Merge branch 'foliage-gpu' of git.elphel.com:Elphel/imagej-elphel into foliage-gpu

.gitignore

@@ -17,6 +17,7 @@ __pycache__
 CLAUDE.md
 GEMINI.md
 MEMORY.md
+ANDREY_CONTINUE.md
 .claude/
 .gemini/
 *.orig

pom.xml

@@ -40,6 +40,12 @@
         </dependencyManagement>
 
         <dependencies>
+			<!-- JNA: call the native CUDA tile-processor shim (libtileproc.so) for the JCuda->JNA GPU-layer migration. By Claude on 2026-06-25 -->
+			<dependency>
+			    <groupId>net.java.dev.jna</groupId>
+			    <artifactId>jna</artifactId>
+			    <version>5.14.0</version>
+			</dependency>
 			<!-- https://mvnrepository.com/artifact/com.google.code.gson/gson -->
 			<dependency>
 			    <groupId>com.google.code.gson</groupId>
@@ -314,7 +320,41 @@
 		            -->
 	           	</dependencies>
 	        </profile>
-		</profiles>	
+	        <!-- Opt-in (mvn -Plibtorch ...): unpack the libtorch native runtime (cu128, ~3.8GB zip) from the
+	             Elphel mirror into target/libtorch-dist for the native DNN backend (libtpdnn.so / CuasDnnLocal).
+	             OFF by default so the normal build never downloads it. Publish the artifact to the mirror with
+	             tile_processor_gpu/jna/publish_libtorch_mirror.sh. By Claude on 06/27/2026. -->
+	        <profile>
+	            <id>libtorch</id>
+	            <build>
+	                <plugins>
+	                    <plugin>
+	                        <groupId>org.apache.maven.plugins</groupId>
+	                        <artifactId>maven-dependency-plugin</artifactId>
+	                        <version>3.1.2</version>
+	                        <executions>
+	                            <execution>
+	                                <id>unpack-libtorch</id>
+	                                <phase>generate-resources</phase>
+	                                <goals><goal>unpack</goal></goals>
+	                                <configuration>
+	                                    <artifactItems>
+	                                        <artifactItem>
+	                                            <groupId>org.pytorch</groupId>
+	                                            <artifactId>libtorch-cxx11-cu128</artifactId>
+	                                            <version>2.7.1</version>
+	                                            <type>zip</type>
+	                                            <outputDirectory>${project.build.directory}/libtorch-dist</outputDirectory>
+	                                        </artifactItem>
+	                                    </artifactItems>
+	                                </configuration>
+	                            </execution>
+	                        </executions>
+	                    </plugin>
+	                </plugins>
+	            </build>
+	        </profile>
+		</profiles>
 
 	<build>
 		<resources>

scripts/migrate_curt_config.py

+#!/usr/bin/env python3
+# By Claude on 07/04/2026
+"""Migrate corr-xml configuration files to the current curt_* key format.
+
+CuasRtParameters history:
+  pre-07/2026   keys CLT_PARAMETERS._imp_curt_<name>   (curt_* fields inside IntersceneMatchParameters,
+                then the extracted class still saved under imp with the same keys)
+  07/2026 -     keys CLT_PARAMETERS._curt_<name>       (CuasRtParameters is a CLTParameters peer,
+                like imp/ofp/ilp)
+
+The Java reader keeps a legacy fallback (it reads _imp_curt_* when present, then
+_curt_* overrides), so unmigrated files still load. This script rewrites the keys
+so files are in the current format and future removal of the fallback is safe.
+
+Usage:
+  migrate_curt_config.py FILE [FILE ...]        # in-place, keeps FILE.bak
+  migrate_curt_config.py --dry-run FILE ...     # report only, no changes
+  migrate_curt_config.py --no-backup FILE ...   # in-place without .bak
+
+Only the literal substring '_imp_curt_' inside key="..." attributes is renamed to
+'_curt_'; everything else (values, formatting, comments) is byte-preserved. If a
+file already contains a _curt_ key that a rename would duplicate, the old key is
+dropped (the new one wins) and a warning is printed.
+
+A provenance XML comment (absolute path of this script + timestamp) is inserted
+right after the <properties> line of every modified file. Java's XML properties
+loader ignores XML comments, but note it also DROPS them if the application
+re-saves the file - the marker survives only until the next save from ImageJ.
+"""
+
+import argparse
+import datetime
+import os
+import re
+import shutil
+import sys
+
+KEY_RE = re.compile(r'(<entry key=")([^"]*)_imp_curt_([^"]*)(")')
+
+
+def migrate_text(text):
+    """Return (new_text, n_renamed, dropped_keys)."""
+    existing_new = set(re.findall(r'<entry key="([^"]*_curt_[^"]*)"', text))
+    existing_new = {k for k in existing_new if '_imp_curt_' not in k}
+    renamed = [0]
+    dropped = []
+    out_lines = []
+    for line in text.splitlines(keepends=True):
+        m = KEY_RE.search(line)
+        if m:
+            new_key = m.group(2) + '_curt_' + m.group(3)
+            if new_key in existing_new:
+                dropped.append(m.group(2) + '_imp_curt_' + m.group(3))
+                continue  # drop the whole legacy entry line - the new key already exists
+            line = KEY_RE.sub(r'\g<1>\g<2>_curt_\g<3>\g<4>', line)
+            renamed[0] += 1
+        out_lines.append(line)
+    return ''.join(out_lines), renamed[0], dropped
+
+
+def add_provenance_comment(text):
+    """Insert a provenance XML comment after the <properties> line."""
+    stamp = datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S')
+    marker = ('<!-- curt_* keys migrated (_imp_curt_* to _curt_*) by %s on %s -->\n'
+              % (os.path.abspath(__file__), stamp))
+    lines = text.splitlines(keepends=True)
+    for i, line in enumerate(lines):
+        if '<properties>' in line:
+            lines.insert(i + 1, marker)
+            return ''.join(lines)
+    return marker + text  # no <properties> line found - prepend (still valid for grep)
+
+
+def main():
+    ap = argparse.ArgumentParser(description=__doc__.splitlines()[0])
+    ap.add_argument('files', nargs='+', help='corr-xml files to migrate')
+    ap.add_argument('--dry-run', action='store_true', help='report only, do not modify')
+    ap.add_argument('--no-backup', action='store_true', help='do not keep a .bak copy')
+    args = ap.parse_args()
+
+    status = 0
+    for path in args.files:
+        try:
+            with open(path, encoding='utf-8') as f:
+                text = f.read()
+        except OSError as e:
+            print(f"{path}: ERROR - {e}", file=sys.stderr)
+            status = 1
+            continue
+        new_text, n, dropped = migrate_text(text)
+        for k in dropped:
+            print(f"{path}: WARNING - dropped legacy entry '{k}' (current-format key already present)")
+        if n == 0 and not dropped:
+            print(f"{path}: already current (no _imp_curt_ keys)")
+            continue
+        if args.dry_run:
+            print(f"{path}: would rename {n} key(s)" +
+                  (f", drop {len(dropped)} duplicate legacy entrie(s)" if dropped else ""))
+            continue
+        if not args.no_backup:
+            shutil.copy2(path, path + '.bak')
+        with open(path, 'w', encoding='utf-8') as f:
+            f.write(add_provenance_comment(new_text))
+        print(f"{path}: renamed {n} key(s)" +
+              (f", dropped {len(dropped)} duplicate legacy entrie(s)" if dropped else "") +
+              ("" if args.no_backup else f" (backup: {path}.bak)"))
+    return status
+
+
+if __name__ == '__main__':
+    sys.exit(main())

src/main/java/com/elphel/imagej/cameras/CLTParameters.java

@@ -40,6 +40,7 @@ import com.elphel.imagej.common.WindowTools;
 import com.elphel.imagej.correction.CorrectionColorProc;
 import com.elphel.imagej.lwir.LwirReaderParameters;
 import com.elphel.imagej.tileprocessor.BiQuadParameters;
+import com.elphel.imagej.tileprocessor.CuasRtParameters; // By Claude on 07/04/2026
 import com.elphel.imagej.tileprocessor.ImageDtt;
 import com.elphel.imagej.tileprocessor.ImageDttParameters;
 import com.elphel.imagej.tileprocessor.IntersceneGlobalLmaParameters;
@@ -75,6 +76,7 @@ public class CLTParameters {
 	private double    scale_strength_main = 1.0;// leave as is
 	private double    scale_strength_aux =  0.3;// reduce to match lower sigma
 	public boolean    norm_kern =         true; // normalize kernels
+	public boolean    norm_kern_abs =     false;// normalize kernels absolute value (for those with sum=0
 	public boolean    gain_equalize =     false;// equalize green channel gain (bug fix for wrong exposure in Exif ?)
 	public boolean    colors_equalize =   true; // equalize R/G, B/G of the individual channels
 	public boolean    nosat_equalize =    true; // Skip saturated when adjusting gains
@@ -1183,6 +1185,7 @@ public class CLTParameters {
 	public IntersceneGlobalLmaParameters  iglp =    new IntersceneGlobalLmaParameters();
 	public InterNoiseParameters           inp =     new InterNoiseParameters();
 	public LWIRWorldParameters            lwp =     new LWIRWorldParameters();
+	public CuasRtParameters               curt =    new CuasRtParameters(); // CUAS real-time (was imp.curt) // By Claude on 07/04/2026
 			
