def initChordUI(self):
self.m_chordFrame = self.m_chord.m_scrollable_frame
self.m_fileSelectionControl = InputFileListBoxControl(
self.m_chordFrame, lambda e: None)
self.m_fileSelectionControl.grid(row=0,
column=0,
columnspan=4,
sticky="nsew")
self.m_optionsLabel = ttk.Label(
self.m_chordFrame,
text="Processing Options:") #, compound = tk.CENTER)
self.m_optionsLabel.grid(row=3, column=0, columnspan=2, sticky="nsw")
self.m_tCutStartLabel = ttk.Label(self.m_chordFrame,
text="Cut Data Start Temp.:")
self.m_tCutStartLabel.grid(row=4, column=1, sticky="nse")
self.m_tCutStartEntry = EnhancedEntry(self.m_chordFrame)
self.m_tCutStartEntry.grid(row=4, column=2, sticky="nsw")
self.m_tCutEndLabel = ttk.Label(self.m_chordFrame,
text="Cut Data End Temp.:")
self.m_tCutEndLabel.grid(row=5, column=1, sticky="nse")
self.m_tCutEndEntry = EnhancedEntry(self.m_chordFrame)
self.m_tCutEndEntry.grid(row=5, column=2, sticky="nsw")
self.m_testButton = ttk.Button(self.m_chordFrame,
text="test",
command=self.adaptTransformTest)
self.m_testButton.grid(row=6, column=0, columnspan=4, sticky="nsew")
self.m_Label = ttk.Label(self.m_chordFrame, text='Work in Progress')
self.m_Label.grid(row=7, column=0, columnspan=4, sticky="nsew")
self.m_chordFrame.grid_columnconfigure(index=0,
weight=1,
uniform="test1")
self.m_chordFrame.grid_columnconfigure(index=1,
weight=1,
uniform="test1")
self.m_chordFrame.grid_columnconfigure(index=2,
weight=1,
uniform="test2")
self.m_chordFrame.grid_columnconfigure(index=3,
weight=1,
uniform="test3")
def initChordUI(self):
self.m_chordFrame = self.m_chord.m_scrollable_frame
# File selection
self.m_fileSelectionControl = SingleInputFileSelectionControl(
self.m_chordFrame, onSelect=self.onFileSelected)
self.m_fileSelectionControl.grid(row=0,
column=0,
columnspan=4,
sticky="nsew")
# Spectrum selection
self.m_spectrumSelectionLabel = ttk.Label(
self.m_chordFrame, text='Select TPD Spectrum for Integration:')
self.m_spectrumSelectionLabel.grid(row=1,
column=0,
columnspan=2,
sticky="nsw")
self.m_spectrumCB = ttk.Combobox(self.m_chordFrame)
self.m_spectrumCB.configure(state='readonly')
self.m_spectrumCB.bind(
"<<ComboboxSelected>>", self.onSpectrumSelected
) #binding to event because CB does not have 'command' param
self.m_spectrumCB.grid(row=2, column=0, columnspan=3, sticky="nsew")
# self.m_spectrumSelectionLabel = ttk.Label(self.m_chordFrame, text='Select Mass Spectrum for Integration:')
# self.m_spectrumSelectionLabel.grid(row = 3, column = 0, columnspan = 2, sticky="nsw")
# self.m_spectrumCB = ttk.Combobox(self.m_chordFrame)
# # self.m_prefactorCB.bind("<<ComboboxSelected>>", self.plotDataForSelectedPrefactor) #binding to event because CB does not have 'command' param
# self.m_spectrumCB.grid(row = 4, column = 0, columnspan = 3, sticky = "nsew")
# Integration Options
self.m_optionsLabel = ttk.Label(
self.m_chordFrame,
text="Fitting Options:") #, compound = tk.CENTER)
self.m_optionsLabel.grid(row=5, column=0, sticky="nsw")
self.m_tCutStartLabel = ttk.Label(self.m_chordFrame,
text="Lower Boundary")
self.m_tCutStartLabel.grid(row=6, column=1, sticky="nse")
self.m_tCutStartEntry = EnhancedEntry(self.m_chordFrame)
self.m_tCutStartEntry.grid(row=6, column=2, sticky="nsw")
self.m_tCutEndLabel = ttk.Label(self.m_chordFrame,
text="Upper Boundary")
self.m_tCutEndLabel.grid(row=7, column=1, sticky="nse")
self.m_tCutEndEntry = EnhancedEntry(self.m_chordFrame)
self.m_tCutEndEntry.grid(row=7, column=2, sticky="nsw")
self.m_resultTitleLabel = ttk.Label(self.m_chordFrame,
text="Fitting Results:")
self.m_resultTitleLabel.grid(row=8, column=1, sticky="nse")
self.m_resultValueLabel = ttk.Label(self.m_chordFrame, text="N/A")
self.m_resultValueLabel.grid(row=8, column=2, sticky="nsw")
self.m_Label = ttk.Label(self.m_chordFrame, text='Work in Progress')
self.m_Label.grid(row=9, column=0, columnspan=4, sticky="nsew")
class RedheadAnalysisControl(ProcessingControlBase):
def __init__(self, controller, root, accordion):
super().__init__("Redhead Analysis (WIP)", controller, accordion)
self.m_parsedData = None
self.m_plots["Processed Data"] = MPLContainer(
self.m_chord.m_notebookRef, "Processed Data",
"Desorption Rate (arb. U.)", "Temperature (K)", root)
self.m_plots["Arrhenius Plot (Processed)"] = MPLContainer(
self.m_chord.m_notebookRef,
"Arrhenius Plot (Processed)",
"ln(Desorption Rate)",
"Reciprocal Temperature (1/K)",
root,
invertXAxis=True)
def onFileSelected(self):
self.m_parsedData = ProcessedDataWrapper(
self.m_fileSelectionControl.m_inputFilePath)
self.m_parsedData.parseProcessedDataFile()
if (self.m_parsedData.m_normalized):
tk.messagebox.showerror(
"Input Data",
"Please use processed data which has not been normalized to a monolayer!"
)
self.m_spectrumCB["values"] = None
else:
self.m_spectrumCB["values"] = self.m_parsedData.m_includedFiles
# self.m_spectrumCB.current(0)
def plotBounds(self):
# for plot in self.m_plots.values():
# plot.removeVerticalLines()
# plot.addVerticalLine(float(self.m_tCutEndEntry.get()))
# plot.addVerticalLine(float(self.m_tCutStartEntry.get()))
self.m_plots["Processed Data"].removeVerticalLines()
# if(not self.m_integrated):
self.m_plots["Processed Data"].addVerticalLine(
float(self.m_tCutEndEntry.get()))
self.m_plots["Processed Data"].addVerticalLine(
float(self.m_tCutStartEntry.get()))
def plotSelectedSpectrum(self):
targetData = self.m_parsedData.fileNameToExpDesorptionRateVSTemp(
self.m_spectrumCB.get())
targetLabel = self.m_parsedData.fileNameToCoverageLabel(
self.m_spectrumCB.get())
arrheniusData = np.vstack(
(np.reciprocal(targetData[0, :]), np.log(targetData[1, :])))
self.m_plots["Processed Data"].clearPlots()
self.m_plots["Processed Data"].addPrimaryLinePlots(targetData,
targetLabel,
color='b')
self.m_plots["Arrhenius Plot (Processed)"].clearPlots()
self.m_plots["Arrhenius Plot (Processed)"].addPrimaryLinePlots(
arrheniusData, targetLabel, color='b')
self.plotBounds()
# if(self.m_integrated): #shade, currently has performance problems when drawing polygon
# t2 = float(self.m_tCutEndEntry.get())
# t1 = float(self.m_tCutStartEntry.get())
# curve = self.m_parsedData.getProcessedDataBetweenForFile(t1,t2,self.m_spectrumCB.get())
# self.m_plots["Processed Data"].shadeBelowCurve(curve[0],curve[1])
def onSpectrumSelected(self, *args, **kwargs):
if (self.m_parsedData != None):
self.m_integrated = False
self.checkIntegrationBounds()
self.plotSelectedSpectrum()
def tryReadStartCutEntry(self):
if (self.m_tCutStartEntry.get() == ''):
return False
try:
int(self.m_tCutStartEntry.get())
except ValueError:
tk.messagebox.showerror(
"Initial Temperature",
"Please enter an integer for the temperature at which to start integration."
)
return False
return True
def tryReadStopCutEntry(self):
if (self.m_tCutEndEntry.get() == ''):
return False
try:
int(self.m_tCutEndEntry.get())
except ValueError:
tk.messagebox.showerror(
"Final Temperature",
"Please enter an integer for the temperature at which to end integration."
