Index

_

__call__() (IndexingStrategy method) (PatchIndexingStrategy method) (SliceIndexingStrategy method) _apply_model() (InferenceFilter method)

_array_to_subject() (InferenceFilter static method) _get_input_array() (InferenceFilter static method) _infer_on_batch() (InferenceFilter method) _prepare_model() (InferenceFilter method)

A

add_data() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method) (Subject method) (TransformInfo method) add_data_by_key() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method) (Subject method) add_filter() (FilterPipeline method) add_image() (Subject method) add_images() (Subject method) add_logger() (FilterPipeline method) add_modalities_to_info() (ModalityConfiguration method) add_modality_entry() (ModalityConfiguration method) add_modality_to_info() (ModalityConfiguration method) add_selector() (SeriesInfoSelectorPipeline method)

add_transform_info() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method) AddImageFilter (class in pyradise.process.modification) AddImageFilterParams (class in pyradise.process.modification) AFFINE (RegistrationType attribute) AIL (SpatialOrientation attribute) AIR (SpatialOrientation attribute) ALI (SpatialOrientation attribute) AlphabeticOrganSortingFilter (class in pyradise.process.postprocess) AlphabeticOrganSortingFilterParams (class in pyradise.process.postprocess) ALS (SpatialOrientation attribute) Annotator (class in pyradise.data.annotator) AnnotatorExtractor (class in pyradise.fileio.extraction) AnnotatorInfoSelector (class in pyradise.fileio.selection) ARI (SpatialOrientation attribute) ARS (SpatialOrientation attribute) ASL (SpatialOrientation attribute) ASR (SpatialOrientation attribute)

B

BSPLINE (RegistrationType attribute)

C

cast() (DoseImage static method) (Image static method) (IntensityImage static method) (SegmentationImage static method) ClipIntensityFilter (class in pyradise.process.intensity) ClipIntensityFilterParams (class in pyradise.process.intensity) convert() (Converter method) (DicomImageSeriesConverter method) (DicomRTSSSeriesConverter method) (RTSSToSegmentConverter method) (SegmentToRTSSConverter2D method) (SegmentToRTSSConverter3D method) (SubjectToRTSSConverter method)

Converter (class in pyradise.fileio.dicom_conversion) copy_info() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method) Crawler (class in pyradise.fileio.crawling)

D

DatasetDicomCrawler (class in pyradise.fileio.crawling) DatasetFileCrawler (class in pyradise.fileio.crawling) default_intensity_file_name_fn() (in module pyradise.fileio.writing) default_segmentation_file_name_fn() (in module pyradise.fileio.writing) DicomImageSeriesConverter (class in pyradise.fileio.dicom_conversion) DicomRTSSSeriesConverter (class in pyradise.fileio.dicom_conversion) DicomSeriesDoseInfo (class in pyradise.fileio.series_info)

DicomSeriesImageInfo (class in pyradise.fileio.series_info) DicomSeriesInfo (class in pyradise.fileio.series_info) DicomSeriesRegistrationInfo (class in pyradise.fileio.series_info) DicomSeriesRTSSInfo (class in pyradise.fileio.series_info) DicomSeriesSubjectWriter (class in pyradise.fileio.writing) direction (ImageProperties property) DirectorySubjectWriter (class in pyradise.fileio.writing) DoseImage (class in pyradise.data.image)

E

execute() (AddImageFilter method) (AlphabeticOrganSortingFilter method) (AnnotatorInfoSelector method) (ClipIntensityFilter method) (Crawler method) (DatasetDicomCrawler method) (DatasetFileCrawler method) (Filter method) (FilterPipeline method) (GaussianFilter method) (InferenceFilter method) (IntensityFilter method) (IntensityLoopFilter method) (InterSubjectRegistrationFilter method) (IntraInterSubjectRegistrationFilter method) (IntraSubjectRegistrationFilter method) (LaplacianFilter method) (LoopEntryFilter method) (MedianFilter method) (MergeSegmentationFilter method) (ModalityInfoSelector method) (NoRegistrationInfoSelector method) (NoRTSSInfoSelector method) (OrganInfoSelector method) (OrientationFilter method) (PlaybackTransformTapeFilter method) (RemoveImageByAnnotatorFilter method) (RemoveImageByModalityFilter method) (RemoveImageByOrganFilter method) (ResampleFilter method) (RescaleIntensityFilter method) (SeriesInfoSelector method) (SeriesInfoSelectorPipeline method) (SingleConnectedComponentFilter method) (SubjectDicomCrawler method) (SubjectFileCrawler method) (ZeroOneNormFilter method) (ZScoreNormFilter method)

