Implemented enlarged reference window for rendering

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

@@ -102,6 +102,7 @@ public class GPUTileProcessor {
 	static String GPU_CLEAR_TEXTURE_RBGA_NAME =    "clear_texture_rbga";
 	static String GPU_TEXTURES_ACCUMULATE_NAME =   "textures_accumulate";
 	static String GPU_CREATE_NONOVERLAP_LIST_NAME ="create_nonoverlap_list";
+	static String GPU_ERASE_CLT_TILES_NAME =       "erase_clt_tiles";
 
 	
 	
@@ -180,6 +181,7 @@ public class GPUTileProcessor {
     CUfunction GPU_CLEAR_TEXTURE_RBGA_kernel =      null; // "clear_texture_rbga"
     CUfunction GPU_TEXTURES_ACCUMULATE_kernel =     null; // "textures_accumulate"
     CUfunction GPU_CREATE_NONOVERLAP_LIST_kernel =  null; // "create_nonoverlap_list"
+    CUfunction GPU_ERASE_CLT_TILES_kernel =         null; // "erase_clt_tiles"
     
     
 
@@ -331,7 +333,8 @@ public class GPUTileProcessor {
         		GPU_GEN_TEXTURE_LIST_NAME,
         		GPU_CLEAR_TEXTURE_RBGA_NAME,
         		GPU_TEXTURES_ACCUMULATE_NAME,
-        		GPU_CREATE_NONOVERLAP_LIST_NAME
+        		GPU_CREATE_NONOVERLAP_LIST_NAME,
+        		GPU_ERASE_CLT_TILES_NAME
         };
         CUfunction[] functions = createFunctions(kernelSources,
         		                                 func_names,
@@ -356,6 +359,7 @@ public class GPUTileProcessor {
         GPU_CLEAR_TEXTURE_RBGA_kernel =      functions[15];
         GPU_TEXTURES_ACCUMULATE_kernel =     functions[16];
         GPU_CREATE_NONOVERLAP_LIST_kernel =  functions[17];
+        GPU_ERASE_CLT_TILES_kernel =         functions[18];
         
 
         System.out.println("GPU kernel functions initialized");
@@ -378,6 +382,7 @@ public class GPUTileProcessor {
         System.out.println(GPU_CLEAR_TEXTURE_RBGA_kernel.toString());
         System.out.println(GPU_TEXTURES_ACCUMULATE_kernel.toString());
         System.out.println(GPU_CREATE_NONOVERLAP_LIST_kernel.toString());
+        System.out.println(GPU_ERASE_CLT_TILES_kernel.toString());
         // GPU data structures are now initialized through GpuQuad instances
     }
     

