Index

Symbols

--config segmentation command line option --dcm nifti_to_series command line option --dcm_file nifti_to_rtstruct command line option --dcm_img rtstruct_to_nifti command line option --dcm_rt_file rtstruct_to_nifti command line option --default segmentation command line option --dose_format dicom_crawler command line option --file_suffix dicom_crawler command line option --image nifti_to_series command line option --image_format dicom_crawler command line option --input_dir dicom_crawler command line option --mask nifti_to_rtstruct command line option --out_rt_filename nifti_to_rtstruct command line option --output segmentation command line option --output_dir dicom_crawler command line option rtstruct_to_nifti command line option --output_directory nifti_to_series command line option --output_img rtstruct_to_nifti command line option --overwrite dicom_crawler command line option --prefix rtstruct_to_nifti command line option --short_description dicom_crawler command line option --sort_by dicom_crawler command line option

--spacing rtstruct_to_nifti command line option --structure_format dicom_crawler command line option --tag nifti_to_series command line option --verbose dicom_crawler command line option -b dicom_crawler command line option -c segmentation command line option -d nifti_to_rtstruct command line option nifti_to_series command line option segmentation command line option -i dicom_crawler command line option nifti_to_series command line option rtstruct_to_nifti command line option -m nifti_to_rtstruct command line option -o dicom_crawler command line option nifti_to_rtstruct command line option nifti_to_series command line option segmentation command line option -od rtstruct_to_nifti command line option -oi rtstruct_to_nifti command line option -p rtstruct_to_nifti command line option -r rtstruct_to_nifti command line option -s dicom_crawler command line option -t nifti_to_series command line option -v dicom_crawler command line option

A

add_bounding_box() (platipy.imaging.visualisation.visualiser.ImageVisualiser method), [1] add_comparison_overlay() (platipy.imaging.visualisation.visualiser.ImageVisualiser method), [1] add_contour() (platipy.imaging.visualisation.visualiser.ImageVisualiser method), [1] add_scalar_overlay() (platipy.imaging.visualisation.visualiser.ImageVisualiser method), [1] add_vector_overlay() (platipy.imaging.visualisation.visualiser.ImageVisualiser method), [1] ALGORITHM segmentation command line option Algorithm (class in platipy.backend.application) algorithms (platipy.backend.application.FlaskApp attribute) alignment_registration() (in module platipy.imaging.registration.linear), [1]

api (platipy.backend.application.FlaskApp attribute) apply_augmentation() (in module platipy.imaging.generation.augment) apply_deformable_transform() (in module platipy.imaging.registration.utils), [1] apply_linear_transform() (in module platipy.imaging.registration.utils), [1] apply_transform() (in module platipy.imaging.registration.utils), [1] assert_bronchus_mask() (in module platipy.imaging.tests.test_bronchus) assert_lung_mask() (in module platipy.imaging.tests.test_bronchus) augment() (platipy.imaging.generation.augment.ContractAugment method) (platipy.imaging.generation.augment.DeformableAugment method) (platipy.imaging.generation.augment.ExpandAugment method) (platipy.imaging.generation.augment.ShiftAugment method)

B

beat_started (platipy.backend.application.FlaskApp attribute) binary_decode_image() (in module platipy.imaging.label.utils), [1]

binary_encode_structure_list() (in module platipy.imaging.label.utils), [1] bronchus_data() (in module platipy.imaging.tests.test_bronchus) bspline_registration() (in module platipy.imaging.registration.deformable), [1]

C

calculate_d_cc_x() (in module platipy.imaging.dose.dvh) calculate_d_x() (in module platipy.imaging.dose.dvh) calculate_dvh() (in module platipy.imaging.dose.dvh) calculate_dvh_for_labels() (in module platipy.imaging.dose.dvh) calculate_v_x() (in module platipy.imaging.dose.dvh) cardiac_data() (in module platipy.imaging.tests.test_cardiac) celery_started (platipy.backend.application.FlaskApp attribute) clear() (platipy.imaging.visualisation.visualiser.ImageVisualiser method), [1] com_from_image_list() (in module platipy.imaging.utils.vessel) combine_labels() (in module platipy.imaging.label.fusion) combine_labels_staple() (in module platipy.imaging.label.fusion) compute_apl() (in module platipy.imaging.label.comparison), [1] compute_metric_dsc() (in module platipy.imaging.label.comparison), [1] compute_metric_hd() (in module platipy.imaging.label.comparison), [1] compute_metric_masd() (in module platipy.imaging.label.comparison), [1] compute_metric_mean_apl() (in module platipy.imaging.label.comparison), [1] compute_metric_sensitivity() (in module platipy.imaging.label.comparison), [1] compute_metric_specificity() (in module platipy.imaging.label.comparison), [1]