)
return False
return True
def checkIntegrationBounds(self):
minStartCut = int(self.m_parsedData.getMinTemp())
maxStopCut = int(self.m_parsedData.getMaxTemp())
if (self.tryReadStartCutEntry()):
if (minStartCut > int(self.m_tCutStartEntry.get())):
self.m_tCutStartEntry.set(str(minStartCut))
else:
self.m_tCutStartEntry.set(str(minStartCut))
if (self.tryReadStopCutEntry()):
if (maxStopCut < int(self.m_tCutEndEntry.get())):
self.m_tCutEndEntry.set(str(maxStopCut))
else:
self.m_tCutEndEntry.set(str(maxStopCut))
def onBoundsChanged(self):
self.checkIntegrationBounds()
def processInput(self):
self.checkIntegrationBounds()
t2 = float(self.m_tCutEndEntry.get())
t1 = float(self.m_tCutStartEntry.get())
result = self.m_parsedData.integrateDesorptionRate(
t1, t2, self.m_spectrumCB.get())
self.m_integrated = True
self.m_resultValueLabel.configure(text=str(result))
self.plotSelectedSpectrum(
) #should update plot with appropriate shading
def initChordUI(self):
self.m_chordFrame = self.m_chord.m_scrollable_frame
# File selection
self.m_fileSelectionControl = SingleInputFileSelectionControl(
self.m_chordFrame, onSelect=self.onFileSelected)
self.m_fileSelectionControl.grid(row=0,
column=0,
columnspan=4,
sticky="nsew")
# Spectrum selection
self.m_spectrumSelectionLabel = ttk.Label(
self.m_chordFrame, text='Select TPD Spectrum for Integration:')
self.m_spectrumSelectionLabel.grid(row=1,
column=0,
columnspan=2,
sticky="nsw")
self.m_spectrumCB = ttk.Combobox(self.m_chordFrame)
self.m_spectrumCB.configure(state='readonly')
self.m_spectrumCB.bind(
"<<ComboboxSelected>>", self.onSpectrumSelected
) #binding to event because CB does not have 'command' param
self.m_spectrumCB.grid(row=2, column=0, columnspan=3, sticky="nsew")
# self.m_spectrumSelectionLabel = ttk.Label(self.m_chordFrame, text='Select Mass Spectrum for Integration:')
# self.m_spectrumSelectionLabel.grid(row = 3, column = 0, columnspan = 2, sticky="nsw")
# self.m_spectrumCB = ttk.Combobox(self.m_chordFrame)
# # self.m_prefactorCB.bind("<<ComboboxSelected>>", self.plotDataForSelectedPrefactor) #binding to event because CB does not have 'command' param
# self.m_spectrumCB.grid(row = 4, column = 0, columnspan = 3, sticky = "nsew")
# Integration Options
self.m_optionsLabel = ttk.Label(
self.m_chordFrame,
text="Fitting Options:") #, compound = tk.CENTER)
self.m_optionsLabel.grid(row=5, column=0, sticky="nsw")
self.m_tCutStartLabel = ttk.Label(self.m_chordFrame,
text="Lower Boundary")
self.m_tCutStartLabel.grid(row=6, column=1, sticky="nse")
self.m_tCutStartEntry = EnhancedEntry(self.m_chordFrame)
self.m_tCutStartEntry.grid(row=6, column=2, sticky="nsw")
self.m_tCutEndLabel = ttk.Label(self.m_chordFrame,
text="Upper Boundary")
self.m_tCutEndLabel.grid(row=7, column=1, sticky="nse")
self.m_tCutEndEntry = EnhancedEntry(self.m_chordFrame)
self.m_tCutEndEntry.grid(row=7, column=2, sticky="nsw")
self.m_resultTitleLabel = ttk.Label(self.m_chordFrame,
text="Fitting Results:")
self.m_resultTitleLabel.grid(row=8, column=1, sticky="nse")
self.m_resultValueLabel = ttk.Label(self.m_chordFrame, text="N/A")
self.m_resultValueLabel.grid(row=8, column=2, sticky="nsw")
self.m_Label = ttk.Label(self.m_chordFrame, text='Work in Progress')
self.m_Label.grid(row=9, column=0, columnspan=4, sticky="nsew")
def initChordUI(self):
self.m_chordFrame = self.m_chord.m_scrollable_frame
# File selection
self.m_fileSelectionControl = SingleInputFileSelectionControl(
self.m_chordFrame, onSelect=self.onFileSelected)
self.m_fileSelectionControl.grid(row=0,
column=0,
columnspan=4,
sticky="nsew")
# Spectrum selection
self.m_spectrumSelectionLabel = ttk.Label(
self.m_chordFrame, text='Select TPD Spectrum for analysis:')
self.m_spectrumSelectionLabel.grid(row=1,
column=0,
columnspan=2,
sticky="nsw")
self.m_spectrumCB = ttk.Combobox(self.m_chordFrame)
self.m_spectrumCB.configure(state='readonly')
self.m_spectrumCB.bind(
"<<ComboboxSelected>>", self.onSpectrumSelected
) #binding to event because CB does not have 'command' param
self.m_spectrumCB.grid(row=2, column=0, columnspan=3, sticky="nsew")
# self.m_spectrumSelectionLabel = ttk.Label(self.m_chordFrame, text='Select Mass Spectrum for Integration:')
# self.m_spectrumSelectionLabel.grid(row = 3, column = 0, columnspan = 2, sticky="nsw")
# self.m_spectrumCB = ttk.Combobox(self.m_chordFrame)
# # self.m_prefactorCB.bind("<<ComboboxSelected>>", self.plotDataForSelectedPrefactor) #binding to event because CB does not have 'command' param
# self.m_spectrumCB.grid(row = 4, column = 0, columnspan = 3, sticky = "nsew")
# Integration Options
self.m_optionsLabel = ttk.Label(
self.m_chordFrame,
text="Fitting Options:") #, compound = tk.CENTER)
self.m_optionsLabel.grid(row=5, column=0, sticky="nsw")
self.m_tCutStartLabel = ttk.Label(self.m_chordFrame,
text="Lower Boundary (1/T)")
self.m_tCutStartLabel.grid(row=6, column=1, sticky="nse")
self.m_lowerBoundEntry = EnhancedEntry(
self.m_chordFrame,
inputValueType=float,
errorTitle="Lower Boundary",
errorMessage=
"Please enter a decimal for the lower boundary of the leading edge."
)
self.m_lowerBoundEntry.grid(row=6, column=2, sticky="nsw")
self.m_tCutEndLabel = ttk.Label(self.m_chordFrame,
text="Upper Boundary (1/T)")
self.m_tCutEndLabel.grid(row=7, column=1, sticky="nse")
self.m_upperBoundEntry = EnhancedEntry(
self.m_chordFrame,
inputValueType=float,
errorTitle="Upper Boundary",
errorMessage=
"Please enter a decimal for the upper boundary of the leading edge."
)
self.m_upperBoundEntry.grid(row=7, column=2, sticky="nsw")
self.m_resultsLabel = ttk.Label(
self.m_chordFrame, text="Result:") #, compound = tk.CENTER)
self.m_resultsLabel.grid(row=8, column=0, sticky="nsw")
self.m_resultTitleLabel = ttk.Label(self.m_chordFrame,
text="Inv. x-intercept (K):")
self.m_resultTitleLabel.grid(row=9, column=1, sticky="nse")
self.m_resultValueLabel = ttk.Label(self.m_chordFrame, text="N/A")
self.m_resultValueLabel.grid(row=9, column=2, sticky="nsw")
# self.m_Label = ttk.Label(self.m_chordFrame, text='Work in Progress')
# self.m_Label.grid(row = 10, column = 0, columnspan = 4, sticky="nsew")
#Process Button
self.m_processButton = ttk.Button(self.m_chordFrame,
text="Generate Edge Fit",
command=self.processInput)
self.m_processButton.grid(row=10,
column=0,
columnspan=4,
sticky="nsew")
class CoverageCalibrationControl(ProcessingControlBase):
def __init__(self, controller, root, accordion):
super().__init__("Coverage Calibration (WIP)", controller, accordion)
self.m_plots["Coverage"] = MPLContainer(self.m_chord.m_notebookRef,
"Coverage", "Desorption Rate",
"Temperature (K)", root)
self.m_forwardXFactor = 1.0
self.m_inverseXFactor = 1.0
self.m_forwardYFactor = 1.0
self.m_inverseYFactor = 1.0
self.m_plots["Coverage"].addSecondaryScaledXAxis(
self.forwardXTransform, self.inverseXTransform)
self.m_plots["Coverage"].addSecondaryScaledYAxis(
self.forwardYTransform, self.inverseYTransform)
def forwardXTransform(self, x):
return x * self.m_forwardXFactor
def inverseXTransform(self, x):
return x * self.m_inverseXFactor
def forwardYTransform(self, y):
return y * self.m_forwardYFactor
def inverseYTransform(self, y):
return y * self.m_inverseYFactor
def adaptTransformTest(self):
self.m_forwardXFactor = 2.0
self.m_inverseXFactor = 0.5
def initChordUI(self):
self.m_chordFrame = self.m_chord.m_scrollable_frame
self.m_fileSelectionControl = InputFileListBoxControl(
self.m_chordFrame, lambda e: None)
self.m_fileSelectionControl.grid(row=0,
column=0,
columnspan=4,
sticky="nsew")
self.m_optionsLabel = ttk.Label(
self.m_chordFrame,
text="Processing Options:") #, compound = tk.CENTER)
self.m_optionsLabel.grid(row=3, column=0, columnspan=2, sticky="nsw")
self.m_tCutStartLabel = ttk.Label(self.m_chordFrame,
text="Cut Data Start Temp.:")
self.m_tCutStartLabel.grid(row=4, column=1, sticky="nse")
self.m_tCutStartEntry = EnhancedEntry(self.m_chordFrame)
self.m_tCutStartEntry.grid(row=4, column=2, sticky="nsw")
self.m_tCutEndLabel = ttk.Label(self.m_chordFrame,
text="Cut Data End Temp.:")
self.m_tCutEndLabel.grid(row=5, column=1, sticky="nse")
self.m_tCutEndEntry = EnhancedEntry(self.m_chordFrame)
self.m_tCutEndEntry.grid(row=5, column=2, sticky="nsw")
self.m_testButton = ttk.Button(self.m_chordFrame,
text="test",
command=self.adaptTransformTest)
self.m_testButton.grid(row=6, column=0, columnspan=4, sticky="nsew")
self.m_Label = ttk.Label(self.m_chordFrame, text='Work in Progress')
self.m_Label.grid(row=7, column=0, columnspan=4, sticky="nsew")
self.m_chordFrame.grid_columnconfigure(index=0,
weight=1,
uniform="test1")
self.m_chordFrame.grid_columnconfigure(index=1,
weight=1,
uniform="test1")
self.m_chordFrame.grid_columnconfigure(index=2,
weight=1,
uniform="test2")
self.m_chordFrame.grid_columnconfigure(index=3,
weight=1,
uniform="test3")
class LeadingEdgeAnalysisControl(ProcessingControlBase):
def __init__(self, controller, root, accordion):
super().__init__("Leading Edge Analysis", controller, accordion)
self.m_parsedData = None
self.m_1DFitCoefficients = None
# self.m_plots["Processed Data"] = MPLContainer(self.m_chord.m_notebookRef, "Processed Data", "Desorption Rate (arb. U.)", "Temperature (K)", root)
self.m_plots["Arrhenius Plot (Processed)"] = MPLContainer(
self.m_chord.m_notebookRef,
"Arrhenius Plot (Processed)",
"ln(Desorption Rate)",
"Reciprocal Temperature (1/K)",
root,
invertXAxis=True)
def onFileSelected(self):
self.m_parsedData = ProcessedDataWrapper(
self.m_fileSelectionControl.m_inputFilePath)
self.m_parsedData.parseProcessedDataFile()
