fixing model directories after LY

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

@@ -18,6 +18,7 @@ public final class LogTee {
     private static final PrintStream ORIGINAL_OUT = System.out;
     private static final PrintStream ORIGINAL_ERR = System.err;
     private static volatile PrintStream fileStream = null;
+    private static volatile Path sceneLogPath = null;
     private static volatile boolean installed = false;
 
     private LogTee() {
@@ -40,6 +41,7 @@ public final class LogTee {
         synchronized (LOCK) {
             closeFileStream();
             fileStream = new PrintStream(new FileOutputStream(path.toFile(), true), true);
+            sceneLogPath = path;
         }
     }
 
@@ -47,9 +49,14 @@ public final class LogTee {
         synchronized (LOCK) {
             closeFileStream();
             fileStream = null;
+            sceneLogPath = null;
         }
     }
 
+    public static Path getSceneLog() {
+        return sceneLogPath;
+    }
+
     private static void closeFileStream() {
         if (fileStream != null) {
             fileStream.flush();

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

@@ -108,6 +108,7 @@ import com.elphel.imagej.common.CholeskyLDLTMulti;
 import com.elphel.imagej.common.DoubleFHT;
 import com.elphel.imagej.common.DoubleGaussianBlur;
 import com.elphel.imagej.common.GenericJTabbedDialog;
+import com.elphel.imagej.common.LogTee;
 import com.elphel.imagej.common.ShowDoubleFloatArrays;
 import com.elphel.imagej.common.WindowTools;
 import com.elphel.imagej.cuas.CuasMotion;
@@ -519,6 +520,13 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			return;
 		}
 		*/
+		/*
+  LogTee.install();         // once, early
+  LogTee.setSceneLog(path); // when you want to start per‑scene logging
+  LogTee.clearSceneLog();   // stop per‑scene logging
+
+		 */
+		LogTee.install();         // once, early
 		try {
 			loadPrefs();
 		} catch (IOException e1) {

src/main/java/com/elphel/imagej/tileprocessor/Correlation2d.java

@@ -2759,13 +2759,16 @@ public class Correlation2d {
 			boolean    eig_fast2x2,  // use fast eigenvectors for 2x2 matrices
 			boolean    debug)
 	{
+		boolean verbose = false; 
 		int data_height = data.length/data_width;
 		int center_xy = (data_width - 1)/2; //  = transform_size - 1;
 		double x0 = center_xy, y0 = center_xy;
 		int imax= 0;
 		for (int i= 1; i < data.length;i++) {
 			if (Double.isNaN(data[i])) {
-				System.out.println("NaN in getMaxXYCmEig() 2");
+				if (verbose) {
+					System.out.println("NaN in getMaxXYCmEig() 2");
+				}
 				return null;
 			}
 			if (data[i] > data[imax]) {

src/main/java/com/elphel/imagej/tileprocessor/OpticalFlow.java

@@ -51,6 +51,7 @@ import com.elphel.imagej.cameras.CLTParameters;
 import com.elphel.imagej.cameras.ColorProcParameters;
 import com.elphel.imagej.cameras.EyesisCorrectionParameters;
 import com.elphel.imagej.common.DoubleGaussianBlur;
+import com.elphel.imagej.common.LogTee;
 import com.elphel.imagej.common.PolynomialApproximation;
 import com.elphel.imagej.common.ShowDoubleFloatArrays;
 import com.elphel.imagej.correction.CorrectionColorProc;
@@ -4865,6 +4866,10 @@ public class OpticalFlow {
 		boolean [] annotate_mono_color = {clt_parameters.imp.annotate_mono,clt_parameters.imp.annotate_color}; 
 		boolean annotate_transparent_mono = clt_parameters.imp.annotate_transparent_mono;
 		