 	public HashMap<String,Double> z_corr_map = new HashMap<String,Double>(); //old one
 	public HashMap<String,Double> infinity_distace_map = new HashMap<String,Double>(); //new one
@@ -1317,6 +1320,7 @@ public class CLTParameters {
 		properties.setProperty(prefix+"scale_strength_aux",         this.scale_strength_aux+"");
 
 		properties.setProperty(prefix+"norm_kern",                  this.norm_kern+"");
+		properties.setProperty(prefix+"norm_kern_abs",              this.norm_kern_abs+"");
 		properties.setProperty(prefix+"gain_equalize",              this.gain_equalize+"");
 		properties.setProperty(prefix+"colors_equalize",            this.colors_equalize+"");
 		properties.setProperty(prefix+"nosat_equalize",             this.nosat_equalize+"");
@@ -2338,6 +2342,7 @@ public class CLTParameters {
 		iglp.setProperties    (prefix+"_iglp_",   properties);
 		inp.setProperties     (prefix+"_inp_",    properties);
 		lwp.setProperties     (prefix+"_lwp_",    properties);
+		curt.setProperties    (prefix+"_curt_",   properties); // By Claude on 07/04/2026
 
 	}
 
@@ -2374,6 +2379,7 @@ public class CLTParameters {
 		if (properties.getProperty(prefix+"scale_strength_aux")!=null)            this.scale_strength_aux=Double.parseDouble(properties.getProperty(prefix+"scale_strength_aux"));
 
 		if (properties.getProperty(prefix+"norm_kern")!=null)                     this.norm_kern=Boolean.parseBoolean(properties.getProperty(prefix+"norm_kern"));
+		if (properties.getProperty(prefix+"norm_kern_abs")!=null)                 this.norm_kern_abs=Boolean.parseBoolean(properties.getProperty(prefix+"norm_kern_abs"));
 		if (properties.getProperty(prefix+"gain_equalize")!=null)                 this.gain_equalize=Boolean.parseBoolean(properties.getProperty(prefix+"gain_equalize"));
 		if (properties.getProperty(prefix+"colors_equalize")!=null)               this.colors_equalize=Boolean.parseBoolean(properties.getProperty(prefix+"colors_equalize"));
 		if (properties.getProperty(prefix+"nosat_equalize")!=null)                this.nosat_equalize=Boolean.parseBoolean(properties.getProperty(prefix+"nosat_equalize"));
@@ -3408,6 +3414,8 @@ public class CLTParameters {
 		iglp.getProperties    (prefix+"_iglp_",   properties);
 		inp.getProperties     (prefix+"_inp_",    properties);
 		lwp.getProperties     (prefix+"_lwp_",    properties);
+		curt.getProperties    (prefix+"_imp_curt_", properties); // legacy keys (curt was inside imp until 07/2026) // By Claude on 07/04/2026
+		curt.getProperties    (prefix+"_curt_",   properties); // current keys override legacy if both present // By Claude on 07/04/2026
 	}
 
 	public boolean showJDialog() {
@@ -3456,7 +3464,8 @@ public class CLTParameters {
 		gd.addNumericField("Scale all correlation strengths (to compensate correlation sigma) for aux camera",  this.scale_strength_aux,        4);
 
 		gd.addCheckbox    ("Normalize kernels",                                                                 this.norm_kern);
-		gd.addCheckbox    ("Equalize green channel gain of the individual cnannels (bug fix for exposure)",           this.gain_equalize);
+		gd.addCheckbox    ("Normalize kernels absolute values",                                                 this.norm_kern_abs);
+		gd.addCheckbox    ("Equalize green channel gain of the individual cnannels (bug fix for exposure)",     this.gain_equalize);
 		gd.addCheckbox    ("Equalize R/G, B/G balance of the individual channels",                              this.colors_equalize);
 		gd.addCheckbox    ("Skip saturated when adjusting gains",                                               this.nosat_equalize);
 		gd.addNumericField("Saturation level of the most saturated color channel",                              this.sat_level,   4);
@@ -4898,6 +4907,9 @@ public class CLTParameters {
 
 		this.imp.dialogQuestions(gd);
 
+		gd.addTab         ("CUAS RT", "CUAS Real Time");
+		this.curt.dialogQuestions(gd); // By Claude on 07/04/2026
+
 		this.lwp.dialogQuestions(gd);
 		
 		gd.addTab         ("Inter-LMA", "parameters for the interscene LMA fitting");
@@ -4992,6 +5004,7 @@ public class CLTParameters {
 		this.scale_strength_main =  gd.getNextNumber();
 		this.scale_strength_aux =   gd.getNextNumber();
 		this.norm_kern=             gd.getNextBoolean();
+		this.norm_kern_abs=         gd.getNextBoolean();
 		this.gain_equalize=         gd.getNextBoolean();
 		this.colors_equalize=       gd.getNextBoolean();
 		this.nosat_equalize=        gd.getNextBoolean();
@@ -5965,6 +5978,7 @@ public class CLTParameters {
 		this.lwir.dialogAnswers(gd);
 		this.ofp.dialogAnswers(gd);
 		this.imp.dialogAnswers(gd);
+		this.curt.dialogAnswers(gd); // By Claude on 07/04/2026
 		this.lwp.dialogAnswers(gd);
 		this.ilp.dialogAnswers(gd);
 		this.iglp.dialogAnswers(gd);

src/main/java/com/elphel/imagej/cameras/EyesisCorrectionParameters.java

@@ -68,7 +68,9 @@ public class EyesisCorrectionParameters {
     			"resultsDirectory", // 6
     			"cuasSeed",         // 7
     			"uasLogs",          // 8
-    			"skyMask"};         // 9  
+    			"skyMask",          // 9
+    			"cuasSynth",        // 10 shared synthetic-grid dir (curt_synth_src), valid for all sequences. By Claude on 06/24/2026
+    			"cuasNoise"};       // 11 INLINE per-level L2 noise-scale numbers (NOT a path); empty -> sqrt default. By Claude on 06/24/2026
     	public static final int KEY_INDEX_ROOT_DIRECTORY =    0;
     	public static final int KEY_INDEX_SOURCE_DIRECTORY =  1;
     	public static final int KEY_INDEX_LINKED_MODELS =     2;
@@ -79,6 +81,8 @@ public class EyesisCorrectionParameters {
     	public static final int KEY_INDEX_CUAS_SEED =         7;
     	public static final int KEY_INDEX_UAS_LOGS =          8;
     	public static final int KEY_INDEX_SKY_MASK =          9;
+    	public static final int KEY_INDEX_CUAS_SYNTH =       10; // By Claude on 06/24/2026
+    	public static final int KEY_INDEX_CUAS_NOISE =       11; // inline per-level noise scales. By Claude on 06/24/2026
     	
     	public static final String AUX_PREFIX = "AUX-";
     	public boolean swapSubchannels01=      true; // false; // (false: 0-1-2, true - 1-0-2)
@@ -129,6 +133,8 @@ public class EyesisCorrectionParameters {
     	public String cuasSeedDir=             "";
     	public boolean useCuasSeedDir=         false;
     	public String cuasSkyMask =            "";  // TIFF image 640x512 where 1.0 - sky, 0.0 - ground, blurred with GB (now sigma==2.0)
+    	public String cuasSynth =              "";  // shared dir holding the synthetic-grid TIFF (curt_synth_src) - valid for ALL sequences, resolved from the list SET key "cuasSynth" (relative to rootDirectory), like cuasSkyMask; empty -> per-sequence model dir (old behavior). By Claude on 06/24/2026
+    	public String cuasNoise =              "";  // INLINE per-level L2 noise-scale numbers from the list SET key "cuasNoise" (e.g. "0.354,0.5,0.707,1.0,1.414,2.0"); NOT a path. Empty -> theoretical sqrt(2)^(L-3) default (computed in CuasDetectRT). By Claude on 06/24/2026
     	public String cuasUasLogs =            "";  // json file path containing UAS logs
     	public double cuasUasTimeStamp =       0.0; // timestamp corresponding to the UAS time 0.0
     	public double [] cuasCameraATR =       {0, 0, 0};
@@ -322,6 +328,8 @@ public class EyesisCorrectionParameters {
   			cp.useCuasSeedDir=    	    this.useCuasSeedDir;
   			
