ustar jeromejerome00000000000000[egg_info] tag_build = tag_date = 0 tag_svn_revision = 0 fabio-0.1.3/README.txt0000644000175000017500000001032012126623347015057 0ustar jeromejerome00000000000000FabIO ===== FabIO is an I/O library for images produced by 2D X-ray detectors and written in python. FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers (as a python dictionary) and datasets (as a numpy ndarray of integers or floats) Citation: --------- The general philosophy of the library is described in: FabIO: easy access to two-dimensional X-ray detector images in Python E. B. Knudsen, H. O. Sørensen, J. P. Wright, G. Goret and J. Kieffer Journal of Applied Crystallography, Volume 46, Part 2, pages 537-539. http://dx.doi.org/10.1107/S0021889813000150 Transparent handling of compressed files ---------------------------------------- Fabio is expected to handle gzip and bzip2 compressed files transparently. Following a query about the performance of reading compressed data, some benchmarking details have been collected at fabio_compressed_speed. This means that when your python was configured and built you needed the bzip and gzip modules to be present (eg libbz2-dev package for ubuntu) Using fabio in your own python programs Example: >>> import fabio >>> obj = fabio.edfimage("mydata0000.edf") >>> obj.data.shape (2048, 2048) >>> obj.header["Omega"] 23.5 Design Specifications --------------------- Name: Fabio = Fable Input/Output Idea: ..... Have a base class for all our 2D diffraction greyscale images. This consists of a 2D array (numpy ndarray) and a python dictionary of header information in (string key, string value) pairs. Class fabioimage ................ Needs a name which will not to be confused with an RGB color image. Class attributes: * data -> 2D array * header -> dictionary * rows, columns, dim1, dim2 -> data.shape * header_keys -> header.keys() used to retain the order of the header when writing an image to disk * bytecode -> data.typecode() * m, minval, maxval, stddev -> image statistics, could add others, eg roi[slice] Class methods (functions): .......................... integrate_area() -> return sum(self.data) within slice rebin(fact) -> rebins data, adjusts dims toPIL16() -> returns a PILimage getheader() -> returns self.header resetvals() -> resets the statistics getmean() -> (computes) returns self.m getmin() -> (computes) returns self.minval getmax() -> (computes) returns self.maxval getstddev() -> (computes) returns self.stddev read() -> read image from file [or stream, or shared memory] write() -> write image to file [or stream, or shared memory] readheader() -> read only the header [much faster for scanning files] Each individual file format would then inherit all the functionality of this class and just make new read and write methods. There are also fileseries related methods (next(), previous(), ...) which return a fabioimage instance of the next/previous frame in a fileserie Other feature: * possibility for using on-the-fly external compression - i.e. if files are stored as something as .gz, .bz2 etc could decompress them, using an external compression mechanism (if available). This is present in fabian but requires that images are edfs. Known file formats ------------------ * Bruker o brukerimage o bruker100image o kcdimage: Nonius KappaCCD diffractometer * Mar Research o marccd (fileformat derived from Tiff) o mar345 imaging plate with PCK compression * Dectris o cbfimage (implements a fast byte offset decompression scheme in python/cython) o pilatusimage (fileformat derived from Tiff) * ESRF o edfimage: The ESRF data Format o xsdimage: XML serialized image from EDNA o fit2dmaskimage: Fit2d Mask format o fit2dspreadsheetimage: Fit2d ascii tables (spread-sheet) * ADSC o adscimage * GE detector at APS o GEimage * PNM o pnmimage * Tiff o tifimage * D3M o d3mimage * Hamamatsu o HiPiCimage * Oxford Diffraction Sapphire 3 o OXDimage * Nonius o KappaCCD * Raw Binary without compression Installation ------------ Please see doc/source/INSTALL.rst Changelog --------- Please see doc/source/Changelog.rst fabio-0.1.3/pylint/0000755000175000017500000000000012233272207014676 5ustar jeromejerome00000000000000fabio-0.1.3/pylint/test_all.py.lint0000644000175000017500000001143512233243326020030 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.test_all C: 13,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 14,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 28,0: No exception type(s) specified W: 31,0: Relative import 'utilstest', should be 'test.utilstest' W: 37,0: Relative import 'testfabioimage', should be 'test.testfabioimage' W: 38,0: Relative import 'testedfimage', should be 'test.testedfimage' W: 39,0: Relative import 'testcbfimage', should be 'test.testcbfimage' W: 40,0: Relative import 'testfilenames', should be 'test.testfilenames' W: 41,0: Relative import 'test_file_series', should be 'test.test_file_series' W: 42,0: Relative import 'test_filename_steps', should be 'test.test_filename_steps' W: 44,0: Relative import 'testadscimage', should be 'test.testadscimage' W: 45,0: Relative import 'testfit2dmaskimage', should be 'test.testfit2dmaskimage' W: 46,0: Relative import 'testGEimage', should be 'test.testGEimage' W: 47,0: Relative import 'testheadernotsingleton', should be 'test.testheadernotsingleton' W: 48,0: Relative import 'testmar345image', should be 'test.testmar345image' W: 49,0: Relative import 'testbrukerimage', should be 'test.testbrukerimage' W: 50,0: Relative import 'testmccdimage', should be 'test.testmccdimage' W: 51,0: Relative import 'testopenheader', should be 'test.testopenheader' W: 52,0: Relative import 'testopenimage', should be 'test.testopenimage' W: 53,0: Relative import 'testOXDimage', should be 'test.testOXDimage' W: 54,0: Relative import 'testkcdimage', should be 'test.testkcdimage' W: 55,0: Relative import 'testtifimage', should be 'test.testtifimage' W: 56,0: Relative import 'testXSDimage', should be 'test.testXSDimage' C: 58,0:test_suite_all: Missing docstring C: 59,4:test_suite_all: Invalid name "testSuite" (should match [a-z_][a-z0-9_]{2,30}$) C: 84,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 85,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 34,4: Unused import fabio Report ====== 70 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |6 |NC |NC | +-----------+-------+---------+-----------+ |refactor |0 |NC |NC | +-----------+-------+---------+-----------+ |warning |22 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |W0403 |20 | +-----------+------------+ |C0103 |5 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0611 |1 | +-----------+------------+ |C0111 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 6.00/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |70 |86.42 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |3 |3.70 |NC |NC | +----------+-------+------+---------+-----------+ |comment |2 |2.47 |NC |NC | +----------+-------+------+---------+-----------+ |empty |6 |7.41 |NC |NC | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |0 |NC |NC |0 |0 | +---------+-------+-----------+-----------+------------+---------+ |method |0 |NC |NC |0 |0 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/testOXDimage.py.lint0000644000175000017500000001233612233243321020552 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.testOXDimage C: 77,0: Line too long (86/80) C: 81,0: Line too long (81/80) C: 82,0: Line too long (107/80) C: 1,0: Invalid name "testOXDimage" (should match (([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$) C: 10,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 11,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 26,0: No exception type(s) specified W: 29,0: Relative import 'utilstest', should be 'test.utilstest' C: 41,0:testOXD: Invalid name "testOXD" (should match [A-Z_][a-zA-Z0-9]+$) C: 43,8:testOXD.setUp: Invalid name "fn" (should match [a-z_][a-z0-9_]{2,30}$) C: 41,0:testOXD: Missing docstring C: 42,4:testOXD.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C: 49,4:testOXD.tearDown: Invalid name "tearDown" (should match [a-z_][a-z0-9_]{2,30}$) R: 41,0:testOXD: Too many public methods (47/20) C: 84,0:testOXD_same: Invalid name "testOXD_same" (should match [A-Z_][a-zA-Z0-9]+$) C: 86,8:testOXD_same.setUp: Invalid name "fn" (should match [a-z_][a-z0-9_]{2,30}$) C: 84,0:testOXD_same: Missing docstring C: 85,4:testOXD_same.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C: 93,8:testOXD_same.test_same: Invalid name "o1" (should match [a-z_][a-z0-9_]{2,30}$) C: 94,8:testOXD_same.test_same: Invalid name "o2" (should match [a-z_][a-z0-9_]{2,30}$) C: 96,12:testOXD_same.test_same: Invalid name "a1" (should match [a-z_][a-z0-9_]{2,30}$) C: 97,12:testOXD_same.test_same: Invalid name "a2" (should match [a-z_][a-z0-9_]{2,30}$) R: 84,0:testOXD_same: Too many public methods (46/20) C:100,0:testOXD_big: Invalid name "testOXD_big" (should match [A-Z_][a-zA-Z0-9]+$) C:103,8:testOXD_big.setUp: Invalid name "fn" (should match [a-z_][a-z0-9_]{2,30}$) C:102,4:testOXD_big.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C:108,4:testOXD_big.test_same: Missing docstring C:110,8:testOXD_big.test_same: Invalid name "df" (should match [a-z_][a-z0-9_]{2,30}$) R:100,0:testOXD_big: Too many public methods (46/20) C:113,0:test_suite_all_OXD: Invalid name "test_suite_all_OXD" (should match [a-z_][a-z0-9_]{2,30}$) C:113,0:test_suite_all_OXD: Missing docstring C:114,4:test_suite_all_OXD: Invalid name "testSuite" (should match [a-z_][a-z0-9_]{2,30}$) C:122,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:123,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) Report ====== 98 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |29 |NC |NC | +-----------+-------+---------+-----------+ |refactor |3 |NC |NC | +-----------+-------+---------+-----------+ |warning |2 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |22 | +-----------+------------+ |C0111 |4 | +-----------+------------+ |R0904 |3 | +-----------+------------+ |C0301 |3 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0403 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 6.53/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |99 |83.19 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |9 |7.56 |NC |NC | +----------+-------+------+---------+-----------+ |comment |3 |2.52 |NC |NC | +----------+-------+------+---------+-----------+ |empty |8 |6.72 |NC |NC | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |class |3 |NC |NC |33.33 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |8 |NC |NC |87.50 |50.00 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |0.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/testfilenames.py.lint0000644000175000017500000000644412126623347021076 0ustar jeromejerome00000000000000************* Module testfilenames W: 28,0: No exception type(s) specified F: 31,0: Unable to import 'utilstest' C: 83,0:testfilenames: Invalid name "testfilenames" (should match [A-Z_][a-zA-Z0-9]+$) E: 89,18:testfilenames.test_many_cases: Module 'fabio' has no 'FilenameObject' member C: 96,4:testfilenames.test_more_cases: Missing docstring C:101,4:testfilenames.test_more_cases_jump: Missing docstring C:107,0:test_suite_all_filenames: Missing docstring Report ====== 49 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |4 |4 |= | +-----------+-------+---------+-----------+ |refactor |0 |0 |= | +-----------+-------+---------+-----------+ |warning |1 |1 |= | +-----------+-------+---------+-----------+ |error |1 |0 |+1.00 | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0111 |3 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |F0401 |1 | +-----------+------------+ |E1101 |1 | +-----------+------------+ |C0103 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 7.96/10 (previous run: 8.98/10) If you commit now, people should not be making nasty comments about you on c.l.py Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |89 |81.65 |89 |= | +----------+-------+------+---------+-----------+ |docstring |9 |8.26 |9 |= | +----------+-------+------+---------+-----------+ |comment |3 |2.75 |3 |= | +----------+-------+------+---------+-----------+ |empty |8 |7.34 |8 |= | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |1 |= |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |3 |3 |= |33.33 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |1 |= |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ fabio-0.1.3/pylint/mar345image.py.lint0000644000175000017500000001471612233243316020243 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module mar345image C: 41,0: Line too long (81/80) C: 45,0: Line too long (106/80) C: 98,0: Line too long (85/80) C:149,0: Line too long (86/80) C:169,0: Line too long (90/80) C:182,0: Line too long (83/80) C:196,0: Line too long (128/80) C:197,0: Line too long (104/80) C:200,0: Line too long (82/80) C:203,0: Line too long (134/80) C:206,0: Line too long (82/80) C:210,0: Line too long (130/80) C:214,0: Line too long (127/80) C:217,0: Line too long (82/80) C:220,0: Line too long (82/80) C:223,0: Line too long (82/80) C:226,0: Line too long (82/80) C:229,0: Line too long (82/80) C:233,0: Line too long (85/80) C:234,0: Line too long (151/80) C:238,0: Line too long (85/80) C:239,0: Line too long (153/80) C:242,0: Line too long (82/80) C:245,0: Line too long (82/80) C:249,0: Line too long (121/80) C:252,0: Line too long (82/80) C:255,0: Line too long (82/80) C:260,0: Line too long (156/80) C:264,0: Line too long (125/80) C:268,0: Line too long (125/80) C:273,0: Line too long (103/80) C:274,0: Line too long (182/80) C:279,0: Line too long (157/80) C:282,0: Line too long (82/80) C:285,0: Line too long (82/80) C:289,0: Line too long (134/80) C:292,0: Line too long (82/80) W:120,0: TODO: validate these values against the binaries already read W: 4,0: Redefining built-in '__doc__' C: 1,0: Missing docstring C: 24,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) R: 28,0:mar345image: Too many instance attributes (8/7) C: 28,0:mar345image: Invalid name "mar345image" (should match [A-Z_][a-zA-Z0-9]+$) C: 28,0:mar345image: Missing docstring C: 38,8:mar345image.read: Invalid name "f" (should match [a-z_][a-z0-9_]{2,30}$) W: 44,19:mar345image.read: Catching too general exception Exception C: 66,8:mar345image._readheader: Invalid name "f" (should match [a-z_][a-z0-9_]{2,30}$) C: 67,8:mar345image._readheader: Invalid name "h" (should match [a-z_][a-z0-9_]{2,30}$) C: 70,8:mar345image._readheader: Invalid name "l" (should match [a-z_][a-z0-9_]{2,30}$) C: 78,12:mar345image._readheader: Invalid name "fs" (should match [a-z_][a-z0-9_]{2,30}$) C: 80,12:mar345image._readheader: Invalid name "fs" (should match [a-z_][a-z0-9_]{2,30}$) C:121,8:mar345image._readheader: Invalid name "l" (should match [a-z_][a-z0-9_]{2,30}$) C:129,8:mar345image._readheader: Invalid name "l" (should match [a-z_][a-z0-9_]{2,30}$) C:130,12:mar345image._readheader: Invalid name "m" (should match [a-z_][a-z0-9_]{2,30}$) C:133,12:mar345image._readheader: Invalid name "n" (should match [a-z_][a-z0-9_]{2,30}$) C:148,16:mar345image._readheader: Invalid name "n" (should match [a-z_][a-z0-9_]{2,30}$) R: 61,4:mar345image._readheader: Too many branches (13/12) R: 61,4:mar345image._readheader: Too many statements (57/50) W:166,15:mar345image.write: Catching too general exception Exception R:169,4:mar345image._writeheader: Too many branches (28/12) R:169,4:mar345image._writeheader: Too many statements (123/50) C:300,4:mar345image._high_intensity_pixel_records: Missing docstring C:312,4:mar345image.nb_overflow_pixels: Missing docstring C:316,4:mar345image.checkData: Invalid name "checkData" (should match [a-z_][a-z0-9_]{2,30}$) C:324,12:mar345image.checkData: Invalid name "z" (should match [a-z_][a-z0-9_]{2,30}$) R: 28,0:mar345image: Too many public methods (26/20) W: 22,0: Unused import traceback Report ====== 246 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |56 |18 |+38.00 | +-----------+-------+---------+-----------+ |refactor |6 |3 |+3.00 | +-----------+-------+---------+-----------+ |warning |5 |10 |-5.00 | +-----------+-------+---------+-----------+ |error |0 |4 |-4.00 | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0301 |37 | +-----------+------------+ |C0103 |15 | +-----------+------------+ |C0111 |4 | +-----------+------------+ |W0703 |2 | +-----------+------------+ |R0915 |2 | +-----------+------------+ |R0912 |2 | +-----------+------------+ |W0622 |1 | +-----------+------------+ |W0611 |1 | +-----------+------------+ |W0511 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ |R0902 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 7.28/10 (previous run: 4.07/10) Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |265 |83.60 |86 |+179.00 | +----------+-------+------+---------+-----------+ |docstring |16 |5.05 |20 |-4.00 | +----------+-------+------+---------+-----------+ |comment |13 |4.10 |12 |+1.00 | +----------+-------+------+---------+-----------+ |empty |23 |7.26 |20 |+3.00 | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (mar345image) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |1 |= |0.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |8 |4 |+4.00 |75.00 |12.50 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/brukerimage.py.lint0000644000175000017500000001476012233243277020527 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module brukerimage C: 21,0: Line too long (86/80) C: 53,0: Line too long (94/80) C: 54,0: Line too long (84/80) C: 55,0: Line too long (123/80) C: 56,0: Line too long (155/80) C: 62,0: Line too long (102/80) C: 70,0: Line too long (87/80) C: 81,0: Line too long (110/80) C: 83,0: Line too long (91/80) C: 84,0: Line too long (88/80) C: 86,0: Line too long (93/80) C: 87,0: Line too long (89/80) C: 90,0: Line too long (100/80) C: 93,0: Line too long (155/80) C: 99,0: Line too long (90/80) C:100,0: Line too long (145/80) C:101,0: Line too long (131/80) C:103,0: Line too long (146/80) C:104,0: Line too long (97/80) C:105,0: Line too long (138/80) C:106,0: Line too long (122/80) C:107,0: Line too long (84/80) C:108,0: Line too long (207/80) C:110,0: Line too long (89/80) C:111,0: Line too long (119/80) C:112,0: Line too long (92/80) C:113,0: Line too long (91/80) C:116,0: Line too long (84/80) C:117,0: Line too long (98/80) C:118,0: Line too long (99/80) C:119,0: Line too long (145/80) C:121,0: Line too long (158/80) C:122,0: Line too long (118/80) C:123,0: Line too long (93/80) C:124,0: Line too long (91/80) C:126,0: Line too long (81/80) C:128,0: Line too long (88/80) C:129,0: Line too long (90/80) C:131,0: Line too long (201/80) C:132,0: Line too long (87/80) C:133,0: Line too long (84/80) C:134,0: Line too long (88/80) C:135,0: Line too long (90/80) C:136,0: Line too long (93/80) C:137,0: Line too long (139/80) C:139,0: Line too long (108/80) C:178,0: Line too long (99/80) C:216,0: Line too long (101/80) C:239,0: Line too long (117/80) C:246,0: Line too long (137/80) C:269,0: Line too long (121/80) C:280,0: Line too long (87/80) C:339,0: Line too long (86/80) C:355,0: Line too long (103/80) C:356,0: Line too long (92/80) C:367,0: Line too long (102/80) W: 41,0: TODO: int32 -> float32 conversion according to the "linear" keyword. W:245,0: TODO: check that the formula is OK, not reverted. W: 35,4: Redefining built-in 'bytes' W: 6,0: Redefining built-in '__doc__' C: 1,0: Missing docstring C: 30,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 35,4: Invalid name "bytes" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) R: 37,0:brukerimage: Too many instance attributes (8/7) C: 37,0:brukerimage: Invalid name "brukerimage" (should match [A-Z_][a-zA-Z0-9]+$) R:193,4:brukerimage.read: Too many local variables (17/15) E:238,19:brukerimage.read: Undefined variable 'Except' W:226,16:brukerimage.read: Unused variable 'i' E:268,23:brukerimage.write: Undefined variable 'Except' W:341,44:brukerimage.gen_header: Using possibly undefined loop variable 'i' C:343,20:brukerimage.gen_header: Invalid name "f" (should match [a-z_][a-z0-9_]{2,30}$) E:343,24:brukerimage.gen_header: Too many arguments for format string R:318,4:brukerimage.gen_header: Too many branches (13/12) R: 37,0:brukerimage: Too many public methods (29/20) W:402,4:test: Redefining name 'sys' from outer scope (line 27) W:402,4:test: Redefining name 'time' from outer scope (line 29) W:402,4:test: Reimport 'sys' (imported line 27) W:402,4:test: Reimport 'time' (imported line 29) W:407,8:test: Unused variable 'res' Report ====== 215 statements analysed. Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |61 |2 |+59.00 | +-----------+-------+---------+-----------+ |refactor |4 |0 |+4.00 | +-----------+-------+---------+-----------+ |warning |11 |10 |+1.00 | +-----------+-------+---------+-----------+ |error |3 |16 |-13.00 | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0301 |56 | +-----------+------------+ |C0103 |4 | +-----------+------------+ |W0622 |2 | +-----------+------------+ |W0621 |2 | +-----------+------------+ |W0612 |2 | +-----------+------------+ |W0511 |2 | +-----------+------------+ |W0404 |2 | +-----------+------------+ |E0602 |2 | +-----------+------------+ |W0631 |1 | +-----------+------------+ |R0914 |1 | +-----------+------------+ |R0912 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ |R0902 |1 | +-----------+------------+ |E1305 |1 | +-----------+------------+ |C0111 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 5.77/10 (previous run: 1.15/10) Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |244 |59.95 |113 |+131.00 | +----------+-------+------+---------+-----------+ |docstring |124 |30.47 |37 |+87.00 | +----------+-------+------+---------+-----------+ |comment |6 |1.47 |6 |= | +----------+-------+------+---------+-----------+ |empty |33 |8.11 |33 |= | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (brukerimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |1 |= |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |8 |4 |+4.00 |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/testcbfimage.py.lint0000644000175000017500000001222612233243332020652 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.testcbfimage C: 44,0: Line too long (91/80) C: 69,0: Line too long (122/80) C: 79,0: Line too long (82/80) C: 84,0: Line too long (103/80) C: 91,0: Line too long (98/80) C:102,0: Line too long (87/80) C:109,0: Line too long (90/80) C:116,0: Line too long (89/80) C:127,0: Line too long (82/80) C:132,0: Line too long (149/80) C:143,0: Line too long (82/80) C:148,0: Line too long (149/80) C:158,0: Line too long (82/80) C:163,0: Line too long (149/80) C: 12,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 13,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 27,0: No exception type(s) specified W: 30,0: Relative import 'utilstest', should be 'test.utilstest' C: 38,0:test_cbfimage_reader: Invalid name "test_cbfimage_reader" (should match [A-Z_][a-zA-Z0-9]+$) C: 41,4:test_cbfimage_reader.__init__: Invalid name "methodName" (should match [a-z_][a-z0-9_]{2,30}$) C: 41,23:test_cbfimage_reader.__init__: Invalid name "methodName" (should match [a-z_][a-z0-9_]{2,30}$) C: 49,4:test_cbfimage_reader.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C: 55,4:test_cbfimage_reader.tearDown: Invalid name "tearDown" (should match [a-z_][a-z0-9_]{2,30}$) C: 90,8:test_cbfimage_reader.test_byte_offset: Invalid name "startPos" (should match [a-z_][a-z0-9_]{2,30}$) C: 92,8:test_cbfimage_reader.test_byte_offset: Invalid name "startTime" (should match [a-z_][a-z0-9_]{2,30}$) C: 93,8:test_cbfimage_reader.test_byte_offset: Invalid name "numpyRes" (should match [a-z_][a-z0-9_]{2,30}$) C: 94,8:test_cbfimage_reader.test_byte_offset: Invalid name "tNumpy" (should match [a-z_][a-z0-9_]{2,30}$) C:111,8:test_cbfimage_reader.test_byte_offset: Invalid name "startTime" (should match [a-z_][a-z0-9_]{2,30}$) C:112,8:test_cbfimage_reader.test_byte_offset: Invalid name "cythonRes" (should match [a-z_][a-z0-9_]{2,30}$) C:113,8:test_cbfimage_reader.test_byte_offset: Invalid name "tCython" (should match [a-z_][a-z0-9_]{2,30}$) R: 38,0:test_cbfimage_reader: Too many public methods (51/20) C:166,0:test_suite_all_cbf: Missing docstring C:167,4:test_suite_all_cbf: Invalid name "testSuite" (should match [a-z_][a-z0-9_]{2,30}$) C:179,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:180,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) Report ====== 122 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |32 |NC |NC | +-----------+-------+---------+-----------+ |refactor |1 |NC |NC | +-----------+-------+---------+-----------+ |warning |2 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |17 | +-----------+------------+ |C0301 |14 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0403 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ |C0111 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 7.13/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |122 |72.62 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |22 |13.10 |NC |NC | +----------+-------+------+---------+-----------+ |comment |15 |8.93 |NC |NC | +----------+-------+------+---------+-----------+ |empty |9 |5.36 |NC |NC | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |NC |NC |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |9 |NC |NC |100.00 |22.22 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/datIO.py.lint0000644000175000017500000000675512120434325017226 0ustar jeromejerome00000000000000************* Module datIO C: 1,0: Invalid name "datIO" (should match (([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$) C: 14,0:fabiodata: Invalid name "fabiodata" (should match [A-Z_][a-zA-Z0-9]+$) W: 36,31:fabiodata.read: Unused argument 'frame' W: 36,19:fabiodata.read: Unused argument 'fname' R: 36,4:fabiodata.read: Method could be a function R: 14,0:fabiodata: Too few public methods (1/2) C: 45,0:columnfile: Invalid name "columnfile" (should match [A-Z_][a-zA-Z0-9]+$) W: 47,4:columnfile.read: Signature differs from overridden method F: 48,8:columnfile.read: Unable to import 'cf_io' R: 45,0:columnfile: Too few public methods (1/2) Report ====== 27 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |3 |3 |= | +-----------+-------+---------+-----------+ |refactor |3 |3 |= | +-----------+-------+---------+-----------+ |warning |3 |3 |= | +-----------+-------+---------+-----------+ |error |0 |0 |= | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |3 | +-----------+------------+ |W0613 |2 | +-----------+------------+ |R0903 |2 | +-----------+------------+ |W0222 |1 | +-----------+------------+ |R0201 |1 | +-----------+------------+ |F0401 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 6.67/10 (previous run: 6.67/10) This is okay-ish, but I'm sure you can do better. Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |27 |43.55 |27 |= | +----------+-------+------+---------+-----------+ |docstring |23 |37.10 |23 |= | +----------+-------+------+---------+-----------+ |comment |3 |4.84 |3 |= | +----------+-------+------+---------+-----------+ |empty |9 |14.52 |9 |= | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |class |2 |2 |= |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |3 |3 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ fabio-0.1.3/pylint/tifimage.py.lint0000644000175000017500000001376512233243274020020 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module tifimage C: 5,0: Line too long (84/80) C: 48,0: Line too long (167/80) C:108,0: Line too long (112/80) C:131,0: Line too long (98/80) C:139,0: Line too long (120/80) C:155,0: Line too long (112/80) C:156,0: Line too long (101/80) C:157,0: Line too long (106/80) C:160,0: Line too long (100/80) C:176,0: Line too long (100/80) C:216,0: Line too long (85/80) C:226,0: Line too long (89/80) C:248,0: Line too long (94/80) C:273,0: Line too long (88/80) C:276,0: Line too long (84/80) C:281,0: Line too long (84/80) C:287,0: Line too long (84/80) C:289,0: Line too long (170/80) C: 28,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 33,4: Invalid name "Image" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 52,0: Invalid name "baseline_tiff_tags" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) R: 80,0:tifimage: Too many instance attributes (9/7) C: 80,0:tifimage: Invalid name "tifimage" (should match [A-Z_][a-zA-Z0-9]+$) W:130,15:tifimage.read: Catching too general exception Exception C:125,12:tifimage.read: Invalid name "tiffIO" (should match [a-z_][a-z0-9_]{2,30}$) W:147,23:tifimage.read: Catching too general exception Exception R:116,4:tifimage.read: Too many branches (13/12) W:136,38:tifimage.read: Unused variable 'ncol' C:175,8:tifimage.write: Invalid name "tiffIO" (should match [a-z_][a-z0-9_]{2,30}$) R: 80,0:tifimage: Too many public methods (25/20) C:181,0:Tiff_header: Invalid name "Tiff_header" (should match [A-Z_][a-zA-Z0-9]+$) C:181,0:Tiff_header: Missing docstring R:181,0:Tiff_header: Too few public methods (0/2) C:205,0:Image_File_Directory: Invalid name "Image_File_Directory" (should match [A-Z_][a-zA-Z0-9]+$) C:205,0:Image_File_Directory: Missing docstring W:206,23:Image_File_Directory.__init__: Unused argument 'instring' C:211,4:Image_File_Directory.unpack: Missing docstring C:212,27:Image_File_Directory.unpack: More than one statement on a single line C:214,8:Image_File_Directory.unpack: Invalid name "strInput" (should match [a-z_][a-z0-9_]{2,30}$) C:218,12:Image_File_Directory.unpack: Invalid name "e" (should match [a-z_][a-z0-9_]{2,30}$) C:222,16:Image_File_Directory.unpack: Invalid name "e" (should match [a-z_][a-z0-9_]{2,30}$) R:205,0:Image_File_Directory: Too few public methods (1/2) C:229,0:Image_File_Directory_entry: Invalid name "Image_File_Directory_entry" (should match [A-Z_][a-zA-Z0-9]+$) C:229,0:Image_File_Directory_entry: Missing docstring C:237,4:Image_File_Directory_entry.unpack: Invalid name "strInput" (should match [a-z_][a-z0-9_]{2,30}$) C:237,4:Image_File_Directory_entry.unpack: Missing docstring C:237,21:Image_File_Directory_entry.unpack: Invalid name "strInput" (should match [a-z_][a-z0-9_]{2,30}$) C:258,4:Image_File_Directory_entry.extract_data: Missing docstring R:258,4:Image_File_Directory_entry.extract_data: Too many branches (15/12) Report ====== 168 statements analysed. Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |39 |35 |+4.00 | +-----------+-------+---------+-----------+ |refactor |6 |4 |+2.00 | +-----------+-------+---------+-----------+ |warning |4 |3 |+1.00 | +-----------+-------+---------+-----------+ |error |0 |10 |-10.00 | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0301 |18 | +-----------+------------+ |C0103 |14 | +-----------+------------+ |C0111 |6 | +-----------+------------+ |W0703 |2 | +-----------+------------+ |R0912 |2 | +-----------+------------+ |R0903 |2 | +-----------+------------+ |W0613 |1 | +-----------+------------+ |W0612 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ |R0902 |1 | +-----------+------------+ |C0321 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 7.08/10 (previous run: 3.99/10) Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |199 |72.36 |183 |+16.00 | +----------+-------+------+---------+-----------+ |docstring |38 |13.82 |33 |+5.00 | +----------+-------+------+---------+-----------+ |comment |18 |6.55 |18 |= | +----------+-------+------+---------+-----------+ |empty |20 |7.27 |18 |+2.00 | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (tifimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |4 |4 |= |25.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |10 |10 |= |70.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/OXDimage.py.lint0000644000175000017500000001722712233243302017655 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module OXDimage C: 30,0: Line too long (90/80) C: 80,0: Line too long (88/80) C: 81,0: Line too long (94/80) C: 82,0: Line too long (95/80) C: 83,0: Line too long (90/80) C: 84,0: Line too long (91/80) C: 85,0: Line too long (89/80) C: 89,0: Line too long (83/80) C: 90,0: Line too long (83/80) C: 91,0: Line too long (88/80) C: 92,0: Line too long (88/80) C: 93,0: Line too long (84/80) C: 94,0: Line too long (84/80) C: 95,0: Line too long (85/80) C:100,0: Line too long (88/80) C:101,0: Line too long (103/80) C:102,0: Line too long (92/80) C:103,0: Line too long (94/80) C:104,0: Line too long (94/80) C:105,0: Line too long (103/80) C:106,0: Line too long (103/80) C:107,0: Line too long (112/80) C:108,0: Line too long (112/80) C:109,0: Line too long (83/80) C:110,0: Line too long (103/80) C:111,0: Line too long (96/80) C:112,0: Line too long (96/80) C:120,0: Line too long (82/80) C:142,0: Line too long (81/80) C:149,0: Line too long (94/80) C:150,0: Line too long (94/80) C:152,0: Line too long (91/80) C:153,0: Line too long (91/80) C:154,0: Line too long (90/80) C:155,0: Line too long (89/80) C:158,0: Line too long (97/80) C:159,0: Line too long (97/80) C:160,0: Line too long (97/80) C:164,0: Line too long (87/80) C:165,0: Line too long (87/80) C:167,0: Line too long (92/80) C:169,0: Line too long (91/80) C:172,0: Line too long (88/80) C:177,0: Line too long (86/80) C:178,0: Line too long (97/80) C:179,0: Line too long (87/80) W:248,0: Found indentation with tabs instead of spaces W:249,0: Found indentation with tabs instead of spaces C:251,0: Line too long (107/80) C:252,0: Line too long (133/80) C:253,0: Line too long (111/80) C:254,0: Line too long (125/80) C:255,0: Line too long (125/80) C:256,0: Line too long (121/80) C:257,0: Line too long (122/80) C:258,0: Line too long (121/80) C:305,0: Line too long (91/80) C:307,0: Line too long (120/80) C:309,0: Line too long (118/80) C:311,0: Line too long (125/80) C:314,0: Line too long (95/80) C:316,0: Line too long (124/80) C:318,0: Line too long (122/80) C:320,0: Line too long (129/80) C:323,0: Line too long (96/80) C:325,0: Line too long (124/80) C:327,0: Line too long (122/80) C:329,0: Line too long (129/80) C:332,0: Line too long (94/80) C:334,0: Line too long (121/80) C:336,0: Line too long (119/80) C:338,0: Line too long (126/80) C:371,0: Line too long (82/80) C:397,0: Line too long (110/80) W: 5,0: Redefining built-in '__doc__' C: 1,0: Missing docstring C: 23,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 31,4: Invalid name "rad2deg" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 32,4: Invalid name "deg2rad" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) R: 52,0:OXDimage: Too many instance attributes (10/7) R: 56,4:OXDimage._readheader: Too many statements (95/50) C:225,12:OXDimage.read: Invalid name "ReadBytes" (should match [a-z_][a-z0-9_]{2,30}$) C:269,8:OXDimage._writeheader: Invalid name "NG" (should match [a-z_][a-z0-9_]{2,30}$) C:279,8:OXDimage._writeheader: Invalid name "NS" (should match [a-z_][a-z0-9_]{2,30}$) C:299,8:OXDimage._writeheader: Invalid name "KM" (should match [a-z_][a-z0-9_]{2,30}$) C:366,8:OXDimage._writeheader: Invalid name "SS" (should match [a-z_][a-z0-9_]{2,30}$) C:375,8:OXDimage._writeheader: Invalid name "HS" (should match [a-z_][a-z0-9_]{2,30}$) R:237,4:OXDimage._writeheader: Too many branches (25/12) R:237,4:OXDimage._writeheader: Too many statements (102/50) C:395,4:OXDimage.getCompressionRatio: Invalid name "getCompressionRatio" (should match [a-z_][a-z0-9_]{2,30}$) C:400,4:OXDimage.checkData: Invalid name "checkData" (should match [a-z_][a-z0-9_]{2,30}$) R: 52,0:OXDimage: Too many public methods (26/20) W:216,12:OXDimage.read: Attribute 'raw16' defined outside __init__ W:215,12:OXDimage.read: Attribute 'raw8' defined outside __init__ W:217,12:OXDimage.read: Attribute 'raw32' defined outside __init__ C:418,8:Section.__init__: Invalid name "_dictSize" (should match [a-z_][a-z0-9_]{2,30}$) C:417,8:Section.__init__: Invalid name "lstChr" (should match [a-z_][a-z0-9_]{2,30}$) C:410,4:Section.__init__: Invalid name "dictHeader" (should match [a-z_][a-z0-9_]{2,30}$) C:410,29:Section.__init__: Invalid name "dictHeader" (should match [a-z_][a-z0-9_]{2,30}$) C:422,4:Section.getSize: Invalid name "getSize" (should match [a-z_][a-z0-9_]{2,30}$) C:422,4:Section.getSize: Missing docstring C:427,4:Section.setData: Invalid name "setData" (should match [a-z_][a-z0-9_]{2,30}$) W: 22,0: Unused import struct Report ====== 288 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |91 |56 |+35.00 | +-----------+-------+---------+-----------+ |refactor |5 |3 |+2.00 | +-----------+-------+---------+-----------+ |warning |7 |8 |-1.00 | +-----------+-------+---------+-----------+ |error |0 |86 |-86.00 | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0301 |72 | +-----------+------------+ |C0103 |17 | +-----------+------------+ |W0201 |3 | +-----------+------------+ |W0312 |2 | +-----------+------------+ |R0915 |2 | +-----------+------------+ |C0111 |2 | +-----------+------------+ |W0622 |1 | +-----------+------------+ |W0611 |1 | +-----------+------------+ |R0912 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ |R0902 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 6.42/10 (previous run: -22.48/10) Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |322 |78.35 |158 |+164.00 | +----------+-------+------+---------+-----------+ |docstring |42 |10.22 |18 |+24.00 | +----------+-------+------+---------+-----------+ |comment |17 |4.14 |14 |+3.00 | +----------+-------+------+---------+-----------+ |empty |30 |7.30 |25 |+5.00 | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (OXDimage) \-deg2rad (OXDimage) \-rad2deg (OXDimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |2 |1 |+1.00 |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |method |10 |2 |+8.00 |90.00 |40.00 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/pilatusimage.py.lint0000644000175000017500000000566312126623347020721 0ustar jeromejerome00000000000000************* Module pilatusimage C: 26,0:pilatusimage: Invalid name "pilatusimage" (should match [A-Z_][a-zA-Z0-9]+$) W: 53,19:pilatusimage._readheader: Catching too general exception Exception R: 26,0:pilatusimage: Too many public methods (25/20) Report ====== 34 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |1 |1 |= | +-----------+-------+---------+-----------+ |refactor |1 |1 |= | +-----------+-------+---------+-----------+ |warning |1 |1 |= | +-----------+-------+---------+-----------+ |error |0 |0 |= | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |W0703 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ |C0103 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 9.12/10 (previous run: 9.12/10) So close to being perfect... Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |34 |42.50 |34 |= | +----------+-------+------+---------+-----------+ |docstring |26 |32.50 |26 |= | +----------+-------+------+---------+-----------+ |comment |6 |7.50 |6 |= | +----------+-------+------+---------+-----------+ |empty |14 |17.50 |14 |= | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |1 |= |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |2 |2 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ fabio-0.1.3/pylint/dm3image.py.lint0000644000175000017500000001155412233243311017703 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module dm3image C: 67,0: Line too long (81/80) C: 70,0: Line too long (85/80) C:131,0: Line too long (97/80) C:148,0: Line too long (112/80) C:150,0: Line too long (101/80) C:166,0: Line too long (95/80) C:177,0: Line too long (88/80) C:182,0: Line too long (101/80) C:186,0: Line too long (109/80) C:193,0: Line too long (86/80) C:202,0: Line too long (97/80) C:206,0: Line too long (105/80) C:211,0: Line too long (98/80) C:212,0: Line too long (95/80) C:213,0: Line too long (94/80) C:214,0: Line too long (83/80) C:218,0: Line too long (94/80) C: 14,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) R: 46,0:dm3image: Too many instance attributes (19/7) C: 46,0:dm3image: Invalid name "dm3image" (should match [A-Z_][a-zA-Z0-9]+$) W: 62,4:dm3image._readheader: Arguments number differs from overridden method C: 89,56:dm3image.read: More than one statement on a single line W:106,39:dm3image.readbytes: Redefining built-in 'format' C:106,4:dm3image.readbytes: Missing docstring C:118,4:dm3image.read_tag_group: Missing docstring C:127,4:dm3image.read_tag_entry: Missing docstring W:168,12:dm3image.read_tag_type: Redefining built-in 'format' C:144,4:dm3image.read_tag_type: Missing docstring W:180,16:dm3image.read_tag_type: Unused variable 'struct_name_length' W:162,16:dm3image.read_tag_type: Unused variable 'dump' C:217,4:dm3image.read_data: Missing docstring R: 46,0:dm3image: Too many public methods (30/20) W: 67,8:dm3image._readheader: Attribute 'byte_order' defined outside __init__ W:158,12:dm3image.read_tag_type: Attribute 'data_type' defined outside __init__ W: 82,8:dm3image.read: Attribute 'infile' defined outside __init__ W: 75,12:dm3image._readheader: Attribute 'swap' defined outside __init__ Report ====== 135 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |25 |24 |+1.00 | +-----------+-------+---------+-----------+ |refactor |2 |1 |+1.00 | +-----------+-------+---------+-----------+ |warning |9 |24 |-15.00 | +-----------+-------+---------+-----------+ |error |0 |33 |-33.00 | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0301 |17 | +-----------+------------+ |C0111 |5 | +-----------+------------+ |W0201 |4 | +-----------+------------+ |W0622 |2 | +-----------+------------+ |W0612 |2 | +-----------+------------+ |C0103 |2 | +-----------+------------+ |W0221 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ |R0902 |1 | +-----------+------------+ |C0321 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 7.33/10 (previous run: -10.00/10) Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |162 |80.60 |134 |+28.00 | +----------+-------+------+---------+-----------+ |docstring |14 |6.97 |14 |= | +----------+-------+------+---------+-----------+ |comment |5 |2.49 |10 |-5.00 | +----------+-------+------+---------+-----------+ |empty |20 |9.95 |32 |-12.00 | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (dm3image) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |1 |= |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |8 |7 |+1.00 |37.50 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/converters.py.lint0000644000175000017500000000521312120434325020404 0ustar jeromejerome00000000000000************* Module converters W: 14,0: Unused import types Report ====== 17 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |0 |0 |= | +-----------+-------+---------+-----------+ |refactor |0 |0 |= | +-----------+-------+---------+-----------+ |warning |1 |1 |= | +-----------+-------+---------+-----------+ |error |0 |0 |= | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |W0611 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 9.41/10 (previous run: 9.41/10) So close to being perfect... Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |27 |50.00 |27 |= | +----------+-------+------+---------+-----------+ |docstring |19 |35.19 |19 |= | +----------+-------+------+---------+-----------+ |comment |2 |3.70 |2 |= | +----------+-------+------+---------+-----------+ |empty |6 |11.11 |6 |= | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ |method |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ |function |3 |3 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ fabio-0.1.3/pylint/test_filename_steps.py.lint0000644000175000017500000001022212233243324022245 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.test_filename_steps C: 1,0: Missing docstring C: 5,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 6,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 20,0: No exception type(s) specified W: 23,0: Relative import 'utilstest', should be 'test.utilstest' C: 28,0:test_next: Invalid name "test_next" (should match [A-Z_][a-zA-Z0-9]+$) C: 28,0:test_next: Missing docstring W: 30,18:test_next.test_next1: Redefining built-in 'next' C: 29,4:test_next.test_next1: Missing docstring R: 28,0:test_next: Too many public methods (46/20) C: 37,0:test_prev: Invalid name "test_prev" (should match [A-Z_][a-zA-Z0-9]+$) C: 37,0:test_prev: Missing docstring C: 38,4:test_prev.test_prev1: Missing docstring R: 37,0:test_prev: Too many public methods (46/20) C: 46,0:test_jump: Invalid name "test_jump" (should match [A-Z_][a-zA-Z0-9]+$) C: 46,0:test_jump: Missing docstring C: 47,4:test_jump.test_jump1: Missing docstring R: 46,0:test_jump: Too many public methods (46/20) C: 56,0:test_suite_all_steps: Missing docstring C: 57,4:test_suite_all_steps: Invalid name "testSuite" (should match [a-z_][a-z0-9_]{2,30}$) C: 65,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 66,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) Report ====== 44 statements analysed. Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |16 |NC |NC | +-----------+-------+---------+-----------+ |refactor |3 |NC |NC | +-----------+-------+---------+-----------+ |warning |3 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0111 |8 | +-----------+------------+ |C0103 |8 | +-----------+------------+ |R0904 |3 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0622 |1 | +-----------+------------+ |W0403 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 5.00/10 Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |55 |91.67 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |0 |0.00 |NC |NC | +----------+-------+------+---------+-----------+ |comment |2 |3.33 |NC |NC | +----------+-------+------+---------+-----------+ |empty |3 |5.00 |NC |NC | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |3 |NC |NC |0.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |3 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/test_all_images.py.lint0000644000175000017500000000555512233243336021364 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.test_all_images W: 10,0: No exception type(s) specified C: 13,0: Invalid name "times" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 14,0: Invalid name "images" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) Report ====== 72 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |2 |NC |NC | +-----------+-------+---------+-----------+ |refactor |0 |NC |NC | +-----------+-------+---------+-----------+ |warning |1 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |2 | +-----------+------------+ |W0702 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 9.58/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |65 |69.89 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |12 |12.90 |NC |NC | +----------+-------+------+---------+-----------+ |comment |1 |1.08 |NC |NC | +----------+-------+------+---------+-----------+ |empty |15 |16.13 |NC |NC | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |0 |NC |NC |0 |0 | +---------+-------+-----------+-----------+------------+---------+ |method |0 |NC |NC |0 |0 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/pnmimage.py.lint0000644000175000017500000001522012233243303020005 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module pnmimage C: 39,0: Line too long (88/80) C: 56,0: Line too long (83/80) C: 77,0: Line too long (91/80) C: 98,0: Line too long (84/80) C:110,0: Line too long (96/80) C:127,0: Line too long (96/80) C:134,0: Line too long (98/80) C:136,0: Line too long (92/80) C: 15,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) R: 23,0:pnmimage: Too many instance attributes (10/7) C: 23,0:pnmimage: Invalid name "pnmimage" (should match [A-Z_][a-zA-Z0-9]+$) C: 31,8:pnmimage.__init__: Invalid name "m" (should match [a-z_][a-z0-9_]{2,30}$) C: 23,0:pnmimage: Missing docstring C: 35,4:pnmimage._readheader: Invalid name "f" (should match [a-z_][a-z0-9_]{2,30}$) C: 35,26:pnmimage._readheader: Invalid name "f" (should match [a-z_][a-z0-9_]{2,30}$) C: 42,8:pnmimage._readheader: Invalid name "l" (should match [a-z_][a-z0-9_]{2,30}$) C: 52,16:pnmimage._readheader: Invalid name "l" (should match [a-z_][a-z0-9_]{2,30}$) C: 53,36:pnmimage._readheader: More than one statement on a single line C: 53,36:pnmimage._readheader: Invalid name "l" (should match [a-z_][a-z0-9_]{2,30}$) C: 54,16:pnmimage._readheader: Invalid name "s" (should match [a-z_][a-z0-9_]{2,30}$) C: 61,16:pnmimage._readheader: Invalid name "l" (should match [a-z_][a-z0-9_]{2,30}$) C: 62,36:pnmimage._readheader: More than one statement on a single line C: 62,36:pnmimage._readheader: Invalid name "l" (should match [a-z_][a-z0-9_]{2,30}$) C: 70,8:pnmimage._readheader: Invalid name "m" (should match [a-z_][a-z0-9_]{2,30}$) R: 35,4:pnmimage._readheader: Too many branches (13/12) C:103,4:pnmimage.P1dec: Invalid name "P1dec" (should match [a-z_][a-z0-9_]{2,30}$) C:103,4:pnmimage.P1dec: Missing docstring E:104,28:pnmimage.P1dec: Undefined variable 'self' E:104,39:pnmimage.P1dec: Undefined variable 'self' C:106,12:pnmimage.P1dec: Invalid name "l" (should match [a-z_][a-z0-9_]{2,30}$) C:114,4:pnmimage.P4dec: Invalid name "P4dec" (should match [a-z_][a-z0-9_]{2,30}$) C:114,4:pnmimage.P4dec: Missing docstring W:114,14:pnmimage.P4dec: Unused argument 'buf' W:114,19:pnmimage.P4dec: Unused argument 'bytecode' C:120,4:pnmimage.P2dec: Invalid name "P2dec" (should match [a-z_][a-z0-9_]{2,30}$) C:120,4:pnmimage.P2dec: Missing docstring E:121,28:pnmimage.P2dec: Undefined variable 'self' E:121,39:pnmimage.P2dec: Undefined variable 'self' C:123,12:pnmimage.P2dec: Invalid name "l" (should match [a-z_][a-z0-9_]{2,30}$) C:131,4:pnmimage.P5dec: Invalid name "P5dec" (should match [a-z_][a-z0-9_]{2,30}$) C:131,4:pnmimage.P5dec: Missing docstring C:132,8:pnmimage.P5dec: Invalid name "l" (should match [a-z_][a-z0-9_]{2,30}$) E:134,65:pnmimage.P5dec: Undefined variable 'self' E:134,76:pnmimage.P5dec: Undefined variable 'self' C:140,4:pnmimage.P3dec: Invalid name "P3dec" (should match [a-z_][a-z0-9_]{2,30}$) C:140,4:pnmimage.P3dec: Missing docstring W:140,14:pnmimage.P3dec: Unused argument 'buf' W:140,19:pnmimage.P3dec: Unused argument 'bytecode' C:146,4:pnmimage.P6dec: Invalid name "P6dec" (should match [a-z_][a-z0-9_]{2,30}$) C:146,4:pnmimage.P6dec: Missing docstring W:146,14:pnmimage.P6dec: Unused argument 'buf' W:146,19:pnmimage.P6dec: Unused argument 'bytecode' C:152,4:pnmimage.P7dec: Invalid name "P7dec" (should match [a-z_][a-z0-9_]{2,30}$) C:152,4:pnmimage.P7dec: Missing docstring W:152,14:pnmimage.P7dec: Unused argument 'buf' W:152,19:pnmimage.P7dec: Unused argument 'bytecode' C:161,4:pnmimage.checkData: Invalid name "checkData" (should match [a-z_][a-z0-9_]{2,30}$) R: 23,0:pnmimage: Too many public methods (32/20) R: 23,0:pnmimage: Abstract class not referenced Report ====== 110 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |41 |43 |-2.00 | +-----------+-------+---------+-----------+ |refactor |4 |4 |= | +-----------+-------+---------+-----------+ |warning |8 |4 |+4.00 | +-----------+-------+---------+-----------+ |error |6 |12 |-6.00 | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |23 | +-----------+------------+ |W0613 |8 | +-----------+------------+ |C0301 |8 | +-----------+------------+ |C0111 |8 | +-----------+------------+ |E0602 |6 | +-----------+------------+ |C0321 |2 | +-----------+------------+ |R0921 |1 | +-----------+------------+ |R0912 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ |R0902 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 2.45/10 (previous run: -1.44/10) Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |121 |80.67 |98 |+23.00 | +----------+-------+------+---------+-----------+ |docstring |15 |10.00 |10 |+5.00 | +----------+-------+------+---------+-----------+ |comment |8 |5.33 |8 |= | +----------+-------+------+---------+-----------+ |empty |6 |4.00 |10 |-4.00 | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (pnmimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |1 |= |0.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |12 |11 |+1.00 |41.67 |66.67 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/testcompression.py.lint0000644000175000017500000001135612233243325021463 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.testcompression C: 42,0: Line too long (217/80) C: 43,0: Line too long (390/80) C: 55,0: Line too long (84/80) C: 56,0: Line too long (92/80) C: 59,0: Line too long (86/80) C: 61,0: Line too long (89/80) C: 63,0: Line too long (90/80) C: 65,0: Line too long (105/80) C: 67,0: Line too long (103/80) C: 11,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 12,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 26,0: No exception type(s) specified W: 29,0: Relative import 'utilstest', should be 'test.utilstest' C: 37,0:testbyteoffset: Invalid name "testbyteoffset" (should match [A-Z_][a-zA-Z0-9]+$) C: 42,8:testbyteoffset.setUp: Invalid name "ds" (should match [a-z_][a-z0-9_]{2,30}$) C: 41,4:testbyteoffset.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C: 44,4:testbyteoffset.testComp: Invalid name "testComp" (should match [a-z_][a-z0-9_]{2,30}$) C: 44,4:testbyteoffset.testComp: Empty docstring C: 47,8:testbyteoffset.testComp: Invalid name "ds" (should match [a-z_][a-z0-9_]{2,30}$) C: 50,8:testbyteoffset.testComp: Invalid name "ds" (should match [a-z_][a-z0-9_]{2,30}$) C: 53,8:testbyteoffset.testComp: Invalid name "ds" (should match [a-z_][a-z0-9_]{2,30}$) C: 58,4:testbyteoffset.testSC: Invalid name "testSC" (should match [a-z_][a-z0-9_]{2,30}$) R: 37,0:testbyteoffset: Too many public methods (47/20) C: 74,0:test_suite_all_compression: Missing docstring C: 75,4:test_suite_all_compression: Invalid name "testSuite" (should match [a-z_][a-z0-9_]{2,30}$) C: 81,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 82,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 32,0: Unused import fabio Report ====== 57 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |24 |NC |NC | +-----------+-------+---------+-----------+ |refactor |1 |NC |NC | +-----------+-------+---------+-----------+ |warning |3 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |13 | +-----------+------------+ |C0301 |9 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0611 |1 | +-----------+------------+ |W0403 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ |C0112 |1 | +-----------+------------+ |C0111 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 5.09/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |57 |69.51 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |11 |13.41 |NC |NC | +----------+-------+------+---------+-----------+ |comment |2 |2.44 |NC |NC | +----------+-------+------+---------+-----------+ |empty |12 |14.63 |NC |NC | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (test.testcompression) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |NC |NC |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |3 |NC |NC |66.67 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/lintem.py0000744000175000017500000000352012126623347016547 0ustar jeromejerome00000000000000#!/usr/bin/python # coding: utf8 from __future__ import with_statement __author__ = "Jerome Kieffer" __email__ = "jerome.kieffer@esrf.fr" __doc__ = "This runs pylint on all modules from fabio package" __date__ = "20120416" __status__ = "production" __licence__ = "GPL" import os, subprocess, sys, distutils.util import numpy import Image from os.path import dirname arch = "lib.%s-%i.%i" % (distutils.util.get_platform(), sys.version_info[0], sys.version_info[1]) pylint_dir = os.path.dirname(os.path.abspath(__file__)) fabio_root = os.path.dirname(pylint_dir) installDir = os.path.abspath(os.path.join(fabio_root, "build", arch, "fabio")) testDir = os.path.abspath(os.path.join(fabio_root, "test")) sys.path.append(testDir) import utilstest #env = {"PYTHONPATH":":".join([installDir, testDir, dirname(dirname(numpy.__file__)), dirname(Image.__file__)])} env = {"PYTHONPATH":installDir} print env def lintit(infile, outfile): print ("Updating %s" % outfile) process = subprocess.Popen(["pylint", infile], stdout=subprocess.PIPE, stderr=subprocess.PIPE, env=env) result, error = process.communicate() if len(result) > 0: with open(outfile, "wb") as lintfile: if len(error) > 0: lintfile.write(error + os.linesep) lintfile.write(result) else: print ("Error in running pylint on %s:%s%s" % (infile, os.linesep, error)) files = [ os.path.join(installDir, i) for i in os.listdir(installDir) if i.endswith(".py") ] + \ [ os.path.join(testDir, i) for i in os.listdir(testDir) if i.endswith(".py") ] for f in files: outf = os.path.join(pylint_dir, os.path.basename(f) + ".lint") if not os.path.exists(outf) : lintit(f, outf) elif os.stat(f).st_mtime > os.stat(outf).st_mtime: lintit(f, outf) else: print ("Not updating %s" % outf) # lintit(f, outf) fabio-0.1.3/pylint/GEimage.py.lint0000644000175000017500000000746312233243303017520 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module GEimage C: 1,0: Missing docstring C: 17,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) R:181,0:GEimage: Too many instance attributes (9/7) C:181,0:GEimage: Missing docstring W:191,26:GEimage._readheader: Redefining built-in 'format' W:253,4:GEimage.write: Arguments number differs from overridden method W:253,27:GEimage.write: Unused argument 'force_type' W:270,17:GEimage.getframe: Access to a protected member _open of a client class W:271,8:GEimage.getframe: Access to a protected member _readframe of a client class R:181,0:GEimage: Too many public methods (25/20) W:269,8:GEimage.getframe: Attribute 'sequencefilename' defined outside __init__ C:300,0:demo: Missing docstring Report ====== 94 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |4 |4 |= | +-----------+-------+---------+-----------+ |refactor |2 |1 |+1.00 | +-----------+-------+---------+-----------+ |warning |6 |8 |-2.00 | +-----------+-------+---------+-----------+ |error |0 |3 |-3.00 | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0111 |3 | +-----------+------------+ |W0212 |2 | +-----------+------------+ |W0622 |1 | +-----------+------------+ |W0613 |1 | +-----------+------------+ |W0221 |1 | +-----------+------------+ |W0201 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ |R0902 |1 | +-----------+------------+ |C0103 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 8.72/10 (previous run: 6.99/10) Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |262 |82.39 |260 |+2.00 | +----------+-------+------+---------+-----------+ |docstring |24 |7.55 |24 |= | +----------+-------+------+---------+-----------+ |comment |13 |4.09 |13 |= | +----------+-------+------+---------+-----------+ |empty |19 |5.97 |21 |-2.00 | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (GEimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |1 |= |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |method |8 |8 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |1 |= |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/GEimage_old.py.lint0000644000175000017500000001223612233243313020351 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module GEimage_old C: 40,0: Line too long (88/80) C: 41,0: Line too long (97/80) C: 42,0: Line too long (92/80) C: 43,0: Line too long (101/80) C: 45,0: Line too long (89/80) C: 46,0: Line too long (94/80) C: 47,0: Line too long (94/80) C: 48,0: Line too long (87/80) C: 65,0: Line too long (86/80) C: 68,0: Line too long (92/80) C: 71,0: Line too long (112/80) C: 74,0: Line too long (112/80) C: 89,0: Line too long (82/80) C:104,0: Line too long (82/80) C:107,0: Line too long (82/80) C:113,0: Line too long (88/80) C:116,0: Line too long (98/80) C:119,0: Line too long (102/80) C:122,0: Line too long (82/80) C:129,0: Line too long (96/80) C:132,0: Line too long (100/80) C:135,0: Line too long (96/80) C:156,0: Line too long (88/80) C:159,0: Line too long (102/80) C:168,0: Line too long (94/80) C:219,0: Line too long (88/80) C:222,0: Line too long (84/80) C:225,0: Line too long (90/80) C:228,0: Line too long (90/80) C:231,0: Line too long (86/80) C:237,0: Line too long (106/80) C:240,0: Line too long (102/80) C:246,0: Line too long (98/80) C:252,0: Line too long (92/80) C:272,0: Line too long (86/80) C:293,0: Line too long (84/80) C:299,0: Line too long (82/80) C:302,0: Line too long (82/80) C:305,0: Line too long (82/80) C:308,0: Line too long (82/80) C:311,0: Line too long (102/80) C:314,0: Line too long (98/80) C:320,0: Line too long (84/80) C:352,0: Line too long (92/80) C:355,0: Line too long (88/80) C:358,0: Line too long (84/80) C:361,0: Line too long (90/80) C:381,0: Line too long (100/80) C:384,0: Line too long (96/80) C:449,0: Line too long (82/80) C:484,0: Line too long (92/80) C: 1,0: Invalid name "GEimage_old" (should match (([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$) R: 26,0:GEimage: Too many instance attributes (9/7) C: 34,8:GEimage._readheader: Invalid name "ImageFormat" (should match [a-z_][a-z0-9_]{2,30}$) C: 53,8:GEimage._readheader: Invalid name "DUTID" (should match [a-z_][a-z0-9_]{2,30}$) C: 26,0:GEimage: Missing docstring C:486,8:GEimage.read: Invalid name "ReadBytes" (should match [a-z_][a-z0-9_]{2,30}$) R: 26,0:GEimage: Too many public methods (25/20) W: 34,8:GEimage._readheader: Attribute 'ImageFormat' defined outside __init__ W: 53,8:GEimage._readheader: Attribute 'DUTID' defined outside __init__ Report ====== 50 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |56 |57 |-1.00 | +-----------+-------+---------+-----------+ |refactor |2 |2 |= | +-----------+-------+---------+-----------+ |warning |2 |10 |-8.00 | +-----------+-------+---------+-----------+ |error |0 |21 |-21.00 | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0301 |51 | +-----------+------------+ |C0103 |4 | +-----------+------------+ |W0201 |2 | +-----------+------------+ |R0904 |1 | +-----------+------------+ |R0902 |1 | +-----------+------------+ |C0111 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at -2.00/10 (previous run: -24.80/10) Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |50 |10.25 |50 |= | +----------+-------+------+---------+-----------+ |docstring |24 |4.92 |24 |= | +----------+-------+------+---------+-----------+ |comment |267 |54.71 |267 |= | +----------+-------+------+---------+-----------+ |empty |147 |30.12 |147 |= | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (GEimage_old) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |1 |= |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |method |2 |2 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/testGEimage.py.lint0000644000175000017500000001014012233243331020403 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.testGEimage C: 34,0: Line too long (86/80) C: 36,0: Line too long (89/80) C: 1,0: Invalid name "testGEimage" (should match (([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$) C: 10,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 11,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 25,0: No exception type(s) specified W: 28,0: Relative import 'utilstest', should be 'test.utilstest' C: 39,0:testGE: Invalid name "testGE" (should match [A-Z_][a-zA-Z0-9]+$) C: 45,8:testGE.setUp: Invalid name "GE" (should match [a-z_][a-z0-9_]{2,30}$) C: 39,0:testGE: Missing docstring C: 41,4:testGE.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C: 48,4:testGE.test_read: Missing docstring R: 39,0:testGE: Too many public methods (46/20) C: 65,0:test_suite_all_GE: Invalid name "test_suite_all_GE" (should match [a-z_][a-z0-9_]{2,30}$) C: 65,0:test_suite_all_GE: Missing docstring C: 66,4:test_suite_all_GE: Invalid name "testSuite" (should match [a-z_][a-z0-9_]{2,30}$) C: 71,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 72,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 31,0: Unused import fabio Report ====== 49 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |15 |NC |NC | +-----------+-------+---------+-----------+ |refactor |1 |NC |NC | +-----------+-------+---------+-----------+ |warning |3 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |10 | +-----------+------------+ |C0111 |3 | +-----------+------------+ |C0301 |2 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0611 |1 | +-----------+------------+ |W0403 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 6.12/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |50 |71.43 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |8 |11.43 |NC |NC | +----------+-------+------+---------+-----------+ |comment |2 |2.86 |NC |NC | +----------+-------+------+---------+-----------+ |empty |10 |14.29 |NC |NC | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |NC |NC |0.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |2 |NC |NC |50.00 |50.00 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |0.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/testedfimage.py.lint0000644000175000017500000002355612233243340020665 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.testedfimage C: 72,0: Line too long (86/80) C: 73,0: Line too long (86/80) C: 75,0: Line too long (106/80) C: 76,0: Line too long (105/80) C: 96,0: Line too long (101/80) W: 96,0: Bad indentation. Found 20 spaces, expected 12 C:105,0: Line too long (98/80) W:105,0: Bad indentation. Found 20 spaces, expected 12 C:124,0: Line too long (85/80) C:140,0: Line too long (89/80) C:141,0: Line too long (87/80) C:143,0: Line too long (89/80) C:144,0: Line too long (87/80) C:145,0: Line too long (95/80) C:154,0: Line too long (123/80) C:179,0: Line too long (83/80) C:183,0: Line too long (86/80) C:187,0: Line too long (92/80) C:188,0: Line too long (93/80) C:189,0: Line too long (104/80) C:199,0: Line too long (82/80) C:200,0: Line too long (82/80) C:207,0: Line too long (105/80) C:211,0: Line too long (89/80) C:215,0: Line too long (89/80) C:219,0: Line too long (110/80) C:221,0: Line too long (100/80) C:222,0: Line too long (110/80) C:226,0: Line too long (109/80) C:228,0: Line too long (108/80) C:232,0: Line too long (106/80) C:234,0: Line too long (102/80) C:238,0: Line too long (105/80) C:240,0: Line too long (101/80) C:245,0: Line too long (104/80) C:247,0: Line too long (104/80) C:252,0: Line too long (103/80) C:254,0: Line too long (105/80) C:257,0: Line too long (84/80) C:258,0: Line too long (145/80) C:259,0: Line too long (147/80) C:260,0: Line too long (147/80) C:274,0: Line too long (83/80) C:292,0: Line too long (94/80) C:300,0: Line too long (94/80) C:308,0: Line too long (94/80) C: 10,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 11,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 25,0: No exception type(s) specified W: 28,0: Relative import 'utilstest', should be 'test.utilstest' C: 38,0:testflatedfs: Invalid name "testflatedfs" (should match [A-Z_][a-zA-Z0-9]+$) C: 58,4:testflatedfs.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R: 38,0:testflatedfs: Too many public methods (47/20) C: 90,0:testbzipedf: Invalid name "testbzipedf" (should match [A-Z_][a-zA-Z0-9]+$) C: 92,4:testbzipedf.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R: 90,0:testbzipedf: Too many public methods (47/20) C: 99,0:testgzipedf: Invalid name "testgzipedf" (should match [A-Z_][a-zA-Z0-9]+$) C:101,4:testgzipedf.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R: 99,0:testgzipedf: Too many public methods (47/20) C:119,0:testedfs: Invalid name "testedfs" (should match [A-Z_][a-zA-Z0-9]+$) C:123,4:testedfs.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C:151,8:testedfs.test_rebin: Invalid name "f" (should match [a-z_][a-z0-9_]{2,30}$) R:119,0:testedfs: Too many public methods (47/20) C:158,0:testedfcompresseddata: Invalid name "testedfcompresseddata" (should match [A-Z_][a-zA-Z0-9]+$) C:163,4:testedfcompresseddata.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C:173,8:testedfcompresseddata.test_read: Invalid name "refFile" (should match [a-z_][a-z0-9_]{2,30}$) C:174,8:testedfcompresseddata.test_read: Invalid name "gzippedFile" (should match [a-z_][a-z0-9_]{2,30}$) C:175,8:testedfcompresseddata.test_read: Invalid name "compressedFile" (should match [a-z_][a-z0-9_]{2,30}$) R:158,0:testedfcompresseddata: Too many public methods (46/20) C:192,0:testedfmultiframe: Invalid name "testedfmultiframe" (should match [A-Z_][a-zA-Z0-9]+$) C:200,8:testedfmultiframe.setUp: Invalid name "Frame1Filename" (should match [a-z_][a-z0-9_]{2,30}$) C:198,8:testedfmultiframe.setUp: Invalid name "multiFrameFilename" (should match [a-z_][a-z0-9_]{2,30}$) C:199,8:testedfmultiframe.setUp: Invalid name "Frame0Filename" (should match [a-z_][a-z0-9_]{2,30}$) C:197,4:testedfmultiframe.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) E:211,73:testedfmultiframe.setUp: Instance of 'testedfmultiframe' has no 'Frame0File' member E:215,73:testedfmultiframe.setUp: Instance of 'testedfmultiframe' has no 'Frame1File' member C:217,4:testedfmultiframe.test_getFrame_multi: Invalid name "test_getFrame_multi" (should match [a-z_][a-z0-9_]{2,30}$) C:224,4:testedfmultiframe.test_getFrame_mono: Invalid name "test_getFrame_mono" (should match [a-z_][a-z0-9_]{2,30}$) W:233,8:testedfmultiframe.test_next_multi: Redefining built-in 'next' W:239,8:testedfmultiframe.text_next_mono: Redefining built-in 'next' C:244,8:testedfmultiframe.test_previous_multi: Invalid name "f1" (should match [a-z_][a-z0-9_]{2,30}$) C:246,8:testedfmultiframe.test_previous_multi: Invalid name "f0" (should match [a-z_][a-z0-9_]{2,30}$) C:251,8:testedfmultiframe.test_previous_mono: Invalid name "f1" (should match [a-z_][a-z0-9_]{2,30}$) R:192,0:testedfmultiframe: Too many public methods (52/20) C:262,0:testedffastread: Invalid name "testedffastread" (should match [A-Z_][a-zA-Z0-9]+$) C:268,8:testedffastread.setUp: Invalid name "refFilename" (should match [a-z_][a-z0-9_]{2,30}$) C:269,8:testedffastread.setUp: Invalid name "fastFilename" (should match [a-z_][a-z0-9_]{2,30}$) C:267,4:testedffastread.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C:270,4:testedffastread.test_fastread: Missing docstring R:262,0:testedffastread: Too many public methods (46/20) C:276,0:testedfwrite: Invalid name "testedfwrite" (should match [A-Z_][a-zA-Z0-9]+$) C:281,4:testedfwrite.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C:285,4:testedfwrite.testFlat: Invalid name "testFlat" (should match [a-z_][a-z0-9_]{2,30}$) C:285,4:testedfwrite.testFlat: Missing docstring C:287,8:testedfwrite.testFlat: Invalid name "e" (should match [a-z_][a-z0-9_]{2,30}$) C:289,8:testedfwrite.testFlat: Invalid name "r" (should match [a-z_][a-z0-9_]{2,30}$) C:293,4:testedfwrite.testGzip: Invalid name "testGzip" (should match [a-z_][a-z0-9_]{2,30}$) C:293,4:testedfwrite.testGzip: Missing docstring C:295,8:testedfwrite.testGzip: Invalid name "e" (should match [a-z_][a-z0-9_]{2,30}$) C:297,8:testedfwrite.testGzip: Invalid name "r" (should match [a-z_][a-z0-9_]{2,30}$) C:301,4:testedfwrite.testBzip2: Invalid name "testBzip2" (should match [a-z_][a-z0-9_]{2,30}$) C:301,4:testedfwrite.testBzip2: Missing docstring C:303,8:testedfwrite.testBzip2: Invalid name "e" (should match [a-z_][a-z0-9_]{2,30}$) C:305,8:testedfwrite.testBzip2: Invalid name "r" (should match [a-z_][a-z0-9_]{2,30}$) C:309,4:testedfwrite.tearDown: Invalid name "tearDown" (should match [a-z_][a-z0-9_]{2,30}$) R:276,0:testedfwrite: Too many public methods (48/20) W:302,8:testedfwrite.testBzip2: Attribute 'filename' defined outside __init__ C:313,0:test_suite_all_edf: Missing docstring C:314,4:test_suite_all_edf: Invalid name "testSuite" (should match [a-z_][a-z0-9_]{2,30}$) C:338,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:339,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) Report ====== 239 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |94 |NC |NC | +-----------+-------+---------+-----------+ |refactor |8 |NC |NC | +-----------+-------+---------+-----------+ |warning |7 |NC |NC | +-----------+-------+---------+-----------+ |error |2 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |45 | +-----------+------------+ |C0301 |44 | +-----------+------------+ |R0904 |8 | +-----------+------------+ |C0111 |5 | +-----------+------------+ |W0622 |2 | +-----------+------------+ |W0311 |2 | +-----------+------------+ |E1101 |2 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0403 |1 | +-----------+------------+ |W0201 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 5.02/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |242 |75.39 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |51 |15.89 |NC |NC | +----------+-------+------+---------+-----------+ |comment |4 |1.25 |NC |NC | +----------+-------+------+---------+-----------+ |empty |24 |7.48 |NC |NC | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (test.testedfimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |8 |NC |NC |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |25 |NC |NC |84.00 |56.00 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/.pylintrc0000644000175000017500000002127012120434325016541 0ustar jeromejerome00000000000000# lint Python modules using external checkers. # # This is the main checker controling the other ones and the reports # generation. It is itself both a raw checker and an astng checker in order # to: # * handle message activation / deactivation at the module level # * handle some basic but necessary stats'data (number of classes, methods...) # [MASTER] # Specify a configuration file. #rcfile= # Profiled execution. profile=no # Add to the black list. It should be a base name, not a # path. You may set this option multiple times. ignore=CVS # Pickle collected data for later comparisons. persistent=yes # Set the cache size for astng objects. cache-size=500 # List of plugins (as comma separated values of python modules names) to load, # usually to register additional checkers. load-plugins= [COMMANDS] # Display a help message for the given message id and exit. The value may be a # comma separated list of message ids. #help-msg= [MESSAGES CONTROL] # Enable only checker(s) with the given id(s). This option conflict with the # disable-checker option #enable-checker= # Enable all checker(s) except those with the given id(s). This option conflict # with the disable-checker option #disable-checker= # Enable all messages in the listed categories. #enable-msg-cat= # Disable all messages in the listed categories. #disable-msg-cat= # Enable the message(s) with the given id(s). #enable-msg= # Disable the message(s) with the given id(s). #disable-msg= [REPORTS] # set the output format. Available formats are text, parseable, colorized and # html output-format=text # Include message's id in output include-ids=yes # Put messages in a separate file for each module / package specified on the # command line instead of printing them on stdout. Reports (if any) will be # written in a file name "pylint_global.[txt|html]". files-output=no # Tells wether to display a full report or only the messages reports=yes # Python expression which should return a note less than 10 (10 is the highest # note).You have access to the variables errors warning, statement which # respectivly contain the number of errors / warnings messages and the total # number of statements analyzed. This is used by the global evaluation report # (R0004). evaluation=10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10) # Add a comment according to your evaluation note. This is used by the global # evaluation report (R0004). comment=no # Enable the report(s) with the given id(s). #enable-report= # Disable the report(s) with the given id(s). #disable-report= # checks for # * unused variables / imports # * undefined variables # * redefinition of variable from builtins or from an outer scope # * use of variable before assigment # [VARIABLES] # Tells wether we should check for unused import in __init__ files. init-import=no # A regular expression matching names used for dummy variables (i.e. not used). dummy-variables-rgx=_|dummy # List of additional names supposed to be defined in builtins. Remember that # you should avoid to define new builtins when possible. additional-builtins= # try to find bugs in the code using type inference # [TYPECHECK] # Tells wether missing members accessed in mixin class should be ignored. A # mixin class is detected if its name ends with "mixin" (case insensitive). ignore-mixin-members=yes # When zope mode is activated, consider the acquired-members option to ignore # access to some undefined attributes. zope=no # List of members which are usually get through zope's acquisition mecanism and # so shouldn't trigger E0201 when accessed (need zope=yes to be considered). acquired-members=REQUEST,acl_users,aq_parent # checks for : # * doc strings # * modules / classes / functions / methods / arguments / variables name # * number of arguments, local variables, branchs, returns and statements in # functions, methods # * required module attributes # * dangerous default values as arguments # * redefinition of function / method / class # * uses of the global statement # [BASIC] # Required attributes for module, separated by a comma required-attributes= # Regular expression which should only match functions or classes name which do # not require a docstring no-docstring-rgx=__.*__ # Regular expression which should only match correct module names module-rgx=(([a-z_][a-z0-9_]*)|([a-z][a-zA-Z0-9]+))$ # Regular expression which should only match correct module level names const-rgx=(([A-Z_]*)|(__.*__))$ # Regular expression which should only match correct class names class-rgx=[a-z_][a-zA-Z0-9]+$ # Regular expression which should only match correct function names function-rgx=[a-z_][a-z0-9_]{2,30}$ # Regular expression which should only match correct method names method-rgx=[a-z_][a-z0-9_]{2,30}$ # Regular expression which should only match correct instance attribute names attr-rgx=[a-z_][a-z0-9_]{2,30}$ # Regular expression which should only match correct argument names argument-rgx=[a-z_][a-z0-9_]{2,30}$ # Regular expression which should only match correct variable names variable-rgx=[a-z_][a-z0-9_]{2,30}$ # Regular expression which should only match correct list comprehension / # generator expression variable names inlinevar-rgx=[A-Za-z_][A-Za-z0-9_]*$ # Good variable names which should always be accepted, separated by a comma good-names=i,j,k,x,y,ex,Run,_ # Bad variable names which should always be refused, separated by a comma bad-names=foo,bar,baz,toto,tutu,tata # List of builtins function names that should not be used, separated by a comma bad-functions=map,filter,apply,input # checks for sign of poor/misdesign: # * number of methods, attributes, local variables... # * size, complexity of functions, methods # [DESIGN] # Maximum number of arguments for function / method max-args=5 # Maximum number of locals for function / method body max-locals=15 # Maximum number of return / yield for function / method body max-returns=6 # Maximum number of branch for function / method body max-branchs=12 # Maximum number of statements in function / method body max-statements=50 # Maximum number of parents for a class (see R0901). max-parents=7 # Maximum number of attributes for a class (see R0902). max-attributes=7 # Minimum number of public methods for a class (see R0903). min-public-methods=2 # Maximum number of public methods for a class (see R0904). max-public-methods=20 # checks for : # * methods without self as first argument # * overridden methods signature # * access only to existant members via self # * attributes not defined in the __init__ method # * supported interfaces implementation # * unreachable code # [CLASSES] # List of interface methods to ignore, separated by a comma. This is used for # instance to not check methods defines in Zope's Interface base class. ignore-iface-methods=isImplementedBy,deferred,extends,names,namesAndDescriptions,queryDescriptionFor,getBases,getDescriptionFor,getDoc,getName,getTaggedValue,getTaggedValueTags,isEqualOrExtendedBy,setTaggedValue,isImplementedByInstancesOf,adaptWith,is_implemented_by # List of method names used to declare (i.e. assign) instance attributes. defining-attr-methods=__init__,__new__,setUp # checks for # * external modules dependencies # * relative / wildcard imports # * cyclic imports # * uses of deprecated modules # [IMPORTS] # Deprecated modules which should not be used, separated by a comma deprecated-modules=regsub,string,TERMIOS,Bastion,rexec # Create a graph of every (i.e. internal and external) dependencies in the # given file (report R0402 must not be disabled) import-graph= # Create a graph of external dependencies in the given file (report R0402 must # not be disabled) ext-import-graph= # Create a graph of internal dependencies in the given file (report R0402 must # not be disabled) int-import-graph= # checks for : # * unauthorized constructions # * strict indentation # * line length # * use of <> instead of != # [FORMAT] # Maximum number of characters on a single line. max-line-length=80 # Maximum number of lines in a module max-module-lines=1000 # String used as indentation unit. This is usually " " (4 spaces) or "\t" (1 # tab). indent-string=' ' # checks for similarities and duplicated code. This computation may be # memory / CPU intensive, so you should disable it if you experiments some # problems. # [SIMILARITIES] # Minimum lines number of a similarity. min-similarity-lines=4 # Ignore comments when computing similarities. ignore-comments=yes # Ignore docstrings when computing similarities. ignore-docstrings=yes # checks for: # * warning notes in the code like FIXME, XXX # * PEP 263: source code with non ascii character but no encoding declaration # [MISCELLANEOUS] # List of note tags to take in consideration, separated by a comma. notes=FIXME,XXX,TODO fabio-0.1.3/pylint/fit2dspreadsheetimage.py.lint0000644000175000017500000000664212233243315022466 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module fit2dspreadsheetimage W: 23,0: TODO : test for minimal attributes? C: 15,0:fit2dspreadsheetimage: Invalid name "fit2dspreadsheetimage" (should match [A-Z_][a-zA-Z0-9]+$) W: 62,16:fit2dspreadsheetimage.read: No exception type(s) specified R: 15,0:fit2dspreadsheetimage: Too many public methods (25/20) C: 78,4: Invalid name "start" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 79,4: Invalid name "img" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) Report ====== 51 statements analysed. Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |3 |3 |= | +-----------+-------+---------+-----------+ |refactor |1 |1 |= | +-----------+-------+---------+-----------+ |warning |2 |9 |-7.00 | +-----------+-------+---------+-----------+ |error |0 |6 |-6.00 | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |3 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0511 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 8.82/10 (previous run: 1.57/10) Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |50 |60.98 |50 |= | +----------+-------+------+---------+-----------+ |docstring |16 |19.51 |16 |= | +----------+-------+------+---------+-----------+ |comment |1 |1.22 |1 |= | +----------+-------+------+---------+-----------+ |empty |15 |18.29 |15 |= | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: matplotlib \-pylab \-imshow (fit2dspreadsheetimage) \-show (fit2dspreadsheetimage) numpy (fit2dspreadsheetimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |1 |= |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |2 |2 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/file_series.py.lint0000644000175000017500000001054112233243304020503 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module file_series C:116,0: Line too long (93/80) C: 18,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 32,4:new_file_series0: Invalid name "im" (should match [a-z_][a-z0-9_]{2,30}$) W: 47,15:new_file_series0: Catching too general exception Exception C: 46,12:new_file_series0: Invalid name "im" (should match [a-z_][a-z0-9_]{2,30}$) W: 54,19:new_file_series0: Catching too general exception Exception C: 95,4:new_file_series: Invalid name "im" (should match [a-z_][a-z0-9_]{2,30}$) W:106,15:new_file_series: Catching too general exception Exception C:104,12:new_file_series: Invalid name "im" (should match [a-z_][a-z0-9_]{2,30}$) C:105,12:new_file_series: Invalid name "retVal" (should match [a-z_][a-z0-9_]{2,30}$) C:107,12:new_file_series: Invalid name "retVal" (should match [a-z_][a-z0-9_]{2,30}$) W:115,19:new_file_series: Catching too general exception Exception C:120,12:new_file_series: Invalid name "retVal" (should match [a-z_][a-z0-9_]{2,30}$) C:121,22:new_file_series: More than one statement on a single line C:126,0:file_series: Invalid name "file_series" (should match [A-Z_][a-zA-Z0-9]+$) R:126,0:file_series: Too many public methods (28/20) C:322,0:numbered_file_series: Invalid name "numbered_file_series" (should match [A-Z_][a-zA-Z0-9]+$) R:328,4:numbered_file_series.__init__: Too many arguments (8/5) R:322,0:numbered_file_series: Too many public methods (28/20) C:349,0:filename_series: Invalid name "filename_series" (should match [A-Z_][a-zA-Z0-9]+$) Report ====== 141 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |13 |11 |+2.00 | +-----------+-------+---------+-----------+ |refactor |3 |3 |= | +-----------+-------+---------+-----------+ |warning |4 |5 |-1.00 | +-----------+-------+---------+-----------+ |error |0 |0 |= | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |11 | +-----------+------------+ |W0703 |4 | +-----------+------------+ |R0904 |2 | +-----------+------------+ |R0913 |1 | +-----------+------------+ |C0321 |1 | +-----------+------------+ |C0301 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 8.58/10 (previous run: 8.64/10) Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |146 |36.68 |145 |+1.00 | +----------+-------+------+---------+-----------+ |docstring |194 |48.74 |101 |+93.00 | +----------+-------+------+---------+-----------+ |comment |7 |1.76 |7 |= | +----------+-------+------+---------+-----------+ |empty |51 |12.81 |33 |+18.00 | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |3 |3 |= |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |34 |34 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |function |2 |2 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/testopenheader.py.lint0000644000175000017500000000736512233243321021235 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.testopenheader C: 36,0: Line too long (83/80) C: 8,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 9,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 23,0: No exception type(s) specified W: 26,0: Relative import 'utilstest', should be 'test.utilstest' C: 33,0:test1: Invalid name "test1" (should match [A-Z_][a-zA-Z0-9]+$) C: 35,4:test1.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R: 33,0:test1: Too many public methods (46/20) C: 50,0:test_suite_all_openheader: Missing docstring C: 51,4:test_suite_all_openheader: Invalid name "testSuite" (should match [a-z_][a-z0-9_]{2,30}$) C: 56,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 57,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 29,0: Unused import fabio Report ====== 40 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |9 |NC |NC | +-----------+-------+---------+-----------+ |refactor |1 |NC |NC | +-----------+-------+---------+-----------+ |warning |3 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |7 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0611 |1 | +-----------+------------+ |W0403 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ |C0301 |1 | +-----------+------------+ |C0111 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 6.75/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |40 |72.73 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |7 |12.73 |NC |NC | +----------+-------+------+---------+-----------+ |comment |2 |3.64 |NC |NC | +----------+-------+------+---------+-----------+ |empty |6 |10.91 |NC |NC | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |NC |NC |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |2 |NC |NC |100.00 |50.00 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/benchheader.py.lint0000644000175000017500000000566012233243334020453 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.benchheader C: 11,0: Line too long (94/80) C: 1,0: Missing docstring C: 6,0: Invalid name "junk" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 11,0: Invalid name "images" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) Report ====== 10 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |4 |NC |NC | +-----------+-------+---------+-----------+ |refactor |0 |NC |NC | +-----------+-------+---------+-----------+ |warning |0 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |2 | +-----------+------------+ |C0301 |1 | +-----------+------------+ |C0111 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 6.00/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |10 |52.63 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |1 |5.26 |NC |NC | +----------+-------+------+---------+-----------+ |comment |3 |15.79 |NC |NC | +----------+-------+------+---------+-----------+ |empty |5 |26.32 |NC |NC | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |0 |NC |NC |0 |0 | +---------+-------+-----------+-----------+------------+---------+ |method |0 |NC |NC |0 |0 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |NC |NC |0 |0 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/HiPiCimage.py.lint0000644000175000017500000001026112233243304020150 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module HiPiCimage C: 93,0: Line too long (81/80) C: 17,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) R: 24,4:HiPiCimage._readheader: Too many local variables (17/15) C: 29,8:HiPiCimage._readheader: Invalid name "Image_tag" (should match [a-z_][a-z0-9_]{2,30}$) C: 31,8:HiPiCimage._readheader: Invalid name "Comment_len" (should match [a-z_][a-z0-9_]{2,30}$) C: 32,8:HiPiCimage._readheader: Invalid name "Dim_1" (should match [a-z_][a-z0-9_]{2,30}$) C: 33,8:HiPiCimage._readheader: Invalid name "Dim_2" (should match [a-z_][a-z0-9_]{2,30}$) C: 34,8:HiPiCimage._readheader: Invalid name "Dim_1_offset" (should match [a-z_][a-z0-9_]{2,30}$) C: 35,8:HiPiCimage._readheader: Invalid name "Dim_2_offset" (should match [a-z_][a-z0-9_]{2,30}$) C: 36,8:HiPiCimage._readheader: Invalid name "HeaderType" (should match [a-z_][a-z0-9_]{2,30}$) C: 37,8:HiPiCimage._readheader: Invalid name "Dump" (should match [a-z_][a-z0-9_]{2,30}$) C: 38,8:HiPiCimage._readheader: Invalid name "Comment" (should match [a-z_][a-z0-9_]{2,30}$) C: 49,8:HiPiCimage._readheader: Invalid name "Comment_split" (should match [a-z_][a-z0-9_]{2,30}$) W: 36,8:HiPiCimage._readheader: Unused variable 'HeaderType' W: 37,8:HiPiCimage._readheader: Unused variable 'Dump' R: 20,0:HiPiCimage: Too many public methods (25/20) Report ====== 58 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |12 |12 |= | +-----------+-------+---------+-----------+ |refactor |2 |2 |= | +-----------+-------+---------+-----------+ |warning |2 |10 |-8.00 | +-----------+-------+---------+-----------+ |error |0 |19 |-19.00 | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |11 | +-----------+------------+ |W0612 |2 | +-----------+------------+ |R0914 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ |C0301 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 7.24/10 (previous run: -10.52/10) Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |61 |59.80 |61 |= | +----------+-------+------+---------+-----------+ |docstring |23 |22.55 |23 |= | +----------+-------+------+---------+-----------+ |comment |8 |7.84 |8 |= | +----------+-------+------+---------+-----------+ |empty |10 |9.80 |10 |= | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (HiPiCimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |method |2 |2 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/testheadernotsingleton.py.lint0000644000175000017500000000740012233243330023005 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.testheadernotsingleton C: 10,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 11,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 25,0: No exception type(s) specified W: 28,0: Relative import 'utilstest', should be 'test.utilstest' C: 34,0:testheadernotsingleton: Invalid name "testheadernotsingleton" (should match [A-Z_][a-zA-Z0-9]+$) C: 34,0:testheadernotsingleton: Missing docstring C: 36,4:testheadernotsingleton.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C: 43,4:testheadernotsingleton.testheader: Missing docstring R: 34,0:testheadernotsingleton: Too many public methods (46/20) C: 55,0:test_suite_all_header: Missing docstring C: 56,4:test_suite_all_header: Invalid name "testSuite" (should match [a-z_][a-z0-9_]{2,30}$) C: 61,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 62,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) Report ====== 44 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |10 |NC |NC | +-----------+-------+---------+-----------+ |refactor |1 |NC |NC | +-----------+-------+---------+-----------+ |warning |2 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |7 | +-----------+------------+ |C0111 |3 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0403 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 7.05/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |44 |74.58 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |8 |13.56 |NC |NC | +----------+-------+------+---------+-----------+ |comment |2 |3.39 |NC |NC | +----------+-------+------+---------+-----------+ |empty |5 |8.47 |NC |NC | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |NC |NC |0.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |2 |NC |NC |50.00 |50.00 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/testmar345image.py.lint0000644000175000017500000001022412233243332021127 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.testmar345image C: 61,0: Line too long (98/80) C: 62,0: Line too long (98/80) C: 63,0: Line too long (101/80) C: 64,0: Line too long (111/80) C: 78,0: Line too long (86/80) C: 82,0: Line too long (81/80) C: 83,0: Line too long (154/80) C: 9,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 10,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 24,0: No exception type(s) specified W: 27,0: Relative import 'utilstest', should be 'test.utilstest' C: 39,0:testMAR345: Invalid name "testMAR345" (should match [A-Z_][a-zA-Z0-9]+$) C: 39,0:testMAR345: Missing docstring C: 40,4:testMAR345.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C: 46,4:testMAR345.tearDown: Invalid name "tearDown" (should match [a-z_][a-z0-9_]{2,30}$) W: 56,18:testMAR345.test_read: Unused variable 'dim2' W: 91,16:testMAR345.test_memoryleak: Unused variable 'img' R: 39,0:testMAR345: Too many public methods (48/20) C: 96,0:test_suite_all_mar345: Missing docstring C: 97,4:test_suite_all_mar345: Invalid name "testSuite" (should match [a-z_][a-z0-9_]{2,30}$) C:105,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:106,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) Report ====== 76 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |17 |NC |NC | +-----------+-------+---------+-----------+ |refactor |1 |NC |NC | +-----------+-------+---------+-----------+ |warning |4 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |8 | +-----------+------------+ |C0301 |7 | +-----------+------------+ |W0612 |2 | +-----------+------------+ |C0111 |2 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0403 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 7.11/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |77 |73.33 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |15 |14.29 |NC |NC | +----------+-------+------+---------+-----------+ |comment |3 |2.86 |NC |NC | +----------+-------+------+---------+-----------+ |empty |10 |9.52 |NC |NC | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |NC |NC |0.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |5 |NC |NC |100.00 |40.00 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/testadscimage.py.lint0000644000175000017500000001021712233243323021030 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.testadscimage C: 63,0: Line too long (115/80) C: 64,0: Line too long (115/80) C: 65,0: Line too long (91/80) C: 13,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 14,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 28,0: No exception type(s) specified W: 31,0: Relative import 'utilstest', should be 'test.utilstest' C: 47,0:testmatch: Invalid name "testmatch" (should match [A-Z_][a-zA-Z0-9]+$) C: 51,4:testmatch.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R: 47,0:testmatch: Too many public methods (46/20) C: 69,0:testflatmccdsadsc: Invalid name "testflatmccdsadsc" (should match [A-Z_][a-zA-Z0-9]+$) C: 69,0:testflatmccdsadsc: Empty docstring C: 72,4:testflatmccdsadsc.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R: 69,0:testflatmccdsadsc: Too many public methods (46/20) C: 97,0:test_suite_all_adsc: Missing docstring C: 98,4:test_suite_all_adsc: Invalid name "testSuite" (should match [a-z_][a-z0-9_]{2,30}$) C:104,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:105,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 34,0: Unused import fabio Report ====== 65 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |14 |NC |NC | +-----------+-------+---------+-----------+ |refactor |2 |NC |NC | +-----------+-------+---------+-----------+ |warning |3 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |9 | +-----------+------------+ |C0301 |3 | +-----------+------------+ |R0904 |2 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0611 |1 | +-----------+------------+ |W0403 |1 | +-----------+------------+ |C0112 |1 | +-----------+------------+ |C0111 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 7.08/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |67 |63.81 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |16 |15.24 |NC |NC | +----------+-------+------+---------+-----------+ |comment |4 |3.81 |NC |NC | +----------+-------+------+---------+-----------+ |empty |18 |17.14 |NC |NC | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |2 |NC |NC |50.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |4 |NC |NC |100.00 |50.00 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/testkcdimage.py.lint0000644000175000017500000000770612233243337020675 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.testkcdimage C: 42,0: Line too long (88/80) C: 69,0: Line too long (81/80) C: 10,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 11,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 25,0: No exception type(s) specified W: 28,0: Relative import 'utilstest', should be 'test.utilstest' C: 38,0:testkcd: Invalid name "testkcd" (should match [A-Z_][a-zA-Z0-9]+$) C: 47,8:testkcd.setUp: Invalid name "fn" (should match [a-z_][a-z0-9_]{2,30}$) C: 45,4:testkcd.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) W: 56,8:testkcd.test_read: Unused variable 'name' R: 38,0:testkcd: Too many public methods (47/20) C: 77,0:test_suite_all_kcd: Missing docstring C: 78,4:test_suite_all_kcd: Invalid name "testSuite" (should match [a-z_][a-z0-9_]{2,30}$) C: 84,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 85,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 33,0: Unused import edfimage Report ====== 62 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |11 |NC |NC | +-----------+-------+---------+-----------+ |refactor |1 |NC |NC | +-----------+-------+---------+-----------+ |warning |4 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |8 | +-----------+------------+ |C0301 |2 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0612 |1 | +-----------+------------+ |W0611 |1 | +-----------+------------+ |W0403 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ |C0111 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 7.42/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |61 |76.25 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |9 |11.25 |NC |NC | +----------+-------+------+---------+-----------+ |comment |2 |2.50 |NC |NC | +----------+-------+------+---------+-----------+ |empty |8 |10.00 |NC |NC | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |NC |NC |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |3 |NC |NC |100.00 |33.33 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/test_file_series.py.lint0000644000175000017500000000766412233243340021556 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.test_file_series C: 12,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 13,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 27,0: No exception type(s) specified W: 30,0: Relative import 'utilstest', should be 'test.utilstest' C: 37,0:testrandomseries: Invalid name "testrandomseries" (should match [A-Z_][a-zA-Z0-9]+$) C: 39,4:testrandomseries.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R: 37,0:testrandomseries: Too many public methods (48/20) C: 55,0:testedfnumbered: Invalid name "testedfnumbered" (should match [A-Z_][a-zA-Z0-9]+$) C: 59,4:testedfnumbered.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R: 55,0:testedfnumbered: Too many public methods (52/20) C:106,0:test_suite_all_series: Missing docstring C:107,4:test_suite_all_series: Invalid name "testSuite" (should match [a-z_][a-z0-9_]{2,30}$) C:125,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:126,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 33,4: Unused import fabio Report ====== 82 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |10 |NC |NC | +-----------+-------+---------+-----------+ |refactor |2 |NC |NC | +-----------+-------+---------+-----------+ |warning |3 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |9 | +-----------+------------+ |R0904 |2 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0611 |1 | +-----------+------------+ |W0403 |1 | +-----------+------------+ |C0111 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 8.17/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |81 |72.32 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |20 |17.86 |NC |NC | +----------+-------+------+---------+-----------+ |comment |2 |1.79 |NC |NC | +----------+-------+------+---------+-----------+ |empty |9 |8.04 |NC |NC | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |2 |NC |NC |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |12 |NC |NC |100.00 |16.67 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/binaryimage.py.lint0000644000175000017500000000766312233243275020523 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module binaryimage C: 46,0: Line too long (98/80) C: 48,0: Line too long (98/80) C: 79,0: Line too long (113/80) C: 84,0: Line too long (86/80) C: 98,0: Line too long (81/80) W: 6,0: Redefining built-in '__doc__' C: 1,0: Missing docstring C: 25,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 27,0:binaryimage: Invalid name "binaryimage" (should match [A-Z_][a-zA-Z0-9]+$) R: 51,4:binaryimage.read: Too many arguments (7/5) W: 51,4:binaryimage.read: Arguments number differs from overridden method C: 68,8:binaryimage.read: Invalid name "f" (should match [a-z_][a-z0-9_]{2,30}$) C: 82,8:binaryimage.read: Invalid name "rawData" (should match [a-z_][a-z0-9_]{2,30}$) C: 92,34:binaryimage.estimate_offset_value: Invalid name "f" (should match [a-z_][a-z0-9_]{2,30}$) R: 90,4:binaryimage.estimate_offset_value: Method could be a function R: 27,0:binaryimage: Too many public methods (27/20) Report ====== 53 statements analysed. Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |11 |NC |NC | +-----------+-------+---------+-----------+ |refactor |3 |NC |NC | +-----------+-------+---------+-----------+ |warning |2 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0301 |5 | +-----------+------------+ |C0103 |5 | +-----------+------------+ |W0622 |1 | +-----------+------------+ |W0221 |1 | +-----------+------------+ |R0913 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ |R0201 |1 | +-----------+------------+ |C0111 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 6.98/10 Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |65 |64.36 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |25 |24.75 |NC |NC | +----------+-------+------+---------+-----------+ |comment |3 |2.97 |NC |NC | +----------+-------+------+---------+-----------+ |empty |8 |7.92 |NC |NC | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (binaryimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |NC |NC |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |5 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |NC |NC |0 |0 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/testmccdimage.py.lint0000644000175000017500000001044412233243326021031 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.testmccdimage C: 50,0: Line too long (89/80) C: 63,0: Line too long (81/80) C: 10,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 11,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 25,0: No exception type(s) specified W: 28,0: Relative import 'utilstest', should be 'test.utilstest' C: 45,0:testnormaltifok: Invalid name "testnormaltifok" (should match [A-Z_][a-zA-Z0-9]+$) C: 51,4:testnormaltifok.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C: 60,4:testnormaltifok.test_read_openimage: Missing docstring R: 45,0:testnormaltifok: Too many public methods (46/20) C: 73,0:testflatmccds: Invalid name "testflatmccds" (should match [A-Z_][a-zA-Z0-9]+$) C: 75,8:testflatmccds.setUp: Invalid name "fn" (should match [a-z_][a-z0-9_]{2,30}$) C: 73,0:testflatmccds: Missing docstring C: 74,4:testflatmccds.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R: 73,0:testflatmccds: Too many public methods (46/20) C:103,0:test_suite_all_mccd: Missing docstring C:104,4:test_suite_all_mccd: Invalid name "testSuite" (should match [a-z_][a-z0-9_]{2,30}$) C:110,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:111,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 31,0: Unused import fabio Report ====== 74 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |15 |NC |NC | +-----------+-------+---------+-----------+ |refactor |2 |NC |NC | +-----------+-------+---------+-----------+ |warning |3 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |10 | +-----------+------------+ |C0111 |3 | +-----------+------------+ |R0904 |2 | +-----------+------------+ |C0301 |2 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0611 |1 | +-----------+------------+ |W0403 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 7.30/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |80 |72.73 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |12 |10.91 |NC |NC | +----------+-------+------+---------+-----------+ |comment |4 |3.64 |NC |NC | +----------+-------+------+---------+-----------+ |empty |14 |12.73 |NC |NC | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (test.testmccdimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |2 |NC |NC |50.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |4 |NC |NC |75.00 |50.00 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/testXSDimage.py.lint0000644000175000017500000001045012233243322020552 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.testXSDimage C: 39,0: Line too long (82/80) C: 70,0: Line too long (91/80) C: 77,0: Line too long (102/80) C: 84,0: Line too long (103/80) C: 1,0: Invalid name "testXSDimage" (should match (([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$) C: 13,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 14,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 28,0: No exception type(s) specified W: 31,0: Relative import 'utilstest', should be 'test.utilstest' C: 42,0:testXSD: Invalid name "testXSD" (should match [A-Z_][a-zA-Z0-9]+$) C: 44,8:testXSD.setUp: Invalid name "fn" (should match [a-z_][a-z0-9_]{2,30}$) C: 42,0:testXSD: Missing docstring C: 43,4:testXSD.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C: 74,8:testXSD.test_invert: Invalid name "m1" (should match [a-z_][a-z0-9_]{2,30}$) C: 75,8:testXSD.test_invert: Invalid name "m2" (should match [a-z_][a-z0-9_]{2,30}$) R: 42,0:testXSD: Too many public methods (48/20) C: 81,0:test_suite_all_XSD: Invalid name "test_suite_all_XSD" (should match [a-z_][a-z0-9_]{2,30}$) C: 81,0:test_suite_all_XSD: Missing docstring C: 82,4:test_suite_all_XSD: Invalid name "testSuite" (should match [a-z_][a-z0-9_]{2,30}$) C: 93,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 94,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) Report ====== 68 statements analysed. Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |18 |NC |NC | +-----------+-------+---------+-----------+ |refactor |1 |NC |NC | +-----------+-------+---------+-----------+ |warning |2 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |12 | +-----------+------------+ |C0301 |4 | +-----------+------------+ |C0111 |2 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0403 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 6.91/10 Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |72 |80.00 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |8 |8.89 |NC |NC | +----------+-------+------+---------+-----------+ |comment |2 |2.22 |NC |NC | +----------+-------+------+---------+-----------+ |empty |8 |8.89 |NC |NC | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (test.testXSDimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |NC |NC |0.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |4 |NC |NC |100.00 |25.00 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |0.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/testtifgz.py.lint0000644000175000017500000001045712233243332020244 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.testtifgz C: 10,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 11,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 25,0: No exception type(s) specified W: 28,0: Relative import 'utilstest', should be 'test.utilstest' C: 34,0:testgziptif: Invalid name "testgziptif" (should match [A-Z_][a-zA-Z0-9]+$) C: 34,0:testgziptif: Missing docstring C: 35,4:testgziptif.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C: 41,4:testgziptif.test1: Missing docstring C: 42,8:testgziptif.test1: Invalid name "o1" (should match [a-z_][a-z0-9_]{2,30}$) C: 43,8:testgziptif.test1: Invalid name "o2" (should match [a-z_][a-z0-9_]{2,30}$) R: 34,0:testgziptif: Too many public methods (46/20) C: 48,0:testtif_rect: Invalid name "testtif_rect" (should match [A-Z_][a-zA-Z0-9]+$) C: 50,8:testtif_rect.setUp: Invalid name "fn" (should match [a-z_][a-z0-9_]{2,30}$) C: 48,0:testtif_rect: Missing docstring C: 49,4:testtif_rect.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C: 52,4:testtif_rect.test1: Missing docstring C: 54,12:testtif_rect.test1: Invalid name "o1" (should match [a-z_][a-z0-9_]{2,30}$) R: 48,0:testtif_rect: Too many public methods (46/20) C: 58,0:test_suite_all_tiff: Missing docstring C: 59,4:test_suite_all_tiff: Invalid name "testSuite" (should match [a-z_][a-z0-9_]{2,30}$) C: 65,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 66,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) Report ====== 49 statements analysed. Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |18 |NC |NC | +-----------+-------+---------+-----------+ |refactor |2 |NC |NC | +-----------+-------+---------+-----------+ |warning |2 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |13 | +-----------+------------+ |C0111 |5 | +-----------+------------+ |R0904 |2 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0403 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 5.51/10 Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |48 |78.69 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |5 |8.20 |NC |NC | +----------+-------+------+---------+-----------+ |comment |2 |3.28 |NC |NC | +----------+-------+------+---------+-----------+ |empty |6 |9.84 |NC |NC | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |2 |NC |NC |0.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |4 |NC |NC |50.00 |50.00 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/compression.py.lint0000644000175000017500000001433512233243273020565 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module compression C: 69,0: Line too long (101/80) C: 73,0: Line too long (127/80) C: 75,0: Line too long (120/80) C: 77,0: Line too long (97/80) C: 87,0: Line too long (105/80) C:162,0: Line too long (98/80) C:211,0: Line too long (110/80) C:273,0: Line too long (96/80) C:313,0: Line too long (89/80) C:319,0: Line too long (89/80) C:399,0: Line too long (83/80) C:420,0: Line too long (84/80) W: 17,4: Redefining built-in 'str' C: 17,4: Invalid name "str" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 18,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 25,4: Invalid name "gzip" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 31,4: Invalid name "bz2" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 37,4: Invalid name "zlib" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) E: 43,28:md5sum: Module 'hashlib' has no 'md5' member C: 56,0:decGzip: Invalid name "decGzip" (should match [a-z_][a-z0-9_]{2,30}$) C: 67,8:decGzip: Invalid name "rawData" (should match [a-z_][a-z0-9_]{2,30}$) W: 76,15:decGzip: Catching too general exception Exception C: 74,12:decGzip: Invalid name "rawData" (should match [a-z_][a-z0-9_]{2,30}$) C: 81,20:decGzip: Invalid name "rawData" (should match [a-z_][a-z0-9_]{2,30}$) C: 91,0:decBzip2: Invalid name "decBzip2" (should match [a-z_][a-z0-9_]{2,30}$) C:102,0:decZlib: Invalid name "decZlib" (should match [a-z_][a-z0-9_]{2,30}$) C:113,0:decByteOffet_python: Invalid name "decByteOffet_python" (should match [a-z_][a-z0-9_]{2,30}$) C:123,4:decByteOffet_python: Invalid name "dataOut" (should match [a-z_][a-z0-9_]{2,30}$) C:148,0:decByteOffet_weave: Invalid name "decByteOffet_weave" (should match [a-z_][a-z0-9_]{2,30}$) C:164,4:decByteOffet_weave: Invalid name "dataIn" (should match [a-z_][a-z0-9_]{2,30}$) C:165,4:decByteOffet_weave: Invalid name "n" (should match [a-z_][a-z0-9_]{2,30}$) C:166,4:decByteOffet_weave: Invalid name "dataOut" (should match [a-z_][a-z0-9_]{2,30}$) C:167,4:decByteOffet_weave: Invalid name "codeC" (should match [a-z_][a-z0-9_]{2,30}$) C:211,4:decByteOffet_weave: Invalid name "rc" (should match [a-z_][a-z0-9_]{2,30}$) W:165,4:decByteOffet_weave: Unused variable 'n' C:218,0:decByteOffet_numpy: Invalid name "decByteOffet_numpy" (should match [a-z_][a-z0-9_]{2,30}$) W:218,31:decByteOffet_numpy: Unused argument 'size' C:259,0:decByteOffet_cython: Invalid name "decByteOffet_cython" (should match [a-z_][a-z0-9_]{2,30}$) W:272,24:decByteOffet_cython: Unused variable 'error' C:278,0:compByteOffet_numpy: Invalid name "compByteOffet_numpy" (should match [a-z_][a-z0-9_]{2,30}$) R:278,0:compByteOffet_numpy: Too many branches (14/12) C:328,0:decTY1: Invalid name "decTY1" (should match [a-z_][a-z0-9_]{2,30}$) C:360,0: Invalid name "decKM4CCD" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:362,0:compTY1: Invalid name "compTY1" (should match [a-z_][a-z0-9_]{2,30}$) C:387,0:decPCK: Invalid name "decPCK" (should match [a-z_][a-z0-9_]{2,30}$) C:387,0:decPCK: Invalid name "overflowPix" (should match [a-z_][a-z0-9_]{2,30}$) C:387,41:decPCK: Invalid name "overflowPix" (should match [a-z_][a-z0-9_]{2,30}$) W:398,24:decPCK: Unused variable 'error' C:409,0:compPCK: Invalid name "compPCK" (should match [a-z_][a-z0-9_]{2,30}$) W:419,24:compPCK: Unused variable 'error' Report ====== 223 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |41 |NC |NC | +-----------+-------+---------+-----------+ |refactor |1 |NC |NC | +-----------+-------+---------+-----------+ |warning |7 |NC |NC | +-----------+-------+---------+-----------+ |error |1 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |29 | +-----------+------------+ |C0301 |12 | +-----------+------------+ |W0612 |4 | +-----------+------------+ |W0703 |1 | +-----------+------------+ |W0622 |1 | +-----------+------------+ |W0613 |1 | +-----------+------------+ |R0912 |1 | +-----------+------------+ |E1101 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 7.58/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |284 |67.78 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |100 |23.87 |NC |NC | +----------+-------+------+---------+-----------+ |comment |2 |0.48 |NC |NC | +----------+-------+------+---------+-----------+ |empty |33 |7.88 |NC |NC | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (compression) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |0 |NC |NC |0 |0 | +---------+-------+-----------+-----------+------------+---------+ |method |0 |NC |NC |0 |0 | +---------+-------+-----------+-----------+------------+---------+ |function |14 |NC |NC |100.00 |85.71 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/fabioimage.py.lint0000644000175000017500000001437212233243300020277 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module fabioimage C: 92,0: Line too long (106/80) C:277,0: Line too long (83/80) C:291,0: Line too long (83/80) C:295,0: Line too long (85/80) C:319,0: Line too long (86/80) C:363,0: Line too long (94/80) C:414,0: Line too long (81/80) C:476,0: Line too long (95/80) C:477,0: Line too long (99/80) W:121,0: FIXME - this should be handled by the libraries now W:372,0: FIXME - what about seek ? W:397,0: FIXME - should we fix that or complain about the daft naming? C: 17,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 23,4: Invalid name "Image" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) R: 27,0:fabioimage: Too many instance attributes (22/7) C: 27,0:fabioimage: Invalid name "fabioimage" (should match [A-Z_][a-zA-Z0-9]+$) C: 70,4:fabioimage.checkHeader: Invalid name "checkHeader" (should match [a-z_][a-z0-9_]{2,30}$) C: 80,4:fabioimage.checkData: Invalid name "checkData" (should match [a-z_][a-z0-9_]{2,30}$) C:117,4:fabioimage.toPIL16: Invalid name "toPIL16" (should match [a-z_][a-z0-9_]{2,30}$) C:261,4:fabioimage.rebin: Invalid name "keep_I" (should match [a-z_][a-z0-9_]{2,30}$) C:261,48:fabioimage.rebin: Invalid name "keep_I" (should match [a-z_][a-z0-9_]{2,30}$) C:280,12:fabioimage.rebin: Invalid name "dataIn" (should match [a-z_][a-z0-9_]{2,30}$) C:281,12:fabioimage.rebin: Invalid name "shapeIn" (should match [a-z_][a-z0-9_]{2,30}$) C:282,12:fabioimage.rebin: Invalid name "shapeOut" (should match [a-z_][a-z0-9_]{2,30}$) W:305,20:fabioimage.write: Unused argument 'fname' R:305,4:fabioimage.write: Method could be a function W:327,26:fabioimage._readheader: Unused argument 'fik_obj' R:327,4:fabioimage._readheader: Method could be a function W:340,29:fabioimage.read: Unused argument 'frame' W:340,19:fabioimage.read: Unused argument 'filename' R:340,4:fabioimage.read: Method could be a function C:351,4:fabioimage.readROI: Invalid name "readROI" (should match [a-z_][a-z0-9_]{2,30}$) C:374,8:fabioimage._open: Invalid name "fileObject" (should match [a-z_][a-z0-9_]{2,30}$) C:384,16:fabioimage._open: Invalid name "fileObject" (should match [a-z_][a-z0-9_]{2,30}$) C:389,16:fabioimage._open: Invalid name "fileObject" (should match [a-z_][a-z0-9_]{2,30}$) C:399,16:fabioimage._open: Invalid name "fileObject" (should match [a-z_][a-z0-9_]{2,30}$) C:418,12:fabioimage._compressed_stream: Invalid name "fo" (should match [a-z_][a-z0-9_]{2,30}$) C:428,12:fabioimage._compressed_stream: Invalid name "fo" (should match [a-z_][a-z0-9_]{2,30}$) W:407,27:fabioimage._compressed_stream: Unused argument 'system_uncompress' W:454,24:fabioimage.convert: No exception type(s) specified R:434,4:fabioimage.convert: Too many branches (15/12) R: 27,0:fabioimage: Too many public methods (25/20) R:480,0:test: Too many local variables (17/15) W:526,12:test.clean: No exception type(s) specified W:533,11:test: Access to a protected member _open of a client class W:539,11:test: Access to a protected member _open of a client class W:545,20:test: Access to a protected member _open of a client class W:547,11:test: Access to a protected member _open of a client class Report ====== 309 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |27 |19 |+8.00 | +-----------+-------+---------+-----------+ |refactor |7 |4 |+3.00 | +-----------+-------+---------+-----------+ |warning |14 |13 |+1.00 | +-----------+-------+---------+-----------+ |error |0 |15 |-15.00 | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |18 | +-----------+------------+ |C0301 |9 | +-----------+------------+ |W0613 |5 | +-----------+------------+ |W0212 |4 | +-----------+------------+ |W0511 |3 | +-----------+------------+ |R0201 |3 | +-----------+------------+ |W0702 |2 | +-----------+------------+ |R0914 |1 | +-----------+------------+ |R0912 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ |R0902 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 8.45/10 (previous run: 5.32/10) Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |350 |66.16 |271 |+79.00 | +----------+-------+------+---------+-----------+ |docstring |119 |22.50 |104 |+15.00 | +----------+-------+------+---------+-----------+ |comment |15 |2.84 |14 |+1.00 | +----------+-------+------+---------+-----------+ |empty |45 |8.51 |41 |+4.00 | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (fabioimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |2 |-1.00 |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |29 |23 |+6.00 |100.00 |13.79 | +---------+-------+-----------+-----------+------------+---------+ |function |2 |2 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/adscimage.py.lint0000644000175000017500000000612212233243312020126 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module adscimage W: 91,0: FIXME ??? - made padding match header bytes keyword C: 18,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 20,0:adscimage: Invalid name "adscimage" (should match [A-Z_][a-zA-Z0-9]+$) R: 20,0:adscimage: Too many public methods (25/20) Report ====== 80 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |2 |2 |= | +-----------+-------+---------+-----------+ |refactor |1 |0 |+1.00 | +-----------+-------+---------+-----------+ |warning |1 |6 |-5.00 | +-----------+-------+---------+-----------+ |error |0 |31 |-31.00 | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |2 | +-----------+------------+ |W0511 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 9.50/10 (previous run: -10.90/10) Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |86 |64.66 |84 |+2.00 | +----------+-------+------+---------+-----------+ |docstring |24 |18.05 |24 |= | +----------+-------+------+---------+-----------+ |comment |9 |6.77 |9 |= | +----------+-------+------+---------+-----------+ |empty |14 |10.53 |16 |-2.00 | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (adscimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |1 |= |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |4 |3 |+1.00 |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/cbfimage.py.lint0000644000175000017500000003741712233243307017765 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module cbfimage C: 7,0: Line too long (81/80) C: 88,0: Line too long (128/80) C:131,0: Line too long (91/80) C:140,0: Line too long (131/80) C:142,0: Line too long (115/80) C:166,0: Line too long (93/80) C:204,0: Line too long (84/80) C:217,0: Line too long (128/80) C:237,0: Line too long (102/80) C:296,0: Line too long (90/80) C:301,0: Line too long (102/80) C:339,0: Line too long (98/80) C:350,0: Line too long (107/80) C:354,0: Line too long (106/80) C:546,0: Line too long (93/80) C:547,0: Line too long (93/80) C:548,0: Line too long (93/80) C:550,0: Line too long (81/80) C:606,0: Line too long (92/80) C:634,0: Line too long (83/80) C:638,0: Line too long (87/80) C:703,0: Line too long (84/80) C:739,0: Line too long (99/80) C:741,0: Line too long (91/80) C: 23,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) R: 46,0:cbfimage: Too many instance attributes (9/7) C: 46,0:cbfimage: Invalid name "cbfimage" (should match [A-Z_][a-zA-Z0-9]+$) C: 63,4:cbfimage.checkData: Invalid name "checkData" (should match [a-z_][a-z0-9_]{2,30}$) C: 72,4:cbfimage._readheader: Invalid name "inStream" (should match [a-z_][a-z0-9_]{2,30}$) C: 72,26:cbfimage._readheader: Invalid name "inStream" (should match [a-z_][a-z0-9_]{2,30}$) E: 88,117:cbfimage._readheader: Instance of 'cbfimage' has no 'fname' member C: 90,8:cbfimage._readheader: Invalid name "inStream2" (should match [a-z_][a-z0-9_]{2,30}$) C: 92,8:cbfimage._readheader: Invalid name "iSepPos" (should match [a-z_][a-z0-9_]{2,30}$) C: 97,12:cbfimage._readheader: Invalid name "oneLine" (should match [a-z_][a-z0-9_]{2,30}$) C:152,4:cbfimage._readbinary_byte_offset: Invalid name "inStream" (should match [a-z_][a-z0-9_]{2,30}$) C:152,38:cbfimage._readbinary_byte_offset: Invalid name "inStream" (should match [a-z_][a-z0-9_]{2,30}$) C:161,8:cbfimage._readbinary_byte_offset: Invalid name "startPos" (should match [a-z_][a-z0-9_]{2,30}$) C:167,12:cbfimage._readbinary_byte_offset: Invalid name "myData" (should match [a-z_][a-z0-9_]{2,30}$) C:169,12:cbfimage._readbinary_byte_offset: Invalid name "myData" (should match [a-z_][a-z0-9_]{2,30}$) C:215,12:cbfimage.write: Invalid name "nonCifHeaders" (should match [a-z_][a-z0-9_]{2,30}$) C:217,12:cbfimage.write: Invalid name "nonCifHeaders" (should match [a-z_][a-z0-9_]{2,30}$) R:175,4:cbfimage.write: Too many branches (17/12) R: 46,0:cbfimage: Too many public methods (25/20) C:255,4:CIF.__init__: Invalid name "_strFilename" (should match [a-z_][a-z0-9_]{2,30}$) C:255,23:CIF.__init__: Invalid name "_strFilename" (should match [a-z_][a-z0-9_]{2,30}$) C:283,4:CIF.loadCIF: Invalid name "loadCIF" (should match [a-z_][a-z0-9_]{2,30}$) C:283,4:CIF.loadCIF: Invalid name "_strFilename" (should match [a-z_][a-z0-9_]{2,30}$) C:283,4:CIF.loadCIF: Invalid name "_bKeepComment" (should match [a-z_][a-z0-9_]{2,30}$) C:283,22:CIF.loadCIF: Invalid name "_strFilename" (should match [a-z_][a-z0-9_]{2,30}$) C:283,36:CIF.loadCIF: Invalid name "_bKeepComment" (should match [a-z_][a-z0-9_]{2,30}$) C:309,4:CIF.isAscii: Invalid name "isAscii" (should match [a-z_][a-z0-9_]{2,30}$) C:309,4:CIF.isAscii: Invalid name "_strIn" (should match [a-z_][a-z0-9_]{2,30}$) C:309,16:CIF.isAscii: Invalid name "_strIn" (should match [a-z_][a-z0-9_]{2,30}$) C:318,8:CIF.isAscii: Invalid name "bIsAcii" (should match [a-z_][a-z0-9_]{2,30}$) C:321,16:CIF.isAscii: Invalid name "bIsAcii" (should match [a-z_][a-z0-9_]{2,30}$) C:327,4:CIF._readCIF: Invalid name "_readCIF" (should match [a-z_][a-z0-9_]{2,30}$) C:341,8:CIF._readCIF: Invalid name "lLinesRead" (should match [a-z_][a-z0-9_]{2,30}$) C:342,8:CIF._readCIF: Invalid name "sText" (should match [a-z_][a-z0-9_]{2,30}$) C:343,12:CIF._readCIF: Invalid name "sLine" (should match [a-z_][a-z0-9_]{2,30}$) C:344,12:CIF._readCIF: Invalid name "iPos" (should match [a-z_][a-z0-9_]{2,30}$) C:347,20:CIF._readCIF: Invalid name "sText" (should match [a-z_][a-z0-9_]{2,30}$) C:352,16:CIF._readCIF: Invalid name "sText" (should match [a-z_][a-z0-9_]{2,30}$) C:358,4:CIF._parseCIF: Invalid name "_parseCIF" (should match [a-z_][a-z0-9_]{2,30}$) C:358,4:CIF._parseCIF: Invalid name "sText" (should match [a-z_][a-z0-9_]{2,30}$) C:358,24:CIF._parseCIF: Invalid name "sText" (should match [a-z_][a-z0-9_]{2,30}$) C:374,8:CIF._parseCIF: Invalid name "lFields" (should match [a-z_][a-z0-9_]{2,30}$) C:387,16:CIF._parseCIF: Invalid name "f1" (should match [a-z_][a-z0-9_]{2,30}$) C:388,16:CIF._parseCIF: Invalid name "lFields" (should match [a-z_][a-z0-9_]{2,30}$) C:394,42:CIF._parseCIF: More than one statement on a single line C:399,4:CIF._splitCIF: Invalid name "_splitCIF" (should match [a-z_][a-z0-9_]{2,30}$) C:399,4:CIF._splitCIF: Invalid name "sText" (should match [a-z_][a-z0-9_]{2,30}$) C:399,18:CIF._splitCIF: Invalid name "sText" (should match [a-z_][a-z0-9_]{2,30}$) C:408,8:CIF._splitCIF: Invalid name "lFields" (should match [a-z_][a-z0-9_]{2,30}$) C:414,16:CIF._splitCIF: Invalid name "bFinished" (should match [a-z_][a-z0-9_]{2,30}$) C:421,24:CIF._splitCIF: Invalid name "sText" (should match [a-z_][a-z0-9_]{2,30}$) C:422,24:CIF._splitCIF: Invalid name "bFinished" (should match [a-z_][a-z0-9_]{2,30}$) C:427,24:CIF._splitCIF: Invalid name "sText1" (should match [a-z_][a-z0-9_]{2,30}$) C:428,24:CIF._splitCIF: Invalid name "sText" (should match [a-z_][a-z0-9_]{2,30}$) C:429,24:CIF._splitCIF: Invalid name "bFinished" (should match [a-z_][a-z0-9_]{2,30}$) C:433,16:CIF._splitCIF: Invalid name "bFinished" (should match [a-z_][a-z0-9_]{2,30}$) C:441,24:CIF._splitCIF: Invalid name "sText" (should match [a-z_][a-z0-9_]{2,30}$) C:442,24:CIF._splitCIF: Invalid name "bFinished" (should match [a-z_][a-z0-9_]{2,30}$) C:448,24:CIF._splitCIF: Invalid name "sText1" (should match [a-z_][a-z0-9_]{2,30}$) C:449,24:CIF._splitCIF: Invalid name "sText" (should match [a-z_][a-z0-9_]{2,30}$) C:450,24:CIF._splitCIF: Invalid name "bFinished" (should match [a-z_][a-z0-9_]{2,30}$) C:460,16:CIF._splitCIF: Invalid name "bFinished" (should match [a-z_][a-z0-9_]{2,30}$) C:465,24:CIF._splitCIF: Invalid name "sText1" (should match [a-z_][a-z0-9_]{2,30}$) C:466,24:CIF._splitCIF: Invalid name "sText" (should match [a-z_][a-z0-9_]{2,30}$) C:467,24:CIF._splitCIF: Invalid name "bFinished" (should match [a-z_][a-z0-9_]{2,30}$) C:469,16:CIF._splitCIF: Invalid name "f" (should match [a-z_][a-z0-9_]{2,30}$) C:472,16:CIF._splitCIF: Invalid name "sText1" (should match [a-z_][a-z0-9_]{2,30}$) C:473,16:CIF._splitCIF: Invalid name "sText" (should match [a-z_][a-z0-9_]{2,30}$) R:399,4:CIF._splitCIF: Too many branches (18/12) R:399,4:CIF._splitCIF: Too many statements (53/50) C:478,4:CIF._analyseOneLoop: Invalid name "_analyseOneLoop" (should match [a-z_][a-z0-9_]{2,30}$) C:478,4:CIF._analyseOneLoop: Invalid name "lFields" (should match [a-z_][a-z0-9_]{2,30}$) C:478,4:CIF._analyseOneLoop: Invalid name "iStart" (should match [a-z_][a-z0-9_]{2,30}$) C:478,24:CIF._analyseOneLoop: Invalid name "lFields" (should match [a-z_][a-z0-9_]{2,30}$) C:478,33:CIF._analyseOneLoop: Invalid name "iStart" (should match [a-z_][a-z0-9_]{2,30}$) C:494,8:CIF._analyseOneLoop: Invalid name "bFinished" (should match [a-z_][a-z0-9_]{2,30}$) C:500,16:CIF._analyseOneLoop: Invalid name "bFinished" (should match [a-z_][a-z0-9_]{2,30}$) R:478,4:CIF._analyseOneLoop: Too many branches (16/12) C:550,4:CIF.saveCIF: Invalid name "saveCIF" (should match [a-z_][a-z0-9_]{2,30}$) C:550,4:CIF.saveCIF: Invalid name "_strFilename" (should match [a-z_][a-z0-9_]{2,30}$) C:550,22:CIF.saveCIF: Invalid name "_strFilename" (should match [a-z_][a-z0-9_]{2,30}$) C:562,12:CIF.saveCIF: Invalid name "fFile" (should match [a-z_][a-z0-9_]{2,30}$) R:575,4:CIF.tostring: Too many local variables (16/15) C:575,4:CIF.tostring: Invalid name "_strFilename" (should match [a-z_][a-z0-9_]{2,30}$) C:575,23:CIF.tostring: Invalid name "_strFilename" (should match [a-z_][a-z0-9_]{2,30}$) C:585,8:CIF.tostring: Invalid name "lstStrCif" (should match [a-z_][a-z0-9_]{2,30}$) C:587,12:CIF.tostring: Invalid name "t" (should match [a-z_][a-z0-9_]{2,30}$) C:589,12:CIF.tostring: Invalid name "t" (should match [a-z_][a-z0-9_]{2,30}$) C:591,12:CIF.tostring: Invalid name "t" (should match [a-z_][a-z0-9_]{2,30}$) C:594,8:CIF.tostring: Invalid name "lKeys" (should match [a-z_][a-z0-9_]{2,30}$) C:601,12:CIF.tostring: Invalid name "sKey" (should match [a-z_][a-z0-9_]{2,30}$) C:608,12:CIF.tostring: Invalid name "sValue" (should match [a-z_][a-z0-9_]{2,30}$) C:610,16:CIF.tostring: Invalid name "lLine" (should match [a-z_][a-z0-9_]{2,30}$) C:612,16:CIF.tostring: Invalid name "sLine" (should match [a-z_][a-z0-9_]{2,30}$) C:614,20:CIF.tostring: Invalid name "lLine" (should match [a-z_][a-z0-9_]{2,30}$) C:616,20:CIF.tostring: Invalid name "lLine" (should match [a-z_][a-z0-9_]{2,30}$) C:618,16:CIF.tostring: Invalid name "sLine" (should match [a-z_][a-z0-9_]{2,30}$) C:620,20:CIF.tostring: Invalid name "lLine" (should match [a-z_][a-z0-9_]{2,30}$) C:622,20:CIF.tostring: Invalid name "lLine" (should match [a-z_][a-z0-9_]{2,30}$) C:623,12:CIF.tostring: Invalid name "lstStrCif" (should match [a-z_][a-z0-9_]{2,30}$) C:627,16:CIF.tostring: Invalid name "lKeys" (should match [a-z_][a-z0-9_]{2,30}$) C:628,16:CIF.tostring: Invalid name "llData" (should match [a-z_][a-z0-9_]{2,30}$) C:629,16:CIF.tostring: Invalid name "lstStrCif" (should match [a-z_][a-z0-9_]{2,30}$) C:630,20:CIF.tostring: Invalid name "lData" (should match [a-z_][a-z0-9_]{2,30}$) C:631,20:CIF.tostring: Invalid name "sLine" (should match [a-z_][a-z0-9_]{2,30}$) C:633,24:CIF.tostring: Invalid name "sRawValue" (should match [a-z_][a-z0-9_]{2,30}$) C:635,28:CIF.tostring: Invalid name "lstStrCif" (should match [a-z_][a-z0-9_]{2,30}$) C:636,28:CIF.tostring: Invalid name "sLine" (should match [a-z_][a-z0-9_]{2,30}$) C:643,32:CIF.tostring: Invalid name "lstStrCif" (should match [a-z_][a-z0-9_]{2,30}$) C:644,32:CIF.tostring: Invalid name "sLine" (should match [a-z_][a-z0-9_]{2,30}$) C:646,32:CIF.tostring: Invalid name "sLine" (should match [a-z_][a-z0-9_]{2,30}$) R:575,4:CIF.tostring: Too many branches (25/12) R:575,4:CIF.tostring: Too many statements (58/50) C:652,4:CIF.exists: Invalid name "sKey" (should match [a-z_][a-z0-9_]{2,30}$) C:652,21:CIF.exists: Invalid name "sKey" (should match [a-z_][a-z0-9_]{2,30}$) C:661,8:CIF.exists: Invalid name "bExists" (should match [a-z_][a-z0-9_]{2,30}$) C:665,20:CIF.exists: Invalid name "bExists" (should match [a-z_][a-z0-9_]{2,30}$) C:669,4:CIF.existsInLoop: Invalid name "existsInLoop" (should match [a-z_][a-z0-9_]{2,30}$) C:669,4:CIF.existsInLoop: Invalid name "sKey" (should match [a-z_][a-z0-9_]{2,30}$) C:669,27:CIF.existsInLoop: Invalid name "sKey" (should match [a-z_][a-z0-9_]{2,30}$) C:680,8:CIF.existsInLoop: Invalid name "bExists" (should match [a-z_][a-z0-9_]{2,30}$) C:685,24:CIF.existsInLoop: Invalid name "bExists" (should match [a-z_][a-z0-9_]{2,30}$) C:689,4:CIF.loadCHIPLOT: Invalid name "loadCHIPLOT" (should match [a-z_][a-z0-9_]{2,30}$) C:689,4:CIF.loadCHIPLOT: Invalid name "_strFilename" (should match [a-z_][a-z0-9_]{2,30}$) C:689,26:CIF.loadCHIPLOT: Invalid name "_strFilename" (should match [a-z_][a-z0-9_]{2,30}$) C:702,8:CIF.loadCHIPLOT: Invalid name "lInFile" (should match [a-z_][a-z0-9_]{2,30}$) C:707,12:CIF.loadCHIPLOT: Invalid name "iLenData" (should match [a-z_][a-z0-9_]{2,30}$) C:709,12:CIF.loadCHIPLOT: Invalid name "iLenData" (should match [a-z_][a-z0-9_]{2,30}$) C:710,8:CIF.loadCHIPLOT: Invalid name "lOneLoop" (should match [a-z_][a-z0-9_]{2,30}$) C:712,12:CIF.loadCHIPLOT: Invalid name "f2ThetaMin" (should match [a-z_][a-z0-9_]{2,30}$) C:714,16:CIF.loadCHIPLOT: Invalid name "sLine" (should match [a-z_][a-z0-9_]{2,30}$) C:717,12:CIF.loadCHIPLOT: Invalid name "f2ThetaMax" (should match [a-z_][a-z0-9_]{2,30}$) C:718,12:CIF.loadCHIPLOT: Invalid name "limitsOK" (should match [a-z_][a-z0-9_]{2,30}$) C:721,12:CIF.loadCHIPLOT: Invalid name "limitsOK" (should match [a-z_][a-z0-9_]{2,30}$) C:722,12:CIF.loadCHIPLOT: Invalid name "f2ThetaMin" (should match [a-z_][a-z0-9_]{2,30}$) C:723,12:CIF.loadCHIPLOT: Invalid name "f2ThetaMax" (should match [a-z_][a-z0-9_]{2,30}$) C:725,12:CIF.loadCHIPLOT: Invalid name "sLine" (should match [a-z_][a-z0-9_]{2,30}$) C:726,12:CIF.loadCHIPLOT: Invalid name "sCleaned" (should match [a-z_][a-z0-9_]{2,30}$) C:730,20:CIF.loadCHIPLOT: Invalid name "f2Theta" (should match [a-z_][a-z0-9_]{2,30}$) C:732,24:CIF.loadCHIPLOT: Invalid name "f2ThetaMin" (should match [a-z_][a-z0-9_]{2,30}$) C:734,24:CIF.loadCHIPLOT: Invalid name "f2ThetaMax" (should match [a-z_][a-z0-9_]{2,30}$) C:737,12:CIF.loadCHIPLOT: Invalid name "iLenData" (should match [a-z_][a-z0-9_]{2,30}$) C:743,12:CIF.loadCHIPLOT: Invalid name "f2ThetaMax" (should match [a-z_][a-z0-9_]{2,30}$) C:744,12:CIF.loadCHIPLOT: Invalid name "f2ThetaMin" (should match [a-z_][a-z0-9_]{2,30}$) C:752,4:CIF.LoopHasKey: Invalid name "LoopHasKey" (should match [a-z_][a-z0-9_]{2,30}$) R:245,0:CIF: Too many public methods (25/20) Report ====== 442 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |159 |168 |-9.00 | +-----------+-------+---------+-----------+ |refactor |10 |6 |+4.00 | +-----------+-------+---------+-----------+ |warning |0 |11 |-11.00 | +-----------+-------+---------+-----------+ |error |1 |22 |-21.00 | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |134 | +-----------+------------+ |C0301 |24 | +-----------+------------+ |R0912 |4 | +-----------+------------+ |R0915 |2 | +-----------+------------+ |R0904 |2 | +-----------+------------+ |R0914 |1 | +-----------+------------+ |R0902 |1 | +-----------+------------+ |E1101 |1 | +-----------+------------+ |C0321 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 6.06/10 (previous run: 3.20/10) Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |471 |64.08 |514 |-43.00 | +----------+-------+------+---------+-----------+ |docstring |172 |23.40 |173 |-1.00 | +----------+-------+------+---------+-----------+ |comment |17 |2.31 |15 |+2.00 | +----------+-------+------+---------+-----------+ |empty |75 |10.20 |92 |-17.00 | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (cbfimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |2 |2 |= |100.00 |50.00 | +---------+-------+-----------+-----------+------------+---------+ |method |22 |21 |+1.00 |100.00 |50.00 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/templateimage.py.lint0000644000175000017500000000771212233243301021033 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module templateimage C: 5,0: Line too long (117/80) C: 6,0: Line too long (91/80) C: 13,0: Line too long (94/80) C: 14,0: Line too long (91/80) C: 16,0: Line too long (99/80) C: 23,0: Line too long (83/80) C: 26,0: Line too long (81/80) C: 27,0: Line too long (81/80) C: 28,0: Line too long (84/80) C: 31,0: Line too long (99/80) C: 33,0: Line too long (102/80) W: 7,0: XXXimage where XXX means something (eg tifimage). W: 58,0: XXX detector W: 38,0: Redefining built-in '__doc__' C: 1,0: Missing docstring C: 53,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) R: 56,0:templateimage: Too many instance attributes (10/7) C: 56,0:templateimage: Invalid name "templateimage" (should match [A-Z_][a-zA-Z0-9]+$) C: 68,8:templateimage.__init__: Invalid name "m" (should match [a-z_][a-z0-9_]{2,30}$) W: 72,26:templateimage._readheader: Unused argument 'infile' R: 56,0:templateimage: Too many public methods (25/20) Report ====== 29 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |15 |NC |NC | +-----------+-------+---------+-----------+ |refactor |2 |NC |NC | +-----------+-------+---------+-----------+ |warning |4 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0301 |11 | +-----------+------------+ |C0103 |3 | +-----------+------------+ |W0511 |2 | +-----------+------------+ |W0622 |1 | +-----------+------------+ |W0613 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ |R0902 |1 | +-----------+------------+ |C0111 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 2.76/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |35 |36.08 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |16 |16.49 |NC |NC | +----------+-------+------+---------+-----------+ |comment |36 |37.11 |NC |NC | +----------+-------+------+---------+-----------+ |empty |10 |10.31 |NC |NC | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (templateimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |NC |NC |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |3 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |NC |NC |0 |0 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/fabioutils.py.lint0000644000175000017500000001531412233243314020357 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module fabioutils C: 82,0: Line too long (123/80) C: 95,0: Line too long (106/80) C:234,0: Line too long (81/80) C:444,0: Line too long (101/80) C:454,0: Line too long (84/80) C:493,0: Line too long (85/80) W:569,0: Bad indentation. Found 16 spaces, expected 12 W:572,0: Bad indentation. Found 16 spaces, expected 12 C: 10,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 51,0: Invalid name "dictAscii" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 61,7: Catching too general exception Exception C: 55,4: Invalid name "lines" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 71,7: Catching too general exception Exception C: 65,4: Invalid name "lines" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W:103,4:getnum: Unused variable 'stem' W:103,16:getnum: Unused variable 'post_num' R:109,0:FilenameObject: Too many instance attributes (8/7) R:113,4:FilenameObject.__init__: Too many arguments (9/5) W:116,12:FilenameObject.__init__: Redefining built-in 'format' W:207,19:FilenameObject.deconstruct_filename: Catching too general exception Exception W:228,23:FilenameObject.deconstruct_filename: Catching too general exception Exception R:182,4:FilenameObject.deconstruct_filename: Too many statements (60/50) C:313,0:isAscii: Invalid name "isAscii" (should match [a-z_][a-z0-9_]{2,30}$) C:313,0:isAscii: Invalid name "listExcluded" (should match [a-z_][a-z0-9_]{2,30}$) C:313,18:isAscii: Invalid name "listExcluded" (should match [a-z_][a-z0-9_]{2,30}$) W:339,12:toAscii: Redefining name 'i' from outer scope (line 51) C:331,0:toAscii: Invalid name "toAscii" (should match [a-z_][a-z0-9_]{2,30}$) E:343,29:toAscii: Unsupported format character 'n' (0x6e) at index 11 C:350,0:nice_int: Invalid name "s" (should match [a-z_][a-z0-9_]{2,30}$) C:350,13:nice_int: Invalid name "s" (should match [a-z_][a-z0-9_]{2,30}$) C:379,4:StringIO.getSize: Invalid name "getSize" (should match [a-z_][a-z0-9_]{2,30}$) C:379,4:StringIO.getSize: Missing docstring C:388,4:StringIO.setSize: Invalid name "setSize" (should match [a-z_][a-z0-9_]{2,30}$) C:388,4:StringIO.setSize: Missing docstring W:390,11:StringIO: Use of "property" on an old style class C:418,4:File.getSize: Invalid name "getSize" (should match [a-z_][a-z0-9_]{2,30}$) C:418,4:File.getSize: Missing docstring C:427,4:File.setSize: Invalid name "setSize" (should match [a-z_][a-z0-9_]{2,30}$) C:427,4:File.setSize: Missing docstring C:448,4: Invalid name "GzipFile" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:488,12:GzipFile.getSize: Invalid name "getSize" (should match [a-z_][a-z0-9_]{2,30}$) C:488,12:GzipFile.getSize: Missing docstring C:491,54:GzipFile.getSize: Invalid name "f" (should match [a-z_][a-z0-9_]{2,30}$) E:493,38:GzipFile.getSize: Undefined variable 'numpy' E:493,72:GzipFile.getSize: Undefined variable 'numpy' C:495,12:GzipFile.setSize: Invalid name "setSize" (should match [a-z_][a-z0-9_]{2,30}$) C:495,12:GzipFile.setSize: Missing docstring R:450,4:GzipFile: Too many public methods (24/20) C:532,4: Invalid name "BZ2File" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W:561,20:BZ2File.getSize: Redefining built-in 'all' C:556,8:BZ2File.getSize: Invalid name "getSize" (should match [a-z_][a-z0-9_]{2,30}$) C:556,8:BZ2File.getSize: Missing docstring W:561,20:BZ2File.getSize: Unused variable 'all' C:565,8:BZ2File.setSize: Invalid name "setSize" (should match [a-z_][a-z0-9_]{2,30}$) C:565,8:BZ2File.setSize: Missing docstring Report ====== 297 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |35 |30 |+5.00 | +-----------+-------+---------+-----------+ |refactor |4 |3 |+1.00 | +-----------+-------+---------+-----------+ |warning |13 |19 |-6.00 | +-----------+-------+---------+-----------+ |error |3 |13 |-10.00 | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |21 | +-----------+------------+ |C0111 |8 | +-----------+------------+ |C0301 |6 | +-----------+------------+ |W0703 |4 | +-----------+------------+ |W0612 |3 | +-----------+------------+ |W0622 |2 | +-----------+------------+ |W0311 |2 | +-----------+------------+ |E0602 |2 | +-----------+------------+ |W1001 |1 | +-----------+------------+ |W0621 |1 | +-----------+------------+ |R0915 |1 | +-----------+------------+ |R0913 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ |R0902 |1 | +-----------+------------+ |E1300 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 7.74/10 (previous run: 5.36/10) Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |324 |56.94 |283 |+41.00 | +----------+-------+------+---------+-----------+ |docstring |187 |32.86 |149 |+38.00 | +----------+-------+------+---------+-----------+ |comment |8 |1.41 |33 |-25.00 | +----------+-------+------+---------+-----------+ |empty |50 |8.79 |40 |+10.00 | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |6 |6 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |method |25 |15 |+10.00 |68.00 |32.00 | +---------+-------+-----------+-----------+------------+---------+ |function |14 |11 |+3.00 |100.00 |14.29 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/testopenimage.py.lint0000644000175000017500000001527412233243334021071 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.testopenimage C: 54,0: Line too long (84/80) C: 81,0: Line too long (84/80) C:112,0: Line too long (84/80) C:113,0: Line too long (84/80) C:140,0: Line too long (84/80) C:166,0: Line too long (84/80) C:193,0: Line too long (84/80) C: 9,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 10,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 24,0: No exception type(s) specified W: 27,0: Relative import 'utilstest', should be 'test.utilstest' W: 32,0: Relative import 'utilstest', should be 'test.utilstest' W: 32,0: Reimport 'UtilsTest' (imported line 27) C: 41,0:testopenedf: Invalid name "testopenedf" (should match [A-Z_][a-zA-Z0-9]+$) C: 44,4:testopenedf.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R: 41,0:testopenedf: Too many public methods (46/20) C: 58,0:testedfgz: Invalid name "testedfgz" (should match [A-Z_][a-zA-Z0-9]+$) R: 58,0:testedfgz: Too many public methods (46/20) C: 63,0:testedfbz2: Invalid name "testedfbz2" (should match [A-Z_][a-zA-Z0-9]+$) R: 63,0:testedfbz2: Too many public methods (46/20) C: 69,0:testopenmccd: Invalid name "testopenmccd" (should match [A-Z_][a-zA-Z0-9]+$) C: 72,4:testopenmccd.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R: 69,0:testopenmccd: Too many public methods (46/20) C: 85,0:testmccdgz: Invalid name "testmccdgz" (should match [A-Z_][a-zA-Z0-9]+$) R: 85,0:testmccdgz: Too many public methods (46/20) C: 90,0:testmccdbz2: Invalid name "testmccdbz2" (should match [A-Z_][a-zA-Z0-9]+$) R: 90,0:testmccdbz2: Too many public methods (46/20) C: 98,0:testmask: Invalid name "testmask" (should match [A-Z_][a-zA-Z0-9]+$) C:101,4:testmask.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R: 98,0:testmask: Too many public methods (46/20) C:116,0:testmaskgz: Invalid name "testmaskgz" (should match [A-Z_][a-zA-Z0-9]+$) R:116,0:testmaskgz: Too many public methods (46/20) C:120,0:testmaskbz2: Invalid name "testmaskbz2" (should match [A-Z_][a-zA-Z0-9]+$) R:120,0:testmaskbz2: Too many public methods (46/20) C:128,0:testbruker: Invalid name "testbruker" (should match [A-Z_][a-zA-Z0-9]+$) C:131,4:testbruker.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R:128,0:testbruker: Too many public methods (46/20) C:143,0:testbrukergz: Invalid name "testbrukergz" (should match [A-Z_][a-zA-Z0-9]+$) R:143,0:testbrukergz: Too many public methods (46/20) C:147,0:testbrukerbz2: Invalid name "testbrukerbz2" (should match [A-Z_][a-zA-Z0-9]+$) R:147,0:testbrukerbz2: Too many public methods (46/20) C:154,0:testadsc: Invalid name "testadsc" (should match [A-Z_][a-zA-Z0-9]+$) C:157,4:testadsc.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R:154,0:testadsc: Too many public methods (46/20) C:169,0:testadscgz: Invalid name "testadscgz" (should match [A-Z_][a-zA-Z0-9]+$) R:169,0:testadscgz: Too many public methods (46/20) C:173,0:testadscbz2: Invalid name "testadscbz2" (should match [A-Z_][a-zA-Z0-9]+$) R:173,0:testadscbz2: Too many public methods (46/20) C:181,0:testOXD: Invalid name "testOXD" (should match [A-Z_][a-zA-Z0-9]+$) C:184,4:testOXD.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R:181,0:testOXD: Too many public methods (46/20) C:197,0:testOXDUNC: Invalid name "testOXDUNC" (should match [A-Z_][a-zA-Z0-9]+$) C:200,4:testOXDUNC.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R:197,0:testOXDUNC: Too many public methods (46/20) C:204,0:test_suite_all_openimage: Missing docstring C:205,4:test_suite_all_openimage: Invalid name "testSuite" (should match [a-z_][a-z0-9_]{2,30}$) C:232,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:233,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 30,0: Unused import fabio Report ====== 145 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |37 |NC |NC | +-----------+-------+---------+-----------+ |refactor |17 |NC |NC | +-----------+-------+---------+-----------+ |warning |5 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |29 | +-----------+------------+ |R0904 |17 | +-----------+------------+ |C0301 |7 | +-----------+------------+ |W0403 |2 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0611 |1 | +-----------+------------+ |W0404 |1 | +-----------+------------+ |C0111 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 5.93/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |144 |68.57 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |29 |13.81 |NC |NC | +----------+-------+------+---------+-----------+ |comment |4 |1.90 |NC |NC | +----------+-------+------+---------+-----------+ |empty |33 |15.71 |NC |NC | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |17 |NC |NC |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |13 |NC |NC |100.00 |53.85 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/testbrukerimage.py.lint0000644000175000017500000001170512233243320021410 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.testbrukerimage C: 98,0: Line too long (93/80) C:107,0: Line too long (90/80) C:125,0: Line too long (88/80) C:143,0: Line too long (82/80) C:175,0: Line too long (86/80) C:180,0: Line too long (102/80) C:182,0: Line too long (164/80) C: 10,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 11,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 25,0: No exception type(s) specified W: 28,0: Relative import 'utilstest', should be 'test.utilstest' W: 35,0: Reimport 'tempfile' (imported line 9) C: 60,0:testbruker: Invalid name "testbruker" (should match [A-Z_][a-zA-Z0-9]+$) C: 64,4:testbruker.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R: 60,0:testbruker: Too many public methods (46/20) C: 92,0:testbzipbruker: Invalid name "testbzipbruker" (should match [A-Z_][a-zA-Z0-9]+$) C: 94,4:testbzipbruker.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R: 92,0:testbzipbruker: Too many public methods (46/20) C:101,0:testgzipbruker: Invalid name "testgzipbruker" (should match [A-Z_][a-zA-Z0-9]+$) C:103,4:testgzipbruker.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R:101,0:testgzipbruker: Too many public methods (46/20) C:112,0:testbrukerLinear: Invalid name "testbrukerLinear" (should match [A-Z_][a-zA-Z0-9]+$) R:112,0:testbrukerLinear: Too many public methods (46/20) C:136,0:test_real_im: Invalid name "test_real_im" (should match [A-Z_][a-zA-Z0-9]+$) C:138,4:test_real_im.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R:136,0:test_real_im: Too many public methods (47/20) C:184,0:test_suite_all_bruker: Missing docstring C:185,4:test_suite_all_bruker: Invalid name "testSuite" (should match [a-z_][a-z0-9_]{2,30}$) C:195,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:196,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 31,0: Unused import fabio Report ====== 131 statements analysed. Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |22 |NC |NC | +-----------+-------+---------+-----------+ |refactor |5 |NC |NC | +-----------+-------+---------+-----------+ |warning |4 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |14 | +-----------+------------+ |C0301 |7 | +-----------+------------+ |R0904 |5 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0611 |1 | +-----------+------------+ |W0404 |1 | +-----------+------------+ |W0403 |1 | +-----------+------------+ |C0111 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 7.63/10 Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |138 |75.00 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |27 |14.67 |NC |NC | +----------+-------+------+---------+-----------+ |comment |6 |3.26 |NC |NC | +----------+-------+------+---------+-----------+ |empty |13 |7.07 |NC |NC | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (test.testbrukerimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |5 |NC |NC |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |8 |NC |NC |100.00 |50.00 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/testfabioimage.py.lint0000644000175000017500000001262212233243335021203 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.testfabioimage C:100,0: Line too long (90/80) C:198,0: Line too long (81/80) C: 9,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 10,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 24,0: No exception type(s) specified W: 27,0: Relative import 'utilstest', should be 'test.utilstest' C: 35,0:test50000: Invalid name "test50000" (should match [A-Z_][a-zA-Z0-9]+$) C: 37,4:test50000.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R: 35,0:test50000: Too many public methods (49/20) C: 61,0:testslices: Invalid name "testslices" (should match [A-Z_][a-zA-Z0-9]+$) C: 63,4:testslices.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C: 94,4:testslices.testRebin: Invalid name "testRebin" (should match [a-z_][a-z0-9_]{2,30}$) R: 61,0:testslices: Too many public methods (49/20) C:103,0:testopen: Invalid name "testopen" (should match [A-Z_][a-zA-Z0-9]+$) C:106,4:testopen.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C:116,4:testopen.testFlat: Invalid name "testFlat" (should match [a-z_][a-z0-9_]{2,30}$) W:118,14:testopen.testFlat: Access to a protected member _open of a client class W:123,14:testopen.testgz: Access to a protected member _open of a client class W:128,14:testopen.testbz2: Access to a protected member _open of a client class R:103,0:testopen: Too many public methods (48/20) C:142,0:testPILimage: Invalid name "testPILimage" (should match [A-Z_][a-zA-Z0-9]+$) C:144,4:testPILimage.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R:155,4:testPILimage.mkdata: Method could be a function C:160,4:testPILimage.testpil: Missing docstring R:142,0:testPILimage: Too many public methods (47/20) C:188,0:testPILimage2: Invalid name "testPILimage2" (should match [A-Z_][a-zA-Z0-9]+$) R:188,0:testPILimage2: Too many public methods (47/20) C:194,0:testPILimage3: Invalid name "testPILimage3" (should match [A-Z_][a-zA-Z0-9]+$) R:194,0:testPILimage3: Too many public methods (47/20) C:200,0:test_suite_all_fabio: Missing docstring C:201,4:test_suite_all_fabio: Invalid name "testSuite" (should match [a-z_][a-z0-9_]{2,30}$) C:225,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:226,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 30,0: Unused import fabio Report ====== 136 statements analysed. Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |21 |NC |NC | +-----------+-------+---------+-----------+ |refactor |7 |NC |NC | +-----------+-------+---------+-----------+ |warning |6 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |17 | +-----------+------------+ |R0904 |6 | +-----------+------------+ |W0212 |3 | +-----------+------------+ |C0301 |2 | +-----------+------------+ |C0111 |2 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0611 |1 | +-----------+------------+ |W0403 |1 | +-----------+------------+ |R0201 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 7.50/10 Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |154 |78.97 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |29 |14.87 |NC |NC | +----------+-------+------+---------+-----------+ |comment |3 |1.54 |NC |NC | +----------+-------+------+---------+-----------+ |empty |9 |4.62 |NC |NC | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (test.testfabioimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |6 |NC |NC |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |19 |NC |NC |94.74 |31.58 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/profile_compressed.py.lint0000644000175000017500000001105212233243327022101 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.profile_compressed W: 10,0: No exception type(s) specified C: 18,0: Invalid name "npts" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 19,0: Invalid name "data" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 20,0: Invalid name "sdata" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 20,8: Used * or ** magic C: 33,4:tst: Invalid name "fo" (should match [a-z_][a-z0-9_]{2,30}$) C: 40,0: Invalid name "start" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 42,0: Invalid name "p" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 49,0: Invalid name "p" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 55,4:tstsys: Invalid name "fo" (should match [a-z_][a-z0-9_]{2,30}$) C: 61,0: Invalid name "p" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 67,0: Invalid name "p" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 74,0: Invalid name "cl" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 97,4: Invalid name "start" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 98,4: Invalid name "s" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:101,4: Invalid name "start" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:102,4: Invalid name "s" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:105,4: Invalid name "start" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:106,4: Invalid name "s" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:109,4: Invalid name "start" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:110,4: Invalid name "s" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:116,4: Invalid name "s" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:120,4: Invalid name "s" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:124,4: Invalid name "s" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:128,4: Invalid name "s" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 6,0: Unused import bz2 W: 6,0: Unused import gzip Report ====== 93 statements analysed. Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |23 |NC |NC | +-----------+-------+---------+-----------+ |refactor |0 |NC |NC | +-----------+-------+---------+-----------+ |warning |4 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |23 | +-----------+------------+ |W0611 |2 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0142 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 7.10/10 Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |88 |72.73 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |17 |14.05 |NC |NC | +----------+-------+------+---------+-----------+ |comment |1 |0.83 |NC |NC | +----------+-------+------+---------+-----------+ |empty |15 |12.40 |NC |NC | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |0 |NC |NC |0 |0 | +---------+-------+-----------+-----------+------------+---------+ |method |0 |NC |NC |0 |0 | +---------+-------+-----------+-----------+------------+---------+ |function |2 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/openimage.py.lint0000644000175000017500000000737012233243310020161 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module openimage C: 77,0: Line too long (92/80) C: 96,0: Line too long (84/80) C: 14,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 90,15:openimage: Catching too general exception Exception W:120,15:_openimage: Access to a protected member _open of a client class W: 22,0: Unused import fit2dmaskimage W: 32,0: Unused import kcdimage W: 24,0: Unused import bruker100image W: 35,0: Unused import binaryimage W: 30,0: Unused import pilatusimage W: 29,0: Unused import HiPiCimage W: 18,0: Unused import adscimage W: 21,0: Unused import mar345image W: 31,0: Unused import fit2dspreadsheetimage W: 25,0: Unused import pnmimage W: 28,0: Unused import dm3image W: 34,0: Unused import xsdimage W: 20,0: Unused import marccdimage W: 26,0: Unused import GEimage W: 33,0: Unused import cbfimage W: 17,0: Unused import edfimage W: 27,0: Unused import OXDimage W: 19,0: Unused import tifimage W: 23,0: Unused import brukerimage Report ====== 89 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |3 |2 |+1.00 | +-----------+-------+---------+-----------+ |refactor |0 |0 |= | +-----------+-------+---------+-----------+ |warning |21 |22 |-1.00 | +-----------+-------+---------+-----------+ |error |0 |0 |= | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |W0611 |19 | +-----------+------------+ |C0301 |2 | +-----------+------------+ |W0703 |1 | +-----------+------------+ |W0212 |1 | +-----------+------------+ |C0103 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 7.30/10 (previous run: 6.96/10) Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |116 |72.96 |102 |+14.00 | +----------+-------+------+---------+-----------+ |docstring |19 |11.95 |19 |= | +----------+-------+------+---------+-----------+ |comment |10 |6.29 |11 |-1.00 | +----------+-------+------+---------+-----------+ |empty |14 |8.81 |15 |-1.00 | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ |method |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ |function |4 |4 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/readbytestream.py.lint0000644000175000017500000000535412120434325021233 0ustar jeromejerome00000000000000************* Module readbytestream W: 49,0: TODO : Read in regions of interest Report ====== 27 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |0 |0 |= | +-----------+-------+---------+-----------+ |refactor |0 |0 |= | +-----------+-------+---------+-----------+ |warning |1 |1 |= | +-----------+-------+---------+-----------+ |error |0 |0 |= | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |W0511 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 9.63/10 (previous run: 9.63/10) So close to being perfect... Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |46 |56.79 |46 |= | +----------+-------+------+---------+-----------+ |docstring |25 |30.86 |25 |= | +----------+-------+------+---------+-----------+ |comment |4 |4.94 |4 |= | +----------+-------+------+---------+-----------+ |empty |6 |7.41 |6 |= | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (readbytestream) Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ |method |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/marccdimage.py.lint0000644000175000017500000000576612233243272020467 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module marccdimage C: 28,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W:234,4:make_format: Unused variable 'expected' C:291,0:marccdimage: Invalid name "marccdimage" (should match [A-Z_][a-zA-Z0-9]+$) R:291,0:marccdimage: Too many public methods (25/20) Report ====== 63 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |2 |2 |= | +-----------+-------+---------+-----------+ |refactor |1 |1 |= | +-----------+-------+---------+-----------+ |warning |1 |3 |-2.00 | +-----------+-------+---------+-----------+ |error |0 |0 |= | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |2 | +-----------+------------+ |W0612 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 9.37/10 (previous run: 9.05/10) Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |236 |75.88 |236 |= | +----------+-------+------+---------+-----------+ |docstring |45 |14.47 |41 |+4.00 | +----------+-------+------+---------+-----------+ |comment |9 |2.89 |9 |= | +----------+-------+------+---------+-----------+ |empty |21 |6.75 |21 |= | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |1 |= |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |2 |2 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |function |2 |2 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/TiffIO.py.lint0000644000175000017500000002434612120434325017342 0ustar jeromejerome00000000000000************* Module TiffIO C: 1,0: Too many lines in module (1197) C: 1,0: Missing docstring C:122,12:TiffIO._initInternalVariables: Invalid name "fd" (should match [a-z_][a-zA-Z0-9_]{2,30}$) C: 94,0:TiffIO: Missing docstring W: 95,23:TiffIO.__init__: Redefining name 'filename' from outer scope (line 1170) C:107,12:TiffIO.__init__: Invalid name "fd" (should match [a-z_][a-zA-Z0-9_]{2,30}$) C:111,12:TiffIO.__init__: Invalid name "fd" (should match [a-z_][a-zA-Z0-9_]{2,30}$) C:118,4:TiffIO._initInternalVariables: Invalid name "fd" (should match [a-z_][a-zA-Z0-9_]{2,30}$) C:118,4:TiffIO._initInternalVariables: Missing docstring C:118,37:TiffIO._initInternalVariables: Invalid name "fd" (should match [a-z_][a-zA-Z0-9_]{2,30}$) C:120,12:TiffIO._initInternalVariables: Invalid name "fd" (should match [a-z_][a-zA-Z0-9_]{2,30}$) C:137,12:TiffIO._initInternalVariables: Invalid name "a" (should match [a-z_][a-zA-Z0-9_]{2,30}$) C:162,4:TiffIO.__makeSureFileIsOpen: Missing docstring C:176,4:TiffIO.__makeSureFileIsClosed: Missing docstring C:186,4:TiffIO.getNumberOfImages: Missing docstring C:191,4:TiffIO._updateIFD: Missing docstring C:196,4:TiffIO.getImageFileDirectories: Invalid name "fd" (should match [a-z_][a-zA-Z0-9_]{2,30}$) C:196,4:TiffIO.getImageFileDirectories: Missing docstring C:196,38:TiffIO.getImageFileDirectories: Invalid name "fd" (should match [a-z_][a-zA-Z0-9_]{2,30}$) C:198,12:TiffIO.getImageFileDirectories: Invalid name "fd" (should match [a-z_][a-zA-Z0-9_]{2,30}$) C:201,8:TiffIO.getImageFileDirectories: Invalid name "st" (should match [a-z_][a-zA-Z0-9_]{2,30}$) W:247,12:TiffIO._parseImageFileDirectory: Redefining name 'i' from outer scope (line 1186) C:232,4:TiffIO._parseImageFileDirectory: Missing docstring C:234,8:TiffIO._parseImageFileDirectory: Invalid name "st" (should match [a-z_][a-zA-Z0-9_]{2,30}$) C:235,8:TiffIO._parseImageFileDirectory: Invalid name "fd" (should match [a-z_][a-zA-Z0-9_]{2,30}$) W:247,12:TiffIO._parseImageFileDirectory: Unused variable 'i' C:280,4:TiffIO._readIFDEntry: Missing docstring C:281,8:TiffIO._readIFDEntry: Invalid name "fd" (should match [a-z_][a-zA-Z0-9_]{2,30}$) C:282,8:TiffIO._readIFDEntry: Invalid name "st" (should match [a-z_][a-zA-Z0-9_]{2,30}$) W:286,8:TiffIO._readIFDEntry: Unused variable 'ftype' W:294,12:TiffIO._readIFDEntry: Unused variable 'offset' C:298,4:TiffIO.getData: Missing docstring C:304,4:TiffIO.getImage: Missing docstring C:307,4:TiffIO.getInfo: Missing docstring W:311,8:TiffIO.getInfo: Unused variable 'current' W:307,0:TiffIO.getInfo: Unused argument 'kw' R:314,4:TiffIO._readInfo: Too many local variables (37/25) W:490,16:TiffIO._readInfo: Redefining name 'key' from outer scope (line 1188) W:460,8:TiffIO._readInfo: Redefining name 'info' from outer scope (line 1187) W:489,16:TiffIO._readInfo: Redefining name 'i' from outer scope (line 1186) C:314,4:TiffIO._readInfo: Missing docstring E:347,36:TiffIO._readInfo: Instance of 'list' has no 'shape' member (but some types could not be inferred) E:347,63:TiffIO._readInfo: Instance of 'list' has no 'dtype' member (but some types could not be inferred) E:348,29:TiffIO._readInfo: Instance of 'list' has no 'T' member (but some types could not be inferred) W:411,12:TiffIO._readInfo: No exception type(s) specified E:404,23:TiffIO._readInfo: Instance of 'list' has no 'upper' member (but some types could not be inferred) E:405,35:TiffIO._readInfo: Instance of 'list' has no 'split' member (but some types could not be inferred) E:407,32:TiffIO._readInfo: Instance of 'list' has no 'decode' member (but some types could not be inferred) C:438,20:TiffIO._readInfo: Invalid name "n" (should match [a-z_][a-zA-Z0-9_]{2,30}$) E:485,40:TiffIO._readInfo: Instance of 'list' has no 'decode' member (but some types could not be inferred) R:314,4:TiffIO._readInfo: Too many branches (51/15) R:314,4:TiffIO._readInfo: Too many statements (143/50) R:504,4:TiffIO._readImage: Too many local variables (35/25) W:583,16:TiffIO._readImage: Redefining name 'dtype' from outer scope (line 1171) W:525,12:TiffIO._readImage: Redefining name 'info' from outer scope (line 1187) W:643,16:TiffIO._readImage: Redefining name 'i' from outer scope (line 1186) C:504,4:TiffIO._readImage: Missing docstring E:573,12:TiffIO._readImage: NotImplemented raised - should raise NotImplementedError C:620,8:TiffIO._readImage: Invalid name "fd" (should match [a-z_][a-zA-Z0-9_]{2,30}$) C:621,8:TiffIO._readImage: Invalid name "st" (should match [a-z_][a-zA-Z0-9_]{2,30}$) W:659,20:TiffIO._readImage: No exception type(s) specified C:667,24:TiffIO._readImage: Invalid name "n" (should match [a-z_][a-zA-Z0-9_]{2,30}$) R:504,4:TiffIO._readImage: Too many branches (77/15) R:504,4:TiffIO._readImage: Too many statements (190/50) W:742,33:TiffIO.writeImage: Redefining name 'info' from outer scope (line 1187) W:816,16:TiffIO.writeImage: Redefining name 'key' from outer scope (line 1188) C:742,4:TiffIO.writeImage: Missing docstring C:749,8:TiffIO.writeImage: Invalid name "fd" (should match [a-z_][a-zA-Z0-9_]{2,30}$) C:768,12:TiffIO.writeImage: Invalid name "fd" (should match [a-z_][a-zA-Z0-9_]{2,30}$) C:771,12:TiffIO.writeImage: Invalid name "fd" (should match [a-z_][a-zA-Z0-9_]{2,30}$) C:777,8:TiffIO.writeImage: Invalid name "fd" (should match [a-z_][a-zA-Z0-9_]{2,30}$) C:787,8:TiffIO.writeImage: Invalid name "st" (should match [a-z_][a-zA-Z0-9_]{2,30}$) R:742,4:TiffIO.writeImage: Too many branches (16/15) R:742,4:TiffIO.writeImage: Too many statements (67/50) C:837,4:TiffIO._initEmptyFile: Invalid name "fd" (should match [a-z_][a-zA-Z0-9_]{2,30}$) C:837,4:TiffIO._initEmptyFile: Missing docstring C:837,29:TiffIO._initEmptyFile: Invalid name "fd" (should match [a-z_][a-zA-Z0-9_]{2,30}$) C:839,12:TiffIO._initEmptyFile: Invalid name "fd" (should match [a-z_][a-zA-Z0-9_]{2,30}$) C:850,8:TiffIO._initEmptyFile: Invalid name "st" (should match [a-z_][a-zA-Z0-9_]{2,30}$) R:866,4:TiffIO._getOutputIFD: Too many local variables (34/25) W:930,8:TiffIO._getOutputIFD: Redefining name 'dtype' from outer scope (line 1171) W:1023,8:TiffIO._getOutputIFD: Redefining name 'info' from outer scope (line 1187) W:999,16:TiffIO._getOutputIFD: Redefining name 'i' from outer scope (line 1186) C:866,4:TiffIO._getOutputIFD: Missing docstring C:989,8:TiffIO._getOutputIFD: Invalid name "st" (should match [a-z_][a-zA-Z0-9_]{2,30}$) R:866,4:TiffIO._getOutputIFD: Too many branches (54/15) R:866,4:TiffIO._getOutputIFD: Too many statements (177/50) W:501,16:TiffIO._readInfo: Attribute '_imageInfoCache' defined outside __init__ W:849,12:TiffIO._initEmptyFile: Attribute '_structChar' defined outside __init__ W:203,8:TiffIO.getImageFileDirectories: Attribute '_IFD' defined outside __init__ W:738,16:TiffIO._readImage: Attribute '_imageDataCache' defined outside __init__ W:737,16:TiffIO._readImage: Attribute '_imageDataCacheIndex' defined outside __init__ W:834,8:TiffIO.writeImage: Attribute 'fd' defined outside __init__ W:854,12:TiffIO._initEmptyFile: Attribute '_swap' defined outside __init__ W:500,16:TiffIO._readInfo: Attribute '_imageInfoCacheIndex' defined outside __init__ Report ====== 797 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |48 |48 |= | +-----------+-------+---------+-----------+ |refactor |11 |11 |= | +-----------+-------+---------+-----------+ |warning |28 |28 |= | +-----------+-------+---------+-----------+ |error |8 |8 |= | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |29 | +-----------+------------+ |C0111 |18 | +-----------+------------+ |W0621 |13 | +-----------+------------+ |W0201 |8 | +-----------+------------+ |E1103 |7 | +-----------+------------+ |W0612 |4 | +-----------+------------+ |R0915 |4 | +-----------+------------+ |R0912 |4 | +-----------+------------+ |R0914 |3 | +-----------+------------+ |W0702 |2 | +-----------+------------+ |W0613 |1 | +-----------+------------+ |E0711 |1 | +-----------+------------+ |C0302 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 8.41/10 (previous run: 8.41/10) That's pretty good. Good work mate. Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |959 |87.82 |959 |= | +----------+-------+------+---------+-----------+ |docstring |11 |1.01 |11 |= | +----------+-------+------+---------+-----------+ |comment |62 |5.68 |62 |= | +----------+-------+------+---------+-----------+ |empty |60 |5.49 |60 |= | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |1 |= |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |method |17 |17 |= |5.88 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ External dependencies --------------------- :: numpy (TiffIO) Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ fabio-0.1.3/pylint/bruker100image.py.lint0000644000175000017500000000767112233243316020745 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module bruker100image C: 58,0: Line too long (81/80) C: 66,0: Line too long (89/80) C: 1,0: Missing docstring C: 4,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 9,4: Invalid name "Image" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 14,0:bruker100image: Invalid name "bruker100image" (should match [A-Z_][a-zA-Z0-9]+$) C: 14,0:bruker100image: Missing docstring C: 17,4:bruker100image.toPIL16: Invalid name "toPIL16" (should match [a-z_][a-z0-9_]{2,30}$) C: 23,8:bruker100image.toPIL16: Invalid name "PILimage" (should match [a-z_][a-z0-9_]{2,30}$) C: 31,8:bruker100image.read: Invalid name "f" (should match [a-z_][a-z0-9_]{2,30}$) C: 58,12:bruker100image.read: Invalid name "ar" (should match [a-z_][a-z0-9_]{2,30}$) C: 66,12:bruker100image.read: Invalid name "M" (should match [a-z_][a-z0-9_]{2,30}$) R: 14,0:bruker100image: Too many public methods (29/20) C: 85,4: Invalid name "b" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 88,8: Invalid name "r" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 95,4: Invalid name "e" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) Report ====== 61 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |15 |16 |-1.00 | +-----------+-------+---------+-----------+ |refactor |1 |0 |+1.00 | +-----------+-------+---------+-----------+ |warning |0 |6 |-6.00 | +-----------+-------+---------+-----------+ |error |0 |22 |-22.00 | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |11 | +-----------+------------+ |C0301 |2 | +-----------+------------+ |C0111 |2 | +-----------+------------+ |R0904 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 7.38/10 (previous run: -14.00/10) Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |66 |76.74 |63 |+3.00 | +----------+-------+------+---------+-----------+ |docstring |5 |5.81 |7 |-2.00 | +----------+-------+------+---------+-----------+ |comment |7 |8.14 |7 |= | +----------+-------+------+---------+-----------+ |empty |8 |9.30 |10 |-2.00 | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (bruker100image) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |1 |= |0.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |2 |2 |= |100.00 |50.00 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/fit2dmaskimage.py.lint0000644000175000017500000000600012233243305021075 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module fit2dmaskimage C: 15,0:fit2dmaskimage: Invalid name "fit2dmaskimage" (should match [A-Z_][a-zA-Z0-9]+$) C: 90,4:fit2dmaskimage.checkData: Invalid name "checkData" (should match [a-z_][a-z0-9_]{2,30}$) R: 15,0:fit2dmaskimage: Too many public methods (25/20) Report ====== 43 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |2 |1 |+1.00 | +-----------+-------+---------+-----------+ |refactor |1 |1 |= | +-----------+-------+---------+-----------+ |warning |0 |8 |-8.00 | +-----------+-------+---------+-----------+ |error |0 |18 |-18.00 | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |2 | +-----------+------------+ |R0904 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 9.30/10 (previous run: -16.32/10) Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |50 |56.18 |43 |+7.00 | +----------+-------+------+---------+-----------+ |docstring |18 |20.22 |18 |= | +----------+-------+------+---------+-----------+ |comment |7 |7.87 |7 |= | +----------+-------+------+---------+-----------+ |empty |14 |15.73 |14 |= | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (fit2dmaskimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |1 |= |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |4 |3 |+1.00 |100.00 |25.00 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/fabian_mar_header.py.lint0000644000175000017500000006346712120434325021620 0ustar jeromejerome00000000000000************* Module fabian_mar_header C: 11:obselete: Invalid name "obselete" (should match [A-Z_][a-zA-Z0-9]+$) C: 11:obselete: Missing docstring W: 11:obselete: Class has no __init__ method C: 18:obselete._readheader_fabian: Invalid name "l" (should match [a-z_][a-zA-Z0-9_]{2,30}$) C: 19:obselete._readheader_fabian: Invalid name "l" (should match [a-z_][a-zA-Z0-9_]{2,30}$) E: 24:obselete._readheader_fabian: Undefined variable 'N' E: 24:obselete._readheader_fabian: Undefined variable 'N' C: 27:obselete._readheader_fabian: Comma not followed by a space self.header['header_major_version'] = N.fromstring(l[20:24],N.uint32)[0] # UINT32 ; /* header_major_version (n.) */ ^^ E: 27:obselete._readheader_fabian: Undefined variable 'N' E: 27:obselete._readheader_fabian: Undefined variable 'N' C: 28:obselete._readheader_fabian: Comma not followed by a space self.header['header_minor_version'] = N.fromstring(l[24:28],N.uint32)[0] # UINT32 ; /* header_minor_version (.n) */ ^^ E: 28:obselete._readheader_fabian: Undefined variable 'N' E: 28:obselete._readheader_fabian: Undefined variable 'N' C: 29:obselete._readheader_fabian: Comma not followed by a space self.header['header_byte_orde'] = N.fromstring(l[28:32],N.uint32)[0] # UINT32 r;/* BIG_ENDIAN (Motorola,MIPS); LITTLE_ENDIAN (DEC, Intel) */ ^^ E: 29:obselete._readheader_fabian: Undefined variable 'N' E: 29:obselete._readheader_fabian: Undefined variable 'N' C: 30:obselete._readheader_fabian: Comma not followed by a space self.header['data_byte_order'] = N.fromstring(l[32:36],N.uint32)[0] # UINT32 ; /* BIG_ENDIAN (Motorola,MIPS); LITTLE_ENDIAN (DEC, Intel) */ ^^ E: 30:obselete._readheader_fabian: Undefined variable 'N' E: 30:obselete._readheader_fabian: Undefined variable 'N' C: 31:obselete._readheader_fabian: Comma not followed by a space self.header['header_size'] = N.fromstring(l[36:40],N.uint32)[0] # UINT32 ; /* in bytes */ ^^ E: 31:obselete._readheader_fabian: Undefined variable 'N' E: 31:obselete._readheader_fabian: Undefined variable 'N' C: 32:obselete._readheader_fabian: Comma not followed by a space self.header['frame_type'] = N.fromstring(l[40:44],N.uint32)[0] # UINT32 ; /* flag for frame type */ ^^ E: 32:obselete._readheader_fabian: Undefined variable 'N' E: 32:obselete._readheader_fabian: Undefined variable 'N' C: 42:obselete._readheader_fabian: Comma not followed by a space self.header['nfast'] = N.fromstring(l[80:84],N.uint32)[0] # UINT32 ; /* number of pixels in one line */ ^^ E: 42:obselete._readheader_fabian: Undefined variable 'N' E: 42:obselete._readheader_fabian: Undefined variable 'N' C: 43:obselete._readheader_fabian: Comma not followed by a space self.header['nslow'] = N.fromstring(l[84:88],N.uint32)[0] # UINT32 ; /* number of lines in image */ ^^ E: 43:obselete._readheader_fabian: Undefined variable 'N' E: 43:obselete._readheader_fabian: Undefined variable 'N' C: 44:obselete._readheader_fabian: Comma not followed by a space self.header['depth'] = N.fromstring(l[88:92],N.uint32)[0] # UINT32 ; /* number of bytes per pixel */ ^^ E: 44:obselete._readheader_fabian: Undefined variable 'N' E: 44:obselete._readheader_fabian: Undefined variable 'N' C: 46:obselete._readheader_fabian: Comma not followed by a space self.header['signif_bits'] = N.fromstring(l[96:100],N.uint32)[0] # UINT32 ; /* true depth of data, in bits */ ^^ E: 46:obselete._readheader_fabian: Undefined variable 'N' E: 46:obselete._readheader_fabian: Undefined variable 'N' C: 49:obselete._readheader_fabian: Comma not followed by a space self.header['sequence'] = N.fromstring(l[108:112],N.uint32)[0] # UINT32 ; /* TRUE or FALSE */ ^^ E: 49:obselete._readheader_fabian: Undefined variable 'N' E: 49:obselete._readheader_fabian: Undefined variable 'N' C: 50:obselete._readheader_fabian: Comma not followed by a space self.header['nimages'] = N.fromstring(l[112:116],N.uint32)[0] # UINT32 ; /* total number of images - size of each is nfast*(nslow/nimages) */ ^^ E: 50:obselete._readheader_fabian: Undefined variable 'N' E: 50:obselete._readheader_fabian: Undefined variable 'N' C: 51:obselete._readheader_fabian: Comma not followed by a space self.header['origin'] = N.fromstring(l[116:120],N.uint32)[0] # UINT32 ; /* corner of origin */ ^^ E: 51:obselete._readheader_fabian: Undefined variable 'N' E: 51:obselete._readheader_fabian: Undefined variable 'N' C: 52:obselete._readheader_fabian: Comma not followed by a space self.header['orientation'] = N.fromstring(l[120:124],N.uint32)[0] # UINT32 ; /* direction of fast axis */ ^^ E: 52:obselete._readheader_fabian: Undefined variable 'N' E: 52:obselete._readheader_fabian: Undefined variable 'N' C: 53:obselete._readheader_fabian: Comma not followed by a space self.header['view_direction'] = N.fromstring(l[124:128],N.uint32)[0] # UINT32 ; /* direction to view frame */ ^^ E: 53:obselete._readheader_fabian: Undefined variable 'N' E: 53:obselete._readheader_fabian: Undefined variable 'N' C: 54:obselete._readheader_fabian: Comma not followed by a space self.header['overflow_locatio'] = N.fromstring(l[128:132],N.uint32)[0] # UINT32 n;/* FOLLOWING_HEADER, FOLLOWING_DATA */ ^^ E: 54:obselete._readheader_fabian: Undefined variable 'N' E: 54:obselete._readheader_fabian: Undefined variable 'N' C: 55:obselete._readheader_fabian: Comma not followed by a space self.header['over_8_bits'] = N.fromstring(l[132:136],N.uint32)[0] # UINT32 ; /* # of pixels with counts > 255 */ ^^ E: 55:obselete._readheader_fabian: Undefined variable 'N' E: 55:obselete._readheader_fabian: Undefined variable 'N' C: 56:obselete._readheader_fabian: Comma not followed by a space self.header['over_16_bits'] = N.fromstring(l[136:140],N.uint32)[0] # UINT32 ; /* # of pixels with count > 65535 */ ^^ E: 56:obselete._readheader_fabian: Undefined variable 'N' E: 56:obselete._readheader_fabian: Undefined variable 'N' C: 57:obselete._readheader_fabian: Comma not followed by a space self.header['multiplexed'] = N.fromstring(l[140:144],N.uint32)[0] # UINT32 ; /* multiplex flag */ ^^ E: 57:obselete._readheader_fabian: Undefined variable 'N' E: 57:obselete._readheader_fabian: Undefined variable 'N' C: 58:obselete._readheader_fabian: Comma not followed by a space self.header['nfastimages'] = N.fromstring(l[144:148],N.uint32)[0] # UINT32 ; /* # of images in fast direction */ ^^ E: 58:obselete._readheader_fabian: Undefined variable 'N' E: 58:obselete._readheader_fabian: Undefined variable 'N' C: 59:obselete._readheader_fabian: Comma not followed by a space self.header['nslowimages'] = N.fromstring(l[148:152],N.uint32)[0] # UINT32 ; /* # of images in slow direction */ ^^ E: 59:obselete._readheader_fabian: Undefined variable 'N' E: 59:obselete._readheader_fabian: Undefined variable 'N' C: 60:obselete._readheader_fabian: Comma not followed by a space self.header['background_applied'] = N.fromstring(l[152:156],N.uint32)[0] # UINT32 ; /* flags correction has been applied hold magic number ? */ ^^ E: 60:obselete._readheader_fabian: Undefined variable 'N' E: 60:obselete._readheader_fabian: Undefined variable 'N' C: 61:obselete._readheader_fabian: Comma not followed by a space self.header['bias_applied'] = N.fromstring(l[156:160],N.uint32)[0] # UINT32 ; /* flags correction has been applied - hold magic number ? */ ^^ E: 61:obselete._readheader_fabian: Undefined variable 'N' E: 61:obselete._readheader_fabian: Undefined variable 'N' C: 62:obselete._readheader_fabian: Comma not followed by a space self.header['flatfield_applied'] = N.fromstring(l[160:164],N.uint32)[0] # UINT32 ; /* flags correction has been applied hold magic number ? */ ^^ E: 62:obselete._readheader_fabian: Undefined variable 'N' E: 62:obselete._readheader_fabian: Undefined variable 'N' C: 63:obselete._readheader_fabian: Comma not followed by a space self.header['distortion_applied'] = N.fromstring(l[164:168],N.uint32)[0] # UINT32 ; /* flags correction has been applied hold magic number ? */ ^^ E: 63:obselete._readheader_fabian: Undefined variable 'N' E: 63:obselete._readheader_fabian: Undefined variable 'N' C: 67:obselete._readheader_fabian: Comma not followed by a space self.header['xtal_to_detector'] = N.fromstring(l[640:644],N.int32)[0]*1000 #INT32 ; /* 1000*distance in millimeters */ ^^ E: 67:obselete._readheader_fabian: Undefined variable 'N' E: 67:obselete._readheader_fabian: Undefined variable 'N' C: 68:obselete._readheader_fabian: Comma not followed by a space self.header['beam_x'] = N.fromstring(l[644:648],N.int32)[0]*1000 #INT32 ; /* 1000*x beam position (pixels) */ ^^ E: 68:obselete._readheader_fabian: Undefined variable 'N' E: 68:obselete._readheader_fabian: Undefined variable 'N' C: 69:obselete._readheader_fabian: Comma not followed by a space self.header['beam_y'] = N.fromstring(l[648:652],N.int32)[0]*1000 #INT32 ; /* 1000*y beam position (pixels) */ ^^ E: 69:obselete._readheader_fabian: Undefined variable 'N' E: 69:obselete._readheader_fabian: Undefined variable 'N' C: 70:obselete._readheader_fabian: Comma not followed by a space self.header['integration_time'] = N.fromstring(l[652:656],N.int32)[0] #INT32 ; /* integration time in milliseconds */ ^^ E: 70:obselete._readheader_fabian: Undefined variable 'N' E: 70:obselete._readheader_fabian: Undefined variable 'N' C: 71:obselete._readheader_fabian: Comma not followed by a space self.header['exposure_time'] = N.fromstring(l[656:660],N.int32)[0] #INT32 ; /* exposure time in milliseconds */ ^^ E: 71:obselete._readheader_fabian: Undefined variable 'N' E: 71:obselete._readheader_fabian: Undefined variable 'N' C: 72:obselete._readheader_fabian: Comma not followed by a space self.header['readout_time'] = N.fromstring(l[660:664],N.int32)[0] #INT32 ; /* readout time in milliseconds */ ^^ E: 72:obselete._readheader_fabian: Undefined variable 'N' E: 72:obselete._readheader_fabian: Undefined variable 'N' C: 73:obselete._readheader_fabian: Comma not followed by a space self.header['nreads'] = N.fromstring(l[664:668],N.int32)[0] #INT32 ; /* number of readouts to get this image */ ^^ E: 73:obselete._readheader_fabian: Undefined variable 'N' E: 73:obselete._readheader_fabian: Undefined variable 'N' C: 74:obselete._readheader_fabian: Comma not followed by a space self.header['start_twotheta'] = N.fromstring(l[668:672],N.int32)[0]*1000 #INT32 ; /* 1000*two_theta angle */ ^^ E: 74:obselete._readheader_fabian: Undefined variable 'N' E: 74:obselete._readheader_fabian: Undefined variable 'N' C: 75:obselete._readheader_fabian: Comma not followed by a space self.header['start_omega'] = N.fromstring(l[676:680],N.int32)[0]*1000 #INT32 ; /* 1000*omega angle */ ^^ E: 75:obselete._readheader_fabian: Undefined variable 'N' E: 75:obselete._readheader_fabian: Undefined variable 'N' C: 76:obselete._readheader_fabian: Comma not followed by a space self.header['start_chi'] = N.fromstring(l[680:684],N.int32)[0]*1000 #INT32 ; /* 1000*chi angle */ ^^ E: 76:obselete._readheader_fabian: Undefined variable 'N' E: 76:obselete._readheader_fabian: Undefined variable 'N' C: 77:obselete._readheader_fabian: Comma not followed by a space self.header['start_kappa'] = N.fromstring(l[684:688],N.int32)[0]*1000 #INT32 ; /* 1000*kappa angle */ ^^ E: 77:obselete._readheader_fabian: Undefined variable 'N' E: 77:obselete._readheader_fabian: Undefined variable 'N' C: 78:obselete._readheader_fabian: Comma not followed by a space self.header['start_phi'] = N.fromstring(l[688:692],N.int32)[0]*1000 #INT32 ; /* 1000*phi angle */ ^^ E: 78:obselete._readheader_fabian: Undefined variable 'N' E: 78:obselete._readheader_fabian: Undefined variable 'N' C: 79:obselete._readheader_fabian: Comma not followed by a space self.header['start_delta'] = N.fromstring(l[692:696],N.int32)[0]*1000 #INT32 ; /* 1000*delta angle */ ^^ E: 79:obselete._readheader_fabian: Undefined variable 'N' E: 79:obselete._readheader_fabian: Undefined variable 'N' C: 80:obselete._readheader_fabian: Comma not followed by a space self.header['start_gamma'] = N.fromstring(l[696:700],N.int32)[0]*1000 #INT32 ; /* 1000*gamma angle */ ^^ E: 80:obselete._readheader_fabian: Undefined variable 'N' E: 80:obselete._readheader_fabian: Undefined variable 'N' C: 81:obselete._readheader_fabian: Comma not followed by a space self.header['start_xtal_to_detector'] = N.fromstring(l[700:704],N.int32)[0]*1000 #INT32 ; /* 1000*distance in mm (dist in um)*/ ^^ E: 81:obselete._readheader_fabian: Undefined variable 'N' E: 81:obselete._readheader_fabian: Undefined variable 'N' C: 82:obselete._readheader_fabian: Comma not followed by a space self.header['end_twotheta'] = N.fromstring(l[704:708],N.int32)[0]*1000 #INT32 ; /* 1000*two_theta angle */ ^^ E: 82:obselete._readheader_fabian: Undefined variable 'N' E: 82:obselete._readheader_fabian: Undefined variable 'N' C: 83:obselete._readheader_fabian: Comma not followed by a space self.header['end_omega'] = N.fromstring(l[708:712],N.int32)[0]*1000 #INT32 ; /* 1000*omega angle */ ^^ E: 83:obselete._readheader_fabian: Undefined variable 'N' E: 83:obselete._readheader_fabian: Undefined variable 'N' C: 84:obselete._readheader_fabian: Comma not followed by a space self.header['end_chi'] = N.fromstring(l[712:716],N.int32)[0]*1000 #INT32 ; /* 1000*chi angle */ ^^ E: 84:obselete._readheader_fabian: Undefined variable 'N' E: 84:obselete._readheader_fabian: Undefined variable 'N' C: 85:obselete._readheader_fabian: Comma not followed by a space self.header['end_kappa'] = N.fromstring(l[716:720],N.int32)[0]*1000 #INT32 ; /* 1000*kappa angle */ ^^ E: 85:obselete._readheader_fabian: Undefined variable 'N' E: 85:obselete._readheader_fabian: Undefined variable 'N' C: 86:obselete._readheader_fabian: Comma not followed by a space self.header['end_phi'] = N.fromstring(l[720:724],N.int32)[0]*1000 #INT32 ; /* 1000*phi angle */ ^^ E: 86:obselete._readheader_fabian: Undefined variable 'N' E: 86:obselete._readheader_fabian: Undefined variable 'N' C: 87:obselete._readheader_fabian: Comma not followed by a space self.header['end_delta'] = N.fromstring(l[724:728],N.int32)[0]*1000 #INT32 ; /* 1000*delta angle */ ^^ E: 87:obselete._readheader_fabian: Undefined variable 'N' E: 87:obselete._readheader_fabian: Undefined variable 'N' C: 88:obselete._readheader_fabian: Comma not followed by a space self.header['end_gamma'] = N.fromstring(l[728:732],N.int32)[0]*1000 #INT32 ; /* 1000*gamma angle */ ^^ E: 88:obselete._readheader_fabian: Undefined variable 'N' E: 88:obselete._readheader_fabian: Undefined variable 'N' C: 89:obselete._readheader_fabian: Comma not followed by a space self.header['end_xtal_to_detector'] = N.fromstring(l[732:736],N.int32)[0]*1000 #INT32 ; /* 1000*distance in mm (dist in um)*/ ^^ E: 89:obselete._readheader_fabian: Undefined variable 'N' E: 89:obselete._readheader_fabian: Undefined variable 'N' C: 90:obselete._readheader_fabian: Comma not followed by a space self.header['rotation_axis'] = N.fromstring(l[736:740],N.int32)[0] #INT32 ; /* active rotation axis */ ^^ E: 90:obselete._readheader_fabian: Undefined variable 'N' E: 90:obselete._readheader_fabian: Undefined variable 'N' C: 91:obselete._readheader_fabian: Comma not followed by a space self.header['rotation_range'] = N.fromstring(l[740:744],N.int32)[0]*1000 #INT32 ; /* 1000*rotation angle */ ^^ E: 91:obselete._readheader_fabian: Undefined variable 'N' E: 91:obselete._readheader_fabian: Undefined variable 'N' C: 92:obselete._readheader_fabian: Comma not followed by a space self.header['detector_rotx'] = N.fromstring(l[744:748],N.int32)[0]*1000 #INT32 ; /* 1000*rotation of detector around X */ ^^ E: 92:obselete._readheader_fabian: Undefined variable 'N' E: 92:obselete._readheader_fabian: Undefined variable 'N' C: 93:obselete._readheader_fabian: Comma not followed by a space self.header['detector_roty'] = N.fromstring(l[748:752],N.int32)[0]*1000 #INT32 ; /* 1000*rotation of detector around Y */ ^^ E: 93:obselete._readheader_fabian: Undefined variable 'N' E: 93:obselete._readheader_fabian: Undefined variable 'N' C: 94:obselete._readheader_fabian: Comma not followed by a space self.header['detector_rotz'] = N.fromstring(l[752:756],N.int32)[0]*1000 #INT32 ; /* 1000*rotation of detector around Z */ ^^ E: 94:obselete._readheader_fabian: Undefined variable 'N' E: 94:obselete._readheader_fabian: Undefined variable 'N' C: 96:obselete._readheader_fabian: Comma not followed by a space self.header['detector_type'] = N.fromstring(l[768:772],N.int32)[0] #INT32 ; /* detector type */ ^^ E: 96:obselete._readheader_fabian: Undefined variable 'N' E: 96:obselete._readheader_fabian: Undefined variable 'N' C: 97:obselete._readheader_fabian: Comma not followed by a space self.header['pixelsize_x'] = N.fromstring(l[772:776],N.int32)[0] #INT32 ; /* pixel size (nanometers) */ ^^ E: 97:obselete._readheader_fabian: Undefined variable 'N' E: 97:obselete._readheader_fabian: Undefined variable 'N' C: 98:obselete._readheader_fabian: Comma not followed by a space self.header['pixelsize_y'] = N.fromstring(l[776:780],N.int32)[0] #INT32 ; /* pixel size (nanometers) */ ^^ E: 98:obselete._readheader_fabian: Undefined variable 'N' E: 98:obselete._readheader_fabian: Undefined variable 'N' C: 99:obselete._readheader_fabian: Comma not followed by a space self.header['mean_bias'] = N.fromstring(l[780:784],N.int32)[0]*1000 #INT32 ; /* 1000*mean bias value */ ^^ E: 99:obselete._readheader_fabian: Undefined variable 'N' E: 99:obselete._readheader_fabian: Undefined variable 'N' C:100:obselete._readheader_fabian: Comma not followed by a space self.header['photons_per_100adu'] = N.fromstring(l[784:788],N.int32)[0] #INT32 ; /* photons / 100 ADUs */ ^^ E:100:obselete._readheader_fabian: Undefined variable 'N' E:100:obselete._readheader_fabian: Undefined variable 'N' C:101:obselete._readheader_fabian: Comma not followed by a space self.header['measured_bias'] = N.fromstring(l[788:792],N.int32)[0]*1000 #INT32 [MAXIMAGES]; /* 1000*mean bias value for each image*/ ^^ E:101:obselete._readheader_fabian: Undefined variable 'N' E:101:obselete._readheader_fabian: Undefined variable 'N' C:102:obselete._readheader_fabian: Comma not followed by a space self.header['measured_temperature'] = N.fromstring(l[792:796],N.int32)[0] #INT32 [MAXIMAGES]; /* Temperature of each detector in milliKelvins */ ^^ E:102:obselete._readheader_fabian: Undefined variable 'N' E:102:obselete._readheader_fabian: Undefined variable 'N' C:103:obselete._readheader_fabian: Comma not followed by a space self.header['measured_pressure'] = N.fromstring(l[796:800],N.int32)[0] #INT32 [MAXIMAGES] ; /* Pressure of each chamber in microTorr */ ^^ E:103:obselete._readheader_fabian: Undefined variable 'N' E:103:obselete._readheader_fabian: Undefined variable 'N' C:108:obselete._readheader_fabian: Comma not followed by a space self.header['source_wavelength'] = N.fromstring(l[908:912],N.int32)[0] #INT32 ; /* wavelength (femtoMeters) */ ^^ E:108:obselete._readheader_fabian: Undefined variable 'N' E:108:obselete._readheader_fabian: Undefined variable 'N' R: 12:obselete._readheader_fabian: Too many statements (74/50) W: 16:obselete._readheader_fabian: Attribute 'header' defined outside __init__ R: 11:obselete: Too few public methods (0/2) Report ====== 75 statements analysed. Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |77 |55.80 |77 |= | +----------+-------+------+---------+-----------+ |docstring |10 |7.25 |10 |= | +----------+-------+------+---------+-----------+ |comment |35 |25.36 |35 |= | +----------+-------+------+---------+-----------+ |empty |16 |11.59 |16 |= | +----------+-------+------+---------+-----------+ Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |1 |= |0.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |0 |= |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |66 |66 |= | +-----------+-------+---------+-----------+ |refactor |2 |2 |= | +-----------+-------+---------+-----------+ |warning |2 |2 |= | +-----------+-------+---------+-----------+ |error |126 |126 |= | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |E0602 |126 | +-----------+------------+ |C0324 |62 | +-----------+------------+ |C0103 |3 | +-----------+------------+ |W0232 |1 | +-----------+------------+ |W0201 |1 | +-----------+------------+ |R0915 |1 | +-----------+------------+ |R0903 |1 | +-----------+------------+ |C0111 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at -83.33/10 (previous run: -83.33/10) You have to do something quick ! fabio-0.1.3/pylint/__init__.py.lint0000644000175000017500000000560012233243277017762 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module __init__ W: 26,0: Redefining built-in 'open' C: 14,0: Invalid name "version" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 24,0: Invalid name "filename_object" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) Report ====== 16 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |2 |73 |-71.00 | +-----------+-------+---------+-----------+ |refactor |0 |0 |= | +-----------+-------+---------+-----------+ |warning |1 |23 |-22.00 | +-----------+-------+---------+-----------+ |error |0 |3 |-3.00 | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |2 | +-----------+------------+ |W0622 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 8.12/10 (previous run: 3.76/10) Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |17 |68.00 |183 |-166.00 | +----------+-------+------+---------+-----------+ |docstring |4 |16.00 |52 |-48.00 | +----------+-------+------+---------+-----------+ |comment |3 |12.00 |48 |-45.00 | +----------+-------+------+---------+-----------+ |empty |1 |4.00 |27 |-26.00 | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ |method |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |13 |-13.00 |0 |0 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/edfimage.py.lint0000644000175000017500000004025012233243313017753 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module edfimage C: 89,0: Line too long (91/80) C:109,0: Line too long (113/80) C:162,0: Line too long (137/80) C:167,0: Line too long (141/80) C:177,0: Line too long (141/80) C:192,0: Line too long (108/80) C:207,0: Line too long (85/80) C:216,0: Line too long (125/80) C:217,0: Line too long (118/80) C:230,0: Line too long (93/80) C:231,0: Line too long (93/80) C:233,0: Line too long (94/80) C:234,0: Line too long (92/80) C:255,0: Line too long (89/80) C:262,0: Line too long (115/80) C:269,0: Line too long (81/80) C:277,0: Line too long (105/80) C:279,0: Line too long (92/80) C:294,0: Line too long (81/80) C:303,0: Line too long (104/80) C:306,0: Line too long (113/80) C:309,0: Line too long (96/80) C:311,0: Line too long (85/80) C:318,0: Line too long (104/80) C:359,0: Line too long (110/80) C:367,0: Line too long (85/80) C:402,0: Line too long (82/80) C:418,0: Line too long (117/80) C:424,0: Line too long (90/80) C:425,0: Line too long (89/80) C:446,0: Line too long (92/80) C:493,0: Line too long (95/80) C:497,0: Line too long (87/80) C:508,0: Line too long (89/80) C:513,0: Line too long (112/80) C:556,0: Line too long (126/80) C:560,0: Line too long (113/80) C:570,0: Line too long (118/80) C:589,0: Line too long (127/80) C:599,0: Line too long (93/80) C:600,0: Line too long (93/80) C:602,0: Line too long (94/80) C:603,0: Line too long (92/80) C:622,0: Line too long (90/80) C:625,0: Line too long (107/80) C:672,0: Line too long (92/80) C:708,0: Line too long (119/80) C:718,0: Line too long (82/80) C:730,0: Line too long (119/80) C:740,0: Line too long (94/80) C:756,0: Line too long (82/80) C:774,0: Line too long (90/80) C:798,0: Line too long (86/80) C:823,0: Line too long (108/80) C:880,0: Line too long (150/80) C: 23,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) R: 93,0:Frame: Too many instance attributes (13/7) C:128,12:Frame.__init__: Invalid name "iFrame" (should match [a-z_][a-z0-9_]{2,30}$) C:112,8:Frame.__init__: Invalid name "capsHeader" (should match [a-z_][a-z0-9_]{2,30}$) C:183,8:Frame.parseheader: Invalid name "iDim" (should match [a-z_][a-z0-9_]{2,30}$) C:186,12:Frame.parseheader: Invalid name "strDim" (should match [a-z_][a-z0-9_]{2,30}$) C:194,20:Frame.parseheader: Invalid name "iDim" (should match [a-z_][a-z0-9_]{2,30}$) C:200,20:Frame.parseheader: Invalid name "iDim" (should match [a-z_][a-z0-9_]{2,30}$) C:204,16:Frame.parseheader: Invalid name "iDim" (should match [a-z_][a-z0-9_]{2,30}$) C:220,15:Frame.parseheader: Invalid name "n" (should match [a-z_][a-z0-9_]{2,30}$) R:132,4:Frame.parseheader: Too many branches (25/12) R:132,4:Frame.parseheader: Too many statements (70/50) C:241,4:Frame.getData: Invalid name "getData" (should match [a-z_][a-z0-9_]{2,30}$) C:266,20:Frame.getData: Invalid name "fileData" (should match [a-z_][a-z0-9_]{2,30}$) C:279,24:Frame.getData: Invalid name "myData" (should match [a-z_][a-z0-9_]{2,30}$) C:280,24:Frame.getData: Invalid name "rawData" (should match [a-z_][a-z0-9_]{2,30}$) C:283,20:Frame.getData: Invalid name "rawData" (should match [a-z_][a-z0-9_]{2,30}$) C:285,20:Frame.getData: Invalid name "rawData" (should match [a-z_][a-z0-9_]{2,30}$) C:288,20:Frame.getData: Invalid name "rawData" (should match [a-z_][a-z0-9_]{2,30}$) C:291,20:Frame.getData: Invalid name "rawData" (should match [a-z_][a-z0-9_]{2,30}$) C:295,20:Frame.getData: Invalid name "rawData" (should match [a-z_][a-z0-9_]{2,30}$) C:298,16:Frame.getData: Invalid name "rawData" (should match [a-z_][a-z0-9_]{2,30}$) C:304,16:Frame.getData: Invalid name "rawData" (should match [a-z_][a-z0-9_]{2,30}$) C:307,16:Frame.getData: Invalid name "rawData" (should match [a-z_][a-z0-9_]{2,30}$) R:241,4:Frame.getData: Too many branches (23/12) R:241,4:Frame.getData: Too many statements (63/50) C:315,4:Frame.setData: Invalid name "setData" (should match [a-z_][a-z0-9_]{2,30}$) C:319,4:Frame.getByteCode: Invalid name "getByteCode" (should match [a-z_][a-z0-9_]{2,30}$) C:319,4:Frame.getByteCode: Missing docstring C:324,4:Frame.setByteCode: Invalid name "setByteCode" (should match [a-z_][a-z0-9_]{2,30}$) C:324,4:Frame.setByteCode: Invalid name "_iVal" (should match [a-z_][a-z0-9_]{2,30}$) C:324,4:Frame.setByteCode: Missing docstring C:324,26:Frame.setByteCode: Invalid name "_iVal" (should match [a-z_][a-z0-9_]{2,30}$) R:328,4:Frame.getEdfBlock: Too many local variables (22/15) C:328,4:Frame.getEdfBlock: Invalid name "getEdfBlock" (should match [a-z_][a-z0-9_]{2,30}$) C:328,4:Frame.getEdfBlock: Invalid name "fit2dMode" (should match [a-z_][a-z0-9_]{2,30}$) C:328,43:Frame.getEdfBlock: Invalid name "fit2dMode" (should match [a-z_][a-z0-9_]{2,30}$) C:341,8:Frame.getEdfBlock: Invalid name "fit2dMode" (should match [a-z_][a-z0-9_]{2,30}$) C:343,12:Frame.getEdfBlock: Invalid name "KEY" (should match [a-z_][a-z0-9_]{2,30}$) C:351,8:Frame.getEdfBlock: Invalid name "capsHeader" (should match [a-z_][a-z0-9_]{2,30}$) C:353,8:Frame.getEdfBlock: Invalid name "listHeader" (should match [a-z_][a-z0-9_]{2,30}$) C:359,12:Frame.getEdfBlock: Invalid name "KEY" (should match [a-z_][a-z0-9_]{2,30}$) C:392,8:Frame.getEdfBlock: Invalid name "approxHeaderSize" (should match [a-z_][a-z0-9_]{2,30}$) C:394,12:Frame.getEdfBlock: Invalid name "approxHeaderSize" (should match [a-z_][a-z0-9_]{2,30}$) C:395,8:Frame.getEdfBlock: Invalid name "approxHeaderSize" (should match [a-z_][a-z0-9_]{2,30}$) C:403,8:Frame.getEdfBlock: Invalid name "preciseSize" (should match [a-z_][a-z0-9_]{2,30}$) C:406,12:Frame.getEdfBlock: Invalid name "strKey" (should match [a-z_][a-z0-9_]{2,30}$) C:410,12:Frame.getEdfBlock: Invalid name "strValue" (should match [a-z_][a-z0-9_]{2,30}$) C:415,12:Frame.getEdfBlock: Invalid name "preciseSize" (should match [a-z_][a-z0-9_]{2,30}$) C:421,20:Frame.getEdfBlock: Invalid name "headerSize" (should match [a-z_][a-z0-9_]{2,30}$) C:425,24:Frame.getEdfBlock: Invalid name "headerSize" (should match [a-z_][a-z0-9_]{2,30}$) C:427,20:Frame.getEdfBlock: Invalid name "preciseSize" (should match [a-z_][a-z0-9_]{2,30}$) C:431,12:Frame.getEdfBlock: Invalid name "headerSize" (should match [a-z_][a-z0-9_]{2,30}$) R:328,4:Frame.getEdfBlock: Too many branches (24/12) R:328,4:Frame.getEdfBlock: Too many statements (82/50) C:437,0:edfimage: Invalid name "edfimage" (should match [A-Z_][a-zA-Z0-9]+$) W:445,15:edfimage.__init__: Catching too general exception Exception C:471,4:edfimage.checkHeader: Invalid name "checkHeader" (should match [a-z_][a-z0-9_]{2,30}$) C:483,4:edfimage._readHeaderBlock: Invalid name "_readHeaderBlock" (should match [a-z_][a-z0-9_]{2,30}$) C:490,8:edfimage._readHeaderBlock: Invalid name "MAX_HEADER_SIZE" (should match [a-z_][a-z0-9_]{2,30}$) W:504,19:edfimage._readHeaderBlock: Catching too general exception Exception C:509,20:edfimage._readHeaderBlock: Invalid name "MAX_HEADER_SIZE" (should match [a-z_][a-z0-9_]{2,30}$) C:538,8:edfimage._readheader: Invalid name "bContinue" (should match [a-z_][a-z0-9_]{2,30}$) C:542,16:edfimage._readheader: Invalid name "bContinue" (should match [a-z_][a-z0-9_]{2,30}$) C:561,16:edfimage._readheader: Invalid name "bContinue" (should match [a-z_][a-z0-9_]{2,30}$) C:620,8:edfimage.getframe: Invalid name "newImage" (should match [a-z_][a-z0-9_]{2,30}$) C:623,12:edfimage.getframe: Invalid name "newImage" (should match [a-z_][a-z0-9_]{2,30}$) C:626,12:edfimage.getframe: Invalid name "newImage" (should match [a-z_][a-z0-9_]{2,30}$) C:638,8:edfimage.previous: Invalid name "newImage" (should match [a-z_][a-z0-9_]{2,30}$) C:640,12:edfimage.previous: Invalid name "newImage" (should match [a-z_][a-z0-9_]{2,30}$) C:642,12:edfimage.previous: Invalid name "newFrameId" (should match [a-z_][a-z0-9_]{2,30}$) C:643,12:edfimage.previous: Invalid name "newImage" (should match [a-z_][a-z0-9_]{2,30}$) C:649,8:edfimage.next: Invalid name "newImage" (should match [a-z_][a-z0-9_]{2,30}$) C:651,12:edfimage.next: Invalid name "newImage" (should match [a-z_][a-z0-9_]{2,30}$) C:653,12:edfimage.next: Invalid name "newFrameId" (should match [a-z_][a-z0-9_]{2,30}$) C:654,12:edfimage.next: Invalid name "newImage" (should match [a-z_][a-z0-9_]{2,30}$) W:658,4:edfimage.write: Arguments number differs from overridden method C:658,4:edfimage.write: Invalid name "fit2dMode" (should match [a-z_][a-z0-9_]{2,30}$) C:658,44:edfimage.write: Invalid name "fit2dMode" (should match [a-z_][a-z0-9_]{2,30}$) C:675,4:edfimage.appendFrame: Invalid name "appendFrame" (should match [a-z_][a-z0-9_]{2,30}$) C:688,4:edfimage.deleteFrame: Invalid name "deleteFrame" (should match [a-z_][a-z0-9_]{2,30}$) C:688,4:edfimage.deleteFrame: Invalid name "frameNb" (should match [a-z_][a-z0-9_]{2,30}$) C:688,26:edfimage.deleteFrame: Invalid name "frameNb" (should match [a-z_][a-z0-9_]{2,30}$) C:700,4:edfimage.fastReadData: Invalid name "fastReadData" (should match [a-z_][a-z0-9_]{2,30}$) C:711,36:edfimage.fastReadData: Invalid name "f" (should match [a-z_][a-z0-9_]{2,30}$) W:717,15:edfimage.fastReadData: Catching too general exception Exception C:721,4:edfimage.fastReadROI: Invalid name "fastReadROI" (should match [a-z_][a-z0-9_]{2,30}$) C:742,8:edfimage.fastReadROI: Invalid name "d1" (should match [a-z_][a-z0-9_]{2,30}$) C:749,36:edfimage.fastReadROI: Invalid name "f" (should match [a-z_][a-z0-9_]{2,30}$) W:755,15:edfimage.fastReadROI: Catching too general exception Exception C:763,4:edfimage.getNbFrames: Invalid name "getNbFrames" (should match [a-z_][a-z0-9_]{2,30}$) C:768,4:edfimage.setNbFrames: Invalid name "setNbFrames" (should match [a-z_][a-z0-9_]{2,30}$) C:777,4:edfimage.getHeader: Invalid name "getHeader" (should match [a-z_][a-z0-9_]{2,30}$) C:782,4:edfimage.setHeader: Invalid name "setHeader" (should match [a-z_][a-z0-9_]{2,30}$) C:782,4:edfimage.setHeader: Invalid name "_dictHeader" (should match [a-z_][a-z0-9_]{2,30}$) C:782,24:edfimage.setHeader: Invalid name "_dictHeader" (should match [a-z_][a-z0-9_]{2,30}$) C:793,4:edfimage.delHeader: Invalid name "delHeader" (should match [a-z_][a-z0-9_]{2,30}$) C:800,4:edfimage.getHeaderKeys: Invalid name "getHeaderKeys" (should match [a-z_][a-z0-9_]{2,30}$) C:805,4:edfimage.setHeaderKeys: Invalid name "setHeaderKeys" (should match [a-z_][a-z0-9_]{2,30}$) C:805,4:edfimage.setHeaderKeys: Invalid name "_listtHeader" (should match [a-z_][a-z0-9_]{2,30}$) C:805,28:edfimage.setHeaderKeys: Invalid name "_listtHeader" (should match [a-z_][a-z0-9_]{2,30}$) C:818,4:edfimage.delHeaderKeys: Invalid name "delHeaderKeys" (should match [a-z_][a-z0-9_]{2,30}$) C:825,4:edfimage.getData: Invalid name "getData" (should match [a-z_][a-z0-9_]{2,30}$) C:831,8:edfimage.getData: Invalid name "npaData" (should match [a-z_][a-z0-9_]{2,30}$) C:833,12:edfimage.getData: Invalid name "npaData" (should match [a-z_][a-z0-9_]{2,30}$) C:836,12:edfimage.getData: Invalid name "npaData" (should match [a-z_][a-z0-9_]{2,30}$) C:840,16:edfimage.getData: Invalid name "npaData" (should match [a-z_][a-z0-9_]{2,30}$) C:843,4:edfimage.setData: Invalid name "setData" (should match [a-z_][a-z0-9_]{2,30}$) C:855,4:edfimage.delData: Invalid name "delData" (should match [a-z_][a-z0-9_]{2,30}$) C:862,4:edfimage.getCapsHeader: Invalid name "getCapsHeader" (should match [a-z_][a-z0-9_]{2,30}$) C:869,4:edfimage.setCapsHeader: Invalid name "setCapsHeader" (should match [a-z_][a-z0-9_]{2,30}$) C:875,4:edfimage.delCapsHeader: Invalid name "delCapsHeader" (should match [a-z_][a-z0-9_]{2,30}$) C:882,4:edfimage.getDim1: Invalid name "getDim1" (should match [a-z_][a-z0-9_]{2,30}$) C:882,4:edfimage.getDim1: Missing docstring C:884,4:edfimage.setDim1: Invalid name "setDim1" (should match [a-z_][a-z0-9_]{2,30}$) C:884,4:edfimage.setDim1: Invalid name "_iVal" (should match [a-z_][a-z0-9_]{2,30}$) C:884,4:edfimage.setDim1: Missing docstring C:884,22:edfimage.setDim1: Invalid name "_iVal" (should match [a-z_][a-z0-9_]{2,30}$) C:894,4:edfimage.getDim2: Invalid name "getDim2" (should match [a-z_][a-z0-9_]{2,30}$) C:894,4:edfimage.getDim2: Missing docstring C:896,4:edfimage.setDim2: Invalid name "setDim2" (should match [a-z_][a-z0-9_]{2,30}$) C:896,4:edfimage.setDim2: Invalid name "_iVal" (should match [a-z_][a-z0-9_]{2,30}$) C:896,4:edfimage.setDim2: Missing docstring C:896,22:edfimage.setDim2: Invalid name "_iVal" (should match [a-z_][a-z0-9_]{2,30}$) C:907,4:edfimage.getDims: Invalid name "getDims" (should match [a-z_][a-z0-9_]{2,30}$) C:907,4:edfimage.getDims: Missing docstring C:910,4:edfimage.getByteCode: Invalid name "getByteCode" (should match [a-z_][a-z0-9_]{2,30}$) C:910,4:edfimage.getByteCode: Missing docstring C:912,4:edfimage.setByteCode: Invalid name "setByteCode" (should match [a-z_][a-z0-9_]{2,30}$) C:912,4:edfimage.setByteCode: Invalid name "_iVal" (should match [a-z_][a-z0-9_]{2,30}$) C:912,4:edfimage.setByteCode: Missing docstring C:912,26:edfimage.setByteCode: Invalid name "_iVal" (should match [a-z_][a-z0-9_]{2,30}$) C:922,4:edfimage.getBpp: Invalid name "getBpp" (should match [a-z_][a-z0-9_]{2,30}$) C:922,4:edfimage.getBpp: Missing docstring C:924,4:edfimage.setBpp: Invalid name "setBpp" (should match [a-z_][a-z0-9_]{2,30}$) C:924,4:edfimage.setBpp: Invalid name "_iVal" (should match [a-z_][a-z0-9_]{2,30}$) C:924,4:edfimage.setBpp: Missing docstring C:924,21:edfimage.setBpp: Invalid name "_iVal" (should match [a-z_][a-z0-9_]{2,30}$) R:437,0:edfimage: Too many public methods (54/20) Report ====== 597 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |180 |180 |= | +-----------+-------+---------+-----------+ |refactor |9 |9 |= | +-----------+-------+---------+-----------+ |warning |5 |15 |-10.00 | +-----------+-------+---------+-----------+ |error |0 |5 |-5.00 | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |114 | +-----------+------------+ |C0301 |55 | +-----------+------------+ |C0111 |11 | +-----------+------------+ |W0703 |4 | +-----------+------------+ |R0915 |3 | +-----------+------------+ |R0912 |3 | +-----------+------------+ |W0221 |1 | +-----------+------------+ |R0914 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ |R0902 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 6.75/10 (previous run: 6.12/10) Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |631 |69.26 |623 |+8.00 | +----------+-------+------+---------+-----------+ |docstring |202 |22.17 |205 |-3.00 | +----------+-------+------+---------+-----------+ |comment |11 |1.21 |11 |= | +----------+-------+------+---------+-----------+ |empty |67 |7.35 |70 |-3.00 | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (edfimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |2 |2 |= |100.00 |50.00 | +---------+-------+-----------+-----------+------------+---------+ |method |46 |47 |-1.00 |76.09 |73.91 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/testfit2dmaskimage.py.lint0000644000175000017500000000765012233243330022007 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.testfit2dmaskimage C: 14,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 15,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 29,0: No exception type(s) specified W: 32,0: Relative import 'utilstest', should be 'test.utilstest' C: 39,0:testfacemask: Invalid name "testfacemask" (should match [A-Z_][a-zA-Z0-9]+$) C: 42,4:testfacemask.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R: 39,0:testfacemask: Too many public methods (46/20) C: 63,0:testclickedmask: Invalid name "testclickedmask" (should match [A-Z_][a-zA-Z0-9]+$) C: 66,4:testclickedmask.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) R: 63,0:testclickedmask: Too many public methods (47/20) C: 99,0:test_suite_all_fit2d: Missing docstring C:100,4:test_suite_all_fit2d: Invalid name "testSuite" (should match [a-z_][a-z0-9_]{2,30}$) C:107,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:108,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) Report ====== 70 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |10 |NC |NC | +-----------+-------+---------+-----------+ |refactor |2 |NC |NC | +-----------+-------+---------+-----------+ |warning |2 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |9 | +-----------+------------+ |R0904 |2 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0403 |1 | +-----------+------------+ |C0111 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 8.00/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |70 |67.31 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |15 |14.42 |NC |NC | +----------+-------+------+---------+-----------+ |comment |4 |3.85 |NC |NC | +----------+-------+------+---------+-----------+ |empty |15 |14.42 |NC |NC | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (test.testfit2dmaskimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |2 |NC |NC |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |5 |NC |NC |100.00 |40.00 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/utilstest.py.lint0000644000175000017500000000765712233243324020272 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.utilstest C: 62,0: Line too long (86/80) C: 71,0: Line too long (95/80) C: 84,0: Line too long (99/80) C: 1,0: Missing docstring C: 42,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 71,12:UtilsTest: Used * or ** magic W: 73,4:UtilsTest: Specify string format arguments as logging function parameters C: 76,4:UtilsTest.forceBuild: Invalid name "forceBuild" (should match [a-z_][a-z0-9_]{2,30}$) C: 81,8:UtilsTest.forceBuild: Invalid name "p" (should match [a-z_][a-z0-9_]{2,30}$) C: 91,4:UtilsTest.timeoutDuringDownload: Invalid name "timeoutDuringDownload" (should match [a-z_][a-z0-9_]{2,30}$) C:114,16:UtilsTest.getimage: Invalid name "dictProxies" (should match [a-z_][a-z0-9_]{2,30}$) R:103,4:UtilsTest.getimage: Too many branches (16/12) R:103,4:UtilsTest.getimage: Too many statements (52/50) C:180,4:UtilsTest.recursive_delete: Invalid name "strDirname" (should match [a-z_][a-z0-9_]{2,30}$) C:180,25:UtilsTest.recursive_delete: Invalid name "strDirname" (should match [a-z_][a-z0-9_]{2,30}$) Report ====== 104 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |11 |NC |NC | +-----------+-------+---------+-----------+ |refactor |2 |NC |NC | +-----------+-------+---------+-----------+ |warning |2 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |7 | +-----------+------------+ |C0301 |3 | +-----------+------------+ |W1201 |1 | +-----------+------------+ |W0142 |1 | +-----------+------------+ |R0915 |1 | +-----------+------------+ |R0912 |1 | +-----------+------------+ |C0111 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 8.56/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |133 |69.27 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |24 |12.50 |NC |NC | +----------+-------+------+---------+-----------+ |comment |26 |13.54 |NC |NC | +----------+-------+------+---------+-----------+ |empty |9 |4.69 |NC |NC | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |method |4 |NC |NC |100.00 |50.00 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |NC |NC |0 |0 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/test_flat_binary.py.lint0000644000175000017500000001030212233243327021543 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.test_flat_binary C: 58,0: Line too long (91/80) C: 1,0: Missing docstring C: 3,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 4,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 18,0: No exception type(s) specified W: 21,0: Relative import 'utilstest', should be 'test.utilstest' C: 27,0:test_flat_binary: Invalid name "test_flat_binary" (should match [A-Z_][a-zA-Z0-9]+$) C: 27,0:test_flat_binary: Missing docstring C: 35,4:test_flat_binary.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C: 37,12:test_flat_binary.setUp: Invalid name "f" (should match [a-z_][a-z0-9_]{2,30}$) C: 42,4:test_flat_binary.NOtest_openimage: Invalid name "NOtest_openimage" (should match [a-z_][a-z0-9_]{2,30}$) W: 55,12:test_flat_binary.NOtest_openimage: No exception type(s) specified C: 50,16:test_flat_binary.NOtest_openimage: Invalid name "im" (should match [a-z_][a-z0-9_]{2,30}$) C: 60,4:test_flat_binary.tearDown: Invalid name "tearDown" (should match [a-z_][a-z0-9_]{2,30}$) R: 27,0:test_flat_binary: Too many public methods (46/20) C: 71,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) E: 71,14: Undefined variable 'test_suite_all_flat' C: 72,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) Report ====== 48 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |13 |NC |NC | +-----------+-------+---------+-----------+ |refactor |1 |NC |NC | +-----------+-------+---------+-----------+ |warning |3 |NC |NC | +-----------+-------+---------+-----------+ |error |1 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |10 | +-----------+------------+ |W0702 |2 | +-----------+------------+ |C0111 |2 | +-----------+------------+ |W0403 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ |E0602 |1 | +-----------+------------+ |C0301 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 5.42/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |48 |71.64 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |8 |11.94 |NC |NC | +----------+-------+------+---------+-----------+ |comment |5 |7.46 |NC |NC | +----------+-------+------+---------+-----------+ |empty |6 |8.96 |NC |NC | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |NC |NC |0.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |3 |NC |NC |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |NC |NC |0 |0 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/kcdimage.py.lint0000644000175000017500000001074712233243306017770 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module kcdimage C: 6,0: Line too long (97/80) C: 49,0: Line too long (92/80) C:113,0: Line too long (104/80) W: 11,0: Uses of a deprecated module 'string' C: 13,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 29,0:kcdimage: Invalid name "kcdimage" (should match [A-Z_][a-zA-Z0-9]+$) C: 39,8:kcdimage._readheader: Invalid name "oneLine" (should match [a-z_][a-z0-9_]{2,30}$) C: 41,8:kcdimage._readheader: Invalid name "asciiHeader" (should match [a-z_][a-z0-9_]{2,30}$) C: 42,12:kcdimage._readheader: Invalid name "oneChar" (should match [a-z_][a-z0-9_]{2,30}$) C: 44,16:kcdimage._readheader: Invalid name "asciiHeader" (should match [a-z_][a-z0-9_]{2,30}$) C: 50,8:kcdimage._readheader: Invalid name "endOfHeaders" (should match [a-z_][a-z0-9_]{2,30}$) C: 52,12:kcdimage._readheader: Invalid name "oneLine" (should match [a-z_][a-z0-9_]{2,30}$) C: 54,16:kcdimage._readheader: Invalid name "endOfHeaders" (should match [a-z_][a-z0-9_]{2,30}$) C: 57,16:kcdimage._readheader: Invalid name "oneLine" (should match [a-z_][a-z0-9_]{2,30}$) W: 60,12:kcdimage._readheader: No exception type(s) specified C: 61,16:kcdimage._readheader: Invalid name "endOfHeaders" (should match [a-z_][a-z0-9_]{2,30}$) C: 97,12:kcdimage.read: Invalid name "nbReadOut" (should match [a-z_][a-z0-9_]{2,30}$) C:100,12:kcdimage.read: Invalid name "nbReadOut" (should match [a-z_][a-z0-9_]{2,30}$) C:101,8:kcdimage.read: Invalid name "fileSize" (should match [a-z_][a-z0-9_]{2,30}$) C:127,4:kcdimage.checkData: Invalid name "checkData" (should match [a-z_][a-z0-9_]{2,30}$) R: 29,0:kcdimage: Too many public methods (25/20) Report ====== 83 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |18 |17 |+1.00 | +-----------+-------+---------+-----------+ |refactor |1 |1 |= | +-----------+-------+---------+-----------+ |warning |2 |10 |-8.00 | +-----------+-------+---------+-----------+ |error |0 |11 |-11.00 | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |15 | +-----------+------------+ |C0301 |3 | +-----------+------------+ |W0702 |1 | +-----------+------------+ |W0402 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 7.47/10 (previous run: -0.51/10) Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |85 |66.41 |79 |+6.00 | +----------+-------+------+---------+-----------+ |docstring |23 |17.97 |23 |= | +----------+-------+------+---------+-----------+ |comment |2 |1.56 |2 |= | +----------+-------+------+---------+-----------+ |empty |18 |14.06 |18 |= | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (kcdimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |1 |= |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |3 |2 |+1.00 |100.00 |33.33 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/oldtifimage.py.lint0000644000175000017500000001021712120434325020476 0ustar jeromejerome00000000000000************* Module oldtifimage C0301: 80: Line too long (84/80) W0704: 40:tifimage._readheader: Except doesn't do anything W0702: 41:tifimage._readheader: No exception's type specified C0111: 43:tifimage._readheader: Missing docstring E0102: 43:tifimage._readheader: method already defined line 34 C0324: 43:tifimage._readheader: Comma not followed by a space def _readheader(self,infile): ^^ C0324: 45:tifimage._readheader: Comma not followed by a space header = N.fromstring(infile.read(64),N.uint16) ^^ W0107: 50:tifimage._readheader: Unnecessary pass statement E1103: 60:tifimage.read: Instance of 'str' has no 'seek' member (but some types could not be inferred) W0702: 64:tifimage.read: No exception's type specified E1103: 64:tifimage.read: Instance of 'str' has no 'seek' member (but some types could not be inferred) E1103: 65:tifimage.read: Instance of 'str' has no 'read' member (but some types could not be inferred) W0201: 48:tifimage._readheader: Attribute 'nbits' defined outside __init__ Report ====== 52 statements analysed. Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |72 |61.54 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |30 |25.64 |NC |NC | +----------+-------+------+---------+-----------+ |comment |4 |3.42 |NC |NC | +----------+-------+------+---------+-----------+ |empty |11 |9.40 |NC |NC | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (oldtifimage) fabio \-fabioimage (oldtifimage) PIL \-Image (oldtifimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |method |4 |NC |NC |75.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |4 |NC |NC | +-----------+-------+---------+-----------+ |refactor |0 |NC |NC | +-----------+-------+---------+-----------+ |warning |5 |NC |NC | +-----------+-------+---------+-----------+ |error |4 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+-----------+ |message id |occurences | +===========+===========+ |E1103 |3 | +-----------+-----------+ |W0702 |2 | +-----------+-----------+ |C0324 |2 | +-----------+-----------+ |W0704 |1 | +-----------+-----------+ |W0201 |1 | +-----------+-----------+ |W0107 |1 | +-----------+-----------+ |E0102 |1 | +-----------+-----------+ |C0301 |1 | +-----------+-----------+ |C0111 |1 | +-----------+-----------+ Global evaluation ----------------- Your code has been rated at 4.42/10 fabio-0.1.3/pylint/xsdimage.py.lint0000644000175000017500000001023112233243317020013 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module xsdimage C: 21,0: Line too long (110/80) C: 80,0: Line too long (158/80) C: 86,0: Line too long (92/80) C:106,0: Line too long (102/80) C:111,0: Line too long (101/80) C: 15,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 22,4: Invalid name "etree" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) R: 24,0:xsdimage: Too many instance attributes (14/7) C: 24,0:xsdimage: Invalid name "xsdimage" (should match [A-Z_][a-zA-Z0-9]+$) C: 40,8:xsdimage.__init__: Invalid name "rawData" (should match [a-z_][a-z0-9_]{2,30}$) C: 72,8:xsdimage.read: Invalid name "decData" (should match [a-z_][a-z0-9_]{2,30}$) C: 74,12:xsdimage.read: Invalid name "decData" (should match [a-z_][a-z0-9_]{2,30}$) C: 76,12:xsdimage.read: Invalid name "decData" (should match [a-z_][a-z0-9_]{2,30}$) C: 78,12:xsdimage.read: Invalid name "decData" (should match [a-z_][a-z0-9_]{2,30}$) C: 81,12:xsdimage.read: Invalid name "decData" (should match [a-z_][a-z0-9_]{2,30}$) E: 83,20:xsdimage.read: Module 'hashlib' has no 'md5' member W:110,19:xsdimage._readheader: Catching too general exception Exception R: 24,0:xsdimage: Too many public methods (25/20) C:130,4: Invalid name "xsdimage" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) Report ====== 95 statements analysed. Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |0 |= | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |0.000 |= | +-------------------------+------+---------+-----------+ Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |15 |16 |-1.00 | +-----------+-------+---------+-----------+ |refactor |2 |2 |= | +-----------+-------+---------+-----------+ |warning |1 |8 |-7.00 | +-----------+-------+---------+-----------+ |error |1 |9 |-8.00 | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |10 | +-----------+------------+ |C0301 |5 | +-----------+------------+ |W0703 |1 | +-----------+------------+ |R0904 |1 | +-----------+------------+ |R0902 |1 | +-----------+------------+ |E1101 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 7.58/10 (previous run: 2.53/10) Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |96 |73.85 |96 |= | +----------+-------+------+---------+-----------+ |docstring |22 |16.92 |22 |= | +----------+-------+------+---------+-----------+ |comment |2 |1.54 |2 |= | +----------+-------+------+---------+-----------+ |empty |10 |7.69 |10 |= | +----------+-------+------+---------+-----------+ External dependencies --------------------- :: numpy (xsdimage) Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |1 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |1 |1 |= |100.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |3 |3 |= |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |function |0 |0 |= |0 |0 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/pylint/testtifimage.py.lint0000644000175000017500000001322612233243336020707 0ustar jeromejerome00000000000000No config file found, using default configuration ************* Module test.testtifimage C: 13,0: Invalid name "logger" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C: 14,0: Invalid name "force_build" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) W: 28,0: No exception type(s) specified W: 31,0: Relative import 'utilstest', should be 'test.utilstest' W: 35,0: Relative import 'testtifgz', should be 'test.testtifgz' C: 37,0:testtifimage_pilatus: Invalid name "testtifimage_pilatus" (should match [A-Z_][a-zA-Z0-9]+$) C: 39,8:testtifimage_pilatus.setUp: Invalid name "fn" (should match [a-z_][a-z0-9_]{2,30}$) C: 37,0:testtifimage_pilatus: Missing docstring C: 38,4:testtifimage_pilatus.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C: 50,8:testtifimage_pilatus.test1: Invalid name "o1" (should match [a-z_][a-z0-9_]{2,30}$) C: 51,8:testtifimage_pilatus.test1: Invalid name "o2" (should match [a-z_][a-z0-9_]{2,30}$) R: 37,0:testtifimage_pilatus: Too many public methods (46/20) C: 54,0:testtifimage_packbits: Invalid name "testtifimage_packbits" (should match [A-Z_][a-zA-Z0-9]+$) C: 56,8:testtifimage_packbits.setUp: Invalid name "fn" (should match [a-z_][a-z0-9_]{2,30}$) C: 54,0:testtifimage_packbits: Missing docstring C: 55,4:testtifimage_packbits.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C: 66,8:testtifimage_packbits.test1: Invalid name "o1" (should match [a-z_][a-z0-9_]{2,30}$) C: 67,8:testtifimage_packbits.test1: Invalid name "o2" (should match [a-z_][a-z0-9_]{2,30}$) R: 54,0:testtifimage_packbits: Too many public methods (46/20) C: 70,0:testtifimage_fit2d: Invalid name "testtifimage_fit2d" (should match [A-Z_][a-zA-Z0-9]+$) C: 72,8:testtifimage_fit2d.setUp: Invalid name "fn" (should match [a-z_][a-z0-9_]{2,30}$) C: 70,0:testtifimage_fit2d: Missing docstring C: 71,4:testtifimage_fit2d.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C: 82,8:testtifimage_fit2d.test1: Invalid name "o1" (should match [a-z_][a-z0-9_]{2,30}$) C: 83,8:testtifimage_fit2d.test1: Invalid name "o2" (should match [a-z_][a-z0-9_]{2,30}$) R: 70,0:testtifimage_fit2d: Too many public methods (46/20) C: 86,0:testtifimage_a0009: Invalid name "testtifimage_a0009" (should match [A-Z_][a-zA-Z0-9]+$) C: 95,8:testtifimage_a0009.setUp: Invalid name "fn" (should match [a-z_][a-z0-9_]{2,30}$) C: 94,4:testtifimage_a0009.setUp: Invalid name "setUp" (should match [a-z_][a-z0-9_]{2,30}$) C:105,8:testtifimage_a0009.test1: Invalid name "o1" (should match [a-z_][a-z0-9_]{2,30}$) C:106,8:testtifimage_a0009.test1: Invalid name "o2" (should match [a-z_][a-z0-9_]{2,30}$) R: 86,0:testtifimage_a0009: Too many public methods (46/20) C:110,0:test_suite_all_tiffimage: Missing docstring C:111,4:test_suite_all_tiffimage: Invalid name "testSuite" (should match [a-z_][a-z0-9_]{2,30}$) C:121,4: Invalid name "mysuite" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) C:122,4: Invalid name "runner" (should match (([A-Z_][A-Z0-9_]*)|(__.*__))$) Report ====== 83 statements analysed. Messages by category -------------------- +-----------+-------+---------+-----------+ |type |number |previous |difference | +===========+=======+=========+===========+ |convention |29 |NC |NC | +-----------+-------+---------+-----------+ |refactor |4 |NC |NC | +-----------+-------+---------+-----------+ |warning |3 |NC |NC | +-----------+-------+---------+-----------+ |error |0 |NC |NC | +-----------+-------+---------+-----------+ Messages -------- +-----------+------------+ |message id |occurrences | +===========+============+ |C0103 |25 | +-----------+------------+ |R0904 |4 | +-----------+------------+ |C0111 |4 | +-----------+------------+ |W0403 |2 | +-----------+------------+ |W0702 |1 | +-----------+------------+ Global evaluation ----------------- Your code has been rated at 5.66/10 Duplication ----------- +-------------------------+------+---------+-----------+ | |now |previous |difference | +=========================+======+=========+===========+ |nb duplicated lines |0 |NC |NC | +-------------------------+------+---------+-----------+ |percent duplicated lines |0.000 |NC |NC | +-------------------------+------+---------+-----------+ Raw metrics ----------- +----------+-------+------+---------+-----------+ |type |number |% |previous |difference | +==========+=======+======+=========+===========+ |code |82 |69.49 |NC |NC | +----------+-------+------+---------+-----------+ |docstring |24 |20.34 |NC |NC | +----------+-------+------+---------+-----------+ |comment |2 |1.69 |NC |NC | +----------+-------+------+---------+-----------+ |empty |10 |8.47 |NC |NC | +----------+-------+------+---------+-----------+ Statistics by type ------------------ +---------+-------+-----------+-----------+------------+---------+ |type |number |old number |difference |%documented |%badname | +=========+=======+===========+===========+============+=========+ |module |1 |NC |NC |100.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ |class |4 |NC |NC |25.00 |100.00 | +---------+-------+-----------+-----------+------------+---------+ |method |8 |NC |NC |100.00 |50.00 | +---------+-------+-----------+-----------+------------+---------+ |function |1 |NC |NC |0.00 |0.00 | +---------+-------+-----------+-----------+------------+---------+ fabio-0.1.3/test/0000755000175000017500000000000012233272207014336 5ustar jeromejerome00000000000000fabio-0.1.3/test/testbrukerimage.py0000644000175000017500000001557512233175220020117 0ustar jeromejerome00000000000000#!/usr/bin/env python # -*- coding: utf8 -*- """ #bruker Unit tests #built on testedfimage """ import unittest, sys, os, logging, tempfile logger = logging.getLogger("testbrukerimage") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio from fabio.brukerimage import brukerimage import numpy import bz2, gzip import tempfile #this is actually a violation of the bruker format since the order of # the header items is specified #in the standard, whereas the order of a python dictionary is not MYHEADER = {"FORMAT":'86', 'NPIXELB':'2', 'VERSION':'9', 'HDRBLKS':'5', 'NOVERFL':'4', 'NCOLS':'256', 'NROWS':'256', 'WORDORD':'0'} MYIMAGE = numpy.ones((256, 256), numpy.uint16) * 16 MYIMAGE[0, 0] = 0 MYIMAGE[1, 1] = 32 MYIMAGE[127:129, 127:129] = 65535 OVERFLOWS = [ ["%09d" % 4194304, ("%07d" % (127 * 256 + 127))], ["%09d" % 4194304, ("%07d" % (127 * 256 + 128))], ["%09d" % 4194304, ("%07d" % (128 * 256 + 127))], ["%09d" % 4194304, ("%07d" % (128 * 256 + 128))] ] class testbruker(unittest.TestCase): """basic test""" filename = os.path.join(UtilsTest.test_home, "testimages", "image.0000") def setUp(self): """ Generate a test bruker image """ if not os.path.isfile(self.filename): fout = open(self.filename, 'wb') wrb = 0 for key, val in MYHEADER.iteritems(): fout.write(("%-7s" % key) + ':' + ("%-72s" % val)) wrb = wrb + 80 hdrblks = int(MYHEADER['HDRBLKS']) while (wrb < hdrblks * 512): fout.write("\x1a\x04") fout.write('.' * 78) wrb = wrb + 80 fout.write(MYIMAGE.tostring()) noverfl = int(MYHEADER['NOVERFL']) for ovf in OVERFLOWS: fout.write(ovf[0] + ovf[1]) fout.write('.' * (512 - (16 * noverfl) % 512)) def test_read(self): """ see if we can read the test image """ obj = brukerimage() obj.read(self.filename) self.assertAlmostEqual(obj.getmean() , 272.0, 2) self.assertEqual(obj.getmin() , 0) self.assertEqual(obj.getmax() , 4194304) class testbzipbruker(testbruker): """ test for a bzipped image """ def setUp(self): """ create the image """ testbruker.setUp(self) if not os.path.isfile(self.filename + ".bz2"): bz2.BZ2File(self.filename + ".bz2", "wb").write(open(self.filename, "rb").read()) self.filename += ".bz2" class testgzipbruker(testbruker): """ test for a gzipped image """ def setUp(self): """ Create the image """ testbruker.setUp(self) if not os.path.isfile(self.filename + ".gz"): gzip.open(self.filename + ".gz", "wb").write(open(self.filename, "rb").read()) # os.system("gzip %s" % (self.filename)) self.filename += ".gz" class testbrukerLinear(unittest.TestCase): """basic test, test a random array of float32""" fd, filename = tempfile.mkstemp('0000', "bruker") os.close(fd) data = numpy.random.random((500, 550)).astype("float32") def test_linear(self): """ test for self consitency of random data read/write """ obj = brukerimage(data=self.data) obj.write(self.filename) new = brukerimage() new.read(self.filename) error = abs(new.data - self.data).max() self.assert_(error < numpy.finfo(numpy.float32).eps, "Error is %s>1e-7" % error) # statistics come from fit2d I think # filename dim1 dim2 min max mean stddev TESTIMAGES = """Cr8F8140k103.0026 512 512 0 145942 289.37 432.17 Cr8F8140k103.0026.gz 512 512 0 145942 289.37 432.17 Cr8F8140k103.0026.bz2 512 512 0 145942 289.37 432.17 """ class test_real_im(unittest.TestCase): """ check some read data from bruker detector""" def setUp(self): """ download images """ self.im_dir = os.path.dirname(UtilsTest.getimage("Cr8F8140k103.0026.bz2")) self.tempdir = tempfile.mkdtemp() def test_read(self): """ check we can read bruker images""" for line in TESTIMAGES.split("\n"): vals = line.split() name = vals[0] dim1, dim2 = [int(x) for x in vals[1:3]] mini, maxi, mean, stddev = [float(x) for x in vals[3:]] obj = brukerimage() obj.read(os.path.join(self.im_dir, name)) self.assertAlmostEqual(mini, obj.getmin(), 2, "getmin") self.assertAlmostEqual(maxi, obj.getmax(), 2, "getmax") self.assertAlmostEqual(mean, obj.getmean(), 2, "getmean") self.assertAlmostEqual(stddev, obj.getstddev(), 2, "getstddev") self.assertEqual(dim1, obj.dim1, "dim1") self.assertEqual(dim2, obj.dim2, "dim2") def test_write(self): "Test writing with self consistency at the fabio level" for line in TESTIMAGES.split("\n"): vals = line.split() name = vals[0] obj = brukerimage() ref = brukerimage() fname = os.path.join(self.im_dir, name) obj.read(fname) obj.write(os.path.join(self.tempdir, name)) other = brukerimage() other.read(os.path.join(self.tempdir, name)) ref.read(fname) self.assertEqual(abs(obj.data - other.data).max(), 0, "data are the same") for key in ref.header: if key in ("filename",): continue if key not in other.header: logger.warning("Key %s is missing in new header, was %s" % (key, ref.header[key])) else: self.assertEqual(ref.header[key], other.header[key], "value are the same for key %s: was %s now %s" % (key, ref.header[key], other.header[key])) def test_suite_all_bruker(): testSuite = unittest.TestSuite() testSuite.addTest(testbruker("test_read")) testSuite.addTest(testbzipbruker("test_read")) testSuite.addTest(testgzipbruker("test_read")) testSuite.addTest(test_real_im("test_read")) testSuite.addTest(test_real_im("test_write")) testSuite.addTest(testbrukerLinear("test_linear")) return testSuite if __name__ == '__main__': mysuite = test_suite_all_bruker() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/testopenheader.py0000644000175000017500000000313112120434325017714 0ustar jeromejerome00000000000000#!/usr/bin/env python # -*- coding: utf8 -*- """ # Unit tests """ import unittest, sys, os, logging logger = logging.getLogger("testopenheader") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio from fabio.openimage import openheader class test1(unittest.TestCase): """openheader opening edf""" def setUp(self): self.name = UtilsTest.getimage("F2K_Seb_Lyso0675_header_only.edf.bz2")[:-4] def testcase(self): """ check openheader can read edf headers""" for ext in ["", ".bz2", ".gz"]: name = self.name + ext obj = openheader(name) logger.debug(" %s obj = %s" % (name, obj.header)) self.assertEqual(obj.header["title"], "ESPIA FRELON Image", "Error on file %s" % name) def test_suite_all_openheader(): testSuite = unittest.TestSuite() testSuite.addTest(test1("testcase")) return testSuite if __name__ == '__main__': mysuite = test_suite_all_openheader() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/testOXDimage.py0000644000175000017500000001102112120434325017234 0ustar jeromejerome00000000000000#!/usr/bin/env python # -*- coding: utf8 -*- """ # Unit tests # builds on stuff from ImageD11.test.testpeaksearch """ import unittest, sys, os, logging, tempfile logger = logging.getLogger("testOXDimage") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio from fabio.OXDimage import OXDimage # filename dim1 dim2 min max mean stddev values are from OD Sapphire 3.0 TESTIMAGES = """b191_1_9_1_uncompressed.img 512 512 -500 11975 25.70 90.2526 b191_1_9_1_uncompressed.img 512 512 -500 11975 25.70 90.2526""" class testOXD(unittest.TestCase): def setUp(self): self.fn = {} for i in ["b191_1_9_1.img", "b191_1_9_1_uncompressed.img"]: self.fn[i] = UtilsTest.getimage(i + ".bz2")[:-4] for i in self.fn: assert os.path.exists(self.fn[i]) self.tempdir = tempfile.mkdtemp() def tearDown(self): UtilsTest.recursive_delete(self.tempdir) def test_read(self): "Test reading of compressed OXD images" for line in TESTIMAGES.split("\n"): vals = line.split() name = vals[0] dim1, dim2 = [int(x) for x in vals[1:3]] mini, maxi, mean, stddev = [float(x) for x in vals[3:]] obj = OXDimage() obj.read(self.fn[name]) self.assertAlmostEqual(mini, obj.getmin(), 2, "getmin") self.assertAlmostEqual(maxi, obj.getmax(), 2, "getmax") self.assertAlmostEqual(mean, obj.getmean(), 2, "getmean") self.assertAlmostEqual(stddev, obj.getstddev(), 2, "getstddev") self.assertEqual(dim1, obj.dim1, "dim1") self.assertEqual(dim2, obj.dim2, "dim2") def test_write(self): "Test writing with self consistency at the fabio level" for line in TESTIMAGES.split("\n"): vals = line.split() name = vals[0] obj = OXDimage() obj.read(self.fn[name]) obj.write(os.path.join(self.tempdir, name)) other = OXDimage() other.read(os.path.join(self.tempdir, name)) self.assertEqual(abs(obj.data - other.data).max(), 0, "data are the same") for key in obj.header: if key == "filename": continue self.assertTrue(key in other.header, "Key %s is in header" % key) self.assertEqual(obj.header[key], other.header[key], "value are the same for key %s" % key) class testOXD_same(unittest.TestCase): def setUp(self): self.fn = {} for i in ["b191_1_9_1.img", "b191_1_9_1_uncompressed.img"]: self.fn[i] = UtilsTest.getimage(i + ".bz2")[:-4] for i in self.fn: assert os.path.exists(self.fn[i]) def test_same(self): """test if images are actually the same""" o1 = fabio.open(self.fn["b191_1_9_1.img"]) o2 = fabio.open(self.fn["b191_1_9_1_uncompressed.img"]) for attr in ["getmin", "getmax", "getmean", "getstddev"]: a1 = getattr(o1, attr)() a2 = getattr(o2, attr)() self.assertEqual(a1, a2, "testing %s: %s | %s" % (attr, a1, a2)) class testOXD_big(unittest.TestCase): """class to test bugs if OI is large (lot of exceptions 16 bits)""" def setUp(self): self.fn = {} for i in ["d80_60s.img", "d80_60s.edf"]: self.fn[i] = UtilsTest.getimage(i + ".bz2")[:-4] for i in self.fn: self.assertTrue(os.path.exists(self.fn[i]), self.fn[i]) def test_same(self): # print self.fn df = [fabio.open(i).data for i in self.fn.values()] self.assertEqual(abs(df[0] - df[1]).max(), 0, "Data are the same") def test_suite_all_OXD(): testSuite = unittest.TestSuite() testSuite.addTest(testOXD("test_read")) testSuite.addTest(testOXD("test_write")) testSuite.addTest(testOXD_same("test_same")) testSuite.addTest(testOXD_big("test_same")) return testSuite if __name__ == '__main__': mysuite = test_suite_all_OXD() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/testXSDimage.py0000755000175000017500000000630312120434325017252 0ustar jeromejerome00000000000000#!/usr/bin/env python # -*- coding: utf8 -*- """ # Unit tests # builds on stuff from ImageD11.test.testpeaksearch """ import unittest import os import logging import sys logger = logging.getLogger("testXSDimage") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio from fabio.xsdimage import xsdimage import numpy # filename dim1 dim2 min max mean stddev values are from OD Sapphire 3.0 TESTIMAGES = """XSDataImage.xml 512 512 86 61204 511.63 667.15 XSDataImageInv.xml 512 512 -0.2814 0.22705039 2.81e-08 0.010""" class testXSD(unittest.TestCase): def setUp(self): self.fn = {} for i in ["XSDataImage.edf", "XSDataImage.xml", "XSDataImageInv.xml"]: self.fn[i] = UtilsTest.getimage(i) def test_read(self): "Test reading of XSD images" for line in TESTIMAGES.split("\n"): vals = line.split() name = vals[0] dim1, dim2 = [int(x) for x in vals[1:3]] mini, maxi, mean, stddev = [float(x) for x in vals[3:]] obj = xsdimage() obj.read(self.fn[name]) self.assertAlmostEqual(mini, obj.getmin(), 2, "getmin") self.assertAlmostEqual(maxi, obj.getmax(), 2, "getmax") self.assertAlmostEqual(mean, obj.getmean(), 2, "getmean") logger.info("%s %s %s" % (name, stddev, obj.getstddev())) self.assertAlmostEqual(stddev, obj.getstddev(), 2, "getstddev") self.assertEqual(dim1, obj.dim1, "dim1") self.assertEqual(dim2, obj.dim2, "dim2") def test_same(self): """ test if an image is the same as the EDF equivalent""" xsd = fabio.open(self.fn["XSDataImage.xml"]) edf = fabio.open(self.fn["XSDataImage.edf"]) self.assertAlmostEqual(0, abs(xsd.data - edf.data).max(), 1, "images are the same") def test_invert(self): """ Tests that 2 matrixes are invert """ m1 = fabio.open(self.fn["XSDataImage.xml"]) m2 = fabio.open(self.fn["XSDataImageInv.xml"]) self.assertAlmostEqual( abs((numpy.matrix(m1.data) * numpy.matrix(m2.data)) - numpy.identity(m1.data.shape[0])).max(), 0, 3, "matrices are invert of each other") def test_suite_all_XSD(): testSuite = unittest.TestSuite() if xsdimage is None: logging.warning("xsdimage is None ... probably an import error related to lxml. Skipping test") else: testSuite.addTest(testXSD("test_read")) testSuite.addTest(testXSD("test_same")) testSuite.addTest(testXSD("test_invert")) return testSuite if __name__ == '__main__': mysuite = test_suite_all_XSD() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/testadscimage.py0000644000175000017500000000662312120434325017530 0ustar jeromejerome00000000000000#!/usr/bin/env python # -*- coding: utf8 -*- """ # Unit tests # builds on stuff from ImageD11.test.testpeaksearch Updated by Jerome Kieffer (jerome.kieffer@esrf.eu), 2011 """ import unittest, sys, os, logging logger = logging.getLogger("testadscimage") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio from fabio.adscimage import adscimage from fabio.edfimage import edfimage # statistics come from fit2d I think # filename dim1 dim2 min max mean stddev TESTIMAGES = """mb_LP_1_001.img 3072 3072 0.0000 65535. 120.33 147.38 mb_LP_1_001.img.gz 3072 3072 0.0000 65535. 120.33 147.38 mb_LP_1_001.img.bz2 3072 3072 0.0000 65535. 120.33 147.38 """ class testmatch(unittest.TestCase): """ check the ??fit2d?? conversion to edf gives same numbers """ def setUp(self): """ Download images """ self.fn_adsc = UtilsTest.getimage("mb_LP_1_001.img.bz2")[:-4] self.fn_edf = UtilsTest.getimage("mb_LP_1_001.edf.bz2")[:-4] def testsame(self): """test ADSC image match to EDF""" im1 = edfimage() im1.read(self.fn_edf) im2 = adscimage() im2.read(self.fn_adsc) diff = (im1.data.astype("float32") - im2.data.astype("float32")) logger.debug("type: %s %s shape %s %s " % (im1.data.dtype, im2.data.dtype, im1.data.shape, im2.data.shape)) logger.debug("im1 min %s %s max %s %s " % (im1.data.min(), im2.data.min(), im1.data.max(), im2.data.max())) logger.debug("delta min %s max %s mean %s" % (diff.min(), diff.max(), diff.mean())) self.assertEqual(abs(diff).max(), 0.0, "asdc data == edf data") class testflatmccdsadsc(unittest.TestCase): """ """ def setUp(self): """ Download images """ self.im_dir = os.path.dirname(UtilsTest.getimage("mb_LP_1_001.img.bz2")) def test_read(self): """ check we can read flat ADSC images""" for line in TESTIMAGES.split("\n"): vals = line.split() name = vals[0] dim1, dim2 = [int(x) for x in vals[1:3]] mini, maxi, mean, stddev = [float(x) for x in vals[3:]] obj = adscimage() obj.read(os.path.join(self.im_dir, name)) self.assertAlmostEqual(mini, obj.getmin(), 2, "getmin") self.assertAlmostEqual(maxi, obj.getmax(), 2, "getmax") self.assertAlmostEqual(mean, obj.getmean(), 2, "getmean") self.assertAlmostEqual(stddev, obj.getstddev(), 2, "getstddev") self.assertEqual(dim1, obj.dim1, "dim1") self.assertEqual(dim2, obj.dim2, "dim2") def test_suite_all_adsc(): testSuite = unittest.TestSuite() testSuite.addTest(testmatch("testsame")) testSuite.addTest(testflatmccdsadsc("test_read")) return testSuite if __name__ == '__main__': mysuite = test_suite_all_adsc() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/utilstest.py0000644000175000017500000001720412120434325016750 0ustar jeromejerome00000000000000# coding: utf8 # # Project: Fabio tests class utilities # http://www.edna-site.org # # File: "$Id:$" # # Copyright (C) 2010 European Synchrotron Radiation Facility # Grenoble, France # # Principal authors: Jérôme KIEFFER (jerome.kieffer@esrf.fr) # # This program is free software: you can redistribute it and/or modify # it under the terms of the Lesser GNU General Public License as # published by the Free Software Foundation, either version 3 of the # License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see . # __authors__ = ["Jérôme Kieffer"] __contact__ = "jerome.kieffer@esrf.eu" __license__ = "LGPLv3+" __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" import os, imp, sys, subprocess, threading import distutils.util import logging import bz2 import gzip if sys.version_info >= (3, 0): import urllib as urllib2 else: import urllib2 logger = logging.getLogger("utilstest") class UtilsTest(object): """ Static class providing useful stuff for preparing tests. """ timeout = 60 #timeout in seconds for downloading images url_base = "http://downloads.sourceforge.net/fable" test_home = os.path.dirname(os.path.abspath(__file__)) name = "fabio" image_home = os.path.join(test_home, "testimages") if not os.path.isdir(image_home): os.makedirs(image_home) platform = distutils.util.get_platform() architecture = "lib.%s-%i.%i" % (platform, sys.version_info[0], sys.version_info[1]) fabio_home = os.path.dirname(test_home) fabio_build_home = os.path.join(fabio_home, "build", architecture) logger.info("Fabio Home is: " + fabio_build_home) if "fabio" in sys.modules: logger.info("Fabio module was already loaded from %s" % sys.modules["fabio"]) fabio = None sys.modules.pop("fabio") if not os.path.isdir(fabio_build_home): logger.warning("Building Fabio to %s" % fabio_build_home) p = subprocess.Popen([sys.executable, "setup.py", "build"], shell=False, cwd=os.path.dirname(test_home)) logger.info("subprocess ended with rc= %s" % p.wait()) fabio = imp.load_module(*((name,) + imp.find_module(name, [fabio_build_home, fabio_home]))) sys.modules[name] = fabio logging.info("pyFAI loaded from %s" % fabio.__file__) @classmethod def forceBuild(cls): """ force the recompilation of Fabio """ logger.info("Building Fabio to %s" % cls.fabio_build_home) p = subprocess.Popen([sys.executable, "setup.py", "build"], shell=False, cwd=os.path.dirname(cls.test_home)) logger.info("subprocess ended with rc= %s" % p.wait()) fabio = imp.load_module(*((cls.name,) + imp.find_module(cls.name, [cls.fabio_build_home]))) sys.modules[cls.name] = fabio logger.info("fabio loaded from %s" % fabio.__file__) @classmethod def timeoutDuringDownload(cls): """ Function called after a timeout in the download part ... just raise an Exception. """ raise RuntimeError("""Could not automatically download test images! If you are behind a firewall, please set the environment variable http_proxy. Otherwise please try to download the images manually from """ + cls.url_base) @classmethod def getimage(cls, imagename): """ Downloads the requested image @return: path of the image, locally """ logger.info("UtilsTest.getimage('%s')" % imagename) fullimagename = os.path.join(cls.image_home, imagename) if not os.path.isfile(fullimagename): logger.info("Trying to download image %s, timeout set to %ss" % (imagename, cls.timeout)) if "http_proxy" in os.environ: dictProxies = {'http': os.environ["http_proxy"]} proxy_handler = urllib2.ProxyHandler(dictProxies) opener = urllib2.build_opener(proxy_handler).open else: opener = urllib2.urlopen # Nota: since python2.6 there is a timeout in the urllib2 timer = threading.Timer(cls.timeout + 1, cls.timeoutDuringDownload) timer.start() logger.info("wget %s/%s" % (cls.url_base, imagename)) if sys.version > (2, 6): data = opener("%s/%s" % (cls.url_base, imagename), data=None, timeout=cls.timeout).read() else: data = opener("%s/%s" % (cls.url_base, imagename), data=None).read() timer.cancel() logger.info("Image %s successfully downloaded." % imagename) try: open(fullimagename, "wb").write(data) except IOError: raise IOError("unable to write downloaded \ data to disk at %s" % cls.image_home) if not os.path.isfile(fullimagename): raise RuntimeError("Could not automatically \ download test images %s!\n \ If you are behind a firewall, \ please set the environment variable http_proxy.\n \ Otherwise please try to download the images manually from \n \ %s" % (cls.url_base, imagename)) if imagename.endswith(".bz2"): decompressed = bz2.decompress(data) basename = fullimagename[:-4] elif imagename.endswith(".gz"): decompressed = gzip.open(fullimagename).read() basename = fullimagename[:-3] else: decompressed = data basename = fullimagename gzipname = basename + ".gz" bzip2name = basename + ".bz2" if basename != fullimagename: try: open(basename, "wb").write(decompressed) except IOError: raise IOError("unable to write decompressed \ data to disk at %s" % cls.image_home) if gzipname != fullimagename: try: gzip.open(gzipname, "wb").write(decompressed) except IOError: raise IOError("unable to write gzipped \ data to disk at %s" % cls.image_home) if bzip2name != fullimagename: try: bz2.BZ2File(bzip2name, "wb").write(decompressed) except IOError: raise IOError("unable to write bzipped2 \ data to disk at %s" % cls.image_home) return fullimagename @staticmethod def recursive_delete(strDirname): """ Delete everything reachable from the directory named in "top", assuming there are no symbolic links. CAUTION: This is dangerous! For example, if top == '/', it could delete all your disk files. @param strDirname: top directory to delete @type strDirname: string """ for root, dirs, files in os.walk(strDirname, topdown=False): for name in files: os.remove(os.path.join(root, name)) for name in dirs: os.rmdir(os.path.join(root, name)) os.rmdir(strDirname) fabio-0.1.3/test/test_filename_steps.py0000644000175000017500000000425112120434325020743 0ustar jeromejerome00000000000000#!/usr/bin/env python # -*- coding: utf8 -*- import unittest, sys, os, logging logger = logging.getLogger("test_filename_steps") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio class test_next(unittest.TestCase): def test_next1(self): for name, next in [ [ "data0001.edf", "data0002.edf" ], [ "bob1.edf", "bob2.edf" ], [ "1.edf", "2.edf" ], [ "1.mar2300", "2.mar2300" ], ]: self.assertEqual(next, fabio.next_filename(name)) class test_prev(unittest.TestCase): def test_prev1(self): for name, prev in [ [ "data0001.edf", "data0000.edf" ], [ "bob1.edf", "bob0.edf" ], [ "1.edf", "0.edf" ], [ "1.mar2300", "0.mar2300" ], ]: self.assertEqual(prev, fabio.previous_filename(name)) class test_jump(unittest.TestCase): def test_jump1(self): for name, res, num in [ [ "data0001.edf", "data99993.edf" , 99993 ], [ "bob1.edf", "bob0.edf", 0 ], [ "1.edf", "123456.edf" , 123456], [ "mydata001.mar2300.gz", "mydata003.mar2300.gz", 3 ], ]: self.assertEqual(res, fabio.jump_filename(name, num)) def test_suite_all_steps(): testSuite = unittest.TestSuite() testSuite.addTest(test_next("test_next1")) testSuite.addTest(test_prev("test_prev1")) testSuite.addTest(test_jump("test_jump1")) return testSuite if __name__ == '__main__': mysuite = test_suite_all_steps() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/testfilenames.py0000644000175000017500000000770612126623347017573 0ustar jeromejerome00000000000000#!/usr/bin/env python # -*- coding: utf8 -*- """ Test cases for filename deconstruction testsuite by Jerome Kieffer (Jerome.Kieffer@esrf.eu) """ import unittest, sys, os, logging logger = logging.getLogger("testfilenames") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio CASES = [ (1, 'edf', "data0001.edf"), (10001, 'edf', "data10001.edf"), (10001, 'edf', "data10001.edf.gz"), (10001, 'edf', "data10001.edf.bz2"), (2, 'marccd', "data0002.mccd"), (12345, 'marccd', "data12345.mccd"), (10001, 'marccd', "data10001.mccd.gz"), (10001, 'marccd', "data10001.mccd.bz2"), (123, 'marccd', "data123.mccd.gz"), (3, 'tif', "data0003.tif"), (4, 'tif', "data0004.tiff"), (12, 'bruker', "sucrose101.012.gz"), (99, 'bruker', "sucrose101.099"), (99, 'bruker', "sucrose101.0099"), (99, 'bruker', "sucrose101.0099.bz2"), (99, 'bruker', "sucrose101.0099.gz"), (2, 'fit2dmask', "fit2d.msk"), (None, 'fit2dmask', "mymask.msk"), (670005, 'edf' , 'S82P670005.edf'), (670005, 'edf' , 'S82P670005.edf.gz'), # based on only the name it can be either img or oxd (1 , 'adsc_or_OXD_or_HiPiC' , 'mb_LP_1_001.img'), (2 , 'adsc_or_OXD_or_HiPiC' , 'mb_LP_1_002.img.gz'), (3 , 'adsc_or_OXD_or_HiPiC' , 'mb_LP_1_003.img.bz2'), (3 , 'adsc_or_OXD_or_HiPiC' , os.path.join("data", 'mb_LP_1_003.img.bz2')), ] MORE_CASES = [ ("data0010.edf", "data0012.edf", 10), ("data1000.pnm", "data999.pnm", 1000), ("data0999.pnm", "data1000.pnm", 999), ("data123457.edf", "data123456.edf", 123457), ("d0ata000100.mccd", "d0ata000012.mccd", 100), (os.path.join("images/sampledir", "P33S670003.edf"), os.path.join("images/sampledir", "P33S670002.edf"), 670003), (os.path.join("images/P33S67", "P33S670003.edf"), os.path.join("images/P33S67", "P33S670002.edf"), 670003), ("image2301.mar2300", "image2300.mar2300", 2301), ("image2300.mar2300", "image2301.mar2300", 2300), ("image.0123", "image.1234", 123), ("mymask.msk", "mymask.msk", None), ("data_123.mccd.bz2", "data_001.mccd.bz2", 123) ] class testfilenames(unittest.TestCase): """ check the name -> number, type conversions """ def test_many_cases(self): """ loop over CASES """ for num, typ, name in CASES: obj = fabio.FilenameObject(filename=name) self.assertEqual(num, obj.num , name + " num=" + str(num) + \ " != obj.num=" + str(obj.num)) self.assertEqual(typ, "_or_".join(obj.format), name + " " + "_or_".join(obj.format)) self.assertEqual(name, obj.tostring() , name + " " + obj.tostring()) def test_more_cases(self): for nname, oname, num in MORE_CASES: name = fabio.construct_filename(oname, num) self.assertEqual(name, nname) def test_more_cases_jump(self): for nname, oname, num in MORE_CASES: name = fabio.jump_filename(oname, num) self.assertEqual(name, nname) def test_suite_all_filenames(): testSuite = unittest.TestSuite() testSuite.addTest(testfilenames("test_many_cases")) testSuite.addTest(testfilenames("test_more_cases")) testSuite.addTest(testfilenames("test_more_cases_jump")) return testSuite if __name__ == '__main__': mysuite = test_suite_all_filenames() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/testcompression.py0000755000175000017500000000636512120434325020162 0ustar jeromejerome00000000000000#!/usr/bin/env python # -*- coding: utf8 -*- """ # Unit tests Updated by Jerome Kieffer (jerome.kieffer@esrf.eu), 2011 """ import unittest, sys, os, logging logger = logging.getLogger("testcompression") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio import fabio.compression as compression import numpy class testbyteoffset(unittest.TestCase): """ test the byte offset compression and decompression """ def setUp(self): self.ds = numpy.array([0, 1, 2, 127, 0, 1, 2, 128, 0, 1, 2, 32767, 0, 1, 2, 32768, 0, 1, 2, 2147483647, 0, 1, 2, 2147483648, 0, 1, 2, 128, 129, 130, 32767, 32768, 128, 129, 130, 32768, 2147483647, 2147483648]) self.ref = '\x00\x01\x01}\x81\x01\x01~\x80\x80\xff\x01\x01\x80\xfd\x7f\x80\x01\x80\x01\x01\x80\xfe\x7f\x80\x00\x80\x00\x80\xff\xff\x01\x01\x80\x00\x80\xfd\xff\xff\x7f\x80\x00\x80\x01\x00\x00\x80\x01\x01\x80\x00\x80\xfe\xff\xff\x7f\x80\x00\x80\x00\x00\x00\x80\x00\x00\x00\x80\xff\xff\xff\xff\x01\x01~\x01\x01\x80}\x7f\x01\x80\x80\x80\x01\x01\x80~\x7f\x80\x00\x80\xff\x7f\xff\x7f\x01' def testComp(self): """ """ ds = numpy.array([0, 128]) ref = "\x00\x80\x80\00" self.assertEqual(ref, compression.compByteOffet_numpy(ds) , "test +128") ds = numpy.array([0, -128]) ref = '\x00\x80\x80\xff' self.assertEqual(ref, compression.compByteOffet_numpy(ds) , "test -128") ds = numpy.array([10, -128]) ref = '\n\x80v\xff' self.assertEqual(ref, compression.compByteOffet_numpy(ds) , "test +10 -128") self.assertEqual(self.ref, compression.compByteOffet_numpy(self.ds) , "test larger") def testSC(self): """test that datasets are unchanged after various comression/decompressions""" obt_np = compression.decByteOffet_numpy(compression.compByteOffet_numpy(self.ds)) self.assertEqual(abs(self.ds - obt_np).max(), 0.0, "numpy algo") obt_cy = compression.decByteOffet_cython(compression.compByteOffet_numpy(self.ds)) self.assertEqual(abs(self.ds - obt_cy).max(), 0.0, "cython algo") obt_cy2 = compression.decByteOffet_cython(compression.compByteOffet_numpy(self.ds), self.ds.size) self.assertEqual(abs(self.ds - obt_cy2).max(), 0.0, "cython algo_orig") obt_we = compression.decByteOffet_weave(compression.compByteOffet_numpy(self.ds), self.ds.size) self.assertEqual(abs(self.ds - obt_we).max(), 0.0, "weave algo") def test_suite_all_compression(): testSuite = unittest.TestSuite() testSuite.addTest(testbyteoffset("testSC")) testSuite.addTest(testbyteoffset("testSC")) return testSuite if __name__ == '__main__': mysuite = test_suite_all_compression() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/__init__.py0000644000175000017500000000000112120434325016432 0ustar jeromejerome00000000000000 fabio-0.1.3/test/testmccdimage.py0000644000175000017500000000745412120434325017527 0ustar jeromejerome00000000000000#!/usr/bin/env python # -*- coding: utf8 -*- """ # Unit tests # builds on stuff from ImageD11.test.testpeaksearch """ import unittest, sys, os, logging logger = logging.getLogger("testmccdimage") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio from fabio.marccdimage import marccdimage from fabio.tifimage import tifimage import numpy # statistics come from fit2d I think # filename dim1 dim2 min max mean stddev TESTIMAGES = """corkcont2_H_0089.mccd 2048 2048 0 354 7.2611 14.639 corkcont2_H_0089.mccd.bz2 2048 2048 0 354 7.2611 14.639 corkcont2_H_0089.mccd.gz 2048 2048 0 354 7.2611 14.639 somedata_0001.mccd 1024 1024 0 20721 128.37 136.23 somedata_0001.mccd.bz2 1024 1024 0 20721 128.37 136.23 somedata_0001.mccd.gz 1024 1024 0 20721 128.37 136.23""" class testnormaltifok(unittest.TestCase): """ check we can read normal tifs as well as mccd """ imdata = None image = os.path.join(UtilsTest.test_home, "testimages", "tifimagewrite_test0000.tif") def setUp(self): """ create an image """ self.imdata = numpy.zeros((24, 24), numpy.uint16) self.imdata[ 12:14, 15:17 ] = 42 obj = tifimage(self.imdata, { }) obj.write(self.image) def test_read_openimage(self): from fabio.openimage import openimage obj = openimage(self.image) if obj.data.astype(int).tostring() != self.imdata.astype(int).tostring(): logger.info("%s %s" % (type(self.imdata), self.imdata.dtype)) logger.info("%s %s" % (type(obj.data), obj.data.dtype)) logger.info("%s %s" % (obj.data - self.imdata)) self.assertEqual(obj.data.astype(int).tostring(), self.imdata.astype(int).tostring()) class testflatmccds(unittest.TestCase): def setUp(self): self.fn = {} for i in ["corkcont2_H_0089.mccd", "somedata_0001.mccd"]: self.fn[i] = UtilsTest.getimage(i + ".bz2")[:-4] self.fn[i + ".bz2"] = self.fn[i] + ".bz2" self.fn[i + ".gz"] = self.fn[i] + ".gz" for i in self.fn: assert os.path.exists(self.fn[i]) def test_read(self): """ check we can read MarCCD images""" for line in TESTIMAGES.split("\n"): vals = line.split() name = vals[0] dim1, dim2 = [int(x) for x in vals[1:3]] mini, maxi, mean, stddev = [float(x) for x in vals[3:]] obj = marccdimage() obj.read(self.fn[name]) self.assertAlmostEqual(mini, obj.getmin(), 2, "getmin") self.assertAlmostEqual(maxi, obj.getmax(), 2, "getmax") self.assertAlmostEqual(mean, obj.getmean(), 2, "getmean") self.assertAlmostEqual(stddev, obj.getstddev(), 2, "getstddev") self.assertEqual(dim1, obj.dim1, "dim1") self.assertEqual(dim2, obj.dim2, "dim2") def test_suite_all_mccd(): testSuite = unittest.TestSuite() testSuite.addTest(testnormaltifok("test_read_openimage")) testSuite.addTest(testflatmccds("test_read")) return testSuite if __name__ == '__main__': mysuite = test_suite_all_mccd() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/test_all.py0000755000175000017500000000574112120434325016525 0ustar jeromejerome00000000000000#!/usr/bin/env python # -*- coding: utf8 -*- """ Test suite for all fabio modules. """ import unittest import os import logging import sys logger = logging.getLogger("test_all_fabio") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio from testfabioimage import test_suite_all_fabio from testedfimage import test_suite_all_edf from testcbfimage import test_suite_all_cbf from testfilenames import test_suite_all_filenames from test_file_series import test_suite_all_series from test_filename_steps import test_suite_all_steps #from test_flat_binary import test_suite_all_flat from testadscimage import test_suite_all_adsc from testfit2dmaskimage import test_suite_all_fit2d from testGEimage import test_suite_all_GE from testheadernotsingleton import test_suite_all_header from testmar345image import test_suite_all_mar345 from testbrukerimage import test_suite_all_bruker from testmccdimage import test_suite_all_mccd from testopenheader import test_suite_all_openheader from testopenimage import test_suite_all_openimage from testOXDimage import test_suite_all_OXD from testkcdimage import test_suite_all_kcd from testtifimage import test_suite_all_tiffimage from testXSDimage import test_suite_all_XSD def test_suite_all(): testSuite = unittest.TestSuite() testSuite.addTest(test_suite_all_fabio()) testSuite.addTest(test_suite_all_filenames()) testSuite.addTest(test_suite_all_series()) testSuite.addTest(test_suite_all_steps()) # testSuite.addTest(test_suite_all_flat()) testSuite.addTest(test_suite_all_adsc()) testSuite.addTest(test_suite_all_edf()) testSuite.addTest(test_suite_all_cbf()) testSuite.addTest(test_suite_all_fit2d()) testSuite.addTest(test_suite_all_GE()) testSuite.addTest(test_suite_all_header()) testSuite.addTest(test_suite_all_mar345()) testSuite.addTest(test_suite_all_bruker()) testSuite.addTest(test_suite_all_mccd()) testSuite.addTest(test_suite_all_openheader()) testSuite.addTest(test_suite_all_openimage()) testSuite.addTest(test_suite_all_OXD()) testSuite.addTest(test_suite_all_kcd()) testSuite.addTest(test_suite_all_tiffimage()) testSuite.addTest(test_suite_all_XSD()) return testSuite if __name__ == '__main__': mysuite = test_suite_all() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/profile_compressed.py0000644000175000017500000000715112120434325020574 0ustar jeromejerome00000000000000 """ Benchmark the bz2 and gzip modules compared to their system counterparts """ import cProfile, os, time, random, gzip, bz2, struct, sys try: import pstats except: print "Your package manager is probably teasing you" print "try sudo apt-get install python-profiler" sys.exit() print "Setting up" npts = int(1e6) data = [ random.random() for i in range(npts) ] sdata = struct.pack( "d"*npts, *tuple(data) ) open("prof.dat","wb").write(sdata) open("prof2.dat","wb").write(" "*npts*8) os.system("gzip -c prof.dat > prof.dat.gz") os.system("bzip2 -c prof.dat > prof.dat.bz2") os.system("gzip -c prof2.dat > prof2.dat.gz") os.system("bzip2 -c prof2.dat > prof2.dat.bz2") print "Done setup" sys.stdout.flush() def tst(fobj, fname): """test""" fo = fobj(fname, "rb") fo.read() return print "Python gzip module" start = time.time() cProfile.run( "tst(gzip.GzipFile, 'prof.dat.gz')", "gzstats") p = pstats.Stats("gzstats") p.strip_dirs().sort_stats(-1).print_stats() del p print "Python bz2 module" cProfile.run( "tst(bz2.BZ2File, 'prof.dat.bz2')", "bz2stats") p = pstats.Stats("bz2stats") p.strip_dirs().sort_stats(-1).print_stats() del p def tstsys(cmd): """ test system""" fo = os.popen(cmd,"rb") fo.read() return print "System gzip" cProfile.run( "tstsys('gzip -cd prof.dat.gz')", "gzosstats") p = pstats.Stats("gzosstats") p.strip_dirs().sort_stats(-1).print_stats() del p print "System bz2" cProfile.run( "tstsys('bzip2 -cd prof.dat.bz2')", "bz2osstats") p = pstats.Stats("bz2osstats") p.strip_dirs().sort_stats(-1).print_stats() del p import timeit cl = ["ret = gzip.GzipFile( 'prof.dat.gz' ,'rb').read()", "ret = os.popen( 'gzip -dc prof.dat.gz' ,'rb').read()", "ret = bz2.BZ2File( 'prof.dat.bz2','rb').read()", "ret = os.popen( 'bzip2 -dc prof.dat.bz2','rb').read()", "ret = gzip.GzipFile( 'prof2.dat.gz' ,'rb').read()", "ret = os.popen( 'gzip -dc prof2.dat.gz' ,'rb').read()", "ret = bz2.BZ2File( 'prof2.dat.bz2','rb').read()", "ret = os.popen('bzip2 -dc prof2.dat.bz2','rb').read()", ] if sys.platform != "win32": cl.append("ret = os.popen( 'gzip -dc prof.dat.gz' ,'rb',2**20).read()") cl.append("ret = os.popen( 'bzip2 -dc prof.dat.bz2','rb',2**20).read()") cl.append("ret = os.popen( 'gzip -dc prof2.dat.gz' ,'rb',2**20).read()") cl.append("ret = os.popen(' bzip2 -dc prof2.dat.bz2','rb',2**20).read()") for s in cl: t = timeit.Timer(s, setup="import os, gzip, bz2") print s, ":", t.timeit(5)/5 # Finally - shell version if sys.platform == 'win32': start = time.time() s = "gzip -cd prof.dat.gz > junk" os.system(s) print s, ":", time.time()-start, "seconds via shell" start = time.time() s = "bzip2 -cd prof.dat.bz2 > junk" os.system(s) print s, ":", time.time()-start, "seconds via shell" start = time.time() s = "gzip -cd prof2.dat.gz > junk" os.system(s) print s, ":", time.time()-start, "seconds via shell" start = time.time() s = "bzip2 -cd prof2.dat.bz2 > junk" os.system(s) print s, ":", time.time()-start, "seconds via shell" os.remove("junk") else: sys.stdout.flush() s = "time gzip -cd prof.dat.gz > /dev/null" print "Time shell gzip:", s os.system(s) sys.stdout.flush() s = "time bzip2 -cd prof.dat.bz2 > /dev/null" print "Time shell bzip2:", s os.system(s) sys.stdout.flush() s = "time gzip -cd prof2.dat.gz > /dev/null" print "Time shell gzip:", s os.system(s) sys.stdout.flush() s = "time bzip2 -cd prof2.dat.bz2 > /dev/null" print "Time shell bzip2:", s os.system(s) fabio-0.1.3/test/profile/0000755000175000017500000000000012233272207015776 5ustar jeromejerome00000000000000fabio-0.1.3/test/profile/profile_compressed.py0000644000175000017500000000715112120434325022234 0ustar jeromejerome00000000000000 """ Benchmark the bz2 and gzip modules compared to their system counterparts """ import cProfile, os, time, random, gzip, bz2, struct, sys try: import pstats except: print "Your package manager is probably teasing you" print "try sudo apt-get install python-profiler" sys.exit() print "Setting up" npts = int(1e6) data = [ random.random() for i in range(npts) ] sdata = struct.pack( "d"*npts, *tuple(data) ) open("prof.dat","wb").write(sdata) open("prof2.dat","wb").write(" "*npts*8) os.system("gzip -c prof.dat > prof.dat.gz") os.system("bzip2 -c prof.dat > prof.dat.bz2") os.system("gzip -c prof2.dat > prof2.dat.gz") os.system("bzip2 -c prof2.dat > prof2.dat.bz2") print "Done setup" sys.stdout.flush() def tst(fobj, fname): """test""" fo = fobj(fname, "rb") fo.read() return print "Python gzip module" start = time.time() cProfile.run( "tst(gzip.GzipFile, 'prof.dat.gz')", "gzstats") p = pstats.Stats("gzstats") p.strip_dirs().sort_stats(-1).print_stats() del p print "Python bz2 module" cProfile.run( "tst(bz2.BZ2File, 'prof.dat.bz2')", "bz2stats") p = pstats.Stats("bz2stats") p.strip_dirs().sort_stats(-1).print_stats() del p def tstsys(cmd): """ test system""" fo = os.popen(cmd,"rb") fo.read() return print "System gzip" cProfile.run( "tstsys('gzip -cd prof.dat.gz')", "gzosstats") p = pstats.Stats("gzosstats") p.strip_dirs().sort_stats(-1).print_stats() del p print "System bz2" cProfile.run( "tstsys('bzip2 -cd prof.dat.bz2')", "bz2osstats") p = pstats.Stats("bz2osstats") p.strip_dirs().sort_stats(-1).print_stats() del p import timeit cl = ["ret = gzip.GzipFile( 'prof.dat.gz' ,'rb').read()", "ret = os.popen( 'gzip -dc prof.dat.gz' ,'rb').read()", "ret = bz2.BZ2File( 'prof.dat.bz2','rb').read()", "ret = os.popen( 'bzip2 -dc prof.dat.bz2','rb').read()", "ret = gzip.GzipFile( 'prof2.dat.gz' ,'rb').read()", "ret = os.popen( 'gzip -dc prof2.dat.gz' ,'rb').read()", "ret = bz2.BZ2File( 'prof2.dat.bz2','rb').read()", "ret = os.popen('bzip2 -dc prof2.dat.bz2','rb').read()", ] if sys.platform != "win32": cl.append("ret = os.popen( 'gzip -dc prof.dat.gz' ,'rb',2**20).read()") cl.append("ret = os.popen( 'bzip2 -dc prof.dat.bz2','rb',2**20).read()") cl.append("ret = os.popen( 'gzip -dc prof2.dat.gz' ,'rb',2**20).read()") cl.append("ret = os.popen(' bzip2 -dc prof2.dat.bz2','rb',2**20).read()") for s in cl: t = timeit.Timer(s, setup="import os, gzip, bz2") print s, ":", t.timeit(5)/5 # Finally - shell version if sys.platform == 'win32': start = time.time() s = "gzip -cd prof.dat.gz > junk" os.system(s) print s, ":", time.time()-start, "seconds via shell" start = time.time() s = "bzip2 -cd prof.dat.bz2 > junk" os.system(s) print s, ":", time.time()-start, "seconds via shell" start = time.time() s = "gzip -cd prof2.dat.gz > junk" os.system(s) print s, ":", time.time()-start, "seconds via shell" start = time.time() s = "bzip2 -cd prof2.dat.bz2 > junk" os.system(s) print s, ":", time.time()-start, "seconds via shell" os.remove("junk") else: sys.stdout.flush() s = "time gzip -cd prof.dat.gz > /dev/null" print "Time shell gzip:", s os.system(s) sys.stdout.flush() s = "time bzip2 -cd prof.dat.bz2 > /dev/null" print "Time shell bzip2:", s os.system(s) sys.stdout.flush() s = "time gzip -cd prof2.dat.gz > /dev/null" print "Time shell gzip:", s os.system(s) sys.stdout.flush() s = "time bzip2 -cd prof2.dat.bz2 > /dev/null" print "Time shell bzip2:", s os.system(s) fabio-0.1.3/test/profile/benchheader.py0000644000175000017500000000105512120434325020575 0ustar jeromejerome00000000000000 import timeit, os, sys sys.path.insert(0, os.path.abspath("../build/lib.linux-x86_64-2.6")) junk = [".svn", "testfile", "testfile.bz2", "testfile.gz"] #for fname in : # if fname.find("") == -1: # images.append(fname) images = [os.path.join("testimages", i) for i in os.listdir("testimages") if (i not in junk) ] images.sort() for im in images: s = "ret = fabio.openimage.openheader(r\"%s\")" % (im) t = timeit.Timer(s, setup="import fabio.openimage") print "%10.6f" % (t.timeit(10) / 10.0), im fabio-0.1.3/test/test_flat_binary.py0000644000175000017500000000404212120434325020235 0ustar jeromejerome00000000000000 import unittest, sys, os, logging logger = logging.getLogger("test_flat_binary") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio class test_flat_binary(unittest.TestCase): filenames = [ "not.a.file", "bad_news_1234", "empty_files_suck_1234.edf", "notRUBY_1234.dat"] def setUp(self): for filename in self.filenames: f = open(filename, "wb") # A 2048 by 2048 blank image f.write("\0x0" * 2048 * 2048 * 2) f.close() def NOtest_openimage(self): """ test the opening of "junk" empty images ... JK: I wonder if this test makes sense ! """ nfail = 0 for filename in self.filenames: try: im = fabio.open(filename) if im.data.tostring() != "\0x0" * 2048 * 2048 * 2: nfail += 1 else: logger.info("**** Passed: %s" % filename) except: logger.warning("failed for: %s" % filename) nfail += 1 self.assertEqual(nfail, 0, " %s failures out of %s" % (nfail, len(self.filenames))) def tearDown(self): for filename in self.filenames: os.remove(filename) #def test_suite_all_flat(): # testSuite = unittest.TestSuite() # # testSuite.addTest(test_flat_binary("test_openimage")) # return testSuite if __name__ == '__main__': mysuite = test_suite_all_flat() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/testfit2dmaskimage.py0000644000175000017500000000615212120434325020477 0ustar jeromejerome00000000000000#!/usr/bin/env python # -*- coding: utf8 -*- ## Automatically adapted for numpy.oldnumeric Oct 05, 2007 by alter_code1.py # Unit tests """ Test the fit2d mask reader Updated by Jerome Kieffer (jerome.kieffer@esrf.eu), 2011 """ import unittest, sys, os, logging logger = logging.getLogger("testfit2dmaskdfimage") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio from fabio.fit2dmaskimage import fit2dmaskimage import numpy class testfacemask(unittest.TestCase): """ test the picture of a face """ def setUp(self): """ download images """ self.filename = UtilsTest.getimage("face.msk.bz2")[:-4] self.edffilename = UtilsTest.getimage("face.edf.bz2") [:-4] def test_getmatch(self): """ test edf and msk are the same """ i = fit2dmaskimage() i.read(self.filename) j = fabio.open(self.edffilename) # print "edf: dim1",oe.dim1,"dim2",oe.dim2 self.assertEqual(i.dim1, j.dim1) self.assertEqual(i.dim2, j.dim2) self.assertEqual(i.data.shape, j.data.shape) diff = j.data - i.data sumd = abs(diff).sum(dtype=float) self.assertEqual(sumd , 0.0) class testclickedmask(unittest.TestCase): """ A few random clicks to make a test mask """ def setUp(self): """ download images """ self.filename = UtilsTest.getimage("fit2d_click.msk.bz2")[:-4] self.edffilename = UtilsTest.getimage("fit2d_click.edf.bz2")[:-4] def test_read(self): """ Check it reads a mask OK """ i = fit2dmaskimage() i.read(self.filename) self.assertEqual(i.dim1 , 1024) self.assertEqual(i.dim2 , 1024) self.assertEqual(i.bpp , 1) self.assertEqual(i.bytecode, numpy.uint8) self.assertEqual(i.data.shape, (1024, 1024)) def test_getmatch(self): """ test edf and msk are the same """ i = fit2dmaskimage() j = fabio.open(self.edffilename) i.read(self.filename) self.assertEqual(i.data.shape, j.data.shape) diff = j.data - i.data self.assertEqual(i.getmax(), 1) self.assertEqual(i.getmin(), 0) sumd = abs(diff).sum(dtype=float) self.assertEqual(sumd , 0) def test_suite_all_fit2d(): testSuite = unittest.TestSuite() testSuite.addTest(testfacemask("test_getmatch")) testSuite.addTest(testclickedmask("test_read")) testSuite.addTest(testclickedmask("test_getmatch")) return testSuite if __name__ == '__main__': mysuite = test_suite_all_fit2d() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/testheadernotsingleton.py0000644000175000017500000000343312120434325021503 0ustar jeromejerome00000000000000#!/usr/bin/python # -*- coding: utf8 -*- """ # Unit tests # builds on stuff from ImageD11.test.testpeaksearch """ import unittest, sys, os, logging logger = logging.getLogger("testheadernotsingleton") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio import shutil class testheadernotsingleton(unittest.TestCase): def setUp(self): """ download images """ self.file1 = UtilsTest.getimage("mb_LP_1_001.img.bz2")[:-4] def testheader(self): file2 = self.file1.replace("mb_LP_1_001.img", "mb_LP_1_002.img") self.assertTrue(os.path.exists(self.file1)) if not os.path.exists(file2): shutil.copy(self.file1, file2) image1 = fabio.open(self.file1) image2 = fabio.open(file2) self.assertEqual(image1.header['filename'] , self.file1) self.assertEqual(image2.header['filename'] , file2) self.assertNotEqual(image1.header['filename'] , image2.header['filename']) def test_suite_all_header(): testSuite = unittest.TestSuite() testSuite.addTest(testheadernotsingleton("testheader")) return testSuite if __name__ == '__main__': mysuite = test_suite_all_header() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/testGEimage.py0000644000175000017500000000437312120434325017111 0ustar jeromejerome00000000000000#!/usr/bin/env python # -*- coding: utf8 -*- """ # Unit tests # builds on stuff from ImageD11.test.testpeaksearch """ import unittest, sys, os, logging logger = logging.getLogger("testfit2dmaskdfimage") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio from fabio.GEimage import GEimage # filename dim1 dim2 min max mean stddev TESTIMAGES = """GE_aSI_detector_image_1529 2048 2048 1515 16353 1833.0311 56.9124 GE_aSI_detector_image_1529.gz 2048 2048 1515 16353 1833.0311 56.9124 GE_aSI_detector_image_1529.bz2 2048 2048 1515 16353 1833.0311 56.9124""" class testGE(unittest.TestCase): def setUp(self): """ download images """ self.GE = UtilsTest.getimage("GE_aSI_detector_image_1529.bz2") def test_read(self): for line in TESTIMAGES.split("\n"): vals = line.split() name = vals[0] dim1, dim2 = [int(x) for x in vals[1:3]] mini, maxi, mean, stddev = [float(x) for x in vals[3:]] obj = GEimage() obj.read(os.path.join(os.path.dirname(self.GE), name)) self.assertAlmostEqual(mini, obj.getmin(), 4, "getmin") self.assertAlmostEqual(maxi, obj.getmax(), 4, "getmax") self.assertAlmostEqual(mean, obj.getmean(), 4, "getmean") self.assertAlmostEqual(stddev, obj.getstddev(), 4, "getstddev") self.assertEqual(dim1, obj.dim1, "dim1") self.assertEqual(dim2, obj.dim2, "dim2") def test_suite_all_GE(): testSuite = unittest.TestSuite() testSuite.addTest(testGE("test_read")) return testSuite if __name__ == '__main__': mysuite = test_suite_all_GE() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/testcbfimage.py0000755000175000017500000001644412233175156017366 0ustar jeromejerome00000000000000#!/usr/bin/env python # coding: utf8 """ 2011: Jerome Kieffer for ESRF. Unit tests for CBF images based on references images taken from: http://pilatus.web.psi.ch/DATA/DATASETS/insulin_0.2/ """ import unittest, sys, os, logging, tempfile logger = logging.getLogger("testcbfimage") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio from fabio.cbfimage import cbfimage from fabio.compression import decByteOffet_numpy, decByteOffet_cython import time class test_cbfimage_reader(unittest.TestCase): """ test cbf image reader """ def __init__(self, methodName): "Constructor of the class" unittest.TestCase.__init__(self, methodName) testimgdir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "testimages") self.edf_filename = os.path.join(testimgdir, "run2_1_00148.edf") self.cbf_filename = os.path.join(testimgdir, "run2_1_00148.cbf") def setUp(self): """Download images""" UtilsTest.getimage(os.path.basename(self.edf_filename + ".bz2")) UtilsTest.getimage(os.path.basename(self.cbf_filename)) self.tempdir = tempfile.mkdtemp() def tearDown(self): UtilsTest.recursive_delete(self.tempdir) def test_read(self): """ check whole reader""" times = [] times.append(time.time()) cbf = fabio.open(self.cbf_filename) times.append(time.time()) edf = fabio.open(self.edf_filename) times.append(time.time()) self.assertAlmostEqual(0, abs(cbf.data - edf.data).max()) logger.info("Reading CBF took %.3fs whereas the same EDF took %.3fs" % (times[1] - times[0], times[2] - times[1])) def test_write(self): "Rest writing with self consistency at the fabio level" name = os.path.basename(self.cbf_filename) obj = cbfimage() obj.read(self.cbf_filename) obj.write(os.path.join(self.tempdir, name)) other = cbfimage() other.read(os.path.join(self.tempdir, name)) self.assertEqual(abs(obj.data - other.data).max(), 0, "data are the same") for key in obj.header: if key in[ "filename", "X-Binary-Size-Padding"]: continue self.assertTrue(key in other.header, "Key %s is in header" % key) self.assertEqual(obj.header[key], other.header[key], "value are the same for key %s" % key) def test_byte_offset(self): """ check byte offset algorythm""" cbf = fabio.open(self.cbf_filename) starter = "\x0c\x1a\x04\xd5" startPos = cbf.cif["_array_data.data"].find(starter) + 4 data = cbf.cif["_array_data.data"][ startPos: startPos + int(cbf.header["X-Binary-Size"])] startTime = time.time() numpyRes = decByteOffet_numpy(data, size=cbf.dim1 * cbf.dim2) tNumpy = time.time() - startTime logger.info("Timing for Numpy method : %.3fs" % tNumpy) # startTime = time.time() # weaveRes = cbfimage.analyseWeave(data, size=cbf.dim1 * cbf.dim2) # tWeave = time.time() - startTime # delta = abs(numpyRes - weaveRes).max() # self.assertAlmostEqual(0, delta) # logger.info("Timing for Weave method : %.3fs, max delta=%s" % (tWeave, delta)) # # startTime = time.time() # pythonRes = decByteOffet_numpy(data, size=cbf.dim1 * cbf.dim2) # tPython = time.time() - startTime # delta = abs(numpyRes - pythonRes).max() # self.assertAlmostEqual(0, delta) # logger.info("Timing for Python method : %.3fs, max delta= %s" % (tPython, delta)) startTime = time.time() cythonRes = decByteOffet_cython(stream=data, size=cbf.dim1 * cbf.dim2) tCython = time.time() - startTime delta = abs(numpyRes - cythonRes).max() self.assertAlmostEqual(0, delta) logger.info("Timing for Cython method : %.3fs, max delta= %s" % (tCython, delta)) def test_consitency_manual(self): """ Test if an image can be read and saved and the results are "similar" """ name = os.path.basename(self.cbf_filename) obj = fabio.open(self.cbf_filename) new = fabio.cbfimage.cbfimage(data=obj.data, header=obj.header) new.write(os.path.join(self.tempdir, name)) other = fabio.open(os.path.join(self.tempdir, name)) self.assertEqual(abs(obj.data - other.data).max(), 0, "data are the same") for key in obj.header: if key in[ "filename", "X-Binary-Size-Padding"]: continue self.assertTrue(key in other.header, "Key %s is in header" % key) self.assertEqual(obj.header[key], other.header[key], "value are the same for key %s [%s|%s]" % (key, obj.header[key], other.header[key])) def test_consitency_convert(self): """ Test if an image can be read and saved and the results are "similar" """ name = os.path.basename(self.cbf_filename) obj = fabio.open(self.cbf_filename) new = obj.convert("cbf") new.write(os.path.join(self.tempdir, name)) other = fabio.open(os.path.join(self.tempdir, name)) self.assertEqual(abs(obj.data - other.data).max(), 0, "data are the same") for key in obj.header: if key in[ "filename", "X-Binary-Size-Padding"]: continue self.assertTrue(key in other.header, "Key %s is in header" % key) self.assertEqual(obj.header[key], other.header[key], "value are the same for key %s [%s|%s]" % (key, obj.header[key], other.header[key])) def test_unicode(self): """ Test if an image can be read and saved to an unicode named """ name = unicode(os.path.basename(self.cbf_filename)) obj = fabio.open(self.cbf_filename) obj.write(os.path.join(self.tempdir, name)) other = fabio.open(os.path.join(self.tempdir, name)) self.assertEqual(abs(obj.data - other.data).max(), 0, "data are the same") for key in obj.header: if key in[ "filename", "X-Binary-Size-Padding"]: continue self.assertTrue(key in other.header, "Key %s is in header" % key) self.assertEqual(obj.header[key], other.header[key], "value are the same for key %s [%s|%s]" % (key, obj.header[key], other.header[key])) def test_suite_all_cbf(): testSuite = unittest.TestSuite() testSuite.addTest(test_cbfimage_reader("test_read")) testSuite.addTest(test_cbfimage_reader("test_write")) testSuite.addTest(test_cbfimage_reader("test_byte_offset")) testSuite.addTest(test_cbfimage_reader("test_consitency_manual")) testSuite.addTest(test_cbfimage_reader("test_consitency_convert")) testSuite.addTest(test_cbfimage_reader("test_unicode")) return testSuite if __name__ == '__main__': mysuite = test_suite_all_cbf() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/testmar345image.py0000644000175000017500000000756112233175156017644 0ustar jeromejerome00000000000000#!/usr/bin/env python # -*- coding: utf8 -*- """ # Unit tests # builds on stuff from ImageD11.test.testpeaksearch """ import unittest, sys, os, logging, tempfile logger = logging.getLogger("testmar345image") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio from fabio.mar345image import mar345image # filename dim1 dim2 min max mean stddev TESTIMAGES = """example.mar2300 2300 2300 0 999999 180.15 4122.67 example.mar2300.bz2 2300 2300 0 999999 180.15 4122.67 example.mar2300.gz 2300 2300 0 999999 180.15 4122.67""" class testMAR345(unittest.TestCase): def setUp(self): """ download images """ self.mar = UtilsTest.getimage("example.mar2300.bz2")[:-4] self.tempdir = tempfile.mkdtemp() def tearDown(self): UtilsTest.recursive_delete(self.tempdir) def test_read(self): """ Test the reading of Mar345 images """ for line in TESTIMAGES.split('\n'): vals = line.strip().split() name = vals[0] dim1, dim2 = [int(x) for x in vals[1:3]] mini, maxi, mean, stddev = [float(x) for x in vals[3:]] obj = mar345image() obj.read(os.path.join(os.path.dirname(self.mar), name)) self.assertAlmostEqual(mini, obj.getmin(), 2, "getmin [%s,%s]" % (mini, obj.getmin())) self.assertAlmostEqual(maxi, obj.getmax(), 2, "getmax [%s,%s]" % (maxi, obj.getmax())) self.assertAlmostEqual(mean, obj.getmean(), 2, "getmean [%s,%s]" % (mean, obj.getmean())) self.assertAlmostEqual(stddev, obj.getstddev(), 2, "getstddev [%s,%s]" % (stddev, obj.getstddev())) self.assertEqual(dim1, obj.dim1, "dim1") self.assertEqual(obj.dim1, obj.dim2, "dim2!=dim1") def test_write(self): "Test writing with self consistency at the fabio level" for line in TESTIMAGES.split("\n"): logger.debug("Processing file: %s" % line) vals = line.split() name = vals[0] obj = mar345image() obj.read(os.path.join(os.path.dirname(self.mar), name)) obj.write(os.path.join(self.tempdir, name)) other = mar345image() other.read(os.path.join(self.tempdir, name)) self.assertEqual(abs(obj.data - other.data).max(), 0, "data are the same") for key in obj.header: if key == "filename": continue self.assertTrue(key in other.header, "Key %s is in header" % key) self.assertEqual(obj.header[key], other.header[key], "value are the same for key %s: [%s|%s]" % (key, obj.header[key], other.header[key])) def test_memoryleak(self): """ This test takes a lot of time, so only in debug mode. """ if logger.getEffectiveLevel() <= logging.INFO: logger.debug("Testing for memory leak") for i in range(1000): img = fabio.open(self.mar) print i def test_suite_all_mar345(): testSuite = unittest.TestSuite() testSuite.addTest(testMAR345("test_read")) testSuite.addTest(testMAR345("test_write")) testSuite.addTest(testMAR345("test_memoryleak")) return testSuite if __name__ == '__main__': mysuite = test_suite_all_mar345() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/testtifgz.py0000644000175000017500000000343012120434325016727 0ustar jeromejerome00000000000000#!/usr/bin/env python # -*- coding: utf8 -*- """ #gipped Tiff Unit tests #built on testedfimage """ import unittest, sys, os, logging logger = logging.getLogger("testtifgz") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio class testgziptif(unittest.TestCase): def setUp(self): self.unzipped = UtilsTest.getimage("oPPA_5grains_0001.tif.bz2")[:-4] self.zipped = self.unzipped + ".gz" assert os.path.exists(self.zipped) assert os.path.exists(self.unzipped) def test1(self): o1 = fabio.open(self.zipped) o2 = fabio.open(self.unzipped) self.assertEqual(o1.data[0, 0], 10) self.assertEqual(o2.data[0, 0], 10) class testtif_rect(unittest.TestCase): def setUp(self): self.fn = UtilsTest.getimage("testmap1_0002.tif.bz2")[:-4] def test1(self): for ext in ["", ".gz", ".bz2"]: o1 = fabio.open(self.fn + ext) self.assertEqual(o1.data.shape, (100, 120)) def test_suite_all_tiff(): testSuite = unittest.TestSuite() testSuite.addTest(testgziptif("test1")) testSuite.addTest(testtif_rect("test1")) return testSuite if __name__ == '__main__': mysuite = test_suite_all_tiff() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/testopenimage.py0000644000175000017500000001543312120434325017556 0ustar jeromejerome00000000000000#!/usr/bin/env python # -*- coding: utf8 -*- """ # Unit tests # builds on stuff from ImageD11.test.testpeaksearch """ import unittest, sys, os, logging logger = logging.getLogger("testopenimage") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio from utilstest import UtilsTest from fabio.openimage import openimage from fabio.edfimage import edfimage from fabio.marccdimage import marccdimage from fabio.fit2dmaskimage import fit2dmaskimage from fabio.OXDimage import OXDimage from fabio.brukerimage import brukerimage from fabio.adscimage import adscimage class testopenedf(unittest.TestCase): """openimage opening edf""" fname = "F2K_Seb_Lyso0675.edf.bz2" def setUp(self): self.fname = UtilsTest.getimage(self.__class__.fname) def testcase(self): """ check we can read EDF image with openimage""" obj = openimage(self.fname) obj2 = edfimage() obj2.read(self.fname) self.assertEqual(obj.data[10, 10], obj2.data[10, 10]) self.assertEqual(type(obj), type(obj2)) self.assertEqual(abs(obj.data.astype(int) - obj2.data.astype(int)).sum(), 0) # etc class testedfgz(testopenedf): """openimage opening edf gzip""" fname = "F2K_Seb_Lyso0675.edf.gz" class testedfbz2(testopenedf): """openimage opening edf bzip""" fname = "F2K_Seb_Lyso0675.edf.bz2" class testopenmccd(unittest.TestCase): """openimage opening mccd""" fname = "somedata_0001.mccd" def setUp(self): self.fname = UtilsTest.getimage(self.__class__.fname) def testcase(self): """ check we can read it""" obj = openimage(self.fname) obj2 = marccdimage() obj2.read(self.fname) self.assertEqual(obj.data[10, 10], obj2.data[10, 10]) self.assertEqual(type(obj), type(obj2)) self.assertEqual(abs(obj.data.astype(int) - obj2.data.astype(int)).sum(), 0) # etc class testmccdgz(testopenmccd): """openimage opening mccd gzip""" fname = "somedata_0001.mccd.gz" class testmccdbz2(testopenmccd): """openimage opening mccd bzip""" fname = "somedata_0001.mccd.bz2" class testmask(unittest.TestCase): """openimage opening mccd""" fname = "face.msk" def setUp(self): """ check file exists """ self.fname = UtilsTest.getimage(self.__class__.fname) def testcase(self): """ check we can read Fit2D mask with openimage""" obj = openimage(self.fname) obj2 = fit2dmaskimage() obj2.read(self.fname) self.assertEqual(obj.data[10, 10], obj2.data[10, 10]) self.assertEqual(type(obj), type(obj2)) self.assertEqual(abs(obj.data.astype(int) - obj2.data.astype(int)).sum(), 0) self.assertEqual(abs(obj.data.astype(int) - obj2.data.astype(int)).sum(), 0) # etc class testmaskgz(testmask): """openimage opening mccd gzip""" fname = "face.msk.gz" class testmaskbz2(testmask): """openimage opening mccd bzip""" fname = "face.msk.bz2" class testbruker(unittest.TestCase): """openimage opening bruker""" fname = "Cr8F8140k103.0026" def setUp(self): self.fname = UtilsTest.getimage(self.__class__.fname) def testcase(self): """ check we can read it""" obj = openimage(self.fname) obj2 = brukerimage() obj2.read(self.fname) self.assertEqual(obj.data[10, 10], obj2.data[10, 10]) self.assertEqual(type(obj), type(obj2)) self.assertEqual(abs(obj.data.astype(int) - obj2.data.astype(int)).sum(), 0) # etc class testbrukergz(testbruker): """openimage opening bruker gzip""" fname = "Cr8F8140k103.0026.gz" class testbrukerbz2(testbruker): """openimage opening bruker bzip""" fname = "Cr8F8140k103.0026.bz2" class testadsc(unittest.TestCase): """openimage opening adsc""" fname = os.path.join("testimages", "mb_LP_1_001.img") def setUp(self): self.fname = UtilsTest.getimage("mb_LP_1_001.img.bz2") def testcase(self): """ check we can read it""" obj = openimage(self.fname) obj2 = adscimage() obj2.read(self.fname) self.assertEqual(obj.data[10, 10], obj2.data[10, 10]) self.assertEqual(type(obj), type(obj2)) self.assertEqual(abs(obj.data.astype(int) - obj2.data.astype(int)).sum(), 0) # etc class testadscgz(testadsc): """openimage opening adsc gzip""" fname = os.path.join("testimages", "mb_LP_1_001.img.gz") class testadscbz2(testadsc): """openimage opening adsc bzip""" fname = os.path.join("testimages", "mb_LP_1_001.img.bz2") class testOXD(unittest.TestCase): """openimage opening adsc""" fname = "b191_1_9_1.img.bz2" def setUp(self): self.fname = UtilsTest.getimage(self.__class__.fname)[:-4] def testcase(self): """ check we can read OXD images with openimage""" obj = openimage(self.fname) obj2 = OXDimage() obj2.read(self.fname) self.assertEqual(obj.data[10, 10], obj2.data[10, 10]) self.assertEqual(type(obj), type(obj2)) self.assertEqual(abs(obj.data.astype(int) - obj2.data.astype(int)).sum(), 0) # etc class testOXDUNC(testOXD): """openimage opening oxd""" fname = "b191_1_9_1_uncompressed.img.bz2" def setUp(self): self.fname = UtilsTest.getimage(self.__class__.fname)[:-4] def test_suite_all_openimage(): testSuite = unittest.TestSuite() testSuite.addTest(testedfbz2("testcase")) testSuite.addTest(testopenedf("testcase")) testSuite.addTest(testedfgz("testcase")) testSuite.addTest(testmccdbz2("testcase")) testSuite.addTest(testopenmccd("testcase")) testSuite.addTest(testmccdgz("testcase")) testSuite.addTest(testmaskbz2("testcase")) testSuite.addTest(testmask("testcase")) testSuite.addTest(testmaskgz("testcase")) testSuite.addTest(testbrukerbz2("testcase")) testSuite.addTest(testbruker("testcase")) testSuite.addTest(testbrukergz("testcase")) testSuite.addTest(testadscbz2("testcase")) testSuite.addTest(testadsc("testcase")) testSuite.addTest(testadscgz("testcase")) testSuite.addTest(testOXD("testcase")) testSuite.addTest(testOXDUNC("testcase")) return testSuite if __name__ == '__main__': mysuite = test_suite_all_openimage() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/benchheader.py0000644000175000017500000000105512120434325017135 0ustar jeromejerome00000000000000 import timeit, os, sys sys.path.insert(0, os.path.abspath("../build/lib.linux-x86_64-2.6")) junk = [".svn", "testfile", "testfile.bz2", "testfile.gz"] #for fname in : # if fname.find("") == -1: # images.append(fname) images = [os.path.join("testimages", i) for i in os.listdir("testimages") if (i not in junk) ] images.sort() for im in images: s = "ret = fabio.openimage.openheader(r\"%s\")" % (im) t = timeit.Timer(s, setup="import fabio.openimage") print "%10.6f" % (t.timeit(10) / 10.0), im fabio-0.1.3/test/testfabioimage.py0000644000175000017500000001652412233175156017710 0ustar jeromejerome00000000000000#!/usr/bin/env python # -*- coding: utf8 -*- """ Test cases for the fabioimage class testsuite by Jerome Kieffer (Jerome.Kieffer@esrf.eu) """ import unittest, sys, os, logging logger = logging.getLogger("testfabioimage") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio from fabio.fabioimage import fabioimage import numpy import gzip, bz2 class test50000(unittest.TestCase): """ test with 50000 everywhere""" def setUp(self): """make the image""" dat = numpy.ones((1024, 1024), numpy.uint16) dat = (dat * 50000).astype(numpy.uint16) assert dat.dtype.char == numpy.ones((1), numpy.uint16).dtype.char hed = {"Title":"50000 everywhere"} self.obj = fabioimage(dat, hed) def testgetmax(self): """check max""" self.assertEqual(self.obj.getmax(), 50000) def testgetmin(self): """check min""" self.assertEqual(self.obj.getmin(), 50000) def testgetmean(self): """check mean""" self.assertEqual(self.obj.getmean(), 50000) def getstddev(self): """check stddev""" self.assertEqual(self.obj.getstddev(), 0) class testslices(unittest.TestCase): """check slicing""" def setUp(self): """make test data""" dat2 = numpy.zeros((1024, 1024), numpy.uint16) hed = {"Title":"zeros and 100"} self.cord = [ 256, 256, 790, 768 ] self.obj = fabioimage(dat2, hed) self.slic = slic = self.obj.make_slice(self.cord) # Note - d2 is modified *after* fabioimage is made dat2[slic] = dat2[slic] + 100 assert self.obj.maxval is None assert self.obj.minval is None self.npix = (slic[0].stop - slic[0].start) * \ (slic[1].stop - slic[1].start) def testgetmax(self): """check max""" self.assertEqual(self.obj.getmax(), 100) def testgetmin(self): """check min""" self.assertEqual(self.obj.getmin(), 0) def testintegratearea(self): """ check integrations""" self.obj.resetvals() area1 = self.obj.integrate_area(self.cord) self.obj.resetvals() area2 = self.obj.integrate_area(self.slic) self.assertEqual(area1, area2) self.assertEqual(area1, self.npix * 100) def testRebin(self): """Test the rebin method""" big = numpy.arange(64).reshape((8, 8)) res = numpy.array([[13, 17], [45, 49]]) fabimg = fabioimage(data=big, header={}) fabimg.rebin(4, 4) self.assertEqual(abs(res - fabimg.data).max(), 0, "data are the same after rebin") class testopen(unittest.TestCase): """check opening compressed files""" testfile = os.path.join(UtilsTest.test_home, "testimages", "testfile") def setUp(self): """ create test files""" if not os.path.isfile(self.testfile): open(self.testfile, "wb").write("{ hello }") if not os.path.isfile(self.testfile + ".gz"): gzip.open(self.testfile + ".gz", "wb").write("{ hello }") if not os.path.isfile(self.testfile + ".bz2"): bz2.BZ2File(self.testfile + ".bz2", "wb").write("{ hello }") self.obj = fabioimage() def testFlat(self): """ no compression""" res = self.obj._open(self.testfile).read() self.assertEqual(res , "{ hello }") def testgz(self): """ gzipped """ res = self.obj._open(self.testfile + ".gz").read() self.assertEqual(res , "{ hello }") def testbz2(self): """ bzipped""" res = self.obj._open(self.testfile + ".bz2").read() self.assertEqual(res , "{ hello }") NAMES = { numpy.uint8 : "numpy.uint8", numpy.int8 : "numpy.int8" , numpy.uint16: "numpy.uint16", numpy.int16 : "numpy.int16" , numpy.uint32: "numpy.uint32" , numpy.int32 : "numpy.int32" , numpy.float32: "numpy.float32" , numpy.float64: "numpy.float64"} class testPILimage(unittest.TestCase): """ check PIL creation""" def setUp(self): """ list of working numeric types""" self.okformats = [numpy.uint8, numpy.int8, numpy.uint16, numpy.int16, numpy.uint32, numpy.int32, numpy.float32] def mkdata(self, shape, typ): """ generate [01] testdata """ return (numpy.random.random(shape)).astype(typ) def testpil(self): for typ in self.okformats: name = NAMES[typ] for shape in [(10, 20), (431, 1325)]: testdata = self.mkdata(shape, typ) img = fabioimage(testdata, {"title":"Random data"}) pim = img.toPIL16() for i in [ 0, 5, 6, shape[1] - 1 ]: for j in [0, 5, 7, shape[0] - 1 ]: errstr = name + " %d %d %f %f t=%s" % ( i, j, testdata[j, i], pim.getpixel((i, j)), typ) er1 = img.data[j, i] - pim.getpixel((i, j)) er2 = img.data[j, i] + pim.getpixel((i, j)) # difference as % error in case of rounding if er2 != 0.: err = er1 / er2 else: err = er1 self.assertAlmostEquals(err, 0, 6, errstr) class testPILimage2(testPILimage): """ check with different numbers""" def mkdata(self, shape, typ): """ positive and big""" return (numpy.random.random(shape) * sys.maxint / 10).astype(typ) class testPILimage3(testPILimage): """ check with different numbers""" def mkdata(self, shape, typ): """ positive, negative and big""" return ((numpy.random.random(shape) - 0.5) * sys.maxint / 10).astype(typ) def test_suite_all_fabio(): testSuite = unittest.TestSuite() testSuite.addTest(test50000("testgetmax")) testSuite.addTest(test50000("testgetmin")) testSuite.addTest(test50000("testgetmean")) testSuite.addTest(test50000("getstddev")) testSuite.addTest(testslices("testgetmax")) testSuite.addTest(testslices("testgetmin")) testSuite.addTest(testslices("testintegratearea")) testSuite.addTest(testslices("testRebin")) testSuite.addTest(testopen("testFlat")) testSuite.addTest(testopen("testgz")) testSuite.addTest(testopen("testbz2")) testSuite.addTest(testPILimage("testpil")) testSuite.addTest(testPILimage2("testpil")) testSuite.addTest(testPILimage3("testpil")) return testSuite if __name__ == '__main__': mysuite = test_suite_all_fabio() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/test_all_images.py0000644000175000017500000000524212120434325020043 0ustar jeromejerome00000000000000 """ Check we can read all the test images """ import glob, os, time, fabio.openimage, gzip, bz2, pstats, sys try: import cProfile except: import profile as cProfile times = {} images = [] for fname in glob.glob(os.path.join("testimages","*")): if fname.find("header_only")==-1: images.append(fname) images.sort() def shellbench(cmd, imname): """ The shell appears to be lying about it's performance. It claims zero time to gunzip a file when it actually takes 200 ms. This is cheating via a cache I suspect. We shall try to avoid this problem """ if sys.platform != "win32": os.system("touch "+imname) astart = time.time() dummy_file = os.popen(cmd + " " + imname, "rb").read() return time.time() - astart print "I/O 1 : Time to read the image" print "I/O 2 : Time to read the image (repeat" print "Fabio : Time for fabio to read the image" print "Shell : Time for shell to do decompression" print "Python : Time for python to do decompression\n" print "I/O 1 I/O 2 Fabio Shell Python Size/MB" for im in images: # Network/disk io time first start = time.clock() the_file = open(im,"rb").read() times[im] = [ time.clock()-start ] start = time.clock() # Network/disk should be cached the_file = open(im,"rb").read() times[im].append( time.clock() - start ) start = time.clock() try: fim = fabio.openimage.openimage(im) except KeyboardInterrupt: raise except: print "Problem with", im continue # raise times[im].append( time.clock() - start ) nt = 3 ns = 2 # Now check for a fabio slowdown effect if im[-3:] == '.gz': times[im].append(shellbench("gzip -cd ", im)) nt += 1 ns -= 1 start = time.clock() the_file = gzip.GzipFile(im,"rb").read() times[im].append( time.clock()-start ) nt += 1 ns -= 1 if im[-4:] == '.bz2': times[im].append(shellbench("bzip2 -cd ", im)) nt += 1 ns -= 1 start = time.clock() the_file = bz2.BZ2File(im,"rb").read() times[im].append( time.clock()-start ) nt += 1 ns -= 1 # Speed ratings in megabytes per second (for fabio) MB = len(the_file) / 1024.0 / 1024.0 try: print ("%.4f "*nt + " "*7*ns)% tuple(times[im]), "%8.3f"%(MB), im except: print times[im], MB, im raise cProfile.run("fabio.openimage.openimage(im)","stats") p = pstats.Stats("stats") # Hack around python2.4 s = sys.stdout sys.stdout = open("profile.txt","a") p.strip_dirs().sort_stats(-1).print_stats() sys.stdout = s fabio-0.1.3/test/testtifimage.py0000755000175000017500000000743512120434325017405 0ustar jeromejerome00000000000000#!/usr/bin/env python # -*- coding: utf8 -*- """ # Tiff Unit tests #built on testedfimage """ import unittest import os import logging import sys logger = logging.getLogger("testTiff") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio from testtifgz import testtif_rect, testgziptif class testtifimage_pilatus(unittest.TestCase): def setUp(self): self.fn = {} for i in ["pilatus2M.tif", "pilatus2M.edf"]: self.fn[i] = UtilsTest.getimage(i + ".bz2") for i in self.fn: assert os.path.exists(self.fn[i]) def test1(self): """ Testing pilatus tif bug """ o1 = fabio.open(self.fn["pilatus2M.tif"]).data o2 = fabio.open(self.fn["pilatus2M.edf"]).data self.assertEqual(abs(o1 - o2).max(), 0.0) class testtifimage_packbits(unittest.TestCase): def setUp(self): self.fn = {} for i in ["oPPA_5grains_0001.tif", "oPPA_5grains_0001.edf"]: self.fn[i] = UtilsTest.getimage(i + ".bz2") for i in self.fn: assert os.path.exists(self.fn[i]) def test1(self): """ Testing packbit comressed data tif bug """ o1 = fabio.open(self.fn["oPPA_5grains_0001.tif"]).data o2 = fabio.open(self.fn["oPPA_5grains_0001.edf"]).data self.assertEqual(abs(o1 - o2).max(), 0.0) class testtifimage_fit2d(unittest.TestCase): def setUp(self): self.fn = {} for i in ["fit2d.tif", "fit2d.edf"]: self.fn[i] = UtilsTest.getimage(i + ".bz2") for i in self.fn: assert os.path.exists(self.fn[i]) def test1(self): """ Testing packbit comressed data tif bug """ o1 = fabio.open(self.fn["fit2d.tif"]).data o2 = fabio.open(self.fn["fit2d.edf"]).data self.assertEqual(abs(o1 - o2).max(), 0.0) class testtifimage_a0009(unittest.TestCase): """ test image from ??? with this error a0009.tif TIFF 1024x1024 1024x1024+0+0 16-bit Grayscale DirectClass 2MiB 0.000u 0:00.010 identify: a0009.tif: invalid TIFF directory; tags are not sorted in ascending order. `TIFFReadDirectory' @ tiff.c/TIFFWarnings/703. identify: a0009.tif: TIFF directory is missing required "StripByteCounts" field, calculating from imagelength. `TIFFReadDirectory' @ tiff.c/TIFFWarnings/703. """ def setUp(self): self.fn = {} for i in ["a0009.tif", "a0009.edf"]: self.fn[i] = UtilsTest.getimage(i + ".bz2")[:-4] for i in self.fn: assert os.path.exists(self.fn[i]) def test1(self): """ Testing packbit comressed data tif bug """ o1 = fabio.open(self.fn["a0009.tif"]).data o2 = fabio.open(self.fn["a0009.edf"]).data self.assertEqual(abs(o1 - o2).max(), 0.0) def test_suite_all_tiffimage(): testSuite = unittest.TestSuite() testSuite.addTest(testtifimage_packbits("test1")) testSuite.addTest(testtifimage_pilatus("test1")) testSuite.addTest(testtifimage_fit2d("test1")) testSuite.addTest(testgziptif("test1")) testSuite.addTest(testtif_rect("test1")) testSuite.addTest(testtifimage_a0009("test1")) return testSuite if __name__ == '__main__': mysuite = test_suite_all_tiffimage() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/testkcdimage.py0000755000175000017500000000515512120434325017361 0ustar jeromejerome00000000000000#!/usr/bin/env python # -*- coding: utf8 -*- """ Test for Nonius Kappa CCD cameras. """ import unittest, sys, os, logging logger = logging.getLogger("testkcdimage") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio from fabio.kcdimage import kcdimage from fabio.edfimage import edfimage from fabio.openimage import openimage class testkcd(unittest.TestCase): """basic test""" kcdfilename = 'i01f0001.kcd' edffilename = 'i01f0001.edf' results = """i01f0001.kcd 625 576 96 66814.0 195.3862972 243.58150990245315""" def setUp(self): """Download files""" self.fn = {} for i in ["i01f0001.kcd", "i01f0001.edf"]: self.fn[i] = UtilsTest.getimage(i + ".bz2")[:-4] for i in self.fn: assert os.path.exists(self.fn[i]) def test_read(self): """ check we can read kcd images""" vals = self.results.split() name = vals[0] dim1, dim2 = [int(x) for x in vals[1:3]] mini, maxi, mean, stddev = [float(x) for x in vals[3:]] obj = openimage(self.fn[self.kcdfilename]) self.assertAlmostEqual(mini, obj.getmin(), 4, "getmin") self.assertAlmostEqual(maxi, obj.getmax(), 4, "getmax") self.assertAlmostEqual(mean, obj.getmean(), 4, "getmean") self.assertAlmostEqual(stddev, obj.getstddev(), 4, "getstddev") self.assertEqual(dim1, obj.dim1, "dim1") self.assertEqual(dim2, obj.dim2, "dim2") def test_same(self): """ see if we can read kcd images and if they are the same as the EDF """ kcd = kcdimage() kcd.read(self.fn[self.kcdfilename]) edf = fabio.open(self.fn[self.edffilename]) diff = (kcd.data.astype("int32") - edf.data.astype("int32")) self.assertAlmostEqual(abs(diff).sum(dtype=int), 0, 4) def test_suite_all_kcd(): testSuite = unittest.TestSuite() testSuite.addTest(testkcd("test_read")) testSuite.addTest(testkcd("test_same")) return testSuite if __name__ == '__main__': mysuite = test_suite_all_kcd() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/testedfimage.py0000755000175000017500000003400412233175220017352 0ustar jeromejerome00000000000000#!/usr/bin/env python # -*- coding: utf8 -*- """ # Unit tests # builds on stuff from ImageD11.test.testpeaksearch """ import unittest, sys, os, logging, tempfile logger = logging.getLogger("testedfimage") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio from fabio.edfimage import edfimage import numpy import gzip, bz2 class testflatedfs(unittest.TestCase): """ test some flat images """ filename = os.path.join(UtilsTest.test_home, "testimages", "im0000.edf") MYHEADER = "{\n%-1020s}\n" % ( """Omega = 0.0 ; Dim_1 = 256 ; Dim_2 = 256 ; DataType = FloatValue ; ByteOrder = LowByteFirst ; Image = 1; History-1 = something=something else; \n\n""") MYIMAGE = numpy.ones((256, 256), numpy.float32) * 10 MYIMAGE[0, 0] = 0 MYIMAGE[1, 1] = 20 assert len(MYIMAGE[0:1, 0:1].tostring()) == 4, \ len(MYIMAGE[0:1, 0:1].tostring()) def setUp(self): """ initialize""" if not os.path.isfile(self.filename): outf = open(self.filename, "wb") assert len(self.MYHEADER) % 1024 == 0 outf.write(self.MYHEADER) outf.write(self.MYIMAGE.tostring()) outf.close() def test_read(self): """ check readable""" obj = edfimage() obj.read(self.filename) self.assertEqual(obj.dim1 , 256, msg="dim1!=256 for file: %s" % self.filename) self.assertEqual(obj.dim2 , 256, msg="dim2!=256 for file: %s" % self.filename) self.assertEqual(obj.bpp , 4, msg="bpp!=4 for file: %s" % self.filename) self.assertEqual(obj.bytecode, numpy.float32, msg="bytecode!=flot32 for file: %s" % self.filename) self.assertEqual(obj.data.shape, (256, 256), msg="shape!=(256,256) for file: %s" % self.filename) self.assertEqual(obj.header['History-1'], "something=something else") def test_getstats(self): """ test statistics""" obj = edfimage() obj.read(self.filename) self.assertEqual(obj.getmean() , 10) self.assertEqual(obj.getmin() , 0) self.assertEqual(obj.getmax() , 20) class testbzipedf(testflatedfs): """ same for bzipped versions """ def setUp(self): """set it up""" testflatedfs.setUp(self) if not os.path.isfile(self.filename + ".bz2"): bz2.BZ2File(self.filename + ".bz2", "wb").write(open(self.filename, "rb").read()) self.filename += ".bz2" class testgzipedf(testflatedfs): """ same for gzipped versions """ def setUp(self): """ set it up """ testflatedfs.setUp(self) if not os.path.isfile(self.filename + ".gz"): gzip.open(self.filename + ".gz", "wb").write(open(self.filename, "rb").read()) self.filename += ".gz" # statistics come from fit2d I think # filename dim1 dim2 min max mean stddev TESTIMAGES = """F2K_Seb_Lyso0675.edf 2048 2048 982 17467 1504.29 217.61 F2K_Seb_Lyso0675.edf.bz2 2048 2048 982 17467 1504.29 217.61 F2K_Seb_Lyso0675.edf.gz 2048 2048 982 17467 1504.29 217.61 id13_badPadding.edf 512 512 85 61947 275.62 583.44 """ class testedfs(unittest.TestCase): """ Read some test images """ def setUp(self): self.im_dir = os.path.dirname(UtilsTest.getimage("F2K_Seb_Lyso0675.edf.bz2")) UtilsTest.getimage("id13_badPadding.edf.bz2") def test_read(self): """ check we can read these images""" for line in TESTIMAGES.split("\n"): vals = line.split() name = vals[0] dim1, dim2 = [int(x) for x in vals[1:3]] mini, maxi, mean, stddev = [float(x) for x in vals[3:]] obj = edfimage() try: obj.read(os.path.join(self.im_dir, name)) except: print "Cannot read image", name raise self.assertAlmostEqual(mini, obj.getmin(), 2, "testedfs: %s getmin()" % name) self.assertAlmostEqual(maxi, obj.getmax(), 2, "testedfs: %s getmax" % name) logger.info("%s Mean: exp=%s, obt=%s" % (name, mean, obj.getmean())) self.assertAlmostEqual(mean, obj.getmean(), 2, "testedfs: %s getmean" % name) logger.info("%s StdDev: exp=%s, obt=%s" % (name, stddev, obj.getstddev())) self.assertAlmostEqual(stddev, obj.getstddev(), 2, "testedfs: %s getstddev" % name) self.assertEqual(dim1, obj.dim1, "testedfs: %s dim1" % name) self.assertEqual(dim2, obj.dim2, "testedfs: %s dim2" % name) def test_rebin(self): """test the rebin of edfdata""" f = edfimage() f.read(os.path.join(self.im_dir, "F2K_Seb_Lyso0675.edf")) f.rebin(1024, 1024) self.assertEqual(abs(numpy.array([[1547, 1439], [1536, 1494]]) - f.data).max(), 0, "data are the same after rebin") class testedfcompresseddata(unittest.TestCase): """ Read some test images with their data-block compressed. Z-Compression and Gzip compression are implemented Bzip2 and byte offet are experimental """ def setUp(self): self.im_dir = os.path.dirname(UtilsTest.getimage("edfGzip_U16.edf.bz2")) UtilsTest.getimage("edfCompressed_U16.edf.bz2") UtilsTest.getimage("edfUncompressed_U16.edf.bz2") def test_read(self): """ check we can read these images""" ref = edfimage() gzipped = edfimage() compressed = edfimage() refFile = "edfUncompressed_U16.edf" gzippedFile = "edfGzip_U16.edf" compressedFile = "edfCompressed_U16.edf" try: ref.read(os.path.join(self.im_dir, refFile)) except: raise RuntimeError("Cannot read image Uncompressed image %s" % refFile) try: gzipped.read(os.path.join(self.im_dir, gzippedFile)) except: raise RuntimeError("Cannot read image gzippedFile image %s" % gzippedFile) try: compressed.read(os.path.join(self.im_dir, compressedFile)) except: raise RuntimeError("Cannot read image compressedFile image %s" % compressedFile) self.assertEqual((ref.data - gzipped.data).max(), 0, "Gzipped data block is correct") self.assertEqual((ref.data - compressed.data).max(), 0, "Zlib compressed data block is correct") class testedfmultiframe(unittest.TestCase): """ Read some test images with their data-block compressed. Z-Compression and Gzip compression are implemented Bzip2 and byte offet are experimental """ def setUp(self): self.multiFrameFilename = UtilsTest.getimage("MultiFrame.edf.bz2")[:-4] self.Frame0Filename = UtilsTest.getimage("MultiFrame-Frame0.edf.bz2")[:-4] self.Frame1Filename = UtilsTest.getimage("MultiFrame-Frame1.edf.bz2")[:-4] self.ref = edfimage() self.frame0 = edfimage() self.frame1 = edfimage() try: self.ref.read(self.multiFrameFilename) except: raise RuntimeError("Cannot read image multiFrameFilename image %s" % self.multiFrameFilename) try: self.frame0.read(self.Frame0Filename) except: raise RuntimeError("Cannot read image Frame0File image %s" % self.Frame0File) try: self.frame1.read(self.Frame1Filename) except: raise RuntimeError("Cannot read image Frame1File image %s" % self.Frame1File) def test_getFrame_multi(self): """testedfmultiframe.test_getFrame_multi""" self.assertEqual((self.ref.data - self.frame0.data).max(), 0, "getFrame_multi: Same data for frame 0") f1_multi = self.ref.getframe(1) # logger.warning("f1_multi.header=%s\nf1_multi.data= %s" % (f1_multi.header, f1_multi.data)) self.assertEqual((f1_multi.data - self.frame1.data).max(), 0, "getFrame_multi: Same data for frame 1") def test_getFrame_mono(self): "testedfmultiframe.test_getFrame_mono" self.assertEqual((self.ref.data - self.frame0.data).max(), 0, "getFrame_mono: Same data for frame 0") f1_mono = self.frame0.getframe(1) self.assertEqual((f1_mono.data - self.frame1.data).max(), 0, "getFrame_mono: Same data for frame 1") def test_next_multi(self): """testedfmultiframe.test_getFrame_mono""" self.assertEqual((self.ref.data - self.frame0.data).max(), 0, "next_multi: Same data for frame 0") next = self.ref.next() self.assertEqual((next.data - self.frame1.data).max(), 0, "next_multi: Same data for frame 1") def text_next_mono(self): "testedfmultiframe.text_next_mono" self.assertEqual((self.ref.data - self.frame0.data).max(), 0, "next_mono: Same data for frame 0") next = self.frame0.next() self.assertEqual((next.data - self.frame1.data).max(), 0, "next_mono: Same data for frame 1") def test_previous_multi(self): """testedfmultiframe.test_previous_multi""" f1 = self.ref.getframe(1) self.assertEqual((f1.data - self.frame1.data).max(), 0, "previous_multi: Same data for frame 1") f0 = f1.previous() self.assertEqual((f0.data - self.frame1.data).max(), 0, "previous_multi: Same data for frame 0") def test_previous_mono(self): "testedfmultiframe.test_previous_mono" f1 = self.ref.getframe(1) self.assertEqual((f1.data - self.frame1.data).max(), 0, "previous_mono: Same data for frame 1") prev = self.frame1.previous() self.assertEqual((prev.data - self.frame0.data).max(), 0, "previous_mono: Same data for frame 0") def test_openimage_multiframes(self): "test if openimage can directly read first or second frame of a multi-frame" self.assertEqual((fabio.open(self.multiFrameFilename).data - self.frame0.data).max(), 0, "openimage_multiframes: Same data for default ") self.assertEqual((fabio.open(self.multiFrameFilename, 0).data - self.frame0.data).max(), 0, "openimage_multiframes: Same data for frame 0") self.assertEqual((fabio.open(self.multiFrameFilename, 1).data - self.frame1.data).max(), 0, "openimage_multiframes: Same data for frame 1") class testedffastread(unittest.TestCase): """ Read some test images with their data-block compressed. Z-Compression and Gzip compression are implemented Bzip2 and byte offet are experimental """ def setUp(self): self.refFilename = UtilsTest.getimage("MultiFrame-Frame0.edf.bz2") self.fastFilename = self.refFilename[:-4] def test_fastread(self): ref = fabio.open(self.refFilename) refdata = ref.data obt = ref.fastReadData(self.fastFilename) self.assertEqual(abs(obt - refdata).max(), 0, "testedffastread: Same data") class testedfwrite(unittest.TestCase): """ Write dummy edf files with various compression schemes """ def setUp(self): self.data = numpy.arange(100).reshape((10, 10)) self.header = {"toto": "tutu"} self.tmpdir = tempfile.mkdtemp(prefix="testedfwrite") def testFlat(self): self.filename = os.path.join(self.tmpdir, "merged.azim") e = edfimage(data=self.data, header=self.header) e.write(self.filename) r = fabio.open(self.filename) self.assert_(r.header["toto"] == self.header["toto"], "header are OK") self.assert_(abs(r.data - self.data).max() == 0, "data are OK") self.assertEqual(int(r.header["EDF_HeaderSize"]), 512, "header size is one 512 block") def testGzip(self): self.filename = os.path.join(self.tmpdir, "merged.azim.gz") e = edfimage(data=self.data, header=self.header) e.write(self.filename) r = fabio.open(self.filename) self.assert_(r.header["toto"] == self.header["toto"], "header are OK") self.assert_(abs(r.data - self.data).max() == 0, "data are OK") self.assertEqual(int(r.header["EDF_HeaderSize"]), 512, "header size is one 512 block") def testBzip2(self): self.filename = os.path.join(self.tmpdir, "merged.azim.gz") e = edfimage(data=self.data, header=self.header) e.write(self.filename) r = fabio.open(self.filename) self.assert_(r.header["toto"] == self.header["toto"], "header are OK") self.assert_(abs(r.data - self.data).max() == 0, "data are OK") self.assertEqual(int(r.header["EDF_HeaderSize"]), 512, "header size is one 512 block") def tearDown(self): os.unlink(self.filename) os.rmdir(self.tmpdir) def test_suite_all_edf(): testSuite = unittest.TestSuite() testSuite.addTest(testflatedfs("test_read")) testSuite.addTest(testflatedfs("test_getstats")) testSuite.addTest(testbzipedf("test_read")) testSuite.addTest(testbzipedf("test_getstats")) testSuite.addTest(testgzipedf("test_read")) testSuite.addTest(testgzipedf("test_getstats")) testSuite.addTest(testedfs("test_read")) testSuite.addTest(testedfs("test_rebin")) testSuite.addTest(testedfcompresseddata("test_read")) testSuite.addTest(testedfmultiframe("test_getFrame_multi")) testSuite.addTest(testedfmultiframe("test_getFrame_mono")) testSuite.addTest(testedfmultiframe("test_next_multi")) testSuite.addTest(testedfmultiframe("text_next_mono")) testSuite.addTest(testedfmultiframe("test_previous_multi")) testSuite.addTest(testedfmultiframe("test_openimage_multiframes")) testSuite.addTest(testedffastread("test_fastread")) testSuite.addTest(testedfwrite("testFlat")) testSuite.addTest(testedfwrite("testGzip")) testSuite.addTest(testedfwrite("testBzip2")) return testSuite if __name__ == '__main__': mysuite = test_suite_all_edf() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/test/test_file_series.py0000644000175000017500000000702012120434325020233 0ustar jeromejerome00000000000000#!/usr/bin/env python # -*- coding: utf8 -*- """ test cases for fileseries """ import unittest import os import logging import sys logger = logging.getLogger("test_file_series") force_build = False for opts in sys.argv[:]: if opts in ["-d", "--debug"]: logging.basicConfig(level=logging.DEBUG) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-i", "--info"]: logging.basicConfig(level=logging.INFO) sys.argv.pop(sys.argv.index(opts)) elif opts in ["-f", "--force"]: force_build = True sys.argv.pop(sys.argv.index(opts)) try: logger.debug("Tests loaded from file: %s" % __file__) except: __file__ = os.getcwd() from utilstest import UtilsTest if force_build: UtilsTest.forceBuild() import fabio from fabio.file_series import numbered_file_series , file_series class testrandomseries(unittest.TestCase): """arbitrary series""" def setUp(self): """sets up""" self.fso = file_series(["first", "second", "last" ]) def testfirst(self): """check first""" self.assertEqual("first", self.fso.first()) def testlast(self): """check first""" self.assertEqual("last" , self.fso.last()) def testjump(self): """check jump""" self.assertEqual("second", self.fso.jump(1)) class testedfnumbered(unittest.TestCase): """ Typical sequence of edf files """ def setUp(self): """ note extension has the . in it""" self.fso = numbered_file_series("mydata", 0, 10005, ".edf") def testfirst(self): """ first in series""" self.assertEqual(self.fso.first(), "mydata0000.edf") def testlast(self): """ last in series""" self.assertEqual(self.fso.last(), "mydata10005.edf") def testnext(self): """ check all in order """ mylist = [ "mydata%04d.edf" % (i) for i in range(0, 10005) ] i = 1 while i < len(mylist): self.assertEqual(mylist[i], self.fso.next()) i += 1 def testprevious(self): """ check all in order """ mylist = [ "mydata%04d.edf" % (i) for i in range(0, 10005) ] i = 10003 self.fso.jump(10004) while i > 0 : self.assertEqual(mylist[i], self.fso.previous()) i -= 1 def testprevjump(self): """check current""" self.fso.jump(9999) self.assertEqual("mydata9999.edf", self.fso.current()) self.assertEqual("mydata9998.edf", self.fso.previous()) def testnextjump(self): """check current""" self.fso.jump(9999) self.assertEqual("mydata9999.edf", self.fso.current()) self.assertEqual("mydata10000.edf", self.fso.next()) def testlen(self): """check len""" self.assertEqual(self.fso.len() , 10006)# +1 for 0000 def test_suite_all_series(): testSuite = unittest.TestSuite() testSuite.addTest(testrandomseries("testfirst")) testSuite.addTest(testrandomseries("testlast")) testSuite.addTest(testrandomseries("testjump")) testSuite.addTest(testedfnumbered("testfirst")) testSuite.addTest(testedfnumbered("testprevious")) testSuite.addTest(testedfnumbered("testlast")) testSuite.addTest(testedfnumbered("testnext")) testSuite.addTest(testedfnumbered("testprevjump")) testSuite.addTest(testedfnumbered("testnextjump")) testSuite.addTest(testedfnumbered("testlen")) return testSuite if __name__ == '__main__': mysuite = test_suite_all_series() runner = unittest.TextTestRunner() runner.run(mysuite) fabio-0.1.3/setup.py0000644000175000017500000001013012233175156015071 0ustar jeromejerome00000000000000#!/usr/bin/env python # coding: utf8 """ Setup script for python distutils package and fabio """ import os, sys import os.path as op try: from setuptools import setup except ImportError: from distutils.core import setup from distutils.core import Extension, Command from numpy.distutils.misc_util import get_numpy_include_dirs cf_backend = Extension('cf_io', include_dirs=get_numpy_include_dirs(), sources=['src/cf_iomodule.c', 'src/columnfile.c']) byteOffset_backend = Extension("byte_offset", include_dirs=get_numpy_include_dirs(), sources=['src/byte_offset.c']) mar345_backend = Extension('mar345_IO', include_dirs=get_numpy_include_dirs(), sources=['src/mar345_IO.c', 'src/ccp4_pack.c', ]) version = [eval(l.split("=")[1]) for l in open(op.join(op.dirname(op.abspath(__file__)), "fabio-src", "__init__.py")) if l.strip().startswith("version")][0] ####################### # build_doc commandes # ####################### cmdclass = {} try: import sphinx import sphinx.util.console sphinx.util.console.color_terminal = lambda: False from sphinx.setup_command import BuildDoc except ImportError: sphinx = None if sphinx: class build_doc(BuildDoc): def run(self): # make sure the python path is pointing to the newly built # code so that the documentation is built on this and not a # previously installed version build = self.get_finalized_command('build') print(os.path.abspath(build.build_lib)) sys.path.insert(0, os.path.abspath(build.build_lib)) # we need to reload PyMca from the build directory and not # the one from the source directory which does not contain # the extensions BuildDoc.run(self) sys.path.pop(0) cmdclass['build_doc'] = build_doc class PyTest(Command): user_options = [] def initialize_options(self): pass def finalize_options(self): pass def run(self): import subprocess os.chdir(os.path.join(os.path.dirname(os.path.abspath(__file__)), "test")) errno = subprocess.call([sys.executable, 'test_all.py']) if errno != 0: raise SystemExit(errno) else: os.chdir("..") cmdclass['test'] = PyTest # See the distutils docs... setup(name='fabio', version=version, author="Henning Sorensen, Erik Knudsen, Jon Wright, Regis Perdreau, Jérôme Kieffer and Gael Goret", author_email="fable-talk@lists.sourceforge.net", description='Image IO for fable', url="http://fable.wiki.sourceforge.net/fabio", download_url="http://sourceforge.net/projects/fable/files/fabio/0.1.2", ext_package="fabio", ext_modules=[mar345_backend, cf_backend, byteOffset_backend], packages=["fabio"], package_dir={"fabio": "fabio-src" }, test_suite="test", cmdclass=cmdclass, classifiers=[ 'Development Status :: 5 - Production/Stable', 'Environment :: Console', 'Intended Audience :: End Users/Desktop', 'Intended Audience :: Developers', 'Intended Audience :: Science/Research', "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)", 'Operating System :: MacOS :: MacOS X', 'Operating System :: Microsoft :: Windows', 'Operating System :: POSIX', 'Programming Language :: Python', 'Programming Language :: Cython', 'Programming Language :: C', 'Topic :: Scientific/Engineering :: Chemistry', 'Topic :: Scientific/Engineering :: Bio-Informatics', 'Topic :: Scientific/Engineering :: Physics', 'Topic :: Scientific/Engineering :: Visualization', 'Topic :: Software Development :: Libraries :: Python Modules', ],) fabio-0.1.3/stdeb.cfg0000644000175000017500000000033112120434325015132 0ustar jeromejerome00000000000000[DEFAULT] Package: python-fabio Depends: python-numpy XS-Python-Version: >= 2.5 Maintainer: Jerome Kieffer Build-Depends: python-dev Recommends: python-imaging, python-numpy-ext, python-lxml fabio-0.1.3/PKG-INFO0000644000175000017500000000242112233272207014453 0ustar jeromejerome00000000000000Metadata-Version: 1.1 Name: fabio Version: 0.1.3 Summary: Image IO for fable Home-page: http://fable.wiki.sourceforge.net/fabio Author: Henning Sorensen, Erik Knudsen, Jon Wright, Regis Perdreau, Jérôme Kieffer and Gael Goret Author-email: fable-talk@lists.sourceforge.net License: UNKNOWN Download-URL: http://sourceforge.net/projects/fable/files/fabio/0.1.2 Description: UNKNOWN Platform: UNKNOWN Classifier: Development Status :: 5 - Production/Stable Classifier: Environment :: Console Classifier: Intended Audience :: End Users/Desktop Classifier: Intended Audience :: Developers Classifier: Intended Audience :: Science/Research Classifier: License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+) Classifier: Operating System :: MacOS :: MacOS X Classifier: Operating System :: Microsoft :: Windows Classifier: Operating System :: POSIX Classifier: Programming Language :: Python Classifier: Programming Language :: Cython Classifier: Programming Language :: C Classifier: Topic :: Scientific/Engineering :: Chemistry Classifier: Topic :: Scientific/Engineering :: Bio-Informatics Classifier: Topic :: Scientific/Engineering :: Physics Classifier: Topic :: Scientific/Engineering :: Visualization Classifier: Topic :: Software Development :: Libraries :: Python Modules fabio-0.1.3/doc/0000755000175000017500000000000012233272206014123 5ustar jeromejerome00000000000000fabio-0.1.3/doc/Makefile0000644000175000017500000001076112121354612015566 0ustar jeromejerome00000000000000# Makefile for Sphinx documentation # # You can set these variables from the command line. SPHINXOPTS = SPHINXBUILD = sphinx-build PAPER = BUILDDIR = build # Internal variables. PAPEROPT_a4 = -D latex_paper_size=a4 PAPEROPT_letter = -D latex_paper_size=letter ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source .PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest help: @echo "Please use \`make ' where is one of" @echo " html to make standalone HTML files" @echo " dirhtml to make HTML files named index.html in directories" @echo " singlehtml to make a single large HTML file" @echo " pickle to make pickle files" @echo " json to make JSON files" @echo " htmlhelp to make HTML files and a HTML help project" @echo " qthelp to make HTML files and a qthelp project" @echo " devhelp to make HTML files and a Devhelp project" @echo " epub to make an epub" @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" @echo " latexpdf to make LaTeX files and run them through pdflatex" @echo " text to make text files" @echo " man to make manual pages" @echo " changes to make an overview of all changed/added/deprecated items" @echo " linkcheck to check all external links for integrity" @echo " doctest to run all doctests embedded in the documentation (if enabled)" clean: -rm -rf $(BUILDDIR)/* html: $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html @echo @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." dirhtml: $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml @echo @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." singlehtml: $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml @echo @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." pickle: $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle @echo @echo "Build finished; now you can process the pickle files." json: $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json @echo @echo "Build finished; now you can process the JSON files." htmlhelp: $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp @echo @echo "Build finished; now you can run HTML Help Workshop with the" \ ".hhp project file in $(BUILDDIR)/htmlhelp." qthelp: $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp @echo @echo "Build finished; now you can run "qcollectiongenerator" with the" \ ".qhcp project file in $(BUILDDIR)/qthelp, like this:" @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/FabIO.qhcp" @echo "To view the help file:" @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/FabIO.qhc" devhelp: $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp @echo @echo "Build finished." @echo "To view the help file:" @echo "# mkdir -p $$HOME/.local/share/devhelp/FabIO" @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/FabIO" @echo "# devhelp" epub: $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub @echo @echo "Build finished. The epub file is in $(BUILDDIR)/epub." latex: $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex @echo @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." @echo "Run \`make' in that directory to run these through (pdf)latex" \ "(use \`make latexpdf' here to do that automatically)." latexpdf: $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex @echo "Running LaTeX files through pdflatex..." $(MAKE) -C $(BUILDDIR)/latex all-pdf @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." text: $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text @echo @echo "Build finished. The text files are in $(BUILDDIR)/text." man: $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man @echo @echo "Build finished. The manual pages are in $(BUILDDIR)/man." changes: $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes @echo @echo "The overview file is in $(BUILDDIR)/changes." linkcheck: $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck @echo @echo "Link check complete; look for any errors in the above output " \ "or in $(BUILDDIR)/linkcheck/output.txt." doctest: $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest @echo "Testing of doctests in the sources finished, look at the " \ "results in $(BUILDDIR)/doctest/output.txt." fabio-0.1.3/doc/make.bat0000644000175000017500000001064112121354612015530 0ustar jeromejerome00000000000000@ECHO OFF REM Command file for Sphinx documentation if "%SPHINXBUILD%" == "" ( set SPHINXBUILD=sphinx-build ) set BUILDDIR=build set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% source if NOT "%PAPER%" == "" ( set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% ) if "%1" == "" goto help if "%1" == "help" ( :help echo.Please use `make ^` where ^ is one of echo. html to make standalone HTML files echo. dirhtml to make HTML files named index.html in directories echo. singlehtml to make a single large HTML file echo. pickle to make pickle files echo. json to make JSON files echo. htmlhelp to make HTML files and a HTML help project echo. qthelp to make HTML files and a qthelp project echo. devhelp to make HTML files and a Devhelp project echo. epub to make an epub echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter echo. text to make text files echo. man to make manual pages echo. changes to make an overview over all changed/added/deprecated items echo. linkcheck to check all external links for integrity echo. doctest to run all doctests embedded in the documentation if enabled goto end ) if "%1" == "clean" ( for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i del /q /s %BUILDDIR%\* goto end ) if "%1" == "html" ( %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html if errorlevel 1 exit /b 1 echo. echo.Build finished. The HTML pages are in %BUILDDIR%/html. goto end ) if "%1" == "dirhtml" ( %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml if errorlevel 1 exit /b 1 echo. echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. goto end ) if "%1" == "singlehtml" ( %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml if errorlevel 1 exit /b 1 echo. echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml. goto end ) if "%1" == "pickle" ( %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle if errorlevel 1 exit /b 1 echo. echo.Build finished; now you can process the pickle files. goto end ) if "%1" == "json" ( %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json if errorlevel 1 exit /b 1 echo. echo.Build finished; now you can process the JSON files. goto end ) if "%1" == "htmlhelp" ( %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp if errorlevel 1 exit /b 1 echo. echo.Build finished; now you can run HTML Help Workshop with the ^ .hhp project file in %BUILDDIR%/htmlhelp. goto end ) if "%1" == "qthelp" ( %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp if errorlevel 1 exit /b 1 echo. echo.Build finished; now you can run "qcollectiongenerator" with the ^ .qhcp project file in %BUILDDIR%/qthelp, like this: echo.^> qcollectiongenerator %BUILDDIR%\qthelp\FabIO.qhcp echo.To view the help file: echo.^> assistant -collectionFile %BUILDDIR%\qthelp\FabIO.ghc goto end ) if "%1" == "devhelp" ( %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp if errorlevel 1 exit /b 1 echo. echo.Build finished. goto end ) if "%1" == "epub" ( %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub if errorlevel 1 exit /b 1 echo. echo.Build finished. The epub file is in %BUILDDIR%/epub. goto end ) if "%1" == "latex" ( %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex if errorlevel 1 exit /b 1 echo. echo.Build finished; the LaTeX files are in %BUILDDIR%/latex. goto end ) if "%1" == "text" ( %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text if errorlevel 1 exit /b 1 echo. echo.Build finished. The text files are in %BUILDDIR%/text. goto end ) if "%1" == "man" ( %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man if errorlevel 1 exit /b 1 echo. echo.Build finished. The manual pages are in %BUILDDIR%/man. goto end ) if "%1" == "changes" ( %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes if errorlevel 1 exit /b 1 echo. echo.The overview file is in %BUILDDIR%/changes. goto end ) if "%1" == "linkcheck" ( %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck if errorlevel 1 exit /b 1 echo. echo.Link check complete; look for any errors in the above output ^ or in %BUILDDIR%/linkcheck/output.txt. goto end ) if "%1" == "doctest" ( %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest if errorlevel 1 exit /b 1 echo. echo.Testing of doctests in the sources finished, look at the ^ results in %BUILDDIR%/doctest/output.txt. goto end ) :end fabio-0.1.3/doc/pdf/0000755000175000017500000000000012233272207014675 5ustar jeromejerome00000000000000fabio-0.1.3/doc/pdf/FabIO.pdf0000644000175000017500000067766412233250060016333 0ustar jeromejerome00000000000000%PDF-1.5 %ÐÔÅØ 2 0 obj << /Type /ObjStm /N 100 /First 804 /Length 1027 /Filter 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FabIO Package¶

