Add exact pattern matching to list_files #333
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ngreenwald
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Nov 12, 2020
ngreenwald
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Nov 13, 2020
alex-l-kong
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Jan 14, 2021
* Add exact pattern matching to list_files and patch up load_imgs_from_tree bug * Change extensions to is_extensions to make argument clearer * Change extensions to is_extensions in io_utils_test * Change from is_extensions to exact_match * Documentation fix
y2kbugger
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Jul 29, 2021
* Add exact pattern matching to list_files and patch up load_imgs_from_tree bug * Change extensions to is_extensions to make argument clearer * Change extensions to is_extensions in io_utils_test * Change from is_extensions to exact_match * Documentation fix
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What is the purpose of this PR?
Addresses and closes #332. Our current substr matching scheme doesn't work if we pass in file names for exact matching (as opposed to file extensions, which we do most but not all of the time). This has caused problems when implementing FlowSOM preprocessing, so we patch this up.
How did you implement your changes
We add a control flag
extensionsinlist_fileswhich will handle both file extension generic matching and file name exact matching.We also patch up bugs in
load_imgs_from_treewhen the user passes in some channel names without file extensions and make the variable names more distinguished from each other.