Connectivity: compute_matrices script

[EmmaRenauld]

Refactored the scil_connectivity_compute_matrices.py script:

• Took out the main computation part and put it in connectivity.connectivity file
• (also renamed connectivity.connectivity_tools to connectivity.matrix_too0ls)
• Clarified the docstring
  • Note that I already mention the scil_connectivity_compute_simple_matrix.py, which does not exist, but in the end I think that this PR is big enough. Will add it soon in another PR.
  • Please help me describe the --similarity option better.
• Removed the --maps option, as discussed with François and Arnaud offline.
• Removed one buggy logging.info: the -len(label_list) could end up in a negative number of total_elem if some diagonal values were not found.

• Now all headers compatibility are done before loading (except for the --similarity folder)

In short, the code is simplified a lot, but the result should be exactly the same, if you want to test with some data!

[codecov]

Codecov Report

Attention: Patch coverage is 62.03704% with 82 lines in your changes missing coverage. Please review.

Project coverage is 68.99%. Comparing base (546f1a9) to head (a112c4f).
Report is 12 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1031      +/-   ##
==========================================
+ Coverage   68.89%   68.99%   +0.09%     
==========================================
  Files         434      435       +1     
  Lines       22646    22662      +16     
  Branches     3078     3077       -1     
==========================================
+ Hits        15603    15635      +32     
+ Misses       5727     5710      -17     
- Partials     1316     1317       +1     

Components	Coverage Δ
Scripts	69.91% <72.64%> (+0.29%)	⬆️
Library	67.72% <49.49%> (-0.18%)	⬇️

[frheault]

I used the new script on older data to compare before vs after.

My command was scil_connectivity_compute_matrices.py Transform_Data/sub-001_ses-1__decompose_warped_mni.h5 Transform_Data/sub-001_ses-1__labels_warped_mni_int16.nii.gz --volume vol.npy --streamline_count sc.npy --length len.npy --metrics Transform_Metrics/sub-001_ses-1__fa_mni.nii.gz fa.npy --include_dps dps -f (works with the master)

This is my error:

Traceback (most recent call last):
  File "/home/rhef1902/VirtualEnvs/basic_scilpy_3_10/bin/scil_connectivity_compute_matrices.py", line 33, in <module>
    sys.exit(load_entry_point('scilpy', 'console_scripts', 'scil_connectivity_compute_matrices.py')())
  File "/home/rhef1902/Libraries/scilpy/scripts/scil_connectivity_compute_matrices.py", line 260, in main
    outputs.append(compute_connectivity_matrices_from_hdf5(
  File "/home/rhef1902/Libraries/scilpy/scilpy/connectivity/connectivity.py", line 188, in compute_connectivity_matrices_from_hdf5
    for dps_key in hdf5_file[key].keys():
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "/home/rhef1902/VirtualEnvs/basic_scilpy_3_10/lib/python3.10/site-packages/h5py/_hl/group.py", line 357, in __getitem__
    oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5o.pyx", line 189, in h5py.h5o.open
KeyError: 'Unable to synchronously open object (invalid identifier type to function)'

I am one Python 3.10.12 (and I got the same error in Python 3.11.6)

[EmmaRenauld]

I used the new script on older data to compare before vs after.

Could you please send me your data? Thanks!