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

@@ -1464,33 +1464,44 @@ public class GpuQuad{ // quad camera description
 	/**
 	 * Direct CLT conversion and aberration correction 
 	 */
-	public void execConvertDirect() {
+	public void execConvertDirect(int  erase_clt) {
 		execConvertDirect(
 				false,
-				null);
+				null,
+				erase_clt);
 	}
 	/**
 	 * Convert and save TD representation in either normal or reference scene. Reference scene TD representation
 	 * is used for interscene correlation (for "IMU")
 	 * @param ref_scene save result into a separate buffer for interscene correlation when true.
 	 * @param wh window width, height (or null)
+	 * @param erase_clt erase CLT data. Only needed before execImcltRbgAll() if not all the
+	 *                  tiles are converted. <0 - do not erase, 0 - erase to 0, 1 - erase to NaN 
 	 */
 	public void execConvertDirect(
-			boolean ref_scene,
-			int [] wh) {
+			boolean  ref_scene,
+			int []   wh,
+			int      erase_clt) {
 		if (this.gpuTileProcessor.GPU_CONVERT_DIRECT_kernel == null) 
 		{
 			IJ.showMessage("Error", "No GPU kernel: GPU_CONVERT_DIRECT_kernel");
 			return;
 		}
+		if (this.gpuTileProcessor.GPU_ERASE_CLT_TILES_kernel == null) 
+		{
+			IJ.showMessage("Error", "No GPU kernel: GPU_ERASE_CLT_TILES_kernel");
+			return;
+		}
+		
+		
 		if (wh == null) {
 			wh = new int[] {img_width, img_height};
 		}
 		setConvolutionKernels(false); // set kernels if they are not set already
 		setBayerImages(false); // set Bayer images if this.quadCLT instance has new ones
 		// kernel parameters: pointer to pointers
-//		int tilesX =  img_width / GPUTileProcessor.DTT_SIZE;
 		int tilesX =  wh[0] / GPUTileProcessor.DTT_SIZE;
+		int tilesY =  wh[1] / GPUTileProcessor.DTT_SIZE;
 		// De-allocate if size mismatch, allocate if needed. Now it is the only place where clt is allocated
 		if (ref_scene) {
 			if ((gpu_clt_ref_wh != null) && ((gpu_clt_ref_wh[0] != wh[0]) || (gpu_clt_ref_wh[1] != wh[1]))) {
@@ -1503,8 +1514,6 @@ public class GpuQuad{ // quad camera description
 			}
 			if (gpu_clt_ref == null) { // Allocate memory, create pointers for reference scene TD representation
 				long [] gpu_clt_ref_l = new long [num_cams];
-//				int tilesY =  img_height / GPUTileProcessor.DTT_SIZE;
-				int tilesY =  wh[1] / GPUTileProcessor.DTT_SIZE;
 				gpu_clt_ref_h =    new CUdeviceptr[num_cams];
 				for (int ncam = 0; ncam < num_cams; ncam++) {
 					gpu_clt_ref_h[ncam] = new CUdeviceptr();
@@ -1530,8 +1539,6 @@ public class GpuQuad{ // quad camera description
 			}
 			if (gpu_clt == null) { // Allocate memory, create pointers for reference scene TD representation
 				long [] gpu_clt_l = new long [num_cams];
-//				int tilesY =  img_height / GPUTileProcessor.DTT_SIZE;
-				int tilesY =  wh[1] / GPUTileProcessor.DTT_SIZE;
 				gpu_clt_h =    new CUdeviceptr[num_cams];
 				for (int ncam = 0; ncam < num_cams; ncam++) {
 					gpu_clt_h[ncam] = new CUdeviceptr();
@@ -1547,28 +1554,32 @@ public class GpuQuad{ // quad camera description
 				gpu_clt_wh = wh.clone();
 			}
 		}
-		/*
-		if (ref_scene && (gpu_clt_ref == null)) { // Allocate memory, create pointers for reference scene TD representation
-			long [] gpu_clt_ref_l = new long [num_cams];
-			int tilesY =  img_height / GPUTileProcessor.DTT_SIZE;
-			gpu_clt_ref_h =    new CUdeviceptr[num_cams];
-			for (int ncam = 0; ncam < num_cams; ncam++) {
-				gpu_clt_ref_h[ncam] = new CUdeviceptr();
-				cuMemAlloc(gpu_clt_ref_h[ncam],
-						   tilesY * tilesX * num_colors * 4 * GPUTileProcessor.DTT_SIZE * GPUTileProcessor.DTT_SIZE * Sizeof.FLOAT );
-			}
-			gpu_clt_ref =  new CUdeviceptr();
-			cuMemAlloc(gpu_clt_ref, num_cams * Sizeof.POINTER);
-			for (int ncam = 0; ncam < num_cams; ncam++) {
-				gpu_clt_ref_l[ncam] = GPUTileProcessor.getPointerAddress(gpu_clt_ref_h[ncam]);
-			}
-			cuMemcpyHtoD(gpu_clt_ref, Pointer.to(gpu_clt_ref_l), num_cams * Sizeof.POINTER);
-			gpu_clt_ref_wh = wh.clone();
-		}
-		*/
 		CUdeviceptr gpu_clt_selected = ref_scene ? gpu_clt_ref : gpu_clt;
 		int [] GridFullWarps =    {1, 1, 1};
 		int [] ThreadsFullWarps = {1, 1, 1};
+		
+		if (erase_clt >= 0) {
+			float fill_data = (erase_clt > 0) ? Float.NaN : 0.0f;
+			Pointer kernelParametersEraseClt = Pointer.to(
+					Pointer.to(new int[] { num_cams}),   // int      num_cams,
+					Pointer.to(new int[] { num_colors}), // int      num_colors,
+					Pointer.to(new int[] { tilesX}),     // int      tiles_x,
+					Pointer.to(new int[] { tilesY}),     // int      tiles_y,
+					Pointer.to(gpu_clt_selected),        // float ** gpu_clt,// [num_cams][tiles_y][tiles_x][num_colors][4*DTT_SIZE*DTT_SIZE]
+					Pointer.to(new float[] { fill_data})); // float    fill_data
+			cuCtxSynchronize();
+			// Call the kernel function
+			cuLaunchKernel(this.gpuTileProcessor.GPU_ERASE_CLT_TILES_kernel,
+					GridFullWarps[0],    GridFullWarps[1],   GridFullWarps[2],   // Grid dimension
+					ThreadsFullWarps[0], ThreadsFullWarps[1],ThreadsFullWarps[2],// Block dimension
+					0, null,                           // Shared memory size and stream (shared - only dynamic, static is in code)
+					kernelParametersEraseClt, null);   // Kernel- and extra parameters
+			cuCtxSynchronize(); // remove later CUDA_ERROR_ILLEGAL_ADDRESS
+			if (getGpu_debug_level() > -1) {
+				System.out.println("======execConvertDirect(): erased CLT");
+			}
+		}
+		
 		Pointer kernelParameters = Pointer.to(
 				Pointer.to(new int[] { num_cams}),              // int                  num_cams,
 				Pointer.to(new int[] { num_colors}),            // int                  num_colors,
@@ -1598,7 +1609,7 @@ public class GpuQuad{ // quad camera description
 				kernelParameters, null);   // Kernel- and extra parameters
 		cuCtxSynchronize(); // remove later CUDA_ERROR_ILLEGAL_ADDRESS
 		if (getGpu_debug_level() > -1) {
-			System.out.println("======execConvertDirect("+ref_scene+")");
+			System.out.println("======execConvertDirect("+ref_scene+", "+erase_clt+")");
 		}
 	}
 

