Tested GPU building DSI with multi-tile mode for low-contrast areas

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

@@ -1413,10 +1413,10 @@ Panel panel1,panel2;
       }
 /* Filter pattern coefficients to make sure they all match between quadrtants (match to the center one?)*/
      boolean patternsMatchedInitially=matchPatterns(quarter_patterns,quarter_patterns[4]);    // uses pattern in the center quadrant
-     if (DEBUG_LEVEL>1) {
-          System.out.println(patternsMatchedInitially?"Sim: All quadrant wave vectors matched initially, no correction needed":
-        	  "Some quadrant wave vectors were adjusted to match");
-     }
+//     if (DEBUG_LEVEL>1) {
+//          System.out.println(patternsMatchedInitially?"Sim: All quadrant wave vectors matched initially, no correction needed":
+//        	  "Some quadrant wave vectors were adjusted to match");
+//     }
      
       patternCorr=calcPatternNonLinear(quarter_patterns); // divide results by ,(FFTSize/2)^2
       if (DEBUG_LEVEL>1) { /* increase LEVEL later */

src/main/java/com/elphel/imagej/cameras/CLTParameters.java

@@ -337,6 +337,8 @@ public class CLTParameters {
 	// not used anywhere so far
 	public double     min_smth         = 0.25;  // 0.25 minimal noise-normalized pixel difference in a channel to suspect something
 	public double     sure_smth        = 2.0;   // reliable noise-normalized pixel difference in a channel to have something
+	public double     rsure_smth       = 0.5;   // reliable noise-normalized pixel difference in a channel to have something
+	public double     cold_sky_above   = 50.0;  // "Cold sky" - LWIR only, bgnd for all colder than found BG by this value
 	public double     bgnd_range       = 0.3;   // disparity range to be considered background
 	public double     other_range      = 2.0;   // disparity difference from center (provided) disparity to trust
 
@@ -1239,6 +1241,8 @@ public class CLTParameters {
 
 		properties.setProperty(prefix+"min_smth",                   this.min_smth +"");
 		properties.setProperty(prefix+"sure_smth",                  this.sure_smth +"");
+		properties.setProperty(prefix+"rsure_smth",                 this.rsure_smth +"");
+		properties.setProperty(prefix+"cold_sky_above",             this.cold_sky_above +"");
 		properties.setProperty(prefix+"bgnd_range",                 this.bgnd_range +"");
 		properties.setProperty(prefix+"other_range",                this.other_range +"");
 
@@ -2059,6 +2063,8 @@ public class CLTParameters {
 
 		if (properties.getProperty(prefix+"min_smth")!=null)                      this.min_smth=Double.parseDouble(properties.getProperty(prefix+"min_smth"));
 		if (properties.getProperty(prefix+"sure_smth")!=null)                     this.sure_smth=Double.parseDouble(properties.getProperty(prefix+"sure_smth"));
+		if (properties.getProperty(prefix+"rsure_smth")!=null)                    this.rsure_smth=Double.parseDouble(properties.getProperty(prefix+"rsure_smth"));
+		if (properties.getProperty(prefix+"cold_sky_above")!=null)                this.cold_sky_above=Double.parseDouble(properties.getProperty(prefix+"cold_sky_above"));
 		if (properties.getProperty(prefix+"bgnd_range")!=null)                    this.bgnd_range=Double.parseDouble(properties.getProperty(prefix+"bgnd_range"));
 		if (properties.getProperty(prefix+"other_range")!=null)                   this.other_range=Double.parseDouble(properties.getProperty(prefix+"other_range"));
 
