nested Patlak and generalized Patlak OSMAPOSL (POSMAPOSL & GPOSMAPOSL) and nested Richardson-Lucy Motion Deconvolution Image Reconstruction (RLMCIR) by nkarakatsanis · Pull Request #1685 · UCL/STIR

Commits on Feb 13, 2012

also print image sum() in list_image_info

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Commits on Jun 4, 2012

corrected case scatter_parameter 4|5|9|10

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Commits on Jun 5, 2012

no longer have "using std::vector; using std::ios;" etc in .h files

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minor change to constructor to use base-type as opposed to private typedef (as this confuses SWIG). This change makes sense anyway.

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Commits on Jun 6, 2012

overloading IterativeReconstruction::get_objective_function() with a return-type specifying it'll always be a Poisson log likelihood.

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added get/set pair for (sub)sensitivity_filename(s)

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added new option SWIG_PYTHON, and CMakeLists.txt inswig subdir

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sorted out a few problems with shared_ptr, added 2D coordinates, some filters and some of the reconstruction classes

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added a few more libraries etc, but this file is now obsolete

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some minor simplifications, and added license header

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Commits on Jun 11, 2012

added some extra comments to avoid confusion, and use -march=native in one example

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Commits on Jun 23, 2012

adjusted location of registries to swig directory in CMakeFiles build

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- corrected Python 'slot' statements for get/setitem to more modern version

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added at() functions (checking out-of-range conditions) and empty()

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- use at() functions in get/setitem (checking out-of-range conditions) and add some better exception handling for these

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fixed html error (unclosed ul)

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added tests on at() and empty()

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Commits on Jun 24, 2012

add checks if files are read ok. if not, abort with error message (as opposed to crash)

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- added basic Python iterator-support, __len__, __nonzero__, __bool__ to VectorWithOffset

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Commits on Jul 31, 2012

preliminary commit with basic info

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Commits on Sep 18, 2012

- BasicCoordinate: add constructor-from-tuple, str, repr, nonzero and bool (Python)

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Commits on Oct 28, 2012

swig python: use new $parentclasssymname if it exists for BasicCoordinate __repr__

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Commits on Oct 29, 2012

added install target

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Commits on Nov 1, 2012

first checkin

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Commits on Nov 3, 2012

make library depend on buildblock and IO

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add extra dependencies of libraries such that shared libraries are working better (still some work to do)

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added stirextra.py to install target

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add extra dependencies of libraries such that shared libraries are working better (still some work to do)

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correct --builting option to -builtin

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uncomment line that actualy runs simset

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set templ_dir to full path of local working directory to prevent problems when changing directory

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first check-in

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Commits on Nov 5, 2012

in stir.i, a few more %newobj, index accessing for Octave and some clean-up

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Commits on Nov 17, 2012

added lines for wrapping to Octave

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Commits on Nov 19, 2012

- add "flat" iterator for Array's in Python, using some code from SWIG

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- use "flat" iterator for Arrays

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Commits on Nov 30, 2012

moved option to build swig_python to swig/CMakeLists.txt

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- moved option to build swig_python here (from main CMakeLists.txt)

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Commits on Jan 2, 2013

clarifications for scatter and attenuation

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enabled support for auto_ptr

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call error() if interfile-reading failed (e.g. because it wasn't an image). This change means that read_from_file etc always call error() when the reading failed, as opposed to silently proceeding …

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corrected syntax error in previous update

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clarified usage and other messages

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clarified in doxygen that we're calling error() if read_from_file fails

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corrected bracket in doxygen

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added 1 argument version that writes to stream, i.e. like info()

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include "fake" normalisation data (filled with 1) in test of POSMAPOSL

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if projection data and norm are incompatible, include parameter_info in warning

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Commits on Jan 4, 2013

added 1 argument version that writes to stream, i.e. like info()

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corrected boost::format examples in doxygen

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removed a few lines in interfile.cxx creating local variables min_ring_num_per_segment etc, which were never used

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- removed _scanner_sptr member of MultipleProjData, added a few set_*() functions.

