def getInfo(self):
text = ""
text += "<nobr><H2><FONT color=#0000cc>"
text += "Computed File : "
text += "</FONT>"
text += "<FONT color=#000000>"
if self.fitfile is not None:
if os.path.basename(self.fitfile) == self.fitfile:
text += "<b><I>%s</I></b>" % (os.getcwd() + "/" + self.fitfile)
else:
text += "<b><I>%s</I></b>" % (self.fitfile)
else:
text += "<b><I>%s</I></b>" % (self.outdir + "/" + self.outfile +
".fit")
#and I have to generate it!!!!!!!!!!!!"
d = ConfigDict.ConfigDict(self.fitresult)
try:
os.remove(self.outdir + "/" + self.outfile + ".fit")
except:
pass
if self.concentrations is not None:
d['concentrations'] = self.concentrations
d.write(self.outdir + "/" + self.outfile + ".fit")
text += "</FONT>"
text += "</H2>"
text += "</nobr>"
text += "<LEFT>"
text += "<TABLE border=0>"
text += "<TR><TD><SPACER TYPE=BLOCK WIDTH=50></TD><TD>"
text += "<TABLE border=0 cellpadding=1 cellspacing=2>"
text += " <TR><TH ALIGN=LEFT>Source : </TH><TD ALIGN=LEFT>%s</TD></TR>" % (
self.sourcename)
text += " <TR><TH ALIGN=LEFT>Selection : </TH><TD ALIGN=LEFT>%s</TD></TR>" % (
self.selection)
text += " <TR><TH ALIGN=LEFT>Parameters : </TH><TD ALIGN=LEFT>"
d = ConfigDict.ConfigDict(self.fitresult['result']['config'])
try:
os.remove(self.outdir + "/" + self.outfile + ".txt")
except:
pass
d.write(self.outdir + "/" + self.outfile + ".txt")
text += "<a HREF=" "%s" ">%s</a>" % (self.outfile + ".txt",
self.outfile + ".txt")
text += "</TD></TR>"
"""
text+= " <TR><TH ALIGN=RIGHT>Source : </TH><TD ALIGN=LEFT>%s</TD>"%(self.sourcename)
text+= " <TH ALIGN=RIGHT>Selection : </TH><TD ALIGN=LEFT>%s</TD></TR>"%(self.selection)
keys= [ key for key in info.keys() if key not in ['paramfile', 'peakfile'] ]
for idx in range(0, len(keys), 2):
text+= " <TR><TH ALIGN=RIGHT>%s : </TH><TD ALIGN=LEFT>%s</TD>"%(keys[idx], info[keys[idx]])
if idx+1<len(keys):
text+= " <TH ALIGN=RIGHT>%s : </TH><TD ALIGN=LEFT>%s</TD></TR>"%(keys[idx+1], info[keys[idx+1]])
else:
text+= " <TD COLSPAN=2></TD></TR>"
"""
text += "</TABLE>"
text += "</TD></TR></TABLE>"
text += "</LEFT>"
return text
def testConfigDictIO(self):
# create a dictionnary
from PyMca import ConfigDict
testDict = {}
testDict['simple_types'] = {}
testDict['simple_types']['float'] = 1.0
testDict['simple_types']['int'] = 1
testDict['simple_types']['string'] = "Hello World"
testDict['containers'] = {}
testDict['containers']['list'] = [-1, 'string', 3.0]
if ConfigDict.USE_NUMPY:
import numpy
testDict['containers']['array'] = numpy.array([1.0, 2.0, 3.0])
testDict['containers']['dict'] = {'key1': 'Hello World', 'key2': 2.0}
tmpFile = tempfile.mkstemp(text=False)
os.close(tmpFile[0])
self._tmpFileName = tmpFile[1]
writeInstance = ConfigDict.ConfigDict(initdict=testDict)
writeInstance.write(self._tmpFileName)
#read the data back
readInstance = ConfigDict.ConfigDict()
readInstance.read(self._tmpFileName)
# get read key list
testDictKeys = list(testDict.keys())
readKeys = list(readInstance.keys())
self.assertTrue(
len(readKeys) == len(testDictKeys),
"Number of read keys not equal to number of written keys")
topKey = 'simple_types'
for key in testDict[topKey]:
original = testDict[topKey][key]
read = readInstance[topKey][key]
self.assertTrue(read == original,
"Read <%s> instead of <%s>" % (read, original))
