skrt package

Subpackages

• skrt.better_viewer package
  • Submodules
    • skrt.better_viewer.options module
      • set_viewer_options()
  • Module contents
    • BetterViewer
      • BetterViewer.__init__()
      • BetterViewer.any_attr()
      • BetterViewer.apply_translation()
      • BetterViewer.get_input_list()
      • BetterViewer.load_comparison()
      • BetterViewer.make_comparison_ui()
      • BetterViewer.make_fig()
      • BetterViewer.make_lower_ui()
      • BetterViewer.make_reset_zoom()
      • BetterViewer.make_translation_ui()
      • BetterViewer.make_ui()
      • BetterViewer.match_axes()
      • BetterViewer.on_key()
      • BetterViewer.on_scroll()
      • BetterViewer.plot()
      • BetterViewer.set_callbacks()
      • BetterViewer.set_slider_widths()
      • BetterViewer.show()
      • BetterViewer.write_translation_to_file()
    • SingleViewer
      • SingleViewer.__init__()
      • SingleViewer.centre_on_roi()
      • SingleViewer.decrease_slice()
      • SingleViewer.get_intensity_range()
      • SingleViewer.get_visible_rois()
      • SingleViewer.increase_slice()
      • SingleViewer.jump_to_roi()
      • SingleViewer.load_df()
      • SingleViewer.load_dose()
      • SingleViewer.load_grid()
      • SingleViewer.load_jacobian()
      • SingleViewer.load_rois()
      • SingleViewer.make_image()
      • SingleViewer.make_lower_ui()
      • SingleViewer.make_ui()
      • SingleViewer.on_key()
      • SingleViewer.on_scroll()
      • SingleViewer.on_view_change()
      • SingleViewer.plot()
      • SingleViewer.plot_image()
      • SingleViewer.reset_zoom()
      • SingleViewer.roi_is_visible()
      • SingleViewer.save_fig()
      • SingleViewer.save_roi_comparison_table()
      • SingleViewer.save_roi_info_table()
      • SingleViewer.set_callbacks()
      • SingleViewer.set_slice()
      • SingleViewer.set_slice_and_view()
      • SingleViewer.set_slice_from_idx()
      • SingleViewer.set_slice_from_pos()
      • SingleViewer.show()
      • SingleViewer.show_in_notebook()
      • SingleViewer.slice_to_slider()
      • SingleViewer.slider_to_slice()
      • SingleViewer.update_roi_comparison()
      • SingleViewer.update_roi_info_table()
      • SingleViewer.update_roi_sliders()
      • SingleViewer.update_slice_slider()
      • SingleViewer.update_slice_slider_desc()
      • SingleViewer.update_slider()
      • SingleViewer.update_zoom_sliders()
    • in_notebook()
    • to_inches()
• skrt.viewer package
  • Submodules
    • skrt.viewer.core module
      • DeformationImage
      • Image
      • ImageComparison
      • MultiImage
      • OrthogonalImage
      • Struct
      • StructComparison
      • StructureSet
      • contours_to_indices()
      • contours_to_mask()
      • find_date()
      • find_files()
      • get_dicom_sequence()
      • get_rotation_matrix()
      • get_translation_matrix()
      • get_unique_path()
      • is_list()
      • is_nested()
      • load_dicom()
      • load_dicom_multiple_files()
      • load_dicom_single_file()
      • load_image()
      • load_structs()
      • make_name_nice()
      • make_three()
      • standard_str()
      • to_inches()
    • skrt.viewer.viewer module
      • OrthogViewer
      • QuickViewer
      • SingleViewer
      • in_notebook()
      • write_translation_to_file()
  • Module contents

Submodules

• skrt.application module
  • Algorithm
    • Algorithm.__init__()
    • Algorithm.execute()
    • Algorithm.finalise()
    • Algorithm.initialise()
    • Algorithm.set_attributes()
  • Application
    • Application.__init__()
    • Application.execute()
    • Application.finalise()
    • Application.from_alg_specs()
    • Application.initialise()
    • Application.run()
  • Status
    • Status.__init__()
    • Status.__repr__()