   			cp.cuasSkyMask =            this.cuasSkyMask;
+  			cp.cuasSynth =              this.cuasSynth;
+  			cp.cuasNoise =              this.cuasNoise;
   			cp.cuasUasLogs =            this.cuasUasLogs;
   			cp.cuasUasTimeStamp =       this.cuasUasTimeStamp;
   			cp.cuasCameraATR =          this.cuasCameraATR.clone();
@@ -1833,7 +1841,7 @@ public class EyesisCorrectionParameters {
             		if (dir_map.get(KEY_DIRS[i]).length() > 0){
             			Path dir_path=base_path.resolve(Paths.get(dir_map.get(KEY_DIRS[i])));
             			File dir_file = new File(dir_path.toString());
-            			if ((i != KEY_INDEX_UAS_LOGS) && (i != KEY_INDEX_SKY_MASK)) { // cuasUasLogs, cuasSkyMask are files, not directories
+            			if ((i != KEY_INDEX_UAS_LOGS) && (i != KEY_INDEX_SKY_MASK) && (i != KEY_INDEX_CUAS_SYNTH) && (i != KEY_INDEX_CUAS_NOISE)) { // cuasUasLogs/cuasSkyMask=files; cuasSynth=input dir; cuasNoise=inline numbers (not a path) - don't auto-create. By Claude on 06/24/2026
             				if (!dir_file.exists()) {
             					if (MKDIRS_ALLOW) {
             						dir_file.mkdirs();
@@ -1901,7 +1909,20 @@ public class EyesisCorrectionParameters {
             		case KEY_INDEX_SKY_MASK: // 9:  // cuasSeed
             			this.cuasSkyMask =     dir_string; // dir_path.toString();
             			System.out.println("this.cuasSkyMask=" + this.cuasSkyMask);
-            			
+
+            			break;
+            		case KEY_INDEX_CUAS_SYNTH: // 10: shared synthetic-grid dir (curt_synth_src), all sequences. By Claude on 06/24/2026
+            			this.cuasSynth =       dir_string;
+            			System.out.println("this.cuasSynth=" + this.cuasSynth);
+            			break;
+            		case KEY_INDEX_CUAS_NOISE: // 11: INLINE per-level noise scales (numbers, NOT a path). By Claude on 06/24/2026
+            			{
+            				StringBuilder nsb = new StringBuilder(dir_map.get(KEY_DIRS[i])); // first number
+            				ArrayList<String> nx = extra_map.get(KEY_DIRS[i]);              // remaining numbers
+            				if (nx != null) for (String v : nx) nsb.append(",").append(v);
+            				this.cuasNoise = nsb.toString();
+            			}
+            			System.out.println("this.cuasNoise=" + this.cuasNoise);
             			break;
             		}
             	}

src/main/java/com/elphel/imagej/common/GenericJTabbedDialog.java

@@ -315,7 +315,13 @@ public class GenericJTabbedDialog implements ActionListener {
 					label.setHorizontalAlignment(JLabel.RIGHT);
 	            	tab.add(label,gbc);
 	        		gbc.gridx = 1;
-	        		tab.add(component,gbc);
+	        		if (component instanceof JCheckBox) { // don't stretch checkboxes - keep the click target at the box, not the whole half-width cell (a near-scrollbar click was toggling them) // By Claude on 06/20/2026
+	        			gbc.fill = GridBagConstraints.NONE; gbc.anchor = GridBagConstraints.WEST;
+	        			tab.add(component,gbc);
+	        			gbc.fill = GridBagConstraints.HORIZONTAL; gbc.anchor = GridBagConstraints.CENTER; // restore for the following rows
+	        		} else {
+	        			tab.add(component,gbc);
+	        		}
 				}
 			}
 			// Add empty label that would push up all other rows

src/main/java/com/elphel/imagej/common/GenericJTabbedDialogMcp.java

@@ -38,6 +38,7 @@ public class GenericJTabbedDialogMcp extends GenericJTabbedDialog{
 	private static long dialogTimeoutMs = 30000L;
 	public boolean mcp_mode = false;
 	private boolean mcpCanceled = false;
+	private McpDialogSession mcpSession = null; // this dialog's OWN session: the registry is cleared on submit BEFORE the getNext*() reads run, so reads must not go through it // By Claude on 07/07/2026
 	private final List<McpDialogField> mcpFields = new ArrayList<McpDialogField>();
 	private final String dialogTitle;
 	private String currentTab = "";
@@ -192,7 +193,8 @@ public class GenericJTabbedDialogMcp extends GenericJTabbedDialog{
 		if (mcp_mode) {
 			// codex 2026-01-25: publish dialog schema to MCP registry
 			readIndex = 0;
-			boolean applied = McpDialogRegistry.setCurrent(new McpDialogSession(dialogTitle, mcpFields));
+			mcpSession = new McpDialogSession(dialogTitle, mcpFields); // By Claude on 07/07/2026: keep own reference (see field comment)
+			boolean applied = McpDialogRegistry.setCurrent(mcpSession);
 			if (!applied) {
 				System.out.println("MCP: dialog already active, ignoring \"" + dialogTitle + "\"");
 			}
@@ -218,7 +220,7 @@ public class GenericJTabbedDialogMcp extends GenericJTabbedDialog{
 	}
 
 	private String getValueOrDefault(McpDialogField field) {
-		McpDialogSession session = McpDialogRegistry.getCurrent();
+		McpDialogSession session = mcpSession; // By Claude on 07/07/2026: was McpDialogRegistry.getCurrent() - always null here (registry cleared on submit before the reads), so /mcp/dialog/values was silently discarded
 		if (session != null && field != null) {
 			String value = session.getValue(field.label);
 			if (value != null) {
@@ -299,7 +301,7 @@ public class GenericJTabbedDialogMcp extends GenericJTabbedDialog{
 	public boolean showDialog() {
 		if (mcp_mode) {
 			buildDialog();
-			McpDialogSession session = McpDialogRegistry.getCurrent();
+			McpDialogSession session = mcpSession; // By Claude on 07/07/2026: own session (registry may hold another dialog / be cleared by submit)
 			if (session != null) {
 				long timeout = dialogTimeoutMs;
 				Boolean ok = (timeout <= 0) ? session.awaitSubmit(Long.MAX_VALUE) : session.awaitSubmit(timeout);
@@ -309,7 +311,9 @@ public class GenericJTabbedDialogMcp extends GenericJTabbedDialog{
 					mcpCanceled = false;
 				}
 			}
-			McpDialogRegistry.setCurrent(null);
+			if (McpDialogRegistry.getCurrent() == mcpSession) { // By Claude on 07/07/2026: clear only OUR session (submit normally cleared it; this covers the timeout path without clobbering a newer dialog)
+				McpDialogRegistry.setCurrent(null);
+			}
 			return true;
 		}
 		else return super.showDialog();

