#!/usr/bin/env python3
"""
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]
"""
import shutil
import tifffile
import numpy as np
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.img_tools import reverse_reorient_axes
from unravel.core.img_io import load_3D_img
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 dir with the .tif files to copy or path to a 3D image', 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')
opts.add_argument('-td', '--target_dir', help='path/target_dir to copy TIF files to. Default: current dir', action=SM)
opts.add_argument('-c', '--channel', help='.czi channel number (if this is the input image type). Default: 1 (i.e., the 2nd channel)', default=1, type=int, metavar='')
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()
[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:
input_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()
if input_path.is_dir() and any(input_path.glob("*.tif")):
copy_specific_tifs(sample_path, input_path, target_dir, args.slices, args.verbose)
else:
# Load the image, extract the specified slices, and save them to the target directory
matches = sorted(Path(sample_path).glob(args.input))
if not matches:
raise FileNotFoundError(f"No files matching '{args.input}' found in {sample_path}")
image_path = matches[0] # Use the first match after sorting
if args.verbose:
print(f" Using {image_path} as the input image.")
img = load_3D_img(image_path, channel=args.channel, verbose=args.verbose)
# Validate the slice indices
try:
slices = [int(slice_number) for slice_number in args.slices]
except ValueError:
raise ValueError("Slice numbers must be integers.")
if any(slice_idx >= img.shape[2] or slice_idx < 0 for slice_idx in slices):
raise ValueError(
f"Invalid slice index. Valid range is 0 to {img.shape[2] - 1}. "
f"Provided slices: {args.slices}"
)
Path(target_dir).mkdir(exist_ok=True, parents=True)
for slice_number in slices:
slice_img = img[:, :, int(slice_number)] # Access the z slice
# Reorient the slice to account for the xyz axis order change
slice_img = reverse_reorient_axes(slice_img)
slice_path = target_dir / f"{Path(sample_path).stem}_{slice_number:04d}.tif"
tifffile.imwrite(str(slice_path), slice_img)
if args.verbose:
print(f" Saved {slice_path}")
progress.update(task_id, advance=1)
verbose_end_msg()
if __name__ == '__main__':
main()