Index

A

Address (class in wsipipe.utils.geometry) Annotation (class in wsipipe.load.annotations.annotation) annotation_from_tag() (in module wsipipe.load.annotations.asapxml)

AnnotationSet (class in wsipipe.load.annotations.annotation) as_shape() (Size method) as_size() (Shape method) as_values() (Region method)

B

balanced_sample() (in module wsipipe.preprocess.sample.sampler)

C

Camelyon16Loader (class in wsipipe.load.datasets.camelyon16) check_level() (OSSlide method) close() (OSSlide method) (SlideBase method), [1]

col (Address property) combine() (in module wsipipe.preprocess.patching.patchset_utils) convert_region() (OSSlide method) convert_to_pyramids() (in module wsipipe.datasets.stripai)

D

description() (PatchSet method) dimensions (OSSlide property) (SlideBase property)

dimensions() (SlideBase method) draw() (Annotation method)

E

export_patches() (PatchSet method)

F

FillHolesTransform (class in wsipipe.preprocess.tissue_detection.morphology_transforms)

from_sdict() (PatchSetting class method)

G

GaussianBlur (class in wsipipe.preprocess.tissue_detection.filters) get_loader() (in module wsipipe.load.datasets.registry)

get_thumbnail() (SlideBase method), [1] GridPatchFinder (class in wsipipe.preprocess.patching.patch_finder)

H

height (Size property)

I

invert() (in module wsipipe.utils.convert)

L

labels (Camelyon16Loader property) (Loader property) (StripaiLoader property) labels_level (PatchFinder property) labels_level() (GridPatchFinder method) (RandomPatchFinder method) level (PatchSetting attribute) (Region property) load() (PatchSet class method) load_annotations() (Camelyon16Loader method) (Loader method) (StripaiLoader method)

load_annotations_asapxml() (in module wsipipe.load.annotations.asapxml) load_patchsets_from_directory() (in module wsipipe.preprocess.patching.patchset_utils) load_slide() (Camelyon16Loader method) (Loader method) (StripaiLoader method) Loader (class in wsipipe.load.datasets.loader) loader (PatchSetting attribute) location (Region property)

M

make() (Region class method) make_and_save_patchsets_for_dataset() (in module wsipipe.preprocess.patching.patchset_utils) make_patchset_for_slide() (in module wsipipe.preprocess.patching.patchset_utils) make_patchsets_for_dataset() (in module wsipipe.preprocess.patching.patchset_utils) MaxPoolTransform (class in wsipipe.preprocess.tissue_detection.morphology_transforms) MedianBlur (class in wsipipe.preprocess.tissue_detection.filters) module wsipipe.datasets wsipipe.datasets.camelyon16 wsipipe.datasets.dataset_utils wsipipe.datasets.stripai wsipipe.load wsipipe.load.annotations wsipipe.load.annotations.annotation wsipipe.load.annotations.asapxml wsipipe.load.datasets wsipipe.load.datasets.camelyon16 wsipipe.load.datasets.loader wsipipe.load.datasets.registry wsipipe.load.datasets.stripai wsipipe.load.slides wsipipe.load.slides.openslide wsipipe.load.slides.region wsipipe.load.slides.slide wsipipe.preprocess wsipipe.preprocess.patching wsipipe.preprocess.patching.patch_finder wsipipe.preprocess.patching.patchset wsipipe.preprocess.patching.patchset_utils wsipipe.preprocess.sample.sampler wsipipe.preprocess.tissue_detection wsipipe.preprocess.tissue_detection.filters wsipipe.preprocess.tissue_detection.morphology_transforms wsipipe.preprocess.tissue_detection.tissue_detector wsipipe.preprocess.tissue_detection.visualise wsipipe.utils wsipipe.utils.convert wsipipe.utils.filters wsipipe.utils.geometry

MorphologyTransform (class in wsipipe.preprocess.tissue_detection.morphology_transforms)

N

name (Camelyon16Loader property) (Loader property) (StripaiLoader property) np_to_pil() (in module wsipipe.utils.convert)

NullBlur (class in wsipipe.preprocess.tissue_detection.filters) NullTransform (class in wsipipe.preprocess.tissue_detection.morphology_transforms) num_cols (Shape property) num_rows (Shape property)

