/usr/lib/python2.7/dist-packages/PyMca/XiaEdf.py is in pymca 4.7.4+dfsg-1.
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.
#############################################################################*/
import os, os.path
import numpy
from PyMca.PyMcaIO import EdfFile
__version__="$Revision: 1.15 $"
XiaStatIndex= {
"det": 0,
"evt": 1,
"icr": 2,
"ocr": 3,
"lt" : 4,
"dt" : 5
}
XiaStatNb= len(XiaStatIndex.keys())
XiaStatLabels= ["xdet", "xevt", "xicr", "xocr", "xlt", "xdt"]
def checkEdfForRead(filename):
if not os.path.isfile(filename):
raise XiaEdfError("Cannot find file <%s>"%filename)
else:
try:
if os.path.getsize(filename)==0:
raise XiaEdfError("File <%s> has a null size "%filename)
except:
raise XiaEdfError("Cannot open file <%s>"%filename)
def openEdf(filename, read=0, write=0, force=0):
if read:
checkEdfForRead(filename)
if write:
checkEdfForWrite(filename, force)
try:
edf= EdfFile.EdfFile(filename)
except:
raise XiaEdfError("Cannot open EDF file <%s>"%filename)
return edf
def checkEdfForWrite(filename, force=0):
if os.path.isfile(filename):
if not force:
raise XiaEdfError("<%s> already exist. Abort saving."%filename)
else:
os.remove(filename)
if os.path.isfile(filename):
raise XiaEdfError("Cannot remove <%s>. Abort saving."%filename)
class XiaEdfError(Exception):
def __init__(self, message):
self.msg= message
def __str__(self):
return "XiaEdf ERROR: %s"%self.msg
class XiaEdfCountFile:
def __init__(self, filename):
self.filename= filename
self.edf= openEdf(filename, read=1)
self.reset()
def reset(self):
self.data= None
self.header= None
try:
self.__readStat()
except:
raise XiaEdfError("Cannot parse header in <%s>"%filename)
def __readStat(self):
self.header= self.edf.GetHeader(0)
self.nbDet= int(self.header.get("xnb", 0))
if not self.nbDet:
self.detList= []
self.statArray= None
return self.nbDet
self.detList= range(self.nbDet)
det= self.header.get("xdet", None)
if det is not None:
dets= det.split()
if len(dets)==self.nbDet:
self.detList= map(int, dets)
self.statArray = numpy.zeros(XiaStatNb*self.nbDet, numpy.int)
idx= 0
for det in self.detList:
self.statArray[idx+XiaStatIndex["det"]]= int(self.header.get("xdet%02d"%det, det))
self.statArray[idx+XiaStatIndex["evt"]]= int(self.header.get("xevt%02d"%det, 0))
self.statArray[idx+XiaStatIndex["icr"]]= int(self.header.get("xicr%02d"%det, 1))
self.statArray[idx+XiaStatIndex["ocr"]]= int(self.header.get("xocr%02d"%det, 1))
self.statArray[idx+XiaStatIndex["lt"]]= int(self.header.get("xlt%02d"%det, 1))
self.statArray[idx+XiaStatIndex["dt"]]= int(self.header.get("xdt%02d"%det, 0))
idx += 6
def __getData(self):
self.__readData()
return self.data
def __readData(self):
if self.data is None:
try:
self.data= self.edf.GetData(0)
except:
raise XiaEdfError("Cannot read data in <%s>"%self.filename)
def getDetList(self):
return self.detList
def getData(self, detector=-1):
# --- WARNING: first index is channels
data= self.__getData()
if detector==-1:
return data[1:]
else:
if detector not in self.detList:
return None
idx= self.detList.index(detector)
return data[idx+1]
def getStat(self, detector=-1):
if detector==-1:
return self.statArray
else:
if detector not in self.detList:
return None
idx= self.detList.index(detector)
return self.statArray[(idx*XiaStatNb):((idx+1)*XiaStatNb)]
def correct(self, deadtime=1, livetime=0):
message= []
corrflag= int(self.header.get("xcorr", 0))
if livetime and corrflag&2:
raise XiaEdfError("<%s> seems already livetime corrected"%self.filename)
if deadtime and corrflag&1:
raise XiaEdfError("<%s> seems already deadtime corrected"%self.filename)
self.__readData()
self.data= self.data.astype(numpy.float)
if livetime:
lvt= numpy.zeros((self.nbDet,1), numpy.float)
derr= []
for idx in range(len(self.detList)):
lvt[idx]= self.statArray[idx*XiaStatNb + XiaStatIndex["lt"]] / 1000.0
if lvt[idx]==0.:
lvt[idx]= 1.
