bioimg.ingestion

cloud.bioimg.ingestion

Functions

Name	Description
ingest	The function ingests microscopy images into TileDB arrays

ingest

cloud.bioimg.ingestion.ingest(
    source
    output
    config
    *args
    acn=''
    taskgraph_name=None
    num_batches=None
    threads=0
    resources=None
    ingest_resources=None
    compute=True
    register=True
    mode=Mode.BATCH
    namespace
    verbose=False
    exclude_metadata=False
    converter=None
    output_ext=''
    tile_scale=128
    **kwargs
)

The function ingests microscopy images into TileDB arrays

Parameters

Name	Type	Description	Default
source	Union[Sequence[str], str]	uri / iterable of uris of input files. If the uri points to a directory of files make sure it ends with a trailing ‘/’	required
output	Union[Sequence[str], str]	uri / iterable of uris of output files. If the uri points to a directory of files make sure it ends with a trailing ‘/’	required
config	Mapping[str, Any]	dict configuration to pass on tiledb.VFS for the source’s resolution	required
acn	str	Access Credentials Name (ACN) registered in TileDB Cloud (ARN type)	''
taskgraph_name	Optional[str]	Optional name for taskgraph, defaults to None	None
num_batches	Optional[int]	Number of graph nodes to spawn. Performs it sequentially if default, defaults to 1	None
threads	Optional[int]	Number of threads for node side multiprocessing, defaults to 0	0
resources	Optional[Mapping[str, Any]]	configuration for node specs e.g. {“cpu”: “8”, “memory”: “4Gi”}, defaults to None	None
ingest_resources	Optional[Mapping[str, Any]]	configuration for node specs e.g. {“cpu”: “8”, “memory”: “4Gi”}. This parameter is intended to be used with the as_batch() wrapper and with the TileDB UI ingest endpoint. It defaults to None and will be superseded by the resources parameter described above.	None
compute	bool	When True the DAG returned will be computed inside the function otherwise DAG will only be returned.	True
register	bool	When True the ingested images are also being registered under the namespace in which were ingested. Should be False when tiledb uris are given as destination paths, registration node is merged with the ingestion stage.	True
mode	Optional[Mode]	By default runs Mode.Batch	Mode.BATCH
namespace	Optional[str]	The namespace where the DAG will run	required
verbose	bool	verbose logging, defaults to False	False
exclude_metadata	bool	a boolean for excluding all the metadata from the ingested image	False
converter	Optional[str]	The converter to be used for the image ingestion, when None the default TIFF converter is used. Available converters are one of the (“tiff”, “zarr”, “osd”).	None
output_ext	str	extension for the output images in tiledb	''
tile_scale	int	The scaling factor applied to each tile during I/O. Larger scale factors will result in less I/O operations.	128
access_credentials_name		[TBDeprecated] Access Credentials Name (ACN) registered in TileDB Cloud (ARN type) if acn is not set.	required
dest_config		dict configuration to pass on tiledb.VFS for the destination’s resolution	required
reader		The selected reader backend implementation either “experimental” or “production”. Default[“production”]	required