Releases | Open Source Science

https://github.com/clesperanto/pyclesperanto_prototype - 0.24.5

What's Changed

allow non-prototype array as parameter values by @haesleinhuepf in https://github.com/clEsperanto/pyclesperanto_prototype/pull/341
silent bia-bob suggestions in case the non-prototype pyclesperanto is installed. by @haesleinhuepf in https://github.com/clEsperanto/pyclesperanto_prototype/pull/342

Full Changelog: https://github.com/clEsperanto/pyclesperanto_prototype/compare/0.24.4...0.24.5

- Jupyter Notebook
Published by haesleinhuepf over 1 year ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.24.4

What's Changed

removed print statement by @thawn in https://github.com/clEsperanto/pyclesperanto_prototype/pull/334
deprecated imshow and imread by @haesleinhuepf in https://github.com/clEsperanto/pyclesperanto_prototype/pull/335
Reduce bia bob suggestions by @haesleinhuepf in https://github.com/clEsperanto/pyclesperanto_prototype/pull/336
added stitching functions by @haesleinhuepf in https://github.com/clEsperanto/pyclesperanto_prototype/pull/337
mute warnings when showing images using reprhtml by @haesleinhuepf in https://github.com/clEsperanto/pyclesperantoprototype/pull/338

New Contributors

@thawn made their first contribution in https://github.com/clEsperanto/pyclesperanto_prototype/pull/334

Full Changelog: https://github.com/clEsperanto/pyclesperanto_prototype/compare/0.24.2...0.24.4

- Jupyter Notebook
Published by haesleinhuepf about 2 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.24.2

What's Changed

Extend bia-bob by adding suggestions by @haesleinhuepf in https://github.com/clEsperanto/pyclesperanto_prototype/pull/327

Full Changelog: https://github.com/clEsperanto/pyclesperanto_prototype/compare/0.24.1...0.24.2

- Jupyter Notebook
Published by haesleinhuepf over 2 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.24.1

Bug fixes * The parameters exlude_in_x, exlude_in_y and exlude_in_z of the function exclude_labels_on_edges() were renamed to exclude_.... This change was made in a backwards-compatible fashion. Aliases of the olde names were added and using them will result in a deprecation warning.

- Jupyter Notebook
Published by haesleinhuepf about 3 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.24.0

Backwards compatibility breacking bug fixes

range/slice didn't work with negative values (e.g. image[::-1]) and out-of-range values (e.g. image[100:1000] for an image with shape (2,3)). More precisely: results were different than when using numpy. Fixed in https://github.com/clEsperanto/pyclesperanto_prototype/pull/295 (Thanks to @thawn for reporting)

Full Changelog: https://github.com/clEsperanto/pyclesperanto_prototype/compare/0.23.6...0.24.0

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Published by haesleinhuepf about 3 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.23.6

Bugfix

force kernel size parameter to be integer to prevent endless loops when a float is passed as radius parameter, e.g. to cle.standard_deviation_box() by @haesleinhuepf in https://github.com/clEsperanto/pyclesperanto_prototype/pull/293

Full Changelog: https://github.com/clEsperanto/pyclesperanto_prototype/compare/0.23.5...0.23.6

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Published by haesleinhuepf about 3 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.23.5

What's Changed

mode_box and mode_sphere filters by @haesleinhuepf in https://github.com/clEsperanto/pyclesperanto_prototype/pull/292

Full Changelog: https://github.com/clEsperanto/pyclesperanto_prototype/compare/0.23.4...0.23.5

- Jupyter Notebook
Published by haesleinhuepf about 3 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.23.4

What's Changed

fix issue with enumerate and zip reported by @thawn, fixed by @haesleinhuepf in https://github.com/clEsperanto/pyclesperanto_prototype/pull/291

Full Changelog: https://github.com/clEsperanto/pyclesperanto_prototype/compare/0.23.3...0.23.4

- Jupyter Notebook
Published by haesleinhuepf about 3 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.23.3

What's Changed

New functions x_position_of_minimum_x_projection, y_position_of_minimum_y_projection and minimum_position by @ClementCaporal in https://github.com/clEsperanto/pyclesperanto_prototype/pull/277
add fill_diagonal alias for set_where_x_equals_y by @haesleinhuepf in https://github.com/clEsperanto/pyclesperanto_prototype/pull/282

Miscelaneous

prevent dependency scikit-image 0.20.0 because saving images doesn't work then by @haesleinhuepf in https://github.com/clEsperanto/pyclesperanto_prototype/pull/273

New Contributors

@ClementCaporal made their first contribution in https://github.com/clEsperanto/pyclesperanto_prototype/pull/277

Full Changelog: https://github.com/clEsperanto/pyclesperanto_prototype/compare/0.23.2...0.23.3

- Jupyter Notebook
Published by haesleinhuepf about 3 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.23.2