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small mods to test_modelling to use Interfile format for the dynamic projection data

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support time frame definitions in Interfile headers (todo: current code issues warnings about unknown keywords)

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updated, e.g. with dynamic proj data

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Commits on Jan 5, 2013

let print-make-vars also print $(AR) and $(ARFLAGS)

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set FAST_CFLAG to -Ofast if gcc supports it, and use xiar for Intel C (required when using -fast)

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updated (compilers, FORE, parametric etc)

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incorporated a few terms for motion compensation into the glossary (Harry Tsoumpas)

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Commits on Jan 13, 2013

a few more updates, also adding the STIR 2.0 paper

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Commits on Feb 15, 2013

changes to RunTests to avoid problems with 64bit Visual Studio (conversion of std::size_t) bu adding "long long" functions. Some explicit "float" to avoid warnings

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change to introduce counters instead of directly working with iterators to avoid (faulty?) debug assertion in Visual Studio 2010

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Commits on Mar 6, 2013

removed ECAT6 test as it is no longer supported

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removed ecat6 tests

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updated version number

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updated version number and some extra clarifications

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updated release info

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inserted comment that this Makefile is for development only

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added listmode_buildblock as depend library for recon_buildblock

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addition of more convenience functions to use STIR from python

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addition of some documentation and examples to use STIR from python

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Commits on Mar 7, 2013

removed examples directory from the main CMakeLists.txt, and provide examples/extra_stir_dirs.cmake. Update examples/README.txt for building with cmake.

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- updated for release of version 2.3beta

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updated version to 2.3beta

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corrected closing tt tag

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update version to 2.3

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Commits on May 4, 2013

fixed typos in documentation

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updated dates and version number for release 2.3

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- updated for release of version 2.3

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Commits on May 5, 2013

added input files for python examples

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Commits on May 17, 2013

- removed some "using std::cerr" etc from .h or .inl files to avoid conflicts. This then needed changes in some files that include these files

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Commits on May 19, 2013

- use CMake FOLDER properties to group projects in Visual Studio (and XCode etc?), needs CMake 2.8.3

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Commits on May 22, 2013

added std:: to cout and endl

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Commits on Jun 2, 2013

added newline after printing an "unknown" event

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Commits on Jun 10, 2013

corrected error()/warning() calls using __LINE__ (where using %s as opposed to %d)

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Commits on Jun 24, 2013

check-in of Charalampos Tsoumpas' (KCL) contributions to STIR

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corrected name of spatial_transformation_buildblock

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check-in of CMake files for Charalampos Tsoumpas' additions

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minor clean-up of PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData.txx:

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changed version number to 2.4a

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- updated for release of version 2.4a

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Commits on Jun 25, 2013

relaxed test on OSSPS to avoid failure on cygwin (and others?)

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updated version and content of README.txt in recon_test_pack

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added 2.4 release

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- added motion stuff in contrib/README.txt

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Commits on Jun 27, 2013

updates of user's guide for version 2.4

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merged Harry's motion related documentation

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Commits on Jun 28, 2013

added "-t tolerance" option to compare_projdata

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Commits on Jul 4, 2013

fixed compilation problem in Debug mode for PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData. also added it to the modelling doxygen group

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fixed documentation for coordinate system for motion vectors (and minor other changes)

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Commits on Jul 14, 2013

minor changes for swig compatibility

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Commits on Jul 16, 2013

updates to swig files

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Commits on Jul 19, 2013

added a few tests for python numpy capabilities

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Commits on Jul 20, 2013

inserted using std::cout in a few utilities to compensate for its removal in .h files

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small updates to test scrips

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InputStreamWithRecords: corrected BUG in memory allocation (introduced in STIR 2.3)

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changed version numbers and updated release notes

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removed contrib/Motion_files_KCL/Documentation/Software_Description.tex as it's incorporated into the UsersGuide

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Commits on Jul 23, 2013

fixes for MPI

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Commits on Jul 24, 2013

added spatial_transformation as doxygengroup

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minor corrections to STIR-UsersGuide

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minor changes to test_Array

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Commits on Jul 29, 2013

update copyright

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Commits on Jul 30, 2013

revised IO-tests in test_Array.

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changes to test-macros for CMake to allow linking without the registries (such as IO_registries), speeding up the linking process

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updated release_2.3.htm to add memory allocation bug in list mode processing

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Commits on Jul 31, 2013

changes related to reading file signature

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updated Doxyfile

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test_Array update, now also succeeds on gcc 4.8.1 (which give larger rounding errors)

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update to RunTests to accept std::string as opposed to const char *const

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interfile parsing of image header: removed warning about setting origin (as it is expected behaviour)

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added run_scatter_tests.sh to the recon_test_pack (comparing with result generated before)

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modifications to the scatter estimation code

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list_lm_events: reset output-format to decimal after printing a gating info (previously all remaining output was in hex)

