Index

A

add_annotation() (wsiprocess.converters.wsiprocess_to_coco.ToCOCOConverter method) add_annotation_args() (wsiprocess.cli.Args method) add_base_text() (wsiprocess.converters.wsiprocess_to_voc.VOCTree method) add_binarization_method() (wsiprocess.cli.Args method) add_categories() (wsiprocess.converters.wsiprocess_to_coco.ToCOCOConverter method) add_category() (wsiprocess.converters.wsiprocess_to_coco.ToCOCOConverter method) add_class() (wsiprocess.annotation.Annotation method) add_image() (wsiprocess.converters.wsiprocess_to_coco.ToCOCOConverter method) add_images_and_annotations() (wsiprocess.converters.wsiprocess_to_coco.ToCOCOConverter method) add_info() (wsiprocess.converters.wsiprocess_to_coco.ToCOCOConverter method) add_main_branches() (wsiprocess.converters.wsiprocess_to_voc.VOCTree method) add_objects() (wsiprocess.converters.wsiprocess_to_voc.VOCTree method) add_on_annotation() (wsiprocess.cli.Args method) add_on_foreground() (wsiprocess.cli.Args method) add_sub_branches() (wsiprocess.converters.wsiprocess_to_voc.VOCTree method) add_text() (wsiprocess.converters.wsiprocess_to_voc.VOCTree method)

all_as_int() (wsiprocess.annotationparser.QuPath_parser.QuPathAnnotation method) Annotation (class in wsiprocess.annotation) (class in wsiprocess.annotationparser.NDPView_parser) annotation (wsiprocess.annotationparser.WSIDissector_parser.WSIDissectorAnnotation attribute) (wsiprocess.patcher.Patcher attribute) annotation() (in module wsiprocess.converters.wsiprocess_to_coco) annotation_cover_patch() (wsiprocess.patcher.Patcher method) annotation_groups (wsiprocess.annotationparser.ASAP_parser.ASAPAnnotation attribute) (wsiprocess.annotationparser.NDPView_parser.NDPViewAnnotation attribute) AnnotationLabelError annotations (wsiprocess.annotationparser.ASAP_parser.ASAPAnnotation attribute) (wsiprocess.annotationparser.NDPView_parser.NDPViewAnnotation attribute) (wsiprocess.annotationparser.QuPath_parser.QuPathAnnotation attribute) Args (class in wsiprocess.cli) ASAPAnnotation (class in wsiprocess.annotationparser.ASAP_parser) assert_annotation() (wsiprocess.converters.wsiprocess_to_coco.ToCOCOConverter method) assert_incl_excl() (wsiprocess.rule.Rule method)

B

base() (in module wsiprocess.converters.wsiprocess_to_coco) base_mask() (wsiprocess.annotation.Annotation method) base_masks() (wsiprocess.annotation.Annotation method)

BaseConverter (class in wsiprocess.converters.base_converter) BaseParser (class in wsiprocess.annotationparser.parser_utils) bbox_to_circle() (wsiprocess.annotationparser.SlideRunner_parser.SlideRunnerAnnotation method) build_args() (wsiprocess.cli.Args method)

C

category() (in module wsiprocess.converters.wsiprocess_to_coco) check_classes() (wsiprocess.annotation.Annotation method) check_memory_consumption() (wsiprocess.annotation.Annotation method) classes (wsiprocess.annotationparser.ASAP_parser.ASAPAnnotation attribute) (wsiprocess.annotationparser.NDPView_parser.NDPViewAnnotation attribute) (wsiprocess.annotationparser.QuPath_parser.QuPathAnnotation attribute) (wsiprocess.annotationparser.SlideRunner_parser.SlideRunnerAnnotation attribute) (wsiprocess.annotationparser.WSIDissector_parser.WSIDissectorAnnotation attribute) (wsiprocess.patcher.Patcher attribute) (wsiprocess.rule.Rule attribute)

ClassificationDataset (class in wsiprocess.pytorch.utils) convert() (wsiprocess.converters.wsiprocess_to_coco.ToCOCOConverter method) (wsiprocess.converters.wsiprocess_to_voc.ToVOCConverter method) (wsiprocess.converters.wsiprocess_to_yolo.ToYOLOConverter method) Converter (class in wsiprocess.converter) Coord (class in wsiprocess.annotationparser.NDPView_parser) coordformat (wsiprocess.annotationparser.NDPView_parser.Annotation attribute) coords (wsiprocess.annotationparser.NDPView_parser.Annotation property) corner_on_patch() (wsiprocess.patcher.Patcher method) crop() (wsiprocess.slide.Slide method) crop_patch() (wsiprocess.patcher.Patcher method)

