scilus · EmmaRenauld · May 10, 2024 · May 9, 2024 · May 9, 2024 · May 9, 2024
diff --git a/scripts/legacy/scil_apply_transform_to_bvecs.py b/scripts/legacy/scil_apply_transform_to_bvecs.py
diff --git a/scripts/legacy/scil_apply_transform_to_hdf5.py b/scripts/legacy/scil_apply_transform_to_hdf5.py
diff --git a/scripts/legacy/scil_assign_custom_color_to_tractogram.py b/scripts/legacy/scil_assign_custom_color_to_tractogram.py
diff --git a/scripts/legacy/scil_assign_uniform_color_to_tractograms.py b/scripts/legacy/scil_assign_uniform_color_to_tractograms.py
diff --git a/scripts/legacy/scil_clean_qbx_clusters.py b/scripts/legacy/scil_clean_qbx_clusters.py
diff --git a/scripts/legacy/scil_compute_bundle_mean_std.py b/scripts/legacy/scil_compute_bundle_mean_std.py
diff --git a/scripts/legacy/scil_compute_bundle_mean_std_per_point.py b/scripts/legacy/scil_compute_bundle_mean_std_per_point.py
diff --git a/scripts/legacy/scil_compute_bundle_volume.py b/scripts/legacy/scil_compute_bundle_volume.py
diff --git a/scripts/legacy/scil_compute_bundle_volume_per_label.py b/scripts/legacy/scil_compute_bundle_volume_per_label.py
diff --git a/scripts/legacy/scil_compute_centroid.py b/scripts/legacy/scil_compute_centroid.py
diff --git a/scripts/legacy/scil_compute_endpoints_map.py b/scripts/legacy/scil_compute_endpoints_map.py
diff --git a/scripts/legacy/scil_compute_hdf5_average_density_map.py b/scripts/legacy/scil_compute_hdf5_average_density_map.py
diff --git a/scripts/legacy/scil_compute_mean_fixel_afd_from_bundles.py b/scripts/legacy/scil_compute_mean_fixel_afd_from_bundles.py
diff --git a/scripts/legacy/scil_compute_mean_fixel_afd_from_hdf5.py b/scripts/legacy/scil_compute_mean_fixel_afd_from_hdf5.py
diff --git a/scripts/legacy/scil_compute_mean_fixel_lobe_metric_from_bundles.py b/scripts/legacy/scil_compute_mean_fixel_lobe_metric_from_bundles.py
diff --git a/scripts/legacy/scil_compute_seed_by_labels.py b/scripts/legacy/scil_compute_seed_by_labels.py
diff --git a/scripts/legacy/scil_compute_seed_density_map.py b/scripts/legacy/scil_compute_seed_density_map.py
diff --git a/scripts/legacy/scil_compute_streamlines_density_map.py b/scripts/legacy/scil_compute_streamlines_density_map.py
diff --git a/scripts/legacy/scil_compute_streamlines_length_stats.py b/scripts/legacy/scil_compute_streamlines_length_stats.py
diff --git a/scripts/legacy/scil_convert_rgb.py b/scripts/legacy/scil_convert_rgb.py
diff --git a/scripts/legacy/scil_convert_tractogram.py b/scripts/legacy/scil_convert_tractogram.py
diff --git a/scripts/legacy/scil_decompose_connectivity.py b/scripts/legacy/scil_decompose_connectivity.py
diff --git a/scripts/legacy/scil_estimate_bundles_diameter.py b/scripts/legacy/scil_estimate_bundles_diameter.py
diff --git a/scripts/legacy/scil_evaluate_bundles_binary_classification_measures.py b/scripts/legacy/scil_evaluate_bundles_binary_classification_measures.py
diff --git a/scripts/legacy/scil_evaluate_bundles_individual_measures.py b/scripts/legacy/scil_evaluate_bundles_individual_measures.py
diff --git a/scripts/legacy/scil_evaluate_bundles_pairwise_agreement_measures.py b/scripts/legacy/scil_evaluate_bundles_pairwise_agreement_measures.py
diff --git a/scripts/legacy/scil_fix_dsi_studio_trk.py b/scripts/legacy/scil_fix_dsi_studio_trk.py
diff --git a/scripts/legacy/scil_generate_gradient_sampling.py b/scripts/legacy/scil_generate_gradient_sampling.py
diff --git a/scripts/legacy/scil_merge_sh.py b/scripts/legacy/scil_merge_sh.py
diff --git a/scripts/legacy/scil_perform_majority_vote.py b/scripts/legacy/scil_perform_majority_vote.py
diff --git a/scripts/legacy/scil_print_header.py b/scripts/legacy/scil_print_header.py
diff --git a/scripts/legacy/scil_save_connections_from_hdf5.py b/scripts/legacy/scil_save_connections_from_hdf5.py
diff --git a/scripts/legacy/scil_score_bundles.py b/scripts/legacy/scil_score_bundles.py
diff --git a/scripts/legacy/scil_score_tractogram.py b/scripts/legacy/scil_score_tractogram.py
diff --git a/scripts/legacy/scil_uniformize_streamlines_endpoints.py b/scripts/legacy/scil_uniformize_streamlines_endpoints.py
@@ -2,11 +2,11 @@
 # -*- coding: utf-8 -*-
 
