Updating batch mode of the 3d scene processing

src/main/java/CorrectionColorProc.java

@@ -25,12 +25,12 @@
 **
 */
 
-import ij.ImageStack;
-import ij.gui.GenericDialog;
-
 import java.util.Properties;
 import java.util.concurrent.atomic.AtomicInteger;
 
+import ij.ImageStack;
+import ij.gui.GenericDialog;
+
 
 public class CorrectionColorProc {
 	showDoubleFloatArrays SDFA_INSTANCE=   new showDoubleFloatArrays();
@@ -241,7 +241,7 @@ public class CorrectionColorProc {
     		//TODO: null DENOISE_MASK if it is not calculated
     		if (colorProcParameters.combineWithSharpnessMask) {
     			if (denoiseMask==null) {
-    				System.out.println ( "Can not combine masks as denoiseMask is null (i.e. no denoise was performed)");
+    				System.out.println ( "Can not combine masks as denoiseMask is null (i.e. no denoise was performed)"); // here
     			} else if (denoiseMask.length!=dmask.length) {
     				System.out.println ( "Can not combine masks as denoiseMask length is different from that of dmask");
     			} else {

src/main/java/EyesisCorrectionParameters.java

@@ -3004,6 +3004,9 @@ public class EyesisCorrectionParameters {
   		public HashMap<String,Double> z_corr_map = new HashMap<String,Double>();
   		public static String Z_CORR_PREFIX = "z_corr.";
 
+  		public boolean   batch_run =               false; // turned on only while running in batch mode
+
+
 
   		public CLTParameters(){}
   		public void setProperties(String prefix,Properties properties){

src/main/java/EyesisDCT.java

@@ -25,7 +25,6 @@
 import java.util.Properties;
 import java.util.concurrent.atomic.AtomicInteger;
 
-
 import ij.CompositeImage;
 import ij.IJ;
 import ij.ImagePlus;
@@ -150,6 +149,7 @@ public class EyesisDCT {
 		  System.out.println("calculateDCTKernel():numberOfKernels="+numberOfKernels);
 		  for (int ithread = 0; ithread < threads.length; ithread++) {
 			  threads[ithread] = new Thread() {
+				  @Override
 				public void run() {
 					  DoubleGaussianBlur gb=null;
 					  if (dct_parameters.decimateSigma > 0)	 gb=new DoubleGaussianBlur();
@@ -1439,7 +1439,9 @@ public class EyesisDCT {
 		  }
 
 		  if (toRGB) {
+			  if (debugLevel > 0){
 				  System.out.println("correctionColorProc.YPrPbToRGB");
+			  }
 			  stack =  YPrPbToRGB(yPrPb,
 					  colorProcParameters.kr,        // 0.299;
 					  colorProcParameters.kb,        // 0.114;
@@ -1636,6 +1638,7 @@ public class EyesisDCT {
 
 		  for (int ithread = 0; ithread < threads.length; ithread++) {
 			  threads[ithread] = new Thread() {
+				  @Override
 				public void run() {
 					  int tileY,tileX;
 					  double [] neibs =   new double[9]; // pixels around current, first Y, then each color diff
@@ -1749,6 +1752,7 @@ public class EyesisDCT {
 
 		  for (int ithread = 0; ithread < threads.length; ithread++) {
 			  threads[ithread] = new Thread() {
+				  @Override
 				public void run() {
 					  int tileY,tileX;
 					  double [] neibs =   new double[9]; // pixels around current, first Y, then each color diff

src/main/java/Eyesis_Correction.java

@@ -776,7 +776,7 @@ private Panel panel1,
 	Runtime runtime = Runtime.getRuntime();
     runtime.gc();
 	if (DEBUG_LEVEL>0) System.out.println("--- Free memory="+runtime.freeMemory()+" (of "+runtime.totalMemory()+")");
-
+	CLT_PARAMETERS.batch_run = false;
     if (label==null) return;
 /* ======================================================================== */
     if (label.equals("Configure spilt")) {
@@ -5051,7 +5051,6 @@ private Panel panel1,
         		RGB_PARAMETERS,  // EyesisCorrectionParameters.RGBParameters             rgbParameters,
         		THREADS_MAX,     // final int          threadsMax,  // maximal number of threads to launch
         		UPDATE_STATUS,   // final boolean    updateStatus,
-        		false,           // final boolean    batch_mode,
         		DEBUG_LEVEL); //final int        debugLevel);
         if (!OK) {
         	String msg="Image data not initialized, run 'CLT 3D' command first";
@@ -5059,18 +5058,9 @@ private Panel panel1,
         	IJ.showMessage("Error",msg);
         }
 