src/main/java/com/elphel/imagej/cuas/Cuas.java

@@ -692,9 +692,80 @@ public class Cuas {
     	return center_CLT;
     }
 
-    
-    
-    
+    /**
+     * Rebuild the center IMAGE from the current in-memory scene image data (e.g. after
+     * subtracting a just-computed FPN) WITHOUT persisting or mutating anything: no
+     * .cuas / -CLT / DSI / IMS files are written and center_CLT.center_clt /
+     * center_CLT.image_center are left untouched. Always a NEW average - no parent
+     * cumulative is folded in (unlike stepCenterClt() which seeds from the current
+     * center and would keep its content residual). Used by the FPN second
+     * back-propagation iteration in CorrectionFPN.cuasSubtractFpn(), where the rebuilt
+     * center is only a temporary measurement reference.
+     * By Claude on 07/06/2026
+     * @param clt_parameters processing parameters
+     * @param quadCLTs scenes to accumulate; pass a slice covering an integer number of
+     *        camera rotations so azimuth sectors are equally weighted
+     * @param center_CLT existing center (geometry/poses reference), must have center CLT
+     * @param disparity_center center-grid disparity (from backPrepareCenter()/getDisparityCenter())
+     * @param sensor_mask -1 - all
+     * @param debugLevel debug level
+     * @return image-domain center as convertCenterClt() returns, or null on failure
+     */
+    public static double [][] rebuildCenterImageInMemory( // By Claude on 07/06/2026
+    		CLTParameters  clt_parameters,
+    		QuadCLT []     quadCLTs,
+    		QuadCLT        center_CLT,
+    		double []      disparity_center,
+    		int            sensor_mask, // -1 - all;
+    		int            debugLevel) {
+    	if (!center_CLT.hasCenterClt()) {
+    		System.out.println("rebuildCenterImageInMemory(): center_CLT does not have .center_clt data, bailing out");
+    		return null;
+    	}
+    	double  cuas_clt_variant =   clt_parameters.imp.cuas_clt_variant;   // 10;
+    	double  cuas_clt_threshold = clt_parameters.imp.cuas_clt_threshold; // 20;
+    	double  cuas_decay_average = clt_parameters.imp.cuas_decay_average; // 100;
+    	double  cuas_keep_fraction = clt_parameters.imp.cuas_keep_fraction; // 0.9;
+    	double  cuas_clt_decrease =  clt_parameters.imp.cuas_clt_decrease;  // 0.01;
+    	double  dts =                center_CLT.getTimeStamp();
+    	CuasData newCuasData = getTDComboSceneSequence(
+    			clt_parameters,      // CLTParameters  clt_parameters,
+    			null,                // double [][]    ref_pXpYD,
+    			true,                // boolean        save_weights,
+    			sensor_mask,         // int            sensor_mask,
+    			null,                // Rectangle      fov_tiles,
+    			OpticalFlow.ZERO3,   // double []      stereo_xyz, // offset reference camera {x,y,z}
+    			OpticalFlow.ZERO3,   // double []      stereo_atr_in, // center already exists - zero ATR
+    			disparity_center,    // double []      ref_disparity,
+    			quadCLTs,            // QuadCLT []     quadCLTs,
+    			center_CLT,          // QuadCLT        refCLT,
+    			null,                // CuasData       cuasData - no parent cumulative: new average only
+    			true,                // final boolean  clt_create, // create new variants
+    			cuas_clt_variant,    // final double   clt_threshold,
+    			cuas_decay_average,  // final double   clt_decay,
+    			cuas_clt_decrease,   // final double   clt_decrease,
+    			debugLevel);         // int            debugLevel)
+    	if (newCuasData == null) {
+    		System.out.println("rebuildCenterImageInMemory(): getTDComboSceneSequence() failed");
+    		return null;
+    	}
+    	if (cuas_keep_fraction < 1.0) { // same filtering as createCenterClt() applies before collapse
+    		newCuasData = filter(
+    				newCuasData,        // final CuasData   cuasData,
+    				cuas_decay_average, // final double     cuas_decay,    // seconds e times
+    				cuas_keep_fraction, // final double     keep_fraction,
+    				debugLevel);        // final int        debugLevel)
+    	}
+    	float [] fclt = newCuasData.collapse(
+    			cuas_clt_threshold, // final double tolerance, // NaN works as infinity
+    			cuas_decay_average, // final double decay,
+    			dts)[0];            // final double ts_now)
+    	return center_CLT.convertCenterClt(new float [][] {fclt}); // does NOT touch center_CLT state
+    }
+
+
+
+
     public static void fillNanDsi(
 			double [][] ref_pXpYD,
 			double [][] dsi,

src/main/java/com/elphel/imagej/cuas/CuasQC.java

+/**
+ **
+ ** CuasQC.java - per-product quality metrics with pass bands (regression protection)
+ **
+ ** Copyright (C) 2026 Elphel, Inc.
+ **
+ ** -----------------------------------------------------------------------------**
+ **
+ **  CuasQC.java is free software: you can redistribute it and/or modify
+ **  it under the terms of the GNU General Public License as published by
+ **  the Free Software Foundation, either version 3 of the License, or
+ **  (at your option) any later version.
+ **
+ **  This program is distributed in the hope that it will be useful,
+ **  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ **  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ **  GNU General Public License for more details.
+ **
+ **  You should have received a copy of the GNU General Public License
+ **  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ ** -----------------------------------------------------------------------------**
+ **
+ */
+package com.elphel.imagej.cuas;
+
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Date;
+import java.util.LinkedHashMap;
+
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
+
+/**
+ * Quality-metrics harness (Andrey's design 07/07/2026, after the v013-ROWCOL-01 junk):
+ * once a pipeline step is "done and verified", detect regressions by per-product HEALTH
+ * STATISTICS with pass bands - NOT bit comparison (a photometric recalibration shifts
+ * values a little; these invariants survive it and transfer across image sequences).
+ * Bands are sequence-independent (defined here in code, in physical/calibrated units for
+ * this LWIR16 hardware class); per-sequence VALUES land in <center>-QC.json next to the
+ * products (append-per-run, with timestamps), so any run answers "was it healthy" and
+ * trends are visible. A FAIL prints loudly but never aborts the run.
+ *
+ * Increment 1 (07/07/2026): ROWCOL vectors + FPN. The ROWCOL bands would have caught both
+ * of today's defects (baseline-mix rms 83, edge-column p95 ~1000 vs legacy 8.5/338).
+ * By Claude on 07/07/2026, from Andrey's design.
+ */
+public class CuasQC {
+	public static final int    QC_VERSION = 1;
+	public static final String SUFFIX = "-QC.json";
+	private static final Gson  GSON = new GsonBuilder().setPrettyPrinting().create();
+
+	// --- pass bands (sequence-independent, LWIR16 class; reference measurements in comments) ---
+	public static final double ROWCOL_MAX_RMS =        25.0;  // legacy method 8.5; broken baseline-mix 83; broken edges 53
+	public static final double ROWCOL_MAX_SCENE_P95 = 500.0;  // p95 of per-scene max |vector|; legacy 338 (own x=2 edge artifact included)
+	public static final double FPN_MAX_RMS =          150.0;  // measured 40.5 (2026-07-07 vintage, rot 164.9)
+	public static final double FPN_MAX_LINE_ROW =      25.0;  // FPN line-structure rms, per-row means; measured 6.4
+	public static final double FPN_MAX_LINE_COL =      25.0;  // per-col means; measured 12.3
+
+	public static class Check {
+		public String  name;
+		public double  value;
+		public double  max;
+		public boolean pass;
+		public Check(String name, double value, double max) {
+			this.name = name; this.value = value; this.max = max; this.pass = (value <= max);
+		}
+	}
+	public static class Entry {
+		public String                        saved;      // timestamp of this QC evaluation
+		public String                        product;    // "ROWCOL", "FPN", ...
+		public boolean                       calculated; // true - just calculated this run; false - reused from file
+		public boolean                       pass;
+		public LinkedHashMap<String, Double> metrics;
+		public ArrayList<Check>              checks;
+	}
+	public static class QcFile {
+		public int              qc_version = QC_VERSION;
+		public ArrayList<Entry> entries = new ArrayList<Entry>();
+	}
+
+	/** ROWCOL health: vector magnitudes must stay at the line-noise scale.
+	 *  @param row_col {rows[scene][sensor][width], cols[scene][sensor][height]} */
+	public static boolean checkRowCol(
+			String          x3d_directory,
+			String          center_name,
+			double [][][][] row_col,
+			boolean         calculated) {
+		double sum2 = 0.0; long n = 0;
+		final int num_scenes = row_col[0].length;
+		final double [] scene_max = new double [num_scenes];
+		for (int f = 0; f < row_col.length; f++) {
+			for (int nscene = 0; nscene < num_scenes; nscene++) if (row_col[f][nscene] != null) {
+				for (double [] vec : row_col[f][nscene]) if (vec != null) {
+					for (double v : vec) if (!Double.isNaN(v)) {
+						sum2 += v*v; n++;
+						final double a = Math.abs(v);
+						if (a > scene_max[nscene]) scene_max[nscene] = a;
+					}
+				}
+			}
+		}
+		final double rms = Math.sqrt(sum2/Math.max(n,1));
+		final LinkedHashMap<String,Double> metrics = new LinkedHashMap<String,Double>();
+		metrics.put("rms",            rms);
+		metrics.put("scene_max_med",  percentile(scene_max, 50));
+		metrics.put("scene_max_p95",  percentile(scene_max, 95));
+		metrics.put("scene_max_max",  percentile(scene_max, 100));
+		final ArrayList<Check> checks = new ArrayList<Check>();
+		checks.add(new Check("rms",           rms,                          ROWCOL_MAX_RMS));
+		checks.add(new Check("scene_max_p95", metrics.get("scene_max_p95"), ROWCOL_MAX_SCENE_P95));
+		return report(x3d_directory, center_name, "ROWCOL", calculated, metrics, checks);
+	}
+
+	/** FPN health: overall scale + row/col line-structure energy (per-sensor line means
+	 *  after removing each sensor's global mean, rms pooled over sensors). */
+	public static boolean checkFpn(
+			String        x3d_directory,
+			String        center_name,
+			double [][][] fpn,
+			int           width,
+			boolean       calculated) {
+		double sum2 = 0.0; long n = 0;
+		double line_row2 = 0.0, line_col2 = 0.0; long nrow = 0, ncol = 0;
+		for (int nsens = 0; nsens < fpn.length; nsens++) if ((fpn[nsens] != null) && (fpn[nsens][0] != null)) {
+			final double [] px = fpn[nsens][0];
+			final int height = px.length/width;
+			double mean = 0.0; long nm = 0;
+			for (double v : px) if (!Double.isNaN(v)) { mean += v; nm++; }
+			mean /= Math.max(nm,1);
+			final double [] rowm = new double [height];
+			final double [] coln = new double [width];
+			final double [] rown = new double [height];
+			final double [] colm = new double [width];
+			int idx = 0;
+			for (int y = 0; y < height; y++) for (int x = 0; x < width; x++) {
+				final double v = px[idx++];
+				if (Double.isNaN(v)) continue;
+				final double d = v - mean;
+				sum2 += d*d; n++;
+				rowm[y] += d; rown[y]++;
+				colm[x] += d; coln[x]++;
+			}
+			for (int y = 0; y < height; y++) if (rown[y] > 0) { final double d = rowm[y]/rown[y]; line_row2 += d*d; nrow++; }
+			for (int x = 0; x < width;  x++) if (coln[x] > 0) { final double d = colm[x]/coln[x]; line_col2 += d*d; ncol++; }
+		}
+		final LinkedHashMap<String,Double> metrics = new LinkedHashMap<String,Double>();
+		metrics.put("rms",      Math.sqrt(sum2/Math.max(n,1)));
+		metrics.put("line_row", Math.sqrt(line_row2/Math.max(nrow,1)));
+		metrics.put("line_col", Math.sqrt(line_col2/Math.max(ncol,1)));
+		final ArrayList<Check> checks = new ArrayList<Check>();
+		checks.add(new Check("rms",      metrics.get("rms"),      FPN_MAX_RMS));
+		checks.add(new Check("line_row", metrics.get("line_row"), FPN_MAX_LINE_ROW));
+		checks.add(new Check("line_col", metrics.get("line_col"), FPN_MAX_LINE_COL));
+		return report(x3d_directory, center_name, "FPN", calculated, metrics, checks);
+	}
+
+	private static double percentile(double [] a, double pct) {
+		final double [] s = a.clone();
+		Arrays.sort(s);
+		final int k = (int) Math.min(s.length-1, Math.round(0.01*pct*(s.length-1)));
+		return s[k];
+	}
+
+	/** Print the QC block, append the entry to <center>-QC.json, return overall pass. */
+	private static boolean report(
+			String x3d_directory, String center_name, String product, boolean calculated,
+			LinkedHashMap<String,Double> metrics, ArrayList<Check> checks) {
+		final Entry entry = new Entry();
+		entry.saved =      new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(new Date());
+		entry.product =    product;
+		entry.calculated = calculated;
+		entry.metrics =    metrics;
+		entry.checks =     checks;
+		entry.pass = true;
+		for (Check c : checks) entry.pass &= c.pass;
+		final StringBuilder sb = new StringBuilder();
+		sb.append("QC: ").append(product).append(calculated ? " (calculated)" : " (reused)")
+		  .append(entry.pass ? " PASS" : " *** FAIL ***");
+		for (Check c : checks) if (!c.pass) {
+			sb.append(String.format(" [%s=%.2f > %.2f]", c.name, c.value, c.max));
+		}
+		sb.append(" metrics: ");
+		for (java.util.Map.Entry<String,Double> m : metrics.entrySet()) {
+			sb.append(String.format("%s=%.2f ", m.getKey(), m.getValue()));
+		}
+		System.out.println(sb.toString());
+		if (!entry.pass) {
+			System.out.println("QC: *** "+product+" is OUT OF ITS HEALTH BANDS - the product is suspect, "+
+					"inspect before trusting this run (bands in CuasQC.java) ***");
+		}
+		try {
+			final String path = x3d_directory + java.io.File.separator + center_name + SUFFIX;
+			QcFile qc = null;
+			if (Files.exists(Paths.get(path))) {
+				try (FileReader fr = new FileReader(path)) {
+					qc = GSON.fromJson(fr, QcFile.class);
+				} catch (Exception e) {
+					System.out.println("QC: could not parse existing "+path+" ("+e.getMessage()+") - starting a new file");
+				}
+			}
+			if ((qc == null) || (qc.entries == null)) qc = new QcFile();
+			qc.entries.add(entry);
+			try (FileWriter fw = new FileWriter(path)) {
+				GSON.toJson(qc, fw);
+			}
+		} catch (IOException e) {
+			System.out.println("QC: failed to save QC json: "+e.getMessage());
+		}
+		return entry.pass;
+	}
+}

