Implementing quasi-parallel processing using GUI and MCP

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

@@ -3407,13 +3407,19 @@ public class CLTParameters {
 	}
 
 	public boolean showJDialog() {
-		return showJDialog(false);
+		return showJDialog(false, GenericJTabbedDialogMcp.isDefaultMcpMode());
 	}
 
 	// codex 2026-01-27: optional modeless dialog for MCP/GUI co-use
 	public boolean showJDialog(boolean nonBlocking) {
+		return showJDialog(nonBlocking, GenericJTabbedDialogMcp.isDefaultMcpMode());
+	}
+
+	// codex 2026-01-28: allow forcing GUI vs MCP mode per call
+	public boolean showJDialog(boolean nonBlocking, boolean useMcp) {
 		//  			GenericDialog gd = new GenericDialog("Set CLT parameters");
 		GenericJTabbedDialogMcp gd = new GenericJTabbedDialogMcp("Set CLT parameters",1090,900, !nonBlocking); // codex 2026-01-25
+		gd.setMcpMode(useMcp);
 		gd.addTab         ("General", "General parameters");
 		gd.addNumericField("Nominal (rectilinear) disparity between side of square cameras (pix)",              this.disparity,  3,7,"pix",
 				"Used when rendering 4 images");

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

@@ -1195,17 +1195,26 @@ public class EyesisCorrectionParameters {
     	}
 
 
-    	public boolean showCLTBatchDialog(String title,
-    			CLTParameters clt_parameters) {
-    		return showCLTBatchDialog(title, clt_parameters, false);
-    	}
+    public boolean showCLTBatchDialog(String title,
+            CLTParameters clt_parameters) {
+        return showCLTBatchDialog(title, clt_parameters, false, GenericJTabbedDialogMcp.isDefaultMcpMode());
+    }
 
-    	// codex 2026-01-27: optional modeless dialog for MCP/GUI co-use
-    	public boolean showCLTBatchDialog(String title,
-    			CLTParameters clt_parameters,
-    			boolean nonBlocking) {
-    		GenericJTabbedDialogMcp gd = new GenericJTabbedDialogMcp(title,1000,1000, !nonBlocking); // codex 2026-01-25
-    		updateAuxFromMain();
+    // codex 2026-01-27: optional modeless dialog for MCP/GUI co-use
+    public boolean showCLTBatchDialog(String title,
+            CLTParameters clt_parameters,
+            boolean nonBlocking) {
+        return showCLTBatchDialog(title, clt_parameters, nonBlocking, GenericJTabbedDialogMcp.isDefaultMcpMode());
+    }
+
+    // codex 2026-01-28: allow forcing GUI vs MCP mode per call
+    public boolean showCLTBatchDialog(String title,
+            CLTParameters clt_parameters,
+            boolean nonBlocking,
+            boolean useMcp) {
+        GenericJTabbedDialogMcp gd = new GenericJTabbedDialogMcp(title,1000,1000, !nonBlocking); // codex 2026-01-25
+        gd.setMcpMode(useMcp);
+        updateAuxFromMain();
 
 
     		gd.addTab         ("File paths", "Select files and directories paths (common to main and optional auxiliary)");
@@ -1792,7 +1801,8 @@ public class EyesisCorrectionParameters {
             	base_path=base_path.resolve(Paths.get(dir_map.get("rootDirectory")));
     			File base_dir = new File(base_path.toString());
     			if (!base_dir.exists()) {
-    				base_dir.mkdirs(); // codex 2026-01-28: mkdirs side-effect (consider guarding)
+    				System.out.println("Root directory "+base_path.toString()+" does not exist, ignoring "+seq_str);
+    				return null;
     			}
             }
             // set sourceDirectory: 
@@ -1808,7 +1818,8 @@ public class EyesisCorrectionParameters {
     		Path source_path = Paths.get(this.sourceDirectory);
 			File source_dir = new File(source_path.toString());
 			if (!source_dir.exists()) {
-				source_dir.mkdirs(); // codex 2026-01-28: mkdirs side-effect (consider guarding)
+				System.out.println("Source directory "+source_path.toString()+" does not exist, ignoring "+seq_str);
+				return null;
 			}
 			
             useCuasSeedDir = false;
@@ -1821,7 +1832,8 @@ public class EyesisCorrectionParameters {
             			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 (!dir_file.exists()) {
-            					dir_file.mkdirs(); // codex 2026-01-28: mkdirs side-effect (consider guarding)
+            					System.out.println(KEY_DIRS[i]+" directory "+dir_path.toString()+" does not exist, ignoring "+seq_str);
+            					return null;
             				}
             			}
             			dir_string =  dir_path.toString();

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

@@ -12,7 +12,9 @@ import ij.IJ;
 public class GenericJTabbedDialogMcp extends GenericJTabbedDialog{
 	// codex 2026-01-25: MCP dialog capture state
 	private static boolean defaultMcpMode = false;
+	private static long dialogTimeoutMs = 30000L;
 	public boolean mcp_mode = false;
+	private boolean mcpCanceled = false;
 	private final List<McpDialogField> mcpFields = new ArrayList<McpDialogField>();
 	private final String dialogTitle;
 	private String currentTab = "";
@@ -42,6 +44,14 @@ public class GenericJTabbedDialogMcp extends GenericJTabbedDialog{
 	public static boolean isDefaultMcpMode() {
 		return defaultMcpMode;
 	}
+	// codex 2026-01-28: configurable MCP dialog submit timeout (0 = wait forever)
+	public static void setDialogTimeoutMs(long timeoutMs) {
+		dialogTimeoutMs = timeoutMs;
+	}
+	// codex 2026-01-28: override MCP mode per dialog instance
+	public void setMcpMode(boolean enabled) {
+		this.mcp_mode = enabled;
+	}
 
 	private void addMcpField(McpDialogField field) {
 		mcpFields.add(field);
@@ -121,6 +131,16 @@ public class GenericJTabbedDialogMcp extends GenericJTabbedDialog{
 		else super.addChoice(label, items, defaultItem, tooltip, count);
 	}	
 
