def DataFile2hgeFile(ListOpt):
List = ListOpt.copy()
List.pop(0)
ValidFileList = []
for File in List:
if isValidSpectrumFile(File):
ValidFileList.append(File)
if len(ValidFileList) != 0:
for File in ValidFileList:
myExtension = File.split('.')[-1]
mySpecialDict = functionDictAdv[myExtension](File)
hgeFilename = File.split('.')[0] + '_factor.hge'
exitcode = WritehgeFile(hgeFilename,mySpecialDict)
else:
print('There is not a valid file to be converted to .hge file.')
return 1050
return exitcode
def SumFun(ListOpt):
List = ListOpt.copy()
List.pop(0)
#functionDict = {"SPE": getDictFromSPE,"mca": getDictFromMCA,"Txt": getDictFromGammaVision,"info":getDictFromInfoFile}
if '--noCal' in List:
noCalFlag = True
List.remove('--noCal')
else:
noCalFlag = False
if '--noPlot' in List:
noPlotFlag = True
List.remove('--noPlot')
else:
noPlotFlag = False
if '--wof' in List:
wofFlag = True
List.remove('--wof')
else:
wofFlag = False
if '--log' in List:
logFlag = True
List.remove('--log')
else:
logFlag = False
if len(List) == 1:
if isValidSpecFile(List[0]):
print('----------------------------------------------')
print(
'WARNING: At least two files are needed to make the sum between them.'
)
print(
'No sum was performed. If option --noPlot is disabled then plot is shown.'
)
print('Otherwise, nothing is shown.')
print('----------------------------------------------')
myFilename = List[0]
myExtension = myFilename.split(".")[-1]
if noCalFlag:
mySubsDict = functionDict[myExtension](myFilename, False)
else:
mySubsDict = functionDict[myExtension](myFilename)
mySubsList = mySubsDict["theList"]
if noPlotFlag:
print('----------------------------------------------')
print('--noPlot is activated, so there is no figure display.')
else:
simplePlot(mySubsList,
logFlag,
noCalFlag,
Label=None,
show=True,
Title=myFilename.split('/')[-1])
else:
print('----------------------------------------------')
print('WARNING: No .mca, .Txt or .SPE files was indicated.')
print('Please, introduce two or more valid files.')
return 41
elif len(List) > 1:
count = 0
Title = ''
for myFilename in List:
count += 1
Title += myFilename.split('/')[-1] + '+'
if isValidSpecFile(myFilename):
myExtension = myFilename.split(".")[-1]
if noCalFlag:
mySubsDict = functionDict[myExtension](myFilename, False)
if count == 1:
mySubsDictOut = mySubsDict.copy()
else:
mySubsDict = functionDict[myExtension](myFilename)
if count == 1:
mySubsDictOut = mySubsDict.copy()
if count != 1:
mySubsDictOut = SumSpectra(mySubsDictOut, mySubsDict)
if not noPlotFlag:
simplePlot(mySubsDictOut["theList"],
logFlag,
noCalFlag,
Label=None,
show=True,
Title=Title[:-1])
if wofFlag:
myOutFile = myFilename.strip(
myFilename.split('/')[-1]) + Title + '.txt'
try:
WritehgeFile(myOutFile, mySubsDictOut)
print('-----------------------------------------')
print('The file was saved as:')
print(myOutFile)
print('-----------------------------------------')
except:
try:
WriteOutputFile(mySubsDictOut, myOutFile, Title)
print('-----------------------------------------')
print('The file was saved as:')
print(myOutFile)
print('-----------------------------------------')
except IOError:
print(
'An unexpected error ocurred while saving the data to file.'
