Smoothing#

Smoothing

Smooth a binary image based on the local configuration of voxels in a cube.

See also

The, parallel

R2(cube)[source]#

S3(cube)[source]#

U0(cube)[source]#

U1(cube)[source]#

U2(cube)[source]#

cube_to_smoothing(cube)[source]#: Match cube configurations to delete, add or keep a voxel.

generate_lookup_table(function=<function index_to_smoothing>, verbose=True, processes=None)[source]#: Generates lookup table for templates

index_to_smoothing(index, verbose=True)[source]#: Match index of configuration to smoothing action

initialize_lookup_table(function=<function index_to_smoothing>, filename='Smoothing.npy', verbose=True, processes=None)[source]#: Initialize the lookup table

rotations_edges(cube)[source]#

rotations_faces(cube)[source]#

rotations_node_faces(cube)[source]#

rotations_nodes(cube)[source]#

smooth_by_configuration(source, sink=None, iterations=1, processing_parameter=None, processes=None, verbose=False)[source]#

Smooth a binary source using the local configuration around each pixel.

Arguments

sourcearray or Source: The binary source to smooth.
sinkarray, Source or None: The sink to write result of smoothing. If None, return array.
iterationsint: Number of smoothing iterations.
processing_parameterNone or dict: The parameter passed to ClearMap.ParallelProcessing.BlockProcessing.process().
processesint or None: number of processes to use.
verbosebool: If True, print progress information.

Returns

smoothedarray or Source: Thre smoothed binary array.

Note

The algorithm is based on a topological smoothing operation defined by adding or removing forground pixels based on the local topology of the binary array.

smooth_by_configuration_block(source, iterations=1, verbose=False)[source]#

Smooth a binary source using the local configuration around each pixel.

Arguments

sourcearray: The binary source to smooth.
iterationsint: Number of smoothing iterations.
verbosebool: If True, print progress information.

Returns

smoothedarray: The smoothed binary array.

smooth_by_counting(source, sink=None, low=5, high=10, shape=None)[source]#

Smooth binary image by counting neighbours.

Arguments

sourcearray: The binary source to smooth.
sinkarray or None.: The sink to write the smoothed source to.
lowint: If a voxel has less then this number of 26-neighbours it is set to False.
highint: If a voxel has more then this number of 26-neighbours it is set to True.
shapetuple of int or None: The shape of the square structuring element to consider.

Returns

sinkarray: The smoothed sbinary source.

Note

The algorithm uses a sequence of 1d convoluions for speed, allowing only rectangular like structuring elements.

smooth_by_configuration_filename = 'Smoothing.npy'#: Filename for the look up table mapping a cube configuration to the smoothing action for the center pixel.