SIRF Synergistic Image Reconstruction Framework

What's Changed

Summary

• SIRF/STIR

  • The implementation of the creation of sirf.STIR.ImageData from sirf.STIR.AcquisitionData has been revised to ensure compatibility of ImageData dimensions and voxel sizes with AcquisitionData.
  • Missing __del__ added to sirf.STIR.AcquisitionModel.

• SIRF/Registration

  • sirf.Reg.ImageData stores voxels values in a 3D Fortran-style array, hence strides had to be set in ImageData.__array_interface__ accordingly (other SIRF ImageData objects use default C-style).

• Python interface

  • Restored functionality for algebraic operations mixing SIRF data containers and numpy arrays and corrected the description of the result type in User Guide.
  • Error raised if AcquisitionModel.adjoint ran when the model is not linear.

• SIRF

  • Adjoint operator added in common/SIRF.py.
  • Added initial pytorch wrappers and examples, check torch/README.md.
  • Simplified sirf.Utilities.Handle for SWIG backend calls.

Contributions details

• CITATION.cff and mailmap updated by @KrisThielemans in https://github.com/SyneRBI/SIRF/pull/1354.
• Bugs in Release 3.9 fixed by @casperdcl in https://github.com/SyneRBI/SIRF/pull/1355.
• Quick fix for MR data views in the case of numpy version 1.* implemented by @evgueni-ovtchinnikov in https://github.com/SyneRBI/SIRF/pull/1366.
• README revised for clarity and documentation links added by @KrisThielemans in https://github.com/SyneRBI/SIRF/pull/1368.
• SIRF data algebra possible operands extended to numpy arrays by @evgueni-ovtchinnikov in https://github.com/SyneRBI/SIRF/pull/1358.
• Creating compatible ImageData from AcquisitionData and voxels grid dimensions x and y implemented by @evgueni-ovtchinnikov in https://github.com/SyneRBI/SIRF/pull/1364.
• Namespace packages allowed by @casperdcl in https://github.com/SyneRBI/SIRF/pull/1371.
• Mixed data algebra fixed based on __array_priority__ by @evgueni-ovtchinnikov in https://github.com/SyneRBI/SIRF/pull/1373.
• Numerical test for Hessian diagonal added by @ColomboMatte0 in https://github.com/SyneRBI/SIRF/pull/1385.
• Hessian diagonal test tolerance relaxed to 2% by @ColomboMatte0 in https://github.com/SyneRBI/SIRF/pull/1386.
• STIR.AcquisitionModel base class fixed by @evgueni-ovtchinnikov in https://github.com/SyneRBI/SIRF/pull/1387.
• Adding Hessian diagonal Implemented in SIRF by @evgueni-ovtchinnikov in https://github.com/SyneRBI/SIRF/pull/1370.
• Handle usage expanded by @casperdcl in https://github.com/SyneRBI/SIRF/pull/1388.
• Method sirf.Reg.ImageData.asarray() fixed by @evgueni-ovtchinnikov in https://github.com/SyneRBI/SIRF/pull/1376.
• Minor tidy introduced by @casperdcl in https://github.com/SyneRBI/SIRF/pull/1389.
• Handle.__del__ fixed by @evgueni-ovtchinnikov in https://github.com/SyneRBI/SIRF/pull/1394.
• Handle conveniences implemented by @casperdcl in https://github.com/SyneRBI/SIRF/pull/1390.
• Release 3.10.0 prepared by @evgueni-ovtchinnikov in https://github.com/SyneRBI/SIRF/pull/1396.
• Import of deprecated Python package cgitb removed by @evgueni-ovtchinnikov in https://github.com/SyneRBI/SIRF/pull/1397.

New Contributors

• @ColomboMatte0 made their first contribution in https://github.com/SyneRBI/SIRF/pull/1385

Full Changelog: https://github.com/SyneRBI/SIRF/compare/v3.9.0...v3.10.0