execute_inverse() (AddImageFilter method) (AlphabeticOrganSortingFilter method) (ClipIntensityFilter method) (Filter method) (GaussianFilter method) (InferenceFilter method) (IntensityFilter method) (IntensityLoopFilter method) (InterSubjectRegistrationFilter method) (IntraInterSubjectRegistrationFilter method) (IntraSubjectRegistrationFilter method) (LaplacianFilter method) (LoopEntryFilter method) (MedianFilter method) (MergeSegmentationFilter method) (OrientationFilter method) (PlaybackTransformTapeFilter method) (RemoveImageByAnnotatorFilter method) (RemoveImageByModalityFilter method) (RemoveImageByOrganFilter method) (ResampleFilter method) (RescaleIntensityFilter method) (SingleConnectedComponentFilter method) (ZeroOneNormFilter method) (ZScoreNormFilter method) execute_iteratively() (FilterPipeline method) ExplicitLoader (class in pyradise.fileio.loading) extract() (AnnotatorExtractor method) (Extractor method) (ModalityExtractor method) (OrganExtractor method) (SimpleAnnotatorExtractor method) (SimpleModalityExtractor method) (SimpleOrganExtractor method) extract_from_dicom() (ModalityExtractor method) (SimpleModalityExtractor method) extract_from_path() (ModalityExtractor method) (SimpleModalityExtractor method) Extractor (class in pyradise.fileio.extraction)

F

FileSeriesInfo (class in pyradise.fileio.series_info) Filter (class in pyradise.process.base) FilterParams (class in pyradise.process.base)

FilterPipeline (class in pyradise.process.base) from_dicom_series_info() (ModalityConfiguration class method) from_file() (ModalityConfiguration class method)

G

GaussianFilter (class in pyradise.process.intensity) GaussianFilterParams (class in pyradise.process.intensity) get_abbreviation() (Annotator method) get_annotator() (DicomSeriesRTSSInfo method) (SegmentationFileSeriesInfo method) (SegmentationImage method) get_annotators() (Subject method) get_data() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method) (Subject method) (TransformInfo method) get_data_by_key() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method) (Subject method) get_default() (Annotator class method) (Modality class method) get_dimensions() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method) get_direction() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method) get_entry() (ImageProperties method) get_filter() (TransformInfo method) get_general_params() (RTSSConverter2DConfiguration method) (RTSSConverter3DConfiguration method) get_image_by_modality() (Subject method) get_image_by_organ() (Subject method) get_image_by_organ_and_annotator() (Subject method) get_image_data() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method) get_image_data_as_np() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method) get_image_infos() (DicomSeriesRegistrationInfo method) get_image_itk_type() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method) get_image_params() (RTSSConverter2DConfiguration method) (RTSSConverter3DConfiguration method) get_image_properties() (TransformInfo method) get_images() (Subject method) get_images_by_annotator() (Subject method) get_images_by_type() (Subject method) get_modalities() (Subject method) get_modality() (DicomSeriesDoseInfo method) (DicomSeriesImageInfo method) (DoseImage method) (IntensityFileSeriesInfo method) (IntensityImage method)

get_name() (Annotator method) (Modality method) (Organ method) (Subject method) get_organ() (SegmentationFileSeriesInfo method) (SegmentationImage method) get_organ_annotator_combination() (SegmentationImage method) get_organs() (Subject method) get_orientation() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method) get_origin() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method) get_params() (TransformInfo method) get_path() (DicomSeriesDoseInfo method) (DicomSeriesImageInfo method) (DicomSeriesInfo method) (DicomSeriesRegistrationInfo method) (DicomSeriesRTSSInfo method) (FileSeriesInfo method) (IntensityFileSeriesInfo method) (SegmentationFileSeriesInfo method) (SeriesInfo method) get_patient_id() (DicomSeriesDoseInfo method) (DicomSeriesImageInfo method) (DicomSeriesInfo method) (DicomSeriesRegistrationInfo method) (DicomSeriesRTSSInfo method) (FileSeriesInfo method) (IntensityFileSeriesInfo method) (SegmentationFileSeriesInfo method) (SeriesInfo method) get_patient_name() (DicomSeriesDoseInfo method) (DicomSeriesImageInfo method) (DicomSeriesInfo method) (DicomSeriesRegistrationInfo method) (DicomSeriesRTSSInfo method) (FileSeriesInfo method) (IntensityFileSeriesInfo method) (SegmentationFileSeriesInfo method) (SeriesInfo method) get_recorded_elements() (Tape method) (TransformTape method) get_referenced_series_info() (DicomSeriesRegistrationInfo static method) get_registration_infos() (DicomSeriesRegistrationInfo static method) get_size() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method) get_spacing() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method) get_transform() (TransformInfo method) get_transform_tape() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method)

