[EXPERIMENTAL]: Integrate cp-measure

[timtreis]

Associated notebook: https://github.com/scverse/squidpy_notebooks/blob/add_cpmeasure_notebook/tutorials/tutorial_cpmeasure.ipynb

[timtreis]

Note to self:

• Doesn't correctly parse str names of channels
  INFO Calculating 'cpmeasure' correlation features between channels '0' and '1'.

• Should show, for permutations, the total number of iterations (in general, the progress bar should contain a (step n out m) readout so one can know how far in the featurisation is. Can easily take more than a day given the amount of cells and cpu_cores. Should also maybe show the total runtime so far for the steps that are done

• Fails if labels and image don't have the same dimensions, despite transformation to align them

[pakiessling]

Tried it out and it worked very well!

One quality of life feature would be the ability to specify channels that should be measured.

Often times there are channels that are not informative / used only for segmentation and those slow down the calculations.

[pakiessling]

Ah I noticed another thing.

For the created morphology table .uns["spatialdata_attrs"] needs to be set, otherwise this runs into problem when querying the Spatialdata afterwards.

[codecov]

Codecov Report

❌ Patch coverage is 51.54185% with 220 lines in your changes missing coverage. Please review.
✅ Project coverage is 65.34%. Comparing base (f976fb0) to head (8da641b).

Files with missing lines	Patch %	Lines
src/squidpy/experimental/im/_feature.py	51.54%	185 Missing and 35 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #982      +/-   ##
==========================================
- Coverage   66.21%   65.34%   -0.88%     
==========================================
  Files          44       45       +1     
  Lines        7163     7617     +454     
  Branches     1217     1330     +113     
==========================================
+ Hits         4743     4977     +234     
- Misses       1943     2128     +185     
- Partials      477      512      +35     

Files with missing lines	Coverage Δ
src/squidpy/experimental/im/_feature.py	51.54% <51.54%> (ø)

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[LucaMarconato]

Looking forward to this PR 👀🥸