5.10 Peak Analysis with Labtalk

Tutorial-Peak-Analysis

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.

// 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!;

2. Use a loop and the subtract_line X-Function to subtract a simple baseline of end points connection.

//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;
	}
}

3. Create new sheet for summary report

// 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";

4. 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

 //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[$(ii-1)] = %(rData[L]$);
}

5. Create a graph of the quantities as a function of excitation wavelength with the plotxy X-Function

//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

// Open an Origin Project file
string fname$ = system.path.program$ + "Samples\Batch Processing\Batch Peak Analysis.opj";
doc -o %(fname$);   // Abbreviation of ''document -open''

3. Perform the peak analysis batch processing with the pre-saved theme with the pamultiY X-Function

paMultiY iy:=2:end theme:="BatchPA" append:=4 dataid:="My Parameter";