debian/ 0000755 0000000 0000000 00000000000 12252540724 007171 5 ustar debian/gofigure2.desktop 0000644 0000000 0000000 00000000474 12147712515 012464 0 ustar [Desktop Entry]
Type=Application
Terminal=false
Version=0.9.0
Name=GoFigure2
GenericName=Data Viewer
Comment=Visualization and Analysis of 3D+t bio-images
TryExec=gofigure
Exec=gofigure &
Categories=Education;Science;DataVisualization;ImageProcessing;MedicalSoftware
Icon=gofigure2
MimeType=application/x-gofigure2;
debian/rules 0000755 0000000 0000000 00000004017 12252336441 010252 0 ustar #!/usr/bin/make -f
#export DH_VERBOSE=1
export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
# deduce documentation option (build-indep target)
ifeq "" "$(filter %-doc,$(shell dh_listpackages))"
BUILDDOC=OFF
else
BUILDDOC=ON
endif
CMAKE_EXTRA_FLAGS = \
-DCMAKE_INSTALL_PREFIX:PATH=/usr \
-DCMAKE_BUILD_TYPE:STRING=None \
-DCMAKE_SKIP_RPATH:BOOL=OFF \
-DBUILD_SHARED_LIBS:BOOL=ON \
-DGOFIGURE2_INSTALL_LIB_DIR:STRING=lib/$(DEB_HOST_MULTIARCH) \
-DBUILD_TESTING:BOOL=ON \
-DBUILD_DOCUMENTATION:BOOL=$(BUILDDOC) \
-DBUILD_PLUGINS:BOOL=ON \
-DENABLE_VIDEO_RECORD_FFMPEG:BOOL=ON \
-DBUILD_COMPARETOOL:BOOL=ON \
-DSUPERBUILD:BOOL=OFF \
-DLINK_EXTERNAL_DOC:BOOL=ON \
-DDOXYGEN_NIGHTLY_LINK:BOOL=OFF \
-DQT_DOC_DIR=/usr/share/qt4/doc/
%:
dh $@ --parallel --builddirectory=build
override_dh_auto_configure:
dh_auto_configure -- $(CMAKE_EXTRA_FLAGS)
# Let's be smart with building doc
override_dh_auto_build-indep:
$(MAKE) -C build doc
rm build/Documentation/html/jquery.js
# No tests needed for docs
override_dh_auto_test-indep:
override_dh_install-arch:
dh_install --list-missing
pkg_doc=gofigure2-doc
override_dh_installdocs:
dh_installdocs -p$(pkg_doc) build/Documentation/html
dh_installdocs
debian/gofigure.1: debian/gofigure.1.in
help2man --include=debian/gofigure.1.in \
--output=debian/gofigure.1 --no-info gofigure
VER_FULL = $(shell dpkg-parsechangelog | grep '^Version' | cut -d' ' -f2 | cut -f1 -d-)
UPSTREAM_SRC = GoFigure2-v$(VER_FULL).tar.gz
DEBIAN_SRC_DIR = GoFigure2-v$(VER_FULL)
DEBIAN_SRC_TAR = gofigure2_$(VER_FULL).orig.tar.gz
$(UPSTREAM_SRC):
wget http://voxel.dl.sourceforge.net/sourceforge/gofigure2/$@
get-orig-source: $(UPSTREAM_SRC)
#uscan --verbose --force-download --repack --rename
tar xzf $(UPSTREAM_SRC)
# save some disk space, removing test data:
rm -rf $(DEBIAN_SRC_DIR)/Testing/Data