fabio Package¶

FabIO module

fabio.fabioimage Module¶

Authors: Henning O. Sorensen & Erik Knudsen

Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk

and Jon Wright, Jerome Kieffer: ESRF

class fabio.fabioimage.fabioimage(data=None, header=None)[source]¶

Bases: object

A common object for images in fable Contains a numpy array (.data) and dict of meta data (.header)

add(other)[source]¶

Add another Image - warning, does not clip to 16 bit images by default

static checkData(data=None)[source]¶

Empty for fabioimage but may be populated by others classes, especially for format accepting only integers

static checkHeader(header=None)[source]¶

Empty for fabioimage but may be populated by others classes

classname¶

Retrieves the name of the class :return: the name of the class

convert(dest)[source]¶

Convert a fabioimage object into another fabioimage object (with possible conversions) :param dest: destination type “EDF”, “edfimage” or the class itself

getclassname()[source]¶

Retrieves the name of the class :return: the name of the class

getframe(num)[source]¶

returns the file numbered ‘num’ in the series as a fabioimage

getheader()[source]¶

returns self.header

getmax()[source]¶

Find max value in self.data, caching for the future

getmean()[source]¶

return the mean

getmin()[source]¶

Find min value in self.data, caching for the future

getstddev()[source]¶

return the standard deviation

integrate_area(coords)[source]¶

Sums up a region of interest if len(coords) == 4 -> convert coords to slices if len(coords) == 2 -> use as slices floor -> ? removed as unused in the function.

load(*arg, **kwarg)[source]¶

Wrapper for read

make_slice(coords)[source]¶

Convert a len(4) set of coords into a len(2) tuple (pair) of slice objects the latter are immutable, meaning the roi can be cached

next()[source]¶

returns the next file in the series as a fabioimage

previous()[source]¶

returns the previous file in the series as a fabioimage

read(filename, frame=None)[source]¶

To be overridden - fill in self.header and self.data

readROI(filename, frame=None, coords=None)[source]¶

Method reading Region of Interest. This implementation is the trivial one, just doing read and crop

readheader(filename)[source]¶

Call the _readheader function...

rebin(x_rebin_fact, y_rebin_fact, keep_I=True)[source]¶

Rebin the data and adjust dims :param x_rebin_fact: x binning factor :param y_rebin_fact: y binning factor :param keep_I: shall the signal increase ? :type x_rebin_fact: int :type y_rebin_fact: int :type keep_I: boolean

resetvals()[source]¶

Reset cache - call on changing data

save(fname)[source]¶

wrapper for write

toPIL16(filename=None)[source]¶

Convert to Python Imaging Library 16 bit greyscale image

FIXME - this should be handled by the libraries now

update_header(**kwds)[source]¶

update the header entries by default pass in a dict of key, values.

write(fname)[source]¶

To be overwritten - write the file

fabio.fabioimage.test()[source]¶

check some basic fabioimage functionality

fabio.fabioutils Module¶

General purpose utilities functions for fabio

class fabio.fabioutils.BZ2File(name, mode='r', buffering=0, compresslevel=9)[source]¶

Bases: bz2.BZ2File

Wrapper with lock

getSize()[source]¶
setSize(value)[source]¶
size¶
class fabio.fabioutils.File(name, mode='rb', buffering=0)[source]¶

Bases: file

wrapper for “file” with locking

getSize()[source]¶
setSize(size)[source]¶
size¶
class fabio.fabioutils.FilenameObject(stem=None, num=None, directory=None, format=None, extension=None, postnum=None, digits=4, filename=None)[source]¶

Bases: object

The ‘meaning’ of a filename ...

deconstruct_filename(filename)[source]¶

Break up a filename to get image type and number

str()[source]¶

Return a string representation

tostring()[source]¶

convert yourself to a string

class fabio.fabioutils.GzipFile(filename=None, mode=None, compresslevel=9, fileobj=None)[source]¶

Bases: gzip.GzipFile

Just a wrapper forgzip.GzipFile providing the correct seek capabilities for python 2.5

class fabio.fabioutils.StringIO(data, fname=None, mode='r')[source]¶

Bases: StringIO.StringIO

just an interface providing the name and mode property to a StringIO

BugFix for MacOSX mainly

getSize()[source]¶
setSize(size)[source]¶
size¶
class fabio.fabioutils.UnknownCompressedFile(name, mode='rb', buffering=0)[source]¶

Bases: fabio.fabioutils.File

wrapper for “File” with locking

fabio.fabioutils.construct_filename(filename, frame=None)[source]¶

Try to construct the filename for a given frame

fabio.fabioutils.deconstruct_filename(filename)[source]¶

Function for backward compatibility. Deprecated

fabio.fabioutils.deprecated(func)[source]¶

used to deprecate a function/method: prints a lot of warning messages to enforce the modifaction of the code

fabio.fabioutils.extract_filenumber(name)[source]¶

extract file number

fabio.fabioutils.getnum(name)[source]¶

# try to figure out a file number # guess it starts at the back

fabio.fabioutils.isAscii(name, listExcluded=None)[source]¶
Parameters:
  • name – string to check
  • listExcluded – list of char or string excluded.
Returns:

True of False whether name is pure ascii or not
fabio.fabioutils.jump_filename(name, num, padding=True)[source]¶

jump to number

fabio.fabioutils.next_filename(name, padding=True)[source]¶

increment number

fabio.fabioutils.nice_int(s)[source]¶

Workaround that int(‘1.0’) raises an exception

Parameters:s – string to be converted to integer
fabio.fabioutils.numstem(name)[source]¶

cant see how to do without reversing strings Match 1 or more digits going backwards from the end of the string

fabio.fabioutils.pad(mystr, pattern=' ', size=80)[source]¶

Performs the padding of the string to the right size with the right pattern

fabio.fabioutils.previous_filename(name, padding=True)[source]¶

decrement number

fabio.fabioutils.toAscii(name, excluded=None)[source]¶
Parameters:
  • name – string to check
  • excluded – tuple of char or string excluded (not list: they are mutable).
Returns:

the name with all non valid char removed

fabio.file_series Module¶

Authors:¶

  • Henning O. Sorensen & Erik Knudsen Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk
  • Jon Wright, ESRF
class fabio.file_series.file_series(list_of_strings)[source]¶

Bases: list

Represents a series of files to iterate has an idea of a current position to do next and prev

You also get from the list python superclass:
append count extend insert pop remove reverse sort
current()[source]¶

Current position in a sequence

current_image()[source]¶

Current image in sequence

Returns:fabioimage
current_object()[source]¶

Current image in sequence

Returns:file_object
first()[source]¶

First image in series

first_image()[source]¶

First image in a sequence

Returns:fabioimage
first_object()[source]¶

First image in a sequence

Returns:file_object
jump(num)[source]¶

Goto a position in sequence

jump_image(num)[source]¶

Jump to and read image

Returns:fabioimage
jump_object(num)[source]¶

Jump to and read image

Returns:file_object
last()[source]¶

Last in series

last_image()[source]¶

Last image in a sequence

Returns:fabioimage
last_object()[source]¶

Last image in a sequence

Returns:file_object
len()[source]¶

Number of files

next()[source]¶

Next in a sequence

next_image()[source]¶

Return the next image

Returns:fabioimage
next_object()[source]¶

Return the next image

Returns:file_object
previous()[source]¶

Prev in a sequence

previous_image()[source]¶

Return the previous image

Returns:fabioimage
previous_object()[source]¶

Return the previous image

Returns:file_object
class fabio.file_series.filename_series(filename)[source]¶

Much like the others, but created from a string filename

current()[source]¶

return current filename string

current_image()[source]¶

returns the current image as a fabioimage

current_object()[source]¶

returns the current filename as a fabio.FilenameObject

jump(num)[source]¶

jump to a specific number

jump_image(num)[source]¶

returns the image number as a fabioimage

jump_object(num)[source]¶

returns the filename num as a fabio.FilenameObject

next()[source]¶

increment number

next_image()[source]¶

returns the next image as a fabioimage

next_object()[source]¶

returns the next filename as a fabio.FilenameObject

prev_image()[source]¶

returns the previos image as a fabioimage

previous()[source]¶

decrement number

previous_object()[source]¶

returns the previous filename as a fabio.FilenameObject

fabio.file_series.new_file_series(first_object, nimages=0, step=1, traceback=False)[source]¶

A generator function that creates a file series starting from a a fabioimage. Iterates through all images in a file (if more than 1), then proceeds to the next file as determined by fabio.next_filename.

Parameters:
  • first_object – the starting fabioimage, which will be the first one yielded in the sequence
  • nimages – the maximum number of images to consider step: step size, will yield the first and every step’th image until nimages is reached. (e.g. nimages = 5, step = 2 will yield 3 images (0, 2, 4)
  • traceback – if True causes it to print a traceback in the event of an exception (missing image, etc.). Otherwise the calling routine can handle the exception as it chooses
  • yields – the next fabioimage in the series. In the event there is an exception, it yields the sys.exec_info for the exception instead. sys.exec_info is a tuple: ( exceptionType, exceptionValue, exceptionTraceback ) from which all the exception information can be obtained.

Suggested usage:

for obj in new_file_series( ... ):
  if not isinstance(obj, fabio.fabioimage.fabioimage ):
    # deal with errors like missing images, non readable files, etc
    # e.g.
    traceback.print_exception(obj[0], obj[1], obj[2])
fabio.file_series.new_file_series0(first_object, first=None, last=None, step=1)[source]¶

Created from a fabio image first and last are file numbers

class fabio.file_series.numbered_file_series(stem, first, last, extension, digits=4, padding='Y', step=1)[source]¶

Bases: fabio.file_series.file_series

mydata0001.edf = “mydata” + 0001 + ”.edf” mydata0002.edf = “mydata” + 0002 + ”.edf” mydata0003.edf = “mydata” + 0003 + ”.edf”

fabio.openimage Module¶

Authors: Henning O. Sorensen & Erik Knudsen
Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:henning.sorensen@risoe.dk

mods for fabio by JPW

fabio.openimage.do_magic(byts)[source]¶

Try to interpret the bytes starting the file as a magic number

fabio.openimage.openheader(filename)[source]¶

return only the header

fabio.openimage.openimage(filename, frame=None)[source]¶

Try to open an image

fabio.adscimage Module¶

Authors: Henning O. Sorensen & Erik Knudsen
Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk
  • mods for fabio by JPW
class fabio.adscimage.adscimage(*args, **kwargs)[source]¶

Bases: fabio.fabioimage.fabioimage

Read an image in ADSC format (quite similar to edf?)

read(fname, frame=None)[source]¶

read in the file

write(fname)[source]¶

Write adsc format

fabio.adscimage.test()[source]¶

testcase

fabio.binaryimage Module¶

Authors: Gael Goret, Jerome Kieffer, ESRF, France Emails: gael.goret@esrf.fr, jerome.kieffer@esrf.fr

Brian Richard Pauw <brian@stack.nl>

Binary files images are simple none-compressed 2D images only defined by their : data-type, dimensions, byte order and offset

This simple library has been made for manipulating exotic/unknown files format.

class fabio.binaryimage.binaryimage(*args, **kwargs)[source]¶

Bases: fabio.fabioimage.fabioimage

This simple library has been made for manipulating exotic/unknown files format.

Binary files images are simple none-compressed 2D images only defined by their : data-type, dimensions, byte order and offset

if offset is set to a negative value, the image is read using the last data but n data in the file, skipping any header.

estimate_offset_value(fname, dim1, dim2, bytecode='int32')[source]¶

Estimates the size of a file

read(fname, dim1, dim2, offset=0, bytecode='int32', endian='<')[source]¶

Read a binary image

Parameters:
  • fname (string) – file name
  • dim1 – image dimensions (Fast index)
  • dim2 – image dimensions (Slow index)
  • offset – starting position of the data-block. If negative, starts at the end.
  • bytecode – can be “int8”,”int16”,”int32”,”int64”,”uint8”,”uint16”,”uint32”,”uint64”,”float32”,”float64”,...
  • endian – among short or long endian (“<” or “>”)
static swap_needed(endian)[source]¶

Decide if we need to byteswap

write(fname)[source]¶

fabio.bruker100image Module¶

class fabio.bruker100image.bruker100image(data=None, header=None)[source]¶

Bases: fabio.brukerimage.brukerimage

read(fname, frame=None)[source]¶
toPIL16(filename=None)[source]¶

fabio.brukerimage Module¶

Authors: Henning O. Sorensen & Erik Knudsen
Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk
Based on: openbruker,readbruker, readbrukerheader functions in the opendata
module of ImageD11 written by Jon Wright, ESRF, Grenoble, France

Writer by Jérôme Kieffer, ESRF, Grenoble, France

class fabio.brukerimage.brukerimage(data=None, header=None)[source]¶

Bases: fabio.fabioimage.fabioimage

Read and eventually write ID11 bruker (eg smart6500) images

TODO: int32 -> float32 conversion according to the “linear” keyword. This is done and works but we need to check with other program that we are appliing the right formula and not the reciprocal one.

HEADERS_KEYS = ['FORMAT', 'VERSION', 'HDRBLKS', 'TYPE', 'SITE', 'MODEL', 'USER', 'SAMPLE', 'SETNAME', 'RUN', 'SAMPNUM', 'TITLE', 'NCOUNTS', 'NOVERFL', 'MINIMUM', 'MAXIMUM', 'NONTIME', 'NLATE', 'FILENAM', 'CREATED', 'CUMULAT', 'ELAPSDR', 'ELAPSDA', 'OSCILLA', 'NSTEPS', 'RANGE', 'START', 'INCREME', 'NUMBER', 'NFRAMES', 'ANGLES', 'NOVER64', 'NPIXELB', 'NROWS', 'NCOLS', 'WORDORD', 'LONGORD', 'TARGET', 'SOURCEK', 'SOURCEM', 'FILTER', 'CELL', 'MATRIX', 'LOWTEMP', 'TEMP', 'HITEMP', 'ZOOM', 'CENTER', 'DISTANC', 'TRAILER', 'COMPRES', 'LINEAR', 'PHD', 'PREAMP', 'CORRECT', 'WARPFIL', 'WAVELEN', 'MAXXY', 'AXIS', 'ENDING', 'DETPAR', 'LUT', 'DISPLIM', 'PROGRAM', 'ROTATE', 'BITMASK', 'OCTMASK', 'ESDCELL', 'DETTYPE', 'NEXP', 'CCDPARM', 'BIS', 'CHEM', 'MORPH', 'CCOLOR', 'CSIZE', 'DNSMET', 'DARK', 'AUTORNG', 'ZEROADJ', 'XTRANS', 'HKL&XY', 'AXES2', 'ENDING2', 'FILTER2', 'LEPTOS', 'CFR']¶
SPACER = '\x1a\x04'¶
basic_translate(fname=None)[source]¶

Does some basic population of the headers so that the writing is possible

bpp_to_numpy = {1: <type 'numpy.uint8'>, 2: <type 'numpy.uint16'>, 4: <type 'numpy.uint32'>}¶
calc_bpp(data=None, max_entry=4096)[source]¶

Calculate the number of byte per pixel to get an optimal overflow table.

Returns:byte per pixel
gen_header()[source]¶

Generate headers (with some magic and guesses) :param format can be 86 or 100

gen_overflow()[source]¶

Generate an overflow table

read(fname, frame=None)[source]¶

Read in and unpack the pixels (including overflow table

write(fname)[source]¶

Write a bruker image

fabio.brukerimage.test()[source]¶

a testcase

fabio.cbfimage Module¶

Authors: Jérôme Kieffer, ESRF
email:jerome.kieffer@esrf.fr

Cif Binary Files images are 2D images written by the Pilatus detector and others. They use a modified (simplified) byte-offset algorithm.

CIF is a library for manipulating Crystallographic information files and tries to conform to the specification of the IUCR

class fabio.cbfimage.CIF(_strFilename=None)[source]¶

Bases: dict

This is the CIF class, it represents the CIF dictionary; and as a a python dictionary thus inherits from the dict built in class.

BINARY_MARKER = '--CIF-BINARY-FORMAT-SECTION--'¶
BLANK = [' ', '\t', '\r', '\n', '\r\n', '\n\r']¶
EOL = ['\r', '\n', '\r\n', '\n\r']¶
static LoopHasKey(loop, key)[source]¶

Returns True if the key (string) exist in the array called loop

START_COMMENT = ['"', "'"]¶
exists(sKey)[source]¶

Check if the key exists in the CIF and is non empty. :param sKey: CIF key :type sKey: string :param cif: CIF dictionary :return: True if the key exists in the CIF dictionary and is non empty :rtype: boolean

existsInLoop(sKey)[source]¶

Check if the key exists in the CIF dictionary. :param sKey: CIF key :type sKey: string :param cif: CIF dictionary :return: True if the key exists in the CIF dictionary and is non empty :rtype: boolean

static isAscii(_strIn)[source]¶

Check if all characters in a string are ascii,

Parameters:_strIn (python string) – input string
Returns:boolean
Return type:boolean
loadCHIPLOT(_strFilename)[source]¶

Load the powder diffraction CHIPLOT file and returns the pd_CIF dictionary in the object

Parameters:_strFilename (string) – the name of the file to open
Returns:the CIF object corresponding to the powder diffraction
Return type:dictionary
loadCIF(_strFilename, _bKeepComment=False)[source]¶

Load the CIF file and populates the CIF dictionary into the object :param _strFilename: the name of the file to open :type _strFilename: string :param _strFilename: the name of the file to open :type _strFilename: string :return: None

pop(key)[source]¶
popitem(key)[source]¶
readCIF(_strFilename, _bKeepComment=False)¶

Load the CIF file and populates the CIF dictionary into the object :param _strFilename: the name of the file to open :type _strFilename: string :param _strFilename: the name of the file to open :type _strFilename: string :return: None

saveCIF(_strFilename='test.cif', linesep='n', binary=False)[source]¶

Transforms the CIF object in string then write it into the given file :param _strFilename: the of the file to be written :param linesep: line separation used (to force compatibility with windows/unix) :param binary: Shall we write the data as binary (True only for imageCIF/CBF) :type param: string

tostring(_strFilename=None, linesep='n')[source]¶

Converts a cif dictionnary to a string according to the CIF syntax

Parameters:_strFilename (string) – the name of the filename to be appended in the header of the CIF file
Returns:a sting that corresponds to the content of the CIF - file.
class fabio.cbfimage.cbfimage(data=None, header=None, fname=None)[source]¶

Bases: fabio.fabioimage.fabioimage

Read the Cif Binary File data format

static checkData(data=None)[source]¶
read(fname, frame=None)[source]¶

Read in header into self.header and the data into self.data

write(fname)[source]¶

write the file in CBF format :param fname: name of the file :type: string

fabio.dm3image Module¶

Authors: Henning O. Sorensen & Erik Knudsen
Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk
  • Jon Wright, ESRF
class fabio.dm3image.dm3image(*args, **kwargs)[source]¶

Bases: fabio.fabioimage.fabioimage

Read and try to write the dm3 data format

read(fname, frame=None)[source]¶
read_data()[source]¶
read_tag_entry()[source]¶
read_tag_group()[source]¶
read_tag_type()[source]¶
readbytes(bytes_to_read, format, swap=True)[source]¶

fabio.edfimage Module¶

License: GPLv2+

Authors:¶

  • Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions; Risoe National Laboratory; Frederiksborgvej 399; DK-4000 Roskilde; email:erik.knudsen@risoe.dk
  • Jon Wright & Jérôme Kieffer: European Synchrotron Radiation Facility; Grenoble (France)
class fabio.edfimage.Frame(data=None, header=None, header_keys=None, number=None)[source]¶

Bases: object

A class representing a single frame in an EDF file

bytecode¶
data¶

Unpack a binary blob according to the specification given in the header

Returns:dataset as numpy.ndarray
getByteCode()[source]¶
getData()[source]¶

Unpack a binary blob according to the specification given in the header

Returns:dataset as numpy.ndarray
getEdfBlock(force_type=None, fit2dMode=False)[source]¶
Parameters:
  • force_type (string or numpy.dtype) – type of the dataset to be enforced like “float64” or “uint16”
  • fit2dMode (boolean) – enforce compatibility with fit2d and starts countimg number of images at 1
Returns:

ascii header block
Return type:

python string with the concatenation of the ascii header and the binary data block
parseheader(block)[source]¶

Parse the header in some EDF format from an already open file

Parameters:block (string, should be full ascii) – string representing the header block
Returns:size of the binary blob
setByteCode(_iVal)[source]¶
setData(npa=None)[source]¶

Setter for data in edf frame

swap_needed()[source]¶

Decide if we need to byteswap

class fabio.edfimage.edfimage(data=None, header=None, header_keys=None, frames=None)[source]¶

Bases: fabio.fabioimage.fabioimage

Read and try to write the ESRF edf data format

appendFrame(frame=None, data=None, header=None)[source]¶

Method used add a frame to an EDF file :param frame: frame to append to edf image :type frame: instance of Frame :return: None

bpp¶
bytecode¶
capsHeader¶

property: capsHeader of EDF file, i.e. the keys of the header in UPPER case.

static checkHeader(header=None)[source]¶

Empty for fabioimage but may be populated by others classes

data¶

property: data of EDF file

delCapsHeader()[source]¶

deleter for edf capsHeader

delData()[source]¶

deleter for edf Data

delHeader()[source]¶

Deleter for edf header

delHeaderKeys()[source]¶

Deleter for edf header_keys

deleteFrame(frameNb=None)[source]¶

Method used to remove a frame from an EDF image. by default the last one is removed. :param frameNb: frame number to remove, by default the last. :type frameNb: integer :return: None

dim1¶
dim2¶
dims¶
fastReadData(filename=None)[source]¶

This is a special method that will read and return the data from another file ... The aim is performances, ... but only supports uncompressed files.

Returns:data from another file using positions from current edfimage
fastReadROI(filename, coords=None)[source]¶

Method reading Region of Interest of another file based on metadata available in current edfimage. The aim is performances, ... but only supports uncompressed files.

Returns:ROI-data from another file using positions from current edfimage
Return type:numpy 2darray
getBpp()[source]¶
getByteCode()[source]¶
getCapsHeader()[source]¶

getter for edf headers keys in upper case :return: data for current frame :rtype: dict

getData()[source]¶

getter for edf Data :return: data for current frame :rtype: numpy.ndarray

getDim1()[source]¶
getDim2()[source]¶
getDims()[source]¶
getHeader()[source]¶

Getter for the headers. used by the property header,

getHeaderKeys()[source]¶

Getter for edf header_keys

getNbFrames()[source]¶

Getter for number of frames

getframe(num)[source]¶

returns the file numbered ‘num’ in the series as a fabioimage

header¶

property: header of EDF file

header_keys¶

property: header_keys of EDF file

next()[source]¶

returns the next file in the series as a fabioimage

nframes¶

Getter for number of frames

previous()[source]¶

returns the previous file in the series as a fabioimage

read(fname, frame=None)[source]¶

Read in header into self.header and the data into self.data

setBpp(_iVal)[source]¶
setByteCode(_iVal)[source]¶
setCapsHeader(_data)[source]¶

Enforces the propagation of the header_keys to the list of frames :param _data: numpy array representing data

setData(_data)[source]¶

Enforces the propagation of the data to the list of frames :param _data: numpy array representing data

setDim1(_iVal)[source]¶
setDim2(_iVal)[source]¶
setHeader(_dictHeader)[source]¶

Enforces the propagation of the header to the list of frames

setHeaderKeys(_listtHeader)[source]¶

Enforces the propagation of the header_keys to the list of frames :param _listtHeader: list of the (ordered) keys in the header :type _listtHeader: python list

setNbFrames(val)[source]¶

Setter for number of frames ... should do nothing. Here just to avoid bugs

swap_needed()[source]¶

Decide if we need to byteswap

unpack()[source]¶

Unpack a binary blob according to the specification given in the header and return the dataset

Returns:dataset as numpy.ndarray
write(fname, force_type=None, fit2dMode=False)[source]¶

Try to write a file check we can write zipped also mimics that fabian was writing uint16 (we sometimes want floats)

Parameters:force_type – can be numpy.uint16 or simply “float”
Returns:None

fabio.fit2dmaskimage Module¶

Author: Andy Hammersley, ESRF Translation into python/fabio: Jon Wright, ESRF

class fabio.fit2dmaskimage.fit2dmaskimage(data=None, header=None)[source]¶

Bases: fabio.fabioimage.fabioimage

Read and try to write Andy Hammersley’s mask format

static checkData(data=None)[source]¶
read(fname, frame=None)[source]¶

Read in header into self.header and the data into self.data

write(fname)[source]¶

Try to write a file check we can write zipped also mimics that fabian was writing uint16 (we sometimes want floats)

fabio.fit2dspreadsheetimage Module¶

Read the fit2d ascii image output
  • Jon Wright, ESRF
class fabio.fit2dspreadsheetimage.fit2dspreadsheetimage(data=None, header=None)[source]¶

Bases: fabio.fabioimage.fabioimage

Read a fit2d ascii format

read(fname, frame=None)[source]¶

Read in header into self.header and the data into self.data

fabio.GEimage Module¶

class fabio.GEimage.GEimage(data=None, header=None)[source]¶

Bases: fabio.fabioimage.fabioimage

getframe(num)[source]¶

Returns a frame as a new fabioimage object

next()[source]¶

Get the next image in a series as a fabio image

previous()[source]¶

Get the previous image in a series as a fabio image

read(fname, frame=None)[source]¶

Read in header into self.header and the data into self.data

write(fname, force_type=<type 'numpy.uint16'>)[source]¶

Not yet implemented

fabio.GEimage.demo()[source]¶

fabio.HiPiCimage Module¶

Authors: Henning O. Sorensen & Erik Knudsen
Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk
  • Jon Wright, ESRF

Information about the file format from Masakatzu Kobayashi is highly appreciated

class fabio.HiPiCimage.HiPiCimage(data=None, header=None)[source]¶

Bases: fabio.fabioimage.fabioimage

Read HiPic images e.g. collected with a Hamamatsu CCD camera

read(fname, frame=None)[source]¶

Read in header into self.header and the data into self.data

fabio.kcdimage Module¶

Authors: Jerome Kieffer, ESRF
email:jerome.kieffer@esrf.fr

kcd images are 2D images written by the old KappaCCD diffractometer built by Nonius in the 1990’s Based on the edfimage.py parser.

class fabio.kcdimage.kcdimage(data=None, header=None)[source]¶

Bases: fabio.fabioimage.fabioimage

Read the Nonius kcd data format

static checkData(data=None)[source]¶
read(fname, frame=None)[source]¶

Read in header into self.header and the data into self.data

fabio.mar345image Module¶

Authors:¶

  • Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions; Risoe National Laboratory; Frederiksborgvej 399; DK-4000 Roskilde; email:erik.knudsen@risoe.dk
  • Jon Wright, Jérôme Kieffer & Gaël Goret: European Synchrotron Radiation Facility; Grenoble (France)
class fabio.mar345image.mar345image(*args, **kwargs)[source]¶

Bases: fabio.fabioimage.fabioimage

static checkData(data=None)[source]¶
nb_overflow_pixels()[source]¶
read(fname, frame=None)[source]¶

Read a mar345 image

write(fname)[source]¶

Try to write mar345 file. This is still in beta version. It uses CCP4 (LGPL) PCK1 algo from JPA

fabio.marccdimage Module¶

Authors:¶

  • Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions; Risoe National Laboratory; Frederiksborgvej 399; DK-4000 Roskilde; email:erik.knudsen@risoe.dk
  • Jon Wright: European Synchrotron Radiation Facility; Grenoble (France)

marccdimage can read MarCCD and MarMosaic images including header info.

JPW : Use a parser in case of typos (sorry?)

fabio.marccdimage.interpret_header(header, fmt, names)[source]¶

given a format and header interpret it

fabio.marccdimage.make_format(c_def_string)[source]¶

Reads the header definition in c and makes the format string to pass to struct.unpack

class fabio.marccdimage.marccdimage(*args, **kwds)[source]¶

Bases: fabio.tifimage.tifimage

Read in data in mar ccd format, also MarMosaic images, including header info

fabio.OXDimage Module¶

Reads Oxford Diffraction Sapphire 3 images

Authors:¶

  • Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions; Risoe National Laboratory; Frederiksborgvej 399; DK-4000 Roskilde; email:erik.knudsen@risoe.dk
  • Jon Wright, Jérôme Kieffer & Gaël Goret: European Synchrotron Radiation Facility; Grenoble (France)
class fabio.OXDimage.OXDimage(data=None, header=None)[source]¶

Bases: fabio.fabioimage.fabioimage

Oxford Diffraction Sapphire 3 images reader/writer class

static checkData(data=None)[source]¶
getCompressionRatio()[source]¶

calculate the compression factor obtained vs raw data

read(fname, frame=None)[source]¶

Read in header into self.header and the data into self.data

write(fname)[source]¶

Write Oxford diffraction images: this is still beta :param fname: output filename

class fabio.OXDimage.Section(size, dictHeader)[source]¶

Bases: object

Small helper class for writing binary headers

getSize(dtype)[source]¶
setData(key, offset, dtype, default=None)[source]¶
Parameters:
  • offset – int, starting position in the section
  • key – name of the header key
  • dtype – type of the data to insert (defines the size!)

fabio.pilatusimage Module¶

Authors:¶

  • Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions; Risoe National Laboratory; Frederiksborgvej 399; DK-4000 Roskilde; email:erik.knudsen@risoe.dk
  • Jon Wright: European Synchrotron Radiation Facility; Grenoble (France)
class fabio.pilatusimage.pilatusimage(*args, **kwds)[source]¶

Bases: fabio.tifimage.tifimage

Read in Pilatus format, also pilatus images, including header info

fabio.pnmimage Module¶

Authors: Henning O. Sorensen & Erik Knudsen
Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:henning.sorensen@risoe.dk
class fabio.pnmimage.pnmimage(*arg, **kwargs)[source]¶

Bases: fabio.fabioimage.fabioimage

static P1dec(buf, bytecode)[source]¶
static P2dec(buf, bytecode)[source]¶
static P3dec(buf, bytecode)[source]¶
static P4dec(buf, bytecode)[source]¶
static P5dec(buf, bytecode)[source]¶
static P6dec(buf, bytecode)[source]¶
static P7dec(buf, bytecode)[source]¶
static checkData(data=None)[source]¶
read(fname, frame=None)[source]¶

try to read PNM images :param fname: name of the file :param frame: not relevant here! PNM is always single framed

write(filename)[source]¶

fabio.tifimage Module¶

FabIO class for dealing with TIFF images. In facts wraps TiffIO from V. Armando Solé (available in PyMca) or falls back to PIL

Authors:¶

  • Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions; Risoe National Laboratory; Frederiksborgvej 399; DK-4000 Roskilde; email:erik.knudsen@risoe.dk
  • Jérôme Kieffer: European Synchrotron Radiation Facility; Grenoble (France)

License: GPLv3+

class fabio.tifimage.Image_File_Directory(instring=None, offset=-1)[source]¶

Bases: object

unpack(instring, offset=-1)[source]¶
class fabio.tifimage.Image_File_Directory_entry(tag=0, tag_type=0, count=0, offset=0)[source]¶

Bases: object

extract_data(full_string)[source]¶
unpack(strInput)[source]¶
class fabio.tifimage.Tiff_header(string)[source]¶

Bases: object

class fabio.tifimage.tifimage(*args, **kwds)[source]¶

Bases: fabio.fabioimage.fabioimage

Images in TIF format Wraps TiffIO

read(fname, frame=None)[source]¶

Wrapper for TiffIO.

write(fname)[source]¶

Overrides the fabioimage.write method and provides a simple TIFF image writer. :param fname: name of the file to save the image to @tag_type fname: string or unicode (file?)...

fabio.xsdimage Module¶

Authors: Jérôme Kieffer, ESRF
email:jerome.kieffer@esrf.fr

XSDimge are XML files containing numpy arrays

class fabio.xsdimage.xsdimage(data=None, header=None, fname=None)[source]¶

Bases: fabio.fabioimage.fabioimage

Read the XSDataImage XML File data format

read(fname, frame=None)[source]¶

fabio.compression Module¶

Authors: Jérôme Kieffer, ESRF
email:jerome.kieffer@esrf.fr

FabIO library containing compression and decompression algorithm for various

fabio.compression.compByteOffet_numpy(data)[source]¶

Compress a dataset into a string using the byte_offet algorithm

Parameters:data – ndarray
Returns:string/bytes with compressed data

test = numpy.array([0,1,2,127,0,1,2,128,0,1,2,32767,0,1,2,32768,0,1,2,2147483647,0,1,2,2147483648,0,1,2,128,129,130,32767,32768,128,129,130,32768,2147483647,2147483648])

fabio.compression.compPCK(data)[source]¶

Modified CCP4 pck compressor used in MAR345 images

Parameters:data – numpy.ndarray (square array)
Returns:compressed stream
fabio.compression.compTY1(data)[source]¶

Modified byte offset compressor used in Oxford Diffraction images

Parameters:data – numpy.ndarray with the input data (integers!)
Returns:3-tuple of strings: raw_8,raw_16,raw_32 containing raw data with integer of the given size
fabio.compression.decByteOffet_cython(stream, size=None)[source]¶
Analyze a stream of char with any length of exception:
2, 4, or 8 bytes integers
Parameters:
  • stream – string representing the compressed data
  • size – the size of the output array (of longInts)
Returns:

1D-ndarray
fabio.compression.decByteOffet_numpy(stream, size=None)[source]¶
Analyze a stream of char with any length of exception:
2, 4, or 8 bytes integers
Parameters:
  • stream – string representing the compressed data
  • size – the size of the output array (of longInts)
Returns:

1D-ndarray
fabio.compression.decByteOffet_python(stream, size)[source]¶

Analyze a stream of char with any length of exception (2,4, or 8 bytes integers)

Parameters:
  • stream – string representing the compressed data
  • size – the size of the output array (of longInts)
Returns:

1D-ndarray
fabio.compression.decByteOffet_weave(stream, size)[source]¶

Analyze a stream of char with any length of exception (2,4, or 8 bytes integers)

Parameters:
  • stream – string representing the compressed data
  • size – the size of the output array (of longInts)
Returns:

1D-ndarray
fabio.compression.decBzip2(stream)[source]¶

Decompress a chunk of data using the bzip2 algorithm from Python

fabio.compression.decGzip(stream)[source]¶

Decompress a chunk of data using the gzip algorithm from Python or alternatives if possible

fabio.compression.decKM4CCD(raw_8, raw_16=None, raw_32=None)¶

Modified byte offset decompressor used in Oxford Diffraction images

Parameters:
  • raw_8 – strings containing raw data with integer 8 bits
  • raw_16 – strings containing raw data with integer 16 bits
  • raw_32 – strings containing raw data with integer 32 bits
Returns:

numpy.ndarray
fabio.compression.decPCK(stream, dim1=None, dim2=None, overflowPix=None, version=None)[source]¶

Modified CCP4 pck decompressor used in MAR345 images

Parameters:stream – string or file
Returns:numpy.ndarray (square array)
fabio.compression.decTY1(raw_8, raw_16=None, raw_32=None)[source]¶

Modified byte offset decompressor used in Oxford Diffraction images

Parameters:
  • raw_8 – strings containing raw data with integer 8 bits
  • raw_16 – strings containing raw data with integer 16 bits
  • raw_32 – strings containing raw data with integer 32 bits
Returns:

numpy.ndarray
fabio.compression.decZlib(stream)[source]¶

Decompress a chunk of data using the zlib algorithm from Python

fabio.compression.endianness()[source]¶

Return the native endianness of the system

fabio.compression.md5sum(blob)[source]¶

returns the md5sum of an object...

fabio.converters Module¶

Converter module. This is for the moment empty (populated only with almost pass through anonymous functions) but aims to be populated with more sofisticated translators ...

fabio.converters.convert_data(inp, outp, data)[source]¶

Return data converted to the output format ... over-simplistic implementation for the moment ... :param inp,outp: input/output format like “cbfimage” :param data(ndarray): the actual dataset to be transformed

fabio.converters.convert_data_integer(data)[source]¶

convert data to integer

fabio.converters.convert_header(inp, outp, header)[source]¶

return header converted to the output format :param inp,outp: input/output format like “cbfimage” :param header(dict):the actual set of headers to be transformed

fabio.datIO Module¶

Authors: Henning O. Sorensen & Erik Knudsen

Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk

and Jon Wright, ESRF

class fabio.datIO.columnfile(data=None, clabels=None, rlabels=None, fname=None)[source]¶

Bases: fabio.datIO.fabiodata

Concrete fabiodata class

read(fname, frame=None)[source]¶
class fabio.datIO.fabiodata(data=None, clabels=None, rlabels=None, fname=None)[source]¶

Bases: object

A common class for dataIO in fable Contains a 2d numpy array for keeping data, and two lists (clabels and rlabels) containing labels for columns and rows respectively

read(fname=None, frame=None)[source]¶

To be overridden by format specific subclasses

fabio.TiffIO Module¶

class fabio.TiffIO.TiffIO(filename, mode=None, cache_length=20, mono_output=False)[source]¶

Bases: object

getData(nImage, **kw)[source]¶
getImage(nImage)[source]¶
getImageFileDirectories(fd=None)[source]¶
getInfo(nImage, **kw)[source]¶
getNumberOfImages()[source]¶
writeImage(image0, info=None, software=None, date=None)[source]¶

fabio.readbytestream Module¶

Reads a bytestream

Authors: Jon Wright Henning O. Sorensen & Erik Knudsen
ESRF Risoe National Laboratory
fabio.readbytestream.readbytestream(fil, offset, x, y, nbytespp, datatype='int', signed='n', swap='n', typeout=<type 'numpy.uint16'>)[source]¶

Reads in a bytestream from a file (which may be a string indicating a filename, or an already opened file (should be “rb”)) offset is the position (in bytes) where the pixel data start nbytespp = number of bytes per pixel type can be int or float (4 bytes pp) or double (8 bytes pp) signed: normally signed data ‘y’, but ‘n’ to try to get back the right numbers when unsigned data are converted to signed (python once had no unsigned numeric types.) swap, normally do not bother, but ‘y’ to swap bytes typeout is the numpy type to output, normally uint16, but more if overflows occurred x and y are the pixel dimensions

TODO : Read in regions of interest

PLEASE LEAVE THE STRANGE INTERFACE ALONE - IT IS USEFUL FOR THE BRUKER FORMAT

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Source code for fabio.HiPiCimage

#!/usr/bin/env python
"""
Authors: Henning O. Sorensen & Erik Knudsen
         Center for Fundamental Research: Metal Structures in Four Dimensions
         Risoe National Laboratory
         Frederiksborgvej 399
         DK-4000 Roskilde
         email:erik.knudsen@risoe.dk

        + Jon Wright, ESRF

Information about the file format from Masakatzu Kobayashi is highly appreciated
"""

import numpy, logging
logger = logging.getLogger("HiPiCimage")
from fabioimage import fabioimage

class HiPiCimage(fabioimage):

[docs]    """ Read HiPic images e.g. collected with a Hamamatsu CCD camera"""


    def _readheader(self, infile):
        """
        Read in a header from an already open file

        """
        Image_tag = infile.read(2)
        print Image_tag
        Comment_len = numpy.fromstring(infile.read(2), numpy.uint16)
        Dim_1 = numpy.fromstring(infile.read(2), numpy.uint16)[0]
        Dim_2 = numpy.fromstring(infile.read(2), numpy.uint16)[0]
        Dim_1_offset = numpy.fromstring(infile.read(2), numpy.uint16)[0]
        Dim_2_offset = numpy.fromstring(infile.read(2), numpy.uint16)[0]
        HeaderType = numpy.fromstring(infile.read(2), numpy.uint16)[0]
        Dump = infile.read(50)
        Comment = infile.read(Comment_len)
        self.header['Image_tag'] = Image_tag
        self.header['Dim_1'] = Dim_1
        self.header['Dim_2'] = Dim_2
        self.header['Dim_1_offset'] = Dim_1_offset
        self.header['Dim_2_offset'] = Dim_2_offset
        #self.header['Comment'] = Comment
        if Image_tag != 'IM' :
            # This does not look like an HiPic file
            logging.warning("no opening.  Corrupt header of HiPic file " + \
                            str(infile.name))
        Comment_split = Comment[:Comment.find('\x00')].split('\r\n')

        for topcomment in Comment_split:
            topsplit = topcomment.split(',')
            for line in topsplit:
                if '=' in line:
                    key, val = line.split('=' , 1)
                    # Users cannot type in significant whitespace
                    key = key.rstrip().lstrip()
                    self.header_keys.append(key)
                    self.header[key] = val.lstrip().rstrip()
                    self.header[key] = val.lstrip('"').rstrip('"')

    def read(self, fname, frame=None):

[docs]        """
        Read in header into self.header and
            the data   into self.data
        """
        self.header = {}
        self.resetvals()
        infile = self._open(fname, "rb")
        self._readheader(infile)
        # Compute image size
        try:
            self.dim1 = int(self.header['Dim_1'])
            self.dim2 = int(self.header['Dim_2'])
        except:
            raise Exception("HiPic file", str(fname) + \
                                "is corrupt, cannot read it")
        bytecode = numpy.uint16
        self.bpp = len(numpy.array(0, bytecode).tostring())

        # Read image data
        block = infile.read(self.dim1 * self.dim2 * self.bpp)
        infile.close()

        #now read the data into the array
        try:
            self.data = numpy.reshape(
                numpy.fromstring(block, bytecode),
                [self.dim2, self.dim1])
        except:
            print len(block), bytecode, self.bpp, self.dim2, self.dim1
            raise IOError, \
              'Size spec in HiPic-header does not match size of image data field'
        self.bytecode = self.data.dtype.type

        # Sometimes these files are not saved as 12 bit,
        # But as 16 bit after bg subtraction - which results 
        # negative values saved as 16bit. Therefore values higher 
        # 4095 is really negative values
        if self.data.max() > 4095:
            gt12bit = self.data > 4095
            self.data = self.data - gt12bit * (2 ** 16 - 1)

        # ensure the PIL image is reset
        self.pilimage = None
        return self

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Source code for fabio.kcdimage

#!/usr/bin/env python
"""
Authors: Jerome Kieffer, ESRF 
         email:jerome.kieffer@esrf.fr

kcd images are 2D images written by the old KappaCCD diffractometer built by Nonius in the 1990's
Based on the edfimage.py parser.
"""

import numpy, logging
import os, string
from fabioimage import fabioimage
logger = logging.getLogger("kcdimage")

DATA_TYPES = {"u16"  :  numpy.uint16 }

MINIMUM_KEYS = [
                'ByteOrder',
                'Data type',
                'X dimension',
                'Y dimension',
                'Number of readouts']

DEFAULT_VALUES = { "Data type": "u16" }





[docs]class kcdimage(fabioimage):
    """ 
    Read the Nonius kcd data format """


    def _readheader(self, infile):
        """
        Read in a header in some KCD format from an already open file
        @
        """
        oneLine = infile.readline()
        alphanum = string.digits + string.letters + ". "
        asciiHeader = True
        for oneChar in oneLine.strip():
            if not oneChar in alphanum:
                asciiHeader = False


        if asciiHeader is False:
            # This does not look like an edf file
            logger.warning("First line of %s does not seam to be ascii text!" % infile.name)
        endOfHeaders = False
        while not endOfHeaders:
            oneLine = infile.readline()
            if len(oneLine) > 100:
                endOfHeaders = True
                break
            if oneLine.strip() == "Binned mode":
                oneLine = "Mode = Binned"
            try:
                key, val = oneLine.split('=' , 1)
            except:
                endOfHeaders = True
                break
            key = key.strip()
            self.header_keys.append(key)
            self.header[key] = val.strip()
        missing = []
        for item in MINIMUM_KEYS:
            if item not in self.header_keys:
                missing.append(item)
        if len(missing) > 0:
            logger.debug("KCD file misses the keys " + " ".join(missing))



[docs]    def read(self, fname, frame=None):
        """
        Read in header into self.header and
            the data   into self.data
        """
        self.header = {}
        self.resetvals()
        infile = self._open(fname, "rb")
        self._readheader(infile)
        # Compute image size
        try:
            self.dim1 = int(self.header['X dimension'])
            self.dim2 = int(self.header['Y dimension'])
        except:
            raise Exception("KCD file %s is corrupt, cannot read it" % fname)
        try:
            bytecode = DATA_TYPES[self.header['Data type']]
            self.bpp = len(numpy.array(0, bytecode).tostring())
        except KeyError:
            bytecode = numpy.uint16
            self.bpp = 2
            logger.warning("Defaulting type to uint16")
        try:
            nbReadOut = int(self.header['Number of readouts'])
        except KeyError:
            logger.warning("Defaulting number of ReadOut to 1")
            nbReadOut = 1
        fileSize = os.stat(fname)[6]
        expected_size = self.dim1 * self.dim2 * self.bpp * nbReadOut
        infile.seek(fileSize - expected_size)
        block = infile.read()
        assert len(block) == expected_size
        infile.close()

        #now read the data into the array
        self.data = numpy.zeros((self.dim2, self.dim1))
        try:
            for i in range(nbReadOut):
                self.data += numpy.reshape(numpy.fromstring(
                    block[i * expected_size / nbReadOut:(i + 1) * expected_size / nbReadOut], bytecode),
                    [self.dim2, self.dim1])
        except:
            print len(block), bytecode, self.bpp, self.dim2, self.dim1
            raise IOError, \
              'Size spec in kcd-header does not match size of image data field'
        self.bytecode = self.data.dtype.type
        self.resetvals()
        # ensure the PIL image is reset
        self.pilimage = None
        return self



    @staticmethod

[docs]    def checkData(data=None):
        if data is None:
            return None
        else:
            return data.astype(int)

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Source code for fabio.marccdimage

#!/usr/bin/env python
"""

Authors:
........
* Henning O. Sorensen & Erik Knudsen:
  Center for Fundamental Research: Metal Structures in Four Dimensions;
  Risoe National Laboratory;
  Frederiksborgvej 399;
  DK-4000 Roskilde;
  email:erik.knudsen@risoe.dk
* Jon Wright:
  European Synchrotron Radiation Facility;
  Grenoble (France)
         
marccdimage can read MarCCD and MarMosaic images including header info.

JPW : Use a parser in case of typos (sorry?)

"""


# Base this on the tifimage (as marccd seems to be tiff with a 
# special header 

from tifimage import tifimage
import logging
logger = logging.getLogger("marccdimage")

# Now for the c definition (found on mar webpage)
# The following string is therefore copyrighted by Mar I guess

CDEFINITION = """
typedef struct frame_header_type {
         /* File/header format parameters (256 bytes) */
         UINT32        header_type;  /* flag for header type  
                                           (can be  used as magic number) */
         char header_name[16];           /* header name (MMX) */
         UINT32        header_major_version;   /* header_major_version  (n.) */
         UINT32        header_minor_version;   /* header_minor_version  (.n) */
         UINT32        header_byte_order;/* BIG_ENDIAN (Motorola,MIPS);  
                                            LITTLE_ENDIAN (DEC, Intel) */
         UINT32        data_byte_order;  /* BIG_ENDIAN (Motorola,MIPS);  
                                            LITTLE_ENDIAN (DEC, Intel) */
         UINT32        header_size;      /* in bytes                     */
         UINT32        frame_type;       /* flag for frame type */
         UINT32        magic_number;     /* to be used as a flag - 
                                            usually  to indicate new file */
         UINT32        compression_type; /* type of image compression    */
         UINT32        compression1;     /* compression parameter 1 */
         UINT32        compression2;     /* compression parameter 2 */
         UINT32        compression3;     /* compression parameter 3 */
         UINT32        compression4;     /* compression parameter 4 */
         UINT32        compression5;     /* compression parameter 4 */
         UINT32        compression6;     /* compression parameter 4 */
         UINT32        nheaders;         /* total number of headers      */
         UINT32        nfast;            /* number of pixels in one line */
         UINT32        nslow;            /* number of lines in image     */
         UINT32        depth;            /* number of bytes per pixel    */
         UINT32        record_length;    /* number of pixels between 
                                            succesive rows */
         UINT32        signif_bits;      /* true depth of data, in bits  */
         UINT32        data_type;        /* (signed,unsigned,float...) */
         UINT32        saturated_value;  /* value marks pixel as saturated */
         UINT32        sequence;         /* TRUE or FALSE */
         UINT32        nimages;          /* total number of images - size of 
                                            each is nfast*(nslow/nimages) */
         UINT32        origin;           /* corner of origin             */
         UINT32        orientation;      /* direction of fast axis       */
         UINT32        view_direction;   /* direction to view frame      */
         UINT32        overflow_location;/* FOLLOWING_HEADER,  FOLLOWING_DATA */
         UINT32        over_8_bits;      /* # of pixels with counts  255 */
         UINT32        over_16_bits;     /* # of pixels with count  65535 */
         UINT32        multiplexed;      /* multiplex flag */
         UINT32        nfastimages;      /* # of images in fast direction */
         UINT32        nslowimages;      /* # of images in slow direction */
         UINT32        background_applied;/* flags correction has been applied 
                                              hold magic number ? */
         UINT32        bias_applied;     /* flags correction has been applied
                                             hold magic number ? */
         UINT32        flatfield_applied;/* flags correction has been applied -
                                              hold magic number ? */
         UINT32        distortion_applied;/*flags correction has been applied - 
                                              hold magic number ? */
         UINT32        original_header_type;    /* Header/frame type from  file 
                                                    that frame is read from */
         UINT32        file_saved;         /* Flag that file has been  saved, 
                                              should be zeroed if modified */
         char reserve1[(64-40)*sizeof(INT32)-16];

         /* Data statistics (128) */
         UINT32        total_counts[2];  /* 64 bit integer range = 1.85E19*/
         UINT32        special_counts1[2];
         UINT32        special_counts2[2];
         UINT32        min;
         UINT32        max;
         UINT32        mean;
         UINT32        rms;
         UINT32        p10;
         UINT32        p90;
         UINT32        stats_uptodate;
         UINT32        pixel_noise[MAXIMAGES]; /*1000*base noise value (ADUs) */
         char reserve2[(32-13-MAXIMAGES)*sizeof(INT32)];

         /* More statistics (256) */
         UINT16 percentile[128];


         /* Goniostat parameters (128 bytes) */
         INT32 xtal_to_detector;  /* 1000*distance in millimeters */
         INT32 beam_x;            /* 1000*x beam position (pixels) */
         INT32 beam_y;            /* 1000*y beam position (pixels) */
         INT32 integration_time;  /* integration time in  milliseconds */
         INT32 exposure_time;     /* exposure time in milliseconds */
         INT32 readout_time;      /* readout time in milliseconds */
         INT32 nreads;            /* number of readouts to get this  image */
         INT32 start_twotheta;    /* 1000*two_theta angle */
         INT32 start_omega;       /* 1000*omega angle */
         INT32 start_chi;         /* 1000*chi angle */
         INT32 start_kappa;       /* 1000*kappa angle */
         INT32 start_phi;         /* 1000*phi angle */
         INT32 start_delta;       /* 1000*delta angle */
         INT32 start_gamma;       /* 1000*gamma angle */
         INT32 start_xtal_to_detector; /* 1000*distance in mm (dist in um)*/
         INT32 end_twotheta;           /* 1000*two_theta angle */
         INT32 end_omega;              /* 1000*omega angle */
         INT32 end_chi;                /* 1000*chi angle */
         INT32 end_kappa;              /* 1000*kappa angle */
         INT32 end_phi;                /* 1000*phi angle */
         INT32 end_delta;              /* 1000*delta angle */
         INT32 end_gamma;              /* 1000*gamma angle */
         INT32 end_xtal_to_detector;   /* 1000*distance in mm (dist in um)*/
         INT32 rotation_axis;          /* active rotation axis */
         INT32 rotation_range;         /* 1000*rotation angle */
         INT32 detector_rotx;          /* 1000*rotation of detector  around X */
         INT32 detector_roty;          /* 1000*rotation of detector  around Y */
         INT32 detector_rotz;          /* 1000*rotation of detector  around Z */
         char reserve3[(32-28)*sizeof(INT32)];

         /* Detector parameters (128 bytes) */
         INT32 detector_type;            /* detector type */
         INT32 pixelsize_x;              /* pixel size (nanometers) */
         INT32 pixelsize_y;              /* pixel size (nanometers) */
         INT32 mean_bias;                        /* 1000*mean bias value */
         INT32 photons_per_100adu;       /* photons / 100 ADUs */
         INT32 measured_bias[MAXIMAGES];/* 1000*mean bias value for each image*/
         INT32 measured_temperature[MAXIMAGES];  /* Temperature of each  
                                                    detector in milliKelvins */
         INT32 measured_pressure[MAXIMAGES]; /* Pressure of each  chamber 
                                               in microTorr */
         /* Retired reserve4 when MAXIMAGES set to 9 from 16 and 
            two fields removed, and temp and pressure added
          char reserve4[(32-(5+3*MAXIMAGES))*sizeof(INT32)]
         */

         /* X-ray source and optics parameters (128 bytes) */
         /* X-ray source parameters (8*4 bytes) */
         INT32 source_type;              /* (code) - target, synch. etc */
         INT32 source_dx;                /* Optics param. - (size  microns) */
         INT32 source_dy;                /* Optics param. - (size  microns) */
         INT32 source_wavelength;        /* wavelength  (femtoMeters) */
         INT32 source_power;             /* (Watts) */
         INT32 source_voltage;           /* (Volts) */
         INT32 source_current;           /* (microAmps) */
         INT32 source_bias;              /* (Volts) */
         INT32 source_polarization_x;    /* () */
         INT32 source_polarization_y;    /* () */
         char reserve_source[4*sizeof(INT32)];

         /* X-ray optics_parameters (8*4 bytes) */
         INT32 optics_type;              /* Optics type (code)*/
         INT32 optics_dx;                /* Optics param. - (size  microns) */
         INT32 optics_dy;                /* Optics param. - (size  microns) */
         INT32 optics_wavelength;        /* Optics param. - (size  microns) */
         INT32 optics_dispersion;        /* Optics param. - (*10E6) */
         INT32 optics_crossfire_x;       /* Optics param. - (microRadians) */
         INT32 optics_crossfire_y;       /* Optics param. - (microRadians) */
         INT32 optics_angle;             /* Optics param. - (monoch.  
                                                    2theta - microradians) */
         INT32 optics_polarization_x;    /* () */
         INT32 optics_polarization_y;    /* () */
         char reserve_optics[4*sizeof(INT32)];

         char reserve5[((32-28)*sizeof(INT32))];

         /* File parameters (1024 bytes) */
         char filetitle[128];            /*  Title                  */
         char filepath[128];             /* path name for data  file  */
         char filename[64];              /* name of data  file  */
         char acquire_timestamp[32];     /* date and time of  acquisition */
         char header_timestamp[32];      /* date and time of header  update  */
         char save_timestamp[32];        /* date and time file  saved */
         char file_comments[512];        /* comments, use as desired   */
         char reserve6[1024-(128+128+64+(3*32)+512)];

         /* Dataset parameters (512 bytes) */
         char dataset_comments[512];     /* comments, used as desired   */
         /* pad out to  3072 bytes */
         char pad[3072-(256+128+256+(3*128)+1024+512)];     

         } frame_header;
"""

import struct

# Convert mar c header file types to python struct module types
C_TO_STRUCT = {
    "INT32"  : "i",
    "UINT32" : "I",
    "char"   : "c",
    "UINT16" : "H"
    }

# Sizes (bytes) of mar c header objects
C_SIZES = {
    "INT32"  : 4,
    "UINT32" : 4,
    "char"   : 1,
    "UINT16" : 2
    }

# This was worked out by trial and error from a trial image I think
MAXIMAGES = 9



[docs]def make_format(c_def_string):
    """
    Reads the header definition in c and makes the format 
    string to pass to struct.unpack
    """
    lines = c_def_string.split("\n")
    fmt = ""
    names = []
    expected = 0
    for line in lines:
        if line.find(";") == -1:
            continue
        decl = line.split(";")[0].lstrip().rstrip()
        try:
            [typ, name] = decl.split()
        except ValueError:
            logger.debug("skipping: %s" , line)
            continue

        if name.find("[") > -1:
            # repeated ... times
            try:
                num = name.split("[")[1].split("]")[0]
                num = num.replace("MAXIMAGES", str(MAXIMAGES))
                num = num.replace("sizeof(INT32)", "4")
                times = eval(num)
            except Exception, error:
                logger.error("%s Please decode %s", error, decl)
                raise error
        else:
            times = 1
        try:
            fmt += C_TO_STRUCT[typ] * times
            names += [name] * times
            expected += C_SIZES[typ] * times
        except KeyError:
            continue
    return names, fmt

# Make these be compiled on loading module

HEADER_NAMES, HEADER_FORMAT = make_format(CDEFINITION)


[docs]def interpret_header(header, fmt, names):
    """
    given a format and header interpret it
    """
    values = struct.unpack(fmt, header)
    hdr = {}
    i = 0
    for name in names:
        if hdr.has_key(name):
            if type(values[i]) == type("string"):
                hdr[name] = hdr[name] + values[i]
            else:
                try:
                    hdr[name].append(values[i])
                except AttributeError:
                    hdr[name] = [hdr[name], values[i]]
        else:
            hdr[name] = values[i]
        i = i + 1

    return hdr




[docs]class marccdimage(tifimage):
    """ Read in data in mar ccd format, also 
        MarMosaic images, including header info """


    def _readheader(self, infile):
        """
        Parser based approach
        Gets all entries
        """
        infile.seek(1024)
        hstr = infile.read(3072)
        self.header = interpret_header(hstr, HEADER_FORMAT, HEADER_NAMES)



    def _read(self, fname):
        """
        inherited from tifimage
        ... a marccd image *is a* tif image
        just with a header
        """
        return tifimage.read(self, fname)

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Source code for fabio.converters

#!/usr/bin/env python 
#coding: utf8
"""
Converter module. 
This is for the moment empty (populated only with almost pass through anonymous functions)
but aims to be populated with more sofisticated translators ...  

"""
__author__ = "Jérôme Kieffer"
__contact__ = "jerome.kieffer@esrf.eu"
__license__ = "GPLv3+"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"

import types, logging
logger = logging.getLogger("converter")


[docs]def convert_data_integer(data):
    """
    convert data to integer
    """
    if data is not None:
        return data.astype(int)
    else:
        return data



CONVERSION_HEADER = {
                     ("edfimage", "edfimage"): lambda header:header,
                     }
CONVERSION_DATA = {
                   ("edfimage", "edfimage"): lambda data:data,
                   ("edfimage", "cbfimage"): convert_data_integer,
                   ("edfimage", "mar345image"): convert_data_integer,
                   ("edfimage", "fit2dmaskimage"): convert_data_integer,
                   ("edfimage", "kcdimage"): convert_data_integer,
                   ("edfimage", "OXDimage"): convert_data_integer,
                   ("edfimage", "pnmimage"): convert_data_integer,
                   }


[docs]def convert_data(inp, outp, data):
    """
    Return data converted to the output format ... over-simplistic implementation for the moment ...
    @param inp,outp: input/output format like "cbfimage"
    @param data(ndarray): the actual dataset to be transformed
    """
    return CONVERSION_DATA.get((inp, outp), lambda data:data)(data)



[docs]def convert_header(inp, outp, header):
    """
    return header converted to the output format
    @param inp,outp: input/output format like "cbfimage"
    @param header(dict):the actual set of headers to be transformed 
    """
    return CONVERSION_HEADER.get((inp, outp), lambda header:header)(header)

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Source code for fabio.GEimage

#!/usr/bin/env python

#
# Reads the header from a GE a-Si Angio Detector
# Using version 8001 of the header from file:
#     c:\adept\core\DefaultImageInfoConfig.csv
#
#  Antonino Miceli
#  Thu Jan  4 13:46:31 CST 2007
#

# modifications by Jon Wright for style, pychecker and fabio
# 

import numpy
import struct, logging
logger = logging.getLogger("GEimage")
from fabioimage import fabioimage
from fabioutils import next_filename, previous_filename

GE_HEADER_INFO = [
    # Name, length in bytes, format for struct (None means string)
    ('ImageFormat', 10, None),
    ('VersionOfStandardHeader', 2, '=H'),
    ('StandardHeaderSizeInBytes', 4, '=L'),
    ('VersionOfUserHeader', 2, '=H'),
    ('UserHeaderSizeInBytes', 4, '=L'),
    ('NumberOfFrames', 2, '=H'),
    ('NumberOfRowsInFrame', 2, '=H'),
    ('NumberOfColsInFrame', 2, '=H'),
    ('ImageDepthInBits', 2, '=H'),
    ('AcquisitionDate', 20, None),
    ('AcquisitionTime', 20, None),
    ('DUTID', 20, None),
    ('Operator', 50, None),
    ('DetectorSignature', 20, None),
    ('TestSystemName', 20, None),
    ('TestStationRevision', 20, None),
    ('CoreBundleRevision', 20, None),
    ('AcquisitionName', 40, None),
    ('AcquisitionParameterRevision', 20, None),
    ('OriginalNumberOfRows', 2, '=H'),
    ('OriginalNumberOfColumns', 2, '=H'),
    ('RowNumberUpperLeftPointArchiveROI', 2, '=H'),
    ('ColNumberUpperLeftPointArchiveROI', 2, '=H'),
    ('Swapped', 2, '=H'),
    ('Reordered', 2, '=H'),
    ('HorizontalFlipped', 2, '=H'),
    ('VerticalFlipped', 2, '=H'),
    ('WindowValueDesired', 2, '=H'),
    ('LevelValueDesired', 2, '=H'),
    ('AcquisitionMode', 2, '=H'),
    ('AcquisitionType', 2, '=H'),
    ('UserAcquisitionCoffFileName1', 100, None),
    ('UserAcquisitionCoffFileName2', 100, None),
    ('FramesBeforeExpose', 2, '=H'),
    ('FramesDuringExpose', 2, '=H'),
    ('FramesAfterExpose', 2, '=H'),
    ('IntervalBetweenFrames', 2, '=H'),
    ('ExposeTimeDelayInMicrosecs', 8, '=d'),
    ('TimeBetweenFramesInMicrosecs', 8, '=d'),
    ('FramesToSkipExpose', 2, '=H'),
    ('ExposureMode', 2, '=H'),
    ('PrepPresetTimeInMicrosecs', 8, '=d'),
    ('ExposePresetTimeInMicrosecs', 8, '=d'),
    ('AcquisitionFrameRateInFps', 4, '=f'),
    ('FOVSelect', 2, '=H'),
    ('ExpertMode', 2, '=H'),
    ('SetVCommon1', 8, '=d'),
    ('SetVCommon2', 8, '=d'),
    ('SetAREF', 8, '=d'),
    ('SetAREFTrim', 4, '=L'),
    ('SetSpareVoltageSource', 8, '=d'),
    ('SetCompensationVoltageSource', 8, '=d'),
    ('SetRowOffVoltage', 8, '=d'),
    ('SetRowOnVoltage', 8, '=d'),
    ('StoreCompensationVoltage', 4, '=L'),
    ('RampSelection', 2, '=H'),
    ('TimingMode', 2, '=H'),
    ('Bandwidth', 2, '=H'),
    ('ARCIntegrator', 2, '=H'),
    ('ARCPostIntegrator', 2, '=H'),
    ('NumberOfRows', 4, '=L'),
    ('RowEnable', 2, '=H'),
    ('EnableStretch', 2, '=H'),
    ('CompEnable', 2, '=H'),
    ('CompStretch', 2, '=H'),
    ('LeftEvenTristate', 2, '=H'),
    ('RightOddTristate', 2, '=H'),
    ('TestModeSelect', 4, '=L'),
    ('AnalogTestSource', 4, '=L'),
    ('VCommonSelect', 4, '=L'),
    ('DRCColumnSum', 4, '=L'),
    ('TestPatternFrameDelta', 4, '=L'),
    ('TestPatternRowDelta', 4, '=L'),
    ('TestPatternColumnDelta', 4, '=L'),
    ('DetectorHorizontalFlip', 2, '=H'),
    ('DetectorVerticalFlip', 2, '=H'),
    ('DFNAutoScrubOnOff', 2, '=H'),
    ('FiberChannelTimeOutInMicrosecs', 4, '=L'),
    ('DFNAutoScrubDelayInMicrosecs', 4, '=L'),
    ('StoreAECROI', 2, '=H'),
    ('TestPatternSaturationValue', 2, '=H'),
    ('TestPatternSeed', 4, '=L'),
    ('ExposureTimeInMillisecs', 4, '=f'),
    ('FrameRateInFps', 4, '=f'),
    ('kVp', 4, '=f'),
    ('mA', 4, '=f'),
    ('mAs', 4, '=f'),
    ('FocalSpotInMM', 4, '=f'),
    ('GeneratorType', 20, None),
    ('StrobeIntensityInFtL', 4, '=f'),
    ('NDFilterSelection', 2, '=H'),
    ('RefRegTemp1', 8, '=d'),
    ('RefRegTemp2', 8, '=d'),
    ('RefRegTemp3', 8, '=d'),
    ('Humidity1', 4, '=f'),
    ('Humidity2', 4, '=f'),
    ('DetectorControlTemp', 8, '=d'),
    ('DoseValueInmR', 8, '=d'),
    ('TargetLevelROIRow0', 2, '=H'),
    ('TargetLevelROICol0', 2, '=H'),
    ('TargetLevelROIRow1', 2, '=H'),
    ('TargetLevelROICol1', 2, '=H'),
    ('FrameNumberForTargetLevelROI', 2, '=H'),
    ('PercentRangeForTargetLevel', 2, '=H'),
    ('TargetValue', 2, '=H'),
    ('ComputedMedianValue', 2, '=H'),
    ('LoadZero', 2, '=H'),
    ('MaxLUTOut', 2, '=H'),
    ('MinLUTOut', 2, '=H'),
    ('MaxLinear', 2, '=H'),
    ('Reserved', 2, '=H'),
    ('ElectronsPerCount', 2, '=H'),
    ('ModeGain', 2, '=H'),
    ('TemperatureInDegC', 8, '=d'),
    ('LineRepaired', 2, '=H'),
    ('LineRepairFileName', 100, None),
    ('CurrentLongitudinalInMM', 4, '=f'),
    ('CurrentTransverseInMM', 4, '=f'),
    ('CurrentCircularInMM', 4, '=f'),
    ('CurrentFilterSelection', 4, '=L'),
    ('DisableScrubAck', 2, '=H'),
    ('ScanModeSelect', 2, '=H'),
    ('DetectorAppSwVersion', 20, None),
    ('DetectorNIOSVersion', 20, None),
    ('DetectorPeripheralSetVersion', 20, None),
    ('DetectorPhysicalAddress', 20, None),
    ('PowerDown', 2, '=H'),
    ('InitialVoltageLevel_VCOMMON', 8, '=d'),
    ('FinalVoltageLevel_VCOMMON', 8, '=d'),
    ('DmrCollimatorSpotSize', 10, None),
    ('DmrTrack', 5, None),
    ('DmrFilter', 5, None),
    ('FilterCarousel', 2, '=H'),
    ('Phantom', 20, None),
    ('SetEnableHighTime', 2, '=H'),
    ('SetEnableLowTime', 2, '=H'),
    ('SetCompHighTime', 2, '=H'),
    ('SetCompLowTime', 2, '=H'),
    ('SetSyncLowTime', 2, '=H'),
    ('SetConvertLowTime', 2, '=H'),
    ('SetSyncHighTime', 2, '=H'),
    ('SetEOLTime', 2, '=H'),
    ('SetRampOffsetTime', 2, '=H'),
    ('FOVStartingValue', 2, '=H'),
    ('ColumnBinning', 2, '=H'),
    ('RowBinning', 2, '=H'),
    ('BorderColumns64', 2, '=H'),
    ('BorderRows64', 2, '=H'),
    ('FETOffRows64', 2, '=H'),
    ('FOVStartColumn128', 2, '=H'),
    ('FOVStartRow128', 2, '=H'),
    ('NumberOfColumns128', 2, '=H'),
    ('NumberOfRows128', 2, '=H'),
    ('VFPAquisition', 2000, None),
    ('Comment', 200, None)
    ]



[docs]class GEimage(fabioimage):

    _need_a_seek_to_read = True

    def _readheader(self, infile):
        """ Read a GE image header """

        infile.seek(0)

        self.header = {}
        for name, nbytes, format in GE_HEADER_INFO:
            if format is None:
                self.header[ name ] = infile.read(nbytes)
            else:
                self.header[ name ] = struct.unpack(format,
                                                     infile.read(nbytes))[0]


[docs]    def read(self, fname, frame=None):
        """
        Read in header into self.header and
        the data   into self.data
        """
        if frame is None:
            frame = 0
        self.header = {}
        self.resetvals()
        infile = self._open(fname, "rb")
        self.sequencefilename = fname
        self._readheader(infile)
        self.nframes = self.header['NumberOfFrames']
        self._readframe(infile, frame)
        infile.close()
        return self


    def _makeframename(self):
        """ The thing to be printed for the user to represent a frame inside
        a file """
        self.filename = "%s$%04d" % (self.sequencefilename,
                                   self.currentframe)

    def _readframe(self, filepointer, img_num):
        """
        # Load only one image from the sequence
        #    Note: the first image in the sequence 0
        # raises an exception if you give an invalid image
        # otherwise fills in self.data
        """
        if(img_num > self.nframes or img_num < 0):
            raise Exception("Bad image number")
        imgstart = self.header['StandardHeaderSizeInBytes'] + \
                   self.header['UserHeaderSizeInBytes'] + \
                   img_num * self.header['NumberOfRowsInFrame'] * \
                   self.header['NumberOfColsInFrame'] * \
                   self.header['ImageDepthInBits'] / 8
        # whence = 0 means seek from start of file
        filepointer.seek(imgstart, 0)

        self.bpp = self.header['ImageDepthInBits'] / 8 # hopefully 2        
        imglength = self.header['NumberOfRowsInFrame'] * \
                    self.header['NumberOfColsInFrame'] * self.bpp
        if self.bpp != 2:
            logging.warning("Using uint16 for GE but seems to be wrong")

        # Guessing it is always unsigned int?
        self.data = numpy.fromstring(filepointer.read(imglength), numpy.uint16)
        self.data.shape = (self.header['NumberOfRowsInFrame'],
                            self.header['NumberOfColsInFrame'])
        self.dim2 , self.dim1 = self.data.shape
        self.currentframe = int(img_num)
        self._makeframename()



[docs]    def write(self, fname, force_type=numpy.uint16):
        """ Not yet implemented"""
        raise Exception("Write is not implemented")



[docs]    def getframe(self, num):
        """
        Returns a frame as a new fabioimage object
        """
        if num < 0 or num > self.nframes:
            raise Exception("Requested frame number is out of range")
        # Do a deep copy of the header to make a new one
        newheader = {}
        for k in self.header.keys():
            newheader[k] = self.header[k]
        frame = GEimage(header=newheader)
        frame.nframes = self.nframes
        frame.sequencefilename = self.sequencefilename
        infile = frame._open(self.sequencefilename, "rb")
        frame._readframe(infile, num)
        infile.close()
        return frame



[docs]    def next(self):
        """
        Get the next image in a series as a fabio image
        """
        if self.currentframe < (self.nframes - 1) and self.nframes > 1:
            return self.getframe(self.currentframe + 1)
        else:
            newobj = GEimage()
            newobj.read(next_filename(
                self.sequencefilename))
            return newobj



[docs]    def previous(self):
        """
        Get the previous image in a series as a fabio image
        """
        if self.currentframe > 0:
            return self.getframe(self.currentframe - 1)
        else:
            newobj = GEimage()
            newobj.read(previous_filename(
                self.sequencefilename))
            return newobj




[docs]def demo():
    import sys, time

    if len(sys.argv) < 2:
        print "USAGE: GE_script.py <GEaSi_raw_image_file>"
        sys.exit()

    image_file = sys.argv[1]

    print "init read_GEaSi_data class and load header.."
    sequence1 = GEimage()
    sequence1.read(image_file)

    print "TimeBetweenFramesInMicrosecs = ",
    print sequence1.header['TimeBetweenFramesInMicrosecs']
    print "AcquisitionTime = ",
    print sequence1.header['AcquisitionTime']


    print "Mean = ", sequence1.data.ravel().mean()

    while 1:
        start = time.time()
        try:
            sequence1 = sequence1.next()
            print sequence1.currentframe, sequence1.data.ravel().mean(), \
                  time.time() - start
        except Exception, ex:
            raise ex





if __name__ == '__main__':
    demo()

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Source code for fabio.cbfimage

#!/usr/bin/env python
# coding: utf8
"""
Authors: Jérôme Kieffer, ESRF
         email:jerome.kieffer@esrf.fr

Cif Binary Files images are 2D images written by the Pilatus detector and others.
They use a modified (simplified) byte-offset algorithm.

CIF is a library for manipulating Crystallographic information files and tries
to conform to the specification of the IUCR
"""
__author__ = "Jérôme Kieffer"
__contact__ = "jerome.kieffer@esrf.eu"
__license__ = "GPLv3+"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__version__ = ["Generated by CIF.py: Jan 2005 - April 2012",
              "Written by Jerome Kieffer: Jerome.Kieffer@esrf.eu",
              "On-line data analysis / ISDD ", "ESRF Grenoble (France)"]


import os, logging
logger = logging.getLogger("cbfimage")
import numpy
from fabioimage import fabioimage
from compression import decByteOffet_numpy, md5sum, compByteOffet_numpy
#import time

DATA_TYPES = { "signed 8-bit integer"   : numpy.int8,
               "signed 16-bit integer"  : numpy.int16,
               "signed 32-bit integer"  : numpy.int32,
               "signed 64-bit integer"  : numpy.int64
                }

MINIMUM_KEYS = ["X-Binary-Size-Fastest-Dimension",
                'ByteOrder',
                'Data type',
                'X dimension',
                'Y dimension',
                'Number of readouts']


STARTER = "\x0c\x1a\x04\xd5"
PADDING = 512


[docs]class cbfimage(fabioimage):
    """
    Read the Cif Binary File data format
    """
    def __init__(self, data=None , header=None, fname=None):
        """
        Constructor of the class CIF Binary File reader.

        @param _strFilename: the name of the file to open
        @type  _strFilename: string
        """
        fabioimage.__init__(self, data, header)
        self.cif = CIF()
        if fname is not None: #load the file)
            self.read(fname)

    @staticmethod

[docs]    def checkData(data=None):
        if data is None:
            return None
        elif numpy.issubdtype(data.dtype, int):
            return data
        else:
            return data.astype(int)



    def _readheader(self, inStream):
        """
        Read in a header in some CBF format from a string representing binary stuff

        @param inStream: file containing the Cif Binary part.
        @type inStream: opened file.
        """
        self.cif.loadCIF(inStream, _bKeepComment=True)

#        backport contents of the CIF data to the headers
        for key in self.cif:
            if key != "_array_data.data":
                self.header_keys.append(key)
                self.header[key] = self.cif[key].strip(" \"\n\r\t")

        if not "_array_data.data" in self.cif:
            raise Exception("cbfimage: CBF file %s is corrupt, cannot find data block with '_array_data.data' key" % self.fname)

        inStream2 = self.cif["_array_data.data"]
        sep = "\r\n"
        iSepPos = inStream2.find(sep)
        if iSepPos < 0 or iSepPos > 80:
            sep = "\n" #switch back to unix representation

        lines = inStream2.split(sep)
        for oneLine in lines[1:]:
            if len(oneLine) < 10:
                break
            try:
                key, val = oneLine.split(':' , 1)
            except ValueError:
                key, val = oneLine.split('=' , 1)
            key = key.strip()
            self.header_keys.append(key)
            self.header[key] = val.strip(" \"\n\r\t")
        missing = []
        for item in MINIMUM_KEYS:
            if item not in self.header_keys:
                missing.append(item)
        if len(missing) > 0:
            logger.debug("CBF file misses the keys " + " ".join(missing))



[docs]    def read(self, fname, frame=None):
        """
        Read in header into self.header and
            the data   into self.data
        """
        self.filename = fname
        self.header = {}
        self.resetvals()

        infile = self._open(fname, "rb")
        self._readheader(infile)
        # Compute image size
        try:
            self.dim1 = int(self.header['X-Binary-Size-Fastest-Dimension'])
            self.dim2 = int(self.header['X-Binary-Size-Second-Dimension'])
        except:
            raise Exception(IOError, "CBF file %s is corrupt, no dimensions in it" % fname)
        try:
            bytecode = DATA_TYPES[self.header['X-Binary-Element-Type']]
            self.bpp = len(numpy.array(0, bytecode).tostring())
        except KeyError:
            bytecode = numpy.int32
            self.bpp = 32
            logger.warning("Defaulting type to int32")
        if self.header["conversions"] == "x-CBF_BYTE_OFFSET":
            self.data = self._readbinary_byte_offset(self.cif["_array_data.data"]).astype(bytecode).reshape((self.dim2, self.dim1))
        else:
            raise Exception(IOError, "Compression scheme not yet supported, please contact FABIO development team")

        self.bytecode = self.data.dtype.type
        self.resetvals()
#        # ensure the PIL image is reset
        self.pilimage = None
        return self




    def _readbinary_byte_offset(self, inStream):
        """
        Read in a binary part of an x-CBF_BYTE_OFFSET compressed image

        @param inStream: the binary image (without any CIF decorators)
        @type inStream: python string.
        @return: a linear numpy array without shape and dtype set
        @rtype: numpy array
        """
        startPos = inStream.find(STARTER) + 4
        data = inStream[ startPos: startPos + int(self.header["X-Binary-Size"])]
        try:
            import byte_offset
        except ImportError:
            logger.warning("Error in byte_offset part: Falling back to Numpy implementation")
            myData = decByteOffet_numpy(data, size=self.dim1 * self.dim2)
        else:
            myData = byte_offset.analyseCython(data, size=self.dim1 * self.dim2)

        assert len(myData) == self.dim1 * self.dim2
        return myData



[docs]    def write(self, fname):
        """
        write the file in CBF format
        @param fname: name of the file
        @type: string
        """
        if self.data is not None:
            self.dim2, self.dim1 = self.data.shape
        else:
            raise RuntimeError("CBF image contains no data")
        binary_blob = compByteOffet_numpy(self.data)
#        l = len(binary_blob)
#        if (l % PADDING) != 0:
#            rem = PADDING - (l % PADDING)
#            binary_blob += "\x00" * rem
        dtype = "Unknown"
        for key, value in DATA_TYPES.iteritems():
            if value == self.data.dtype:
                dtype = key
        binary_block = [
                        "--CIF-BINARY-FORMAT-SECTION--",
                        "Content-Type: application/octet-stream;",
                        '     conversions="x-CBF_BYTE_OFFSET"',
                        'Content-Transfer-Encoding: BINARY',
                        "X-Binary-Size: %d" % (len(binary_blob)),
                        "X-Binary-ID: 1",
                        'X-Binary-Element-Type: "%s"' % (dtype),
                        "X-Binary-Element-Byte-Order: LITTLE_ENDIAN" ,
                        "Content-MD5: %s" % md5sum(binary_blob),
                        "X-Binary-Number-of-Elements: %s" % (self.dim1 * self.dim2),
                        "X-Binary-Size-Fastest-Dimension: %d" % self.dim1,
                        "X-Binary-Size-Second-Dimension: %d" % self.dim2,
                        "X-Binary-Size-Padding: %d" % 1,
                        "",
                        STARTER + binary_blob,
                        "",
                        "--CIF-BINARY-FORMAT-SECTION----"
                        ]

        if "_array_data.header_contents" not in self.header:
            nonCifHeaders = []
        else:
            nonCifHeaders = [i.strip()[2:] for i in self.header["_array_data.header_contents"].split("\n") if i.find("# ") >= 0]

        for key in self.header:
            if (key not in self.header_keys):
                self.header_keys.append(key)
        for key in self.header_keys:
            if key.startswith("_") :
                if key not in self.cif or self.cif[key] != self.header[key]:
                    self.cif[key] = self.header[key]
            elif key.startswith("X-Binary-"):
                pass
            elif key.startswith("Content-"):
                pass
            elif key.startswith("conversions"):
                pass
            elif key.startswith("filename"):
                pass
            elif key in self.header:
                nonCifHeaders.append("%s %s" % (key, self.header[key]))
        if len(nonCifHeaders) > 0:
            self.cif["_array_data.header_contents"] = "\r\n".join(["# %s" % i for i in nonCifHeaders])

        self.cif["_array_data.data"] = "\r\n".join(binary_block)
        self.cif.saveCIF(fname, linesep="\r\n", binary=True)

################################################################################
# CIF class
################################################################################


[docs]class CIF(dict):
    """
    This is the CIF class, it represents the CIF dictionary;
    and as a a python dictionary thus inherits from the dict built in class.
    """
    EOL = ["\r", "\n", "\r\n", "\n\r"]
    BLANK = [" ", "\t"] + EOL
    START_COMMENT = ["\"", "\'"]
    BINARY_MARKER = "--CIF-BINARY-FORMAT-SECTION--"

    def __init__(self, _strFilename=None):
        """
        Constructor of the class.

        @param _strFilename: the name of the file to open
        @type  _strFilename: filename (str) or file object
        """
        dict.__init__(self)
        self._ordered = []
        if _strFilename is not None: #load the file)
            self.loadCIF(_strFilename)

    def __setitem__(self, key, value):
        if key not in self._ordered:
            self._ordered.append(key)
        return dict.__setitem__(self, key, value)


[docs]    def pop(self, key):
        if key  in self._ordered:
            self._ordered.remove(key)
        return dict.pop(self, key)



[docs]    def popitem(self, key):
        if key  in self._ordered:
            self._ordered.remove(key)
        return dict.popitem(self, key)




[docs]    def loadCIF(self, _strFilename, _bKeepComment=False):
        """Load the CIF file and populates the CIF dictionary into the object
        @param _strFilename: the name of the file to open
        @type  _strFilename: string
        @param _strFilename: the name of the file to open
        @type  _strFilename: string
        @return: None
        """

        if isinstance(_strFilename, (str, unicode)):
            if os.path.isfile(_strFilename):
                infile = open(_strFilename, "rb")
            else:
                raise RuntimeError("CIF.loadCIF: No such file to open: %s" % _strFilename)
        #elif isinstance(_strFilename, file, bz2.BZ2File, ):
        elif "read" in dir(_strFilename):
            infile = _strFilename
        else:
            raise RuntimeError("CIF.loadCIF: what is %s type %s" % (_strFilename, type(_strFilename)))
        if _bKeepComment:
            self._parseCIF(infile.read())
        else:
            self._parseCIF(CIF._readCIF(infile))

    readCIF = loadCIF

    @staticmethod

[docs]    def isAscii(_strIn):
        """
        Check if all characters in a string are ascii,

        @param _strIn: input string
        @type _strIn: python string
        @return: boolean
        @rtype: boolean
        """
        bIsAcii = True
        for i in _strIn:
            if ord(i) > 127:
                bIsAcii = False
                break
        return bIsAcii



    @staticmethod
    def _readCIF(_instream):
        """
        - Check if the filename containing the CIF data exists
        - read the cif file
        - removes the comments

        @param _instream: the file containing the CIF data
        @type _instream: open file in read mode
        @return: a string containing the raw data
        @rtype: string
        """
        if not "readlines" in dir(_instream):
            raise RuntimeError("CIF._readCIF(instream): I expected instream to be an opened file,\
             here I got %s type %s" % (_instream, type(_instream)))
        lLinesRead = _instream.readlines()
        sText = ""
        for sLine in lLinesRead:
            iPos = sLine.find("#")
            if iPos >= 0:
                if CIF.isAscii(sLine):
                    sText += sLine[:iPos] + os.linesep

                if iPos > 80 :
                    logger.warning("This line is too long and could cause problems in PreQuest: %s", sLine)
            else :
                sText += sLine
                if len(sLine.strip()) > 80 :
                    logger.warning("This line is too long and could cause problems in PreQues: %s", sLine)
        return sText


    def _parseCIF(self, sText):
        """
        - Parses the text of a CIF file
        - Cut it in fields
        - Find all the loops and process
        - Find all the keys and values

        @param sText: the content of the CIF - file
        @type sText: string
        @return: Nothing, the data are incorporated at the CIF object dictionary
        @rtype: None
        """
        loopidx = []
        looplen = []
        loop = []
        #first of all : separate the cif file in fields
        lFields = CIF._splitCIF(sText.strip())
        #Then : look for loops
        for i in range(len(lFields)):
            if lFields[i].lower() == "loop_":
                loopidx.append(i)
        if len(loopidx) > 0:
            for i in loopidx:
                loopone, length, keys = CIF._analyseOneLoop(lFields, i)
                loop.append([keys, loopone])
                looplen.append(length)


            for i in range(len(loopidx) - 1, -1, -1):
                f1 = lFields[:loopidx[i]] + lFields[loopidx[i] + looplen[i]:]
                lFields = f1

            self["loop_"] = loop

        for i in range(len(lFields) - 1):
    #        print lFields[i], lFields[i+1]
            if len(lFields[i + 1]) == 0 : lFields[i + 1] = "?"
            if lFields[i][0] == "_" and lFields[i + 1][0] != "_":
                self[lFields[i]] = lFields[i + 1]

    @staticmethod
    def _splitCIF(sText):
        """
        Separate the text in fields as defined in the CIF

        @param sText: the content of the CIF - file
        @type sText: string
        @return: list of all the fields of the CIF
        @rtype: list
        """
        lFields = []
        while True:
            if len(sText) == 0:
                break
            elif sText[0] == "'":
                idx = 0
                bFinished = False
                while not  bFinished:
                    idx += 1 + sText[idx + 1:].find("'")
    ##########debuging    in case we arrive at the end of the text
                    if idx >= len(sText) - 1:
    #                    print sText,idx,len(sText)
                        lFields.append(sText[1:-1].strip())
                        sText = ""
                        bFinished = True
                        break

                    if sText[idx + 1] in CIF.BLANK:
                        lFields.append(sText[1:idx].strip())
                        sText1 = sText[idx + 1:]
                        sText = sText1.strip()
                        bFinished = True

            elif sText[0] == '"':
                idx = 0
                bFinished = False
                while not  bFinished:
                    idx += 1 + sText[idx + 1:].find('"')
    ##########debuging    in case we arrive at the end of the text
                    if idx >= len(sText) - 1:
    #                    print sText,idx,len(sText)
                        lFields.append(sText[1:-1].strip())
#                        print lFields[-1]
                        sText = ""
                        bFinished = True
                        break

                    if sText[idx + 1] in CIF.BLANK:
                        lFields.append(sText[1:idx].strip())
#                        print lFields[-1]
                        sText1 = sText[idx + 1:]
                        sText = sText1.strip()
                        bFinished = True
            elif sText[0] == ';':
                if sText[1:].strip().find(CIF.BINARY_MARKER) == 0:
                    idx = sText[32:].find(CIF.BINARY_MARKER)
                    if idx == -1:
                        idx = 0
                    else:
                        idx += 32 + len(CIF.BINARY_MARKER)
                else:
                    idx = 0
                bFinished = False
                while not  bFinished:
                    idx += 1 + sText[idx + 1:].find(';')
                    if sText[idx - 1] in CIF.EOL:
                        lFields.append(sText[1:idx - 1].strip())
                        sText1 = sText[idx + 1:]
                        sText = sText1.strip()
                        bFinished = True
            else:
                f = sText.split(None, 1)[0]
                lFields.append(f)
#                print lFields[-1]
                sText1 = sText[len(f):].strip()
                sText = sText1
        return lFields


    @staticmethod
    def _analyseOneLoop(lFields, iStart):
        """Processes one loop in the data extraction of the CIF file
        @param lFields: list of all the words contained in the cif file
        @type lFields: list
        @param iStart: the starting index corresponding to the "loop_" key
        @type iStart: integer
        @return: the list of loop dictionaries, the length of the data
            extracted from the lFields and the list of all the keys of the loop.
        @rtype: tuple
        """
    #    in earch loop we first search the length of the loop
    #    print lFields
#        curloop = {}
        loop = []
        keys = []
        i = iStart + 1
        bFinished = False
        while not bFinished:
            if lFields[i][0] == "_":
                keys.append(lFields[i])#.lower())
                i += 1
            else:
                bFinished = True
        data = []
        while True:
            if i >= len(lFields):
                break
            elif len(lFields[i]) == 0:
                break
            elif lFields[i][0] == "_":
                break
            elif lFields[i] in ["loop_", "stop_", "global_", "data_", "save_"]:
                break
            else:
                data.append(lFields[i])
                i += 1
        #print len(keys), len(data)
        k = 0

        if len(data) < len(keys):
            element = {}
            for j in keys:
                if k < len(data):
                    element[j] = data[k]
                else :
                    element[j] = "?"
                k += 1
            #print element
            loop.append(element)

        else:
            #print data
            #print keys
            for i in range(len(data) / len(keys)):
                element = {}
                for j in keys:
                    element[j] = data[k]
                    k += 1
    #            print element
                loop.append(element)
    #    print loop
        return loop, 1 + len(keys) + len(data), keys






#############################################################################################
########     everything needed to  write a cif file #########################################
#############################################################################################


[docs]    def saveCIF(self, _strFilename="test.cif", linesep=os.linesep, binary=False):
        """Transforms the CIF object in string then write it into the given file
        @param _strFilename: the of the file to be written
        @param linesep: line separation used (to force compatibility with windows/unix)
        @param binary: Shall we write the data as binary (True only for imageCIF/CBF)
        @type param: string
        """
        if binary:
            mode = "wb"
        else:
            mode = "w"
        try:
            fFile = open(_strFilename, mode)
        except IOError:
            print("Error during the opening of file for write: %s" %
                                                            _strFilename)
            return
        fFile.write(self.tostring(_strFilename, linesep))
        try:
            fFile.close()
        except IOError:
            print("Error during the closing of file for write: %s" %
                                                             _strFilename)




[docs]    def tostring(self, _strFilename=None, linesep=os.linesep):
        """
        Converts a cif dictionnary to a string according to the CIF syntax
        
        @param _strFilename: the name of the filename to be appended in the header of the CIF file
        @type _strFilename: string
        @return: a sting that corresponds to the content of the CIF - file.
        
        """
#        sCifText = ""
        lstStrCif = ["# " + i for i in __version__]
        if "_chemical_name_common" in self:
            t = self["_chemical_name_common"].split()[0]
        elif _strFilename is not None:
            t = os.path.splitext(os.path.split(str(_strFilename).strip())[1])[0]
        else:
            t = ""
        lstStrCif.append("data_%s" % (t))
        #first of all get all the keys :
        lKeys = self.keys()
        lKeys.sort()
        for key in lKeys[:]:
            if key in self._ordered:
                lKeys.remove(key)
        self._ordered += lKeys

        for sKey in self._ordered:
            if sKey == "loop_":
                continue
            if sKey not in self:
                self._ordered.remove(sKey)
                logger.debug("Skipping key %s from ordered list as no more present in dict")
                continue
            sValue = str(self[sKey])
            if sValue.find("\n") > -1: #should add value  between ;;
                lLine = [sKey, ";", sValue, ";", ""]
            elif len(sValue.split()) > 1: #should add value between ''
                sLine = "%s        '%s'" % (sKey, sValue)
                if len(sLine) > 80:
                    lLine = [str(sKey), sValue]
                else:
                    lLine = [sLine]
            else:
                sLine = "%s        %s" % (sKey, sValue)
                if len(sLine) > 80:
                    lLine = [str(sKey), sValue]
                else:
                    lLine = [sLine]
            lstStrCif += lLine
        if self.has_key("loop_"):
            for loop in self["loop_"]:
                lstStrCif.append("loop_ ")
                lKeys = loop[0]
                llData = loop[1]
                lstStrCif += [" %s" % (sKey) for sKey in lKeys]
                for lData in llData:
                    sLine = " "
                    for key in lKeys:
                        sRawValue = lData[key]
                        if sRawValue.find("\n") > -1: #should add value  between ;;
                            lstStrCif += [sLine, ";", str(sRawValue), ";"]
                            sLine = " "
                        else:
                            if len(sRawValue.split()) > 1: #should add value between ''
                                value = "'%s'" % (sRawValue)
                            else:
                                value = str(sRawValue)
                            if len(sLine) + len(value) > 78:
                                lstStrCif += [sLine]
                                sLine = " " + value
                            else:
                                sLine += " " + value
                    lstStrCif.append(sLine)
                lstStrCif.append("")
        return linesep.join(lstStrCif)




[docs]    def exists(self, sKey):
        """
        Check if the key exists in the CIF and is non empty.
        @param sKey: CIF key
        @type sKey: string
        @param cif: CIF dictionary
        @return: True if the key exists in the CIF dictionary and is non empty
        @rtype: boolean
        """
        bExists = False
        if self.has_key(sKey):
            if len(self[sKey]) >= 1:
                if self[sKey][0] not in ["?", "."]:
                    bExists = True
        return bExists




[docs]    def existsInLoop(self, sKey):
        """
        Check if the key exists in the CIF dictionary.
        @param sKey: CIF key
        @type sKey: string
        @param cif: CIF dictionary
        @return: True if the key exists in the CIF dictionary and is non empty
        @rtype: boolean
        """
        if not self.exists("loop_"):
            return False
        bExists = False
        if not bExists:
            for i in self["loop_"]:
                for j in i[0]:
                    if j == sKey:
                        bExists = True
        return bExists




[docs]    def loadCHIPLOT(self, _strFilename):
        """
        Load the powder diffraction CHIPLOT file and returns the
        pd_CIF dictionary in the object

        @param _strFilename: the name of the file to open
        @type  _strFilename: string
        @return: the CIF object corresponding to the powder diffraction
        @rtype: dictionary
        """
        if not os.path.isfile(_strFilename):
            print "I cannot find the file %s" % _strFilename
            raise
        lInFile = open(_strFilename, "r").readlines()
        self["_audit_creation_method"] = 'From 2-D detector using FIT2D and CIFfile'
        self["_pd_meas_scan_method"] = "fixed"
        self["_pd_spec_description"] = lInFile[0].strip()
        try:
            iLenData = int(lInFile[3])
        except ValueError:
            iLenData = None
        lOneLoop = []
        try:
            f2ThetaMin = float(lInFile[4].split()[0])
            last = ""
            for sLine in lInFile[-20:]:
                if sLine.strip() != "":
                    last = sLine.strip()
            f2ThetaMax = float(last.split()[0])
            limitsOK = True

        except (ValueError, IndexError):
            limitsOK = False
            f2ThetaMin = 180.0
            f2ThetaMax = 0
#        print "limitsOK:", limitsOK
        for sLine in lInFile[4:]:
            sCleaned = sLine.split("#")[0].strip()
            data = sCleaned.split()
            if len(data) == 2 :
                if not limitsOK:
                    f2Theta = float(data[0])
                    if f2Theta < f2ThetaMin :
                        f2ThetaMin = f2Theta
                    if f2Theta > f2ThetaMax :
                        f2ThetaMax = f2Theta
                lOneLoop.append({ "_pd_meas_intensity_total": data[1] })
        if not iLenData:
            iLenData = len(lOneLoop)
        assert (iLenData == len(lOneLoop))
        self[ "_pd_meas_2theta_range_inc" ] = "%.4f" % ((f2ThetaMax - f2ThetaMin) / (iLenData - 1))
        if self[ "_pd_meas_2theta_range_inc" ] < 0:
            self[ "_pd_meas_2theta_range_inc" ] = abs (self[ "_pd_meas_2theta_range_inc" ])
            tmp = f2ThetaMax
            f2ThetaMax = f2ThetaMin
            f2ThetaMin = tmp
        self[ "_pd_meas_2theta_range_max" ] = "%.4f" % f2ThetaMax
        self[ "_pd_meas_2theta_range_min" ] = "%.4f" % f2ThetaMin
        self[ "_pd_meas_number_of_points" ] = str(iLenData)
        self["loop_"] = [ [ ["_pd_meas_intensity_total" ], lOneLoop ] ]



    @staticmethod

[docs]    def LoopHasKey(loop, key):
        "Returns True if the key (string) exist in the array called loop"""
        try:
            loop.index(key)
            return True
        except ValueError:
            return False

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© Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
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Source code for fabio.pnmimage

#!/usr/bin/env python
#coding: utf8
"""

Authors: Henning O. Sorensen & Erik Knudsen
         Center for Fundamental Research: Metal Structures in Four Dimensions
         Risoe National Laboratory
         Frederiksborgvej 399
         DK-4000 Roskilde
         email:henning.sorensen@risoe.dk

"""

import numpy, logging
logger = logging.getLogger("pnmimage")
from fabioimage import fabioimage

SUBFORMATS = ['P1', 'P2', 'P3', 'P4', 'P5', 'P6', 'P7']

HEADERITEMS = ['SUBFORMAT', 'DIMENSIONS', 'MAXVAL']
P7HEADERITEMS = ['WIDTH', 'HEIGHT', 'DEPTH', 'MAXVAL', 'TUPLTYPE', 'ENDHDR']


[docs]class pnmimage(fabioimage):
    def __init__(self, *arg, **kwargs):
        fabioimage.__init__(self, *arg, **kwargs)
        fun = getattr(fabioimage, '__init__', lambda x: None)
        fun(self)
        self.data = None
        self.header = {'Subformat':'P5'}
        self.dim1 = self.dim2 = 0
        self.m = self.maxval = self.stddev = self.minval = None
        self.header_keys = self.header.keys()
        self.bytecode = None

    def _readheader(self, f):
        #pnm images have a 3-line header but ignore lines starting with '#'
        #1st line contains the pnm image sub format
        #2nd line contains the image pixel dimension
        #3rd line contains the maximum pixel value (at least for grayscale - check this)
        self.header_keys = ['SUBFORMAT', 'DIMENSIONS', 'MAXVAL']

        l = f.readline().strip()
        if l not in SUBFORMATS:
            raise IOError, ('unknown subformat of pnm: %s' % l)
        else:
            self.header['SUBFORMAT'] = l

        if self.header['SUBFORMAT'] == 'P7':
            self.header_keys = P7HEADERITEMS
            #this one has a special header
            while 'ENDHDR' not in l:
                l = f.readline()
                while(l[0] == '#'): l = f.readline()
                s = l.lsplit(' ', 1)
                if s[0] not in P7HEADERITEMS:
                    raise IOError, ('Illegal pam (netpnm p7) headeritem %s' % s[0])
                self.header[s[0]] = s[1]
        else:
            self.header_keys = HEADERITEMS
            for k in self.header_keys[1:]:
                l = f.readline()
                while(l[0] == '#'): l = f.readline()
                self.header[k] = l.strip()

        #set the dimensions
        dims = (self.header['DIMENSIONS'].split())
        self.dim1, self.dim2 = int(dims[0]), int(dims[1])
        #figure out how many bytes are used to store the data
        #case construct here!
        m = int(self.header['MAXVAL'])
        if m < 256:
            self.bytecode = numpy.uint8
        elif m < 65536:
            self.bytecode = numpy.uint16
        elif m < 2147483648L:
            self.bytecode = numpy.uint32
            logger.warning('32-bit pixels are not really supported by the netpgm standard')
        else:
            raise IOError, 'could not figure out what kind of pixels you have'


[docs]    def read(self, fname, frame=None):
        """
        try to read PNM images
        @param fname: name of the file
        @param frame: not relevant here! PNM is always single framed
        """
        self.header = {}
        self.resetvals()
        infile = self._open(fname)
        self._readheader(infile)

        #read the image data
        decoder_name = "%sdec" % self.header['SUBFORMAT']
        if decoder_name in dir(pnmimage):
            decoder = getattr(pnmimage, decoder_name)
            self.data = decoder(infile, self.bytecode)
        else:
            raise IOError("No decoder named %s for file %s" % (decoder_name, fname))
        self.resetvals()
        return self


    @staticmethod

[docs]    def P1dec(buf, bytecode):
        data = numpy.zeros((self.dim2, self.dim1))
        i = 0
        for l in buf.readlines():
            try:
                data[i, :] = numpy.array(l.split()).astype(bytecode)
            except ValueError:
                raise IOError, 'Size spec in pnm-header does not match size of image data field'
        return data


    @staticmethod

[docs]    def P4dec(buf, bytecode):
        err = 'single bit (pbm) images are not supported - yet'
        logger.error(err)
        raise NotImplementedError(err)


    @staticmethod

[docs]    def P2dec(buf, bytecode):
        data = numpy.zeros((self.dim2, self.dim1))
        i = 0
        for l in buf.readlines():
            try:
                data[i, :] = numpy.array(l.split()).astype(bytecode)
            except ValueError:
                raise IOError, 'Size spec in pnm-header does not match size of image data field'
        return data


    @staticmethod

[docs]    def P5dec(buf, bytecode):
        l = buf.read()
        try:
            data = numpy.reshape(numpy.fromstring(l, bytecode), [self.dim2, self.dim1]).byteswap()
        except ValueError:
            raise IOError, 'Size spec in pnm-header does not match size of image data field'
        return data


    @staticmethod

[docs]    def P3dec(buf, bytecode):
        err = '(plain-ppm) RGB images are not supported - yet'
        logger.error(err)
        raise NotImplementedError(err)


    @staticmethod

[docs]    def P6dec(buf, bytecode):
        err = '(ppm) RGB images are not supported - yet'
        logger.error(err)
        raise NotImplementedError(err)


    @staticmethod

[docs]    def P7dec(buf, bytecode):
        err = '(pam) images are not supported - yet'
        logger.error(err)
        raise NotImplementedError(err)



[docs]    def write(self, filename):
        raise NotImplementedError('write pnm images is not implemented yet.')


    @staticmethod

[docs]    def checkData(data=None):
        if data is None:
            return None
        else:
            return data.astype(int)

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© Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
fabio-0.1.3/doc/html/_modules/fabio/edfimage.html0000644000175000017500000052103512233250022022403 0ustar jeromejerome00000000000000 fabio.edfimage — FabIO 0.1.3 documentation

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Source code for fabio.edfimage

#!/usr/bin/env python
# -*- coding: utf8 -*-
"""

License: GPLv2+

Authors:
........
* Henning O. Sorensen & Erik Knudsen:
  Center for Fundamental Research: Metal Structures in Four Dimensions;
  Risoe National Laboratory;
  Frederiksborgvej 399;
  DK-4000 Roskilde;
  email:erik.knudsen@risoe.dk
* Jon Wright & Jérôme Kieffer:
  European Synchrotron Radiation Facility;
  Grenoble (France)


"""
from __future__ import with_statement
import os, logging, types
logger = logging.getLogger("edfimage")
import numpy
from fabioimage import fabioimage
from fabioutils import isAscii, toAscii, nice_int
from compression import decBzip2, decGzip, decZlib


BLOCKSIZE = 512
DATA_TYPES = {  "SignedByte"    :  numpy.int8,
                "Signed8"       :  numpy.int8,
                "UnsignedByte"  :  numpy.uint8,
                "Unsigned8"     :  numpy.uint8,
                "SignedShort"   :  numpy.int16,
                "Signed16"      :  numpy.int16,
                "UnsignedShort" :  numpy.uint16,
                "Unsigned16"    :  numpy.uint16,
                "UnsignedShortInteger" : numpy.uint16,
                "SignedInteger" :  numpy.int32,
                "Signed32"      :  numpy.int32,
                "UnsignedInteger":  numpy.uint32,
                "Unsigned32"    :  numpy.uint32,
                "SignedLong"    :  numpy.int32,
                "UnsignedLong"  :  numpy.uint32,
                "Signed64"      :  numpy.int64,
                "Unsigned64"    :  numpy.uint64,
                "FloatValue"    :  numpy.float32,
                "FLOATVALUE"    :  numpy.float32,
                "FLOAT"         :  numpy.float32, # fit2d
                "Float"         :  numpy.float32, # fit2d
                "FloatIEEE32"   :  numpy.float32,
                "Float32"       :  numpy.float32,
                "Double"        :  numpy.float64,
                "DoubleValue"   :  numpy.float64,
                "FloatIEEE64"   :  numpy.float64,
                "DoubleIEEE64"  :  numpy.float64}
try:
    DATA_TYPES["FloatIEEE128" ] =  numpy.float128
    DATA_TYPES["DoubleIEEE128" ] =  numpy.float128
    DATA_TYPES["QuadrupleValue" ] =  numpy.float128

except AttributeError:
    # not in your numpy
    pass

NUMPY_EDF_DTYPE = {"int8"       :"SignedByte",
                   "int16"      :"SignedShort",
                   "int32"      :"SignedInteger",
                   "int64"      :"Signed64",
                   "uint8"      :"UnsignedByte",
                   "uint16"     :"UnsignedShort",
                   "uint32"     :"UnsignedInteger",
                   "uint64"     :"Unsigned64",
                   "float32"    :"FloatValue",
                   "float64"    :"DoubleValue",
                   "float128"   :"QuadrupleValue",
             }

MINIMUM_KEYS = ['HEADERID',
                'IMAGE',
                'BYTEORDER',
                'DATATYPE',
                'DIM_1',
                'DIM_2',
                'SIZE'] # Size is thought to be essential for writing at least

DEFAULT_VALUES = {
                  # I do not define default values as they will be calculated at write time
                  # JK20110415
                  }


[docs]class Frame(object):
    """
    A class representing a single frame in an EDF file
    """
    def __init__(self, data=None, header=None, header_keys=None, number=None):
        if header is None:
            self.header = {}
        else:
            self.header = dict(header)

        if header_keys is None:
            self.header_keys = self.header.keys()
        else:
            self.header_keys = header_keys[:]
            for key in header_keys:
                if key not in self.header:
                    logger.warning("Header key %s, in header_keys is not in header dictionary, poping !!!" % key)
                    self.header_keys.remove(key)

        self.capsHeader = {}
        for key in self.header_keys:
            try:
                self.capsHeader[key.upper()] = key
            except AttributeError:
                logger.warning("Header key %s is not a string" % key)
        self._data = data
        self.dims = []
        self.dim1 = 0
        self.dim2 = 0
        self.start = None # Position of start of raw data in file
        self.size = None  # size of raw data in file
        self.file = None  # opened file object with locking capabilities !!!
        self.bpp = None
        self._bytecode = None
        if (number is not None) and isinstance(number, int):
            self.iFrame = number
        else:
            self.iFrame = 0


[docs]    def parseheader(self, block):
        """
        Parse the header in some EDF format from an already open file

        @param block: string representing the header block
        @type block: string, should be full ascii
        @return: size of the binary blob
        """
        #reset values ...
        self.header = {}
        self.capsHeader = {}
        self.header_keys = []
        self.size = None
        calcsize = 1
        self.dims = []

        for line in block.split(';'):
            if '=' in line:
                key, val = line.split('=' , 1)
                # Why would someone put null bytes in a header?
                key = key.replace("\x00"," ").strip()
                self.header[key] = val.replace("\x00"," ").strip()
                self.capsHeader[key.upper()] = key
                self.header_keys.append(key)

        # Compute image size
        if "SIZE" in self.capsHeader:
            try:
                self.size = nice_int(self.header[self.capsHeader["SIZE"]])
            except ValueError:
                logger.warning("Unable to convert to integer : %s %s " % (self.capsHeader["SIZE"], self.header[self.capsHeader["SIZE"]]))
        if "DIM_1" in self.capsHeader:
            try:
                dim1 = nice_int(self.header[self.capsHeader['DIM_1']])
            except ValueError:
                logger.error("Unable to convert to integer Dim_1: %s %s" % (self.capsHeader["DIM_1"], self.header[self.capsHeader["DIM_1"]]))
            else:
                calcsize *= dim1
                self.dims.append(dim1)
        else:
            logger.error("No Dim_1 in headers !!!")
        if "DIM_2" in self.capsHeader:
            try:
                dim2 = nice_int(self.header[self.capsHeader['DIM_2']])
            except ValueError:
                logger.error("Unable to convert to integer Dim_3: %s %s" % (self.capsHeader["DIM_2"], self.header[self.capsHeader["DIM_2"]]))
            else:
                calcsize *= dim2
                self.dims.append(dim2)
        else:
            logger.error("No Dim_2 in headers !!!")
        iDim = 3
        # JON: this appears to be for nD images, but we don't treat those
        while iDim is not None:
            strDim = "DIM_%i" % iDim
            if strDim in self.capsHeader:
                try:
                    dim3 = nice_int(self.header[self.capsHeader[strDim]])
                except ValueError:
                    logger.error("Unable to convert to integer %s: %s %s"
                                  % (strDim, self.capsHeader[strDim], self.header[self.capsHeader[strDim]]))
                    dim3 = None
                    iDim = None
                else:
                    if dim3 > 1:
                        # Otherwise treat dim3==1 as a 2D image
                        calcsize *= dim3
                        self.dims.append(dim3)
                    iDim += 1

            else:
                logger.debug("No Dim_3 -> it is a 2D image")
                iDim = None
        if self._bytecode is None:
            if "DATATYPE" in self.capsHeader:
                self._bytecode = DATA_TYPES[self.header[self.capsHeader['DATATYPE']]]
            else:
                self._bytecode = numpy.uint16
                logger.warning("Defaulting type to uint16")
        self.bpp = len(numpy.array(0, self._bytecode).tostring())
        calcsize *= self.bpp
        if (self.size is None):
            self.size = calcsize
        elif (self.size != calcsize):
            if ("COMPRESSION" in self.capsHeader) and (self.header[self.capsHeader['COMPRESSION']].upper().startswith("NO")):
                logger.info("Mismatch between the expected size %s and the calculated one %s" % (self.size, calcsize))
                self.size = calcsize

        for i, n in enumerate(self.dims):
            setattr(self, "dim%i" % (i + 1), n)

        return self.size




[docs]    def swap_needed(self):
        """
        Decide if we need to byteswap
        """
        if ('Low'  in self.header[self.capsHeader['BYTEORDER']] and numpy.little_endian) or \
           ('High' in self.header[self.capsHeader['BYTEORDER']] and not numpy.little_endian):
            return False
        if ('High'  in self.header[self.capsHeader['BYTEORDER']] and numpy.little_endian) or \
           ('Low' in self.header[self.capsHeader['BYTEORDER']] and not numpy.little_endian):
            if self.bpp in [2, 4, 8]:
                return True
            else:
                return False




[docs]    def getData(self):
        """
        Unpack a binary blob according to the specification given in the header

        @return: dataset as numpy.ndarray
        """
        data = None
        if self._data is not None:
            data = self._data
        elif self.file is None:
            data = self._data
        else:
            if self._bytecode is None:
                if "DATATYPE" in self.capsHeader:
                    self._bytecode = DATA_TYPES[self.header[self.capsHeader["DATATYPE"]]]
                else:
                    self._bytecode = numpy.uint16
            dims = self.dims[:]
            dims.reverse()
            with self.file.lock:
                if self.file.closed:
                    logger.error("file: %s from %s is closed. Cannot read data." % (self.file, self.file.filename))
                    return
                else:
                    self.file.seek(self.start)
                    fileData = self.file.read(self.size)

            if ("COMPRESSION" in self.capsHeader):
                compression = self.header[self.capsHeader["COMPRESSION"]].upper()
                uncompressed_size = self.bpp
                for i in dims:
                    uncompressed_size *= i
                if "OFFSET" in compression :
                    try:
                        import byte_offset#IGNORE:F0401
                    except ImportError, error:
                        logger.error("Unimplemented compression scheme:  %s (%s)" % (compression, error))
                    else:
                        myData = byte_offset.analyseCython(fileData, size=uncompressed_size)
                        rawData = myData.astype(self._bytecode).tostring()
                        self.size = uncompressed_size
                elif compression == "NONE":
                    rawData = fileData
                elif "GZIP" in compression:
                    rawData = decGzip(fileData)
                    self.size = uncompressed_size
                elif "BZ" in compression :
                    rawData = decBzip2(fileData)
                    self.size = uncompressed_size
                elif "Z" in compression :
                    rawData = decZlib(fileData)
                    self.size = uncompressed_size
                else:
                    logger.warning("Unknown compression scheme %s" % compression)
                    rawData = fileData

            else:
                rawData = fileData

            expected = self.size
            obtained = len(rawData)
            if expected > obtained:
                logger.error("Data stream is incomplete: %s < expected %s bytes" % (obtained, expected))
                rawData += "\x00" * (expected - obtained)
            elif expected < len(rawData):
                logger.info("Data stream contains trailing junk : %s > expected %s bytes" % (obtained, expected))
                rawData = rawData[:expected]
            if self.swap_needed():
                data = numpy.fromstring(rawData, self._bytecode).byteswap().reshape(tuple(dims))
            else:
                data = numpy.fromstring(rawData, self._bytecode).reshape(tuple(dims))
            self._data = data
            self._bytecode = data.dtype.type
        return data


[docs]    def setData(self, npa=None):
        """Setter for data in edf frame"""
        self._data = npa

    data = property(getData, setData, "property: (edf)frame.data, uncompress the datablock when needed")

[docs]    def getByteCode(self):
        if self._bytecode is None:
            self._bytecode = self.data.dtype.type

        return self._bytecode


[docs]    def setByteCode(self, _iVal):
        self._bytecode = _iVal

    bytecode = property(getByteCode, setByteCode)


[docs]    def getEdfBlock(self, force_type=None, fit2dMode=False):
        """
        @param force_type: type of the dataset to be enforced like "float64" or "uint16"
        @type force_type: string or numpy.dtype
        @param fit2dMode: enforce compatibility with fit2d and starts countimg number of images at 1
        @type fit2dMode: boolean
        @return: ascii header block
        @rtype: python string with the concatenation of the ascii header and the binary data block
        """
        if force_type is not None:
            data = self.data.astype(force_type)
        else:
            data = self.data
        fit2dMode = bool(fit2dMode)
        for key in self.header:
            KEY = key.upper()
            if KEY not in self.capsHeader:
                self.capsHeader[KEY] = key
            if key not in self.header_keys:
                self.header_keys.append(key)

        header = self.header.copy()
        header_keys = self.header_keys[:]
        capsHeader = self.capsHeader.copy()

        listHeader = ["{\n"]
#        First of all clean up the headers:
        for i in capsHeader:
            if "DIM_" in i:
                header.pop(capsHeader[i])
                header_keys.remove(capsHeader[i])
        for KEY in ["SIZE", "EDF_BINARYSIZE", "EDF_HEADERSIZE", "BYTEORDER", "DATATYPE", "HEADERID", "IMAGE"]:
            if KEY in capsHeader:
                header.pop(capsHeader[KEY])
                header_keys.remove(capsHeader[KEY])
        if "EDF_DATABLOCKID" in capsHeader:
            header_keys.remove(capsHeader["EDF_DATABLOCKID"])
            #but do not remove the value from dict, instead reset the key ...
            if capsHeader["EDF_DATABLOCKID"] != "EDF_DataBlockID":
                header["EDF_DataBlockID"] = header.pop(capsHeader["EDF_DATABLOCKID"])
                capsHeader["EDF_DATABLOCKID"] = "EDF_DataBlockID"

#            Then update static headers freshly deleted
        header_keys.insert(0, "Size")
        header["Size"] = len(data.tostring())
        header_keys.insert(0, "HeaderID")
        header["HeaderID"] = "EH:%06d:000000:000000" % (self.iFrame + fit2dMode)
        header_keys.insert(0, "Image")
        header["Image"] = str(self.iFrame + fit2dMode)

        dims = list(data.shape)
        nbdim = len(dims)
        for i in dims:
            key = "Dim_%i" % nbdim
            header[key] = i
            header_keys.insert(0, key)
            nbdim -= 1
        header_keys.insert(0, "DataType")
        header["DataType"] = NUMPY_EDF_DTYPE[str(numpy.dtype(data.dtype))]
        header_keys.insert(0, "ByteOrder")
        if numpy.little_endian:
            header["ByteOrder"] = "LowByteFirst"
        else:
            header["ByteOrder"] = "HighByteFirst"
        approxHeaderSize = 100
        for key in header:
            approxHeaderSize += 7 + len(key) + len(str(header[key]))
        approxHeaderSize = BLOCKSIZE * (approxHeaderSize // BLOCKSIZE + 1)
        header_keys.insert(0, "EDF_HeaderSize")
        header["EDF_HeaderSize"] = "%5s" % (approxHeaderSize)
        header_keys.insert(0, "EDF_BinarySize")
        header["EDF_BinarySize"] = len(data.tostring())
        header_keys.insert(0, "EDF_DataBlockID")
        if not "EDF_DataBlockID" in header:
            header["EDF_DataBlockID"] = "%i.Image.Psd" % (self.iFrame + fit2dMode)
        preciseSize = 4 #2 before {\n 2 after }\n
        for key in header_keys:
            #Escape keys or values that are no ascii
            strKey = str(key)
            if not isAscii(strKey, listExcluded=["}", "{"]):
                logger.warning("Non ascii key %s, skipping" % strKey)
                continue
            strValue = str(header[key])
            if not isAscii(strValue, listExcluded=["}", "{"]):
                logger.warning("Non ascii value %s, skipping" % strValue)
                continue
            line = strKey + " = " + strValue + " ;\n"
            preciseSize += len(line)
            listHeader.append(line)
        if preciseSize > approxHeaderSize:
            logger.error("I expected the header block only at %s in fact it is %s" % (approxHeaderSize, preciseSize))
            for  idx, line in enumerate(listHeader[:]):
                if line.startswith("EDF_HeaderSize"):
                    headerSize = BLOCKSIZE * (preciseSize // BLOCKSIZE + 1)
                    newline = "EDF_HeaderSize = %5s ;\n" % headerSize
                    delta = len(newline) - len(line)
                    if (preciseSize // BLOCKSIZE) != ((preciseSize + delta) // BLOCKSIZE):
                        headerSize = BLOCKSIZE * ((preciseSize + delta) // BLOCKSIZE + 1)
                        newline = "EDF_HeaderSize = %5s ;\n" % headerSize
                    preciseSize = preciseSize + delta
                    listHeader[idx] = newline
                    break
        else:
            headerSize = approxHeaderSize
        listHeader.append(" "*(headerSize - preciseSize) + "}\n")
        return "".join(listHeader) + data.tostring()





[docs]class edfimage(fabioimage):
    """ Read and try to write the ESRF edf data format """

    def __init__(self, data=None , header=None, header_keys=None, frames=None):
        self.currentframe = 0
        self.filesize = None
        try:
            dim = len(data.shape)
        except Exception, error: #IGNORE:W0703
            logger.debug("Data don't look like a numpy array (%s), resetting all!!" % error)
            data = None
            dim = 0
            fabioimage.__init__(self, data, header)
        if dim == 2:
            fabioimage.__init__(self, data, header)
        elif dim == 1 :
            data.shape = (0, len(data))
            fabioimage.__init__(self, data, header)
        elif dim == 3 :
            fabioimage.__init__(self, data[0, :, :], header)
        elif dim == 4 :
            fabioimage.__init__(self, data[0, 0, :, :], header)
        elif dim == 5 :
            fabioimage.__init__(self, data[0, 0, 0, :, :], header)

        if frames is None:
            frame = Frame(data=self.data, header=self.header,
                          header_keys=header_keys ,
                          number=self.currentframe)
            self.__frames = [frame]
        else:
            self.__frames = frames

    @staticmethod

[docs]    def checkHeader(header=None):
        """
        Empty for fabioimage but may be populated by others classes
        """
        if type(header) != types.DictionaryType:
            return {}
        new = {}
        for key, value in header.items():
            new[toAscii(key, ";{}")] = toAscii(value, ";{}")
        return new


    @staticmethod
    def _readHeaderBlock(infile):
        """
        Read in a header in some EDF format from an already open file

        @param infile: file object open in read mode
        @return: string (or None if no header was found.
        """
        MAX_HEADER_SIZE = BLOCKSIZE * 20
        block = infile.read(BLOCKSIZE)
        if len(block) < BLOCKSIZE:
            logger.debug("Under-short header: only %i bytes in %s" % (len(block), infile.name))
            return
        if (block.find("{") < 0) :
            # This does not look like an edf file
            logger.warning("no opening {. Corrupt header of EDF file %s" % infile.name)
            return
        if "EDF_HeaderSize" in block:
            start = block.index("EDF_HeaderSize")
            chunk = block[start:].split("=")[1].strip()
            try:
                new_max_header_size = int(chunk.split(";")[0].strip())
            except Exception:
                logger.warning("Unable to read header size in %s" % chunk)
            else:
                if new_max_header_size > MAX_HEADER_SIZE:
                    logger.info("Redefining MAX_HEADER_SIZE to %s" % new_max_header_size)
                    MAX_HEADER_SIZE = new_max_header_size
        while '}' not in block:
            block = block + infile.read(BLOCKSIZE)
            if len(block) > MAX_HEADER_SIZE:
                logger.warning("Runaway header in EDF file MAX_HEADER_SIZE: %s \n%s" % (MAX_HEADER_SIZE, block))
                return
        start = block.find("{") + 1
        end = block.find("}")

        # Now it is essential to go to the start of the binary part
        if block[end: end + 3] == "}\r\n":
            offset = end + 3 - len(block)
        elif block[end: end + 2] == "}\n":
            offset = end + 2 - len(block)
        else:
            logger.error("Unable to locate start of the binary section")
            offset = None
        if offset is not None:
            infile.seek(offset, os.SEEK_CUR)
        return block[start:end]


    def _readheader(self, infile):
        """
        Read all headers in a file and populate self.header
        data is not yet populated
        @type infile: file object open in read mode
        """
        self.__frames = []
        bContinue = True
        while bContinue:
            block = self._readHeaderBlock(infile)
            if block is None:
                bContinue = False
                break
            frame = Frame(number=self.nframes)
            size = frame.parseheader(block)
            frame.file = infile
            frame.start = infile.tell()
            frame.size = size
            self.__frames += [frame]
            try:
                infile.seek(size, os.SEEK_CUR)
            except Exception, error:
                logger.warning("infile is %s" % infile)
                logger.warning("Position is %s" % infile.tell())
                logger.warning("size is %s" % size)
                logger.error("It seams this error occurs under windows when reading a (large-) file over network: %s ", error)
                raise Exception(error)

            if  frame.start + size > infile.size:
                logger.warning("Non complete datablock: got %s, expected %s" % (infile.size - frame.start, size))
                bContinue = False
                break

        for i, frame in enumerate(self.__frames):
            missing = []
            for item in MINIMUM_KEYS:
                if item not in frame.capsHeader:
                    missing.append(item)
            if len(missing) > 0:
                logger.info("EDF file %s frame %i misses mandatory keys: %s " % (self.filename, i, " ".join(missing)))
        self.currentframe = 0



[docs]    def read(self, fname, frame=None):
        """
        Read in header into self.header and
            the data   into self.data
        """
        self.resetvals()
        self.filename = fname

        infile = self._open(fname, "rb")
        self._readheader(infile)
        if frame is None:
            pass
        elif frame < self.nframes:
            self = self.getframe(frame)
        else:
            logger.error("Reading file %s You requested frame %s but only %s frames are available", fname, frame, self.nframes)
        self.resetvals()
        # ensure the PIL image is reset
        self.pilimage = None
        return self



[docs]    def swap_needed(self):
        """
        Decide if we need to byteswap
        """
        if ('Low'  in self.header[self.capsHeader['BYTEORDER']] and numpy.little_endian) or \
           ('High' in self.header[self.capsHeader['BYTEORDER']] and not numpy.little_endian):
            return False
        if ('High'  in self.header[self.capsHeader['BYTEORDER']] and numpy.little_endian) or \
           ('Low' in self.header[self.capsHeader['BYTEORDER']] and not numpy.little_endian):
            if self.bpp in [2, 4, 8]:
                return True
            else:
                return False



[docs]    def unpack(self):
        """
        Unpack a binary blob according to the specification given in the header and return the dataset

        @return: dataset as numpy.ndarray
        """
        return self.__frames[self.currentframe].getData()




[docs]    def getframe(self, num):
        """ returns the file numbered 'num' in the series as a fabioimage """
        newImage = None
        if self.nframes == 1:
            logger.debug("Single frame EDF; having fabioimage default behavour: %s" % num)
            newImage = fabioimage.getframe(self, num)
        elif num in xrange(self.nframes):
            logger.debug("Multi frame EDF; having edfimage specific behavour: %s/%s" % (num, self.nframes))
            newImage = edfimage(frames=self.__frames)
            newImage.currentframe = num
            newImage.filename = self.filename
        else:
            txt = "Cannot access frame: %s/%s" % (num, self.nframes)
            logger.error(txt)
            raise ValueError("edfimage.getframe:" + txt)
        return newImage




[docs]    def previous(self):
        """ returns the previous file in the series as a fabioimage """
        newImage = None
        if self.nframes == 1:
            newImage = fabioimage.previous(self)
        else:
            newFrameId = self.currentframe - 1
            newImage = self.getframe(newFrameId)
        return newImage




[docs]    def next(self):
        """ returns the next file in the series as a fabioimage """
        newImage = None
        if self.nframes == 1:
            newImage = fabioimage.next(self)
        else:
            newFrameId = self.currentframe + 1
            newImage = self.getframe(newFrameId)
        return newImage




[docs]    def write(self, fname, force_type=None, fit2dMode=False):
        """
        Try to write a file
        check we can write zipped also
        mimics that fabian was writing uint16 (we sometimes want floats)

        @param force_type: can be numpy.uint16 or simply "float"
        @return: None

        """

        with self._open(fname, mode="wb") as outfile:
            for i, frame in enumerate(self.__frames):
                frame.iFrame = i
                outfile.write(frame.getEdfBlock(force_type=force_type, fit2dMode=fit2dMode))




[docs]    def appendFrame(self, frame=None, data=None, header=None):
        """
        Method used add a frame to an EDF file
        @param frame: frame to append to edf image
        @type frame: instance of Frame
        @return: None
        """
        if isinstance(frame, Frame):
            self.__frames.append(frame)
        else:
            self.__frames.append(Frame(data, header))




[docs]    def deleteFrame(self, frameNb=None):
        """
        Method used to remove a frame from an EDF image. by default the last one is removed.
        @param frameNb: frame number to remove, by  default the last.
        @type frameNb: integer
        @return: None
        """
        if frameNb is None:
            self.__frames.pop()
        else:
            self.__frames.pop(frameNb)



[docs]    def fastReadData(self, filename=None):
        """
        This is a special method that will read and return the data from another file ...
        The aim is performances, ... but only supports uncompressed files. 
         
        @return: data from another file using positions from current edfimage
        """
        if (filename is None) or not os.path.isfile(filename):
            raise RuntimeError("edfimage.fastReadData is only valid with another file: %s does not exist" % (filename))
        data = None
        frame = self.__frames[self.currentframe]
        with open(filename, "rb")as f:
            f.seek(frame.start)
            raw = f.read(frame.size)
        try:
            data = numpy.fromstring(raw, dtype=self.bytecode)
            data.shape = self.data.shape
        except Exception, err :
            logger.error("unable to convert file content to numpy array: %s", err)
        return data



[docs]    def fastReadROI(self, filename, coords=None):
        """
        Method reading Region of Interest of another file  based on metadata available in current edfimage.
        The aim is performances, ... but only supports uncompressed files.
        
        @return: ROI-data from another file using positions from current edfimage
        @rtype: numpy 2darray
        """
        if (filename is None) or not os.path.isfile(filename):
            raise RuntimeError("edfimage.fastReadData is only valid with another file: %s does not exist" % (filename))
        data = None
        frame = self.__frames[self.currentframe]

        if len(coords) == 4:
            slice1 = self.make_slice(coords)
        elif len(coords) == 2 and isinstance(coords[0], slice) and \
                                  isinstance(coords[1], slice):
            slice1 = coords
        else:
            logger.warning('readROI: Unable to understand Region Of Interest: got %s', coords)
            return
        d1 = self.data.shape[-1]
        start0 = slice1[0].start
        start1 = slice1[1].start
        slice2 = (slice(0, slice1[0].stop - start0, slice1[0].step),
                   slice(0, slice1[1].stop - start1, slice1[1].step))
        start = frame.start + self.bpp * (d1 * start0 + start1)
        size = self.bpp * ((slice2[0].stop) * d1)
        with open(filename, "rb")as f:
            f.seek(start)
            raw = f.read(size)
        try:
            data = numpy.fromstring(raw, dtype=self.bytecode)
            data.shape = -1, d1
        except Exception, err :
            logger.error("unable to convert file content to numpy array: %s", err)
        return data[slice2]


################################################################################
# Properties definition for header, data, header_keys and capsHeader
################################################################################


[docs]    def getNbFrames(self):
        """
        Getter for number of frames
        """
        return len(self.__frames)


[docs]    def setNbFrames(self, val):
        """
        Setter for number of frames ... should do nothing. Here just to avoid bugs
        """
        if val != len(self.__frames):
            logger.warning("trying to set the number of frames ")

    nframes = property(getNbFrames, setNbFrames, "property: number of frames in EDF file")



[docs]    def getHeader(self):
        """
        Getter for the headers. used by the property header,
        """
        return self.__frames[self.currentframe].header


[docs]    def setHeader(self, _dictHeader):
        """
        Enforces the propagation of the header to the list of frames
        """
        try:
            self.__frames[self.currentframe].header = _dictHeader
        except AttributeError:
            self.__frames = [Frame(header=_dictHeader)]
        except IndexError:
            if self.currentframe < len(self.__frames):
                self.__frames.append(Frame(header=_dictHeader))


[docs]    def delHeader(self):
        """
        Deleter for edf header
        """
        self.__frames[self.currentframe].header = {}

    header = property(getHeader, setHeader, delHeader, "property: header of EDF file")


[docs]    def getHeaderKeys(self):
        """
        Getter for edf header_keys
        """
        return self.__frames[self.currentframe].header_keys


[docs]    def setHeaderKeys(self, _listtHeader):
        """
        Enforces the propagation of the header_keys to the list of frames
        @param _listtHeader: list of the (ordered) keys in the header
        @type _listtHeader: python list
        """
        try:
            self.__frames[self.currentframe].header_keys = _listtHeader
        except AttributeError:
            self.__frames = [Frame(header_keys=_listtHeader)]
        except IndexError:
            if self.currentframe < len(self.__frames):
                self.__frames.append(Frame(header_keys=_listtHeader))


[docs]    def delHeaderKeys(self):
        """
        Deleter for edf header_keys
        """
        self.__frames[self.currentframe].header_keys = []

    header_keys = property(getHeaderKeys, setHeaderKeys, delHeaderKeys, "property: header_keys of EDF file")


[docs]    def getData(self):
        """
        getter for edf Data
        @return: data for current frame
        @rtype: numpy.ndarray
        """
        npaData = None
        try:
            npaData = self.__frames[self.currentframe].data
        except AttributeError:
            self.__frames = [Frame()]
            npaData = self.__frames[self.currentframe].data
        except IndexError:
            if self.currentframe < len(self.__frames):
                self.__frames.append(Frame())
                npaData = self.__frames[self.currentframe].data
        return npaData



[docs]    def setData(self, _data):
        """
        Enforces the propagation of the data to the list of frames
        @param _data: numpy array representing data
        """
        try:
            self.__frames[self.currentframe].data = _data
        except AttributeError:
            self.__frames = [Frame(data=_data)]
        except IndexError:
            if self.currentframe < len(self.__frames):
                self.__frames.append(Frame(data=_data))


[docs]    def delData(self):
        """
        deleter for edf Data
        """
        self.__frames[self.currentframe].data = None

    data = property(getData, setData, delData, "property: data of EDF file")


[docs]    def getCapsHeader(self):
        """
        getter for edf headers keys in upper case
        @return: data for current frame
        @rtype: dict
        """
        return self.__frames[self.currentframe].capsHeader


[docs]    def setCapsHeader(self, _data):
        """
        Enforces the propagation of the header_keys to the list of frames
        @param _data: numpy array representing data
        """
        self.__frames[self.currentframe].capsHeader = _data


[docs]    def delCapsHeader(self):
        """
        deleter for edf capsHeader
        """
        self.__frames[self.currentframe].capsHeader = {}

    capsHeader = property(getCapsHeader, setCapsHeader, delCapsHeader, "property: capsHeader of EDF file, i.e. the keys of the header in UPPER case.")


[docs]    def getDim1(self):
        return self.__frames[self.currentframe].dim1


[docs]    def setDim1(self, _iVal):
        try:
            self.__frames[self.currentframe].dim1 = _iVal
        except AttributeError:
            self.__frames = [Frame()]
        except IndexError:
            if self.currentframe < len(self.__frames):
                self.__frames.append(Frame())
                self.__frames[self.currentframe].dim1 = _iVal

    dim1 = property(getDim1, setDim1)

[docs]    def getDim2(self):
        return self.__frames[self.currentframe].dim2


[docs]    def setDim2(self, _iVal):
        try:
            self.__frames[self.currentframe].dim2 = _iVal
        except AttributeError:
            self.__frames = [Frame()]
        except IndexError:
            if self.currentframe < len(self.__frames):
                self.__frames.append(Frame())
                self.__frames[self.currentframe].dim2 = _iVal

    dim2 = property(getDim2, setDim2)


[docs]    def getDims(self):
        return self.__frames[self.currentframe].dims

    dims = property(getDims)

[docs]    def getByteCode(self):
        return self.__frames[self.currentframe].bytecode


[docs]    def setByteCode(self, _iVal):
        try:
            self.__frames[self.currentframe].bytecode = _iVal
        except AttributeError:
            self.__frames = [Frame()]
        except IndexError:
            if self.currentframe < len(self.__frames):
                self.__frames.append(Frame())
                self.__frames[self.currentframe].bytecode = _iVal

    bytecode = property(getByteCode, setByteCode)

[docs]    def getBpp(self):
        return self.__frames[self.currentframe].bpp


[docs]    def setBpp(self, _iVal):
        try:
            self.__frames[self.currentframe].bpp = _iVal
        except AttributeError:
            self.__frames = [Frame()]
        except IndexError:
            if self.currentframe < len(self.__frames):
                self.__frames.append(Frame())
                self.__frames[self.currentframe].bpp = _iVal

    bpp = property(getBpp, setBpp)

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Source code for fabio.binaryimage

#!/usr/bin/env python
# coding: utf8

# Get ready for python3:
from __future__ import with_statement, print_function
__doc__ = """
Authors: Gael Goret, Jerome Kieffer, ESRF, France
Emails: gael.goret@esrf.fr, jerome.kieffer@esrf.fr
        Brian Richard Pauw <brian@stack.nl>

Binary files images are simple none-compressed 2D images only defined by their :
data-type, dimensions, byte order and offset

This simple library has been made for manipulating exotic/unknown files format.
"""

__authors__ = ["Gaël Goret", "Jérôme Kieffer", "Brian Pauw"]
__contact__ = "gael.goret@esrf.fr"
__license__ = "GPLv3+"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__version__ = "17 Oct 2012"

from fabioimage import fabioimage
import numpy, logging
logger = logging.getLogger("binaryimage")


[docs]class binaryimage(fabioimage):
    """
    This simple library has been made for manipulating exotic/unknown files format.

