SIRF Release 3.8.0

What's Changed

• SIRF/STIR (PET and SPECT)

  • use direct STIR operations for arrays, potentially resulting in speed-up when using STIR 6.2 or later
  • fixed STIR linking problems by adding STIR_REGISTRIES to Reg executables
  • added compute_attenuation_factors method to AcquisitionSensitivityModel
  • added means for setting maximal and minimal value for scale factor in stir::ScatterEstimation
  • added support for the STIR 6.2 (somewhat experimental) Cuda Relative Difference Prior

• MR

  • fixed density_weight shape issue caused by upgrading numpy to version 2.0

• CMake/building:

  • set CMP0074 policy to NEW, i.e. honour _ROOT env variables

SIRF Release 3.7.0

What's Changed

• CMake improvements when coping with old Gadgetron by @KrisThielemans in #1236
• Enabling PET reconstruction from list mode data by @evgueni-ovtchinnikov in #1103
• Added optional argument out in all gradient-computing methods by @evgueni-ovtchinnikov in #1246
• sapyb to return even if out is not None by @paskino in #1254
• Computing Hessian products with image data objects and related stuff by @evgueni-ovtchinnikov in #1253
• Updated data submodule by @evgueni-ovtchinnikov in #1256
• V3.7.0 prep by @KrisThielemans in #1258

Full Changelog: v3.6.0...v3.7.0

v3.6.0

• PET:

  • ensured compatibility with STIR 6.0, which supports Time-of-Flight data.
  • added extra members to ScatterEstimation to set behaviour of OSEM used during scatter estimation.
  • added missing set/get methods for OSSPS relaxation_parameter, relaxation_gamma and upper_bound.
  • added test for scatter simulation and estimation.

• CMake/building:

  • default DISABLE_MATLAB to ON as our Matlab support is out-of-date and could
    generate conflicts with Python shared libraries.

• Demo scripts:

  • replaced importing reconstruction engines from calling exec to importing via importlib.import_module thus enabling code completion (and getting rid of Codacy complaints about undefined modules).

• Python interfaces for the reconstruction engines:

  • Several allocate methods in STIR.py, Gadgetron.py and Reg.py are replaced with just one allocate in DataContainer class that does not copy data between Python and C++.
  • return None in the method Datacontainer.shape() replaced with more Pythonesque return (0,).

• MR

  • Improved handling of "irregular" ISMRMRD acquisitions by providing IgnoreMask object that allows the user to specify which kind of acquisitions is to be ignored. By default, no acquisition is ignored when reading from file.

• Registration

  • fixed handling of complex images in NiftiImageData.cpp.

v3.5.0

• SIRF/common:

  • Replaced Python implementation of DataContainer methods with simple Python wraps of their C++ implementation.

  • Provided C++ tools for accessing the examples data (examples_data_path and utility functions such as append_path in common/utilities.h).

• MR

  • Re-designed handling of "irregular" ISMRMRD acquisitions, making it user-controlled and more flexible. See #1174 for more information.

  • Allow user to set radial, goldenangle, spiral and rpe trajectories.

  • Added setter for acquisition header information and encoding limits. This allows the user to modify the reconstructed k-space dimensions and enables e.g. retrospective motion resolved or time-resolved reconstructions, or combinations of such dimensions. The acquisition model picks up these changes automatically if the encoding limits are set correctly.

  • Added Gadgetron gadgets that allow for k-space filtering, coil compression and partial fourier reconstruction.

• PET/SPECT

  • Added SIRF interfaces to STIR functions to know where its files are: get_STIR_doc_dir() and get_STIR_examples_dir().

  • Added SIRF interfaces to STIR functions for LogcoshPrior and RelativeDifferencePrior.

  • Added SIRF interfaces to STIR functions for kappa (spatially variant penalty strengths) for QP, Log-cosh, and RDP.

  • Fixed IterativeReconstructor.get_objective_function().

v3.4.0

• MR:

  • Added support for spiral trajectories that are pre-computed by the user (by exposing a trajectory setter).
  • Writing images to .dcm files fixed.
  • Running image processing chains after reconstruction fixed.
  • Use C++ 17 if Gadgetron-support is enabled.
  • Support Gadgetron master of end November 2022
    • using find_package(gadgetron) in CMake, but still support old version by looking for toolboxes.

