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

@@ -1197,14 +1197,23 @@ public class EyesisCorrectionParameters {
 
     public boolean showCLTBatchDialog(String title,
             CLTParameters clt_parameters) {
-    		return showCLTBatchDialog(title, clt_parameters, false);
+        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) {
+        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();
 
 
@@ -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/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());
@@ -62,8 +63,10 @@ public class McpServer {
         server.createContext("/mcp/fs/glob", new FsGlobHandler());
         server.setExecutor(null);
         server.start();
+        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 {
         @Override
@@ -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);
+            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}");
         }
     }