/usr/share/pyshared/PyMca/McaAdvancedFitBatch.py is in pymca 4.5.0-4.
This file is owned by root:root, with mode 0o644.
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# Copyright (C) 2004-2011 European Synchrotron Radiation Facility
#
# This file is part of the PyMCA X-ray Fluorescence Toolkit developed at
# the ESRF by the Beamline Instrumentation Software Support (BLISS) 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., 59 Temple Place,
# Suite 330, Boston, MA 02111-1307, USA.
#
# PyMCA follows the dual licensing model of Trolltech's Qt and 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.
#############################################################################*/
__revision__ = "$Revision: 1.32 $"
import ClassMcaTheory
import SpecFileLayer
import EdfFileLayer
import EdfFile
import LuciaMap
import AifiraMap
import EDFStack
try:
import h5py
import HDF5Stack1D
HDF5SUPPORT = True
except ImportError:
HDF5SUPPORT = False
import numpy
import numpy.oldnumeric as Numeric
import os
import sys
import ConfigDict
import ConcentrationsTool
class McaAdvancedFitBatch:
def __init__(self,initdict,filelist=None,outputdir=None,
roifit=None,roiwidth=None,
overwrite=1, filestep=1, mcastep=1,
concentrations=0, fitfiles=1, fitimages=1,
filebeginoffset = 0, fileendoffset=0,
mcaoffset=0, chunk = None,
selection=None, lock=None):
#for the time being the concentrations are bound to the .fit files
#that is not necessary, but it will be correctly implemented in
#future releases
self._lock = lock
self.fitFiles = fitfiles
self._concentrations = concentrations
if type(initdict) == type([]):
self.mcafit = ClassMcaTheory.McaTheory(initdict[mcaoffset])
self.__configList = initdict
else:
self.__configList = None
self.mcafit = ClassMcaTheory.McaTheory(initdict)
self.__concentrationsKeys = []
if self._concentrations:
self._tool = ConcentrationsTool.ConcentrationsTool()
self._toolConversion = ConcentrationsTool.ConcentrationsConversion()
self.setFileList(filelist)
self.setOutputDir(outputdir)
if fitimages:
self.fitImages= 1
self.__ncols = None
else:
self.fitImages = False
self.__ncols = None
self.fileStep = filestep
self.mcaStep = mcastep
self.useExistingFiles = not overwrite
self.savedImages=[]
if roifit is None:roifit = False
if roiwidth is None:roiwidth = 100.
self.pleaseBreak = 0
self.roiFit = roifit
self.roiWidth = roiwidth
self.fileBeginOffset = filebeginoffset
self.fileEndOffset = fileendoffset
self.mcaOffset = mcaoffset
self.chunk = chunk
self.selection = selection
def setFileList(self,filelist=None):
self._rootname = ""
if filelist is None:filelist = []
if type(filelist) == type(" "):filelist = [filelist]
self._filelist = filelist
self._rootname = self.getRootName(filelist)
def getRootName(self,filelist=None):
if filelist is None:filelist = self._filelist
first = os.path.basename(filelist[ 0])
last = os.path.basename(filelist[-1])
if first == last:return os.path.splitext(first)[0]
name1,ext1 = os.path.splitext(first)
name2,ext2 = os.path.splitext(last )
i0=0
for i in range(len(name1)):
if i >= len(name2):
break
elif name1[i] == name2[i]:
pass
else:
break
i0 = i
for i in range(i0,len(name1)):
if i >= len(name2):
break
elif name1[i] != name2[i]:
pass
else:
break
i1 = i
if i1 > 0:
delta=1
while (i1-delta):
if (last[(i1-delta)] in ['0', '1', '2',
'3', '4', '5',
'6', '7', '8',
'9']):
delta = delta + 1
else:
if delta > 1: delta = delta -1
break
rootname = name1[0:]+"_to_"+last[(i1-delta):]
else:
rootname = name1[0:]+"_to_"+last[0:]
return rootname
def setOutputDir(self,outputdir=None):
if outputdir is None:outputdir=os.getcwd()
self._outputdir = outputdir