# if(self.m_parsedData.m_normalized):
# tk.messagebox.showerror("Input Data", "Please use processed data which has not been normalized to a monolayer!")
# self.m_spectrumCB["values"] = None
# else:
self.m_spectrumCB["values"] = self.m_parsedData.m_includedFiles
# self.m_spectrumCB.current(0)
def calc1DPoly(self, coef, xData):
result = list()
for i in range(len(xData)):
result.append(coef[0] + coef[1] * xData[i])
return result
def plotFit(self, coef):
x1 = float(self.m_lowerBoundEntry.get())
x2 = float(self.m_upperBoundEntry.get())
xdat = [x2, x1]
linearFitData = np.vstack((xdat, self.calc1DPoly(coef, xdat)))
self.m_plots["Arrhenius Plot (Processed)"].addPrimaryLinePlots(
linearFitData, "Leading Edge Fit",
color='g') #, shouldRelim = False)
def plotBounds(self):
# for plot in self.m_plots.values():
# plot.removeVerticalLines()
# plot.addVerticalLine(float(self.m_tCutEndEntry.get()))
# plot.addVerticalLine(float(self.m_tCutStartEntry.get()))
self.m_plots["Arrhenius Plot (Processed)"].removeVerticalLines()
# if(not self.m_integrated):
self.m_plots["Arrhenius Plot (Processed)"].addVerticalLine(
float(self.m_upperBoundEntry.get()))
self.m_plots["Arrhenius Plot (Processed)"].addVerticalLine(
float(self.m_lowerBoundEntry.get()))
def plotSelectedSpectrum(self):
targetData = self.m_parsedData.fileNameToExpDesorptionRateVSTemp(
self.m_spectrumCB.get())
targetLabel = self.m_parsedData.fileNameToCoverageLabel(
self.m_spectrumCB.get())
arrheniusData = np.vstack(
(np.reciprocal(targetData[0, :]), np.log(targetData[1, :])))
# self.m_plots["Processed Data"].clearPlots()
# self.m_plots["Processed Data"].addPrimaryLinePlots(targetData,targetLabel, color = 'b')
self.m_plots["Arrhenius Plot (Processed)"].clearPlots()
self.m_plots["Arrhenius Plot (Processed)"].addPrimaryLinePlots(
arrheniusData, targetLabel, color='b')
if (self.m_1DFitCoefficients.any()):
self.plotFit(self.m_1DFitCoefficients)
self.plotBounds()
# if(self.m_integrated): #shade, currently has performance problems when drawing polygon
# t2 = float(self.m_tCutEndEntry.get())
# t1 = float(self.m_tCutStartEntry.get())
# curve = self.m_parsedData.getProcessedDataBetweenForFile(t1,t2,self.m_spectrumCB.get())
# self.m_plots["Processed Data"].shadeBelowCurve(curve[0],curve[1])
def onSpectrumSelected(self, *args, **kwargs):
if (self.m_parsedData != None):
self.m_fitted = False
self.checkFitBounds()
self.plotSelectedSpectrum()
def checkFitBounds(self):
minStartCut = float(1.0 / self.m_parsedData.getMaxTemp())
maxStopCut = float(1.0 / self.m_parsedData.getMinTemp())
if (self.m_lowerBoundEntry.InputIsValid()):
if (minStartCut > float(self.m_lowerBoundEntry.get())):
self.m_lowerBoundEntry.set(str(minStartCut))
else:
self.m_lowerBoundEntry.set(str(minStartCut))
if (self.m_upperBoundEntry.InputIsValid()):
if (maxStopCut < float(self.m_upperBoundEntry.get())):
self.m_upperBoundEntry.set(str(maxStopCut))
else:
self.m_upperBoundEntry.set(str(maxStopCut))
def onBoundsChanged(self):
self.checkFitBounds()
def processInput(self):
self.checkFitBounds()
t2 = float(self.m_upperBoundEntry.get())
t1 = float(self.m_lowerBoundEntry.get())
targetData = self.m_parsedData.fileNameToExpDesorptionRateVSTemp(
self.m_spectrumCB.get())
# targetLabel = self.m_parsedData.fileNameToCoverageLabel(self.m_spectrumCB.get())
# arrheniusData = np.vstack((np.reciprocal(targetData[0,:]),np.log(targetData[1,:])))
reciprocalTemp = np.reciprocal(targetData[0, :])
logCountRate = np.log(targetData[1, :])
maxIdx = (np.abs(reciprocalTemp - t1)).argmin()
minIdx = (np.abs(reciprocalTemp - t2)).argmin()
# result = self.m_parsedData.integrateDesorptionRate(t1,t2,self.m_spectrumCB.get())
# coef = np.polyfit(reciprocalTemp,logCountRate,1)
self.m_1DFitCoefficients = npp.polynomial.polyfit(
reciprocalTemp[minIdx:maxIdx], logCountRate[minIdx:maxIdx], 1)
# linearFitPoly = np.poly1d(coef)
# self.plotFit(self.m_1DFitCoefficients)
leadingEdgeTempXIntercept = -self.m_1DFitCoefficients[
1] / self.m_1DFitCoefficients[0]
self.m_fitted = True
self.m_resultValueLabel.configure(text=str(leadingEdgeTempXIntercept))
self.plotSelectedSpectrum(
) #should update plot with appropriate shading
def initChordUI(self):
self.m_chordFrame = self.m_chord.m_scrollable_frame
# File selection
self.m_fileSelectionControl = SingleInputFileSelectionControl(
self.m_chordFrame, onSelect=self.onFileSelected)
self.m_fileSelectionControl.grid(row=0,
column=0,
columnspan=4,
sticky="nsew")
# Spectrum selection
self.m_spectrumSelectionLabel = ttk.Label(
self.m_chordFrame, text='Select TPD Spectrum for analysis:')
self.m_spectrumSelectionLabel.grid(row=1,
column=0,
columnspan=2,
sticky="nsw")
self.m_spectrumCB = ttk.Combobox(self.m_chordFrame)
self.m_spectrumCB.configure(state='readonly')
self.m_spectrumCB.bind(
"<<ComboboxSelected>>", self.onSpectrumSelected
) #binding to event because CB does not have 'command' param
self.m_spectrumCB.grid(row=2, column=0, columnspan=3, sticky="nsew")
# self.m_spectrumSelectionLabel = ttk.Label(self.m_chordFrame, text='Select Mass Spectrum for Integration:')
# self.m_spectrumSelectionLabel.grid(row = 3, column = 0, columnspan = 2, sticky="nsw")
# self.m_spectrumCB = ttk.Combobox(self.m_chordFrame)
# # self.m_prefactorCB.bind("<<ComboboxSelected>>", self.plotDataForSelectedPrefactor) #binding to event because CB does not have 'command' param
# self.m_spectrumCB.grid(row = 4, column = 0, columnspan = 3, sticky = "nsew")
# Integration Options
self.m_optionsLabel = ttk.Label(
self.m_chordFrame,
text="Fitting Options:") #, compound = tk.CENTER)
self.m_optionsLabel.grid(row=5, column=0, sticky="nsw")
self.m_tCutStartLabel = ttk.Label(self.m_chordFrame,
text="Lower Boundary (1/T)")
self.m_tCutStartLabel.grid(row=6, column=1, sticky="nse")
self.m_lowerBoundEntry = EnhancedEntry(
self.m_chordFrame,
inputValueType=float,
errorTitle="Lower Boundary",
errorMessage=
"Please enter a decimal for the lower boundary of the leading edge."
