Verify that reference is always checked

scripts/scil_bundle_compute_centroid.py

@@ -46,7 +46,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_bundle)
+    assert_inputs_exist(parser, args.in_bundle, args.reference)
     assert_outputs_exist(parser, args, args.out_centroid)
 
     if args.nb_points < 2:

scripts/scil_bundle_diameter.py

@@ -213,7 +213,8 @@ def main():
     tmp = args.in_bundles + args.in_labels
     args.in_labels = args.in_bundles[(len(tmp) // 2):] + args.in_labels
     args.in_bundles = args.in_bundles[0:len(tmp) // 2]
-    assert_inputs_exist(parser, args.in_bundles+args.in_labels)
+    assert_inputs_exist(parser, args.in_bundles + args.in_labels,
+                        args.reference)
     assert_output_dirs_exist_and_empty(parser, args, [],
                                        optional=args.save_rendering)
 

scripts/scil_bundle_filter_by_occurence.py

@@ -70,7 +70,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_bundles)
+    assert_inputs_exist(parser, args.in_bundles, args.reference)
     output_streamlines_filename = '{}streamlines.trk'.format(
         args.output_prefix)
     output_voxels_filename = '{}voxels.nii.gz'.format(args.output_prefix)

scripts/scil_bundle_generate_priors.py

@@ -78,8 +78,8 @@ def main():
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
     required = [args.in_bundle, args.in_fodf, args.in_mask]
-    assert_inputs_exist(parser, required)
-    assert_headers_compatible(parser, required)
+    assert_inputs_exist(parser, required, args.reference)
+    assert_headers_compatible(parser, required, reference=args.reference)
 
     out_efod = os.path.join(args.out_dir,
                             '{0}efod.nii.gz'.format(args.out_prefix))

scripts/scil_bundle_mean_fixel_afd.py

@@ -63,7 +63,8 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, [args.in_bundle, args.in_fodf])
+    assert_inputs_exist(parser, [args.in_bundle, args.in_fodf],
+                        args.reference)
     assert_outputs_exist(parser, args, [args.afd_mean_map])
 
     sft = load_tractogram_with_reference(parser, args, args.in_bundle)

scripts/scil_bundle_mean_fixel_bingham_metric.py

@@ -73,9 +73,9 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, [args.in_bundle,
-                                 args.in_bingham,
-                                 args.in_bingham_metric])
+    assert_inputs_exist(parser, [args.in_bundle, args.in_bingham,
+                                 args.in_bingham_metric],
+                        args.reference)
     assert_outputs_exist(parser, args, [args.out_mean_map])
 
     sft = load_tractogram_with_reference(parser, args, args.in_bundle)

scripts/scil_bundle_pairwise_comparison.py

@@ -286,7 +286,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_bundles)
+    assert_inputs_exist(parser, args.in_bundles, args.reference)
     assert_outputs_exist(parser, args, [args.out_json])
 
     if args.ratio and not args.single_compare:

scripts/scil_bundle_score_many_bundles_one_tractogram.py

@@ -94,7 +94,7 @@ def _build_arg_parser():
 
 def load_and_verify_everything(parser, args):
 
-    assert_inputs_exist(parser, [args.gt_config])
+    assert_inputs_exist(parser, args.gt_config, args.reference)
     if not os.path.isdir(args.bundles_dir):
         parser.error("Bundles dir ({}) does not exist."
                      .format(args.bundles_dir))

scripts/scil_bundle_score_same_bundle_many_segmentations.py

@@ -159,7 +159,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_bundles)
+    assert_inputs_exist(parser, args.in_bundles, args.reference)
     assert_outputs_exist(parser, args, args.out_json)
 
     if (not args.streamlines_measures) and (not args.voxels_measures):

scripts/scil_bundle_shape_measures.py

@@ -199,7 +199,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_bundles)
+    assert_inputs_exist(parser, args.in_bundles, args.reference)
     assert_outputs_exist(parser, args, [], args.out_json)
 
     nbr_cpu = validate_nbr_processes(parser, args)

scripts/scil_clean_qbx_clusters.py

@@ -151,7 +151,7 @@ def keypress_callback(obj, _):
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_bundles)
+    assert_inputs_exist(parser, args.in_bundles, args.reference)
     assert_outputs_exist(parser, args, [args.out_accepted, args.out_rejected])
 
     if args.out_accepted_dir:

scripts/scil_header_validate_compatibility.py

@@ -38,7 +38,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_files)
+    assert_inputs_exist(parser, args.in_files, args.reference)
     assert_headers_compatible(parser, args.in_files,
                               verbose_all_compatible=True,
                               reference=args.reference)