+	@Override
+	public void addChoice(String label, String[] items, String defaultItem) {
+		addChoice(label, items, defaultItem, null, 0);
+	}
+
+	@Override
+	public void addChoice(String label, String[] items, String defaultItem, String tooltip) {
+		addChoice(label, items, defaultItem, tooltip, 0);
+	}
+
 	@Override
 	public void addDefaultButtons() { // not used
 		if (mcp_mode) {
@@ -149,7 +169,10 @@ public class GenericJTabbedDialogMcp extends GenericJTabbedDialog{
 		if (mcp_mode) {
 			// codex 2026-01-25: publish dialog schema to MCP registry
 			readIndex = 0;
-			McpDialogRegistry.setCurrent(new McpDialogSession(dialogTitle, mcpFields));
+			boolean applied = McpDialogRegistry.setCurrent(new McpDialogSession(dialogTitle, mcpFields));
+			if (!applied) {
+				System.out.println("MCP: dialog already active, ignoring \"" + dialogTitle + "\"");
+			}
 		}
 		else super.buildDialog();
 	}
@@ -253,6 +276,17 @@ public class GenericJTabbedDialogMcp extends GenericJTabbedDialog{
 	public boolean showDialog() {
 		if (mcp_mode) {
 			buildDialog();
+			McpDialogSession session = McpDialogRegistry.getCurrent();
+			if (session != null) {
+				long timeout = dialogTimeoutMs;
+				Boolean ok = (timeout <= 0) ? session.awaitSubmit(Long.MAX_VALUE) : session.awaitSubmit(timeout);
+				if (ok != null && !ok.booleanValue()) {
+					mcpCanceled = true;
+				} else {
+					mcpCanceled = false;
+				}
+			}
+			McpDialogRegistry.setCurrent(null);
 			return true;
 		}
 		else return super.showDialog();
@@ -279,7 +313,7 @@ public class GenericJTabbedDialogMcp extends GenericJTabbedDialog{
 	@Override
 	public boolean wasCanceled() {
 		if (mcp_mode) {
-			return false;
+			return mcpCanceled;
 		}
 		else return super.wasCanceled();
 	}

src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java

@@ -479,6 +479,11 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 	public static String DEFAULT_DIRECTORY = null;
 	// codex 2026-01-28: remember last MCP-selected paths per dialog title
 	private static final HashMap<String, String> MCP_LAST_PATHS = new HashMap<String, String>();
+	// codex 2026-01-28: current command origin (MCP vs GUI) for file dialogs
+	private static volatile boolean MCP_COMMAND_CONTEXT = false;
+	// codex 2026-01-28: MCP debug output control
+	public static final int MINIMAL_DEBUG_MCP = -2;
+	public static int MCP_DEBUG_LEVEL = -1;
 	public static boolean ADVANCED_MODE = false; // true; // show all buttons
 	public static boolean DCT_MODE = false; // true; // show all buttons
 	public static boolean MODE_3D = false; // 3D-related commands
@@ -489,7 +494,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 	public ImagePlus CORRELATE_IMP = null;
 	public TensorflowInferModel TENSORFLOW_INFER_MODEL = null;
 
-	public boolean use_swing = true; // false;
+//	public boolean use_swing = true; // false;
 	private PlugInFrame plugInFrame;
 	private JFrame plugInJFrame;
 //	static Frame instance;
@@ -499,6 +504,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 	private JPanel jpanel1, jpanel2, jpanel3, jpanel4, jpanel5, jpanel5a, jpanel6, jpanel7, jpanelPostProcessing1,
 	jpanelPostProcessing2, jpanelPostProcessing3, jpanelDct1, jpanelClt1, jpanelClt2, jpanelClt3, jpanelClt4,
 	jpanelClt5, jpanelClt5aux, jpanelClt_GPU, jpanelLWIR, jpanelLWIR16, jpanelLWIRWorld, jpanelOrange;
+	private boolean commandFromMcp = false;
 	
 //	EyesisTopFrame eyesisTopFrame = new EyesisTopFrame();	
 //	System.out.println("Launched EyesisTopFrame");
@@ -535,6 +541,8 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		LogTee.install();         // once, early
 		// codex 2026-01-25: start MCP server + enable MCP dialog mode by default
 		GenericJTabbedDialogMcp.setDefaultMcpMode(getMcpMode());
+		GenericJTabbedDialogMcp.setDialogTimeoutMs(getMcpDialogTimeoutMs());
+		MCP_DEBUG_LEVEL = DEBUG_LEVEL-2;
 		// codex 2026-01-27: enable MCP-mode SyncCommand control
 		SYNC_COMMAND.setMcpMode(getMcpMode());
 		McpServer.startIfNeeded(this, getMcpPort());
@@ -550,11 +558,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		if (options != null || headless) {
 			processFiles();
 		} else {
-			if (use_swing) {
-				initGuiSwing();
-			} else {
-				initGuiAWT();
-			}
+			initGuiSwing();
 		}
 	}
 
@@ -954,6 +958,8 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 					}
 					if (this.SYNC_COMMAND.stopRequested.get() == 0) {
 						try {
+							this.commandFromMcp = this.SYNC_COMMAND.fromMcp;
+							this.SYNC_COMMAND.fromMcp = false;
 							runMenuCommand(this.SYNC_COMMAND.buttonLabel);
 						} catch (Exception e) {
 							// TODO Auto-generated catch block
@@ -962,418 +968,13 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 							IJ.showMessage("Exception", stack2string(e));
 						}
 					}
+					this.commandFromMcp = false;
 					this.SYNC_COMMAND.isRunning = false;
 					this.SYNC_COMMAND.stopRequested.set(0);
 				}
 
