Added support of command interruption.

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

@@ -1520,14 +1520,18 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		String label = e.getActionCommand();
 		if (label.equals("Abort")) {
 			this.SYNC_COMMAND.stopRequested.set(1);
+			this.SYNC_COMMAND.confirm = true;
 			return;
 		} else if (label.equals("Stop")) {
 			this.SYNC_COMMAND.stopRequested.set(2);
+			this.SYNC_COMMAND.confirm = true;
 			return;
 		}
 //		System.out.println("actionPerformed: SwingUtilities.isEventDispatchThread()="+SwingUtilities.isEventDispatchThread());
 		// executed in EDT, so no need to synchronize additionally?
 		if (this.SYNC_COMMAND.isRunning) {
+			this.SYNC_COMMAND.interruptCommand(); 
+			/*
 			GenericDialog gd = new GenericDialog("Busy");
 			gd.addMessage("Command \"" + this.SYNC_COMMAND.buttonLabel + "\" is running. Ask it to stop "
 					+ ((this.SYNC_COMMAND.stopRequested.get() != 0) ? "(again!) " : "") + "(when possible)?");
@@ -1536,6 +1540,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			if (gd.wasCanceled())
 				return;
 			this.SYNC_COMMAND.stopRequested.set(gd.wasOKed() ? 1 : 2);
+			*/
 			return;
 		}
 		synchronized (this.SYNC_COMMAND) {
@@ -7742,7 +7747,9 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		CLT_PARAMETERS.setRGBParameters(RGB_PARAMETERS);
 