def processList(self):
self.counter = 0
self.__row = self.fileBeginOffset - 1
self.__stack = None
for i in range(0+self.fileBeginOffset,
len(self._filelist)-self.fileEndOffset,
self.fileStep):
if not self.roiFit:
if self.__configList is not None:
if i != 0:
self.mcafit = ClassMcaTheory.McaTheory(self.__configList[i])
self.mcafit.enableOptimizedLinearFit()
inputfile = self._filelist[i]
self.__row += 1
self.onNewFile(inputfile, self._filelist)
self.file = self.getFileHandle(inputfile)
if self.pleaseBreak: break
if self.__stack is None:
self.__stack = False
if hasattr(self.file, "info"):
if "SourceType" in self.file.info:
if self.file.info["SourceType"] in\
["EdfFileStack", "HDF5Stack1D"]:
self.__stack = True
if self.__stack:
self.__processStack()
else:
self.__processOneFile()
if self.counter:
if not self.roiFit:
if self.fitFiles:
self.listfile.write(']\n')
self.listfile.close()
if self.__ncols is not None:
if self.__ncols:self.saveImage()
self.onEnd()
def getFileHandle(self,inputfile):
try:
self._HDF5 = False
if HDF5SUPPORT:
if h5py.is_hdf5(inputfile):
self._HDF5 = True
try:
return HDF5Stack1D.HDF5Stack1D([inputfile], self.selection)
except:
raise
ffile = self.__tryEdf(inputfile)
if ffile is None:
ffile = self.__tryLucia(inputfile)
if ffile is None:
if inputfile[-3:] == "DAT":
ffile = self.__tryAifira(inputfile)
if (ffile is None):
del ffile
ffile = SpecFileLayer.SpecFileLayer()
ffile.SetSource(inputfile)
return ffile
except:
raise IOError("I do not know what to do with file %s" % inputfile)
def onNewFile(self,ffile, filelist):
self.__log(ffile)
def onImage(self,image,imagelist):
pass
def onMca(self,mca,nmca, filename=None, key=None, info=None):
pass
def onEnd(self):
pass
def __log(self,text):
print(text)
def __tryEdf(self,inputfile):
try:
ffile = EdfFileLayer.EdfFileLayer(fastedf=0)
ffile.SetSource(inputfile)
fileinfo = ffile.GetSourceInfo()
if fileinfo['KeyList'] == []:
ffile=None
elif len(self._filelist) == 1:
#Is it a Diamond stack?
if len(fileinfo['KeyList']) > 1:
info, data = ffile.LoadSource(fileinfo['KeyList'][0])
shape = data.shape
if len(shape) == 2:
if min(shape) == 1:
#It is a Diamond Stack
ffile=EDFStack.EDFStack(inputfile)
return ffile
except:
return None
def __tryLucia(self, inputfile):
f = open(inputfile)
line = f.readline()
f.close()
ffile = None
if line.startswith('#\tDate:'):
ffile = LuciaMap.LuciaMap(inputfile)
return ffile
def __tryAifira(self, inputfile):
if sys.platform == "win32":
f = open(inputfile,"rb")
else:
f = open(inputfile,"r")
line = f.read(3)
f.close()
if '#' in line:
#specfile
return None
ffile = None
try:
ffile = AifiraMap.AifiraMap(inputfile)
except:
ffile = None
return ffile
def __processStack(self):
stack = self.file
info = stack.info
data = stack.data
nimages = stack.info['Dim_1']
self.__nrows = nimages
numberofmca = stack.info['Dim_2']
keylist = ["1.1"] * nimages
for i in range(nimages):
keylist[i] = "1.%04d" % i
for i in range(nimages):
if self.pleaseBreak: break
self.onImage(keylist[i], keylist)
self.__ncols = numberofmca
colsToIter = range(0+self.mcaOffset,
numberofmca,
self.mcaStep)
self.__row = i
self.__col = -1
try:
cache_data = data[i, :, :]
except:
print("Error reading dataset row %d" % i)
print(sys.exc_info())
print("Batch resumed")
continue
for mca in colsToIter:
if self.pleaseBreak: break
self.__col = mca
mcadata = cache_data[mca, :]
if 'MCA start ch' in info:
xmin = float(info['MCA start ch'])
else:
xmin = 0.0
#key = "%s.%s.%02d.%02d" % (scan,order,row,col)
key = "%s.%04d" % (keylist[i], mca)
y0 = Numeric.array(mcadata)
x = Numeric.arange(len(y0))*1.0 + xmin
#I only process the first file of the stack?
