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)
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)
