Index

_

__call__() (zarrdataset._augs.ToDtype method) (zarrdataset._maskfuncs.MaskGenerator method) (zarrdataset.MaskGenerator method) (zarrdataset.ToDtype method) __del__() (zarrdataset._imageloaders.ImageLoader method) (zarrdataset.ImageLoader method) __getitem__() (zarrdataset._imageloaders.ImageBase method) (zarrdataset._imageloaders.ImageCollection method) (zarrdataset._zarrdataset.ZarrDataset method) (zarrdataset.ImageBase method) (zarrdataset.ImageCollection method) (zarrdataset.ZarrDataset method) __iter__() (zarrdataset._zarrdataset.ZarrDataset method) (zarrdataset.ZarrDataset method) __repr__() (zarrdataset._augs.ToDtype method) (zarrdataset._samplers.PatchSampler method) (zarrdataset._zarrdataset.ZarrDataset method) (zarrdataset.PatchSampler method) (zarrdataset.ToDtype method) (zarrdataset.ZarrDataset method) _allow_incomplete_patches (zarrdataset._samplers.PatchSampler attribute) (zarrdataset.PatchSampler attribute) _allow_overlap (zarrdataset._samplers.BlueNoisePatchSampler attribute) (zarrdataset.BlueNoisePatchSampler attribute) _area_threshold_2 (zarrdataset._maskfuncs.WSITissueMaskGenerator attribute) (zarrdataset.WSITissueMaskGenerator attribute) _arr_lists (zarrdataset._zarrdataset.ZarrDataset attribute) (zarrdataset.ZarrDataset attribute) _base_chunk_tls (zarrdataset._samplers.BlueNoisePatchSampler attribute) (zarrdataset.BlueNoisePatchSampler attribute) _cache_chunk() (zarrdataset._imageloaders.ImageBase method) (zarrdataset.ImageBase method) _cached_coords (zarrdataset._imageloaders.ImageBase attribute) (zarrdataset.ImageBase attribute) _chunk_size (zarrdataset._imageloaders.ImageBase attribute) (zarrdataset.ImageBase attribute) _collections (zarrdataset._zarrdataset.ZarrDataset attribute) (zarrdataset.ZarrDataset attribute) _compute_corners() (zarrdataset._samplers.PatchSampler method) (zarrdataset.PatchSampler method) _compute_grid() (zarrdataset._samplers.PatchSampler method) (zarrdataset.PatchSampler method) _compute_overlap() (zarrdataset._samplers.PatchSampler method) (zarrdataset.PatchSampler method) _compute_reference_indices() (zarrdataset._samplers.PatchSampler method) (zarrdataset.PatchSampler method) _compute_shapes() (zarrdataset._imageloaders.ImageBase method) (zarrdataset.ImageBase method) _compute_toplefts_slices() (zarrdataset._samplers.PatchSampler method) (zarrdataset.PatchSampler method) _compute_transform() (zarrdataset._maskfuncs.MaskGenerator method) (zarrdataset._maskfuncs.WSITissueMaskGenerator method) (zarrdataset.MaskGenerator method) (zarrdataset.WSITissueMaskGenerator method) _compute_valid_toplefts() (zarrdataset._samplers.BlueNoisePatchSampler method) (zarrdataset._samplers.PatchSampler method) (zarrdataset.BlueNoisePatchSampler method) (zarrdataset.PatchSampler method) _current_patch_idx (zarrdataset._zarrdataset.ImageSample attribute) _draw_same_chunk (zarrdataset._zarrdataset.ZarrDataset attribute) (zarrdataset.ZarrDataset attribute) _drop_axes (zarrdataset._imageloaders.ImageBase attribute) (zarrdataset.ImageBase attribute) _dtype (zarrdataset._augs.ToDtype attribute) (zarrdataset.ToDtype attribute) _generate_mask() (zarrdataset._imageloaders.ImageCollection method) (zarrdataset.ImageCollection method) _image_func (zarrdataset._imageloaders.ImageBase attribute) (zarrdataset._imageloaders.ImageLoader attribute) (zarrdataset.ImageBase attribute) (zarrdataset.ImageLoader attribute)

