Index

_

__init__() (import_analysis.patient.ImportPatient method) (skrt.application.Algorithm method) (skrt.application.Application method) (skrt.application.Status method) (skrt.better_viewer.BetterViewer method) (skrt.better_viewer.SingleViewer method) (skrt.core.Archive method) (skrt.core.Data method) (skrt.core.Dated method) (skrt.core.Defaults method) (skrt.core.DicomFile method) (skrt.core.PathData method) (skrt.core.TicToc method) (skrt.dicom_writer.DicomWriter method) (skrt.dose.Constraint method) (skrt.dose.Dose method) (skrt.dose.ImageOverlay method) (skrt.dose.Plan method) (skrt.image.Image method) (skrt.image.ImageComparison method) (skrt.multi.PatientDataset method) (skrt.multi.PatientIterator method) (skrt.patient.Patient method) (skrt.patient.Study method) (skrt.registration.DeformationField method) (skrt.registration.Elastix method) (skrt.registration.Grid method) (skrt.registration.Jacobian method) (skrt.registration.NiftyReg method) (skrt.registration.Registration method) (skrt.registration.RegistrationEngine method) (skrt.segmentation.MultiAtlasSegmentation method) (skrt.segmentation.SasTuner method) (skrt.segmentation.SingleAtlasSegmentation method) (skrt.simulation.Cuboid method) (skrt.simulation.Cylinder method) (skrt.simulation.Grid method) (skrt.simulation.ShapeGroup method) (skrt.simulation.Sphere method) (skrt.simulation.SyntheticImage method) (skrt.structures.ROI method) (skrt.structures.ROIDefaults method) (skrt.structures.StructureSet method) (skrt.structures.StructureSetIterator method) (skrt.viewer.core.DeformationImage method) (skrt.viewer.core.Image method) (skrt.viewer.core.ImageComparison method) (skrt.viewer.core.MultiImage method) (skrt.viewer.core.OrthogonalImage method) (skrt.viewer.core.Struct method) (skrt.viewer.core.StructComparison method) (skrt.viewer.core.StructureSet method) (skrt.viewer.viewer.QuickViewer method) (skrt.viewer.viewer.SingleViewer method) (voxtox.structures.ROI method) (voxtox.structures.StructureSet method)

__repr__() (skrt.application.Status method) (skrt.core.Data method) (skrt.core.Defaults method) (skrt.core.TicToc method)

A

abs_centroid_distance() (skrt.viewer.core.StructComparison method) add_cube() (skrt.simulation.SyntheticImage method) add_cuboid() (skrt.simulation.SyntheticImage method) add_cylinder() (skrt.simulation.SyntheticImage method) add_default_pfile() (skrt.registration.Registration method) add_dose() (skrt.dose.Plan method) (skrt.image.Image method) add_engine() (in module skrt.registration) add_file() (skrt.registration.Registration method) add_files() (skrt.registration.Registration method) add_grid() (skrt.simulation.SyntheticImage method) add_image() (skrt.patient.Study method) add_image_info() (skrt.dicom_writer.DicomWriter method) add_path() (skrt.multi.PatientDataset method) add_pfile() (skrt.registration.Registration method) add_plan() (skrt.image.Image method) (skrt.structures.ROI method) (skrt.structures.StructureSet method) add_roi() (skrt.structures.StructureSet method) add_rois() (skrt.structures.ROI method) (skrt.structures.StructureSet method) add_shape() (skrt.simulation.ShapeGroup method) (skrt.simulation.SyntheticImage method) add_sinogram_noise() (skrt.image.Image method) add_sphere() (skrt.simulation.SyntheticImage method) add_struct_array() (skrt.viewer.core.StructureSet method) add_struct_file() (skrt.viewer.core.StructureSet method) add_structure_set() (skrt.image.Image method) add_structure_set_info() (skrt.dicom_writer.DicomWriter method)

add_study() (skrt.patient.Patient method) adjust_ax() (skrt.viewer.core.Image method) adjust_file() (skrt.registration.Registration method) adjust_parameters() (in module skrt.registration) (skrt.registration.Elastix method) (skrt.registration.Matlab method) (skrt.registration.NiftyReg method) (skrt.registration.RegistrationEngine method) adjust_pfile() (skrt.registration.Registration method) adjust_reg_files() (skrt.segmentation.SingleAtlasSegmentation method) Algorithm (class in skrt.application) alphanumeric() (in module skrt.core) any_attr() (skrt.better_viewer.BetterViewer method) (skrt.viewer.viewer.QuickViewer method) Application (class in skrt.application) apply_banding() (skrt.image.Image method) apply_couch_shifts() (voxtox.image.Image method) (voxtox.structures.ROI method) (voxtox.structures.StructureSet method) apply_filter() (skrt.image.Sinogram method) apply_noise() (skrt.simulation.SyntheticImage method) apply_selective_banding() (skrt.image.Image method) apply_translation() (skrt.better_viewer.BetterViewer method) (skrt.viewer.viewer.QuickViewer method) Archive (class in skrt.core) area_ratio() (skrt.viewer.core.StructComparison method) assign_color() (skrt.viewer.core.Struct method) assign_intensity_to_rois() (skrt.image.Image method) assign_structure_set() (skrt.image.Image method) astype() (skrt.image.Image method)

B

backprojected() (skrt.image.Sinogram method)

best_text_color() (in module skrt.structures) BetterViewer (class in skrt.better_viewer)

C

centre_at_struct() (skrt.viewer.viewer.SingleViewer method) centre_on_roi() (skrt.better_viewer.SingleViewer method) centroid() (skrt.viewer.core.Struct method) centroid_distance() (skrt.viewer.core.StructComparison method) checked_crop_limits() (in module skrt.image) clear() (skrt.registration.Registration method) clear_doses() (skrt.dose.Plan method) (skrt.image.Image method) clear_plans() (skrt.image.Image method) (skrt.structures.ROI method) (skrt.structures.StructureSet method) clear_structure_sets() (skrt.image.Image method) clone() (skrt.core.Data method) clone_attrs() (skrt.core.Data method) (skrt.structures.ROI method) (skrt.structures.StructureSet method) clone_with_structure_set() (skrt.image.Image method) combine_rois() (skrt.structures.StructureSet method) combined_files() (skrt.patient.Patient method) combined_files_by_dir() (skrt.patient.Patient method) combined_objs() (skrt.patient.Patient method) combined_types() (skrt.patient.Patient method) compare_roi_pairs() (in module skrt.structures) compress_user() (in module skrt.core) Constraint (class in skrt.dose) containing_image() (skrt.structures.StructureSet method) contains() (skrt.structures.StructureSet method) contour_to_polygon() (in module skrt.structures) contours_mean_z() (in module voxtox.structures) contours_to_indices() (in module skrt.viewer.core) contours_to_mask() (in module skrt.viewer.core) convert_spacing() (skrt.registration.DeformationField method) convert_to_3d() (skrt.viewer.core.Image method)

convert_xy_contours() (skrt.viewer.core.Struct method) copy() (skrt.patient.Patient method) copy_attributes() (skrt.application.Status method) copy_dicom() (skrt.core.Dated method) (skrt.dose.Dose method) (skrt.image.Image method) (skrt.patient.Patient method) (skrt.patient.Study method) copy_dicom_files() (skrt.core.Dated method) correct_dose_image_position() (skrt.patient.Study method) create_contours() (skrt.structures.ROI method) create_dummy_image() (in module skrt.structures) create_file_dataset() (skrt.dicom_writer.DicomWriter method) create_majority_vote() (in module skrt.structures) create_mask() (skrt.structures.ROI method) create_objects() (skrt.core.PathData method) create_roi_overlap() (in module skrt.structures) create_roi_sum() (in module skrt.structures) create_staple() (in module skrt.structures) create_structure_sets_from_nifti() (in module skrt.structures) crop() (skrt.image.Image method) (skrt.structures.ROI method) (skrt.structures.StructureSet method) crop_about_point() (skrt.image.Image method) crop_by_amounts() (in module skrt.image) (skrt.image.Image method) (skrt.structures.ROI method) crop_to_image() (skrt.image.Image method) crop_to_roi() (skrt.image.Image method) (skrt.structures.ROI method) crop_to_roi_length() (skrt.structures.ROI method) Cuboid (class in skrt.simulation) Cylinder (class in skrt.simulation)