+		if ((index_scenes[0] != null) && (LogTee.getSceneLog()==null)) {
+			index_scenes[0].startLogging();
+		}
+		
 		
 		boolean [] generate_modes3d = {
 				clt_parameters.imp.generate_raw,
@@ -5431,7 +5436,18 @@ public class OpticalFlow {
 			if (index_scenes[1] == null) { // not yet implemented, to create an index of all sequences indices ) 
 				index_scenes[1] = quadCLTs[last_index];
 			}
-		}
+			if ((index_scenes[0] != null) && (LogTee.getSceneLog() == null)) {
+				index_scenes[0].startLogging();
+			}
+	   	}
+		/*
+  LogTee.install();         // once, early
+  LogTee.setSceneLog(path); // when you want to start per‑scene logging
+  LogTee.clearSceneLog();   // stop per‑scene logging
+  LogTee.getSceneLog()
+		 */
+		
+		
 		// reduce some conditions as they are implied by (operation_mode == RESULTS_BUILD_SEQ_LY)
 		// && run_ly && (run_ly_mode > 0)  && (run_ly_mode <= 3)  && is_first_scene 
 		boolean exec_ly_correction = (operation_mode == RESULTS_BUILD_SEQ_LY) && force_initial_orientations;
@@ -6275,7 +6291,19 @@ public class OpticalFlow {
 					threadsMax,                // final int        threadsMax,  // maximal number of threads to launch
 					updateStatus,              // final boolean    updateStatus,
 					debugLevel);               // final int        debugLevel)  throws Exception
-			oriented_scenes[oriented_ref_index].saveConfInModelDirectory(); // save all (global) configurations in model/version directory
+			
+//			oriented_scenes[oriented_ref_index].saveConfInModelDirectory(); // save all (global) configurations in model/version directory
+			// temporary fix save/restore linkedModels, sourceDirectory, sourcePaths
+			// that are copied main-> aux in EyesisCorrectionParameters.updateAuxFromMain()
+			// quadCLT_main.correctionsParameters
+
+			wrappedSaveConfInModelDirectory(
+			quadCLTs,     // QuadCLT [] quadCLTs,
+			quadCLT_main, // QuadCLT quadCLT_main,
+			master_CLT,   // QuadCLT master_CLT,
+			ref_index);   // int     ref_index)
+			
+			
 			// Copy LY calibration to the index scene (last in the sequence)
 			CorrVector corr_vector = oriented_scenes[oriented_ref_index].getGeometryCorrection().getCorrVector();
 			index_scenes[0].getGeometryCorrection().setCorrVector(corr_vector); // updated system corr vector with the current updated one
@@ -8037,6 +8065,14 @@ public class OpticalFlow {
 		// temporary fix save/restore linkedModels, sourceDirectory, sourcePaths
 		// that are copied main-> aux in EyesisCorrectionParameters.updateAuxFromMain()
 		// quadCLT_main.correctionsParameters
+		wrappedSaveConfInModelDirectory(
+		quadCLTs,     // QuadCLT [] quadCLTs,
+		quadCLT_main, // QuadCLT quadCLT_main,
+		master_CLT,   // QuadCLT master_CLT,
+		ref_index);   // int     ref_index)
+		/*
+		
+		
 		String bkp_linkedModels = quadCLT_main.correctionsParameters.linkedModels;
 		String bkp_linkedCenters = quadCLT_main.correctionsParameters.linkedCenters;
 ///		String bkp_cuasSeed = quadCLT_main.correctionsParameters.cuasSeed;
@@ -8054,9 +8090,6 @@ public class OpticalFlow {
     	double [] bkp_cuasCameraATR =       quadCLT_main.correctionsParameters.cuasCameraATR;    //{0, 0, 0};
     	double [] bkp_cuasUASHome =       quadCLT_main.correctionsParameters.cuasUASHome;    //{0, 0, 0};
 		boolean bkp_cuasSetHome = quadCLT_main.correctionsParameters.cuasSetHome;
-		
-		
-		
 		master_CLT.saveConfInModelDirectory(); // save all (global) configurations in model/version directory
 		if (master_CLT != quadCLTs[ref_index]) {
 			quadCLTs[ref_index].saveConfInModelDirectory(); // save all (global) configurations in model/version directory
@@ -8077,12 +8110,62 @@ public class OpticalFlow {
     	quadCLT_main.correctionsParameters.cuasUASHome =      bkp_cuasUASHome;
 		quadCLT_main.correctionsParameters.cuasSetHome =      bkp_cuasSetHome;
 		quadCLT_main.correctionsParameters.cuasSkyMask =      bkp_cuasSkyMask;
-		
+		*/
 		System.out.println("buildSeries(): DONE"); //
 //		String top_dir0=quadCLTs[ref_index].getX3dTopDirectory();
 		return quadCLTs[ref_index].getX3dTopDirectory(); // top_dir; // keep?
     }
     
