Pyclesperanto

Latest version: v0.16.0

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0.19.4

New features
* Added new columns to `statistics_of_labeled_neighbors` for statistics of dilated label images. (thanks to lcferme for proposing)

Bug fixes
* The touch count and touch portion measurements in `statistics_of_labeled_neighbors` considered background as something that touches. This has been corrected. Background is ignored now, In case you want to measure touching with background, add `1` to the image. This makes background a valid label and allows quantifying touches with background.

0.19.3

New features
* `crop_border`
* `draw_distance_mesh_between_n_nearest_labels`
* added auto-generated docs

0.19.2

Bug fix
* touch portion ratio mesh was distorted because `NaN`s resulting from `ratio = ... / 0` were drawn along lines

0.19.1

New features
* The first four label colours correspond now to matplotlibs default colours when visualizing label images
* `merge_labels_according_to_touch_matrix`

Bugfix:
* Visualization of label images did not result in similar views, depending on maximum number of labels
* Warngings in `statistics_of_labelleld_neighbors` are now suppressed when division by zero happens. The result in `NaN` anyway.

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.

0.18.4

What's Changed
* Improved dask array support by pr4deepr in https://github.com/clEsperanto/pyclesperanto_prototype/pull/204
* Optional linear_interpolation in deskewing functions by pr4deepr in https://github.com/clEsperanto/pyclesperanto_prototype/pull/204

**Full Changelog**: https://github.com/clEsperanto/pyclesperanto_prototype/compare/0.18.3...0.18.4

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