rm -rf $(DEBIAN_SRC_DIR)/Testing/Sikuli
GZIP="--best --no-name" tar czf $(DEBIAN_SRC_TAR) $(DEBIAN_SRC_DIR)
rm -rf $(DEBIAN_SRC_DIR)
debian/gofigure2.xml 0000644 0000000 0000000 00000000512 11411253400 011566 0 ustar
GoFigure2 Document
GoFigure2 Document
debian/libgofigure0.lintian-overrides 0000644 0000000 0000000 00000000250 11745031114 015116 0 ustar libgofigure0: package-name-doesnt-match-sonames libPoissonReconstruction0.9 libQGoGui0.9 libQGoIO0.9 libctk0.9 libitkQt0.9 libvtkLSMReader0.9 libvtkRenderingAddOn2-0.9
debian/gofigure2.install 0000644 0000000 0000000 00000000501 12147712515 012450 0 ustar debian/gofigure.1 usr/share/man/man1
debian/gofigure2.xpm usr/share/pixmaps
debian/gofigure2.xml usr/share/mime/packages
debian/gofigure2.desktop usr/share/applications
usr/bin/gofigure
usr/share/doc/gofigure2/Licenses/
usr/share/gofigure2/icons/
usr/share/doc/gofigure2/Resources/BugEntry.txt
#usr/bin/GoFigure2.desktop
debian/libgofigure-dev.install 0000644 0000000 0000000 00000000204 12147712515 013631 0 ustar usr/lib/*/lib*.so
usr/include/gofigure2/*.h
usr/include/gofigure2/*.txx
usr/include/gofigure2/*.inl
usr/lib/*/GoFigure2Config.cmake
debian/watch 0000644 0000000 0000000 00000000100 11536177413 010216 0 ustar version=3
http://sf.net/gofigure2/GoFigure2-v([\d\.]+)\.tar\.gz
debian/gofigure.1 0000644 0000000 0000000 00000001747 12147707032 011073 0 ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
.TH GOFIGURE "1" "December 2011" "gofigure GoFigure2-v0.9.0" "User Commands"
.SH NAME
gofigure \- Tool for visualizing, processing and analysing of bioimages
.SH SYNOPSIS
.B gofigure
.RI [ options ] " files" ...
.SH DESCRIPTION
The prime goal of GoFigure2 is the automatic segmentation of nuclei and cell
membranes and in temporally tracking them amidst cell division to create
lineages.
.SS "Usage:"
.IP
gofigure [options]:
.SS "Generic Options:"
.TP
\fB\-h\fR [ \fB\-\-help\fR ]
Display this information
.TP
\fB\-v\fR [ \fB\-\-version\fR ]
Display GoFigure2 version information
.TP
\fB\-\-shortcuts\fR
Display all shortcuts
.SS "Configuration:"
.TP
\fB\-i\fR [ \fB\-\-input\fR ] arg
input file (single file)
.TP
\fB\-\-max\-meshes\fR arg
Maximum number of meshes to load in memory (default
5000)
.SH AUTHORS
This manual page was written by Mathieu Malaterre ,
for the Debian project (and may be used by others).
