Hi Chang:
If it is the right form, I have a Python program which will convert them
along with a description of the file format. I have attached the
description below and the python program to the email. If it does not get
through the mailing list filter, just email me directly and I will send
it.
Carlo
------------------------------------------------------------------------
The first column is in motor steps (!), and the angle is a linear function
of motor steps, and the rest is just Bragg's law. Things are referenced
physically to the copper edge.
Key parameters used in the data acquisition program are in the header:
dspace is obvious, stepdeg is steps per degree in the mono, cuedge is
the position of the Cu edge as measured in motor step units.
I think the channel offsets (dark currents) are already subtracted from the
other columns; the offsets are just listed for documentation.
In addition, there are two different file types, the ones which have a
header beginning with NPTS and containing DSPACE and the older files which
begin with CUEDGE and do not contain d-spacing information.
For the latter, we make the following assumptions:
dSpacing = 1.92017
stepDegree = 2000 * int(edgeCu / 42000)
The guts of the calculation are as follows:
theta = ((steps - edgeCu) / stepDegree) * (pi / 180.) + thetaCu
energy = hc / (2 * d * numpy.sin(theta))
where steps - the current step value in the original file
edgeCu - the position of the Cu edge in steps
stepDegree - the steps per degree theta
thetaCu - the angle of the Cu edge (from d-spacing information)
On Fri, 8 Dec 2017, woschangqi...@126.com wrote:
Hello, dear everyone.
I downloaded a XAFS data about mettalic Ru from the website of ixs.iit.edu.
There are 4 groups of information in the data, and each ranges between ~67800
with ~63000 in energy. So how to import the data to Athena, and how this kind
of data was produced? Does anyone come across this situation? Thanks for your
time and help in advance.
Q. CHANG
Unversity of Chinese of Academy of Sciences
--
Carlo U. Segre -- Duchossois Leadership Professor of Physics
Interim Chair, Department of Chemistry
Director, Center for Synchrotron Radiation Research and Instrumentation
Illinois Institute of Technology
Voice: 312.567.3498 Fax: 312.567.3494
se...@iit.edu http://phys.iit.edu/~segre se...@debian.org
#!/usr/bin/env python
# Name: lytle_convert
# Purpose: Convert Farrel Lytle data files from steps to energy
# and output in SFF format. This program supports
# conversion of two different file types. Those which
# have a header beginning with NPTS and containing DSPACE and
# the older files with begin with CUEDGE and do not contain
# d-spacing information.
# Author: Carlo U. Segre <se...@iit.edu>
#
# Copyright 2009 Illinois Institute of Technology
#
# Version:
# 1.0 2009/02/03 Carlo Segre
# * Initial release
# 1.1 2009/02/11 Carlo Segre
# * Replace Numeric with numpy
# * Open output file after checking for supported input
# file format
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation the rights to use, copy, modify, merge, publish,
# distribute, sublicense, and/or sell copies of the Software, and to
# permit persons to whom the Software is furnished to do so, subject to
# the following conditions:
#
# The above copyright notice and this permission notice shall be
# included in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
# IN NO EVENT SHALL ILLINOIS INSTITUTE OF TECHNOLOGY BE LIABLE FOR ANY
# CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
# SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
#
# Except as contained in this notice, the name of Illinois Institute
# of Technology shall not be used in advertising or otherwise to promote
# the sale, use or other dealings in this Software without prior written
# authorization from Illinois Institute of Technology.
#
__version__ = '1.1'
__rcsid__ = '$Id$'
__source__ = '$Source$'
import os
import sys
import getopt
from string import *
from struct import *
import commands
import time
import numpy
def usage(error=1):
usage = """\
Usage: %s [OPTION]... INFILE0 [INFILE1 ... INFILEn]
Converts Farrel Lytle data files from steps to energy.
Options:
-h, --help Print this message
""" % os.path.basename(sys.argv[0])
if error:
sys.stderr.write(usage)
sys.exit(1)
else:
sys.stdout.write(usage)
sys.exit()
def main(rawFile, convFile):
inFile = open(rawFile, "r")
lines = inFile.readlines()
vars = lines[0].split()
if vars[0] == "NPTS" :
fileType = "new"
vals = lines[1].split()
elif vars[0] == "CUEDGE" :
fileType = "old"
vals = vars[5:]
vars = vars[:5]
else :
sys.stderr.write("Unknown file format!\n")
sys.exit(1)
ouFile = open(convFile, "w")
pi = numpy.arccos(-1.)
