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CHANGELOG.md

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Change Log

All notable changes to COMMIT will be documented in this file.

v2.3.1
2024-09-24

🐛Fixed

  • Revert changes when save results in results.pickle
  • Add checks on group_weights_extra

v2.3.0
2024-07-04

✨Added

  • Added support for Windows (requires the pthread-win32 library)
  • Precompiled wheels for Windows, MacOS, and Linux are now available on PyPI

🛠️Changed

  • operator.pyx no more compiled at runtime
  • Restict the numpy version to <2.0.0

🐛Fixed

  • Improved output when running from Jupyter notebooks

v2.2.0
2024-04-12

🐛Fixed

  • Fix set_thread isotropic compartment voxel distribution

✨Added

  • Add do_reweighting parameter to save_results()
  • Add logging module to handle console output

v2.1.0
2024-01-22

✨Added

  • Work In Progress (WIP) models
  • Different regularizers

🐛Fixed

  • Merged PR #127: [FIX] Operator is not recompiled when some parameters are changed
  • Merged PR #129: [FIX] Fista update

v2.0.1
2023-10-31

🛠️Changed

  • Bump dependencies

🐛Fixed

  • Add dtype=np.object_ to inhomogemeous shape arrays
  • Fix egg_base option in setup.cfg (create the build folder before running setup())
  • Fix trk2didtionary crash when run from Jupyter notebooks (removed C-level stdout from Jupyter notebook)

v2.0.0
2023-09-14

🛠️Changed

  • Default ndirs=500 in core.generate_kernels() and in trk2dictionary.run()
  • Expire the deprecated ndirs parameter in amico.core.setup()
  • Expire the deprecated filename_trk and gen_trk parameters in trk2dictionary.run()
  • Removed unused parameter ndirs from trk2dictionary_c.cpp()
  • Build output goes into build
  • Switched to proprietary license (see LICENSE file)

✨Added

  • Added clustering in trk2dictionary.run()

    • geometry-based clustering using blur_clust_thr parameter
    • anatomical information streamlines clustering based on their endpoints using blur_clust_groupby parameter

  • Added trk2dictionary.run() parallel computation using n_threads parameter

  • Changed internal streamlines representation using blur_core_extent and blur_gauss_extent parameters

  • Added possibility to keep temporal files created by parallel trk2dictionary.run() and clustering using keep_temp parameter

  • Parallel compilation

🐛Fixed

  • Bugfixes

[1.6.5] - 2023-08-03

Changed

  • Build output goes into 'build'
  • Require dmri-amico>=1.3.2,<2.0.0

Fixed

[1.6.4] - 2023-02-14

Fixed

  • Invalid command 'bdist_wheel' error when install with pip<=20.0.2

[1.6.3] - 2022-10-21

Changed

  • Ensure non-negative values in the 'y' vector before fit

Added

  • 'replace_bad_voxels' parameter in 'load_data()' to replace NaN and Inf values in the signal

[1.6.2] - 2022-05-05

Fixed

  • Problem with very anisotropic voxelsizes

[1.6.1] - 2022-01-31

Changed

  • generate_kernels: forcing 'ndirs' to 1 in case of 'VolumeFraction' model
  • core.setup: removed 'ndirs' parameter, now precomputes all directions

Added

  • Shortcut 'commit.core.setup' to 'commit.setup'

[1.6.0] - 2021-12-03

Changed

  • Improved the blur functionality

[1.5.3] - 2021-12-03

Added

  • Option 'coeffs_format' to 'save_results()'

Changed

  • Install information are stored (and taken from) commit/info.py

[1.5.2] - 2021-10-27

Fixed

  • Missing dependencies

[1.5.1] - 2021-10-11

Added

  • Option 'get_normalized' to 'save_coeffs()'

[1.5.0] - 2021-06-19

Added

  • Possibility to specify a voxel confidence map

Fixed

  • Set license: BSD-3-Clause License
  • Indices of groups in case of streamlines that were pre-filtered during trk2dictionary

Changed

  • Loading of nii data using (np.asanyarray( nii.dataobj )) in core and trk2dictionary
  • confidence_map from float64 to float32

[1.4.6] - 2021-03-25

Fixed

  • Length of short segments to neglect
  • Streamline weights, in case of blur, are properly scaled