 		try {
-			TWO_QUAD_CLT.batchLwirRig(QUAD_CLT, // QuadCLT quadCLT_main,
+			TWO_QUAD_CLT.batchLwirRig(
+					SYNC_COMMAND,  // SyncCommand sync_command,
+					QUAD_CLT, // QuadCLT quadCLT_main,
 					QUAD_CLT_AUX, // QuadCLT quadCLT_aux,
 					CLT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters,
 					COLOR_PROC_PARAMETERS, // EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
@@ -7829,6 +7836,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		ColorProcParameters colorProcParameters = use_aux ? COLOR_PROC_PARAMETERS_AUX : COLOR_PROC_PARAMETERS;
 		try {
 			TWO_QUAD_CLT.TestInterScene(
+					SYNC_COMMAND,  // SyncCommand sync_command,
 					// use_aux, // boolean is_aux,
 					quadCLT, // QUAD_CLT, // QuadCLT quadCLT_main,
 					// QUAD_CLT_AUX, // QuadCLT quadCLT_aux,
@@ -7922,6 +7930,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		
 		try {
 			TwoQuadCLT.buildSeriesTQ(
+					SYNC_COMMAND,               // SyncCommand sync_command,
 					cuas_proc_mode,             // int  cuas_proc_mode, // 0 - old, 1 combine scene series
 					quadCLT,                    // QUAD_CLT, // QuadCLT quadCLT_main,
 					-1,                         // int  ref_index,
@@ -8102,7 +8111,9 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		QuadCLT quadCLT = use_aux ? QUAD_CLT_AUX : QUAD_CLT;
 		ColorProcParameters colorProcParameters = use_aux ? COLOR_PROC_PARAMETERS_AUX : COLOR_PROC_PARAMETERS;
 		try {
-			TWO_QUAD_CLT.TestInterLMA(quadCLT, // QUAD_CLT, // QuadCLT quadCLT_main,
+			TWO_QUAD_CLT.TestInterLMA(
+					SYNC_COMMAND,  // SyncCommand sync_command,
+					quadCLT, // QUAD_CLT, // QuadCLT quadCLT_main,
 					CLT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters,
 					colorProcParameters, // COLOR_PROC_PARAMETERS, //EyesisCorrectionParameters.ColorProcParameters
 					CHANNEL_GAINS_PARAMETERS, // CorrectionColorProc.ColorGainsParameters channelGainParameters,
@@ -8187,7 +8198,9 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		QuadCLT quadCLT = use_aux ? QUAD_CLT_AUX : QUAD_CLT;
 		ColorProcParameters colorProcParameters = use_aux ? COLOR_PROC_PARAMETERS_AUX : COLOR_PROC_PARAMETERS;
 		try {
-			TWO_QUAD_CLT.interPairsLMA(quadCLT, // QUAD_CLT, // QuadCLT quadCLT_main,
+			TWO_QUAD_CLT.interPairsLMA(
+					SYNC_COMMAND,  // SyncCommand sync_command,
+					quadCLT, // QUAD_CLT, // QuadCLT quadCLT_main,
 					CLT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters,
 					colorProcParameters, // COLOR_PROC_PARAMETERS, //EyesisCorrectionParameters.ColorProcParameters
 					CHANNEL_GAINS_PARAMETERS, // CorrectionColorProc.ColorGainsParameters channelGainParameters,
@@ -8271,7 +8284,9 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		QuadCLT quadCLT = use_aux ? QUAD_CLT_AUX : QUAD_CLT;
 		ColorProcParameters colorProcParameters = use_aux ? COLOR_PROC_PARAMETERS_AUX : COLOR_PROC_PARAMETERS;
 		try {
-			TWO_QUAD_CLT.interSeriesLMA(quadCLT, // QUAD_CLT, // QuadCLT quadCLT_main,
+			TWO_QUAD_CLT.interSeriesLMA(
+					SYNC_COMMAND,  // SyncCommand sync_command,
+					quadCLT, // QUAD_CLT, // QuadCLT quadCLT_main,
 					-1, // int  ref_index,
 					0,  // int  ref_step, 
 					CLT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters,
@@ -8358,7 +8373,9 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		QuadCLT quadCLT = use_aux ? QUAD_CLT_AUX : QUAD_CLT;
 		ColorProcParameters colorProcParameters = use_aux ? COLOR_PROC_PARAMETERS_AUX : COLOR_PROC_PARAMETERS;
 		try {
-			TWO_QUAD_CLT.intersceneAccumulate(quadCLT, // QUAD_CLT, // QuadCLT quadCLT_main,
+			TWO_QUAD_CLT.intersceneAccumulate(
+					SYNC_COMMAND,  // SyncCommand sync_command,
+					quadCLT, // QUAD_CLT, // QuadCLT quadCLT_main,
 					CLT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters,
 					colorProcParameters, // COLOR_PROC_PARAMETERS, //EyesisCorrectionParameters.ColorProcParameters
 					CHANNEL_GAINS_PARAMETERS, // CorrectionColorProc.ColorGainsParameters channelGainParameters,
@@ -8442,6 +8459,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		ColorProcParameters colorProcParameters = use_aux ? COLOR_PROC_PARAMETERS_AUX : COLOR_PROC_PARAMETERS;
 		try {
 			TWO_QUAD_CLT.interIntraExportML(
+					SYNC_COMMAND,              // SyncCommand sync_command,
 					quadCLT, // QuadCLT quadCLT_main,
 					-1, // use last // int  indx_ref,     // = num_scenes - 1; 
 					0,  // int                                                  ref_step, 
@@ -8528,7 +8546,9 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 
 		try {
 			if (batch_noise) {
-				TWO_QUAD_CLT.intersceneNoiseBatch(quadCLT, // QuadCLT quadCLT_main,
+				TWO_QUAD_CLT.intersceneNoiseBatch(
+						SYNC_COMMAND,  // SyncCommand sync_command,
+						quadCLT, // QuadCLT quadCLT_main,
 						CLT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters,
 						colorProcParameters, // EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
 						CHANNEL_GAINS_PARAMETERS, // CorrectionColorProc.ColorGainsParameters channelGainParameters,
@@ -8540,7 +8560,9 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 						UPDATE_STATUS, // final boolean updateStatus,
 						DEBUG_LEVEL);
 			} else {
-				TWO_QUAD_CLT.intersceneNoise(quadCLT, // QuadCLT quadCLT_main,
+				TWO_QUAD_CLT.intersceneNoise(
+						SYNC_COMMAND,  // SyncCommand sync_command,
+						quadCLT, // QuadCLT quadCLT_main,
 						CLT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters,
 						colorProcParameters, // EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
 						CHANNEL_GAINS_PARAMETERS, // CorrectionColorProc.ColorGainsParameters channelGainParameters,

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

@@ -2,8 +2,48 @@ package com.elphel.imagej.correction;
 
 import java.util.concurrent.atomic.AtomicInteger;
 