    • Status.copy_attributes()
    • Status.is_ok()
  • get_paths()
• skrt.core module
  • Archive
    • Archive.__init__()
    • Archive.get_file_size()
    • Archive.get_n_file()
  • Data
    • Data.__init__()
    • Data.__repr__()
    • Data.clone()
    • Data.clone_attrs()
    • Data.get_dict()
    • Data.get_item_string()
    • Data.get_print_depth()
    • Data.print()
    • Data.set_print_depth()
  • Dated
    • Dated.__init__()
    • Dated.copy_dicom()
    • Dated.copy_dicom_files()
    • Dated.get_matched_timestamps()
    • Dated.get_pandas_timestamp()
    • Dated.in_date_interval()
  • Defaults
    • Defaults.__init__()
    • Defaults.__repr__()
    • Defaults.instance
  • DicomFile
    • DicomFile.__init__()
    • DicomFile.get_matched_attributes()
    • DicomFile.get_object()
    • DicomFile.set_dates_and_times()
    • DicomFile.set_referenced_sop_instance_uids()
    • DicomFile.set_slice_thickness()
  • File
  • PathData
    • PathData.__init__()
    • PathData.create_objects()
    • PathData.get_file_size()
    • PathData.get_n_file()
    • PathData.get_n_file_below()
    • PathData.print_paths()
  • TicToc
    • TicToc.__init__()
    • TicToc.__repr__()
    • TicToc.instance
  • alphanumeric()
  • compress_user()
  • download()
  • filter_on_paths()
  • filtered_dict()
  • fullpath()
  • generate_timestamp()
  • get_associated_image()
  • get_basenames()
  • get_data_by_filename()
  • get_data_indices()
  • get_day_in_week()
  • get_dict_permutations()
  • get_file_size()
  • get_float()
  • get_hour_in_day()
  • get_hour_in_week()
  • get_indexed_objs()
  • get_interval_in_days()
  • get_interval_in_whole_days()
  • get_logger()
  • get_n_file()
  • get_n_file_below()
  • get_qualified_class_name()
  • get_referenced_image()
  • get_referenced_object()
  • get_single_path()
  • get_stat()
  • get_stat_functions()
  • get_subdir_paths()
  • get_time_and_date()
  • get_time_separated_objects()
  • get_uid_without_slice()
  • get_value_from_json()
  • hu_to_mu()
  • is_list()
  • is_timestamp()
  • load_json()
  • load_toml()
  • make_dir()
  • matches_suffix()
  • mu_to_hu()
  • prepend_path()
  • print_paths()
  • qualified__name()
  • qualified_name()
  • relative_path()
  • set_matlab_runtime()
  • tic()
  • to_list()
  • toc()
  • year_fraction()
• skrt.dicom_writer module
  • DicomWriter
    • DicomWriter.__init__()
    • DicomWriter.add_image_info()
    • DicomWriter.add_structure_set_info()
    • DicomWriter.create_file_dataset()
    • DicomWriter.generate_shortened_uid()
    • DicomWriter.get_file_dataset()
    • DicomWriter.get_media_storage_sop_class_uid()
    • DicomWriter.get_path_with_timestamp()
    • DicomWriter.initialise_outdir()
    • DicomWriter.new_roi_contour()
    • DicomWriter.new_rt_roi_observation()
    • DicomWriter.set_date_and_time()
    • DicomWriter.set_geometry_and_scaling()
    • DicomWriter.set_image()
    • DicomWriter.set_image_slice()
    • DicomWriter.set_referenced_frame_of_reference_sequence()
    • DicomWriter.set_structure_set()
    • DicomWriter.update_dataset()
    • DicomWriter.write()
• skrt.dose module
  • Constraint
    • Constraint.__init__()
    • Constraint.get_weight_and_objectives()
  • Dose
    • Dose.__init__()
    • Dose.copy_dicom()
    • Dose.get_bed()
    • Dose.get_biologically_effective_dose()
    • Dose.get_dose_in_roi()
    • Dose.get_dose_in_roi_3d()
    • Dose.get_dose_quantile()
    • Dose.get_dose_summation_type()
    • Dose.get_dose_type()
    • Dose.get_dose_units()
    • Dose.get_eqd()
    • Dose.get_equivalent_dose()
    • Dose.get_max_dose_in_rois()
    • Dose.get_mean_dose()
    • Dose.get_n_fraction()
    • Dose.load()
    • Dose.plot_DVH()
    • Dose.plot_dvh()
    • Dose.set_image()
    • Dose.set_plan()