• PET/SPECT

  • Require STIR 5.0 and support 5.1.
  • If SIRF is compiled with STIR 5.1, we now support Pinhole SPECT via the PinholeSPECTUBMatrix acquisition model. Examples are provided (but the code is not yet tested).
  • sirf.STIR.AcquisitionData constructor taking a scanner now has an extra optional argument
    tof_mash_factor (defaulting to 1). This is only functional if a STIR version supporting TOF is used.
  • C++: Renamed PETAcquisitionData and derived classes to STIRAcquisitionData* as STIR now supports SPECT in addition to PET modality. Backward compatibility ensured by defining old nomenclature via typedefs until the release of SIRF 4.

• Documentation

  • revision of READMEs for the examples.

• Changed Python test framework to pytest.

• Added support for the extraction of subsets of STIR and Gadgetron acquisition data.

v3.3.0

• Added a new acquisition model SPECTUBMatrix for (simple) usage in SPECT.
  sirf.STIR.ImageData has now a way to set/get the modality.

• interactive Python demos superseded by SIRF-Exercises notebooks removed.

• arguments setting number of CG iterations and verbosity of output
  of acquisition models method norm() added.

• path for ISMRMRD shared library when generating MR data fixed.

• extension processing in ISMRMRDImageData::write fixed.

• Python int array check/conversion ensuring C++ compatibility added.

• C/Python interfaces for computing prior value added.

• added CITATION.cff file (replacing .zenodo.json`)

v3.2.0

• To avoid appending to an existing .h5 file, writing methods now first check whether the file to which data is to be written already exists, and if so, delete it before writing.

• A version.h is created by CMake and installed to access version minor and major from C++.

• MR

  • added acquisition models for 2D non-cartesian encoding.
  • The 2D radial, golden-angle increment radial and stack-of-stars trajectory are supported.

• MR Geometry

  • fixed GadgetronImagesVector::reorient() to only consider slice index
    and ignore dimensions such as contrast, repetition etc.

• PET/STIR

  • (C++) Replaced where possible returning stir::Succeeded::no with throwing exception.
  • (C++) Fixed a bug in PETAcquisitionDataInMemory::norm.
  • (C++) Expose advanced parameters from STIR to sirf.STIR.RayTracingMatrix
  • (Python) Expose advanced parameters from STIR to sirf.STIR.RayTracingMatrix and add get_info()

• SIRF Python interface

  • Removed __div__ , __idiv__ operators for DataContainers required for Python2.
  • Added __truediv__ and __itruediv__ Python3 operators to DataContainer algebra.

• Build system

  • export a CMake config file such that external C++ projects can use SIRF via CMake,
    see the examples/C++ directory for basic usage.
  • during the build step the executable ismrmrd_generate_cartesian_shepp_logan is called
    to generate simulated data to be used in tests such that the test data are compatible with
    the installed ISMRMRD version.
  • we now require ISMRMRD v1.4.2.1 to allow for the -w flag for the creation of Shepp
    Logan test data during build.

• Other changes

  • added conjugation methods to DataContainer

v3.1.1

minor fixes w.r.t. v3.1.0

v3.1.0

v3.1.0

• MR/Gadgetron

  • Golden-angle radial phase encoding (RPE) trajectory is supported if Gadgetron toolboxes were found during building
    
    WARNING if Gadgetron was compiled with CUDA support, you need to build SIRF with the Gadgetron_USE_CUDA CMake variable set to ON.
  • Automatic calling of sort_by_time() in most places. This ensures that only consistent images are reconstructed.
  • Encoding classes perform the Fourier transformations instead of the MRAcquisitionModel
  • CoilSensitivitiesVector class now has forward and backward method using the encoding classes getting rid of the duplicate FFT code used to compute coil sensitivities from MRAcquisitionData.
  • Added constructor for GadgetronImagesVector from MRAcquisitionData. This allows setting up an MR acquisition model without having to perform a reconstruction first.

• PET/STIR

  • iterative reconstructors set_current_estimate and get_current_estimate now create a clone to avoid surprising modifications of arguments. The old behaviour of set_current_estimate can still be achieved by set_estimate.
    
    Warning This is backwards incompatible, but arguably a bug fix.

• SIRF Python interface

  • range_geometry and domain_geometry methods of AcquisitionModel classes, required by CIL algorithms, now obtain data via respective C++ AcquisitionModel classes accessors, in line with our strategy of keeping interface code minimal
  • sirf.Gadgetron.AcquisitionData.get_info was renamed to get_ISMRMRD_info to avoid
    confusion with the other get_info() methods that return a string. (get_info still works but issues a deprecation warning).

