# 4.5.4 Peaks Analysis

## Integrate Active Curve in Graph over a Specific X Range

The following example shows how to integrate the active curve in a graph over a specific range of x values, using the integ1 X-Function.

// Purpose: This example demonstrates the following:
//	1. import a file
//	2. create a graph
//	3. integrate the curve over a specific x range

// Create new book and import a sample file
newbook;
string fname$= system.path.program$ + "samples\curve fitting\multiple peaks.dat";
impasc;

// Plot 4th column against 1st column as a line plot
plotxy iy:=(1,4) plot:=200;

// Get row index for x values of 6.5 and 9.5, which covers the 3rd peak in the graph
int ix1=xindex(6.5,%c);
int ix2=xindex(9.5,%c);

// Integrate this range of the curve, and list the results of integration
range rr=(%c)[$(ix1):$(ix2)];
integ1 rr;
integ1.=;

## Subtract Baseline and Integrate Peaks

The following example process a single file but it can be easily modify to loop through to process multiple files.

// Purpose:		This example demonstrates the following:
//	1. import a file
//	2. find and subtract baseline
//	3. find peaks
//	4. integrate each peaks
//	5. put integration area of each peak to append to a summary sheet

doc -s;doc -n;{win -cd};

// Create new book to save results from analysis of multiple peaks
newbook name:="Integ Peaks" sheet:=0;
string result$= %h; newsheet cols:=5 xy:="NXYXY" name:="Results"; // Define ranges for all cols and give names to the columns range rFilename=1, rPkindex=2, rArea=3, rCenter=4, rHeight=5; rFilename[L]$ = "File Name";
rPkindex[L]$= "Peak Index"; rArea[L]$ = "Area";
rCenter[L]$= "Center"; rHeight[L]$ = "Height";
// filename col need to be wider
wcolwidth irng:= col(1) width:=20;

// Find data files
fname$= system.path.program$ + "Samples\Spectroscopy\Peaks with Base.dat";

newbook;// use a new book to store data, so results book can be in separate book

//impfile filtername:="ASCII.oif";
impASC;
// we will use only the 1st two col
wks.ncols = 2;
range baseline=3;// put before anchor XY so we can share data's X of col(1)
range subtracted=4;// data subtracted to find peaks and integrate
range -x anchors = (5,6);
//columns to hold peak finding results
range pcenter=7, pleft=8, pright=9;
// Find baseline anchor points to put into col(5),(6)
blauto iy:=(1,2) oy:=anchors;

// Interpolate with Cubic B-Spline to put into col(5)
interp1 ix:=1 iy:=anchors method:=spline ox:=baseline;
baseline[L]$="Baseline"; baseline[C]$="Interpolated from Found Anchor Pts";
//Subtract baseline
subtracted = col(2) - baseline;
subtracted[L]$="Subtracted"; //Find peak pkfind subtracted ocenter:=pcenter oleft:=pleft oright:=pright; //loop each peak to compute area for(int ipeak = 1; ipeak <= pcenter.GetSize(); ipeak++) { int n1 = pleft[ipeak]; int n2 = pright[ipeak]; range rint = subtracted[$(n1):$(n2)]; // range of data to be integrated double aa, x0, y0; integ1 rint oy:=<optional> area:=aa x0:=xx y0:=yy; rFilename[ipeak]$ = %(page.info.system.import.filename$); rPkindex[ipeak] = ipeak; rArea[ipeak] = aa; rCenter[ipeak] = xx; rHeight[ipeak] = yy; } ## Process Multiple DSC Files to Find and Integrate Peaks In this example, we find all files under a sample subfolder to loop over each and process them and generate a summary sheet. /////////////////////////////////////////////////////////////////////////////////////////////////////// // Purpose: This example demonstrates the following: // 1. Import files with dsc extension // 2. Loop through each data to : find and subtract baseline; // find peaks; integrate peaks; put integration area and other result in a separate worksheet // 3. Sort summary sheet by indices of peaks. // // Note that this code is in 'OGS' style with various sections that can be independently accessed. // Save the code as a file with OGS extension to your User Files Folder. // Run with run.section(filename,Main) // OR // Type DIR *.OGS<Enter> to scan for OGS files then type filename<Enter> to run. ///////////////////////////////////////////////////////////////////////////////////////////////////////// [Help] type Load one more files with dsc extension and then integrate area of each peak.; type One argument : %1 = number of files to load, 0 to load all.; [Main] int nfiles = %1; string LoadDSCogsPath$=system.path.program$+ "Samples\LabTalk Script Examples\LoadDSC.ogs"; %A=LoadDSCogsPath$;
if(!run.section(%A, Main, nfiles))
return 0;
string dscBook$=%H; if(dscBook.GetLength() < 1 ) { type "new book " + dscBook$ + " is not valid";
return 0;
}
nfiles = page.nLayers;