)
return 44
else:
print('ERROR: Not a valid argument in "Sum" function.')
return 40
return 0
def efficencyFun(Command):
List = Command.copy()
List.pop(0)
PlotFlag = False
if '--Plot' in List or '--plot' in List:
PlotFlag = True
List.remove('--Plot')
ValidFileList = []
EffFile = ''
for File in List:
if isValidSpectrumFile(File):
ValidFileList.append(File)
elif '.eff' in File:
EffFile = File
if EffFile == '':
sys.stderr.write('An efficiency file for the detector is required.\n')
return 2000
else:
try:
Effdf = pd.read_csv(EffFile,header=None,names=['energy','eff'])
except IOError:
sys.stderr.write('ERROR: The .eff file could not be read.\n')
return 2001
else:
Effenernp = Effdf['energy'].values
Effnp = Effdf['eff'].values
PolyCoeff = curve_fit(PolyFun,Effenernp,Effnp,absolute_sigma=True)
R2PolyCoeff = R2PolyFun(Effenernp,Effnp,PolyCoeff[0])
Fun1Coeff = curve_fit(Fun1,Effenernp,Effnp,absolute_sigma=True,bounds=([-np.inf,-np.inf,-np.inf,-np.inf],[np.inf,np.inf,np.inf,np.inf]))
R2Fun1Coeff = R2Fun1(Effenernp,Effnp,Fun1Coeff[0])
LinearCoeff = curve_fit(LinearFun,Effenernp,Effnp,absolute_sigma=True)
R2LinearCoeff = R2LinearFun(Effenernp,Effnp,LinearCoeff[0])
if PlotFlag:
XPoly = np.linspace(min(Effenernp),max(Effenernp),num=len(Effenernp)*50)
R2List = [R2PolyCoeff,R2Fun1Coeff,R2LinearCoeff]
R2max = max(R2List)
if R2max == R2PolyCoeff:
Ypoly = np.polyval(PolyCoeff[0],XPoly)
elif R2max == R2Fun1Coeff:
Ypoly = Fun1(XPoly,Fun1Coeff[0][0],Fun1Coeff[0][1],Fun1Coeff[0][2],Fun1Coeff[0][3])
elif R2max == R2LinearCoeff:
Ypoly = LinearFun(XPoly,LinearCoeff[0][0],LinearCoeff[0][1])
plt.plot(XPoly,Ypoly,label='Curve fitting')
plt.scatter(Effenernp,Effnp,label='Data')
plt.xscale('log')
plt.yscale('log')
plt.xlabel('Energy/keV')
plt.ylabel('Efficiency')
plt.title('Detector Efficiency')
plt.legend(loc='upper right')
if R2max == R2PolyCoeff:
textstr = f'Eight grade polynomial.\na1={str(PolyCoeff[0][0])},a2={str(PolyCoeff[0][1])}\na3={str(PolyCoeff[0][2])},a4={str(PolyCoeff[0][3])}\na5={str(PolyCoeff[0][4])},a6={str(PolyCoeff[0][5])}\na7={str(PolyCoeff[0][6])},a8={str(PolyCoeff[0][7])}\nR²={str(R2PolyCoeff)}'
elif R2max == R2Fun1Coeff:
textstr = f'f(x) = (ax+b)/(x²+cx+d)\na={str(Fun1Coeff[0][0])}\nb={str(Fun1Coeff[0][1])}\nc={str(Fun1Coeff[0][2])}\nd={str(Fun1Coeff[0][3])}\nR²={str(R2Fun1Coeff)}'
elif R2max == R2LinearCoeff:
textstr = f'f(x) = (ax+b)\na={str(LinearCoeff[0][0])}\nb={str(LinearCoeff[0][1])}\nR²={str(R2LinearCoeff)}'
plt.annotate(textstr,xy=(0, 0.1), xytext=(12, -12),va='bottom',xycoords='axes fraction', textcoords='offset points',fontsize=10)
plt.show()
return 0
elif not PlotFlag:
for File in ValidFileList:
myExtension = File.split('.')[-1]
mySpecialDict = functionDictAdv[myExtension](File)
xVals = np.array(mySpecialDict['theList'][0])
yVals = np.array(mySpecialDict['theList'][1])
R2List = [R2PolyCoeff,R2Fun1Coeff,R2LinearCoeff]
R2max = max(R2List)
if R2max == R2PolyCoeff:
EffGe = np.polyval(PolyCoeff[0],xVals)
elif R2max == R2Fun1Coeff:
EffGe = Fun1(xVals,Fun1Coeff[0][0],Fun1Coeff[0][1],Fun1Coeff[0][2],Fun1Coeff[0][3])
elif R2max == R2LinearCoeff:
EffGe = LinearFun(xVals,LinearCoeff[0][0],LinearCoeff[0][1])
CorrectedSpec = mySpecialDict.copy()
CorrectedSpec['theList'][1] = yVals/EffGe
