Merge pull request scilus#1297 from EmmaRenauld/small_changes_from_my_tests

Small changes from my tests

Author: arnaudbore

src/scilpy/cli/scil_bundle_explore_bundleseg.py

@@ -478,11 +478,16 @@ def main():
     offset = 0
     count = 0
     for bundle in mapping.keys():
-        filename = glob.glob(f'{os.path.join(args.in_folder, bundle)}.t?k')[0]
-
-        if not os.path.exists(filename):
-            logging.warning(f'File {filename} not found.')
+        files = glob.glob(f'{os.path.join(args.in_folder, bundle)}.t?k')
+        if len(files) == 0:
+            logging.warning("Could not find any file fitting pattern {}"
+                            .format(os.path.join(args.in_folder, bundle)))
             continue
+        elif len(files) > 1:
+            logging.warning("Found two files for bundle {}. Selecting the "
+                            "first one. Verify your files!".format(bundle))
+
+        filename = files[0]
         count += 1
 
         tmp_sft = load_tractogram(filename, ref_img)

src/scilpy/cli/scil_tractogram_compute_density_map.py

@@ -77,13 +77,15 @@ def main():
     transformation, dimensions, _, _ = sft.space_attributes
 
     # Processing
+    logging.info("Computing density map...")
     if args.endpoints_only:
         streamline_count = get_endpoints_density_map(sft)
     else:
         streamline_count = compute_tract_counts_map(sft.streamlines,
                                                     dimensions)
 
     # Saving
+    logging.info("Saving density map {}".format(args.out_img))
     dtype_to_use = np.int32
     if args.binary is not None:
         if args.binary == 1:

src/scilpy/cli/scil_tractogram_segment_with_bundleseg.py

@@ -55,7 +55,8 @@
                              add_reference_arg, add_verbose_arg,
                              assert_inputs_exist,
                              assert_output_dirs_exist_and_empty,
-                             load_matrix_in_any_format, ranged_type)
+                             load_matrix_in_any_format, ranged_type,
+                             assert_inputs_dirs_exist)
 from scilpy.segment.voting_scheme import VotingScheme
 from scilpy.version import version_string
 
@@ -136,6 +137,7 @@ def main():
     logging.getLogger().setLevel(logging.getLevelName('INFO'))
 
     # Verifications
+    assert_inputs_dirs_exist(parser, args.in_directory)
     in_models_directories = [
         os.path.join(args.in_directory, x)
         for x in os.listdir(args.in_directory)

src/scilpy/cli/scil_tractogram_segment_with_recobundles.py

@@ -112,8 +112,8 @@ def main():
     if args.tractogram_clustering_thr and args.in_pickle:
         parser.error("Option --tractogram_clustering_thr should not be "
                      "used with --in_pickle.")
-    else:
-        # Setting default value. (Will be ignored in args.in_pickle)
+    elif args.tractogram_clustering_thr is not None:
+        # Setting default value. (Will be ignored if args.in_pickle)
         args.tractogram_clustering_thr = 8.0
 
     # Loading