compute_metric_total_apl() (in module platipy.imaging.label.comparison), [1] compute_surface_dsc() (in module platipy.imaging.label.comparison), [1] compute_surface_metrics() (in module platipy.imaging.label.comparison), [1] compute_volume() (in module platipy.imaging.label.comparison), [1] compute_volume_metrics() (in module platipy.imaging.label.comparison), [1] compute_weight_map() (in module platipy.imaging.label.fusion) ContractAugment (class in platipy.imaging.generation.augment) control_point_spacing_distance_to_number() (in module platipy.imaging.registration.utils), [1] convert_mask_to_distance_map() (in module platipy.imaging.registration.utils), [1] convert_mask_to_reg_structure() (in module platipy.imaging.registration.utils), [1] convert_nifti() (in module platipy.dicom.io.nifti_to_rtstruct), [1] convert_nifti_to_dicom_series() (in module platipy.dicom.io.nifti_to_series) convert_rtdose() (in module platipy.dicom.io.rtdose_to_nifti) convert_rtstruct() (in module platipy.dicom.io.rtstruct_to_nifti), [1] convert_simpleitk_to_vtk() (in module platipy.imaging.utils.vessel) correct_volume_overlap() (in module platipy.imaging.label.utils), [1] crop_to_label_extent() (in module platipy.imaging.utils.crop), [1] crop_to_roi() (in module platipy.imaging.utils.crop), [1]

D

deformable_registration_command_iteration() (in module platipy.imaging.registration.utils), [1] DeformableAugment (class in platipy.imaging.generation.augment) detect_holes() (in module platipy.imaging.utils.lung) dicom_crawler command line option --dose_format --file_suffix --image_format --input_dir --output_dir --overwrite --short_description --sort_by --structure_format --verbose -b -i -o -s -v

dicom_data() (in module platipy.dicom.tests.test_convert) dicom_listener_aetitle (platipy.backend.application.FlaskApp attribute) dicom_listener_port (platipy.backend.application.FlaskApp attribute) DicomConnector (class in platipy.dicom.communication.connector) display_open_cardiac_zip_url_locations() (in module platipy.imaging.projects.cardiac.run) do_find() (platipy.dicom.communication.connector.DicomConnector method) download_series() (platipy.dicom.communication.connector.DicomConnector method) draw_bounding_box_on_axes() (platipy.imaging.visualisation.visualiser.ImageVisualiser method)

E

environment variable FLASK_DEBUG evaluate_distance_on_surface() (in module platipy.imaging.label.projection)

evaluate_distance_to_reference() (in module platipy.imaging.label.projection) ExpandAugment (class in platipy.imaging.generation.augment) extend_mask() (in module platipy.imaging.generation.mask) extract() (in module platipy.imaging.utils.ventricle)

F

fast_mask() (in module platipy.imaging.projects.bronchus.bronchus) fast_symmetric_forces_demons_registration() (in module platipy.imaging.registration.deformable), [1] fetch_data() (in module platipy.dicom.download.tcia) fill_holes() (in module platipy.imaging.utils.lung)

fix_missing_data() (in module platipy.dicom.io.crawl) (in module platipy.dicom.io.rtstruct_to_nifti), [1] FLASK_DEBUG FlaskApp (class in platipy.backend.application) flatten() (in module platipy.dicom.io.crawl)