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

@@ -339,7 +339,7 @@ public class ImageDtt extends ImageDttCPU {
 		}
 		
 		
-		gpuQuad.execConvertDirect();
+		gpuQuad.execConvertDirect(-1); // boolean erase_clt
 		if (iclt_fimg != null) {
 			gpuQuad.execImcltRbgAll(isMonochrome());  // execute GPU kernel
 			for (int ncam = 0; ncam < iclt_fimg.length; ncam++) {
@@ -958,7 +958,7 @@ public class ImageDtt extends ImageDttCPU {
 		
        	// Skipping if ((fdisp_dist != null) || (fpxpy != null)) {...
 
-		gpuQuad.execConvertDirect();
+		gpuQuad.execConvertDirect(-1); // boolean erase_clt
 		if (mcorr_sel == 0) { // no correlation at all
 			return;
 		}
@@ -1124,7 +1124,7 @@ public class ImageDtt extends ImageDttCPU {
 		
        	// Skipping if ((fdisp_dist != null) || (fpxpy != null)) {...
 
-		gpuQuad.execConvertDirect();
+		gpuQuad.execConvertDirect(-1); // boolean erase_clt
 		if (sensor_mask_inter == 0) { // no correlation at all
 			return;
 		}
@@ -1143,6 +1143,9 @@ public class ImageDtt extends ImageDttCPU {
 	/**
 	 * Convert reference scene to FD and save result in extra GPU array for the future interscene correlation
 	 * Geometry correction and images will come from gpuQuad instance - 
+	 * @param erase_clt erase CLT (<0 - do not erase, 0 - erase to 0.0, >0 - erase to NaN). Needed only for later IMCLT
+	 *                  end rendering images. NaN produces sharp, distinct borders; 0f - blended
+	 * @param wh if null, will uses sensor dimensions. Otherwise {width, height} in pixels
 	 * @param imgdtt_params
 	 * @param use_reference_buffer true - use extra GPU array, false - use main one
 	 * @param tp_tasks
@@ -1154,6 +1157,7 @@ public class ImageDtt extends ImageDttCPU {
 	 * @param globalDebugLevel
 	 */
 	public void setReferenceTD(
+			final int                 erase_clt,
 			final int []              wh,               // null (use sensor dimensions) or pair {width, height} in pixels
 			final ImageDttParameters  imgdtt_params,    // Now just extra correlation parameters, later will include, most others
 			final boolean             use_reference_buffer,
@@ -1186,7 +1190,8 @@ public class ImageDtt extends ImageDttCPU {
 				false); // boolean use_aux    // while is it in class member? - just to be able to free
 		// Skipping if ((fdisp_dist != null) || (fpxpy != null)) {...
 //		int [] wh = null;
-		gpuQuad.execConvertDirect(use_reference_buffer, wh); // put results into a "reference" buffer
+//		int  erase_clt = 1; // NaN;
+		gpuQuad.execConvertDirect(use_reference_buffer, wh, erase_clt); // put results into a "reference" buffer
 	}
 
 
@@ -1297,7 +1302,7 @@ public class ImageDtt extends ImageDttCPU {
 ///		gpuQuad.execSetTilesOffsets(); // prepare tiles offsets in GPU memory
        	// Skipping if ((fdisp_dist != null) || (fpxpy != null)) {...
        	
-		gpuQuad.execConvertDirect();
+		gpuQuad.execConvertDirect(-1); // boolean erase_clt
 
 		//Generate 2D phase correlations from the CLT representation
 		int mcorr_sel = Correlation2d.corrSelEncode(imgdtt_params,numSensors);
@@ -1688,7 +1693,7 @@ public class ImageDtt extends ImageDttCPU {
 //		GPUTileProcessor.TpTask[] tp_tasks_full2)
 		
 		
-		gpuQuad.execConvertDirect();
+		gpuQuad.execConvertDirect(-1); // boolean erase_clt
 		if (iclt_fimg != null) {
 			gpuQuad.execImcltRbgAll(isMonochrome());  // execute GPU kernel
 			for (int ncam = 0; ncam < iclt_fimg.length; ncam++) {

