def OnSimulate(self, event):
#---------- Retrive values from panel --------------
AtomList = []
ConcList = []
Atoms = []
text = self.textENERGY.GetValue()
eV0 = float(text) # incident energy
text = self.textANGLE.GetValue()
angle0 = float(text) # incident angle
if eV0 <= 1000: eV0 = 1010
text = self.textELEMENT.GetValue(
) # list of elements and concentrations
words = text.split()
junk = ["'", ",", ":", ";", "/", "\\"]
for (ix, word) in enumerate(words):
concentration = 1.0
skip = 0
for test in junk:
if word == test: skip = 1
if word.startswith(test): word = word[1:]
if word.endswith(test): word = word[:-1]
if skip == 1: continue
if (word.isalpha()): # element name
word = word[0].upper() + word[1:]
AtomList.append(str(word))
else: # concentration
concentration = float(word)
ConcList.append(concentration)
# appending to Atoms is done later.
#
text = self.textSUBSTRATE.GetValue()
substrate1 = str(text) # substrate1 material
text = self.textDENSITY.GetValue()
density1 = float(text) # substrate1 density in g/cc
text = self.textTOP.GetValue()
thickness1 = float(text) # substrate1 thickness in cm
#
text = self.textSUBSTRATE2.GetValue()
substrate2 = str(text) # substrate2 material
text = self.textDENSITY2.GetValue()
density2 = float(text) # substrate2 density
text = self.textBOT.GetValue()
thickness2 = float(text) # substrate2 thickness
text = self.cbLOCATION.GetValue()
loc = text # location of elements
#
unit_PPM = self.cbPPM.GetValue(
) # unit for concentration atomic fraction or weight fraction
#
if unit_PPM == 'weight fraction': # concentrations are in weight fraction
substrate1_material = fluo_det.Material(substrate1, density1)
AtomicWeight_substrate1 = substrate1_material.AtWt # g/mol of substrate1
for (ii, item) in enumerate(AtomList):
AtomicSymbol = item # dilute elements
AtomicWeight = fluo_elem.AtSym2AtWt(AtomicSymbol) # g/mol
concentration_AtWtFract = ConcList[
ii] # concentration in weight fraction
Conversion = AtomicWeight_substrate1 / AtomicWeight # weight fraction to atomic fraction
ConcList[ii] = Conversion * concentration_AtWtFract
#print(AtomicSymbol, concentration_AtWtFract, Conversion, Conversion * concentration_AtWtFract)
# concentrations are in atomic percent now
#
for (ii, item) in enumerate(AtomList):
AtSym = item # name of element
con = ConcList[
ii] / 1.0e6 # concentration, from ppm(1e-6) to fraction
atom1 = fluo_det.ElemFY(
AtSym, con) # atom1.AtomicSybol, atom1.Concentration
Atoms.append(atom1) # Atoms is a list of objects with attributes
#
text = self.cbHE.GetValue()
if text == 'Yes':
xHe = 1
else:
xHe = 0
text = self.textAL.GetValue()
xAl = float(text)
text = self.textKAPTON.GetValue()
xKap = float(text)
text = self.textWD.GetValue()
WD = float(text)
text = self.cbXSW.GetValue() # collimator
if text == 'WD60mm(XRM)': xsw = 0
if text == 'WD30mm(XSW)': xsw = 1
if text == 'none': xsw = -1
# -------------- run functions in fluo.py -----------------------------
reload(fluo_det)
self.input = fluo_det.input_param(eV0, Atoms, xHe, xAl, xKap, WD, xsw)
matrix = fluo_det.SampleMatrix2(substrate1, density1, thickness1,
substrate2, density2, thickness2,
angle0, loc)
#print('####', substrate1, density1, thickness1,substrate2, density2, thickness2)
