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4.5.4 Peaks Analysis
Contents
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): $(ix2)]; integ1 rr; integ1.=;
Subtract Baseline and Integrate Peaks
The following example process a single file but it can be easily modify to loop through to process multiple files.
// Purpose: This example demonstrates the following: // 1. import a file // 2. find and subtract baseline // 3. find peaks // 4. integrate each peaks // 5. put integration area of each peak to append to a summary sheet //clean the project to start with empty space doc -s;doc -n;{win -cd}; // Create new book to save results from analysis of multiple peaks newbook name:="Integ Peaks" sheet:=0; string result$ = %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$; if(!run.section(%A, Main, nfiles)) return 0; // load success, data should be loaded into active book string dscBook$=%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 wks.AddCol(); 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.
(Please unzip the dialog theme from this zip file to your User Files Folder\Themes\AnalysisAndReportTable\ in advance.)
// 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$; int nfrom =3; int nto=5; range ww = !; ww.ncols = nto - nfrom + 1 + 1; //the first column is for label of variable list //format comparison variables range rLabel = 1!1; rLabel[1]$ = "Peak Curve"; rLabel[2]$ = "xc"; rLabel[3]$ = "A"; rLabel[4]$ = "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!$(ii-1)[1]; peak3$ = 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[1] = trRes.Parameters.xc__3.Value; r_info[2] = trRes.Parameters.A__3.Value; r_info[3] = trRes.Parameters.w__3.Value; } page.active=1;