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

@@ -37,6 +37,8 @@ public class IntersceneMatchParameters {
 	public  boolean show_images =        false; // color, infinity
 	public  boolean show_images_bgfg =   false; // bg and fg
 	public  boolean show_images_mono =   false; // float, monochrome 16-slice images (same disparity, COMBO_DSN_INDX_DISP_FG and COMBO_DSN_INDX_DISP_BG_ALL,
+	public  boolean show_color_nan =     true;  // use NAN background for color images (sharp, but distinct black)
+	public  boolean show_mono_nan =      false; // use NAN background for monochrome images (sharp, but distinct black)
 	public  boolean show_ranges =        true;
 	
 	public  double  range_disparity_offset =   -0.08;
@@ -120,9 +122,13 @@ public class IntersceneMatchParameters {
 				"Show foreground and background exported images");
 		gd.addCheckbox ("Show floating-point monochrome images",     this.show_images_mono,
 				"Display generated/saved monochrome images");
+		gd.addCheckbox ("Color NaN background",                      this.show_color_nan,
+				"Use NaN for undefined tiles (false - 0.0f). NaN produces sharp distinct result, 0.0f - blended");
+		gd.addCheckbox ("Mono NaN background",                       this.show_mono_nan,
+				"Use NaN for undefined tiles (false - 0.0f). NaN produces sharp distinct result, 0.0f - blended");
+	
 		gd.addCheckbox ("Show distances in meters",                  this.show_ranges,
 				"Calculate strength, distance, X, and Y in meters");
-		
 		gd.addNumericField("Disparity at infinity",                  this.range_disparity_offset, 5,7,"pix",
 				"Disparity at infinity - subtract from measured disparity when converting to ranges.");
 		gd.addNumericField("Minimal strength for range calculation", this.range_min_strength, 5,7,"",
@@ -234,6 +240,8 @@ public class IntersceneMatchParameters {
 		this.show_images =              gd.getNextBoolean();
 		this.show_images_bgfg =         gd.getNextBoolean();
 		this.show_images_mono =         gd.getNextBoolean();
+		this.show_color_nan =           gd.getNextBoolean();
+		this.show_mono_nan =            gd.getNextBoolean();
 		this.show_ranges =              gd.getNextBoolean();
 		this.range_disparity_offset =   gd.getNextNumber();
 		this.range_min_strength =       gd.getNextNumber();
@@ -292,12 +300,12 @@ public class IntersceneMatchParameters {
 		properties.setProperty(prefix+"show_images",          this.show_images + "");       // boolean
 		properties.setProperty(prefix+"show_images_bgfg",     this.show_images_bgfg + "");  // boolean
 		properties.setProperty(prefix+"show_images_mono",     this.show_images_mono + "");  // boolean
+		properties.setProperty(prefix+"show_color_nan",       this.show_color_nan + "");  // boolean
+		properties.setProperty(prefix+"show_mono_nan",       this.show_mono_nan + "");  // boolean
 		properties.setProperty(prefix+"show_ranges",          this.show_ranges + "");       // boolean
-
 		properties.setProperty(prefix+"range_disparity_offset",this.range_disparity_offset+""); // double
 		properties.setProperty(prefix+"range_min_strength",   this.range_min_strength+"");  // double
 		properties.setProperty(prefix+"range_max",            this.range_max+"");           // double
-		
 		properties.setProperty(prefix+"margin",               this.margin+"");              // int
 		properties.setProperty(prefix+"sensor_mask_inter",    this.sensor_mask_inter+"");   // int
 		properties.setProperty(prefix+"use_partial",          this.use_partial+"");         // boolean
@@ -349,6 +357,8 @@ public class IntersceneMatchParameters {
 		if (properties.getProperty(prefix+"show_images")!=null)          this.show_images=Boolean.parseBoolean(properties.getProperty(prefix+"show_images"));		
 		if (properties.getProperty(prefix+"show_images_bgfg")!=null)     this.show_images_bgfg=Boolean.parseBoolean(properties.getProperty(prefix+"show_images_bgfg"));		
 		if (properties.getProperty(prefix+"show_images_mono")!=null)     this.show_images_mono=Boolean.parseBoolean(properties.getProperty(prefix+"show_images_mono"));		
+		if (properties.getProperty(prefix+"show_color_nan")!=null)       this.show_color_nan=Boolean.parseBoolean(properties.getProperty(prefix+"show_color_nan"));		
+		if (properties.getProperty(prefix+"show_mono_nan")!=null)        this.show_mono_nan=Boolean.parseBoolean(properties.getProperty(prefix+"show_mono_nan"));		
 		if (properties.getProperty(prefix+"show_ranges")!=null)          this.show_images=Boolean.parseBoolean(properties.getProperty(prefix+"show_ranges"));
 		if (properties.getProperty(prefix+"range_disparity_offset")!=null) this.range_disparity_offset=Double.parseDouble(properties.getProperty(prefix+"range_disparity_offset"));
 		if (properties.getProperty(prefix+"range_min_strength")!=null)   this.range_min_strength=Double.parseDouble(properties.getProperty(prefix+"range_min_strength"));
@@ -406,6 +416,8 @@ public class IntersceneMatchParameters {
 		imp.show_images           = this.show_images;
 		imp.show_images_bgfg      = this.show_images_bgfg;
 		imp.show_images_mono      = this.show_images_mono;
+		imp.show_color_nan        = this.show_color_nan;
+		imp.show_mono_nan         = this.show_mono_nan;
 		imp.show_ranges           = this.show_ranges;
 		imp.range_disparity_offset = this.range_disparity_offset;
 		imp.range_min_strength    = this.range_min_strength;

