Index A | C | D | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W A adapt_dataset_from_bytes() (in module pydicer.input.orthanc) add_dose_object() (in module pydicer.generate.object) (pydicer.tool.PyDicer method) add_entry() (pydicer.convert.data.ConvertData method) add_image_object() (in module pydicer.generate.object) (pydicer.tool.PyDicer method) add_input() (pydicer.tool.PyDicer method) add_object() (in module pydicer.generate.object) (pydicer.tool.PyDicer method) add_object_to_dataset() (pydicer.dataset.preparation.PrepareDataset method) add_structure_name_mapping() (in module pydicer.utils) (pydicer.tool.PyDicer method) add_structure_object() (in module pydicer.generate.object) (pydicer.tool.PyDicer method) add_testing_cases() (pydicer.dataset.nnunet.NNUNetDataset method) AnalyseData (class in pydicer.analyse.data) C check_dataset() (pydicer.dataset.nnunet.NNUNetDataset method) check_duplicates_train_test() (pydicer.dataset.nnunet.NNUNetDataset method) check_overlapping_structures() (pydicer.dataset.nnunet.NNUNetDataset method) check_structure_names() (pydicer.dataset.nnunet.NNUNetDataset method) compute_contour_similarity_metrics() (in module pydicer.analyse.compare) compute_dose_metrics() (pydicer.analyse.data.AnalyseData method) compute_dvh() (pydicer.analyse.data.AnalyseData method) compute_radiomics() (pydicer.analyse.data.AnalyseData method) convert() (pydicer.convert.data.ConvertData method) convert_dicom_headers() (in module pydicer.convert.headers) convert_dicom_to_nifti_pt() (in module pydicer.convert.pt) convert_rtstruct() (in module pydicer.convert.rtstruct) ConvertData (class in pydicer.convert.data) copy_doc() (in module pydicer.utils) D determine_dcm_datetime() (in module pydicer.utils) DICOMPACSInput (class in pydicer.input.pacs) download_and_extract_zip_file() (in module pydicer.utils) F fetch_converted_test_data() (in module pydicer.utils) fetch_data() (pydicer.input.orthanc.OrthancInput method) (pydicer.input.pacs.DICOMPACSInput method) (pydicer.input.tcia.TCIAInput method) (pydicer.input.web.WebInput method) FileSystemInput (class in pydicer.input.filesystem) G generate_training_scripts() (pydicer.dataset.nnunet.NNUNetDataset method) get_all_computed_radiomics_for_dataset() (pydicer.analyse.data.AnalyseData method) get_all_dvhs_for_dataset() (pydicer.analyse.data.AnalyseData method) get_all_similarity_metrics_for_dataset() (in module pydicer.analyse.compare) get_available_mhub_models() (in module pydicer.generate.models) get_config() (pydicer.config.PyDicerConfig method) get_iterator() (in module pydicer.utils) get_linked_for_and_ref_uid() (in module pydicer.generate.object) get_mapped_structure_name() (pydicer.dataset.structureset.StructureSet method) get_mapping_for_structure_set() (in module pydicer.dataset.structureset) get_object_type() (in module pydicer.convert.data) get_physical_values_pt() (in module pydicer.convert.pt) get_segmentation_log_path() (in module pydicer.generate.segmentation) get_sitk_volume_from_np() (in module pydicer.convert.pt) get_standardised_structure_name() (pydicer.dataset.structureset.StructureSet method) get_structures_linked_to_dose() (in module pydicer.utils) (pydicer.tool.PyDicer method) get_suv_from_bqml() (in module pydicer.convert.pt) get_suv_philips() (in module pydicer.convert.pt) get_unmapped_structures() (pydicer.dataset.structureset.StructureSet method) get_working_dir() (pydicer.config.PyDicerConfig method) H handle_missing_slice() (in module pydicer.convert.data) hash_uid() (in module pydicer.utils) I is_approx_equal() (in module pydicer.convert.pt) items() (pydicer.dataset.structureset.StructureSet method) K keys() (pydicer.dataset.structureset.StructureSet method) L link_via_frame_of_reference() (in module pydicer.convert.data) load_dvh() (in