@@ -2991,6 +2997,11 @@ public class CLTParameters {
 
 		gd.addNumericField("Minimal noise-normalized pixel difference in a channel to suspect something",            this.min_smth,  3);
 		gd.addNumericField("Reliable noise-normalized pixel difference in a channel to have something ",             this.sure_smth,  3);
+
+		gd.addNumericField("Relative inter-channel variation meaning there is something non-bg",                     this.rsure_smth,  4,6,"",
+				"Absolute difference ratio to average of mean and max meaning that there is something there");
+		gd.addNumericField("Cold sky",                                                                               this.cold_sky_above,  4,6,"counts",
+				"LWIR-only: tiles that are higher than the lowest BG and are colder by this value than BG");
 		gd.addNumericField("Disparity range to be considered background",                                            this.bgnd_range,  3);
 		gd.addNumericField("Disparity difference from the center (provided) disparity to trust",                     this.other_range,  3);
 
@@ -3933,6 +3944,8 @@ public class CLTParameters {
 		this.debug_filters=         gd.getNextBoolean();
 		this.min_smth=              gd.getNextNumber();
 		this.sure_smth=             gd.getNextNumber();
+		this.rsure_smth=            gd.getNextNumber();
+		this.cold_sky_above=        gd.getNextNumber();
 		this.bgnd_range=            gd.getNextNumber();
 		this.other_range=           gd.getNextNumber();
 

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

@@ -6757,8 +6757,6 @@ private Panel panel1,
 		
 		try {
 			TWO_QUAD_CLT.batchLwirRig(
-//					GPU_QUAD,     // GPUTileProcessor.GpuQuad gpuQuad_main, // may be null if GPU for MAIN is not use3d
-//					GPU_QUAD_AUX, // GPUTileProcessor.GpuQuad gpuQuad_aux,  // may be null if GPU for AUX is not use3d
 					QUAD_CLT, // QuadCLT quadCLT_main,
 					QUAD_CLT_AUX, // QuadCLT quadCLT_aux,
 					CLT_PARAMETERS,  // EyesisCorrectionParameters.DCTParameters           dct_parameters,

src/main/java/com/elphel/imagej/gpu/ExportForGPUDevelopment.java

@@ -34,7 +34,7 @@ public class ExportForGPUDevelopment {
 		//		  int mcorr_sel = Correlation2d.corrSelEncode(clt_parameters.img_dtt, getNumSensors());
 		TpTask[] tp_tasks = GpuQuad.setTasks(
 				quadCLT.getNumSensors(),       // final int                      num_cams,
-				clt_parameters.transform_size, // final int                      transform_size,
+//				clt_parameters.transform_size, // final int                      transform_size,
 				disparity_array,               // final double [][]	           disparity_array,  // [tilesY][tilesX] - individual per-tile expected disparity
 				disparity_corr,                // final double                   disparity_corr,
 				tile_op,                       // final int [][]                 tile_op,          // [tilesY][tilesX] - what to do - 0 - nothing for this tile

src/main/java/com/elphel/imagej/gpu/TpTask.java

@@ -38,7 +38,7 @@ public class TpTask {
 	}
 	/**
 	 * Initialize from the float array (read from the GPU)
-	 * @param num_sensors number of sesnors in an array
+	 * @param num_sensors number of sensors in an array
 	 * @param flt float array containing tasks data
 	 * @param indx task number to use
 	 * @param use_aux (always false now)
@@ -101,24 +101,6 @@ public class TpTask {
 		}
 		return ddisp_dist;
 	}
-	@Deprecated
-	public float [][] getXY(boolean use_aux){
-		return use_aux? xy_aux : xy;
-	}
-	@Deprecated
-	public double [][] getDoubleXY(boolean use_aux){
-		float [][] fXY = getXY(use_aux);
-		if (fXY == null) {
-			return null;
-		}
-		double [][] dXY = new double [fXY.length][fXY[0].length];
-		for (int nsens = 0; nsens < fXY.length; nsens++) {
-			for (int i = 0; i < fXY[nsens].length; i++) {
-				dXY[nsens][i] = fXY[nsens][i]; 
-			}
-		}
-		return dXY;
-	}
 