 			}
-	
-	
-	public void initGuiAWT() {
-///		EyesisTopFrame eyesisTopFrame = new EyesisTopFrame();	
-		Color color_configure = new Color(200, 200, 160);
-		Color color_configure_aux = new Color(190, 190, 180);
-		Color color_process = new Color(180, 180, 240);
-		Color color_process_aux = new Color(175, 175, 250);
-		Color color_conf_process = new Color(180, 240, 240);
-		Color color_conf_process_aux = new Color(175, 235, 250);
-		Color color_restore = new Color(160, 240, 160);
-		Color color_stop = new Color(255, 160, 160);
-		Color color_report = new Color(180, 220, 180);
-		plugInFrame = new PlugInFrame("Eyesis_Correction") {
-			private static final long serialVersionUID = -4138832568507690332L;
-
-			@Override
-			public void processWindowEvent(WindowEvent e) {
-				super.processWindowEvent(e);
-				if (e.getID() == WindowEvent.WINDOW_CLOSING) {
-					plugInFrame=null; // instance = null;
-				}
-			}
-		};
-//		Font font = plugInFrame.getFont();
-//		instance = plugInFrame;
-		plugInFrame.addKeyListener(IJ.getInstance());
-//		int menuRows=4 + (ADVANCED_MODE?4:0) + (MODE_3D?3:0) + (DCT_MODE?6:0) + (GPU_MODE?1:0) +(LWIR_MODE?2:0);
-		int menuRows = 4 + (ADVANCED_MODE ? 4 : 0) + (MODE_3D ? 3 : 0) + (DCT_MODE ? 7 : 0) + (GPU_MODE ? 1 : 0)
-				+ (LWIR_MODE ? 4 : 0);
-		plugInFrame.setLayout(new GridLayout(menuRows, 1));
-		panel6 = new Panel();
-		panel6.setLayout(new GridLayout(1, 0, 5, 5));
-		addButton("Save", panel6, color_process); // , "Save configuration");
-		addButton("Save Clean", panel6, color_process); // , "Save clean configuration");
-		addButton("Restore", panel6, color_restore); // , "Restore configuration");
-		addButton("Stop", panel6, color_stop);
-		addButton("Abort", panel6, color_stop);
-
-		plugInFrame.add(panel6);
-
-		panel5 = new Panel();
-		panel5.setLayout(new GridLayout(1, 0, 5, 5));
-		addButton("Configure spilt", panel5, color_configure);
-		addButton("Configure demosaic", panel5, color_configure);
-		plugInFrame.add(panel5);
-		panel5a = new Panel();
-		panel5a.setLayout(new GridLayout(1, 0, 5, 5));
-		addButton("Configure convolution", panel5a, color_configure);
-		addButton("Configure denoise", panel5a, color_configure);
-		addButton("Configure color", panel5a, color_configure);
-		addButton("Configure AUX color", panel5a, color_configure_aux);
-//		addButton("Channel gains", panel5a, color_configure);
-		addButton("Configure RGB", panel5a, color_configure);
-		plugInFrame.add(panel5a);
-
-		// Debug/development options
-
-		if (ADVANCED_MODE) {
-			panel1 = new Panel();
-			panel1.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
-			addButton("Split Image", panel1, null);
-			addButton("Debayer Image", panel1, null);
-			plugInFrame.add(panel1);
-
-			panel2 = new Panel();
-			panel2.setLayout(new GridLayout(1, 0, 5, 5));
-			addButton("Select kernel stack", panel2, null);
-			addButton("Convolve with stack", panel2, null);
-			plugInFrame.add(panel2);
-
-			panel3 = new Panel();
-			panel3.setLayout(new GridLayout(1, 0, 5, 5));
-			addButton("Select lo-res", panel3, null);
-			addButton("Combine pair", panel3, null);
-			addButton("Colors", panel3, null);
-			addButton("RGB", panel3, null);
-			plugInFrame.add(panel3);
-
-			panel4 = new Panel();
-			panel4.setLayout(new GridLayout(1, 0, 5, 5));
-			addButton("Test", panel4, null);
-			addButton("Test Debayer", panel4, null);
-			plugInFrame.add(panel4);
-		}
-		panel7 = new Panel();
-		panel7.setLayout(new GridLayout(1, 0, 5, 5));
-		addButton("Configure correction", panel7, color_configure);
-		addButton("Channel gains/colors", panel7, color_configure);
-		addButton("Configure warping", panel7, color_conf_process);
-		addButton("Select source files", panel7, color_configure);
-		addButton("Select source sets", panel7, color_configure);
-		addButton("Process files", panel7, color_process);
-		if (ADVANCED_MODE) {
-			addButton("Tiff Writer", panel7, null);
-			addButton("Tiff Properties", panel7, null);
-			addButton("Add TIFF resolution", panel7, null);
-		}
-		plugInFrame.add(panel7);
-
-		if (MODE_3D) {
-			panelPostProcessing1 = new Panel();
-			panelPostProcessing1.setLayout(new GridLayout(1, 0, 5, 5));
-			addButton("Configure PP", panelPostProcessing1, color_configure);
-			addButton("Source PP", panelPostProcessing1, color_configure);
-			addButton("ConvertPP", panelPostProcessing1, color_process);
-			addButton("Linear Features", panelPostProcessing1, null);
-			addButton("Intercam correlations", panelPostProcessing1, null);
-			plugInFrame.add(panelPostProcessing1, null);
-
-			panelPostProcessing2 = new Panel();
-			panelPostProcessing2.setLayout(new GridLayout(1, 0, 5, 5));
-			addButton("Tile correlations", panelPostProcessing2, null);
-			addButton("Load correlations", panelPostProcessing2, null);
-			addButton("Section correlations", panelPostProcessing2, null);
-			addButton("Setup Z-map", panelPostProcessing2, null);
-			addButton("Fill FG gaps", panelPostProcessing2, null);
-			addButton("Filter Z-map", panelPostProcessing2, null);
-			addButton("Occluding FG", panelPostProcessing2, null);
-			plugInFrame.add(panelPostProcessing2, null);
-
-			panelPostProcessing3 = new Panel();
-			panelPostProcessing3.setLayout(new GridLayout(1, 0, 5, 5));
-			addButton("Refine Disparities", panelPostProcessing3, null);
-			addButton("Init Photometry", panelPostProcessing3, null);
-			addButton("Plane Likely", panelPostProcessing3, null);
-			plugInFrame.add(panelPostProcessing3, null);
-		}
-		if (DCT_MODE) {
-			panelDct1 = new Panel();
-			panelDct1.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
-			addButton("DCT test 1", panelDct1, color_process);
-			addButton("select MDCT image", panelDct1, color_configure);
-			addButton("MDCT scale", panelDct1, color_process);
-			addButton("MDCT stack", panelDct1, color_process);
-			addButton("DCT test 3", panelDct1, color_process);
-			addButton("DCT test 4", panelDct1, color_process);
-			addButton("Test Kernel Factorization", panelDct1, color_process);
-			addButton("Min Kernel Factorization", panelDct1, color_process);
-			addButton("Select kernels image", panelDct1, color_configure);
-			addButton("Create DCT kernels", panelDct1, color_process);
-			addButton("Read DCT kernels", panelDct1, color_process);
-			addButton("Reset DCT kernels", panelDct1, color_stop);
-			addButton("Setup DCT parameters", panelDct1, color_configure);
