Remove file extensions from fovs in generate_cell_data #311
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Verified that this passes wtih |
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Looks good. I think it makes sense to hold off on integrating this until the jupyter notebook testing is up and running. Partly to give the high school students more time, and also because of all the different possible permutations of mibi-tiffs, multiple channels, etc, that aren't currently tested
| print(f"These files still have \".\" in them after file extension removal: " | ||
| f"{','.join(bad_names)}, " | ||
| f"please double check that these are the correct names") | ||
| warnings.warn("remaining periods in file names") |
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Why have both a print statement and a warning? Does one not show up in certain locations?
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warnings.warn doesn't actually print the desired warning message, only provides something that you can catch and do something with. I didn't know if we were planning to write code to explicitly catch these in the future, so I left them in.
You're right, though: we need to stick to one or the other. I should open an issue that addresses these inconsistencies. My opinion is that we should drop warnings.warn and simply do print statements. Normally, I would go the other route, but these functions that throw warnings are mostly used directly in the notebooks, and we don't want to handle the warnings in the notebooks themselves.
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The functionality in this branch has moved over to #318, closing. |
What is the purpose of this PR?
Addresses and closes #303. As it stands, the user cannot specify fovs with file extensions in
generate_cell_data. This PR will fix that.How did you implement your changes
We simply remove the file extensions as a precaution before running the rest of
generate_cell_data. Because we're seeing this functionality being used in several places, we'll branch this off fromextract_delimited_namesinto a separate function. By extension, this means we'll need to update the places in the repo where we call this.