+    
+    public void wrappedSaveConfInModelDirectory(
+    		QuadCLT [] quadCLTs,
+    		QuadCLT quadCLT_main,
+    		QuadCLT master_CLT,
+    		int     ref_index
+    		) {
+		// temporary fix save/restore linkedModels, sourceDirectory, sourcePaths
+		// that are copied main-> aux in EyesisCorrectionParameters.updateAuxFromMain()
+		// quadCLT_main.correctionsParameters
+    	
+    	String bkp_linkedModels = quadCLT_main.correctionsParameters.linkedModels;
+    	String bkp_linkedCenters = quadCLT_main.correctionsParameters.linkedCenters;
+    	///		String bkp_cuasSeed = quadCLT_main.correctionsParameters.cuasSeed;
+    	String bkp_cuasSeedDir = quadCLT_main.correctionsParameters.cuasSeedDir;
+    	String bkp_videoDirectory = quadCLT_main.correctionsParameters.videoDirectory;
+    	String bkp_x3dDirectory = quadCLT_main.correctionsParameters.x3dDirectory;
+    	String bkp_mlDirectory = quadCLT_main.correctionsParameters.mlDirectory;
+    	String bkp_sourceDirectory =  quadCLT_main.correctionsParameters.sourceDirectory;
+    	String [] bkp_sourcePaths =   quadCLT_main.correctionsParameters.sourcePaths;
+    	boolean bkp_use_set_dirs = quadCLT_main.correctionsParameters.use_set_dirs;
+    	String bkp_cuasUasLogs =            quadCLT_main.correctionsParameters.cuasUasLogs;      // TIFF image 640x512 where 1.0 - sky, 0.0 - ground, blurred with GB (now sigma==2.0)
+    	String bkp_cuasSkyMask =            quadCLT_main.correctionsParameters.cuasSkyMask;      // json file path containing UAS logs
+    	double bkp_cuasUasTimeStamp =       quadCLT_main.correctionsParameters.cuasUasTimeStamp; // 0.0; // timestamp corresponding to the UAS time 0.0
+    	double [] bkp_cuasCameraATR =       quadCLT_main.correctionsParameters.cuasCameraATR;    //{0, 0, 0};
+    	double [] bkp_cuasUASHome =       quadCLT_main.correctionsParameters.cuasUASHome;    //{0, 0, 0};
+    	boolean bkp_cuasSetHome = quadCLT_main.correctionsParameters.cuasSetHome;
+    	master_CLT.saveConfInModelDirectory(); // save all (global) configurations in model/version directory
+    	if (master_CLT != quadCLTs[ref_index]) {
+    		quadCLTs[ref_index].saveConfInModelDirectory(); // save all (global) configurations in model/version directory
+    	}
+    	quadCLT_main.correctionsParameters.linkedModels =     bkp_linkedModels;
+    	quadCLT_main.correctionsParameters.linkedCenters =    bkp_linkedCenters;
+    	quadCLT_main.correctionsParameters.cuasSeedDir =      bkp_cuasSeedDir;
+    	quadCLT_main.correctionsParameters.videoDirectory =   bkp_videoDirectory;
+    	quadCLT_main.correctionsParameters.x3dDirectory =     bkp_x3dDirectory;
+    	quadCLT_main.correctionsParameters.mlDirectory =      bkp_mlDirectory;
+    	quadCLT_main.correctionsParameters.sourceDirectory =  bkp_sourceDirectory;
+    	quadCLT_main.correctionsParameters.sourceDirectory =  bkp_sourceDirectory;
+    	quadCLT_main.correctionsParameters.sourcePaths =      bkp_sourcePaths;
+    	quadCLT_main.correctionsParameters.use_set_dirs =     bkp_use_set_dirs;
+    	quadCLT_main.correctionsParameters.cuasUasLogs =      bkp_cuasUasLogs;   
+    	quadCLT_main.correctionsParameters.cuasUasTimeStamp = bkp_cuasUasTimeStamp;
+    	quadCLT_main.correctionsParameters.cuasCameraATR =    bkp_cuasCameraATR;
+    	quadCLT_main.correctionsParameters.cuasUASHome =      bkp_cuasUASHome;
+    	quadCLT_main.correctionsParameters.cuasSetHome =      bkp_cuasSetHome;
+    	quadCLT_main.correctionsParameters.cuasSkyMask =      bkp_cuasSkyMask;
+    	return;
+    }
+    
     public static double getImsDisparityCorrection(
     		QuadCLT []       quadCLTs,
     		QuadCLT          master_CLT,