hc = 12398.5
energyCu = 8980.3
edgeCu = float(vals[vars.index('CUEDGE')])
if fileType == "new" :
stepDegree = float(vals[vars.index('STPDEG')])
d = float(vals[vars.index('DSPACE')])
numPts = int(vals[vars.index('NPTS')])
numScalers = int(vals[vars.index('NS')])
scale = float(vals[vars.index('SCALE')])
else:
# For the "old" file type, the following assumptions are made:
# dSpacing = 1.92017
# stepDegree = 2000 * int(edgeCu / 42000)
# make sure to change these if converted files do not have the
# correct energy.
stepDegree = int((edgeCu / 42000) + 0.5) * 2000
d = 1.92017
numPts = (len(lines) - 5) * 4
numScalers = 1
start = float(vals[vars.index('START')])
stop = float(vals[vars.index('STOP')])
thetaCu=numpy.arcsin(hc/(2*d*energyCu))
steps = numpy.zeros((numPts), dtype=float)
scalers = numpy.zeros((numPts, numScalers), dtype=float)
if fileType == "new" :
i = 0
while i < numPts :
try :
tmp = lines[i + 7].split()
except IndexError :
numPts = i
break
try :
steps[i] = float(tmp[0])
except IndexError :
numPts = i
break
j = 0
while j < numScalers :
scalers[i,j] = float(tmp[j + 1])
j = j + 1
i = i + 1
else :
i = 0
while i < numPts :
try :
tmp = lines[(i / 4) + 5].split()
except IndexError :
numPts = i
break
k = 0
while k < 4 :
try :
steps[i] = float(tmp[2 * k])
scalers[i,0] = float(tmp[(2 * k)+1])
except IndexError :
numPts = i
break
k = k + 1
i = i + 1
theta = ((steps - edgeCu) / stepDegree) * (pi / 180.) + thetaCu
energy = hc / (2 * d * numpy.sin(theta))
if fileType == "new" :
ouFile.write('# SFF main_header 12\n')
else :
ouFile.write('# SFF main_header 11\n')
ouFile.write('# raw_data_file = "' + rawFile +'";\n')
ouFile.write('# source = "Farrel Lytle Database";\n')
timestamp = time.strftime('%m-%d-%G %H:%M:%S').split()
ouFile.write('# conversion_timestamp = ' + str(timestamp) + ';\n')
ouFile.write('# d_spacing = "' + str(d) + '";\n')
ouFile.write('# steps_per_degree = "' + str(stepDegree) + '";\n')
ouFile.write('# step_start = "' + str(vals[vars.index('START')]) + '";\n')
if fileType == "new" :
ouFile.write('# step_deltas = "' +
lines[2][lines[2].find('DELTA:') + 6:].strip() + '";\n')
ouFile.write('# region_ends = "' +
lines[3][lines[3].find('DELEND:') + 7:].strip() + '";\n')
ouFile.write('# count_times = "' +
lines[4][lines[4].find('SEC:') + 4:].strip() + '";\n')
ouFile.write('# offsets = "' +
lines[5][lines[5].find('OFFSET:') + 7:].strip() + '";\n')
ouFile.write('# sample = "' + lines[6].strip() + '";\n')
scalerList = ""
j = 0
while j < numScalers :
scalerList = scalerList + 'scaler' + str(j) + ' '
j = j + 1
ouFile.write('# %devices = "energy ' + scalerList + 'steps";\n')
else :
ouFile.write('# step_deltas = "' +
lines[1][lines[1].find('DELTA:') + 6:].strip() + '";\n')
ouFile.write('# region_ends = "' +
lines[2][lines[2].find('DELEND:') + 7:].strip() + '";\n')
ouFile.write('# count_times = "' +
lines[3][lines[3].find('SEC:') + 4:].strip() + '";\n')
ouFile.write('# full_scale_counts = "' +
str(vals[vars.index('FSCTS:')]) + '";\n')
ouFile.write('# sample = "' + lines[4].strip() + '";\n')
ouFile.write('# %devices = "energy mu(E) steps";\n')
i = 0
while i < numPts :
if energy[i] < 0 :
break
ouFile.write('%8.2f' % energy[i] + '\t')
if fileType == "new" :
j = 0
while j < numScalers :
ouFile.write('%10.2f' % scalers[i,j] + '\t')
j = j + 1
else :
ouFile.write('%10.6f' % scalers[i,0] + '\t')
ouFile.write('%8.0f' % steps[i] + '\n')
i = i + 1
inFile.close()
ouFile.close()
if __name__ == '__main__':
try:
opts, args = getopt.getopt(sys.argv[1:], 'h', ['help'])
except getopt.error:
sys.stderr.write("%s: %s \nTry `%s --help` for more informatIon\n"
% (PROGNAME, e, PROGNAME))
sys.exit(1)
for o in opts:
if o in ('-h', '--help'):
usage(error=0)
if len(args) == 0:
usage()
for infile in args:
oufile = '_'.join(infile.split('.')) + '.sff'
main(infile, oufile)
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