Cell Scan Converter

cell-scan-conv.py

#!/usr/bin/env python
"""
cell-scan-conv.py - A simple script to mass convert images while keeping only
                    some of the RGB channels to make cells more visible on cell
                    scans. Please note that ImageMagick's convert command needs
                    to be installed and in your $PATH.

Copyright (c) 2015, Jan Holthuis
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this
   list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its contributors
   may be used to endorse or promote products derived from this software
   without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
"""
import logging
import sys
import os
import subprocess
import multiprocessing
import distutils.spawn
import argparse

IM_CONVERT_EXE = distutils.spawn.find_executable('convert')
if IM_CONVERT_EXE is None:
    print('ERROR: ImageMagick convert not found')
    sys.exit(1)

CHANNEL_RED = 1    # 0000 0001
CHANNEL_GREEN = 2  # 0000 0010
CHANNEL_BLUE = 4   # 0000 0100


def copy_image_channels_to_img(src, dst, channels):
    removed_channels = []
    if not channels & CHANNEL_RED:
        removed_channels.append('Red')
    if not channels & CHANNEL_GREEN:
        removed_channels.append('Green')
    if not channels & CHANNEL_BLUE:
        removed_channels.append('Blue')
    kept_channels = list(set(['Red', 'Green', 'Blue']) - set(removed_channels))

    logger = logging.getLogger(__name__)
    if not kept_channels:
        logger.error('Removing all channels from "%s" would result in a' +
                     'black image. Conversion canceled.', src)
        return -1

    cmd = [IM_CONVERT_EXE, src]
    if removed_channels:
        cmd.extend(['-channel', ','.join(removed_channels),
                    '-evaluate', 'set', '0'])
    cmd.append(dst)
    status = subprocess.call(cmd)
    if status != 0:
        logger.error('Copying "%s" to "%s" while keeping channels {%s} ' +
                     'failed with status "%d"', src, dst,
                     ', '.join(kept_channels), status)
    else:
        logger.info('Successfully copied "%s" to "%s" while keeping ' +
                    'channels {%s}!', src, dst, ', '.join(kept_channels))


def make_channeldesc(channels):
    channeldesc = ''
    if channels & CHANNEL_RED:
        channeldesc += 'R'
    if channels & CHANNEL_GREEN:
        channeldesc += 'G'
    if channels & CHANNEL_BLUE:
        channeldesc += 'B'
    return channeldesc


def process_image(filepath):
    path = os.path.dirname(filepath)
    base = os.path.splitext(os.path.basename(filepath))[0]

    for channels in [CHANNEL_BLUE,
                     CHANNEL_BLUE | CHANNEL_RED,
                     CHANNEL_BLUE | CHANNEL_GREEN]:
        dst = os.path.join(path,
                           "%s_%s.tif" % (base, make_channeldesc(channels)))
        copy_image_channels_to_img(filepath, dst, channels)


def gather_files(input_directory):
    logger = logging.getLogger(__name__)
    gathered_files = []
    for directory, dirs, files in os.walk(input_directory):
        logger.info('Gathering files in "%s"...', directory)
        for filename in files:
            if filename.lower().endswith('.tif'):
                gathered_files.append(os.path.join(directory, filename))
    logger.info('Gathered %d files for processing.', len(gathered_files))
    return gathered_files


def process_directory(directory, num_processes=4):
    logger = logging.getLogger(__name__)
    # First we gather the files
    files = gather_files(directory)
    num_files = len(files)

    if num_files > 0:
        num_chars = len(str(num_files))

        # Setting up the multiprocessing pool
        pool = multiprocessing.Pool(processes=num_processes)

        # Now let's process them
        for i, filename in enumerate(files):
            pool.apply(process_image, args=(filename,))
            logger.info('Processing %s/%d: %s',
                        str(i+1).zfill(num_chars),
                        num_files,
                        filename)
    logger.info('Done.')


if __name__ == "__main__":
    logging.basicConfig(level=logging.INFO)

    parser = argparse.ArgumentParser(
        prog='cell-scan-conv.py',
        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
    parser.add_argument('-j', type=int, default=4, metavar='num_processes',
                        help='Number of processes to use')
    parser.add_argument('directory', help='The directory to scan for files')
    args = parser.parse_args()
    process_directory(directory=args.directory, num_processes=args.j)