)
self.m_lowerBoundEntry.grid(row=6, column=2, sticky="nsw")
self.m_tCutEndLabel = ttk.Label(self.m_chordFrame,
text="Upper Boundary (1/T)")
self.m_tCutEndLabel.grid(row=7, column=1, sticky="nse")
self.m_upperBoundEntry = EnhancedEntry(
self.m_chordFrame,
inputValueType=float,
errorTitle="Upper Boundary",
errorMessage=
"Please enter a decimal for the upper boundary of the leading edge."
)
self.m_upperBoundEntry.grid(row=7, column=2, sticky="nsw")
self.m_resultsLabel = ttk.Label(
self.m_chordFrame, text="Result:") #, compound = tk.CENTER)
self.m_resultsLabel.grid(row=8, column=0, sticky="nsw")
self.m_resultTitleLabel = ttk.Label(self.m_chordFrame,
text="Inv. x-intercept (K):")
self.m_resultTitleLabel.grid(row=9, column=1, sticky="nse")
self.m_resultValueLabel = ttk.Label(self.m_chordFrame, text="N/A")
self.m_resultValueLabel.grid(row=9, column=2, sticky="nsw")
# self.m_Label = ttk.Label(self.m_chordFrame, text='Work in Progress')
# self.m_Label.grid(row = 10, column = 0, columnspan = 4, sticky="nsew")
#Process Button
self.m_processButton = ttk.Button(self.m_chordFrame,
text="Generate Edge Fit",
command=self.processInput)
self.m_processButton.grid(row=10,
column=0,
columnspan=4,
sticky="nsew")
def initChordUI(self):
self.m_chordFrame = self.m_chord.m_scrollable_frame
# File selection
self.m_fileSelectionControl = SingleInputFileSelectionControl(
self.m_chordFrame)
self.m_fileSelectionControl.grid(row=0,
column=0,
columnspan=4,
sticky="nsew")
#Options
self.m_optionsLabel = ttk.Label(
self.m_chordFrame,
text="Inversion Options:") #, compound = tk.CENTER)
self.m_optionsLabel.grid(row=3, column=0, columnspan=2, sticky="nsw")
#Radiobutton var
self.m_RBVariable = tk.IntVar(self.m_chordFrame)
#Single Prefactor
self.m_singleRB = ttk.Radiobutton(self.m_chordFrame,
text="Single Prefactor",
variable=self.m_RBVariable,
value=0,
command=self.changeRB)
self.m_singleRB.grid(row=4, column=1, sticky="nsw")
self.m_tPrefactorLabel = ttk.Label(self.m_chordFrame,
text="Prefactor Value:")
self.m_tPrefactorLabel.grid(row=5, column=1, sticky="nse")
self.m_tPrefactorEntry = EnhancedEntry(
self.m_chordFrame,
inputValueType=float,
errorTitle="Prefactor Value",
errorMessage=
"Please enter a float for the prefactor. For example 1e17.")
self.m_tPrefactorEntry.grid(row=5, column=2, sticky="nsw")
#Or Prefactor Range
self.m_linearRB = ttk.Radiobutton(self.m_chordFrame,
text="Prefactor Range - Linear",
variable=self.m_RBVariable,
value=1,
command=self.changeRB)
self.m_linearRB.grid(row=6, column=1, sticky="nsw")
self.m_tPrefactorIncrementLabel = ttk.Label(self.m_chordFrame,
text="Increment:")
self.m_tPrefactorIncrementLabel.grid(row=7, column=1, sticky="nse")
self.m_tPrefactorIncrementEntry = EnhancedEntry(
self.m_chordFrame,
inputValueType=float,
errorTitle="Increment",
errorMessage="Please enter a float for the prefactor increment.")
self.m_tPrefactorIncrementEntry.grid(row=7, column=2, sticky="nsw")
self.m_multiplicativeRB = ttk.Radiobutton(
self.m_chordFrame,
text="Prefactor Range - Multiplicative (10x)",
variable=self.m_RBVariable,
value=2,
command=self.changeRB)
self.m_multiplicativeRB.grid(row=8, column=1, sticky="nsw")
self.m_tPrefactorStartLabel = ttk.Label(self.m_chordFrame,
text="Lowest Prefactor:")
self.m_tPrefactorStartLabel.grid(row=9, column=1, sticky="nse")
self.m_tPrefactorStartEntry = EnhancedEntry(
self.m_chordFrame,
inputValueType=float,
errorTitle="Lowest Prefactor",
errorMessage=
"Please enter a float for the lowest prefactor. For example 1e13.")
self.m_tPrefactorStartEntry.grid(row=9, column=2, sticky="nsw")
self.m_tPrefactorEndLabel = ttk.Label(self.m_chordFrame,
text="Highest Prefactor:")
self.m_tPrefactorEndLabel.grid(row=10, column=1, sticky="nse")
self.m_tPrefactorEndEntry = EnhancedEntry(
self.m_chordFrame,
inputValueType=float,
errorTitle="Highest Prefactor",
errorMessage=
"Please enter a float for the highest prefactor. For example 1e21."
)
self.m_tPrefactorEndEntry.grid(row=10, column=2, sticky="nsw")
#default values
self.m_tPrefactorStartEntry.setBackingVar("1e15")
self.m_tPrefactorEndEntry.setBackingVar("1e17")
self.m_RBVariable.set(2)
self.changeRB()
#Process Button
self.m_processButton = ttk.Button(self.m_chordFrame,
text="Process Input",
command=self.processInput)
self.m_processButton.grid(row=11,
column=1,
columnspan=2,
sticky="nsew")
# self.m_prbar = ttk.Progressbar(self.m_chordFrame, orient ="horizontal", mode ="determinate", length = 50) #int(self.m_chordFrame.winfo_width() / 2))
# self.m_prbar.grid(row = 12, column = 1, columnspan = 2, sticky="nsw")
# self.m_prbar["value"] = 10
#Display options
self.m_displayOptionsLabel = ttk.Label(self.m_chordFrame,
text='Display Options:')
self.m_displayOptionsLabel.grid(row=12,
column=0,
columnspan=2,
sticky="nsw")
self.m_toggleMarkersButton = ttk.Button(self.m_chordFrame,
text="Toggle Markers",
command=self.toggleMarkers)
self.m_toggleMarkersButton.grid(row=13,
column=1,
columnspan=2,
sticky="nsew")
self.m_prefactorCBLabel = ttk.Label(
self.m_chordFrame, text='Select prefactor to display data for:')
self.m_prefactorCBLabel.grid(row=14,
column=1,
columnspan=2,
sticky="nsw")
self.m_prefactorCB = ttk.Combobox(self.m_chordFrame)
self.m_prefactorCB.bind(
"<<ComboboxSelected>>", self.plotDataForSelectedPrefactor
) #binding to event because CB does not have 'command' param
self.m_prefactorCB.grid(row=15, column=1, columnspan=2, sticky="nsew")
#Save Button
self.m_saveDataButton = ttk.Button(self.m_chordFrame,
text="Save Inverted Data",
command=self.saveData)
self.m_saveDataButton.grid(row=16,
column=1,
columnspan=2,
sticky="nsew")
for child in self.m_chordFrame.winfo_children():
child.grid_configure(padx=3, pady=3)
self.m_chordFrame.grid_columnconfigure(index=0, weight=1)
self.m_chordFrame.grid_columnconfigure(index=1, weight=1)
self.m_chordFrame.grid_columnconfigure(index=2, weight=1)
class InvertDataControl(ProcessingControlBase):
def __init__(self, controller, root, accordion):
super().__init__("Inversion Analysis", controller, accordion)
self.m_parsedData = None
self.m_prefactors = []
# self.m_inputFilePath = None
self.m_plots["Input Data"] = MPLContainer(self.m_chord.m_notebookRef,
"Input Data",
"Desorption Rate (arb. U.)",
"Temperature (K)", root)
self.m_plots["Coverage vs. Temp."] = MPLContainer(
self.m_chord.m_notebookRef, "Coverage vs. Temp.", "Coverage",
"Temperature (K)", root)
self.m_plots["Energy vs. Coverage"] = MPLContainer(
self.m_chord.m_notebookRef, "Energy vs. Coverage", "Energy (eV)",
"Coverage", root)
self.m_plots["Sim. Coverage vs Temp."] = MPLContainer(
self.m_chord.m_notebookRef, "Sim. Coverage vs Temp.",
"Coverge (ML)", "Temperature (K)", root)
self.m_plots["Sim. Desorption Rate vs Coverage"] = MPLContainer(
self.m_chord.m_notebookRef, "Sim. Desorption Rate vs Coverage",
"Desorption Rate (ML/K)", "Coverage", root)
self.m_plots["Chi Squared vs Prefactor"] = MPLContainer(
self.m_chord.m_notebookRef, "Chi Squared vs Prefactor",
"Chi Squared Value", "Prefactor", root)
def checkInput(self):
# if(self.m_inputFilePath == None): #check for file selection
if (self.m_fileSelectionControl.m_inputFilePath == None):
tk.messagebox.showerror(
"Input File",
"Please select a preprocessed file on which to perform the inversion analysis."
)
return False
if (self.m_RBVariable.get() == 0): #single prefactor
if not self.m_tPrefactorEntry.InputIsValid(): return False
else: #prefactor range
if not self.m_tPrefactorStartEntry.InputIsValid(): return False
if not self.m_tPrefactorEndEntry.InputIsValid(): return False
currentEntry = float(self.m_tPrefactorStartEntry.get())
lastEntry = float(self.m_tPrefactorEndEntry.get())
if (self.m_RBVariable.get() == 1): #linear range
if not self.m_tPrefactorIncrementEntry.InputIsValid():
return False
incrementEntry = float(self.m_tPrefactorIncrementEntry.get())
if ((lastEntry - currentEntry) / incrementEntry > 20):
tk.messagebox.showerror(
"Number of Data Points",
"Too many simulated data points required. Adapt range so that less than 20 simulations are necessary per spectrum."