G

gaussian_curve() (in module platipy.imaging.label.iar) generate_airway_mask() (in module platipy.imaging.projects.bronchus.bronchus) generate_comparison_colormix() (in module platipy.imaging.visualisation.utils) generate_field_asymmetric_contract() (in module platipy.imaging.generation.dvf) generate_field_asymmetric_extend() (in module platipy.imaging.generation.dvf) generate_field_expand() (in module platipy.imaging.generation.dvf) generate_field_radial_bend() (in module platipy.imaging.generation.dvf) generate_field_shift() (in module platipy.imaging.generation.dvf) generate_left_ventricle_segments() (in module platipy.imaging.utils.ventricle) generate_lung_mask() (in module platipy.imaging.projects.bronchus.bronchus) generate_primes() (in module platipy.imaging.label.utils), [1] generate_random_augmentation() (in module platipy.imaging.generation.augment) generate_valve_from_great_vessel() (in module platipy.imaging.utils.valve) generate_valve_using_cylinder() (in module platipy.imaging.utils.valve) get_bone_mask() (in module platipy.imaging.generation.mask) get_collections() (in module platipy.dicom.download.tcia)

get_com() (in module platipy.imaging.label.utils), [1] get_dicom_info_from_description() (in module platipy.dicom.io.crawl) get_distance() (in module platipy.imaging.projects.bronchus.bronchus) get_external_mask() (in module platipy.imaging.generation.mask) (in module platipy.imaging.utils.lung) get_hn_data() (in module platipy.dicom.download.tcia) get_hn_nifti() (in module platipy.imaging.tests.data) get_lung_data() (in module platipy.dicom.download.tcia) get_lung_dicom() (in module platipy.imaging.tests.data) get_lung_mask() (in module platipy.imaging.utils.lung) get_lung_nifti() (in module platipy.imaging.tests.data) get_modalities_in_collection() (in module platipy.dicom.download.tcia) get_patients_in_collection() (in module platipy.dicom.download.tcia) get_series_for_study() (platipy.dicom.communication.connector.DicomConnector method) get_studies_for_patient() (platipy.dicom.communication.connector.DicomConnector method) get_suv_bw_scale_factor() (in module platipy.dicom.io.crawl)

I

image (platipy.imaging.visualisation.visualiser.ImageVisualiser property) ImageVisualiser (class in platipy.imaging.visualisation.visualiser), [1] INPUT_PATH segmentation command line option insert_cylinder() (in module platipy.imaging.generation.image)

insert_cylinder_image() (in module platipy.imaging.generation.image) insert_sphere() (in module platipy.imaging.generation.image) insert_sphere_image() (in module platipy.imaging.generation.image) install_atlas_from_zipfile() (in module platipy.imaging.projects.cardiac.run) install_hybrid_cardiac_from_zip() (in module platipy.imaging.projects.cardiac.run) install_open_atlas() (in module platipy.imaging.projects.cardiac.run)

L

label_to_roi() (in module platipy.imaging.utils.crop), [1] labelmap (platipy.imaging.visualisation.visualiser.ImageVisualiser property)

linear_registration() (in module platipy.imaging.registration.linear), [1] listen() (platipy.dicom.communication.connector.DicomConnector method) logger (in module platipy.imaging.visualisation.visualiser)

M

median_absolute_deviation() (in module platipy.imaging.label.iar) module platipy platipy.backend.application platipy.cli platipy.cli.dicom_crawler platipy.cli.nifti_to_rtstruct platipy.cli.nifti_to_series platipy.cli.rtstruct_to_nifti platipy.cli.segmentation platipy.cli.tcia_download platipy.dicom platipy.dicom.communication platipy.dicom.communication.connector platipy.dicom.download platipy.dicom.download.tcia platipy.dicom.io platipy.dicom.io.crawl platipy.dicom.io.nifti_to_rtstruct, [1] platipy.dicom.io.nifti_to_series platipy.dicom.io.rtdose_to_nifti platipy.dicom.io.rtstruct_to_nifti, [1] platipy.dicom.tests platipy.dicom.tests.test_convert platipy.imaging platipy.imaging.dose.dvh platipy.imaging.generation platipy.imaging.generation.augment platipy.imaging.generation.dvf platipy.imaging.generation.image platipy.imaging.generation.mask platipy.imaging.label platipy.imaging.label.comparison, [1] platipy.imaging.label.fusion platipy.imaging.label.iar platipy.imaging.label.projection platipy.imaging.label.utils, [1] platipy.imaging.projects platipy.imaging.projects.bronchus platipy.imaging.projects.bronchus.bronchus platipy.imaging.projects.bronchus.run platipy.imaging.projects.cardiac platipy.imaging.projects.cardiac.run platipy.imaging.registration platipy.imaging.registration.deformable, [1] platipy.imaging.registration.linear, [1] platipy.imaging.registration.utils, [1] platipy.imaging.tests platipy.imaging.tests.data platipy.imaging.tests.test_bronchus platipy.imaging.tests.test_cardiac platipy.imaging.tests.test_visualiser platipy.imaging.utils platipy.imaging.utils.crop, [1] platipy.imaging.utils.geometry platipy.imaging.utils.io platipy.imaging.utils.lung platipy.imaging.utils.valve platipy.imaging.utils.ventricle platipy.imaging.utils.vessel platipy.imaging.visualisation platipy.imaging.visualisation.utils platipy.imaging.visualisation.visualiser