topKey = 'containers'
for key in testDict[topKey]:
original = testDict[topKey][key]
read = readInstance[topKey][key]
if key == 'array':
self.assertTrue(read.all() == original.all(),
"Read <%s> instead of <%s>" % (read, original))
else:
self.assertTrue(read == original,
"Read <%s> instead of <%s>" % (read, original))
def __init__(self, *args, **kwargs):
XRFSpectrum.__init__(self, *args, **kwargs)
self.mca_hwobj = self.getObjectByRole("mca")
self.ctrl_hwobj = self.getObjectByRole("controller")
self.fname = self.getProperty("cfgfile")
self.config = ConfigDict.ConfigDict()
self.mcafit = ClassMcaTheory.McaTheory(self.fname)
def loadDict(self):
openDir = PyMcaDirs.outputDir
filter = 'PyMca (*.shift)'
filename = qt.QFileDialog.\
getOpenFileName(self,
'Load Shifts obtained from FFTAlignment',
openDir,
filter)
if len(filename) == 0:
return
inDict = ConfigDict.ConfigDict()
try:
inDict.read(filename)
except IOError:
msg = qt.QMessageBox()
msg.setTitle('FFTAlignment Load Error')
msg.setText('Unable to read shifts form file \'%s\''%filename)
msg.exec_()
return
if 'Shifts' not in inDict.keys():
# Only if the shift file consists exclusively of ShiftList
orderedLegends = [legend for legend in self.plugin.getOrder()]
try:
shiftList = inDict['ShiftList']['ShiftList']
except KeyError:
msg = qt.QMessageBox()
msg.setWindowTitle('FFTAlignment Load Error')
msg.setText('No shift information found in file \'%s\''%filename)
msg.exec_()
ddict = dict(zip(orderedLegends, shiftList))
llist = self.plugin.getOrder()
else:
llist = inDict['Order']['Order']
ddict = inDict['Shifts']
self.setDict(llist, ddict)
def saveDict(self):
saveDir = PyMcaDirs.outputDir
filter = ['PyMca (*.shift)']
try:
filename = PyMcaFileDialogs.\
getFileList(parent=self,
filetypelist=filter,
message='Safe FFT Alignment shifts',
mode='SAVE',
single=True)[0]
except IndexError:
# Returned list is empty
return False
if len(filename) == 0:
return False
if not str(filename).endswith('.shift'):
filename += '.shift'
if DEBUG:
print('saveOptions -- Filename: "%s"' % filename)
currentOrder = self.plugin.getOrder()
outDict = ConfigDict.ConfigDict()
llist, ddict = self.getDict()
outDict['Order'] = {'Order': currentOrder}
outDict['Shifts'] = ddict
outDict['ShiftList'] = {
'ShiftList':[ddict[legend] for legend in currentOrder]}
try:
outDict.write(filename)
except IOError:
msg = qt.QMessageBox()
msg.setWindowTitle('FFTAlignment Save Error')
msg.setText('Unable to write configuration to \'%s\''%filename)
msg.exec_()
return True
def generateReportFromFitFile(self):
d = ConfigDict.ConfigDict()
d.read(self.fitfile)
sourcename = "Unknown Source"
selection = "Unknown Selection"
if 'info' in d:
if 'key' in d['info']:
selection = d['info']['key']
elif 'Key' in d['info']:
selection = d['info']['Key']
for key in d['info'].keys():
if key.upper() == 'SOURCENAME':
sourcename = d['info'][key]
elif (key.upper() == 'SELECTION') or\
(key.upper() == 'LEGEND'):
selection = d['info'][key]
self.sourcename = sourcename
self.selection = selection
if self.outfile is None:
if self.outdir is None:
self.outdir = os.getcwd()
self.outfile = os.path.basename(self.fitfile)
else:
if self.outdir is None:
self.outdir = os.path.dirname(self.outfile)
self.outfile = os.path.basename(self.outfile)
if self.outdir == '': self.outdir = "."
