cellmap_segmentation_challenge.utils.fetch_data#
Functions
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Iterate over the keys, copying them from the source store to the dest store |
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Get a list of the objects supporting this array. |
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Get the keys for all the chunks in a Zarr array as a generator of strings. |
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Get the path to the reconstructed FIB-SEM data used to create the crop. |
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- cellmap_segmentation_challenge.utils.fetch_data.copy_store(*, keys: Iterable[str], source_store: Store, dest_store: Store)[source]#
Iterate over the keys, copying them from the source store to the dest store
- Parameters:
keys (Iterable[str])
source_store (Store)
dest_store (Store)
- cellmap_segmentation_challenge.utils.fetch_data.partition_copy_store(*, keys, source_store, dest_store, batch_size, pool: ThreadPoolExecutor, log: BoundLogger | None = None)[source]#
- Parameters:
pool (ThreadPoolExecutor)
log (BoundLogger | None)
- cellmap_segmentation_challenge.utils.fetch_data.get_url(node: Group | Array) URL [source]#
- Parameters:
node (Group | Array)
- Return type:
URL
- cellmap_segmentation_challenge.utils.fetch_data.get_store_url(store: BaseStore, path: str)[source]#
- Parameters:
store (BaseStore)
path (str)
- cellmap_segmentation_challenge.utils.fetch_data.get_fibsem_path(crop_path: str) str [source]#
Get the path to the reconstructed FIB-SEM data used to create the crop. Returns a uri that resolves to a zarr group
- Parameters:
crop_path (str)
- Return type:
str
- cellmap_segmentation_challenge.utils.fetch_data.get_chunk_keys(array: Array, region: tuple[slice, ...] = ()) Generator[str, None, None] [source]#
Get the keys for all the chunks in a Zarr array as a generator of strings. Returns keys relative to the path of the array.
copied with modifications from janelia-cellmap/fibsem-tools
- Parameters:
array (zarr.core.Array) – The zarr array to get the chunk keys from
region (tuple[slice, ...]) – The region in the zarr array get chunks keys from. Defaults to (), which will result in all the chunk keys being returned.
- Return type:
Generator[str, None, None]
- cellmap_segmentation_challenge.utils.fetch_data.get_array_objects(node: Array, region: tuple[slice, ...] = ()) tuple[str, ...] [source]#
Get a list of the objects supporting this array. These objects may or may not exist in storage.
- Parameters:
node (Array)
region (tuple[slice, ...])
- Return type:
tuple[str, …]
- cellmap_segmentation_challenge.utils.fetch_data.get_group_objects(node: Group) tuple[str, ...] [source]#
- Parameters:
node (Group)
- Return type:
tuple[str, …]
- cellmap_segmentation_challenge.utils.fetch_data.read_group(path: str, **kwargs) Group [source]#
- Parameters:
path (str)
- Return type:
Group