O

open() (OSSlide method) (SlideBase method), [1]

OSSlide (class in wsipipe.load.slides.openslide)

P

patch_size (PatchSetting attribute) PatchFinder (class in wsipipe.preprocess.patching.patch_finder) PatchSet (class in wsipipe.preprocess.patching.patchset) PatchSetting (class in wsipipe.preprocess.patching.patchset) path (OSSlide property) (SlideBase property)

path() (SlideBase method) pil_to_np() (in module wsipipe.utils.convert) Point (class in wsipipe.utils.geometry) PointF (class in wsipipe.utils.geometry) pool2d() (in module wsipipe.utils.filters) PreFilter (class in wsipipe.preprocess.tissue_detection.filters)

R

RandomPatchFinder (class in wsipipe.preprocess.patching.patch_finder) read_region() (OSSlide method) (SlideBase method), [1] read_regions() (OSSlide method) (SlideBase method), [1]

Region (class in wsipipe.load.slides.region) remove_item_from_dict() (in module wsipipe.utils.convert) render() (AnnotationSet method) row (Address property)

S

sample_dataset() (in module wsipipe.datasets.dataset_utils) save() (PatchSet method) Shape (class in wsipipe.utils.geometry) simple_random() (in module wsipipe.preprocess.sample.sampler) simple_random_replacement() (in module wsipipe.preprocess.sample.sampler) SimpleClosingTransform (class in wsipipe.preprocess.tissue_detection.morphology_transforms) SimpleOpeningTransform (class in wsipipe.preprocess.tissue_detection.morphology_transforms)

Size (class in wsipipe.utils.geometry) size (Region property) SizedClosingTransform (class in wsipipe.preprocess.tissue_detection.morphology_transforms) slide_path (PatchSetting attribute) slide_weighted_random() (in module wsipipe.preprocess.sample.sampler) SlideBase (class in wsipipe.load.slides.slide) StripaiLoader (class in wsipipe.load.datasets.stripai)

T

testing() (in module wsipipe.datasets.camelyon16) TissueDetector (class in wsipipe.preprocess.tissue_detection.tissue_detector) TissueDetectorAll (class in wsipipe.preprocess.tissue_detection.tissue_detector) TissueDetectorGreyScale (class in wsipipe.preprocess.tissue_detection.tissue_detector)

TissueDetectorOTSU (class in wsipipe.preprocess.tissue_detection.tissue_detector) to_frame_with_locations() (in module wsipipe.utils.convert) to_sdict() (PatchSetting method) training() (in module wsipipe.datasets.camelyon16) (in module wsipipe.datasets.stripai)

V

visualise_annotations() (in module wsipipe.load.annotations.annotation)

visualise_patches_on_slide() (in module wsipipe.preprocess.patching.patchset_utils) visualise_tissue_detection_for_slide() (in module wsipipe.preprocess.tissue_detection.visualise)

W

width (Size property) wsipipe.datasets module wsipipe.datasets.camelyon16 module wsipipe.datasets.dataset_utils module wsipipe.datasets.stripai module wsipipe.load module wsipipe.load.annotations module wsipipe.load.annotations.annotation module wsipipe.load.annotations.asapxml module wsipipe.load.datasets module wsipipe.load.datasets.camelyon16 module wsipipe.load.datasets.loader module wsipipe.load.datasets.registry module wsipipe.load.datasets.stripai module wsipipe.load.slides module wsipipe.load.slides.openslide module wsipipe.load.slides.region module

wsipipe.load.slides.slide module wsipipe.preprocess module wsipipe.preprocess.patching module wsipipe.preprocess.patching.patch_finder module wsipipe.preprocess.patching.patchset module wsipipe.preprocess.patching.patchset_utils module wsipipe.preprocess.sample.sampler module wsipipe.preprocess.tissue_detection module wsipipe.preprocess.tissue_detection.filters module wsipipe.preprocess.tissue_detection.morphology_transforms module wsipipe.preprocess.tissue_detection.tissue_detector module wsipipe.preprocess.tissue_detection.visualise module wsipipe.utils module wsipipe.utils.convert module wsipipe.utils.filters module wsipipe.utils.geometry module

X

x (Point property) (PointF property)

Y

y (Point property) (PointF property)