derr.append("#%02d"%self.detList[idx])
if len(derr):
message.append("Null livetime on det %s"% " ".join(derr))
self.data[1:,:]= self.data[1:,:] / lvt
self.header["xcorr"]= corrflag|2
if deadtime:
rate= numpy.zeros((self.nbDet,1), numpy.float)
for idx in range(len(self.detList)):
derr= []
try:
rate[idx]= float(self.statArray[idx*XiaStatNb + XiaStatIndex["icr"]]) / \
float(self.statArray[idx*XiaStatNb + XiaStatIndex["ocr"]])
except:
rate[idx]= 1.
derr.append("#%02d"%idx)
if len(derr):
message.append("Null OCR on det %s" % " ".join(derr))
self.data[1:,:]= self.data[1:,:] * rate
self.header["xcorr"]= corrflag|1
return message
def sum(self, sums=[], deadtime=0, livetime=0, average=0):
message= []
if not len(sums):
return message
self.__readData()
if deadtime or livetime:
message+= self.correct(deadtime, livetime)
else:
self.data= self.data.astype(numpy.float)
sumdata= numpy.zeros((len(sums), self.data.shape[1]), numpy.float)
for idx in range(len(sums)):
if not len(sums[idx]):
sumdata[idx,:] = numpy.sum(self.data[1:,], 0)
xdet= self.detList
else:
mask= numpy.zeros((self.nbDet+1,1), numpy.int)
xdet= []
for det in sums[idx]:
if det in self.detList:
detidx= self.detList.index(det)
mask[detidx+1]= 1
xdet.append(det)
sumdata[idx,:]= numpy.sum(self.data*mask, 0)
self.header["xcorr%d"%idx] = self.header.get("xcorr", 0)
self.header["xdet%d"%idx] = " ".join([str(det) for det in xdet])
if average:
self.data= sumdata / len(xdet)
else:
self.data= sumdata
for key in self.header.keys():
if key[0]=='x':
try:
det= int(key[-2:])
del self.header[key]
except:
pass
dataflag= int(self.header.get("xdata", 0))
self.header["xdata"]= dataflag | (1<<2)
self.header["xnb"]= len(sums)
return message
def save(self, filename, force=0):
edf= openEdf(filename, write=1, force=force)
self.__readData()
edf.WriteImage(self.header, self.data)
class XiaEdfScanFile:
def __init__(self, statfile, detfiles):
self.statfile= statfile
self.detfiles= detfiles
self.detector= None
self.data= None
self.header= None
checkEdfForRead(self.statfile)
for file in self.detfiles:
checkEdfForRead(file)
try:
self.__readStat()
except:
raise XiaEdfError("Cannot parse header in <%s>"%self.statfile)
def __readStat(self):
edf= openEdf(self.statfile)
header= edf.GetHeader(0)
self.nbDet= int(header.get("xnb", 0))
if not self.nbDet:
self.detList= []
self.statArray= None
return self.nbDet
self.detList= range(self.nbDet)
det= header.get("xdet", None)
if det is not None:
dets= det.split()
if len(dets)==self.nbDet:
self.detList= map(int, dets)
self.statArray= edf.GetData(0)
return self.nbDet
def __readData(self, detector):
if detector!=self.detector:
self.detector= None
self.data= None
self.header= None
#try:
if 1:
if detector in self.detList:
idx= self.detList.index(detector)
if idx < len(self.detfiles):
file= self.detfiles[idx]
edf= openEdf(self.detfiles[idx])
header= edf.GetHeader(0)
xdet= int(header.get("xdet", -1))
if xdet==-1 or xdet==detector:
self.data= edf.GetData(0)
self.header= header
self.detector= xdet
if self.data is None:
for file in self.detfiles:
edf= openEdf(file)
