various fixes

Author: timjarsky

Packages/MIES/MIES_SweepFormula_PSX.ipf

@@ -367,7 +367,7 @@ static Function/WAVE PSX_DeconvoluteSweepData(WAVE sweepData, WAVE/C psxKernelFF
 	// no window function on purpose
 	WAVE/C outputFFT = DoFFT(sweepData, padSize = numPoints)
 
-	Multithread outputFFT[] = outputFFT[p] / psxKernelFFT[p]
+	Multithread outputFFT[] = outputFFT[p] / (psxKernelFFT[p] + 1e-5)
 
 	IFFT/DEST=Deconv/FREE outputFFT
 
@@ -376,7 +376,8 @@ static Function/WAVE PSX_DeconvoluteSweepData(WAVE sweepData, WAVE/C psxKernelFF
 
 	CopyScales sweepData, Deconv
 	FilterIIR/LO=(lowFrac)/HI=(highFrac)/ORD=(order) Deconv; err = GetRTError(0)
-
+//	FilterIIR/LO=(lowFrac)/ORD=(order) Deconv; err = GetRTError(0)
+//	smooth/E=2 47, Deconv
 	if(err)
 		printf "Error applying deconvolution filter: %s\r", GetRTErrMessage()
 		ClearRTError()
@@ -476,7 +477,7 @@ static Function [WAVE/D peakX, WAVE/D peakY] PSX_FindPeaks(WAVE sweepDataOffFilt
 	Make/FREE/D/N=(numPeaksMax) peakX, peakY
 
 	for(i = 0; i < numPeaksMax; i += 1)
-		FindPeak/B=10/M=(threshold)/Q/R=(start, stop) sweepDataOffFiltDeconv
+		FindPeak/B=100/M=(threshold)/Q/R=(start, stop) sweepDataOffFiltDeconv
 
 		if(V_Flag != 0)
 			break
@@ -593,11 +594,11 @@ static Function [variable peak_t, variable peak] PSX_CalculateEventPeak(WAVE pea
 	return [peak_t, peak]
 End
 
-static Function [variable baseline_t, variable baseline] PSX_CalculateEventBaseline(WAVE sweepDataOffFilt, variable peak_t, variable kernelAmp, variable kernelRiseTau)
+static Function [variable baseline_t, variable baseline] PSX_CalculateEventBaseline(WAVE sweepDataOffFilt,variable peak_t_prev, variable peak_t, variable kernelAmp, variable kernelRiseTau)
 
 	variable range
 
-	WaveStats/M=1/Q/R=(peak_t - PSX_BASELINE_RANGE_FACTOR * kernelRiseTau, peak_t) sweepDataOffFilt
+	WaveStats/M=1/Q/R=(max(peak_t - PSX_BASELINE_RANGE_FACTOR * kernelRiseTau, peak_t_prev), peak_t) sweepDataOffFilt
 
 	if(kernelAmp > 0)
 		baseline_t = V_minloc
@@ -616,8 +617,16 @@ End
 
 static Function [variable peak, variable peak_t, variable baseline, variable baseline_t, variable amplitude] PSX_CalculateEventProperties(WAVE peakX, WAVE peakY, WAVE sweepDataOffFilt, variable kernelAmp, variable kernelRiseTau, variable kernelDecayTau, variable index)
 
+	variable peak_t_prev = -inf
+	variable peak_prev
+
 	[peak_t, peak]         = PSX_CalculateEventPeak(peakX, peakY, sweepDataOffFilt, kernelAmp, kernelRiseTau, kernelDecayTau, index)
-	[baseline_t, baseline] = PSX_CalculateEventBaseline(sweepDataOffFilt, peak_t, kernelAmp, kernelRiseTau)
+
+	if(index > 0)
+		[peak_t_prev, peak_prev]         = PSX_CalculateEventPeak(peakX, peakY, sweepDataOffFilt, kernelAmp, kernelRiseTau, kernelDecayTau, index - 1)
+	endif
+	
+	[baseline_t, baseline] = PSX_CalculateEventBaseline(sweepDataOffFilt, peak_t_prev, peak_t, kernelAmp, kernelRiseTau)
 
 	amplitude = peak - baseline
 
@@ -764,7 +773,7 @@ static Function [variable start, variable stop] PSX_GetEventFitRange(WAVE sweepD
 
 	variable calcLength, maxLength
 
-	start = psxEvent[eventIndex][%deconvPeak_t]
+	start = psxEvent[eventIndex][%peak_t]
 
 	maxLength = PSX_FIT_RANGE_FACTOR * JWN_GetNumberFromWaveNote(psxEvent, SF_META_USER_GROUP + PSX_JWN_PARAMETERS + "/psxKernel/decayTau")
 
