/usr/bin/pyFAI-waxs is in pyfai 0.10.2-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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# -*- 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>
# Picca Frédéric-Emmanuel <picca@synchrotron-soleil.fr>
#
# 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-waxs is the Waxs script of pyFAI that allows data reduction for
Wide Angle Scattering, producing output in 2-theta range output in
radial dimension (and in degrees).
"""
__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 time
import fabio
import pyFAI
import pyFAI.units
import pyFAI.utils
hc = pyFAI.units.hc
import logging
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger("PyFAI")
try:
from argparse import ArgumentParser
except ImportError:
from pyFAI.argparse import ArgumentParser
def main():
usage = "usage: pyFAI-waxs [options] -p ponifile file1.edf file2.edf ..."
version = "pyFAI-waxs version %s from %s" % (pyFAI.version, pyFAI.date)
description = "Azimuthal integration for powder diffraction."
epilog = """pyFAI-waxs is the script of pyFAI that allows data reduction
(azimuthal integration) for Wide Angle Scattering to produce X-Ray Powder
Diffraction Pattern with output axis in 2-theta space.
"""
parser = ArgumentParser(usage=usage, description=description, epilog=epilog)
parser.add_argument("-v", "--version", action='version', version=version)
parser.add_argument("-p", dest="ponifile",
type=str, default=None,
help="PyFAI parameter file (.poni)")
parser.add_argument("-n", dest="npt",
type=int, default=None,
help="Number of points in radial dimension")
parser.add_argument("-w", "--wavelength", dest="wavelength", type=float,
help="wavelength of the X-Ray beam in Angstrom", default=None)
parser.add_argument("-e", "--energy", dest="energy", type=float,
help="energy of the X-Ray beam in keV (hc=%skeV.A)" % hc,
default=None)
parser.add_argument("-u", "--dummy", dest="dummy",
type=float, default=None,
help="dummy value for dead pixels")
parser.add_argument("-U", "--delta_dummy", dest="delta_dummy",
type=float, default=None,
help="delta dummy value")
parser.add_argument("-m", "--mask", dest="mask",
type=str, default=None,
help="name of the file containing the mask image")
parser.add_argument("-d", "--dark", dest="dark",
type=str, default=None,
help="name of the file containing the dark current")
parser.add_argument("-f", "--flat", dest="flat",
type=str, default=None,
help="name of the file containing the flat field")
parser.add_argument("-P", "--polarization", dest="polarization_factor",
type=float, default=None,
help="Polarization factor, from -1 (vertical) to +1 (horizontal), \
default is None for no correction, synchrotrons are around 0.95")
# parser.add_argument("-b", "--background", dest="background",
# type=str, default=None,
# help="name of the file containing the background")
parser.add_argument("--error-model", dest="error_model",
type=str, default=None,
help="Error model to use. Currently on 'poisson' is implemented ")
parser.add_argument("--unit", dest="unit",
type=str, default="2th_deg",
help="unit for the radial dimension: can be q_nm^-1, q_A^-1, 2th_deg, \
2th_rad or r_mm")
parser.add_argument("--ext", dest="ext",
type=str, default=".xy",
help="extension of the regrouped filename (.xy) ")
parser.add_argument("--multi", dest="multiframe", #type=bool,
default=False, action="store_true",
help="Average out all frame in a file before integrating")
parser.add_argument("--average", dest="average", type=str,
default="mean",
help="Method for averaging out: can be 'mean' (default), 'min', 'max' or 'median")
parser.add_argument("--do-2D", dest="do_2d",
default=False, action="store_true",
help="Perform 2D integration in addition to 1D")
parser.add_argument("args", metavar='FILE', type=str, nargs='+',
help="Files to integrated")
options = parser.parse_args()
if len(options.args) < 1:
logger.error("incorrect number of arguments")
processFile = pyFAI.utils.expand_args(options.args)
if options.ponifile and processFile:
integrator = pyFAI.load(options.ponifile)
if options.wavelength:
integrator.wavelength = options.wavelength*1e-10
elif options.energy:
integrator.wavelength = hc / options.energy*1e-10
if options.mask and os.path.exists(options.mask): # override with the command line mask
integrator.maskfile = options.mask
if options.dark and os.path.exists(options.dark): # set dark current
integrator.darkcurrent = fabio.open(options.dark).data
if options.flat and os.path.exists(options.flat): # set Flat field
integrator.flatfield = fabio.open(options.flat).data
if len(processFile) > 5:
method = "csr"
else:
method = "splitpixel"
print(integrator)
print("Mask: %s\tMethod: %s" % (integrator.maskfile, method))
for oneFile in processFile:
sys.stdout.write("Integrating %s --> " % oneFile)
outFile = os.path.splitext(oneFile)[0] + options.ext
azimFile = os.path.splitext(oneFile)[0] + ".azim"
t0 = time.time()
fabioFile = fabio.open(oneFile)
if options.multiframe:
data = pyFAI.utils.averageDark([fabioFile.getframe(i).data for i in range(fabioFile.nframes)], center_method=options.average)
else:
data=fabioFile.data
t1 = time.time()
integrator.integrate1d(data,
nbPt=options.npt or min(fabioFile.data.shape),
filename=outFile,
dummy=options.dummy,
delta_dummy=options.delta_dummy,
method=method,
unit=options.unit,
error_model=options.error_model,
polarization_factor=options.polarization_factor
)
t2 = time.time()
if options.do_2d:
integrator.integrate2d(data,
options.npt or min(fabioFile.data.shape),
360,
filename=azimFile,
dummy=options.dummy,
delta_dummy=options.delta_dummy,
method=method,
unit=options.unit,
error_model=options.error_model,
polarization_factor=options.polarization_factor
)
print("%s\t reading: %.3fs\t 1D integration: %.3fs,\t 2D integration %.3fs." %
(outFile, t1 - t0, t2 - t1, time.time() - t2))
else:
print("%s\t reading: %.3fs\t 1D integration: %.3fs." %
(outFile, t1 - t0, t2 - t1))
if __name__ == "__main__":
main()
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