From 5414f9dacd6971f5b9e8ae96b489a16cd10e6e97 Mon Sep 17 00:00:00 2001
From: salman <zaher.salman@psi.ch>
Date: Wed, 17 Jun 2026 16:52:19 +0200
Subject: [PATCH] Fix regressions

---
 TrimSPelec.js |  7 +++++++
 TrimSPlib.js  | 22 +++++++++++++++-------
 main.js       |  7 ++++---
 3 files changed, 26 insertions(+), 10 deletions(-)

diff --git a/TrimSPelec.js b/TrimSPelec.js
index 388ce25..0e60de0 100644
--- a/TrimSPelec.js
+++ b/TrimSPelec.js
@@ -46,6 +46,10 @@ function getParallelJobCount() {
 
 function checkDir(directory) {
     // Check whether directory exists, if not create it
+    if (typeof directory !== 'string' || directory.length === 0) {
+	console.log('Invalid directory passed to checkDir:', directory);
+	return(0);
+    }
     if (!fs.existsSync(directory)) {
 	// Folder does not exist try to create it
 	fs.mkdir(directory,{recursive: true}, (err) => {
@@ -83,6 +87,9 @@ function readAsciiFile(filename) {
 }
 	       
 function fileExists(filename) {
+    if (typeof filename !== 'string' || filename.length === 0) {
+	return 0;
+    }
     try {
 	if (fs.existsSync(filename)) {
 	    return 1;
diff --git a/TrimSPlib.js b/TrimSPlib.js
index 7ddf7dc..b2cc718 100644
--- a/TrimSPlib.js
+++ b/TrimSPlib.js
@@ -3433,6 +3433,13 @@ function prep_cfg(toggle) {
     let valtmp = "";
 
     All['trimPath']=document.getElementById("trimPath").value;
+    // Keep file output settings in the runtime state even though they are not
+    // part of the projectile block. The scan runner depends on both values.
+    All["fileNamePrefix"] = document.getElementById("fileNamePrefix").value;
+    All["workPath"] = document.getElementById("workPath").value;
+    // Thread count is a local GUI/runtime setting only. It must stay out of
+    // TrimSP.cfg, but the local parallel runner still needs to read it.
+    All["scanThreads"] = document.getElementById("scanThreads").value;
     
     // Prepare Layers section
     let LayersSec = "[Layers]\n";
@@ -3762,21 +3769,22 @@ async function startSequence() {
 	    }
 	}
 
-	if (All["comboScan"]==1) {
+	if (All["comboScan"]=="SigEScan") {
 	    ScanName = "SigE";
 	    ScanAttrib = "sigEnergy";
-	} else if (All["comboScan"]==2) {
+	} else if (All["comboScan"]=="AngleScan") {
 	    ScanName = "Angle";
 	    ScanAttrib = "valAngle";
-	} else if (All["comboScan"]==3) {
+	} else if (All["comboScan"]=="SigAngleScan") {
 	    ScanName = "SigAngle";
 	    ScanAttrib = "sigAngle";
-	} else if (All["comboScan"]==4) {
+	} else if (All["comboScan"]=="NProjScan") {
 	    ScanName = "N";
 	    ScanAttrib = "numberProj";
-	} else if (All["comboScan"]==5) { 
-	    ScanName = "Ld"+All["scandL"];
-	    ScanAttrib = "L"+All["scandL"]+"d";
+	} else if (All["comboScan"]=="dScan") {
+	    // The GUI currently exposes the thickness scan only for layer 1.
+	    ScanName = "Ld1";
+	    ScanAttrib = "L1d";
 	}
     } else {
 	// For single run, array with single value of valEnergy
diff --git a/main.js b/main.js
index 4495230..197c38b 100644
--- a/main.js
+++ b/main.js
@@ -46,13 +46,13 @@ function parseStartupOptions(argv) {
 		    for (const candidate of candidates) {
 			if (!matcher) {
 			    const nextPath = path.join(candidate, segment);
-			    if (fs.existsSync(nextPath)) {
+			    if (typeof nextPath === 'string' && fs.existsSync(nextPath)) {
 				nextCandidates.push(nextPath);
 			    }
 			    continue;
 			}
 
-			if (!fs.existsSync(candidate) || !fs.statSync(candidate).isDirectory()) {
+			if (typeof candidate !== 'string' || !fs.existsSync(candidate) || !fs.statSync(candidate).isDirectory()) {
 			    continue;
 			}
 
@@ -71,12 +71,13 @@ function parseStartupOptions(argv) {
 		}
 
 		candidates = candidates
-		    .filter((candidate) => fs.existsSync(candidate) && fs.statSync(candidate).isFile())
+		    .filter((candidate) => typeof candidate === 'string' && fs.existsSync(candidate) && fs.statSync(candidate).isFile())
 		    .sort();
 	    }
 
 	    for (const candidate of candidates) {
 		if (
+		    typeof candidate === 'string' &&
 		    path.extname(candidate).toLowerCase() === '.cfg' &&
 		    fs.existsSync(candidate) &&
 		    fs.statSync(candidate).isFile() &&