// Create new sheet for summary report and define ranges
newsheet cols:=8 xy:="LYYYYYYY" name:="Summary";
range rColName = 1, rIndex = 2, rCntrInd = 3, rLtInd = 4, rRtInd = 5;
range rArea = 6, rCntr = 7, rHt = 8;
rColName[L]$= "Data Name"; rIndex[L]$   = "Peak Index";
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";

for(int ii = 1; ii<= nfiles; ii++)
{
if(!run.section(, IntegOneData, $(ii))) return 0; } page.active =$(page.nLayers);
dataset sbc = {2};  //Select indecies of peaks for the primary sort order
dataset sodr= {1};  //Ascending
wsort nestcols:=sbc order:=sodr; //Perform the sorting

return 1;// for success

[IntegOneData]
int sheet = %1;
page.active = $(sheet); range rinput =$(sheet)!2;
string strData$= rinput[C]$;

//alloc space for baseline and subtracted with same X of data
int n = wks.nCols;
range baseline = $(n); baseline[L]$="Baseline";
baseline[C]$="Interpolated from Found Anchor Pts"; wks.AddCol(); n = wks.nCols; range subtracted =$(n);
subtracted[L]$="Subtracted"; // Find baseline anchor points range -x anchors = (AnchorX, AnchorsY); blauto iy:=rinput oy:=anchors; // Interpolate with Spline interp1 ix:=1 iy:=anchors method:=spline ox:=baseline; //Subtract baseline subtracted = rinput - baseline; //columns to hold peak finding results int nn = wks.ncols; loop(cc, 1, 7) { wks.addcol(); } //Find peak range pindex =$(nn+1), pcenter= $(nn+2), pleft=$(nn+3), pright= $(nn+4), parea=$(nn+5), px =  $(nn+6), py =$(nn+7);
pkfind subtracted ocenter:=pcenter oleft:=pleft oright:=pright;

//loop each peak to compute area
int nNumPeaks = pcenter.GetSize();
for(int ipeak = 1; ipeak <= nNumPeaks; ipeak++)
{
int n1 = pleft[ipeak];
int n2 = pright[ipeak];
range rint = subtracted[$(n1):$(n2)]; // range of data to be integrated
double aa, x0, y0;
integ1 rint area:=aa x0:=xx y0:=yy oy:=<optional>;

pindex[ipeak] = ipeak;
parea[ipeak] = aa;
px[ipeak] = xx;
py[ipeak] = yy;

// Copy results for current peak, to the summary sheet
int irow = (($(sheet)-1)*$(nNumPeaks))+$(ipeak) ; rColName[$(irow)]$= rinput[C]$;
rIndex[$(irow)] = ipeak; rCntrInd[$(irow)] = pcenter[ipeak];
rLtInd[$(irow)] = pleft[ipeak]; rRtInd[$(irow)] = pright[ipeak];
rArea[$(irow)] = parea[ipeak]; rCntr[$(irow)] = px[ipeak];
rHt[$(irow)] = py[ipeak]; } pindex[L]$ = "Peak Index";
pcenter[L]$= "Peak Center Index"; pleft[L]$ = "Peak Left Index";
pright[L]$= "Peak Right Index"; parea[L]$ = "Area";
px[L]$= "Center"; py[L]$ = "Height";

return 1;

## Compare Fitting Results of PA

This example shows how to compare a particular peak with its fit after running PA on a series of sample data.

// Purpose:		This example demonstrates the following:
//	1. import a series of dsc files
//	2. auto find and subtract baseline
//	3. find peaks and fit peaks with same setting loading form theme file.
//	4. Plot the fit curve of third peak to the first sheet
//	5. Append primary parameters of this peak under the graph cell.
//      6. At the end, get the comparsion sheet about the same peak in the source data.

path$= system.path.program$ + "Samples\Spectroscopy\DSC\Data\";

newbook s:=1 result:=bkn$; int nfrom =3; int nto=5; range ww = !; ww.ncols = nto - nfrom + 1 + 1; //the first column is for label of variable list //format comparison variables range rLabel = 1!1; rLabel$ = "Peak Curve";
rLabel$= "xc"; rLabel$ = "A";
rLabel$= "w"; int ii; loop(ii,nfrom,nto) { //1, import two data files in a series ind$ = $(ii); filename$ = "tcal"+ ind$+".dsc"; file$ = path$+ filename$;
newsheet bkn$; impfile file$ ;

//2, run pa script mode and save result wks name and report tree.
aa$="(1,2)"; pa iy:=aa$ theme:=the3ndpeaks;

//3, get result and make plot of the 3nd peak
string pp, fitc, resid, peak3;
pp$=__PEAK$;
fitc$= __FITCURVE$;
resid$= __RESIDUAL$;
getresults tr:=trRes iw:=__REPORT$; //4, plot the 3nd peak to sheet1 for comparison range r_peak = 1!$(ii-1);
peak3$= fitc$ + "(7,8)";

plotxy iy:=peak3$plot:=200; graphname$ = %H;
insertGraph gname:=graphname$embed:=1 resizecell:=1 cell:=r_peak; //5, append peak information range r_info = 1!$(ii-1)[2:4];
r_info = trRes.Parameters.xc__3.Value;
r_info = trRes.Parameters.A__3.Value;
r_info = trRes.Parameters.w__3.Value;

}
page.active=1;