self.fitresult = d
if 'concentrations' in d:
self.concentrations = d['concentrations']
def save(self, filename):
d= ConfigDict.ConfigDict()
d['ROI'] = {}
d['ROI'] = {'roilist': self.mcaROITable.roilist * 1,
'roidict':{}}
d['ROI']['roidict'].update(self.mcaROITable.roidict)
d.write(filename)
def __init__(self, *args, **kwargs):
XRFSpectrum.__init__(self, *args, **kwargs)
self.mca_hwobj = self.getObjectByRole('mca')
self.ctrl_hwobj = self.getObjectByRole('controller')
self.fname = "/users/blissadm/local/beamline_configuration/misc/15keV.cfg"
self.config = ConfigDict.ConfigDict()
self.mcafit = ClassMcaTheory.McaTheory(self.fname)
def fitFileChanged(self, ddict):
#for the time being only one ...
fitfile= ddict['filelist'][0]
self.fitConfiguration = ConfigDict.ConfigDict()
self.fitConfiguration.read(fitfile)
if 'result' in self.fitConfiguration:
matrix = self.fitConfiguration['result']\
['config']['attenuators'].get('Matrix', None)
else:
matrix = self.fitConfiguration\
['attenuators'].get('Matrix', None)
if matrix is None:
text = 'Undefined sample matrix in file %s' % fitfile
title = "Invalid Matrix"
self.errorMessage(text, title)
return
if matrix[0] != 1:
text = 'Undefined sample matrix in file %s' % fitfile
title = "Matrix not considered in fit"
self.errorMessage(text, title)
return
if matrix[1] == '-':
text = 'Invalid sample Composition "%s"' % matrix[1]
title = "Invalid Sample"
self.errorMessage(text, title)
return
if self.fitConfiguration.has_key('xrfmc'):
if self.fitConfiguration['xrfmc'].has_key('setup'):
self.parametersWidget.setParameters(self.fitConfiguration)
if matrix[1] != "MULTILAYER":
self.parametersWidget.setParameters({'layer':1})
self.parametersWidget.fitLayer.setMaximum(0)
def configurationFileChanged(self, ddict):
configFile= ddict['filelist'][0]
configuration = ConfigDict.ConfigDict()
configuration.read(configFile)
if not configuration['xrfmc'].has_key('setup'):
title = "Invalid file"
text = "Invalid configuration file."