)
# raise ValueError #ridiculous amount of data points
else: #multiplicative range
if (math.log10(lastEntry) - math.log10(currentEntry) > 20):
tk.messagebox.showerror(
"Number of Data Points",
"Too many simulated data points required. Adapt range so that less than 20 simulations are necessary per spectrum."
)
# raise ValueError #ridiculous amount of data points
return True
def processInput(self):
if (not self.checkInput()): return
self.m_invertedData = None
self.m_parsedData = ProcessedDataWrapper(
self.m_fileSelectionControl.m_inputFilePath)
self.m_parsedData.parseProcessedDataFile()
if (not self.m_parsedData.m_normalized):
tk.messagebox.showerror(
"Input File",
"Please use an input file with normalized coverages!")
return
if (not self.m_parsedData.m_normalized):
return #need a normalized monolayer coverage for inversion + simulation to make sense
# self.m_parsedData.clearInvertedData() #incase we are reusing the wrapper
# for c in self.m_plots:
# c.clearPlots()
if (self.m_RBVariable.get() == 0): #single prefactor
self.m_prefactors = [
"{:e}".format(float(self.m_tPrefactorEntry.get()))
]
elif (self.m_RBVariable.get() == 1): #linear range
currentEntry = float(self.m_tPrefactorStartEntry.get())
lastEntry = float(self.m_tPrefactorEndEntry.get())
incrementEntry = float(self.m_tPrefactorIncrementEntry.get())
self.m_prefactors = []
while (currentEntry <= lastEntry):
self.m_prefactors.append("{:e}".format(currentEntry))
currentEntry += incrementEntry #increase by order of magnitude
else: #multiplicative range
currentEntry = float(self.m_tPrefactorStartEntry.get())
lastEntry = float(self.m_tPrefactorEndEntry.get())
self.m_prefactors = []
while (currentEntry <= lastEntry):
self.m_prefactors.append("{:e}".format(currentEntry))
currentEntry *= 10.0 #increase by order of magnitude
for p in self.m_prefactors:
self.m_parsedData.invertProcessedData(
float(p)) #do the calculations
self.m_parsedData.simulateCoveragesFromInvertedData()
self.m_parsedData.evaluateData()
#plot chi-squared value vs prefactor for all input coverages
self.m_plots["Chi Squared vs Prefactor"].clearPlots()
self.m_plots["Chi Squared vs Prefactor"].addPrimaryLinePlots(
self.m_parsedData.getChiSquaredVSPrefactor(),
self.m_parsedData.getCoverageLabels(),
logXAxis=True) #, logYAxis = True)
self.m_plots["Chi Squared vs Prefactor"].addPrimaryLinePlots(
self.m_parsedData.getChiSquaredSumVSPrefactor(), ["Sum"],
logXAxis=True) #, logYAxis = True)
self.m_prefactorCB["values"] = self.m_prefactors
self.plotDataForSelectedPrefactor()
def plotDataForSelectedPrefactor(self, *args, **kwargs):
if (len(self.m_prefactors) == 0):
return
else:
selectedPrefactor = self.m_prefactorCB.get()
if (selectedPrefactor == ''):
self.m_prefactorCB.current(0) #set to first entry
selectedPrefactor = self.m_prefactorCB.get()
#plot input data
self.m_plots["Input Data"].clearPlots()
self.m_plots["Input Data"].addPrimaryLinePlots(
self.m_parsedData.getInputData(),
self.m_parsedData.getCoverageLabels())
#plot coverage vs temperature from experimental data
self.m_plots["Coverage vs. Temp."].clearPlots()
self.m_plots["Coverage vs. Temp."].addPrimaryLinePlots(
self.m_parsedData.getExpCoverageVSTemp(
float(selectedPrefactor)),
self.m_parsedData.getCoverageLabels())
#plot desorption energy vs coverage from experimental data
self.m_plots["Energy vs. Coverage"].clearPlots()
for e, lbl in zip(
self.m_parsedData.getDesEnergyVSCoverageList(
float(selectedPrefactor)),
self.m_parsedData.getCoverageLabels()):
self.m_plots["Energy vs. Coverage"].addPrimaryLinePlots(e, lbl)
#plot simulated coverage vs temperature
self.m_plots["Sim. Coverage vs Temp."].clearPlots()
# self.m_plots[3].addLinePlots(self.m_parsedData.getExpDesorptionRateVSTemp())
self.m_plots["Sim. Coverage vs Temp."].addPrimaryLinePlots(
self.m_parsedData.getSimCoverageVSTemp(
float(selectedPrefactor)),
self.m_parsedData.getCoverageLabels())
#plot simulated desorption rate vs temperature
self.m_plots["Sim. Desorption Rate vs Coverage"].clearPlots()
self.m_plots[
"Sim. Desorption Rate vs Coverage"].addPrimaryLinePlots(
self.m_parsedData.getSimDesRateVSTemp(
float(selectedPrefactor)),
self.m_parsedData.getCoverageLabels())
def changeRB(self):
self.m_tPrefactorEntry.configure(state='disabled')
self.m_tPrefactorIncrementEntry.configure(state='disabled')
self.m_tPrefactorStartEntry.configure(state='disabled')
self.m_tPrefactorEndEntry.configure(state='disabled')
if (self.m_RBVariable.get() == 0): #single prefactor
self.m_tPrefactorEntry.configure(state='normal')
elif (self.m_RBVariable.get() == 1): #linear range
self.m_tPrefactorIncrementEntry.configure(state='normal')
self.m_tPrefactorStartEntry.configure(state='normal')
self.m_tPrefactorEndEntry.configure(state='normal')
else: #multiplicative range
self.m_tPrefactorIncrementEntry.configure(state='disabled')
self.m_tPrefactorStartEntry.configure(state='normal')
self.m_tPrefactorEndEntry.configure(state='normal')
def toggleMarkers(self):
for c in self.m_plots.values():
c.toggleMarkers()
def saveData(self):
if (self.m_parsedData == None):
return
outputFilePath = asksaveasfilename()
substrings = outputFilePath.split('/')
#consider using s = '/' result = s.join(substrings[x:y])
outputFilePath = substrings[0]
for s in substrings[1:-1]:
outputFilePath = outputFilePath + '/' + s
substrings = substrings[-1].split('.')
fileName = substrings[0]
if (len(substrings) > 1):
for s in substrings[1:-1]:
fileName = fileName + '.' + s
# dateTimeString = str(datetime.now()).replace('-','').replace(' ', '_').replace(':','')
# fileName = fileName + '.' + dateTimeString
outputFilePath = outputFilePath + '/' + fileName
self.m_parsedData.saveInvertedDataToFile(outputFilePath)
def initChordUI(self):
self.m_chordFrame = self.m_chord.m_scrollable_frame
# File selection
self.m_fileSelectionControl = SingleInputFileSelectionControl(
self.m_chordFrame)
self.m_fileSelectionControl.grid(row=0,
column=0,
columnspan=4,
sticky="nsew")
#Options
self.m_optionsLabel = ttk.Label(
self.m_chordFrame,
text="Inversion Options:") #, compound = tk.CENTER)
self.m_optionsLabel.grid(row=3, column=0, columnspan=2, sticky="nsw")
#Radiobutton var
self.m_RBVariable = tk.IntVar(self.m_chordFrame)
#Single Prefactor
self.m_singleRB = ttk.Radiobutton(self.m_chordFrame,
text="Single Prefactor",
variable=self.m_RBVariable,
value=0,
command=self.changeRB)
self.m_singleRB.grid(row=4, column=1, sticky="nsw")
self.m_tPrefactorLabel = ttk.Label(self.m_chordFrame,
text="Prefactor Value:")
self.m_tPrefactorLabel.grid(row=5, column=1, sticky="nse")
self.m_tPrefactorEntry = EnhancedEntry(
self.m_chordFrame,
inputValueType=float,
errorTitle="Prefactor Value",
errorMessage=
"Please enter a float for the prefactor. For example 1e17.")
self.m_tPrefactorEntry.grid(row=5, column=2, sticky="nsw")
#Or Prefactor Range
self.m_linearRB = ttk.Radiobutton(self.m_chordFrame,
text="Prefactor Range - Linear",
variable=self.m_RBVariable,
value=1,
command=self.changeRB)
self.m_linearRB.grid(row=6, column=1, sticky="nsw")
self.m_tPrefactorIncrementLabel = ttk.Label(self.m_chordFrame,
text="Increment:")
self.m_tPrefactorIncrementLabel.grid(row=7, column=1, sticky="nse")
self.m_tPrefactorIncrementEntry = EnhancedEntry(
self.m_chordFrame,
inputValueType=float,
errorTitle="Increment",
errorMessage="Please enter a float for the prefactor increment.")
self.m_tPrefactorIncrementEntry.grid(row=7, column=2, sticky="nsw")
self.m_multiplicativeRB = ttk.Radiobutton(
self.m_chordFrame,
text="Prefactor Range - Multiplicative (10x)",
variable=self.m_RBVariable,
value=2,
command=self.changeRB)
self.m_multiplicativeRB.grid(row=8, column=1, sticky="nsw")
self.m_tPrefactorStartLabel = ttk.Label(self.m_chordFrame,
text="Lowest Prefactor:")
self.m_tPrefactorStartLabel.grid(row=9, column=1, sticky="nse")
self.m_tPrefactorStartEntry = EnhancedEntry(
self.m_chordFrame,
inputValueType=float,
errorTitle="Lowest Prefactor",
errorMessage=
"Please enter a float for the lowest prefactor. For example 1e13.")
self.m_tPrefactorStartEntry.grid(row=9, column=2, sticky="nsw")
self.m_tPrefactorEndLabel = ttk.Label(self.m_chordFrame,
text="Highest Prefactor:")
self.m_tPrefactorEndLabel.grid(row=10, column=1, sticky="nse")
self.m_tPrefactorEndEntry = EnhancedEntry(
self.m_chordFrame,
inputValueType=float,
errorTitle="Highest Prefactor",
errorMessage=
"Please enter a float for the highest prefactor. For example 1e21."