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

@@ -3963,6 +3963,9 @@ public class OpticalFlow {
     	boolean export_images =      clt_parameters.imp.export_images;
     	boolean export_dsi_image =   clt_parameters.imp.show_ranges;
     	boolean show_images =        clt_parameters.imp.show_images;
+    	boolean show_color_nan =     clt_parameters.imp.show_color_nan;
+    	boolean show_mono_nan =      clt_parameters.imp.show_mono_nan;
+    	
     	boolean show_images_bgfg =   clt_parameters.imp.show_images_bgfg;
     	boolean show_images_mono =   clt_parameters.imp.show_images_mono;
 
@@ -4279,11 +4282,12 @@ public class OpticalFlow {
 			Arrays.fill(constant_disparity,clt_parameters.disparity);
 			Rectangle testr = new Rectangle(10, 8, 100,80);
 			ImagePlus imp_constant = QuadCLT.renderGPUFromDSI(
-					testr, // null,                // final Rectangle   full_woi_in,      // show larger than sensor WOI (or null)
+					-1,                  // final int         sensor_mask,
+					null, // testr, // null,                // final Rectangle   full_woi_in,      // show larger than sensor WOI (or null)
 					clt_parameters,      // CLTParameters     clt_parameters,
 					constant_disparity,  // double []         disparity_ref,
 					ZERO3,               // final double []   scene_xyz, // camera center in world coordinates
-					new double[] {.1,0.1,.1}, // ZERO3,               // final double []   scene_atr, // camera orientation relative to world frame
+					ZERO3, // new double[] {.1,0.1,.1}, // ZERO3,               // final double []   scene_atr, // camera orientation relative to world frame
 					quadCLTs[ref_index], // final QuadCLT     scene,
 					true, // toRGB,               // final boolean     toRGB,
 					"GPU-SHIFTED-D"+clt_parameters.disparity, // String            suffix,
@@ -4293,7 +4297,8 @@ public class OpticalFlow {
 					null, // "GPU-SHIFTED-D"+clt_parameters.disparity, // String      suffix,
 					imp_constant); // ImagePlus   imp)
 			ImagePlus imp_constant_mono = QuadCLT.renderGPUFromDSI(
-					testr, // null,                // final Rectangle   full_woi_in,      // show larger than sensor WOI (or null)
+					-1,                  // final int         sensor_mask,
+					null, // testr, // null,                // final Rectangle   full_woi_in,      // show larger than sensor WOI (or null)
 					clt_parameters,      // CLTParameters     clt_parameters,
 					constant_disparity,  // double []         disparity_ref,
 					ZERO3,               // final double []   scene_xyz, // camera center in world coordinates
@@ -4313,6 +4318,7 @@ public class OpticalFlow {
 				}
 			}
 			ImagePlus imp_fg = QuadCLT.renderGPUFromDSI(
+					-1,                  // final int         sensor_mask,
 					null,                // final Rectangle   full_woi_in,      // show larger than sensor WOI (or null)
 					clt_parameters,      // CLTParameters     clt_parameters,
 					fg_disparity,  // double []         disparity_ref,
@@ -4327,6 +4333,7 @@ public class OpticalFlow {
 					null, // "GPU-SHIFTED-FOREGROUND", // String      suffix,
 					imp_fg); // ImagePlus   imp)
 			ImagePlus imp_fg_mono = QuadCLT.renderGPUFromDSI(
+					-1,                  // final int         sensor_mask,
 					null,                // final Rectangle   full_woi_in,      // show larger than sensor WOI (or null)
 					clt_parameters,      // CLTParameters     clt_parameters,
 					fg_disparity,  // double []         disparity_ref,
@@ -4347,6 +4354,7 @@ public class OpticalFlow {
 				}
 			}
 			ImagePlus imp_bg = QuadCLT.renderGPUFromDSI(
+					-1,                  // final int         sensor_mask,
 					null,                // final Rectangle   full_woi_in,      // show larger than sensor WOI (or null)
 					clt_parameters,      // CLTParameters     clt_parameters,
 					bg_disparity,        // double []         disparity_ref,
@@ -4361,6 +4369,7 @@ public class OpticalFlow {
 					null, // "GPU-SHIFTED-BACKGROUND", // String      suffix,
 					imp_bg); // ImagePlus   imp)
 			ImagePlus imp_bg_mono = QuadCLT.renderGPUFromDSI(
+					-1,                  // final int         sensor_mask,
 					null,                // final Rectangle   full_woi_in,      // show larger than sensor WOI (or null)
 					clt_parameters,      // CLTParameters     clt_parameters,
 					bg_disparity,        // double []         disparity_ref,
@@ -9812,6 +9821,7 @@ public double[][] correlateIntersceneDebug( // only uses GPU and quad
 			final float [][][]   accum_2d_corr, // if [1][][] - return accumulated 2d correlations (all pairs)final float [][][]   accum_2d_corr, // if [1][][] - return accumulated 2d correlations (all pairs)
 			int              debug_level)
 	{
+		
 		TileProcessor tp = ref_scene.getTileProcessor();
 		// Temporary reusing same ref scene ******
 		boolean scene_is_ref_test =    clt_parameters.imp.scene_is_ref_test; // false; // true;
@@ -9821,6 +9831,8 @@ public double[][] correlateIntersceneDebug( // only uses GPU and quad
 		boolean show_render_scene =    clt_parameters.imp.renderScene(); // false; // true;
 		boolean toRGB =                clt_parameters.imp.toRGB  ; // true;
 		boolean show_coord_motion =    clt_parameters.imp.showCorrMotion(); // mae its own
+	    int     erase_clt = (toRGB? clt_parameters.imp.show_color_nan : clt_parameters.imp.show_mono_nan) ? 1:0;
+
 		if (scene_is_ref_test) {
 			scene_xyz = ZERO3.clone();
 			scene_atr = ZERO3.clone();
@@ -9907,6 +9919,7 @@ public double[][] correlateIntersceneDebug( // only uses GPU and quad
 			float  [][][][]     fcorr_td =  null; // no accumulation, use data in GPU
 			ref_scene.saveQuadClt(); // to re-load new set of Bayer images to the GPU (do nothing for CPU) and Geometry
 			image_dtt.setReferenceTD(
+					erase_clt,
 					null,                       // final int []              wh,               // null (use sensor dimensions) or pair {width, height} in pixels
 					clt_parameters.img_dtt,     // final ImageDttParameters  imgdtt_params,    // Now just extra correlation parameters, later will include, most others
 					true, // final boolean             use_reference_buffer,
@@ -9919,6 +9932,7 @@ public double[][] correlateIntersceneDebug( // only uses GPU and quad
 					debug_level);               // final int                 globalDebugLevel);
 			if (show_render_ref) {
 				ImagePlus imp_render_ref = ref_scene.renderFromTD (
+						-1,                  // final int         sensor_mask,
 						clt_parameters,                                 // CLTParameters clt_parameters,
 						clt_parameters.getColorProcParameters(ref_scene.isAux()), //ColorProcParameters colorProcParameters,
 						clt_parameters.getRGBParameters(),              //EyesisCorrectionParameters.RGBParameters rgbParameters,
@@ -9948,6 +9962,7 @@ public double[][] correlateIntersceneDebug( // only uses GPU and quad
 					debug_level);               // final int                 globalDebugLevel);
 			if (show_render_scene) {
 				ImagePlus imp_render_scene = scene.renderFromTD (
+						-1,                  // final int         sensor_mask,
 						clt_parameters,                                 // CLTParameters clt_parameters,
 						clt_parameters.getColorProcParameters(ref_scene.isAux()), //ColorProcParameters colorProcParameters,
 						clt_parameters.getRGBParameters(),              //EyesisCorrectionParameters.RGBParameters rgbParameters,

