intake_io.io

Module Contents

Functions

imload(uri: str, partition: Optional[Any] = None, metadata_only: bool = False, **kwargs) → xarray.Dataset	Load image, autodetect source type.
imsave(image: Any, uri: str, compress: Optional[bool] = None, partition: Optional[str] = None, **kwargs)	Save image, autodetect format.

intake_io.io.imload(uri: str, partition: Optional[Any] = None, metadata_only: bool = False, **kwargs) → xarray.Dataset

Load image, autodetect source type.

Parameters

• uri (str) –

• partition (Optional[Any]) – Load only a partition of the image

• metadata_only (bool) – Load metadata only

• kwargs –

  Additional arguments passed to the source constructor. Notable fields supported by all subclasses of intake_io.source.base.ImageSource are:

  • output_axis_order (Optional[str]) – Deviate from default “itczyx” output axis ordering, or None to use original axis ordering of the data

  • metadata (Optional[Dict[str, Any]]) – Add or overrule metadata fields, for instance:

    metadata={
        "axes": "tcxy",                      # specify input axis order
        "spacing": {"t": 0.3},               # overrule spacing
        "spacing_units": {"t": "ms"},        # overrule spacing unit
        "coords": {"c": ["nuclei", "actin"]} # use specific channel names
    }
    

Returns

image

Return type

xarray.Dataset

intake_io.io.imsave(image: Any, uri: str, compress: Optional[bool] = None, partition: Optional[str] = None, **kwargs)

Save image, autodetect format.

Format is chosen based on URI extension. Defaults to .zarr if no extension is given.

image is automatically split into multiple files if the output format doesn’t support saving it in a single file. For instance, TIF hyperstacks support single arrays with up to tzcyx axes. An xarray.Dataset with multiple variables (e.g. “image” and “segmentation”) and extra axes (e.g. multiple image arrays along the i-axis) is saved as multiple files according to the following pattern (axes are separated by ., key and value are separated by _):

/path/to/filename.var_image.i_00.tif
/path/to/filename.var_image.i_01.tif
...
/path/to/filename.var_segmentation.i_00.tif
/path/to/filename.var_segmentation.i_01.tif
...

The indexes used in the file name are the actual xarray.DataArray coordinates along their respective axes, e.g. if our i coordinates are [3, 10] or ["control", "treatment"] then we’ll get file names containing “i_03” or “i_treatment”. The data variable key (e.g. “var_segmentation” in the example above) is omitted from the output file name if image doesn’t have multiple data variables or if it isn’t an xarray.Dataset.

The partition argument controls the partitioning scheme. By default, image is split only if needed, and into as few files as possible. In contrast, e.g. partition="tyx" partitions the data into files containing only the given axes, in order (axes are reordered as needed), yielding e.g. the following file pattern:

/path/to/filename.var_image.i_03.c_actin.tif
/path/to/filename.var_image.i_03.c_nuclei.tif
/path/to/filename.var_image.i_21.c_actin.tif
/path/to/filename.var_image.i_21.c_nuclei.tif
...
/path/to/filename.var_segmentation.i_03.c_actin.tif
/path/to/filename.var_segmentation.i_03.c_nuclei.tif
/path/to/filename.var_segmentation.i_21.c_actin.tif
/path/to/filename.var_segmentation.i_21.c_nuclei.tif
...

See File patterns section of this documentation for help with loading these file patterns.

Parameters

• image (Any) –

• uri (str) –

• compress (Optional[bool]) – Whether or not to compress the data. Default value None defers decision to backend. Where applicable, compression algorithm and parameters are chosen as a trade-off of compatibility, compression ratio and I/O performance. If compression is requested but unsupported, the data is saved uncompressed and no exception is raised.

• partition (Optional[str]) – Partition the data as needed into multiple files, each containing the given axes, in the given order. By default, as few files as possible are created.