aliby.io.image.ImageDummy

class ImageDummy(tiler_parameters)

Bases: BaseLocalImage

Dummy Image class.

ImageDummy mimics the other Image classes in such a way that it is accepted by Tiler. The purpose of this class is for testing, in particular, identifying silent failures. If something goes wrong, we should be able to know whether it is because of bad parameters or bad input data.

For the purposes of testing parameters, ImageDummy assumes that we already know the tiler parameters before Image instances are instantiated. This is true for a typical pipeline run.

Attributes

data

dimorder

metadata

name

Methods

get_data_lazy()	Return 5D dask array.
pad_array(image_array, dim, n_empty_slices)	Extends a dimension in a dask array and pads with zeros

rechunk_data

Builds image instance

Parameters

tiler_parametersdict

Tiler parameters, in dict form. Following aliby.tile.tiler.TilerParameters, the keys are: “tile_size” (size of tile), “ref_channel” (reference channel for tiling), and “ref_z” (reference z-stack, 0 to choose a default).

Attributes

data

dimorder

metadata

name

Methods

get_data_lazy()	Return 5D dask array.
pad_array(image_array, dim, n_empty_slices)	Extends a dimension in a dask array and pads with zeros

rechunk_data

__init__(tiler_parameters)

Builds image instance

Parameters

tiler_parametersdict

Tiler parameters, in dict form. Following aliby.tile.tiler.TilerParameters, the keys are: “tile_size” (size of tile), “ref_channel” (reference channel for tiling), and “ref_z” (reference z-stack, 0 to choose a default).

Methods

__init__(tiler_parameters)	Builds image instance
get_data_lazy()	Return 5D dask array.
pad_array(image_array, dim, n_empty_slices)	Extends a dimension in a dask array and pads with zeros
rechunk_data(img)

Attributes

data
dimorder
metadata
name

get_data_lazy()

Return 5D dask array. For lazy-loading multidimensional tiff files. Dummy image.

Return type

Array

static pad_array(image_array, dim, n_empty_slices, image_position=0)

Extends a dimension in a dask array and pads with zeros

Extends a dimension in a dask array that has existing content, then pads with zeros.

Parameters

image_arrayda.Array

Input dask array

dimint

Dimension in which to extend the dask array.

n_empty_slicesint

Number of empty slices to extend the dask array by, in the specified dimension/axis.

image_positionint

Position within the new dimension to place the input arary, default 0 (the beginning).

Examples

``` extended_array = pad_array(

my_da_array, dim = 2, n_empty_slices = 4, image_position = 1)

``` Extends a dask array called my_da_array in the 3rd dimension (dimensions start from 0) by 4 slices, filled with zeros. And puts the original content in slice 1 of the 3rd dimension