aliby.io.image.ImageDummy¶
- class ImageDummy(tiler_parameters)[source]¶
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
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
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)[source]¶
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
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()[source]¶
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)[source]¶
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