Software for Tomographic Image Reconstruction
This version is 100% backwards compatible with STIR 6.0 for the user, except for the bug-fix in the RDP (see below).
This version adds capability of using Parallelproj (CPU and GPU versions) for TOF data. In addition, the list-mode objective function has several improvements, including speed-up by using multi-threading if caching was not enabled.
Of course, there is also the usual code-cleanup and improvements to the documentation.
This release contains mainly code written by Nicole Jurjew (UCL) and Kris Thielemans (UCL).
PoissonLogLikelihoodWithLinearModelForMeanAndListModeDataWithProjMatrixByBin can now compute the value as well as
accumulate_Hessian_times_input. PR #1418
GeneralisedObjectiveFunction has 2 new members to compute the full gradient (compute_gradient and compute_gradient_without_penalty`). Previously, only subset gradients were available. PR #1418
PoissonLogLikelihoodWithLinearModelForMeanAndListModeDataWithProjMatrixByBin now computes the gradient multi-threaded (if OpenMP is enabled), even if caching to file of the list-mode file is not enabled. PR #1418
CMAKE_CXX_BYTE_ORDER (available since CMake 3.20). This could potentially affect reading of list-mode data (which would otherwise be garbled). Fixed in PR #1412.See our issue tracker.
GeometryBlocksOnCylindrical scanner configuration, which may lead to an error being raised, while previously the code silently proceeded.PoissonLogLikelihoodWithLinearModelForMeanAndProjData had a (minor?) problem with TOF data that when computing the gradient, the normalisation object was not set-up with the TOF data, but non-TOF instead. This did not happen in our normal reconstruction code, and would have thrown an error if it occured. Fixed in issue #1427.root-config.accumulate_Hessian_times_inputFull Changelog: https://github.com/UCL/STIR/compare/rel_6.0.0...rel_6.1.0
This version is 99% backwards compatible with STIR 5.x for the user (see below). Developers might need to make code changes as detailed below. Note though that the locations of installed files have changed. Developers of other software that uses STIR via CMake will therefore need to adapt (see below).
This release is a major upgrade adding Time of Flight (TOF) capabilities to STIR.
This version has a major code-cleanup related to removing old compiler work-arounds, consistent use of override and white-space enforcement.
Overall code management and assistance was Kris Thielemans (UCL and ASC). Other main contributors include: Nikos Efthimiou (UCL, University of Hull, UPenn, MGH) for the TOF framework and list-mode reconstruction, Elise Emond (UCL) for adapting TOF framework for projection-data, Palak Wadhwa (University of Leeds) for adaptations and testing on GE Signa PET/MR data, Robert Twyman for extending projector symmetries to TOF and formalising ROOT-based testing, Nicole Jurjew (UCL) for adaptations and testing on Siemens Vision 600 data. Non-TOF contributors include Daniel Deidda (NPL) and Markus Jehl (Positrigo).
originating system is not recognised, the previous version of STIR tried to guess the scanner based on the number of views or rings. This was using very old scanners though, and could lead to confusion. These guesses have now been removed.CMAKE_INSTALL_PREFIX, where V.v indicates the major.minor version number, e.g. 6.0:
documentation (including examples as subfolder): share/doc/STIR-V.v (was share/doc/stir-V.v)
JSON files with radionuclide database: share/STIR-V.v/config (was share/stir/config)
Developers also need to check the new location to use for STIR_DIR documented below.
ProjDataInfo::ask_parameters() and therefore create_projdata_template has changed:
false.make_num_tangential_poss_odd argument (defaulting to false), which made the returned argument a different size. This has been deprecated since version 5.0. Setting this argument to true will now raise an error.FloatLOR to LOR, and same for derived classes.The new TOF support is mostly transparent, i.e. normally no changes are required to the reconstruction code etc. When using Interfile or ROOT files, certain new keywords are required, see examples/samples/PET_TOF_Interfile_header_Signa_PETMR.hs and examples/samples/root_header.hroot. See also the updated STIR_glossary. Please cite the following papers:
See also the (enormous) PR #304.