[1.4.5] - 2021-02-08

Fixed

  • operator.pyxbld: Changed the condition to create a new operator
  • trk2dictionary.pyx: Check that the tractogram exists before trying to load it and remove the try section
  • trk2dictionary.run(): fixed bug with blur parameters and computing the blur

Added

  • core.pyx: Add to the function build_operator the parameter build_dir

Changed

  • core.pyx: The function build_operator checks if the LUT configuration changed before build a new operator
  • verbose variables in core.pyx and solvers.py changed to be boolean
  • trk2dictionary.run(): removed 'points_to_skip' option

[1.4.4] - 2020-10-28

Changed

  • Option to set one single direction in the resolution of the LUT

[1.4.3] - 2020-10-22

Added

  • store model parameters to results.pickle

[1.4.2] - 2020-10-22

Fixed

  • trk2dictionary.run(): check for invalid parameters passed to the blur

[1.4.1] - 2020-10-21

Fixed

  • operator.pyxbld: Changed the condition to create a new operator

Added

  • COMMIT version is stored in results.pickle
  • COMMIT version is stored in output NIFTI files

[1.4.0.4] - 2020-09-24

Fixed

  • trk2dictionary.run(): bug in the blurring functionality
  • trk2dictionary.run(): 'blur_sigma' defaults to 0

[1.4.0.3] - 2020-08-07

Fixed

  • COMMIT_debugger: compilation problem
  • COMMIT_debugger: wrong visualization in Linux

[1.4.0.2] - 2020-08-07

Changed

  • Moved the documentation to the Wiki

[1.4.0.1] - 2020-08-03

Changed

  • Updated the installation guide

[1.4.0.0] - 2020-07-30

Changed

  • trk2dictionary.run(): removed 'gen_trk' option
  • save_results(): removed 'save_coeff' and 'save_opt_details' parameters
  • save_results(): now saving only streamline_weights.txt (not anymore xic.txt, xec.txt, xiso.txt)
  • load_dictionary(): renamed 'use_mask' to 'use_all_voxels_in_mask'
  • Removed unused 'dictionary_ndirs.dict' file
  • trk2dictionary.run(): 'min_fiber_len' defaults to 0.0 for backward compatibility

Added

  • added 'get_coeffs()' function to get all estimated coefficients
  • save_results(): added 'stat_coeffs' parameter for saving streamline weights
  • trk2dictionary.run(): added 'max_fiber_len' parameter to discard long streamlines
  • load_data(): added 'b0_min_signal' to discard voxels with very low signal

[1.3.9] - 2020-06-09

Changed

  • Modify setup.py and fix spams dependencies

[1.3.8] - 2020-05-12

Changed

  • Improvements to the COMMIT_debugger.

[1.3.7] - 2020-04-25

Changed

  • Adapt demos to use d_perps instead of ICVFs for setting model parameters.

[1.3.6] - 2020-04-22

Fixed

  • Bug when the selected model has EC compartments but no peaks are provided (in trk2dictionary).

[1.3.5] - 2020-04-08

Added

  • Parameter 'min_fiber_len' in trk2dictionary to discard streamlines shorter than a given length in mm.

Fixed

  • Bug when 'points_to_skip' was higher then streamline length.
  • Few corrections to docstring of trk2dictionary.

[1.3.4] - 2020-04-02

Changed

  • Added colorized output. NB: needs AMICO 1.2.0 or above.

[1.3.3] - 2020-03-31

Added

  • Added possibility to save the predicted DW-MR signal in save_results.

Fixed

  • Minor cleanup.

[1.3.2] - 2020-03-27

Added

  • Check if dictionary (upon loading) and data have the same geometry.

Fixed

  • Bug while saving coefficients in save_results.

[1.3.1] - 2020-03-27

Fixed

  • Improved the loading of the streamlines in trk2dictionary

[1.3] - 2019-10-30

This version of COMMIT is not compatible with AMICO v1.0.1 of below. If you update COMMIT to this version, please update AMICO to version 1.1.0 or above.

Added

  • Changelog file to keep tracking of the COMMIT versions.

Changed

  • Added compatibility with low resolution LUTs.

Fixed

  • Nothing.