scripts/scil_lesions_info.py

@@ -81,7 +81,7 @@ def main():
 
     assert_inputs_exist(parser, [args.in_lesion],
                         optional=[args.bundle, args.bundle_mask,
-                                  args.bundle_labels_map])
+                                  args.bundle_labels_map, args.reference])
     assert_outputs_exist(parser, args, args.out_json,
                          optional=[args.out_lesion_stats,
                                    args.out_streamlines_stats])

scripts/scil_outlier_rejection.py

@@ -53,7 +53,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_bundle)
+    assert_inputs_exist(parser, args.in_bundle, args.reference)
     assert_outputs_exist(parser, args, args.out_bundle, args.remaining_bundle)
     if args.alpha <= 0 or args.alpha > 1:
         parser.error('--alpha should be ]0, 1]')

scripts/scil_score_tractogram.py

@@ -173,7 +173,7 @@ def load_and_verify_everything(parser, args):
     args.json_prefix = os.path.join(args.out_dir, args.json_prefix)
     json_outputs = [args.json_prefix + 'processing_stats.json',
                     args.json_prefix + 'results.json']
-    assert_inputs_exist(parser, args.gt_config)
+    assert_inputs_exist(parser, args.gt_config, args.reference)
     assert_output_dirs_exist_and_empty(parser, args, args.out_dir,
                                        create_dir=True)
     assert_outputs_exist(parser, args, json_outputs)

scripts/scil_tractogram_apply_transform.py

@@ -105,7 +105,8 @@ def main():
 
     assert_inputs_exist(parser, [args.in_moving_tractogram,
                                  args.in_target_file,
-                                 args.in_transfo], args.in_deformation)
+                                 args.in_transfo],
+                        [args.in_deformation, args.reference])
     assert_outputs_exist(parser, args, args.out_tractogram)
 
     args.bbox_check = False  # Adding manually bbox_check argument.

scripts/scil_tractogram_apply_transform_to_hdf5.py

@@ -71,7 +71,8 @@ def main():
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
     assert_inputs_exist(parser, [args.in_hdf5, args.in_target_file,
-                                 args.in_transfo], args.in_deformation)
+                                 args.in_transfo],
+                        [args.in_deformation, args.reference])
     assert_outputs_exist(parser, args, args.out_hdf5)
 
     # HDF5 will not overwrite the file

scripts/scil_tractogram_assign_custom_color.py

@@ -172,7 +172,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram,
                          optional=args.out_colorbar)
 

scripts/scil_tractogram_assign_uniform_color.py

@@ -70,7 +70,7 @@ def main():
     if len(args.in_tractograms) > 1 and args.out_tractogram:
         parser.error('Using multiple inputs, use --out_suffix.')
 
-    assert_inputs_exist(parser, args.in_tractograms)
+    assert_inputs_exist(parser, args.in_tractograms, args.reference)
 
     if args.out_suffix:
         if args.out_tractogram:

scripts/scil_tractogram_cut_streamlines.py

@@ -73,7 +73,8 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, [args.in_tractogram, args.in_mask])
+    assert_inputs_exist(parser, [args.in_tractogram, args.in_mask],
+                        args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram)
     assert_headers_compatible(parser, [args.in_tractogram, args.in_mask],
                               reference=args.reference)

scripts/scil_tractogram_detect_loops.py

@@ -80,7 +80,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram,
                          optional=args.looping_tractogram)
     check_tracts_same_format(parser, [args.in_tractogram, args.out_tractogram,

scripts/scil_tractogram_dpp_math.py

@@ -106,7 +106,7 @@ def main():
     if args.verbose:
         logging.getLogger().setLevel(logging.INFO)
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram)
 
     # Load the input files.

scripts/scil_tractogram_extract_ushape.py

@@ -65,7 +65,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram,
                          optional=args.remaining_tractogram)
     check_tracts_same_format(parser, [args.in_tractogram, args.out_tractogram,

scripts/scil_tractogram_filter_by_anatomy.py

@@ -277,7 +277,7 @@ def main():
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
     assert_inputs_exist(parser, [args.in_tractogram, args.in_wmparc],
-                        args.csf_bin)
+                        [args.csf_bin, args.reference])
     assert_output_dirs_exist_and_empty(parser, args, args.out_path,
                                        create_dir=True)
     assert_headers_compatible(parser, [args.in_tractogram, args.in_wmparc],

scripts/scil_tractogram_filter_by_length.py

@@ -56,7 +56,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram)
 
     if args.minL == 0 and np.isinf(args.maxL):

scripts/scil_tractogram_filter_by_orientation.py

@@ -88,7 +88,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram, args.save_rejected)
 
     if args.min_x == 0 and np.isinf(args.max_x) and \

scripts/scil_tractogram_filter_by_roi.py

@@ -242,7 +242,7 @@ def main():
 
