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clabtoolkit 0.5.0

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@yasseraleman yasseraleman released this 21 Oct 16:34
· 103 commits to main since this release
v0.5.0
3ec31bc

clabtoolkit 0.5.0

pip install clabtoolkit==0.5.0 · PyPI

Breaking changes

  • DWI maps: the FA, VF, RA and GA maps of maps_from_tensor_eigenvalues were computed with wrong formulas and are now fixed. Maps made with earlier versions will change.
  • DICOM session names: the study time lost its leading zero (09:15:30 gave ses-2024031291530). It is now ses-20240312091530, so sessions acquired before 10:00 get different folder names.
  • BIDS tables: the suffix column is now Type, and the pipelinetools tables use the original BIDS entity names (Participant, Session, Run, ...). Code reading the old column names must be updated.
  • Renamed: get_ids2process is now get_fullids2process, with a new source parameter ('folders' or 'files').
  • entities_to_table raises ValueError instead of TypeError when filepath is None.

Added

  • DiffusionScheme.simulate_dwi_acq_scheme for shelled and Cartesian (DSI) schemes, and save_path, non_blocking and window_size for DiffusionScheme.plot.
  • window_size for BrainPlotter.plot, plot_hemispheres and plot_scene.
  • pathlib.Path support in es_file.
  • The param entity and the dwimap suffix in the BIDS configuration. - Example notebooks for imagels and pipelinetools.
  • Test suites for pipelinetools, dicomtools, imagetools, segmentativisualizationtools`.
    ### Fixed
  • dwitools: gradient signs from DiffusionScheme.from_bmatrix_array; delete_dwi_volumes and get_from bval files stored as acolumn; get_b0s` crashing without an output name or bval file; inconsistent return types.
  • imagetools: Gaussian smorom_volume andextract_mesh_from_volume; closingremoving voxels on the image border; crop_image_from_maskdroppin;create_spamswith adictionary lookup table;spams2maxprob_from_volumeandregion_growing` no longer modify their inputs.
  • dicomtools: overwrite=True deleting a file without copying it again; ses_id being ignored; create_sessionm_file failing on missing tags or non-DICOM files; org_conv_dicoms exiting Python when no subjects were found, plus exact subject-ID matching and
  • visualizationtools: update_figure_config now validates every parameter before applying any, so one invalid vfiguration half-updated.
    ### Documentation
    Updated CONTRIBUTING.rst, tox.ini and DOCUMENTATION.md; corrected the BrainPlotter and pipelinetools docstringsrnings.

Full changelog:HISTORY.rst

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