Limitations
matrix based projectors support TOF. Note that the implementation is generic but slow: a non-TOF row is computed and then multiplied with the TOF kernel. This is somewhat alleviated by the use of caching. However, as not all symmetries are supported yet, caching of the projection matrix needs substantially more memory than in the non-TOF situation.list_lm_events now has an additional option --event-bin which lists the bin assigned for the event (according to the "native" projection data, i.e. without any mashing).
In addition, the --event-LOR option now also works for SPECT (it was disabled by accident).stir_list_registries is a new utility that list possible values of various registries, which can be useful to know what to use in a .par file.ProjMatrixByBinPinholeSPECTUB
PR #1366
ListRecord etc, such that loops over list-mode data can now be performed in Python (although this will be somewhat slow). See examples/python/listmode_loop_demo.py.LORAs2Points,LORInCylinderCoordinates, LORInAxialAndSinogramCoordinates and PointOnCylinder.
Warning: renamed FloatLOR to LOR, and same for derived classes.DetectionPositionPair.__repr__ for printing and change order of text in DetectionPosition.__repr__ to fit with constructor to avoid confusion.
PR #1316
ProjDataInfo*NoArcCorr) if number of tangential positions in the projection data exceeds the maximum number of non arc-corrected bins set for the scanner. If it is, an error is raised. You might therefore have to adapt your interfile header.STIR6.0 as Interfile key version to denote TOF changes. This is currently ignored for parsing though.effective central bin size (cm) keyword for projection data is now only used for arc-corrected data. It is no longer written to the header for non-arccorrected data.CMakeLists.txt accordingly.STIR_CONFIG_DIR is no longer a CMake cached variable, such that it automatically moves along with CMAKE_INSTALL_PREFIX. However, if you are upgrading an existing STIR build, you might have to delete the cached variable, or it will point to the old location.: in a keyword (e.g., used by Siemens for dates).
PR #1267
See our issue tracker.
examples/C++/using_installed_STIR to illustrate how to use STIR as a "library".examples/C++/src to examples/C++/using_STIR_LOCAL.STIR_USE_BOOST_SHARED_PTR will be removed. It probably no longer works anyway. Therefore stir::shared_ptr will always be std::shared_ptr.clang-format to enforce C++-style, including white-space settings, line-breaks etc. This uses the .clang-format file in the root directory of STIR. Developers should configure their editor encordingly, and ideally use pre-commit. It also has consequences for existing branches as you might experience more conflicts than usual during a merge. More detail is in documentation/devel/README.md.
PR #1368.ListModeData now has a shared_ptr<const ProjDataInfo> proj_data_info_sptr protected member, and the scanner_sptr member has been removed.
Warning: If your derived class had its own proj_data_info_sptr, it should be removed.
virtual ListModeData::get_scanner_ptr() is replaced by ListModeData::get_scanner().
ProjDataInfo*NoArcCorr::get_bin_for_det_pair is now private. Use get_bin_for_det_pos_pair instead.
The GeneralisedObjectiveFunction hierarchy now has a already_set_up member variable that needs to be set to false by set_* functions and checked by callers.
(deprecated) members/functions have been removed
BinNormalisation::undo and apply members that take explicit time argumentsextend_sinogram_in_views, extend_segment_in_views and interpolate_axial_position
As mentioned above, installation locations are now versioned. New locations that could affect developers that use STIR as an external project:
include/STIR-V.v (was include). This should be transparant if you use find_package(STIR).STIRConfig.cmake etc: lib/cmake/STIR-V.v (was share/lib).
