/usr/lib/python2.7/dist-packages/PyMca/XiaCorrect.py is in pymca 4.7.1+dfsg-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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# Copyright (C) 2004-2012 European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF by the Software group.
#
# This toolkit 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 2 of the License, or (at your option)
# any later version.
#
# PyMca 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
# PyMca; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# PyMca follows the dual licensing model of Riverbank's PyQt and cannot be
# used as a free plugin for a non-free program.
#
# Please contact the ESRF industrial unit (industry@esrf.fr) if this license
# is a problem for you.
#############################################################################*/
__author__ = "E. Papillon - ESRF Software group"
from PyMca import XiaEdf
import sys
import os
import time
__version__="$Revision: 1.11 $"
def defaultErrorCB(message):
print(message)
def defaultLogCB(message, verbose_level=None, verbose_ask=None):
if verbose_level is None:
print(message)
elif verbose_level <= verbose_ask:
print(message)
def defaultDoneCB(nbdone, total):
pass
def checkCB(log_cb=None, done_cb=None, error_cb=None):
if log_cb is None:
log_cb= defaultLogCB
if done_cb is None:
done_cb= defaultDoneCB
if error_cb is None:
error_cb= defaultErrorCB
return (log_cb, done_cb, error_cb)
def parseFiles(filelist, verbose=0, keep_sum=0, log_cb=None, done_cb=None, error_cb=None):
(log_cb, done_cb, error_cb)= checkCB(log_cb, done_cb, error_cb)
log_cb("Checking xia files ...")
xiafiles= []
for file in filelist:
xf= XiaEdf.XiaFilename(file)
if xf.isValid():
log_cb(" - Parsing %s (OK - %s)"%(file, xf.getType()), 1, verbose)
if not keep_sum:
if not xf.isSum():
xiafiles.append(xf)
else:
xiafiles.append(xf)
else:
log_cb(" - Parsing %s (Not Xia)"%file, 1, verbose)
if len(xiafiles):
log_cb("Sorting xia files ...")
xiafiles.sort()
groupfiles= []
group= None
for xf in xiafiles:
if group is None:
group= [ xf ]
else:
if xf.isGroupedWith(group[0]):
group.append(xf)
else:
groupfiles.append(group)
group= [ xf ]
if group is not None:
groupfiles.append(group)
grouperrors= []
for group in groupfiles:
if group[0].isScan():
if not group[-1].isStat():
stat= group[0].findStatFile()
if stat is not None:
log_cb(" - Find stat file for group <%s>"%stat.get(), 1, verbose)
group.append(stat)
else:
error_cb("XiaCorrect ERROR: no stat file in current group <%s>"%group[0].get())
grouperrors.append(group)
for group in grouperrors:
groupfiles.remove(group)
if not len(groupfiles):
error_cb("XiaCorrect ERROR: No valid XIA group files")
return None
return groupfiles
else:
error_cb("XiaCorrect ERROR: No XIA files found.")
return None
def correctFiles(xiafiles, deadtime=1, livetime=0, sums=None, avgflag=0, outdir=None, outname="corr", force=0, \
verbose=0, log_cb=None, done_cb=None, error_cb=None):
(log_cb, done_cb, error_cb)= checkCB(log_cb, done_cb, error_cb)
processed= 0
saved= 0
total= 0
errors= 0
tps= time.time()
done_cb(0, total)
total= len(xiafiles)
log_cb("Correcting xia files ...")
for group in xiafiles:
if not group[0].isScan():
file= group[0]
name= file.get()
log_cb("Working on %s"%name, 1, verbose)
try:
xia= XiaEdf.XiaEdfCountFile(name)
file.setDirectory(outdir)
file.appendPrefix(outname)
name= file.get()
if sums is not None:
err= xia.sum(sums, deadtime, livetime, avgflag)
file.setType("sum", -1)
else:
err= xia.correct(deadtime, livetime)
if len(err):
error_cb(" - WARNING: in %s"%name)
for msg in err:
error_cb(" * " + msg)
log_cb(" - Saving %s"%name)
xia.save(name, force)
saved += 1
except XiaEdf.XiaEdfError:
errors += 1
log_cb(sys.exc_info()[1])
else:
groupfiles= [ file.get() for file in group ]
name= groupfiles[-1]
log_cb("Reading %s"%name, 1, verbose)
try:
xia= XiaEdf.XiaEdfScanFile(name, groupfiles[:-1])
except XiaEdf.XiaEdfError:
xia= None
errors += 1
error_cb(sys.exc_info()[1])
if xia is not None:
for file in group:
file.setDirectory(outdir)
file.appendPrefix(outname)
if sums is None:
for file in group[:-1]:
det= file.getDetector()
if det is not None:
log_cb("Working on detector #%02d"%det, 1, verbose)
try:
err= xia.correct(det, deadtime, livetime)
name= file.get()
if len(err):
error_cb(" - WARNING: in %s"%name)
for msg in err:
error_cb(" * " + msg)
log_cb(" - Saving %s"%name)
xia.save(name, force)
saved += 1
except XiaEdf.XiaEdfError:
errors += 1
error_cb(sys.exc_info()[1])
else:
log_cb("Working on group %s"%name, 1, verbose)
file= group[-1]
for isum in range(len(sums)):
try:
err= xia.sum(sums[isum], deadtime, livetime, avgflag)
file.setType("sum", isum+1)
name= file.get()
if len(err):
error_cb(" - WARNING: in %s"%name)
for msg in err:
error_cb(" * " + msg)
log_cb(" - Saving %s"%name)
xia.save(name, force)
saved += 1
except XiaEdf.XiaEdfError:
errors += 1
error_cb(sys.exc_info()[1])
processed += 1
done_cb(processed, total)
done_cb(total, total)
