filter_by_roi: add more tests. Fixes.

scripts/scil_tractogram_filter_by_roi.py

@@ -156,15 +156,18 @@ def _build_arg_parser():
 
 
 def _convert_filering_list_to_roi_args(parser, args):
-    with open(args.filtering_list) as txt:
+    assert_inputs_exist(parser, args.filtering_list)
+
+    with open(args.filtering_list, 'r') as txt:
         content = txt.readlines()
+
     for roi_opt in content:
-        if "\"" in roi_opt:
-            # Hein?? À tester
-            tmp_opt = [i.strip() for i in roi_opt.strip().split("\"")]
-            tmp_opt = [tmp_opt[0].split() + [tmp_opt[1]] + tmp_opt[2].split()]
-        else:
-            tmp_opt = roi_opt.strip().split()
+        # Convert the line with spaces to a list of args.
+        tmp_opt = roi_opt.split()
+
+        # Manage cases with " " or ' ' around options
+        tmp_opt = [i.replace("\"", '') for i in tmp_opt]
+        tmp_opt = [i.replace("'", '') for i in tmp_opt]
 
         if tmp_opt[0] == 'drawn_roi':
             args.drawn_roi.append(tmp_opt[1:])
@@ -221,6 +224,7 @@ def _read_and_check_overwrite_distance(parser, args):
 def _check_values(parser, mode, criteria, distance):
     if mode not in ['any', 'all', 'either_end', 'both_ends']:
         parser.error('{} is not a valid option for filter_mode'.format(mode))
+
     if criteria not in ['include', 'exclude']:
         parser.error('{} is not a valid option for filter_criteria'
                      .format(criteria))
@@ -251,28 +255,34 @@ def _prepare_filtering_criteria(
     for roi_opt in bdo:
         roi_opt_list.append(['bdo'] + roi_opt)
     for roi_opt in x_plane:
-        if not (0 <= roi_opt[0] < dim[0]):
+        roi_opt[0] = float(roi_opt[0])
+        if not roi_opt[0].is_integer():
+            parser.error("x_plane's plane number must be and integer.")
+        roi_opt[0] = int(roi_opt[0])
+        if not (0 <= roi_opt[0] < int(dim[0])):
             parser.error('x_plane is not valid according to the tractogram '
                          'header. Expecting a value between {} and {}'
                          .format(0, dim[0]))
-        if not roi_opt.is_integer():
-            parser.error("x_plane must be an integer value")
         roi_opt_list.append(['x_plane'] + roi_opt)
     for roi_opt in y_plane:
-        if not (0 <= roi_opt[0] < dim[1]):
+        roi_opt[0] = float(roi_opt[0])
+        if not roi_opt[0].is_integer():
+            parser.error("y_plane's plane number must be and integer.")
+        roi_opt[0] = int(roi_opt[0])
+        if not (0 <= roi_opt[0] < int(dim[1])):
             parser.error('y_plane is not valid according to the tractogram '
                          'header. Expecting a value between {} and {}'
                          .format(0, dim[1]))
-        if not roi_opt.is_integer():
-            parser.error("y_plane must be an integer value")
         roi_opt_list.append(['y_plane'] + roi_opt)
     for roi_opt in z_plane:
-        if not (0 <= roi_opt[0] < dim[2]):
+        roi_opt[0] = float(roi_opt[0])
+        if not roi_opt[0].is_integer():
+            parser.error("z_plane's plane number must be and integer.")
+        roi_opt[0] = int(roi_opt[0])
+        if not (0 <= roi_opt[0] < int(dim[2])):
             parser.error('z_plane is not valid according to the tractogram '
                          'header. Expecting a value between {} and {}'
                          .format(0, dim[2]))
-        if not roi_opt.is_integer():
-            parser.error("z_plane must be an integer value")
         roi_opt_list.append(['z_plane'] + roi_opt)
 