The CMake variable STIR_DIR should now be set to <STIR_CMAKE_INSTALL_PREFIX>/lib/cmake/STIR-V.v. However, this new
location increases chances that find_package finds STIR as it follows conventions better. For instance, STIR can now by found by
find_package when setting CMAKE_PREFIX_PATH to what was used for CMAKE_INSTALL_PREFIX when installing STIR (indicated as
STIR_CMAKE_INSTALL_PREFIX above). Moreover, if you use the same CMAKE_INSTALL_PREFIX for your project as for STIR, you
shouldn't need to set STIR_DIR nor CMAKE_PREFIX_PATH.Scanner now allows storing TOF information. This is currently not yet done for all TOF-capable scanners though. Contributions welcome!
All projection-data related classes and their members now have a TOF bin index and related information. At present, old-style accessors are in an awkward format such as
auto sino = proj_data.get_sinogram(ax_pos_num, segment_num, false, timing_pos_num);
These are deprecated since version 5.2 and should be replaced by
const SinogramIndices sinogram_idxs{ax_pos_num, segment_num, timing_pos_num};
auto sino = proj_data.get_sinogram(sinogram_idxs);
List-mode data for TOF-capable scanners need to pass the relevant information through appropriately of course.
clone() member, currently returning a bare pointer (like other STIR classes).Bin can now be output to stream as text.RunTests::check_if_equal for Bin.KeyParser has a new facility to add an alias to a keyword. This can be used to rename a keyword for instance while remaining backwards compatible. By default, a warning will be written, but this can be disabled.ProjDataInfoCylindricalNoArcCorr::get_all_det_pos_pairs_for_bin is in most places intended to return the physical locations. However, a `DetectionPositionPair` also contains (unmashed) TOF bin information. This will be further complicated once energy windows are supported. The method therefore has an extra boolean argument ignore_non_spatial_dimensions, which defaults to true.multiply_crystal_factors is essentially a non-TOF calculation. When given TOF projection data, it will "spread" the non-TOF result equally over all TOF bins. This is also appropriate for randoms_from_singles.STIR_NO_NAMESPACES, STIR_NO_MUTABLE, BOOST_NO_TEMPLATE_SPECIALIZATION, BOOST_NO_STRINGSTREAM and various items specifically for VC 6.0.override in derived classes, via clang-tidy --modernize-use-override.This version is 100% backwards compatible with STIR 5.0 as far as usage goes. However, there are changes in the output of scatter estimation and ECAT8 normalisation, see below for more information.
Of course, there is also the usual code-cleanup and improvements to the documentation. See also the 5.2 milestone on GitHub.
Overall code management and assistance by Kris Thielemans (UCL and ASC). Other main contributors were Daniel Deidda (NPL) and Markus Jehl (Positrigo).
use_axial_effects_factors:=0 to the parameter file (see an example in examples/Siemens-mMR/correct_projdata_no_axial_effects.par), or the class member of the same name.
In addition, the Siemens normalisation header is now read (using a new class InterfileNormHeaderSiemens) such that hard-coded variables for the Siemens mMR have been removed. Further testing of this functionality is still required however.
PR #1182.:=.set_up() method of the ray-tracing projection matrix now skips further processing if it was already called with data of the same characteristics. This will means that any cached data will be re-used, potentially leading to a speed-up when re-using it from Python.
PR #1281.The Discretised Shape3D shape/ROI has now an extra value label index. For ROIs, this allows using a single volume with multiple ROIs encoded as labels, such as output by ITKSnap and many others. When used as a shape in generate_image, it could be used to extract a single ROI from such a label image.
PR #1196.
Global variables in SPECTUB have been substituted by class members, such that multiple SPECTUB projectors can be used. PR #1169.
Global variables in PinholeSPECTUB have been substituted by class members, such that multiple PinholeSPECTUB projectors can be used. PR #1212.
Scatter estimation is now smoothed in axial direction for BlocksOnCylindrical scanners. PR #1172.
InverseSSRB now works for BlocksOnCylindrical after a rewrite.
PR #1172. /
Parallelised function set_fan_data_add_gaps_help across segments to reduce computation time.