D

Data (class in skrt.core) Dated (class in skrt.core) decrease_slice() (skrt.better_viewer.SingleViewer method) (skrt.viewer.viewer.SingleViewer method) def_signs (skrt.registration.NiftyReg attribute) (skrt.registration.RegistrationEngine attribute) default_aspect() (in module skrt.image) Defaults (class in skrt.core) define_translation() (skrt.registration.Elastix method) (skrt.registration.Matlab method) (skrt.registration.NiftyReg method) (skrt.registration.RegistrationEngine method)

DeformationField (class in skrt.registration) DeformationImage (class in skrt.viewer.core) df_to_html() (in module skrt.structures) dice() (skrt.viewer.core.StructComparison method) DicomFile (class in skrt.core) DicomWriter (class in skrt.dicom_writer) Dose (class in skrt.dose) download() (in module skrt.core) downsample() (in module skrt.image) (skrt.image.Image method) (skrt.viewer.core.Image method) downsample_array() (skrt.viewer.core.Image method)

E

Elastix (class in skrt.registration) ensure_dict() (in module skrt.segmentation) ensure_image() (in module skrt.segmentation) ensure_registered() (skrt.registration.Registration method) ensure_structure_set() (in module skrt.segmentation) entropy() (in module skrt.image) execute() (skrt.application.Algorithm method) (skrt.application.Application method)

exes (skrt.registration.Elastix attribute) (skrt.registration.Matlab attribute) (skrt.registration.NiftyReg attribute) (skrt.registration.RegistrationEngine attribute) expand_slice_stats() (in module skrt.structures) extent_ratio() (skrt.viewer.core.StructComparison method)

F

File (class in skrt.core) filter_on_paths() (in module skrt.core) filter_rois() (skrt.structures.StructureSet method) filtered() (skrt.image.Sinogram method) filtered_copy() (skrt.structures.StructureSet method) filtered_dict() (in module skrt.core) finalise() (skrt.application.Algorithm method) (skrt.application.Application method) find_color_match() (skrt.viewer.core.StructureSet method) find_comparisons() (skrt.viewer.core.StructureSet method)

find_date() (in module skrt.viewer.core) find_files() (in module skrt.viewer.core) find_matching_object() (in module skrt.patient) find_most_populated_slice() (skrt.structures.StructureSet method) find_name_match() (skrt.viewer.core.StructureSet method) find_translation_file() (skrt.viewer.viewer.QuickViewer method) flattened() (skrt.image.Image method) (skrt.structures.ROI method) from_alg_specs() (skrt.application.Application class method) fullpath() (in module skrt.core)