    Binary files images are simple none-compressed 2D images only defined by their :
    data-type, dimensions, byte order and offset

    if offset is set to a negative value, the image is read using the last data but n
    data in the file, skipping any header.
    """

    def __init__(self, *args, **kwargs):
        fabioimage.__init__(self, *args, **kwargs)

    @staticmethod

[docs]    def swap_needed(endian):
        """
        Decide if we need to byteswap
        """
        if (endian == '<' and numpy.little_endian) or (endian == '>' and not numpy.little_endian):
            return False
        if (endian == '>' and numpy.little_endian) or (endian == '<' and not numpy.little_endian):
            return True



[docs]    def read(self, fname, dim1, dim2, offset=0, bytecode="int32", endian="<"):
        """
        Read a binary image

        @param fname: file name
        @type fname: string
        @param dim1: image dimensions (Fast index)
        @param dim2: image dimensions (Slow index)
        @param offset: starting position of the data-block. If negative, starts at the end.
        @param bytecode: can be "int8","int16","int32","int64","uint8","uint16","uint32","uint64","float32","float64",...
        @param endian:  among short or long endian ("<" or ">")

        """
        self.filename = fname
        self.dim1 = dim1
        self.dim2 = dim2
        self.bytecode = bytecode
        f = open(self.filename, "rb")
        dims = [dim2, dim1]
        bpp = len(numpy.array(0, bytecode).tostring())
        size = dims[0] * dims[1] * bpp

        if offset >= 0:
            f.seek(offset)
        else:
            try:
                f.seek(-size + offset + 1, 2) #seek from EOF backwards
            except IOError:
                logging.warn('expected datablock too large, please check bytecode settings: {}'.format(bytecode))
            except:
                logging.error('Uncommon error encountered when reading file')
        rawData = f.read(size)
        if  self.swap_needed(endian):
            data = numpy.fromstring(rawData, bytecode).byteswap().reshape(tuple(dims))
        else:
            data = numpy.fromstring(rawData, bytecode).reshape(tuple(dims))
        self.data = data
        return self



[docs]    def estimate_offset_value(self, fname, dim1, dim2, bytecode="int32"):
        "Estimates the size of a file"
        with open(fname, "rb") as f:
            bpp = len(numpy.array(0, bytecode).tostring())
            size = dim1 * dim2 * bpp
            totsize = len(f.read())
        logger.info('total size (bytes): %s', totsize)
        logger.info('expected data size given parameters (bytes): %s', size)
        logger.info('estimation of the offset value (bytes): %s', totsize - size)



[docs]    def write(self, fname):
        with open(fname, mode="wb") as outfile:
            outfile.write(self.data.tostring())

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© Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
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Source code for fabio.fabioimage

#!/usr/bin/env python

"""

Authors: Henning O. Sorensen & Erik Knudsen
         Center for Fundamental Research: Metal Structures in Four Dimensions
         Risoe National Laboratory
         Frederiksborgvej 399
         DK-4000 Roskilde
         email:erik.knudsen@risoe.dk

         and Jon Wright, Jerome Kieffer: ESRF

"""
from __future__ import with_statement
import os, types, logging, sys, tempfile
logger = logging.getLogger("fabioimage")
import numpy
try:
    from PIL import Image
except ImportError:
    logger.warning("PIL is not installed ... trying to do without")
    Image = None
import fabioutils, converters



[docs]class fabioimage(object):
    """
    A common object for images in fable
    Contains a numpy array (.data) and dict of meta data (.header)
    """

    _need_a_seek_to_read = False
    _need_a_real_file = False

    def __init__(self, data=None , header=None):
        """
        Set up initial values
        """
        self._classname = None
        if type(data) in types.StringTypes:
            raise Exception("fabioimage.__init__ bad argument - " + \
                            "data should be numpy array")
        self.data = self.checkData(data)
        self.pilimage = None
        if header is None:
            self.header = {}
        else:
            self.header = self.checkHeader(header)
        self.header_keys = self.header.keys() # holds key ordering
        if self.data is not None:
            self.dim2, self.dim1 = self.data.shape
        else:
            self.dim1 = self.dim2 = 0
        self.bytecode = None     # numpy typecode
        self.bpp = 2             # bytes per pixel
        # cache for image statistics
        self.mean = self.maxval = self.stddev = self.minval = None
        # Cache roi
        self.roi = None
        self.area_sum = None
        self.slice = None
        # New for multiframe files
        self.nframes = 1
        self.currentframe = 0
        self.filename = None
        self.filenumber = None

    @staticmethod

[docs]    def checkHeader(header=None):
        """
        Empty for fabioimage but may be populated by others classes
        """
        if header is None:
            return {}
        else:
            return header


    @staticmethod

[docs]    def checkData(data=None):
        """
        Empty for fabioimage but may be populated by others classes, especially for format accepting only integers
        """
        return data



[docs]    def getclassname(self):
        """
        Retrieves the name of the class
        @return: the name of the class
        """
        if self._classname is None:
            self._classname = str(self.__class__).replace("<class '", "").replace("'>", "").split(".")[-1]
        return self._classname

    classname = property(getclassname)


[docs]    def getframe(self, num):
        """ returns the file numbered 'num' in the series as a fabioimage """
        if self.nframes == 1:
            # single image per file
            import openimage
            return openimage.openimage(
                fabioutils.jump_filename(self.filename, num))
        raise Exception("getframe out of range")



[docs]    def previous(self):
        """ returns the previous file in the series as a fabioimage """
        import openimage
        return openimage.openimage(
            fabioutils.previous_filename(self.filename))



[docs]    def next(self):
        """ returns the next file in the series as a fabioimage """
        import openimage
        return openimage.openimage(
            fabioutils.next_filename(self.filename))



[docs]    def toPIL16(self, filename=None):
        """
        Convert to Python Imaging Library 16 bit greyscale image

        FIXME - this should be handled by the libraries now
        """
        if not Image:
            raise RuntimeError("PIL is not installed !!! ")
        if filename:
            self.read(filename)
        if self.pilimage is not None:
            return self.pilimage
        # mode map
        size = self.data.shape[:2][::-1]
        typmap = {
            'float32' : "F"     ,
            'int32'   : "F;32S" ,
            'uint32'  : "F;32"  ,
            'int16'   : "F;16S" ,
            'uint16'  : "F;16"  ,
            'int8'    : "F;8S"  ,
            'uint8'   : "F;8"  }
        if typmap.has_key(self.data.dtype.name):
            mode2 = typmap[ self.data.dtype.name ]
            mode1 = mode2[0]
        else:
            raise Exception("Unknown numpy type " + str(self.data.dtype.type))
        #
        # hack for byteswapping for PIL in MacOS
        testval = numpy.array((1, 0), numpy.uint8).view(numpy.uint16)[0]
        if  testval == 1:
            dats = self.data.tostring()
        elif testval == 256:
            dats = self.data.byteswap().tostring()
        else:
            raise Exception("Endian unknown in fabioimage.toPIL16")

        self.pilimage = Image.frombuffer(mode1,
                                         size,
                                         dats,
                                         "raw",
                                         mode2,
                                         0,
                                         1)

        return self.pilimage



[docs]    def getheader(self):
        """ returns self.header """
        return self.header



[docs]    def getmax(self):
        """ Find max value in self.data, caching for the future """
        if self.maxval is None:
            self.maxval = self.data.max()
        return self.maxval



[docs]    def getmin(self):
        """ Find min value in self.data, caching for the future """
        if self.minval is None:
            self.minval = self.data.min()
        return self.minval



[docs]    def make_slice(self, coords):
        """
        Convert a len(4) set of coords into a len(2)
        tuple (pair) of slice objects
        the latter are immutable, meaning the roi can be cached
        """
        assert len(coords) == 4
        if len(coords) == 4:
            # fabian edfimage preference
            if coords[0] > coords[2]:
                coords[0:3:2] = [coords[2], coords[0]]
            if coords[1] > coords[3]:
                coords[1:4:2] = [coords[3], coords[1]]
            #in fabian: normally coordinates are given as (x,y) whereas
            # a matrix is given as row,col
            # also the (for whichever reason) the image is flipped upside
            # down wrt to the matrix hence these tranformations
            fixme = (self.dim2 - coords[3] - 1,
                     coords[0] ,
                     self.dim2 - coords[1] - 1,
                     coords[2])
        return (slice(int(fixme[0]), int(fixme[2]) + 1) ,
                 slice(int(fixme[1]), int(fixme[3]) + 1))




[docs]    def integrate_area(self, coords):
        """
        Sums up a region of interest
        if len(coords) == 4 -> convert coords to slices
        if len(coords) == 2 -> use as slices
        floor -> ? removed as unused in the function.
        """
        if self.data == None:
            # This should return NAN, not zero ?
            return 0
        if len(coords) == 4:
            sli = self.make_slice(coords)
        elif len(coords) == 2 and isinstance(coords[0], slice) and \
                                  isinstance(coords[1], slice):
            sli = coords

        if sli == self.slice and self.area_sum is not None:
            pass
        elif sli == self.slice and self.roi is not None:
            self.area_sum = self.roi.sum(dtype=numpy.float)
        else:
            self.slice = sli
            self.roi = self.data[ self.slice ]
            self.area_sum = self.roi.sum(dtype=numpy.float)
        return self.area_sum



[docs]    def getmean(self):
        """ return the mean """
        if self.mean is None:
            self.mean = self.data.mean(dtype=numpy.double)
        return self.mean



[docs]    def getstddev(self):
        """ return the standard deviation """
        if self.stddev == None:
            self.stddev = self.data.std(dtype=numpy.double)
        return self.stddev



[docs]    def add(self, other):
        """
        Add another Image - warning, does not clip to 16 bit images by default
        """
        if not hasattr(other, 'data'):
            logger.warning('edfimage.add() called with something that ' + \
                'does not have a data field')
        assert self.data.shape == other.data.shape , \
                  'incompatible images - Do they have the same size?'
        self.data = self.data + other.data
        self.resetvals()




[docs]    def resetvals(self):
        """ Reset cache - call on changing data """
        self.mean = self.stddev = self.maxval = self.minval = None
        self.roi = self.slice = self.area_sum = None



[docs]    def rebin(self, x_rebin_fact, y_rebin_fact, keep_I=True):
        """
        Rebin the data and adjust dims
        @param x_rebin_fact: x binning factor
        @param y_rebin_fact: y binning factor
        @param keep_I: shall the signal increase ?
        @type x_rebin_fact: int
        @type y_rebin_fact: int
        @type keep_I: boolean


        """
        if self.data == None:
            raise Exception('Please read in the file you wish to rebin first')

        if (self.dim1 % x_rebin_fact != 0) or (self.dim2 % y_rebin_fact != 0):
            raise RuntimeError('image size is not divisible by rebin factor - ' + \
                  'skipping rebin')
        else:
            dataIn = self.data.astype("float64")
            shapeIn = self.data.shape
            shapeOut = (shapeIn[0] / y_rebin_fact, shapeIn[1] / x_rebin_fact)
            binsize = y_rebin_fact * x_rebin_fact
            if binsize < 50: #method faster for small binning (4x4)
                out = numpy.zeros(shapeOut, dtype="float64")
                for j in range(x_rebin_fact):
                    for i in range(y_rebin_fact):
                        out += dataIn[i::y_rebin_fact, j::x_rebin_fact]
            else: #method faster for large binning (8x8)
                temp = self.data.astype("float64")
                temp.shape = (shapeOut[0], y_rebin_fact, shapeOut[1], x_rebin_fact)
                out = temp.sum(axis=3).sum(axis=1)
        self.resetvals()
        if keep_I:
            self.data = (out / (y_rebin_fact * x_rebin_fact)).astype(self.data.dtype)
        else:
            self.data = out.astype(self.data.dtype)

        self.dim1 = self.dim1 / x_rebin_fact
        self.dim2 = self.dim2 / y_rebin_fact

        #update header
        self.update_header()



[docs]    def write(self, fname):
        """
        To be overwritten - write the file
        """
        raise Exception("Class has not implemented readheader method yet")



[docs]    def save(self, fname):
        'wrapper for write'
        self.write(fname)



[docs]    def readheader(self, filename):
        """
        Call the _readheader function...
        """
        # Override the needs asserting that all headers can be read via python modules
        save_state = self._need_a_real_file , self._need_a_seek_to_read
        self._need_a_real_file , self._need_a_seek_to_read = False, False
        fin = self._open(filename)
        self._readheader(fin)
        fin.close()
        self._need_a_real_file , self._need_a_seek_to_read = save_state


    def _readheader(self, fik_obj):
        """
        Must be overridden in classes
        """
        raise Exception("Class has not implemented _readheader method yet")


[docs]    def update_header(self , **kwds):
        """
        update the header entries
        by default pass in a dict of key, values.
        """
        self.header.update(kwds)



[docs]    def read(self, filename, frame=None):
        """
        To be overridden - fill in self.header and self.data
        """
        raise Exception("Class has not implemented read method yet")
#        return self



[docs]    def load(self, *arg, **kwarg):
        "Wrapper for read"
        return self.read(*arg, **kwarg)



[docs]    def readROI(self, filename, frame=None, coords=None):
        """
        Method reading Region of Interest.
        This implementation is the trivial one, just doing read and crop
        """
        self.read(filename, frame)
        if len(coords) == 4:
            self.slice = self.make_slice(coords)
        elif len(coords) == 2 and isinstance(coords[0], slice) and \
                                  isinstance(coords[1], slice):
            self.slice = coords
        else:
            logger.warning('readROI: Unable to understand Region Of Interest: got %s', coords)
        self.roi = self.data[ self.slice ]
        return self.roi



    def _open(self, fname, mode="rb"):
        """
        Try to handle compressed files, streams, shared memory etc
        Return an object which can be used for "read" and "write"
        ... FIXME - what about seek ?
        """
        fileObject = None
        self.filename = fname
        self.filenumber = fabioutils.extract_filenumber(fname)

        if hasattr(fname, "read") and hasattr(fname, "write"):
            # It is already something we can use
            return fname
        if isinstance(fname, (str, unicode)):
            self.header["filename"] = fname
            if os.path.splitext(fname)[1] == ".gz":
                fileObject = self._compressed_stream(fname,
                                       fabioutils.COMPRESSORS['.gz'],
                                       fabioutils.GzipFile,
                                       mode)
            elif os.path.splitext(fname)[1] == '.bz2':
                fileObject = self._compressed_stream(fname,
                                       fabioutils.COMPRESSORS['.bz2'],
                                       fabioutils.BZ2File,
                                       mode)
            #
            # Here we return the file even though it may be bzipped or gzipped
            # but named incorrectly...
            #
            # FIXME - should we fix that or complain about the daft naming?
            else:
                fileObject = fabioutils.File(fname, mode)
            if "name" not in dir(fileObject):
                fileObject.name = fname

        return fileObject

    def _compressed_stream(self,
                           fname,
                           system_uncompress,
                           python_uncompress,
                           mode='rb'):
        """
        Try to transparently handle gzip / bzip without always getting python
        performance
        """
        # assert that python modules are always OK based on performance benchmark
        # Try to fix the way we are using them?
        fobj = None
        if self._need_a_real_file and mode[0] == "r":
            fo = python_uncompress(fname, mode)
#            fobj = os.tmpfile()
            #problem when not administrator under certain flavors of windows
            tmpfd, tmpfn = tempfile.mkstemp()
            os.close(tmpfd)
            fobj = fabioutils.File(tmpfn, "w+b")
            fobj.write(fo.read())
            fo.close()
            fobj.seek(0)
        elif self._need_a_seek_to_read and mode[0] == "r":
            fo = python_uncompress(fname, mode)
            fobj = fabioutils.StringIO(fo.read(), fname, mode)
        else:
            fobj = python_uncompress(fname, mode)
        return fobj


[docs]    def convert(self, dest):
        """
        Convert a fabioimage object into another fabioimage object (with possible conversions)
        @param dest: destination type "EDF", "edfimage" or the class itself
        """
        if type(dest) in types.StringTypes:
            dest = dest.lower()
            modules = []
            for val  in fabioutils.FILETYPES.values():
                modules += [i + "image" for i in val if i not in modules]
            klass = None
            module = None
            klass_name = None
            for klass_name in modules:
                if  klass_name.startswith(dest):
                    try:
                        module = sys.modules["fabio." + klass_name]
                    except KeyError:
                        try:
                            module = __import__(klass_name)
                        except:
                            logger.error("Failed to import %s", klass_name)
                        else:
                            logger.debug("imported %simage", klass_name)
                    if module is not None:
                        break
            if module is not None:
                if hasattr(module, klass_name):
                    klass = getattr(module, klass_name)
                else:
                    logger.error("Module %s has no image class" % module)
        elif isinstance(dest, self.__class__):
            klass = dest.__class__
        elif ("__new__" in dir(dest)) and isinstance(dest(), fabioimage):
            klass = dest
        else:
            logger.warning("Unrecognized destination format: %s " % dest)
            return self
        if klass is None:
            logger.warning("Unrecognized destination format: %s " % dest)
            return self
        other = klass() #temporary instance (to be overwritten)
        other = klass(data=converters.convert_data(self.classname, other.classname, self.data),
                    header=converters.convert_header(self.classname, other.classname, self.header))
        return other



[docs]def test():
    """
    check some basic fabioimage functionality
    """
    import time
    start = time.time()

    dat = numpy.ones((1024, 1024), numpy.uint16)
    dat = (dat * 50000).astype(numpy.uint16)
    assert dat.dtype.char == numpy.ones((1), numpy.uint16).dtype.char
    hed = {"Title":"50000 everywhere"}
    obj = fabioimage(dat, hed)

    assert obj.getmax() == 50000
    assert obj.getmin() == 50000
    assert obj.getmean() == 50000 , obj.getmean()
    assert obj.getstddev() == 0.

    dat2 = numpy.zeros((1024, 1024), numpy.uint16, savespace=1)
    cord = [ 256, 256, 790, 768 ]
    slic = obj.make_slice(cord)
    dat2[slic] = dat2[slic] + 100

    obj = fabioimage(dat2, hed)

    # New object, so...
    assert obj.maxval is None
    assert obj.minval is None

    assert obj.getmax() == 100, obj.getmax()
    assert obj.getmin() == 0 , obj.getmin()
    npix = (slic[0].stop - slic[0].start) * (slic[1].stop - slic[1].start)
    obj.resetvals()
    area1 = obj.integrate_area(cord)
    obj.resetvals()
    area2 = obj.integrate_area(slic)
    assert area1 == area2
    assert obj.integrate_area(cord) == obj.integrate_area(slic)
    assert obj.integrate_area(cord) == npix * 100, obj.integrate_area(cord)


    def clean():
        """ clean up the created testfiles"""
        for name in ["testfile", "testfile.gz", "testfile.bz2"]:
            try:
                os.remove(name)
            except:
                continue


    clean()
    import gzip, bz2
    gzip.open("testfile.gz", "wb").write("{ hello }")
    fout = obj._open("testfile.gz")
    readin = fout.read()
    assert readin == "{ hello }", readin + " gzipped file"


    bz2.BZ2File("testfilebz", "wb").write("{ hello }")
    fout = obj._open("testfile.bz2")
    readin = fout.read()
    assert readin == "{ hello }", readin + " bzipped file"

    ftest = open("testfile", "wb")
    ftest.write("{ hello }")
    assert ftest == obj._open(ftest)
    ftest.close()
    fout = obj._open("testfile")
    readin = fout.read()
    assert readin == "{ hello }", readin + "plain file"
    fout.close()
    ftest.close()
    clean()

    print "Passed in", time.time() - start, "s"


if __name__ == '__main__':
    test()

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© Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
fabio-0.1.3/doc/html/_modules/fabio/dm3image.html0000644000175000017500000013424312233250022022331 0ustar jeromejerome00000000000000 fabio.dm3image — FabIO 0.1.3 documentation

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Source code for fabio.dm3image

"""
Authors: Henning O. Sorensen & Erik Knudsen
         Center for Fundamental Research: Metal Structures in Four Dimensions
         Risoe National Laboratory
         Frederiksborgvej 399
         DK-4000 Roskilde
         email:erik.knudsen@risoe.dk

        + Jon Wright, ESRF
"""
import logging
import numpy
from fabioimage import fabioimage
logger = logging.getLogger("dm3image")

DATA_TYPES = {  2     :  numpy.int16,
                4     :  numpy.uint16,
                3     :  numpy.int32,
                5     :  numpy.uint32,
                6     :  numpy.float32,
                7     :  numpy.float,
                8     :  numpy.int8,
                9     :  None,
                10    :  None,
                15    :  'Struct',
                18    :  None,
                20    :  None
                }

DATA_BYTES = {  2     :  2,
                4     :  2,
                3     :  4,
                5     :  4,
                6     :  4,
                7     :  8,
                8     :  1,
                9     :  None,
                10    :  None,
                15    :  'Struct',
                18    :  None,
                20    :  None
                }




[docs]class dm3image(fabioimage):
    """ Read and try to write the dm3 data format """
    def __init__(self, *args, **kwargs):
        fabioimage.__init__(self, *args, **kwargs)
        self.encoded_datatype = None
        self.no_data_elements = None
        self.grouptag_is_sorted = None
        self.grouptag_is_open = None
        self.tag_encoded_type = None
        self.tag_data_type = None
        self.tag_is_data = None
        self.grouptag_no_tags = None
        self.bytes_in_file = None
        self.tag_label_length = None
        self.go_on = None

    def _readheader(self):
        self.infile.seek(0)
        file_format = self.readbytes(4, numpy.uint32)[0] # should be 3
        assert file_format == 3, 'Wrong file type '
        self.bytes_in_file = self.readbytes(4, numpy.uint32)[0]
        self.byte_order = self.readbytes(4, numpy.uint32)[0] # 0 = big, 1= little
        print 'read dm3 file - file format ', file_format
        print 'Bytes in file : ' , self.bytes_in_file
        print 'Byte order :', self.byte_order, '  - 0 = bigEndian , 1 = littleEndian'

        if self.byte_order == 0:
            self.swap = True
        elif self.byte_order == 1:
            self.swap = False
        else:
            raise ValueError


[docs]    def read(self, fname, frame=None):
        self.header = {}
        self.resetvals()
        self.infile = self._open(fname, "rb")
        self._readheader()
        self.go_on = True
        print self.go_on
        while self.go_on:
            self.read_tag_group()
            self.read_tag_entry()
            if self.infile.tell() > self.bytes_in_file: break

            while self.tag_is_data == 21:
                self.read_tag_entry()
                if self.infile.tell() > self.bytes_in_file:
                    self.go_on = False

        (dim1_raw, dim2_raw) = self.header['Active Size (pixels)'].split()
        (dim1_raw, dim2_raw) = (eval(dim1_raw), eval(dim2_raw))
        (dim1_binning, dim2_binning) = self.header['Binning'].split()
        (dim1_binning, dim2_binning) = (eval(dim1_binning), eval(dim2_binning))
        self.dim1 = dim1_raw / dim1_binning
        self.dim2 = dim2_raw / dim2_binning
        #print dim1,dim2
        if self.header.has_key('Data'):
            self.data = self.header['Data'].reshape(self.dim1, self.dim2)



[docs]    def readbytes(self, bytes_to_read, format, swap=True):
        raw = self.infile.read(bytes_to_read)
        if format != None:
            data = numpy.fromstring(raw, format)
        else:
            data = raw
        if swap:
            data = data.byteswap()
        return data





[docs]    def read_tag_group(self):

        self.grouptag_is_sorted = self.readbytes(1, numpy.uint8)[0]
        self.grouptag_is_open = self.readbytes(1, numpy.uint8)[0]
        self.grouptag_no_tags = self.readbytes(4, numpy.uint32)[0]
        logger.debug('TagGroup is sorted? %s', self.grouptag_is_sorted)
        logger.debug('TagGroup is open? %s', self.grouptag_is_open)
        logger.debug('no of tags in TagGroup %s', self.grouptag_no_tags)



[docs]    def read_tag_entry(self):

        self.tag_is_data = self.readbytes(1, numpy.uint8)[0]
        self.tag_label_length = self.readbytes(2, numpy.uint16)[0]
        logger.debug('does Tag have data ? %s  -  20 = Tag group , 21 = data ', self.tag_is_data)
        logger.debug('length of tag_label ', self.tag_label_length)
        if self.tag_label_length != 0:
            tag_label = self.infile.read(self.tag_label_length)
        else:
            tag_label = None

        if self.tag_is_data == 21:
            # This is data
            self.header[tag_label] = self.read_tag_type()
            logger.debug("%s: %s", tag_label, self.header[tag_label])




[docs]    def read_tag_type(self):
        if self.infile.read(4) != '%%%%':
            raise IOError
        self.tag_data_type = self.readbytes(4, numpy.uint32)[0]
        logger.debug('data is of type : %s  - 1 = simple, 2= string, 3 = array, >3 structs', self.tag_data_type)
        self.tag_encoded_type = self.readbytes(4, numpy.uint32)[0]
        logger.debug('encode type: %s %s', self.tag_encoded_type, DATA_TYPES[ self.tag_encoded_type])
        if self.tag_data_type == 1:
            # simple type
            return self.readbytes(DATA_BYTES[ self.tag_encoded_type],
                                  DATA_TYPES[ self.tag_encoded_type],
                                  swap=self.swap)[0]
        # are the data stored in a simple array?
        if self.tag_encoded_type == 20 and self.tag_data_type == 3 :
            self.data_type = self.readbytes(4, numpy.uint32)[0]
            self.no_data_elements = self.readbytes(4, numpy.uint32)[0]
            if self.data_type == 10:
                logger.debug('skip bytes %s', self.no_data_elements)
                dump = self.infile.read(self.no_data_elements)
                return None

            logger.debug('Data are stored as a simple a array -')
            logger.debug('%s data elemets stored as %s', self.no_data_elements, self.data_type)
            read_no_bytes = DATA_BYTES[self.data_type] * self.no_data_elements
            format = DATA_TYPES[self.data_type]
            return self.readbytes(read_no_bytes, format, swap=self.swap)

        # are the data stored in a complex array ?
        # print 'tag_type + data_type', self.tag_encoded_type,self.tag_data_type

        #print self.tag_encoded_type , self.tag_data_type 
        if self.tag_encoded_type == 20 and self.tag_data_type > 3 :
            self.tag_encoded_type = self.readbytes(4, numpy.uint32)[0]
            logger.debug('found array - new tag_encoded_type %s', self.tag_encoded_type)
            if self.tag_encoded_type == 15:            # struct type
                 ###type = self.readbytes(4,numpy.int32)
                struct_name_length = self.readbytes(4, numpy.int32)[0]
                struct_number_fields = self.readbytes(4, numpy.int32)[0]
                #print 'struct - name_length, number_field',  struct_name_length,struct_number_fields
                #print self.infile.read(struct_name_length)
                field_info = []
                for i in range(struct_number_fields):
                    field_info.append([self.readbytes(4, numpy.int32)[0], self.readbytes(4, numpy.int32)[0]])
                #print field_info
                self.no_data_elements = self.readbytes(4, numpy.int32)[0]
                #print '%i data elemets stored as ' %self.no_data_elements
                bytes_in_struct = 0
                for i in range(struct_number_fields):
                    bytes_in_struct += DATA_BYTES[field_info[i][1]]
                logger.debug('skip bytes %s', self.no_data_elements * bytes_in_struct)
                dump = self.infile.read(self.no_data_elements * bytes_in_struct)
                return None


        if self.tag_encoded_type == 15:            # struct type
            ###type = self.readbytes(4,numpy.int32)
            struct_name_length = self.readbytes(4, numpy.int32)[0]
            struct_number_fields = self.readbytes(4, numpy.int32)[0]
            #print 'struct - name_length, number_field',  struct_name_length,struct_number_fields
            #print self.infile.read(struct_name_length)
            field_info = []
            for i in range(struct_number_fields):
                field_info.append([self.readbytes(4, numpy.int32)[0], self.readbytes(4, numpy.int32)[0]])
            #print field_info
            field_data = ''
            for i in range(struct_number_fields):
                #print type(i)
                field_data = field_data + self.readbytes(field_info[i][0], None, swap=False) + ' '
                field_data = field_data + '%i  ' % self.readbytes(DATA_BYTES[field_info[i][1]],
                                                                 DATA_TYPES[field_info[i][1]],
                                                                 swap=self.swap)[0]
            return field_data



[docs]    def read_data(self):
        self.encoded_datatype = numpy.fromstring(self.infile.read(4), numpy.uint32).byteswap()

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© Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
fabio-0.1.3/doc/html/_modules/fabio/readbytestream.html0000644000175000017500000003267312233250022023662 0ustar jeromejerome00000000000000 fabio.readbytestream — FabIO 0.1.3 documentation

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Source code for fabio.readbytestream

#!/usr/bin/env python
#coding: utf8

"""
Reads a bytestream

Authors: Jon Wright    Henning O. Sorensen & Erik Knudsen
         ESRF          Risoe National Laboratory
"""

import numpy, logging
logger = logging.getLogger("readbytestream")
DATATYPES = {
    # type  sign bytes
    ("int", 'n', 1) : numpy.uint8,
    ("int", 'n', 2) : numpy.uint16,
    ("int", 'n', 4) : numpy.uint32,
    ("int", 'y', 1) : numpy.int8,
    ("int", 'y', 2) : numpy.int16,
    ("int", 'y', 4) : numpy.int32,
    ('float', 'y', 4) : numpy.float32, # does this occur in bruker?
    ('double', 'y', 4): numpy.float64
    }



[docs]def readbytestream(fil,
                   offset,
                   x,
                   y,
                   nbytespp,
                   datatype='int',
                   signed='n',
                   swap='n',
                   typeout=numpy.uint16):
    """
    Reads in a bytestream from a file (which may be a string indicating
    a filename, or an already opened file (should be "rb"))
    offset is the position (in bytes) where the pixel data start
    nbytespp = number of bytes per pixel
    type can be int or float (4 bytes pp) or double (8 bytes pp)
    signed: normally signed data 'y', but 'n' to try to get back the 
    right numbers when unsigned data are converted to signed 
    (python once had no unsigned numeric types.)
    swap, normally do not bother, but 'y' to swap bytes
    typeout is the numpy type to output, normally uint16, 
    but more if overflows occurred
    x and y are the pixel dimensions
    
    TODO : Read in regions of interest
    
    PLEASE LEAVE THE STRANGE INTERFACE ALONE - 
    IT IS USEFUL FOR THE BRUKER FORMAT
    """
    tin = "dunno"
    length = nbytespp * x * y # bytes per pixel times number of pixels
    if datatype in ['float', 'double']:
        signed = 'y'

    key = (datatype, signed, nbytespp)
    try:
        tin = DATATYPES[key]
    except:
        logging.warning("datatype,signed,nbytespp " + str(key))
        raise Exception("Unknown combination of types to readbytestream")

    # Did we get a string (filename) or a readable stream object?
    if hasattr(fil, "read") and hasattr(fil, "seek"):
        infile = fil
        opened = False
    else:
        infile = open(fil, 'rb')
        opened = True

    infile.seek(offset)

    arr = numpy.array(numpy.reshape(
            numpy.fromstring(
                infile.read(length), tin) , (x, y)), typeout)

    if swap == 'y':
        arr = arr.byteswap()

    if opened:
        infile.close()

    return arr

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© Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
fabio-0.1.3/doc/html/_modules/fabio/OXDimage.html0000644000175000017500000035611612233250022022305 0ustar jeromejerome00000000000000 fabio.OXDimage — FabIO 0.1.3 documentation

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Source code for fabio.OXDimage

#!/usr/bin/env python
#coding: utf8

from __future__ import with_statement
__doc__ = """
Reads Oxford Diffraction Sapphire 3 images

Authors:
........
* Henning O. Sorensen & Erik Knudsen:
  Center for Fundamental Research: Metal Structures in Four Dimensions;
  Risoe National Laboratory;
  Frederiksborgvej 399;
  DK-4000 Roskilde;
  email:erik.knudsen@risoe.dk
* Jon Wright, Jérôme Kieffer & Gaël Goret:
  European Synchrotron Radiation Facility;
  Grenoble (France)

"""

import time, logging, struct
logger = logging.getLogger("OXDimage")
import numpy
from fabioimage import fabioimage
from compression import decTY1, compTY1

try:
    from numpy import rad2deg, deg2rad
except ImportError: #naive implementation for very old numpy (v1.0.1 on MacOSX from Risoe)
    rad2deg = lambda x: 180.0 * x / numpy.pi
    deg2rad = lambda x: x * numpy.pi / 180.

DETECTOR_TYPES = {0: 'Sapphire/KM4CCD (1x1: 0.06mm, 2x2: 0.12mm)',
1: 'Sapphire2-Kodak (1x1: 0.06mm, 2x2: 0.12mm)',
2: 'Sapphire3-Kodak (1x1: 0.03mm, 2x2: 0.06mm, 4x4: 0.12mm)',
3: 'Onyx-Kodak (1x1: 0.06mm, 2x2: 0.12mm, 4x4: 0.24mm)',
4: 'Unknown Oxford diffraction detector'}

DEFAULT_HEADERS = {'Header Version':  'OD SAPPHIRE  3.0',
                   'Compression': "TY1",
                   'Header Size In Bytes': 5120,
                   "ASCII Section size in Byte": 256,
                   "General Section size in Byte": 512,
                   "Special Section size in Byte": 768,
                   "KM4 Section size in Byte": 1024,
                   "Statistic Section in Byte": 512,
                   "History Section in Byte": 2048,
                   'NSUPPLEMENT':0
                   }


[docs]class OXDimage(fabioimage):
    """
    Oxford Diffraction Sapphire 3 images reader/writer class
    """
    def _readheader(self, infile):

        infile.seek(0)

        # Ascii header part 256 byes long
        self.header['Header Version'] = infile.readline()[:-2]
        block = infile.readline()
        self.header['Compression'] = block[12:15]
        block = infile.readline()
        self.header['NX'] = int(block[3:7])
        self.header['NY'] = int(block[11:15])
        self.header['OI'] = int(block[19:26])
        self.header['OL'] = int(block[30:37])
        block = infile.readline()
        self.header['Header Size In Bytes'] = int(block[8:15])
        self.header['General Section size in Byte'] = int(block[19:26])
        self.header['Special Section size in Byte'] = int(block[30:37])
        self.header['KM4 Section size in Byte'] = int(block[41:48])
        self.header['Statistic Section in Byte'] = int(block[52:59])
        self.header['History Section in Byte'] = int(block[63:])
        block = infile.readline()
        self.header['NSUPPLEMENT'] = int(block[12:19])
        block = infile.readline()
        self.header['Time'] = block[5:29]
        self.header["ASCII Section size in Byte"] = self.header['Header Size In Bytes']\
                                                - self.header['General Section size in Byte']\
                                                - self.header['Special Section size in Byte'] \
                                                - self.header['KM4 Section size in Byte']\
                                                - self.header['Statistic Section in Byte']\
                                                - self.header['History Section in Byte']\
        # Skip to general section (NG) 512 byes long <<<<<<"
        infile.seek(self.header["ASCII Section size in Byte"])
        block = infile.read(self.header['General Section size in Byte'])
        self.header['Binning in x'] = numpy.fromstring(block[0:2], numpy.uint16)[0]
        self.header['Binning in y'] = numpy.fromstring(block[2:4], numpy.uint16)[0]
        self.header['Detector size x'] = numpy.fromstring(block[22:24], numpy.uint16)[0]
        self.header['Detector size y'] = numpy.fromstring(block[24:26], numpy.uint16)[0]
        self.header['Pixels in x'] = numpy.fromstring(block[26:28], numpy.uint16)[0]
        self.header['Pixels in y'] = numpy.fromstring(block[28:30], numpy.uint16)[0]
        self.header['No of pixels'] = numpy.fromstring(block[36:40], numpy.uint32)[0]

        # Speciel section (NS) 768 bytes long
        block = infile.read(self.header['Special Section size in Byte'])
        self.header['Gain'] = numpy.fromstring(block[56:64], numpy.float)[0]
        self.header['Overflows flag'] = numpy.fromstring(block[464:466], numpy.int16)[0]
        self.header['Overflow after remeasure flag'] = numpy.fromstring(block[466:468], numpy.int16)[0]
        self.header['Overflow threshold'] = numpy.fromstring(block[472:476], numpy.int32)[0]
        self.header['Exposure time in sec'] = numpy.fromstring(block[480:488], numpy.float)[0]
        self.header['Overflow time in sec'] = numpy.fromstring(block[488:496], numpy.float)[0]
        self.header['Monitor counts of raw image 1'] = numpy.fromstring(block[528:532], numpy.int32)[0]
        self.header['Monitor counts of raw image 2'] = numpy.fromstring(block[532:536], numpy.int32)[0]
        self.header['Monitor counts of overflow raw image 1'] = numpy.fromstring(block[536:540], numpy.int32)[0]
        self.header['Monitor counts of overflow raw image 2'] = numpy.fromstring(block[540:544], numpy.int32)[0]
        self.header['Unwarping'] = numpy.fromstring(block[544:548], numpy.int32)[0]
        self.header['Detector type'] = DETECTOR_TYPES[numpy.fromstring(block[548:552], numpy.int32)[0]]
        self.header['Real pixel size x (mm)'] = numpy.fromstring(block[568:576], numpy.float)[0]
        self.header['Real pixel size y (mm)'] = numpy.fromstring(block[576:584], numpy.float)[0]

        # KM4 goniometer section (NK) 1024 bytes long
        block = infile.read(self.header['KM4 Section size in Byte'])
        # Spatial correction file
        self.header['Spatial correction file'] = block[26:272].strip("\x00")
        self.header['Spatial correction file date'] = block[0:26].strip("\x00")
        # Angles are in steps due to stepper motors - conversion factor RAD
        # angle[0] = omega, angle[1] = theta, angle[2] = kappa, angle[3] = phi,   
        start_angles_step = numpy.fromstring(block[284:304], numpy.int32)
        end_angles_step = numpy.fromstring(block[324:344], numpy.int32)
        step2rad = numpy.fromstring(block[368:408], numpy.float)
        step_angles_deg = rad2deg(step2rad)
        # calc angles
        start_angles_deg = start_angles_step * step_angles_deg
        end_angles_deg = end_angles_step * step_angles_deg
        self.header['Omega start in deg'] = start_angles_deg[0]
        self.header['Theta start in deg'] = start_angles_deg[1]
        self.header['Kappa start in deg'] = start_angles_deg[2]
        self.header['Phi start in deg'] = start_angles_deg[3]
        self.header['Omega end in deg'] = end_angles_deg[0]
        self.header['Theta end in deg'] = end_angles_deg[1]
        self.header['Kappa end in deg'] = end_angles_deg[2]
        self.header['Phi end in deg'] = end_angles_deg[3]
        self.header['Omega step in deg'] = step_angles_deg[0]
        self.header['Theta step in deg'] = step_angles_deg[1]
        self.header['Kappa step in deg'] = step_angles_deg[2]
        self.header['Phi step in deg'] = step_angles_deg[3]


        zero_correction_soft_step = numpy.fromstring(block[512:532], numpy.int32)
        zero_correction_soft_deg = zero_correction_soft_step * step_angles_deg
        self.header['Omega zero corr. in deg'] = zero_correction_soft_deg[0]
        self.header['Theta zero corr. in deg'] = zero_correction_soft_deg[1]
        self.header['Kappa zero corr. in deg'] = zero_correction_soft_deg[2]
        self.header['Phi zero corr. in deg'] = zero_correction_soft_deg[3]
        # Beam rotation about e2,e3
        self.header['Beam rot in deg (e2)'] = numpy.fromstring(block[552:560], numpy.float)[0]
        self.header['Beam rot in deg (e3)'] = numpy.fromstring(block[560:568], numpy.float)[0]
        # Wavelenghts alpha1, alpha2, beta
        self.header['Wavelength alpha1'] = numpy.fromstring(block[568:576], numpy.float)[0]
        self.header['Wavelength alpha2'] = numpy.fromstring(block[576:584], numpy.float)[0]
        self.header['Wavelength alpha'] = numpy.fromstring(block[584:592], numpy.float)[0]
        self.header['Wavelength beta'] = numpy.fromstring(block[592:600], numpy.float)[0]

        # Detector tilts around e1,e2,e3 in deg
        self.header['Detector tilt e1 in deg'] = numpy.fromstring(block[640:648], numpy.float)[0]
        self.header['Detector tilt e2 in deg'] = numpy.fromstring(block[648:656], numpy.float)[0]
        self.header['Detector tilt e3 in deg'] = numpy.fromstring(block[656:664], numpy.float)[0]


        # Beam center
        self.header['Beam center x'] = numpy.fromstring(block[664:672], numpy.float)[0]
        self.header['Beam center y'] = numpy.fromstring(block[672:680], numpy.float)[0]
        # Angle (alpha) between kappa rotation axis and e3 (ideally 50 deg)
        self.header['Alpha angle in deg'] = numpy.fromstring(block[672:680], numpy.float)[0]
        # Angle (beta) between phi rotation axis and e3 (ideally 0 deg)
        self.header['Beta angle in deg'] = numpy.fromstring(block[672:680], numpy.float)[0]

        # Detector distance
        self.header['Distance in mm'] = numpy.fromstring(block[712:720], numpy.float)[0]
        # Statistics section (NS) 512 bytes long
        block = infile.read(self.header['Statistic Section in Byte'])
        self.header['Stat: Min '] = numpy.fromstring(block[0:4], numpy.int32)[0]
        self.header['Stat: Max '] = numpy.fromstring(block[4:8], numpy.int32)[0]
        self.header['Stat: Average '] = numpy.fromstring(block[24:32], numpy.float)[0]
        self.header['Stat: Stddev '] = numpy.sqrt(numpy.fromstring(block[32:40], numpy.float)[0])
        self.header['Stat: Skewness '] = numpy.fromstring(block[40:48], numpy.float)[0]

        # History section (NH) 2048 bytes long
        block = infile.read(self.header['History Section in Byte'])
        self.header['Flood field image'] = block[99:126].strip("\x00")


[docs]    def read(self, fname, frame=None):
        """
        Read in header into self.header and
            the data   into self.data
        """
        self.header = {}
        self.resetvals()
        infile = self._open(fname)
        self._readheader(infile)

        infile.seek(self.header['Header Size In Bytes'])

        # Compute image size
        try:
            self.dim1 = int(self.header['NX'])
            self.dim2 = int(self.header['NY'])
        except:
            raise Exception("Oxford  file", str(fname) + \
                                "is corrupt, cannot read it")
        #
        if self.header['Compression'] == 'TY1':
            #Compressed with the KM4CCD compression
            raw8 = infile.read(self.dim1 * self.dim2)
            raw16 = None
            raw32 = None
            if self.header['OI'] > 0:
                raw16 = infile.read(self.header['OI'] * 2)
            if self.header['OL'] > 0:
                raw32 = infile.read(self.header['OL'] * 4)
            #DEBUG stuff ... 
            self.raw8 = raw8
            self.raw16 = raw16
            self.raw32 = raw32
            #END DEBUG
            block = decTY1(raw8, raw16, raw32)
            bytecode = block.dtype

        else:
            bytecode = numpy.int32
            self.bpp = len(numpy.array(0, bytecode).tostring())
            ReadBytes = self.dim1 * self.dim2 * self.bpp
            block = numpy.fromstring(infile.read(ReadBytes), bytecode)

        logger.debug('OVER_SHORT2: %s', block.dtype)
        logger.debug("%s" % (block < 0).sum())
        infile.close()
        logger.debug("BYTECODE: %s", bytecode)
        self.data = block.reshape((self.dim2, self.dim1))
        self.bytecode = self.data.dtype.type
        self.pilimage = None
        return self


    def _writeheader(self):
        """
        @return a string containing the header for Oxford images
        """
        linesep = "\r\n"
        for key in DEFAULT_HEADERS:
            if key not in self.header_keys:
                self.header_keys.append(key)
                self.header[key] = DEFAULT_HEADERS[key]

        if "NX" not in self.header.keys() or "NY" not in self.header.keys():
			self.header['NX'] = self.dim1
			self.header['NY'] = self.dim2
        ascii_headers = [self.header['Header Version'],
                       "COMPRESSION=%s (%5.1f)" % (self.header["Compression"], self.getCompressionRatio()),
                       "NX=%4i NY=%4i OI=%7i OL=%7i " % (self.header["NX"], self.header["NY"], self.header["OI"], self.header["OL"]),
                       "NHEADER=%7i NG=%7i NS=%7i NK=%7i NS=%7i NH=%7i" % (self.header['Header Size In Bytes'],
                                                                                 self.header['General Section size in Byte'],
                                                                                 self.header['Special Section size in Byte'],
                                                                                 self.header['KM4 Section size in Byte'],
                                                                                 self.header['Statistic Section in Byte'],
                                                                                 self.header['History Section in Byte']),
                        "NSUPPLEMENT=%7i" % (self.header["NSUPPLEMENT"])]
        if "Time" in self.header:
            ascii_headers.append("TIME=%s" % self.header["Time"])
        else:

            ascii_headers.append("TIME=%s" % time.ctime())

        header = (linesep.join(ascii_headers)).ljust(256)


        NG = Section(self.header['General Section size in Byte'], self.header)
        NG.setData('Binning in x', 0, numpy.uint16)
        NG.setData('Binning in y', 2, numpy.uint16)
        NG.setData('Detector size x', 22, numpy.uint16)
        NG.setData('Detector size y', 24, numpy.uint16)
        NG.setData('Pixels in x', 26, numpy.uint16)
        NG.setData('Pixels in y', 28, numpy.uint16)
        NG.setData('No of pixels', 36, numpy.uint32)
        header += NG.__repr__()

        NS = Section(self.header['Special Section size in Byte'], self.header)
        NS.setData('Gain', 56, numpy.float)
        NS.setData('Overflows flag', 464, numpy.int16)
        NS.setData('Overflow after remeasure flag', 466, numpy.int16)
        NS.setData('Overflow threshold', 472, numpy.int32)
        NS.setData('Exposure time in sec', 480, numpy.float)
        NS.setData('Overflow time in sec', 488, numpy.float)
        NS.setData('Monitor counts of raw image 1', 528, numpy.int32)
        NS.setData('Monitor counts of raw image 2', 532, numpy.int32)
        NS.setData('Monitor counts of overflow raw image 1', 536, numpy.int32)
        NS.setData('Monitor counts of overflow raw image 2', 540, numpy.int32)
        NS.setData('Unwarping', 544, numpy.int32)
        if 'Detector type' in  self.header:
            for key, value in  DETECTOR_TYPES.items():
                if value == self.header['Detector type']:
                    NS.setData(None, 548, numpy.int32, default=key)
        NS.setData('Real pixel size x (mm)', 568, numpy.float)
        NS.setData('Real pixel size y (mm)', 576, numpy.float)
        header += NS.__repr__()

        KM = Section(self.header['KM4 Section size in Byte'], self.header)
        KM.setData('Spatial correction file date', 0, "|S26")
        KM.setData('Spatial correction file', 26, "|S246")
        # Angles are in steps due to stepper motors - conversion factor RAD
        # angle[0] = omega, angle[1] = theta, angle[2] = kappa, angle[3] = phi,
        if self.header.get('Omega step in deg', None):
            KM.setData(None, 368, numpy.float64, deg2rad(self.header["Omega step in deg"]))
            if self.header.get('Omega start in deg', None):
                KM.setData(None, 284, numpy.int32, self.header["Omega start in deg"] / self.header["Omega step in deg"])
            if self.header.get('Omega end in deg', None):
                KM.setData(None, 324, numpy.int32, self.header["Omega end in deg"] / self.header["Omega step in deg"])
            if self.header.get('Omega zero corr. in deg', None):
                KM.setData(None, 512, numpy.int32, self.header['Omega zero corr. in deg'] / self.header["Omega step in deg"])

        if self.header.get('Theta step in deg', None):
            KM.setData(None, 368 + 8, numpy.float64, deg2rad(self.header["Theta step in deg"]))
            if self.header.get('Theta start in deg', None):
                KM.setData(None, 284 + 4, numpy.int32, self.header["Theta start in deg"] / self.header["Theta step in deg"])
            if self.header.get('Theta end in deg', None):
                KM.setData(None, 324 + 4, numpy.int32, self.header["Theta end in deg"] / self.header["Theta step in deg"])
            if self.header.get('Theta zero corr. in deg', None):
                KM.setData(None, 512 + 4, numpy.int32, self.header['Theta zero corr. in deg'] / self.header["Theta step in deg"])

        if self.header.get('Kappa step in deg', None):
            KM.setData(None, 368 + 16, numpy.float64, deg2rad(self.header["Kappa step in deg"]))
            if self.header.get('Kappa start in deg', None):
                KM.setData(None, 284 + 8, numpy.int32, self.header["Kappa start in deg"] / self.header["Kappa step in deg"])
            if self.header.get('Kappa end in deg', None):
                KM.setData(None, 324 + 8, numpy.int32, self.header["Kappa end in deg"] / self.header["Kappa step in deg"])
            if self.header.get('Kappa zero corr. in deg', None):
                KM.setData(None, 512 + 8, numpy.int32, self.header['Kappa zero corr. in deg'] / self.header["Kappa step in deg"])

        if self.header.get('Phi step in deg', None):
            KM.setData(None, 368 + 24, numpy.float64, deg2rad(self.header["Phi step in deg"]))
            if self.header.get('Phi start in deg', None):
                KM.setData(None, 284 + 12, numpy.int32, self.header["Phi start in deg"] / self.header["Phi step in deg"])
            if self.header.get('Phi end in deg', None):
                KM.setData(None, 324 + 12, numpy.int32, self.header["Phi end in deg"] / self.header["Phi step in deg"])
            if self.header.get('Phi zero corr. in deg', None):
                KM.setData(None, 512 + 12, numpy.int32, self.header['Phi zero corr. in deg'] / self.header["Phi step in deg"])

        # Beam rotation about e2,e3
        KM.setData('Beam rot in deg (e2)', 552, numpy.float64)
        KM.setData('Beam rot in deg (e3)', 560, numpy.float64)
        # Wavelenghts alpha1, alpha2, beta
        KM.setData('Wavelength alpha1', 568, numpy.float64)
        KM.setData('Wavelength alpha2', 576, numpy.float64)
        KM.setData('Wavelength alpha', 584, numpy.float64)
        KM.setData('Wavelength beta', 592, numpy.float64)

        # Detector tilts around e1,e2,e3 in deg
        KM.setData('Detector tilt e1 in deg', 640, numpy.float64)
        KM.setData('Detector tilt e2 in deg', 648, numpy.float64)
        KM.setData('Detector tilt e3 in deg', 656, numpy.float64)

        # Beam center
        KM.setData('Beam center x', 664, numpy.float64)
        KM.setData('Beam center y', 672, numpy.float64)
        # Angle (alpha) between kappa rotation axis and e3 (ideally 50 deg)
        KM.setData('Alpha angle in deg', 672, numpy.float64)
        # Angle (beta) between phi rotation axis and e3 (ideally 0 deg)
        KM.setData('Beta angle in deg', 672, numpy.float64)

        # Detector distance
        KM.setData('Distance in mm', 712, numpy.float64)
        header += KM.__repr__()

        SS = Section(self.header['Statistic Section in Byte'], self.header)
        SS.setData('Stat: Min ', 0, numpy.int32)
        SS.setData('Stat: Max ', 4, numpy.int32)
        SS.setData('Stat: Average ', 24, numpy.float64)
        if self.header.get('Stat: Stddev ', None):
            SS.setData(None, 32, numpy.float64, self.header['Stat: Stddev '] ** 2)
        SS.setData('Stat: Skewness ', 40, numpy.float64)
        header += SS.__repr__()

        HS = Section(self.header['History Section in Byte'], self.header)
        HS.setData('Flood field image', 99, "|S27")
        header += HS.__repr__()

        return header



[docs]    def write(self, fname):
        """Write Oxford diffraction images: this is still beta
        @param fname: output filename 
        """
        datablock8, datablock16, datablock32 = compTY1(self.data)
        self.header["OI"] = len(datablock16) / 2
        self.header["OL"] = len(datablock32) / 4
        with self._open(fname, mode="wb") as outfile:
            outfile.write(self._writeheader())
            outfile.write(datablock8)
            outfile.write(datablock16)
            outfile.write(datablock32)



[docs]    def getCompressionRatio(self):
        "calculate the compression factor obtained vs raw data"
        return 100.0 * (self.data.size + 2 * self.header["OI"] + 4 * self.header["OL"]) / (self.data.size * 4)


    @staticmethod

[docs]    def checkData(data=None):
        if data is None:
            return None
        else:
            return data.astype(int)



[docs]class Section(object):
    """
    Small helper class for writing binary headers
    """
    def __init__(self, size, dictHeader):
        """
        @param size: size of the header section in bytes
        @param dictHeader: headers of the image
        """
        self.size = size
        self.header = dictHeader
        self.lstChr = ["\x00"] * size
        self._dictSize = {}
    def __repr__(self):
        return "".join(self.lstChr)


[docs]    def getSize(self, dtype):
        if not dtype in self._dictSize:
            self._dictSize[dtype] = len(numpy.zeros(1, dtype=dtype).tostring())
        return self._dictSize[dtype]



[docs]    def setData(self, key, offset, dtype, default=None):
        """
        @param offset: int, starting position in the section
        @param key: name of the header key
        @param dtype: type of the data to insert (defines the size!)
        """
        if key in self.header:
            value = self.header[key]
        elif key in DEFAULT_HEADERS:
            value = DEFAULT_HEADERS[key]
        else:
            value = default
        if value is None:
            value = "\x00" * self.getSize(dtype)
        else:
            value = numpy.array(value).astype(dtype).tostring()
        self.lstChr[offset:offset + self.getSize(dtype)] = value

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© Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
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Source code for fabio.compression

#!/usr/bin/env python
# coding: utf8
"""
Authors: Jérôme Kieffer, ESRF
         email:jerome.kieffer@esrf.fr

FabIO library containing compression and decompression algorithm for various
"""
__author__ = "Jérôme Kieffer"
__contact__ = "jerome.kieffer@esrf.eu"
__license__ = "GPLv3+"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"


import logging, struct, hashlib, base64, StringIO, sys
if sys.version_info >= (3,):
    str = bytes
logger = logging.getLogger("compression")
import numpy

try:
    import gzip
except ImportError:
    logger.error("Unable to import gzip module: disabling gzip compression")
    gzip = None

try:
    import bz2
except ImportError:
    logger.error("Unable to import bz2 module: disabling bz2 compression")
    bz2 = None

try:
    import zlib
except ImportError:
    logger.error("Unable to import zlib module: disabling zlib compression")
    zlib = None


[docs]def md5sum(blob):
    """
    returns the md5sum of an object...
    """
    return base64.b64encode(hashlib.md5(blob).digest())




[docs]def endianness():
    """
    Return the native endianness of the system
    """
    if numpy.little_endian:
        return "LITTLE_ENDIAN"
    else:
        return "BIG_ENDIAN"




[docs]def decGzip(stream):
    """

    Decompress a chunk of data using the gzip algorithm from Python or alternatives if possible

    """

    if gzip is None:
        raise ImportError("gzip module is not available")
    fileobj = StringIO.StringIO(stream)
    try:
        rawData = gzip.GzipFile(fileobj=fileobj).read()
    except IOError:
        logger.warning("Encounter the python-gzip bug with trailing garbage, trying subprocess gzip")
        try:
            #This is as an ugly hack against a bug in Python gzip
            import subprocess
            sub = subprocess.Popen(["gzip", "-d", "-f"], stdout=subprocess.PIPE, stdin=subprocess.PIPE, stderr=subprocess.PIPE)
            rawData, err = sub.communicate(input=stream)
            logger.debug("Gzip subprocess ended with %s err= %s; I got %s bytes back" % (sub.wait(), err, len(rawData)))
        except Exception, error: #IGNORE:W0703
            logger.warning("Unable to use the subprocess gzip (%s). Is gzip available? " % error)
            for i in range(1, 513):
                try:
                    fileobj = StringIO.StringIO(stream[:-i])
                    rawData = gzip.GzipFile(fileobj=fileobj).read()
                except IOError:
                    logger.debug("trying with %s bytes less, doesn't work" % i)
                else:
                    break
            else:
                logger.error("I am totally unable to read this gzipped compressed data block, giving up")
    return rawData




[docs]def decBzip2(stream):
    """

    Decompress a chunk of data using the bzip2 algorithm from Python

    """
    if bz2 is None:
        raise ImportError("bz2 module is not available")
    return bz2.decompress(stream)




[docs]def decZlib(stream):
    """

    Decompress a chunk of data using the zlib algorithm from Python

    """
    if zlib is None:
        raise ImportError("zlib module is not available")
    return zlib.decompress(stream)




[docs]def decByteOffet_python(stream, size):
    """
    Analyze a stream of char with any length of exception (2,4, or 8 bytes integers)

    @param stream: string representing the compressed data
    @param size: the size of the output array (of longInts)
    @return: 1D-ndarray

    """
    logger.debug("CBF decompression using Python with Cython loops")
    dataOut = numpy.zeros((size), dtype=numpy.int64)
    i = 0
    j = 0
    last = 0
    current = 0
    while ((i < len(stream)) and (j < size)):
        if (stream[i] == '\x80'):
            if (stream[i + 1:i + 3] == "\x00\x80"):
                if (stream[i + 3:i + 7] == "\x00\x00\x00\x80"):
                    current = struct.unpack("<q", stream[i + 7:i + 15])[0]
                    i += 15
                else:
                    current = struct.unpack("<i", stream[i + 3:i + 7])[0]
                    i += 7
            else:
                current = struct.unpack("<h", stream[i + 1:i + 3])[0]
                i += 3
        else:
            current = struct.unpack("<b", stream[i])[0]
            i += 1
        last += current
        dataOut[j] = last
        j += 1
    return dataOut



[docs]def decByteOffet_weave(stream, size):
    """
    Analyze a stream of char with any length of exception (2,4, or 8 bytes integers)

    @param stream: string representing the compressed data
    @param size: the size of the output array (of longInts)
    @return: 1D-ndarray

    """
    logger.debug("CBF decompression using Weave")
    try:
        from scipy import weave
        from scipy.weave import converters
    except ImportError:
        logger.warning("scipy.weave is not available, falling back on slow Numpy implementations")
        return decByteOffet_numpy(stream, size)
    dataIn = numpy.fromstring(stream, dtype="uint8")
    n = dataIn.size
    dataOut = numpy.zeros(size, dtype="int64")
    codeC = """
unsigned char key = 0x80;
long   j = 0;
long   last=0;
long   current=0;
for (int i=0; i< n; i++){
   if (j>=size){
   //printf("i= %i<%i, j=%i < size= %i %i\\n",i,n,j,size,dataIn(i));
       break;
  }
  if (dataIn(i) == key){
      if ( (dataIn(i+1)==0) and (dataIn(i+2)==key) ){
          if ( (dataIn(i+3)==0) and (dataIn(i+4)==0) and (dataIn(i+5)==0) and (dataIn(i+6)==key) )  {
               // 64 bits mode
               char tmp = dataIn(i+14) ;
               current = (long(tmp)<<56) | (long(dataIn(i+13))<<48) | (long(dataIn(i+12))<<40) | (long(dataIn(i+11))<<32) | (long(dataIn(i+10))<<24) | (long(dataIn(i+9))<<16) | (long(dataIn(i+8))<<8) | (long(dataIn(i+7)));
//                printf("64 bit int at pos %i, %i, value=%ld \\n",i,j,current);
               i+=14;
           }else{
               // 32 bits mode
               char tmp = dataIn(i+6) ;
               current = (long(tmp)<<24) | (long(dataIn(i+5))<<16) | (long(dataIn(i+4))<<8) | (long(dataIn(i+3)));
//                printf("32 bit int at pos %i, %i, value=%ld was %i %i %i %i %i %i %i\\n",i,j,current,dataIn(i),dataIn(i+1),dataIn(i+2),dataIn(i+3),dataIn(i+4),dataIn(i+5),dataIn(i+6));
//                printf("%ld %ld %ld %ld\\n",(long(tmp)<<24) , (long(dataIn(i+5))<<16) , (long(dataIn(i+4))<<8) ,long(dataIn(i+3)));
               i+=6;
           }
      }else{
           // 16 bit mode
           char tmp = dataIn(i+2);
           current = (long(tmp)<<8) | (long (dataIn(i+1)));
//           printf("16 bit int at pos %i, %i, value=%ld was %i %i %i\\n",i,j,current,dataIn(i),dataIn(i+1),dataIn(i+2));
           i+=2;
      }
  }else{
      // 8 bit mode
      char tmp = dataIn(i) ;
      current= long(tmp) ;
  }
  last+=current;
  dataOut(j)=last;
  j++ ;
}
return_val=0;
     """
    rc = weave.inline(codeC, ["dataIn", "dataOut", "n", "size" ], verbose=2, type_converters=converters.blitz)
    if rc != 0:
        logger.warning("weave binary module return error code %s" % rc)
    return dataOut





[docs]def decByteOffet_numpy(stream, size=None):
    """
    Analyze a stream of char with any length of exception:
                2, 4, or 8 bytes integers

    @param stream: string representing the compressed data
    @param size: the size of the output array (of longInts)
    @return: 1D-ndarray

    """
    logger.debug("CBF decompression using Numpy")
    listnpa = []
    key16 = "\x80"
    key32 = "\x00\x80"
    key64 = "\x00\x00\x00\x80"
    shift = 1
    while True:
        idx = stream.find(key16)
        if idx == -1:
            listnpa.append(numpy.fromstring(stream, dtype="int8"))
            break
        listnpa.append(numpy.fromstring(stream[:idx], dtype="int8"))

        if stream[idx + 1:idx + 3] == key32:
            if stream[idx + 3:idx + 7] == key64:
#                        long int 64 bits
                listnpa.append(numpy.fromstring(stream[idx + 7:idx + 15],
                                             dtype="int64"))
                shift = 15
            else: #32 bit int
                listnpa.append(numpy.fromstring(stream[idx + 3:idx + 7],
                                             dtype="int32"))
                shift = 7
        else:  # int16
            listnpa.append(numpy.fromstring(stream[idx + 1:idx + 3],
                                         dtype="int16"))
            shift = 3
        stream = stream[idx + shift:]
    return  (numpy.hstack(listnpa)).astype("int64").cumsum()




[docs]def decByteOffet_cython(stream, size=None):
    """
    Analyze a stream of char with any length of exception:
                2, 4, or 8 bytes integers

    @param stream: string representing the compressed data
    @param size: the size of the output array (of longInts)
    @return: 1D-ndarray

    """
    logger.debug("CBF decompression using cython")
    try:
        from fabio.byte_offset import analyseCython
    except ImportError, error:
        logger.error("Failed to import byte_offset cython module, falling back on numpy method")
        return decByteOffet_numpy(stream, size)
    else:
        return analyseCython(stream, size)



[docs]def compByteOffet_numpy(data):
    """
    Compress a dataset into a string using the byte_offet algorithm

    @param data: ndarray
    @return: string/bytes with compressed data

    test = numpy.array([0,1,2,127,0,1,2,128,0,1,2,32767,0,1,2,32768,0,1,2,2147483647,0,1,2,2147483648,0,1,2,128,129,130,32767,32768,128,129,130,32768,2147483647,2147483648])

    """
    flat = data.astype("int64").ravel()
    delta = numpy.zeros_like(flat)
    delta[0] = flat[0]
    delta[1:] = flat[1:] - flat[:-1]
    mask = ((delta > 127) + (delta < -127))
    exceptions = numpy.nonzero(mask)[0]
    if numpy.little_endian:
        byteswap = False
    else:
        byteswap = True
    start = 0
    binary_blob = ""
    for stop in exceptions:
        if stop - start > 0:
            binary_blob += delta[start:stop].astype("int8").tostring()
        exc = delta[stop]
        if (exc > 2147483647) or (exc < -2147483647): #2**31-1
            binary_blob += "\x80\x00\x80\x00\x00\x00\x80"
            if byteswap:
                binary_blob += delta[stop:stop + 1].byteswap().tostring()
            else:
                binary_blob += delta[stop:stop + 1].tostring()
        elif (exc > 32767) or (exc < -32767): #2**15-1
            binary_blob += "\x80\x00\x80"
            if byteswap:
                binary_blob += delta[stop:stop + 1].astype("int32").byteswap().tostring()
            else:
                binary_blob += delta[stop:stop + 1].astype("int32").tostring()
        else: #>127
            binary_blob += "\x80"
            if byteswap:
                binary_blob += delta[stop:stop + 1].astype("int16").byteswap().tostring()
            else:
                binary_blob += delta[stop:stop + 1].astype("int16").tostring()
        start = stop + 1
    if start < delta.size:
        binary_blob += delta[start:].astype("int8").tostring()
    return binary_blob




[docs]def decTY1(raw_8, raw_16=None, raw_32=None):
    """
    Modified byte offset decompressor used in Oxford Diffraction images
    
    @param raw_8:  strings containing raw data with integer 8 bits
    @param raw_16: strings containing raw data with integer 16 bits
    @param raw_32: strings containing raw data with integer 32 bits
    @return: numpy.ndarray
    
    """
    data = numpy.fromstring(raw_8, dtype="uint8").astype(int)
    data -= 127
    if raw_32 is not None:
        int32 = numpy.fromstring(raw_32, dtype="int32").astype(int)
        exception32 = numpy.nonzero(data == 128)
    if raw_16 is not None:
        int16 = numpy.fromstring(raw_16, dtype="int16").astype(int)
        exception16 = numpy.nonzero(data == 127)
        data[exception16] = int16
    if raw_32:
        data[exception32] = int32
    summed = data.cumsum()
    smax = summed.max()
    if (smax > (2 ** 31 - 1)):
        bytecode = "int64"
    elif (smax > (2 ** 15 - 1)):
        bytecode = "int32"
    elif (smax > (2 ** 7 - 1)):
        bytecode = "int16"
    else:
        bytecode = "int8"
    return summed.astype(bytecode)

decKM4CCD = decTY1


[docs]def compTY1(data):
    """
    Modified byte offset compressor used in Oxford Diffraction images

    @param data: numpy.ndarray with the input data (integers!)
    @return: 3-tuple of strings: raw_8,raw_16,raw_32 containing raw data with integer of the given size

    """
    fdata = data.flatten()
    diff = numpy.zeros_like(fdata)
    diff[0] = fdata[0]
    diff[1:] = fdata[1:] - fdata[:-1]
    adiff = abs(diff)
    exception32 = (adiff > 32767)#2**15-1
    exception16 = (adiff >= 127) - exception32 #2**7-1)
    we16 = numpy.where(exception16)
    we32 = numpy.where(exception32)
    raw_16 = diff[we16].astype("int16").tostring()
    raw_32 = diff[we32].astype("int32").tostring()
    diff[we16] = 127
    diff[we32] = 128
    diff += 127
    raw_8 = diff.astype("uint8").tostring()
    return  raw_8, raw_16, raw_32



[docs]def decPCK(stream, dim1=None, dim2=None, overflowPix=None, version=None):
    """
    Modified CCP4  pck decompressor used in MAR345 images

    @param stream: string or file
    @return: numpy.ndarray (square array)

    """

    try:
        from mar345_IO import uncompress_pck
    except ImportError, error:
        raise RuntimeError("Unable to import mar345_IO to read compressed dataset")
    if "seek" in dir(stream):
        stream.seek(0)
        raw = stream.read()
    else:
        raw = str(stream)

    return uncompress_pck(raw, dim1, dim2, overflowPix, version)




[docs]def compPCK(data):
    """
    Modified CCP4  pck compressor used in MAR345 images

    @param data: numpy.ndarray (square array)
    @return:  compressed stream

    """
    try:
        from mar345_IO import compress_pck
    except ImportError, error:
        raise RuntimeError("Unable to import mar345_IO to write compressed dataset")
    return compress_pck(data)

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© Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
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Source code for fabio.xsdimage

#!/usr/bin/env python
# coding: utf8
"""
Authors: Jérôme Kieffer, ESRF 
         email:jerome.kieffer@esrf.fr

XSDimge are XML files containing numpy arrays 
"""
__author__ = "Jérôme Kieffer"
__contact__ = "jerome.kieffer@esrf.eu"
__license__ = "GPLv3+"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"

import logging, numpy
logger = logging.getLogger("xsdimage")
from fabioimage import fabioimage
import base64, hashlib
try:
    from lxml import etree
except ImportError:
    logger.warning("lxml library is probably not part of your python installation: disabling xsdimage format")
    etree = None


[docs]class xsdimage(fabioimage):
    """ 
    Read the XSDataImage XML File data format 
    """
    def __init__(self, data=None, header=None, fname=None):
        """
        Constructor of the class XSDataImage.

        @param _strFilename: the name of the file to open
        @type  _strFilename: string
        """
        fabioimage.__init__(self, data=data, header=header)
        self.dims = []
        self.size = None
        self.coding = None
        self.dtype = None
        self.rawData = None
        self.md5 = None
        if fname is not None:
            self.filename = fname
            self.read(fname)


[docs]    def read(self, fname, frame=None):
        """
        """
        self.header = {}
        self.resetvals()
        self.filename = fname
        infile = self._open(fname, "rb")
        self._readheader(infile)

        try:
            self.dim1, self.dim2 = self.dims[:2]
        except:
            raise IOError("XSD file %s is corrupt, no dimensions in it" % fname)
        try:
            self.bytecode = numpy.dtype(self.dtype).type
            self.bpp = len(numpy.array(0, self.bytecode).tostring())
        except TypeError:
            self.bytecode = numpy.int32
            self.bpp = 32
            logger.warning("Defaulting type to int32")

        exp_size = 1
        for i in self.dims:
            exp_size *= i
        assert exp_size == self.size

        decData = None
        if self.coding == "base64":
            decData = base64.b64decode(self.rawData)
        elif self.coding == "base32":
            decData = base64.b32decode(self.rawData)
        elif self.coding == "base16":
            decData = base64.b16decode(self.rawData)
        else:
            logger.warning("Unable to recognize the encoding of the data !!! got %s, expected base64, base32 or base16, I assume it is base64 " % self.coding)
            decData = base64.b64decode(self.rawData)
        if self.md5:
            assert  hashlib.md5(decData).hexdigest() == self.md5


        self.data = numpy.fromstring(decData, dtype=self.bytecode).reshape(tuple(self.dims))
        if not numpy.little_endian: #by default little endian
            self.data.byteswap(inplace=True)
        self.resetvals()
#        # ensure the PIL image is reset
        self.pilimage = None
        return self


    def _readheader(self, infile):
        """
        Read all headers in a file and populate self.header
        data is not yet populated
        @type infile: file object open in read mode
        """
        xml = etree.parse(infile)
        self.dims = []
        for i in xml.xpath("//shape"):
            try:
                self.dims.append(int(i.text))
            except ValueError, error:
                logger.warning("%s Shape: Unable to convert %s to integer in %s" % (error, i.text, i))
        for i in xml.xpath("//size"):
            try:
                self.size = int(i.text)
            except Exception, error:#IGNORE:W0703
                logger.warning("%s Size: Unable to convert %s to integer in %s" % (error, i.text, i))
        self.dtype = None
        for i in xml.xpath("//dtype"):
            self.dtype = i.text
        self.coding = None
        for i in xml.xpath("//coding"):
            j = i.find("value")
            if j is not None:
                self.coding = j.text
        self.rawData = None
        for i in xml.xpath("//data"):
            self.rawData = i.text
        self.md5 = None
        for i in xml.xpath("//md5sum"):
            j = i.find("value")
            if j is not None:
                self.md5 = j.text


if etree is None:
    xsdimage = None

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© Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
fabio-0.1.3/doc/html/_modules/fabio/fabioutils.html0000644000175000017500000025325312233250022023007 0ustar jeromejerome00000000000000 fabio.fabioutils — FabIO 0.1.3 documentation

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Source code for fabio.fabioutils

#!/usr/bin/env python
#coding: utf8

"""
General purpose utilities functions for fabio
"""
from __future__ import with_statement
import re, os, logging, threading, sys
import StringIO as stringIO
logger = logging.getLogger("fabioutils")
from compression import bz2, gzip
import traceback
from math import ceil



FILETYPES = {
    # extension NNNimage fabioclass
    # type consistency - always use a list if one case is
    'edf'    : ['edf'],
    'cor'    : ['edf'],
    'pnm'    : ['pnm'],
    'pgm'    : ['pnm'],
    'pbm'    : ['pnm'],
    'tif'    : ['tif'],
    'tiff'   : ['tif'],
    'img'    : ['adsc', 'OXD', 'HiPiC'],
    'mccd'   : ['marccd'],
    'mar2300': ['mar345'],
    'sfrm'   : ['bruker100'],
    'msk'    : ['fit2dmask'],
    'spr'    : ['fit2dspreadsheet'],
    'dm3'    : ['dm3'],
    'kcd'    : ['kcd'],
    'cbf'    : ['cbf'],
    'xml'    : ["xsd"],
    'xsd'    : ["xsd"],
             }

# Add bzipped and gzipped
for key in FILETYPES.keys():
    FILETYPES[key + ".bz2"] = FILETYPES[key]
    FILETYPES[key + ".gz"] = FILETYPES[key]


# Compressors

COMPRESSORS = {}


dictAscii = {None:[chr(i) for i in range(32, 127)],
           }

try:
    lines = os.popen("gzip -h 2>&1").read()
    # Looking for "usage"
    if "sage" in lines:
        COMPRESSORS['.gz'] = 'gzip -dc '
    else:
        COMPRESSORS['.gz'] = None
except Exception:
    COMPRESSORS['.gz'] = None

try:
    lines = os.popen("bzip2 -h 2>&1").read()
    # Looking for "usage"
    if "sage" in lines:
        COMPRESSORS['.bz2'] = 'bzip2 -dc '
    else:
        COMPRESSORS['.bz2'] = None
except Exception:
    COMPRESSORS['.bz2'] = None


[docs]def deprecated(func):
    """
    used to deprecate a function/method: prints a lot of warning messages to enforce the modifaction of the code
    """
    def wrapper(*arg, **kw):
        """
        decorator that deprecates the use of a function  
        """
        logger.warning("%s is Deprecated !!! %s" % (func.func_name, os.linesep.join([""] + traceback.format_stack()[:-1])))
        return func(*arg, **kw)
    return wrapper



[docs]def pad(mystr, pattern=" ", size=80):
    """
    Performs the padding of the string to the right size with the right pattern 
    """
    size = int(size)
    padded_size = int(ceil(float(len(mystr)) / size) * size)
    if len(pattern) == 1:
        return mystr.ljust(padded_size, pattern)
    else:
        return (mystr + pattern * int(ceil(float(padded_size - len(mystr)) / len(pattern))))[:padded_size]




[docs]def getnum(name):
    """
    # try to figure out a file number
    # guess it starts at the back
    """
    stem , num, post_num = numstem(name)
    try:
        return int(num)
    except ValueError:
        return None



[docs]class FilenameObject(object):
    """
    The 'meaning' of a filename ... 
    """
    def __init__(self, stem=None,
            num=None,
            directory=None,
            format=None,
            extension=None,
            postnum=None,
            digits=4,
            filename=None):
        """
        This class can either be instanciated by a set of parameters like  directory, prefix, num, extension, ...   
        
        @param stem: the stem is a kind of prefix (str)
        @param num: image number in the serie (int)
        @param directory: name of the directory (str)
        @param format: ??
        @param extension: 
        @param postnum: 
        @param digits: Number of digits used to print num
        
        Alternative constructor: 
        
        @param filename: fullpath of an image file to be deconstructed into directory, prefix, num, extension, ... 
        
        """


        self.stem = stem
        self.num = num
        self.format = format
        self.extension = extension
        self.digits = digits
        self.postnum = postnum
        self.directory = directory
        self.compressed = None
        if filename is not None:
            self.deconstruct_filename(filename)



[docs]    def str(self):
        """ Return a string representation """
        fmt = "stem %s, num %s format %s extension %s " + \
                "postnum = %s digits %s dir %s"
        return fmt % tuple([str(x) for x in [
                    self.stem ,
                    self.num ,
                    self.format ,
                    self.extension ,
                    self.postnum ,
                    self.digits ,
                    self.directory ] ])

    __repr__ = str


[docs]    def tostring(self):
        """
        convert yourself to a string
        """
        name = self.stem
        if self.digits is not None and self.num is not None:
            fmt = "%0" + str(self.digits) + "d"
            name += fmt % self.num
        if self.postnum is not None:
            name += self.postnum
        if self.extension is not None:
            name += self.extension
        if self.directory is not None:
            name = os.path.join(self.directory, name)
        return name




[docs]    def deconstruct_filename(self, filename):
        """
        Break up a filename to get image type and number
        """
        direc, name = os.path.split(filename)
        direc = direc or None
        parts = name.split(".")
        compressed = False
        stem = parts[0]
        extn = ""
        postnum = ""
        ndigit = 4
        num = None
        typ = None
        if parts[-1] in ["gz", "bz2"]:
            extn = "." + parts[-1]
            parts = parts[:-1]
            compressed = True
        if parts[-1] in FILETYPES.keys():
            typ = FILETYPES[parts[-1]]
            extn = "." + parts[-1] + extn
            try:
                stem, numstring, postnum = numstem(".".join(parts[:-1]))
                num = int(numstring)
                ndigit = len(numstring)
            except Exception, err:
                # There is no number - hence make num be None, not 0
                logger.debug("l176: %s" % err)
                num = None
                stem = "".join(parts[:-1])
        else:
            # Probably two type left
            if len(parts) == 1:
                # Probably GE format stem_numb
                parts2 = parts[0].split("_")
                if parts2[-1].isdigit():
                    num = int(parts2[-1])
                    ndigit = len(parts2[-1])
                    typ = ['GE']
                    stem = "_".join(parts2[:-1]) + "_"
            else:
                try:
                    num = int(parts[-1])
                    ndigit = len(parts[-1])
                    typ = ['bruker']
                    stem = ".".join(parts[:-1]) + "."
                except Exception, err:
                    logger.debug("l196: %s" % err)
                    typ = None
                    extn = "." + parts[-1] + extn
                    numstring = ""
                    try:
                        stem , numstring, postnum = numstem(".".join(parts[:-1]))
                    except Exception, err:
                        logger.debug("l202: %s" % err)
                        raise
                    if numstring.isdigit():
                        num = int(numstring)
                        ndigit = len(numstring)
                #            raise Exception("Cannot decode "+filename)

        self.stem = stem
        self.num = num
        self.directory = direc
        self.format = typ
        self.extension = extn
        self.postnum = postnum
        self.digits = ndigit
        self.compressed = compressed



[docs]def numstem(name):
    """ cant see how to do without reversing strings
    Match 1 or more digits going backwards from the end of the string
    """
    reg = re.compile(r"^(.*?)(-?[0-9]{0,9})(\D*)$")
    #reg = re.compile("""(\D*)(\d\d*)(\w*)""")
    try:
        res = reg.match(name).groups()
        #res = reg.match(name[::-1]).groups()
        #return [ r[::-1] for r in res[::-1]]
        if len(res[0]) == len(res[1]) == 0: # Hack for file without number
            return [res[2], '', '']
        return [ r for r in res]
    except AttributeError: # no digits found
        return [name, "", ""]

#@deprecated


[docs]def deconstruct_filename(filename):
    """
    Function for backward compatibility.
    Deprecated
    """
    return FilenameObject(filename=filename)



[docs]def construct_filename(filename, frame=None):
    "Try to construct the filename for a given frame"
    fobj = FilenameObject(filename=filename)
    if frame is not None:
        fobj.num = frame
    return fobj.tostring()



[docs]def next_filename(name, padding=True):
    """ increment number """
    fobj = FilenameObject(filename=name)
    fobj.num += 1
    if not padding:
        fobj.digits = 0
    return fobj.tostring()



[docs]def previous_filename(name, padding=True):
    """ decrement number """
    fobj = FilenameObject(filename=name)
    fobj.num -= 1
    if not padding:
        fobj.digits = 0
    return fobj.tostring()



[docs]def jump_filename(name, num, padding=True):
    """ jump to number """
    fobj = FilenameObject(filename=name)
    fobj.num = num
    if not padding:
        fobj.digits = 0
    return fobj.tostring()




[docs]def extract_filenumber(name):
    """ extract file number """
    fobj = FilenameObject(filename=name)
    return fobj.num



[docs]def isAscii(name, listExcluded=None):
    """
    @param name: string to check
    @param listExcluded: list of char or string excluded.
    @return: True of False whether  name is pure ascii or not
    """
    isascii = None
    try:
        name.decode("ascii")
    except UnicodeDecodeError:
        isascii = False
    else:
        if listExcluded:
            isascii = not(any(bad in  name for bad in listExcluded))
        else:
            isascii = True
    return isascii



[docs]def toAscii(name, excluded=None):
    """
    @param name: string to check
    @param excluded: tuple of char or string excluded (not list: they are mutable).
    @return: the name with all non valid char removed
    """
    if excluded not in dictAscii:
        ascii = dictAscii[None][:]
        for i in excluded:
            if i in ascii:
                ascii.remove(i)
            else:
                logger.error("toAscii: % not in ascii table" % i)
        dictAscii[excluded] = ascii
    else:
        ascii = dictAscii[excluded]
    out = [i for i in str(name) if i in ascii]
    return "".join(out)



[docs]def nice_int(s):
    """ 
    Workaround that int('1.0') raises an exception 
    
    @param s: string to be converted to integer
    """
    try:
        return int(s)
    except ValueError:
        return int(float(s))




[docs]class StringIO(stringIO.StringIO):
    """
    just an interface providing the name and mode property to a StringIO

    BugFix for MacOSX mainly
    """
    def __init__(self, data, fname=None, mode="r"):
        stringIO.StringIO.__init__(self, data)
        self.closed = False
        if fname == None:
            self.name = "fabioStream"
        else:
            self.name = fname
        self.mode = mode
        self.lock = threading.Semaphore()
        self.__size = None


[docs]    def getSize(self):
        if self.__size is None:
            logger.debug("Measuring size of %s" % self.name)
            with self.lock:
                pos = self.tell()
                self.seek(0, os.SEEK_END)
                self.__size = self.tell()
                self.seek(pos)
        return self.__size


[docs]    def setSize(self, size):
        self.__size = size

    size = property(getSize, setSize)



[docs]class File(file):
    """
    wrapper for "file" with locking
    """
    def __init__(self, name, mode="rb", buffering=0):
        """file(name[, mode[, buffering]]) -> file object
            
        Open a file.  The mode can be 'r', 'w' or 'a' for reading (default),
        writing or appending.  The file will be created if it doesn't exist
        when opened for writing or appending; it will be truncated when
        opened for writing.  Add a 'b' to the mode for binary files.
        Add a '+' to the mode to allow simultaneous reading and writing.
        If the buffering argument is given, 0 means unbuffered, 1 means line
        buffered, and larger numbers specify the buffer size.  The preferred way
        to open a file is with the builtin open() function.
        Add a 'U' to mode to open the file for input with universal newline
        support.  Any line ending in the input file will be seen as a '\n'
        in Python.  Also, a file so opened gains the attribute 'newlines';
        the value for this attribute is one of None (no newline read yet),
        '\r', '\n', '\r\n' or a tuple containing all the newline types seen.
        
        'U' cannot be combined with 'w' or '+' mode.
        """
        file.__init__(self, name, mode, buffering)
        self.lock = threading.Semaphore()
        self.__size = None

[docs]    def getSize(self):
        if self.__size is None:
            logger.debug("Measuring size of %s" % self.name)
            with self.lock:
                pos = self.tell()
                self.seek(0, os.SEEK_END)
                self.__size = self.tell()
                self.seek(pos)
        return self.__size


[docs]    def setSize(self, size):
        self.__size = size

    def __exit__(self, *args, **kwargs):
        """
        Close the file.
        """
        return file.close(self)
    def __enter__(self, *args, **kwargs):
        return self
    size = property(getSize, setSize)




[docs]class UnknownCompressedFile(File):
    """
    wrapper for "File" with locking
    """
    def __init__(self, name, mode="rb", buffering=0):
        logger.warning("No decompressor found for this type of file (are gzip anf bz2 installed ???")
        File.__init__(self, name, mode, buffering)


if gzip is None:
    GzipFile = UnknownCompressedFile
else:

[docs]    class GzipFile(gzip.GzipFile):
        """
        Just a wrapper forgzip.GzipFile providing the correct seek capabilities for python 2.5   
        """
        def __init__(self, filename=None, mode=None, compresslevel=9, fileobj=None):
            """
            Wrapper with locking for constructor for the GzipFile class.
            
            At least one of fileobj and filename must be given a
            non-trivial value.
            
            The new class instance is based on fileobj, which can be a regular
            file, a StringIO object, or any other object which simulates a file.
            It defaults to None, in which case filename is opened to provide
            a file object.
            
            When fileobj is not None, the filename argument is only used to be
            included in the gzip file header, which may includes the original
            filename of the uncompressed file.  It defaults to the filename of
            fileobj, if discernible; otherwise, it defaults to the empty string,
            and in this case the original filename is not included in the header.
            
            The mode argument can be any of 'r', 'rb', 'a', 'ab', 'w', or 'wb',
            depending on whether the file will be read or written.  The default
            is the mode of fileobj if discernible; otherwise, the default is 'rb'.
            Be aware that only the 'rb', 'ab', and 'wb' values should be used
            for cross-platform portability.
            
            The compresslevel argument is an integer from 1 to 9 controlling the
            level of compression; 1 is fastest and produces the least compression,
            and 9 is slowest and produces the most compression.  The default is 9.
            """
            gzip.GzipFile.__init__(self, filename, mode, compresslevel, fileobj)
            self.lock = threading.Semaphore()
            self.__size = None


        if sys.version_info < (2, 7):
            def getSize(self):
                if self.__size is None:
                    logger.debug("Measuring size of %s" % self.name)
                    with open(self.filename, "rb") as f:
                        f.seek(-4)
                        self.__size = numpy.fromstring(f.read(4), dtype=numpy.uint32)
                return self.__size
            def setSize(self, value):
                self.__size = value
            size = property(getSize, setSize)
            @property
            def closed(self):
                return self.fileobj is None

            def seek(self, offset, whence=os.SEEK_SET):
                """
                Move to new file position.
        
                Argument offset is a byte count.  Optional argument whence defaults to
                0 (offset from start of file, offset should be >= 0); other values are 1
                (move relative to current position, positive or negative), and 2 (move
                relative to end of file, usually negative, although many platforms allow
                seeking beyond the end of a file).  If the file is opened in text mode,
                only offsets returned by tell() are legal.  Use of other offsets causes
                undefined behavior.
                
                This is a wrapper for seek to ensure compatibility with old python 2.5
                """
                if whence == os.SEEK_SET:
                    gzip.GzipFile.seek(self, offset)
                elif whence == os.SEEK_CUR:
                    gzip.GzipFile.seek(self, offset + self.tell())
                elif whence == os.SEEK_END:
                    gzip.GzipFile.seek(self, -1)
                    gzip.GzipFile.seek(self, offset + self.tell())
            def __enter__(self, *args, **kwargs):
                return self
            def __exit__(self, *args, **kwargs):
                """
                Close the file.
                """
                return gzip.GzipFile.close(self)


if bz2 is None:
    BZ2File = UnknownCompressedFile
else:

[docs]    class BZ2File(bz2.BZ2File):
        "Wrapper with lock"
        def __init__(self, name , mode='r', buffering=0, compresslevel=9):
            """
            BZ2File(name [, mode='r', buffering=0, compresslevel=9]) -> file object
            
            Open a bz2 file. The mode can be 'r' or 'w', for reading (default) or
            writing. When opened for writing, the file will be created if it doesn't
            exist, and truncated otherwise. If the buffering argument is given, 0 means
            unbuffered, and larger numbers specify the buffer size. If compresslevel
            is given, must be a number between 1 and 9.
            
            Add a 'U' to mode to open the file for input with universal newline
            support. Any line ending in the input file will be seen as a '\n' in
            Python. Also, a file so opened gains the attribute 'newlines'; the value
            for this attribute is one of None (no newline read yet), '\r', '\n',
            '\r\n' or a tuple containing all the newline types seen. Universal
            newlines are available only when reading.
            """
            bz2.BZ2File.__init__(self, name , mode, buffering, compresslevel)
            self.lock = threading.Semaphore()
            self.__size = None

[docs]        def getSize(self):
            if self.__size is None:
                logger.debug("Measuring size of %s" % self.name)
                with self.lock:
                    pos = self.tell()
                    all = self.read()
                    self.__size = self.tell()
                    self.seek(pos)
            return self.__size


[docs]        def setSize(self, value):
            self.__size = value

        size = property(getSize, setSize)
        def __exit__(self, *args, **kwargs):
                """
                Close the file.
                """
                return bz2.BZ2File.close(self)
        def __enter__(self, *args, **kwargs):
            return self

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Source code for fabio.datIO

#!/usr/bin/env python
#coding: utf8
"""
Authors: Henning O. Sorensen & Erik Knudsen
         Center for Fundamental Research: Metal Structures in Four Dimensions
         Risoe National Laboratory
         Frederiksborgvej 399
         DK-4000 Roskilde
         email:erik.knudsen@risoe.dk
         
         and Jon Wright, ESRF
"""


[docs]class fabiodata(object):
    """
    A common class for dataIO in fable
    Contains a 2d numpy array for keeping data, and two lists (clabels and rlabels)
    containing labels for columns and rows respectively
    """

    def __init__(self, data=None, clabels=None, rlabels=None, fname=None):
        """
        set up initial values
        """
        if type(data) == type("string"):
            raise Exception("fabioimage.__init__ bad argument - " + \
                                "data should be numpy array")
        self.data = data
        if (self.data):
            self.dims = self.data.shape
        self.clabels = clabels
        self.rlabels = rlabels
        if (fname):
            self.read(fname)


[docs]    def read(self, fname=None, frame=None):
        """
        To be overridden by format specific subclasses
        """
        raise Exception("Class has not implemented read method yet")

#import stuff from Jon's columnfile things




[docs]class columnfile(fabiodata):
    "Concrete fabiodata class"

[docs]    def read(self, fname, frame=None):
        import cf_io
        try:
            infile = open(fname, 'rb')
        except:
            raise Exception("columnfile: file" + str(fname) + "not found.")
        try:
            (self.data, self.clabels) = cf_io.read(infile)
        except:
            raise Exception("columnfile: read error, file " + str(fname) + " possibly corrupt")
        self.dims = self.data.shape
        infile.close()

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Source code for fabio.file_series

#!/usr/bin/env python

"""

Authors:
........

* Henning O. Sorensen & Erik Knudsen
  Center for Fundamental Research: Metal Structures in Four Dimensions
  Risoe National Laboratory
  Frederiksborgvej 399
  DK-4000 Roskilde
  email:erik.knudsen@risoe.dk
* Jon Wright, ESRF

"""
import logging, sys
logger = logging.getLogger("fileseries")
import traceback as pytraceback

from fabioutils import FilenameObject, next_filename

from openimage import openimage



[docs]def new_file_series0(first_object, first=None, last=None, step=1):
    """
    Created from a fabio image
    first and last are file numbers

    """
    im = first_object
    nimages = 0
    # for counting images
    if None in (first, last):
        step = 0
        total = 1
    else:
        total = last - first

    yield im
    while nimages < total:
        nimages += step
        try:
            newim = im.next()
            im = newim
        except Exception, error:
            pytraceback.print_exc()

            # Skip bad images
            logger.warning("Got a problem here: %s", error)
            try:
                im.filename = next_filename(im.filename)
            except Exception, error:
                # KE: This will not work and will throw an exception
                # fabio.next_filename doesn't understand %nnnn on the end
                logger.warning("Got another problem here: %s", error)
                im.filename = next_filename(im.sequencefilename)
            yield None
        yield im





[docs]def new_file_series(first_object, nimages=0, step=1, traceback=False):
    """
    A generator function that creates a file series starting from a a fabioimage.
    Iterates through all images in a file (if more than 1), then proceeds to
    the next file as determined by fabio.next_filename.

    @param first_object: the starting fabioimage, which will be the first one yielded
        in the sequence
    @param nimages:  the maximum number of images to consider
        step: step size, will yield the first and every step'th image until nimages
        is reached.  (e.g. nimages = 5, step = 2 will yield 3 images (0, 2, 4)
    @param traceback: if True causes it to print a traceback in the event of an
        exception (missing image, etc.).  Otherwise the calling routine can handle
        the exception as it chooses
    @param yields: the next fabioimage in the series.
        In the event there is an exception, it yields the sys.exec_info for the
        exception instead.  sys.exec_info is a tuple:
        ( exceptionType, exceptionValue, exceptionTraceback )
        from which all the exception information can be obtained.

    Suggested usage:
    
    ::
    
        for obj in new_file_series( ... ):
          if not isinstance(obj, fabio.fabioimage.fabioimage ):
            # deal with errors like missing images, non readable files, etc
            # e.g.
            traceback.print_exception(obj[0], obj[1], obj[2])

    """
    im = first_object
    nprocessed = 0
    abort = False
    if nimages > 0:
        yield im
        nprocessed += 1
    while nprocessed < nimages:
        try:
            newim = im.next()
            im = newim
            retVal = im
        except Exception, ex:
            retVal = sys.exc_info()
            if(traceback):
                pytraceback.print_exc()
                # Skip bad images
                logger.warning("Got a problem here: next() failed %s", ex)
            # Skip bad images
            try:
                im.filename = next_filename(im.filename)
            except Exception, ex:
                logger.warning("Got another problem here: next_filename(im.filename) %s", ex)
        if nprocessed % step == 0:
            yield retVal
            # Avoid cyclic references with exc_info ?
            retVal = None
            if abort: break
        nprocessed += 1





[docs]class file_series(list):
    """
    Represents a series of files to iterate
    has an idea of a current position to do next and prev

    You also get from the list python superclass:
       append
       count
       extend
       insert
       pop
       remove
       reverse
       sort
    """
    def __init__(self, list_of_strings):
        """
        Constructor:

        @param list_of_strings: arg should be a list of strings which are filenames

        """
        super(file_series, self).__init__(list_of_strings)
        # track current position in list
        self._current = 0


    # methods which return a filename


[docs]    def first(self):
        """
        First image in series

        """
        return self[0]



[docs]    def last(self):
        """
        Last in series

        """
        return self[-1]



[docs]    def previous(self):
        """
        Prev in a sequence

        """
        self._current -= 1
        return self[self._current]



[docs]    def current(self):
        """Current position in a sequence

        """
        return self[self._current]



[docs]    def next(self):
        """
        Next in a sequence

        """
        self._current += 1
        return self[self._current]



[docs]    def jump(self, num):
        """
        Goto a position in sequence

        """
        assert num < len(self) and num > 0, "num out of range"
        self._current = num
        return self[self._current]



[docs]    def len(self):
        """
        Number of files

        """
        return len(self)


    # Methods which return a fabioimage



[docs]    def first_image(self):
        """
        First image in a sequence

        @return: fabioimage

        """
        return openimage(self.first())



[docs]    def last_image(self):
        """
        Last image in a sequence

        @return: fabioimage

        """
        return openimage(self.last())



[docs]    def next_image(self):
        """
        Return the next image

        @return: fabioimage

        """
        return openimage(self.next())



[docs]    def previous_image(self):
        """
        Return the previous image

        @return: fabioimage

        """
        return openimage(self.previous())



[docs]    def jump_image(self, num):
        """
        Jump to and read image

        @return: fabioimage

        """
        return openimage(self.jump(num))



[docs]    def current_image(self):
        """
        Current image in sequence

        @return: fabioimage

        """
        return openimage(self.current())

    # methods which return a file_object



[docs]    def first_object(self):
        """
        First image in a sequence

        @return: file_object
        """
        return FilenameObject(self.first())



[docs]    def last_object(self):
        """
        Last image in a sequence

        @return: file_object

        """
        return FilenameObject(self.last())



[docs]    def next_object(self):
        """
        Return the next image

        @return: file_object

        """
        return FilenameObject(self.next())



[docs]    def previous_object(self):
        """
        Return the previous image

        @return: file_object

        """
        return FilenameObject(self.previous())



[docs]    def jump_object(self, num):
        """
        Jump to and read image

        @return: file_object

        """
        return FilenameObject(self.jump(num))



[docs]    def current_object(self):
        """
        Current image in sequence

        @return: file_object

        """
        return FilenameObject(self.current())






[docs]class numbered_file_series(file_series):
    """
    mydata0001.edf = "mydata" + 0001 + ".edf"
    mydata0002.edf = "mydata" + 0002 + ".edf"
    mydata0003.edf = "mydata" + 0003 + ".edf"
    """
    def __init__(self, stem, first, last, extension,
                 digits=4, padding='Y', step=1):
        """
        Constructor

        @param stem: first part of the name
        @param step: in case of every nth file
        @param padding: possibility for specifying that numbers are not padded with zeroes up to digits

        """
        if padding == 'Y':
            fmt = "%s%0" + str(digits) + "d%s"
        else:
            fmt = "%s%i%s"

        super(numbered_file_series, self).__init__(
            [ fmt % (stem, i, extension) for i in range(first,
                                                          last + 1,
                                                          step) ])




[docs]class filename_series:
    """ Much like the others, but created from a string filename """
    def __init__(self, filename):
        """ create from a filename (String)"""
        self.obj = FilenameObject(filename)


[docs]    def next(self):
        """ increment number """
        self.obj.num += 1
        return self.obj.tostring()



[docs]    def previous(self):
        """ decrement number """
        self.obj.num -= 1
        return self.obj.tostring()



[docs]    def current(self):
        """ return current filename string"""
        return self.obj.tostring()



[docs]    def jump(self, num):
        """ jump to a specific number """
        self.obj.num = num
        return self.obj.tostring()

    # image methods


[docs]    def next_image(self):
        """ returns the next image as a fabioimage """
        return openimage(self.next())


[docs]    def prev_image(self):
        """ returns the previos image as a fabioimage """
        return openimage(self.previous())


[docs]    def current_image(self):
        """ returns the current image as a fabioimage"""
        return openimage(self.current())


[docs]    def jump_image(self, num):
        """ returns the image number as a fabioimage"""
        return openimage(self.jump(num))
    # object methods


[docs]    def next_object(self):
        """ returns the next filename as a fabio.FilenameObject"""
        self.obj.num += 1
        return self.obj


[docs]    def previous_object(self):
        """ returns the previous filename as a fabio.FilenameObject"""
        self.obj.num -= 1
        return self.obj


[docs]    def current_object(self):
        """ returns the current filename as a fabio.FilenameObject"""
        return self.obj


[docs]    def jump_object(self, num):
        """ returns the filename num as a fabio.FilenameObject"""
        self.obj.num = num
        return self.obj

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Source code for fabio.fit2dmaskimage

## Automatically adapted for numpy.oldnumeric Oct 05, 2007 by alter_code1.py

#!/usr/bin/env python
"""

Author: Andy Hammersley, ESRF
Translation into python/fabio: Jon Wright, ESRF
"""

import numpy

from fabioimage import fabioimage



[docs]class fit2dmaskimage(fabioimage):
    """ Read and try to write Andy Hammersley's mask format """


    def _readheader(self, infile):
        """
        Read in a header from an already open file
        """
        # 1024 bytes gives 256x32 bit integers
        header = infile.read(1024)
        for i, j in [ ("M", 0),
                      ("A", 4),
                      ("S", 8),
                      ("K", 12)  ]:
            if header[j] != i:
                raise Exception("Not a fit2d mask file")
        fit2dhdr = numpy.fromstring(header, numpy.int32)
        self.dim1 = fit2dhdr[4] # 1 less than Andy's fortran
        self.dim2 = fit2dhdr[5]



[docs]    def read(self, fname, frame=None):
        """
        Read in header into self.header and
            the data   into self.data
        """
        fin = self._open(fname)
        self._readheader(fin)
        # Compute image size
        self.bytecode = numpy.uint8
        self.bpp = len(numpy.array(0, self.bytecode).tostring())

        # integer division
        num_ints = (self.dim1 + 31) // 32
        total = self.dim2 * num_ints * 4
        data = fin.read(total)
        assert len(data) == total
        fin.close()

        # Now to unpack it
        data = numpy.fromstring(data, numpy.uint8)
        data = numpy.reshape(data, (self.dim2, num_ints * 4))

        result = numpy.zeros((self.dim2, num_ints * 4 * 8), numpy.uint8)

        # Unpack using bitwise comparisons to 2**n
        bits = numpy.ones((1), numpy.uint8)
        for i in range(8):
            temp = numpy.bitwise_and(bits, data)
            result[:, i::8] = temp.astype(numpy.uint8)
            bits = bits * 2
        # Extra rows needed for packing odd dimensions
        spares = num_ints * 4 * 8 - self.dim1
        if spares == 0:
            self.data = numpy.where(result == 0, 0, 1)
        else:
            self.data = numpy.where(result[:, :-spares] == 0, 0, 1)
        # Transpose appears to be needed to match edf reader (scary??)
#        self.data = numpy.transpose(self.data)
        self.data = numpy.reshape(self.data.astype(numpy.uint16),
                                    (self.dim2, self.dim1))
        self.pilimage = None
        return self





[docs]    def write(self, fname):
        """
        Try to write a file
        check we can write zipped also
        mimics that fabian was writing uint16 (we sometimes want floats)
        """
        raise Exception("Not implemented yet")


    @staticmethod

[docs]    def checkData(data=None):
        if data is None:
            return None
        else:
            return data.astype(int)

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fabio-0.1.3/doc/html/_modules/fabio/TiffIO.html0000644000175000017500000061022112233250023021757 0ustar jeromejerome00000000000000 fabio.TiffIO — FabIO 0.1.3 documentation

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Source code for fabio.TiffIO

#/*##########################################################################
# Copyright (C) 2012 European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF by the Software group.
#
# This file is free software; you can redistribute it and/or modify it 
# under the terms of the GNU Lesser General Public License as published by the Free
# Software Foundation; either version 2 of the License, or (at your option) 
# any later version.
#
# PyMca is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
# details.
#
#############################################################################*/
__author__ = "V.A. Sole - ESRF Data Analysis"
__revision__ = 1501

import sys
import os
import struct
import numpy

DEBUG = 0
ALLOW_MULTIPLE_STRIPS = False

TAG_ID = { 256:"NumberOfColumns", # S or L ImageWidth
            257:"NumberOfRows", # S or L ImageHeight
            258:"BitsPerSample", # S Number of bits per component
            259:"Compression", # SHORT (1 - NoCompression, ... 
            262:"PhotometricInterpretation", # SHORT (0 - WhiteIsZero, 1 -BlackIsZero, 2 - RGB, 3 - Palette color
            270:"ImageDescription", # ASCII
            273:"StripOffsets", # S or L, for each strip, the byte offset of the strip
            278:"RowsPerStrip", # S or L, number of rows in each back may be not for the last
            279:"StripByteCounts", # S or L, The number of bytes in the strip AFTER any compression
            305:"Software", # ASCII
            306:"Date", # ASCII
            320:"Colormap", # Colormap of Palette-color Images 
            339:"SampleFormat", # SHORT Interpretation of data in each pixel
            }

#TILES ARE TO BE SUPPORTED TOO ...
TAG_NUMBER_OF_COLUMNS = 256
TAG_NUMBER_OF_ROWS = 257
TAG_BITS_PER_SAMPLE = 258
TAG_PHOTOMETRIC_INTERPRETATION = 262
TAG_COMPRESSION = 259
TAG_IMAGE_DESCRIPTION = 270
TAG_STRIP_OFFSETS = 273
TAG_ROWS_PER_STRIP = 278
TAG_STRIP_BYTE_COUNTS = 279
TAG_SOFTWARE = 305
TAG_DATE = 306
TAG_COLORMAP = 320
TAG_SAMPLE_FORMAT = 339

FIELD_TYPE = {1:('BYTE', "B"),
               2:('ASCII', "s"), #string ending with binary zero
               3:('SHORT', "H"),
               4:('LONG', "I"),
               5:('RATIONAL', "II"),
               6:('SBYTE', "b"),
               7:('UNDEFINED', "B"),
               8:('SSHORT', "h"),
               9:('SLONG', "i"),
               10:('SRATIONAL', "ii"),
               11:('FLOAT', "f"),
               12:('DOUBLE', "d")}

FIELD_TYPE_OUT = { 'B':   1,
                   's':   2,
                   'H':   3,
                   'I':   4,
                   'II':  5,
                   'b':   6,
                   'h':   8,
                   'i':   9,
                   'ii': 10,
                   'f':  11,
                   'd':  12}

#sample formats (http://www.awaresystems.be/imaging/tiff/tiffflags/sampleformat.html)
SAMPLE_FORMAT_UINT = 1
SAMPLE_FORMAT_INT = 2
SAMPLE_FORMAT_FLOAT = 3   #floating point
SAMPLE_FORMAT_VOID = 4   #undefined data, usually assumed UINT
SAMPLE_FORMAT_COMPLEXINT = 5
SAMPLE_FORMAT_COMPLEXIEEEFP = 6




[docs]class TiffIO(object):
    def __init__(self, filename, mode=None, cache_length=20, mono_output=False):
        if mode is None:
            mode = 'rb'
        if 'b' not in mode:
            mode = mode + 'b'
        if 'a' in mode.lower():
            raise IOError("Mode %s makes no sense on TIFF files. Consider 'rb+'" % mode)
        if ('w' in mode):
            if '+' not in mode:
                mode += '+'
        #if isinstance(filename, file): #does not work in python 3
        if hasattr(filename, "seek"):
            fd = filename
            self._access = None
        else:
            #the b is needed for windows and python 3
            fd = open(filename, mode)
            self._access = mode

        self._initInternalVariables(fd)
        self._maxImageCacheLength = cache_length
        self._forceMonoOutput = mono_output

    def _initInternalVariables(self, fd=None):
        if fd is None:
            fd = self.fd
        else:
            self.fd = fd
        # read the order
        fd.seek(0)
        order = fd.read(2).decode()
        if len(order):
            if order == "II":
                #intel, little endian
                fileOrder = "little"
                self._structChar = '<'
            elif order == "MM":
                #motorola, high endian
                fileOrder = "big"
                self._structChar = '>'
            else:
                raise IOError("File is not a Mar CCD file, nor a TIFF file")
            a = fd.read(2)
            fortyTwo = struct.unpack(self._structChar + "H", a)[0]
            if fortyTwo != 42:
                raise IOError("Invalid TIFF version %d" % fortyTwo)
            else:
                if DEBUG:
                    print("VALID TIFF VERSION")
            if sys.byteorder != fileOrder:
                swap = True
            else:
                swap = False
        else:
            if sys.byteorder == "little":
                self._structChar = '<'
            else:
                self._structChar = '>'
            swap = False
        self._swap = swap
        self._IFD = []
        self._imageDataCacheIndex = []
        self._imageDataCache = []
        self._imageInfoCacheIndex = []
        self._imageInfoCache = []
        self.getImageFileDirectories(fd)

    def __makeSureFileIsOpen(self):
        if not self.fd.closed:
            return
        if DEBUG:
            print("Reopening closed file")
        fileName = self.fd.name
        if self._access is None:
            #we do not own the file
            #open in read mode
            newFile = open(fileName, 'rb')
        else:
            newFile = open(fileName, self._access)
        self.fd = newFile

    def __makeSureFileIsClosed(self):
        if self._access is None:
            #we do not own the file
            if DEBUG:
                print("Not closing not owned file")
            return

        if not self.fd.closed:
            self.fd.close()


[docs]    def getNumberOfImages(self):
        #update for the case someone has done anything?
        self._updateIFD()
        return len(self._IFD)


    def _updateIFD(self):
        self.__makeSureFileIsOpen()
        self.getImageFileDirectories()
        self.__makeSureFileIsClosed()


[docs]    def getImageFileDirectories(self, fd=None):
        if fd is None:
            fd = self.fd
        else:
            self.fd = fd
        st = self._structChar
        fd.seek(4)
        self._IFD = []
        nImages = 0
        fmt = st + 'I'
        inStr = fd.read(struct.calcsize(fmt))
        if not len(inStr):
            offsetToIFD = 0
        else:
            offsetToIFD = struct.unpack(fmt, inStr)[0]
        if DEBUG:
            print("Offset to first IFD = %d" % offsetToIFD)
        while offsetToIFD != 0:
            self._IFD.append(offsetToIFD)
            nImages += 1
            fd.seek(offsetToIFD)
            fmt = st + 'H'
            numberOfDirectoryEntries = struct.unpack(fmt, fd.read(struct.calcsize(fmt)))[0]
            if DEBUG:
                print("Number of directory entries = %d" % numberOfDirectoryEntries)

            fmt = st + 'I'
            fd.seek(offsetToIFD + 2 + 12 * numberOfDirectoryEntries)
            offsetToIFD = struct.unpack(fmt, fd.read(struct.calcsize(fmt)))[0]
            if DEBUG:
                print("Next Offset to IFD = %d" % offsetToIFD)
            #offsetToIFD = 0 
        if DEBUG:
            print("Number of images found = %d" % nImages)
        return nImages


    def _parseImageFileDirectory(self, nImage):
        offsetToIFD = self._IFD[nImage]
        st = self._structChar
        fd = self.fd
        fd.seek(offsetToIFD)
        fmt = st + 'H'
        numberOfDirectoryEntries = struct.unpack(fmt, fd.read(struct.calcsize(fmt)))[0]
        if DEBUG:
            print("Number of directory entries = %d" % numberOfDirectoryEntries)

        fmt = st + 'HHI4s'
        tagIDList = []
        fieldTypeList = []
        nValuesList = []
        valueOffsetList = []
        for i in range(numberOfDirectoryEntries):
            tagID, fieldType, nValues, valueOffset = struct.unpack(fmt, fd.read(12))
            tagIDList.append(tagID)
            fieldTypeList.append(fieldType)
            nValuesList.append(nValues)
            if nValues == 1:
                ftype, vfmt = FIELD_TYPE[fieldType]
                if ftype not in ['ASCII', 'RATIONAL', 'SRATIONAL']:
                    vfmt = st + vfmt
                    actualValue = struct.unpack(vfmt, valueOffset[0: struct.calcsize(vfmt)])[0]
                    valueOffsetList.append(actualValue)
                else:
                    valueOffsetList.append(valueOffset)
            elif (nValues < 5) and (fieldType == 2):
                ftype, vfmt = FIELD_TYPE[fieldType]
                vfmt = st + "%d%s" % (nValues, vfmt)
                actualValue = struct.unpack(vfmt, valueOffset[0: struct.calcsize(vfmt)])[0]
                valueOffsetList.append(actualValue)
            else:
                valueOffsetList.append(valueOffset)
            if DEBUG:
                if tagID in TAG_ID:
                    print("tagID = %s" % TAG_ID[tagID])
                else:
                    print("tagID        = %d" % tagID)
                print("fieldType    = %s" % FIELD_TYPE[fieldType][0])
                print("nValues      = %d" % nValues)
                #if nValues == 1:
                #    print("valueOffset =  %s" % valueOffset)
        return tagIDList, fieldTypeList, nValuesList, valueOffsetList



    def _readIFDEntry(self, tag, tagIDList, fieldTypeList, nValuesList, valueOffsetList):
        fd = self.fd
        st = self._structChar
        idx = tagIDList.index(tag)
        nValues = nValuesList[idx]
        output = []
        ftype, vfmt = FIELD_TYPE[fieldTypeList[idx]]
        vfmt = st + "%d%s" % (nValues, vfmt)
        requestedBytes = struct.calcsize(vfmt)
        if nValues == 1:
            output.append(valueOffsetList[idx])
        elif requestedBytes < 5:
            output.append(valueOffsetList[idx])
        else:
            offset = fd.seek(struct.unpack(st + "I", valueOffsetList[idx])[0])
            output = struct.unpack(vfmt, fd.read(requestedBytes))
        return output


[docs]    def getData(self, nImage, **kw):
        if nImage >= len(self._IFD):
            #update prior to raise an index error error
            self._updateIFD()
        return self._readImage(nImage, **kw)



[docs]    def getImage(self, nImage):
        return self.getData(nImage)



[docs]    def getInfo(self, nImage, **kw):
        if nImage >= len(self._IFD):
            #update prior to raise an index error error
            self._updateIFD()
        current = self._IFD[nImage]
        return self._readInfo(nImage)


    def _readInfo(self, nImage, close=True):
        if nImage in self._imageInfoCacheIndex:
            if DEBUG:
                print("Reading info from cache")
            return self._imageInfoCache[self._imageInfoCacheIndex.index(nImage)]

        #read the header
        self.__makeSureFileIsOpen()
        tagIDList, fieldTypeList, nValuesList, valueOffsetList = self._parseImageFileDirectory(nImage)

        #rows and columns
        nColumns = valueOffsetList[tagIDList.index(TAG_NUMBER_OF_COLUMNS)]
        nRows = valueOffsetList[tagIDList.index(TAG_NUMBER_OF_ROWS)]

        #bits per sample
        idx = tagIDList.index(TAG_BITS_PER_SAMPLE)
        nBits = valueOffsetList[idx]
        if nValuesList[idx] != 1:
            #this happens with RGB and friends, nBits is not a single value
            nBits = self._readIFDEntry(TAG_BITS_PER_SAMPLE,
                                          tagIDList, fieldTypeList, nValuesList, valueOffsetList)


        if TAG_COLORMAP in tagIDList:
            idx = tagIDList.index(TAG_COLORMAP)
            tmpColormap = self._readIFDEntry(TAG_COLORMAP,
                                          tagIDList, fieldTypeList, nValuesList, valueOffsetList)
            if max(tmpColormap) > 255:
                tmpColormap = numpy.array(tmpColormap, dtype=numpy.uint16)
                tmpColormap = (tmpColormap / 256.).astype(numpy.uint8)
            else:
                tmpColormap = numpy.array(tmpColormap, dtype=numpy.uint8)
            tmpColormap.shape = 3, -1
            colormap = numpy.zeros((tmpColormap.shape[-1], 3), tmpColormap.dtype)
            colormap[:, :] = tmpColormap.T
            tmpColormap = None
        else:
            colormap = None

        #sample format
        if TAG_SAMPLE_FORMAT in tagIDList:
            sampleFormat = valueOffsetList[tagIDList.index(TAG_SAMPLE_FORMAT)]
        else:
            #set to unknown
            sampleFormat = SAMPLE_FORMAT_VOID

        # compression
        compression = False
        compression_type = 1
        if TAG_COMPRESSION in tagIDList:
            compression_type = valueOffsetList[tagIDList.index(TAG_COMPRESSION)]
            if compression_type == 1:
                compression = False
            else:
                compression = True

        #photometric interpretation
        interpretation = 1
        if TAG_PHOTOMETRIC_INTERPRETATION in tagIDList:
            interpretation = valueOffsetList[tagIDList.index(TAG_PHOTOMETRIC_INTERPRETATION)]
        else:
            print("WARNING: Non standard TIFF. Photometric interpretation TAG missing")
        helpString = ""
        if sys.version > '2.6':
            helpString = eval('b""')

        if TAG_IMAGE_DESCRIPTION in tagIDList:
            imageDescription = self._readIFDEntry(TAG_IMAGE_DESCRIPTION,
                    tagIDList, fieldTypeList, nValuesList, valueOffsetList)
            if type(imageDescription) in [type([1]), type((1,))]:
                imageDescription = helpString.join(imageDescription)
        else:
            imageDescription = "%d/%d" % (nImage + 1, len(self._IFD))

        if sys.version < '3.0':
            defaultSoftware = "Unknown Software"
        else:
            defaultSoftware = bytes("Unknown Software",
                                    encoding='utf-8')
        if TAG_SOFTWARE in tagIDList:
            software = self._readIFDEntry(TAG_SOFTWARE,
                    tagIDList, fieldTypeList, nValuesList, valueOffsetList)
            if type(software) in [type([1]), type((1,))]:
                software = helpString.join(software)
        else:
            software = defaultSoftware

        if software == defaultSoftware:
            try:
                if sys.version < '3.0':
                    if imageDescription.upper().startswith("IMAGEJ"):
                        software = imageDescription.split("=")[0]
                else:
                    tmpString = imageDescription.decode()
                    if tmpString.upper().startswith("IMAGEJ"):
                        software = bytes(tmpString.split("=")[0],
                                         encoding='utf-8')
            except:
                pass

        if TAG_DATE in tagIDList:
            date = self._readIFDEntry(TAG_DATE,
                    tagIDList, fieldTypeList, nValuesList, valueOffsetList)
            if type(date) in [type([1]), type((1,))]:
                date = helpString.join(date)
        else:
            date = "Unknown Date"

        stripOffsets = self._readIFDEntry(TAG_STRIP_OFFSETS,
                        tagIDList, fieldTypeList, nValuesList, valueOffsetList)
        if TAG_ROWS_PER_STRIP in tagIDList:
            rowsPerStrip = self._readIFDEntry(TAG_ROWS_PER_STRIP,
                        tagIDList, fieldTypeList, nValuesList, valueOffsetList)[0]
        else:
            rowsPerStrip = nRows
            print("WARNING: Non standard TIFF. Rows per strip TAG missing")

        if TAG_STRIP_BYTE_COUNTS in tagIDList:
            stripByteCounts = self._readIFDEntry(TAG_STRIP_BYTE_COUNTS,
                        tagIDList, fieldTypeList, nValuesList, valueOffsetList)
        else:
            print("WARNING: Non standard TIFF. Strip byte counts TAG missing")
            if hasattr(nBits, 'index'):
                expectedSum = 0
                for n in nBits:
                    expectedSum += int(nRows * nColumns * n / 8)
            else:
                expectedSum = int(nRows * nColumns * nBits / 8)
            stripByteCounts = [expectedSum]

        if close:
            self.__makeSureFileIsClosed()

        if self._forceMonoOutput and (interpretation > 1):
            #color image but asked monochrome output
            nBits = 32
            colormap = None
            sampleFormat = SAMPLE_FORMAT_FLOAT
            interpretation = 1
            #we cannot rely on any cache in this case
            useInfoCache = False
            if DEBUG:
                print("FORCED MONO")
        else:
            useInfoCache = True

        info = {}
        info["nRows"] = nRows
        info["nColumns"] = nColumns
        info["nBits"] = nBits
        info["compression"] = compression
        info["compression_type"] = compression_type
        info["imageDescription"] = imageDescription
        info["stripOffsets"] = stripOffsets #This contains the file offsets to the data positions
        info["rowsPerStrip"] = rowsPerStrip
        info["stripByteCounts"] = stripByteCounts #bytes in strip since I do not support compression
        info["software"] = software
        info["date"] = date
        info["colormap"] = colormap
        info["sampleFormat"] = sampleFormat
        info["photometricInterpretation"] = interpretation
        infoDict = {}
        if sys.version < '3.0':
            testString = 'PyMca'
        else:
            testString = eval('b"PyMca"')
        if software.startswith(testString):
            #str to make sure python 2.x sees it as string and not unicode
            if sys.version < '3.0':
                descriptionString = imageDescription
            else:
                descriptionString = str(imageDescription.decode())
            #interpret the image description in terms of supplied
            #information at writing time
            items = descriptionString.split('=')
            for i in range(int(len(items) / 2)):
                key = "%s" % items[i * 2]
                #get rid of the \n at the end of the value 
                value = "%s" % items[i * 2 + 1][:-1]
                infoDict[key] = value
        info['info'] = infoDict

        if (self._maxImageCacheLength > 0) and useInfoCache:
            self._imageInfoCacheIndex.insert(0, nImage)
            self._imageInfoCache.insert(0, info)
            if len(self._imageInfoCacheIndex) > self._maxImageCacheLength:
                self._imageInfoCacheIndex = self._imageInfoCacheIndex[:self._maxImageCacheLength]
                self._imageInfoCache = self._imageInfoCache[:self._maxImageCacheLength]
        return info

    def _readImage(self, nImage, **kw):
        if DEBUG:
            print("Reading image %d" % nImage)
        if 'close' in kw:
            close = kw['close']
        else:
            close = True
        rowMin = kw.get('rowMin', None)
        rowMax = kw.get('rowMax', None)
        if nImage in self._imageDataCacheIndex:
            if DEBUG:
                print("Reading image data from cache")
            return self._imageDataCache[self._imageDataCacheIndex.index(nImage)]

        self.__makeSureFileIsOpen()
        if self._forceMonoOutput:
            oldMono = True
        else:
            oldMono = False
        try:
            self._forceMonoOutput = False
            info = self._readInfo(nImage, close=False)
            self._forceMonoOutput = oldMono
        except:
            self._forceMonoOutput = oldMono
            raise
        compression = info['compression']
        compression_type = info['compression_type']
        if compression:
            if compression_type != 32773:
                raise IOError("Compressed TIFF images not supported except packbits")
            else:
                #PackBits compression
                if DEBUG:
                    print("Using PackBits compression")

        interpretation = info["photometricInterpretation"]
        if interpretation == 2:
            #RGB
            pass
            #raise IOError("RGB Image. Only grayscale images supported")
        elif interpretation == 3:
            #Palette Color Image
            pass
            #raise IOError("Palette-color Image. Only grayscale images supported")
        elif interpretation > 2:
            #Palette Color Image
            raise IOError("Only grayscale images supported")

        nRows = info["nRows"]
        nColumns = info["nColumns"]
        nBits = info["nBits"]
        colormap = info["colormap"]
        sampleFormat = info["sampleFormat"]

        if rowMin is None:
            rowMin = 0

        if rowMax is None:
            rowMax = nRows - 1

        if rowMin < 0:
            rowMin = nRows - rowMin

        if rowMax < 0:
            rowMax = nRows - rowMax

        if rowMax < rowMin:
            txt = "Max Row smaller than Min Row. Reverse selection not supported"
            raise NotImplemented(txt)

        if rowMin >= nRows:
            raise IndexError("Image only has %d rows" % nRows)

        if rowMax >= nRows:
            raise IndexError("Image only has %d rows" % nRows)

        if sampleFormat == SAMPLE_FORMAT_FLOAT:
            if nBits == 32:
                dtype = numpy.float32
            elif nBits == 64:
                dtype = numpy.float64
            else:
                raise ValueError("Unsupported number of bits for a float: %d" % nBits)
        elif sampleFormat in [SAMPLE_FORMAT_UINT, SAMPLE_FORMAT_VOID]:
            if nBits in [8, (8, 8, 8), [8, 8, 8]]:
                dtype = numpy.uint8
            elif nBits in [16, (16, 16, 16), [16, 16, 16]]:
                dtype = numpy.uint16
            elif nBits in [32, (32, 32, 32), [32, 32, 32]]:
                dtype = numpy.uint32
            elif nBits in [64, (64, 64, 64), [64, 64, 64]]:
                dtype = numpy.uint64
            else:
                raise ValueError("Unsupported number of bits for unsigned int: %s" % (nBits,))
        elif sampleFormat == SAMPLE_FORMAT_INT:
            if nBits in [8, (8, 8, 8), [8, 8, 8]]:
                dtype = numpy.int8
            elif nBits in [16, (16, 16, 16), [16, 16, 16]]:
                dtype = numpy.int16
            elif nBits in [32, (32, 32, 32), [32, 32, 32]]:
                dtype = numpy.int32
            elif nBits in [64, (64, 64, 64), [64, 64, 64]]:
                dtype = numpy.int64
            else:
                raise ValueError("Unsupported number of bits for signed int: %s" % (nBits,))
        else:
            raise ValueError("Unsupported combination. Bits = %s  Format = %d" % (nBits, sampleFormat))
        if hasattr(nBits, 'index'):
            image = numpy.zeros((nRows, nColumns, len(nBits)), dtype=dtype)
        elif colormap is not None:
            #should I use colormap dtype?
            image = numpy.zeros((nRows, nColumns, 3), dtype=dtype)
        else:
            image = numpy.zeros((nRows, nColumns), dtype=dtype)

        fd = self.fd
        st = self._structChar
        stripOffsets = info["stripOffsets"] #This contains the file offsets to the data positions
        rowsPerStrip = info["rowsPerStrip"]
        stripByteCounts = info["stripByteCounts"] #bytes in strip since I do not support compression

        rowStart = 0
        if len(stripOffsets) == 1:
            bytesPerRow = int(stripByteCounts[0] / rowsPerStrip)
            fd.seek(stripOffsets[0] + rowMin * bytesPerRow)
            nBytes = (rowMax - rowMin + 1) * bytesPerRow
            if self._swap:
                readout = numpy.fromstring(fd.read(nBytes), dtype).byteswap()
            else:
                readout = numpy.fromstring(fd.read(nBytes), dtype)
            if hasattr(nBits, 'index'):
                readout.shape = -1, nColumns, len(nBits)
            elif info['colormap'] is not None:
                readout = colormap[readout]
            else:
                readout.shape = -1, nColumns
            image[rowMin:rowMax + 1, :] = readout
        else:
            for i in range(len(stripOffsets)):
                #the amount of rows
                nRowsToRead = rowsPerStrip
                rowEnd = int(min(rowStart + nRowsToRead, nRows))
                if rowEnd < rowMin:
                    rowStart += nRowsToRead
                    continue
                if (rowStart > rowMax):
                    break
                #we are in position
                fd.seek(stripOffsets[i])
                #the amount of bytes to read
                nBytes = stripByteCounts[i]
                if compression_type == 32773:
                    try:
                        bufferBytes = bytes()
                    except:
                        #python 2.5 ...
                        bufferBytes = ""
                    #packBits
                    readBytes = 0
                    #intermediate buffer
                    tmpBuffer = fd.read(nBytes)
                    while readBytes < nBytes:
                        n = struct.unpack('b', tmpBuffer[readBytes:(readBytes + 1)])[0]
                        readBytes += 1
                        if n >= 0:
                            #should I prevent reading more than the
                            #length of the chain? Let's python raise
                            #the exception...
                            bufferBytes += tmpBuffer[readBytes:\
                                                      readBytes + (n + 1)]
                            readBytes += (n + 1)
                        elif n > -128:
                            bufferBytes += (-n + 1) * tmpBuffer[readBytes:(readBytes + 1)]
                            readBytes += 1
                        else:
                            #if read -128 ignore the byte
                            continue
                    if self._swap:
                        readout = numpy.fromstring(bufferBytes, dtype).byteswap()
                    else:
                        readout = numpy.fromstring(bufferBytes, dtype)
                    if hasattr(nBits, 'index'):
                        readout.shape = -1, nColumns, len(nBits)
                    elif info['colormap'] is not None:
                        readout = colormap[readout]
                        readout.shape = -1, nColumns, 3
                    else:
                        readout.shape = -1, nColumns
                    image[rowStart:rowEnd, :] = readout
                else:
                    if 1:
                        #use numpy
                        if self._swap:
                            readout = numpy.fromstring(fd.read(nBytes), dtype).byteswap()
                        else:
                            readout = numpy.fromstring(fd.read(nBytes), dtype)
                        if hasattr(nBits, 'index'):
                            readout.shape = -1, nColumns, len(nBits)
                        elif colormap is not None:
                            readout = colormap[readout]
                            readout.shape = -1, nColumns, 3
                        else:
                            readout.shape = -1, nColumns
                        image[rowStart:rowEnd, :] = readout
                    else:
                        #using struct
                        readout = numpy.array(struct.unpack(st + "%df" % int(nBytes / 4), fd.read(nBytes)),
                                              dtype=dtype)
                        if hasattr(nBits, 'index'):
                            readout.shape = -1, nColumns, len(nBits)
                        elif colormap is not None:
                            readout = colormap[readout]
                            readout.shape = -1, nColumns, 3
                        else:
                            readout.shape = -1, nColumns
                        image[rowStart:rowEnd, :] = readout
                rowStart += nRowsToRead
        if close:
            self.__makeSureFileIsClosed()

        if len(image.shape) == 3:
            #color image
            if self._forceMonoOutput:
                #color image, convert to monochrome
                image = (image[:, :, 0] * 0.114 + \
                         image[:, :, 1] * 0.587 + \
                         image[:, :, 2] * 0.299).astype(numpy.float32)

        if (rowMin == 0) and (rowMax == (nRows - 1)):
            self._imageDataCacheIndex.insert(0, nImage)
            self._imageDataCache.insert(0, image)
            if len(self._imageDataCacheIndex) > self._maxImageCacheLength:
                self._imageDataCacheIndex = self._imageDataCacheIndex[:self._maxImageCacheLength]
                self._imageDataCache = self._imageDataCache[:self._maxImageCacheLength]

        return image


[docs]    def writeImage(self, image0, info=None, software=None, date=None):
        if software is None:
            software = 'PyMca.TiffIO'
        #if date is None:
        #    date = time.ctime()

        self.__makeSureFileIsOpen()
        fd = self.fd
        #prior to do anything, perform some tests
        if not len(image0.shape):
            raise ValueError("Empty image")
        if len(image0.shape) == 1:
            #get a different view
            image = image0[:]
            image.shape = 1, -1
        else:
            image = image0

        if image.dtype == numpy.float64:
            image = image.astype(numpy.float32)
        fd.seek(0)
        mode = fd.mode
        name = fd.name
        if 'w' in mode:
            #we have to overwrite the file
            self.__makeSureFileIsClosed()
            fd = None
            if os.path.exists(name):
                os.remove(name)
            fd = open(name, mode='wb+')
            self._initEmptyFile(fd)
        self.fd = fd

        #read the file size
        self.__makeSureFileIsOpen()
        fd = self.fd
        fd.seek(0, os.SEEK_END)
        endOfFile = fd.tell()
        if fd.tell() == 0:
            self._initEmptyFile(fd)
            fd.seek(0, os.SEEK_END)
            endOfFile = fd.tell()

        #init internal variables
        self._initInternalVariables(fd)
        st = self._structChar

        #get the image file directories
        nImages = self.getImageFileDirectories()
        if DEBUG:
            print("File contains %d images" % nImages)
        if nImages == 0:
            fd.seek(4)
            fmt = st + 'I'
            fd.write(struct.pack(fmt, endOfFile))
        else:
            fd.seek(self._IFD[-1])
            fmt = st + 'H'
            numberOfDirectoryEntries = struct.unpack(fmt, fd.read(struct.calcsize(fmt)))[0]
            fmt = st + 'I'
            pos = self._IFD[-1] + 2 + 12 * numberOfDirectoryEntries
            fd.seek(pos)
            fmt = st + 'I'
            fd.write(struct.pack(fmt, endOfFile))
        fd.flush()

        #and we can write at the end of the file, find out the file length
        fd.seek(0, os.SEEK_END)

        #get the description information from the input information
        if info is None:
            description = info
        else:
            description = "%s" % ""
            for key in info.keys():
                description += "%s=%s\n" % (key, info[key])

        #get the image file directory
        outputIFD = self._getOutputIFD(image, description=description,
                                              software=software,
                                              date=date)

        #write the new IFD
        fd.write(outputIFD)

        #write the image
        if self._swap:
            fd.write(image.byteswap().tostring())
        else:
            fd.write(image.tostring())

        fd.flush()
        self.fd = fd
        self.__makeSureFileIsClosed()


    def _initEmptyFile(self, fd=None):
        if fd is None:
            fd = self.fd
        if sys.byteorder == "little":
            order = "II"
            #intel, little endian
            fileOrder = "little"
            self._structChar = '<'
        else:
            order = "MM"
            #motorola, high endian
            fileOrder = "big"
            self._structChar = '>'
        st = self._structChar
        if fileOrder == sys.byteorder:
            self._swap = False
        else:
            self._swap = True
        fd.seek(0)
        if sys.version < '3.0':
            fd.write(struct.pack(st + '2s', order))
            fd.write(struct.pack(st + 'H', 42))
            fd.write(struct.pack(st + 'I', 0))
        else:
            fd.write(struct.pack(st + '2s', bytes(order, 'utf-8')))
            fd.write(struct.pack(st + 'H', 42))
            fd.write(struct.pack(st + 'I', 0))
        fd.flush()

    def _getOutputIFD(self, image, description=None, software=None, date=None):
        #the tags have to be in order
        #the very minimum is
        #256:"NumberOfColumns",           # S or L ImageWidth
        #257:"NumberOfRows",              # S or L ImageHeight
        #258:"BitsPerSample",             # S Number of bits per component
        #259:"Compression",               # SHORT (1 - NoCompression, ... 
        #262:"PhotometricInterpretation", # SHORT (0 - WhiteIsZero, 1 -BlackIsZero, 2 - RGB, 3 - Palette color
        #270:"ImageDescription",          # ASCII
        #273:"StripOffsets",              # S or L, for each strip, the byte offset of the strip
        #278:"RowsPerStrip",              # S or L, number of rows in each back may be not for the last
        #279:"StripByteCounts",           # S or L, The number of bytes in the strip AFTER any compression
        #305:"Software",                  # ASCII
        #306:"Date",                      # ASCII
        #339:"SampleFormat",              # SHORT Interpretation of data in each pixel

        nDirectoryEntries = 9
        imageDescription = None
        if description is not None:
            descriptionLength = len(description)
            while descriptionLength < 4:
                description = description + " "
                descriptionLength = len(description)
            if sys.version >= '3.0':
                description = bytes(description, 'utf-8')
            elif type(description) != type(""):
                try:
                    description = description.decode('utf-8')
                except UnicodeDecodeError:
                    try:
                        description = description.decode('latin-1')
                    except UnicodeDecodeError:
                        description = "%s" % description
                if sys.version > '2.6':
                    description = description.encode('utf-8', errors="ignore")
                description = "%s" % description
            descriptionLength = len(description)
            imageDescription = struct.pack("%ds" % descriptionLength, description)
            nDirectoryEntries += 1

        #software
        if software is not None:
            softwareLength = len(software)
            while softwareLength < 4:
                software = software + " "
                softwareLength = len(software)
            if sys.version >= '3.0':
                software = bytes(software, 'utf-8')
            softwarePackedString = struct.pack("%ds" % softwareLength, software)
            nDirectoryEntries += 1
        else:
            softwareLength = 0

        if date is not None:
            dateLength = len(date)
            if sys.version >= '3.0':
                date = bytes(date, 'utf-8')
            datePackedString = struct.pack("%ds" % dateLength, date)
            dateLength = len(datePackedString)
            nDirectoryEntries += 1
        else:
            dateLength = 0

        nRows, nColumns = image.shape
        dtype = image.dtype
        bitsPerSample = int(dtype.str[-1]) * 8

        #only uncompressed data
        compression = 1

        #interpretation, black is zero
        interpretation = 1

        #image description
        if imageDescription is not None:
            descriptionLength = len(imageDescription)
        else:
            descriptionLength = 0

        #strip offsets
        #we are putting them after the directory and the directory is
        #at the end of the file
        self.fd.seek(0, os.SEEK_END)
        endOfFile = self.fd.tell()
        if endOfFile == 0:
            #empty file
            endOfFile = 8

        #rows per strip
        if ALLOW_MULTIPLE_STRIPS:
            #try to segment the image in several pieces
            if not (nRows % 4):
                rowsPerStrip = int(nRows / 4)
            elif not (nRows % 10):
                rowsPerStrip = int(nRows / 10)
            elif not (nRows % 8):
                rowsPerStrip = int(nRows / 8)
            elif not (nRows % 4):
                rowsPerStrip = int(nRows / 4)
            elif not (nRows % 2):
                rowsPerStrip = int(nRows / 2)
            else:
                rowsPerStrip = nRows
        else:
            rowsPerStrip = nRows

        #stripByteCounts
        stripByteCounts = int(nColumns * rowsPerStrip * bitsPerSample / 8)

        if descriptionLength > 4:
            stripOffsets0 = endOfFile + dateLength + descriptionLength + \
                        2 + 12 * nDirectoryEntries + 4
        else:
            stripOffsets0 = endOfFile + dateLength + \
                        2 + 12 * nDirectoryEntries + 4

        if softwareLength > 4:
            stripOffsets0 += softwareLength

        stripOffsets = [stripOffsets0]
        stripOffsetsLength = 0
        stripOffsetsString = None

        st = self._structChar

        if rowsPerStrip != nRows:
            nStripOffsets = int(nRows / rowsPerStrip)
            fmt = st + 'I'
            stripOffsetsLength = struct.calcsize(fmt) * nStripOffsets
            stripOffsets0 += stripOffsetsLength
            #the length for the stripByteCounts will be the same
            stripOffsets0 += stripOffsetsLength
            stripOffsets = []
            for i in range(nStripOffsets):
                value = stripOffsets0 + i * stripByteCounts
                stripOffsets.append(value)
                if i == 0:
                    stripOffsetsString = struct.pack(fmt, value)
                    stripByteCountsString = struct.pack(fmt, stripByteCounts)
                else:
                    stripOffsetsString += struct.pack(fmt, value)
                    stripByteCountsString += struct.pack(fmt, stripByteCounts)

        if DEBUG:
            print("IMAGE WILL START AT %d" % stripOffsets[0])

        #sample format
        if dtype in [numpy.float32, numpy.float64] or\
           dtype.str[-2] == 'f':
            sampleFormat = SAMPLE_FORMAT_FLOAT
        elif dtype in [numpy.uint8, numpy.uint16, numpy.uint32, numpy.uint64]:
            sampleFormat = SAMPLE_FORMAT_UINT
        elif dtype in [numpy.int8, numpy.int16, numpy.int32, numpy.int64]:
            sampleFormat = SAMPLE_FORMAT_INT
        else:
            raise ValueError("Unsupported data type %s" % dtype)

        info = {}
        info["nColumns"] = nColumns
        info["nRows"] = nRows
        info["nBits"] = bitsPerSample
        info["compression"] = compression
        info["photometricInterpretation"] = interpretation
        info["stripOffsets"] = stripOffsets
        info["rowsPerStrip"] = rowsPerStrip
        info["stripByteCounts"] = stripByteCounts
        info["date"] = date
        info["sampleFormat"] = sampleFormat

        outputIFD = ""
        if sys.version > '2.6':
            outputIFD = eval('b""')

        fmt = st + "H"
        outputIFD += struct.pack(fmt, nDirectoryEntries)

        fmt = st + "HHII"
        outputIFD += struct.pack(fmt, TAG_NUMBER_OF_COLUMNS,
                                         FIELD_TYPE_OUT['I'],
                                         1,
                                         info["nColumns"])
        outputIFD += struct.pack(fmt, TAG_NUMBER_OF_ROWS,
                                         FIELD_TYPE_OUT['I'],
                                         1,
                                         info["nRows"])

        fmt = st + 'HHIHH'
        outputIFD += struct.pack(fmt, TAG_BITS_PER_SAMPLE,
                                         FIELD_TYPE_OUT['H'],
                                         1,
                                         info["nBits"], 0)
        fmt = st + 'HHIHH'
        outputIFD += struct.pack(fmt, TAG_COMPRESSION,
                                         FIELD_TYPE_OUT['H'],
                                         1,
                                         info["compression"], 0)
        fmt = st + 'HHIHH'
        outputIFD += struct.pack(fmt, TAG_PHOTOMETRIC_INTERPRETATION,
                                         FIELD_TYPE_OUT['H'],
                                         1,
                                         info["photometricInterpretation"], 0)

        if imageDescription is not None:
            descriptionLength = len(imageDescription)
            if descriptionLength > 4:
                fmt = st + 'HHII'
                outputIFD += struct.pack(fmt, TAG_IMAGE_DESCRIPTION,
                                         FIELD_TYPE_OUT['s'],
                                         descriptionLength,
                                         info["stripOffsets"][0] - \
                                         2 * stripOffsetsLength - \
                                         descriptionLength)
            else:
                #it has to have length 4
                fmt = st + 'HHI%ds' % descriptionLength
                outputIFD += struct.pack(fmt, TAG_IMAGE_DESCRIPTION,
                                         FIELD_TYPE_OUT['s'],
                                         descriptionLength,
                                         description)

        if len(stripOffsets) == 1:
            fmt = st + 'HHII'
            outputIFD += struct.pack(fmt, TAG_STRIP_OFFSETS,
                                             FIELD_TYPE_OUT['I'],
                                             1,
                                             info["stripOffsets"][0])
        else:
            fmt = st + 'HHII'
            outputIFD += struct.pack(fmt, TAG_STRIP_OFFSETS,
                                             FIELD_TYPE_OUT['I'],
                                             len(stripOffsets),
                    info["stripOffsets"][0] - 2 * stripOffsetsLength)

        fmt = st + 'HHII'
        outputIFD += struct.pack(fmt, TAG_ROWS_PER_STRIP,
                                         FIELD_TYPE_OUT['I'],
                                         1,
                                         info["rowsPerStrip"])

        if len(stripOffsets) == 1:
            fmt = st + 'HHII'
            outputIFD += struct.pack(fmt, TAG_STRIP_BYTE_COUNTS,
                                             FIELD_TYPE_OUT['I'],
                                             1,
                                             info["stripByteCounts"])
        else:
            fmt = st + 'HHII'
            outputIFD += struct.pack(fmt, TAG_STRIP_BYTE_COUNTS,
                                             FIELD_TYPE_OUT['I'],
                                             len(stripOffsets),
                    info["stripOffsets"][0] - stripOffsetsLength)

        if software is not None:
            if softwareLength > 4:
                fmt = st + 'HHII'
                outputIFD += struct.pack(fmt, TAG_SOFTWARE,
                                         FIELD_TYPE_OUT['s'],
                                         softwareLength,
                                         info["stripOffsets"][0] - \
                                         2 * stripOffsetsLength - \
                            descriptionLength - softwareLength - dateLength)
            else:
                #it has to have length 4
                fmt = st + 'HHI%ds' % softwareLength
                outputIFD += struct.pack(fmt, TAG_SOFTWARE,
                                         FIELD_TYPE_OUT['s'],
                                         softwareLength,
                                         softwarePackedString)

        if date is not None:
            fmt = st + 'HHII'
            outputIFD += struct.pack(fmt, TAG_DATE,
                                      FIELD_TYPE_OUT['s'],
                                      dateLength,
                                      info["stripOffsets"][0] - \
                                         2 * stripOffsetsLength - \
                                      descriptionLength - dateLength)

        fmt = st + 'HHIHH'
        outputIFD += struct.pack(fmt, TAG_SAMPLE_FORMAT,
                                         FIELD_TYPE_OUT['H'],
                                         1,
                                         info["sampleFormat"], 0)
        fmt = st + 'I'
        outputIFD += struct.pack(fmt, 0)

        if softwareLength > 4:
            outputIFD += softwarePackedString

        if date is not None:
            outputIFD += datePackedString

        if imageDescription is not None:
            if descriptionLength > 4:
                outputIFD += imageDescription

        if stripOffsetsString is not None:
            outputIFD += stripOffsetsString
            outputIFD += stripByteCountsString

        return outputIFD



if __name__ == "__main__":
    filename = sys.argv[1]
    dtype = numpy.uint16
    if not os.path.exists(filename):
        print("Testing file creation")
        tif = TiffIO(filename, mode='wb+')
        data = numpy.arange(10000).astype(dtype)
        data.shape = 100, 100
        tif.writeImage(data, info={'Title':'1st'})
        tif = None
        if os.path.exists(filename):
            print("Testing image appending")
            tif = TiffIO(filename, mode='rb+')
            tif.writeImage((data * 2).astype(dtype), info={'Title':'2nd'})
            tif = None
    tif = TiffIO(filename)
    print("Number of images = %d" % tif.getNumberOfImages())
    for i in range(tif.getNumberOfImages()):
        info = tif.getInfo(i)
        for key in info:
            if key not in ["colormap"]:
                print("%s = %s" % (key, info[key]))
            elif info['colormap'] is not None:
                print("RED   %s = %s" % (key, info[key][0:10, 0]))
                print("GREEN %s = %s" % (key, info[key][0:10, 1]))
                print("BLUE  %s = %s" % (key, info[key][0:10, 2]))
        data = tif.getImage(i)[0, 0:10]
        print("data [0, 0:10] = ", data)

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© Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
fabio-0.1.3/doc/html/_modules/fabio/pilatusimage.html0000644000175000017500000003045312233250022023325 0ustar jeromejerome00000000000000 fabio.pilatusimage — FabIO 0.1.3 documentation

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Source code for fabio.pilatusimage

#!/usr/bin/env python
#coding: utf8
"""

Authors:
........
* Henning O. Sorensen & Erik Knudsen:
  Center for Fundamental Research: Metal Structures in Four Dimensions;
  Risoe National Laboratory;
  Frederiksborgvej 399;
  DK-4000 Roskilde;
  email:erik.knudsen@risoe.dk
* Jon Wright:
  European Synchrotron Radiation Facility;
  Grenoble (France)

"""


# Base this on the tifimage (as Pilatus is tiff with a
# tiff header

from fabio.tifimage import tifimage



[docs]class pilatusimage(tifimage):
    """ Read in Pilatus format, also 
        pilatus images, including header info """


    def _readheader(self, infile):
        """
        Parser based approach
        Gets all entries
        """

        self.header = {}

#        infile = open(infile)
        hstr = infile.read(4096)
        # well not very pretty - but seems to find start of
        # header information
        if (hstr.find('# ') == -1):
            return self.header

        hstr = hstr[hstr.index('# '):]
        hstr = hstr[:hstr.index('\x00')]
        hstr = hstr.split('#')
        go_on = True
        while go_on:
            try:
                hstr.remove('')
            except Exception:
                go_on = False

        for line in hstr:
            line = line[1:line.index('\r\n')]
            if line.find(':') > -1:
                dump = line.split(':')
                self.header[dump[0]] = dump[1]
            elif line.find('=') > -1:
                dump = line.split('=')
                self.header[dump[0]] = dump[1]
            elif line.find(' ') > -1:
                i = line.find(' ')
                self.header[line[:i]] = line[i:]
            elif line.find(',') > -1:
                dump = line.split(',')
                self.header[dump[0]] = dump[1]

        return self.header



    def _read(self, fname):
        """
        inherited from tifimage
        ... a Pilatus image *is a* tif image
        just with a header
        """
        return tifimage.read(self, fname)

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© Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
fabio-0.1.3/doc/html/_modules/fabio/openimage.html0000644000175000017500000006707512233250022022617 0ustar jeromejerome00000000000000 fabio.openimage — FabIO 0.1.3 documentation

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Source code for fabio.openimage

"""

Authors: Henning O. Sorensen & Erik Knudsen
         Center for Fundamental Research: Metal Structures in Four Dimensions
         Risoe National Laboratory
         Frederiksborgvej 399
         DK-4000 Roskilde
         email:henning.sorensen@risoe.dk

mods for fabio by JPW

"""
import sys, logging
logger = logging.getLogger("openimage")
from fabioutils  import FilenameObject
from fabioimage import fabioimage
import edfimage
import adscimage
import tifimage
import marccdimage
import mar345image
import fit2dmaskimage
import brukerimage
import bruker100image
import pnmimage
import GEimage
import OXDimage
import dm3image
import HiPiCimage
import pilatusimage
import fit2dspreadsheetimage
import kcdimage
import cbfimage
import xsdimage
import binaryimage

MAGIC_NUMBERS = [
    # "\42\5a" : 'bzipped'
    # "\1f\8b" : 'gzipped'
    ("FORMAT :        86" , 'bruker'),
    ("\x4d\x4d\x00\x2a"   , 'tif') ,
    # The marCCD and Pilatus formats are both standard tif with a header
    # hopefully these byte patterns are unique for the formats
    # If not the image will be read, but the is missing 
    ("\x49\x49\x2a\x00\x08\x00"   , 'marccd') ,
    ("\x49\x49\x2a\x00\x82\x00"   , 'pilatus') ,
    ("\x49\x49\x2a\x00"   , 'tif') ,
    # ADSC must come before edf
    ("{\nHEA"             , 'adsc'),
    ("{"                  , 'edf'),
    ("\r{"                , 'edf'),
    ("\n{"                , 'edf'),
    ("ADEPT"              , 'GE'),
    ("OD"                 , 'OXD'),
    ("IM"                 , 'HiPiC'),
    ('\x2d\x04'           , 'mar345'),
    ('\xd2\x04'           , 'mar345'),
    ('\x04\x2d'           , 'mar345'), #some machines may need byteswapping
    ('\x04\xd2'           , 'mar345'),
    # hint : MASK in 32 bit
    ('M\x00\x00\x00A\x00\x00\x00S\x00\x00\x00K\x00\x00\x00' , 'fit2dmask') ,
    ('\x00\x00\x00\x03'   , 'dm3'),
    ("No"                 , "kcd"),
    ("<"                  , "xsd")
    ]


[docs]def do_magic(byts):
    """ Try to interpret the bytes starting the file as a magic number """
    for magic, format_type in MAGIC_NUMBERS:
        if byts.find(magic) == 0:
            return format_type
        if 0: # debugging - bruker needed 18 bytes below
            logger.debug("m: %s f: %s", magic, format_type)
            logger.debug("bytes: %s len(bytes) %s", magic, len(magic))
            logger.debug("found: %s", byts.find(magic))
            for i in range(len(magic)):
                logger.debug("%s %s %s %s ", ord(magic[i]), ord(byts[i]), magic[i], byts[i])
    raise Exception("Could not interpret magic string")




[docs]def openimage(filename, frame=None):
    """ Try to open an image """
    if isinstance(filename, FilenameObject):
        try:
            logger.debug("Attempting to open %s" % (filename.tostring()))
            obj = _openimage(filename.tostring())
            logger.debug("Attempting to read frame %s from %s" % (frame,
                filename.tostring()))
            obj = obj.read(filename.tostring(), frame)
        except Exception, ex:
            # multiframe file
            #logger.debug( "DEBUG: multiframe file, start # %d"%(
            #    filename.num)
            logger.debug("Exception %s, trying name %s" % (ex, filename.stem))
            obj = _openimage(filename.stem)
            logger.debug("Reading frame %s from %s" % (filename.num, filename.stem))
            obj.read(filename.stem, frame=filename.num)
    else:
        logger.debug("Attempting to open %s" % (filename))
        obj = _openimage(filename)
        logger.debug("Attempting to read frame %s from %s" % (frame, filename))
        obj = obj.read(filename, frame)
    return obj




[docs]def openheader(filename):
    """ return only the header"""
    obj = _openimage(filename)
    obj.readheader(filename)
    return obj



def _openimage(filename):
    """ 
    determine which format for a filename
    and return appropriate class which can be used for opening the image
    """
    try:
        imo = fabioimage()
        byts = imo._open(filename).read(18)
        filetype = do_magic(byts)
        if filetype == "marccd" and filename.find("mccd") == -1:
            # Cannot see a way around this. Need to find something
            # to distinguish mccd from regular tif...
            filetype = "tif"
    except IOError, error:
        logger.error("%s: File probably does not exist", error)
        raise error
    except:
        try:
            file_obj = FilenameObject(filename=filename)
            if file_obj == None:
                raise Exception("Unable to deconstruct filename")
            if (file_obj.format is not None) and\
                len(file_obj.format) != 1 and \
                type(file_obj.format) != type(["list"]):
                # one of OXD/ ADSC - should have got in previous
                raise Exception("openimage failed on magic bytes & name guess")
            filetype = file_obj.format
            #UNUSED filenumber = file_obj.num
        except Exception, error:
            logger.error(error)
            import traceback
            traceback.print_exc()
            raise Exception("Fabio could not identify " + filename)
    klass_name = "".join(filetype) + 'image'
    module = sys.modules.get("fabio." + klass_name, None)
    if module is not None:
        if hasattr(module, klass_name):
            klass = getattr(module, klass_name)
        else:
            raise Exception("Module %s has no image class" % module)
    else:
        raise Exception("Filetype not known %s %s" % (filename, klass_name))
    obj = klass()
    # skip the read for read header
    return obj

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© Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
fabio-0.1.3/doc/html/_modules/fabio/adscimage.html0000644000175000017500000006311312233250022022555 0ustar jeromejerome00000000000000 fabio.adscimage — FabIO 0.1.3 documentation

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Source code for fabio.adscimage

#!/usr/bin/env python
#coding: utf8
"""

Authors: Henning O. Sorensen & Erik Knudsen
         Center for Fundamental Research: Metal Structures in Four Dimensions
         Risoe National Laboratory
         Frederiksborgvej 399
         DK-4000 Roskilde
         email:erik.knudsen@risoe.dk

+ mods for fabio by JPW

"""

import numpy, logging
from fabioimage import fabioimage
logger = logging.getLogger("adscimage")


[docs]class adscimage(fabioimage):
    """ Read an image in ADSC format (quite similar to edf?) """
    def __init__(self, *args, **kwargs):
        fabioimage.__init__(self, *args, **kwargs)


[docs]    def read(self, fname, frame=None):
        """ read in the file """
        infile = self._open(fname, "rb")
        try:
            self._readheader(infile)
        except:
            raise Exception("Error processing adsc header")
        # banned by bzip/gzip???
        try:
            infile.seek(int(self.header['HEADER_BYTES']), 0)
        except TypeError:
            # Gzipped does not allow a seek and read header is not
            # promising to stop in the right place
            infile.close()
            infile = self._open(fname, "rb")
            infile.read(int(self.header['HEADER_BYTES']))
        binary = infile.read()
        infile.close()

        #now read the data into the array
        self.dim1 = int(self.header['SIZE1'])
        self.dim2 = int(self.header['SIZE2'])
        if 'little' in self.header['BYTE_ORDER']:
            try:
                self.data = numpy.reshape(
                    numpy.fromstring(binary, numpy.uint16),
                    (self.dim2, self.dim1))
            except ValueError:
                raise IOError, 'Size spec in ADSC-header does not match ' + \
                    'size of image data field'
            self.bytecode = numpy.uint16
            logger.info("adscimage read in using low byte first (x386-order)")
        else:
            try:
                self.data = numpy.reshape(
                    numpy.fromstring(binary, numpy.uint16),
                    (self.dim2, self.dim1)).byteswap()
            except ValueError:
                raise IOError, 'Size spec in ADSC-header does not match ' + \
                    'size of image data field'
            self.bytecode = numpy.uint16
            logger.info('adscimage using high byte first (network order)')
        self.resetvals()
        return self



    def _readheader(self, infile):
        """ read an adsc header """
        line = infile.readline()
        bytesread = len(line)
        while '}' not in line:
            if '=' in line:
                (key, val) = line.split('=')
                self.header_keys.append(key.strip())
                self.header[key.strip()] = val.strip(' ;\n')
            line = infile.readline()
            bytesread = bytesread + len(line)



[docs]    def write(self, fname):
        """
        Write adsc format
        """
        out = '{\n'
        for key in self.header_keys:
            out += "%s = %s;\n" % (key, self.header[key])
        # FIXME ??? - made padding match header bytes keyword            
        #        the cbflib example image has exactly 512...
        if self.header.has_key("HEADER_BYTES"):
            pad = int(self.header["HEADER_BYTES"]) - len(out) - 2
        else:
            # integer division
            # 1234567890123456789012
            # HEADER_BYTES = 1234;\n
            hsize = ((len(out) + 23) / 512 + 1) * 512
            out += "HEADER_BYTES=%d;\n" % (hsize)
            pad = hsize - len(out) - 2
        out += pad * ' ' + "}\n"
        assert len(out) % 512 == 0 , "Header is not multiple of 512"
        outf = open(fname, "wb")
        outf.write(out)
        # it says "unsigned_short" ? ... jpw example has:
        # BYTE_ORDER=big_endian;
        # TYPE=unsigned_short;
        if "little" in self.header["BYTE_ORDER"]:
            outf.write(self.data.astype(numpy.uint16).tostring())
        else:
            outf.write(self.data.byteswap().astype(
                    numpy.uint16).tostring())
        outf.close()




[docs]def test():
    """ testcase """
    import sys, time
    img = adscimage()
    begin = time.clock()
    while (sys.argv[1:]):
        img.read(sys.argv[1])
#        rim = img.toPIL16()
        img.rebin(2, 2)
        img.write('jegErEnFil0000.img')
        print sys.argv[1] + ": max=%d, min=%d, mean=%.2e, stddev=%.2e" % (\
              img.getmax(), img.getmin(), img.getmean(), img.getstddev())
        print 'integrated intensity (%d %d %d %d) =%.3f' % (\
              10, 20, 20, 40, img.integrate_area((10, 20, 20, 40)))
        sys.argv[1:] = sys.argv[2:]
    end = time.clock()
    print end - begin



if __name__ == '__main__':
    test()

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© Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
fabio-0.1.3/doc/html/_modules/fabio/bruker100image.html0000644000175000017500000005113412233250022023356 0ustar jeromejerome00000000000000 fabio.bruker100image — FabIO 0.1.3 documentation

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Source code for fabio.bruker100image

import numpy
import math
import logging
logger = logging.getLogger("bruker100image")
try:
    from PIL import Image
except ImportError:
    logger.warning("PIL is not installed ... trying to do without")
    Image = None

from brukerimage import brukerimage
from readbytestream import readbytestream 


[docs]class bruker100image(brukerimage):



[docs]    def toPIL16(self, filename=None):
        if not Image:
            raise RuntimeError("PIL is not installed !!! ")

        if filename:
            self.read(filename)
        PILimage = Image.frombuffer("F",
                                        (self.dim1, self.dim2),
                                        self.data,
                                        "raw",
                                        "F;16", 0, -1)
        return PILimage



[docs]    def read(self, fname, frame=None):
        f = open(fname, "rb")
        try:
            self._readheader(f)
        except:
            raise

        rows = int(self.header['NROWS'])
        cols = int(self.header['NCOLS'])
        npixelb = int(self.header['NPIXELB'][0])
        # you had to read the Bruker docs to know this!

        # We are now at the start of the image - assuming 
        #   readbrukerheader worked
        # size = rows * cols * npixelb
        self.data = readbytestream(f, f.tell(), rows, cols, npixelb,
                                    datatype="int", signed='n', swap='n')

        noverfl = self.header['NOVERFL'].split() # now process the overflows
        #read the set of "underflow pixels" - these will be completely 
        # disregarded for now
        data = self.data
        k = 0

        while k < 2:#for the time being things - are done in 16 bits
            datatype = {'1' : numpy.uint8,
                        '2' : numpy.uint16,
                        '4' : numpy.uint32 }[("%d" % 2 ** k)]
            ar = numpy.array(numpy.fromstring(f.read(int(noverfl[k]) * (2 ** k)),
                                        datatype), numpy.uint16)
            #insert the the overflow pixels in the image array:
            #this is probably a memory intensive way of doing this - 
            # might be done in a more clever way
            lim = 2 ** (8 * k) - 1
            #generate an array comprising of the indices into data.ravel() 
            # where its value equals lim.
            M = numpy.compress(numpy.equal(data.ravel(), lim), numpy.arange(rows * cols))
            #now put values from ar into those indices
            numpy.put(data.ravel(), M, ar)
            padding = 16 * int(math.ceil(int(noverfl[k]) * (2 ** k) / 16.)) - \
                         int(noverfl[k]) * (2 ** k)
            f.seek(padding, 1)
            print noverfl[k] + " bytes read + %d bytes padding" % padding
            k = k + 1

        f.close()

        (self.dim1, self.dim2) = (rows, cols)
        print self.dim1, self.dim2
        self.resetvals()
        return self


if __name__ == '__main__':
    import sys, time
    I = bruker100image()
    b = time.clock()
    while (sys.argv[1:]):
        I.read(sys.argv[1])
        r = I.toPIL16()
        I.rebin(2, 2)
        print sys.argv[1] + (": max=%d, min=%d, mean=%.2e, stddev=%.2e") % (
            I.getmax(), I.getmin(), I.getmean(), I.getstddev())
        print 'integrated intensity (%d %d %d %d) =%.3f' % (
            10, 20, 20, 40, I.integrate_area((10, 20, 20, 40)))
        sys.argv[1:] = sys.argv[2:]
    e = time.clock()
    print (e - b)

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© Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
fabio-0.1.3/doc/html/_modules/fabio/fit2dspreadsheetimage.html0000644000175000017500000003274412233250022025111 0ustar jeromejerome00000000000000 fabio.fit2dspreadsheetimage — FabIO 0.1.3 documentation

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Source code for fabio.fit2dspreadsheetimage

"""
Read the fit2d ascii image output
        + Jon Wright, ESRF
"""

import numpy

from fabioimage import fabioimage




class fit2dspreadsheetimage(fabioimage):
    """

[docs]    Read a fit2d ascii format
    """

    def _readheader(self, infile):
        """

        TODO : test for minimal attributes?
        """
        line = infile.readline()
        try:
            items = line.split()
            xdim = int(items[0])
            ydim = int(items[1])
        except:
            raise
        self.header['title'] = line
        self.header['Dim_1'] = xdim
        self.header['Dim_2'] = ydim

    def read(self, fname, frame=None):
        """

[docs]        Read in header into self.header and
            the data   into self.data
        """
        self.header = {}
        self.resetvals()
        infile = self._open(fname)
        self._readheader(infile)
        # Compute image size
        try:
            self.dim1 = int(self.header['Dim_1'])
            self.dim2 = int(self.header['Dim_2'])
        except:
            raise Exception("file", str(fname) + \
                                "is corrupt, cannot read it")
        bytecode = numpy.float32

        self.bpp = len(numpy.array(0, bytecode).tostring())

        #now read the data into the array
        try:
            vals = []
            for line in infile.readlines():
                try:
                    vals.append([float(x) for x in line.split()])
                except:
                    pass
            self.data = numpy.array(vals).astype(bytecode)
            assert self.data.shape == (self.dim2, self.dim1)

        except:
            raise IOError, "Error reading ascii"

        self.resetvals()
        # ensure the PIL image is reset
        self.pilimage = None
        return self


if __name__ == "__main__":
    import sys, time

    start = time.time()
    img = fit2dspreadsheetimage()
    img.read(sys.argv[1])
    print time.time() - start
    print img.dim1, img.dim2, img.data.shape
    from matplotlib.pylab import imshow, show
    imshow(img.data.T)
    show()

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© Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
fabio-0.1.3/doc/html/_modules/fabio/brukerimage.html0000644000175000017500000023456312233250022023146 0ustar jeromejerome00000000000000 fabio.brukerimage — FabIO 0.1.3 documentation

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Source code for fabio.brukerimage

#!/usr/bin/env python
#coding: utf8

from __future__ import with_statement

__doc__ = """

Authors: Henning O. Sorensen & Erik Knudsen
         Center for Fundamental Research: Metal Structures in Four Dimensions
         Risoe National Laboratory
         Frederiksborgvej 399
         DK-4000 Roskilde
         email:erik.knudsen@risoe.dk

Based on: openbruker,readbruker, readbrukerheader functions in the opendata
         module of ImageD11 written by Jon Wright, ESRF, Grenoble, France

Writer by Jérôme Kieffer, ESRF, Grenoble, France

"""
__authors__ = ["Henning O. Sorensen" , "Erik Knudsen", "Jon Wright", "Jérôme Kieffer"]
__date__ = "20130502"
__status__ = "development"
__copyright__ = "2007-2009 Risoe National Laboratory; 2010-2013 ESRF"
__licence__ = "GPL"

import numpy, logging, sys
from math import ceil
import os, getpass, time
logger = logging.getLogger("brukerimage")
from fabioimage import fabioimage
from fabioutils import pad
from types import StringTypes
if sys.version_info[0] < 3:
    bytes = str


[docs]class brukerimage(fabioimage):
    """
    Read and eventually write ID11 bruker (eg smart6500) images

    TODO: int32 -> float32 conversion according to the "linear" keyword.
    This is done and works but we need to check with other program that we
    are appliing the right formula and not the reciprocal one.
    
    """
    bpp_to_numpy = {1:numpy.uint8,
                    2:numpy.uint16,
                    4:numpy.uint32}

    # needed if you feel like writing - see ImageD11/scripts/edf2bruker.py

    SPACER = "\x1a\x04" #this is CTRL-Z CTRL-D
    HEADERS_KEYS = ["FORMAT",    #Frame format. Always “86†or "100" for Bruker-format frames.
                   "VERSION",   #Header version #, such as: 1 to 17 (6 is obsolete).
                   "HDRBLKS",   #Header size in 512-byte blocks, such as 10 or 15. Determines where the image block begins.
                   "TYPE",      #String indicating kind of data in the frame. Used to determine if a spatial correction table was applied to the frame imag
                   "SITE",      #Site name
                   "MODEL",     #Diffractometer model
                   "USER",      #Username
                   "SAMPLE",    #Sample ID,
                   "SETNAME",   #Basic data set name
                   "RUN",       #Run number within the data set, usually starts at 0, but 1 for APEX2.
                   "SAMPNUM",   #Specimen number within the data set
                   "TITLE",     #User comments (8 lines)
                   "NCOUNTS",   #Total frame counts
                   "NOVERFL",   #Number of overflows when compression frame.
                   "MINIMUM",   #Minimum counts in a pixel (uncompressed value)
                   "MAXIMUM",   #Maximum counts in a pixel (uncompressed value)
                   "NONTIME",   #Number of on-time events
                   "NLATE",     #Number of late events. Always zero for many detectors.
                   "FILENAM",   #(Original) frame filename
                   "CREATED",   #Date and time of creation
                   "CUMULAT",   #Accumulated frame exposure time in seconds
                   "ELAPSDR",   #Requested time for last exposure in seconds
                   "ELAPSDA",   #Actual time for last exposure in seconds.
                   "OSCILLA",   #Nonzero if acquired by oscillation
                   "NSTEPS",    #steps or oscillations in this frame
                   "RANGE",     #Scan range in decimal degrees (unsigned)
                   "START",     #Starting scan angle value, decimal degrees
                   "INCREME",   #Scan angle increment between frames (signed)
                   "NUMBER",    #Sequence number of this frame in series, usually starts at 0, but 1 for APEX2
                   "NFRAMES",   #Total number of frames in the series
                   "ANGLES",    #Diffractometer angles in Eulerian space ( 2T, OM, PH, CH).
                   "NOVER64",   #Number of pixels > 64K (actually LinearThreshold value)
                   "NPIXELB",   #Number of bytes/pixel, such as 1, 2, or 4.
                   "NROWS",     #Number of rasters in frame, such as 512, 1024, 2048, or 4096
                   "NCOLS",     #Number of pixels/raster, such as 512, 1024, 2048 or 4096
                   "WORDORD",   #Order of bytes in word (0=LSB first)
                   "LONGORD",   #Order of words in a longword (0=LSW first)
                   "TARGET" ,   #X-ray target material: Cu, Mo, Ag, Fe, Cr, Co, Ni, W, Mn, or other.
                   "SOURCEK",   #X-ray source voltage in kV
                   "SOURCEM",   #X-ray source current in mA
                   "FILTER" ,   #Filter/monochromator setting: Such as: Parallel, graphite, Ni Filter, C Filter, Zr Filter,Cross coupled Goebel Mirrors ...
                   "CELL" ,     #Unit cell A,B,C,ALPHA,BETA,GAMMA
                   "MATRIX" ,   #9R Orientation matrix (P3 conventions)
                   "LOWTEMP",   #Low temp flag.
                   "TEMP",      #set temperature
                   "HITEMP",    #Acquired at high temperature
                   "ZOOM" ,     #Zoom: Xc, Yc, Mag used for HI-STAR detectors: 0.5 0.5 1.0
                   "CENTER" ,   #X, Y of direct beam at 2-theta = 0. These are raw center for raw frames and unwarped center for unwarped frames.
                   "DISTANC",   #Sample-detector distance, cm (see CmToGrid value) Adds: Sample-detector grid/phosphor distance, cm
                   "TRAILER",   #Byte pointer to trailer info
                   "COMPRES",   #Compression scheme ID, if any. Such as: NONE, LINEAR (Linear scale, offset for pixel values, typically 1.0, 0.0).
                   "LINEAR",    #Linear scale (1.0 0.0 for no change; 0.1 0 for divided by 10...)
                   "PHD" ,      # Discriminator: Pulse height settings. X100 and X1000 only. Stores CCD phosphor efficiency (first field).
                   "PREAMP" ,   #Preamp gain setting. X100 and X1000 only. SMART: Stores Roper CCD gain table index value.
                   "CORRECT",   #Flood table correction filename, UNKNOWN or LINEAR.
                   "WARPFIL",   #Brass plate correction filename, UNKNOWN or LINEAR. Note: A filename here does NOT mean that spatial correction was performed. See TYPE and string “UNWARP†to determine that.
                   "WAVELEN",   #Wavelengths (average, a1, a2)
                   "MAXXY",     #X,Y pixel # of maximum counts (from lower corner of 0,0)
                   "AXIS",      #Scan axis ib Eulerian space (1-4 for 2-theta, omega, phi, chi) (0 =none, 2 = default).
                   "ENDING" ,   #Actual goniometer angles at end of frame in Eulerian space.
                   "DETPAR" ,   #Detector position corrections (dX,dY,dDist,Pitch,Roll,Yaw)
                   "LUT",       #Recommended display lookup table
                   "DISPLIM",   #Recommended display limits
                   "PROGRAM",   #Name and version of program writing frame, such as:
                   "ROTATE",    #Non zero if acquired by rotation of phi during scan (or oscilate)
                   "BITMASK",   #File name of active pixel mask associated with this frame or $NULL
                   "OCTMASK",   #Octagon mask parameters to use if BITMASK=$null. Min X, Min X+Y, Min Y, Max X-Y, Max X, Max X+Y, Max Y, Max Y-X.
                   "ESDCELL",   #Unit cell parameter standard deviations
                   "DETTYPE",   #Detector or CCD chip type (as displayed on CEU). Default is MULTIWIRE but UNKNOWN is advised, can contain PIXPERCM: CMTOGRID:
                   "NEXP",      #Number of exposures: 1=single, 2=correlated sum.32 for most ccds, and 64 for 2K ccds.
                   "CCDPARM",   #CCD parameters: readnoise, e/ADU, e/photon, bias, full scale
                   "BIS",       #Potential full linear scale if rescan and attenuator used.
                   "CHEM",      #Chemical formula in CIFTAB string, such as “?â€
                   "MORPH",     #Crystal morphology in CIFTAB string, such as “?â€
                   "CCOLOR",    #Crystal color in CIFTAB string, such as “?â€
                   "CSIZE",     #Crystal dimensions (3 ea) in CIFTAB string, such as “?â€
                   "DNSMET",     #Density measurement method in CIFTAB string, such as “?â€
                   "DARK",       #Name of dark current correction or NONE.
                   "AUTORNG",   #Auto-ranging: gain, high-speed time, scale, offset, full linear scale Note: If full linear scale is zero, then CCDPARM full scale is the full linear scale (BIS frames).
                   "ZEROADJ",   #Goniometer zero corrections (refined in least squares)
                   "XTRANS",    #Crystal XYZ translations (refined in least squares)
                   "HKL&XY",    #HKL and pixel XY for reciprocal space scan. GADDS only.
                   "AXES2",     #Diffractometer setting linear axes (4 ea). (X, Y, Z, Aux)
                   "ENDING2",   #Actual goniometer linear axes @ end of frame. (X, Y, Z, Aux)
                   "FILTER2",   #Monochromator 2-theta angle and monochromator roll angle. v15: Adds beam tilt angle and attenuator factor.
                   "LEPTOS",    # String for LEPTOS.
                   "CFR",       #Only in 21CFRPart11 mode, writes the checksum for header and image (2str).]
           ]

    def __init__(self, data=None , header=None):
        fabioimage.__init__(self, data, header)
        self.__bpp_file = None
        self.version = 86
        self.__headerstring__ = ""


    def _readheader(self, infile):
        """
        The bruker format uses 80 char lines in key : value format
        In the first 512*5 bytes of the header there should be a
        HDRBLKS key, whose value denotes how many 512 byte blocks
        are in the total header. The header is always n*5*512 bytes,
        otherwise it wont contain whole key: value pairs
        """
        line = 80
        blocksize = 512
        nhdrblks = 5 #by default we always read 5 blocks of 512
        self.__headerstring__ = infile.read(blocksize * nhdrblks)
        self.header = {}
        for i in range(0, nhdrblks * blocksize, line):
            if self.__headerstring__[i: i + line].find(":") > 0:
                key, val = self.__headerstring__[i: i + line].split(":", 1)
                key = key.strip()         # remove the whitespace (why?)
                val = val.strip()
                if key in self.header:
                    # append lines if key already there
                    self.header[key] = self.header[key] + os.linesep + val
                else:
                    self.header[key] = val
                    self.header_keys.append(key)
        # we must have read this in the first 5*512 bytes.
        nhdrblks = int(self.header['HDRBLKS'])
        # Now read in the rest of the header blocks, appending
        self.__headerstring__ += infile.read(blocksize * (nhdrblks - 5))
        for i in range(5 * blocksize, nhdrblks * blocksize, line):
            if self.__headerstring__[i: i + line].find(":") > 0: # as for first 512 bytes of header
                key, val = self.__headerstring__[i: i + line].split(":", 1)
                key = key.strip()
                val = val.strip()
                if key in self.header:
                    self.header[key] = self.header[key] + os.linesep + val
                else:
                    self.header[key] = val
                    self.header_keys.append(key)
        # make a (new) header item called "datastart"
        self.header['datastart'] = blocksize * nhdrblks
        #set the image dimensions
        self.dim1 = int(self.header['NROWS'])
        self.dim2 = int(self.header['NCOLS'])


[docs]    def read(self, fname, frame=None):
        """
        Read in and unpack the pixels (including overflow table
        """
        infile = self._open(fname, "rb")
        try:
            self._readheader(infile)
        except:
            raise

        rows = self.dim1
        cols = self.dim2

        try:
            # you had to read the Bruker docs to know this!
            npixelb = int(self.header['NPIXELB'])
        except Exception:
            errmsg = "length " + str(len(self.header['NPIXELB'])) + "\n"
            for byt in self.header['NPIXELB']:
                errmsg += "char: " + str(byt) + " " + str(ord(byt)) + "\n"
            logger.warning(errmsg)
            raise RuntimeError(errmsg)

        data = numpy.fromstring(infile.read(rows * cols * npixelb), dtype=self.bpp_to_numpy[npixelb])

        #handle overflows
        nov = int(self.header['NOVERFL'])
        if nov > 0:   # Read in the overflows
            # need at least int32 sized data I guess - can reach 2^21
            data = data.astype(numpy.uint32)
            # 16 character overflows:
            #      9 characters of intensity
            #      7 character position
            for i in range(nov):
                ovfl = infile.read(16)
                intensity = int(ovfl[0: 9])
                position = int(ovfl[9: 16])
                data[position] = intensity
        infile.close()
        # Handle Float images ...
        if "LINEAR" in self.header:
            try:
                slope, offset = self.header["LINEAR"].split(None, 1)
                slope = float(slope)
                offset = float(offset)
            except Except:
                logger.warning("Error in converting to float data with linear parameter: %s" % self.header["LINEAR"])
                self.data = data
            else:
                if slope == 1 and offset == 0:
                    self.data = data
                else:
                    #TODO: check that the formula is OK, not reverted.
                    logger.warning("performing correction with slope=%s, offset=%s (LINEAR=%s)" % (slope, offset, self.header["LINEAR"]))
                    self.data = (data * slope + offset).astype(numpy.float32)
        else:
            self.data = data
        self.data.shape = self.dim1, self.dim2

        self.resetvals()
        self.pilimage = None
        return self




[docs]    def write(self, fname):
        """
        Write a bruker image 

        """
        if numpy.issubdtype(self.data.dtype, float):
            if "LINEAR" in self.header:
                try:
                    slope, offset = self.header["LINEAR"].split(None, 1)
                    slope = float(slope)
                    offset = float(offset)
                except Except:
                    logger.warning("Error in converting to float data with linear parameter: %s" % self.header["LINEAR"])
                    slope, offset = 1.0, 0.0

            else:
                offset = self.data.min()
                max_data = self.data.max()
                max_range = 2 ** 24 - 1 #similar to the mantissa of a float32
                if max_data > offset:
                    slope = (max_data - offset) / float(max_range)
                else:
                    slope = 1.0
            tmp_data = numpy.round(((self.data - offset) / slope)).astype(numpy.uint32)
            self.header["LINEAR"] = "%s %s" % (slope, offset)

        else:
            tmp_data = self.data

        bpp = self.calc_bpp(tmp_data)
        self.basic_translate(fname)
        limit = 2 ** (8 * bpp) - 1
        data = tmp_data.astype(self.bpp_to_numpy[bpp])
        reset = numpy.where(tmp_data >= limit)
        data[reset] = limit
        data = data.newbyteorder("<") #Bruker enforces little endian
        with self._open(fname, "wb") as bruker:
            bruker.write(self.gen_header())
            bruker.write(data.tostring())
            bruker.write(self.gen_overflow())





[docs]    def calc_bpp(self, data=None, max_entry=4096):
        """
        Calculate the number of byte per pixel to get an optimal overflow table. 
        
        @return: byte per pixel 
        """
        if data is None:
            data = self.data
        if self.__bpp_file is None:
            for i in [1, 2]:
                overflown = (data >= (2 ** (8 * i) - 1))
                if overflown.sum() < max_entry:
                    self.__bpp_file = i
                    break
            else:
                self.__bpp_file = 4
        return self.__bpp_file



[docs]    def gen_header(self):
        """
        Generate headers (with some magic and guesses)
        @param format can be 86 or 100
        """
        headers = []
        for key in self.HEADERS_KEYS:
            if key in self.header:
                value = self.header[key]
                line = key.ljust(7) + ":"
                if type(value) in StringTypes:
                    if os.linesep in value:
                        lines = value.split(os.linesep)
                        for i in lines[:-1] :
                            headers.append((line + bytes(i)).ljust(80, " "))
                            line = key.ljust(7) + ":"
                        line += bytes(lines[-1])
                    elif len(value) < 72:
                        line += bytes(value)
                    else:
                        for i in range(len(value) // 72):
                            headers.append((line + bytes(value[72 * i:72 * (i + 1)])))
                            line = key.ljust(7) + ":"
                        line += value[72 * (i + 1):]
                elif "__len__" in dir(value):
                    f = "\%.%is" % 72 // len(value) - 1
                    line += " ".join([f % i for i in value])
                else:
                    line += bytes(value)
                headers.append(line.ljust(80, " "))

        header = "".join(headers)
        if len(header) > 512 * self.header["HDRBLKS"]:
            tmp = ceil(len(header) / 512.0)
            self.header["HDRBLKS"] = int(ceil(tmp / 5.0) * 5.0)
            for i in range(len(headers)):
                if headers[i].startswith("HDRBLKS"):
                    headers[i] = headers.append(("HDRBLKS:%s" % self.header["HDRBLKS"]).ljust(80, " "))
        res = pad("".join(headers), self.SPACER + "."*78, 512 * int(self.header["HDRBLKS"]))
        return res



[docs]    def gen_overflow(self):
        """
        Generate an overflow table  
        """
        limit = 2 ** (8 * self.calc_bpp()) - 1
        flat = self.data.ravel()                     #flat memory view
        overflow_pos = numpy.where(flat >= limit)[0] #list of indexes
        overflow_val = flat[overflow_pos]
        overflow = "".join(["%09i%07i" % (val, pos) for pos, val  in zip(overflow_pos, overflow_val)])
        return pad(overflow, ".", 512)



[docs]    def basic_translate(self, fname=None):
        """
        Does some basic population of the headers so that the writing is possible 
        """
        if not "FORMAT" in self.header:
            self.header["FORMAT"] = "86"
        if not "HDRBLKS" in self.header:
            self.header["HDRBLKS"] = 5
        if not "TYPE" in self.header:
            self.header["TYPE"] = "UNWARPED"
        if not "USER" in self.header:
            self.header["USER"] = getpass.getuser()
        if not "FILENAM" in self.header:
            self.header["FILENAM"] = "%s" % fname
        if not "CREATED" in self.header:
            self.header["CREATED"] = time.ctime()
        if not "NOVERFL" in self.header:
            self.header["NOVERFL"] = "0"
#        if not "NPIXELB" in self.header:
        self.header["NPIXELB"] = self.calc_bpp()
        #if not "NROWS" in self.header:
        self.header["NROWS"] = self.data.shape[0]
        #if not "NCOLS" in self.header:
        self.header["NCOLS"] = self.data.shape[1]
        if not "WORDORD" in self.header:
            self.header["WORDORD"] = "0"
        if not "LONGORD" in self.header:
            self.header["LONGORD"] = "0"




[docs]def test():
    """ a testcase """
    import sys, time
    img = brukerimage()
    start = time.clock()
    for filename in sys.argv[1:]:
        img.read(filename)
        res = img.toPIL16()
        img.rebin(2, 2)
        print(filename + (": max=%d, min=%d, mean=%.2e, stddev=%.2e") % (
            img.getmax(), img.getmin(), img.getmean(), img.getstddev()))
        print('integrated intensity (%d %d %d %d) =%.3f' % (
            10, 20, 20, 40, img.integrate_area((10, 20, 20, 40))))
    end = time.clock()
    print (end - start)




if __name__ == '__main__':
    test()

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© Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
fabio-0.1.3/doc/html/_modules/fabio/tifimage.html0000644000175000017500000016154712233250022022437 0ustar jeromejerome00000000000000 fabio.tifimage — FabIO 0.1.3 documentation

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Source code for fabio.tifimage

#!/usr/bin/env python
#-*- coding: utf8 -*-
"""
FabIO class for dealing with TIFF images. 
In facts wraps TiffIO from V. Armando Solé (available in PyMca) or falls back to PIL

Authors:
........
* Henning O. Sorensen & Erik Knudsen:
  Center for Fundamental Research: Metal Structures in Four Dimensions;
  Risoe National Laboratory;
  Frederiksborgvej 399;
  DK-4000 Roskilde;
  email:erik.knudsen@risoe.dk
* Jérôme Kieffer:
  European Synchrotron Radiation Facility;
  Grenoble (France)
   
License: GPLv3+        
"""

__authors__ = ["Jérôme Kieffer", "Henning O. Sorensen", "Erik Knudsen"]
__date__ = "11/07/2011"
__license__ = "GPLv3+"
__copyright__ = "ESRF, Grenoble & Risoe National Laboratory"
__status__ = "stable"
import time, logging, struct
logger = logging.getLogger("tifimage")
try:
    from PIL import Image
except ImportError:
    logger.warning("PIL is not installed ... trying to do without")
    Image = None
import numpy
from fabioimage import fabioimage
from TiffIO     import TiffIO

PIL_TO_NUMPY = { "I;16": numpy.uint16,
                   "F": numpy.float32,
                   "1": numpy.bool,
                   "I": numpy.int32,
                   "L": numpy.uint8,
                    }

LITTLE_ENDIAN = 1234
BIG_ENDIAN = 3412

TYPES = {0:'invalid', 1:'byte', 2:'ascii', 3:'short', 4:'long', 5:'rational', 6:'sbyte', 7:'undefined', 8:'sshort', 9:'slong', 10:'srational', 11:'float', 12:'double'}

TYPESIZES = {0:0, 1:1, 2:1, 3:2, 4:4, 5:8, 6:1, 7:1, 8:2, 9:4, 10:8, 11:4, 12:8}

baseline_tiff_tags = {
  256:'ImageWidth',
  257:'ImageLength',
  306:'DateTime',
  315:'Artist',
  258:'BitsPerSample',
  265:'CellLength',
  264:'CellWidth',
  259:'Compression',

  262:'PhotometricInterpretation',
  296:'ResolutionUnit',
  282:'XResolution',
  283:'YResolution',

  278:'RowsPerStrip',
  273:'StripOffset',
  279:'StripByteCounts',

  270:'ImageDescription',
  271:'Make',
  272:'Model',
  320:'ColorMap',
  305:'Software',
  339:'SampleFormat',
  33432:'Copyright'
  }


[docs]class tifimage(fabioimage):
    """
    Images in TIF format
    Wraps TiffIO
    """
    _need_a_seek_to_read = True

    def __init__(self, *args, **kwds):
        """ Tifimage constructor adds an nbits member attribute """
        self.nbits = None
        fabioimage.__init__(self, *args, **kwds)
        self.lib = None

    def _readheader(self, infile):
        """
        Try to read Tiff images header...
        """
#        try:
#            self.header = { "filename" : infile.name }
#        except AttributeError:
#            self.header = {}
#
#        t = Tiff_header(infile.read())
#        self.header = t.header
#        try:
#            self.dim1 = int(self.header['ImageWidth'])
#            self.dim2 = int(self.header['ImageLength'])
#        except (KeyError):
#            logger.warning("image dimensions could not be determined from header tags, trying to go on anyway")
#         read the first 32 bytes to determine size
        header = numpy.fromstring(infile.read(64), numpy.uint16)
        self.dim1 = int(header[9])
        self.dim2 = int(header[15])
#         nbits is not a fabioimage attribute...
        self.nbits = int(header[21]) # number of bits


[docs]    def read(self, fname, frame=None):
        """
        Wrapper for TiffIO.
        """
        infile = self._open(fname, "rb")
        self._readheader(infile)
        infile.seek(0)
        self.lib = None
        try:
            tiffIO = TiffIO(infile)
            if tiffIO.getNumberOfImages() > 0:
                #No support for now of multi-frame tiff images
                self.data = tiffIO.getImage(0)
                self.header = tiffIO.getInfo(0)
        except Exception, error:
            logger.warning("Unable to read %s with TiffIO due to %s, trying PIL" % (fname, error))
        else:
            if self.data.ndim == 2:
                self.dim2, self.dim1 = self.data.shape
            elif self.data.ndim == 3:
                self.dim2, self.dim1, ncol = self.data.shape
                logger.warning("Third dimension is the color")
            else:
                logger.warning("dataset has %s dimensions (%s), check for errors !!!!", self.data.ndim, self.data.shape)
            self.lib = "TiffIO"

        if (self.lib is None):
            if Image:
                try:
                    infile.seek(0)
                    self.pilimage = Image.open(infile)
                except Exception:
                    logger.error("Error in opening %s  with PIL" % fname)
                    self.lib = None
                    infile.seek(0)
                else:
                    self.lib = "PIL"
                    self.dim1, self.dim2 = self.pilimage.size
                    if self.pilimage.mode in PIL_TO_NUMPY:
                        self.data = numpy.fromstring(self.pilimage.tostring(), PIL_TO_NUMPY[self.pilimage.mode])
                    else: #probably RGB or RGBA images: rely on PIL to convert it to greyscale float.
                        self.data = numpy.fromstring(self.pilimage.convert("F").tostring(), numpy.float32)
                    self.data.shape = (self.dim2, self.dim1)
            else:
                logger.error("Error in opening %s: no tiff reader managed to read the file.", fname)
                self.lib = None
                infile.seek(0)

        self.bpp = len(numpy.zeros(1, dtype=self.data.dtype).tostring())
        self.bytecode = self.data.dtype.name
        self.resetvals()
        return self



[docs]    def write(self, fname):
        """
        Overrides the fabioimage.write method and provides a simple TIFF image writer.
        @param fname: name of the file to save the image to
        @tag_type fname: string or unicode (file?)...
        """
        tiffIO = TiffIO(fname, mode="w")
        tiffIO.writeImage(self.data, info=self.header, software="fabio.tifimage", date=time.ctime())



#define a couple of helper classes here:         


[docs]class Tiff_header(object):
    def __init__(self, string):
        if string[:4] == "II\x2a\x00":
            self.byteorder = LITTLE_ENDIAN
        elif string[:4] == 'MM\x00\x2a':
            self.byteorder = BIG_ENDIAN
        else:
            logger.warning("Warning: This does not appear to be a tiff file")
        #the next two bytes contains the offset of the oth IFD
        offset_first_ifd = struct.unpack_from("h", string[4:])[0]
        self.ifd = [Image_File_Directory()]
        offset_next = self.ifd[0].unpack(string, offset_first_ifd)
        while (offset_next != 0):
            self.ifd.append(Image_File_Directory())
            offset_next = self.ifd[-1].unpack(string, offset_next)

        self.header = {}
        #read the values of the header items into a dictionary
        for entry in self.ifd[0].entries:
            if entry.tag in baseline_tiff_tags.keys():
                self.header[baseline_tiff_tags[entry.tag]] = entry.val
            else:
                self.header[entry.tag] = entry.val



[docs]class Image_File_Directory(object):
    def __init__(self, instring=None, offset= -1):
        self.entries = []
        self.offset = offset
        self.count = None


[docs]    def unpack(self, instring, offset= -1):
        if (offset == -1): offset = self.offset

        strInput = instring[offset:]
        self.count = struct.unpack_from("H", strInput[:2])[0]
        #0th IFD contains count-1 entries (count includes the adress of the next IFD)
        for i in range(self.count - 1):
            e = Image_File_Directory_entry().unpack(strInput[2 + 12 * (i + 1):])
            if (e != None):
                self.entries.append(e)
            #extract data associated with tags
            for e in self.entries:
                if (e.val == None):
                    e.extract_data(instring)
        #do we have some more ifds in this file 
        offset_next = struct.unpack_from("L", instring[offset + 2 + self.count * 12:])[0]
        return offset_next



[docs]class Image_File_Directory_entry(object):
    def __init__(self, tag=0, tag_type=0, count=0, offset=0):
        self.tag = tag
        self.tag_type = tag_type
        self.count = count
        self.val_offset = offset
        self.val = None


[docs]    def unpack(self, strInput):
        idfentry = strInput[:12]
################################################################################
# #        TOFIX: How is it possible that HHL (2+2+4 bytes has a size of )
################################################################################
        (tag, tag_type, count) = struct.unpack_from("HHL", idfentry)
        self.tag = tag
        self.count = count
        self.tag_type = tag_type
        self.val = None
        if (count <= 0):
            logger.warning("Tag # %s has an invalid count: %s. Tag is ignored" % (tag, count))
            return
        if(count * TYPESIZES[tag_type] <= 4):
            self.val_offset = 8
            self.extract_data(idfentry)
            self.val_offset = None
        else:
            self.val_offset = struct.unpack_from("L", idfentry[8:])[0]
        return self



[docs]    def extract_data(self, full_string):
        tag_type = self.tag_type
        if (TYPES[tag_type] == 'byte'):
            self.val = struct.unpack_from("B", full_string[self.val_offset:])[0]
        elif (TYPES[tag_type] == 'short'):
            self.val = struct.unpack_from("H", full_string[self.val_offset:])[0]
        elif (TYPES[tag_type] == 'long'):
            self.val = struct.unpack_from("L", full_string[self.val_offset:])[0]
        elif (TYPES[tag_type] == 'sbyte'):
            self.val = struct.unpack_from("b", full_string[self.val_offset:])[0]
        elif (TYPES[tag_type] == 'sshort'):
            self.val = struct.unpack_from("h", full_string[self.val_offset:])[0]
        elif (TYPES[tag_type] == 'slong'):
            self.val = struct.unpack_from("l", full_string[self.val_offset:])[0]
        elif (TYPES[tag_type] == 'ascii'):
            self.val = full_string[self.val_offset:self.val_offset + max(self.count, 4)]
        elif (TYPES[tag_type] == 'rational'):
            if self.val_offset != None:
                (num, den) = struct.unpack_from("LL", full_string[self.val_offset:])
                print self.val_offset
                self.val = float(num) / den
        elif (TYPES[tag_type] == 'srational'):
            if self.val_offset != None:
                (num, den) = struct.unpack_from("ll", full_string[self.val_offset:])
                self.val = float(num) / den,
        elif (TYPES[tag_type] == 'float'):
            self.val = struct.unpack_from("f", full_string[self.val_offset:])[0]
        elif (TYPES[tag_type] == 'double'):
            if  self.val_offset != None:
                self.val = struct.unpack_from("d", full_string[self.val_offset:])[0]
        else:
            logger.warning("unrecognized type of strInputentry self: %s tag: %s type: %s TYPE: %s" % (self, baseline_tiff_tags[self.tag], self.tag_type, TYPES[tag_type]))

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© Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
fabio-0.1.3/doc/html/_modules/fabio/mar345image.html0000644000175000017500000026306612233250022022667 0ustar jeromejerome00000000000000 fabio.mar345image — FabIO 0.1.3 documentation

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Source code for fabio.mar345image

#!/usr/bin/env python
#coding: utf8 
from __future__ import with_statement
__doc__ = """

Authors:
........
* Henning O. Sorensen & Erik Knudsen:
  Center for Fundamental Research: Metal Structures in Four Dimensions;
  Risoe National Laboratory;
  Frederiksborgvej 399;
  DK-4000 Roskilde;
  email:erik.knudsen@risoe.dk
* Jon Wright, Jérôme Kieffer & Gaël Goret:
  European Synchrotron Radiation Facility;
  Grenoble (France)

         
"""

from fabioimage import fabioimage
import numpy, struct, time, sys, traceback
import logging
logger = logging.getLogger("mar345image")
from compression import compPCK, decPCK



[docs]class mar345image(fabioimage):
    _need_a_real_file = True
    def __init__(self, *args, **kwargs):
        fabioimage.__init__(self, *args, **kwargs)
        self.numhigh = None
        self.numpixels = None


[docs]    def read(self, fname, frame=None):
        """ Read a mar345 image"""
        self.filename = fname
        f = self._open(self.filename, "rb")
        self._readheader(f)
        if 'compressed' in self.header['Format']:
#            self.data = decPCK(f, self.dim1, self.dim2, self.numhigh, version=1)
            try:
                self.data = decPCK(f, self.dim1, self.dim2)
            except Exception, error:
                logger.error('%s. importing the mar345_io backend: generate an empty 1x1 picture' % error)
                f.close()
                self.dim1 = 1
                self.dim2 = 1
                self.bytecode = numpy.int #
                self.data = numpy.resize(numpy.array([0], numpy.int), [1, 1])
                return self

        else:
            logger.error("cannot handle these formats yet " + \
                "due to lack of documentation")
            return None
        self.bytecode = numpy.uint
        f.close()
        return self


    def _readheader(self, infile=None):
        """ Read a mar345 image header """
        # clip was not used anywhere - commented out
        # clip = '\x00'
        #using a couple of local variables inside this function
        f = infile
        h = {}

        #header is 4096 bytes long
        l = f.read(64)
        #the contents of the mar345 header is taken to be as
        # described in
        # http://www.mar-usa.com/support/downloads/mar345_formats.pdf
        #the first 64 bytes are 4-byte integers (but in the CBFlib
        # example image it seems to 128 bytes?)
        #first 4-byte integer is a marker to check endianness
        if struct.unpack("<i", l[0:4])[0] == 1234:
            fs = '<i'
        else:
            fs = '>i'

        #image dimensions
        self.dim1 = self.dim2 = int(struct.unpack(fs, l[4:8])[0])
        #number of high intensity pixels
        self.numhigh = struct.unpack(fs, l[2 * 4 : (2 + 1) * 4])[0]
        h['NumHigh'] = self.numhigh
        #Image format
        i = struct.unpack(fs, l[3 * 4 : (3 + 1) * 4])[0]
        if i == 1:
            h['Format'] = 'compressed'
        elif i == 2:
            h['Format'] = 'spiral'
        else:
            h['Format'] = 'compressed'
            logger.warning("image format could not be detetermined" + \
                "- assuming compressed mar345")
        #collection mode
        h['Mode'] = {0:'Dose', 1: 'Time'}[struct.unpack(fs, l[4 * 4:(4 + 1) * 4])[0]]
        #total number of pixels
        self.numpixels = struct.unpack(fs, l[5 * 4:(5 + 1) * 4])[0]
        h['NumPixels'] = str(self.numpixels)
        #pixel dimensions (length,height) in mm
        h['PixelLength'] = struct.unpack(fs, l[6 * 4:(6 + 1) * 4])[0] / 1000.0
        h['PixelHeight'] = struct.unpack(fs, l[7 * 4:(7 + 1) * 4])[0] / 1000.0
        #x-ray wavelength in AA
        h['Wavelength'] = struct.unpack(fs, l[8 * 4:(8 + 1) * 4])[0] / 1000000.0
        #used distance
        h['Distance'] = struct.unpack(fs, l[9 * 4:(9 + 1) * 4])[0] / 1000.0
        #starting and ending phi
        h['StartPhi'] = struct.unpack(fs, l[10 * 4:11 * 4])[0] / 1000.0
        h['EndPhi'] = struct.unpack(fs, l[11 * 4:12 * 4])[0] / 1000.0
        #starting and ending omega
        h['StartOmega'] = struct.unpack(fs, l[12 * 4:13 * 4])[0] / 1000.0
        h['EndOmega'] = struct.unpack(fs, l[13 * 4:14 * 4])[0] / 1000.0
        #Chi and Twotheta angles
        h['Chi'] = struct.unpack(fs, l[14 * 4:15 * 4])[0] / 1000.0
        h['TwoTheta'] = struct.unpack(fs, l[15 * 4:16 * 4])[0] / 1000.0

        #the rest of the header is ascii
        # TODO: validate these values against the binaries already read
        l = f.read(128)
        if not 'mar research' in l:
            logger.warning("the string \"mar research\" should be in " + \
                "bytes 65-76 of the header but was not")
            start = 128
        else:
            start = l.index('mar research')
            f.seek(64 + start)
        l = f.read(4096 - start - 64).strip()
        for m in l.splitlines():
            if m == 'END OF HEADER':
                break
            n = m.split(' ', 1)
            if n[0] == '':
                continue
            if n[0] in ('PROGRAM', 'DATE', 'SCANNER', 'HIGH', 'MULTIPLIER',
                        'GAIN', 'WAVELENGTH', 'DISTANCE', 'RESOLUTION',
                        'CHI', 'TWOTHETA', 'MODE', 'TIME', 'GENERATOR',
                        'MONOCHROMATOR', 'REMARK'):
                logger.debug("reading: %s %s", n[0], n[1])
                h[n[0]] = n[1].strip()
                continue
            if n[0] in ('FORMAT'):
                (h['DIM'], h['FORMAT_TYPE'], h['NO_PIXELS']) = n[1].split()
                continue
            if n[0] in ('PIXEL', 'OFFSET', 'PHI', 'OMEGA', 'COUNTS',
                        'CENTER', 'INTENSITY', 'HISTOGRAM', 'COLLIMATOR'):
                n = m.split()
                h.update([(n[0] + '_' + n[j], n[j + 1]) for j in range(1, len(n), 2)])
                continue
        self.header = h
        return h


[docs]    def write(self, fname):
        """Try to write mar345 file. This is still in beta version.
        It uses CCP4 (LGPL) PCK1 algo from JPA"""
        headers = self._writeheader()
        hotpixels = self._high_intensity_pixel_records()
        compressed_stream = compPCK(self.data)
        try:
            outfile = self._open(fname, mode="wb")
            outfile.write(headers)
            outfile.write(hotpixels)
            outfile.write(compressed_stream)
            outfile.close()
        except Exception, error:
            logger.error("Error in writing file %s: %s" % (fname, error))


    def _writeheader(self, linesep="\n", size=4096):#the standard padding does not inclued
        """
        @param linesep: end of line separator
        @return string/bytes containing the mar345 header
        """
        try:
            version = sys.modules["fabio"].version
        except (KeyError, AttributeError):
            version = "0.1.1"
        lnsep = len(linesep)

        self.header["HIGH"] = str(self.nb_overflow_pixels())
        binheader = numpy.zeros(16, "int32")
        binheader[:4] = numpy.array([1234, self.dim1, int(self.header["HIGH"]), 1])
        binheader[4] = (self.header.get("MODE", "TIME") == "TIME")
        binheader[5] = self.dim1 * self.dim2
        binheader[6] = int(self.header.get("PIXEL_LENGTH", 1))
        binheader[7] = int(self.header.get("PIXEL_HEIGHT", 1))
        binheader[8] = int(float(self.header.get("WAVELENGTH", 1)) * 1e6)
        binheader[9] = int(float(self.header.get("DISTANCE", 1)) * 1e3)
        binheader[10] = int(float(self.header.get("PHI_START", 1)) * 1e3)
        binheader[11] = int(float(self.header.get("PHI_END", 1)) * 1e3)
        binheader[12] = int(float(self.header.get("OMEGA_START", 1)) * 1e3)
        binheader[13] = int(float(self.header.get("OMEGA_END", 1)) * 1e3)
        binheader[14] = int(float(self.header.get("CHI", 1)) * 1e3)
        binheader[15] = int(float(self.header.get("TWOTHETA", 1)) * 1e3)
        lstout = [binheader.tostring() + 'mar research'.ljust(64 - lnsep)]
        lstout.append("PROGRAM".ljust(15) + (str(self.header.get("PROGRAM", "FabIO Version %s" % (version))).ljust(49 - lnsep)))
        lstout.append("DATE".ljust(15) + (str(self.header.get("DATE", time.ctime()))).ljust(49 - lnsep))
        key = "SCANNER"
        if key in self.header:
            lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
        key = "FORMAT_TYPE"
        if key in self.header:
            lstout.append("FORMAT".ljust(15) + ("%s  %s %s" % (self.dim1, self.header[key], self.dim1 * self.dim2)).ljust(49 - lnsep))
        key = "HIGH"
        if key in self.header:
            lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
        key1 = "PIXEL_LENGTH"
        key2 = "PIXEL_HEIGHT"
        if (key1 in self.header) and (key2 in self.header):
            lstout.append("PIXEL".ljust(15) + ("LENGTH %s  HEIGHT %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep))
        key1 = "OFFSET_ROFF"
        key2 = "OFFSET_TOFF"
        if key1 in self.header and key2 in self.header:
            lstout.append("OFFSET".ljust(15) + ("ROFF %s  TOFF %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep))
        key = "MULTIPLIER"
        if key in self.header:
            lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
        key = "GAIN"
        if key in self.header:
            lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
        key = "WAVELENGTH"
        if key in self.header:
            lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
        key = "DISTANCE"
        if key in self.header:
            lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
        key = "RESOLUTION"
        if key in self.header:
            lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
        key1 = "PHI_START"
        key2 = "PHI_END"
        key3 = "PHI_OSC"
        if (key1 in self.header) and (key2 in self.header) and (key3 in self.header):
            lstout.append("PHI".ljust(15) + ("START %s  END %s  OSC %s" % (self.header[key1], self.header[key2], self.header[key3])).ljust(49 - lnsep))
        key1 = "OMEGA_START"
        key2 = "OMEGA_END"
        key3 = "OMEGA_OSC"
        if (key1 in self.header) and (key2 in self.header) and (key3 in self.header):
            lstout.append("OMEGA".ljust(15) + ("START %s  END %s  OSC %s" % (self.header[key1], self.header[key2], self.header[key3])).ljust(49 - lnsep))
        key = "CHI"
        if key in self.header:
            lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
        key = "TWOTHETA"
        if key in self.header:
            lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
        key1 = "CENTER_X"
        key2 = "CENTER_Y"
        if (key1 in self.header) and (key2 in self.header):
            lstout.append("CENTER".ljust(15) + ("X %s  Y %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep))
        key = "MODE"
        if key in self.header:
            lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
        key = "TIME"
        if key in self.header:
            lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
        key1 = "COUNTS_START"
        key2 = "COUNTS_END"
        key3 = "COUNTS_NMEAS"
        if key1 in self.header and key2 in self.header and key3 in self.header:
            lstout.append("COUNTS".ljust(15) + ("START %s  END %s  NMEAS %s" % (self.header[key1], self.header[key2], self.header[key3])).ljust(49 - lnsep))
        key1 = "COUNTS_MIN"
        key2 = "COUNTS_MAX"
        if key1 in self.header and key2 in self.header:
            lstout.append("COUNTS".ljust(15) + ("MIN %s  MAX %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep))
        key1 = "COUNTS_AVE"
        key2 = "COUNTS_SIG"
        if key1 in self.header and key2 in self.header:
            lstout.append("COUNTS".ljust(15) + ("AVE %s  SIG %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep))
        key1 = "INTENSITY_MIN"
        key2 = "INTENSITY_MAX"
        key3 = "INTENSITY_AVE"
        key4 = "INTENSITY_SIG"
        if key1 in self.header and key2 in self.header and key3 in self.header and key4 in self.header:
            lstout.append("INTENSITY".ljust(15) + ("MIN %s  MAX %s  AVE %s  SIG %s" % (self.header[key1], self.header[key2], self.header[key3], self.header[key4])).ljust(49 - lnsep))
        key1 = "HISTOGRAM_START"
        key2 = "HISTOGRAM_END"
        key3 = "HISTOGRAM_MAX"
        if key1 in self.header and key2 in self.header and key3 in self.header:
            lstout.append("HISTOGRAM".ljust(15) + ("START %s  END %s  MAX %s" % (self.header[key1], self.header[key2], self.header[key3])).ljust(49 - lnsep))
        key = "GENERATOR"
        if key in self.header:
            lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
        key = "MONOCHROMATOR"
        if key in self.header:
            lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
        key1 = "COLLIMATOR_WIDTH"
        key2 = "COLLIMATOR_HEIGHT"
        if key1 in self.header and key2 in self.header:
            lstout.append("COLLIMATOR".ljust(15) + ("WIDTH %s  HEIGHT %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep))
        key = "REMARK"
        if key in self.header:
            lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
        else:
            lstout.append(key.ljust(64 - lnsep))
        key = "END OF HEADER"
        lstout.append(key)
        return linesep.join(lstout).ljust(size)


    def _high_intensity_pixel_records(self):
        flt_data = self.data.flatten()
        pix_location = numpy.where(flt_data > 65535)[0]
        nb_pix = pix_location.size
        if nb_pix % 8 == 0:
            tmp = numpy.zeros((nb_pix, 2), dtype="int32")
        else:
            tmp = numpy.zeros(((nb_pix // 8 + 1) * 8, 2), dtype="int32")
        tmp[:nb_pix, 0] = pix_location + 1
        tmp[:nb_pix, 1] = flt_data[pix_location]
        return tmp.tostring()


[docs]    def nb_overflow_pixels(self):
        return (self.data > 65535).sum()


    @staticmethod

[docs]    def checkData(data=None):
        if data is None:
            return None
        else:
#            enforce square image 
            shape = data.shape
            assert len(shape) == 2, "image has 2 dimensions"
            mshape = max(shape)
            z = numpy.zeros((mshape, mshape), dtype=int)
            z[:shape[0], :shape[1]] = data
            return z

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© Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
fabio-0.1.3/doc/html/_modules/index.html0000644000175000017500000001136312233250023020670 0ustar jeromejerome00000000000000 Overview: module code — FabIO 0.1.3 documentation

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© Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
fabio-0.1.3/doc/html/_static/0000755000175000017500000000000012233272207016516 5ustar jeromejerome00000000000000fabio-0.1.3/doc/html/_static/ajax-loader.gif0000644000175000017500000000124111644410761021376 0ustar jeromejerome00000000000000GIF89aòÿÿÿU|ÆÖßN€U|l–®Š«¾™¶Æ!þCreated with ajaxload.info!ù !ÿ NETSCAPE2.0,3ºÜþ0ÊIkc:œN˜f E±1º™Á¶.`ÄÂqÐ-[9ݦ9 JkçH!ù ,4ºÜþNŒ! „ »°æŠDqBQT`1 `LE[¨|µußía€ ×â†C²%$*!ù ,6º2#+ÊAÈÌ”V/…côNñIBa˜«pð ̳½ƨ+YíüƒÃ2©dŸ¿!ù ,3ºb%+Ê2†‘ìœV_…‹¦ …! 1D‡aªF‚°ÑbR]ó=08,Ȥr9L!ù ,2ºr'+JçdðóL &vÃ`\bT”…„¹hYB)ÏÊ@é<Ã&,ȤR’!ù ,3º Â9ãtç¼Úž0Çà!.B¶ÊW¬¢1  sa»°5÷•0° ‰»Ÿm)J!ù ,2ºÜþð ÙœU]šîÚqp•`ˆÝaœÝ4–…AFÅ0`›¶ Â@›1€ÂÖΑ!ù ,2ºÜþ0ÊI«eBÔœ)×à ŽÇq10©Ê°®PÂaVÚ¥ ub‚ž[;fabio-0.1.3/doc/html/_static/comment-close.png0000644000175000017500000000677211644410761022011 0ustar jeromejerome00000000000000‰PNG  IHDRóÿa OiCCPPhotoshop ICC profilexÚSgTSé=÷ÞôBKˆ€”KoR RB‹€‘&*! Jˆ!¡ÙQÁEEÈ ˆŽŽ€ŒQ, Š Øä!¢Žƒ£ˆŠÊûá{£kÖ¼÷æÍþµ×>ç¬ó³ÏÀ –H3Q5€ ©BàƒÇÄÆáä.@ $p³d!sý#ø~<<+"À¾xÓ ÀM›À0‡ÿêB™\€„Àt‘8K€@zŽB¦@F€˜&S `ËcbãP-`'æÓ€ø™{[”! ‘ eˆDh;¬ÏVŠEX0fKÄ9Ø-0IWfH°·ÀÎ ² 0Qˆ…){`È##x„™FòW<ñ+®ç*x™²<¹$9E[-qWW.(ÎI+6aaš@.Ây™24àóÌ ‘àƒóýxήÎÎ6Ž¶_-ê¿ÿ"bbãþåÏ«p@át~Ñþ,/³€;€mþ¢%îh^  u÷‹f²@µ éÚWópø~<ß5°j>{‘-¨]cöK'XtÀâ÷ò»oÁÔ(€hƒáÏwÿï?ýG %€fI’q^D$.Tʳ?ÇD *°AôÁ,ÀÁÜÁ ü`6„B$ÄÂBB d€r`)¬‚B(†Í°*`/Ô@4ÀQh†“p.ÂU¸=púažÁ(¼ AÈa!ÚˆbŠX#Ž™…ø!ÁH‹$ ɈQ"K‘5H1RŠT UHò=r9‡\Fº‘;È2‚ü†¼G1”²Q=Ô µC¹¨7„F¢ Ðdt1š ›Ðr´=Œ6¡çЫhÚ>CÇ0Àè3Äl0.ÆÃB±8, “c˱"¬ «Æ°V¬»‰õcϱwEÀ 6wB aAHXLXNØH¨ $4Ú 7 „QÂ'"“¨K´&ºùÄb21‡XH,#Ö/{ˆCÄ7$‰C2'¹I±¤TÒÒFÒnR#é,©›4H#“ÉÚdk²9”, +È…ääÃä3ää!ò[ b@q¤øSâ(RÊjJåå4åe˜2AU£šRݨ¡T5ZB­¡¶R¯Q‡¨4uš9̓IK¥­¢•Óhh÷i¯ètºÝ•N—ÐWÒËéGè—èôw †ƒÇˆg(›gw¯˜L¦Ó‹ÇT071ë˜ç™™oUX*¶*|‘Ê •J•&•*/T©ª¦ªÞª UóUËT©^S}®FU3Sã© Ô–«UªPëSSg©;¨‡ªg¨oT?¤~Yý‰YÃLÃOC¤Q ±_ã¼Æ c³x,!k «†u5Ä&±ÍÙ|v*»˜ý»‹=ª©¡9C3J3W³Ró”f?ã˜qøœtN ç(§—ó~ŠÞï)â)¦4L¹1e\kª–—–X«H«Q«Gë½6®í§¦½E»YûAÇJ'\'GgÎçSÙSݧ §M=:õ®.ªk¥¡»Dw¿n§î˜ž¾^€žLo§Þy½çú}/ýTýmú§õG X³ $Û Î<Å5qo</ÇÛñQC]Ã@C¥a•a—á„‘¹Ñ<£ÕFFŒiÆ\ã$ãmÆmÆ£&&!&KMêMîšRM¹¦)¦;L;LÇÍÌÍ¢ÍÖ™5›=1×2ç›ç›×›ß·`ZxZ,¶¨¶¸eI²äZ¦Yn…Z9Y¥XUZ]³F­­%Ö»­»§§¹N“N«žÖgðñ¶É¶©·°åØÛ®¶m¶}agbg·Å®Ã“}º}ý= ‡Ù«Z~s´r:V:ޚΜî?}Åô–é/gXÏÏØ3ã¶Ë)ÄiS›ÓGgg¹sƒóˆ‹‰K‚Ë.—>.›ÆÝȽäJtõq]ázÒõ›³›Âí¨Û¯î6îiî‡ÜŸÌ4Ÿ)žY3sÐÃÈCàQåÑ? Ÿ•0k߬~OCOgµç#/c/‘W­×°·¥wª÷aï>ö>rŸã>ã<7Þ2ÞY_Ì7À·È·ËOÃož_…ßC#ÿdÿzÿѧ€%g‰A[ûøz|!¿Ž?:Ûeö²ÙíAŒ ¹AA‚­‚åÁ­!hÈì­!÷ç˜Î‘Îi…P~èÖÐaæa‹Ã~ '…‡…W†?ŽpˆXÑ1—5wÑÜCsßDúD–DÞ›g1O9¯-J5*>ª.j<Ú7º4º?Æ.fYÌÕXXIlK9.*®6nl¾ßüíó‡ââ ã{˜/È]py¡ÎÂô…§©.,:–@LˆN8”ðA*¨Œ%òw%Ž yÂÂg"/Ñ6шØC\*NòH*Mz’쑼5y$Å3¥,幄'©¼L LÝ›:žšv m2=:½1ƒ’‘qBª!M“¶gêgæfvˬe…²þÅn‹·/•Ék³¬Y- ¶B¦èTZ(×*²geWf¿Í‰Ê9–«ž+Íí̳ÊÛ7œïŸÿíÂá’¶¥†KW-X潬j9²‰Š®Û—Ø(Üxå‡oÊ¿™Ü”´©«Ä¹dÏfÒféæÞ-ž[–ª—æ—n ÙÚ´ ßV´íõöEÛ/—Í(Û»ƒ¶C¹£¿<¸¼e§ÉÎÍ;?T¤TôTúT6îÒݵa×ønÑî{¼ö4ìÕÛ[¼÷ý>ɾÛUUMÕfÕeûIû³÷?®‰ªéø–ûm]­NmqíÇÒý#¶×¹ÔÕÒ=TRÖ+ëGǾþïw- 6 UœÆâ#pDyäé÷ ß÷ :ÚvŒ{¬áÓvg/jBšòšF›Sšû[b[ºOÌ>ÑÖêÞzüGÛœ499â?rýéü§CÏdÏ&žþ¢þË®/~øÕë×Îјѡ—ò—“¿m|¥ýêÀë¯ÛÆÂƾÉx31^ôVûíÁwÜwï£ßOä| (ÿhù±õSЧû“““ÿ˜óüc3-ÛbKGDÿÿÿ ½§“ pHYs  šœtIMEÚ!â›ÈÝ,IDAT8Ëe’_HuÇ?Ïï}ßsŽž3ÍyòË•¶¦‹U2MvQÉÖŠFÔE¬.ŠÑÍÃÅ‚­ÄŠbÑE$DD­‹ËZF5b@QÌ"š:2§›š¦¾ïû{Ÿn.êsõåçû<_ø yî?ô½m÷²ýè·wV™ê@t£R`}Z íÄÐ_£# _=œá_@ÝËý ßw^óRë®·•%6gC-έ(K>ä| $„Éï{¯} 0) { var start = document.cookie.indexOf('sortBy='); if (start != -1) { start = start + 7; var end = document.cookie.indexOf(";", start); if (end == -1) { end = document.cookie.length; by = unescape(document.cookie.substring(start, end)); } } } setComparator(); } /** * Show a comment div. */ function show(id) { $('#ao' + id).hide(); $('#ah' + id).show(); var context = $.extend({id: id}, opts); var popup = $(renderTemplate(popupTemplate, context)).hide(); popup.find('textarea[name="proposal"]').hide(); popup.find('a.by' + by).addClass('sel'); var form = popup.find('#cf' + id); form.submit(function(event) { event.preventDefault(); addComment(form); }); $('#s' + id).after(popup); popup.slideDown('fast', function() { getComments(id); }); } /** * Hide a comment div. */ function hide(id) { $('#ah' + id).hide(); $('#ao' + id).show(); var div = $('#sc' + id); div.slideUp('fast', function() { div.remove(); }); } /** * Perform an ajax request to get comments for a node * and insert the comments into the comments tree. */ function getComments(id) { $.ajax({ type: 'GET', url: opts.getCommentsURL, data: {node: id}, success: function(data, textStatus, request) { var ul = $('#cl' + id); var speed = 100; $('#cf' + id) .find('textarea[name="proposal"]') .data('source', data.source); if (data.comments.length === 0) { ul.html('
  • No comments yet.
    • '); ul.data('empty', true); } else { // If there are comments, sort them and put them in the list. var comments = sortComments(data.comments); speed = data.comments.length * 100; appendComments(comments, ul); ul.data('empty', false); } $('#cn' + id).slideUp(speed + 200); ul.slideDown(speed); }, error: function(request, textStatus, error) { showError('Oops, there was a problem retrieving the comments.'); }, dataType: 'json' }); } /** * Add a comment via ajax and insert the comment into the comment tree. */ function addComment(form) { var node_id = form.find('input[name="node"]').val(); var parent_id = form.find('input[name="parent"]').val(); var text = form.find('textarea[name="comment"]').val(); var proposal = form.find('textarea[name="proposal"]').val(); if (text == '') { showError('Please enter a comment.'); return; } // Disable the form that is being submitted. form.find('textarea,input').attr('disabled', 'disabled'); // Send the comment to the server. $.ajax({ type: "POST", url: opts.addCommentURL, dataType: 'json', data: { node: node_id, parent: parent_id, text: text, proposal: proposal }, success: function(data, textStatus, error) { // Reset the form. if (node_id) { hideProposeChange(node_id); } form.find('textarea') .val('') .add(form.find('input')) .removeAttr('disabled'); var ul = $('#cl' + (node_id || parent_id)); if (ul.data('empty')) { $(ul).empty(); ul.data('empty', false); } insertComment(data.comment); var ao = $('#ao' + node_id); ao.find('img').attr({'src': opts.commentBrightImage}); if (node_id) { // if this was a "root" comment, remove the commenting box // (the user can get it back by reopening the comment popup) $('#ca' + node_id).slideUp(); } }, error: function(request, textStatus, error) { form.find('textarea,input').removeAttr('disabled'); showError('Oops, there was a problem adding the comment.'); } }); } /** * Recursively append comments to the main comment list and children * lists, creating the comment tree. */ function appendComments(comments, ul) { $.each(comments, function() { var div = createCommentDiv(this); ul.append($(document.createElement('li')).html(div)); appendComments(this.children, div.find('ul.comment-children')); // To avoid stagnating data, don't store the comments children in data. this.children = null; div.data('comment', this); }); } /** * After adding a new comment, it must be inserted in the correct * location in the comment tree. */ function insertComment(comment) { var div = createCommentDiv(comment); // To avoid stagnating data, don't store the comments children in data. comment.children = null; div.data('comment', comment); var ul = $('#cl' + (comment.node || comment.parent)); var siblings = getChildren(ul); var li = $(document.createElement('li')); li.hide(); // Determine where in the parents children list to insert this comment. for(i=0; i < siblings.length; i++) { if (comp(comment, siblings[i]) <= 0) { $('#cd' + siblings[i].id) .parent() .before(li.html(div)); li.slideDown('fast'); return; } } // If we get here, this comment rates lower than all the others, // or it is the only comment in the list. ul.append(li.html(div)); li.slideDown('fast'); } function acceptComment(id) { $.ajax({ type: 'POST', url: opts.acceptCommentURL, data: {id: id}, success: function(data, textStatus, request) { $('#cm' + id).fadeOut('fast'); $('#cd' + id).removeClass('moderate'); }, error: function(request, textStatus, error) { showError('Oops, there was a problem accepting the comment.'); } }); } function deleteComment(id) { $.ajax({ type: 'POST', url: opts.deleteCommentURL, data: {id: id}, success: function(data, textStatus, request) { var div = $('#cd' + id); if (data == 'delete') { // Moderator mode: remove the comment and all children immediately div.slideUp('fast', function() { div.remove(); }); return; } // User mode: only mark the comment as deleted div .find('span.user-id:first') .text('[deleted]').end() .find('div.comment-text:first') .text('[deleted]').end() .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id + ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id) .remove(); var comment = div.data('comment'); comment.username = '[deleted]'; comment.text = '[deleted]'; div.data('comment', comment); }, error: function(request, textStatus, error) { showError('Oops, there was a problem deleting the comment.'); } }); } function showProposal(id) { $('#sp' + id).hide(); $('#hp' + id).show(); $('#pr' + id).slideDown('fast'); } function hideProposal(id) { $('#hp' + id).hide(); $('#sp' + id).show(); $('#pr' + id).slideUp('fast'); } function showProposeChange(id) { $('#pc' + id).hide(); $('#hc' + id).show(); var textarea = $('#pt' + id); textarea.val(textarea.data('source')); $.fn.autogrow.resize(textarea[0]); textarea.slideDown('fast'); } function hideProposeChange(id) { $('#hc' + id).hide(); $('#pc' + id).show(); var textarea = $('#pt' + id); textarea.val('').removeAttr('disabled'); textarea.slideUp('fast'); } function toggleCommentMarkupBox(id) { $('#mb' + id).toggle(); } /** Handle when the user clicks on a sort by link. */ function handleReSort(link) { var classes = link.attr('class').split(/\s+/); for (var i=0; iThank you! Your comment will show up ' + 'once it is has been approved by a moderator.'); } // Prettify the comment rating. comment.pretty_rating = comment.rating + ' point' + (comment.rating == 1 ? '' : 's'); // Make a class (for displaying not yet moderated comments differently) comment.css_class = comment.displayed ? '' : ' moderate'; // Create a div for this comment. var context = $.extend({}, opts, comment); var div = $(renderTemplate(commentTemplate, context)); // If the user has voted on this comment, highlight the correct arrow. if (comment.vote) { var direction = (comment.vote == 1) ? 'u' : 'd'; div.find('#' + direction + 'v' + comment.id).hide(); div.find('#' + direction + 'u' + comment.id).show(); } if (opts.moderator || comment.text != '[deleted]') { div.find('a.reply').show(); if (comment.proposal_diff) div.find('#sp' + comment.id).show(); if (opts.moderator && !comment.displayed) div.find('#cm' + comment.id).show(); if (opts.moderator || (opts.username == comment.username)) div.find('#dc' + comment.id).show(); } return div; } /** * A simple template renderer. Placeholders such as <%id%> are replaced * by context['id'] with items being escaped. Placeholders such as <#id#> * are not escaped. */ function renderTemplate(template, context) { var esc = $(document.createElement('div')); function handle(ph, escape) { var cur = context; $.each(ph.split('.'), function() { cur = cur[this]; }); return escape ? esc.text(cur || "").html() : cur; } return template.replace(/<([%#])([\w\.]*)\1>/g, function() { return handle(arguments[2], arguments[1] == '%' ? true : false); }); } /** Flash an error message briefly. */ function showError(message) { $(document.createElement('div')).attr({'class': 'popup-error'}) .append($(document.createElement('div')) .attr({'class': 'error-message'}).text(message)) .appendTo('body') .fadeIn("slow") .delay(2000) .fadeOut("slow"); } /** Add a link the user uses to open the comments popup. */ $.fn.comment = function() { return this.each(function() { var id = $(this).attr('id').substring(1); var count = COMMENT_METADATA[id]; var title = count + ' comment' + (count == 1 ? '' : 's'); var image = count > 0 ? opts.commentBrightImage : opts.commentImage; var addcls = count == 0 ? ' nocomment' : ''; $(this) .append( $(document.createElement('a')).attr({ href: '#', 'class': 'sphinx-comment-open' + addcls, id: 'ao' + id }) .append($(document.createElement('img')).attr({ src: image, alt: 'comment', title: title })) .click(function(event) { event.preventDefault(); show($(this).attr('id').substring(2)); }) ) .append( $(document.createElement('a')).attr({ href: '#', 'class': 'sphinx-comment-close hidden', id: 'ah' + id }) .append($(document.createElement('img')).attr({ src: opts.closeCommentImage, alt: 'close', title: 'close' })) .click(function(event) { event.preventDefault(); hide($(this).attr('id').substring(2)); }) ); }); }; var opts = { processVoteURL: '/_process_vote', addCommentURL: '/_add_comment', getCommentsURL: '/_get_comments', acceptCommentURL: '/_accept_comment', deleteCommentURL: '/_delete_comment', commentImage: '/static/_static/comment.png', closeCommentImage: '/static/_static/comment-close.png', loadingImage: '/static/_static/ajax-loader.gif', commentBrightImage: '/static/_static/comment-bright.png', upArrow: '/static/_static/up.png', downArrow: '/static/_static/down.png', upArrowPressed: '/static/_static/up-pressed.png', downArrowPressed: '/static/_static/down-pressed.png', voting: false, moderator: false }; if (typeof COMMENT_OPTIONS != "undefined") { opts = jQuery.extend(opts, COMMENT_OPTIONS); } var popupTemplate = '\
    \

    \ Sort by:\ best rated\ newest\ oldest\

    \
    Comments
    \
    \ loading comments...
    \
      \
      \

      Add a comment\ (markup):

      \
      \ reStructured text markup: *emph*, **strong**, \ ``code``, \ code blocks: :: and an indented block after blank line
      \
      \ \

      \ \ Propose a change ▹\ \ \ Propose a change ▿\ \

      \ \ \ \ \
      \
      \
      '; var commentTemplate = '\
      \
      \
      \ \ \ \ \ \ \
      \
      \ \ \ \ \ \ \
      \
      \
      \