 	public float [][] getXY(){
 		return  xy;
@@ -149,6 +131,11 @@ public class TpTask {
 	public double getTargetDisparity() {
 		return target_disparity;
 	}
+
+	public void updateTargetDisparity(float td) {
+		target_disparity = td;
+	}
+	
 	
 	public float [] getCenterXY() {
 		return centerXY;
@@ -188,15 +175,6 @@ public class TpTask {
 				indx+= 2;
 			}
 		}
-		/*
-		for (int i = 0; i < num_sensors; i++) { // actually disp_dist will be initialized by the GPU
-			indx+= 4;
-			flt[indx++] = disp_dist[i][0];
-			flt[indx++] = disp_dist[i][1];
-			flt[indx++] = disp_dist[i][2];
-			flt[indx++] = disp_dist[i][3];
-		}
-		*/
 		return flt;
 	}
 }
\ No newline at end of file

src/main/java/com/elphel/imagej/tileprocessor/CLTPass3d.java

@@ -1027,7 +1027,37 @@ public class CLTPass3d{
 			}
 			return num_op_tiles;
 		}
+		
+		public void setTileOp(
+				int  tile_op)
+		{
+			final int tilesX = tileProcessor.getTilesX();
+			final int tilesY = tileProcessor.getTilesY();
+			this.tile_op =     new int [tilesY][tilesX];
+
+			for (int ty = 0; ty < tilesY; ty++) for (int tx = 0; tx <tilesX; tx++){
+				this.tile_op[ty][tx] = tile_op;
+			}
+		}
+
+		public double [] getDA() {
+			final int tilesX = tileProcessor.getTilesX();
+			final int tilesY = tileProcessor.getTilesY();
+			double [] da = new double [tilesX*tilesY];
+			for (int ty = 0; ty < tilesY; ty++) for (int tx = 0; tx <tilesX; tx++){
+				da[tilesX * ty + tx] = this.disparity[ty][tx];
+			}
+			return da;
+		}
 
+		public void setDA(double [] da) {
+			final int tilesX = tileProcessor.getTilesX();
+			final int tilesY = tileProcessor.getTilesY();
+			for (int ty = 0; ty < tilesY; ty++) for (int tx = 0; tx <tilesX; tx++){
+				this.disparity[ty][tx] = da[tilesX * ty + tx];
+			}
+		}
+		
 		/**
 		 * Set next measurement disparity from last calculated
 		 */

src/main/java/com/elphel/imagej/tileprocessor/Corr2dLMA.java

@@ -500,7 +500,7 @@ public class Corr2dLMA {
 			if ((disp_str[nTile] != null) && (disp_str[nTile][1] > 0.0) && used_tiles[nTile]) {
 				this.all_pars[DISP_INDEX + nTile*tile_params] = -disp_str[nTile][0]; // disp0;
 			} else {
-				this.all_pars[DISP_INDEX + nTile*tile_params] = 0.0; // disp0;
+				this.all_pars[DISP_INDEX + nTile*tile_params] = 0.0; // disp0; // null pointer
 			}
 		}
 	}
@@ -2535,10 +2535,13 @@ public class Corr2dLMA {
 			}
 		}
 		Matrix y_minus_fx_weighted = new Matrix(this.last_ymfx, this.last_ymfx.length);
-
-		Matrix wjtjlambda = new Matrix(getWJtJlambda(
+		double [][] awjtjlambda = getWJtJlambda( // null
 				lambda, // *10, // temporary
-				this.last_jt)); // double [][] jt)
+				this.last_jt); // double [][] jt)
+		if ((awjtjlambda ==  null) || (awjtjlambda.length==0)) {
+			return null;
+		}
+		Matrix wjtjlambda = new Matrix(awjtjlambda); // double [][] jt)
 		if (debug_level>2) {
 			System.out.println("JtJ + lambda*diag(JtJ");
 			wjtjlambda.print(18, 6);