-/*
-        if (configPath!=null) {
-        	saveTimestampedProperties( // save config again
-        			configPath,      // full path or null
-        			null, // use as default directory if path==null
-        			true,
-        			PROPERTIES);
-        }
-
-*/
     } else if (label.equals("CLT batch process")) {
     	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
+        CLT_PARAMETERS.batch_run = true;
     	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
         if (QUAD_CLT == null){
         	QUAD_CLT = new  QuadCLT (

src/main/java/MacroCorrelation.java

@@ -269,7 +269,7 @@ public class MacroCorrelation {
 				clt_parameters.corr_magic_scale, // still not understood coefficient that reduces reported disparity value.  Seems to be around 0.85
 				clt_parameters.shift_x,       // final int               shiftX, // shift image horizontally (positive - right) - just for testing
 				clt_parameters.shift_y,       // final int               shiftY, // shift image vertically (positive - down)
-				31, // clt_parameters.tileX,         // final int               debug_tileX,
+				clt_parameters.batch_run? -1: 31, // clt_parameters.tileX,         // final int               debug_tileX,
 				10, // clt_parameters.tileY,         // final int               debug_tileY,
 				(clt_parameters.dbg_mode & 64) != 0, // no fract shift
 				true,                        // no convolve

src/main/java/MeasuredLayers.java

@@ -732,7 +732,7 @@ public class MeasuredLayers {
 		int st2 = 2 * superTileSize;
 		int st_half = superTileSize/2;
 		double [][] ds = new double [2][st2*st2];
-		final int dbg_tile = ((stX == 22) && (stY == 19)) ? (5 + 7*16) : -1;// 50397;
+		final int dbg_tile = -1; // = ((stX == 22) && (stY == 19)) ? (5 + 7*16) : -1;// 50397;
 
 		int num_selected = 0;
 		int smpl_center = mlfp.smplSide /2;
@@ -1023,7 +1023,7 @@ public class MeasuredLayers {
 		int st2 = 2 * superTileSize;
 		int st_half = superTileSize/2;
 		double [][] ds = new double [2][st2*st2];
-		final int dbg_tile = ((stX == 22) && (stY == 19)) ? (5 + 7*16) : -1;// 50397;
+		final int dbg_tile =-1; //  ((stX == 22) && (stY == 19)) ? (5 + 7*16) : -1;// 50397;
 
 		int num_selected = 0;
 		int smpl_center = mlfp.smplSide /2;

src/main/java/SuperTiles.java

@@ -663,9 +663,9 @@ public class SuperTiles{
 							int numMax = 0;
 							int lo = 0;
 							int hi = 1;
-							if ((globalDebugLevel > -1 ) && (nsTile == 795)) {
-								System.out.println(nsTile);
-							}
+//							if ((globalDebugLevel > -1 ) && (nsTile == 795)) {
+//								System.out.println("getMaxMinMax(): nsTile="+nsTile);
+//							}
 							while (hi < numBins) {
 								// looking for next max
 								while ((hi < numBins) && (dh[hi] >= dh[hi - 1])) hi++; // flat or higher - continue
@@ -949,9 +949,9 @@ public class SuperTiles{
 			}
 		}
 		for (int nsTile = 0; nsTile < sTiles; nsTile++){
-			if (nsTile == 795){
-				System.out.println("showMaxMinMax(), nsTile="+nsTile);
-			}
+//			if (nsTile == 795){
+//				System.out.println("showMaxMinMax(), nsTile="+nsTile);
+//			}
 			int stileY = nsTile / sTilesX;
 			int stileX = nsTile % sTilesX;
 			int x0 = stileX * (numBins + 1);
@@ -1580,6 +1580,9 @@ public class SuperTiles{
 		final double [][][][] plane_disp_strength = new double [nStiles][][][];
 		// DEBUG feature:
 		final double [][] zero_tilts = {{0.0,0.0}}; // set to null for float
+		if (debugLevel > -1) {
+			System.out.println("getPlaneDispStrengthsST(x): debugLevel == "+debugLevel);
+		}
 		for (int ithread = 0; ithread < threads.length; ithread++) {
 			threads[ithread] = new Thread() {
 				@Override

src/main/java/TileAssignment.java

@@ -175,6 +175,7 @@ diff_best= 0.06731 diff9=  1.09087 weak_fgnd= 0.22250 flaps= 0.07229 ml_mismatch
 			return titles;
 		}
 