G

generate_shortened_uid() (skrt.dicom_writer.DicomWriter method) generate_timestamp() (in module skrt.core) get_abs_centroid_distance() (skrt.structures.ROI method) get_added_path_length() (skrt.structures.ROI method) get_affine() (skrt.image.Image method) (skrt.structures.ROI method) get_age() (skrt.patient.Patient method) get_alignment_strategy() (in module skrt.image) get_alignment_translation() (in module skrt.image) (skrt.image.Image method) get_all_rois() (in module skrt.structures) get_alpha_beta_ratios() (skrt.structures.StructureSet method) get_alpha_over_beta() (skrt.structures.ROI method) get_approval_status() (skrt.dose.Plan method) get_area() (skrt.structures.ROI method) (skrt.viewer.core.Struct method) get_area_diff() (skrt.structures.ROI method) get_area_ratio() (skrt.structures.ROI method) get_aspect_ratio() (skrt.structures.ROI method) get_associated_image() (in module skrt.core) get_atlases() (in module skrt.segmentation) get_auto_steps() (skrt.segmentation.SingleAtlasSegmentation method) get_ax_dict() (skrt.viewer.core.Image method) get_axes() (skrt.image.Image method) get_background() (skrt.simulation.SyntheticImage method) get_basenames() (in module skrt.core) get_bbox_centre_and_widths() (skrt.structures.ROI method) (skrt.structures.StructureSet method) get_bed() (skrt.dose.Dose method) get_biologically_effective_dose() (skrt.dose.Dose method) get_birth_date() (skrt.patient.Patient method) get_box_mask_from_mask() (in module skrt.image) get_by_slice_methods() (in module skrt.structures) get_centre() (skrt.image.Image method) (skrt.structures.ROI method) (skrt.structures.StructureSet method) (skrt.viewer.core.Struct method) get_centroid() (skrt.structures.ROI method) get_centroid_distance() (skrt.structures.ROI method) get_centroid_idx() (skrt.image.Image method) get_centroid_pos() (skrt.image.Image method) get_centroid_slice() (skrt.image.Image method) get_centroid_translation() (import_analysis.patient.ImportPatient method) get_color_from_kwargs() (skrt.structures.ROI method) get_colored_roi_string() (in module skrt.structures) get_colors() (skrt.structures.StructureSet method) get_comparison() (skrt.image.Image method) (skrt.registration.Registration method) (skrt.segmentation.MultiAtlasSegmentation method) (skrt.segmentation.SingleAtlasSegmentation method) (skrt.structures.ROI method) (skrt.structures.StructureSet method) get_comparison_dict() (skrt.viewer.core.StructureSet method) get_comparison_metrics() (in module skrt.structures) get_comparison_name() (skrt.structures.ROI method) get_comparison_pairs() (skrt.structures.StructureSet method) get_comparison_steps() (skrt.segmentation.SingleAtlasSegmentation method) get_comparisons() (skrt.viewer.core.StructureSet method) get_conformity_index() (in module skrt.structures) (skrt.structures.StructureSet method) get_consensus() (skrt.segmentation.MultiAtlasSegmentation method) (skrt.structures.StructureSet method) get_consensus_types() (in module skrt.structures) get_contour_propagation_strategies() (in module skrt.segmentation) get_contour_slice() (skrt.viewer.core.Struct method) get_contours() (skrt.structures.ROI method) get_contours_on_slice() (skrt.structures.ROI method) get_coordinate_arrays() (skrt.image.Image method) get_coords() (skrt.image.Image method) (skrt.viewer.core.Image method) get_correlation_quality() (skrt.image.Image method) (skrt.registration.Registration method) get_couch_rotations() (in module voxtox.core) get_couch_shifts() (in module voxtox.core) get_couch_translations() (in module voxtox.core) get_crop_limits() (skrt.structures.ROI method) (skrt.structures.StructureSet method) get_ct_plan() (import_analysis.patient.ImportPatient method) get_ct_relapse() (import_analysis.patient.ImportPatient method) get_data() (skrt.image.Image method) (skrt.simulation.Cuboid method) (skrt.simulation.Cylinder method) (skrt.simulation.Grid method) (skrt.simulation.ShapeGroup method) (skrt.simulation.Sphere method) (skrt.simulation.SyntheticImage method) (skrt.viewer.core.Image method) get_data_by_filename() (in module skrt.core) get_data_dir() (in module skrt.registration) get_data_indices() (in module skrt.core) get_date_dict() (skrt.viewer.core.MultiImage method) get_day_in_week() (in module skrt.core) get_def_cmd() (skrt.registration.Elastix method) (skrt.registration.Matlab method) (skrt.registration.NiftyReg method) (skrt.registration.RegistrationEngine method) get_default_params() (skrt.registration.Registration method) get_default_pfiles() (in module skrt.registration) (skrt.registration.RegistrationEngine method) get_default_pfiles_dir() (in module skrt.registration) (skrt.registration.RegistrationEngine method) get_default_roi_color() (skrt.structures.ROIDefaults method) get_default_roi_name() (skrt.structures.ROIDefaults method) get_default_structure_set_name() (skrt.structures.ROIDefaults method) get_deformation_field() (skrt.registration.Registration method) get_deformation_slice() (skrt.viewer.core.DeformationImage method) get_description() (skrt.dose.Plan method) (skrt.patient.Study method) get_dice() (skrt.structures.ROI method) get_dicom_affine() (in module skrt.image) get_dicom_array_and_affine() (skrt.image.Image method) get_dicom_dataset() (skrt.dose.Plan method) (skrt.image.Image method) (skrt.structures.ROI method) (skrt.structures.StructureSet method) get_dicom_filepath() (skrt.image.Image method) get_dicom_orientation() (in module skrt.image) get_dicom_paths() (in module skrt.image) get_dicom_sequence() (in module skrt.structures) (in module skrt.viewer.core) get_dicom_voxel_size() (in module skrt.image) get_dicom_window() (in module skrt.image) get_dict() (skrt.core.Data method) get_dict_permutations() (in module skrt.core) get_difference() (skrt.image.ImageComparison method) get_displacement_image() (skrt.registration.DeformationField method) get_dose_in_roi() (skrt.dose.Dose method) get_dose_in_roi_3d() (skrt.dose.Dose method) get_dose_info() (skrt.patient.Patient method) get_dose_objective() (skrt.dose.Plan method) get_dose_params() (skrt.registration.Elastix method) (skrt.registration.RegistrationEngine method) get_dose_quantile() (skrt.dose.Dose method) get_dose_sum() (import_analysis.patient.ImportPatient method) (skrt.patient.Patient method) get_dose_summation_type() (skrt.dose.Dose method) get_dose_summation_types() (import_analysis.patient.ImportPatient method) get_dose_type() (skrt.dose.Dose method) get_dose_units() (skrt.dose.Dose method) get_doses() (skrt.dose.Plan method) (skrt.image.Image method) (skrt.patient.Patient method) (skrt.patient.Study method) get_dta() (skrt.image.ImageComparison method) (skrt.viewer.core.ImageComparison method) get_dummy_image() (skrt.structures.ROI method) (skrt.structures.StructureSet method) get_enclosing_roi() (skrt.structures.ROI method) get_engine_cls() (in module skrt.registration) get_engine_name() (in module skrt.registration) get_engines() (in module skrt.registration) get_eqd() (skrt.dose.Dose method) get_equivalent_dose() (skrt.dose.Dose method) get_extent() (skrt.structures.ROI method) (skrt.structures.StructureSet method) get_extent_diff() (skrt.structures.ROI method) get_extents() (skrt.image.Image method) (skrt.structures.ROI method) (skrt.structures.StructureSet method) get_fidelity() (skrt.image.Image method) (skrt.registration.Registration method) get_file_dataset() (skrt.dicom_writer.DicomWriter method) get_file_size() (in module skrt.core) (skrt.core.Archive method) (skrt.core.PathData method) get_fixed_and_moving() (in module skrt.segmentation) get_float() (in module skrt.core) get_foreground_bbox() (skrt.image.Image method) get_foreground_bbox_centre_and_widths() (skrt.image.Image method) get_foreground_box_mask() (skrt.image.Image method) get_foreground_comparison() (skrt.image.Image method) (skrt.registration.Registration method) get_foreground_mask() (skrt.image.Image method) get_foreground_roi() (skrt.image.Image method) get_gamma() (skrt.image.ImageComparison method) (skrt.viewer.core.ImageComparison method) get_geometry() (in module skrt.image) (skrt.structures.ROI method) (skrt.structures.StructureSet method) get_groupings() (skrt.patient.Patient method) get_hausdorff_distance() (skrt.structures.ROI method) get_hour_in_day() (in module skrt.core) get_hour_in_week() (in module skrt.core) get_hu_range() (skrt.viewer.viewer.SingleViewer method) get_idx() (skrt.image.Image method) (skrt.structures.ROI method) (skrt.viewer.core.Image method) get_image() (skrt.dose.ImageOverlay method) (skrt.dose.Plan method) (skrt.simulation.SyntheticImage method) (skrt.structures.ROI method) (skrt.structures.StructureSet method) get_image_centre() (skrt.viewer.core.Image method) get_image_comparison_metrics() (in module skrt.image) get_image_info() (skrt.patient.Patient method) get_image_transform_parameters() (in module skrt.registration) get_images() (skrt.patient.Patient method) (skrt.patient.Study method) get_indexed_objs() (in module skrt.core) get_indices() (skrt.structures.ROI method) get_info() (skrt.patient.Patient method) get_input_list() (skrt.better_viewer.BetterViewer method) (skrt.viewer.viewer.QuickViewer method) get_input_parameters() (skrt.registration.Registration method) get_intensities() (skrt.structures.ROI method) get_intensities_3d() (skrt.structures.ROI method) get_intensity_mask() (skrt.image.Image method) get_intensity_range() (skrt.better_viewer.SingleViewer method) get_intersection() (in module skrt.structures) get_intersection_union_size() (skrt.structures.ROI method) get_interval_in_days() (in module skrt.core) get_interval_in_whole_days() (in module skrt.core) get_item_string() (skrt.core.Data method) get_jac_cmd() (skrt.registration.Elastix method) (skrt.registration.Matlab method) (skrt.registration.NiftyReg method) (skrt.registration.RegistrationEngine method) get_jaccard() (skrt.structures.ROI method) get_jacobian() (skrt.registration.Registration method) get_jacobian_colormap() (in module skrt.registration) get_key() (in module voxtox.structures) get_kwargs() (skrt.viewer.core.Image method) get_label() (skrt.structures.StructureSet method) get_length() (skrt.image.Image method) (skrt.structures.ROI method) (skrt.structures.StructureSet method) (skrt.viewer.core.Struct method) get_lengths() (skrt.viewer.core.Image method) get_logger() (in module skrt.core) get_machine() (skrt.dose.Plan method) (skrt.image.Image method)