log_cb("\n* %d groups processed and %d files saved in %.2f sec"%(processed, saved, time.time()-tps))
if not errors:
log_cb("* No errors found")
else:
log_cb("* %d errors found"%errors)
log_cb("\n")
def parseArguments():
import getopt, os.path
prog= os.path.basename(sys.argv[0])
long = ["help", "input=", "output=", "force", "verbose", "deadtime", "livetime", "sum=", "avg", "name=", "parsing"]
short= ["h", "i:", "o:", "f", "v", "d", "l", "s:", "a", "n:", "p"]
try:
opts, args= getopt.getopt(sys.argv[1:], " ".join(short), long)
except getopt.error:
print("XiaCorrect ERROR: Cannot parse command line arguments")
print("\t%s" % sys.exc_info()[1])
sys.exit(0)
parsing= 0
options= {"input": [], "files": [], "output": None, "force": 0, "name": "corr",
"verbose": 0, "deadtime": 0, "livetime": 0, "sums": None, "avgflag": 0, "parsing": 0}
for opt, arg in opts:
if opt in ("-h", "--help"):
printHelp()
sys.exit(0)
if opt in ("-i", "--input"):
options["input"].append(os.path.normpath(arg))
if opt in ("-o", "--output"):
options["output"]= os.path.normpath(arg)
if opt in ("-f", "--force"):
options["force"]= 1
if opt in ("-v", "--verbose"):
options["verbose"]= 1
if opt in ("-d", "--deadtime"):
options["deadtime"]= 1
if opt in ("-l", "--livetime"):
options["livetime"]= 1
if opt in ("-n", "--name"):
options["name"]= str(arg)
if opt in ("-s", "--sum"):
if options["sums"] is None:
options["sums"]= []
try:
ssum= [ int(det) for det in arg.split(",") ]
if ssum[0]==-1:
ssum= []
options["sums"].append(ssum)
except:
print("XiaCorrect ERROR: Cannot parse sum detectors")
print("\t%s"%arg)
sys.exit(0)
if opt in ("-a", "--avg"):
options["avgflag"]= 1
if opt in ("-p", "--parsing"):
options["parsing"]= 1
for iinput in options["input"]:
if not os.path.isdir(iinput):
print("XiaCorrect WARNING: Input directory <%s> is not valid"%\
iinput)
files= [ os.path.join(iinput, file) for file in os.listdir(iinput) ]
if not len(files):
print("XiaCorrect WARNING: Input directory <%s> is empty"%\
(iinput, prog))
else:
options["files"]+= files
if len(args):
options["files"]+= args
if not len(options["files"]):
print("XiaCorrect ERROR: No input datafiles")
sys.exit(0)
if not options["parsing"]:
if not options["deadtime"] and not options["livetime"] and options["sums"] is None:
print("XiaCorrect ERROR: Must have at least deadtime, livetime or sum options")
sys.exit(0)
if options["output"] is not None:
if not os.path.isdir(options["output"]):
print("XiaCorrect ERROR: output directory is not valid")
sys.exit(0)
return options
def printHelp():
prog= os.path.basename(sys.argv[0])
msg= """
%s [-h] [-v] [-f] [-d] [-l] [-a] [-s <detlist>] [-i <directory>] [-o <directory>] [<files ...>]
Options:
[-h]/[--help]
Print help message
[-v]/[--verbose]
Switch ON verbose mode
[-f]/[--force]
Force writing output files if they already exists
[-d]/[--deadtime]
Perform deadtime correction
[-l]/[--livetime]
Perform livetime normalization
[-s]/[--sum] <detector_list_comma_separated>
Sum given detectors. if detector list is set to (-1),
all detectors are used:
%s -s 2,4,8 --> will sum detectors 2,4 and 8
%s -s -1 --> will sum ALL detectors
Several sums can be added:
-s 2,4,6,7 -s 8,9,10,11
[-a]/[--avg]
Sum(s) are averaged.
Need <-s> to specify list of detectors:
-s 2,3,4 -a --> will average detectors 2,3 and 4
[-i]/[--input] <directory>
Specify input directory: all files in this directory
which appears to be xia edf files are processed.
Several [-i] options can be added:
%s -d -i /tmp -i /data/opidXX
[-o]/[--output]
Specify output directories. If not specified, output
files are saved in the same place as input file.
[-n]/[--name]
String to be appended to prefix for output filename.
Default is \"corr\".
[<files ...>]
Specify one or several input files. Wildcards can be used:
%s -l file1.edf file2.edf /tmp/test*.edf
Minimum options to work:
[-l] , [-d] or [-s]
[-i input] or <files ...>
"""%(prog, prog, prog, prog, prog)
print(msg)
def mainCommandLine():
options= parseArguments()
files= parseFiles(options["files"], options["verbose"])
if files is not None:
if options["parsing"]:
for group in files:
print("FileGroup:")
for file in group:
print(" - ", file.get())
else:
correctFiles(files, options["deadtime"], options["livetime"], options["sums"], options["avgflag"], \
options["output"], options["name"], options["force"], options["verbose"])
def mainGUI(app=None):
import PyMcaQt as qt
import XiaCorrectWizard
if app is None:
app= qt.QApplication(sys.argv)
wid= XiaCorrectWizard.XiaCorrectWizard()
ret= wid.exec_()
if ret==qt.QDialog.Accepted:
options= wid.get()
files= parseFiles(options["files"], options["verbose"])
if files is not None:
correctFiles(files, options["deadtime"], options["livetime"], options["sums"], options["avgflag"], \
options["output"], options["name"], options["force"], options["verbose"])
if __name__=="__main__":
import sys
if len(sys.argv)==1:
mainGUI()
else:
mainCommandLine()
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