H

has_default_modalities() (ModalityConfiguration method)

has_duplicate_modalities() (ModalityConfiguration method) has_equal_origin_direction() (ImageProperties method)

I

IAL (SpatialOrientation attribute) IAR (SpatialOrientation attribute) ILA (SpatialOrientation attribute) ILP (SpatialOrientation attribute) Image (class in pyradise.data.image) ImageFileFormat (class in pyradise.fileio.writing) ImageProperties (class in pyradise.data.image) IndexingStrategy (class in pyradise.process.inference) InferenceFilter (class in pyradise.process.inference) InferenceFilterParams (class in pyradise.process.inference) IntensityFileSeriesInfo (class in pyradise.fileio.series_info) IntensityFilter (class in pyradise.process.intensity) IntensityFilterParams (class in pyradise.process.intensity) IntensityImage (class in pyradise.data.image) IntensityLoopFilter (class in pyradise.process.intensity) IntensityLoopFilterParams (class in pyradise.process.intensity) InterSubjectRegistrationFilter (class in pyradise.process.registration) InterSubjectRegistrationFilterParams (class in pyradise.process.registration) IntraInterSubjectRegistrationFilter (class in pyradise.process.registration) IntraInterSubjectRegistrationFilterParams (class in pyradise.process.registration) IntraSubjectRegistrationFilter (class in pyradise.process.registration) IntraSubjectRegistrationFilterParams (class in pyradise.process.registration) INVALID (SpatialOrientation attribute) IPL (SpatialOrientation attribute) IPR (SpatialOrientation attribute) IRA (SpatialOrientation attribute) IRP (SpatialOrientation attribute) is_binary() (SegmentationImage method) is_default() (Annotator method) (Modality method) is_enumerated_default_modality() (ModalityExtractor method) (SimpleModalityExtractor method) is_intensity_image() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method)

is_invertible() (AddImageFilter static method) (AlphabeticOrganSortingFilter static method) (ClipIntensityFilter static method) (Filter static method) (GaussianFilter method) (InferenceFilter static method) (InterSubjectRegistrationFilter static method) (IntraInterSubjectRegistrationFilter static method) (IntraSubjectRegistrationFilter static method) (LaplacianFilter static method) (LoopEntryFilter static method) (MedianFilter static method) (MergeSegmentationFilter static method) (OrientationFilter static method) (PlaybackTransformTapeFilter static method) (RemoveImageByAnnotatorFilter static method) (RemoveImageByModalityFilter static method) (RemoveImageByOrganFilter static method) (ResampleFilter static method) (RescaleIntensityFilter static method) (SingleConnectedComponentFilter static method) (ZeroOneNormFilter static method) (ZScoreNormFilter static method) is_updated() (DicomSeriesDoseInfo method) (DicomSeriesImageInfo method) (DicomSeriesInfo method) (DicomSeriesRegistrationInfo method) (DicomSeriesRTSSInfo method) (FileSeriesInfo method) (IntensityFileSeriesInfo method) (SegmentationFileSeriesInfo method) (SeriesInfo method) IterableSubjectLoader (class in pyradise.fileio.loading)

L

LAI (SpatialOrientation attribute) LaplacianFilter (class in pyradise.process.intensity) LaplacianFilterParams (class in pyradise.process.intensity) LAS (SpatialOrientation attribute) LIA (SpatialOrientation attribute) LIP (SpatialOrientation attribute) load() (ExplicitLoader method) (SubjectLoader method)

Loader (class in pyradise.fileio.loading) loop_entries() (LoopEntryFilter static method) LoopEntryFilter (class in pyradise.process.base) LoopEntryFilterParams (class in pyradise.process.base) LPI (SpatialOrientation attribute) LPS (SpatialOrientation attribute) LSA (SpatialOrientation attribute) LSP (SpatialOrientation attribute)