      \ <%username%>\ <%pretty_rating%>\ <%time.delta%>\

      \
      <#text#>
      \

      \ \ reply ▿\ proposal ▹\ proposal ▿\ \ \

      \ 
      \
<#proposal_diff#>\
      \
        \
        \
        \
        \ '; var replyTemplate = '\
      • \
        \
        \ \ \ \ \ \
        \
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See #6781 readyWait: 1, // Hold (or release) the ready event holdReady: function( hold ) { if ( hold ) { jQuery.readyWait++; } else { jQuery.ready( true ); } }, // Handle when the DOM is ready ready: function( wait ) { // Either a released hold or an DOMready/load event and not yet ready if ( (wait === true && !--jQuery.readyWait) || (wait !== true && !jQuery.isReady) ) { // Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443). if ( !document.body ) { return setTimeout( jQuery.ready, 1 ); } // Remember that the DOM is ready jQuery.isReady = true; // If a normal DOM Ready event fired, decrement, and wait if need be if ( wait !== true && --jQuery.readyWait > 0 ) { return; } // If there are functions bound, to execute readyList.fireWith( document, [ jQuery ] ); // Trigger any bound ready events if ( jQuery.fn.trigger ) { jQuery( document ).trigger( "ready" ).off( "ready" ); } } }, bindReady: function() { if ( readyList ) { return; } readyList = jQuery.Callbacks( "once memory" ); // Catch cases where $(document).ready() is called after the // browser event has already occurred. if ( document.readyState === "complete" ) { // Handle it asynchronously to allow scripts the opportunity to delay ready return setTimeout( jQuery.ready, 1 ); } // Mozilla, Opera and webkit nightlies currently support this event if ( document.addEventListener ) { // Use the handy event callback document.addEventListener( "DOMContentLoaded", DOMContentLoaded, false ); // A fallback to window.onload, that will always work window.addEventListener( "load", jQuery.ready, false ); // If IE event model is used } else if ( document.attachEvent ) { // ensure firing before onload, // maybe late but safe also for iframes document.attachEvent( "onreadystatechange", DOMContentLoaded ); // A fallback to window.onload, that will always work window.attachEvent( "onload", jQuery.ready ); // If IE and not a frame // continually check to see if the document is ready var toplevel = false; try { toplevel = window.frameElement == null; } catch(e) {} if ( document.documentElement.doScroll && toplevel ) { doScrollCheck(); } } }, // See test/unit/core.js for details concerning isFunction. // Since version 1.3, DOM methods and functions like alert // aren't supported. They return false on IE (#2968). isFunction: function( obj ) { return jQuery.type(obj) === "function"; }, isArray: Array.isArray || function( obj ) { return jQuery.type(obj) === "array"; }, isWindow: function( obj ) { return obj != null && obj == obj.window; }, isNumeric: function( obj ) { return !isNaN( parseFloat(obj) ) && isFinite( obj ); }, type: function( obj ) { return obj == null ? String( obj ) : class2type[ toString.call(obj) ] || "object"; }, isPlainObject: function( obj ) { // Must be an Object. // Because of IE, we also have to check the presence of the constructor property. // Make sure that DOM nodes and window objects don't pass through, as well if ( !obj || jQuery.type(obj) !== "object" || obj.nodeType || jQuery.isWindow( obj ) ) { return false; } try { // Not own constructor property must be Object if ( obj.constructor && !hasOwn.call(obj, "constructor") && !hasOwn.call(obj.constructor.prototype, "isPrototypeOf") ) { return false; } } catch ( e ) { // IE8,9 Will throw exceptions on certain host objects #9897 return false; } // Own properties are enumerated firstly, so to speed up, // if last one is own, then all properties are own. var key; for ( key in obj ) {} return key === undefined || hasOwn.call( obj, key ); }, isEmptyObject: function( obj ) { for ( var name in obj ) { return false; } return true; }, error: function( msg ) { throw new Error( msg ); }, parseJSON: function( data ) { if ( typeof data !== "string" || !data ) { return null; } // Make sure leading/trailing whitespace is removed (IE can't handle it) data = jQuery.trim( data ); // Attempt to parse using the native JSON parser first if ( window.JSON && window.JSON.parse ) { return window.JSON.parse( data ); } // Make sure the incoming data is actual JSON // Logic borrowed from http://json.org/json2.js if ( rvalidchars.test( data.replace( rvalidescape, "@" ) .replace( rvalidtokens, "]" ) .replace( rvalidbraces, "")) ) { return ( new Function( "return " + data ) )(); } jQuery.error( "Invalid JSON: " + data ); }, // Cross-browser xml parsing parseXML: function( data ) { if ( typeof data !== "string" || !data ) { return null; } var xml, tmp; try { if ( window.DOMParser ) { // Standard tmp = new DOMParser(); xml = tmp.parseFromString( data , "text/xml" ); } else { // IE xml = new ActiveXObject( "Microsoft.XMLDOM" ); xml.async = "false"; xml.loadXML( data ); } } catch( e ) { xml = undefined; } if ( !xml || !xml.documentElement || xml.getElementsByTagName( "parsererror" ).length ) { jQuery.error( "Invalid XML: " + data ); } return xml; }, noop: function() {}, // Evaluates a script in a global context // Workarounds based on findings by Jim Driscoll // http://weblogs.java.net/blog/driscoll/archive/2009/09/08/eval-javascript-global-context globalEval: function( data ) { if ( data && rnotwhite.test( data ) ) { // We use execScript on Internet Explorer // We use an anonymous function so that context is window // rather than jQuery in Firefox ( window.execScript || function( data ) { window[ "eval" ].call( window, data ); } )( data ); } }, // Convert dashed to camelCase; used by the css and data modules // Microsoft forgot to hump their vendor prefix (#9572) camelCase: function( string ) { return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase ); }, nodeName: function( elem, name ) { return elem.nodeName && elem.nodeName.toUpperCase() === name.toUpperCase(); }, // args is for internal usage only each: function( object, callback, args ) { var name, i = 0, length = object.length, isObj = length === undefined || jQuery.isFunction( object ); if ( args ) { if ( isObj ) { for ( name in object ) { if ( callback.apply( object[ name ], args ) === false ) { break; } } } else { for ( ; i < length; ) { if ( callback.apply( object[ i++ ], args ) === false ) { break; } } } // A special, fast, case for the most common use of each } else { if ( isObj ) { for ( name in object ) { if ( callback.call( object[ name ], name, object[ name ] ) === false ) { break; } } } else { for ( ; i < length; ) { if ( callback.call( object[ i ], i, object[ i++ ] ) === false ) { break; } } } } return object; }, // Use native String.trim function wherever possible trim: trim ? function( text ) { return text == null ? "" : trim.call( text ); } : // Otherwise use our own trimming functionality function( text ) { return text == null ? "" : text.toString().replace( trimLeft, "" ).replace( trimRight, "" ); }, // results is for internal usage only makeArray: function( array, results ) { var ret = results || []; if ( array != null ) { // The window, strings (and functions) also have 'length' // Tweaked logic slightly to handle Blackberry 4.7 RegExp issues #6930 var type = jQuery.type( array ); if ( array.length == null || type === "string" || type === "function" || type === "regexp" || jQuery.isWindow( array ) ) { push.call( ret, array ); } else { jQuery.merge( ret, array ); } } return ret; }, inArray: function( elem, array, i ) { var len; if ( array ) { if ( indexOf ) { return indexOf.call( array, elem, i ); } len = array.length; i = i ? i < 0 ? Math.max( 0, len + i ) : i : 0; for ( ; i < len; i++ ) { // Skip accessing in sparse arrays if ( i in array && array[ i ] === elem ) { return i; } } } return -1; }, merge: function( first, second ) { var i = first.length, j = 0; if ( typeof second.length === "number" ) { for ( var l = second.length; j < l; j++ ) { first[ i++ ] = second[ j ]; } } else { while ( second[j] !== undefined ) { first[ i++ ] = second[ j++ ]; } } first.length = i; return first; }, grep: function( elems, callback, inv ) { var ret = [], retVal; inv = !!inv; // Go through the array, only saving the items // that pass the validator function for ( var i = 0, length = elems.length; i < length; i++ ) { retVal = !!callback( elems[ i ], i ); if ( inv !== retVal ) { ret.push( elems[ i ] ); } } return ret; }, // arg is for internal usage only map: function( elems, callback, arg ) { var value, key, ret = [], i = 0, length = elems.length, // jquery objects are treated as arrays isArray = elems instanceof jQuery || length !== undefined && typeof length === "number" && ( ( length > 0 && elems[ 0 ] && elems[ length -1 ] ) || length === 0 || jQuery.isArray( elems ) ) ; // Go through the array, translating each of the items to their if ( isArray ) { for ( ; i < length; i++ ) { value = callback( elems[ i ], i, arg ); if ( value != null ) { ret[ ret.length ] = value; } } // Go through every key on the object, } else { for ( key in elems ) { value = callback( elems[ key ], key, arg ); if ( value != null ) { ret[ ret.length ] = value; } } } // Flatten any nested arrays return ret.concat.apply( [], ret ); }, // A global GUID counter for objects guid: 1, // Bind a function to a context, optionally partially applying any // arguments. proxy: function( fn, context ) { if ( typeof context === "string" ) { var tmp = fn[ context ]; context = fn; fn = tmp; } // Quick check to determine if target is callable, in the spec // this throws a TypeError, but we will just return undefined. if ( !jQuery.isFunction( fn ) ) { return undefined; } // Simulated bind var args = slice.call( arguments, 2 ), proxy = function() { return fn.apply( context, args.concat( slice.call( arguments ) ) ); }; // Set the guid of unique handler to the same of original handler, so it can be removed proxy.guid = fn.guid = fn.guid || proxy.guid || jQuery.guid++; return proxy; }, // Mutifunctional method to get and set values to a collection // The value/s can optionally be executed if it's a function access: function( elems, fn, key, value, chainable, emptyGet, pass ) { var exec, bulk = key == null, i = 0, length = elems.length; // Sets many values if ( key && typeof key === "object" ) { for ( i in key ) { jQuery.access( elems, fn, i, key[i], 1, emptyGet, value ); } chainable = 1; // Sets one value } else if ( value !== undefined ) { // Optionally, function values get executed if exec is true exec = pass === undefined && jQuery.isFunction( value ); if ( bulk ) { // Bulk operations only iterate when executing function values if ( exec ) { exec = fn; fn = function( elem, key, value ) { return exec.call( jQuery( elem ), value ); }; // Otherwise they run against the entire set } else { fn.call( elems, value ); fn = null; } } if ( fn ) { for (; i < length; i++ ) { fn( elems[i], key, exec ? value.call( elems[i], i, fn( elems[i], key ) ) : value, pass ); } } chainable = 1; } return chainable ? elems : // Gets bulk ? fn.call( elems ) : length ? fn( elems[0], key ) : emptyGet; }, now: function() { return ( new Date() ).getTime(); }, // Use of jQuery.browser is frowned upon. // More details: http://docs.jquery.com/Utilities/jQuery.browser uaMatch: function( ua ) { ua = ua.toLowerCase(); var match = rwebkit.exec( ua ) || ropera.exec( ua ) || rmsie.exec( ua ) || ua.indexOf("compatible") < 0 && rmozilla.exec( ua ) || []; return { browser: match[1] || "", version: match[2] || "0" }; }, sub: function() { function jQuerySub( selector, context ) { return new jQuerySub.fn.init( selector, context ); } jQuery.extend( true, jQuerySub, this ); jQuerySub.superclass = this; jQuerySub.fn = jQuerySub.prototype = this(); jQuerySub.fn.constructor = jQuerySub; jQuerySub.sub = this.sub; jQuerySub.fn.init = function init( selector, context ) { if ( context && context instanceof jQuery && !(context instanceof jQuerySub) ) { context = jQuerySub( context ); } return jQuery.fn.init.call( this, selector, context, rootjQuerySub ); }; jQuerySub.fn.init.prototype = jQuerySub.fn; var rootjQuerySub = jQuerySub(document); return jQuerySub; }, browser: {} }); // Populate the class2type map jQuery.each("Boolean Number String Function Array Date RegExp Object".split(" "), function(i, name) { class2type[ "[object " + name + "]" ] = name.toLowerCase(); }); browserMatch = jQuery.uaMatch( userAgent ); if ( browserMatch.browser ) { jQuery.browser[ browserMatch.browser ] = true; jQuery.browser.version = browserMatch.version; } // Deprecated, use jQuery.browser.webkit instead if ( jQuery.browser.webkit ) { jQuery.browser.safari = true; } // IE doesn't match non-breaking spaces with \s if ( rnotwhite.test( "\xA0" ) ) { trimLeft = /^[\s\xA0]+/; trimRight = /[\s\xA0]+$/; } // All jQuery objects should point back to these rootjQuery = jQuery(document); // Cleanup functions for the document ready method if ( document.addEventListener ) { DOMContentLoaded = function() { document.removeEventListener( "DOMContentLoaded", DOMContentLoaded, false ); jQuery.ready(); }; } else if ( document.attachEvent ) { DOMContentLoaded = function() { // Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443). if ( document.readyState === "complete" ) { document.detachEvent( "onreadystatechange", DOMContentLoaded ); jQuery.ready(); } }; } // The DOM ready check for Internet Explorer function doScrollCheck() { if ( jQuery.isReady ) { return; } try { // If IE is used, use the trick by Diego Perini // http://javascript.nwbox.com/IEContentLoaded/ document.documentElement.doScroll("left"); } catch(e) { setTimeout( doScrollCheck, 1 ); return; } // and execute any waiting functions jQuery.ready(); } return jQuery; })(); // String to Object flags format cache var flagsCache = {}; // Convert String-formatted flags into Object-formatted ones and store in cache function createFlags( flags ) { var object = flagsCache[ flags ] = {}, i, length; flags = flags.split( /\s+/ ); for ( i = 0, length = flags.length; i < length; i++ ) { object[ flags[i] ] = true; } return object; } /* * Create a callback list using the following parameters: * * flags: an optional list of space-separated flags that will change how * the callback list behaves * * By default a callback list will act like an event callback list and can be * "fired" multiple times. * * Possible flags: * * once: will ensure the callback list can only be fired once (like a Deferred) * * memory: will keep track of previous values and will call any callback added * after the list has been fired right away with the latest "memorized" * values (like a Deferred) * * unique: will ensure a callback can only be added once (no duplicate in the list) * * stopOnFalse: interrupt callings when a callback returns false * */ jQuery.Callbacks = function( flags ) { // Convert flags from String-formatted to Object-formatted // (we check in cache first) flags = flags ? ( flagsCache[ flags ] || createFlags( flags ) ) : {}; var // Actual callback list list = [], // Stack of fire calls for repeatable lists stack = [], // Last fire value (for non-forgettable lists) memory, // Flag to know if list was already fired fired, // Flag to know if list is currently firing firing, // First callback to fire (used internally by add and fireWith) firingStart, // End of the loop when firing firingLength, // Index of currently firing callback (modified by remove if needed) firingIndex, // Add one or several callbacks to the list add = function( args ) { var i, length, elem, type, actual; for ( i = 0, length = args.length; i < length; i++ ) { elem = args[ i ]; type = jQuery.type( elem ); if ( type === "array" ) { // Inspect recursively add( elem ); } else if ( type === "function" ) { // Add if not in unique mode and callback is not in if ( !flags.unique || !self.has( elem ) ) { list.push( elem ); } } } }, // Fire callbacks fire = function( context, args ) { args = args || []; memory = !flags.memory || [ context, args ]; fired = true; firing = true; firingIndex = firingStart || 0; firingStart = 0; firingLength = list.length; for ( ; list && firingIndex < firingLength; firingIndex++ ) { if ( list[ firingIndex ].apply( context, args ) === false && flags.stopOnFalse ) { memory = true; // Mark as halted break; } } firing = false; if ( list ) { if ( !flags.once ) { if ( stack && stack.length ) { memory = stack.shift(); self.fireWith( memory[ 0 ], memory[ 1 ] ); } } else if ( memory === true ) { self.disable(); } else { list = []; } } }, // Actual Callbacks object self = { // Add a callback or a collection of callbacks to the list add: function() { if ( list ) { var length = list.length; add( arguments ); // Do we need to add the callbacks to the // current firing batch? if ( firing ) { firingLength = list.length; // With memory, if we're not firing then // we should call right away, unless previous // firing was halted (stopOnFalse) } else if ( memory && memory !== true ) { firingStart = length; fire( memory[ 0 ], memory[ 1 ] ); } } return this; }, // Remove a callback from the list remove: function() { if ( list ) { var args = arguments, argIndex = 0, argLength = args.length; for ( ; argIndex < argLength ; argIndex++ ) { for ( var i = 0; i < list.length; i++ ) { if ( args[ argIndex ] === list[ i ] ) { // Handle firingIndex and firingLength if ( firing ) { if ( i <= firingLength ) { firingLength--; if ( i <= firingIndex ) { firingIndex--; } } } // Remove the element list.splice( i--, 1 ); // If we have some unicity property then // we only need to do this once if ( flags.unique ) { break; } } } } } return this; }, // Control if a given callback is in the list has: function( fn ) { if ( list ) { var i = 0, length = list.length; for ( ; i < length; i++ ) { if ( fn === list[ i ] ) { return true; } } } return false; }, // Remove all callbacks from the list empty: function() { list = []; return this; }, // Have the list do nothing anymore disable: function() { list = stack = memory = undefined; return this; }, // Is it disabled? disabled: function() { return !list; }, // Lock the list in its current state lock: function() { stack = undefined; if ( !memory || memory === true ) { self.disable(); } return this; }, // Is it locked? locked: function() { return !stack; }, // Call all callbacks with the given context and arguments fireWith: function( context, args ) { if ( stack ) { if ( firing ) { if ( !flags.once ) { stack.push( [ context, args ] ); } } else if ( !( flags.once && memory ) ) { fire( context, args ); } } return this; }, // Call all the callbacks with the given arguments fire: function() { self.fireWith( this, arguments ); return this; }, // To know if the callbacks have already been called at least once fired: function() { return !!fired; } }; return self; }; var // Static reference to slice sliceDeferred = [].slice; jQuery.extend({ Deferred: function( func ) { var doneList = jQuery.Callbacks( "once memory" ), failList = jQuery.Callbacks( "once memory" ), progressList = jQuery.Callbacks( "memory" ), state = "pending", lists = { resolve: doneList, reject: failList, notify: progressList }, promise = { done: doneList.add, fail: failList.add, progress: progressList.add, state: function() { return state; }, // Deprecated isResolved: doneList.fired, isRejected: failList.fired, then: function( doneCallbacks, failCallbacks, progressCallbacks ) { deferred.done( doneCallbacks ).fail( failCallbacks ).progress( progressCallbacks ); return this; }, always: function() { deferred.done.apply( deferred, arguments ).fail.apply( deferred, arguments ); return this; }, pipe: function( fnDone, fnFail, fnProgress ) { return jQuery.Deferred(function( newDefer ) { jQuery.each( { done: [ fnDone, "resolve" ], fail: [ fnFail, "reject" ], progress: [ fnProgress, "notify" ] }, function( handler, data ) { var fn = data[ 0 ], action = data[ 1 ], returned; if ( jQuery.isFunction( fn ) ) { deferred[ handler ](function() { returned = fn.apply( this, arguments ); if ( returned && jQuery.isFunction( returned.promise ) ) { returned.promise().then( newDefer.resolve, newDefer.reject, newDefer.notify ); } else { newDefer[ action + "With" ]( this === deferred ? newDefer : this, [ returned ] ); } }); } else { deferred[ handler ]( newDefer[ action ] ); } }); }).promise(); }, // Get a promise for this deferred // If obj is provided, the promise aspect is added to the object promise: function( obj ) { if ( obj == null ) { obj = promise; } else { for ( var key in promise ) { obj[ key ] = promise[ key ]; } } return obj; } }, deferred = promise.promise({}), key; for ( key in lists ) { deferred[ key ] = lists[ key ].fire; deferred[ key + "With" ] = lists[ key ].fireWith; } // Handle state deferred.done( function() { state = "resolved"; }, failList.disable, progressList.lock ).fail( function() { state = "rejected"; }, doneList.disable, progressList.lock ); // Call given func if any if ( func ) { func.call( deferred, deferred ); } // All done! return deferred; }, // Deferred helper when: function( firstParam ) { var args = sliceDeferred.call( arguments, 0 ), i = 0, length = args.length, pValues = new Array( length ), count = length, pCount = length, deferred = length <= 1 && firstParam && jQuery.isFunction( firstParam.promise ) ? firstParam : jQuery.Deferred(), promise = deferred.promise(); function resolveFunc( i ) { return function( value ) { args[ i ] = arguments.length > 1 ? sliceDeferred.call( arguments, 0 ) : value; if ( !( --count ) ) { deferred.resolveWith( deferred, args ); } }; } function progressFunc( i ) { return function( value ) { pValues[ i ] = arguments.length > 1 ? sliceDeferred.call( arguments, 0 ) : value; deferred.notifyWith( promise, pValues ); }; } if ( length > 1 ) { for ( ; i < length; i++ ) { if ( args[ i ] && args[ i ].promise && jQuery.isFunction( args[ i ].promise ) ) { args[ i ].promise().then( resolveFunc(i), deferred.reject, progressFunc(i) ); } else { --count; } } if ( !count ) { deferred.resolveWith( deferred, args ); } } else if ( deferred !== firstParam ) { deferred.resolveWith( deferred, length ? [ firstParam ] : [] ); } return promise; } }); jQuery.support = (function() { var support, all, a, select, opt, input, fragment, tds, events, eventName, i, isSupported, div = document.createElement( "div" ), documentElement = document.documentElement; // Preliminary tests div.setAttribute("className", "t"); div.innerHTML = "
        a"; all = div.getElementsByTagName( "*" ); a = div.getElementsByTagName( "a" )[ 0 ]; // Can't get basic test support if ( !all || !all.length || !a ) { return {}; } // First batch of supports tests select = document.createElement( "select" ); opt = select.appendChild( document.createElement("option") ); input = div.getElementsByTagName( "input" )[ 0 ]; support = { // IE strips leading whitespace when .innerHTML is used leadingWhitespace: ( div.firstChild.nodeType === 3 ), // Make sure that tbody elements aren't automatically inserted // IE will insert them into empty tables tbody: !div.getElementsByTagName("tbody").length, // Make sure that link elements get serialized correctly by innerHTML // This requires a wrapper element in IE htmlSerialize: !!div.getElementsByTagName("link").length, // Get the style information from getAttribute // (IE uses .cssText instead) style: /top/.test( a.getAttribute("style") ), // Make sure that URLs aren't manipulated // (IE normalizes it by default) hrefNormalized: ( a.getAttribute("href") === "/a" ), // Make sure that element opacity exists // (IE uses filter instead) // Use a regex to work around a WebKit issue. See #5145 opacity: /^0.55/.test( a.style.opacity ), // Verify style float existence // (IE uses styleFloat instead of cssFloat) cssFloat: !!a.style.cssFloat, // Make sure that if no value is specified for a checkbox // that it defaults to "on". // (WebKit defaults to "" instead) checkOn: ( input.value === "on" ), // Make sure that a selected-by-default option has a working selected property. // (WebKit defaults to false instead of true, IE too, if it's in an optgroup) optSelected: opt.selected, // Test setAttribute on camelCase class. If it works, we need attrFixes when doing get/setAttribute (ie6/7) getSetAttribute: div.className !== "t", // Tests for enctype support on a form(#6743) enctype: !!document.createElement("form").enctype, // Makes sure cloning an html5 element does not cause problems // Where outerHTML is undefined, this still works html5Clone: document.createElement("nav").cloneNode( true ).outerHTML !== "<:nav>", // Will be defined later submitBubbles: true, changeBubbles: true, focusinBubbles: false, deleteExpando: true, noCloneEvent: true, inlineBlockNeedsLayout: false, shrinkWrapBlocks: false, reliableMarginRight: true, pixelMargin: true }; // jQuery.boxModel DEPRECATED in 1.3, use jQuery.support.boxModel instead jQuery.boxModel = support.boxModel = (document.compatMode === "CSS1Compat"); // Make sure checked status is properly cloned input.checked = true; support.noCloneChecked = input.cloneNode( true ).checked; // Make sure that the options inside disabled selects aren't marked as disabled // (WebKit marks them as disabled) select.disabled = true; support.optDisabled = !opt.disabled; // Test to see if it's possible to delete an expando from an element // Fails in Internet Explorer try { delete div.test; } catch( e ) { support.deleteExpando = false; } if ( !div.addEventListener && div.attachEvent && div.fireEvent ) { div.attachEvent( "onclick", function() { // Cloning a node shouldn't copy over any // bound event handlers (IE does this) support.noCloneEvent = false; }); div.cloneNode( true ).fireEvent( "onclick" ); } // Check if a radio maintains its value // after being appended to the DOM input = document.createElement("input"); input.value = "t"; input.setAttribute("type", "radio"); support.radioValue = input.value === "t"; input.setAttribute("checked", "checked"); // #11217 - WebKit loses check when the name is after the checked attribute input.setAttribute( "name", "t" ); div.appendChild( input ); fragment = document.createDocumentFragment(); fragment.appendChild( div.lastChild ); // WebKit doesn't clone checked state correctly in fragments support.checkClone = fragment.cloneNode( true ).cloneNode( true ).lastChild.checked; // Check if a disconnected checkbox will retain its checked // value of true after appended to the DOM (IE6/7) support.appendChecked = input.checked; fragment.removeChild( input ); fragment.appendChild( div ); // Technique from Juriy Zaytsev // http://perfectionkills.com/detecting-event-support-without-browser-sniffing/ // We only care about the case where non-standard event systems // are used, namely in IE. Short-circuiting here helps us to // avoid an eval call (in setAttribute) which can cause CSP // to go haywire. See: https://developer.mozilla.org/en/Security/CSP if ( div.attachEvent ) { for ( i in { submit: 1, change: 1, focusin: 1 }) { eventName = "on" + i; isSupported = ( eventName in div ); if ( !isSupported ) { div.setAttribute( eventName, "return;" ); isSupported = ( typeof div[ eventName ] === "function" ); } support[ i + "Bubbles" ] = isSupported; } } fragment.removeChild( div ); // Null elements to avoid leaks in IE fragment = select = opt = div = input = null; // Run tests that need a body at doc ready jQuery(function() { var container, outer, inner, table, td, offsetSupport, marginDiv, conMarginTop, style, html, positionTopLeftWidthHeight, paddingMarginBorderVisibility, paddingMarginBorder, body = document.getElementsByTagName("body")[0]; if ( !body ) { // Return for frameset docs that don't have a body return; } conMarginTop = 1; paddingMarginBorder = "padding:0;margin:0;border:"; positionTopLeftWidthHeight = "position:absolute;top:0;left:0;width:1px;height:1px;"; paddingMarginBorderVisibility = paddingMarginBorder + "0;visibility:hidden;"; style = "style='" + positionTopLeftWidthHeight + paddingMarginBorder + "5px solid #000;"; html = "
        " + "" + "
        "; container = document.createElement("div"); container.style.cssText = paddingMarginBorderVisibility + "width:0;height:0;position:static;top:0;margin-top:" + conMarginTop + "px"; body.insertBefore( container, body.firstChild ); // Construct the test element div = document.createElement("div"); container.appendChild( div ); // Check if table cells still have offsetWidth/Height when they are set // to display:none and there are still other visible table cells in a // table row; if so, offsetWidth/Height are not reliable for use when // determining if an element has been hidden directly using // display:none (it is still safe to use offsets if a parent element is // hidden; don safety goggles and see bug #4512 for more information). // (only IE 8 fails this test) div.innerHTML = "
        t
        "; tds = div.getElementsByTagName( "td" ); isSupported = ( tds[ 0 ].offsetHeight === 0 ); tds[ 0 ].style.display = ""; tds[ 1 ].style.display = "none"; // Check if empty table cells still have offsetWidth/Height // (IE <= 8 fail this test) support.reliableHiddenOffsets = isSupported && ( tds[ 0 ].offsetHeight === 0 ); // Check if div with explicit width and no margin-right incorrectly // gets computed margin-right based on width of container. For more // info see bug #3333 // Fails in WebKit before Feb 2011 nightlies // WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right if ( window.getComputedStyle ) { div.innerHTML = ""; marginDiv = document.createElement( "div" ); marginDiv.style.width = "0"; marginDiv.style.marginRight = "0"; div.style.width = "2px"; div.appendChild( marginDiv ); support.reliableMarginRight = ( parseInt( ( window.getComputedStyle( marginDiv, null ) || { marginRight: 0 } ).marginRight, 10 ) || 0 ) === 0; } if ( typeof div.style.zoom !== "undefined" ) { // Check if natively block-level elements act like inline-block // elements when setting their display to 'inline' and giving // them layout // (IE < 8 does this) div.innerHTML = ""; div.style.width = div.style.padding = "1px"; div.style.border = 0; div.style.overflow = "hidden"; div.style.display = "inline"; div.style.zoom = 1; support.inlineBlockNeedsLayout = ( div.offsetWidth === 3 ); // Check if elements with layout shrink-wrap their children // (IE 6 does this) div.style.display = "block"; div.style.overflow = "visible"; div.innerHTML = "
        "; support.shrinkWrapBlocks = ( div.offsetWidth !== 3 ); } div.style.cssText = positionTopLeftWidthHeight + paddingMarginBorderVisibility; div.innerHTML = html; outer = div.firstChild; inner = outer.firstChild; td = outer.nextSibling.firstChild.firstChild; offsetSupport = { doesNotAddBorder: ( inner.offsetTop !== 5 ), doesAddBorderForTableAndCells: ( td.offsetTop === 5 ) }; inner.style.position = "fixed"; inner.style.top = "20px"; // safari subtracts parent border width here which is 5px offsetSupport.fixedPosition = ( inner.offsetTop === 20 || inner.offsetTop === 15 ); inner.style.position = inner.style.top = ""; outer.style.overflow = "hidden"; outer.style.position = "relative"; offsetSupport.subtractsBorderForOverflowNotVisible = ( inner.offsetTop === -5 ); offsetSupport.doesNotIncludeMarginInBodyOffset = ( body.offsetTop !== conMarginTop ); if ( window.getComputedStyle ) { div.style.marginTop = "1%"; support.pixelMargin = ( window.getComputedStyle( div, null ) || { marginTop: 0 } ).marginTop !== "1%"; } if ( typeof container.style.zoom !== "undefined" ) { container.style.zoom = 1; } body.removeChild( container ); marginDiv = div = container = null; jQuery.extend( support, offsetSupport ); }); return support; })(); var rbrace = /^(?:\{.*\}|\[.*\])$/, rmultiDash = /([A-Z])/g; jQuery.extend({ cache: {}, // Please use with caution uuid: 0, // Unique for each copy of jQuery on the page // Non-digits removed to match rinlinejQuery expando: "jQuery" + ( jQuery.fn.jquery + Math.random() ).replace( /\D/g, "" ), // The following elements throw uncatchable exceptions if you // attempt to add expando properties to them. noData: { "embed": true, // Ban all objects except for Flash (which handle expandos) "object": "clsid:D27CDB6E-AE6D-11cf-96B8-444553540000", "applet": true }, hasData: function( elem ) { elem = elem.nodeType ? jQuery.cache[ elem[jQuery.expando] ] : elem[ jQuery.expando ]; return !!elem && !isEmptyDataObject( elem ); }, data: function( elem, name, data, pvt /* Internal Use Only */ ) { if ( !jQuery.acceptData( elem ) ) { return; } var privateCache, thisCache, ret, internalKey = jQuery.expando, getByName = typeof name === "string", // We have to handle DOM nodes and JS objects differently because IE6-7 // can't GC object references properly across the DOM-JS boundary isNode = elem.nodeType, // Only DOM nodes need the global jQuery cache; JS object data is // attached directly to the object so GC can occur automatically cache = isNode ? jQuery.cache : elem, // Only defining an ID for JS objects if its cache already exists allows // the code to shortcut on the same path as a DOM node with no cache id = isNode ? elem[ internalKey ] : elem[ internalKey ] && internalKey, isEvents = name === "events"; // Avoid doing any more work than we need to when trying to get data on an // object that has no data at all if ( (!id || !cache[id] || (!isEvents && !pvt && !cache[id].data)) && getByName && data === undefined ) { return; } if ( !id ) { // Only DOM nodes need a new unique ID for each element since their data // ends up in the global cache if ( isNode ) { elem[ internalKey ] = id = ++jQuery.uuid; } else { id = internalKey; } } if ( !cache[ id ] ) { cache[ id ] = {}; // Avoids exposing jQuery metadata on plain JS objects when the object // is serialized using JSON.stringify if ( !isNode ) { cache[ id ].toJSON = jQuery.noop; } } // An object can be passed to jQuery.data instead of a key/value pair; this gets // shallow copied over onto the existing cache if ( typeof name === "object" || typeof name === "function" ) { if ( pvt ) { cache[ id ] = jQuery.extend( cache[ id ], name ); } else { cache[ id ].data = jQuery.extend( cache[ id ].data, name ); } } privateCache = thisCache = cache[ id ]; // jQuery data() is stored in a separate object inside the object's internal data // cache in order to avoid key collisions between internal data and user-defined // data. if ( !pvt ) { if ( !thisCache.data ) { thisCache.data = {}; } thisCache = thisCache.data; } if ( data !== undefined ) { thisCache[ jQuery.camelCase( name ) ] = data; } // Users should not attempt to inspect the internal events object using jQuery.data, // it is undocumented and subject to change. But does anyone listen? No. if ( isEvents && !thisCache[ name ] ) { return privateCache.events; } // Check for both converted-to-camel and non-converted data property names // If a data property was specified if ( getByName ) { // First Try to find as-is property data ret = thisCache[ name ]; // Test for null|undefined property data if ( ret == null ) { // Try to find the camelCased property ret = thisCache[ jQuery.camelCase( name ) ]; } } else { ret = thisCache; } return ret; }, removeData: function( elem, name, pvt /* Internal Use Only */ ) { if ( !jQuery.acceptData( elem ) ) { return; } var thisCache, i, l, // Reference to internal data cache key internalKey = jQuery.expando, isNode = elem.nodeType, // See jQuery.data for more information cache = isNode ? jQuery.cache : elem, // See jQuery.data for more information id = isNode ? elem[ internalKey ] : internalKey; // If there is already no cache entry for this object, there is no // purpose in continuing if ( !cache[ id ] ) { return; } if ( name ) { thisCache = pvt ? cache[ id ] : cache[ id ].data; if ( thisCache ) { // Support array or space separated string names for data keys if ( !jQuery.isArray( name ) ) { // try the string as a key before any manipulation if ( name in thisCache ) { name = [ name ]; } else { // split the camel cased version by spaces unless a key with the spaces exists name = jQuery.camelCase( name ); if ( name in thisCache ) { name = [ name ]; } else { name = name.split( " " ); } } } for ( i = 0, l = name.length; i < l; i++ ) { delete thisCache[ name[i] ]; } // If there is no data left in the cache, we want to continue // and let the cache object itself get destroyed if ( !( pvt ? isEmptyDataObject : jQuery.isEmptyObject )( thisCache ) ) { return; } } } // See jQuery.data for more information if ( !pvt ) { delete cache[ id ].data; // Don't destroy the parent cache unless the internal data object // had been the only thing left in it if ( !isEmptyDataObject(cache[ id ]) ) { return; } } // Browsers that fail expando deletion also refuse to delete expandos on // the window, but it will allow it on all other JS objects; other browsers // don't care // Ensure that `cache` is not a window object #10080 if ( jQuery.support.deleteExpando || !cache.setInterval ) { delete cache[ id ]; } else { cache[ id ] = null; } // We destroyed the cache and need to eliminate the expando on the node to avoid // false lookups in the cache for entries that no longer exist if ( isNode ) { // IE does not allow us to delete expando properties from nodes, // nor does it have a removeAttribute function on Document nodes; // we must handle all of these cases if ( jQuery.support.deleteExpando ) { delete elem[ internalKey ]; } else if ( elem.removeAttribute ) { elem.removeAttribute( internalKey ); } else { elem[ internalKey ] = null; } } }, // For internal use only. _data: function( elem, name, data ) { return jQuery.data( elem, name, data, true ); }, // A method for determining if a DOM node can handle the data expando acceptData: function( elem ) { if ( elem.nodeName ) { var match = jQuery.noData[ elem.nodeName.toLowerCase() ]; if ( match ) { return !(match === true || elem.getAttribute("classid") !== match); } } return true; } }); jQuery.fn.extend({ data: function( key, value ) { var parts, part, attr, name, l, elem = this[0], i = 0, data = null; // Gets all values if ( key === undefined ) { if ( this.length ) { data = jQuery.data( elem ); if ( elem.nodeType === 1 && !jQuery._data( elem, "parsedAttrs" ) ) { attr = elem.attributes; for ( l = attr.length; i < l; i++ ) { name = attr[i].name; if ( name.indexOf( "data-" ) === 0 ) { name = jQuery.camelCase( name.substring(5) ); dataAttr( elem, name, data[ name ] ); } } jQuery._data( elem, "parsedAttrs", true ); } } return data; } // Sets multiple values if ( typeof key === "object" ) { return this.each(function() { jQuery.data( this, key ); }); } parts = key.split( ".", 2 ); parts[1] = parts[1] ? "." + parts[1] : ""; part = parts[1] + "!"; return jQuery.access( this, function( value ) { if ( value === undefined ) { data = this.triggerHandler( "getData" + part, [ parts[0] ] ); // Try to fetch any internally stored data first if ( data === undefined && elem ) { data = jQuery.data( elem, key ); data = dataAttr( elem, key, data ); } return data === undefined && parts[1] ? this.data( parts[0] ) : data; } parts[1] = value; this.each(function() { var self = jQuery( this ); self.triggerHandler( "setData" + part, parts ); jQuery.data( this, key, value ); self.triggerHandler( "changeData" + part, parts ); }); }, null, value, arguments.length > 1, null, false ); }, removeData: function( key ) { return this.each(function() { jQuery.removeData( this, key ); }); } }); function dataAttr( elem, key, data ) { // If nothing was found internally, try to fetch any // data from the HTML5 data-* attribute if ( data === undefined && elem.nodeType === 1 ) { var name = "data-" + key.replace( rmultiDash, "-$1" ).toLowerCase(); data = elem.getAttribute( name ); if ( typeof data === "string" ) { try { data = data === "true" ? true : data === "false" ? false : data === "null" ? null : jQuery.isNumeric( data ) ? +data : rbrace.test( data ) ? jQuery.parseJSON( data ) : data; } catch( e ) {} // Make sure we set the data so it isn't changed later jQuery.data( elem, key, data ); } else { data = undefined; } } return data; } // checks a cache object for emptiness function isEmptyDataObject( obj ) { for ( var name in obj ) { // if the public data object is empty, the private is still empty if ( name === "data" && jQuery.isEmptyObject( obj[name] ) ) { continue; } if ( name !== "toJSON" ) { return false; } } return true; } function handleQueueMarkDefer( elem, type, src ) { var deferDataKey = type + "defer", queueDataKey = type + "queue", markDataKey = type + "mark", defer = jQuery._data( elem, deferDataKey ); if ( defer && ( src === "queue" || !jQuery._data(elem, queueDataKey) ) && ( src === "mark" || !jQuery._data(elem, markDataKey) ) ) { // Give room for hard-coded callbacks to fire first // and eventually mark/queue something else on the element setTimeout( function() { if ( !jQuery._data( elem, queueDataKey ) && !jQuery._data( elem, markDataKey ) ) { jQuery.removeData( elem, deferDataKey, true ); defer.fire(); } }, 0 ); } } jQuery.extend({ _mark: function( elem, type ) { if ( elem ) { type = ( type || "fx" ) + "mark"; jQuery._data( elem, type, (jQuery._data( elem, type ) || 0) + 1 ); } }, _unmark: function( force, elem, type ) { if ( force !== true ) { type = elem; elem = force; force = false; } if ( elem ) { type = type || "fx"; var key = type + "mark", count = force ? 0 : ( (jQuery._data( elem, key ) || 1) - 1 ); if ( count ) { jQuery._data( elem, key, count ); } else { jQuery.removeData( elem, key, true ); handleQueueMarkDefer( elem, type, "mark" ); } } }, queue: function( elem, type, data ) { var q; if ( elem ) { type = ( type || "fx" ) + "queue"; q = jQuery._data( elem, type ); // Speed up dequeue by getting out quickly if this is just a lookup if ( data ) { if ( !q || jQuery.isArray(data) ) { q = jQuery._data( elem, type, jQuery.makeArray(data) ); } else { q.push( data ); } } return q || []; } }, dequeue: function( elem, type ) { type = type || "fx"; var queue = jQuery.queue( elem, type ), fn = queue.shift(), hooks = {}; // If the fx queue is dequeued, always remove the progress sentinel if ( fn === "inprogress" ) { fn = queue.shift(); } if ( fn ) { // Add a progress sentinel to prevent the fx queue from being // automatically dequeued if ( type === "fx" ) { queue.unshift( "inprogress" ); } jQuery._data( elem, type + ".run", hooks ); fn.call( elem, function() { jQuery.dequeue( elem, type ); }, hooks ); } if ( !queue.length ) { jQuery.removeData( elem, type + "queue " + type + ".run", true ); handleQueueMarkDefer( elem, type, "queue" ); } } }); jQuery.fn.extend({ queue: function( type, data ) { var setter = 2; if ( typeof type !== "string" ) { data = type; type = "fx"; setter--; } if ( arguments.length < setter ) { return jQuery.queue( this[0], type ); } return data === undefined ? this : this.each(function() { var queue = jQuery.queue( this, type, data ); if ( type === "fx" && queue[0] !== "inprogress" ) { jQuery.dequeue( this, type ); } }); }, dequeue: function( type ) { return this.each(function() { jQuery.dequeue( this, type ); }); }, // Based off of the plugin by Clint Helfers, with permission. // http://blindsignals.com/index.php/2009/07/jquery-delay/ delay: function( time, type ) { time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time; type = type || "fx"; return this.queue( type, function( next, hooks ) { var timeout = setTimeout( next, time ); hooks.stop = function() { clearTimeout( timeout ); }; }); }, clearQueue: function( type ) { return this.queue( type || "fx", [] ); }, // Get a promise resolved when queues of a certain type // are emptied (fx is the type by default) promise: function( type, object ) { if ( typeof type !== "string" ) { object = type; type = undefined; } type = type || "fx"; var defer = jQuery.Deferred(), elements = this, i = elements.length, count = 1, deferDataKey = type + "defer", queueDataKey = type + "queue", markDataKey = type + "mark", tmp; function resolve() { if ( !( --count ) ) { defer.resolveWith( elements, [ elements ] ); } } while( i-- ) { if (( tmp = jQuery.data( elements[ i ], deferDataKey, undefined, true ) || ( jQuery.data( elements[ i ], queueDataKey, undefined, true ) || jQuery.data( elements[ i ], markDataKey, undefined, true ) ) && jQuery.data( elements[ i ], deferDataKey, jQuery.Callbacks( "once memory" ), true ) )) { count++; tmp.add( resolve ); } } resolve(); return defer.promise( object ); } }); var rclass = /[\n\t\r]/g, rspace = /\s+/, rreturn = /\r/g, rtype = /^(?:button|input)$/i, rfocusable = /^(?:button|input|object|select|textarea)$/i, rclickable = /^a(?:rea)?$/i, rboolean = /^(?:autofocus|autoplay|async|checked|controls|defer|disabled|hidden|loop|multiple|open|readonly|required|scoped|selected)$/i, getSetAttribute = jQuery.support.getSetAttribute, nodeHook, boolHook, fixSpecified; jQuery.fn.extend({ attr: function( name, value ) { return jQuery.access( this, jQuery.attr, name, value, arguments.length > 1 ); }, removeAttr: function( name ) { return this.each(function() { jQuery.removeAttr( this, name ); }); }, prop: function( name, value ) { return jQuery.access( this, jQuery.prop, name, value, arguments.length > 1 ); }, removeProp: function( name ) { name = jQuery.propFix[ name ] || name; return this.each(function() { // try/catch handles cases where IE balks (such as removing a property on window) try { this[ name ] = undefined; delete this[ name ]; } catch( e ) {} }); }, addClass: function( value ) { var classNames, i, l, elem, setClass, c, cl; if ( jQuery.isFunction( value ) ) { return this.each(function( j ) { jQuery( this ).addClass( value.call(this, j, this.className) ); }); } if ( value && typeof value === "string" ) { classNames = value.split( rspace ); for ( i = 0, l = this.length; i < l; i++ ) { elem = this[ i ]; if ( elem.nodeType === 1 ) { if ( !elem.className && classNames.length === 1 ) { elem.className = value; } else { setClass = " " + elem.className + " "; for ( c = 0, cl = classNames.length; c < cl; c++ ) { if ( !~setClass.indexOf( " " + classNames[ c ] + " " ) ) { setClass += classNames[ c ] + " "; } } elem.className = jQuery.trim( setClass ); } } } } return this; }, removeClass: function( value ) { var classNames, i, l, elem, className, c, cl; if ( jQuery.isFunction( value ) ) { return this.each(function( j ) { jQuery( this ).removeClass( value.call(this, j, this.className) ); }); } if ( (value && typeof value === "string") || value === undefined ) { classNames = ( value || "" ).split( rspace ); for ( i = 0, l = this.length; i < l; i++ ) { elem = this[ i ]; if ( elem.nodeType === 1 && elem.className ) { if ( value ) { className = (" " + elem.className + " ").replace( rclass, " " ); for ( c = 0, cl = classNames.length; c < cl; c++ ) { className = className.replace(" " + classNames[ c ] + " ", " "); } elem.className = jQuery.trim( className ); } else { elem.className = ""; } } } } return this; }, toggleClass: function( value, stateVal ) { var type = typeof value, isBool = typeof stateVal === "boolean"; if ( jQuery.isFunction( value ) ) { return this.each(function( i ) { jQuery( this ).toggleClass( value.call(this, i, this.className, stateVal), stateVal ); }); } return this.each(function() { if ( type === "string" ) { // toggle individual class names var className, i = 0, self = jQuery( this ), state = stateVal, classNames = value.split( rspace ); while ( (className = classNames[ i++ ]) ) { // check each className given, space seperated list state = isBool ? state : !self.hasClass( className ); self[ state ? "addClass" : "removeClass" ]( className ); } } else if ( type === "undefined" || type === "boolean" ) { if ( this.className ) { // store className if set jQuery._data( this, "__className__", this.className ); } // toggle whole className this.className = this.className || value === false ? "" : jQuery._data( this, "__className__" ) || ""; } }); }, hasClass: function( selector ) { var className = " " + selector + " ", i = 0, l = this.length; for ( ; i < l; i++ ) { if ( this[i].nodeType === 1 && (" " + this[i].className + " ").replace(rclass, " ").indexOf( className ) > -1 ) { return true; } } return false; }, val: function( value ) { var hooks, ret, isFunction, elem = this[0]; if ( !arguments.length ) { if ( elem ) { hooks = jQuery.valHooks[ elem.type ] || jQuery.valHooks[ elem.nodeName.toLowerCase() ]; if ( hooks && "get" in hooks && (ret = hooks.get( elem, "value" )) !== undefined ) { return ret; } ret = elem.value; return typeof ret === "string" ? // handle most common string cases ret.replace(rreturn, "") : // handle cases where value is null/undef or number ret == null ? "" : ret; } return; } isFunction = jQuery.isFunction( value ); return this.each(function( i ) { var self = jQuery(this), val; if ( this.nodeType !== 1 ) { return; } if ( isFunction ) { val = value.call( this, i, self.val() ); } else { val = value; } // Treat null/undefined as ""; convert numbers to string if ( val == null ) { val = ""; } else if ( typeof val === "number" ) { val += ""; } else if ( jQuery.isArray( val ) ) { val = jQuery.map(val, function ( value ) { return value == null ? "" : value + ""; }); } hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ]; // If set returns undefined, fall back to normal setting if ( !hooks || !("set" in hooks) || hooks.set( this, val, "value" ) === undefined ) { this.value = val; } }); } }); jQuery.extend({ valHooks: { option: { get: function( elem ) { // attributes.value is undefined in Blackberry 4.7 but // uses .value. See #6932 var val = elem.attributes.value; return !val || val.specified ? elem.value : elem.text; } }, select: { get: function( elem ) { var value, i, max, option, index = elem.selectedIndex, values = [], options = elem.options, one = elem.type === "select-one"; // Nothing was selected if ( index < 0 ) { return null; } // Loop through all the selected options i = one ? index : 0; max = one ? index + 1 : options.length; for ( ; i < max; i++ ) { option = options[ i ]; // Don't return options that are disabled or in a disabled optgroup if ( option.selected && (jQuery.support.optDisabled ? !option.disabled : option.getAttribute("disabled") === null) && (!option.parentNode.disabled || !jQuery.nodeName( option.parentNode, "optgroup" )) ) { // Get the specific value for the option value = jQuery( option ).val(); // We don't need an array for one selects if ( one ) { return value; } // Multi-Selects return an array values.push( value ); } } // Fixes Bug #2551 -- select.val() broken in IE after form.reset() if ( one && !values.length && options.length ) { return jQuery( options[ index ] ).val(); } return values; }, set: function( elem, value ) { var values = jQuery.makeArray( value ); jQuery(elem).find("option").each(function() { this.selected = jQuery.inArray( jQuery(this).val(), values ) >= 0; }); if ( !values.length ) { elem.selectedIndex = -1; } return values; } } }, attrFn: { val: true, css: true, html: true, text: true, data: true, width: true, height: true, offset: true }, attr: function( elem, name, value, pass ) { var ret, hooks, notxml, nType = elem.nodeType; // don't get/set attributes on text, comment and attribute nodes if ( !elem || nType === 3 || nType === 8 || nType === 2 ) { return; } if ( pass && name in jQuery.attrFn ) { return jQuery( elem )[ name ]( value ); } // Fallback to prop when attributes are not supported if ( typeof elem.getAttribute === "undefined" ) { return jQuery.prop( elem, name, value ); } notxml = nType !== 1 || !jQuery.isXMLDoc( elem ); // All attributes are lowercase // Grab necessary hook if one is defined if ( notxml ) { name = name.toLowerCase(); hooks = jQuery.attrHooks[ name ] || ( rboolean.test( name ) ? boolHook : nodeHook ); } if ( value !== undefined ) { if ( value === null ) { jQuery.removeAttr( elem, name ); return; } else if ( hooks && "set" in hooks && notxml && (ret = hooks.set( elem, value, name )) !== undefined ) { return ret; } else { elem.setAttribute( name, "" + value ); return value; } } else if ( hooks && "get" in hooks && notxml && (ret = hooks.get( elem, name )) !== null ) { return ret; } else { ret = elem.getAttribute( name ); // Non-existent attributes return null, we normalize to undefined return ret === null ? undefined : ret; } }, removeAttr: function( elem, value ) { var propName, attrNames, name, l, isBool, i = 0; if ( value && elem.nodeType === 1 ) { attrNames = value.toLowerCase().split( rspace ); l = attrNames.length; for ( ; i < l; i++ ) { name = attrNames[ i ]; if ( name ) { propName = jQuery.propFix[ name ] || name; isBool = rboolean.test( name ); // See #9699 for explanation of this approach (setting first, then removal) // Do not do this for boolean attributes (see #10870) if ( !isBool ) { jQuery.attr( elem, name, "" ); } elem.removeAttribute( getSetAttribute ? name : propName ); // Set corresponding property to false for boolean attributes if ( isBool && propName in elem ) { elem[ propName ] = false; } } } } }, attrHooks: { type: { set: function( elem, value ) { // We can't allow the type property to be changed (since it causes problems in IE) if ( rtype.test( elem.nodeName ) && elem.parentNode ) { jQuery.error( "type property can't be changed" ); } else if ( !jQuery.support.radioValue && value === "radio" && jQuery.nodeName(elem, "input") ) { // Setting the type on a radio button after the value resets the value in IE6-9 // Reset value to it's default in case type is set after value // This is for element creation var val = elem.value; elem.setAttribute( "type", value ); if ( val ) { elem.value = val; } return value; } } }, // Use the value property for back compat // Use the nodeHook for button elements in IE6/7 (#1954) value: { get: function( elem, name ) { if ( nodeHook && jQuery.nodeName( elem, "button" ) ) { return nodeHook.get( elem, name ); } return name in elem ? elem.value : null; }, set: function( elem, value, name ) { if ( nodeHook && jQuery.nodeName( elem, "button" ) ) { return nodeHook.set( elem, value, name ); } // Does not return so that setAttribute is also used elem.value = value; } } }, propFix: { tabindex: "tabIndex", readonly: "readOnly", "for": "htmlFor", "class": "className", maxlength: "maxLength", cellspacing: "cellSpacing", cellpadding: "cellPadding", rowspan: "rowSpan", colspan: "colSpan", usemap: "useMap", frameborder: "frameBorder", contenteditable: "contentEditable" }, prop: function( elem, name, value ) { var ret, hooks, notxml, nType = elem.nodeType; // don't get/set properties on text, comment and attribute nodes if ( !elem || nType === 3 || nType === 8 || nType === 2 ) { return; } notxml = nType !== 1 || !jQuery.isXMLDoc( elem ); if ( notxml ) { // Fix name and attach hooks name = jQuery.propFix[ name ] || name; hooks = jQuery.propHooks[ name ]; } if ( value !== undefined ) { if ( hooks && "set" in hooks && (ret = hooks.set( elem, value, name )) !== undefined ) { return ret; } else { return ( elem[ name ] = value ); } } else { if ( hooks && "get" in hooks && (ret = hooks.get( elem, name )) !== null ) { return ret; } else { return elem[ name ]; } } }, propHooks: { tabIndex: { get: function( elem ) { // elem.tabIndex doesn't always return the correct value when it hasn't been explicitly set // http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/ var attributeNode = elem.getAttributeNode("tabindex"); return attributeNode && attributeNode.specified ? parseInt( attributeNode.value, 10 ) : rfocusable.test( elem.nodeName ) || rclickable.test( elem.nodeName ) && elem.href ? 0 : undefined; } } } }); // Add the tabIndex propHook to attrHooks for back-compat (different case is intentional) jQuery.attrHooks.tabindex = jQuery.propHooks.tabIndex; // Hook for boolean attributes boolHook = { get: function( elem, name ) { // Align boolean attributes with corresponding properties // Fall back to attribute presence where some booleans are not supported var attrNode, property = jQuery.prop( elem, name ); return property === true || typeof property !== "boolean" && ( attrNode = elem.getAttributeNode(name) ) && attrNode.nodeValue !== false ? name.toLowerCase() : undefined; }, set: function( elem, value, name ) { var propName; if ( value === false ) { // Remove boolean attributes when set to false jQuery.removeAttr( elem, name ); } else { // value is true since we know at this point it's type boolean and not false // Set boolean attributes to the same name and set the DOM property propName = jQuery.propFix[ name ] || name; if ( propName in elem ) { // Only set the IDL specifically if it already exists on the element elem[ propName ] = true; } elem.setAttribute( name, name.toLowerCase() ); } return name; } }; // IE6/7 do not support getting/setting some attributes with get/setAttribute if ( !getSetAttribute ) { fixSpecified = { name: true, id: true, coords: true }; // Use this for any attribute in IE6/7 // This fixes almost every IE6/7 issue nodeHook = jQuery.valHooks.button = { get: function( elem, name ) { var ret; ret = elem.getAttributeNode( name ); return ret && ( fixSpecified[ name ] ? ret.nodeValue !== "" : ret.specified ) ? ret.nodeValue : undefined; }, set: function( elem, value, name ) { // Set the existing or create a new attribute node var ret = elem.getAttributeNode( name ); if ( !ret ) { ret = document.createAttribute( name ); elem.setAttributeNode( ret ); } return ( ret.nodeValue = value + "" ); } }; // Apply the nodeHook to tabindex jQuery.attrHooks.tabindex.set = nodeHook.set; // Set width and height to auto instead of 0 on empty string( Bug #8150 ) // This is for removals jQuery.each([ "width", "height" ], function( i, name ) { jQuery.attrHooks[ name ] = jQuery.extend( jQuery.attrHooks[ name ], { set: function( elem, value ) { if ( value === "" ) { elem.setAttribute( name, "auto" ); return value; } } }); }); // Set contenteditable to false on removals(#10429) // Setting to empty string throws an error as an invalid value jQuery.attrHooks.contenteditable = { get: nodeHook.get, set: function( elem, value, name ) { if ( value === "" ) { value = "false"; } nodeHook.set( elem, value, name ); } }; } // Some attributes require a special call on IE if ( !jQuery.support.hrefNormalized ) { jQuery.each([ "href", "src", "width", "height" ], function( i, name ) { jQuery.attrHooks[ name ] = jQuery.extend( jQuery.attrHooks[ name ], { get: function( elem ) { var ret = elem.getAttribute( name, 2 ); return ret === null ? undefined : ret; } }); }); } if ( !jQuery.support.style ) { jQuery.attrHooks.style = { get: function( elem ) { // Return undefined in the case of empty string // Normalize to lowercase since IE uppercases css property names return elem.style.cssText.toLowerCase() || undefined; }, set: function( elem, value ) { return ( elem.style.cssText = "" + value ); } }; } // Safari mis-reports the default selected property of an option // Accessing the parent's selectedIndex property fixes it if ( !jQuery.support.optSelected ) { jQuery.propHooks.selected = jQuery.extend( jQuery.propHooks.selected, { get: function( elem ) { var parent = elem.parentNode; if ( parent ) { parent.selectedIndex; // Make sure that it also works with optgroups, see #5701 if ( parent.parentNode ) { parent.parentNode.selectedIndex; } } return null; } }); } // IE6/7 call enctype encoding if ( !jQuery.support.enctype ) { jQuery.propFix.enctype = "encoding"; } // Radios and checkboxes getter/setter if ( !jQuery.support.checkOn ) { jQuery.each([ "radio", "checkbox" ], function() { jQuery.valHooks[ this ] = { get: function( elem ) { // Handle the case where in Webkit "" is returned instead of "on" if a value isn't specified return elem.getAttribute("value") === null ? "on" : elem.value; } }; }); } jQuery.each([ "radio", "checkbox" ], function() { jQuery.valHooks[ this ] = jQuery.extend( jQuery.valHooks[ this ], { set: function( elem, value ) { if ( jQuery.isArray( value ) ) { return ( elem.checked = jQuery.inArray( jQuery(elem).val(), value ) >= 0 ); } } }); }); var rformElems = /^(?:textarea|input|select)$/i, rtypenamespace = /^([^\.]*)?(?:\.(.+))?$/, rhoverHack = /(?:^|\s)hover(\.\S+)?\b/, rkeyEvent = /^key/, rmouseEvent = /^(?:mouse|contextmenu)|click/, rfocusMorph = /^(?:focusinfocus|focusoutblur)$/, rquickIs = /^(\w*)(?:#([\w\-]+))?(?:\.([\w\-]+))?$/, quickParse = function( selector ) { var quick = rquickIs.exec( selector ); if ( quick ) { // 0 1 2 3 // [ _, tag, id, class ] quick[1] = ( quick[1] || "" ).toLowerCase(); quick[3] = quick[3] && new RegExp( "(?:^|\\s)" + quick[3] + "(?:\\s|$)" ); } return quick; }, quickIs = function( elem, m ) { var attrs = elem.attributes || {}; return ( (!m[1] || elem.nodeName.toLowerCase() === m[1]) && (!m[2] || (attrs.id || {}).value === m[2]) && (!m[3] || m[3].test( (attrs[ "class" ] || {}).value )) ); }, hoverHack = function( events ) { return jQuery.event.special.hover ? events : events.replace( rhoverHack, "mouseenter$1 mouseleave$1" ); }; /* * Helper functions for managing events -- not part of the public interface. * Props to Dean Edwards' addEvent library for many of the ideas. */ jQuery.event = { add: function( elem, types, handler, data, selector ) { var elemData, eventHandle, events, t, tns, type, namespaces, handleObj, handleObjIn, quick, handlers, special; // Don't attach events to noData or text/comment nodes (allow plain objects tho) if ( elem.nodeType === 3 || elem.nodeType === 8 || !types || !handler || !(elemData = jQuery._data( elem )) ) { return; } // Caller can pass in an object of custom data in lieu of the handler if ( handler.handler ) { handleObjIn = handler; handler = handleObjIn.handler; selector = handleObjIn.selector; } // Make sure that the handler has a unique ID, used to find/remove it later if ( !handler.guid ) { handler.guid = jQuery.guid++; } // Init the element's event structure and main handler, if this is the first events = elemData.events; if ( !events ) { elemData.events = events = {}; } eventHandle = elemData.handle; if ( !eventHandle ) { elemData.handle = eventHandle = function( e ) { // Discard the second event of a jQuery.event.trigger() and // when an event is called after a page has unloaded return typeof jQuery !== "undefined" && (!e || jQuery.event.triggered !== e.type) ? jQuery.event.dispatch.apply( eventHandle.elem, arguments ) : undefined; }; // Add elem as a property of the handle fn to prevent a memory leak with IE non-native events eventHandle.elem = elem; } // Handle multiple events separated by a space // jQuery(...).bind("mouseover mouseout", fn); types = jQuery.trim( hoverHack(types) ).split( " " ); for ( t = 0; t < types.length; t++ ) { tns = rtypenamespace.exec( types[t] ) || []; type = tns[1]; namespaces = ( tns[2] || "" ).split( "." ).sort(); // If event changes its type, use the special event handlers for the changed type special = jQuery.event.special[ type ] || {}; // If selector defined, determine special event api type, otherwise given type type = ( selector ? special.delegateType : special.bindType ) || type; // Update special based on newly reset type special = jQuery.event.special[ type ] || {}; // handleObj is passed to all event handlers handleObj = jQuery.extend({ type: type, origType: tns[1], data: data, handler: handler, guid: handler.guid, selector: selector, quick: selector && quickParse( selector ), namespace: namespaces.join(".") }, handleObjIn ); // Init the event handler queue if we're the first handlers = events[ type ]; if ( !handlers ) { handlers = events[ type ] = []; handlers.delegateCount = 0; // Only use addEventListener/attachEvent if the special events handler returns false if ( !special.setup || special.setup.call( elem, data, namespaces, eventHandle ) === false ) { // Bind the global event handler to the element if ( elem.addEventListener ) { elem.addEventListener( type, eventHandle, false ); } else if ( elem.attachEvent ) { elem.attachEvent( "on" + type, eventHandle ); } } } if ( special.add ) { special.add.call( elem, handleObj ); if ( !handleObj.handler.guid ) { handleObj.handler.guid = handler.guid; } } // Add to the element's handler list, delegates in front if ( selector ) { handlers.splice( handlers.delegateCount++, 0, handleObj ); } else { handlers.push( handleObj ); } // Keep track of which events have ever been used, for event optimization jQuery.event.global[ type ] = true; } // Nullify elem to prevent memory leaks in IE elem = null; }, global: {}, // Detach an event or set of events from an element remove: function( elem, types, handler, selector, mappedTypes ) { var elemData = jQuery.hasData( elem ) && jQuery._data( elem ), t, tns, type, origType, namespaces, origCount, j, events, special, handle, eventType, handleObj; if ( !elemData || !(events = elemData.events) ) { return; } // Once for each type.namespace in types; type may be omitted types = jQuery.trim( hoverHack( types || "" ) ).split(" "); for ( t = 0; t < types.length; t++ ) { tns = rtypenamespace.exec( types[t] ) || []; type = origType = tns[1]; namespaces = tns[2]; // Unbind all events (on this namespace, if provided) for the element if ( !type ) { for ( type in events ) { jQuery.event.remove( elem, type + types[ t ], handler, selector, true ); } continue; } special = jQuery.event.special[ type ] || {}; type = ( selector? special.delegateType : special.bindType ) || type; eventType = events[ type ] || []; origCount = eventType.length; namespaces = namespaces ? new RegExp("(^|\\.)" + namespaces.split(".").sort().join("\\.(?:.*\\.)?") + "(\\.|$)") : null; // Remove matching events for ( j = 0; j < eventType.length; j++ ) { handleObj = eventType[ j ]; if ( ( mappedTypes || origType === handleObj.origType ) && ( !handler || handler.guid === handleObj.guid ) && ( !namespaces || namespaces.test( handleObj.namespace ) ) && ( !selector || selector === handleObj.selector || selector === "**" && handleObj.selector ) ) { eventType.splice( j--, 1 ); if ( handleObj.selector ) { eventType.delegateCount--; } if ( special.remove ) { special.remove.call( elem, handleObj ); } } } // Remove generic event handler if we removed something and no more handlers exist // (avoids potential for endless recursion during removal of special event handlers) if ( eventType.length === 0 && origCount !== eventType.length ) { if ( !special.teardown || special.teardown.call( elem, namespaces ) === false ) { jQuery.removeEvent( elem, type, elemData.handle ); } delete events[ type ]; } } // Remove the expando if it's no longer used if ( jQuery.isEmptyObject( events ) ) { handle = elemData.handle; if ( handle ) { handle.elem = null; } // removeData also checks for emptiness and clears the expando if empty // so use it instead of delete jQuery.removeData( elem, [ "events", "handle" ], true ); } }, // Events that are safe to short-circuit if no handlers are attached. // Native DOM events should not be added, they may have inline handlers. customEvent: { "getData": true, "setData": true, "changeData": true }, trigger: function( event, data, elem, onlyHandlers ) { // Don't do events on text and comment nodes if ( elem && (elem.nodeType === 3 || elem.nodeType === 8) ) { return; } // Event object or event type var type = event.type || event, namespaces = [], cache, exclusive, i, cur, old, ontype, special, handle, eventPath, bubbleType; // focus/blur morphs to focusin/out; ensure we're not firing them right now if ( rfocusMorph.test( type + jQuery.event.triggered ) ) { return; } if ( type.indexOf( "!" ) >= 0 ) { // Exclusive events trigger only for the exact event (no namespaces) type = type.slice(0, -1); exclusive = true; } if ( type.indexOf( "." ) >= 0 ) { // Namespaced trigger; create a regexp to match event type in handle() namespaces = type.split("."); type = namespaces.shift(); namespaces.sort(); } if ( (!elem || jQuery.event.customEvent[ type ]) && !jQuery.event.global[ type ] ) { // No jQuery handlers for this event type, and it can't have inline handlers return; } // Caller can pass in an Event, Object, or just an event type string event = typeof event === "object" ? // jQuery.Event object event[ jQuery.expando ] ? event : // Object literal new jQuery.Event( type, event ) : // Just the event type (string) new jQuery.Event( type ); event.type = type; event.isTrigger = true; event.exclusive = exclusive; event.namespace = namespaces.join( "." ); event.namespace_re = event.namespace? new RegExp("(^|\\.)" + namespaces.join("\\.(?:.*\\.)?") + "(\\.|$)") : null; ontype = type.indexOf( ":" ) < 0 ? "on" + type : ""; // Handle a global trigger if ( !elem ) { // TODO: Stop taunting the data cache; remove global events and always attach to document cache = jQuery.cache; for ( i in cache ) { if ( cache[ i ].events && cache[ i ].events[ type ] ) { jQuery.event.trigger( event, data, cache[ i ].handle.elem, true ); } } return; } // Clean up the event in case it is being reused event.result = undefined; if ( !event.target ) { event.target = elem; } // Clone any incoming data and prepend the event, creating the handler arg list data = data != null ? jQuery.makeArray( data ) : []; data.unshift( event ); // Allow special events to draw outside the lines special = jQuery.event.special[ type ] || {}; if ( special.trigger && special.trigger.apply( elem, data ) === false ) { return; } // Determine event propagation path in advance, per W3C events spec (#9951) // Bubble up to document, then to window; watch for a global ownerDocument var (#9724) eventPath = [[ elem, special.bindType || type ]]; if ( !onlyHandlers && !special.noBubble && !jQuery.isWindow( elem ) ) { bubbleType = special.delegateType || type; cur = rfocusMorph.test( bubbleType + type ) ? elem : elem.parentNode; old = null; for ( ; cur; cur = cur.parentNode ) { eventPath.push([ cur, bubbleType ]); old = cur; } // Only add window if we got to document (e.g., not plain obj or detached DOM) if ( old && old === elem.ownerDocument ) { eventPath.push([ old.defaultView || old.parentWindow || window, bubbleType ]); } } // Fire handlers on the event path for ( i = 0; i < eventPath.length && !event.isPropagationStopped(); i++ ) { cur = eventPath[i][0]; event.type = eventPath[i][1]; handle = ( jQuery._data( cur, "events" ) || {} )[ event.type ] && jQuery._data( cur, "handle" ); if ( handle ) { handle.apply( cur, data ); } // Note that this is a bare JS function and not a jQuery handler handle = ontype && cur[ ontype ]; if ( handle && jQuery.acceptData( cur ) && handle.apply( cur, data ) === false ) { event.preventDefault(); } } event.type = type; // If nobody prevented the default action, do it now if ( !onlyHandlers && !event.isDefaultPrevented() ) { if ( (!special._default || special._default.apply( elem.ownerDocument, data ) === false) && !(type === "click" && jQuery.nodeName( elem, "a" )) && jQuery.acceptData( elem ) ) { // Call a native DOM method on the target with the same name name as the event. // Can't use an .isFunction() check here because IE6/7 fails that test. // Don't do default actions on window, that's where global variables be (#6170) // IE<9 dies on focus/blur to hidden element (#1486) if ( ontype && elem[ type ] && ((type !== "focus" && type !== "blur") || event.target.offsetWidth !== 0) && !jQuery.isWindow( elem ) ) { // Don't re-trigger an onFOO event when we call its FOO() method old = elem[ ontype ]; if ( old ) { elem[ ontype ] = null; } // Prevent re-triggering of the same event, since we already bubbled it above jQuery.event.triggered = type; elem[ type ](); jQuery.event.triggered = undefined; if ( old ) { elem[ ontype ] = old; } } } } return event.result; }, dispatch: function( event ) { // Make a writable jQuery.Event from the native event object event = jQuery.event.fix( event || window.event ); var handlers = ( (jQuery._data( this, "events" ) || {} )[ event.type ] || []), delegateCount = handlers.delegateCount, args = [].slice.call( arguments, 0 ), run_all = !event.exclusive && !event.namespace, special = jQuery.event.special[ event.type ] || {}, handlerQueue = [], i, j, cur, jqcur, ret, selMatch, matched, matches, handleObj, sel, related; // Use the fix-ed jQuery.Event rather than the (read-only) native event args[0] = event; event.delegateTarget = this; // Call the preDispatch hook for the mapped type, and let it bail if desired if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) { return; } // Determine handlers that should run if there are delegated events // Avoid non-left-click bubbling in Firefox (#3861) if ( delegateCount && !(event.button && event.type === "click") ) { // Pregenerate a single jQuery object for reuse with .is() jqcur = jQuery(this); jqcur.context = this.ownerDocument || this; for ( cur = event.target; cur != this; cur = cur.parentNode || this ) { // Don't process events on disabled elements (#6911, #8165) if ( cur.disabled !== true ) { selMatch = {}; matches = []; jqcur[0] = cur; for ( i = 0; i < delegateCount; i++ ) { handleObj = handlers[ i ]; sel = handleObj.selector; if ( selMatch[ sel ] === undefined ) { selMatch[ sel ] = ( handleObj.quick ? quickIs( cur, handleObj.quick ) : jqcur.is( sel ) ); } if ( selMatch[ sel ] ) { matches.push( handleObj ); } } if ( matches.length ) { handlerQueue.push({ elem: cur, matches: matches }); } } } } // Add the remaining (directly-bound) handlers if ( handlers.length > delegateCount ) { handlerQueue.push({ elem: this, matches: handlers.slice( delegateCount ) }); } // Run delegates first; they may want to stop propagation beneath us for ( i = 0; i < handlerQueue.length && !event.isPropagationStopped(); i++ ) { matched = handlerQueue[ i ]; event.currentTarget = matched.elem; for ( j = 0; j < matched.matches.length && !event.isImmediatePropagationStopped(); j++ ) { handleObj = matched.matches[ j ]; // Triggered event must either 1) be non-exclusive and have no namespace, or // 2) have namespace(s) a subset or equal to those in the bound event (both can have no namespace). if ( run_all || (!event.namespace && !handleObj.namespace) || event.namespace_re && event.namespace_re.test( handleObj.namespace ) ) { event.data = handleObj.data; event.handleObj = handleObj; ret = ( (jQuery.event.special[ handleObj.origType ] || {}).handle || handleObj.handler ) .apply( matched.elem, args ); if ( ret !== undefined ) { event.result = ret; if ( ret === false ) { event.preventDefault(); event.stopPropagation(); } } } } } // Call the postDispatch hook for the mapped type if ( special.postDispatch ) { special.postDispatch.call( this, event ); } return event.result; }, // Includes some event props shared by KeyEvent and MouseEvent // *** attrChange attrName relatedNode srcElement are not normalized, non-W3C, deprecated, will be removed in 1.8 *** props: "attrChange attrName relatedNode srcElement altKey bubbles cancelable ctrlKey currentTarget eventPhase metaKey relatedTarget shiftKey target timeStamp view which".split(" "), fixHooks: {}, keyHooks: { props: "char charCode key keyCode".split(" "), filter: function( event, original ) { // Add which for key events if ( event.which == null ) { event.which = original.charCode != null ? original.charCode : original.keyCode; } return event; } }, mouseHooks: { props: "button buttons clientX clientY fromElement offsetX offsetY pageX pageY screenX screenY toElement".split(" "), filter: function( event, original ) { var eventDoc, doc, body, button = original.button, fromElement = original.fromElement; // Calculate pageX/Y if missing and clientX/Y available if ( event.pageX == null && original.clientX != null ) { eventDoc = event.target.ownerDocument || document; doc = eventDoc.documentElement; body = eventDoc.body; event.pageX = original.clientX + ( doc && doc.scrollLeft || body && body.scrollLeft || 0 ) - ( doc && doc.clientLeft || body && body.clientLeft || 0 ); event.pageY = original.clientY + ( doc && doc.scrollTop || body && body.scrollTop || 0 ) - ( doc && doc.clientTop || body && body.clientTop || 0 ); } // Add relatedTarget, if necessary if ( !event.relatedTarget && fromElement ) { event.relatedTarget = fromElement === event.target ? original.toElement : fromElement; } // Add which for click: 1 === left; 2 === middle; 3 === right // Note: button is not normalized, so don't use it if ( !event.which && button !== undefined ) { event.which = ( button & 1 ? 1 : ( button & 2 ? 3 : ( button & 4 ? 2 : 0 ) ) ); } return event; } }, fix: function( event ) { if ( event[ jQuery.expando ] ) { return event; } // Create a writable copy of the event object and normalize some properties var i, prop, originalEvent = event, fixHook = jQuery.event.fixHooks[ event.type ] || {}, copy = fixHook.props ? this.props.concat( fixHook.props ) : this.props; event = jQuery.Event( originalEvent ); for ( i = copy.length; i; ) { prop = copy[ --i ]; event[ prop ] = originalEvent[ prop ]; } // Fix target property, if necessary (#1925, IE 6/7/8 & Safari2) if ( !event.target ) { event.target = originalEvent.srcElement || document; } // Target should not be a text node (#504, Safari) if ( event.target.nodeType === 3 ) { event.target = event.target.parentNode; } // For mouse/key events; add metaKey if it's not there (#3368, IE6/7/8) if ( event.metaKey === undefined ) { event.metaKey = event.ctrlKey; } return fixHook.filter? fixHook.filter( event, originalEvent ) : event; }, special: { ready: { // Make sure the ready event is setup setup: jQuery.bindReady }, load: { // Prevent triggered image.load events from bubbling to window.load noBubble: true }, focus: { delegateType: "focusin" }, blur: { delegateType: "focusout" }, beforeunload: { setup: function( data, namespaces, eventHandle ) { // We only want to do this special case on windows if ( jQuery.isWindow( this ) ) { this.onbeforeunload = eventHandle; } }, teardown: function( namespaces, eventHandle ) { if ( this.onbeforeunload === eventHandle ) { this.onbeforeunload = null; } } } }, simulate: function( type, elem, event, bubble ) { // Piggyback on a donor event to simulate a different one. // Fake originalEvent to avoid donor's stopPropagation, but if the // simulated event prevents default then we do the same on the donor. var e = jQuery.extend( new jQuery.Event(), event, { type: type, isSimulated: true, originalEvent: {} } ); if ( bubble ) { jQuery.event.trigger( e, null, elem ); } else { jQuery.event.dispatch.call( elem, e ); } if ( e.isDefaultPrevented() ) { event.preventDefault(); } } }; // Some plugins are using, but it's undocumented/deprecated and will be removed. // The 1.7 special event interface should provide all the hooks needed now. jQuery.event.handle = jQuery.event.dispatch; jQuery.removeEvent = document.removeEventListener ? function( elem, type, handle ) { if ( elem.removeEventListener ) { elem.removeEventListener( type, handle, false ); } } : function( elem, type, handle ) { if ( elem.detachEvent ) { elem.detachEvent( "on" + type, handle ); } }; jQuery.Event = function( src, props ) { // Allow instantiation without the 'new' keyword if ( !(this instanceof jQuery.Event) ) { return new jQuery.Event( src, props ); } // Event object if ( src && src.type ) { this.originalEvent = src; this.type = src.type; // Events bubbling up the document may have been marked as prevented // by a handler lower down the tree; reflect the correct value. this.isDefaultPrevented = ( src.defaultPrevented || src.returnValue === false || src.getPreventDefault && src.getPreventDefault() ) ? returnTrue : returnFalse; // Event type } else { this.type = src; } // Put explicitly provided properties onto the event object if ( props ) { jQuery.extend( this, props ); } // Create a timestamp if incoming event doesn't have one this.timeStamp = src && src.timeStamp || jQuery.now(); // Mark it as fixed this[ jQuery.expando ] = true; }; function returnFalse() { return false; } function returnTrue() { return true; } // jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding // http://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html jQuery.Event.prototype = { preventDefault: function() { this.isDefaultPrevented = returnTrue; var e = this.originalEvent; if ( !e ) { return; } // if preventDefault exists run it on the original event if ( e.preventDefault ) { e.preventDefault(); // otherwise set the returnValue property of the original event to false (IE) } else { e.returnValue = false; } }, stopPropagation: function() { this.isPropagationStopped = returnTrue; var e = this.originalEvent; if ( !e ) { return; } // if stopPropagation exists run it on the original event if ( e.stopPropagation ) { e.stopPropagation(); } // otherwise set the cancelBubble property of the original event to true (IE) e.cancelBubble = true; }, stopImmediatePropagation: function() { this.isImmediatePropagationStopped = returnTrue; this.stopPropagation(); }, isDefaultPrevented: returnFalse, isPropagationStopped: returnFalse, isImmediatePropagationStopped: returnFalse }; // Create mouseenter/leave events using mouseover/out and event-time checks jQuery.each({ mouseenter: "mouseover", mouseleave: "mouseout" }, function( orig, fix ) { jQuery.event.special[ orig ] = { delegateType: fix, bindType: fix, handle: function( event ) { var target = this, related = event.relatedTarget, handleObj = event.handleObj, selector = handleObj.selector, ret; // For mousenter/leave call the handler if related is outside the target. // NB: No relatedTarget if the mouse left/entered the browser window if ( !related || (related !== target && !jQuery.contains( target, related )) ) { event.type = handleObj.origType; ret = handleObj.handler.apply( this, arguments ); event.type = fix; } return ret; } }; }); // IE submit delegation if ( !jQuery.support.submitBubbles ) { jQuery.event.special.submit = { setup: function() { // Only need this for delegated form submit events if ( jQuery.nodeName( this, "form" ) ) { return false; } // Lazy-add a submit handler when a descendant form may potentially be submitted jQuery.event.add( this, "click._submit keypress._submit", function( e ) { // Node name check avoids a VML-related crash in IE (#9807) var elem = e.target, form = jQuery.nodeName( elem, "input" ) || jQuery.nodeName( elem, "button" ) ? elem.form : undefined; if ( form && !form._submit_attached ) { jQuery.event.add( form, "submit._submit", function( event ) { event._submit_bubble = true; }); form._submit_attached = true; } }); // return undefined since we don't need an event listener }, postDispatch: function( event ) { // If form was submitted by the user, bubble the event up the tree if ( event._submit_bubble ) { delete event._submit_bubble; if ( this.parentNode && !event.isTrigger ) { jQuery.event.simulate( "submit", this.parentNode, event, true ); } } }, teardown: function() { // Only need this for delegated form submit events if ( jQuery.nodeName( this, "form" ) ) { return false; } // Remove delegated handlers; cleanData eventually reaps submit handlers attached above jQuery.event.remove( this, "._submit" ); } }; } // IE change delegation and checkbox/radio fix if ( !jQuery.support.changeBubbles ) { jQuery.event.special.change = { setup: function() { if ( rformElems.test( this.nodeName ) ) { // IE doesn't fire change on a check/radio until blur; trigger it on click // after a propertychange. Eat the blur-change in special.change.handle. // This still fires onchange a second time for check/radio after blur. if ( this.type === "checkbox" || this.type === "radio" ) { jQuery.event.add( this, "propertychange._change", function( event ) { if ( event.originalEvent.propertyName === "checked" ) { this._just_changed = true; } }); jQuery.event.add( this, "click._change", function( event ) { if ( this._just_changed && !event.isTrigger ) { this._just_changed = false; jQuery.event.simulate( "change", this, event, true ); } }); } return false; } // Delegated event; lazy-add a change handler on descendant inputs jQuery.event.add( this, "beforeactivate._change", function( e ) { var elem = e.target; if ( rformElems.test( elem.nodeName ) && !elem._change_attached ) { jQuery.event.add( elem, "change._change", function( event ) { if ( this.parentNode && !event.isSimulated && !event.isTrigger ) { jQuery.event.simulate( "change", this.parentNode, event, true ); } }); elem._change_attached = true; } }); }, handle: function( event ) { var elem = event.target; // Swallow native change events from checkbox/radio, we already triggered them above if ( this !== elem || event.isSimulated || event.isTrigger || (elem.type !== "radio" && elem.type !== "checkbox") ) { return event.handleObj.handler.apply( this, arguments ); } }, teardown: function() { jQuery.event.remove( this, "._change" ); return rformElems.test( this.nodeName ); } }; } // Create "bubbling" focus and blur events if ( !jQuery.support.focusinBubbles ) { jQuery.each({ focus: "focusin", blur: "focusout" }, function( orig, fix ) { // Attach a single capturing handler while someone wants focusin/focusout var attaches = 0, handler = function( event ) { jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ), true ); }; jQuery.event.special[ fix ] = { setup: function() { if ( attaches++ === 0 ) { document.addEventListener( orig, handler, true ); } }, teardown: function() { if ( --attaches === 0 ) { document.removeEventListener( orig, handler, true ); } } }; }); } jQuery.fn.extend({ on: function( types, selector, data, fn, /*INTERNAL*/ one ) { var origFn, type; // Types can be a map of types/handlers if ( typeof types === "object" ) { // ( types-Object, selector, data ) if ( typeof selector !== "string" ) { // && selector != null // ( types-Object, data ) data = data || selector; selector = undefined; } for ( type in types ) { this.on( type, selector, data, types[ type ], one ); } return this; } if ( data == null && fn == null ) { // ( types, fn ) fn = selector; data = selector = undefined; } else if ( fn == null ) { if ( typeof selector === "string" ) { // ( types, selector, fn ) fn = data; data = undefined; } else { // ( types, data, fn ) fn = data; data = selector; selector = undefined; } } if ( fn === false ) { fn = returnFalse; } else if ( !fn ) { return this; } if ( one === 1 ) { origFn = fn; fn = function( event ) { // Can use an empty set, since event contains the info jQuery().off( event ); return origFn.apply( this, arguments ); }; // Use same guid so caller can remove using origFn fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ ); } return this.each( function() { jQuery.event.add( this, types, fn, data, selector ); }); }, one: function( types, selector, data, fn ) { return this.on( types, selector, data, fn, 1 ); }, off: function( types, selector, fn ) { if ( types && types.preventDefault && types.handleObj ) { // ( event ) dispatched jQuery.Event var handleObj = types.handleObj; jQuery( types.delegateTarget ).off( handleObj.namespace ? handleObj.origType + "." + handleObj.namespace : handleObj.origType, handleObj.selector, handleObj.handler ); return this; } if ( typeof types === "object" ) { // ( types-object [, selector] ) for ( var type in types ) { this.off( type, selector, types[ type ] ); } return this; } if ( selector === false || typeof selector === "function" ) { // ( types [, fn] ) fn = selector; selector = undefined; } if ( fn === false ) { fn = returnFalse; } return this.each(function() { jQuery.event.remove( this, types, fn, selector ); }); }, bind: function( types, data, fn ) { return this.on( types, null, data, fn ); }, unbind: function( types, fn ) { return this.off( types, null, fn ); }, live: function( types, data, fn ) { jQuery( this.context ).on( types, this.selector, data, fn ); return this; }, die: function( types, fn ) { jQuery( this.context ).off( types, this.selector || "**", fn ); return this; }, delegate: function( selector, types, data, fn ) { return this.on( types, selector, data, fn ); }, undelegate: function( selector, types, fn ) { // ( namespace ) or ( selector, types [, fn] ) return arguments.length == 1? this.off( selector, "**" ) : this.off( types, selector, fn ); }, trigger: function( type, data ) { return this.each(function() { jQuery.event.trigger( type, data, this ); }); }, triggerHandler: function( type, data ) { if ( this[0] ) { return jQuery.event.trigger( type, data, this[0], true ); } }, toggle: function( fn ) { // Save reference to arguments for access in closure var args = arguments, guid = fn.guid || jQuery.guid++, i = 0, toggler = function( event ) { // Figure out which function to execute var lastToggle = ( jQuery._data( this, "lastToggle" + fn.guid ) || 0 ) % i; jQuery._data( this, "lastToggle" + fn.guid, lastToggle + 1 ); // Make sure that clicks stop event.preventDefault(); // and execute the function return args[ lastToggle ].apply( this, arguments ) || false; }; // link all the functions, so any of them can unbind this click handler toggler.guid = guid; while ( i < args.length ) { args[ i++ ].guid = guid; } return this.click( toggler ); }, hover: function( fnOver, fnOut ) { return this.mouseenter( fnOver ).mouseleave( fnOut || fnOver ); } }); jQuery.each( ("blur focus focusin focusout load resize scroll unload click dblclick " + "mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave " + "change select submit keydown keypress keyup error contextmenu").split(" "), function( i, name ) { // Handle event binding jQuery.fn[ name ] = function( data, fn ) { if ( fn == null ) { fn = data; data = null; } return arguments.length > 0 ? this.on( name, null, data, fn ) : this.trigger( name ); }; if ( jQuery.attrFn ) { jQuery.attrFn[ name ] = true; } if ( rkeyEvent.test( name ) ) { jQuery.event.fixHooks[ name ] = jQuery.event.keyHooks; } if ( rmouseEvent.test( name ) ) { jQuery.event.fixHooks[ name ] = jQuery.event.mouseHooks; } }); /*! * Sizzle CSS Selector Engine * Copyright 2011, The Dojo Foundation * Released under the MIT, BSD, and GPL Licenses. * More information: http://sizzlejs.com/ */ (function(){ var chunker = /((?:\((?:\([^()]+\)|[^()]+)+\)|\[(?:\[[^\[\]]*\]|['"][^'"]*['"]|[^\[\]'"]+)+\]|\\.|[^ >+~,(\[\\]+)+|[>+~])(\s*,\s*)?((?:.|\r|\n)*)/g, expando = "sizcache" + (Math.random() + '').replace('.', ''), done = 0, toString = Object.prototype.toString, hasDuplicate = false, baseHasDuplicate = true, rBackslash = /\\/g, rReturn = /\r\n/g, rNonWord = /\W/; // Here we check if the JavaScript engine is using some sort of // optimization where it does not always call our comparision // function. If that is the case, discard the hasDuplicate value. // Thus far that includes Google Chrome. [0, 0].sort(function() { baseHasDuplicate = false; return 0; }); var Sizzle = function( selector, context, results, seed ) { results = results || []; context = context || document; var origContext = context; if ( context.nodeType !== 1 && context.nodeType !== 9 ) { return []; } if ( !selector || typeof selector !== "string" ) { return results; } var m, set, checkSet, extra, ret, cur, pop, i, prune = true, contextXML = Sizzle.isXML( context ), parts = [], soFar = selector; // Reset the position of the chunker regexp (start from head) do { chunker.exec( "" ); m = chunker.exec( soFar ); if ( m ) { soFar = m[3]; parts.push( m[1] ); if ( m[2] ) { extra = m[3]; break; } } } while ( m ); if ( parts.length > 1 && origPOS.exec( selector ) ) { if ( parts.length === 2 && Expr.relative[ parts[0] ] ) { set = posProcess( parts[0] + parts[1], context, seed ); } else { set = Expr.relative[ parts[0] ] ? [ context ] : Sizzle( parts.shift(), context ); while ( parts.length ) { selector = parts.shift(); if ( Expr.relative[ selector ] ) { selector += parts.shift(); } set = posProcess( selector, set, seed ); } } } else { // Take a shortcut and set the context if the root selector is an ID // (but not if it'll be faster if the inner selector is an ID) if ( !seed && parts.length > 1 && context.nodeType === 9 && !contextXML && Expr.match.ID.test(parts[0]) && !Expr.match.ID.test(parts[parts.length - 1]) ) { ret = Sizzle.find( parts.shift(), context, contextXML ); context = ret.expr ? Sizzle.filter( ret.expr, ret.set )[0] : ret.set[0]; } if ( context ) { ret = seed ? { expr: parts.pop(), set: makeArray(seed) } : Sizzle.find( parts.pop(), parts.length === 1 && (parts[0] === "~" || parts[0] === "+") && context.parentNode ? context.parentNode : context, contextXML ); set = ret.expr ? Sizzle.filter( ret.expr, ret.set ) : ret.set; if ( parts.length > 0 ) { checkSet = makeArray( set ); } else { prune = false; } while ( parts.length ) { cur = parts.pop(); pop = cur; if ( !Expr.relative[ cur ] ) { cur = ""; } else { pop = parts.pop(); } if ( pop == null ) { pop = context; } Expr.relative[ cur ]( checkSet, pop, contextXML ); } } else { checkSet = parts = []; } } if ( !checkSet ) { checkSet = set; } if ( !checkSet ) { Sizzle.error( cur || selector ); } if ( toString.call(checkSet) === "[object Array]" ) { if ( !prune ) { results.push.apply( results, checkSet ); } else if ( context && context.nodeType === 1 ) { for ( i = 0; checkSet[i] != null; i++ ) { if ( checkSet[i] && (checkSet[i] === true || checkSet[i].nodeType === 1 && Sizzle.contains(context, checkSet[i])) ) { results.push( set[i] ); } } } else { for ( i = 0; checkSet[i] != null; i++ ) { if ( checkSet[i] && checkSet[i].nodeType === 1 ) { results.push( set[i] ); } } } } else { makeArray( checkSet, results ); } if ( extra ) { Sizzle( extra, origContext, results, seed ); Sizzle.uniqueSort( results ); } return results; }; Sizzle.uniqueSort = function( results ) { if ( sortOrder ) { hasDuplicate = baseHasDuplicate; results.sort( sortOrder ); if ( hasDuplicate ) { for ( var i = 1; i < results.length; i++ ) { if ( results[i] === results[ i - 1 ] ) { results.splice( i--, 1 ); } } } } return results; }; Sizzle.matches = function( expr, set ) { return Sizzle( expr, null, null, set ); }; Sizzle.matchesSelector = function( node, expr ) { return Sizzle( expr, null, null, [node] ).length > 0; }; Sizzle.find = function( expr, context, isXML ) { var set, i, len, match, type, left; if ( !expr ) { return []; } for ( i = 0, len = Expr.order.length; i < len; i++ ) { type = Expr.order[i]; if ( (match = Expr.leftMatch[ type ].exec( expr )) ) { left = match[1]; match.splice( 1, 1 ); if ( left.substr( left.length - 1 ) !== "\\" ) { match[1] = (match[1] || "").replace( rBackslash, "" ); set = Expr.find[ type ]( match, context, isXML ); if ( set != null ) { expr = expr.replace( Expr.match[ type ], "" ); break; } } } } if ( !set ) { set = typeof context.getElementsByTagName !== "undefined" ? context.getElementsByTagName( "*" ) : []; } return { set: set, expr: expr }; }; Sizzle.filter = function( expr, set, inplace, not ) { var match, anyFound, type, found, item, filter, left, i, pass, old = expr, result = [], curLoop = set, isXMLFilter = set && set[0] && Sizzle.isXML( set[0] ); while ( expr && set.length ) { for ( type in Expr.filter ) { if ( (match = Expr.leftMatch[ type ].exec( expr )) != null && match[2] ) { filter = Expr.filter[ type ]; left = match[1]; anyFound = false; match.splice(1,1); if ( left.substr( left.length - 1 ) === "\\" ) { continue; } if ( curLoop === result ) { result = []; } if ( Expr.preFilter[ type ] ) { match = Expr.preFilter[ type ]( match, curLoop, inplace, result, not, isXMLFilter ); if ( !match ) { anyFound = found = true; } else if ( match === true ) { continue; } } if ( match ) { for ( i = 0; (item = curLoop[i]) != null; i++ ) { if ( item ) { found = filter( item, match, i, curLoop ); pass = not ^ found; if ( inplace && found != null ) { if ( pass ) { anyFound = true; } else { curLoop[i] = false; } } else if ( pass ) { result.push( item ); anyFound = true; } } } } if ( found !== undefined ) { if ( !inplace ) { curLoop = result; } expr = expr.replace( Expr.match[ type ], "" ); if ( !anyFound ) { return []; } break; } } } // Improper expression if ( expr === old ) { if ( anyFound == null ) { Sizzle.error( expr ); } else { break; } } old = expr; } return curLoop; }; Sizzle.error = function( msg ) { throw new Error( "Syntax error, unrecognized expression: " + msg ); }; /** * Utility function for retreiving the text value of an array of DOM nodes * @param {Array|Element} elem */ var getText = Sizzle.getText = function( elem ) { var i, node, nodeType = elem.nodeType, ret = ""; if ( nodeType ) { if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) { // Use textContent || innerText for elements if ( typeof elem.textContent === 'string' ) { return elem.textContent; } else if ( typeof elem.innerText === 'string' ) { // Replace IE's carriage returns return elem.innerText.replace( rReturn, '' ); } else { // Traverse it's children for ( elem = elem.firstChild; elem; elem = elem.nextSibling) { ret += getText( elem ); } } } else if ( nodeType === 3 || nodeType === 4 ) { return elem.nodeValue; } } else { // If no nodeType, this is expected to be an array for ( i = 0; (node = elem[i]); i++ ) { // Do not traverse comment nodes if ( node.nodeType !== 8 ) { ret += getText( node ); } } } return ret; }; var Expr = Sizzle.selectors = { order: [ "ID", "NAME", "TAG" ], match: { ID: /#((?:[\w\u00c0-\uFFFF\-]|\\.)+)/, CLASS: /\.((?:[\w\u00c0-\uFFFF\-]|\\.)+)/, NAME: /\[name=['"]*((?:[\w\u00c0-\uFFFF\-]|\\.)+)['"]*\]/, ATTR: /\[\s*((?:[\w\u00c0-\uFFFF\-]|\\.)+)\s*(?:(\S?=)\s*(?:(['"])(.*?)\3|(#?(?:[\w\u00c0-\uFFFF\-]|\\.)*)|)|)\s*\]/, TAG: /^((?:[\w\u00c0-\uFFFF\*\-]|\\.)+)/, CHILD: /:(only|nth|last|first)-child(?:\(\s*(even|odd|(?:[+\-]?\d+|(?:[+\-]?\d*)?n\s*(?:[+\-]\s*\d+)?))\s*\))?/, POS: /:(nth|eq|gt|lt|first|last|even|odd)(?:\((\d*)\))?(?=[^\-]|$)/, PSEUDO: /:((?:[\w\u00c0-\uFFFF\-]|\\.)+)(?:\((['"]?)((?:\([^\)]+\)|[^\(\)]*)+)\2\))?/ }, leftMatch: {}, attrMap: { "class": "className", "for": "htmlFor" }, attrHandle: { href: function( elem ) { return elem.getAttribute( "href" ); }, type: function( elem ) { return elem.getAttribute( "type" ); } }, relative: { "+": function(checkSet, part){ var isPartStr = typeof part === "string", isTag = isPartStr && !rNonWord.test( part ), isPartStrNotTag = isPartStr && !isTag; if ( isTag ) { part = part.toLowerCase(); } for ( var i = 0, l = checkSet.length, elem; i < l; i++ ) { if ( (elem = checkSet[i]) ) { while ( (elem = elem.previousSibling) && elem.nodeType !== 1 ) {} checkSet[i] = isPartStrNotTag || elem && elem.nodeName.toLowerCase() === part ? elem || false : elem === part; } } if ( isPartStrNotTag ) { Sizzle.filter( part, checkSet, true ); } }, ">": function( checkSet, part ) { var elem, isPartStr = typeof part === "string", i = 0, l = checkSet.length; if ( isPartStr && !rNonWord.test( part ) ) { part = part.toLowerCase(); for ( ; i < l; i++ ) { elem = checkSet[i]; if ( elem ) { var parent = elem.parentNode; checkSet[i] = parent.nodeName.toLowerCase() === part ? parent : false; } } } else { for ( ; i < l; i++ ) { elem = checkSet[i]; if ( elem ) { checkSet[i] = isPartStr ? elem.parentNode : elem.parentNode === part; } } if ( isPartStr ) { Sizzle.filter( part, checkSet, true ); } } }, "": function(checkSet, part, isXML){ var nodeCheck, doneName = done++, checkFn = dirCheck; if ( typeof part === "string" && !rNonWord.test( part ) ) { part = part.toLowerCase(); nodeCheck = part; checkFn = dirNodeCheck; } checkFn( "parentNode", part, doneName, checkSet, nodeCheck, isXML ); }, "~": function( checkSet, part, isXML ) { var nodeCheck, doneName = done++, checkFn = dirCheck; if ( typeof part === "string" && !rNonWord.test( part ) ) { part = part.toLowerCase(); nodeCheck = part; checkFn = dirNodeCheck; } checkFn( "previousSibling", part, doneName, checkSet, nodeCheck, isXML ); } }, find: { ID: function( match, context, isXML ) { if ( typeof context.getElementById !== "undefined" && !isXML ) { var m = context.getElementById(match[1]); // Check parentNode to catch when Blackberry 4.6 returns // nodes that are no longer in the document #6963 return m && m.parentNode ? [m] : []; } }, NAME: function( match, context ) { if ( typeof context.getElementsByName !== "undefined" ) { var ret = [], results = context.getElementsByName( match[1] ); for ( var i = 0, l = results.length; i < l; i++ ) { if ( results[i].getAttribute("name") === match[1] ) { ret.push( results[i] ); } } return ret.length === 0 ? null : ret; } }, TAG: function( match, context ) { if ( typeof context.getElementsByTagName !== "undefined" ) { return context.getElementsByTagName( match[1] ); } } }, preFilter: { CLASS: function( match, curLoop, inplace, result, not, isXML ) { match = " " + match[1].replace( rBackslash, "" ) + " "; if ( isXML ) { return match; } for ( var i = 0, elem; (elem = curLoop[i]) != null; i++ ) { if ( elem ) { if ( not ^ (elem.className && (" " + elem.className + " ").replace(/[\t\n\r]/g, " ").indexOf(match) >= 0) ) { if ( !inplace ) { result.push( elem ); } } else if ( inplace ) { curLoop[i] = false; } } } return false; }, ID: function( match ) { return match[1].replace( rBackslash, "" ); }, TAG: function( match, curLoop ) { return match[1].replace( rBackslash, "" ).toLowerCase(); }, CHILD: function( match ) { if ( match[1] === "nth" ) { if ( !match[2] ) { Sizzle.error( match[0] ); } match[2] = match[2].replace(/^\+|\s*/g, ''); // parse equations like 'even', 'odd', '5', '2n', '3n+2', '4n-1', '-n+6' var test = /(-?)(\d*)(?:n([+\-]?\d*))?/.exec( match[2] === "even" && "2n" || match[2] === "odd" && "2n+1" || !/\D/.test( match[2] ) && "0n+" + match[2] || match[2]); // calculate the numbers (first)n+(last) including if they are negative match[2] = (test[1] + (test[2] || 1)) - 0; match[3] = test[3] - 0; } else if ( match[2] ) { Sizzle.error( match[0] ); } // TODO: Move to normal caching system match[0] = done++; return match; }, ATTR: function( match, curLoop, inplace, result, not, isXML ) { var name = match[1] = match[1].replace( rBackslash, "" ); if ( !isXML && Expr.attrMap[name] ) { match[1] = Expr.attrMap[name]; } // Handle if an un-quoted value was used match[4] = ( match[4] || match[5] || "" ).replace( rBackslash, "" ); if ( match[2] === "~=" ) { match[4] = " " + match[4] + " "; } return match; }, PSEUDO: function( match, curLoop, inplace, result, not ) { if ( match[1] === "not" ) { // If we're dealing with a complex expression, or a simple one if ( ( chunker.exec(match[3]) || "" ).length > 1 || /^\w/.test(match[3]) ) { match[3] = Sizzle(match[3], null, null, curLoop); } else { var ret = Sizzle.filter(match[3], curLoop, inplace, true ^ not); if ( !inplace ) { result.push.apply( result, ret ); } return false; } } else if ( Expr.match.POS.test( match[0] ) || Expr.match.CHILD.test( match[0] ) ) { return true; } return match; }, POS: function( match ) { match.unshift( true ); return match; } }, filters: { enabled: function( elem ) { return elem.disabled === false && elem.type !== "hidden"; }, disabled: function( elem ) { return elem.disabled === true; }, checked: function( elem ) { return elem.checked === true; }, selected: function( elem ) { // Accessing this property makes selected-by-default // options in Safari work properly if ( elem.parentNode ) { elem.parentNode.selectedIndex; } return elem.selected === true; }, parent: function( elem ) { return !!elem.firstChild; }, empty: function( elem ) { return !elem.firstChild; }, has: function( elem, i, match ) { return !!Sizzle( match[3], elem ).length; }, header: function( elem ) { return (/h\d/i).test( elem.nodeName ); }, text: function( elem ) { var attr = elem.getAttribute( "type" ), type = elem.type; // IE6 and 7 will map elem.type to 'text' for new HTML5 types (search, etc) // use getAttribute instead to test this case return elem.nodeName.toLowerCase() === "input" && "text" === type && ( attr === type || attr === null ); }, radio: function( elem ) { return elem.nodeName.toLowerCase() === "input" && "radio" === elem.type; }, checkbox: function( elem ) { return elem.nodeName.toLowerCase() === "input" && "checkbox" === elem.type; }, file: function( elem ) { return elem.nodeName.toLowerCase() === "input" && "file" === elem.type; }, password: function( elem ) { return elem.nodeName.toLowerCase() === "input" && "password" === elem.type; }, submit: function( elem ) { var name = elem.nodeName.toLowerCase(); return (name === "input" || name === "button") && "submit" === elem.type; }, image: function( elem ) { return elem.nodeName.toLowerCase() === "input" && "image" === elem.type; }, reset: function( elem ) { var name = elem.nodeName.toLowerCase(); return (name === "input" || name === "button") && "reset" === elem.type; }, button: function( elem ) { var name = elem.nodeName.toLowerCase(); return name === "input" && "button" === elem.type || name === "button"; }, input: function( elem ) { return (/input|select|textarea|button/i).test( elem.nodeName ); }, focus: function( elem ) { return elem === elem.ownerDocument.activeElement; } }, setFilters: { first: function( elem, i ) { return i === 0; }, last: function( elem, i, match, array ) { return i === array.length - 1; }, even: function( elem, i ) { return i % 2 === 0; }, odd: function( elem, i ) { return i % 2 === 1; }, lt: function( elem, i, match ) { return i < match[3] - 0; }, gt: function( elem, i, match ) { return i > match[3] - 0; }, nth: function( elem, i, match ) { return match[3] - 0 === i; }, eq: function( elem, i, match ) { return match[3] - 0 === i; } }, filter: { PSEUDO: function( elem, match, i, array ) { var name = match[1], filter = Expr.filters[ name ]; if ( filter ) { return filter( elem, i, match, array ); } else if ( name === "contains" ) { return (elem.textContent || elem.innerText || getText([ elem ]) || "").indexOf(match[3]) >= 0; } else if ( name === "not" ) { var not = match[3]; for ( var j = 0, l = not.length; j < l; j++ ) { if ( not[j] === elem ) { return false; } } return true; } else { Sizzle.error( name ); } }, CHILD: function( elem, match ) { var first, last, doneName, parent, cache, count, diff, type = match[1], node = elem; switch ( type ) { case "only": case "first": while ( (node = node.previousSibling) ) { if ( node.nodeType === 1 ) { return false; } } if ( type === "first" ) { return true; } node = elem; /* falls through */ case "last": while ( (node = node.nextSibling) ) { if ( node.nodeType === 1 ) { return false; } } return true; case "nth": first = match[2]; last = match[3]; if ( first === 1 && last === 0 ) { return true; } doneName = match[0]; parent = elem.parentNode; if ( parent && (parent[ expando ] !== doneName || !elem.nodeIndex) ) { count = 0; for ( node = parent.firstChild; node; node = node.nextSibling ) { if ( node.nodeType === 1 ) { node.nodeIndex = ++count; } } parent[ expando ] = doneName; } diff = elem.nodeIndex - last; if ( first === 0 ) { return diff === 0; } else { return ( diff % first === 0 && diff / first >= 0 ); } } }, ID: function( elem, match ) { return elem.nodeType === 1 && elem.getAttribute("id") === match; }, TAG: function( elem, match ) { return (match === "*" && elem.nodeType === 1) || !!elem.nodeName && elem.nodeName.toLowerCase() === match; }, CLASS: function( elem, match ) { return (" " + (elem.className || elem.getAttribute("class")) + " ") .indexOf( match ) > -1; }, ATTR: function( elem, match ) { var name = match[1], result = Sizzle.attr ? Sizzle.attr( elem, name ) : Expr.attrHandle[ name ] ? Expr.attrHandle[ name ]( elem ) : elem[ name ] != null ? elem[ name ] : elem.getAttribute( name ), value = result + "", type = match[2], check = match[4]; return result == null ? type === "!=" : !type && Sizzle.attr ? result != null : type === "=" ? value === check : type === "*=" ? value.indexOf(check) >= 0 : type === "~=" ? (" " + value + " ").indexOf(check) >= 0 : !check ? value && result !== false : type === "!=" ? value !== check : type === "^=" ? value.indexOf(check) === 0 : type === "$=" ? value.substr(value.length - check.length) === check : type === "|=" ? value === check || value.substr(0, check.length + 1) === check + "-" : false; }, POS: function( elem, match, i, array ) { var name = match[2], filter = Expr.setFilters[ name ]; if ( filter ) { return filter( elem, i, match, array ); } } } }; var origPOS = Expr.match.POS, fescape = function(all, num){ return "\\" + (num - 0 + 1); }; for ( var type in Expr.match ) { Expr.match[ type ] = new RegExp( Expr.match[ type ].source + (/(?![^\[]*\])(?![^\(]*\))/.source) ); Expr.leftMatch[ type ] = new RegExp( /(^(?:.|\r|\n)*?)/.source + Expr.match[ type ].source.replace(/\\(\d+)/g, fescape) ); } // Expose origPOS // "global" as in regardless of relation to brackets/parens Expr.match.globalPOS = origPOS; var makeArray = function( array, results ) { array = Array.prototype.slice.call( array, 0 ); if ( results ) { results.push.apply( results, array ); return results; } return array; }; // Perform a simple check to determine if the browser is capable of // converting a NodeList to an array using builtin methods. // Also verifies that the returned array holds DOM nodes // (which is not the case in the Blackberry browser) try { Array.prototype.slice.call( document.documentElement.childNodes, 0 )[0].nodeType; // Provide a fallback method if it does not work } catch( e ) { makeArray = function( array, results ) { var i = 0, ret = results || []; if ( toString.call(array) === "[object Array]" ) { Array.prototype.push.apply( ret, array ); } else { if ( typeof array.length === "number" ) { for ( var l = array.length; i < l; i++ ) { ret.push( array[i] ); } } else { for ( ; array[i]; i++ ) { ret.push( array[i] ); } } } return ret; }; } var sortOrder, siblingCheck; if ( document.documentElement.compareDocumentPosition ) { sortOrder = function( a, b ) { if ( a === b ) { hasDuplicate = true; return 0; } if ( !a.compareDocumentPosition || !b.compareDocumentPosition ) { return a.compareDocumentPosition ? -1 : 1; } return a.compareDocumentPosition(b) & 4 ? -1 : 1; }; } else { sortOrder = function( a, b ) { // The nodes are identical, we can exit early if ( a === b ) { hasDuplicate = true; return 0; // Fallback to using sourceIndex (in IE) if it's available on both nodes } else if ( a.sourceIndex && b.sourceIndex ) { return a.sourceIndex - b.sourceIndex; } var al, bl, ap = [], bp = [], aup = a.parentNode, bup = b.parentNode, cur = aup; // If the nodes are siblings (or identical) we can do a quick check if ( aup === bup ) { return siblingCheck( a, b ); // If no parents were found then the nodes are disconnected } else if ( !aup ) { return -1; } else if ( !bup ) { return 1; } // Otherwise they're somewhere else in the tree so we need // to build up a full list of the parentNodes for comparison while ( cur ) { ap.unshift( cur ); cur = cur.parentNode; } cur = bup; while ( cur ) { bp.unshift( cur ); cur = cur.parentNode; } al = ap.length; bl = bp.length; // Start walking down the tree looking for a discrepancy for ( var i = 0; i < al && i < bl; i++ ) { if ( ap[i] !== bp[i] ) { return siblingCheck( ap[i], bp[i] ); } } // We ended someplace up the tree so do a sibling check return i === al ? siblingCheck( a, bp[i], -1 ) : siblingCheck( ap[i], b, 1 ); }; siblingCheck = function( a, b, ret ) { if ( a === b ) { return ret; } var cur = a.nextSibling; while ( cur ) { if ( cur === b ) { return -1; } cur = cur.nextSibling; } return 1; }; } // Check to see if the browser returns elements by name when // querying by getElementById (and provide a workaround) (function(){ // We're going to inject a fake input element with a specified name var form = document.createElement("div"), id = "script" + (new Date()).getTime(), root = document.documentElement; form.innerHTML = ""; // Inject it into the root element, check its status, and remove it quickly root.insertBefore( form, root.firstChild ); // The workaround has to do additional checks after a getElementById // Which slows things down for other browsers (hence the branching) if ( document.getElementById( id ) ) { Expr.find.ID = function( match, context, isXML ) { if ( typeof context.getElementById !== "undefined" && !isXML ) { var m = context.getElementById(match[1]); return m ? m.id === match[1] || typeof m.getAttributeNode !== "undefined" && m.getAttributeNode("id").nodeValue === match[1] ? [m] : undefined : []; } }; Expr.filter.ID = function( elem, match ) { var node = typeof elem.getAttributeNode !== "undefined" && elem.getAttributeNode("id"); return elem.nodeType === 1 && node && node.nodeValue === match; }; } root.removeChild( form ); // release memory in IE root = form = null; })(); (function(){ // Check to see if the browser returns only elements // when doing getElementsByTagName("*") // Create a fake element var div = document.createElement("div"); div.appendChild( document.createComment("") ); // Make sure no comments are found if ( div.getElementsByTagName("*").length > 0 ) { Expr.find.TAG = function( match, context ) { var results = context.getElementsByTagName( match[1] ); // Filter out possible comments if ( match[1] === "*" ) { var tmp = []; for ( var i = 0; results[i]; i++ ) { if ( results[i].nodeType === 1 ) { tmp.push( results[i] ); } } results = tmp; } return results; }; } // Check to see if an attribute returns normalized href attributes div.innerHTML = ""; if ( div.firstChild && typeof div.firstChild.getAttribute !== "undefined" && div.firstChild.getAttribute("href") !== "#" ) { Expr.attrHandle.href = function( elem ) { return elem.getAttribute( "href", 2 ); }; } // release memory in IE div = null; })(); if ( document.querySelectorAll ) { (function(){ var oldSizzle = Sizzle, div = document.createElement("div"), id = "__sizzle__"; div.innerHTML = "

        "; // Safari can't handle uppercase or unicode characters when // in quirks mode. if ( div.querySelectorAll && div.querySelectorAll(".TEST").length === 0 ) { return; } Sizzle = function( query, context, extra, seed ) { context = context || document; // Only use querySelectorAll on non-XML documents // (ID selectors don't work in non-HTML documents) if ( !seed && !Sizzle.isXML(context) ) { // See if we find a selector to speed up var match = /^(\w+$)|^\.([\w\-]+$)|^#([\w\-]+$)/.exec( query ); if ( match && (context.nodeType === 1 || context.nodeType === 9) ) { // Speed-up: Sizzle("TAG") if ( match[1] ) { return makeArray( context.getElementsByTagName( query ), extra ); // Speed-up: Sizzle(".CLASS") } else if ( match[2] && Expr.find.CLASS && context.getElementsByClassName ) { return makeArray( context.getElementsByClassName( match[2] ), extra ); } } if ( context.nodeType === 9 ) { // Speed-up: Sizzle("body") // The body element only exists once, optimize finding it if ( query === "body" && context.body ) { return makeArray( [ context.body ], extra ); // Speed-up: Sizzle("#ID") } else if ( match && match[3] ) { var elem = context.getElementById( match[3] ); // Check parentNode to catch when Blackberry 4.6 returns // nodes that are no longer in the document #6963 if ( elem && elem.parentNode ) { // Handle the case where IE and Opera return items // by name instead of ID if ( elem.id === match[3] ) { return makeArray( [ elem ], extra ); } } else { return makeArray( [], extra ); } } try { return makeArray( context.querySelectorAll(query), extra ); } catch(qsaError) {} // qSA works strangely on Element-rooted queries // We can work around this by specifying an extra ID on the root // and working up from there (Thanks to Andrew Dupont for the technique) // IE 8 doesn't work on object elements } else if ( context.nodeType === 1 && context.nodeName.toLowerCase() !== "object" ) { var oldContext = context, old = context.getAttribute( "id" ), nid = old || id, hasParent = context.parentNode, relativeHierarchySelector = /^\s*[+~]/.test( query ); if ( !old ) { context.setAttribute( "id", nid ); } else { nid = nid.replace( /'/g, "\\$&" ); } if ( relativeHierarchySelector && hasParent ) { context = context.parentNode; } try { if ( !relativeHierarchySelector || hasParent ) { return makeArray( context.querySelectorAll( "[id='" + nid + "'] " + query ), extra ); } } catch(pseudoError) { } finally { if ( !old ) { oldContext.removeAttribute( "id" ); } } } } return oldSizzle(query, context, extra, seed); }; for ( var prop in oldSizzle ) { Sizzle[ prop ] = oldSizzle[ prop ]; } // release memory in IE div = null; })(); } (function(){ var html = document.documentElement, matches = html.matchesSelector || html.mozMatchesSelector || html.webkitMatchesSelector || html.msMatchesSelector; if ( matches ) { // Check to see if it's possible to do matchesSelector // on a disconnected node (IE 9 fails this) var disconnectedMatch = !matches.call( document.createElement( "div" ), "div" ), pseudoWorks = false; try { // This should fail with an exception // Gecko does not error, returns false instead matches.call( document.documentElement, "[test!='']:sizzle" ); } catch( pseudoError ) { pseudoWorks = true; } Sizzle.matchesSelector = function( node, expr ) { // Make sure that attribute selectors are quoted expr = expr.replace(/\=\s*([^'"\]]*)\s*\]/g, "='$1']"); if ( !Sizzle.isXML( node ) ) { try { if ( pseudoWorks || !Expr.match.PSEUDO.test( expr ) && !/!=/.test( expr ) ) { var ret = matches.call( node, expr ); // IE 9's matchesSelector returns false on disconnected nodes if ( ret || !disconnectedMatch || // As well, disconnected nodes are said to be in a document // fragment in IE 9, so check for that node.document && node.document.nodeType !== 11 ) { return ret; } } } catch(e) {} } return Sizzle(expr, null, null, [node]).length > 0; }; } })(); (function(){ var div = document.createElement("div"); div.innerHTML = "
        "; // Opera can't find a second classname (in 9.6) // Also, make sure that getElementsByClassName actually exists if ( !div.getElementsByClassName || div.getElementsByClassName("e").length === 0 ) { return; } // Safari caches class attributes, doesn't catch changes (in 3.2) div.lastChild.className = "e"; if ( div.getElementsByClassName("e").length === 1 ) { return; } Expr.order.splice(1, 0, "CLASS"); Expr.find.CLASS = function( match, context, isXML ) { if ( typeof context.getElementsByClassName !== "undefined" && !isXML ) { return context.getElementsByClassName(match[1]); } }; // release memory in IE div = null; })(); function dirNodeCheck( dir, cur, doneName, checkSet, nodeCheck, isXML ) { for ( var i = 0, l = checkSet.length; i < l; i++ ) { var elem = checkSet[i]; if ( elem ) { var match = false; elem = elem[dir]; while ( elem ) { if ( elem[ expando ] === doneName ) { match = checkSet[elem.sizset]; break; } if ( elem.nodeType === 1 && !isXML ){ elem[ expando ] = doneName; elem.sizset = i; } if ( elem.nodeName.toLowerCase() === cur ) { match = elem; break; } elem = elem[dir]; } checkSet[i] = match; } } } function dirCheck( dir, cur, doneName, checkSet, nodeCheck, isXML ) { for ( var i = 0, l = checkSet.length; i < l; i++ ) { var elem = checkSet[i]; if ( elem ) { var match = false; elem = elem[dir]; while ( elem ) { if ( elem[ expando ] === doneName ) { match = checkSet[elem.sizset]; break; } if ( elem.nodeType === 1 ) { if ( !isXML ) { elem[ expando ] = doneName; elem.sizset = i; } if ( typeof cur !== "string" ) { if ( elem === cur ) { match = true; break; } } else if ( Sizzle.filter( cur, [elem] ).length > 0 ) { match = elem; break; } } elem = elem[dir]; } checkSet[i] = match; } } } if ( document.documentElement.contains ) { Sizzle.contains = function( a, b ) { return a !== b && (a.contains ? a.contains(b) : true); }; } else if ( document.documentElement.compareDocumentPosition ) { Sizzle.contains = function( a, b ) { return !!(a.compareDocumentPosition(b) & 16); }; } else { Sizzle.contains = function() { return false; }; } Sizzle.isXML = function( elem ) { // documentElement is verified for cases where it doesn't yet exist // (such as loading iframes in IE - #4833) var documentElement = (elem ? elem.ownerDocument || elem : 0).documentElement; return documentElement ? documentElement.nodeName !== "HTML" : false; }; var posProcess = function( selector, context, seed ) { var match, tmpSet = [], later = "", root = context.nodeType ? [context] : context; // Position selectors must be done after the filter // And so must :not(positional) so we move all PSEUDOs to the end while ( (match = Expr.match.PSEUDO.exec( selector )) ) { later += match[0]; selector = selector.replace( Expr.match.PSEUDO, "" ); } selector = Expr.relative[selector] ? selector + "*" : selector; for ( var i = 0, l = root.length; i < l; i++ ) { Sizzle( selector, root[i], tmpSet, seed ); } return Sizzle.filter( later, tmpSet ); }; // EXPOSE // Override sizzle attribute retrieval Sizzle.attr = jQuery.attr; Sizzle.selectors.attrMap = {}; jQuery.find = Sizzle; jQuery.expr = Sizzle.selectors; jQuery.expr[":"] = jQuery.expr.filters; jQuery.unique = Sizzle.uniqueSort; jQuery.text = Sizzle.getText; jQuery.isXMLDoc = Sizzle.isXML; jQuery.contains = Sizzle.contains; })(); var runtil = /Until$/, rparentsprev = /^(?:parents|prevUntil|prevAll)/, // Note: This RegExp should be improved, or likely pulled from Sizzle rmultiselector = /,/, isSimple = /^.[^:#\[\.,]*$/, slice = Array.prototype.slice, POS = jQuery.expr.match.globalPOS, // methods guaranteed to produce a unique set when starting from a unique set guaranteedUnique = { children: true, contents: true, next: true, prev: true }; jQuery.fn.extend({ find: function( selector ) { var self = this, i, l; if ( typeof selector !== "string" ) { return jQuery( selector ).filter(function() { for ( i = 0, l = self.length; i < l; i++ ) { if ( jQuery.contains( self[ i ], this ) ) { return true; } } }); } var ret = this.pushStack( "", "find", selector ), length, n, r; for ( i = 0, l = this.length; i < l; i++ ) { length = ret.length; jQuery.find( selector, this[i], ret ); if ( i > 0 ) { // Make sure that the results are unique for ( n = length; n < ret.length; n++ ) { for ( r = 0; r < length; r++ ) { if ( ret[r] === ret[n] ) { ret.splice(n--, 1); break; } } } } } return ret; }, has: function( target ) { var targets = jQuery( target ); return this.filter(function() { for ( var i = 0, l = targets.length; i < l; i++ ) { if ( jQuery.contains( this, targets[i] ) ) { return true; } } }); }, not: function( selector ) { return this.pushStack( winnow(this, selector, false), "not", selector); }, filter: function( selector ) { return this.pushStack( winnow(this, selector, true), "filter", selector ); }, is: function( selector ) { return !!selector && ( typeof selector === "string" ? // If this is a positional selector, check membership in the returned set // so $("p:first").is("p:last") won't return true for a doc with two "p". POS.test( selector ) ? jQuery( selector, this.context ).index( this[0] ) >= 0 : jQuery.filter( selector, this ).length > 0 : this.filter( selector ).length > 0 ); }, closest: function( selectors, context ) { var ret = [], i, l, cur = this[0]; // Array (deprecated as of jQuery 1.7) if ( jQuery.isArray( selectors ) ) { var level = 1; while ( cur && cur.ownerDocument && cur !== context ) { for ( i = 0; i < selectors.length; i++ ) { if ( jQuery( cur ).is( selectors[ i ] ) ) { ret.push({ selector: selectors[ i ], elem: cur, level: level }); } } cur = cur.parentNode; level++; } return ret; } // String var pos = POS.test( selectors ) || typeof selectors !== "string" ? jQuery( selectors, context || this.context ) : 0; for ( i = 0, l = this.length; i < l; i++ ) { cur = this[i]; while ( cur ) { if ( pos ? pos.index(cur) > -1 : jQuery.find.matchesSelector(cur, selectors) ) { ret.push( cur ); break; } else { cur = cur.parentNode; if ( !cur || !cur.ownerDocument || cur === context || cur.nodeType === 11 ) { break; } } } } ret = ret.length > 1 ? jQuery.unique( ret ) : ret; return this.pushStack( ret, "closest", selectors ); }, // Determine the position of an element within // the matched set of elements index: function( elem ) { // No argument, return index in parent if ( !elem ) { return ( this[0] && this[0].parentNode ) ? this.prevAll().length : -1; } // index in selector if ( typeof elem === "string" ) { return jQuery.inArray( this[0], jQuery( elem ) ); } // Locate the position of the desired element return jQuery.inArray( // If it receives a jQuery object, the first element is used elem.jquery ? elem[0] : elem, this ); }, add: function( selector, context ) { var set = typeof selector === "string" ? jQuery( selector, context ) : jQuery.makeArray( selector && selector.nodeType ? [ selector ] : selector ), all = jQuery.merge( this.get(), set ); return this.pushStack( isDisconnected( set[0] ) || isDisconnected( all[0] ) ? all : jQuery.unique( all ) ); }, andSelf: function() { return this.add( this.prevObject ); } }); // A painfully simple check to see if an element is disconnected // from a document (should be improved, where feasible). function isDisconnected( node ) { return !node || !node.parentNode || node.parentNode.nodeType === 11; } jQuery.each({ parent: function( elem ) { var parent = elem.parentNode; return parent && parent.nodeType !== 11 ? parent : null; }, parents: function( elem ) { return jQuery.dir( elem, "parentNode" ); }, parentsUntil: function( elem, i, until ) { return jQuery.dir( elem, "parentNode", until ); }, next: function( elem ) { return jQuery.nth( elem, 2, "nextSibling" ); }, prev: function( elem ) { return jQuery.nth( elem, 2, "previousSibling" ); }, nextAll: function( elem ) { return jQuery.dir( elem, "nextSibling" ); }, prevAll: function( elem ) { return jQuery.dir( elem, "previousSibling" ); }, nextUntil: function( elem, i, until ) { return jQuery.dir( elem, "nextSibling", until ); }, prevUntil: function( elem, i, until ) { return jQuery.dir( elem, "previousSibling", until ); }, siblings: function( elem ) { return jQuery.sibling( ( elem.parentNode || {} ).firstChild, elem ); }, children: function( elem ) { return jQuery.sibling( elem.firstChild ); }, contents: function( elem ) { return jQuery.nodeName( elem, "iframe" ) ? elem.contentDocument || elem.contentWindow.document : jQuery.makeArray( elem.childNodes ); } }, function( name, fn ) { jQuery.fn[ name ] = function( until, selector ) { var ret = jQuery.map( this, fn, until ); if ( !runtil.test( name ) ) { selector = until; } if ( selector && typeof selector === "string" ) { ret = jQuery.filter( selector, ret ); } ret = this.length > 1 && !guaranteedUnique[ name ] ? jQuery.unique( ret ) : ret; if ( (this.length > 1 || rmultiselector.test( selector )) && rparentsprev.test( name ) ) { ret = ret.reverse(); } return this.pushStack( ret, name, slice.call( arguments ).join(",") ); }; }); jQuery.extend({ filter: function( expr, elems, not ) { if ( not ) { expr = ":not(" + expr + ")"; } return elems.length === 1 ? jQuery.find.matchesSelector(elems[0], expr) ? [ elems[0] ] : [] : jQuery.find.matches(expr, elems); }, dir: function( elem, dir, until ) { var matched = [], cur = elem[ dir ]; while ( cur && cur.nodeType !== 9 && (until === undefined || cur.nodeType !== 1 || !jQuery( cur ).is( until )) ) { if ( cur.nodeType === 1 ) { matched.push( cur ); } cur = cur[dir]; } return matched; }, nth: function( cur, result, dir, elem ) { result = result || 1; var num = 0; for ( ; cur; cur = cur[dir] ) { if ( cur.nodeType === 1 && ++num === result ) { break; } } return cur; }, sibling: function( n, elem ) { var r = []; for ( ; n; n = n.nextSibling ) { if ( n.nodeType === 1 && n !== elem ) { r.push( n ); } } return r; } }); // Implement the identical functionality for filter and not function winnow( elements, qualifier, keep ) { // Can't pass null or undefined to indexOf in Firefox 4 // Set to 0 to skip string check qualifier = qualifier || 0; if ( jQuery.isFunction( qualifier ) ) { return jQuery.grep(elements, function( elem, i ) { var retVal = !!qualifier.call( elem, i, elem ); return retVal === keep; }); } else if ( qualifier.nodeType ) { return jQuery.grep(elements, function( elem, i ) { return ( elem === qualifier ) === keep; }); } else if ( typeof qualifier === "string" ) { var filtered = jQuery.grep(elements, function( elem ) { return elem.nodeType === 1; }); if ( isSimple.test( qualifier ) ) { return jQuery.filter(qualifier, filtered, !keep); } else { qualifier = jQuery.filter( qualifier, filtered ); } } return jQuery.grep(elements, function( elem, i ) { return ( jQuery.inArray( elem, qualifier ) >= 0 ) === keep; }); } function createSafeFragment( document ) { var list = nodeNames.split( "|" ), safeFrag = document.createDocumentFragment(); if ( safeFrag.createElement ) { while ( list.length ) { safeFrag.createElement( list.pop() ); } } return safeFrag; } var nodeNames = "abbr|article|aside|audio|bdi|canvas|data|datalist|details|figcaption|figure|footer|" + "header|hgroup|mark|meter|nav|output|progress|section|summary|time|video", rinlinejQuery = / jQuery\d+="(?:\d+|null)"/g, rleadingWhitespace = /^\s+/, rxhtmlTag = /<(?!area|br|col|embed|hr|img|input|link|meta|param)(([\w:]+)[^>]*)\/>/ig, rtagName = /<([\w:]+)/, rtbody = /]", "i"), // checked="checked" or checked rchecked = /checked\s*(?:[^=]|=\s*.checked.)/i, rscriptType = /\/(java|ecma)script/i, rcleanScript = /^\s*", "" ], legend: [ 1, "
        ", "
        " ], thead: [ 1, "", "
        " ], tr: [ 2, "", "
        " ], td: [ 3, "", "
        " ], col: [ 2, "", "
        " ], area: [ 1, "", "" ], _default: [ 0, "", "" ] }, safeFragment = createSafeFragment( document ); wrapMap.optgroup = wrapMap.option; wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead; wrapMap.th = wrapMap.td; // IE can't serialize and

        Navigation

        Changelog¶

        From FabIO-0.1.2 to FabIO-0.1.3:¶

        • Fixed a memory-leak in mar345 module
        • Improved support for bruker format (writer & reader)
        • Fixed a bug in EDF headers (very long headers)
        • Provide template for new file-formats
        • Fix a bug related to PIL in new MacOSX
        • Allow binary-images to be read from end

        From FabIO-0.1.1 to FabIO-0.1.2:¶

        • Fixed a bug in fabioimage.write (impacted all writers)
        • added Sphinx documentation “python setup.py build_doc”
        • PyLint compliance of some classes (rename, ...)
        • tests from installer with “python setup.py build test”

        From FabIO-0.1.0 to FabIO-0.1.1:¶

        • Merged Mar345 image reader and writer with cython bindings (towards python3 compliance)
        • Improve CBF image writing under windows
        • Bz2, Gzip and Flat files are managed through a common way ... classes are more (python v2.5) or less (python v2.7) overloaded
        • Fast EDF reading if one assumes offsets are the same between files, same for ROIs

        From FabIO-0.0.8 to FabIO-0.1.0:¶

        • OXD reader improved and writer implemented
        • Mar345 reader improved and writer implemented
        • CBF writer implemented
        • Clean-up of the code & bug fixes
        • Move towards python3
        • Make PIL optional dependency

        Python3 is not yet tested but some blocking points have been identified and some fixed.

        From FabIO-0.0.7 to FabIO-0.0.8:¶

        • Support for Tiff using TiffIO module from V.A.Solé
        • Clean-up of the code & bug fixes

        From FabIO-0.0.6 to FabIO-0.0.7:¶

        • Support for multi-frames EDF files
        • Support for XML images/2D arrays used in EDNA
        • new method: fabio.open(filename) that is an alias for fabio.openimage.openimage(filename)

        From FabIO-0.0.4 to FabIO-0.0.6:¶

        • Support for CBF files from Pilatus detectors
        • Support for KCD files from Nonius Kappa CCD images
        • write EDF with their native data type (instead of uint16 by default)

        Table Of Contents

        Previous topic

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        Next topic

        FabIO Package

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        fabio-0.1.3/doc/html/genindex.html0000644000175000017500000014211212233250023017550 0ustar jeromejerome00000000000000 Index — FabIO 0.1.3 documentation

        Navigation

        Index

        A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | W | X

        A

        add() (fabio.fabioimage.fabioimage method)
        adscimage (class in fabio.adscimage)
        appendFrame() (fabio.edfimage.edfimage method)

        B

        basic_translate() (fabio.brukerimage.brukerimage method)
        BINARY_MARKER (fabio.cbfimage.CIF attribute)
        binaryimage (class in fabio.binaryimage)
        BLANK (fabio.cbfimage.CIF attribute)
        bpp (fabio.edfimage.edfimage attribute)
        bpp_to_numpy (fabio.brukerimage.brukerimage attribute)
        bruker100image (class in fabio.bruker100image)
        brukerimage (class in fabio.brukerimage)
        bytecode (fabio.edfimage.edfimage attribute)
        (fabio.edfimage.Frame attribute)
        BZ2File (class in fabio.fabioutils)

        C

        calc_bpp() (fabio.brukerimage.brukerimage method)
        capsHeader (fabio.edfimage.edfimage attribute)
        cbfimage (class in fabio.cbfimage)
        checkData() (fabio.cbfimage.cbfimage static method)
        (fabio.OXDimage.OXDimage static method)
        (fabio.fabioimage.fabioimage static method)
        (fabio.fit2dmaskimage.fit2dmaskimage static method)
        (fabio.kcdimage.kcdimage static method)
        (fabio.mar345image.mar345image static method)
        (fabio.pnmimage.pnmimage static method)
        checkHeader() (fabio.edfimage.edfimage static method)
        (fabio.fabioimage.fabioimage static method)
        CIF (class in fabio.cbfimage)
        classname (fabio.fabioimage.fabioimage attribute)
        columnfile (class in fabio.datIO)
        compByteOffet_numpy() (in module fabio.compression)
        compPCK() (in module fabio.compression)
        compTY1() (in module fabio.compression)
        construct_filename() (in module fabio.fabioutils)
        convert() (fabio.fabioimage.fabioimage method)
        convert_data() (in module fabio.converters)
        convert_data_integer() (in module fabio.converters)
        convert_header() (in module fabio.converters)
        current() (fabio.file_series.file_series method)
        (fabio.file_series.filename_series method)
        current_image() (fabio.file_series.file_series method)
        (fabio.file_series.filename_series method)
        current_object() (fabio.file_series.file_series method)
        (fabio.file_series.filename_series method)

        D

        data (fabio.edfimage.edfimage attribute)
        (fabio.edfimage.Frame attribute)
        decByteOffet_cython() (in module fabio.compression)
        decByteOffet_numpy() (in module fabio.compression)
        decByteOffet_python() (in module fabio.compression)
        decByteOffet_weave() (in module fabio.compression)
        decBzip2() (in module fabio.compression)
        decGzip() (in module fabio.compression)
        decKM4CCD() (in module fabio.compression)
        deconstruct_filename() (fabio.fabioutils.FilenameObject method)
        (in module fabio.fabioutils)
        decPCK() (in module fabio.compression)
        decTY1() (in module fabio.compression)
        decZlib() (in module fabio.compression)
        delCapsHeader() (fabio.edfimage.edfimage method)
        delData() (fabio.edfimage.edfimage method)
        deleteFrame() (fabio.edfimage.edfimage method)
        delHeader() (fabio.edfimage.edfimage method)
        delHeaderKeys() (fabio.edfimage.edfimage method)
        demo() (in module fabio.GEimage)
        deprecated() (in module fabio.fabioutils)
        dim1 (fabio.edfimage.edfimage attribute)
        dim2 (fabio.edfimage.edfimage attribute)
        dims (fabio.edfimage.edfimage attribute)
        dm3image (class in fabio.dm3image)
        do_magic() (in module fabio.openimage)

        E

        edfimage (class in fabio.edfimage)
        endianness() (in module fabio.compression)
        EOL (fabio.cbfimage.CIF attribute)
        estimate_offset_value() (fabio.binaryimage.binaryimage method)
        exists() (fabio.cbfimage.CIF method)
        existsInLoop() (fabio.cbfimage.CIF method)
        extract_data() (fabio.tifimage.Image_File_Directory_entry method)
        extract_filenumber() (in module fabio.fabioutils)

        F

        fabio.__init__ (module)
        fabio.adscimage (module)
        fabio.binaryimage (module)
        fabio.bruker100image (module)
        fabio.brukerimage (module)
        fabio.cbfimage (module)
        fabio.compression (module)
        fabio.converters (module)
        fabio.datIO (module)
        fabio.dm3image (module)
        fabio.edfimage (module)
        fabio.fabioimage (module)
        fabio.fabioutils (module)
        fabio.file_series (module)
        fabio.fit2dmaskimage (module)
        fabio.fit2dspreadsheetimage (module)
        fabio.GEimage (module)
        fabio.HiPiCimage (module)
        fabio.kcdimage (module)
        fabio.mar345image (module)
        fabio.marccdimage (module)
        fabio.openimage (module)
        fabio.OXDimage (module)
        fabio.pilatusimage (module)
        fabio.pnmimage (module)
        fabio.readbytestream (module)
        fabio.TiffIO (module)
        fabio.tifimage (module)
        fabio.xsdimage (module)
        fabiodata (class in fabio.datIO)
        fabioimage (class in fabio.fabioimage)
        fastReadData() (fabio.edfimage.edfimage method)
        fastReadROI() (fabio.edfimage.edfimage method)
        File (class in fabio.fabioutils)
        file_series (class in fabio.file_series)
        filename_series (class in fabio.file_series)
        FilenameObject (class in fabio.fabioutils)
        first() (fabio.file_series.file_series method)
        first_image() (fabio.file_series.file_series method)
        first_object() (fabio.file_series.file_series method)
        fit2dmaskimage (class in fabio.fit2dmaskimage)
        fit2dspreadsheetimage (class in fabio.fit2dspreadsheetimage)
        Frame (class in fabio.edfimage)

        G

        GEimage (class in fabio.GEimage)
        gen_header() (fabio.brukerimage.brukerimage method)
        gen_overflow() (fabio.brukerimage.brukerimage method)
        getBpp() (fabio.edfimage.edfimage method)
        getByteCode() (fabio.edfimage.edfimage method)
        (fabio.edfimage.Frame method)
        getCapsHeader() (fabio.edfimage.edfimage method)
        getclassname() (fabio.fabioimage.fabioimage method)
        getCompressionRatio() (fabio.OXDimage.OXDimage method)
        getData() (fabio.edfimage.edfimage method)
        (fabio.TiffIO.TiffIO method)
        (fabio.edfimage.Frame method)
        getDim1() (fabio.edfimage.edfimage method)
        getDim2() (fabio.edfimage.edfimage method)
        getDims() (fabio.edfimage.edfimage method)
        getEdfBlock() (fabio.edfimage.Frame method)
        getframe() (fabio.edfimage.edfimage method)
        (fabio.GEimage.GEimage method)
        (fabio.fabioimage.fabioimage method)
        getHeader() (fabio.edfimage.edfimage method)
        getheader() (fabio.fabioimage.fabioimage method)
        getHeaderKeys() (fabio.edfimage.edfimage method)
        getImage() (fabio.TiffIO.TiffIO method)
        getImageFileDirectories() (fabio.TiffIO.TiffIO method)
        getInfo() (fabio.TiffIO.TiffIO method)
        getmax() (fabio.fabioimage.fabioimage method)
        getmean() (fabio.fabioimage.fabioimage method)
        getmin() (fabio.fabioimage.fabioimage method)
        getNbFrames() (fabio.edfimage.edfimage method)
        getnum() (in module fabio.fabioutils)
        getNumberOfImages() (fabio.TiffIO.TiffIO method)
        getSize() (fabio.fabioutils.BZ2File method)
        (fabio.OXDimage.Section method)
        (fabio.fabioutils.File method)
        (fabio.fabioutils.StringIO method)
        getstddev() (fabio.fabioimage.fabioimage method)
        GzipFile (class in fabio.fabioutils)

        H

        header (fabio.edfimage.edfimage attribute)
        header_keys (fabio.edfimage.edfimage attribute)
        HEADERS_KEYS (fabio.brukerimage.brukerimage attribute)
        HiPiCimage (class in fabio.HiPiCimage)

        I

        Image_File_Directory (class in fabio.tifimage)
        Image_File_Directory_entry (class in fabio.tifimage)
        integrate_area() (fabio.fabioimage.fabioimage method)
        interpret_header() (in module fabio.marccdimage)
        isAscii() (fabio.cbfimage.CIF static method)
        (in module fabio.fabioutils)

        J

        jump() (fabio.file_series.file_series method)
        (fabio.file_series.filename_series method)
        jump_filename() (in module fabio.fabioutils)
        jump_image() (fabio.file_series.file_series method)
        (fabio.file_series.filename_series method)
        jump_object() (fabio.file_series.file_series method)
        (fabio.file_series.filename_series method)

        K

        kcdimage (class in fabio.kcdimage)

        L

        last() (fabio.file_series.file_series method)
        last_image() (fabio.file_series.file_series method)
        last_object() (fabio.file_series.file_series method)
        len() (fabio.file_series.file_series method)
        load() (fabio.fabioimage.fabioimage method)
        loadCHIPLOT() (fabio.cbfimage.CIF method)
        loadCIF() (fabio.cbfimage.CIF method)
        LoopHasKey() (fabio.cbfimage.CIF static method)

        M

        make_format() (in module fabio.marccdimage)
        make_slice() (fabio.fabioimage.fabioimage method)
        mar345image (class in fabio.mar345image)
        marccdimage (class in fabio.marccdimage)
        md5sum() (in module fabio.compression)

        N

        nb_overflow_pixels() (fabio.mar345image.mar345image method)
        new_file_series() (in module fabio.file_series)
        new_file_series0() (in module fabio.file_series)
        next() (fabio.edfimage.edfimage method)
        (fabio.GEimage.GEimage method)
        (fabio.fabioimage.fabioimage method)
        (fabio.file_series.file_series method)
        (fabio.file_series.filename_series method)
        next_filename() (in module fabio.fabioutils)
        next_image() (fabio.file_series.file_series method)
        (fabio.file_series.filename_series method)
        next_object() (fabio.file_series.file_series method)
        (fabio.file_series.filename_series method)
        nframes (fabio.edfimage.edfimage attribute)
        nice_int() (in module fabio.fabioutils)
        numbered_file_series (class in fabio.file_series)
        numstem() (in module fabio.fabioutils)

        O

        openheader() (in module fabio.openimage)
        openimage() (in module fabio.openimage)
        OXDimage (class in fabio.OXDimage)

        P

        P1dec() (fabio.pnmimage.pnmimage static method)
        P2dec() (fabio.pnmimage.pnmimage static method)
        P3dec() (fabio.pnmimage.pnmimage static method)
        P4dec() (fabio.pnmimage.pnmimage static method)
        P5dec() (fabio.pnmimage.pnmimage static method)
        P6dec() (fabio.pnmimage.pnmimage static method)
        P7dec() (fabio.pnmimage.pnmimage static method)
        pad() (in module fabio.fabioutils)
        parseheader() (fabio.edfimage.Frame method)
        pilatusimage (class in fabio.pilatusimage)
        pnmimage (class in fabio.pnmimage)
        pop() (fabio.cbfimage.CIF method)
        popitem() (fabio.cbfimage.CIF method)
        prev_image() (fabio.file_series.filename_series method)
        previous() (fabio.edfimage.edfimage method)
        (fabio.GEimage.GEimage method)
        (fabio.fabioimage.fabioimage method)
        (fabio.file_series.file_series method)
        (fabio.file_series.filename_series method)
        previous_filename() (in module fabio.fabioutils)
        previous_image() (fabio.file_series.file_series method)
        previous_object() (fabio.file_series.file_series method)
        (fabio.file_series.filename_series method)

        R

        read() (fabio.adscimage.adscimage method)
        (fabio.GEimage.GEimage method)
        (fabio.HiPiCimage.HiPiCimage method)
        (fabio.OXDimage.OXDimage method)
        (fabio.binaryimage.binaryimage method)
        (fabio.bruker100image.bruker100image method)
        (fabio.brukerimage.brukerimage method)
        (fabio.cbfimage.cbfimage method)
        (fabio.datIO.columnfile method)
        (fabio.datIO.fabiodata method)
        (fabio.dm3image.dm3image method)
        (fabio.edfimage.edfimage method)
        (fabio.fabioimage.fabioimage method)
        (fabio.fit2dmaskimage.fit2dmaskimage method)
        (fabio.fit2dspreadsheetimage.fit2dspreadsheetimage method)
        (fabio.kcdimage.kcdimage method)
        (fabio.mar345image.mar345image method)
        (fabio.pnmimage.pnmimage method)
        (fabio.tifimage.tifimage method)
        (fabio.xsdimage.xsdimage method)
        read_data() (fabio.dm3image.dm3image method)
        read_tag_entry() (fabio.dm3image.dm3image method)
        read_tag_group() (fabio.dm3image.dm3image method)
        read_tag_type() (fabio.dm3image.dm3image method)
        readbytes() (fabio.dm3image.dm3image method)
        readbytestream() (in module fabio.readbytestream)
        readCIF() (fabio.cbfimage.CIF method)
        readheader() (fabio.fabioimage.fabioimage method)
        readROI() (fabio.fabioimage.fabioimage method)
        rebin() (fabio.fabioimage.fabioimage method)
        resetvals() (fabio.fabioimage.fabioimage method)

        S

        save() (fabio.fabioimage.fabioimage method)
        saveCIF() (fabio.cbfimage.CIF method)
        Section (class in fabio.OXDimage)
        setBpp() (fabio.edfimage.edfimage method)
        setByteCode() (fabio.edfimage.edfimage method)
        (fabio.edfimage.Frame method)
        setCapsHeader() (fabio.edfimage.edfimage method)
        setData() (fabio.edfimage.edfimage method)
        (fabio.OXDimage.Section method)
        (fabio.edfimage.Frame method)
        setDim1() (fabio.edfimage.edfimage method)
        setDim2() (fabio.edfimage.edfimage method)
        setHeader() (fabio.edfimage.edfimage method)
        setHeaderKeys() (fabio.edfimage.edfimage method)
        setNbFrames() (fabio.edfimage.edfimage method)
        setSize() (fabio.fabioutils.BZ2File method)
        (fabio.fabioutils.File method)
        (fabio.fabioutils.StringIO method)
        size (fabio.fabioutils.BZ2File attribute)
        (fabio.fabioutils.File attribute)
        (fabio.fabioutils.StringIO attribute)
        SPACER (fabio.brukerimage.brukerimage attribute)
        START_COMMENT (fabio.cbfimage.CIF attribute)
        str() (fabio.fabioutils.FilenameObject method)
        StringIO (class in fabio.fabioutils)
        swap_needed() (fabio.binaryimage.binaryimage static method)
        (fabio.edfimage.Frame method)
        (fabio.edfimage.edfimage method)

        T

        test() (in module fabio.adscimage)
        (in module fabio.brukerimage)
        (in module fabio.fabioimage)
        Tiff_header (class in fabio.tifimage)
        TiffIO (class in fabio.TiffIO)
        tifimage (class in fabio.tifimage)
        toAscii() (in module fabio.fabioutils)
        toPIL16() (fabio.bruker100image.bruker100image method)
        (fabio.fabioimage.fabioimage method)
        tostring() (fabio.cbfimage.CIF method)
        (fabio.fabioutils.FilenameObject method)

        U

        UnknownCompressedFile (class in fabio.fabioutils)
        unpack() (fabio.edfimage.edfimage method)
        (fabio.tifimage.Image_File_Directory method)
        (fabio.tifimage.Image_File_Directory_entry method)
        update_header() (fabio.fabioimage.fabioimage method)

        W

        write() (fabio.adscimage.adscimage method)
        (fabio.GEimage.GEimage method)
        (fabio.OXDimage.OXDimage method)
        (fabio.binaryimage.binaryimage method)
        (fabio.brukerimage.brukerimage method)
        (fabio.cbfimage.cbfimage method)
        (fabio.edfimage.edfimage method)
        (fabio.fabioimage.fabioimage method)
        (fabio.fit2dmaskimage.fit2dmaskimage method)
        (fabio.mar345image.mar345image method)
        (fabio.pnmimage.pnmimage method)
        (fabio.tifimage.tifimage method)
        writeImage() (fabio.TiffIO.TiffIO method)

        X

        xsdimage (class in fabio.xsdimage)

        Navigation

        © Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
        fabio-0.1.3/doc/html/getting_started.html0000644000175000017500000005722212233250022021144 0ustar jeromejerome00000000000000 Getting Started — FabIO 0.1.3 documentation

        Navigation

        Getting Started¶

        FabIO is a Python module for reading and handling data from two-dimensional X-ray detectors.

        FabIO is a Python module written for easy and transparent reading of raw two-dimensional data from various X-ray detectors. The module provides a function for reading any image and returning a fabioimage object which contains both metadata (header information) and the raw data. All fabioimage object offer additional methods to extract information about the image and to open other detector images from the same data series.

        Introduction¶

        One obstacle when writing software to analyse data collected from a two-dimensional detector is to read the raw data into the program, not least because the data can be stored in many different formats depending on the instrument used. To overcome this problem we decided to develop a general module, FabIO (FABle I/O), to handle reading and writing of two-dimensional data. The code-base was initiated by merging parts of our fabian imageviewer and ImageD11 peak-search programs and has been developed since 2007 as part of the TotalCryst program suite for analysis of 3DXRD microscopy data. During integration into a range of scientific programs like the FABLE graphical interface, EDNA and the fast azimuthal integration library, pyFAI; FabIO has gained several features like handling multi-frame image formats as well as writing many of the file formats.

        FabIO Python module¶

        Python is a scripting language that is very popular among scientists and which also allows well structured applications and libraries to be developed.

        Philosophy¶

        The intention behind this development was to create a Python module which would enable easy reading of 2D data images, from any detector without having to worry about the file format. Therefore FabIO just needs a file name to open a file and it determines the file format automatically and deals with gzip and bzip2 compression transparently. Opening a file returns an object which stores the image in memory as a 2D NumPy array and the metadata, called header, in a Python dictionary. Beside the data and header attributes, some methods are provided for reading the previous or next image in a series of images as well as jumping to a specific file number. For the user, these auxiliary methods are intended to be independent of the image format (as far as is reasonably possible).

        FabIO is written in an object-oriented style (with classes) but aims at being used in a scripting environment: special care has been taken to ensure the library remains easy to use. Therefore no knowledge of object-oriented programming is required to get full benefits of the library. As the development is done in a collaborative and decentralized way; a comprehensive test suite has been added to reduce the number of regressions when new features are added or old problems are repaired. The software is very modular and allows new classes to be added for handling other data formats easily. FabIO and its source-code are freely available to everyone on-line, licensed under the GNU General Public License version 3 (GPLv3). FabIO is also available directly from popular Linux distributions like Debian and Ubuntu.

        Implementation¶

        The main language used in the development of FabIO is Python; however, some image formats are compressed and require compression algorithms for reading and writing data. When such algorithms could not be implemented efficiently using Python or NumPy native modules were developed, in i.e. standard C code callable from Python (sometimes generated using Cython). This code has to be compiled for each computer architecture and offers excellent performance. FabIO is only dependent on the NumPy module and has extra features if two other optional Python modules are available. For reading XML files (that are used in EDNA) the Lxml module is required and the Python Image Library, PIL is needed for producing a PIL image for displaying the image in graphical user interfaces and several image-processing operations that are not re-implemented in FabIO. A variety of useful image processing is also available in the scipy.ndimage module and in scikits-image.

        Images can also be displayed in a convenient interactive manner using matplotlib and an IPython shell , which is mainly used for developing data analysis algorithms. Reading and writing procedure of the various TIFF formats is based on the TiffIO code from PyMCA.

        In the Python shell, the fabio module must be imported prior to reading an image in one of the supported file formats (see Table Supported formats, hereafter). The fabio.open function creates an instance of the Python class fabioimage, from the name of a file. This instance, named img hereafter, stores the image data in img.data as a 2D NumPy array. Often the image file contains more information than just the intensities of the pixels, e.g. information about how the image is stored and the instrument parameters at the time of the image acquisition, these metadata are usually stored in the file header. Header information, are available in img.header as a Python dictionary where keys are strings and values are usually strings or numeric values.

        Information in the header about the binary part of the image (compression, endianness, shape) are interpreted however, other metadata are exposed as they are recorded in the file. FabIO allows the user to modify and, where possible, to save this information (the table Supported formats summarizes writable formats). Automatic translation between file-formats, even if desirable, is sometimes impossible because not all format have the capability to be extended with additional metadata. Nevertheless FabIO is capable of converting one image data-format into another by taking care of the numerical specifics: for example float arrays are converted to integer arrays if the output format only accepts integers.

        FabIO methods¶

        One strength of the implementation in an object oriented language is the possibility to combine functions (or methods) together with data appropriate for specific formats. In addition to the header information and image data, every fabioimage instance (returned by fabio.open) has methods inherited from fabioimage which provide information about the image minimum, maximum and mean values. In addition there are methods which return the file number, name etc. Some of the most important methods are specific for certain formats because the methods are related to how frames in a sequence are handled; these methods are img.next(), img.previous(), and img.getframe(n). The behaviour of such methods varies depending on the image format: for single-frame format (like mar345), img.next() will return the image in next file; for multi-frame format (like GE), img.next() will return the next frame within the same file. For formats which are possibly multi-framed like EDF, the behaviour depends on the actual number of frames per file (accessible via the img.nframes attribute).

        Usage¶

        Examples¶

        In this section we have collected some basic examples of how FabIO can be employed.

        Opening an image:

        import fabio
im100 = fabio.open('Quartz_0100.tif') # Open image file
print(im0.data[1024,1024])            # Check a pixel value
im101 = im100.next()                  # Open next image
im270 = im1.getframe(270)             # Jump to file number 270: Quartz_0270.tif

        Normalising the intensity to a value in the header:

        img = fabio.open('exampleimage0001.edf')
print(img.header)
{'ByteOrder': 'LowByteFirst',
 'DATE (scan begin)': 'Mon Jun 28 21:22:16 2010',
 'ESRFCurrent': '198.099',
...
}
# Normalise to beam current and save data
srcur = float(img.header['ESRFCurrent'])
img.data *= 200.0/srcur
img.write('normed_0001.edf')

        Interactive viewing with matplotlib:

        from matplotlib import pyplot       # Load matplotlib
pyplot.imshow(img.data)             # Display as an image
pyplot.show()                       # Show GUI window

        Future and perspectives¶

        The Hierarchical Data Format version 5 (hdf5) is a data format which is increasingly popular for storage of X-ray and neutron data. To name a few facilities the synchrotron Soleil and the neutron sources ISIS, SNS and SINQ already use HDF extensively through the NeXus format. For now, mainly processed or curated data are stored in this format but new detectors are rumoured to provide native output in HDF5. FabIO will rely on H5Py, which already provides a good HDF5 binding for Python, as an external dependency, to be able to read and write such HDF5 files.

        In the near future FabIO will be upgraded to work with Python3 (a new version of Python); this change of version will affect some internals FabIO as string and file handling have been altered. This change is already ongoing as many parts of native code in C have already been translated into Cython to smoothe the transition, since Cython generates code compatible with Python3. This also makes it easier to retain backwards compatibility with the earlier Python versions.

        Conclusion¶

        FabIO gives an easy way to read and write 2D images when using the Python computer language. It was originally developed for X-ray diffraction data but now gives an easy way for scientists to access and manipulate their data from a wide range of 2D X-ray detectors. We welcome contributions to further improve the code and hope to add more file formats in the future as well as port the existing code base to the emerging Python3.

        Acknoledgements¶

        We acknowledge Andy Götz and Kenneth Evans for extensive testing when including the FabIO reader in the Fable image viewer (Götz et al., 2007).We also thank V. Armando Solé for assistance with his TiffIO reader and Carsten Gundlach for deployment of FabIO at the beamlines i711 and i811, MAX IV, and providing bug reports. We finally acknowledge our colleagues who have reported bugs and helped to improve FabIO. Financial support was granted by the EU 6th Framework NEST/ADVENTURE project TotalCryst (Poulsen et al., 2006).

        Citation¶

        Knudsen, E. B., Sørensen, H. O., Wright, J. P., Goret, G. & Kieffer, J. (2013). J. Appl. Cryst. 46, 537-539.

        http://dx.doi.org/10.1107/S0021889813000150

        List of file formats that FabIO can read and write¶

        In alphabetical order. The listed filename extensions are typical examples. FabIO tries to deduce the actual format from the file itself and only uses extensions as a fallback if that fails.

        Supported formats
        Python Module Detector / Format Extension Read Multi-image Write
        ADSC ADSC Quantum .img Yes No Yes
        Bruker Bruker formats .sfrm Yes No Yes
        DM3 Gatan Digital Micrograph .dm3 Yes No No
        EDF ESRF data format .edf Yes Yes Yes
        EDNA-XML Used by EDNA .xml Yes No No
        CBF CIF binary files .cbf Yes No Yes
        kcd Nonius KappaCCD .kccd Yes No No
        fit2d mask Used by Fit2D .msk Yes No Yes
        fit2d spreadsheet Used by Fit2D .spr Yes No Yes
        GE General Electric No Yes Yes No
        HiPiC Hamamatsu CCD .tif Yes No No
        marccd MarCCD/Mar165 .mccd Yes No Yes
        mar345 Mar345 image plate .mar3450 Yes No Yes
        OXD Oxford Diffraction .img Yes No Yes
        pilatus Dectris Pilatus Tiff .tif Yes No Yes
        PNM Portable aNy Map .pnm Yes No No
        TIFF Tagged Image File Format .tif Yes No Yes

        Adding new file formats¶

        We hope it will be relatively easy to add new file formats to fabio in the future. The basic idea is the following:
        1. inherit from fabioimage overriding the methods _readheader, read and optionally write. Name your new module XXXimage where XXX means something (eg tifimage).
        2. readheader fills in a dictionary of “name”:”value” pairs in self.header. No one expects to find anything much in there.
        3. read fills in self.data with a numpy array holding the image. Some redundant info which also appears are self.dim1 and self.dim2: the image dimensions, self.bpp is the bytes per pixel and self.bytecode is the numpy.dtype.type of the data.
        4. The member variables “_need_a_seek_to_read” and “_need_a_real_file” are there in case you have trouble with the transparent handling of bz2 and gz files.
        5. Register the file type (extension naming) in fabioutils.py:FILETYPES
        6. Add your new module as an import into fabio.openimage
        7. Fill out the magic numbers for your format in fabio.openimage if you know them (the characteristic first few bytes in the file)
        8. Upload a testimage to the file release system and create a unittest testcase which opens an example of your new format, confirming the image has actually been read in successfully (eg check the mean, max, min and esd are all correct, perhaps orientation too)
        9. Run pylint on your code and then please go clean it up. Have a go at mine while you are at it.
        10. Bask in the warm glow of appreciation when someone unexpectedly learns they don’t need to convert their data into another format

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        © Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
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to FabIO’s documentation!","Changelog","Getting Started","Installation","FabIO Package"],objnames:{"0":["py","module","Python module"],"1":["py","method","Python method"],"2":["py","function","Python function"],"3":["py","staticmethod","Python static method"],"4":["py","attribute","Python attribute"],"5":["py","class","Python class"]},filenames:["index","Changelog","getting_started","INSTALL","api/modules"]})fabio-0.1.3/doc/html/.buildinfo0000644000175000017500000000034612233250023017037 0ustar jeromejerome00000000000000# Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. config: 59333a03b9d7fc243eb1812d88ec7e8e tags: fbb0d17656682115ca4d033fb2f83ba1 fabio-0.1.3/doc/html/_sources/0000755000175000017500000000000012233272207016712 5ustar jeromejerome00000000000000fabio-0.1.3/doc/html/_sources/api/0000755000175000017500000000000012233272207017463 5ustar jeromejerome00000000000000fabio-0.1.3/doc/html/_sources/api/modules.txt0000644000175000017500000001064512121354612021677 0ustar jeromejerome00000000000000FabIO Package ============= .. toctree:: :maxdepth: 4 :mod:`fabio` Package -------------------- .. automodule:: fabio.__init__ :members: :undoc-members: :show-inheritance: :mod:`fabio.fabioimage` Module ------------------------------ .. automodule:: fabio.fabioimage :members: :undoc-members: :show-inheritance: :mod:`fabio.fabioutils` Module ------------------------------ .. automodule:: fabio.fabioutils :members: :undoc-members: :show-inheritance: :mod:`fabio.file_series` Module ------------------------------- .. automodule:: fabio.file_series :members: :undoc-members: :show-inheritance: :mod:`fabio.openimage` Module ----------------------------- .. automodule:: fabio.openimage :members: :undoc-members: :show-inheritance: :mod:`fabio.adscimage` Module ----------------------------- .. automodule:: fabio.adscimage :members: :undoc-members: :show-inheritance: :mod:`fabio.binaryimage` Module ------------------------------- .. automodule:: fabio.binaryimage :members: :undoc-members: :show-inheritance: :mod:`fabio.bruker100image` Module ---------------------------------- .. automodule:: fabio.bruker100image :members: :undoc-members: :show-inheritance: :mod:`fabio.brukerimage` Module ------------------------------- .. automodule:: fabio.brukerimage :members: :undoc-members: :show-inheritance: :mod:`fabio.cbfimage` Module ---------------------------- .. automodule:: fabio.cbfimage :members: :undoc-members: :show-inheritance: :mod:`fabio.dm3image` Module ---------------------------- .. automodule:: fabio.dm3image :members: :undoc-members: :show-inheritance: :mod:`fabio.edfimage` Module ---------------------------- .. automodule:: fabio.edfimage :members: :undoc-members: :show-inheritance: :mod:`fabio.fit2dmaskimage` Module ---------------------------------- .. automodule:: fabio.fit2dmaskimage :members: :undoc-members: :show-inheritance: :mod:`fabio.fit2dspreadsheetimage` Module ----------------------------------------- .. automodule:: fabio.fit2dspreadsheetimage :members: :undoc-members: :show-inheritance: :mod:`fabio.GEimage` Module --------------------------- .. automodule:: fabio.GEimage :members: :undoc-members: :show-inheritance: :mod:`fabio.HiPiCimage` Module ------------------------------ .. automodule:: fabio.HiPiCimage :members: :undoc-members: :show-inheritance: :mod:`fabio.kcdimage` Module ---------------------------- .. automodule:: fabio.kcdimage :members: :undoc-members: :show-inheritance: :mod:`fabio.mar345image` Module ------------------------------- .. automodule:: fabio.mar345image :members: :undoc-members: :show-inheritance: :mod:`fabio.marccdimage` Module ------------------------------- .. automodule:: fabio.marccdimage :members: :undoc-members: :show-inheritance: :mod:`fabio.OXDimage` Module ---------------------------- .. automodule:: fabio.OXDimage :members: :undoc-members: :show-inheritance: :mod:`fabio.pilatusimage` Module -------------------------------- .. automodule:: fabio.pilatusimage :members: :undoc-members: :show-inheritance: :mod:`fabio.pnmimage` Module ---------------------------- .. automodule:: fabio.pnmimage :members: :undoc-members: :show-inheritance: :mod:`fabio.tifimage` Module ---------------------------- .. automodule:: fabio.tifimage :members: :undoc-members: :show-inheritance: :mod:`fabio.xsdimage` Module ---------------------------- .. automodule:: fabio.xsdimage :members: :undoc-members: :show-inheritance: :mod:`fabio.compression` Module ------------------------------- .. automodule:: fabio.compression :members: :undoc-members: :show-inheritance: :mod:`fabio.converters` Module ------------------------------ .. automodule:: fabio.converters :members: :undoc-members: :show-inheritance: :mod:`fabio.datIO` Module ------------------------- .. automodule:: fabio.datIO :members: :undoc-members: :show-inheritance: :mod:`fabio.TiffIO` Module -------------------------- .. automodule:: fabio.TiffIO :members: :undoc-members: :show-inheritance: :mod:`fabio.readbytestream` Module ---------------------------------- .. automodule:: fabio.readbytestream :members: :undoc-members: :show-inheritance: fabio-0.1.3/doc/html/_sources/api/fabio.txt0000644000175000017500000000024112121354612021276 0ustar jeromejerome00000000000000FabIO Package ============= :mod:`fabio` Package -------------------- .. automodule:: fabio.__init__ :members: :undoc-members: :show-inheritance: fabio-0.1.3/doc/html/_sources/getting_started.txt0000644000175000017500000003240412121415346022644 0ustar jeromejerome00000000000000Getting Started =============== FabIO is a Python module for reading and handling data from two-dimensional X-ray detectors. FabIO is a Python module written for easy and transparent reading of raw two-dimensional data from various X-ray detectors. The module provides a function for reading any image and returning a fabioimage object which contains both metadata (header information) and the raw data. All fabioimage object offer additional methods to extract information about the image and to open other detector images from the same data series. Introduction ------------ One obstacle when writing software to analyse data collected from a two-dimensional detector is to read the raw data into the program, not least because the data can be stored in many different formats depending on the instrument used. To overcome this problem we decided to develop a general module, FabIO (FABle I/O), to handle reading and writing of two-dimensional data. The code-base was initiated by merging parts of our fabian imageviewer and ImageD11 peak-search programs and has been developed since 2007 as part of the TotalCryst program suite for analysis of 3DXRD microscopy data. During integration into a range of scientific programs like the FABLE graphical interface, EDNA and the fast azimuthal integration library, pyFAI; FabIO has gained several features like handling multi-frame image formats as well as writing many of the file formats. FabIO Python module ------------------- Python is a scripting language that is very popular among scientists and which also allows well structured applications and libraries to be developed. Philosophy .......... The intention behind this development was to create a Python module which would enable easy reading of 2D data images, from any detector without having to worry about the file format. Therefore FabIO just needs a file name to open a file and it determines the file format automatically and deals with gzip and bzip2 compression transparently. Opening a file returns an object which stores the image in memory as a 2D NumPy array and the metadata, called header, in a Python dictionary. Beside the data and header attributes, some methods are provided for reading the previous or next image in a series of images as well as jumping to a specific file number. For the user, these auxiliary methods are intended to be independent of the image format (as far as is reasonably possible). FabIO is written in an object-oriented style (with classes) but aims at being used in a scripting environment: special care has been taken to ensure the library remains easy to use. Therefore no knowledge of object-oriented programming is required to get full benefits of the library. As the development is done in a collaborative and decentralized way; a comprehensive test suite has been added to reduce the number of regressions when new features are added or old problems are repaired. The software is very modular and allows new classes to be added for handling other data formats easily. FabIO and its source-code are freely available to everyone on-line, licensed under the GNU General Public License version 3 (GPLv3). FabIO is also available directly from popular Linux distributions like Debian and Ubuntu. Implementation .............. The main language used in the development of FabIO is Python; however, some image formats are compressed and require compression algorithms for reading and writing data. When such algorithms could not be implemented efficiently using Python or NumPy native modules were developed, in i.e. standard C code callable from Python (sometimes generated using Cython). This code has to be compiled for each computer architecture and offers excellent performance. FabIO is only dependent on the NumPy module and has extra features if two other optional Python modules are available. For reading XML files (that are used in EDNA) the Lxml module is required and the Python Image Library, PIL is needed for producing a PIL image for displaying the image in graphical user interfaces and several image-processing operations that are not re-implemented in FabIO. A variety of useful image processing is also available in the scipy.ndimage module and in scikits-image. Images can also be displayed in a convenient interactive manner using matplotlib and an IPython shell , which is mainly used for developing data analysis algorithms. Reading and writing procedure of the various TIFF formats is based on the TiffIO code from PyMCA. In the Python shell, the `fabio` module must be imported prior to reading an image in one of the supported file formats (see Table `Supported formats`, hereafter). The `fabio.open` function creates an instance of the Python class `fabioimage`, from the name of a file. This instance, named `img` hereafter, stores the image data in `img.data` as a 2D NumPy array. Often the image file contains more information than just the intensities of the pixels, e.g. information about how the image is stored and the instrument parameters at the time of the image acquisition, these metadata are usually stored in the file header. Header information, are available in `img.header` as a Python dictionary where keys are strings and values are usually strings or numeric values. Information in the header about the binary part of the image (compression, endianness, shape) are interpreted however, other metadata are exposed as they are recorded in the file. FabIO allows the user to modify and, where possible, to save this information (the table `Supported formats` summarizes writable formats). Automatic translation between file-formats, even if desirable, is sometimes impossible because not all format have the capability to be extended with additional metadata. Nevertheless FabIO is capable of converting one image data-format into another by taking care of the numerical specifics: for example float arrays are converted to integer arrays if the output format only accepts integers. FabIO methods ............. One strength of the implementation in an object oriented language is the possibility to combine functions (or methods) together with data appropriate for specific formats. In addition to the header information and image data, every `fabioimage` instance (returned by `fabio.open`) has methods inherited from `fabioimage` which provide information about the image minimum, maximum and mean values. In addition there are methods which return the file number, name etc. Some of the most important methods are specific for certain formats because the methods are related to how frames in a sequence are handled; these methods are `img.next()`, `img.previous()`, and `img.getframe(n)`. The behaviour of such methods varies depending on the image format: for single-frame format (like mar345), `img.next()` will return the image in next file; for multi-frame format (like GE), `img.next()` will return the next frame within the same file. For formats which are possibly multi-framed like EDF, the behaviour depends on the actual number of frames per file (accessible via the `img.nframes` attribute). Usage ----- Examples ........ In this section we have collected some basic examples of how FabIO can be employed. Opening an image: :: import fabio im100 = fabio.open('Quartz_0100.tif') # Open image file print(im0.data[1024,1024]) # Check a pixel value im101 = im100.next() # Open next image im270 = im1.getframe(270) # Jump to file number 270: Quartz_0270.tif Normalising the intensity to a value in the header: :: img = fabio.open('exampleimage0001.edf') print(img.header) {'ByteOrder': 'LowByteFirst', 'DATE (scan begin)': 'Mon Jun 28 21:22:16 2010', 'ESRFCurrent': '198.099', ... } # Normalise to beam current and save data srcur = float(img.header['ESRFCurrent']) img.data *= 200.0/srcur img.write('normed_0001.edf') Interactive viewing with matplotlib: :: from matplotlib import pyplot # Load matplotlib pyplot.imshow(img.data) # Display as an image pyplot.show() # Show GUI window Future and perspectives ----------------------- The Hierarchical Data Format version 5 (`hdf5`) is a data format which is increasingly popular for storage of X-ray and neutron data. To name a few facilities the synchrotron Soleil and the neutron sources ISIS, SNS and SINQ already use HDF extensively through the NeXus format. For now, mainly processed or curated data are stored in this format but new detectors are rumoured to provide native output in HDF5. FabIO will rely on H5Py, which already provides a good HDF5 binding for Python, as an external dependency, to be able to read and write such HDF5 files. In the near future FabIO will be upgraded to work with Python3 (a new version of Python); this change of version will affect some internals FabIO as string and file handling have been altered. This change is already ongoing as many parts of native code in C have already been translated into Cython to smoothe the transition, since Cython generates code compatible with Python3. This also makes it easier to retain backwards compatibility with the earlier Python versions. Conclusion ---------- FabIO gives an easy way to read and write 2D images when using the Python computer language. It was originally developed for X-ray diffraction data but now gives an easy way for scientists to access and manipulate their data from a wide range of 2D X-ray detectors. We welcome contributions to further improve the code and hope to add more file formats in the future as well as port the existing code base to the emerging Python3. Acknoledgements ............... We acknowledge Andy Götz and Kenneth Evans for extensive testing when including the FabIO reader in the Fable image viewer (Götz et al., 2007).We also thank V. Armando Solé for assistance with his TiffIO reader and Carsten Gundlach for deployment of FabIO at the beamlines i711 and i811, MAX IV, and providing bug reports. We finally acknowledge our colleagues who have reported bugs and helped to improve FabIO. Financial support was granted by the EU 6th Framework NEST/ADVENTURE project TotalCryst (Poulsen et al., 2006). Citation ........ Knudsen, E. B., Sørensen, H. O., Wright, J. P., Goret, G. & Kieffer, J. (2013). J. Appl. Cryst. 46, 537-539. http://dx.doi.org/10.1107/S0021889813000150 List of file formats that FabIO can read and write .................................................. In alphabetical order. The listed filename extensions are typical examples. FabIO tries to deduce the actual format from the file itself and only uses extensions as a fallback if that fails. .. csv-table:: Supported formats :header: "Python Module", "Detector / Format", "Extension", "Read", "Multi-image", "Write" :widths: 30, 30, 20, 10, 15, 10 "ADSC", "ADSC Quantum", ".img ", "Yes", "No", "Yes" "Bruker", "Bruker formats", ".sfrm ", "Yes", "No", "Yes" "DM3", "Gatan Digital Micrograph ", ".dm3 ", "Yes", "No", "No" "EDF", "ESRF data format ", ".edf ", "Yes", "Yes ", "Yes" "EDNA-XML", "Used by EDNA", ".xml ", "Yes", "No", "No" "CBF", "CIF binary files", ".cbf ", "Yes", "No", "Yes" "kcd", "Nonius KappaCCD", ".kccd ", "Yes", "No", "No" "fit2d mask", "Used by Fit2D", ".msk ", "Yes", "No", "Yes" "fit2d spreadsheet", "Used by Fit2D", ".spr ", "Yes", "No", "Yes" "GE", "General Electric", "No", "Yes", "Yes ", "No" "HiPiC", "Hamamatsu CCD", ".tif ", "Yes", "No", "No" "marccd", "MarCCD/Mar165", ".mccd ", "Yes", "No", "Yes" "mar345", "Mar345 image plate", ".mar3450 ", "Yes", "No", "Yes" "OXD", "Oxford Diffraction", ".img ", "Yes", "No", "Yes" "pilatus", "Dectris Pilatus Tiff", ".tif ", "Yes", "No", "Yes" "PNM", "Portable aNy Map", ".pnm ", "Yes", "No", "No" "TIFF", "Tagged Image File Format", ".tif ", "Yes", "No", "Yes" Adding new file formats ....................... We hope it will be relatively easy to add new file formats to fabio in the future. The basic idea is the following: 1. inherit from fabioimage overriding the methods _readheader, read and optionally write. Name your new module XXXimage where XXX means something (eg tifimage). 2. readheader fills in a dictionary of "name":"value" pairs in self.header. No one expects to find anything much in there. 3. read fills in self.data with a numpy array holding the image. Some redundant info which also appears are self.dim1 and self.dim2: the image dimensions, self.bpp is the bytes per pixel and self.bytecode is the numpy.dtype.type of the data. 4. The member variables "_need_a_seek_to_read" and "_need_a_real_file" are there in case you have trouble with the transparent handling of bz2 and gz files. 5. Register the file type (extension naming) in fabioutils.py:FILETYPES 6. Add your new module as an import into fabio.openimage 7. Fill out the magic numbers for your format in fabio.openimage if you know them (the characteristic first few bytes in the file) 8. Upload a testimage to the file release system and create a unittest testcase which opens an example of your new format, confirming the image has actually been read in successfully (eg check the mean, max, min and esd are all correct, perhaps orientation too) 9. Run pylint on your code and then please go clean it up. Have a go at mine while you are at it. 10. Bask in the warm glow of appreciation when someone unexpectedly learns they don't need to convert their data into another format fabio-0.1.3/doc/html/_sources/index.txt0000644000175000017500000000073612121413504020561 0ustar jeromejerome00000000000000.. FabIO documentation master file, created by sphinx-quickstart on Fri Mar 15 09:03:50 2013. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. Welcome to FabIO's documentation! ================================= Contents: .. toctree:: :maxdepth: 2 getting_started INSTALL Changelog api/modules Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search` fabio-0.1.3/doc/html/_sources/Changelog.txt0000644000175000017500000000400512233242527021343 0ustar jeromejerome00000000000000Changelog ========= From FabIO-0.1.2 to FabIO-0.1.3: ................................ - Fixed a memory-leak in mar345 module - Improved support for bruker format (writer & reader) - Fixed a bug in EDF headers (very long headers) - Provide template for new file-formats - Fix a bug related to PIL in new MacOSX - Allow binary-images to be read from end From FabIO-0.1.1 to FabIO-0.1.2: ................................ - Fixed a bug in fabioimage.write (impacted all writers) - added Sphinx documentation "python setup.py build_doc" - PyLint compliance of some classes (rename, ...) - tests from installer with "python setup.py build test" From FabIO-0.1.0 to FabIO-0.1.1: ................................ - Merged Mar345 image reader and writer with cython bindings (towards python3 compliance) - Improve CBF image writing under windows - Bz2, Gzip and Flat files are managed through a common way ... classes are more (python v2.5) or less (python v2.7) overloaded - Fast EDF reading if one assumes offsets are the same between files, same for ROIs From FabIO-0.0.8 to FabIO-0.1.0: ................................ - OXD reader improved and writer implemented - Mar345 reader improved and writer implemented - CBF writer implemented - Clean-up of the code & bug fixes - Move towards python3 - Make PIL optional dependency Python3 is not yet tested but some blocking points have been identified and some fixed. From FabIO-0.0.7 to FabIO-0.0.8: ................................ - Support for Tiff using TiffIO module from V.A.Solé - Clean-up of the code & bug fixes From FabIO-0.0.6 to FabIO-0.0.7: ................................ - Support for multi-frames EDF files - Support for XML images/2D arrays used in EDNA - new method: fabio.open(filename) that is an alias for fabio.openimage.openimage(filename) From FabIO-0.0.4 to FabIO-0.0.6: ................................ - Support for CBF files from Pilatus detectors - Support for KCD files from Nonius Kappa CCD images - write EDF with their native data type (instead of uint16 by default) fabio-0.1.3/doc/html/_sources/INSTALL.txt0000644000175000017500000000720312233247462020570 0ustar jeromejerome00000000000000Installation ============ FabIO can, as any Python module, be installed from its sources, available on sourceforge but we advice to use binary packages provided for the most common platforms on sourceforge: Windows, MacOSX and Linux. Moreover FabIO is part of the common Linux distributions Ubuntu (since 11.10) and Debian7 where the package is named python-fabio and can be installed via: :: # apt-get install python-fabio If you are using MS Windows or MacOSX; binary version have been packaged. Windows installers are executable, just download the one corresponding to you python version and run it. MacOSX builds are zipped: unzip them at the right place. Dependencies ------------ * Python 2.5 or later (python 3.x is not yet ready) * numpy - http://www.numpy.org For full functionality of Fabio the following modules need to be installed: * PIL (python imaging library) - http://www.pythonware.com * lxml (library for reading XSDimages) Installation from sources ------------------------- FabIO can be downloaded from the fable download page on sourceforge.net. Presently the source code has been distributed as a zip package and a compressed tarball. Download either one and unpack it. :: http://sourceforge.net/projects/fable/files/fabio/ e.g. :: tar xvzf fabio-0.1.3.tar.gz or :: unzip fabio-0.1.3.zip all files are unpacked into the directory fabio-0.1.3. To install these do :: cd fabio-0.1.3 and install fabio with :: python setup.py build sudo python setup.py install most likely you will need to gain root privileges (with sudo in front of the command) to install the built package. Development versions -------------------- The newest development version can be obtained by checking it out from the subversion (SVN) repository: :: svn checkout https://svn.sourceforge.net/svnroot/fable/fabio/trunk fabio cd fabio python setup.py build sudo python setup.py install For Ubuntu/Debian users, you will need: * python-imaging * python-imaging-tk * python-numpy * python-dev :: sudo apt-get install python-imaging python-imaging-tk python-numpy We provide also a debian-package builder based on stdeb: :: sudo apt-get install python-stdeb ./build-deb.sh which builds a debian package and installs it in a single command. Handy for testing. Test suite ---------- FabIO has a comprehensive test-suite to ensure non regression (about 100 tests). When you run the test for the first time, many test images will be download and converted into various compressed format like gzip and bzip2 (this takes a lot of time). Be sure you have an internet connection (and your environment variable http_proxy is correctly set-up, if you are behind a proxy). :: python setup.py build cd test python test_all.py ........................................WARNING:compression:Encounter the python-gzip bug with trailing garbage, trying subprocess gzip ..............................WARNING:edfimage:Non complete datablock: got 6928, expected 8388608 WARNING:edfimage:Non complete datablock: got 6928, expected 8388608 WARNING:edfimage:Non complete datablock: got 6928, expected 8388608 .....................WARNING:edfimage:Unknown compression scheme TY1 .....WARNING:edfimage:Unknown compression scheme FALSE ...WARNING: Non standard TIFF. Rows per strip TAG missing WARNING: Non standard TIFF. Strip byte counts TAG missing .... ---------------------------------------------------------------------- Ran 103 tests in 21.696s OK Many tests are there to deal with malformed files, don't worry if the programs comaplins in warnings about "bad files", it is done on purpose. fabio-0.1.3/doc/html/INSTALL.html0000644000175000017500000002270312233250021017056 0ustar jeromejerome00000000000000 Installation — FabIO 0.1.3 documentation

        Navigation

        Installation¶

        FabIO can, as any Python module, be installed from its sources, available on sourceforge but we advice to use binary packages provided for the most common platforms on sourceforge: Windows, MacOSX and Linux. Moreover FabIO is part of the common Linux distributions Ubuntu (since 11.10) and Debian7 where the package is named python-fabio and can be installed via:

        # apt-get install python-fabio

        If you are using MS Windows or MacOSX; binary version have been packaged. Windows installers are executable, just download the one corresponding to you python version and run it. MacOSX builds are zipped: unzip them at the right place.

        Dependencies¶

        For full functionality of Fabio the following modules need to be installed:

        Installation from sources¶

        FabIO can be downloaded from the fable download page on sourceforge.net. Presently the source code has been distributed as a zip package and a compressed tarball. Download either one and unpack it.

        http://sourceforge.net/projects/fable/files/fabio/

        e.g.

        tar xvzf fabio-0.1.3.tar.gz

        or

        unzip fabio-0.1.3.zip

        all files are unpacked into the directory fabio-0.1.3. To install these do

        cd fabio-0.1.3

        and install fabio with

        python setup.py build
sudo python setup.py install

        most likely you will need to gain root privileges (with sudo in front of the command) to install the built package.

        Development versions¶

        The newest development version can be obtained by checking it out from the subversion (SVN) repository:

        svn checkout https://svn.sourceforge.net/svnroot/fable/fabio/trunk fabio
cd fabio
python setup.py build
sudo python setup.py install

        For Ubuntu/Debian users, you will need:

        • python-imaging
        • python-imaging-tk
        • python-numpy
        • python-dev
        sudo apt-get install python-imaging python-imaging-tk python-numpy

        We provide also a debian-package builder based on stdeb:

        sudo apt-get install python-stdeb
./build-deb.sh

        which builds a debian package and installs it in a single command. Handy for testing.

        Test suite¶

        FabIO has a comprehensive test-suite to ensure non regression (about 100 tests). When you run the test for the first time, many test images will be download and converted into various compressed format like gzip and bzip2 (this takes a lot of time). Be sure you have an internet connection (and your environment variable http_proxy is correctly set-up, if you are behind a proxy).

        python setup.py build
cd test
python test_all.py
........................................WARNING:compression:Encounter the python-gzip bug with trailing garbage, trying subprocess gzip
..............................WARNING:edfimage:Non complete datablock: got 6928, expected 8388608
WARNING:edfimage:Non complete datablock: got 6928, expected 8388608
WARNING:edfimage:Non complete datablock: got 6928, expected 8388608
.....................WARNING:edfimage:Unknown compression scheme TY1
.....WARNING:edfimage:Unknown compression scheme FALSE
...WARNING: Non standard TIFF. Rows per strip TAG missing
WARNING: Non standard TIFF. Strip byte counts TAG missing
....
----------------------------------------------------------------------
Ran 103 tests in 21.696s
OK

        Many tests are there to deal with malformed files, don’t worry if the programs comaplins in warnings about “bad files”, it is done on purpose.

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        © Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
        fabio-0.1.3/doc/html/py-modindex.html0000644000175000017500000002253012233250023020205 0ustar jeromejerome00000000000000 Python Module Index — FabIO 0.1.3 documentation

        Navigation

        Python Module Index

        f
         
        f
        fabio
            fabio.__init__
            fabio.adscimage
            fabio.binaryimage
            fabio.bruker100image
            fabio.brukerimage
            fabio.cbfimage
            fabio.compression
            fabio.converters
            fabio.datIO
            fabio.dm3image
            fabio.edfimage
            fabio.fabioimage
            fabio.fabioutils
            fabio.file_series
            fabio.fit2dmaskimage
            fabio.fit2dspreadsheetimage
            fabio.GEimage
            fabio.HiPiCimage
            fabio.kcdimage
            fabio.mar345image
            fabio.marccdimage
            fabio.openimage
            fabio.OXDimage
            fabio.pilatusimage
            fabio.pnmimage
            fabio.readbytestream
            fabio.TiffIO
            fabio.tifimage
            fabio.xsdimage