debian/changelog 0000644 0000000 0000000 00000004300 12252541166 011041 0 ustar gofigure2 (0.9.0-3) unstable; urgency=low
* Set CMAKE_BUILD_TYPE to None
* Bump Std-Vers to 3.9.5, no changes needed
-- Mathieu Malaterre Fri, 13 Dec 2013 09:13:41 +0100
gofigure2 (0.9.0-2) unstable; urgency=low
* Remove explicit B-D to libgdcm since not needed anymore
* Remove DMUA flag, use my @d.o alias
* Bump Std-Vers to 3.9.4, no changes needed
* Fix building against newer VTK:
- debian/patches/missingx11link.patch
* Use hardening flags thanks to dh/9
* Fix lintian about d/copyright empty lines
* Add a gofigure2-doc package for documentation
-- Mathieu Malaterre Fri, 24 May 2013 16:31:50 +0200
gofigure2 (0.9.0-1) unstable; urgency=low
* New upstream
- Many actions are parallelized with Open MP
-- Mathieu Malaterre Sun, 11 Dec 2011 16:38:51 +0100
gofigure2 (0.8.4-1) unstable; urgency=low
* New upstream
* Update gofigure2.desktop (upstream)
* Fix Vcs-Browser URL
* Remove all patches
-- Mathieu Malaterre Thu, 10 Nov 2011 21:03:37 +0100
gofigure2 (0.8.2-1) unstable; urgency=low
[ Andreas Tille ]
* New upstream version
debian/patches/qreal_getrgb.patch: removed because applied upstream
debian/patches/apple_bundle_fix.patch: adapted to new version
* debian/control:
- Added myself to Uploaders
- Standards-Version: 3.9.2 (no changes needed)
- Build-Depends: libfftw3-dev which is needed in new version
* Debhelper 8 (control+compat)
* Remove wrongly placed file libgofigure0.lintian-overrides
* debian/rules: --parallel option needs to be added in the end
[ Mathieu Malaterre ]
* Change get-orig-source target to remove testing data
* Add suggests on mysql-server. Closes: #634921
-- Mathieu Malaterre Mon, 29 Aug 2011 15:20:21 +0200
gofigure2 (0.8.1-2) unstable; urgency=low
* Fix armel compilation
* Add missing license files in help
-- Mathieu Malaterre Mon, 18 Apr 2011 21:08:58 +0200
gofigure2 (0.8.1-1) unstable; urgency=low
* Initial release (Closes: #587051)
-- Mathieu Malaterre Thu, 10 Mar 2011 17:28:10 +0100
debian/README.Debian 0000644 0000000 0000000 00000000357 12252336441 011236 0 ustar GoFigure2 for Debian
-------------------
As of release 0.8.2 GoFigure2 requires that mysql be installed locally. See bug #634921
http://bugs.debian.org/634921#17
-- Mathieu Malaterre Mon, 29 Aug 2011 15:19:23 +0200
debian/control 0000644 0000000 0000000 00000006274 12252541166 010606 0 ustar Source: gofigure2
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team
Uploaders: Mathieu Malaterre ,
Andreas Tille
Build-Depends: debhelper (>= 9), cmake (>= 2.8.2), libboost-all-dev, libqt4-dev,
libinsighttoolkit3-dev (>= 3.20), libvtk5-qt4-dev (>= 5.6), libfftw3-dev,
libqtwebkit-dev | libqt4-dev (<< 4.7)
Build-Depends-Indep: qt4-doc-html, doxygen (>= 1.7.4) , graphviz, vtk-doc
Standards-Version: 3.9.5
Homepage: http://gofigure2.sourceforge.net
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/gofigure2/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/gofigure2/trunk/
Package: gofigure2
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
Suggests: mysql-server
Description: Tool for visualizing, processing and analysing of bioimages
Main objectives of GoFigure2 are to provide
* interaction/visualization/navigation into 4D multichannels bio-images;
* save/retrieve information related to the imaging process, analysis results;
* extracting objects from bio-images (e.g. nucleii, cell-membranes...);
* tracking sub-cellular structure, cells;
* detecting and tracking cell-division through time;
* generating and visualizing cell-lineage.
Package: libgofigure0
Section: libs
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
Pre-Depends: ${misc:Pre-Depends}
Description: Tool for visualizing, processing and analysing of bioimages
Main objectives of GoFigure2 are to provide
* interaction/visualization/navigation into 4D multichannels bio-images;
* save/retrieve information related to the imaging process, analysis results;
* extracting objects from bio-images (e.g. nucleii, cell-membranes...);
* tracking sub-cellular structure, cells;
* detecting and tracking cell-division through time;
* generating and visualizing cell-lineage.
.
The runtime libraries
Package: libgofigure-dev
Section: libdevel
Architecture: any
Depends: libgofigure0 (= ${binary:Version}), ${misc:Depends}
Description: Tool for visualizing, processing and analysing of bioimages
Main objectives of GoFigure2 are to provide
* interaction/visualization/navigation into 4D multichannels bio-images;
* save/retrieve information related to the imaging process, analysis results;
* extracting objects from bio-images (e.g. nucleii, cell-membranes...);
* tracking sub-cellular structure, cells;
* detecting and tracking cell-division through time;
* generating and visualizing cell-lineage.