)
self.m_tPrefactorEndEntry.grid(row=10, column=2, sticky="nsw")
#default values
self.m_tPrefactorStartEntry.setBackingVar("1e15")
self.m_tPrefactorEndEntry.setBackingVar("1e17")
self.m_RBVariable.set(2)
self.changeRB()
#Process Button
self.m_processButton = ttk.Button(self.m_chordFrame,
text="Process Input",
command=self.processInput)
self.m_processButton.grid(row=11,
column=1,
columnspan=2,
sticky="nsew")
# self.m_prbar = ttk.Progressbar(self.m_chordFrame, orient ="horizontal", mode ="determinate", length = 50) #int(self.m_chordFrame.winfo_width() / 2))
# self.m_prbar.grid(row = 12, column = 1, columnspan = 2, sticky="nsw")
# self.m_prbar["value"] = 10
#Display options
self.m_displayOptionsLabel = ttk.Label(self.m_chordFrame,
text='Display Options:')
self.m_displayOptionsLabel.grid(row=12,
column=0,
columnspan=2,
sticky="nsw")
self.m_toggleMarkersButton = ttk.Button(self.m_chordFrame,
text="Toggle Markers",
command=self.toggleMarkers)
self.m_toggleMarkersButton.grid(row=13,
column=1,
columnspan=2,
sticky="nsew")
self.m_prefactorCBLabel = ttk.Label(
self.m_chordFrame, text='Select prefactor to display data for:')
self.m_prefactorCBLabel.grid(row=14,
column=1,
columnspan=2,
sticky="nsw")
self.m_prefactorCB = ttk.Combobox(self.m_chordFrame)
self.m_prefactorCB.bind(
"<<ComboboxSelected>>", self.plotDataForSelectedPrefactor
) #binding to event because CB does not have 'command' param
self.m_prefactorCB.grid(row=15, column=1, columnspan=2, sticky="nsew")
#Save Button
self.m_saveDataButton = ttk.Button(self.m_chordFrame,
text="Save Inverted Data",
command=self.saveData)
self.m_saveDataButton.grid(row=16,
column=1,
columnspan=2,
sticky="nsew")
for child in self.m_chordFrame.winfo_children():
child.grid_configure(padx=3, pady=3)
self.m_chordFrame.grid_columnconfigure(index=0, weight=1)
self.m_chordFrame.grid_columnconfigure(index=1, weight=1)
self.m_chordFrame.grid_columnconfigure(index=2, weight=1)
def initChordUI(self):
self.m_chordFrame = self.m_chord.m_scrollable_frame
# File selection
self.m_fileSelectionControl = InputFileListBoxControl(
self.m_chordFrame, self.onUpdateFileList)
self.m_fileSelectionControl.grid(row=0,
column=0,
columnspan=4,
sticky="nsew")
# Processing options:
self.m_optionsLabel = ttk.Label(
self.m_chordFrame,
text="Processing Options:") #, compound = tk.CENTER)
self.m_optionsLabel.grid(row=3, column=0, columnspan=2, sticky="nsw")
self.m_tCutStartLabel = ttk.Label(self.m_chordFrame,
text="Lower Boundary (Temp.):")
self.m_tCutStartLabel.grid(row=4, column=1, sticky="nse")
self.m_lowerBoundEntry = EnhancedEntry(
self.m_chordFrame,
inputValueType=int,
errorTitle="Lower Boundary (Temp.)",
errorMessage=
"Please enter an integer for the lower temperature boundary")
self.m_lowerBoundEntry.grid(row=4, column=2, sticky="nsw")
self.m_tCutEndLabel = ttk.Label(self.m_chordFrame,
text="Upper Boundary (Temp.):")
self.m_tCutEndLabel.grid(row=5, column=1, sticky="nse")
self.m_upperBoundEntry = EnhancedEntry(
self.m_chordFrame,
inputValueType=int,
errorTitle="Upper Boundary (Temp.)",
errorMessage=
"Please enter an integer for the upper temperature boundary.")
self.m_upperBoundEntry.grid(row=5, column=2, sticky="nsw")
#Temperature (thermocouple) calibration options:
self.m_calibLabel = ttk.Label(
self.m_chordFrame,
text="Temperature Calibration:") #, compound = tk.CENTER)
self.m_calibLabel.grid(row=6, column=0, columnspan=2, sticky="nsw")
self.m_calibFormulaLabel = ttk.Label(
self.m_chordFrame,
text="( T_Calibrated = Scale * T_RawData + Offset )")
self.m_calibFormulaLabel.grid(row=7, column=0,
columnspan=3) #, sticky = "nse")
self.m_calibOffsetLabel = ttk.Label(self.m_chordFrame, text="Offset:")
self.m_calibOffsetLabel.grid(row=8, column=1, sticky="nse")
self.m_calibOffsetEntry = EnhancedEntry(
self.m_chordFrame,
inputValueType=float,
errorTitle="Calibration Offset",
errorMessage=
"Please enter a decimal for the temperature calibration offset.")
self.m_calibOffsetEntry.grid(row=8, column=2, sticky="nsw")
self.m_calibOffsetEntry.setBackingVar("0.836") #default
self.m_calibScaleLabel = ttk.Label(self.m_chordFrame, text="Scale:")
self.m_calibScaleLabel.grid(row=9, column=1, sticky="nse")
self.m_calibScaleEntry = EnhancedEntry(
self.m_chordFrame,
inputValueType=float,
errorTitle="Calibration Scale",
errorMessage=
"Please enter a decimal for the temperature calibration scale.")
self.m_calibScaleEntry.grid(row=9, column=2, sticky="nsw")
self.m_calibScaleEntry.setBackingVar("0.985") #default
# Checkbuttons + Comboboxes for options:
self.m_smoothTempCB = EnhancedCheckButton(self.m_chordFrame,
text="Smooth Temperature")
self.m_smoothTempCB.grid(row=10, column=1, sticky="nsw")
self.m_smoothTempCB.set(1)
self.m_smoothTempCB.configure(state=tk.DISABLED)
self.m_smoothCountsCB = EnhancedCheckButton(self.m_chordFrame,
text="Smooth Counts/s")
self.m_smoothCountsCB.grid(row=10, column=2, sticky="nsw")
self.m_normalizeCB = EnhancedCheckButton(
self.m_chordFrame,
text="Normalize to coverage of (select file):",
command=self.toggleNormalizeCB)
self.m_normalizeCB.grid(row=11, column=1, sticky="nsw")
self.m_removeBackgroundCB = EnhancedCheckButton(
self.m_chordFrame, text="Remove Background")
self.m_removeBackgroundCB.grid(row=11, column=2, sticky="nsw")
self.m_normSelection = ttk.Combobox(self.m_chordFrame,
state=tk.DISABLED)
self.m_normSelection.grid(row=12,
column=1,
columnspan=2,
sticky="nsew")
self.m_subtractCB = EnhancedCheckButton(
self.m_chordFrame,
text="Subtract Spectrum (select file):",
command=self.toggleSubtractCB,
state=tk.DISABLED)
self.m_subtractCB.grid(row=13, column=1, sticky="nsw")
self.m_subtractSelection = ttk.Combobox(self.m_chordFrame,
state=tk.DISABLED)
self.m_subtractSelection.grid(row=14,
column=1,
columnspan=2,
sticky="nsew")
#Process Button
self.m_processButton = ttk.Button(self.m_chordFrame,
text="Process Input",
command=self.processInput)
self.m_processButton.grid(row=15,
column=1,
columnspan=2,
sticky="nsew")
#Display options
self.m_displayOptionsLabel = ttk.Label(self.m_chordFrame,
text='Display Options:')
self.m_displayOptionsLabel.grid(row=16,
column=0,
columnspan=2,
sticky="nsw")
self.m_toggleMarkersButton = ttk.Button(self.m_chordFrame,
text="Toggle Markers",
command=self.toggleMarkers)
self.m_toggleMarkersButton.grid(row=17,
column=1,
columnspan=2,
sticky="nsew")
self.m_massDisplayOptions = DisplayOptionsFrame(
self.m_chordFrame, self.plotSelectedMasses)
self.m_massDisplayOptions.grid(row=18,
column=0,
columnspan=4,
sticky="nsew")
# self.m_massDisplayOptions.m_availableMassesListBox
self.m_saveDataButton = ttk.Button(self.m_chordFrame,
text="Save Processed Data",
command=self.saveData)
self.m_saveDataButton.grid(row=19,
column=1,
columnspan=3,
sticky="nsew")
# for child in self.m_chordFrame.winfo_children():
# child.grid_configure(padx=3, pady=3)
# for child in self.m_fileButtonFrame.winfo_children():
# child.pack_configure(padx=3, pady=3)
# for child in self.m_massDisplayOptions.winfo_children():
# child.grid_configure(padx=3, pady=3)
self.m_chordFrame.grid_columnconfigure(index=0, weight=1)
self.m_chordFrame.grid_columnconfigure(index=1, weight=1)
self.m_chordFrame.grid_columnconfigure(index=2, weight=1)
self.m_chordFrame.grid_columnconfigure(index=3, weight=1)
class RawDataControl(ProcessingControlBase):