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        © Copyright 2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer. Created using Sphinx 1.1.3.
        fabio-0.1.3/doc/source/0000755000175000017500000000000012233272207015424 5ustar jeromejerome00000000000000fabio-0.1.3/doc/source/api/0000755000175000017500000000000012233272207016175 5ustar jeromejerome00000000000000fabio-0.1.3/doc/source/api/modules.rst0000644000175000017500000001064512121354612020402 0ustar jeromejerome00000000000000FabIO Package ============= .. toctree:: :maxdepth: 4 :mod:`fabio` Package -------------------- .. automodule:: fabio.__init__ :members: :undoc-members: :show-inheritance: :mod:`fabio.fabioimage` Module ------------------------------ .. automodule:: fabio.fabioimage :members: :undoc-members: :show-inheritance: :mod:`fabio.fabioutils` Module ------------------------------ .. automodule:: fabio.fabioutils :members: :undoc-members: :show-inheritance: :mod:`fabio.file_series` Module ------------------------------- .. automodule:: fabio.file_series :members: :undoc-members: :show-inheritance: :mod:`fabio.openimage` Module ----------------------------- .. automodule:: fabio.openimage :members: :undoc-members: :show-inheritance: :mod:`fabio.adscimage` Module ----------------------------- .. automodule:: fabio.adscimage :members: :undoc-members: :show-inheritance: :mod:`fabio.binaryimage` Module ------------------------------- .. automodule:: fabio.binaryimage :members: :undoc-members: :show-inheritance: :mod:`fabio.bruker100image` Module ---------------------------------- .. automodule:: fabio.bruker100image :members: :undoc-members: :show-inheritance: :mod:`fabio.brukerimage` Module ------------------------------- .. automodule:: fabio.brukerimage :members: :undoc-members: :show-inheritance: :mod:`fabio.cbfimage` Module ---------------------------- .. automodule:: fabio.cbfimage :members: :undoc-members: :show-inheritance: :mod:`fabio.dm3image` Module ---------------------------- .. automodule:: fabio.dm3image :members: :undoc-members: :show-inheritance: :mod:`fabio.edfimage` Module ---------------------------- .. automodule:: fabio.edfimage :members: :undoc-members: :show-inheritance: :mod:`fabio.fit2dmaskimage` Module ---------------------------------- .. automodule:: fabio.fit2dmaskimage :members: :undoc-members: :show-inheritance: :mod:`fabio.fit2dspreadsheetimage` Module ----------------------------------------- .. automodule:: fabio.fit2dspreadsheetimage :members: :undoc-members: :show-inheritance: :mod:`fabio.GEimage` Module --------------------------- .. automodule:: fabio.GEimage :members: :undoc-members: :show-inheritance: :mod:`fabio.HiPiCimage` Module ------------------------------ .. automodule:: fabio.HiPiCimage :members: :undoc-members: :show-inheritance: :mod:`fabio.kcdimage` Module ---------------------------- .. automodule:: fabio.kcdimage :members: :undoc-members: :show-inheritance: :mod:`fabio.mar345image` Module ------------------------------- .. automodule:: fabio.mar345image :members: :undoc-members: :show-inheritance: :mod:`fabio.marccdimage` Module ------------------------------- .. automodule:: fabio.marccdimage :members: :undoc-members: :show-inheritance: :mod:`fabio.OXDimage` Module ---------------------------- .. automodule:: fabio.OXDimage :members: :undoc-members: :show-inheritance: :mod:`fabio.pilatusimage` Module -------------------------------- .. automodule:: fabio.pilatusimage :members: :undoc-members: :show-inheritance: :mod:`fabio.pnmimage` Module ---------------------------- .. automodule:: fabio.pnmimage :members: :undoc-members: :show-inheritance: :mod:`fabio.tifimage` Module ---------------------------- .. automodule:: fabio.tifimage :members: :undoc-members: :show-inheritance: :mod:`fabio.xsdimage` Module ---------------------------- .. automodule:: fabio.xsdimage :members: :undoc-members: :show-inheritance: :mod:`fabio.compression` Module ------------------------------- .. automodule:: fabio.compression :members: :undoc-members: :show-inheritance: :mod:`fabio.converters` Module ------------------------------ .. automodule:: fabio.converters :members: :undoc-members: :show-inheritance: :mod:`fabio.datIO` Module ------------------------- .. automodule:: fabio.datIO :members: :undoc-members: :show-inheritance: :mod:`fabio.TiffIO` Module -------------------------- .. automodule:: fabio.TiffIO :members: :undoc-members: :show-inheritance: :mod:`fabio.readbytestream` Module ---------------------------------- .. automodule:: fabio.readbytestream :members: :undoc-members: :show-inheritance: fabio-0.1.3/doc/source/getting_started.rst0000644000175000017500000003240412121415346021347 0ustar jeromejerome00000000000000Getting Started =============== FabIO is a Python module for reading and handling data from two-dimensional X-ray detectors. FabIO is a Python module written for easy and transparent reading of raw two-dimensional data from various X-ray detectors. The module provides a function for reading any image and returning a fabioimage object which contains both metadata (header information) and the raw data. All fabioimage object offer additional methods to extract information about the image and to open other detector images from the same data series. Introduction ------------ One obstacle when writing software to analyse data collected from a two-dimensional detector is to read the raw data into the program, not least because the data can be stored in many different formats depending on the instrument used. To overcome this problem we decided to develop a general module, FabIO (FABle I/O), to handle reading and writing of two-dimensional data. The code-base was initiated by merging parts of our fabian imageviewer and ImageD11 peak-search programs and has been developed since 2007 as part of the TotalCryst program suite for analysis of 3DXRD microscopy data. During integration into a range of scientific programs like the FABLE graphical interface, EDNA and the fast azimuthal integration library, pyFAI; FabIO has gained several features like handling multi-frame image formats as well as writing many of the file formats. FabIO Python module ------------------- Python is a scripting language that is very popular among scientists and which also allows well structured applications and libraries to be developed. Philosophy .......... The intention behind this development was to create a Python module which would enable easy reading of 2D data images, from any detector without having to worry about the file format. Therefore FabIO just needs a file name to open a file and it determines the file format automatically and deals with gzip and bzip2 compression transparently. Opening a file returns an object which stores the image in memory as a 2D NumPy array and the metadata, called header, in a Python dictionary. Beside the data and header attributes, some methods are provided for reading the previous or next image in a series of images as well as jumping to a specific file number. For the user, these auxiliary methods are intended to be independent of the image format (as far as is reasonably possible). FabIO is written in an object-oriented style (with classes) but aims at being used in a scripting environment: special care has been taken to ensure the library remains easy to use. Therefore no knowledge of object-oriented programming is required to get full benefits of the library. As the development is done in a collaborative and decentralized way; a comprehensive test suite has been added to reduce the number of regressions when new features are added or old problems are repaired. The software is very modular and allows new classes to be added for handling other data formats easily. FabIO and its source-code are freely available to everyone on-line, licensed under the GNU General Public License version 3 (GPLv3). FabIO is also available directly from popular Linux distributions like Debian and Ubuntu. Implementation .............. The main language used in the development of FabIO is Python; however, some image formats are compressed and require compression algorithms for reading and writing data. When such algorithms could not be implemented efficiently using Python or NumPy native modules were developed, in i.e. standard C code callable from Python (sometimes generated using Cython). This code has to be compiled for each computer architecture and offers excellent performance. FabIO is only dependent on the NumPy module and has extra features if two other optional Python modules are available. For reading XML files (that are used in EDNA) the Lxml module is required and the Python Image Library, PIL is needed for producing a PIL image for displaying the image in graphical user interfaces and several image-processing operations that are not re-implemented in FabIO. A variety of useful image processing is also available in the scipy.ndimage module and in scikits-image. Images can also be displayed in a convenient interactive manner using matplotlib and an IPython shell , which is mainly used for developing data analysis algorithms. Reading and writing procedure of the various TIFF formats is based on the TiffIO code from PyMCA. In the Python shell, the `fabio` module must be imported prior to reading an image in one of the supported file formats (see Table `Supported formats`, hereafter). The `fabio.open` function creates an instance of the Python class `fabioimage`, from the name of a file. This instance, named `img` hereafter, stores the image data in `img.data` as a 2D NumPy array. Often the image file contains more information than just the intensities of the pixels, e.g. information about how the image is stored and the instrument parameters at the time of the image acquisition, these metadata are usually stored in the file header. Header information, are available in `img.header` as a Python dictionary where keys are strings and values are usually strings or numeric values. Information in the header about the binary part of the image (compression, endianness, shape) are interpreted however, other metadata are exposed as they are recorded in the file. FabIO allows the user to modify and, where possible, to save this information (the table `Supported formats` summarizes writable formats). Automatic translation between file-formats, even if desirable, is sometimes impossible because not all format have the capability to be extended with additional metadata. Nevertheless FabIO is capable of converting one image data-format into another by taking care of the numerical specifics: for example float arrays are converted to integer arrays if the output format only accepts integers. FabIO methods ............. One strength of the implementation in an object oriented language is the possibility to combine functions (or methods) together with data appropriate for specific formats. In addition to the header information and image data, every `fabioimage` instance (returned by `fabio.open`) has methods inherited from `fabioimage` which provide information about the image minimum, maximum and mean values. In addition there are methods which return the file number, name etc. Some of the most important methods are specific for certain formats because the methods are related to how frames in a sequence are handled; these methods are `img.next()`, `img.previous()`, and `img.getframe(n)`. The behaviour of such methods varies depending on the image format: for single-frame format (like mar345), `img.next()` will return the image in next file; for multi-frame format (like GE), `img.next()` will return the next frame within the same file. For formats which are possibly multi-framed like EDF, the behaviour depends on the actual number of frames per file (accessible via the `img.nframes` attribute). Usage ----- Examples ........ In this section we have collected some basic examples of how FabIO can be employed. Opening an image: :: import fabio im100 = fabio.open('Quartz_0100.tif') # Open image file print(im0.data[1024,1024]) # Check a pixel value im101 = im100.next() # Open next image im270 = im1.getframe(270) # Jump to file number 270: Quartz_0270.tif Normalising the intensity to a value in the header: :: img = fabio.open('exampleimage0001.edf') print(img.header) {'ByteOrder': 'LowByteFirst', 'DATE (scan begin)': 'Mon Jun 28 21:22:16 2010', 'ESRFCurrent': '198.099', ... } # Normalise to beam current and save data srcur = float(img.header['ESRFCurrent']) img.data *= 200.0/srcur img.write('normed_0001.edf') Interactive viewing with matplotlib: :: from matplotlib import pyplot # Load matplotlib pyplot.imshow(img.data) # Display as an image pyplot.show() # Show GUI window Future and perspectives ----------------------- The Hierarchical Data Format version 5 (`hdf5`) is a data format which is increasingly popular for storage of X-ray and neutron data. To name a few facilities the synchrotron Soleil and the neutron sources ISIS, SNS and SINQ already use HDF extensively through the NeXus format. For now, mainly processed or curated data are stored in this format but new detectors are rumoured to provide native output in HDF5. FabIO will rely on H5Py, which already provides a good HDF5 binding for Python, as an external dependency, to be able to read and write such HDF5 files. In the near future FabIO will be upgraded to work with Python3 (a new version of Python); this change of version will affect some internals FabIO as string and file handling have been altered. This change is already ongoing as many parts of native code in C have already been translated into Cython to smoothe the transition, since Cython generates code compatible with Python3. This also makes it easier to retain backwards compatibility with the earlier Python versions. Conclusion ---------- FabIO gives an easy way to read and write 2D images when using the Python computer language. It was originally developed for X-ray diffraction data but now gives an easy way for scientists to access and manipulate their data from a wide range of 2D X-ray detectors. We welcome contributions to further improve the code and hope to add more file formats in the future as well as port the existing code base to the emerging Python3. Acknoledgements ............... We acknowledge Andy Götz and Kenneth Evans for extensive testing when including the FabIO reader in the Fable image viewer (Götz et al., 2007).We also thank V. Armando Solé for assistance with his TiffIO reader and Carsten Gundlach for deployment of FabIO at the beamlines i711 and i811, MAX IV, and providing bug reports. We finally acknowledge our colleagues who have reported bugs and helped to improve FabIO. Financial support was granted by the EU 6th Framework NEST/ADVENTURE project TotalCryst (Poulsen et al., 2006). Citation ........ Knudsen, E. B., Sørensen, H. O., Wright, J. P., Goret, G. & Kieffer, J. (2013). J. Appl. Cryst. 46, 537-539. http://dx.doi.org/10.1107/S0021889813000150 List of file formats that FabIO can read and write .................................................. In alphabetical order. The listed filename extensions are typical examples. FabIO tries to deduce the actual format from the file itself and only uses extensions as a fallback if that fails. .. csv-table:: Supported formats :header: "Python Module", "Detector / Format", "Extension", "Read", "Multi-image", "Write" :widths: 30, 30, 20, 10, 15, 10 "ADSC", "ADSC Quantum", ".img ", "Yes", "No", "Yes" "Bruker", "Bruker formats", ".sfrm ", "Yes", "No", "Yes" "DM3", "Gatan Digital Micrograph ", ".dm3 ", "Yes", "No", "No" "EDF", "ESRF data format ", ".edf ", "Yes", "Yes ", "Yes" "EDNA-XML", "Used by EDNA", ".xml ", "Yes", "No", "No" "CBF", "CIF binary files", ".cbf ", "Yes", "No", "Yes" "kcd", "Nonius KappaCCD", ".kccd ", "Yes", "No", "No" "fit2d mask", "Used by Fit2D", ".msk ", "Yes", "No", "Yes" "fit2d spreadsheet", "Used by Fit2D", ".spr ", "Yes", "No", "Yes" "GE", "General Electric", "No", "Yes", "Yes ", "No" "HiPiC", "Hamamatsu CCD", ".tif ", "Yes", "No", "No" "marccd", "MarCCD/Mar165", ".mccd ", "Yes", "No", "Yes" "mar345", "Mar345 image plate", ".mar3450 ", "Yes", "No", "Yes" "OXD", "Oxford Diffraction", ".img ", "Yes", "No", "Yes" "pilatus", "Dectris Pilatus Tiff", ".tif ", "Yes", "No", "Yes" "PNM", "Portable aNy Map", ".pnm ", "Yes", "No", "No" "TIFF", "Tagged Image File Format", ".tif ", "Yes", "No", "Yes" Adding new file formats ....................... We hope it will be relatively easy to add new file formats to fabio in the future. The basic idea is the following: 1. inherit from fabioimage overriding the methods _readheader, read and optionally write. Name your new module XXXimage where XXX means something (eg tifimage). 2. readheader fills in a dictionary of "name":"value" pairs in self.header. No one expects to find anything much in there. 3. read fills in self.data with a numpy array holding the image. Some redundant info which also appears are self.dim1 and self.dim2: the image dimensions, self.bpp is the bytes per pixel and self.bytecode is the numpy.dtype.type of the data. 4. The member variables "_need_a_seek_to_read" and "_need_a_real_file" are there in case you have trouble with the transparent handling of bz2 and gz files. 5. Register the file type (extension naming) in fabioutils.py:FILETYPES 6. Add your new module as an import into fabio.openimage 7. Fill out the magic numbers for your format in fabio.openimage if you know them (the characteristic first few bytes in the file) 8. Upload a testimage to the file release system and create a unittest testcase which opens an example of your new format, confirming the image has actually been read in successfully (eg check the mean, max, min and esd are all correct, perhaps orientation too) 9. Run pylint on your code and then please go clean it up. Have a go at mine while you are at it. 10. Bask in the warm glow of appreciation when someone unexpectedly learns they don't need to convert their data into another format fabio-0.1.3/doc/source/_static/0000755000175000017500000000000012233272207017052 5ustar jeromejerome00000000000000fabio-0.1.3/doc/source/_static/placeholder0000644000175000017500000000006612121417527021263 0ustar jeromejerome00000000000000#This empty file is there to keep the directory in Gitfabio-0.1.3/doc/source/conf.py0000644000175000017500000001714712233242132016727 0ustar jeromejerome00000000000000# -*- coding: utf-8 -*- # # FabIO documentation build configuration file, created by # sphinx-quickstart on Fri Mar 15 09:03:50 2013. # # This file is execfile()d with the current directory set to its containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. import sys, os # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. #sys.path.insert(0, os.path.abspath('.')) # -- General configuration ----------------------------------------------------- # If your documentation needs a minimal Sphinx version, state it here. #needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be extensions # coming with Sphinx (named 'sphinx.ext.*') or your custom ones. extensions = ['sphinx.ext.autodoc', 'sphinx.ext.todo', 'sphinx.ext.viewcode', "sphinx.ext.pngmath"] # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix of source filenames. source_suffix = '.rst' # The encoding of source files. #source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # General information about the project. project = u'FabIO' copyright = u'2006-2013, Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. version = '0.1.3' # The full version, including alpha/beta/rc tags. release = '0.1.3' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. #language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: #today = '' # Else, today_fmt is used as the format for a strftime call. #today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. exclude_patterns = [] # The reST default role (used for this markup: `text`) to use for all documents. #default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. #add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). #add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. #show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. #modindex_common_prefix = [] # -- Options for HTML output --------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. html_theme = 'default' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. #html_theme_options = {} # Add any paths that contain custom themes here, relative to this directory. #html_theme_path = [] # The name for this set of Sphinx documents. If None, it defaults to # " v documentation". #html_title = None # A shorter title for the navigation bar. Default is the same as html_title. #html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. #html_logo = None # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. #html_favicon = None # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. #html_last_updated_fmt = '%b %d, %Y' # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. #html_use_smartypants = True # Custom sidebar templates, maps document names to template names. #html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. #html_additional_pages = {} # If false, no module index is generated. #html_domain_indices = True # If false, no index is generated. #html_use_index = True # If true, the index is split into individual pages for each letter. #html_split_index = False # If true, links to the reST sources are added to the pages. #html_show_sourcelink = True # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. #html_show_sphinx = True # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. #html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. #html_use_opensearch = '' # This is the file name suffix for HTML files (e.g. ".xhtml"). #html_file_suffix = None # Output file base name for HTML help builder. htmlhelp_basename = 'FabIOdoc' # -- Options for LaTeX output -------------------------------------------------- # The paper size ('letter' or 'a4'). #latex_paper_size = 'letter' # The font size ('10pt', '11pt' or '12pt'). #latex_font_size = '10pt' # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ ('index', 'FabIO.tex', u'FabIO Documentation', u'H. Sorensen, E. Knudsen, J. Wright, G. Goret and J. Kieffer', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. #latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. #latex_use_parts = False # If true, show page references after internal links. #latex_show_pagerefs = False # If true, show URL addresses after external links. #latex_show_urls = False # Additional stuff for the LaTeX preamble. #latex_preamble = '' # Documents to append as an appendix to all manuals. #latex_appendices = [] # If false, no module index is generated. #latex_domain_indices = True # -- Options for manual page output -------------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ ('index', 'fabio', u'FabIO Documentation', [u'Henning Sorensen, Erik Knudsen, Jon Wright, Gael Goret and Jerome Kieffer'], 1) ] # Documents to append as an appendix to all manuals. #texinfo_appendices = [] # If false, no module index is generated. #texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. #texinfo_show_urls = 'footnote' # still use the epydoc markup for now import re re_field = re.compile('@(param|type|rtype|return)') def fix_docstring(app, what, name, obj, options, lines): for i in xrange(len(lines)): lines[i] = re_field.sub(r':\1', lines[i]) def setup(app): app.connect('autodoc-process-docstring', fix_docstring) fabio-0.1.3/doc/source/Changelog.rst0000644000175000017500000000400512233242527020046 0ustar jeromejerome00000000000000Changelog ========= From FabIO-0.1.2 to FabIO-0.1.3: ................................ - Fixed a memory-leak in mar345 module - Improved support for bruker format (writer & reader) - Fixed a bug in EDF headers (very long headers) - Provide template for new file-formats - Fix a bug related to PIL in new MacOSX - Allow binary-images to be read from end From FabIO-0.1.1 to FabIO-0.1.2: ................................ - Fixed a bug in fabioimage.write (impacted all writers) - added Sphinx documentation "python setup.py build_doc" - PyLint compliance of some classes (rename, ...) - tests from installer with "python setup.py build test" From FabIO-0.1.0 to FabIO-0.1.1: ................................ - Merged Mar345 image reader and writer with cython bindings (towards python3 compliance) - Improve CBF image writing under windows - Bz2, Gzip and Flat files are managed through a common way ... classes are more (python v2.5) or less (python v2.7) overloaded - Fast EDF reading if one assumes offsets are the same between files, same for ROIs From FabIO-0.0.8 to FabIO-0.1.0: ................................ - OXD reader improved and writer implemented - Mar345 reader improved and writer implemented - CBF writer implemented - Clean-up of the code & bug fixes - Move towards python3 - Make PIL optional dependency Python3 is not yet tested but some blocking points have been identified and some fixed. From FabIO-0.0.7 to FabIO-0.0.8: ................................ - Support for Tiff using TiffIO module from V.A.Solé - Clean-up of the code & bug fixes From FabIO-0.0.6 to FabIO-0.0.7: ................................ - Support for multi-frames EDF files - Support for XML images/2D arrays used in EDNA - new method: fabio.open(filename) that is an alias for fabio.openimage.openimage(filename) From FabIO-0.0.4 to FabIO-0.0.6: ................................ - Support for CBF files from Pilatus detectors - Support for KCD files from Nonius Kappa CCD images - write EDF with their native data type (instead of uint16 by default) fabio-0.1.3/doc/source/INSTALL.rst0000644000175000017500000000720312233247462017273 0ustar jeromejerome00000000000000Installation ============ FabIO can, as any Python module, be installed from its sources, available on sourceforge but we advice to use binary packages provided for the most common platforms on sourceforge: Windows, MacOSX and Linux. Moreover FabIO is part of the common Linux distributions Ubuntu (since 11.10) and Debian7 where the package is named python-fabio and can be installed via: :: # apt-get install python-fabio If you are using MS Windows or MacOSX; binary version have been packaged. Windows installers are executable, just download the one corresponding to you python version and run it. MacOSX builds are zipped: unzip them at the right place. Dependencies ------------ * Python 2.5 or later (python 3.x is not yet ready) * numpy - http://www.numpy.org For full functionality of Fabio the following modules need to be installed: * PIL (python imaging library) - http://www.pythonware.com * lxml (library for reading XSDimages) Installation from sources ------------------------- FabIO can be downloaded from the fable download page on sourceforge.net. Presently the source code has been distributed as a zip package and a compressed tarball. Download either one and unpack it. :: http://sourceforge.net/projects/fable/files/fabio/ e.g. :: tar xvzf fabio-0.1.3.tar.gz or :: unzip fabio-0.1.3.zip all files are unpacked into the directory fabio-0.1.3. To install these do :: cd fabio-0.1.3 and install fabio with :: python setup.py build sudo python setup.py install most likely you will need to gain root privileges (with sudo in front of the command) to install the built package. Development versions -------------------- The newest development version can be obtained by checking it out from the subversion (SVN) repository: :: svn checkout https://svn.sourceforge.net/svnroot/fable/fabio/trunk fabio cd fabio python setup.py build sudo python setup.py install For Ubuntu/Debian users, you will need: * python-imaging * python-imaging-tk * python-numpy * python-dev :: sudo apt-get install python-imaging python-imaging-tk python-numpy We provide also a debian-package builder based on stdeb: :: sudo apt-get install python-stdeb ./build-deb.sh which builds a debian package and installs it in a single command. Handy for testing. Test suite ---------- FabIO has a comprehensive test-suite to ensure non regression (about 100 tests). When you run the test for the first time, many test images will be download and converted into various compressed format like gzip and bzip2 (this takes a lot of time). Be sure you have an internet connection (and your environment variable http_proxy is correctly set-up, if you are behind a proxy). :: python setup.py build cd test python test_all.py ........................................WARNING:compression:Encounter the python-gzip bug with trailing garbage, trying subprocess gzip ..............................WARNING:edfimage:Non complete datablock: got 6928, expected 8388608 WARNING:edfimage:Non complete datablock: got 6928, expected 8388608 WARNING:edfimage:Non complete datablock: got 6928, expected 8388608 .....................WARNING:edfimage:Unknown compression scheme TY1 .....WARNING:edfimage:Unknown compression scheme FALSE ...WARNING: Non standard TIFF. Rows per strip TAG missing WARNING: Non standard TIFF. Strip byte counts TAG missing .... ---------------------------------------------------------------------- Ran 103 tests in 21.696s OK Many tests are there to deal with malformed files, don't worry if the programs comaplins in warnings about "bad files", it is done on purpose. fabio-0.1.3/doc/source/index.rst0000644000175000017500000000073612121413504017264 0ustar jeromejerome00000000000000.. FabIO documentation master file, created by sphinx-quickstart on Fri Mar 15 09:03:50 2013. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. Welcome to FabIO's documentation! ================================= Contents: .. toctree:: :maxdepth: 2 getting_started INSTALL Changelog api/modules Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search` fabio-0.1.3/fabio-src/0000755000175000017500000000000012233272207015224 5ustar jeromejerome00000000000000fabio-0.1.3/fabio-src/marccdimage.py0000644000175000017500000003272012233175156020043 0ustar jeromejerome00000000000000#!/usr/bin/env python """ Authors: ........ * Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions; Risoe National Laboratory; Frederiksborgvej 399; DK-4000 Roskilde; email:erik.knudsen@risoe.dk * Jon Wright: European Synchrotron Radiation Facility; Grenoble (France) marccdimage can read MarCCD and MarMosaic images including header info. JPW : Use a parser in case of typos (sorry?) """ # Base this on the tifimage (as marccd seems to be tiff with a # special header from tifimage import tifimage import logging logger = logging.getLogger("marccdimage") # Now for the c definition (found on mar webpage) # The following string is therefore copyrighted by Mar I guess CDEFINITION = """ typedef struct frame_header_type { /* File/header format parameters (256 bytes) */ UINT32 header_type; /* flag for header type (can be used as magic number) */ char header_name[16]; /* header name (MMX) */ UINT32 header_major_version; /* header_major_version (n.) */ UINT32 header_minor_version; /* header_minor_version (.n) */ UINT32 header_byte_order;/* BIG_ENDIAN (Motorola,MIPS); LITTLE_ENDIAN (DEC, Intel) */ UINT32 data_byte_order; /* BIG_ENDIAN (Motorola,MIPS); LITTLE_ENDIAN (DEC, Intel) */ UINT32 header_size; /* in bytes */ UINT32 frame_type; /* flag for frame type */ UINT32 magic_number; /* to be used as a flag - usually to indicate new file */ UINT32 compression_type; /* type of image compression */ UINT32 compression1; /* compression parameter 1 */ UINT32 compression2; /* compression parameter 2 */ UINT32 compression3; /* compression parameter 3 */ UINT32 compression4; /* compression parameter 4 */ UINT32 compression5; /* compression parameter 4 */ UINT32 compression6; /* compression parameter 4 */ UINT32 nheaders; /* total number of headers */ UINT32 nfast; /* number of pixels in one line */ UINT32 nslow; /* number of lines in image */ UINT32 depth; /* number of bytes per pixel */ UINT32 record_length; /* number of pixels between succesive rows */ UINT32 signif_bits; /* true depth of data, in bits */ UINT32 data_type; /* (signed,unsigned,float...) */ UINT32 saturated_value; /* value marks pixel as saturated */ UINT32 sequence; /* TRUE or FALSE */ UINT32 nimages; /* total number of images - size of each is nfast*(nslow/nimages) */ UINT32 origin; /* corner of origin */ UINT32 orientation; /* direction of fast axis */ UINT32 view_direction; /* direction to view frame */ UINT32 overflow_location;/* FOLLOWING_HEADER, FOLLOWING_DATA */ UINT32 over_8_bits; /* # of pixels with counts 255 */ UINT32 over_16_bits; /* # of pixels with count 65535 */ UINT32 multiplexed; /* multiplex flag */ UINT32 nfastimages; /* # of images in fast direction */ UINT32 nslowimages; /* # of images in slow direction */ UINT32 background_applied;/* flags correction has been applied hold magic number ? */ UINT32 bias_applied; /* flags correction has been applied hold magic number ? */ UINT32 flatfield_applied;/* flags correction has been applied - hold magic number ? */ UINT32 distortion_applied;/*flags correction has been applied - hold magic number ? */ UINT32 original_header_type; /* Header/frame type from file that frame is read from */ UINT32 file_saved; /* Flag that file has been saved, should be zeroed if modified */ char reserve1[(64-40)*sizeof(INT32)-16]; /* Data statistics (128) */ UINT32 total_counts[2]; /* 64 bit integer range = 1.85E19*/ UINT32 special_counts1[2]; UINT32 special_counts2[2]; UINT32 min; UINT32 max; UINT32 mean; UINT32 rms; UINT32 p10; UINT32 p90; UINT32 stats_uptodate; UINT32 pixel_noise[MAXIMAGES]; /*1000*base noise value (ADUs) */ char reserve2[(32-13-MAXIMAGES)*sizeof(INT32)]; /* More statistics (256) */ UINT16 percentile[128]; /* Goniostat parameters (128 bytes) */ INT32 xtal_to_detector; /* 1000*distance in millimeters */ INT32 beam_x; /* 1000*x beam position (pixels) */ INT32 beam_y; /* 1000*y beam position (pixels) */ INT32 integration_time; /* integration time in milliseconds */ INT32 exposure_time; /* exposure time in milliseconds */ INT32 readout_time; /* readout time in milliseconds */ INT32 nreads; /* number of readouts to get this image */ INT32 start_twotheta; /* 1000*two_theta angle */ INT32 start_omega; /* 1000*omega angle */ INT32 start_chi; /* 1000*chi angle */ INT32 start_kappa; /* 1000*kappa angle */ INT32 start_phi; /* 1000*phi angle */ INT32 start_delta; /* 1000*delta angle */ INT32 start_gamma; /* 1000*gamma angle */ INT32 start_xtal_to_detector; /* 1000*distance in mm (dist in um)*/ INT32 end_twotheta; /* 1000*two_theta angle */ INT32 end_omega; /* 1000*omega angle */ INT32 end_chi; /* 1000*chi angle */ INT32 end_kappa; /* 1000*kappa angle */ INT32 end_phi; /* 1000*phi angle */ INT32 end_delta; /* 1000*delta angle */ INT32 end_gamma; /* 1000*gamma angle */ INT32 end_xtal_to_detector; /* 1000*distance in mm (dist in um)*/ INT32 rotation_axis; /* active rotation axis */ INT32 rotation_range; /* 1000*rotation angle */ INT32 detector_rotx; /* 1000*rotation of detector around X */ INT32 detector_roty; /* 1000*rotation of detector around Y */ INT32 detector_rotz; /* 1000*rotation of detector around Z */ char reserve3[(32-28)*sizeof(INT32)]; /* Detector parameters (128 bytes) */ INT32 detector_type; /* detector type */ INT32 pixelsize_x; /* pixel size (nanometers) */ INT32 pixelsize_y; /* pixel size (nanometers) */ INT32 mean_bias; /* 1000*mean bias value */ INT32 photons_per_100adu; /* photons / 100 ADUs */ INT32 measured_bias[MAXIMAGES];/* 1000*mean bias value for each image*/ INT32 measured_temperature[MAXIMAGES]; /* Temperature of each detector in milliKelvins */ INT32 measured_pressure[MAXIMAGES]; /* Pressure of each chamber in microTorr */ /* Retired reserve4 when MAXIMAGES set to 9 from 16 and two fields removed, and temp and pressure added char reserve4[(32-(5+3*MAXIMAGES))*sizeof(INT32)] */ /* X-ray source and optics parameters (128 bytes) */ /* X-ray source parameters (8*4 bytes) */ INT32 source_type; /* (code) - target, synch. etc */ INT32 source_dx; /* Optics param. - (size microns) */ INT32 source_dy; /* Optics param. - (size microns) */ INT32 source_wavelength; /* wavelength (femtoMeters) */ INT32 source_power; /* (Watts) */ INT32 source_voltage; /* (Volts) */ INT32 source_current; /* (microAmps) */ INT32 source_bias; /* (Volts) */ INT32 source_polarization_x; /* () */ INT32 source_polarization_y; /* () */ char reserve_source[4*sizeof(INT32)]; /* X-ray optics_parameters (8*4 bytes) */ INT32 optics_type; /* Optics type (code)*/ INT32 optics_dx; /* Optics param. - (size microns) */ INT32 optics_dy; /* Optics param. - (size microns) */ INT32 optics_wavelength; /* Optics param. - (size microns) */ INT32 optics_dispersion; /* Optics param. - (*10E6) */ INT32 optics_crossfire_x; /* Optics param. - (microRadians) */ INT32 optics_crossfire_y; /* Optics param. - (microRadians) */ INT32 optics_angle; /* Optics param. - (monoch. 2theta - microradians) */ INT32 optics_polarization_x; /* () */ INT32 optics_polarization_y; /* () */ char reserve_optics[4*sizeof(INT32)]; char reserve5[((32-28)*sizeof(INT32))]; /* File parameters (1024 bytes) */ char filetitle[128]; /* Title */ char filepath[128]; /* path name for data file */ char filename[64]; /* name of data file */ char acquire_timestamp[32]; /* date and time of acquisition */ char header_timestamp[32]; /* date and time of header update */ char save_timestamp[32]; /* date and time file saved */ char file_comments[512]; /* comments, use as desired */ char reserve6[1024-(128+128+64+(3*32)+512)]; /* Dataset parameters (512 bytes) */ char dataset_comments[512]; /* comments, used as desired */ /* pad out to 3072 bytes */ char pad[3072-(256+128+256+(3*128)+1024+512)]; } frame_header; """ import struct # Convert mar c header file types to python struct module types C_TO_STRUCT = { "INT32" : "i", "UINT32" : "I", "char" : "c", "UINT16" : "H" } # Sizes (bytes) of mar c header objects C_SIZES = { "INT32" : 4, "UINT32" : 4, "char" : 1, "UINT16" : 2 } # This was worked out by trial and error from a trial image I think MAXIMAGES = 9 def make_format(c_def_string): """ Reads the header definition in c and makes the format string to pass to struct.unpack """ lines = c_def_string.split("\n") fmt = "" names = [] expected = 0 for line in lines: if line.find(";") == -1: continue decl = line.split(";")[0].lstrip().rstrip() try: [typ, name] = decl.split() except ValueError: logger.debug("skipping: %s" , line) continue if name.find("[") > -1: # repeated ... times try: num = name.split("[")[1].split("]")[0] num = num.replace("MAXIMAGES", str(MAXIMAGES)) num = num.replace("sizeof(INT32)", "4") times = eval(num) except Exception, error: logger.error("%s Please decode %s", error, decl) raise error else: times = 1 try: fmt += C_TO_STRUCT[typ] * times names += [name] * times expected += C_SIZES[typ] * times except KeyError: continue return names, fmt # Make these be compiled on loading module HEADER_NAMES, HEADER_FORMAT = make_format(CDEFINITION) def interpret_header(header, fmt, names): """ given a format and header interpret it """ values = struct.unpack(fmt, header) hdr = {} i = 0 for name in names: if hdr.has_key(name): if type(values[i]) == type("string"): hdr[name] = hdr[name] + values[i] else: try: hdr[name].append(values[i]) except AttributeError: hdr[name] = [hdr[name], values[i]] else: hdr[name] = values[i] i = i + 1 return hdr class marccdimage(tifimage): """ Read in data in mar ccd format, also MarMosaic images, including header info """ def _readheader(self, infile): """ Parser based approach Gets all entries """ infile.seek(1024) hstr = infile.read(3072) self.header = interpret_header(hstr, HEADER_FORMAT, HEADER_NAMES) def _read(self, fname): """ inherited from tifimage ... a marccd image *is a* tif image just with a header """ return tifimage.read(self, fname) fabio-0.1.3/fabio-src/compression.py0000644000175000017500000003317512233175156020155 0ustar jeromejerome00000000000000#!/usr/bin/env python # coding: utf8 """ Authors: Jérôme Kieffer, ESRF email:jerome.kieffer@esrf.fr FabIO library containing compression and decompression algorithm for various """ __author__ = "Jérôme Kieffer" __contact__ = "jerome.kieffer@esrf.eu" __license__ = "GPLv3+" __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" import logging, struct, hashlib, base64, StringIO, sys if sys.version_info >= (3,): str = bytes logger = logging.getLogger("compression") import numpy try: import gzip except ImportError: logger.error("Unable to import gzip module: disabling gzip compression") gzip = None try: import bz2 except ImportError: logger.error("Unable to import bz2 module: disabling bz2 compression") bz2 = None try: import zlib except ImportError: logger.error("Unable to import zlib module: disabling zlib compression") zlib = None def md5sum(blob): """ returns the md5sum of an object... """ return base64.b64encode(hashlib.md5(blob).digest()) def endianness(): """ Return the native endianness of the system """ if numpy.little_endian: return "LITTLE_ENDIAN" else: return "BIG_ENDIAN" def decGzip(stream): """ Decompress a chunk of data using the gzip algorithm from Python or alternatives if possible """ if gzip is None: raise ImportError("gzip module is not available") fileobj = StringIO.StringIO(stream) try: rawData = gzip.GzipFile(fileobj=fileobj).read() except IOError: logger.warning("Encounter the python-gzip bug with trailing garbage, trying subprocess gzip") try: #This is as an ugly hack against a bug in Python gzip import subprocess sub = subprocess.Popen(["gzip", "-d", "-f"], stdout=subprocess.PIPE, stdin=subprocess.PIPE, stderr=subprocess.PIPE) rawData, err = sub.communicate(input=stream) logger.debug("Gzip subprocess ended with %s err= %s; I got %s bytes back" % (sub.wait(), err, len(rawData))) except Exception, error: #IGNORE:W0703 logger.warning("Unable to use the subprocess gzip (%s). Is gzip available? " % error) for i in range(1, 513): try: fileobj = StringIO.StringIO(stream[:-i]) rawData = gzip.GzipFile(fileobj=fileobj).read() except IOError: logger.debug("trying with %s bytes less, doesn't work" % i) else: break else: logger.error("I am totally unable to read this gzipped compressed data block, giving up") return rawData def decBzip2(stream): """ Decompress a chunk of data using the bzip2 algorithm from Python """ if bz2 is None: raise ImportError("bz2 module is not available") return bz2.decompress(stream) def decZlib(stream): """ Decompress a chunk of data using the zlib algorithm from Python """ if zlib is None: raise ImportError("zlib module is not available") return zlib.decompress(stream) def decByteOffet_python(stream, size): """ Analyze a stream of char with any length of exception (2,4, or 8 bytes integers) @param stream: string representing the compressed data @param size: the size of the output array (of longInts) @return: 1D-ndarray """ logger.debug("CBF decompression using Python with Cython loops") dataOut = numpy.zeros((size), dtype=numpy.int64) i = 0 j = 0 last = 0 current = 0 while ((i < len(stream)) and (j < size)): if (stream[i] == '\x80'): if (stream[i + 1:i + 3] == "\x00\x80"): if (stream[i + 3:i + 7] == "\x00\x00\x00\x80"): current = struct.unpack("=size){ //printf("i= %i<%i, j=%i < size= %i %i\\n",i,n,j,size,dataIn(i)); break; } if (dataIn(i) == key){ if ( (dataIn(i+1)==0) and (dataIn(i+2)==key) ){ if ( (dataIn(i+3)==0) and (dataIn(i+4)==0) and (dataIn(i+5)==0) and (dataIn(i+6)==key) ) { // 64 bits mode char tmp = dataIn(i+14) ; current = (long(tmp)<<56) | (long(dataIn(i+13))<<48) | (long(dataIn(i+12))<<40) | (long(dataIn(i+11))<<32) | (long(dataIn(i+10))<<24) | (long(dataIn(i+9))<<16) | (long(dataIn(i+8))<<8) | (long(dataIn(i+7))); // printf("64 bit int at pos %i, %i, value=%ld \\n",i,j,current); i+=14; }else{ // 32 bits mode char tmp = dataIn(i+6) ; current = (long(tmp)<<24) | (long(dataIn(i+5))<<16) | (long(dataIn(i+4))<<8) | (long(dataIn(i+3))); // printf("32 bit int at pos %i, %i, value=%ld was %i %i %i %i %i %i %i\\n",i,j,current,dataIn(i),dataIn(i+1),dataIn(i+2),dataIn(i+3),dataIn(i+4),dataIn(i+5),dataIn(i+6)); // printf("%ld %ld %ld %ld\\n",(long(tmp)<<24) , (long(dataIn(i+5))<<16) , (long(dataIn(i+4))<<8) ,long(dataIn(i+3))); i+=6; } }else{ // 16 bit mode char tmp = dataIn(i+2); current = (long(tmp)<<8) | (long (dataIn(i+1))); // printf("16 bit int at pos %i, %i, value=%ld was %i %i %i\\n",i,j,current,dataIn(i),dataIn(i+1),dataIn(i+2)); i+=2; } }else{ // 8 bit mode char tmp = dataIn(i) ; current= long(tmp) ; } last+=current; dataOut(j)=last; j++ ; } return_val=0; """ rc = weave.inline(codeC, ["dataIn", "dataOut", "n", "size" ], verbose=2, type_converters=converters.blitz) if rc != 0: logger.warning("weave binary module return error code %s" % rc) return dataOut def decByteOffet_numpy(stream, size=None): """ Analyze a stream of char with any length of exception: 2, 4, or 8 bytes integers @param stream: string representing the compressed data @param size: the size of the output array (of longInts) @return: 1D-ndarray """ logger.debug("CBF decompression using Numpy") listnpa = [] key16 = "\x80" key32 = "\x00\x80" key64 = "\x00\x00\x00\x80" shift = 1 while True: idx = stream.find(key16) if idx == -1: listnpa.append(numpy.fromstring(stream, dtype="int8")) break listnpa.append(numpy.fromstring(stream[:idx], dtype="int8")) if stream[idx + 1:idx + 3] == key32: if stream[idx + 3:idx + 7] == key64: # long int 64 bits listnpa.append(numpy.fromstring(stream[idx + 7:idx + 15], dtype="int64")) shift = 15 else: #32 bit int listnpa.append(numpy.fromstring(stream[idx + 3:idx + 7], dtype="int32")) shift = 7 else: # int16 listnpa.append(numpy.fromstring(stream[idx + 1:idx + 3], dtype="int16")) shift = 3 stream = stream[idx + shift:] return (numpy.hstack(listnpa)).astype("int64").cumsum() def decByteOffet_cython(stream, size=None): """ Analyze a stream of char with any length of exception: 2, 4, or 8 bytes integers @param stream: string representing the compressed data @param size: the size of the output array (of longInts) @return: 1D-ndarray """ logger.debug("CBF decompression using cython") try: from fabio.byte_offset import analyseCython except ImportError, error: logger.error("Failed to import byte_offset cython module, falling back on numpy method") return decByteOffet_numpy(stream, size) else: return analyseCython(stream, size) def compByteOffet_numpy(data): """ Compress a dataset into a string using the byte_offet algorithm @param data: ndarray @return: string/bytes with compressed data test = numpy.array([0,1,2,127,0,1,2,128,0,1,2,32767,0,1,2,32768,0,1,2,2147483647,0,1,2,2147483648,0,1,2,128,129,130,32767,32768,128,129,130,32768,2147483647,2147483648]) """ flat = data.astype("int64").ravel() delta = numpy.zeros_like(flat) delta[0] = flat[0] delta[1:] = flat[1:] - flat[:-1] mask = ((delta > 127) + (delta < -127)) exceptions = numpy.nonzero(mask)[0] if numpy.little_endian: byteswap = False else: byteswap = True start = 0 binary_blob = "" for stop in exceptions: if stop - start > 0: binary_blob += delta[start:stop].astype("int8").tostring() exc = delta[stop] if (exc > 2147483647) or (exc < -2147483647): #2**31-1 binary_blob += "\x80\x00\x80\x00\x00\x00\x80" if byteswap: binary_blob += delta[stop:stop + 1].byteswap().tostring() else: binary_blob += delta[stop:stop + 1].tostring() elif (exc > 32767) or (exc < -32767): #2**15-1 binary_blob += "\x80\x00\x80" if byteswap: binary_blob += delta[stop:stop + 1].astype("int32").byteswap().tostring() else: binary_blob += delta[stop:stop + 1].astype("int32").tostring() else: #>127 binary_blob += "\x80" if byteswap: binary_blob += delta[stop:stop + 1].astype("int16").byteswap().tostring() else: binary_blob += delta[stop:stop + 1].astype("int16").tostring() start = stop + 1 if start < delta.size: binary_blob += delta[start:].astype("int8").tostring() return binary_blob def decTY1(raw_8, raw_16=None, raw_32=None): """ Modified byte offset decompressor used in Oxford Diffraction images @param raw_8: strings containing raw data with integer 8 bits @param raw_16: strings containing raw data with integer 16 bits @param raw_32: strings containing raw data with integer 32 bits @return: numpy.ndarray """ data = numpy.fromstring(raw_8, dtype="uint8").astype(int) data -= 127 if raw_32 is not None: int32 = numpy.fromstring(raw_32, dtype="int32").astype(int) exception32 = numpy.nonzero(data == 128) if raw_16 is not None: int16 = numpy.fromstring(raw_16, dtype="int16").astype(int) exception16 = numpy.nonzero(data == 127) data[exception16] = int16 if raw_32: data[exception32] = int32 summed = data.cumsum() smax = summed.max() if (smax > (2 ** 31 - 1)): bytecode = "int64" elif (smax > (2 ** 15 - 1)): bytecode = "int32" elif (smax > (2 ** 7 - 1)): bytecode = "int16" else: bytecode = "int8" return summed.astype(bytecode) decKM4CCD = decTY1 def compTY1(data): """ Modified byte offset compressor used in Oxford Diffraction images @param data: numpy.ndarray with the input data (integers!) @return: 3-tuple of strings: raw_8,raw_16,raw_32 containing raw data with integer of the given size """ fdata = data.flatten() diff = numpy.zeros_like(fdata) diff[0] = fdata[0] diff[1:] = fdata[1:] - fdata[:-1] adiff = abs(diff) exception32 = (adiff > 32767)#2**15-1 exception16 = (adiff >= 127) - exception32 #2**7-1) we16 = numpy.where(exception16) we32 = numpy.where(exception32) raw_16 = diff[we16].astype("int16").tostring() raw_32 = diff[we32].astype("int32").tostring() diff[we16] = 127 diff[we32] = 128 diff += 127 raw_8 = diff.astype("uint8").tostring() return raw_8, raw_16, raw_32 def decPCK(stream, dim1=None, dim2=None, overflowPix=None, version=None): """ Modified CCP4 pck decompressor used in MAR345 images @param stream: string or file @return: numpy.ndarray (square array) """ try: from mar345_IO import uncompress_pck except ImportError, error: raise RuntimeError("Unable to import mar345_IO to read compressed dataset") if "seek" in dir(stream): stream.seek(0) raw = stream.read() else: raw = str(stream) return uncompress_pck(raw, dim1, dim2, overflowPix, version) def compPCK(data): """ Modified CCP4 pck compressor used in MAR345 images @param data: numpy.ndarray (square array) @return: compressed stream """ try: from mar345_IO import compress_pck except ImportError, error: raise RuntimeError("Unable to import mar345_IO to write compressed dataset") return compress_pck(data) fabio-0.1.3/fabio-src/tifimage.py0000644000175000017500000002530712233175220017367 0ustar jeromejerome00000000000000#!/usr/bin/env python #-*- coding: utf8 -*- """ FabIO class for dealing with TIFF images. In facts wraps TiffIO from V. Armando Solé (available in PyMca) or falls back to PIL Authors: ........ * Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions; Risoe National Laboratory; Frederiksborgvej 399; DK-4000 Roskilde; email:erik.knudsen@risoe.dk * Jérôme Kieffer: European Synchrotron Radiation Facility; Grenoble (France) License: GPLv3+ """ __authors__ = ["Jérôme Kieffer", "Henning O. Sorensen", "Erik Knudsen"] __date__ = "11/07/2011" __license__ = "GPLv3+" __copyright__ = "ESRF, Grenoble & Risoe National Laboratory" __status__ = "stable" import time, logging, struct logger = logging.getLogger("tifimage") try: from PIL import Image except ImportError: logger.warning("PIL is not installed ... trying to do without") Image = None import numpy from fabioimage import fabioimage from TiffIO import TiffIO PIL_TO_NUMPY = { "I;16": numpy.uint16, "F": numpy.float32, "1": numpy.bool, "I": numpy.int32, "L": numpy.uint8, } LITTLE_ENDIAN = 1234 BIG_ENDIAN = 3412 TYPES = {0:'invalid', 1:'byte', 2:'ascii', 3:'short', 4:'long', 5:'rational', 6:'sbyte', 7:'undefined', 8:'sshort', 9:'slong', 10:'srational', 11:'float', 12:'double'} TYPESIZES = {0:0, 1:1, 2:1, 3:2, 4:4, 5:8, 6:1, 7:1, 8:2, 9:4, 10:8, 11:4, 12:8} baseline_tiff_tags = { 256:'ImageWidth', 257:'ImageLength', 306:'DateTime', 315:'Artist', 258:'BitsPerSample', 265:'CellLength', 264:'CellWidth', 259:'Compression', 262:'PhotometricInterpretation', 296:'ResolutionUnit', 282:'XResolution', 283:'YResolution', 278:'RowsPerStrip', 273:'StripOffset', 279:'StripByteCounts', 270:'ImageDescription', 271:'Make', 272:'Model', 320:'ColorMap', 305:'Software', 339:'SampleFormat', 33432:'Copyright' } class tifimage(fabioimage): """ Images in TIF format Wraps TiffIO """ _need_a_seek_to_read = True def __init__(self, *args, **kwds): """ Tifimage constructor adds an nbits member attribute """ self.nbits = None fabioimage.__init__(self, *args, **kwds) self.lib = None def _readheader(self, infile): """ Try to read Tiff images header... """ # try: # self.header = { "filename" : infile.name } # except AttributeError: # self.header = {} # # t = Tiff_header(infile.read()) # self.header = t.header # try: # self.dim1 = int(self.header['ImageWidth']) # self.dim2 = int(self.header['ImageLength']) # except (KeyError): # logger.warning("image dimensions could not be determined from header tags, trying to go on anyway") # read the first 32 bytes to determine size header = numpy.fromstring(infile.read(64), numpy.uint16) self.dim1 = int(header[9]) self.dim2 = int(header[15]) # nbits is not a fabioimage attribute... self.nbits = int(header[21]) # number of bits def read(self, fname, frame=None): """ Wrapper for TiffIO. """ infile = self._open(fname, "rb") self._readheader(infile) infile.seek(0) self.lib = None try: tiffIO = TiffIO(infile) if tiffIO.getNumberOfImages() > 0: #No support for now of multi-frame tiff images self.data = tiffIO.getImage(0) self.header = tiffIO.getInfo(0) except Exception, error: logger.warning("Unable to read %s with TiffIO due to %s, trying PIL" % (fname, error)) else: if self.data.ndim == 2: self.dim2, self.dim1 = self.data.shape elif self.data.ndim == 3: self.dim2, self.dim1, ncol = self.data.shape logger.warning("Third dimension is the color") else: logger.warning("dataset has %s dimensions (%s), check for errors !!!!", self.data.ndim, self.data.shape) self.lib = "TiffIO" if (self.lib is None): if Image: try: infile.seek(0) self.pilimage = Image.open(infile) except Exception: logger.error("Error in opening %s with PIL" % fname) self.lib = None infile.seek(0) else: self.lib = "PIL" self.dim1, self.dim2 = self.pilimage.size if self.pilimage.mode in PIL_TO_NUMPY: self.data = numpy.fromstring(self.pilimage.tostring(), PIL_TO_NUMPY[self.pilimage.mode]) else: #probably RGB or RGBA images: rely on PIL to convert it to greyscale float. self.data = numpy.fromstring(self.pilimage.convert("F").tostring(), numpy.float32) self.data.shape = (self.dim2, self.dim1) else: logger.error("Error in opening %s: no tiff reader managed to read the file.", fname) self.lib = None infile.seek(0) self.bpp = len(numpy.zeros(1, dtype=self.data.dtype).tostring()) self.bytecode = self.data.dtype.name self.resetvals() return self def write(self, fname): """ Overrides the fabioimage.write method and provides a simple TIFF image writer. @param fname: name of the file to save the image to @tag_type fname: string or unicode (file?)... """ tiffIO = TiffIO(fname, mode="w") tiffIO.writeImage(self.data, info=self.header, software="fabio.tifimage", date=time.ctime()) #define a couple of helper classes here: class Tiff_header(object): def __init__(self, string): if string[:4] == "II\x2a\x00": self.byteorder = LITTLE_ENDIAN elif string[:4] == 'MM\x00\x2a': self.byteorder = BIG_ENDIAN else: logger.warning("Warning: This does not appear to be a tiff file") #the next two bytes contains the offset of the oth IFD offset_first_ifd = struct.unpack_from("h", string[4:])[0] self.ifd = [Image_File_Directory()] offset_next = self.ifd[0].unpack(string, offset_first_ifd) while (offset_next != 0): self.ifd.append(Image_File_Directory()) offset_next = self.ifd[-1].unpack(string, offset_next) self.header = {} #read the values of the header items into a dictionary for entry in self.ifd[0].entries: if entry.tag in baseline_tiff_tags.keys(): self.header[baseline_tiff_tags[entry.tag]] = entry.val else: self.header[entry.tag] = entry.val class Image_File_Directory(object): def __init__(self, instring=None, offset= -1): self.entries = [] self.offset = offset self.count = None def unpack(self, instring, offset= -1): if (offset == -1): offset = self.offset strInput = instring[offset:] self.count = struct.unpack_from("H", strInput[:2])[0] #0th IFD contains count-1 entries (count includes the adress of the next IFD) for i in range(self.count - 1): e = Image_File_Directory_entry().unpack(strInput[2 + 12 * (i + 1):]) if (e != None): self.entries.append(e) #extract data associated with tags for e in self.entries: if (e.val == None): e.extract_data(instring) #do we have some more ifds in this file offset_next = struct.unpack_from("L", instring[offset + 2 + self.count * 12:])[0] return offset_next class Image_File_Directory_entry(object): def __init__(self, tag=0, tag_type=0, count=0, offset=0): self.tag = tag self.tag_type = tag_type self.count = count self.val_offset = offset self.val = None def unpack(self, strInput): idfentry = strInput[:12] ################################################################################ # # TOFIX: How is it possible that HHL (2+2+4 bytes has a size of ) ################################################################################ (tag, tag_type, count) = struct.unpack_from("HHL", idfentry) self.tag = tag self.count = count self.tag_type = tag_type self.val = None if (count <= 0): logger.warning("Tag # %s has an invalid count: %s. Tag is ignored" % (tag, count)) return if(count * TYPESIZES[tag_type] <= 4): self.val_offset = 8 self.extract_data(idfentry) self.val_offset = None else: self.val_offset = struct.unpack_from("L", idfentry[8:])[0] return self def extract_data(self, full_string): tag_type = self.tag_type if (TYPES[tag_type] == 'byte'): self.val = struct.unpack_from("B", full_string[self.val_offset:])[0] elif (TYPES[tag_type] == 'short'): self.val = struct.unpack_from("H", full_string[self.val_offset:])[0] elif (TYPES[tag_type] == 'long'): self.val = struct.unpack_from("L", full_string[self.val_offset:])[0] elif (TYPES[tag_type] == 'sbyte'): self.val = struct.unpack_from("b", full_string[self.val_offset:])[0] elif (TYPES[tag_type] == 'sshort'): self.val = struct.unpack_from("h", full_string[self.val_offset:])[0] elif (TYPES[tag_type] == 'slong'): self.val = struct.unpack_from("l", full_string[self.val_offset:])[0] elif (TYPES[tag_type] == 'ascii'): self.val = full_string[self.val_offset:self.val_offset + max(self.count, 4)] elif (TYPES[tag_type] == 'rational'): if self.val_offset != None: (num, den) = struct.unpack_from("LL", full_string[self.val_offset:]) print self.val_offset self.val = float(num) / den elif (TYPES[tag_type] == 'srational'): if self.val_offset != None: (num, den) = struct.unpack_from("ll", full_string[self.val_offset:]) self.val = float(num) / den, elif (TYPES[tag_type] == 'float'): self.val = struct.unpack_from("f", full_string[self.val_offset:])[0] elif (TYPES[tag_type] == 'double'): if self.val_offset != None: self.val = struct.unpack_from("d", full_string[self.val_offset:])[0] else: logger.warning("unrecognized type of strInputentry self: %s tag: %s type: %s TYPE: %s" % (self, baseline_tiff_tags[self.tag], self.tag_type, TYPES[tag_type])) fabio-0.1.3/fabio-src/binaryimage.py0000644000175000017500000000735112233247673020104 0ustar jeromejerome00000000000000#!/usr/bin/env python # coding: utf8 # Get ready for python3: from __future__ import with_statement, print_function __doc__ = """ Authors: Gael Goret, Jerome Kieffer, ESRF, France Emails: gael.goret@esrf.fr, jerome.kieffer@esrf.fr Brian Richard Pauw Binary files images are simple none-compressed 2D images only defined by their : data-type, dimensions, byte order and offset This simple library has been made for manipulating exotic/unknown files format. """ __authors__ = ["Gaël Goret", "Jérôme Kieffer", "Brian Pauw"] __contact__ = "gael.goret@esrf.fr" __license__ = "GPLv3+" __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" __version__ = "17 Oct 2012" from fabioimage import fabioimage import numpy, logging logger = logging.getLogger("binaryimage") class binaryimage(fabioimage): """ This simple library has been made for manipulating exotic/unknown files format. Binary files images are simple none-compressed 2D images only defined by their : data-type, dimensions, byte order and offset if offset is set to a negative value, the image is read using the last data but n data in the file, skipping any header. """ def __init__(self, *args, **kwargs): fabioimage.__init__(self, *args, **kwargs) @staticmethod def swap_needed(endian): """ Decide if we need to byteswap """ if (endian == '<' and numpy.little_endian) or (endian == '>' and not numpy.little_endian): return False if (endian == '>' and numpy.little_endian) or (endian == '<' and not numpy.little_endian): return True def read(self, fname, dim1, dim2, offset=0, bytecode="int32", endian="<"): """ Read a binary image @param fname: file name @type fname: string @param dim1: image dimensions (Fast index) @param dim2: image dimensions (Slow index) @param offset: starting position of the data-block. If negative, starts at the end. @param bytecode: can be "int8","int16","int32","int64","uint8","uint16","uint32","uint64","float32","float64",... @param endian: among short or long endian ("<" or ">") """ self.filename = fname self.dim1 = dim1 self.dim2 = dim2 self.bytecode = bytecode f = open(self.filename, "rb") dims = [dim2, dim1] bpp = len(numpy.array(0, bytecode).tostring()) size = dims[0] * dims[1] * bpp if offset >= 0: f.seek(offset) else: try: f.seek(-size + offset + 1, 2) #seek from EOF backwards except IOError: logging.warn('expected datablock too large, please check bytecode settings: {}'.format(bytecode)) except: logging.error('Uncommon error encountered when reading file') rawData = f.read(size) if self.swap_needed(endian): data = numpy.fromstring(rawData, bytecode).byteswap().reshape(tuple(dims)) else: data = numpy.fromstring(rawData, bytecode).reshape(tuple(dims)) self.data = data return self def estimate_offset_value(self, fname, dim1, dim2, bytecode="int32"): "Estimates the size of a file" with open(fname, "rb") as f: bpp = len(numpy.array(0, bytecode).tostring()) size = dim1 * dim2 * bpp totsize = len(f.read()) logger.info('total size (bytes): %s', totsize) logger.info('expected data size given parameters (bytes): %s', size) logger.info('estimation of the offset value (bytes): %s', totsize - size) def write(self, fname): with open(fname, mode="wb") as outfile: outfile.write(self.data.tostring()) fabio-0.1.3/fabio-src/pilatusimage.py0000644000175000017500000000372212126623347020274 0ustar jeromejerome00000000000000#!/usr/bin/env python #coding: utf8 """ Authors: ........ * Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions; Risoe National Laboratory; Frederiksborgvej 399; DK-4000 Roskilde; email:erik.knudsen@risoe.dk * Jon Wright: European Synchrotron Radiation Facility; Grenoble (France) """ # Base this on the tifimage (as Pilatus is tiff with a # tiff header from fabio.tifimage import tifimage class pilatusimage(tifimage): """ Read in Pilatus format, also pilatus images, including header info """ def _readheader(self, infile): """ Parser based approach Gets all entries """ self.header = {} # infile = open(infile) hstr = infile.read(4096) # well not very pretty - but seems to find start of # header information if (hstr.find('# ') == -1): return self.header hstr = hstr[hstr.index('# '):] hstr = hstr[:hstr.index('\x00')] hstr = hstr.split('#') go_on = True while go_on: try: hstr.remove('') except Exception: go_on = False for line in hstr: line = line[1:line.index('\r\n')] if line.find(':') > -1: dump = line.split(':') self.header[dump[0]] = dump[1] elif line.find('=') > -1: dump = line.split('=') self.header[dump[0]] = dump[1] elif line.find(' ') > -1: i = line.find(' ') self.header[line[:i]] = line[i:] elif line.find(',') > -1: dump = line.split(',') self.header[dump[0]] = dump[1] return self.header def _read(self, fname): """ inherited from tifimage ... a Pilatus image *is a* tif image just with a header """ return tifimage.read(self, fname) fabio-0.1.3/fabio-src/TiffIO.py0000644000175000017500000013343112120434325016717 0ustar jeromejerome00000000000000#/*########################################################################## # Copyright (C) 2012 European Synchrotron Radiation Facility # # This file is part of the PyMca X-ray Fluorescence Toolkit developed at # the ESRF by the Software group. # # This file is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by the Free # Software Foundation; either version 2 of the License, or (at your option) # any later version. # # PyMca is distributed in the hope that it will be useful, but WITHOUT ANY # WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS # FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more # details. # #############################################################################*/ __author__ = "V.A. Sole - ESRF Data Analysis" __revision__ = 1501 import sys import os import struct import numpy DEBUG = 0 ALLOW_MULTIPLE_STRIPS = False TAG_ID = { 256:"NumberOfColumns", # S or L ImageWidth 257:"NumberOfRows", # S or L ImageHeight 258:"BitsPerSample", # S Number of bits per component 259:"Compression", # SHORT (1 - NoCompression, ... 262:"PhotometricInterpretation", # SHORT (0 - WhiteIsZero, 1 -BlackIsZero, 2 - RGB, 3 - Palette color 270:"ImageDescription", # ASCII 273:"StripOffsets", # S or L, for each strip, the byte offset of the strip 278:"RowsPerStrip", # S or L, number of rows in each back may be not for the last 279:"StripByteCounts", # S or L, The number of bytes in the strip AFTER any compression 305:"Software", # ASCII 306:"Date", # ASCII 320:"Colormap", # Colormap of Palette-color Images 339:"SampleFormat", # SHORT Interpretation of data in each pixel } #TILES ARE TO BE SUPPORTED TOO ... TAG_NUMBER_OF_COLUMNS = 256 TAG_NUMBER_OF_ROWS = 257 TAG_BITS_PER_SAMPLE = 258 TAG_PHOTOMETRIC_INTERPRETATION = 262 TAG_COMPRESSION = 259 TAG_IMAGE_DESCRIPTION = 270 TAG_STRIP_OFFSETS = 273 TAG_ROWS_PER_STRIP = 278 TAG_STRIP_BYTE_COUNTS = 279 TAG_SOFTWARE = 305 TAG_DATE = 306 TAG_COLORMAP = 320 TAG_SAMPLE_FORMAT = 339 FIELD_TYPE = {1:('BYTE', "B"), 2:('ASCII', "s"), #string ending with binary zero 3:('SHORT', "H"), 4:('LONG', "I"), 5:('RATIONAL', "II"), 6:('SBYTE', "b"), 7:('UNDEFINED', "B"), 8:('SSHORT', "h"), 9:('SLONG', "i"), 10:('SRATIONAL', "ii"), 11:('FLOAT', "f"), 12:('DOUBLE', "d")} FIELD_TYPE_OUT = { 'B': 1, 's': 2, 'H': 3, 'I': 4, 'II': 5, 'b': 6, 'h': 8, 'i': 9, 'ii': 10, 'f': 11, 'd': 12} #sample formats (http://www.awaresystems.be/imaging/tiff/tiffflags/sampleformat.html) SAMPLE_FORMAT_UINT = 1 SAMPLE_FORMAT_INT = 2 SAMPLE_FORMAT_FLOAT = 3 #floating point SAMPLE_FORMAT_VOID = 4 #undefined data, usually assumed UINT SAMPLE_FORMAT_COMPLEXINT = 5 SAMPLE_FORMAT_COMPLEXIEEEFP = 6 class TiffIO(object): def __init__(self, filename, mode=None, cache_length=20, mono_output=False): if mode is None: mode = 'rb' if 'b' not in mode: mode = mode + 'b' if 'a' in mode.lower(): raise IOError("Mode %s makes no sense on TIFF files. Consider 'rb+'" % mode) if ('w' in mode): if '+' not in mode: mode += '+' #if isinstance(filename, file): #does not work in python 3 if hasattr(filename, "seek"): fd = filename self._access = None else: #the b is needed for windows and python 3 fd = open(filename, mode) self._access = mode self._initInternalVariables(fd) self._maxImageCacheLength = cache_length self._forceMonoOutput = mono_output def _initInternalVariables(self, fd=None): if fd is None: fd = self.fd else: self.fd = fd # read the order fd.seek(0) order = fd.read(2).decode() if len(order): if order == "II": #intel, little endian fileOrder = "little" self._structChar = '<' elif order == "MM": #motorola, high endian fileOrder = "big" self._structChar = '>' else: raise IOError("File is not a Mar CCD file, nor a TIFF file") a = fd.read(2) fortyTwo = struct.unpack(self._structChar + "H", a)[0] if fortyTwo != 42: raise IOError("Invalid TIFF version %d" % fortyTwo) else: if DEBUG: print("VALID TIFF VERSION") if sys.byteorder != fileOrder: swap = True else: swap = False else: if sys.byteorder == "little": self._structChar = '<' else: self._structChar = '>' swap = False self._swap = swap self._IFD = [] self._imageDataCacheIndex = [] self._imageDataCache = [] self._imageInfoCacheIndex = [] self._imageInfoCache = [] self.getImageFileDirectories(fd) def __makeSureFileIsOpen(self): if not self.fd.closed: return if DEBUG: print("Reopening closed file") fileName = self.fd.name if self._access is None: #we do not own the file #open in read mode newFile = open(fileName, 'rb') else: newFile = open(fileName, self._access) self.fd = newFile def __makeSureFileIsClosed(self): if self._access is None: #we do not own the file if DEBUG: print("Not closing not owned file") return if not self.fd.closed: self.fd.close() def getNumberOfImages(self): #update for the case someone has done anything? self._updateIFD() return len(self._IFD) def _updateIFD(self): self.__makeSureFileIsOpen() self.getImageFileDirectories() self.__makeSureFileIsClosed() def getImageFileDirectories(self, fd=None): if fd is None: fd = self.fd else: self.fd = fd st = self._structChar fd.seek(4) self._IFD = [] nImages = 0 fmt = st + 'I' inStr = fd.read(struct.calcsize(fmt)) if not len(inStr): offsetToIFD = 0 else: offsetToIFD = struct.unpack(fmt, inStr)[0] if DEBUG: print("Offset to first IFD = %d" % offsetToIFD) while offsetToIFD != 0: self._IFD.append(offsetToIFD) nImages += 1 fd.seek(offsetToIFD) fmt = st + 'H' numberOfDirectoryEntries = struct.unpack(fmt, fd.read(struct.calcsize(fmt)))[0] if DEBUG: print("Number of directory entries = %d" % numberOfDirectoryEntries) fmt = st + 'I' fd.seek(offsetToIFD + 2 + 12 * numberOfDirectoryEntries) offsetToIFD = struct.unpack(fmt, fd.read(struct.calcsize(fmt)))[0] if DEBUG: print("Next Offset to IFD = %d" % offsetToIFD) #offsetToIFD = 0 if DEBUG: print("Number of images found = %d" % nImages) return nImages def _parseImageFileDirectory(self, nImage): offsetToIFD = self._IFD[nImage] st = self._structChar fd = self.fd fd.seek(offsetToIFD) fmt = st + 'H' numberOfDirectoryEntries = struct.unpack(fmt, fd.read(struct.calcsize(fmt)))[0] if DEBUG: print("Number of directory entries = %d" % numberOfDirectoryEntries) fmt = st + 'HHI4s' tagIDList = [] fieldTypeList = [] nValuesList = [] valueOffsetList = [] for i in range(numberOfDirectoryEntries): tagID, fieldType, nValues, valueOffset = struct.unpack(fmt, fd.read(12)) tagIDList.append(tagID) fieldTypeList.append(fieldType) nValuesList.append(nValues) if nValues == 1: ftype, vfmt = FIELD_TYPE[fieldType] if ftype not in ['ASCII', 'RATIONAL', 'SRATIONAL']: vfmt = st + vfmt actualValue = struct.unpack(vfmt, valueOffset[0: struct.calcsize(vfmt)])[0] valueOffsetList.append(actualValue) else: valueOffsetList.append(valueOffset) elif (nValues < 5) and (fieldType == 2): ftype, vfmt = FIELD_TYPE[fieldType] vfmt = st + "%d%s" % (nValues, vfmt) actualValue = struct.unpack(vfmt, valueOffset[0: struct.calcsize(vfmt)])[0] valueOffsetList.append(actualValue) else: valueOffsetList.append(valueOffset) if DEBUG: if tagID in TAG_ID: print("tagID = %s" % TAG_ID[tagID]) else: print("tagID = %d" % tagID) print("fieldType = %s" % FIELD_TYPE[fieldType][0]) print("nValues = %d" % nValues) #if nValues == 1: # print("valueOffset = %s" % valueOffset) return tagIDList, fieldTypeList, nValuesList, valueOffsetList def _readIFDEntry(self, tag, tagIDList, fieldTypeList, nValuesList, valueOffsetList): fd = self.fd st = self._structChar idx = tagIDList.index(tag) nValues = nValuesList[idx] output = [] ftype, vfmt = FIELD_TYPE[fieldTypeList[idx]] vfmt = st + "%d%s" % (nValues, vfmt) requestedBytes = struct.calcsize(vfmt) if nValues == 1: output.append(valueOffsetList[idx]) elif requestedBytes < 5: output.append(valueOffsetList[idx]) else: offset = fd.seek(struct.unpack(st + "I", valueOffsetList[idx])[0]) output = struct.unpack(vfmt, fd.read(requestedBytes)) return output def getData(self, nImage, **kw): if nImage >= len(self._IFD): #update prior to raise an index error error self._updateIFD() return self._readImage(nImage, **kw) def getImage(self, nImage): return self.getData(nImage) def getInfo(self, nImage, **kw): if nImage >= len(self._IFD): #update prior to raise an index error error self._updateIFD() current = self._IFD[nImage] return self._readInfo(nImage) def _readInfo(self, nImage, close=True): if nImage in self._imageInfoCacheIndex: if DEBUG: print("Reading info from cache") return self._imageInfoCache[self._imageInfoCacheIndex.index(nImage)] #read the header self.__makeSureFileIsOpen() tagIDList, fieldTypeList, nValuesList, valueOffsetList = self._parseImageFileDirectory(nImage) #rows and columns nColumns = valueOffsetList[tagIDList.index(TAG_NUMBER_OF_COLUMNS)] nRows = valueOffsetList[tagIDList.index(TAG_NUMBER_OF_ROWS)] #bits per sample idx = tagIDList.index(TAG_BITS_PER_SAMPLE) nBits = valueOffsetList[idx] if nValuesList[idx] != 1: #this happens with RGB and friends, nBits is not a single value nBits = self._readIFDEntry(TAG_BITS_PER_SAMPLE, tagIDList, fieldTypeList, nValuesList, valueOffsetList) if TAG_COLORMAP in tagIDList: idx = tagIDList.index(TAG_COLORMAP) tmpColormap = self._readIFDEntry(TAG_COLORMAP, tagIDList, fieldTypeList, nValuesList, valueOffsetList) if max(tmpColormap) > 255: tmpColormap = numpy.array(tmpColormap, dtype=numpy.uint16) tmpColormap = (tmpColormap / 256.).astype(numpy.uint8) else: tmpColormap = numpy.array(tmpColormap, dtype=numpy.uint8) tmpColormap.shape = 3, -1 colormap = numpy.zeros((tmpColormap.shape[-1], 3), tmpColormap.dtype) colormap[:, :] = tmpColormap.T tmpColormap = None else: colormap = None #sample format if TAG_SAMPLE_FORMAT in tagIDList: sampleFormat = valueOffsetList[tagIDList.index(TAG_SAMPLE_FORMAT)] else: #set to unknown sampleFormat = SAMPLE_FORMAT_VOID # compression compression = False compression_type = 1 if TAG_COMPRESSION in tagIDList: compression_type = valueOffsetList[tagIDList.index(TAG_COMPRESSION)] if compression_type == 1: compression = False else: compression = True #photometric interpretation interpretation = 1 if TAG_PHOTOMETRIC_INTERPRETATION in tagIDList: interpretation = valueOffsetList[tagIDList.index(TAG_PHOTOMETRIC_INTERPRETATION)] else: print("WARNING: Non standard TIFF. Photometric interpretation TAG missing") helpString = "" if sys.version > '2.6': helpString = eval('b""') if TAG_IMAGE_DESCRIPTION in tagIDList: imageDescription = self._readIFDEntry(TAG_IMAGE_DESCRIPTION, tagIDList, fieldTypeList, nValuesList, valueOffsetList) if type(imageDescription) in [type([1]), type((1,))]: imageDescription = helpString.join(imageDescription) else: imageDescription = "%d/%d" % (nImage + 1, len(self._IFD)) if sys.version < '3.0': defaultSoftware = "Unknown Software" else: defaultSoftware = bytes("Unknown Software", encoding='utf-8') if TAG_SOFTWARE in tagIDList: software = self._readIFDEntry(TAG_SOFTWARE, tagIDList, fieldTypeList, nValuesList, valueOffsetList) if type(software) in [type([1]), type((1,))]: software = helpString.join(software) else: software = defaultSoftware if software == defaultSoftware: try: if sys.version < '3.0': if imageDescription.upper().startswith("IMAGEJ"): software = imageDescription.split("=")[0] else: tmpString = imageDescription.decode() if tmpString.upper().startswith("IMAGEJ"): software = bytes(tmpString.split("=")[0], encoding='utf-8') except: pass if TAG_DATE in tagIDList: date = self._readIFDEntry(TAG_DATE, tagIDList, fieldTypeList, nValuesList, valueOffsetList) if type(date) in [type([1]), type((1,))]: date = helpString.join(date) else: date = "Unknown Date" stripOffsets = self._readIFDEntry(TAG_STRIP_OFFSETS, tagIDList, fieldTypeList, nValuesList, valueOffsetList) if TAG_ROWS_PER_STRIP in tagIDList: rowsPerStrip = self._readIFDEntry(TAG_ROWS_PER_STRIP, tagIDList, fieldTypeList, nValuesList, valueOffsetList)[0] else: rowsPerStrip = nRows print("WARNING: Non standard TIFF. Rows per strip TAG missing") if TAG_STRIP_BYTE_COUNTS in tagIDList: stripByteCounts = self._readIFDEntry(TAG_STRIP_BYTE_COUNTS, tagIDList, fieldTypeList, nValuesList, valueOffsetList) else: print("WARNING: Non standard TIFF. Strip byte counts TAG missing") if hasattr(nBits, 'index'): expectedSum = 0 for n in nBits: expectedSum += int(nRows * nColumns * n / 8) else: expectedSum = int(nRows * nColumns * nBits / 8) stripByteCounts = [expectedSum] if close: self.__makeSureFileIsClosed() if self._forceMonoOutput and (interpretation > 1): #color image but asked monochrome output nBits = 32 colormap = None sampleFormat = SAMPLE_FORMAT_FLOAT interpretation = 1 #we cannot rely on any cache in this case useInfoCache = False if DEBUG: print("FORCED MONO") else: useInfoCache = True info = {} info["nRows"] = nRows info["nColumns"] = nColumns info["nBits"] = nBits info["compression"] = compression info["compression_type"] = compression_type info["imageDescription"] = imageDescription info["stripOffsets"] = stripOffsets #This contains the file offsets to the data positions info["rowsPerStrip"] = rowsPerStrip info["stripByteCounts"] = stripByteCounts #bytes in strip since I do not support compression info["software"] = software info["date"] = date info["colormap"] = colormap info["sampleFormat"] = sampleFormat info["photometricInterpretation"] = interpretation infoDict = {} if sys.version < '3.0': testString = 'PyMca' else: testString = eval('b"PyMca"') if software.startswith(testString): #str to make sure python 2.x sees it as string and not unicode if sys.version < '3.0': descriptionString = imageDescription else: descriptionString = str(imageDescription.decode()) #interpret the image description in terms of supplied #information at writing time items = descriptionString.split('=') for i in range(int(len(items) / 2)): key = "%s" % items[i * 2] #get rid of the \n at the end of the value value = "%s" % items[i * 2 + 1][:-1] infoDict[key] = value info['info'] = infoDict if (self._maxImageCacheLength > 0) and useInfoCache: self._imageInfoCacheIndex.insert(0, nImage) self._imageInfoCache.insert(0, info) if len(self._imageInfoCacheIndex) > self._maxImageCacheLength: self._imageInfoCacheIndex = self._imageInfoCacheIndex[:self._maxImageCacheLength] self._imageInfoCache = self._imageInfoCache[:self._maxImageCacheLength] return info def _readImage(self, nImage, **kw): if DEBUG: print("Reading image %d" % nImage) if 'close' in kw: close = kw['close'] else: close = True rowMin = kw.get('rowMin', None) rowMax = kw.get('rowMax', None) if nImage in self._imageDataCacheIndex: if DEBUG: print("Reading image data from cache") return self._imageDataCache[self._imageDataCacheIndex.index(nImage)] self.__makeSureFileIsOpen() if self._forceMonoOutput: oldMono = True else: oldMono = False try: self._forceMonoOutput = False info = self._readInfo(nImage, close=False) self._forceMonoOutput = oldMono except: self._forceMonoOutput = oldMono raise compression = info['compression'] compression_type = info['compression_type'] if compression: if compression_type != 32773: raise IOError("Compressed TIFF images not supported except packbits") else: #PackBits compression if DEBUG: print("Using PackBits compression") interpretation = info["photometricInterpretation"] if interpretation == 2: #RGB pass #raise IOError("RGB Image. Only grayscale images supported") elif interpretation == 3: #Palette Color Image pass #raise IOError("Palette-color Image. Only grayscale images supported") elif interpretation > 2: #Palette Color Image raise IOError("Only grayscale images supported") nRows = info["nRows"] nColumns = info["nColumns"] nBits = info["nBits"] colormap = info["colormap"] sampleFormat = info["sampleFormat"] if rowMin is None: rowMin = 0 if rowMax is None: rowMax = nRows - 1 if rowMin < 0: rowMin = nRows - rowMin if rowMax < 0: rowMax = nRows - rowMax if rowMax < rowMin: txt = "Max Row smaller than Min Row. Reverse selection not supported" raise NotImplemented(txt) if rowMin >= nRows: raise IndexError("Image only has %d rows" % nRows) if rowMax >= nRows: raise IndexError("Image only has %d rows" % nRows) if sampleFormat == SAMPLE_FORMAT_FLOAT: if nBits == 32: dtype = numpy.float32 elif nBits == 64: dtype = numpy.float64 else: raise ValueError("Unsupported number of bits for a float: %d" % nBits) elif sampleFormat in [SAMPLE_FORMAT_UINT, SAMPLE_FORMAT_VOID]: if nBits in [8, (8, 8, 8), [8, 8, 8]]: dtype = numpy.uint8 elif nBits in [16, (16, 16, 16), [16, 16, 16]]: dtype = numpy.uint16 elif nBits in [32, (32, 32, 32), [32, 32, 32]]: dtype = numpy.uint32 elif nBits in [64, (64, 64, 64), [64, 64, 64]]: dtype = numpy.uint64 else: raise ValueError("Unsupported number of bits for unsigned int: %s" % (nBits,)) elif sampleFormat == SAMPLE_FORMAT_INT: if nBits in [8, (8, 8, 8), [8, 8, 8]]: dtype = numpy.int8 elif nBits in [16, (16, 16, 16), [16, 16, 16]]: dtype = numpy.int16 elif nBits in [32, (32, 32, 32), [32, 32, 32]]: dtype = numpy.int32 elif nBits in [64, (64, 64, 64), [64, 64, 64]]: dtype = numpy.int64 else: raise ValueError("Unsupported number of bits for signed int: %s" % (nBits,)) else: raise ValueError("Unsupported combination. Bits = %s Format = %d" % (nBits, sampleFormat)) if hasattr(nBits, 'index'): image = numpy.zeros((nRows, nColumns, len(nBits)), dtype=dtype) elif colormap is not None: #should I use colormap dtype? image = numpy.zeros((nRows, nColumns, 3), dtype=dtype) else: image = numpy.zeros((nRows, nColumns), dtype=dtype) fd = self.fd st = self._structChar stripOffsets = info["stripOffsets"] #This contains the file offsets to the data positions rowsPerStrip = info["rowsPerStrip"] stripByteCounts = info["stripByteCounts"] #bytes in strip since I do not support compression rowStart = 0 if len(stripOffsets) == 1: bytesPerRow = int(stripByteCounts[0] / rowsPerStrip) fd.seek(stripOffsets[0] + rowMin * bytesPerRow) nBytes = (rowMax - rowMin + 1) * bytesPerRow if self._swap: readout = numpy.fromstring(fd.read(nBytes), dtype).byteswap() else: readout = numpy.fromstring(fd.read(nBytes), dtype) if hasattr(nBits, 'index'): readout.shape = -1, nColumns, len(nBits) elif info['colormap'] is not None: readout = colormap[readout] else: readout.shape = -1, nColumns image[rowMin:rowMax + 1, :] = readout else: for i in range(len(stripOffsets)): #the amount of rows nRowsToRead = rowsPerStrip rowEnd = int(min(rowStart + nRowsToRead, nRows)) if rowEnd < rowMin: rowStart += nRowsToRead continue if (rowStart > rowMax): break #we are in position fd.seek(stripOffsets[i]) #the amount of bytes to read nBytes = stripByteCounts[i] if compression_type == 32773: try: bufferBytes = bytes() except: #python 2.5 ... bufferBytes = "" #packBits readBytes = 0 #intermediate buffer tmpBuffer = fd.read(nBytes) while readBytes < nBytes: n = struct.unpack('b', tmpBuffer[readBytes:(readBytes + 1)])[0] readBytes += 1 if n >= 0: #should I prevent reading more than the #length of the chain? Let's python raise #the exception... bufferBytes += tmpBuffer[readBytes:\ readBytes + (n + 1)] readBytes += (n + 1) elif n > -128: bufferBytes += (-n + 1) * tmpBuffer[readBytes:(readBytes + 1)] readBytes += 1 else: #if read -128 ignore the byte continue if self._swap: readout = numpy.fromstring(bufferBytes, dtype).byteswap() else: readout = numpy.fromstring(bufferBytes, dtype) if hasattr(nBits, 'index'): readout.shape = -1, nColumns, len(nBits) elif info['colormap'] is not None: readout = colormap[readout] readout.shape = -1, nColumns, 3 else: readout.shape = -1, nColumns image[rowStart:rowEnd, :] = readout else: if 1: #use numpy if self._swap: readout = numpy.fromstring(fd.read(nBytes), dtype).byteswap() else: readout = numpy.fromstring(fd.read(nBytes), dtype) if hasattr(nBits, 'index'): readout.shape = -1, nColumns, len(nBits) elif colormap is not None: readout = colormap[readout] readout.shape = -1, nColumns, 3 else: readout.shape = -1, nColumns image[rowStart:rowEnd, :] = readout else: #using struct readout = numpy.array(struct.unpack(st + "%df" % int(nBytes / 4), fd.read(nBytes)), dtype=dtype) if hasattr(nBits, 'index'): readout.shape = -1, nColumns, len(nBits) elif colormap is not None: readout = colormap[readout] readout.shape = -1, nColumns, 3 else: readout.shape = -1, nColumns image[rowStart:rowEnd, :] = readout rowStart += nRowsToRead if close: self.__makeSureFileIsClosed() if len(image.shape) == 3: #color image if self._forceMonoOutput: #color image, convert to monochrome image = (image[:, :, 0] * 0.114 + \ image[:, :, 1] * 0.587 + \ image[:, :, 2] * 0.299).astype(numpy.float32) if (rowMin == 0) and (rowMax == (nRows - 1)): self._imageDataCacheIndex.insert(0, nImage) self._imageDataCache.insert(0, image) if len(self._imageDataCacheIndex) > self._maxImageCacheLength: self._imageDataCacheIndex = self._imageDataCacheIndex[:self._maxImageCacheLength] self._imageDataCache = self._imageDataCache[:self._maxImageCacheLength] return image def writeImage(self, image0, info=None, software=None, date=None): if software is None: software = 'PyMca.TiffIO' #if date is None: # date = time.ctime() self.__makeSureFileIsOpen() fd = self.fd #prior to do anything, perform some tests if not len(image0.shape): raise ValueError("Empty image") if len(image0.shape) == 1: #get a different view image = image0[:] image.shape = 1, -1 else: image = image0 if image.dtype == numpy.float64: image = image.astype(numpy.float32) fd.seek(0) mode = fd.mode name = fd.name if 'w' in mode: #we have to overwrite the file self.__makeSureFileIsClosed() fd = None if os.path.exists(name): os.remove(name) fd = open(name, mode='wb+') self._initEmptyFile(fd) self.fd = fd #read the file size self.__makeSureFileIsOpen() fd = self.fd fd.seek(0, os.SEEK_END) endOfFile = fd.tell() if fd.tell() == 0: self._initEmptyFile(fd) fd.seek(0, os.SEEK_END) endOfFile = fd.tell() #init internal variables self._initInternalVariables(fd) st = self._structChar #get the image file directories nImages = self.getImageFileDirectories() if DEBUG: print("File contains %d images" % nImages) if nImages == 0: fd.seek(4) fmt = st + 'I' fd.write(struct.pack(fmt, endOfFile)) else: fd.seek(self._IFD[-1]) fmt = st + 'H' numberOfDirectoryEntries = struct.unpack(fmt, fd.read(struct.calcsize(fmt)))[0] fmt = st + 'I' pos = self._IFD[-1] + 2 + 12 * numberOfDirectoryEntries fd.seek(pos) fmt = st + 'I' fd.write(struct.pack(fmt, endOfFile)) fd.flush() #and we can write at the end of the file, find out the file length fd.seek(0, os.SEEK_END) #get the description information from the input information if info is None: description = info else: description = "%s" % "" for key in info.keys(): description += "%s=%s\n" % (key, info[key]) #get the image file directory outputIFD = self._getOutputIFD(image, description=description, software=software, date=date) #write the new IFD fd.write(outputIFD) #write the image if self._swap: fd.write(image.byteswap().tostring()) else: fd.write(image.tostring()) fd.flush() self.fd = fd self.__makeSureFileIsClosed() def _initEmptyFile(self, fd=None): if fd is None: fd = self.fd if sys.byteorder == "little": order = "II" #intel, little endian fileOrder = "little" self._structChar = '<' else: order = "MM" #motorola, high endian fileOrder = "big" self._structChar = '>' st = self._structChar if fileOrder == sys.byteorder: self._swap = False else: self._swap = True fd.seek(0) if sys.version < '3.0': fd.write(struct.pack(st + '2s', order)) fd.write(struct.pack(st + 'H', 42)) fd.write(struct.pack(st + 'I', 0)) else: fd.write(struct.pack(st + '2s', bytes(order, 'utf-8'))) fd.write(struct.pack(st + 'H', 42)) fd.write(struct.pack(st + 'I', 0)) fd.flush() def _getOutputIFD(self, image, description=None, software=None, date=None): #the tags have to be in order #the very minimum is #256:"NumberOfColumns", # S or L ImageWidth #257:"NumberOfRows", # S or L ImageHeight #258:"BitsPerSample", # S Number of bits per component #259:"Compression", # SHORT (1 - NoCompression, ... #262:"PhotometricInterpretation", # SHORT (0 - WhiteIsZero, 1 -BlackIsZero, 2 - RGB, 3 - Palette color #270:"ImageDescription", # ASCII #273:"StripOffsets", # S or L, for each strip, the byte offset of the strip #278:"RowsPerStrip", # S or L, number of rows in each back may be not for the last #279:"StripByteCounts", # S or L, The number of bytes in the strip AFTER any compression #305:"Software", # ASCII #306:"Date", # ASCII #339:"SampleFormat", # SHORT Interpretation of data in each pixel nDirectoryEntries = 9 imageDescription = None if description is not None: descriptionLength = len(description) while descriptionLength < 4: description = description + " " descriptionLength = len(description) if sys.version >= '3.0': description = bytes(description, 'utf-8') elif type(description) != type(""): try: description = description.decode('utf-8') except UnicodeDecodeError: try: description = description.decode('latin-1') except UnicodeDecodeError: description = "%s" % description if sys.version > '2.6': description = description.encode('utf-8', errors="ignore") description = "%s" % description descriptionLength = len(description) imageDescription = struct.pack("%ds" % descriptionLength, description) nDirectoryEntries += 1 #software if software is not None: softwareLength = len(software) while softwareLength < 4: software = software + " " softwareLength = len(software) if sys.version >= '3.0': software = bytes(software, 'utf-8') softwarePackedString = struct.pack("%ds" % softwareLength, software) nDirectoryEntries += 1 else: softwareLength = 0 if date is not None: dateLength = len(date) if sys.version >= '3.0': date = bytes(date, 'utf-8') datePackedString = struct.pack("%ds" % dateLength, date) dateLength = len(datePackedString) nDirectoryEntries += 1 else: dateLength = 0 nRows, nColumns = image.shape dtype = image.dtype bitsPerSample = int(dtype.str[-1]) * 8 #only uncompressed data compression = 1 #interpretation, black is zero interpretation = 1 #image description if imageDescription is not None: descriptionLength = len(imageDescription) else: descriptionLength = 0 #strip offsets #we are putting them after the directory and the directory is #at the end of the file self.fd.seek(0, os.SEEK_END) endOfFile = self.fd.tell() if endOfFile == 0: #empty file endOfFile = 8 #rows per strip if ALLOW_MULTIPLE_STRIPS: #try to segment the image in several pieces if not (nRows % 4): rowsPerStrip = int(nRows / 4) elif not (nRows % 10): rowsPerStrip = int(nRows / 10) elif not (nRows % 8): rowsPerStrip = int(nRows / 8) elif not (nRows % 4): rowsPerStrip = int(nRows / 4) elif not (nRows % 2): rowsPerStrip = int(nRows / 2) else: rowsPerStrip = nRows else: rowsPerStrip = nRows #stripByteCounts stripByteCounts = int(nColumns * rowsPerStrip * bitsPerSample / 8) if descriptionLength > 4: stripOffsets0 = endOfFile + dateLength + descriptionLength + \ 2 + 12 * nDirectoryEntries + 4 else: stripOffsets0 = endOfFile + dateLength + \ 2 + 12 * nDirectoryEntries + 4 if softwareLength > 4: stripOffsets0 += softwareLength stripOffsets = [stripOffsets0] stripOffsetsLength = 0 stripOffsetsString = None st = self._structChar if rowsPerStrip != nRows: nStripOffsets = int(nRows / rowsPerStrip) fmt = st + 'I' stripOffsetsLength = struct.calcsize(fmt) * nStripOffsets stripOffsets0 += stripOffsetsLength #the length for the stripByteCounts will be the same stripOffsets0 += stripOffsetsLength stripOffsets = [] for i in range(nStripOffsets): value = stripOffsets0 + i * stripByteCounts stripOffsets.append(value) if i == 0: stripOffsetsString = struct.pack(fmt, value) stripByteCountsString = struct.pack(fmt, stripByteCounts) else: stripOffsetsString += struct.pack(fmt, value) stripByteCountsString += struct.pack(fmt, stripByteCounts) if DEBUG: print("IMAGE WILL START AT %d" % stripOffsets[0]) #sample format if dtype in [numpy.float32, numpy.float64] or\ dtype.str[-2] == 'f': sampleFormat = SAMPLE_FORMAT_FLOAT elif dtype in [numpy.uint8, numpy.uint16, numpy.uint32, numpy.uint64]: sampleFormat = SAMPLE_FORMAT_UINT elif dtype in [numpy.int8, numpy.int16, numpy.int32, numpy.int64]: sampleFormat = SAMPLE_FORMAT_INT else: raise ValueError("Unsupported data type %s" % dtype) info = {} info["nColumns"] = nColumns info["nRows"] = nRows info["nBits"] = bitsPerSample info["compression"] = compression info["photometricInterpretation"] = interpretation info["stripOffsets"] = stripOffsets info["rowsPerStrip"] = rowsPerStrip info["stripByteCounts"] = stripByteCounts info["date"] = date info["sampleFormat"] = sampleFormat outputIFD = "" if sys.version > '2.6': outputIFD = eval('b""') fmt = st + "H" outputIFD += struct.pack(fmt, nDirectoryEntries) fmt = st + "HHII" outputIFD += struct.pack(fmt, TAG_NUMBER_OF_COLUMNS, FIELD_TYPE_OUT['I'], 1, info["nColumns"]) outputIFD += struct.pack(fmt, TAG_NUMBER_OF_ROWS, FIELD_TYPE_OUT['I'], 1, info["nRows"]) fmt = st + 'HHIHH' outputIFD += struct.pack(fmt, TAG_BITS_PER_SAMPLE, FIELD_TYPE_OUT['H'], 1, info["nBits"], 0) fmt = st + 'HHIHH' outputIFD += struct.pack(fmt, TAG_COMPRESSION, FIELD_TYPE_OUT['H'], 1, info["compression"], 0) fmt = st + 'HHIHH' outputIFD += struct.pack(fmt, TAG_PHOTOMETRIC_INTERPRETATION, FIELD_TYPE_OUT['H'], 1, info["photometricInterpretation"], 0) if imageDescription is not None: descriptionLength = len(imageDescription) if descriptionLength > 4: fmt = st + 'HHII' outputIFD += struct.pack(fmt, TAG_IMAGE_DESCRIPTION, FIELD_TYPE_OUT['s'], descriptionLength, info["stripOffsets"][0] - \ 2 * stripOffsetsLength - \ descriptionLength) else: #it has to have length 4 fmt = st + 'HHI%ds' % descriptionLength outputIFD += struct.pack(fmt, TAG_IMAGE_DESCRIPTION, FIELD_TYPE_OUT['s'], descriptionLength, description) if len(stripOffsets) == 1: fmt = st + 'HHII' outputIFD += struct.pack(fmt, TAG_STRIP_OFFSETS, FIELD_TYPE_OUT['I'], 1, info["stripOffsets"][0]) else: fmt = st + 'HHII' outputIFD += struct.pack(fmt, TAG_STRIP_OFFSETS, FIELD_TYPE_OUT['I'], len(stripOffsets), info["stripOffsets"][0] - 2 * stripOffsetsLength) fmt = st + 'HHII' outputIFD += struct.pack(fmt, TAG_ROWS_PER_STRIP, FIELD_TYPE_OUT['I'], 1, info["rowsPerStrip"]) if len(stripOffsets) == 1: fmt = st + 'HHII' outputIFD += struct.pack(fmt, TAG_STRIP_BYTE_COUNTS, FIELD_TYPE_OUT['I'], 1, info["stripByteCounts"]) else: fmt = st + 'HHII' outputIFD += struct.pack(fmt, TAG_STRIP_BYTE_COUNTS, FIELD_TYPE_OUT['I'], len(stripOffsets), info["stripOffsets"][0] - stripOffsetsLength) if software is not None: if softwareLength > 4: fmt = st + 'HHII' outputIFD += struct.pack(fmt, TAG_SOFTWARE, FIELD_TYPE_OUT['s'], softwareLength, info["stripOffsets"][0] - \ 2 * stripOffsetsLength - \ descriptionLength - softwareLength - dateLength) else: #it has to have length 4 fmt = st + 'HHI%ds' % softwareLength outputIFD += struct.pack(fmt, TAG_SOFTWARE, FIELD_TYPE_OUT['s'], softwareLength, softwarePackedString) if date is not None: fmt = st + 'HHII' outputIFD += struct.pack(fmt, TAG_DATE, FIELD_TYPE_OUT['s'], dateLength, info["stripOffsets"][0] - \ 2 * stripOffsetsLength - \ descriptionLength - dateLength) fmt = st + 'HHIHH' outputIFD += struct.pack(fmt, TAG_SAMPLE_FORMAT, FIELD_TYPE_OUT['H'], 1, info["sampleFormat"], 0) fmt = st + 'I' outputIFD += struct.pack(fmt, 0) if softwareLength > 4: outputIFD += softwarePackedString if date is not None: outputIFD += datePackedString if imageDescription is not None: if descriptionLength > 4: outputIFD += imageDescription if stripOffsetsString is not None: outputIFD += stripOffsetsString outputIFD += stripByteCountsString return outputIFD if __name__ == "__main__": filename = sys.argv[1] dtype = numpy.uint16 if not os.path.exists(filename): print("Testing file creation") tif = TiffIO(filename, mode='wb+') data = numpy.arange(10000).astype(dtype) data.shape = 100, 100 tif.writeImage(data, info={'Title':'1st'}) tif = None if os.path.exists(filename): print("Testing image appending") tif = TiffIO(filename, mode='rb+') tif.writeImage((data * 2).astype(dtype), info={'Title':'2nd'}) tif = None tif = TiffIO(filename) print("Number of images = %d" % tif.getNumberOfImages()) for i in range(tif.getNumberOfImages()): info = tif.getInfo(i) for key in info: if key not in ["colormap"]: print("%s = %s" % (key, info[key])) elif info['colormap'] is not None: print("RED %s = %s" % (key, info[key][0:10, 0])) print("GREEN %s = %s" % (key, info[key][0:10, 1])) print("BLUE %s = %s" % (key, info[key][0:10, 2])) data = tif.getImage(i)[0, 0:10] print("data [0, 0:10] = ", data) fabio-0.1.3/fabio-src/brukerimage.py0000644000175000017500000004762512233175220020106 0ustar jeromejerome00000000000000#!/usr/bin/env python #coding: utf8 from __future__ import with_statement __doc__ = """ Authors: Henning O. Sorensen & Erik Knudsen Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk Based on: openbruker,readbruker, readbrukerheader functions in the opendata module of ImageD11 written by Jon Wright, ESRF, Grenoble, France Writer by Jérôme Kieffer, ESRF, Grenoble, France """ __authors__ = ["Henning O. Sorensen" , "Erik Knudsen", "Jon Wright", "Jérôme Kieffer"] __date__ = "20130502" __status__ = "development" __copyright__ = "2007-2009 Risoe National Laboratory; 2010-2013 ESRF" __licence__ = "GPL" import numpy, logging, sys from math import ceil import os, getpass, time logger = logging.getLogger("brukerimage") from fabioimage import fabioimage from fabioutils import pad from types import StringTypes if sys.version_info[0] < 3: bytes = str class brukerimage(fabioimage): """ Read and eventually write ID11 bruker (eg smart6500) images TODO: int32 -> float32 conversion according to the "linear" keyword. This is done and works but we need to check with other program that we are appliing the right formula and not the reciprocal one. """ bpp_to_numpy = {1:numpy.uint8, 2:numpy.uint16, 4:numpy.uint32} # needed if you feel like writing - see ImageD11/scripts/edf2bruker.py SPACER = "\x1a\x04" #this is CTRL-Z CTRL-D HEADERS_KEYS = ["FORMAT", #Frame format. Always “86†or "100" for Bruker-format frames. "VERSION", #Header version #, such as: 1 to 17 (6 is obsolete). "HDRBLKS", #Header size in 512-byte blocks, such as 10 or 15. Determines where the image block begins. "TYPE", #String indicating kind of data in the frame. Used to determine if a spatial correction table was applied to the frame imag "SITE", #Site name "MODEL", #Diffractometer model "USER", #Username "SAMPLE", #Sample ID, "SETNAME", #Basic data set name "RUN", #Run number within the data set, usually starts at 0, but 1 for APEX2. "SAMPNUM", #Specimen number within the data set "TITLE", #User comments (8 lines) "NCOUNTS", #Total frame counts "NOVERFL", #Number of overflows when compression frame. "MINIMUM", #Minimum counts in a pixel (uncompressed value) "MAXIMUM", #Maximum counts in a pixel (uncompressed value) "NONTIME", #Number of on-time events "NLATE", #Number of late events. Always zero for many detectors. "FILENAM", #(Original) frame filename "CREATED", #Date and time of creation "CUMULAT", #Accumulated frame exposure time in seconds "ELAPSDR", #Requested time for last exposure in seconds "ELAPSDA", #Actual time for last exposure in seconds. "OSCILLA", #Nonzero if acquired by oscillation "NSTEPS", #steps or oscillations in this frame "RANGE", #Scan range in decimal degrees (unsigned) "START", #Starting scan angle value, decimal degrees "INCREME", #Scan angle increment between frames (signed) "NUMBER", #Sequence number of this frame in series, usually starts at 0, but 1 for APEX2 "NFRAMES", #Total number of frames in the series "ANGLES", #Diffractometer angles in Eulerian space ( 2T, OM, PH, CH). "NOVER64", #Number of pixels > 64K (actually LinearThreshold value) "NPIXELB", #Number of bytes/pixel, such as 1, 2, or 4. "NROWS", #Number of rasters in frame, such as 512, 1024, 2048, or 4096 "NCOLS", #Number of pixels/raster, such as 512, 1024, 2048 or 4096 "WORDORD", #Order of bytes in word (0=LSB first) "LONGORD", #Order of words in a longword (0=LSW first) "TARGET" , #X-ray target material: Cu, Mo, Ag, Fe, Cr, Co, Ni, W, Mn, or other. "SOURCEK", #X-ray source voltage in kV "SOURCEM", #X-ray source current in mA "FILTER" , #Filter/monochromator setting: Such as: Parallel, graphite, Ni Filter, C Filter, Zr Filter,Cross coupled Goebel Mirrors ... "CELL" , #Unit cell A,B,C,ALPHA,BETA,GAMMA "MATRIX" , #9R Orientation matrix (P3 conventions) "LOWTEMP", #Low temp flag. "TEMP", #set temperature "HITEMP", #Acquired at high temperature "ZOOM" , #Zoom: Xc, Yc, Mag used for HI-STAR detectors: 0.5 0.5 1.0 "CENTER" , #X, Y of direct beam at 2-theta = 0. These are raw center for raw frames and unwarped center for unwarped frames. "DISTANC", #Sample-detector distance, cm (see CmToGrid value) Adds: Sample-detector grid/phosphor distance, cm "TRAILER", #Byte pointer to trailer info "COMPRES", #Compression scheme ID, if any. Such as: NONE, LINEAR (Linear scale, offset for pixel values, typically 1.0, 0.0). "LINEAR", #Linear scale (1.0 0.0 for no change; 0.1 0 for divided by 10...) "PHD" , # Discriminator: Pulse height settings. X100 and X1000 only. Stores CCD phosphor efficiency (first field). "PREAMP" , #Preamp gain setting. X100 and X1000 only. SMART: Stores Roper CCD gain table index value. "CORRECT", #Flood table correction filename, UNKNOWN or LINEAR. "WARPFIL", #Brass plate correction filename, UNKNOWN or LINEAR. Note: A filename here does NOT mean that spatial correction was performed. See TYPE and string “UNWARP†to determine that. "WAVELEN", #Wavelengths (average, a1, a2) "MAXXY", #X,Y pixel # of maximum counts (from lower corner of 0,0) "AXIS", #Scan axis ib Eulerian space (1-4 for 2-theta, omega, phi, chi) (0 =none, 2 = default). "ENDING" , #Actual goniometer angles at end of frame in Eulerian space. "DETPAR" , #Detector position corrections (dX,dY,dDist,Pitch,Roll,Yaw) "LUT", #Recommended display lookup table "DISPLIM", #Recommended display limits "PROGRAM", #Name and version of program writing frame, such as: "ROTATE", #Non zero if acquired by rotation of phi during scan (or oscilate) "BITMASK", #File name of active pixel mask associated with this frame or $NULL "OCTMASK", #Octagon mask parameters to use if BITMASK=$null. Min X, Min X+Y, Min Y, Max X-Y, Max X, Max X+Y, Max Y, Max Y-X. "ESDCELL", #Unit cell parameter standard deviations "DETTYPE", #Detector or CCD chip type (as displayed on CEU). Default is MULTIWIRE but UNKNOWN is advised, can contain PIXPERCM: CMTOGRID: "NEXP", #Number of exposures: 1=single, 2=correlated sum.32 for most ccds, and 64 for 2K ccds. "CCDPARM", #CCD parameters: readnoise, e/ADU, e/photon, bias, full scale "BIS", #Potential full linear scale if rescan and attenuator used. "CHEM", #Chemical formula in CIFTAB string, such as “?†"MORPH", #Crystal morphology in CIFTAB string, such as “?†"CCOLOR", #Crystal color in CIFTAB string, such as “?†"CSIZE", #Crystal dimensions (3 ea) in CIFTAB string, such as “?†"DNSMET", #Density measurement method in CIFTAB string, such as “?†"DARK", #Name of dark current correction or NONE. "AUTORNG", #Auto-ranging: gain, high-speed time, scale, offset, full linear scale Note: If full linear scale is zero, then CCDPARM full scale is the full linear scale (BIS frames). "ZEROADJ", #Goniometer zero corrections (refined in least squares) "XTRANS", #Crystal XYZ translations (refined in least squares) "HKL&XY", #HKL and pixel XY for reciprocal space scan. GADDS only. "AXES2", #Diffractometer setting linear axes (4 ea). (X, Y, Z, Aux) "ENDING2", #Actual goniometer linear axes @ end of frame. (X, Y, Z, Aux) "FILTER2", #Monochromator 2-theta angle and monochromator roll angle. v15: Adds beam tilt angle and attenuator factor. "LEPTOS", # String for LEPTOS. "CFR", #Only in 21CFRPart11 mode, writes the checksum for header and image (2str).] ] def __init__(self, data=None , header=None): fabioimage.__init__(self, data, header) self.__bpp_file = None self.version = 86 self.__headerstring__ = "" def _readheader(self, infile): """ The bruker format uses 80 char lines in key : value format In the first 512*5 bytes of the header there should be a HDRBLKS key, whose value denotes how many 512 byte blocks are in the total header. The header is always n*5*512 bytes, otherwise it wont contain whole key: value pairs """ line = 80 blocksize = 512 nhdrblks = 5 #by default we always read 5 blocks of 512 self.__headerstring__ = infile.read(blocksize * nhdrblks) self.header = {} for i in range(0, nhdrblks * blocksize, line): if self.__headerstring__[i: i + line].find(":") > 0: key, val = self.__headerstring__[i: i + line].split(":", 1) key = key.strip() # remove the whitespace (why?) val = val.strip() if key in self.header: # append lines if key already there self.header[key] = self.header[key] + os.linesep + val else: self.header[key] = val self.header_keys.append(key) # we must have read this in the first 5*512 bytes. nhdrblks = int(self.header['HDRBLKS']) # Now read in the rest of the header blocks, appending self.__headerstring__ += infile.read(blocksize * (nhdrblks - 5)) for i in range(5 * blocksize, nhdrblks * blocksize, line): if self.__headerstring__[i: i + line].find(":") > 0: # as for first 512 bytes of header key, val = self.__headerstring__[i: i + line].split(":", 1) key = key.strip() val = val.strip() if key in self.header: self.header[key] = self.header[key] + os.linesep + val else: self.header[key] = val self.header_keys.append(key) # make a (new) header item called "datastart" self.header['datastart'] = blocksize * nhdrblks #set the image dimensions self.dim1 = int(self.header['NROWS']) self.dim2 = int(self.header['NCOLS']) def read(self, fname, frame=None): """ Read in and unpack the pixels (including overflow table """ infile = self._open(fname, "rb") try: self._readheader(infile) except: raise rows = self.dim1 cols = self.dim2 try: # you had to read the Bruker docs to know this! npixelb = int(self.header['NPIXELB']) except Exception: errmsg = "length " + str(len(self.header['NPIXELB'])) + "\n" for byt in self.header['NPIXELB']: errmsg += "char: " + str(byt) + " " + str(ord(byt)) + "\n" logger.warning(errmsg) raise RuntimeError(errmsg) data = numpy.fromstring(infile.read(rows * cols * npixelb), dtype=self.bpp_to_numpy[npixelb]) #handle overflows nov = int(self.header['NOVERFL']) if nov > 0: # Read in the overflows # need at least int32 sized data I guess - can reach 2^21 data = data.astype(numpy.uint32) # 16 character overflows: # 9 characters of intensity # 7 character position for i in range(nov): ovfl = infile.read(16) intensity = int(ovfl[0: 9]) position = int(ovfl[9: 16]) data[position] = intensity infile.close() # Handle Float images ... if "LINEAR" in self.header: try: slope, offset = self.header["LINEAR"].split(None, 1) slope = float(slope) offset = float(offset) except Except: logger.warning("Error in converting to float data with linear parameter: %s" % self.header["LINEAR"]) self.data = data else: if slope == 1 and offset == 0: self.data = data else: #TODO: check that the formula is OK, not reverted. logger.warning("performing correction with slope=%s, offset=%s (LINEAR=%s)" % (slope, offset, self.header["LINEAR"])) self.data = (data * slope + offset).astype(numpy.float32) else: self.data = data self.data.shape = self.dim1, self.dim2 self.resetvals() self.pilimage = None return self def write(self, fname): """ Write a bruker image """ if numpy.issubdtype(self.data.dtype, float): if "LINEAR" in self.header: try: slope, offset = self.header["LINEAR"].split(None, 1) slope = float(slope) offset = float(offset) except Except: logger.warning("Error in converting to float data with linear parameter: %s" % self.header["LINEAR"]) slope, offset = 1.0, 0.0 else: offset = self.data.min() max_data = self.data.max() max_range = 2 ** 24 - 1 #similar to the mantissa of a float32 if max_data > offset: slope = (max_data - offset) / float(max_range) else: slope = 1.0 tmp_data = numpy.round(((self.data - offset) / slope)).astype(numpy.uint32) self.header["LINEAR"] = "%s %s" % (slope, offset) else: tmp_data = self.data bpp = self.calc_bpp(tmp_data) self.basic_translate(fname) limit = 2 ** (8 * bpp) - 1 data = tmp_data.astype(self.bpp_to_numpy[bpp]) reset = numpy.where(tmp_data >= limit) data[reset] = limit data = data.newbyteorder("<") #Bruker enforces little endian with self._open(fname, "wb") as bruker: bruker.write(self.gen_header()) bruker.write(data.tostring()) bruker.write(self.gen_overflow()) def calc_bpp(self, data=None, max_entry=4096): """ Calculate the number of byte per pixel to get an optimal overflow table. @return: byte per pixel """ if data is None: data = self.data if self.__bpp_file is None: for i in [1, 2]: overflown = (data >= (2 ** (8 * i) - 1)) if overflown.sum() < max_entry: self.__bpp_file = i break else: self.__bpp_file = 4 return self.__bpp_file def gen_header(self): """ Generate headers (with some magic and guesses) @param format can be 86 or 100 """ headers = [] for key in self.HEADERS_KEYS: if key in self.header: value = self.header[key] line = key.ljust(7) + ":" if type(value) in StringTypes: if os.linesep in value: lines = value.split(os.linesep) for i in lines[:-1] : headers.append((line + bytes(i)).ljust(80, " ")) line = key.ljust(7) + ":" line += bytes(lines[-1]) elif len(value) < 72: line += bytes(value) else: for i in range(len(value) // 72): headers.append((line + bytes(value[72 * i:72 * (i + 1)]))) line = key.ljust(7) + ":" line += value[72 * (i + 1):] elif "__len__" in dir(value): f = "\%.%is" % 72 // len(value) - 1 line += " ".join([f % i for i in value]) else: line += bytes(value) headers.append(line.ljust(80, " ")) header = "".join(headers) if len(header) > 512 * self.header["HDRBLKS"]: tmp = ceil(len(header) / 512.0) self.header["HDRBLKS"] = int(ceil(tmp / 5.0) * 5.0) for i in range(len(headers)): if headers[i].startswith("HDRBLKS"): headers[i] = headers.append(("HDRBLKS:%s" % self.header["HDRBLKS"]).ljust(80, " ")) res = pad("".join(headers), self.SPACER + "."*78, 512 * int(self.header["HDRBLKS"])) return res def gen_overflow(self): """ Generate an overflow table """ limit = 2 ** (8 * self.calc_bpp()) - 1 flat = self.data.ravel() #flat memory view overflow_pos = numpy.where(flat >= limit)[0] #list of indexes overflow_val = flat[overflow_pos] overflow = "".join(["%09i%07i" % (val, pos) for pos, val in zip(overflow_pos, overflow_val)]) return pad(overflow, ".", 512) def basic_translate(self, fname=None): """ Does some basic population of the headers so that the writing is possible """ if not "FORMAT" in self.header: self.header["FORMAT"] = "86" if not "HDRBLKS" in self.header: self.header["HDRBLKS"] = 5 if not "TYPE" in self.header: self.header["TYPE"] = "UNWARPED" if not "USER" in self.header: self.header["USER"] = getpass.getuser() if not "FILENAM" in self.header: self.header["FILENAM"] = "%s" % fname if not "CREATED" in self.header: self.header["CREATED"] = time.ctime() if not "NOVERFL" in self.header: self.header["NOVERFL"] = "0" # if not "NPIXELB" in self.header: self.header["NPIXELB"] = self.calc_bpp() #if not "NROWS" in self.header: self.header["NROWS"] = self.data.shape[0] #if not "NCOLS" in self.header: self.header["NCOLS"] = self.data.shape[1] if not "WORDORD" in self.header: self.header["WORDORD"] = "0" if not "LONGORD" in self.header: self.header["LONGORD"] = "0" def test(): """ a testcase """ import sys, time img = brukerimage() start = time.clock() for filename in sys.argv[1:]: img.read(filename) res = img.toPIL16() img.rebin(2, 2) print(filename + (": max=%d, min=%d, mean=%.2e, stddev=%.2e") % ( img.getmax(), img.getmin(), img.getmean(), img.getstddev())) print('integrated intensity (%d %d %d %d) =%.3f' % ( 10, 20, 20, 40, img.integrate_area((10, 20, 20, 40)))) end = time.clock() print (end - start) if __name__ == '__main__': test() fabio-0.1.3/fabio-src/__init__.py0000644000175000017500000000131112233175156017336 0ustar jeromejerome00000000000000#!/usr/bin/env python #coding: utf8 """ FabIO module """ __author__ = "Jérôme Kieffer" __contact__ = "Jerome.Kieffer@ESRF.eu" __license__ = "GPLv3+" __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" __date__ = "30/04/2013" __status__ = "stable" version = "0.1.3" import logging logging.basicConfig() import fabioimage import openimage from fabioutils import COMPRESSORS, jump_filename, FilenameObject, \ previous_filename, next_filename, deconstruct_filename, \ extract_filenumber, getnum, construct_filename # Compatibility with outside world: filename_object = FilenameObject from openimage import openimage as open from openimage import openheader as openheader fabio-0.1.3/fabio-src/fabioimage.py0000644000175000017500000004614312233175220017666 0ustar jeromejerome00000000000000#!/usr/bin/env python """ Authors: Henning O. Sorensen & Erik Knudsen Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk and Jon Wright, Jerome Kieffer: ESRF """ from __future__ import with_statement import os, types, logging, sys, tempfile logger = logging.getLogger("fabioimage") import numpy try: from PIL import Image except ImportError: logger.warning("PIL is not installed ... trying to do without") Image = None import fabioutils, converters class fabioimage(object): """ A common object for images in fable Contains a numpy array (.data) and dict of meta data (.header) """ _need_a_seek_to_read = False _need_a_real_file = False def __init__(self, data=None , header=None): """ Set up initial values """ self._classname = None if type(data) in types.StringTypes: raise Exception("fabioimage.__init__ bad argument - " + \ "data should be numpy array") self.data = self.checkData(data) self.pilimage = None if header is None: self.header = {} else: self.header = self.checkHeader(header) self.header_keys = self.header.keys() # holds key ordering if self.data is not None: self.dim2, self.dim1 = self.data.shape else: self.dim1 = self.dim2 = 0 self.bytecode = None # numpy typecode self.bpp = 2 # bytes per pixel # cache for image statistics self.mean = self.maxval = self.stddev = self.minval = None # Cache roi self.roi = None self.area_sum = None self.slice = None # New for multiframe files self.nframes = 1 self.currentframe = 0 self.filename = None self.filenumber = None @staticmethod def checkHeader(header=None): """ Empty for fabioimage but may be populated by others classes """ if header is None: return {} else: return header @staticmethod def checkData(data=None): """ Empty for fabioimage but may be populated by others classes, especially for format accepting only integers """ return data def getclassname(self): """ Retrieves the name of the class @return: the name of the class """ if self._classname is None: self._classname = str(self.__class__).replace("", "").split(".")[-1] return self._classname classname = property(getclassname) def getframe(self, num): """ returns the file numbered 'num' in the series as a fabioimage """ if self.nframes == 1: # single image per file import openimage return openimage.openimage( fabioutils.jump_filename(self.filename, num)) raise Exception("getframe out of range") def previous(self): """ returns the previous file in the series as a fabioimage """ import openimage return openimage.openimage( fabioutils.previous_filename(self.filename)) def next(self): """ returns the next file in the series as a fabioimage """ import openimage return openimage.openimage( fabioutils.next_filename(self.filename)) def toPIL16(self, filename=None): """ Convert to Python Imaging Library 16 bit greyscale image FIXME - this should be handled by the libraries now """ if not Image: raise RuntimeError("PIL is not installed !!! ") if filename: self.read(filename) if self.pilimage is not None: return self.pilimage # mode map size = self.data.shape[:2][::-1] typmap = { 'float32' : "F" , 'int32' : "F;32S" , 'uint32' : "F;32" , 'int16' : "F;16S" , 'uint16' : "F;16" , 'int8' : "F;8S" , 'uint8' : "F;8" } if typmap.has_key(self.data.dtype.name): mode2 = typmap[ self.data.dtype.name ] mode1 = mode2[0] else: raise Exception("Unknown numpy type " + str(self.data.dtype.type)) # # hack for byteswapping for PIL in MacOS testval = numpy.array((1, 0), numpy.uint8).view(numpy.uint16)[0] if testval == 1: dats = self.data.tostring() elif testval == 256: dats = self.data.byteswap().tostring() else: raise Exception("Endian unknown in fabioimage.toPIL16") self.pilimage = Image.frombuffer(mode1, size, dats, "raw", mode2, 0, 1) return self.pilimage def getheader(self): """ returns self.header """ return self.header def getmax(self): """ Find max value in self.data, caching for the future """ if self.maxval is None: self.maxval = self.data.max() return self.maxval def getmin(self): """ Find min value in self.data, caching for the future """ if self.minval is None: self.minval = self.data.min() return self.minval def make_slice(self, coords): """ Convert a len(4) set of coords into a len(2) tuple (pair) of slice objects the latter are immutable, meaning the roi can be cached """ assert len(coords) == 4 if len(coords) == 4: # fabian edfimage preference if coords[0] > coords[2]: coords[0:3:2] = [coords[2], coords[0]] if coords[1] > coords[3]: coords[1:4:2] = [coords[3], coords[1]] #in fabian: normally coordinates are given as (x,y) whereas # a matrix is given as row,col # also the (for whichever reason) the image is flipped upside # down wrt to the matrix hence these tranformations fixme = (self.dim2 - coords[3] - 1, coords[0] , self.dim2 - coords[1] - 1, coords[2]) return (slice(int(fixme[0]), int(fixme[2]) + 1) , slice(int(fixme[1]), int(fixme[3]) + 1)) def integrate_area(self, coords): """ Sums up a region of interest if len(coords) == 4 -> convert coords to slices if len(coords) == 2 -> use as slices floor -> ? removed as unused in the function. """ if self.data == None: # This should return NAN, not zero ? return 0 if len(coords) == 4: sli = self.make_slice(coords) elif len(coords) == 2 and isinstance(coords[0], slice) and \ isinstance(coords[1], slice): sli = coords if sli == self.slice and self.area_sum is not None: pass elif sli == self.slice and self.roi is not None: self.area_sum = self.roi.sum(dtype=numpy.float) else: self.slice = sli self.roi = self.data[ self.slice ] self.area_sum = self.roi.sum(dtype=numpy.float) return self.area_sum def getmean(self): """ return the mean """ if self.mean is None: self.mean = self.data.mean(dtype=numpy.double) return self.mean def getstddev(self): """ return the standard deviation """ if self.stddev == None: self.stddev = self.data.std(dtype=numpy.double) return self.stddev def add(self, other): """ Add another Image - warning, does not clip to 16 bit images by default """ if not hasattr(other, 'data'): logger.warning('edfimage.add() called with something that ' + \ 'does not have a data field') assert self.data.shape == other.data.shape , \ 'incompatible images - Do they have the same size?' self.data = self.data + other.data self.resetvals() def resetvals(self): """ Reset cache - call on changing data """ self.mean = self.stddev = self.maxval = self.minval = None self.roi = self.slice = self.area_sum = None def rebin(self, x_rebin_fact, y_rebin_fact, keep_I=True): """ Rebin the data and adjust dims @param x_rebin_fact: x binning factor @param y_rebin_fact: y binning factor @param keep_I: shall the signal increase ? @type x_rebin_fact: int @type y_rebin_fact: int @type keep_I: boolean """ if self.data == None: raise Exception('Please read in the file you wish to rebin first') if (self.dim1 % x_rebin_fact != 0) or (self.dim2 % y_rebin_fact != 0): raise RuntimeError('image size is not divisible by rebin factor - ' + \ 'skipping rebin') else: dataIn = self.data.astype("float64") shapeIn = self.data.shape shapeOut = (shapeIn[0] / y_rebin_fact, shapeIn[1] / x_rebin_fact) binsize = y_rebin_fact * x_rebin_fact if binsize < 50: #method faster for small binning (4x4) out = numpy.zeros(shapeOut, dtype="float64") for j in range(x_rebin_fact): for i in range(y_rebin_fact): out += dataIn[i::y_rebin_fact, j::x_rebin_fact] else: #method faster for large binning (8x8) temp = self.data.astype("float64") temp.shape = (shapeOut[0], y_rebin_fact, shapeOut[1], x_rebin_fact) out = temp.sum(axis=3).sum(axis=1) self.resetvals() if keep_I: self.data = (out / (y_rebin_fact * x_rebin_fact)).astype(self.data.dtype) else: self.data = out.astype(self.data.dtype) self.dim1 = self.dim1 / x_rebin_fact self.dim2 = self.dim2 / y_rebin_fact #update header self.update_header() def write(self, fname): """ To be overwritten - write the file """ raise Exception("Class has not implemented readheader method yet") def save(self, fname): 'wrapper for write' self.write(fname) def readheader(self, filename): """ Call the _readheader function... """ # Override the needs asserting that all headers can be read via python modules save_state = self._need_a_real_file , self._need_a_seek_to_read self._need_a_real_file , self._need_a_seek_to_read = False, False fin = self._open(filename) self._readheader(fin) fin.close() self._need_a_real_file , self._need_a_seek_to_read = save_state def _readheader(self, fik_obj): """ Must be overridden in classes """ raise Exception("Class has not implemented _readheader method yet") def update_header(self , **kwds): """ update the header entries by default pass in a dict of key, values. """ self.header.update(kwds) def read(self, filename, frame=None): """ To be overridden - fill in self.header and self.data """ raise Exception("Class has not implemented read method yet") # return self def load(self, *arg, **kwarg): "Wrapper for read" return self.read(*arg, **kwarg) def readROI(self, filename, frame=None, coords=None): """ Method reading Region of Interest. This implementation is the trivial one, just doing read and crop """ self.read(filename, frame) if len(coords) == 4: self.slice = self.make_slice(coords) elif len(coords) == 2 and isinstance(coords[0], slice) and \ isinstance(coords[1], slice): self.slice = coords else: logger.warning('readROI: Unable to understand Region Of Interest: got %s', coords) self.roi = self.data[ self.slice ] return self.roi def _open(self, fname, mode="rb"): """ Try to handle compressed files, streams, shared memory etc Return an object which can be used for "read" and "write" ... FIXME - what about seek ? """ fileObject = None self.filename = fname self.filenumber = fabioutils.extract_filenumber(fname) if hasattr(fname, "read") and hasattr(fname, "write"): # It is already something we can use return fname if isinstance(fname, (str, unicode)): self.header["filename"] = fname if os.path.splitext(fname)[1] == ".gz": fileObject = self._compressed_stream(fname, fabioutils.COMPRESSORS['.gz'], fabioutils.GzipFile, mode) elif os.path.splitext(fname)[1] == '.bz2': fileObject = self._compressed_stream(fname, fabioutils.COMPRESSORS['.bz2'], fabioutils.BZ2File, mode) # # Here we return the file even though it may be bzipped or gzipped # but named incorrectly... # # FIXME - should we fix that or complain about the daft naming? else: fileObject = fabioutils.File(fname, mode) if "name" not in dir(fileObject): fileObject.name = fname return fileObject def _compressed_stream(self, fname, system_uncompress, python_uncompress, mode='rb'): """ Try to transparently handle gzip / bzip without always getting python performance """ # assert that python modules are always OK based on performance benchmark # Try to fix the way we are using them? fobj = None if self._need_a_real_file and mode[0] == "r": fo = python_uncompress(fname, mode) # fobj = os.tmpfile() #problem when not administrator under certain flavors of windows tmpfd, tmpfn = tempfile.mkstemp() os.close(tmpfd) fobj = fabioutils.File(tmpfn, "w+b") fobj.write(fo.read()) fo.close() fobj.seek(0) elif self._need_a_seek_to_read and mode[0] == "r": fo = python_uncompress(fname, mode) fobj = fabioutils.StringIO(fo.read(), fname, mode) else: fobj = python_uncompress(fname, mode) return fobj def convert(self, dest): """ Convert a fabioimage object into another fabioimage object (with possible conversions) @param dest: destination type "EDF", "edfimage" or the class itself """ if type(dest) in types.StringTypes: dest = dest.lower() modules = [] for val in fabioutils.FILETYPES.values(): modules += [i + "image" for i in val if i not in modules] klass = None module = None klass_name = None for klass_name in modules: if klass_name.startswith(dest): try: module = sys.modules["fabio." + klass_name] except KeyError: try: module = __import__(klass_name) except: logger.error("Failed to import %s", klass_name) else: logger.debug("imported %simage", klass_name) if module is not None: break if module is not None: if hasattr(module, klass_name): klass = getattr(module, klass_name) else: logger.error("Module %s has no image class" % module) elif isinstance(dest, self.__class__): klass = dest.__class__ elif ("__new__" in dir(dest)) and isinstance(dest(), fabioimage): klass = dest else: logger.warning("Unrecognized destination format: %s " % dest) return self if klass is None: logger.warning("Unrecognized destination format: %s " % dest) return self other = klass() #temporary instance (to be overwritten) other = klass(data=converters.convert_data(self.classname, other.classname, self.data), header=converters.convert_header(self.classname, other.classname, self.header)) return other def test(): """ check some basic fabioimage functionality """ import time start = time.time() dat = numpy.ones((1024, 1024), numpy.uint16) dat = (dat * 50000).astype(numpy.uint16) assert dat.dtype.char == numpy.ones((1), numpy.uint16).dtype.char hed = {"Title":"50000 everywhere"} obj = fabioimage(dat, hed) assert obj.getmax() == 50000 assert obj.getmin() == 50000 assert obj.getmean() == 50000 , obj.getmean() assert obj.getstddev() == 0. dat2 = numpy.zeros((1024, 1024), numpy.uint16, savespace=1) cord = [ 256, 256, 790, 768 ] slic = obj.make_slice(cord) dat2[slic] = dat2[slic] + 100 obj = fabioimage(dat2, hed) # New object, so... assert obj.maxval is None assert obj.minval is None assert obj.getmax() == 100, obj.getmax() assert obj.getmin() == 0 , obj.getmin() npix = (slic[0].stop - slic[0].start) * (slic[1].stop - slic[1].start) obj.resetvals() area1 = obj.integrate_area(cord) obj.resetvals() area2 = obj.integrate_area(slic) assert area1 == area2 assert obj.integrate_area(cord) == obj.integrate_area(slic) assert obj.integrate_area(cord) == npix * 100, obj.integrate_area(cord) def clean(): """ clean up the created testfiles""" for name in ["testfile", "testfile.gz", "testfile.bz2"]: try: os.remove(name) except: continue clean() import gzip, bz2 gzip.open("testfile.gz", "wb").write("{ hello }") fout = obj._open("testfile.gz") readin = fout.read() assert readin == "{ hello }", readin + " gzipped file" bz2.BZ2File("testfilebz", "wb").write("{ hello }") fout = obj._open("testfile.bz2") readin = fout.read() assert readin == "{ hello }", readin + " bzipped file" ftest = open("testfile", "wb") ftest.write("{ hello }") assert ftest == obj._open(ftest) ftest.close() fout = obj._open("testfile") readin = fout.read() assert readin == "{ hello }", readin + "plain file" fout.close() ftest.close() clean() print "Passed in", time.time() - start, "s" if __name__ == '__main__': test() fabio-0.1.3/fabio-src/templateimage.py0000644000175000017500000000634212233175220020416 0ustar jeromejerome00000000000000#!/usr/bin/env python #coding: utf8 #This is a template for adding new file formats to FabIO # We hope it will be relatively easy to add new file formats to fabio in the future. The basic idea is the following: # 1) inherit from fabioimage overriding the methods _readheader, read and optionally write. # Name your new module XXXimage where XXX means something (eg tifimage). # # 2) readheader fills in a dictionary of "name":"value" pairs in self.header. # No one expects to find anything much in there. # # 3) read fills in self.data with a numpy array holding the image. # Some redundant info which also appears are self.dim1 and self.dim2: the image dimensions, # self.bpp is the bytes per pixel and self.bytecode is the numpy.dtype.type of the data. # # 4) The member variables "_need_a_seek_to_read" and "_need_a_real_file" are there in case you have # trouble with the transparent handling of bz2 and gz files. # # 5) Register the file type (extension naming) in fabioutils.FILETYPES # # 6) Add your new module as an import into fabio.openimage # # 7) Fill out the magic numbers for your format in fabio.openimage if you know them # (the characteristic first few bytes in the file) # # 8) Upload a testimage to the file release system and create a unittest testcase # which opens an example of your new format, confirming the image has actually # been read in successfully (eg check the mean, max, min and esd are all correct, # perhaps orientation too) # # 9) Run pylint on your code and then please go clean it up. Have a go at mine while you are at it. # #10) Bask in the warm glow of appreciation when someone unexpectedly learns they don't need to convert # their data into another format # Get ready for python3: from __future__ import with_statement, print_function __doc__ = """ Template for FabIO Authors: Who are you ? email: Where can you be reached ? """ __authors__ = ["author"] __contact__ = "name@institut.org" __license__ = "GPLv3+" __copyright__ = "Institut" __version__ = "17 Oct 2012" import numpy, logging from fabioimage import fabioimage logger = logging.getLogger("templateimage") class templateimage(fabioimage): """ FabIO image class for Images for XXX detector """ def __init__(self, *arg, **kwargs): """ Generic constructor """ fabioimage.__init__(self, *arg, **kwargs) self.data = None self.header = {} self.dim1 = self.dim2 = 0 self.m = self.maxval = self.stddev = self.minval = None self.header_keys = self.header.keys() self.bytecode = None def _readheader(self, infile): """ Read and decode the header of an image: @param infile: Opened python file (can be stringIO or bipped file) """ #list of header key to keep the order (when writing) self.header = {} self.header_keys = [] def read(self, fname, frame=None): """ try to read image @param fname: name of the file @param frame: """ self.resetvals() infile = self._open(fname) self._readheader(infile) #read the image data self.data = numpy.zeros((self.dim2, self.dim1), dtype=self.bytecode) return self fabio-0.1.3/fabio-src/OXDimage.py0000644000175000017500000005475512233175156017260 0ustar jeromejerome00000000000000#!/usr/bin/env python #coding: utf8 from __future__ import with_statement __doc__ = """ Reads Oxford Diffraction Sapphire 3 images Authors: ........ * Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions; Risoe National Laboratory; Frederiksborgvej 399; DK-4000 Roskilde; email:erik.knudsen@risoe.dk * Jon Wright, Jérôme Kieffer & Gaël Goret: European Synchrotron Radiation Facility; Grenoble (France) """ import time, logging, struct logger = logging.getLogger("OXDimage") import numpy from fabioimage import fabioimage from compression import decTY1, compTY1 try: from numpy import rad2deg, deg2rad except ImportError: #naive implementation for very old numpy (v1.0.1 on MacOSX from Risoe) rad2deg = lambda x: 180.0 * x / numpy.pi deg2rad = lambda x: x * numpy.pi / 180. DETECTOR_TYPES = {0: 'Sapphire/KM4CCD (1x1: 0.06mm, 2x2: 0.12mm)', 1: 'Sapphire2-Kodak (1x1: 0.06mm, 2x2: 0.12mm)', 2: 'Sapphire3-Kodak (1x1: 0.03mm, 2x2: 0.06mm, 4x4: 0.12mm)', 3: 'Onyx-Kodak (1x1: 0.06mm, 2x2: 0.12mm, 4x4: 0.24mm)', 4: 'Unknown Oxford diffraction detector'} DEFAULT_HEADERS = {'Header Version': 'OD SAPPHIRE 3.0', 'Compression': "TY1", 'Header Size In Bytes': 5120, "ASCII Section size in Byte": 256, "General Section size in Byte": 512, "Special Section size in Byte": 768, "KM4 Section size in Byte": 1024, "Statistic Section in Byte": 512, "History Section in Byte": 2048, 'NSUPPLEMENT':0 } class OXDimage(fabioimage): """ Oxford Diffraction Sapphire 3 images reader/writer class """ def _readheader(self, infile): infile.seek(0) # Ascii header part 256 byes long self.header['Header Version'] = infile.readline()[:-2] block = infile.readline() self.header['Compression'] = block[12:15] block = infile.readline() self.header['NX'] = int(block[3:7]) self.header['NY'] = int(block[11:15]) self.header['OI'] = int(block[19:26]) self.header['OL'] = int(block[30:37]) block = infile.readline() self.header['Header Size In Bytes'] = int(block[8:15]) self.header['General Section size in Byte'] = int(block[19:26]) self.header['Special Section size in Byte'] = int(block[30:37]) self.header['KM4 Section size in Byte'] = int(block[41:48]) self.header['Statistic Section in Byte'] = int(block[52:59]) self.header['History Section in Byte'] = int(block[63:]) block = infile.readline() self.header['NSUPPLEMENT'] = int(block[12:19]) block = infile.readline() self.header['Time'] = block[5:29] self.header["ASCII Section size in Byte"] = self.header['Header Size In Bytes']\ - self.header['General Section size in Byte']\ - self.header['Special Section size in Byte'] \ - self.header['KM4 Section size in Byte']\ - self.header['Statistic Section in Byte']\ - self.header['History Section in Byte']\ # Skip to general section (NG) 512 byes long <<<<<<" infile.seek(self.header["ASCII Section size in Byte"]) block = infile.read(self.header['General Section size in Byte']) self.header['Binning in x'] = numpy.fromstring(block[0:2], numpy.uint16)[0] self.header['Binning in y'] = numpy.fromstring(block[2:4], numpy.uint16)[0] self.header['Detector size x'] = numpy.fromstring(block[22:24], numpy.uint16)[0] self.header['Detector size y'] = numpy.fromstring(block[24:26], numpy.uint16)[0] self.header['Pixels in x'] = numpy.fromstring(block[26:28], numpy.uint16)[0] self.header['Pixels in y'] = numpy.fromstring(block[28:30], numpy.uint16)[0] self.header['No of pixels'] = numpy.fromstring(block[36:40], numpy.uint32)[0] # Speciel section (NS) 768 bytes long block = infile.read(self.header['Special Section size in Byte']) self.header['Gain'] = numpy.fromstring(block[56:64], numpy.float)[0] self.header['Overflows flag'] = numpy.fromstring(block[464:466], numpy.int16)[0] self.header['Overflow after remeasure flag'] = numpy.fromstring(block[466:468], numpy.int16)[0] self.header['Overflow threshold'] = numpy.fromstring(block[472:476], numpy.int32)[0] self.header['Exposure time in sec'] = numpy.fromstring(block[480:488], numpy.float)[0] self.header['Overflow time in sec'] = numpy.fromstring(block[488:496], numpy.float)[0] self.header['Monitor counts of raw image 1'] = numpy.fromstring(block[528:532], numpy.int32)[0] self.header['Monitor counts of raw image 2'] = numpy.fromstring(block[532:536], numpy.int32)[0] self.header['Monitor counts of overflow raw image 1'] = numpy.fromstring(block[536:540], numpy.int32)[0] self.header['Monitor counts of overflow raw image 2'] = numpy.fromstring(block[540:544], numpy.int32)[0] self.header['Unwarping'] = numpy.fromstring(block[544:548], numpy.int32)[0] self.header['Detector type'] = DETECTOR_TYPES[numpy.fromstring(block[548:552], numpy.int32)[0]] self.header['Real pixel size x (mm)'] = numpy.fromstring(block[568:576], numpy.float)[0] self.header['Real pixel size y (mm)'] = numpy.fromstring(block[576:584], numpy.float)[0] # KM4 goniometer section (NK) 1024 bytes long block = infile.read(self.header['KM4 Section size in Byte']) # Spatial correction file self.header['Spatial correction file'] = block[26:272].strip("\x00") self.header['Spatial correction file date'] = block[0:26].strip("\x00") # Angles are in steps due to stepper motors - conversion factor RAD # angle[0] = omega, angle[1] = theta, angle[2] = kappa, angle[3] = phi, start_angles_step = numpy.fromstring(block[284:304], numpy.int32) end_angles_step = numpy.fromstring(block[324:344], numpy.int32) step2rad = numpy.fromstring(block[368:408], numpy.float) step_angles_deg = rad2deg(step2rad) # calc angles start_angles_deg = start_angles_step * step_angles_deg end_angles_deg = end_angles_step * step_angles_deg self.header['Omega start in deg'] = start_angles_deg[0] self.header['Theta start in deg'] = start_angles_deg[1] self.header['Kappa start in deg'] = start_angles_deg[2] self.header['Phi start in deg'] = start_angles_deg[3] self.header['Omega end in deg'] = end_angles_deg[0] self.header['Theta end in deg'] = end_angles_deg[1] self.header['Kappa end in deg'] = end_angles_deg[2] self.header['Phi end in deg'] = end_angles_deg[3] self.header['Omega step in deg'] = step_angles_deg[0] self.header['Theta step in deg'] = step_angles_deg[1] self.header['Kappa step in deg'] = step_angles_deg[2] self.header['Phi step in deg'] = step_angles_deg[3] zero_correction_soft_step = numpy.fromstring(block[512:532], numpy.int32) zero_correction_soft_deg = zero_correction_soft_step * step_angles_deg self.header['Omega zero corr. in deg'] = zero_correction_soft_deg[0] self.header['Theta zero corr. in deg'] = zero_correction_soft_deg[1] self.header['Kappa zero corr. in deg'] = zero_correction_soft_deg[2] self.header['Phi zero corr. in deg'] = zero_correction_soft_deg[3] # Beam rotation about e2,e3 self.header['Beam rot in deg (e2)'] = numpy.fromstring(block[552:560], numpy.float)[0] self.header['Beam rot in deg (e3)'] = numpy.fromstring(block[560:568], numpy.float)[0] # Wavelenghts alpha1, alpha2, beta self.header['Wavelength alpha1'] = numpy.fromstring(block[568:576], numpy.float)[0] self.header['Wavelength alpha2'] = numpy.fromstring(block[576:584], numpy.float)[0] self.header['Wavelength alpha'] = numpy.fromstring(block[584:592], numpy.float)[0] self.header['Wavelength beta'] = numpy.fromstring(block[592:600], numpy.float)[0] # Detector tilts around e1,e2,e3 in deg self.header['Detector tilt e1 in deg'] = numpy.fromstring(block[640:648], numpy.float)[0] self.header['Detector tilt e2 in deg'] = numpy.fromstring(block[648:656], numpy.float)[0] self.header['Detector tilt e3 in deg'] = numpy.fromstring(block[656:664], numpy.float)[0] # Beam center self.header['Beam center x'] = numpy.fromstring(block[664:672], numpy.float)[0] self.header['Beam center y'] = numpy.fromstring(block[672:680], numpy.float)[0] # Angle (alpha) between kappa rotation axis and e3 (ideally 50 deg) self.header['Alpha angle in deg'] = numpy.fromstring(block[672:680], numpy.float)[0] # Angle (beta) between phi rotation axis and e3 (ideally 0 deg) self.header['Beta angle in deg'] = numpy.fromstring(block[672:680], numpy.float)[0] # Detector distance self.header['Distance in mm'] = numpy.fromstring(block[712:720], numpy.float)[0] # Statistics section (NS) 512 bytes long block = infile.read(self.header['Statistic Section in Byte']) self.header['Stat: Min '] = numpy.fromstring(block[0:4], numpy.int32)[0] self.header['Stat: Max '] = numpy.fromstring(block[4:8], numpy.int32)[0] self.header['Stat: Average '] = numpy.fromstring(block[24:32], numpy.float)[0] self.header['Stat: Stddev '] = numpy.sqrt(numpy.fromstring(block[32:40], numpy.float)[0]) self.header['Stat: Skewness '] = numpy.fromstring(block[40:48], numpy.float)[0] # History section (NH) 2048 bytes long block = infile.read(self.header['History Section in Byte']) self.header['Flood field image'] = block[99:126].strip("\x00") def read(self, fname, frame=None): """ Read in header into self.header and the data into self.data """ self.header = {} self.resetvals() infile = self._open(fname) self._readheader(infile) infile.seek(self.header['Header Size In Bytes']) # Compute image size try: self.dim1 = int(self.header['NX']) self.dim2 = int(self.header['NY']) except: raise Exception("Oxford file", str(fname) + \ "is corrupt, cannot read it") # if self.header['Compression'] == 'TY1': #Compressed with the KM4CCD compression raw8 = infile.read(self.dim1 * self.dim2) raw16 = None raw32 = None if self.header['OI'] > 0: raw16 = infile.read(self.header['OI'] * 2) if self.header['OL'] > 0: raw32 = infile.read(self.header['OL'] * 4) #DEBUG stuff ... self.raw8 = raw8 self.raw16 = raw16 self.raw32 = raw32 #END DEBUG block = decTY1(raw8, raw16, raw32) bytecode = block.dtype else: bytecode = numpy.int32 self.bpp = len(numpy.array(0, bytecode).tostring()) ReadBytes = self.dim1 * self.dim2 * self.bpp block = numpy.fromstring(infile.read(ReadBytes), bytecode) logger.debug('OVER_SHORT2: %s', block.dtype) logger.debug("%s" % (block < 0).sum()) infile.close() logger.debug("BYTECODE: %s", bytecode) self.data = block.reshape((self.dim2, self.dim1)) self.bytecode = self.data.dtype.type self.pilimage = None return self def _writeheader(self): """ @return a string containing the header for Oxford images """ linesep = "\r\n" for key in DEFAULT_HEADERS: if key not in self.header_keys: self.header_keys.append(key) self.header[key] = DEFAULT_HEADERS[key] if "NX" not in self.header.keys() or "NY" not in self.header.keys(): self.header['NX'] = self.dim1 self.header['NY'] = self.dim2 ascii_headers = [self.header['Header Version'], "COMPRESSION=%s (%5.1f)" % (self.header["Compression"], self.getCompressionRatio()), "NX=%4i NY=%4i OI=%7i OL=%7i " % (self.header["NX"], self.header["NY"], self.header["OI"], self.header["OL"]), "NHEADER=%7i NG=%7i NS=%7i NK=%7i NS=%7i NH=%7i" % (self.header['Header Size In Bytes'], self.header['General Section size in Byte'], self.header['Special Section size in Byte'], self.header['KM4 Section size in Byte'], self.header['Statistic Section in Byte'], self.header['History Section in Byte']), "NSUPPLEMENT=%7i" % (self.header["NSUPPLEMENT"])] if "Time" in self.header: ascii_headers.append("TIME=%s" % self.header["Time"]) else: ascii_headers.append("TIME=%s" % time.ctime()) header = (linesep.join(ascii_headers)).ljust(256) NG = Section(self.header['General Section size in Byte'], self.header) NG.setData('Binning in x', 0, numpy.uint16) NG.setData('Binning in y', 2, numpy.uint16) NG.setData('Detector size x', 22, numpy.uint16) NG.setData('Detector size y', 24, numpy.uint16) NG.setData('Pixels in x', 26, numpy.uint16) NG.setData('Pixels in y', 28, numpy.uint16) NG.setData('No of pixels', 36, numpy.uint32) header += NG.__repr__() NS = Section(self.header['Special Section size in Byte'], self.header) NS.setData('Gain', 56, numpy.float) NS.setData('Overflows flag', 464, numpy.int16) NS.setData('Overflow after remeasure flag', 466, numpy.int16) NS.setData('Overflow threshold', 472, numpy.int32) NS.setData('Exposure time in sec', 480, numpy.float) NS.setData('Overflow time in sec', 488, numpy.float) NS.setData('Monitor counts of raw image 1', 528, numpy.int32) NS.setData('Monitor counts of raw image 2', 532, numpy.int32) NS.setData('Monitor counts of overflow raw image 1', 536, numpy.int32) NS.setData('Monitor counts of overflow raw image 2', 540, numpy.int32) NS.setData('Unwarping', 544, numpy.int32) if 'Detector type' in self.header: for key, value in DETECTOR_TYPES.items(): if value == self.header['Detector type']: NS.setData(None, 548, numpy.int32, default=key) NS.setData('Real pixel size x (mm)', 568, numpy.float) NS.setData('Real pixel size y (mm)', 576, numpy.float) header += NS.__repr__() KM = Section(self.header['KM4 Section size in Byte'], self.header) KM.setData('Spatial correction file date', 0, "|S26") KM.setData('Spatial correction file', 26, "|S246") # Angles are in steps due to stepper motors - conversion factor RAD # angle[0] = omega, angle[1] = theta, angle[2] = kappa, angle[3] = phi, if self.header.get('Omega step in deg', None): KM.setData(None, 368, numpy.float64, deg2rad(self.header["Omega step in deg"])) if self.header.get('Omega start in deg', None): KM.setData(None, 284, numpy.int32, self.header["Omega start in deg"] / self.header["Omega step in deg"]) if self.header.get('Omega end in deg', None): KM.setData(None, 324, numpy.int32, self.header["Omega end in deg"] / self.header["Omega step in deg"]) if self.header.get('Omega zero corr. in deg', None): KM.setData(None, 512, numpy.int32, self.header['Omega zero corr. in deg'] / self.header["Omega step in deg"]) if self.header.get('Theta step in deg', None): KM.setData(None, 368 + 8, numpy.float64, deg2rad(self.header["Theta step in deg"])) if self.header.get('Theta start in deg', None): KM.setData(None, 284 + 4, numpy.int32, self.header["Theta start in deg"] / self.header["Theta step in deg"]) if self.header.get('Theta end in deg', None): KM.setData(None, 324 + 4, numpy.int32, self.header["Theta end in deg"] / self.header["Theta step in deg"]) if self.header.get('Theta zero corr. in deg', None): KM.setData(None, 512 + 4, numpy.int32, self.header['Theta zero corr. in deg'] / self.header["Theta step in deg"]) if self.header.get('Kappa step in deg', None): KM.setData(None, 368 + 16, numpy.float64, deg2rad(self.header["Kappa step in deg"])) if self.header.get('Kappa start in deg', None): KM.setData(None, 284 + 8, numpy.int32, self.header["Kappa start in deg"] / self.header["Kappa step in deg"]) if self.header.get('Kappa end in deg', None): KM.setData(None, 324 + 8, numpy.int32, self.header["Kappa end in deg"] / self.header["Kappa step in deg"]) if self.header.get('Kappa zero corr. in deg', None): KM.setData(None, 512 + 8, numpy.int32, self.header['Kappa zero corr. in deg'] / self.header["Kappa step in deg"]) if self.header.get('Phi step in deg', None): KM.setData(None, 368 + 24, numpy.float64, deg2rad(self.header["Phi step in deg"])) if self.header.get('Phi start in deg', None): KM.setData(None, 284 + 12, numpy.int32, self.header["Phi start in deg"] / self.header["Phi step in deg"]) if self.header.get('Phi end in deg', None): KM.setData(None, 324 + 12, numpy.int32, self.header["Phi end in deg"] / self.header["Phi step in deg"]) if self.header.get('Phi zero corr. in deg', None): KM.setData(None, 512 + 12, numpy.int32, self.header['Phi zero corr. in deg'] / self.header["Phi step in deg"]) # Beam rotation about e2,e3 KM.setData('Beam rot in deg (e2)', 552, numpy.float64) KM.setData('Beam rot in deg (e3)', 560, numpy.float64) # Wavelenghts alpha1, alpha2, beta KM.setData('Wavelength alpha1', 568, numpy.float64) KM.setData('Wavelength alpha2', 576, numpy.float64) KM.setData('Wavelength alpha', 584, numpy.float64) KM.setData('Wavelength beta', 592, numpy.float64) # Detector tilts around e1,e2,e3 in deg KM.setData('Detector tilt e1 in deg', 640, numpy.float64) KM.setData('Detector tilt e2 in deg', 648, numpy.float64) KM.setData('Detector tilt e3 in deg', 656, numpy.float64) # Beam center KM.setData('Beam center x', 664, numpy.float64) KM.setData('Beam center y', 672, numpy.float64) # Angle (alpha) between kappa rotation axis and e3 (ideally 50 deg) KM.setData('Alpha angle in deg', 672, numpy.float64) # Angle (beta) between phi rotation axis and e3 (ideally 0 deg) KM.setData('Beta angle in deg', 672, numpy.float64) # Detector distance KM.setData('Distance in mm', 712, numpy.float64) header += KM.__repr__() SS = Section(self.header['Statistic Section in Byte'], self.header) SS.setData('Stat: Min ', 0, numpy.int32) SS.setData('Stat: Max ', 4, numpy.int32) SS.setData('Stat: Average ', 24, numpy.float64) if self.header.get('Stat: Stddev ', None): SS.setData(None, 32, numpy.float64, self.header['Stat: Stddev '] ** 2) SS.setData('Stat: Skewness ', 40, numpy.float64) header += SS.__repr__() HS = Section(self.header['History Section in Byte'], self.header) HS.setData('Flood field image', 99, "|S27") header += HS.__repr__() return header def write(self, fname): """Write Oxford diffraction images: this is still beta @param fname: output filename """ datablock8, datablock16, datablock32 = compTY1(self.data) self.header["OI"] = len(datablock16) / 2 self.header["OL"] = len(datablock32) / 4 with self._open(fname, mode="wb") as outfile: outfile.write(self._writeheader()) outfile.write(datablock8) outfile.write(datablock16) outfile.write(datablock32) def getCompressionRatio(self): "calculate the compression factor obtained vs raw data" return 100.0 * (self.data.size + 2 * self.header["OI"] + 4 * self.header["OL"]) / (self.data.size * 4) @staticmethod def checkData(data=None): if data is None: return None else: return data.astype(int) class Section(object): """ Small helper class for writing binary headers """ def __init__(self, size, dictHeader): """ @param size: size of the header section in bytes @param dictHeader: headers of the image """ self.size = size self.header = dictHeader self.lstChr = ["\x00"] * size self._dictSize = {} def __repr__(self): return "".join(self.lstChr) def getSize(self, dtype): if not dtype in self._dictSize: self._dictSize[dtype] = len(numpy.zeros(1, dtype=dtype).tostring()) return self._dictSize[dtype] def setData(self, key, offset, dtype, default=None): """ @param offset: int, starting position in the section @param key: name of the header key @param dtype: type of the data to insert (defines the size!) """ if key in self.header: value = self.header[key] elif key in DEFAULT_HEADERS: value = DEFAULT_HEADERS[key] else: value = default if value is None: value = "\x00" * self.getSize(dtype) else: value = numpy.array(value).astype(dtype).tostring() self.lstChr[offset:offset + self.getSize(dtype)] = value fabio-0.1.3/fabio-src/GEimage.py0000644000175000017500000002614512233175156017111 0ustar jeromejerome00000000000000#!/usr/bin/env python # # Reads the header from a GE a-Si Angio Detector # Using version 8001 of the header from file: # c:\adept\core\DefaultImageInfoConfig.csv # # Antonino Miceli # Thu Jan 4 13:46:31 CST 2007 # # modifications by Jon Wright for style, pychecker and fabio # import numpy import struct, logging logger = logging.getLogger("GEimage") from fabioimage import fabioimage from fabioutils import next_filename, previous_filename GE_HEADER_INFO = [ # Name, length in bytes, format for struct (None means string) ('ImageFormat', 10, None), ('VersionOfStandardHeader', 2, '=H'), ('StandardHeaderSizeInBytes', 4, '=L'), ('VersionOfUserHeader', 2, '=H'), ('UserHeaderSizeInBytes', 4, '=L'), ('NumberOfFrames', 2, '=H'), ('NumberOfRowsInFrame', 2, '=H'), ('NumberOfColsInFrame', 2, '=H'), ('ImageDepthInBits', 2, '=H'), ('AcquisitionDate', 20, None), ('AcquisitionTime', 20, None), ('DUTID', 20, None), ('Operator', 50, None), ('DetectorSignature', 20, None), ('TestSystemName', 20, None), ('TestStationRevision', 20, None), ('CoreBundleRevision', 20, None), ('AcquisitionName', 40, None), ('AcquisitionParameterRevision', 20, None), ('OriginalNumberOfRows', 2, '=H'), ('OriginalNumberOfColumns', 2, '=H'), ('RowNumberUpperLeftPointArchiveROI', 2, '=H'), ('ColNumberUpperLeftPointArchiveROI', 2, '=H'), ('Swapped', 2, '=H'), ('Reordered', 2, '=H'), ('HorizontalFlipped', 2, '=H'), ('VerticalFlipped', 2, '=H'), ('WindowValueDesired', 2, '=H'), ('LevelValueDesired', 2, '=H'), ('AcquisitionMode', 2, '=H'), ('AcquisitionType', 2, '=H'), ('UserAcquisitionCoffFileName1', 100, None), ('UserAcquisitionCoffFileName2', 100, None), ('FramesBeforeExpose', 2, '=H'), ('FramesDuringExpose', 2, '=H'), ('FramesAfterExpose', 2, '=H'), ('IntervalBetweenFrames', 2, '=H'), ('ExposeTimeDelayInMicrosecs', 8, '=d'), ('TimeBetweenFramesInMicrosecs', 8, '=d'), ('FramesToSkipExpose', 2, '=H'), ('ExposureMode', 2, '=H'), ('PrepPresetTimeInMicrosecs', 8, '=d'), ('ExposePresetTimeInMicrosecs', 8, '=d'), ('AcquisitionFrameRateInFps', 4, '=f'), ('FOVSelect', 2, '=H'), ('ExpertMode', 2, '=H'), ('SetVCommon1', 8, '=d'), ('SetVCommon2', 8, '=d'), ('SetAREF', 8, '=d'), ('SetAREFTrim', 4, '=L'), ('SetSpareVoltageSource', 8, '=d'), ('SetCompensationVoltageSource', 8, '=d'), ('SetRowOffVoltage', 8, '=d'), ('SetRowOnVoltage', 8, '=d'), ('StoreCompensationVoltage', 4, '=L'), ('RampSelection', 2, '=H'), ('TimingMode', 2, '=H'), ('Bandwidth', 2, '=H'), ('ARCIntegrator', 2, '=H'), ('ARCPostIntegrator', 2, '=H'), ('NumberOfRows', 4, '=L'), ('RowEnable', 2, '=H'), ('EnableStretch', 2, '=H'), ('CompEnable', 2, '=H'), ('CompStretch', 2, '=H'), ('LeftEvenTristate', 2, '=H'), ('RightOddTristate', 2, '=H'), ('TestModeSelect', 4, '=L'), ('AnalogTestSource', 4, '=L'), ('VCommonSelect', 4, '=L'), ('DRCColumnSum', 4, '=L'), ('TestPatternFrameDelta', 4, '=L'), ('TestPatternRowDelta', 4, '=L'), ('TestPatternColumnDelta', 4, '=L'), ('DetectorHorizontalFlip', 2, '=H'), ('DetectorVerticalFlip', 2, '=H'), ('DFNAutoScrubOnOff', 2, '=H'), ('FiberChannelTimeOutInMicrosecs', 4, '=L'), ('DFNAutoScrubDelayInMicrosecs', 4, '=L'), ('StoreAECROI', 2, '=H'), ('TestPatternSaturationValue', 2, '=H'), ('TestPatternSeed', 4, '=L'), ('ExposureTimeInMillisecs', 4, '=f'), ('FrameRateInFps', 4, '=f'), ('kVp', 4, '=f'), ('mA', 4, '=f'), ('mAs', 4, '=f'), ('FocalSpotInMM', 4, '=f'), ('GeneratorType', 20, None), ('StrobeIntensityInFtL', 4, '=f'), ('NDFilterSelection', 2, '=H'), ('RefRegTemp1', 8, '=d'), ('RefRegTemp2', 8, '=d'), ('RefRegTemp3', 8, '=d'), ('Humidity1', 4, '=f'), ('Humidity2', 4, '=f'), ('DetectorControlTemp', 8, '=d'), ('DoseValueInmR', 8, '=d'), ('TargetLevelROIRow0', 2, '=H'), ('TargetLevelROICol0', 2, '=H'), ('TargetLevelROIRow1', 2, '=H'), ('TargetLevelROICol1', 2, '=H'), ('FrameNumberForTargetLevelROI', 2, '=H'), ('PercentRangeForTargetLevel', 2, '=H'), ('TargetValue', 2, '=H'), ('ComputedMedianValue', 2, '=H'), ('LoadZero', 2, '=H'), ('MaxLUTOut', 2, '=H'), ('MinLUTOut', 2, '=H'), ('MaxLinear', 2, '=H'), ('Reserved', 2, '=H'), ('ElectronsPerCount', 2, '=H'), ('ModeGain', 2, '=H'), ('TemperatureInDegC', 8, '=d'), ('LineRepaired', 2, '=H'), ('LineRepairFileName', 100, None), ('CurrentLongitudinalInMM', 4, '=f'), ('CurrentTransverseInMM', 4, '=f'), ('CurrentCircularInMM', 4, '=f'), ('CurrentFilterSelection', 4, '=L'), ('DisableScrubAck', 2, '=H'), ('ScanModeSelect', 2, '=H'), ('DetectorAppSwVersion', 20, None), ('DetectorNIOSVersion', 20, None), ('DetectorPeripheralSetVersion', 20, None), ('DetectorPhysicalAddress', 20, None), ('PowerDown', 2, '=H'), ('InitialVoltageLevel_VCOMMON', 8, '=d'), ('FinalVoltageLevel_VCOMMON', 8, '=d'), ('DmrCollimatorSpotSize', 10, None), ('DmrTrack', 5, None), ('DmrFilter', 5, None), ('FilterCarousel', 2, '=H'), ('Phantom', 20, None), ('SetEnableHighTime', 2, '=H'), ('SetEnableLowTime', 2, '=H'), ('SetCompHighTime', 2, '=H'), ('SetCompLowTime', 2, '=H'), ('SetSyncLowTime', 2, '=H'), ('SetConvertLowTime', 2, '=H'), ('SetSyncHighTime', 2, '=H'), ('SetEOLTime', 2, '=H'), ('SetRampOffsetTime', 2, '=H'), ('FOVStartingValue', 2, '=H'), ('ColumnBinning', 2, '=H'), ('RowBinning', 2, '=H'), ('BorderColumns64', 2, '=H'), ('BorderRows64', 2, '=H'), ('FETOffRows64', 2, '=H'), ('FOVStartColumn128', 2, '=H'), ('FOVStartRow128', 2, '=H'), ('NumberOfColumns128', 2, '=H'), ('NumberOfRows128', 2, '=H'), ('VFPAquisition', 2000, None), ('Comment', 200, None) ] class GEimage(fabioimage): _need_a_seek_to_read = True def _readheader(self, infile): """ Read a GE image header """ infile.seek(0) self.header = {} for name, nbytes, format in GE_HEADER_INFO: if format is None: self.header[ name ] = infile.read(nbytes) else: self.header[ name ] = struct.unpack(format, infile.read(nbytes))[0] def read(self, fname, frame=None): """ Read in header into self.header and the data into self.data """ if frame is None: frame = 0 self.header = {} self.resetvals() infile = self._open(fname, "rb") self.sequencefilename = fname self._readheader(infile) self.nframes = self.header['NumberOfFrames'] self._readframe(infile, frame) infile.close() return self def _makeframename(self): """ The thing to be printed for the user to represent a frame inside a file """ self.filename = "%s$%04d" % (self.sequencefilename, self.currentframe) def _readframe(self, filepointer, img_num): """ # Load only one image from the sequence # Note: the first image in the sequence 0 # raises an exception if you give an invalid image # otherwise fills in self.data """ if(img_num > self.nframes or img_num < 0): raise Exception("Bad image number") imgstart = self.header['StandardHeaderSizeInBytes'] + \ self.header['UserHeaderSizeInBytes'] + \ img_num * self.header['NumberOfRowsInFrame'] * \ self.header['NumberOfColsInFrame'] * \ self.header['ImageDepthInBits'] / 8 # whence = 0 means seek from start of file filepointer.seek(imgstart, 0) self.bpp = self.header['ImageDepthInBits'] / 8 # hopefully 2 imglength = self.header['NumberOfRowsInFrame'] * \ self.header['NumberOfColsInFrame'] * self.bpp if self.bpp != 2: logging.warning("Using uint16 for GE but seems to be wrong") # Guessing it is always unsigned int? self.data = numpy.fromstring(filepointer.read(imglength), numpy.uint16) self.data.shape = (self.header['NumberOfRowsInFrame'], self.header['NumberOfColsInFrame']) self.dim2 , self.dim1 = self.data.shape self.currentframe = int(img_num) self._makeframename() def write(self, fname, force_type=numpy.uint16): """ Not yet implemented""" raise Exception("Write is not implemented") def getframe(self, num): """ Returns a frame as a new fabioimage object """ if num < 0 or num > self.nframes: raise Exception("Requested frame number is out of range") # Do a deep copy of the header to make a new one newheader = {} for k in self.header.keys(): newheader[k] = self.header[k] frame = GEimage(header=newheader) frame.nframes = self.nframes frame.sequencefilename = self.sequencefilename infile = frame._open(self.sequencefilename, "rb") frame._readframe(infile, num) infile.close() return frame def next(self): """ Get the next image in a series as a fabio image """ if self.currentframe < (self.nframes - 1) and self.nframes > 1: return self.getframe(self.currentframe + 1) else: newobj = GEimage() newobj.read(next_filename( self.sequencefilename)) return newobj def previous(self): """ Get the previous image in a series as a fabio image """ if self.currentframe > 0: return self.getframe(self.currentframe - 1) else: newobj = GEimage() newobj.read(previous_filename( self.sequencefilename)) return newobj def demo(): import sys, time if len(sys.argv) < 2: print "USAGE: GE_script.py " sys.exit() image_file = sys.argv[1] print "init read_GEaSi_data class and load header.." sequence1 = GEimage() sequence1.read(image_file) print "TimeBetweenFramesInMicrosecs = ", print sequence1.header['TimeBetweenFramesInMicrosecs'] print "AcquisitionTime = ", print sequence1.header['AcquisitionTime'] print "Mean = ", sequence1.data.ravel().mean() while 1: start = time.time() try: sequence1 = sequence1.next() print sequence1.currentframe, sequence1.data.ravel().mean(), \ time.time() - start except Exception, ex: raise ex if __name__ == '__main__': demo() fabio-0.1.3/fabio-src/pnmimage.py0000644000175000017500000001303312233175156017400 0ustar jeromejerome00000000000000#!/usr/bin/env python #coding: utf8 """ Authors: Henning O. Sorensen & Erik Knudsen Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:henning.sorensen@risoe.dk """ import numpy, logging logger = logging.getLogger("pnmimage") from fabioimage import fabioimage SUBFORMATS = ['P1', 'P2', 'P3', 'P4', 'P5', 'P6', 'P7'] HEADERITEMS = ['SUBFORMAT', 'DIMENSIONS', 'MAXVAL'] P7HEADERITEMS = ['WIDTH', 'HEIGHT', 'DEPTH', 'MAXVAL', 'TUPLTYPE', 'ENDHDR'] class pnmimage(fabioimage): def __init__(self, *arg, **kwargs): fabioimage.__init__(self, *arg, **kwargs) fun = getattr(fabioimage, '__init__', lambda x: None) fun(self) self.data = None self.header = {'Subformat':'P5'} self.dim1 = self.dim2 = 0 self.m = self.maxval = self.stddev = self.minval = None self.header_keys = self.header.keys() self.bytecode = None def _readheader(self, f): #pnm images have a 3-line header but ignore lines starting with '#' #1st line contains the pnm image sub format #2nd line contains the image pixel dimension #3rd line contains the maximum pixel value (at least for grayscale - check this) self.header_keys = ['SUBFORMAT', 'DIMENSIONS', 'MAXVAL'] l = f.readline().strip() if l not in SUBFORMATS: raise IOError, ('unknown subformat of pnm: %s' % l) else: self.header['SUBFORMAT'] = l if self.header['SUBFORMAT'] == 'P7': self.header_keys = P7HEADERITEMS #this one has a special header while 'ENDHDR' not in l: l = f.readline() while(l[0] == '#'): l = f.readline() s = l.lsplit(' ', 1) if s[0] not in P7HEADERITEMS: raise IOError, ('Illegal pam (netpnm p7) headeritem %s' % s[0]) self.header[s[0]] = s[1] else: self.header_keys = HEADERITEMS for k in self.header_keys[1:]: l = f.readline() while(l[0] == '#'): l = f.readline() self.header[k] = l.strip() #set the dimensions dims = (self.header['DIMENSIONS'].split()) self.dim1, self.dim2 = int(dims[0]), int(dims[1]) #figure out how many bytes are used to store the data #case construct here! m = int(self.header['MAXVAL']) if m < 256: self.bytecode = numpy.uint8 elif m < 65536: self.bytecode = numpy.uint16 elif m < 2147483648L: self.bytecode = numpy.uint32 logger.warning('32-bit pixels are not really supported by the netpgm standard') else: raise IOError, 'could not figure out what kind of pixels you have' def read(self, fname, frame=None): """ try to read PNM images @param fname: name of the file @param frame: not relevant here! PNM is always single framed """ self.header = {} self.resetvals() infile = self._open(fname) self._readheader(infile) #read the image data decoder_name = "%sdec" % self.header['SUBFORMAT'] if decoder_name in dir(pnmimage): decoder = getattr(pnmimage, decoder_name) self.data = decoder(infile, self.bytecode) else: raise IOError("No decoder named %s for file %s" % (decoder_name, fname)) self.resetvals() return self @staticmethod def P1dec(buf, bytecode): data = numpy.zeros((self.dim2, self.dim1)) i = 0 for l in buf.readlines(): try: data[i, :] = numpy.array(l.split()).astype(bytecode) except ValueError: raise IOError, 'Size spec in pnm-header does not match size of image data field' return data @staticmethod def P4dec(buf, bytecode): err = 'single bit (pbm) images are not supported - yet' logger.error(err) raise NotImplementedError(err) @staticmethod def P2dec(buf, bytecode): data = numpy.zeros((self.dim2, self.dim1)) i = 0 for l in buf.readlines(): try: data[i, :] = numpy.array(l.split()).astype(bytecode) except ValueError: raise IOError, 'Size spec in pnm-header does not match size of image data field' return data @staticmethod def P5dec(buf, bytecode): l = buf.read() try: data = numpy.reshape(numpy.fromstring(l, bytecode), [self.dim2, self.dim1]).byteswap() except ValueError: raise IOError, 'Size spec in pnm-header does not match size of image data field' return data @staticmethod def P3dec(buf, bytecode): err = '(plain-ppm) RGB images are not supported - yet' logger.error(err) raise NotImplementedError(err) @staticmethod def P6dec(buf, bytecode): err = '(ppm) RGB images are not supported - yet' logger.error(err) raise NotImplementedError(err) @staticmethod def P7dec(buf, bytecode): err = '(pam) images are not supported - yet' logger.error(err) raise NotImplementedError(err) def write(self, filename): raise NotImplementedError('write pnm images is not implemented yet.') @staticmethod def checkData(data=None): if data is None: return None else: return data.astype(int) fabio-0.1.3/fabio-src/datIO.py0000644000175000017500000000341612120434325016576 0ustar jeromejerome00000000000000#!/usr/bin/env python #coding: utf8 """ Authors: Henning O. Sorensen & Erik Knudsen Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk and Jon Wright, ESRF """ class fabiodata(object): """ A common class for dataIO in fable Contains a 2d numpy array for keeping data, and two lists (clabels and rlabels) containing labels for columns and rows respectively """ def __init__(self, data=None, clabels=None, rlabels=None, fname=None): """ set up initial values """ if type(data) == type("string"): raise Exception("fabioimage.__init__ bad argument - " + \ "data should be numpy array") self.data = data if (self.data): self.dims = self.data.shape self.clabels = clabels self.rlabels = rlabels if (fname): self.read(fname) def read(self, fname=None, frame=None): """ To be overridden by format specific subclasses """ raise Exception("Class has not implemented read method yet") #import stuff from Jon's columnfile things class columnfile(fabiodata): "Concrete fabiodata class" def read(self, fname, frame=None): import cf_io try: infile = open(fname, 'rb') except: raise Exception("columnfile: file" + str(fname) + "not found.") try: (self.data, self.clabels) = cf_io.read(infile) except: raise Exception("columnfile: read error, file " + str(fname) + " possibly corrupt") self.dims = self.data.shape infile.close() fabio-0.1.3/fabio-src/file_series.py0000644000175000017500000002356612233175156020110 0ustar jeromejerome00000000000000#!/usr/bin/env python """ Authors: ........ * Henning O. Sorensen & Erik Knudsen Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk * Jon Wright, ESRF """ import logging, sys logger = logging.getLogger("fileseries") import traceback as pytraceback from fabioutils import FilenameObject, next_filename from openimage import openimage def new_file_series0(first_object, first=None, last=None, step=1): """ Created from a fabio image first and last are file numbers """ im = first_object nimages = 0 # for counting images if None in (first, last): step = 0 total = 1 else: total = last - first yield im while nimages < total: nimages += step try: newim = im.next() im = newim except Exception, error: pytraceback.print_exc() # Skip bad images logger.warning("Got a problem here: %s", error) try: im.filename = next_filename(im.filename) except Exception, error: # KE: This will not work and will throw an exception # fabio.next_filename doesn't understand %nnnn on the end logger.warning("Got another problem here: %s", error) im.filename = next_filename(im.sequencefilename) yield None yield im def new_file_series(first_object, nimages=0, step=1, traceback=False): """ A generator function that creates a file series starting from a a fabioimage. Iterates through all images in a file (if more than 1), then proceeds to the next file as determined by fabio.next_filename. @param first_object: the starting fabioimage, which will be the first one yielded in the sequence @param nimages: the maximum number of images to consider step: step size, will yield the first and every step'th image until nimages is reached. (e.g. nimages = 5, step = 2 will yield 3 images (0, 2, 4) @param traceback: if True causes it to print a traceback in the event of an exception (missing image, etc.). Otherwise the calling routine can handle the exception as it chooses @param yields: the next fabioimage in the series. In the event there is an exception, it yields the sys.exec_info for the exception instead. sys.exec_info is a tuple: ( exceptionType, exceptionValue, exceptionTraceback ) from which all the exception information can be obtained. Suggested usage: :: for obj in new_file_series( ... ): if not isinstance(obj, fabio.fabioimage.fabioimage ): # deal with errors like missing images, non readable files, etc # e.g. traceback.print_exception(obj[0], obj[1], obj[2]) """ im = first_object nprocessed = 0 abort = False if nimages > 0: yield im nprocessed += 1 while nprocessed < nimages: try: newim = im.next() im = newim retVal = im except Exception, ex: retVal = sys.exc_info() if(traceback): pytraceback.print_exc() # Skip bad images logger.warning("Got a problem here: next() failed %s", ex) # Skip bad images try: im.filename = next_filename(im.filename) except Exception, ex: logger.warning("Got another problem here: next_filename(im.filename) %s", ex) if nprocessed % step == 0: yield retVal # Avoid cyclic references with exc_info ? retVal = None if abort: break nprocessed += 1 class file_series(list): """ Represents a series of files to iterate has an idea of a current position to do next and prev You also get from the list python superclass: append count extend insert pop remove reverse sort """ def __init__(self, list_of_strings): """ Constructor: @param list_of_strings: arg should be a list of strings which are filenames """ super(file_series, self).__init__(list_of_strings) # track current position in list self._current = 0 # methods which return a filename def first(self): """ First image in series """ return self[0] def last(self): """ Last in series """ return self[-1] def previous(self): """ Prev in a sequence """ self._current -= 1 return self[self._current] def current(self): """Current position in a sequence """ return self[self._current] def next(self): """ Next in a sequence """ self._current += 1 return self[self._current] def jump(self, num): """ Goto a position in sequence """ assert num < len(self) and num > 0, "num out of range" self._current = num return self[self._current] def len(self): """ Number of files """ return len(self) # Methods which return a fabioimage def first_image(self): """ First image in a sequence @return: fabioimage """ return openimage(self.first()) def last_image(self): """ Last image in a sequence @return: fabioimage """ return openimage(self.last()) def next_image(self): """ Return the next image @return: fabioimage """ return openimage(self.next()) def previous_image(self): """ Return the previous image @return: fabioimage """ return openimage(self.previous()) def jump_image(self, num): """ Jump to and read image @return: fabioimage """ return openimage(self.jump(num)) def current_image(self): """ Current image in sequence @return: fabioimage """ return openimage(self.current()) # methods which return a file_object def first_object(self): """ First image in a sequence @return: file_object """ return FilenameObject(self.first()) def last_object(self): """ Last image in a sequence @return: file_object """ return FilenameObject(self.last()) def next_object(self): """ Return the next image @return: file_object """ return FilenameObject(self.next()) def previous_object(self): """ Return the previous image @return: file_object """ return FilenameObject(self.previous()) def jump_object(self, num): """ Jump to and read image @return: file_object """ return FilenameObject(self.jump(num)) def current_object(self): """ Current image in sequence @return: file_object """ return FilenameObject(self.current()) class numbered_file_series(file_series): """ mydata0001.edf = "mydata" + 0001 + ".edf" mydata0002.edf = "mydata" + 0002 + ".edf" mydata0003.edf = "mydata" + 0003 + ".edf" """ def __init__(self, stem, first, last, extension, digits=4, padding='Y', step=1): """ Constructor @param stem: first part of the name @param step: in case of every nth file @param padding: possibility for specifying that numbers are not padded with zeroes up to digits """ if padding == 'Y': fmt = "%s%0" + str(digits) + "d%s" else: fmt = "%s%i%s" super(numbered_file_series, self).__init__( [ fmt % (stem, i, extension) for i in range(first, last + 1, step) ]) class filename_series: """ Much like the others, but created from a string filename """ def __init__(self, filename): """ create from a filename (String)""" self.obj = FilenameObject(filename) def next(self): """ increment number """ self.obj.num += 1 return self.obj.tostring() def previous(self): """ decrement number """ self.obj.num -= 1 return self.obj.tostring() def current(self): """ return current filename string""" return self.obj.tostring() def jump(self, num): """ jump to a specific number """ self.obj.num = num return self.obj.tostring() # image methods def next_image(self): """ returns the next image as a fabioimage """ return openimage(self.next()) def prev_image(self): """ returns the previos image as a fabioimage """ return openimage(self.previous()) def current_image(self): """ returns the current image as a fabioimage""" return openimage(self.current()) def jump_image(self, num): """ returns the image number as a fabioimage""" return openimage(self.jump(num)) # object methods def next_object(self): """ returns the next filename as a fabio.FilenameObject""" self.obj.num += 1 return self.obj def previous_object(self): """ returns the previous filename as a fabio.FilenameObject""" self.obj.num -= 1 return self.obj def current_object(self): """ returns the current filename as a fabio.FilenameObject""" return self.obj def jump_object(self, num): """ returns the filename num as a fabio.FilenameObject""" self.obj.num = num return self.obj fabio-0.1.3/fabio-src/HiPiCimage.py0000644000175000017500000000752112233175156017547 0ustar jeromejerome00000000000000 #!/usr/bin/env python """ Authors: Henning O. Sorensen & Erik Knudsen Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk + Jon Wright, ESRF Information about the file format from Masakatzu Kobayashi is highly appreciated """ import numpy, logging logger = logging.getLogger("HiPiCimage") from fabioimage import fabioimage class HiPiCimage(fabioimage): """ Read HiPic images e.g. collected with a Hamamatsu CCD camera""" def _readheader(self, infile): """ Read in a header from an already open file """ Image_tag = infile.read(2) print Image_tag Comment_len = numpy.fromstring(infile.read(2), numpy.uint16) Dim_1 = numpy.fromstring(infile.read(2), numpy.uint16)[0] Dim_2 = numpy.fromstring(infile.read(2), numpy.uint16)[0] Dim_1_offset = numpy.fromstring(infile.read(2), numpy.uint16)[0] Dim_2_offset = numpy.fromstring(infile.read(2), numpy.uint16)[0] HeaderType = numpy.fromstring(infile.read(2), numpy.uint16)[0] Dump = infile.read(50) Comment = infile.read(Comment_len) self.header['Image_tag'] = Image_tag self.header['Dim_1'] = Dim_1 self.header['Dim_2'] = Dim_2 self.header['Dim_1_offset'] = Dim_1_offset self.header['Dim_2_offset'] = Dim_2_offset #self.header['Comment'] = Comment if Image_tag != 'IM' : # This does not look like an HiPic file logging.warning("no opening. Corrupt header of HiPic file " + \ str(infile.name)) Comment_split = Comment[:Comment.find('\x00')].split('\r\n') for topcomment in Comment_split: topsplit = topcomment.split(',') for line in topsplit: if '=' in line: key, val = line.split('=' , 1) # Users cannot type in significant whitespace key = key.rstrip().lstrip() self.header_keys.append(key) self.header[key] = val.lstrip().rstrip() self.header[key] = val.lstrip('"').rstrip('"') def read(self, fname, frame=None): """ Read in header into self.header and the data into self.data """ self.header = {} self.resetvals() infile = self._open(fname, "rb") self._readheader(infile) # Compute image size try: self.dim1 = int(self.header['Dim_1']) self.dim2 = int(self.header['Dim_2']) except: raise Exception("HiPic file", str(fname) + \ "is corrupt, cannot read it") bytecode = numpy.uint16 self.bpp = len(numpy.array(0, bytecode).tostring()) # Read image data block = infile.read(self.dim1 * self.dim2 * self.bpp) infile.close() #now read the data into the array try: self.data = numpy.reshape( numpy.fromstring(block, bytecode), [self.dim2, self.dim1]) except: print len(block), bytecode, self.bpp, self.dim2, self.dim1 raise IOError, \ 'Size spec in HiPic-header does not match size of image data field' self.bytecode = self.data.dtype.type # Sometimes these files are not saved as 12 bit, # But as 16 bit after bg subtraction - which results # negative values saved as 16bit. Therefore values higher # 4095 is really negative values if self.data.max() > 4095: gt12bit = self.data > 4095 self.data = self.data - gt12bit * (2 ** 16 - 1) # ensure the PIL image is reset self.pilimage = None return self fabio-0.1.3/fabio-src/fit2dmaskimage.py0000644000175000017500000000544312233175156020500 0ustar jeromejerome00000000000000## Automatically adapted for numpy.oldnumeric Oct 05, 2007 by alter_code1.py #!/usr/bin/env python """ Author: Andy Hammersley, ESRF Translation into python/fabio: Jon Wright, ESRF """ import numpy from fabioimage import fabioimage class fit2dmaskimage(fabioimage): """ Read and try to write Andy Hammersley's mask format """ def _readheader(self, infile): """ Read in a header from an already open file """ # 1024 bytes gives 256x32 bit integers header = infile.read(1024) for i, j in [ ("M", 0), ("A", 4), ("S", 8), ("K", 12) ]: if header[j] != i: raise Exception("Not a fit2d mask file") fit2dhdr = numpy.fromstring(header, numpy.int32) self.dim1 = fit2dhdr[4] # 1 less than Andy's fortran self.dim2 = fit2dhdr[5] def read(self, fname, frame=None): """ Read in header into self.header and the data into self.data """ fin = self._open(fname) self._readheader(fin) # Compute image size self.bytecode = numpy.uint8 self.bpp = len(numpy.array(0, self.bytecode).tostring()) # integer division num_ints = (self.dim1 + 31) // 32 total = self.dim2 * num_ints * 4 data = fin.read(total) assert len(data) == total fin.close() # Now to unpack it data = numpy.fromstring(data, numpy.uint8) data = numpy.reshape(data, (self.dim2, num_ints * 4)) result = numpy.zeros((self.dim2, num_ints * 4 * 8), numpy.uint8) # Unpack using bitwise comparisons to 2**n bits = numpy.ones((1), numpy.uint8) for i in range(8): temp = numpy.bitwise_and(bits, data) result[:, i::8] = temp.astype(numpy.uint8) bits = bits * 2 # Extra rows needed for packing odd dimensions spares = num_ints * 4 * 8 - self.dim1 if spares == 0: self.data = numpy.where(result == 0, 0, 1) else: self.data = numpy.where(result[:, :-spares] == 0, 0, 1) # Transpose appears to be needed to match edf reader (scary??) # self.data = numpy.transpose(self.data) self.data = numpy.reshape(self.data.astype(numpy.uint16), (self.dim2, self.dim1)) self.pilimage = None return self def write(self, fname): """ Try to write a file check we can write zipped also mimics that fabian was writing uint16 (we sometimes want floats) """ raise Exception("Not implemented yet") @staticmethod def checkData(data=None): if data is None: return None else: return data.astype(int) fabio-0.1.3/fabio-src/kcdimage.py0000644000175000017500000001003412233175156017345 0ustar jeromejerome00000000000000#!/usr/bin/env python """ Authors: Jerome Kieffer, ESRF email:jerome.kieffer@esrf.fr kcd images are 2D images written by the old KappaCCD diffractometer built by Nonius in the 1990's Based on the edfimage.py parser. """ import numpy, logging import os, string from fabioimage import fabioimage logger = logging.getLogger("kcdimage") DATA_TYPES = {"u16" : numpy.uint16 } MINIMUM_KEYS = [ 'ByteOrder', 'Data type', 'X dimension', 'Y dimension', 'Number of readouts'] DEFAULT_VALUES = { "Data type": "u16" } class kcdimage(fabioimage): """ Read the Nonius kcd data format """ def _readheader(self, infile): """ Read in a header in some KCD format from an already open file @ """ oneLine = infile.readline() alphanum = string.digits + string.letters + ". " asciiHeader = True for oneChar in oneLine.strip(): if not oneChar in alphanum: asciiHeader = False if asciiHeader is False: # This does not look like an edf file logger.warning("First line of %s does not seam to be ascii text!" % infile.name) endOfHeaders = False while not endOfHeaders: oneLine = infile.readline() if len(oneLine) > 100: endOfHeaders = True break if oneLine.strip() == "Binned mode": oneLine = "Mode = Binned" try: key, val = oneLine.split('=' , 1) except: endOfHeaders = True break key = key.strip() self.header_keys.append(key) self.header[key] = val.strip() missing = [] for item in MINIMUM_KEYS: if item not in self.header_keys: missing.append(item) if len(missing) > 0: logger.debug("KCD file misses the keys " + " ".join(missing)) def read(self, fname, frame=None): """ Read in header into self.header and the data into self.data """ self.header = {} self.resetvals() infile = self._open(fname, "rb") self._readheader(infile) # Compute image size try: self.dim1 = int(self.header['X dimension']) self.dim2 = int(self.header['Y dimension']) except: raise Exception("KCD file %s is corrupt, cannot read it" % fname) try: bytecode = DATA_TYPES[self.header['Data type']] self.bpp = len(numpy.array(0, bytecode).tostring()) except KeyError: bytecode = numpy.uint16 self.bpp = 2 logger.warning("Defaulting type to uint16") try: nbReadOut = int(self.header['Number of readouts']) except KeyError: logger.warning("Defaulting number of ReadOut to 1") nbReadOut = 1 fileSize = os.stat(fname)[6] expected_size = self.dim1 * self.dim2 * self.bpp * nbReadOut infile.seek(fileSize - expected_size) block = infile.read() assert len(block) == expected_size infile.close() #now read the data into the array self.data = numpy.zeros((self.dim2, self.dim1)) try: for i in range(nbReadOut): self.data += numpy.reshape(numpy.fromstring( block[i * expected_size / nbReadOut:(i + 1) * expected_size / nbReadOut], bytecode), [self.dim2, self.dim1]) except: print len(block), bytecode, self.bpp, self.dim2, self.dim1 raise IOError, \ 'Size spec in kcd-header does not match size of image data field' self.bytecode = self.data.dtype.type self.resetvals() # ensure the PIL image is reset self.pilimage = None return self @staticmethod def checkData(data=None): if data is None: return None else: return data.astype(int) fabio-0.1.3/fabio-src/cbfimage.py0000644000175000017500000006564612233175156017361 0ustar jeromejerome00000000000000#!/usr/bin/env python # coding: utf8 """ Authors: Jérôme Kieffer, ESRF email:jerome.kieffer@esrf.fr Cif Binary Files images are 2D images written by the Pilatus detector and others. They use a modified (simplified) byte-offset algorithm. CIF is a library for manipulating Crystallographic information files and tries to conform to the specification of the IUCR """ __author__ = "Jérôme Kieffer" __contact__ = "jerome.kieffer@esrf.eu" __license__ = "GPLv3+" __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" __version__ = ["Generated by CIF.py: Jan 2005 - April 2012", "Written by Jerome Kieffer: Jerome.Kieffer@esrf.eu", "On-line data analysis / ISDD ", "ESRF Grenoble (France)"] import os, logging logger = logging.getLogger("cbfimage") import numpy from fabioimage import fabioimage from compression import decByteOffet_numpy, md5sum, compByteOffet_numpy #import time DATA_TYPES = { "signed 8-bit integer" : numpy.int8, "signed 16-bit integer" : numpy.int16, "signed 32-bit integer" : numpy.int32, "signed 64-bit integer" : numpy.int64 } MINIMUM_KEYS = ["X-Binary-Size-Fastest-Dimension", 'ByteOrder', 'Data type', 'X dimension', 'Y dimension', 'Number of readouts'] STARTER = "\x0c\x1a\x04\xd5" PADDING = 512 class cbfimage(fabioimage): """ Read the Cif Binary File data format """ def __init__(self, data=None , header=None, fname=None): """ Constructor of the class CIF Binary File reader. @param _strFilename: the name of the file to open @type _strFilename: string """ fabioimage.__init__(self, data, header) self.cif = CIF() if fname is not None: #load the file) self.read(fname) @staticmethod def checkData(data=None): if data is None: return None elif numpy.issubdtype(data.dtype, int): return data else: return data.astype(int) def _readheader(self, inStream): """ Read in a header in some CBF format from a string representing binary stuff @param inStream: file containing the Cif Binary part. @type inStream: opened file. """ self.cif.loadCIF(inStream, _bKeepComment=True) # backport contents of the CIF data to the headers for key in self.cif: if key != "_array_data.data": self.header_keys.append(key) self.header[key] = self.cif[key].strip(" \"\n\r\t") if not "_array_data.data" in self.cif: raise Exception("cbfimage: CBF file %s is corrupt, cannot find data block with '_array_data.data' key" % self.fname) inStream2 = self.cif["_array_data.data"] sep = "\r\n" iSepPos = inStream2.find(sep) if iSepPos < 0 or iSepPos > 80: sep = "\n" #switch back to unix representation lines = inStream2.split(sep) for oneLine in lines[1:]: if len(oneLine) < 10: break try: key, val = oneLine.split(':' , 1) except ValueError: key, val = oneLine.split('=' , 1) key = key.strip() self.header_keys.append(key) self.header[key] = val.strip(" \"\n\r\t") missing = [] for item in MINIMUM_KEYS: if item not in self.header_keys: missing.append(item) if len(missing) > 0: logger.debug("CBF file misses the keys " + " ".join(missing)) def read(self, fname, frame=None): """ Read in header into self.header and the data into self.data """ self.filename = fname self.header = {} self.resetvals() infile = self._open(fname, "rb") self._readheader(infile) # Compute image size try: self.dim1 = int(self.header['X-Binary-Size-Fastest-Dimension']) self.dim2 = int(self.header['X-Binary-Size-Second-Dimension']) except: raise Exception(IOError, "CBF file %s is corrupt, no dimensions in it" % fname) try: bytecode = DATA_TYPES[self.header['X-Binary-Element-Type']] self.bpp = len(numpy.array(0, bytecode).tostring()) except KeyError: bytecode = numpy.int32 self.bpp = 32 logger.warning("Defaulting type to int32") if self.header["conversions"] == "x-CBF_BYTE_OFFSET": self.data = self._readbinary_byte_offset(self.cif["_array_data.data"]).astype(bytecode).reshape((self.dim2, self.dim1)) else: raise Exception(IOError, "Compression scheme not yet supported, please contact FABIO development team") self.bytecode = self.data.dtype.type self.resetvals() # # ensure the PIL image is reset self.pilimage = None return self def _readbinary_byte_offset(self, inStream): """ Read in a binary part of an x-CBF_BYTE_OFFSET compressed image @param inStream: the binary image (without any CIF decorators) @type inStream: python string. @return: a linear numpy array without shape and dtype set @rtype: numpy array """ startPos = inStream.find(STARTER) + 4 data = inStream[ startPos: startPos + int(self.header["X-Binary-Size"])] try: import byte_offset except ImportError: logger.warning("Error in byte_offset part: Falling back to Numpy implementation") myData = decByteOffet_numpy(data, size=self.dim1 * self.dim2) else: myData = byte_offset.analyseCython(data, size=self.dim1 * self.dim2) assert len(myData) == self.dim1 * self.dim2 return myData def write(self, fname): """ write the file in CBF format @param fname: name of the file @type: string """ if self.data is not None: self.dim2, self.dim1 = self.data.shape else: raise RuntimeError("CBF image contains no data") binary_blob = compByteOffet_numpy(self.data) # l = len(binary_blob) # if (l % PADDING) != 0: # rem = PADDING - (l % PADDING) # binary_blob += "\x00" * rem dtype = "Unknown" for key, value in DATA_TYPES.iteritems(): if value == self.data.dtype: dtype = key binary_block = [ "--CIF-BINARY-FORMAT-SECTION--", "Content-Type: application/octet-stream;", ' conversions="x-CBF_BYTE_OFFSET"', 'Content-Transfer-Encoding: BINARY', "X-Binary-Size: %d" % (len(binary_blob)), "X-Binary-ID: 1", 'X-Binary-Element-Type: "%s"' % (dtype), "X-Binary-Element-Byte-Order: LITTLE_ENDIAN" , "Content-MD5: %s" % md5sum(binary_blob), "X-Binary-Number-of-Elements: %s" % (self.dim1 * self.dim2), "X-Binary-Size-Fastest-Dimension: %d" % self.dim1, "X-Binary-Size-Second-Dimension: %d" % self.dim2, "X-Binary-Size-Padding: %d" % 1, "", STARTER + binary_blob, "", "--CIF-BINARY-FORMAT-SECTION----" ] if "_array_data.header_contents" not in self.header: nonCifHeaders = [] else: nonCifHeaders = [i.strip()[2:] for i in self.header["_array_data.header_contents"].split("\n") if i.find("# ") >= 0] for key in self.header: if (key not in self.header_keys): self.header_keys.append(key) for key in self.header_keys: if key.startswith("_") : if key not in self.cif or self.cif[key] != self.header[key]: self.cif[key] = self.header[key] elif key.startswith("X-Binary-"): pass elif key.startswith("Content-"): pass elif key.startswith("conversions"): pass elif key.startswith("filename"): pass elif key in self.header: nonCifHeaders.append("%s %s" % (key, self.header[key])) if len(nonCifHeaders) > 0: self.cif["_array_data.header_contents"] = "\r\n".join(["# %s" % i for i in nonCifHeaders]) self.cif["_array_data.data"] = "\r\n".join(binary_block) self.cif.saveCIF(fname, linesep="\r\n", binary=True) ################################################################################ # CIF class ################################################################################ class CIF(dict): """ This is the CIF class, it represents the CIF dictionary; and as a a python dictionary thus inherits from the dict built in class. """ EOL = ["\r", "\n", "\r\n", "\n\r"] BLANK = [" ", "\t"] + EOL START_COMMENT = ["\"", "\'"] BINARY_MARKER = "--CIF-BINARY-FORMAT-SECTION--" def __init__(self, _strFilename=None): """ Constructor of the class. @param _strFilename: the name of the file to open @type _strFilename: filename (str) or file object """ dict.__init__(self) self._ordered = [] if _strFilename is not None: #load the file) self.loadCIF(_strFilename) def __setitem__(self, key, value): if key not in self._ordered: self._ordered.append(key) return dict.__setitem__(self, key, value) def pop(self, key): if key in self._ordered: self._ordered.remove(key) return dict.pop(self, key) def popitem(self, key): if key in self._ordered: self._ordered.remove(key) return dict.popitem(self, key) def loadCIF(self, _strFilename, _bKeepComment=False): """Load the CIF file and populates the CIF dictionary into the object @param _strFilename: the name of the file to open @type _strFilename: string @param _strFilename: the name of the file to open @type _strFilename: string @return: None """ if isinstance(_strFilename, (str, unicode)): if os.path.isfile(_strFilename): infile = open(_strFilename, "rb") else: raise RuntimeError("CIF.loadCIF: No such file to open: %s" % _strFilename) #elif isinstance(_strFilename, file, bz2.BZ2File, ): elif "read" in dir(_strFilename): infile = _strFilename else: raise RuntimeError("CIF.loadCIF: what is %s type %s" % (_strFilename, type(_strFilename))) if _bKeepComment: self._parseCIF(infile.read()) else: self._parseCIF(CIF._readCIF(infile)) readCIF = loadCIF @staticmethod def isAscii(_strIn): """ Check if all characters in a string are ascii, @param _strIn: input string @type _strIn: python string @return: boolean @rtype: boolean """ bIsAcii = True for i in _strIn: if ord(i) > 127: bIsAcii = False break return bIsAcii @staticmethod def _readCIF(_instream): """ - Check if the filename containing the CIF data exists - read the cif file - removes the comments @param _instream: the file containing the CIF data @type _instream: open file in read mode @return: a string containing the raw data @rtype: string """ if not "readlines" in dir(_instream): raise RuntimeError("CIF._readCIF(instream): I expected instream to be an opened file,\ here I got %s type %s" % (_instream, type(_instream))) lLinesRead = _instream.readlines() sText = "" for sLine in lLinesRead: iPos = sLine.find("#") if iPos >= 0: if CIF.isAscii(sLine): sText += sLine[:iPos] + os.linesep if iPos > 80 : logger.warning("This line is too long and could cause problems in PreQuest: %s", sLine) else : sText += sLine if len(sLine.strip()) > 80 : logger.warning("This line is too long and could cause problems in PreQues: %s", sLine) return sText def _parseCIF(self, sText): """ - Parses the text of a CIF file - Cut it in fields - Find all the loops and process - Find all the keys and values @param sText: the content of the CIF - file @type sText: string @return: Nothing, the data are incorporated at the CIF object dictionary @rtype: None """ loopidx = [] looplen = [] loop = [] #first of all : separate the cif file in fields lFields = CIF._splitCIF(sText.strip()) #Then : look for loops for i in range(len(lFields)): if lFields[i].lower() == "loop_": loopidx.append(i) if len(loopidx) > 0: for i in loopidx: loopone, length, keys = CIF._analyseOneLoop(lFields, i) loop.append([keys, loopone]) looplen.append(length) for i in range(len(loopidx) - 1, -1, -1): f1 = lFields[:loopidx[i]] + lFields[loopidx[i] + looplen[i]:] lFields = f1 self["loop_"] = loop for i in range(len(lFields) - 1): # print lFields[i], lFields[i+1] if len(lFields[i + 1]) == 0 : lFields[i + 1] = "?" if lFields[i][0] == "_" and lFields[i + 1][0] != "_": self[lFields[i]] = lFields[i + 1] @staticmethod def _splitCIF(sText): """ Separate the text in fields as defined in the CIF @param sText: the content of the CIF - file @type sText: string @return: list of all the fields of the CIF @rtype: list """ lFields = [] while True: if len(sText) == 0: break elif sText[0] == "'": idx = 0 bFinished = False while not bFinished: idx += 1 + sText[idx + 1:].find("'") ##########debuging in case we arrive at the end of the text if idx >= len(sText) - 1: # print sText,idx,len(sText) lFields.append(sText[1:-1].strip()) sText = "" bFinished = True break if sText[idx + 1] in CIF.BLANK: lFields.append(sText[1:idx].strip()) sText1 = sText[idx + 1:] sText = sText1.strip() bFinished = True elif sText[0] == '"': idx = 0 bFinished = False while not bFinished: idx += 1 + sText[idx + 1:].find('"') ##########debuging in case we arrive at the end of the text if idx >= len(sText) - 1: # print sText,idx,len(sText) lFields.append(sText[1:-1].strip()) # print lFields[-1] sText = "" bFinished = True break if sText[idx + 1] in CIF.BLANK: lFields.append(sText[1:idx].strip()) # print lFields[-1] sText1 = sText[idx + 1:] sText = sText1.strip() bFinished = True elif sText[0] == ';': if sText[1:].strip().find(CIF.BINARY_MARKER) == 0: idx = sText[32:].find(CIF.BINARY_MARKER) if idx == -1: idx = 0 else: idx += 32 + len(CIF.BINARY_MARKER) else: idx = 0 bFinished = False while not bFinished: idx += 1 + sText[idx + 1:].find(';') if sText[idx - 1] in CIF.EOL: lFields.append(sText[1:idx - 1].strip()) sText1 = sText[idx + 1:] sText = sText1.strip() bFinished = True else: f = sText.split(None, 1)[0] lFields.append(f) # print lFields[-1] sText1 = sText[len(f):].strip() sText = sText1 return lFields @staticmethod def _analyseOneLoop(lFields, iStart): """Processes one loop in the data extraction of the CIF file @param lFields: list of all the words contained in the cif file @type lFields: list @param iStart: the starting index corresponding to the "loop_" key @type iStart: integer @return: the list of loop dictionaries, the length of the data extracted from the lFields and the list of all the keys of the loop. @rtype: tuple """ # in earch loop we first search the length of the loop # print lFields # curloop = {} loop = [] keys = [] i = iStart + 1 bFinished = False while not bFinished: if lFields[i][0] == "_": keys.append(lFields[i])#.lower()) i += 1 else: bFinished = True data = [] while True: if i >= len(lFields): break elif len(lFields[i]) == 0: break elif lFields[i][0] == "_": break elif lFields[i] in ["loop_", "stop_", "global_", "data_", "save_"]: break else: data.append(lFields[i]) i += 1 #print len(keys), len(data) k = 0 if len(data) < len(keys): element = {} for j in keys: if k < len(data): element[j] = data[k] else : element[j] = "?" k += 1 #print element loop.append(element) else: #print data #print keys for i in range(len(data) / len(keys)): element = {} for j in keys: element[j] = data[k] k += 1 # print element loop.append(element) # print loop return loop, 1 + len(keys) + len(data), keys ############################################################################################# ######## everything needed to write a cif file ######################################### ############################################################################################# def saveCIF(self, _strFilename="test.cif", linesep=os.linesep, binary=False): """Transforms the CIF object in string then write it into the given file @param _strFilename: the of the file to be written @param linesep: line separation used (to force compatibility with windows/unix) @param binary: Shall we write the data as binary (True only for imageCIF/CBF) @type param: string """ if binary: mode = "wb" else: mode = "w" try: fFile = open(_strFilename, mode) except IOError: print("Error during the opening of file for write: %s" % _strFilename) return fFile.write(self.tostring(_strFilename, linesep)) try: fFile.close() except IOError: print("Error during the closing of file for write: %s" % _strFilename) def tostring(self, _strFilename=None, linesep=os.linesep): """ Converts a cif dictionnary to a string according to the CIF syntax @param _strFilename: the name of the filename to be appended in the header of the CIF file @type _strFilename: string @return: a sting that corresponds to the content of the CIF - file. """ # sCifText = "" lstStrCif = ["# " + i for i in __version__] if "_chemical_name_common" in self: t = self["_chemical_name_common"].split()[0] elif _strFilename is not None: t = os.path.splitext(os.path.split(str(_strFilename).strip())[1])[0] else: t = "" lstStrCif.append("data_%s" % (t)) #first of all get all the keys : lKeys = self.keys() lKeys.sort() for key in lKeys[:]: if key in self._ordered: lKeys.remove(key) self._ordered += lKeys for sKey in self._ordered: if sKey == "loop_": continue if sKey not in self: self._ordered.remove(sKey) logger.debug("Skipping key %s from ordered list as no more present in dict") continue sValue = str(self[sKey]) if sValue.find("\n") > -1: #should add value between ;; lLine = [sKey, ";", sValue, ";", ""] elif len(sValue.split()) > 1: #should add value between '' sLine = "%s '%s'" % (sKey, sValue) if len(sLine) > 80: lLine = [str(sKey), sValue] else: lLine = [sLine] else: sLine = "%s %s" % (sKey, sValue) if len(sLine) > 80: lLine = [str(sKey), sValue] else: lLine = [sLine] lstStrCif += lLine if self.has_key("loop_"): for loop in self["loop_"]: lstStrCif.append("loop_ ") lKeys = loop[0] llData = loop[1] lstStrCif += [" %s" % (sKey) for sKey in lKeys] for lData in llData: sLine = " " for key in lKeys: sRawValue = lData[key] if sRawValue.find("\n") > -1: #should add value between ;; lstStrCif += [sLine, ";", str(sRawValue), ";"] sLine = " " else: if len(sRawValue.split()) > 1: #should add value between '' value = "'%s'" % (sRawValue) else: value = str(sRawValue) if len(sLine) + len(value) > 78: lstStrCif += [sLine] sLine = " " + value else: sLine += " " + value lstStrCif.append(sLine) lstStrCif.append("") return linesep.join(lstStrCif) def exists(self, sKey): """ Check if the key exists in the CIF and is non empty. @param sKey: CIF key @type sKey: string @param cif: CIF dictionary @return: True if the key exists in the CIF dictionary and is non empty @rtype: boolean """ bExists = False if self.has_key(sKey): if len(self[sKey]) >= 1: if self[sKey][0] not in ["?", "."]: bExists = True return bExists def existsInLoop(self, sKey): """ Check if the key exists in the CIF dictionary. @param sKey: CIF key @type sKey: string @param cif: CIF dictionary @return: True if the key exists in the CIF dictionary and is non empty @rtype: boolean """ if not self.exists("loop_"): return False bExists = False if not bExists: for i in self["loop_"]: for j in i[0]: if j == sKey: bExists = True return bExists def loadCHIPLOT(self, _strFilename): """ Load the powder diffraction CHIPLOT file and returns the pd_CIF dictionary in the object @param _strFilename: the name of the file to open @type _strFilename: string @return: the CIF object corresponding to the powder diffraction @rtype: dictionary """ if not os.path.isfile(_strFilename): print "I cannot find the file %s" % _strFilename raise lInFile = open(_strFilename, "r").readlines() self["_audit_creation_method"] = 'From 2-D detector using FIT2D and CIFfile' self["_pd_meas_scan_method"] = "fixed" self["_pd_spec_description"] = lInFile[0].strip() try: iLenData = int(lInFile[3]) except ValueError: iLenData = None lOneLoop = [] try: f2ThetaMin = float(lInFile[4].split()[0]) last = "" for sLine in lInFile[-20:]: if sLine.strip() != "": last = sLine.strip() f2ThetaMax = float(last.split()[0]) limitsOK = True except (ValueError, IndexError): limitsOK = False f2ThetaMin = 180.0 f2ThetaMax = 0 # print "limitsOK:", limitsOK for sLine in lInFile[4:]: sCleaned = sLine.split("#")[0].strip() data = sCleaned.split() if len(data) == 2 : if not limitsOK: f2Theta = float(data[0]) if f2Theta < f2ThetaMin : f2ThetaMin = f2Theta if f2Theta > f2ThetaMax : f2ThetaMax = f2Theta lOneLoop.append({ "_pd_meas_intensity_total": data[1] }) if not iLenData: iLenData = len(lOneLoop) assert (iLenData == len(lOneLoop)) self[ "_pd_meas_2theta_range_inc" ] = "%.4f" % ((f2ThetaMax - f2ThetaMin) / (iLenData - 1)) if self[ "_pd_meas_2theta_range_inc" ] < 0: self[ "_pd_meas_2theta_range_inc" ] = abs (self[ "_pd_meas_2theta_range_inc" ]) tmp = f2ThetaMax f2ThetaMax = f2ThetaMin f2ThetaMin = tmp self[ "_pd_meas_2theta_range_max" ] = "%.4f" % f2ThetaMax self[ "_pd_meas_2theta_range_min" ] = "%.4f" % f2ThetaMin self[ "_pd_meas_number_of_points" ] = str(iLenData) self["loop_"] = [ [ ["_pd_meas_intensity_total" ], lOneLoop ] ] @staticmethod def LoopHasKey(loop, key): "Returns True if the key (string) exist in the array called loop""" try: loop.index(key) return True except ValueError: return False fabio-0.1.3/fabio-src/openimage.py0000644000175000017500000001276412233175156017561 0ustar jeromejerome00000000000000""" Authors: Henning O. Sorensen & Erik Knudsen Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:henning.sorensen@risoe.dk mods for fabio by JPW """ import sys, logging logger = logging.getLogger("openimage") from fabioutils import FilenameObject from fabioimage import fabioimage import edfimage import adscimage import tifimage import marccdimage import mar345image import fit2dmaskimage import brukerimage import bruker100image import pnmimage import GEimage import OXDimage import dm3image import HiPiCimage import pilatusimage import fit2dspreadsheetimage import kcdimage import cbfimage import xsdimage import binaryimage MAGIC_NUMBERS = [ # "\42\5a" : 'bzipped' # "\1f\8b" : 'gzipped' ("FORMAT : 86" , 'bruker'), ("\x4d\x4d\x00\x2a" , 'tif') , # The marCCD and Pilatus formats are both standard tif with a header # hopefully these byte patterns are unique for the formats # If not the image will be read, but the is missing ("\x49\x49\x2a\x00\x08\x00" , 'marccd') , ("\x49\x49\x2a\x00\x82\x00" , 'pilatus') , ("\x49\x49\x2a\x00" , 'tif') , # ADSC must come before edf ("{\nHEA" , 'adsc'), ("{" , 'edf'), ("\r{" , 'edf'), ("\n{" , 'edf'), ("ADEPT" , 'GE'), ("OD" , 'OXD'), ("IM" , 'HiPiC'), ('\x2d\x04' , 'mar345'), ('\xd2\x04' , 'mar345'), ('\x04\x2d' , 'mar345'), #some machines may need byteswapping ('\x04\xd2' , 'mar345'), # hint : MASK in 32 bit ('M\x00\x00\x00A\x00\x00\x00S\x00\x00\x00K\x00\x00\x00' , 'fit2dmask') , ('\x00\x00\x00\x03' , 'dm3'), ("No" , "kcd"), ("<" , "xsd") ] def do_magic(byts): """ Try to interpret the bytes starting the file as a magic number """ for magic, format_type in MAGIC_NUMBERS: if byts.find(magic) == 0: return format_type if 0: # debugging - bruker needed 18 bytes below logger.debug("m: %s f: %s", magic, format_type) logger.debug("bytes: %s len(bytes) %s", magic, len(magic)) logger.debug("found: %s", byts.find(magic)) for i in range(len(magic)): logger.debug("%s %s %s %s ", ord(magic[i]), ord(byts[i]), magic[i], byts[i]) raise Exception("Could not interpret magic string") def openimage(filename, frame=None): """ Try to open an image """ if isinstance(filename, FilenameObject): try: logger.debug("Attempting to open %s" % (filename.tostring())) obj = _openimage(filename.tostring()) logger.debug("Attempting to read frame %s from %s" % (frame, filename.tostring())) obj = obj.read(filename.tostring(), frame) except Exception, ex: # multiframe file #logger.debug( "DEBUG: multiframe file, start # %d"%( # filename.num) logger.debug("Exception %s, trying name %s" % (ex, filename.stem)) obj = _openimage(filename.stem) logger.debug("Reading frame %s from %s" % (filename.num, filename.stem)) obj.read(filename.stem, frame=filename.num) else: logger.debug("Attempting to open %s" % (filename)) obj = _openimage(filename) logger.debug("Attempting to read frame %s from %s" % (frame, filename)) obj = obj.read(filename, frame) return obj def openheader(filename): """ return only the header""" obj = _openimage(filename) obj.readheader(filename) return obj def _openimage(filename): """ determine which format for a filename and return appropriate class which can be used for opening the image """ try: imo = fabioimage() byts = imo._open(filename).read(18) filetype = do_magic(byts) if filetype == "marccd" and filename.find("mccd") == -1: # Cannot see a way around this. Need to find something # to distinguish mccd from regular tif... filetype = "tif" except IOError, error: logger.error("%s: File probably does not exist", error) raise error except: try: file_obj = FilenameObject(filename=filename) if file_obj == None: raise Exception("Unable to deconstruct filename") if (file_obj.format is not None) and\ len(file_obj.format) != 1 and \ type(file_obj.format) != type(["list"]): # one of OXD/ ADSC - should have got in previous raise Exception("openimage failed on magic bytes & name guess") filetype = file_obj.format #UNUSED filenumber = file_obj.num except Exception, error: logger.error(error) import traceback traceback.print_exc() raise Exception("Fabio could not identify " + filename) klass_name = "".join(filetype) + 'image' module = sys.modules.get("fabio." + klass_name, None) if module is not None: if hasattr(module, klass_name): klass = getattr(module, klass_name) else: raise Exception("Module %s has no image class" % module) else: raise Exception("Filetype not known %s %s" % (filename, klass_name)) obj = klass() # skip the read for read header return obj fabio-0.1.3/fabio-src/dm3image.py0000644000175000017500000002211212233175156017267 0ustar jeromejerome00000000000000""" Authors: Henning O. Sorensen & Erik Knudsen Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk + Jon Wright, ESRF """ import logging import numpy from fabioimage import fabioimage logger = logging.getLogger("dm3image") DATA_TYPES = { 2 : numpy.int16, 4 : numpy.uint16, 3 : numpy.int32, 5 : numpy.uint32, 6 : numpy.float32, 7 : numpy.float, 8 : numpy.int8, 9 : None, 10 : None, 15 : 'Struct', 18 : None, 20 : None } DATA_BYTES = { 2 : 2, 4 : 2, 3 : 4, 5 : 4, 6 : 4, 7 : 8, 8 : 1, 9 : None, 10 : None, 15 : 'Struct', 18 : None, 20 : None } class dm3image(fabioimage): """ Read and try to write the dm3 data format """ def __init__(self, *args, **kwargs): fabioimage.__init__(self, *args, **kwargs) self.encoded_datatype = None self.no_data_elements = None self.grouptag_is_sorted = None self.grouptag_is_open = None self.tag_encoded_type = None self.tag_data_type = None self.tag_is_data = None self.grouptag_no_tags = None self.bytes_in_file = None self.tag_label_length = None self.go_on = None def _readheader(self): self.infile.seek(0) file_format = self.readbytes(4, numpy.uint32)[0] # should be 3 assert file_format == 3, 'Wrong file type ' self.bytes_in_file = self.readbytes(4, numpy.uint32)[0] self.byte_order = self.readbytes(4, numpy.uint32)[0] # 0 = big, 1= little print 'read dm3 file - file format ', file_format print 'Bytes in file : ' , self.bytes_in_file print 'Byte order :', self.byte_order, ' - 0 = bigEndian , 1 = littleEndian' if self.byte_order == 0: self.swap = True elif self.byte_order == 1: self.swap = False else: raise ValueError def read(self, fname, frame=None): self.header = {} self.resetvals() self.infile = self._open(fname, "rb") self._readheader() self.go_on = True print self.go_on while self.go_on: self.read_tag_group() self.read_tag_entry() if self.infile.tell() > self.bytes_in_file: break while self.tag_is_data == 21: self.read_tag_entry() if self.infile.tell() > self.bytes_in_file: self.go_on = False (dim1_raw, dim2_raw) = self.header['Active Size (pixels)'].split() (dim1_raw, dim2_raw) = (eval(dim1_raw), eval(dim2_raw)) (dim1_binning, dim2_binning) = self.header['Binning'].split() (dim1_binning, dim2_binning) = (eval(dim1_binning), eval(dim2_binning)) self.dim1 = dim1_raw / dim1_binning self.dim2 = dim2_raw / dim2_binning #print dim1,dim2 if self.header.has_key('Data'): self.data = self.header['Data'].reshape(self.dim1, self.dim2) def readbytes(self, bytes_to_read, format, swap=True): raw = self.infile.read(bytes_to_read) if format != None: data = numpy.fromstring(raw, format) else: data = raw if swap: data = data.byteswap() return data def read_tag_group(self): self.grouptag_is_sorted = self.readbytes(1, numpy.uint8)[0] self.grouptag_is_open = self.readbytes(1, numpy.uint8)[0] self.grouptag_no_tags = self.readbytes(4, numpy.uint32)[0] logger.debug('TagGroup is sorted? %s', self.grouptag_is_sorted) logger.debug('TagGroup is open? %s', self.grouptag_is_open) logger.debug('no of tags in TagGroup %s', self.grouptag_no_tags) def read_tag_entry(self): self.tag_is_data = self.readbytes(1, numpy.uint8)[0] self.tag_label_length = self.readbytes(2, numpy.uint16)[0] logger.debug('does Tag have data ? %s - 20 = Tag group , 21 = data ', self.tag_is_data) logger.debug('length of tag_label ', self.tag_label_length) if self.tag_label_length != 0: tag_label = self.infile.read(self.tag_label_length) else: tag_label = None if self.tag_is_data == 21: # This is data self.header[tag_label] = self.read_tag_type() logger.debug("%s: %s", tag_label, self.header[tag_label]) def read_tag_type(self): if self.infile.read(4) != '%%%%': raise IOError self.tag_data_type = self.readbytes(4, numpy.uint32)[0] logger.debug('data is of type : %s - 1 = simple, 2= string, 3 = array, >3 structs', self.tag_data_type) self.tag_encoded_type = self.readbytes(4, numpy.uint32)[0] logger.debug('encode type: %s %s', self.tag_encoded_type, DATA_TYPES[ self.tag_encoded_type]) if self.tag_data_type == 1: # simple type return self.readbytes(DATA_BYTES[ self.tag_encoded_type], DATA_TYPES[ self.tag_encoded_type], swap=self.swap)[0] # are the data stored in a simple array? if self.tag_encoded_type == 20 and self.tag_data_type == 3 : self.data_type = self.readbytes(4, numpy.uint32)[0] self.no_data_elements = self.readbytes(4, numpy.uint32)[0] if self.data_type == 10: logger.debug('skip bytes %s', self.no_data_elements) dump = self.infile.read(self.no_data_elements) return None logger.debug('Data are stored as a simple a array -') logger.debug('%s data elemets stored as %s', self.no_data_elements, self.data_type) read_no_bytes = DATA_BYTES[self.data_type] * self.no_data_elements format = DATA_TYPES[self.data_type] return self.readbytes(read_no_bytes, format, swap=self.swap) # are the data stored in a complex array ? # print 'tag_type + data_type', self.tag_encoded_type,self.tag_data_type #print self.tag_encoded_type , self.tag_data_type if self.tag_encoded_type == 20 and self.tag_data_type > 3 : self.tag_encoded_type = self.readbytes(4, numpy.uint32)[0] logger.debug('found array - new tag_encoded_type %s', self.tag_encoded_type) if self.tag_encoded_type == 15: # struct type ###type = self.readbytes(4,numpy.int32) struct_name_length = self.readbytes(4, numpy.int32)[0] struct_number_fields = self.readbytes(4, numpy.int32)[0] #print 'struct - name_length, number_field', struct_name_length,struct_number_fields #print self.infile.read(struct_name_length) field_info = [] for i in range(struct_number_fields): field_info.append([self.readbytes(4, numpy.int32)[0], self.readbytes(4, numpy.int32)[0]]) #print field_info self.no_data_elements = self.readbytes(4, numpy.int32)[0] #print '%i data elemets stored as ' %self.no_data_elements bytes_in_struct = 0 for i in range(struct_number_fields): bytes_in_struct += DATA_BYTES[field_info[i][1]] logger.debug('skip bytes %s', self.no_data_elements * bytes_in_struct) dump = self.infile.read(self.no_data_elements * bytes_in_struct) return None if self.tag_encoded_type == 15: # struct type ###type = self.readbytes(4,numpy.int32) struct_name_length = self.readbytes(4, numpy.int32)[0] struct_number_fields = self.readbytes(4, numpy.int32)[0] #print 'struct - name_length, number_field', struct_name_length,struct_number_fields #print self.infile.read(struct_name_length) field_info = [] for i in range(struct_number_fields): field_info.append([self.readbytes(4, numpy.int32)[0], self.readbytes(4, numpy.int32)[0]]) #print field_info field_data = '' for i in range(struct_number_fields): #print type(i) field_data = field_data + self.readbytes(field_info[i][0], None, swap=False) + ' ' field_data = field_data + '%i ' % self.readbytes(DATA_BYTES[field_info[i][1]], DATA_TYPES[field_info[i][1]], swap=self.swap)[0] return field_data def read_data(self): self.encoded_datatype = numpy.fromstring(self.infile.read(4), numpy.uint32).byteswap() fabio-0.1.3/fabio-src/adscimage.py0000644000175000017500000001120112233175156017513 0ustar jeromejerome00000000000000#!/usr/bin/env python #coding: utf8 """ Authors: Henning O. Sorensen & Erik Knudsen Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk + mods for fabio by JPW """ import numpy, logging from fabioimage import fabioimage logger = logging.getLogger("adscimage") class adscimage(fabioimage): """ Read an image in ADSC format (quite similar to edf?) """ def __init__(self, *args, **kwargs): fabioimage.__init__(self, *args, **kwargs) def read(self, fname, frame=None): """ read in the file """ infile = self._open(fname, "rb") try: self._readheader(infile) except: raise Exception("Error processing adsc header") # banned by bzip/gzip??? try: infile.seek(int(self.header['HEADER_BYTES']), 0) except TypeError: # Gzipped does not allow a seek and read header is not # promising to stop in the right place infile.close() infile = self._open(fname, "rb") infile.read(int(self.header['HEADER_BYTES'])) binary = infile.read() infile.close() #now read the data into the array self.dim1 = int(self.header['SIZE1']) self.dim2 = int(self.header['SIZE2']) if 'little' in self.header['BYTE_ORDER']: try: self.data = numpy.reshape( numpy.fromstring(binary, numpy.uint16), (self.dim2, self.dim1)) except ValueError: raise IOError, 'Size spec in ADSC-header does not match ' + \ 'size of image data field' self.bytecode = numpy.uint16 logger.info("adscimage read in using low byte first (x386-order)") else: try: self.data = numpy.reshape( numpy.fromstring(binary, numpy.uint16), (self.dim2, self.dim1)).byteswap() except ValueError: raise IOError, 'Size spec in ADSC-header does not match ' + \ 'size of image data field' self.bytecode = numpy.uint16 logger.info('adscimage using high byte first (network order)') self.resetvals() return self def _readheader(self, infile): """ read an adsc header """ line = infile.readline() bytesread = len(line) while '}' not in line: if '=' in line: (key, val) = line.split('=') self.header_keys.append(key.strip()) self.header[key.strip()] = val.strip(' ;\n') line = infile.readline() bytesread = bytesread + len(line) def write(self, fname): """ Write adsc format """ out = '{\n' for key in self.header_keys: out += "%s = %s;\n" % (key, self.header[key]) # FIXME ??? - made padding match header bytes keyword # the cbflib example image has exactly 512... if self.header.has_key("HEADER_BYTES"): pad = int(self.header["HEADER_BYTES"]) - len(out) - 2 else: # integer division # 1234567890123456789012 # HEADER_BYTES = 1234;\n hsize = ((len(out) + 23) / 512 + 1) * 512 out += "HEADER_BYTES=%d;\n" % (hsize) pad = hsize - len(out) - 2 out += pad * ' ' + "}\n" assert len(out) % 512 == 0 , "Header is not multiple of 512" outf = open(fname, "wb") outf.write(out) # it says "unsigned_short" ? ... jpw example has: # BYTE_ORDER=big_endian; # TYPE=unsigned_short; if "little" in self.header["BYTE_ORDER"]: outf.write(self.data.astype(numpy.uint16).tostring()) else: outf.write(self.data.byteswap().astype( numpy.uint16).tostring()) outf.close() def test(): """ testcase """ import sys, time img = adscimage() begin = time.clock() while (sys.argv[1:]): img.read(sys.argv[1]) # rim = img.toPIL16() img.rebin(2, 2) img.write('jegErEnFil0000.img') print sys.argv[1] + ": max=%d, min=%d, mean=%.2e, stddev=%.2e" % (\ img.getmax(), img.getmin(), img.getmean(), img.getstddev()) print 'integrated intensity (%d %d %d %d) =%.3f' % (\ 10, 20, 20, 40, img.integrate_area((10, 20, 20, 40))) sys.argv[1:] = sys.argv[2:] end = time.clock() print end - begin if __name__ == '__main__': test() fabio-0.1.3/fabio-src/edfimage.py0000644000175000017500000010742712233175220017347 0ustar jeromejerome00000000000000#!/usr/bin/env python # -*- coding: utf8 -*- """ License: GPLv2+ Authors: ........ * Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions; Risoe National Laboratory; Frederiksborgvej 399; DK-4000 Roskilde; email:erik.knudsen@risoe.dk * Jon Wright & Jérôme Kieffer: European Synchrotron Radiation Facility; Grenoble (France) """ from __future__ import with_statement import os, logging, types logger = logging.getLogger("edfimage") import numpy from fabioimage import fabioimage from fabioutils import isAscii, toAscii, nice_int from compression import decBzip2, decGzip, decZlib BLOCKSIZE = 512 DATA_TYPES = { "SignedByte" : numpy.int8, "Signed8" : numpy.int8, "UnsignedByte" : numpy.uint8, "Unsigned8" : numpy.uint8, "SignedShort" : numpy.int16, "Signed16" : numpy.int16, "UnsignedShort" : numpy.uint16, "Unsigned16" : numpy.uint16, "UnsignedShortInteger" : numpy.uint16, "SignedInteger" : numpy.int32, "Signed32" : numpy.int32, "UnsignedInteger": numpy.uint32, "Unsigned32" : numpy.uint32, "SignedLong" : numpy.int32, "UnsignedLong" : numpy.uint32, "Signed64" : numpy.int64, "Unsigned64" : numpy.uint64, "FloatValue" : numpy.float32, "FLOATVALUE" : numpy.float32, "FLOAT" : numpy.float32, # fit2d "Float" : numpy.float32, # fit2d "FloatIEEE32" : numpy.float32, "Float32" : numpy.float32, "Double" : numpy.float64, "DoubleValue" : numpy.float64, "FloatIEEE64" : numpy.float64, "DoubleIEEE64" : numpy.float64} try: DATA_TYPES["FloatIEEE128" ] = numpy.float128 DATA_TYPES["DoubleIEEE128" ] = numpy.float128 DATA_TYPES["QuadrupleValue" ] = numpy.float128 except AttributeError: # not in your numpy pass NUMPY_EDF_DTYPE = {"int8" :"SignedByte", "int16" :"SignedShort", "int32" :"SignedInteger", "int64" :"Signed64", "uint8" :"UnsignedByte", "uint16" :"UnsignedShort", "uint32" :"UnsignedInteger", "uint64" :"Unsigned64", "float32" :"FloatValue", "float64" :"DoubleValue", "float128" :"QuadrupleValue", } MINIMUM_KEYS = ['HEADERID', 'IMAGE', 'BYTEORDER', 'DATATYPE', 'DIM_1', 'DIM_2', 'SIZE'] # Size is thought to be essential for writing at least DEFAULT_VALUES = { # I do not define default values as they will be calculated at write time # JK20110415 } class Frame(object): """ A class representing a single frame in an EDF file """ def __init__(self, data=None, header=None, header_keys=None, number=None): if header is None: self.header = {} else: self.header = dict(header) if header_keys is None: self.header_keys = self.header.keys() else: self.header_keys = header_keys[:] for key in header_keys: if key not in self.header: logger.warning("Header key %s, in header_keys is not in header dictionary, poping !!!" % key) self.header_keys.remove(key) self.capsHeader = {} for key in self.header_keys: try: self.capsHeader[key.upper()] = key except AttributeError: logger.warning("Header key %s is not a string" % key) self._data = data self.dims = [] self.dim1 = 0 self.dim2 = 0 self.start = None # Position of start of raw data in file self.size = None # size of raw data in file self.file = None # opened file object with locking capabilities !!! self.bpp = None self._bytecode = None if (number is not None) and isinstance(number, int): self.iFrame = number else: self.iFrame = 0 def parseheader(self, block): """ Parse the header in some EDF format from an already open file @param block: string representing the header block @type block: string, should be full ascii @return: size of the binary blob """ #reset values ... self.header = {} self.capsHeader = {} self.header_keys = [] self.size = None calcsize = 1 self.dims = [] for line in block.split(';'): if '=' in line: key, val = line.split('=' , 1) # Why would someone put null bytes in a header? key = key.replace("\x00"," ").strip() self.header[key] = val.replace("\x00"," ").strip() self.capsHeader[key.upper()] = key self.header_keys.append(key) # Compute image size if "SIZE" in self.capsHeader: try: self.size = nice_int(self.header[self.capsHeader["SIZE"]]) except ValueError: logger.warning("Unable to convert to integer : %s %s " % (self.capsHeader["SIZE"], self.header[self.capsHeader["SIZE"]])) if "DIM_1" in self.capsHeader: try: dim1 = nice_int(self.header[self.capsHeader['DIM_1']]) except ValueError: logger.error("Unable to convert to integer Dim_1: %s %s" % (self.capsHeader["DIM_1"], self.header[self.capsHeader["DIM_1"]])) else: calcsize *= dim1 self.dims.append(dim1) else: logger.error("No Dim_1 in headers !!!") if "DIM_2" in self.capsHeader: try: dim2 = nice_int(self.header[self.capsHeader['DIM_2']]) except ValueError: logger.error("Unable to convert to integer Dim_3: %s %s" % (self.capsHeader["DIM_2"], self.header[self.capsHeader["DIM_2"]])) else: calcsize *= dim2 self.dims.append(dim2) else: logger.error("No Dim_2 in headers !!!") iDim = 3 # JON: this appears to be for nD images, but we don't treat those while iDim is not None: strDim = "DIM_%i" % iDim if strDim in self.capsHeader: try: dim3 = nice_int(self.header[self.capsHeader[strDim]]) except ValueError: logger.error("Unable to convert to integer %s: %s %s" % (strDim, self.capsHeader[strDim], self.header[self.capsHeader[strDim]])) dim3 = None iDim = None else: if dim3 > 1: # Otherwise treat dim3==1 as a 2D image calcsize *= dim3 self.dims.append(dim3) iDim += 1 else: logger.debug("No Dim_3 -> it is a 2D image") iDim = None if self._bytecode is None: if "DATATYPE" in self.capsHeader: self._bytecode = DATA_TYPES[self.header[self.capsHeader['DATATYPE']]] else: self._bytecode = numpy.uint16 logger.warning("Defaulting type to uint16") self.bpp = len(numpy.array(0, self._bytecode).tostring()) calcsize *= self.bpp if (self.size is None): self.size = calcsize elif (self.size != calcsize): if ("COMPRESSION" in self.capsHeader) and (self.header[self.capsHeader['COMPRESSION']].upper().startswith("NO")): logger.info("Mismatch between the expected size %s and the calculated one %s" % (self.size, calcsize)) self.size = calcsize for i, n in enumerate(self.dims): setattr(self, "dim%i" % (i + 1), n) return self.size def swap_needed(self): """ Decide if we need to byteswap """ if ('Low' in self.header[self.capsHeader['BYTEORDER']] and numpy.little_endian) or \ ('High' in self.header[self.capsHeader['BYTEORDER']] and not numpy.little_endian): return False if ('High' in self.header[self.capsHeader['BYTEORDER']] and numpy.little_endian) or \ ('Low' in self.header[self.capsHeader['BYTEORDER']] and not numpy.little_endian): if self.bpp in [2, 4, 8]: return True else: return False def getData(self): """ Unpack a binary blob according to the specification given in the header @return: dataset as numpy.ndarray """ data = None if self._data is not None: data = self._data elif self.file is None: data = self._data else: if self._bytecode is None: if "DATATYPE" in self.capsHeader: self._bytecode = DATA_TYPES[self.header[self.capsHeader["DATATYPE"]]] else: self._bytecode = numpy.uint16 dims = self.dims[:] dims.reverse() with self.file.lock: if self.file.closed: logger.error("file: %s from %s is closed. Cannot read data." % (self.file, self.file.filename)) return else: self.file.seek(self.start) fileData = self.file.read(self.size) if ("COMPRESSION" in self.capsHeader): compression = self.header[self.capsHeader["COMPRESSION"]].upper() uncompressed_size = self.bpp for i in dims: uncompressed_size *= i if "OFFSET" in compression : try: import byte_offset#IGNORE:F0401 except ImportError, error: logger.error("Unimplemented compression scheme: %s (%s)" % (compression, error)) else: myData = byte_offset.analyseCython(fileData, size=uncompressed_size) rawData = myData.astype(self._bytecode).tostring() self.size = uncompressed_size elif compression == "NONE": rawData = fileData elif "GZIP" in compression: rawData = decGzip(fileData) self.size = uncompressed_size elif "BZ" in compression : rawData = decBzip2(fileData) self.size = uncompressed_size elif "Z" in compression : rawData = decZlib(fileData) self.size = uncompressed_size else: logger.warning("Unknown compression scheme %s" % compression) rawData = fileData else: rawData = fileData expected = self.size obtained = len(rawData) if expected > obtained: logger.error("Data stream is incomplete: %s < expected %s bytes" % (obtained, expected)) rawData += "\x00" * (expected - obtained) elif expected < len(rawData): logger.info("Data stream contains trailing junk : %s > expected %s bytes" % (obtained, expected)) rawData = rawData[:expected] if self.swap_needed(): data = numpy.fromstring(rawData, self._bytecode).byteswap().reshape(tuple(dims)) else: data = numpy.fromstring(rawData, self._bytecode).reshape(tuple(dims)) self._data = data self._bytecode = data.dtype.type return data def setData(self, npa=None): """Setter for data in edf frame""" self._data = npa data = property(getData, setData, "property: (edf)frame.data, uncompress the datablock when needed") def getByteCode(self): if self._bytecode is None: self._bytecode = self.data.dtype.type return self._bytecode def setByteCode(self, _iVal): self._bytecode = _iVal bytecode = property(getByteCode, setByteCode) def getEdfBlock(self, force_type=None, fit2dMode=False): """ @param force_type: type of the dataset to be enforced like "float64" or "uint16" @type force_type: string or numpy.dtype @param fit2dMode: enforce compatibility with fit2d and starts countimg number of images at 1 @type fit2dMode: boolean @return: ascii header block @rtype: python string with the concatenation of the ascii header and the binary data block """ if force_type is not None: data = self.data.astype(force_type) else: data = self.data fit2dMode = bool(fit2dMode) for key in self.header: KEY = key.upper() if KEY not in self.capsHeader: self.capsHeader[KEY] = key if key not in self.header_keys: self.header_keys.append(key) header = self.header.copy() header_keys = self.header_keys[:] capsHeader = self.capsHeader.copy() listHeader = ["{\n"] # First of all clean up the headers: for i in capsHeader: if "DIM_" in i: header.pop(capsHeader[i]) header_keys.remove(capsHeader[i]) for KEY in ["SIZE", "EDF_BINARYSIZE", "EDF_HEADERSIZE", "BYTEORDER", "DATATYPE", "HEADERID", "IMAGE"]: if KEY in capsHeader: header.pop(capsHeader[KEY]) header_keys.remove(capsHeader[KEY]) if "EDF_DATABLOCKID" in capsHeader: header_keys.remove(capsHeader["EDF_DATABLOCKID"]) #but do not remove the value from dict, instead reset the key ... if capsHeader["EDF_DATABLOCKID"] != "EDF_DataBlockID": header["EDF_DataBlockID"] = header.pop(capsHeader["EDF_DATABLOCKID"]) capsHeader["EDF_DATABLOCKID"] = "EDF_DataBlockID" # Then update static headers freshly deleted header_keys.insert(0, "Size") header["Size"] = len(data.tostring()) header_keys.insert(0, "HeaderID") header["HeaderID"] = "EH:%06d:000000:000000" % (self.iFrame + fit2dMode) header_keys.insert(0, "Image") header["Image"] = str(self.iFrame + fit2dMode) dims = list(data.shape) nbdim = len(dims) for i in dims: key = "Dim_%i" % nbdim header[key] = i header_keys.insert(0, key) nbdim -= 1 header_keys.insert(0, "DataType") header["DataType"] = NUMPY_EDF_DTYPE[str(numpy.dtype(data.dtype))] header_keys.insert(0, "ByteOrder") if numpy.little_endian: header["ByteOrder"] = "LowByteFirst" else: header["ByteOrder"] = "HighByteFirst" approxHeaderSize = 100 for key in header: approxHeaderSize += 7 + len(key) + len(str(header[key])) approxHeaderSize = BLOCKSIZE * (approxHeaderSize // BLOCKSIZE + 1) header_keys.insert(0, "EDF_HeaderSize") header["EDF_HeaderSize"] = "%5s" % (approxHeaderSize) header_keys.insert(0, "EDF_BinarySize") header["EDF_BinarySize"] = len(data.tostring()) header_keys.insert(0, "EDF_DataBlockID") if not "EDF_DataBlockID" in header: header["EDF_DataBlockID"] = "%i.Image.Psd" % (self.iFrame + fit2dMode) preciseSize = 4 #2 before {\n 2 after }\n for key in header_keys: #Escape keys or values that are no ascii strKey = str(key) if not isAscii(strKey, listExcluded=["}", "{"]): logger.warning("Non ascii key %s, skipping" % strKey) continue strValue = str(header[key]) if not isAscii(strValue, listExcluded=["}", "{"]): logger.warning("Non ascii value %s, skipping" % strValue) continue line = strKey + " = " + strValue + " ;\n" preciseSize += len(line) listHeader.append(line) if preciseSize > approxHeaderSize: logger.error("I expected the header block only at %s in fact it is %s" % (approxHeaderSize, preciseSize)) for idx, line in enumerate(listHeader[:]): if line.startswith("EDF_HeaderSize"): headerSize = BLOCKSIZE * (preciseSize // BLOCKSIZE + 1) newline = "EDF_HeaderSize = %5s ;\n" % headerSize delta = len(newline) - len(line) if (preciseSize // BLOCKSIZE) != ((preciseSize + delta) // BLOCKSIZE): headerSize = BLOCKSIZE * ((preciseSize + delta) // BLOCKSIZE + 1) newline = "EDF_HeaderSize = %5s ;\n" % headerSize preciseSize = preciseSize + delta listHeader[idx] = newline break else: headerSize = approxHeaderSize listHeader.append(" "*(headerSize - preciseSize) + "}\n") return "".join(listHeader) + data.tostring() class edfimage(fabioimage): """ Read and try to write the ESRF edf data format """ def __init__(self, data=None , header=None, header_keys=None, frames=None): self.currentframe = 0 self.filesize = None try: dim = len(data.shape) except Exception, error: #IGNORE:W0703 logger.debug("Data don't look like a numpy array (%s), resetting all!!" % error) data = None dim = 0 fabioimage.__init__(self, data, header) if dim == 2: fabioimage.__init__(self, data, header) elif dim == 1 : data.shape = (0, len(data)) fabioimage.__init__(self, data, header) elif dim == 3 : fabioimage.__init__(self, data[0, :, :], header) elif dim == 4 : fabioimage.__init__(self, data[0, 0, :, :], header) elif dim == 5 : fabioimage.__init__(self, data[0, 0, 0, :, :], header) if frames is None: frame = Frame(data=self.data, header=self.header, header_keys=header_keys , number=self.currentframe) self.__frames = [frame] else: self.__frames = frames @staticmethod def checkHeader(header=None): """ Empty for fabioimage but may be populated by others classes """ if type(header) != types.DictionaryType: return {} new = {} for key, value in header.items(): new[toAscii(key, ";{}")] = toAscii(value, ";{}") return new @staticmethod def _readHeaderBlock(infile): """ Read in a header in some EDF format from an already open file @param infile: file object open in read mode @return: string (or None if no header was found. """ MAX_HEADER_SIZE = BLOCKSIZE * 20 block = infile.read(BLOCKSIZE) if len(block) < BLOCKSIZE: logger.debug("Under-short header: only %i bytes in %s" % (len(block), infile.name)) return if (block.find("{") < 0) : # This does not look like an edf file logger.warning("no opening {. Corrupt header of EDF file %s" % infile.name) return if "EDF_HeaderSize" in block: start = block.index("EDF_HeaderSize") chunk = block[start:].split("=")[1].strip() try: new_max_header_size = int(chunk.split(";")[0].strip()) except Exception: logger.warning("Unable to read header size in %s" % chunk) else: if new_max_header_size > MAX_HEADER_SIZE: logger.info("Redefining MAX_HEADER_SIZE to %s" % new_max_header_size) MAX_HEADER_SIZE = new_max_header_size while '}' not in block: block = block + infile.read(BLOCKSIZE) if len(block) > MAX_HEADER_SIZE: logger.warning("Runaway header in EDF file MAX_HEADER_SIZE: %s \n%s" % (MAX_HEADER_SIZE, block)) return start = block.find("{") + 1 end = block.find("}") # Now it is essential to go to the start of the binary part if block[end: end + 3] == "}\r\n": offset = end + 3 - len(block) elif block[end: end + 2] == "}\n": offset = end + 2 - len(block) else: logger.error("Unable to locate start of the binary section") offset = None if offset is not None: infile.seek(offset, os.SEEK_CUR) return block[start:end] def _readheader(self, infile): """ Read all headers in a file and populate self.header data is not yet populated @type infile: file object open in read mode """ self.__frames = [] bContinue = True while bContinue: block = self._readHeaderBlock(infile) if block is None: bContinue = False break frame = Frame(number=self.nframes) size = frame.parseheader(block) frame.file = infile frame.start = infile.tell() frame.size = size self.__frames += [frame] try: infile.seek(size, os.SEEK_CUR) except Exception, error: logger.warning("infile is %s" % infile) logger.warning("Position is %s" % infile.tell()) logger.warning("size is %s" % size) logger.error("It seams this error occurs under windows when reading a (large-) file over network: %s ", error) raise Exception(error) if frame.start + size > infile.size: logger.warning("Non complete datablock: got %s, expected %s" % (infile.size - frame.start, size)) bContinue = False break for i, frame in enumerate(self.__frames): missing = [] for item in MINIMUM_KEYS: if item not in frame.capsHeader: missing.append(item) if len(missing) > 0: logger.info("EDF file %s frame %i misses mandatory keys: %s " % (self.filename, i, " ".join(missing))) self.currentframe = 0 def read(self, fname, frame=None): """ Read in header into self.header and the data into self.data """ self.resetvals() self.filename = fname infile = self._open(fname, "rb") self._readheader(infile) if frame is None: pass elif frame < self.nframes: self = self.getframe(frame) else: logger.error("Reading file %s You requested frame %s but only %s frames are available", fname, frame, self.nframes) self.resetvals() # ensure the PIL image is reset self.pilimage = None return self def swap_needed(self): """ Decide if we need to byteswap """ if ('Low' in self.header[self.capsHeader['BYTEORDER']] and numpy.little_endian) or \ ('High' in self.header[self.capsHeader['BYTEORDER']] and not numpy.little_endian): return False if ('High' in self.header[self.capsHeader['BYTEORDER']] and numpy.little_endian) or \ ('Low' in self.header[self.capsHeader['BYTEORDER']] and not numpy.little_endian): if self.bpp in [2, 4, 8]: return True else: return False def unpack(self): """ Unpack a binary blob according to the specification given in the header and return the dataset @return: dataset as numpy.ndarray """ return self.__frames[self.currentframe].getData() def getframe(self, num): """ returns the file numbered 'num' in the series as a fabioimage """ newImage = None if self.nframes == 1: logger.debug("Single frame EDF; having fabioimage default behavour: %s" % num) newImage = fabioimage.getframe(self, num) elif num in xrange(self.nframes): logger.debug("Multi frame EDF; having edfimage specific behavour: %s/%s" % (num, self.nframes)) newImage = edfimage(frames=self.__frames) newImage.currentframe = num newImage.filename = self.filename else: txt = "Cannot access frame: %s/%s" % (num, self.nframes) logger.error(txt) raise ValueError("edfimage.getframe:" + txt) return newImage def previous(self): """ returns the previous file in the series as a fabioimage """ newImage = None if self.nframes == 1: newImage = fabioimage.previous(self) else: newFrameId = self.currentframe - 1 newImage = self.getframe(newFrameId) return newImage def next(self): """ returns the next file in the series as a fabioimage """ newImage = None if self.nframes == 1: newImage = fabioimage.next(self) else: newFrameId = self.currentframe + 1 newImage = self.getframe(newFrameId) return newImage def write(self, fname, force_type=None, fit2dMode=False): """ Try to write a file check we can write zipped also mimics that fabian was writing uint16 (we sometimes want floats) @param force_type: can be numpy.uint16 or simply "float" @return: None """ with self._open(fname, mode="wb") as outfile: for i, frame in enumerate(self.__frames): frame.iFrame = i outfile.write(frame.getEdfBlock(force_type=force_type, fit2dMode=fit2dMode)) def appendFrame(self, frame=None, data=None, header=None): """ Method used add a frame to an EDF file @param frame: frame to append to edf image @type frame: instance of Frame @return: None """ if isinstance(frame, Frame): self.__frames.append(frame) else: self.__frames.append(Frame(data, header)) def deleteFrame(self, frameNb=None): """ Method used to remove a frame from an EDF image. by default the last one is removed. @param frameNb: frame number to remove, by default the last. @type frameNb: integer @return: None """ if frameNb is None: self.__frames.pop() else: self.__frames.pop(frameNb) def fastReadData(self, filename=None): """ This is a special method that will read and return the data from another file ... The aim is performances, ... but only supports uncompressed files. @return: data from another file using positions from current edfimage """ if (filename is None) or not os.path.isfile(filename): raise RuntimeError("edfimage.fastReadData is only valid with another file: %s does not exist" % (filename)) data = None frame = self.__frames[self.currentframe] with open(filename, "rb")as f: f.seek(frame.start) raw = f.read(frame.size) try: data = numpy.fromstring(raw, dtype=self.bytecode) data.shape = self.data.shape except Exception, err : logger.error("unable to convert file content to numpy array: %s", err) return data def fastReadROI(self, filename, coords=None): """ Method reading Region of Interest of another file based on metadata available in current edfimage. The aim is performances, ... but only supports uncompressed files. @return: ROI-data from another file using positions from current edfimage @rtype: numpy 2darray """ if (filename is None) or not os.path.isfile(filename): raise RuntimeError("edfimage.fastReadData is only valid with another file: %s does not exist" % (filename)) data = None frame = self.__frames[self.currentframe] if len(coords) == 4: slice1 = self.make_slice(coords) elif len(coords) == 2 and isinstance(coords[0], slice) and \ isinstance(coords[1], slice): slice1 = coords else: logger.warning('readROI: Unable to understand Region Of Interest: got %s', coords) return d1 = self.data.shape[-1] start0 = slice1[0].start start1 = slice1[1].start slice2 = (slice(0, slice1[0].stop - start0, slice1[0].step), slice(0, slice1[1].stop - start1, slice1[1].step)) start = frame.start + self.bpp * (d1 * start0 + start1) size = self.bpp * ((slice2[0].stop) * d1) with open(filename, "rb")as f: f.seek(start) raw = f.read(size) try: data = numpy.fromstring(raw, dtype=self.bytecode) data.shape = -1, d1 except Exception, err : logger.error("unable to convert file content to numpy array: %s", err) return data[slice2] ################################################################################ # Properties definition for header, data, header_keys and capsHeader ################################################################################ def getNbFrames(self): """ Getter for number of frames """ return len(self.__frames) def setNbFrames(self, val): """ Setter for number of frames ... should do nothing. Here just to avoid bugs """ if val != len(self.__frames): logger.warning("trying to set the number of frames ") nframes = property(getNbFrames, setNbFrames, "property: number of frames in EDF file") def getHeader(self): """ Getter for the headers. used by the property header, """ return self.__frames[self.currentframe].header def setHeader(self, _dictHeader): """ Enforces the propagation of the header to the list of frames """ try: self.__frames[self.currentframe].header = _dictHeader except AttributeError: self.__frames = [Frame(header=_dictHeader)] except IndexError: if self.currentframe < len(self.__frames): self.__frames.append(Frame(header=_dictHeader)) def delHeader(self): """ Deleter for edf header """ self.__frames[self.currentframe].header = {} header = property(getHeader, setHeader, delHeader, "property: header of EDF file") def getHeaderKeys(self): """ Getter for edf header_keys """ return self.__frames[self.currentframe].header_keys def setHeaderKeys(self, _listtHeader): """ Enforces the propagation of the header_keys to the list of frames @param _listtHeader: list of the (ordered) keys in the header @type _listtHeader: python list """ try: self.__frames[self.currentframe].header_keys = _listtHeader except AttributeError: self.__frames = [Frame(header_keys=_listtHeader)] except IndexError: if self.currentframe < len(self.__frames): self.__frames.append(Frame(header_keys=_listtHeader)) def delHeaderKeys(self): """ Deleter for edf header_keys """ self.__frames[self.currentframe].header_keys = [] header_keys = property(getHeaderKeys, setHeaderKeys, delHeaderKeys, "property: header_keys of EDF file") def getData(self): """ getter for edf Data @return: data for current frame @rtype: numpy.ndarray """ npaData = None try: npaData = self.__frames[self.currentframe].data except AttributeError: self.__frames = [Frame()] npaData = self.__frames[self.currentframe].data except IndexError: if self.currentframe < len(self.__frames): self.__frames.append(Frame()) npaData = self.__frames[self.currentframe].data return npaData def setData(self, _data): """ Enforces the propagation of the data to the list of frames @param _data: numpy array representing data """ try: self.__frames[self.currentframe].data = _data except AttributeError: self.__frames = [Frame(data=_data)] except IndexError: if self.currentframe < len(self.__frames): self.__frames.append(Frame(data=_data)) def delData(self): """ deleter for edf Data """ self.__frames[self.currentframe].data = None data = property(getData, setData, delData, "property: data of EDF file") def getCapsHeader(self): """ getter for edf headers keys in upper case @return: data for current frame @rtype: dict """ return self.__frames[self.currentframe].capsHeader def setCapsHeader(self, _data): """ Enforces the propagation of the header_keys to the list of frames @param _data: numpy array representing data """ self.__frames[self.currentframe].capsHeader = _data def delCapsHeader(self): """ deleter for edf capsHeader """ self.__frames[self.currentframe].capsHeader = {} capsHeader = property(getCapsHeader, setCapsHeader, delCapsHeader, "property: capsHeader of EDF file, i.e. the keys of the header in UPPER case.") def getDim1(self): return self.__frames[self.currentframe].dim1 def setDim1(self, _iVal): try: self.__frames[self.currentframe].dim1 = _iVal except AttributeError: self.__frames = [Frame()] except IndexError: if self.currentframe < len(self.__frames): self.__frames.append(Frame()) self.__frames[self.currentframe].dim1 = _iVal dim1 = property(getDim1, setDim1) def getDim2(self): return self.__frames[self.currentframe].dim2 def setDim2(self, _iVal): try: self.__frames[self.currentframe].dim2 = _iVal except AttributeError: self.__frames = [Frame()] except IndexError: if self.currentframe < len(self.__frames): self.__frames.append(Frame()) self.__frames[self.currentframe].dim2 = _iVal dim2 = property(getDim2, setDim2) def getDims(self): return self.__frames[self.currentframe].dims dims = property(getDims) def getByteCode(self): return self.__frames[self.currentframe].bytecode def setByteCode(self, _iVal): try: self.__frames[self.currentframe].bytecode = _iVal except AttributeError: self.__frames = [Frame()] except IndexError: if self.currentframe < len(self.__frames): self.__frames.append(Frame()) self.__frames[self.currentframe].bytecode = _iVal bytecode = property(getByteCode, setByteCode) def getBpp(self): return self.__frames[self.currentframe].bpp def setBpp(self, _iVal): try: self.__frames[self.currentframe].bpp = _iVal except AttributeError: self.__frames = [Frame()] except IndexError: if self.currentframe < len(self.__frames): self.__frames.append(Frame()) self.__frames[self.currentframe].bpp = _iVal bpp = property(getBpp, setBpp) fabio-0.1.3/fabio-src/readbytestream.py0000644000175000017500000000477212120434325020617 0ustar jeromejerome00000000000000#!/usr/bin/env python #coding: utf8 """ Reads a bytestream Authors: Jon Wright Henning O. Sorensen & Erik Knudsen ESRF Risoe National Laboratory """ import numpy, logging logger = logging.getLogger("readbytestream") DATATYPES = { # type sign bytes ("int", 'n', 1) : numpy.uint8, ("int", 'n', 2) : numpy.uint16, ("int", 'n', 4) : numpy.uint32, ("int", 'y', 1) : numpy.int8, ("int", 'y', 2) : numpy.int16, ("int", 'y', 4) : numpy.int32, ('float', 'y', 4) : numpy.float32, # does this occur in bruker? ('double', 'y', 4): numpy.float64 } def readbytestream(fil, offset, x, y, nbytespp, datatype='int', signed='n', swap='n', typeout=numpy.uint16): """ Reads in a bytestream from a file (which may be a string indicating a filename, or an already opened file (should be "rb")) offset is the position (in bytes) where the pixel data start nbytespp = number of bytes per pixel type can be int or float (4 bytes pp) or double (8 bytes pp) signed: normally signed data 'y', but 'n' to try to get back the right numbers when unsigned data are converted to signed (python once had no unsigned numeric types.) swap, normally do not bother, but 'y' to swap bytes typeout is the numpy type to output, normally uint16, but more if overflows occurred x and y are the pixel dimensions TODO : Read in regions of interest PLEASE LEAVE THE STRANGE INTERFACE ALONE - IT IS USEFUL FOR THE BRUKER FORMAT """ tin = "dunno" length = nbytespp * x * y # bytes per pixel times number of pixels if datatype in ['float', 'double']: signed = 'y' key = (datatype, signed, nbytespp) try: tin = DATATYPES[key] except: logging.warning("datatype,signed,nbytespp " + str(key)) raise Exception("Unknown combination of types to readbytestream") # Did we get a string (filename) or a readable stream object? if hasattr(fil, "read") and hasattr(fil, "seek"): infile = fil opened = False else: infile = open(fil, 'rb') opened = True infile.seek(offset) arr = numpy.array(numpy.reshape( numpy.fromstring( infile.read(length), tin) , (x, y)), typeout) if swap == 'y': arr = arr.byteswap() if opened: infile.close() return arr fabio-0.1.3/fabio-src/GEimage_old.py0000644000175000017500000005016712233175156017750 0ustar jeromejerome00000000000000 #!/usr/bin/env python """ Reads the header from a GE a-Si Angio Detector Authors: Henning O. Sorensen & Erik Knudsen Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk + Jon Wright, ESRF The header information has been taken from the script read_GEaSi_data.py by Antonino Miceli Thu Jan 4 13:46:31 CST 2007 """ import numpy from fabioimage import fabioimage class GEimage(fabioimage): def _readheader(self, infile): infile.seek(0) # ADEPT self.ImageFormat = infile.read(10) # USHORT --> "=H" # ULONG --> "=L" # = means byte order is native self.header['HeaderVersion'] = numpy.fromstring(infile.read(2), numpy.uint16)[0] self.header['HeaderSizeInBytes'] = int(numpy.fromstring(infile.read(4), numpy.uint32)[0]) self.header['UserHeaderVersion'] = numpy.fromstring(infile.read(2), numpy.uint16)[0] self.header['UserHeaderSizeInBytes'] = int(numpy.fromstring(infile.read(4), numpy.uint32)[0]) self.header['NumberOfFrames'] = numpy.fromstring(infile.read(2), numpy.uint16)[0] self.header['NumberOfRowsInFrame'] = numpy.fromstring(infile.read(2), numpy.uint16)[0] self.header['NumberOfColsInFrame'] = numpy.fromstring(infile.read(2), numpy.uint16)[0] self.header['BitsPerPixel'] = numpy.fromstring(infile.read(2), numpy.uint16)[0] self.header['AcquisitionDate'] = infile.read(20) self.header['AcquisitionTime'] = infile.read(20) self.DUTID = infile.read(20) self.header['Operator'] = infile.read(50) self.header['DetectorSignature'] = infile.read(20) self.header['TestSystemName'] = infile.read(20) self.header['TestStationRevision'] = infile.read(20) self.header['CoreBundleRevision'] = infile.read(20) self.header['AcquisitionName'] = infile.read(40) self.header['AcquisitionParameterRevision'] = infile.read(20) # self.OriginalNumberOfRows = infile.read(2) # self.OriginalNumberOfRows = struct.unpack("=H",self.OriginalNumberOfRows)[0] # self.OriginalNumberOfColumns = infile.read(2) # self.OriginalNumberOfColumns = struct.unpack("=H",self.OriginalNumberOfColumns)[0] # self.RowNumberUpperLeftPointArchiveROI = infile.read(2) # self.RowNumberUpperLeftPointArchiveROI = struct.unpack("=H",self.RowNumberUpperLeftPointArchiveROI)[0] # self.ColNumberUpperLeftPointArchiveROI = infile.read(2) # self.ColNumberUpperLeftPointArchiveROI = struct.unpack("=H",self.ColNumberUpperLeftPointArchiveROI)[0] # self.Swapped = infile.read(2) # self.Swapped = struct.unpack("=H",self.Swapped)[0] # self.Reordered = infile.read(2) # self.Reordered = struct.unpack("=H",self.Reordered)[0] # self.HorizontalFlipped = infile.read(2) # self.HorizontalFlipped = struct.unpack("=H",self.HorizontalFlipped)[0] # self.VerticalFlipped = infile.read(2) # self.VerticalFlipped = struct.unpack("=H",self.VerticalFlipped)[0] # self.WindowValueDesired = infile.read(2) # self.WindowValueDesired = struct.unpack("=H",self.WindowValueDesired)[0] # self.LevelValueDesired = infile.read(2) # self.LevelValueDesired = struct.unpack("=H",self.LevelValueDesired)[0] # self.AcquisitionMode = infile.read(2) # self.AcquisitionMode = struct.unpack("=H",self.AcquisitionMode)[0] # self.AcquisitionType = infile.read(2) # self.AcquisitionType = struct.unpack("=H",self.AcquisitionType)[0] # self.UserAcquisitionCoffFileName1 = infile.read(100) # self.UserAcquisitionCoffFileName2 = infile.read(100) # self.FramesBeforeExpose = infile.read(2) # self.FramesBeforeExpose = struct.unpack("=H",self.FramesBeforeExpose)[0] # self.FramesDuringExpose = infile.read(2) # self.FramesDuringExpose = struct.unpack("=H",self.FramesDuringExpose)[0] # self.FramesAfterExpose = infile.read(2) # self.FramesAfterExpose = struct.unpack("=H",self.FramesAfterExpose)[0] # self.IntervalBetweenFrames = infile.read(2) # self.IntervalBetweenFrames = struct.unpack("=H",self.IntervalBetweenFrames)[0] # self.ExposeTimeDelayInMicrosecs = infile.read(8) # self.ExposeTimeDelayInMicrosecs = struct.unpack("=d",self.ExposeTimeDelayInMicrosecs)[0] # self.TimeBetweenFramesInMicrosecs = infile.read(8) # self.TimeBetweenFramesInMicrosecs = struct.unpack("=d",self.TimeBetweenFramesInMicrosecs)[0] # self.FramesToSkipExpose = infile.read(2) # self.FramesToSkipExpose = struct.unpack("=H",self.FramesToSkipExpose)[0] # # Rad --> ExposureMode = 1 # self.ExposureMode = infile.read(2) # self.ExposureMode = struct.unpack("=H",self.ExposureMode)[0] # self.PrepPresetTimeInMicrosecs = infile.read(8) # self.PrepPresetTimeInMicrosecs = struct.unpack("=d",self.PrepPresetTimeInMicrosecs)[0] # self.ExposePresetTimeInMicrosecs = infile.read(8) # self.ExposePresetTimeInMicrosecs = struct.unpack("=d",self.ExposePresetTimeInMicrosecs)[0] # self.AcquisitionFrameRateInFps = infile.read(4) # self.AcquisitionFrameRateInFps = struct.unpack("=f",self.AcquisitionFrameRateInFps)[0] # self.FOVSelect = infile.read(2) # self.FOVSelect = struct.unpack("=H",self.FOVSelect)[0] # self.ExpertMode = infile.read(2) # self.ExpertMode = struct.unpack("=H",self.ExpertMode)[0] # self.SetVCommon1 = infile.read(8) # self.SetVCommon1 = struct.unpack("=d",self.SetVCommon1)[0] # self.SetVCommon2 = infile.read(8) # self.SetVCommon2 = struct.unpack("=d",self.SetVCommon2)[0] # self.SetAREF = infile.read(8) # self.SetAREF = struct.unpack("=d",self.SetAREF)[0] # self.SetAREFTrim = infile.read(4) # self.SetAREFTrim = struct.unpack("=L",self.SetAREFTrim)[0] # self.SetSpareVoltageSource = infile.read(8) # self.SetSpareVoltageSource = struct.unpack("=d",self.SetSpareVoltageSource)[0] # self.SetCompensationVoltageSource = infile.read(8) # self.SetCompensationVoltageSource = struct.unpack("=d",self.SetCompensationVoltageSource)[0] # self.SetRowOffVoltage = infile.read(8) # self.SetRowOffVoltage = struct.unpack("=d",self.SetRowOffVoltage)[0] # self.SetRowOnVoltage = infile.read(8) # self.SetRowOnVoltage = struct.unpack("=d",self.SetRowOnVoltage)[0] # self.StoreCompensationVoltage = infile.read(4) # self.StoreCompensationVoltage = struct.unpack("=L",self.StoreCompensationVoltage)[0] # self.RampSelection = infile.read(2) # self.RampSelection = struct.unpack("=H",self.RampSelection)[0] # self.TimingMode = infile.read(2) # self.TimingMode = struct.unpack("=H",self.TimingMode)[0] # self.Bandwidth = infile.read(2) # self.Bandwidth = struct.unpack("=H",self.Bandwidth)[0] # self.ARCIntegrator = infile.read(2) # self.ARCIntegrator = struct.unpack("=H",self.ARCIntegrator)[0] # self.ARCPostIntegrator = infile.read(2) # self.ARCPostIntegrator = struct.unpack("=H",self.ARCPostIntegrator)[0] # self.NumberOfRows = infile.read(4) # self.NumberOfRows = struct.unpack("=L",self.NumberOfRows)[0] # self.RowEnable = infile.read(2) # self.RowEnable = struct.unpack("=H",self.RowEnable)[0] # self.EnableStretch = infile.read(2) # self.EnableStretch = struct.unpack("=H",self.EnableStretch)[0] # self.CompEnable = infile.read(2) # self.CompEnable = struct.unpack("=H",self.CompEnable)[0] # self.CompStretch = infile.read(2) # self.CompStretch = struct.unpack("=H",self.CompStretch)[0] # self.LeftEvenTristate = infile.read(2) # self.LeftEvenTristate = struct.unpack("=H",self.LeftEvenTristate)[0] # self.RightOddTristate = infile.read(2) # self.RightOddTristate = struct.unpack("=H",self.RightOddTristate)[0] # self.TestModeSelect = infile.read(4) # self.TestModeSelect = struct.unpack("=L",self.TestModeSelect)[0] # self.AnalogTestSource = infile.read(4) # self.AnalogTestSource = struct.unpack("=L",self.AnalogTestSource)[0] # self.VCommonSelect = infile.read(4) # self.VCommonSelect = struct.unpack("=L",self.VCommonSelect)[0] # self.DRCColumnSum = infile.read(4) # self.DRCColumnSum = struct.unpack("=L",self.DRCColumnSum)[0] # self.TestPatternFrameDelta = infile.read(4) # self.TestPatternFrameDelta = struct.unpack("=L",self.TestPatternFrameDelta)[0] # self.TestPatternRowDelta = infile.read(4) # self.TestPatternRowDelta = struct.unpack("=L",self.TestPatternRowDelta)[0] # self.TestPatternColumnDelta = infile.read(4) # self.TestPatternColumnDelta = struct.unpack("=L",self.TestPatternColumnDelta)[0] # self.DetectorHorizontalFlip = infile.read(2) # self.DetectorHorizontalFlip = struct.unpack("=H",self.DetectorHorizontalFlip)[0] # self.DetectorVerticalFlip = infile.read(2) # self.DetectorVerticalFlip = struct.unpack("=H",self.DetectorVerticalFlip)[0] # self.DFNAutoScrubOnOff = infile.read(2) # self.DFNAutoScrubOnOff = struct.unpack("=H",self.DFNAutoScrubOnOff)[0] # self.FiberChannelTimeOutInMicrosecs = infile.read(4) # self.FiberChannelTimeOutInMicrosecs = struct.unpack("=L",self.FiberChannelTimeOutInMicrosecs)[0] # self.DFNAutoScrubDelayInMicrosecs = infile.read(4) # self.DFNAutoScrubDelayInMicrosecs = struct.unpack("=L",self.DFNAutoScrubDelayInMicrosecs)[0] # self.StoreAECROI = infile.read(2) # self.StoreAECROI = struct.unpack("=H",self.StoreAECROI)[0] # self.TestPatternSaturationValue = infile.read(2) # self.TestPatternSaturationValue = struct.unpack("=H",self.TestPatternSaturationValue)[0] # self.TestPatternSeed = infile.read(4) # self.TestPatternSeed = struct.unpack("=L",self.TestPatternSeed)[0] # self.ExposureTimeInMillisecs = infile.read(4) # self.ExposureTimeInMillisecs = struct.unpack("=f",self.ExposureTimeInMillisecs)[0] # self.FrameRateInFps = infile.read(4) # self.FrameRateInFps = struct.unpack("=f",self.FrameRateInFps)[0] # self.kVp = infile.read(4) # self.kVp = struct.unpack("=f",self.kVp)[0] # self.mA = infile.read(4) # self.mA = struct.unpack("=f",self.mA)[0] # self.mAs = infile.read(4) # self.mAs = struct.unpack("=f",self.mAs)[0] # self.FocalSpotInMM = infile.read(4) # self.FocalSpotInMM = struct.unpack("=f",self.FocalSpotInMM)[0] # self.GeneratorType = infile.read(20) # self.StrobeIntensityInFtL = infile.read(4) # self.StrobeIntensityInFtL = struct.unpack("=f",self.StrobeIntensityInFtL)[0] # self.NDFilterSelection = infile.read(2) # self.NDFilterSelection = struct.unpack("=H",self.NDFilterSelection)[0] # self.RefRegTemp1 = infile.read(8) # self.RefRegTemp1 = struct.unpack("=d",self.RefRegTemp1)[0] # self.RefRegTemp2 = infile.read(8) # self.RefRegTemp2 = struct.unpack("=d",self.RefRegTemp2)[0] # self.RefRegTemp3 = infile.read(8) # self.RefRegTemp3 = struct.unpack("=d",self.RefRegTemp3)[0] # self.Humidity1 = infile.read(4) # self.Humidity1 = struct.unpack("=f",self.Humidity1)[0] # self.Humidity2 = infile.read(4) # self.Humidity2 = struct.unpack("=f",self.Humidity2)[0] # self.DetectorControlTemp = infile.read(8) # self.DetectorControlTemp = struct.unpack("=d",self.DetectorControlTemp)[0] # self.DoseValueInmR = infile.read(8) # self.DoseValueInmR = struct.unpack("=d",self.DoseValueInmR)[0] # self.TargetLevelROIRow0 = infile.read(2) # self.TargetLevelROIRow0 = struct.unpack("=H",self.TargetLevelROIRow0)[0] # self.TargetLevelROICol0 = infile.read(2) # self.TargetLevelROICol0 = struct.unpack("=H",self.TargetLevelROICol0)[0] # self.TargetLevelROIRow1 = infile.read(2) # self.TargetLevelROIRow1 = struct.unpack("=H",self.TargetLevelROIRow1)[0] # self.TargetLevelROICol1 = infile.read(2) # self.TargetLevelROICol1 = struct.unpack("=H",self.TargetLevelROICol1)[0] # self.FrameNumberForTargetLevelROI = infile.read(2) # self.FrameNumberForTargetLevelROI = struct.unpack("=H",self.FrameNumberForTargetLevelROI)[0] # self.PercentRangeForTargetLevel = infile.read(2) # self.PercentRangeForTargetLevel = struct.unpack("=H",self.PercentRangeForTargetLevel)[0] # self.TargetValue = infile.read(2) # self.TargetValue = struct.unpack("=H",self.TargetValue)[0] # self.ComputedMedianValue = infile.read(2) # self.ComputedMedianValue = struct.unpack("=H",self.ComputedMedianValue)[0] # self.LoadZero = infile.read(2) # self.LoadZero = struct.unpack("=H",self.LoadZero)[0] # self.MaxLUTOut = infile.read(2) # self.MaxLUTOut = struct.unpack("=H",self.MaxLUTOut)[0] # self.MinLUTOut = infile.read(2) # self.MinLUTOut = struct.unpack("=H",self.MinLUTOut)[0] # self.MaxLinear = infile.read(2) # self.MaxLinear = struct.unpack("=H",self.MaxLinear)[0] # self.Reserved = infile.read(2) # self.Reserved = struct.unpack("=H",self.Reserved)[0] # self.ElectronsPerCount = infile.read(2) # self.ElectronsPerCount = struct.unpack("=H",self.ElectronsPerCount)[0] # self.ModeGain = infile.read(2) # self.ModeGain = struct.unpack("=H",self.ModeGain)[0] # self.TemperatureInDegC = infile.read(8) # self.TemperatureInDegC = struct.unpack("=d",self.TemperatureInDegC)[0] # self.LineRepaired = infile.read(2) # self.LineRepaired = struct.unpack("=H",self.LineRepaired)[0] # self.LineRepairFileName = infile.read(100) # self.CurrentLongitudinalInMM = infile.read(4) # self.CurrentLongitudinalInMM = struct.unpack("=f",self.CurrentLongitudinalInMM)[0] # self.CurrentTransverseInMM = infile.read(4) # self.CurrentTransverseInMM = struct.unpack("=f",self.CurrentTransverseInMM)[0] # self.CurrentCircularInMM = infile.read(4) # self.CurrentCircularInMM = struct.unpack("=f",self.CurrentCircularInMM)[0] # self.CurrentFilterSelection = infile.read(4) # self.CurrentFilterSelection = struct.unpack("=L",self.CurrentFilterSelection)[0] # self.DisableScrubAck = infile.read(2) # self.DisableScrubAck = struct.unpack("=H",self.DisableScrubAck)[0] # self.ScanModeSelect = infile.read(2) # self.ScanModeSelect = struct.unpack("=H",self.ScanModeSelect)[0] # self.DetectorAppSwVersion = infile.read(20) # self.DetectorNIOSVersion = infile.read(20) # self.DetectorPeripheralSetVersion = infile.read(20) # self.DetectorPhysicalAddress = infile.read(20) # self.PowerDown = infile.read(2) # self.PowerDown = struct.unpack("=H",self.PowerDown)[0] # self.InitialVoltageLevel_VCOMMON = infile.read(8) # self.InitialVoltageLevel_VCOMMON = struct.unpack("=d",self.InitialVoltageLevel_VCOMMON)[0] # self.FinalVoltageLevel_VCOMMON = infile.read(8) # self.FinalVoltageLevel_VCOMMON = struct.unpack("=d",self.FinalVoltageLevel_VCOMMON)[0] # self.DmrCollimatorSpotSize = infile.read(10) # self.DmrTrack = infile.read(5) # self.DmrFilter = infile.read(5) # self.FilterCarousel = infile.read(2) # self.FilterCarousel = struct.unpack("=H",self.FilterCarousel)[0] # self.Phantom = infile.read(20) # self.SetEnableHighTime = infile.read(2) # self.SetEnableHighTime = struct.unpack("=H",self.SetEnableHighTime)[0] # self.SetEnableLowTime = infile.read(2) # self.SetEnableLowTime = struct.unpack("=H",self.SetEnableLowTime)[0] # self.SetCompHighTime = infile.read(2) # self.SetCompHighTime = struct.unpack("=H",self.SetCompHighTime)[0] # self.SetCompLowTime = infile.read(2) # self.SetCompLowTime = struct.unpack("=H",self.SetCompLowTime)[0] # self.SetSyncLowTime = infile.read(2) # self.SetSyncLowTime = struct.unpack("=H",self.SetSyncLowTime)[0] # self.SetConvertLowTime = infile.read(2) # self.SetConvertLowTime = struct.unpack("=H",self.SetConvertLowTime)[0] # self.SetSyncHighTime = infile.read(2) # self.SetSyncHighTime = struct.unpack("=H",self.SetSyncHighTime)[0] # self.SetEOLTime = infile.read(2) # self.SetEOLTime = struct.unpack("=H",self.SetEOLTime)[0] # self.SetRampOffsetTime = infile.read(2) # self.SetRampOffsetTime = struct.unpack("=H",self.SetRampOffsetTime)[0] # self.FOVStartingValue = infile.read(2) # self.FOVStartingValue = struct.unpack("=H",self.FOVStartingValue)[0] # self.ColumnBinning = infile.read(2) # self.ColumnBinning = struct.unpack("=H",self.ColumnBinning)[0] # self.RowBinning = infile.read(2) # self.RowBinning = struct.unpack("=H",self.RowBinning)[0] # self.BorderColumns64 = infile.read(2) # self.BorderColumns64 = struct.unpack("=H",self.BorderColumns64)[0] # self.BorderRows64 = infile.read(2) # self.BorderRows64 = struct.unpack("=H",self.BorderRows64)[0] # self.FETOffRows64 = infile.read(2) # self.FETOffRows64 = struct.unpack("=H",self.FETOffRows64)[0] # self.FOVStartColumn128 = infile.read(2) # self.FOVStartColumn128 = struct.unpack("=H",self.FOVStartColumn128)[0] # self.FOVStartRow128 = infile.read(2) # self.FOVStartRow128 = struct.unpack("=H",self.FOVStartRow128)[0] # self.NumberOfColumns128 = infile.read(2) # self.NumberOfColumns128 = struct.unpack("=H",self.NumberOfColumns128)[0] # self.NumberOfRows128 = infile.read(2) # self.NumberOfRows128 = struct.unpack("=H",self.NumberOfRows128)[0] # self.VFPAquisition = infile.read(2000) # self.Comment = infile.read(200) def read(self, fname, frame=None): """ Read in header into self.header and the data into self.data """ self.header = {} self.resetvals() infile = self._open(fname, "rb") self._readheader(infile) # Compute image size try: self.dim1 = int(self.header['NumberOfRowsInFrame']) self.dim2 = int(self.header['NumberOfColsInFrame']) self.bpp = int(self.header['BitsPerPixel']) except: raise Exception("GE file", str(fname) + \ "is corrupt, cannot read it") # More than one image can be saved in a GE file # Will only load the first one # Go to the beginning of the file infile.seek(0) infile.seek(self.header['HeaderSizeInBytes'] + self.header['UserHeaderSizeInBytes']) ReadBytes = self.dim1 * self.dim2 * (self.bpp / 8) block = infile.read(ReadBytes) block = numpy.fromstring(block, numpy.uint16) infile.close() try: self.data = numpy.reshape(block, [self.dim2, self.dim1]) except: print len(block), self.dim2, self.dim1 raise IOError, \ 'Size spec in GE-header does not match size of image data field' self.bytecode = self.data.dtype.type self.pilimage = None return self fabio-0.1.3/fabio-src/fabioutils.py0000644000175000017500000004643412233175220017747 0ustar jeromejerome00000000000000#!/usr/bin/env python #coding: utf8 """ General purpose utilities functions for fabio """ from __future__ import with_statement import re, os, logging, threading, sys import StringIO as stringIO logger = logging.getLogger("fabioutils") from compression import bz2, gzip import traceback from math import ceil FILETYPES = { # extension NNNimage fabioclass # type consistency - always use a list if one case is 'edf' : ['edf'], 'cor' : ['edf'], 'pnm' : ['pnm'], 'pgm' : ['pnm'], 'pbm' : ['pnm'], 'tif' : ['tif'], 'tiff' : ['tif'], 'img' : ['adsc', 'OXD', 'HiPiC'], 'mccd' : ['marccd'], 'mar2300': ['mar345'], 'sfrm' : ['bruker100'], 'msk' : ['fit2dmask'], 'spr' : ['fit2dspreadsheet'], 'dm3' : ['dm3'], 'kcd' : ['kcd'], 'cbf' : ['cbf'], 'xml' : ["xsd"], 'xsd' : ["xsd"], } # Add bzipped and gzipped for key in FILETYPES.keys(): FILETYPES[key + ".bz2"] = FILETYPES[key] FILETYPES[key + ".gz"] = FILETYPES[key] # Compressors COMPRESSORS = {} dictAscii = {None:[chr(i) for i in range(32, 127)], } try: lines = os.popen("gzip -h 2>&1").read() # Looking for "usage" if "sage" in lines: COMPRESSORS['.gz'] = 'gzip -dc ' else: COMPRESSORS['.gz'] = None except Exception: COMPRESSORS['.gz'] = None try: lines = os.popen("bzip2 -h 2>&1").read() # Looking for "usage" if "sage" in lines: COMPRESSORS['.bz2'] = 'bzip2 -dc ' else: COMPRESSORS['.bz2'] = None except Exception: COMPRESSORS['.bz2'] = None def deprecated(func): """ used to deprecate a function/method: prints a lot of warning messages to enforce the modifaction of the code """ def wrapper(*arg, **kw): """ decorator that deprecates the use of a function """ logger.warning("%s is Deprecated !!! %s" % (func.func_name, os.linesep.join([""] + traceback.format_stack()[:-1]))) return func(*arg, **kw) return wrapper def pad(mystr, pattern=" ", size=80): """ Performs the padding of the string to the right size with the right pattern """ size = int(size) padded_size = int(ceil(float(len(mystr)) / size) * size) if len(pattern) == 1: return mystr.ljust(padded_size, pattern) else: return (mystr + pattern * int(ceil(float(padded_size - len(mystr)) / len(pattern))))[:padded_size] def getnum(name): """ # try to figure out a file number # guess it starts at the back """ stem , num, post_num = numstem(name) try: return int(num) except ValueError: return None class FilenameObject(object): """ The 'meaning' of a filename ... """ def __init__(self, stem=None, num=None, directory=None, format=None, extension=None, postnum=None, digits=4, filename=None): """ This class can either be instanciated by a set of parameters like directory, prefix, num, extension, ... @param stem: the stem is a kind of prefix (str) @param num: image number in the serie (int) @param directory: name of the directory (str) @param format: ?? @param extension: @param postnum: @param digits: Number of digits used to print num Alternative constructor: @param filename: fullpath of an image file to be deconstructed into directory, prefix, num, extension, ... """ self.stem = stem self.num = num self.format = format self.extension = extension self.digits = digits self.postnum = postnum self.directory = directory self.compressed = None if filename is not None: self.deconstruct_filename(filename) def str(self): """ Return a string representation """ fmt = "stem %s, num %s format %s extension %s " + \ "postnum = %s digits %s dir %s" return fmt % tuple([str(x) for x in [ self.stem , self.num , self.format , self.extension , self.postnum , self.digits , self.directory ] ]) __repr__ = str def tostring(self): """ convert yourself to a string """ name = self.stem if self.digits is not None and self.num is not None: fmt = "%0" + str(self.digits) + "d" name += fmt % self.num if self.postnum is not None: name += self.postnum if self.extension is not None: name += self.extension if self.directory is not None: name = os.path.join(self.directory, name) return name def deconstruct_filename(self, filename): """ Break up a filename to get image type and number """ direc, name = os.path.split(filename) direc = direc or None parts = name.split(".") compressed = False stem = parts[0] extn = "" postnum = "" ndigit = 4 num = None typ = None if parts[-1] in ["gz", "bz2"]: extn = "." + parts[-1] parts = parts[:-1] compressed = True if parts[-1] in FILETYPES.keys(): typ = FILETYPES[parts[-1]] extn = "." + parts[-1] + extn try: stem, numstring, postnum = numstem(".".join(parts[:-1])) num = int(numstring) ndigit = len(numstring) except Exception, err: # There is no number - hence make num be None, not 0 logger.debug("l176: %s" % err) num = None stem = "".join(parts[:-1]) else: # Probably two type left if len(parts) == 1: # Probably GE format stem_numb parts2 = parts[0].split("_") if parts2[-1].isdigit(): num = int(parts2[-1]) ndigit = len(parts2[-1]) typ = ['GE'] stem = "_".join(parts2[:-1]) + "_" else: try: num = int(parts[-1]) ndigit = len(parts[-1]) typ = ['bruker'] stem = ".".join(parts[:-1]) + "." except Exception, err: logger.debug("l196: %s" % err) typ = None extn = "." + parts[-1] + extn numstring = "" try: stem , numstring, postnum = numstem(".".join(parts[:-1])) except Exception, err: logger.debug("l202: %s" % err) raise if numstring.isdigit(): num = int(numstring) ndigit = len(numstring) # raise Exception("Cannot decode "+filename) self.stem = stem self.num = num self.directory = direc self.format = typ self.extension = extn self.postnum = postnum self.digits = ndigit self.compressed = compressed def numstem(name): """ cant see how to do without reversing strings Match 1 or more digits going backwards from the end of the string """ reg = re.compile(r"^(.*?)(-?[0-9]{0,9})(\D*)$") #reg = re.compile("""(\D*)(\d\d*)(\w*)""") try: res = reg.match(name).groups() #res = reg.match(name[::-1]).groups() #return [ r[::-1] for r in res[::-1]] if len(res[0]) == len(res[1]) == 0: # Hack for file without number return [res[2], '', ''] return [ r for r in res] except AttributeError: # no digits found return [name, "", ""] #@deprecated def deconstruct_filename(filename): """ Function for backward compatibility. Deprecated """ return FilenameObject(filename=filename) def construct_filename(filename, frame=None): "Try to construct the filename for a given frame" fobj = FilenameObject(filename=filename) if frame is not None: fobj.num = frame return fobj.tostring() def next_filename(name, padding=True): """ increment number """ fobj = FilenameObject(filename=name) fobj.num += 1 if not padding: fobj.digits = 0 return fobj.tostring() def previous_filename(name, padding=True): """ decrement number """ fobj = FilenameObject(filename=name) fobj.num -= 1 if not padding: fobj.digits = 0 return fobj.tostring() def jump_filename(name, num, padding=True): """ jump to number """ fobj = FilenameObject(filename=name) fobj.num = num if not padding: fobj.digits = 0 return fobj.tostring() def extract_filenumber(name): """ extract file number """ fobj = FilenameObject(filename=name) return fobj.num def isAscii(name, listExcluded=None): """ @param name: string to check @param listExcluded: list of char or string excluded. @return: True of False whether name is pure ascii or not """ isascii = None try: name.decode("ascii") except UnicodeDecodeError: isascii = False else: if listExcluded: isascii = not(any(bad in name for bad in listExcluded)) else: isascii = True return isascii def toAscii(name, excluded=None): """ @param name: string to check @param excluded: tuple of char or string excluded (not list: they are mutable). @return: the name with all non valid char removed """ if excluded not in dictAscii: ascii = dictAscii[None][:] for i in excluded: if i in ascii: ascii.remove(i) else: logger.error("toAscii: % not in ascii table" % i) dictAscii[excluded] = ascii else: ascii = dictAscii[excluded] out = [i for i in str(name) if i in ascii] return "".join(out) def nice_int(s): """ Workaround that int('1.0') raises an exception @param s: string to be converted to integer """ try: return int(s) except ValueError: return int(float(s)) class StringIO(stringIO.StringIO): """ just an interface providing the name and mode property to a StringIO BugFix for MacOSX mainly """ def __init__(self, data, fname=None, mode="r"): stringIO.StringIO.__init__(self, data) self.closed = False if fname == None: self.name = "fabioStream" else: self.name = fname self.mode = mode self.lock = threading.Semaphore() self.__size = None def getSize(self): if self.__size is None: logger.debug("Measuring size of %s" % self.name) with self.lock: pos = self.tell() self.seek(0, os.SEEK_END) self.__size = self.tell() self.seek(pos) return self.__size def setSize(self, size): self.__size = size size = property(getSize, setSize) class File(file): """ wrapper for "file" with locking """ def __init__(self, name, mode="rb", buffering=0): """file(name[, mode[, buffering]]) -> file object Open a file. The mode can be 'r', 'w' or 'a' for reading (default), writing or appending. The file will be created if it doesn't exist when opened for writing or appending; it will be truncated when opened for writing. Add a 'b' to the mode for binary files. Add a '+' to the mode to allow simultaneous reading and writing. If the buffering argument is given, 0 means unbuffered, 1 means line buffered, and larger numbers specify the buffer size. The preferred way to open a file is with the builtin open() function. Add a 'U' to mode to open the file for input with universal newline support. Any line ending in the input file will be seen as a '\n' in Python. Also, a file so opened gains the attribute 'newlines'; the value for this attribute is one of None (no newline read yet), '\r', '\n', '\r\n' or a tuple containing all the newline types seen. 'U' cannot be combined with 'w' or '+' mode. """ file.__init__(self, name, mode, buffering) self.lock = threading.Semaphore() self.__size = None def getSize(self): if self.__size is None: logger.debug("Measuring size of %s" % self.name) with self.lock: pos = self.tell() self.seek(0, os.SEEK_END) self.__size = self.tell() self.seek(pos) return self.__size def setSize(self, size): self.__size = size def __exit__(self, *args, **kwargs): """ Close the file. """ return file.close(self) def __enter__(self, *args, **kwargs): return self size = property(getSize, setSize) class UnknownCompressedFile(File): """ wrapper for "File" with locking """ def __init__(self, name, mode="rb", buffering=0): logger.warning("No decompressor found for this type of file (are gzip anf bz2 installed ???") File.__init__(self, name, mode, buffering) if gzip is None: GzipFile = UnknownCompressedFile else: class GzipFile(gzip.GzipFile): """ Just a wrapper forgzip.GzipFile providing the correct seek capabilities for python 2.5 """ def __init__(self, filename=None, mode=None, compresslevel=9, fileobj=None): """ Wrapper with locking for constructor for the GzipFile class. At least one of fileobj and filename must be given a non-trivial value. The new class instance is based on fileobj, which can be a regular file, a StringIO object, or any other object which simulates a file. It defaults to None, in which case filename is opened to provide a file object. When fileobj is not None, the filename argument is only used to be included in the gzip file header, which may includes the original filename of the uncompressed file. It defaults to the filename of fileobj, if discernible; otherwise, it defaults to the empty string, and in this case the original filename is not included in the header. The mode argument can be any of 'r', 'rb', 'a', 'ab', 'w', or 'wb', depending on whether the file will be read or written. The default is the mode of fileobj if discernible; otherwise, the default is 'rb'. Be aware that only the 'rb', 'ab', and 'wb' values should be used for cross-platform portability. The compresslevel argument is an integer from 1 to 9 controlling the level of compression; 1 is fastest and produces the least compression, and 9 is slowest and produces the most compression. The default is 9. """ gzip.GzipFile.__init__(self, filename, mode, compresslevel, fileobj) self.lock = threading.Semaphore() self.__size = None if sys.version_info < (2, 7): def getSize(self): if self.__size is None: logger.debug("Measuring size of %s" % self.name) with open(self.filename, "rb") as f: f.seek(-4) self.__size = numpy.fromstring(f.read(4), dtype=numpy.uint32) return self.__size def setSize(self, value): self.__size = value size = property(getSize, setSize) @property def closed(self): return self.fileobj is None def seek(self, offset, whence=os.SEEK_SET): """ Move to new file position. Argument offset is a byte count. Optional argument whence defaults to 0 (offset from start of file, offset should be >= 0); other values are 1 (move relative to current position, positive or negative), and 2 (move relative to end of file, usually negative, although many platforms allow seeking beyond the end of a file). If the file is opened in text mode, only offsets returned by tell() are legal. Use of other offsets causes undefined behavior. This is a wrapper for seek to ensure compatibility with old python 2.5 """ if whence == os.SEEK_SET: gzip.GzipFile.seek(self, offset) elif whence == os.SEEK_CUR: gzip.GzipFile.seek(self, offset + self.tell()) elif whence == os.SEEK_END: gzip.GzipFile.seek(self, -1) gzip.GzipFile.seek(self, offset + self.tell()) def __enter__(self, *args, **kwargs): return self def __exit__(self, *args, **kwargs): """ Close the file. """ return gzip.GzipFile.close(self) if bz2 is None: BZ2File = UnknownCompressedFile else: class BZ2File(bz2.BZ2File): "Wrapper with lock" def __init__(self, name , mode='r', buffering=0, compresslevel=9): """ BZ2File(name [, mode='r', buffering=0, compresslevel=9]) -> file object Open a bz2 file. The mode can be 'r' or 'w', for reading (default) or writing. When opened for writing, the file will be created if it doesn't exist, and truncated otherwise. If the buffering argument is given, 0 means unbuffered, and larger numbers specify the buffer size. If compresslevel is given, must be a number between 1 and 9. Add a 'U' to mode to open the file for input with universal newline support. Any line ending in the input file will be seen as a '\n' in Python. Also, a file so opened gains the attribute 'newlines'; the value for this attribute is one of None (no newline read yet), '\r', '\n', '\r\n' or a tuple containing all the newline types seen. Universal newlines are available only when reading. """ bz2.BZ2File.__init__(self, name , mode, buffering, compresslevel) self.lock = threading.Semaphore() self.__size = None def getSize(self): if self.__size is None: logger.debug("Measuring size of %s" % self.name) with self.lock: pos = self.tell() all = self.read() self.__size = self.tell() self.seek(pos) return self.__size def setSize(self, value): self.__size = value size = property(getSize, setSize) def __exit__(self, *args, **kwargs): """ Close the file. """ return bz2.BZ2File.close(self) def __enter__(self, *args, **kwargs): return self fabio-0.1.3/fabio-src/fit2dspreadsheetimage.py0000644000175000017500000000404012233175156022044 0ustar jeromejerome00000000000000 """ Read the fit2d ascii image output + Jon Wright, ESRF """ import numpy from fabioimage import fabioimage class fit2dspreadsheetimage(fabioimage): """ Read a fit2d ascii format """ def _readheader(self, infile): """ TODO : test for minimal attributes? """ line = infile.readline() try: items = line.split() xdim = int(items[0]) ydim = int(items[1]) except: raise self.header['title'] = line self.header['Dim_1'] = xdim self.header['Dim_2'] = ydim def read(self, fname, frame=None): """ Read in header into self.header and the data into self.data """ self.header = {} self.resetvals() infile = self._open(fname) self._readheader(infile) # Compute image size try: self.dim1 = int(self.header['Dim_1']) self.dim2 = int(self.header['Dim_2']) except: raise Exception("file", str(fname) + \ "is corrupt, cannot read it") bytecode = numpy.float32 self.bpp = len(numpy.array(0, bytecode).tostring()) #now read the data into the array try: vals = [] for line in infile.readlines(): try: vals.append([float(x) for x in line.split()]) except: pass self.data = numpy.array(vals).astype(bytecode) assert self.data.shape == (self.dim2, self.dim1) except: raise IOError, "Error reading ascii" self.resetvals() # ensure the PIL image is reset self.pilimage = None return self if __name__ == "__main__": import sys, time start = time.time() img = fit2dspreadsheetimage() img.read(sys.argv[1]) print time.time() - start print img.dim1, img.dim2, img.data.shape from matplotlib.pylab import imshow, show imshow(img.data.T) show() fabio-0.1.3/fabio-src/converters.py0000644000175000017500000000355212120434325017771 0ustar jeromejerome00000000000000#!/usr/bin/env python #coding: utf8 """ Converter module. This is for the moment empty (populated only with almost pass through anonymous functions) but aims to be populated with more sofisticated translators ... """ __author__ = "Jérôme Kieffer" __contact__ = "jerome.kieffer@esrf.eu" __license__ = "GPLv3+" __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" import types, logging logger = logging.getLogger("converter") def convert_data_integer(data): """ convert data to integer """ if data is not None: return data.astype(int) else: return data CONVERSION_HEADER = { ("edfimage", "edfimage"): lambda header:header, } CONVERSION_DATA = { ("edfimage", "edfimage"): lambda data:data, ("edfimage", "cbfimage"): convert_data_integer, ("edfimage", "mar345image"): convert_data_integer, ("edfimage", "fit2dmaskimage"): convert_data_integer, ("edfimage", "kcdimage"): convert_data_integer, ("edfimage", "OXDimage"): convert_data_integer, ("edfimage", "pnmimage"): convert_data_integer, } def convert_data(inp, outp, data): """ Return data converted to the output format ... over-simplistic implementation for the moment ... @param inp,outp: input/output format like "cbfimage" @param data(ndarray): the actual dataset to be transformed """ return CONVERSION_DATA.get((inp, outp), lambda data:data)(data) def convert_header(inp, outp, header): """ return header converted to the output format @param inp,outp: input/output format like "cbfimage" @param header(dict):the actual set of headers to be transformed """ return CONVERSION_HEADER.get((inp, outp), lambda header:header)(header) fabio-0.1.3/fabio-src/mar345image.py0000644000175000017500000003441412233175156017627 0ustar jeromejerome00000000000000#!/usr/bin/env python #coding: utf8 from __future__ import with_statement __doc__ = """ Authors: ........ * Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions; Risoe National Laboratory; Frederiksborgvej 399; DK-4000 Roskilde; email:erik.knudsen@risoe.dk * Jon Wright, Jérôme Kieffer & Gaël Goret: European Synchrotron Radiation Facility; Grenoble (France) """ from fabioimage import fabioimage import numpy, struct, time, sys, traceback import logging logger = logging.getLogger("mar345image") from compression import compPCK, decPCK class mar345image(fabioimage): _need_a_real_file = True def __init__(self, *args, **kwargs): fabioimage.__init__(self, *args, **kwargs) self.numhigh = None self.numpixels = None def read(self, fname, frame=None): """ Read a mar345 image""" self.filename = fname f = self._open(self.filename, "rb") self._readheader(f) if 'compressed' in self.header['Format']: # self.data = decPCK(f, self.dim1, self.dim2, self.numhigh, version=1) try: self.data = decPCK(f, self.dim1, self.dim2) except Exception, error: logger.error('%s. importing the mar345_io backend: generate an empty 1x1 picture' % error) f.close() self.dim1 = 1 self.dim2 = 1 self.bytecode = numpy.int # self.data = numpy.resize(numpy.array([0], numpy.int), [1, 1]) return self else: logger.error("cannot handle these formats yet " + \ "due to lack of documentation") return None self.bytecode = numpy.uint f.close() return self def _readheader(self, infile=None): """ Read a mar345 image header """ # clip was not used anywhere - commented out # clip = '\x00' #using a couple of local variables inside this function f = infile h = {} #header is 4096 bytes long l = f.read(64) #the contents of the mar345 header is taken to be as # described in # http://www.mar-usa.com/support/downloads/mar345_formats.pdf #the first 64 bytes are 4-byte integers (but in the CBFlib # example image it seems to 128 bytes?) #first 4-byte integer is a marker to check endianness if struct.unpack(" 65535)[0] nb_pix = pix_location.size if nb_pix % 8 == 0: tmp = numpy.zeros((nb_pix, 2), dtype="int32") else: tmp = numpy.zeros(((nb_pix // 8 + 1) * 8, 2), dtype="int32") tmp[:nb_pix, 0] = pix_location + 1 tmp[:nb_pix, 1] = flt_data[pix_location] return tmp.tostring() def nb_overflow_pixels(self): return (self.data > 65535).sum() @staticmethod def checkData(data=None): if data is None: return None else: # enforce square image shape = data.shape assert len(shape) == 2, "image has 2 dimensions" mshape = max(shape) z = numpy.zeros((mshape, mshape), dtype=int) z[:shape[0], :shape[1]] = data return z fabio-0.1.3/fabio-src/bruker100image.py0000644000175000017500000000660412233175220020317 0ustar jeromejerome00000000000000import numpy import math import logging logger = logging.getLogger("bruker100image") try: from PIL import Image except ImportError: logger.warning("PIL is not installed ... trying to do without") Image = None from brukerimage import brukerimage from readbytestream import readbytestream class bruker100image(brukerimage): def toPIL16(self, filename=None): if not Image: raise RuntimeError("PIL is not installed !!! ") if filename: self.read(filename) PILimage = Image.frombuffer("F", (self.dim1, self.dim2), self.data, "raw", "F;16", 0, -1) return PILimage def read(self, fname, frame=None): f = open(fname, "rb") try: self._readheader(f) except: raise rows = int(self.header['NROWS']) cols = int(self.header['NCOLS']) npixelb = int(self.header['NPIXELB'][0]) # you had to read the Bruker docs to know this! # We are now at the start of the image - assuming # readbrukerheader worked # size = rows * cols * npixelb self.data = readbytestream(f, f.tell(), rows, cols, npixelb, datatype="int", signed='n', swap='n') noverfl = self.header['NOVERFL'].split() # now process the overflows #read the set of "underflow pixels" - these will be completely # disregarded for now data = self.data k = 0 while k < 2:#for the time being things - are done in 16 bits datatype = {'1' : numpy.uint8, '2' : numpy.uint16, '4' : numpy.uint32 }[("%d" % 2 ** k)] ar = numpy.array(numpy.fromstring(f.read(int(noverfl[k]) * (2 ** k)), datatype), numpy.uint16) #insert the the overflow pixels in the image array: #this is probably a memory intensive way of doing this - # might be done in a more clever way lim = 2 ** (8 * k) - 1 #generate an array comprising of the indices into data.ravel() # where its value equals lim. M = numpy.compress(numpy.equal(data.ravel(), lim), numpy.arange(rows * cols)) #now put values from ar into those indices numpy.put(data.ravel(), M, ar) padding = 16 * int(math.ceil(int(noverfl[k]) * (2 ** k) / 16.)) - \ int(noverfl[k]) * (2 ** k) f.seek(padding, 1) print noverfl[k] + " bytes read + %d bytes padding" % padding k = k + 1 f.close() (self.dim1, self.dim2) = (rows, cols) print self.dim1, self.dim2 self.resetvals() return self if __name__ == '__main__': import sys, time I = bruker100image() b = time.clock() while (sys.argv[1:]): I.read(sys.argv[1]) r = I.toPIL16() I.rebin(2, 2) print sys.argv[1] + (": max=%d, min=%d, mean=%.2e, stddev=%.2e") % ( I.getmax(), I.getmin(), I.getmean(), I.getstddev()) print 'integrated intensity (%d %d %d %d) =%.3f' % ( 10, 20, 20, 40, I.integrate_area((10, 20, 20, 40))) sys.argv[1:] = sys.argv[2:] e = time.clock() print (e - b) fabio-0.1.3/fabio-src/xsdimage.py0000644000175000017500000001026512233175156017410 0ustar jeromejerome00000000000000#!/usr/bin/env python # coding: utf8 """ Authors: Jérôme Kieffer, ESRF email:jerome.kieffer@esrf.fr XSDimge are XML files containing numpy arrays """ __author__ = "Jérôme Kieffer" __contact__ = "jerome.kieffer@esrf.eu" __license__ = "GPLv3+" __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" import logging, numpy logger = logging.getLogger("xsdimage") from fabioimage import fabioimage import base64, hashlib try: from lxml import etree except ImportError: logger.warning("lxml library is probably not part of your python installation: disabling xsdimage format") etree = None class xsdimage(fabioimage): """ Read the XSDataImage XML File data format """ def __init__(self, data=None, header=None, fname=None): """ Constructor of the class XSDataImage. @param _strFilename: the name of the file to open @type _strFilename: string """ fabioimage.__init__(self, data=data, header=header) self.dims = [] self.size = None self.coding = None self.dtype = None self.rawData = None self.md5 = None if fname is not None: self.filename = fname self.read(fname) def read(self, fname, frame=None): """ """ self.header = {} self.resetvals() self.filename = fname infile = self._open(fname, "rb") self._readheader(infile) try: self.dim1, self.dim2 = self.dims[:2] except: raise IOError("XSD file %s is corrupt, no dimensions in it" % fname) try: self.bytecode = numpy.dtype(self.dtype).type self.bpp = len(numpy.array(0, self.bytecode).tostring()) except TypeError: self.bytecode = numpy.int32 self.bpp = 32 logger.warning("Defaulting type to int32") exp_size = 1 for i in self.dims: exp_size *= i assert exp_size == self.size decData = None if self.coding == "base64": decData = base64.b64decode(self.rawData) elif self.coding == "base32": decData = base64.b32decode(self.rawData) elif self.coding == "base16": decData = base64.b16decode(self.rawData) else: logger.warning("Unable to recognize the encoding of the data !!! got %s, expected base64, base32 or base16, I assume it is base64 " % self.coding) decData = base64.b64decode(self.rawData) if self.md5: assert hashlib.md5(decData).hexdigest() == self.md5 self.data = numpy.fromstring(decData, dtype=self.bytecode).reshape(tuple(self.dims)) if not numpy.little_endian: #by default little endian self.data.byteswap(inplace=True) self.resetvals() # # ensure the PIL image is reset self.pilimage = None return self def _readheader(self, infile): """ Read all headers in a file and populate self.header data is not yet populated @type infile: file object open in read mode """ xml = etree.parse(infile) self.dims = [] for i in xml.xpath("//shape"): try: self.dims.append(int(i.text)) except ValueError, error: logger.warning("%s Shape: Unable to convert %s to integer in %s" % (error, i.text, i)) for i in xml.xpath("//size"): try: self.size = int(i.text) except Exception, error:#IGNORE:W0703 logger.warning("%s Size: Unable to convert %s to integer in %s" % (error, i.text, i)) self.dtype = None for i in xml.xpath("//dtype"): self.dtype = i.text self.coding = None for i in xml.xpath("//coding"): j = i.find("value") if j is not None: self.coding = j.text self.rawData = None for i in xml.xpath("//data"): self.rawData = i.text self.md5 = None for i in xml.xpath("//md5sum"): j = i.find("value") if j is not None: self.md5 = j.text if etree is None: xsdimage = None fabio-0.1.3/MANIFEST.in0000644000175000017500000000070312126623347015123 0ustar jeromejerome00000000000000include README.txt include stdeb.cfg recursive-include src *.c *.h *.pyx recursive-include test *.py recursive-include doc * recursive-include pylint * recursive-include epydoc * # recursive-exclude pylint * # recursive-exclude pydoc * # recursive-exclude epydoc * recursive-exclude build * recursive-exclude dist * recursive-exclude test/tiftest * recursive-exclude test/testimages * recursive-exclude fabio.egg-info * # recursive-exclude debian * fabio-0.1.3/src/0000755000175000017500000000000012233272207014146 5ustar jeromejerome00000000000000fabio-0.1.3/src/mar345_IO.c0000644000175000017500000123044512233175156015732 0ustar jeromejerome00000000000000/* Generated by Cython 0.18 on Mon Apr 29 17:23:19 2013 */ #define PY_SSIZE_T_CLEAN #include "Python.h" #ifndef Py_PYTHON_H #error Python headers needed to compile C extensions, please install development version of Python. #elif PY_VERSION_HEX < 0x02040000 #error Cython requires Python 2.4+. #else #include /* For offsetof */ #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) #endif #if !defined(WIN32) && !defined(MS_WINDOWS) #ifndef __stdcall #define __stdcall #endif #ifndef __cdecl #define __cdecl #endif #ifndef __fastcall #define __fastcall #endif #endif #ifndef DL_IMPORT #define DL_IMPORT(t) t #endif #ifndef DL_EXPORT #define DL_EXPORT(t) t #endif #ifndef PY_LONG_LONG #define PY_LONG_LONG LONG_LONG #endif #ifndef Py_HUGE_VAL #define Py_HUGE_VAL HUGE_VAL #endif #ifdef PYPY_VERSION #define CYTHON_COMPILING_IN_PYPY 1 #define CYTHON_COMPILING_IN_CPYTHON 0 #else #define CYTHON_COMPILING_IN_PYPY 0 #define CYTHON_COMPILING_IN_CPYTHON 1 #endif #if PY_VERSION_HEX < 0x02050000 typedef int Py_ssize_t; #define PY_SSIZE_T_MAX INT_MAX #define PY_SSIZE_T_MIN INT_MIN #define PY_FORMAT_SIZE_T "" #define CYTHON_FORMAT_SSIZE_T "" #define PyInt_FromSsize_t(z) PyInt_FromLong(z) #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o) #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? 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/* "numpy.pxd":732 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< * ctypedef npy_uint64 uint64_t * #ctypedef npy_uint96 uint96_t */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; /* "numpy.pxd":733 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< * #ctypedef npy_uint96 uint96_t * #ctypedef npy_uint128 uint128_t */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; /* "numpy.pxd":737 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< * ctypedef npy_float64 float64_t * #ctypedef npy_float80 float80_t */ typedef npy_float32 __pyx_t_5numpy_float32_t; /* "numpy.pxd":738 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< * #ctypedef npy_float80 float80_t * #ctypedef npy_float128 float128_t */ typedef npy_float64 __pyx_t_5numpy_float64_t; /* "numpy.pxd":747 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t */ typedef npy_long __pyx_t_5numpy_int_t; /* "numpy.pxd":748 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< * ctypedef npy_longlong longlong_t * */ typedef npy_longlong __pyx_t_5numpy_long_t; /* "numpy.pxd":749 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< * * ctypedef npy_ulong uint_t */ typedef npy_longlong __pyx_t_5numpy_longlong_t; /* "numpy.pxd":751 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t */ typedef npy_ulong __pyx_t_5numpy_uint_t; /* "numpy.pxd":752 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< * ctypedef npy_ulonglong ulonglong_t * */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; /* "numpy.pxd":753 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< * * ctypedef npy_intp intp_t */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; /* "numpy.pxd":755 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< * ctypedef npy_uintp uintp_t * */ typedef npy_intp __pyx_t_5numpy_intp_t; /* "numpy.pxd":756 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< * * ctypedef npy_double float_t */ typedef npy_uintp __pyx_t_5numpy_uintp_t; /* "numpy.pxd":758 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t */ typedef npy_double __pyx_t_5numpy_float_t; /* "numpy.pxd":759 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< * ctypedef npy_longdouble longdouble_t * */ typedef npy_double __pyx_t_5numpy_double_t; /* "numpy.pxd":760 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< * * ctypedef npy_cfloat cfloat_t */ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; #if CYTHON_CCOMPLEX #ifdef __cplusplus typedef ::std::complex< float > __pyx_t_float_complex; #else typedef float _Complex __pyx_t_float_complex; #endif #else typedef struct { float real, imag; } __pyx_t_float_complex; #endif #if CYTHON_CCOMPLEX #ifdef __cplusplus typedef ::std::complex< double > __pyx_t_double_complex; #else typedef double _Complex __pyx_t_double_complex; #endif #else typedef struct { double real, imag; } __pyx_t_double_complex; #endif /*--- Type declarations ---*/ /* "numpy.pxd":762 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; /* "numpy.pxd":763 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< * ctypedef npy_clongdouble clongdouble_t * */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; /* "numpy.pxd":764 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< * * ctypedef npy_cdouble complex_t */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; 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static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ typedef struct { Py_ssize_t shape, strides, suboffsets; } __Pyx_Buf_DimInfo; typedef struct { size_t refcount; Py_buffer pybuffer; } __Pyx_Buffer; typedef struct { __Pyx_Buffer *rcbuffer; char *data; __Pyx_Buf_DimInfo diminfo[8]; } __Pyx_LocalBuf_ND; #if PY_MAJOR_VERSION < 3 static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags); static void __Pyx_ReleaseBuffer(Py_buffer *view); #else #define __Pyx_GetBuffer PyObject_GetBuffer #define __Pyx_ReleaseBuffer PyBuffer_Release #endif static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0}; static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1}; static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); /*proto*/ #ifndef __PYX_FORCE_INIT_THREADS #define __PYX_FORCE_INIT_THREADS 0 #endif static int __Pyx_Print(PyObject*, PyObject *, int); /*proto*/ #if CYTHON_COMPILING_IN_PYPY || PY_MAJOR_VERSION >= 3 static PyObject* __pyx_print = 0; static PyObject* __pyx_print_kwargs = 0; #endif static int __Pyx_PrintOne(PyObject* stream, PyObject *o); /*proto*/ #if CYTHON_CCOMPLEX #ifdef __cplusplus #define __Pyx_CREAL(z) ((z).real()) #define __Pyx_CIMAG(z) ((z).imag()) #else #define __Pyx_CREAL(z) (__real__(z)) #define __Pyx_CIMAG(z) (__imag__(z)) #endif #else #define __Pyx_CREAL(z) ((z).real) #define __Pyx_CIMAG(z) ((z).imag) #endif #if defined(_WIN32) && defined(__cplusplus) && CYTHON_CCOMPLEX #define __Pyx_SET_CREAL(z,x) ((z).real(x)) #define __Pyx_SET_CIMAG(z,y) ((z).imag(y)) #else #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x) #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y) #endif static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float); #if CYTHON_CCOMPLEX #define __Pyx_c_eqf(a, b) ((a)==(b)) #define __Pyx_c_sumf(a, b) ((a)+(b)) #define __Pyx_c_difff(a, b) ((a)-(b)) #define __Pyx_c_prodf(a, b) ((a)*(b)) #define __Pyx_c_quotf(a, b) ((a)/(b)) #define __Pyx_c_negf(a) (-(a)) #ifdef __cplusplus #define __Pyx_c_is_zerof(z) ((z)==(float)0) #define __Pyx_c_conjf(z) (::std::conj(z)) #if 1 #define __Pyx_c_absf(z) (::std::abs(z)) #define __Pyx_c_powf(a, b) (::std::pow(a, b)) #endif #else #define __Pyx_c_is_zerof(z) ((z)==0) #define __Pyx_c_conjf(z) (conjf(z)) #if 1 #define __Pyx_c_absf(z) (cabsf(z)) #define __Pyx_c_powf(a, b) (cpowf(a, b)) #endif #endif #else static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex, __pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex, __pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex, __pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex, __pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex, __pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex); static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex); #if 1 static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex, __pyx_t_float_complex); #endif #endif static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double); #if CYTHON_CCOMPLEX #define __Pyx_c_eq(a, b) ((a)==(b)) #define __Pyx_c_sum(a, b) ((a)+(b)) #define __Pyx_c_diff(a, b) ((a)-(b)) #define __Pyx_c_prod(a, b) ((a)*(b)) #define __Pyx_c_quot(a, b) ((a)/(b)) #define __Pyx_c_neg(a) (-(a)) #ifdef __cplusplus #define __Pyx_c_is_zero(z) ((z)==(double)0) #define __Pyx_c_conj(z) (::std::conj(z)) #if 1 #define __Pyx_c_abs(z) (::std::abs(z)) #define __Pyx_c_pow(a, b) (::std::pow(a, b)) #endif #else #define __Pyx_c_is_zero(z) ((z)==0) #define __Pyx_c_conj(z) (conj(z)) #if 1 #define __Pyx_c_abs(z) (cabs(z)) #define __Pyx_c_pow(a, b) (cpow(a, b)) #endif #endif #else static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex, __pyx_t_double_complex); 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= 0; /* "numpy.pxd":975 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< * if arr.base is NULL: * return None */ goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); if (__pyx_m) { __Pyx_AddTraceback("init mar345_IO", __pyx_clineno, __pyx_lineno, __pyx_filename); Py_DECREF(__pyx_m); __pyx_m = 0; } else if (!PyErr_Occurred()) { PyErr_SetString(PyExc_ImportError, "init mar345_IO"); } __pyx_L0:; __Pyx_RefNannyFinishContext(); #if PY_MAJOR_VERSION < 3 return; #else return __pyx_m; #endif } /* Runtime support code */ #if CYTHON_REFNANNY static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) { PyObject *m = NULL, *p = NULL; void *r = NULL; m = PyImport_ImportModule((char *)modname); if (!m) goto end; p = PyObject_GetAttrString(m, (char *)"RefNannyAPI"); if (!p) goto end; r = PyLong_AsVoidPtr(p); end: Py_XDECREF(p); Py_XDECREF(m); return (__Pyx_RefNannyAPIStruct *)r; } #endif /* CYTHON_REFNANNY */ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) { PyObject *result; result = PyObject_GetAttr(dict, name); if (!result) { if (dict != __pyx_b) { PyErr_Clear(); result = PyObject_GetAttr(__pyx_b, name); } if (!result) { PyErr_SetObject(PyExc_NameError, name); } } return result; } static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, const char *name, int exact) { if (!type) { PyErr_Format(PyExc_SystemError, "Missing type object"); return 0; } if (none_allowed && obj == Py_None) return 1; else if (exact) { if (Py_TYPE(obj) == type) return 1; } else { if (PyObject_TypeCheck(obj, type)) return 1; } PyErr_Format(PyExc_TypeError, "Argument '%s' has incorrect type (expected %s, got %s)", name, type->tp_name, Py_TYPE(obj)->tp_name); return 0; } static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { if (unlikely(!type)) { PyErr_Format(PyExc_SystemError, "Missing type object"); return 0; } if (likely(PyObject_TypeCheck(obj, type))) return 1; PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", Py_TYPE(obj)->tp_name, type->tp_name); return 0; } static CYTHON_INLINE int __Pyx_IsLittleEndian(void) { unsigned int n = 1; return *(unsigned char*)(&n) != 0; } static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, __Pyx_BufFmt_StackElem* stack, __Pyx_TypeInfo* type) { stack[0].field = &ctx->root; stack[0].parent_offset = 0; ctx->root.type = type; ctx->root.name = "buffer dtype"; ctx->root.offset = 0; ctx->head = stack; ctx->head->field = &ctx->root; ctx->fmt_offset = 0; ctx->head->parent_offset = 0; ctx->new_packmode = '@'; ctx->enc_packmode = '@'; ctx->new_count = 1; ctx->enc_count = 0; ctx->enc_type = 0; ctx->is_complex = 0; ctx->is_valid_array = 0; ctx->struct_alignment = 0; while (type->typegroup == 'S') { ++ctx->head; ctx->head->field = type->fields; ctx->head->parent_offset = 0; type = type->fields->type; } } static int __Pyx_BufFmt_ParseNumber(const char** ts) { int count; const char* t = *ts; if (*t < '0' || *t > '9') { return -1; } else { count = *t++ - '0'; while (*t >= '0' && *t < '9') { count *= 10; count += *t++ - '0'; } } *ts = t; return count; } static int __Pyx_BufFmt_ExpectNumber(const char **ts) { int number = __Pyx_BufFmt_ParseNumber(ts); if (number == -1) /* First char was not a digit */ PyErr_Format(PyExc_ValueError,\ "Does not understand character buffer dtype format string ('%c')", **ts); return number; } static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { PyErr_Format(PyExc_ValueError, "Unexpected format string character: '%c'", ch); } static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { switch (ch) { case 'c': return "'char'"; case 'b': return "'signed char'"; case 'B': return "'unsigned char'"; case 'h': return "'short'"; case 'H': return "'unsigned short'"; case 'i': return "'int'"; case 'I': return "'unsigned int'"; case 'l': return "'long'"; case 'L': return "'unsigned long'"; case 'q': return "'long long'"; case 'Q': return "'unsigned long long'"; case 'f': return (is_complex ? "'complex float'" : "'float'"); case 'd': return (is_complex ? "'complex double'" : "'double'"); case 'g': return (is_complex ? "'complex long double'" : "'long double'"); case 'T': return "a struct"; case 'O': return "Python object"; case 'P': return "a pointer"; case 's': case 'p': return "a string"; case 0: return "end"; default: return "unparseable format string"; } } static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { switch (ch) { case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; case 'h': case 'H': return 2; case 'i': case 'I': case 'l': case 'L': return 4; case 'q': case 'Q': return 8; case 'f': return (is_complex ? 8 : 4); case 'd': return (is_complex ? 16 : 8); case 'g': { PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); return 0; } case 'O': case 'P': return sizeof(void*); default: __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { switch (ch) { case 'c': case 'b': case 'B': case 's': case 'p': return 1; case 'h': case 'H': return sizeof(short); case 'i': case 'I': return sizeof(int); case 'l': case 'L': return sizeof(long); #ifdef HAVE_LONG_LONG case 'q': case 'Q': return sizeof(PY_LONG_LONG); #endif case 'f': return sizeof(float) * (is_complex ? 2 : 1); case 'd': return sizeof(double) * (is_complex ? 2 : 1); case 'g': return sizeof(long double) * (is_complex ? 2 : 1); case 'O': case 'P': return sizeof(void*); default: { __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } } typedef struct { char c; short x; } __Pyx_st_short; typedef struct { char c; int x; } __Pyx_st_int; typedef struct { char c; long x; } __Pyx_st_long; typedef struct { char c; float x; } __Pyx_st_float; typedef struct { char c; double x; } __Pyx_st_double; typedef struct { char c; long double x; } __Pyx_st_longdouble; typedef struct { char c; void *x; } __Pyx_st_void_p; #ifdef HAVE_LONG_LONG typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; #endif static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { switch (ch) { case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); #ifdef HAVE_LONG_LONG case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); #endif case 'f': return sizeof(__Pyx_st_float) - sizeof(float); case 'd': return sizeof(__Pyx_st_double) - sizeof(double); case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); default: __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } /* These are for computing the padding at the end of the struct to align on the first member of the struct. This will probably the same as above, but we don't have any guarantees. */ typedef struct { short x; char c; } __Pyx_pad_short; typedef struct { int x; char c; } __Pyx_pad_int; typedef struct { long x; char c; } __Pyx_pad_long; typedef struct { float x; char c; } __Pyx_pad_float; typedef struct { double x; char c; } __Pyx_pad_double; typedef struct { long double x; char c; } __Pyx_pad_longdouble; typedef struct { void *x; char c; } __Pyx_pad_void_p; #ifdef HAVE_LONG_LONG typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; #endif static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { switch (ch) { case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); #ifdef HAVE_LONG_LONG case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); #endif case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); default: __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { switch (ch) { case 'c': return 'H'; case 'b': case 'h': case 'i': case 'l': case 'q': case 's': case 'p': return 'I'; case 'B': case 'H': case 'I': case 'L': case 'Q': return 'U'; case 'f': case 'd': case 'g': return (is_complex ? 'C' : 'R'); case 'O': return 'O'; case 'P': return 'P'; default: { __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } } static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { if (ctx->head == NULL || ctx->head->field == &ctx->root) { const char* expected; const char* quote; if (ctx->head == NULL) { expected = "end"; quote = ""; } else { expected = ctx->head->field->type->name; quote = "'"; } PyErr_Format(PyExc_ValueError, "Buffer dtype mismatch, expected %s%s%s but got %s", quote, expected, quote, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); } else { __Pyx_StructField* field = ctx->head->field; __Pyx_StructField* parent = (ctx->head - 1)->field; PyErr_Format(PyExc_ValueError, "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), parent->type->name, field->name); } } static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { char group; size_t size, offset, arraysize = 1; if (ctx->enc_type == 0) return 0; if (ctx->head->field->type->arraysize[0]) { int i, ndim = 0; if (ctx->enc_type == 's' || ctx->enc_type == 'p') { ctx->is_valid_array = ctx->head->field->type->ndim == 1; ndim = 1; if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { PyErr_Format(PyExc_ValueError, "Expected a dimension of size %zu, got %zu", ctx->head->field->type->arraysize[0], ctx->enc_count); return -1; } } if (!ctx->is_valid_array) { PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", ctx->head->field->type->ndim, ndim); return -1; } for (i = 0; i < ctx->head->field->type->ndim; i++) { arraysize *= ctx->head->field->type->arraysize[i]; } ctx->is_valid_array = 0; ctx->enc_count = 1; } group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); do { __Pyx_StructField* field = ctx->head->field; __Pyx_TypeInfo* type = field->type; if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); } else { size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); } if (ctx->enc_packmode == '@') { size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); size_t align_mod_offset; if (align_at == 0) return -1; align_mod_offset = ctx->fmt_offset % align_at; if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; if (ctx->struct_alignment == 0) ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, ctx->is_complex); } if (type->size != size || type->typegroup != group) { if (type->typegroup == 'C' && type->fields != NULL) { size_t parent_offset = ctx->head->parent_offset + field->offset; ++ctx->head; ctx->head->field = type->fields; ctx->head->parent_offset = parent_offset; continue; } if ((type->typegroup == 'H' || group == 'H') && type->size == size) { } else { __Pyx_BufFmt_RaiseExpected(ctx); return -1; } } offset = ctx->head->parent_offset + field->offset; if (ctx->fmt_offset != offset) { PyErr_Format(PyExc_ValueError, "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); return -1; } ctx->fmt_offset += size; if (arraysize) ctx->fmt_offset += (arraysize - 1) * size; --ctx->enc_count; /* Consume from buffer string */ while (1) { if (field == &ctx->root) { ctx->head = NULL; if (ctx->enc_count != 0) { __Pyx_BufFmt_RaiseExpected(ctx); return -1; } break; /* breaks both loops as ctx->enc_count == 0 */ } ctx->head->field = ++field; if (field->type == NULL) { --ctx->head; field = ctx->head->field; continue; } else if (field->type->typegroup == 'S') { size_t parent_offset = ctx->head->parent_offset + field->offset; if (field->type->fields->type == NULL) continue; /* empty struct */ field = field->type->fields; ++ctx->head; ctx->head->field = field; ctx->head->parent_offset = parent_offset; break; } else { break; } } } while (ctx->enc_count); ctx->enc_type = 0; ctx->is_complex = 0; return 0; } static CYTHON_INLINE PyObject * __pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) { const char *ts = *tsp; int i = 0, number; int ndim = ctx->head->field->type->ndim; ; ++ts; if (ctx->new_count != 1) { PyErr_SetString(PyExc_ValueError, "Cannot handle repeated arrays in format string"); return NULL; } if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; while (*ts && *ts != ')') { if (isspace(*ts)) continue; number = __Pyx_BufFmt_ExpectNumber(&ts); if (number == -1) return NULL; if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) return PyErr_Format(PyExc_ValueError, "Expected a dimension of size %zu, got %d", ctx->head->field->type->arraysize[i], number); if (*ts != ',' && *ts != ')') return PyErr_Format(PyExc_ValueError, "Expected a comma in format string, got '%c'", *ts); if (*ts == ',') ts++; i++; } if (i != ndim) return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", ctx->head->field->type->ndim, i); if (!*ts) { PyErr_SetString(PyExc_ValueError, "Unexpected end of format string, expected ')'"); return NULL; } ctx->is_valid_array = 1; ctx->new_count = 1; *tsp = ++ts; return Py_None; } static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { int got_Z = 0; while (1) { switch(*ts) { case 0: if (ctx->enc_type != 0 && ctx->head == NULL) { __Pyx_BufFmt_RaiseExpected(ctx); return NULL; } if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; if (ctx->head != NULL) { __Pyx_BufFmt_RaiseExpected(ctx); return NULL; } return ts; case ' ': case 10: case 13: ++ts; break; case '<': if (!__Pyx_IsLittleEndian()) { PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); return NULL; } ctx->new_packmode = '='; ++ts; break; case '>': case '!': if (__Pyx_IsLittleEndian()) { PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); return NULL; } ctx->new_packmode = '='; ++ts; break; case '=': case '@': case '^': ctx->new_packmode = *ts++; break; case 'T': /* substruct */ { const char* ts_after_sub; size_t i, struct_count = ctx->new_count; size_t struct_alignment = ctx->struct_alignment; ctx->new_count = 1; ++ts; if (*ts != '{') { PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); return NULL; } if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; ctx->enc_type = 0; /* Erase processed last struct element */ ctx->enc_count = 0; ctx->struct_alignment = 0; ++ts; ts_after_sub = ts; for (i = 0; i != struct_count; ++i) { ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); if (!ts_after_sub) return NULL; } ts = ts_after_sub; if (struct_alignment) ctx->struct_alignment = struct_alignment; } break; case '}': /* end of substruct; either repeat or move on */ { size_t alignment = ctx->struct_alignment; ++ts; if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; ctx->enc_type = 0; /* Erase processed last struct element */ if (alignment && ctx->fmt_offset % alignment) { ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); } } return ts; case 'x': if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; ctx->fmt_offset += ctx->new_count; ctx->new_count = 1; ctx->enc_count = 0; ctx->enc_type = 0; ctx->enc_packmode = ctx->new_packmode; ++ts; break; case 'Z': got_Z = 1; ++ts; if (*ts != 'f' && *ts != 'd' && *ts != 'g') { __Pyx_BufFmt_RaiseUnexpectedChar('Z'); return NULL; } /* fall through */ case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': case 'l': case 'L': case 'q': case 'Q': case 'f': case 'd': case 'g': case 'O': case 's': case 'p': if (ctx->enc_type == *ts && got_Z == ctx->is_complex && ctx->enc_packmode == ctx->new_packmode) { ctx->enc_count += ctx->new_count; } else { if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; ctx->enc_count = ctx->new_count; ctx->enc_packmode = ctx->new_packmode; ctx->enc_type = *ts; ctx->is_complex = got_Z; } ++ts; ctx->new_count = 1; got_Z = 0; break; case ':': ++ts; while(*ts != ':') ++ts; ++ts; break; case '(': if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; break; default: { int number = __Pyx_BufFmt_ExpectNumber(&ts); if (number == -1) return NULL; ctx->new_count = (size_t)number; } } } } static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) { buf->buf = NULL; buf->obj = NULL; buf->strides = __Pyx_zeros; buf->shape = __Pyx_zeros; buf->suboffsets = __Pyx_minusones; } static CYTHON_INLINE int __Pyx_GetBufferAndValidate( Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack) { if (obj == Py_None || obj == NULL) { __Pyx_ZeroBuffer(buf); return 0; } buf->buf = NULL; if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail; if (buf->ndim != nd) { PyErr_Format(PyExc_ValueError, "Buffer has wrong number of dimensions (expected %d, got %d)", nd, buf->ndim); goto fail; } if (!cast) { __Pyx_BufFmt_Context ctx; __Pyx_BufFmt_Init(&ctx, stack, dtype); if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; } if ((unsigned)buf->itemsize != dtype->size) { PyErr_Format(PyExc_ValueError, "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)", buf->itemsize, (buf->itemsize > 1) ? "s" : "", dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : ""); goto fail; } if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; return 0; fail:; __Pyx_ZeroBuffer(buf); return -1; } static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { if (info->buf == NULL) return; if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; __Pyx_ReleaseBuffer(info); } static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { PyErr_Format(PyExc_ValueError, "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); } static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { PyErr_Format(PyExc_ValueError, "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack", index, (index == 1) ? "" : "s"); } static CYTHON_INLINE int __Pyx_IterFinish(void) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); PyObject* exc_type = tstate->curexc_type; if (unlikely(exc_type)) { if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) { PyObject *exc_value, *exc_tb; exc_value = tstate->curexc_value; exc_tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; Py_DECREF(exc_type); Py_XDECREF(exc_value); Py_XDECREF(exc_tb); return 0; } else { return -1; } } return 0; #else if (unlikely(PyErr_Occurred())) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) { PyErr_Clear(); return 0; } else { return -1; } } return 0; #endif } static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { if (unlikely(retval)) { Py_DECREF(retval); __Pyx_RaiseTooManyValuesError(expected); return -1; } else { return __Pyx_IterFinish(); } return 0; } static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { PyObject *local_type, *local_value, *local_tb; #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); local_type = tstate->curexc_type; local_value = tstate->curexc_value; local_tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; #else PyErr_Fetch(&local_type, &local_value, &local_tb); #endif PyErr_NormalizeException(&local_type, &local_value, &local_tb); #if CYTHON_COMPILING_IN_CPYTHON if (unlikely(tstate->curexc_type)) #else if (unlikely(PyErr_Occurred())) #endif goto bad; #if PY_MAJOR_VERSION >= 3 if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) goto bad; #endif Py_INCREF(local_type); Py_INCREF(local_value); Py_INCREF(local_tb); *type = local_type; *value = local_value; *tb = local_tb; #if CYTHON_COMPILING_IN_CPYTHON tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; tstate->exc_type = local_type; tstate->exc_value = local_value; tstate->exc_traceback = local_tb; /* Make sure tstate is in a consistent state when we XDECREF these objects (DECREF may run arbitrary code). */ Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); #else PyErr_SetExcInfo(local_type, local_value, local_tb); #endif return 0; bad: *type = 0; *value = 0; *tb = 0; Py_XDECREF(local_type); Py_XDECREF(local_value); Py_XDECREF(local_tb); return -1; } static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->curexc_type; tmp_value = tstate->curexc_value; tmp_tb = tstate->curexc_traceback; tstate->curexc_type = type; tstate->curexc_value = value; tstate->curexc_traceback = tb; Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); #else PyErr_Restore(type, value, tb); #endif } static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); *type = tstate->curexc_type; *value = tstate->curexc_value; *tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; #else PyErr_Fetch(type, value, tb); #endif } static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); } static void __Pyx_RaiseDoubleKeywordsError( const char* func_name, PyObject* kw_name) { PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION >= 3 "%s() got multiple values for keyword argument '%U'", func_name, kw_name); #else "%s() got multiple values for keyword argument '%s'", func_name, PyString_AsString(kw_name)); #endif } static int __Pyx_ParseOptionalKeywords( PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name) { PyObject *key = 0, *value = 0; Py_ssize_t pos = 0; PyObject*** name; PyObject*** first_kw_arg = argnames + num_pos_args; while (PyDict_Next(kwds, &pos, &key, &value)) { name = first_kw_arg; while (*name && (**name != key)) name++; if (*name) { values[name-argnames] = value; continue; } name = first_kw_arg; #if PY_MAJOR_VERSION < 3 if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { while (*name) { if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) && _PyString_Eq(**name, key)) { values[name-argnames] = value; break; } name++; } if (*name) continue; else { PyObject*** argname = argnames; while (argname != first_kw_arg) { if ((**argname == key) || ( (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) && _PyString_Eq(**argname, key))) { goto arg_passed_twice; } argname++; } } } else #endif if (likely(PyUnicode_Check(key))) { while (*name) { int cmp = (**name == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : #endif PyUnicode_Compare(**name, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; if (cmp == 0) { values[name-argnames] = value; break; } name++; } if (*name) continue; else { PyObject*** argname = argnames; while (argname != first_kw_arg) { int cmp = (**argname == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : #endif PyUnicode_Compare(**argname, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; if (cmp == 0) goto arg_passed_twice; argname++; } } } else goto invalid_keyword_type; if (kwds2) { if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; } else { goto invalid_keyword; } } return 0; arg_passed_twice: __Pyx_RaiseDoubleKeywordsError(function_name, key); goto bad; invalid_keyword_type: PyErr_Format(PyExc_TypeError, "%s() keywords must be strings", function_name); goto bad; invalid_keyword: PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION < 3 "%s() got an unexpected keyword argument '%s'", function_name, PyString_AsString(key)); #else "%s() got an unexpected keyword argument '%U'", function_name, key); #endif bad: return -1; } static void __Pyx_RaiseArgtupleInvalid( const char* func_name, int exact, Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found) { Py_ssize_t num_expected; const char *more_or_less; if (num_found < num_min) { num_expected = num_min; more_or_less = "at least"; } else { num_expected = num_max; more_or_less = "at most"; } if (exact) { more_or_less = "exactly"; } PyErr_Format(PyExc_TypeError, "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)", func_name, more_or_less, num_expected, (num_expected == 1) ? "" : "s", num_found); } #if PY_MAJOR_VERSION < 3 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, CYTHON_UNUSED PyObject *cause) { Py_XINCREF(type); if (!value || value == Py_None) value = NULL; else Py_INCREF(value); if (!tb || tb == Py_None) tb = NULL; else { Py_INCREF(tb); if (!PyTraceBack_Check(tb)) { PyErr_SetString(PyExc_TypeError, "raise: arg 3 must be a traceback or None"); goto raise_error; } } #if PY_VERSION_HEX < 0x02050000 if (PyClass_Check(type)) { #else if (PyType_Check(type)) { #endif #if CYTHON_COMPILING_IN_PYPY if (!value) { Py_INCREF(Py_None); value = Py_None; } #endif PyErr_NormalizeException(&type, &value, &tb); } else { if (value) { PyErr_SetString(PyExc_TypeError, "instance exception may not have a separate value"); goto raise_error; } value = type; #if PY_VERSION_HEX < 0x02050000 if (PyInstance_Check(type)) { type = (PyObject*) ((PyInstanceObject*)type)->in_class; Py_INCREF(type); } else { type = 0; PyErr_SetString(PyExc_TypeError, "raise: exception must be an old-style class or instance"); goto raise_error; } #else type = (PyObject*) Py_TYPE(type); Py_INCREF(type); if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { PyErr_SetString(PyExc_TypeError, "raise: exception class must be a subclass of BaseException"); goto raise_error; } #endif } __Pyx_ErrRestore(type, value, tb); return; raise_error: Py_XDECREF(value); Py_XDECREF(type); Py_XDECREF(tb); return; } #else /* Python 3+ */ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { PyObject* owned_instance = NULL; if (tb == Py_None) { tb = 0; } else if (tb && !PyTraceBack_Check(tb)) { PyErr_SetString(PyExc_TypeError, "raise: arg 3 must be a traceback or None"); goto bad; } if (value == Py_None) value = 0; if (PyExceptionInstance_Check(type)) { if (value) { PyErr_SetString(PyExc_TypeError, "instance exception may not have a separate value"); goto bad; } value = type; type = (PyObject*) Py_TYPE(value); } else if (PyExceptionClass_Check(type)) { PyObject *args; if (!value) args = PyTuple_New(0); else if (PyTuple_Check(value)) { Py_INCREF(value); args = value; } else args = PyTuple_Pack(1, value); if (!args) goto bad; owned_instance = PyEval_CallObject(type, args); Py_DECREF(args); if (!owned_instance) goto bad; value = owned_instance; if (!PyExceptionInstance_Check(value)) { PyErr_Format(PyExc_TypeError, "calling %R should have returned an instance of " "BaseException, not %R", type, Py_TYPE(value)); goto bad; } } else { PyErr_SetString(PyExc_TypeError, "raise: exception class must be a subclass of BaseException"); goto bad; } if (cause && cause != Py_None) { PyObject *fixed_cause; if (PyExceptionClass_Check(cause)) { fixed_cause = PyObject_CallObject(cause, NULL); if (fixed_cause == NULL) goto bad; } else if (PyExceptionInstance_Check(cause)) { fixed_cause = cause; Py_INCREF(fixed_cause); } else { PyErr_SetString(PyExc_TypeError, "exception causes must derive from " "BaseException"); goto bad; } PyException_SetCause(value, fixed_cause); } PyErr_SetObject(type, value); if (tb) { PyThreadState *tstate = PyThreadState_GET(); PyObject* tmp_tb = tstate->curexc_traceback; if (tb != tmp_tb) { Py_INCREF(tb); tstate->curexc_traceback = tb; Py_XDECREF(tmp_tb); } } bad: Py_XDECREF(owned_instance); return; } #endif static void __Pyx_RaiseBufferFallbackError(void) { PyErr_Format(PyExc_ValueError, "Buffer acquisition failed on assignment; and then reacquiring the old buffer failed too!"); } static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); } static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); *type = tstate->exc_type; *value = tstate->exc_value; *tb = tstate->exc_traceback; Py_XINCREF(*type); Py_XINCREF(*value); Py_XINCREF(*tb); #else PyErr_GetExcInfo(type, value, tb); #endif } static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) { #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; tstate->exc_type = type; tstate->exc_value = value; tstate->exc_traceback = tb; Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); #else PyErr_SetExcInfo(type, value, tb); #endif } #if PY_MAJOR_VERSION < 3 static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { CYTHON_UNUSED PyObject *getbuffer_cobj; #if PY_VERSION_HEX >= 0x02060000 if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); #endif if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); #if PY_VERSION_HEX < 0x02060000 if (obj->ob_type->tp_dict && (getbuffer_cobj = PyMapping_GetItemString(obj->ob_type->tp_dict, "__pyx_getbuffer"))) { getbufferproc func; #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0) func = (getbufferproc) PyCapsule_GetPointer(getbuffer_cobj, "getbuffer(obj, view, flags)"); #else func = (getbufferproc) PyCObject_AsVoidPtr(getbuffer_cobj); #endif Py_DECREF(getbuffer_cobj); if (!func) goto fail; return func(obj, view, flags); } else { PyErr_Clear(); } #endif PyErr_Format(PyExc_TypeError, "'%100s' does not have the buffer interface", Py_TYPE(obj)->tp_name); #if PY_VERSION_HEX < 0x02060000 fail: #endif return -1; } static void __Pyx_ReleaseBuffer(Py_buffer *view) { PyObject *obj = view->obj; CYTHON_UNUSED PyObject *releasebuffer_cobj; if (!obj) return; #if PY_VERSION_HEX >= 0x02060000 if (PyObject_CheckBuffer(obj)) { PyBuffer_Release(view); return; } #endif if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } #if PY_VERSION_HEX < 0x02060000 if (obj->ob_type->tp_dict && (releasebuffer_cobj = PyMapping_GetItemString(obj->ob_type->tp_dict, "__pyx_releasebuffer"))) { releasebufferproc func; #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0) func = (releasebufferproc) PyCapsule_GetPointer(releasebuffer_cobj, "releasebuffer(obj, view)"); #else func = (releasebufferproc) PyCObject_AsVoidPtr(releasebuffer_cobj); #endif Py_DECREF(releasebuffer_cobj); if (!func) goto fail; func(obj, view); return; } else { PyErr_Clear(); } #endif goto nofail; #if PY_VERSION_HEX < 0x02060000 fail: #endif PyErr_WriteUnraisable(obj); nofail: Py_DECREF(obj); view->obj = NULL; } #endif /* PY_MAJOR_VERSION < 3 */ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { PyObject *empty_list = 0; PyObject *module = 0; PyObject *global_dict = 0; PyObject *empty_dict = 0; PyObject *list; #if PY_VERSION_HEX < 0x03030000 PyObject *py_import = 0; py_import = __Pyx_GetAttrString(__pyx_b, "__import__"); if (!py_import) goto bad; #endif if (from_list) list = from_list; else { empty_list = PyList_New(0); if (!empty_list) goto bad; list = empty_list; } global_dict = PyModule_GetDict(__pyx_m); if (!global_dict) goto bad; empty_dict = PyDict_New(); if (!empty_dict) goto bad; #if PY_VERSION_HEX >= 0x02050000 { #if PY_MAJOR_VERSION >= 3 if (level == -1) { if (strchr(__Pyx_MODULE_NAME, '.')) { #if PY_VERSION_HEX < 0x03030000 PyObject *py_level = PyInt_FromLong(1); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); #else module = PyImport_ImportModuleLevelObject( name, global_dict, empty_dict, list, 1); #endif if (!module) { if (!PyErr_ExceptionMatches(PyExc_ImportError)) goto bad; PyErr_Clear(); } } level = 0; /* try absolute import on failure */ } #endif if (!module) { #if PY_VERSION_HEX < 0x03030000 PyObject *py_level = PyInt_FromLong(level); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); #else module = PyImport_ImportModuleLevelObject( name, global_dict, empty_dict, list, level); #endif } } #else if (level>0) { PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4."); goto bad; } module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, NULL); #endif bad: #if PY_VERSION_HEX < 0x03030000 Py_XDECREF(py_import); #endif Py_XDECREF(empty_list); Py_XDECREF(empty_dict); return module; } #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION < 3 static PyObject *__Pyx_GetStdout(void) { PyObject *f = PySys_GetObject((char *)"stdout"); if (!f) { PyErr_SetString(PyExc_RuntimeError, "lost sys.stdout"); } return f; } static int __Pyx_Print(PyObject* f, PyObject *arg_tuple, int newline) { int i; if (!f) { if (!(f = __Pyx_GetStdout())) return -1; } Py_INCREF(f); for (i=0; i < PyTuple_GET_SIZE(arg_tuple); i++) { PyObject* v; if (PyFile_SoftSpace(f, 1)) { if (PyFile_WriteString(" ", f) < 0) goto error; } v = PyTuple_GET_ITEM(arg_tuple, i); if (PyFile_WriteObject(v, f, Py_PRINT_RAW) < 0) goto error; if (PyString_Check(v)) { char *s = PyString_AsString(v); Py_ssize_t len = PyString_Size(v); if (len > 0 && isspace(Py_CHARMASK(s[len-1])) && s[len-1] != ' ') PyFile_SoftSpace(f, 0); } } if (newline) { if (PyFile_WriteString("\n", f) < 0) goto error; PyFile_SoftSpace(f, 0); } Py_DECREF(f); return 0; error: Py_DECREF(f); return -1; } #else /* Python 3 has a print function */ static int __Pyx_Print(PyObject* stream, PyObject *arg_tuple, int newline) { PyObject* kwargs = 0; PyObject* result = 0; PyObject* end_string; if (unlikely(!__pyx_print)) { __pyx_print = __Pyx_GetAttrString(__pyx_b, "print"); if (!__pyx_print) return -1; } if (stream) { kwargs = PyDict_New(); if (unlikely(!kwargs)) return -1; if (unlikely(PyDict_SetItemString(kwargs, "file", stream) < 0)) goto bad; if (!newline) { end_string = PyUnicode_FromStringAndSize(" ", 1); if (unlikely(!end_string)) goto bad; if (PyDict_SetItemString(kwargs, "end", end_string) < 0) { Py_DECREF(end_string); goto bad; } Py_DECREF(end_string); } } else if (!newline) { if (unlikely(!__pyx_print_kwargs)) { __pyx_print_kwargs = PyDict_New(); if (unlikely(!__pyx_print_kwargs)) return -1; end_string = PyUnicode_FromStringAndSize(" ", 1); if (unlikely(!end_string)) return -1; if (PyDict_SetItemString(__pyx_print_kwargs, "end", end_string) < 0) { Py_DECREF(end_string); return -1; } Py_DECREF(end_string); } kwargs = __pyx_print_kwargs; } result = PyObject_Call(__pyx_print, arg_tuple, kwargs); if (unlikely(kwargs) && (kwargs != __pyx_print_kwargs)) Py_DECREF(kwargs); if (!result) return -1; Py_DECREF(result); return 0; bad: if (kwargs != __pyx_print_kwargs) Py_XDECREF(kwargs); return -1; } #endif #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION < 3 static int __Pyx_PrintOne(PyObject* f, PyObject *o) { if (!f) { if (!(f = __Pyx_GetStdout())) return -1; } Py_INCREF(f); if (PyFile_SoftSpace(f, 0)) { if (PyFile_WriteString(" ", f) < 0) goto error; } if (PyFile_WriteObject(o, f, Py_PRINT_RAW) < 0) goto error; if (PyFile_WriteString("\n", f) < 0) goto error; Py_DECREF(f); return 0; error: Py_DECREF(f); return -1; /* the line below is just to avoid C compiler * warnings about unused functions */ return __Pyx_Print(f, NULL, 0); } #else /* Python 3 has a print function */ static int __Pyx_PrintOne(PyObject* stream, PyObject *o) { int res; PyObject* arg_tuple = PyTuple_Pack(1, o); if (unlikely(!arg_tuple)) return -1; res = __Pyx_Print(stream, arg_tuple, 1); Py_DECREF(arg_tuple); return res; } #endif #if CYTHON_CCOMPLEX #ifdef __cplusplus static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { return ::std::complex< float >(x, y); } #else static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { return x + y*(__pyx_t_float_complex)_Complex_I; } #endif #else static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { __pyx_t_float_complex z; z.real = x; z.imag = y; return z; } #endif #if CYTHON_CCOMPLEX #else static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) { return (a.real == b.real) && (a.imag == b.imag); } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; z.real = a.real + b.real; z.imag = a.imag + b.imag; return z; } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; z.real = a.real - b.real; z.imag = a.imag - b.imag; return z; } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; z.real = a.real * b.real - a.imag * b.imag; z.imag = a.real * b.imag + a.imag * b.real; return z; } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; float denom = b.real * b.real + b.imag * b.imag; z.real = (a.real * b.real + a.imag * b.imag) / denom; z.imag = (a.imag * b.real - a.real * b.imag) / denom; return z; } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) { __pyx_t_float_complex z; z.real = -a.real; z.imag = -a.imag; return z; } static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) { return (a.real == 0) && (a.imag == 0); } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) { __pyx_t_float_complex z; z.real = a.real; z.imag = -a.imag; return z; } #if 1 static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) { #if !defined(HAVE_HYPOT) || defined(_MSC_VER) return sqrtf(z.real*z.real + z.imag*z.imag); #else return hypotf(z.real, z.imag); #endif } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; float r, lnr, theta, z_r, z_theta; if (b.imag == 0 && b.real == (int)b.real) { if (b.real < 0) { float denom = a.real * a.real + a.imag * a.imag; a.real = a.real / denom; a.imag = -a.imag / denom; b.real = -b.real; } switch ((int)b.real) { case 0: z.real = 1; z.imag = 0; return z; case 1: return a; case 2: z = __Pyx_c_prodf(a, a); return __Pyx_c_prodf(a, a); case 3: z = __Pyx_c_prodf(a, a); return __Pyx_c_prodf(z, a); case 4: z = __Pyx_c_prodf(a, a); return __Pyx_c_prodf(z, z); } } if (a.imag == 0) { if (a.real == 0) { return a; } r = a.real; theta = 0; } else { r = __Pyx_c_absf(a); theta = atan2f(a.imag, a.real); } lnr = logf(r); z_r = expf(lnr * b.real - theta * b.imag); z_theta = theta * b.real + lnr * b.imag; z.real = z_r * cosf(z_theta); z.imag = z_r * sinf(z_theta); return z; } #endif #endif #if CYTHON_CCOMPLEX #ifdef __cplusplus static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { return ::std::complex< double >(x, y); } #else static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { return x + y*(__pyx_t_double_complex)_Complex_I; } #endif #else static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { __pyx_t_double_complex z; z.real = x; z.imag = y; return z; } #endif #if CYTHON_CCOMPLEX #else static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) { return (a.real == b.real) && (a.imag == b.imag); } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; z.real = a.real + b.real; z.imag = a.imag + b.imag; return z; } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; z.real = a.real - b.real; z.imag = a.imag - b.imag; return z; } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; z.real = a.real * b.real - a.imag * b.imag; z.imag = a.real * b.imag + a.imag * b.real; return z; } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; double denom = b.real * b.real + b.imag * b.imag; z.real = (a.real * b.real + a.imag * b.imag) / denom; z.imag = (a.imag * b.real - a.real * b.imag) / denom; return z; } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) { __pyx_t_double_complex z; z.real = -a.real; z.imag = -a.imag; return z; } static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) { return (a.real == 0) && (a.imag == 0); } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) { __pyx_t_double_complex z; z.real = a.real; z.imag = -a.imag; return z; } #if 1 static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) { #if !defined(HAVE_HYPOT) || defined(_MSC_VER) return sqrt(z.real*z.real + z.imag*z.imag); #else return hypot(z.real, z.imag); #endif } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; double r, lnr, theta, z_r, z_theta; if (b.imag == 0 && b.real == (int)b.real) { if (b.real < 0) { double denom = a.real * a.real + a.imag * a.imag; a.real = a.real / denom; a.imag = -a.imag / denom; b.real = -b.real; } switch ((int)b.real) { case 0: z.real = 1; z.imag = 0; return z; case 1: return a; case 2: z = __Pyx_c_prod(a, a); return __Pyx_c_prod(a, a); case 3: z = __Pyx_c_prod(a, a); return __Pyx_c_prod(z, a); case 4: z = __Pyx_c_prod(a, a); return __Pyx_c_prod(z, z); } } if (a.imag == 0) { if (a.real == 0) { return a; } r = a.real; theta = 0; } else { r = __Pyx_c_abs(a); theta = atan2(a.imag, a.real); } lnr = log(r); z_r = exp(lnr * b.real - theta * b.imag); z_theta = theta * b.real + lnr * b.imag; z.real = z_r * cos(z_theta); z.imag = z_r * sin(z_theta); return z; } #endif #endif static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { const unsigned char neg_one = (unsigned char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned char" : "value too large to convert to unsigned char"); } return (unsigned char)-1; } return (unsigned char)val; } return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { const unsigned short neg_one = (unsigned short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned short" : "value too large to convert to unsigned short"); } return (unsigned short)-1; } return (unsigned short)val; } return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { const unsigned int neg_one = (unsigned int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned int" : "value too large to convert to unsigned int"); } return (unsigned int)-1; } return (unsigned int)val; } return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { const char neg_one = (char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to char" : "value too large to convert to char"); } return (char)-1; } return (char)val; } return (char)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { const short neg_one = (short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to short" : "value too large to convert to short"); } return (short)-1; } return (short)val; } return (short)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { const signed char neg_one = (signed char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed char" : "value too large to convert to signed char"); } return (signed char)-1; } return (signed char)val; } return (signed char)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { const signed short neg_one = (signed short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed short" : "value too large to convert to signed short"); } return (signed short)-1; } return (signed short)val; } return (signed short)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { const signed int neg_one = (signed int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed int" : "value too large to convert to signed int"); } return (signed int)-1; } return (signed int)val; } return (signed int)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) { const unsigned long neg_one = (unsigned long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)PyLong_AsUnsignedLong(x); } else { return (unsigned long)PyLong_AsLong(x); } } else { unsigned long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned long)-1; val = __Pyx_PyInt_AsUnsignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) { const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x); } } else { unsigned PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned PY_LONG_LONG)-1; val = __Pyx_PyInt_AsUnsignedLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) { const long neg_one = (long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)PyLong_AsUnsignedLong(x); } else { return (long)PyLong_AsLong(x); } } else { long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (long)-1; val = __Pyx_PyInt_AsLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (PY_LONG_LONG)PyLong_AsLongLong(x); } } else { PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (PY_LONG_LONG)-1; val = __Pyx_PyInt_AsLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) { const signed long neg_one = (signed long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)PyLong_AsUnsignedLong(x); } else { return (signed long)PyLong_AsLong(x); } } else { signed long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed long)-1; val = __Pyx_PyInt_AsSignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (signed PY_LONG_LONG)PyLong_AsLongLong(x); } } else { signed PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed PY_LONG_LONG)-1; val = __Pyx_PyInt_AsSignedLongLong(tmp); Py_DECREF(tmp); return val; } } static int __Pyx_check_binary_version(void) { char ctversion[4], rtversion[4]; PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { char message[200]; PyOS_snprintf(message, sizeof(message), "compiletime version %s of module '%.100s' " "does not match runtime version %s", ctversion, __Pyx_MODULE_NAME, rtversion); #if PY_VERSION_HEX < 0x02050000 return PyErr_Warn(NULL, message); #else return PyErr_WarnEx(NULL, message, 1); #endif } return 0; } #ifndef __PYX_HAVE_RT_ImportModule #define __PYX_HAVE_RT_ImportModule static PyObject *__Pyx_ImportModule(const char *name) { PyObject *py_name = 0; PyObject *py_module = 0; py_name = __Pyx_PyIdentifier_FromString(name); if (!py_name) goto bad; py_module = PyImport_Import(py_name); Py_DECREF(py_name); return py_module; bad: Py_XDECREF(py_name); return 0; } #endif #ifndef __PYX_HAVE_RT_ImportType #define __PYX_HAVE_RT_ImportType static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict) { PyObject *py_module = 0; PyObject *result = 0; PyObject *py_name = 0; char warning[200]; Py_ssize_t basicsize; #ifdef Py_LIMITED_API PyObject *py_basicsize; #endif py_module = __Pyx_ImportModule(module_name); if (!py_module) goto bad; py_name = __Pyx_PyIdentifier_FromString(class_name); if (!py_name) goto bad; result = PyObject_GetAttr(py_module, py_name); Py_DECREF(py_name); py_name = 0; Py_DECREF(py_module); py_module = 0; if (!result) goto bad; if (!PyType_Check(result)) { PyErr_Format(PyExc_TypeError, "%s.%s is not a type object", module_name, class_name); goto bad; } #ifndef Py_LIMITED_API basicsize = ((PyTypeObject *)result)->tp_basicsize; #else py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); if (!py_basicsize) goto bad; basicsize = PyLong_AsSsize_t(py_basicsize); Py_DECREF(py_basicsize); py_basicsize = 0; if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) goto bad; #endif if (!strict && (size_t)basicsize > size) { PyOS_snprintf(warning, sizeof(warning), "%s.%s size changed, may indicate binary incompatibility", module_name, class_name); #if PY_VERSION_HEX < 0x02050000 if (PyErr_Warn(NULL, warning) < 0) goto bad; #else if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; #endif } else if ((size_t)basicsize != size) { PyErr_Format(PyExc_ValueError, "%s.%s has the wrong size, try recompiling", module_name, class_name); goto bad; } return (PyTypeObject *)result; bad: Py_XDECREF(py_module); Py_XDECREF(result); return NULL; } #endif static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { int start = 0, mid = 0, end = count - 1; if (end >= 0 && code_line > entries[end].code_line) { return count; } while (start < end) { mid = (start + end) / 2; if (code_line < entries[mid].code_line) { end = mid; } else if (code_line > entries[mid].code_line) { start = mid + 1; } else { return mid; } } if (code_line <= entries[mid].code_line) { return mid; } else { return mid + 1; } } static PyCodeObject *__pyx_find_code_object(int code_line) { PyCodeObject* code_object; int pos; if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { return NULL; } pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { return NULL; } code_object = __pyx_code_cache.entries[pos].code_object; Py_INCREF(code_object); return code_object; } static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { int pos, i; __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; if (unlikely(!code_line)) { return; } if (unlikely(!entries)) { entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); if (likely(entries)) { __pyx_code_cache.entries = entries; __pyx_code_cache.max_count = 64; __pyx_code_cache.count = 1; entries[0].code_line = code_line; entries[0].code_object = code_object; Py_INCREF(code_object); } return; } pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { PyCodeObject* tmp = entries[pos].code_object; entries[pos].code_object = code_object; Py_DECREF(tmp); return; } if (__pyx_code_cache.count == __pyx_code_cache.max_count) { int new_max = __pyx_code_cache.max_count + 64; entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry)); if (unlikely(!entries)) { return; } __pyx_code_cache.entries = entries; __pyx_code_cache.max_count = new_max; } for (i=__pyx_code_cache.count; i>pos; i--) { entries[i] = entries[i-1]; } entries[pos].code_line = code_line; entries[pos].code_object = code_object; __pyx_code_cache.count++; Py_INCREF(code_object); } #include "compile.h" #include "frameobject.h" #include "traceback.h" static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( const char *funcname, int c_line, int py_line, const char *filename) { PyCodeObject *py_code = 0; PyObject *py_srcfile = 0; PyObject *py_funcname = 0; #if PY_MAJOR_VERSION < 3 py_srcfile = PyString_FromString(filename); #else py_srcfile = PyUnicode_FromString(filename); #endif if (!py_srcfile) goto bad; if (c_line) { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); #else py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); #endif } else { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromString(funcname); #else py_funcname = PyUnicode_FromString(funcname); #endif } if (!py_funcname) goto bad; py_code = __Pyx_PyCode_New( 0, /*int argcount,*/ 0, /*int kwonlyargcount,*/ 0, /*int nlocals,*/ 0, /*int stacksize,*/ 0, /*int flags,*/ __pyx_empty_bytes, /*PyObject *code,*/ __pyx_empty_tuple, /*PyObject *consts,*/ __pyx_empty_tuple, /*PyObject *names,*/ __pyx_empty_tuple, /*PyObject *varnames,*/ __pyx_empty_tuple, /*PyObject *freevars,*/ __pyx_empty_tuple, /*PyObject *cellvars,*/ py_srcfile, /*PyObject *filename,*/ py_funcname, /*PyObject *name,*/ py_line, /*int firstlineno,*/ __pyx_empty_bytes /*PyObject *lnotab*/ ); Py_DECREF(py_srcfile); Py_DECREF(py_funcname); return py_code; bad: Py_XDECREF(py_srcfile); Py_XDECREF(py_funcname); return NULL; } static void __Pyx_AddTraceback(const char *funcname, int c_line, int py_line, const char *filename) { PyCodeObject *py_code = 0; PyObject *py_globals = 0; PyFrameObject *py_frame = 0; py_code = __pyx_find_code_object(c_line ? c_line : py_line); if (!py_code) { py_code = __Pyx_CreateCodeObjectForTraceback( funcname, c_line, py_line, filename); if (!py_code) goto bad; __pyx_insert_code_object(c_line ? c_line : py_line, py_code); } py_globals = PyModule_GetDict(__pyx_m); if (!py_globals) goto bad; py_frame = PyFrame_New( PyThreadState_GET(), /*PyThreadState *tstate,*/ py_code, /*PyCodeObject *code,*/ py_globals, /*PyObject *globals,*/ 0 /*PyObject *locals*/ ); if (!py_frame) goto bad; py_frame->f_lineno = py_line; PyTraceBack_Here(py_frame); bad: Py_XDECREF(py_code); Py_XDECREF(py_frame); } static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { while (t->p) { #if PY_MAJOR_VERSION < 3 if (t->is_unicode) { *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); } else if (t->intern) { *t->p = PyString_InternFromString(t->s); } else { *t->p = PyString_FromStringAndSize(t->s, t->n - 1); } #else /* Python 3+ has unicode identifiers */ if (t->is_unicode | t->is_str) { if (t->intern) { *t->p = PyUnicode_InternFromString(t->s); } else if (t->encoding) { *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); } else { *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); } } else { *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); } #endif if (!*t->p) return -1; ++t; } return 0; } static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { int is_true = x == Py_True; if (is_true | (x == Py_False) | (x == Py_None)) return is_true; else return PyObject_IsTrue(x); } static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { PyNumberMethods *m; const char *name = NULL; PyObject *res = NULL; #if PY_VERSION_HEX < 0x03000000 if (PyInt_Check(x) || PyLong_Check(x)) #else if (PyLong_Check(x)) #endif return Py_INCREF(x), x; m = Py_TYPE(x)->tp_as_number; #if PY_VERSION_HEX < 0x03000000 if (m && m->nb_int) { name = "int"; res = PyNumber_Int(x); } else if (m && m->nb_long) { name = "long"; res = PyNumber_Long(x); } #else if (m && m->nb_int) { name = "int"; res = PyNumber_Long(x); } #endif if (res) { #if PY_VERSION_HEX < 0x03000000 if (!PyInt_Check(res) && !PyLong_Check(res)) { #else if (!PyLong_Check(res)) { #endif PyErr_Format(PyExc_TypeError, "__%s__ returned non-%s (type %.200s)", name, name, Py_TYPE(res)->tp_name); Py_DECREF(res); return NULL; } } else if (!PyErr_Occurred()) { PyErr_SetString(PyExc_TypeError, "an integer is required"); } return res; } static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { Py_ssize_t ival; PyObject* x = PyNumber_Index(b); if (!x) return -1; ival = PyInt_AsSsize_t(x); Py_DECREF(x); return ival; } static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { #if PY_VERSION_HEX < 0x02050000 if (ival <= LONG_MAX) return PyInt_FromLong((long)ival); else { unsigned char *bytes = (unsigned char *) &ival; int one = 1; int little = (int)*(unsigned char*)&one; return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0); } #else return PyInt_FromSize_t(ival); #endif } static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x); if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) { return (size_t)-1; } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) { PyErr_SetString(PyExc_OverflowError, "value too large to convert to size_t"); return (size_t)-1; } return (size_t)val; } #endif /* Py_PYTHON_H */ fabio-0.1.3/src/byte_offset.c0000644000175000017500000072072512233175156016645 0ustar jeromejerome00000000000000/* Generated by Cython 0.15.1+ on Fri Dec 9 12:19:09 2011 */ #define PY_SSIZE_T_CLEAN #include "Python.h" #ifndef Py_PYTHON_H #error Python headers needed to compile C extensions, please install development version of Python. #elif PY_VERSION_HEX < 0x02040000 #error Cython requires Python 2.4+. #else #include /* For offsetof */ #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) #endif #if !defined(WIN32) && !defined(MS_WINDOWS) #ifndef __stdcall #define __stdcall #endif #ifndef __cdecl #define __cdecl #endif #ifndef __fastcall #define __fastcall #endif #endif #ifndef DL_IMPORT #define DL_IMPORT(t) t #endif #ifndef DL_EXPORT #define DL_EXPORT(t) t #endif #ifndef PY_LONG_LONG #define PY_LONG_LONG LONG_LONG #endif #if PY_VERSION_HEX < 0x02050000 typedef int Py_ssize_t; #define PY_SSIZE_T_MAX INT_MAX #define PY_SSIZE_T_MIN INT_MIN #define PY_FORMAT_SIZE_T "" #define PyInt_FromSsize_t(z) PyInt_FromLong(z) #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o) #define PyNumber_Index(o) PyNumber_Int(o) #define PyIndex_Check(o) PyNumber_Check(o) #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message) #endif #if PY_VERSION_HEX < 0x02060000 #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt) #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type) #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size) #define PyVarObject_HEAD_INIT(type, size) \ PyObject_HEAD_INIT(type) size, #define PyType_Modified(t) typedef struct { void *buf; PyObject *obj; Py_ssize_t len; Py_ssize_t itemsize; int readonly; int ndim; char *format; Py_ssize_t *shape; Py_ssize_t *strides; Py_ssize_t *suboffsets; void *internal; } Py_buffer; #define PyBUF_SIMPLE 0 #define PyBUF_WRITABLE 0x0001 #define PyBUF_FORMAT 0x0004 #define PyBUF_ND 0x0008 #define PyBUF_STRIDES (0x0010 | PyBUF_ND) #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES) #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES) #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES) #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES) #endif #if PY_MAJOR_VERSION < 3 #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #else #define __Pyx_BUILTIN_MODULE_NAME "builtins" #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s) #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #endif #if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6 #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict") #endif #if PY_MAJOR_VERSION >= 3 #define Py_TPFLAGS_CHECKTYPES 0 #define Py_TPFLAGS_HAVE_INDEX 0 #endif #if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3) #define Py_TPFLAGS_HAVE_NEWBUFFER 0 #endif /* new Py3.3 unicode representation (PEP 393) */ #if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_GET_LENGTH) #define CYTHON_PEP393_ENABLED #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) #else #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) #endif #if PY_MAJOR_VERSION >= 3 #define PyBaseString_Type PyUnicode_Type #define PyStringObject PyUnicodeObject #define PyString_Type PyUnicode_Type #define PyString_Check PyUnicode_Check #define PyString_CheckExact PyUnicode_CheckExact #endif #if PY_VERSION_HEX < 0x02060000 #define PyBytesObject PyStringObject #define PyBytes_Type PyString_Type #define PyBytes_Check PyString_Check #define PyBytes_CheckExact PyString_CheckExact #define PyBytes_FromString PyString_FromString #define PyBytes_FromStringAndSize PyString_FromStringAndSize #define PyBytes_FromFormat PyString_FromFormat #define PyBytes_DecodeEscape PyString_DecodeEscape #define PyBytes_AsString PyString_AsString #define PyBytes_AsStringAndSize PyString_AsStringAndSize #define PyBytes_Size PyString_Size #define PyBytes_AS_STRING PyString_AS_STRING #define PyBytes_GET_SIZE PyString_GET_SIZE #define PyBytes_Repr PyString_Repr #define PyBytes_Concat PyString_Concat #define PyBytes_ConcatAndDel PyString_ConcatAndDel #endif #if PY_VERSION_HEX < 0x02060000 #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type) #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type) #endif #ifndef PySet_CheckExact #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) #endif #define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) #if PY_MAJOR_VERSION >= 3 #define PyIntObject PyLongObject #define PyInt_Type PyLong_Type #define PyInt_Check(op) PyLong_Check(op) #define PyInt_CheckExact(op) PyLong_CheckExact(op) #define PyInt_FromString PyLong_FromString #define PyInt_FromUnicode PyLong_FromUnicode #define PyInt_FromLong PyLong_FromLong #define PyInt_FromSize_t PyLong_FromSize_t #define PyInt_FromSsize_t PyLong_FromSsize_t #define PyInt_AsLong PyLong_AsLong #define PyInt_AS_LONG PyLong_AS_LONG #define PyInt_AsSsize_t PyLong_AsSsize_t #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask #endif #if PY_MAJOR_VERSION >= 3 #define PyBoolObject PyLongObject #endif #if PY_VERSION_HEX < 0x03020000 typedef long Py_hash_t; #define __Pyx_PyInt_FromHash_t PyInt_FromLong #define __Pyx_PyInt_AsHash_t PyInt_AsLong #else #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t #endif #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) #else #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) #endif #if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300) #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b) #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value) #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b) #else #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0))) #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1))) #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1))) #endif #if PY_MAJOR_VERSION >= 3 #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func)) #endif #if PY_VERSION_HEX < 0x02050000 #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n))) #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a)) #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n))) #else #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n)) #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a)) #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n)) #endif #if PY_VERSION_HEX < 0x02050000 #define __Pyx_NAMESTR(n) ((char *)(n)) #define __Pyx_DOCSTR(n) ((char *)(n)) #else #define __Pyx_NAMESTR(n) (n) #define __Pyx_DOCSTR(n) (n) #endif #ifndef __PYX_EXTERN_C #ifdef __cplusplus #define __PYX_EXTERN_C extern "C" #else #define __PYX_EXTERN_C extern #endif #endif #if defined(WIN32) || defined(MS_WINDOWS) #define _USE_MATH_DEFINES #endif #include #define __PYX_HAVE__byte_offset #define __PYX_HAVE_API__byte_offset #include "stdio.h" #include "stdlib.h" #include "numpy/arrayobject.h" #include "numpy/ufuncobject.h" #ifdef _OPENMP #include #endif /* _OPENMP */ #ifdef PYREX_WITHOUT_ASSERTIONS #define CYTHON_WITHOUT_ASSERTIONS #endif /* inline attribute */ #ifndef CYTHON_INLINE #if defined(__GNUC__) #define CYTHON_INLINE __inline__ #elif defined(_MSC_VER) #define CYTHON_INLINE __inline #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L #define CYTHON_INLINE inline #else #define CYTHON_INLINE #endif #endif /* unused attribute */ #ifndef CYTHON_UNUSED # if defined(__GNUC__) # if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) # define CYTHON_UNUSED __attribute__ ((__unused__)) # else # define CYTHON_UNUSED # endif # elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) # define CYTHON_UNUSED __attribute__ ((__unused__)) # else # define CYTHON_UNUSED # endif #endif typedef struct {PyObject **p; char *s; const long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/ /* Type Conversion Predeclarations */ #define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s) #define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s)) #define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None) #define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False)) static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x); static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*); #define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) #ifdef __GNUC__ /* Test for GCC > 2.95 */ #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)) #define likely(x) __builtin_expect(!!(x), 1) #define unlikely(x) __builtin_expect(!!(x), 0) #else /* __GNUC__ > 2 ... */ #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ > 2 ... */ #else /* __GNUC__ */ #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ */ static PyObject *__pyx_m; static PyObject *__pyx_b; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; static int __pyx_lineno; static int __pyx_clineno = 0; static const char * __pyx_cfilenm= __FILE__; static const char *__pyx_filename; #if !defined(CYTHON_CCOMPLEX) #if defined(__cplusplus) #define CYTHON_CCOMPLEX 1 #elif defined(_Complex_I) #define CYTHON_CCOMPLEX 1 #else #define CYTHON_CCOMPLEX 0 #endif #endif #if CYTHON_CCOMPLEX #ifdef __cplusplus #include #else #include #endif #endif #if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__) #undef _Complex_I #define _Complex_I 1.0fj #endif static const char *__pyx_f[] = { "byte_offset.pyx", "numpy.pxd", }; /* "numpy.pxd":719 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t */ typedef npy_int8 __pyx_t_5numpy_int8_t; /* "numpy.pxd":720 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t */ typedef npy_int16 __pyx_t_5numpy_int16_t; /* "numpy.pxd":721 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< * ctypedef npy_int64 int64_t * #ctypedef npy_int96 int96_t */ typedef npy_int32 __pyx_t_5numpy_int32_t; /* "numpy.pxd":722 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< * #ctypedef npy_int96 int96_t * #ctypedef npy_int128 int128_t */ typedef npy_int64 __pyx_t_5numpy_int64_t; /* "numpy.pxd":726 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; /* "numpy.pxd":727 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; /* "numpy.pxd":728 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< * ctypedef npy_uint64 uint64_t * #ctypedef npy_uint96 uint96_t */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; /* "numpy.pxd":729 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< * #ctypedef npy_uint96 uint96_t * #ctypedef npy_uint128 uint128_t */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; /* "numpy.pxd":733 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< * ctypedef npy_float64 float64_t * #ctypedef npy_float80 float80_t */ typedef npy_float32 __pyx_t_5numpy_float32_t; /* "numpy.pxd":734 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< * #ctypedef npy_float80 float80_t * #ctypedef npy_float128 float128_t */ typedef npy_float64 __pyx_t_5numpy_float64_t; /* "numpy.pxd":743 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t */ typedef npy_long __pyx_t_5numpy_int_t; /* "numpy.pxd":744 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< * ctypedef npy_longlong longlong_t * */ typedef npy_longlong __pyx_t_5numpy_long_t; /* "numpy.pxd":745 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< * * ctypedef npy_ulong uint_t */ typedef npy_longlong __pyx_t_5numpy_longlong_t; /* "numpy.pxd":747 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t */ typedef npy_ulong __pyx_t_5numpy_uint_t; /* "numpy.pxd":748 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< * ctypedef npy_ulonglong ulonglong_t * */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; /* "numpy.pxd":749 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< * * ctypedef npy_intp intp_t */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; /* "numpy.pxd":751 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< * ctypedef npy_uintp uintp_t * */ typedef npy_intp __pyx_t_5numpy_intp_t; /* "numpy.pxd":752 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< * * ctypedef npy_double float_t */ typedef npy_uintp __pyx_t_5numpy_uintp_t; /* "numpy.pxd":754 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t */ typedef npy_double __pyx_t_5numpy_float_t; /* "numpy.pxd":755 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< * ctypedef npy_longdouble longdouble_t * */ typedef npy_double __pyx_t_5numpy_double_t; /* "numpy.pxd":756 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< * * ctypedef npy_cfloat cfloat_t */ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; #if CYTHON_CCOMPLEX #ifdef __cplusplus typedef ::std::complex< float > __pyx_t_float_complex; #else typedef float _Complex __pyx_t_float_complex; #endif #else typedef struct { float real, imag; } __pyx_t_float_complex; #endif #if CYTHON_CCOMPLEX #ifdef __cplusplus typedef ::std::complex< double > __pyx_t_double_complex; #else typedef double _Complex __pyx_t_double_complex; #endif #else typedef struct { double real, imag; } __pyx_t_double_complex; #endif /*--- Type declarations ---*/ /* "numpy.pxd":758 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; /* "numpy.pxd":759 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< * ctypedef npy_clongdouble clongdouble_t * */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; /* "numpy.pxd":760 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< * * ctypedef npy_cdouble complex_t */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; 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/*proto*/ static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/ static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, const char *name, int exact); /*proto*/ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/ static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/ #define IS_UNSIGNED(type) (((type) -1) > 0) /* Run-time type information about structs used with buffers */ struct __Pyx_StructField_; #define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0) typedef struct { const char* name; /* for error messages only */ struct __Pyx_StructField_* fields; size_t size; /* sizeof(type) */ char typegroup; /* _R_eal, _C_omplex, Signed _I_nt, _U_nsigned int, _S_truct, _P_ointer, _O_bject */ char is_unsigned; int flags; } __Pyx_TypeInfo; typedef struct __Pyx_StructField_ { __Pyx_TypeInfo* type; const char* name; size_t offset; } __Pyx_StructField; 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/*proto*/ #ifndef __PYX_FORCE_INIT_THREADS #define __PYX_FORCE_INIT_THREADS 0 #endif #if CYTHON_CCOMPLEX #ifdef __cplusplus #define __Pyx_CREAL(z) ((z).real()) #define __Pyx_CIMAG(z) ((z).imag()) #else #define __Pyx_CREAL(z) (__real__(z)) #define __Pyx_CIMAG(z) (__imag__(z)) #endif #else #define __Pyx_CREAL(z) ((z).real) #define __Pyx_CIMAG(z) ((z).imag) #endif #if defined(_WIN32) && defined(__cplusplus) && CYTHON_CCOMPLEX #define __Pyx_SET_CREAL(z,x) ((z).real(x)) #define __Pyx_SET_CIMAG(z,y) ((z).imag(y)) #else #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x) #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y) #endif static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float); #if CYTHON_CCOMPLEX #define __Pyx_c_eqf(a, b) ((a)==(b)) #define __Pyx_c_sumf(a, b) ((a)+(b)) #define __Pyx_c_difff(a, b) ((a)-(b)) #define __Pyx_c_prodf(a, b) ((a)*(b)) #define __Pyx_c_quotf(a, b) ((a)/(b)) #define __Pyx_c_negf(a) (-(a)) #ifdef __cplusplus #define __Pyx_c_is_zerof(z) ((z)==(float)0) #define __Pyx_c_conjf(z) (::std::conj(z)) #if 1 #define __Pyx_c_absf(z) (::std::abs(z)) #define __Pyx_c_powf(a, b) (::std::pow(a, b)) #endif #else #define __Pyx_c_is_zerof(z) ((z)==0) #define __Pyx_c_conjf(z) (conjf(z)) #if 1 #define __Pyx_c_absf(z) (cabsf(z)) #define __Pyx_c_powf(a, b) (cpowf(a, b)) #endif #endif #else static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex, __pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex, __pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex, __pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex, __pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex, __pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex); static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex); #if 1 static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex, __pyx_t_float_complex); #endif #endif static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double); #if CYTHON_CCOMPLEX #define __Pyx_c_eq(a, b) ((a)==(b)) #define __Pyx_c_sum(a, b) ((a)+(b)) #define __Pyx_c_diff(a, b) ((a)-(b)) #define __Pyx_c_prod(a, b) ((a)*(b)) #define __Pyx_c_quot(a, b) ((a)/(b)) #define __Pyx_c_neg(a) (-(a)) #ifdef __cplusplus #define __Pyx_c_is_zero(z) ((z)==(double)0) #define __Pyx_c_conj(z) (::std::conj(z)) #if 1 #define __Pyx_c_abs(z) (::std::abs(z)) #define __Pyx_c_pow(a, b) (::std::pow(a, b)) #endif #else #define __Pyx_c_is_zero(z) ((z)==0) #define __Pyx_c_conj(z) (conj(z)) #if 1 #define __Pyx_c_abs(z) (cabs(z)) #define __Pyx_c_pow(a, b) (cpow(a, b)) #endif #endif #else static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex, __pyx_t_double_complex); static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex, __pyx_t_double_complex); static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex, __pyx_t_double_complex); static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex, __pyx_t_double_complex); static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex, __pyx_t_double_complex); static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex); static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex); static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex); #if 1 static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex); static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex, __pyx_t_double_complex); #endif #endif static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *); static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *); static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *); static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject *); static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject *); static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject *); static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject *); static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *); static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject *); static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject *); static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *); static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *); static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject *); static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *); static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *); static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *); static int __Pyx_check_binary_version(void); static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/ static PyObject *__Pyx_ImportModule(const char *name); /*proto*/ static void __Pyx_AddTraceback(const char *funcname, int __pyx_clineno, int __pyx_lineno, const char *__pyx_filename); /*proto*/ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/ /* Module declarations from 'cpython.buffer' */ /* Module declarations from 'cpython.ref' */ /* Module declarations from 'libc.stdio' */ /* Module declarations from 'cpython.object' */ /* Module declarations from 'libc.stdlib' */ /* Module declarations from 'numpy' */ /* Module declarations from 'numpy' */ static PyTypeObject *__pyx_ptype_5numpy_dtype = 0; static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0; static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0; static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0; static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0; static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/ /* Module declarations from 'cython' */ /* Module declarations from 'byte_offset' */ static __Pyx_TypeInfo __Pyx_TypeInfo_PY_LONG_LONG = { "long long", NULL, sizeof(PY_LONG_LONG), 'I', IS_UNSIGNED(PY_LONG_LONG), 0 }; #define __Pyx_MODULE_NAME "byte_offset" int __pyx_module_is_main_byte_offset = 0; /* Implementation of 'byte_offset' */ static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_RuntimeError; static char __pyx_k_1[] = "ndarray is not C contiguous"; static char __pyx_k_3[] = "ndarray is not Fortran contiguous"; static char __pyx_k_5[] = "Non-native byte order not supported"; static char __pyx_k_7[] = "unknown dtype code in numpy.pxd (%d)"; static char __pyx_k_8[] = "Format string allocated too short, see comment in numpy.pxd"; static char __pyx_k_11[] = "Format string allocated too short."; static char __pyx_k_13[] = "\nAuthors: Jerome Kieffer, ESRF \nEmail: jerome.kieffer@esrf.eu\n\nCif Binary Files images are 2D images written by the Pilatus detector and others.\nThey use a modified (simplified) byte-offset algorithm. 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if (value) { values[1] = value; kw_args--; } } } if (unlikely(kw_args > 0)) { if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "analyseCython") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } __pyx_v_stream = ((PyObject*)values[0]); __pyx_v_size = values[1]; } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; } } __pyx_v_stream = ((PyObject*)values[0]); __pyx_v_size = values[1]; } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("analyseCython", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("byte_offset.analyseCython", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); 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/* "byte_offset.pyx":51 * cdef long long tmp64b = 0 * cdef long long tmp64c = 0 * cdef long long tmp64d = 0 # <<<<<<<<<<<<<< * cdef long long tmp64e = 0 * cdef long long tmp64f = 0 */ __pyx_v_tmp64d = 0; /* "byte_offset.pyx":52 * cdef long long tmp64c = 0 * cdef long long tmp64d = 0 * cdef long long tmp64e = 0 # <<<<<<<<<<<<<< * cdef long long tmp64f = 0 * cdef long long tmp64g = 0 */ __pyx_v_tmp64e = 0; /* "byte_offset.pyx":53 * cdef long long tmp64d = 0 * cdef long long tmp64e = 0 * cdef long long tmp64f = 0 # <<<<<<<<<<<<<< * cdef long long tmp64g = 0 * */ __pyx_v_tmp64f = 0; /* "byte_offset.pyx":54 * cdef long long tmp64e = 0 * cdef long long tmp64f = 0 * cdef long long tmp64g = 0 # <<<<<<<<<<<<<< * * cdef char key8 = 0x80 */ __pyx_v_tmp64g = 0; /* "byte_offset.pyx":56 * cdef long long tmp64g = 0 * * cdef char key8 = 0x80 # <<<<<<<<<<<<<< * cdef char key0 = 0x00 * */ __pyx_v_key8 = 0x80; /* "byte_offset.pyx":57 * * cdef char key8 = 0x80 * cdef char key0 = 0x00 # <<<<<<<<<<<<<< * * cdef int csize */ __pyx_v_key0 = 0x00; 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#else if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) && _PyString_Eq(**name, key)) goto arg_passed_twice; #endif } if (kwds2) { if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; } else { goto invalid_keyword; } } } } } return 0; arg_passed_twice: __Pyx_RaiseDoubleKeywordsError(function_name, **name); goto bad; invalid_keyword_type: PyErr_Format(PyExc_TypeError, "%s() keywords must be strings", function_name); goto bad; invalid_keyword: PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION < 3 "%s() got an unexpected keyword argument '%s'", function_name, PyString_AsString(key)); #else "%s() got an unexpected keyword argument '%U'", function_name, key); #endif bad: return -1; } static void __Pyx_RaiseArgtupleInvalid( const char* func_name, int exact, Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found) { Py_ssize_t num_expected; const char *more_or_less; if (num_found < num_min) { num_expected = num_min; more_or_less = "at least"; } else { num_expected = num_max; more_or_less = "at most"; } if (exact) { more_or_less = "exactly"; } PyErr_Format(PyExc_TypeError, "%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)", func_name, more_or_less, num_expected, (num_expected == 1) ? "" : "s", num_found); } static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, const char *name, int exact) { if (!type) { PyErr_Format(PyExc_SystemError, "Missing type object"); return 0; } if (none_allowed && obj == Py_None) return 1; else if (exact) { if (Py_TYPE(obj) == type) return 1; } else { if (PyObject_TypeCheck(obj, type)) return 1; } PyErr_Format(PyExc_TypeError, "Argument '%s' has incorrect type (expected %s, got %s)", name, type->tp_name, Py_TYPE(obj)->tp_name); return 0; } static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) { PyObject *result; result = PyObject_GetAttr(dict, name); if (!result) { if (dict != __pyx_b) { PyErr_Clear(); result = PyObject_GetAttr(__pyx_b, name); } if (!result) { PyErr_SetObject(PyExc_NameError, name); } } return result; } static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { if (unlikely(!type)) { PyErr_Format(PyExc_SystemError, "Missing type object"); return 0; } if (likely(PyObject_TypeCheck(obj, type))) return 1; PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", Py_TYPE(obj)->tp_name, type->tp_name); return 0; } static CYTHON_INLINE int __Pyx_IsLittleEndian(void) { unsigned int n = 1; return *(unsigned char*)(&n) != 0; } static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, __Pyx_BufFmt_StackElem* stack, __Pyx_TypeInfo* type) { stack[0].field = &ctx->root; stack[0].parent_offset = 0; ctx->root.type = type; ctx->root.name = "buffer dtype"; ctx->root.offset = 0; ctx->head = stack; ctx->head->field = &ctx->root; ctx->fmt_offset = 0; ctx->head->parent_offset = 0; ctx->new_packmode = '@'; ctx->enc_packmode = '@'; ctx->new_count = 1; ctx->enc_count = 0; ctx->enc_type = 0; ctx->is_complex = 0; while (type->typegroup == 'S') { ++ctx->head; ctx->head->field = type->fields; ctx->head->parent_offset = 0; type = type->fields->type; } } static int __Pyx_BufFmt_ParseNumber(const char** ts) { int count; const char* t = *ts; if (*t < '0' || *t > '9') { return -1; } else { count = *t++ - '0'; while (*t >= '0' && *t < '9') { count *= 10; count += *t++ - '0'; } } *ts = t; return count; } static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { PyErr_Format(PyExc_ValueError, "Unexpected format string character: '%c'", ch); } static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { switch (ch) { case 'b': return "'char'"; case 'B': return "'unsigned char'"; case 'h': return "'short'"; case 'H': return "'unsigned short'"; case 'i': return "'int'"; case 'I': return "'unsigned int'"; case 'l': return "'long'"; case 'L': return "'unsigned long'"; case 'q': return "'long long'"; case 'Q': return "'unsigned long long'"; case 'f': return (is_complex ? "'complex float'" : "'float'"); case 'd': return (is_complex ? "'complex double'" : "'double'"); case 'g': return (is_complex ? "'complex long double'" : "'long double'"); case 'T': return "a struct"; case 'O': return "Python object"; case 'P': return "a pointer"; case 0: return "end"; default: return "unparseable format string"; } } static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { switch (ch) { case '?': case 'c': case 'b': case 'B': return 1; case 'h': case 'H': return 2; case 'i': case 'I': case 'l': case 'L': return 4; case 'q': case 'Q': return 8; case 'f': return (is_complex ? 8 : 4); case 'd': return (is_complex ? 16 : 8); case 'g': { PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); return 0; } case 'O': case 'P': return sizeof(void*); default: __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { switch (ch) { case 'c': case 'b': case 'B': return 1; case 'h': case 'H': return sizeof(short); case 'i': case 'I': return sizeof(int); case 'l': case 'L': return sizeof(long); #ifdef HAVE_LONG_LONG case 'q': case 'Q': return sizeof(PY_LONG_LONG); #endif case 'f': return sizeof(float) * (is_complex ? 2 : 1); case 'd': return sizeof(double) * (is_complex ? 2 : 1); case 'g': return sizeof(long double) * (is_complex ? 2 : 1); case 'O': case 'P': return sizeof(void*); default: { __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } } typedef struct { char c; short x; } __Pyx_st_short; typedef struct { char c; int x; } __Pyx_st_int; typedef struct { char c; long x; } __Pyx_st_long; typedef struct { char c; float x; } __Pyx_st_float; typedef struct { char c; double x; } __Pyx_st_double; typedef struct { char c; long double x; } __Pyx_st_longdouble; typedef struct { char c; void *x; } __Pyx_st_void_p; #ifdef HAVE_LONG_LONG typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; #endif static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, int is_complex) { switch (ch) { case '?': case 'c': case 'b': case 'B': return 1; case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); #ifdef HAVE_LONG_LONG case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); #endif case 'f': return sizeof(__Pyx_st_float) - sizeof(float); case 'd': return sizeof(__Pyx_st_double) - sizeof(double); case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); default: __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { switch (ch) { case 'c': case 'b': case 'h': case 'i': case 'l': case 'q': return 'I'; case 'B': case 'H': case 'I': case 'L': case 'Q': return 'U'; case 'f': case 'd': case 'g': return (is_complex ? 'C' : 'R'); case 'O': return 'O'; case 'P': return 'P'; default: { __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } } static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { if (ctx->head == NULL || ctx->head->field == &ctx->root) { const char* expected; const char* quote; if (ctx->head == NULL) { expected = "end"; quote = ""; } else { expected = ctx->head->field->type->name; quote = "'"; } PyErr_Format(PyExc_ValueError, "Buffer dtype mismatch, expected %s%s%s but got %s", quote, expected, quote, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); } else { __Pyx_StructField* field = ctx->head->field; __Pyx_StructField* parent = (ctx->head - 1)->field; PyErr_Format(PyExc_ValueError, "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), parent->type->name, field->name); } } static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { char group; size_t size, offset; if (ctx->enc_type == 0) return 0; group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); do { __Pyx_StructField* field = ctx->head->field; __Pyx_TypeInfo* type = field->type; if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); } else { size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); } if (ctx->enc_packmode == '@') { size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); size_t align_mod_offset; if (align_at == 0) return -1; align_mod_offset = ctx->fmt_offset % align_at; if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; } if (type->size != size || type->typegroup != group) { if (type->typegroup == 'C' && type->fields != NULL) { /* special case -- treat as struct rather than complex number */ size_t parent_offset = ctx->head->parent_offset + field->offset; ++ctx->head; ctx->head->field = type->fields; ctx->head->parent_offset = parent_offset; continue; } __Pyx_BufFmt_RaiseExpected(ctx); return -1; } offset = ctx->head->parent_offset + field->offset; if (ctx->fmt_offset != offset) { PyErr_Format(PyExc_ValueError, "Buffer dtype mismatch; next field is at offset %"PY_FORMAT_SIZE_T"d but %"PY_FORMAT_SIZE_T"d expected", (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); return -1; } ctx->fmt_offset += size; --ctx->enc_count; /* Consume from buffer string */ /* Done checking, move to next field, pushing or popping struct stack if needed */ while (1) { if (field == &ctx->root) { ctx->head = NULL; if (ctx->enc_count != 0) { __Pyx_BufFmt_RaiseExpected(ctx); return -1; } break; /* breaks both loops as ctx->enc_count == 0 */ } ctx->head->field = ++field; if (field->type == NULL) { --ctx->head; field = ctx->head->field; continue; } else if (field->type->typegroup == 'S') { size_t parent_offset = ctx->head->parent_offset + field->offset; if (field->type->fields->type == NULL) continue; /* empty struct */ field = field->type->fields; ++ctx->head; ctx->head->field = field; ctx->head->parent_offset = parent_offset; break; } else { break; } } } while (ctx->enc_count); ctx->enc_type = 0; ctx->is_complex = 0; return 0; } static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { int got_Z = 0; while (1) { switch(*ts) { case 0: if (ctx->enc_type != 0 && ctx->head == NULL) { __Pyx_BufFmt_RaiseExpected(ctx); return NULL; } if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; if (ctx->head != NULL) { __Pyx_BufFmt_RaiseExpected(ctx); return NULL; } return ts; case ' ': case 10: case 13: ++ts; break; case '<': if (!__Pyx_IsLittleEndian()) { PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); return NULL; } ctx->new_packmode = '='; ++ts; break; case '>': case '!': if (__Pyx_IsLittleEndian()) { PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); return NULL; } ctx->new_packmode = '='; ++ts; break; case '=': case '@': case '^': ctx->new_packmode = *ts++; break; case 'T': /* substruct */ { const char* ts_after_sub; size_t i, struct_count = ctx->new_count; ctx->new_count = 1; ++ts; if (*ts != '{') { PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); return NULL; } ++ts; ts_after_sub = ts; for (i = 0; i != struct_count; ++i) { ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); if (!ts_after_sub) return NULL; } ts = ts_after_sub; } break; case '}': /* end of substruct; either repeat or move on */ ++ts; return ts; case 'x': if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; ctx->fmt_offset += ctx->new_count; ctx->new_count = 1; ctx->enc_count = 0; ctx->enc_type = 0; ctx->enc_packmode = ctx->new_packmode; ++ts; break; case 'Z': got_Z = 1; ++ts; if (*ts != 'f' && *ts != 'd' && *ts != 'g') { __Pyx_BufFmt_RaiseUnexpectedChar('Z'); return NULL; } /* fall through */ case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': case 'l': case 'L': case 'q': case 'Q': case 'f': case 'd': case 'g': case 'O': if (ctx->enc_type == *ts && got_Z == ctx->is_complex && ctx->enc_packmode == ctx->new_packmode) { /* Continue pooling same type */ ctx->enc_count += ctx->new_count; } else { /* New type */ if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; ctx->enc_count = ctx->new_count; ctx->enc_packmode = ctx->new_packmode; ctx->enc_type = *ts; ctx->is_complex = got_Z; } ++ts; ctx->new_count = 1; got_Z = 0; break; case ':': ++ts; while(*ts != ':') ++ts; ++ts; break; default: { int number = __Pyx_BufFmt_ParseNumber(&ts); if (number == -1) { /* First char was not a digit */ PyErr_Format(PyExc_ValueError, "Does not understand character buffer dtype format string ('%c')", *ts); return NULL; } ctx->new_count = (size_t)number; } } } } static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) { buf->buf = NULL; buf->obj = NULL; buf->strides = __Pyx_zeros; buf->shape = __Pyx_zeros; buf->suboffsets = __Pyx_minusones; } static CYTHON_INLINE int __Pyx_GetBufferAndValidate( Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack) { if (obj == Py_None || obj == NULL) { __Pyx_ZeroBuffer(buf); return 0; } buf->buf = NULL; if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail; if (buf->ndim != nd) { PyErr_Format(PyExc_ValueError, "Buffer has wrong number of dimensions (expected %d, got %d)", nd, buf->ndim); goto fail; } if (!cast) { __Pyx_BufFmt_Context ctx; __Pyx_BufFmt_Init(&ctx, stack, dtype); if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; } if ((unsigned)buf->itemsize != dtype->size) { PyErr_Format(PyExc_ValueError, "Item size of buffer (%"PY_FORMAT_SIZE_T"d byte%s) does not match size of '%s' (%"PY_FORMAT_SIZE_T"d byte%s)", buf->itemsize, (buf->itemsize > 1) ? "s" : "", dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : ""); goto fail; } if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; return 0; fail:; __Pyx_ZeroBuffer(buf); return -1; } static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { if (info->buf == NULL) return; if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; __Pyx_ReleaseBuffer(info); } static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->curexc_type; tmp_value = tstate->curexc_value; tmp_tb = tstate->curexc_traceback; tstate->curexc_type = type; tstate->curexc_value = value; tstate->curexc_traceback = tb; Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); } static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { PyThreadState *tstate = PyThreadState_GET(); *type = tstate->curexc_type; *value = tstate->curexc_value; *tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; } #if PY_MAJOR_VERSION < 3 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { /* cause is unused */ Py_XINCREF(type); Py_XINCREF(value); Py_XINCREF(tb); /* First, check the traceback argument, replacing None with NULL. */ if (tb == Py_None) { Py_DECREF(tb); tb = 0; } else if (tb != NULL && !PyTraceBack_Check(tb)) { PyErr_SetString(PyExc_TypeError, "raise: arg 3 must be a traceback or None"); goto raise_error; } /* Next, replace a missing value with None */ if (value == NULL) { value = Py_None; Py_INCREF(value); } #if PY_VERSION_HEX < 0x02050000 if (!PyClass_Check(type)) #else if (!PyType_Check(type)) #endif { /* Raising an instance. The value should be a dummy. */ if (value != Py_None) { PyErr_SetString(PyExc_TypeError, "instance exception may not have a separate value"); goto raise_error; } /* Normalize to raise , */ Py_DECREF(value); value = type; #if PY_VERSION_HEX < 0x02050000 if (PyInstance_Check(type)) { type = (PyObject*) ((PyInstanceObject*)type)->in_class; Py_INCREF(type); } else { type = 0; PyErr_SetString(PyExc_TypeError, "raise: exception must be an old-style class or instance"); goto raise_error; } #else type = (PyObject*) Py_TYPE(type); Py_INCREF(type); if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { PyErr_SetString(PyExc_TypeError, "raise: exception class must be a subclass of BaseException"); goto raise_error; } #endif } __Pyx_ErrRestore(type, value, tb); return; raise_error: Py_XDECREF(value); Py_XDECREF(type); Py_XDECREF(tb); return; } #else /* Python 3+ */ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { if (tb == Py_None) { tb = 0; } else if (tb && !PyTraceBack_Check(tb)) { PyErr_SetString(PyExc_TypeError, "raise: arg 3 must be a traceback or None"); goto bad; } if (value == Py_None) value = 0; if (PyExceptionInstance_Check(type)) { if (value) { PyErr_SetString(PyExc_TypeError, "instance exception may not have a separate value"); goto bad; } value = type; type = (PyObject*) Py_TYPE(value); } else if (!PyExceptionClass_Check(type)) { PyErr_SetString(PyExc_TypeError, "raise: exception class must be a subclass of BaseException"); goto bad; } if (cause) { PyObject *fixed_cause; if (PyExceptionClass_Check(cause)) { fixed_cause = PyObject_CallObject(cause, NULL); if (fixed_cause == NULL) goto bad; } else if (PyExceptionInstance_Check(cause)) { fixed_cause = cause; Py_INCREF(fixed_cause); } else { PyErr_SetString(PyExc_TypeError, "exception causes must derive from " "BaseException"); goto bad; } if (!value) { value = PyObject_CallObject(type, NULL); } PyException_SetCause(value, fixed_cause); } PyErr_SetObject(type, value); if (tb) { PyThreadState *tstate = PyThreadState_GET(); PyObject* tmp_tb = tstate->curexc_traceback; if (tb != tmp_tb) { Py_INCREF(tb); tstate->curexc_traceback = tb; Py_XDECREF(tmp_tb); } } bad: return; } #endif static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { PyErr_Format(PyExc_ValueError, "need more than %"PY_FORMAT_SIZE_T"d value%s to unpack", index, (index == 1) ? "" : "s"); } static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { PyErr_Format(PyExc_ValueError, "too many values to unpack (expected %"PY_FORMAT_SIZE_T"d)", expected); } static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); } static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) { if (t == Py_None) { __Pyx_RaiseNoneNotIterableError(); } else if (PyTuple_GET_SIZE(t) < index) { __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(t)); } else { __Pyx_RaiseTooManyValuesError(index); } } #if PY_MAJOR_VERSION < 3 static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { #if PY_VERSION_HEX >= 0x02060000 if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); #endif if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pf_5numpy_7ndarray___getbuffer__(obj, view, flags); else { PyErr_Format(PyExc_TypeError, "'%100s' does not have the buffer interface", Py_TYPE(obj)->tp_name); return -1; } } static void __Pyx_ReleaseBuffer(Py_buffer *view) { PyObject* obj = view->obj; if (obj) { #if PY_VERSION_HEX >= 0x02060000 if (PyObject_CheckBuffer(obj)) {PyBuffer_Release(view); return;} #endif if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) __pyx_pf_5numpy_7ndarray_1__releasebuffer__(obj, view); Py_DECREF(obj); view->obj = NULL; } } #endif static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) { PyObject *py_import = 0; PyObject *empty_list = 0; PyObject *module = 0; PyObject *global_dict = 0; PyObject *empty_dict = 0; PyObject *list; py_import = __Pyx_GetAttrString(__pyx_b, "__import__"); if (!py_import) goto bad; if (from_list) list = from_list; else { empty_list = PyList_New(0); if (!empty_list) goto bad; list = empty_list; } global_dict = PyModule_GetDict(__pyx_m); if (!global_dict) goto bad; empty_dict = PyDict_New(); if (!empty_dict) goto bad; #if PY_VERSION_HEX >= 0x02050000 { PyObject *py_level = PyInt_FromLong(level); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); } #else if (level>0) { PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4."); goto bad; } module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, NULL); #endif bad: Py_XDECREF(empty_list); Py_XDECREF(py_import); Py_XDECREF(empty_dict); return module; } #if CYTHON_CCOMPLEX #ifdef __cplusplus static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { return ::std::complex< float >(x, y); } #else static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { return x + y*(__pyx_t_float_complex)_Complex_I; } #endif #else static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { __pyx_t_float_complex z; z.real = x; z.imag = y; return z; } #endif #if CYTHON_CCOMPLEX #else static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) { return (a.real == b.real) && (a.imag == b.imag); } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; z.real = a.real + b.real; z.imag = a.imag + b.imag; return z; } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; z.real = a.real - b.real; z.imag = a.imag - b.imag; return z; } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; z.real = a.real * b.real - a.imag * b.imag; z.imag = a.real * b.imag + a.imag * b.real; return z; } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; float denom = b.real * b.real + b.imag * b.imag; z.real = (a.real * b.real + a.imag * b.imag) / denom; z.imag = (a.imag * b.real - a.real * b.imag) / denom; return z; } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) { __pyx_t_float_complex z; z.real = -a.real; z.imag = -a.imag; return z; } static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) { return (a.real == 0) && (a.imag == 0); } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) { __pyx_t_float_complex z; z.real = a.real; z.imag = -a.imag; return z; } #if 1 static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) { #if !defined(HAVE_HYPOT) || defined(_MSC_VER) return sqrtf(z.real*z.real + z.imag*z.imag); #else return hypotf(z.real, z.imag); #endif } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; float r, lnr, theta, z_r, z_theta; if (b.imag == 0 && b.real == (int)b.real) { if (b.real < 0) { float denom = a.real * a.real + a.imag * a.imag; a.real = a.real / denom; a.imag = -a.imag / denom; b.real = -b.real; } switch ((int)b.real) { case 0: z.real = 1; z.imag = 0; return z; case 1: return a; case 2: z = __Pyx_c_prodf(a, a); return __Pyx_c_prodf(a, a); case 3: z = __Pyx_c_prodf(a, a); return __Pyx_c_prodf(z, a); case 4: z = __Pyx_c_prodf(a, a); return __Pyx_c_prodf(z, z); } } if (a.imag == 0) { if (a.real == 0) { return a; } r = a.real; theta = 0; } else { r = __Pyx_c_absf(a); theta = atan2f(a.imag, a.real); } lnr = logf(r); z_r = expf(lnr * b.real - theta * b.imag); z_theta = theta * b.real + lnr * b.imag; z.real = z_r * cosf(z_theta); z.imag = z_r * sinf(z_theta); return z; } #endif #endif #if CYTHON_CCOMPLEX #ifdef __cplusplus static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { return ::std::complex< double >(x, y); } #else static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { return x + y*(__pyx_t_double_complex)_Complex_I; } #endif #else static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { __pyx_t_double_complex z; z.real = x; z.imag = y; return z; } #endif #if CYTHON_CCOMPLEX #else static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) { return (a.real == b.real) && (a.imag == b.imag); } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; z.real = a.real + b.real; z.imag = a.imag + b.imag; return z; } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; z.real = a.real - b.real; z.imag = a.imag - b.imag; return z; } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; z.real = a.real * b.real - a.imag * b.imag; z.imag = a.real * b.imag + a.imag * b.real; return z; } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; double denom = b.real * b.real + b.imag * b.imag; z.real = (a.real * b.real + a.imag * b.imag) / denom; z.imag = (a.imag * b.real - a.real * b.imag) / denom; return z; } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) { __pyx_t_double_complex z; z.real = -a.real; z.imag = -a.imag; return z; } static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) { return (a.real == 0) && (a.imag == 0); } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) { __pyx_t_double_complex z; z.real = a.real; z.imag = -a.imag; return z; } #if 1 static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) { #if !defined(HAVE_HYPOT) || defined(_MSC_VER) return sqrt(z.real*z.real + z.imag*z.imag); #else return hypot(z.real, z.imag); #endif } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; double r, lnr, theta, z_r, z_theta; if (b.imag == 0 && b.real == (int)b.real) { if (b.real < 0) { double denom = a.real * a.real + a.imag * a.imag; a.real = a.real / denom; a.imag = -a.imag / denom; b.real = -b.real; } switch ((int)b.real) { case 0: z.real = 1; z.imag = 0; return z; case 1: return a; case 2: z = __Pyx_c_prod(a, a); return __Pyx_c_prod(a, a); case 3: z = __Pyx_c_prod(a, a); return __Pyx_c_prod(z, a); case 4: z = __Pyx_c_prod(a, a); return __Pyx_c_prod(z, z); } } if (a.imag == 0) { if (a.real == 0) { return a; } r = a.real; theta = 0; } else { r = __Pyx_c_abs(a); theta = atan2(a.imag, a.real); } lnr = log(r); z_r = exp(lnr * b.real - theta * b.imag); z_theta = theta * b.real + lnr * b.imag; z.real = z_r * cos(z_theta); z.imag = z_r * sin(z_theta); return z; } #endif #endif static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { const unsigned char neg_one = (unsigned char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned char" : "value too large to convert to unsigned char"); } return (unsigned char)-1; } return (unsigned char)val; } return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { const unsigned short neg_one = (unsigned short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned short" : "value too large to convert to unsigned short"); } return (unsigned short)-1; } return (unsigned short)val; } return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { const unsigned int neg_one = (unsigned int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned int" : "value too large to convert to unsigned int"); } return (unsigned int)-1; } return (unsigned int)val; } return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { const char neg_one = (char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to char" : "value too large to convert to char"); } return (char)-1; } return (char)val; } return (char)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { const short neg_one = (short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to short" : "value too large to convert to short"); } return (short)-1; } return (short)val; } return (short)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { const signed char neg_one = (signed char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed char" : "value too large to convert to signed char"); } return (signed char)-1; } return (signed char)val; } return (signed char)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { const signed short neg_one = (signed short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed short" : "value too large to convert to signed short"); } return (signed short)-1; } return (signed short)val; } return (signed short)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { const signed int neg_one = (signed int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed int" : "value too large to convert to signed int"); } return (signed int)-1; } return (signed int)val; } return (signed int)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) { const unsigned long neg_one = (unsigned long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)PyLong_AsUnsignedLong(x); } else { return (unsigned long)PyLong_AsLong(x); } } else { unsigned long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned long)-1; val = __Pyx_PyInt_AsUnsignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) { const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x); } } else { unsigned PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned PY_LONG_LONG)-1; val = __Pyx_PyInt_AsUnsignedLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) { const long neg_one = (long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)PyLong_AsUnsignedLong(x); } else { return (long)PyLong_AsLong(x); } } else { long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (long)-1; val = __Pyx_PyInt_AsLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (PY_LONG_LONG)PyLong_AsLongLong(x); } } else { PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (PY_LONG_LONG)-1; val = __Pyx_PyInt_AsLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) { const signed long neg_one = (signed long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)PyLong_AsUnsignedLong(x); } else { return (signed long)PyLong_AsLong(x); } } else { signed long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed long)-1; val = __Pyx_PyInt_AsSignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (signed PY_LONG_LONG)PyLong_AsLongLong(x); } } else { signed PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed PY_LONG_LONG)-1; val = __Pyx_PyInt_AsSignedLongLong(tmp); Py_DECREF(tmp); return val; } } static int __Pyx_check_binary_version(void) { char ctversion[4], rtversion[4]; PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { char message[200]; PyOS_snprintf(message, sizeof(message), "compiletime version %s of module '%.100s' " "does not match runtime version %s", ctversion, __Pyx_MODULE_NAME, rtversion); #if PY_VERSION_HEX < 0x02050000 return PyErr_Warn(NULL, message); #else return PyErr_WarnEx(NULL, message, 1); #endif } return 0; } #ifndef __PYX_HAVE_RT_ImportType #define __PYX_HAVE_RT_ImportType static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict) { PyObject *py_module = 0; PyObject *result = 0; PyObject *py_name = 0; char warning[200]; py_module = __Pyx_ImportModule(module_name); if (!py_module) goto bad; py_name = __Pyx_PyIdentifier_FromString(class_name); if (!py_name) goto bad; result = PyObject_GetAttr(py_module, py_name); Py_DECREF(py_name); py_name = 0; Py_DECREF(py_module); py_module = 0; if (!result) goto bad; if (!PyType_Check(result)) { PyErr_Format(PyExc_TypeError, "%s.%s is not a type object", module_name, class_name); goto bad; } if (!strict && ((PyTypeObject *)result)->tp_basicsize > (Py_ssize_t)size) { PyOS_snprintf(warning, sizeof(warning), "%s.%s size changed, may indicate binary incompatibility", module_name, class_name); #if PY_VERSION_HEX < 0x02050000 if (PyErr_Warn(NULL, warning) < 0) goto bad; #else if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; #endif } else if (((PyTypeObject *)result)->tp_basicsize != (Py_ssize_t)size) { PyErr_Format(PyExc_ValueError, "%s.%s has the wrong size, try recompiling", module_name, class_name); goto bad; } return (PyTypeObject *)result; bad: Py_XDECREF(py_module); Py_XDECREF(result); return NULL; } #endif #ifndef __PYX_HAVE_RT_ImportModule #define __PYX_HAVE_RT_ImportModule static PyObject *__Pyx_ImportModule(const char *name) { PyObject *py_name = 0; PyObject *py_module = 0; py_name = __Pyx_PyIdentifier_FromString(name); if (!py_name) goto bad; py_module = PyImport_Import(py_name); Py_DECREF(py_name); return py_module; bad: Py_XDECREF(py_name); return 0; } #endif #include "compile.h" #include "frameobject.h" #include "traceback.h" static void __Pyx_AddTraceback(const char *funcname, int __pyx_clineno, int __pyx_lineno, const char *__pyx_filename) { PyObject *py_srcfile = 0; PyObject *py_funcname = 0; PyObject *py_globals = 0; PyCodeObject *py_code = 0; PyFrameObject *py_frame = 0; #if PY_MAJOR_VERSION < 3 py_srcfile = PyString_FromString(__pyx_filename); #else py_srcfile = PyUnicode_FromString(__pyx_filename); #endif if (!py_srcfile) goto bad; if (__pyx_clineno) { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno); #else py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno); #endif } else { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromString(funcname); #else py_funcname = PyUnicode_FromString(funcname); #endif } if (!py_funcname) goto bad; py_globals = PyModule_GetDict(__pyx_m); if (!py_globals) goto bad; py_code = __Pyx_PyCode_New( 0, /*int argcount,*/ 0, /*int kwonlyargcount,*/ 0, /*int nlocals,*/ 0, /*int stacksize,*/ 0, /*int flags,*/ __pyx_empty_bytes, /*PyObject *code,*/ __pyx_empty_tuple, /*PyObject *consts,*/ __pyx_empty_tuple, /*PyObject *names,*/ __pyx_empty_tuple, /*PyObject *varnames,*/ __pyx_empty_tuple, /*PyObject *freevars,*/ __pyx_empty_tuple, /*PyObject *cellvars,*/ py_srcfile, /*PyObject *filename,*/ py_funcname, /*PyObject *name,*/ __pyx_lineno, /*int firstlineno,*/ __pyx_empty_bytes /*PyObject *lnotab*/ ); if (!py_code) goto bad; py_frame = PyFrame_New( PyThreadState_GET(), /*PyThreadState *tstate,*/ py_code, /*PyCodeObject *code,*/ py_globals, /*PyObject *globals,*/ 0 /*PyObject *locals*/ ); if (!py_frame) goto bad; py_frame->f_lineno = __pyx_lineno; PyTraceBack_Here(py_frame); bad: Py_XDECREF(py_srcfile); Py_XDECREF(py_funcname); Py_XDECREF(py_code); Py_XDECREF(py_frame); } static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { while (t->p) { #if PY_MAJOR_VERSION < 3 if (t->is_unicode) { *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); } else if (t->intern) { *t->p = PyString_InternFromString(t->s); } else { *t->p = PyString_FromStringAndSize(t->s, t->n - 1); } #else /* Python 3+ has unicode identifiers */ if (t->is_unicode | t->is_str) { if (t->intern) { *t->p = PyUnicode_InternFromString(t->s); } else if (t->encoding) { *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); } else { *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); } } else { *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); } #endif if (!*t->p) return -1; ++t; } return 0; } /* Type Conversion Functions */ static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { int is_true = x == Py_True; if (is_true | (x == Py_False) | (x == Py_None)) return is_true; else return PyObject_IsTrue(x); } static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { PyNumberMethods *m; const char *name = NULL; PyObject *res = NULL; #if PY_VERSION_HEX < 0x03000000 if (PyInt_Check(x) || PyLong_Check(x)) #else if (PyLong_Check(x)) #endif return Py_INCREF(x), x; m = Py_TYPE(x)->tp_as_number; #if PY_VERSION_HEX < 0x03000000 if (m && m->nb_int) { name = "int"; res = PyNumber_Int(x); } else if (m && m->nb_long) { name = "long"; res = PyNumber_Long(x); } #else if (m && m->nb_int) { name = "int"; res = PyNumber_Long(x); } #endif if (res) { #if PY_VERSION_HEX < 0x03000000 if (!PyInt_Check(res) && !PyLong_Check(res)) { #else if (!PyLong_Check(res)) { #endif PyErr_Format(PyExc_TypeError, "__%s__ returned non-%s (type %.200s)", name, name, Py_TYPE(res)->tp_name); Py_DECREF(res); return NULL; } } else if (!PyErr_Occurred()) { PyErr_SetString(PyExc_TypeError, "an integer is required"); } return res; } static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { Py_ssize_t ival; PyObject* x = PyNumber_Index(b); if (!x) return -1; ival = PyInt_AsSsize_t(x); Py_DECREF(x); return ival; } static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { #if PY_VERSION_HEX < 0x02050000 if (ival <= LONG_MAX) return PyInt_FromLong((long)ival); else { unsigned char *bytes = (unsigned char *) &ival; int one = 1; int little = (int)*(unsigned char*)&one; return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0); } #else return PyInt_FromSize_t(ival); #endif } static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x); if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) { return (size_t)-1; } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) { PyErr_SetString(PyExc_OverflowError, "value too large to convert to size_t"); return (size_t)-1; } return (size_t)val; } #endif /* Py_PYTHON_H */ fabio-0.1.3/src/ccp4_pack.c0000644000175000017500000010035512137541670016153 0ustar jeromejerome00000000000000/* Fabio Mar345 ccp4_pack decompressor Copyright (C) 2007-2009 Henning O. Sorensen & Erik Knudsen 2012 ESRF This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA */ /* part of this code is freely adaped from pack_c.c from CCP4 distribution * (which is also LGPL). The original author is Jan Pieter Abrahams * jpa@mrc-lmb.cam.ac.uk This file contains functions capable of compressing and decompressing images. It is especially suited for X-ray diffraction patterns, or other image formats in which orthogonal pixels contain "grey-levels" and vary smoothly accross the image. Clean images measured by a MAR-research image plate scanner containing two bytes per pixel can be compressed by a factor of 3.5 to 4.5 . Since the images are encoded in a byte-stream, there should be no problem concerning big- or little ended machines: both will produce an identical packed image. Compression is achieved by first calculating the differences between every pixel and the truncated value of four of its neighbours. For example: the difference for a pixel at img[x, y] is: img[x, y] - (int) (img[x-1, y-1] + img[x-1, y] + img[x-1, y+1] + img[x, y-1]) / 4 After calculating the differences, they are encoded in a packed array. A packed array consists of consequitive chunks which have the following format: - Three bits containing the logarithm base 2 of the number of pixels encoded in the chunk. - Three bits defining the number of bits used to encode one element of the chunk. The value of these three bits is used as index in a lookup table to get the actual number of bits of the elements of the chunk. Note: in version 2, there are four bits in this position!! This allows more efficient packing of synchrotron data! The routines in this sourcefile are backwards compatible. JPA, 26 June 1995 - The truncated pixel differences. To compress an image, call pack_wordimage_c() or pack_longimage_c(). These will append the packed image to any header information already written to disk (take care that the file containing this information is closed before calling). To decompress an image, call readpack_word_c() or readpack_long_c(). These functions will find the start of the packed image themselves, irrespective of the header format. Jan Pieter Abrahams, 6 Jan 1993 */ #ifndef _MSC_VER #include #else #include "stdint.h" #endif #include #include #include #include #define PACKIDENTIFIER "\nCCP4 packed image, X: %04d, Y: %04d\n" /* This string defines the start of a packed image. An image file is scanned until this string is encountered, the size of the unpacked image is determined from the values of X and Y (which are written out as formatted ascii numbers), and the packed image is expected to start immediately after the null-character ending the string. */ #define V2IDENTIFIER "\nCCP4 packed image V2, X: %04d, Y: %04d\n" /* This string defines the start of a packed image. An image file is scanned until this string is encountered, the size of the unpacked image is determined from the values of X and Y (which are written out as formatted ascii numbers), and the packed image is expected to start immediately after the null-character ending the string. */ #define PACKBUFSIZ BUFSIZ /* Size of internal buffer in which the packed array is stored during transit form an unpacked image to a packed image on disk. It is set to the size used by the buffered io-routines given in , but it could be anything. */ #define DIFFBUFSIZ 16384L /* Size of the internal buffer in which the differences between neighbouring pixels are stored prior to compression. The image is therefore compressed in DIFFBUFSIZ chunks. Decompression does not need to know what DIFFBUFSIZ was when the image was compressed. By increasing this value, the image can be compressed into a packed image which is a few bytes smaller. Do not decrease the value of DIFFBUFSIZ below 128L. */ #define CCP4_PCK_BLOCK_HEADER_LENGTH 6 #define CCP4_PCK_BLOCK_HEADER_LENGTH_V2 8 /*array translating the number of errors per block*/ static unsigned int CCP4_PCK_ERR_COUNT[] = {1,2,4,8,16,32,64,128}; /*array translating the number of bits per error*/ static unsigned int CCP4_PCK_BIT_COUNT[]= {0,4,5,6,7,8,16,32}; /*array translating the number of errors per block - can use shifts as well actually*/ static unsigned int CCP4_PCK_ERR_COUNT_V2[] = {1,2,4,8,16,32,64,128,256,512,1024,2048,4096,8192,16384,32768}; /*array translating the number of bits per error*/ static unsigned int CCP4_PCK_BIT_COUNT_V2[]= {0,4,5,6,7,8,9,10,11,12,13,14,15,16,32}; static const unsigned char CCP4_PCK_MASK[]={0x00, 0x01, 0x03, 0x07, 0x0F, 0x1F, 0x3F, 0x7F, 0xFF}; static const unsigned int CCP4_PCK_MASK_16[]={0x00, 0x01, 0x03, 0x07, 0x0F, 0x1F, 0x3F, 0x7F, 0xFF, 0x1FF, 0x3FF, 0x7FF, 0xFFF, 0x1FFF, 0x3FFF, 0x7FFF, 0xFFFF}; static const unsigned long CCP4_PCK_MASK_32[]={0x00, 0x01, 0x03, 0x07, 0x0F, 0x1F, 0x3F, 0x7F, 0xFF, 0x1FF, 0x3FF, 0x7FF, 0xFFF, 0x1FFF, 0x3FFF, 0x7FFF, 0xFFFF, 0x1FFFF, 0x3FFFF, 0x7FFFF, 0xFFFFF, 0x1FFFFF, 0x3FFFFF, 0x7FFFFF, 0xFFFFFF, 0x1FFFFFF, 0x3FFFFFF, 0x7FFFFFF, 0xFFFFFFF, 0x1FFFFFFF, 0x3FFFFFFF, 0x7FFFFFFF, 0xFFFFFFFF}; #define pfail_nonzero(a) if ((a)) return NULL; #define max(x, y) (((x) > (y)) ? (x) : (y)) #define min(x, y) (((x) < (y)) ? (x) : (y)) #define shift_left(x, n) (((x) & CCP4_PCK_MASK_32[32 - (n)]) << (n)) /* This macro is included because the C standard does not properly define a left shift: on some machines the bits which are pushed out at the left are popped back in at the right. By masking, the macro prevents this behaviour. If you are sure that your machine does not pops bits back in, you can speed up the code insignificantly by taking out the masking. */ #define shift_right(x, n) (((x) >> (n)) & CCP4_PCK_MASK_32[32 - (n)]) void *mar345_read_data(FILE *file, int ocount, int dim1, int dim2); void *mar345_read_data_string(char *instring, int ocount, int dim1, int dim2); void *ccp4_unpack(void *unpacked_array, void *packed, size_t dim1, size_t dim2, size_t max_num_int); void *ccp4_unpack_v2(void *unpacked_array, void *packed, size_t dim1, size_t dim2, size_t max_num_int); void *ccp4_unpack_string(void *unpacked_array, void *packed, size_t dim1, size_t dim2, size_t max_num_int); void *ccp4_unpack_v2_string(void *unpacked_array, void *packed, size_t dim1, size_t dim2, size_t max_num_int); void *mar345_read_data_string(char *instring, int ocount, int dim1, int dim2){ /* first process overflow bytes - for now we just ignore them * these are stored in 64 byte records*/ int orecords=(int)(ocount/8.0+0.875); int *odata,x,y,version=0; char *c,cbuffer[64]=""; char *t_; unsigned int *unpacked_array; odata=(int*)malloc(64*8*orecords); if (!odata) return NULL; //pfail_nonzero (orecords-fread(odata,64,orecords,file)); memcpy(odata, instring, 64*orecords); t_ = instring + (64*orecords); /* there is no stdout in a gui, sorry*/ //printf("have %d overflows in %d recs\n",ocount,orecords); /* now after they have been read find the CCP4.....string and compare to dim1*/ c=cbuffer; while((*c)!=EOF){ if (c==cbuffer+63){ c=cbuffer; } // *c=(char)getc(file); *c = (char) *t_; t_++; /*set the next character to a \0 so the string is always terminated*/ *(c+1)='\0'; if (*c=='\n'){ /*check for the CCP- string*/ x=y=0; sscanf(cbuffer,"CCP4 packed image, X: %04d, Y: %04d", &x,&y); if (x==dim1 || y ==dim2){ version=1; break; } x=y=0; sscanf(cbuffer,"CCP4 packed image V2, X: %04d, Y: %04d", &x,&y); if (x==dim1 || y ==dim2){ version=2; break; } c=cbuffer; } else c++; } //printf("%d %d %d %d version %d\n",x,y,dim1,dim2,version); /* allocate memory for the arrays*/ unpacked_array=(unsigned int*) malloc(sizeof(unsigned int)*dim1*dim2); if (!unpacked_array) return NULL; /*relay to whichever version of ccp4_unpack is appropriate*/ switch(version){ case 1: ccp4_unpack_string(unpacked_array,(void*)t_,dim1,dim2,0); break; case 2: ccp4_unpack_v2_string(unpacked_array,(void*)t_,dim1,dim2,0); break; default: return NULL; } //printf("finished, %d \n",dim1*dim2*sizeof(unsigned int)); /*handle overflows*/ while (ocount>0){ unsigned int adress,value; adress=odata[2*ocount-2]; if (adress){ value=odata[2*ocount-1]; /*adresses start at 1*/ // printf("address %d %d\n",address,value); unpacked_array[adress-1]=value; } ocount--; } return unpacked_array; } /**unpack a new style mar345 image a'la what is done in CBFlib * assumes the file is already positioned after the ascii header * Perhaps the positioning should be done here as well. */ void * mar345_read_data(FILE *file, int ocount, int dim1, int dim2){ /* first process overflow bytes - for now we just ignore them * these are stored in 64 byte records*/ int orecords=(int)(ocount/8.0+0.875); int *odata,x,y,version=0; char *c,cbuffer[64]=""; unsigned int *unpacked_array; odata=(int*)malloc(64*8*orecords); if (!odata) return NULL; pfail_nonzero (orecords-fread(odata,64,orecords,file)); /* there is no stdout in a gui, sorry printf("have %d overflows in %d recs\n",ocount,orecords); */ /* now after they have been read find the CCP4.....string and compare to dim1*/ c=cbuffer; while((*c)!=EOF){ if (c==cbuffer+63){ c=cbuffer; } *c=(char)getc(file); /*set the next character to a \0 so the string is always terminated*/ *(c+1)='\0'; if (*c=='\n'){ /*check for the CCP- string*/ x=y=0; sscanf(cbuffer,"CCP4 packed image, X: %04d, Y: %04d", &x,&y); if (x==dim1 || y ==dim2){ version=1; break; } x=y=0; sscanf(cbuffer,"CCP4 packed image V2, X: %04d, Y: %04d", &x,&y); if (x==dim1 || y ==dim2){ version=2; break; } c=cbuffer; } else c++; } /* allocate memory for the arrays*/ unpacked_array=(unsigned int*) malloc(sizeof(unsigned int)*dim1*dim2); if (!unpacked_array) return NULL; /*relay to whichever version of ccp4_unpack is appropriate*/ switch(version){ case 1: ccp4_unpack(unpacked_array,(void*)file,dim1,dim2,0); break; case 2: ccp4_unpack_v2(unpacked_array,(void*)file,dim1,dim2,0); break; default: return NULL; } /*handle overflows*/ while (ocount>0){ unsigned int adress,value; adress=odata[2*ocount-2]; if (adress){ value=odata[2*ocount-1]; /*adresses start at 1*/ unpacked_array[adress-1]=value; } ocount--; } return unpacked_array; } /**unpack a ccp4-style packed array into the memory location pointed to by unpacked_array * if this is null allocate memory and return a pointer to it * \return NULL if unsuccessful * TODO change this to read directly from the FILE to not waste memory*/ void * ccp4_unpack( void *unpacked_array, void *packed, size_t dim1,size_t dim2, size_t max_num_int ){ uint8_t t_,t2,_conv; int err_val,bit_offset,num_error=0,num_bits=0,read_bits; int i; int x4,x3,x2,x1; unsigned int *int_arr=(unsigned int *) unpacked_array; FILE *instream=(FILE *)packed; //printf("file "); /*if no maximum integers are give read the whole nine yards*/ if (max_num_int==0){ max_num_int=dim1*dim2; } /*if a NULL pointer is passed allocate some new memory*/ if (unpacked_array==NULL){ if ( (unpacked_array=malloc(sizeof(unsigned int)*max_num_int))==NULL){ errno=ENOMEM; return NULL; } } /*packed bits always start at byte boundary after header*/ bit_offset=0; /*read the first byte of the current_block*/ t_=(unsigned char)fgetc(instream); //printf("%02X \n",t_); /*while less than num ints have been unpacked*/ i=0; while(i=(8-CCP4_PCK_BLOCK_HEADER_LENGTH)){ /*we'll be reading past the next byte boundary*/ t2=(unsigned char ) fgetc(instream); t_=(t_>>bit_offset) + ((unsigned char)t2 <<(8-bit_offset) ); num_error=CCP4_PCK_ERR_COUNT[t_ & CCP4_PCK_MASK[3]]; num_bits=CCP4_PCK_BIT_COUNT[(t_>>3) & CCP4_PCK_MASK[3]]; bit_offset=CCP4_PCK_BLOCK_HEADER_LENGTH+bit_offset-8; t_=t2; }else{ num_error=CCP4_PCK_ERR_COUNT[(t_>>bit_offset) & CCP4_PCK_MASK[3]]; num_bits=CCP4_PCK_BIT_COUNT[(t_>>(3+bit_offset)) & CCP4_PCK_MASK[3]]; bit_offset+=CCP4_PCK_BLOCK_HEADER_LENGTH; } } else { /*reading the data in the block*/ while(num_error>0){ err_val=0; read_bits=0; while(read_bits=8) { /*read to next full byte boundary and convert*/ _conv= (t_>>bit_offset) & CCP4_PCK_MASK[8-bit_offset]; err_val|= (unsigned int) _conv << read_bits; read_bits+=(8-bit_offset); /*have read to byte boundary - set offset to 0 and read next byte*/ bit_offset=0; t_=(unsigned char) fgetc(instream); } else { /*must stop before next byte boundary - also this means that these are the last bits in the error*/ _conv= (t_ >>bit_offset) & CCP4_PCK_MASK[num_bits-read_bits]; err_val|= _conv<dim1){ /*the current pixel is not in the first row - averaging is possible *n.b. the averaging calculation is performed in the 2's complement domain*/ x4=(int16_t) int_arr[i-1]; x3=(int16_t) int_arr[i-dim1+1]; x2=(int16_t) int_arr[i-dim1]; x1=(int16_t) int_arr[i-dim1-1]; int_arr[i]=(uint16_t) (err_val + (x4 + x3 + x2 + x1 +2) /4 ); i=i; } else if (i!=0){ /*current pixel is in the 1st row but is not first pixel*/ int_arr[i]=(uint16_t) (err_val + int_arr[i-1]); } else { int_arr[i]=(uint16_t) err_val; } i++; num_error--; } }/*else*/ } return (void *) unpacked_array; } void * ccp4_unpack_string( void *unpacked_array, void *packed, size_t dim1,size_t dim2, size_t max_num_int ){ uint8_t t_,t2,_conv; int err_val,bit_offset,num_error=0,num_bits=0,read_bits; int i; int x4,x3,x2,x1; unsigned int *int_arr; char *instream = (char *)packed; // printf("string "); // int toto; // for (toto=0;toto<16;toto++){ // printf("%02X ",(unsigned char)instream[toto]); // } // printf("\n"); /*if no maximum integers are give read the whole nine yards*/ if (max_num_int==0){ max_num_int=dim1*dim2; } /*if a NULL pointer is passed allocate some new memory*/ if (unpacked_array==NULL){ if ( (unpacked_array=malloc(sizeof(unsigned int)*max_num_int))==NULL){ errno=ENOMEM; return NULL; } } int_arr = (unsigned int *) unpacked_array; /*packed bits always start at byte boundary after header*/ bit_offset=0; /*read the first byte of the current_block*/ t_=(unsigned char)*instream; instream++; //printf("%02X \n",t_); /*while less than num ints have been unpacked*/ i=0; while(i=(8-CCP4_PCK_BLOCK_HEADER_LENGTH)){ /*we'll be reading past the next byte boundary*/ t2=(unsigned char ) *instream; instream++; t_=(t_>>bit_offset) + ((unsigned char)t2 <<(8-bit_offset) ); num_error=CCP4_PCK_ERR_COUNT[t_ & CCP4_PCK_MASK[3]]; num_bits=CCP4_PCK_BIT_COUNT[(t_>>3) & CCP4_PCK_MASK[3]]; bit_offset=CCP4_PCK_BLOCK_HEADER_LENGTH+bit_offset-8; t_=t2; }else{ num_error=CCP4_PCK_ERR_COUNT[(t_>>bit_offset) & CCP4_PCK_MASK[3]]; num_bits=CCP4_PCK_BIT_COUNT[(t_>>(3+bit_offset)) & CCP4_PCK_MASK[3]]; bit_offset+=CCP4_PCK_BLOCK_HEADER_LENGTH; } } else { /*reading the data in the block*/ while(num_error>0){ err_val=0; read_bits=0; while(read_bits=8) { /*read to next full byte boundary and convert*/ _conv= (t_>>bit_offset) & CCP4_PCK_MASK[8-bit_offset]; err_val|= (unsigned int) _conv << read_bits; read_bits+=(8-bit_offset); /*have read to byte boundary - set offset to 0 and read next byte*/ bit_offset=0; t_=(unsigned char) *instream; instream++; } else { /*must stop before next byte boundary - also this means that these are the last bits in the error*/ _conv= (t_ >>bit_offset) & CCP4_PCK_MASK[num_bits-read_bits]; err_val|= _conv<dim1){ /*the current pixel is not in the first row - averaging is possible *n.b. the averaging calculation is performed in the 2's complement domain*/ x4=(int16_t) int_arr[i-1]; x3=(int16_t) int_arr[i-dim1+1]; x2=(int16_t) int_arr[i-dim1]; x1=(int16_t) int_arr[i-dim1-1]; int_arr[i]=(uint16_t) (err_val + (x4 + x3 + x2 + x1 +2) /4 ); i=i; } else if (i!=0){ /*current pixel is in the 1st row but is not first pixel*/ int_arr[i]=(uint16_t) (err_val + int_arr[i-1]); } else { int_arr[i]=(uint16_t) err_val; } i++; num_error--; } }/*else*/ } return (void *) unpacked_array; } void * ccp4_unpack_v2( void *unpacked_array, void *packed, size_t dim1,size_t dim2, size_t max_num_int){ uint8_t t_,t2,_conv; int err_val,bit_offset,num_error=0,num_bits=0,read_bits; int i; unsigned int x4=0,x3=0,x2=0,x1=0; unsigned int *int_arr=(unsigned int *) unpacked_array; FILE *instream=(FILE *)packed; /*if no maximum integers are give read the whole nine yards*/ if (max_num_int==0){ max_num_int=dim1*dim2; } /*if a NULL pointer is passed allocate some new memory*/ if (unpacked_array==NULL){ if ( (unpacked_array=malloc(sizeof(unsigned int)*max_num_int))==NULL){ errno=ENOMEM; return NULL; } } /*packed bits always start at byte boundary after header*/ bit_offset=0; /*read the first byte of the current_block*/ t_=(unsigned char)fgetc(instream); /*while less than num ints have been unpacked*/ i=0; while(i=(8-CCP4_PCK_BLOCK_HEADER_LENGTH_V2)){ /*we'll be reading past the next byte boundary*/ t2=(unsigned char ) fgetc(instream); t_=(t_>>bit_offset) + ((unsigned char)t2 <<(8-bit_offset) ); num_error=CCP4_PCK_ERR_COUNT_V2[t_ & CCP4_PCK_MASK[4]]; num_bits=CCP4_PCK_BIT_COUNT_V2[(t_>>4) & CCP4_PCK_MASK[4]]; bit_offset=CCP4_PCK_BLOCK_HEADER_LENGTH_V2+bit_offset-8; t_=t2; }else{ num_error=CCP4_PCK_ERR_COUNT_V2[ (t_>>bit_offset) & CCP4_PCK_MASK[4] ]; num_bits=CCP4_PCK_BIT_COUNT_V2[ (t_>>(4+bit_offset)) & CCP4_PCK_MASK[4] ]; bit_offset+=CCP4_PCK_BLOCK_HEADER_LENGTH_V2; } } else { /*reading the data in the block*/ while(num_error>0){ err_val=0; read_bits=0; while(read_bits=8) { /*read to next full byte boundary and convert*/ _conv= (t_>>bit_offset) & CCP4_PCK_MASK[8-bit_offset]; err_val|= (unsigned int) _conv << read_bits; read_bits+=(8-bit_offset); /*have read to byte boundary - set offset to 0 and read next byte*/ bit_offset=0; t_=(unsigned char) fgetc(instream); } else { /*must stop before next byte boundary - also this means that these are the last bits in the error*/ _conv= (t_ >>bit_offset) & CCP4_PCK_MASK[num_bits-read_bits]; err_val|= _conv<dim1){ /*the current pixel is not in the first row - averaging is possible *n.b. the averaging calculation is performed in the 2's complement domain*/ x4=(int16_t) int_arr[i-1]; x3=(int16_t) int_arr[i-dim1+1]; x2=(int16_t) int_arr[i-dim1]; x1=(int16_t) int_arr[i-dim1-1]; int_arr[i]=(uint16_t) (err_val + (x4 + x3 + x2 + x1 +2) /4 ); i=i; } else if (i!=0){ /*current pixel is in the 1st row but is not first pixel*/ int_arr[i]=(uint16_t) (err_val + int_arr[i-1]); } else { int_arr[i]=(uint16_t) err_val; } i++; num_error--; } }/*else*/ } return (void *) unpacked_array; } void * ccp4_unpack_v2_string( void *unpacked_array, void *packed, size_t dim1,size_t dim2, size_t max_num_int){ uint8_t t_,t2,_conv; int err_val,bit_offset,num_error=0,num_bits=0,read_bits; int i; unsigned int x4=0,x3=0,x2=0,x1=0; unsigned int *int_arr=(unsigned int *) unpacked_array; char *instream=(char *)packed; /*if no maximum integers are give read the whole nine yards*/ if (max_num_int==0){ max_num_int=dim1*dim2; } /*if a NULL pointer is passed allocate some new memory*/ if (unpacked_array==NULL){ if ( (unpacked_array=malloc(sizeof(unsigned int)*max_num_int))==NULL){ errno=ENOMEM; return NULL; } } /*packed bits always start at byte boundary after header*/ bit_offset=0; /*read the first byte of the current_block*/ t_=(unsigned char)*instream; instream++; /*while less than num ints have been unpacked*/ i=0; while(i=(8-CCP4_PCK_BLOCK_HEADER_LENGTH_V2)){ /*we'll be reading past the next byte boundary*/ t2=(unsigned char ) *instream; instream++; t_=(t_>>bit_offset) + ((unsigned char)t2 <<(8-bit_offset) ); num_error=CCP4_PCK_ERR_COUNT_V2[t_ & CCP4_PCK_MASK[4]]; num_bits=CCP4_PCK_BIT_COUNT_V2[(t_>>4) & CCP4_PCK_MASK[4]]; bit_offset=CCP4_PCK_BLOCK_HEADER_LENGTH_V2+bit_offset-8; t_=t2; }else{ num_error=CCP4_PCK_ERR_COUNT_V2[ (t_>>bit_offset) & CCP4_PCK_MASK[4] ]; num_bits=CCP4_PCK_BIT_COUNT_V2[ (t_>>(4+bit_offset)) & CCP4_PCK_MASK[4] ]; bit_offset+=CCP4_PCK_BLOCK_HEADER_LENGTH_V2; } } else { /*reading the data in the block*/ while(num_error>0){ err_val=0; read_bits=0; while(read_bits=8) { /*read to next full byte boundary and convert*/ _conv= (t_>>bit_offset) & CCP4_PCK_MASK[8-bit_offset]; err_val|= (unsigned int) _conv << read_bits; read_bits+=(8-bit_offset); /*have read to byte boundary - set offset to 0 and read next byte*/ bit_offset=0; t_=(unsigned char) *instream; instream++; } else { /*must stop before next byte boundary - also this means that these are the last bits in the error*/ _conv= (t_ >>bit_offset) & CCP4_PCK_MASK[num_bits-read_bits]; err_val|= _conv<dim1){ /*the current pixel is not in the first row - averaging is possible *n.b. the averaging calculation is performed in the 2's complement domain*/ x4=(int16_t) int_arr[i-1]; x3=(int16_t) int_arr[i-dim1+1]; x2=(int16_t) int_arr[i-dim1]; x1=(int16_t) int_arr[i-dim1-1]; int_arr[i]=(uint16_t) (err_val + (x4 + x3 + x2 + x1 +2) /4 ); i=i; } else if (i!=0){ /*current pixel is in the 1st row but is not first pixel*/ int_arr[i]=(uint16_t) (err_val + int_arr[i-1]); } else { int_arr[i]=(uint16_t) err_val; } i++; num_error--; } }/*else*/ } return (void *) unpacked_array; } /* ############################################################################# ################### Everything to write Mar345 ############################## ############################################################################# */ /* Returns the number of bits neccesary to encode the longword-array 'chunk' of size 'n' The size in bits of one encoded element can be 0, 4, 5, 6, 7, 8, 16 or 32. */ int bits( int32_t *chunk, int n){ int size, maxsize, i; for (i = 1, maxsize = abs(chunk[0]); i < n; ++i) maxsize = max(maxsize, abs(chunk[i])); if (maxsize == 0) size = 0; else if (maxsize < 8) size = 4 * n; else if (maxsize < 16) size = 5 * n; else if (maxsize < 32) size = 6 * n; else if (maxsize < 64) size = 7 * n; else if (maxsize < 128) size = 8 * n; else if (maxsize < 32768) size = 16 * n; else size = 32 * n; return(size); } /* Calculates the difference of WORD-sized pixels of an image with the truncated mean value of four of its neighbours. 'x' is the number of fast coordinates of the image 'img', 'y' is the number of slow coordinates, 'diffs' will contain the differences, 'done' defines the index of the pixel where calculating the differences should start. A pointer to the last difference is returned. Maximally DIFFBUFSIZ differences are returned in 'diffs'.*/ int *diff_words( short int *word, int x, int y, int *diffs, int done){ int i = 0; int tot = x * y; if (done == 0) { *diffs = word[0]; ++diffs; ++done; ++i;} while ((done <= x) && (i < DIFFBUFSIZ)) { *diffs = word[done] - word[done - 1]; ++diffs; ++done; ++i;} while ((done < tot) && (i < DIFFBUFSIZ)) { *diffs = word[done] - (word[done - 1] + word[done - x + 1] + word[done - x] + word[done - x - 1] + 2) / 4; ++diffs; ++done; ++i;} return(--diffs); } /* Pack 'n' WORDS, starting with 'lng[0]' into the packed array 'target'. The elements of such a packed array do not obey BYTE-boundaries, but are put one behind the other without any spacing. Only the 'bitsiz' number of least significant bits are used. The starting bit of 'target' is 'bit' (bits range from 0 to 7). After completion of 'pack_words()', both '**target' and '*bit' are updated and define the next position in 'target' from which packing could continue. */ void pack_longs(int32_t *lng, int n, char **target, int *bit, int size){ int32_t mask, window; int valids, i, temp; int temp_bit = *bit; char *temp_target = *target; if (size > 0) { mask = CCP4_PCK_MASK_32[size]; for (i = 0; i < n; ++i) { window = lng[i] & mask; valids = size; if (temp_bit == 0) *temp_target = (char) window; else { temp = shift_left(window, temp_bit); *temp_target |= temp;} window = shift_right(window, 8 - temp_bit); valids = valids - (8 - temp_bit); if (valids < 0) temp_bit += size; else { while (valids > 0) { *++temp_target = (char) window; window = shift_right(window, 8); valids -= 8;} temp_bit = 8 + valids;} if (valids == 0) { temp_bit = 0; ++temp_target;}} *target = temp_target; *bit = (*bit + (size * n)) % 8;} } /* Packs 'nmbr' LONGs starting at 'lng[0]' into a packed array of 'bitsize' sized elements. If the internal buffer in which the array is packed is full, it is flushed to 'file', making room for more of the packed array. If ('lng == NULL'), the buffer is flushed a swell. */ void pack_chunk(int32_t *lng, int nmbr, int bitsize, FILE *packfile){ static int32_t bitsize_encode[33] = {0, 0, 0, 0, 1, 2, 3, 4, 5, 0, 0, 0, 0, 0, 0, 0, 6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 7}; int32_t descriptor[2], i, j; static char *buffer = NULL; static char *buffree = NULL; static int bitmark; if (buffer == NULL) { buffree = buffer = (char *) malloc(PACKBUFSIZ); bitmark = 0;} if (lng != NULL) { for (i = nmbr, j = 0; i > 1; i /= 2, ++j); descriptor[0] = j; descriptor[1] = bitsize_encode[bitsize]; if ((buffree - buffer) > (PACKBUFSIZ - (130 * 4))) { fwrite(buffer, sizeof(char), buffree - buffer, packfile); buffer[0] = buffree[0]; buffree = buffer;} pack_longs(descriptor, 2, &buffree, &bitmark, 3); pack_longs(lng, nmbr, &buffree, &bitmark, bitsize);} else { int len=buffree-buffer; if (bitmark!=0) len++; fwrite(buffer, sizeof(char), len, packfile); free((void *) buffer); buffer = NULL;}} /* Pack image 'img', containing 'x * y' WORD-sized pixels into 'filename'. */ void pack_wordimage_copen(short int *img, int x, int y, FILE *packfile){ int chunksiz, packsiz, nbits, next_nbits, tot_nbits; int32_t buffer[DIFFBUFSIZ]; int32_t *diffs = buffer; int32_t *end = diffs - 1; int32_t done = 0; fprintf(packfile, PACKIDENTIFIER, x, y); while (done < (x * y)) { end = diff_words(img, x, y, buffer, done); done += (end - buffer) + 1; diffs = buffer; while (diffs <= end) { packsiz = 0; chunksiz = 1; nbits = bits(diffs, 1); while (packsiz == 0) { if (end <= (diffs + chunksiz * 2)) packsiz = chunksiz; else { next_nbits = bits(diffs + chunksiz, chunksiz); tot_nbits = 2 * max(nbits, next_nbits); if (tot_nbits >= (nbits + next_nbits + 6)) packsiz = chunksiz; else { nbits = tot_nbits; if (chunksiz == 64) packsiz = 128; else chunksiz *= 2;}}} pack_chunk(diffs, packsiz, nbits / packsiz, packfile); diffs += packsiz;}} pack_chunk(NULL, 0, 0, packfile); } void pack_wordimage_c( short int *img, int x, int y, char *filename){ FILE *packfile = fopen(filename, "ab"); if (packfile == NULL) { fprintf(stderr,"The file %s cannot be created!\n ...giving up...\n", filename); exit(1); } else { pack_wordimage_copen(img, x, y, packfile); fclose(packfile); } } fabio-0.1.3/src/mar345_IO.pyx0000644000175000017500000001241512137541667016331 0ustar jeromejerome00000000000000""" New Cython version of mar345_io for preparing the migration to Python3 Compressor & decompressor for "pack" algorithm by JPA, binding to CCP4 libraries Warning: decompressor is just a cython porting of mar345_io, but in cython so (soon) python3 compliant. Future: make those algorithm actually generate strings not go via files; it will allow a broader use of the algorithm. """ __authors__ = ["Jerome Kieffer", "Gael Goret"] __contact__ = "jerome.kieffer@esrf.eu" __license__ = "LGPLv3+" __copyright__ = "2012, European Synchrotron Radiation Facility, Grenoble, France" import cython cimport numpy import numpy import os,tempfile from libc.string cimport memcpy #from libc.stdlib cimport free, malloc cdef extern from "ccp4_pack.h": void* mar345_read_data_string(char *instream, int ocount, int dim1, int dim2) nogil void pack_wordimage_c(short int*, int , int , char*) nogil void* ccp4_unpack_string (void *, void *, size_t, size_t, size_t) nogil void* ccp4_unpack_v2_string(void *, void *, size_t, size_t, size_t) nogil @cython.boundscheck(False) def compress_pck(numpy.ndarray inputArray not None): """ @param inputArray: numpy array as input @param filename: file to write data to """ cdef long size = inputArray.size cdef int dim0, dim1, i, j, fd, ret cdef char* name assert inputArray.ndim == 2, "shape is 2D" dim0 = inputArray.shape[0] dim1 = inputArray.shape[1] cdef numpy.ndarray[numpy.uint16_t, ndim = 1] data = numpy.ascontiguousarray(inputArray.astype(numpy.uint16).ravel(), dtype=numpy.uint16) cdef short int * cdata cdata = < short int *> data.data (fd,fname) = tempfile.mkstemp() name = fname with nogil: pack_wordimage_c(cdata, dim1, dim0, name) with open(name,"rb") as f: f.seek(0) output = f.read() os.close(fd) os.remove(name) return output @cython.boundscheck(False) def uncompress_pck(raw not None, dim1=None, dim2=None, overflowPix=None, version=None, normal_start=None): """ Unpack a mar345 compressed image @param raw: input string (bytes in python3) @param dim1,dim2: optional parameters size @param overflowPix: optional parameters: number of overflowed pixels @param version: PCK version 1 or 2 @param normal_start: position of the normal value section (can be auto-guessed) @return : ndarray of 2D with the right size """ cdef int cdimx, cdimy, chigh, cversion, orecords, normal_offset cdef numpy.ndarray[numpy.uint32_t, ndim = 2] data cdef numpy.ndarray[numpy.uint32_t, ndim = 1] flat cdef numpy.ndarray[numpy.uint8_t, ndim = 1] instream cdef void* out end=None key1 = "CCP4 packed image, X: " key2 = "CCP4 packed image V2, X: " if (dim1 is None) or (dim2 is None) or (version not in [1,2]) or (version is None) or (normal_start is None): start = raw.find(key2) key = key2 cversion = 2 if start == -1: start = raw.find(key1) key = key1 cversion = 1 lenkey = len(key) start = raw.index(key) + lenkey sizes = raw[start:start + 13] cdimx = < int > int(sizes[:4]) cdimy = < int > int(sizes[-4:]) normal_offset = start + 13 else: cdimx = < int > dim1 cdimy = < int > dim2 cversion = version normal_offset = normal_start if cversion==1: lenkey = len(key1) else: lenkey = len(key2) if cversion not in [1,2]: raise RuntimeError("Cannot determine the compression scheme for PCK compression (either version 1 or 2)") if (overflowPix is None): end = raw.find("END OF HEADER") start = raw[:end].find("HIGH") hiLine = raw[start:end] hiLine = hiLine.split("\n")[0] word = hiLine.split() if len(word) > 1: chigh = int(word[1]) else: print("Error while looking for overflowed pixels in line %s" % hiLine.strip()) chigh = 0 else: chigh = < int > overflowPix orecords = (chigh/8.0+0.875) data = numpy.empty((cdimy, cdimx), dtype=numpy.uint32) flat = data.ravel() #flat view on the data instream = numpy.fromstring(raw[normal_offset:].lstrip(),dtype=numpy.uint8) with nogil: ################################################################################ # relay to whichever version of ccp4_unpack is appropriate ################################################################################ if cversion == 1: ccp4_unpack_string( &data[0,0], &instream[0], cdimx, cdimy,0); else:# cversion == 2: ccp4_unpack_v2_string( &data[0,0], &instream[0], cdimx, cdimy,0); ################################################################################ # handle overflows ################################################################################ stop = normal_offset-lenkey-14 odata = numpy.fromstring(raw[stop-64*orecords: stop],dtype=numpy.int32) odata.shape = -1,2 addresses = odata[:,0] values = odata[:,1] valid = (addresses>0) addresses = addresses[valid]-1 #addresses start at 1 !! values = values[valid] flat[addresses] = values.astype(numpy.uint32) return data fabio-0.1.3/src/ccp4_pack.h0000644000175000017500000000570112137541667016165 0ustar jeromejerome00000000000000/* Fabio Mar345 ccp4_pack decompressor Copyright (C) 2007-2009 Henning O. Sorensen & Erik Knudsen This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA */ #ifndef _MSC_VER #include #else #include "stdint.h" #endif #include #include #include #define CCP4_PCK_BLOCK_HEADER_LENGTH 6 #define CCP4_PCK_BLOCK_HEADER_LENGTH_V2 8 /*array translating the number of errors per block*/ static unsigned int CCP4_PCK_ERR_COUNT[] = {1,2,4,8,16,32,64,128}; /*array translating the number of bits per error*/ static unsigned int CCP4_PCK_BIT_COUNT[]= {0,4,5,6,7,8,16,32}; /*array translating the number of errors per block - can use shifts as well actually*/ static unsigned int CCP4_PCK_ERR_COUNT_V2[] = {1,2,4,8,16,32,64,128,256,512,1024,2048,4096,8192,16384,32768}; /*array translating the number of bits per error*/ static unsigned int CCP4_PCK_BIT_COUNT_V2[]= {0,4,5,6,7,8,9,10,11,12,13,14,15,16,32}; static const unsigned char CCP4_PCK_MASK[]={0x00, 0x01, 0x03, 0x07, 0x0F, 0x1F, 0x3F, 0x7F, 0xFF}; static const unsigned int CCP4_PCK_MASK_16[]={0x00, 0x01, 0x03, 0x07, 0x0F, 0x1F, 0x3F, 0x7F, 0xFF, 0x1FF, 0x3FF, 0x7FF, 0xFFF, 0x1FFF, 0x3FFF, 0x7FFF, 0xFFFF}; static const unsigned long CCP4_PCK_MASK_32[]={0x00, 0x01, 0x03, 0x07, 0x0F, 0x1F, 0x3F, 0x7F, 0xFF, 0x1FF, 0x3FF, 0x7FF, 0xFFF, 0x1FFF, 0x3FFF, 0x7FFF, 0xFFFF, 0x1FFFF, 0x3FFFF, 0x7FFFF, 0xFFFFF, 0x1FFFFF, 0x3FFFFF, 0x7FFFFF, 0xFFFFFF, 0x1FFFFFF, 0x3FFFFFF, 0x7FFFFFF, 0xFFFFFFF, 0x1FFFFFFF, 0x3FFFFFFF, 0x7FFFFFFF, 0xFFFFFFFF}; #define pfail_nonzero(a) if ((a)) return NULL; void *mar345_read_data(FILE *file, int ocount, int dim1, int dim2); void *mar345_read_data_string(char *instring, int ocount, int dim1, int dim2); void *ccp4_unpack(void *unpacked_array, void *packed, size_t dim1, size_t dim2, size_t max_num_int); void *ccp4_unpack_v2(void *unpacked_array, void *packed, size_t dim1, size_t dim2, size_t max_num_int); void *ccp4_unpack_string(void *unpacked_array, void *packed, size_t dim1, size_t dim2, size_t max_num_int); void *ccp4_unpack_v2_string(void *unpacked_array, void *packed, size_t dim1, size_t dim2, size_t max_num_int); void pack_wordimage_c(short int *img, int x, int y, char *filename); fabio-0.1.3/src/cf_iomodule.c0000644000175000017500000000450412120434325016576 0ustar jeromejerome00000000000000#include #include #include #include #include "columnfile.h" static PyObject *cf_read(PyObject *self, PyObject *args, PyObject *keywds){ cf_data *cf__; PyArrayObject *py_data; PyStringObject *str; PyListObject *clabels; static char *kwlist[]={"file","mode",NULL}; const char mode[]="a "; unsigned int flags=0; /* perhaps not const */ int dim1,dim2,ocount; int dims[2]; int i; FILE *file; PyObject *py_file; if (!PyArg_ParseTupleAndKeywords(args,keywds,"O|s",kwlist,&py_file,&mode)) return NULL; file=PyFile_AsFile(py_file); if (strchr(mode,'z')){ flags|=CF_GZ_COMP; } if(strchr(mode,'b')){ cf__=(cf_data *) cf_read_bin(file,NULL,flags); }else if (strchr(mode,'a')) { cf__=(cf_data *) cf_read_ascii(file,NULL,flags); }else{ fprintf(stderr,"unrecognized mode for columnfile %s (assuming ascii)\n",mode); cf__= (cf_data *)cf_read_ascii(file,NULL,flags); } /*check for failure to read*/ if (cf__==NULL){ return Py_BuildValue("OO",Py_None,Py_None); } dims[0]=cf__->nrows;dims[1]=cf__->ncols; /*since data may be non-contigous we can't simply create a numpy-array from cf__->data, as Numpy's memory model prohibits it*/ /*i.e. py_data=(PyArrayObject*)PyArray_SimpleNewFromData(2, dims, NPY_DOUBLE, (void*)(&(cf__->data[0][0]))); * won't work*/ py_data=(PyArrayObject *)PyArray_SimpleNew(2,dims,NPY_DOUBLE); for (i=0;inrows;i++){ memcpy((double *)PyArray_GETPTR2(py_data,i,0),cf__->data[i],cf__->ncols*sizeof(double)); } clabels=(PyListObject *)PyList_New(0); for (i=0;incols;i++){ str = (PyStringObject*)PyString_FromString(cf__->clabels[i]); if (PyList_Append((PyObject*)clabels,(PyObject*)str)){ fprintf(stderr,"cannot insert column label %d\n",i); } } cf_free(cf__); return Py_BuildValue("OO", PyArray_Return(py_data),clabels); } static PyMethodDef cf_io_Methods[] = { {"read",(PyCFunction)cf_read, METH_VARARGS | METH_KEYWORDS, "call the c-columnfile reading interface. The mode keyword argument is either:\n \"a\" for ascii (the default)\n \"b\" for binary"}, {NULL, NULL, 0, NULL} }; PyMODINIT_FUNC initcf_io(void) { (void) Py_InitModule("cf_io",cf_io_Methods); import_array(); if (PyErr_Occurred()) Py_FatalError("cannot initialize cf_iomodule.c"); } fabio-0.1.3/src/stdint.h0000644000175000017500000001746112120434325015631 0ustar jeromejerome00000000000000// ISO C9x compliant stdint.h for Microsoft Visual Studio // Based on ISO/IEC 9899:TC2 Committee draft (May 6, 2005) WG14/N1124 // // Copyright (c) 2006-2008 Alexander Chemeris // // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are met: // // 1. Redistributions of source code must retain the above copyright notice, // this list of conditions and the following disclaimer. // // 2. Redistributions in binary form must reproduce the above copyright // notice, this list of conditions and the following disclaimer in the // documentation and/or other materials provided with the distribution. // // 3. The name of the author may be used to endorse or promote products // derived from this software without specific prior written permission. // // THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED // WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF // MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO // EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, // SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // /////////////////////////////////////////////////////////////////////////////// #ifndef _MSC_VER // [ #error "Use this header only with Microsoft Visual C++ compilers!" #endif // _MSC_VER ] #ifndef _MSC_STDINT_H_ // [ #define _MSC_STDINT_H_ #if _MSC_VER > 1000 #pragma once #endif #include // For Visual Studio 6 in C++ mode and for many Visual Studio versions when // compiling for ARM we should wrap include with 'extern "C++" {}' // or compiler give many errors like this: // error C2733: second C linkage of overloaded function 'wmemchr' not allowed #ifdef __cplusplus extern "C" { #endif # include #ifdef __cplusplus } #endif // Define _W64 macros to mark types changing their size, like intptr_t. #ifndef _W64 # if !defined(__midl) && (defined(_X86_) || defined(_M_IX86)) && _MSC_VER >= 1300 # define _W64 __w64 # else # define _W64 # endif #endif // 7.18.1 Integer types // 7.18.1.1 Exact-width integer types // Visual Studio 6 and Embedded Visual C++ 4 doesn't // realize that, e.g. char has the same size as __int8 // so we give up on __intX for them. #if (_MSC_VER < 1300) typedef char int8_t; typedef short int16_t; typedef int int32_t; typedef unsigned char uint8_t; typedef unsigned short uint16_t; typedef unsigned int uint32_t; #else typedef __int8 int8_t; typedef __int16 int16_t; typedef __int32 int32_t; typedef unsigned __int8 uint8_t; typedef unsigned __int16 uint16_t; typedef unsigned __int32 uint32_t; #endif typedef __int64 int64_t; typedef unsigned __int64 uint64_t; // 7.18.1.2 Minimum-width integer types typedef int8_t int_least8_t; typedef int16_t int_least16_t; typedef int32_t int_least32_t; typedef int64_t int_least64_t; typedef uint8_t uint_least8_t; typedef uint16_t uint_least16_t; typedef uint32_t uint_least32_t; typedef uint64_t uint_least64_t; // 7.18.1.3 Fastest minimum-width integer types typedef int8_t int_fast8_t; typedef int16_t int_fast16_t; typedef int32_t int_fast32_t; typedef int64_t int_fast64_t; typedef uint8_t uint_fast8_t; typedef uint16_t uint_fast16_t; typedef uint32_t uint_fast32_t; typedef uint64_t uint_fast64_t; // 7.18.1.4 Integer types capable of holding object pointers #ifdef _WIN64 // [ typedef __int64 intptr_t; typedef unsigned __int64 uintptr_t; #else // _WIN64 ][ typedef _W64 int intptr_t; typedef _W64 unsigned int uintptr_t; #endif // _WIN64 ] // 7.18.1.5 Greatest-width integer types typedef int64_t intmax_t; typedef uint64_t uintmax_t; // 7.18.2 Limits of specified-width integer types #if !defined(__cplusplus) || defined(__STDC_LIMIT_MACROS) // [ See footnote 220 at page 257 and footnote 221 at page 259 // 7.18.2.1 Limits of exact-width integer types #define INT8_MIN ((int8_t)_I8_MIN) #define INT8_MAX _I8_MAX #define INT16_MIN ((int16_t)_I16_MIN) #define INT16_MAX _I16_MAX #define INT32_MIN ((int32_t)_I32_MIN) #define INT32_MAX _I32_MAX #define INT64_MIN ((int64_t)_I64_MIN) #define INT64_MAX _I64_MAX #define UINT8_MAX _UI8_MAX #define UINT16_MAX _UI16_MAX #define UINT32_MAX _UI32_MAX #define UINT64_MAX _UI64_MAX // 7.18.2.2 Limits of minimum-width integer types #define INT_LEAST8_MIN INT8_MIN #define INT_LEAST8_MAX INT8_MAX #define INT_LEAST16_MIN INT16_MIN #define INT_LEAST16_MAX INT16_MAX #define INT_LEAST32_MIN INT32_MIN #define INT_LEAST32_MAX INT32_MAX #define INT_LEAST64_MIN INT64_MIN #define INT_LEAST64_MAX INT64_MAX #define UINT_LEAST8_MAX UINT8_MAX #define UINT_LEAST16_MAX UINT16_MAX #define UINT_LEAST32_MAX UINT32_MAX #define UINT_LEAST64_MAX UINT64_MAX // 7.18.2.3 Limits of fastest minimum-width integer types #define INT_FAST8_MIN INT8_MIN #define INT_FAST8_MAX INT8_MAX #define INT_FAST16_MIN INT16_MIN #define INT_FAST16_MAX INT16_MAX #define INT_FAST32_MIN INT32_MIN #define INT_FAST32_MAX INT32_MAX #define INT_FAST64_MIN INT64_MIN #define INT_FAST64_MAX INT64_MAX #define UINT_FAST8_MAX UINT8_MAX #define UINT_FAST16_MAX UINT16_MAX #define UINT_FAST32_MAX UINT32_MAX #define UINT_FAST64_MAX UINT64_MAX // 7.18.2.4 Limits of integer types capable of holding object pointers #ifdef _WIN64 // [ # define INTPTR_MIN INT64_MIN # define INTPTR_MAX INT64_MAX # define UINTPTR_MAX UINT64_MAX #else // _WIN64 ][ # define INTPTR_MIN INT32_MIN # define INTPTR_MAX INT32_MAX # define UINTPTR_MAX UINT32_MAX #endif // _WIN64 ] // 7.18.2.5 Limits of greatest-width integer types #define INTMAX_MIN INT64_MIN #define INTMAX_MAX INT64_MAX #define UINTMAX_MAX UINT64_MAX // 7.18.3 Limits of other integer types #ifdef _WIN64 // [ # define PTRDIFF_MIN _I64_MIN # define PTRDIFF_MAX _I64_MAX #else // _WIN64 ][ # define PTRDIFF_MIN _I32_MIN # define PTRDIFF_MAX _I32_MAX #endif // _WIN64 ] #define SIG_ATOMIC_MIN INT_MIN #define SIG_ATOMIC_MAX INT_MAX #ifndef SIZE_MAX // [ # ifdef _WIN64 // [ # define SIZE_MAX _UI64_MAX # else // _WIN64 ][ # define SIZE_MAX _UI32_MAX # endif // _WIN64 ] #endif // SIZE_MAX ] // WCHAR_MIN and WCHAR_MAX are also defined in #ifndef WCHAR_MIN // [ # define WCHAR_MIN 0 #endif // WCHAR_MIN ] #ifndef WCHAR_MAX // [ # define WCHAR_MAX _UI16_MAX #endif // WCHAR_MAX ] #define WINT_MIN 0 #define WINT_MAX _UI16_MAX #endif // __STDC_LIMIT_MACROS ] // 7.18.4 Limits of other integer types #if !defined(__cplusplus) || defined(__STDC_CONSTANT_MACROS) // [ See footnote 224 at page 260 // 7.18.4.1 Macros for minimum-width integer constants #define INT8_C(val) val##i8 #define INT16_C(val) val##i16 #define INT32_C(val) val##i32 #define INT64_C(val) val##i64 #define UINT8_C(val) val##ui8 #define UINT16_C(val) val##ui16 #define UINT32_C(val) val##ui32 #define UINT64_C(val) val##ui64 // 7.18.4.2 Macros for greatest-width integer constants #define INTMAX_C INT64_C #define UINTMAX_C UINT64_C #endif // __STDC_CONSTANT_MACROS ] #endif // _MSC_STDINT_H_ ] fabio-0.1.3/src/columnfile.c0000644000175000017500000001360312120434325016446 0ustar jeromejerome00000000000000#include #include #include #ifndef HAVE_ZLIB_H #define HAVE_ZLIB_H 0 #else #include #endif #include "columnfile.h" static char hdr_ctl[]="# %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s"; int compression_yes(char *fname){ /*should we use compression*/ char *p; if ( HAVE_ZLIB_H && (p=strstr(fname,".gz"))!=NULL && pnralloc;i++){ if (p->data[i]!=NULL) free(p->data[i]); } if( p->data!=NULL){free(p->data);} for (i=0;incols;i++){ if(p->clabels[i]!=NULL) free(p->clabels[i]); } if(p->clabels!=NULL){free(p->clabels);} free(p); } } int cf_write(char *fname,void *cf_handle, unsigned int FLAGS){ int status; #if HAVE_ZLIB_H if (FLAGS & CF_GZ_COMP){ gzFile gzfp=gzopen(fname,"wbh"); if (gzfp==NULL) return -1; status=-1; if (FLAGS && CF_BIN){ status=cf_write_bin_gz(gzfp,cf_handle); }else{ status=cf_write_ascii_gz(gzfp,cf_handle); } gzclose(gzfp); return status; }else{ #else if(1){ #endif FILE *fp=fopen(fname,"wb"); if (fp==NULL) return -1; status=-1; if (FLAGS && CF_BIN){ /*status=cf_write_bin(fp,cf_handle); */ }else{ status=cf_write_ascii(fp,cf_handle,0); } fclose(fp); return status; } } int cf_write_ascii(void *fp, void *cf_handle, unsigned int FLAGS){/*{{{*/ int r,c; cf_data *cf_=(cf_data *) cf_handle; #if HAVE_ZLIB_H if (FLAGS & CF_GZ_COMP){ gzprintf((gzFile)fp,"#"); for (i=0;incols;i++){ gzprintf((gzFile)fp," %s",cf_->clabels[i]); } gzprintf((gzFile)fp,"\n"); for (r=0;rnrows;r++){ for (i=0;incols;i++){ gzprintf((gzFile)fp," %g",cf_->data[i][r]); } gzprintf((gzFile)fp,"\n"); } return 0; }else{ #endif fprintf((FILE *)fp,"#"); for (c=0;cncols;c++){ fprintf((FILE *)fp," %s",cf_->clabels[c]); } fprintf((FILE *)fp,"\n"); for (r=0;rnrows;r++){ for (c=0;cncols;c++){ fprintf((FILE *)fp," %g",cf_->data[c][r]); } fprintf((FILE *)fp,"\n"); } return 0; #if HAVE_ZLIB_H } #endif }/*}}}*/ void *cf_read_ascii(void *fp, void *dest, unsigned int FLAGS){/*{{{*/ /*read the first line and figure out how many columns we have*/ char line[2048]; char *fi; /* returned by fgets */ int i,r; int nr_alloc=CF_INIT_ROWS; int nc_alloc=CF_INIT_COLS; int ncols,nrows; char **clabels,**cp; double **data,**dp; char *p; cf_data *dest_local; /*read the first line into buffer*/ #if HAVE_ZLIB_H if (FLAGS & CF_GZ_COMP){ if ((gzgets((gzFile )fp,line,2048))==Z_NULL) {fprintf(stderr,"zlib io error in %s \n",__FILE__);return NULL;} }else{ if((fgets(line,2048,(FILE *)fp))==NULL){fprintf(stderr,"io-error in %s\n",__FILE__);return NULL;} } #else if((fgets(line,2048,(FILE *)fp))==NULL){fprintf(stderr,"io-error in %s\n",__FILE__);return NULL;} #endif /*initially allocate room for 32 columns - if that is not enough should reallocate*/ clabels=(char**) malloc(CF_INIT_COLS* sizeof(char*)); for (cp=clabels;cpnon-ws slopes. when one is found read from pc-1 into header storage. exit when line is exhausted*/ /*count the number of entries*/ ncols=0; /*headers are supposed to start with # so skip that*/ if (*line=='#') p=line+1; else p=line; while (*p!='\0' || *p!='\n' || pncols=ncols; ((cf_data *) dest_local)->nrows=r; ((cf_data *) dest_local)->nralloc=nr_alloc; ((cf_data *) dest_local)->clabels=clabels; ((cf_data *) dest_local)->data=data; return (void *) dest_local; }/*}}}*/ void *cf_read_bin(void *fp, void *dest, unsigned int FLAGS){ return NULL; } fabio-0.1.3/src/columnfile.h0000644000175000017500000000302512120434325016450 0ustar jeromejerome00000000000000#ifndef CF_H #define CF_H 1 #include #include #include #define CF_INIT_ROWS 8192 #define CF_INIT_COLS 32 #define CF_HEADER_ITEM 128 #define CF_GZ_COMP 1 #define CF_BIN 2 #define repeat16_inc(name,offset) \ *((name)+(offset)),*((name)+(offset)+1),*((name)+(offset)+2),*((name)+(offset)+3),*((name)+(offset)+4), \ *((name)+(offset)+5),*((name)+(offset)+6),*((name)+(offset)+7),*((name)+(offset)+8),*((name)+(offset)+9), \ *((name)+(offset)+10),*((name)+(offset)+11),*((name)+(offset)+12),*((name)+(offset)+13),*((name)+(offset)+14),*((name)+(offset)+15) #define cf_check_realloc(p,i,chunk_size,item_size) \ do {\ if((i)%(chunk_size)==0){\ } while (0); #define cf_sscan_column(source,conversion,dest,prefix) \ do {\ int tmpi=0;\ if ((prefix)!=NULL) sscanf(source,prefix);\ while (sscanf( (source) , (conversion) , ((dest) +tmpi))){\ tmpi++;\ }\ } while (0); #define is_ws(character) \ ( (character==' ') || ((character)=='\t') || ((character)=='\v') || ((character) =='\r') || ((character) =='\n') ) typedef struct cf_data{ int ncols,nrows; unsigned int nralloc; double **data; char **clabels; } cf_data; void * cf_read_ascii(void *fp, void *dest, unsigned int FLAGS); void * cf_read_bin(void *fp, void *dest, unsigned int FLAGS); int cf_write(char *fname, void *cf_handle, unsigned int FLAGS); int cf_write_bin(void *fp, void *cf_handle); int cf_write_ascii(void *fp, void *cf_handle,unsigned int FLAGS); void cf_free( cf_data *cf_handle); #endif fabio-0.1.3/src/byte_offset.pyx0000644000175000017500000001073612120434325017224 0ustar jeromejerome00000000000000""" Authors: Jerome Kieffer, ESRF Email: jerome.kieffer@esrf.eu Cif Binary Files images are 2D images written by the Pilatus detector and others. They use a modified (simplified) byte-offset algorithm. This file contains the decompression function from a string to an int64 numpy array. This is Cython: convert it to pure C then compile it with gcc $ cython byte_offset.pyx """ __author__ = "Jerome Kieffer" __contact__ = "jerome.kieffer@esrf.eu" __license__ = "LGPLv3+" __copyright__ = "2010-2012, European Synchrotron Radiation Facility, Grenoble, France" cimport numpy import numpy import cython @cython.boundscheck(False) def analyseCython(bytes stream not None, size=None): """ Analyze a stream of char with any length of exception (2,4, or 8 bytes integers) @param stream: string representing the compressed data @param size: the size of the output array (of longInts) @return : int64 ndArrays """ cdef int i = 0 cdef int j = 0 cdef long long last = 0 cdef long long current = 0 cdef char tmp8 = 0 cdef unsigned char utmp8a = 0 cdef unsigned char utmp8b = 0 cdef unsigned char utmp8c = 0 cdef unsigned char utmp8d = 0 cdef unsigned char utmp8e = 0 cdef unsigned char utmp8f = 0 cdef unsigned char utmp8g = 0 cdef long long tmp64 = 0 cdef long long tmp64a = 0 cdef long long tmp64b = 0 cdef long long tmp64c = 0 cdef long long tmp64d = 0 cdef long long tmp64e = 0 cdef long long tmp64f = 0 cdef long long tmp64g = 0 cdef char key8 = 0x80 cdef char key0 = 0x00 cdef int csize cdef int lenStream = < int > len(stream) cdef char * cstream = stream if size is None: csize = lenStream else: csize = < int > size cdef numpy.ndarray[ long long , ndim = 1] dataOut = numpy.zeros(csize, dtype=numpy.int64) with nogil: while (i < lenStream) and (j < csize): if (cstream[i] == key8): if ((cstream[i + 1] == key0) and (cstream[i + 2] == key8)): if (cstream[i + 3] == key0) and (cstream[i + 4] == key0) and (cstream[i + 5] == key0) and (cstream[i + 6] == key8): #Retrieve the interesting Bytes of data tmp8 = cstream[i + 14] utmp8a = cstream[i + 13] utmp8b = cstream[i + 12] utmp8c = cstream[i + 11] utmp8d = cstream[i + 10] utmp8e = cstream[i + 9] utmp8f = cstream[i + 8] utmp8g = cstream[i + 7] # cast them in 64 bit tmp64 = tmp8 tmp64a = utmp8a tmp64b = utmp8b tmp64c = utmp8c tmp64d = utmp8d tmp64e = utmp8e tmp64f = utmp8f tmp64g = utmp8g current = (tmp64 << 56) | (tmp64a << 48) | (tmp64b << 40) | (tmp64c << 32) | (tmp64d << 24) | (tmp64e << 16) | (tmp64f << 8) | (tmp64g) i += 15 else: #Retrieve the interesting Bytes of data tmp8 = cstream[i + 6] utmp8a = cstream[i + 5] utmp8b = cstream[i + 4] utmp8c = cstream[i + 3] # cast them in 64 bit tmp64 = tmp8 tmp64a = utmp8a tmp64b = utmp8b tmp64c = utmp8c #Assemble data into a long long current = (tmp64 << 24) | (tmp64a << 16) | (tmp64b << 8) | (tmp64c); i += 7 else: tmp8 = cstream[i + 2]; utmp8a = cstream[i + 1] # cast them in 64 bit tmp64 = tmp8 tmp64a = utmp8a current = (tmp64 << 8) | (tmp64a); i += 3 else: tmp8 = cstream[i] current = tmp8 i += 1 last += current dataOut[j] = last j += 1 return dataOut[:j] fabio-0.1.3/src/cf_io.pyx0000644000175000017500000000510712233175156015777 0ustar jeromejerome00000000000000""" New Cython version of cf_iomodule.c for preparing the migration to Python3 """ __authors__ = ["Jerome Kieffer"] __contact__ = "jerome.kieffer@esrf.eu" __license__ = "LGPLv3+" __copyright__ = "2013, European Synchrotron Radiation Facility, Grenoble, France" import cython cimport numpy import numpy import os,tempfile, sys from libc.string cimport memcpy from libc.stdio cimport fopen, FILE CF_H=1 CF_INIT_ROWS=8192 CF_INIT_COLS=32 CF_HEADER_ITEM=128 CF_GZ_COMP=1 CF_BIN=2 cdef extern from "columnfile.h": struct cf_data: int ncols,nrows unsigned int nralloc double **data char **clabels void * cf_read_ascii(void *fp, void *dest, unsigned int FLAGS)nogil void * cf_read_bin(void *fp, void *dest, unsigned int FLAGS)nogil int cf_write(char *fname, void *cf_handle, unsigned int FLAGS)nogil int cf_write_bin(void *fp, void *cf_handle)nogil int cf_write_ascii(void *fp, void *cf_handle,unsigned int FLAGS)nogil void cf_free( cf_data *cf_handle)nogil def read(py_file, mode="a"): """ Call the c-columnfile reading interface. The mode keyword argument is either: "a" for ascii (the default) "b" for binary """ cdef cf_data *cf__ cdef unsigned int flags=0,fd # /* perhaps not const */ cdef int i cdef FILE *file # PyObject *py_file; #Here is a big issue !!! and I got an even worse solution ! # file=PyFile_AsFile(py_file); (fd,fname) = tempfile.mkstemp() os.fdopen(fd,mode="wb").write(py_file.read()) os.close(fd) file=fopen(fname, "r"); if "z" in mode: flags|=CF_GZ_COMP if "b" in mode: cf__= cf_read_bin(file,NULL,flags) elif "a" in mode: cf__= cf_read_ascii(file,NULL,flags) else: sys.stderr.write("unrecognized mode for columnfile %s (assuming ascii)\n",mode) cf__= cf_read_ascii(file,NULL,flags); # check for failure to read if (cf__==NULL): return None, None dims=(cf__.nrows,cf__.ncols) #since data may be non-contigous we can't simply create a numpy-array from cf__->data, as Numpy's memory model prohibits it # i.e. py_data=(PyArrayObject*)PyArray_SimpleNewFromData(2, dims, NPY_DOUBLE, (void*)(&(cf__->data[0][0]))); # won't work cdef numpy.ndarray[numpy.float64_t, ndim = 2] py_data=numpy.empty(dims,dtype=numpy.float64) for i in range(cf__.nrows): memcpy(&py_data[i,0], cf__.data[i],cf__.ncols*sizeof(double)) clabels=[] for i in range(cf__.ncols): clabels.append(str(cf__.clabels[i])) cf_free(cf__) return py_data, clabels fabio-0.1.3/epydoc/0000755000175000017500000000000012233272207014642 5ustar jeromejerome00000000000000fabio-0.1.3/epydoc/fabio.fabioutils.FilenameObject-class.html0000644000175000017500000003376512126623347024745 0ustar jeromejerome00000000000000 fabio.fabioutils.FilenameObject
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        Package fabio :: Module fabioutils :: Class FilenameObject
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        Class FilenameObject

