b-heifets/UNRAVEL: v1.0.0-beta.8

Summary of Changes

New Features:

• New Scripts:
  • filter_csv.py: Allows filtering of a CSV file by a specified column based on a list of values (useful for filtering out data from one hemisphere).
  • gubra_to_CCF_50um.py and gubra_to_CCF.py: For warping from Gubra space to CCF space.
  • points_compressor.py: Compresses coordinate points per region and can output a regional summary.
  • points_to_atlas.py: Warps a point coordinate image to atlas space.
  • resample_points.py: esampling points and saving them as NIfTI images.
  • points_to_img.py: Converts point data into images for visualization.
  • img_to_points.py: Converts images back into point data for further analysis.

Updates and Improvements:

• Script and Function Updates:

  • Converted generators to lists to handle scenarios where no files match, and the script needs to iterate over the list of matched files.
  • Added an option to move files instead of copying them.
  • Refactored functions to work with a DataFrame instead of ndarray for point data.
  • Corrected handling of single float values for current_res and target_res in the resample_and_convert_points function.
  • Fixed logic for saving output and determining whether to use the -o option.
  • Improved the code for updating the affine matrix to avoid affecting the origin and refactored resample_nii() to reduce parameters.

• Documentation:

  • Slicer 3D installation link and functions of dependencies are now mentioned.
  • Updated the installation guide and terminal cheat sheet, adding new video links for beginners.
  • Fixed multiple Sphinx warnings by updating docstrings and removing problematic parameters like *args and **kwargs.
  • Added __doc__ to epilog and improved the clarity of argument descriptions.

• Configuration and Dependency Management:

  • Fixed the default path for the -fri option.
  • Pinned Python version to 3.11 in GitHub Actions due to compatibility issues with distutils in Python 3.12.
  • Updated command names starting with cluster_ to cstats_ for consistency with vstats and rstats commands.

• Bug Fixes:

  • Fixed a warning related to plotting bar graphs.
  • Resolved issues when using small terminal windows with nargs='+' and action=SM.
  • Corrected typos and addressed minor bugs in the handling of command options and argument processing.

These changes introduce new functionality, improve existing scripts, and address bugs.