def __init__(self, controller, root, accordion):
super().__init__("Process TPD Data", controller, accordion)
self.m_filePaths = []
self.m_parsedData = []
# self.m_notebook.bind("<<NotebookTabChanged>>", self.onNotebookTabChanged)
# self.m_plots.append(MPLContainer(self.m_notebook, "Raw Data", "Desorption Rate", "Temperature (K)"))
self.m_plots["Raw Data vs. Temp."] = MPLContainer(
self.m_chord.m_notebookRef, "Raw Data vs. Temp.",
"Desorption Rate", "Temperature (K)", root)
self.m_plots["Raw Data vs. Time"] = MPLContainer(
self.m_chord.m_notebookRef,
"Raw Data vs. Time.",
"Desorption Rate",
"Time (ms)",
root,
secondaryYAxis=True,
secondaryYAxisName="Temperature (K)",
legendLoc='center right')
self.m_plots["Processed Data"] = MPLContainer(
self.m_chord.m_notebookRef, "Processed Data", "Desorption Rate",
"Temperature (K)", root)
self.m_plots["Log Plot (Processed)"] = MPLContainer(
self.m_chord.m_notebookRef, "Log Plot (Processed)",
"ln(Desorption Rate)", "Temperature (K)", root)
self.m_plots["Arrhenius Plot (Processed)"] = MPLContainer(
self.m_chord.m_notebookRef,
"Arrhenius Plot (Processed)",
"ln(Desorption Rate)",
"Reciprocal Temperature (1/K)",
root,
invertXAxis=True)
# self.m_plots["Temperature Ramp"] = MPLContainer(self.m_chord.m_notebookRef, "Temperature Ramp", "Temperature (K)", "Time (ms)", root)
def onUpdateFileList(self, fileList):
self.m_subtractSelection["values"] = fileList
self.m_normSelection["values"] = fileList
def toggleSubtractCB(self):
if (self.m_subtractCB.instate(['!selected'])):
self.m_subtractSelection.configure(state=tk.DISABLED)
else:
self.m_subtractSelection.configure(state='readonly')
def toggleNormalizeCB(self):
if (self.m_normalizeCB.instate(['!selected'])):
self.m_removeBackgroundCB.configure(state=tk.NORMAL)
self.m_normSelection.configure(state=tk.DISABLED)
else:
self.m_removeBackgroundCB.set(
1
) #if we want to normalize, we also have to remove the background, otherwise it does not make sense
self.m_removeBackgroundCB.configure(state=tk.DISABLED)
self.m_normSelection.configure(state='readonly')
def toggleMarkers(self):
for c in self.m_plots.values():
c.toggleMarkers()
def plotSelectedMasses(self):
for c in self.m_plots.values():
c.clearPlots()
tempMasses = self.m_massDisplayOptions.getMassesToDisplay()
if (len(tempMasses) == 0):
return
for d in self.m_parsedData:
self.m_plots["Raw Data vs. Temp."].addPrimaryLinePlots(
d.getRawDataVSRawTemp(tempMasses),
d.getLangmuirLabels(tempMasses))
self.m_plots["Raw Data vs. Time"].addPrimaryLinePlots(
d.getRawDataVSRawTime(tempMasses),
d.getLangmuirLabels(tempMasses))
self.m_plots["Raw Data vs. Time"].addSecondaryLinePlots(
d.getRawTempVSRawTime())
self.m_plots["Processed Data"].addPrimaryLinePlots(
d.getProcessedData(tempMasses),
d.getCoverageLabels(tempMasses))
self.m_plots["Log Plot (Processed)"].addPrimaryLinePlots(
d.getProcessedLNData(tempMasses),
d.getCoverageLabels(tempMasses))
self.m_plots["Arrhenius Plot (Processed)"].addPrimaryLinePlots(
d.getProcessedArrheniusData(tempMasses),
d.getCoverageLabels(tempMasses))
# self.m_plots[3].addPrimaryLinePlots(d.getRawTempVSRawTime(), d.getCoverageLabels(tempMasses))
# self.m_plots[0].setLegendCenterRight()
# self.m_plots["Arrhenius Plot (Processed)"].autoScaleTopY()
#if(showTempBounds)
# self.m_plots["Raw Data vs. Temp."].addVerticalLine(float(self.m_tCutStartEntry.get()))
# self.m_plots["Raw Data vs. Temp."].addVerticalLine(float(self.m_tCutEndEntry.get()))
def checkInput(self):
if (len(self.m_fileSelectionControl.m_filePaths) == 0
): #check for file selection
tk.messagebox.showerror(
"Input Files", "Please select at least one file to process.")
return False
if not self.m_calibOffsetEntry.InputIsValid(): return False
if not self.m_calibScaleEntry.InputIsValid(): return False
return True
def prepareStartStopCutValues(self):
t_Minima = [d.getRawTempMin() for d in self.m_parsedData]
minStartCut = int(np.amin(t_Minima))
if (minStartCut == 0):
minStartCut = 1 #otherwise arrhenius plot will have 1/T -> 1/0 -> Inf value which causes bounds error
t_Maxima = [d.getRawTempMax() for d in self.m_parsedData]
maxStopCut = int(np.amax(t_Maxima))
if (self.m_lowerBoundEntry.InputIsValid()):
if (minStartCut > int(self.m_lowerBoundEntry.get())):
self.m_lowerBoundEntry.set(str(minStartCut))
else:
self.m_lowerBoundEntry.set(str(minStartCut))
if (self.m_upperBoundEntry.InputIsValid()):
if (maxStopCut < int(self.m_upperBoundEntry.get())):
self.m_upperBoundEntry.set(str(maxStopCut))
else:
self.m_upperBoundEntry.set(str(maxStopCut))
def processInput(self):
if (not self.checkInput()): return False
self.m_parsedData = []
#TODO: check input, maybe highlight missing entries!
for f in self.m_fileSelectionControl.m_filePaths:
wrapper = RawDataWrapper(f)
wrapper.parseRawDataFile()
self.m_parsedData.append(wrapper)
self.prepareStartStopCutValues()
wrapper.processParsedData(
0,
0,
int(self.m_lowerBoundEntry.get()), #lower temperature boundary
int(self.m_upperBoundEntry.get()), #upper temperature boundary
self.m_removeBackgroundCB.instate(['selected']),
self.m_smoothCountsCB.instate(['selected']),
float(self.m_calibScaleEntry.get()
), #calibration slope 'm' in y=mx+b
float(self.m_calibOffsetEntry.get())
) #calibration offset 'b' in y=mx+b
if (self.m_normalizeCB.instate([
'selected'
])): #if we want to normalize data to a specific coverage
monolayerData = None
#find the coverage by fileName
for w in self.m_parsedData:
if (w.m_fileName == self.m_normSelection.get()):
monolayerData = w
break
if (monolayerData == None):
print("No reference coverage file selected")
raise ValueError
#normalize everything except the reference
for w in [d for d in self.m_parsedData if not d == monolayerData]:
w.normalizeDataTo(monolayerData)
#normalize reference data last
monolayerData.normalizeDataTo(monolayerData)
#sort input data by coverage
indexMapBuffer = [
] #index i will contain tuple of (oldIndex,coverage) sorted by coverage
for i in range(len(self.m_parsedData)):
indexMapBuffer.append(
(i, self.m_parsedData[i].getParsedCoverageAsFloat()
)) #sorting input files by coverage
indexMapBuffer.sort(reverse=False, key=lambda a: a[
1]) #sort, such that old index and coverage are preserved
#buffers for different ordering
sortedParsedDataBuffer = []
sortedFilePathsBuffer = []
for i in range(len(indexMapBuffer)):
sortedParsedDataBuffer.append(
self.m_parsedData[indexMapBuffer[i][0]])
sortedFilePathsBuffer.append(
self.m_fileSelectionControl.m_filePaths[indexMapBuffer[i][0]])
self.m_fileSelectionControl.m_filePaths = sortedFilePathsBuffer #reference-copy
self.m_parsedData = sortedParsedDataBuffer #reference-copy
self.m_fileSelectionControl.prepareFileSelections()
# self.m_fileSelectionControl.onUpdateSelection(self.m_fileSelectionControl.m_fileList)
self.m_massDisplayOptions.resetMasses(self.m_parsedData)
self.plotSelectedMasses()
def saveData(self):
if (len(self.m_parsedData) == 0):
tk.messagebox.showerror(
"Save Error",
"Please process some data before attempting to save it.")
return
outputFilePath = asksaveasfilename()
substrings = outputFilePath.split('/')
#consider using s = '/' result = s.join(substrings[x:y])
outputFilePath = substrings[0]
for s in substrings[1:-1]:
outputFilePath = outputFilePath + '/' + s
substrings = substrings[-1].split('.')