move_series() (platipy.dicom.communication.connector.DicomConnector method) multiscale_demons() (in module platipy.imaging.registration.deformable), [1] mutual_information() (in module platipy.imaging.label.fusion)

N

nifti_data() (in module platipy.dicom.tests.test_convert) (in module platipy.imaging.tests.test_visualiser) nifti_to_rtstruct command line option --dcm_file --mask --out_rt_filename -d -m -o

nifti_to_series command line option --dcm --image --output_directory --tag -d -i -o -t

O

on_association_accepted() (platipy.dicom.communication.connector.DicomConnector method) on_association_released() (platipy.dicom.communication.connector.DicomConnector method)

on_c_echo() (platipy.dicom.communication.connector.DicomConnector method) on_c_store() (platipy.dicom.communication.connector.DicomConnector method)

P

platipy module platipy.backend.application module platipy.cli module platipy.cli.dicom_crawler module platipy.cli.nifti_to_rtstruct module platipy.cli.nifti_to_series module platipy.cli.rtstruct_to_nifti module platipy.cli.segmentation module platipy.cli.tcia_download module platipy.dicom module platipy.dicom.communication module platipy.dicom.communication.connector module platipy.dicom.download module platipy.dicom.download.tcia module platipy.dicom.io module platipy.dicom.io.crawl module platipy.dicom.io.nifti_to_rtstruct module, [1] platipy.dicom.io.nifti_to_series module platipy.dicom.io.rtdose_to_nifti module platipy.dicom.io.rtstruct_to_nifti module, [1] platipy.dicom.tests module platipy.dicom.tests.test_convert module platipy.imaging module platipy.imaging.dose.dvh module platipy.imaging.generation module platipy.imaging.generation.augment module platipy.imaging.generation.dvf module platipy.imaging.generation.image module platipy.imaging.generation.mask module platipy.imaging.label module platipy.imaging.label.comparison module, [1] platipy.imaging.label.fusion module

platipy.imaging.label.iar module platipy.imaging.label.projection module platipy.imaging.label.utils module, [1] platipy.imaging.projects module platipy.imaging.projects.bronchus module platipy.imaging.projects.bronchus.bronchus module platipy.imaging.projects.bronchus.run module platipy.imaging.projects.cardiac module platipy.imaging.projects.cardiac.run module platipy.imaging.registration module platipy.imaging.registration.deformable module, [1] platipy.imaging.registration.linear module, [1] platipy.imaging.registration.utils module, [1] platipy.imaging.tests module platipy.imaging.tests.data module platipy.imaging.tests.test_bronchus module platipy.imaging.tests.test_cardiac module platipy.imaging.tests.test_visualiser module platipy.imaging.utils module platipy.imaging.utils.crop module, [1] platipy.imaging.utils.geometry module platipy.imaging.utils.io module platipy.imaging.utils.lung module platipy.imaging.utils.valve module platipy.imaging.utils.ventricle module platipy.imaging.utils.vessel module platipy.imaging.visualisation module platipy.imaging.visualisation.utils module platipy.imaging.visualisation.visualiser module prime_decode_image() (in module platipy.imaging.label.utils), [1] prime_encode_structure_list() (in module platipy.imaging.label.utils), [1] process_dicom_directory() (in module platipy.dicom.io.crawl) process_dicom_file_list() (in module platipy.dicom.io.crawl) process_dicom_series() (in module platipy.dicom.io.crawl) process_probability_image() (in module platipy.imaging.label.fusion) project_onto_arbitrary_plane() (in module platipy.imaging.visualisation.utils)

