From 2fbbe5f0c12f5ecf7b919e0e35c567c1eb13d5c3 Mon Sep 17 00:00:00 2001 From: arnaudbore Date: Thu, 9 May 2024 14:29:46 -0400 Subject: [PATCH 1/3] fix mask type --- scripts/scil_dwi_apply_bias_field.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/scil_dwi_apply_bias_field.py b/scripts/scil_dwi_apply_bias_field.py index 03e20a799..150bc1394 100755 --- 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 From c95ab836cea15e19531e47cab143bbcab2454444 Mon Sep 17 00:00:00 2001 From: arnaudbore Date: Thu, 9 May 2024 14:36:01 -0400 Subject: [PATCH 2/3] fix executable scripts, and rename script --- scripts/legacy/scil_apply_transform_to_bvecs.py | 0 scripts/legacy/scil_apply_transform_to_hdf5.py | 0 scripts/legacy/scil_assign_custom_color_to_tractogram.py | 0 scripts/legacy/scil_assign_uniform_color_to_tractograms.py | 0 scripts/legacy/scil_clean_qbx_clusters.py | 0 scripts/legacy/scil_compute_bundle_mean_std.py | 0 scripts/legacy/scil_compute_bundle_mean_std_per_point.py | 0 scripts/legacy/scil_compute_bundle_volume.py | 0 scripts/legacy/scil_compute_bundle_volume_per_label.py | 0 scripts/legacy/scil_compute_centroid.py | 0 scripts/legacy/scil_compute_endpoints_map.py | 0 scripts/legacy/scil_compute_hdf5_average_density_map.py | 0 scripts/legacy/scil_compute_mean_fixel_afd_from_bundles.py | 0 scripts/legacy/scil_compute_mean_fixel_afd_from_hdf5.py | 0 .../scil_compute_mean_fixel_lobe_metric_from_bundles.py | 0 scripts/legacy/scil_compute_seed_by_labels.py | 0 scripts/legacy/scil_compute_seed_density_map.py | 0 scripts/legacy/scil_compute_streamlines_density_map.py | 0 scripts/legacy/scil_compute_streamlines_length_stats.py | 0 scripts/legacy/scil_convert_rgb.py | 0 scripts/legacy/scil_convert_tractogram.py | 0 scripts/legacy/scil_decompose_connectivity.py | 0 scripts/legacy/scil_estimate_bundles_diameter.py | 0 .../scil_evaluate_bundles_binary_classification_measures.py | 0 scripts/legacy/scil_evaluate_bundles_individual_measures.py | 0 .../scil_evaluate_bundles_pairwise_agreement_measures.py | 0 scripts/legacy/scil_fix_dsi_studio_trk.py | 0 scripts/legacy/scil_generate_gradient_sampling.py | 0 scripts/legacy/scil_merge_sh.py | 0 scripts/legacy/scil_perform_majority_vote.py | 0 scripts/legacy/scil_print_header.py | 0 scripts/legacy/scil_save_connections_from_hdf5.py | 0 scripts/legacy/scil_score_bundles.py | 0 scripts/legacy/scil_score_tractogram.py | 0 scripts/legacy/scil_uniformize_streamlines_endpoints.py | 4 ++-- scripts/legacy/scil_validate_and_correct_bvecs.py | 0 scripts/legacy/scil_validate_and_correct_eddy_gradients.py | 0 scripts/legacy/scil_validate_bids.py | 0 scripts/legacy/scil_verify_space_attributes_compatibility.py | 0 ...rmize_endpoints.py => scil_bundle_uniformize_endpoints.py} | 0 scripts/scil_mti_adjust_B1_header.py | 0 scripts/scil_tractogram_pairwise_comparison.py | 0 scripts/scil_volume_b0_synthesis.py | 0 43 files changed, 2 insertions(+), 2 deletions(-) mode change 100644 => 100755 scripts/legacy/scil_apply_transform_to_bvecs.py mode change 100644 => 100755 scripts/legacy/scil_apply_transform_to_hdf5.py mode change 100644 => 100755 scripts/legacy/scil_assign_custom_color_to_tractogram.py mode change 100644 => 100755 scripts/legacy/scil_assign_uniform_color_to_tractograms.py mode change 100644 => 100755 scripts/legacy/scil_clean_qbx_clusters.py mode change 100644 => 100755 scripts/legacy/scil_compute_bundle_mean_std.py mode change 100644 => 100755 scripts/legacy/scil_compute_bundle_mean_std_per_point.py mode change 100644 => 100755 scripts/legacy/scil_compute_bundle_volume.py mode change 100644 => 100755 scripts/legacy/scil_compute_bundle_volume_per_label.py mode change 100644 => 100755 scripts/legacy/scil_compute_centroid.py mode change 100644 => 100755 scripts/legacy/scil_compute_endpoints_map.py mode change 100644 => 100755 scripts/legacy/scil_compute_hdf5_average_density_map.py mode change 100644 => 100755 scripts/legacy/scil_compute_mean_fixel_afd_from_bundles.py mode change 100644 => 100755 scripts/legacy/scil_compute_mean_fixel_afd_from_hdf5.py mode change 100644 => 100755 scripts/legacy/scil_compute_mean_fixel_lobe_metric_from_bundles.py mode change 100644 => 100755 scripts/legacy/scil_compute_seed_by_labels.py mode change 100644 => 100755 scripts/legacy/scil_compute_seed_density_map.py mode change 100644 => 100755 scripts/legacy/scil_compute_streamlines_density_map.py mode change 100644 => 100755 scripts/legacy/scil_compute_streamlines_length_stats.py mode change 100644 => 100755 scripts/legacy/scil_convert_rgb.py mode change 100644 => 100755 scripts/legacy/scil_convert_tractogram.py mode change 100644 => 100755 scripts/legacy/scil_decompose_connectivity.py mode change 100644 => 100755 scripts/legacy/scil_estimate_bundles_diameter.py mode change 100644 => 100755 scripts/legacy/scil_evaluate_bundles_binary_classification_measures.py mode change 100644 => 100755 scripts/legacy/scil_evaluate_bundles_individual_measures.py mode change 100644 => 100755 scripts/legacy/scil_evaluate_bundles_pairwise_agreement_measures.py mode change 100644 => 100755 scripts/legacy/scil_fix_dsi_studio_trk.py mode change 100644 => 100755 scripts/legacy/scil_generate_gradient_sampling.py mode change 100644 => 100755 scripts/legacy/scil_merge_sh.py mode change 100644 => 100755 scripts/legacy/scil_perform_majority_vote.py mode change 100644 => 100755 scripts/legacy/scil_print_header.py mode change 100644 => 100755 scripts/legacy/scil_save_connections_from_hdf5.py mode change 100644 => 100755 scripts/legacy/scil_score_bundles.py mode change 100644 => 100755 scripts/legacy/scil_score_tractogram.py mode change 100644 => 100755 scripts/legacy/scil_validate_and_correct_bvecs.py mode change 100644 => 100755 scripts/legacy/scil_validate_and_correct_eddy_gradients.py mode change 100644 => 100755 scripts/legacy/scil_validate_bids.py mode change 100644 => 100755 scripts/legacy/scil_verify_space_attributes_compatibility.py rename scripts/{scil_tractogram_uniformize_endpoints.py => scil_bundle_uniformize_endpoints.py} (100%) mode change 100644 => 100755 scripts/scil_mti_adjust_B1_header.py mode change 100644 => 100755 scripts/scil_tractogram_pairwise_comparison.py mode change 100644 => 100755 scripts/scil_volume_b0_synthesis.py diff --git a/scripts/legacy/scil_apply_transform_to_bvecs.py b/scripts/legacy/scil_apply_transform_to_bvecs.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_apply_transform_to_hdf5.py b/scripts/legacy/scil_apply_transform_to_hdf5.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_assign_custom_color_to_tractogram.py b/scripts/legacy/scil_assign_custom_color_to_tractogram.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_assign_uniform_color_to_tractograms.py b/scripts/legacy/scil_assign_uniform_color_to_tractograms.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_clean_qbx_clusters.py b/scripts/legacy/scil_clean_qbx_clusters.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_compute_bundle_mean_std.py b/scripts/legacy/scil_compute_bundle_mean_std.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_compute_bundle_mean_std_per_point.py b/scripts/legacy/scil_compute_bundle_mean_std_per_point.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_compute_bundle_volume.py b/scripts/legacy/scil_compute_bundle_volume.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_compute_bundle_volume_per_label.py b/scripts/legacy/scil_compute_bundle_volume_per_label.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_compute_centroid.py b/scripts/legacy/scil_compute_centroid.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_compute_endpoints_map.py b/scripts/legacy/scil_compute_endpoints_map.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_compute_hdf5_average_density_map.py b/scripts/legacy/scil_compute_hdf5_average_density_map.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_compute_mean_fixel_afd_from_bundles.py b/scripts/legacy/scil_compute_mean_fixel_afd_from_bundles.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_compute_mean_fixel_afd_from_hdf5.py b/scripts/legacy/scil_compute_mean_fixel_afd_from_hdf5.py old mode 100644 new mode 100755 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 old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_compute_seed_by_labels.py b/scripts/legacy/scil_compute_seed_by_labels.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_compute_seed_density_map.py b/scripts/legacy/scil_compute_seed_density_map.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_compute_streamlines_density_map.py b/scripts/legacy/scil_compute_streamlines_density_map.