M

MedianFilter (class in pyradise.process.intensity) MedianFilterParams (class in pyradise.process.intensity) MergeSegmentationFilter (class in pyradise.process.modification) MergeSegmentationFilterParams (class in pyradise.process.modification) MHA (ImageFileFormat attribute) Modality (class in pyradise.data.modality) ModalityConfiguration (class in pyradise.fileio.modality_config) ModalityExtractor (class in pyradise.fileio.extraction) ModalityInfoSelector (class in pyradise.fileio.selection) module pyradise.data pyradise.data.annotator pyradise.data.image pyradise.data.modality pyradise.data.organ pyradise.data.subject pyradise.data.taping pyradise.fileio pyradise.fileio.crawling pyradise.fileio.dicom_conversion pyradise.fileio.extraction pyradise.fileio.loading pyradise.fileio.modality_config pyradise.fileio.selection pyradise.fileio.series_info pyradise.fileio.writing pyradise.process pyradise.process.base pyradise.process.inference pyradise.process.intensity pyradise.process.invertibility pyradise.process.modification pyradise.process.orientation pyradise.process.postprocess pyradise.process.registration pyradise.process.resampling

N

name (OrganAnnotatorCombination property) NIFTI (ImageFileFormat attribute) NIFTI_GZ (ImageFileFormat attribute)

NoRegistrationInfoSelector (class in pyradise.fileio.selection) NoRTSSInfoSelector (class in pyradise.fileio.selection) NRRD (ImageFileFormat attribute)

O

Organ (class in pyradise.data.organ) OrganAnnotatorCombination (class in pyradise.data.organ) OrganExtractor (class in pyradise.fileio.extraction)

OrganInfoSelector (class in pyradise.fileio.selection) OrientationFilter (class in pyradise.process.orientation) OrientationFilterParams (class in pyradise.process.orientation) origin (ImageProperties property)

P

PatchIndexingStrategy (class in pyradise.process.inference) PIL (SpatialOrientation attribute) PIR (SpatialOrientation attribute) playback() (Tape static method) (TransformTape static method) playback_transform_tapes() (Subject method) PlaybackTransformTapeFilter (class in pyradise.process.invertibility) PlaybackTransformTapeFilterParams (class in pyradise.process.invertibility) PLI (SpatialOrientation attribute) PLS (SpatialOrientation attribute) preprocess_image() (SegmentToRTSSConverter3D method) PRI (SpatialOrientation attribute) PRS (SpatialOrientation attribute) PSL (SpatialOrientation attribute) PSR (SpatialOrientation attribute) pyradise.data module pyradise.data.annotator module pyradise.data.image module pyradise.data.modality module pyradise.data.organ module pyradise.data.subject module pyradise.data.taping module pyradise.fileio module pyradise.fileio.crawling module

pyradise.fileio.dicom_conversion module pyradise.fileio.extraction module pyradise.fileio.loading module pyradise.fileio.modality_config module pyradise.fileio.selection module pyradise.fileio.series_info module pyradise.fileio.writing module pyradise.process module pyradise.process.base module pyradise.process.inference module pyradise.process.intensity module pyradise.process.invertibility module pyradise.process.modification module pyradise.process.orientation module pyradise.process.postprocess module pyradise.process.registration module pyradise.process.resampling module

R

RAI (SpatialOrientation attribute) RAS (SpatialOrientation attribute) record() (Tape method) (TransformTape method) ReferenceInfo (class in pyradise.fileio.series_info) RegistrationInfo (class in pyradise.fileio.series_info) RegistrationSequenceInfo (class in pyradise.fileio.series_info) RegistrationType (class in pyradise.process.registration) remove_additional_data() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method) (Subject method) remove_additional_data_by_key() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method) (Subject method) remove_image() (Subject method) remove_image_by_annotator() (Subject method) remove_image_by_modality() (Subject method) remove_image_by_organ() (Subject method) remove_image_by_organ_and_annotator() (Subject method) RemoveImageByAnnotatorFilter (class in pyradise.process.modification) RemoveImageByAnnotatorFilterParams (class in pyradise.process.modification) RemoveImageByModalityFilter (class in pyradise.process.modification)

