procedure to generate a wave that would be the mean of several waves

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Wed, 02/27/2013 - 07:21 am

In my experiments, I have different waves, all of them called subsequently (e.g. 0__temp, 1__temp, ...).
If I want to make the average of these waves, I have to type in a console:
duplicate 0__temp, ave__temp
ave__temp = (0__temp+1__temp+...)/"number_of_waves"


I would like to make a procedure to do this more automatically and not to type every time these lines. It should be a smart way to do it.

Thanks in advance
Thanks for your advice. It was very helpful.

But if I want to call the procedure for example like this:

average(temp)

I would need that the procedure take all the wave ending with "temp" and make the average. should it be valid this procedure to do it?

Function average(whatever_I_choose)
Wave WaveList(*_waves_to_average)
string name_of_wave = nameofwave(waves_to_average)

do
fWaveAverage(WaveList("*_waves_to_average", ";", ""), 0, 3, "$name_of_wave_ave", "")

End


Thanks in advance

February 27, 2013 at 10:51 am - Permalink

Here give this one a try. Copy the following two functions to a procedure file and compile it. Then select the desired source waves in the Igor Data Browser using the shift or control/command keys, and then with these highlighted enter AverageSelected() in the command window.

At the prompt, the "Include NAN points" option will average waves even if some are missing intermediary values (ie, those set to NAN). The "Generate error wave" option computes the standard error on a per point basis for the population of waves. The function will by default move the selected source waves to a folder called "Averaged", or you can use the drop-down menu to leave them alone, delete the source waves, or move them to a custom folder name specified in the "Custom Folder" field.

Function AverageSelected()
    string selected=SelectedWaveList()
    if(itemsinlist(selected)>1)
        variable option=3
        variable truncate=2
        variable generr=1
        string newFolder
        string keystr=getdatafolder(1)[0,strlen(getdatafolder(1))-1]
        string name="waveAverage"
        prompt option, "Manage source waves:", popup, "Do nothing;Delete waves;Move waves to \"Averaged\" folder;Move waves to custom folder..."
        prompt newFolder, "Custom Folder:"
        prompt name, "Base name for average wave"
        prompt truncate, "Include NAN points?",popup,"yes;no"
        prompt generr, "Generate error wave?",popup,"yes;no"
        DoPrompt "Average Waves", name, option,newFolder,truncate,generr
   
        if(!V_Flag && itemsinlist(selected)>1)
            string avgName=UniqueName(name,1,0)
            make/n=(numpnts($stringfromlist(0,selected))) $avgName=0
            make/o/n=0 indexnans
            WAVE indexnans=$nameofwave(indexnans)
   
            WAVE avg=$avgName
            SetScale/P x 0,deltax($stringfromlist(0,selected)), stringbykey("XUNITS",waveinfo($stringfromlist(0,selected),0)), avg
   
            variable i,j
            string avgnote
            Print "Waves averaged:"
            for(i=0;i<itemsinlist(selected);i+=1)
                WAVE wavenm=$stringfromlist(i,selected)
                if(truncate==1)
                    for(j=0;j<numpnts(wavenm);j+=1)
                        FindValue/V=(j) indexnans
                        if(numtype(wavenm[j])==2 && V_value==-1)
                            insertpoints 0,1,indexnans
                            indexnans[0]=j
                        endif
                    endfor
                endif
                avg+=wavenm
                print "     "+nameofwave(wavenm)
                //manage options
                if(option==2)
                    killwaves/z wavenm
                endif
                if(option==3)
                    newdatafolder/o Averaged
                    //execute "ModifyBrowser expand="+num2str(GetBrowserLine(":Averaged:"))
                    MoveWave wavenm, :Averaged:
                endif
            endfor
           
            avg/=itemsinlist(selected)
           
            //generate std err wave here
            if(generr==1)
                make/n=(numpnts($stringfromlist(0,selected))) $(avgName+"_err")=0
                wave err=$(avgName+"_err")
                //perform error for full wave
                for(i=0;i<itemsinlist(selected);i+=1)
                    WAVE wavenm=$stringfromlist(i,selected)
                    err+=(wavenm-avg)^2
                endfor
                err=sqrt(err/(itemsinlist(selected)))/sqrt(itemsinlist(selected)-1)
            endif
           
            if(truncate==1)
                variable numnans
                for(i=0;i<numpnts(indexnans);i+=1)
                    numnans=0
                    avg[indexnans[i]]=0
                    for(j=0;j<itemsinlist(selected);j+=1)
                        WAVE wavenm=$stringfromlist(j,selected)
                        if(numtype(wavenm[indexnans[i]])==0)
                            numnans+=1
                            avg[indexnans[i]]+=wavenm[indexnans[i]]
                        endif
                    endfor
                    avg[indexnans[i]]/=numnans
                    //perform per-point error for index wave
                   
                    if(generr==1)
                        //zero error point
                        err[indexnans[i]]=0
                        for(j=0;j<itemsinlist(selected);j+=1)
                            WAVE wavenm=$stringfromlist(j,selected)
                            if(numtype(wavenm[indexnans[i]])==0)
                                numnans+=1
                                err[indexnans[i]]+=(wavenm[indexnans[i]]-avg[indexnans[i]])^2
                            endif
                        endfor
                        err[indexnans[i]]=sqrt(err[indexnans[i]]/numnans)/sqrt(numnans-1)
                    endif
                   
                endfor
            endif
           
            killwaves indexnans
            Print "Average wave: "+nameofwave(avg)
        endif
    else
        Abort "Select more than one wave to average."
    endif
end

Function/S SelectedWaveList() //all selected waves...
    string SelectedWaves=""
    variable i
    do
        if(waveexists($(GetBrowserSelection(i))))
            SelectedWaves+=GetBrowserSelection(i)+";"
        endif
        i+=1
    while(strlen(GetBrowserSelection(i))>0)
    return SelectedWaves
end

February 27, 2013 at 01:51 pm - Permalink

If you want to average all the waves in the current data folder that end in "temp", using the fWaveAverage() function, you would use something like this:
#include <Waves Average>

Function averageTempWaves(NameforNewWave)
    String NameforNewWave

    String listofwaves = WaveList("*temp", ";", "")
    fWaveAverage(listofwaves, "", 3, 1, NameforNewWave, NameforNewWave+"_STE")
end

WaveList is a function that returns a string containing a semicolon-separated list of waves that match the input criteria. The way I have written it, it lists all waves whose names end in "temp", it puts a semicolon between names, and it doesn't apply any WaveList options (that's the final empty quotes). The function takes a string as input that is used to name the output waves. It creates an average wave and a standard error wave that has the same name with "_STE" appended to the name.

If you have waves data1, data2, data3, data1temp, data2temp, and data3temp, it will list average the last three of those waves. You might invoke it like this:

averageTempWaves("myAverage")

The output will be two waves: myAverage containing the averages, and myAverage_STE containing the standard error. Of course, three inputs isn't enough to make the standard error meaningful, but you get the idea.

Or you can use the Wave Average control panel as a GUI, select by Name in the top menu, and enter "*temp" in the Name Template box.

There is a demo experiment about this package: File->Example Experiments->Ave, Box Plot, Percentile.

John Weeks
WaveMetrics, Inc.
support@wavemetrics.com

February 27, 2013 at 03:42 pm - Permalink