[RELEASE] v2.3.1

CHANGELOG.md

@@ -1,6 +1,14 @@
 # Change Log
 ### All notable changes to `COMMIT` will be documented in this file.
 
+## `v2.3.1`<br>_2024-09-24_
+### 🐛Fixed
+- Revert changes when save results in `results.pickle`
+- Add checks on `group_weights_extra`
+
+---
+---
+
 ## `v2.3.0`<br>_2024-07-04_
 ### ✨Added
 - Added support for Windows (requires the `pthread-win32` library) 

commit/core.pyx

@@ -986,6 +986,9 @@ cdef class Evaluation :
 
         # check if group_weights_extra is consistent with the number of groups
         if (regularisation['regIC'] == 'group_lasso' or regularisation['regIC'] == 'sparse_group_lasso') and 'group_weights_extra' in dictIC_params:
+            if type(dictIC_params['group_weights_extra']) not in [list, np.ndarray]:
+                logger.error('"group_weights_extra" must be a list or a numpy array')
+            dictIC_params['group_weights_extra'] = np.array(dictIC_params['group_weights_extra'], dtype=np.float64)
             if np.any(dictIC_params['group_weights_extra'] < 0):
                 logger.error('All group weights must be non-negative')
             if dictIC_params['group_weights_extra'].size != dictIC_params['group_idx'].size:
@@ -1074,7 +1077,7 @@ cdef class Evaluation :
             logger.debug( f'Lambda used: {regularisation["lambdaIC"]}' )
         if regularisation['regIC'] == 'group_lasso' or regularisation['regIC'] == 'sparse_group_lasso':
             logger.debug( f'Number of groups: {len(dictIC_params["group_idx_kept"])}' )
-            if dictIC_params['group_weights_cardinality']==False and dictIC_params['group_weights_adaptive']==False and dictIC_params['group_weights_extra'] is None:
+            if dictIC_params['group_weights_cardinality']==False and dictIC_params['group_weights_adaptive']==False and not ('group_weights_extra' in dictIC_params):
                 logger.debug( 'Group weights are not considered (all ones)' )
             else:
                 str_weights = 'Group weights computed using '
@@ -1595,14 +1598,10 @@ cdef class Evaluation :
         log_list = []
         ret_subinfo = logger.subinfo('results.pickle', indent_char='-', indent_lvl=2, with_progress=True)
         with ProgressBar(disable=self.verbose < 3, hide_on_exit=True, subinfo=ret_subinfo, log_list=log_list):
-            xic, xec, xiso = self.get_coeffs()
-            x = self.x
-            if self.get_config('doNormalizeKernels') :
-                x = x * np.hstack( (norm1*norm_fib,norm2,norm3) )
             with open( pjoin(RESULTS_path,'results.pickle'), 'wb+' ) as fid :
                 self.CONFIG['optimization']['regularisation'].pop('omega', None)
                 self.CONFIG['optimization']['regularisation'].pop('prox', None)
-                pickle.dump( [self.CONFIG, x, self.x], fid, protocol=2 )
+                pickle.dump( [self.CONFIG, self.x, x], fid, protocol=2 )
 
         if save_est_dwi:
             log_list = []

commit/trk2dictionary/trk2dictionary.pyx

@@ -324,14 +324,14 @@ cpdef run( filename_tractogram=None, path_out=None, filename_peaks=None, filenam
             log_list = []
             ret_subinfo = logger.subinfo(f'Clustering with threshold = {blur_clust_thr[0]}', indent_lvl=2, indent_char='-', with_progress=verbose>2)
             with ProgressBar(disable=verbose<3, hide_on_exit=True, subinfo=ret_subinfo, log_list=log_list):
-                idx_centroids = run_clustering(tractogram_in=filename_tractogram, tractogram_out=filename_out,
+                idx_centroids, _ = run_clustering(tractogram_in=filename_tractogram, tractogram_out=filename_out,
                                             temp_folder=path_temp, atlas=blur_clust_groupby, clust_thr=blur_clust_thr[0],
                                             n_threads=n_threads, keep_temp_files=True, force=True, verbose=1, log_list=log_list)
         else:
             log_list = []
             ret_subinfo = logger.subinfo(f'Clustering with threshold = {blur_clust_thr[0]}', indent_lvl=2, indent_char='-', with_progress=verbose>2)
             with ProgressBar(disable=verbose<3, hide_on_exit=True, subinfo=ret_subinfo, log_list=log_list):
-                idx_centroids = run_clustering(tractogram_in=filename_tractogram, tractogram_out=filename_out,
+                idx_centroids, _ = run_clustering(tractogram_in=filename_tractogram, tractogram_out=filename_out,
                                             temp_folder=path_temp, clust_thr=blur_clust_thr[0],
                                             keep_temp_files=True, force=True, verbose=1)
         filename_tractogram = filename_out

pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "dmri-commit"
-version = "2.3.0"
+version = "2.3.1"
 dependencies = [
     "dmri-amico>=2.0.1",
     "dmri-dicelib>=1.1.0",