  • ImageOverlay
    • ImageOverlay.__init__()
    • ImageOverlay.get_image()
    • ImageOverlay.max
    • ImageOverlay.plot()
    • ImageOverlay.set_image()
  • Plan
    • Plan.__init__()
    • Plan.add_dose()
    • Plan.clear_doses()
    • Plan.get_approval_status()
    • Plan.get_description()
    • Plan.get_dicom_dataset()
    • Plan.get_dose_objective()
    • Plan.get_doses()
    • Plan.get_image()
    • Plan.get_machine()
    • Plan.get_n_beam_seq()
    • Plan.get_n_fraction()
    • Plan.get_n_fraction_group()
    • Plan.get_name()
    • Plan.get_organs_at_risk()
    • Plan.get_prescription_description()
    • Plan.get_station_name()
    • Plan.get_structure_set()
    • Plan.get_target_dose()
    • Plan.get_targets()
    • Plan.load()
    • Plan.load_constraints()
    • Plan.set_image()
    • Plan.set_structure_set()
  • remove_duplicate_doses()
  • sum_doses()
• skrt.image module
  • Image
    • Image.__init__()
    • Image.add_dose()
    • Image.add_plan()
    • Image.add_sinogram_noise()
    • Image.add_structure_set()
    • Image.apply_banding()
    • Image.apply_selective_banding()
    • Image.assign_intensity_to_rois()
    • Image.assign_structure_set()
    • Image.astype()
    • Image.clear_doses()
    • Image.clear_plans()
    • Image.clear_structure_sets()
    • Image.clone_with_structure_set()
    • Image.copy_dicom()
    • Image.crop()
    • Image.crop_about_point()
    • Image.crop_by_amounts()
    • Image.crop_to_image()
    • Image.crop_to_roi()
    • Image.downsample()
    • Image.flattened()
    • Image.get_affine()
    • Image.get_alignment_translation()
    • Image.get_axes()
    • Image.get_centre()
    • Image.get_centroid_idx()
    • Image.get_centroid_pos()
    • Image.get_centroid_slice()
    • Image.get_comparison()
    • Image.get_coordinate_arrays()
    • Image.get_coords()
    • Image.get_correlation_quality()
    • Image.get_data()
    • Image.get_dicom_array_and_affine()
    • Image.get_dicom_dataset()
    • Image.get_dicom_filepath()
    • Image.get_doses()
    • Image.get_extents()
    • Image.get_fidelity()
    • Image.get_foreground_bbox()
    • Image.get_foreground_bbox_centre_and_widths()
    • Image.get_foreground_box_mask()
    • Image.get_foreground_comparison()
    • Image.get_foreground_mask()
    • Image.get_foreground_roi()
    • Image.get_idx()
    • Image.get_intensity_mask()
    • Image.get_length()
    • Image.get_machine()
    • Image.get_manufacturer()
    • Image.get_masked_image()
    • Image.get_max()
    • Image.get_min()
    • Image.get_model()
    • Image.get_mpl_kwargs()
    • Image.get_mutual_information()
    • Image.get_n_voxels()
    • Image.get_nifti_array_and_affine()
    • Image.get_orientation_codes()
    • Image.get_orientation_vector()
    • Image.get_orientation_view()
    • Image.get_origin()
    • Image.get_plans()
    • Image.get_plot_aspect_ratio()
    • Image.get_quality()
    • Image.get_range()
    • Image.get_relative_structural_content()
    • Image.get_rois()
    • Image.get_sinogram()
    • Image.get_size()
    • Image.get_slice()
    • Image.get_slice_foreground()
    • Image.get_standardised_affine()
    • Image.get_standardised_data()
    • Image.get_standardised_origin()
    • Image.get_standardised_voxel_size()
    • Image.get_station_name()
    • Image.get_structure_sets()
    • Image.get_translation_to_align()
    • Image.get_translation_to_align_image_rois()
    • Image.get_volume()
    • Image.get_voxel_coords()
    • Image.get_voxel_size()
    • Image.has_same_data()
    • Image.has_same_geometry()
    • Image.hu_to_mu()
    • Image.idx_to_pos()
    • Image.idx_to_slice()
    • Image.label_ax()
    • Image.load()
    • Image.map_hu()
    • Image.match_size()
    • Image.match_voxel_size()
    • Image.mu_to_hu()
    • Image.plot()
