unravel.segment.copy_tifs module

Use seg_copy_tifs (sct) from UNRAVEL to copy or save specified slices from each sample?? dir to a target dir for training ilastik with TIFFs.

Note

• reg_inputs/autofl_50um_tifs is from reg_prep and is used to make a brain mask using seg_brain_mask.

Next command:

seg_brain_mask for reg or seg_ilastik for pixel classification.

Usage to prep for seg_brain_mask:

seg_copy_tifs -i reg_inputs/autofl_50um_tifs -s 0000 0005 0050 [-td brain_mask] [-d list of paths] [-p sample??] [-v]

Usage to copy tifs for ilastik:

seg_copy_tifs -i <path to dir with tifs or to a 3D image> -s 0100 0500 1000 [-td ilastik_segmentation] [-d list of paths] [-p sample??] [-v]

unravel.segment.copy_tifs.parse_args()

unravel.segment.copy_tifs.copy_specific_tifs(sample_path, source_dir, target_dir, slice_numbers, verbose=False)

Copy the specified tif slices from the source directory to the target directory.

Parameters:

sample_pathPath or str

Path to the sample directory (appended to the destination file name).

source_dirPath or str

Path to the source directory containing the .tif files.

target_dirPath or str

Path to the target directory where the selected slices will be copied.

slice_numberslist

List of slice numbers to copy (4 digits each).

verbosebool

Print verbose output.

unravel.segment.copy_tifs.main()