module pydicer.utils) load_object_metadata() (in module pydicer.utils) load_output_nifti() (in module pydicer.generate.models) M map_structure_name() (in module pydicer.utils) module pydicer.analyse.compare pydicer.analyse.data pydicer.convert.data pydicer.convert.headers pydicer.convert.pt pydicer.convert.rtstruct pydicer.dataset.functions pydicer.dataset.preparation pydicer.dataset.structureset pydicer.generate.models pydicer.generate.object pydicer.generate.segmentation pydicer.input.filesystem pydicer.input.orthanc pydicer.input.pacs pydicer.input.tcia pydicer.input.test pydicer.input.web pydicer.preprocess.data pydicer.utils pydicer.visualise.data N NNUNetDataset (class in pydicer.dataset.nnunet) O OrthancInput (class in pydicer.input.orthanc) P parse_patient_kwarg() (in module pydicer.utils) prep_label_map_from_one_hot() (pydicer.dataset.nnunet.NNUNetDataset method) prepare() (pydicer.dataset.preparation.PrepareDataset method) prepare_dataset() (pydicer.dataset.nnunet.NNUNetDataset method) prepare_from_dataframe() (pydicer.dataset.preparation.PrepareDataset method) prepare_similarity_metric_analysis() (in module pydicer.analyse.compare) PrepareDataset (class in pydicer.dataset.preparation) preprocess() (pydicer.preprocess.data.PreprocessData method) (pydicer.tool.PyDicer method) PreprocessData (class in pydicer.preprocess.data) PyDicer (class in pydicer.tool) pydicer.analyse.compare module pydicer.analyse.data module pydicer.convert.data module pydicer.convert.headers module pydicer.convert.pt module pydicer.convert.rtstruct module pydicer.dataset.functions module pydicer.dataset.preparation module pydicer.dataset.structureset module pydicer.generate.models module pydicer.generate.object module pydicer.generate.segmentation module pydicer.input.filesystem module pydicer.input.orthanc module pydicer.input.pacs module pydicer.input.tcia module pydicer.input.test module pydicer.input.web module pydicer.preprocess.data module pydicer.utils module pydicer.visualise.data module PyDicerConfig (class in pydicer.config) R read_all_segmentation_logs() (in module pydicer.generate.segmentation) (pydicer.tool.PyDicer method) read_converted_data() (in module pydicer.utils) (pydicer.tool.PyDicer method) read_preprocessed_data() (in module pydicer.utils) (pydicer.tool.PyDicer method) read_quarantined_data() (pydicer.tool.PyDicer method) read_segmentation_log() (in module pydicer.generate.segmentation) read_simple_itk_image() (in module pydicer.utils) rt_latest_dose() (in module pydicer.dataset.functions) rt_latest_struct() (in module pydicer.dataset.functions) run_mhub_model() (in module pydicer.generate.models) run_pipeline() (pydicer.tool.PyDicer method) run_total_segmentator() (in module pydicer.generate.models) S save_config() (pydicer.config.PyDicerConfig method) scan_file() (pydicer.preprocess.data.PreprocessData method) segment_dataset() (in module pydicer.generate.segmentation) (pydicer.tool.PyDicer method) segment_image() (in module pydicer.generate.segmentation) (pydicer.tool.PyDicer method) set_config() (pydicer.config.PyDicerConfig method) set_verbosity() (pydicer.tool.PyDicer method) split_dataset() (pydicer.dataset.nnunet.NNUNetDataset method) StructureSet (class in pydicer.dataset.structureset) T TCIAInput (class in pydicer.input.tcia) TestInput (class in pydicer.input.test) train() (pydicer.dataset.nnunet.NNUNetDataset method) U update_logging() (pydicer.tool.PyDicer method) V values() (pydicer.dataset.structureset.StructureSet method) visualise() (pydicer.visualise.data.VisualiseData method) VisualiseData (class in pydicer.visualise.data) W WebInput (class in pydicer.input.web) write_autoseg_log() (in module pydicer.generate.segmentation) write_nrrd_from_mask_directory() (in module pydicer.convert.rtstruct)