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added Siemens mMR details (and add 1080 as a "name" for the Biograph 16)

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fixed possible race-condition in OPENMP version of FBP2D

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minor change in test_Array

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added latest features/bug-fixes to release_2.4

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moved a few tests in test/CMakeLists.txt back to compilation "with registries" as otherwise external libraries didn't get dragged in for some reason

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Commits on Aug 7, 2013

final changes to release_2.4.htm

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Commits on Aug 9, 2013

added thanks to Irene in release notes

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Commits on Nov 3, 2013

commit of changes related to SPECT (authors: Berta Marti Fuster, Carles Falcon, some support by Kris Thielemans):

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some clean-up of SPECTUB code (moved to SPECTUB namespace, some doxygen, call stir::error as opposed to exit() etc)

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Commits on Nov 4, 2013

minor fix for std::auto_ptr to get it to compile with CLang 5.0

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small fixes to interfile_keyword_functions.* (guard against multiple inclusion of .h and remove "using std::string" etc in .h)

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Commits on Nov 6, 2013

various fixes for ITK IO and added tests. It works now (aside from orientation)

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added 2 sample parameter files (for SPECT and for ITK image output)

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Commits on Nov 14, 2013

added interpolation matrix to user's guide (somehow got forgotten before)

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modified ProjDataInfoCylindrical::get_tantheta slightly to allow s>R if the ring difference is zero anyway.

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in main CMakeLists.txt, no longer add local subdirectory. Leave that to local/stir_extra_dirs.cmake

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added more examples of shapes to sample generate_image.par

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corrected doxygen in EllipsoidalCylinder

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Commits on Nov 16, 2013

addition of samples/PET_simulation

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Commits on Dec 24, 2013

removed unused typedefs in BSplines_coef.inl to avoid compiler warnings

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fix small memory leak in ProjMatrixByBinSPECTUB (delete Rrad)

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Commits on Dec 27, 2013

corrected BUG in writing usage message of conv_SimSET_projdata_to_STIR

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Commits on Dec 30, 2013

in run_eat_tests.sh, remove all output of a previous run as otherwise the test fails.

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add optional bool to KeyParser::parse to silence warnings

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when not using c++11, disable 2 constructors in LORCoordinates which are implemented using delegating constructors (and are not currently used in STIR anyway)

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Commits on Dec 31, 2013

corrected spelling mistake in test/CMakeLists.txt (test_ITKDefaultOutputFileFormat.in)

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moved ITK before ECAT6 in InputFileFormatRegistry such that it's tried first

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first version of release_3.0.htm

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Major update related to IO keeping more information such as modality, patient position and timing.

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Commits on Jan 2, 2014

CMake changes for tests

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corrected ECAT7 code in TimeFrameDefinitions.cxx

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attempt at removing warning in IRfilters.inl, but it didn't work, so new code is commented out.

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read in data sinogram by sinogram as opposed to one big chunck.

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minor updates to release notes for 3.0

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in conv_gipl_to_interfile, handle upper boundaries of arrays in a safer way (not relying on float arithmetic)

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add 3rd argument to BSplines templates to specify type of internal constants (with a good default).

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Commits on Jan 3, 2014

small fixes to SPECT Interfile IO

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fix keeping ExamInfo in fwdtest

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CMake changes for tests

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Minor fixes to reduce number of warnings by MSVC

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Changed reporting of timings in SPECTUB proj matrix

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Let list_projdata_info write a bit more info suitable for SPECT Data

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changes to Interfile IO

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Commits on Jan 4, 2014

BUG FIX: ECAT966ListmodeInputFileFormat never worked before

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Updates to CListModeData (WARNING: NOT BACKWARDS COMPATIBLE) and BUG FIX in list mode reconstruction

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updated copyright

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removed unused variables in interfile.cxx

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BUG fix in MPI code

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fixes in MPI code (and test) for POSMAPOSL and PSOSSPS

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updates to recon_test_pack to be able to run MPI executables (and bumped version number to 3.0)

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added parameters in doxygen of ITKOutputFileFormat

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Commits on Jan 5, 2014

updated User's Guide

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STIR MPI programs now exit immediatelly when only 1 processor is available

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report azimuthal angle extent as absolute value

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corrected azimuthal angle increment and start for SPECT UB

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Commits on Jan 6, 2014

Modify CMake files such that STIR MPI tests work properly

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SPECT Interfile IO: fix z-spacing