    • Image.pos_to_idx()
    • Image.pos_to_slice()
    • Image.print_geometry()
    • Image.remove_bolus()
    • Image.resample()
    • Image.rescale()
    • Image.resize()
    • Image.select_foreground()
    • Image.set_ax()
    • Image.set_geometry()
    • Image.slice_to_idx()
    • Image.slice_to_pos()
    • Image.standardise_data()
    • Image.transform()
    • Image.translate_origin()
    • Image.view()
    • Image.write()
    • Image.zoom_ax()
  • ImageComparison
    • ImageComparison.__init__()
    • ImageComparison.get_difference()
    • ImageComparison.get_dta()
    • ImageComparison.get_gamma()
    • ImageComparison.get_plot_aspect_ratio()
    • ImageComparison.load()
    • ImageComparison.plot()
    • ImageComparison.set_slices()
    • ImageComparison.view()
  • Sinogram
    • Sinogram.apply_filter()
    • Sinogram.backprojected()
    • Sinogram.filtered()
  • checked_crop_limits()
  • crop_by_amounts()
  • default_aspect()
  • downsample()
  • entropy()
  • get_alignment_strategy()
  • get_alignment_translation()
  • get_box_mask_from_mask()
  • get_dicom_affine()
  • get_dicom_orientation()
  • get_dicom_paths()
  • get_dicom_voxel_size()
  • get_dicom_window()
  • get_geometry()
  • get_image_comparison_metrics()
  • get_mask()
  • get_mask_bbox()
  • get_mi_metrics()
  • get_quality_metrics()
  • get_translation_to_align()
  • get_translation_to_align_image_rois()
  • kv_to_mv()
  • load_dicom()
  • load_dicom_many_files()
  • load_dicom_single_file()
  • load_nifti()
  • load_npy()
  • load_rgb()
  • match_image_voxel_sizes()
  • match_images()
  • match_images_for_comparison()
  • pad_transpose()
  • remove_duplicate_images()
  • rescale_dicom_data()
  • rescale_images()
  • set_ax()
  • set_image_orientation_patient()
  • sum_images()
  • to_inches()
  • write_nifti()
  • write_npy()
• skrt.multi module
  • PatientDataset
    • PatientDataset.__init__()
    • PatientDataset.add_path()
  • PatientIterator
    • PatientIterator.__init__()
• skrt.patient module
  • Patient
    • Patient.__init__()
    • Patient.add_study()
    • Patient.combined_files()
    • Patient.combined_files_by_dir()
    • Patient.combined_objs()
    • Patient.combined_types()
    • Patient.copy()
    • Patient.copy_dicom()
    • Patient.get_age()
    • Patient.get_birth_date()
    • Patient.get_dose_info()
    • Patient.get_dose_sum()
    • Patient.get_doses()
    • Patient.get_groupings()
    • Patient.get_image_info()
    • Patient.get_images()
    • Patient.get_info()
    • Patient.get_objs()
    • Patient.get_plan_info()
    • Patient.get_plans()
    • Patient.get_sex()
    • Patient.get_structure_set_info()
    • Patient.get_structure_set_with_image()
    • Patient.get_structure_sets()
    • Patient.get_studies()
    • Patient.get_subdir_studies()
    • Patient.last_in_interval()
    • Patient.link_study_data_to_patient()
    • Patient.load_demographics()
    • Patient.sort_dicom()
    • Patient.write()
    • Patient.write_non_image_data()
  • Study
    • Study.__init__()
    • Study.add_image()
    • Study.copy_dicom()
    • Study.correct_dose_image_position()
    • Study.get_description()
    • Study.get_doses()
    • Study.get_images()
    • Study.get_machine_sublist()
    • Study.get_mvct_selection()
    • Study.get_objs()
    • Study.get_patient()
    • Study.get_patient_id()
    • Study.get_plan_data()
    • Study.get_plan_dose()
    • Study.get_plans()
    • Study.get_structure_sets()
    • Study.link_plan_to_doses()
    • Study.load_from_subdir()
    • Study.load_images()
    • Study.save_images_as_nifti()
    • Study.save_structure_sets_as_nifti()
    • Study.sum_dose_plans()
  • find_matching_object()
• skrt.registration module
  • DeformationField
    • DeformationField.__init__()