.
The development libraries
Package: gofigure2-doc
Architecture: all
Section: doc
Depends: ${misc:Depends}, vtk-doc, doc-base
Description: Tool for visualizing, processing and analysing of bioimages - doc
Main objectives of GoFigure2 are to provide
* interaction/visualization/navigation into 4D multichannels bio-images;
* save/retrieve information related to the imaging process, analysis results;
* extracting objects from bio-images (e.g. nucleii, cell-membranes...);
* tracking sub-cellular structure, cells;
* detecting and tracking cell-division through time;
* generating and visualizing cell-lineage.
.
This is the documentation for gofigure2
debian/gofigure2.xpm 0000644 0000000 0000000 00000002564 11540342732 011615 0 ustar /* XPM */
static char *gofigure2[] = {
/* columns rows colors chars-per-pixel */
"32 32 9 1",
" c #800000",
". c #008000",
"X c #808000",
"o c #0000FF",
"O c #FF00FF",
"+ c #00FFFF",
"@ c #808080",
"# c #C0C0C0",
"$ c #FFFFFF",
/* pixels */
" $$$$$$$$$$$$$$$$$$$$$$$$",
" $$$$$$$ $$$$$$$$$",
" @@@###$$$$$#@ $$$$$$$$$",
" $$$$$$$$$#X......XX.X#$$$$$$$$",
" $ $$@XXX.. XX@..X.@$$$$$$$",
" $ $@XXXX$ X$$$$$$.O$$$$$$",
" $ @@@ #XXXX.$ XX $$$$@$$$$$$",
" $$$$$ @XXX.$XXX $$$$$#$$$$$",
" ##@@@ #X.@ XX @@@@$$$$$.+$$$$",
" $#.$X $ $$$$$$$$..#$$$$",
" $$$XX$$ $ $$$.@$$$$",
"$$$$$$$$$$oX $$ $ $$$..$$$$",
"$$$$$$$$$$O. $$ $$$$ $$$..$$$$",
"$$$$$$$$$.o.$$$$$$ $$$$..$$$$",
"$$$$$$$$$$..$$$$$$ $$$$$$.X$$$$",
"$$$$$$$$$$.#.$$.$$ $$$XX$$$$",
"$$$$$$$$$$$.@$$$$$ $..X@$$$$",
"$$$$$$$$$$$$...$$$$.$$$$$XX$$$$$",
"$$$$$$$$$$$$$$$#....$$$$.XXO$$$$",
"$$$$$$$$$$$$$$.$..#.$$$$.X@$$$$$",
"$$$$$$$$$$$$$$$$$$..$$$.XX#$$$$$",
"$$$$$$$$$$$$$$$$$$#.$$$.XX$$$$$$",
"$$$$$$$$$$$$$$$$$..$$$$XX@$$$$$$",
"$$$$$$$$$$$$$$$$$@$$$$.XX#$$$$$$",
"$$$$$$$$$$$$$$$.#.$$$$XXX$$$$$$$",
"$$$$$$$$$$$$$$$O.$$$$.XX$$$$$$$$",
"$$$$$$$$$$$$$$.@$$$$.XX@$$$$$$$$",
"$$$$$$$$o$$$$ @$$$$$XXXO$$$$$$$$",
"$$$$$$$@.@##@.$.$$$XXXo$$$$$$$$$",
"$$$$$$$#X..$$$$$$.XXX$$$$$$$$$$$",
"$$$$$$$$#..........@o$$$$$$$$$$$",
"$$$$$$$$$$@X...XX@O$$$$$$$$$$$$$"
};
debian/gofigure2.manpages 0000644 0000000 0000000 00000000022 12147712515 012573 0 ustar debian/gofigure.1
debian/get-orig-source 0000755 0000000 0000000 00000001150 11570214572 012130 0 ustar #!/bin/sh
set -ex
PACKAGE=gofigure2
VERSION=${VERSION:-$2}
TARFILE=${TARFILE:-$3}
if [ -z ${VERSION}]; then
VERSION=`dpkg-parsechangelog | sed -n -e 's/^Version: \(.*\)-[^-]*$/\1/p'`
fi
REVISION=`echo $VERSION | sed -e 's/^.*svn//g'`
FOLDER=${PACKAGE}-${VERSION}
if [ -z ${TARFILE}]; then
TARFILE=${PACKAGE}_${VERSION}.orig.tar.gz
fi
svn export --quiet https://gofigure2.svn.sourceforge.net/svnroot/gofigure2/tags/GoFigure2-v${VERSION} ${FOLDER}
GZIP="--best --no-name" tar czf ${TARFILE} ${FOLDER}
rm -rf ${FOLDER}
# curl -L https://github.com/gofigure2/GoFigure2/tarball/master -o gofigure2-master.tar.gz
debian/libgofigure0.install 0000644 0000000 0000000 00000000024 12147712515 013135 0 ustar usr/lib/*/lib*.so.*
debian/copyright 0000644 0000000 0000000 00000026172 12147707032 011134 0 ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: gofigure2