filename = os.path.basename(info['SourceName'][0])
infoDict = {}
infoDict['SourceName'] = info['SourceName']
infoDict['Key'] = key
self.__processOneMca(x,y0,filename,key,info=infoDict)
self.onMca(mca, numberofmca, filename=filename,
key=key,
info=infoDict)
def __processOneFile(self):
ffile=self.file
fileinfo = ffile.GetSourceInfo()
nimages = nscans = len(fileinfo['KeyList'])
if 1:
i = 0
for scankey in fileinfo['KeyList']:
if self.pleaseBreak: break
self.onImage(scankey, fileinfo['KeyList'])
if 0:
scan,rc = string.split(scankey,".")
info,data = ffile.LoadSource({'Key':int(image)-1})
else:
scan,order = scankey.split(".")
info,data = ffile.LoadSource(scankey)
if info['SourceType'] == "EdfFile":
nrows = int(info['Dim_1'])
ncols = int(info['Dim_2'])
numberofmca = min(nrows,ncols)
self.__ncols = len(range(0+self.mcaOffset,numberofmca,self.mcaStep))
self.__col = -1
for mca_index in range(self.__ncols):
mca = 0 + self.mcaOffset + mca_index * self.mcaStep
if self.pleaseBreak: break
self.__col += 1
if int(nrows) > int(ncols):
row=mca
col=0
mcadata = data[mca,:]
else:
col=mca
row=0
mcadata = data[:,mca]
if 'MCA start ch' in info:
xmin = float(info['MCA start ch'])
else:
xmin = 0.0
#key = "%s.%s.%02d.%02d" % (scan,order,row,col)
key = "%s.%s.%04d" % (scan,order,mca)
if 0:
#slow
y0 = Numeric.array(mcadata.tolist())
else:
#fast
y0 = Numeric.array(mcadata)
x = Numeric.arange(len(y0))*1.0 + xmin
filename = os.path.basename(info['SourceName'])
infoDict = {}
infoDict['SourceName'] = info['SourceName']
infoDict['Key'] = key
self.__processOneMca(x,y0,filename,key,info=infoDict)
self.onMca(mca, numberofmca, filename=filename,
key=key,
info=infoDict)
else:
if info['NbMca'] > 0:
self.fitImages = True
numberofmca = info['NbMca'] * 1
self.__ncols = len(range(0+self.mcaOffset,
numberofmca,self.mcaStep))
self.__col = -1
scan_key = "%s.%s" % (scan,order)
scan_obj= ffile.Source.select(scan_key)
#I assume always same number of detectors and
#same offset for each detector otherways I would
#slow down everything to deal with not very common
#situations
#if self.__row == 0:
if self.counter == 0:
self.__chann0List = Numeric.zeros(info['NbMcaDet'])
chan0list = scan_obj.header('@CHANN')
if len(chan0list):
for i in range(info['NbMcaDet']):
self.__chann0List[i] = int(chan0list[i].split()[2])
#import time
for mca_index in range(self.__ncols):
i = 0 + self.mcaOffset + mca_index * self.mcaStep
#e0 = time.time()
if self.pleaseBreak: break
self.__col += 1
point = int(i/info['NbMcaDet']) + 1
mca = (i % info['NbMcaDet']) + 1
key = "%s.%s.%05d.%d" % (scan,order,point,mca)
#get rid of slow info reading methods
#mcainfo,mcadata = ffile.LoadSource(key)
mcadata = scan_obj.mca(i+1)
y0 = Numeric.array(mcadata)
x = Numeric.arange(len(y0))*1.0 + \
self.__chann0List[mca-1]
filename = os.path.basename(info['SourceName'])
infoDict = {}
infoDict['SourceName'] = info['SourceName']
infoDict['Key'] = key
self.__processOneMca(x,y0,filename,key,info=infoDict)
self.onMca(i, info['NbMca'],filename=filename,
key=key,
info=infoDict)
#print "remaining = ",(time.time()-e0) * (info['NbMca'] - i)
def __getFitFile(self, filename, key):
fitdir = os.path.join(self._outputdir,"FIT")
fitdir = os.path.join(fitdir,filename+"_FITDIR")
outfile = filename +"_"+key+".fit"
outfile = os.path.join(fitdir, outfile)
return outfile
def __processOneMca(self,x,y,filename,key,info=None):
self._concentrationsAsAscii = ""
if not self.roiFit:
result = None
concentrationsdone = 0
concentrations = None
outfile=os.path.join(self._outputdir,filename)
fitfile = self.__getFitFile(filename,key)
if self.chunk is not None:
con_extension = "_%06d_partial_concentrations.txt" % self.chunk
else:
con_extension = "_concentrations.txt"
self._concentrationsFile = os.path.join(self._outputdir,
self._rootname+ con_extension)
# self._rootname+"_concentrationsNEW.txt")
if self.counter == 0:
if os.path.exists(self._concentrationsFile):
try:
os.remove(self._concentrationsFile)
except:
print("I could not delete existing concentrations file %s" %\
self._concentrationsFile)
#print "self._concentrationsFile", self._concentrationsFile
if self.useExistingFiles and os.path.exists(fitfile):
useExistingResult = 1
try:
dict = ConfigDict.ConfigDict()
dict.read(fitfile)
result = dict['result']
if 'concentrations' in dict:
concentrationsdone = 1
except:
print("Error trying to use result file %s" % fitfile)
print("Please, consider deleting it.")
