porespy.filters.chunked_func#

porespy.filters.chunked_func(func, parallel_kw={'divs': 2, 'overlap': None, 'cores': None}, im_arg=['input', 'image', 'im'], strel_arg=['strel', 'structure', 'footprint'], **kwargs)#

Performs the specfied operation “chunk-wise” in parallel using dask.

This can be used to save memory by doing one chunk at a time (cores=1) or to increase computation speed by spreading the work across multiple cores (e.g. cores=8)

This function can be used with any operation that applies a structuring element of some sort, since this implies that the operation is local and can be chunked.

Parameters:

func (function handle) – The function which should be applied to each chunk, such as spipy.ndimage.binary_dilation.
parallel_kw (dict) –
Dictionary containing the settings for parallelization by chunking. The optional settings include divs (scalar or list of scalars, default = [2, 2, 2]), overlap (scalar or list of scalars, optional), and cores (scalar, default is all available cores).

Divs is the number of times to divide the image for parallel processing. If 1 then parallel processing does not occur. 2 is equivalent to [2, 2, 2] for a 3D image.

Overlap is the amount of overlap to include when dividing up the image. This value will almost always be the size (i.e. raduis) of the structuring element. If not specified then the amount of overlap is inferred from the size of the structuring element, in which case the strel_arg must be specified.

Cores is the number of cores that will be used to parallel process all domains. If None then all cores will be used but user can specify any integer values to control the memory usage. Setting value to 1 will effectively process the chunks in serial to minimize memory usage.
im_arg (str) – The keyword used by func for the image to be operated on. By default this function will look for image, input, and im which are commonly used by scipy.ndimage and skimage.
strel_arg (str) – The keyword used by func for the structuring element to apply. This is only needed if overlap is not specified. By default this function will look for strel, structure, and footprint which are commonly used by scipy.ndimage and skimage.
kwargs – All other arguments are passed to func as keyword arguments. Note that PoreSpy will fetch the image from this list of keywords using the value provided to im_arg.

Returns:

result – An image the same size as the input image, with the specified filter applied as though done on a single large image. There should be no difference.

Return type:

ndarray

Notes

This function divides the image into the specified number of chunks, but also applies a padding to each chunk to create an overlap with neighboring chunks. This way the operation does not have any edge artifacts. The amount of padding is usually equal to the radius of the structuring element but some functions do not use one, such as the distance transform and Gaussian blur. In these cases the user can specify overlap.