_image_loader_func (zarrdataset._zarrdataset.ZarrDataset attribute) (zarrdataset.ZarrDataset attribute) _initialize() (zarrdataset._zarrdataset.ZarrDataset method) (zarrdataset.ZarrDataset method) _initialized (zarrdataset._zarrdataset.ZarrDataset attribute) (zarrdataset.ZarrDataset attribute) _iscached() (zarrdataset._imageloaders.ImageBase method) (zarrdataset.ImageBase method) _mask_scale (zarrdataset._maskfuncs.WSITissueMaskGenerator attribute) (zarrdataset.WSITissueMaskGenerator attribute) _max_chunk_size (zarrdataset._samplers.PatchSampler attribute) (zarrdataset.PatchSampler attribute) _min_area (zarrdataset._samplers.PatchSampler attribute) (zarrdataset.PatchSampler attribute) _min_size (zarrdataset._maskfuncs.WSITissueMaskGenerator attribute) (zarrdataset.WSITissueMaskGenerator attribute) _new_axes (zarrdataset._imageloaders.ImageBase attribute) (zarrdataset.ImageBase attribute) _num_workers (zarrdataset._zarrdataset.ZarrDataset attribute) (zarrdataset.ZarrDataset attribute) _ordering (zarrdataset._zarrdataset.ImageSample attribute) _output_order (zarrdataset._zarrdataset.ZarrDataset attribute) (zarrdataset.ZarrDataset attribute) _pad (zarrdataset._samplers.PatchSampler attribute) (zarrdataset.PatchSampler attribute) _patch_sampler (zarrdataset._zarrdataset.ZarrDataset attribute) (zarrdataset.ZarrDataset attribute) _patch_size (zarrdataset._samplers.PatchSampler attribute) (zarrdataset.PatchSampler attribute) _progress_bar (zarrdataset._zarrdataset.ZarrDataset attribute) (zarrdataset.ZarrDataset attribute) _ref_mod (zarrdataset._zarrdataset.ZarrDataset attribute) (zarrdataset.ZarrDataset attribute) _resample_positions (zarrdataset._samplers.BlueNoisePatchSampler attribute) (zarrdataset.BlueNoisePatchSampler attribute) _return_positions (zarrdataset._zarrdataset.ZarrDataset attribute) (zarrdataset.ZarrDataset attribute) _return_worker_id (zarrdataset._zarrdataset.ZarrDataset attribute) (zarrdataset.ZarrDataset attribute) _rng_seed (zarrdataset._zarrdataset.ImageSample attribute) _scale (zarrdataset._imageloaders.ImageBase attribute) (zarrdataset.ImageBase attribute) _shape (zarrdataset._imageloaders.ImageBase attribute) (zarrdataset.ImageBase attribute) _shuffle (zarrdataset._zarrdataset.ImageSample attribute) (zarrdataset._zarrdataset.ZarrDataset attribute) (zarrdataset.ZarrDataset attribute) _spatial_reference_axes (zarrdataset._imageloaders.ImageBase attribute) (zarrdataset.ImageBase attribute) _spatial_reference_shape (zarrdataset._imageloaders.ImageBase attribute) (zarrdataset.ImageBase attribute) _store (zarrdataset._imageloaders.ImageBase attribute) (zarrdataset.ImageBase attribute) _stride (zarrdataset._samplers.PatchSampler attribute) (zarrdataset.PatchSampler attribute) _thresh (zarrdataset._maskfuncs.WSITissueMaskGenerator attribute) (zarrdataset.WSITissueMaskGenerator attribute) _toplefts (zarrdataset._zarrdataset.ZarrDataset attribute) (zarrdataset.ZarrDataset attribute) _transforms (zarrdataset._zarrdataset.ZarrDataset attribute) (zarrdataset.ZarrDataset attribute) _worker_id (zarrdataset._zarrdataset.ZarrDataset attribute) (zarrdataset.ZarrDataset attribute) _worker_sel (zarrdataset._zarrdataset.ZarrDataset attribute) (zarrdataset.ZarrDataset attribute) _zarr_store (zarrdataset._zarrdataset.ZarrDataset attribute) (zarrdataset.ZarrDataset attribute)

A

add_modality() (zarrdataset._zarrdataset.ZarrDataset method) (zarrdataset.ZarrDataset method) add_transform() (zarrdataset._zarrdataset.ZarrDataset method) (zarrdataset.ZarrDataset method) arr (zarrdataset._imageloaders.ImageBase attribute) (zarrdataset.ImageBase attribute)

axes (zarrdataset._imageloaders.ImageBase attribute) (zarrdataset._imageloaders.ImageLoader attribute) (zarrdataset._maskfuncs.MaskGenerator attribute) (zarrdataset.ImageBase attribute) (zarrdataset.ImageLoader attribute) (zarrdataset.MaskGenerator attribute)

B

BlueNoisePatchSampler (class in zarrdataset) (class in zarrdataset._samplers)

C

chained_zarrdataset_worker_init_fn() (in module zarrdataset) (in module zarrdataset._zarrdataset) chk_id (zarrdataset._zarrdataset.ImageSample attribute) chunk_size (zarrdataset._imageloaders.ImageBase property) (zarrdataset.ImageBase property) collection (zarrdataset._imageloaders.ImageCollection attribute) (zarrdataset.ImageCollection attribute)

compute_chunks() (zarrdataset._samplers.PatchSampler method) (zarrdataset.PatchSampler method) compute_patches() (zarrdataset._samplers.PatchSampler method) (zarrdataset.PatchSampler method) compute_sampling_positions() (zarrdataset._samplers.BlueNoisePatchSampler method) (zarrdataset.BlueNoisePatchSampler method) connect_s3() (in module zarrdataset) (in module zarrdataset._utils)