PR #1168.
New utility SPECT_dicom_to_interfile which reads a DICOM file with SPECT projection data and extracts the data and writes one or more Interfile 3.3 headers (still somewhat preliminary).
PR #1182.
The new stir_timings utility is mostly useful for developers, but you could use it to optimise the number of OpenMP threads to use for your data.
PR #1237.
New classes SegmentIndices, ViewgramIndices and SinogramIndices, used by ProjData related classes, as opposed to having to specify all the elements directly, e.g. in C++
auto sinogram = proj_data.get_sinogram(sinogram_indices);
This makes these functions more future proof, in particular for TOF. The older functions are now deprecated. Note that as Bin is now derived from ViewgramIndices, instantations of Bin can now be used to specify the indices as well in most places.
There is still more work to do here, mostly related to the symmetries.
PR #1273.
stir.ProjData.read_from_file as opposed to stir.ProjData_read_from_file. The former is supported since SWIG 3.0, and the default from SWIG 4.1.DetectionPosition and DetectionPositionPair.bin.time_frame_num is now no longer a function in Python, but acts like a variable (as the other Bin members).RadionuclideDB
examples/python/construct_projdata_demo.py illustrates constructing a ProjDataInMemory
restart_reconstruction_every_scatter_iteration to true either via a parameter file or via the set_restart_reconstruction_every_scatter_iteration() function.
PR #1160.Scanner::check_consistency also checks if the energy resolution is less than 20 (as it is FWHM/reference_energy).
PR #1149.std::runtime_error instead of std::string.
PR #1131.use_view_offset was removed from the interpolate_projdata functions. View-offset is now always taken into account.
PR #1172.distributable.cxx was changed from verbosity 2 (which is the STIR default) to verbosity 3. This is to reduce the default output during iterative reconstructions.
PR #1243.Succeeded class has a new method bool succeeded() enabling more concise code (avoiding the need for comparing with Succeeded::yes which is especially verbose in Python).interpolate_axial_position, extend_sinogram_in_views and extend_segment_in_views
ProjData related classes that explicitly use axial_pos_num, view_num etc in their arguments are now deprecated, and should be replaced by their respective versions that use SegmentIndices, ViewgramIndices or SinogramIndices. The former will not be compatible with TOF information that will be introduced in version 6.0.0.error and warning functions are now no longer included from common.h and need to be included manually when used (as was already the case for #include "stir/info.h").
PR #1192.CListEventCylindricalScannerWithDiscreteDetectors to template class CListEventScannerWithDiscreteDetectors (templated in ProjDataInfoT). This enables re-use for generic/blocksoncylindrical scanners.
PR #1222.ProjDataInMemory to avoid streams, causing a speed-up of some operations, and removing a limit of total size of 2GB.
PR #1260.extend_segment_in_views does not handle view offsets correctly and does not work for BlocksOnCylindrical scanners
issue #1177. A new function extend_segment was added that works for Cylindrical and BlocksOnCylindrical and allows extension in tangential and axial direction as well.
PR #1172.sample_function_on_regular_grid did not handle offset correctly in all places
issue #1178.
PR #1172.Code is identical to 5.1.0 and 5.1.1, aside from handling the scatter test with a slightly larger threshold due to occasional failures (as it uses random placements). This change is a backport from STIR master.
Code is identical to 5.1.0, aside from handling numerical precision in 2 tests, which otherwise can fail.
This version is 100% backwards compatible with STIR 5.0.
examples/python) by Robert Twyman (UCL).Of course, there is also the usual code-cleanup and improvements to the documentation. See also the 5.1 milestone on GitHub and the full release notes
Overall code management and assistance by Kris Thielemans (UCL and ASC).
bug-fix release:
get_phi() which could cause 180 degrees swapsbug-fix release
This version is 95% backwards compatible with STIR 4.0 for the user (see below). Developers might need to make code changes as detailed below.