D

detect_type() (in module wsiprocess.annotationparser.parser_utils)

dot_to_bbox() (wsiprocess.annotation.Annotation method) dryrun (wsiprocess.patcher.Patcher attribute)

E

element (wsiprocess.annotationparser.NDPView_parser.Annotation attribute) exclude_coords() (wsiprocess.annotation.Annotation method) exclude_masks() (wsiprocess.annotation.Annotation method) export_mask() (wsiprocess.annotation.Annotation method) export_masks() (wsiprocess.annotation.Annotation method)

export_thumb_mask() (wsiprocess.annotation.Annotation method) export_thumb_masks() (wsiprocess.annotation.Annotation method) export_thumbnail() (wsiprocess.slide.Slide method) ext (wsiprocess.patcher.Patcher attribute) extract_patches (wsiprocess.patcher.Patcher attribute) (wsiprocess.verify.Verify attribute)

F

filename (wsiprocess.annotationparser.WSIDissector_parser.WSIDissectorAnnotation attribute) filepath (wsiprocess.patcher.Patcher attribute) filestem (wsiprocess.patcher.Patcher attribute) (wsiprocess.verify.Verify attribute) fillattr() (wsiprocess.cli.Args method) fillattrs() (wsiprocess.cli.Args method)

find_bbs() (wsiprocess.patcher.Patcher method) find_masks() (wsiprocess.patcher.Patcher method) finished_sample (wsiprocess.patcher.Patcher attribute) (wsiprocess.verify.Verify attribute) fix_mask_size() (wsiprocess.annotation.Annotation method) foreground_mask() (wsiprocess.annotation.Annotation method) from_image() (wsiprocess.annotation.Annotation method)

G

GeoJsonAnnotation (class in wsiprocess.annotationparser.GeoJson_parser) get_base() (wsiprocess.converters.wsiprocess_to_coco.ToCOCOConverter method) get_circle_coords() (wsiprocess.annotationparser.NDPView_parser.Annotation method) get_coords() (wsiprocess.annotationparser.NDPView_parser.Annotation method) get_image_paths() (wsiprocess.converters.wsiprocess_to_yolo.ToYOLOConverter method) get_iterator() (wsiprocess.patcher.Patcher method) get_mini_patch_parallel() (wsiprocess.patcher.Patcher method) get_mpp() (in module wsiprocess.annotationparser.NDPView_parser) get_origin() (in module wsiprocess.annotationparser.NDPView_parser) get_patch() (wsiprocess.patcher.Patcher method)

get_patch_mask() (wsiprocess.annotation.Annotation method) get_patch_parallel() (wsiprocess.patcher.Patcher method) get_pin_coords() (wsiprocess.annotationparser.NDPView_parser.Annotation method) get_polygon_coords() (wsiprocess.annotationparser.NDPView_parser.Annotation method) get_random_sample() (wsiprocess.patcher.Patcher method) get_ratio() (wsiprocess.converters.wsiprocess_to_coco.ToCOCOConverter method) get_scale() (wsiprocess.annotation.Annotation method) get_thumbnail() (wsiprocess.slide.Slide method) getargs() (wsiprocess.converters.wsiprocess_to_coco.ToCOCOConverter method) (wsiprocess.converters.wsiprocess_to_voc.ToVOCConverter method) (wsiprocess.converters.wsiprocess_to_yolo.ToYOLOConverter method)

I

image() (in module wsiprocess.converters.wsiprocess_to_coco) include_masks() (wsiprocess.annotation.Annotation method)

info() (in module wsiprocess.converters.wsiprocess_to_coco) iterator (wsiprocess.patcher.Patcher attribute)

L

last_x (wsiprocess.patcher.Patcher attribute) last_y (wsiprocess.patcher.Patcher attribute)

load_rule() (wsiprocess.rule.Rule method) load_slide() (wsiprocess.slide.Slide method)

