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Inconsistent seg_suffix causing error in pixel clustering notebook #842

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cliu72 opened this issue Nov 29, 2022 · 0 comments · Fixed by #848
Closed

Inconsistent seg_suffix causing error in pixel clustering notebook #842

cliu72 opened this issue Nov 29, 2022 · 0 comments · Fixed by #848
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@cliu72
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cliu72 commented Nov 29, 2022

Please refer to our FAQ and look at our known issues before opening a bug report.

Describe the bug
In the pixel clustering notebook, one of the user-specified parameters is seg_suffix = '_whole_cell.tiff' (which I changed to '_feature_0.tif' to test on some old datasets). The create_mantis_dir function has an argument seg_suffix_name, which is default to 'whole_cell', without the .tiff extension (https://github.com/angelolab/ark-analysis/blob/main/ark/utils/plot_utils.py#L392-L399). In the Pixie notebook, I tried to add seg_suffix_name = seg_suffix as an argument to create_mantix_dir. However, doing this currently throws an error because seg_suffix for the notebook requires .tif at the end, while seg_suffix_name does not require an extension

Expected behavior
Add seg_suffix_name=seg_suffix to the create_mantis_dir function in the pixel clustering notebook. I think it would probably be best to have seg_suffix_name in create_mantis_dir to require an extension, just in case people are using other image formats for their segmentation.

To Reproduce
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