Merge branch 'lwir-distort' of git.elphel.com:Elphel/imagej-elphel into lwir-distort

src/main/java/com/elphel/imagej/calibration/Aberration_Calibration.java

@@ -10465,6 +10465,7 @@ if (MORE_BUTTONS) {
         String [][] sourceFilesList=LWIR_PARAMETERS.getSourceFiles(sourceSetList, sel_chn);
         boolean saveGrids=DISTORTION_PROCESS_CONFIGURATION.saveGridImages;
         boolean overwriteGrids=DISTORTION_PROCESS_CONFIGURATION.overwriteResultFiles;
+        int minGridFileSize = PATTERN_DETECT.minGridFileSize;
         if (sourceSetList==null) return;
         showPatternMinMaxPeriodDialog(PATTERN_DETECT, true);
         int saved_file = 0;
@@ -10485,7 +10486,8 @@ if (MORE_BUTTONS) {
         		if (!set_dir.exists()) {
         			set_dir.mkdirs(); // including parent
         		}
-        	}
+        	}        						
+
 
         	for (int nfile = 0; nfile < sourceFilesList[nset].length; nfile++) if (sourceFilesList[nset][nfile] != null){
         		in_file++;
@@ -10497,7 +10499,7 @@ if (MORE_BUTTONS) {
         		}
         		String grid_path = null;
         		/*
-        		if (saveGrids && !overwriteGrids){ // check if result already exists
+        		if (saveGrids && !ovminGridFileSizeerwriteGrids){ // check if result already exists
         			i = sourceFilesList[nset][nfile].lastIndexOf('/');
         			if (i>0){
         				String grid_name = prefix+sourceFilesList[nset][nfile].substring(i+1);
@@ -10508,6 +10510,7 @@ if (MORE_BUTTONS) {
     					}
         			}
         		}
+        		patternDetectParameters.minGridFileSize
         		 */
 
         		if (saveGrids){ // check if result already exists
@@ -10515,10 +10518,23 @@ if (MORE_BUTTONS) {
         			if (i>0){
         				String grid_name = prefix+sourceFilesList[nset][nfile].substring(i+1);
         				grid_path = gridSetPath + Prefs.getFileSeparator() + grid_name;
-        				if (!overwriteGrids && ((new File(grid_path)).exists())){ // check if result already exists
-    						if (DEBUG_LEVEL>0) System.out.println("-->>> Skipping existing "+grid_path+" (as requested in \"Configure Process Distortions\")");
-    						continue;
-    					}
+        				File grid_file = new File(grid_path);
+        				if (!overwriteGrids && (grid_file.exists())){ // check if result already exists
+        					if (grid_file.length() >= minGridFileSize) {
+        						if (DEBUG_LEVEL>0) {
+        							System.out.println("-->>> Skipping existing large enough ("+(grid_file.length())+
+        									" bytes >= "+minGridFileSize+" bytes)"+grid_path+" (as requested in \"Configure Process Distortions\")");
+        						}
+        						continue;
+        					} else {
+        						if (DEBUG_LEVEL>0) {
+        							System.out.println("-->>> Deleting small ("+(grid_file.length())+
+        									" bytes < "+minGridFileSize+" bytes)"+grid_path+" (as requested in \"Configure Process Distortions\")");
+        							grid_file.delete();
+        						}
+        						
+        					}
+        				}
         			}
         		}
         		imp_sel=new ImagePlus(sourceFilesList[nset][nfile]); // read source file
@@ -10549,7 +10565,10 @@ if (MORE_BUTTONS) {
         				noMessageBoxes);
 
         		if (DEBUG_LEVEL>1) System.out.println("numAbsolutePoints="+numAbsolutePoints);
-        		if ((numAbsolutePoints==DISTORTION.errPatternNotFound) || (numAbsolutePoints==DISTORTION.errTooFewCells)) {
+        		if ((numAbsolutePoints==DISTORTION.errPatternNotFound) ||
+        				(numAbsolutePoints==DISTORTION.errTooFewCells) ||
+        				(numAbsolutePoints==DISTORTION.errRefineFailed)
+        				) {
         			if (DEBUG_LEVEL>0) System.out.println("Grid "+(in_file)+" not found or too small ("+numAbsolutePoints+"), wasted "+
         					IJ.d2s(0.000000001*(System.nanoTime()-startFileTime),3)+" seconds )\n");
         			if (this.SYNC_COMMAND.stopRequested.get()>0) {
@@ -21107,6 +21126,9 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
 			gd.addNumericField("Minimal pattern grid period for LWIR sensors (<=0.0 - do not check)" ,         patternDetectParameters.minGridPeriodLwir, 2,5,"pix");
 			gd.addNumericField("Maximal pattern grid period for LWIR sensors (<=0.0 - do not check)" ,         patternDetectParameters.maxGridPeriodLwir, 2,5,"pix");
 		}
+		gd.addNumericField("Minimal grid file size to overwrite" ,         patternDetectParameters.minGridFileSize, 0, 8, "bytes");
+		//		public double minGridFileSize = 25000; // Minimal file size (to overwirite) 
+
 		gd.showDialog();
 		if (gd.wasCanceled()) return false;
 		patternDetectParameters.minGridPeriod=            gd.getNextNumber();
@@ -21115,6 +21137,7 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
 			patternDetectParameters.minGridPeriodLwir=            gd.getNextNumber();
 			patternDetectParameters.maxGridPeriodLwir=            gd.getNextNumber();
 		}
+		patternDetectParameters.minGridFileSize = (int) gd.getNextNumber();
 		return true;
 	}
 

