Merge pull request #646 from EmmaRenauld/fix_bbox_score_bundles

Add check_bbox_false (only in scil_score_bundles)
scilus · Nov 9, 2022 · e838867 · e838867
2 parents 4714ce3 + 2430b1d
commit e838867
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Showing 2 changed files with 9 additions and 7 deletions.
diff --git a/scripts/scil_score_bundles.py b/scripts/scil_score_bundles.py
@@ -72,8 +72,8 @@ def _build_arg_parser():
                         "file are considered \nas absolute paths.")
 
     g = p.add_argument_group("Preprocessing")
-    g.add_argument("--remove_invalid", action="store_true",
-                   help="Remove invalid streamlines before scoring.")
+    g.add_argument("--ignore_invalid", action="store_true",
+                   help="Ignore invalid streamlines in loaded tractograms.")
 
     add_json_args(p)
     add_overwrite_arg(p)
@@ -84,6 +84,7 @@ def _build_arg_parser():
 
 
 def load_and_verify_everything(parser, args):
+    bbox_check = False if args.ignore_invalid else True
 
     assert_inputs_exist(parser, [args.gt_config])
     if not os.path.isdir(args.bundles_dir):
@@ -137,7 +138,7 @@ def load_and_verify_everything(parser, args):
     for bundle in bundle_names:
         vb_name = os.path.join(vb_path, bundle + '_VS.trk')
         if os.path.isfile(vb_name):
-            sft = load_tractogram(vb_name, 'same')
+            sft = load_tractogram(vb_name, 'same', bbox_valid_check=bbox_check)
             vb_sft_list.append(sft)
             if ref_sft is None:
                 ref_sft = sft
@@ -150,7 +151,7 @@ def load_and_verify_everything(parser, args):
     if wpc_path is not None:
         logging.info("Loading WPC bundles")
         for bundle in glob.glob(wpc_path + '/*'):
-            sft = load_tractogram(bundle, 'same')
+            sft = load_tractogram(bundle, 'same', bbox_valid_check=bbox_check)
             wpc_sft_list.append(sft)
             if ref_sft is None:
                 ref_sft = sft
@@ -164,7 +165,7 @@ def load_and_verify_everything(parser, args):
         logging.info("Loading invalid bundles")
         for bundle in glob.glob(ib_path + '/*'):
             ib_names.append(os.path.basename(bundle))
-            sft = load_tractogram(bundle, 'same')
+            sft = load_tractogram(bundle, 'same', bbox_valid_check=bbox_check)
             ib_sft_list.append(ref_sft)
             if ref_sft is None:
                 ref_sft = sft
@@ -173,7 +174,8 @@ def load_and_verify_everything(parser, args):
 
     # Load either NC or IS
     if nc_filename is not None:
-        nc_sft = load_tractogram(nc_filename, 'same')
+        nc_sft = load_tractogram(nc_filename, 'same',
+                                 bbox_valid_check=bbox_check)
         ref_sft = nc_sft
     else:
         nc_sft = None

diff --git a/scripts/tests/test_score_bundles.py b/scripts/tests/test_score_bundles.py
@@ -43,6 +43,6 @@ def test_score_bundles(script_runner):
         json.dump(json_contents, f)
 
     ret = script_runner.run('scil_score_bundles.py',
-                            "config_file.json", "./")
+                            "config_file.json", "./", '--ignore_invalid')
 
     assert ret.success