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

@@ -1594,7 +1594,7 @@ public class Correlation2d {
      * @param lpf optional final low-pass filter applied to mixed colors
      * @param lpf_rb optional low-pass filter (extra) for R,B components only
      * @param scale_value scale correlation results to compensate for lpf changes and other factors
-     * @param col_weights [3] - color weights {R, B, G} - green is last, normalized to sum =1.0
+     * @param col_weights [3] - color weights {R, B, G} - green is last, normalized to sum =1.0 
      * @return correlation result (Transform Domain) [quadrant][index]
      */
     public double[][]   correlateCompositeTD(
@@ -4069,7 +4069,7 @@ public class Correlation2d {
     		
     		if (disp != null) {
     			disp_str2[0] = disp;
-    			lma.initDisparity( // USED in lwir
+    			lma.initDisparity( // USED in lwir null pointer
     					disp_str2); // double [][] disp_str         // initial value of disparity
 
     			if (debug_level > 1) {

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

@@ -282,6 +282,15 @@ public class ImageDttParameters {
 		return (numSens > mcorr_multi) ? mcorr_topis0_multi : mcorr_topis0;
 	}
 	
+	public int getMcorr(int numSens) {
+		return  (getMcorrAll (numSens) ?  1 : 0) |
+				(getMcorrDia (numSens) ?  2 : 0) |
+				(getMcorrSq  (numSens) ?  8 : 0) |
+				(getMcorrNeib(numSens) ? 16 : 0) |
+				(getMcorrHor (numSens) ? 32 : 0) |
+				(getMcorrVert(numSens) ? 64 : 0);
+	}
+	
 	public boolean getMcorrAll(int numSens) {
 		return (numSens > mcorr_multi) ? mcorr_all_multi : mcorr_all;
 	}
@@ -310,6 +319,42 @@ public class ImageDttParameters {
 		return (numSens > mcorr_multi) ? mcorr_sel_ly_multi : mcorr_sel_ly;
 	}
 	
+	public void setMcorr(int numSens, int sel ) {
+		setMcorrAll (numSens, (sel & (1 << 0)) != 0);
+		setMcorrDia (numSens, (sel & (1 << 1)) != 0);
+		setMcorrSq  (numSens, (sel & (1 << 2)) != 0);
+		setMcorrNeib(numSens, (sel & (1 << 3)) != 0);
+		setMcorrHor (numSens, (sel & (1 << 4)) != 0);
+		setMcorrVert(numSens, (sel & (1 << 5)) != 0);
+	}
+	
+	
+	public void setMcorrAll(int numSens, boolean b) {
+		if (numSens > mcorr_multi) mcorr_all_multi = b; else mcorr_all = b;
+	}
+
+	public void setMcorrDia(int numSens, boolean b) {
+		if (numSens > mcorr_multi) mcorr_dia_multi = b; else mcorr_dia = b;
+	}
+
+	public void setMcorrSq(int numSens, boolean b) {
+		if (numSens > mcorr_multi) mcorr_sq_multi = b; else mcorr_sq = b;
+	}
+
+	public void setMcorrNeib(int numSens, boolean b) {
+		if (numSens > mcorr_multi) mcorr_neib_multi = b; else mcorr_neib = b;
+	}
+
+	public void setMcorrHor(int numSens, boolean b) {
+		if (numSens > mcorr_multi) mcorr_hor_multi = b; else mcorr_hor = b;
+	}
+
+	public void setMcorrVert(int numSens, boolean b) {
+		if (numSens > mcorr_multi) mcorr_vert_multi = b; else mcorr_vert = b;
+	}
+
+	
+	
 	public void dialogQuestions(GenericJTabbedDialog gd) {
 		
 		    gd.addCheckbox    ("Debug CPU->GPU matching",                                         this.gpu_mode_debug,

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

@@ -283,7 +283,7 @@ public class MacroCorrelation {
 		double min_corr_selected = clt_parameters.min_corr;
 