src/main/java/com/elphel/imagej/calibration/MatchSimulatedPattern.java

@@ -4372,11 +4372,13 @@ public class MatchSimulatedPattern {
 									continue;
 								} else if ((refCell[0] != null) && (refCell[0].length > 3)) {
 									double dbg_contrast = (refCell[0].length > 2) ? refCell[0][2] : Double.NaN;
-									System.out.println("**** refCell was deleted **** u=" + iUVRef[0] + " v="
-											+ iUVRef[1] + " current=" + iUVdir[0] + "/" + iUVdir[1] + " ncell=" + ncell
-											+ " waveFrontList.size()=" + waveFrontList.size() + " ref_x="
-											+ IJ.d2s(refCell[0][0], 3) + " ref_y=" + IJ.d2s(refCell[0][1], 3)
-											+ " contrast=" + IJ.d2s(dbg_contrast, 3));
+									if (debugLevel > debugThreshold) {
+										System.out.println("**** refCell was deleted **** u=" + iUVRef[0] + " v="
+												+ iUVRef[1] + " current=" + iUVdir[0] + "/" + iUVdir[1] + " ncell=" + ncell
+												+ " waveFrontList.size()=" + waveFrontList.size() + " ref_x="
+												+ IJ.d2s(refCell[0][0], 3) + " ref_y=" + IJ.d2s(refCell[0][1], 3)
+												+ " contrast=" + IJ.d2s(dbg_contrast, 3));
+									}
 								}
 								// found reference cell, calculate x/y, make sure it is inside the selection w/o
 								// borders
@@ -6855,7 +6857,7 @@ public class MatchSimulatedPattern {
 				IJ.showMessage("Error", "Pattern not found");
 			return distortionParameters.errPatternNotFound;
 		} else {
-			if (global_debug_level > (debugThreshold + 1))
+			if (global_debug_level > 0) // (debugThreshold + 1))
 				System.out.println("Initial pattern cluster has " + patternCells + " cells");
 		}
 		if (global_debug_level > (debugThreshold + 1))
@@ -6878,7 +6880,7 @@ public class MatchSimulatedPattern {
 			imp_eq = imp;
 
 		if (distortionParameters.refineCorrelations) {
-			refineDistortionCorrelation(
+			double maxActualCorr = refineDistortionCorrelation(
 					lwirReaderParameters, // LwirReaderParameters lwirReaderParameters, // null is OK
 					distortionParameters, //
 					patternDetectParameters,
@@ -6889,7 +6891,10 @@ public class MatchSimulatedPattern {
 					threadsMax,
 					updateStatus,
 					debug_level); // debug level
-
+			System.out.println(".... maxActualCorr="+maxActualCorr);
+			if (maxActualCorr <= 0.0) {
+				return distortionParameters.errRefineFailed; // 2021
+			}
 			recalculateWaveVectors(
 					updateStatus,
 					debug_level);// debug level used inside loops
@@ -10560,6 +10565,7 @@ public class MatchSimulatedPattern {
 		}
 		contrast = contrasts[0];
 		result[2] = contrast;
+//		System.out.println("cobntrasts = "+contrasts[0]+", "+contrasts[1]);
 		if (Double.isNaN(contrasts[0]) || ((distortionParameters.correlationMinContrast > 0)
 				&& (contrasts[0] < distortionParameters.correlationMinContrast))) {
 			if ((debug_level > (debug_threshold - 1)))
@@ -12400,6 +12406,7 @@ public class MatchSimulatedPattern {
 		public double minGridPeriod;
 		public double maxGridPeriod;
 		public double minGridPeriodLwir;
+		public int    minGridFileSize = 15000; // Minimal file size (to overwrite) 
 		public double maxGridPeriodLwir;
 		public double debugX;
 		public double debugY;
@@ -12623,8 +12630,10 @@ public class MatchSimulatedPattern {
 												// the grig brightness
 
 		// match pointers errors
-		public  int errTooFewCells = -10;
+		public  int errTooFewCells =     -10;
 		public  int errPatternNotFound = -11;
+		public  int errRefineFailed =    -12;
+		
 		public  boolean legacyMode = false; // legacy mode