    • DeformationField.convert_spacing()
    • DeformationField.get_displacement_image()
    • DeformationField.get_slice()
    • DeformationField.load()
    • DeformationField.plot()
    • DeformationField.view()
  • Elastix
    • Elastix.__init__()
    • Elastix.adjust_parameters()
    • Elastix.define_translation()
    • Elastix.exes
    • Elastix.get_def_cmd()
    • Elastix.get_dose_params()
    • Elastix.get_jac_cmd()
    • Elastix.get_registration_cmd()
    • Elastix.get_roi_params()
    • Elastix.get_transform_cmd()
    • Elastix.get_transform_strategies()
    • Elastix.read_parameters()
    • Elastix.set_exe_paths()
    • Elastix.shift_translation_parameters()
    • Elastix.transform_log
    • Elastix.transform_points_implemented
    • Elastix.write_parameters()
  • Grid
    • Grid.__init__()
  • Jacobian
    • Jacobian.__init__()
  • Matlab
    • Matlab.adjust_parameters()
    • Matlab.define_translation()
    • Matlab.exes
    • Matlab.get_def_cmd()
    • Matlab.get_jac_cmd()
    • Matlab.get_registration_cmd()
    • Matlab.get_roi_params()
    • Matlab.get_transform_cmd()
    • Matlab.get_transform_strategies()
    • Matlab.read_affine()
    • Matlab.read_parameters()
    • Matlab.recursive_transform
    • Matlab.set_exe_env()
    • Matlab.shift_translation_parameters()
    • Matlab.write_affine()
    • Matlab.write_parameters()
  • NiftyReg
    • NiftyReg.__init__()
    • NiftyReg.adjust_parameters()
    • NiftyReg.def_signs
    • NiftyReg.define_translation()
    • NiftyReg.exes
    • NiftyReg.get_def_cmd()
    • NiftyReg.get_jac_cmd()
    • NiftyReg.get_registration_cmd()
    • NiftyReg.get_roi_params()
    • NiftyReg.get_transform_cmd()
    • NiftyReg.get_transform_strategies()
    • NiftyReg.read_affine()
    • NiftyReg.read_parameters()
    • NiftyReg.set_exe_paths()
    • NiftyReg.shift_translation_parameters()
    • NiftyReg.write_affine()
    • NiftyReg.write_parameters()
  • Registration
    • Registration.__init__()
    • Registration.add_default_pfile()
    • Registration.add_file()
    • Registration.add_files()
    • Registration.add_pfile()
    • Registration.adjust_file()
    • Registration.adjust_pfile()
    • Registration.clear()
    • Registration.ensure_registered()
    • Registration.get_comparison()
    • Registration.get_correlation_quality()
    • Registration.get_default_params()
    • Registration.get_deformation_field()
    • Registration.get_fidelity()
    • Registration.get_foreground_comparison()
    • Registration.get_input_parameters()
    • Registration.get_jacobian()
    • Registration.get_mutual_information()
    • Registration.get_quality()
    • Registration.get_registration_cmd()
    • Registration.get_relative_structural_content()
    • Registration.get_step_name()
    • Registration.get_step_number()
    • Registration.get_tfile()
    • Registration.get_transform_parameters()
    • Registration.get_transformed_grid()
    • Registration.get_transformed_image()
    • Registration.is_registered()
    • Registration.list_default_pfiles()
    • Registration.load_existing_input_images()
    • Registration.load_files()
    • Registration.make_tmp_dir()
    • Registration.manually_adjust_translation()
    • Registration.print_log()
    • Registration.register()
    • Registration.register_step()
    • Registration.rm_tmp_dir()
    • Registration.run_transformix_on_all()
    • Registration.set_fixed_image()
    • Registration.set_fixed_mask()
    • Registration.set_image()
    • Registration.set_moving_grid()
    • Registration.set_moving_image()
    • Registration.set_moving_mask()
    • Registration.transform()
    • Registration.transform_data()
    • Registration.transform_image()
    • Registration.transform_moving_image()
    • Registration.transform_roi()
