Fix for pep8

scripts/scil_ft_reconstruction_metrics.py

@@ -72,11 +72,11 @@ def _build_arg_parser():
         formatter_class=argparse.RawTextHelpFormatter)
 
     p.add_argument('in_fibertubes',
-                help='Path to the tractogram file containing the \n'
-                    'fibertubes with their respective diameter saved \n'
-                    'data_per_streamline (must be .trk). \n'
-                    'The fibertubes must be void of any collision \n'
-                    '(see scil_filter_intersections.py). \n')
+                   help='Path to the tractogram file containing the \n'
+                   'fibertubes with their respective diameter saved \n'
+                   'data_per_streamline (must be .trk). \n'
+                   'The fibertubes must be void of any collision \n'
+                   '(see scil_filter_intersections.py). \n')
 
     p.add_argument('in_tractogram',
                    help='Path to a text file containing the ground-truth \n'
@@ -134,22 +134,29 @@ def main():
     our_origin = Origin('center')
 
     logging.debug('Loading centerline tractogram & diameters')
-    truth_sft = load_tractogram(args.in_fibertubes, 'same', our_space, our_origin)
+    truth_sft = load_tractogram(args.in_fibertubes, 'same', our_space,
+                                our_origin)
     centerlines = truth_sft.get_streamlines_copy()
-    centerlines, centerlines_length = get_streamlines_as_fixed_array(centerlines)
+    centerlines, centerlines_length = get_streamlines_as_fixed_array(
+        centerlines)
 
     if "diameters" not in truth_sft.data_per_streamline:
-        parser.error('No diameters found as data per streamline on ' + args.in_fibertubes)
-    diameters = np.reshape(truth_sft.data_per_streamline['diameters'], len(centerlines))
+        parser.error('No diameters found as data per streamline on ' +
+                     args.in_fibertubes)
+    diameters = np.reshape(truth_sft.data_per_streamline['diameters'],
+                           len(centerlines))
 
     logging.debug('Loading reconstructed tractogram')
-    in_sft = load_tractogram(args.in_tractogram, 'same', our_space, our_origin)
+    in_sft = load_tractogram(args.in_tractogram, 'same', our_space,
+                             our_origin)
     streamlines = in_sft.get_streamlines_copy()
-    streamlines, streamlines_length = get_streamlines_as_fixed_array(streamlines)
+    streamlines, streamlines_length = get_streamlines_as_fixed_array(
+        streamlines)
 
     logging.debug("Loading seeds")
     if "seeds" not in in_sft.data_per_streamline:
-        parser.error('No seeds found as data per streamline on ' + args.in_tractogram)
+        parser.error('No seeds found as data per streamline on ' +
+                     args.in_tractogram)
 
     seeds = in_sft.data_per_streamline['seeds']
     seeds_fiber = resolve_origin_seeding(seeds, centerlines, diameters)
@@ -176,13 +183,9 @@ def main():
         seeds_fiber, rand_gen)
 
     logging.debug("Computing reconstruction error")
-    (mean_errors,
-     error_tractogram) = mean_reconstruction_error(centerlines, centerlines_length,
-                                                   diameters,
-                                                   streamlines,
-                                                   streamlines_length,
-                                                   seeds_fiber,
-                                                   args.save_error_tractogram)
+    (mean_errors, error_tractogram) = mean_reconstruction_error(
+        centerlines, centerlines_length, diameters, streamlines,
+        streamlines_length, seeds_fiber, args.save_error_tractogram)
 
     metrics = {
         'truth_vc_ratio': len(truth_vc)/len(streamlines),

scripts/scil_ft_tracking.py

@@ -112,7 +112,7 @@ def _build_arg_parser():
              'Note that points obtained after an invalid direction \n'
              '(based on the propagator\'s definition of invalid) \n'
              'are never added.')
-    
+
     seed_group = p.add_argument_group(
         'Seeding options',
         'When no option is provided, uses --nb_seeds_per_fiber 5.')
@@ -198,7 +198,8 @@ def main():
     logging.debug('Loading tractogram & diameters')
     in_sft = load_tractogram(args.in_fibertubes, 'same', our_space, our_origin)
     centerlines = list(in_sft.get_streamlines_copy())
-    diameters = np.reshape(in_sft.data_per_streamline['diameters'], len(centerlines))
+    diameters = np.reshape(in_sft.data_per_streamline['diameters'],
+                           len(centerlines))
 
     logging.debug("Instantiating datavolumes")
     fake_mask_data = np.ones(in_sft.dimensions)

scripts/scil_ft_visualize_collisions.py

@@ -72,7 +72,7 @@ def main():
                              "(must be trk): {0}".format(args.invalid))
 
     invalid_sft = load_tractogram(args.invalid, 'same',
-                                    bbox_valid_check=False)
+                                  bbox_valid_check=False)
     invalid_sft.to_voxmm()
     invalid_sft.to_center()
 
@@ -94,7 +94,7 @@ def main():
     # Make display objects and add them to canvas
     s = window.Scene()
     invalid_actor = actor.line(invalid_sft.streamlines,
-                                 colors=[1., 0., 0.])
+                               colors=[1., 0., 0.])
     s.add(invalid_actor)
 
     if (args.obstacle):

scripts/scil_tractogram_filter_collisions.py

@@ -187,7 +187,7 @@ def main():
         streamlines = streamlines[indexes]
         diameters = diameters[indexes]
         in_sft = StatefulTractogram.from_sft(streamlines, in_sft)
-    
+
     # Casting ArraySequence as a list to improve speed
     streamlines = list(streamlines[indexes])
 
@@ -256,6 +256,5 @@ def main():
                        max_voxel_rotated_transform)
 
 
-
 if __name__ == "__main__":
     main()