• Build system

  • fix bug with older CMake (pre-3.12?) that the Python interface was not built
    #939.

SIRF v3.0.0

New features

• PET
  • Addition of sirf.STIR.ScatterEstimation and ScatterSimulation to allow (non-TOF) scatter estimation in PET
  • GE Signa PET/MR reading of listmode data, sinograms, normalisation and randoms support added.
  • If STIR is at least version 5 or built from the master branch, [Georg Schramm's parallel (computing) projector](https://github.com/gschramm/parallelproj proj) is now made available from SIRF (use AcquisitionModelUsingParallelproj). This uses Joseph interpolation, but importantly can use your GPU (if CUDA was found during building).
  • Implemented extraction of the operator representing the linear part of PET acquisition model and computation of its norm.
  • When adding a shape to a sirf.STIR.ImageData, optionally give the number of times to sample a voxel. This is useful when the shape partially - but not completely - fills a voxel.
  • If storage_scheme is set to memory, PETAcquisitionData allows direct modification, whereas before a copy would need to be created first. (Internally, it uses STIR ProjDataInMemory, instead of ProjDataFromStream).
• Registration
  • Registration of 2d images is now supported with aladin and f3d.
• examples data:
  • Installs examples, data and doc to the install directory, i.e. ${CMAKE_INSTALL_PREFIX}/share/SIRF-<version_major>.<version_minor> directory.
  • If the SIRF_DATA_PATH environment variable is set, examples_data_path will search for the examples data there, or in SIRF_INSTALL_PATH/share/SIRF-<version_major>.<version_minor>/data directory. In MATLAB, the example_data_path function has the version set by CMake at install time.
• Other Python features:
  • Define __version__ in sirf python package.
  • Added implementation of division and multiplication for NiftiImageData.
  • Data validity checks return NotImplemented instead of throwing error, opening the door for future implementations of operations on data.

Backwards incompatible changes

• STIR version 4.1.0 is now required.
• Python 2 is no longer supported. Most code might still work, but we do not check. A warning is written when the Python version found is 2. This will be changed to FATAL_ERROR at a later stage.
• Handling of coil images and sensitivities in C++ code simplified by inheriting CoilImagesVector from GadgetronImagesVector and replacing CoilSensitivitiesAsImages with CoilSensitivitiesVector, also inheriting from GadgetronImagesVector. All methods of CoilImagesVector and CoilSensitivitiesVector other than those inherited from GadgetronImagesVector are no longer supported except methods named compute(), which are renamed to calculate().

Deprecations (will be errors in SIRF 4.0)

• Registration: renamed Resample to Resampler and NiftyResample to NiftyResampler. Old names are now deprecated but should still work.
• STIR AcquisitionModel forward, direct, backward and adjoint signatures have changed in Python. Subset information should now be set via num_subsets and subset_num members. The forwardandbackwardmembers can still be called with the previous syntax but this will be removed in a later version. Note that default values ofnum_subsetsandsubset_num` are 0 and 1 respectively, such that default behaviour is default behaviour (i.e. process all data) is unchanged.
• MR acquisition data storage scheme restricted to memory only (a message will be printed but no error thrown)
• Use CMake variable names from find_package(Python) which are available with CMake 3.12+. SIRF CMake files will accept both Python_EXECUTABLE or PYTHON_EXECUTABLE, for the latter it will send a deprecation warning.

Other changes

• When registering, internally the forward displacement is no longer stored, replaced by the forward deformation. The inverse is no longer stored, and is calculated as needed.
• PETAcquisitionData.axpby now uses STIR's axpby and is therefore faster.
• Speed-up in stir::AcquisitionDataInMemory of as_array, fill, dot, norm, etc. (by using STIR iterators).
• Added common Python DataContainer algebra unit tests for all DataContainer inherited classes.
• Continuous Integration now uses Github Actions. Travis-CI has been dropped.
• New CMake option BUILD_DOCUMENTATION to use doxygen to build C++ documentation.
  It will be installed in the share/SIRF-version/doc/doxygen.

Bug fixes

• Python fill method in MR DataContainer accepts numpy array, number or DataContainer.
• get_index_to_physical_point_matrix() returned a wrong matrix in MATLAB and Python.
• path manipulation of examples_data_path now should work for any platform, not just linux.