get_machine_sublist() (skrt.patient.Study method) get_majority_vote() (skrt.structures.StructureSet method) get_manufacturer() (skrt.image.Image method) get_mask() (in module skrt.image) (skrt.structures.ROI method) get_mask_bbox() (in module skrt.image) get_mask_image() (skrt.structures.ROI method) (skrt.structures.StructureSet method) get_mask_plan() (import_analysis.patient.ImportPatient method) get_mask_relapse() (import_analysis.patient.ImportPatient method) get_mask_to_contour_volume_ratio() (skrt.structures.ROI method) get_masked_image() (skrt.image.Image method) get_matched_attributes() (skrt.core.DicomFile method) get_matched_timestamps() (skrt.core.Dated method) get_max() (skrt.image.Image method) get_max_dose_in_rois() (skrt.dose.Dose method) get_mean_distance_to_conformity() (skrt.structures.ROI method) get_mean_dose() (skrt.dose.Dose method) get_mean_surface_distance() (skrt.structures.ROI method) get_media_storage_sop_class_uid() (skrt.dicom_writer.DicomWriter method) get_metric_by_slice() (skrt.structures.ROI method) get_metric_method() (in module skrt.structures) get_mi_metrics() (in module skrt.image) get_mid_idx() (skrt.structures.ROI method) (skrt.structures.StructureSet method) get_min() (skrt.image.Image method) (skrt.viewer.core.Image method) get_min_hu() (skrt.viewer.core.Image method) get_model() (skrt.image.Image method) get_mpl_kwargs() (skrt.image.Image method) get_mutual_information() (skrt.image.Image method) (skrt.registration.Registration method) get_mvct_selection() (skrt.patient.Study method) get_n_beam_seq() (skrt.dose.Plan method) get_n_colorbars() (skrt.viewer.core.MultiImage method) get_n_file() (in module skrt.core) (skrt.core.Archive method) (skrt.core.PathData method) get_n_file_below() (in module skrt.core) (skrt.core.PathData method) get_n_fraction() (skrt.dose.Dose method) (skrt.dose.Plan method) get_n_fraction_group() (skrt.dose.Plan method) get_n_voxels() (skrt.image.Image method) get_name() (skrt.dose.Plan method) (skrt.structures.ROI method) (skrt.structures.StructureSet method) get_nifti_array_and_affine() (skrt.image.Image method) get_np_voxel_size() (skrt.structures.ROI method) get_nz_contours() (skrt.structures.ROI method) get_object() (skrt.core.DicomFile method) get_objs() (skrt.patient.Patient method) (skrt.patient.Study method) get_option() (in module skrt.segmentation) get_options() (in module skrt.segmentation) get_organs_at_risk() (skrt.dose.Plan method) get_orientation_codes() (skrt.image.Image method) get_orientation_vector() (skrt.image.Image method) get_orientation_view() (skrt.image.Image method) get_origin() (skrt.image.Image method) (skrt.structures.ROI method) get_overlap() (skrt.structures.StructureSet method) get_pandas_timestamp() (skrt.core.Dated method) get_parameters() (in module skrt.registration) get_patch() (skrt.structures.ROI method) get_path_with_timestamp() (skrt.dicom_writer.DicomWriter method) get_paths() (in module skrt.application) (in module voxtox.data) get_paths_djn_253() (in module voxtox.data) get_paths_jes_109() (in module voxtox.data) get_patient() (skrt.patient.Study method) get_patient_id() (skrt.patient.Study method) get_plan_data() (skrt.patient.Study method) get_plan_dose() (skrt.patient.Study method) get_plan_info() (skrt.patient.Patient method) get_plans() (skrt.image.Image method) (skrt.patient.Patient method) (skrt.patient.Study method) (skrt.structures.ROI method) (skrt.structures.StructureSet method) get_plot_aspect_ratio() (skrt.image.Image method) (skrt.image.ImageComparison method) get_polygons() (skrt.structures.ROI method) get_polygons_on_slice() (skrt.structures.ROI method) get_prescription_description() (skrt.dose.Plan method) get_print_depth() (skrt.core.Data method) get_qualified_class_name() (in module skrt.core) get_quality() (skrt.image.Image method) (skrt.registration.Registration method) get_quality_metrics() (in module skrt.image) get_range() (skrt.image.Image method) get_referenced_image() (in module skrt.core) get_referenced_object() (in module skrt.core) get_reg_steps() (skrt.segmentation.SingleAtlasSegmentation method) get_registration() (skrt.segmentation.SingleAtlasSegmentation method) get_registration_cmd() (skrt.registration.Elastix method) (skrt.registration.Matlab method) (skrt.registration.NiftyReg method) (skrt.registration.Registration method) (skrt.registration.RegistrationEngine method) get_relative_area_diff() (skrt.structures.ROI method) get_relative_structural_content() (skrt.image.Image method) (skrt.registration.Registration method) get_relative_volume_diff() (skrt.structures.ROI method) get_relative_width() (skrt.viewer.core.Image method) (skrt.viewer.core.ImageComparison method) (skrt.viewer.core.MultiImage method) (skrt.viewer.core.OrthogonalImage method) get_rms_surface_distance() (skrt.structures.ROI method) get_roi() (in module voxtox.roi_names) (skrt.simulation.SyntheticImage method) (skrt.structures.StructureSet method) get_roi_data() (skrt.simulation.SyntheticImage method) get_roi_dict() (skrt.structures.StructureSet method) get_roi_names() (skrt.structures.StructureSet method) get_roi_params() (skrt.registration.Elastix method) (skrt.registration.Matlab method) (skrt.registration.NiftyReg method) (skrt.registration.RegistrationEngine method) get_roi_slice() (in module skrt.structures) (skrt.structures.ROI method) get_rois() (skrt.image.Image method) (skrt.simulation.SyntheticImage method) (skrt.structures.StructureSet method) get_rois_wildcard() (skrt.structures.StructureSet method) get_rotation_matrix() (in module skrt.viewer.core) get_sas() (skrt.segmentation.MultiAtlasSegmentation method) get_sas_segmentations() (skrt.segmentation.MultiAtlasSegmentation method) get_segmentation() (skrt.segmentation.SingleAtlasSegmentation method) get_segmentation_steps() (in module skrt.segmentation) get_series_description() (skrt.structures.StructureSet method) get_sex() (skrt.patient.Patient method) get_similarity_scores() (skrt.segmentation.MultiAtlasSegmentation method) get_single_path() (in module skrt.core) get_sinogram() (skrt.image.Image method) get_size() (skrt.image.Image method) get_slice() (skrt.image.Image method) (skrt.registration.DeformationField method) (skrt.structures.ROI method) (skrt.viewer.core.Image method) get_slice_foreground() (skrt.image.Image method) get_slice_positions() (in module skrt.structures) (skrt.structures.ROI method) get_slice_stat() (skrt.structures.ROI method) get_slice_stats() (skrt.structures.ROI method) get_slice_thickness_contours() (skrt.structures.ROI method) get_ss_clinical() (import_analysis.patient.ImportPatient method) get_ss_plan() (import_analysis.patient.ImportPatient method) get_ss_recurrence() (import_analysis.patient.ImportPatient method) get_ss_relapse() (import_analysis.patient.ImportPatient method) get_standalone_structs() (skrt.viewer.core.StructureSet method) get_standardised_affine() (skrt.image.Image method) get_standardised_data() (skrt.image.Image method) get_standardised_origin() (skrt.image.Image method) get_standardised_voxel_size() (skrt.image.Image method) get_staple() (skrt.structures.StructureSet method) get_stat() (in module skrt.core) get_stat_functions() (in module skrt.core) get_station_name() (skrt.dose.Plan method) (skrt.image.Image method) get_step_name() (skrt.registration.Registration method) get_step_number() (skrt.registration.Registration method) get_steps() (in module skrt.segmentation) get_strategy() (in module skrt.segmentation) get_struct() (skrt.viewer.core.StructureSet method) get_struct_centre() (skrt.viewer.core.Struct method) get_struct_dict() (skrt.viewer.core.StructureSet method) get_struct_html() (skrt.viewer.viewer.SingleViewer method) get_struct_visibility() (skrt.viewer.viewer.SingleViewer method) get_structs() (skrt.viewer.core.StructureSet method) get_structure_set() (skrt.dose.Plan method) (skrt.simulation.SyntheticImage method) get_structure_set_index() (in module skrt.segmentation) get_structure_set_info() (skrt.patient.Patient method) get_structure_set_with_image() (skrt.patient.Patient method) get_structure_sets() (skrt.image.Image method) (skrt.patient.Patient method) (skrt.patient.Study method) get_structuring_element() (in module skrt.structures) get_studies() (skrt.patient.Patient method) get_subdir_paths() (in module skrt.core) get_subdir_studies() (skrt.patient.Patient method) get_sum() (skrt.structures.StructureSet method) get_surface_area() (skrt.structures.ROI method) get_surface_distance_metrics() (skrt.structures.ROI method) get_surface_distances() (skrt.structures.ROI method) get_target_dose() (skrt.dose.Plan method) get_targets() (skrt.dose.Plan method) get_tfile() (skrt.registration.Registration method) get_time_and_date() (in module skrt.core) get_time_separated_objects() (in module skrt.core) get_transform_cmd() (skrt.registration.Elastix method) (skrt.registration.Matlab method) (skrt.registration.NiftyReg method) (skrt.registration.RegistrationEngine method) get_transform_log() (skrt.registration.RegistrationEngine method) get_transform_parameters() (skrt.registration.Registration method) get_transform_strategies() (skrt.registration.Elastix static method) (skrt.registration.Matlab static method) (skrt.registration.NiftyReg static method) (skrt.registration.RegistrationEngine static method) get_transformed_grid() (skrt.registration.Registration method) get_transformed_image() (skrt.registration.Registration method) get_translation_matrix() (in module skrt.viewer.core) get_translation_to_align() (in module skrt.image) (in module skrt.structures) (skrt.image.Image method) (skrt.structures.ROI method) (skrt.structures.StructureSet method) get_translation_to_align_image_rois() (in module skrt.image) (skrt.image.Image method) get_uid_without_slice() (in module skrt.core) get_unique_path() (in module skrt.viewer.core) get_value() (in module skrt.simulation) get_value_from_json() (in module skrt.core) get_values() (in module skrt.simulation) get_visible_rois() (skrt.better_viewer.SingleViewer method) get_volume() (skrt.image.Image method) (skrt.structures.ROI method) (skrt.viewer.core.Struct method) get_volume_diff() (skrt.structures.ROI method) get_volume_ratio() (skrt.structures.ROI method) get_voxel_coords() (skrt.image.Image method) get_voxel_size() (skrt.image.Image method) (skrt.structures.ROI method) get_weight_and_objectives() (skrt.dose.Constraint class method) get_zoom_centre() (skrt.structures.ROI method) get_zoomed_lims() (skrt.viewer.core.Image method) Grid (class in skrt.registration) (class in skrt.simulation)