+import com.elphel.imagej.common.GenericJTabbedDialog;
+
 public class SyncCommand {
+	public static final int STOP_NO =         0;
+	public static final int STOP_ASAP =       1;
+	public static final int STOP_CONVENIENT = 2;
 	public boolean isRunning = false;
 	public AtomicInteger stopRequested = new AtomicInteger(0); // 0 - not requested, 1 - ASAP, 2 - gracefully
 	public String buttonLabel = "";
+	public boolean confirm = true;
+	
+	public boolean interruptCommand() {
+		boolean asap = false;
+		GenericJTabbedDialog gd = new GenericJTabbedDialog("Interrupt Command",600,300);
+		gd.addCheckbox ("Ask for confirmation",                              this.confirm,
+				"If checked, program will pause at a checkpoint allowing to cancel the stop request and continue.");
+		gd.addCheckbox ("ASAP",                                              asap,
+				"Stop ASAP.  If uncheked, stop at more convenient stage.");
+		gd.showDialog();
+		if (gd.wasCanceled()) 
+			return false;
+		this.confirm=               gd.getNextBoolean();
+		this.stopRequested.set(gd.getNextBoolean() ? STOP_ASAP : STOP_CONVENIENT );
+		return true;
+	}
+	public boolean stopNow(boolean convenient) {
+		if (stopRequested.get()==STOP_NO){
+			return false;
+		}
+		//if (stopRequested.get() ==)
+		if (!convenient && (stopRequested.get()==STOP_CONVENIENT)) {
+			return false;
+		}
+		if (!confirm) {
+			return true;
+		}
+		GenericJTabbedDialog gd = new GenericJTabbedDialog("Stop requested, "+(convenient?"convenient point":"ASAP point"),600,300);
+		gd.addMessage ("OK to stop, Cancel to continue");
+		stopRequested.set(STOP_NO); // reset pending stop in any case.
+		gd.showDialog();
+		if (gd.wasCanceled()) 
+			return false;
+		return true;
+	}
 }
\ No newline at end of file

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

@@ -225,7 +225,8 @@ public class GroundPlane {
 			final int        debugLevel) {
 	
 		final boolean [] good_tiles = new boolean[ref_scene.getTilesX()*ref_scene.getTilesY()];
-		String     dbg_title =ref_scene.getImageName()+"-ground_tilts"; 
+//		String     dbg_title =ref_scene.getImageName()+"-ground_tilts"; 
+		String     dbg_title ="-ground_tilts"; 
 		double [][] to_ground_xyzatr_frac= getPlaneDualPassMetric( // returns to_ground_xyzatr (rotated around the ground point nadir of teh drone)
 				clt_parameters,        // final CLTParameters    clt_parameters,
 				ref_scene,             // final QuadCLT    ref_Clt,
@@ -237,7 +238,6 @@ public class GroundPlane {
 		if (to_ground_xyzatr_frac == null) {
 			to_ground_xyzatr_frac = new double [][] {new double[3], new double[3], new double[1]};
 		}
-		
 		// To get terrain disparity (until rotation is fixed) use "good_tiles" from getPlaneDualPassMetric and re-calculate ground disparity plane
 		
 		double [][] to_ground_xyzatr = {to_ground_xyzatr_frac[0],to_ground_xyzatr_frac[1]};
@@ -254,18 +254,6 @@ public class GroundPlane {
 				dbg_title+"-disp",     // final String     dbg_title,
 				debugLevel); // final int        debugLevel)
 		
-/*		
-		double [] disparity_plane = getDisparityPlaneDualPass( // returns to_ground_xyzatr (rotated around the ground point nadir of the drone)
-				clt_parameters,        // final CLTParameters clt_parameters,
-				ref_scene,             // final QuadCLT    ref_Clt,
-				ref_scene.getTilesX(),// final int        width,
-				good_tiles,            // final boolean [] good_tiles, // null or boolean[data.length] // should all be false
-				gnd_disp,              // final double []  gnd_disp, // if not null
-				dbg_title+"-disp",     // final String     dbg_title,
-				debugLevel); // final int        debugLevel)
-*/		
-		
-		
 		return new GroundPlane(
 				to_ground_xyzatr,     // double [][] to_ground_xyzatr,
 				disparity_plane,      // double []   disparity_plane,
@@ -274,8 +262,6 @@ public class GroundPlane {
 				ref_scene.getQEnu()); // double []   quat_enu) {
 	}
 	
