Peak Analysis with Labtalk

Summary

This tutorial demonstrates using labtalk for peak analysis.

What You Will Learn

This tutorial will show you how to use Labtalk script to:

  • Subtract a line from source data
  • Find the highest peaks of each dataset
  • Calculate the area, height and FWHM of the highest peak
  • Create a graph of the quantities of the peak
  • Create a theme of Peak Analyzer and run batch processing with the pre-saved theme

Steps

Example 1: Peak Analysis with Scripts

  1. Import the data file Waterfall.dat under <Origin EXE folder>\Samples\Graphing folder with the associated import filter into the workbook Waterfall.
  2. // Create a newbook and name it Waterfall (both long and short name)
    newbook name:="Waterfall" option:=lsname;
    // Define the file name and filter name
    string fname$ = system.path.program$ + "Samples\Graphing\Waterfall.dat";
    string filtername$ = "waterfall.oif";  
    // Use the impfile x-function to import the specified file with the import filter
    impfile fname:=fname$ filtername:=filtername$ location:=data orng:=[Waterfall]1!;
  3. Use a loop and the subtract_line X-Function to subtract a simple baseline of end points connection.
  4. //Create new sheet named as SubtractedData
    newsheet name:=SubtractedData;
    //Define the newly created worksheet(current active) as a range variable
    range sdwk = !;
    //Active the "Waterfall" worksheet by its name
    page.active$ = "Waterfall";
    //Define an integer to hold the number of columns in Waterfall sheet
    int nc = wks.nCols;
    
    //Find out the columns for excitation wavelength = 600, 610, 620, 630 ect
    //Use the loop and subtract_line x-function to subtract baseline
    //The first and last data points are found and connected linearly
    //This line will be subtracted as baseline from source data
    //Subtracted data will be named by excitation wavelength of source data
    int nexc;
    loop(ii, 2, nc)
    {
    	range ry = [Waterfall]Waterfall!col($(ii));
    	int nWave = %(ry[D1]$);
    	if (mod(nWave, 10)==0)
    	{
    		nexc = nexc + 1;
    		range rx = [Waterfall]Waterfall!col(1);
    		range rr = [Waterfall]SubtractedData!(1,$(nexc));
    		subtract_line iy:=ry 
    		x1:=rx[1] /* Specifies the X value of the first point*/
    		y1:=ry[1] /* Specifies the Y value of the first point*/
    		x2:=rx[$(wks.maxRows)] /* Specifies the X value of the last point*/
    		y2:=ry[$(wks.maxRows)] /* Specifies the Y value of the last point*/
    		oy:=rr;
    	//Rename the column long names in SubtractedData sheet
    	//Use the User Defined Parameter Wavelength in Waterfall sheet 
    	 rr[L]$ = ry[D1]$;
    	 
    	 //add a new column for next loop
    	 wks.addcol();
    	}
    	else
    	{
    		continue;
    	}
    }
  5. Create new sheet for summary report
  6. // Create new sheet for summary report and define ranges
    newsheet cols:=7 xy:="XYYYYYY" name:="Summary";
    range rWaveLength = 1, rCntrInd = 2, rLtInd =3, rRtInd = 4;
    range rArea = 5, rCntr = 6, rHt = 7, rFWHM = 8;
    rWaveLength[L]$ = "WaveLength";
    rCntrInd[L]$ = "Peak Center Index";
    rLtInd[L]$   = "Peak Left Index";
    rRtInd[L]$   = "Peak Right Index";
    rArea[L]$    = "Peak Area";
    rCntr[L]$    = "Peak Center";
    rHt[L]$      = "Peak Height";
    rFWHM[L]$	 = "FWHM";
  7. To calculate the quantities of the highest peak of the data, we should find the highest peak with the pkfind X-Function and then calculate the quantities of the peak with the integ1 X-Function
  8.  //active the SubtractedData sheet
    page.active$="SubtractedData";
    
    //add columns for temp results of the finded peaks
    loop(cc, 1, 2)
    {
        wks.addcol();
    };
    
    loop(ii, 2, nexc)
    { 
    	//find the highest peak
    	range rData = col($(ii));
    	range pcenter= $(nexc+1), pleft= $(nexc+2), pright= $(nexc+3);
    	pkfind rData filter:=num value:= 1 ocenter:=pcenter oleft:=pleft oright:=pright; //find a highest peak
    
    	//copy the result from the temp columns to summary sheet
    	wrcopy iw:=SubtractedData ow:=Summary c1:=nexc+1 c2:=nexc+3 r1:=1 r2:=1 dc1:=2 dr1:= ii-1;
    	
    	//compute the quantities of the highest peak with integ1
    	int n1 = pleft[1]; //specify the peak left index 
    	int n2 = pright[1]; //specify the peak right index 
    	range rint = rData[$(n1):$(n2)]; // range of data to be integrated
    	double aa, cc, hh, fw; 
    	integ1 iy:=rint area:=aa x0:=cc y0:=hh dx:=fw oy:=<optional>;
    	//put the quantities to summary sheet
    	rArea[$(ii-1)] = aa;
    	rCntr[$(ii-1)] = cc;
    	rHt[$(ii-1)] = hh;
    	rFWHM[$(ii-1)] =fw;
    	//copy the longname of calculated data to summary sheet
    	rWaveLength[$(ii-1)] = %(rData[L]$);
    }
  9. Create a graph of the quantities as a function of excitation wavelength with the plotxy X-Function
  10. //create a graph of the quantities as a function of excitation wavelength
    plotxy iy:=(rWaveLength, rArea) plot:=202 ogl:=[<new>];
    plotxy iy:=(rWaveLength, rHt) plot:=202 ogl:=[<new>];
    plotxy iy:=(rWaveLength, rFWHM) plot:=202 ogl:=[<new>];

Example 2: Running Batch Processing with pre-saved Theme

  1. Drag and drop the prepared theme,0-PA-BatchPA.ois, under the <Origin EXE folder>\Samples\Batch Processing folder into Origin.
  2. Open the project file with data for peak analysis
  3. // Open an Origin Project file
    string fname$ = system.path.program$ + "Samples\Batch Processing\Batch Peak Analysis.opj";
    doc -o %(fname$);   // Abbreviation of ''document -open''
  4. Perform the peak analysis batch processing with the pre-saved theme with the pamultiY X-Function
  5. paMultiY iy:=2:end theme:="BatchPA" append:=4 dataid:="My Parameter";