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

@@ -2031,6 +2031,7 @@ public class QuadCLT extends QuadCLTCPU {
 	}
 	
 	public static ImagePlus renderGPUFromDSI(
+			final int         sensor_mask,
 			final Rectangle   full_woi_in,      // show larger than sensor WOI in tiles (or null)
 			CLTParameters     clt_parameters,
 			double []         disparity_ref,
@@ -2041,6 +2042,7 @@ public class QuadCLT extends QuadCLTCPU {
 			String            suffix,
 			int               threadsMax,
 			final int         debugLevel){
+		boolean show_nan = toRGB? clt_parameters.imp.show_color_nan : clt_parameters.imp.show_mono_nan;
 		double [][] pXpYD =OpticalFlow.transformToScenePxPyD(
 				full_woi_in,   // final Rectangle [] extra_woi,    // show larger than sensor WOI (or null)
 				disparity_ref, // final double []   disparity_ref, // invalid tiles - NaN in disparity
@@ -2080,7 +2082,9 @@ public class QuadCLT extends QuadCLTCPU {
 	    		full_woi_in.width * GPUTileProcessor.DTT_SIZE,
 	    		full_woi_in.height * GPUTileProcessor.DTT_SIZE};
 //	    boolean toRGB =         true; // does not work here, define in ColorProcParameters
+	    int                 erase_clt = show_nan ? 1:0;
 	    image_dtt.setReferenceTD( // change to main?
+	    		erase_clt, //final int                 erase_clt,
 	    		wh, // null,                       // final int []              wh,               // null (use sensor dimensions) or pair {width, height} in pixels
 	            clt_parameters.img_dtt,     // final ImageDttParameters  imgdtt_params,    // Now just extra correlation parameters, later will include, most others
 	            use_reference, // true, // final boolean             use_reference_buffer,
@@ -2092,6 +2096,7 @@ public class QuadCLT extends QuadCLTCPU {
 	            threadsMax,                 // final int                 threadsMax,       // maximal number of threads to launch
 	            debugLevel);                // final int                 globalDebugLevel);
         ImagePlus imp_render = scene.renderFromTD (
+        		sensor_mask,                  // final int         sensor_mask,
                 clt_parameters,                                 // CLTParameters clt_parameters,
                 clt_parameters.getColorProcParameters(scene.isAux()), //ColorProcParameters colorProcParameters,
                 clt_parameters.getRGBParameters(),              //EyesisCorrectionParameters.RGBParameters rgbParameters,\
@@ -2102,72 +2107,9 @@ public class QuadCLT extends QuadCLTCPU {
 		return imp_render;
 	}
 	
