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remove_file_extensions is more robust to various fov naming schemes #577

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merged 7 commits into from
Jun 3, 2022

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srivarra
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@srivarra srivarra commented May 31, 2022

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What is the purpose of this PR?

Closes #537.

Allows more complex fov name parsing in remove_file_extensions.
Removes the extensions correctly for files named such as:

"fov.1" -> "fov.1"
"fov.2.tiff" -> "fov.2"
"fov3" -> "fov3"
"fov4.tar.gz" -> "fov4.tar"

How did you implement your changes

Added explicit checks for the following file extensions:

"tiff", "tif", "png", "jpg", "jpeg", "tar", "gz", "csv", "feather".

Added an extra test for more complicated fov filenames.

Remaining issues

Should we account for more file extensions?

@srivarra srivarra self-assigned this May 31, 2022
@srivarra srivarra requested a review from ngreenwald May 31, 2022 23:17
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Not sure why coverage is dropping, can you see if this is real or an artifact?

@srivarra srivarra requested a review from ngreenwald June 2, 2022 02:04
@ngreenwald ngreenwald merged commit daf0104 into master Jun 3, 2022
@ngreenwald ngreenwald deleted the fov_name_parsing_fix branch June 3, 2022 04:52
@srivarra srivarra added the bug Something isn't working label Jun 15, 2022
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create_deepcell_output fails if FOV names with . specified
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