 //		double [][] disparity_map = new double [ImageDtt.DISPARITY_TITLES.length][]; //[0] -residual disparity, [1] - orthogonal (just for debugging)
-		double [][] disparity_map = new double [ImageDtt.getDisparityTitles(geometryCorrection.getNumSensors()).length][]; //[0] -residual disparity, [1] - orthogonal (just for debugging)
+		double [][] disparity_map = new double [ImageDtt.getDisparityTitles(geometryCorrection.getNumSensors(), this.mtp.isMonochrome()).length][]; //[0] -residual disparity, [1] - orthogonal (just for debugging)
 
 		double [][] shiftXY = {{0.0,0.0},{0.0,0.0},{0.0,0.0},{0.0,0.0}};
 

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

@@ -1399,12 +1399,12 @@ public class TwoQuadCLT {
 		double [][] sub_disparity_map = new double [sub_titles.length][];
 		for (int ncam = 0; ncam < numSensors; ncam++) {
 			sub_disparity_map[ncam] = disparity_map[ncam + ImageDtt.IMG_DIFF0_INDEX];
-			sub_titles[ncam] = ImageDtt.getDisparityTitles(numSensors)[ncam + ImageDtt.IMG_DIFF0_INDEX];
+			sub_titles[ncam] = ImageDtt.getDisparityTitles(numSensors, quadCLT_main.isMonochrome())[ncam + ImageDtt.IMG_DIFF0_INDEX];
 			for (int ncol = 0; ncol < num_colors_main; ncol++) {
 				sub_disparity_map[ncam + (ncol + 1)* numSensors] =
 						disparity_map[ncam +ncol* numSensors+ ImageDtt.getImgToneRGB(numSensors)];
 				sub_titles[ncam + (ncol + 1)* numSensors] =
-						ImageDtt.getDisparityTitles(numSensors)[ncam +ncol* numSensors+ ImageDtt.getImgToneRGB(numSensors)];
+						ImageDtt.getDisparityTitles(numSensors,quadCLT_main.isMonochrome())[ncam +ncol* numSensors+ ImageDtt.getImgToneRGB(numSensors)];
 			}
 		}
 		(new ShowDoubleFloatArrays()).showArrays(
@@ -8253,8 +8253,8 @@ if (debugLevel > -100) return true; // temporarily !
 		QuadCLT.SetChannels [] set_channels=quadCLT_main.setChannels(debugLevel);
 //		String set_name = set_channels[0].set_name;
 		
-//		QuadCLT [] quadCLTs = new QuadCLT [set_channels.length]; 
-		QuadCLTCPU [] quadCLTs = new QuadCLTCPU [set_channels.length]; 
+		QuadCLT [] quadCLTs = new QuadCLT [set_channels.length]; // Was line below
+//		QuadCLTCPU [] quadCLTs = new QuadCLTCPU [set_channels.length]; 
 		for (int i = 0; i < quadCLTs.length; i++) {
 			quadCLTs[i] = quadCLT_main.spawnQuadCLT(
 					set_channels[i].set_name,
@@ -11176,15 +11176,6 @@ if (debugLevel > -100) return true; // temporarily !
 		}
 		