src/main/java/com/elphel/imagej/cuas/CuasRanging.java

@@ -75,6 +75,7 @@ public class CuasRanging {
 	}
 	
 	public ImagePlus prepareFpixels(){
+		boolean dbg_save_fpixels = clt_parameters.curt.dbg_fpixels; // was hardcoded true: gates the EXTRA per-sensor -CUAS-INDIVIDUAL-CUAS-DBG render pass (~11GB) + the -CUAS-MERGED-CUAS-DBG save; -CUAS-RT-RENDER (rend_test) is the RT-chain full render // By Claude on 07/05/2026
 		double [][]combo_dsi = getCenter_CLT().comboFromMain();
     	double [][] dls = { 
     			combo_dsi[OpticalFlow.COMBO_DSN_INDX_DISP], // **** null on second scene sequence
@@ -135,6 +136,52 @@ public class CuasRanging {
 		double [] cuas_atr = OpticalFlow.ZERO3;
 
 		String scenes_suffix = getCenter_CLT().getImageName()+"-CUAS"; // "1747829900_781803-SEQ-FG-MONO-FPN";
+    	boolean merge_all = false; // clt_parameters.imp.merge_all || !um_mono; // no unsharp mask -> terrain->merge_all
+    	int     sensor_mask = merge_all? 1 : -1;
+    	if (dbg_save_fpixels) {
+    		// By Claude on 07/02/2026: per-sensor averages can only be calculated from slices (the precalculated CLT center
+    		// average is merged-channels only), so add_average implies calculating here. Number of average frames is
+    		// variable: 0, 1 (full) or 2 (full + center fraction), matching the merged sequence convention.
+    		boolean dbg_add_average = clt_parameters.imp.add_average || clt_parameters.imp.calculate_average; // By Claude on 07/02/2026
+    		int []  dbg_average_range = (clt_parameters.imp.add_center_average && dbg_add_average)? new int[2] : null; // By Claude on 07/02/2026
+    		if (dbg_average_range != null) { // By Claude on 07/02/2026: same as in renderSceneSequence() wrapper
+    			int num_scenes = scenes.length;
+    			dbg_average_range[0] = (int) Math.round (num_scenes * (1 - clt_parameters.imp.center_avg_frac)/2);
+    			dbg_average_range[0] = Math.max(0, dbg_average_range[0]);
+    			dbg_average_range[0] = Math.min(num_scenes-1, dbg_average_range[0]);
+    			dbg_average_range[1] = num_scenes-1 - dbg_average_range[0];
+    			dbg_average_range[1] = Math.max(dbg_average_range[0], dbg_average_range[1]);
+    			dbg_average_range[1] = Math.min(num_scenes-1, dbg_average_range[1]);
+    		}
+    		ImagePlus imp_targets= OpticalFlow.renderSceneSequence(
+    				clt_parameters,     // CLTParameters clt_parameters,
+    				true,  // center_CLT.hasCenterClt(), // boolean        mode_cuas,
+    				false, // clt_parameters.imp.um_mono, // boolean        um_mono,
+    				dbg_add_average,      // boolean        insert_average, // By Claude on 07/02/2026: was clt_parameters.imp.calculate_average
+    				dbg_average_range,    // int []         average_range, // By Claude on 07/02/2026: was null
+    				null, // average_channels,     //  average_slice,
+    				clt_parameters.imp.subtract_average, // boolean    subtract_average,
+    				clt_parameters.imp.running_average,  // int            running_average,
+    				null, // fov_tiles,   // Rectangle     fov_tiles,
+    				1, // mode3d,         // int           mode3d,
+    				false, // toRGB,      // boolean       toRGB,
+    				xyz_offset,           // double []     stereo_offset, // offset reference camera {x,y,z}
+    				cuas_atr,             // double []      stereo_atr, // offset reference orientation (cuas)
+    				sensor_mask,          // sensor_mask,    // int           sensor_mask,
+    				merge_all,            // boolean       merge_all,
+    				2,                    // int           make_hyper, // By Claude on 07/02/2026: hyperstack, per-timestamp sensor average as first channel
+    				scenes_suffix,        // String        suffix,
+    				ds_vantage[0],        // selected_disparity, // double []     ref_disparity,			
+    				scenes,               // QuadCLT []    quadCLTs,
+    				getCenter_CLT(),           // ref_index,          // int           ref_index,
+    				ImageDtt.THREADS_MAX, // threadsMax,         // int           threadsMax,
+    				debugLevel);          // int           debugLevel);
+    		getCenter_CLT().saveImagePlusInModelDirectory(
+    				imp_targets.getTitle()+"-DBG", // "GPU-SHIFTED-D"+clt_parameters.disparity, // String      suffix,
+    				imp_targets); // imp_scenes); // ImagePlus   imp)
+    	}
+    	merge_all =   true; // clt_parameters.imp.merge_all || !um_mono; // no unsharp mask -> terrain->merge_all
+    	sensor_mask = merge_all? 1 : -1;
 		ImagePlus imp_targets= OpticalFlow.renderSceneSequence(
 				clt_parameters,     // CLTParameters clt_parameters,
 				true,  // center_CLT.hasCenterClt(), // boolean        mode_cuas,
@@ -149,13 +196,20 @@ public class CuasRanging {
 				false, // toRGB,      // boolean       toRGB,
 				xyz_offset,           // double []     stereo_offset, // offset reference camera {x,y,z}
 				cuas_atr,             // double []      stereo_atr, // offset reference orientation (cuas)
-				1, // sensor_mask,    // int           sensor_mask,
+				sensor_mask,          // sensor_mask,    // int           sensor_mask,
+				merge_all,            // boolean       merge_all,
+				0,                    // int           make_hyper, // By Claude on 07/02/2026: flat stack - keep old behavior
 				scenes_suffix,        // String        suffix,
 				ds_vantage[0],        // selected_disparity, // double []     ref_disparity,			
 				scenes,               // QuadCLT []    quadCLTs,
 				getCenter_CLT(),           // ref_index,          // int           ref_index,
 				ImageDtt.THREADS_MAX, // threadsMax,         // int           threadsMax,
 				debugLevel);          // int           debugLevel);
+		if (dbg_save_fpixels) {
+        	getCenter_CLT().saveImagePlusInModelDirectory(
+        			imp_targets.getTitle()+"-DBG", // "GPU-SHIFTED-D"+clt_parameters.disparity, // String      suffix,
+                    imp_targets); // imp_scenes); // ImagePlus   imp)
+		}
         return imp_targets;
 	}
 	