Kris Thielemans
authored and
Kris Thielemans
committed
SPECTUB matrix: corrected 3D PSF (author: Carles Falcon)

Kris Thielemans
authored and
Kris Thielemans
committed

Commits on Jan 9, 2014

small modifications to the example PET_simulation scripts

Kris Thielemans
authored and
Kris Thielemans
committed

Commits on Jan 11, 2014

minor update of parameter file parsing of the SPECT UB projection matrix

Kris Thielemans
authored and
Kris Thielemans
committed
more SPECT into the User's Guide

Kris Thielemans
authored and
Kris Thielemans
committed
minor edits to STIR-UsersGuide

Kris Thielemans
authored and
Kris Thielemans
committed

Commits on Jan 12, 2014

tiny fixes in PoissonLogLikelihoodWithLinearModelForMeanAndProjData.cxx

Kris Thielemans
authored and
Kris Thielemans
committed
added extra set/get pairs to ProjMatrixByBinUsingRayTracing

Kris Thielemans
authored and
Kris Thielemans
committed
make the ray-tracing projection matrix the default projector in most applications

Kris Thielemans
authored and
Kris Thielemans
committed

Commits on Jan 13, 2014

CMake files: make BUILD_SWIG_OCTAVE an advanced option (to hide it for most users) as it doesn't work very well yet

Kris Thielemans
authored and
Kris Thielemans
committed
documentation Makefile: add "doc_as_html" target and clean-up

Kris Thielemans
authored and
Kris Thielemans
committed
documentation Makefile: fixed copyright

Kris Thielemans
authored and
Kris Thielemans
committed
PoissonLogLikelihoodWithLinearModelForMean: change default of use_subset_sensitivities to true (WARNING: NOT BACKWARDS COMPATIBLE)

Kris Thielemans
authored and
Kris Thielemans
committed
updates to documentation

Kris Thielemans
authored and
Kris Thielemans
committed
removed obsolete project files for Visual Studio. Use CMake instead

Kris Thielemans
authored and
Kris Thielemans
committed
- updated for release of version 3.0alpha

Kris Thielemans
authored and
Kris Thielemans
committed
added recon_test_pack tests for SPECT reconstruction (KT with Berta Marti)

Kris Thielemans
authored and
Kris Thielemans
committed
final updates to documentation before release of 3.0alpha

Kris Thielemans
authored and
Kris Thielemans
committed

Commits on Jan 27, 2014

disable some warnings for Visual Studio in OutputFileFormat.cxx

Kris Thielemans
authored and
Kris Thielemans
committed
Handle multi-file DICOMs via ITK IO

Kris Thielemans
authored and
Kris Thielemans
committed
modified get_directory_name in utilities.cxx to return "." if the directory info was not given

Kris Thielemans
authored and
Kris Thielemans
committed
removed spurious text in comments (copy-paste mistake) in conv_GATE_raw_ECAT_projdata_to_interfile.cxx

Kris Thielemans
authored and
Kris Thielemans
committed
minor code-cleanup (mostly due to removing "using std::*" statements in utilities.h)

Kris Thielemans
authored and
Kris Thielemans
committed

Commits on Jan 30, 2014

corrected script in PET_simulation

Kris Thielemans
authored and
Kris Thielemans
committed

Commits on Feb 13, 2014

small update to contrib documentation

Kris Thielemans
authored and
Kris Thielemans
committed

Commits on Feb 14, 2014

remove CVS keywords

Kris Thielemans
authored and
Kris Thielemans
committed

Commits on Feb 15, 2014

Commits on Feb 17, 2014

fixed SSRB command line processing
KrisThielemans
committed

Commits on Feb 18, 2014

updates to git configuration files
KrisThielemans
committed

Commits on Feb 21, 2014

fixed error in auto-removing of CVS keyword
KrisThielemans
committed

Commits on Mar 1, 2014

updated values for Siemens mMR a bit (arc-corrected bin-size and buckets)
KrisThielemans
committed

Commits

Commits on Feb 13, 2012

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Commits on Sep 18, 2012

Commits on Oct 28, 2012

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Commits on Nov 1, 2012

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Commits on Nov 5, 2012

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Commits on Nov 19, 2012

Commits on Nov 30, 2012

Commits on Jan 2, 2013

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Commits on Jan 5, 2013

Commits on Jan 13, 2013

Commits on Feb 15, 2013

Commits on Mar 6, 2013

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Commits on May 4, 2013

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Commits on May 17, 2013