H

has_rois() (skrt.structures.StructureSet method) has_same_data() (skrt.image.Image method) has_same_geometry() (skrt.image.Image method)

hausdorff_distance() (skrt.viewer.core.StructComparison method) hu_to_mu() (in module skrt.core) (skrt.image.Image method) (skrt.simulation.SyntheticImage method)

I

idx_to_pos() (skrt.image.Image method) (skrt.structures.ROI method) (skrt.viewer.core.Image method) idx_to_slice() (skrt.image.Image method) (skrt.structures.ROI method) (skrt.viewer.core.Image method) Image (class in skrt.image) (class in skrt.viewer.core) (class in voxtox.image) ImageComparison (class in skrt.image) (class in skrt.viewer.core) ImageOverlay (class in skrt.dose) import_analysis module import_analysis.patient module import_analysis.roi_names module import_analysis.viewer module ImportPatient (class in import_analysis.patient) in_date_interval() (skrt.core.Dated method)

in_notebook() (in module skrt.better_viewer) (in module skrt.viewer.viewer) increase_slice() (skrt.better_viewer.SingleViewer method) (skrt.viewer.viewer.SingleViewer method) initialise() (skrt.application.Algorithm method) (skrt.application.Application method) initialise_outdir() (skrt.dicom_writer.DicomWriter method) instance (skrt.core.Defaults attribute) (skrt.core.TicToc attribute) (skrt.structures.ROIDefaults attribute) interpolate_points() (skrt.structures.ROI method) (skrt.structures.StructureSet method) interpolate_points_single_contour() (in module skrt.structures) intersect_rois() (skrt.structures.ROI method) is_available() (skrt.registration.RegistrationEngine method) is_empty() (skrt.structures.ROI method) is_list() (in module skrt.core) (in module skrt.viewer.core) is_nested() (in module skrt.viewer.core) is_ok() (skrt.application.Status method) is_registered() (skrt.registration.Registration method) is_timestamp() (in module skrt.core) is_valid() (skrt.viewer.core.StructComparison method)

J

Jacobian (class in skrt.registration) jump_to_roi() (skrt.better_viewer.SingleViewer method)

jump_to_struct() (skrt.viewer.viewer.OrthogViewer method) (skrt.viewer.viewer.SingleViewer method)

K

keep_struct() (skrt.viewer.core.StructureSet method)

kv_to_mv() (in module skrt.image)

L

label_ax() (skrt.image.Image method) (skrt.viewer.core.Image method) last_in_interval() (skrt.patient.Patient method) length_to_voxels() (skrt.viewer.core.Image method) link_plan_to_doses() (skrt.patient.Study method) link_study_data_to_patient() (skrt.patient.Patient method) list_default_pfiles() (skrt.registration.Registration method) load() (skrt.dose.Dose method) (skrt.dose.Plan method) (skrt.image.Image method) (skrt.image.ImageComparison method) (skrt.registration.DeformationField method) (skrt.structures.ROI method) (skrt.structures.StructureSet method) (skrt.viewer.core.Struct method) (voxtox.structures.ROI method) (voxtox.structures.StructureSet method) load_all() (skrt.viewer.core.StructureSet method) load_comparison() (skrt.better_viewer.BetterViewer method) (skrt.viewer.viewer.QuickViewer method) load_constraints() (skrt.dose.Plan method) load_demographics() (skrt.patient.Patient method) load_df() (skrt.better_viewer.SingleViewer method) (skrt.viewer.core.MultiImage method) load_dicom() (in module skrt.image) (in module skrt.viewer.core) load_dicom_many_files() (in module skrt.image)

load_dicom_multiple_files() (in module skrt.viewer.core) load_dicom_single_file() (in module skrt.image) (in module skrt.viewer.core) load_dose() (skrt.better_viewer.SingleViewer method) load_existing_input_images() (skrt.registration.Registration method) load_files() (skrt.registration.Registration method) load_from_subdir() (skrt.patient.Study method) load_grid() (skrt.better_viewer.SingleViewer method) load_image() (in module skrt.viewer.core) load_images() (skrt.patient.Study method) load_jacobian() (skrt.better_viewer.SingleViewer method) load_json() (in module skrt.core) load_key_data() (import_analysis.patient.ImportPatient method) load_nifti() (in module skrt.image) load_npy() (in module skrt.image) load_rgb() (in module skrt.image) load_rois() (skrt.better_viewer.SingleViewer method) load_rois_dicom() (in module skrt.structures) load_settings() (skrt.viewer.core.StructureSet method) load_struct_pairs() (skrt.viewer.core.StructureSet method) load_structs() (in module skrt.viewer.core) (skrt.viewer.core.MultiImage method) (skrt.viewer.core.StructureSet method) load_structs_from_dicom() (skrt.viewer.core.StructureSet method) load_structs_from_file() (skrt.viewer.core.StructureSet method) load_to() (skrt.viewer.core.MultiImage method) load_toml() (in module skrt.core) load_transformix_points() (skrt.structures.ROI method)