ProjDataInfoSubsetByView class has been implemented which allows for subsets of projection data. Previously, subset projections could only be stored in fully sampled ProjData. This is still possible, the implementation is backward compatible, and subset reconstructions such as OSMAPSOL have not been changed. However, there is now an option to create subsets with ProjData::get_subset which only store a subset of views and so are more memory efficient when subsets might be handled separately. ProjDataInfoSubsetByView currently does not support file I/O.ROOT files produced by GATE can now be interpreted using "virtual crystals", see PR #617.BinNormalisation derived class BinNormalisationWithCalibration; Interfile now reads/writes isotope name and calibration factor. See PR 672. This code was contributed by Daniel Deidda (NPL) and Kris Thielemans (UCL)Radionuclide and RadionuclideDB; This code was contributed by Daniel Deidda (NPL) and Kris Thielemans (UCL)dynamic instead of runtime, resulting in faster performance.Of course, there is also the usual code-cleanup and improvements to the documentation.
This release contains mainly code written by Kris Thielemans (UCL), Richard Brown (UCL), Parisa Khateri and Michael Roethlisberger (ETHZ), Robert Twyman (UCL), Daniel Deidda (NPL), Tahereh Nikjenad (PETsys), Palak Wadhwa (Univ of Leeds), Viet Ahn Dao (Univ of Leeds), Ashley Gillman (CSIRO), Georg Schramm (KUL), Markus Jehl (Positrigo), Gefei Chen (Univ of Macao)
View Offset Support enabled for the PET scanners.
WARNING This means that reconstructed PET images will not be identical when either the scanner has non-zero view-offset, or view-mashing is on.
To reflect this change, Scanner::get_default_intrinsic_tilt() has been renamed to get_intrinsic_azimuthal_tilt().
Note: start angle was already supported for SPECT
Backward compatibility for reconstructed images can be achieved by setting the STIR_LEGACY_IGNORE_VIEW_OFFSET CMake option to ON. (However, copied sinogram data will then always have the offset set to 0, in contrast to earlier versions of STIR).
PoissonLogLikelihood Hessian methods have been corrected to reflect the concavity of the function. Hessian vector products now return non-positive voxels, if the vector (input) is non-negative. STIR usages of these methods (OSSPS and SqrtHessianRowSum) have been updated to see no effective change in functionality. However, calling the Hessian vector product methods, via python etc., will result in a change in functionality as the sign of the output voxel values has changed.
Python/MATLAB wrappers no longer have ProjDataInfo::ProjDataInfoCTI, use ProjDataInfo::construct_proj_data_info instead. However, this now returns an object of the appropriate (derived) type as opposed to just ProjDataInfo. This should be transparent, except apparently for testing equality of objects.
use_subset_sensitivities was false and num_subsets greater than 1. Fixing this isssue means that images reconstructed with OSSPS are different from previous versions of STIR when the above conditions are met. See Issue #873 and associated PR #893.POSMAPOSL could lead to zeroes being introduced gradually during reconstruction. See Issue #906 and associated PR #978.Capability to model block and generic PET detectors was added. This is currently limited to span=1, no view mashing and the ray-tracing matrix (single LOR). It is enabled by specifying appropriate keywords in the Interfile header of the projection data.
Scanner parameters:=
normal parameters...
Scanner geometry (BlocksOnCylindrical/Cylindrical/Generic) := BlocksOnCylindrical
Distance between crystals in axial direction (cm) := 0.22
Distance between crystals in transaxial direction (cm) := 0.22
Distance between blocks in axial direction (cm) := 0.22
Distance between blocks in transaxial direction (cm) := 3.3
end scanner parameters:=
Scatter and normalisation code are still pending changes.
Georg's Schramm parallelproj is an implementation of the Joseph algorithm for projection. If it has been installed in your system, and you tell CMake where to find it (`parallelproj_DIR=/wherever/lib/cmake`), the STIR user is now able to select an additional projector, called Parallelproj. This will use the CUDA version if available, otherwise will fall-back to the OpenMP version. Check the new sample files in examples/samples and the section in the User's Guide.
