Which yabplot version is compatible with `automate_create_meshes_and_SVGs.py`?

[RuiHe1999]

Hi,

I am trying to use the semi-automated atlas pipeline in subcortex_visualization. The mesh-generation step appears to work correctly. The script successfully parses the lookup table and saves the meshes. However, the script fails during the SVG-generation step when calling plot_subcortical():

TypeError: plot_subcortical() got an unexpected keyword argument 'plot_regions_separately'

The relevant call in automate_create_meshes_and_SVGs.py is:

plot_subcortical(
    custom_atlas_path=mesh_path,
    views=views,
    cmap=cmap,
    figsize=figsize,
    bmesh_alpha=bmesh_alpha,
    style=style,
    zoom=zoom,
    plot_regions_separately=True,
    export_path=export_path
)

I am using yabplot==0.5.0. In this version, plot_subcortical() does not seem to have the argument plot_regions_separately. Also, yabplot.plotting does not seem to expose get_base_name, although the pipeline imports it with: from yabplot.plotting import get_base_name, plot_subcortical.

I also tried checking other available yabplot versions, but I could not find one where both get_base_name and plot_regions_separately are available.

Could you let me know which yabplot version was used when this pipeline was developed/tested? Alternatively, should the pipeline now be updated to work with the current yabplot API?

Thank you very much in advance!

[anniegbryant]

Hi Rui, thank you for checking out this package and for providing this really helpful issue report! 😊

As it happens, I introduced a couple tweaks to my own forked version of yabplot to work with the semi-automated pipeline in subcortex_visualization (including the two helper functions quoted in your issue). My apologies for that oversight, in the flurry of responding to reviewers for the associated manuscript, this slipped my mind.

I've opened one PR with the yabplot package so far and working on the second one, with the hope of incorporating this functionality into yabplot directly so there's bi-directional compatibility between our packages.

In the meantime, you are welcome to use my forked version of the yabplot package that includes the added feature patches to work for the semi-automated workflow of subcortex_visualization: https://github.com/anniegbryant/yabplot/tree/feature/subcortical-new-params
(Note: please ensure you refer to the specific branch linked above, called subcortical-new-params, as this contains the plot_regions_separately and get_base_regions functions while the main branch does not).

I hope that's helpful for the time being, and please do let me know if any other issues come up. I'll ping you back here with any updates to share from the PR(s) at yabplot.

All the best,
Annie