        source code

        object --+
         |
        FilenameObject

        The 'meaning' of a filename ...

        Instance Methods [hide private]
         
        __init__(self, stem=None, num=None, directory=None, format=None, extension=None, postnum=None, digits=4, filename=None)
        This class can either be instanciated by a set of parameters like directory, prefix, num, extension, ...        		 source code
         
        str(self)
        Return a string representation        		 source code
         
        __repr__(self)
        Return a string representation        		 source code
         
        tostring(self)
        convert yourself to a string        		 source code
         
        deconstruct_filename(self, filename)
        Break up a filename to get image type and number        		 source code

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __str__, __subclasshook__

        Properties [hide private]

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, stem=None, num=None, directory=None, format=None, extension=None, postnum=None, digits=4, filename=None)
        (Constructor)

        		source code 

        This class can either be instanciated by a set of parameters like directory, prefix, num, extension, ...

        Parameters:
        • stem - the stem is a kind of prefix (str)
        • num - image number in the serie (int)
        • directory - name of the directory (str)
        • format - ??
        • extension
        • postnum
        • digits - Number of digits used to print num

          Alternative constructor:

        • filename - fullpath of an image file to be deconstructed into directory, prefix, num, extension, ...
        Overrides: object.__init__

        __repr__(self)
        (Representation operator)

        		source code 

        Return a string representation

        Overrides: object.__repr__

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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:40 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/fabio.xsdimage-pysrc.html0000644000175000017500000016572212126623347021571 0ustar jeromejerome00000000000000 fabio.xsdimage
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        Package fabio :: Module xsdimage
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        [frames] | no frames]

        Source Code for Module fabio.xsdimage

          1  #!/usr/bin/env python 
  2  # coding: utf8 
  3  """ 
  4  Authors: Jérôme Kieffer, ESRF  
  5           email:jerome.kieffer@esrf.fr 
  6   
  7  XSDimge are XML files containing numpy arrays  
  8  """ 
  9  __author__ = "Jérôme Kieffer" 
 10  __contact__ = "jerome.kieffer@esrf.eu" 
 11  __license__ = "GPLv3+" 
 12  __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" 
 13   
 14  import logging, numpy 
 15  logger = logging.getLogger("xsdimage") 
 16  from fabioimage import fabioimage 
 17  import base64, hashlib 
 18  try: 
 19      from lxml import etree 
 20  except ImportError: 
 21      logger.warning("lxml library is probably not part of your python installation: disabling xsdimage format") 
 22      etree = None 
 23   

         24 -class xsdimage(fabioimage): 

         25      """  
 26      Read the XSDataImage XML File data format  
 27      """ 

         28 -    def __init__(self, data=None, header=None, fname=None): 

         29          """ 
 30          Constructor of the class XSDataImage. 
 31   
 32          @param _strFilename: the name of the file to open 
 33          @type  _strFilename: string 
 34          """ 
 35          fabioimage.__init__(self, data=data, header=header) 
 36          self.dims = [] 
 37          self.size = None 
 38          self.coding = None 
 39          self.dtype = None 
 40          self.rawData = None 
 41          self.md5 = None 
 42          if fname is not None: 
 43              self.filename = fname 
 44              self.read(fname) 

         45   

         46 -    def read(self, fname, frame=None): 

         47          """ 
 48          """ 
 49          self.header = {} 
 50          self.resetvals() 
 51          self.filename = fname 
 52          infile = self._open(fname, "rb") 
 53          self._readheader(infile) 
 54   
 55          try: 
 56              self.dim1, self.dim2 = self.dims[:2] 
 57          except: 
 58              raise IOError("XSD file %s is corrupt, no dimensions in it" % fname) 
 59          try: 
 60              self.bytecode = numpy.dtype(self.dtype).type 
 61              self.bpp = len(numpy.array(0, self.bytecode).tostring()) 
 62          except TypeError: 
 63              self.bytecode = numpy.int32 
 64              self.bpp = 32 
 65              logger.warning("Defaulting type to int32") 
 66   
 67          exp_size = 1 
 68          for i in self.dims: 
 69              exp_size *= i 
 70          assert exp_size == self.size 
 71   
 72          decData = None 
 73          if self.coding == "base64": 
 74              decData = base64.b64decode(self.rawData) 
 75          elif self.coding == "base32": 
 76              decData = base64.b32decode(self.rawData) 
 77          elif self.coding == "base16": 
 78              decData = base64.b16decode(self.rawData) 
 79          else: 
 80              logger.warning("Unable to recognize the encoding of the data !!! got %s, expected base64, base32 or base16, I assume it is base64 " % self.coding) 
 81              decData = base64.b64decode(self.rawData) 
 82          if self.md5: 
 83              assert  hashlib.md5(decData).hexdigest() == self.md5 
 84   
 85   
 86          self.data = numpy.fromstring(decData, dtype=self.bytecode).reshape(tuple(self.dims)) 
 87          if not numpy.little_endian: #by default little endian 
 88              self.data.byteswap(inplace=True) 
 89          self.resetvals() 
 90  #        # ensure the PIL image is reset 
 91          self.pilimage = None 
 92          return self 

         93   

         94 -    def _readheader(self, infile): 

         95          """ 
 96          Read all headers in a file and populate self.header 
 97          data is not yet populated 
 98          @type infile: file object open in read mode 
 99          """ 
100          xml = etree.parse(infile) 
101          self.dims = [] 
102          for i in xml.xpath("//shape"): 
103              try: 
104                  self.dims.append(int(i.text)) 
105              except ValueError, error: 
106                  logger.warning("%s Shape: Unable to convert %s to integer in %s" % (error, i.text, i)) 
107          for i in xml.xpath("//size"): 
108              try: 
109                  self.size = int(i.text) 
110              except Exception, error:#IGNORE:W0703 
111                  logger.warning("%s Size: Unable to convert %s to integer in %s" % (error, i.text, i)) 
112          self.dtype = None 
113          for i in xml.xpath("//dtype"): 
114              self.dtype = i.text 
115          self.coding = None 
116          for i in xml.xpath("//coding"): 
117              j = i.find("value") 
118              if j is not None: 
119                  self.coding = j.text 
120          self.rawData = None 
121          for i in xml.xpath("//data"): 
122              self.rawData = i.text 
123          self.md5 = None 
124          for i in xml.xpath("//md5sum"): 
125              j = i.find("value") 
126              if j is not None: 
127                  self.md5 = j.text 

        128   
129  if etree is None: 
130      xsdimage = None 
131

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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:41 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/fabio.GEimage.GEimage-class.html0000644000175000017500000005550012126623347022520 0ustar jeromejerome00000000000000 fabio.GEimage.GEimage
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        Package fabio :: Module GEimage :: Class GEimage
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        Class GEimage

        source code

                   object --+    
                    |    
fabioimage.fabioimage --+
                        |
                       GEimage
        Instance Methods [hide private]
         
        _readheader(self, infile)
        Read a GE image header        		 source code
         
        read(self, fname, frame=None)
        Read in header into self.header and the data into self.data        		 source code
         
        _makeframename(self)
        The thing to be printed for the user to represent a frame inside a file        		 source code
         
        _readframe(self, filepointer, img_num)
        # Load only one image from the sequence # Note: the first image in the sequence 0 # raises an exception if you give an invalid image # otherwise fills in self.data        		 source code
         
        write(self, fname, force_type=<type 'numpy.uint16'>)
        Not yet implemented        		 source code
         
        getframe(self, num)
        Returns a frame as a new fabioimage object        		 source code
         
        next(self)
        Get the next image in a series as a fabio image        		 source code
         
        previous(self)
        Get the previous image in a series as a fabio image        		 source code

        Inherited from fabioimage.fabioimage: __init__, add, convert, getclassname, getheader, getmax, getmean, getmin, getstddev, integrate_area, load, make_slice, readROI, readheader, rebin, resetvals, save, toPIL16, update_header

        Inherited from fabioimage.fabioimage (private): _compressed_stream, _open

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Static Methods [hide private]

        Inherited from fabioimage.fabioimage: checkData, checkHeader

        Class Variables [hide private]
          _need_a_seek_to_read = True

        Inherited from fabioimage.fabioimage (private): _need_a_real_file

        Properties [hide private]

        Inherited from fabioimage.fabioimage: classname

        Inherited from object: __class__

        Method Details [hide private]

        _readheader(self, infile)

        		source code 

        Read a GE image header

        Overrides: fabioimage.fabioimage._readheader

        read(self, fname, frame=None)

        		source code 

        Read in header into self.header and the data into self.data

        Overrides: fabioimage.fabioimage.read

        write(self, fname, force_type=<type 'numpy.uint16'>)

        		source code 

        Not yet implemented

        Overrides: fabioimage.fabioimage.write

        getframe(self, num)

        		source code 

        Returns a frame as a new fabioimage object

        Overrides: fabioimage.fabioimage.getframe

        next(self)

        		source code 

        Get the next image in a series as a fabio image

        Overrides: fabioimage.fabioimage.next

        previous(self)

        		source code 

        Get the previous image in a series as a fabio image

        Overrides: fabioimage.fabioimage.previous

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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:40 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/toc-fabio.pilatusimage-module.html0000644000175000017500000000234012120434325023334 0ustar jeromejerome00000000000000 pilatusimage

        Module pilatusimage

        Classes

        pilatusimage

        Variables

        __package__
        [hide private] fabio-0.1.3/epydoc/fabio.TiffIO-module.html0000644000175000017500000005772712126623347021242 0ustar jeromejerome00000000000000 fabio.TiffIO
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        Package fabio :: Module TiffIO
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        Module TiffIO

        source code

        Author: V.A. Sole - ESRF Data Analysis

        Classes [hide private]
          TiffIO
        Variables [hide private]
          __revision__ = 1501
          DEBUG = 0
          ALLOW_MULTIPLE_STRIPS = False
          TAG_ID = {256: 'NumberOfColumns', 257: 'NumberOfRows', 258: 'B...
          TAG_NUMBER_OF_COLUMNS = 256
          TAG_NUMBER_OF_ROWS = 257
          TAG_BITS_PER_SAMPLE = 258
          TAG_PHOTOMETRIC_INTERPRETATION = 262
          TAG_COMPRESSION = 259
          TAG_IMAGE_DESCRIPTION = 270
          TAG_STRIP_OFFSETS = 273
          TAG_ROWS_PER_STRIP = 278
          TAG_STRIP_BYTE_COUNTS = 279
          TAG_SOFTWARE = 305
          TAG_DATE = 306
          TAG_COLORMAP = 320
          TAG_SAMPLE_FORMAT = 339
          FIELD_TYPE = {1: ('BYTE', 'B'), 2: ('ASCII', 's'), 3: ('SHORT'...
          FIELD_TYPE_OUT = {'B': 1, 'H': 3, 'I': 4, 'II': 5, 'b': 6, 'd'...
          SAMPLE_FORMAT_UINT = 1
          SAMPLE_FORMAT_INT = 2
          SAMPLE_FORMAT_FLOAT = 3
          SAMPLE_FORMAT_VOID = 4
          SAMPLE_FORMAT_COMPLEXINT = 5
          SAMPLE_FORMAT_COMPLEXIEEEFP = 6
          __package__ = 'fabio'
        Variables Details [hide private]

        TAG_ID

        Value:
        {256: 'NumberOfColumns',
 257: 'NumberOfRows',
 258: 'BitsPerSample',
 259: 'Compression',
 262: 'PhotometricInterpretation',
 270: 'ImageDescription',
 273: 'StripOffsets',
 278: 'RowsPerStrip',
...

        FIELD_TYPE

        Value:
        {1: ('BYTE', 'B'),
 2: ('ASCII', 's'),
 3: ('SHORT', 'H'),
 4: ('LONG', 'I'),
 5: ('RATIONAL', 'II'),
 6: ('SBYTE', 'b'),
 7: ('UNDEFINED', 'B'),
 8: ('SSHORT', 'h'),
...

        FIELD_TYPE_OUT

        Value:
        {'B': 1,
 'H': 3,
 'I': 4,
 'II': 5,
 'b': 6,
 'd': 12,
 'f': 11,
 'h': 8,
...

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        fabio-0.1.3/epydoc/toc-fabio.GEimage_old-module.html0000644000175000017500000000232212120434325023004 0ustar jeromejerome00000000000000 GEimage_old

        Module GEimage_old

        Classes

        GEimage

        Variables

        __package__
        [hide private] fabio-0.1.3/epydoc/fabio.readbytestream-pysrc.html0000644000175000017500000006537512126623347023006 0ustar jeromejerome00000000000000 fabio.readbytestream
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        Package fabio :: Module readbytestream
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        Source Code for Module fabio.readbytestream

         1  #!/usr/bin/env python 
 2  #coding: utf8 
 3   
 4  """ 
 5  Reads a bytestream 
 6   
 7  Authors: Jon Wright    Henning O. Sorensen & Erik Knudsen 
 8           ESRF          Risoe National Laboratory 
 9  """ 
10   
11  import numpy, logging 
12  logger = logging.getLogger("readbytestream") 
13  DATATYPES = { 
14      # type  sign bytes 
15      ("int", 'n', 1) : numpy.uint8, 
16      ("int", 'n', 2) : numpy.uint16, 
17      ("int", 'n', 4) : numpy.uint32, 
18      ("int", 'y', 1) : numpy.int8, 
19      ("int", 'y', 2) : numpy.int16, 
20      ("int", 'y', 4) : numpy.int32, 
21      ('float', 'y', 4) : numpy.float32, # does this occur in bruker? 
22      ('double', 'y', 4): numpy.float64 
23      } 
24   
25   

        26 -def readbytestream(fil, 
27                     offset, 
28                     x, 
29                     y, 
30                     nbytespp, 
31                     datatype='int', 
32                     signed='n', 
33                     swap='n', 
34                     typeout=numpy.uint16): 

        35      """ 
36      Reads in a bytestream from a file (which may be a string indicating 
37      a filename, or an already opened file (should be "rb")) 
38      offset is the position (in bytes) where the pixel data start 
39      nbytespp = number of bytes per pixel 
40      type can be int or float (4 bytes pp) or double (8 bytes pp) 
41      signed: normally signed data 'y', but 'n' to try to get back the  
42      right numbers when unsigned data are converted to signed  
43      (python once had no unsigned numeric types.) 
44      swap, normally do not bother, but 'y' to swap bytes 
45      typeout is the numpy type to output, normally uint16,  
46      but more if overflows occurred 
47      x and y are the pixel dimensions 
48       
49      TODO : Read in regions of interest 
50       
51      PLEASE LEAVE THE STRANGE INTERFACE ALONE -  
52      IT IS USEFUL FOR THE BRUKER FORMAT 
53      """ 
54      tin = "dunno" 
55      length = nbytespp * x * y # bytes per pixel times number of pixels 
56      if datatype in ['float', 'double']: 
57          signed = 'y' 
58   
59      key = (datatype, signed, nbytespp) 
60      try: 
61          tin = DATATYPES[key] 
62      except: 
63          logging.warning("datatype,signed,nbytespp " + str(key)) 
64          raise Exception("Unknown combination of types to readbytestream") 
65   
66      # Did we get a string (filename) or a readable stream object? 
67      if hasattr(fil, "read") and hasattr(fil, "seek"): 
68          infile = fil 
69          opened = False 
70      else: 
71          infile = open(fil, 'rb') 
72          opened = True 
73   
74      infile.seek(offset) 
75   
76      arr = numpy.array(numpy.reshape( 
77              numpy.fromstring( 
78                  infile.read(length), tin) , (x, y)), typeout) 
79   
80      if swap == 'y': 
81          arr = arr.byteswap() 
82   
83      if opened: 
84          infile.close() 
85   
86      return arr 

        87

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        fabio-0.1.3/epydoc/toc.html0000644000175000017500000001626312120434325016321 0ustar jeromejerome00000000000000 Table of Contents

        Table of Contents

        Everything

        Modules

        fabio
        fabio.GEimage
        fabio.GEimage_old
        fabio.HiPiCimage
        fabio.OXDimage
        fabio.TiffIO
        fabio.adscimage
        fabio.binaryimage
        fabio.bruker100image
        fabio.brukerimage
        fabio.byte_offset
        fabio.cbfimage
        fabio.cf_io
        fabio.compression
        fabio.converters
        fabio.datIO
        fabio.dm3image
        fabio.edfimage
        fabio.fabioimage
        fabio.fabioutils
        fabio.file_series
        fabio.fit2dmaskimage
        fabio.fit2dspreadsheetimage
        fabio.kcdimage
        fabio.mar345_IO
        fabio.mar345image
        fabio.marccdimage
        fabio.openimage
        fabio.pilatusimage
        fabio.pnmimage
        fabio.readbytestream
        fabio.tifimage
        fabio.xsdimage
        [hide private] fabio-0.1.3/epydoc/api-objects.txt0000644000175000017500000027267712126623347017636 0ustar jeromejerome00000000000000fabio fabio-module.html fabio.getnum fabio.fabioutils-module.html#getnum fabio.construct_filename fabio.fabioutils-module.html#construct_filename fabio.open fabio.openimage-module.html#openimage fabio.deconstruct_filename fabio.fabioutils-module.html#deconstruct_filename fabio.__package__ fabio-module.html#__package__ fabio.version fabio-module.html#version fabio.openheader fabio.openimage-module.html#openheader fabio.next_filename fabio.fabioutils-module.html#next_filename fabio.extract_filenumber fabio.fabioutils-module.html#extract_filenumber fabio.__status__ fabio-module.html#__status__ fabio.previous_filename fabio.fabioutils-module.html#previous_filename fabio.jump_filename fabio.fabioutils-module.html#jump_filename fabio.GEimage fabio.GEimage-module.html fabio.GEimage.previous_filename fabio.fabioutils-module.html#previous_filename fabio.GEimage.GE_HEADER_INFO fabio.GEimage-module.html#GE_HEADER_INFO fabio.GEimage.__package__ fabio.GEimage-module.html#__package__ fabio.GEimage.next_filename fabio.fabioutils-module.html#next_filename fabio.GEimage.demo fabio.GEimage-module.html#demo fabio.GEimage.logger fabio.GEimage-module.html#logger fabio.GEimage_old fabio.GEimage_old-module.html fabio.GEimage_old.__package__ fabio.GEimage_old-module.html#__package__ fabio.HiPiCimage fabio.HiPiCimage-module.html fabio.HiPiCimage.__package__ fabio.HiPiCimage-module.html#__package__ fabio.HiPiCimage.logger fabio.HiPiCimage-module.html#logger fabio.OXDimage fabio.OXDimage-module.html fabio.OXDimage.deg2rad fabio.OXDimage-module.html#deg2rad fabio.OXDimage.rad2deg fabio.OXDimage-module.html#rad2deg fabio.OXDimage.__package__ fabio.OXDimage-module.html#__package__ fabio.OXDimage.decTY1 fabio.compression-module.html#decTY1 fabio.OXDimage.__doc__ fabio.OXDimage-module.html#__doc__ fabio.OXDimage.compTY1 fabio.compression-module.html#compTY1 fabio.OXDimage.logger fabio.OXDimage-module.html#logger fabio.OXDimage.DEFAULT_HEADERS fabio.OXDimage-module.html#DEFAULT_HEADERS fabio.OXDimage.DETECTOR_TYPES fabio.OXDimage-module.html#DETECTOR_TYPES fabio.TiffIO fabio.TiffIO-module.html fabio.TiffIO.FIELD_TYPE fabio.TiffIO-module.html#FIELD_TYPE fabio.TiffIO.FIELD_TYPE_OUT fabio.TiffIO-module.html#FIELD_TYPE_OUT fabio.TiffIO.TAG_ROWS_PER_STRIP fabio.TiffIO-module.html#TAG_ROWS_PER_STRIP fabio.TiffIO.TAG_PHOTOMETRIC_INTERPRETATION fabio.TiffIO-module.html#TAG_PHOTOMETRIC_INTERPRETATION fabio.TiffIO.TAG_IMAGE_DESCRIPTION fabio.TiffIO-module.html#TAG_IMAGE_DESCRIPTION fabio.TiffIO.TAG_COMPRESSION fabio.TiffIO-module.html#TAG_COMPRESSION fabio.TiffIO.TAG_DATE fabio.TiffIO-module.html#TAG_DATE fabio.TiffIO.TAG_SOFTWARE fabio.TiffIO-module.html#TAG_SOFTWARE fabio.TiffIO.TAG_NUMBER_OF_ROWS fabio.TiffIO-module.html#TAG_NUMBER_OF_ROWS fabio.TiffIO.TAG_BITS_PER_SAMPLE 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fabio.fabioimage.fabioimage.checkHeader fabio.fabioimage.fabioimage-class.html#checkHeader fabio.fabioimage.fabioimage.integrate_area fabio.fabioimage.fabioimage-class.html#integrate_area fabio.fabioimage.fabioimage.next fabio.fabioimage.fabioimage-class.html#next fabio.pnmimage.pnmimage.__init__ fabio.pnmimage.pnmimage-class.html#__init__ fabio.fabioimage.fabioimage.previous fabio.fabioimage.fabioimage-class.html#previous fabio.fabioimage.fabioimage.getmean fabio.fabioimage.fabioimage-class.html#getmean fabio.fabioimage.fabioimage.rebin fabio.fabioimage.fabioimage-class.html#rebin fabio.fabioimage.fabioimage._open fabio.fabioimage.fabioimage-class.html#_open fabio.pnmimage.pnmimage.P2dec fabio.pnmimage.pnmimage-class.html#P2dec fabio.pnmimage.pnmimage.write fabio.pnmimage.pnmimage-class.html#write fabio.fabioimage.fabioimage.add fabio.fabioimage.fabioimage-class.html#add fabio.pnmimage.pnmimage.P6dec fabio.pnmimage.pnmimage-class.html#P6dec fabio.fabioimage.fabioimage.getstddev fabio.fabioimage.fabioimage-class.html#getstddev fabio.fabioimage.fabioimage.getmin fabio.fabioimage.fabioimage-class.html#getmin fabio.fabioimage.fabioimage.readROI fabio.fabioimage.fabioimage-class.html#readROI fabio.fabioimage.fabioimage.getmax fabio.fabioimage.fabioimage-class.html#getmax fabio.fabioimage.fabioimage.save fabio.fabioimage.fabioimage-class.html#save fabio.fabioimage.fabioimage.make_slice fabio.fabioimage.fabioimage-class.html#make_slice fabio.pnmimage.pnmimage.P3dec fabio.pnmimage.pnmimage-class.html#P3dec fabio.pnmimage.pnmimage.read fabio.pnmimage.pnmimage-class.html#read fabio.fabioimage.fabioimage._compressed_stream fabio.fabioimage.fabioimage-class.html#_compressed_stream fabio.pnmimage.pnmimage.P5dec fabio.pnmimage.pnmimage-class.html#P5dec fabio.fabioimage.fabioimage.getframe fabio.fabioimage.fabioimage-class.html#getframe fabio.fabioimage.fabioimage.readheader fabio.fabioimage.fabioimage-class.html#readheader fabio.pnmimage.pnmimage.P1dec fabio.pnmimage.pnmimage-class.html#P1dec fabio.pnmimage.pnmimage.checkData fabio.pnmimage.pnmimage-class.html#checkData fabio.fabioimage.fabioimage.update_header fabio.fabioimage.fabioimage-class.html#update_header fabio.fabioimage.fabioimage.convert fabio.fabioimage.fabioimage-class.html#convert fabio.fabioimage.fabioimage._need_a_real_file fabio.fabioimage.fabioimage-class.html#_need_a_real_file fabio.fabioimage.fabioimage.toPIL16 fabio.fabioimage.fabioimage-class.html#toPIL16 fabio.pnmimage.pnmimage.P4dec fabio.pnmimage.pnmimage-class.html#P4dec fabio.pnmimage.pnmimage._readheader fabio.pnmimage.pnmimage-class.html#_readheader fabio.fabioimage.fabioimage.getclassname fabio.fabioimage.fabioimage-class.html#getclassname fabio.tifimage.Image_File_Directory fabio.tifimage.Image_File_Directory-class.html fabio.tifimage.Image_File_Directory.unpack fabio.tifimage.Image_File_Directory-class.html#unpack fabio.tifimage.Image_File_Directory.__init__ fabio.tifimage.Image_File_Directory-class.html#__init__ fabio.tifimage.Image_File_Directory_entry fabio.tifimage.Image_File_Directory_entry-class.html fabio.tifimage.Image_File_Directory_entry.extract_data fabio.tifimage.Image_File_Directory_entry-class.html#extract_data fabio.tifimage.Image_File_Directory_entry.unpack fabio.tifimage.Image_File_Directory_entry-class.html#unpack fabio.tifimage.Image_File_Directory_entry.__init__ fabio.tifimage.Image_File_Directory_entry-class.html#__init__ fabio.tifimage.Tiff_header fabio.tifimage.Tiff_header-class.html fabio.tifimage.Tiff_header.__init__ fabio.tifimage.Tiff_header-class.html#__init__ fabio.tifimage.tifimage fabio.tifimage.tifimage-class.html fabio.fabioimage.fabioimage.load fabio.fabioimage.fabioimage-class.html#load fabio.tifimage.tifimage._need_a_seek_to_read fabio.tifimage.tifimage-class.html#_need_a_seek_to_read fabio.fabioimage.fabioimage.getheader fabio.fabioimage.fabioimage-class.html#getheader fabio.fabioimage.fabioimage.resetvals fabio.fabioimage.fabioimage-class.html#resetvals fabio.fabioimage.fabioimage.classname fabio.fabioimage.fabioimage-class.html#classname fabio.fabioimage.fabioimage.checkHeader fabio.fabioimage.fabioimage-class.html#checkHeader fabio.fabioimage.fabioimage.integrate_area fabio.fabioimage.fabioimage-class.html#integrate_area fabio.tifimage.tifimage.__init__ fabio.tifimage.tifimage-class.html#__init__ fabio.fabioimage.fabioimage.previous fabio.fabioimage.fabioimage-class.html#previous fabio.tifimage.tifimage.write fabio.tifimage.tifimage-class.html#write fabio.fabioimage.fabioimage.rebin fabio.fabioimage.fabioimage-class.html#rebin fabio.fabioimage.fabioimage._open fabio.fabioimage.fabioimage-class.html#_open fabio.fabioimage.fabioimage.next fabio.fabioimage.fabioimage-class.html#next fabio.fabioimage.fabioimage.getmean fabio.fabioimage.fabioimage-class.html#getmean fabio.fabioimage.fabioimage.add fabio.fabioimage.fabioimage-class.html#add fabio.fabioimage.fabioimage.getstddev fabio.fabioimage.fabioimage-class.html#getstddev fabio.fabioimage.fabioimage.getmin fabio.fabioimage.fabioimage-class.html#getmin fabio.fabioimage.fabioimage.readROI fabio.fabioimage.fabioimage-class.html#readROI fabio.fabioimage.fabioimage.getmax fabio.fabioimage.fabioimage-class.html#getmax fabio.fabioimage.fabioimage.save fabio.fabioimage.fabioimage-class.html#save fabio.fabioimage.fabioimage.make_slice fabio.fabioimage.fabioimage-class.html#make_slice fabio.tifimage.tifimage.read fabio.tifimage.tifimage-class.html#read fabio.fabioimage.fabioimage._compressed_stream fabio.fabioimage.fabioimage-class.html#_compressed_stream fabio.fabioimage.fabioimage.getframe fabio.fabioimage.fabioimage-class.html#getframe fabio.fabioimage.fabioimage.readheader fabio.fabioimage.fabioimage-class.html#readheader fabio.fabioimage.fabioimage.checkData fabio.fabioimage.fabioimage-class.html#checkData fabio.fabioimage.fabioimage.update_header fabio.fabioimage.fabioimage-class.html#update_header fabio.fabioimage.fabioimage.convert fabio.fabioimage.fabioimage-class.html#convert fabio.fabioimage.fabioimage._need_a_real_file fabio.fabioimage.fabioimage-class.html#_need_a_real_file fabio.fabioimage.fabioimage.toPIL16 fabio.fabioimage.fabioimage-class.html#toPIL16 fabio.tifimage.tifimage._readheader fabio.tifimage.tifimage-class.html#_readheader fabio.fabioimage.fabioimage.getclassname fabio.fabioimage.fabioimage-class.html#getclassname fabio.xsdimage.xsdimage fabio.xsdimage.xsdimage-class.html fabio.fabioimage.fabioimage.load fabio.fabioimage.fabioimage-class.html#load fabio.fabioimage.fabioimage._need_a_seek_to_read fabio.fabioimage.fabioimage-class.html#_need_a_seek_to_read fabio.fabioimage.fabioimage.getheader fabio.fabioimage.fabioimage-class.html#getheader fabio.fabioimage.fabioimage.resetvals fabio.fabioimage.fabioimage-class.html#resetvals fabio.fabioimage.fabioimage.classname fabio.fabioimage.fabioimage-class.html#classname fabio.fabioimage.fabioimage.checkHeader fabio.fabioimage.fabioimage-class.html#checkHeader fabio.fabioimage.fabioimage.integrate_area fabio.fabioimage.fabioimage-class.html#integrate_area fabio.xsdimage.xsdimage.__init__ fabio.xsdimage.xsdimage-class.html#__init__ fabio.fabioimage.fabioimage.previous fabio.fabioimage.fabioimage-class.html#previous fabio.fabioimage.fabioimage.getmean fabio.fabioimage.fabioimage-class.html#getmean fabio.fabioimage.fabioimage.rebin fabio.fabioimage.fabioimage-class.html#rebin fabio.fabioimage.fabioimage._open fabio.fabioimage.fabioimage-class.html#_open fabio.fabioimage.fabioimage.next fabio.fabioimage.fabioimage-class.html#next fabio.fabioimage.fabioimage.write fabio.fabioimage.fabioimage-class.html#write fabio.fabioimage.fabioimage.add fabio.fabioimage.fabioimage-class.html#add fabio.fabioimage.fabioimage.getstddev fabio.fabioimage.fabioimage-class.html#getstddev fabio.fabioimage.fabioimage.getmin fabio.fabioimage.fabioimage-class.html#getmin fabio.fabioimage.fabioimage.readROI fabio.fabioimage.fabioimage-class.html#readROI fabio.fabioimage.fabioimage.getmax fabio.fabioimage.fabioimage-class.html#getmax fabio.fabioimage.fabioimage.save fabio.fabioimage.fabioimage-class.html#save fabio.fabioimage.fabioimage.make_slice fabio.fabioimage.fabioimage-class.html#make_slice fabio.xsdimage.xsdimage.read fabio.xsdimage.xsdimage-class.html#read fabio.fabioimage.fabioimage._compressed_stream fabio.fabioimage.fabioimage-class.html#_compressed_stream fabio.fabioimage.fabioimage.getframe fabio.fabioimage.fabioimage-class.html#getframe fabio.fabioimage.fabioimage.readheader fabio.fabioimage.fabioimage-class.html#readheader fabio.fabioimage.fabioimage.checkData fabio.fabioimage.fabioimage-class.html#checkData fabio.fabioimage.fabioimage.update_header fabio.fabioimage.fabioimage-class.html#update_header fabio.fabioimage.fabioimage.convert fabio.fabioimage.fabioimage-class.html#convert fabio.fabioimage.fabioimage._need_a_real_file fabio.fabioimage.fabioimage-class.html#_need_a_real_file fabio.fabioimage.fabioimage.toPIL16 fabio.fabioimage.fabioimage-class.html#toPIL16 fabio.xsdimage.xsdimage._readheader fabio.xsdimage.xsdimage-class.html#_readheader fabio.fabioimage.fabioimage.getclassname fabio.fabioimage.fabioimage-class.html#getclassname str str-class.html str.upper str-class.html#upper str.__getslice__ str-class.html#__getslice__ str.__ne__ str-class.html#__ne__ str.lstrip str-class.html#lstrip str.__str__ str-class.html#__str__ str.__getattribute__ str-class.html#__getattribute__ str.rpartition str-class.html#rpartition str.replace str-class.html#replace str.isdigit str-class.html#isdigit str.endswith str-class.html#endswith str.splitlines str-class.html#splitlines str.rfind str-class.html#rfind str.strip str-class.html#strip str.__rmul__ str-class.html#__rmul__ str.__lt__ str-class.html#__lt__ str.__getnewargs__ str-class.html#__getnewargs__ str.__rmod__ str-class.html#__rmod__ str.index str-class.html#index str.ljust str-class.html#ljust str.__new__ str-class.html#__new__ str.isalnum str-class.html#isalnum str.__contains__ str-class.html#__contains__ str.rindex str-class.html#rindex str.rsplit str-class.html#rsplit str.__format__ str-class.html#__format__ str.find str-class.html#find str.decode str-class.html#decode str.isalpha str-class.html#isalpha str.__eq__ str-class.html#__eq__ str.split str-class.html#split str.rstrip str-class.html#rstrip str.encode str-class.html#encode str._formatter_parser str-class.html#_formatter_parser str.translate str-class.html#translate str.isspace str-class.html#isspace str.__len__ str-class.html#__len__ str.__repr__ str-class.html#__repr__ str.startswith str-class.html#startswith str.__getitem__ str-class.html#__getitem__ str.format str-class.html#format str.rjust str-class.html#rjust str.swapcase str-class.html#swapcase str.__hash__ str-class.html#__hash__ str.zfill str-class.html#zfill str.__add__ str-class.html#__add__ str.__gt__ str-class.html#__gt__ str.capitalize str-class.html#capitalize str.__sizeof__ str-class.html#__sizeof__ str.count str-class.html#count str.lower str-class.html#lower str.join str-class.html#join str.center str-class.html#center str.__mod__ str-class.html#__mod__ str.partition str-class.html#partition str.expandtabs str-class.html#expandtabs str.istitle str-class.html#istitle str.__le__ str-class.html#__le__ str.__mul__ str-class.html#__mul__ str._formatter_field_name_split str-class.html#_formatter_field_name_split str.islower str-class.html#islower str.title str-class.html#title str.isupper str-class.html#isupper str.__ge__ str-class.html#__ge__ fabio-0.1.3/epydoc/fabio.fit2dspreadsheetimage.fit2dspreadsheetimage-class.html0000644000175000017500000003704712126623347030440 0ustar jeromejerome00000000000000 fabio.fit2dspreadsheetimage.fit2dspreadsheetimage
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        Package fabio :: Module fit2dspreadsheetimage :: Class fit2dspreadsheetimage
        [hide private]
        [frames] | no frames]

        Class fit2dspreadsheetimage

        source code

                   object --+    
                    |    
fabioimage.fabioimage --+
                        |
                       fit2dspreadsheetimage

        Read a fit2d ascii format

        Instance Methods [hide private]
         
        _readheader(self, infile)
        TODO : test for minimal attributes?        		 source code
         
        read(self, fname, frame=None)
        Read in header into self.header and...        		 source code

        Inherited from fabioimage.fabioimage: __init__, add, convert, getclassname, getframe, getheader, getmax, getmean, getmin, getstddev, integrate_area, load, make_slice, next, previous, readROI, readheader, rebin, resetvals, save, toPIL16, update_header, write

        Inherited from fabioimage.fabioimage (private): _compressed_stream, _open

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Static Methods [hide private]

        Inherited from fabioimage.fabioimage: checkData, checkHeader

        Class Variables [hide private]

        Inherited from fabioimage.fabioimage (private): _need_a_real_file, _need_a_seek_to_read

        Properties [hide private]

        Inherited from fabioimage.fabioimage: classname

        Inherited from object: __class__

        Method Details [hide private]

        _readheader(self, infile)

        		source code 

        TODO : test for minimal attributes?

        Overrides: fabioimage.fabioimage._readheader

        read(self, fname, frame=None)

        		source code  
        
Read in header into self.header and
    the data   into self.data
        Overrides: fabioimage.fabioimage.read

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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:40 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/fabio.dm3image.dm3image-class.html0000644000175000017500000005026512126623347023103 0ustar jeromejerome00000000000000 fabio.dm3image.dm3image
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        Package fabio :: Module dm3image :: Class dm3image
        [hide private]
        [frames] | no frames]

        Class dm3image

        source code

                   object --+    
                    |    
fabioimage.fabioimage --+
                        |
                       dm3image

        Read and try to write the dm3 data format

        Instance Methods [hide private]
         
        __init__(self, *args, **kwargs)
        Set up initial values        		 source code
         
        _readheader(self)
        Must be overridden in classes        		 source code
         
        read(self, fname, frame=None)
        To be overridden - fill in self.header and self.data        		 source code
         
        readbytes(self, bytes_to_read, format, swap=True) source code
         
        read_tag_group(self) source code
         
        read_tag_entry(self) source code
         
        read_tag_type(self) source code
         
        read_data(self) source code

        Inherited from fabioimage.fabioimage: add, convert, getclassname, getframe, getheader, getmax, getmean, getmin, getstddev, integrate_area, load, make_slice, next, previous, readROI, readheader, rebin, resetvals, save, toPIL16, update_header, write

        Inherited from fabioimage.fabioimage (private): _compressed_stream, _open

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Static Methods [hide private]

        Inherited from fabioimage.fabioimage: checkData, checkHeader

        Class Variables [hide private]

        Inherited from fabioimage.fabioimage (private): _need_a_real_file, _need_a_seek_to_read

        Properties [hide private]

        Inherited from fabioimage.fabioimage: classname

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, *args, **kwargs)
        (Constructor)

        		source code 

        Set up initial values

        Overrides: object.__init__
        (inherited documentation)

        _readheader(self)

        		source code 

        Must be overridden in classes

        Overrides: fabioimage.fabioimage._readheader
        (inherited documentation)

        read(self, fname, frame=None)

        		source code 

        To be overridden - fill in self.header and self.data

        Overrides: fabioimage.fabioimage.read
        (inherited documentation)

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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:40 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/fabio.TiffIO.TiffIO-class.html0000644000175000017500000005145012126623347022164 0ustar jeromejerome00000000000000 fabio.TiffIO.TiffIO
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        Package fabio :: Module TiffIO :: Class TiffIO
        [hide private]
        [frames] | no frames]

        Class TiffIO

        source code

        object --+
         |
        TiffIO
        Instance Methods [hide private]
         
        __init__(self, filename, mode=None, cache_length=20, mono_output=False)
        x.__init__(...) initializes x; see x.__class__.__doc__ for signature        		 source code
         
        _initInternalVariables(self, fd=None) source code
         
        __makeSureFileIsOpen(self) source code
         
        __makeSureFileIsClosed(self) source code
         
        getNumberOfImages(self) source code
         
        _updateIFD(self) source code
         
        getImageFileDirectories(self, fd=None) source code
         
        _parseImageFileDirectory(self, nImage) source code
         
        _readIFDEntry(self, tag, tagIDList, fieldTypeList, nValuesList, valueOffsetList) source code
         
        getData(self, nImage, **kw) source code
         
        getImage(self, nImage) source code
         
        getInfo(self, nImage, **kw) source code
         
        _readInfo(self, nImage, close=True) source code
         
        _readImage(self, nImage, **kw) source code
         
        writeImage(self, image0, info=None, software=None, date=None) source code
         
        _initEmptyFile(self, fd=None) source code
         
        _getOutputIFD(self, image, description=None, software=None, date=None) source code

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Properties [hide private]

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, filename, mode=None, cache_length=20, mono_output=False)
        (Constructor)

        		source code 

        x.__init__(...) initializes x; see x.__class__.__doc__ for signature

        Overrides: object.__init__
        (inherited documentation)

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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:40 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/fabio.adscimage-module.html0000644000175000017500000001673312126623347022027 0ustar jeromejerome00000000000000 fabio.adscimage
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        Package fabio :: Module adscimage
        [hide private]
        [frames] | no frames]

        Module adscimage

        source code

        

Authors: Henning O. Sorensen & Erik Knudsen
         Center for Fundamental Research: Metal Structures in Four Dimensions
         Risoe National Laboratory
         Frederiksborgvej 399
         DK-4000 Roskilde
         email:erik.knudsen@risoe.dk

+ mods for fabio by JPW
        Classes [hide private]
          adscimage
        Read an image in ADSC format (quite similar to edf?)
        Functions [hide private]
         
        test()
        testcase        		 source code
        Variables [hide private]
          logger = logging.getLogger("adscimage")
          __package__ = 'fabio'
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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:40 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/fabio.cbfimage-pysrc.html0000644000175000017500000075143012126623347021522 0ustar jeromejerome00000000000000 fabio.cbfimage
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        Package fabio :: Module cbfimage
        [hide private]
        [frames] | no frames]

        Source Code for Module fabio.cbfimage

          1  #!/usr/bin/env python 
  2  # coding: utf8 
  3  """ 
  4  Authors: Jérôme Kieffer, ESRF 
  5           email:jerome.kieffer@esrf.fr 
  6   
  7  Cif Binary Files images are 2D images written by the Pilatus detector and others. 
  8  They use a modified (simplified) byte-offset algorithm. 
  9   
 10  CIF is a library for manipulating Crystallographic information files and tries 
 11  to conform to the specification of the IUCR 
 12  """ 
 13  __author__ = "Jérôme Kieffer" 
 14  __contact__ = "jerome.kieffer@esrf.eu" 
 15  __license__ = "GPLv3+" 
 16  __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" 
 17  __version__ = ["Generated by CIF.py: Jan 2005 - April 2012", 
 18                "Written by Jerome Kieffer: Jerome.Kieffer@esrf.eu", 
 19                "On-line data analysis / ISDD ", "ESRF Grenoble (France)"] 
 20   
 21   
 22  import os, logging 
 23  logger = logging.getLogger("cbfimage") 
 24  import numpy 
 25  from fabioimage import fabioimage 
 26  from compression import decByteOffet_numpy, md5sum, compByteOffet_numpy 
 27  #import time 
 28   
 29  DATA_TYPES = { "signed 8-bit integer"   : numpy.int8, 
 30                 "signed 16-bit integer"  : numpy.int16, 
 31                 "signed 32-bit integer"  : numpy.int32, 
 32                 "signed 64-bit integer"  : numpy.int64 
 33                  } 
 34   
 35  MINIMUM_KEYS = ["X-Binary-Size-Fastest-Dimension", 
 36                  'ByteOrder', 
 37                  'Data type', 
 38                  'X dimension', 
 39                  'Y dimension', 
 40                  'Number of readouts'] 
 41   
 42   
 43  STARTER = "\x0c\x1a\x04\xd5" 
 44  PADDING = 512 

         45   
 46 -class cbfimage(fabioimage): 

         47      """ 
 48      Read the Cif Binary File data format 
 49      """ 

         50 -    def __init__(self, data=None , header=None, fname=None): 

         51          """ 
 52          Constructor of the class CIF Binary File reader. 
 53   
 54          @param _strFilename: the name of the file to open 
 55          @type  _strFilename: string 
 56          """ 
 57          fabioimage.__init__(self, data, header) 
 58          self.cif = CIF() 
 59          if fname is not None: #load the file) 
 60              self.read(fname) 

         61   
 62      @staticmethod 

         63 -    def checkData(data=None): 

         64          if data is None: 
 65              return None 
 66          elif numpy.issubdtype(data.dtype, int): 
 67              return data 
 68          else: 
 69              return data.astype(int) 

         70   
 71   

         72 -    def _readheader(self, inStream): 

         73          """ 
 74          Read in a header in some CBF format from a string representing binary stuff 
 75   
 76          @param inStream: file containing the Cif Binary part. 
 77          @type inStream: opened file. 
 78          """ 
 79          self.cif.loadCIF(inStream, _bKeepComment=True) 
 80   
 81  #        backport contents of the CIF data to the headers 
 82          for key in self.cif: 
 83              if key != "_array_data.data": 
 84                  self.header_keys.append(key) 
 85                  self.header[key] = self.cif[key].strip(" \"\n\r\t") 
 86   
 87          if not "_array_data.data" in self.cif: 
 88              raise Exception("cbfimage: CBF file %s is corrupt, cannot find data block with '_array_data.data' key" % self.fname) 
 89   
 90          inStream2 = self.cif["_array_data.data"] 
 91          sep = "\r\n" 
 92          iSepPos = inStream2.find(sep) 
 93          if iSepPos < 0 or iSepPos > 80: 
 94              sep = "\n" #switch back to unix representation 
 95   
 96          lines = inStream2.split(sep) 
 97          for oneLine in lines[1:]: 
 98              if len(oneLine) < 10: 
 99                  break 
100              try: 
101                  key, val = oneLine.split(':' , 1) 
102              except ValueError: 
103                  key, val = oneLine.split('=' , 1) 
104              key = key.strip() 
105              self.header_keys.append(key) 
106              self.header[key] = val.strip(" \"\n\r\t") 
107          missing = [] 
108          for item in MINIMUM_KEYS: 
109              if item not in self.header_keys: 
110                  missing.append(item) 
111          if len(missing) > 0: 
112              logger.debug("CBF file misses the keys " + " ".join(missing)) 

        113   
114   

        115 -    def read(self, fname, frame=None): 

        116          """ 
117          Read in header into self.header and 
118              the data   into self.data 
119          """ 
120          self.filename = fname 
121          self.header = {} 
122          self.resetvals() 
123   
124          infile = self._open(fname, "rb") 
125          self._readheader(infile) 
126          # Compute image size 
127          try: 
128              self.dim1 = int(self.header['X-Binary-Size-Fastest-Dimension']) 
129              self.dim2 = int(self.header['X-Binary-Size-Second-Dimension']) 
130          except: 
131              raise Exception(IOError, "CBF file %s is corrupt, no dimensions in it" % fname) 
132          try: 
133              bytecode = DATA_TYPES[self.header['X-Binary-Element-Type']] 
134              self.bpp = len(numpy.array(0, bytecode).tostring()) 
135          except KeyError: 
136              bytecode = numpy.int32 
137              self.bpp = 32 
138              logger.warning("Defaulting type to int32") 
139          if self.header["conversions"] == "x-CBF_BYTE_OFFSET": 
140              self.data = self._readbinary_byte_offset(self.cif["_array_data.data"]).astype(bytecode).reshape((self.dim2, self.dim1)) 
141          else: 
142              raise Exception(IOError, "Compression scheme not yet supported, please contact FABIO development team") 
143   
144          self.bytecode = self.data.dtype.type 
145          self.resetvals() 
146  #        # ensure the PIL image is reset 
147          self.pilimage = None 
148          return self 

        149   
150   
151   

        152 -    def _readbinary_byte_offset(self, inStream): 

        153          """ 
154          Read in a binary part of an x-CBF_BYTE_OFFSET compressed image 
155   
156          @param inStream: the binary image (without any CIF decorators) 
157          @type inStream: python string. 
158          @return: a linear numpy array without shape and dtype set 
159          @rtype: numpy array 
160          """ 
161          startPos = inStream.find(STARTER) + 4 
162          data = inStream[ startPos: startPos + int(self.header["X-Binary-Size"])] 
163          try: 
164              import byte_offset 
165          except ImportError: 
166              logger.warning("Error in byte_offset part: Falling back to Numpy implementation") 
167              myData = decByteOffet_numpy(data, size=self.dim1 * self.dim2) 
168          else: 
169              myData = byte_offset.analyseCython(data, size=self.dim1 * self.dim2) 
170   
171          assert len(myData) == self.dim1 * self.dim2 
172          return myData 

        173   
174   

        175 -    def write(self, fname): 

        176          """ 
177          write the file in CBF format 
178          @param fname: name of the file 
179          @type: string 
180          """ 
181          if self.data is not None: 
182              self.dim2, self.dim1 = self.data.shape 
183          else: 
184              raise RuntimeError("CBF image contains no data") 
185          binary_blob = compByteOffet_numpy(self.data) 
186  #        l = len(binary_blob) 
187  #        if (l % PADDING) != 0: 
188  #            rem = PADDING - (l % PADDING) 
189  #            binary_blob += "\x00" * rem 
190          dtype = "Unknown" 
191          for key, value in DATA_TYPES.iteritems(): 
192              if value == self.data.dtype: 
193                  dtype = key 
194          binary_block = [ 
195                          "--CIF-BINARY-FORMAT-SECTION--", 
196                          "Content-Type: application/octet-stream;", 
197                          '     conversions="x-CBF_BYTE_OFFSET"', 
198                          'Content-Transfer-Encoding: BINARY', 
199                          "X-Binary-Size: %d" % (len(binary_blob)), 
200                          "X-Binary-ID: 1", 
201                          'X-Binary-Element-Type: "%s"' % (dtype), 
202                          "X-Binary-Element-Byte-Order: LITTLE_ENDIAN" , 
203                          "Content-MD5: %s" % md5sum(binary_blob), 
204                          "X-Binary-Number-of-Elements: %s" % (self.dim1 * self.dim2), 
205                          "X-Binary-Size-Fastest-Dimension: %d" % self.dim1, 
206                          "X-Binary-Size-Second-Dimension: %d" % self.dim2, 
207                          "X-Binary-Size-Padding: %d" % 1, 
208                          "", 
209                          STARTER + binary_blob, 
210                          "", 
211                          "--CIF-BINARY-FORMAT-SECTION----" 
212                          ] 
213   
214          if "_array_data.header_contents" not in self.header: 
215              nonCifHeaders = [] 
216          else: 
217              nonCifHeaders = [i.strip()[2:] for i in self.header["_array_data.header_contents"].split("\n") if i.find("# ") >= 0] 
218   
219          for key in self.header: 
220              if (key not in self.header_keys): 
221                  self.header_keys.append(key) 
222          for key in self.header_keys: 
223              if key.startswith("_") : 
224                  if key not in self.cif or self.cif[key] != self.header[key]: 
225                      self.cif[key] = self.header[key] 
226              elif key.startswith("X-Binary-"): 
227                  pass 
228              elif key.startswith("Content-"): 
229                  pass 
230              elif key.startswith("conversions"): 
231                  pass 
232              elif key.startswith("filename"): 
233                  pass 
234              elif key in self.header: 
235                  nonCifHeaders.append("%s %s" % (key, self.header[key])) 
236          if len(nonCifHeaders) > 0: 
237              self.cif["_array_data.header_contents"] = "\r\n".join(["# %s" % i for i in nonCifHeaders]) 
238   
239          self.cif["_array_data.data"] = "\r\n".join(binary_block) 
240          self.cif.saveCIF(fname, linesep="\r\n", binary=True) 

        241   

        242  ################################################################################ 
243  # CIF class 
244  ################################################################################ 
245 -class CIF(dict): 

        246      """ 
247      This is the CIF class, it represents the CIF dictionary; 
248      and as a a python dictionary thus inherits from the dict built in class. 
249      """ 
250      EOL = ["\r", "\n", "\r\n", "\n\r"] 
251      BLANK = [" ", "\t"] + EOL 
252      START_COMMENT = ["\"", "\'"] 
253      BINARY_MARKER = "--CIF-BINARY-FORMAT-SECTION--" 
254   

        255 -    def __init__(self, _strFilename=None): 

        256          """ 
257          Constructor of the class. 
258   
259          @param _strFilename: the name of the file to open 
260          @type  _strFilename: filename (str) or file object 
261          """ 
262          dict.__init__(self) 
263          self._ordered = [] 
264          if _strFilename is not None: #load the file) 
265              self.loadCIF(_strFilename) 

        266   

        267 -    def __setitem__(self, key, value): 

        268          if key not in self._ordered: 
269              self._ordered.append(key) 
270          return dict.__setitem__(self, key, value) 

        271   

        272 -    def pop(self, key): 

        273          if key  in self._ordered: 
274              self._ordered.remove(key) 
275          return dict.pop(self, key) 

        276   

        277 -    def popitem(self, key): 

        278          if key  in self._ordered: 
279              self._ordered.remove(key) 
280          return dict.popitem(self, key) 

        281   
282   

        283 -    def loadCIF(self, _strFilename, _bKeepComment=False): 

        284          """Load the CIF file and populates the CIF dictionary into the object 
285          @param _strFilename: the name of the file to open 
286          @type  _strFilename: string 
287          @param _strFilename: the name of the file to open 
288          @type  _strFilename: string 
289          @return: None 
290          """ 
291   
292          if isinstance(_strFilename, (str, unicode)): 
293              if os.path.isfile(_strFilename): 
294                  infile = open(_strFilename, "rb") 
295              else: 
296                  raise RuntimeError("CIF.loadCIF: No such file to open: %s" % _strFilename) 
297          #elif isinstance(_strFilename, file, bz2.BZ2File, ): 
298          elif "read" in dir(_strFilename): 
299              infile = _strFilename 
300          else: 
301              raise RuntimeError("CIF.loadCIF: what is %s type %s" % (_strFilename, type(_strFilename))) 
302          if _bKeepComment: 
303              self._parseCIF(infile.read()) 
304          else: 
305              self._parseCIF(CIF._readCIF(infile)) 

        306      readCIF = loadCIF 
307   
308      @staticmethod 

        309 -    def isAscii(_strIn): 

        310          """ 
311          Check if all characters in a string are ascii, 
312   
313          @param _strIn: input string 
314          @type _strIn: python string 
315          @return: boolean 
316          @rtype: boolean 
317          """ 
318          bIsAcii = True 
319          for i in _strIn: 
320              if ord(i) > 127: 
321                  bIsAcii = False 
322                  break 
323          return bIsAcii 

        324   
325   
326      @staticmethod 

        327 -    def _readCIF(_instream): 

        328          """ 
329          - Check if the filename containing the CIF data exists 
330          - read the cif file 
331          - removes the comments 
332   
333          @param _instream: the file containing the CIF data 
334          @type _instream: open file in read mode 
335          @return: a string containing the raw data 
336          @rtype: string 
337          """ 
338          if not "readlines" in dir(_instream): 
339              raise RuntimeError("CIF._readCIF(instream): I expected instream to be an opened file,\ 
340               here I got %s type %s" % (_instream, type(_instream))) 
341          lLinesRead = _instream.readlines() 
342          sText = "" 
343          for sLine in lLinesRead: 
344              iPos = sLine.find("#") 
345              if iPos >= 0: 
346                  if CIF.isAscii(sLine): 
347                      sText += sLine[:iPos] + os.linesep 
348   
349                  if iPos > 80 : 
350                      logger.warning("This line is too long and could cause problems in PreQuest: %s", sLine) 
351              else : 
352                  sText += sLine 
353                  if len(sLine.strip()) > 80 : 
354                      logger.warning("This line is too long and could cause problems in PreQues: %s", sLine) 
355          return sText 

        356   
357   

        358 -    def _parseCIF(self, sText): 

        359          """ 
360          - Parses the text of a CIF file 
361          - Cut it in fields 
362          - Find all the loops and process 
363          - Find all the keys and values 
364   
365          @param sText: the content of the CIF - file 
366          @type sText: string 
367          @return: Nothing, the data are incorporated at the CIF object dictionary 
368          @rtype: None 
369          """ 
370          loopidx = [] 
371          looplen = [] 
372          loop = [] 
373          #first of all : separate the cif file in fields 
374          lFields = CIF._splitCIF(sText.strip()) 
375          #Then : look for loops 
376          for i in range(len(lFields)): 
377              if lFields[i].lower() == "loop_": 
378                  loopidx.append(i) 
379          if len(loopidx) > 0: 
380              for i in loopidx: 
381                  loopone, length, keys = CIF._analyseOneLoop(lFields, i) 
382                  loop.append([keys, loopone]) 
383                  looplen.append(length) 
384   
385   
386              for i in range(len(loopidx) - 1, -1, -1): 
387                  f1 = lFields[:loopidx[i]] + lFields[loopidx[i] + looplen[i]:] 
388                  lFields = f1 
389   
390              self["loop_"] = loop 
391   
392          for i in range(len(lFields) - 1): 
393      #        print lFields[i], lFields[i+1] 
394              if len(lFields[i + 1]) == 0 : lFields[i + 1] = "?" 
395              if lFields[i][0] == "_" and lFields[i + 1][0] != "_": 
396                  self[lFields[i]] = lFields[i + 1] 

        397   
398      @staticmethod 

        399 -    def _splitCIF(sText): 

        400          """ 
401          Separate the text in fields as defined in the CIF 
402   
403          @param sText: the content of the CIF - file 
404          @type sText: string 
405          @return: list of all the fields of the CIF 
406          @rtype: list 
407          """ 
408          lFields = [] 
409          while True: 
410              if len(sText) == 0: 
411                  break 
412              elif sText[0] == "'": 
413                  idx = 0 
414                  bFinished = False 
415                  while not  bFinished: 
416                      idx += 1 + sText[idx + 1:].find("'") 
417      ##########debuging    in case we arrive at the end of the text 
418                      if idx >= len(sText) - 1: 
419      #                    print sText,idx,len(sText) 
420                          lFields.append(sText[1:-1].strip()) 
421                          sText = "" 
422                          bFinished = True 
423                          break 
424   
425                      if sText[idx + 1] in CIF.BLANK: 
426                          lFields.append(sText[1:idx].strip()) 
427                          sText1 = sText[idx + 1:] 
428                          sText = sText1.strip() 
429                          bFinished = True 
430   
431              elif sText[0] == '"': 
432                  idx = 0 
433                  bFinished = False 
434                  while not  bFinished: 
435                      idx += 1 + sText[idx + 1:].find('"') 
436      ##########debuging    in case we arrive at the end of the text 
437                      if idx >= len(sText) - 1: 
438      #                    print sText,idx,len(sText) 
439                          lFields.append(sText[1:-1].strip()) 
440  #                        print lFields[-1] 
441                          sText = "" 
442                          bFinished = True 
443                          break 
444   
445                      if sText[idx + 1] in CIF.BLANK: 
446                          lFields.append(sText[1:idx].strip()) 
447  #                        print lFields[-1] 
448                          sText1 = sText[idx + 1:] 
449                          sText = sText1.strip() 
450                          bFinished = True 
451              elif sText[0] == ';': 
452                  if sText[1:].strip().find(CIF.BINARY_MARKER) == 0: 
453                      idx = sText[32:].find(CIF.BINARY_MARKER) 
454                      if idx == -1: 
455                          idx = 0 
456                      else: 
457                          idx += 32 + len(CIF.BINARY_MARKER) 
458                  else: 
459                      idx = 0 
460                  bFinished = False 
461                  while not  bFinished: 
462                      idx += 1 + sText[idx + 1:].find(';') 
463                      if sText[idx - 1] in CIF.EOL: 
464                          lFields.append(sText[1:idx - 1].strip()) 
465                          sText1 = sText[idx + 1:] 
466                          sText = sText1.strip() 
467                          bFinished = True 
468              else: 
469                  f = sText.split(None, 1)[0] 
470                  lFields.append(f) 
471  #                print lFields[-1] 
472                  sText1 = sText[len(f):].strip() 
473                  sText = sText1 
474          return lFields 

        475   
476   
477      @staticmethod 

        478 -    def _analyseOneLoop(lFields, iStart): 

        479          """Processes one loop in the data extraction of the CIF file 
480          @param lFields: list of all the words contained in the cif file 
481          @type lFields: list 
482          @param iStart: the starting index corresponding to the "loop_" key 
483          @type iStart: integer 
484          @return: the list of loop dictionaries, the length of the data 
485              extracted from the lFields and the list of all the keys of the loop. 
486          @rtype: tuple 
487          """ 
488      #    in earch loop we first search the length of the loop 
489      #    print lFields 
490  #        curloop = {} 
491          loop = [] 
492          keys = [] 
493          i = iStart + 1 
494          bFinished = False 
495          while not bFinished: 
496              if lFields[i][0] == "_": 
497                  keys.append(lFields[i])#.lower()) 
498                  i += 1 
499              else: 
500                  bFinished = True 
501          data = [] 
502          while True: 
503              if i >= len(lFields): 
504                  break 
505              elif len(lFields[i]) == 0: 
506                  break 
507              elif lFields[i][0] == "_": 
508                  break 
509              elif lFields[i] in ["loop_", "stop_", "global_", "data_", "save_"]: 
510                  break 
511              else: 
512                  data.append(lFields[i]) 
513                  i += 1 
514          #print len(keys), len(data) 
515          k = 0 
516   
517          if len(data) < len(keys): 
518              element = {} 
519              for j in keys: 
520                  if k < len(data): 
521                      element[j] = data[k] 
522                  else : 
523                      element[j] = "?" 
524                  k += 1 
525              #print element 
526              loop.append(element) 
527   
528          else: 
529              #print data 
530              #print keys 
531              for i in range(len(data) / len(keys)): 
532                  element = {} 
533                  for j in keys: 
534                      element[j] = data[k] 
535                      k += 1 
536      #            print element 
537                  loop.append(element) 
538      #    print loop 
539          return loop, 1 + len(keys) + len(data), keys 

        540   
541   
542   
543   
544   
545   
546  ############################################################################################# 
547  ########     everything needed to  write a cif file ######################################### 
548  ############################################################################################# 
549   

        550 -    def saveCIF(self, _strFilename="test.cif", linesep=os.linesep, binary=False): 

        551          """Transforms the CIF object in string then write it into the given file 
552          @param _strFilename: the of the file to be written 
553          @param linesep: line separation used (to force compatibility with windows/unix) 
554          @param binary: Shall we write the data as binary (True only for imageCIF/CBF) 
555          @type param: string 
556          """ 
557          if binary: 
558              mode = "wb" 
559          else: 
560              mode = "w" 
561          try: 
562              fFile = open(_strFilename, mode) 
563          except IOError: 
564              print("Error during the opening of file for write: %s" % 
565                                                              _strFilename) 
566              return 
567          fFile.write(self.tostring(_strFilename, linesep)) 
568          try: 
569              fFile.close() 
570          except IOError: 
571              print("Error during the closing of file for write: %s" % 
572                                                               _strFilename) 

        573   
574   

        575 -    def tostring(self, _strFilename=None, linesep=os.linesep): 

        576          """ 
577          Converts a cif dictionnary to a string according to the CIF syntax 
578           
579          @param _strFilename: the name of the filename to be appended in the header of the CIF file 
580          @type _strFilename: string 
581          @return: a sting that corresponds to the content of the CIF - file. 
582           
583          """ 
584  #        sCifText = "" 
585          lstStrCif = ["# " + i for i in __version__] 
586          if "_chemical_name_common" in self: 
587              t = self["_chemical_name_common"].split()[0] 
588          elif _strFilename is not None: 
589              t = os.path.splitext(os.path.split(str(_strFilename).strip())[1])[0] 
590          else: 
591              t = "" 
592          lstStrCif.append("data_%s" % (t)) 
593          #first of all get all the keys : 
594          lKeys = self.keys() 
595          lKeys.sort() 
596          for key in lKeys[:]: 
597              if key in self._ordered: 
598                  lKeys.remove(key) 
599          self._ordered += lKeys 
600   
601          for sKey in self._ordered: 
602              if sKey == "loop_": 
603                  continue 
604              if sKey not in self: 
605                  self._ordered.remove(sKey) 
606                  logger.debug("Skipping key %s from ordered list as no more present in dict") 
607                  continue 
608              sValue = str(self[sKey]) 
609              if sValue.find("\n") > -1: #should add value  between ;; 
610                  lLine = [sKey, ";", sValue, ";", ""] 
611              elif len(sValue.split()) > 1: #should add value between '' 
612                  sLine = "%s        '%s'" % (sKey, sValue) 
613                  if len(sLine) > 80: 
614                      lLine = [str(sKey), sValue] 
615                  else: 
616                      lLine = [sLine] 
617              else: 
618                  sLine = "%s        %s" % (sKey, sValue) 
619                  if len(sLine) > 80: 
620                      lLine = [str(sKey), sValue] 
621                  else: 
622                      lLine = [sLine] 
623              lstStrCif += lLine 
624          if self.has_key("loop_"): 
625              for loop in self["loop_"]: 
626                  lstStrCif.append("loop_ ") 
627                  lKeys = loop[0] 
628                  llData = loop[1] 
629                  lstStrCif += [" %s" % (sKey) for sKey in lKeys] 
630                  for lData in llData: 
631                      sLine = " " 
632                      for key in lKeys: 
633                          sRawValue = lData[key] 
634                          if sRawValue.find("\n") > -1: #should add value  between ;; 
635                              lstStrCif += [sLine, ";", str(sRawValue), ";"] 
636                              sLine = " " 
637                          else: 
638                              if len(sRawValue.split()) > 1: #should add value between '' 
639                                  value = "'%s'" % (sRawValue) 
640                              else: 
641                                  value = str(sRawValue) 
642                              if len(sLine) + len(value) > 78: 
643                                  lstStrCif += [sLine] 
644                                  sLine = " " + value 
645                              else: 
646                                  sLine += " " + value 
647                      lstStrCif.append(sLine) 
648                  lstStrCif.append("") 
649          return linesep.join(lstStrCif) 

        650   
651   

        652 -    def exists(self, sKey): 

        653          """ 
654          Check if the key exists in the CIF and is non empty. 
655          @param sKey: CIF key 
656          @type sKey: string 
657          @param cif: CIF dictionary 
658          @return: True if the key exists in the CIF dictionary and is non empty 
659          @rtype: boolean 
660          """ 
661          bExists = False 
662          if self.has_key(sKey): 
663              if len(self[sKey]) >= 1: 
664                  if self[sKey][0] not in ["?", "."]: 
665                      bExists = True 
666          return bExists 

        667   
668   

        669 -    def existsInLoop(self, sKey): 

        670          """ 
671          Check if the key exists in the CIF dictionary. 
672          @param sKey: CIF key 
673          @type sKey: string 
674          @param cif: CIF dictionary 
675          @return: True if the key exists in the CIF dictionary and is non empty 
676          @rtype: boolean 
677          """ 
678          if not self.exists("loop_"): 
679              return False 
680          bExists = False 
681          if not bExists: 
682              for i in self["loop_"]: 
683                  for j in i[0]: 
684                      if j == sKey: 
685                          bExists = True 
686          return bExists 

        687   
688   

        689 -    def loadCHIPLOT(self, _strFilename): 

        690          """ 
691          Load the powder diffraction CHIPLOT file and returns the 
692          pd_CIF dictionary in the object 
693   
694          @param _strFilename: the name of the file to open 
695          @type  _strFilename: string 
696          @return: the CIF object corresponding to the powder diffraction 
697          @rtype: dictionary 
698          """ 
699          if not os.path.isfile(_strFilename): 
700              print "I cannot find the file %s" % _strFilename 
701              raise 
702          lInFile = open(_strFilename, "r").readlines() 
703          self["_audit_creation_method"] = 'From 2-D detector using FIT2D and CIFfile' 
704          self["_pd_meas_scan_method"] = "fixed" 
705          self["_pd_spec_description"] = lInFile[0].strip() 
706          try: 
707              iLenData = int(lInFile[3]) 
708          except ValueError: 
709              iLenData = None 
710          lOneLoop = [] 
711          try: 
712              f2ThetaMin = float(lInFile[4].split()[0]) 
713              last = "" 
714              for sLine in lInFile[-20:]: 
715                  if sLine.strip() != "": 
716                      last = sLine.strip() 
717              f2ThetaMax = float(last.split()[0]) 
718              limitsOK = True 
719   
720          except (ValueError, IndexError): 
721              limitsOK = False 
722              f2ThetaMin = 180.0 
723              f2ThetaMax = 0 
724  #        print "limitsOK:", limitsOK 
725          for sLine in lInFile[4:]: 
726              sCleaned = sLine.split("#")[0].strip() 
727              data = sCleaned.split() 
728              if len(data) == 2 : 
729                  if not limitsOK: 
730                      f2Theta = float(data[0]) 
731                      if f2Theta < f2ThetaMin : 
732                          f2ThetaMin = f2Theta 
733                      if f2Theta > f2ThetaMax : 
734                          f2ThetaMax = f2Theta 
735                  lOneLoop.append({ "_pd_meas_intensity_total": data[1] }) 
736          if not iLenData: 
737              iLenData = len(lOneLoop) 
738          assert (iLenData == len(lOneLoop)) 
739          self[ "_pd_meas_2theta_range_inc" ] = "%.4f" % ((f2ThetaMax - f2ThetaMin) / (iLenData - 1)) 
740          if self[ "_pd_meas_2theta_range_inc" ] < 0: 
741              self[ "_pd_meas_2theta_range_inc" ] = abs (self[ "_pd_meas_2theta_range_inc" ]) 
742              tmp = f2ThetaMax 
743              f2ThetaMax = f2ThetaMin 
744              f2ThetaMin = tmp 
745          self[ "_pd_meas_2theta_range_max" ] = "%.4f" % f2ThetaMax 
746          self[ "_pd_meas_2theta_range_min" ] = "%.4f" % f2ThetaMin 
747          self[ "_pd_meas_number_of_points" ] = str(iLenData) 
748          self["loop_"] = [ [ ["_pd_meas_intensity_total" ], lOneLoop ] ] 

        749   
750   
751      @staticmethod 

        752 -    def LoopHasKey(loop, key): 

        753          "Returns True if the key (string) exist in the array called loop""" 
754          try: 
755              loop.index(key) 
756              return True 
757          except ValueError: 
758              return False 

        759

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        Package fabio :: Module cf_io
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        Module cf_io

        Functions [hide private]
         
        read(...)
        call the c-columnfile reading interface.
        Variables [hide private]
          __package__ = None
        hash(x)
        Function Details [hide private]

        read(...)

        		 

        call the c-columnfile reading interface. The mode keyword argument is either: "a" for ascii (the default) "b" for binary


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        Module mar345image

        source code

        

Authors:
........
* Henning O. Sorensen & Erik Knudsen:
  Center for Fundamental Research: Metal Structures in Four Dimensions;
  Risoe National Laboratory;
  Frederiksborgvej 399;
  DK-4000 Roskilde;
  email:erik.knudsen@risoe.dk
* Jon Wright, Jérôme Kieffer & Gaël Goret:
  European Synchrotron Radiation Facility;
  Grenoble (France)
        Classes [hide private]
          mar345image
        Variables [hide private]
          __doc__ = ...
          logger = logging.getLogger("mar345image")
          __package__ = 'fabio'
        Variables Details [hide private]

        __doc__

        Value:
        """

Authors:
........
* Henning O. Sorensen & Erik Knudsen:
  Center for Fundamental Research: Metal Structures in Four Dimensions\
;
  Risoe National Laboratory;
...

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        Package fabio :: Module datIO :: Class columnfile
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        Class columnfile

        source code

        object --+    
         |    
 fabiodata --+
             |
            columnfile

        Concrete fabiodata class

        Instance Methods [hide private]
         
        read(self, fname, frame=None)
        To be overridden by format specific subclasses        		 source code

        Inherited from fabiodata: __init__

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Properties [hide private]

        Inherited from object: __class__

        Method Details [hide private]

        read(self, fname, frame=None)

        		source code 

        To be overridden by format specific subclasses

        Overrides: fabiodata.read
        (inherited documentation)

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        Module fabioimage

        Classes

        fabioimage

        Functions

        test

        Variables

        __package__
        logger
        [hide private] fabio-0.1.3/epydoc/fabio.marccdimage-pysrc.html0000644000175000017500000021721012126623347022212 0ustar jeromejerome00000000000000 fabio.marccdimage
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        Source Code for Module fabio.marccdimage

          1  #!/usr/bin/env python 
  2  """ 
  3   
  4  Authors: 
  5  ........ 
  6  * Henning O. Sorensen & Erik Knudsen: 
  7    Center for Fundamental Research: Metal Structures in Four Dimensions; 
  8    Risoe National Laboratory; 
  9    Frederiksborgvej 399; 
 10    DK-4000 Roskilde; 
 11    email:erik.knudsen@risoe.dk 
 12  * Jon Wright: 
 13    European Synchrotron Radiation Facility; 
 14    Grenoble (France) 
 15            
 16  marccdimage can read MarCCD and MarMosaic images including header info. 
 17   
 18  JPW : Use a parser in case of typos (sorry?) 
 19   
 20  """ 
 21   
 22   
 23  # Base this on the tifimage (as marccd seems to be tiff with a  
 24  # special header  
 25   
 26  from tifimage import tifimage 
 27  import logging 
 28  logger = logging.getLogger("marccdimage") 
 29   
 30  # Now for the c definition (found on mar webpage) 
 31  # The following string is therefore copyrighted by Mar I guess 
 32   
 33  CDEFINITION = """ 
 34  typedef struct frame_header_type { 
 35           /* File/header format parameters (256 bytes) */ 
 36           UINT32        header_type;  /* flag for header type   
 37                                             (can be  used as magic number) */ 
 38           char header_name[16];           /* header name (MMX) */ 
 39           UINT32        header_major_version;   /* header_major_version  (n.) */ 
 40           UINT32        header_minor_version;   /* header_minor_version  (.n) */ 
 41           UINT32        header_byte_order;/* BIG_ENDIAN (Motorola,MIPS);   
 42                                              LITTLE_ENDIAN (DEC, Intel) */ 
 43           UINT32        data_byte_order;  /* BIG_ENDIAN (Motorola,MIPS);   
 44                                              LITTLE_ENDIAN (DEC, Intel) */ 
 45           UINT32        header_size;      /* in bytes                     */ 
 46           UINT32        frame_type;       /* flag for frame type */ 
 47           UINT32        magic_number;     /* to be used as a flag -  
 48                                              usually  to indicate new file */ 
 49           UINT32        compression_type; /* type of image compression    */ 
 50           UINT32        compression1;     /* compression parameter 1 */ 
 51           UINT32        compression2;     /* compression parameter 2 */ 
 52           UINT32        compression3;     /* compression parameter 3 */ 
 53           UINT32        compression4;     /* compression parameter 4 */ 
 54           UINT32        compression5;     /* compression parameter 4 */ 
 55           UINT32        compression6;     /* compression parameter 4 */ 
 56           UINT32        nheaders;         /* total number of headers      */ 
 57           UINT32        nfast;            /* number of pixels in one line */ 
 58           UINT32        nslow;            /* number of lines in image     */ 
 59           UINT32        depth;            /* number of bytes per pixel    */ 
 60           UINT32        record_length;    /* number of pixels between  
 61                                              succesive rows */ 
 62           UINT32        signif_bits;      /* true depth of data, in bits  */ 
 63           UINT32        data_type;        /* (signed,unsigned,float...) */ 
 64           UINT32        saturated_value;  /* value marks pixel as saturated */ 
 65           UINT32        sequence;         /* TRUE or FALSE */ 
 66           UINT32        nimages;          /* total number of images - size of  
 67                                              each is nfast*(nslow/nimages) */ 
 68           UINT32        origin;           /* corner of origin             */ 
 69           UINT32        orientation;      /* direction of fast axis       */ 
 70           UINT32        view_direction;   /* direction to view frame      */ 
 71           UINT32        overflow_location;/* FOLLOWING_HEADER,  FOLLOWING_DATA */ 
 72           UINT32        over_8_bits;      /* # of pixels with counts  255 */ 
 73           UINT32        over_16_bits;     /* # of pixels with count  65535 */ 
 74           UINT32        multiplexed;      /* multiplex flag */ 
 75           UINT32        nfastimages;      /* # of images in fast direction */ 
 76           UINT32        nslowimages;      /* # of images in slow direction */ 
 77           UINT32        background_applied;/* flags correction has been applied  
 78                                                hold magic number ? */ 
 79           UINT32        bias_applied;     /* flags correction has been applied 
 80                                               hold magic number ? */ 
 81           UINT32        flatfield_applied;/* flags correction has been applied - 
 82                                                hold magic number ? */ 
 83           UINT32        distortion_applied;/*flags correction has been applied -  
 84                                                hold magic number ? */ 
 85           UINT32        original_header_type;    /* Header/frame type from  file  
 86                                                      that frame is read from */ 
 87           UINT32        file_saved;         /* Flag that file has been  saved,  
 88                                                should be zeroed if modified */ 
 89           char reserve1[(64-40)*sizeof(INT32)-16]; 
 90   
 91           /* Data statistics (128) */ 
 92           UINT32        total_counts[2];  /* 64 bit integer range = 1.85E19*/ 
 93           UINT32        special_counts1[2]; 
 94           UINT32        special_counts2[2]; 
 95           UINT32        min; 
 96           UINT32        max; 
 97           UINT32        mean; 
 98           UINT32        rms; 
 99           UINT32        p10; 
100           UINT32        p90; 
101           UINT32        stats_uptodate; 
102           UINT32        pixel_noise[MAXIMAGES]; /*1000*base noise value (ADUs) */ 
103           char reserve2[(32-13-MAXIMAGES)*sizeof(INT32)]; 
104   
105           /* More statistics (256) */ 
106           UINT16 percentile[128]; 
107   
108   
109           /* Goniostat parameters (128 bytes) */ 
110           INT32 xtal_to_detector;  /* 1000*distance in millimeters */ 
111           INT32 beam_x;            /* 1000*x beam position (pixels) */ 
112           INT32 beam_y;            /* 1000*y beam position (pixels) */ 
113           INT32 integration_time;  /* integration time in  milliseconds */ 
114           INT32 exposure_time;     /* exposure time in milliseconds */ 
115           INT32 readout_time;      /* readout time in milliseconds */ 
116           INT32 nreads;            /* number of readouts to get this  image */ 
117           INT32 start_twotheta;    /* 1000*two_theta angle */ 
118           INT32 start_omega;       /* 1000*omega angle */ 
119           INT32 start_chi;         /* 1000*chi angle */ 
120           INT32 start_kappa;       /* 1000*kappa angle */ 
121           INT32 start_phi;         /* 1000*phi angle */ 
122           INT32 start_delta;       /* 1000*delta angle */ 
123           INT32 start_gamma;       /* 1000*gamma angle */ 
124           INT32 start_xtal_to_detector; /* 1000*distance in mm (dist in um)*/ 
125           INT32 end_twotheta;           /* 1000*two_theta angle */ 
126           INT32 end_omega;              /* 1000*omega angle */ 
127           INT32 end_chi;                /* 1000*chi angle */ 
128           INT32 end_kappa;              /* 1000*kappa angle */ 
129           INT32 end_phi;                /* 1000*phi angle */ 
130           INT32 end_delta;              /* 1000*delta angle */ 
131           INT32 end_gamma;              /* 1000*gamma angle */ 
132           INT32 end_xtal_to_detector;   /* 1000*distance in mm (dist in um)*/ 
133           INT32 rotation_axis;          /* active rotation axis */ 
134           INT32 rotation_range;         /* 1000*rotation angle */ 
135           INT32 detector_rotx;          /* 1000*rotation of detector  around X */ 
136           INT32 detector_roty;          /* 1000*rotation of detector  around Y */ 
137           INT32 detector_rotz;          /* 1000*rotation of detector  around Z */ 
138           char reserve3[(32-28)*sizeof(INT32)]; 
139   
140           /* Detector parameters (128 bytes) */ 
141           INT32 detector_type;            /* detector type */ 
142           INT32 pixelsize_x;              /* pixel size (nanometers) */ 
143           INT32 pixelsize_y;              /* pixel size (nanometers) */ 
144           INT32 mean_bias;                        /* 1000*mean bias value */ 
145           INT32 photons_per_100adu;       /* photons / 100 ADUs */ 
146           INT32 measured_bias[MAXIMAGES];/* 1000*mean bias value for each image*/ 
147           INT32 measured_temperature[MAXIMAGES];  /* Temperature of each   
148                                                      detector in milliKelvins */ 
149           INT32 measured_pressure[MAXIMAGES]; /* Pressure of each  chamber  
150                                                 in microTorr */ 
151           /* Retired reserve4 when MAXIMAGES set to 9 from 16 and  
152              two fields removed, and temp and pressure added 
153            char reserve4[(32-(5+3*MAXIMAGES))*sizeof(INT32)] 
154           */ 
155   
156           /* X-ray source and optics parameters (128 bytes) */ 
157           /* X-ray source parameters (8*4 bytes) */ 
158           INT32 source_type;              /* (code) - target, synch. etc */ 
159           INT32 source_dx;                /* Optics param. - (size  microns) */ 
160           INT32 source_dy;                /* Optics param. - (size  microns) */ 
161           INT32 source_wavelength;        /* wavelength  (femtoMeters) */ 
162           INT32 source_power;             /* (Watts) */ 
163           INT32 source_voltage;           /* (Volts) */ 
164           INT32 source_current;           /* (microAmps) */ 
165           INT32 source_bias;              /* (Volts) */ 
166           INT32 source_polarization_x;    /* () */ 
167           INT32 source_polarization_y;    /* () */ 
168           char reserve_source[4*sizeof(INT32)]; 
169   
170           /* X-ray optics_parameters (8*4 bytes) */ 
171           INT32 optics_type;              /* Optics type (code)*/ 
172           INT32 optics_dx;                /* Optics param. - (size  microns) */ 
173           INT32 optics_dy;                /* Optics param. - (size  microns) */ 
174           INT32 optics_wavelength;        /* Optics param. - (size  microns) */ 
175           INT32 optics_dispersion;        /* Optics param. - (*10E6) */ 
176           INT32 optics_crossfire_x;       /* Optics param. - (microRadians) */ 
177           INT32 optics_crossfire_y;       /* Optics param. - (microRadians) */ 
178           INT32 optics_angle;             /* Optics param. - (monoch.   
179                                                      2theta - microradians) */ 
180           INT32 optics_polarization_x;    /* () */ 
181           INT32 optics_polarization_y;    /* () */ 
182           char reserve_optics[4*sizeof(INT32)]; 
183   
184           char reserve5[((32-28)*sizeof(INT32))]; 
185   
186           /* File parameters (1024 bytes) */ 
187           char filetitle[128];            /*  Title                  */ 
188           char filepath[128];             /* path name for data  file  */ 
189           char filename[64];              /* name of data  file  */ 
190           char acquire_timestamp[32];     /* date and time of  acquisition */ 
191           char header_timestamp[32];      /* date and time of header  update  */ 
192           char save_timestamp[32];        /* date and time file  saved */ 
193           char file_comments[512];        /* comments, use as desired   */ 
194           char reserve6[1024-(128+128+64+(3*32)+512)]; 
195   
196           /* Dataset parameters (512 bytes) */ 
197           char dataset_comments[512];     /* comments, used as desired   */ 
198           /* pad out to  3072 bytes */ 
199           char pad[3072-(256+128+256+(3*128)+1024+512)];      
200   
201           } frame_header; 
202  """ 
203   
204  import struct 
205   
206  # Convert mar c header file types to python struct module types 
207  C_TO_STRUCT = { 
208      "INT32"  : "i", 
209      "UINT32" : "I", 
210      "char"   : "c", 
211      "UINT16" : "H" 
212      } 
213   
214  # Sizes (bytes) of mar c header objects 
215  C_SIZES = { 
216      "INT32"  : 4, 
217      "UINT32" : 4, 
218      "char"   : 1, 
219      "UINT16" : 2 
220      } 
221   
222  # This was worked out by trial and error from a trial image I think 
223  MAXIMAGES = 9 
224   
225   

        226 -def make_format(c_def_string): 

        227      """ 
228      Reads the header definition in c and makes the format  
229      string to pass to struct.unpack 
230      """ 
231      lines = c_def_string.split("\n") 
232      fmt = "" 
233      names = [] 
234      expected = 0 
235      for line in lines: 
236          if line.find(";") == -1: 
237              continue 
238          decl = line.split(";")[0].lstrip().rstrip() 
239          try: 
240              [typ, name] = decl.split() 
241          except ValueError: 
242              logger.debug("skipping: %s" , line) 
243              continue 
244   
245          if name.find("[") > -1: 
246              # repeated ... times 
247              try: 
248                  num = name.split("[")[1].split("]")[0] 
249                  num = num.replace("MAXIMAGES", str(MAXIMAGES)) 
250                  num = num.replace("sizeof(INT32)", "4") 
251                  times = eval(num) 
252              except Exception, error: 
253                  logger.error("%s Please decode %s", error, decl) 
254                  raise error 
255          else: 
256              times = 1 
257          try: 
258              fmt += C_TO_STRUCT[typ] * times 
259              names += [name] * times 
260              expected += C_SIZES[typ] * times 
261          except KeyError: 
262              continue 
263      return names, fmt 

        264   
265  # Make these be compiled on loading module 
266  HEADER_NAMES, HEADER_FORMAT = make_format(CDEFINITION) 
267   

        268 -def interpret_header(header, fmt, names): 

        269      """ 
270      given a format and header interpret it 
271      """ 
272      values = struct.unpack(fmt, header) 
273      hdr = {} 
274      i = 0 
275      for name in names: 
276          if hdr.has_key(name): 
277              if type(values[i]) == type("string"): 
278                  hdr[name] = hdr[name] + values[i] 
279              else: 
280                  try: 
281                      hdr[name].append(values[i]) 
282                  except AttributeError: 
283                      hdr[name] = [hdr[name], values[i]] 
284          else: 
285              hdr[name] = values[i] 
286          i = i + 1 
287   
288      return hdr 

        289   
290   

        291 -class marccdimage(tifimage): 

        292      """ Read in data in mar ccd format, also  
293          MarMosaic images, including header info """ 
294   
295   

        296 -    def _readheader(self, infile): 

        297          """ 
298          Parser based approach 
299          Gets all entries 
300          """ 
301          infile.seek(1024) 
302          hstr = infile.read(3072) 
303          self.header = interpret_header(hstr, HEADER_FORMAT, HEADER_NAMES) 

        304   
305   
306   

        307 -    def _read(self, fname): 

        308          """ 
309          inherited from tifimage 
310          ... a marccd image *is a* tif image 
311          just with a header 
312          """ 
313          return tifimage.read(self, fname) 

        314

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        Package fabio :: Module mar345_IO
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        Module mar345_IO

        
New Cython version of mar345_io for preparing the migration to Python3

Compressor & decompressor for "pack" algorithm by JPA, binding to CCP4 libraries 

Warning: decompressor is just a cython porting of mar345_io, but in cython so (soon) python3 compliant.

Future: make those algorithm actually generate strings not go via files;
        it will allow a broader use of the algorithm.
        Authors:
        Jerome Kieffer, Gael Goret

        Contact: jerome.kieffer@esrf.eu

        Copyright: 2012, European Synchrotron Radiation Facility, Grenoble, France

        License: LGPLv3+

        Variables [hide private]
          __package__ = 'fabio'
          __test__ = {}
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        Package fabio :: Module OXDimage
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        Module OXDimage

        source code

        
Reads Oxford Diffraction Sapphire 3 images

Authors:
........
* Henning O. Sorensen & Erik Knudsen:
  Center for Fundamental Research: Metal Structures in Four Dimensions;
  Risoe National Laboratory;
  Frederiksborgvej 399;
  DK-4000 Roskilde;
  email:erik.knudsen@risoe.dk
* Jon Wright, Jérôme Kieffer & Gaël Goret:
  European Synchrotron Radiation Facility;
  Grenoble (France)
        Classes [hide private]
          OXDimage
        Oxford Diffraction Sapphire 3 images reader/writer class
          Section
        Small helper class for writing binary headers
        Variables [hide private]
          __doc__ = "...
          logger = logging.getLogger("OXDimage")
          rad2deg = <ufunc 'rad2deg'>
          deg2rad = <ufunc 'deg2rad'>
          DETECTOR_TYPES = {0: 'Sapphire/KM4CCD (1x1: 0.06mm, 2x2: 0.12m...
          DEFAULT_HEADERS = {'ASCII Section size in Byte': 256, 'Compres...
          __package__ = 'fabio'
        Variables Details [hide private]

        __doc__

        Value:
        """
Reads Oxford Diffraction Sapphire 3 images

Authors:
........
* Henning O. Sorensen & Erik Knudsen:
  Center for Fundamental Research: Metal Structures in Four Dimensions\
;
...

        DETECTOR_TYPES

        Value:
        {0: 'Sapphire/KM4CCD (1x1: 0.06mm, 2x2: 0.12mm)',
 1: 'Sapphire2-Kodak (1x1: 0.06mm, 2x2: 0.12mm)',
 2: 'Sapphire3-Kodak (1x1: 0.03mm, 2x2: 0.06mm, 4x4: 0.12mm)',
 3: 'Onyx-Kodak (1x1: 0.06mm, 2x2: 0.12mm, 4x4: 0.24mm)',
 4: 'Unknown Oxford diffraction detector'}

        DEFAULT_HEADERS

        Value:
        {'ASCII Section size in Byte': 256,
 'Compression': 'TY1',
 'General Section size in Byte': 512,
 'Header Size In Bytes': 5120,
 'Header Version': 'OD SAPPHIRE  3.0',
 'History Section in Byte': 2048,
 'KM4 Section size in Byte': 1024,
 'NSUPPLEMENT': 0,
...

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        Package fabio :: Module tifimage
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        Source Code for Module fabio.tifimage

          1  #!/usr/bin/env python 
  2  #-*- coding: utf8 -*- 
  3  """ 
  4  FabIO class for dealing with TIFF images.  
  5  In facts wraps TiffIO from V. Armando Solé (available in PyMca) or falls back to PIL 
  6   
  7  Authors: 
  8  ........ 
  9  * Henning O. Sorensen & Erik Knudsen: 
 10    Center for Fundamental Research: Metal Structures in Four Dimensions; 
 11    Risoe National Laboratory; 
 12    Frederiksborgvej 399; 
 13    DK-4000 Roskilde; 
 14    email:erik.knudsen@risoe.dk 
 15  * Jérôme Kieffer: 
 16    European Synchrotron Radiation Facility; 
 17    Grenoble (France) 
 18      
 19  License: GPLv3+         
 20  """ 
 21   
 22  __authors__ = ["Jérôme Kieffer", "Henning O. Sorensen", "Erik Knudsen"] 
 23  __date__ = "11/07/2011" 
 24  __license__ = "GPLv3+" 
 25  __copyright__ = "ESRF, Grenoble & Risoe National Laboratory" 
 26  __status__ = "stable" 
 27  import time, logging, struct 
 28  logger = logging.getLogger("tifimage") 
 29  try: 
 30      import Image 
 31  except ImportError: 
 32      logger.warning("PIL is not installed ... trying to do without") 
 33      Image = None 
 34  import numpy 
 35  from fabioimage import fabioimage 
 36  from TiffIO     import TiffIO 
 37   
 38  PIL_TO_NUMPY = { "I;16": numpy.uint16, 
 39                     "F": numpy.float32, 
 40                     "1": numpy.bool, 
 41                     "I": numpy.int32, 
 42                     "L": numpy.uint8, 
 43                      } 
 44   
 45  LITTLE_ENDIAN = 1234 
 46  BIG_ENDIAN = 3412 
 47   
 48  TYPES = {0:'invalid', 1:'byte', 2:'ascii', 3:'short', 4:'long', 5:'rational', 6:'sbyte', 7:'undefined', 8:'sshort', 9:'slong', 10:'srational', 11:'float', 12:'double'} 
 49   
 50  TYPESIZES = {0:0, 1:1, 2:1, 3:2, 4:4, 5:8, 6:1, 7:1, 8:2, 9:4, 10:8, 11:4, 12:8} 
 51   
 52  baseline_tiff_tags = { 
 53    256:'ImageWidth', 
 54    257:'ImageLength', 
 55    306:'DateTime', 
 56    315:'Artist', 
 57    258:'BitsPerSample', 
 58    265:'CellLength', 
 59    264:'CellWidth', 
 60    259:'Compression', 
 61   
 62    262:'PhotometricInterpretation', 
 63    296:'ResolutionUnit', 
 64    282:'XResolution', 
 65    283:'YResolution', 
 66   
 67    278:'RowsPerStrip', 
 68    273:'StripOffset', 
 69    279:'StripByteCounts', 
 70   
 71    270:'ImageDescription', 
 72    271:'Make', 
 73    272:'Model', 
 74    320:'ColorMap', 
 75    305:'Software', 
 76    339:'SampleFormat', 
 77    33432:'Copyright' 
 78    } 
 79   

         80 -class tifimage(fabioimage): 

         81      """ 
 82      Images in TIF format 
 83      Wraps TiffIO 
 84      """ 
 85      _need_a_seek_to_read = True 
 86   

         87 -    def __init__(self, *args, **kwds): 

         88          """ Tifimage constructor adds an nbits member attribute """ 
 89          self.nbits = None 
 90          fabioimage.__init__(self, *args, **kwds) 
 91          self.lib = None 

         92   

         93 -    def _readheader(self, infile): 

         94          """ 
 95          Try to read Tiff images header... 
 96          """ 
 97  #        try: 
 98  #            self.header = { "filename" : infile.name } 
 99  #        except AttributeError: 
100  #            self.header = {} 
101  # 
102  #        t = Tiff_header(infile.read()) 
103  #        self.header = t.header 
104  #        try: 
105  #            self.dim1 = int(self.header['ImageWidth']) 
106  #            self.dim2 = int(self.header['ImageLength']) 
107  #        except (KeyError): 
108  #            logger.warning("image dimensions could not be determined from header tags, trying to go on anyway") 
109  #         read the first 32 bytes to determine size 
110          header = numpy.fromstring(infile.read(64), numpy.uint16) 
111          self.dim1 = int(header[9]) 
112          self.dim2 = int(header[15]) 
113  #         nbits is not a fabioimage attribute... 
114          self.nbits = int(header[21]) # number of bits 

        115   

        116 -    def read(self, fname, frame=None): 

        117          """ 
118          Wrapper for TiffIO. 
119          """ 
120          infile = self._open(fname, "rb") 
121          self._readheader(infile) 
122          infile.seek(0) 
123          self.lib = None 
124          try: 
125              tiffIO = TiffIO(infile) 
126              if tiffIO.getNumberOfImages() > 0: 
127                  #No support for now of multi-frame tiff images 
128                  self.data = tiffIO.getImage(0) 
129                  self.header = tiffIO.getInfo(0) 
130          except Exception, error: 
131              logger.warning("Unable to read %s with TiffIO due to %s, trying PIL" % (fname, error)) 
132          else: 
133              if self.data.ndim == 2: 
134                  self.dim2, self.dim1 = self.data.shape 
135              elif self.data.ndim == 3: 
136                  self.dim2, self.dim1, ncol = self.data.shape 
137                  logger.warning("Third dimension is the color") 
138              else: 
139                  logger.warning("dataset has %s dimensions (%s), check for errors !!!!", self.data.ndim, self.data.shape) 
140              self.lib = "TiffIO" 
141   
142          if (self.lib is None): 
143              if Image: 
144                  try: 
145                      infile.seek(0) 
146                      self.pilimage = Image.open(infile) 
147                  except Exception: 
148                      logger.error("Error in opening %s  with PIL" % fname) 
149                      self.lib = None 
150                      infile.seek(0) 
151                  else: 
152                      self.lib = "PIL" 
153                      self.dim1, self.dim2 = self.pilimage.size 
154                      if self.pilimage.mode in PIL_TO_NUMPY: 
155                          self.data = numpy.fromstring(self.pilimage.tostring(), PIL_TO_NUMPY[self.pilimage.mode]) 
156                      else: #probably RGB or RGBA images: rely on PIL to convert it to greyscale float. 
157                          self.data = numpy.fromstring(self.pilimage.convert("F").tostring(), numpy.float32) 
158                      self.data.shape = (self.dim2, self.dim1) 
159              else: 
160                  logger.error("Error in opening %s: no tiff reader managed to read the file.", fname) 
161                  self.lib = None 
162                  infile.seek(0) 
163   
164          self.bpp = len(numpy.zeros(1, dtype=self.data.dtype).tostring()) 
165          self.bytecode = self.data.dtype.name 
166          self.resetvals() 
167          return self 

        168   

        169 -    def write(self, fname): 

        170          """ 
171          Overrides the fabioimage.write method and provides a simple TIFF image writer. 
172          @param fname: name of the file to save the image to 
173          @tag_type fname: string or unicode (file?)... 
174          """ 
175          tiffIO = TiffIO(fname, mode="w") 
176          tiffIO.writeImage(self.data, info=self.header, software="fabio.tifimage", date=time.ctime()) 

        177   
178   
179   
180  #define a couple of helper classes here:          

        181 -class Tiff_header(object): 

        182 -    def __init__(self, string): 

        183          if string[:4] == "II\x2a\x00": 
184              self.byteorder = LITTLE_ENDIAN 
185          elif string[:4] == 'MM\x00\x2a': 
186              self.byteorder = BIG_ENDIAN 
187          else: 
188              logger.warning("Warning: This does not appear to be a tiff file") 
189          #the next two bytes contains the offset of the oth IFD 
190          offset_first_ifd = struct.unpack_from("h", string[4:])[0] 
191          self.ifd = [Image_File_Directory()] 
192          offset_next = self.ifd[0].unpack(string, offset_first_ifd) 
193          while (offset_next != 0): 
194              self.ifd.append(Image_File_Directory()) 
195              offset_next = self.ifd[-1].unpack(string, offset_next) 
196   
197          self.header = {} 
198          #read the values of the header items into a dictionary 
199          for entry in self.ifd[0].entries: 
200              if entry.tag in baseline_tiff_tags.keys(): 
201                  self.header[baseline_tiff_tags[entry.tag]] = entry.val 
202              else: 
203                  self.header[entry.tag] = entry.val 

        204   

        205 -class Image_File_Directory(object): 

        206 -    def __init__(self, instring=None, offset= -1): 

        207          self.entries = [] 
208          self.offset = offset 
209          self.count = None 

        210   

        211 -    def unpack(self, instring, offset= -1): 

        212          if (offset == -1): offset = self.offset 
213   
214          strInput = instring[offset:] 
215          self.count = struct.unpack_from("H", strInput[:2])[0] 
216          #0th IFD contains count-1 entries (count includes the adress of the next IFD) 
217          for i in range(self.count - 1): 
218              e = Image_File_Directory_entry().unpack(strInput[2 + 12 * (i + 1):]) 
219              if (e != None): 
220                  self.entries.append(e) 
221              #extract data associated with tags 
222              for e in self.entries: 
223                  if (e.val == None): 
224                      e.extract_data(instring) 
225          #do we have some more ifds in this file  
226          offset_next = struct.unpack_from("L", instring[offset + 2 + self.count * 12:])[0] 
227          return offset_next 

        228   

        229 -class Image_File_Directory_entry(object): 

        230 -    def __init__(self, tag=0, tag_type=0, count=0, offset=0): 

        231          self.tag = tag 
232          self.tag_type = tag_type 
233          self.count = count 
234          self.val_offset = offset 
235          self.val = None 

        236   

        237 -    def unpack(self, strInput): 

        238          idfentry = strInput[:12] 
239  ################################################################################ 
240  # #        TOFIX: How is it possible that HHL (2+2+4 bytes has a size of ) 
241  ################################################################################ 
242          (tag, tag_type, count) = struct.unpack_from("HHL", idfentry) 
243          self.tag = tag 
244          self.count = count 
245          self.tag_type = tag_type 
246          self.val = None 
247          if (count <= 0): 
248              logger.warning("Tag # %s has an invalid count: %s. Tag is ignored" % (tag, count)) 
249              return 
250          if(count * TYPESIZES[tag_type] <= 4): 
251              self.val_offset = 8 
252              self.extract_data(idfentry) 
253              self.val_offset = None 
254          else: 
255              self.val_offset = struct.unpack_from("L", idfentry[8:])[0] 
256          return self 

        257   

        258 -    def extract_data(self, full_string): 

        259          tag_type = self.tag_type 
260          if (TYPES[tag_type] == 'byte'): 
261              self.val = struct.unpack_from("B", full_string[self.val_offset:])[0] 
262          elif (TYPES[tag_type] == 'short'): 
263              self.val = struct.unpack_from("H", full_string[self.val_offset:])[0] 
264          elif (TYPES[tag_type] == 'long'): 
265              self.val = struct.unpack_from("L", full_string[self.val_offset:])[0] 
266          elif (TYPES[tag_type] == 'sbyte'): 
267              self.val = struct.unpack_from("b", full_string[self.val_offset:])[0] 
268          elif (TYPES[tag_type] == 'sshort'): 
269              self.val = struct.unpack_from("h", full_string[self.val_offset:])[0] 
270          elif (TYPES[tag_type] == 'slong'): 
271              self.val = struct.unpack_from("l", full_string[self.val_offset:])[0] 
272          elif (TYPES[tag_type] == 'ascii'): 
273              self.val = full_string[self.val_offset:self.val_offset + max(self.count, 4)] 
274          elif (TYPES[tag_type] == 'rational'): 
275              if self.val_offset != None: 
276                  (num, den) = struct.unpack_from("LL", full_string[self.val_offset:]) 
277                  print self.val_offset 
278                  self.val = float(num) / den 
279          elif (TYPES[tag_type] == 'srational'): 
280              if self.val_offset != None: 
281                  (num, den) = struct.unpack_from("ll", full_string[self.val_offset:]) 
282                  self.val = float(num) / den, 
283          elif (TYPES[tag_type] == 'float'): 
284              self.val = struct.unpack_from("f", full_string[self.val_offset:])[0] 
285          elif (TYPES[tag_type] == 'double'): 
286              if  self.val_offset != None: 
287                  self.val = struct.unpack_from("d", full_string[self.val_offset:])[0] 
288          else: 
289              logger.warning("unrecognized type of strInputentry self: %s tag: %s type: %s TYPE: %s" % (self, baseline_tiff_tags[self.tag], self.tag_type, TYPES[tag_type])) 

        290

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        fabio-0.1.3/epydoc/fabio.dm3image-pysrc.html0000644000175000017500000031555212126623347021454 0ustar jeromejerome00000000000000 fabio.dm3image
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        Package fabio :: Module dm3image
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        Source Code for Module fabio.dm3image

          1  """ 
  2  Authors: Henning O. Sorensen & Erik Knudsen 
  3           Center for Fundamental Research: Metal Structures in Four Dimensions 
  4           Risoe National Laboratory 
  5           Frederiksborgvej 399 
  6           DK-4000 Roskilde 
  7           email:erik.knudsen@risoe.dk 
  8   
  9          + Jon Wright, ESRF 
 10  """ 
 11  import logging 
 12  import numpy 
 13  from fabioimage import fabioimage 
 14  logger = logging.getLogger("dm3image") 
 15   
 16  DATA_TYPES = {  2     :  numpy.int16, 
 17                  4     :  numpy.uint16, 
 18                  3     :  numpy.int32, 
 19                  5     :  numpy.uint32, 
 20                  6     :  numpy.float32, 
 21                  7     :  numpy.float, 
 22                  8     :  numpy.int8, 
 23                  9     :  None, 
 24                  10    :  None, 
 25                  15    :  'Struct', 
 26                  18    :  None, 
 27                  20    :  None 
 28                  } 
 29   
 30  DATA_BYTES = {  2     :  2, 
 31                  4     :  2, 
 32                  3     :  4, 
 33                  5     :  4, 
 34                  6     :  4, 
 35                  7     :  8, 
 36                  8     :  1, 
 37                  9     :  None, 
 38                  10    :  None, 
 39                  15    :  'Struct', 
 40                  18    :  None, 
 41                  20    :  None 
 42                  } 
 43   
 44   
 45   

         46 -class dm3image(fabioimage): 

         47      """ Read and try to write the dm3 data format """ 

         48 -    def __init__(self, *args, **kwargs): 

         49          fabioimage.__init__(self, *args, **kwargs) 
 50          self.encoded_datatype = None 
 51          self.no_data_elements = None 
 52          self.grouptag_is_sorted = None 
 53          self.grouptag_is_open = None 
 54          self.tag_encoded_type = None 
 55          self.tag_data_type = None 
 56          self.tag_is_data = None 
 57          self.grouptag_no_tags = None 
 58          self.bytes_in_file = None 
 59          self.tag_label_length = None 
 60          self.go_on = None 

         61   

         62 -    def _readheader(self): 

         63          self.infile.seek(0) 
 64          file_format = self.readbytes(4, numpy.uint32)[0] # should be 3 
 65          assert file_format == 3, 'Wrong file type ' 
 66          self.bytes_in_file = self.readbytes(4, numpy.uint32)[0] 
 67          self.byte_order = self.readbytes(4, numpy.uint32)[0] # 0 = big, 1= little 
 68          print 'read dm3 file - file format ', file_format 
 69          print 'Bytes in file : ' , self.bytes_in_file 
 70          print 'Byte order :', self.byte_order, '  - 0 = bigEndian , 1 = littleEndian' 
 71   
 72          if self.byte_order == 0: 
 73              self.swap = True 
 74          elif self.byte_order == 1: 
 75              self.swap = False 
 76          else: 
 77              raise ValueError 

         78   

         79 -    def read(self, fname, frame=None): 

         80          self.header = {} 
 81          self.resetvals() 
 82          self.infile = self._open(fname, "rb") 
 83          self._readheader() 
 84          self.go_on = True 
 85          print self.go_on 
 86          while self.go_on: 
 87              self.read_tag_group() 
 88              self.read_tag_entry() 
 89              if self.infile.tell() > self.bytes_in_file: break 
 90   
 91              while self.tag_is_data == 21: 
 92                  self.read_tag_entry() 
 93                  if self.infile.tell() > self.bytes_in_file: 
 94                      self.go_on = False 
 95   
 96          (dim1_raw, dim2_raw) = self.header['Active Size (pixels)'].split() 
 97          (dim1_raw, dim2_raw) = (eval(dim1_raw), eval(dim2_raw)) 
 98          (dim1_binning, dim2_binning) = self.header['Binning'].split() 
 99          (dim1_binning, dim2_binning) = (eval(dim1_binning), eval(dim2_binning)) 
100          self.dim1 = dim1_raw / dim1_binning 
101          self.dim2 = dim2_raw / dim2_binning 
102          #print dim1,dim2 
103          if self.header.has_key('Data'): 
104              self.data = self.header['Data'].reshape(self.dim1, self.dim2) 

        105   

        106 -    def readbytes(self, bytes_to_read, format, swap=True): 

        107          raw = self.infile.read(bytes_to_read) 
108          if format != None: 
109              data = numpy.fromstring(raw, format) 
110          else: 
111              data = raw 
112          if swap: 
113              data = data.byteswap() 
114          return data 

        115   
116   
117   

        118 -    def read_tag_group(self): 

        119   
120          self.grouptag_is_sorted = self.readbytes(1, numpy.uint8)[0] 
121          self.grouptag_is_open = self.readbytes(1, numpy.uint8)[0] 
122          self.grouptag_no_tags = self.readbytes(4, numpy.uint32)[0] 
123          logger.debug('TagGroup is sorted? %s', self.grouptag_is_sorted) 
124          logger.debug('TagGroup is open? %s', self.grouptag_is_open) 
125          logger.debug('no of tags in TagGroup %s', self.grouptag_no_tags) 

        126   

        127 -    def read_tag_entry(self): 

        128   
129          self.tag_is_data = self.readbytes(1, numpy.uint8)[0] 
130          self.tag_label_length = self.readbytes(2, numpy.uint16)[0] 
131          logger.debug('does Tag have data ? %s  -  20 = Tag group , 21 = data ', self.tag_is_data) 
132          logger.debug('length of tag_label ', self.tag_label_length) 
133          if self.tag_label_length != 0: 
134              tag_label = self.infile.read(self.tag_label_length) 
135          else: 
136              tag_label = None 
137   
138          if self.tag_is_data == 21: 
139              # This is data 
140              self.header[tag_label] = self.read_tag_type() 
141              logger.debug("%s: %s", tag_label, self.header[tag_label]) 

        142   
143   

        144 -    def read_tag_type(self): 

        145          if self.infile.read(4) != '%%%%': 
146              raise IOError 
147          self.tag_data_type = self.readbytes(4, numpy.uint32)[0] 
148          logger.debug('data is of type : %s  - 1 = simple, 2= string, 3 = array, >3 structs', self.tag_data_type) 
149          self.tag_encoded_type = self.readbytes(4, numpy.uint32)[0] 
150          logger.debug('encode type: %s %s', self.tag_encoded_type, DATA_TYPES[ self.tag_encoded_type]) 
151          if self.tag_data_type == 1: 
152              # simple type 
153              return self.readbytes(DATA_BYTES[ self.tag_encoded_type], 
154                                    DATA_TYPES[ self.tag_encoded_type], 
155                                    swap=self.swap)[0] 
156          # are the data stored in a simple array? 
157          if self.tag_encoded_type == 20 and self.tag_data_type == 3 : 
158              self.data_type = self.readbytes(4, numpy.uint32)[0] 
159              self.no_data_elements = self.readbytes(4, numpy.uint32)[0] 
160              if self.data_type == 10: 
161                  logger.debug('skip bytes %s', self.no_data_elements) 
162                  dump = self.infile.read(self.no_data_elements) 
163                  return None 
164   
165              logger.debug('Data are stored as a simple a array -') 
166              logger.debug('%s data elemets stored as %s', self.no_data_elements, self.data_type) 
167              read_no_bytes = DATA_BYTES[self.data_type] * self.no_data_elements 
168              format = DATA_TYPES[self.data_type] 
169              return self.readbytes(read_no_bytes, format, swap=self.swap) 
170   
171          # are the data stored in a complex array ? 
172          # print 'tag_type + data_type', self.tag_encoded_type,self.tag_data_type 
173   
174          #print self.tag_encoded_type , self.tag_data_type  
175          if self.tag_encoded_type == 20 and self.tag_data_type > 3 : 
176              self.tag_encoded_type = self.readbytes(4, numpy.uint32)[0] 
177              logger.debug('found array - new tag_encoded_type %s', self.tag_encoded_type) 
178              if self.tag_encoded_type == 15:            # struct type 
179                   ###type = self.readbytes(4,numpy.int32) 
180                  struct_name_length = self.readbytes(4, numpy.int32)[0] 
181                  struct_number_fields = self.readbytes(4, numpy.int32)[0] 
182                  #print 'struct - name_length, number_field',  struct_name_length,struct_number_fields 
183                  #print self.infile.read(struct_name_length) 
184                  field_info = [] 
185                  for i in range(struct_number_fields): 
186                      field_info.append([self.readbytes(4, numpy.int32)[0], self.readbytes(4, numpy.int32)[0]]) 
187                  #print field_info 
188                  self.no_data_elements = self.readbytes(4, numpy.int32)[0] 
189                  #print '%i data elemets stored as ' %self.no_data_elements 
190                  bytes_in_struct = 0 
191                  for i in range(struct_number_fields): 
192                      bytes_in_struct += DATA_BYTES[field_info[i][1]] 
193                  logger.debug('skip bytes %s', self.no_data_elements * bytes_in_struct) 
194                  dump = self.infile.read(self.no_data_elements * bytes_in_struct) 
195                  return None 
196   
197   
198          if self.tag_encoded_type == 15:            # struct type 
199              ###type = self.readbytes(4,numpy.int32) 
200              struct_name_length = self.readbytes(4, numpy.int32)[0] 
201              struct_number_fields = self.readbytes(4, numpy.int32)[0] 
202              #print 'struct - name_length, number_field',  struct_name_length,struct_number_fields 
203              #print self.infile.read(struct_name_length) 
204              field_info = [] 
205              for i in range(struct_number_fields): 
206                  field_info.append([self.readbytes(4, numpy.int32)[0], self.readbytes(4, numpy.int32)[0]]) 
207              #print field_info 
208              field_data = '' 
209              for i in range(struct_number_fields): 
210                  #print type(i) 
211                  field_data = field_data + self.readbytes(field_info[i][0], None, swap=False) + ' ' 
212                  field_data = field_data + '%i  ' % self.readbytes(DATA_BYTES[field_info[i][1]], 
213                                                                   DATA_TYPES[field_info[i][1]], 
214                                                                   swap=self.swap)[0] 
215              return field_data 

        216   

        217 -    def read_data(self): 

        218          self.encoded_datatype = numpy.fromstring(self.infile.read(4), numpy.uint32).byteswap() 

        219

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        fabio-0.1.3/epydoc/fabio.file_series.filename_series-class.html0000644000175000017500000003304112126623347025343 0ustar jeromejerome00000000000000 fabio.file_series.filename_series
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        Package fabio :: Module file_series :: Class filename_series
        [hide private]
        [frames] | no frames]

        Class filename_series

        source code

        Much like the others, but created from a string filename

        Instance Methods [hide private]
         
        __init__(self, filename)
        create from a filename (String)        		 source code
         
        next(self)
        increment number        		 source code
         
        previous(self)
        decrement number        		 source code
         
        current(self)
        return current filename string        		 source code
         
        jump(self, num)
        jump to a specific number        		 source code
         
        next_image(self)
        returns the next image as a fabioimage        		 source code
         
        prev_image(self)
        returns the previos image as a fabioimage        		 source code
         
        current_image(self)
        returns the current image as a fabioimage        		 source code
         
        jump_image(self, num)
        returns the image number as a fabioimage        		 source code
         
        next_object(self)
        returns the next filename as a fabio.FilenameObject        		 source code
         
        previous_object(self)
        returns the previous filename as a fabio.FilenameObject        		 source code
         
        current_object(self)
        returns the current filename as a fabio.FilenameObject        		 source code
         
        jump_object(self, num)
        returns the filename num as a fabio.FilenameObject        		 source code
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        fabio-0.1.3/epydoc/fabio.binaryimage.binaryimage-class.html0000644000175000017500000005072612126623347024507 0ustar jeromejerome00000000000000 fabio.binaryimage.binaryimage
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        Package fabio :: Module binaryimage :: Class binaryimage
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        Class binaryimage

        source code

                   object --+    
                    |    
fabioimage.fabioimage --+
                        |
                       binaryimage

        This simple library has been made for manipulating exotic/unknown files format.

