crop_ome_tiff.py

import pytiff
import skimage.io

try:
    import pathlib
except ImportError:
    import pathlib2 as pathlib
import argparse
import warnings
import sys

parser = argparse.ArgumentParser(
    description='Crop a pyramidal OME-TIFF with supplied starting and ending row and starting and ending column'
)
parser.add_argument(
    'input_filepath', metavar='ASHLAR_OMETIFF',
    help='A OME-TIFF generated by ashlar'
)
parser.add_argument(
    'start_row', metavar='START_ROW',
    help='Starting row, starts from zero, this row is included'
)
parser.add_argument(
    'end_row', metavar='END_ROW',
    help='Ending row, this row is not included'
)
parser.add_argument(
    'start_column', metavar='START_COLUMN',
    help='Starting column, starts from zero, this column is included'
)
parser.add_argument(
    'end_column', metavar='END_COLUMN',
    help='Ending column, this column is not included'
)
parser.add_argument(
    'output_filepath', metavar='OUTPUT_FILEPATH',
    help='Conmplete output filepath, must ends with .ome.tif'
)
args = parser.parse_args()

input_filepath = pathlib.Path(args.input_filepath)
output_filepath = pathlib.Path(args.output_filepath)
if output_filepath.exists:
    output_filepath.unlink()
tiff = pytiff.Tiff(str(input_filepath))

print('{} -> {}'.format(input_filepath.name, output_filepath.name))

page = 0
tiff.set_page(page)
size = tiff.size

while tiff.size == size:
    cropped = tiff[
        int(args.start_row):int(args.end_row), 
        int(args.start_column):int(args.end_column)
    ]
    sys.stdout.write('\rsaving page {}'.format(page))
    sys.stdout.flush()
    with warnings.catch_warnings():
        warnings.filterwarnings(
            'ignore', r'.* is a low contrast image', UserWarning,
            '^skimage\.io'
        )
        skimage.io.imsave(
            str(output_filepath), cropped, bigtiff=True, 
            photometric='minisblack', metadata=None, append=True
        )
    page += 1
    tiff.set_page(page)