header= edf.GetHeader(0)
xdet= int(header.get("xdet", -1))
if xdet==detector:
self.data= edf.GetData(0)
self.header= header
self.detector= xdet
break
else: #except:
raise XiaEdfError("Cannot read data on det #%02d in <%s>"%(detector, file))
if self.data is None:
raise XiaEdfError("Cannot read data on det #%02d"%detector)
def getDetList(self):
return self.detList
def getData(self, detector):
self.__readData(detector)
return self.data
def getStat(self, detector=-1):
if detector==-1:
return self.statArray
else:
if detector not in self.detList:
return None
idx= self.detList.index(detector)
return self.statArray[:,(idx*XiaStatNb):((idx+1)*XiaStatNb)]
def correct(self, detector, deadtime=1, livetime=0):
message= []
if detector!=self.detector:
self.__readData(detector)
corrflag= int(self.header.get("xcorr", 0))
if livetime and corrflag&2:
raise XiaEdfError("det #%02d seems already livetime corrected"%detector)
if deadtime and corrflag&1:
raise XiaEdfError("det #%02d seems already deadtime corrected"%detector)
self.data= self.data.astype(numpy.float)
idx= self.detList.index(detector)
pts= self.statArray.shape[0]
if livetime:
lvt= numpy.zeros((pts, 1), numpy.float)
lvt[:,0]= self.statArray[:,((XiaStatNb*idx)+XiaStatIndex["lt"])] / 1000.0
perr= self.__checkNullLivetime(lvt, pts)
if len(perr):
message.append("Null livetime on det #%02d points %s"%(detector, self.__pointRange(perr)))
self.data= self.data / lvt
self.header["xcorr"]= corrflag|2
if deadtime:
rate= numpy.zeros((self.statArray.shape[0], 1), numpy.float)
count= numpy.zeros((self.statArray.shape[0], 2), numpy.float)
count[:,0]= self.statArray[:, (XiaStatNb*idx)+XiaStatIndex["ocr"]]
count[:,1]= self.statArray[:, (XiaStatNb*idx)+XiaStatIndex["icr"]]
perr= self.__checkNullCount(count, pts)
if len(perr):
message.append("Null ICR|OCR on det #%02d points %s"%(detector, self.__pointRange(perr)))
perr= []
for ipt in range(pts):
if count[ipt,0]>0 and count[ipt,1]>0:
rate[ipt,0]= count[ipt,1]/count[ipt,0]
else:
rate[ipt,0]= 1.
perr.append(ipt)
if len(perr):
message.append("No DeadTime correction perfomed on det #%02d points %s"%(detector, self.__pointRange(perr)))
self.data= self.data * rate
self.header["xcorr"]= corrflag|1
return message
def __checkNullCount(self, count, pts):
perr= []
check= numpy.sum(numpy.greater(count,0.), 1)
for ipt in range(pts):
if check[ipt]!=2:
perr.append(ipt)
if (ipt!=0 and check[ipt-1]==2) and (ipt!=pts-1 and check[ipt+1]==2):
count[ipt,:]= (count[ipt-1,:]+count[ipt+1,:])/2.
elif (ipt!=0 and check[ipt-1]==2):
count[ipt,:]= count[ipt-1,:]
elif (ipt!=pts-1 and check[ipt+1]==2):
count[ipt,:]= count[ipt+1,:]
else:
count[ipt,:]= -1
return perr
def __checkNullLivetime(self, lvt, pts):
perr= []
check= numpy.greater(lvt, 0.)
for ipt in range(pts):
if check[ipt]==0:
perr.append(ipt)
if (ipt!=0 and check[ipt-1]==1) and (ipt!=pts-1 and check[ipt+1]==1):
lvt[ipt,0]= (lvt[ipt+1]+lvt[ipt-1])/2.
elif (ipt!=0 and check[ipt-1]==1):
lvt[ipt,0]= lvt[ipt-1,0]
elif (ipt!=pts-1 and check[ipt+1]==1):
lvt[ipt,0]= lvt[ipt+1,0]
else:
lvt[ipt,0]= 1.