    • Registration.transform_structure_set()
    • Registration.view_init()
    • Registration.view_result()
    • Registration.write_steps()
  • RegistrationEngine
    • RegistrationEngine.__init__()
    • RegistrationEngine.adjust_parameters()
    • RegistrationEngine.def_signs
    • RegistrationEngine.define_translation()
    • RegistrationEngine.exes
    • RegistrationEngine.get_def_cmd()
    • RegistrationEngine.get_default_pfiles()
    • RegistrationEngine.get_default_pfiles_dir()
    • RegistrationEngine.get_dose_params()
    • RegistrationEngine.get_jac_cmd()
    • RegistrationEngine.get_registration_cmd()
    • RegistrationEngine.get_roi_params()
    • RegistrationEngine.get_transform_cmd()
    • RegistrationEngine.get_transform_log()
    • RegistrationEngine.get_transform_strategies()
    • RegistrationEngine.is_available()
    • RegistrationEngine.read_parameters()
    • RegistrationEngine.recursive_transform
    • RegistrationEngine.set_exe_env()
    • RegistrationEngine.set_exe_paths()
    • RegistrationEngine.shift_translation_parameters()
    • RegistrationEngine.transform_points_implemented
    • RegistrationEngine.write_parameters()
  • add_engine()
  • adjust_parameters()
  • get_data_dir()
  • get_default_pfiles()
  • get_default_pfiles_dir()
  • get_engine_cls()
  • get_engine_name()
  • get_engines()
  • get_image_transform_parameters()
  • get_jacobian_colormap()
  • get_parameters()
  • read_parameters()
  • set_elastix_dir()
  • set_engine_dir()
  • shift_translation_parameters()
  • write_parameters()
• skrt.segmentation module
  • MultiAtlasSegmentation
    • MultiAtlasSegmentation.__init__()
    • MultiAtlasSegmentation.get_comparison()
    • MultiAtlasSegmentation.get_consensus()
    • MultiAtlasSegmentation.get_sas()
    • MultiAtlasSegmentation.get_sas_segmentations()
    • MultiAtlasSegmentation.get_similarity_scores()
    • MultiAtlasSegmentation.segment()
    • MultiAtlasSegmentation.set_consensuses()
  • SasTuner
    • SasTuner.__init__()
  • SingleAtlasSegmentation
    • SingleAtlasSegmentation.__init__()
    • SingleAtlasSegmentation.adjust_reg_files()
    • SingleAtlasSegmentation.get_auto_steps()
    • SingleAtlasSegmentation.get_comparison()
    • SingleAtlasSegmentation.get_comparison_steps()
    • SingleAtlasSegmentation.get_reg_steps()
    • SingleAtlasSegmentation.get_registration()
    • SingleAtlasSegmentation.get_segmentation()
    • SingleAtlasSegmentation.segment()
    • SingleAtlasSegmentation.segment_roi()
    • SingleAtlasSegmentation.segment_structure_set()
  • ensure_dict()
  • ensure_image()
  • ensure_structure_set()
  • get_atlases()
  • get_contour_propagation_strategies()
  • get_fixed_and_moving()
  • get_option()
  • get_options()
  • get_segmentation_steps()
  • get_steps()
  • get_strategy()
  • get_structure_set_index()
  • select_atlases()
• skrt.simulation module
  • Cuboid
    • Cuboid.__init__()
    • Cuboid.get_data()
  • Cylinder
    • Cylinder.__init__()
    • Cylinder.get_data()
  • Grid
    • Grid.__init__()
    • Grid.get_data()
  • ShapeGroup
    • ShapeGroup.__init__()
    • ShapeGroup.add_shape()
    • ShapeGroup.get_data()
  • Sphere
    • Sphere.__init__()
    • Sphere.get_data()
  • SyntheticImage
    • SyntheticImage.__init__()
    • SyntheticImage.add_cube()
    • SyntheticImage.add_cuboid()
    • SyntheticImage.add_cylinder()
    • SyntheticImage.add_grid()
    • SyntheticImage.add_shape()
    • SyntheticImage.add_sphere()
    • SyntheticImage.apply_noise()
    • SyntheticImage.get_background()
    • SyntheticImage.get_data()
    • SyntheticImage.get_image()
    • SyntheticImage.get_roi()
    • SyntheticImage.get_roi_data()
    • SyntheticImage.get_rois()
    • SyntheticImage.get_structure_set()
    • SyntheticImage.hu_to_mu()