# --- change directory for pc executable: py2exe makes exe-file in dist folder. put outputfiles one folder up.
exeExists = 0
if os.path.exists(
'fluo_panel.exe'
): # run from exe file put outputs in different folder
exeExists = 1
path0 = os.getcwd()
if self.path == path0 and exeExists == 1: # current directory is the original location
num = len(path0)
range0 = range(num - 1, -1, -1)
for ix in range0:
if path0[ix] == '\\': # find position for right-most '\'
pos0 = ix
break
path0 = path0[:pos0]
os.chdir(path0) # go up one level in directory
# ------------------------------------------------------------------------
textOut = fluo_det.sim_spectra(eV0,
Atoms,
xHe,
xAl,
xKap,
WD,
xsw,
sample=matrix)
printout = 'output: simSpectrum_table.txt, simSpectrum_plot.txt, Elemental_Sensitivity.txt'
printout += ' saved in ' + path0
print(printout)
#self.cbLINES.Destroy()
#self.fyList=[]
#self.cbLINES = wx.ComboBox(self, 3, 'Press [Plot!] to update', (120, 30), (165, 10), self.fyList, wx.CB_DROPDOWN)
self.cbLINES.Clear(
) # use these three lines instead of above 3, 8/27/2010
self.cbLINES.SetValue(str('Press [Plot!] to update'))
self.cbLINES.AppendItems(self.fyList)
# ------------- display output message from fluo.sim_spectra -------------
textList = textOut.split()
self.TextOutputList = []
#self.TextOutput.Destroy() # 8/27/2010
for ii in range(0, len(textList), 2):
temp = textList[ii] + ' ' + textList[ii + 1]
self.TextOutputList.append(temp)
#self.TextOutput = wx.ComboBox(self, 26, 'concentration list', (10, 410), (280, 20), self.TextOutputList, wx.CB_DROPDOWN)
self.TextOutput.Clear()
self.TextOutput.AppendItems(self.TextOutputList)
def __init__(self, parent, id, title):
wx.Dialog.__init__(self, parent, id, 'SimFluo: fluorescence spectrum simulation', size=(350, 480))
#------------- read simulated spectrum and set plot limits --------------------------
self.data=[]; self.data2=[]
self.plot_on=0
self.path=os.getcwd() # remembers current directory
inputfile='simSpectrum_plot.txt'
if os.path.exists(inputfile)==0:
fo=open(inputfile, 'w')
out1=str(1e3)+' '+str(1e6)+'\n'
fo.write(out1)
out1=str(10e3)+' '+str(10e6)+'\n'
fo.write(out1)
fo.close()
f=open(inputfile)
lines=f.readlines()
self.xMin=1e6; self.xMax=-1e6; self.yMin=1e6; self.yMax=-1e6
for line in lines:
if line.startswith('#'): continue
words=line.split()
xx=float(words[0])
if self.xMin>xx: self.xMin=xx
if self.xMax<=xx: self.xMax=xx
yy=float(words[1])
if self.yMin>yy: self.yMin=yy
if self.yMax<=yy: self.yMax=yy
self.data.append((xx, yy))
f.close()
HeList=['Yes', 'No']
xswList=['WD60mm(XRM)', 'WD30mm(XSW)', 'none']
self.fyList=[]
self.locationList=['all', 'top', 'bottom', 'surface']
self.ppmList=['atomic fraction', 'weight fraction']
self.TextOutputList=[]
self.input=fluo_det.input_param()
#--------------------------------------------------------------------------
btnSim = wx.Button(self, 1, 'Simulate!', (30,10))
btnPlot = wx.Button(self, 2, 'Plot!', (30,35))
self.cbLINES = wx.ComboBox(self, 3, 'emission lines', (120, 30), (165, 10), self.fyList, wx.CB_DROPDOWN)
#
wx.StaticText(self, -1, "incident x-ray energy (eV)", (5, 60))
self.textENERGY = wx.TextCtrl(self, 10, '7500', (10, 75))
wx.StaticText(self, -1, "incident x-ray angle (Deg.)", (165, 60))
self.textANGLE = wx.TextCtrl(self, 11, '45.', (170, 75))
#
wx.StaticText(self, -1, "elements and concentrations (ppm of top substrate material)", (5, 100))
wx.StaticText(self, -1, "in atomic fraction or weight fraction", (5, 115))