src/main/java/com/elphel/imagej/tileprocessor/QuadCLTCPU.java

@@ -67,6 +67,7 @@ import com.elphel.imagej.cameras.EyesisCorrectionParameters;
 import com.elphel.imagej.cameras.ThermalColor;
 import com.elphel.imagej.common.DoubleGaussianBlur;
 import com.elphel.imagej.common.GenericJTabbedDialog;
+import com.elphel.imagej.common.LogTee;
 import com.elphel.imagej.common.PolynomialApproximation;
 import com.elphel.imagej.common.ShowDoubleFloatArrays;
 import com.elphel.imagej.correction.CorrectionColorProc;
@@ -111,6 +112,7 @@ public class QuadCLTCPU {
 	public static final String    ORIENTATION_LOGS_SUFFIX =  "-ORIENTATION.log";
 	public static final String    INTERFRAME_SUFFIX =        "-INTERFRAME";
 	public static final String    FIELD_CALIBRATION_SUFFIX = "-FIELD_CALIBRATION";
+	public static final String    SYSTEM_OUT_LOG_SUFFIX =    "-SYSTEM_OUT.log";
 	public static final String    CONFIGURATION_EXTENSION =  ".corr-xml";
 	
 	public static final String [] DSI_SUFFIXES = {"-INTER-INTRA-LMA","-INTER-INTRA","-DSI_MAIN"};
@@ -5417,6 +5419,24 @@ public class QuadCLTCPU {
         }
     }
     
+	/*
+LogTee.install();         // once, early
+LogTee.setSceneLog(path); // when you want to start per‑scene logging
+LogTee.clearSceneLog();   // stop per‑scene logging
+	 */
+    public void startLogging() {
+    	String x3d_path = getX3dTopDirectory();
+    	Path log_path = Paths.get(x3d_path).resolve(getImageName()+SYSTEM_OUT_LOG_SUFFIX);  
+    	try {
+			LogTee.setSceneLog(log_path);
+		} catch (IOException e) {
+			System.err.println("startLogging(): failed to start logging to "+x3d_path);
+		} // when you want to start per‑scene logging	
+    }
+    
+    public void stopLogging() {
+    	LogTee.clearSceneLog();   // stop per‑scene logging
+    }
     
     
     /**

src/main/java/com/elphel/imagej/tileprocessor/TwoQuadCLT.java

@@ -52,6 +52,7 @@ import com.elphel.imagej.cameras.CLTParameters;
 import com.elphel.imagej.cameras.ColorProcParameters;
 import com.elphel.imagej.cameras.EyesisCorrectionParameters;
 import com.elphel.imagej.common.GenericJTabbedDialog;
+import com.elphel.imagej.common.LogTee;
 import com.elphel.imagej.common.ShowDoubleFloatArrays;
 import com.elphel.imagej.correction.CorrectionColorProc;
 import com.elphel.imagej.correction.EyesisCorrections;
@@ -8614,6 +8615,7 @@ if (debugLevel > -100) return true; // temporarily !
 								threadsMax,                // final int        threadsMax,  // maximal number of threads to launch
 								updateStatus,              // final boolean    updateStatus,
 								debugLevel+2);             // final int        debugLevel)
+						LogTee.clearSceneLog();   // stop per‑scene logging
 						if (debugLevel > -4){
 							System.out.println("3. cuas_centers="+((cuas_centers != null)?("[\""+cuas_centers[0]+"\",\""+cuas_centers[1]+"\"]"):"null"));
 						}