M

make_comparison_ui() (skrt.better_viewer.BetterViewer method) (skrt.viewer.viewer.QuickViewer method) make_dir() (in module skrt.core) make_fig() (skrt.better_viewer.BetterViewer method) (skrt.viewer.viewer.QuickViewer method) make_grid() (in module skrt.simulation) make_head() (in module skrt.simulation) make_image() (skrt.better_viewer.SingleViewer method) (skrt.viewer.viewer.OrthogViewer method) (skrt.viewer.viewer.SingleViewer method) make_lower_ui() (skrt.better_viewer.BetterViewer method) (skrt.better_viewer.SingleViewer method) (skrt.viewer.viewer.QuickViewer method) (skrt.viewer.viewer.SingleViewer method) make_name_nice() (in module skrt.viewer.core) make_reset_zoom() (skrt.better_viewer.BetterViewer method) (skrt.viewer.viewer.QuickViewer method) make_three() (in module skrt.viewer.core) make_tmp_dir() (skrt.registration.Registration method) make_translation_ui() (skrt.better_viewer.BetterViewer method) (skrt.viewer.viewer.QuickViewer method) make_ui() (skrt.better_viewer.BetterViewer method) (skrt.better_viewer.SingleViewer method) (skrt.viewer.viewer.QuickViewer method) (skrt.viewer.viewer.SingleViewer method) manually_adjust_translation() (skrt.registration.Registration method) map_hu() (skrt.image.Image method) mask_to_contours() (skrt.structures.ROI method) match_axes() (skrt.better_viewer.BetterViewer method) (skrt.viewer.viewer.QuickViewer method) match_image_voxel_sizes() (in module skrt.image) match_images() (in module skrt.image) match_images_for_comparison() (in module skrt.image) match_mask_voxel_size() (skrt.structures.ROI method) match_rois() (in module skrt.structures) match_size() (skrt.image.Image method) (skrt.viewer.core.Image method) match_voxel_size() (skrt.image.Image method) (skrt.structures.ROI method) matches_suffix() (in module skrt.core) Matlab (class in skrt.registration)

max (skrt.dose.ImageOverlay property) mean_surface_distance() (skrt.viewer.core.StructComparison method) mid_slice() (skrt.viewer.core.Struct method) missing() (skrt.structures.StructureSet method) module import_analysis import_analysis.patient import_analysis.roi_names import_analysis.viewer skrt skrt.application skrt.better_viewer skrt.better_viewer.options skrt.core skrt.dicom_writer skrt.dose skrt.image skrt.multi skrt.patient skrt.registration skrt.segmentation skrt.simulation skrt.structures skrt.viewer skrt.viewer.core skrt.viewer.viewer voxtox voxtox.core voxtox.data voxtox.data.djn_253 voxtox.data.jes_109 voxtox.image voxtox.roi_names voxtox.roi_names.head_and_neck_roi_names voxtox.roi_names.prostate_roi_names voxtox.structures mu_to_hu() (in module skrt.core) (skrt.image.Image method) (skrt.simulation.SyntheticImage method) MultiAtlasSegmentation (class in skrt.segmentation) MultiImage (class in skrt.viewer.core)

N

new_roi_contour() (skrt.dicom_writer.DicomWriter method)

new_rt_roi_observation() (skrt.dicom_writer.DicomWriter method) NiftyReg (class in skrt.registration)

O

on_key() (skrt.better_viewer.BetterViewer method) (skrt.better_viewer.SingleViewer method) (skrt.viewer.viewer.QuickViewer method) (skrt.viewer.viewer.SingleViewer method) on_scroll() (skrt.better_viewer.BetterViewer method) (skrt.better_viewer.SingleViewer method) (skrt.viewer.viewer.QuickViewer method) (skrt.viewer.viewer.SingleViewer method)

on_slice() (skrt.structures.ROI method) (skrt.viewer.core.Struct method) (skrt.viewer.core.StructComparison method) on_view_change() (skrt.better_viewer.SingleViewer method) (skrt.viewer.viewer.SingleViewer method) order_rois() (skrt.structures.StructureSet method) OrthogonalImage (class in skrt.viewer.core) OrthogViewer (class in skrt.viewer.viewer)

P

pad_transpose() (in module skrt.image) PathData (class in skrt.core) Patient (class in skrt.patient) PatientDataset (class in skrt.multi) PatientIterator (class in skrt.multi) Plan (class in skrt.dose) plot() (skrt.better_viewer.BetterViewer method) (skrt.better_viewer.SingleViewer method) (skrt.dose.ImageOverlay method) (skrt.image.Image method) (skrt.image.ImageComparison method) (skrt.registration.DeformationField method) (skrt.simulation.SyntheticImage method) (skrt.structures.ROI method) (skrt.structures.StructureSet method) (skrt.viewer.core.DeformationImage method) (skrt.viewer.core.Image method) (skrt.viewer.core.ImageComparison method) (skrt.viewer.core.MultiImage method) (skrt.viewer.core.OrthogonalImage method) (skrt.viewer.core.Struct method) (skrt.viewer.core.StructComparison method) (skrt.viewer.viewer.QuickViewer method) (skrt.viewer.viewer.SingleViewer method) plot_chequerboard() (skrt.viewer.core.ImageComparison method) plot_comparison() (skrt.structures.ROI method) plot_comparisons() (skrt.structures.StructureSet method) plot_consensus() (skrt.structures.StructureSet method) plot_contour() (skrt.viewer.core.Struct method)

plot_difference() (skrt.viewer.core.ImageComparison method) plot_dta() (skrt.viewer.core.ImageComparison method) plot_DVH() (skrt.dose.Dose method) plot_dvh() (skrt.dose.Dose method) plot_gamma() (skrt.viewer.core.ImageComparison method) plot_grid() (skrt.viewer.core.DeformationImage method) plot_image() (skrt.better_viewer.SingleViewer method) (skrt.viewer.viewer.SingleViewer method) plot_mask() (skrt.viewer.core.Struct method) (skrt.viewer.core.StructComparison method) plot_overlay() (skrt.viewer.core.ImageComparison method) plot_quiver() (skrt.viewer.core.DeformationImage method) plot_surface_distances() (skrt.structures.ROI method) (skrt.structures.StructureSet method) polygon_to_contour() (in module skrt.structures) pos_to_idx() (skrt.image.Image method) (skrt.structures.ROI method) (skrt.viewer.core.Image method) pos_to_slice() (skrt.image.Image method) (skrt.structures.ROI method) (skrt.viewer.core.Image method) prepend_path() (in module skrt.core) print() (skrt.core.Data method) print_geometry() (skrt.image.Image method) print_log() (skrt.registration.Registration method) print_paths() (in module skrt.core) (skrt.core.PathData method) print_rois() (skrt.structures.StructureSet method) process_mask() (skrt.viewer.core.Image method)