self.cbPPM = wx.ComboBox(self, 12, 'atomic fraction', (200, 113), (140, 10), self.ppmList, wx.CB_DROPDOWN)
self.textELEMENT = wx.TextCtrl(self, 13, 'La 10 Ce 10 Nd 10', (10,135), size=(280, 20))
#
wx.StaticText(self, -1, "top substrate material", (5, 155))
self.textSUBSTRATE = wx.TextCtrl(self, 14, 'CaCO3', (10, 170), (80, 20))
wx.StaticText(self, -1, "density (g/cc)", (135, 155))
self.textDENSITY = wx.TextCtrl(self, 15, '2.71', (140, 170), (80, 20))
wx.StaticText(self, -1, "thickness (cm)", (235, 155))
self.textTOP = wx.TextCtrl(self, 16, '0.001', (240, 170), (80, 20))
#
wx.StaticText(self, -1, "bottom substrate material", (5, 195))
self.textSUBSTRATE2 = wx.TextCtrl(self, 17, 'Al2O3', (10, 210), (80, 20))
wx.StaticText(self, -1, "density (g/cc)", (135, 195))
self.textDENSITY2 = wx.TextCtrl(self, 18, '3.97', (140, 210), (80, 20))
wx.StaticText(self, -1, "thickness (cm)", (235, 195))
self.textBOT = wx.TextCtrl(self, 19, '0.001', (240, 210), (80, 20))
#
wx.StaticText(self, -1, 'location of fluorescence elements', (5, 235))
self.cbLOCATION = wx.ComboBox(self, 20, 'all', (10, 250), (165, 10), \
self.locationList, wx.CB_DROPDOWN)
#
wx.StaticText(self, -1, "He-path used?", (5, 275))
self.cbHE = wx.ComboBox(self, 21, 'No', (10, 290), (95, 10), HeList, wx.CB_DROPDOWN)
wx.StaticText(self, -1, '# of Al film (1.5mil)', (5, 315))
self.textAL = wx.TextCtrl(self, 22, '0', (10, 330))
wx.StaticText(self, -1, "# of Kapton film (0.3mil)", (165, 315))
self.textKAPTON = wx.TextCtrl(self, 23, '0', (170, 330))
wx.StaticText(self, -1, "Vortex detector distance (cm)", (5, 355))
self.textWD = wx.TextCtrl(self, 24, '6.0', (10, 370))
wx.StaticText(self, -1, "detector collimator", (165, 355))
self.cbXSW = wx.ComboBox(self, 25, 'WD60mm(XRM)', (170, 370), (120, 10), xswList, wx.CB_DROPDOWN)
self.TextOutput = wx.ComboBox(self, 26, 'output message', (10, 410), (250, 20), self.TextOutputList, wx.CB_DROPDOWN)
#
wx.EVT_BUTTON(self, 1, self.OnSimulate)
wx.EVT_BUTTON(self, 2, self.OnPlot)
wx.EVT_TEXT(self, 14, self.OntextSUBSTRATE)
wx.EVT_TEXT(self, 17, self.OntextSUBSTRATE2)
wx.EVT_TEXT(self, 25, self.OnCBXSW)
wx.EVT_CLOSE(self, self.OnQuit)
def __init__(self, parent, id, title):
wx.Dialog.__init__(self,
parent,
id,
'SimFluo: fluorescence spectrum simulation',
size=(350, 480))
#------------- read simulated spectrum and set plot limits --------------------------
self.data = []
self.data2 = []
self.plot_on = 0
self.path = os.getcwd() # remembers current directory
inputfile = 'simSpectrum_plot.txt'
if os.path.exists(inputfile) == 0:
fo = open(inputfile, 'w')
out1 = str(1e3) + ' ' + str(1e6) + '\n'
fo.write(out1)
out1 = str(10e3) + ' ' + str(10e6) + '\n'
fo.write(out1)
fo.close()
f = open(inputfile)
lines = f.readlines()
self.xMin = 1e6
self.xMax = -1e6
self.yMin = 1e6
self.yMax = -1e6
for line in lines:
if line.startswith('#'): continue
words = line.split()
xx = float(words[0])
if self.xMin > xx: self.xMin = xx
if self.xMax <= xx: self.xMax = xx
yy = float(words[1])
if self.yMin > yy: self.yMin = yy
if self.yMax <= yy: self.yMax = yy
self.data.append((xx, yy))
f.close()
HeList = ['Yes', 'No']
xswList = ['WD60mm(XRM)', 'WD30mm(XSW)', 'none']
self.fyList = []
self.locationList = ['all', 'top', 'bottom', 'surface']
self.ppmList = ['atomic fraction', 'weight fraction']
self.TextOutputList = []
self.input = fluo_det.input_param()
#--------------------------------------------------------------------------
btnSim = wx.Button(self, 1, 'Simulate!', (30, 10))
