Automatically findpeaks

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Thu, 12/12/2019 - 08:41 am

Hello everyone!! 

I really need your help. 

Each experiment is stored in an individual folder, and each folder contain X and Y datas. I used those data to create a graph. 

I have been able to obtain a great peak recognition using the Automatically Detect Peaks package, but this only allows me to identify peaks in one graph curve at a time.

I would like to used this package Automatically find peaks. I found the code relative to it:

Function MyAutomaticallyFindPeaks()
    String wname, xdata="_calculated_"

    Variable maxPeaks=100, minPeakPercent=5
    wave current_nb, mob_nb
    Prompt wname, "Peak Wave", popup, WaveList("*",";","DIMS:1,TEXT:0,CMPLX:0")+"_none_;"
    Prompt xdata, "X values", popup, "_calculated_;"+WaveList("*",";","DIMS:1,TEXT:0,CMPLX:0")
    Prompt maxPeaks, "Maximum Peaks"
    Prompt minPeakPercent, "Minimum Peak Amplitude (% max)"

    DoPrompt"Automatically Find Peaks", wname, xdata, maxPeaks, minPeakPercent
    if( V_Flag != 0)
        return 0    // user cancelled
    endif

    WAVE/Z w=$wname
    WAVE/Z wx=$xdata

    Variable pBegin=0, pEnd= numpnts(w)-1
    Variable/C estimates= EstPeakNoiseAndSmfact(w,pBegin, pEnd)
    Variable noiselevel=real(estimates)
    Variable smoothingFactor=imag(estimates)

    Variable peaksFound= AutoFindPeaks(w,pBegin,pEnd,noiseLevel,smoothingFactor,maxPeaks)

    if( peaksFound >0)
        WAVE W_AutoPeakInfo

        // Remove too-small peaks
        peaksFound= TrimAmpAutoPeakInfo(W_AutoPeakInfo,minPeakPercent/100)
        if( peaksFound >0)
            // Make waves to display in a graph
            // The x values in W_AutoPeakInfo are still actually points, not X
            Make/O/N=(peaksFound) WA_PeakCentersY = w[W_AutoPeakInfo[p][0]]
            AdjustAutoPeakInfoForX(W_AutoPeakInfo,w,wx)
            Make/O/N=(peaksFound) WA_PeakCentersX = W_AutoPeakInfo[p][0]

            // Show W_AutoPeakInfo in a table, with dimension labels
            SetDimLabel 1, 0, center, W_AutoPeakInfo
            SetDimLabel 1, 1, width, W_AutoPeakInfo
            SetDimLabel 1, 2, height, W_AutoPeakInfo

            CheckDisplayed/A W_AutoPeakInfo
            if( V_Flag == 0)
                Edit W_AutoPeakInfo.ld
            endif

            DoWindow ShowPeaks
            if( V_Flag == 0)
                if(WaveExists(wx))
                    Display/N=ShowPeaks w vs wx                
                else
                    Display/N=ShowPeaks w
                endif
                AppendToGraph/W=ShowPeaks WA_PeakCentersY vs WA_PeakCentersX
                ModifyGraph/W=ShowPeaks rgb(WA_PeakCentersY)=(0,0,65535)
                ModifyGraph/W=ShowPeaks mode(WA_PeakCentersY)=3
                ModifyGraph/W=ShowPeaks marker(WA_PeakCentersY)=19
            endif
        endif
    endif

    if( peaksFound <1)
        DoAlert 0, "No Peaks found!"
    endif

    return peaksFound
End

My problem is to know where in the code I can enter directly the name of the waves corresponding to the values X and Y, I don't want to have the prompt window to fill "peakwave", "Xvalues...".

Thanks you so much

 The popup window i would like to delete miracle.pxp

By coincidence I just prepared a function for a customer that might provide a starting point for what you want to do. Here is the function:

#include <Peak AutoFind> menus=0

Function FindPeaksForJL(String listOfWaves, String listOfXWaves, Variable maxPeaks, Variable minPeakPercent, Variable noiseLevel, Variable smoothingFactor)
    Variable nwaves = ItemsInList(listOfWaves)
    Variable i
   
    for (i = 0; i < nwaves; i++)
        Wave w = $StringFromList(i, listOfWaves)
        Wave/Z wx = $StringFromList(i, listOfXWaves)
        Variable pBegin = 0
        Variable pEnd = numpnts(w)-1

        Variable peaksFound= AutoFindPeaks(w,pBegin,pEnd,noiseLevel,smoothingFactor,maxPeaks)
        if (peaksFound > 0)
            WAVE W_AutoPeakInfo
            // Remove too-small peaks
            peaksFound= TrimAmpAutoPeakInfo(W_AutoPeakInfo,minPeakPercent/100)
            if( peaksFound > 0 )
                Make/O/N=(peaksFound) $("WA_PeakCentersY_"+NameOfWave(w))/WAVE=peakCentersY
                peakCentersY = w[W_AutoPeakInfo[p][0]]
                AdjustAutoPeakInfoForX(W_AutoPeakInfo,w,wx)
                Make/O/N=(peaksFound) $("WA_PeakCentersX_"+NameOfWave(w))/WAVE=peakCentersX
                peakCentersX = W_AutoPeakInfo[p][0]
            endif
        endif
    endfor
end

The function is intended to take a list of waves, possibly XY pairs, and apply the Automatically Find Peaks functionality to it. The customer's request included being able to set the parameters of the peak finder as in Find Peaks Custom Parameters. If you are OK with the automatic parameters, you could remove the noiseLevel and smoothingFactor inputs and call something like this:

    Variable/C estimates= EstPeakNoiseAndSmfact(w,pBegin, pEnd)
    Variable noiselevel=real(estimates)
    Variable smoothingFactor=imag(estimates)

which is copied from the function AutomaticallyFindPeaks().

December 12, 2019 at 09:32 am - Permalink