-	
-	
 	public static double [][] getPlaneDualPassMetric( // returns to_ground_xyzatr (rotated around the ground point nadir of teh drone)
 			final CLTParameters    clt_parameters,
 			final QuadCLT    ref_Clt,
@@ -547,19 +533,43 @@ public class GroundPlane {
      	double [][] virtual_camera_from_camera =     ErsCorrection.combineXYZATR(ground_xyzatr, virtual_camera_from_ground_xyz);
      	// FIXME: Next is correct (at least approximately, "-"/invert, order,), find out why
      	System.out.println("FIXME: Inverted X, Y, kept Z, and ATR. Find out why.");
-     	
+//     	double [][] vcfs_test = {
+//     			{-virtual_camera_from_camera[0][0], -virtual_camera_from_camera[0][1],  virtual_camera_from_camera[0][2]},
+//     			{ virtual_camera_from_camera[1][0],  virtual_camera_from_camera[1][1],  virtual_camera_from_camera[1][2]}};
      	double [][] vcfs_test = {
-     			{-virtual_camera_from_camera[0][0], -virtual_camera_from_camera[0][1],  virtual_camera_from_camera[0][2]},
-     			{ virtual_camera_from_camera[1][0],  virtual_camera_from_camera[1][1],  virtual_camera_from_camera[1][2]}};
+     			{virtual_camera_from_camera[0][0], virtual_camera_from_camera[0][1],  virtual_camera_from_camera[0][2]},
+     			{ to_ground_xyzatr[1][0],  to_ground_xyzatr[1][1],  to_ground_xyzatr[1][2]}};
      	
      	if ((dbg_title != null) || (gnd_disp != null)) {
      		// expand macrotiles results to match tiles
      		// rotate ref_disparity and show
+     		/*
      		double [][] pXpYD_ground = OpticalFlow.transformToScenePxPyD(
      				null,                      // final Rectangle   full_woi_in,      // show larger than sensor WOI (or null) IN TILES
      				ref_disparity,             // final double []   disparity_ref,    // invalid tiles - NaN in disparity
      				vcfs_test, // virtual_camera_from_camera,// final double [][] scene_xyzatr,     // camera center in world coordinates, camera orientation relative to world frame
      				ref_Clt);                  // final QuadCLT     scene_QuadClt)
+     		*/
+     		double [][] fgnd_pXpYD = OpticalFlow.refDisparityFromGroundDisparity(
+     				ref_disparity, // final double [] ground_disparity,
+     				vcfs_test,     // final double [][] ground_xyzatr,   		
+     				ref_Clt);      //final QuadCLT ref_scene)
+     		double [][] pXpYD_ground = OpticalFlow.transformToScenePxPyD(
+					fgnd_pXpYD,         // final double [][] reference_pXpYD,// invalid tiles - NaN in disparity. Should be no nulls, no NaN disparity
+					ground_xyzatr[0],   // final double []   scene_xyz,         // camera center in world (reference) coordinates
+					ground_xyzatr[1],   // final double []   scene_atr,         // camera orientation relative to world (reference) frame
+					ref_Clt,          // final QuadCLT     reference_QuadClt) //
+					null);              // final QuadCLT     scene_QuadClt) //
+     		
+/*
+			ref_pXpYD = OpticalFlow.transformToScenePxPyD(
+					fgnd_pXpYD,         // final double [][] reference_pXpYD,// invalid tiles - NaN in disparity. Should be no nulls, no NaN disparity
+					ground_xyzatr[0],   // final double []   scene_xyz,         // camera center in world (reference) coordinates
+					ground_xyzatr[1],   // final double []   scene_atr,         // camera orientation relative to world (reference) frame
+					ref_scene,          // final QuadCLT     reference_QuadClt) //
+					null);              // final QuadCLT     scene_QuadClt) //
+     		
+ */
      		double [] gnd_disparity = (gnd_disp != null) ? gnd_disp.clone() : new double [ref_disparity.length];
      		Arrays.fill(gnd_disparity, Double.NaN);
      		for (int i = 0; i <ref_disparity.length; i++) {

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

@@ -5437,6 +5437,8 @@ LogTee.clearSceneLog();   // stop per‑scene logging
 		} catch (IOException e) {
 			System.err.println("startLogging(): failed to start logging to "+x3d_path);
 		} // when you want to start per‑scene logging	
+    	System.out.println("\n***** STARTING LOGGING: "+
+    			(new SimpleDateFormat("yyyy/MM/dd HH:mm:ss").format(Calendar.getInstance().getTime())+" *****\n"));
     }
     
     public void stopLogging() {