-			addButton("DCT process files", panelDct1, color_process);
-			plugInFrame.add(panelDct1);
-		}
-		if (DCT_MODE) {
-			panelClt1 = new Panel();
-			panelClt1.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
-			addButton("Select CLT image", panelClt1, color_configure);
-			addButton("CLT stack", panelClt1, color_process);
-			addButton("Select second CLT image", panelClt1, color_configure);
-			addButton("CLT correlate", panelClt1, color_process);
-			addButton("Reset Geometry", panelClt1, color_stop);
-			addButton("Reset AUX Geometry", panelClt1, color_stop);
-			addButton("Create CLT kernels", panelClt1, color_process);
-			addButton("Create AUX CLT kernels", panelClt1, color_process);
-			addButton("Read CLT kernels", panelClt1, color_process_aux);
-			addButton("Reset CLT kernels", panelClt1, color_stop);
-
-			addButton("CLT process files", panelClt1, color_process);
-			addButton("CLT process sets", panelClt1, color_process);
-
-			plugInFrame.add(panelClt1);
-		}
-		if (DCT_MODE) {
-			panelClt2 = new Panel();
-			panelClt2.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
-			addButton("Setup CLT parameters", panelClt2, color_configure);
-			addButton("CLT 4 images", panelClt2, color_conf_process);
-			addButton("CLT disparity scan", panelClt2, color_conf_process);
-			addButton("CLT reset fine corr", panelClt2, color_stop);
-			addButton("CLT reset extrinsic corr", panelClt2, color_stop);
-			addButton("ERS reset", panelClt2, color_stop);
-			addButton("CLT show geometry", panelClt2, color_configure);
-			addButton("CLT show fine corr", panelClt2, color_report);
-			addButton("CLT apply fine corr", panelClt2, color_process);
-			addButton("CLT test fine corr", panelClt2, color_process);
-			addButton("CLT process fine corr", panelClt2, color_conf_process);
-			addButton("CLT infinity corr", panelClt2, color_conf_process);
-			addButton("CLT ext infinity corr", panelClt2, color_conf_process);
-			addButton("CLT reset 3D", panelClt2, color_stop);
-			addButton("MAIN extrinsics", panelClt2, color_process);
-			addButton("CLT Poly corr", panelClt2, color_process);
-			addButton("DRY RUN", panelClt2, color_configure);
-			addButton("CLT 3D", panelClt2, color_process);
-			addButton("CLT planes", panelClt2, color_conf_process);
-			addButton("CLT ASSIGN", panelClt2, color_process);
-			addButton("CLT OUT 3D", panelClt2, color_process);
-
-			plugInFrame.add(panelClt2);
-		}
-		if (DCT_MODE) {
-			panelClt3 = new Panel();
-			panelClt3.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
-			addButton("Setup CLT", panelClt3, color_configure);
-			addButton("Infinity offset", panelClt3, color_configure);
-			addButton("Setup CLT Batch parameters", panelClt3, color_configure);
-			addButton("CLT batch process", panelClt3, color_process);
-			addButton("CM Test", panelClt3, color_stop);
-			addButton("Show scan", panelClt3, color_report);
-			addButton("Show all scans", panelClt3, color_report);
-			addButton("Periodic", panelClt3, color_configure);
-			plugInFrame.add(panelClt3);
-		}
-
-		if (DCT_MODE) {
-			panelClt4 = new Panel();
-			panelClt4.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
-			addButton("Import Aux", panelClt4, color_restore);
-			addButton("Setup CLT Batch parameters", panelClt4, color_configure);
-			addButton("CLT rig edit", panelClt4, color_configure);
-			addButton("Rig offset", panelClt4, color_configure);
-			addButton("Save offset", panelClt4, color_process);
-			addButton("SHOW extrinsics", panelClt4, color_report);
-			addButton("RIG DSI", panelClt4, color_conf_process);
-			addButton("MAIN extrinsics", panelClt4, color_process);
-			addButton("AUX extrinsics", panelClt4, color_process);
-			addButton("RIG extrinsics", panelClt4, color_conf_process);
-			addButton("SAVE extrinsics", panelClt4, color_process); // , "Save configuration");
-
-			addButton("Rig8 images", panelClt4, color_conf_process);
-
-			addButton("Reset GT", panelClt4, color_stop);
-			addButton("Ground truth", panelClt4, color_conf_process);
-			addButton("Show biscan", panelClt4, color_report);
-			addButton("Poles GT", panelClt4, color_process);
-			addButton("ML export", panelClt4, color_conf_process);
-			addButton("JP4 copy", panelClt4, color_conf_process);
-			addButton("DSI show", panelClt4, color_report);
-			addButton("Rig batch", panelClt4, color_process);
-			plugInFrame.add(panelClt4);
-		}
-
-		if (DCT_MODE) {
-			panelClt5 = new Panel();
-			panelClt5.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
-			addButton("LIST extrinsics", panelClt5, color_report);
-			addButton("DSI histogram", panelClt5, color_report);
-			addButton("ML recalc", panelClt5, color_process);
-			addButton("Inter Test", panelClt5, color_stop);
-			addButton("Inter Pairs", panelClt5, color_process);
-			addButton("Inter LMA", panelClt5, color_stop);
-			addButton("Inter Series", panelClt5, color_process);
-			addButton("Inter Accumulate", panelClt5, color_process);
-			addButton("Inter Noise", panelClt5, color_process);
-			addButton("Inter Debug Noise", panelClt5, color_report);
-			addButton("Noise Stats", panelClt5, color_process);
-			addButton("Test 1D", panelClt5, color_process);
-			addButton("Colorize Depth", panelClt5, color_process);
-			addButton("Main LY series", panelClt5, color_process);
-			plugInFrame.add(panelClt5);
-		}
-
-		if (DCT_MODE) {
-			panelClt5aux = new Panel();
-			panelClt5aux.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
-			addButton("LIST extrinsics", panelClt5aux, color_report);
-			addButton("Aux Build Series", panelClt5aux, color_stop);
-			addButton("Aux Inter Test", panelClt5aux, color_stop);
-			addButton("Aux Inter Pairs", panelClt5aux, color_process);
-			addButton("Aux Inter LMA", panelClt5aux, color_stop);
-			addButton("Aux Inter Series", panelClt5aux, color_process);
-			addButton("Aux Inter Accumulate", panelClt5aux, color_process);
-			addButton("Inter Noise Aux", panelClt5aux, color_process);
-			addButton("Batch Noise Aux", panelClt5aux, color_report);
-			addButton("Noise Stats Aux", panelClt5aux, color_process);
-			addButton("Colorize Depth", panelClt5aux, color_process);
-			addButton("Inter Intra ML", panelClt5aux, color_report);
-			addButton("Aux LY series", panelClt5aux, color_process);
-			plugInFrame.add(panelClt5aux);
-		}
-
-		if (GPU_MODE) {
-			panelClt_GPU = new Panel();