@@ -2880,8 +2934,66 @@ public class CuasRanging {
 			getCenter_CLT().saveStringInModelDirectory(tsv.toString(), UAS_DATA_SUFFIX, false);
 		}
 	}
-	
-	// relies on calcMatchingTargetsLengths(.., true,...) called from recalcOmegas() to set [RSLT_GLOBAL] 
+
+	/** Standalone UAS flight-log extraction for the mode-0 RT path (NO CuasMotion / targets array): project the
+	 *  DJI flight log to per-scene px,py,range using center_CLT pose + uasLogReader, accumulate a TSV (same columns
+	 *  + UAS_DATA_SUFFIX as addUasData), save via the QuadCLT model dir. Timestamps = imp_targets slice labels
+	 *  (skip leading non-digit "average" slices, == CuasDetectRT.ingest). Needs QuadCLT pose, so mode-0 only (not
+	 *  the mode=3 file path). By Claude on 06/24/2026 */
+	public void saveUasFlightLogCsv(UasLogReader uasLogReader, ImagePlus imp_targets) {
+		if (uasLogReader == null) {
+			System.out.println("saveUasFlightLogCsv(): no UAS log reader - skipping flight-log CSV");
+			return;
+		}
+		if ((imp_targets == null) || (imp_targets.getStackSize() < 1)) {
+			System.out.println("saveUasFlightLogCsv(): no imp_targets - skipping flight-log CSV");
+			return;
+		}
+		// camera reference LLA from center_CLT (mirror addUasData)
+		if ((getCenter_CLT() != null) && getCenter_CLT().hasIns()) {
+			double [] cameraLla = getCenter_CLT().getLla();
+			if ((cameraLla != null) && ((cameraLla[0] != 0.0) || (cameraLla[1] != 0.0))) {
+				uasLogReader.setCameraLLA(cameraLla);
+			}
+		}
+		double [] cam_atr = uasLogReader.getCameraATR();
+		int tilesX = getCenter_CLT().getTileProcessor().getTilesX();
+		int tilesY = getCenter_CLT().getTileProcessor().getTilesY();
+		ij.ImageStack stack = imp_targets.getStack();
+		int num_slices = stack.getSize();
+		int first_slice = 1;
+		for (; (first_slice <= num_slices) && !Character.isDigit(stack.getSliceLabel(first_slice).charAt(0)); first_slice++);
+		StringBuffer sb = new StringBuffer();
+		sb.append("seq\tts\tstatus\tpx\tpy\ttile_x\ttile_y\trange\tlat\tlon\talt\tnorth\teast\tdown\tcam_az\tcam_tilt\tcam_roll\n");
+		int nseq = 0;
+		for (int slice = first_slice; slice <= num_slices; slice++, nseq++) {
+			// slice labels can carry a suffix (e.g. "1773135457.547099-0"); extract the bare timestamp the
+			// same way as QuadCLT.getTimeStamp (regex \d{5,10}\.\d{6}), but keep it a STRING - the double
+			// round-trip would lose microsecond precision at this magnitude. By Claude on 06/24/2026
+			String norm = stack.getSliceLabel(slice).replace("_", ".");
+			java.util.regex.Matcher tm = java.util.regex.Pattern.compile("\\d{5,10}\\.\\d{6}").matcher(norm);
+			String timestamp = tm.find() ? norm.substring(tm.start(), tm.end()) : norm;
+			double [] uas =    uasLogReader.getUasPxPyDRange(timestamp); // px, py, disparity, range
+			double [] llaned = uasLogReader.getUasLlaNed(timestamp);     // lat, lon, alt, N, E, D
+			if (uas != null) {
+				double px = uas[0], py = uas[1], range = uas[3];
+				int tileX = (int) (px / GPUTileProcessor.DTT_SIZE);
+				int tileY = (int) (py / GPUTileProcessor.DTT_SIZE);
+				String status = ((tileX >= 0) && (tileY >= 0) && (tileX < tilesX) && (tileY < tilesY)) ? "IN FoV" : "OUT OF FoV";
+				sb.append(nseq+"\t"+timestamp+"\t"+status+"\t"+px+"\t"+py+"\t"+tileX+"\t"+tileY+"\t"+range+"\t"+
+						llaned[0]+"\t"+llaned[1]+"\t"+llaned[2]+"\t"+llaned[3]+"\t"+llaned[4]+"\t"+llaned[5]+"\t"+
+						cam_atr[0]+"\t"+cam_atr[1]+"\t"+cam_atr[2]+"\n");
+			} else {
+				sb.append(nseq+"\t"+timestamp+"\tno entry\t\t\t\t\t\t"+
+						((llaned != null) ? (llaned[0]+"\t"+llaned[1]+"\t"+llaned[2]) : "\t\t")+
+						"\t\t\t\t"+cam_atr[0]+"\t"+cam_atr[1]+"\t"+cam_atr[2]+"\n");
+			}
+		}
+		getCenter_CLT().saveStringInModelDirectory(sb.toString(), UAS_DATA_SUFFIX, false);
+		System.out.println("saveUasFlightLogCsv(): wrote UAS flight log ("+nseq+" scenes) -> "+getCenter_CLT().getImageName()+UAS_DATA_SUFFIX);
+	}
+
+	// relies on calcMatchingTargetsLengths(.., true,...) called from recalcOmegas() to set [RSLT_GLOBAL]
 	public void saveTargetStats(
 			final double [][][] targets_single) {
 		UasLogReader  uasLogReader = cuasMotion.getUasLogReader();

src/main/java/com/elphel/imagej/cuas/rt/CuasDnnBackend.java

+package com.elphel.imagej.cuas.rt;
+
+import java.awt.Rectangle;
+
+/**
+ * DNN inference backend for the CUAS L1+L2 pipeline. Implemented by {@link CuasDnnRemote} (TCP to the
+ * Python infer_server, e.g. on the DGX) and {@link CuasDnnLocal} (in-process native LibTorch via JNA /
+ * libtpdnn.so). CuasDetectRT.runDnnRemote() talks to this interface so the two are drop-in swappable;
+ * the result type {@link CuasDnnRemote.BatchResult} is shared. By Claude on 06/27/2026.
+ */
+public interface CuasDnnBackend extends AutoCloseable {
+	/** Upload the conditioned stack frames[T][H*W] (row-major) once; the backend builds the temporal
+	 *  pyramid. Returns the per-level frame counts (and sets {@link #getNFrames()}). */
+	int [] upload(float [][] frames, int H, int W) throws Exception;
+
+	/** Temporal depth N of the loaded model (window length), known after {@link #upload}. */
+	int getNFrames();
+
+	/** Infer `count` scenes of a level in one call (newest_s = start + s*stride). rmaxCells>0 enables the
+	 *  on-GPU ghostbuster. l2Enable/l2Reset drive Layer-2; noiseScale is the per-level L1-input scale. */
+	CuasDnnRemote.BatchResult inferBatch(int level, int start, int count, int stride, Rectangle roi,
+			double rmaxCells, boolean l2Enable, boolean l2Reset, double noiseScale) throws Exception;
+
+	@Override
+	void close();
+}

src/main/java/com/elphel/imagej/cuas/rt/CuasDnnInfer.java

@@ -38,6 +38,9 @@ public class CuasDnnInfer implements AutoCloseable {
         String local = resolveModel(modelSpec);
         this.env = OrtEnvironment.getEnvironment();
         OrtSession.SessionOptions opts = new OrtSession.SessionOptions();
+        // Only log errors (not warnings): suppresses the benign dynamic-batch VerifyOutputSizes W-spam
+        // (reg head's cat pins the graph's declared batch to 1) that was yellow-on-white in Eclipse. By Claude on 06/17/2026
+        try { opts.setSessionLogLevel(ai.onnxruntime.OrtLoggingLevel.ORT_LOGGING_LEVEL_ERROR); } catch (Exception e) {}
         // CPU EP by default. GPU later: opts.addCUDA(deviceId) once cuDNN 9 is present.
         this.session = env.createSession(local, opts);
         this.inputName = session.getInputNames().iterator().next();  // "frames"
@@ -154,8 +157,12 @@ public class CuasDnnInfer implements AutoCloseable {
     }
 