fileName = substrings[0]
if (len(substrings) > 1):
for s in substrings[1:-1]:
fileName = fileName + '.' + s
# dateTimeString = str(datetime.now()).replace('-','').replace(' ', '_').replace(':','')
# fileName = fileName + '.' + dateTimeString
outputFilePath = outputFilePath + '/' + fileName
self.SaveProcessedDataToFile(outputFilePath,
self.m_massDisplayOptions.getAllMasses(),
self.m_parsedData)
def SaveProcessedDataToFile(self, outputFilePath, massList,
rawDataWrappers):
if (massList == None or rawDataWrappers == None):
raise ValueError
for m in massList: #generate one .pdat file per mass (cleanest way to seperate data for masses, and keep things in an easily readable format)
headerString = "Processed TPD data for mass " + m + \
"\nHeader length is " + str(len(rawDataWrappers) + 4) + \
"\nThe following files are included in this data set:\n"
#outputData starts out column-major
outputData = rawDataWrappers[0].m_interpolatedTemp.copy(
) # start with temperature column
labels = ["Temperature"]
coverages = [str(0.0)]
for w in rawDataWrappers: #for each raw data file, do....
headerString = headerString + w.m_fileName + "\n" #write filename to header for quick overview
outputData = np.vstack(
(outputData, w.m_interpolatedData[m]
)) #append data column for mass m in outputdata
if (w.m_parsedCoverageAvailable):
labels.append(
w.m_parsedCoverage
) #will append dosed coverage in Langmuir with "L" at the end
else:
labels.append(w.m_fileName.split(" ")
[0]) # this should append file number
coverages.append(str(w.m_coverages[m]))
headerString = headerString + "Calibration params: Temperature offset = " + str(
self.m_calibOffsetEntry.get()) + " Temperature scale = " + str(
self.m_calibScaleEntry.get())
if (outputFilePath[-5:] == ".pdat"):
outputFilePath = outputFilePath[:
-5] #removing .pdat extension from user-written output file path, if it is there
#making one file per mass, so making name based on mass number
namedOutputFilePath = outputFilePath + ".M" + str(
m) + ".pdat" #pdat for processed data
if (path.exists(namedOutputFilePath)):
tk.messagebox.showerror(
"File exists!",
"Please choose another name, or explicitly delete the " +
outputFilePath + "to overwrite in the file explorer.")
stringData = np.vstack(
(np.array(labels, dtype=str), np.array(coverages, dtype=str)))
with open(namedOutputFilePath,
mode='a') as fileHandle: #actually write file
#write header and stringData first
np.savetxt(fileHandle,
stringData,
fmt="%s",
delimiter=' ',
header=headerString)
#then write float data (after transposing it)
np.savetxt(fileHandle, outputData.transpose(), delimiter=' ')
def initChordUI(self):
self.m_chordFrame = self.m_chord.m_scrollable_frame
# File selection
self.m_fileSelectionControl = InputFileListBoxControl(
self.m_chordFrame, self.onUpdateFileList)
self.m_fileSelectionControl.grid(row=0,
column=0,
columnspan=4,
sticky="nsew")
# Processing options:
self.m_optionsLabel = ttk.Label(
self.m_chordFrame,
text="Processing Options:") #, compound = tk.CENTER)
self.m_optionsLabel.grid(row=3, column=0, columnspan=2, sticky="nsw")
self.m_tCutStartLabel = ttk.Label(self.m_chordFrame,
text="Lower Boundary (Temp.):")
self.m_tCutStartLabel.grid(row=4, column=1, sticky="nse")
self.m_lowerBoundEntry = EnhancedEntry(
self.m_chordFrame,
inputValueType=int,
errorTitle="Lower Boundary (Temp.)",
errorMessage=
"Please enter an integer for the lower temperature boundary")
self.m_lowerBoundEntry.grid(row=4, column=2, sticky="nsw")
self.m_tCutEndLabel = ttk.Label(self.m_chordFrame,
text="Upper Boundary (Temp.):")
self.m_tCutEndLabel.grid(row=5, column=1, sticky="nse")
self.m_upperBoundEntry = EnhancedEntry(
self.m_chordFrame,
inputValueType=int,
errorTitle="Upper Boundary (Temp.)",
errorMessage=
"Please enter an integer for the upper temperature boundary.")
self.m_upperBoundEntry.grid(row=5, column=2, sticky="nsw")
#Temperature (thermocouple) calibration options:
self.m_calibLabel = ttk.Label(
self.m_chordFrame,
text="Temperature Calibration:") #, compound = tk.CENTER)
self.m_calibLabel.grid(row=6, column=0, columnspan=2, sticky="nsw")
self.m_calibFormulaLabel = ttk.Label(
self.m_chordFrame,
text="( T_Calibrated = Scale * T_RawData + Offset )")
self.m_calibFormulaLabel.grid(row=7, column=0,
columnspan=3) #, sticky = "nse")
self.m_calibOffsetLabel = ttk.Label(self.m_chordFrame, text="Offset:")
self.m_calibOffsetLabel.grid(row=8, column=1, sticky="nse")
self.m_calibOffsetEntry = EnhancedEntry(
self.m_chordFrame,
inputValueType=float,
errorTitle="Calibration Offset",
errorMessage=
"Please enter a decimal for the temperature calibration offset.")
self.m_calibOffsetEntry.grid(row=8, column=2, sticky="nsw")
self.m_calibOffsetEntry.setBackingVar("0.836") #default
self.m_calibScaleLabel = ttk.Label(self.m_chordFrame, text="Scale:")
self.m_calibScaleLabel.grid(row=9, column=1, sticky="nse")
self.m_calibScaleEntry = EnhancedEntry(
self.m_chordFrame,
inputValueType=float,
errorTitle="Calibration Scale",
errorMessage=
"Please enter a decimal for the temperature calibration scale.")
self.m_calibScaleEntry.grid(row=9, column=2, sticky="nsw")
self.m_calibScaleEntry.setBackingVar("0.985") #default
# Checkbuttons + Comboboxes for options:
self.m_smoothTempCB = EnhancedCheckButton(self.m_chordFrame,
text="Smooth Temperature")
self.m_smoothTempCB.grid(row=10, column=1, sticky="nsw")
self.m_smoothTempCB.set(1)
self.m_smoothTempCB.configure(state=tk.DISABLED)
self.m_smoothCountsCB = EnhancedCheckButton(self.m_chordFrame,
text="Smooth Counts/s")
self.m_smoothCountsCB.grid(row=10, column=2, sticky="nsw")
self.m_normalizeCB = EnhancedCheckButton(
self.m_chordFrame,
text="Normalize to coverage of (select file):",
command=self.toggleNormalizeCB)
self.m_normalizeCB.grid(row=11, column=1, sticky="nsw")
self.m_removeBackgroundCB = EnhancedCheckButton(
self.m_chordFrame, text="Remove Background")
self.m_removeBackgroundCB.grid(row=11, column=2, sticky="nsw")
self.m_normSelection = ttk.Combobox(self.m_chordFrame,
state=tk.DISABLED)
self.m_normSelection.grid(row=12,
column=1,
columnspan=2,
sticky="nsew")
self.m_subtractCB = EnhancedCheckButton(
self.m_chordFrame,
text="Subtract Spectrum (select file):",
command=self.toggleSubtractCB,
state=tk.DISABLED)
self.m_subtractCB.grid(row=13, column=1, sticky="nsw")
self.m_subtractSelection = ttk.Combobox(self.m_chordFrame,
state=tk.DISABLED)
self.m_subtractSelection.grid(row=14,
column=1,
columnspan=2,
sticky="nsew")
#Process Button
self.m_processButton = ttk.Button(self.m_chordFrame,
text="Process Input",
command=self.processInput)
self.m_processButton.grid(row=15,
column=1,
columnspan=2,
sticky="nsew")
#Display options
self.m_displayOptionsLabel = ttk.Label(self.m_chordFrame,
text='Display Options:')
self.m_displayOptionsLabel.grid(row=16,
column=0,
columnspan=2,
sticky="nsw")
self.m_toggleMarkersButton = ttk.Button(self.m_chordFrame,
text="Toggle Markers",
command=self.toggleMarkers)
self.m_toggleMarkersButton.grid(row=17,
column=1,
columnspan=2,
sticky="nsew")
self.m_massDisplayOptions = DisplayOptionsFrame(
self.m_chordFrame, self.plotSelectedMasses)
self.m_massDisplayOptions.grid(row=18,
column=0,
columnspan=4,
sticky="nsew")
# self.m_massDisplayOptions.m_availableMassesListBox
self.m_saveDataButton = ttk.Button(self.m_chordFrame,
text="Save Processed Data",
command=self.saveData)
self.m_saveDataButton.grid(row=19,
column=1,
columnspan=3,
sticky="nsew")
# for child in self.m_chordFrame.winfo_children():
# child.grid_configure(padx=3, pady=3)
# for child in self.m_fileButtonFrame.winfo_children():
# child.pack_configure(padx=3, pady=3)
# for child in self.m_massDisplayOptions.winfo_children():
# child.grid_configure(padx=3, pady=3)
self.m_chordFrame.grid_columnconfigure(index=0, weight=1)
self.m_chordFrame.grid_columnconfigure(index=1, weight=1)
self.m_chordFrame.grid_columnconfigure(index=2, weight=1)
self.m_chordFrame.grid_columnconfigure(index=3, weight=1)