+		@Override
 		public String toString()
 		{
 			String s = "";
@@ -334,6 +335,7 @@ diff_best= 0.06731 diff9=  1.09087 weak_fgnd= 0.22250 flaps= 0.07229 ml_mismatch
 		final AtomicInteger ai = new AtomicInteger(0);
 		for (int ithread = 0; ithread < threads.length; ithread++) {
 			threads[ithread] = new Thread() {
+				@Override
 				public void run() {
 					for (int nSurfTile = ai.getAndIncrement(); nSurfTile < tone_diff_weight.length; nSurfTile = ai.getAndIncrement()) {
 						if (nSurfTile >= 0){
@@ -383,6 +385,7 @@ diff_best= 0.06731 diff9=  1.09087 weak_fgnd= 0.22250 flaps= 0.07229 ml_mismatch
 
 		for (int ithread = 0; ithread < threads.length; ithread++) {
 			threads[ithread] = new Thread() {
+				@Override
 				public void run() {
 					for (int dir = ai.getAndIncrement(); dir < 4; dir = ai.getAndIncrement()) {
 						for (int nSurfTile = 0; nSurfTile < num_tiles; nSurfTile++){
@@ -803,7 +806,7 @@ diff_best= 0.06731 diff9=  1.09087 weak_fgnd= 0.22250 flaps= 0.07229 ml_mismatch
 	{
 		TACosts costs = new TACosts();
 		int debugLevel = 0;
-		if (nSurfTile == 51360) { //  44831) { // 47459){
+		if (nSurfTile == -51360) { //  44831) { // 47459){
 			System.out.println("getTileCosts() nSurfTile="+nSurfTile);
 			debugLevel = 1;
 		}
@@ -1093,6 +1096,7 @@ diff_best= 0.06731 diff9=  1.09087 weak_fgnd= 0.22250 flaps= 0.07229 ml_mismatch
 		if (noEdge) {
 			for (int ithread = 0; ithread < threads.length; ithread++) {
 				threads[ithread] = new Thread() {
+					@Override
 					public void run() {
 						for (int nSurfTile = ai.getAndIncrement(); nSurfTile < num_tiles; nSurfTile = ai.getAndIncrement()) {
 							if (tileData[nSurfTile] != null){
@@ -1122,6 +1126,7 @@ diff_best= 0.06731 diff9=  1.09087 weak_fgnd= 0.22250 flaps= 0.07229 ml_mismatch
 				ai_numThread.set(0);
 				for (int ithread = 0; ithread < threads.length; ithread++) {
 					threads[ithread] = new Thread() {
+						@Override
 						public void run() {
 							int numThread = ai_numThread.getAndIncrement(); // unique number of thread to write to rslt_diffs[numThread]
 							for (int iTile = ai.getAndIncrement(); iTile < tile_indices[fnSeries].length; iTile = ai.getAndIncrement()) {
@@ -1305,6 +1310,7 @@ diff_best= 0.06731 diff9=  1.09087 weak_fgnd= 0.22250 flaps= 0.07229 ml_mismatch
 		if (noEdge) {
 			for (int ithread = 0; ithread < threads.length; ithread++) {
 				threads[ithread] = new Thread() {
+					@Override
 					public void run() {
 						for (int nSurfTile = ai.getAndIncrement(); nSurfTile < num_tiles; nSurfTile = ai.getAndIncrement()) {
 							if (tileData[nSurfTile] != null){
@@ -1334,6 +1340,7 @@ diff_best= 0.06731 diff9=  1.09087 weak_fgnd= 0.22250 flaps= 0.07229 ml_mismatch
 				ai_numThread.set(0);
 				for (int ithread = 0; ithread < threads.length; ithread++) {
 					threads[ithread] = new Thread() {
+						@Override
 						public void run() {
 							int numThread = ai_numThread.getAndIncrement(); // unique number of thread to write to rslt_diffs[numThread]
 							for (int iTile = ai.getAndIncrement(); iTile < tile_indices[fnSeries].length; iTile = ai.getAndIncrement()) {

src/main/java/TilePlanes.java

@@ -3504,12 +3504,14 @@ public class TilePlanes {
 				System.out.println("mergePlaneToThisWorld()");
 			}
 			if (wvalues == null ) {
+				if (debugLevel > -2) {
 					System.out.println("mergePlaneToThisWorld(): wvalues=null:\n"+toString());
+				}
 				return null;
 
 			}
 			if (otherPd.wvalues == null ) {
-				System.out.println("mergePlaneToThisWorld(): otherPd.wvalues=null:\n"+otherPd.toString());
+				if (debugLevel > -1) System.out.println("mergePlaneToThisWorld(): otherPd.wvalues=null:\n"+otherPd.toString());
 				return null;
 			}
 			double [][] this_eig_avals = {
@@ -4036,6 +4038,9 @@ public class TilePlanes {
 			if (debugLevel > 2) {
 				debugLevel += 0; // +=1 // no show all eigen stuff (debugLevel > 3)
 			}
+			if (debugLevel > 0) {
+				System.out.println("Debug debugLevel"); // +=1 // no show all eigen stuff (debugLevel > 3)
+			}
 
