unravel.utilities.clean_tif_dirs module#

Use utils_clean_tifs (clean_tiffs) from UNRAVEL to clean directories w/ tif series.

Tif directory clean up involves:

  • Finding .tif or .ome.tif files in the tif directory

  • Moving subdirectories to parent dir

  • Moving non-TIF files to parent dir

  • Replacing spaces in TIF file names

Note

  • If -d is not provided, the current directory is used to search for sample?? dirs to process.

  • If the current dir is a sample?? dir, it will be processed.

  • If -d is provided, the specified dirs and/or dirs containing sample?? dirs will be processed.

  • If -p is not provided, the default pattern for dirs to process is ‘sample??’.

Usage:#

utils_clean_tifs -t <list of tif dir> –move [-d list of paths] [-p sample??] [-v]

unravel.utilities.clean_tif_dirs.parse_args()[source]#
unravel.utilities.clean_tif_dirs.clean_tifs_dir(path_to_tif_dir, move, verbose)[source]#
Clean up a directory containing TIF files:

  • Move subdirs to parent dir

  • Move non-TIF files to parent dir.

  • Replace spaces in TIF file names with underscores.

Parameters:

  • path_to_tif_dir (str) – Path to the directory containing the TIF files.

  • move (bool) – Enable moving of subdirs and non-TIF files to parent dir.

  • verbose (bool) – Increase verbosity.

unravel.utilities.clean_tif_dirs.main()[source]#