M

magnification (wsiprocess.patcher.Patcher attribute) (wsiprocess.slide.Slide attribute) magnification() (wsiprocess.verify.Verify method) main() (in module wsiprocess.cli) (in module wsiprocess.pytorch.utils) main_mask() (wsiprocess.annotation.Annotation method) main_masks() (wsiprocess.annotation.Annotation method) make_dir() (wsiprocess.verify.Verify static method) make_dirs() (wsiprocess.verify.Verify method) make_images() (wsiprocess.converters.wsiprocess_to_yolo.ToYOLOConverter method) make_labels() (wsiprocess.converters.wsiprocess_to_yolo.ToYOLOConverter method) make_link_to_images() (wsiprocess.converters.wsiprocess_to_coco.ToCOCOConverter method) make_masks() (wsiprocess.annotation.Annotation method) make_paths() (wsiprocess.converters.wsiprocess_to_yolo.ToYOLOConverter method) make_template() (wsiprocess.converters.wsiprocess_to_voc.VOCTree method) make_tree() (wsiprocess.converters.wsiprocess_to_voc.ToVOCConverter method) makedirs() (wsiprocess.converters.wsiprocess_to_voc.ToVOCConverter method) (wsiprocess.converters.wsiprocess_to_yolo.ToYOLOConverter method) mask_coords (wsiprocess.annotationparser.ASAP_parser.ASAPAnnotation attribute) (wsiprocess.annotationparser.NDPView_parser.NDPViewAnnotation attribute) (wsiprocess.annotationparser.QuPath_parser.QuPathAnnotation attribute) (wsiprocess.annotationparser.SlideRunner_parser.SlideRunnerAnnotation attribute) (wsiprocess.annotationparser.WSIDissector_parser.WSIDissectorAnnotation attribute) masks (wsiprocess.patcher.Patcher attribute) merge_include_coords() (wsiprocess.annotation.Annotation method) meter2px() (wsiprocess.annotationparser.NDPView_parser.MPP method) method (wsiprocess.patcher.Patcher attribute) (wsiprocess.verify.Verify attribute) MissCombinationError mkdirs() (wsiprocess.converters.wsiprocess_to_voc.ToVOCConverter method)

module wsiprocess wsiprocess.annotation wsiprocess.annotationparser wsiprocess.annotationparser.ASAP_parser wsiprocess.annotationparser.GeoJson_parser wsiprocess.annotationparser.NDPView_parser wsiprocess.annotationparser.parser_utils wsiprocess.annotationparser.QuPath_parser wsiprocess.annotationparser.SlideRunner_parser wsiprocess.annotationparser.WSIDissector_parser wsiprocess.cli wsiprocess.converter wsiprocess.converters wsiprocess.converters.base_converter wsiprocess.converters.wsiprocess_to_coco wsiprocess.converters.wsiprocess_to_voc wsiprocess.converters.wsiprocess_to_yolo wsiprocess.error wsiprocess.patcher wsiprocess.pytorch wsiprocess.pytorch.utils wsiprocess.pytorch.wsidataloader wsiprocess.pytorch.wsidataset wsiprocess.rule wsiprocess.slide wsiprocess.utils wsiprocess.verify move_to_test() (wsiprocess.converters.wsiprocess_to_voc.ToVOCConverter method) MPP (class in wsiprocess.annotationparser.NDPView_parser)

N

NDPViewAnnotation (class in wsiprocess.annotationparser.NDPView_parser)

no_patches (wsiprocess.patcher.Patcher attribute) (wsiprocess.verify.Verify attribute)

O

o_height (wsiprocess.patcher.Patcher attribute) o_width (wsiprocess.patcher.Patcher attribute) offset_x (wsiprocess.patcher.Patcher attribute) offset_y (wsiprocess.patcher.Patcher attribute)

on_annotation (wsiprocess.patcher.Patcher attribute) on_foreground (wsiprocess.patcher.Patcher attribute) on_params() (wsiprocess.verify.Verify method) OnParamError

P

p_area (wsiprocess.patcher.Patcher attribute) p_height (wsiprocess.patcher.Patcher attribute) p_scale (wsiprocess.patcher.Patcher attribute) p_width (wsiprocess.patcher.Patcher attribute) parse_mask_coords() (wsiprocess.annotationparser.SlideRunner_parser.SlideRunnerAnnotation method) parse_ratio() (wsiprocess.converters.wsiprocess_to_yolo.ToYOLOConverter method) patch_on_annotation() (wsiprocess.patcher.Patcher method) patch_on_foreground() (wsiprocess.patcher.Patcher method)