Q

qualified__name() (in module skrt.core)

qualified_name() (in module skrt.core) QuickViewer (class in skrt.viewer.viewer)

R

read_affine() (skrt.registration.Matlab method) (skrt.registration.NiftyReg method) read_parameters() (in module skrt.registration) (skrt.registration.Elastix method) (skrt.registration.Matlab method) (skrt.registration.NiftyReg method) (skrt.registration.RegistrationEngine method) reassign_colors() (skrt.viewer.core.StructureSet method) recolor_rois() (skrt.structures.StructureSet method) recursive_transform (skrt.registration.Matlab attribute) (skrt.registration.RegistrationEngine attribute) register() (skrt.registration.Registration method) register_step() (skrt.registration.Registration method) Registration (class in skrt.registration) RegistrationEngine (class in skrt.registration) relative_area() (skrt.viewer.core.StructComparison method) relative_path() (in module skrt.core) relative_vol() (skrt.viewer.core.StructComparison method) remove_bolus() (skrt.image.Image method) remove_duplicate_doses() (in module skrt.dose) remove_duplicate_images() (in module skrt.image) rename_rois() (skrt.structures.StructureSet method) renamed() (skrt.structures.ROI method) (skrt.structures.StructureSet method) resample() (skrt.image.Image method) (skrt.structures.ROI method) (skrt.viewer.core.Image method)

rescale() (skrt.image.Image method) (skrt.simulation.SyntheticImage method) rescale_dicom_data() (in module skrt.image) rescale_images() (in module skrt.image) reset() (skrt.simulation.SyntheticImage method) (skrt.structures.StructureSet method) (skrt.viewer.core.Image method) reset_contours() (skrt.structures.ROI method) (skrt.structures.StructureSet method) reset_mask() (skrt.structures.ROI method) reset_transforms() (skrt.simulation.SyntheticImage method) reset_zoom() (skrt.better_viewer.SingleViewer method) (skrt.viewer.viewer.SingleViewer method) resize() (skrt.image.Image method) resize_contours() (skrt.structures.ROI method) resized() (skrt.structures.ROI method) rm_tmp_dir() (skrt.registration.Registration method) rms_surface_distance() (skrt.viewer.core.StructComparison method) ROI (class in skrt.structures) (class in voxtox.structures) roi_is_visible() (skrt.better_viewer.SingleViewer method) ROIDefaults (class in skrt.structures) rotate() (skrt.simulation.SyntheticImage method) (skrt.viewer.core.Image method) run() (skrt.application.Application method) run_transformix_on_all() (skrt.registration.Registration method)

S

same_frame() (skrt.viewer.core.Image method) SasTuner (class in skrt.segmentation) save_fig() (skrt.better_viewer.SingleViewer method) (skrt.viewer.viewer.SingleViewer method) save_images_as_nifti() (skrt.patient.Study method) save_roi_comparison_table() (skrt.better_viewer.SingleViewer method) save_roi_info_table() (skrt.better_viewer.SingleViewer method) save_struct_comp_table() (skrt.viewer.viewer.SingleViewer method) save_struct_info_table() (skrt.viewer.viewer.SingleViewer method) save_structure_sets_as_nifti() (skrt.patient.Study method) save_table() (skrt.viewer.viewer.SingleViewer method) segment() (skrt.segmentation.MultiAtlasSegmentation method) (skrt.segmentation.SingleAtlasSegmentation method) segment_roi() (skrt.segmentation.SingleAtlasSegmentation method) segment_structure_set() (skrt.segmentation.SingleAtlasSegmentation method) select_atlases() (in module skrt.segmentation) select_foreground() (skrt.image.Image method) set_alpha_beta_ratios() (skrt.structures.StructureSet method) set_alpha_over_beta() (skrt.structures.ROI method) set_attributes() (skrt.application.Algorithm method) set_ax() (in module skrt.image) (skrt.image.Image method) (skrt.structures.ROI method) (skrt.viewer.core.Image method) set_ax_lims() (skrt.viewer.viewer.SingleViewer method) set_axes() (skrt.viewer.core.OrthogonalImage method) set_callbacks() (skrt.better_viewer.BetterViewer method) (skrt.better_viewer.SingleViewer method) (skrt.viewer.viewer.QuickViewer method) (skrt.viewer.viewer.SingleViewer method) set_color() (skrt.structures.ROI method) set_consensuses() (skrt.segmentation.MultiAtlasSegmentation method) set_contours() (skrt.viewer.core.Struct method) set_date() (skrt.viewer.core.MultiImage method) set_date_and_time() (skrt.dicom_writer.DicomWriter method) set_dates_and_times() (skrt.core.DicomFile method) set_elastix_dir() (in module skrt.registration) set_engine_dir() (in module skrt.registration) set_exe_env() (skrt.registration.Matlab method) (skrt.registration.RegistrationEngine method) set_exe_paths() (skrt.registration.Elastix method) (skrt.registration.NiftyReg method) (skrt.registration.RegistrationEngine method) set_fixed_image() (skrt.registration.Registration method) set_fixed_mask() (skrt.registration.Registration method) set_geom() (skrt.viewer.core.Image method) set_geometry() (skrt.image.Image method) set_geometry_and_scaling() (skrt.dicom_writer.DicomWriter method) set_image() (skrt.dicom_writer.DicomWriter method) (skrt.dose.Dose method) (skrt.dose.ImageOverlay method) (skrt.dose.Plan method) (skrt.registration.Registration method) (skrt.structures.ROI method) (skrt.structures.StructureSet method) set_image_orientation_patient() (in module skrt.image) set_image_slice() (skrt.dicom_writer.DicomWriter method) set_image_to_dummy() (skrt.structures.ROI method) (skrt.structures.StructureSet method) set_label() (skrt.viewer.core.Struct method) set_mask() (skrt.viewer.core.Image method) (skrt.viewer.core.Struct method) set_masks() (skrt.viewer.core.MultiImage method) set_matlab_runtime() (in module skrt.core) set_moving_grid() (skrt.registration.Registration method) set_moving_image() (skrt.registration.Registration method) set_moving_mask() (skrt.registration.Registration method) set_name() (skrt.structures.ROI method) (skrt.structures.StructureSet method) set_noise_std() (skrt.simulation.SyntheticImage method) set_plan() (skrt.dose.Dose method) set_plotting_defaults() (skrt.viewer.core.DeformationImage method) (skrt.viewer.core.Image method) (skrt.viewer.core.MultiImage method) (skrt.viewer.core.Struct method) set_print_depth() (skrt.core.Data method) set_referenced_frame_of_reference_sequence() (skrt.dicom_writer.DicomWriter method) set_referenced_sop_instance_uids() (skrt.core.DicomFile method) set_shift() (skrt.viewer.core.Image method) set_slice() (skrt.better_viewer.SingleViewer method) (skrt.viewer.core.DeformationImage method) (skrt.viewer.core.Image method) (skrt.viewer.viewer.SingleViewer method) set_slice_and_view() (skrt.better_viewer.SingleViewer method) (skrt.viewer.viewer.SingleViewer method) set_slice_from_idx() (skrt.better_viewer.SingleViewer method) set_slice_from_pos() (skrt.better_viewer.SingleViewer method) (skrt.viewer.viewer.SingleViewer method) set_slice_thickness() (skrt.core.DicomFile method) set_slice_thickness_contours() (skrt.structures.ROI method) set_slices() (skrt.image.ImageComparison method)

