aicsimageio.readers.reader.Reader

class aicsimageio.readers.reader.Reader(image: Any, **kwargs: Any)

A small class to build standardized image reader objects that deal with the raw image and metadata.

Parameters

• image (Any) – Some type of object to read and follow the Reader specification.

• fs_kwargs (Dict[str, Any]) – Any specific keyword arguments to pass down to the fsspec created filesystem. Default: {}

Notes

It is up to the implementer of the Reader to decide which types they would like to accept (certain readers may not support buffers for example).

__init__(image: Any, **kwargs: Any)

Methods

__init__(image, **kwargs)
get_dask_stack(**kwargs)	Get all scenes stacked in to a single array.
get_image_dask_data([dimension_order_out])	Get specific dimension image data out of an image as a dask array.
get_image_data([dimension_order_out])	Read the image as a numpy array then return specific dimension image data.
get_mosaic_tile_position(mosaic_tile_index, ...)	Get the absolute position of the top left point for a single mosaic tile.
get_mosaic_tile_positions(**kwargs)	Get the absolute positions of the top left points for each mosaic tile matching the specified dimensions and current scene.
get_stack(**kwargs)	Get all scenes stacked in to a single array.
get_xarray_dask_stack(**kwargs)	Get all scenes stacked in to a single array.
get_xarray_stack(**kwargs)	Get all scenes stacked in to a single array.
is_supported_image(image[, fs_kwargs])	Asserts that the provided image like object is supported by the current Reader.
set_scene(scene_id)	Set the operating scene.

Attributes

channel_names	returns channel_names -- Using available metadata, the list of strings representing channel names.
current_scene	returns scene -- The current operating scene.
current_scene_index	returns scene_index -- The current operating scene index in the file.
dask_data	returns dask_data -- The image as a dask array with the native dimension ordering.
data	returns data -- The image as a numpy array with native dimension ordering.
dims	returns dims -- Object with the paired dimension names and their sizes.
dtype	returns dtype -- Data-type of the image array's elements.
metadata	returns metadata -- The metadata for the formats supported by the inhereting Reader.
mosaic_dask_data	returns dask_data -- The stitched together mosaic image as a dask array.
mosaic_data	returns data -- The stitched together mosaic image as a numpy array.
mosaic_tile_dims	returns tile_dims -- The dimensions for each tile in the mosaic image.
mosaic_xarray_dask_data	returns xarray_dask_data -- The delayed mosaic image and metadata as an annotated data array.
mosaic_xarray_data	returns xarray_dask_data -- The in-memory mosaic image and metadata as an annotated data array.
ome_metadata	returns metadata -- The original metadata transformed into the OME specfication.
physical_pixel_sizes	returns sizes -- Using available metadata, the floats representing physical pixel sizes for
scenes	returns scenes -- A tuple of valid scene ids in the file.
shape	returns shape -- Tuple of the image array's dimensions.
xarray_dask_data	returns xarray_dask_data -- The delayed image and metadata as an annotated data array.
xarray_data	returns xarray_data -- The fully read image and metadata as an annotated data array.