- Revert changes when save results in
results.pickle
- Add checks on
group_weights_extra
- Added support for Windows (requires the
pthread-win32
library) - Precompiled wheels for Windows, MacOS, and Linux are now available on PyPI
operator.pyx
no more compiled at runtime- Restict the
numpy
version to<2.0.0
- Improved output when running from Jupyter notebooks
- Fix
set_thread
isotropic compartment voxel distribution
- Add
do_reweighting
parameter tosave_results()
- Add logging module to handle console output
- Work In Progress (WIP) models
- Different regularizers
- Merged PR #127: [FIX] Operator is not recompiled when some parameters are changed
- Merged PR #129: [FIX] Fista update
- Bump dependencies
- Add
dtype=np.object_
to inhomogemeous shape arrays - Fix
egg_base
option insetup.cfg
(create thebuild
folder before runningsetup()
) - Fix
trk2didtionary
crash when run from Jupyter notebooks (removed C-level stdout from Jupyter notebook)
- Default
ndirs=500
incore.generate_kernels()
and intrk2dictionary.run()
- Expire the deprecated
ndirs
parameter inamico.core.setup()
- Expire the deprecated
filename_trk
andgen_trk
parameters intrk2dictionary.run()
- Removed unused parameter
ndirs
fromtrk2dictionary_c.cpp()
- Build output goes into
build
- Switched to proprietary license (see
LICENSE
file)
-
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
- geometry-based clustering using
-
Added trk2dictionary.run() parallel computation using
n_threads
parameter -
Changed internal streamlines representation using
blur_core_extent
andblur_gauss_extent
parameters -
Added possibility to keep temporal files created by parallel trk2dictionary.run() and clustering using
keep_temp
parameter -
Parallel compilation
- Bugfixes
- Build output goes into 'build'
- Require
dmri-amico>=1.3.2,<2.0.0
- Solve #121
- Invalid command 'bdist_wheel' error when install with pip<=20.0.2
- Ensure non-negative values in the 'y' vector before fit
- 'replace_bad_voxels' parameter in 'load_data()' to replace NaN and Inf values in the signal
- Problem with very anisotropic voxelsizes
- generate_kernels: forcing 'ndirs' to 1 in case of 'VolumeFraction' model
- core.setup: removed 'ndirs' parameter, now precomputes all directions
- Shortcut 'commit.core.setup' to 'commit.setup'
- Improved the blur functionality
- Option 'coeffs_format' to 'save_results()'
- Install information are stored (and taken from) commit/info.py
- Missing dependencies
- Option 'get_normalized' to 'save_coeffs()'
- Possibility to specify a voxel confidence map
- Set license: BSD-3-Clause License
- Indices of groups in case of streamlines that were pre-filtered during trk2dictionary
- Loading of nii data using (np.asanyarray( nii.dataobj )) in core and trk2dictionary
- confidence_map from float64 to float32
- Length of short segments to neglect
- Streamline weights, in case of blur, are properly scaled
- 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
- core.pyx: Add to the function build_operator the parameter build_dir
- 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
- Option to set one single direction in the resolution of the LUT
- store model parameters to results.pickle
- trk2dictionary.run(): check for invalid parameters passed to the blur
- operator.pyxbld: Changed the condition to create a new operator
- COMMIT version is stored in results.pickle
- COMMIT version is stored in output NIFTI files
- trk2dictionary.run(): bug in the blurring functionality
- trk2dictionary.run(): 'blur_sigma' defaults to 0
- COMMIT_debugger: compilation problem
- COMMIT_debugger: wrong visualization in Linux
- Moved the documentation to the Wiki
- Updated the installation guide
- 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 '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
- Modify setup.py and fix spams dependencies
- Improvements to the COMMIT_debugger.
- Adapt demos to use d_perps instead of ICVFs for setting model parameters.
- Bug when the selected model has EC compartments but no peaks are provided (in trk2dictionary).
- Parameter 'min_fiber_len' in trk2dictionary to discard streamlines shorter than a given length in mm.
- Bug when 'points_to_skip' was higher then streamline length.
- Few corrections to docstring of trk2dictionary.
- Added colorized output. NB: needs AMICO 1.2.0 or above.
- Added possibility to save the predicted DW-MR signal in save_results.
- Minor cleanup.
- Check if dictionary (upon loading) and data have the same geometry.
- Bug while saving coefficients in save_results.
- Improved the loading of the streamlines in trk2dictionary
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.
- Changelog file to keep tracking of the COMMIT versions.
- Added compatibility with low resolution LUTs.
- Nothing.