RF - Input to volume stats scripts

[gabknight]

Quick description

Add new input features to

• scil_volume_stats_in_labels.py

  • in_map was replaced by the argument group Metrics input options, allowing for a list of metric filenames or a metric folder;
  • if the scripts as multiple input metrics, the output json file has a new top level dict metric;
  • add add_json_args and corresponding formatting to the output json;
  • this PR changes the interface of the script, i.e. it will break other scripts using it.

• scil_volume_stats_in_ROI.py

  • change the positional argument in_mask to in_rois, allowing for multiple input mask.
  • if the scripts as multiple input ROIs, the output json file has a new top level dict roi_name;

...

Type of change

Check the relevant options.

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

Provide data, screenshots, command line to test (if relevant)

...

Checklist

• My code follows the style guidelines of this project (run autopep8)
• I added relevant citations to scripts, modules and functions docstrings and descriptions
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I moved all functions from the script file (except the argparser and main) to scilpy modules
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes

[pep8speaks]

Hello @gabknight, Thank you for updating !

• In the file scripts/scil_volume_stats_in_ROI.py:

Line 79:80: E501 line too long (85 > 79 characters)

• In the file scripts/scil_volume_stats_in_labels.py:

Line 67:80: E501 line too long (85 > 79 characters)

Comment last updated at 2025-01-08 18:53:16 UTC

[codecov]

Codecov Report

Attention: Patch coverage is 69.49153% with 18 lines in your changes missing coverage. Please review.

Project coverage is 69.57%. Comparing base (4d2715b) to head (bd62183).
Report is 114 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1068      +/-   ##
==========================================
+ Coverage   69.41%   69.57%   +0.16%     
==========================================
  Files         447      448       +1     
  Lines       24046    24092      +46     
  Branches     3280     3295      +15     
==========================================
+ Hits        16691    16762      +71     
+ Misses       5960     5936      -24     
+ Partials     1395     1394       -1     

Components	Coverage Δ
Scripts	70.30% <69.49%> (+0.02%)	⬆️
Library	68.60% <ø> (+0.34%)	⬆️

[arnaudbore]

@gabknight I gave it a try and there are some errors when I use the metrics_dir.

[gabknight]

hmm, it seems the error was unrelated to this PR. Should have tested it though, thanks for checking.

Could you re-test now?

[EmmaRenauld]

Code seems ok! Small comment on the --help.

[EmmaRenauld]

(a binary mask), or (binary masks.)
(a weighting mask) or (weighting masks)

[EmmaRenauld]

weighting masks, they

[EmmaRenauld]

In the description above, can you change input map for input metric (s)?. Then, maybe something like "if more than one metric maps are provided, statistics are computed separately for each".