aicsimageio.readers.tiff_reader.TiffReader

class aicsimageio.readers.tiff_reader.TiffReader(image: Union[str, Path], chunk_dims: Union[str, List[str]] = ['Z', 'Y', 'X', 'S'], dim_order: Optional[Union[List[str], str]] = None, channel_names: Optional[Union[List[str], List[List[str]]]] = None, fs_kwargs: Dict[str, Any] = {}, **kwargs: Any)[source]

Wraps the tifffile API to provide the same aicsimageio Reader API but for volumetric Tiff (and other tifffile supported) images. :Parameters: * image (types.PathLike) – Path to image file to construct Reader for.

chunk_dims (Union[str, List[str]]) – Which dimensions to create chunks for. Default: DEFAULT_CHUNK_DIMS Note: Dimensions.SpatialY, Dimensions.SpatialX, and DimensionNames.Samples, will always be added to the list if not present during dask array construction.

dim_order (Optional[Union[List[str], str]]) – A string of dimensions to be applied to all array(s) or a list of string dimension names to be mapped onto the list of arrays provided to image. I.E. “TYX”. Default: None (guess dimensions for single array or multiple arrays)

channel_names (Optional[Union[List[str], List[List[str]]]]) – A list of string channel names to be applied to all array(s) or a list of lists of string channel names to be mapped onto the list of arrays provided to image. Default: None (create OME channel IDs for names for single or multiple arrays)

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

__init__(image: Union[str, Path], chunk_dims: Union[str, List[str]] = ['Z', 'Y', 'X', 'S'], dim_order: Optional[Union[List[str], str]] = None, channel_names: Optional[Union[List[str], List[List[str]]]] = None, fs_kwargs: Dict[str, Any] = {}, **kwargs: Any)[source]

Methods

`__init__`(image[, chunk_dims, dim_order, ...])
`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`	Return the physical pixel sizes of the image.
`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.