 from scilpy.io.deprecator import deprecate_script
-from scripts.scil_tractogram_uniformize_endpoints import main as new_main
+from scripts.scil_bundle_uniformize_endpoints import main as new_main
 
 
 DEPRECATION_MSG = """
-This script has been renamed scil_tractogram_uniformize_endpoints.py. Please
+This script has been renamed scil_bundle_uniformize_endpoints.py. Please
 change your existing pipelines accordingly.
 """
 

diff --git a/scripts/legacy/scil_validate_and_correct_bvecs.py b/scripts/legacy/scil_validate_and_correct_bvecs.py
diff --git a/scripts/legacy/scil_validate_and_correct_eddy_gradients.py b/scripts/legacy/scil_validate_and_correct_eddy_gradients.py
diff --git a/scripts/legacy/scil_validate_bids.py b/scripts/legacy/scil_validate_bids.py
diff --git a/scripts/legacy/scil_verify_space_attributes_compatibility.py b/scripts/legacy/scil_verify_space_attributes_compatibility.py
diff --git a/...s/scil_tractogram_uniformize_endpoints.py → scripts/scil_bundle_uniformize_endpoints.py b/...s/scil_tractogram_uniformize_endpoints.py → scripts/scil_bundle_uniformize_endpoints.py
diff --git a/scripts/scil_dwi_apply_bias_field.py b/scripts/scil_dwi_apply_bias_field.py
@@ -62,7 +62,7 @@ def main():
     bias_field_data = bias_field_img.get_fdata(dtype=np.float32)
 
     if args.mask:
-        mask_data = get_data_as_mask(nib.load(args.mask))
+        mask_data = get_data_as_mask(nib.load(args.mask), dtype=bool)
     else:
         mask_data = np.average(dwi_data, axis=-1) != 0
 

diff --git a/scripts/scil_mti_adjust_B1_header.py b/scripts/scil_mti_adjust_B1_header.py
diff --git a/scripts/scil_tractogram_pairwise_comparison.py b/scripts/scil_tractogram_pairwise_comparison.py
diff --git a/scripts/scil_volume_b0_synthesis.py b/scripts/scil_volume_b0_synthesis.py
diff --git a/...s/test_tractogram_uniformize_endpoints.py → ...tests/test_bundle_uniformize_endpoints.py b/...s/test_tractogram_uniformize_endpoints.py → ...tests/test_bundle_uniformize_endpoints.py
@@ -13,15 +13,15 @@
 
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_tractogram_uniformize_endpoints.py',
+    ret = script_runner.run('scil_bundle_uniformize_endpoints.py',
                             '--help')
     assert ret.success
 
 
 def test_execution_auto(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
     in_bundle = os.path.join(SCILPY_HOME, 'tractometry', 'IFGWM.trk')
-    ret = script_runner.run('scil_tractogram_uniformize_endpoints.py',
+    ret = script_runner.run('scil_bundle_uniformize_endpoints.py',
                             in_bundle, 'IFGWM_uni.trk', '--auto')
     assert ret.success
 
@@ -30,7 +30,7 @@ def test_execution_target_atlas(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
     in_bundle = os.path.join(SCILPY_HOME, 'tractometry', 'IFGWM.trk')
     label = os.path.join(SCILPY_HOME, 'tractometry', 'IFGWM_labels_map.nii.gz')
-    ret = script_runner.run('scil_tractogram_uniformize_endpoints.py',
+    ret = script_runner.run('scil_bundle_uniformize_endpoints.py',
                             in_bundle, 'IFGWM_uni2.trk', '--target_roi', label,
                             '3', '10')
     assert ret.success