-	@Deprecated
-	public static ImagePlus renderGPUFromDSI( // being replaced by the above
-			CLTParameters     clt_parameters,
-			double []         disparity_ref,
-			final double []   scene_xyz, // camera center in world coordinates
-			final double []   scene_atr, // camera orientation relative to world frame
-			final QuadCLT     scene,
-			final boolean     toRGB,
-			String            suffix,
-			int               threadsMax,
-			final int         debugLevel){
-		double [][] pXpYD =OpticalFlow.transformToScenePxPyD(
-				null,          // final Rectangle [] extra_woi,    // show larger than sensor WOI (or null)
-				disparity_ref, // final double []   disparity_ref, // invalid tiles - NaN in disparity
-				scene_xyz,     // final double []   scene_xyz, // camera center in world coordinates
-				scene_atr,     // final double []   scene_atr, // camera orientation relative to world frame
-				scene,         // final QuadCLT     scene_QuadClt,
-				scene,         // final QuadCLT     reference_QuadClt, // now - may be null - for testing if scene is rotated ref
-				threadsMax);   // int               threadsMax)
-	    TpTask[] tp_tasks_ref =  GpuQuad.setInterTasks(
-	    		scene.getNumSensors(),
-	    		scene.getErsCorrection().getSensorWH()[0],
-	            !scene.hasGPU(),              // final boolean             calcPortsCoordinatesAndDerivatives, // GPU can calculate them centreXY
-	            pXpYD,                        // final double [][]         pXpYD, // per-tile array of pX,pY,disparity triplets (or nulls)
-	            null,                         // final boolean []          selection, // may be null, if not null do not  process unselected tiles
-	            scene.getErsCorrection(), // final GeometryCorrection  geometryCorrection,
-	            0.0,                          // final double              disparity_corr,
-	            0, // margin,                 // final int                 margin,      // do not use tiles if their centers are closer to the edges
-	            null,                         // final boolean []          valid_tiles,            
-	            threadsMax);                  // final int                 threadsMax)  // maximal number of threads to launch
-	    scene.saveQuadClt(); // to re-load new set of Bayer images to the GPU (do nothing for CPU) and Geometry
-	    ImageDtt image_dtt = new ImageDtt(
-	    		scene.getNumSensors(),
-	    		clt_parameters.transform_size,
-	    		clt_parameters.img_dtt,
-	    		scene.isAux(),
-	    		scene.isMonochrome(),
-	    		scene.isLwir(),
-	    		clt_parameters.getScaleStrength(scene.isAux()),
-	    		scene.getGPU());
-	    boolean use_reference = false;
-//	    boolean toRGB =         true; // does not work here, define in ColorProcParameters
-	    image_dtt.setReferenceTD( // change to main?
-				null,                       // final int []              wh,               // null (use sensor dimensions) or pair {width, height} in pixels
-	            clt_parameters.img_dtt,     // final ImageDttParameters  imgdtt_params,    // Now just extra correlation parameters, later will include, most others
-	            use_reference, // true, // final boolean             use_reference_buffer,
-	            tp_tasks_ref,               // final TpTask[]            tp_tasks,
-	            clt_parameters.gpu_sigma_r, // final double              gpu_sigma_r,     // 0.9, 1.1
-	            clt_parameters.gpu_sigma_b, // final double              gpu_sigma_b,     // 0.9, 1.1
-	            clt_parameters.gpu_sigma_g, // final double              gpu_sigma_g,     // 0.6, 0.7
-	            clt_parameters.gpu_sigma_m, // final double              gpu_sigma_m,     //  =       0.4; // 0.7;
-	            threadsMax,                 // final int                 threadsMax,       // maximal number of threads to launch
-	            debugLevel);                // final int                 globalDebugLevel);
-        ImagePlus imp_render = scene.renderFromTD (
-                clt_parameters,                                 // CLTParameters clt_parameters,
-                clt_parameters.getColorProcParameters(scene.isAux()), //ColorProcParameters colorProcParameters,
-                clt_parameters.getRGBParameters(),              //EyesisCorrectionParameters.RGBParameters rgbParameters,
-				null, // int []  wh,
-                toRGB, // boolean toRGB,
-                use_reference, //boolean use_reference
-                suffix); // String  suffix)
-		return imp_render;
-	}
-	
 	
