Fibertube Density

scripts/scil_fibertube_compute_density.py

@@ -12,6 +12,11 @@
 3. By doing the same steps for samples that landed within 2 or more
 fibertubes, we can create a density map of the fibertube collisions.
 
+To form fibertubes from a set of streamlines, you can use the scripts:
+- scil_tractogram_filter_collisions.py to assign a diameter to each streamline
+  and remove all colliding fibertubes.
+- scil_tractogram_dps_math.py to assign a diameter without filtering.
+
 See also:
     - docs/source/documentation/fibertube_tracking.rst
 """
@@ -39,12 +44,8 @@ def _build_arg_parser():
 
     p.add_argument('in_fibertubes',
                    help='Path to the tractogram (must be .trk) file \n'
-                        'containing fibertubes. They must be: \n'
-                        '1- Void of any collision. \n'
-                        '2- With their respective diameter saved \n'
-                        'as data_per_streamline. \n'
-                        'For both of these requirements, see \n'
-                        'scil_tractogram_filter_collisions.py.')
+                        'containing fibertubes. They must have their \n'
+                        'respective diameter saved as data_per_streamline.')
 
     p.add_argument('--out_density_map', default=None, type=str,
                    help='Path of the density Nifti image.')

scripts/scil_fibertube_score_tractogram.py

@@ -80,13 +80,9 @@ def _build_arg_parser():
         formatter_class=argparse.RawTextHelpFormatter)
 
     p.add_argument('in_fibertubes',
-                   help='Path to the tractogram file (must be .trk) \n'
-                   'containing ground-truth fibertubes. They must be: \n'
-                   '1- Void of any collision. \n'
-                   '2- With their respective diameter saved \n'
-                   'as data_per_streamline. \n'
-                   'For both of these requirements, see \n'
-                   'scil_tractogram_filter_collisions.')
+                   help='Path to the tractogram (must be .trk) file \n'
+                        'containing fibertubes. They must have their \n'
+                        'respective diameter saved as data_per_streamline.')
 
     p.add_argument('in_tracking',
                    help='Path to the tractogram file (must be .trk) \n'

scripts/scil_fibertube_tracking.py

@@ -22,6 +22,11 @@
 
 Seeding is done within the first segment of each fibertube.
 
+To form fibertubes from a set of streamlines, you can use the scripts:
+- scil_tractogram_filter_collisions.py to assign a diameter to each streamline
+  and remove all colliding fibertubes.
+- scil_tractogram_dps_math.py to assign a diameter without filtering.
+
 For a better understanding of Fibertube Tracking please see:
     - docs/source/documentation/fibertube_tracking.rst
 """
@@ -57,12 +62,8 @@ def _build_arg_parser():
 
     p.add_argument('in_fibertubes',
                    help='Path to the tractogram (must be .trk) file \n'
-                        'containing fibertubes. They must be: \n'
-                        '1- Void of any collision. \n'
-                        '2- With their respective diameter saved \n'
-                        'as data_per_streamline. \n'
-                        'For both of these requirements, see \n'
-                        'scil_tractogram_filter_collisions.py.')
+                        'containing fibertubes. They must have their \n'
+                        'respective diameter saved as data_per_streamline.')
 
     p.add_argument('out_tractogram',
                    help='Tractogram output file (must be .trk or .tck).')

scripts/scil_tractogram_dps_math.py

@@ -61,9 +61,15 @@ def _build_arg_parser():
                         '"delete" operations.')
 
     import_args = p.add_argument_group('Operation "import" mandatory options')
-    import_args.add_argument('--in_dps_file',
+    import_excl = import_args.add_mutually_exclusive_group()
+    import_excl.add_argument('--in_dps_file',
                              help='File containing the data to import to\n'
-                                  'streamlines (.txt, .npy or .mat).')
+                                  'streamlines (.txt, .npy or .mat). There\n'
+                                  'must be the same amount of entries as\n'
+                                  'there are streamlines.')
+    import_excl.add_argument('--in_dps_file_single_value',
+                             help='File containing a single value to import\n'
+                                  'to each streamlines (.txt, .npy or .mat).')
 
     export_args = p.add_argument_group('Operation "export" mandatory options')
     export_args.add_argument('--out_dps_file',
@@ -98,9 +104,15 @@ def main():
     sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
 
     if args.operation == 'import':
-        if args.in_dps_file is None:
-            parser.error('The --in_dps_file option is required for ' +
-                         'the "import" operation.')
+        if args.in_dps_file:
+            dps_file = args.in_dps_file
+        else:
+            dps_file = args.in_dps_file_single_value
+
+        if dps_file is None:
+            parser.error('One of --in_dps_file or ' +
+                         '--in_dps_file_single_value is required for the ' +
+                         '"import" operation.')
 
         if args.out_tractogram is None:
             parser.error('The --out_tractogram option is required for ' +
@@ -113,13 +125,15 @@ def main():
                          ' overwriting.'.format(args.dps_key))
 
         # Load data and remove extraneous dimensions
-        data = np.squeeze(load_matrix_in_any_format(args.in_dps_file))
-
-        # Quick check as the built-in error from sft is not too explicit
-        if len(sft) != data.shape[0]:
-            raise ValueError('Data must have as many entries ({}) as there are'
-                             ' streamlines ({}).'.format(data.shape[0],
-                                                         len(sft)))
+        data = np.squeeze(load_matrix_in_any_format(dps_file))
+
+        # Validate data shape
+        if args.in_dps_file and len(sft) != data.shape[0]:
+            raise ValueError(
+                'Data must have as many entries ({}) as there are '
+                'streamlines ({}).'.format(data.shape[0], len(sft)))
+        if args.in_dps_file_single_value:
+            data = [data] * len(sft.streamlines)
 
         sft.data_per_streamline[args.dps_key] = data
 

scripts/tests/test_tractogram_dps_math.py

@@ -37,6 +37,22 @@ def test_execution_dps_math_import(script_runner, monkeypatch):
     assert ret.success
 
 
+def test_execution_dps_math_import_single_value(script_runner,
+                                                monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_bundle = os.path.join(SCILPY_HOME, 'filtering',
+                             'bundle_4.trk')
+    filename = 'vals.npy'
+    outname = 'out.trk'
+    np.save(filename, [1.1])
+    ret = script_runner.run('scil_tractogram_dps_math.py',
+                            in_bundle, 'import', 'key',
+                            '--in_dps_file_single_value', filename,
+                            '--out_tractogram', outname,
+                            '-f')
+    assert ret.success
+
+
 def test_execution_dps_math_import_with_missing_vals(script_runner,
                                                      monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))