btnPlot = wx.Button(self, 2, 'Plot!', (30, 35))
self.cbLINES = wx.ComboBox(self, 3, 'emission lines', (120, 30),
(165, 10), self.fyList, wx.CB_DROPDOWN)
#
wx.StaticText(self, -1, "incident x-ray energy (eV)", (5, 60))
self.textENERGY = wx.TextCtrl(self, 10, '7500', (10, 75))
wx.StaticText(self, -1, "incident x-ray angle (Deg.)", (165, 60))
self.textANGLE = wx.TextCtrl(self, 11, '45.', (170, 75))
#
wx.StaticText(
self, -1,
"elements and concentrations (ppm of top substrate material)",
(5, 100))
wx.StaticText(self, -1, "in atomic fraction or weight fraction",
(5, 115))
self.cbPPM = wx.ComboBox(self, 12, 'atomic fraction', (200, 113),
(140, 10), self.ppmList, wx.CB_DROPDOWN)
self.textELEMENT = wx.TextCtrl(self,
13,
'La 10 Ce 10 Nd 10', (10, 135),
size=(280, 20))
#
wx.StaticText(self, -1, "top substrate material", (5, 155))
self.textSUBSTRATE = wx.TextCtrl(self, 14, 'CaCO3', (10, 170),
(80, 20))
wx.StaticText(self, -1, "density (g/cc)", (135, 155))
self.textDENSITY = wx.TextCtrl(self, 15, '2.71', (140, 170), (80, 20))
wx.StaticText(self, -1, "thickness (cm)", (235, 155))
self.textTOP = wx.TextCtrl(self, 16, '0.001', (240, 170), (80, 20))
#
wx.StaticText(self, -1, "bottom substrate material", (5, 195))
self.textSUBSTRATE2 = wx.TextCtrl(self, 17, 'Al2O3', (10, 210),
(80, 20))
wx.StaticText(self, -1, "density (g/cc)", (135, 195))
self.textDENSITY2 = wx.TextCtrl(self, 18, '3.97', (140, 210), (80, 20))
wx.StaticText(self, -1, "thickness (cm)", (235, 195))
self.textBOT = wx.TextCtrl(self, 19, '0.001', (240, 210), (80, 20))
#
wx.StaticText(self, -1, 'location of fluorescence elements', (5, 235))
self.cbLOCATION = wx.ComboBox(self, 20, 'all', (10, 250), (165, 10), \
self.locationList, wx.CB_DROPDOWN)
#
wx.StaticText(self, -1, "He-path used?", (5, 275))
self.cbHE = wx.ComboBox(self, 21, 'No', (10, 290), (95, 10), HeList,
wx.CB_DROPDOWN)
wx.StaticText(self, -1, '# of Al film (1.5mil)', (5, 315))
self.textAL = wx.TextCtrl(self, 22, '0', (10, 330))
wx.StaticText(self, -1, "# of Kapton film (0.3mil)", (165, 315))
self.textKAPTON = wx.TextCtrl(self, 23, '0', (170, 330))
wx.StaticText(self, -1, "Vortex detector distance (cm)", (5, 355))
self.textWD = wx.TextCtrl(self, 24, '6.0', (10, 370))
wx.StaticText(self, -1, "detector collimator", (165, 355))
self.cbXSW = wx.ComboBox(self, 25, 'WD60mm(XRM)', (170, 370),
(120, 10), xswList, wx.CB_DROPDOWN)
self.TextOutput = wx.ComboBox(self, 26, 'output message', (10, 410),
(250, 20), self.TextOutputList,
wx.CB_DROPDOWN)
#
wx.EVT_BUTTON(self, 1, self.OnSimulate)
wx.EVT_BUTTON(self, 2, self.OnPlot)
wx.EVT_TEXT(self, 14, self.OntextSUBSTRATE)
wx.EVT_TEXT(self, 17, self.OntextSUBSTRATE2)
wx.EVT_TEXT(self, 25, self.OnCBXSW)
wx.EVT_CLOSE(self, self.OnQuit)
def OnSimulate(self, event):
#---------- Retrive values from panel --------------
AtomList=[]; ConcList=[]; Atoms=[]
text=self.textENERGY.GetValue()
eV0=float(text) # incident energy
text=self.textANGLE.GetValue()
angle0=float(text) # incident angle
if eV0<=1000: eV0=1010
text=self.textELEMENT.GetValue() # list of elements and concentrations
words=text.split()
junk=["'", ",", ":", ";", "/", "\\"]
for (ix,word) in enumerate(words):
concentration=1.0; skip=0
for test in junk:
if word==test: skip=1
if word.startswith(test): word=word[1:]
if word.endswith(test): word=word[:-1]
if skip==1: continue
if (word.isalpha()): # element name
word=word[0].upper()+word[1:]
AtomList.append(str(word))
else: # concentration
concentration=float(word)
ConcList.append(concentration)