        Binary files images are simple none-compressed 2D images only defined by their : data-type, dimensions, byte order and offset

        Instance Methods [hide private]
         
        __init__(self, *args, **kwargs)
        Set up initial values        		 source code
         
        read(self, fname, dim1, dim2, offset=0, bytecode='int32', endian='<')
        Read a binary image Parameters : fname, dim1, dim2, offset, bytecode, endian fname : file name : str dim1,dim2 : image dimensions : int offset : size of the : int bytecode among : "int8","int16","int32","int64","uint8","uint16","uint32","uint64","float32","float64",...        		 source code
         
        estimate_offset_value(self, fname, dim1, dim2, bytecode='int32')
        Estimates the size of a file        		 source code
         
        write(self, fname)
        To be overwritten - write the file        		 source code

        Inherited from fabioimage.fabioimage: add, convert, getclassname, getframe, getheader, getmax, getmean, getmin, getstddev, integrate_area, load, make_slice, next, previous, readROI, readheader, rebin, resetvals, save, toPIL16, update_header

        Inherited from fabioimage.fabioimage (private): _compressed_stream, _open, _readheader

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Static Methods [hide private]
         
        swap_needed(endian)
        Decide if we need to byteswap        		 source code

        Inherited from fabioimage.fabioimage: checkData, checkHeader

        Class Variables [hide private]

        Inherited from fabioimage.fabioimage (private): _need_a_real_file, _need_a_seek_to_read

        Properties [hide private]

        Inherited from fabioimage.fabioimage: classname

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, *args, **kwargs)
        (Constructor)

        		source code 

        Set up initial values

        Overrides: object.__init__
        (inherited documentation)

        read(self, fname, dim1, dim2, offset=0, bytecode='int32', endian='<')

        		source code 

        Read a binary image Parameters : fname, dim1, dim2, offset, bytecode, endian fname : file name : str dim1,dim2 : image dimensions : int offset : size of the : int bytecode among : "int8","int16","int32","int64","uint8","uint16","uint32","uint64","float32","float64",... endian among short or long endian ("<" or ">")

        Overrides: fabioimage.fabioimage.read

        write(self, fname)

        		source code 

        To be overwritten - write the file

        Overrides: fabioimage.fabioimage.write
        (inherited documentation)

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        fabio-0.1.3/epydoc/fabio.bruker100image-pysrc.html0000644000175000017500000013364112126623347022501 0ustar jeromejerome00000000000000 fabio.bruker100image
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        Package fabio :: Module bruker100image
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        [frames] | no frames]

        Source Code for Module fabio.bruker100image

         1  import numpy 
 2  import math 
 3  import logging 
 4  logger = logging.getLogger("bruker100image") 
 5  try: 
 6      import Image 
 7  except ImportError: 
 8      logger.warning("PIL is not installed ... trying to do without") 
 9      Image = None 
10   
11  from brukerimage import brukerimage 
12  from readbytestream import readbytestream  
13   

        14 -class bruker100image(brukerimage): 

        15   
16   

        17 -    def toPIL16(self, filename=None): 

        18          if not Image: 
19              raise RuntimeError("PIL is not installed !!! ") 
20   
21          if filename: 
22              self.read(filename) 
23          PILimage = Image.frombuffer("F", 
24                                          (self.dim1, self.dim2), 
25                                          self.data, 
26                                          "raw", 
27                                          "F;16", 0, -1) 
28          return PILimage 

        29   

        30 -    def read(self, fname, frame=None): 

        31          f = open(fname, "rb") 
32          try: 
33              self._readheader(f) 
34          except: 
35              raise 
36   
37          rows = int(self.header['NROWS']) 
38          cols = int(self.header['NCOLS']) 
39          npixelb = int(self.header['NPIXELB'][0]) 
40          # you had to read the Bruker docs to know this! 
41   
42          # We are now at the start of the image - assuming  
43          #   readbrukerheader worked 
44          # size = rows * cols * npixelb 
45          self.data = readbytestream(f, f.tell(), rows, cols, npixelb, 
46                                      datatype="int", signed='n', swap='n') 
47   
48          noverfl = self.header['NOVERFL'].split() # now process the overflows 
49          #read the set of "underflow pixels" - these will be completely  
50          # disregarded for now 
51          data = self.data 
52          k = 0 
53   
54          while k < 2:#for the time being things - are done in 16 bits 
55              datatype = {'1' : numpy.uint8, 
56                          '2' : numpy.uint16, 
57                          '4' : numpy.uint32 }[("%d" % 2 ** k)] 
58              ar = numpy.array(numpy.fromstring(f.read(int(noverfl[k]) * (2 ** k)), 
59                                          datatype), numpy.uint16) 
60              #insert the the overflow pixels in the image array: 
61              #this is probably a memory intensive way of doing this -  
62              # might be done in a more clever way 
63              lim = 2 ** (8 * k) - 1 
64              #generate an array comprising of the indices into data.ravel()  
65              # where its value equals lim. 
66              M = numpy.compress(numpy.equal(data.ravel(), lim), numpy.arange(rows * cols)) 
67              #now put values from ar into those indices 
68              numpy.put(data.ravel(), M, ar) 
69              padding = 16 * int(math.ceil(int(noverfl[k]) * (2 ** k) / 16.)) - \ 
70                           int(noverfl[k]) * (2 ** k) 
71              f.seek(padding, 1) 
72              print noverfl[k] + " bytes read + %d bytes padding" % padding 
73              k = k + 1 
74   
75          f.close() 
76   
77          (self.dim1, self.dim2) = (rows, cols) 
78          print self.dim1, self.dim2 
79          self.resetvals() 
80          return self 

        81   
82  if __name__ == '__main__': 
83      import sys, time 
84      I = bruker100image() 
85      b = time.clock() 
86      while (sys.argv[1:]): 
87          I.read(sys.argv[1]) 
88          r = I.toPIL16() 
89          I.rebin(2, 2) 
90          print sys.argv[1] + (": max=%d, min=%d, mean=%.2e, stddev=%.2e") % ( 
91              I.getmax(), I.getmin(), I.getmean(), I.getstddev()) 
92          print 'integrated intensity (%d %d %d %d) =%.3f' % ( 
93              10, 20, 20, 40, I.integrate_area((10, 20, 20, 40))) 
94          sys.argv[1:] = sys.argv[2:] 
95      e = time.clock() 
96      print (e - b) 
97

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        fabio-0.1.3/epydoc/fabio.tifimage-module.html0000644000175000017500000004715012126623347021674 0ustar jeromejerome00000000000000 fabio.tifimage
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        Package fabio :: Module tifimage
        [hide private]
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        Module tifimage

        source code

        
FabIO class for dealing with TIFF images. 
In facts wraps TiffIO from V. Armando Solé (available in PyMca) or falls back to PIL

Authors:
........
* Henning O. Sorensen & Erik Knudsen:
  Center for Fundamental Research: Metal Structures in Four Dimensions;
  Risoe National Laboratory;
  Frederiksborgvej 399;
  DK-4000 Roskilde;
  email:erik.knudsen@risoe.dk
* Jérôme Kieffer:
  European Synchrotron Radiation Facility;
  Grenoble (France)
   
License: GPLv3+

        Date: 11/07/2011

        Authors:
        J\xc3\xa9r\xc3\xb4me Kieffer, Henning O. Sorensen, Erik Knudsen

        Copyright: ESRF, Grenoble & Risoe National Laboratory

        License: GPLv3+

        Classes [hide private]
          tifimage
        Images in TIF format Wraps TiffIO
          Tiff_header
          Image_File_Directory
          Image_File_Directory_entry
        Variables [hide private]
          __status__ = 'stable'
          logger = logging.getLogger("tifimage")
          PIL_TO_NUMPY = {'1': <type 'bool'>, 'F': <type 'numpy.float32'...
          LITTLE_ENDIAN = 1234
          BIG_ENDIAN = 3412
          TYPES = {0: 'invalid', 1: 'byte', 2: 'ascii', 3: 'short', 4: '...
          TYPESIZES = {0: 0, 1: 1, 2: 1, 3: 2, 4: 4, 5: 8, 6: 1, 7: 1, 8...
          baseline_tiff_tags = {256: 'ImageWidth', 257: 'ImageLength', 2...
          __package__ = 'fabio'
        Variables Details [hide private]

        PIL_TO_NUMPY

        Value:
        {'1': <type 'bool'>,
 'F': <type 'numpy.float32'>,
 'I': <type 'numpy.int32'>,
 'I;16': <type 'numpy.uint16'>,
 'L': <type 'numpy.uint8'>}

        TYPES

        Value:
        {0: 'invalid',
 1: 'byte',
 2: 'ascii',
 3: 'short',
 4: 'long',
 5: 'rational',
 6: 'sbyte',
 7: 'undefined',
...

        TYPESIZES

        Value:
        {0: 0,
 1: 1,
 2: 1,
 3: 2,
 4: 4,
 5: 8,
 6: 1,
 7: 1,
...

        baseline_tiff_tags

        Value:
        {256: 'ImageWidth',
 257: 'ImageLength',
 258: 'BitsPerSample',
 259: 'Compression',
 262: 'PhotometricInterpretation',
 264: 'CellWidth',
 265: 'CellLength',
 270: 'ImageDescription',
...

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        fabio-0.1.3/epydoc/toc-fabio.converters-module.html0000644000175000017500000000336612120434325023053 0ustar jeromejerome00000000000000 converters

        Module converters

        Functions

        convert_data
        convert_data_integer
        convert_header

        Variables

        CONVERSION_DATA
        CONVERSION_HEADER
        __package__
        logger
        [hide private] fabio-0.1.3/epydoc/toc-fabio.mar345image-module.html0000644000175000017500000000262412120434325022673 0ustar jeromejerome00000000000000 mar345image

        Module mar345image

        Classes

        mar345image

        Variables

        __doc__
        __package__
        logger
        [hide private] fabio-0.1.3/epydoc/crarr.png0000644000175000017500000000052412120434325016456 0ustar jeromejerome00000000000000‰PNG  IHDR e¢E,tEXtCreation TimeTue 22 Aug 2006 00:43:10 -0500` XtIMEÖ)Ó}Ö pHYsÂÂnÐu>gAMA± üaEPLTEÿÿÿÍð×ÏÀ€f4sW áÛЊrD`@bCÜÕÈéäÜ–X{`,¯Ÿ€lN‡o@õóðª™xdEðí螊dÐÆ´”~TÖwÅvtRNS@æØfMIDATxÚc`@¼ì¼0&+š—Šˆ°»(’ˆ€ ;; /ðEXùØ‘?Ð n ƒª†— b;'ª+˜˜YÐ#œ(r<£"IEND®B`‚fabio-0.1.3/epydoc/fabio.GEimage-module.html0000644000175000017500000003074212126623347021404 0ustar jeromejerome00000000000000 fabio.GEimage
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        Package fabio :: Module GEimage
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        Module GEimage

        source code

        Classes [hide private]
          GEimage
        Functions [hide private]
         
        demo() source code
        Variables [hide private]
          logger = logging.getLogger("GEimage")
          GE_HEADER_INFO = [('ImageFormat', 10, None), ('VersionOfStanda...
          __package__ = 'fabio'
        Variables Details [hide private]

        GE_HEADER_INFO

        Value:
        [('ImageFormat', 10, None),
 ('VersionOfStandardHeader', 2, '=H'),
 ('StandardHeaderSizeInBytes', 4, '=L'),
 ('VersionOfUserHeader', 2, '=H'),
 ('UserHeaderSizeInBytes', 4, '=L'),
 ('NumberOfFrames', 2, '=H'),
 ('NumberOfRowsInFrame', 2, '=H'),
 ('NumberOfColsInFrame', 2, '=H'),
...

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        fabio-0.1.3/epydoc/toc-fabio.binaryimage-module.html0000644000175000017500000000262412120434325023144 0ustar jeromejerome00000000000000 binaryimage

        Module binaryimage

        Classes

        binaryimage

        Variables

        __doc__
        __package__
        logger
        [hide private] fabio-0.1.3/epydoc/fabio.file_series.file_series-class.html0000644000175000017500000007766312126623347024524 0ustar jeromejerome00000000000000 fabio.file_series.file_series
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        Package fabio :: Module file_series :: Class file_series
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        Class file_series

        source code

        object --+    
         |    
      list --+
             |
            file_series
        Known Subclasses:
        
Represents a series of files to iterate
has an idea of a current position to do next and prev

You also get from the list python superclass:
   append
   count
   extend
   insert
   pop
   remove
   reverse
   sort
        Instance Methods [hide private]
        new empty list
        __init__(self, list_of_strings)
        Constructor:        		 source code
         
        first(self)
        First image in series        		 source code
         
        last(self)
        Last in series        		 source code
         
        previous(self)
        Prev in a sequence        		 source code
         
        current(self)
        Current position in a sequence        		 source code
         
        next(self)
        Next in a sequence        		 source code
         
        jump(self, num)
        Goto a position in sequence        		 source code
         
        len(self)
        Number of files        		 source code
         
        first_image(self)
        First image in a sequence        		 source code
         
        last_image(self)
        Last image in a sequence        		 source code
         
        next_image(self)
        Return the next image        		 source code
         
        previous_image(self)
        Return the previous image        		 source code
         
        jump_image(self, num)
        Jump to and read image        		 source code
         
        current_image(self)
        Current image in sequence        		 source code
         
        first_object(self)
        First image in a sequence        		 source code
         
        last_object(self)
        Last image in a sequence        		 source code
         
        next_object(self)
        Return the next image        		 source code
         
        previous_object(self)
        Return the previous image        		 source code
         
        jump_object(self, num)
        Jump to and read image        		 source code
         
        current_object(self)
        Current image in sequence        		 source code

        Inherited from list: __add__, __contains__, __delitem__, __delslice__, __eq__, __ge__, __getattribute__, __getitem__, __getslice__, __gt__, __iadd__, __imul__, __iter__, __le__, __len__, __lt__, __mul__, __ne__, __new__, __repr__, __reversed__, __rmul__, __setitem__, __setslice__, __sizeof__, append, count, extend, index, insert, pop, remove, reverse, sort

        Inherited from object: __delattr__, __format__, __reduce__, __reduce_ex__, __setattr__, __str__, __subclasshook__

        Class Variables [hide private]

        Inherited from list: __hash__

        Properties [hide private]

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, list_of_strings)
        (Constructor)

        		source code 

        Constructor:

        Parameters:
        • list_of_strings - arg should be a list of strings which are filenames
        Returns: new empty list
        Overrides: object.__init__

        first_image(self)

        		source code 

        First image in a sequence

        Returns:
        fabioimage

        last_image(self)

        		source code 

        Last image in a sequence

        Returns:
        fabioimage

        next_image(self)

        		source code 

        Return the next image

        Returns:
        fabioimage

        previous_image(self)

        		source code 

        Return the previous image

        Returns:
        fabioimage

        jump_image(self, num)

        		source code 

        Jump to and read image

        Returns:
        fabioimage

        current_image(self)

        		source code 

        Current image in sequence

        Returns:
        fabioimage

        first_object(self)

        		source code 

        First image in a sequence

        Returns:
        file_object

        last_object(self)

        		source code 

        Last image in a sequence

        Returns:
        file_object

        next_object(self)

        		source code 

        Return the next image

        Returns:
        file_object

        previous_object(self)

        		source code 

        Return the previous image

        Returns:
        file_object

        jump_object(self, num)

        		source code 

        Jump to and read image

        Returns:
        file_object

        current_object(self)

        		source code 

        Current image in sequence

        Returns:
        file_object

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        fabio-0.1.3/epydoc/fabio.pnmimage-pysrc.html0000644000175000017500000022302312126623347021552 0ustar jeromejerome00000000000000 fabio.pnmimage
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        Package fabio :: Module pnmimage
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        Source Code for Module fabio.pnmimage

          1  #!/usr/bin/env python 
  2  #coding: utf8 
  3  """ 
  4   
  5  Authors: Henning O. Sorensen & Erik Knudsen 
  6           Center for Fundamental Research: Metal Structures in Four Dimensions 
  7           Risoe National Laboratory 
  8           Frederiksborgvej 399 
  9           DK-4000 Roskilde 
 10           email:henning.sorensen@risoe.dk 
 11   
 12  """ 
 13   
 14  import numpy, logging 
 15  logger = logging.getLogger("pnmimage") 
 16  from fabioimage import fabioimage 
 17   
 18  SUBFORMATS = ['P1', 'P2', 'P3', 'P4', 'P5', 'P6', 'P7'] 
 19   
 20  HEADERITEMS = ['SUBFORMAT', 'DIMENSIONS', 'MAXVAL'] 
 21  P7HEADERITEMS = ['WIDTH', 'HEIGHT', 'DEPTH', 'MAXVAL', 'TUPLTYPE', 'ENDHDR'] 

         22   
 23 -class pnmimage(fabioimage): 

         24 -    def __init__(self, *arg, **kwargs): 

         25          fabioimage.__init__(self, *arg, **kwargs) 
 26          fun = getattr(fabioimage, '__init__', lambda x: None) 
 27          fun(self) 
 28          self.data = None 
 29          self.header = {'Subformat':'P5'} 
 30          self.dim1 = self.dim2 = 0 
 31          self.m = self.maxval = self.stddev = self.minval = None 
 32          self.header_keys = self.header.keys() 
 33          self.bytecode = None 

         34   

         35 -    def _readheader(self, f): 

         36          #pnm images have a 3-line header but ignore lines starting with '#' 
 37          #1st line contains the pnm image sub format 
 38          #2nd line contains the image pixel dimension 
 39          #3rd line contains the maximum pixel value (at least for grayscale - check this) 
 40          self.header_keys = ['SUBFORMAT', 'DIMENSIONS', 'MAXVAL'] 
 41   
 42          l = f.readline().strip() 
 43          if l not in SUBFORMATS: 
 44              raise IOError, ('unknown subformat of pnm: %s' % l) 
 45          else: 
 46              self.header['SUBFORMAT'] = l 
 47   
 48          if self.header['SUBFORMAT'] == 'P7': 
 49              self.header_keys = P7HEADERITEMS 
 50              #this one has a special header 
 51              while 'ENDHDR' not in l: 
 52                  l = f.readline() 
 53                  while(l[0] == '#'): l = f.readline() 
 54                  s = l.lsplit(' ', 1) 
 55                  if s[0] not in P7HEADERITEMS: 
 56                      raise IOError, ('Illegal pam (netpnm p7) headeritem %s' % s[0]) 
 57                  self.header[s[0]] = s[1] 
 58          else: 
 59              self.header_keys = HEADERITEMS 
 60              for k in self.header_keys[1:]: 
 61                  l = f.readline() 
 62                  while(l[0] == '#'): l = f.readline() 
 63                  self.header[k] = l.strip() 
 64   
 65          #set the dimensions 
 66          dims = (self.header['DIMENSIONS'].split()) 
 67          self.dim1, self.dim2 = int(dims[0]), int(dims[1]) 
 68          #figure out how many bytes are used to store the data 
 69          #case construct here! 
 70          m = int(self.header['MAXVAL']) 
 71          if m < 256: 
 72              self.bytecode = numpy.uint8 
 73          elif m < 65536: 
 74              self.bytecode = numpy.uint16 
 75          elif m < 2147483648L: 
 76              self.bytecode = numpy.uint32 
 77              logger.warning('32-bit pixels are not really supported by the netpgm standard') 
 78          else: 
 79              raise IOError, 'could not figure out what kind of pixels you have' 

         80   

         81 -    def read(self, fname, frame=None): 

         82          """ 
 83          try to read PNM images 
 84          @param fname: name of the file 
 85          @param frame: not relevant here! PNM is always single framed 
 86          """ 
 87          self.header = {} 
 88          self.resetvals() 
 89          infile = self._open(fname) 
 90          self._readheader(infile) 
 91   
 92          #read the image data 
 93          decoder_name = "%sdec" % self.header['SUBFORMAT'] 
 94          if decoder_name in dir(pnmimage): 
 95              decoder = getattr(pnmimage, decoder_name) 
 96              self.data = decoder(infile, self.bytecode) 
 97          else: 
 98              raise IOError("No decoder named %s for file %s" % (decoder_name, fname)) 
 99          self.resetvals() 
100          return self 

        101   
102      @staticmethod 

        103 -    def P1dec(buf, bytecode): 

        104          data = numpy.zeros((self.dim2, self.dim1)) 
105          i = 0 
106          for l in buf.readlines(): 
107              try: 
108                  data[i, :] = numpy.array(l.split()).astype(bytecode) 
109              except ValueError: 
110                  raise IOError, 'Size spec in pnm-header does not match size of image data field' 
111          return data 

        112   
113      @staticmethod 

        114 -    def P4dec(buf, bytecode): 

        115          err = 'single bit (pbm) images are not supported - yet' 
116          logger.error(err) 
117          raise NotImplementedError(err) 

        118   
119      @staticmethod 

        120 -    def P2dec(buf, bytecode): 

        121          data = numpy.zeros((self.dim2, self.dim1)) 
122          i = 0 
123          for l in buf.readlines(): 
124              try: 
125                  data[i, :] = numpy.array(l.split()).astype(bytecode) 
126              except ValueError: 
127                  raise IOError, 'Size spec in pnm-header does not match size of image data field' 
128          return data 

        129   
130      @staticmethod 

        131 -    def P5dec(buf, bytecode): 

        132          l = buf.read() 
133          try: 
134              data = numpy.reshape(numpy.fromstring(l, bytecode), [self.dim2, self.dim1]).byteswap() 
135          except ValueError: 
136              raise IOError, 'Size spec in pnm-header does not match size of image data field' 
137          return data 

        138   
139      @staticmethod 

        140 -    def P3dec(buf, bytecode): 

        141          err = '(plain-ppm) RGB images are not supported - yet' 
142          logger.error(err) 
143          raise NotImplementedError(err) 

        144   
145      @staticmethod 

        146 -    def P6dec(buf, bytecode): 

        147          err = '(ppm) RGB images are not supported - yet' 
148          logger.error(err) 
149          raise NotImplementedError(err) 

        150   
151      @staticmethod 

        152 -    def P7dec(buf, bytecode): 

        153          err = '(pam) images are not supported - yet' 
154          logger.error(err) 
155          raise NotImplementedError(err) 

        156   

        157 -    def write(self, filename): 

        158          raise NotImplementedError('write pnm images is not implemented yet.') 

        159   
160      @staticmethod 

        161 -    def checkData(data=None): 

        162          if data is None: 
163              return None 
164          else: 
165              return data.astype(int) 

        166

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        fabio-0.1.3/epydoc/toc-fabio.mar345_IO-module.html0000644000175000017500000000225612120434325022260 0ustar jeromejerome00000000000000 mar345_IO

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        [hide private] fabio-0.1.3/epydoc/fabio.fit2dmaskimage-pysrc.html0000644000175000017500000011641112126623347022646 0ustar jeromejerome00000000000000 fabio.fit2dmaskimage
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        Package fabio :: Module fit2dmaskimage
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        Source Code for Module fabio.fit2dmaskimage

         1  ## Automatically adapted for numpy.oldnumeric Oct 05, 2007 by alter_code1.py 
 2   
 3  #!/usr/bin/env python 
 4  """ 
 5   
 6  Author: Andy Hammersley, ESRF 
 7  Translation into python/fabio: Jon Wright, ESRF 
 8  """ 
 9   
10  import numpy 
11   
12  from fabioimage import fabioimage 

        13   
14   
15 -class fit2dmaskimage(fabioimage): 

        16      """ Read and try to write Andy Hammersley's mask format """ 
17   
18   

        19 -    def _readheader(self, infile): 

        20          """ 
21          Read in a header from an already open file 
22          """ 
23          # 1024 bytes gives 256x32 bit integers 
24          header = infile.read(1024) 
25          for i, j in [ ("M", 0), 
26                        ("A", 4), 
27                        ("S", 8), 
28                        ("K", 12)  ]: 
29              if header[j] != i: 
30                  raise Exception("Not a fit2d mask file") 
31          fit2dhdr = numpy.fromstring(header, numpy.int32) 
32          self.dim1 = fit2dhdr[4] # 1 less than Andy's fortran 
33          self.dim2 = fit2dhdr[5] 

        34   
35   

        36 -    def read(self, fname, frame=None): 

        37          """ 
38          Read in header into self.header and 
39              the data   into self.data 
40          """ 
41          fin = self._open(fname) 
42          self._readheader(fin) 
43          # Compute image size 
44          self.bytecode = numpy.uint8 
45          self.bpp = len(numpy.array(0, self.bytecode).tostring()) 
46   
47          # integer division 
48          num_ints = (self.dim1 + 31) // 32 
49          total = self.dim2 * num_ints * 4 
50          data = fin.read(total) 
51          assert len(data) == total 
52          fin.close() 
53   
54          # Now to unpack it 
55          data = numpy.fromstring(data, numpy.uint8) 
56          data = numpy.reshape(data, (self.dim2, num_ints * 4)) 
57   
58          result = numpy.zeros((self.dim2, num_ints * 4 * 8), numpy.uint8) 
59   
60          # Unpack using bitwise comparisons to 2**n 
61          bits = numpy.ones((1), numpy.uint8) 
62          for i in range(8): 
63              temp = numpy.bitwise_and(bits, data) 
64              result[:, i::8] = temp.astype(numpy.uint8) 
65              bits = bits * 2 
66          # Extra rows needed for packing odd dimensions 
67          spares = num_ints * 4 * 8 - self.dim1 
68          if spares == 0: 
69              self.data = numpy.where(result == 0, 0, 1) 
70          else: 
71              self.data = numpy.where(result[:, :-spares] == 0, 0, 1) 
72          # Transpose appears to be needed to match edf reader (scary??) 
73  #        self.data = numpy.transpose(self.data) 
74          self.data = numpy.reshape(self.data.astype(numpy.uint16), 
75                                      (self.dim2, self.dim1)) 
76          self.pilimage = None 
77          return self 

        78   
79   
80   

        81 -    def write(self, fname): 

        82          """ 
83          Try to write a file 
84          check we can write zipped also 
85          mimics that fabian was writing uint16 (we sometimes want floats) 
86          """ 
87          raise Exception("Not implemented yet") 

        88   
89      @staticmethod 

        90 -    def checkData(data=None): 

        91          if data is None: 
92              return None 
93          else: 
94              return data.astype(int) 

        95

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        fabio-0.1.3/epydoc/fabio.file_series-pysrc.html0000644000175000017500000033347412126623347022262 0ustar jeromejerome00000000000000 fabio.file_series
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        Package fabio :: Module file_series
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        Source Code for Module fabio.file_series

          1  #!/usr/bin/env python 
  2   
  3  """ 
  4   
  5  Authors: 
  6  ........ 
  7   
  8  * Henning O. Sorensen & Erik Knudsen 
  9    Center for Fundamental Research: Metal Structures in Four Dimensions 
 10    Risoe National Laboratory 
 11    Frederiksborgvej 399 
 12    DK-4000 Roskilde 
 13    email:erik.knudsen@risoe.dk 
 14  * Jon Wright, ESRF 
 15   
 16  """ 
 17  import logging, sys 
 18  logger = logging.getLogger("fileseries") 
 19  import traceback as pytraceback 
 20   
 21  from fabioutils import FilenameObject, next_filename 
 22   
 23  from openimage import openimage 
 24   
 25   

         26 -def new_file_series0(first_object, first=None, last=None, step=1): 

         27      """ 
 28      Created from a fabio image 
 29      first and last are file numbers 
 30   
 31      """ 
 32      im = first_object 
 33      nimages = 0 
 34      # for counting images 
 35      if None in (first, last): 
 36          step = 0 
 37          total = 1 
 38      else: 
 39          total = last - first 
 40   
 41      yield im 
 42      while nimages < total: 
 43          nimages += step 
 44          try: 
 45              newim = im.next() 
 46              im = newim 
 47          except Exception, error: 
 48              pytraceback.print_exc() 
 49   
 50              # Skip bad images 
 51              logger.warning("Got a problem here: %s", error) 
 52              try: 
 53                  im.filename = next_filename(im.filename) 
 54              except Exception, error: 
 55                  # KE: This will not work and will throw an exception 
 56                  # fabio.next_filename doesn't understand %nnnn on the end 
 57                  logger.warning("Got another problem here: %s", error) 
 58                  im.filename = next_filename(im.sequencefilename) 
 59              yield None 
 60          yield im 

         61   
 62   
 63   

         64 -def new_file_series(first_object, nimages=0, step=1, traceback=False): 

         65      """ 
 66      A generator function that creates a file series starting from a a fabioimage. 
 67      Iterates through all images in a file (if more than 1), then proceeds to 
 68      the next file as determined by fabio.next_filename. 
 69   
 70      @param first_object: the starting fabioimage, which will be the first one yielded 
 71          in the sequence 
 72      @param nimages:  the maximum number of images to consider 
 73          step: step size, will yield the first and every step'th image until nimages 
 74          is reached.  (e.g. nimages = 5, step = 2 will yield 3 images (0, 2, 4) 
 75      @param traceback: if True causes it to print a traceback in the event of an 
 76          exception (missing image, etc.).  Otherwise the calling routine can handle 
 77          the exception as it chooses 
 78      @param yields: the next fabioimage in the series. 
 79          In the event there is an exception, it yields the sys.exec_info for the 
 80          exception instead.  sys.exec_info is a tuple: 
 81          ( exceptionType, exceptionValue, exceptionTraceback ) 
 82          from which all the exception information can be obtained. 
 83   
 84      Suggested usage: 
 85       
 86      :: 
 87       
 88          for obj in new_file_series( ... ): 
 89            if not isinstance(obj, fabio.fabioimage.fabioimage ): 
 90              # deal with errors like missing images, non readable files, etc 
 91              # e.g. 
 92              traceback.print_exception(obj[0], obj[1], obj[2]) 
 93   
 94      """ 
 95      im = first_object 
 96      nprocessed = 0 
 97      abort = False 
 98      if nimages > 0: 
 99          yield im 
100          nprocessed += 1 
101      while nprocessed < nimages: 
102          try: 
103              newim = im.next() 
104              im = newim 
105              retVal = im 
106          except Exception, ex: 
107              retVal = sys.exc_info() 
108              if(traceback): 
109                  pytraceback.print_exc() 
110                  # Skip bad images 
111                  logger.warning("Got a problem here: next() failed %s", ex) 
112              # Skip bad images 
113              try: 
114                  im.filename = next_filename(im.filename) 
115              except Exception, ex: 
116                  logger.warning("Got another problem here: next_filename(im.filename) %s", ex) 
117          if nprocessed % step == 0: 
118              yield retVal 
119              # Avoid cyclic references with exc_info ? 
120              retVal = None 
121              if abort: break 
122          nprocessed += 1 

        123   
124   
125   

        126 -class file_series(list): 

        127      """ 
128      Represents a series of files to iterate 
129      has an idea of a current position to do next and prev 
130   
131      You also get from the list python superclass: 
132         append 
133         count 
134         extend 
135         insert 
136         pop 
137         remove 
138         reverse 
139         sort 
140      """ 

        141 -    def __init__(self, list_of_strings): 

        142          """ 
143          Constructor: 
144   
145          @param list_of_strings: arg should be a list of strings which are filenames 
146   
147          """ 
148          super(file_series, self).__init__(list_of_strings) 
149          # track current position in list 
150          self._current = 0 

        151   
152   
153      # methods which return a filename 
154   

        155 -    def first(self): 

        156          """ 
157          First image in series 
158   
159          """ 
160          return self[0] 

        161   

        162 -    def last(self): 

        163          """ 
164          Last in series 
165   
166          """ 
167          return self[-1] 

        168   

        169 -    def previous(self): 

        170          """ 
171          Prev in a sequence 
172   
173          """ 
174          self._current -= 1 
175          return self[self._current] 

        176   

        177 -    def current(self): 

        178          """Current position in a sequence 
179   
180          """ 
181          return self[self._current] 

        182   

        183 -    def next(self): 

        184          """ 
185          Next in a sequence 
186   
187          """ 
188          self._current += 1 
189          return self[self._current] 

        190   

        191 -    def jump(self, num): 

        192          """ 
193          Goto a position in sequence 
194   
195          """ 
196          assert num < len(self) and num > 0, "num out of range" 
197          self._current = num 
198          return self[self._current] 

        199   

        200 -    def len(self): 

        201          """ 
202          Number of files 
203   
204          """ 
205          return len(self) 

        206   
207   
208      # Methods which return a fabioimage 
209   

        210 -    def first_image(self): 

        211          """ 
212          First image in a sequence 
213   
214          @return: fabioimage 
215   
216          """ 
217          return openimage(self.first()) 

        218   

        219 -    def last_image(self): 

        220          """ 
221          Last image in a sequence 
222   
223          @return: fabioimage 
224   
225          """ 
226          return openimage(self.last()) 

        227   

        228 -    def next_image(self): 

        229          """ 
230          Return the next image 
231   
232          @return: fabioimage 
233   
234          """ 
235          return openimage(self.next()) 

        236   

        237 -    def previous_image(self): 

        238          """ 
239          Return the previous image 
240   
241          @return: fabioimage 
242   
243          """ 
244          return openimage(self.previous()) 

        245   

        246 -    def jump_image(self, num): 

        247          """ 
248          Jump to and read image 
249   
250          @return: fabioimage 
251   
252          """ 
253          return openimage(self.jump(num)) 

        254   

        255 -    def current_image(self): 

        256          """ 
257          Current image in sequence 
258   
259          @return: fabioimage 
260   
261          """ 
262          return openimage(self.current()) 

        263   
264      # methods which return a file_object 
265   

        266 -    def first_object(self): 

        267          """ 
268          First image in a sequence 
269   
270          @return: file_object 
271          """ 
272          return FilenameObject(self.first()) 

        273   

        274 -    def last_object(self): 

        275          """ 
276          Last image in a sequence 
277   
278          @return: file_object 
279   
280          """ 
281          return FilenameObject(self.last()) 

        282   

        283 -    def next_object(self): 

        284          """ 
285          Return the next image 
286   
287          @return: file_object 
288   
289          """ 
290          return FilenameObject(self.next()) 

        291   

        292 -    def previous_object(self): 

        293          """ 
294          Return the previous image 
295   
296          @return: file_object 
297   
298          """ 
299          return FilenameObject(self.previous()) 

        300   

        301 -    def jump_object(self, num): 

        302          """ 
303          Jump to and read image 
304   
305          @return: file_object 
306   
307          """ 
308          return FilenameObject(self.jump(num)) 

        309   

        310 -    def current_object(self): 

        311          """ 
312          Current image in sequence 
313   
314          @return: file_object 
315   
316          """ 
317          return FilenameObject(self.current()) 

        318   
319   
320   
321   

        322 -class numbered_file_series(file_series): 

        323      """ 
324      mydata0001.edf = "mydata" + 0001 + ".edf" 
325      mydata0002.edf = "mydata" + 0002 + ".edf" 
326      mydata0003.edf = "mydata" + 0003 + ".edf" 
327      """ 

        328 -    def __init__(self, stem, first, last, extension, 
329                   digits=4, padding='Y', step=1): 

        330          """ 
331          Constructor 
332   
333          @param stem: first part of the name 
334          @param step: in case of every nth file 
335          @param padding: possibility for specifying that numbers are not padded with zeroes up to digits 
336   
337          """ 
338          if padding == 'Y': 
339              fmt = "%s%0" + str(digits) + "d%s" 
340          else: 
341              fmt = "%s%i%s" 
342   
343          super(numbered_file_series, self).__init__( 
344              [ fmt % (stem, i, extension) for i in range(first, 
345                                                            last + 1, 
346                                                            step) ]) 

        347   
348   

        349 -class filename_series: 

        350      """ Much like the others, but created from a string filename """ 

        351 -    def __init__(self, filename): 

        352          """ create from a filename (String)""" 
353          self.obj = FilenameObject(filename) 

        354   

        355 -    def next(self): 

        356          """ increment number """ 
357          self.obj.num += 1 
358          return self.obj.tostring() 

        359   

        360 -    def previous(self): 

        361          """ decrement number """ 
362          self.obj.num -= 1 
363          return self.obj.tostring() 

        364   

        365 -    def current(self): 

        366          """ return current filename string""" 
367          return self.obj.tostring() 

        368   

        369 -    def jump(self, num): 

        370          """ jump to a specific number """ 
371          self.obj.num = num 
372          return self.obj.tostring() 

        373   
374      # image methods 

        375 -    def next_image(self): 

        376          """ returns the next image as a fabioimage """ 
377          return openimage(self.next()) 

        378 -    def prev_image(self): 

        379          """ returns the previos image as a fabioimage """ 
380          return openimage(self.previous()) 

        381 -    def current_image(self): 

        382          """ returns the current image as a fabioimage""" 
383          return openimage(self.current()) 

        384 -    def jump_image(self, num): 

        385          """ returns the image number as a fabioimage""" 
386          return openimage(self.jump(num)) 

        387      # object methods 

        388 -    def next_object(self): 

        389          """ returns the next filename as a fabio.FilenameObject""" 
390          self.obj.num += 1 
391          return self.obj 

        392 -    def previous_object(self): 

        393          """ returns the previous filename as a fabio.FilenameObject""" 
394          self.obj.num -= 1 
395          return self.obj 

        396 -    def current_object(self): 

        397          """ returns the current filename as a fabio.FilenameObject""" 
398          return self.obj 

        399 -    def jump_object(self, num): 

        400          """ returns the filename num as a fabio.FilenameObject""" 
401          self.obj.num = num 
402          return self.obj 

        403

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        fabio-0.1.3/epydoc/toc-fabio.GEimage-module.html0000644000175000017500000000276712120434325022163 0ustar jeromejerome00000000000000 GEimage

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        fabio.cbfimage.MINIMUM_KEYS
        fabio.cbfimage.PADDING
        fabio.cbfimage.STARTER
        fabio.cbfimage.__package__
        fabio.cbfimage.logger
        fabio.cf_io.__package__
        fabio.compression.__package__
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        fabio.converters.CONVERSION_DATA
        fabio.converters.CONVERSION_HEADER
        fabio.converters.__package__
        fabio.converters.logger
        fabio.datIO.__package__
        fabio.dm3image.DATA_BYTES
        fabio.dm3image.DATA_TYPES
        fabio.dm3image.__package__
        fabio.dm3image.logger
        fabio.edfimage.BLOCKSIZE
        fabio.edfimage.DATA_TYPES
        fabio.edfimage.DEFAULT_VALUES
        fabio.edfimage.MINIMUM_KEYS
        fabio.edfimage.NUMPY_EDF_DTYPE
        fabio.edfimage.__package__
        fabio.edfimage.logger
        fabio.fabioimage.__package__
        fabio.fabioimage.logger
        fabio.fabioutils.COMPRESSORS
        fabio.fabioutils.FILETYPES
        fabio.fabioutils.__package__
        fabio.fabioutils.dictAscii
        fabio.fabioutils.i
        fabio.fabioutils.key
        fabio.fabioutils.lines
        fabio.fabioutils.logger
        fabio.file_series.__package__
        fabio.file_series.logger
        fabio.fit2dmaskimage.__package__
        fabio.fit2dspreadsheetimage.__package__
        fabio.kcdimage.DATA_TYPES
        fabio.kcdimage.DEFAULT_VALUES
        fabio.kcdimage.MINIMUM_KEYS
        fabio.kcdimage.__package__
        fabio.kcdimage.logger
        fabio.mar345_IO.__package__
        fabio.mar345_IO.__test__
        fabio.mar345image.__doc__
        fabio.mar345image.__package__
        fabio.mar345image.logger
        fabio.marccdimage.CDEFINITION
        fabio.marccdimage.C_SIZES
        fabio.marccdimage.C_TO_STRUCT
        fabio.marccdimage.HEADER_FORMAT
        fabio.marccdimage.HEADER_NAMES
        fabio.marccdimage.MAXIMAGES
        fabio.marccdimage.__package__
        fabio.marccdimage.logger
        fabio.openimage.MAGIC_NUMBERS
        fabio.openimage.__package__
        fabio.openimage.logger
        fabio.pilatusimage.__package__
        fabio.pnmimage.HEADERITEMS
        fabio.pnmimage.P7HEADERITEMS
        fabio.pnmimage.SUBFORMATS
        fabio.pnmimage.__package__
        fabio.pnmimage.logger
        fabio.readbytestream.DATATYPES
        fabio.readbytestream.__package__
        fabio.readbytestream.logger
        fabio.tifimage.BIG_ENDIAN
        fabio.tifimage.LITTLE_ENDIAN
        fabio.tifimage.PIL_TO_NUMPY
        fabio.tifimage.TYPES
        fabio.tifimage.TYPESIZES
        fabio.tifimage.__package__
        fabio.tifimage.__status__
        fabio.tifimage.baseline_tiff_tags
        fabio.tifimage.logger
        fabio.version
        fabio.xsdimage.__package__
        fabio.xsdimage.logger
        [hide private] fabio-0.1.3/epydoc/toc-fabio.TiffIO-module.html0000644000175000017500000000752712120434325022004 0ustar jeromejerome00000000000000 TiffIO

        Module TiffIO

        Classes

        TiffIO

        Variables

        ALLOW_MULTIPLE_STRIPS
        DEBUG
        FIELD_TYPE
        FIELD_TYPE_OUT
        SAMPLE_FORMAT_COMPLEXIEEEFP
        SAMPLE_FORMAT_COMPLEXINT
        SAMPLE_FORMAT_FLOAT
        SAMPLE_FORMAT_INT
        SAMPLE_FORMAT_UINT
        SAMPLE_FORMAT_VOID
        TAG_BITS_PER_SAMPLE
        TAG_COLORMAP
        TAG_COMPRESSION
        TAG_DATE
        TAG_ID
        TAG_IMAGE_DESCRIPTION
        TAG_NUMBER_OF_COLUMNS
        TAG_NUMBER_OF_ROWS
        TAG_PHOTOMETRIC_INTERPRETATION
        TAG_ROWS_PER_STRIP
        TAG_SAMPLE_FORMAT
        TAG_SOFTWARE
        TAG_STRIP_BYTE_COUNTS
        TAG_STRIP_OFFSETS
        __package__
        __revision__
        [hide private] fabio-0.1.3/epydoc/class-tree.html0000644000175000017500000003243512126623347017607 0ustar jeromejerome00000000000000 Class Hierarchy
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        [ Module Hierarchy | Class Hierarchy ]

        Class Hierarchy

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        fabio-0.1.3/epydoc/toc-fabio.xsdimage-module.html0000644000175000017500000000244112120434325022453 0ustar jeromejerome00000000000000 xsdimage

        Module xsdimage

        Classes

        xsdimage

        Variables

        __package__
        logger
        [hide private] fabio-0.1.3/epydoc/toc-fabio.tifimage-module.html0000644000175000017500000000445412126623347022457 0ustar jeromejerome00000000000000 tifimage

        Module tifimage

        Classes

        Image_File_Directory
        Image_File_Directory_entry
        Tiff_header
        tifimage

        Variables

        BIG_ENDIAN
        LITTLE_ENDIAN
        PIL_TO_NUMPY
        TYPES
        TYPESIZES
        __package__
        __status__
        baseline_tiff_tags
        logger
        [hide private] fabio-0.1.3/epydoc/fabio.fabioutils.GzipFile-class.html0000644000175000017500000004220012126623347023567 0ustar jeromejerome00000000000000 fabio.fabioutils.GzipFile
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        Package fabio :: Module fabioutils :: Class GzipFile
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        Class GzipFile

        source code

        gzip.GzipFile --+
                |
               GzipFile

        Just a wrapper forgzip.GzipFile providing the correct seek capabilities for python 2.5

        Instance Methods [hide private]
         
        __init__(self, filename=None, mode=None, compresslevel=9, fileobj=None)
        Wrapper with locking for constructor for the GzipFile class.        		 source code
         
        getSize(self) source code
         
        setSize(self, value) source code
         
        seek(self, offset, whence=0)
        Move to new file position.        		 source code

        Inherited from gzip.GzipFile: __del__, __iter__, __repr__, close, fileno, flush, isatty, next, read, readline, readlines, rewind, tell, write, writelines

        Inherited from gzip.GzipFile (private): _add_read_data, _init_read, _init_write, _read, _read_eof, _read_gzip_header, _unread, _write_gzip_header

        Class Variables [hide private]

        Inherited from gzip.GzipFile: max_read_chunk, myfileobj

        Properties [hide private]
          size
          closed

        Inherited from gzip.GzipFile: filename

        Method Details [hide private]

        __init__(self, filename=None, mode=None, compresslevel=9, fileobj=None)
        (Constructor)

        		source code 

        Wrapper with locking for constructor for the GzipFile class.

        At least one of fileobj and filename must be given a non-trivial value.

        The new class instance is based on fileobj, which can be a regular file, a StringIO object, or any other object which simulates a file. It defaults to None, in which case filename is opened to provide a file object.

        When fileobj is not None, the filename argument is only used to be included in the gzip file header, which may includes the original filename of the uncompressed file. It defaults to the filename of fileobj, if discernible; otherwise, it defaults to the empty string, and in this case the original filename is not included in the header.

        The mode argument can be any of 'r', 'rb', 'a', 'ab', 'w', or 'wb', depending on whether the file will be read or written. The default is the mode of fileobj if discernible; otherwise, the default is 'rb'. Be aware that only the 'rb', 'ab', and 'wb' values should be used for cross-platform portability.

        The compresslevel argument is an integer from 1 to 9 controlling the level of compression; 1 is fastest and produces the least compression, and 9 is slowest and produces the most compression. The default is 9.

        Overrides: gzip.GzipFile.__init__

        seek(self, offset, whence=0)

        		source code 

        Move to new file position.

        Argument offset is a byte count. Optional argument whence defaults to 0 (offset from start of file, offset should be >= 0); other values are 1 (move relative to current position, positive or negative), and 2 (move relative to end of file, usually negative, although many platforms allow seeking beyond the end of a file). If the file is opened in text mode, only offsets returned by tell() are legal. Use of other offsets causes undefined behavior.

        This is a wrapper for seek to ensure compatibility with old python 2.5

        Overrides: gzip.GzipFile.seek

        Property Details [hide private]

        size

        Get Method:
        getSize(self)
        Set Method:
        setSize(self, value)

        closed

        Get Method:
        unreachable.closed(self)

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        fabio-0.1.3/epydoc/fabio.fabioimage.fabioimage-class.html0000644000175000017500000012074112126623347024072 0ustar jeromejerome00000000000000 fabio.fabioimage.fabioimage
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        Package fabio :: Module fabioimage :: Class fabioimage
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        Class fabioimage

        source code

        object --+
         |
        fabioimage
        Known Subclasses:

        A common object for images in fable Contains a numpy array (.data) and dict of meta data (.header)

        Instance Methods [hide private]
         
        __init__(self, data=None, header=None)
        Set up initial values        		 source code
         
        getclassname(self)
        Retrieves the name of the class        		 source code
         
        getframe(self, num)
        returns the file numbered 'num' in the series as a fabioimage        		 source code
         
        previous(self)
        returns the previous file in the series as a fabioimage        		 source code
         
        next(self)
        returns the next file in the series as a fabioimage        		 source code
         
        toPIL16(self, filename=None)
        Convert to Python Imaging Library 16 bit greyscale image        		 source code
         
        getheader(self)
        returns self.header        		 source code
         
        getmax(self)
        Find max value in self.data, caching for the future        		 source code
         
        getmin(self)
        Find min value in self.data, caching for the future        		 source code
         
        make_slice(self, coords)
        Convert a len(4) set of coords into a len(2) tuple (pair) of slice objects the latter are immutable, meaning the roi can be cached        		 source code
         
        integrate_area(self, coords)
        Sums up a region of interest if len(coords) == 4 -> convert coords to slices if len(coords) == 2 -> use as slices floor -> ? removed as unused in the function.        		 source code
         
        getmean(self)
        return the mean        		 source code
         
        getstddev(self)
        return the standard deviation        		 source code
         
        add(self, other)
        Add another Image - warning, does not clip to 16 bit images by default        		 source code
         
        resetvals(self)
        Reset cache - call on changing data        		 source code
         
        rebin(self, x_rebin_fact, y_rebin_fact, keep_I=True)
        Rebin the data and adjust dims        		 source code
         
        write(self, fname)
        To be overwritten - write the file        		 source code
         
        save(self, fname)
        wrapper for write        		 source code
         
        readheader(self, filename)
        Call the _readheader function...        		 source code
         
        _readheader(self, fik_obj)
        Must be overridden in classes        		 source code
         
        update_header(self, **kwds)
        update the header entries by default pass in a dict of key, values.        		 source code
         
        read(self, filename, frame=None)
        To be overridden - fill in self.header and self.data        		 source code
         
        load(self, *arg, **kwarg)
        Wrapper for read        		 source code
         
        readROI(self, filename, frame=None, coords=None)
        Method reading Region of Interest.        		 source code
         
        _open(self, fname, mode='rb')
        Try to handle compressed files, streams, shared memory etc Return an object which can be used for "read" and "write" ...        		 source code
         
        _compressed_stream(self, fname, system_uncompress, python_uncompress, mode='rb')
        Try to transparently handle gzip / bzip without always getting python performance        		 source code
         
        convert(self, dest)
        Convert a fabioimage object into another fabioimage object (with possible conversions)        		 source code

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Static Methods [hide private]
         
        checkHeader(header=None)
        Empty for fabioimage but may be populated by others classes
         
        checkData(data=None)
        Empty for fabioimage but may be populated by others classes, especially for format accepting only integers
        Class Variables [hide private]
          _need_a_seek_to_read = False
          _need_a_real_file = False
        Properties [hide private]
          classname
        Retrieves the name of the class

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, data=None, header=None)
        (Constructor)

        		source code 

        Set up initial values

        Overrides: object.__init__

        getclassname(self)

        		source code 

        Retrieves the name of the class

        Returns:
        the name of the class

        toPIL16(self, filename=None)

        		source code 

        Convert to Python Imaging Library 16 bit greyscale image

        FIXME - this should be handled by the libraries now

        rebin(self, x_rebin_fact, y_rebin_fact, keep_I=True)

        		source code 

        Rebin the data and adjust dims

        Parameters:
        • x_rebin_fact (int) - x binning factor
        • y_rebin_fact (int) - y binning factor
        • keep_I (boolean) - shall the signal increase ?

        readROI(self, filename, frame=None, coords=None)

        		source code 

        Method reading Region of Interest. This implementation is the trivial one, just doing read and crop

        _open(self, fname, mode='rb')

        		source code 

        Try to handle compressed files, streams, shared memory etc Return an object which can be used for "read" and "write" ... FIXME - what about seek ?

        convert(self, dest)

        		source code 

        Convert a fabioimage object into another fabioimage object (with possible conversions)

        Parameters:
        • dest - destination type "EDF", "edfimage" or the class itself

        Property Details [hide private]

        classname

        Retrieves the name of the class

        Get Method:
        getclassname(self) - Retrieves the name of the class

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        fabio-0.1.3/epydoc/toc-fabio.compression-module.html0000644000175000017500000000546112120434325023220 0ustar jeromejerome00000000000000 compression

        Module compression

        Classes

        str

        Functions

        compByteOffet_numpy
        compPCK
        compTY1
        decByteOffet_cython
        decByteOffet_numpy
        decByteOffet_python
        decByteOffet_weave
        decBzip2
        decGzip
        decKM4CCD
        decPCK
        decTY1
        decZlib
        endianness
        md5sum

        Variables

        __package__
        logger
        [hide private] fabio-0.1.3/epydoc/fabio.compression-module.html0000644000175000017500000007415612126623347022456 0ustar jeromejerome00000000000000 fabio.compression
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        Package fabio :: Module compression
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        Module compression

        source code

        
Authors: Jérôme Kieffer, ESRF
         email:jerome.kieffer@esrf.fr

FabIO library containing compression and decompression algorithm for various

        Author: J\xc3\xa9r\xc3\xb4me Kieffer

        Contact: jerome.kieffer@esrf.eu

        Copyright: European Synchrotron Radiation Facility, Grenoble, France

        License: GPLv3+

        Classes [hide private]
          str
        str(object) -> string
        Functions [hide private]
         
        md5sum(blob)
        returns the md5sum of an object...        		 source code
         
        endianness()
        Return the native endianness of the system        		 source code
         
        decGzip(stream)
        Decompress a chunk of data using the gzip algorithm from Python or alternatives if possible        		 source code
         
        decBzip2(stream)
        Decompress a chunk of data using the bzip2 algorithm from Python        		 source code
         
        decZlib(stream)
        Decompress a chunk of data using the zlib algorithm from Python        		 source code
         
        decByteOffet_python(stream, size)
        Analyze a stream of char with any length of exception (2,4, or 8 bytes integers)        		 source code
         
        decByteOffet_weave(stream, size)
        Analyze a stream of char with any length of exception (2,4, or 8 bytes integers)        		 source code
         
        decByteOffet_numpy(stream, size=None)
        Analyze a stream of char with any length of exception: 2, 4, or 8 bytes integers        		 source code
         
        decByteOffet_cython(stream, size=None)
        Analyze a stream of char with any length of exception: 2, 4, or 8 bytes integers        		 source code
         
        compByteOffet_numpy(data)
        Compress a dataset into a string using the byte_offet algorithm        		 source code
         
        decTY1(raw_8, raw_16=None, raw_32=None)
        Modified byte offset decompressor used in Oxford Diffraction images        		 source code
         
        decKM4CCD(raw_8, raw_16=None, raw_32=None)
        Modified byte offset decompressor used in Oxford Diffraction images        		 source code
         
        compTY1(data)
        Modified byte offset compressor used in Oxford Diffraction images        		 source code
         
        decPCK(stream, dim1=None, dim2=None, overflowPix=None)
        Modified CCP4 pck decompressor used in MAR345 images        		 source code
         
        compPCK(data)
        Modified CCP4 pck compressor used in MAR345 images        		 source code
        Variables [hide private]
          logger = logging.getLogger("compression")
          __package__ = 'fabio'
        Function Details [hide private]

        decByteOffet_python(stream, size)

        		source code 

        Analyze a stream of char with any length of exception (2,4, or 8 bytes integers)

        Parameters:
        • stream - string representing the compressed data
        • size - the size of the output array (of longInts)
        Returns:
        1D-ndarray

        decByteOffet_weave(stream, size)

        		source code 

        Analyze a stream of char with any length of exception (2,4, or 8 bytes integers)

        Parameters:
        • stream - string representing the compressed data
        • size - the size of the output array (of longInts)
        Returns:
        1D-ndarray

        decByteOffet_numpy(stream, size=None)

        		source code  
        
Analyze a stream of char with any length of exception:
            2, 4, or 8 bytes integers

@param stream: string representing the compressed data
@param size: the size of the output array (of longInts)
@return: 1D-ndarray

        decByteOffet_cython(stream, size=None)

        		source code  
        
Analyze a stream of char with any length of exception:
            2, 4, or 8 bytes integers

@param stream: string representing the compressed data
@param size: the size of the output array (of longInts)
@return: 1D-ndarray

        compByteOffet_numpy(data)

        		source code 

        Compress a dataset into a string using the byte_offet algorithm

        Parameters:
        • data - ndarray
        Returns:
        string/bytes with compressed data

        test = numpy.array([0,1,2,127,0,1,2,128,0,1,2,32767,0,1,2,32768,0,1,2,2147483647,0,1,2,2147483648,0,1,2,128,129,130,32767,32768,128,129,130,32768,2147483647,2147483648])

        decTY1(raw_8, raw_16=None, raw_32=None)

        		source code 

        Modified byte offset decompressor used in Oxford Diffraction images

        Parameters:
        • raw_8 - strings containing raw data with integer 8 bits
        • raw_16 - strings containing raw data with integer 16 bits
        • raw_32 - strings containing raw data with integer 32 bits
        Returns:
        numpy.ndarray

        decKM4CCD(raw_8, raw_16=None, raw_32=None)

        		source code 

        Modified byte offset decompressor used in Oxford Diffraction images

        Parameters:
        • raw_8 - strings containing raw data with integer 8 bits
        • raw_16 - strings containing raw data with integer 16 bits
        • raw_32 - strings containing raw data with integer 32 bits
        Returns:
        numpy.ndarray

        compTY1(data)

        		source code 

        Modified byte offset compressor used in Oxford Diffraction images

        Parameters:
        • data - numpy.ndarray with the input data (integers!)
        Returns:
        3-tuple of strings: raw_8,raw_16,raw_32 containing raw data with integer of the given size

        decPCK(stream, dim1=None, dim2=None, overflowPix=None)

        		source code 

        Modified CCP4 pck decompressor used in MAR345 images

        Parameters:
        • stream - string or file
        Returns:
        numpy.ndarray (square array)

        compPCK(data)

        		source code 

        Modified CCP4 pck compressor used in MAR345 images

        Parameters:
        • data - numpy.ndarray (square array)
        Returns:
        compressed stream

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        Package fabio :: Module readbytestream
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        Module readbytestream

        source code

        
Reads a bytestream

Authors: Jon Wright    Henning O. Sorensen & Erik Knudsen
         ESRF          Risoe National Laboratory
        Functions [hide private]
         
        readbytestream(fil, offset, x, y, nbytespp, datatype='int', signed='n', swap='n', typeout=<type 'numpy.uint16'>)
        Reads in a bytestream from a file (which may be a string indicating a filename, or an already opened file (should be "rb")) offset is the position (in bytes) where the pixel data start nbytespp = number of bytes per pixel type can be int or float (4 bytes pp) or double (8 bytes pp) signed: normally signed data 'y', but 'n' to try to get back the right numbers when unsigned data are converted to signed (python once had no unsigned numeric types.) swap, normally do not bother, but 'y' to swap bytes typeout is the numpy type to output, normally uint16, but more if overflows occurred x and y are the pixel dimensions        		 source code
        Variables [hide private]
          logger = logging.getLogger("readbytestream")
          DATATYPES = {('double', 'y', 4): <type 'numpy.float64'>, ('flo...
          __package__ = 'fabio'
        Function Details [hide private]

        readbytestream(fil, offset, x, y, nbytespp, datatype='int', signed='n', swap='n', typeout=<type 'numpy.uint16'>)

        		source code 

        Reads in a bytestream from a file (which may be a string indicating a filename, or an already opened file (should be "rb")) offset is the position (in bytes) where the pixel data start nbytespp = number of bytes per pixel type can be int or float (4 bytes pp) or double (8 bytes pp) signed: normally signed data 'y', but 'n' to try to get back the right numbers when unsigned data are converted to signed (python once had no unsigned numeric types.) swap, normally do not bother, but 'y' to swap bytes typeout is the numpy type to output, normally uint16, but more if overflows occurred x and y are the pixel dimensions

        TODO : Read in regions of interest

        PLEASE LEAVE THE STRANGE INTERFACE ALONE - IT IS USEFUL FOR THE BRUKER FORMAT


        Variables Details [hide private]

        DATATYPES

        Value:
        {('double', 'y', 4): <type 'numpy.float64'>,
 ('float', 'y', 4): <type 'numpy.float32'>,
 ('int', 'n', 1): <type 'numpy.uint8'>,
 ('int', 'n', 2): <type 'numpy.uint16'>,
 ('int', 'n', 4): <type 'numpy.uint32'>,
 ('int', 'y', 1): <type 'numpy.int8'>,
 ('int', 'y', 2): <type 'numpy.int16'>,
 ('int', 'y', 4): <type 'numpy.int32'>}

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        Package fabio :: Module dm3image
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        Module dm3image

        source code

        
Authors: Henning O. Sorensen & Erik Knudsen
         Center for Fundamental Research: Metal Structures in Four Dimensions
         Risoe National Laboratory
         Frederiksborgvej 399
         DK-4000 Roskilde
         email:erik.knudsen@risoe.dk

        + Jon Wright, ESRF
        Classes [hide private]
          dm3image
        Read and try to write the dm3 data format
        Variables [hide private]
          logger = logging.getLogger("dm3image")
          DATA_TYPES = {2: <type 'numpy.int16'>, 3: <type 'numpy.int32'>...
          DATA_BYTES = {2: 2, 3: 4, 4: 2, 5: 4, 6: 4, 7: 8, 8: 1, 9: Non...
          __package__ = 'fabio'
        Variables Details [hide private]

        DATA_TYPES

        Value:
        {2: <type 'numpy.int16'>,
 3: <type 'numpy.int32'>,
 4: <type 'numpy.uint16'>,
 5: <type 'numpy.uint32'>,
 6: <type 'numpy.float32'>,
 7: <type 'float'>,
 8: <type 'numpy.int8'>,
 9: None,
...

        DATA_BYTES

        Value:
        {2: 2,
 3: 4,
 4: 2,
 5: 4,
 6: 4,
 7: 8,
 8: 1,
 9: None,
...

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        Package fabio :: Module byte_offset
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        Module byte_offset

        Authors: Jerome Kieffer, ESRF Email: jerome.kieffer@esrf.eu

        Cif Binary Files images are 2D images written by the Pilatus detector and others. They use a modified (simplified) byte-offset algorithm. This file contains the decompression function from a string to an int64 numpy array.

        This is Cython: convert it to pure C then compile it with gcc $ cython byte_offset.pyx

        Author: J\xc3\xa9r\xc3\xb4me Kieffer

        Contact: jerome.kieffer@esrf.eu

        Copyright: 2010, European Synchrotron Radiation Facility, Grenoble, France

        License: GPLv3+

        Variables [hide private]
          __package__ = 'fabio'
          __test__ = {}
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        Package fabio :: Module fabioutils
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        Source Code for Module fabio.fabioutils

          1  #!/usr/bin/env python 
  2  #coding: utf8 
  3   
  4  """ 
  5  General purpose utilities functions for fabio 
  6  """ 
  7  from __future__ import with_statement 
  8  import re, os, logging, threading, sys 
  9  import StringIO as stringIO 
 10  logger = logging.getLogger("fabioutils") 
 11  from compression import bz2, gzip 
 12  import traceback 
 13   
 14   
 15   
 16  FILETYPES = { 
 17      # extension NNNimage fabioclass 
 18      # type consistency - always use a list if one case is 
 19      'edf'    : ['edf'], 
 20      'cor'    : ['edf'], 
 21      'pnm'    : ['pnm'], 
 22      'pgm'    : ['pnm'], 
 23      'pbm'    : ['pnm'], 
 24      'tif'    : ['tif'], 
 25      'tiff'   : ['tif'], 
 26      'img'    : ['adsc', 'OXD', 'HiPiC'], 
 27      'mccd'   : ['marccd'], 
 28      'mar2300': ['mar345'], 
 29      'sfrm'   : ['bruker100'], 
 30      'msk'    : ['fit2dmask'], 
 31      'spr'    : ['fit2dspreadsheet'], 
 32      'dm3'    : ['dm3'], 
 33      'kcd'    : ['kcd'], 
 34      'cbf'    : ['cbf'], 
 35      'xml'    : ["xsd"], 
 36      'xsd'    : ["xsd"], 
 37               } 
 38   
 39  # Add bzipped and gzipped 
 40  for key in FILETYPES.keys(): 
 41      FILETYPES[key + ".bz2"] = FILETYPES[key] 
 42      FILETYPES[key + ".gz"] = FILETYPES[key] 
 43   
 44   
 45  # Compressors 
 46   
 47  COMPRESSORS = {} 
 48   
 49   
 50  dictAscii = {None:[chr(i) for i in range(32, 127)], 
 51             } 
 52   
 53  try: 
 54      lines = os.popen("gzip -h 2>&1").read() 
 55      # Looking for "usage" 
 56      if "sage" in lines: 
 57          COMPRESSORS['.gz'] = 'gzip -dc ' 
 58      else: 
 59          COMPRESSORS['.gz'] = None 
 60  except Exception: 
 61      COMPRESSORS['.gz'] = None 
 62   
 63  try: 
 64      lines = os.popen("bzip2 -h 2>&1").read() 
 65      # Looking for "usage"  
 66      if "sage" in lines: 
 67          COMPRESSORS['.bz2'] = 'bzip2 -dc ' 
 68      else: 
 69          COMPRESSORS['.bz2'] = None 
 70  except Exception: 
 71      COMPRESSORS['.bz2'] = None 

         72   
 73 -def deprecated(func): 

         74      """ 
 75      used to deprecate a function/method: prints a lot of warning messages to enforce the modifaction of the code 
 76      """ 
 77      def wrapper(*arg, **kw): 
 78          """ 
 79          decorator that deprecates the use of a function   
 80          """ 
 81          logger.warning("%s is Deprecated !!! %s" % (func.func_name, os.linesep.join([""] + traceback.format_stack()[:-1]))) 
 82          return func(*arg, **kw) 

         83      return wrapper 
 84   

         85   
 86 -def getnum(name): 

         87      """ 
 88      # try to figure out a file number 
 89      # guess it starts at the back 
 90      """ 
 91      stem , num, post_num = numstem(name) 
 92      try: 
 93          return int(num) 
 94      except ValueError: 
 95          return None 

         96   

         97 -class FilenameObject(object): 

         98      """ 
 99      The 'meaning' of a filename ...  
100      """ 

        101 -    def __init__(self, stem=None, 
102              num=None, 
103              directory=None, 
104              format=None, 
105              extension=None, 
106              postnum=None, 
107              digits=4, 
108              filename = None): 

        109          """ 
110          This class can either be instanciated by a set of parameters like  directory, prefix, num, extension, ...    
111           
112          @param stem: the stem is a kind of prefix (str) 
113          @param num: image number in the serie (int) 
114          @param directory: name of the directory (str) 
115          @param format: ?? 
116          @param extension:  
117          @param postnum:  
118          @param digits: Number of digits used to print num 
119           
120          Alternative constructor:  
121           
122          @param filename: fullpath of an image file to be deconstructed into directory, prefix, num, extension, ...  
123           
124          """ 
125   
126   
127          self.stem = stem 
128          self.num = num 
129          self.format = format 
130          self.extension = extension 
131          self.digits = digits 
132          self.postnum = postnum 
133          self.directory = directory 
134          self.compressed = None 
135          if filename is not None: 
136              self.deconstruct_filename(filename) 

        137               
138   

        139 -    def str(self): 

        140          """ Return a string representation """ 
141          fmt = "stem %s, num %s format %s extension %s " + \ 
142                  "postnum = %s digits %s dir %s" 
143          return fmt % tuple([str(x) for x in [ 
144                      self.stem , 
145                      self.num , 
146                      self.format , 
147                      self.extension , 
148                      self.postnum , 
149                      self.digits , 
150                      self.directory ] ]) 

        151      __repr__ = str 
152   

        153 -    def tostring(self): 

        154          """ 
155          convert yourself to a string 
156          """ 
157          name = self.stem 
158          if self.digits is not None and self.num is not None: 
159              fmt = "%0" + str(self.digits) + "d" 
160              name += fmt % self.num 
161          if self.postnum is not None: 
162              name += self.postnum 
163          if self.extension is not None: 
164              name += self.extension 
165          if self.directory is not None: 
166              name = os.path.join(self.directory, name) 
167          return name 

        168   
169   

        170 -    def deconstruct_filename(self, filename): 

        171          """ 
172          Break up a filename to get image type and number 
173          """ 
174          direc, name = os.path.split(filename) 
175          direc = direc or None 
176          parts = name.split(".") 
177          compressed = False 
178          stem = parts[0] 
179          extn = "" 
180          postnum = "" 
181          ndigit = 4 
182          num = None 
183          typ = None 
184          if parts[-1] in ["gz", "bz2"]: 
185              extn = "." + parts[-1] 
186              parts = parts[:-1] 
187              compressed = True 
188          if parts[-1] in FILETYPES.keys(): 
189              typ = FILETYPES[parts[-1]] 
190              extn = "." + parts[-1] + extn 
191              try: 
192                  stem, numstring, postnum = numstem(".".join(parts[:-1])) 
193                  num = int(numstring) 
194                  ndigit = len(numstring) 
195              except Exception, err: 
196                  # There is no number - hence make num be None, not 0 
197                  logger.debug("l176: %s" % err) 
198                  num = None 
199                  stem = "".join(parts[:-1]) 
200          else: 
201              # Probably two type left 
202              if len(parts) == 1: 
203                  # Probably GE format stem_numb 
204                  parts2 = parts[0].split("_") 
205                  if parts2[-1].isdigit(): 
206                      num = int(parts2[-1]) 
207                      ndigit = len(parts2[-1]) 
208                      typ = ['GE'] 
209                      stem = "_".join(parts2[:-1]) + "_" 
210              else: 
211                  try: 
212                      num = int(parts[-1]) 
213                      ndigit = len(parts[-1]) 
214                      typ = ['bruker'] 
215                      stem = ".".join(parts[:-1]) + "." 
216                  except Exception, err: 
217                      logger.debug("l196: %s" % err) 
218                      typ = None 
219                      extn = "." + parts[-1] + extn 
220                      numstring = "" 
221                      try: 
222                          stem , numstring, postnum = numstem(".".join(parts[:-1])) 
223                      except Exception, err: 
224                          logger.debug("l202: %s" % err) 
225                          raise 
226                      if numstring.isdigit(): 
227                          num = int(numstring) 
228                          ndigit = len(numstring) 
229                  #            raise Exception("Cannot decode "+filename) 
230   
231          self.stem = stem 
232          self.num = num 
233          self.directory = direc 
234          self.format = typ 
235          self.extension = extn 
236          self.postnum = postnum 
237          self.digits = ndigit 
238          self.compressed = compressed 

        239   

        240 -def numstem(name): 

        241      """ cant see how to do without reversing strings 
242      Match 1 or more digits going backwards from the end of the string 
243      """ 
244      reg = re.compile(r"^(.*?)(-?[0-9]{0,9})(\D*)$") 
245      #reg = re.compile("""(\D*)(\d\d*)(\w*)""") 
246      try: 
247          res = reg.match(name).groups() 
248          #res = reg.match(name[::-1]).groups() 
249          #return [ r[::-1] for r in res[::-1]] 
250          if len(res[0]) == len(res[1]) == 0: # Hack for file without number 
251              return [res[2], '', ''] 
252          return [ r for r in res] 
253      except AttributeError: # no digits found 
254          return [name, "", ""] 

        255   

        256  @deprecated 
257 -def deconstruct_filename(filename): 

        258      """ 
259      Function for backward compatibility. 
260      Deprecated 
261      """ 
262      return FilenameObject(filename=filename) 

        263   

        264 -def construct_filename(filename, frame=None): 

        265      "Try to construct the filename for a given frame" 
266      fobj = FilenameObject(filename=filename) 
267      if frame is not None: 
268          fobj.num = frame 
269      return fobj.tostring() 

        270   

        271 -def next_filename(name, padding=True): 

        272      """ increment number """ 
273      fobj = FilenameObject(filename=name) 
274      fobj.num += 1 
275      if not padding: 
276          fobj.digits = 0 
277      return fobj.tostring() 

        278   

        279 -def previous_filename(name, padding=True): 

        280      """ decrement number """ 
281      fobj = FilenameObject(filename=name) 
282      fobj.num -= 1 
283      if not padding: 
284          fobj.digits = 0 
285      return fobj.tostring() 

        286   

        287 -def jump_filename(name, num, padding=True): 

        288      """ jump to number """ 
289      fobj = FilenameObject(filename=name) 
290      fobj.num = num 
291      if not padding: 
292          fobj.digits = 0 
293      return fobj.tostring() 

        294   

        295   
296 -def extract_filenumber(name): 

        297      """ extract file number """ 
298      fobj = FilenameObject(filename=name) 
299      return fobj.num 

        300   

        301 -def isAscii(name, listExcluded=None): 

        302      """ 
303      @param name: string to check 
304      @param listExcluded: list of char or string excluded. 
305      @return: True of False whether  name is pure ascii or not 
306      """ 
307      isascii = None 
308      try: 
309          name.decode("ascii") 
310      except UnicodeDecodeError: 
311          isascii = False 
312      else: 
313          if listExcluded: 
314              isascii = not(any(bad in  name for bad in listExcluded)) 
315          else: 
316              isascii = True 
317      return isascii 

        318   

        319 -def toAscii(name, excluded=None): 

        320      """ 
321      @param name: string to check 
322      @param excluded: tuple of char or string excluded (not list: they are mutable). 
323      @return: the name with all non valid char removed 
324      """ 
325      if excluded not in dictAscii: 
326          ascii = dictAscii[None][:] 
327          for i in excluded: 
328              if i in ascii: 
329                  ascii.remove(i) 
330              else: 
331                  logger.error("toAscii: % not in ascii table" % i) 
332          dictAscii[excluded] = ascii 
333      else: 
334          ascii = dictAscii[excluded] 
335      out = [i for i in str(name) if i in ascii] 
336      return "".join(out) 

        337   

        338 -def nice_int(s): 

        339      """  
340      Workaround that int('1.0') raises an exception  
341       
342      @param s: string to be converted to integer 
343      """ 
344      try: 
345          return int(s) 
346      except ValueError: 
347          return int(float(s)) 

        348   

        349   
350 -class StringIO(stringIO.StringIO): 

        351      """ 
352      just an interface providing the name and mode property to a StringIO 
353   
354      BugFix for MacOSX mainly 
355      """ 

        356 -    def __init__(self, data, fname=None, mode="r"): 

        357          stringIO.StringIO.__init__(self, data) 
358          self.closed = False 
359          if fname == None: 
360              self.name = "fabioStream" 
361          else: 
362              self.name = fname 
363          self.mode = mode 
364          self.lock = threading.Semaphore() 
365          self.__size = None 

        366       

        367 -    def getSize(self): 

        368          if self.__size is None: 
369              logger.debug("Measuring size of %s" % self.name) 
370              with self.lock: 
371                  pos = self.tell() 
372                  self.seek(0, os.SEEK_END) 
373                  self.__size = self.tell() 
374                  self.seek(pos) 
375          return self.__size 

        376 -    def setSize(self, size): 

        377          self.__size = size 

        378      size = property(getSize, setSize) 

        379   

        380 -class File(file): 

        381      """ 
382      wrapper for "file" with locking 
383      """ 

        384 -    def __init__(self, name, mode="rb", buffering=0): 

        385          """file(name[, mode[, buffering]]) -> file object 
386               
387          Open a file.  The mode can be 'r', 'w' or 'a' for reading (default), 
388          writing or appending.  The file will be created if it doesn't exist 
389          when opened for writing or appending; it will be truncated when 
390          opened for writing.  Add a 'b' to the mode for binary files. 
391          Add a '+' to the mode to allow simultaneous reading and writing. 
392          If the buffering argument is given, 0 means unbuffered, 1 means line 
393          buffered, and larger numbers specify the buffer size.  The preferred way 
394          to open a file is with the builtin open() function. 
395          Add a 'U' to mode to open the file for input with universal newline 
396          support.  Any line ending in the input file will be seen as a '\n' 
397          in Python.  Also, a file so opened gains the attribute 'newlines'; 
398          the value for this attribute is one of None (no newline read yet), 
399          '\r', '\n', '\r\n' or a tuple containing all the newline types seen. 
400           
401          'U' cannot be combined with 'w' or '+' mode. 
402          """ 
403          file.__init__(self, name, mode, buffering) 
404          self.lock = threading.Semaphore() 
405          self.__size = None 

        406 -    def getSize(self): 

        407          if self.__size is None: 
408              logger.debug("Measuring size of %s" % self.name) 
409              with self.lock: 
410                  pos = self.tell() 
411                  self.seek(0, os.SEEK_END) 
412                  self.__size = self.tell() 
413                  self.seek(pos) 
414          return self.__size 

        415 -    def setSize(self, size): 

        416          self.__size = size 

        417      size = property(getSize, setSize) 

        418   

        419 -class UnknownCompressedFile(File): 

        420      """ 
421      wrapper for "File" with locking 
422      """ 

        423 -    def __init__(self, name, mode="rb", buffering=0): 

        424          logger.warning("No decompressor found for this type of file (are gzip anf bz2 installed ???") 
425          File.__init__(self, name, mode, buffering) 

        426   
427  if gzip is None: 
428      GzipFile = UnknownCompressedFile 
429  else: 

        430 -    class GzipFile(gzip.GzipFile): 

        431          """ 
432          Just a wrapper forgzip.GzipFile providing the correct seek capabilities for python 2.5    
433          """ 

        434 -        def __init__(self, filename=None, mode=None, compresslevel=9, fileobj=None): 

        435              """ 
436              Wrapper with locking for constructor for the GzipFile class. 
437               
438              At least one of fileobj and filename must be given a 
439              non-trivial value. 
440               
441              The new class instance is based on fileobj, which can be a regular 
442              file, a StringIO object, or any other object which simulates a file. 
443              It defaults to None, in which case filename is opened to provide 
444              a file object. 
445               
446              When fileobj is not None, the filename argument is only used to be 
447              included in the gzip file header, which may includes the original 
448              filename of the uncompressed file.  It defaults to the filename of 
449              fileobj, if discernible; otherwise, it defaults to the empty string, 
450              and in this case the original filename is not included in the header. 
451               
452              The mode argument can be any of 'r', 'rb', 'a', 'ab', 'w', or 'wb', 
453              depending on whether the file will be read or written.  The default 
454              is the mode of fileobj if discernible; otherwise, the default is 'rb'. 
455              Be aware that only the 'rb', 'ab', and 'wb' values should be used 
456              for cross-platform portability. 
457               
458              The compresslevel argument is an integer from 1 to 9 controlling the 
459              level of compression; 1 is fastest and produces the least compression, 
460              and 9 is slowest and produces the most compression.  The default is 9. 
461              """ 
462              gzip.GzipFile.__init__(self, filename, mode, compresslevel, fileobj) 
463              self.lock = threading.Semaphore() 
464              self.__size = None 

        465   
466   
467          if sys.version_info < (2, 7): 

        468 -            def getSize(self): 

        469                  if self.__size is None: 
470                      logger.debug("Measuring size of %s" % self.name) 
471                      with open(self.filename, "rb") as f: 
472                          f.seek(-4) 
473                          self.__size = numpy.fromstring(f.read(4), dtype=numpy.uint32) 
474                  return self.__size 

        475 -            def setSize(self, value): 

        476                  self.__size = value 

        477              size = property(getSize, setSize) 
478              @property 

        479 -            def closed(self): 

        480                  return self.fileobj is None 

        481   

        482 -            def seek(self, offset, whence=os.SEEK_SET): 

        483                  """ 
484                  Move to new file position. 
485           
486                  Argument offset is a byte count.  Optional argument whence defaults to 
487                  0 (offset from start of file, offset should be >= 0); other values are 1 
488                  (move relative to current position, positive or negative), and 2 (move 
489                  relative to end of file, usually negative, although many platforms allow 
490                  seeking beyond the end of a file).  If the file is opened in text mode, 
491                  only offsets returned by tell() are legal.  Use of other offsets causes 
492                  undefined behavior. 
493                   
494                  This is a wrapper for seek to ensure compatibility with old python 2.5 
495                  """ 
496                  if whence == os.SEEK_SET: 
497                      gzip.GzipFile.seek(self, offset) 
498                  elif whence == os.SEEK_CUR: 
499                      gzip.GzipFile.seek(self, offset + self.tell()) 
500                  elif whence == os.SEEK_END: 
501                      gzip.GzipFile.seek(self, -1) 
502                      gzip.GzipFile.seek(self, offset + self.tell()) 

        503   
504  if bz2 is None: 
505      BZ2File = UnknownCompressedFile 
506  else: 

        507 -    class BZ2File(bz2.BZ2File): 

        508          "Wrapper with lock" 

        509 -        def __init__(self, name , mode='r', buffering=0, compresslevel=9): 

        510              """ 
511              BZ2File(name [, mode='r', buffering=0, compresslevel=9]) -> file object 
512               
513              Open a bz2 file. The mode can be 'r' or 'w', for reading (default) or 
514              writing. When opened for writing, the file will be created if it doesn't 
515              exist, and truncated otherwise. If the buffering argument is given, 0 means 
516              unbuffered, and larger numbers specify the buffer size. If compresslevel 
517              is given, must be a number between 1 and 9. 
518               
519              Add a 'U' to mode to open the file for input with universal newline 
520              support. Any line ending in the input file will be seen as a '\n' in 
521              Python. Also, a file so opened gains the attribute 'newlines'; the value 
522              for this attribute is one of None (no newline read yet), '\r', '\n', 
523              '\r\n' or a tuple containing all the newline types seen. Universal 
524              newlines are available only when reading. 
525              """ 
526              bz2.BZ2File.__init__(self, name , mode, buffering, compresslevel) 
527              self.lock = threading.Semaphore() 
528              self.__size = None 

        529 -        def getSize(self): 

        530              if self.__size is None: 
531                  logger.debug("Measuring size of %s" % self.name) 
532                  with self.lock: 
533                      pos = self.tell() 
534                      all = self.read() 
535                      self.__size = self.tell() 
536                      self.seek(pos) 
537              return self.__size 

        538 -        def setSize(self, value): 

        539              self.__size = value 

        540          size = property(getSize, setSize) 

        541

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        fabio-0.1.3/epydoc/fabio.edfimage.edfimage-class.html0000644000175000017500000021537112126623347023232 0ustar jeromejerome00000000000000 fabio.edfimage.edfimage
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        Package fabio :: Module edfimage :: Class edfimage
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        Class edfimage

        source code

                   object --+    
                    |    
fabioimage.fabioimage --+
                        |
                       edfimage

        Read and try to write the ESRF edf data format

        Instance Methods [hide private]
         
        __init__(self, data=None, header=None, header_keys=None, frames=None)
        Set up initial values        		 source code
         
        _readheader(self, infile)
        Read all headers in a file and populate self.header data is not yet populated        		 source code
         
        read(self, fname, frame=None)
        Read in header into self.header and...        		 source code
         
        swap_needed(self)
        Decide if we need to byteswap        		 source code
         
        unpack(self)
        Unpack a binary blob according to the specification given in the header and return the dataset        		 source code
         
        getframe(self, num)
        returns the file numbered 'num' in the series as a fabioimage        		 source code
         
        previous(self)
        returns the previous file in the series as a fabioimage        		 source code
         
        next(self)
        returns the next file in the series as a fabioimage        		 source code
         
        write(self, fname, force_type=None, fit2dMode=False)
        Try to write a file check we can write zipped also mimics that fabian was writing uint16 (we sometimes want floats)        		 source code
         
        appendFrame(self, frame=None, data=None, header=None)
        Method used add a frame to an EDF file        		 source code
         
        deleteFrame(self, frameNb=None)
        Method used to remove a frame from an EDF image.        		 source code
         
        fastReadData(self, filename=None)
        This is a special method that will read and return the data from another file ...        		 source code
        numpy 2darray
        fastReadROI(self, filename, coords=None)
        Method reading Region of Interest of another file based on metadata available in current edfimage.        		 source code
         
        getNbFrames(self)
        Getter for number of frames        		 source code
         
        setNbFrames(self, val)
        Setter for number of frames ...        		 source code
         
        getHeader(self)
        Getter for the headers.        		 source code
         
        setHeader(self, _dictHeader)
        Enforces the propagation of the header to the list of frames        		 source code
         
        delHeader(self)
        Deleter for edf header        		 source code
         
        getHeaderKeys(self)
        Getter for edf header_keys        		 source code
         
        setHeaderKeys(self, _listtHeader)
        Enforces the propagation of the header_keys to the list of frames        		 source code
         
        delHeaderKeys(self)
        Deleter for edf header_keys        		 source code
        numpy.ndarray
        getData(self)
        getter for edf Data        		 source code
         
        setData(self, _data)
        Enforces the propagation of the data to the list of frames        		 source code
         
        delData(self)
        deleter for edf Data        		 source code
        dict
        getCapsHeader(self)
        getter for edf headers keys in upper case        		 source code
         
        setCapsHeader(self, _data)
        Enforces the propagation of the header_keys to the list of frames        		 source code
         
        delCapsHeader(self)
        deleter for edf capsHeader        		 source code
         
        getDim1(self) source code
         
        setDim1(self, _iVal) source code
         
        getDim2(self) source code
         
        setDim2(self, _iVal) source code
         
        getDims(self) source code
         
        getByteCode(self) source code
         
        setByteCode(self, _iVal) source code
         
        getBpp(self) source code
         
        setBpp(self, _iVal) source code

        Inherited from fabioimage.fabioimage: add, convert, getclassname, getheader, getmax, getmean, getmin, getstddev, integrate_area, load, make_slice, readROI, readheader, rebin, resetvals, save, toPIL16, update_header

        Inherited from fabioimage.fabioimage (private): _compressed_stream, _open

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Static Methods [hide private]
         
        checkHeader(header=None)
        Empty for fabioimage but may be populated by others classes        		 source code
         
        _readHeaderBlock(infile)
        Read in a header in some EDF format from an already open file        		 source code

        Inherited from fabioimage.fabioimage: checkData

        Class Variables [hide private]

        Inherited from fabioimage.fabioimage (private): _need_a_real_file, _need_a_seek_to_read

        Properties [hide private]
          nframes
        Getter for number of frames
          header
        property: header of EDF file
          header_keys
        property: header_keys of EDF file
          data
        property: data of EDF file
          capsHeader
        property: capsHeader of EDF file, i.e.
          dim1
          dim2
          dims
          bytecode
          bpp

        Inherited from fabioimage.fabioimage: classname

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, data=None, header=None, header_keys=None, frames=None)
        (Constructor)

        		source code 

        Set up initial values

        Overrides: object.__init__
        (inherited documentation)

        checkHeader(header=None)
        Static Method

        		source code 

        Empty for fabioimage but may be populated by others classes

        Overrides: fabioimage.fabioimage.checkHeader

        _readHeaderBlock(infile)
        Static Method

        		source code 

        Read in a header in some EDF format from an already open file

        Parameters:
        • infile - file object open in read mode
        Returns:
        string (or None if no header was found.

        _readheader(self, infile)

        		source code 

        Read all headers in a file and populate self.header data is not yet populated

        Parameters:
        • infile (file object open in read mode)
        Overrides: fabioimage.fabioimage._readheader

        read(self, fname, frame=None)

        		source code  
        
Read in header into self.header and
    the data   into self.data
        Overrides: fabioimage.fabioimage.read

        unpack(self)

        		source code 

        Unpack a binary blob according to the specification given in the header and return the dataset

        Returns:
        dataset as numpy.ndarray

        getframe(self, num)

        		source code 

        returns the file numbered 'num' in the series as a fabioimage

        Overrides: fabioimage.fabioimage.getframe

        previous(self)

        		source code 

        returns the previous file in the series as a fabioimage

        Overrides: fabioimage.fabioimage.previous

        next(self)

        		source code 

        returns the next file in the series as a fabioimage

        Overrides: fabioimage.fabioimage.next

        write(self, fname, force_type=None, fit2dMode=False)

        		source code 

        Try to write a file check we can write zipped also mimics that fabian was writing uint16 (we sometimes want floats)

        Parameters:
        • force_type - can be numpy.uint16 or simply "float"
        Returns:
        None
        Overrides: fabioimage.fabioimage.write

        appendFrame(self, frame=None, data=None, header=None)

        		source code 

        Method used add a frame to an EDF file

        Parameters:
        • frame (instance of Frame) - frame to append to edf image
        Returns:
        None

        deleteFrame(self, frameNb=None)

        		source code 

        Method used to remove a frame from an EDF image. by default the last one is removed.

        Parameters:
        • frameNb (integer) - frame number to remove, by default the last.
        Returns:
        None

        fastReadData(self, filename=None)

        		source code 

        This is a special method that will read and return the data from another file ... The aim is performances, ... but only supports uncompressed files.

        Returns:
        data from another file using positions from current edfimage

        fastReadROI(self, filename, coords=None)

        		source code 

        Method reading Region of Interest of another file based on metadata available in current edfimage. The aim is performances, ... but only supports uncompressed files.

        Returns: numpy 2darray
        ROI-data from another file using positions from current edfimage

        setNbFrames(self, val)

        		source code 

        Setter for number of frames ... should do nothing. Here just to avoid bugs

        getHeader(self)

        		source code 

        Getter for the headers. used by the property header,

        setHeaderKeys(self, _listtHeader)

        		source code 

        Enforces the propagation of the header_keys to the list of frames

        Parameters:
        • _listtHeader (python list) - list of the (ordered) keys in the header

        getData(self)

        		source code 

        getter for edf Data

        Returns: numpy.ndarray
        data for current frame

        setData(self, _data)

        		source code 

        Enforces the propagation of the data to the list of frames

        Parameters:
        • _data - numpy array representing data

        getCapsHeader(self)

        		source code 

        getter for edf headers keys in upper case

        Returns: dict
        data for current frame

        setCapsHeader(self, _data)

        		source code 

        Enforces the propagation of the header_keys to the list of frames

        Parameters:
        • _data - numpy array representing data

        Property Details [hide private]

        nframes

        Getter for number of frames

        Get Method:
        getNbFrames(self) - Getter for number of frames
        Set Method:
        setNbFrames(self, val) - Setter for number of frames ...
        Delete Method:
        'property: number of frames in EDF file'

        header

        property: header of EDF file

        Get Method:
        getHeader(self) - Getter for the headers.
        Set Method:
        setHeader(self, _dictHeader) - Enforces the propagation of the header to the list of frames
        Delete Method:
        delHeader(self) - Deleter for edf header

        header_keys

        property: header_keys of EDF file

        Get Method:
        getHeaderKeys(self) - Getter for edf header_keys
        Set Method:
        setHeaderKeys(self, _listtHeader) - Enforces the propagation of the header_keys to the list of frames
        Delete Method:
        delHeaderKeys(self) - Deleter for edf header_keys

        data

        property: data of EDF file

        Get Method:
        getData(self) - getter for edf Data
        Set Method:
        setData(self, _data) - Enforces the propagation of the data to the list of frames
        Delete Method:
        delData(self) - deleter for edf Data

        capsHeader

        property: capsHeader of EDF file, i.e. the keys of the header in UPPER case.

        Get Method:
        getCapsHeader(self) - getter for edf headers keys in upper case
        Set Method:
        setCapsHeader(self, _data) - Enforces the propagation of the header_keys to the list of frames
        Delete Method:
        delCapsHeader(self) - deleter for edf capsHeader

        dim1

        Get Method:
        getDim1(self)
        Set Method:
        setDim1(self, _iVal)

        dim2

        Get Method:
        getDim2(self)
        Set Method:
        setDim2(self, _iVal)

        dims

        Get Method:
        getDims(self)

        bytecode

        Get Method:
        getByteCode(self)
        Set Method:
        setByteCode(self, _iVal)

        bpp

        Get Method:
        getBpp(self)
        Set Method:
        setBpp(self, _iVal)

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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:40 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/toc-fabio.cbfimage-module.html0000644000175000017500000000335712120434325022416 0ustar jeromejerome00000000000000 cbfimage

        Module cbfimage

        Classes

        CIF
        cbfimage

        Variables

        DATA_TYPES
        MINIMUM_KEYS
        PADDING
        STARTER
        __package__
        logger
        [hide private] fabio-0.1.3/epydoc/fabio.openimage-pysrc.html0000644000175000017500000020336412126623347021727 0ustar jeromejerome00000000000000 fabio.openimage
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        Package fabio :: Module openimage
        [hide private]
        [frames] | no frames]

        Source Code for Module fabio.openimage

          1  """ 
  2   
  3  Authors: Henning O. Sorensen & Erik Knudsen 
  4           Center for Fundamental Research: Metal Structures in Four Dimensions 
  5           Risoe National Laboratory 
  6           Frederiksborgvej 399 
  7           DK-4000 Roskilde 
  8           email:henning.sorensen@risoe.dk 
  9   
 10  mods for fabio by JPW 
 11   
 12  """ 
 13  import sys, logging 
 14  logger = logging.getLogger("openimage") 
 15  from fabioutils  import FilenameObject 
 16  from fabioimage import fabioimage 
 17  import edfimage 
 18  import adscimage 
 19  import tifimage 
 20  import marccdimage 
 21  import mar345image 
 22  import fit2dmaskimage 
 23  import brukerimage 
 24  import bruker100image 
 25  import pnmimage 
 26  import GEimage 
 27  import OXDimage 
 28  import dm3image 
 29  import HiPiCimage 
 30  import pilatusimage 
 31  import fit2dspreadsheetimage 
 32  import kcdimage 
 33  import cbfimage 
 34  import xsdimage 
 35  import binaryimage 
 36   
 37  MAGIC_NUMBERS = [ 
 38      # "\42\5a" : 'bzipped' 
 39      # "\1f\8b" : 'gzipped' 
 40      ("FORMAT :        86" , 'bruker'), 
 41      ("\x4d\x4d\x00\x2a"   , 'tif') , 
 42      # The marCCD and Pilatus formats are both standard tif with a header 
 43      # hopefully these byte patterns are unique for the formats 
 44      # If not the image will be read, but the is missing  
 45      ("\x49\x49\x2a\x00\x08\x00"   , 'marccd') , 
 46      ("\x49\x49\x2a\x00\x82\x00"   , 'pilatus') , 
 47      ("\x49\x49\x2a\x00"   , 'tif') , 
 48      # ADSC must come before edf 
 49      ("{\nHEA"             , 'adsc'), 
 50      ("{"                  , 'edf'), 
 51      ("\r{"                , 'edf'), 
 52      ("\n{"                , 'edf'), 
 53      ("ADEPT"              , 'GE'), 
 54      ("OD"                 , 'OXD'), 
 55      ("IM"                 , 'HiPiC'), 
 56      ('\x2d\x04'           , 'mar345'), 
 57      ('\xd2\x04'           , 'mar345'), 
 58      ('\x04\x2d'           , 'mar345'), #some machines may need byteswapping 
 59      ('\x04\xd2'           , 'mar345'), 
 60      # hint : MASK in 32 bit 
 61      ('M\x00\x00\x00A\x00\x00\x00S\x00\x00\x00K\x00\x00\x00' , 'fit2dmask') , 
 62      ('\x00\x00\x00\x03'   , 'dm3'), 
 63      ("No"                 , "kcd"), 
 64      ("<"                  , "xsd") 
 65      ] 
 66   

         67 -def do_magic(byts): 

         68      """ Try to interpret the bytes starting the file as a magic number """ 
 69      for magic, format_type in MAGIC_NUMBERS: 
 70          if byts.find(magic) == 0: 
 71              return format_type 
 72          if 0: # debugging - bruker needed 18 bytes below 
 73              logger.debug("m: %s f: %s", magic, format_type) 
 74              logger.debug("bytes: %s len(bytes) %s", magic, len(magic)) 
 75              logger.debug("found: %s", byts.find(magic)) 
 76              for i in range(len(magic)): 
 77                  logger.debug("%s %s %s %s ", ord(magic[i]), ord(byts[i]), magic[i], byts[i]) 
 78      raise Exception("Could not interpret magic string") 

         79   
 80   

         81 -def openimage(filename, frame=None): 

         82      """ Try to open an image """ 
 83      if isinstance(filename, FilenameObject): 
 84          try: 
 85              logger.debug("Attempting to open %s" % (filename.tostring())) 
 86              obj = _openimage(filename.tostring()) 
 87              logger.debug("Attempting to read frame %s from %s" % (frame, 
 88                  filename.tostring())) 
 89              obj = obj.read(filename.tostring(), frame) 
 90          except Exception, ex: 
 91              # multiframe file 
 92              #logger.debug( "DEBUG: multiframe file, start # %d"%( 
 93              #    filename.num) 
 94              logger.debug("Exception %s, trying name %s" % (ex, filename.stem)) 
 95              obj = _openimage(filename.stem) 
 96              logger.debug("Reading frame %s from %s" % (filename.num, filename.stem)) 
 97              obj.read(filename.stem, frame=filename.num) 
 98      else: 
 99          logger.debug("Attempting to open %s" % (filename)) 
100          obj = _openimage(filename) 
101          logger.debug("Attempting to read frame %s from %s" % (frame, filename)) 
102          obj = obj.read(filename, frame) 
103      return obj 

        104   
105   

        106 -def openheader(filename): 

        107      """ return only the header""" 
108      obj = _openimage(filename) 
109      obj.readheader(filename) 
110      return obj 

        111   
112   

        113 -def _openimage(filename): 

        114      """  
115      determine which format for a filename 
116      and return appropriate class which can be used for opening the image 
117      """ 
118      try: 
119          imo = fabioimage() 
120          byts = imo._open(filename).read(18) 
121          filetype = do_magic(byts) 
122          if filetype == "marccd" and filename.find("mccd") == -1: 
123              # Cannot see a way around this. Need to find something 
124              # to distinguish mccd from regular tif... 
125              filetype = "tif" 
126      except IOError, error: 
127          logger.error("%s: File probably does not exist", error) 
128          raise error 
129      except: 
130          try: 
131              file_obj = FilenameObject(filename=filename) 
132              if file_obj == None: 
133                  raise Exception("Unable to deconstruct filename") 
134              if (file_obj.format is not None) and\ 
135                  len(file_obj.format) != 1 and \ 
136                  type(file_obj.format) != type(["list"]): 
137                  # one of OXD/ ADSC - should have got in previous 
138                  raise Exception("openimage failed on magic bytes & name guess") 
139              filetype = file_obj.format 
140              #UNUSED filenumber = file_obj.num 
141          except Exception, error: 
142              logger.error(error) 
143              import traceback 
144              traceback.print_exc() 
145              raise Exception("Fabio could not identify " + filename) 
146      klass_name = "".join(filetype) + 'image' 
147      module = sys.modules.get("fabio." + klass_name, None) 
148      if module is not None: 
149          if hasattr(module, klass_name): 
150              klass = getattr(module, klass_name) 
151          else: 
152              raise Exception("Module %s has no image class" % module) 
153      else: 
154          raise Exception("Filetype not known %s %s" % (filename, klass_name)) 
155      obj = klass() 
156      # skip the read for read header 
157      return obj 

        158

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        fabio-0.1.3/epydoc/fabio.marccdimage.marccdimage-class.html0000644000175000017500000003721612126623347024420 0ustar jeromejerome00000000000000 fabio.marccdimage.marccdimage
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        Package fabio :: Module marccdimage :: Class marccdimage
        [hide private]
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        Class marccdimage

        source code

                   object --+        
                    |        
fabioimage.fabioimage --+    
                        |    
        tifimage.tifimage --+
                            |
                           marccdimage

        Read in data in mar ccd format, also MarMosaic images, including header info

        Instance Methods [hide private]
         
        _readheader(self, infile)
        Parser based approach Gets all entries        		 source code
         
        _read(self, fname)
        inherited from tifimage ...        		 source code

        Inherited from tifimage.tifimage: __init__, read, write

        Inherited from fabioimage.fabioimage: add, convert, getclassname, getframe, getheader, getmax, getmean, getmin, getstddev, integrate_area, load, make_slice, next, previous, readROI, readheader, rebin, resetvals, save, toPIL16, update_header

        Inherited from fabioimage.fabioimage (private): _compressed_stream, _open

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Static Methods [hide private]

        Inherited from fabioimage.fabioimage: checkData, checkHeader

        Class Variables [hide private]

        Inherited from tifimage.tifimage (private): _need_a_seek_to_read

        Inherited from fabioimage.fabioimage (private): _need_a_real_file

        Properties [hide private]

        Inherited from fabioimage.fabioimage: classname

        Inherited from object: __class__

        Method Details [hide private]

        _readheader(self, infile)

        		source code 

        Parser based approach Gets all entries

        Overrides: fabioimage.fabioimage._readheader

        _read(self, fname)

        		source code 

        inherited from tifimage ... a marccd image *is a* tif image just with a header


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        Module mytest

        source code

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        fabio-0.1.3/epydoc/fabio.pilatusimage.pilatusimage-class.html0000644000175000017500000003723012126623347025074 0ustar jeromejerome00000000000000 fabio.pilatusimage.pilatusimage
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        Package fabio :: Module pilatusimage :: Class pilatusimage
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        Class pilatusimage

        source code

                   object --+        
                    |        
fabioimage.fabioimage --+    
                        |    
        tifimage.tifimage --+
                            |
                           pilatusimage

        Read in Pilatus format, also pilatus images, including header info

        Instance Methods [hide private]
         
        _readheader(self, infile)
        Parser based approach Gets all entries        		 source code
         
        _read(self, fname)
        inherited from tifimage ...        		 source code

        Inherited from tifimage.tifimage: __init__, read, write

        Inherited from fabioimage.fabioimage: add, convert, getclassname, getframe, getheader, getmax, getmean, getmin, getstddev, integrate_area, load, make_slice, next, previous, readROI, readheader, rebin, resetvals, save, toPIL16, update_header

        Inherited from fabioimage.fabioimage (private): _compressed_stream, _open

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Static Methods [hide private]

        Inherited from fabioimage.fabioimage: checkData, checkHeader

        Class Variables [hide private]

        Inherited from tifimage.tifimage (private): _need_a_seek_to_read

        Inherited from fabioimage.fabioimage (private): _need_a_real_file

        Properties [hide private]

        Inherited from fabioimage.fabioimage: classname

        Inherited from object: __class__

        Method Details [hide private]

        _readheader(self, infile)

        		source code 

        Parser based approach Gets all entries

        Overrides: fabioimage.fabioimage._readheader

        _read(self, fname)

        		source code 

        inherited from tifimage ... a Pilatus image *is a* tif image just with a header


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        fabio-0.1.3/epydoc/toc-fabio.marccdimage-module.html0000644000175000017500000000421312120434325023105 0ustar jeromejerome00000000000000 marccdimage

        Module marccdimage

        Classes

        marccdimage

        Functions

        interpret_header
        make_format

        Variables

        CDEFINITION
        C_SIZES
        C_TO_STRUCT
        HEADER_FORMAT
        HEADER_NAMES
        MAXIMAGES
        __package__
        logger
        [hide private] fabio-0.1.3/epydoc/fabio.xsdimage-module.html0000644000175000017500000001462312126623347021707 0ustar jeromejerome00000000000000 fabio.xsdimage
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        Package fabio :: Module xsdimage
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        Module xsdimage

        source code

        
Authors: Jérôme Kieffer, ESRF 
         email:jerome.kieffer@esrf.fr

XSDimge are XML files containing numpy arrays

        Author: J\xc3\xa9r\xc3\xb4me Kieffer

        Contact: jerome.kieffer@esrf.eu

        Copyright: European Synchrotron Radiation Facility, Grenoble, France

        License: GPLv3+

        Classes [hide private]
          xsdimage
        Read the XSDataImage XML File data format
        Variables [hide private]
          logger = logging.getLogger("xsdimage")
          __package__ = 'fabio'
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        fabio-0.1.3/epydoc/fabio.OXDimage.Section-class.html0000644000175000017500000003117612126623347022770 0ustar jeromejerome00000000000000 fabio.OXDimage.Section
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        Package fabio :: Module OXDimage :: Class Section
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        Class Section

        source code

        object --+
         |
        Section

        Small helper class for writing binary headers

        Instance Methods [hide private]
         
        __init__(self, size, dictHeader)
        x.__init__(...) initializes x; see x.__class__.__doc__ for signature        		 source code
         
        __repr__(self)
        repr(x)        		 source code
         
        getSize(self, dtype) source code
         
        setData(self, key, offset, dtype, default=None) source code

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __str__, __subclasshook__

        Properties [hide private]

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, size, dictHeader)
        (Constructor)

        		source code 

        x.__init__(...) initializes x; see x.__class__.__doc__ for signature

        Parameters:
        • size - size of the header section in bytes
        • dictHeader - headers of the image
        Overrides: object.__init__

        __repr__(self)
        (Representation operator)

        		source code 

        repr(x)

        Overrides: object.__repr__
        (inherited documentation)

        setData(self, key, offset, dtype, default=None)

        		source code 
        Parameters:
        • offset - int, starting position in the section
        • key - name of the header key
        • dtype - type of the data to insert (defines the size!)

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        fabio-0.1.3/epydoc/toc-fabio.brukerimage-module.html0000644000175000017500000000265712120434325023160 0ustar jeromejerome00000000000000 brukerimage

        Module brukerimage

        Classes

        brukerimage

        Functions

        test

        Variables

        __package__
        logger
        [hide private] fabio-0.1.3/epydoc/fabio.OXDimage.OXDimage-class.html0000644000175000017500000005012512126623347023014 0ustar jeromejerome00000000000000 fabio.OXDimage.OXDimage
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        Package fabio :: Module OXDimage :: Class OXDimage
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        Class OXDimage

        source code

                   object --+    
                    |    
fabioimage.fabioimage --+
                        |
                       OXDimage

        Oxford Diffraction Sapphire 3 images reader/writer class

        Instance Methods [hide private]
         
        _readheader(self, infile)
        Must be overridden in classes        		 source code
         
        read(self, fname, frame=None)
        Read in header into self.header and...        		 source code
         
        _writeheader(self)
        @return a string containing the header for Oxford images        		 source code
         
        write(self, fname)
        Write Oxford diffraction images: this is still beta        		 source code
         
        getCompressionRatio(self)
        calculate the compression factor obtained vs raw data        		 source code

        Inherited from fabioimage.fabioimage: __init__, add, convert, getclassname, getframe, getheader, getmax, getmean, getmin, getstddev, integrate_area, load, make_slice, next, previous, readROI, readheader, rebin, resetvals, save, toPIL16, update_header

        Inherited from fabioimage.fabioimage (private): _compressed_stream, _open

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Static Methods [hide private]
         
        checkData(data=None)
        Empty for fabioimage but may be populated by others classes, especially for format accepting only integers        		 source code

        Inherited from fabioimage.fabioimage: checkHeader

        Class Variables [hide private]

        Inherited from fabioimage.fabioimage (private): _need_a_real_file, _need_a_seek_to_read

        Properties [hide private]

        Inherited from fabioimage.fabioimage: classname

        Inherited from object: __class__

        Method Details [hide private]

        _readheader(self, infile)

        		source code 

        Must be overridden in classes

        Overrides: fabioimage.fabioimage._readheader
        (inherited documentation)

        read(self, fname, frame=None)

        		source code  
        
Read in header into self.header and
    the data   into self.data
        Overrides: fabioimage.fabioimage.read

        write(self, fname)

        		source code 

        Write Oxford diffraction images: this is still beta

        Parameters:
        • fname - output filename
        Overrides: fabioimage.fabioimage.write

        checkData(data=None)
        Static Method

        		source code 

        Empty for fabioimage but may be populated by others classes, especially for format accepting only integers

        Overrides: fabioimage.fabioimage.checkData
        (inherited documentation)

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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:40 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/fabio.mar345image-pysrc.html0000644000175000017500000055143712126623347022010 0ustar jeromejerome00000000000000 fabio.mar345image
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        Package fabio :: Module mar345image
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        Source Code for Module fabio.mar345image

          1  #!/usr/bin/env python 
  2  #coding: utf8  
  3  from __future__ import with_statement 
  4  __doc__ = """ 
  5   
  6  Authors: 
  7  ........ 
  8  * Henning O. Sorensen & Erik Knudsen: 
  9    Center for Fundamental Research: Metal Structures in Four Dimensions; 
 10    Risoe National Laboratory; 
 11    Frederiksborgvej 399; 
 12    DK-4000 Roskilde; 
 13    email:erik.knudsen@risoe.dk 
 14  * Jon Wright, Jérôme Kieffer & Gaël Goret: 
 15    European Synchrotron Radiation Facility; 
 16    Grenoble (France) 
 17   
 18            
 19  """ 
 20   
 21  from fabioimage import fabioimage 
 22  import numpy, struct, time, sys 
 23  import logging 
 24  logger = logging.getLogger("mar345image") 
 25  from compression import compPCK, decPCK 

         26   
 27 -class mar345image(fabioimage): 

         28      _need_a_real_file = True 

         29 -    def __init__(self, *args, **kwargs): 

         30          fabioimage.__init__(self, *args, **kwargs) 
 31          self.numhigh = None 
 32          self.numpixels = None 

         33   

         34 -    def read(self, fname, frame=None): 

         35          """ Read a mar345 image""" 
 36          self.filename = fname 
 37          f = self._open(self.filename, "rb") 
 38          self._readheader(f) 
 39          if 'compressed' in self.header['Format']: 
 40              try: 
 41                  self.data = decPCK(f, self.dim1, self.dim2, self.numhigh) 
 42              except Exception, error: 
 43                  logger.error('%s. importing the mar345_io backend: generate an empty 1x1 picture' % error) 
 44                  f.close() 
 45                  self.dim1 = 1 
 46                  self.dim2 = 1 
 47                  self.bytecode = numpy.int # 
 48                  self.data = numpy.resize(numpy.array([0], numpy.int), [1, 1]) 
 49                  return self 
 50   
 51          else: 
 52              logger.error("cannot handle these formats yet " + \ 
 53                  "due to lack of documentation") 
 54              return None 
 55          self.bytecode = numpy.uint 
 56          f.close() 
 57          return self 

         58   

         59 -    def _readheader(self, infile=None): 

         60          """ Read a mar345 image header """ 
 61          # clip was not used anywhere - commented out 
 62          # clip = '\x00' 
 63          #using a couple of local variables inside this function 
 64          f = infile 
 65          h = {} 
 66   
 67          #header is 4096 bytes long 
 68          l = f.read(64) 
 69          #the contents of the mar345 header is taken to be as 
 70          # described in 
 71          # http://www.mar-usa.com/support/downloads/mar345_formats.pdf 
 72          #the first 64 bytes are 4-byte integers (but in the CBFlib 
 73          # example image it seems to 128 bytes?) 
 74          #first 4-byte integer is a marker to check endianness 
 75          if struct.unpack("<i", l[0:4])[0] == 1234: 
 76              fs = '<i' 
 77          else: 
 78              fs = '>i' 
 79   
 80          #image dimensions 
 81          self.dim1 = self.dim2 = int(struct.unpack(fs, l[4:8])[0]) 
 82          #number of high intensity pixels 
 83          self.numhigh = struct.unpack(fs, l[2 * 4 : (2 + 1) * 4])[0] 
 84          h['NumHigh'] = self.numhigh 
 85          #Image format 
 86          i = struct.unpack(fs, l[3 * 4 : (3 + 1) * 4])[0] 
 87          if i == 1: 
 88              h['Format'] = 'compressed' 
 89          elif i == 2: 
 90              h['Format'] = 'spiral' 
 91          else: 
 92              h['Format'] = 'compressed' 
 93              logger.warning("image format could not be detetermined" + \ 
 94                  "- assuming compressed mar345") 
 95          #collection mode 
 96          h['Mode'] = {0:'Dose', 1: 'Time'}[struct.unpack(fs, l[4 * 4:(4 + 1) * 4])[0]] 
 97          #total number of pixels 
 98          self.numpixels = struct.unpack(fs, l[5 * 4:(5 + 1) * 4])[0] 
 99          h['NumPixels'] = str(self.numpixels) 
100          #pixel dimensions (length,height) in mm 
101          h['PixelLength'] = struct.unpack(fs, l[6 * 4:(6 + 1) * 4])[0] / 1000.0 
102          h['PixelHeight'] = struct.unpack(fs, l[7 * 4:(7 + 1) * 4])[0] / 1000.0 
103          #x-ray wavelength in AA 
104          h['Wavelength'] = struct.unpack(fs, l[8 * 4:(8 + 1) * 4])[0] / 1000000.0 
105          #used distance 
106          h['Distance'] = struct.unpack(fs, l[9 * 4:(9 + 1) * 4])[0] / 1000.0 
107          #starting and ending phi 
108          h['StartPhi'] = struct.unpack(fs, l[10 * 4:11 * 4])[0] / 1000.0 
109          h['EndPhi'] = struct.unpack(fs, l[11 * 4:12 * 4])[0] / 1000.0 
110          #starting and ending omega 
111          h['StartOmega'] = struct.unpack(fs, l[12 * 4:13 * 4])[0] / 1000.0 
112          h['EndOmega'] = struct.unpack(fs, l[13 * 4:14 * 4])[0] / 1000.0 
113          #Chi and Twotheta angles 
114          h['Chi'] = struct.unpack(fs, l[14 * 4:15 * 4])[0] / 1000.0 
115          h['TwoTheta'] = struct.unpack(fs, l[15 * 4:16 * 4])[0] / 1000.0 
116   
117          #the rest of the header is ascii 
118          # TODO: validate these values against the binaries already read 
119          l = f.read(128) 
120          if not 'mar research' in l: 
121              logger.warning("the string \"mar research\" should be in " + \ 
122                  "bytes 65-76 of the header but was not") 
123              start = 128 
124          else: 
125              start = l.index('mar research') 
126              f.seek(64 + start) 
127          l = f.read(4096 - start - 64).strip() 
128          for m in l.splitlines(): 
129              if m == 'END OF HEADER': 
130                  break 
131              n = m.split(' ', 1) 
132              if n[0] == '': 
133                  continue 
134              if n[0] in ('PROGRAM', 'DATE', 'SCANNER', 'HIGH', 'MULTIPLIER', 
135                          'GAIN', 'WAVELENGTH', 'DISTANCE', 'RESOLUTION', 
136                          'CHI', 'TWOTHETA', 'MODE', 'TIME', 'GENERATOR', 
137                          'MONOCHROMATOR', 'REMARK'): 
138                  logger.debug("reading: %s %s", n[0], n[1]) 
139                  h[n[0]] = n[1].strip() 
140                  continue 
141              if n[0] in ('FORMAT'): 
142                  (h['DIM'], h['FORMAT_TYPE'], h['NO_PIXELS']) = n[1].split() 
143                  continue 
144              if n[0] in ('PIXEL', 'OFFSET', 'PHI', 'OMEGA', 'COUNTS', 
145                          'CENTER', 'INTENSITY', 'HISTOGRAM', 'COLLIMATOR'): 
146                  n = m.split() 
147                  h.update([(n[0] + '_' + n[j], n[j + 1]) for j in range(1, len(n), 2)]) 
148                  continue 
149          self.header = h 
150          return h 

        151   

        152 -    def write(self, fname): 

        153          """Try to write mar345 file. This is still in beta version. 
154          It uses CCP4 (LGPL) PCK1 algo from JPA""" 
155          headers = self._writeheader() 
156          hotpixels = self._high_intensity_pixel_records() 
157          compressed_stream = compPCK(self.data) 
158          try: 
159              outfile = self._open(fname, mode="wb") 
160              outfile.write(headers) 
161              outfile.write(hotpixels) 
162              outfile.write(compressed_stream) 
163              outfile.close() 
164          except Exception, error: 
165              logger.error("Error in writing file %s: %s" % (fname, error)) 

        166   

        167 -    def _writeheader(self, linesep="\n", size=4096):#the standard padding does not inclued 

        168          """ 
169          @param linesep: end of line separator 
170          @return string/bytes containing the mar345 header 
171          """ 
172          try: 
173              version = sys.modules["fabio"].version 
174          except (KeyError, AttributeError): 
175              version = "0.1.1" 
176          lnsep = len(linesep) 
177   
178          self.header["HIGH"] = str(self.nb_overflow_pixels()) 
179          binheader = numpy.zeros(16, "int32") 
180          binheader[:4] = numpy.array([1234, self.dim1, int(self.header["HIGH"]), 1]) 
181          binheader[4] = (self.header.get("MODE", "TIME") == "TIME") 
182          binheader[5] = self.dim1 * self.dim2 
183          binheader[6] = int(self.header.get("PIXEL_LENGTH", 1)) 
184          binheader[7] = int(self.header.get("PIXEL_HEIGHT", 1)) 
185          binheader[8] = int(float(self.header.get("WAVELENGTH", 1)) * 1e6) 
186          binheader[9] = int(float(self.header.get("DISTANCE", 1)) * 1e3) 
187          binheader[10] = int(float(self.header.get("PHI_START", 1)) * 1e3) 
188          binheader[11] = int(float(self.header.get("PHI_END", 1)) * 1e3) 
189          binheader[12] = int(float(self.header.get("OMEGA_START", 1)) * 1e3) 
190          binheader[13] = int(float(self.header.get("OMEGA_END", 1)) * 1e3) 
191          binheader[14] = int(float(self.header.get("CHI", 1)) * 1e3) 
192          binheader[15] = int(float(self.header.get("TWOTHETA", 1)) * 1e3) 
193          lstout = [binheader.tostring() + 'mar research'.ljust(64 - lnsep)] 
194          lstout.append("PROGRAM".ljust(15) + (str(self.header.get("PROGRAM", "FabIO Version %s" % (version))).ljust(49 - lnsep))) 
195          lstout.append("DATE".ljust(15) + (str(self.header.get("DATE", time.ctime()))).ljust(49 - lnsep)) 
196          key = "SCANNER" 
197          if key in self.header: 
198              lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep)) 
199          key = "FORMAT_TYPE" 
200          if key in self.header: 
201              lstout.append("FORMAT".ljust(15) + ("%s  %s %s" % (self.dim1, self.header[key], self.dim1 * self.dim2)).ljust(49 - lnsep)) 
202          key = "HIGH" 
203          if key in self.header: 
204              lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep)) 
205          key1 = "PIXEL_LENGTH" 
206          key2 = "PIXEL_HEIGHT" 
207          if (key1 in self.header) and (key2 in self.header): 
208              lstout.append("PIXEL".ljust(15) + ("LENGTH %s  HEIGHT %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep)) 
209          key1 = "OFFSET_ROFF" 
210          key2 = "OFFSET_TOFF" 
211          if key1 in self.header and key2 in self.header: 
212              lstout.append("OFFSET".ljust(15) + ("ROFF %s  TOFF %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep)) 
213          key = "MULTIPLIER" 
214          if key in self.header: 
215              lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep)) 
216          key = "GAIN" 
217          if key in self.header: 
218              lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep)) 
219          key = "WAVELENGTH" 
220          if key in self.header: 
221              lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep)) 
222          key = "DISTANCE" 
223          if key in self.header: 
224              lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep)) 
225          key = "RESOLUTION" 
226          if key in self.header: 
227              lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep)) 
228          key1 = "PHI_START" 
229          key2 = "PHI_END" 
230          key3 = "PHI_OSC" 
231          if (key1 in self.header) and (key2 in self.header) and (key3 in self.header): 
232              lstout.append("PHI".ljust(15) + ("START %s  END %s  OSC %s" % (self.header[key1], self.header[key2], self.header[key3])).ljust(49 - lnsep)) 
233          key1 = "OMEGA_START" 
234          key2 = "OMEGA_END" 
235          key3 = "OMEGA_OSC" 
236          if (key1 in self.header) and (key2 in self.header) and (key3 in self.header): 
237              lstout.append("OMEGA".ljust(15) + ("START %s  END %s  OSC %s" % (self.header[key1], self.header[key2], self.header[key3])).ljust(49 - lnsep)) 
238          key = "CHI" 
239          if key in self.header: 
240              lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep)) 
241          key = "TWOTHETA" 
242          if key in self.header: 
243              lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep)) 
244          key1 = "CENTER_X" 
245          key2 = "CENTER_Y" 
246          if (key1 in self.header) and (key2 in self.header): 
247              lstout.append("CENTER".ljust(15) + ("X %s  Y %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep)) 
248          key = "MODE" 
249          if key in self.header: 
250              lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep)) 
251          key = "TIME" 
252          if key in self.header: 
253              lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep)) 
254          key1 = "COUNTS_START" 
255          key2 = "COUNTS_END" 
256          key3 = "COUNTS_NMEAS" 
257          if key1 in self.header and key2 in self.header and key3 in self.header: 
258              lstout.append("COUNTS".ljust(15) + ("START %s  END %s  NMEAS %s" % (self.header[key1], self.header[key2], self.header[key3])).ljust(49 - lnsep)) 
259          key1 = "COUNTS_MIN" 
260          key2 = "COUNTS_MAX" 
261          if key1 in self.header and key2 in self.header: 
262              lstout.append("COUNTS".ljust(15) + ("MIN %s  MAX %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep)) 
263          key1 = "COUNTS_AVE" 
264          key2 = "COUNTS_SIG" 
265          if key1 in self.header and key2 in self.header: 
266              lstout.append("COUNTS".ljust(15) + ("AVE %s  SIG %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep)) 
267          key1 = "INTENSITY_MIN" 
268          key2 = "INTENSITY_MAX" 
269          key3 = "INTENSITY_AVE" 
270          key4 = "INTENSITY_SIG" 
271          if key1 in self.header and key2 in self.header and key3 in self.header and key4 in self.header: 
272              lstout.append("INTENSITY".ljust(15) + ("MIN %s  MAX %s  AVE %s  SIG %s" % (self.header[key1], self.header[key2], self.header[key3], self.header[key4])).ljust(49 - lnsep)) 
273          key1 = "HISTOGRAM_START" 
274          key2 = "HISTOGRAM_END" 
275          key3 = "HISTOGRAM_MAX" 
276          if key1 in self.header and key2 in self.header and key3 in self.header: 
277              lstout.append("HISTOGRAM".ljust(15) + ("START %s  END %s  MAX %s" % (self.header[key1], self.header[key2], self.header[key3])).ljust(49 - lnsep)) 
278          key = "GENERATOR" 
279          if key in self.header: 
280              lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep)) 
281          key = "MONOCHROMATOR" 
282          if key in self.header: 
283              lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep)) 
284          key1 = "COLLIMATOR_WIDTH" 
285          key2 = "COLLIMATOR_HEIGHT" 
286          if key1 in self.header and key2 in self.header: 
287              lstout.append("COLLIMATOR".ljust(15) + ("WIDTH %s  HEIGHT %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep)) 
288          key = "REMARK" 
289          if key in self.header: 
290              lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep)) 
291          else: 
292              lstout.append(key.ljust(64 - lnsep)) 
293          key = "END OF HEADER" 
294          lstout.append(key) 
295          return linesep.join(lstout).ljust(size) 

        296   
297   

        299          flt_data = self.data.flatten() 
300          pix_location = numpy.where(flt_data > 65535)[0] 
301          nb_pix = pix_location.size 
302          if nb_pix % 8 == 0: 
303              tmp = numpy.zeros((nb_pix, 2), dtype="int32") 
304          else: 
305              tmp = numpy.zeros(((nb_pix // 8 + 1) * 8, 2), dtype="int32") 
306          tmp[:nb_pix, 0] = pix_location + 1 
307          tmp[:nb_pix, 1] = flt_data[pix_location] 
308          return tmp.tostring() 

        309   

        310 -    def nb_overflow_pixels(self): 

        311          return (self.data > 65535).sum() 

        312   
313      @staticmethod 

        314 -    def checkData(data=None): 

        315          if data is None: 
316              return None 
317          else: 
318  #            enforce square image  
319              shape = data.shape 
320              assert len(shape) == 2, "image has 2 dimensions" 
321              mshape = max(shape) 
322              z = numpy.zeros((mshape, mshape), dtype=int) 
323              z[:shape[0], :shape[1]] = data 
324              return z 

        325

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        fabio-0.1.3/epydoc/fabio.fabioimage-module.html0000644000175000017500000001712412126623347022170 0ustar jeromejerome00000000000000 fabio.fabioimage
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        Package fabio :: Module fabioimage
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        Module fabioimage

        source code

        

Authors: Henning O. Sorensen & Erik Knudsen
         Center for Fundamental Research: Metal Structures in Four Dimensions
         Risoe National Laboratory
         Frederiksborgvej 399
         DK-4000 Roskilde
         email:erik.knudsen@risoe.dk

         and Jon Wright, Jerome Kieffer: ESRF
        Classes [hide private]
          fabioimage
        A common object for images in fable Contains a numpy array (.data) and dict of meta data (.header)
        Functions [hide private]
         
        test()
        check some basic fabioimage functionality        		 source code
        Variables [hide private]
          logger = logging.getLogger("fabioimage")
          __package__ = 'fabio'
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        Package fabio :: Module datIO :: Class fabiodata
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        Class fabiodata

        source code

        object --+
         |
        fabiodata
        Known Subclasses:

        A common class for dataIO in fable Contains a 2d numpy array for keeping data, and two lists (clabels and rlabels) containing labels for columns and rows respectively

        Instance Methods [hide private]
         
        __init__(self, data=None, clabels=None, rlabels=None, fname=None)
        set up initial values        		 source code
         
        read(self, fname=None, frame=None)
        To be overridden by format specific subclasses        		 source code

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Properties [hide private]

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, data=None, clabels=None, rlabels=None, fname=None)
        (Constructor)

        		source code 

        set up initial values

        Overrides: object.__init__

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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:40 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/toc-fabio.openimage-module.html0000644000175000017500000000332612120434325022621 0ustar jeromejerome00000000000000 openimage

        Module openimage

        Functions

        _openimage
        do_magic
        openheader
        openimage

        Variables

        MAGIC_NUMBERS
        __package__
        logger
        [hide private] fabio-0.1.3/epydoc/fabio.fabioutils.BZ2File-class.html0000644000175000017500000003173512126623347023266 0ustar jeromejerome00000000000000 fabio.fabioutils.BZ2File
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        Package fabio :: Module fabioutils :: Class BZ2File
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        Class BZ2File

        source code

         object --+    
          |    
bz2.BZ2File --+
              |
             BZ2File

        Wrapper with lock

        Instance Methods [hide private]
        file object
        __init__(name, mode='r', buffering=0, compresslevel=9)
        Open a bz2 file.        		 source code
         
        getSize(self) source code
         
        setSize(self, value) source code

        Inherited from bz2.BZ2File: __delattr__, __getattribute__, __iter__, __new__, __setattr__, close, next, read, readline, readlines, seek, tell, write, writelines, xreadlines

        Inherited from object: __format__, __hash__, __reduce__, __reduce_ex__, __repr__, __sizeof__, __str__, __subclasshook__

        Properties [hide private]
          size

        Inherited from bz2.BZ2File: closed, mode, name, newlines, softspace

        Inherited from object: __class__

        Method Details [hide private]

        __init__(name, mode='r', buffering=0, compresslevel=9)
        (Constructor)

        		source code  
                    Open a bz2 file. The mode can be 'r' or 'w', for reading (default) or
            writing. When opened for writing, the file will be created if it doesn't
            exist, and truncated otherwise. If the buffering argument is given, 0 means
            unbuffered, and larger numbers specify the buffer size. If compresslevel
            is given, must be a number between 1 and 9.
            
            Add a 'U' to mode to open the file for input with universal newline
            support. Any line ending in the input file will be seen as a '
' in
            Python. Also, a file so opened gains the attribute 'newlines'; the value
            for this attribute is one of None (no newline read yet), '
', '
',
            '
' or a tuple containing all the newline types seen. Universal
            newlines are available only when reading.
        Returns: file object
        Overrides: object.__init__

        Property Details [hide private]

        size

        Get Method:
        getSize(self)
        Set Method:
        setSize(self, value)

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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:40 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/fabio.OXDimage-pysrc.html0000644000175000017500000073370412126623347021426 0ustar jeromejerome00000000000000 fabio.OXDimage
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        Package fabio :: Module OXDimage
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        Source Code for Module fabio.OXDimage

          1  #!/usr/bin/env python
 
  2  #coding: utf8
 
  3  
 
  4  from __future__ import with_statement 
  5  __doc__ = """
 
  6  Reads Oxford Diffraction Sapphire 3 images
 
  7  
 
  8  Authors:
 
  9  ........
 
 10  * Henning O. Sorensen & Erik Knudsen:
 
 11    Center for Fundamental Research: Metal Structures in Four Dimensions;
 
 12    Risoe National Laboratory;
 
 13    Frederiksborgvej 399;
 
 14    DK-4000 Roskilde;
 
 15    email:erik.knudsen@risoe.dk
 
 16  * Jon Wright, Jérôme Kieffer & Gaël Goret:
 
 17    European Synchrotron Radiation Facility;
 
 18    Grenoble (France)
 
 19  
 
 20  """ 
 21  
 
 22  import time, logging, struct 
 23  logger = logging.getLogger("OXDimage") 
 24  import numpy 
 25  from fabioimage import fabioimage 
 26  from compression import decTY1, compTY1 
 27  
 
 28  try: 
 29      from numpy import rad2deg, deg2rad 
 30  except ImportError: #naive implementation for very old numpy (v1.0.1 on MacOSX from Risoe) 
 31      rad2deg = lambda x: 180.0 * x / numpy.pi 
 32      deg2rad = lambda x: x * numpy.pi / 180. 
 33  
 
 34  DETECTOR_TYPES = {0: 'Sapphire/KM4CCD (1x1: 0.06mm, 2x2: 0.12mm)',
 
 35  1: 'Sapphire2-Kodak (1x1: 0.06mm, 2x2: 0.12mm)',
 
 36  2: 'Sapphire3-Kodak (1x1: 0.03mm, 2x2: 0.06mm, 4x4: 0.12mm)',
 
 37  3: 'Onyx-Kodak (1x1: 0.06mm, 2x2: 0.12mm, 4x4: 0.24mm)',
 
 38  4: 'Unknown Oxford diffraction detector'} 
 39  
 
 40  DEFAULT_HEADERS = {'Header Version':  'OD SAPPHIRE  3.0',
 
 41                     'Compression': "TY1",
 
 42                     'Header Size In Bytes': 5120,
 
 43                     "ASCII Section size in Byte": 256,
 
 44                     "General Section size in Byte": 512,
 
 45                     "Special Section size in Byte": 768,
 
 46                     "KM4 Section size in Byte": 1024,
 
 47                     "Statistic Section in Byte": 512,
 
 48                     "History Section in Byte": 2048,
 
 49                     'NSUPPLEMENT':0
 
 50                     } 

         51  
 
 52 -class OXDimage(fabioimage): 

         53      """
 
 54      Oxford Diffraction Sapphire 3 images reader/writer class
 
 55      """ 

         56 -    def _readheader(self, infile): 

         57  
 
 58          infile.seek(0) 
 59  
 
 60          # Ascii header part 256 byes long
 
 61          self.header['Header Version'] = infile.readline()[:-2] 
 62          block = infile.readline() 
 63          self.header['Compression'] = block[12:15] 
 64          block = infile.readline() 
 65          self.header['NX'] = int(block[3:7]) 
 66          self.header['NY'] = int(block[11:15]) 
 67          self.header['OI'] = int(block[19:26]) 
 68          self.header['OL'] = int(block[30:37]) 
 69          block = infile.readline() 
 70          self.header['Header Size In Bytes'] = int(block[8:15]) 
 71          self.header['General Section size in Byte'] = int(block[19:26]) 
 72          self.header['Special Section size in Byte'] = int(block[30:37]) 
 73          self.header['KM4 Section size in Byte'] = int(block[41:48]) 
 74          self.header['Statistic Section in Byte'] = int(block[52:59]) 
 75          self.header['History Section in Byte'] = int(block[63:]) 
 76          block = infile.readline() 
 77          self.header['NSUPPLEMENT'] = int(block[12:19]) 
 78          block = infile.readline() 
 79          self.header['Time'] = block[5:29] 
 80          self.header["ASCII Section size in Byte"] = self.header['Header Size In Bytes']\
 
 81                                                  - self.header['General Section size in Byte']\
 
 82                                                  - self.header['Special Section size in Byte'] \
 
 83                                                  - self.header['KM4 Section size in Byte']\
 
 84                                                  - self.header['Statistic Section in Byte']\
 
 85                                                  - self.header['History Section in Byte']\
 
 86          # Skip to general section (NG) 512 byes long <<<<<<" 
 87          infile.seek(self.header["ASCII Section size in Byte"]) 
 88          block = infile.read(self.header['General Section size in Byte']) 
 89          self.header['Binning in x'] = numpy.fromstring(block[0:2], numpy.uint16)[0] 
 90          self.header['Binning in y'] = numpy.fromstring(block[2:4], numpy.uint16)[0] 
 91          self.header['Detector size x'] = numpy.fromstring(block[22:24], numpy.uint16)[0] 
 92          self.header['Detector size y'] = numpy.fromstring(block[24:26], numpy.uint16)[0] 
 93          self.header['Pixels in x'] = numpy.fromstring(block[26:28], numpy.uint16)[0] 
 94          self.header['Pixels in y'] = numpy.fromstring(block[28:30], numpy.uint16)[0] 
 95          self.header['No of pixels'] = numpy.fromstring(block[36:40], numpy.uint32)[0] 
 96  
 
 97          # Speciel section (NS) 768 bytes long
 
 98          block = infile.read(self.header['Special Section size in Byte']) 
 99          self.header['Gain'] = numpy.fromstring(block[56:64], numpy.float)[0] 
100          self.header['Overflows flag'] = numpy.fromstring(block[464:466], numpy.int16)[0] 
101          self.header['Overflow after remeasure flag'] = numpy.fromstring(block[466:468], numpy.int16)[0] 
102          self.header['Overflow threshold'] = numpy.fromstring(block[472:476], numpy.int32)[0] 
103          self.header['Exposure time in sec'] = numpy.fromstring(block[480:488], numpy.float)[0] 
104          self.header['Overflow time in sec'] = numpy.fromstring(block[488:496], numpy.float)[0] 
105          self.header['Monitor counts of raw image 1'] = numpy.fromstring(block[528:532], numpy.int32)[0] 
106          self.header['Monitor counts of raw image 2'] = numpy.fromstring(block[532:536], numpy.int32)[0] 
107          self.header['Monitor counts of overflow raw image 1'] = numpy.fromstring(block[536:540], numpy.int32)[0] 
108          self.header['Monitor counts of overflow raw image 2'] = numpy.fromstring(block[540:544], numpy.int32)[0] 
109          self.header['Unwarping'] = numpy.fromstring(block[544:548], numpy.int32)[0] 
110          self.header['Detector type'] = DETECTOR_TYPES[numpy.fromstring(block[548:552], numpy.int32)[0]] 
111          self.header['Real pixel size x (mm)'] = numpy.fromstring(block[568:576], numpy.float)[0] 
112          self.header['Real pixel size y (mm)'] = numpy.fromstring(block[576:584], numpy.float)[0] 
113  
 
114          # KM4 goniometer section (NK) 1024 bytes long
 
115          block = infile.read(self.header['KM4 Section size in Byte']) 
116          # Spatial correction file
 
117          self.header['Spatial correction file'] = block[26:272].strip("\x00") 
118          self.header['Spatial correction file date'] = block[0:26].strip("\x00") 
119          # Angles are in steps due to stepper motors - conversion factor RAD
 
120          # angle[0] = omega, angle[1] = theta, angle[2] = kappa, angle[3] = phi,   
 
121          start_angles_step = numpy.fromstring(block[284:304], numpy.int32) 
122          end_angles_step = numpy.fromstring(block[324:344], numpy.int32) 
123          step2rad = numpy.fromstring(block[368:408], numpy.float) 
124          step_angles_deg = rad2deg(step2rad) 
125          # calc angles
 
126          start_angles_deg = start_angles_step * step_angles_deg 
127          end_angles_deg = end_angles_step * step_angles_deg 
128          self.header['Omega start in deg'] = start_angles_deg[0] 
129          self.header['Theta start in deg'] = start_angles_deg[1] 
130          self.header['Kappa start in deg'] = start_angles_deg[2] 
131          self.header['Phi start in deg'] = start_angles_deg[3] 
132          self.header['Omega end in deg'] = end_angles_deg[0] 
133          self.header['Theta end in deg'] = end_angles_deg[1] 
134          self.header['Kappa end in deg'] = end_angles_deg[2] 
135          self.header['Phi end in deg'] = end_angles_deg[3] 
136          self.header['Omega step in deg'] = step_angles_deg[0] 
137          self.header['Theta step in deg'] = step_angles_deg[1] 
138          self.header['Kappa step in deg'] = step_angles_deg[2] 
139          self.header['Phi step in deg'] = step_angles_deg[3] 
140  
 
141  
 
142          zero_correction_soft_step = numpy.fromstring(block[512:532], numpy.int32) 
143          zero_correction_soft_deg = zero_correction_soft_step * step_angles_deg 
144          self.header['Omega zero corr. in deg'] = zero_correction_soft_deg[0] 
145          self.header['Theta zero corr. in deg'] = zero_correction_soft_deg[1] 
146          self.header['Kappa zero corr. in deg'] = zero_correction_soft_deg[2] 
147          self.header['Phi zero corr. in deg'] = zero_correction_soft_deg[3] 
148          # Beam rotation about e2,e3
 
149          self.header['Beam rot in deg (e2)'] = numpy.fromstring(block[552:560], numpy.float)[0] 
150          self.header['Beam rot in deg (e3)'] = numpy.fromstring(block[560:568], numpy.float)[0] 
151          # Wavelenghts alpha1, alpha2, beta
 
152          self.header['Wavelength alpha1'] = numpy.fromstring(block[568:576], numpy.float)[0] 
153          self.header['Wavelength alpha2'] = numpy.fromstring(block[576:584], numpy.float)[0] 
154          self.header['Wavelength alpha'] = numpy.fromstring(block[584:592], numpy.float)[0] 
155          self.header['Wavelength beta'] = numpy.fromstring(block[592:600], numpy.float)[0] 
156  
 
157          # Detector tilts around e1,e2,e3 in deg
 
158          self.header['Detector tilt e1 in deg'] = numpy.fromstring(block[640:648], numpy.float)[0] 
159          self.header['Detector tilt e2 in deg'] = numpy.fromstring(block[648:656], numpy.float)[0] 
160          self.header['Detector tilt e3 in deg'] = numpy.fromstring(block[656:664], numpy.float)[0] 
161  
 
162  
 
163          # Beam center
 
164          self.header['Beam center x'] = numpy.fromstring(block[664:672], numpy.float)[0] 
165          self.header['Beam center y'] = numpy.fromstring(block[672:680], numpy.float)[0] 
166          # Angle (alpha) between kappa rotation axis and e3 (ideally 50 deg)
 
167          self.header['Alpha angle in deg'] = numpy.fromstring(block[672:680], numpy.float)[0] 
168          # Angle (beta) between phi rotation axis and e3 (ideally 0 deg)
 
169          self.header['Beta angle in deg'] = numpy.fromstring(block[672:680], numpy.float)[0] 
170  
 
171          # Detector distance
 
172          self.header['Distance in mm'] = numpy.fromstring(block[712:720], numpy.float)[0] 
173          # Statistics section (NS) 512 bytes long
 
174          block = infile.read(self.header['Statistic Section in Byte']) 
175          self.header['Stat: Min '] = numpy.fromstring(block[0:4], numpy.int32)[0] 
176          self.header['Stat: Max '] = numpy.fromstring(block[4:8], numpy.int32)[0] 
177          self.header['Stat: Average '] = numpy.fromstring(block[24:32], numpy.float)[0] 
178          self.header['Stat: Stddev '] = numpy.sqrt(numpy.fromstring(block[32:40], numpy.float)[0]) 
179          self.header['Stat: Skewness '] = numpy.fromstring(block[40:48], numpy.float)[0] 
180  
 
181          # History section (NH) 2048 bytes long
 
182          block = infile.read(self.header['History Section in Byte']) 
183          self.header['Flood field image'] = block[99:126].strip("\x00") 

        184  
 

        185 -    def read(self, fname, frame=None): 

        186          """
 
187          Read in header into self.header and
 
188              the data   into self.data
 
189          """ 
190          self.header = {} 
191          self.resetvals() 
192          infile = self._open(fname) 
193          self._readheader(infile) 
194  
 
195          infile.seek(self.header['Header Size In Bytes']) 
196  
 
197          # Compute image size
 
198          try: 
199              self.dim1 = int(self.header['NX']) 
200              self.dim2 = int(self.header['NY']) 
201          except: 
202              raise Exception("Oxford  file", str(fname) + \
 
203                                  "is corrupt, cannot read it") 
204          #
 
205          if self.header['Compression'] == 'TY1': 
206              #Compressed with the KM4CCD compression
 
207              raw8 = infile.read(self.dim1 * self.dim2) 
208              raw16 = None 
209              raw32 = None 
210              if self.header['OI'] > 0: 
211                  raw16 = infile.read(self.header['OI'] * 2) 
212              if self.header['OL'] > 0: 
213                  raw32 = infile.read(self.header['OL'] * 4) 
214              #DEBUG stuff ... 
 
215              self.raw8 = raw8 
216              self.raw16 = raw16 
217              self.raw32 = raw32 
218              #END DEBUG
 
219              block = decTY1(raw8, raw16, raw32) 
220              bytecode = block.dtype 
221  
 
222          else: 
223              bytecode = numpy.int32 
224              self.bpp = len(numpy.array(0, bytecode).tostring()) 
225              ReadBytes = self.dim1 * self.dim2 * self.bpp 
226              block = numpy.fromstring(infile.read(ReadBytes), bytecode) 
227  
 
228          logger.debug('OVER_SHORT2: %s', block.dtype) 
229          logger.debug("%s" % (block < 0).sum()) 
230          infile.close() 
231          logger.debug("BYTECODE: %s", bytecode) 
232          self.data = block.reshape((self.dim2, self.dim1)) 
233          self.bytecode = self.data.dtype.type 
234          self.pilimage = None 
235          return self 

        236  
 

        237 -    def _writeheader(self): 

        238          """
 
239          @return a string containing the header for Oxford images
 
240          """ 
241          linesep = "\r\n" 
242          for key in DEFAULT_HEADERS: 
243              if key not in self.header_keys: 
244                  self.header_keys.append(key) 
245                  self.header[key] = DEFAULT_HEADERS[key] 
246  
 
247          if "NX" not in self.header.keys() or "NY" not in self.header.keys(): 
248                          self.header['NX'] = self.dim1 
249                          self.header['NY'] = self.dim2 
250          ascii_headers = [self.header['Header Version'],
 
251                         "COMPRESSION=%s (%5.1f)" % (self.header["Compression"], self.getCompressionRatio()),
 
252                         "NX=%4i NY=%4i OI=%7i OL=%7i " % (self.header["NX"], self.header["NY"], self.header["OI"], self.header["OL"]),
 
253                         "NHEADER=%7i NG=%7i NS=%7i NK=%7i NS=%7i NH=%7i" % (self.header['Header Size In Bytes'],
 
254                                                                                   self.header['General Section size in Byte'],
 
255                                                                                   self.header['Special Section size in Byte'],
 
256                                                                                   self.header['KM4 Section size in Byte'],
 
257                                                                                   self.header['Statistic Section in Byte'],
 
258                                                                                   self.header['History Section in Byte']),
 
259                          "NSUPPLEMENT=%7i" % (self.header["NSUPPLEMENT"])] 
260          if "Time" in self.header: 
261              ascii_headers.append("TIME=%s" % self.header["Time"]) 
262          else: 
263  
 
264              ascii_headers.append("TIME=%s" % time.ctime()) 
265  
 
266          header = (linesep.join(ascii_headers)).ljust(256) 
267  
 
268  
 
269          NG = Section(self.header['General Section size in Byte'], self.header) 
270          NG.setData('Binning in x', 0, numpy.uint16) 
271          NG.setData('Binning in y', 2, numpy.uint16) 
272          NG.setData('Detector size x', 22, numpy.uint16) 
273          NG.setData('Detector size y', 24, numpy.uint16) 
274          NG.setData('Pixels in x', 26, numpy.uint16) 
275          NG.setData('Pixels in y', 28, numpy.uint16) 
276          NG.setData('No of pixels', 36, numpy.uint32) 
277          header += NG.__repr__() 
278  
 
279          NS = Section(self.header['Special Section size in Byte'], self.header) 
280          NS.setData('Gain', 56, numpy.float) 
281          NS.setData('Overflows flag', 464, numpy.int16) 
282          NS.setData('Overflow after remeasure flag', 466, numpy.int16) 
283          NS.setData('Overflow threshold', 472, numpy.int32) 
284          NS.setData('Exposure time in sec', 480, numpy.float) 
285          NS.setData('Overflow time in sec', 488, numpy.float) 
286          NS.setData('Monitor counts of raw image 1', 528, numpy.int32) 
287          NS.setData('Monitor counts of raw image 2', 532, numpy.int32) 
288          NS.setData('Monitor counts of overflow raw image 1', 536, numpy.int32) 
289          NS.setData('Monitor counts of overflow raw image 2', 540, numpy.int32) 
290          NS.setData('Unwarping', 544, numpy.int32) 
291          if 'Detector type' in  self.header: 
292              for key, value in  DETECTOR_TYPES.items(): 
293                  if value == self.header['Detector type']: 
294                      NS.setData(None, 548, numpy.int32, default=key) 
295          NS.setData('Real pixel size x (mm)', 568, numpy.float) 
296          NS.setData('Real pixel size y (mm)', 576, numpy.float) 
297          header += NS.__repr__() 
298  
 
299          KM = Section(self.header['KM4 Section size in Byte'], self.header) 
300          KM.setData('Spatial correction file date', 0, "|S26") 
301          KM.setData('Spatial correction file', 26, "|S246") 
302          # Angles are in steps due to stepper motors - conversion factor RAD
 
303          # angle[0] = omega, angle[1] = theta, angle[2] = kappa, angle[3] = phi,
 
304          if self.header.get('Omega step in deg', None): 
305              KM.setData(None, 368, numpy.float64, deg2rad(self.header["Omega step in deg"])) 
306              if self.header.get('Omega start in deg', None): 
307                  KM.setData(None, 284, numpy.int32, self.header["Omega start in deg"] / self.header["Omega step in deg"]) 
308              if self.header.get('Omega end in deg', None): 
309                  KM.setData(None, 324, numpy.int32, self.header["Omega end in deg"] / self.header["Omega step in deg"]) 
310              if self.header.get('Omega zero corr. in deg', None): 
311                  KM.setData(None, 512, numpy.int32, self.header['Omega zero corr. in deg'] / self.header["Omega step in deg"]) 
312  
 
313          if self.header.get('Theta step in deg', None): 
314              KM.setData(None, 368 + 8, numpy.float64, deg2rad(self.header["Theta step in deg"])) 
315              if self.header.get('Theta start in deg', None): 
316                  KM.setData(None, 284 + 4, numpy.int32, self.header["Theta start in deg"] / self.header["Theta step in deg"]) 
317              if self.header.get('Theta end in deg', None): 
318                  KM.setData(None, 324 + 4, numpy.int32, self.header["Theta end in deg"] / self.header["Theta step in deg"]) 
319              if self.header.get('Theta zero corr. in deg', None): 
320                  KM.setData(None, 512 + 4, numpy.int32, self.header['Theta zero corr. in deg'] / self.header["Theta step in deg"]) 
321  
 
322          if self.header.get('Kappa step in deg', None): 
323              KM.setData(None, 368 + 16, numpy.float64, deg2rad(self.header["Kappa step in deg"])) 
324              if self.header.get('Kappa start in deg', None): 
325                  KM.setData(None, 284 + 8, numpy.int32, self.header["Kappa start in deg"] / self.header["Kappa step in deg"]) 
326              if self.header.get('Kappa end in deg', None): 
327                  KM.setData(None, 324 + 8, numpy.int32, self.header["Kappa end in deg"] / self.header["Kappa step in deg"]) 
328              if self.header.get('Kappa zero corr. in deg', None): 
329                  KM.setData(None, 512 + 8, numpy.int32, self.header['Kappa zero corr. in deg'] / self.header["Kappa step in deg"]) 
330  
 
331          if self.header.get('Phi step in deg', None): 
332              KM.setData(None, 368 + 24, numpy.float64, deg2rad(self.header["Phi step in deg"])) 
333              if self.header.get('Phi start in deg', None): 
334                  KM.setData(None, 284 + 12, numpy.int32, self.header["Phi start in deg"] / self.header["Phi step in deg"]) 
335              if self.header.get('Phi end in deg', None): 
336                  KM.setData(None, 324 + 12, numpy.int32, self.header["Phi end in deg"] / self.header["Phi step in deg"]) 
337              if self.header.get('Phi zero corr. in deg', None): 
338                  KM.setData(None, 512 + 12, numpy.int32, self.header['Phi zero corr. in deg'] / self.header["Phi step in deg"]) 
339  
 
340          # Beam rotation about e2,e3
 
341          KM.setData('Beam rot in deg (e2)', 552, numpy.float64) 
342          KM.setData('Beam rot in deg (e3)', 560, numpy.float64) 
343          # Wavelenghts alpha1, alpha2, beta
 
344          KM.setData('Wavelength alpha1', 568, numpy.float64) 
345          KM.setData('Wavelength alpha2', 576, numpy.float64) 
346          KM.setData('Wavelength alpha', 584, numpy.float64) 
347          KM.setData('Wavelength beta', 592, numpy.float64) 
348  
 
349          # Detector tilts around e1,e2,e3 in deg
 
350          KM.setData('Detector tilt e1 in deg', 640, numpy.float64) 
351          KM.setData('Detector tilt e2 in deg', 648, numpy.float64) 
352          KM.setData('Detector tilt e3 in deg', 656, numpy.float64) 
353  
 
354          # Beam center
 
355          KM.setData('Beam center x', 664, numpy.float64) 
356          KM.setData('Beam center y', 672, numpy.float64) 
357          # Angle (alpha) between kappa rotation axis and e3 (ideally 50 deg)
 
358          KM.setData('Alpha angle in deg', 672, numpy.float64) 
359          # Angle (beta) between phi rotation axis and e3 (ideally 0 deg)
 
360          KM.setData('Beta angle in deg', 672, numpy.float64) 
361  
 
362          # Detector distance
 
363          KM.setData('Distance in mm', 712, numpy.float64) 
364          header += KM.__repr__() 
365  
 
366          SS = Section(self.header['Statistic Section in Byte'], self.header) 
367          SS.setData('Stat: Min ', 0, numpy.int32) 
368          SS.setData('Stat: Max ', 4, numpy.int32) 
369          SS.setData('Stat: Average ', 24, numpy.float64) 
370          if self.header.get('Stat: Stddev ', None): 
371              SS.setData(None, 32, numpy.float64, self.header['Stat: Stddev '] ** 2) 
372          SS.setData('Stat: Skewness ', 40, numpy.float64) 
373          header += SS.__repr__() 
374  
 
375          HS = Section(self.header['History Section in Byte'], self.header) 
376          HS.setData('Flood field image', 99, "|S27") 
377          header += HS.__repr__() 
378  
 
379          return header 

        380  
 
381  
 

        382 -    def write(self, fname): 

        383          """Write Oxford diffraction images: this is still beta
 
384          @param fname: output filename 
 
385          """ 
386          datablock8, datablock16, datablock32 = compTY1(self.data) 
387          self.header["OI"] = len(datablock16) / 2 
388          self.header["OL"] = len(datablock32) / 4 
389          with self._open(fname, mode="wb") as outfile: 
390              outfile.write(self._writeheader()) 
391              outfile.write(datablock8) 
392              outfile.write(datablock16) 
393              outfile.write(datablock32) 

        394  
 

        395 -    def getCompressionRatio(self): 

        396          "calculate the compression factor obtained vs raw data" 
397          return 100.0 * (self.data.size + 2 * self.header["OI"] + 4 * self.header["OL"]) / (self.data.size * 4) 

        398  
 
399      @staticmethod 

        400 -    def checkData(data=None): 

        401          if data is None: 
402              return None 
403          else: 
404              return data.astype(int) 

        405  
 

        406 -class Section(object): 

        407      """
 
408      Small helper class for writing binary headers
 
409      """ 

        410 -    def __init__(self, size, dictHeader): 

        411          """
 
412          @param size: size of the header section in bytes
 
413          @param dictHeader: headers of the image
 
414          """ 
415          self.size = size 
416          self.header = dictHeader 
417          self.lstChr = ["\x00"] * size 
418          self._dictSize = {} 

        419 -    def __repr__(self): 

        420          return "".join(self.lstChr) 

        421  
 

        422 -    def getSize(self, dtype): 

        423          if not dtype in self._dictSize: 
424              self._dictSize[dtype] = len(numpy.zeros(1, dtype=dtype).tostring()) 
425          return self._dictSize[dtype] 

        426  
 

        427 -    def setData(self, key, offset, dtype, default=None): 

        428          """
 
429          @param offset: int, starting position in the section
 
430          @param key: name of the header key
 
431          @param dtype: type of the data to insert (defines the size!)
 
432          """ 
433          if key in self.header: 
434              value = self.header[key] 
435          elif key in DEFAULT_HEADERS: 
436              value = DEFAULT_HEADERS[key] 
437          else: 
438              value = default 
439          if value is None: 
440              value = "\x00" * self.getSize(dtype) 
441          else: 
442              value = numpy.array(value).astype(dtype).tostring() 
443          self.lstChr[offset:offset + self.getSize(dtype)] = value 

        444

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        Package fabio :: Module converters
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        Source Code for Module fabio.converters

         1  #!/usr/bin/env python  
 2  #coding: utf8 
 3  """ 
 4  Converter module.  
 5  This is for the moment empty (populated only with almost pass through anonymous functions) 
 6  but aims to be populated with more sofisticated translators ...   
 7   
 8  """ 
 9  __author__ = "Jérôme Kieffer" 
10  __contact__ = "jerome.kieffer@esrf.eu" 
11  __license__ = "GPLv3+" 
12  __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" 
13   
14  import types, logging 
15  logger = logging.getLogger("converter") 
16   

        17 -def convert_data_integer(data): 

        18      """ 
19      convert data to integer 
20      """ 
21      if data is not None: 
22          return data.astype(int) 
23      else: 
24          return data 

        25   
26   
27  CONVERSION_HEADER = { 
28                       ("edfimage", "edfimage"): lambda header:header, 
29                       } 
30  CONVERSION_DATA = { 
31                     ("edfimage", "edfimage"): lambda data:data, 
32                     ("edfimage", "cbfimage"): convert_data_integer, 
33                     ("edfimage", "mar345image"): convert_data_integer, 
34                     ("edfimage", "fit2dmaskimage"): convert_data_integer, 
35                     ("edfimage", "kcdimage"): convert_data_integer, 
36                     ("edfimage", "OXDimage"): convert_data_integer, 
37                     ("edfimage", "pnmimage"): convert_data_integer, 
38                     } 
39   

        40 -def convert_data(inp, outp, data): 

        41      """ 
42      Return data converted to the output format ... over-simplistic implementation for the moment ... 
43      @param inp,outp: input/output format like "cbfimage" 
44      @param data(ndarray): the actual dataset to be transformed 
45      """ 
46      return CONVERSION_DATA.get((inp, outp), lambda data:data)(data) 

        47   

        48 -def convert_header(inp, outp, header): 

        49      """ 
50      return header converted to the output format 
51      @param inp,outp: input/output format like "cbfimage" 
52      @param header(dict):the actual set of headers to be transformed  
53      """ 
54      return CONVERSION_HEADER.get((inp, outp), lambda header:header)(header) 

        55

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        Package fabio :: Module edfimage
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        Source Code for Module fabio.edfimage

          1  #!/usr/bin/env python 
  2  # -*- coding: utf8 -*- 
  3  """ 
  4   
  5  License: GPLv2+ 
  6   
  7  Authors: 
  8  ........ 
  9  * Henning O. Sorensen & Erik Knudsen: 
 10    Center for Fundamental Research: Metal Structures in Four Dimensions; 
 11    Risoe National Laboratory; 
 12    Frederiksborgvej 399; 
 13    DK-4000 Roskilde; 
 14    email:erik.knudsen@risoe.dk 
 15  * Jon Wright & Jérôme Kieffer: 
 16    European Synchrotron Radiation Facility; 
 17    Grenoble (France) 
 18   
 19   
 20  """ 
 21  from __future__ import with_statement 
 22  import os, logging, types 
 23  logger = logging.getLogger("edfimage") 
 24  import numpy 
 25  from fabioimage import fabioimage 
 26  from fabioutils import isAscii, toAscii, nice_int 
 27  from compression import decBzip2, decGzip, decZlib 
 28   
 29   
 30  BLOCKSIZE = 512 
 31  DATA_TYPES = {  "SignedByte"    :  numpy.int8, 
 32                  "Signed8"       :  numpy.int8, 
 33                  "UnsignedByte"  :  numpy.uint8, 
 34                  "Unsigned8"     :  numpy.uint8, 
 35                  "SignedShort"   :  numpy.int16, 
 36                  "Signed16"      :  numpy.int16, 
 37                  "UnsignedShort" :  numpy.uint16, 
 38                  "Unsigned16"    :  numpy.uint16, 
 39                  "UnsignedShortInteger" : numpy.uint16, 
 40                  "SignedInteger" :  numpy.int32, 
 41                  "Signed32"      :  numpy.int32, 
 42                  "UnsignedInteger":  numpy.uint32, 
 43                  "Unsigned32"    :  numpy.uint32, 
 44                  "SignedLong"    :  numpy.int32, 
 45                  "UnsignedLong"  :  numpy.uint32, 
 46                  "Signed64"      :  numpy.int64, 
 47                  "Unsigned64"    :  numpy.uint64, 
 48                  "FloatValue"    :  numpy.float32, 
 49                  "FLOATVALUE"    :  numpy.float32, 
 50                  "FLOAT"         :  numpy.float32, # fit2d 
 51                  "Float"         :  numpy.float32, # fit2d 
 52                  "FloatIEEE32"   :  numpy.float32, 
 53                  "Float32"       :  numpy.float32, 
 54                  "Double"        :  numpy.float64, 
 55                  "DoubleValue"   :  numpy.float64, 
 56                  "FloatIEEE64"   :  numpy.float64, 
 57                  "DoubleIEEE64"  :  numpy.float64} 
 58  try: 
 59      DATA_TYPES["FloatIEEE128" ] =  numpy.float128 
 60      DATA_TYPES["DoubleIEEE128" ] =  numpy.float128 
 61      DATA_TYPES["QuadrupleValue" ] =  numpy.float128 
 62   
 63  except AttributeError: 
 64      # not in your numpy 
 65      pass 
 66   
 67  NUMPY_EDF_DTYPE = {"int8"       :"SignedByte", 
 68                     "int16"      :"SignedShort", 
 69                     "int32"      :"SignedInteger", 
 70                     "int64"      :"Signed64", 
 71                     "uint8"      :"UnsignedByte", 
 72                     "uint16"     :"UnsignedShort", 
 73                     "uint32"     :"UnsignedInteger", 
 74                     "uint64"     :"Unsigned64", 
 75                     "float32"    :"FloatValue", 
 76                     "float64"    :"DoubleValue", 
 77                     "float128"   :"QuadrupleValue", 
 78               } 
 79   
 80  MINIMUM_KEYS = ['HEADERID', 
 81                  'IMAGE', 
 82                  'BYTEORDER', 
 83                  'DATATYPE', 
 84                  'DIM_1', 
 85                  'DIM_2', 
 86                  'SIZE'] # Size is thought to be essential for writing at least 
 87   
 88  DEFAULT_VALUES = { 
 89                    # I do not define default values as they will be calculated at write time 
 90                    # JK20110415 
 91                    } 

         92   
 93 -class Frame(object): 

         94      """ 
 95      A class representing a single frame in an EDF file 
 96      """ 

         97 -    def __init__(self, data=None, header=None, header_keys=None, number=None): 

         98          if header is None: 
 99              self.header = {} 
100          else: 
101              self.header = dict(header) 
102   
103          if header_keys is None: 
104              self.header_keys = self.header.keys() 
105          else: 
106              self.header_keys = header_keys[:] 
107              for key in header_keys: 
108                  if key not in self.header: 
109                      logger.warning("Header key %s, in header_keys is not in header dictionary, poping !!!" % key) 
110                      self.header_keys.remove(key) 
111   
112          self.capsHeader = {} 
113          for key in self.header_keys: 
114              try: 
115                  self.capsHeader[key.upper()] = key 
116              except AttributeError: 
117                  logger.warning("Header key %s is not a string" % key) 
118          self._data = data 
119          self.dims = [] 
120          self.dim1 = 0 
121          self.dim2 = 0 
122          self.start = None # Position of start of raw data in file 
123          self.size = None  # size of raw data in file 
124          self.file = None  # opened file object with locking capabilities !!! 
125          self.bpp = None 
126          self._bytecode = None 
127          if (number is not None) and isinstance(number, int): 
128              self.iFrame = number 
129          else: 
130              self.iFrame = 0 

        131   

        132 -    def parseheader(self, block): 

        133          """ 
134          Parse the header in some EDF format from an already open file 
135   
136          @param block: string representing the header block 
137          @type block: string, should be full ascii 
138          @return: size of the binary blob 
139          """ 
140          #reset values ... 
141          self.header = {} 
142          self.capsHeader = {} 
143          self.header_keys = [] 
144          self.size = None 
145          calcsize = 1 
146          self.dims = [] 
147   
148          for line in block.split(';'): 
149              if '=' in line: 
150                  key, val = line.split('=' , 1) 
151                  # Why would someone put null bytes in a header? 
152                  key = key.replace("\x00"," ").strip() 
153                  self.header[key] = val.replace("\x00"," ").strip() 
154                  self.capsHeader[key.upper()] = key 
155                  self.header_keys.append(key) 
156   
157          # Compute image size 
158          if "SIZE" in self.capsHeader: 
159              try: 
160                  self.size = nice_int(self.header[self.capsHeader["SIZE"]]) 
161              except ValueError: 
162                  logger.warning("Unable to convert to integer : %s %s " % (self.capsHeader["SIZE"], self.header[self.capsHeader["SIZE"]])) 
163          if "DIM_1" in self.capsHeader: 
164              try: 
165                  dim1 = nice_int(self.header[self.capsHeader['DIM_1']]) 
166              except ValueError: 
167                  logger.error("Unable to convert to integer Dim_1: %s %s" % (self.capsHeader["DIM_1"], self.header[self.capsHeader["DIM_1"]])) 
168              else: 
169                  calcsize *= dim1 
170                  self.dims.append(dim1) 
171          else: 
172              logger.error("No Dim_1 in headers !!!") 
173          if "DIM_2" in self.capsHeader: 
174              try: 
175                  dim2 = nice_int(self.header[self.capsHeader['DIM_2']]) 
176              except ValueError: 
177                  logger.error("Unable to convert to integer Dim_3: %s %s" % (self.capsHeader["DIM_2"], self.header[self.capsHeader["DIM_2"]])) 
178              else: 
179                  calcsize *= dim2 
180                  self.dims.append(dim2) 
181          else: 
182              logger.error("No Dim_2 in headers !!!") 
183          iDim = 3 
184          # JON: this appears to be for nD images, but we don't treat those 
185          while iDim is not None: 
186              strDim = "DIM_%i" % iDim 
187              if strDim in self.capsHeader: 
188                  try: 
189                      dim3 = nice_int(self.header[self.capsHeader[strDim]]) 
190                  except ValueError: 
191                      logger.error("Unable to convert to integer %s: %s %s" 
192                                    % (strDim, self.capsHeader[strDim], self.header[self.capsHeader[strDim]])) 
193                      dim3 = None 
194                      iDim = None 
195                  else: 
196                      if dim3 > 1: 
197                          # Otherwise treat dim3==1 as a 2D image 
198                          calcsize *= dim3 
199                          self.dims.append(dim3) 
200                      iDim += 1 
201   
202              else: 
203                  logger.debug("No Dim_3 -> it is a 2D image") 
204                  iDim = None 
205          if self._bytecode is None: 
206              if "DATATYPE" in self.capsHeader: 
207                  self._bytecode = DATA_TYPES[self.header[self.capsHeader['DATATYPE']]] 
208              else: 
209                  self._bytecode = numpy.uint16 
210                  logger.warning("Defaulting type to uint16") 
211          self.bpp = len(numpy.array(0, self._bytecode).tostring()) 
212          calcsize *= self.bpp 
213          if (self.size is None): 
214              self.size = calcsize 
215          elif (self.size != calcsize): 
216              if ("COMPRESSION" in self.capsHeader) and (self.header[self.capsHeader['COMPRESSION']].upper().startswith("NO")): 
217                  logger.info("Mismatch between the expected size %s and the calculated one %s" % (self.size, calcsize)) 
218                  self.size = calcsize 
219   
220          for i, n in enumerate(self.dims): 
221              setattr(self, "dim%i" % (i + 1), n) 
222   
223          return self.size 

        224   
225   

        226 -    def swap_needed(self): 

        227          """ 
228          Decide if we need to byteswap 
229          """ 
230          if ('Low'  in self.header[self.capsHeader['BYTEORDER']] and numpy.little_endian) or \ 
231             ('High' in self.header[self.capsHeader['BYTEORDER']] and not numpy.little_endian): 
232              return False 
233          if ('High'  in self.header[self.capsHeader['BYTEORDER']] and numpy.little_endian) or \ 
234             ('Low' in self.header[self.capsHeader['BYTEORDER']] and not numpy.little_endian): 
235              if self.bpp in [2, 4, 8]: 
236                  return True 
237              else: 
238                  return False 

        239   
240   

        241 -    def getData(self): 

        242          """ 
243          Unpack a binary blob according to the specification given in the header 
244   
245          @return: dataset as numpy.ndarray 
246          """ 
247          data = None 
248          if self._data is not None: 
249              data = self._data 
250          elif self.file is None: 
251              data = self._data 
252          else: 
253              if self._bytecode is None: 
254                  if "DATATYPE" in self.capsHeader: 
255                      self._bytecode = DATA_TYPES[self.header[self.capsHeader["DATATYPE"]]] 
256                  else: 
257                      self._bytecode = numpy.uint16 
258              dims = self.dims[:] 
259              dims.reverse() 
260              with self.file.lock: 
261                  if self.file.closed: 
262                      logger.error("file: %s from %s is closed. Cannot read data." % (self.file, self.file.filename)) 
263                      return 
264                  else: 
265                      self.file.seek(self.start) 
266                      fileData = self.file.read(self.size) 
267   
268              if ("COMPRESSION" in self.capsHeader): 
269                  compression = self.header[self.capsHeader["COMPRESSION"]].upper() 
270                  uncompressed_size = self.bpp 
271                  for i in dims: 
272                      uncompressed_size *= i 
273                  if "OFFSET" in compression : 
274                      try: 
275                          import byte_offset#IGNORE:F0401 
276                      except ImportError, error: 
277                          logger.error("Unimplemented compression scheme:  %s (%s)" % (compression, error)) 
278                      else: 
279                          myData = byte_offset.analyseCython(fileData, size=uncompressed_size) 
280                          rawData = myData.astype(self._bytecode).tostring() 
281                          self.size = uncompressed_size 
282                  elif compression == "NONE": 
283                      rawData = fileData 
284                  elif "GZIP" in compression: 
285                      rawData = decGzip(fileData) 
286                      self.size = uncompressed_size 
287                  elif "BZ" in compression : 
288                      rawData = decBzip2(fileData) 
289                      self.size = uncompressed_size 
290                  elif "Z" in compression : 
291                      rawData = decZlib(fileData) 
292                      self.size = uncompressed_size 
293                  else: 
294                      logger.warning("Unknown compression scheme %s" % compression) 
295                      rawData = fileData 
296   
297              else: 
298                  rawData = fileData 
299   
300              expected = self.size 
301              obtained = len(rawData) 
302              if expected > obtained: 
303                  logger.error("Data stream is incomplete: %s < expected %s bytes" % (obtained, expected)) 
304                  rawData += "\x00" * (expected - obtained) 
305              elif expected < len(rawData): 
306                  logger.info("Data stream contains trailing junk : %s > expected %s bytes" % (obtained, expected)) 
307                  rawData = rawData[:expected] 
308              if self.swap_needed(): 
309                  data = numpy.fromstring(rawData, self._bytecode).byteswap().reshape(tuple(dims)) 
310              else: 
311                  data = numpy.fromstring(rawData, self._bytecode).reshape(tuple(dims)) 
312              self._data = data 
313              self._bytecode = data.dtype.type 
314          return data 

        315 -    def setData(self, npa=None): 

        316          """Setter for data in edf frame""" 
317          self._data = npa 

        318      data = property(getData, setData, "property: (edf)frame.data, uncompress the datablock when needed") 

        319 -    def getByteCode(self): 

        320          if self._bytecode is None: 
321              self._bytecode = self.data.dtype.type 
322   
323          return self._bytecode 

        324 -    def setByteCode(self, _iVal): 

        325          self._bytecode = _iVal 

        326      bytecode = property(getByteCode, setByteCode) 
327   

        328 -    def getEdfBlock(self, force_type=None, fit2dMode=False): 

        329          """ 
330          @param force_type: type of the dataset to be enforced like "float64" or "uint16" 
331          @type force_type: string or numpy.dtype 
332          @param fit2dMode: enforce compatibility with fit2d and starts countimg number of images at 1 
333          @type fit2dMode: boolean 
334          @return: ascii header block 
335          @rtype: python string with the concatenation of the ascii header and the binary data block 
336          """ 
337          if force_type is not None: 
338              data = self.data.astype(force_type) 
339          else: 
340              data = self.data 
341          fit2dMode = bool(fit2dMode) 
342          for key in self.header: 
343              KEY = key.upper() 
344              if KEY not in self.capsHeader: 
345                  self.capsHeader[KEY] = key 
346              if key not in self.header_keys: 
347                  self.header_keys.append(key) 
348   
349          header = self.header.copy() 
350          header_keys = self.header_keys[:] 
351          capsHeader = self.capsHeader.copy() 
352   
353          listHeader = ["{\n"] 
354  #        First of all clean up the headers: 
355          for i in capsHeader: 
356              if "DIM_" in i: 
357                  header.pop(capsHeader[i]) 
358                  header_keys.remove(capsHeader[i]) 
359          for KEY in ["SIZE", "EDF_BINARYSIZE", "EDF_HEADERSIZE", "BYTEORDER", "DATATYPE", "HEADERID", "IMAGE"]: 
360              if KEY in capsHeader: 
361                  header.pop(capsHeader[KEY]) 
362                  header_keys.remove(capsHeader[KEY]) 
363          if "EDF_DATABLOCKID" in capsHeader: 
364              header_keys.remove(capsHeader["EDF_DATABLOCKID"]) 
365              #but do not remove the value from dict, instead reset the key ... 
366              if capsHeader["EDF_DATABLOCKID"] != "EDF_DataBlockID": 
367                  header["EDF_DataBlockID"] = header.pop(capsHeader["EDF_DATABLOCKID"]) 
368                  capsHeader["EDF_DATABLOCKID"] = "EDF_DataBlockID" 
369   
370  #            Then update static headers freshly deleted 
371          header_keys.insert(0, "Size") 
372          header["Size"] = len(data.tostring()) 
373          header_keys.insert(0, "HeaderID") 
374          header["HeaderID"] = "EH:%06d:000000:000000" % (self.iFrame + fit2dMode) 
375          header_keys.insert(0, "Image") 
376          header["Image"] = str(self.iFrame + fit2dMode) 
377   
378          dims = list(data.shape) 
379          nbdim = len(dims) 
380          for i in dims: 
381              key = "Dim_%i" % nbdim 
382              header[key] = i 
383              header_keys.insert(0, key) 
384              nbdim -= 1 
385          header_keys.insert(0, "DataType") 
386          header["DataType"] = NUMPY_EDF_DTYPE[str(numpy.dtype(data.dtype))] 
387          header_keys.insert(0, "ByteOrder") 
388          if numpy.little_endian: 
389              header["ByteOrder"] = "LowByteFirst" 
390          else: 
391              header["ByteOrder"] = "HighByteFirst" 
392          approxHeaderSize = 100 
393          for key in header: 
394              approxHeaderSize += 7 + len(key) + len(str(header[key])) 
395          approxHeaderSize = BLOCKSIZE * (approxHeaderSize // BLOCKSIZE + 1) 
396          header_keys.insert(0, "EDF_HeaderSize") 
397          header["EDF_HeaderSize"] = str(BLOCKSIZE * (approxHeaderSize // BLOCKSIZE + 1)) 
398          header_keys.insert(0, "EDF_BinarySize") 
399          header["EDF_BinarySize"] = len(data.tostring()) 
400          header_keys.insert(0, "EDF_DataBlockID") 
401          if not "EDF_DataBlockID" in header: 
402              header["EDF_DataBlockID"] = "%i.Image.Psd" % (self.iFrame + fit2dMode) 
403          preciseSize = 4 #2 before {\n 2 after }\n 
404          for key in header_keys: 
405              #Escape keys or values that are no ascii 
406              strKey = str(key) 
407              if not isAscii(strKey, listExcluded=["}", "{"]): 
408                  logger.warning("Non ascii key %s, skipping" % strKey) 
409                  continue 
410              strValue = str(header[key]) 
411              if not isAscii(strValue, listExcluded=["}", "{"]): 
412                  logger.warning("Non ascii value %s, skipping" % strValue) 
413                  continue 
414              line = strKey + " = " + strValue + " ;\n" 
415              preciseSize += len(line) 
416              listHeader.append(line) 
417          if preciseSize > approxHeaderSize: 
418              logger.error("I expected the header block only at %s in fact it is %s" % (approxHeaderSize, preciseSize)) 
419              for  idx, line in enumerate(listHeader[:]): 
420                  if line.startswith("EDF_HeaderSize"): 
421                      headerSize = BLOCKSIZE * (preciseSize // BLOCKSIZE + 1) 
422                      newline = "EDF_HeaderSize = %s ;\n" % headerSize 
423                      delta = len(newline) - len(line) 
424                      if (preciseSize // BLOCKSIZE) != ((preciseSize + delta) // BLOCKSIZE): 
425                          headerSize = BLOCKSIZE * ((preciseSize + delta) // BLOCKSIZE + 1) 
426                          newline = "EDF_HeaderSize = %s ;\n" % headerSize 
427                      preciseSize = preciseSize + delta 
428                      listHeader[idx] = newline 
429                      break 
430          else: 
431              headerSize = approxHeaderSize 
432          listHeader.append(" "*(headerSize - preciseSize) + "}\n") 
433          return "".join(listHeader) + data.tostring() 

        434   

        435   
436   
437 -class edfimage(fabioimage): 

        438      """ Read and try to write the ESRF edf data format """ 
439   

        440 -    def __init__(self, data=None , header=None, header_keys=None, frames=None): 

        441          self.currentframe = 0 
442          self.filesize = None 
443          try: 
444              dim = len(data.shape) 
445          except Exception, error: #IGNORE:W0703 
446              logger.debug("Data don't look like a numpy array (%s), resetting all!!" % error) 
447              data = None 
448              dim = 0 
449              fabioimage.__init__(self, data, header) 
450          if dim == 2: 
451              fabioimage.__init__(self, data, header) 
452          elif dim == 1 : 
453              data.shape = (0, len(data)) 
454              fabioimage.__init__(self, data, header) 
455          elif dim == 3 : 
456              fabioimage.__init__(self, data[0, :, :], header) 
457          elif dim == 4 : 
458              fabioimage.__init__(self, data[0, 0, :, :], header) 
459          elif dim == 5 : 
460              fabioimage.__init__(self, data[0, 0, 0, :, :], header) 
461   
462          if frames is None: 
463              frame = Frame(data=self.data, header=self.header, 
464                            header_keys=header_keys , 
465                            number=self.currentframe) 
466              self.__frames = [frame] 
467          else: 
468              self.__frames = frames 

        469   
470      @staticmethod 

        471 -    def checkHeader(header=None): 

        472          """ 
473          Empty for fabioimage but may be populated by others classes 
474          """ 
475          if type(header) != types.DictionaryType: 
476              return {} 
477          new = {} 
478          for key, value in header.items(): 
479              new[toAscii(key, ";{}")] = toAscii(value, ";{}") 
480          return new 

        481   
482      @staticmethod 

        483 -    def _readHeaderBlock(infile): 

        484          """ 
485          Read in a header in some EDF format from an already open file 
486   
487          @param infile: file object open in read mode 
488          @return: string (or None if no header was found. 
489          """ 
490   
491          block = infile.read(BLOCKSIZE) 
492          if len(block) < BLOCKSIZE: 
493              logger.debug("Under-short header: only %i bytes in %s" % (len(block), infile.name)) 
494              return 
495          if (block.find("{") < 0) : 
496              # This does not look like an edf file 
497              logger.warning("no opening {. Corrupt header of EDF file %s" % infile.name) 
498              return 
499          while '}' not in block: 
500              block = block + infile.read(BLOCKSIZE) 
501              if len(block) > BLOCKSIZE * 20: 
502                  logger.warning("Runaway header in EDF file") 
503                  return 
504          start = block.find("{") + 1 
505          end = block.find("}") 
506   
507          # Now it is essential to go to the start of the binary part 
508          if block[end: end + 3] == "}\r\n": 
509              offset = end + 3 - len(block) 
510          elif block[end: end + 2] == "}\n": 
511              offset = end + 2 - len(block) 
512          else: 
513              logger.error("Unable to locate start of the binary section") 
514              offset = None 
515          if offset is not None: 
516              infile.seek(offset, os.SEEK_CUR) 
517          return block[start:end] 

        518   
519   

        520 -    def _readheader(self, infile): 

        521          """ 
522          Read all headers in a file and populate self.header 
523          data is not yet populated 
524          @type infile: file object open in read mode 
525          """ 
526          self.__frames = [] 
527          bContinue = True 
528          while bContinue: 
529              block = self._readHeaderBlock(infile) 
530              if block is None: 
531                  bContinue = False 
532                  break 
533              frame = Frame(number=self.nframes) 
534              size = frame.parseheader(block) 
535              frame.file = infile 
536              frame.start = infile.tell() 
537              frame.size = size 
538              self.__frames += [frame] 
539              try: 
540                  infile.seek(size, os.SEEK_CUR) 
541              except Exception, error: 
542                  logger.warning("infile is %s" % infile) 
543                  logger.warning("Position is %s" % infile.tell()) 
544                  logger.warning("size is %s" % size) 
545                  logger.error("It seams this error occurs under windows when reading a (large-) file over network: %s ", error) 
546                  raise Exception(error) 
547   
548              if  frame.start + size > infile.size: 
549                  logger.warning("Non complete datablock: got %s, expected %s" % (infile.size - frame.start, size)) 
550                  bContinue = False 
551                  break 
552   
553          for i, frame in enumerate(self.__frames): 
554              missing = [] 
555              for item in MINIMUM_KEYS: 
556                  if item not in frame.capsHeader: 
557                      missing.append(item) 
558              if len(missing) > 0: 
559                  logger.info("EDF file %s frame %i misses mandatory keys: %s " % (self.filename, i, " ".join(missing))) 
560          self.currentframe = 0 

        561   
562   

        563 -    def read(self, fname, frame=None): 

        564          """ 
565          Read in header into self.header and 
566              the data   into self.data 
567          """ 
568          self.resetvals() 
569          self.filename = fname 
570   
571          infile = self._open(fname, "rb") 
572          self._readheader(infile) 
573          if frame is None: 
574              pass 
575          elif frame < self.nframes: 
576              self = self.getframe(frame) 
577          else: 
578              logger.error("Reading file %s You requested frame %s but only %s frames are available", fname, frame, self.nframes) 
579          self.resetvals() 
580          # ensure the PIL image is reset 
581          self.pilimage = None 
582          return self 

        583   

        584 -    def swap_needed(self): 

        585          """ 
586          Decide if we need to byteswap 
587          """ 
588          if ('Low'  in self.header[self.capsHeader['BYTEORDER']] and numpy.little_endian) or \ 
589             ('High' in self.header[self.capsHeader['BYTEORDER']] and not numpy.little_endian): 
590              return False 
591          if ('High'  in self.header[self.capsHeader['BYTEORDER']] and numpy.little_endian) or \ 
592             ('Low' in self.header[self.capsHeader['BYTEORDER']] and not numpy.little_endian): 
593              if self.bpp in [2, 4, 8]: 
594                  return True 
595              else: 
596                  return False 

        597   

        598 -    def unpack(self): 

        599          """ 
600          Unpack a binary blob according to the specification given in the header and return the dataset 
601   
602          @return: dataset as numpy.ndarray 
603          """ 
604          return self.__frames[self.currentframe].getData() 

        605   
606   

        607 -    def getframe(self, num): 

        608          """ returns the file numbered 'num' in the series as a fabioimage """ 
609          newImage = None 
610          if self.nframes == 1: 
611              logger.debug("Single frame EDF; having fabioimage default behavour: %s" % num) 
612              newImage = fabioimage.getframe(self, num) 
613          elif num in xrange(self.nframes): 
614              logger.debug("Multi frame EDF; having edfimage specific behavour: %s/%s" % (num, self.nframes)) 
615              newImage = edfimage(frames=self.__frames) 
616              newImage.currentframe = num 
617              newImage.filename = self.filename 
618          else: 
619              txt = "Cannot access frame: %s/%s" % (num, self.nframes) 
620              logger.error(txt) 
621              raise ValueError("edfimage.getframe:" + txt) 
622          return newImage 

        623   
624   

        625 -    def previous(self): 

        626          """ returns the previous file in the series as a fabioimage """ 
627          newImage = None 
628          if self.nframes == 1: 
629              newImage = fabioimage.previous(self) 
630          else: 
631              newFrameId = self.currentframe - 1 
632              newImage = self.getframe(newFrameId) 
633          return newImage 

        634   
635   

        636 -    def next(self): 

        637          """ returns the next file in the series as a fabioimage """ 
638          newImage = None 
639          if self.nframes == 1: 
640              newImage = fabioimage.next(self) 
641          else: 
642              newFrameId = self.currentframe + 1 
643              newImage = self.getframe(newFrameId) 
644          return newImage 

        645   
646   

        647 -    def write(self, fname, force_type=None, fit2dMode=False): 

        648          """ 
649          Try to write a file 
650          check we can write zipped also 
651          mimics that fabian was writing uint16 (we sometimes want floats) 
652   
653          @param force_type: can be numpy.uint16 or simply "float" 
654          @return: None 
655   
656          """ 
657   
658          outfile = self._open(fname, mode="wb") 
659          for i, frame in enumerate(self.__frames): 
660              frame.iFrame = i 
661              outfile.write(frame.getEdfBlock(force_type=force_type, fit2dMode=fit2dMode)) 
662          outfile.close() 

        663   
664   

        665 -    def appendFrame(self, frame=None, data=None, header=None): 

        666          """ 
667          Method used add a frame to an EDF file 
668          @param frame: frame to append to edf image 
669          @type frame: instance of Frame 
670          @return: None 
671          """ 
672          if isinstance(frame, Frame): 
673              self.__frames.append(frame) 
674          else: 
675              self.__frames.append(Frame(data, header)) 

        676   
677   

        678 -    def deleteFrame(self, frameNb=None): 

        679          """ 
680          Method used to remove a frame from an EDF image. by default the last one is removed. 
681          @param frameNb: frame number to remove, by  default the last. 
682          @type frameNb: integer 
683          @return: None 
684          """ 
685          if frameNb is None: 
686              self.__frames.pop() 
687          else: 
688              self.__frames.pop(frameNb) 

        689   

        690 -    def fastReadData(self, filename=None): 

        691          """ 
692          This is a special method that will read and return the data from another file ... 
693          The aim is performances, ... but only supports uncompressed files.  
694            
695          @return: data from another file using positions from current edfimage 
696          """ 
697          if (filename is None) or not os.path.isfile(filename): 
698              raise RuntimeError("edfimage.fastReadData is only valid with another file: %s does not exist" % (filename)) 
699          data = None 
700          frame = self.__frames[self.currentframe] 
701          with open(filename, "rb")as f: 
702              f.seek(frame.start) 
703              raw = f.read(frame.size) 
704          try: 
705              data = numpy.fromstring(raw, dtype=self.bytecode) 
706              data.shape = self.data.shape 
707          except Exception, err : 
708              logger.error("unable to convert file content to numpy array: %s", err) 
709          return data 

        710   

        711 -    def fastReadROI(self, filename, coords=None): 

        712          """ 
713          Method reading Region of Interest of another file  based on metadata available in current edfimage. 
714          The aim is performances, ... but only supports uncompressed files. 
715           
716          @return: ROI-data from another file using positions from current edfimage 
717          @rtype: numpy 2darray 
718          """ 
719          if (filename is None) or not os.path.isfile(filename): 
720              raise RuntimeError("edfimage.fastReadData is only valid with another file: %s does not exist" % (filename)) 
721          data = None 
722          frame = self.__frames[self.currentframe] 
723   
724          if len(coords) == 4: 
725              slice1 = self.make_slice(coords) 
726          elif len(coords) == 2 and isinstance(coords[0], slice) and \ 
727                                    isinstance(coords[1], slice): 
728              slice1 = coords 
729          else: 
730              logger.warning('readROI: Unable to understand Region Of Interest: got %s', coords) 
731              return 
732          d1 = self.data.shape[-1] 
733          start0 = slice1[0].start 
734          start1 = slice1[1].start 
735          slice2 = (slice(0, slice1[0].stop - start0, slice1[0].step), 
736                     slice(0, slice1[1].stop - start1, slice1[1].step)) 
737          start = frame.start + self.bpp * (d1 * start0 + start1) 
738          size = self.bpp * ((slice2[0].stop) * d1) 
739          with open(filename, "rb")as f: 
740              f.seek(start) 
741              raw = f.read(size) 
742          try: 
743              data = numpy.fromstring(raw, dtype=self.bytecode) 
744              data.shape = -1, d1 
745          except Exception, err : 
746              logger.error("unable to convert file content to numpy array: %s", err) 
747          return data[slice2] 

        748   
749   
750  ################################################################################ 
751  # Properties definition for header, data, header_keys and capsHeader 
752  ################################################################################ 

        753 -    def getNbFrames(self): 

        754          """ 
755          Getter for number of frames 
756          """ 
757          return len(self.__frames) 

        758 -    def setNbFrames(self, val): 

        759          """ 
760          Setter for number of frames ... should do nothing. Here just to avoid bugs 
761          """ 
762          if val != len(self.__frames): 
763              logger.warning("trying to set the number of frames ") 

        764      nframes = property(getNbFrames, setNbFrames, "property: number of frames in EDF file") 
765   
766   

        767 -    def getHeader(self): 

        768          """ 
769          Getter for the headers. used by the property header, 
770          """ 
771          return self.__frames[self.currentframe].header 

        772 -    def setHeader(self, _dictHeader): 

        773          """ 
774          Enforces the propagation of the header to the list of frames 
775          """ 
776          try: 
777              self.__frames[self.currentframe].header = _dictHeader 
778          except AttributeError: 
779              self.__frames = [Frame(header=_dictHeader)] 
780          except IndexError: 
781              if self.currentframe < len(self.__frames): 
782                  self.__frames.append(Frame(header=_dictHeader)) 

        783 -    def delHeader(self): 

        784          """ 
785          Deleter for edf header 
786          """ 
787          self.__frames[self.currentframe].header = {} 

        788      header = property(getHeader, setHeader, delHeader, "property: header of EDF file") 
789   

        790 -    def getHeaderKeys(self): 

        791          """ 
792          Getter for edf header_keys 
793          """ 
794          return self.__frames[self.currentframe].header_keys 

        795 -    def setHeaderKeys(self, _listtHeader): 

        796          """ 
797          Enforces the propagation of the header_keys to the list of frames 
798          @param _listtHeader: list of the (ordered) keys in the header 
799          @type _listtHeader: python list 
800          """ 
801          try: 
802              self.__frames[self.currentframe].header_keys = _listtHeader 
803          except AttributeError: 
804              self.__frames = [Frame(header_keys=_listtHeader)] 
805          except IndexError: 
806              if self.currentframe < len(self.__frames): 
807                  self.__frames.append(Frame(header_keys=_listtHeader)) 

        808 -    def delHeaderKeys(self): 

        809          """ 
810          Deleter for edf header_keys 
811          """ 
812          self.__frames[self.currentframe].header_keys = [] 

        813      header_keys = property(getHeaderKeys, setHeaderKeys, delHeaderKeys, "property: header_keys of EDF file") 
814   

        815 -    def getData(self): 

        816          """ 
817          getter for edf Data 
818          @return: data for current frame 
819          @rtype: numpy.ndarray 
820          """ 
821          npaData = None 
822          try: 
823              npaData = self.__frames[self.currentframe].data 
824          except AttributeError: 
825              self.__frames = [Frame()] 
826              npaData = self.__frames[self.currentframe].data 
827          except IndexError: 
828              if self.currentframe < len(self.__frames): 
829                  self.__frames.append(Frame()) 
830                  npaData = self.__frames[self.currentframe].data 
831          return npaData 

        832   

        833 -    def setData(self, _data): 

        834          """ 
835          Enforces the propagation of the data to the list of frames 
836          @param _data: numpy array representing data 
837          """ 
838          try: 
839              self.__frames[self.currentframe].data = _data 
840          except AttributeError: 
841              self.__frames = [Frame(data=_data)] 
842          except IndexError: 
843              if self.currentframe < len(self.__frames): 
844                  self.__frames.append(Frame(data=_data)) 

        845 -    def delData(self): 

        846          """ 
847          deleter for edf Data 
848          """ 
849          self.__frames[self.currentframe].data = None 

        850      data = property(getData, setData, delData, "property: data of EDF file") 
851   

        852 -    def getCapsHeader(self): 

        853          """ 
854          getter for edf headers keys in upper case 
855          @return: data for current frame 
856          @rtype: dict 
857          """ 
858          return self.__frames[self.currentframe].capsHeader 

        859 -    def setCapsHeader(self, _data): 

        860          """ 
861          Enforces the propagation of the header_keys to the list of frames 
862          @param _data: numpy array representing data 
863          """ 
864          self.__frames[self.currentframe].capsHeader = _data 

        865 -    def delCapsHeader(self): 

        866          """ 
867          deleter for edf capsHeader 
868          """ 
869          self.__frames[self.currentframe].capsHeader = {} 

        870      capsHeader = property(getCapsHeader, setCapsHeader, delCapsHeader, "property: capsHeader of EDF file, i.e. the keys of the header in UPPER case.") 
871   

        872 -    def getDim1(self): 

        873          return self.__frames[self.currentframe].dim1 

        874 -    def setDim1(self, _iVal): 

        875          try: 
876              self.__frames[self.currentframe].dim1 = _iVal 
877          except AttributeError: 
878              self.__frames = [Frame()] 
879          except IndexError: 
880              if self.currentframe < len(self.__frames): 
881                  self.__frames.append(Frame()) 
882                  self.__frames[self.currentframe].dim1 = _iVal 

        883      dim1 = property(getDim1, setDim1) 

        884 -    def getDim2(self): 

        885          return self.__frames[self.currentframe].dim2 

        886 -    def setDim2(self, _iVal): 

        887          try: 
888              self.__frames[self.currentframe].dim2 = _iVal 
889          except AttributeError: 
890              self.__frames = [Frame()] 
891          except IndexError: 
892              if self.currentframe < len(self.__frames): 
893                  self.__frames.append(Frame()) 
894                  self.__frames[self.currentframe].dim2 = _iVal 

        895      dim2 = property(getDim2, setDim2) 
896   

        897 -    def getDims(self): 

        898          return self.__frames[self.currentframe].dims 

        899      dims = property(getDims) 

        900 -    def getByteCode(self): 

        901          return self.__frames[self.currentframe].bytecode 

        902 -    def setByteCode(self, _iVal): 

        903          try: 
904              self.__frames[self.currentframe].bytecode = _iVal 
905          except AttributeError: 
906              self.__frames = [Frame()] 
907          except IndexError: 
908              if self.currentframe < len(self.__frames): 
909                  self.__frames.append(Frame()) 
910                  self.__frames[self.currentframe].bytecode = _iVal 

        911      bytecode = property(getByteCode, setByteCode) 

        912 -    def getBpp(self): 

        913          return self.__frames[self.currentframe].bpp 

        914 -    def setBpp(self, _iVal): 

        915          try: 
916              self.__frames[self.currentframe].bpp = _iVal 
917          except AttributeError: 
918              self.__frames = [Frame()] 
919          except IndexError: 
920              if self.currentframe < len(self.__frames): 
921                  self.__frames.append(Frame()) 
922                  self.__frames[self.currentframe].bpp = _iVal 

        923      bpp = property(getBpp, setBpp) 

        924

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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:42 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/toc-fabio.dm3image-module.html0000644000175000017500000000274312120434325022345 0ustar jeromejerome00000000000000 dm3image

        Module dm3image

        Classes

        dm3image

        Variables

        DATA_BYTES
        DATA_TYPES
        __package__
        logger
        [hide private] fabio-0.1.3/epydoc/fabio.cbfimage.cbfimage-class.html0000644000175000017500000005546712126623347023232 0ustar jeromejerome00000000000000 fabio.cbfimage.cbfimage
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        Package fabio :: Module cbfimage :: Class cbfimage
        [hide private]
        [frames] | no frames]

        Class cbfimage

        source code

                   object --+    
                    |    
fabioimage.fabioimage --+
                        |
                       cbfimage

        Read the Cif Binary File data format

        Instance Methods [hide private]
         
        __init__(self, data=None, header=None, fname=None)
        Constructor of the class CIF Binary File reader.        		 source code
         
        _readheader(self, inStream)
        Read in a header in some CBF format from a string representing binary stuff        		 source code
         
        read(self, fname, frame=None)
        Read in header into self.header and...        		 source code
        numpy array
        _readbinary_byte_offset(self, inStream)
        Read in a binary part of an x-CBF_BYTE_OFFSET compressed image        		 source code
         
        write(self, fname)
        write the file in CBF format        		 source code

        Inherited from fabioimage.fabioimage: add, convert, getclassname, getframe, getheader, getmax, getmean, getmin, getstddev, integrate_area, load, make_slice, next, previous, readROI, readheader, rebin, resetvals, save, toPIL16, update_header

        Inherited from fabioimage.fabioimage (private): _compressed_stream, _open

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Static Methods [hide private]
         
        checkData(data=None)
        Empty for fabioimage but may be populated by others classes, especially for format accepting only integers        		 source code

        Inherited from fabioimage.fabioimage: checkHeader

        Class Variables [hide private]

        Inherited from fabioimage.fabioimage (private): _need_a_real_file, _need_a_seek_to_read

        Properties [hide private]

        Inherited from fabioimage.fabioimage: classname

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, data=None, header=None, fname=None)
        (Constructor)

        		source code 

        Constructor of the class CIF Binary File reader.

        Parameters:
        • _strFilename (string) - the name of the file to open
        Overrides: object.__init__

        checkData(data=None)
        Static Method

        		source code 

        Empty for fabioimage but may be populated by others classes, especially for format accepting only integers

        Overrides: fabioimage.fabioimage.checkData
        (inherited documentation)

        _readheader(self, inStream)

        		source code 

        Read in a header in some CBF format from a string representing binary stuff

        Parameters:
        • inStream (opened file.) - file containing the Cif Binary part.
        Overrides: fabioimage.fabioimage._readheader

        read(self, fname, frame=None)

        		source code  
        
Read in header into self.header and
    the data   into self.data
        Overrides: fabioimage.fabioimage.read

        _readbinary_byte_offset(self, inStream)

        		source code 

        Read in a binary part of an x-CBF_BYTE_OFFSET compressed image

        Parameters:
        • inStream (python string.) - the binary image (without any CIF decorators)
        Returns: numpy array
        a linear numpy array without shape and dtype set

        write(self, fname)

        		source code 

        write the file in CBF format

        Parameters:
        • fname - name of the file
        Overrides: fabioimage.fabioimage.write

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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:40 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/toc-fabio.mytest-module.html0000644000175000017500000000170512120434325022201 0ustar jeromejerome00000000000000 mytest

        Module mytest

        [hide private] fabio-0.1.3/epydoc/toc-fabio.fit2dmaskimage-module.html0000644000175000017500000000235412120434325023544 0ustar jeromejerome00000000000000 fit2dmaskimage

        Module fit2dmaskimage

        Classes

        fit2dmaskimage

        Variables

        __package__
        [hide private] fabio-0.1.3/epydoc/toc-fabio-module.html0000644000175000017500000000235012126623347020664 0ustar jeromejerome00000000000000 fabio

        Module fabio

        Variables

        __package__
        __status__
        version
        [hide private] fabio-0.1.3/epydoc/fabio.binaryimage-module.html0000644000175000017500000002136312126623347022374 0ustar jeromejerome00000000000000 fabio.binaryimage
           Home       Trees       Indices       Help   
        Package fabio :: Module binaryimage
        [hide private]
        [frames] | no frames]

        Module binaryimage

        source code

        Authors: Gael Goret, Jerome Kieffer, ESRF, France Emails: gael.goret@esrf.fr, jerome.kieffer@esrf.fr

        Binary files images are simple none-compressed 2D images only defined by their : data-type, dimensions, byte order and offset

        This simple library has been made for manipulating exotic/unknown files format.

        Version: 17 Apr 2012

        Authors:
        Ga\xc3\xabl Goret, J\xc3\xa9r\xc3\xb4me Kieffer

        Contact: gael.goret@esrf.fr

        Copyright: European Synchrotron Radiation Facility, Grenoble, France

        License: GPLv3+

        Classes [hide private]
          binaryimage
        This simple library has been made for manipulating exotic/unknown files format.
        Variables [hide private]
          __doc__ = ...
          logger = logging.getLogger("binaryimage")
          __package__ = 'fabio'
        Variables Details [hide private]

        __doc__

        Value:
        """
Authors: Gael Goret, Jerome Kieffer, ESRF, France
Emails: gael.goret@esrf.fr, jerome.kieffer@esrf.fr

Binary files images are simple none-compressed 2D images only defined \
by their : 
data-type, dimensions, byte order and offset

...

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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:40 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/fabio.GEimage-pysrc.html0000644000175000017500000035022312126623347021256 0ustar jeromejerome00000000000000 fabio.GEimage
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        Package fabio :: Module GEimage
        [hide private]
        [frames] | no frames]

        Source Code for Module fabio.GEimage

          1  #!/usr/bin/env python
 
  2  
 
  3  #
 
  4  # Reads the header from a GE a-Si Angio Detector
 
  5  # Using version 8001 of the header from file:
 
  6  #     c:\adept\core\DefaultImageInfoConfig.csv
 
  7  #
 
  8  #  Antonino Miceli
 
  9  #  Thu Jan  4 13:46:31 CST 2007
 
 10  #
 
 11  
 
 12  # modifications by Jon Wright for style, pychecker and fabio
 
 13  # 
 
 14  
 
 15  import numpy 
 16  import struct, logging 
 17  logger = logging.getLogger("GEimage") 
 18  from fabioimage import fabioimage 
 19  from fabioutils import next_filename, previous_filename 
 20  
 
 21  GE_HEADER_INFO = [
 
 22      # Name, length in bytes, format for struct (None means string)
 
 23      ('ImageFormat', 10, None),
 
 24      ('VersionOfStandardHeader', 2, '=H'),
 
 25      ('StandardHeaderSizeInBytes', 4, '=L'),
 
 26      ('VersionOfUserHeader', 2, '=H'),
 
 27      ('UserHeaderSizeInBytes', 4, '=L'),
 
 28      ('NumberOfFrames', 2, '=H'),
 
 29      ('NumberOfRowsInFrame', 2, '=H'),
 
 30      ('NumberOfColsInFrame', 2, '=H'),
 
 31      ('ImageDepthInBits', 2, '=H'),
 
 32      ('AcquisitionDate', 20, None),
 
 33      ('AcquisitionTime', 20, None),
 
 34      ('DUTID', 20, None),
 
 35      ('Operator', 50, None),
 
 36      ('DetectorSignature', 20, None),
 
 37      ('TestSystemName', 20, None),
 
 38      ('TestStationRevision', 20, None),
 
 39      ('CoreBundleRevision', 20, None),
 
 40      ('AcquisitionName', 40, None),
 
 41      ('AcquisitionParameterRevision', 20, None),
 
 42      ('OriginalNumberOfRows', 2, '=H'),
 
 43      ('OriginalNumberOfColumns', 2, '=H'),
 
 44      ('RowNumberUpperLeftPointArchiveROI', 2, '=H'),
 
 45      ('ColNumberUpperLeftPointArchiveROI', 2, '=H'),
 
 46      ('Swapped', 2, '=H'),
 
 47      ('Reordered', 2, '=H'),
 
 48      ('HorizontalFlipped', 2, '=H'),
 
 49      ('VerticalFlipped', 2, '=H'),
 
 50      ('WindowValueDesired', 2, '=H'),
 
 51      ('LevelValueDesired', 2, '=H'),
 
 52      ('AcquisitionMode', 2, '=H'),
 
 53      ('AcquisitionType', 2, '=H'),
 
 54      ('UserAcquisitionCoffFileName1', 100, None),
 
 55      ('UserAcquisitionCoffFileName2', 100, None),
 
 56      ('FramesBeforeExpose', 2, '=H'),
 
 57      ('FramesDuringExpose', 2, '=H'),
 
 58      ('FramesAfterExpose', 2, '=H'),
 
 59      ('IntervalBetweenFrames', 2, '=H'),
 
 60      ('ExposeTimeDelayInMicrosecs', 8, '=d'),
 
 61      ('TimeBetweenFramesInMicrosecs', 8, '=d'),
 
 62      ('FramesToSkipExpose', 2, '=H'),
 
 63      ('ExposureMode', 2, '=H'),
 
 64      ('PrepPresetTimeInMicrosecs', 8, '=d'),
 
 65      ('ExposePresetTimeInMicrosecs', 8, '=d'),
 
 66      ('AcquisitionFrameRateInFps', 4, '=f'),
 
 67      ('FOVSelect', 2, '=H'),
 
 68      ('ExpertMode', 2, '=H'),
 
 69      ('SetVCommon1', 8, '=d'),
 
 70      ('SetVCommon2', 8, '=d'),
 
 71      ('SetAREF', 8, '=d'),
 
 72      ('SetAREFTrim', 4, '=L'),
 
 73      ('SetSpareVoltageSource', 8, '=d'),
 
 74      ('SetCompensationVoltageSource', 8, '=d'),
 
 75      ('SetRowOffVoltage', 8, '=d'),
 
 76      ('SetRowOnVoltage', 8, '=d'),
 
 77      ('StoreCompensationVoltage', 4, '=L'),
 
 78      ('RampSelection', 2, '=H'),
 
 79      ('TimingMode', 2, '=H'),
 
 80      ('Bandwidth', 2, '=H'),
 
 81      ('ARCIntegrator', 2, '=H'),
 
 82      ('ARCPostIntegrator', 2, '=H'),
 
 83      ('NumberOfRows', 4, '=L'),
 
 84      ('RowEnable', 2, '=H'),
 
 85      ('EnableStretch', 2, '=H'),
 
 86      ('CompEnable', 2, '=H'),
 
 87      ('CompStretch', 2, '=H'),
 
 88      ('LeftEvenTristate', 2, '=H'),
 
 89      ('RightOddTristate', 2, '=H'),
 
 90      ('TestModeSelect', 4, '=L'),
 
 91      ('AnalogTestSource', 4, '=L'),
 
 92      ('VCommonSelect', 4, '=L'),
 
 93      ('DRCColumnSum', 4, '=L'),
 
 94      ('TestPatternFrameDelta', 4, '=L'),
 
 95      ('TestPatternRowDelta', 4, '=L'),
 
 96      ('TestPatternColumnDelta', 4, '=L'),
 
 97      ('DetectorHorizontalFlip', 2, '=H'),
 
 98      ('DetectorVerticalFlip', 2, '=H'),
 
 99      ('DFNAutoScrubOnOff', 2, '=H'),
 
100      ('FiberChannelTimeOutInMicrosecs', 4, '=L'),
 
101      ('DFNAutoScrubDelayInMicrosecs', 4, '=L'),
 
102      ('StoreAECROI', 2, '=H'),
 
103      ('TestPatternSaturationValue', 2, '=H'),
 
104      ('TestPatternSeed', 4, '=L'),
 
105      ('ExposureTimeInMillisecs', 4, '=f'),
 
106      ('FrameRateInFps', 4, '=f'),
 
107      ('kVp', 4, '=f'),
 
108      ('mA', 4, '=f'),
 
109      ('mAs', 4, '=f'),
 
110      ('FocalSpotInMM', 4, '=f'),
 
111      ('GeneratorType', 20, None),
 
112      ('StrobeIntensityInFtL', 4, '=f'),
 
113      ('NDFilterSelection', 2, '=H'),
 
114      ('RefRegTemp1', 8, '=d'),
 
115      ('RefRegTemp2', 8, '=d'),
 
116      ('RefRegTemp3', 8, '=d'),
 
117      ('Humidity1', 4, '=f'),
 
118      ('Humidity2', 4, '=f'),
 
119      ('DetectorControlTemp', 8, '=d'),
 
120      ('DoseValueInmR', 8, '=d'),
 
121      ('TargetLevelROIRow0', 2, '=H'),
 
122      ('TargetLevelROICol0', 2, '=H'),
 
123      ('TargetLevelROIRow1', 2, '=H'),
 
124      ('TargetLevelROICol1', 2, '=H'),
 
125      ('FrameNumberForTargetLevelROI', 2, '=H'),
 
126      ('PercentRangeForTargetLevel', 2, '=H'),
 
127      ('TargetValue', 2, '=H'),
 
128      ('ComputedMedianValue', 2, '=H'),
 
129      ('LoadZero', 2, '=H'),
 
130      ('MaxLUTOut', 2, '=H'),
 
131      ('MinLUTOut', 2, '=H'),
 
132      ('MaxLinear', 2, '=H'),
 
133      ('Reserved', 2, '=H'),
 
134      ('ElectronsPerCount', 2, '=H'),
 
135      ('ModeGain', 2, '=H'),
 
136      ('TemperatureInDegC', 8, '=d'),
 
137      ('LineRepaired', 2, '=H'),
 
138      ('LineRepairFileName', 100, None),
 
139      ('CurrentLongitudinalInMM', 4, '=f'),
 
140      ('CurrentTransverseInMM', 4, '=f'),
 
141      ('CurrentCircularInMM', 4, '=f'),
 
142      ('CurrentFilterSelection', 4, '=L'),
 
143      ('DisableScrubAck', 2, '=H'),
 
144      ('ScanModeSelect', 2, '=H'),
 
145      ('DetectorAppSwVersion', 20, None),
 
146      ('DetectorNIOSVersion', 20, None),
 
147      ('DetectorPeripheralSetVersion', 20, None),
 
148      ('DetectorPhysicalAddress', 20, None),
 
149      ('PowerDown', 2, '=H'),
 
150      ('InitialVoltageLevel_VCOMMON', 8, '=d'),
 
151      ('FinalVoltageLevel_VCOMMON', 8, '=d'),
 
152      ('DmrCollimatorSpotSize', 10, None),
 
153      ('DmrTrack', 5, None),
 
154      ('DmrFilter', 5, None),
 
155      ('FilterCarousel', 2, '=H'),
 
156      ('Phantom', 20, None),
 
157      ('SetEnableHighTime', 2, '=H'),
 
158      ('SetEnableLowTime', 2, '=H'),
 
159      ('SetCompHighTime', 2, '=H'),
 
160      ('SetCompLowTime', 2, '=H'),
 
161      ('SetSyncLowTime', 2, '=H'),
 
162      ('SetConvertLowTime', 2, '=H'),
 
163      ('SetSyncHighTime', 2, '=H'),
 
164      ('SetEOLTime', 2, '=H'),
 
165      ('SetRampOffsetTime', 2, '=H'),
 
166      ('FOVStartingValue', 2, '=H'),
 
167      ('ColumnBinning', 2, '=H'),
 
168      ('RowBinning', 2, '=H'),
 
169      ('BorderColumns64', 2, '=H'),
 
170      ('BorderRows64', 2, '=H'),
 
171      ('FETOffRows64', 2, '=H'),
 
172      ('FOVStartColumn128', 2, '=H'),
 
173      ('FOVStartRow128', 2, '=H'),
 
174      ('NumberOfColumns128', 2, '=H'),
 
175      ('NumberOfRows128', 2, '=H'),
 
176      ('VFPAquisition', 2000, None),
 
177      ('Comment', 200, None)
 
178      ] 
179  
 
180  
 

        181 -class GEimage(fabioimage): 

        182  
 
183      _need_a_seek_to_read = True 
184  
 

        185 -    def _readheader(self, infile): 

        186          """ Read a GE image header """ 
187  
 
188          infile.seek(0) 
189  
 
190          self.header = {} 
191          for name, nbytes, format in GE_HEADER_INFO: 
192              if format is None: 
193                  self.header[ name ] = infile.read(nbytes) 
194              else: 
195                  self.header[ name ] = struct.unpack(format,
 
196                                                       infile.read(nbytes))[0] 

        197  
 

        198 -    def read(self, fname, frame=None): 

        199          """
 
200          Read in header into self.header and
 
201          the data   into self.data
 
202          """ 
203          if frame is None: 
204              frame = 0 
205          self.header = {} 
206          self.resetvals() 
207          infile = self._open(fname, "rb") 
208          self.sequencefilename = fname 
209          self._readheader(infile) 
210          self.nframes = self.header['NumberOfFrames'] 
211          self._readframe(infile, frame) 
212          infile.close() 
213          return self 

        214  
 

        215 -    def _makeframename(self): 

        216          """ The thing to be printed for the user to represent a frame inside
 
217          a file """ 
218          self.filename = "%s$%04d" % (self.sequencefilename,
 
219                                     self.currentframe) 

        220  
 

        221 -    def _readframe(self, filepointer, img_num): 

        222          """
 
223          # Load only one image from the sequence
 
224          #    Note: the first image in the sequence 0
 
225          # raises an exception if you give an invalid image
 
226          # otherwise fills in self.data
 
227          """ 
228          if(img_num > self.nframes or img_num < 0): 
229              raise Exception("Bad image number") 
230          imgstart = self.header['StandardHeaderSizeInBytes'] + \
 
231                     self.header['UserHeaderSizeInBytes'] + \
 
232                     img_num * self.header['NumberOfRowsInFrame'] * \
 
233                     self.header['NumberOfColsInFrame'] * \
 
234                     self.header['ImageDepthInBits'] / 8 
235          # whence = 0 means seek from start of file
 
236          filepointer.seek(imgstart, 0) 
237  
 
238          self.bpp = self.header['ImageDepthInBits'] / 8 # hopefully 2         
239          imglength = self.header['NumberOfRowsInFrame'] * \
 
240                      self.header['NumberOfColsInFrame'] * self.bpp 
241          if self.bpp != 2: 
242              logging.warning("Using uint16 for GE but seems to be wrong") 
243  
 
244          # Guessing it is always unsigned int?
 
245          self.data = numpy.fromstring(filepointer.read(imglength), numpy.uint16) 
246          self.data.shape = (self.header['NumberOfRowsInFrame'],
 
247                              self.header['NumberOfColsInFrame']) 
248          self.dim2 , self.dim1 = self.data.shape 
249          self.currentframe = int(img_num) 
250          self._makeframename() 

        251  
 
252  
 

        253 -    def write(self, fname, force_type=numpy.uint16): 

        254          """ Not yet implemented""" 
255          raise Exception("Write is not implemented") 

        256  
 

        257 -    def getframe(self, num): 

        258          """
 
259          Returns a frame as a new fabioimage object
 
260          """ 
261          if num < 0 or num > self.nframes: 
262              raise Exception("Requested frame number is out of range") 
263          # Do a deep copy of the header to make a new one
 
264          newheader = {} 
265          for k in self.header.keys(): 
266              newheader[k] = self.header[k] 
267          frame = GEimage(header=newheader) 
268          frame.nframes = self.nframes 
269          frame.sequencefilename = self.sequencefilename 
270          infile = frame._open(self.sequencefilename, "rb") 
271          frame._readframe(infile, num) 
272          infile.close() 
273          return frame 

        274  
 

        275 -    def next(self): 

        276          """
 
277          Get the next image in a series as a fabio image
 
278          """ 
279          if self.currentframe < (self.nframes - 1) and self.nframes > 1: 
280              return self.getframe(self.currentframe + 1) 
281          else: 
282              newobj = GEimage() 
283              newobj.read(next_filename(
 
284                  self.sequencefilename)) 
285              return newobj 

        286  
 

        287 -    def previous(self): 

        288          """
 
289          Get the previous image in a series as a fabio image
 
290          """ 
291          if self.currentframe > 0: 
292              return self.getframe(self.currentframe - 1) 
293          else: 
294              newobj = GEimage() 
295              newobj.read(previous_filename(
 
296                  self.sequencefilename)) 
297              return newobj 

        298  
 
299  
 

        300 -def demo(): 

        301      import sys, time 
302  
 
303      if len(sys.argv) < 2: 
304          print "USAGE: GE_script.py <GEaSi_raw_image_file>" 
305          sys.exit() 
306  
 
307      image_file = sys.argv[1] 
308  
 
309      print "init read_GEaSi_data class and load header.." 
310      sequence1 = GEimage() 
311      sequence1.read(image_file) 
312  
 
313      print "TimeBetweenFramesInMicrosecs = ", 
314      print sequence1.header['TimeBetweenFramesInMicrosecs'] 
315      print "AcquisitionTime = ", 
316      print sequence1.header['AcquisitionTime'] 
317  
 
318  
 
319      print "Mean = ", sequence1.data.ravel().mean() 
320  
 
321      while 1: 
322          start = time.time() 
323          try: 
324              sequence1 = sequence1.next() 
325              print sequence1.currentframe, sequence1.data.ravel().mean(), \
 
326                    time.time() - start 
327          except Exception, ex: 
328              raise ex 

        329  
 
330  
 
331  
 
332  
 
333  if __name__ == '__main__': 
334      demo() 
335

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        Package fabio :: Module fit2dmaskimage
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        Module fit2dmaskimage

        source code

        Author: Andy Hammersley, ESRF Translation into python/fabio: Jon Wright, ESRF

        Classes [hide private]
          fit2dmaskimage
        Read and try to write Andy Hammersley's mask format
        Variables [hide private]
          __package__ = 'fabio'
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        fabio-0.1.3/epydoc/fabio.kcdimage-pysrc.html0000644000175000017500000015506512126623347021533 0ustar jeromejerome00000000000000 fabio.kcdimage
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        Package fabio :: Module kcdimage
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        Source Code for Module fabio.kcdimage

          1  #!/usr/bin/env python 
  2  """ 
  3  Authors: Jerome Kieffer, ESRF  
  4           email:jerome.kieffer@esrf.fr 
  5   
  6  kcd images are 2D images written by the old KappaCCD diffractometer built by Nonius in the 1990's 
  7  Based on the edfimage.py parser. 
  8  """ 
  9   
 10  import numpy, logging 
 11  import os, string 
 12  from fabioimage import fabioimage 
 13  logger = logging.getLogger("kcdimage") 
 14   
 15  DATA_TYPES = {"u16"  :  numpy.uint16 } 
 16   
 17  MINIMUM_KEYS = [ 
 18                  'ByteOrder', 
 19                  'Data type', 
 20                  'X dimension', 
 21                  'Y dimension', 
 22                  'Number of readouts'] 
 23   
 24  DEFAULT_VALUES = { "Data type": "u16" } 

         25   
 26   
 27   
 28   
 29 -class kcdimage(fabioimage): 

         30      """  
 31      Read the Nonius kcd data format """ 
 32   
 33   

         34 -    def _readheader(self, infile): 

         35          """ 
 36          Read in a header in some KCD format from an already open file 
 37          @ 
 38          """ 
 39          oneLine = infile.readline() 
 40          alphanum = string.digits + string.letters + ". " 
 41          asciiHeader = True 
 42          for oneChar in oneLine.strip(): 
 43              if not oneChar in alphanum: 
 44                  asciiHeader = False 
 45   
 46   
 47          if asciiHeader is False: 
 48              # This does not look like an edf file 
 49              logger.warning("First line of %s does not seam to be ascii text!" % infile.name) 
 50          endOfHeaders = False 
 51          while not endOfHeaders: 
 52              oneLine = infile.readline() 
 53              if len(oneLine) > 100: 
 54                  endOfHeaders = True 
 55                  break 
 56              if oneLine.strip() == "Binned mode": 
 57                  oneLine = "Mode = Binned" 
 58              try: 
 59                  key, val = oneLine.split('=' , 1) 
 60              except: 
 61                  endOfHeaders = True 
 62                  break 
 63              key = key.strip() 
 64              self.header_keys.append(key) 
 65              self.header[key] = val.strip() 
 66          missing = [] 
 67          for item in MINIMUM_KEYS: 
 68              if item not in self.header_keys: 
 69                  missing.append(item) 
 70          if len(missing) > 0: 
 71              logger.debug("KCD file misses the keys " + " ".join(missing)) 

         72   
 73   

         74 -    def read(self, fname, frame=None): 

         75          """ 
 76          Read in header into self.header and 
 77              the data   into self.data 
 78          """ 
 79          self.header = {} 
 80          self.resetvals() 
 81          infile = self._open(fname, "rb") 
 82          self._readheader(infile) 
 83          # Compute image size 
 84          try: 
 85              self.dim1 = int(self.header['X dimension']) 
 86              self.dim2 = int(self.header['Y dimension']) 
 87          except: 
 88              raise Exception("KCD file %s is corrupt, cannot read it" % fname) 
 89          try: 
 90              bytecode = DATA_TYPES[self.header['Data type']] 
 91              self.bpp = len(numpy.array(0, bytecode).tostring()) 
 92          except KeyError: 
 93              bytecode = numpy.uint16 
 94              self.bpp = 2 
 95              logger.warning("Defaulting type to uint16") 
 96          try: 
 97              nbReadOut = int(self.header['Number of readouts']) 
 98          except KeyError: 
 99              logger.warning("Defaulting number of ReadOut to 1") 
100              nbReadOut = 1 
101          fileSize = os.stat(fname)[6] 
102          expected_size = self.dim1 * self.dim2 * self.bpp * nbReadOut 
103          infile.seek(fileSize - expected_size) 
104          block = infile.read() 
105          assert len(block) == expected_size 
106          infile.close() 
107   
108          #now read the data into the array 
109          self.data = numpy.zeros((self.dim2, self.dim1)) 
110          try: 
111              for i in range(nbReadOut): 
112                  self.data += numpy.reshape(numpy.fromstring( 
113                      block[i * expected_size / nbReadOut:(i + 1) * expected_size / nbReadOut], bytecode), 
114                      [self.dim2, self.dim1]) 
115          except: 
116              print len(block), bytecode, self.bpp, self.dim2, self.dim1 
117              raise IOError, \ 
118                'Size spec in kcd-header does not match size of image data field' 
119          self.bytecode = self.data.dtype.type 
120          self.resetvals() 
121          # ensure the PIL image is reset 
122          self.pilimage = None 
123          return self 

        124   
125   
126      @staticmethod 

        127 -    def checkData(data=None): 

        128          if data is None: 
129              return None 
130          else: 
131              return data.astype(int) 

        132

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        Package fabio :: Module kcdimage :: Class kcdimage
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        Class kcdimage

        source code

                   object --+    
                    |    
fabioimage.fabioimage --+
                        |
                       kcdimage

        Read the Nonius kcd data format

        Instance Methods [hide private]
         
        _readheader(self, infile)
        Read in a header in some KCD format from an already open file @        		 source code
         
        read(self, fname, frame=None)
        Read in header into self.header and...        		 source code

        Inherited from fabioimage.fabioimage: __init__, add, convert, getclassname, getframe, getheader, getmax, getmean, getmin, getstddev, integrate_area, load, make_slice, next, previous, readROI, readheader, rebin, resetvals, save, toPIL16, update_header, write

        Inherited from fabioimage.fabioimage (private): _compressed_stream, _open

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Static Methods [hide private]
         
        checkData(data=None)
        Empty for fabioimage but may be populated by others classes, especially for format accepting only integers        		 source code

        Inherited from fabioimage.fabioimage: checkHeader

        Class Variables [hide private]

        Inherited from fabioimage.fabioimage (private): _need_a_real_file, _need_a_seek_to_read

        Properties [hide private]

        Inherited from fabioimage.fabioimage: classname

        Inherited from object: __class__

        Method Details [hide private]

        _readheader(self, infile)

        		source code 

        Read in a header in some KCD format from an already open file @

        Overrides: fabioimage.fabioimage._readheader

        read(self, fname, frame=None)

        		source code  
        
Read in header into self.header and
    the data   into self.data
        Overrides: fabioimage.fabioimage.read

        checkData(data=None)
        Static Method

        		source code 

        Empty for fabioimage but may be populated by others classes, especially for format accepting only integers

        Overrides: fabioimage.fabioimage.checkData
        (inherited documentation)

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        fabio-0.1.3/epydoc/fabio.brukerimage.brukerimage-class.html0000644000175000017500000004511612126623347024520 0ustar jeromejerome00000000000000 fabio.brukerimage.brukerimage
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        Package fabio :: Module brukerimage :: Class brukerimage
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        Class brukerimage

        source code

                   object --+    
                    |    
fabioimage.fabioimage --+
                        |
                       brukerimage
        Known Subclasses:

        Read and eventually write ID11 bruker (eg smart6500) images

        Instance Methods [hide private]
         
        _readheader(self, infile)
        the bruker format uses 80 char lines in key : value format In the fisrt 512*5 bytes of the header there should be a HDRBLKS key, whose value denotes how many 512 byte blocks are in the total header.        		 source code
         
        read(self, fname, frame=None)
        Read in and unpack the pixels (including overflow table        		 source code
         
        write(self, fname)
        Writes the image as EDF        		 source code
         
        write2(self, fname)
        FIXME: what is this?

        Inherited from fabioimage.fabioimage: __init__, add, convert, getclassname, getframe, getheader, getmax, getmean, getmin, getstddev, integrate_area, load, make_slice, next, previous, readROI, readheader, rebin, resetvals, save, toPIL16, update_header

        Inherited from fabioimage.fabioimage (private): _compressed_stream, _open

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Static Methods [hide private]

        Inherited from fabioimage.fabioimage: checkData, checkHeader

        Class Variables [hide private]
          __headerstring__ = ''

        Inherited from fabioimage.fabioimage (private): _need_a_real_file, _need_a_seek_to_read

        Properties [hide private]

        Inherited from fabioimage.fabioimage: classname

        Inherited from object: __class__

        Method Details [hide private]

        _readheader(self, infile)

        		source code 

        the bruker format uses 80 char lines in key : value format In the fisrt 512*5 bytes of the header there should be a HDRBLKS key, whose value denotes how many 512 byte blocks are in the total header. The header is always n*5*512 bytes, otherwise it wont contain whole key: value pairs

        Overrides: fabioimage.fabioimage._readheader

        read(self, fname, frame=None)

        		source code 

        Read in and unpack the pixels (including overflow table

        Overrides: fabioimage.fabioimage.read

        write(self, fname)

        		source code  
        
Writes the image as EDF

FIXME:  this should call edfimage.write if that is wanted?
        obj = edfimage(data = self.data, header = self.header)
        obj.write(fname)
        or maybe something like: edfimage.write(self, fname)
        Overrides: fabioimage.fabioimage.write

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        Package fabio :: Module datIO
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        Source Code for Module fabio.datIO

         1  #!/usr/bin/env python 
 2  #coding: utf8 
 3  """ 
 4  Authors: Henning O. Sorensen & Erik Knudsen 
 5           Center for Fundamental Research: Metal Structures in Four Dimensions 
 6           Risoe National Laboratory 
 7           Frederiksborgvej 399 
 8           DK-4000 Roskilde 
 9           email:erik.knudsen@risoe.dk 
10            
11           and Jon Wright, ESRF 
12  """ 
13   

        14 -class fabiodata(object): 

        15      """ 
16      A common class for dataIO in fable 
17      Contains a 2d numpy array for keeping data, and two lists (clabels and rlabels) 
18      containing labels for columns and rows respectively 
19      """ 
20   

        21 -    def __init__(self, data=None, clabels=None, rlabels=None, fname=None): 

        22          """ 
23          set up initial values 
24          """ 
25          if type(data) == type("string"): 
26              raise Exception("fabioimage.__init__ bad argument - " + \ 
27                                  "data should be numpy array") 
28          self.data = data 
29          if (self.data): 
30              self.dims = self.data.shape 
31          self.clabels = clabels 
32          self.rlabels = rlabels 
33          if (fname): 
34              self.read(fname) 

        35   

        36 -    def read(self, fname=None, frame=None): 

        37          """ 
38          To be overridden by format specific subclasses 
39          """ 
40          raise Exception("Class has not implemented read method yet") 

        41   
42  #import stuff from Jon's columnfile things 
43   
44   

        45 -class columnfile(fabiodata): 

        46      "Concrete fabiodata class" 

        47 -    def read(self, fname, frame=None): 

        48          import cf_io 
49          try: 
50              infile = open(fname, 'rb') 
51          except: 
52              raise Exception("columnfile: file" + str(fname) + "not found.") 
53          try: 
54              (self.data, self.clabels) = cf_io.read(infile) 
55          except: 
56              raise Exception("columnfile: read error, file " + str(fname) + " possibly corrupt") 
57          self.dims = self.data.shape 
58          infile.close() 

        59

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        Package fabio :: Module fit2dspreadsheetimage
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        Module fit2dspreadsheetimage

        source code

        
Read the fit2d ascii image output
        + Jon Wright, ESRF
        Classes [hide private]
          fit2dspreadsheetimage
        Read a fit2d ascii format
        Variables [hide private]
          __package__ = 'fabio'
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        str :: Class str
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        Class str

        object --+    
         |    
basestring --+
             |
            str

        str(object) -> string

        Return a nice string representation of the object. If the argument is a string, the return value is the same object.

        Instance Methods [hide private]
         
        __add__(x, y)
        x+y
         
        __contains__(x, y)
        y in x
         
        __eq__(x, y)
        x==y
        string
        __format__(S, format_spec)
        default object formatter
         
        __ge__(x, y)
        x>=y
         
        __getattribute__(...)
        x.__getattribute__('name') <==> x.name
         
        __getitem__(x, y)
        x[y]
         
        __getnewargs__(...)
         
        __getslice__(x, i, j)
        x[i:j]
         
        __gt__(x, y)
        x>y
         
        __hash__(x)
        hash(x)
         
        __le__(x, y)
        x<=y
         
        __len__(x)
        len(x)
         
        __lt__(x, y)
        x<y
         
        __mod__(x, y)
        x%y
         
        __mul__(x, n)
        x*n
         
        __ne__(x, y)
        x!=y
        a new object with type S, a subtype of T
        __new__(T, S, ...)
         
        __repr__(x)
        repr(x)
         
        __rmod__(x, y)
        y%x
         
        __rmul__(x, n)
        n*x
        size of S in memory, in bytes
        __sizeof__(S)
         
        __str__(x)
        str(x)
         
        _formatter_field_name_split(...)
         
        _formatter_parser(...)
        string
        capitalize(S)
        Return a copy of the string S with only its first character capitalized.
        string
        center(S, width, fillchar=...)
        Return S centered in a string of length width.
        int
        count(S, sub, start=..., end=...)
        Return the number of non-overlapping occurrences of substring sub in string S[start:end].
        object
        decode(S, encoding=..., errors=...)
        Decodes S using the codec registered for encoding.
        object
        encode(S, encoding=..., errors=...)
        Encodes S using the codec registered for encoding.
        bool
        endswith(S, suffix, start=..., end=...)
        Return True if S ends with the specified suffix, False otherwise.
        string
        expandtabs(S, tabsize=...)
        Return a copy of S where all tab characters are expanded using spaces.
        int
        find(S, sub, start=... , end=...)
        Return the lowest index in S where substring sub is found, such that sub is contained within s[start:end].
        string
        format(S, *args, **kwargs)
        int
        index(S, sub, start=... , end=...)
        Like S.find() but raise ValueError when the substring is not found.
        bool
        isalnum(S)
        Return True if all characters in S are alphanumeric and there is at least one character in S, False otherwise.
        bool
        isalpha(S)
        Return True if all characters in S are alphabetic and there is at least one character in S, False otherwise.
        bool
        isdigit(S)
        Return True if all characters in S are digits and there is at least one character in S, False otherwise.
        bool
        islower(S)
        Return True if all cased characters in S are lowercase and there is at least one cased character in S, False otherwise.
        bool
        isspace(S)
        Return True if all characters in S are whitespace and there is at least one character in S, False otherwise.
        bool
        istitle(S)
        Return True if S is a titlecased string and there is at least one character in S, i.e.
        bool
        isupper(S)
        Return True if all cased characters in S are uppercase and there is at least one cased character in S, False otherwise.
        string
        join(S, iterable)
        Return a string which is the concatenation of the strings in the iterable.
        string
        ljust(S, width, fillchar=...)
        Return S left-justified in a string of length width.
        string
        lower(S)
        Return a copy of the string S converted to lowercase.
        string or unicode
        lstrip(S, chars=...)
        Return a copy of the string S with leading whitespace removed.
        (head, sep, tail)
        partition(S, sep)
        Search for the separator sep in S, and return the part before it, the separator itself, and the part after it.
        string
        replace(S, old, new, count=...)
        Return a copy of string S with all occurrences of substring old replaced by new.
        int
        rfind(S, sub, start=... , end=...)
        Return the highest index in S where substring sub is found, such that sub is contained within s[start:end].
        int
        rindex(S, sub, start=... , end=...)
        Like S.rfind() but raise ValueError when the substring is not found.
        string
        rjust(S, width, fillchar=...)
        Return S right-justified in a string of length width.
        (head, sep, tail)
        rpartition(S, sep)
        Search for the separator sep in S, starting at the end of S, and return the part before it, the separator itself, and the part after it.
        list of strings
        rsplit(S, sep=... , maxsplit=...)
        Return a list of the words in the string S, using sep as the delimiter string, starting at the end of the string and working to the front.
        string or unicode
        rstrip(S, chars=...)
        Return a copy of the string S with trailing whitespace removed.
        list of strings
        split(S, sep=... , maxsplit=...)
        Return a list of the words in the string S, using sep as the delimiter string.
        list of strings
        splitlines(S, keepends=...)
        Return a list of the lines in S, breaking at line boundaries.
        bool
        startswith(S, prefix, start=..., end=...)
        Return True if S starts with the specified prefix, False otherwise.
        string or unicode
        strip(S, chars=...)
        Return a copy of the string S with leading and trailing whitespace removed.
        string
        swapcase(S)
        Return a copy of the string S with uppercase characters converted to lowercase and vice versa.
        string
        title(S)
        Return a titlecased version of S, i.e.
        string
        translate(S, table, deletechars=...)
        Return a copy of the string S, where all characters occurring in the optional argument deletechars are removed, and the remaining characters have been mapped through the given translation table, which must be a string of length 256.
        string
        upper(S)
        Return a copy of the string S converted to uppercase.
        string
        zfill(S, width)
        Pad a numeric string S with zeros on the left, to fill a field of the specified width.

        Inherited from object: __delattr__, __init__, __reduce__, __reduce_ex__, __setattr__, __subclasshook__

        Properties [hide private]

        Inherited from object: __class__

        Method Details [hide private]

        __format__(S, format_spec)

        		 

        default object formatter

        Returns: string
        Overrides: object.__format__

        __getattribute__(...)

        		 

        x.__getattribute__('name') <==> x.name

        Overrides: object.__getattribute__

        __getslice__(x, i, j)
        (Slicling operator)

        		 

        x[i:j]

        Use of negative indices is not supported.

        __hash__(x)
        (Hashing function)

        		 

        hash(x)

        Overrides: object.__hash__

        __new__(T, S, ...)

        		 
        Returns: a new object with type S, a subtype of T
        Overrides: object.__new__

        __repr__(x)
        (Representation operator)

        		 

        repr(x)

        Overrides: object.__repr__

        __sizeof__(S)

        		 
        Returns: size of S in memory, in bytes
        Overrides: object.__sizeof__

        __str__(x)
        (Informal representation operator)

        		 

        str(x)

        Overrides: object.__str__

        center(S, width, fillchar=...)

        		 

        Return S centered in a string of length width. Padding is done using the specified fill character (default is a space)

        Returns: string

        count(S, sub, start=..., end=...)

        		 

        Return the number of non-overlapping occurrences of substring sub in string S[start:end]. Optional arguments start and end are interpreted as in slice notation.

        Returns: int

        decode(S, encoding=..., errors=...)

        		 

        Decodes S using the codec registered for encoding. encoding defaults to the default encoding. errors may be given to set a different error handling scheme. Default is 'strict' meaning that encoding errors raise a UnicodeDecodeError. Other possible values are 'ignore' and 'replace' as well as any other name registered with codecs.register_error that is able to handle UnicodeDecodeErrors.

        Returns: object

        encode(S, encoding=..., errors=...)

        		 

        Encodes S using the codec registered for encoding. encoding defaults to the default encoding. errors may be given to set a different error handling scheme. Default is 'strict' meaning that encoding errors raise a UnicodeEncodeError. Other possible values are 'ignore', 'replace' and 'xmlcharrefreplace' as well as any other name registered with codecs.register_error that is able to handle UnicodeEncodeErrors.

        Returns: object

        endswith(S, suffix, start=..., end=...)

        		 

        Return True if S ends with the specified suffix, False otherwise. With optional start, test S beginning at that position. With optional end, stop comparing S at that position. suffix can also be a tuple of strings to try.

        Returns: bool

        expandtabs(S, tabsize=...)

        		 

        Return a copy of S where all tab characters are expanded using spaces. If tabsize is not given, a tab size of 8 characters is assumed.

        Returns: string

        find(S, sub, start=... , end=...)

        		 

        Return the lowest index in S where substring sub is found, such that sub is contained within s[start:end]. Optional arguments start and end are interpreted as in slice notation.

        Return -1 on failure.

        Returns: int

        istitle(S)

        		 

        Return True if S is a titlecased string and there is at least one character in S, i.e. uppercase characters may only follow uncased characters and lowercase characters only cased ones. Return False otherwise.

        Returns: bool

        join(S, iterable)

        		 

        Return a string which is the concatenation of the strings in the iterable. The separator between elements is S.

        Returns: string

        ljust(S, width, fillchar=...)

        		 

        Return S left-justified in a string of length width. Padding is done using the specified fill character (default is a space).

        Returns: string

        lstrip(S, chars=...)

        		 

        Return a copy of the string S with leading whitespace removed. If chars is given and not None, remove characters in chars instead. If chars is unicode, S will be converted to unicode before stripping

        Returns: string or unicode

        partition(S, sep)

        		 

        Search for the separator sep in S, and return the part before it, the separator itself, and the part after it. If the separator is not found, return S and two empty strings.

        Returns: (head, sep, tail)

        replace(S, old, new, count=...)

        		 

        Return a copy of string S with all occurrences of substring old replaced by new. If the optional argument count is given, only the first count occurrences are replaced.

        Returns: string

        rfind(S, sub, start=... , end=...)

        		 

        Return the highest index in S where substring sub is found, such that sub is contained within s[start:end]. Optional arguments start and end are interpreted as in slice notation.

        Return -1 on failure.

        Returns: int

        rjust(S, width, fillchar=...)

        		 

        Return S right-justified in a string of length width. Padding is done using the specified fill character (default is a space)

        Returns: string

        rpartition(S, sep)

        		 

        Search for the separator sep in S, starting at the end of S, and return the part before it, the separator itself, and the part after it. If the separator is not found, return two empty strings and S.

        Returns: (head, sep, tail)

        rsplit(S, sep=... , maxsplit=...)

        		 

        Return a list of the words in the string S, using sep as the delimiter string, starting at the end of the string and working to the front. If maxsplit is given, at most maxsplit splits are done. If sep is not specified or is None, any whitespace string is a separator.

        Returns: list of strings

        rstrip(S, chars=...)

        		 

        Return a copy of the string S with trailing whitespace removed. If chars is given and not None, remove characters in chars instead. If chars is unicode, S will be converted to unicode before stripping

        Returns: string or unicode

        split(S, sep=... , maxsplit=...)

        		 

        Return a list of the words in the string S, using sep as the delimiter string. If maxsplit is given, at most maxsplit splits are done. If sep is not specified or is None, any whitespace string is a separator and empty strings are removed from the result.

        Returns: list of strings

        splitlines(S, keepends=...)

        		 

        Return a list of the lines in S, breaking at line boundaries. Line breaks are not included in the resulting list unless keepends is given and true.

        Returns: list of strings

        startswith(S, prefix, start=..., end=...)

        		 

        Return True if S starts with the specified prefix, False otherwise. With optional start, test S beginning at that position. With optional end, stop comparing S at that position. prefix can also be a tuple of strings to try.

        Returns: bool

        strip(S, chars=...)

        		 

        Return a copy of the string S with leading and trailing whitespace removed. If chars is given and not None, remove characters in chars instead. If chars is unicode, S will be converted to unicode before stripping

        Returns: string or unicode

        title(S)

        		 

        Return a titlecased version of S, i.e. words start with uppercase characters, all remaining cased characters have lowercase.