self.errorMessage(text, title)
else:
self.parametersWidget.setParameters(configuration['xrfmc']['setup'])
def _configure(self,config):
d = ConfigDict.ConfigDict()
d.read(config["file"])
if not d.has_key('concentrations'):
d['concentrations']= {}
if not d.has_key('attenuators'):
d['attenuators']= {}
d['attenuators']['Matrix'] = [1, 'Water', 1.0, 0.01, 45.0, 45.0]
if config.has_key('flux'):
d['concentrations']['flux'] = float(config['flux'])
if config.has_key('time'):
d['concentrations']['time'] = float(config['time'])
self.mcafit_widget.mcafit.configure(d)
def saveConfiguration(self, filename):
cfg = ConfigDict.ConfigDict(self.getConfiguration())
if DEBUG:
cfg.write(filename)
self.initDir = os.path.dirname(filename)
else:
try:
cfg.write(filename)
self.initDir = os.path.dirname(filename)
except:
qt.QMessageBox.critical(self, "Save Parameters",
"ERROR while saving parameters to\n%s"%filename,
qt.QMessageBox.Ok, qt.QMessageBox.NoButton, qt.QMessageBox.NoButton)
def _configure(self,config):
d = ConfigDict.ConfigDict()
d.read(config["file"])
if 'concentrations' not in d:
d['concentrations']= {}
if 'attenuators' not in d:
d['attenuators']= {}
d['attenuators']['Matrix'] = [1, 'Water', 1.0, 0.01, 45.0, 45.0]
if 'flux' in config:
d['concentrations']['flux'] = float(config['flux'])
if 'time' in config:
d['concentrations']['time'] = float(config['time'])
self.mcafit_widget.mcafit.configure(d)
def loadConfiguration(self, filename):
cfg= ConfigDict.ConfigDict()
try:
cfg.read(filename)
self.initDir = os.path.dirname(filename)
self.setConfiguration(cfg)
except:
if DEBUG:
raise
qt.QMessageBox.critical(self, "Load Parameters",
"ERROR while loading parameters from\n%s"%filename,
qt.QMessageBox.Ok,
qt.QMessageBox.NoButton,
qt.QMessageBox.NoButton)
def test(filename):
fitConfig = ConfigDict.ConfigDict()
fitConfig.read(filename)
ddict = getXRFMCCorrectionFactors(fitConfig, verbose=True)
fitConfig = None
for element in ddict:
for line in ddict[element]:
if line == "z":
#atomic number
continue
if line in ['K', 'Ka', 'Kb', 'L', 'L1', 'L2', 'L3', 'M']:
correction1 = ddict[element][line]['correction_factor'][1]
correctionn = ddict[element][line]['correction_factor'][-1]
print("Element %s Line %s Correction 2 = %f Correction n = %f" %\
(element, line,correction1, correctionn))
def saveConfiguration(self):
wdir = Object3DDirs.outputDir
message = "Enter output scene configuration file name"
filename = qt.QFileDialog.getSaveFileName(self, message, wdir,
"*.scene")
filename = str(filename)
if not len(filename):
return
Object3DDirs.outputDir = os.path.dirname(filename)
config = self.glWindow.scene.getConfiguration()
d = ConfigDict.ConfigDict()
if os.path.exists(filename):
os.remove(filename)
d.update(config)
d.write(filename)
def _saveCounterTableConfiguration(self):
fname = self.getOutputFilename()
if not len(fname):
return
if not fname.endswith('.ini'):
fname += '.ini'
ddict = ConfigDict.ConfigDict()
if "PyMcaDirs" in sys.modules:
ddict['PyMca'] = {}
ddict['PyMca']['HDF5'] = {'WidgetConfiguration':\
self.getWidgetConfiguration()}
else:
ddict['HDF5'] ={'WidgetConfiguration':\
self.getWidgetConfiguration()}
ddict.write(fname)
def load(self, filename):
d = ConfigDict.ConfigDict()
d.read(filename)
current = ""
if self.mcaROITable.rowCount():
row = self.mcaROITable.currentRow()
item = self.mcaROITable.item(row, 0)
if item is not None:
current = str(item.text())
self.fillfromroidict(roilist=d['ROI']['roilist'],
roidict=d['ROI']['roidict'])