     # Todo. Prepare now the names of other files (ex, ROI) and verify if
     #  exist and compatible.
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram, args.save_rejected)
 
     if overwrite_distance:

scripts/scil_tractogram_flip.py

@@ -51,7 +51,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram)
 
     sft = load_tractogram_with_reference(parser, args, args.in_tractogram)

scripts/scil_tractogram_math.py

@@ -113,7 +113,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractograms)
+    assert_inputs_exist(parser, args.in_tractograms, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram,
                          optional=args.save_indices)
 

scripts/scil_tractogram_print_info.py

@@ -47,7 +47,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
 
     sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
 

scripts/scil_tractogram_project_map_to_streamlines.py

@@ -87,8 +87,8 @@ def main():
     parser = _build_arg_parser()
     args = parser.parse_args()
 
-    assert_inputs_exist(parser, [args.in_tractogram] + args.in_maps)
-
+    assert_inputs_exist(parser, [args.in_tractogram] + args.in_maps,
+                        args.reference)
     assert_outputs_exist(parser, args, [args.out_tractogram])
 
     if args.verbose:

scripts/scil_tractogram_project_streamlines_to_map.py

@@ -173,7 +173,7 @@ def main():
 
     # -------- General checks ----------
     assert_inputs_exist(parser, [args.in_bundle],
-                        args.load_dps + args.load_dpp)
+                        args.load_dps + args.load_dpp + [args.reference])
 
     # Find all final output files (one per metric).
     if args.load_dps or args.load_dpp:

scripts/scil_tractogram_qbx.py

@@ -58,7 +58,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, [], optional=args.out_centroids)
     assert_output_dirs_exist_and_empty(parser, args,
                                        args.out_clusters_dir,

scripts/scil_tractogram_register.py

@@ -63,7 +63,9 @@ def main():
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
     assert_inputs_exist(parser, [args.moving_tractogram,
-                                 args.static_tractogram])
+                                 args.static_tractogram],
+                        [args.moving_tractogram_ref,
+                         args.static_tractogram_ref])
 
     if args.only_rigid:
         matrix_filename = os.path.splitext(args.out_name)[0] + '_rigid.txt'

scripts/scil_tractogram_resample.py

@@ -122,7 +122,7 @@ def main():
              args.streamline_wise_std <= 0):
         parser.error('STD needs to be above 0.')
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram)
 
     logging.info("Loading sft.")

scripts/scil_tractogram_resample_nb_points.py

@@ -49,7 +49,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram)
 
     sft = load_tractogram_with_reference(parser, args, args.in_tractogram)

scripts/scil_tractogram_segment_bundles.py

@@ -101,8 +101,8 @@ def main():
                                                     args.in_directory, x))]
 
     assert_inputs_exist(parser, args.in_tractograms +
-                        [args.in_config_file,
-                         args.in_transfo])
+                        [args.in_config_file, args.in_transfo],
+                        args.reference)
 
     for in_tractogram in args.in_tractograms:
         ext = os.path.splitext(in_tractogram)[1]

scripts/scil_tractogram_segment_one_bundles.py

@@ -98,7 +98,8 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, [args.in_tractogram, args.in_transfo])
+    assert_inputs_exist(parser, [args.in_tractogram, args.in_transfo],
+                        args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram)
 
     wb_file = load_tractogram_with_reference(parser, args, args.in_tractogram)

scripts/scil_tractogram_shuffle.py

@@ -43,7 +43,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram)
 
     sft = load_tractogram_with_reference(parser, args, args.in_tractogram)

scripts/scil_tractogram_smooth.py

@@ -79,7 +79,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram)
 
     sft = load_tractogram_with_reference(parser, args, args.in_tractogram)

scripts/scil_tractogram_split.py

@@ -84,7 +84,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     _, out_extension = os.path.splitext(args.in_tractogram)
 
     assert_output_dirs_exist_and_empty(parser, args, [], optional=args.out_dir)

scripts/scil_tractogram_uniformize_endpoints.py

@@ -77,7 +77,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_bundle)
+    assert_inputs_exist(parser, args.in_bundle, args.reference)
     assert_outputs_exist(parser, args, args.out_bundle)
 
     sft = load_tractogram_with_reference(parser, args, args.in_bundle)