D

DatasetSpecs (class in zarrdataset) (class in zarrdataset._zarrdataset)

F

free_sampler() (zarrdataset._zarrdataset.ImageSample method)

I

im_id (zarrdataset._zarrdataset.ImageSample attribute) image2array() (in module zarrdataset) (in module zarrdataset._imageloaders) ImageBase (class in zarrdataset) (class in zarrdataset._imageloaders) ImageCollection (class in zarrdataset) (class in zarrdataset._imageloaders)

ImageLoader (class in zarrdataset) (class in zarrdataset._imageloaders) ImageSample (class in zarrdataset._zarrdataset) ImagesDatasetSpecs (class in zarrdataset) (class in zarrdataset._zarrdataset) isconsolidated() (in module zarrdataset) (in module zarrdataset._utils)

L

LabelsDatasetSpecs (class in zarrdataset) (class in zarrdataset._zarrdataset)

M

map_axes_order() (in module zarrdataset) (in module zarrdataset._utils) MaskGenerator (class in zarrdataset) (class in zarrdataset._maskfuncs) MasksDatasetSpecs (class in zarrdataset) (class in zarrdataset._zarrdataset) mode (zarrdataset._imageloaders.ImageBase attribute) (zarrdataset._imageloaders.ImageLoader attribute) (zarrdataset.ImageBase attribute) (zarrdataset.ImageLoader attribute)

module zarrdataset zarrdataset._augs zarrdataset._imageloaders zarrdataset._maskfuncs zarrdataset._samplers zarrdataset._utils zarrdataset._zarrdataset

N

next_patch() (zarrdataset._zarrdataset.ImageSample method)

num_patches (zarrdataset._zarrdataset.ImageSample attribute)

P

parse_metadata() (in module zarrdataset) (in module zarrdataset._utils) parse_rois() (in module zarrdataset) (in module zarrdataset._utils)

PatchSampler (class in zarrdataset) (class in zarrdataset._samplers) permute_order (zarrdataset._imageloaders.ImageBase attribute) (zarrdataset.ImageBase attribute) PYTORCH_SUPPORT (in module zarrdataset._zarrdataset)

R

reference_mode (zarrdataset._imageloaders.ImageCollection attribute) (zarrdataset.ImageCollection attribute) rescale() (zarrdataset._imageloaders.ImageBase method) (zarrdataset.ImageBase method) reset_scales() (zarrdataset._imageloaders.ImageCollection method) (zarrdataset.ImageCollection method)

roi (zarrdataset._imageloaders.ImageBase attribute) (zarrdataset._imageloaders.ImageLoader attribute) (zarrdataset.ImageBase attribute) (zarrdataset.ImageLoader attribute) roi_slices (zarrdataset._imageloaders.ImageLoader attribute) (zarrdataset.ImageLoader attribute)

S

scale (zarrdataset._imageloaders.ImageBase property) (zarrdataset.ImageBase property) scale_coords() (in module zarrdataset) (in module zarrdataset._utils) select_axes() (in module zarrdataset) (in module zarrdataset._utils) shape (zarrdataset._imageloaders.ImageBase property) (zarrdataset.ImageBase property) source_axes (zarrdataset._imageloaders.ImageBase attribute) (zarrdataset._imageloaders.ImageLoader attribute) (zarrdataset.ImageBase attribute) (zarrdataset.ImageLoader attribute)

spatial_axes (zarrdataset._imageloaders.ImageBase attribute) (zarrdataset._imageloaders.ImageCollection attribute) (zarrdataset._imageloaders.ImageLoader attribute) (zarrdataset._samplers.PatchSampler attribute) (zarrdataset.ImageBase attribute) (zarrdataset.ImageCollection attribute) (zarrdataset.ImageLoader attribute) (zarrdataset.PatchSampler attribute)

T

TIFFFILE_SUPPORT (in module zarrdataset._imageloaders) ToDtype (class in zarrdataset) (class in zarrdataset._augs)

TQDM_SUPPORT (in module zarrdataset._zarrdataset) translate2roi() (in module zarrdataset) (in module zarrdataset._utils)

W

WSITissueMaskGenerator (class in zarrdataset) (class in zarrdataset._maskfuncs)

Z

zarrdataset module ZarrDataset (class in zarrdataset) (class in zarrdataset._zarrdataset) zarrdataset._augs module zarrdataset._imageloaders module zarrdataset._maskfuncs module

zarrdataset._samplers module zarrdataset._utils module zarrdataset._zarrdataset module zarrdataset_worker_init_fn() (in module zarrdataset) (in module zarrdataset._zarrdataset)