The (still preliminary) code for Maximum Likelihood estimation of normalisation factors now includes estimation of geometric factors in 3D as well
The (also preliminary) ProjDataInfoSubsetByView is backwards compatible and allows a new, memory efficient method for subset projections. Subset projections are created with with ProjData::get_subset, which is the only addition to the ProjData class (additions are mostly in the aforementioned new Info class). ProjDataInfoSubsetByView can be used to set up projectors, which will project only the subset. ProjDataInfoSubsetByView currently does not support file I/O. Therefore, the interface is not yet accessible through parameter files, only through C++ interface.
PR #969
calculate_attenuation_coefficients utility now accepts an optional forward projection parameter file in the same format as the forward_project utility. Example usage has been added to src/recon_test_pack/simulate_data.sh.
ROOT files produced by GATE can now be interpreted using ``virtual crystals", i.e. by inserting ``dummy" crystals before converting to cylindrical geometry (as is done on many Siemens scanners). LmToProjData and list mode reconstructions will then put the LORs more accurately (at least when the ``virtual crystals" roughly correspond to gaps between blocks). See the update .hroot file in examples/samples.
Warning: if you use the originating system to specify the scanner, this will be automatically enabled. (If you do not want this, set it to User_defined_scanner and specify all values).
PR #617
Moved most code from the ctac_to_mu_values.cxx utility to a new HUToMuImageProcessor class (derived from DataProcessor. This allows combining it with filtering etc, also from in Python. It means that the ctac_to_mu_values.cxx utility itself is now obsolete, but it still exists in this version. (Note that this functionality depends on an external JSON library.)
Addition of a new utility create_multi_header which can be used to create a single header pointing to several files (e.g. one image per time frame). The header uses the (STIR-specific) multi format.
Addition of a new utility extract_single_images_from_parametric_image to get each parametric image in a single file.
generate_image parameter files now support the originating system keyword.
list_image_info now works for dynamic images, with a new --per-volume option to list min/max/sum for every volume.
SSRB now has the option of taking a template sinogram.
KOSMAPOSL (HKEM) allows now to freeze the iterative part of the kernel at a specific subiteration. This can be set in the parameter file through the keyword freeze_iterative_kernel_at_subiter_num
BinNormalisationWithCalibration is a new class derived from BinNormalisation. This class allows to apply calibration factor from the scanner and save the information into the interfile header. To use this, a specific BinNormalisation class should be derived from BinNormalisationWithCalibration, the information about the calibration factor read, and the function get_uncalibrated_bin_efficiencies() needs to be overwritten. Note that also the isotope name and branching ratio can be set here (the latter will need to be set according to the isotope by reading into a radionuclide database, see below). BinNormalisationSPECT already reads Calibration factor and isotope name and apply the calibration factor read from interfile. Since not all SPECT scanner do quantitative reconstruction an option of setting the calibration factor from the parameter file is added. Factors for BinNormalisationECA8/ECAT7 and GEHDF5 are set to one at the moment as we need to double check on the meaning of cross calibration factor for ECAT and find out how to read them for GEHDF5. Documentation for this is pending and will be added in the following PR.
Radionuclide is a new class which contains radionuclide information such as halflife, branching ratio, energy etc. This class allows to propagate infrmation trough the reconstruction as it is now a member in the ExamInfo. It is populated from the information extracted from RadionuclideDB which allows to create a Radionuclide object from the information stored in the radionuclide_info.json in the STIR configuration directory. Different vendors, as we saw with SPECT, may have different standards for the isotope name. Three different ones were observed, therefore a lookup table has been added to allow the use of the data base for any different isotope name format. The lookup table is a JSON file stored in radionuclide_names.json.
Logcosh Prior.