Source: http://gofigure2.sourceforge.net/
Files: *
Copyright: © 2009-10, President and Fellows of Harvard College.
License: BSD
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
.
Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
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.
Neither the name of the President and Fellows of Harvard College
nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written
permission.
.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"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 COPYRIGHT OWNER OR CONTRIBUTORS
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.
Files: Resources/fig/system-quit.png
Resources/fig/UseDatabase.png
Resources/fig/EyeIcon.png
Copyright: © Crystal Project
Source: http://everaldo.com/crystal/
License: LGPL-2.1
Files: Resources/fig/ContourEditing.png
Resources/fig/manual-editing.png
Resources/fig/MeshEditing.png
Resources/fig/document-open.png
Resources/fig/zoom.png
Copyright: © Nuvola
Source: http://www.icon-king.com/projects/nuvola/
License: LGPL-2.1
Files: Resources/fig/video.png
Copyright: © Oxygen Project (http://www.oxygen-icons.org/)
Source: http://www.icon-king.com/projects/oxygen/
License: LGPL-2.1
Files: Code/ExternalCode/MegaVTK/vtkItk/*
Code/ExternalCode/itkQt/*
Code/Filters/itk*
Copyright: © Insight Software Consortium. All rights reserved.
License: BSD
Copyright (c) 1999-2008 Insight Software Consortium
All rights reserved.
.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
.
* Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
.
* 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.
.
* The name of the Insight Software Consortium, or the names of any
consortium members, or of any contributors, may not be used to endorse or
promote products derived from this software without specific prior written
permission.
.
* Modified source versions must be plainly marked as such, and must not be
misrepresented as being the original software.
.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS ``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 AUTHORS OR CONTRIBUTORS 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.
Files: Code/ExternalCode/MegaVTK/vtkRenderingAddOn/*
Copyright: © 2006-2010 INRIA - ASCLEPIOS Project (http://www-sop.inria.fr/asclepios).
Source: http://www-sop.inria.fr/asclepios/software/vtkINRIA3D/
License: BSD
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
.
* Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
.
* 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.
.
* Neither the name of INRIA or ASCLEPIOS, nor the names of any contributors
may be used to endorse or promote products derived from this software
without specific prior written permission.
.
* Modified source versions must be plainly marked as such, and must not be
misrepresented as being the original software.
.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS ``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 AUTHORS OR CONTRIBUTORS 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.