    • SyntheticImage.mu_to_hu()
    • SyntheticImage.plot()
    • SyntheticImage.rescale()
    • SyntheticImage.reset()
    • SyntheticImage.reset_transforms()
    • SyntheticImage.rotate()
    • SyntheticImage.set_noise_std()
    • SyntheticImage.translate()
    • SyntheticImage.update()
    • SyntheticImage.update_roi()
    • SyntheticImage.update_rois()
    • SyntheticImage.view()
    • SyntheticImage.write()
    • SyntheticImage.write_dicom_dataset()
  • get_value()
  • get_values()
  • make_grid()
  • make_head()
• skrt.structures module
  • ROI
    • ROI.__init__()
    • ROI.add_plan()
    • ROI.add_rois()
    • ROI.clear_plans()
    • ROI.clone_attrs()
    • ROI.create_contours()
    • ROI.create_mask()
    • ROI.crop()
    • ROI.crop_by_amounts()
    • ROI.crop_to_roi()
    • ROI.crop_to_roi_length()
    • ROI.flattened()
    • ROI.get_abs_centroid_distance()
    • ROI.get_added_path_length()
    • ROI.get_affine()
    • ROI.get_alpha_over_beta()
    • ROI.get_area()
    • ROI.get_area_diff()
    • ROI.get_area_ratio()
    • ROI.get_aspect_ratio()
    • ROI.get_bbox_centre_and_widths()
    • ROI.get_centre()
    • ROI.get_centroid()
    • ROI.get_centroid_distance()
    • ROI.get_color_from_kwargs()
    • ROI.get_comparison()
    • ROI.get_comparison_name()
    • ROI.get_contours()
    • ROI.get_contours_on_slice()
    • ROI.get_crop_limits()
    • ROI.get_dice()
    • ROI.get_dicom_dataset()
    • ROI.get_dummy_image()
    • ROI.get_enclosing_roi()
    • ROI.get_extent()
    • ROI.get_extent_diff()
    • ROI.get_extents()
    • ROI.get_geometry()
    • ROI.get_hausdorff_distance()
    • ROI.get_idx()
    • ROI.get_image()
    • ROI.get_indices()
    • ROI.get_intensities()
    • ROI.get_intensities_3d()
    • ROI.get_intersection_union_size()
    • ROI.get_jaccard()
    • ROI.get_length()
    • ROI.get_mask()
    • ROI.get_mask_image()
    • ROI.get_mask_to_contour_volume_ratio()
    • ROI.get_mean_distance_to_conformity()
    • ROI.get_mean_surface_distance()
    • ROI.get_metric_by_slice()
    • ROI.get_mid_idx()
    • ROI.get_name()
    • ROI.get_np_voxel_size()
    • ROI.get_nz_contours()
    • ROI.get_origin()
    • ROI.get_patch()
    • ROI.get_plans()
    • ROI.get_polygons()
    • ROI.get_polygons_on_slice()
    • ROI.get_relative_area_diff()
    • ROI.get_relative_volume_diff()
    • ROI.get_rms_surface_distance()
    • ROI.get_roi_slice()
    • ROI.get_slice()
    • ROI.get_slice_positions()
    • ROI.get_slice_stat()
    • ROI.get_slice_stats()
    • ROI.get_slice_thickness_contours()
    • ROI.get_surface_area()
    • ROI.get_surface_distance_metrics()
    • ROI.get_surface_distances()
    • ROI.get_translation_to_align()
    • ROI.get_volume()
    • ROI.get_volume_diff()
    • ROI.get_volume_ratio()
    • ROI.get_voxel_size()
    • ROI.get_zoom_centre()
    • ROI.idx_to_pos()
    • ROI.idx_to_slice()
    • ROI.interpolate_points()
    • ROI.intersect_rois()
    • ROI.is_empty()
    • ROI.load()
    • ROI.load_transformix_points()
    • ROI.mask_to_contours()
    • ROI.match_mask_voxel_size()
    • ROI.match_voxel_size()
    • ROI.on_slice()
    • ROI.plot()
    • ROI.plot_comparison()
    • ROI.plot_surface_distances()
    • ROI.pos_to_idx()
    • ROI.pos_to_slice()
    • ROI.renamed()
    • ROI.resample()
    • ROI.reset_contours()
    • ROI.reset_mask()
    • ROI.resize_contours()
    • ROI.resized()
    • ROI.set_alpha_over_beta()
    • ROI.set_ax()
    • ROI.set_color()
    • ROI.set_image()
    • ROI.set_image_to_dummy()
    • ROI.set_name()
    • ROI.set_slice_thickness_contours()
    • ROI.slice_to_idx()
    • ROI.slice_to_pos()
    • ROI.split()
    • ROI.split_in_two()
    • ROI.subtract_rois()
    • ROI.transform()
    • ROI.view()
    • ROI.write()
  • ROIDefaults
    • ROIDefaults.__init__()