set_slider_widths() (skrt.better_viewer.BetterViewer method) (skrt.viewer.viewer.QuickViewer method) set_spacing() (skrt.viewer.core.DeformationImage method) set_structure_set() (skrt.dicom_writer.DicomWriter method) (skrt.dose.Plan method) set_unique_name() (skrt.viewer.core.StructureSet method) set_viewer_options() (in module import_analysis.viewer) (in module skrt.better_viewer.options) ShapeGroup (class in skrt.simulation) shift_translation_parameters() (in module skrt.registration) (skrt.registration.Elastix method) (skrt.registration.Matlab method) (skrt.registration.NiftyReg method) (skrt.registration.RegistrationEngine method) show() (skrt.better_viewer.BetterViewer method) (skrt.better_viewer.SingleViewer method) (skrt.viewer.viewer.QuickViewer method) (skrt.viewer.viewer.SingleViewer method) show_in_notebook() (skrt.better_viewer.SingleViewer method) (skrt.viewer.viewer.SingleViewer method) SingleAtlasSegmentation (class in skrt.segmentation) SingleViewer (class in skrt.better_viewer) (class in skrt.viewer.viewer) Sinogram (class in skrt.image) skrt module skrt.application module skrt.better_viewer module skrt.better_viewer.options module skrt.core module skrt.dicom_writer module skrt.dose module skrt.image module skrt.multi module skrt.patient module skrt.registration module skrt.segmentation module skrt.simulation module skrt.structures module skrt.viewer module skrt.viewer.core module skrt.viewer.viewer module slice_to_idx() (skrt.image.Image method) (skrt.structures.ROI method) (skrt.viewer.core.Image method) slice_to_pos() (skrt.image.Image method) (skrt.structures.ROI method) (skrt.viewer.core.Image method) slice_to_slider() (skrt.better_viewer.SingleViewer method) (skrt.viewer.viewer.SingleViewer method) slices() (skrt.viewer.core.Struct method) slider_to_sl() (skrt.viewer.viewer.SingleViewer method) slider_to_slice() (skrt.better_viewer.SingleViewer method) sort_dicom() (skrt.patient.Patient method) Sphere (class in skrt.simulation) split() (skrt.structures.ROI method) split_in_two() (skrt.structures.ROI method) split_rois_in_two() (skrt.structures.StructureSet method) standard_str() (in module skrt.viewer.core) standardise_data() (skrt.image.Image method) Status (class in skrt.application) Struct (class in skrt.viewer.core) struct_extent() (skrt.viewer.core.Struct method) StructComparison (class in skrt.viewer.core) StructureSet (class in skrt.structures) (class in skrt.viewer.core) (class in voxtox.structures) StructureSetIterator (class in skrt.structures) Study (class in skrt.patient) subtract_rois() (skrt.structures.ROI method) sum_dose_plans() (skrt.patient.Study method) sum_doses() (in module skrt.dose) sum_images() (in module skrt.image) surface_distances() (skrt.viewer.core.StructComparison method) SyntheticImage (class in skrt.simulation)

T

tic() (in module skrt.core) TicToc (class in skrt.core) to_inches() (in module skrt.better_viewer) (in module skrt.image) (in module skrt.viewer.core) to_list() (in module skrt.core) toc() (in module skrt.core) transform() (skrt.image.Image method) (skrt.registration.Registration method) (skrt.structures.ROI method) (skrt.structures.StructureSet method)

transform_data() (skrt.registration.Registration method) transform_image() (skrt.registration.Registration method) transform_log (skrt.registration.Elastix attribute) transform_moving_image() (skrt.registration.Registration method) transform_points_implemented (skrt.registration.Elastix attribute) (skrt.registration.RegistrationEngine attribute) transform_roi() (skrt.registration.Registration method) transform_structure_set() (skrt.registration.Registration method) translate() (skrt.simulation.SyntheticImage method) (skrt.viewer.core.Image method) translate_origin() (skrt.image.Image method)

U

unpack_couch_shifts() (in module voxtox.core) update() (skrt.simulation.SyntheticImage method) update_dataset() (skrt.dicom_writer.DicomWriter method) update_roi() (skrt.simulation.SyntheticImage method) update_roi_comparison() (skrt.better_viewer.SingleViewer method) update_roi_info_table() (skrt.better_viewer.SingleViewer method) update_roi_sliders() (skrt.better_viewer.SingleViewer method) update_rois() (skrt.simulation.SyntheticImage method) update_s2_data() (skrt.viewer.core.StructComparison method) update_slice_slider() (skrt.better_viewer.SingleViewer method) (skrt.viewer.viewer.SingleViewer method)

update_slice_slider_desc() (skrt.better_viewer.SingleViewer method) (skrt.viewer.viewer.SingleViewer method) update_slider() (skrt.better_viewer.SingleViewer method) (skrt.viewer.viewer.SingleViewer method) update_struct_comparisons() (skrt.viewer.viewer.SingleViewer method) update_struct_info() (skrt.viewer.viewer.SingleViewer method) update_struct_sliders() (skrt.viewer.viewer.SingleViewer method) update_zoom_sliders() (skrt.better_viewer.SingleViewer method) (skrt.viewer.viewer.SingleViewer method)

V

view() (skrt.image.Image method) (skrt.image.ImageComparison method) (skrt.registration.DeformationField method) (skrt.simulation.SyntheticImage method) (skrt.structures.ROI method) (skrt.structures.StructureSet method) view_init() (skrt.registration.Registration method) view_result() (skrt.registration.Registration method) vol_ratio() (skrt.viewer.core.StructComparison method) voxtox module voxtox.core module voxtox.data module

voxtox.data.djn_253 module voxtox.data.jes_109 module voxtox.image module voxtox.roi_names module voxtox.roi_names.head_and_neck_roi_names module voxtox.roi_names.prostate_roi_names module voxtox.structures module

W

write() (skrt.dicom_writer.DicomWriter method) (skrt.image.Image method) (skrt.patient.Patient method) (skrt.simulation.SyntheticImage method) (skrt.structures.ROI method) (skrt.structures.StructureSet method) (voxtox.structures.ROI method) (voxtox.structures.StructureSet method) write_affine() (skrt.registration.Matlab method) (skrt.registration.NiftyReg method) write_dicom_dataset() (skrt.simulation.SyntheticImage method)

write_nifti() (in module skrt.image) write_non_image_data() (skrt.patient.Patient method) write_npy() (in module skrt.image) write_parameters() (in module skrt.registration) (skrt.registration.Elastix method) (skrt.registration.Matlab method) (skrt.registration.NiftyReg method) (skrt.registration.RegistrationEngine method) write_steps() (skrt.registration.Registration method) write_translation_to_file() (in module skrt.viewer.viewer) (skrt.better_viewer.BetterViewer method) (skrt.viewer.viewer.QuickViewer method)

Y

year_fraction() (in module skrt.core)

Z

zoom_ax() (skrt.image.Image method)