clEsperanto/pyclesperanto_prototype: 0.19.0

New functions

• draw_mesh_between_labels_with_touch_portion_in_range
• draw_mesh_between_n_most_touching_labels
• generate_n_most_touching_neighbors_matrix
• generate_touch_mean_intensity_matrix
• generate_touch_mean_intensity_within_range_matrix
• generate_touch_portion_within_range_neighbor_matrix
• is_matrix_symmetric
• maximum_of_n_most_touching_neighbors_map
• maximum_of_touch_portion_within_range_neighbors_map
• mean_of_n_most_touching_neighbors_map
• mean_of_touch_portion_within_range_neighbors_map
• merge_labels_with_border_intensity_within_range
• minimum_of_n_most_touching_neighbors_map
• minimum_of_touch_portion_within_range_neighbors_map
• mode_of_n_most_touching_neighbors_map
• mode_of_touch_portion_within_range_neighbors_map
• smooth_labels
• standard_deviation_of_n_most_touching_neighbors_map
• standard_deviation_of_touch_portion_within_range_neighbors_map
• symmetric_maximum_matrix
• symmetric_mean_matrix
• symmetric_minimum_matrix
• symmetric_sum_matrix
• touch_portion_within_range_neighbor_count
• touch_portion_within_range_neighbor_count_map

New parameters

• count_touching_neighbors has a new optional parameter ignore_background

New measurements

• statistics_of_labelled_neighbors has new columns: touch_portion_above_?_neighbor_count with ? in [0, 0.16, 0.2, 0.33, 0.5, 0.75]

Bug fixes

• erode_labels with radius>1 eroded one pixel too much.
• opening_labels with radius>1 left a 1 pixel gap between labels unintentionally

Miscellaneous

• Added hints to documentation in case functions need images with isotropic voxels as input.

Deprecated methods

• touch_matrix_to_adjacency_matrix is deprecated, use symmetric_maximum_matrix or symmetric_minimum_matrix, symmetric_mean_matrix or symmetric_sum_matrix instead.

Backwards compatibility breaking changes

• generate_touch_matrix now produces a symmetric matrix as "touching" is bi-directional. In case label A touches label B, also label B touches A. If you want to have a matrix like in pyclesperanto_prototype < 0.19.0, you need to call cle.set_where_x_greater_than_y(matrix, 0) on the matrix after generating it.
• touch_matrix_to_mesh and all draw_*_mesh functions will now process asymmetric matrices when drawing meshes. The mesh line intensity will be the maximum of the potentially two different values stored in any touch/distance/...-matrix. If you prefer the old way of how matrices were handled, you need to call this before drawing the mesh: cle.set_where_x_greater_than_y(matrix, 0). This will ensure that only the lower half of the matrix will be taken into account for drawing the mesh, which is pretty much the old behaviour in pyclesperanto_prototype < 0.19.0 .
• count_touching_neighbors ignores touching background. If you want to have the old behaviour back, set ignore_background=False when calling the function.