        Returns: string

        zfill(S, width)

        		 

        Pad a numeric string S with zeros on the left, to fill a field of the specified width. The string S is never truncated.

        Returns: string

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        fabio-0.1.3/epydoc/fabio.adscimage.adscimage-class.html0000644000175000017500000004420712126623347023560 0ustar jeromejerome00000000000000 fabio.adscimage.adscimage
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        Package fabio :: Module adscimage :: Class adscimage
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        Class adscimage

        source code

                   object --+    
                    |    
fabioimage.fabioimage --+
                        |
                       adscimage

        Read an image in ADSC format (quite similar to edf?)

        Instance Methods [hide private]
         
        __init__(self, *args, **kwargs)
        Set up initial values        		 source code
         
        read(self, fname, frame=None)
        read in the file        		 source code
         
        _readheader(self, infile)
        read an adsc header        		 source code
         
        write(self, fname)
        Write adsc format        		 source code

        Inherited from fabioimage.fabioimage: add, convert, getclassname, getframe, getheader, getmax, getmean, getmin, getstddev, integrate_area, load, make_slice, next, previous, readROI, readheader, rebin, resetvals, save, toPIL16, update_header

        Inherited from fabioimage.fabioimage (private): _compressed_stream, _open

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Static Methods [hide private]

        Inherited from fabioimage.fabioimage: checkData, checkHeader

        Class Variables [hide private]

        Inherited from fabioimage.fabioimage (private): _need_a_real_file, _need_a_seek_to_read

        Properties [hide private]

        Inherited from fabioimage.fabioimage: classname

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, *args, **kwargs)
        (Constructor)

        		source code 

        Set up initial values

        Overrides: object.__init__
        (inherited documentation)

        read(self, fname, frame=None)

        		source code 

        read in the file

        Overrides: fabioimage.fabioimage.read

        _readheader(self, infile)

        		source code 

        read an adsc header

        Overrides: fabioimage.fabioimage._readheader

        write(self, fname)

        		source code 

        Write adsc format

        Overrides: fabioimage.fabioimage.write

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        Package fabio :: Module GEimage_old :: Class GEimage
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        Class GEimage

        source code

                   object --+    
                    |    
fabioimage.fabioimage --+
                        |
                       GEimage
        Instance Methods [hide private]
         
        _readheader(self, infile)
        Must be overridden in classes        		 source code
         
        read(self, fname, frame=None)
        Read in header into self.header and...        		 source code

        Inherited from fabioimage.fabioimage: __init__, add, convert, getclassname, getframe, getheader, getmax, getmean, getmin, getstddev, integrate_area, load, make_slice, next, previous, readROI, readheader, rebin, resetvals, save, toPIL16, update_header, write

        Inherited from fabioimage.fabioimage (private): _compressed_stream, _open

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Static Methods [hide private]

        Inherited from fabioimage.fabioimage: checkData, checkHeader

        Class Variables [hide private]

        Inherited from fabioimage.fabioimage (private): _need_a_real_file, _need_a_seek_to_read

        Properties [hide private]

        Inherited from fabioimage.fabioimage: classname

        Inherited from object: __class__

        Method Details [hide private]

        _readheader(self, infile)

        		source code 

        Must be overridden in classes

        Overrides: fabioimage.fabioimage._readheader
        (inherited documentation)

        read(self, fname, frame=None)

        		source code  
        
Read in header into self.header and
    the data   into self.data
        Overrides: fabioimage.fabioimage.read

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        Package fabio :: Module tifimage :: Class Tiff_header
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        Class Tiff_header

        source code

        object --+
         |
        Tiff_header
        Instance Methods [hide private]
         
        __init__(self, string)
        x.__init__(...) initializes x; see x.__class__.__doc__ for signature        		 source code

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Properties [hide private]

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, string)
        (Constructor)

        		source code 

        x.__init__(...) initializes x; see x.__class__.__doc__ for signature

        Overrides: object.__init__
        (inherited documentation)

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        Package fabio :: Module file_series :: Class numbered_file_series
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        Class numbered_file_series

        source code

        object --+        
         |        
      list --+    
             |    
   file_series --+
                 |
                numbered_file_series

        mydata0001.edf = "mydata" + 0001 + ".edf" mydata0002.edf = "mydata" + 0002 + ".edf" mydata0003.edf = "mydata" + 0003 + ".edf"

        Instance Methods [hide private]
        new empty list
        __init__(self, stem, first, last, extension, digits=4, padding='Y', step=1)
        Constructor        		 source code

        Inherited from file_series: current, current_image, current_object, first, first_image, first_object, jump, jump_image, jump_object, last, last_image, last_object, len, next, next_image, next_object, previous, previous_image, previous_object

        Inherited from list: __add__, __contains__, __delitem__, __delslice__, __eq__, __ge__, __getattribute__, __getitem__, __getslice__, __gt__, __iadd__, __imul__, __iter__, __le__, __len__, __lt__, __mul__, __ne__, __new__, __repr__, __reversed__, __rmul__, __setitem__, __setslice__, __sizeof__, append, count, extend, index, insert, pop, remove, reverse, sort

        Inherited from object: __delattr__, __format__, __reduce__, __reduce_ex__, __setattr__, __str__, __subclasshook__

        Class Variables [hide private]

        Inherited from list: __hash__

        Properties [hide private]

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, stem, first, last, extension, digits=4, padding='Y', step=1)
        (Constructor)

        		source code 

        Constructor

        Parameters:
        • stem - first part of the name
        • step - in case of every nth file
        • padding - possibility for specifying that numbers are not padded with zeroes up to digits
        Returns: new empty list
        Overrides: object.__init__

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        Package fabio :: Module compression
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        Source Code for Module fabio.compression

          1  #!/usr/bin/env python 
  2  # coding: utf8 
  3  """ 
  4  Authors: Jérôme Kieffer, ESRF 
  5           email:jerome.kieffer@esrf.fr 
  6   
  7  FabIO library containing compression and decompression algorithm for various 
  8  """ 
  9  __author__ = "Jérôme Kieffer" 
 10  __contact__ = "jerome.kieffer@esrf.eu" 
 11  __license__ = "GPLv3+" 
 12  __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" 
 13   
 14   
 15  import logging, struct, hashlib, base64, StringIO, sys 
 16  if sys.version_info >= (3,): 
 17      str = bytes 
 18  logger = logging.getLogger("compression") 
 19  import numpy 
 20   
 21  try: 
 22      import gzip 
 23  except ImportError: 
 24      logger.error("Unable to import gzip module: disabling gzip compression") 
 25      gzip = None 
 26   
 27  try: 
 28      import bz2 
 29  except ImportError: 
 30      logger.error("Unable to import bz2 module: disabling bz2 compression") 
 31      bz2 = None 
 32   
 33  try: 
 34      import zlib 
 35  except ImportError: 
 36      logger.error("Unable to import zlib module: disabling zlib compression") 
 37      zlib = None 
 38   

         39 -def md5sum(blob): 

         40      """ 
 41      returns the md5sum of an object... 
 42      """ 
 43      return base64.b64encode(hashlib.md5(blob).digest()) 

         44   
 45   

         46 -def endianness(): 

         47      """ 
 48      Return the native endianness of the system 
 49      """ 
 50      if numpy.little_endian: 
 51          return "LITTLE_ENDIAN" 
 52      else: 
 53          return "BIG_ENDIAN" 

         54   
 55   

         56 -def decGzip(stream): 

         57      """ 
 58   
 59      Decompress a chunk of data using the gzip algorithm from Python or alternatives if possible 
 60   
 61      """ 
 62   
 63      if gzip is None: 
 64          raise ImportError("gzip module is not available") 
 65      fileobj = StringIO.StringIO(stream) 
 66      try: 
 67          rawData = gzip.GzipFile(fileobj=fileobj).read() 
 68      except IOError: 
 69          logger.warning("Encounter the python-gzip bug with trailing garbage, trying subprocess gzip") 
 70          try: 
 71              #This is as an ugly hack against a bug in Python gzip 
 72              import subprocess 
 73              sub = subprocess.Popen(["gzip", "-d", "-f"], stdout=subprocess.PIPE, stdin=subprocess.PIPE, stderr=subprocess.PIPE) 
 74              rawData, err = sub.communicate(input=stream) 
 75              logger.debug("Gzip subprocess ended with %s err= %s; I got %s bytes back" % (sub.wait(), err, len(rawData))) 
 76          except Exception, error: #IGNORE:W0703 
 77              logger.warning("Unable to use the subprocess gzip (%s). Is gzip available? " % error) 
 78              for i in range(1, 513): 
 79                  try: 
 80                      fileobj = StringIO.StringIO(stream[:-i]) 
 81                      rawData = gzip.GzipFile(fileobj=fileobj).read() 
 82                  except IOError: 
 83                      logger.debug("trying with %s bytes less, doesn't work" % i) 
 84                  else: 
 85                      break 
 86              else: 
 87                  logger.error("I am totally unable to read this gzipped compressed data block, giving up") 
 88      return rawData 

         89   
 90   

         91 -def decBzip2(stream): 

         92      """ 
 93   
 94      Decompress a chunk of data using the bzip2 algorithm from Python 
 95   
 96      """ 
 97      if bz2 is None: 
 98          raise ImportError("bz2 module is not available") 
 99      return bz2.decompress(stream) 

        100   
101   

        102 -def decZlib(stream): 

        103      """ 
104   
105      Decompress a chunk of data using the zlib algorithm from Python 
106   
107      """ 
108      if zlib is None: 
109          raise ImportError("zlib module is not available") 
110      return zlib.decompress(stream) 

        111   
112   

        113 -def decByteOffet_python(stream, size): 

        114      """ 
115      Analyze a stream of char with any length of exception (2,4, or 8 bytes integers) 
116   
117      @param stream: string representing the compressed data 
118      @param size: the size of the output array (of longInts) 
119      @return: 1D-ndarray 
120   
121      """ 
122      logger.debug("CBF decompression using Python with Cython loops") 
123      dataOut = numpy.zeros((size), dtype=numpy.int64) 
124      i = 0 
125      j = 0 
126      last = 0 
127      current = 0 
128      while ((i < len(stream)) and (j < size)): 
129          if (stream[i] == '\x80'): 
130              if (stream[i + 1:i + 3] == "\x00\x80"): 
131                  if (stream[i + 3:i + 7] == "\x00\x00\x00\x80"): 
132                      current = struct.unpack("<q", stream[i + 7:i + 15])[0] 
133                      i += 15 
134                  else: 
135                      current = struct.unpack("<i", stream[i + 3:i + 7])[0] 
136                      i += 7 
137              else: 
138                  current = struct.unpack("<h", stream[i + 1:i + 3])[0] 
139                  i += 3 
140          else: 
141              current = struct.unpack("<b", stream[i])[0] 
142              i += 1 
143          last += current 
144          dataOut[j] = last 
145          j += 1 
146      return dataOut 

        147   

        148 -def decByteOffet_weave(stream, size): 

        149      """ 
150      Analyze a stream of char with any length of exception (2,4, or 8 bytes integers) 
151   
152      @param stream: string representing the compressed data 
153      @param size: the size of the output array (of longInts) 
154      @return: 1D-ndarray 
155   
156      """ 
157      logger.debug("CBF decompression using Weave") 
158      try: 
159          from scipy import weave 
160          from scipy.weave import converters 
161      except ImportError: 
162          logger.warning("scipy.weave is not available, falling back on slow Numpy implementations") 
163          return decByteOffet_numpy(stream, size) 
164      dataIn = numpy.fromstring(stream, dtype="uint8") 
165      n = dataIn.size 
166      dataOut = numpy.zeros(size, dtype="int64") 
167      codeC = """ 
168  unsigned char key = 0x80; 
169  long   j = 0; 
170  long   last=0; 
171  long   current=0; 
172  for (int i=0; i< n; i++){ 
173     if (j>=size){ 
174     //printf("i= %i<%i, j=%i < size= %i %i\\n",i,n,j,size,dataIn(i)); 
175         break; 
176    } 
177    if (dataIn(i) == key){ 
178        if ( (dataIn(i+1)==0) and (dataIn(i+2)==key) ){ 
179            if ( (dataIn(i+3)==0) and (dataIn(i+4)==0) and (dataIn(i+5)==0) and (dataIn(i+6)==key) )  { 
180                 // 64 bits mode 
181                 char tmp = dataIn(i+14) ; 
182                 current = (long(tmp)<<56) | (long(dataIn(i+13))<<48) | (long(dataIn(i+12))<<40) | (long(dataIn(i+11))<<32) | (long(dataIn(i+10))<<24) | (long(dataIn(i+9))<<16) | (long(dataIn(i+8))<<8) | (long(dataIn(i+7))); 
183  //                printf("64 bit int at pos %i, %i, value=%ld \\n",i,j,current); 
184                 i+=14; 
185             }else{ 
186                 // 32 bits mode 
187                 char tmp = dataIn(i+6) ; 
188                 current = (long(tmp)<<24) | (long(dataIn(i+5))<<16) | (long(dataIn(i+4))<<8) | (long(dataIn(i+3))); 
189  //                printf("32 bit int at pos %i, %i, value=%ld was %i %i %i %i %i %i %i\\n",i,j,current,dataIn(i),dataIn(i+1),dataIn(i+2),dataIn(i+3),dataIn(i+4),dataIn(i+5),dataIn(i+6)); 
190  //                printf("%ld %ld %ld %ld\\n",(long(tmp)<<24) , (long(dataIn(i+5))<<16) , (long(dataIn(i+4))<<8) ,long(dataIn(i+3))); 
191                 i+=6; 
192             } 
193        }else{ 
194             // 16 bit mode 
195             char tmp = dataIn(i+2); 
196             current = (long(tmp)<<8) | (long (dataIn(i+1))); 
197  //           printf("16 bit int at pos %i, %i, value=%ld was %i %i %i\\n",i,j,current,dataIn(i),dataIn(i+1),dataIn(i+2)); 
198             i+=2; 
199        } 
200    }else{ 
201        // 8 bit mode 
202        char tmp = dataIn(i) ; 
203        current= long(tmp) ; 
204    } 
205    last+=current; 
206    dataOut(j)=last; 
207    j++ ; 
208  } 
209  return_val=0; 
210       """ 
211      rc = weave.inline(codeC, ["dataIn", "dataOut", "n", "size" ], verbose=2, type_converters=converters.blitz) 
212      if rc != 0: 
213          logger.warning("weave binary module return error code %s" % rc) 
214      return dataOut 

        215   
216   
217   

        218 -def decByteOffet_numpy(stream, size=None): 

        219      """ 
220      Analyze a stream of char with any length of exception: 
221                  2, 4, or 8 bytes integers 
222   
223      @param stream: string representing the compressed data 
224      @param size: the size of the output array (of longInts) 
225      @return: 1D-ndarray 
226   
227      """ 
228      logger.debug("CBF decompression using Numpy") 
229      listnpa = [] 
230      key16 = "\x80" 
231      key32 = "\x00\x80" 
232      key64 = "\x00\x00\x00\x80" 
233      shift = 1 
234      while True: 
235          idx = stream.find(key16) 
236          if idx == -1: 
237              listnpa.append(numpy.fromstring(stream, dtype="int8")) 
238              break 
239          listnpa.append(numpy.fromstring(stream[:idx], dtype="int8")) 
240   
241          if stream[idx + 1:idx + 3] == key32: 
242              if stream[idx + 3:idx + 7] == key64: 
243  #                        long int 64 bits 
244                  listnpa.append(numpy.fromstring(stream[idx + 7:idx + 15], 
245                                               dtype="int64")) 
246                  shift = 15 
247              else: #32 bit int 
248                  listnpa.append(numpy.fromstring(stream[idx + 3:idx + 7], 
249                                               dtype="int32")) 
250                  shift = 7 
251          else:  # int16 
252              listnpa.append(numpy.fromstring(stream[idx + 1:idx + 3], 
253                                           dtype="int16")) 
254              shift = 3 
255          stream = stream[idx + shift:] 
256      return  (numpy.hstack(listnpa)).astype("int64").cumsum() 

        257   
258   

        259 -def decByteOffet_cython(stream, size=None): 

        260      """ 
261      Analyze a stream of char with any length of exception: 
262                  2, 4, or 8 bytes integers 
263   
264      @param stream: string representing the compressed data 
265      @param size: the size of the output array (of longInts) 
266      @return: 1D-ndarray 
267   
268      """ 
269      logger.debug("CBF decompression using cython") 
270      try: 
271          from fabio.byte_offset import analyseCython 
272      except ImportError, error: 
273          logger.error("Failed to import byte_offset cython module, falling back on numpy method") 
274          return decByteOffet_numpy(stream, size) 
275      else: 
276          return analyseCython(stream, size) 

        277   

        278 -def compByteOffet_numpy(data): 

        279      """ 
280      Compress a dataset into a string using the byte_offet algorithm 
281   
282      @param data: ndarray 
283      @return: string/bytes with compressed data 
284   
285      test = numpy.array([0,1,2,127,0,1,2,128,0,1,2,32767,0,1,2,32768,0,1,2,2147483647,0,1,2,2147483648,0,1,2,128,129,130,32767,32768,128,129,130,32768,2147483647,2147483648]) 
286   
287      """ 
288      flat = data.astype("int64").ravel() 
289      delta = numpy.zeros_like(flat) 
290      delta[0] = flat[0] 
291      delta[1:] = flat[1:] - flat[:-1] 
292      mask = ((delta > 127) + (delta < -127)) 
293      exceptions = numpy.nonzero(mask)[0] 
294      if numpy.little_endian: 
295          byteswap = False 
296      else: 
297          byteswap = True 
298      start = 0 
299      binary_blob = "" 
300      for stop in exceptions: 
301          if stop - start > 0: 
302              binary_blob += delta[start:stop].astype("int8").tostring() 
303          exc = delta[stop] 
304          if (exc > 2147483647) or (exc < -2147483647): #2**31-1 
305              binary_blob += "\x80\x00\x80\x00\x00\x00\x80" 
306              if byteswap: 
307                  binary_blob += delta[stop:stop + 1].byteswap().tostring() 
308              else: 
309                  binary_blob += delta[stop:stop + 1].tostring() 
310          elif (exc > 32767) or (exc < -32767): #2**15-1 
311              binary_blob += "\x80\x00\x80" 
312              if byteswap: 
313                  binary_blob += delta[stop:stop + 1].astype("int32").byteswap().tostring() 
314              else: 
315                  binary_blob += delta[stop:stop + 1].astype("int32").tostring() 
316          else: #>127 
317              binary_blob += "\x80" 
318              if byteswap: 
319                  binary_blob += delta[stop:stop + 1].astype("int16").byteswap().tostring() 
320              else: 
321                  binary_blob += delta[stop:stop + 1].astype("int16").tostring() 
322          start = stop + 1 
323      if start < delta.size: 
324          binary_blob += delta[start:].astype("int8").tostring() 
325      return binary_blob 

        326   
327   

        328 -def decTY1(raw_8, raw_16=None, raw_32=None): 

        329      """ 
330      Modified byte offset decompressor used in Oxford Diffraction images 
331       
332      @param raw_8:  strings containing raw data with integer 8 bits 
333      @param raw_16: strings containing raw data with integer 16 bits 
334      @param raw_32: strings containing raw data with integer 32 bits 
335      @return: numpy.ndarray 
336       
337      """ 
338      data = numpy.fromstring(raw_8, dtype="uint8").astype(int) 
339      data -= 127 
340      if raw_32 is not None: 
341          int32 = numpy.fromstring(raw_32, dtype="int32").astype(int) 
342          exception32 = numpy.nonzero(data == 128) 
343      if raw_16 is not None: 
344          int16 = numpy.fromstring(raw_16, dtype="int16").astype(int) 
345          exception16 = numpy.nonzero(data == 127) 
346          data[exception16] = int16 
347      if raw_32: 
348          data[exception32] = int32 
349      summed = data.cumsum() 
350      smax = summed.max() 
351      if (smax > (2 ** 31 - 1)): 
352          bytecode = "int64" 
353      elif (smax > (2 ** 15 - 1)): 
354          bytecode = "int32" 
355      elif (smax > (2 ** 7 - 1)): 
356          bytecode = "int16" 
357      else: 
358          bytecode = "int8" 
359      return summed.astype(bytecode) 

        360  decKM4CCD = decTY1 
361   

        362 -def compTY1(data): 

        363      """ 
364      Modified byte offset compressor used in Oxford Diffraction images 
365   
366      @param data: numpy.ndarray with the input data (integers!) 
367      @return: 3-tuple of strings: raw_8,raw_16,raw_32 containing raw data with integer of the given size 
368   
369      """ 
370      fdata = data.flatten() 
371      diff = numpy.zeros_like(fdata) 
372      diff[0] = fdata[0] 
373      diff[1:] = fdata[1:] - fdata[:-1] 
374      adiff = abs(diff) 
375      exception32 = (adiff > 32767)#2**15-1 
376      exception16 = (adiff >= 127) - exception32 #2**7-1) 
377      we16 = numpy.where(exception16) 
378      we32 = numpy.where(exception32) 
379      raw_16 = diff[we16].astype("int16").tostring() 
380      raw_32 = diff[we32].astype("int32").tostring() 
381      diff[we16] = 127 
382      diff[we32] = 128 
383      diff += 127 
384      raw_8 = diff.astype("uint8").tostring() 
385      return  raw_8, raw_16, raw_32 

        386   

        387 -def decPCK(stream, dim1=None, dim2=None, overflowPix=None): 

        388      """ 
389      Modified CCP4  pck decompressor used in MAR345 images 
390   
391      @param stream: string or file 
392      @return: numpy.ndarray (square array) 
393   
394      """ 
395   
396      try: 
397          from mar345_IO import uncompress_pck 
398      except ImportError, error: 
399          raise RuntimeError("Unable to import mar345_IO to read compressed dataset") 
400      if "seek" in dir(stream): 
401          stream.seek(0) 
402          raw = stream.read() 
403      else: 
404          raw = str(stream) 
405   
406      return uncompress_pck(raw, dim1, dim2, overflowPix) 

        407   
408   

        409 -def compPCK(data): 

        410      """ 
411      Modified CCP4  pck compressor used in MAR345 images 
412   
413      @param data: numpy.ndarray (square array) 
414      @return:  compressed stream 
415   
416      """ 
417      try: 
418          from mar345_IO import compress_pck 
419      except ImportError, error: 
420          raise RuntimeError("Unable to import mar345_IO to write compressed dataset") 
421      return compress_pck(data) 

        422

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        fabio-0.1.3/epydoc/fabio.brukerimage-pysrc.html0000644000175000017500000024176312126623347022265 0ustar jeromejerome00000000000000 fabio.brukerimage
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        Package fabio :: Module brukerimage
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        Source Code for Module fabio.brukerimage

          1  #!/usr/bin/env python 
  2  """ 
  3   
  4  Authors: Henning O. Sorensen & Erik Knudsen 
  5           Center for Fundamental Research: Metal Structures in Four Dimensions 
  6           Risoe National Laboratory 
  7           Frederiksborgvej 399 
  8           DK-4000 Roskilde 
  9           email:erik.knudsen@risoe.dk 
 10   
 11  Based on: openbruker,readbruker, readbrukerheader functions in the opendata 
 12           module of ImageD11 written by Jon Wright, ESRF, Grenoble, France 
 13   
 14  """ 
 15   
 16  import numpy, logging 
 17  logger = logging.getLogger("brukerimage") 
 18  from fabioimage import fabioimage 
 19  from readbytestream import readbytestream 
 20   
 21   

         22 -class brukerimage(fabioimage): 

         23      """ 
 24      Read and eventually write ID11 bruker (eg smart6500) images 
 25      """ 
 26   
 27      # needed if you feel like writing - see ImageD11/scripts/edf2bruker.py 
 28   
 29      __headerstring__ = "" 
 30   
 31   

         32 -    def _readheader(self, infile): 

         33          """ 
 34          the bruker format uses 80 char lines in key : value format 
 35          In the fisrt 512*5 bytes of the header there should be a 
 36          HDRBLKS key, whose value denotes how many 512 byte blocks 
 37          are in the total header. The header is always n*5*512 bytes, 
 38          otherwise it wont contain whole key: value pairs 
 39          """ 
 40          lump = infile.read(512 * 5) 
 41          self.__headerstring__ += lump 
 42          i = 80 
 43          self.header = {} 
 44          while i < 512 * 5: 
 45              if lump[i - 80: i].find(":") > 0: 
 46                  key, val = lump[i - 80: i].split(":", 1) 
 47                  key = key.strip()         # remove the whitespace (why?) 
 48                  val = val.strip() 
 49                  if self.header.has_key(key): 
 50                      # append lines if key already there 
 51                      self.header[key] = self.header[key] + '\n' + val 
 52                  else: 
 53                      self.header[key] = val 
 54                      self.header_keys.append(key) 
 55              i = i + 80                  # next 80 characters 
 56          # we must have read this in the first 512 bytes. 
 57          nhdrblks = int(self.header['HDRBLKS']) 
 58          # Now read in the rest of the header blocks, appending 
 59          rest = infile.read(512 * (nhdrblks - 5)) 
 60          self.__headerstring__ += rest 
 61          lump = lump[i - 80: 512] + rest 
 62          i = 80 
 63          j = 512 * nhdrblks 
 64          while i < j : 
 65              if lump[i - 80: i].find(":") > 0: # as for first 512 bytes of header 
 66                  key, val = lump[i - 80: i].split(":", 1) 
 67                  key = key.strip() 
 68                  val = val.strip() 
 69                  if self.header.has_key(key): 
 70                      self.header[key] = self.header[key] + '\n' + val 
 71                  else: 
 72                      self.header[key] = val 
 73                      self.header_keys.append(key) 
 74              i = i + 80 
 75          # make a (new) header item called "datastart" 
 76          self.header['datastart'] = infile.tell() 
 77          #set the image dimensions 
 78          self.dim1 = int(self.header['NROWS']) 
 79          self.dim2 = int(self.header['NCOLS']) 

         80   

         81 -    def read(self, fname, frame=None): 

         82          """ 
 83          Read in and unpack the pixels (including overflow table 
 84          """ 
 85          infile = self._open(fname, "rb") 
 86          try: 
 87              self._readheader(infile) 
 88          except: 
 89              raise 
 90   
 91          rows = self.dim1 
 92          cols = self.dim2 
 93   
 94          try: 
 95              # you had to read the Bruker docs to know this! 
 96              npixelb = int(self.header['NPIXELB']) 
 97          except: 
 98              errmsg = "length " + str(len(self.header['NPIXELB'])) + "\n" 
 99              for byt in self.header['NPIXELB']: 
100                  errmsg += "char: " + str(byt) + " " + str(ord(byt)) + "\n" 
101              logger.warning(errmsg) 
102              raise 
103   
104          self.data = readbytestream(infile, infile.tell(), 
105                                     rows, cols, npixelb, 
106                                     datatype="int", 
107                                     signed='n', 
108                                     swap='n') 
109   
110          #handle overflows 
111          nov = int(self.header['NOVERFL']) 
112          if nov > 0:   # Read in the overflows 
113              # need at least int32 sized data I guess - can reach 2^21 
114              self.data = self.data.astype(numpy.uint32) 
115              # 16 character overflows: 
116              #      9 characters of intensity 
117              #      7 character position 
118              for i in range(nov): 
119                  ovfl = infile.read(16) 
120                  intensity = int(ovfl[0: 9]) 
121                  position = int(ovfl[9: 16]) 
122                  # relies on python style modulo being always + 
123                  row = position % rows 
124                  # relies on truncation down 
125                  col = position / rows 
126                  #print "Overflow ", r, c, intensity, position,\ 
127                  #    self.data[r,c],self.data[c,r] 
128                  self.data[col, row] = intensity 
129          infile.close() 
130   
131          self.resetvals() 
132          self.pilimage = None 
133          return self 

        134   
135   

        136 -    def write(self, fname): 

        137          """ 
138          Writes the image as EDF 
139   
140          FIXME:  this should call edfimage.write if that is wanted? 
141                  obj = edfimage(data = self.data, header = self.header) 
142                  obj.write(fname) 
143                  or maybe something like: edfimage.write(self, fname) 
144   
145          """ 
146          logger.warning("***warning***: call to unifinished " + \ 
147                  "brukerimage.write. This will write the file" + \ 
148                              fname + "as an edf-file") 
149   
150   
151          outfile = self._open(fname, "wb") 
152          outfile.write('{\n') 
153          i = 4 
154          for k in self.header_keys: 
155              out = (("%s = %s;\n") % (k, self.header[k])) 
156              i = i + len(out) 
157              outfile.write(out) 
158          out = (4096 - i) * ' ' 
159          outfile.write(out) 
160          outfile.write('}\n') 
161          # Assumes a short-circuiting if / or ... 
162          if not self.header.has_key("ByteOrder") or \ 
163                 self.header["ByteOrder"] == "LowByteFirst": 
164              outfile.write(self.data.astype(numpy.uint16).tostring()) 
165          else: 
166              outfile.write(self.data.byteswap().astype( 
167                      numpy.uint16).tostring()) 
168          outfile.close() 

        169   
170   
171   
172   

        173 -def test(): 

        174      """ a testcase """ 
175      import sys, time 
176      img = brukerimage() 
177      start = time.clock() 
178      for filename in sys.argv[1:]: 
179          img.read(filename) 
180          res = img.toPIL16() 
181          img.rebin(2, 2) 
182          print filename + (": max=%d, min=%d, mean=%.2e, stddev=%.2e") % ( 
183              img.getmax(), img.getmin(), img.getmean(), img.getstddev()) 
184          print 'integrated intensity (%d %d %d %d) =%.3f' % ( 
185              10, 20, 20, 40, img.integrate_area((10, 20, 20, 40))) 
186      end = time.clock() 
187      print (end - start) 

        188   
189   
190   
191  if __name__ == '__main__': 
192      test() 
193

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        fabio-0.1.3/epydoc/toc-fabio.datIO-module.html0000644000175000017500000000243312120434325021653 0ustar jeromejerome00000000000000 datIO

        Module datIO

        Classes

        columnfile
        fabiodata

        Variables

        __package__
        [hide private] fabio-0.1.3/epydoc/fabio.tifimage.Image_File_Directory_entry-class.html0000644000175000017500000002444212126623347026740 0ustar jeromejerome00000000000000 fabio.tifimage.Image_File_Directory_entry
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        Package fabio :: Module tifimage :: Class Image_File_Directory_entry
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        Class Image_File_Directory_entry

        source code

        object --+
         |
        Image_File_Directory_entry
        Instance Methods [hide private]
         
        __init__(self, tag=0, tag_type=0, count=0, offset=0)
        x.__init__(...) initializes x; see x.__class__.__doc__ for signature        		 source code
         
        unpack(self, strInput) source code
         
        extract_data(self, full_string) source code

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Properties [hide private]

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, tag=0, tag_type=0, count=0, offset=0)
        (Constructor)

        		source code 

        x.__init__(...) initializes x; see x.__class__.__doc__ for signature

        Overrides: object.__init__
        (inherited documentation)

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        fabio-0.1.3/epydoc/fabio.fabioutils.filename_object-class.html0000644000175000017500000001575612120434325025172 0ustar jeromejerome00000000000000 fabio.fabioutils.filename_object
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        Package fabio :: Module fabioutils :: Class filename_object
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        Class filename_object

        source code

        The 'meaning' of a filename

        Instance Methods [hide private]
         
        __init__(self, stem, num=None, directory=None, format=None, extension=None, postnum=None, digits=4) source code
         
        str(self)
        Return a string representation        		 source code
         
        tostring(self)
        convert yourself to a string        		 source code
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        Package fabio :: Module pilatusimage
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        Module pilatusimage

        source code

        

Authors:
........
* Henning O. Sorensen & Erik Knudsen:
  Center for Fundamental Research: Metal Structures in Four Dimensions;
  Risoe National Laboratory;
  Frederiksborgvej 399;
  DK-4000 Roskilde;
  email:erik.knudsen@risoe.dk
* Jon Wright:
  European Synchrotron Radiation Facility;
  Grenoble (France)
        Classes [hide private]
          pilatusimage
        Read in Pilatus format, also pilatus images, including header info
        Variables [hide private]
          __package__ = 'fabio'
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        fabio-0.1.3/epydoc/fabio.openimage-module.html0000644000175000017500000003400212126623347022043 0ustar jeromejerome00000000000000 fabio.openimage
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        Package fabio :: Module openimage
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        Module openimage

        source code

        

Authors: Henning O. Sorensen & Erik Knudsen
         Center for Fundamental Research: Metal Structures in Four Dimensions
         Risoe National Laboratory
         Frederiksborgvej 399
         DK-4000 Roskilde
         email:henning.sorensen@risoe.dk

mods for fabio by JPW
        Functions [hide private]
         
        do_magic(byts)
        Try to interpret the bytes starting the file as a magic number        		 source code
         
        openimage(filename, frame=None)
        Try to open an image        		 source code
         
        openheader(filename)
        return only the header        		 source code
         
        _openimage(filename)
        determine which format for a filename and return appropriate class which can be used for opening the image        		 source code
        Variables [hide private]
          logger = logging.getLogger("openimage")
          MAGIC_NUMBERS = [('FORMAT : 86', 'bruker'), ('MM\x00*',...
          __package__ = 'fabio'
        Variables Details [hide private]

        MAGIC_NUMBERS

        Value:
        [('FORMAT :        86', 'bruker'),
 ('MM\x00*', 'tif'),
 ('II*\x00\x08\x00', 'marccd'),
 ('II*\x00\x82\x00', 'pilatus'),
 ('II*\x00', 'tif'),
 ('{\nHEA', 'adsc'),
 ('{', 'edf'),
 ('\r{', 'edf'),
...

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        fabio-0.1.3/epydoc/toc-fabio.edfimage-module.html0000644000175000017500000000356012120434325022416 0ustar jeromejerome00000000000000 edfimage

        Module edfimage

        Classes

        Frame
        edfimage

        Variables

        BLOCKSIZE
        DATA_TYPES
        DEFAULT_VALUES
        MINIMUM_KEYS
        NUMPY_EDF_DTYPE
        __package__
        logger
        [hide private] fabio-0.1.3/epydoc/toc-fabio.cf_io-module.html0000644000175000017500000000226712120434325021737 0ustar jeromejerome00000000000000 cf_io

        Module cf_io

        Functions

        read

        Variables

        __package__
        [hide private] fabio-0.1.3/epydoc/toc-fabio.pnmimage-module.html0000644000175000017500000000311412120434325022445 0ustar jeromejerome00000000000000 pnmimage

        Module pnmimage

        Classes

        pnmimage

        Variables

        HEADERITEMS
        P7HEADERITEMS
        SUBFORMATS
        __package__
        logger
        [hide private] fabio-0.1.3/epydoc/fabio.cbfimage.CIF-class.html0000644000175000017500000012653112126623347022065 0ustar jeromejerome00000000000000 fabio.cbfimage.CIF
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        Package fabio :: Module cbfimage :: Class CIF
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        Class CIF

        source code

        object --+    
         |    
      dict --+
             |
            CIF

        This is the CIF class, it represents the CIF dictionary; and as a a python dictionary thus inherits from the dict built in class.

        Instance Methods [hide private] 
        new empty dictionary
        __init__(self, _strFilename=None)
        Constructor of the class.        		 source code
         
        __setitem__(self, key, value)
        x[i]=y        		 source code
        v, remove specified key and return the corresponding value
        pop(self, key)
        If key is not found, d is returned if given, otherwise KeyError is raised        		 source code
        (k, v), remove and return some (key, value) pair as a
        popitem(self, key)
        2-tuple; but raise KeyError if D is empty.        		 source code
         
        loadCIF(self, _strFilename, _bKeepComment=False)
        Load the CIF file and populates the CIF dictionary into the object        		 source code
         
        readCIF(self, _strFilename, _bKeepComment=False)
        Load the CIF file and populates the CIF dictionary into the object        		 source code
        None
        _parseCIF(self, sText)
        Parses the text of a CIF file        		 source code
         
        saveCIF(self, _strFilename='test.cif', linesep='\n', binary=False)
        Transforms the CIF object in string then write it into the given file        		 source code
         
        tostring(self, _strFilename=None, linesep='\n')
        Converts a cif dictionnary to a string according to the CIF syntax        		 source code
        boolean
        exists(self, sKey)
        Check if the key exists in the CIF and is non empty.        		 source code
        boolean
        existsInLoop(self, sKey)
        Check if the key exists in the CIF dictionary.        		 source code
        dictionary
        loadCHIPLOT(self, _strFilename)
        Load the powder diffraction CHIPLOT file and returns the pd_CIF dictionary in the object        		 source code

        Inherited from dict: __cmp__, __contains__, __delitem__, __eq__, __ge__, __getattribute__, __getitem__, __gt__, __iter__, __le__, __len__, __lt__, __ne__, __new__, __repr__, __sizeof__, clear, copy, fromkeys, get, has_key, items, iteritems, iterkeys, itervalues, keys, setdefault, update, values

        Inherited from object: __delattr__, __format__, __reduce__, __reduce_ex__, __setattr__, __str__, __subclasshook__

        Static Methods [hide private]
        boolean
        isAscii(_strIn)
        Check if all characters in a string are ascii,        		 source code
        string
        _readCIF(_instream)
        Check if the filename containing the CIF data exists        		 source code
        list
        _splitCIF(sText)
        Separate the text in fields as defined in the CIF        		 source code
        tuple
        _analyseOneLoop(lFields, iStart)
        Processes one loop in the data extraction of the CIF file        		 source code
         
        LoopHasKey(loop, key)
        Returns True if the key (string) exist in the array called loop        		 source code
        Class Variables [hide private]
          EOL = ['\r', '\n', '\r\n', '\n\r']
          BLANK = [' ', '\t', '\r', '\n', '\r\n', '\n\r']
          START_COMMENT = ['"', '\'']
          BINARY_MARKER = '--CIF-BINARY-FORMAT-SECTION--'

        Inherited from dict: __hash__

        Properties [hide private]

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, _strFilename=None)
        (Constructor)

        		source code 

        Constructor of the class.

        Parameters:
        • _strFilename (filename (str) or file object) - the name of the file to open
        Returns: 
        new empty dictionary
        Overrides: object.__init__

        __setitem__(self, key, value)
        (Index assignment operator)

        		source code 

        x[i]=y

        Overrides: dict.__setitem__
        (inherited documentation)

        pop(self, key)

        		source code 

        If key is not found, d is returned if given, otherwise KeyError is raised

        Returns: v, remove specified key and return the corresponding value
        Overrides: dict.pop
        (inherited documentation)

        popitem(self, key)

        		source code 

        2-tuple; but raise KeyError if D is empty.

        Returns: (k, v), remove and return some (key, value) pair as a
        Overrides: dict.popitem
        (inherited documentation)

        loadCIF(self, _strFilename, _bKeepComment=False)

        		source code 

        Load the CIF file and populates the CIF dictionary into the object

        Parameters:
        • _strFilename (string) - the name of the file to open
        • _strFilename (string) - the name of the file to open
        Returns:
        None

        readCIF(self, _strFilename, _bKeepComment=False)

        		source code 

        Load the CIF file and populates the CIF dictionary into the object

        Parameters:
        • _strFilename (string) - the name of the file to open
        • _strFilename (string) - the name of the file to open
        Returns:
        None

        isAscii(_strIn)
        Static Method

        		source code 

        Check if all characters in a string are ascii,

        Parameters:
        • _strIn (python string) - input string
        Returns: boolean
        boolean

        _readCIF(_instream)
        Static Method

        		source code 
        • Check if the filename containing the CIF data exists
        • read the cif file
        • removes the comments
        Parameters:
        • _instream (open file in read mode) - the file containing the CIF data
        Returns: string
        a string containing the raw data

        _parseCIF(self, sText)

        		source code 
        • Parses the text of a CIF file
        • Cut it in fields
        • Find all the loops and process
        • Find all the keys and values
        Parameters:
        • sText (string) - the content of the CIF - file
        Returns: None
        Nothing, the data are incorporated at the CIF object dictionary

        _splitCIF(sText)
        Static Method

        		source code 

        Separate the text in fields as defined in the CIF

        Parameters:
        • sText (string) - the content of the CIF - file
        Returns: list
        list of all the fields of the CIF

        _analyseOneLoop(lFields, iStart)
        Static Method

        		source code 

        Processes one loop in the data extraction of the CIF file

        Parameters:
        • lFields (list) - list of all the words contained in the cif file
        • iStart (integer) - the starting index corresponding to the "loop_" key
        Returns: tuple
        the list of loop dictionaries, the length of the data extracted from the lFields and the list of all the keys of the loop.

        saveCIF(self, _strFilename='test.cif', linesep='\n', binary=False)

        		source code 

        Transforms the CIF object in string then write it into the given file

        Parameters:
        • _strFilename - the of the file to be written
        • linesep - line separation used (to force compatibility with windows/unix)
        • binary - Shall we write the data as binary (True only for imageCIF/CBF)
        • param (string)

        tostring(self, _strFilename=None, linesep='\n')

        		source code 

        Converts a cif dictionnary to a string according to the CIF syntax

        Parameters:
        • _strFilename (string) - the name of the filename to be appended in the header of the CIF file
        Returns:
        a sting that corresponds to the content of the CIF - file.

        exists(self, sKey)

        		source code 

        Check if the key exists in the CIF and is non empty.

        Parameters:
        • sKey (string) - CIF key
        • cif - CIF dictionary
        Returns: boolean
        True if the key exists in the CIF dictionary and is non empty

        existsInLoop(self, sKey)

        		source code 

        Check if the key exists in the CIF dictionary.

        Parameters:
        • sKey (string) - CIF key
        • cif - CIF dictionary
        Returns: boolean
        True if the key exists in the CIF dictionary and is non empty

        loadCHIPLOT(self, _strFilename)

        		source code 

        Load the powder diffraction CHIPLOT file and returns the pd_CIF dictionary in the object

        Parameters:
        • _strFilename (string) - the name of the file to open
        Returns: dictionary
        the CIF object corresponding to the powder diffraction

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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:40 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/fabio.fabioutils.UnknownCompressedFile-class.html0000644000175000017500000002650312126623347026352 0ustar jeromejerome00000000000000 fabio.fabioutils.UnknownCompressedFile
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        Package fabio :: Module fabioutils :: Class UnknownCompressedFile
        [hide private]
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        Class UnknownCompressedFile

        source code

        object --+        
         |        
      file --+    
             |    
          File --+
                 |
                UnknownCompressedFile

        wrapper for "File" with locking

        Instance Methods [hide private]
        file object
        __init__(self, name, mode='rb', buffering=0)
        Open a file.        		 source code

        Inherited from File: getSize, setSize

        Inherited from file: __delattr__, __enter__, __exit__, __getattribute__, __iter__, __new__, __repr__, __setattr__, close, fileno, flush, isatty, next, read, readinto, readline, readlines, seek, tell, truncate, write, writelines, xreadlines

        Inherited from object: __format__, __hash__, __reduce__, __reduce_ex__, __sizeof__, __str__, __subclasshook__

        Properties [hide private]

        Inherited from File: size

        Inherited from file: closed, encoding, errors, mode, name, newlines, softspace

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, name, mode='rb', buffering=0)
        (Constructor)

        		source code  
                Open a file.  The mode can be 'r', 'w' or 'a' for reading (default),
        writing or appending.  The file will be created if it doesn't exist
        when opened for writing or appending; it will be truncated when
        opened for writing.  Add a 'b' to the mode for binary files.
        Add a '+' to the mode to allow simultaneous reading and writing.
        If the buffering argument is given, 0 means unbuffered, 1 means line
        buffered, and larger numbers specify the buffer size.  The preferred way
        to open a file is with the builtin open() function.
        Add a 'U' to mode to open the file for input with universal newline
        support.  Any line ending in the input file will be seen as a '
'
        in Python.  Also, a file so opened gains the attribute 'newlines';
        the value for this attribute is one of None (no newline read yet),
        '
', '
', '
' or a tuple containing all the newline types seen.
        
        'U' cannot be combined with 'w' or '+' mode.
        Returns: file object
        Overrides: object.__init__
        (inherited documentation)

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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:40 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/toc-fabio.OXDimage-module.html0000644000175000017500000000354012120434325022310 0ustar jeromejerome00000000000000 OXDimage

        Module OXDimage

        Classes

        OXDimage
        Section

        Variables

        DEFAULT_HEADERS
        DETECTOR_TYPES
        __doc__
        __package__
        deg2rad
        logger
        rad2deg
        [hide private] fabio-0.1.3/epydoc/fabio.pnmimage-module.html0000644000175000017500000002654312126623347021707 0ustar jeromejerome00000000000000 fabio.pnmimage
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        Package fabio :: Module pnmimage
        [hide private]
        [frames] | no frames]

        Module pnmimage

        source code

        

Authors: Henning O. Sorensen & Erik Knudsen
         Center for Fundamental Research: Metal Structures in Four Dimensions
         Risoe National Laboratory
         Frederiksborgvej 399
         DK-4000 Roskilde
         email:henning.sorensen@risoe.dk
        Classes [hide private]
          pnmimage
        Variables [hide private]
          logger = logging.getLogger("pnmimage")
          SUBFORMATS = ['P1', 'P2', 'P3', 'P4', 'P5', 'P6', 'P7']
          HEADERITEMS = ['SUBFORMAT', 'DIMENSIONS', 'MAXVAL']
          P7HEADERITEMS = ['WIDTH', 'HEIGHT', 'DEPTH', 'MAXVAL', 'TUPLTY...
          __package__ = 'fabio'
        Variables Details [hide private]

        P7HEADERITEMS

        Value:
        ['WIDTH', 'HEIGHT', 'DEPTH', 'MAXVAL', 'TUPLTYPE', 'ENDHDR']

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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:40 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/identifier-index.html0000644000175000017500000037161712126623347021004 0ustar jeromejerome00000000000000 Identifier Index
           Home       Trees       Indices       Help   
         
        [hide private]
        [frames] | no frames]

        Identifier Index

        		 [ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _ ]

        A
        add()
        (in fabioimage)        		 adscimage
        (in fabio.adscimage)        		 appendFrame()
        (in edfimage)
        adscimage
        (in fabio)        		 ALLOW_MULTIPLE_STRIPS
        (in fabio.TiffIO)        		  

        B
        baseline_tiff_tags
        (in fabio.tifimage)        		 BLOCKSIZE
        (in fabio.edfimage)        		 byte_offset
        (in fabio)
        BIG_ENDIAN
        (in fabio.tifimage)        		 bpp
        (in edfimage)        		 bytecode
        (in Frame)
        BINARY_MARKER
        (in CIF)        		 bruker100image
        (in fabio)        		 bytecode
        (in edfimage)
        binaryimage
        (in fabio)        		 bruker100image
        (in fabio.bruker100image)        		 BZ2File
        (in fabio.fabioutils)
        binaryimage
        (in fabio.binaryimage)        		 brukerimage
        (in fabio)        		  
        BLANK
        (in CIF)        		 brukerimage
        (in fabio.brukerimage)        		  

        C
        C_SIZES
        (in fabio.marccdimage)        		 checkData()
        (in pnmimage)        		 CONVERSION_DATA
        (in fabio.converters)
        C_TO_STRUCT
        (in fabio.marccdimage)        		 checkHeader()
        (in edfimage)        		 CONVERSION_HEADER
        (in fabio.converters)
        capsHeader
        (in edfimage)        		 checkHeader()
        (in fabioimage)        		 convert()
        (in fabioimage)
        cbfimage
        (in fabio)        		 CIF
        (in fabio.cbfimage)        		 convert_data()
        (in fabio.converters)
        cbfimage
        (in fabio.cbfimage)        		 classname
        (in fabioimage)        		 convert_data_integer()
        (in fabio.converters)
        CDEFINITION
        (in fabio.marccdimage)        		 closed
        (in GzipFile)        		 convert_header()
        (in fabio.converters)
        cf_io
        (in fabio)        		 columnfile
        (in fabio.datIO)        		 converters
        (in fabio)
        checkData()
        (in OXDimage)        		 compByteOffet_numpy()
        (in fabio.compression)        		 current()
        (in file_series)
        checkData()
        (in cbfimage)        		 compPCK()
        (in fabio.compression)        		 current()
        (in filename_series)
        checkData()
        (in fabioimage)        		 compression
        (in fabio)        		 current_image()
        (in file_series)
        checkData()
        (in fit2dmaskimage)        		 COMPRESSORS
        (in fabio.fabioutils)        		 current_image()
        (in filename_series)
        checkData()
        (in kcdimage)        		 compTY1()
        (in fabio.compression)        		 current_object()
        (in file_series)
        checkData()
        (in mar345image)        		 construct_filename()
        (in fabio.fabioutils)        		 current_object()
        (in filename_series)

        D
        data
        (in Frame)        		 decBzip2()
        (in fabio.compression)        		 delHeader()
        (in edfimage)
        data
        (in edfimage)        		 decGzip()
        (in fabio.compression)        		 delHeaderKeys()
        (in edfimage)
        DATA_BYTES
        (in fabio.dm3image)        		 deconstruct_filename()
        (in FilenameObject)        		 demo()
        (in fabio.GEimage)
        DATA_TYPES
        (in fabio.cbfimage)        		 deconstruct_filename()
        (in fabio.fabioutils)        		 deprecated()
        (in fabio.fabioutils)
        DATA_TYPES
        (in fabio.dm3image)        		 decPCK()
        (in fabio.compression)        		 DETECTOR_TYPES
        (in fabio.OXDimage)
        DATA_TYPES
        (in fabio.edfimage)        		 decTY1()
        (in fabio.compression)        		 dictAscii
        (in fabio.fabioutils)
        DATA_TYPES
        (in fabio.kcdimage)        		 decZlib()
        (in fabio.compression)        		 dim1
        (in edfimage)
        DATATYPES
        (in fabio.readbytestream)        		 DEFAULT_HEADERS
        (in fabio.OXDimage)        		 dim2
        (in edfimage)
        datIO
        (in fabio)        		 DEFAULT_VALUES
        (in fabio.edfimage)        		 dims
        (in edfimage)
        DEBUG
        (in fabio.TiffIO)        		 DEFAULT_VALUES
        (in fabio.kcdimage)        		 dm3image
        (in fabio)
        decByteOffet_cython()
        (in fabio.compression)        		 deg2rad
        (in fabio.OXDimage)        		 dm3image
        (in fabio.dm3image)
        decByteOffet_numpy()
        (in fabio.compression)        		 delCapsHeader()
        (in edfimage)        		 do_magic()
        (in fabio.openimage)
        decByteOffet_python()
        (in fabio.compression)        		 delData()
        (in edfimage)        		  
        decByteOffet_weave()
        (in fabio.compression)        		 deleteFrame()
        (in edfimage)        		  

        E
        edfimage
        (in fabio)        		 EOL
        (in CIF)        		 existsInLoop()
        (in CIF)
        edfimage
        (in fabio.edfimage)        		 estimate_offset_value()
        (in binaryimage)        		 extract_data()
        (in Image_File_Directory_entry)
        endianness()
        (in fabio.compression)        		 exists()
        (in CIF)        		 extract_filenumber()
        (in fabio.fabioutils)

        F
        fabio FIELD_TYPE_OUT
        (in fabio.TiffIO)        		 first_image()
        (in file_series)
        fabiodata
        (in fabio.datIO)        		 File
        (in fabio.fabioutils)        		 first_object()
        (in file_series)
        fabioimage
        (in fabio)        		 file_series
        (in fabio)        		 fit2dmaskimage
        (in fabio)
        fabioimage
        (in fabio.fabioimage)        		 file_series
        (in fabio.file_series)        		 fit2dmaskimage
        (in fabio.fit2dmaskimage)
        fabioutils
        (in fabio)        		 filename_series
        (in fabio.file_series)        		 fit2dspreadsheetimage
        (in fabio)
        fastReadData()
        (in edfimage)        		 FilenameObject
        (in fabio.fabioutils)        		 fit2dspreadsheetimage
        (in fabio.fit2dspreadsheetimage)
        fastReadROI()
        (in edfimage)        		 FILETYPES
        (in fabio.fabioutils)        		 Frame
        (in fabio.edfimage)
        FIELD_TYPE
        (in fabio.TiffIO)        		 first()
        (in file_series)        		  

        G
        GE_HEADER_INFO
        (in fabio.GEimage)        		 getDim1()
        (in edfimage)        		 getmean()
        (in fabioimage)
        GEimage
        (in fabio)        		 getDim2()
        (in edfimage)        		 getmin()
        (in fabioimage)
        GEimage
        (in fabio.GEimage)        		 getDims()
        (in edfimage)        		 getNbFrames()
        (in edfimage)
        GEimage
        (in fabio.GEimage_old)        		 getEdfBlock()
        (in Frame)        		 getnum()
        (in fabio.fabioutils)
        GEimage_old
        (in fabio)        		 getframe()
        (in GEimage)        		 getNumberOfImages()
        (in TiffIO)
        getBpp()
        (in edfimage)        		 getframe()
        (in edfimage)        		 getSize()
        (in Section)
        getByteCode()
        (in Frame)        		 getframe()
        (in fabioimage)        		 getSize()
        (in BZ2File)
        getByteCode()
        (in edfimage)        		 getHeader()
        (in edfimage)        		 getSize()
        (in File)
        getCapsHeader()
        (in edfimage)        		 getheader()
        (in fabioimage)        		 getSize()
        (in GzipFile)
        getclassname()
        (in fabioimage)        		 getHeaderKeys()
        (in edfimage)        		 getSize()
        (in StringIO)
        getCompressionRatio()
        (in OXDimage)        		 getImage()
        (in TiffIO)        		 getstddev()
        (in fabioimage)
        getData()
        (in TiffIO)        		 getImageFileDirectories()
        (in TiffIO)        		 GzipFile
        (in fabio.fabioutils)
        getData()
        (in Frame)        		 getInfo()
        (in TiffIO)        		  
        getData()
        (in edfimage)        		 getmax()
        (in fabioimage)        		  

        H
        header
        (in edfimage)        		 HEADER_NAMES
        (in fabio.marccdimage)        		 HiPiCimage
        (in fabio.HiPiCimage)
        HEADER_FORMAT
        (in fabio.marccdimage)        		 HEADERITEMS
        (in fabio.pnmimage)        		  
        header_keys
        (in edfimage)        		 HiPiCimage
        (in fabio)        		  

        I
        i
        (in fabio.fabioutils)        		 integrate_area()
        (in fabioimage)        		 isAscii()
        (in fabio.fabioutils)
        Image_File_Directory
        (in fabio.tifimage)        		 interpret_header()
        (in fabio.marccdimage)        		  
        Image_File_Directory_entry
        (in fabio.tifimage)        		 isAscii()
        (in CIF)        		  

        J
        jump()
        (in file_series)        		 jump_image()
        (in file_series)        		 jump_object()
        (in filename_series)
        jump()
        (in filename_series)        		 jump_image()
        (in filename_series)        		  
        jump_filename()
        (in fabio.fabioutils)        		 jump_object()
        (in file_series)        		  

        K
        kcdimage
        (in fabio)        		 kcdimage
        (in fabio.kcdimage)        		 key
        (in fabio.fabioutils)
           

        L
        last()
        (in file_series)        		 logger
        (in fabio.OXDimage)        		 logger
        (in fabio.fabioutils)
        last_image()
        (in file_series)        		 logger
        (in fabio.adscimage)        		 logger
        (in fabio.file_series)
        last_object()
        (in file_series)        		 logger
        (in fabio.binaryimage)        		 logger
        (in fabio.kcdimage)
        len()
        (in file_series)        		 logger
        (in fabio.bruker100image)        		 logger
        (in fabio.mar345image)
        lines
        (in fabio.fabioutils)        		 logger
        (in fabio.brukerimage)        		 logger
        (in fabio.marccdimage)
        LITTLE_ENDIAN
        (in fabio.tifimage)        		 logger
        (in fabio.cbfimage)        		 logger
        (in fabio.openimage)
        load()
        (in fabioimage)        		 logger
        (in fabio.compression)        		 logger
        (in fabio.pnmimage)
        loadCHIPLOT()
        (in CIF)        		 logger
        (in fabio.converters)        		 logger
        (in fabio.readbytestream)
        loadCIF()
        (in CIF)        		 logger
        (in fabio.dm3image)        		 logger
        (in fabio.tifimage)
        logger
        (in fabio.GEimage)        		 logger
        (in fabio.edfimage)        		 logger
        (in fabio.xsdimage)
        logger
        (in fabio.HiPiCimage)        		 logger
        (in fabio.fabioimage)        		 LoopHasKey()
        (in CIF)

        M
        MAGIC_NUMBERS
        (in fabio.openimage)        		 mar345image
        (in fabio.mar345image)        		 MINIMUM_KEYS
        (in fabio.cbfimage)
        make_format()
        (in fabio.marccdimage)        		 marccdimage
        (in fabio)        		 MINIMUM_KEYS
        (in fabio.edfimage)
        make_slice()
        (in fabioimage)        		 marccdimage
        (in fabio.marccdimage)        		 MINIMUM_KEYS
        (in fabio.kcdimage)
        mar345_IO
        (in fabio)        		 MAXIMAGES
        (in fabio.marccdimage)        		  
        mar345image
        (in fabio)        		 md5sum()
        (in fabio.compression)        		  

        N
        nb_overflow_pixels()
        (in mar345image)        		 next()
        (in file_series)        		 next_object()
        (in filename_series)
        new_file_series()
        (in fabio.file_series)        		 next()
        (in filename_series)        		 nframes
        (in edfimage)
        new_file_series0()
        (in fabio.file_series)        		 next_filename()
        (in fabio.fabioutils)        		 nice_int()
        (in fabio.fabioutils)
        next()
        (in GEimage)        		 next_image()
        (in file_series)        		 numbered_file_series
        (in fabio.file_series)
        next()
        (in edfimage)        		 next_image()
        (in filename_series)        		 NUMPY_EDF_DTYPE
        (in fabio.edfimage)
        next()
        (in fabioimage)        		 next_object()
        (in file_series)        		 numstem()
        (in fabio.fabioutils)

        O
        openheader()
        (in fabio.openimage)        		 openimage()
        (in fabio.openimage)        		 OXDimage
        (in fabio.OXDimage)
        openimage
        (in fabio)        		 OXDimage
        (in fabio)        		  

        P
        P1dec()
        (in pnmimage)        		 parseheader()
        (in Frame)        		 previous()
        (in GEimage)
        P2dec()
        (in pnmimage)        		 PIL_TO_NUMPY
        (in fabio.tifimage)        		 previous()
        (in edfimage)
        P3dec()
        (in pnmimage)        		 pilatusimage
        (in fabio)        		 previous()
        (in fabioimage)
        P4dec()
        (in pnmimage)        		 pilatusimage
        (in fabio.pilatusimage)        		 previous()
        (in file_series)
        P5dec()
        (in pnmimage)        		 pnmimage
        (in fabio)        		 previous()
        (in filename_series)
        P6dec()
        (in pnmimage)        		 pnmimage
        (in fabio.pnmimage)        		 previous_filename()
        (in fabio.fabioutils)
        P7dec()
        (in pnmimage)        		 pop()
        (in CIF)        		 previous_image()
        (in file_series)
        P7HEADERITEMS
        (in fabio.pnmimage)        		 popitem()
        (in CIF)        		 previous_object()
        (in file_series)
        PADDING
        (in fabio.cbfimage)        		 prev_image()
        (in filename_series)        		 previous_object()
        (in filename_series)

        R
        rad2deg
        (in fabio.OXDimage)        		 read()
        (in fabiodata)        		 read_tag_entry()
        (in dm3image)
        read()
        (in GEimage)        		 read()
        (in dm3image)        		 read_tag_group()
        (in dm3image)
        read()
        (in GEimage)        		 read()
        (in edfimage)        		 read_tag_type()
        (in dm3image)
        read()
        (in HiPiCimage)        		 read()
        (in fabioimage)        		 readbytes()
        (in dm3image)
        read()
        (in OXDimage)        		 read()
        (in fit2dmaskimage)        		 readbytestream
        (in fabio)
        read()
        (in adscimage)        		 read()
        (in fit2dspreadsheetimage)        		 readbytestream()
        (in fabio.readbytestream)
        read()
        (in binaryimage)        		 read()
        (in kcdimage)        		 readheader()
        (in fabioimage)
        read()
        (in bruker100image)        		 read()
        (in mar345image)        		 readROI()
        (in fabioimage)
        read()
        (in brukerimage)        		 read()
        (in pnmimage)        		 rebin()
        (in fabioimage)
        read()
        (in cbfimage)        		 read()
        (in tifimage)        		 resetvals()
        (in fabioimage)
        read()
        (in fabio.cf_io)        		 read()
        (in xsdimage)        		  
        read()
        (in columnfile)        		 read_data()
        (in dm3image)        		  

        S
        SAMPLE_FORMAT_COMPLEXIEEEFP
        (in fabio.TiffIO)        		 setCapsHeader()
        (in edfimage)        		 size
        (in BZ2File)
        SAMPLE_FORMAT_COMPLEXINT
        (in fabio.TiffIO)        		 setData()
        (in Section)        		 size
        (in File)
        SAMPLE_FORMAT_FLOAT
        (in fabio.TiffIO)        		 setData()
        (in Frame)        		 size
        (in GzipFile)
        SAMPLE_FORMAT_INT
        (in fabio.TiffIO)        		 setData()
        (in edfimage)        		 size
        (in StringIO)
        SAMPLE_FORMAT_UINT
        (in fabio.TiffIO)        		 setDim1()
        (in edfimage)        		 START_COMMENT
        (in CIF)
        SAMPLE_FORMAT_VOID
        (in fabio.TiffIO)        		 setDim2()
        (in edfimage)        		 STARTER
        (in fabio.cbfimage)
        save()
        (in fabioimage)        		 setHeader()
        (in edfimage)        		 str
        saveCIF()
        (in CIF)        		 setHeaderKeys()
        (in edfimage)        		 str()
        (in FilenameObject)
        Section
        (in fabio.OXDimage)        		 setNbFrames()
        (in edfimage)        		 StringIO
        (in fabio.fabioutils)
        seek()
        (in GzipFile)        		 setSize()
        (in BZ2File)        		 SUBFORMATS
        (in fabio.pnmimage)
        setBpp()
        (in edfimage)        		 setSize()
        (in File)        		 swap_needed()
        (in binaryimage)
        setByteCode()
        (in Frame)        		 setSize()
        (in GzipFile)        		 swap_needed()
        (in Frame)
        setByteCode()
        (in edfimage)        		 setSize()
        (in StringIO)        		 swap_needed()
        (in edfimage)

        T
        TAG_BITS_PER_SAMPLE
        (in fabio.TiffIO)        		 TAG_SAMPLE_FORMAT
        (in fabio.TiffIO)        		 tifimage
        (in fabio)
        TAG_COLORMAP
        (in fabio.TiffIO)        		 TAG_SOFTWARE
        (in fabio.TiffIO)        		 tifimage
        (in fabio.tifimage)
        TAG_COMPRESSION
        (in fabio.TiffIO)        		 TAG_STRIP_BYTE_COUNTS
        (in fabio.TiffIO)        		 toAscii()
        (in fabio.fabioutils)
        TAG_DATE
        (in fabio.TiffIO)        		 TAG_STRIP_OFFSETS
        (in fabio.TiffIO)        		 toPIL16()
        (in bruker100image)
        TAG_ID
        (in fabio.TiffIO)        		 test()
        (in fabio.adscimage)        		 toPIL16()
        (in fabioimage)
        TAG_IMAGE_DESCRIPTION
        (in fabio.TiffIO)        		 test()
        (in fabio.brukerimage)        		 tostring()
        (in CIF)
        TAG_NUMBER_OF_COLUMNS
        (in fabio.TiffIO)        		 test()
        (in fabio.fabioimage)        		 tostring()
        (in FilenameObject)
        TAG_NUMBER_OF_ROWS
        (in fabio.TiffIO)        		 Tiff_header
        (in fabio.tifimage)        		 TYPES
        (in fabio.tifimage)
        TAG_PHOTOMETRIC_INTERPRETATION
        (in fabio.TiffIO)        		 TiffIO
        (in fabio)        		 TYPESIZES
        (in fabio.tifimage)
        TAG_ROWS_PER_STRIP
        (in fabio.TiffIO)        		 TiffIO
        (in fabio.TiffIO)        		  

        U
        UnknownCompressedFile
        (in fabio.fabioutils)        		 unpack()
        (in Image_File_Directory)        		 update_header()
        (in fabioimage)
        unpack()
        (in edfimage)        		 unpack()
        (in Image_File_Directory_entry)        		  

        V
        version
        (in fabio)        		    
           

        W
        write()
        (in GEimage)        		 write()
        (in cbfimage)        		 write()
        (in pnmimage)
        write()
        (in OXDimage)        		 write()
        (in edfimage)        		 write()
        (in tifimage)
        write()
        (in adscimage)        		 write()
        (in fabioimage)        		 write2()
        (in brukerimage)
        write()
        (in binaryimage)        		 write()
        (in fit2dmaskimage)        		 writeImage()
        (in TiffIO)
        write()
        (in brukerimage)        		 write()
        (in mar345image)        		  

        X
        xsdimage
        (in fabio)        		 xsdimage
        (in fabio.xsdimage)        		  
           

        _
        __doc__
        (in fabio.OXDimage)        		 __package__
        (in fabio.bruker100image)        		 _need_a_seek_to_read
        (in GEimage)
        __doc__
        (in fabio.binaryimage)        		 __package__
        (in fabio.brukerimage)        		 _need_a_seek_to_read
        (in fabioimage)
        __doc__
        (in fabio.mar345image)        		 __package__
        (in fabio.byte_offset)        		 _need_a_seek_to_read
        (in tifimage)
        __headerstring__
        (in brukerimage)        		 __package__
        (in fabio.cbfimage)        		 _open()
        (in fabioimage)
        __init__()
        (in Section)        		 __package__
        (in fabio.cf_io)        		 _openimage()
        (in fabio.openimage)
        __init__()
        (in TiffIO)        		 __package__
        (in fabio.compression)        		 _parseCIF()
        (in CIF)
        __init__()
        (in adscimage)        		 __package__
        (in fabio.converters)        		 _parseImageFileDirectory()
        (in TiffIO)
        __init__()
        (in binaryimage)        		 __package__
        (in fabio.datIO)        		 _read()
        (in marccdimage)
        __init__()
        (in CIF)        		 __package__
        (in fabio.dm3image)        		 _read()
        (in pilatusimage)
        __init__()
        (in cbfimage)        		 __package__
        (in fabio.edfimage)        		 _readbinary_byte_offset()
        (in cbfimage)
        __init__()
        (in fabiodata)        		 __package__
        (in fabio.fabioimage)        		 _readCIF()
        (in CIF)
        __init__()
        (in dm3image)        		 __package__
        (in fabio.fabioutils)        		 _readframe()
        (in GEimage)
        __init__()
        (in Frame)        		 __package__
        (in fabio.file_series)        		 _readheader()
        (in GEimage)
        __init__()
        (in edfimage)        		 __package__
        (in fabio.fit2dmaskimage)        		 _readheader()
        (in GEimage)
        __init__()
        (in fabioimage)        		 __package__
        (in fabio.fit2dspreadsheetimage)        		 _readheader()
        (in HiPiCimage)
        __init__()
        (in BZ2File)        		 __package__
        (in fabio.kcdimage)        		 _readheader()
        (in OXDimage)
        __init__()
        (in File)        		 __package__
        (in fabio.mar345_IO)        		 _readheader()
        (in adscimage)
        __init__()
        (in FilenameObject)        		 __package__
        (in fabio.mar345image)        		 _readheader()
        (in brukerimage)
        __init__()
        (in GzipFile)        		 __package__
        (in fabio.marccdimage)        		 _readheader()
        (in cbfimage)
        __init__()
        (in StringIO)        		 __package__
        (in fabio.openimage)        		 _readheader()
        (in dm3image)
        __init__()
        (in UnknownCompressedFile)        		 __package__
        (in fabio.pilatusimage)        		 _readheader()
        (in edfimage)
        __init__()
        (in file_series)        		 __package__
        (in fabio.pnmimage)        		 _readheader()
        (in fabioimage)
        __init__()
        (in filename_series)        		 __package__
        (in fabio.readbytestream)        		 _readheader()
        (in fit2dmaskimage)
        __init__()
        (in numbered_file_series)        		 __package__
        (in fabio.tifimage)        		 _readheader()
        (in fit2dspreadsheetimage)
        __init__()
        (in mar345image)        		 __package__
        (in fabio.xsdimage)        		 _readheader()
        (in kcdimage)
        __init__()
        (in pnmimage)        		 __repr__()
        (in Section)        		 _readheader()
        (in mar345image)
        __init__()
        (in Image_File_Directory)        		 __revision__
        (in fabio.TiffIO)        		 _readheader()
        (in marccdimage)
        __init__()
        (in Image_File_Directory_entry)        		 __setitem__()
        (in CIF)        		 _readheader()
        (in pilatusimage)
        __init__()
        (in Tiff_header)        		 __status__
        (in fabio)        		 _readheader()
        (in pnmimage)
        __init__()
        (in tifimage)        		 __status__
        (in fabio.tifimage)        		 _readheader()
        (in tifimage)
        __init__()
        (in xsdimage)        		 __test__
        (in fabio.byte_offset)        		 _readheader()
        (in xsdimage)
        __makeSureFileIsClosed()
        (in TiffIO)        		 __test__
        (in fabio.mar345_IO)        		 _readHeaderBlock()
        (in edfimage)
        __makeSureFileIsOpen()
        (in TiffIO)        		 _analyseOneLoop()
        (in CIF)        		 _readIFDEntry()
        (in TiffIO)
        __package__
        (in fabio.GEimage)        		 _compressed_stream()
        (in fabioimage)        		 _readImage()
        (in TiffIO)
        __package__
        (in fabio.GEimage_old)        		 _getOutputIFD()
        (in TiffIO)        		 _readInfo()
        (in TiffIO)
        __package__
        (in fabio.HiPiCimage)        		 _high_intensity_pixel_records()
        (in mar345image)        		 _splitCIF()
        (in CIF)
        __package__
        (in fabio.OXDimage)        		 _initEmptyFile()
        (in TiffIO)        		 _updateIFD()
        (in TiffIO)
        __package__
        (in fabio.TiffIO)        		 _initInternalVariables()
        (in TiffIO)        		 _writeheader()
        (in OXDimage)
        __package__
        (in fabio)        		 _makeframename()
        (in GEimage)        		 _writeheader()
        (in mar345image)
        __package__
        (in fabio.adscimage)        		 _need_a_real_file
        (in fabioimage)        		  
        __package__
        (in fabio.binaryimage)        		 _need_a_real_file
        (in mar345image)        		  


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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:40 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/fabio.GEimage_old-module.html0000644000175000017500000001402212126623347022233 0ustar jeromejerome00000000000000 fabio.GEimage_old
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        Package fabio :: Module GEimage_old
        [hide private]
        [frames] | no frames]

        Module GEimage_old

        source code

        
Reads the header from a GE a-Si Angio Detector

Authors: Henning O. Sorensen & Erik Knudsen
         Center for Fundamental Research: Metal Structures in Four Dimensions
         Risoe National Laboratory
         Frederiksborgvej 399
         DK-4000 Roskilde
         email:erik.knudsen@risoe.dk

        + Jon Wright, ESRF

        The header information has been taken from the script read_GEaSi_data.py
        by
        Antonino Miceli
        Thu Jan  4 13:46:31 CST 2007
        Classes [hide private]
          GEimage
        Variables [hide private]
          __package__ = 'fabio'
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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:40 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/fabio.marccdimage-module.html0000644000175000017500000005211612126623347022341 0ustar jeromejerome00000000000000 fabio.marccdimage
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        Package fabio :: Module marccdimage
        [hide private]
        [frames] | no frames]

        Module marccdimage

        source code

        

Authors:
........
* Henning O. Sorensen & Erik Knudsen:
  Center for Fundamental Research: Metal Structures in Four Dimensions;
  Risoe National Laboratory;
  Frederiksborgvej 399;
  DK-4000 Roskilde;
  email:erik.knudsen@risoe.dk
* Jon Wright:
  European Synchrotron Radiation Facility;
  Grenoble (France)
         
marccdimage can read MarCCD and MarMosaic images including header info.

JPW : Use a parser in case of typos (sorry?)
        Classes [hide private]
          marccdimage
        Read in data in mar ccd format, also MarMosaic images, including header info
        Functions [hide private]
         
        make_format(c_def_string)
        Reads the header definition in c and makes the format string to pass to struct.unpack        		 source code
         
        interpret_header(header, fmt, names)
        given a format and header interpret it        		 source code
        Variables [hide private]
          logger = logging.getLogger("marccdimage")
          CDEFINITION = '\ntypedef struct frame_header_type {\n ...
          C_TO_STRUCT = {'INT32': 'i', 'UINT16': 'H', 'UINT32': 'I', 'ch...
          C_SIZES = {'INT32': 4, 'UINT16': 2, 'UINT32': 4, 'char': 1}
          MAXIMAGES = 9
          HEADER_FORMAT = 'IccccccccccccccccIIIIIIIIIIIIIIIIIIIIIIIIIIII...
          HEADER_NAMES = ['header_type', 'header_name[16]', 'header_name...
          __package__ = 'fabio'
        Variables Details [hide private]

        CDEFINITION

        Value:
        '''
typedef struct frame_header_type {
         /* File/header format parameters (256 bytes) */
         UINT32        header_type;  /* flag for header type  
                                           (can be  used as magic numb\
er) */
         char header_name[16];           /* header name (MMX) */
         UINT32        header_major_version;   /* header_major_version\
...

        C_TO_STRUCT

        Value:
        {'INT32': 'i', 'UINT16': 'H', 'UINT32': 'I', 'char': 'c'}

        HEADER_FORMAT

        Value:
        'IccccccccccccccccIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIccccccccccccc\
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccIII\
IIIIIIIIIIIIIIIIIIIccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHH\
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH\
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiii\
iiiiicccccccccccccccciiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiccccccc\
ccccccccciiiiiiiiiiccccccccccccccccccccccccccccccccccccccccccccccccccc\
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc\
...

        HEADER_NAMES

        Value:
        ['header_type',
 'header_name[16]',
 'header_name[16]',
 'header_name[16]',
 'header_name[16]',
 'header_name[16]',
 'header_name[16]',
 'header_name[16]',
...

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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:40 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/fabio.edfimage-module.html0000644000175000017500000004275012126623347021651 0ustar jeromejerome00000000000000 fabio.edfimage
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        Package fabio :: Module edfimage
        [hide private]
        [frames] | no frames]

        Module edfimage

        source code

        

License: GPLv2+

Authors:
........
* Henning O. Sorensen & Erik Knudsen:
  Center for Fundamental Research: Metal Structures in Four Dimensions;
  Risoe National Laboratory;
  Frederiksborgvej 399;
  DK-4000 Roskilde;
  email:erik.knudsen@risoe.dk
* Jon Wright & Jérôme Kieffer:
  European Synchrotron Radiation Facility;
  Grenoble (France)
        Classes [hide private]
          Frame
        A class representing a single frame in an EDF file
          edfimage
        Read and try to write the ESRF edf data format
        Variables [hide private]
          logger = logging.getLogger("edfimage")
          BLOCKSIZE = 512
          DATA_TYPES = {'Double': <type 'numpy.float64'>, 'DoubleIEEE128...
          NUMPY_EDF_DTYPE = {'float128': 'QuadrupleValue', 'float32': 'F...
          MINIMUM_KEYS = ['HEADERID', 'IMAGE', 'BYTEORDER', 'DATATYPE', ...
          DEFAULT_VALUES = {}
          __package__ = 'fabio'
        Variables Details [hide private]

        DATA_TYPES

        Value:
        {'Double': <type 'numpy.float64'>,
 'DoubleIEEE128': <type 'numpy.float128'>,
 'DoubleIEEE64': <type 'numpy.float64'>,
 'DoubleValue': <type 'numpy.float64'>,
 'FLOAT': <type 'numpy.float32'>,
 'FLOATVALUE': <type 'numpy.float32'>,
 'Float': <type 'numpy.float32'>,
 'Float32': <type 'numpy.float32'>,
...

        NUMPY_EDF_DTYPE

        Value:
        {'float128': 'QuadrupleValue',
 'float32': 'FloatValue',
 'float64': 'DoubleValue',
 'int16': 'SignedShort',
 'int32': 'SignedInteger',
 'int64': 'Signed64',
 'int8': 'SignedByte',
 'uint16': 'UnsignedShort',
...

        MINIMUM_KEYS

        Value:
        ['HEADERID',
 'IMAGE',
 'BYTEORDER',
 'DATATYPE',
 'DIM_1',
 'DIM_2',
 'SIZE']

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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:40 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/toc-fabio.kcdimage-module.html0000644000175000017500000000312012120434325022411 0ustar jeromejerome00000000000000 kcdimage

        Module kcdimage

        Classes

        kcdimage

        Variables

        DATA_TYPES
        DEFAULT_VALUES
        MINIMUM_KEYS
        __package__
        logger
        [hide private] fabio-0.1.3/epydoc/toc-fabio.readbytestream-module.html0000644000175000017500000000266312120434325023673 0ustar jeromejerome00000000000000 readbytestream

        Module readbytestream

        Functions

        readbytestream

        Variables

        DATATYPES
        __package__
        logger
        [hide private] fabio-0.1.3/epydoc/fabio.HiPiCimage-module.html0000644000175000017500000001442212126623347022042 0ustar jeromejerome00000000000000 fabio.HiPiCimage
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        Package fabio :: Module HiPiCimage
        [hide private]
        [frames] | no frames]

        Module HiPiCimage

        source code

        
Authors: Henning O. Sorensen & Erik Knudsen
         Center for Fundamental Research: Metal Structures in Four Dimensions
         Risoe National Laboratory
         Frederiksborgvej 399
         DK-4000 Roskilde
         email:erik.knudsen@risoe.dk

        + Jon Wright, ESRF

Information about the file format from Masakatzu Kobayashi is highly appreciated
        Classes [hide private]
          HiPiCimage
        Read HiPic images e.g.
        Variables [hide private]
          logger = logging.getLogger("HiPiCimage")
          __package__ = 'fabio'
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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:40 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/fabio.adscimage-pysrc.html0000644000175000017500000020316712126623347021701 0ustar jeromejerome00000000000000 fabio.adscimage
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        Package fabio :: Module adscimage
        [hide private]
        [frames] | no frames]

        Source Code for Module fabio.adscimage

          1  #!/usr/bin/env python 
  2  #coding: utf8 
  3  """ 
  4   
  5  Authors: Henning O. Sorensen & Erik Knudsen 
  6           Center for Fundamental Research: Metal Structures in Four Dimensions 
  7           Risoe National Laboratory 
  8           Frederiksborgvej 399 
  9           DK-4000 Roskilde 
 10           email:erik.knudsen@risoe.dk 
 11   
 12  + mods for fabio by JPW 
 13   
 14  """ 
 15   
 16  import numpy, logging 
 17  from fabioimage import fabioimage 
 18  logger = logging.getLogger("adscimage") 
 19   

         20 -class adscimage(fabioimage): 

         21      """ Read an image in ADSC format (quite similar to edf?) """ 

         22 -    def __init__(self, *args, **kwargs): 

         23          fabioimage.__init__(self, *args, **kwargs) 

         24   

         25 -    def read(self, fname, frame=None): 

         26          """ read in the file """ 
 27          infile = self._open(fname, "rb") 
 28          try: 
 29              self._readheader(infile) 
 30          except: 
 31              raise Exception("Error processing adsc header") 
 32          # banned by bzip/gzip??? 
 33          try: 
 34              infile.seek(int(self.header['HEADER_BYTES']), 0) 
 35          except TypeError: 
 36              # Gzipped does not allow a seek and read header is not 
 37              # promising to stop in the right place 
 38              infile.close() 
 39              infile = self._open(fname, "rb") 
 40              infile.read(int(self.header['HEADER_BYTES'])) 
 41          binary = infile.read() 
 42          infile.close() 
 43   
 44          #now read the data into the array 
 45          self.dim1 = int(self.header['SIZE1']) 
 46          self.dim2 = int(self.header['SIZE2']) 
 47          if 'little' in self.header['BYTE_ORDER']: 
 48              try: 
 49                  self.data = numpy.reshape( 
 50                      numpy.fromstring(binary, numpy.uint16), 
 51                      (self.dim2, self.dim1)) 
 52              except ValueError: 
 53                  raise IOError, 'Size spec in ADSC-header does not match ' + \ 
 54                      'size of image data field' 
 55              self.bytecode = numpy.uint16 
 56              logger.info("adscimage read in using low byte first (x386-order)") 
 57          else: 
 58              try: 
 59                  self.data = numpy.reshape( 
 60                      numpy.fromstring(binary, numpy.uint16), 
 61                      (self.dim2, self.dim1)).byteswap() 
 62              except ValueError: 
 63                  raise IOError, 'Size spec in ADSC-header does not match ' + \ 
 64                      'size of image data field' 
 65              self.bytecode = numpy.uint16 
 66              logger.info('adscimage using high byte first (network order)') 
 67          self.resetvals() 
 68          return self 

         69   
 70   

         71 -    def _readheader(self, infile): 

         72          """ read an adsc header """ 
 73          line = infile.readline() 
 74          bytesread = len(line) 
 75          while '}' not in line: 
 76              if '=' in line: 
 77                  (key, val) = line.split('=') 
 78                  self.header_keys.append(key.strip()) 
 79                  self.header[key.strip()] = val.strip(' ;\n') 
 80              line = infile.readline() 
 81              bytesread = bytesread + len(line) 

         82   
 83   

         84 -    def write(self, fname): 

         85          """ 
 86          Write adsc format 
 87          """ 
 88          out = '{\n' 
 89          for key in self.header_keys: 
 90              out += "%s = %s;\n" % (key, self.header[key]) 
 91          # FIXME ??? - made padding match header bytes keyword             
 92          #        the cbflib example image has exactly 512... 
 93          if self.header.has_key("HEADER_BYTES"): 
 94              pad = int(self.header["HEADER_BYTES"]) - len(out) - 2 
 95          else: 
 96              # integer division 
 97              # 1234567890123456789012 
 98              # HEADER_BYTES = 1234;\n 
 99              hsize = ((len(out) + 23) / 512 + 1) * 512 
100              out += "HEADER_BYTES=%d;\n" % (hsize) 
101              pad = hsize - len(out) - 2 
102          out += pad * ' ' + "}\n" 
103          assert len(out) % 512 == 0 , "Header is not multiple of 512" 
104          outf = open(fname, "wb") 
105          outf.write(out) 
106          # it says "unsigned_short" ? ... jpw example has: 
107          # BYTE_ORDER=big_endian; 
108          # TYPE=unsigned_short; 
109          if "little" in self.header["BYTE_ORDER"]: 
110              outf.write(self.data.astype(numpy.uint16).tostring()) 
111          else: 
112              outf.write(self.data.byteswap().astype( 
113                      numpy.uint16).tostring()) 
114          outf.close() 

        115   
116   

        117 -def test(): 

        118      """ testcase """ 
119      import sys, time 
120      img = adscimage() 
121      begin = time.clock() 
122      while (sys.argv[1:]): 
123          img.read(sys.argv[1]) 
124  #        rim = img.toPIL16() 
125          img.rebin(2, 2) 
126          img.write('jegErEnFil0000.img') 
127          print sys.argv[1] + ": max=%d, min=%d, mean=%.2e, stddev=%.2e" % (\ 
128                img.getmax(), img.getmin(), img.getmean(), img.getstddev()) 
129          print 'integrated intensity (%d %d %d %d) =%.3f' % (\ 
130                10, 20, 20, 40, img.integrate_area((10, 20, 20, 40))) 
131          sys.argv[1:] = sys.argv[2:] 
132      end = time.clock() 
133      print end - begin 

        134   
135   
136  if __name__ == '__main__': 
137      test() 
138

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        Package fabio :: Module datIO
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        Module datIO

        source code

        
Authors: Henning O. Sorensen & Erik Knudsen
         Center for Fundamental Research: Metal Structures in Four Dimensions
         Risoe National Laboratory
         Frederiksborgvej 399
         DK-4000 Roskilde
         email:erik.knudsen@risoe.dk
         
         and Jon Wright, ESRF
        Classes [hide private]
          fabiodata
        A common class for dataIO in fable Contains a 2d numpy array for keeping data, and two lists (clabels and rlabels) containing labels for columns and rows respectively
          columnfile
        Concrete fabiodata class
        Variables [hide private]
          __package__ = None
        hash(x)
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        Package fabio :: Module binaryimage
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        Source Code for Module fabio.binaryimage

         1  #!/usr/bin/env python 
 2  #coding: utf8  
 3  from __future__ import with_statement 
 4  __doc__ = """ 
 5  Authors: Gael Goret, Jerome Kieffer, ESRF, France 
 6  Emails: gael.goret@esrf.fr, jerome.kieffer@esrf.fr 
 7   
 8  Binary files images are simple none-compressed 2D images only defined by their :  
 9  data-type, dimensions, byte order and offset 
10   
11  This simple library has been made for manipulating exotic/unknown files format.   
12  """ 
13   
14  __authors__ = ["Gaël Goret", "Jérôme Kieffer"] 
15  __contact__ = "gael.goret@esrf.fr"#, jerome.kieffer@esrf.eu" 
16  __license__ = "GPLv3+" 
17  __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" 
18  __version__ = "17 Apr 2012" 
19   
20  from fabioimage import fabioimage 
21  import numpy, logging 
22  logger = logging.getLogger("binaryimage") 

        23   
24 -class binaryimage(fabioimage): 

        25      """ 
26      This simple library has been made for manipulating exotic/unknown files format. 
27       
28      Binary files images are simple none-compressed 2D images only defined by their :  
29      data-type, dimensions, byte order and offset 
30      """ 
31   

        32 -    def __init__(self, *args, **kwargs): 

        33          fabioimage.__init__(self, *args, **kwargs) 

        34   
35      @staticmethod 

        36 -    def swap_needed(endian): 

        37          """ 
38          Decide if we need to byteswap 
39          """ 
40          if (endian == '<' and numpy.little_endian) or (endian == '>' and not numpy.little_endian): 
41              return False 
42          if (endian == '>' and numpy.little_endian) or (endian == '<' and not numpy.little_endian): 
43              return True 

        44   

        45 -    def read(self, fname, dim1, dim2, offset=0, bytecode="int32", endian="<"): 

        46          """  
47          Read a binary image 
48          Parameters : fname, dim1, dim2, offset, bytecode, endian 
49          fname : file name : str 
50          dim1,dim2 : image dimensions : int 
51          offset : size of the : int  
52          bytecode among : "int8","int16","int32","int64","uint8","uint16","uint32","uint64","float32","float64",... 
53          endian among short or long endian ("<" or ">") 
54          """ 
55          self.filename = fname 
56          self.dim1 = dim1 
57          self.dim2 = dim2 
58          self.bytecode = bytecode 
59          f = open(self.filename, "rb") 
60          dims = [dim2, dim1] 
61          bpp = len(numpy.array(0, bytecode).tostring()) 
62          size = dims[0] * dims[1] * bpp 
63   
64          f.seek(offset) 
65          rawData = f.read(size) 
66          if  self.swap_needed(endian): 
67              data = numpy.fromstring(rawData, bytecode).byteswap().reshape(tuple(dims)) 
68          else: 
69              data = numpy.fromstring(rawData, bytecode).reshape(tuple(dims)) 
70          self.data = data 
71          return self 

        72   

        73 -    def estimate_offset_value(self, fname, dim1, dim2, bytecode="int32"): 

        74          "Estimates the size of a file" 
75          with open(fname, "rb") as f: 
76              bpp = len(numpy.array(0, bytecode).tostring()) 
77              size = dim1 * dim2 * bpp 
78              totsize = len(f.read()) 
79          logger.info('total size (bytes): %s', totsize) 
80          logger.info('expected data size given parameters (bytes): %s', size) 
81          logger.info('estimation of the offset value (bytes): %s', totsize - size) 

        82   

        83 -    def write(self, fname): 

        84          with open(fname, mode="wb") as outfile: 
85              outfile.write(self.data.tostring()) 

        86

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        API Documentation

        This document contains the API (Application Programming Interface) documentation for this project. Documentation for the Python objects defined by the project is divided into separate pages for each package, module, and class. The API documentation also includes two pages containing information about the project as a whole: a trees page, and an index page.

        Object Documentation

        Each Package Documentation page contains:

        • A description of the package.
        • A list of the modules and sub-packages contained by the package.
        • A summary of the classes defined by the package.
        • A summary of the functions defined by the package.
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        • A detailed description of each function defined by the package.
        • A detailed description of each variable defined by the package.

        Each Module Documentation page contains:

        • A description of the module.
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        • A summary of the functions defined by the module.
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        • A detailed description of each function defined by the module.
        • A detailed description of each variable defined by the module.

        Each Class Documentation page contains:

        • A class inheritance diagram.
        • A list of known subclasses.
        • A description of the class.
        • A summary of the methods defined by the class.
        • A summary of the instance variables defined by the class.
        • A summary of the class (static) variables defined by the class.
        • A detailed description of each method defined by the class.
        • A detailed description of each instance variable defined by the class.
        • A detailed description of each class (static) variable defined by the class.

        Project Documentation

        The Trees page contains the module and class hierarchies:

        • The module hierarchy lists every package and module, with modules grouped into packages. At the top level, and within each package, modules and sub-packages are listed alphabetically.
        • The class hierarchy lists every class, grouped by base class. If a class has more than one base class, then it will be listed under each base class. At the top level, and under each base class, classes are listed alphabetically.

        The Index page contains indices of terms and identifiers:

        • The term index lists every term indexed by any object's documentation. For each term, the index provides links to each place where the term is indexed.
        • The identifier index lists the (short) name of every package, module, class, method, function, variable, and parameter. For each identifier, the index provides a short description, and a link to its documentation.

        The Table of Contents

        The table of contents occupies the two frames on the left side of the window. The upper-left frame displays the project contents, and the lower-left frame displays the module contents:

        Project
        Contents
        ...        		 API
        Documentation
        Frame
        Module
        Contents
         
        ...
         

        The project contents frame contains a list of all packages and modules that are defined by the project. Clicking on an entry will display its contents in the module contents frame. Clicking on a special entry, labeled "Everything," will display the contents of the entire project.

        The module contents frame contains a list of every submodule, class, type, exception, function, and variable defined by a module or package. Clicking on an entry will display its documentation in the API documentation frame. Clicking on the name of the module, at the top of the frame, will display the documentation for the module itself.

        The "frames" and "no frames" buttons below the top navigation bar can be used to control whether the table of contents is displayed or not.

        The Navigation Bar

        A navigation bar is located at the top and bottom of every page. It indicates what type of page you are currently viewing, and allows you to go to related pages. The following table describes the labels on the navigation bar. Note that not some labels (such as [Parent]) are not displayed on all pages.

        Label Highlighted when... Links to...
        [Parent] (never highlighted) the parent of the current package
        [Package] viewing a package the package containing the current object
        [Module] viewing a module the module containing the current object
        [Class] viewing a class the class containing the current object
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        The "show private" and "hide private" buttons below the top navigation bar can be used to control whether documentation for private objects is displayed. Private objects are usually defined as objects whose (short) names begin with a single underscore, but do not end with an underscore. For example, "_x", "__pprint", and "epydoc.epytext._tokenize" are private objects; but "re.sub", "__init__", and "type_" are not. However, if a module defines the "__all__" variable, then its contents are used to decide which objects are private.

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        Package fabio :: Module fabioutils
        [hide private]
        [frames] | no frames]

        Module fabioutils

        source code

        General purpose utilities functions for fabio

        Classes [hide private]
          FilenameObject
        The 'meaning' of a filename ...
          StringIO
        just an interface providing the name and mode property to a StringIO
          File
        wrapper for "file" with locking
          UnknownCompressedFile
        wrapper for "File" with locking
          GzipFile
        Just a wrapper forgzip.GzipFile providing the correct seek capabilities for python 2.5
          BZ2File
        Wrapper with lock
        Functions [hide private]
         
        deprecated(func)
        used to deprecate a function/method: prints a lot of warning messages to enforce the modifaction of the code        		 source code
         
        getnum(name)
        # try to figure out a file number # guess it starts at the back        		 source code
         
        numstem(name)
        cant see how to do without reversing strings Match 1 or more digits going backwards from the end of the string        		 source code
         
        deconstruct_filename(*arg, **kw)
        decorator that deprecates the use of a function        		 source code
         
        construct_filename(filename, frame=None)
        Try to construct the filename for a given frame        		 source code
         
        next_filename(name, padding=True)
        increment number        		 source code
         
        previous_filename(name, padding=True)
        decrement number        		 source code
         
        jump_filename(name, num, padding=True)
        jump to number        		 source code
         
        extract_filenumber(name)
        extract file number        		 source code
         
        isAscii(name, listExcluded=None)
        Returns: True of False whether name is pure ascii or not        		 source code
         
        toAscii(name, excluded=None)
        Returns: the name with all non valid char removed        		 source code
         
        nice_int(s)
        Workaround that int('1.0') raises an exception        		 source code
        Variables [hide private]
          logger = logging.getLogger("fabioutils")
          FILETYPES = {'cbf': ['cbf'], 'cbf.bz2': ['cbf'], 'cbf.gz': ['c...
          COMPRESSORS = {'.bz2': 'bzip2 -dc ', '.gz': 'gzip -dc '}
          dictAscii = {None: [' ', '!', '"', '#', '$', '%', '&', '\'', '...
          lines = 'bzip2, a block-sorting file compressor. Version 1.0....
          __package__ = 'fabio'
          i = 126
          key = 'cbf'
        Function Details [hide private]

        deconstruct_filename(*arg, **kw)

        		source code 

        decorator that deprecates the use of a function

        Decorators:
        • @deprecated

        isAscii(name, listExcluded=None)

        		source code 
        Parameters:
        • name - string to check
        • listExcluded - list of char or string excluded.
        Returns:
        True of False whether name is pure ascii or not

        toAscii(name, excluded=None)

        		source code 
        Parameters:
        • name - string to check
        • excluded - tuple of char or string excluded (not list: they are mutable).
        Returns:
        the name with all non valid char removed

        nice_int(s)

        		source code 

        Workaround that int('1.0') raises an exception

        Parameters:
        • s - string to be converted to integer

        Variables Details [hide private]

        FILETYPES

        Value:
        {'cbf': ['cbf'],
 'cbf.bz2': ['cbf'],
 'cbf.gz': ['cbf'],
 'cor': ['edf'],
 'cor.bz2': ['edf'],
 'cor.gz': ['edf'],
 'dm3': ['dm3'],
 'dm3.bz2': ['dm3'],
...

        dictAscii

        Value:
        {None: [' ',
        '!',
        '"',
        '#',
        '$',
        '%',
        '&',
        '\'',
...

        lines

        Value:
        '''bzip2, a block-sorting file compressor.  Version 1.0.5, 10-Dec-2007\
.

   usage: bzip2 [flags and input files in any order]

   -h --help           print this message
   -d --decompress     force decompression
   -z --compress       force compression
...

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        Package fabio :: Module fabioutils :: Class File
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        Class File

        source code

        object --+    
         |    
      file --+
             |
            File
        Known Subclasses:

        wrapper for "file" with locking

        Instance Methods [hide private]
        file object
        __init__(name, mode=..., buffering=...)
        Open a file.        		 source code
         
        getSize(self) source code
         
        setSize(self, size) source code

        Inherited from file: __delattr__, __enter__, __exit__, __getattribute__, __iter__, __new__, __repr__, __setattr__, close, fileno, flush, isatty, next, read, readinto, readline, readlines, seek, tell, truncate, write, writelines, xreadlines

        Inherited from object: __format__, __hash__, __reduce__, __reduce_ex__, __sizeof__, __str__, __subclasshook__

        Properties [hide private]
          size

        Inherited from file: closed, encoding, errors, mode, name, newlines, softspace

        Inherited from object: __class__

        Method Details [hide private]

        __init__(name, mode=..., buffering=...)
        (Constructor)

        		source code  
                Open a file.  The mode can be 'r', 'w' or 'a' for reading (default),
        writing or appending.  The file will be created if it doesn't exist
        when opened for writing or appending; it will be truncated when
        opened for writing.  Add a 'b' to the mode for binary files.
        Add a '+' to the mode to allow simultaneous reading and writing.
        If the buffering argument is given, 0 means unbuffered, 1 means line
        buffered, and larger numbers specify the buffer size.  The preferred way
        to open a file is with the builtin open() function.
        Add a 'U' to mode to open the file for input with universal newline
        support.  Any line ending in the input file will be seen as a '
'
        in Python.  Also, a file so opened gains the attribute 'newlines';
        the value for this attribute is one of None (no newline read yet),
        '
', '
', '
' or a tuple containing all the newline types seen.
        
        'U' cannot be combined with 'w' or '+' mode.
        Returns: file object
        Overrides: object.__init__

        Property Details [hide private]

        size

        Get Method:
        getSize(self)
        Set Method:
        setSize(self, size)

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        Module bruker100image

        Classes

        bruker100image

        Variables

        __package__
        logger
        [hide private] fabio-0.1.3/epydoc/fabio.pilatusimage-pysrc.html0000644000175000017500000006333012126623347022444 0ustar jeromejerome00000000000000 fabio.pilatusimage
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        Package fabio :: Module pilatusimage
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        Source Code for Module fabio.pilatusimage

         1  #!/usr/bin/env python 
 2  #coding: utf8 
 3  """ 
 4   
 5  Authors: 
 6  ........ 
 7  * Henning O. Sorensen & Erik Knudsen: 
 8    Center for Fundamental Research: Metal Structures in Four Dimensions; 
 9    Risoe National Laboratory; 
10    Frederiksborgvej 399; 
11    DK-4000 Roskilde; 
12    email:erik.knudsen@risoe.dk 
13  * Jon Wright: 
14    European Synchrotron Radiation Facility; 
15    Grenoble (France) 
16   
17  """ 
18   
19   
20  # Base this on the tifimage (as Pilatus is tiff with a 
21  # tiff header 
22   
23  from fabio.tifimage import tifimage 
24   
25   

        26 -class pilatusimage(tifimage): 

        27      """ Read in Pilatus format, also  
28          pilatus images, including header info """ 
29   
30   

        31 -    def _readheader(self, infile): 

        32          """ 
33          Parser based approach 
34          Gets all entries 
35          """ 
36   
37          self.header = {} 
38   
39  #        infile = open(infile) 
40          hstr = infile.read(4096) 
41          # well not very pretty - but seems to find start of 
42          # header information 
43          if (hstr.find('# ') == -1): 
44              return self.header 
45   
46          hstr = hstr[hstr.index('# '):] 
47          hstr = hstr[:hstr.index('\x00')] 
48          hstr = hstr.split('#') 
49          go_on = True 
50          while go_on: 
51              try: 
52                  hstr.remove('') 
53              except Exception: 
54                  go_on = False 
55   
56          for line in hstr: 
57              line = line[1:line.index('\r\n')] 
58              if line.find(':') > -1: 
59                  dump = line.split(':') 
60                  self.header[dump[0]] = dump[1] 
61              elif line.find('=') > -1: 
62                  dump = line.split('=') 
63                  self.header[dump[0]] = dump[1] 
64              elif line.find(' ') > -1: 
65                  i = line.find(' ') 
66                  self.header[line[:i]] = line[i:] 
67              elif line.find(',') > -1: 
68                  dump = line.split(',') 
69                  self.header[dump[0]] = dump[1] 
70   
71          return self.header 

        72   
73   
74   

        75 -    def _read(self, fname): 

        76          """ 
77          inherited from tifimage 
78          ... a Pilatus image *is a* tif image 
79          just with a header 
80          """ 
81          return tifimage.read(self, fname) 

        82

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        Package fabio :: Module converters
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        Module converters

        source code

        Converter module. This is for the moment empty (populated only with almost pass through anonymous functions) but aims to be populated with more sofisticated translators ...

        Author: J\xc3\xa9r\xc3\xb4me Kieffer

        Contact: jerome.kieffer@esrf.eu

        Copyright: European Synchrotron Radiation Facility, Grenoble, France

        License: GPLv3+

        Functions [hide private]
         
        convert_data_integer(data)
        convert data to integer        		 source code
         
        convert_data(inp, outp, data)
        Return data converted to the output format ...        		 source code
         
        convert_header(inp, outp, header)
        return header converted to the output format        		 source code
        Variables [hide private]
          logger = logging.getLogger("converter")
          CONVERSION_HEADER = {('edfimage', 'edfimage'): <function <lamb...
          CONVERSION_DATA = {('edfimage', 'OXDimage'): <function convert...
          __package__ = 'fabio'
        Function Details [hide private]

        convert_data(inp, outp, data)

        		source code 

        Return data converted to the output format ... over-simplistic implementation for the moment ...

        Parameters:
        • inp, outp - input/output format like "cbfimage"
        • data(ndarray) - the actual dataset to be transformed

        convert_header(inp, outp, header)

        		source code 

        return header converted to the output format

        Parameters:
        • inp, outp - input/output format like "cbfimage"
        • header(dict) - the actual set of headers to be transformed

        Variables Details [hide private]

        CONVERSION_HEADER

        Value:
        {('edfimage', 'edfimage'): <function <lambda> at 0x2136500>}

        CONVERSION_DATA

        Value:
        {("edfimage", "edfimage"): lambda data: data, ("edfimage", "cbfimage")\
: convert_data_integer, ("edfimage", "mar345image"): convert_data_inte\
ger, ("edfimage", "fit2dmaskimage"): convert_data_integer, ("edfimage"\
, "kcdimage"): convert_data_integer, ("edfimage", "OXDimage"): convert\
_data_integer, ("edfimage", "pnmimage"): convert_data_integer,}

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        Module byte_offset

        Variables

        __package__
        __test__
        [hide private] fabio-0.1.3/epydoc/fabio.tifimage.tifimage-class.html0000644000175000017500000004553112126623347023301 0ustar jeromejerome00000000000000 fabio.tifimage.tifimage
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        Package fabio :: Module tifimage :: Class tifimage
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        Class tifimage

        source code

                   object --+    
                    |    
fabioimage.fabioimage --+
                        |
                       tifimage
        Known Subclasses:

        Images in TIF format Wraps TiffIO

        Instance Methods [hide private]
         
        __init__(self, *args, **kwds)
        Tifimage constructor adds an nbits member attribute        		 source code
         
        _readheader(self, infile)
        Try to read Tiff images header...        		 source code
         
        read(self, fname, frame=None)
        Wrapper for TiffIO.        		 source code
         
        write(self, fname)
        Overrides the fabioimage.write method and provides a simple TIFF image writer.        		 source code

        Inherited from fabioimage.fabioimage: add, convert, getclassname, getframe, getheader, getmax, getmean, getmin, getstddev, integrate_area, load, make_slice, next, previous, readROI, readheader, rebin, resetvals, save, toPIL16, update_header

        Inherited from fabioimage.fabioimage (private): _compressed_stream, _open

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Static Methods [hide private]

        Inherited from fabioimage.fabioimage: checkData, checkHeader

        Class Variables [hide private]
          _need_a_seek_to_read = True

        Inherited from fabioimage.fabioimage (private): _need_a_real_file

        Properties [hide private]

        Inherited from fabioimage.fabioimage: classname

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, *args, **kwds)
        (Constructor)

        		source code 

        Tifimage constructor adds an nbits member attribute

        Overrides: object.__init__

        _readheader(self, infile)

        		source code 

        Try to read Tiff images header...

        Overrides: fabioimage.fabioimage._readheader

        read(self, fname, frame=None)

        		source code 

        Wrapper for TiffIO.

        Overrides: fabioimage.fabioimage.read

        write(self, fname)

        		source code 

        Overrides the fabioimage.write method and provides a simple TIFF image writer.

        Parameters:
        • fname - name of the file to save the image to
        Overrides: fabioimage.fabioimage.write

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        fabio-0.1.3/epydoc/fabio.GEimage_old-pysrc.html0000644000175000017500000034017012126623347022114 0ustar jeromejerome00000000000000 fabio.GEimage_old
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        Package fabio :: Module GEimage_old
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        [frames] | no frames]

        Source Code for Module fabio.GEimage_old

          1  
 
  2  #!/usr/bin/env python
 
  3  
 
  4  """
 
  5  Reads the header from a GE a-Si Angio Detector
 
  6  
 
  7  Authors: Henning O. Sorensen & Erik Knudsen
 
  8           Center for Fundamental Research: Metal Structures in Four Dimensions
 
  9           Risoe National Laboratory
 
 10           Frederiksborgvej 399
 
 11           DK-4000 Roskilde
 
 12           email:erik.knudsen@risoe.dk
 
 13  
 
 14          + Jon Wright, ESRF
 
 15  
 
 16          The header information has been taken from the script read_GEaSi_data.py
 
 17          by
 
 18          Antonino Miceli
 
 19          Thu Jan  4 13:46:31 CST 2007
 
 20  
 
 21  """ 
 22  
 
 23  import numpy 
 24  from fabioimage import fabioimage 
 25  
 

         26 -class GEimage(fabioimage): 

         27  
 
 28  
 

         29 -    def _readheader(self, infile): 

         30  
 
 31          infile.seek(0) 
 32  
 
 33          # ADEPT
 
 34          self.ImageFormat = infile.read(10) 
 35  
 
 36          # USHORT --> "=H"
 
 37          # ULONG  --> "=L"
 
 38          #   = means byte order is native
 
 39  
 
 40          self.header['HeaderVersion'] = numpy.fromstring(infile.read(2), numpy.uint16)[0] 
 41          self.header['HeaderSizeInBytes'] = int(numpy.fromstring(infile.read(4), numpy.uint32)[0]) 
 42          self.header['UserHeaderVersion'] = numpy.fromstring(infile.read(2), numpy.uint16)[0] 
 43          self.header['UserHeaderSizeInBytes'] = int(numpy.fromstring(infile.read(4), numpy.uint32)[0]) 
 44  
 
 45          self.header['NumberOfFrames'] = numpy.fromstring(infile.read(2), numpy.uint16)[0] 
 46          self.header['NumberOfRowsInFrame'] = numpy.fromstring(infile.read(2), numpy.uint16)[0] 
 47          self.header['NumberOfColsInFrame'] = numpy.fromstring(infile.read(2), numpy.uint16)[0] 
 48          self.header['BitsPerPixel'] = numpy.fromstring(infile.read(2), numpy.uint16)[0] 
 49  
 
 50          self.header['AcquisitionDate'] = infile.read(20) 
 51          self.header['AcquisitionTime'] = infile.read(20) 
 52  
 
 53          self.DUTID = infile.read(20) 
 54  
 
 55          self.header['Operator'] = infile.read(50) 
 56  
 
 57          self.header['DetectorSignature'] = infile.read(20) 
 58          self.header['TestSystemName'] = infile.read(20) 
 59          self.header['TestStationRevision'] = infile.read(20) 
 60          self.header['CoreBundleRevision'] = infile.read(20) 
 61          self.header['AcquisitionName'] = infile.read(40) 
 62          self.header['AcquisitionParameterRevision'] = infile.read(20) 

         63  
 
 64  #         self.OriginalNumberOfRows = infile.read(2)
 
 65  #         self.OriginalNumberOfRows = struct.unpack("=H",self.OriginalNumberOfRows)[0]
 
 66  
 
 67  #         self.OriginalNumberOfColumns = infile.read(2)
 
 68  #         self.OriginalNumberOfColumns = struct.unpack("=H",self.OriginalNumberOfColumns)[0]
 
 69  
 
 70  #         self.RowNumberUpperLeftPointArchiveROI = infile.read(2)
 
 71  #         self.RowNumberUpperLeftPointArchiveROI = struct.unpack("=H",self.RowNumberUpperLeftPointArchiveROI)[0]
 
 72  
 
 73  #         self.ColNumberUpperLeftPointArchiveROI = infile.read(2)
 
 74  #         self.ColNumberUpperLeftPointArchiveROI = struct.unpack("=H",self.ColNumberUpperLeftPointArchiveROI)[0]
 
 75  
 
 76  #         self.Swapped = infile.read(2) 
 
 77  #         self.Swapped = struct.unpack("=H",self.Swapped)[0]
 
 78  
 
 79  #         self.Reordered = infile.read(2) 
 
 80  #         self.Reordered = struct.unpack("=H",self.Reordered)[0]
 
 81  
 
 82  #         self.HorizontalFlipped = infile.read(2) 
 
 83  #         self.HorizontalFlipped = struct.unpack("=H",self.HorizontalFlipped)[0]
 
 84  
 
 85  #         self.VerticalFlipped = infile.read(2) 
 
 86  #         self.VerticalFlipped = struct.unpack("=H",self.VerticalFlipped)[0]
 
 87  
 
 88  #         self.WindowValueDesired = infile.read(2) 
 
 89  #         self.WindowValueDesired = struct.unpack("=H",self.WindowValueDesired)[0]
 
 90  
 
 91  #         self.LevelValueDesired = infile.read(2) 
 
 92  #         self.LevelValueDesired = struct.unpack("=H",self.LevelValueDesired)[0]
 
 93  
 
 94  #         self.AcquisitionMode = infile.read(2) 
 
 95  #         self.AcquisitionMode = struct.unpack("=H",self.AcquisitionMode)[0]
 
 96  
 
 97  #         self.AcquisitionType = infile.read(2) 
 
 98  #         self.AcquisitionType = struct.unpack("=H",self.AcquisitionType)[0]
 
 99  
 
100  #         self.UserAcquisitionCoffFileName1 = infile.read(100) 
 
101  #         self.UserAcquisitionCoffFileName2 = infile.read(100) 
 
102  
 
103  #         self.FramesBeforeExpose = infile.read(2) 
 
104  #         self.FramesBeforeExpose = struct.unpack("=H",self.FramesBeforeExpose)[0]
 
105  
 
106  #         self.FramesDuringExpose = infile.read(2)  
 
107  #         self.FramesDuringExpose = struct.unpack("=H",self.FramesDuringExpose)[0]
 
108  
 
109  #         self.FramesAfterExpose = infile.read(2) 
 
110  #         self.FramesAfterExpose = struct.unpack("=H",self.FramesAfterExpose)[0]
 
111  
 
112  #         self.IntervalBetweenFrames = infile.read(2) 
 
113  #         self.IntervalBetweenFrames = struct.unpack("=H",self.IntervalBetweenFrames)[0]
 
114  
 
115  #         self.ExposeTimeDelayInMicrosecs = infile.read(8) 
 
116  #         self.ExposeTimeDelayInMicrosecs = struct.unpack("=d",self.ExposeTimeDelayInMicrosecs)[0]
 
117  
 
118  #         self.TimeBetweenFramesInMicrosecs = infile.read(8) 
 
119  #         self.TimeBetweenFramesInMicrosecs = struct.unpack("=d",self.TimeBetweenFramesInMicrosecs)[0]
 
120  
 
121  #         self.FramesToSkipExpose = infile.read(2) 
 
122  #         self.FramesToSkipExpose = struct.unpack("=H",self.FramesToSkipExpose)[0]
 
123  
 
124  #         # Rad --> ExposureMode = 1
 
125  #         self.ExposureMode = infile.read(2) 
 
126  #         self.ExposureMode = struct.unpack("=H",self.ExposureMode)[0]
 
127  
 
128  #         self.PrepPresetTimeInMicrosecs = infile.read(8) 
 
129  #         self.PrepPresetTimeInMicrosecs = struct.unpack("=d",self.PrepPresetTimeInMicrosecs)[0]
 
130  
 
131  #         self.ExposePresetTimeInMicrosecs = infile.read(8) 
 
132  #         self.ExposePresetTimeInMicrosecs = struct.unpack("=d",self.ExposePresetTimeInMicrosecs)[0]
 
133  
 
134  #         self.AcquisitionFrameRateInFps = infile.read(4) 
 
135  #         self.AcquisitionFrameRateInFps = struct.unpack("=f",self.AcquisitionFrameRateInFps)[0]
 
136  
 
137  #         self.FOVSelect = infile.read(2)
 
138  #         self.FOVSelect = struct.unpack("=H",self.FOVSelect)[0]
 
139  
 
140  #         self.ExpertMode = infile.read(2)
 
141  #         self.ExpertMode = struct.unpack("=H",self.ExpertMode)[0]
 
142  
 
143  #         self.SetVCommon1 = infile.read(8)
 
144  #         self.SetVCommon1 = struct.unpack("=d",self.SetVCommon1)[0]
 
145  
 
146  #         self.SetVCommon2 = infile.read(8)
 
147  #         self.SetVCommon2 = struct.unpack("=d",self.SetVCommon2)[0]
 
148  
 
149  #         self.SetAREF = infile.read(8)
 
150  #         self.SetAREF = struct.unpack("=d",self.SetAREF)[0]
 
151  
 
152  #         self.SetAREFTrim = infile.read(4)
 
153  #         self.SetAREFTrim = struct.unpack("=L",self.SetAREFTrim)[0]
 
154  
 
155  #         self.SetSpareVoltageSource = infile.read(8)
 
156  #         self.SetSpareVoltageSource = struct.unpack("=d",self.SetSpareVoltageSource)[0]
 
157  
 
158  #         self.SetCompensationVoltageSource = infile.read(8)
 
159  #         self.SetCompensationVoltageSource = struct.unpack("=d",self.SetCompensationVoltageSource)[0]
 
160  
 
161  #         self.SetRowOffVoltage = infile.read(8)
 
162  #         self.SetRowOffVoltage = struct.unpack("=d",self.SetRowOffVoltage)[0]
 
163  
 
164  #         self.SetRowOnVoltage = infile.read(8)
 
165  #         self.SetRowOnVoltage = struct.unpack("=d",self.SetRowOnVoltage)[0]
 
166  
 
167  #         self.StoreCompensationVoltage = infile.read(4)
 
168  #         self.StoreCompensationVoltage = struct.unpack("=L",self.StoreCompensationVoltage)[0]
 
169  
 
170  #         self.RampSelection = infile.read(2)
 
171  #         self.RampSelection = struct.unpack("=H",self.RampSelection)[0]
 
172  
 
173  #         self.TimingMode = infile.read(2)
 
174  #         self.TimingMode = struct.unpack("=H",self.TimingMode)[0]
 
175  
 
176  #         self.Bandwidth = infile.read(2)
 
177  #         self.Bandwidth = struct.unpack("=H",self.Bandwidth)[0]
 
178  
 
179  #         self.ARCIntegrator = infile.read(2)
 
180  #         self.ARCIntegrator = struct.unpack("=H",self.ARCIntegrator)[0]
 
181  
 
182  #         self.ARCPostIntegrator = infile.read(2)
 
183  #         self.ARCPostIntegrator = struct.unpack("=H",self.ARCPostIntegrator)[0]
 
184  
 
185  #         self.NumberOfRows = infile.read(4)
 
186  #         self.NumberOfRows = struct.unpack("=L",self.NumberOfRows)[0]
 
187  
 
188  #         self.RowEnable = infile.read(2)
 
189  #         self.RowEnable = struct.unpack("=H",self.RowEnable)[0]
 
190  
 
191  #         self.EnableStretch = infile.read(2)
 
192  #         self.EnableStretch = struct.unpack("=H",self.EnableStretch)[0]
 
193  
 
194  #         self.CompEnable = infile.read(2)
 
195  #         self.CompEnable = struct.unpack("=H",self.CompEnable)[0]
 
196  
 
197  #         self.CompStretch = infile.read(2)
 
198  #         self.CompStretch = struct.unpack("=H",self.CompStretch)[0]
 
199  
 
200  #         self.LeftEvenTristate = infile.read(2)
 
201  #         self.LeftEvenTristate = struct.unpack("=H",self.LeftEvenTristate)[0]
 
202  
 
203  #         self.RightOddTristate = infile.read(2)
 
204  #         self.RightOddTristate = struct.unpack("=H",self.RightOddTristate)[0]
 
205  
 
206  #         self.TestModeSelect = infile.read(4)
 
207  #         self.TestModeSelect = struct.unpack("=L",self.TestModeSelect)[0]
 
208  
 
209  #         self.AnalogTestSource = infile.read(4)
 
210  #         self.AnalogTestSource = struct.unpack("=L",self.AnalogTestSource)[0]
 
211  
 
212  #         self.VCommonSelect = infile.read(4)
 
213  #         self.VCommonSelect = struct.unpack("=L",self.VCommonSelect)[0]
 
214  
 
215  #         self.DRCColumnSum = infile.read(4)
 
216  #         self.DRCColumnSum = struct.unpack("=L",self.DRCColumnSum)[0]
 
217  
 
218  #         self.TestPatternFrameDelta = infile.read(4)
 
219  #         self.TestPatternFrameDelta = struct.unpack("=L",self.TestPatternFrameDelta)[0]
 
220  
 
221  #         self.TestPatternRowDelta = infile.read(4)
 
222  #         self.TestPatternRowDelta = struct.unpack("=L",self.TestPatternRowDelta)[0]
 
223  
 
224  #         self.TestPatternColumnDelta = infile.read(4)
 
225  #         self.TestPatternColumnDelta = struct.unpack("=L",self.TestPatternColumnDelta)[0]
 
226  
 
227  #         self.DetectorHorizontalFlip = infile.read(2)
 
228  #         self.DetectorHorizontalFlip = struct.unpack("=H",self.DetectorHorizontalFlip)[0]
 
229  
 
230  #         self.DetectorVerticalFlip = infile.read(2)
 
231  #         self.DetectorVerticalFlip = struct.unpack("=H",self.DetectorVerticalFlip)[0]
 
232  
 
233  #         self.DFNAutoScrubOnOff = infile.read(2)
 
234  #         self.DFNAutoScrubOnOff = struct.unpack("=H",self.DFNAutoScrubOnOff)[0]
 
235  
 
236  #         self.FiberChannelTimeOutInMicrosecs = infile.read(4)
 
237  #         self.FiberChannelTimeOutInMicrosecs = struct.unpack("=L",self.FiberChannelTimeOutInMicrosecs)[0]
 
238  
 
239  #         self.DFNAutoScrubDelayInMicrosecs = infile.read(4)
 
240  #         self.DFNAutoScrubDelayInMicrosecs = struct.unpack("=L",self.DFNAutoScrubDelayInMicrosecs)[0]
 
241  
 
242  #         self.StoreAECROI = infile.read(2)
 
243  #         self.StoreAECROI = struct.unpack("=H",self.StoreAECROI)[0]
 
244  
 
245  #         self.TestPatternSaturationValue = infile.read(2)
 
246  #         self.TestPatternSaturationValue = struct.unpack("=H",self.TestPatternSaturationValue)[0]
 
247  
 
248  #         self.TestPatternSeed = infile.read(4)
 
249  #         self.TestPatternSeed = struct.unpack("=L",self.TestPatternSeed)[0]
 
250  
 
251  #         self.ExposureTimeInMillisecs = infile.read(4) 
 
252  #         self.ExposureTimeInMillisecs = struct.unpack("=f",self.ExposureTimeInMillisecs)[0]
 
253  
 
254  #         self.FrameRateInFps = infile.read(4) 
 
255  #         self.FrameRateInFps = struct.unpack("=f",self.FrameRateInFps)[0]
 
256  
 
257  #         self.kVp = infile.read(4) 
 
258  #         self.kVp = struct.unpack("=f",self.kVp)[0]
 
259  
 
260  #         self.mA = infile.read(4) 
 
261  #         self.mA = struct.unpack("=f",self.mA)[0]
 
262  
 
263  #         self.mAs = infile.read(4) 
 
264  #         self.mAs = struct.unpack("=f",self.mAs)[0]
 
265  
 
266  #         self.FocalSpotInMM = infile.read(4) 
 
267  #         self.FocalSpotInMM = struct.unpack("=f",self.FocalSpotInMM)[0]
 
268  
 
269  #         self.GeneratorType = infile.read(20)
 
270  
 
271  #         self.StrobeIntensityInFtL = infile.read(4) 
 
272  #         self.StrobeIntensityInFtL = struct.unpack("=f",self.StrobeIntensityInFtL)[0]
 
273  
 
274  #         self.NDFilterSelection = infile.read(2) 
 
275  #         self.NDFilterSelection = struct.unpack("=H",self.NDFilterSelection)[0]
 
276  
 
277  #         self.RefRegTemp1 = infile.read(8) 
 
278  #         self.RefRegTemp1 = struct.unpack("=d",self.RefRegTemp1)[0]
 
279  
 
280  #         self.RefRegTemp2 = infile.read(8) 
 
281  #         self.RefRegTemp2 = struct.unpack("=d",self.RefRegTemp2)[0]
 
282  
 
283  #         self.RefRegTemp3 = infile.read(8) 
 
284  #         self.RefRegTemp3 = struct.unpack("=d",self.RefRegTemp3)[0]
 
285  
 
286  #         self.Humidity1 = infile.read(4) 
 
287  #         self.Humidity1 = struct.unpack("=f",self.Humidity1)[0]
 
288  
 
289  #         self.Humidity2 = infile.read(4) 
 
290  #         self.Humidity2 = struct.unpack("=f",self.Humidity2)[0]
 
291  
 
292  #         self.DetectorControlTemp = infile.read(8) 
 
293  #         self.DetectorControlTemp = struct.unpack("=d",self.DetectorControlTemp)[0]
 
294  
 
295  #         self.DoseValueInmR = infile.read(8) 
 
296  #         self.DoseValueInmR = struct.unpack("=d",self.DoseValueInmR)[0]
 
297  
 
298  #         self.TargetLevelROIRow0 = infile.read(2)
 
299  #         self.TargetLevelROIRow0 = struct.unpack("=H",self.TargetLevelROIRow0)[0]
 
300  
 
301  #         self.TargetLevelROICol0 = infile.read(2)
 
302  #         self.TargetLevelROICol0 = struct.unpack("=H",self.TargetLevelROICol0)[0]
 
303  
 
304  #         self.TargetLevelROIRow1 = infile.read(2)
 
305  #         self.TargetLevelROIRow1 = struct.unpack("=H",self.TargetLevelROIRow1)[0]
 
306  
 
307  #         self.TargetLevelROICol1 = infile.read(2)
 
308  #         self.TargetLevelROICol1 = struct.unpack("=H",self.TargetLevelROICol1)[0]
 
309  
 
310  #         self.FrameNumberForTargetLevelROI = infile.read(2)
 
311  #         self.FrameNumberForTargetLevelROI = struct.unpack("=H",self.FrameNumberForTargetLevelROI)[0]
 
312  
 
313  #         self.PercentRangeForTargetLevel = infile.read(2)
 
314  #         self.PercentRangeForTargetLevel = struct.unpack("=H",self.PercentRangeForTargetLevel)[0]
 
315  
 
316  #         self.TargetValue = infile.read(2)
 
317  #         self.TargetValue = struct.unpack("=H",self.TargetValue)[0]
 
318  
 
319  #         self.ComputedMedianValue = infile.read(2)
 
320  #         self.ComputedMedianValue = struct.unpack("=H",self.ComputedMedianValue)[0]
 
321  
 
322  #         self.LoadZero = infile.read(2)
 
323  #         self.LoadZero = struct.unpack("=H",self.LoadZero)[0]
 
324  
 
325  #         self.MaxLUTOut = infile.read(2)
 
326  #         self.MaxLUTOut = struct.unpack("=H",self.MaxLUTOut)[0]
 
327  
 
328  #         self.MinLUTOut = infile.read(2)
 
329  #         self.MinLUTOut = struct.unpack("=H",self.MinLUTOut)[0]
 
330  
 
331  #         self.MaxLinear = infile.read(2)
 
332  #         self.MaxLinear = struct.unpack("=H",self.MaxLinear)[0]
 
333  
 
334  #         self.Reserved = infile.read(2)
 
335  #         self.Reserved = struct.unpack("=H",self.Reserved)[0]
 
336  
 
337  #         self.ElectronsPerCount = infile.read(2)
 
338  #         self.ElectronsPerCount = struct.unpack("=H",self.ElectronsPerCount)[0]
 
339  
 
340  #         self.ModeGain = infile.read(2)
 
341  #         self.ModeGain = struct.unpack("=H",self.ModeGain)[0]
 
342  
 
343  #         self.TemperatureInDegC = infile.read(8)
 
344  #         self.TemperatureInDegC = struct.unpack("=d",self.TemperatureInDegC)[0]
 
345  
 
346  #         self.LineRepaired = infile.read(2)
 
347  #         self.LineRepaired = struct.unpack("=H",self.LineRepaired)[0]
 
348  
 
349  #         self.LineRepairFileName = infile.read(100)
 
350  
 
351  #         self.CurrentLongitudinalInMM = infile.read(4)
 
352  #         self.CurrentLongitudinalInMM = struct.unpack("=f",self.CurrentLongitudinalInMM)[0]
 
353  
 
354  #         self.CurrentTransverseInMM = infile.read(4)
 
355  #         self.CurrentTransverseInMM = struct.unpack("=f",self.CurrentTransverseInMM)[0]
 
356  
 
357  #         self.CurrentCircularInMM = infile.read(4)
 
358  #         self.CurrentCircularInMM = struct.unpack("=f",self.CurrentCircularInMM)[0]
 
359  
 
360  #         self.CurrentFilterSelection = infile.read(4)
 
361  #         self.CurrentFilterSelection = struct.unpack("=L",self.CurrentFilterSelection)[0]
 
362  
 
363  #         self.DisableScrubAck = infile.read(2)
 
364  #         self.DisableScrubAck = struct.unpack("=H",self.DisableScrubAck)[0]
 
365  
 
366  #         self.ScanModeSelect = infile.read(2)
 
367  #         self.ScanModeSelect = struct.unpack("=H",self.ScanModeSelect)[0]
 
368  
 
369  #         self.DetectorAppSwVersion = infile.read(20)   
 
370  
 
371  #         self.DetectorNIOSVersion = infile.read(20)    
 
372  
 
373  #         self.DetectorPeripheralSetVersion = infile.read(20)   
 
374  
 
375  #         self.DetectorPhysicalAddress   = infile.read(20)
 
376  
 
377  #         self.PowerDown = infile.read(2)
 
378  #         self.PowerDown = struct.unpack("=H",self.PowerDown)[0]
 
379  
 
380  #         self.InitialVoltageLevel_VCOMMON = infile.read(8)
 
381  #         self.InitialVoltageLevel_VCOMMON = struct.unpack("=d",self.InitialVoltageLevel_VCOMMON)[0]
 
382  
 
383  #         self.FinalVoltageLevel_VCOMMON = infile.read(8)
 
384  #         self.FinalVoltageLevel_VCOMMON = struct.unpack("=d",self.FinalVoltageLevel_VCOMMON)[0]
 
385  
 
386  #         self.DmrCollimatorSpotSize     = infile.read(10)
 
387  
 
388  #         self.DmrTrack  = infile.read(5)
 
389  
 
390  #         self.DmrFilter         = infile.read(5)
 
391  
 
392  #         self.FilterCarousel = infile.read(2)
 
393  #         self.FilterCarousel = struct.unpack("=H",self.FilterCarousel)[0]
 
394  
 
395  #         self.Phantom   = infile.read(20)
 
396  
 
397  #         self.SetEnableHighTime = infile.read(2)
 
398  #         self.SetEnableHighTime = struct.unpack("=H",self.SetEnableHighTime)[0]
 
399  
 
400  #         self.SetEnableLowTime = infile.read(2)
 
401  #         self.SetEnableLowTime = struct.unpack("=H",self.SetEnableLowTime)[0]
 
402  
 
403  #         self.SetCompHighTime = infile.read(2)
 
404  #         self.SetCompHighTime = struct.unpack("=H",self.SetCompHighTime)[0]
 
405  
 
406  #         self.SetCompLowTime = infile.read(2)
 
407  #         self.SetCompLowTime = struct.unpack("=H",self.SetCompLowTime)[0]
 
408  
 
409  #         self.SetSyncLowTime = infile.read(2)
 
410  #         self.SetSyncLowTime = struct.unpack("=H",self.SetSyncLowTime)[0]
 
411  
 
412  #         self.SetConvertLowTime = infile.read(2)
 
413  #         self.SetConvertLowTime = struct.unpack("=H",self.SetConvertLowTime)[0]
 
414  
 
415  #         self.SetSyncHighTime = infile.read(2)
 
416  #         self.SetSyncHighTime = struct.unpack("=H",self.SetSyncHighTime)[0]
 
417  
 
418  #         self.SetEOLTime = infile.read(2)
 
419  #         self.SetEOLTime = struct.unpack("=H",self.SetEOLTime)[0]
 
420  
 
421  #         self.SetRampOffsetTime = infile.read(2)
 
422  #         self.SetRampOffsetTime = struct.unpack("=H",self.SetRampOffsetTime)[0]
 
423  
 
424  #         self.FOVStartingValue = infile.read(2)
 
425  #         self.FOVStartingValue = struct.unpack("=H",self.FOVStartingValue)[0]
 
426  
 
427  #         self.ColumnBinning = infile.read(2)
 
428  #         self.ColumnBinning = struct.unpack("=H",self.ColumnBinning)[0]
 
429  
 
430  #         self.RowBinning = infile.read(2)
 
431  #         self.RowBinning = struct.unpack("=H",self.RowBinning)[0]
 
432  
 
433  #         self.BorderColumns64 = infile.read(2)
 
434  #         self.BorderColumns64 = struct.unpack("=H",self.BorderColumns64)[0]
 
435  
 
436  #         self.BorderRows64 = infile.read(2)
 
437  #         self.BorderRows64 = struct.unpack("=H",self.BorderRows64)[0]
 
438  
 
439  #         self.FETOffRows64 = infile.read(2)
 
440  #         self.FETOffRows64 = struct.unpack("=H",self.FETOffRows64)[0]
 
441  
 
442  #         self.FOVStartColumn128 = infile.read(2)
 
443  #         self.FOVStartColumn128 = struct.unpack("=H",self.FOVStartColumn128)[0]
 
444  
 
445  #         self.FOVStartRow128 = infile.read(2)
 
446  #         self.FOVStartRow128 = struct.unpack("=H",self.FOVStartRow128)[0]
 
447  
 
448  #         self.NumberOfColumns128 = infile.read(2)
 
449  #         self.NumberOfColumns128 = struct.unpack("=H",self.NumberOfColumns128)[0]
 
450  
 
451  #         self.NumberOfRows128 = infile.read(2)
 
452  #         self.NumberOfRows128 = struct.unpack("=H",self.NumberOfRows128)[0]
 
453  
 
454  #         self.VFPAquisition     = infile.read(2000)
 
455  
 
456  #         self.Comment   = infile.read(200)
 
457  
 
458  
 
459  
 

        460 -    def read(self, fname, frame=None): 

        461          """
 
462          Read in header into self.header and
 
463              the data   into self.data
 
464          """ 
465          self.header = {} 
466          self.resetvals() 
467          infile = self._open(fname, "rb") 
468          self._readheader(infile) 
469          # Compute image size
 
470          try: 
471              self.dim1 = int(self.header['NumberOfRowsInFrame']) 
472              self.dim2 = int(self.header['NumberOfColsInFrame']) 
473              self.bpp = int(self.header['BitsPerPixel']) 
474          except: 
475              raise Exception("GE  file", str(fname) + \
 
476                                  "is corrupt, cannot read it") 
477  
 
478          # More than one image can be saved in a GE file
 
479          # Will only load the first one
 
480  
 
481  
 
482          # Go to the beginning of the file
 
483          infile.seek(0) 
484          infile.seek(self.header['HeaderSizeInBytes'] + self.header['UserHeaderSizeInBytes']) 
485  
 
486          ReadBytes = self.dim1 * self.dim2 * (self.bpp / 8) 
487          block = infile.read(ReadBytes) 
488          block = numpy.fromstring(block, numpy.uint16) 
489  
 
490          infile.close() 
491  
 
492          try: 
493              self.data = numpy.reshape(block, [self.dim2, self.dim1]) 
494          except: 
495              print len(block), self.dim2, self.dim1 
496              raise IOError, \
 
497                'Size spec in GE-header does not match size of image data field' 
498  
 
499          self.bytecode = self.data.dtype.type 
500          self.pilimage = None 
501          return self 

        502

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        fabio-0.1.3/epydoc/toc-fabio.fabioutils-module.html0000644000175000017500000000707012126623347023030 0ustar jeromejerome00000000000000 fabioutils

        Module fabioutils

        Classes

        BZ2File
        File
        FilenameObject
        GzipFile
        StringIO
        UnknownCompressedFile

        Functions

        construct_filename
        deconstruct_filename
        deprecated
        extract_filenumber
        getnum
        isAscii
        jump_filename
        next_filename
        nice_int
        numstem
        previous_filename
        toAscii

        Variables

        COMPRESSORS
        FILETYPES
        __package__
        dictAscii
        i
        key
        lines
        logger
        [hide private] fabio-0.1.3/epydoc/fabio.brukerimage-module.html0000644000175000017500000001717012126623347022403 0ustar jeromejerome00000000000000 fabio.brukerimage
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        Package fabio :: Module brukerimage
        [hide private]
        [frames] | no frames]

        Module brukerimage

        source code

        

Authors: Henning O. Sorensen & Erik Knudsen
         Center for Fundamental Research: Metal Structures in Four Dimensions
         Risoe National Laboratory
         Frederiksborgvej 399
         DK-4000 Roskilde
         email:erik.knudsen@risoe.dk

Based on: openbruker,readbruker, readbrukerheader functions in the opendata
         module of ImageD11 written by Jon Wright, ESRF, Grenoble, France
        Classes [hide private]
          brukerimage
        Read and eventually write ID11 bruker (eg smart6500) images
        Functions [hide private]
         
        test()
        a testcase        		 source code
        Variables [hide private]
          logger = logging.getLogger("brukerimage")
          __package__ = 'fabio'
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        fabio-0.1.3/epydoc/fabio.xsdimage.xsdimage-class.html0000644000175000017500000004304712126623347023331 0ustar jeromejerome00000000000000 fabio.xsdimage.xsdimage
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        Package fabio :: Module xsdimage :: Class xsdimage
        [hide private]
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        Class xsdimage

        source code

                   object --+    
                    |    
fabioimage.fabioimage --+
                        |
                       xsdimage

        Read the XSDataImage XML File data format

        Instance Methods [hide private]
         
        __init__(self, data=None, header=None, fname=None)
        Constructor of the class XSDataImage.        		 source code
         
        _readheader(self, infile)
        Read all headers in a file and populate self.header data is not yet populated        		 source code
         
        read(self, fname, frame=None)
        To be overridden - fill in self.header and self.data        		 source code

        Inherited from fabioimage.fabioimage: add, convert, getclassname, getframe, getheader, getmax, getmean, getmin, getstddev, integrate_area, load, make_slice, next, previous, readROI, readheader, rebin, resetvals, save, toPIL16, update_header, write

        Inherited from fabioimage.fabioimage (private): _compressed_stream, _open

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Static Methods [hide private]

        Inherited from fabioimage.fabioimage: checkData, checkHeader

        Class Variables [hide private]

        Inherited from fabioimage.fabioimage (private): _need_a_real_file, _need_a_seek_to_read

        Properties [hide private]

        Inherited from fabioimage.fabioimage: classname

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, data=None, header=None, fname=None)
        (Constructor)

        		source code 

        Constructor of the class XSDataImage.

        Parameters:
        • _strFilename (string) - the name of the file to open
        Overrides: object.__init__

        _readheader(self, infile)

        		source code 

        Read all headers in a file and populate self.header data is not yet populated

        Parameters:
        • infile (file object open in read mode)
        Overrides: fabioimage.fabioimage._readheader

        read(self, fname, frame=None)

        		source code 

        To be overridden - fill in self.header and self.data

        Overrides: fabioimage.fabioimage.read

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        fabio-0.1.3/epydoc/fabio.fit2dmaskimage.fit2dmaskimage-class.html0000644000175000017500000004545112126623347025506 0ustar jeromejerome00000000000000 fabio.fit2dmaskimage.fit2dmaskimage
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        Package fabio :: Module fit2dmaskimage :: Class fit2dmaskimage
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        Class fit2dmaskimage

        source code

                   object --+    
                    |    
fabioimage.fabioimage --+
                        |
                       fit2dmaskimage

        Read and try to write Andy Hammersley's mask format

        Instance Methods [hide private]
         
        _readheader(self, infile)
        Read in a header from an already open file        		 source code
         
        read(self, fname, frame=None)
        Read in header into self.header and...        		 source code
         
        write(self, fname)
        Try to write a file check we can write zipped also mimics that fabian was writing uint16 (we sometimes want floats)        		 source code

        Inherited from fabioimage.fabioimage: __init__, add, convert, getclassname, getframe, getheader, getmax, getmean, getmin, getstddev, integrate_area, load, make_slice, next, previous, readROI, readheader, rebin, resetvals, save, toPIL16, update_header

        Inherited from fabioimage.fabioimage (private): _compressed_stream, _open

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Static Methods [hide private]
         
        checkData(data=None)
        Empty for fabioimage but may be populated by others classes, especially for format accepting only integers        		 source code

        Inherited from fabioimage.fabioimage: checkHeader

        Class Variables [hide private]

        Inherited from fabioimage.fabioimage (private): _need_a_real_file, _need_a_seek_to_read

        Properties [hide private]

        Inherited from fabioimage.fabioimage: classname

        Inherited from object: __class__

        Method Details [hide private]

        _readheader(self, infile)

        		source code 

        Read in a header from an already open file

        Overrides: fabioimage.fabioimage._readheader

        read(self, fname, frame=None)

        		source code  
        
Read in header into self.header and
    the data   into self.data
        Overrides: fabioimage.fabioimage.read

        write(self, fname)

        		source code 

        Try to write a file check we can write zipped also mimics that fabian was writing uint16 (we sometimes want floats)

        Overrides: fabioimage.fabioimage.write

        checkData(data=None)
        Static Method

        		source code 

        Empty for fabioimage but may be populated by others classes, especially for format accepting only integers

        Overrides: fabioimage.fabioimage.checkData
        (inherited documentation)

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        Package fabio :: Module file_series
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        Module file_series

        source code

        

Authors:
........

* Henning O. Sorensen & Erik Knudsen
  Center for Fundamental Research: Metal Structures in Four Dimensions
  Risoe National Laboratory
  Frederiksborgvej 399
  DK-4000 Roskilde
  email:erik.knudsen@risoe.dk
* Jon Wright, ESRF
        Classes [hide private]
          file_series
        Represents a series of files to iterate has an idea of a current position to do next and prev
          numbered_file_series
        mydata0001.edf = "mydata" + 0001 + ".edf" mydata0002.edf = "mydata" + 0002 + ".edf" mydata0003.edf = "mydata" + 0003 + ".edf"
          filename_series
        Much like the others, but created from a string filename
        Functions [hide private]
         
        new_file_series0(first_object, first=None, last=None, step=1)
        Created from a fabio image first and last are file numbers        		 source code
         
        new_file_series(first_object, nimages=0, step=1, traceback=False)
        A generator function that creates a file series starting from a a fabioimage.        		 source code
        Variables [hide private]
          logger = logging.getLogger("fileseries")
          __package__ = 'fabio'
        Function Details [hide private]

        new_file_series(first_object, nimages=0, step=1, traceback=False)

        		source code  
        
A generator function that creates a file series starting from a a fabioimage.
Iterates through all images in a file (if more than 1), then proceeds to
the next file as determined by fabio.next_filename.

@param first_object: the starting fabioimage, which will be the first one yielded
    in the sequence
@param nimages:  the maximum number of images to consider
    step: step size, will yield the first and every step'th image until nimages
    is reached.  (e.g. nimages = 5, step = 2 will yield 3 images (0, 2, 4)
@param traceback: if True causes it to print a traceback in the event of an
    exception (missing image, etc.).  Otherwise the calling routine can handle
    the exception as it chooses
@param yields: the next fabioimage in the series.
    In the event there is an exception, it yields the sys.exec_info for the
    exception instead.  sys.exec_info is a tuple:
    ( exceptionType, exceptionValue, exceptionTraceback )
    from which all the exception information can be obtained.

Suggested usage:

::

    for obj in new_file_series( ... ):
      if not isinstance(obj, fabio.fabioimage.fabioimage ):
        # deal with errors like missing images, non readable files, etc
        # e.g.
        traceback.print_exception(obj[0], obj[1], obj[2])

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        Package fabio :: Module bruker100image
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        Module bruker100image

        source code

        Classes [hide private]
          bruker100image
        Variables [hide private]
          logger = logging.getLogger("bruker100image")
          __package__ = 'fabio'
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        fabio-0.1.3/epydoc/fabio.pnmimage.pnmimage-class.html0000644000175000017500000006154712126623347023326 0ustar jeromejerome00000000000000 fabio.pnmimage.pnmimage
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        Package fabio :: Module pnmimage :: Class pnmimage
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        Class pnmimage

        source code

                   object --+    
                    |    
fabioimage.fabioimage --+
                        |
                       pnmimage
        Instance Methods [hide private]
         
        __init__(self, *arg, **kwargs)
        Set up initial values        		 source code
         
        _readheader(self, f)
        Must be overridden in classes        		 source code
         
        read(self, fname, frame=None)
        try to read PNM images        		 source code
         
        write(self, filename)
        To be overwritten - write the file        		 source code

        Inherited from fabioimage.fabioimage: add, convert, getclassname, getframe, getheader, getmax, getmean, getmin, getstddev, integrate_area, load, make_slice, next, previous, readROI, readheader, rebin, resetvals, save, toPIL16, update_header

        Inherited from fabioimage.fabioimage (private): _compressed_stream, _open

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Static Methods [hide private]
         
        P1dec(buf, bytecode) source code
         
        P4dec(buf, bytecode) source code
         
        P2dec(buf, bytecode) source code
         
        P5dec(buf, bytecode) source code
         
        P3dec(buf, bytecode) source code
         
        P6dec(buf, bytecode) source code
         
        P7dec(buf, bytecode) source code
         
        checkData(data=None)
        Empty for fabioimage but may be populated by others classes, especially for format accepting only integers        		 source code

        Inherited from fabioimage.fabioimage: checkHeader

        Class Variables [hide private]

        Inherited from fabioimage.fabioimage (private): _need_a_real_file, _need_a_seek_to_read

        Properties [hide private]

        Inherited from fabioimage.fabioimage: classname

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, *arg, **kwargs)
        (Constructor)

        		source code 

        Set up initial values

        Overrides: object.__init__
        (inherited documentation)

        _readheader(self, f)

        		source code 

        Must be overridden in classes

        Overrides: fabioimage.fabioimage._readheader
        (inherited documentation)

        read(self, fname, frame=None)

        		source code 

        try to read PNM images

        Parameters:
        • fname - name of the file
        • frame - not relevant here! PNM is always single framed
        Overrides: fabioimage.fabioimage.read

        write(self, filename)

        		source code 

        To be overwritten - write the file

        Overrides: fabioimage.fabioimage.write
        (inherited documentation)

        checkData(data=None)
        Static Method

        		source code 

        Empty for fabioimage but may be populated by others classes, especially for format accepting only integers

        Overrides: fabioimage.fabioimage.checkData
        (inherited documentation)

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        fabio-0.1.3/epydoc/toc-fabio.file_series-module.html0000644000175000017500000000343112120434325023143 0ustar jeromejerome00000000000000 file_series

        Module file_series

        Classes

        file_series
        filename_series
        numbered_file_series

        Functions

        new_file_series
        new_file_series0

        Variables

        __package__
        logger
        [hide private] fabio-0.1.3/epydoc/fabio.mytest-pysrc.html0000644000175000017500000001106312120434325021267 0ustar jeromejerome00000000000000 fabio.mytest
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        Package fabio :: Module mytest
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        Source Code for Module fabio.mytest

        1  import fabioutils 
2  fabioutils.deconstruct_filename("merged.azim") 
3

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        Package fabio :: Module fabioimage
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        Source Code for Module fabio.fabioimage

          1  #!/usr/bin/env python 
  2   
  3  """ 
  4   
  5  Authors: Henning O. Sorensen & Erik Knudsen 
  6           Center for Fundamental Research: Metal Structures in Four Dimensions 
  7           Risoe National Laboratory 
  8           Frederiksborgvej 399 
  9           DK-4000 Roskilde 
 10           email:erik.knudsen@risoe.dk 
 11   
 12           and Jon Wright, Jerome Kieffer: ESRF 
 13   
 14  """ 
 15  from __future__ import with_statement 
 16  import os, types, logging, sys, tempfile 
 17  logger = logging.getLogger("fabioimage") 
 18  import numpy 
 19  try: 
 20      import Image 
 21  except ImportError: 
 22      logger.warning("PIL is not installed ... trying to do without") 
 23      Image = None 
 24  import fabioutils, converters 

         25   
 26   
 27 -class fabioimage(object): 

         28      """ 
 29      A common object for images in fable 
 30      Contains a numpy array (.data) and dict of meta data (.header) 
 31      """ 
 32   
 33      _need_a_seek_to_read = False 
 34      _need_a_real_file = False 
 35   

         36 -    def __init__(self, data=None , header=None): 

         37          """ 
 38          Set up initial values 
 39          """ 
 40          self._classname = None 
 41          if type(data) in types.StringTypes: 
 42              raise Exception("fabioimage.__init__ bad argument - " + \ 
 43                              "data should be numpy array") 
 44          self.data = self.checkData(data) 
 45          self.pilimage = None 
 46          if header is None: 
 47              self.header = {} 
 48          else: 
 49              self.header = self.checkHeader(header) 
 50          self.header_keys = self.header.keys() # holds key ordering 
 51          if self.data is not None: 
 52              self.dim2, self.dim1 = self.data.shape 
 53          else: 
 54              self.dim1 = self.dim2 = 0 
 55          self.bytecode = None     # numpy typecode 
 56          self.bpp = 2             # bytes per pixel 
 57          # cache for image statistics 
 58          self.mean = self.maxval = self.stddev = self.minval = None 
 59          # Cache roi 
 60          self.roi = None 
 61          self.area_sum = None 
 62          self.slice = None 
 63          # New for multiframe files 
 64          self.nframes = 1 
 65          self.currentframe = 0 
 66          self.filename = None 
 67          self.filenumber = None 

         68   
 69      @staticmethod 

         70 -    def checkHeader(header=None): 

         71          """ 
 72          Empty for fabioimage but may be populated by others classes 
 73          """ 
 74          if header is None: 
 75              return {} 
 76          else: 
 77              return header 

         78   
 79      @staticmethod 

         80 -    def checkData(data=None): 

         81          """ 
 82          Empty for fabioimage but may be populated by others classes, especially for format accepting only integers 
 83          """ 
 84          return data 

         85   

         86 -    def getclassname(self): 

         87          """ 
 88          Retrieves the name of the class 
 89          @return: the name of the class 
 90          """ 
 91          if self._classname is None: 
 92              self._classname = str(self.__class__).replace("<class '", "").replace("'>", "").split(".")[-1] 
 93          return self._classname 

         94      classname = property(getclassname) 
 95   

         96 -    def getframe(self, num): 

         97          """ returns the file numbered 'num' in the series as a fabioimage """ 
 98          if self.nframes == 1: 
 99              # single image per file 
100              import openimage 
101              return openimage.openimage( 
102                  fabioutils.jump_filename(self.filename, num)) 
103          raise Exception("getframe out of range") 

        104   

        105 -    def previous(self): 

        106          """ returns the previous file in the series as a fabioimage """ 
107          import openimage 
108          return openimage.openimage( 
109              fabioutils.previous_filename(self.filename)) 

        110   

        111 -    def next(self): 

        112          """ returns the next file in the series as a fabioimage """ 
113          import openimage 
114          return openimage.openimage( 
115              fabioutils.next_filename(self.filename)) 

        116   

        117 -    def toPIL16(self, filename=None): 

        118          """ 
119          Convert to Python Imaging Library 16 bit greyscale image 
120   
121          FIXME - this should be handled by the libraries now 
122          """ 
123          if not Image: 
124              raise RuntimeError("PIL is not installed !!! ") 
125          if filename: 
126              self.read(filename) 
127          if self.pilimage is not None: 
128              return self.pilimage 
129          # mode map 
130          size = self.data.shape[:2][::-1] 
131          typmap = { 
132              'float32' : "F"     , 
133              'int32'   : "F;32S" , 
134              'uint32'  : "F;32"  , 
135              'int16'   : "F;16S" , 
136              'uint16'  : "F;16"  , 
137              'int8'    : "F;8S"  , 
138              'uint8'   : "F;8"  } 
139          if typmap.has_key(self.data.dtype.name): 
140              mode2 = typmap[ self.data.dtype.name ] 
141              mode1 = mode2[0] 
142          else: 
143              raise Exception("Unknown numpy type " + str(self.data.dtype.type)) 
144          # 
145          # hack for byteswapping for PIL in MacOS 
146          testval = numpy.array((1, 0), numpy.uint8).view(numpy.uint16)[0] 
147          if  testval == 1: 
148              dats = self.data.tostring() 
149          elif testval == 256: 
150              dats = self.data.byteswap().tostring() 
151          else: 
152              raise Exception("Endian unknown in fabioimage.toPIL16") 
153   
154          self.pilimage = Image.frombuffer(mode1, 
155                                           size, 
156                                           dats, 
157                                           "raw", 
158                                           mode2, 
159                                           0, 
160                                           1) 
161   
162          return self.pilimage 

        163   

        164 -    def getheader(self): 

        165          """ returns self.header """ 
166          return self.header 

        167   

        168 -    def getmax(self): 

        169          """ Find max value in self.data, caching for the future """ 
170          if self.maxval is None: 
171              self.maxval = self.data.max() 
172          return self.maxval 

        173   

        174 -    def getmin(self): 

        175          """ Find min value in self.data, caching for the future """ 
176          if self.minval is None: 
177              self.minval = self.data.min() 
178          return self.minval 

        179   

        180 -    def make_slice(self, coords): 

        181          """ 
182          Convert a len(4) set of coords into a len(2) 
183          tuple (pair) of slice objects 
184          the latter are immutable, meaning the roi can be cached 
185          """ 
186          assert len(coords) == 4 
187          if len(coords) == 4: 
188              # fabian edfimage preference 
189              if coords[0] > coords[2]: 
190                  coords[0:3:2] = [coords[2], coords[0]] 
191              if coords[1] > coords[3]: 
192                  coords[1:4:2] = [coords[3], coords[1]] 
193              #in fabian: normally coordinates are given as (x,y) whereas 
194              # a matrix is given as row,col 
195              # also the (for whichever reason) the image is flipped upside 
196              # down wrt to the matrix hence these tranformations 
197              fixme = (self.dim2 - coords[3] - 1, 
198                       coords[0] , 
199                       self.dim2 - coords[1] - 1, 
200                       coords[2]) 
201          return (slice(int(fixme[0]), int(fixme[2]) + 1) , 
202                   slice(int(fixme[1]), int(fixme[3]) + 1)) 

        203   
204   

        205 -    def integrate_area(self, coords): 

        206          """ 
207          Sums up a region of interest 
208          if len(coords) == 4 -> convert coords to slices 
209          if len(coords) == 2 -> use as slices 
210          floor -> ? removed as unused in the function. 
211          """ 
212          if self.data == None: 
213              # This should return NAN, not zero ? 
214              return 0 
215          if len(coords) == 4: 
216              sli = self.make_slice(coords) 
217          elif len(coords) == 2 and isinstance(coords[0], slice) and \ 
218                                    isinstance(coords[1], slice): 
219              sli = coords 
220   
221          if sli == self.slice and self.area_sum is not None: 
222              pass 
223          elif sli == self.slice and self.roi is not None: 
224              self.area_sum = self.roi.sum(dtype=numpy.float) 
225          else: 
226              self.slice = sli 
227              self.roi = self.data[ self.slice ] 
228              self.area_sum = self.roi.sum(dtype=numpy.float) 
229          return self.area_sum 

        230   

        231 -    def getmean(self): 

        232          """ return the mean """ 
233          if self.mean is None: 
234              self.mean = self.data.mean(dtype=numpy.double) 
235          return self.mean 

        236   

        237 -    def getstddev(self): 

        238          """ return the standard deviation """ 
239          if self.stddev == None: 
240              self.stddev = self.data.std(dtype=numpy.double) 
241          return self.stddev 

        242   

        243 -    def add(self, other): 

        244          """ 
245          Add another Image - warning, does not clip to 16 bit images by default 
246          """ 
247          if not hasattr(other, 'data'): 
248              logger.warning('edfimage.add() called with something that ' + \ 
249                  'does not have a data field') 
250          assert self.data.shape == other.data.shape , \ 
251                    'incompatible images - Do they have the same size?' 
252          self.data = self.data + other.data 
253          self.resetvals() 

        254   
255   

        256 -    def resetvals(self): 

        257          """ Reset cache - call on changing data """ 
258          self.mean = self.stddev = self.maxval = self.minval = None 
259          self.roi = self.slice = self.area_sum = None 

        260   

        261 -    def rebin(self, x_rebin_fact, y_rebin_fact, keep_I=True): 

        262          """ 
263          Rebin the data and adjust dims 
264          @param x_rebin_fact: x binning factor 
265          @param y_rebin_fact: y binning factor 
266          @param keep_I: shall the signal increase ? 
267          @type x_rebin_fact: int 
268          @type y_rebin_fact: int 
269          @type keep_I: boolean 
270   
271   
272          """ 
273          if self.data == None: 
274              raise Exception('Please read in the file you wish to rebin first') 
275   
276          if (self.dim1 % x_rebin_fact != 0) or (self.dim2 % y_rebin_fact != 0): 
277              raise RuntimeError('image size is not divisible by rebin factor - ' + \ 
278                    'skipping rebin') 
279          else: 
280              dataIn = self.data.astype("float64") 
281              shapeIn = self.data.shape 
282              shapeOut = (shapeIn[0] / y_rebin_fact, shapeIn[1] / x_rebin_fact) 
283              binsize = y_rebin_fact * x_rebin_fact 
284              if binsize < 50: #method faster for small binning (4x4) 
285                  out = numpy.zeros(shapeOut, dtype="float64") 
286                  for j in range(x_rebin_fact): 
287                      for i in range(y_rebin_fact): 
288                          out += dataIn[i::y_rebin_fact, j::x_rebin_fact] 
289              else: #method faster for large binning (8x8) 
290                  temp = self.data.astype("float64") 
291                  temp.shape = (shapeOut[0], y_rebin_fact, shapeOut[1], x_rebin_fact) 
292                  out = temp.sum(axis=3).sum(axis=1) 
293          self.resetvals() 
294          if keep_I: 
295              self.data = (out / (y_rebin_fact * x_rebin_fact)).astype(self.data.dtype) 
296          else: 
297              self.data = out.astype(self.data.dtype) 
298   
299          self.dim1 = self.dim1 / x_rebin_fact 
300          self.dim2 = self.dim2 / y_rebin_fact 
301   
302          #update header 
303          self.update_header() 

        304   

        305 -    def write(self, fname): 

        306          """ 
307          To be overwritten - write the file 
308          """ 
309          raise Exception("Class has not implemented readheader method yet") 

        310   

        311 -    def save(self, fname): 

        312          'wrapper for write' 
313          self.write(fname) 

        314   

        315 -    def readheader(self, filename): 

        316          """ 
317          Call the _readheader function... 
318          """ 
319          # Override the needs asserting that all headers can be read via python modules 
320          save_state = self._need_a_real_file , self._need_a_seek_to_read 
321          self._need_a_real_file , self._need_a_seek_to_read = False, False 
322          fin = self._open(filename) 
323          self._readheader(fin) 
324          fin.close() 
325          self._need_a_real_file , self._need_a_seek_to_read = save_state 

        326   

        327 -    def _readheader(self, fik_obj): 

        328          """ 
329          Must be overridden in classes 
330          """ 
331          raise Exception("Class has not implemented _readheader method yet") 

        332   

        333 -    def update_header(self , **kwds): 

        334          """ 
335          update the header entries 
336          by default pass in a dict of key, values. 
337          """ 
338          self.header.update(kwds) 

        339   

        340 -    def read(self, filename, frame=None): 

        341          """ 
342          To be overridden - fill in self.header and self.data 
343          """ 
344          raise Exception("Class has not implemented read method yet") 

        345  #        return self 
346   

        347 -    def load(self, *arg, **kwarg): 

        348          "Wrapper for read" 
349          return self.read(*arg, **kwarg) 

        350   

        351 -    def readROI(self, filename, frame=None, coords=None): 

        352          """ 
353          Method reading Region of Interest. 
354          This implementation is the trivial one, just doing read and crop 
355          """ 
356          self.read(filename, frame) 
357          if len(coords) == 4: 
358              self.slice = self.make_slice(coords) 
359          elif len(coords) == 2 and isinstance(coords[0], slice) and \ 
360                                    isinstance(coords[1], slice): 
361              self.slice = coords 
362          else: 
363              logger.warning('readROI: Unable to understand Region Of Interest: got %s', coords) 
364          self.roi = self.data[ self.slice ] 
365          return self.roi 

        366   
367   

        368 -    def _open(self, fname, mode="rb"): 

        369          """ 
370          Try to handle compressed files, streams, shared memory etc 
371          Return an object which can be used for "read" and "write" 
372          ... FIXME - what about seek ? 
373          """ 
374          fileObject = None 
375          self.filename = fname 
376          self.filenumber = fabioutils.extract_filenumber(fname) 
377   
378          if hasattr(fname, "read") and hasattr(fname, "write"): 
379              # It is already something we can use 
380              return fname 
381          if isinstance(fname, (str, unicode)): 
382              self.header["filename"] = fname 
383              if os.path.splitext(fname)[1] == ".gz": 
384                  fileObject = self._compressed_stream(fname, 
385                                         fabioutils.COMPRESSORS['.gz'], 
386                                         fabioutils.GzipFile, 
387                                         mode) 
388              elif os.path.splitext(fname)[1] == '.bz2': 
389                  fileObject = self._compressed_stream(fname, 
390                                         fabioutils.COMPRESSORS['.bz2'], 
391                                         fabioutils.BZ2File, 
392                                         mode) 
393              # 
394              # Here we return the file even though it may be bzipped or gzipped 
395              # but named incorrectly... 
396              # 
397              # FIXME - should we fix that or complain about the daft naming? 
398              else: 
399                  fileObject = fabioutils.File(fname, mode) 
400              if "name" not in dir(fileObject): 
401                  fileObject.name = fname 
402   
403          return fileObject 

        404   

        405 -    def _compressed_stream(self, 
406                             fname, 
407                             system_uncompress, 
408                             python_uncompress, 
409                             mode='rb'): 

        410          """ 
411          Try to transparently handle gzip / bzip without always getting python 
412          performance 
413          """ 
414          # assert that python modules are always OK based on performance benchmark 
415          # Try to fix the way we are using them? 
416          fobj = None 
417          if self._need_a_real_file and mode[0] == "r": 
418              fo = python_uncompress(fname, mode) 
419  #            fobj = os.tmpfile() 
420              #problem when not administrator under certain flavors of windows 
421              tmpfd, tmpfn = tempfile.mkstemp() 
422              os.close(tmpfd) 
423              fobj = fabioutils.File(tmpfn, "w+b") 
424              fobj.write(fo.read()) 
425              fo.close() 
426              fobj.seek(0) 
427          elif self._need_a_seek_to_read and mode[0] == "r": 
428              fo = python_uncompress(fname, mode) 
429              fobj = fabioutils.StringIO(fo.read(), fname, mode) 
430          else: 
431              fobj = python_uncompress(fname, mode) 
432          return fobj 

        433   

        434 -    def convert(self, dest): 

        435          """ 
436          Convert a fabioimage object into another fabioimage object (with possible conversions) 
437          @param dest: destination type "EDF", "edfimage" or the class itself 
438          """ 
439          if type(dest) in types.StringTypes: 
440              dest = dest.lower() 
441              modules = [] 
442              for val  in fabioutils.FILETYPES.values(): 
443                  modules += [i + "image" for i in val if i not in modules] 
444              klass = None 
445              module = None 
446              klass_name = None 
447              for klass_name in modules: 
448                  if  klass_name.startswith(dest): 
449                      try: 
450                          module = sys.modules["fabio." + klass_name] 
451                      except KeyError: 
452                          try: 
453                              module = __import__(klass_name) 
454                          except: 
455                              logger.error("Failed to import %s", klass_name) 
456                          else: 
457                              logger.debug("imported %simage", klass_name) 
458                      if module is not None: 
459                          break 
460              if module is not None: 
461                  if hasattr(module, klass_name): 
462                      klass = getattr(module, klass_name) 
463                  else: 
464                      logger.error("Module %s has no image class" % module) 
465          elif isinstance(dest, self.__class__): 
466              klass = dest.__class__ 
467          elif ("__new__" in dir(dest)) and isinstance(dest(), fabioimage): 
468              klass = dest 
469          else: 
470              logger.warning("Unrecognized destination format: %s " % dest) 
471              return self 
472          if klass is None: 
473              logger.warning("Unrecognized destination format: %s " % dest) 
474              return self 
475          other = klass() #temporary instance (to be overwritten) 
476          other = klass(data=converters.convert_data(self.classname, other.classname, self.data), 
477                      header=converters.convert_header(self.classname, other.classname, self.header)) 
478          return other 

        479   

        480 -def test(): 

        481      """ 
482      check some basic fabioimage functionality 
483      """ 
484      import time 
485      start = time.time() 
486   
487      dat = numpy.ones((1024, 1024), numpy.uint16) 
488      dat = (dat * 50000).astype(numpy.uint16) 
489      assert dat.dtype.char == numpy.ones((1), numpy.uint16).dtype.char 
490      hed = {"Title":"50000 everywhere"} 
491      obj = fabioimage(dat, hed) 
492   
493      assert obj.getmax() == 50000 
494      assert obj.getmin() == 50000 
495      assert obj.getmean() == 50000 , obj.getmean() 
496      assert obj.getstddev() == 0. 
497   
498      dat2 = numpy.zeros((1024, 1024), numpy.uint16, savespace=1) 
499      cord = [ 256, 256, 790, 768 ] 
500      slic = obj.make_slice(cord) 
501      dat2[slic] = dat2[slic] + 100 
502   
503      obj = fabioimage(dat2, hed) 
504   
505      # New object, so... 
506      assert obj.maxval is None 
507      assert obj.minval is None 
508   
509      assert obj.getmax() == 100, obj.getmax() 
510      assert obj.getmin() == 0 , obj.getmin() 
511      npix = (slic[0].stop - slic[0].start) * (slic[1].stop - slic[1].start) 
512      obj.resetvals() 
513      area1 = obj.integrate_area(cord) 
514      obj.resetvals() 
515      area2 = obj.integrate_area(slic) 
516      assert area1 == area2 
517      assert obj.integrate_area(cord) == obj.integrate_area(slic) 
518      assert obj.integrate_area(cord) == npix * 100, obj.integrate_area(cord) 
519   
520   
521      def clean(): 
522          """ clean up the created testfiles""" 
523          for name in ["testfile", "testfile.gz", "testfile.bz2"]: 
524              try: 
525                  os.remove(name) 
526              except: 
527                  continue 

        528   
529   
530      clean() 
531      import gzip, bz2 
532      gzip.open("testfile.gz", "wb").write("{ hello }") 
533      fout = obj._open("testfile.gz") 
534      readin = fout.read() 
535      assert readin == "{ hello }", readin + " gzipped file" 
536   
537   
538      bz2.BZ2File("testfilebz", "wb").write("{ hello }") 
539      fout = obj._open("testfile.bz2") 
540      readin = fout.read() 
541      assert readin == "{ hello }", readin + " bzipped file" 
542   
543      ftest = open("testfile", "wb") 
544      ftest.write("{ hello }") 
545      assert ftest == obj._open(ftest) 
546      ftest.close() 
547      fout = obj._open("testfile") 
548      readin = fout.read() 
549      assert readin == "{ hello }", readin + "plain file" 
550      fout.close() 
551      ftest.close() 
552      clean() 
553   
554      print "Passed in", time.time() - start, "s" 
555   
556  if __name__ == '__main__': 
557      test() 
558

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        fabio-0.1.3/epydoc/fabio.HiPiCimage.HiPiCimage-class.html0000644000175000017500000003653312126623347023627 0ustar jeromejerome00000000000000 fabio.HiPiCimage.HiPiCimage
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        Package fabio :: Module HiPiCimage :: Class HiPiCimage
        [hide private]
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        Class HiPiCimage

        source code

                   object --+    
                    |    
fabioimage.fabioimage --+
                        |
                       HiPiCimage

        Read HiPic images e.g. collected with a Hamamatsu CCD camera

        Instance Methods [hide private]
         
        _readheader(self, infile)
        Read in a header from an already open file        		 source code
         
        read(self, fname, frame=None)
        Read in header into self.header and...        		 source code

        Inherited from fabioimage.fabioimage: __init__, add, convert, getclassname, getframe, getheader, getmax, getmean, getmin, getstddev, integrate_area, load, make_slice, next, previous, readROI, readheader, rebin, resetvals, save, toPIL16, update_header, write

        Inherited from fabioimage.fabioimage (private): _compressed_stream, _open

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Static Methods [hide private]

        Inherited from fabioimage.fabioimage: checkData, checkHeader

        Class Variables [hide private]

        Inherited from fabioimage.fabioimage (private): _need_a_real_file, _need_a_seek_to_read

        Properties [hide private]

        Inherited from fabioimage.fabioimage: classname

        Inherited from object: __class__

        Method Details [hide private]

        _readheader(self, infile)

        		source code 

        Read in a header from an already open file

        Overrides: fabioimage.fabioimage._readheader

        read(self, fname, frame=None)

        		source code  
        
Read in header into self.header and
    the data   into self.data
        Overrides: fabioimage.fabioimage.read

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        fabio-0.1.3/epydoc/toc-fabio.fit2dspreadsheetimage-module.html0000644000175000017500000000242612120434325025120 0ustar jeromejerome00000000000000 fit2dspreadsheetimage

        Module fit2dspreadsheetimage

        Classes

        fit2dspreadsheetimage

        Variables

        __package__
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        Package fabio :: Module bruker100image :: Class bruker100image
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        Class bruker100image

        source code

                   object --+        
                    |        
fabioimage.fabioimage --+    
                        |    
  brukerimage.brukerimage --+
                            |
                           bruker100image
        Instance Methods [hide private]
         
        toPIL16(self, filename=None)
        Convert to Python Imaging Library 16 bit greyscale image        		 source code
         
        read(self, fname, frame=None)
        Read in and unpack the pixels (including overflow table        		 source code

        Inherited from brukerimage.brukerimage: write, write2

        Inherited from brukerimage.brukerimage (private): _readheader

        Inherited from fabioimage.fabioimage: __init__, add, convert, getclassname, getframe, getheader, getmax, getmean, getmin, getstddev, integrate_area, load, make_slice, next, previous, readROI, readheader, rebin, resetvals, save, update_header

        Inherited from fabioimage.fabioimage (private): _compressed_stream, _open

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Static Methods [hide private]

        Inherited from fabioimage.fabioimage: checkData, checkHeader

        Class Variables [hide private]

        Inherited from brukerimage.brukerimage: __headerstring__

        Inherited from fabioimage.fabioimage (private): _need_a_real_file, _need_a_seek_to_read

        Properties [hide private]

        Inherited from fabioimage.fabioimage: classname

        Inherited from object: __class__

        Method Details [hide private]

        toPIL16(self, filename=None)

        		source code 

        Convert to Python Imaging Library 16 bit greyscale image

        FIXME - this should be handled by the libraries now

        Overrides: fabioimage.fabioimage.toPIL16
        (inherited documentation)

        read(self, fname, frame=None)

        		source code 

        Read in and unpack the pixels (including overflow table

        Overrides: fabioimage.fabioimage.read
        (inherited documentation)

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        fabio-0.1.3/epydoc/toc-fabio.adscimage-module.html0000644000175000017500000000263712120434325022576 0ustar jeromejerome00000000000000 adscimage

        Module adscimage

        Classes

        adscimage

        Functions

        test

        Variables

        __package__
        logger
        [hide private] fabio-0.1.3/epydoc/fabio.fit2dspreadsheetimage-pysrc.html0000644000175000017500000010226212126623347024221 0ustar jeromejerome00000000000000 fabio.fit2dspreadsheetimage
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        Package fabio :: Module fit2dspreadsheetimage
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        Source Code for Module fabio.fit2dspreadsheetimage

         1   
 2   
 3  """ 
 4  Read the fit2d ascii image output 
 5          + Jon Wright, ESRF 
 6  """ 
 7   
 8  import numpy 
 9   
10  from fabioimage import fabioimage 
11   
12   
13   
14   

        15 -class fit2dspreadsheetimage(fabioimage): 

        16      """ 
17      Read a fit2d ascii format 
18      """ 
19   

        20 -    def _readheader(self, infile): 

        21          """ 
22   
23          TODO : test for minimal attributes? 
24          """ 
25          line = infile.readline() 
26          try: 
27              items = line.split() 
28              xdim = int(items[0]) 
29              ydim = int(items[1]) 
30          except: 
31              raise 
32          self.header['title'] = line 
33          self.header['Dim_1'] = xdim 
34          self.header['Dim_2'] = ydim 

        35   

        36 -    def read(self, fname, frame=None): 

        37          """ 
38          Read in header into self.header and 
39              the data   into self.data 
40          """ 
41          self.header = {} 
42          self.resetvals() 
43          infile = self._open(fname) 
44          self._readheader(infile) 
45          # Compute image size 
46          try: 
47              self.dim1 = int(self.header['Dim_1']) 
48              self.dim2 = int(self.header['Dim_2']) 
49          except: 
50              raise Exception("file", str(fname) + \ 
51                                  "is corrupt, cannot read it") 
52          bytecode = numpy.float32 
53   
54          self.bpp = len(numpy.array(0, bytecode).tostring()) 
55   
56          #now read the data into the array 
57          try: 
58              vals = [] 
59              for line in infile.readlines(): 
60                  try: 
61                      vals.append([float(x) for x in line.split()]) 
62                  except: 
63                      pass 
64              self.data = numpy.array(vals).astype(bytecode) 
65              assert self.data.shape == (self.dim2, self.dim1) 
66   
67          except: 
68              raise IOError, "Error reading ascii" 
69   
70          self.resetvals() 
71          # ensure the PIL image is reset 
72          self.pilimage = None 
73          return self 

        74   
75   
76  if __name__ == "__main__": 
77      import sys, time 
78      start = time.time() 
79      img = fit2dspreadsheetimage() 
80      img.read(sys.argv[1]) 
81      print time.time() - start 
82      print img.dim1, img.dim2, img.data.shape 
83      from matplotlib.pylab import imshow, show 
84      imshow(img.data.T) 
85      show() 
86

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        fabio-0.1.3/epydoc/fabio.TiffIO-pysrc.html0000644000175000017500000135132112126623347021101 0ustar jeromejerome00000000000000 fabio.TiffIO
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        Package fabio :: Module TiffIO
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        Source Code for Module fabio.TiffIO

           1  #/*########################################################################## 
   2  # Copyright (C) 2012 European Synchrotron Radiation Facility 
   3  # 
   4  # This file is part of the PyMca X-ray Fluorescence Toolkit developed at 
   5  # the ESRF by the Software group. 
   6  # 
   7  # This file is free software; you can redistribute it and/or modify it  
   8  # under the terms of the GNU Lesser General Public License as published by the Free 
   9  # Software Foundation; either version 2 of the License, or (at your option)  
  10  # any later version. 
  11  # 
  12  # PyMca is distributed in the hope that it will be useful, but WITHOUT ANY 
  13  # WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS 
  14  # FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more 
  15  # details. 
  16  # 
  17  #############################################################################*/ 
  18  __author__ = "V.A. Sole - ESRF Data Analysis" 
  19  __revision__ = 1501 
  20   
  21  import sys 
  22  import os 
  23  import struct 
  24  import numpy 
  25   
  26  DEBUG = 0 
  27  ALLOW_MULTIPLE_STRIPS = False 
  28   
  29  TAG_ID = { 256:"NumberOfColumns", # S or L ImageWidth 
  30              257:"NumberOfRows", # S or L ImageHeight 
  31              258:"BitsPerSample", # S Number of bits per component 
  32              259:"Compression", # SHORT (1 - NoCompression, ...  
  33              262:"PhotometricInterpretation", # SHORT (0 - WhiteIsZero, 1 -BlackIsZero, 2 - RGB, 3 - Palette color 
  34              270:"ImageDescription", # ASCII 
  35              273:"StripOffsets", # S or L, for each strip, the byte offset of the strip 
  36              278:"RowsPerStrip", # S or L, number of rows in each back may be not for the last 
  37              279:"StripByteCounts", # S or L, The number of bytes in the strip AFTER any compression 
  38              305:"Software", # ASCII 
  39              306:"Date", # ASCII 
  40              320:"Colormap", # Colormap of Palette-color Images  
  41              339:"SampleFormat", # SHORT Interpretation of data in each pixel 
  42              } 
  43   
  44  #TILES ARE TO BE SUPPORTED TOO ... 
  45  TAG_NUMBER_OF_COLUMNS = 256 
  46  TAG_NUMBER_OF_ROWS = 257 
  47  TAG_BITS_PER_SAMPLE = 258 
  48  TAG_PHOTOMETRIC_INTERPRETATION = 262 
  49  TAG_COMPRESSION = 259 
  50  TAG_IMAGE_DESCRIPTION = 270 
  51  TAG_STRIP_OFFSETS = 273 
  52  TAG_ROWS_PER_STRIP = 278 
  53  TAG_STRIP_BYTE_COUNTS = 279 
  54  TAG_SOFTWARE = 305 
  55  TAG_DATE = 306 
  56  TAG_COLORMAP = 320 
  57  TAG_SAMPLE_FORMAT = 339 
  58   
  59  FIELD_TYPE = {1:('BYTE', "B"), 
  60                 2:('ASCII', "s"), #string ending with binary zero 
  61                 3:('SHORT', "H"), 
  62                 4:('LONG', "I"), 
  63                 5:('RATIONAL', "II"), 
  64                 6:('SBYTE', "b"), 
  65                 7:('UNDEFINED', "B"), 
  66                 8:('SSHORT', "h"), 
  67                 9:('SLONG', "i"), 
  68                 10:('SRATIONAL', "ii"), 
  69                 11:('FLOAT', "f"), 
  70                 12:('DOUBLE', "d")} 
  71   
  72  FIELD_TYPE_OUT = { 'B':   1, 
  73                     's':   2, 
  74                     'H':   3, 
  75                     'I':   4, 
  76                     'II':  5, 
  77                     'b':   6, 
  78                     'h':   8, 
  79                     'i':   9, 
  80                     'ii': 10, 
  81                     'f':  11, 
  82                     'd':  12} 
  83   
  84  #sample formats (http://www.awaresystems.be/imaging/tiff/tiffflags/sampleformat.html) 
  85  SAMPLE_FORMAT_UINT = 1 
  86  SAMPLE_FORMAT_INT = 2 
  87  SAMPLE_FORMAT_FLOAT = 3   #floating point 
  88  SAMPLE_FORMAT_VOID = 4   #undefined data, usually assumed UINT 
  89  SAMPLE_FORMAT_COMPLEXINT = 5 
  90  SAMPLE_FORMAT_COMPLEXIEEEFP = 6 
  91   
  92   
  93   

          94 -class TiffIO(object): 

          95 -    def __init__(self, filename, mode=None, cache_length=20, mono_output=False): 

          96          if mode is None: 
  97              mode = 'rb' 
  98          if 'b' not in mode: 
  99              mode = mode + 'b' 
 100          if 'a' in mode.lower(): 
 101              raise IOError("Mode %s makes no sense on TIFF files. Consider 'rb+'" % mode) 
 102          if ('w' in mode): 
 103              if '+' not in mode: 
 104                  mode += '+' 
 105          #if isinstance(filename, file): #does not work in python 3 
 106          if hasattr(filename, "seek"): 
 107              fd = filename 
 108              self._access = None 
 109          else: 
 110              #the b is needed for windows and python 3 
 111              fd = open(filename, mode) 
 112              self._access = mode 
 113   
 114          self._initInternalVariables(fd) 
 115          self._maxImageCacheLength = cache_length 
 116          self._forceMonoOutput = mono_output 

         117   

         118 -    def _initInternalVariables(self, fd=None): 

         119          if fd is None: 
 120              fd = self.fd 
 121          else: 
 122              self.fd = fd 
 123          # read the order 
 124          fd.seek(0) 
 125          order = fd.read(2).decode() 
 126          if len(order): 
 127              if order == "II": 
 128                  #intel, little endian 
 129                  fileOrder = "little" 
 130                  self._structChar = '<' 
 131              elif order == "MM": 
 132                  #motorola, high endian 
 133                  fileOrder = "big" 
 134                  self._structChar = '>' 
 135              else: 
 136                  raise IOError("File is not a Mar CCD file, nor a TIFF file") 
 137              a = fd.read(2) 
 138              fortyTwo = struct.unpack(self._structChar + "H", a)[0] 
 139              if fortyTwo != 42: 
 140                  raise IOError("Invalid TIFF version %d" % fortyTwo) 
 141              else: 
 142                  if DEBUG: 
 143                      print("VALID TIFF VERSION") 
 144              if sys.byteorder != fileOrder: 
 145                  swap = True 
 146              else: 
 147                  swap = False 
 148          else: 
 149              if sys.byteorder == "little": 
 150                  self._structChar = '<' 
 151              else: 
 152                  self._structChar = '>' 
 153              swap = False 
 154          self._swap = swap 
 155          self._IFD = [] 
 156          self._imageDataCacheIndex = [] 
 157          self._imageDataCache = [] 
 158          self._imageInfoCacheIndex = [] 
 159          self._imageInfoCache = [] 
 160          self.getImageFileDirectories(fd) 

         161   

         162 -    def __makeSureFileIsOpen(self): 

         163          if not self.fd.closed: 
 164              return 
 165          if DEBUG: 
 166              print("Reopening closed file") 
 167          fileName = self.fd.name 
 168          if self._access is None: 
 169              #we do not own the file 
 170              #open in read mode 
 171              newFile = open(fileName, 'rb') 
 172          else: 
 173              newFile = open(fileName, self._access) 
 174          self.fd = newFile 

         175   

         176 -    def __makeSureFileIsClosed(self): 

         177          if self._access is None: 
 178              #we do not own the file 
 179              if DEBUG: 
 180                  print("Not closing not owned file") 
 181              return 
 182   
 183          if not self.fd.closed: 
 184              self.fd.close() 

         185   

         186 -    def getNumberOfImages(self): 

         187          #update for the case someone has done anything? 
 188          self._updateIFD() 
 189          return len(self._IFD) 

         190   

         191 -    def _updateIFD(self): 

         195   

         196 -    def getImageFileDirectories(self, fd=None): 

         197          if fd is None: 
 198              fd = self.fd 
 199          else: 
 200              self.fd = fd 
 201          st = self._structChar 
 202          fd.seek(4) 
 203          self._IFD = [] 
 204          nImages = 0 
 205          fmt = st + 'I' 
 206          inStr = fd.read(struct.calcsize(fmt)) 
 207          if not len(inStr): 
 208              offsetToIFD = 0 
 209          else: 
 210              offsetToIFD = struct.unpack(fmt, inStr)[0] 
 211          if DEBUG: 
 212              print("Offset to first IFD = %d" % offsetToIFD) 
 213          while offsetToIFD != 0: 
 214              self._IFD.append(offsetToIFD) 
 215              nImages += 1 
 216              fd.seek(offsetToIFD) 
 217              fmt = st + 'H' 
 218              numberOfDirectoryEntries = struct.unpack(fmt, fd.read(struct.calcsize(fmt)))[0] 
 219              if DEBUG: 
 220                  print("Number of directory entries = %d" % numberOfDirectoryEntries) 
 221   
 222              fmt = st + 'I' 
 223              fd.seek(offsetToIFD + 2 + 12 * numberOfDirectoryEntries) 
 224              offsetToIFD = struct.unpack(fmt, fd.read(struct.calcsize(fmt)))[0] 
 225              if DEBUG: 
 226                  print("Next Offset to IFD = %d" % offsetToIFD) 
 227              #offsetToIFD = 0  
 228          if DEBUG: 
 229              print("Number of images found = %d" % nImages) 
 230          return nImages 

         231   

         232 -    def _parseImageFileDirectory(self, nImage): 

         233          offsetToIFD = self._IFD[nImage] 
 234          st = self._structChar 
 235          fd = self.fd 
 236          fd.seek(offsetToIFD) 
 237          fmt = st + 'H' 
 238          numberOfDirectoryEntries = struct.unpack(fmt, fd.read(struct.calcsize(fmt)))[0] 
 239          if DEBUG: 
 240              print("Number of directory entries = %d" % numberOfDirectoryEntries) 
 241   
 242          fmt = st + 'HHI4s' 
 243          tagIDList = [] 
 244          fieldTypeList = [] 
 245          nValuesList = [] 
 246          valueOffsetList = [] 
 247          for i in range(numberOfDirectoryEntries): 
 248              tagID, fieldType, nValues, valueOffset = struct.unpack(fmt, fd.read(12)) 
 249              tagIDList.append(tagID) 
 250              fieldTypeList.append(fieldType) 
 251              nValuesList.append(nValues) 
 252              if nValues == 1: 
 253                  ftype, vfmt = FIELD_TYPE[fieldType] 
 254                  if ftype not in ['ASCII', 'RATIONAL', 'SRATIONAL']: 
 255                      vfmt = st + vfmt 
 256                      actualValue = struct.unpack(vfmt, valueOffset[0: struct.calcsize(vfmt)])[0] 
 257                      valueOffsetList.append(actualValue) 
 258                  else: 
 259                      valueOffsetList.append(valueOffset) 
 260              elif (nValues < 5) and (fieldType == 2): 
 261                  ftype, vfmt = FIELD_TYPE[fieldType] 
 262                  vfmt = st + "%d%s" % (nValues, vfmt) 
 263                  actualValue = struct.unpack(vfmt, valueOffset[0: struct.calcsize(vfmt)])[0] 
 264                  valueOffsetList.append(actualValue) 
 265              else: 
 266                  valueOffsetList.append(valueOffset) 
 267              if DEBUG: 
 268                  if tagID in TAG_ID: 
 269                      print("tagID = %s" % TAG_ID[tagID]) 
 270                  else: 
 271                      print("tagID        = %d" % tagID) 
 272                  print("fieldType    = %s" % FIELD_TYPE[fieldType][0]) 
 273                  print("nValues      = %d" % nValues) 
 274                  #if nValues == 1: 
 275                  #    print("valueOffset =  %s" % valueOffset) 
 276          return tagIDList, fieldTypeList, nValuesList, valueOffsetList 

         277   
 278   
 279   

         280 -    def _readIFDEntry(self, tag, tagIDList, fieldTypeList, nValuesList, valueOffsetList): 

         281          fd = self.fd 
 282          st = self._structChar 
 283          idx = tagIDList.index(tag) 
 284          nValues = nValuesList[idx] 
 285          output = [] 
 286          ftype, vfmt = FIELD_TYPE[fieldTypeList[idx]] 
 287          vfmt = st + "%d%s" % (nValues, vfmt) 
 288          requestedBytes = struct.calcsize(vfmt) 
 289          if nValues == 1: 
 290              output.append(valueOffsetList[idx]) 
 291          elif requestedBytes < 5: 
 292              output.append(valueOffsetList[idx]) 
 293          else: 
 294              offset = fd.seek(struct.unpack(st + "I", valueOffsetList[idx])[0]) 
 295              output = struct.unpack(vfmt, fd.read(requestedBytes)) 
 296          return output 

         297   

         298 -    def getData(self, nImage, **kw): 

         299          if nImage >= len(self._IFD): 
 300              #update prior to raise an index error error 
 301              self._updateIFD() 
 302          return self._readImage(nImage, **kw) 

         303   

         304 -    def getImage(self, nImage): 

         305          return self.getData(nImage) 

         306   

         307 -    def getInfo(self, nImage, **kw): 

         308          if nImage >= len(self._IFD): 
 309              #update prior to raise an index error error 
 310              self._updateIFD() 
 311          current = self._IFD[nImage] 
 312          return self._readInfo(nImage) 

         313   

         314 -    def _readInfo(self, nImage, close=True): 

         315          if nImage in self._imageInfoCacheIndex: 
 316              if DEBUG: 
 317                  print("Reading info from cache") 
 318              return self._imageInfoCache[self._imageInfoCacheIndex.index(nImage)] 
 319   
 320          #read the header 
 321          self.__makeSureFileIsOpen() 
 322          tagIDList, fieldTypeList, nValuesList, valueOffsetList = self._parseImageFileDirectory(nImage) 
 323   
 324          #rows and columns 
 325          nColumns = valueOffsetList[tagIDList.index(TAG_NUMBER_OF_COLUMNS)] 
 326          nRows = valueOffsetList[tagIDList.index(TAG_NUMBER_OF_ROWS)] 
 327   
 328          #bits per sample 
 329          idx = tagIDList.index(TAG_BITS_PER_SAMPLE) 
 330          nBits = valueOffsetList[idx] 
 331          if nValuesList[idx] != 1: 
 332              #this happens with RGB and friends, nBits is not a single value 
 333              nBits = self._readIFDEntry(TAG_BITS_PER_SAMPLE, 
 334                                            tagIDList, fieldTypeList, nValuesList, valueOffsetList) 
 335   
 336   
 337          if TAG_COLORMAP in tagIDList: 
 338              idx = tagIDList.index(TAG_COLORMAP) 
 339              tmpColormap = self._readIFDEntry(TAG_COLORMAP, 
 340                                            tagIDList, fieldTypeList, nValuesList, valueOffsetList) 
 341              if max(tmpColormap) > 255: 
 342                  tmpColormap = numpy.array(tmpColormap, dtype=numpy.uint16) 
 343                  tmpColormap = (tmpColormap / 256.).astype(numpy.uint8) 
 344              else: 
 345                  tmpColormap = numpy.array(tmpColormap, dtype=numpy.uint8) 
 346              tmpColormap.shape = 3, -1 
 347              colormap = numpy.zeros((tmpColormap.shape[-1], 3), tmpColormap.dtype) 
 348              colormap[:, :] = tmpColormap.T 
 349              tmpColormap = None 
 350          else: 
 351              colormap = None 
 352   
 353          #sample format 
 354          if TAG_SAMPLE_FORMAT in tagIDList: 
 355              sampleFormat = valueOffsetList[tagIDList.index(TAG_SAMPLE_FORMAT)] 
 356          else: 
 357              #set to unknown 
 358              sampleFormat = SAMPLE_FORMAT_VOID 
 359   
 360          # compression 
 361          compression = False 
 362          compression_type = 1 
 363          if TAG_COMPRESSION in tagIDList: 
 364              compression_type = valueOffsetList[tagIDList.index(TAG_COMPRESSION)] 
 365              if compression_type == 1: 
 366                  compression = False 
 367              else: 
 368                  compression = True 
 369   
 370          #photometric interpretation 
 371          interpretation = 1 
 372          if TAG_PHOTOMETRIC_INTERPRETATION in tagIDList: 
 373              interpretation = valueOffsetList[tagIDList.index(TAG_PHOTOMETRIC_INTERPRETATION)] 
 374          else: 
 375              print("WARNING: Non standard TIFF. Photometric interpretation TAG missing") 
 376          helpString = "" 
 377          if sys.version > '2.6': 
 378              helpString = eval('b""') 
 379   
 380          if TAG_IMAGE_DESCRIPTION in tagIDList: 
 381              imageDescription = self._readIFDEntry(TAG_IMAGE_DESCRIPTION, 
 382                      tagIDList, fieldTypeList, nValuesList, valueOffsetList) 
 383              if type(imageDescription) in [type([1]), type((1,))]: 
 384                  imageDescription = helpString.join(imageDescription) 
 385          else: 
 386              imageDescription = "%d/%d" % (nImage + 1, len(self._IFD)) 
 387   
 388          if sys.version < '3.0': 
 389              defaultSoftware = "Unknown Software" 
 390          else: 
 391              defaultSoftware = bytes("Unknown Software", 
 392                                      encoding='utf-8') 
 393          if TAG_SOFTWARE in tagIDList: 
 394              software = self._readIFDEntry(TAG_SOFTWARE, 
 395                      tagIDList, fieldTypeList, nValuesList, valueOffsetList) 
 396              if type(software) in [type([1]), type((1,))]: 
 397                  software = helpString.join(software) 
 398          else: 
 399              software = defaultSoftware 
 400   
 401          if software == defaultSoftware: 
 402              try: 
 403                  if sys.version < '3.0': 
 404                      if imageDescription.upper().startswith("IMAGEJ"): 
 405                          software = imageDescription.split("=")[0] 
 406                  else: 
 407                      tmpString = imageDescription.decode() 
 408                      if tmpString.upper().startswith("IMAGEJ"): 
 409                          software = bytes(tmpString.split("=")[0], 
 410                                           encoding='utf-8') 
 411              except: 
 412                  pass 
 413   
 414          if TAG_DATE in tagIDList: 
 415              date = self._readIFDEntry(TAG_DATE, 
 416                      tagIDList, fieldTypeList, nValuesList, valueOffsetList) 
 417              if type(date) in [type([1]), type((1,))]: 
 418                  date = helpString.join(date) 
 419          else: 
 420              date = "Unknown Date" 
 421   
 422          stripOffsets = self._readIFDEntry(TAG_STRIP_OFFSETS, 
 423                          tagIDList, fieldTypeList, nValuesList, valueOffsetList) 
 424          if TAG_ROWS_PER_STRIP in tagIDList: 
 425              rowsPerStrip = self._readIFDEntry(TAG_ROWS_PER_STRIP, 
 426                          tagIDList, fieldTypeList, nValuesList, valueOffsetList)[0] 
 427          else: 
 428              rowsPerStrip = nRows 
 429              print("WARNING: Non standard TIFF. Rows per strip TAG missing") 
 430   
 431          if TAG_STRIP_BYTE_COUNTS in tagIDList: 
 432              stripByteCounts = self._readIFDEntry(TAG_STRIP_BYTE_COUNTS, 
 433                          tagIDList, fieldTypeList, nValuesList, valueOffsetList) 
 434          else: 
 435              print("WARNING: Non standard TIFF. Strip byte counts TAG missing") 
 436              if hasattr(nBits, 'index'): 
 437                  expectedSum = 0 
 438                  for n in nBits: 
 439                      expectedSum += int(nRows * nColumns * n / 8) 
 440              else: 
 441                  expectedSum = int(nRows * nColumns * nBits / 8) 
 442              stripByteCounts = [expectedSum] 
 443   
 444          if close: 
 445              self.__makeSureFileIsClosed() 
 446   
 447          if self._forceMonoOutput and (interpretation > 1): 
 448              #color image but asked monochrome output 
 449              nBits = 32 
 450              colormap = None 
 451              sampleFormat = SAMPLE_FORMAT_FLOAT 
 452              interpretation = 1 
 453              #we cannot rely on any cache in this case 
 454              useInfoCache = False 
 455              if DEBUG: 
 456                  print("FORCED MONO") 
 457          else: 
 458              useInfoCache = True 
 459   
 460          info = {} 
 461          info["nRows"] = nRows 
 462          info["nColumns"] = nColumns 
 463          info["nBits"] = nBits 
 464          info["compression"] = compression 
 465          info["compression_type"] = compression_type 
 466          info["imageDescription"] = imageDescription 
 467          info["stripOffsets"] = stripOffsets #This contains the file offsets to the data positions 
 468          info["rowsPerStrip"] = rowsPerStrip 
 469          info["stripByteCounts"] = stripByteCounts #bytes in strip since I do not support compression 
 470          info["software"] = software 
 471          info["date"] = date 
 472          info["colormap"] = colormap 
 473          info["sampleFormat"] = sampleFormat 
 474          info["photometricInterpretation"] = interpretation 
 475          infoDict = {} 
 476          if sys.version < '3.0': 
 477              testString = 'PyMca' 
 478          else: 
 479              testString = eval('b"PyMca"') 
 480          if software.startswith(testString): 
 481              #str to make sure python 2.x sees it as string and not unicode 
 482              if sys.version < '3.0': 
 483                  descriptionString = imageDescription 
 484              else: 
 485                  descriptionString = str(imageDescription.decode()) 
 486              #interpret the image description in terms of supplied 
 487              #information at writing time 
 488              items = descriptionString.split('=') 
 489              for i in range(int(len(items) / 2)): 
 490                  key = "%s" % items[i * 2] 
 491                  #get rid of the \n at the end of the value  
 492                  value = "%s" % items[i * 2 + 1][:-1] 
 493                  infoDict[key] = value 
 494          info['info'] = infoDict 
 495   
 496          if (self._maxImageCacheLength > 0) and useInfoCache: 
 497              self._imageInfoCacheIndex.insert(0, nImage) 
 498              self._imageInfoCache.insert(0, info) 
 499              if len(self._imageInfoCacheIndex) > self._maxImageCacheLength: 
 500                  self._imageInfoCacheIndex = self._imageInfoCacheIndex[:self._maxImageCacheLength] 
 501                  self._imageInfoCache = self._imageInfoCache[:self._maxImageCacheLength] 
 502          return info 

         503   

         504 -    def _readImage(self, nImage, **kw): 

         505          if DEBUG: 
 506              print("Reading image %d" % nImage) 
 507          if 'close' in kw: 
 508              close = kw['close'] 
 509          else: 
 510              close = True 
 511          rowMin = kw.get('rowMin', None) 
 512          rowMax = kw.get('rowMax', None) 
 513          if nImage in self._imageDataCacheIndex: 
 514              if DEBUG: 
 515                  print("Reading image data from cache") 
 516              return self._imageDataCache[self._imageDataCacheIndex.index(nImage)] 
 517   
 518          self.__makeSureFileIsOpen() 
 519          if self._forceMonoOutput: 
 520              oldMono = True 
 521          else: 
 522              oldMono = False 
 523          try: 
 524              self._forceMonoOutput = False 
 525              info = self._readInfo(nImage, close=False) 
 526              self._forceMonoOutput = oldMono 
 527          except: 
 528              self._forceMonoOutput = oldMono 
 529              raise 
 530          compression = info['compression'] 
 531          compression_type = info['compression_type'] 
 532          if compression: 
 533              if compression_type != 32773: 
 534                  raise IOError("Compressed TIFF images not supported except packbits") 
 535              else: 
 536                  #PackBits compression 
 537                  if DEBUG: 
 538                      print("Using PackBits compression") 
 539   
 540          interpretation = info["photometricInterpretation"] 
 541          if interpretation == 2: 
 542              #RGB 
 543              pass 
 544              #raise IOError("RGB Image. Only grayscale images supported") 
 545          elif interpretation == 3: 
 546              #Palette Color Image 
 547              pass 
 548              #raise IOError("Palette-color Image. Only grayscale images supported") 
 549          elif interpretation > 2: 
 550              #Palette Color Image 
 551              raise IOError("Only grayscale images supported") 
 552   
 553          nRows = info["nRows"] 
 554          nColumns = info["nColumns"] 
 555          nBits = info["nBits"] 
 556          colormap = info["colormap"] 
 557          sampleFormat = info["sampleFormat"] 
 558   
 559          if rowMin is None: 
 560              rowMin = 0 
 561   
 562          if rowMax is None: 
 563              rowMax = nRows - 1 
 564   
 565          if rowMin < 0: 
 566              rowMin = nRows - rowMin 
 567   
 568          if rowMax < 0: 
 569              rowMax = nRows - rowMax 
 570   
 571          if rowMax < rowMin: 
 572              txt = "Max Row smaller than Min Row. Reverse selection not supported" 
 573              raise NotImplemented(txt) 
 574   
 575          if rowMin >= nRows: 
 576              raise IndexError("Image only has %d rows" % nRows) 
 577   
 578          if rowMax >= nRows: 
 579              raise IndexError("Image only has %d rows" % nRows) 
 580   
 581          if sampleFormat == SAMPLE_FORMAT_FLOAT: 
 582              if nBits == 32: 
 583                  dtype = numpy.float32 
 584              elif nBits == 64: 
 585                  dtype = numpy.float64 
 586              else: 
 587                  raise ValueError("Unsupported number of bits for a float: %d" % nBits) 
 588          elif sampleFormat in [SAMPLE_FORMAT_UINT, SAMPLE_FORMAT_VOID]: 
 589              if nBits in [8, (8, 8, 8), [8, 8, 8]]: 
 590                  dtype = numpy.uint8 
 591              elif nBits in [16, (16, 16, 16), [16, 16, 16]]: 
 592                  dtype = numpy.uint16 
 593              elif nBits in [32, (32, 32, 32), [32, 32, 32]]: 
 594                  dtype = numpy.uint32 
 595              elif nBits in [64, (64, 64, 64), [64, 64, 64]]: 
 596                  dtype = numpy.uint64 
 597              else: 
 598                  raise ValueError("Unsupported number of bits for unsigned int: %s" % (nBits,)) 
 599          elif sampleFormat == SAMPLE_FORMAT_INT: 
 600              if nBits in [8, (8, 8, 8), [8, 8, 8]]: 
 601                  dtype = numpy.int8 
 602              elif nBits in [16, (16, 16, 16), [16, 16, 16]]: 
 603                  dtype = numpy.int16 
 604              elif nBits in [32, (32, 32, 32), [32, 32, 32]]: 
 605                  dtype = numpy.int32 
 606              elif nBits in [64, (64, 64, 64), [64, 64, 64]]: 
 607                  dtype = numpy.int64 
 608              else: 
 609                  raise ValueError("Unsupported number of bits for signed int: %s" % (nBits,)) 
 610          else: 
 611              raise ValueError("Unsupported combination. Bits = %s  Format = %d" % (nBits, sampleFormat)) 
 612          if hasattr(nBits, 'index'): 
 613              image = numpy.zeros((nRows, nColumns, len(nBits)), dtype=dtype) 
 614          elif colormap is not None: 
 615              #should I use colormap dtype? 
 616              image = numpy.zeros((nRows, nColumns, 3), dtype=dtype) 
 617          else: 
 618              image = numpy.zeros((nRows, nColumns), dtype=dtype) 
 619   
 620          fd = self.fd 
 621          st = self._structChar 
 622          stripOffsets = info["stripOffsets"] #This contains the file offsets to the data positions 
 623          rowsPerStrip = info["rowsPerStrip"] 
 624          stripByteCounts = info["stripByteCounts"] #bytes in strip since I do not support compression 
 625   
 626          rowStart = 0 
 627          if len(stripOffsets) == 1: 
 628              bytesPerRow = int(stripByteCounts[0] / rowsPerStrip) 
 629              fd.seek(stripOffsets[0] + rowMin * bytesPerRow) 
 630              nBytes = (rowMax - rowMin + 1) * bytesPerRow 
 631              if self._swap: 
 632                  readout = numpy.fromstring(fd.read(nBytes), dtype).byteswap() 
 633              else: 
 634                  readout = numpy.fromstring(fd.read(nBytes), dtype) 
 635              if hasattr(nBits, 'index'): 
 636                  readout.shape = -1, nColumns, len(nBits) 
 637              elif info['colormap'] is not None: 
 638                  readout = colormap[readout] 
 639              else: 
 640                  readout.shape = -1, nColumns 
 641              image[rowMin:rowMax + 1, :] = readout 
 642          else: 
 643              for i in range(len(stripOffsets)): 
 644                  #the amount of rows 
 645                  nRowsToRead = rowsPerStrip 
 646                  rowEnd = int(min(rowStart + nRowsToRead, nRows)) 
 647                  if rowEnd < rowMin: 
 648                      rowStart += nRowsToRead 
 649                      continue 
 650                  if (rowStart > rowMax): 
 651                      break 
 652                  #we are in position 
 653                  fd.seek(stripOffsets[i]) 
 654                  #the amount of bytes to read 
 655                  nBytes = stripByteCounts[i] 
 656                  if compression_type == 32773: 
 657                      try: 
 658                          bufferBytes = bytes() 
 659                      except: 
 660                          #python 2.5 ... 
 661                          bufferBytes = "" 
 662                      #packBits 
 663                      readBytes = 0 
 664                      #intermediate buffer 
 665                      tmpBuffer = fd.read(nBytes) 
 666                      while readBytes < nBytes: 
 667                          n = struct.unpack('b', tmpBuffer[readBytes:(readBytes + 1)])[0] 
 668                          readBytes += 1 
 669                          if n >= 0: 
 670                              #should I prevent reading more than the 
 671                              #length of the chain? Let's python raise 
 672                              #the exception... 
 673                              bufferBytes += tmpBuffer[readBytes:\ 
 674                                                        readBytes + (n + 1)] 
 675                              readBytes += (n + 1) 
 676                          elif n > -128: 
 677                              bufferBytes += (-n + 1) * tmpBuffer[readBytes:(readBytes + 1)] 
 678                              readBytes += 1 
 679                          else: 
 680                              #if read -128 ignore the byte 
 681                              continue 
 682                      if self._swap: 
 683                          readout = numpy.fromstring(bufferBytes, dtype).byteswap() 
 684                      else: 
 685                          readout = numpy.fromstring(bufferBytes, dtype) 
 686                      if hasattr(nBits, 'index'): 
 687                          readout.shape = -1, nColumns, len(nBits) 
 688                      elif info['colormap'] is not None: 
 689                          readout = colormap[readout] 
 690                          readout.shape = -1, nColumns, 3 
 691                      else: 
 692                          readout.shape = -1, nColumns 
 693                      image[rowStart:rowEnd, :] = readout 
 694                  else: 
 695                      if 1: 
 696                          #use numpy 
 697                          if self._swap: 
 698                              readout = numpy.fromstring(fd.read(nBytes), dtype).byteswap() 
 699                          else: 
 700                              readout = numpy.fromstring(fd.read(nBytes), dtype) 
 701                          if hasattr(nBits, 'index'): 
 702                              readout.shape = -1, nColumns, len(nBits) 
 703                          elif colormap is not None: 
 704                              readout = colormap[readout] 
 705                              readout.shape = -1, nColumns, 3 
 706                          else: 
 707                              readout.shape = -1, nColumns 
 708                          image[rowStart:rowEnd, :] = readout 
 709                      else: 
 710                          #using struct 
 711                          readout = numpy.array(struct.unpack(st + "%df" % int(nBytes / 4), fd.read(nBytes)), 
 712                                                dtype=dtype) 
 713                          if hasattr(nBits, 'index'): 
 714                              readout.shape = -1, nColumns, len(nBits) 
 715                          elif colormap is not None: 
 716                              readout = colormap[readout] 
 717                              readout.shape = -1, nColumns, 3 
 718                          else: 
 719                              readout.shape = -1, nColumns 
 720                          image[rowStart:rowEnd, :] = readout 
 721                  rowStart += nRowsToRead 
 722          if close: 
 723              self.__makeSureFileIsClosed() 
 724   
 725          if len(image.shape) == 3: 
 726              #color image 
 727              if self._forceMonoOutput: 
 728                  #color image, convert to monochrome 
 729                  image = (image[:, :, 0] * 0.114 + \ 
 730                           image[:, :, 1] * 0.587 + \ 
 731                           image[:, :, 2] * 0.299).astype(numpy.float32) 
 732   
 733          if (rowMin == 0) and (rowMax == (nRows - 1)): 
 734              self._imageDataCacheIndex.insert(0, nImage) 
 735              self._imageDataCache.insert(0, image) 
 736              if len(self._imageDataCacheIndex) > self._maxImageCacheLength: 
 737                  self._imageDataCacheIndex = self._imageDataCacheIndex[:self._maxImageCacheLength] 
 738                  self._imageDataCache = self._imageDataCache[:self._maxImageCacheLength] 
 739   
 740          return image 

         741   

         742 -    def writeImage(self, image0, info=None, software=None, date=None): 

         743          if software is None: 
 744              software = 'PyMca.TiffIO' 
 745          #if date is None: 
 746          #    date = time.ctime() 
 747   
 748          self.__makeSureFileIsOpen() 
 749          fd = self.fd 
 750          #prior to do anything, perform some tests 
 751          if not len(image0.shape): 
 752              raise ValueError("Empty image") 
 753          if len(image0.shape) == 1: 
 754              #get a different view 
 755              image = image0[:] 
 756              image.shape = 1, -1 
 757          else: 
 758              image = image0 
 759   
 760          if image.dtype == numpy.float64: 
 761              image = image.astype(numpy.float32) 
 762          fd.seek(0) 
 763          mode = fd.mode 
 764          name = fd.name 
 765          if 'w' in mode: 
 766              #we have to overwrite the file 
 767              self.__makeSureFileIsClosed() 
 768              fd = None 
 769              if os.path.exists(name): 
 770                  os.remove(name) 
 771              fd = open(name, mode='wb+') 
 772              self._initEmptyFile(fd) 
 773          self.fd = fd 
 774   
 775          #read the file size 
 776          self.__makeSureFileIsOpen() 
 777          fd = self.fd 
 778          fd.seek(0, os.SEEK_END) 
 779          endOfFile = fd.tell() 
 780          if fd.tell() == 0: 
 781              self._initEmptyFile(fd) 
 782              fd.seek(0, os.SEEK_END) 
 783              endOfFile = fd.tell() 
 784   
 785          #init internal variables 
 786          self._initInternalVariables(fd) 
 787          st = self._structChar 
 788   
 789          #get the image file directories 
 790          nImages = self.getImageFileDirectories() 
 791          if DEBUG: 
 792              print("File contains %d images" % nImages) 
 793          if nImages == 0: 
 794              fd.seek(4) 
 795              fmt = st + 'I' 
 796              fd.write(struct.pack(fmt, endOfFile)) 
 797          else: 
 798              fd.seek(self._IFD[-1]) 
 799              fmt = st + 'H' 
 800              numberOfDirectoryEntries = struct.unpack(fmt, fd.read(struct.calcsize(fmt)))[0] 
 801              fmt = st + 'I' 
 802              pos = self._IFD[-1] + 2 + 12 * numberOfDirectoryEntries 
 803              fd.seek(pos) 
 804              fmt = st + 'I' 
 805              fd.write(struct.pack(fmt, endOfFile)) 
 806          fd.flush() 
 807   
 808          #and we can write at the end of the file, find out the file length 
 809          fd.seek(0, os.SEEK_END) 
 810   
 811          #get the description information from the input information 
 812          if info is None: 
 813              description = info 
 814          else: 
 815              description = "%s" % "" 
 816              for key in info.keys(): 
 817                  description += "%s=%s\n" % (key, info[key]) 
 818   
 819          #get the image file directory 
 820          outputIFD = self._getOutputIFD(image, description=description, 
 821                                                software=software, 
 822                                                date=date) 
 823   
 824          #write the new IFD 
 825          fd.write(outputIFD) 
 826   
 827          #write the image 
 828          if self._swap: 
 829              fd.write(image.byteswap().tostring()) 
 830          else: 
 831              fd.write(image.tostring()) 
 832   
 833          fd.flush() 
 834          self.fd = fd 
 835          self.__makeSureFileIsClosed() 

         836   

         837 -    def _initEmptyFile(self, fd=None): 

         838          if fd is None: 
 839              fd = self.fd 
 840          if sys.byteorder == "little": 
 841              order = "II" 
 842              #intel, little endian 
 843              fileOrder = "little" 
 844              self._structChar = '<' 
 845          else: 
 846              order = "MM" 
 847              #motorola, high endian 
 848              fileOrder = "big" 
 849              self._structChar = '>' 
 850          st = self._structChar 
 851          if fileOrder == sys.byteorder: 
 852              self._swap = False 
 853          else: 
 854              self._swap = True 
 855          fd.seek(0) 
 856          if sys.version < '3.0': 
 857              fd.write(struct.pack(st + '2s', order)) 
 858              fd.write(struct.pack(st + 'H', 42)) 
 859              fd.write(struct.pack(st + 'I', 0)) 
 860          else: 
 861              fd.write(struct.pack(st + '2s', bytes(order, 'utf-8'))) 
 862              fd.write(struct.pack(st + 'H', 42)) 
 863              fd.write(struct.pack(st + 'I', 0)) 
 864          fd.flush() 

         865   

         866 -    def _getOutputIFD(self, image, description=None, software=None, date=None): 

         867          #the tags have to be in order 
 868          #the very minimum is 
 869          #256:"NumberOfColumns",           # S or L ImageWidth 
 870          #257:"NumberOfRows",              # S or L ImageHeight 
 871          #258:"BitsPerSample",             # S Number of bits per component 
 872          #259:"Compression",               # SHORT (1 - NoCompression, ...  
 873          #262:"PhotometricInterpretation", # SHORT (0 - WhiteIsZero, 1 -BlackIsZero, 2 - RGB, 3 - Palette color 
 874          #270:"ImageDescription",          # ASCII 
 875          #273:"StripOffsets",              # S or L, for each strip, the byte offset of the strip 
 876          #278:"RowsPerStrip",              # S or L, number of rows in each back may be not for the last 
 877          #279:"StripByteCounts",           # S or L, The number of bytes in the strip AFTER any compression 
 878          #305:"Software",                  # ASCII 
 879          #306:"Date",                      # ASCII 
 880          #339:"SampleFormat",              # SHORT Interpretation of data in each pixel 
 881   
 882          nDirectoryEntries = 9 
 883          imageDescription = None 
 884          if description is not None: 
 885              descriptionLength = len(description) 
 886              while descriptionLength < 4: 
 887                  description = description + " " 
 888                  descriptionLength = len(description) 
 889              if sys.version >= '3.0': 
 890                  description = bytes(description, 'utf-8') 
 891              elif type(description) != type(""): 
 892                  try: 
 893                      description = description.decode('utf-8') 
 894                  except UnicodeDecodeError: 
 895                      try: 
 896                          description = description.decode('latin-1') 
 897                      except UnicodeDecodeError: 
 898                          description = "%s" % description 
 899                  if sys.version > '2.6': 
 900                      description = description.encode('utf-8', errors="ignore") 
 901                  description = "%s" % description 
 902              descriptionLength = len(description) 
 903              imageDescription = struct.pack("%ds" % descriptionLength, description) 
 904              nDirectoryEntries += 1 
 905   
 906          #software 
 907          if software is not None: 
 908              softwareLength = len(software) 
 909              while softwareLength < 4: 
 910                  software = software + " " 
 911                  softwareLength = len(software) 
 912              if sys.version >= '3.0': 
 913                  software = bytes(software, 'utf-8') 
 914              softwarePackedString = struct.pack("%ds" % softwareLength, software) 
 915              nDirectoryEntries += 1 
 916          else: 
 917              softwareLength = 0 
 918   
 919          if date is not None: 
 920              dateLength = len(date) 
 921              if sys.version >= '3.0': 
 922                  date = bytes(date, 'utf-8') 
 923              datePackedString = struct.pack("%ds" % dateLength, date) 
 924              dateLength = len(datePackedString) 
 925              nDirectoryEntries += 1 
 926          else: 
 927              dateLength = 0 
 928   
 929          nRows, nColumns = image.shape 
 930          dtype = image.dtype 
 931          bitsPerSample = int(dtype.str[-1]) * 8 
 932   
 933          #only uncompressed data 
 934          compression = 1 
 935   
 936          #interpretation, black is zero 
 937          interpretation = 1 
 938   
 939          #image description 
 940          if imageDescription is not None: 
 941              descriptionLength = len(imageDescription) 
 942          else: 
 943              descriptionLength = 0 
 944   
 945          #strip offsets 
 946          #we are putting them after the directory and the directory is 
 947          #at the end of the file 
 948          self.fd.seek(0, os.SEEK_END) 
 949          endOfFile = self.fd.tell() 
 950          if endOfFile == 0: 
 951              #empty file 
 952              endOfFile = 8 
 953   
 954          #rows per strip 
 955          if ALLOW_MULTIPLE_STRIPS: 
 956              #try to segment the image in several pieces 
 957              if not (nRows % 4): 
 958                  rowsPerStrip = int(nRows / 4) 
 959              elif not (nRows % 10): 
 960                  rowsPerStrip = int(nRows / 10) 
 961              elif not (nRows % 8): 
 962                  rowsPerStrip = int(nRows / 8) 
 963              elif not (nRows % 4): 
 964                  rowsPerStrip = int(nRows / 4) 
 965              elif not (nRows % 2): 
 966                  rowsPerStrip = int(nRows / 2) 
 967              else: 
 968                  rowsPerStrip = nRows 
 969          else: 
 970              rowsPerStrip = nRows 
 971   
 972          #stripByteCounts 
 973          stripByteCounts = int(nColumns * rowsPerStrip * bitsPerSample / 8) 
 974   
 975          if descriptionLength > 4: 
 976              stripOffsets0 = endOfFile + dateLength + descriptionLength + \ 
 977                          2 + 12 * nDirectoryEntries + 4 
 978          else: 
 979              stripOffsets0 = endOfFile + dateLength + \ 
 980                          2 + 12 * nDirectoryEntries + 4 
 981   
 982          if softwareLength > 4: 
 983              stripOffsets0 += softwareLength 
 984   
 985          stripOffsets = [stripOffsets0] 
 986          stripOffsetsLength = 0 
 987          stripOffsetsString = None 
 988   
 989          st = self._structChar 
 990   
 991          if rowsPerStrip != nRows: 
 992              nStripOffsets = int(nRows / rowsPerStrip) 
 993              fmt = st + 'I' 
 994              stripOffsetsLength = struct.calcsize(fmt) * nStripOffsets 
 995              stripOffsets0 += stripOffsetsLength 
 996              #the length for the stripByteCounts will be the same 
 997              stripOffsets0 += stripOffsetsLength 
 998              stripOffsets = [] 
 999              for i in range(nStripOffsets): 
1000                  value = stripOffsets0 + i * stripByteCounts 
1001                  stripOffsets.append(value) 
1002                  if i == 0: 
1003                      stripOffsetsString = struct.pack(fmt, value) 
1004                      stripByteCountsString = struct.pack(fmt, stripByteCounts) 
1005                  else: 
1006                      stripOffsetsString += struct.pack(fmt, value) 
1007                      stripByteCountsString += struct.pack(fmt, stripByteCounts) 
1008   
1009          if DEBUG: 
1010              print("IMAGE WILL START AT %d" % stripOffsets[0]) 
1011   
1012          #sample format 
1013          if dtype in [numpy.float32, numpy.float64] or\ 
1014             dtype.str[-2] == 'f': 
1015              sampleFormat = SAMPLE_FORMAT_FLOAT 
1016          elif dtype in [numpy.uint8, numpy.uint16, numpy.uint32, numpy.uint64]: 
1017              sampleFormat = SAMPLE_FORMAT_UINT 
1018          elif dtype in [numpy.int8, numpy.int16, numpy.int32, numpy.int64]: 
1019              sampleFormat = SAMPLE_FORMAT_INT 
1020          else: 
1021              raise ValueError("Unsupported data type %s" % dtype) 
1022   
1023          info = {} 
1024          info["nColumns"] = nColumns 
1025          info["nRows"] = nRows 
1026          info["nBits"] = bitsPerSample 
1027          info["compression"] = compression 
1028          info["photometricInterpretation"] = interpretation 
1029          info["stripOffsets"] = stripOffsets 
1030          info["rowsPerStrip"] = rowsPerStrip 
1031          info["stripByteCounts"] = stripByteCounts 
1032          info["date"] = date 
1033          info["sampleFormat"] = sampleFormat 
1034   
1035          outputIFD = "" 
1036          if sys.version > '2.6': 
1037              outputIFD = eval('b""') 
1038   
1039          fmt = st + "H" 
1040          outputIFD += struct.pack(fmt, nDirectoryEntries) 
1041   
1042          fmt = st + "HHII" 
1043          outputIFD += struct.pack(fmt, TAG_NUMBER_OF_COLUMNS, 
1044                                           FIELD_TYPE_OUT['I'], 
1045                                           1, 
1046                                           info["nColumns"]) 
1047          outputIFD += struct.pack(fmt, TAG_NUMBER_OF_ROWS, 
1048                                           FIELD_TYPE_OUT['I'], 
1049                                           1, 
1050                                           info["nRows"]) 
1051   
1052          fmt = st + 'HHIHH' 
1053          outputIFD += struct.pack(fmt, TAG_BITS_PER_SAMPLE, 
1054                                           FIELD_TYPE_OUT['H'], 
1055                                           1, 
1056                                           info["nBits"], 0) 
1057          fmt = st + 'HHIHH' 
1058          outputIFD += struct.pack(fmt, TAG_COMPRESSION, 
1059                                           FIELD_TYPE_OUT['H'], 
1060                                           1, 
1061                                           info["compression"], 0) 
1062          fmt = st + 'HHIHH' 
1063          outputIFD += struct.pack(fmt, TAG_PHOTOMETRIC_INTERPRETATION, 
1064                                           FIELD_TYPE_OUT['H'], 
1065                                           1, 
1066                                           info["photometricInterpretation"], 0) 
1067   
1068          if imageDescription is not None: 
1069              descriptionLength = len(imageDescription) 
1070              if descriptionLength > 4: 
1071                  fmt = st + 'HHII' 
1072                  outputIFD += struct.pack(fmt, TAG_IMAGE_DESCRIPTION, 
1073                                           FIELD_TYPE_OUT['s'], 
1074                                           descriptionLength, 
1075                                           info["stripOffsets"][0] - \ 
1076                                           2 * stripOffsetsLength - \ 
1077                                           descriptionLength) 
1078              else: 
1079                  #it has to have length 4 
1080                  fmt = st + 'HHI%ds' % descriptionLength 
1081                  outputIFD += struct.pack(fmt, TAG_IMAGE_DESCRIPTION, 
1082                                           FIELD_TYPE_OUT['s'], 
1083                                           descriptionLength, 
1084                                           description) 
1085   
1086          if len(stripOffsets) == 1: 
1087              fmt = st + 'HHII' 
1088              outputIFD += struct.pack(fmt, TAG_STRIP_OFFSETS, 
1089                                               FIELD_TYPE_OUT['I'], 
1090                                               1, 
1091                                               info["stripOffsets"][0]) 
1092          else: 
1093              fmt = st + 'HHII' 
1094              outputIFD += struct.pack(fmt, TAG_STRIP_OFFSETS, 
1095                                               FIELD_TYPE_OUT['I'], 
1096                                               len(stripOffsets), 
1097                      info["stripOffsets"][0] - 2 * stripOffsetsLength) 
1098   
1099          fmt = st + 'HHII' 
1100          outputIFD += struct.pack(fmt, TAG_ROWS_PER_STRIP, 
1101                                           FIELD_TYPE_OUT['I'], 
1102                                           1, 
1103                                           info["rowsPerStrip"]) 
1104   
1105          if len(stripOffsets) == 1: 
1106              fmt = st + 'HHII' 
1107              outputIFD += struct.pack(fmt, TAG_STRIP_BYTE_COUNTS, 
1108                                               FIELD_TYPE_OUT['I'], 
1109                                               1, 
1110                                               info["stripByteCounts"]) 
1111          else: 
1112              fmt = st + 'HHII' 
1113              outputIFD += struct.pack(fmt, TAG_STRIP_BYTE_COUNTS, 
1114                                               FIELD_TYPE_OUT['I'], 
1115                                               len(stripOffsets), 
1116                      info["stripOffsets"][0] - stripOffsetsLength) 
1117   
1118          if software is not None: 
1119              if softwareLength > 4: 
1120                  fmt = st + 'HHII' 
1121                  outputIFD += struct.pack(fmt, TAG_SOFTWARE, 
1122                                           FIELD_TYPE_OUT['s'], 
1123                                           softwareLength, 
1124                                           info["stripOffsets"][0] - \ 
1125                                           2 * stripOffsetsLength - \ 
1126                              descriptionLength - softwareLength - dateLength) 
1127              else: 
1128                  #it has to have length 4 
1129                  fmt = st + 'HHI%ds' % softwareLength 
1130                  outputIFD += struct.pack(fmt, TAG_SOFTWARE, 
1131                                           FIELD_TYPE_OUT['s'], 
1132                                           softwareLength, 
1133                                           softwarePackedString) 
1134   
1135          if date is not None: 
1136              fmt = st + 'HHII' 
1137              outputIFD += struct.pack(fmt, TAG_DATE, 
1138                                        FIELD_TYPE_OUT['s'], 
1139                                        dateLength, 
1140                                        info["stripOffsets"][0] - \ 
1141                                           2 * stripOffsetsLength - \ 
1142                                        descriptionLength - dateLength) 
1143   
1144          fmt = st + 'HHIHH' 
1145          outputIFD += struct.pack(fmt, TAG_SAMPLE_FORMAT, 
1146                                           FIELD_TYPE_OUT['H'], 
1147                                           1, 
1148                                           info["sampleFormat"], 0) 
1149          fmt = st + 'I' 
1150          outputIFD += struct.pack(fmt, 0) 
1151   
1152          if softwareLength > 4: 
1153              outputIFD += softwarePackedString 
1154   
1155          if date is not None: 
1156              outputIFD += datePackedString 
1157   
1158          if imageDescription is not None: 
1159              if descriptionLength > 4: 
1160                  outputIFD += imageDescription 
1161   
1162          if stripOffsetsString is not None: 
1163              outputIFD += stripOffsetsString 
1164              outputIFD += stripByteCountsString 
1165   
1166          return outputIFD 

        1167   
1168   
1169  if __name__ == "__main__": 
1170      filename = sys.argv[1] 
1171      dtype = numpy.uint16 
1172      if not os.path.exists(filename): 
1173          print("Testing file creation") 
1174          tif = TiffIO(filename, mode='wb+') 
1175          data = numpy.arange(10000).astype(dtype) 
1176          data.shape = 100, 100 
1177          tif.writeImage(data, info={'Title':'1st'}) 
1178          tif = None 
1179          if os.path.exists(filename): 
1180              print("Testing image appending") 
1181              tif = TiffIO(filename, mode='rb+') 
1182              tif.writeImage((data * 2).astype(dtype), info={'Title':'2nd'}) 
1183              tif = None 
1184      tif = TiffIO(filename) 
1185      print("Number of images = %d" % tif.getNumberOfImages()) 
1186      for i in range(tif.getNumberOfImages()): 
1187          info = tif.getInfo(i) 
1188          for key in info: 
1189              if key not in ["colormap"]: 
1190                  print("%s = %s" % (key, info[key])) 
1191              elif info['colormap'] is not None: 
1192                  print("RED   %s = %s" % (key, info[key][0:10, 0])) 
1193                  print("GREEN %s = %s" % (key, info[key][0:10, 1])) 
1194                  print("BLUE  %s = %s" % (key, info[key][0:10, 2])) 
1195          data = tif.getImage(i)[0, 0:10] 
1196          print("data [0, 0:10] = ", data) 
1197

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0000568394 00000 n 0000570452 00000 n 0000571552 00000 n 0000581623 00000 n 0000592001 00000 n 0000598830 00000 n 0000599707 00000 n 0000604629 00000 n 0000610166 00000 n 0000510947 00000 n 0000511553 00000 n 0000512139 00000 n 0000512728 00000 n 0000513594 00000 n 0000514717 00000 n 0000515320 00000 n 0000515865 00000 n 0000516513 00000 n 0000517332 00000 n trailer << /Size 1298 /Root 1 0 R /Info 2 0 R /ID [] >> startxref 632225 %%EOF fabio-0.1.3/epydoc/fabio-module.html0000644000175000017500000002741612126623347020113 0ustar jeromejerome00000000000000 fabio
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        Package fabio
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        Package fabio

        source code

        FabIO module

        Date: 02/04/2013

        Author: J\xc3\xa9r\xc3\xb4me Kieffer

        Contact: Jerome.Kieffer@ESRF.eu

        Copyright: European Synchrotron Radiation Facility, Grenoble, France

        License: GPLv3+

        Submodules [hide private]

        Variables [hide private]
          __status__ = 'stable'
          version = '0.1.2'
          __package__ = 'fabio'
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        fabio-0.1.3/epydoc/fabio.tifimage.Image_File_Directory-class.html0000644000175000017500000002244312126623347025516 0ustar jeromejerome00000000000000 fabio.tifimage.Image_File_Directory
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        Package fabio :: Module tifimage :: Class Image_File_Directory
        [hide private]
        [frames] | no frames]

        Class Image_File_Directory

        source code

        object --+
         |
        Image_File_Directory
        Instance Methods [hide private]
         
        __init__(self, instring=None, offset=-1)
        x.__init__(...) initializes x; see x.__class__.__doc__ for signature        		 source code
         
        unpack(self, instring, offset=-1) source code

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Properties [hide private]

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, instring=None, offset=-1)
        (Constructor)

        		source code 

        x.__init__(...) initializes x; see x.__class__.__doc__ for signature

        Overrides: object.__init__
        (inherited documentation)

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        fabio-0.1.3/epydoc/fabio-pysrc.html0000644000175000017500000003107312126623347017760 0ustar jeromejerome00000000000000 fabio
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        Package fabio
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        Source Code for Package fabio

         1  #!/usr/bin/env python 
 2  #coding: utf8 
 3  """ 
 4  FabIO module 
 5    
 6  """ 
 7  __author__ = "Jérôme Kieffer" 
 8  __contact__ = "Jerome.Kieffer@ESRF.eu" 
 9  __license__ = "GPLv3+" 
10  __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" 
11  __date__ = "02/04/2013" 
12  __status__ = "stable" 
13   
14  version = "0.1.2" 
15  import logging 
16  logging.basicConfig() 
17  import fabioimage 
18  import openimage 
19  from fabioutils import COMPRESSORS, jump_filename, FilenameObject, \ 
20          previous_filename, next_filename, deconstruct_filename, \ 
21          extract_filenumber, getnum, construct_filename 
22   
23  # Compatibility with outside world: 
24  filename_object = FilenameObject 
25   
26  from openimage import openimage as open 
27  from openimage import openheader as openheader 
28

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        fabio-0.1.3/epydoc/epydoc.js0000644000175000017500000002452512120434325016467 0ustar jeromejerome00000000000000function toggle_private() { // Search for any private/public links on this page. Store // their old text in "cmd," so we will know what action to // take; and change their text to the opposite action. var cmd = "?"; var elts = document.getElementsByTagName("a"); for(var i=0; i...
        "; elt.innerHTML = s; } } function toggle(id) { elt = document.getElementById(id+"-toggle"); if (elt.innerHTML == "-") collapse(id); else expand(id); return false; } function highlight(id) { var elt = document.getElementById(id+"-def"); if (elt) elt.className = "py-highlight-hdr"; var elt = document.getElementById(id+"-expanded"); if (elt) elt.className = "py-highlight"; var elt = document.getElementById(id+"-collapsed"); if (elt) elt.className = "py-highlight"; } function num_lines(s) { var n = 1; var pos = s.indexOf("\n"); while ( pos > 0) { n += 1; pos = s.indexOf("\n", pos+1); } return n; } // Collapse all blocks that mave more than `min_lines` lines. function collapse_all(min_lines) { var elts = document.getElementsByTagName("div"); for (var i=0; i 0) if (elt.id.substring(split, elt.id.length) == "-expanded") if (num_lines(elt.innerHTML) > min_lines) collapse(elt.id.substring(0, split)); } } function expandto(href) { var start = href.indexOf("#")+1; if (start != 0 && start != href.length) { if (href.substring(start, href.length) != "-") { collapse_all(4); pos = href.indexOf(".", start); while (pos != -1) { var id = href.substring(start, pos); expand(id); pos = href.indexOf(".", pos+1); } var id = href.substring(start, href.length); expand(id); highlight(id); } } } function kill_doclink(id) { var parent = document.getElementById(id); parent.removeChild(parent.childNodes.item(0)); } function auto_kill_doclink(ev) { if (!ev) var ev = window.event; if (!this.contains(ev.toElement)) { var parent = document.getElementById(this.parentID); parent.removeChild(parent.childNodes.item(0)); } } function doclink(id, name, targets_id) { var elt = document.getElementById(id); // If we already opened the box, then destroy it. // (This case should never occur, but leave it in just in case.) if (elt.childNodes.length > 1) { elt.removeChild(elt.childNodes.item(0)); } else { // The outer box: relative + inline positioning. var box1 = document.createElement("div"); box1.style.position = "relative"; box1.style.display = "inline"; box1.style.top = 0; box1.style.left = 0; // A shadow for fun var shadow = document.createElement("div"); shadow.style.position = "absolute"; shadow.style.left = "-1.3em"; shadow.style.top = "-1.3em"; shadow.style.background = "#404040"; // The inner box: absolute positioning. var box2 = document.createElement("div"); box2.style.position = "relative"; box2.style.border = "1px solid #a0a0a0"; box2.style.left = "-.2em"; box2.style.top = "-.2em"; box2.style.background = "white"; box2.style.padding = ".3em .4em .3em .4em"; box2.style.fontStyle = "normal"; box2.onmouseout=auto_kill_doclink; box2.parentID = id; // Get the targets var targets_elt = document.getElementById(targets_id); var targets = targets_elt.getAttribute("targets"); var links = ""; target_list = targets.split(","); for (var i=0; i" + target[0] + ""; } // Put it all together. elt.insertBefore(box1, elt.childNodes.item(0)); //box1.appendChild(box2); box1.appendChild(shadow); shadow.appendChild(box2); box2.innerHTML = "Which "+name+" do you want to see documentation for?" + ""; } return false; } function get_anchor() { var href = location.href; var start = href.indexOf("#")+1; if ((start != 0) && (start != href.length)) return href.substring(start, href.length); } function redirect_url(dottedName) { // Scan through each element of the "pages" list, and check // if "name" matches with any of them. for (var i=0; i-m" or "-c"; // extract the portion & compare it to dottedName. var pagename = pages[i].substring(0, pages[i].length-2); if (pagename == dottedName.substring(0,pagename.length)) { // We've found a page that matches `dottedName`; // construct its URL, using leftover `dottedName` // content to form an anchor. var pagetype = pages[i].charAt(pages[i].length-1); var url = pagename + ((pagetype=="m")?"-module.html": "-class.html"); if (dottedName.length > pagename.length) url += "#" + dottedName.substring(pagename.length+1, dottedName.length); return url; } } } fabio-0.1.3/epydoc/fabio.kcdimage-module.html0000644000175000017500000002417112126623347021651 0ustar jeromejerome00000000000000 fabio.kcdimage
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        Package fabio :: Module kcdimage
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        Module kcdimage

        source code

        
Authors: Jerome Kieffer, ESRF 
         email:jerome.kieffer@esrf.fr

kcd images are 2D images written by the old KappaCCD diffractometer built by Nonius in the 1990's
Based on the edfimage.py parser.
        Classes [hide private]
          kcdimage
        Read the Nonius kcd data format
        Variables [hide private]
          logger = logging.getLogger("kcdimage")
          DATA_TYPES = {'u16': <type 'numpy.uint16'>}
          MINIMUM_KEYS = ['ByteOrder', 'Data type', 'X dimension', 'Y di...
          DEFAULT_VALUES = {'Data type': 'u16'}
          __package__ = 'fabio'
        Variables Details [hide private]

        MINIMUM_KEYS

        Value:
        ['ByteOrder',
 'Data type',
 'X dimension',
 'Y dimension',
 'Number of readouts']

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        fabio-0.1.3/epydoc/fabio.cbfimage-module.html0000644000175000017500000003111012126623347021631 0ustar jeromejerome00000000000000 fabio.cbfimage
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        Package fabio :: Module cbfimage
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        Module cbfimage

        source code

        
Authors: Jérôme Kieffer, ESRF
         email:jerome.kieffer@esrf.fr

Cif Binary Files images are 2D images written by the Pilatus detector and others.
They use a modified (simplified) byte-offset algorithm.

CIF is a library for manipulating Crystallographic information files and tries
to conform to the specification of the IUCR

        Author: J\xc3\xa9r\xc3\xb4me Kieffer

        Contact: jerome.kieffer@esrf.eu

        Copyright: European Synchrotron Radiation Facility, Grenoble, France

        License: GPLv3+

        Classes [hide private]
          cbfimage
        Read the Cif Binary File data format
          CIF
        This is the CIF class, it represents the CIF dictionary; and as a a python dictionary thus inherits from the dict built in class.
        Variables [hide private]
          logger = logging.getLogger("cbfimage")
          DATA_TYPES = {'signed 16-bit integer': <type 'numpy.int16'>, '...
          MINIMUM_KEYS = ['X-Binary-Size-Fastest-Dimension', 'ByteOrder'...
          STARTER = '\x0c\x1a\x04\xd5'
          PADDING = 512
          __package__ = 'fabio'
        Variables Details [hide private]

        DATA_TYPES

        Value:
        {'signed 16-bit integer': <type 'numpy.int16'>,
 'signed 32-bit integer': <type 'numpy.int32'>,
 'signed 64-bit integer': <type 'numpy.int64'>,
 'signed 8-bit integer': <type 'numpy.int8'>}

        MINIMUM_KEYS

        Value:
        ['X-Binary-Size-Fastest-Dimension',
 'ByteOrder',
 'Data type',
 'X dimension',
 'Y dimension',
 'Number of readouts']

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        fabio-0.1.3/epydoc/toc-fabio.HiPiCimage-module.html0000644000175000017500000000245712120434325022620 0ustar jeromejerome00000000000000 HiPiCimage

        Module HiPiCimage

        Classes

        HiPiCimage

        Variables

        __package__
        logger
        [hide private] fabio-0.1.3/epydoc/fabio.fabioutils.StringIO-class.html0000644000175000017500000002671212126623347023566 0ustar jeromejerome00000000000000 fabio.fabioutils.StringIO
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        Package fabio :: Module fabioutils :: Class StringIO
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        Class StringIO

        source code

        StringIO.StringIO --+
                    |
                   StringIO

        just an interface providing the name and mode property to a StringIO

        BugFix for MacOSX mainly

        Instance Methods [hide private]
         
        __init__(self, data, fname=None, mode='r') source code
         
        getSize(self) source code
         
        setSize(self, size) source code

        Inherited from StringIO.StringIO: __iter__, close, flush, getvalue, isatty, next, read, readline, readlines, seek, tell, truncate, write, writelines

        Properties [hide private]
          size
        Method Details [hide private]

        __init__(self, data, fname=None, mode='r')
        (Constructor)

        		source code 
        Overrides: StringIO.StringIO.__init__

        Property Details [hide private]

        size

        Get Method:
        getSize(self)
        Set Method:
        setSize(self, size)

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        fabio-0.1.3/epydoc/fabio.HiPiCimage-pysrc.html0000644000175000017500000015370012126623347021720 0ustar jeromejerome00000000000000 fabio.HiPiCimage
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        Package fabio :: Module HiPiCimage
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        Source Code for Module fabio.HiPiCimage

          1   
  2  #!/usr/bin/env python 
  3  """ 
  4  Authors: Henning O. Sorensen & Erik Knudsen 
  5           Center for Fundamental Research: Metal Structures in Four Dimensions 
  6           Risoe National Laboratory 
  7           Frederiksborgvej 399 
  8           DK-4000 Roskilde 
  9           email:erik.knudsen@risoe.dk 
 10   
 11          + Jon Wright, ESRF 
 12   
 13  Information about the file format from Masakatzu Kobayashi is highly appreciated 
 14  """ 
 15   
 16  import numpy, logging 
 17  logger = logging.getLogger("HiPiCimage") 
 18  from fabioimage import fabioimage 
 19   

         20 -class HiPiCimage(fabioimage): 

         21      """ Read HiPic images e.g. collected with a Hamamatsu CCD camera""" 
 22   
 23   

         24 -    def _readheader(self, infile): 

         25          """ 
 26          Read in a header from an already open file 
 27   
 28          """ 
 29          Image_tag = infile.read(2) 
 30          print Image_tag 
 31          Comment_len = numpy.fromstring(infile.read(2), numpy.uint16) 
 32          Dim_1 = numpy.fromstring(infile.read(2), numpy.uint16)[0] 
 33          Dim_2 = numpy.fromstring(infile.read(2), numpy.uint16)[0] 
 34          Dim_1_offset = numpy.fromstring(infile.read(2), numpy.uint16)[0] 
 35          Dim_2_offset = numpy.fromstring(infile.read(2), numpy.uint16)[0] 
 36          HeaderType = numpy.fromstring(infile.read(2), numpy.uint16)[0] 
 37          Dump = infile.read(50) 
 38          Comment = infile.read(Comment_len) 
 39          self.header['Image_tag'] = Image_tag 
 40          self.header['Dim_1'] = Dim_1 
 41          self.header['Dim_2'] = Dim_2 
 42          self.header['Dim_1_offset'] = Dim_1_offset 
 43          self.header['Dim_2_offset'] = Dim_2_offset 
 44          #self.header['Comment'] = Comment 
 45          if Image_tag != 'IM' : 
 46              # This does not look like an HiPic file 
 47              logging.warning("no opening.  Corrupt header of HiPic file " + \ 
 48                              str(infile.name)) 
 49          Comment_split = Comment[:Comment.find('\x00')].split('\r\n') 
 50   
 51          for topcomment in Comment_split: 
 52              topsplit = topcomment.split(',') 
 53              for line in topsplit: 
 54                  if '=' in line: 
 55                      key, val = line.split('=' , 1) 
 56                      # Users cannot type in significant whitespace 
 57                      key = key.rstrip().lstrip() 
 58                      self.header_keys.append(key) 
 59                      self.header[key] = val.lstrip().rstrip() 
 60                      self.header[key] = val.lstrip('"').rstrip('"') 

         61   

         62 -    def read(self, fname, frame=None): 

         63          """ 
 64          Read in header into self.header and 
 65              the data   into self.data 
 66          """ 
 67          self.header = {} 
 68          self.resetvals() 
 69          infile = self._open(fname, "rb") 
 70          self._readheader(infile) 
 71          # Compute image size 
 72          try: 
 73              self.dim1 = int(self.header['Dim_1']) 
 74              self.dim2 = int(self.header['Dim_2']) 
 75          except: 
 76              raise Exception("HiPic file", str(fname) + \ 
 77                                  "is corrupt, cannot read it") 
 78          bytecode = numpy.uint16 
 79          self.bpp = len(numpy.array(0, bytecode).tostring()) 
 80   
 81          # Read image data 
 82          block = infile.read(self.dim1 * self.dim2 * self.bpp) 
 83          infile.close() 
 84   
 85          #now read the data into the array 
 86          try: 
 87              self.data = numpy.reshape( 
 88                  numpy.fromstring(block, bytecode), 
 89                  [self.dim2, self.dim1]) 
 90          except: 
 91              print len(block), bytecode, self.bpp, self.dim2, self.dim1 
 92              raise IOError, \ 
 93                'Size spec in HiPic-header does not match size of image data field' 
 94          self.bytecode = self.data.dtype.type 
 95   
 96          # Sometimes these files are not saved as 12 bit, 
 97          # But as 16 bit after bg subtraction - which results  
 98          # negative values saved as 16bit. Therefore values higher  
 99          # 4095 is really negative values 
100          if self.data.max() > 4095: 
101              gt12bit = self.data > 4095 
102              self.data = self.data - gt12bit * (2 ** 16 - 1) 
103   
104          # ensure the PIL image is reset 
105          self.pilimage = None 
106          return self 

        107

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        fabio-0.1.3/epydoc/fabio.edfimage.Frame-class.html0000644000175000017500000005042312126623347022516 0ustar jeromejerome00000000000000 fabio.edfimage.Frame
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        Package fabio :: Module edfimage :: Class Frame
        [hide private]
        [frames] | no frames]

        Class Frame

        source code

        object --+
         |
        Frame

        A class representing a single frame in an EDF file

        Instance Methods [hide private]
         
        __init__(self, data=None, header=None, header_keys=None, number=None)
        x.__init__(...) initializes x; see x.__class__.__doc__ for signature        		 source code
         
        parseheader(self, block)
        Parse the header in some EDF format from an already open file        		 source code
         
        swap_needed(self)
        Decide if we need to byteswap        		 source code
         
        getData(self)
        Unpack a binary blob according to the specification given in the header        		 source code
         
        setData(self, npa=None)
        Setter for data in edf frame        		 source code
         
        getByteCode(self) source code
         
        setByteCode(self, _iVal) source code
        python string with the concatenation of the ascii header and the binary data block
        getEdfBlock(self, force_type=None, fit2dMode=False)
        Returns: ascii header block        		 source code

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Properties [hide private]
          data
        Unpack a binary blob according to the specification given in the header
          bytecode

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, data=None, header=None, header_keys=None, number=None)
        (Constructor)

        		source code 

        x.__init__(...) initializes x; see x.__class__.__doc__ for signature

        Overrides: object.__init__
        (inherited documentation)

        parseheader(self, block)

        		source code 

        Parse the header in some EDF format from an already open file

        Parameters:
        • block (string, should be full ascii) - string representing the header block
        Returns:
        size of the binary blob

        getData(self)

        		source code 

        Unpack a binary blob according to the specification given in the header

        Returns:
        dataset as numpy.ndarray

        getEdfBlock(self, force_type=None, fit2dMode=False)

        		source code 
        Parameters:
        • force_type (string or numpy.dtype) - type of the dataset to be enforced like "float64" or "uint16"
        • fit2dMode (boolean) - enforce compatibility with fit2d and starts countimg number of images at 1
        Returns: python string with the concatenation of the ascii header and the binary data block
        ascii header block

        Property Details [hide private]

        data

        Unpack a binary blob according to the specification given in the header

        Get Method:
        getData(self) - Unpack a binary blob according to the specification given in the header
        Set Method:
        setData(self, npa=None) - Setter for data in edf frame
        Delete Method:
        'property: (edf)frame.data, uncompress the datablock when needed'

        bytecode

        Get Method:
        getByteCode(self)
        Set Method:
        setByteCode(self, _iVal)

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        Generated by Epydoc 3.0.1 on Tue Apr 2 13:31:40 2013 http://epydoc.sourceforge.net
        fabio-0.1.3/epydoc/fabio.mar345image.mar345image-class.html0000644000175000017500000005730512126623347023765 0ustar jeromejerome00000000000000 fabio.mar345image.mar345image
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        Package fabio :: Module mar345image :: Class mar345image
        [hide private]
        [frames] | no frames]

        Class mar345image

        source code

                   object --+    
                    |    
fabioimage.fabioimage --+
                        |
                       mar345image
        Instance Methods [hide private]
         
        __init__(self, *args, **kwargs)
        Set up initial values        		 source code
         
        read(self, fname, frame=None)
        Read a mar345 image        		 source code
         
        _readheader(self, infile=None)
        Read a mar345 image header        		 source code
         
        write(self, fname)
        Try to write mar345 file.        		 source code
         
        _writeheader(self, linesep='\n', size=4096) source code
         
        _high_intensity_pixel_records(self) source code
         
        nb_overflow_pixels(self) source code

        Inherited from fabioimage.fabioimage: add, convert, getclassname, getframe, getheader, getmax, getmean, getmin, getstddev, integrate_area, load, make_slice, next, previous, readROI, readheader, rebin, resetvals, save, toPIL16, update_header

        Inherited from fabioimage.fabioimage (private): _compressed_stream, _open

        Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

        Static Methods [hide private]
         
        checkData(data=None)
        Empty for fabioimage but may be populated by others classes, especially for format accepting only integers        		 source code

        Inherited from fabioimage.fabioimage: checkHeader

        Class Variables [hide private]
          _need_a_real_file = True

        Inherited from fabioimage.fabioimage (private): _need_a_seek_to_read

        Properties [hide private]

        Inherited from fabioimage.fabioimage: classname

        Inherited from object: __class__

        Method Details [hide private]

        __init__(self, *args, **kwargs)
        (Constructor)

        		source code 

        Set up initial values

        Overrides: object.__init__
        (inherited documentation)

        read(self, fname, frame=None)

        		source code 

        Read a mar345 image

        Overrides: fabioimage.fabioimage.read

        _readheader(self, infile=None)

        		source code 

        Read a mar345 image header

        Overrides: fabioimage.fabioimage._readheader

        write(self, fname)

        		source code 

        Try to write mar345 file. This is still in beta version. It uses CCP4 (LGPL) PCK1 algo from JPA

        Overrides: fabioimage.fabioimage.write

        _writeheader(self, linesep='\n', size=4096)

        		source code 
        Parameters:
        • linesep - end of line separator @return string/bytes containing the mar345 header

        checkData(data=None)
        Static Method

        		source code 

        Empty for fabioimage but may be populated by others classes, especially for format accepting only integers

        Overrides: fabioimage.fabioimage.checkData
        (inherited documentation)

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