SAFIR input file format now supports a Gaussian LOR randomization, which is applied on the endpoints of each LOR when sorting the listmode events into virtual scanner projection data.
Scanner has now a new static member get_names_of_predefined_scanners returning a list of names.
Exposed compute_total_ROI_values and ROIValues to Python/MATLAB via swig. Added python example ROI_demo.py to demonstrate usage.
Additional C++ demo demonstrating the use the objective function and gradient ascent optimisation, see examples/src/demo4_obj_fun.cxx.
A few functions related to TOF were added to ProjDataInfo and Scanner for future compatibility. However, this release still does not support TOF. (Check the GitHub site for the relevant PR).
Exposed BinNormalisation, ListModeData, LmToProjData, ProjectorByBinPair, ScatterSimulation, ScatterEstimation and a couple of support classes and functions to Python/MATLAB via swig. Added python example listmode_demo.py to demonstrate usage.
More setter functions on ScatterEstimation.
dynamic instead of runtime. On some machines, this was causing slower projection operations due to a static scheduler being selected by default. See Issue #935 for more details.ProjDataInMemory are now much faster (it now uses an underlying 1D array).ParametricDiscretisedDensity objects can now have an ExamInfo object with multiple time frames (corresponding to the time frames of the data where the parametric image is derived from). In some cases, there could only be a single time frame (start to end of the study).find_ML_normfactors3D and apply_ML_normfactors3D can be used for scanner with virtual crystal (Only verified on mCT). Contributed by Gefei Chen, see PR 833.find_ML_normfactors3D. Otherwise, we use a block. The use of an argument --for-symmetry-per-block in the find_ML_normfactors3D utility will use the symmetry size of a block.apply_patlak_to_images no longer uses an existing file as a template for the dynamic image but will overwrite it.ROOT file I/O improvements. An entire entry's tree is no longer loaded by default and instead individual branches are loaded as needed. ROOT file event processing is now up to 4x faster. In addition, there is now an option to check energy window information (defaulting to on). Futhermore, added functionality to exclude true and unscattered event types from list mode processing.CMAKE_CXX_STANDARD, see the CMake documentation for supported values.
When importing STIR's STIRConfig.cmake via find_package(STIR), your compiler will be set to use at least C++-11 (via CMake's target_compile_features).
Note that some external libraries that STIR depends on (such as ROOT) might increase the required C++ version, depending on how they were built.ROOT library is now preferentially found by searching for its own exported ROOTConfig.cmake. Set the CMake variable ROOT_DIR accordingly. Older behaviour relying on ROOTSYS and root-config will be deprecated in a future version.Python_EXECUTABLE variable to a particular version (see the CMake doc for other hints you can provide).( If the old PYTHON_EXECUTABLE is set, we use it to initialise Python_EXECUTABLE).src/recon_test/test_modelling.sh and associated input files to the recon_test_pack. It is also modified to be independent of ECAT7 and now runs again.test_proj_data_in_memory to also test ProjDataInterfile so renamed the test to test_proj_data.InterfilePDFSHeader now contain a shared_ptr<ProjDataInfo> instead of a raw pointer, removing a memory leak.shared_ptr:
In the previous version of STIR, the use of shared_ptr allowed unsafe access to the objects (although this never happened in distributed STIR code). We now prevent this with changes to the class interface (although there is still work to do):
shared_ptr<ProjDataInfo> now contain a shared_ptr<const ProjDataInfo>, and similar for DiscretisedDensity
get_proj_data_info_sptr used to return shared_ptr<ProjDataInfo>, but now returns shared_ptr<const ProjDataInfo>, similar for ExamInfo.set_up, that accept shared_ptr now take a shared_ptr to a const object.ProjData*::copy_to and fill_from now return the updated iterator (as opposed to the size). This is like std::copy, and more convenient for reusing it.ModelMatrix::set_if_uncalibrated and ModelMatrix::get_if_uncalibrated renamed to ModelMatrix::set_is_uncalibrated and ModelMatrix::get_is_uncalibrated