-			panelClt_GPU.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
-			addButton("JCUDA TEST", panelClt_GPU, null);
-			addButton("TF TEST", panelClt_GPU, null);
-			addButton("GPU simulate", panelClt_GPU, color_conf_process);
-			addButton("GPU RUN", panelClt_GPU, color_conf_process);
-//			addButton("ShowGPU",                    panelClt_GPU, color_conf_process);
-
-			addButton("LWIR_TEST", panelClt_GPU, color_conf_process);
-			addButton("LWIR_ACQUIRE", panelClt_GPU, color_conf_process);
-			addButton("ERS reset", panelClt2, color_stop);
-			addButton("IMU main", panelClt_GPU, color_conf_process);
-			addButton("ERS main", panelClt_GPU, color_process);
-			addButton("IMU aux", panelClt_GPU, color_conf_process_aux);
-			addButton("ERS aux", panelClt_GPU, color_process_aux);
-
-			addButton("Rotations_test", panelClt_GPU, color_stop);
-			addButton("GPU simulate", panelClt_GPU, color_conf_process);
-
-			plugInFrame.add(panelClt_GPU);
-		}
-		if (LWIR_MODE) {
-			panelLWIR = new Panel();
-			panelLWIR.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
-			addButton("Setup CLT Batch parameters", panelLWIR, color_configure);
-			addButton("Reset Geometry", panelLWIR, color_stop);
-			addButton("Reset AUX Geometry", panelLWIR, color_stop);
-			addButton("Create CLT kernels", panelLWIR, color_process);
-			addButton("Create AUX CLT kernels", panelLWIR, color_process_aux);
-			addButton("Select source sets", panelLWIR, color_configure);
-			addButton("Configure color", panelLWIR, color_configure);
-			addButton("CORR TEST", panelLWIR, color_conf_process);
-			addButton("CLT 4 images", panelLWIR, color_conf_process);
-			addButton("CLT 3D", panelLWIR, color_process);
-			addButton("CLT planes", panelLWIR, color_conf_process);
-			addButton("CLT ASSIGN", panelLWIR, color_process);
-			addButton("CLT OUT 3D", panelLWIR, color_process);
-			addButton("Configure AUX color", panelLWIR, color_configure_aux);
-			addButton("AUX 4 images", panelLWIR, color_conf_process_aux);
-			addButton("AUX 3D", panelLWIR, color_process);
-			addButton("AUX planes", panelLWIR, color_conf_process_aux);
-			addButton("AUX ASSIGN", panelLWIR, color_process_aux);
-			addButton("AUX OUT 3D", panelLWIR, color_process_aux);
-			addButton("Main img AUX", panelLWIR, color_process_aux);
-			addButton("Main to AUX", panelLWIR, color_process_aux);
-			addButton("LWIR batch", panelClt4, color_process);
-//			addButton("LWIR_TEST",                  panelLWIR, color_conf_process);
-//			addButton("LWIR_ACQUIRE",               panelLWIR, color_conf_process);
-			plugInFrame.add(panelLWIR);
-
-			panelLWIR16 = new Panel();
-			panelLWIR16.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
-			addButton("SHOW extrinsics", panelLWIR16, color_report);
-			addButton("Reset Geometry", panelLWIR16, color_stop);
-			addButton("Reset AUX Geometry", panelLWIR16, color_stop);
-			addButton("Generate Sym Vectors", panelLWIR16, color_configure);
-			addButton("Image Properties", panelLWIR16, color_conf_process);
-			addButton("Illustrations Configure", panelLWIR16, color_conf_process);
-			addButton("Footage Organize", panelLWIR16, color_conf_process);
-			addButton("Super batch",     panelLWIR16, color_process);
-			addButton("Remove source paths",     panelLWIR16, color_stop);
-			plugInFrame.add(panelLWIR16);
-			panelLWIRWorld = new Panel();
-			panelLWIRWorld.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
-			addButton("Aux Build Series", panelLWIRWorld, color_stop);
-			addButton("CUAS Combine", panelLWIRWorld, color_stop);
-			addButton("Build World", panelLWIRWorld, color_process);
-			addButton("Test IMX5", panelLWIRWorld, color_process);
-			addButton("Show mice", panelLWIRWorld, color_process);
-			addButton("Set pair",  panelLWIRWorld, color_process);
-			addButton("Warp pair",  panelLWIRWorld, color_process);
-			addButton("Read Tiff",  panelLWIRWorld, color_process);
-			addButton("Test video",  panelLWIRWorld, color_process);
-			addButton("Ortho",         panelLWIRWorld, color_process);
-			addButton("Ortho Pairs",  panelLWIRWorld, color_process);
-			addButton("Manual pair",  panelLWIRWorld, color_process);
-			addButton("Extract Objects",  panelLWIRWorld, color_process);
-			addButton("Mismatched resolutions",  panelLWIRWorld, color_process);
-			addButton("Generate DATI",  panelLWIRWorld, color_process);
-			addButton("Create mine",  panelLWIRWorld, color_process);
-			addButton("Pattern correlate",  panelLWIRWorld, color_process);
-			addButton("Properties compare",  panelLWIRWorld, color_process);
-			plugInFrame.add(panelLWIRWorld);
-
-			panelOrange = new Panel();
-			panelOrange.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
-			addButton("Test Orange", panelOrange, color_process);
-			addButton("Process Merged", panelOrange, color_process);
-			addButton("Vegetation LMA", panelOrange, color_process);
-			addButton("Combine LMA Segments", panelOrange, color_process);
-			addButton("Render synthetic", panelOrange, color_process);
-			addButton("Generate LWIR target", panelOrange, color_process);
-//			addButton("Test LDLT Cholesky", panelOrange, color_process);
-			addButton("Test LLT Cholesky",  panelOrange, color_process);
-			addButton("UAS log",  panelOrange, color_process);
-			addButton("DJI SRT",  panelOrange, color_process);
-			addButton("SRT to KML",  panelOrange, color_process);
-			//
-			plugInFrame.add(panelOrange);
-		}
-		plugInFrame.pack(); // Adjusts the window size to fit components
-//"LWIR batch"
-		GUI.center(plugInFrame);
-		plugInFrame.setVisible(true);
-//		FHT_INSTANCE = new DoubleFHT();
-		// main loop
-		while (true) {
-			synchronized (this.SYNC_COMMAND) {
-				try {
-					this.SYNC_COMMAND.wait();
-				} catch (InterruptedException e) {
-					// TODO Auto-generated catch block
-					e.printStackTrace();
-				}
-				this.SYNC_COMMAND.isRunning = true;
-			}
-			if (this.SYNC_COMMAND.stopRequested.get() == 0) {
-				try {
-					runMenuCommand(this.SYNC_COMMAND.buttonLabel);
-				} catch (Exception e) {
-					// TODO Auto-generated catch block
-					e.printStackTrace();
-					System.out.println(stack2string(e));
-					IJ.showMessage("Exception", stack2string(e));
-				}
-			}
-			this.SYNC_COMMAND.isRunning = false;
-			this.SYNC_COMMAND.stopRequested.set(0);
-		}
-
-	}
-
+		
 	private Properties prefsProperties = new Properties();
 