if current in d['ROI']['roidict'].keys():
if current in d['ROI']['roilist']:
row = d['ROI']['roilist'].index(current, 0)
self.mcaROITable.setCurrentCell(row, 0)
self.mcaROITable._cellChangedSlot(row, 2)
return
self.mcaROITable.setCurrentCell(0, 0)
self.mcaROITable._cellChangedSlot(0, 2)
def _getConfigurationFromFile(self, fname):
ddict = ConfigDict.ConfigDict()
ddict.read(fname)
keys = ddict.keys
if 'PyMca' in keys():
ddict = ddict['PyMca']
if 'HDF5' not in ddict.keys():
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Information)
msg.setText("File does not contain HDF5 configuration")
msg.exec_()
return None
if 'WidgetConfiguration' not in ddict['HDF5'].keys():
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Information)
msg.setText("File does not contain HDF5 WidgetConfiguration")
msg.exec_()
return None
ddict = ddict['HDF5']['WidgetConfiguration']
keys = ddict.keys()
if ('counters' not in keys) or\
('aliases' not in keys):
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Information)
msg.setText("File does not contain HDF5 counters information")
msg.exec_()
return None
if len(ddict['counters']) != len(ddict['aliases']):
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Number of counters does not match number of aliases")
msg.exec_()
return None
return ddict
def main():
import sys
import getopt
from PyMca import ConfigDict
if len(sys.argv) > 1:
options = ''
longoptions = [
'flux=', 'time=', 'area=', 'distance=', 'attenuators=',
'usematrix='
]
tool = ConcentrationsTool()
opts, args = getopt.getopt(sys.argv[1:], options, longoptions)
config = tool.configure()
for opt, arg in opts:
if opt in ('--flux'):
config['flux'] = float(arg)
elif opt in ('--area'):
config['area'] = float(arg)
elif opt in ('--time'):
config['time'] = float(arg)
elif opt in ('--distance'):
config['distance'] = float(arg)
elif opt in ('--attenuators'):
config['useattenuators'] = int(float(arg))
elif opt in ('--usematrix'):
config['usematrix'] = int(float(arg))
tool.configure(config)
filelist = args
for filename in filelist:
d = ConfigDict.ConfigDict()
d.read(filename)
for material in d['result']['config']['materials'].keys():
Elements.Material[material] =\
copy.deepcopy(d['result']['config']['materials'][material])
print(tool.processFitResult(fitresult=d, elementsfrommatrix=True))
else:
print("Usage:")
print("ConcentrationsTool [--flux=xxxx --area=xxxx] fitresultfile")
def loadConfiguration(self):
wdir = Object3DDirs.inputDir
message = "Enter input scene configuration file name"
filename = qt.QFileDialog.getOpenFileName(self, message, wdir,
"*.scene")
filename = str(filename)
if not len(filename):
return
Object3DDirs.inputDir = os.path.dirname(filename)
d = ConfigDict.ConfigDict()
d.read(filename)
self.glWindow.scene.setConfiguration(d)
#This partially works but it is awful
current = self.glWindow.scene.getSelectedObject()
if current is None:
current = 'Scene'
self.sceneControl.sceneWidget.setSelectedObject(current)
self.sceneControl.sceneWidget.treeWidget.emitSignal('objectSelected')
ddict = {}
ddict['event'] = 'configurationLoaded'
ddict['object'] = None
ddict['legend'] = None
self.emit(qt.SIGNAL('SceneManagerSignal'), ddict)
def getBasicSubprocessCommand(fitFile, outputDir=None, xmimsim_pymca=None):
ddict = getOutputFileNames(fitFile, outputDir)
scriptFile = getScriptFile(pathToExecutable=xmimsim_pymca,
name=ddict['script'])
if ddict['fit'] != fitFile:
if outputDir is None:
# this should never happen
raise ValueError("Inconsistent internal behaviour!")