@@ -2226,7 +2235,7 @@ static Function PSX_UpdateAverageTraces(string win, WAVE/T eventIndexFromTraces,
 	numEvents = DimSize(eventIndexFromTraces, ROWS)
 
 	Make/WAVE/FREE/N=(numEvents) contAverageAll, contAverageAccept, contAverageReject, contAverageUndet
-	Make/FREE/D/N=(numEvents) eventStopTime
+	Make/FREE/D/N=(numEvents) eventStopTime, eventPeakTime
 
 	for(i = 0; i < numEvents; i += 1)
 		idx = str2num(eventIndexFromTraces[i])
@@ -2249,6 +2258,7 @@ static Function PSX_UpdateAverageTraces(string win, WAVE/T eventIndexFromTraces,
 				// single event waves are zeroed in x-direction to extractStartAbs
 				[extractStartAbs, extractStopAbs] = PSX_GetSingleEventRange(psxEvent, sweepDataOffFilt, idx)
 				eventStopTime[acceptIndex]        = extractStopAbs - extractStartAbs
+				eventPeakTime[acceptIndex]        = psxEvent[idx][%peak_t] - extractStartAbs
 
 				acceptIndex += 1
 				break
@@ -2275,7 +2285,7 @@ static Function PSX_UpdateAverageTraces(string win, WAVE/T eventIndexFromTraces,
 	PSX_UpdateAverageWave(contAverageAll, numEvents, averageDFR, PSX_ALL)
 
 	Redimension/N=(acceptIndex) eventStopTime
-	PSX_FitAcceptAverage(win, averageDFR, eventStopTime)
+	PSX_FitAcceptAverage(win, averageDFR, eventPeakTime, eventStopTime)
 End
 
 /// @brief Helper function to update the average waves for the all event graph
@@ -2299,10 +2309,10 @@ static Function/DF PSX_GetAverageFolder(string win)
 	endif
 End
 
-static Function PSX_FitAcceptAverage(string win, DFREF averageDFR, WAVE eventStopTime)
+static Function PSX_FitAcceptAverage(string win, DFREF averageDFR, WAVE eventPeakTime, WAVE eventStopTime)
 
 	string specialEventPanel, str, htmlStr, rawCode, browser, msg, fitFunc
-	variable err, numAveragePoints, start, stop, meanStopTime
+	variable err, numAveragePoints, start, stop, meanStopTime, meanPeakTime
 
 	WAVE acceptedAverageFit = GetPSXAcceptedAverageFitWaveFromDFR(averageDFR)
 
@@ -2333,10 +2343,17 @@ static Function PSX_FitAcceptAverage(string win, DFREF averageDFR, WAVE eventSto
 	else
 		meanStopTime = Inf
 	endif
+	
+	WAVE/Z eventPeakTimeClean = ZapNaNs(eventPeakTime)
+	if(WaveExists(eventPeakTimeClean))
+		meanPeakTime = mean(eventPeakTime)
+	else
+		ASSERT(0, "Could not find any events with finite peak_t")
+	endif
 
-	start = 0
 	stop  = min(IndexToScale(average, DimSize(average, ROWS) - 1, ROWS), meanStopTime)
-
+	start = 0.1 * meanPeakTime
+	
 	AssertOnAndClearRTError()
 	fitFunc = GetPopupMenuString(specialEventPanel, "popupmenu_accept_fit_function")
 	strswitch(fitFunc)

Packages/MIES/MIES_WaveDataFolderGetters.ipf

@@ -8243,7 +8243,8 @@ End
 ///            in the filtered sweep wave
 /// -  4/peak_t: peak time
 /// -  5/baseline: Maximum (negative kernel amp sign) or minimum (positive kernel amp sign) in the range of
-///                    [peak_t – 10 * kernelRiseTau, peak_t], averaged over +/- 5 points, in the filtered sweep wave
+///                    [peak_t – 10 * kernelRiseTau or peak_t of previous event (whichever comes later),
+///                     peak_t], averaged over +/- 5 points, in the filtered sweep wave
 /// -  6/baseline_t: baseline time
 /// -  7/amplitude: Relative amplitude: [3] - [5]
 /// -  8/iei: Time difference to previous event (inter event interval) [ms]