Patcher (class in wsiprocess.patcher) PatchSizeTooSmallError path (wsiprocess.annotationparser.ASAP_parser.ASAPAnnotation attribute) (wsiprocess.annotationparser.NDPView_parser.NDPViewAnnotation attribute) (wsiprocess.annotationparser.QuPath_parser.QuPathAnnotation attribute) (wsiprocess.annotationparser.SlideRunner_parser.SlideRunnerAnnotation attribute) (wsiprocess.annotationparser.WSIDissector_parser.WSIDissectorAnnotation attribute) (wsiprocess.slide.Slide attribute) process_annotation() (in module wsiprocess.cli)

Q

QuPathAnnotation (class in wsiprocess.annotationparser.QuPath_parser)

R

r (wsiprocess.annotationparser.NDPView_parser.MPP attribute) read_annotation() (wsiprocess.annotation.Annotation method) (wsiprocess.annotationparser.GeoJson_parser.GeoJsonAnnotation method) (wsiprocess.annotationparser.NDPView_parser.NDPViewAnnotation method) (wsiprocess.converters.wsiprocess_to_coco.ToCOCOConverter method) read_annotations() (wsiprocess.annotationparser.SlideRunner_parser.SlideRunnerAnnotation method) read_classes() (wsiprocess.annotationparser.QuPath_parser.QuPathAnnotation method) (wsiprocess.annotationparser.SlideRunner_parser.SlideRunnerAnnotation method) read_coordinates() (wsiprocess.annotationparser.QuPath_parser.QuPathAnnotation method) (wsiprocess.annotationparser.SlideRunner_parser.SlideRunnerAnnotation method) read_coords() (wsiprocess.pytorch.wsidataset.WSIDataset method) read_labels() (wsiprocess.annotationparser.SlideRunner_parser.SlideRunnerAnnotation method) (wsiprocess.pytorch.utils.ClassificationDataset method) read_mask_coord() (wsiprocess.annotationparser.ASAP_parser.ASAPAnnotation method)

read_mask_coords() (wsiprocess.annotationparser.ASAP_parser.ASAPAnnotation method) (wsiprocess.annotationparser.WSIDissector_parser.WSIDissectorAnnotation method) read_masks() (wsiprocess.pytorch.utils.SegmentationDataset method) read_patch() (wsiprocess.pytorch.wsidataset.WSIDataset method) read_patch_from_disk() (wsiprocess.pytorch.wsidataset.WSIDataset method) read_patch_from_wsi() (wsiprocess.pytorch.wsidataset.WSIDataset method) read_result_file() (wsiprocess.converters.wsiprocess_to_voc.ToVOCConverter method) (wsiprocess.converters.wsiprocess_to_yolo.ToYOLOConverter method) read_slides() (wsiprocess.annotationparser.SlideRunner_parser.SlideRunnerAnnotation method) remove_dup_in_results() (wsiprocess.patcher.Patcher method) rename_path() (wsiprocess.converters.wsiprocess_to_yolo.ToYOLOConverter method) resize_mask() (wsiprocess.annotation.Annotation method) resize_masks() (wsiprocess.annotation.Annotation method) result (wsiprocess.patcher.Patcher attribute) Rule (class in wsiprocess.rule)

S

save_data() (wsiprocess.converters.wsiprocess_to_coco.ToCOCOConverter method) save_patch() (wsiprocess.patcher.Patcher method) save_patch_result() (wsiprocess.patcher.Patcher method) save_results() (wsiprocess.patcher.Patcher method) save_to (wsiprocess.patcher.Patcher attribute) (wsiprocess.verify.Verify attribute) SaveTo (class in wsiprocess.converters.wsiprocess_to_coco) SegmentationDataset (class in wsiprocess.pytorch.utils) set_base_parser() (wsiprocess.cli.Args method) set_classification_args() (wsiprocess.cli.Args method) set_common_args() (wsiprocess.cli.Args method) set_detection_args() (wsiprocess.cli.Args method) set_evaluation_args() (wsiprocess.cli.Args method) set_id() (wsiprocess.converters.wsiprocess_to_coco.ToCOCOConverter method) set_magnification() (wsiprocess.patcher.Patcher method) set_method_args() (wsiprocess.cli.Args method)