# recreate input in output directory
new = ConfigDict.ConfigDict()
new.read(fitFile)
if os.path.exists(ddict['fit']):
os.remove(ddict['fit'])
new.write(ddict['fit'])
new = None
speName = ddict['spe']
csvName = ddict['csv']
newFitFile = ddict['fit']
xmsoName = ddict['xmsoName']
args = [
scriptFile,
#"--enable-single-run",
"--verbose",
"--spe-file=%s" % speName,
"--csv-file=%s" % csvName,
#"--enable-roi-normalization",
#"--disable-roi-normalization", #default
#"--enable-pile-up"
#"--disable-pile-up" #default
#"--enable-poisson",
#"--disable-poisson", #default no noise
#"--set-threads=2", #overwrite default maximum
newFitFile,
xmsoName
]
return args
def __processOneMca(self, x, y, filename, key, info=None):
self._concentrationsAsAscii = ""
if not self.roiFit:
result = None
concentrationsdone = 0
concentrations = None
outfile = self.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 = self.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 = self.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 = self.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 = self.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 = self.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 = self.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] = numpy.zeros(
(self.__nrows, self.__ncols), numpy.float)
self.__sigmas[group] = numpy.zeros(
(self.__nrows, self.__ncols), numpy.float)
self.__images['chisq'] = numpy.zeros(
(self.__nrows, self.__ncols), numpy.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] = numpy.zeros(
(self.__nrows, self.__ncols), numpy.float)
if len(layerlist) > 1:
for layer in layerlist:
key = group + " " + layer
self.__concentrationsKeys.append(key)
self.__images[key] = numpy.zeros(
(self.__nrows, self.__ncols),
numpy.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 = self.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] = numpy.zeros(
(self.__nrows, self.__ncols), numpy.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
# # 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 ([email protected]) if this license # is a problem for you. #############################################################################*/ import sys import os from PyMca import ConfigDict from PyMca import PyMcaDataDir dict = ConfigDict.ConfigDict() dirmod = PyMcaDataDir.PYMCA_DATA_DIR dictfile = os.path.join(dirmod, "Scofield1973.dict") if not os.path.exists(dictfile): dirmod = os.path.dirname(dirmod) dictfile = os.path.join(dirmod, "Scofield1973.dict") if not os.path.exists(dictfile): if dirmod.lower().endswith(".zip"): dirmod = os.path.dirname(dirmod) dictfile = os.path.join(dirmod, "Scofield1973.dict") if not os.path.exists(dictfile): print("Cannot find file ", dictfile) raise IOError("Cannot find file %s " % dictfile) dict.read(dictfile)
def setConfigurationFile(self, fname):
if not os.path.exists(fname):
raise IOError("File %s does not exist" % fname)
w = ConfigDict.ConfigDict()
w.read(fname)
self.setConfiguration(w)
ffile = os.path.join(ffile, "incoh.dict")
if not os.path.exists(ffile):
#freeze does bad things with the path ...
dirmod = os.path.dirname(dirmod)
ffile = os.path.join(dirmod, "attdata")
ffile = os.path.join(ffile, "incoh.dict")
if not os.path.exists(ffile):
if dirmod.lower().endswith(".zip"):
dirmod = os.path.dirname(dirmod)
ffile = os.path.join(dirmod, "attdata")
ffile = os.path.join(ffile, "incoh.dict")
if not os.path.exists(ffile):
print("Cannot find file ", ffile)
raise IOError("Cannot find file %s" % ffile)
COEFFICIENTS = ConfigDict.ConfigDict()
COEFFICIENTS.read(ffile)
xvalues = COEFFICIENTS['ISCADT']['XSVAL']
svalues = numpy.reshape(COEFFICIENTS['ISCADT']['SCATF'], (100, len(xvalues)))