PlasmaData::set_if_decay_corrected and PlasmaData::get_if_decay_corrected renamed to PlasmaData::set_is_decay_corrected and PlasmaData::get_is_decay_corrected
PatlakPlot::get_model_matrix, now it can only be called using class membersBinNormalisation::set_up() now need exam_info_sptr as input.BinNormalisation::apply() and undo now no longer accept start_time and end_time as they are taken from exam_info. To allow this to happen, class Bin has now an extra member time_frame(). Note that it defaults to 1. If this is incorrect, it has to be initialised explicitly (not via a constructor).actual_compute_subset_gradient_without_penalty in the derived classes (which has an extra argument add_sensitivity). Therefore developers that created their own derived class will need to adjust their class accordingly. The public class interface is identical though.DetectorCoordinateMapFromfile (used by SAFIR listmode files) has been renamed to DetectorCoordinateMap and moved from listmode to buildblock.Scanner now has a set_up() function. This needs to be called after using any of the set_*() functions (except set_params). For the blocks/generic scanners, this will fill in the detector maps etc. You will get a run-time exception if you forgot to do this.New templated functions stir::copy_to and stir::fill_from in stir/copy_fill.h which can be used to fill most STIR objects from an iterator range (or copy to). The functions normally use stir_object.begin_all() but resort to stir_object::fill_from or copy_to for a few cases where no iterators exist. We use some specialisations to try and find the fastest version.
Introduced ProjData::standard_segment_sequence function returning 0,+1,-1,..., as used by copy_to and fill_from
stir::read_from_file can now be called with a "node", e.g.
auto uptr = read_from_file<VoxelsOnCartesianGrid<float> >(filename);
; To do this, we now need a typedef hierarchy_base_type at the top level, as otherwise we would need multiple registries. However, this was already required by write_to_file anyway.
GeneralisedPrior and QuadraticPrior have a new method accumulate_Hessian_times_input(output, current_estimate, input). This computes the hessian of the prior at the current_image_estimate and multiplies this by input. Before this, the add_multiplication_with_approximate_Hessian(output, input) method was used that assumed a quadratic function and therefore hessian = 1.Exam_info, TimeFrameDefinition and PatientPosition have now a == operatorcompute_total_ROI_values and compute_ROI_values_per_plane functions to allow the passing of aVoxelsOnCartesianGrid object instead of a Shape3D as the ROI shape. This allows the ROI volume to be constructed during preprocessing for multiple image analysis.KeyParser::parameter_info() now outputs vectorised keys as wellDetectionPosition now has all comparison operators.LOR classes now no longer require phi at input to be between 0 and pi, nor psi to be between 0 and 2 pi. They will standardise the input automatically.ProjDataInMemory in the same order as what is used by copy_to and fill_from. This enabled using straight-forward copy. (This change should not affect anyone, except if you relied on a specific order in the buffer before.)These notes only describe a summary of the changes. Please check documentation/release_4.1.htm
stir_math now supports the --output-format option for dynamic and parametric images as well. (An example file using the Multi format is given in the examples/samples folder).list_lm_info - A new script create_fdef_from_listmode.sh that can be used to create a single-time frame definition file for a given listmode file.xapyb and sapyb where a and b can be scalar or vector types.LmToProjData hierarchy has a new member function set_up(), and more set_* functions, such that it can be used without parsing.ScatterEstimation has now many more set* functions such that most (all?) parameters can be set from C++/Python (i.e. without parsing).SinglesRates hierarchy has been revised. The SinglesRates classes assumed that stored singles were rates but in practice were totals-per-time-interval (for both ECAT7 and RDF9). It is convenient to be able to access totals and rates, so SinglesRates has now get_singles (returning the singles in the time interval) and get_singles_rates (returning the rate per second). Due to the previous confusion, "client"-code will need to be adapted to use either get_singles or get_singles_rate, depending on what is needed