 	public void loadPrefs() throws IOException {
@@ -1535,6 +1136,11 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 
 	// codex 2026-01-25: MCP-visible command trigger
 	public void triggerCommand(String label) {
+		triggerCommand(label, false);
+	}
+
+	// codex 2026-01-28: mark MCP-originated commands
+	public void triggerCommand(String label, boolean fromMcp) {
 		if (label == null) {
 			return;
 		}
@@ -1553,6 +1159,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			return;
 		}
 		synchronized (this.SYNC_COMMAND) {
+			this.SYNC_COMMAND.fromMcp = fromMcp;
 			this.SYNC_COMMAND.buttonLabel = label;
 			this.SYNC_COMMAND.notify();
 		}
@@ -1600,6 +1207,19 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		}
 	}
 
+	private long getMcpDialogTimeoutMs() {
+		String value = System.getProperty("elphel.mcp.dialogTimeoutMs");
+		if (value == null || value.isEmpty()) {
+			return 30000L;
+		}
+		try {
+			return Long.parseLong(value);
+		} catch (NumberFormatException e) {
+			return 30000L;
+		}
+	}
+
+
 	private boolean getMcpMode() {
 		String value = System.getProperty("elphel.mcp.mode");
 		if (value == null || value.isEmpty()) {
@@ -1752,6 +1372,8 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 	}
 