return perr
def __pointRange(self, ptlist):
nb= len(ptlist)
ptdiff= []
for idx in range(nb-1):
ptdiff.append(((ptlist[idx+1]-ptlist[idx])==1))
ptdiff.append(0)
ptrange= []
curr= None
for idx in range(nb):
if ptdiff[idx]:
if curr is None:
curr= ptlist[idx]
else:
if curr is None:
ptrange.append(str(ptlist[idx]))
else:
ptrange.append("%d-%d"%(curr,ptlist[idx]))
curr= None
return "["+ ",".join(ptrange)+"]"
def sum(self, detectors=[], deadtime=0, livetime=0, average=0):
message= []
if not len(detectors):
sumdet= self.detList
else:
sumdet= [ det for det in detectors if det in self.detList ]
sumdata= None
for det in sumdet:
if deadtime or livetime:
message+= self.correct(det, deadtime, livetime)
else:
self.__readData(det)
self.data= self.data.astype(numpy.float)
if sumdata is None:
sumdata= self.data * 1.0
else:
sumdata= sumdata + self.data
if average:
self.data= sumdata / len(sumdet)
else:
self.data= sumdata
dataflag= int(self.header.get("xdata", 0))
self.header["xdata"]= dataflag | (1<<2)
self.header["xnb"]= 1
self.header["xdet"]= " ".join([str(det) for det in sumdet])
return message
def save(self, filename, force=0):
if self.data is None:
raise XiaEdfError("Cannot save. No data loaded.")
edf= openEdf(filename, write=1, force=force)
edf.WriteImage(self.header, self.data)
class XiaFilename:
def __init__(self, filename=None):
self.__reset()
if filename is not None:
self.__parseFilename(filename)
def setType(self, type, det=None):
self.type= type
self.det= det
def getType(self):
return self.type
def isValid(self):
return self.type is not None
def isCount(self):
return (self.type=="ct" or (self.type=="sum" and self.det==-1))
def isScan(self):
return (self.type=="det" or self.type=="st" or (self.type=="sum" and self.det>0))
def isSum(self):
return (self.type=="sum")
def isStat(self):
return (self.type=="st")
def findStatFile(self):
xf= XiaFilename(self.get())
xf.setType("st")
if os.path.isfile(xf.get()):
return xf
else:
return None
def isGroupedWith(self, other):
if (self.isScan() and other.isScan()) or (self.isCount() and other.isCount()):
file1= "%s/%s"%(self.dir is None and "." or self.dir, self.prefix is None and "" or self.prefix)
file2= "%s/%s"%(other.dir is None and "." or other.dir, other.prefix is None and "" or other.prefix)
res= cmp(file1, file2)
if res!=0: return 0
res= cmp(self.index, other.index)
if res!=0: return 0
file1= "%s.%s"%(self.suffix is None and "" or self.suffix, self.ext is None and "" or self.ext)
file2= "%s.%s"%(other.suffix is None and "" or other.suffix, other.ext is None and "" or other.ext)
res= cmp(file1, file2)
if res!=0: return 0
return 1
else:
return 0
def setDirectory(self, dirname):
if dirname is None:
self.dir= "."
else:
self.dir= dirname
def appendPrefix(self, name):
if self.prefix is None:
self.prefix= name
elif name is not None:
self.prefix= "%s_%s"%(self.prefix, name)
def getDetector(self):
if self.type!="det":
return None
else:
return self.det
def set(self, filename):
self.__reset()
if filename is not None:
self.__parseFilename(filename)
def get(self):
self.__createFilename()
return self.file
def __reset(self):
self.file= None # --- full filename
self.dir = None # --- directory
self.type= None # --- file type = "ct", "st", "det"
self.index= [] # --- file indexes
self.suffix= None # --- suffix
self.det= None # --- if type=="det", detector number
def __parseFilename(self, filename):
self.file= os.path.basename(filename)
self.dir= os.path.dirname(filename)
if not len(self.dir):
self.dir= "."
