#!/usr/bin/env python3
"""
Use ``seg_copy_tifs`` from UNRAVEL to copy specified TIFFs from each sample?? to a target dir for training ilastik.
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 prep for seg_ilastik:
------------------------------
seg_copy_tifs -i <raw_tif_dir> -s 0100 0500 1000 [-td ilastik_segmentation] [-d list of paths] [-p sample??] [-v]
"""
import shutil
from glob import glob
from pathlib import Path
from rich import print
from rich.live import Live
from rich.traceback import install
from unravel.core.help_formatter import RichArgumentParser, SuppressMetavar, SM
from unravel.core.config import Configuration
from unravel.core.utils import log_command, verbose_start_msg, verbose_end_msg, initialize_progress_bar, get_samples
[docs]
def parse_args():
parser = RichArgumentParser(formatter_class=SuppressMetavar, add_help=False, docstring=__doc__)
reqs = parser.add_argument_group('Required arguments')
reqs.add_argument('-i', '--input', help='Path to input tifs relative to sample??/', required=True, action=SM)
reqs.add_argument('-s', '--slices', help='List of slice numbers to copy (4 digits each; space separated)', nargs='*', type=str, required=True, action=SM)
opts = parser.add_argument_group('Optional arguments')
reqs.add_argument('-td', '--target_dir', help='path/target_dir to copy TIF files to. Default: current dir', action=SM)
general = parser.add_argument_group('General arguments')
general.add_argument('-d', '--dirs', help='Paths to sample?? dirs and/or dirs containing them (space-separated) for batch processing. Default: current dir', nargs='*', default=None, action=SM)
general.add_argument('-p', '--pattern', help='Pattern for directories to process. Default: sample??', default='sample??', action=SM)
general.add_argument('-v', '--verbose', help='Increase verbosity. Default: False', action='store_true', default=False)
return parser.parse_args()
# TODO: Currently this just copies tif files from the source directory to the target directory. Adapt it so that if an input directory does not exist, it loads an image from the source directory and extracts the specified slices from it. These slices should then be saved to the target directory.
[docs]
def 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_path : Path or str
Path to the sample directory (appended to the destination file name).
source_dir : Path or str
Path to the source directory containing the .tif files.
target_dir : Path or str
Path to the target directory where the selected slices will be copied.
slice_numbers : list
List of slice numbers to copy (4 digits each).
verbose : bool
Print verbose output.
"""
tif_files = list(source_dir.glob('*.tif'))
if not tif_files:
print(f"\n [red1]No .tif files found in {source_dir}\n")
return
Path(target_dir).mkdir(exist_ok=True, parents=True)
for file_path in Path(source_dir).glob('*.tif'):
if any(file_path.stem.endswith(f"{slice:04}") for slice in map(int, slice_numbers)):
dest_file = Path(target_dir) / f'{Path(sample_path).name}_{file_path.name}'
shutil.copy(file_path, dest_file)
if verbose:
print(f" Copied {file_path} to {dest_file}")
[docs]
@log_command
def main():
install()
args = parse_args()
Configuration.verbose = args.verbose
verbose_start_msg()
sample_paths = get_samples(args.dirs, args.pattern, args.verbose)
progress, task_id = initialize_progress_bar(len(sample_paths), "[red]Processing samples...")
with Live(progress):
for sample_path in sample_paths:
source_path = Path(sample_path) / args.input # Path to dir w/ the .tif files to copy
target_dir = Path(args.target_dir).resolve() if args.target_dir else Path.cwd()
copy_specific_tifs(sample_path, source_path, target_dir, args.slices, args.verbose)
progress.update(task_id, advance=1)
verbose_end_msg()
if __name__ == '__main__':
main()