# appending to Atoms is done later.
#
text=self.textSUBSTRATE.GetValue()
substrate1=str(text) # substrate1 material
text=self.textDENSITY.GetValue()
density1=float(text) # substrate1 density in g/cc
text=self.textTOP.GetValue()
thickness1=float(text) # substrate1 thickness in cm
#
text=self.textSUBSTRATE2.GetValue()
substrate2=str(text) # substrate2 material
text=self.textDENSITY2.GetValue()
density2=float(text) # substrate2 density
text=self.textBOT.GetValue()
thickness2=float(text) # substrate2 thickness
text=self.cbLOCATION.GetValue()
loc=text # location of elements
#
unit_PPM=self.cbPPM.GetValue() # unit for concentration atomic fraction or weight fraction
#
if unit_PPM=='weight fraction': # concentrations are in weight fraction
substrate1_material = fluo_det.Material(substrate1, density1)
AtomicWeight_substrate1 = substrate1_material.AtWt # g/mol of substrate1
for (ii, item) in enumerate(AtomList):
AtomicSymbol = item # dilute elements
AtomicWeight = fluo_elem.AtSym2AtWt(AtomicSymbol) # g/mol
concentration_AtWtFract = ConcList[ii] # concentration in weight fraction
Conversion = AtomicWeight_substrate1/AtomicWeight # weight fraction to atomic fraction
ConcList[ii] = Conversion * concentration_AtWtFract
#print AtomicSymbol, concentration_AtWtFract, Conversion, Conversion * concentration_AtWtFract
# concentrations are in atomic percent now
#
for (ii, item) in enumerate(AtomList):
AtSym=item # name of element
con=ConcList[ii]/1.0e6 # concentration, from ppm(1e-6) to fraction
atom1=fluo_det.ElemFY(AtSym, con) # atom1.AtomicSybol, atom1.Concentration
Atoms.append(atom1) # Atoms is a list of objects with attributes
#
text=self.cbHE.GetValue()
if text=='Yes':
xHe=1
else:
xHe=0
text=self.textAL.GetValue()
xAl=float(text)
text=self.textKAPTON.GetValue()
xKap=float(text)
text=self.textWD.GetValue()
WD=float(text)
text=self.cbXSW.GetValue() # collimator
if text=='WD60mm(XRM)': xsw=0
if text=='WD30mm(XSW)': xsw=1
if text=='none': xsw=-1
# -------------- run functions in fluo.py -----------------------------
reload(fluo_det)
self.input=fluo_det.input_param(eV0, Atoms, xHe, xAl, xKap, WD, xsw)
matrix=fluo_det.SampleMatrix2(substrate1, density1, thickness1,substrate2, density2, thickness2, angle0, loc)
#print '####', substrate1, density1, thickness1,substrate2, density2, thickness2
# --- change directory for pc executable: py2exe makes exe-file in dist folder. put outputfiles one folder up.
exeExists=0
if os.path.exists('fluo_panel.exe'): # run from exe file put outputs in different folder
exeExists=1
path0=os.getcwd()
if self.path==path0 and exeExists==1: # current directory is the original location
num=len(path0)
range0=range(num-1, -1, -1)
for ix in range0:
if path0[ix]=='\\' : # find position for right-most '\'
pos0=ix
break
path0=path0[:pos0]
os.chdir(path0) # go up one level in directory
# ------------------------------------------------------------------------
textOut=fluo_det.sim_spectra(eV0, Atoms, xHe, xAl, xKap, WD, xsw, sample=matrix)
printout='output: simSpectrum_table.txt, simSpectrum_plot.txt, Elemental_Sensitivity.txt'
printout+=' saved in '+path0
print printout
#self.cbLINES.Destroy()
#self.fyList=[]
#self.cbLINES = wx.ComboBox(self, 3, 'Press [Plot!] to update', (120, 30), (165, 10), self.fyList, wx.CB_DROPDOWN)
self.cbLINES.Clear() # use these three lines instead of above 3, 8/27/2010
self.cbLINES.SetValue(str('Press [Plot!] to update'))
self.cbLINES.AppendItems(self.fyList)
# ------------- display output message from fluo.sim_spectra -------------
textList=textOut.split()
self.TextOutputList=[]
#self.TextOutput.Destroy() # 8/27/2010
for ii in range(0, len(textList), 2):
temp=textList[ii]+' '+textList[ii+1]
self.TextOutputList.append(temp)
#self.TextOutput = wx.ComboBox(self, 26, 'concentration list', (10, 410), (280, 20), self.TextOutputList, wx.CB_DROPDOWN)
self.TextOutput.Clear()
self.TextOutput.AppendItems(self.TextOutputList)