print(sys.exc_info())
return
else:
useExistingResult = 0
try:
#I make sure I take the fit limits configuration
self.mcafit.config['fit']['use_limit'] = 1
self.mcafit.setdata(x,y)
except:
print("Error entering data of file with output = %s" %\
filename)
return
try:
self.mcafit.estimate()
if self.fitFiles:
fitresult, result = self.mcafit.startfit(digest=1)
elif self._concentrations and (self.mcafit._fluoRates is None):
fitresult, result = self.mcafit.startfit(digest=1)
elif self._concentrations:
fitresult = self.mcafit.startfit(digest=0)
try:
fitresult0 = {}
fitresult0['fitresult'] = fitresult
fitresult0['result'] = self.mcafit.imagingDigestResult()
fitresult0['result']['config'] = self.mcafit.config
conf = self.mcafit.configure()
tconf = self._tool.configure()
if 'concentrations' in conf:
tconf.update(conf['concentrations'])
else:
#what to do?
pass
concentrations = self._tool.processFitResult(config=tconf,
fitresult=fitresult0,
elementsfrommatrix=False,
fluorates = self.mcafit._fluoRates)
except:
print("error in concentrations")
print(sys.exc_info()[0:-1])
concentrationsdone = True
else:
#just images
fitresult = self.mcafit.startfit(digest=0)
except:
print("Error fitting file with output = %s: %s)" %\
(filename, sys.exc_info()[1]))
return
if self._concentrations:
if concentrationsdone == 0:
if not ('concentrations' in result):
if useExistingResult:
fitresult0={}
fitresult0['result'] = result
conf = result['config']
else:
fitresult0={}
if result is None:
result = self.mcafit.digestresult()
fitresult0['result'] = result
fitresult0['fitresult'] = fitresult
conf = self.mcafit.configure()
tconf = self._tool.configure()
if 'concentrations' in conf:
tconf.update(conf['concentrations'])
else:
pass
#print "Concentrations not calculated"
#print "Is your fit configuration file correct?"
#return
try:
concentrations = self._tool.processFitResult(config=tconf,
fitresult=fitresult0,
elementsfrommatrix=False)
except:
print("error in concentrations")
print(sys.exc_info()[0:-1])
#return
self._concentrationsAsAscii=self._toolConversion.getConcentrationsAsAscii(concentrations)
if len(self._concentrationsAsAscii) > 1:
text = ""
text += "SOURCE: "+ filename +"\n"
text += "KEY: "+key+"\n"
text += self._concentrationsAsAscii + "\n"
f=open(self._concentrationsFile,"a")
f.write(text)
f.close()
#output options
# .FIT files
if self.fitFiles:
fitdir = os.path.join(self._outputdir,"FIT")
if not os.path.exists(fitdir):
try:
os.mkdir(fitdir)
except:
print("I could not create directory %s" % fitdir)
return
fitdir = os.path.join(fitdir,filename+"_FITDIR")
if not os.path.exists(fitdir):
try:
os.mkdir(fitdir)
except:
print("I could not create directory %s" % fitdir)
return
if not os.path.isdir(fitdir):
print("%s does not seem to be a valid directory" % fitdir)
else:
outfile = filename +"_"+key+".fit"
outfile = os.path.join(fitdir, outfile)
if not useExistingResult:
result = self.mcafit.digestresult(outfile=outfile,
info=info)
if concentrations is not None:
try:
f=ConfigDict.ConfigDict()
f.read(outfile)
f['concentrations'] = concentrations
try:
os.remove(outfile)
except:
print("error deleting fit file")
f.write(outfile)
except:
print("Error writing concentrations to fit file")
print(sys.exc_info())
#python like output list
if not self.counter:
name = os.path.splitext(self._rootname)[0]+"_fitfilelist.py"
name = os.path.join(self._outputdir,name)
try:
os.remove(name)
except:
pass
self.listfile=open(name,"w+")
self.listfile.write("fitfilelist = [")
self.listfile.write('\n'+outfile)
else:
self.listfile.write(',\n'+outfile)
else:
if not useExistingResult:
if 0:
#this is very slow and not needed just for imaging