New features

Added generate_maximum_intensity_between_points_matrix
Added generate_minimum_intensity_between_points_matrix

Full Changelog: https://github.com/clEsperanto/pyclesperanto_prototype/compare/0.23.1...0.23.2

- Jupyter Notebook
Published by haesleinhuepf over 3 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.23.1

Bug fixes

skimage.io.imsave didn't work with cle images anymore

- Jupyter Notebook
Published by haesleinhuepf over 3 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.23.0

New features

Device selection using device index by @haesleinhuepf in https://github.com/clEsperanto/pyclesperanto_prototype/pull/258
Warning in case a selected device name wasn't found @haesleinhuepf in https://github.com/clEsperanto/pyclesperanto_prototype/pull/258
enable color bars in subplots by @haesleinhuepf in https://github.com/clEsperanto/pyclesperanto_prototype/pull/260 (thanks to @somas193 for proposing and providing code)

Bug fixes

cle_image.T did not work as expected
cle.create_like(numpy_array) created an image of wrong size (shape was inverse).
iterating through slices of a 3D stack didn't work

Backwards compatibility breacking changes

The behaviour of cle.create_like() has changed in case a numpy array was passed (see above)
The alias local_threshold was removed. Use greater instead.

Full Changelog: https://github.com/clEsperanto/pyclesperanto_prototype/compare/0.22.1...0.23.0

- Jupyter Notebook
Published by haesleinhuepf over 3 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.22.1

New features

make excluding edges on specific edges optional by @haesleinhuepf in https://github.com/clEsperanto/pyclesperanto_prototype/pull/248
add generatemeanintensitybetweenpointsmatrix and generatestandarddeviationintensitybetweenpointsmatrix by @haesleinhuepf in https://github.com/clEsperanto/pyclesperantoprototype/pull/257

Bug fixes

bugfix EDF result dimensionality by @haesleinhuepf in https://github.com/clEsperanto/pyclesperanto_prototype/pull/256 (thanks to @jaimemcc for reporting)

Full Changelog: https://github.com/clEsperanto/pyclesperanto_prototype/compare/0.22.0...0.22.1

- Jupyter Notebook
Published by haesleinhuepf over 3 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.22.0

Bug fixes * Issue with indexing linux (Thanks to @ENicolay for reporting and support in fixing) * Issue with networkx 3.0, fromnumpymatrix was deprecated and conversion failed.

Backwards compatibility breaking bug fixes * The visualisation of label images was changed: The first two colors were flipped (now new: 1=cyan, 2=orange). The colour order is now identical with matplotlib default colours.

- Jupyter Notebook
Published by haesleinhuepf over 3 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.21.2

Bugfixes * Tests failed because of numpy 1.24 release. Library code remains unchanged

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Published by haesleinhuepf over 3 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.21.1

New features * generate_should_touch_matrix() * merge_annotated_touching_labels()

Bug fixes * merge_labels_according_to_touch_matrix() didn't merge all requested labels in case labels were touching in chains / circles

- Jupyter Notebook
Published by haesleinhuepf over 3 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.21.0

Backwards compatibility breaking changes (MacOS, Intel GPUs only) * This version changes the default device on older MacOS because Intel based GPUs caused trouble. The CPU is now used per default. This gives users of older MacBooks a functional OpenCL device and more available memory.

- Jupyter Notebook
Published by haesleinhuepf over 3 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.20.0

New features * Added maximum position function by @grahamross123 in https://github.com/clEsperanto/pyclesperantoprototype/pull/230 * Pytorch interoperability by @haesleinhuepf as proposed by @alisterburt in https://github.com/clEsperanto/pyclesperantoprototype/pull/232 * Colab example by @haesleinhuepf in https://github.com/clEsperanto/pyclesperanto_prototype/pull/222

Bug fixes * Bugfix cupy backend by @haesleinhuepf in https://github.com/clEsperanto/pyclesperantoprototype/pull/231 * Orthogonal interpolation (Sapoznik et al. (2020) https://doi.org/10.7554/eLife.57681) for deskewing by @pr4deepr with support by @dpshepherd in https://github.com/clEsperanto/pyclesperantoprototype/pull/224 Also thanks for reporting this bug to Sebastian Bundschuh (MPI-CBG)

Backwards compatibility breaking changes * The parameter linear_interpolation in the functions deskew_x and deskew_y have now True as default parameter and the result image looks different because of a bugfix, now using orthogonal interpolation (see above). See this notebook for details

Deprecated functions and parameters * The parameter linear_interpolation in the functions deskew_x and deskew_y is deprecated. It will be removed in a future version.

Full Changelog: https://github.com/clEsperanto/pyclesperanto_prototype/compare/0.19.4...0.20.0

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Published by haesleinhuepf over 3 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 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.

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Published by haesleinhuepf over 3 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.19.3

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

- Jupyter Notebook
Published by haesleinhuepf over 3 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.19.2

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

- Jupyter Notebook
Published by haesleinhuepf over 3 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 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.