 			// first make a plane from all tiles
 			ArrayList<PlaneData> st_planes = new ArrayList<PlaneData>();

src/main/java/TileProcessor.java

@@ -4572,9 +4572,10 @@ public class TileProcessor {
 			GeometryCorrection geometryCorrection,
 			final int         threadsMax,  // maximal number of threads to launch
 			final boolean     updateStatus,
-			final boolean     batch_mode,
+//			final boolean     batch_mode,
 			final int         debugLevel)
 	{
+		final boolean    batch_mode = clt_parameters.batch_run;
 		final int debugLevelInner =  batch_mode ? -5: debugLevel;
 		trimCLTPasses(); // make possible to run this method multiple times - remove extra passes added by it last time
 		CLTPass3d scan_prev = clt_3d_passes.get(clt_3d_passes.size() -1); // get last one
@@ -5140,9 +5141,9 @@ public class TileProcessor {
 			GeometryCorrection geometryCorrection,
 			final int         threadsMax,  // maximal number of threads to launch
 			final boolean     updateStatus,
-			final boolean     batch_mode,
 			final int         debugLevel)
 	{
+		final boolean                       batch_mode = clt_parameters.batch_run; //disable any debug images
 		trimCLTPasses(); // make possible to run this method multiple time - remove extra passes added by it last time
 		CLTPass3d scan_prev = clt_3d_passes.get(clt_3d_passes.size() -1); // get last one
 
@@ -5311,7 +5312,7 @@ public class TileProcessor {
 				clt_parameters.stHighMix,       // stHighMix         = 0.4;   // Consider merging initial planes if jumps between ratio above
 				world_hor,                      // final double []  world_hor, // horizontal plane normal (default [0.0, 1.0, 0.0])
 				clt_parameters.show_histograms, // final boolean    show_histograms,
-				1, // -1,                       // debugLevel,                  // final int        debugLevel)
+				clt_parameters.batch_run?-1:1, // -1,                       // debugLevel,                  // final int        debugLevel)
 				clt_parameters.tileX,
 				clt_parameters.tileY);
 //		showDoubleFloatArrays sdfa_instance = null;
@@ -5334,7 +5335,7 @@ public class TileProcessor {
 		lp.conditionSuperTiles(
 				st.planes,              // final TilePlanes.PlaneData [][] planes,
 				10,                 // final int   max_num_merge_try,
-				0); // 1); // debugLevel);        // final int         debugLevel);
+				clt_parameters.batch_run?-2:0); // 1); // debugLevel);        // final int         debugLevel);
 // Used only by conflicts (not processed currently)
 		lp.calcStarValueStrength(
 				true, // boolean set_start_planes,
@@ -5398,7 +5399,7 @@ public class TileProcessor {
 
 					clt_parameters.plDiscrXMedian,    // final double     plDiscrXMedian, //         = 1.5;   // Remove outliers from the final selection that have distance more than scaled median
 					debugLevel, // -1,                         // debugLevel,                  // final int        debugLevel)
-					clt_parameters.tileX,
+					clt_parameters.batch_run ? -1 : clt_parameters.tileX, // clt_parameters.tileX,
 					clt_parameters.tileY);
 
 			// condition the redefined planes
@@ -6064,9 +6065,9 @@ public class TileProcessor {
 			GeometryCorrection geometryCorrection,
 			final int         threadsMax,  // maximal number of threads to launch
 			final boolean     updateStatus,
-			final boolean     batch_mode,
 			final int         debugLevel)
 	{
+		final boolean                       batch_mode = clt_parameters.batch_run; //disable any debug images
 		int debugLevelInner = batch_mode ? -5: debugLevel;
 		CLTPass3d scan_bg =   clt_3d_passes.get(bg_scan_index); //
 		CLTPass3d scan_prev = clt_3d_passes.get(clt_3d_passes.size() -1); // get last one
@@ -6146,7 +6147,7 @@ public class TileProcessor {
 					true,  // final boolean     keep_raw_fg,  // do not replace raw tiles by the plates, if raw is closer (like poles)
 					0.0, // 					final double      scale_filtered_strength_pre, // scale plate_ds[1] before comparing to raw strength
 					0.0,// final double      scale_filtered_strength_post,// scale plate_ds[1] when replacing raw (generally plate_ds is more reliable if it exists)
-					true, // clt_parameters.show_filter_scan,
+					batch_mode, // true, // clt_parameters.show_filter_scan,
 					clt_parameters.min_clstr_seed, // clt_parameters.min_clstr_seed
 					clt_parameters.min_clstr_weight,  // double     min_weight // minimal total weight of the cluster
 					clt_parameters.min_clstr_max,    // double     min_max_weight // minimal value of the maximal strengh in the cluster