set_properties() (wsiprocess.slide.Slide method) set_scale() (wsiprocess.annotation.Annotation method) set_segmentation_args() (wsiprocess.cli.Args method) set_size() (wsiprocess.converters.wsiprocess_to_voc.VOCTree method) set_wsi_arg() (wsiprocess.cli.Args method) show_bounding_box() (in module wsiprocess.utils) show_mask_on_patch() (in module wsiprocess.utils) side_on_patch() (wsiprocess.patcher.Patcher method) SizeError sizes() (wsiprocess.verify.Verify method) Slide (class in wsiprocess.slide) slide (wsiprocess.patcher.Patcher attribute) (wsiprocess.slide.Slide attribute) SlideLoadError SlideRunnerAnnotation (class in wsiprocess.annotationparser.SlideRunner_parser) start_sample (wsiprocess.patcher.Patcher attribute) (wsiprocess.verify.Verify attribute)

T

title (wsiprocess.annotationparser.NDPView_parser.Annotation attribute) (wsiprocess.annotationparser.NDPView_parser.Annotation property) to_bb() (wsiprocess.patcher.Patcher method) to_coco() (wsiprocess.converter.Converter method) to_jpg() (wsiprocess.converters.wsiprocess_to_voc.ToVOCConverter method) to_voc() (wsiprocess.converter.Converter method)

to_xml() (wsiprocess.converters.wsiprocess_to_voc.VOCTree method) to_yolo() (wsiprocess.converter.Converter method) ToCOCOConverter (class in wsiprocess.converters.wsiprocess_to_coco) ToVOCConverter (class in wsiprocess.converters.wsiprocess_to_voc) ToYOLOConverter (class in wsiprocess.converters.wsiprocess_to_yolo) type (wsiprocess.annotationparser.NDPView_parser.Annotation attribute)

V

verbose (wsiprocess.patcher.Patcher attribute) Verify (class in wsiprocess.verify)

verify_annotations() (wsiprocess.annotationparser.SlideRunner_parser.SlideRunnerAnnotation method) VOCTree (class in wsiprocess.converters.wsiprocess_to_voc)

W

wsi_height (wsiprocess.patcher.Patcher attribute) (wsiprocess.slide.Slide attribute) wsi_width (wsiprocess.patcher.Patcher attribute) (wsiprocess.slide.Slide attribute) WSIDataset (class in wsiprocess.pytorch.wsidataset) WSIDissectorAnnotation (class in wsiprocess.annotationparser.WSIDissector_parser) wsiprocess module wsiprocess.annotation module wsiprocess.annotationparser module wsiprocess.annotationparser.ASAP_parser module wsiprocess.annotationparser.GeoJson_parser module wsiprocess.annotationparser.NDPView_parser module wsiprocess.annotationparser.parser_utils module wsiprocess.annotationparser.QuPath_parser module wsiprocess.annotationparser.SlideRunner_parser module wsiprocess.annotationparser.WSIDissector_parser module wsiprocess.cli module wsiprocess.converter module wsiprocess.converters module

wsiprocess.converters.base_converter module wsiprocess.converters.wsiprocess_to_coco module wsiprocess.converters.wsiprocess_to_voc module wsiprocess.converters.wsiprocess_to_yolo module wsiprocess.error module wsiprocess.patcher module wsiprocess.pytorch module wsiprocess.pytorch.utils module wsiprocess.pytorch.wsidataloader module wsiprocess.pytorch.wsidataset module wsiprocess.rule module wsiprocess.slide module wsiprocess.utils module wsiprocess.verify module WsiProcessError WSIsDataset (class in wsiprocess.pytorch.wsidataset)

X

x (wsiprocess.annotationparser.NDPView_parser.Coord attribute) (wsiprocess.annotationparser.NDPView_parser.MPP attribute)

x_lefttop (wsiprocess.patcher.Patcher attribute)

Y

y (wsiprocess.annotationparser.NDPView_parser.Coord attribute) (wsiprocess.annotationparser.NDPView_parser.MPP attribute)

y_lefttop (wsiprocess.patcher.Patcher attribute)