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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Project: Fast Azimuthal integration
# https://github.com/kif/pyFAI
#
#
# Copyright (C) European Synchrotron Radiation Facility, Grenoble, France
#
# Authors: Jérôme Kieffer <Jerome.Kieffer@ESRF.eu>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
"""
pyFAI-average is a small utility that averages out a serie of files,
for example for dark, or flat or calibration images
"""
__author__ = "Jerome Kieffer, Picca Frédéric-Emmanuel"
__contact__ = "Jerome.Kieffer@ESRF.eu"
__license__ = "GPLv3+"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "29/09/2014"
__status__ = "production"
import os
import sys
import fabio
import logging
import pyFAI
import pyFAI.utils
try:
from argparse import ArgumentParser
except ImportError:
from pyFAI.argparse import ArgumentParser
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger("average")
def main():
usage = "usage: pyFAI-average [options] [options] -o output.edf file1.edf file2.edf ..."
version = "pyFAI-average version %s from %s" % (pyFAI.version, pyFAI.date)
description = """
This tool can be used to average out a set of dark current images using
mean or median filter (along the image stack). One can also reject outliers
be specifying a cutoff (remove cosmic rays / zingers from dark)
"""
epilog = """It can also be used to merge many images from the same sample when using a small beam
and reduce the spotty-ness of Debye-Sherrer rings. In this case the "max-filter" is usually
recommended.
"""
parser = ArgumentParser(usage=usage, description=description, epilog=epilog)
parser.add_argument("-V", "--version", action='version', version=version)
parser.add_argument("-o", "--output", dest="output",
type=str, default=None,
help="Output/ destination of average image")
parser.add_argument("-m", "--method", dest="method",
type=str, default="mean",
help="Method used for averaging, can be 'mean'(default) or 'median', 'min' or 'max'")
parser.add_argument("-c", "--cutoff", dest="cutoff", type=float, default=None,
help="Take the mean of the average +/- cutoff * std_dev.")
parser.add_argument("-F", "--format", dest="format", type=str, default="edf",
help="Output file/image format (by default EDF)")
parser.add_argument("-d", "--dark", dest="dark", type=str, default=None,
help="Dark noise to be subtracted")
parser.add_argument("-f", "--flat", dest="flat", type=str, default=None,
help="Flat field correction")
parser.add_argument("-v", "--verbose", action="store_true", dest="verbose", default=False,
help="switch to verbose/debug mode")
parser.add_argument("args", metavar='FILE', type=str, nargs='+',
help="Files to be processed")
options = parser.parse_args()
# Analyse aruments and options
images = pyFAI.utils.expand_args(options.args)
if options.verbose:
pyFAI.utils.logger.setLevel(logging.DEBUG)
else:
pyFAI.utils.logger.setLevel(logging.INFO)
if options.output:
output = options.output
else:
output = "%s_%s" % (os.path.commonprefix(images), options.method)
if options.cutoff:
output += "_cutoff_%s_std" % options.cutoff
output += "_%s_frames.%s" % (len(images), options.format)
if options.flat:
flats = pyFAI.utils.expand_args([options.flat])
else:
flats = None
if options.dark:
darks = pyFAI.utils.expand_args([options.dark])
else:
darks = None
if images:
dataout = pyFAI.utils.averageImages(images, filter_=options.method, cutoff=options.cutoff,
threshold=0, format=options.format, output=output,
flats=flats, darks=darks)
return dataout
if __name__ == "__main__":
main()
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