if result is None:result = self.mcafit.digestresult()
else:
if result is None:result = self.mcafit.imagingDigestResult()
#IMAGES
if self.fitImages:
#this only works with EDF
if self.__ncols is not None:
if not self.counter:
imgdir = os.path.join(self._outputdir,"IMAGES")
if not os.path.exists(imgdir):
try:
os.mkdir(imgdir)
except:
print("I could not create directory %s" %\
imgdir)
return
elif not os.path.isdir(imgdir):
print("%s does not seem to be a valid directory" %\
imgdir)
self.imgDir = imgdir
self.__peaks = []
self.__images = {}
self.__sigmas = {}
if not self.__stack:
self.__nrows = len(range(0,len(self._filelist),self.fileStep))
for group in result['groups']:
self.__peaks.append(group)
self.__images[group]=Numeric.zeros((self.__nrows,self.__ncols),Numeric.Float)
self.__sigmas[group]=Numeric.zeros((self.__nrows,self.__ncols),Numeric.Float)
self.__images['chisq'] = Numeric.zeros((self.__nrows,self.__ncols),Numeric.Float) - 1.
if self._concentrations:
layerlist = concentrations['layerlist']
if 'mmolar' in concentrations:
self.__conLabel = " mM"
self.__conKey = "mmolar"
else:
self.__conLabel = " mass fraction"
self.__conKey = "mass fraction"
for group in concentrations['groups']:
key = group+self.__conLabel
self.__concentrationsKeys.append(key)
self.__images[key] = Numeric.zeros((self.__nrows,self.__ncols),
Numeric.Float)
if len(layerlist) > 1:
for layer in layerlist:
key = group+" "+layer
self.__concentrationsKeys.append(key)
self.__images[key] = Numeric.zeros((self.__nrows,self.__ncols),
Numeric.Float)
for peak in self.__peaks:
try:
self.__images[peak][self.__row, self.__col] = result[peak]['fitarea']
self.__sigmas[peak][self.__row, self.__col] = result[peak]['sigmaarea']
except:
pass
if self._concentrations:
layerlist = concentrations['layerlist']
for group in concentrations['groups']:
self.__images[group+self.__conLabel][self.__row, self.__col] = \
concentrations[self.__conKey][group]
if len(layerlist) > 1:
for layer in layerlist:
self.__images[group+" "+layer] [self.__row, self.__col] = \
concentrations[layer][self.__conKey][group]
try:
self.__images['chisq'][self.__row, self.__col] = result['chisq']
except:
print("Error on chisq row %d col %d" %\
(self.__row, self.__col))
print("File = %s\n" % filename)
pass
else:
dict=self.mcafit.roifit(x,y,width=self.roiWidth)
#this only works with EDF
if self.__ncols is not None:
if not self.counter:
imgdir = os.path.join(self._outputdir,"IMAGES")
if not os.path.exists(imgdir):
try:
os.mkdir(imgdir)
except:
print("I could not create directory %s" %\
imgdir)
return
elif not os.path.isdir(imgdir):
print("%s does not seem to be a valid directory" %\
imgdir)
self.imgDir = imgdir
self.__ROIpeaks = []
self._ROIimages = {}
if not self.__stack:
self.__nrows = len(self._filelist)
for group in dict.keys():
self.__ROIpeaks.append(group)
self._ROIimages[group]={}
for roi in dict[group].keys():
self._ROIimages[group][roi]=Numeric.zeros((self.__nrows,
self.__ncols),Numeric.Float)
if not hasattr(self, "_ROIimages"):
print("ROI fitting only supported on EDF")
for group in self.__ROIpeaks:
for roi in self._ROIimages[group].keys():
try:
self._ROIimages[group][roi][self.__row, self.__col] = dict[group][roi]
except:
print("error on (row,col) = %d,%d" %\
(self.__row, self.__col))
print("File = %s" % filename)
pass
#update counter
self.counter += 1
def saveImage(self,ffile=None):
self.savedImages=[]
if ffile is None:
ffile = os.path.splitext(self._rootname)[0]
ffile = os.path.join(self.imgDir,ffile)
if not self.roiFit:
if (self.fileStep > 1) or (self.mcaStep > 1):
trailing = "_filestep_%02d_mcastep_%02d" % ( self.fileStep,