#svalues = COEFFICIENTS['ISCADT']['SCATF']
#print svalues[100:110]
KEVTOANG = 12.39852000
R0 = 2.82E-13 #electron radius in cm
def getZ(ele):
if ele in ElementList:
return float(ElementList.index(ele) + 1)
else:
return None
if opt in ('--flux'):
config['flux'] = float(arg)
elif opt in ('--area'):
config['area'] = float(arg)
elif opt in ('--time'):
config['time'] = float(arg)
elif opt in ('--distance'):
config['distance'] = float(arg)
elif opt in ('--attenuators'):
config['useattenuators'] = int(float(arg))
elif opt in ('--usematrix'):
config['usematrix'] = int(float(arg))
demo.setParameters(config)
filelist = args
for file in filelist:
d = ConfigDict.ConfigDict()
d.read(file)
for material in d['result']['config']['materials'].keys():
Elements.Material[material] = copy.deepcopy(d['result']['config']['materials'][material])
demo.processFitResult(fitresult=d, elementsfrommatrix=False)
demo.show()
if QTVERSION < '4.0.0':
app.setMainWidget(demo)
app.exec_loop()
else:
app.exec_()
else:
print("Usage:")
print("ConcentrationsWidget.py [--flux=xxxx --area=xxxx] fitresultfile")
def _start(self):
"""
"""
if self.logWidget is not None:
if self.logWidget.isSubprocessRunning():
text = "A simulation is already started\n"
self.errorMessage(text)
return
pymcaFitFile = self.fitFileWidget.getFileList()
if len(pymcaFitFile) < 1:
text = "PyMca .fit or .cfg file is mandatory\n"
self.errorMessage(text)
return
pymcaFitFile = pymcaFitFile[0]
program = self.programWidget.getFileList()
if len(program) < 1:
text = "Simulation program file is mandatory\n"
self.errorMessage(text)
return
program = program[0]
#This one would only be needed for backup purposes
#self.iniFileWidget.getFileList()
#The output directory
outputDir = self.outputDirWidget.getFileList()
if len(outputDir) < 1:
text = "Output directory is mandatory\n"
self.errorMessage(text)
return
#the actual parameters to be used
ddict = self.parametersWidget.getParameters()
#the output directory
ddict['xrfmc']['setup']['output_dir'] = outputDir[0]
self.__outputDir = outputDir[0]
#the simulation parameters
simPar = self.simulationWidget.getParameters()
ddict['xrfmc']['setup']['histories'] = simPar['histories']
#write a file containing both, PyMca and XRFMC configuration in output dir
if pymcaFitFile.lower().endswith(".cfg"):
# not a fit result but a configuration file
# but this does not work
newFile=ConfigDict.ConfigDict()
newFile.read(pymcaFitFile)
#perform a dummy fit till xmimsim-pymca is upgraded
if 0:
import numpy
from PyMca import ClassMcaTheory
newFile['fit']['linearfitflag']=1
newFile['fit']['stripflag']=0
newFile['fit']['stripiterations']=0
xmin = newFile['fit']['xmin']
xmax = newFile['fit']['xmax']
#xdata = numpy.arange(xmin, xmax + 1) * 1.0
xdata = numpy.arange(0, xmax + 1) * 1.0
ydata = 0.0 + 0.1 * xdata
mcaFit = ClassMcaTheory.McaTheory()
mcaFit.configure(newFile)
mcaFit.setData(x=xdata, y=ydata, xmin=xmin, xmax=xmax)
mcaFit.estimate()
fitresult,result = mcaFit.startfit(digest=1)
newFile = None
nfile=ConfigDict.ConfigDict()
nfile['result'] = result
#nfile.write("tmpFitFileFromConfig.fit")
else:
nfile = ConfigDict.ConfigDict()
nfile.read(pymcaFitFile)
nfile.update(ddict)
newFile = os.path.join(outputDir[0],\
os.path.basename(pymcaFitFile[:-4] + ".fit"))
else:
nfile = ConfigDict.ConfigDict()
nfile.read(pymcaFitFile)
nfile.update(ddict)
newFile = os.path.join(outputDir[0],\
os.path.basename(pymcaFitFile))
if os.path.exists(newFile):
os.remove(newFile)
nfile.write(newFile)
nfile = None
fileNamesDict = XRFMCHelper.getOutputFileNames(newFile,
outputDir=outputDir[0])
if newFile != fileNamesDict['fit']:
raise ValueError("Inconsistent internal behaviour!")
