localization_cp_files

Reliability status: development

Copy and rename files based on folder names

usage: localization_cp_files [-h] --files FILES [FILES ...]
                             --destination_folder DESTINATION_FOLDER

Named Arguments

--files: List of files to copy (will be expanded by shell)
--destination_folder: Destination folder path

Why ?

At the moment the localization files form multiple ROIs have the same name. Thus we cannot copy them onto the same folder to merge.

This script copies the files to a destination folder while renaming them to include the unique folder name from their original path.

Usage Examples

Basic usage with shell wildcard expansion:

localization_cp_files --files /path/to/*/data/file.dat --destination_folder /output/path

For instance:

localization_cp_files --files /home/marcnol/grey/ProcessedData_2024/Experiment_76_David_DNAFISH_HiM_HRKit_G1E_20240711/*/localize_3d/data/localizations_3D_barcode.dat --destination_folder .

With explicit file list:

localization_cp_files --files /path/to/001/data/file.dat /path/to/002/data/file.dat --destination_folder /output/path

Notes

The script automatically detects which part of the path varies (usually a folder number)
Original file metadata (timestamps, permissions) is preserved
Destination folder is created if it doesn’t exist