filename = File.split('.')[0] + '_corrected.hge'
exitcode = WritehgeFile(filename,CorrectedSpec)
return exitcode
def SubFun(ListOpt):
List = ListOpt.copy()
List.pop(0)
if '--noCal' in List:
noCalFlag = True
List.remove('--noCal')
else:
noCalFlag = False
if '--noPlot' in List:
noPlotFlag = True
List.remove('--noPlot')
else:
noPlotFlag = False
if '--wof' in List:
wofFlag = True
List.remove('--wof')
else:
wofFlag = False
if '--log' in List:
logFlag = True
List.remove('--log')
else:
logFlag = False
if '--rebin' in List:
rebinFlag = True
List.remove('--rebin')
rebinNum = None
for Arg in List:
try:
rebinNum = float(Arg)
break
except:
continue
if rebinNum == None:
return 64
else:
rebinFlag = False
FileName1 = List[0]
FileName2 = List[1]
if len(List) == 0:
sys.stderr.write(
'ERROR: "-r" option needs 2 arguments: File1 and File2, which will be substracted to File1.'
)
return 60
if not os.path.isfile(FileName1):
sys.stderr.write("ERROR: %s does not exist.\n" % (FileName1))
return 61
if not os.path.isfile(FileName2):
sys.stderr.write("ERROR: %s does not exist.\n" % (FileName2))
return 62
File1Ext = FileName1.split('.')[-1]
File2Ext = FileName2.split('.')[-1]
if File1Ext != File2Ext:
sys.stderr.write(
"Errror: background substraction needs the same extension as the main file. (for now)"
)
return 65
if noCalFlag:
File1Dict = functionDict[File1Ext](FileName1, True)
File2Dict = functionDict[File2Ext](FileName2, True)
else:
File1Dict = functionDict[File1Ext](FileName1, False)
File2Dict = functionDict[File2Ext](FileName2, False)
if rebinFlag:
File1Dict["theRebinedList"] = getRebinedList(File1Dict["theList"],
rebinNum)
File2Dict["theRebinedList"] = getRebinedList(File2Dict["theList"],
rebinNum)
myLen1 = len(File1Dict["theRebinedList"][1])
myLen2 = len(File2Dict["theRebinedList"][1])
else:
myLen1 = len(File1Dict["theList"][1])
myLen2 = len(File2Dict["theList"][1])
if myLen1 != myLen2:
sys.stderr.write(
"ERROR: histograms do not have the same length and histoGe cannot continue.\n"
)
return 63
time1 = File1Dict["expoTime"]
time2 = File2Dict["expoTime"]
tRatio = time1 / time2
rescaledList = getRescaledList(File2Dict['theList'], tRatio)
if File1Dict['calBoolean'] == File2Dict['calBoolean']:
subsTractedL = getSubstractedList(File1Dict['theList'], rescaledList)
else:
print('--------------------------------------------')
sys.stderr.write(
'ERROR: All files must be calibrated or non-calibrated.\n')
print('Sub cannot be performed between different types of files')
print('--------------------------------------------')
exit(43)
pass
allData = subsTractedL
allData.append(rescaledList[1])
allData.append(File1Dict['theList'][1])
Title = FileName1.split('/')[-1].rstrip(
'.' + File1Ext) + '-' + FileName2.split('/')[-1].rstrip('.' + File2Ext)
IdFile = FileName1.rfind('/')
myOutFile = FileName1[:IdFile + 1] + Title + '.txt'
Labels = [
FileName1.split('/')[-1].rstrip('.' + File1Ext),
FileName2.split('/')[-1].rstrip('.' + File1Ext), Title
]
if not noPlotFlag:
simplePlot(allData,
logFlag,
File1Dict['calBoolean'] and File2Dict['calBoolean'],
Label=Labels,
show=True,
Title=Title,
figTitle=Title) #simple plot of subtracted
if wofFlag:
try:
WritehgeFile(myOutFile, subsTractedL)
print('-----------------------------------------')
print('The file was saved as:')