R

read_dicom_image() (in module platipy.dicom.io.rtstruct_to_nifti), [1] read_dicom_struct_file() (in module platipy.dicom.io.rtstruct_to_nifti), [1] register() (platipy.backend.application.FlaskApp method) registration_command_iteration() (in module platipy.imaging.registration.utils), [1] regrid_spherical_data() (in module platipy.imaging.label.projection) reorientate_vector_field() (in module platipy.imaging.visualisation.utils) return_slice() (in module platipy.imaging.visualisation.utils) rotate_image() (in module platipy.imaging.utils.geometry) rtstruct_to_nifti command line option --dcm_img --dcm_rt_file --output_dir --output_img --prefix --spacing -i -od -oi -p -r

run() (platipy.backend.application.FlaskApp method) run_bronchus_segmentation() (in module platipy.imaging.projects.bronchus.run) run_cardiac_segmentation() (in module platipy.imaging.projects.cardiac.run) run_dicom_listener() (platipy.backend.application.FlaskApp method) run_hybrid_segmentation() (in module platipy.imaging.projects.cardiac.run) run_iar() (in module platipy.imaging.label.iar)

S

safe_sort_dicom_image_list() (in module platipy.dicom.io.crawl) segmentation command line option --config --default --output -c -d -o ALGORITHM INPUT_PATH

send_dcm() (platipy.dicom.communication.connector.DicomConnector method) set_limits_from_label() (platipy.imaging.visualisation.visualiser.ImageVisualiser method), [1] settings_to_json() (platipy.backend.application.Algorithm method) ShiftAugment (class in platipy.imaging.generation.augment) show() (platipy.imaging.visualisation.visualiser.ImageVisualiser method), [1] simpleitk_image_from_vtk_tube() (in module platipy.imaging.utils.vessel) smooth_and_resample() (in module platipy.imaging.registration.utils), [1] stage_iteration() (in module platipy.imaging.registration.utils), [1] subsample_vector_field() (in module platipy.imaging.visualisation.utils)

T

test_bronchus_segmentation() (in module platipy.imaging.tests.test_bronchus) test_cardiac_service() (in module platipy.imaging.tests.test_cardiac) test_cardiac_structure_guided_service() (in module platipy.imaging.tests.test_cardiac) test_comparison_overlay_visualisation() (in module platipy.imaging.tests.test_visualiser) test_contour_visualisation() (in module platipy.imaging.tests.test_visualiser) test_convert_dicom_to_nifti() (in module platipy.dicom.tests.test_convert)

test_convert_nifti_to_dicom() (in module platipy.dicom.tests.test_convert) test_lung_segmentation() (in module platipy.imaging.tests.test_bronchus) test_scalar_overlay_visualisation() (in module platipy.imaging.tests.test_visualiser) transform_point_set_from_dicom_struct() (in module platipy.dicom.io.crawl) (in module platipy.dicom.io.rtstruct_to_nifti), [1] tube_from_com_list() (in module platipy.imaging.utils.vessel)

V

vector_angle() (in module platipy.imaging.utils.geometry) vector_image_grid() (in module platipy.imaging.visualisation.utils) vectorised_transform_index_to_physical_point() (in module platipy.imaging.label.utils), [1] vectorised_transform_physical_point_to_index() (in module platipy.imaging.label.utils), [1] verify() (platipy.dicom.communication.connector.DicomConnector method) vessel_spline_generation() (in module platipy.imaging.utils.vessel)

VisualiseBoundingBox (class in platipy.imaging.visualisation.utils) VisualiseComparisonOverlay (class in platipy.imaging.visualisation.utils) VisualiseContour (class in platipy.imaging.visualisation.utils) VisualiseImage (class in platipy.imaging.visualisation.utils) VisualiseScalarOverlay (class in platipy.imaging.visualisation.utils) VisualiseVectorOverlay (class in platipy.imaging.visualisation.utils)

W

write_nrrd_structure_set() (in module platipy.imaging.utils.io)

write_output_data_to_disk() (in module platipy.dicom.io.crawl) write_vtk_tube_to_file() (in module platipy.imaging.utils.vessel)