     /** Continuous-velocity (reg) inference over an ROI. For each pixel returns
-     *  {S, Vx, Vy, sigma, dx, dy} from the 6-ch reg head (det, Vx, Vy, logvar, dx, dy):
-     *  S=sigmoid(det), Vx/Vy already bounded by the model, sigma=exp(logvar/2). By Claude on 06/17/2026 */
+     *  {S, Vx, Vy, sigma, dx, dy} from the 6-ch reg head (det/S, Vx, Vy, logvar, dx, dy):
+     *  Vx/Vy already bounded by the model, sigma=exp(logvar/2).
+     *  MF-S models (option a, Andrey 2026-06-18): channel 0 is the RAW matched-filter path-sum S
+     *  (clamp>=0), NOT a det logit -> read raw, no sigmoid (sigmoid would re-saturate the unbounded
+     *  response). S is then the informative vote weight directly (CuasDetectRT.voteScatter). By Claude on 06/18/2026
+     *  DEPRECATED 2026-06-20 — may be revisited for Layer 2 // By Claude */
     public double[][] inferROIReg(float[][] frames, int width, int height, Rectangle roi) throws Exception {
         final int N = frames.length;
         final int P = patch, half = P / 2;
@@ -187,7 +194,7 @@ public class CuasDnnInfer implements AutoCloseable {
                 for (int q = 0; q < bs; q++) {
                     float[][][] op = out[q];
                     double[] o = out6[base + q];
-                    o[0] = sigmoid(op[0][0][0]);                 // S
+                    o[0] = Math.max(0.0, op[0][0][0]);           // S = raw MF path-sum (clamp>=0); MF-S model, no sigmoid. By Claude on 06/18/2026
                     o[1] = op[1][0][0]; o[2] = op[2][0][0];      // Vx, Vy (model-bounded)
                     o[3] = Math.exp(0.5 * op[3][0][0]);          // sigma = exp(logvar/2)
                     o[4] = op[4][0][0]; o[5] = op[5][0][0];      // dx, dy

src/main/java/com/elphel/imagej/cuas/rt/CuasDnnLocal.java

+package com.elphel.imagej.cuas.rt;
+
+import java.awt.Rectangle;
+import java.io.File;
+import java.io.InputStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.StandardCopyOption;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import com.sun.jna.Native;
+import com.sun.jna.Pointer;
+
+/**
+ * In-process native DNN backend: runs the SAME L1+L2 inference as {@link CuasDnnRemote}, but via
+ * LibTorch through JNA (libtpdnn.so, tile_processor_gpu/jna/tp_dnn.cpp) instead of TCP to a Python
+ * server. No DGX / no server process. Each model's params (N/P/vr/out_ch, L2 ch_hidden) come from its
+ * bundled {@code <model>.ts.pt.meta.json} sidecar (single source of truth). By Claude on 06/27/2026.
+ *
+ * Model resolution mirrors CuasDnnRemote's bundled-vs-override convention:
+ *   - localDir set  -> &lt;localDir&gt;/&lt;model&gt;/model.ts.pt (+ .meta.json)   [dev/override]
+ *   - localDir empty -> bundled jar resource /cuas_dnn/&lt;basename&gt;/model.ts.pt extracted to temp
+ *
+ * Requires {@code -Djna.library.path=<dir with libtpdnn.so>}; libtpdnn.so finds libtorch via its rpath
+ * (set by build_dnn.sh) or LD_LIBRARY_PATH.
+ */
+public class CuasDnnLocal implements CuasDnnBackend {
+	private static TpDnnJna LIB = null;
+	private static synchronized TpDnnJna lib() {
+		if (LIB == null) LIB = Native.load("tpdnn", TpDnnJna.class);
+		return LIB;
+	}
+
+	private final TpDnnJna   lib;
+	private final Pointer    ctx;
+	private final int        N, P, vr, nvel;
+	private int              nFrames = 0;
+	private int              H = 0, W = 0;
+	private File             tmpDir = null;     // holds extracted bundled models (deleted on close)
+
+	/** @param localDir  override dir holding &lt;model&gt;/model.ts.pt, or empty/null to use bundled resources.
+	 *  @param l1Model   L1 run name (e.g. "runs/weighted9_pm_s").
+	 *  @param l2Model   L2 run name (e.g. "runs/mexhat_gaps_boost40"), or empty/null for L1-only. */
+	public CuasDnnLocal(String localDir, String l1Model, String l2Model) throws Exception {
+		this.lib = lib();
+		String [] l1 = resolveModel(localDir, l1Model, ".ts.pt");      // {tsPath, metaJson}
+		this.N  = metaInt(l1[1], "N", 9);
+		this.P  = metaInt(l1[1], "P", 24);
+		this.vr = metaInt(l1[1], "vr", 5);
+		this.nvel = (2 * vr + 1) * (2 * vr + 1);
+		String l2ts = "";
+		int l2ch = 24;
+		if ((l2Model != null) && !l2Model.isEmpty()) {
+			String [] l2 = resolveModel(localDir, l2Model, ".l2.ts.pt");
+			l2ts = l2[0];
+			l2ch = metaInt(l2[1], "ch_hidden", 24);
+		}
+		this.ctx = lib.tpdnn_init(l1[0], l2ts, N, P, vr, l2ch);
+		if (ctx == null) throw new Exception("tpdnn_init failed (l1=" + l1[0] + ", l2=" + l2ts + ")");
+		System.out.println("CuasDnnLocal: native LibTorch backend up (L1=" + l1Model
+				+ ", L2=" + ((l2Model == null || l2Model.isEmpty()) ? "off" : l2Model)
+				+ "; N=" + N + " P=" + P + " vr=" + vr + " l2_ch=" + l2ch + ")");
+	}
+
+	@Override
+	public int [] upload(float [][] frames, int H, int W) throws Exception {
+		this.H = H; this.W = W;
+		int T = frames.length, hw = H * W;
+		float [] flat = new float [T * hw];                            // [T,H,W] row-major
+		for (int t = 0; t < T; t++) System.arraycopy(frames[t], 0, flat, t * hw, hw);
+		lib.tpdnn_upload(ctx, flat, T, H, W);
+		this.nFrames = N;
+		int nl = lib.tpdnn_num_levels(ctx);
+		int [] counts = new int [nl];
+		for (int i = 0; i < nl; i++) counts[i] = lib.tpdnn_level_frames(ctx, i);
+		return counts;
+	}
+
+	@Override
+	public int getNFrames() { return nFrames; }
+
+	@Override
+	public CuasDnnRemote.BatchResult inferBatch(int level, int start, int count, int stride, Rectangle roi,
+			double rmaxCells, boolean l2Enable, boolean l2Reset, double noiseScale) throws Exception {
+		int hw = H * W, rn = roi.width * roi.height;
+		int nchAlloc = l2Enable ? 6 : 5;                              // native returns 6 with L2 (+age), else 5
+		float [] o5  = new float [count * nchAlloc * hw];
+		float [] rfb = new float [count * rn * nvel];
+		long t0 = System.nanoTime();
+		int nch = lib.tpdnn_infer(ctx, level, start, count, stride,
+				roi.x, roi.y, roi.width, roi.height, rmaxCells,
+				l2Enable ? 1 : 0, l2Reset ? 1 : 0, noiseScale, o5, rfb);
+		double ms = (System.nanoTime() - t0) / 1.0e6;
+
+		CuasDnnRemote.BatchResult r = new CuasDnnRemote.BatchResult();
+		r.gpuMs = ms; r.H = H; r.W = W; r.count = count; r.nch = nch; r.nvel = nvel;
+		r.rh = roi.height; r.rw = roi.width;
+		r.offset5 = new float [count][nch][hw];                       // o5 layout [count][nch][hw]
+		for (int s = 0; s < count; s++)
+			for (int c = 0; c < nch; c++)
+				System.arraycopy(o5, (s * nch + c) * hw, r.offset5[s][c], 0, hw);
+		r.roiField = new float [count][rn][nvel];                     // rfb layout [count][rn][nvel]
+		for (int s = 0; s < count; s++)
+			for (int p = 0; p < rn; p++)
+				System.arraycopy(rfb, (s * rn + p) * nvel, r.roiField[s][p], 0, nvel);
+		return r;
+	}
+
+	@Override
+	public void close() {
+		try { if (ctx != null) lib.tpdnn_free(ctx); } catch (Exception e) { /* ignore */ }
+		if (tmpDir != null) { try { deleteRec(tmpDir); } catch (Exception e) { /* ignore */ } }
+	}
+
+	// ---- model resolution + tiny meta parser ----
+
+	/** Returns {tsPath, metaJsonContent} for the model. localDir override, else bundled resource->temp. */
+	private String [] resolveModel(String localDir, String model, String suffix) throws Exception {
+		String fileName = "model" + suffix;                          // model.ts.pt / model.l2.ts.pt
+		if ((localDir != null) && !localDir.isEmpty()) {
+			File ts   = new File(new File(localDir, model), fileName);
+			File meta = new File(ts.getPath() + ".meta.json");
+			if (!ts.exists()) throw new Exception("local model not found: " + ts);
+			String mj = meta.exists() ? new String(Files.readAllBytes(meta.toPath())) : "";
+			return new String [] { ts.getPath(), mj };
+		}
+		// bundled: /cuas_dnn/<basename(model)>/model.ts.pt (+ .meta.json) -> extract to a temp dir
+		String base = model.substring(model.lastIndexOf('/') + 1);
+		if (tmpDir == null) tmpDir = Files.createTempDirectory("cuas_dnn_").toFile();
+		String res = "/cuas_dnn/" + base + "/" + fileName;
+		Path tsTmp = extractResource(res, base + suffix);
+		String mj = "";
+		try (InputStream is = CuasDnnLocal.class.getResourceAsStream(res + ".meta.json")) {
+			if (is != null) mj = new String(is.readAllBytes());
+		}
+		return new String [] { tsTmp.toString(), mj };
+	}
+
+	private Path extractResource(String res, String tmpName) throws Exception {
+		try (InputStream is = CuasDnnLocal.class.getResourceAsStream(res)) {
+			if (is == null) throw new Exception("bundled resource not found: " + res);
+			Path out = new File(tmpDir, tmpName).toPath();
+			Files.copy(is, out, StandardCopyOption.REPLACE_EXISTING);
+			return out;
+		}
+	}
+
+	private static int metaInt(String json, String key, int dflt) {
+		if (json == null) return dflt;
+		Matcher m = Pattern.compile("\"" + key + "\"\\s*:\\s*(-?\\d+)").matcher(json);
+		return m.find() ? Integer.parseInt(m.group(1)) : dflt;
+	}
+
+	private static void deleteRec(File f) {
+		File [] kids = f.listFiles();
+		if (kids != null) for (File k : kids) deleteRec(k);
+		f.delete();
+	}
+}