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_compute_streamlines_length_stats.py b/scripts/legacy/scil_compute_streamlines_length_stats.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_convert_rgb.py b/scripts/legacy/scil_convert_rgb.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_convert_tractogram.py b/scripts/legacy/scil_convert_tractogram.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_decompose_connectivity.py b/scripts/legacy/scil_decompose_connectivity.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_estimate_bundles_diameter.py b/scripts/legacy/scil_estimate_bundles_diameter.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_evaluate_bundles_binary_classification_measures.py b/scripts/legacy/scil_evaluate_bundles_binary_classification_measures.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_evaluate_bundles_individual_measures.py b/scripts/legacy/scil_evaluate_bundles_individual_measures.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_evaluate_bundles_pairwise_agreement_measures.py b/scripts/legacy/scil_evaluate_bundles_pairwise_agreement_measures.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_fix_dsi_studio_trk.py b/scripts/legacy/scil_fix_dsi_studio_trk.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_generate_gradient_sampling.py b/scripts/legacy/scil_generate_gradient_sampling.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_merge_sh.py b/scripts/legacy/scil_merge_sh.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_perform_majority_vote.py b/scripts/legacy/scil_perform_majority_vote.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_print_header.py b/scripts/legacy/scil_print_header.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_save_connections_from_hdf5.py b/scripts/legacy/scil_save_connections_from_hdf5.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_score_bundles.py b/scripts/legacy/scil_score_bundles.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_score_tractogram.py b/scripts/legacy/scil_score_tractogram.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_uniformize_streamlines_endpoints.py b/scripts/legacy/scil_uniformize_streamlines_endpoints.py index 7ef5a8724..8943896be 100755 --- 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 old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_validate_and_correct_eddy_gradients.py b/scripts/legacy/scil_validate_and_correct_eddy_gradients.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_validate_bids.py b/scripts/legacy/scil_validate_bids.py old mode 100644 new mode 100755 diff --git a/scripts/legacy/scil_verify_space_attributes_compatibility.py b/scripts/legacy/scil_verify_space_attributes_compatibility.py old mode 100644 new mode 100755 diff --git a/scripts/scil_tractogram_uniformize_endpoints.py b/scripts/scil_bundle_uniformize_endpoints.py similarity index 100% rename from scripts/scil_tractogram_uniformize_endpoints.py rename to scripts/scil_bundle_uniformize_endpoints.py diff --git a/scripts/scil_mti_adjust_B1_header.py b/scripts/scil_mti_adjust_B1_header.py old mode 100644 new mode 100755 diff --git a/scripts/scil_tractogram_pairwise_comparison.py b/scripts/scil_tractogram_pairwise_comparison.py old mode 100644 new mode 100755 diff --git a/scripts/scil_volume_b0_synthesis.py b/scripts/scil_volume_b0_synthesis.py old mode 100644 new mode 100755 From 9fe94e731651b50c149849b331315fd8f41fd016 Mon Sep 17 00:00:00 2001 From: arnaudbore Date: Thu, 9 May 2024 16:16:12 -0400 Subject: [PATCH 3/3] fix tests --- ...ize_endpoints.py => test_bundle_uniformize_endpoints.py} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename scripts/tests/{test_tractogram_uniformize_endpoints.py => test_bundle_uniformize_endpoints.py} (84%) diff --git a/scripts/tests/test_tractogram_uniformize_endpoints.py b/scripts/tests/test_bundle_uniformize_endpoints.py similarity index 84% rename from scripts/tests/test_tractogram_uniformize_endpoints.py rename to scripts/tests/test_bundle_uniformize_endpoints.py index 67ee8487a..d022be7ce 100644 --- a/scripts/tests/test_tractogram_uniformize_endpoints.py +++ b/scripts/tests/test_bundle_uniformize_endpoints.py @@ -13,7 +13,7 @@ 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 @@ -21,7 +21,7 @@ def test_help_option(script_runner): 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