 		for (int nSet = 0; nSet < set_channels.length; nSet++){
-			// check it is the same set for both cameras
-			/*
-			if ((set_channels_aux != null) && (set_channels_aux.length <= nSet )) {
-				throw new Exception ("Set names for cameras do not match: main camera: '"+set_channels_main[nSet].name()+"', aux. camera: nothing");
-			}
-			if (!set_channels_main[nSet].name().equals(set_channels_aux[nSet].name())) {
-				throw new Exception ("Set names for cameras do not match: main camera: '"+set_channels_main[nSet].name()+"', aux. camera: '"+set_channels_main[nSet].name()+"'");
-			}
-			*/
 			// nset -> name - n1, n2 (in 
 			String set_name = set_channels[nSet].set_name;
 			int nSet_main = -1, nSet_aux = -1;
@@ -11358,7 +11349,6 @@ if (debugLevel > -100) return true; // temporarily !
 								debugLevel);         // final int        debugLevel);
 					} else {
 						if (updateStatus) IJ.showStatus("CPU: Rendering 4 image set (disparity = 0) for "+quadCLT_main.image_name+ "and a thumb nail");
-
 						quadCLT_main.processCLTQuadCorrCPU( // returns ImagePlus, but it already should be saved/shown
 //								imp_srcs_main, // [srcChannel], // should have properties "name"(base for saving results), "channel","path"
 								saturation_imp_main, // boolean [][] saturation_imp, // (near) saturated pixels or null
@@ -11652,23 +11642,39 @@ if (debugLevel > -100) return true; // temporarily !
 				}
 				// Generate 4 AUX camera images and thumbnail
 				if (quadCLT_main.correctionsParameters.clt_batch_4img_aux){
-					if (updateStatus) IJ.showStatus("Rendering 4 AUX image set (disparity = 0) for "+quadCLT_aux.image_name);
-
-					quadCLT_aux.processCLTQuadCorrCPU( // returns ImagePlus, but it already should be saved/shown
-//							imp_srcs_aux, // [srcChannel], // should have properties "name"(base for saving results), "channel","path"
-							saturation_imp_aux, // boolean [][] saturation_imp, // (near) saturated pixels or null
-							clt_parameters,
-							debayerParameters,
-							colorProcParameters_aux,
-							channelGainParameters,
-							rgbParameters,
-							scaleExposures_aux,
-							false, // calculate and apply additional fine geometry correction
-							false, // calculate and apply geometry correction at infinity
-							threadsMax,  // maximal number of threads to launch
-							updateStatus,
-							debugLevel);
-					quadCLT_aux.tp.resetCLTPasses();
+					if (clt_parameters.gpu_use_aux) {
+						if (updateStatus) IJ.showStatus("GPU: Rendering 4 AUX image set (disparity = 0) for "+quadCLT_aux.image_name+ "and a thumb nail");
+						quadCLT_aux.processCLTQuadCorrGPU(
+								imp_srcs_aux,        // ImagePlus []                                    imp_quad,
+								saturation_imp_aux,  // boolean [][] saturation_imp, // (near) saturated pixels or null
+								clt_parameters,      // CLTParameters                                   clt_parameters,
+								debayerParameters,   // EyesisCorrectionParameters.DebayerParameters    debayerParameters,
+								colorProcParameters_aux, // ColorProcParameters                             colorProcParameters,
+								channelGainParameters,
+								rgbParameters,       // EyesisCorrectionParameters.RGBParameters        rgbParameters,
+								scaleExposures_aux,  // double []	                                    scaleExposures, // probably not needed here - restores brightness of the final image
+								false,               // boolean                                         only4slice,
+								threadsMax,          // final int        threadsMax,  // maximal number of threads to launch
+								updateStatus,        // final boolean    updateStatus,
+								debugLevel);         // final int        debugLevel);
+					} else {
+						if (updateStatus) IJ.showStatus("CPU: Rendering 4 AUX image set (disparity = 0) for "+quadCLT_aux.image_name);
+						quadCLT_aux.processCLTQuadCorrCPU( // returns ImagePlus, but it already should be saved/shown
+								//							imp_srcs_aux, // [srcChannel], // should have properties "name"(base for saving results), "channel","path"
+								saturation_imp_aux, // boolean [][] saturation_imp, // (near) saturated pixels or null
+								clt_parameters,
+								debayerParameters,
+								colorProcParameters_aux,
+								channelGainParameters,
+								rgbParameters,
+								scaleExposures_aux,
+								false, // calculate and apply additional fine geometry correction
+								false, // calculate and apply geometry correction at infinity
+								threadsMax,  // maximal number of threads to launch
+								updateStatus,
+								debugLevel);
+						quadCLT_aux.tp.resetCLTPasses();
+					}
 				}
 				// Currently - no LWIR 3D model generation, maybe it will be added later
 				// Generate AUX DS