Files: Code/ExternalCode/PoissonReconstruction/*
Copyright: © 2006-10, Michael Kazhdan and Matthew Bolitho, Johns Hopkins University.
License: BSD
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
.
Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
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.
Neither the name of the Johns Hopkins University nor the names of its
contributors may be used to endorse or promote products derived from this
software without specific prior written permission.
.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"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 COPYRIGHT OWNER OR CONTRIBUTORS
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.
.
This code has been modified and wrapped to VTK.
Here is the corresponding license:
.
Authors: David Doria at Rensselaer Polytechnic Institute and
Arnaud Gelas at Harvard Medical School
.
Copyright (c) 2010, David Doria at Rensselaer Polytechnic Institute and
Arnaud Gelas at Harvard Medical School,
All rights reserved.
.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
.
Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
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.
Neither the name of the Rensselaer Polytechnic Institute and of Harvard
Medical School nor the names of its contributors may be used to endorse
or promote products derived from this software without specific prior
written permission.
.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"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 COPYRIGHT OWNER OR CONTRIBUTORS
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.
Files: Code/ExternalCode/vtkLSM/*
Copyright: © 2004-2008 BioImageXD Development Team
License: BSD
All rights reserved.
.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
.
* Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
.
* 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.
.
* Modified source versions must be plainly marked as such, and must not be
misrepresented as being the original software.
.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``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 AUTHORS OR CONTRIBUTORS 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.
Files: Code/ExternalCode/ctk/*
Copyright: © Kitware Inc.
License: Apache 2.0
Files: debian/*
Copyright: 2011-2012; Mathieu Malaterre
License: Apache 2.0
License: Apache 2.0
On Debian GNU/Linux system you can find the complete text of the
Apache 2.0 license in '/usr/share/common-licenses/Apache-2.0'.
License: LGPL-2.1
On Debian GNU/Linux system you can find the complete text of the
LGPL license in '/usr/share/common-licenses/LGPL-2.1'.
debian/gofigure2-doc.doc-base 0000644 0000000 0000000 00000000715 12147712515 013231 0 ustar Document: gofigure2-doc
Title: gofigure2 doc
Author: gofigure2 team
Abstract: GoFigure2 is an open-source, cross-platform application for visualizing,
processing and analyzing of multidimensional microscopy data.
Users can visualize, segment and track cells through time, detect cell-division
and ultimately generate lineages.
Section: Programming
Format: HTML
Index: /usr/share/doc/gofigure2-doc/html/index.html
Files: /usr/share/doc/gofigure2-doc/html/*
debian/gofigure.1.in 0000644 0000000 0000000 00000000670 12147707032 011472 0 ustar [NAME]
gofigure \- Tool for visualizing, processing and analysing of bioimages
[SYNOPSIS]
.B gofigure
.RI [ options ] " files" ...
[DESCRIPTION]
The prime goal of GoFigure2 is the automatic segmentation of nuclei and cell
membranes and in temporally tracking them amidst cell division to create
lineages.
[AUTHORS]
This manual page was written by Mathieu Malaterre ,
for the Debian project (and may be used by others).
debian/source/ 0000755 0000000 0000000 00000000000 12252540724 010471 5 ustar debian/source/format 0000644 0000000 0000000 00000000014 11411116725 011673 0 ustar 3.0 (quilt)
debian/docs 0000644 0000000 0000000 00000000013 11671147127 010042 0 ustar ReadMe.rst
debian/compat 0000644 0000000 0000000 00000000002 12147707032 010367 0 ustar 9
debian/patches/ 0000755 0000000 0000000 00000000000 12252540724 010620 5 ustar debian/patches/dotsvgoutput.patch 0000644 0000000 0000000 00000001223 12147712515 014430 0 ustar Index: gofigure2-0.9.0/Documentation/Doxygen/Doxyfile.txt.in
===================================================================
--- gofigure2-0.9.0.orig/Documentation/Doxygen/Doxyfile.txt.in 2011-12-07 21:48:18.000000000 +0000
+++ gofigure2-0.9.0/Documentation/Doxygen/Doxyfile.txt.in 2013-05-24 15:53:04.290636756 +0000
