from pathlib import Path from importlib import import_module ROOT_PATH = Path(__file__ + "/..").resolve() sys.path.append(str(ROOT_PATH)) from common.docopt import docopt from common.version import get_version from common.output import colorize import re from schema import Schema, And, Or, Use, SchemaError, Optional, Regex arguments = docopt(__doc__, version=get_version()) schema = Schema({ 'PROCESSOR': And(len, lambda n: (ROOT_PATH / ('preprocessors/' + str(n) + '.py')).is_file(), error='That preprocessor does not exist'), 'INPUT': And(len, lambda n: os.path.exists(n), error='That folder does not exist'), '--output-dir': len, '--output-name': len, '--img-dir': Or(None, len), '--mip-dir': Or(None, len), '--data-dir': Or(None, len), '--filter-window': And(Use(int), lambda n: n > 0, error='--filter-window must be > 0'), '--gamma': And(Use(float), lambda n: n > 0, error='--gamma must be > 0'), '--channel': And(Use(int), lambda n: n > 0), '--data-set': Or(None, len), '--pixel-size': And(Use(float), lambda n: n >= 0, error='--pixel-size must be > 0'), '--rolling-ball-size': And(Use(int), lambda n: n > 0),
def main(): arguments = docopt(__doc__, version=__version__) server = 'http://home.nabla.mobi:8381/' get_jenkins_jobs(server)
OUTPUT Where the Tiff files should be saved """ import sys import os from common.docopt import docopt from ij import IJ from ij import ImagePlus from ij import ImageStack from ij import CompositeImage from ij.io import FileSaver import glob arguments = docopt(__doc__, version='NER 0.1') input_file = arguments['INPUT'] output_dir = arguments['OUTPUT'] img = IJ.openImage(input_file) dims = img.getDimensions() width = dims[0] height = dims[1] num_channels = dims[2] num_frames = dims[4] # If it's the T index if num_frames == 1: num_frames = dims[3] # If it's the Z index img.setDimensions(num_channels, 1, num_frames)