From 198fb0a41a67a0d6207d20b4676b6aabffec52e1 Mon Sep 17 00:00:00 2001
From: salman <zaher.salman@psi.ch>
Date: Sat, 13 Jun 2026 11:08:10 +0200
Subject: [PATCH] Improve output data handeling from fixed numbered columns to
 base it on column labels.

---
 TrimSPlib.js | 115 +++++++++++++++++++++++++++++++++++++++++----------
 1 file changed, 94 insertions(+), 21 deletions(-)

diff --git a/TrimSPlib.js b/TrimSPlib.js
index bebaa6a..fe8e3c2 100644
--- a/TrimSPlib.js
+++ b/TrimSPlib.js
@@ -3745,22 +3745,31 @@ async function startSequence() {
 	Plot_xy("plotRge",depth,nmuons,['Depth (nm)','Stopped muons (%/nm)',ScanName+'='+Number(SValue)/1000+'keV']);		
 	// Read the sequence data
 	let [cfort,cdata]= readDatFile(All["workPath"]+"/fort.33");
-	let lyrs = [6]; // back scattered muons
-	for (let ilayer=18;ilayer<cdata.length;ilayer++){lyrs.push(ilayer);} // the rest of the layers
+	let seqInfo = getSequenceColumnInfo(cfort, All["numLayer"]);
+	let energy = cdata[seqInfo.indexByName['Energy']];
+	let ntot = cdata[seqInfo.indexByName['ntot']];
+	let plotSeries = [
+	    {
+		index: seqInfo.indexByName['backsc'],
+		label: cfort[seqInfo.indexByName['backsc']],
+	    },
+	    ...seqInfo.layerIndices.map((index, offset) => {
+		let LComp = "L" + (offset + 1) + "Comp";
+		return {
+		    index: index,
+		    label: All[LComp] || seqInfo.layerHeaders[offset],
+		};
+	    }),
+	];
 	// Now loop over all
 	Plotly.purge("plotFrac")
-	for (let ilayer of lyrs) {
+	for (let series of plotSeries) {
 	    // Normalize
-	    let idata = cdata[ilayer];
+	    let idata = cdata[series.index];
 	    for (let i=0; i<idata.length; i++) {
-		idata[i]=100*idata[i]/cdata[4][i];
+		idata[i]=100*idata[i]/ntot[i];
 	    }
-	    let chem = cfort[ilayer];
-	    if (ilayer != 6) {
-		let LComp = "L"+(ilayer-17)+"Comp";
-		chem = All[LComp];
-	    }
-	    Plot_xy("plotFrac",cdata[0],cdata[ilayer],['E (keV)','Fraction of muons (%)',chem]);
+	    Plot_xy("plotFrac",energy,cdata[series.index],['E (keV)','Fraction of muons (%)',series.label]);
 	}
 	await yieldToRenderer();
 	iScan++;
@@ -3820,6 +3829,56 @@ function readDatFile(filename) {
     return [cols,data];
 }
 
+function getSequenceColumnInfo(cols, expectedLayers = null) {
+    // Parse the fort.33 / *_Seq_Results.dat header into fixed summary columns
+    // and per-layer result columns. This avoids hard-coding column offsets in
+    // the plotting routines.
+    const requiredSummaryFields = [
+	'Energy',
+	'SigmaE',
+	'Alpha',
+	'SigAlpha',
+	'ntot',
+	'imp',
+	'backsc',
+	'trans',
+	'tried',
+	'negE',
+	'range',
+	'straggeling',
+	'Eback',
+	'sigEback',
+	'Etrans',
+	'SigEtrans',
+	'red._E',
+	'PRC',
+    ];
+
+    const indexByName = {};
+    for (let i = 0; i < cols.length; i++) {
+	indexByName[cols[i]] = i;
+    }
+
+    const missing = requiredSummaryFields.filter((name) => indexByName[name] == null);
+    if (missing.length > 0) {
+	throw new Error('Unexpected sequence-file header. Missing columns: ' + missing.join(', '));
+    }
+
+    const fixedCount = requiredSummaryFields.length;
+    let layerHeaders = cols.slice(fixedCount);
+    if (expectedLayers != null && expectedLayers >= 0) {
+	layerHeaders = layerHeaders.slice(0, expectedLayers);
+    }
+
+    return {
+	indexByName: indexByName,
+	requiredSummaryFields: requiredSummaryFields,
+	layerStartIndex: fixedCount,
+	layerHeaders: layerHeaders,
+	layerIndices: layerHeaders.map((_, offset) => fixedCount + offset),
+    };
+}
+
 function plotProfiles(filenames) {
     // Plot rge files filenames
 
@@ -3868,16 +3927,28 @@ function plotFractions(filename) {
     var plotDiv=win.document.getElementById("newPlot");
 
     var [cfort,cdata]= readDatFile(filename);
-    let lyrs = [6]; // back scattered muons
-    for (let ilayer=18;ilayer<cdata.length;ilayer++){lyrs.push(ilayer);} // the rest of the layers
+    let seqInfo = getSequenceColumnInfo(cfort);
+    let energy = cdata[seqInfo.indexByName['Energy']];
+    let ntot = cdata[seqInfo.indexByName['ntot']];
+
+    let plotSeries = [
+	{
+	    index: seqInfo.indexByName['backsc'],
+	    label: cfort[seqInfo.indexByName['backsc']],
+	},
+	...seqInfo.layerIndices.map((index, offset) => ({
+	    index: index,
+	    label: seqInfo.layerHeaders[offset],
+	})),
+    ];
     // Now loop over all
-    for (let ilayer of lyrs) {
+    for (let series of plotSeries) {
 	// Normalize
-	let idata = cdata[ilayer];
+	let idata = cdata[series.index];
 	for (let i=0; i<idata.length; i++) {
-	    idata[i]=100*idata[i]/cdata[4][i];
+	    idata[i]=100*idata[i]/ntot[i];
 	}
-	Plot_xy(plotDiv,cdata[0],cdata[ilayer],['E (keV)','Fraction of muons (%)',cfort[ilayer]]);
+	Plot_xy(plotDiv,energy,cdata[series.index],['E (keV)','Fraction of muons (%)',series.label]);
     }
     plotDiv=win.document.getElementById("newPlot");
 }
@@ -3895,14 +3966,16 @@ function plotMean(filename) {
     var plotDiv=win.document.getElementById("newPlot");
     
     let [cfort,cdata]= readDatFile(filename);
-    let mean = cdata[10];
-    let strag = cdata[11];
+    let seqInfo = getSequenceColumnInfo(cfort);
+    let energy = cdata[seqInfo.indexByName['Energy']];
+    let mean = cdata[seqInfo.indexByName['range']];
+    let strag = cdata[seqInfo.indexByName['straggeling']];
     for (let i=0; i<mean.length; i++) {
 	mean[i]=mean[i]/10;
 	strag[i]=strag[i]/10;
     }
-    Plot_xy(plotDiv,cdata[0],mean,['E (keV)','Mean Depth/Stragg. (nm)',cfort[10]]);
-    Plot_xy(plotDiv,cdata[0],strag,['E (keV)','Mean Depth/Stragg. (nm)',cfort[11]]);
+    Plot_xy(plotDiv,energy,mean,['E (keV)','Mean Depth/Stragg. (nm)','range']);
+    Plot_xy(plotDiv,energy,strag,['E (keV)','Mean Depth/Stragg. (nm)','straggeling']);
 }
 
 function startSim() {