ConvolvePointList

Convolution on a subset of points only.

Paralllel convolution of a kernel at specified points of the source only. Useful to speed up processing in large arrays and only a smaller number of convolution points.

Note

This module is heavily used in the :mod”~ClearMap.ImageProcessing.Skeletonization algorithm.

convolve_3d(source, kernel, points=None, indices=None, x=None, y=None, z=None, sink=None, sink_dtype=None, strides=None, check_border=True, processes=8)

Convolves source with a specified kernel at specific points only.

Arguments

sourcearray

3d binary array to convolve.

kernelarray

Convolution kernel.

pointsarray

List of points to convolve.

indicesarray

Indices to convolve.

x,y,zarray

Arrays of x,y,z coordinates of points to convolve on

sinkarray

Optional sink to write result to.

sink_dtypedtype)

Optional type of the sink. If None, the kernel type is used as default.

stridesarray

The strides of the source in case its given as a 1d list.

check_borderbool

If True, check if each kernel element is inside the source array shape.

processesint or None

Number of processes to use.

Returns

convolvedarray

List of results of convolution at specified points

Note

Either points x,y,z or an index array needs to be given. This function wraps more specialized functions

See also

convolve_3d_points(), convolve_3d_xyz(), convolve_3d_indices()

convolve_3d_find_smaller_than(source, search, indices, max_value, sink=None, processes=8)

Convolves source with a specified kernel at specific points given by a flat array indx under conditon the value is smaller than a number

Arguments:

source (array): 3d binary array to convolve kernel (array): binary orinteger kernel to convolve points (array): list of points to convolve given by the flat array coordinates max_value (int): if result of convolution is smaller then this value return True otherwise False in the sink array processes (int): number of processors

Returns:

array: list of results of convolution at specified points

Note:

cython does not support bools -> use view on uint8 as numpy does

convolve_3d_indices(source, kernel, indices, sink=None, sink_dtype=None, strides=None, check_border=True, processes=8)

Convolves source with a specified kernel at specific points given by a flat array index.

Arguments

sourcearray

3d binary array to convolve.

kernelarray

Convolution kernel.

indicesarray

Indices to convolve.

sinkarray

Optional sink to write result to.

sink_dtypedtype)

Optional type of the sink. If None, the kernel type is used as default.

stridesarray

The strides of the source in case its given as a 1d list.

check_borderbool

If True, check if each kernel element is inside the source array shape.

processesint or None

Number of processes to use.

Returns

convolvedarray

List of results of convolution.

convolve_3d_indices_if_smaller_than(source, kernel, indices, max_value, sink=None, strides=None, check_border=True, processes=8)

Convolves source with a specified kernel at specific points given by a flat array indx under conditon the value is smaller than a number

Arguments

sourcearray

3d binary array to convolve.

kernelarray

Convolution kernel.

indicesarray

Indices to convolve.

max_valuefloat

Checks if the convolution result is smaller than this value.

sinkarray

Optional sink to write result to.

stridesarray

The strides of the source in case its given as a 1d list.

check_borderbool

If True, check if each kernel element is inside the source array shape.

processesint or None

Number of processes to use.

Returns

convolvedarray

List of results of convolution at specified points

convolve_3d_points(source, kernel, points, sink=None, sink_dtype=None, check_border=True, processes=8)

Convolves source with a specified kernel at specific points only

Arguments

sourcearray

3d binary array to convolve.

kernelarray

Convolution kernel.

pointsarray

List of points to convolve.

sinkarray

Optional sink to write result to.

sink_dtypedtype)

Optional type of the sink. If None, the kernel type is used as default.

check_borderbool

If True, check if each kernel element is inside the source array shape.

processesint or None

Number of processes to use.

Returns

convolvedarray

List of results of convolution at specified points

convolve_3d_xyz(source, kernel, x, y, z, sink=None, sink_dtype=None, check_border=True, processes=8)

Convolves source with a specified kernel at specific points only

Arguments

sourcearray

3d binary array to convolve.

kernelarray

Convolution kernel.

x,y,zarray

Arrays of x,y,z coordinates of points to convolve on

sinkarray

Optional sink to write result to.

sink_dtypedtype)

Optional type of the sink. If None, the kernel type is used as default.

check_borderbool

If True, check if each kernel element is inside the source array shape.

processesint or None

Number of processes to use.

Returns

convolvedarray

List of results of convolution.

test()