src/main/java/com/elphel/imagej/cuas/rt/CuasRtState.java

+/**
+ ** CuasRtState.java - per-sequence persistent state of the CUAS RT mode (JSON)
+ **
+ ** Copyright (C) 2026 Elphel, Inc.
+ **
+ ** -----------------------------------------------------------------------------**
+ **
+ **  CuasRtState.java is free software: you can redistribute it and/or modify
+ **  it under the terms of the GNU General Public License as published by
+ **  the Free Software Foundation, either version 3 of the License, or
+ **  (at your option) any later version.
+ **
+ **  This program is distributed in the hope that it will be useful,
+ **  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ **  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ **  GNU General Public License for more details.
+ **
+ **  You should have received a copy of the GNU General Public License
+ **  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ ** -----------------------------------------------------------------------------**
+ **
+ */
+package com.elphel.imagej.cuas.rt;
+
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.text.SimpleDateFormat;
+import java.util.Date;
+
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
+
+/**
+ * Persistent RT-ONLY state of ONE scene sequence: <center_name>-RT-STATE.json in the
+ * sequence's CENTER model directory (Andrey's ruling 07/05/2026). Scope split:
+ *  - GLOBAL (all sequences) parameters stay with quadCLT_main / corr-xml (saved from
+ *    the GUI, merged with the compare/combine tool);
+ *  - PER-SEQUENCE derived values (vintage-specific calibrations the RT run computes
+ *    and reuses) live HERE, in modern JSON - easy to read, easy to tell apart from
+ *    the legacy parameter files, easy to erase for a forced re-derive (the
+ *    missing-file rule: absent -> recompute+save, present -> reuse).
+ *
+ * The class is data-pure: it knows file paths, not QuadCLT - callers (CuasRT, the
+ * borrow boundary) pass the directory/name. Unknown JSON fields are ignored on load
+ * (forward compatibility); missing fields stay at their defaults (null = not yet
+ * derived). Add new RT persistent variables as public fields with a provenance
+ * string where useful.
+ *
+ * By Claude on 07/05/2026, from Andrey's design.
+ */
+public class CuasRtState {
+	public static final String SUFFIX = "-RT-STATE.json";
+	private static final Gson GSON = new GsonBuilder().setPrettyPrinting().serializeNulls().create();
+
+	public int    version = 1;
+	public String updated = null;           // timestamp of the last save (informational)
+
+	// ---- persistent RT variables (per scene sequence) ----
+	public Double dc_center = null;         // adopted borrowed-center DC level (counts); null = not yet derived
+	public String dc_center_source = null;  // provenance, e.g. "auto: sky-half median of the reference render"
+
+	/** @return the state file path for this sequence. */
+	public static String path(String x3d_directory, String center_name) {
+		return x3d_directory + java.io.File.separator + center_name + SUFFIX;
+	}
+
+	/**
+	 * Load the sequence state, or return a fresh (all-defaults) instance when the file
+	 * is missing or unreadable (unreadable prints a warning - never breaks the run).
+	 */
+	public static CuasRtState load(String x3d_directory, String center_name) {
+		final String path = path(x3d_directory, center_name);
+		if (!Files.exists(Paths.get(path))) {
+			return new CuasRtState();
+		}
+		try (FileReader reader = new FileReader(path)) {
+			CuasRtState state = GSON.fromJson(reader, CuasRtState.class);
+			return (state != null) ? state : new CuasRtState();
+		} catch (IOException | RuntimeException e) { // malformed JSON -> JsonSyntaxException
+			System.out.println("CuasRtState.load(): FAILED to read "+path+" ("+e.getMessage()+
+					") - starting with a fresh state (derived values will be recomputed)");
+			return new CuasRtState();
+		}
+	}
+
+	/** Save the sequence state (pretty JSON, stamped). @return true on success. */
+	public boolean save(String x3d_directory, String center_name) {
+		final String path = path(x3d_directory, center_name);
+		this.updated = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(new Date());
+		try (FileWriter writer = new FileWriter(path)) {
+			GSON.toJson(this, writer);
+			System.out.println("CuasRtState.save(): wrote "+path);
+			return true;
+		} catch (IOException e) {
+			System.out.println("CuasRtState.save(): FAILED to write "+path+" ("+e.getMessage()+")");
+			return false;
+		}
+	}
+}

src/main/java/com/elphel/imagej/orthomosaic/ComboMatch.java

@@ -897,6 +897,14 @@ public class ComboMatch {
 		
 		// for all modes - needed for create_overlaps || process_correlation || render_match || pattern_match
     	if (GPU_QUAD_AFFINE == null) {
+    		// Fail loud rather than NPE deep in JCuda: the orthomosaic GPU_QUAD_AFFINE (rectilinear) path is
+    		// not on the validated JNA surface yet (wider than CUAS: affine matching). Run orthomosaic on
+    		// JCuda. The CUAS rectilinear path IS ported (GpuQuad.createRectilinear). By Claude on 06/26/2026.
+    		if (GpuQuad.useJnaBackend()) {
+    			throw new UnsupportedOperationException(
+    					"ComboMatch GPU_QUAD_AFFINE (orthomosaic, rectilinear) is not yet ported to the JNA backend "+
+    					"(-Dtp.backend=jna); run orthomosaic with the JCUDA backend.");
+    		}
         	System.out.println("Setting up GPU");
     		try {
     			GPU_QUAD_AFFINE = new GpuQuad(//

src/main/resources/cuas_dnn/mexhat_gaps_boost40/model.l2.ts.pt.meta.json

+{"kind": "L2", "ch_hidden": 24, "vmax": 1.4, "grid": 32, "ch_in": 3}
\ No newline at end of file