 	public void runMenuCommand(String label) {
+		MCP_COMMAND_CONTEXT = this.commandFromMcp;
+		try {
 		int i, j; // ,l,iq;
 //    String label = e.getActionCommand();
 		Runtime runtime = Runtime.getRuntime();
@@ -4762,16 +4384,16 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			/* ======================================================================== */
 		} else if (label.equals("Setup CLT Batch parameters")) {
 			DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
-			CORRECTION_PARAMETERS.showCLTBatchDialog("CLT Batch parameters", CLT_PARAMETERS, true); // codex 2026-01-27
+			CORRECTION_PARAMETERS.showCLTBatchDialog("CLT Batch parameters", CLT_PARAMETERS, true, this.commandFromMcp); // codex 2026-01-27
 			return;
 
 			/* ======================================================================== */
 		} else if (label.equals("Setup CLT parameters")) {
-			CLT_PARAMETERS.showJDialog(true); // codex 2026-01-27
+			CLT_PARAMETERS.showJDialog(true, this.commandFromMcp); // codex 2026-01-27
 			return;
 			/* ======================================================================== */
 		} else if (label.equals("Setup CLT")) {
-			CLT_PARAMETERS.showJDialog(true); // codex 2026-01-27
+			CLT_PARAMETERS.showJDialog(true, this.commandFromMcp); // codex 2026-01-27
 			return;
 			/* ======================================================================== */
 		} else if (label.equals("Infinity offset")) {
@@ -6451,6 +6073,9 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			}
 			*/
 		}
+		} finally {
+			MCP_COMMAND_CONTEXT = false;
+		}
 	}
 	
 	public static boolean testUasLog() {
@@ -10162,7 +9787,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 
 	public static String[] selectDirectoriesOrFiles(boolean save, boolean directory, String title, String button,
 			FileFilter filter, String[] defaultPaths) {
-		if (GenericJTabbedDialogMcp.isDefaultMcpMode()) {
+		if (GenericJTabbedDialogMcp.isDefaultMcpMode() && MCP_COMMAND_CONTEXT) {
 			String defaultPath = null;
 			if (defaultPaths != null && defaultPaths.length > 0) {
 				defaultPath = defaultPaths[0];
@@ -10255,7 +9880,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 
 	public static String selectDirectoryOrFile(boolean save, boolean directory, String title, String button, FileFilter filter,
 			String defaultPath) {
-		if (GenericJTabbedDialogMcp.isDefaultMcpMode()) {
+		if (GenericJTabbedDialogMcp.isDefaultMcpMode() && MCP_COMMAND_CONTEXT) {
 			return selectDirectoryOrFileMcp(directory, title, defaultPath);
 		}
 		File dir = null;
@@ -10930,7 +10555,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			QUAD_CLT.getProperties(QuadCLT.PREFIX);
 		if (QUAD_CLT_AUX != null)
 			QUAD_CLT_AUX.getProperties(QuadCLT.PREFIX_AUX);
-
+		return;
 	}
 
 	/* ======================================================================== */

src/main/java/com/elphel/imagej/correction/SyncCommand.java

@@ -12,6 +12,7 @@ public class SyncCommand {
 	public AtomicInteger stopRequested = new AtomicInteger(0); // 0 - not requested, 1 - ASAP, 2 - gracefully
 	public String buttonLabel = "";
 	public boolean confirm = true;
+	public boolean fromMcp = false;
 	// codex 2026-01-27: MCP-controlled pause/confirm
 	private boolean mcpMode = false;
 	private boolean confirmPending = false;

src/main/java/com/elphel/imagej/mcp/McpDialogRegistry.java

@@ -8,19 +8,58 @@ public class McpDialogRegistry {
     private McpDialogRegistry() {
     }
 
-    public static void setCurrent(McpDialogSession session) {
+    public static boolean setCurrent(McpDialogSession session) {
+        if (session == null) {
+            CURRENT.set(null);
+            return true;
+        }
+        McpDialogSession existing = CURRENT.get();
+        if (existing != null) {
+            return false;
+        }
         CURRENT.set(session);
+        return true;
     }
 
     public static McpDialogSession getCurrent() {
         return CURRENT.get();
     }
 
-    public static void setValue(String label, String value) {
+    public static boolean setValue(String label, String value) {
         McpDialogSession session = CURRENT.get();
         if (session == null) {
-            return;
+            return false;
         }
         session.setValue(label, value);
+        return true;
+    }
+
+    public static boolean setValueForId(String id, String label, String value) {
+        McpDialogSession session = CURRENT.get();
+        if (session == null || id == null || !id.equals(session.getId())) {
+            return false;
+        }
+        session.setValue(label, value);
+        return true;
+    }
+
+    public static boolean submitCurrent(boolean ok) {
+        McpDialogSession session = CURRENT.get();
+        if (session == null) {
+            return false;
+        }
+        session.submit(ok);
+        CURRENT.set(null);
+        return true;
+    }
+
+    public static boolean submitForId(String id, boolean ok) {
+        McpDialogSession session = CURRENT.get();
+        if (session == null || id == null || !id.equals(session.getId())) {
+            return false;
+        }
+        session.submit(ok);
+        CURRENT.set(null);
+        return true;
     }
 }

src/main/java/com/elphel/imagej/mcp/McpDialogSession.java

@@ -8,10 +8,13 @@ import java.util.Map;
 import java.util.UUID;
 
 public class McpDialogSession {
+	public static final int debugLevel = -1; // name in the same case in most other places. Compares if (debugLevel >-3)
     private final String id;
     private final String title;
     private final List<McpDialogField> fields;
     private final Map<String, String> valuesByLabel;
+    private final Object submitLock = new Object();
+    private Boolean submittedOk = null;
 