self.mcaStep )
else:
trailing = ""
#speclabel = "#L row column"
speclabel = "row column"
if self.chunk is None:
suffix = ".edf"
else:
suffix = "_%06d_partial.edf" % self.chunk
iterationList = self.__peaks * 1
iterationList += ['chisq']
if self._concentrations:
iterationList += self.__concentrationsKeys
for peak in iterationList:
if peak in self.__peaks:
a,b = peak.split()
speclabel +=" %s" % (a+"-"+b)
speclabel +=" s(%s)" % (a+"-"+b)
edfname = ffile +"_"+a+"_"+b+trailing+suffix
elif peak in self.__concentrationsKeys:
speclabel +=" %s" % peak.replace(" ","-")
edfname = ffile +"_"+peak.replace(" ","_")+trailing+suffix
elif peak == 'chisq':
speclabel +=" %s" % (peak)
edfname = ffile +"_"+peak+trailing+suffix
else:
print("Unhandled peak name: %s. Not saved." % peak)
continue
dirname = os.path.dirname(edfname)
if not os.path.exists(dirname):
try:
os.mkdir(dirname)
except:
print("I could not create directory %s" % dirname)
Append = 0
if os.path.exists(edfname):
try:
os.remove(edfname)
except:
print("I cannot delete output file")
print("trying to append image to the end")
Append = 1
edfout = EdfFile.EdfFile(edfname, access='ab')
edfout.WriteImage ({'Title':peak} , self.__images[peak], Append=Append)
edfout = None
self.savedImages.append(edfname)
#save specfile format
if self.chunk is None:
specname = ffile+trailing+".dat"
else:
specname = ffile+trailing+"_%06d_partial.dat" % self.chunk
if os.path.exists(specname):
try:
os.remove(specname)
except:
pass
specfile=open(specname,'w+')
#specfile.write('\n')
#specfile.write('#S 1 %s\n' % (file+trailing))
#specfile.write('#N %d\n' % (len(self.__peaks)+2))
specfile.write('%s\n' % speclabel)
specline=""
for row in range(self.__nrows):
for col in range(self.__ncols):
specline += "%d" % row
specline += " %d" % col
for peak in self.__peaks:
#write area
specline +=" %g" % self.__images[peak][row][col]
#write sigma area
specline +=" %g" % self.__sigmas[peak][row][col]
#write global chisq
specline +=" %g" % self.__images['chisq'][row][col]
if self._concentrations:
for peak in self.__concentrationsKeys:
specline +=" %g" % self.__images[peak][row][col]
specline += "\n"
specfile.write("%s" % specline)
specline =""
specfile.write("\n")
specfile.close()
else:
for group in self.__ROIpeaks:
i = 0
grouptext = group.replace(" ","_")
for roi in self._ROIimages[group].keys():
#roitext = roi.replace(" ","-")
if (self.fileStep > 1) or (self.mcaStep > 1):
edfname = ffile+"_"+grouptext+("_%04deVROI_filestep_%02d_mcastep_%02d.edf" % (self.roiWidth,
self.fileStep, self.mcaStep ))
else:
edfname = ffile+"_"+grouptext+("_%04deVROI.edf" % self.roiWidth)
dirname = os.path.dirname(edfname)
if not os.path.exists(dirname):
try:
os.mkdir(dirname)
except:
print("I could not create directory %s" % dirname)
edfout = EdfFile.EdfFile(edfname)
edfout.WriteImage ({'Title':group+" "+roi} , self._ROIimages[group][roi],
Append=i)
if i==0:
self.savedImages.append(edfname)
i=1
if __name__ == "__main__":
import getopt
options = 'f'
longoptions = ['cfg=','pkm=','outdir=','roifit=','roi=','roiwidth=']
filelist = None
outdir = None
cfg = None
roifit = 0
roiwidth = 250.
opts, args = getopt.getopt(
sys.argv[1:],
options,
longoptions)
for opt,arg in opts:
if opt in ('--pkm','--cfg'):
cfg = arg
elif opt in ('--outdir'):
outdir = arg
elif opt in ('--roi','--roifit'):
roifit = int(arg)
elif opt in ('--roiwidth'):
roiwidth = float(arg)
filelist=args
if len(filelist) == 0:
print("No input files, run GUI")
sys.exit(0)
b = McaAdvancedFitBatch(cfg,filelist,outdir,roifit,roiwidth)
b.processList()
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