Merge pull request #1090 from levje/levje/rejected_streamlines_arg

FIX: Filter streamlines by length, use the "save rejection" argument.

scripts/scil_tractogram_filter_by_length.py

@@ -48,8 +48,9 @@ def _build_arg_parser():
                    help='Do not write file if there is no streamline.')
     p.add_argument('--display_counts', action='store_true',
                    help='Print streamline count before and after filtering')
-    p.add_argument('--save_rejected', action='store_true',
-                   help='Save rejected streamlines to output tractogram.')
+    p.add_argument('--out_rejected',
+                   help='If specified, save rejected streamlines to this '
+                   'file.')
     add_json_args(p)
     add_reference_arg(p)
     add_verbose_arg(p)
@@ -75,8 +76,17 @@ def main():
     sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
 
     # Processing
-    new_sft, _, outliers_sft = filter_streamlines_by_length(
-        sft, args.minL, args.maxL, return_rejected=True)
+    return_rejected = args.out_rejected is not None
+
+    # Returns (new_sft, _, [rejected_sft]) in filtered_result
+    filtered_result = filter_streamlines_by_length(
+        sft, args.minL, args.maxL, return_rejected=return_rejected)
+
+    new_sft = filtered_result[0]
+
+    if return_rejected:
+        rejected_sft = filtered_result[2]
+        save_tractogram(rejected_sft, args.out_rejected, args.no_empty)
 
     if args.display_counts:
         sc_bf = len(sft.streamlines)

scripts/tests/test_tractogram_filter_by_length.py

@@ -6,6 +6,7 @@
 
 from scilpy import SCILPY_HOME
 from scilpy.io.fetcher import fetch_data, get_testing_files_dict
+from scilpy.io.streamlines import load_tractogram
 
 # If they already exist, this only takes 5 seconds (check md5sum)
 fetch_data(get_testing_files_dict(), keys=['filtering.zip'])
@@ -20,9 +21,55 @@ def test_help_option(script_runner):
 
 def test_execution_filtering(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    # Effectively, this doesn't filter anything, since bundle_4.trk has
+    # all streamlines with lengths of 130mm. This is just to test the
+    # script execution.
     in_bundle = os.path.join(SCILPY_HOME, 'filtering',
                              'bundle_4.trk')
     ret = script_runner.run('scil_tractogram_filter_by_length.py',
                             in_bundle,  'bundle_4_filtered.trk',
                             '--minL', '125', '--maxL', '130')
+
+    sft = load_tractogram('bundle_4_filtered.trk', 'same')
+    assert len(sft) == 52
+
+    assert ret.success
+
+
+def test_rejected_filtering(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_bundle = os.path.join(SCILPY_HOME, 'filtering',
+                             'bundle_all_1mm.trk')
+    ret = script_runner.run('scil_tractogram_filter_by_length.py',
+                            in_bundle,  'bundle_all_1mm_filtered.trk',
+                            '--minL', '125', '--maxL', '130',
+                            '--out_rejected', 'bundle_all_1mm_rejected.trk')
+    assert ret.success
+    assert os.path.exists('bundle_all_1mm_rejected.trk')
+    assert os.path.exists('bundle_all_1mm_rejected.trk')
+
+    sft = load_tractogram('bundle_all_1mm_filtered.trk', 'same')
+    rejected_sft = load_tractogram('bundle_all_1mm_rejected.trk', 'same')
+
+    assert len(sft) == 266
+    assert len(rejected_sft) == 2824
+
+
+def test_rejected_filtering_no_rejection(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_bundle = os.path.join(SCILPY_HOME, 'filtering',
+                             'bundle_4.trk')
+    ret = script_runner.run('scil_tractogram_filter_by_length.py',
+                            in_bundle,  'bundle_4_filtered_no_rejection.trk',
+                            '--minL', '125', '--maxL', '130',
+                            '--out_rejected', 'bundle_4_rejected.trk')
     assert ret.success
+
+    # File should be created even though there are no rejected streamlines
+    assert os.path.exists('bundle_4_rejected.trk')
+
+    sft = load_tractogram('bundle_4_filtered_no_rejection.trk', 'same')
+    rejected_sft = load_tractogram('bundle_4_rejected.trk', 'same')
+
+    assert len(sft) == 52
+    assert len(rejected_sft) == 0