     public McpDialogSession(String title, List<McpDialogField> fields) {
         this.id = UUID.randomUUID().toString();
@@ -37,6 +40,41 @@ public class McpDialogSession {
             return;
         }
         valuesByLabel.put(label, value);
+        if (debugLevel > -3) {
+        	System.out.println("setValue("+label+","+value+")");
+        }
+    }
+
+    public void submit(boolean ok) {
+        synchronized (submitLock) {
+            submittedOk = Boolean.valueOf(ok);
+            submitLock.notifyAll();
+            if (debugLevel > -3) {
+            	System.out.println("submit("+ok+")");
+            }
+        }
+    }
+
+    public Boolean awaitSubmit(long timeoutMs) {
+        synchronized (submitLock) {
+            if (submittedOk != null) {
+                return submittedOk;
+            }
+            long deadline = System.currentTimeMillis() + timeoutMs;
+            while (submittedOk == null) {
+                long remaining = deadline - System.currentTimeMillis();
+                if (remaining <= 0) {
+                    break;
+                }
+                try {
+                    submitLock.wait(remaining);
+                } catch (InterruptedException e) {
+                    Thread.currentThread().interrupt();
+                    break;
+                }
+            }
+            return submittedOk;
+        }
     }
 
     public String getValue(String label) {

src/main/java/com/elphel/imagej/mcp/McpFsAccess.java

@@ -72,9 +72,9 @@ public class McpFsAccess {
 		if (configPath != null && !configPath.trim().isEmpty()) {
 			Path configFile = Paths.get(configPath).toAbsolutePath().normalize();
 			roots.add(configFile);
-			Path configDir = configFile.getParent();
-			if (configDir != null) {
-				roots.add(configDir);
+			Path configDirFileParent = configFile.getParent();
+			if (configDirFileParent != null) {
+				roots.add(configDirFileParent);
 			}
 			addRootsFromConfig(configFile, roots);
 		}

src/main/java/com/elphel/imagej/mcp/McpServer.java

@@ -51,6 +51,7 @@ public class McpServer {
         server.createContext("/mcp/status", new StatusHandler());
         server.createContext("/mcp/dialog", new DialogHandler());
         server.createContext("/mcp/dialog/values", new DialogValuesHandler());
+        server.createContext("/mcp/dialog/submit", new DialogSubmitHandler());
         server.createContext("/mcp/button", new ButtonHandler());
         server.createContext("/mcp/interrupt", new InterruptHandler());
         server.createContext("/mcp/interrupt/confirm", new InterruptConfirmHandler());
@@ -62,7 +63,9 @@ public class McpServer {
         server.createContext("/mcp/fs/glob", new FsGlobHandler());
         server.setExecutor(null);
         server.start();
-        System.out.println("MCP: server started on http://127.0.0.1:" + port);
+        if (Eyesis_Correction.MCP_DEBUG_LEVEL >= Eyesis_Correction.MINIMAL_DEBUG_MCP) {
+            System.out.println("MCP: server started on http://127.0.0.1:" + port);
+        }
     }
 
     private class StatusHandler implements HttpHandler {
@@ -89,14 +92,40 @@ public class McpServer {
                 return;
             }
             Map<String, String> params = parseParams(exchange);
+            String id = params.get("id");
             String label = params.get("label");
             String value = params.get("value");
             if (label == null) {
                 sendJson(exchange, 400, "{\"ok\":false,\"error\":\"Missing label\"}");
                 return;
             }
-            McpDialogRegistry.setValue(label, value);
-            sendJson(exchange, 200, "{\"ok\":true}");
+            boolean applied = (id == null) ? McpDialogRegistry.setValue(label, value) : McpDialogRegistry.setValueForId(id, label, value);
+            if (applied) {
+                if (Eyesis_Correction.MCP_DEBUG_LEVEL >= Eyesis_Correction.MINIMAL_DEBUG_MCP) {
+                    System.out.println("MCP: dialog value label=\"" + label + "\"");
+                }
+                sendJson(exchange, 200, "{\"ok\":true}");
+            } else {
+                sendJson(exchange, 409, "{\"ok\":false,\"error\":\"No active dialog or id mismatch\"}");
+            }
+        }
+    }
+
+    private class DialogSubmitHandler implements HttpHandler {
+        @Override
+        public void handle(HttpExchange exchange) throws IOException {
+            if (!"POST".equalsIgnoreCase(exchange.getRequestMethod())) {
+                sendJson(exchange, 405, "{\"ok\":false,\"error\":\"POST required\"}");
+                return;
+            }
+            Map<String, String> params = parseParams(exchange);
+            String id = params.get("id");
+            boolean ok = parseBool(params.get("ok"), true);
+            boolean applied = (id == null) ? McpDialogRegistry.submitCurrent(ok) : McpDialogRegistry.submitForId(id, ok);
+            if (applied && Eyesis_Correction.MCP_DEBUG_LEVEL >= Eyesis_Correction.MINIMAL_DEBUG_MCP) {
+                System.out.println("MCP: dialog submit ok=" + ok);
+            }
+            sendJson(exchange, 200, applied ? "{\"ok\":true}" : "{\"ok\":false,\"error\":\"No active dialog\"}");
         }
     }
 
@@ -113,7 +142,10 @@ public class McpServer {
                 sendJson(exchange, 400, "{\"ok\":false,\"error\":\"Missing label\"}");
                 return;
             }
-            owner.triggerCommand(label);
+            owner.triggerCommand(label, true);
+            if (Eyesis_Correction.MCP_DEBUG_LEVEL >= Eyesis_Correction.MINIMAL_DEBUG_MCP) {
+                System.out.println("MCP: button \"" + label + "\"");
+            }
             sendJson(exchange, 200, "{\"ok\":true}");
         }
     }