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Topp-Roots-Lab / 3d-root-crown-analysis-pipeline

A pipeline to process 3-D volumes (.raw) of maize root crowns. Also known as XRCAP.
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Filepaths with spaces not handled when calling MATLAB module #31

Closed tparkerd closed 3 years ago

tparkerd commented 3 years ago

https://github.com/Topp-Roots-Lab/3d-root-crown-analysis-pipeline/blob/0d5c5284dc36ca6f221d5e6069901bd0f3ca6a6d/xrcap/rootCrownImageAnalysis3D.py#L276

Change it to:

biomass_hist, convexhull_hist = asyncio.run(process_kde_with_matlab(f"kde-traits '{os.path.join(fp, subfolder)}' {thickness} {args.sampling}"))

This will also prevent any variable expansions in filepaths.