scriptName = fileNamesDict['script']
scriptFile = XRFMCHelper.getScriptFile(program, name=scriptName)
csvName = fileNamesDict['csv']
speName = fileNamesDict['spe']
xmsoName = fileNamesDict['xmso']
# basic parameters
args = [scriptFile,
#"--enable-single-run",
"--verbose",
"--spe-file=%s" % speName,
"--csv-file=%s" % csvName,
#"--enable-roi-normalization",
#"--disable-roi-normalization", #default
#"--enable-pile-up"
#"--disable-pile-up" #default
#"--enable-poisson",
#"--disable-poisson", #default no noise
#"--set-threads=2", #overwrite default maximum
newFile,
xmsoName]
self.__fileNamesDict = fileNamesDict
# additionalParameters
if self.simulationWidget.getSimulationMode().lower() == "fit":
simulationParameters = []
else:
simulationParameters = ["--enable-single-run",
"--set-threads=2"]
i = 0
for parameter in simulationParameters:
i += 1
args.insert(1, parameter)
# show the command on the log widget
text = "%s" % scriptFile
for arg in args[1:]:
text += " %s" % arg
self.logWidget.clear()
self.logWidget.append(text)
self.logWidget.start(args=args)
def getXRFMCCorrectionFactors(fitConfiguration,
xmimsim_pymca=None,
verbose=False):
outputDir = tempfile.mkdtemp(prefix="pymcaTmp")
if 'result' in fitConfiguration:
# we have to create a .fit file with the information
ddict = ConfigDict.ConfigDict()
ddict.update(fitConfiguration)
else:
# for the time being we have to build a "fit-like" file with the information
import numpy
from PyMca import ClassMcaTheory
fitConfiguration['fit']['linearfitflag'] = 1
fitConfiguration['fit']['stripflag'] = 0
fitConfiguration['fit']['stripiterations'] = 0
xmin = fitConfiguration['fit']['xmin']
xmax = fitConfiguration['fit']['xmax']
#xdata = numpy.arange(xmin, xmax + 1) * 1.0
xdata = numpy.arange(0, xmax + 1) * 1.0
ydata = 0.0 + 0.1 * xdata
mcaFit = ClassMcaTheory.McaTheory()
mcaFit.configure(fitConfiguration)
mcaFit.setData(x=xdata, y=ydata, xmin=xmin, xmax=xmax)
mcaFit.estimate()
fitresult, result = mcaFit.startfit(digest=1)
ddict = ConfigDict.ConfigDict()
ddict['result'] = result
ddict['xrfmc'] = fitConfiguration['xrfmc']
handle, fitFile = tempfile.mkstemp(suffix=".fit",
prefix="pymca",
dir=outputDir,
text=False)
os.close(handle)
ddict.write(fitFile)
ddict = None
# we have the input file ready
fileNamesDict = getOutputFileNames(fitFile, outputDir)
scriptFile = getScriptFile(pathToExecutable=xmimsim_pymca,
name=fileNamesDict['script'])
xmsoName = fileNamesDict['xmso']
# basic parameters
args = [
scriptFile,
"--enable-single-run",
#"--set-threads=2",
#"--verbose",
#"--spe-file=%s" % speName,
#"--csv-file=%s" % csvName,
#"--enable-roi-normalization",
#"--disable-roi-normalization", #default
#"--enable-pile-up"
#"--disable-pile-up" #default
#"--enable-poisson",
#"--disable-poisson", #default no noise
#"--set-threads=2", #overwrite default maximum
fitFile,
xmsoName
]
if verbose:
args.insert(2, "--verbose")
process = subprocess.Popen(args,
bufsize=0,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True)
while process.poll() is None:
# process did not finish yet
time.sleep(0.1)
line = process.stdout.readline()
if verbose:
if len(line) > 1:
print("OUTPUT = <%s>" % line[:-1])
returnCode = process.returncode
line = process.stdout.readline()
while len(line) > 1:
if verbose:
print("OUTPUT = %s" % line[:-1])
line = process.stdout.readline()
if returnCode:
text = ""
line = process.stderr.readline()
while len(line) > 1:
text += line
if verbose:
print("ERROR = %s" % line[:-1])
line = process.stderr.readline()
removeDirectory(outputDir)
raise IOError("Program terminated with error code %d:\n%s" %
(returnCode, text))
corrections = getXMSOFileFluorescenceInformation(xmsoName)
xmsoName = None
removeDirectory(outputDir)
return corrections