    • ROIDefaults.get_default_roi_color()
    • ROIDefaults.get_default_roi_name()
    • ROIDefaults.get_default_structure_set_name()
    • ROIDefaults.instance
  • StructureSet
    • StructureSet.__init__()
    • StructureSet.add_plan()
    • StructureSet.add_roi()
    • StructureSet.add_rois()
    • StructureSet.clear_plans()
    • StructureSet.clone_attrs()
    • StructureSet.combine_rois()
    • StructureSet.containing_image()
    • StructureSet.contains()
    • StructureSet.crop()
    • StructureSet.filter_rois()
    • StructureSet.filtered_copy()
    • StructureSet.find_most_populated_slice()
    • StructureSet.get_alpha_beta_ratios()
    • StructureSet.get_bbox_centre_and_widths()
    • StructureSet.get_centre()
    • StructureSet.get_colors()
    • StructureSet.get_comparison()
    • StructureSet.get_comparison_pairs()
    • StructureSet.get_conformity_index()
    • StructureSet.get_consensus()
    • StructureSet.get_crop_limits()
    • StructureSet.get_dicom_dataset()
    • StructureSet.get_dummy_image()
    • StructureSet.get_extent()
    • StructureSet.get_extents()
    • StructureSet.get_geometry()
    • StructureSet.get_image()
    • StructureSet.get_label()
    • StructureSet.get_length()
    • StructureSet.get_majority_vote()
    • StructureSet.get_mask_image()
    • StructureSet.get_mid_idx()
    • StructureSet.get_name()
    • StructureSet.get_overlap()
    • StructureSet.get_plans()
    • StructureSet.get_roi()
    • StructureSet.get_roi_dict()
    • StructureSet.get_roi_names()
    • StructureSet.get_rois()
    • StructureSet.get_rois_wildcard()
    • StructureSet.get_series_description()
    • StructureSet.get_staple()
    • StructureSet.get_sum()
    • StructureSet.get_translation_to_align()
    • StructureSet.has_rois()
    • StructureSet.interpolate_points()
    • StructureSet.load()
    • StructureSet.missing()
    • StructureSet.order_rois()
    • StructureSet.plot()
    • StructureSet.plot_comparisons()
    • StructureSet.plot_consensus()
    • StructureSet.plot_surface_distances()
    • StructureSet.print_rois()
    • StructureSet.recolor_rois()
    • StructureSet.rename_rois()
    • StructureSet.renamed()
    • StructureSet.reset()
    • StructureSet.reset_contours()
    • StructureSet.set_alpha_beta_ratios()
    • StructureSet.set_image()
    • StructureSet.set_image_to_dummy()
    • StructureSet.set_name()
    • StructureSet.split_rois_in_two()
    • StructureSet.transform()
    • StructureSet.view()
    • StructureSet.write()
  • StructureSetIterator
    • StructureSetIterator.__init__()
  • best_text_color()
  • compare_roi_pairs()
  • contour_to_polygon()
  • create_dummy_image()
  • create_majority_vote()
  • create_roi_overlap()
  • create_roi_sum()
  • create_staple()
  • create_structure_sets_from_nifti()
  • df_to_html()
  • expand_slice_stats()
  • get_all_rois()
  • get_by_slice_methods()
  • get_colored_roi_string()
  • get_comparison_metrics()
  • get_conformity_index()
  • get_consensus_types()
  • get_dicom_sequence()
  • get_intersection()
  • get_metric_method()
  • get_roi_slice()
  • get_slice_positions()
  • get_structuring_element()
  • get_translation_to_align()
  • interpolate_points_single_contour()
  • load_rois_dicom()
  • match_rois()
  • polygon_to_contour()

Module contents

Toolkit for analysis of radiotherapy data.

Scikit-rt, imported as skrt, is a toolkit for loading, plotting, and analysing radiotherapy data in DICOM and NIfTI formats. It includes image registration via elastix, NiftyReg, and MATLAB, single- and multi-atlas segmentation, and region-of-interest (ROI) comparisons.

Documentation: https://scikit-rt.github.io/scikit-rt/ Code repository: https://github.com/scikit-rt/scikit-rt/ PyPI project page: https://pypi.org/project/scikit-rt/