print(myOutFile)
print('-----------------------------------------')
except:
try:
WriteOutputFile(subsTractedL, myOutFile, Title)
print('-----------------------------------------')
print('The file was saved as:')
print(myOutFile)
print('-----------------------------------------')
except IOError:
sys.stderr.write(
'An unexpected error ocurred while saving the data to file.\n'
)
return 66
return 0
def SubFun(ListOpt):
List = ListOpt.copy()
List.pop(0)
if '--noCal' in List:
noCalFlag = True
List.remove('--noCal')
else:
noCalFlag = False
if '--noPlot' in List:
noPlotFlag = True
List.remove('--noPlot')
else:
noPlotFlag = False
if '--wof' in List:
wofFlag = True
List.remove('--wof')
else:
wofFlag = False
if '--log' in List:
logFlag = True
List.remove('--log')
else:
logFlag = False
if '--rebin' in List:
rebinFlag = True
List.remove('--rebin')
rebinNum = None
for Arg in List:
try:
rebinNum = float(Arg)
break
except:
continue
if rebinNum == None:
return 64
else:
rebinFlag = False
FileName1 = List[0]
FileName2 = List[1]
if len(List) == 0:
print(
'ERROR: "-r" option needs 2 arguments: File1 and File2, which will be substracted to File1.'
)
return 60
if not os.path.isfile(FileName1):
print("ERROR: %s does not exist." % (FileName1))
return 61
if not os.path.isfile(FileName2):
print("ERROR: %s does not exist." % (FileName2))
return 62
File1Ext = FileName1.split('.')[-1]
File2Ext = FileName2.split('.')[-1]
if File1Ext != File2Ext:
print(
"Errror: background substraction needs the same extension as the main file. (for now)"
)
return 65
if noCalFlag:
File1Dict = functionDict[File1Ext](FileName1, False)
File2Dict = functionDict[File2Ext](FileName2, False)
else:
File1Dict = functionDict[File1Ext](FileName1)
File2Dict = functionDict[File2Ext](FileName2)
if rebinFlag:
File1Dict["theRebinedList"] = getRebinedList(File1Dict["theList"],
rebinNum)
File2Dict["theRebinedList"] = getRebinedList(File2Dict["theList"],
rebinNum)
myLen1 = len(File1Dict["theRebinedList"][1])
myLen2 = len(File2Dict["theRebinedList"][1])
else:
myLen1 = len(File1Dict["theList"][1])
myLen2 = len(File2Dict["theList"][1])
if myLen1 != myLen2:
print(
"ERROR: histograms do not have the same length and histoGe cannot continue."
)
return 63
time1 = File1Dict["expoTime"]
time2 = File2Dict["expoTime"]
tRatio = time1 / time2
rescaledList = getRescaledList(File2Dict['theList'], tRatio)
subsTractedL = getSubstractedList(File1Dict['theList'], rescaledList)
Title = FileName1.split('/')[-1].rstrip(
'.' + File1Ext) + '-' + FileName2.split('/')[-1].rstrip('.' + File2Ext)
IdFile = FileName1.rfind('/')
myOutFile = FileName1[:IdFile + 1] + Title + '.txt'
if not noPlotFlag:
simplePlot(subsTractedL,
logFlag,
noCalFlag,
Label=None,
show=True,
Title=Title)
if wofFlag:
try:
WritehgeFile(myOutFile, subsTractedL)
print('-----------------------------------------')
print('The file was saved as:')
print(myOutFile)
print('-----------------------------------------')
except:
try:
WriteOutputFile(subsTractedL, myOutFile, Title)
print('-----------------------------------------')
print('The file was saved as:')
print(myOutFile)
print('-----------------------------------------')
except IOError:
print(
'An unexpected error ocurred while saving the data to file.'
)
return 66
return 0