/usr/bin/pyFAI-saxs 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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 | #! /usr/bin/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>
# 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/>.
#
"""
saxs_integrate is the Saxs script of pyFAI that allows data reduction
for Small Angle Scattering.
"""
__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 = "pyFAI-saxs [options] -n 1000 -p ponifile file1.edf file2.edf ..."
version = "PyFAI-saxs version %s from %s " % (pyFAI.version, pyFAI.date)
description = """Azimuthal integration for SAXS users."""
epilog = """pyFAI-saxs is the SAXS script of pyFAI that allows data
reduction (azimuthal integration) for Small Angle Scattering with output
axis in q space."""
parser = ArgumentParser(usage=usage, description=description, epilog=epilog)
parser.add_argument("-v", "--version", action='version', version=version)
parser.add_argument("args", metavar="FILE", help="Files to integrated", nargs='+')
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("-b", "--background", dest="background",
# type="string", default=None,
# help="name of the file containing the background")
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("--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="q_nm^-1",
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=".dat",
help="extension of the regrouped filename (.dat)")
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 = "lut"
else:
method = "BBox"
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"
fabioFile = fabio.open(oneFile)
t0 = time.time()
if fabioFile.nframes > 1:
integrator.integrate1d(data=fabioFile.data,
nbPt=options.npt or min(fabioFile.data.shape),
dummy=options.dummy,
delta_dummy=options.delta_dummy,
filename=outFile,
variance=fabioFile.next().data,
method=method,
unit=options.unit,
error_model=options.error_model,
polarization_factor=options.polarization_factor
)
else:
integrator.integrate1d(data=fabioFile.data,
nbPt=min(fabioFile.data.shape),
dummy=options.dummy,
delta_dummy=options.delta_dummy,
filename=outFile,
method=method,
unit=options.unit,
error_model=options.error_model,
polarization_factor=options.polarization_factor)
t1 = time.time()
print("Integration took %6.3fs %s --> %s" %
(t1 - t0, oneFile, outFile))
if __name__ == "__main__":
main()
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