debian/0000755000000000000000000000000011750756403007176 5ustar debian/rules0000755000000000000000000000251211561272632010253 0ustar #!/usr/bin/make -f # -*- makefile -*- srcpkg = $(shell LC_ALL=C dpkg-parsechangelog | grep '^Source:' | cut -d ' ' -f 2,2) upstreamver = $(shell LC_ALL=C dpkg-parsechangelog | grep '^Version:' | cut -d ' ' -f 2,2 | cut -d '-' -f 1,1) export LDFLAGS = -Wl,--as-needed # one ring to rule them all ... %: dh $@ override_dh_auto_configure: dh_auto_configure -- -DSNAP_USE_FLTK_1_1:BOOL=ON override_dh_auto_install: dh_auto_install # move data files to /usr/share mv $(CURDIR)/debian/itksnap/usr/lib/snap*/ProgramData \ $(CURDIR)/debian/itksnap/usr/share/itksnap/ # get rid of application "forwarder" mv $(CURDIR)/debian/itksnap/usr/lib/snap*/InsightSNAP \ $(CURDIR)/debian/itksnap/usr/bin/itksnap # remove left-overs rm -r $(CURDIR)/debian/itksnap/usr/lib # use one of the pix as an icon convert $(CURDIR)/ProgramData/Images2D/EdgeForcesExample.png -resize 32x32 \ $(CURDIR)/debian/itksnap/usr/share/pixmaps/itksnap.xpm # strip useless CMakeLists find $(CURDIR)/debian/itksnap/usr -name 'CMakeLists.txt' -delete get-orig-source: # orig tarball, turn directory into something nicer touch $(srcpkg)_$(upstreamver).orig.tar.gz tar --exclude='.git*' --exclude=debian --exclude=.pc \ --exclude=$(srcpkg)_$(upstreamver).orig.tar.gz \ --transform 's,^,$(srcpkg)-$(upstreamver)/,' \ -cvzf $(srcpkg)_$(upstreamver).orig.tar.gz . debian/itksnap.manpages0000644000000000000000000000002111561272632012352 0ustar debian/itksnap.1 debian/control0000644000000000000000000000252611561273175010606 0ustar Source: itksnap Priority: extra Maintainer: NeuroDebian Team Uploaders: Michael Hanke , Yaroslav Halchenko Build-Depends: debhelper (>= 7.0.50~), cmake, imagemagick, libvtk5-dev, libinsighttoolkit3-dev, libgdcm2-dev, libfltk1.1-dev, fluid, libopenjpeg-dev, libfftw3-dev, uuid-dev, libxinerama-dev Standards-Version: 3.9.2 Section: science Homepage: http://www.itksnap.org XS-DM-Upload-Allowed: yes Vcs-Browser: http://git.debian.org/?p=debian-med/itksnap.git Vcs-Git: git://git.debian.org/git/debian-med/itksnap.git Package: itksnap Section: science Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: semi-automatic segmentation of structures in 3D images SNAP provides semi-automatic segmentation of structures in medical images (e.g. magnetic resonance images of the brain) using active contour methods, as well as manual delineation and image navigation. Noteworthy features are: . * Linked cursor for seamless 3D navigation * Manual segmentation in three orthogonal planes at once * Support for many different 3D image formats, including NIfTI * Support for concurrent, linked viewing and segmentation of multiple images * Limited support for color images (e.g., diffusion tensor maps) * 3D cut-plane tool for fast post-processing of segmentation results debian/itksnap.menu0000644000000000000000000000034211561272632011531 0ustar ?package(itksnap): \ needs="X11" \ section="Applications/Science/Medicine" \ title="ITK-SNAP" \ longtitle="3D Structure Segmentation" \ icon="itksnap.xpm" \ command="/usr/bin/itksnap" \ hints="MRI" debian/itksnap.10000644000000000000000000000337511561272632010736 0ustar .TH "ITKSNAP" "1" "April 2010" "Michael Hanke" "User Commands" .SH NAME itksnap \- semi-automatic segmentation of structures in 3D images .SH "SYNOPSIS" .B itksnap [options] [grey_image] .SH DESCRIPTION SNAP provides semi-automatic segmentation of structures in medical images (e.g. magnetic resonance images of the brain) using active contour methods, as well as manual delineation and image navigation. Noteworthy features are: .PP * Linked cursor for seamless 3D navigation .PP * Manual segmentation in three orthogonal planes at once .PP * Support for many different 3D image formats, including NIfTI .PP * Support for concurrent, linked viewing and segmentation of multiple images .PP * Limited support for color images (e.g., diffusion tensor maps) .PP * 3D cut-plane tool for fast post-processing of segmentation results .SH OPTIONS .TP \fB\-\-grey\fR, \fB\-g\fR FILE Load greyscale image FILE (optional) .TP \fB\-\-segmentation\fR, \fB\-s\fR FILE Load segmentation image FILE .TP \fB\-\-labels\fR, \fB\-l\fR FILE Load label description file FILE .TP \fB\-\-rgb\fR FILE Load RGB image FILE (as overlay if combined with \fB\-g\fR) .SH "AUTHOR" \fBITK-SNAP\fR was written by Paul A. Yushkevichi, Hui Zhang, Casey Goodlett, Timothy Burke, Nicholas Tustison, Guido Gerig, Silvio Turello, Joachim Schlegel, Gabor Szekely, Chris Wynn, Arun Neelamkavil, David Gregg, Eric Larsen, Sanjay Sthapit, Sean Ho, Ashraf Farrag, Amy Henderson, Robin Munesato, Ming Yu, Nathan Moon, Thorsten Scheuermann, Konstantin Bobkov, Nathan Talbert, Yongjik Kim, Pierre Fillard, Daniel S. Fritsch, Stephen R. Aylward .PP This manual page was written by Michael Hanke , for the Debian project (but may be used by others). .SH "SEE ALSO" \fBManual and tutorial:\fR http://itksnap.org debian/source/0000755000000000000000000000000011561272632010473 5ustar debian/source/format0000644000000000000000000000001411561272632011701 0ustar 3.0 (quilt) debian/changelog0000644000000000000000000000364711750756402011061 0ustar itksnap (2.2.0-1.1) unstable; urgency=low * Non-maintainer upload. * Fix "ftbfs with GCC-4.7": add patch gcc-4.7.patch ("this->" qualifiers). (Closes: #667211) -- gregor herrmann Fri, 04 May 2012 15:43:12 +0200 itksnap (2.2.0-1) unstable; urgency=low * New upstream release. * Bumped Standards to 3.9.2, no changes necessary. * Changed maintainer email. * Removed FLTK patch and wrong-header-file-casing patch -- merged upstream. -- Michael Hanke Fri, 27 May 2011 07:39:03 -0400 itksnap (2.1.4-1) unstable; urgency=low * New upstream release (RC1 for upcoming 2.2.0). Merged all relevant patches with upstream. * Bumped Standards to 3.9.1, no changes necessary. * Added upstream patch to allow building against FLTK 1.1. Thanks to Paul Yushkevich. * Added patch to remove CMake's find_package() version requirements for VTK 5.6 and ITK 3.20. First of all Debian's CMake fails to handle them properly (see #600889), but moreover, ITKSNAP builds and runs fine with VTK 5.4 and ITK 3.18 on Debian. * Added patch to fix a minor header filename casing problem. * Add 'get-orig-source' target to debian/rules to create a tarball from the CVS branch of the Git packaging repository. * Added build-dependency to libxinerama-dev. -- Michael Hanke Sat, 23 Oct 2010 10:54:51 -0400 itksnap (2.0.0+cvs20100615-1) unstable; urgency=low * New CVS snapshot fixing a number of compiler issues. * Add patch to avoid namespace confusion of itk:: and std:: (Closes: #583208). Patch has been forwarded upstream. -- Michael Hanke Wed, 23 Jun 2010 12:17:33 -0400 itksnap (2.0.0-1) unstable; urgency=low * Initial Debian packaging based on debhelper's "dh" and using the new source package format 3.0 (quilt). Closes: #579588. -- Michael Hanke Sun, 25 Apr 2010 12:47:51 -0400 debian/itksnap.install0000644000000000000000000000005611561272632012235 0ustar debian/itksnap.desktop usr/share/applications debian/compat0000644000000000000000000000000211561272632010371 0ustar 7 debian/itksnap.desktop0000644000000000000000000000036411561272632012242 0ustar [Desktop Entry] Encoding=UTF-8 GenericName=3D Structure Segmentation Name=ITK-SNAP Exec=itksnap %F TryExec=itksnap Type=Application Terminal=false Categories=Education;Graphics;Science;DataVisualization;MedicalSoftware;Viewer; Icon=itksnap.xpm debian/patches/0000755000000000000000000000000011750756357010635 5ustar debian/patches/series0000644000000000000000000000006611750756024012043 0ustar debian_path_cfg no_find_package_version gcc-4.7.patch debian/patches/gcc-4.7.patch0000644000000000000000000000500711750756357012722 0ustar Description: add this-> qualifier to avoid FTBFS with gcc 4.7 Origin: vendor Bug-Debian: http://bugs.debian.org/667211 Forwarded: no Author: gregor herrmann Last-Update: 2012-05-04 --- a/Logic/LevelSet/SNAPAdvectionFieldImageFilter.txx +++ b/Logic/LevelSet/SNAPAdvectionFieldImageFilter.txx @@ -85,7 +85,7 @@ // graft the mini-pipeline output back onto this filter's output. // this is needed to get the appropriate regions passed back. - GraftOutput( fltPipeEnd->GetOutput() ); + this->GraftOutput( fltPipeEnd->GetOutput() ); } template --- a/Logic/Preprocessing/EdgePreprocessingImageFilter.txx +++ b/Logic/Preprocessing/EdgePreprocessingImageFilter.txx @@ -117,7 +117,7 @@ // graft the mini-pipeline output back onto this filter's output. // this is needed to get the appropriate regions passed back. - GraftOutput( m_RemappingFilter->GetOutput() ); + this->GraftOutput( m_RemappingFilter->GetOutput() ); } --- a/Logic/Preprocessing/SmoothBinaryThresholdImageFilter.txx +++ b/Logic/Preprocessing/SmoothBinaryThresholdImageFilter.txx @@ -85,7 +85,7 @@ // graft the mini-pipeline output back onto this filter's output. // this is needed to get the appropriate regions passed back. - GraftOutput( m_ThresholdFilter->GetOutput() ); + this->GraftOutput( m_ThresholdFilter->GetOutput() ); } template --- a/UserInterface/BasicComponents/FLTKWidgetActivationManager.h +++ b/UserInterface/BasicComponents/FLTKWidgetActivationManager.h @@ -295,21 +295,21 @@ void AddWidget(Fl_Widget *widget, TFlag flag) { typedef GenericWidgetWrapper WrapperType; - AddWidgetWrapper(new WrapperType(widget), flag); + this->AddWidgetWrapper(new WrapperType(widget), flag); } /** Associate an FLTK menu item with a flag */ void AddMenuItem(Fl_Menu_Item *menu, TFlag flag) { typedef GenericWidgetWrapper WrapperType; - AddWidgetWrapper(new WrapperType(menu), flag); + this->AddWidgetWrapper(new WrapperType(menu), flag); } /** Associate an FLTK checkbox with a flag and two values */ void AddCheckBox(Fl_Check_Button *cb, TFlag flag, bool onState, bool offState) { typedef ValuatorWidgetWrapper WrapperType; - AddWidgetWrapper(new WrapperType(cb,onState ? 1 : 0,offState ? 1 : 0), flag); + this->AddWidgetWrapper(new WrapperType(cb,onState ? 1 : 0,offState ? 1 : 0), flag); } protected: debian/patches/debian_path_cfg0000644000000000000000000000115611561272632013625 0ustar Description: Patch to set proper data paths By default itksnap wants all data to be relavtive to its install directory. On Debian systems, however, it is located in /usr/share/itksnap. Forwarded: not-needed Author: Michael Hanke --- a/Common/SystemInterface.cxx +++ b/Common/SystemInterface.cxx @@ -221,7 +221,7 @@ vPathList.push_back( SystemTools::GetFilenamePath( SystemTools::GetFilenamePath(sExeFullPath)) + - "/share/snap/ProgramData"); + "/share/itksnap/ProgramData"); // Search for the token file in the path list StringType sFoundFile = debian/patches/no_find_package_version0000644000000000000000000000110711561273412015375 0ustar --- a/CMake/standalone.cmake +++ b/CMake/standalone.cmake @@ -1,13 +1,13 @@ ############################################# # REQUIRE ITK 3.20 OR LATER # ############################################# -FIND_PACKAGE(ITK 3.20 REQUIRED) +FIND_PACKAGE(ITK REQUIRED) INCLUDE(${ITK_USE_FILE}) ############################################# # REQUIRE VTK # ############################################# -FIND_PACKAGE(VTK 5.6 REQUIRED) +FIND_PACKAGE(VTK REQUIRED) INCLUDE (${VTK_USE_FILE}) ############################################# debian/copyright0000644000000000000000000000157411561272632011135 0ustar Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat Upstream-Name: ITK-SNAP Upstream-Source: http://www.itksnap.org Files: * Copyright: Copyright 2007-2009 Paul A. Yushkevich Copyright 2003 Insight Software Consortium License: GPL-3 On Debian systems the full text of the GNU General Public License can be found in the `/usr/share/common-licenses/GPL-3' file. Files: Utilities/FLTK/Fl_Native_File_Chooser/* Copyright: Copyright 2004-2005 by Greg Ercolanoa, Nathan Vander Wilt License: LGPL On Debian systems the full text of the GNU Library General Public License can be found in the `/usr/share/common-licenses/LGPL-2' file. Files: debian/* Copyright: Copyright 2010, Michael Hanke License: GPL-3 On Debian systems the full text of the GNU General Public License can be found in the `/usr/share/common-licenses/GPL-3' file. debian/itksnap.dirs0000644000000000000000000000006411561272632011527 0ustar usr/lib/itksnap usr/share/itksnap usr/share/pixmaps debian/itksnap.docs0000644000000000000000000000003511561272632011514 0ustar ReleaseNotes.txt README.html