When trying to run segmentation, an error propped up where a mask file that didn't exist was being loaded for csv writing. After troubleshooting, the problem occurs in marker_quantification.process_lists code. In this example, while only file names with 'R6C1' were desired, files with R6C10' were also being extracted due to the way marker_quantification.process_lists matches substrings in file names. Similar to list_files issue in alpineer.
Expected behavior
marker_quantification.process_lists currently finds files using the code below based on a matching file prefix. Instead of returning "whole_cell" and "nuclear", the returned list is "_whole_cell", "0_whole_cell", etc.
To Reproduce
Ping me for access to my mask files.
Proposed solution:
Similar to the list_files and list_folders fix in alpineer, token matching will be used instead of string subsetting to find matching files (code pic below)
Describe the bug
When trying to run segmentation, an error propped up where a mask file that didn't exist was being loaded for csv writing. After troubleshooting, the problem occurs in
marker_quantification.process_listscode. In this example, while only file names with 'R6C1' were desired, files with R6C10' were also being extracted due to the waymarker_quantification.process_listsmatches substrings in file names. Similar to list_files issue in alpineer.Expected behavior
marker_quantification.process_listscurrently finds files using the code below based on a matching file prefix. Instead of returning "whole_cell" and "nuclear", the returned list is "_whole_cell", "0_whole_cell", etc.To Reproduce Ping me for access to my mask files.
Proposed solution: Similar to the list_files and list_folders fix in alpineer, token matching will be used instead of string subsetting to find matching files (code pic below)