- Jupyter Notebook
Published by haesleinhuepf over 3 years ago

https://github.com/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 pyclesperantoprototype < 0.19.0, you need to call `cle.setwherexgreaterthany(matrix, 0)on the matrix after generating it. *touchmatrixtomeshand alldraw*meshfunctions 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.setwherexgreaterthany(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 . *counttouchingneighborsignores touching background. If you want to have the old behaviour back, setignore_background=False` when calling the function.

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Published by haesleinhuepf over 3 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.18.4

What's Changed

Improved dask array support by @pr4deepr in https://github.com/clEsperanto/pyclesperanto_prototype/pull/204
Optional linearinterpolation in deskewing functions by @pr4deepr in https://github.com/clEsperanto/pyclesperantoprototype/pull/204

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

- Jupyter Notebook
Published by haesleinhuepf over 3 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.18.3

Bug fix: * statistics_of_labelled_neighbors counted background as a neighbor in touching_neighbor_count

- Jupyter Notebook
Published by haesleinhuepf almost 4 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.18.2

New features * divide_scalar_by_image * draw_touch_portion_mesh_between_touching_labels * draw_touch_portion_ratio_mesh_between_touching_labels * fill_zeros_inpainting (thanks to @AlisterBurt for proposing) * generate_touch_count_matrix * generate_touch_portion_matrix * prefix_in_x * proximal_neighbor_count * standard_deviation_touch_portion * standard_deviation_touch_portion_map * statistics_of_labelled_neighbors

Bug fixes * corrected result type of artificial_tissue_2d to uint32 as it's supposed to be a label image

- Jupyter Notebook
Published by haesleinhuepf almost 4 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.18.1

Bugfix * Output images remained empty in deskew_y in case the output image was provided as parameter. Presumably all affine transforms were affected by this, in case auto_size=True was set.

- Jupyter Notebook
Published by haesleinhuepf almost 4 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.18.0

New functions * local_cross_correlation for template matching (big thanks to @grahamross123 for implementing this) * Compatibility with Python 3.9 and 3.10; also automatically tested * Rendering (_repr_html_) of images in Jupyter Notebooks (thanks to @tlambert03 for feedback and pointers in the right direction)

Added new functions for which numpy counterparts exist * square_root and alias sqrt * cubic_root and alias cbrt * modulo_images and aliases mod and remainder * nan_to_num * reciprocal * sign * clip * square * array_equal and alias array_equiv

Added aliases to existing functions to improve numpy interoperability * exp alias for exponential * fabs alias for absolute * logical_and alias for binary_and * logical_or alias for binary_or * logical_xor alias for binary_xor * logical_not alias for binary_not * log alias for logarithm * maximum alias for maximum_images * minimum alias for minimum_images

Bug fixes * Detect minima/maxima missed minima/maxima at image borders (thanks to @StRigaud for reporting this issue)

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Published by haesleinhuepf almost 4 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.17.3

Bug fixes * Output shape of deskew was not rounded correctly (thanks to @pr4deepr for reporting and fixing) * Exception fixed in slicing operations / special cases

- Jupyter Notebook
Published by haesleinhuepf almost 4 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.17.2

See https://github.com/clEsperanto/pyclesperantoprototype/blob/master/docs/releasenotes.md#0172---may-7th-2022

Contributors: @psobolewskiPhD

- Jupyter Notebook
Published by haesleinhuepf about 4 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.17.1

See https://github.com/clEsperanto/pyclesperantoprototype/blob/master/docs/releasenotes.md#0171---may-1st-2022

- Jupyter Notebook
Published by haesleinhuepf about 4 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.17.0

See https://github.com/clEsperanto/pyclesperantoprototype/blob/master/docs/releasenotes.md#0170---april-30th-2022

Contributors: @tlambert03 @pr4deepr

- Jupyter Notebook
Published by haesleinhuepf about 4 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.16.0

See https://github.com/clEsperanto/pyclesperantoprototype/blob/master/docs/releasenotes.md#0160---march-16th-2022

Contributors: @DrLachie

- Jupyter Notebook
Published by haesleinhuepf about 4 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.15.5

Bugfixes: * Deskewing produced wrong results in case voxelsizez was != 0.3. This release contains a temporary workaround for fixing this. The workaround leads to higher memory consumption, longer compute time and tiny interpolation artefacts. A future release will fix those issues. (Thanks to @DrLachie for reporting and also for demonstrating the potential workaround!)

- Jupyter Notebook
Published by haesleinhuepf about 4 years ago

https://github.com/clesperanto/pyclesperanto_prototype - 0.15.4

See https://github.com/clEsperanto/pyclesperantoprototype/blob/master/docs/releasenotes.md#0154---february-20th-2022

Thanks to the contributors: * @psobolewskiPhD