ZarrDataset
Getting started:
ZarrDataset
Examples:
Basic ZarrDataset usage example
Integration of ZarrDataset with PyTorch’s DataLoader
Integration of ZarrDataset with Tensorflow Datasets
Loading patches/windows from masked regions of images with ZarrDataset
Custom masks for sampling specific regions from images with ZarrDataset
Labeled dataset loading with ZarrDataset
Integration of ZarrDataset with PyTorch’s DataLoader (Advanced)
Integration of ZarrDataset with PyTorch’s DataLoader for inference (Advanced)
Contents:
License
API Reference
ZarrDataset
Index
Index
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A
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B
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C
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D
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F
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I
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L
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M
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N
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P
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R
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S
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T
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W
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Z
_
__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)
_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)
_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)
_drop_axes (zarrdataset._imageloaders.ImageBase attribute)
(zarrdataset.ImageBase attribute)
_generate_mask() (zarrdataset._imageloaders.ImageCollection method)
(zarrdataset.ImageCollection method)
_image_func (zarrdataset._imageloaders.ImageBase attribute)
(zarrdataset.ImageBase attribute)
_initialize() (zarrdataset._zarrdataset.ZarrDataset method)
(zarrdataset.ZarrDataset method)
_iscached() (zarrdataset._imageloaders.ImageBase method)
(zarrdataset.ImageBase method)
_new_axes (zarrdataset._imageloaders.ImageBase attribute)
(zarrdataset.ImageBase attribute)
_ordering (zarrdataset._zarrdataset.ImageSample attribute)
_rng_seed (zarrdataset._zarrdataset.ImageSample attribute)
_scale (zarrdataset._imageloaders.ImageBase attribute)
(zarrdataset.ImageBase attribute)
_shape (zarrdataset._imageloaders.ImageBase attribute)
(zarrdataset.ImageBase 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)
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.ImageBase attribute)
B
BlueNoisePatchSampler (class in zarrdataset)
(class in zarrdataset._samplers)
C
chained_zarrdataset_worker_init_fn() (in module zarrdataset)
(in module zarrdataset._zarrdataset)
chunk_size (zarrdataset._imageloaders.ImageBase property)
(zarrdataset.ImageBase property)
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
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.ImageBase 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
rescale() (zarrdataset._imageloaders.ImageBase method)
(zarrdataset.ImageBase method)
reset_scales() (zarrdataset._imageloaders.ImageCollection method)
(zarrdataset.ImageCollection method)
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.ImageBase attribute)
spatial_axes (zarrdataset._imageloaders.ImageBase attribute)
(zarrdataset.ImageBase 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)