     # b) Format to 4-item list, with 0 distance if not specified.
@@ -326,12 +336,11 @@ def main():
 
     assert_inputs_exist(parser, args.in_tractogram,
                         roi_files_with_header + roi_files_no_header +
-                        [args.reference, args.filtering_list])
+                        [args.reference])
     assert_outputs_exist(parser, args, args.out_tractogram,
                          [args.save_rejected] + other_outputs)
     assert_headers_compatible(parser, args.in_tractogram,
-                              roi_files_with_header + [args.filtering_list],
-                              reference=args.reference)
+                              roi_files_with_header, reference=args.reference)
 
     dict_overwrite_distance = _read_and_check_overwrite_distance(parser, args)
 

scripts/tests/test_tractogram_filter_by_roi.py

@@ -11,6 +11,12 @@
 fetch_data(get_testing_files_dict(), keys=['filtering.zip'])
 tmp_dir = tempfile.TemporaryDirectory()
 
+# toDo. Add an altas and test option --atlas_roi
+in_tractogram = os.path.join(SCILPY_HOME, 'filtering',
+                             'bundle_all_1mm_inliers.trk')
+in_roi = os.path.join(SCILPY_HOME, 'filtering', 'mask.nii.gz')
+in_bdo = os.path.join(SCILPY_HOME, 'filtering', 'sc.bdo')
+
 
 def test_help_option(script_runner):
     ret = script_runner.run('scil_tractogram_filter_by_roi.py', '--help')
@@ -19,32 +25,39 @@ def test_help_option(script_runner):
 
 def test_execution_filtering(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
-    in_tractogram = os.path.join(SCILPY_HOME, 'filtering',
-                                 'bundle_all_1mm_inliers.trk')
-    in_roi = os.path.join(SCILPY_HOME, 'filtering',
-                          'mask.nii.gz')
-    in_bdo = os.path.join(SCILPY_HOME, 'filtering',
-                          'sc.bdo')
+
     ret = script_runner.run('scil_tractogram_filter_by_roi.py', in_tractogram,
-                            'bundle_4.trk', '--display_counts',
+                            'bundle_1.trk', '--display_counts',
                             '--drawn_roi', in_roi, 'any', 'include',
                             '--bdo', in_bdo, 'any', 'include',
-                            '--save_rejected', 'bundle_4_rejected.trk')
+                            '--x_plane', '0', 'either_end', 'exclude',
+                            '--y_plane', '0', 'all', 'exclude', '0',
+                            '--z_plane', '0', 'either_end', 'exclude', '1',
+                            '--save_rejected', 'bundle_1_rejected.trk')
     assert ret.success
 
 
-def test_execution_filtering_distance(script_runner, monkeypatch):
+def test_execution_filtering_overwrite_distance(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
-    in_tractogram = os.path.join(SCILPY_HOME, 'filtering',
-                                 'bundle_all_1mm_inliers.trk')
-    in_roi = os.path.join(SCILPY_HOME, 'filtering',
-                          'mask.nii.gz')
-    in_bdo = os.path.join(SCILPY_HOME, 'filtering',
-                          'sc.bdo')
+
     ret = script_runner.run('scil_tractogram_filter_by_roi.py', in_tractogram,
-                            'bundle_5.trk', '--display_counts',
+                            'bundle_2.trk', '--display_counts',
                             '--drawn_roi', in_roi, 'any', 'include', '2',
-                            '--bdo', in_bdo, 'any', 'include', '3',
-                            '--overwrite_distance', 'any', 'include', '2',
-                            '--save_rejected', 'bundle_5_rejected.trk')
+                            '--overwrite_distance', 'any', 'include', '4')
+    assert ret.success
+
+
+def test_execution_filtering_list(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+
+    # Write a list of options
+    filelist = 'my_filelist.txt'
+    with open(filelist, 'w') as f:
+        f.write('drawn_roi {} any include\n'.format(in_roi))
+        f.write('bdo {} "any" "include"\n'.format(in_bdo))
+        f.write("bdo {} 'any' include".format(in_bdo))
+
+    ret = script_runner.run('scil_tractogram_filter_by_roi.py', in_tractogram,
+                            'bundle_3.trk', '--display_counts',
+                            '--filtering_list', filelist)
     assert ret.success