RemoveImageByModalityFilterParams (class in pyradise.process.modification) RemoveImageByOrganFilter (class in pyradise.process.modification) RemoveImageByOrganFilterParams (class in pyradise.process.modification) replace_data() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method) (Subject method) replace_image() (Subject method) ResampleFilter (class in pyradise.process.resampling) ResampleFilterParams (class in pyradise.process.resampling) RescaleIntensityFilter (class in pyradise.process.intensity) RescaleIntensityFilterParams (class in pyradise.process.intensity) reset() (Tape method) (TransformTape method) RIA (SpatialOrientation attribute) RIGID (RegistrationType attribute) RIP (SpatialOrientation attribute) RPI (SpatialOrientation attribute) RPS (SpatialOrientation attribute) RSA (SpatialOrientation attribute) RSP (SpatialOrientation attribute) RTSSConverter2DConfiguration (class in pyradise.fileio.dicom_conversion) RTSSConverter3DConfiguration (class in pyradise.fileio.dicom_conversion) RTSSMetaData (class in pyradise.fileio.dicom_conversion) RTSSToSegmentConverter (class in pyradise.fileio.dicom_conversion)

S

SAL (SpatialOrientation attribute) SAR (SpatialOrientation attribute) SegmentationFileSeriesInfo (class in pyradise.fileio.series_info) SegmentationImage (class in pyradise.data.image) SegmentToRTSSConverter2D (class in pyradise.fileio.dicom_conversion) SegmentToRTSSConverter3D (class in pyradise.fileio.dicom_conversion) SeriesInfo (class in pyradise.fileio.series_info) SeriesInfoSelector (class in pyradise.fileio.selection) SeriesInfoSelectorPipeline (class in pyradise.fileio.selection) set_annotator() (SegmentationFileSeriesInfo method) (SegmentationImage method) set_entry() (ImageProperties method) set_general_params() (RTSSConverter2DConfiguration method) (RTSSConverter3DConfiguration method) set_image_data() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method) set_image_infos() (DicomSeriesRegistrationInfo method) set_image_params() (RTSSConverter2DConfiguration method) (RTSSConverter3DConfiguration method) set_modality() (DicomSeriesDoseInfo method) (DicomSeriesImageInfo method) (DoseImage method) (IntensityFileSeriesInfo method) (IntensityImage method) set_name() (Organ method) set_organ() (SegmentationFileSeriesInfo method) (SegmentationImage method) set_organ_annotator_combination() (SegmentationImage method) set_param() (FilterPipeline method)

set_transform_tape() (DoseImage method) (Image method) (IntensityImage method) (SegmentationImage method) set_verbose() (Filter method) (LoopEntryFilter method) set_verbose_all() (FilterPipeline method) set_warning_on_non_invertible() (Filter method) (LoopEntryFilter method) SIMILARITY (RegistrationType attribute) SimpleAnnotatorExtractor (class in pyradise.fileio.extraction) SimpleModalityExtractor (class in pyradise.fileio.extraction) SimpleOrganExtractor (class in pyradise.fileio.extraction) SingleConnectedComponentFilter (class in pyradise.process.postprocess) SingleConnectedComponentFilterParams (class in pyradise.process.postprocess) size (ImageProperties property) SLA (SpatialOrientation attribute) SliceIndexingStrategy (class in pyradise.process.inference) SLP (SpatialOrientation attribute) spacing (ImageProperties property) SpatialOrientation (class in pyradise.process.orientation) SPL (SpatialOrientation attribute) SPR (SpatialOrientation attribute) SRA (SpatialOrientation attribute) SRP (SpatialOrientation attribute) Subject (class in pyradise.data.subject) SubjectDicomCrawler (class in pyradise.fileio.crawling) SubjectFileCrawler (class in pyradise.fileio.crawling) SubjectLoader (class in pyradise.fileio.loading) SubjectToRTSSConverter (class in pyradise.fileio.dicom_conversion) SubjectWriter (class in pyradise.fileio.writing)

T

Tape (class in pyradise.data.taping) to_file() (ModalityConfiguration method)

TransformInfo (class in pyradise.data.taping) TransformTape (class in pyradise.data.taping)

U

update() (DicomSeriesDoseInfo method) (DicomSeriesImageInfo method) (DicomSeriesInfo method) (DicomSeriesRegistrationInfo method) (DicomSeriesRTSSInfo method) (FileSeriesInfo method) (IntensityFileSeriesInfo method) (SegmentationFileSeriesInfo method) (SeriesInfo method)

W

write() (DicomSeriesSubjectWriter method) (DirectorySubjectWriter method) (SubjectWriter method)

write_to_subject_folder() (SubjectWriter method)

Z

ZeroOneNormFilter (class in pyradise.process.intensity) ZeroOneNormFilterParams (class in pyradise.process.intensity)

ZScoreNormFilter (class in pyradise.process.intensity) ZScoreNormFilterParams (class in pyradise.process.intensity)