fileext= os.path.splitext(self.file)
if len(fileext[1]):
self.ext= fileext[1][1:]
filelist= fileext[0].split("_")
xiaidx= 0
for xiaidx in range(len(filelist)):
if filelist[xiaidx][0:3]=="xia":
break
xiaidx += 1
if xiaidx==len(filelist):
self.type= None
self.prefix= fileext[0]
else:
self.prefix= "_".join(filelist[0:xiaidx])
try:
self.index= map(int, filelist[xiaidx+1:])
except:
self.suffix= "_".join(filelist[xiaidx+1:])
type= filelist[xiaidx][3:]
if type=="ct" or type=="st":
self.type= type
elif type[0]=='S':
self.type= "sum"
if type[1]=='N':
self.det= -1
else:
try:
self.det= int(type[1])
except:
self.type= None
else:
try:
self.type= "det"
self.det= int(type)
except:
self.type= None
def __createFilename(self):
if self.prefix is None or self.type is None:
self.file= None
else:
self.file= "%s/%s"%(self.dir, self.prefix)
xia= None
if self.type=="ct":
xia= "xiact"
elif self.type=="st":
xia= "xiast"
elif self.type=="sum":
if self.det==-1:
xia= "xiaSN"
else:
xia= "xiaS%01d"%self.det
elif self.type=="det":
xia= "xia%02d"%self.det
elif self.type is not None:
xia= "xia%s"%self.type
if xia is not None:
self.file= "%s_%s"%(self.file, xia)
for idx in self.index:
self.file= "%s_%04d"%(self.file, idx)
if self.suffix is not None:
self.file= "%s_%s"%(self.file, self.suffix)
if self.ext is not None:
self.file= "%s.%s"%(self.file, self.ext)
def __cmp__(self, other):
file1= "%s/%s"%(self.dir is None and "." or self.dir, self.prefix is None and "" or self.prefix)
file2= "%s/%s"%(other.dir is None and "." or other.dir, other.prefix is None and "" or other.prefix)
res= cmp(file1, file2)
if res!=0:
return res
res= cmp(self.ext, other.ext)
if res!=0:
return res
res= cmp(self.index, other.index)
if res!=0:
return res
res= cmp(self.type, other.type)
if res!=0:
return res
if self.type=="det" or self.type=="sum":
res= cmp(self.det, other.det)
if res!=0:
return res
file1= "%s.%s"%(self.suffix is None and "" or self.suffix, self.ext is None and "" or self.ext)
file2= "%s.%s"%(other.suffix is None and "" or other.suffix, other.ext is None and "" or other.ext)
return cmp(file1, file2)
def testScan():
x= XiaEdfScanFile("data/test_xiast_0000_0000_0000.edf",
["data/test_xia00_0000_0000_0000.edf",
"data/test_xia01_0000_0000_0000.edf",
"data/test_xia02_0000_0000_0000.edf",
"data/test_xia03_0000_0000_0000.edf",
"data/test_xia04_0000_0000_0000.edf",
"data/test_xia05_0000_0000_0000.edf",
"data/test_xia06_0000_0000_0000.edf",
"data/test_xia07_0000_0000_0000.edf",
"data/test_xia08_0000_0000_0000.edf",
"data/test_xia09_0000_0000_0000.edf",
"data/test_xia10_0000_0000_0000.edf",
"data/test_xia11_0000_0000_0000.edf",
])
x.sum([1,10])
print(x.header)
x.save("test_sum.edf")
#for det in [1, 2, 3, 4, 5, 6]:
# x.correct(det, livetime=1)
# x.save(det, "scan_corr_xia%02d.edf"%det)
def testAcq(infile, outfile=None):
print("Reading ", infile)
x= XiaEdfCountFile(infile)
#print "DeadTime Correction ..."
#x.correct()
x.sum([1,10])
if outfile is not None:
print(x.header)
print("Saving %s" % outfile)
x.save(outfile)
if __name__=="__main__":
import sys
testScan()
sys.exit(0)
if len(sys.argv)<2:
print("%s <ct_filename> [<output_filename>]" % sys.argv[0])
sys.exit(0)
else:
infile= sys.argv[1]
outfile= len(sys.argv)>=3 and sys.argv[2] or None
testAcq(infile, outfile)
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