Auto masking tool

[OliDG]

Tool to automatically generate a mask based on the darkest portion of the image. Quite straightforward, to skip the manual definition of a mask, much faster to apply to different DP as it compensates for possible beam stopper movement (image rotation during acquisition or beam stopper mechanical play). In addition. it cuts out much closer to the beam stopper, keeping in valuable information for the autocenter() operation.

• Fixes Issue: no need for manual mask definition to remove the beam stopper.
• [function to automatically generate a mask from an image] CHANGELOG.rst updated.
• Changes Proposed by this Pull Request: auto_center function can require a mask. This function add an automated generation of a mask from any image, will precisely cut out the beam stopper and spare valuable information from its immediate surrounding. The mask is based on the 10% darkest values as default but can be adjusted (optionally). The tutorial section was updated and tested.

[LaurentRDC]

Hi Olivier,

Very cool, thanks for your contribution.

Before I merge, could you:

• Add at least one unit test? It can be very simple, trivial even;
• Make sure to run the black code formatter, which is causing the lint job to fail.

If you are not used to black, you can install it as follows:

pip install -r dev-requirements.txt
black .

[OliDG]

Thanks. :) I ran "black" earlier but modified further, now it should be Ok. How do I properly update the current merge request? shall I simply push the changes to my fork?

What is a unit test? I ran the pytest as requested:

pytest scikit-ued
=================================================================== test session starts ====================================================================
platform win32 -- Python 3.11.7, pytest-8.2.2, pluggy-1.5.0
rootdir: C:\Users\oldo\scikit-ued
plugins: anyio-4.2.0
collected 569 items

scikit-ued\skued\baseline\tests\test_algorithms.py ...........                                                                                        [  1%]
scikit-ued\skued\baseline\tests\test_dtcwt.py ....................................................................................................... [ 20%]
.............................................................................................................................                         [ 42%]
scikit-ued\skued\image\tests\test_alignment.py .......                                                                                                [ 43%]
scikit-ued\skued\image\tests\test_brillouin.py .                                                                                                      [ 43%]
scikit-ued\skued\image\tests\test_calibration.py .....                                                                                                [ 44%]
scikit-ued\skued\image\tests\test_center.py ......................................................................................................... [ 62%]
.............................................                                                                                                         [ 70%]
scikit-ued\skued\image\tests\test_indexing.py ..                                                                                                      [ 71%]
scikit-ued\skued\image\tests\test_indexing_persistence.py ..                                                                                          [ 71%]
scikit-ued\skued\image\tests\test_metrics.py ...................                                                                                      [ 74%]
scikit-ued\skued\image\tests\test_powder.py ......                                                                                                    [ 75%]
scikit-ued\skued\image\tests\test_symmetry.py ...............                                                                                         [ 78%]
scikit-ued\skued\io\tests\test_io.py .........                                                                                                        [ 79%]
scikit-ued\skued\simulation\tests\test_kinematic.py ....                                                                                              [ 80%]
scikit-ued\skued\simulation\tests\test_potential.py ...                                                                                               [ 81%]
scikit-ued\skued\simulation\tests\test_powdersim.py ..                                                                                                [ 81%]
scikit-ued\skued\simulation\tests\test_structure_factors.py .....                                                                                     [ 82%]
scikit-ued\skued\tests\test_affine.py .................                                                                                               [ 85%]
scikit-ued\skued\tests\test_array_utils.py .............                                                                                              [ 87%]
scikit-ued\skued\tests\test_eproperties.py ........                                                                                                   [ 89%]
scikit-ued\skued\tests\test_patterson.py .                                                                                                            [ 89%]
scikit-ued\skued\tests\test_plot_utils.py ........                                                                                                    [ 90%]
scikit-ued\skued\tests\test_potential_map.py ......                                                                                                   [ 91%]
scikit-ued\skued\tests\test_thin_films.py ..                                                                                                          [ 92%]
scikit-ued\skued\tests\test_voigt.py ..........                                                                                                       [ 93%]
scikit-ued\skued\time_series\tests\test_fitting.py ...........                                                                                        [ 95%]
scikit-ued\skued\time_series\tests\test_nfft.py ...                                                                                                   [ 96%]
scikit-ued\skued\time_series\tests\test_robust.py ....                                                                                                [ 97%]
scikit-ued\skued\time_series\tests\test_selections.py ..........                                                                                      [ 98%]
scikit-ued\skued\time_series\tests\test_time_zero.py .......                                                                                          [100%]

=================================================================== 569 passed in 36.15s ===================================================================

[LaurentRDC]

I will add a unit test once I merge the branch then, don't worry about it.

For your information, unit tests are small, self-contained tests like this one.

[LaurentRDC]

Thank you for your contribution! I will create a new release today

[LaurentRDC]

Your contribution has been released in version 2.1.17