 	public ImagePlus renderFromTD (
+			int         sensor_mask,
 			CLTParameters clt_parameters,
 			ColorProcParameters colorProcParameters,
 			EyesisCorrectionParameters.RGBParameters rgbParameters,
@@ -2183,7 +2125,7 @@ public class QuadCLT extends QuadCLTCPU {
 				wh); //int [] wh
 		// get data back from GPU
 		float [][][] iclt_fimg = new float [getNumSensors()][][];
-		for (int ncam = 0; ncam < iclt_fimg.length; ncam++) {
+		for (int ncam = 0; ncam < iclt_fimg.length; ncam++) if (((1 << ncam) & sensor_mask) != 0){
 			iclt_fimg[ncam] = gpuQuad.getRBG(ncam); // updated window
 		}
 		// 2022/06/15 - handles variable window size
@@ -2213,7 +2155,7 @@ public class QuadCLT extends QuadCLTCPU {
 		}
 		/* Prepare 4-channel images*/
 		ImagePlus [] imps_RGB = new ImagePlus[iclt_fimg.length];
-		for (int ncam = 0; ncam < iclt_fimg.length; ncam++) {
+		for (int ncam = 0; ncam < iclt_fimg.length; ncam++) if (iclt_fimg[ncam] != null){
             String title=String.format("%s%s-%02d",image_name, sAux(), ncam);
 			imps_RGB[ncam] = linearStackToColor( // probably no need to separate and process the second half with quadCLT_aux (!)
 					clt_parameters,
@@ -2243,7 +2185,7 @@ public class QuadCLT extends QuadCLTCPU {
 		int width = imps_RGB[0].getWidth();
 		int height = imps_RGB[0].getHeight();
 		ImageStack array_stack=new ImageStack(width,height);
-		for (int i = 0; i<slice_seq.length; i++){
+		for (int i = 0; i<slice_seq.length; i++) if (imps_RGB[slice_seq[i]] != null){
 			///				if (imps_RGB[slice_seq[i]] != null) {
 			array_stack.addSlice("port_"+slice_seq[i], imps_RGB[slice_seq[i]].getProcessor().getPixels());
 			///				} else {
@@ -2393,7 +2335,7 @@ public class QuadCLT extends QuadCLTCPU {
 		}
 		
 		
-		gpuQuad.execConvertDirect();
+		gpuQuad.execConvertDirect(-1); // boolean erase_clt
 		int mcorr_sel = Correlation2d.corrSelEncode(clt_parameters.img_dtt, getNumSensors());
 
 		if (test_execCorr2D) {
@@ -2961,7 +2903,7 @@ public class QuadCLT extends QuadCLTCPU {
 
 		for (int i = 0; i < NREPEAT; i++ ) {
 			// Direct CLT conversion and aberration correction
-			quadCLT_main.getGPU().execConvertDirect();
+			quadCLT_main.getGPU().execConvertDirect(-1); // boolean erase_clt
 		}
 
 		long startIMCLT=System.nanoTime();

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

@@ -7062,7 +7062,7 @@ public class QuadCLTCPU {
 		  too_cold *= iclt_data.length;
 		  too_hot *= iclt_data.length;
 		  int [] hist = null;
-		  for (int iQuad = 0; iQuad < iclt_data.length; iQuad++) {
+		  for (int iQuad = 0; iQuad < iclt_data.length; iQuad++) if (iclt_data[iQuad] != null){
 			  int [] this_hist = getLwirHistogram(
 					  iclt_data[iQuad][ncol], // double [] data,
 					  hard_cold,
@@ -7079,11 +7079,11 @@ public class QuadCLTCPU {
 		  double [] rel_lim = {
 				  getMarginFromHist(
 						  hist, // histogram
-						  too_cold, // double cumul_val, // cummulative number of items to be ignored
+						  too_cold, // double cumul_val, // cumulative number of items to be ignored
 						  false), // boolean high_marg)
 				  getMarginFromHist(
 						  hist, // histogram
-						  too_hot, // double cumul_val, // cummulative number of items to be ignored
+						  too_hot, // double cumul_val, // cumulative number of items to be ignored
 						  true)}; // boolean high_marg)
 		  double [] abs_lim = {
 				  rel_lim[0] * (hard_hot - hard_cold) + hard_cold,