@@ -1642,7 +1642,7 @@
# generated by dot. Possible values are png, jpg, or gif
# If left blank png will be used.
-DOT_IMAGE_FORMAT = png
+DOT_IMAGE_FORMAT = svg
# The tag DOT_PATH can be used to specify the path where the dot tool can be
# found. If left blank, it is assumed the dot tool can be found in the path.
debian/patches/missingx11link.patch 0000644 0000000 0000000 00000001007 11745031114 014512 0 ustar Description: libQVTK is missing link to X libs
Author: Mathieu Malaterre
Forwarded: not-needed
Last-Update: 2012-04-22
--- gofigure2-0.9.0.orig/Main/CMakeLists.txt
+++ gofigure2-0.9.0/Main/CMakeLists.txt
@@ -146,6 +146,7 @@ ENDIF( WIN32 )
# --------
# gofigure
+find_package(X11 REQUIRED)
ADD_EXECUTABLE( gofigure
MACOSX_BUNDLE
${GOFIGURE_MAIN}
@@ -161,6 +162,7 @@ TARGET_LINK_LIBRARIES( gofigure
QGoIO
itkQt
${Boost_LIBRARIES}
+ ${X11_LIBRARIES}
)
IF( BUILD_COMPARETOOL )
debian/patches/removedocfromall.patch 0000644 0000000 0000000 00000001215 12147707032 015200 0 ustar Description: remove doc from target all
Author: Mathieu Malaterre
Forwarded: not-needed
Index: gofigure2-0.9.0/Documentation/Doxygen/CMakeLists.txt
===================================================================
--- gofigure2-0.9.0.orig/Documentation/Doxygen/CMakeLists.txt 2011-12-07 21:48:18.000000000 +0000
+++ gofigure2-0.9.0/Documentation/Doxygen/CMakeLists.txt 2013-05-24 14:46:28.806681743 +0000
@@ -77,7 +77,7 @@
${GOFIGURE2_BINARY_DIR}/Doxyfile.txt
)
-ADD_CUSTOM_TARGET(doc ALL
+ADD_CUSTOM_TARGET(doc
${DOXYGEN_EXECUTABLE} ${GOFIGURE2_BINARY_DIR}/Doxyfile.txt
DEPENDS ${GOFIGURE2_BINARY_DIR}/Doxyfile.txt
)
debian/patches/fiximagecomp.patch 0000644 0000000 0000000 00000001210 12147707032 014303 0 ustar Description: fix compilation
Author: Mathieu Malaterre
Forwarded: no
--- gofigure2-0.9.0.orig/Main/CMakeLists.txt
+++ gofigure2-0.9.0/Main/CMakeLists.txt
@@ -31,11 +31,13 @@ IF( BUILD_COMPARETOOL )
SET( GOFIGURE_APPLICATION_SOURCE_LIST
${GOFIGURE_APPLICATION_SOURCE_LIST}
- ${QGoSynchronizedViewMainWindow.cxx}
+ QGoSynchronizedViewMainWindow.cxx
)
ENDIF( BUILD_COMPARETOOL )
-INCLUDE_DIRECTORIES( ${GOFIGURE2_BINARY_DIR}/Main/ )
+INCLUDE_DIRECTORIES( ${GOFIGURE2_BINARY_DIR}/Main/
+ ${GOFIGURE2_SOURCE_DIR}/Code/GUI/lib/SynchronizedViews/
+)
QT4_WRAP_UI( QGoMainWindow_UI_H ${QGoMainWindow_UI} )
debian/patches/series 0000644 0000000 0000000 00000000122 12147707032 012030 0 ustar missingx11link.patch
removedocfromall.patch
fiximagecomp.patch
dotsvgoutput.patch