Mixing noise - random and FPN for performance evaluation

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

@@ -28,64 +28,95 @@ package com.elphel.imagej.cameras;
 import java.util.Properties;
 
 import com.elphel.imagej.common.GenericJTabbedDialog;
+import com.elphel.imagej.tileprocessor.NoiseParameters;
 
 
 public class InterNoiseParameters {
-	public double noise_sigma =        1.5;
-	public double noise_scale =        0.01;
-	public double initial_offset =     1.0;
+	public NoiseParameters noise = new NoiseParameters (0.1, 0.0, 1.5, 1.0, 16);
+//	public double noise_sigma =        1.5;
+//	public double noise_scale =        0.01;
+//	public double initial_offset =     1.0;
 	public boolean ref_only =          false; // also see imgdtt_params.dbg_pair_mask to switch between all pairs (63) and binocular only (1)
+	public boolean show_final_2d =     true;  // show 2d correlations during last interation step
 	public int     noise_debug_level = -1; // Noise testing debug level
 
 	
 	public void dialogQuestions(GenericJTabbedDialog gd) {
 		gd.addMessage("Additive noise parameters");
 		gd.addMessage("LMA other parameters");
-		gd.addNumericField("Noise Gaussian sigma",                            this.noise_sigma, 3,5,"pix",
+		gd.addNumericField("Noise Gaussian sigma",                            this.noise.sigma,          3,5,"pix",
 				"Blur noise with 2D Gaussian");
-		gd.addNumericField("Scale noise",                                     this.noise_scale, 6,8,"",
+		gd.addNumericField("Scale noise random (each scene indepemdent)",     this.noise.scale_random,   6,8,"",
+				"Scale noise relative to the average value of the color component");
+		gd.addNumericField("Scale noise FPN (same for each scene)",           this.noise.scale_fpn,      6,8,"",
 				"Scale noise relative to the average value of the color component.");
-		gd.addNumericField("Offset target disparity",                         this.initial_offset, 3,5,"pix",
+		gd.addNumericField("Offset target disparity",                         this.noise.initial_offset, 3,5,"pix",
 				"Offset target disparity before attempting to correlate and refine.");
+		gd.addNumericField("Subset number of sensors (2/4/8/16)",             this.noise.used_sensors,   0,3,"",
+				"Performance comparison - use only some of 16 sensors");
+		
 		gd.addCheckbox    ("Reference scene only",                            this.ref_only,
 				"Process only reference scene (intra-scene, no inter-scene accumulation).");
-		gd.addNumericField("Debug level",                                     this.noise_debug_level, 0,3,"",
+		gd.addCheckbox    ("Show 2d correlations for the last iteration",     this.show_final_2d,
+				"Show single-scene and interframe 2d correlations for the last iteration");
+		gd.addNumericField("Debug level",                                     this.noise_debug_level,    0,3,"",
 				"Debug level of interscene noise testing.");
 		
 	}
 	public void dialogAnswers(GenericJTabbedDialog gd) {
-		this.noise_sigma =                 gd.getNextNumber();
-		this.noise_scale =                 gd.getNextNumber();
-		this.initial_offset =              gd.getNextNumber();
+		this.noise.sigma =                 gd.getNextNumber();
+		this.noise.scale_random =          gd.getNextNumber();
+		this.noise.scale_fpn =             gd.getNextNumber();
+		this.noise.initial_offset =        gd.getNextNumber();
+		this.noise.used_sensors =    (int) gd.getNextNumber();
 		this.ref_only =                    gd.getNextBoolean();
+		this.show_final_2d =               gd.getNextBoolean();
 		this.noise_debug_level =     (int) gd.getNextNumber();
 	}
 	
 	public void setProperties(String prefix,Properties properties){
-		properties.setProperty(prefix+"noise_sigma",          this.noise_sigma+"");	
-		properties.setProperty(prefix+"noise_scale",          this.noise_scale+"");	
-		properties.setProperty(prefix+"initial_offset",       this.initial_offset+"");	
-		properties.setProperty(prefix+"ref_only",       this.ref_only+"");	
-		properties.setProperty(prefix+"noise_debug_level",       this.noise_debug_level+"");	
+		properties.setProperty(prefix+"noise.sigma",          this.noise.sigma+"");	
+		properties.setProperty(prefix+"noise.scale_random",   this.noise.scale_random+"");	
+		properties.setProperty(prefix+"noise.scale_fpn",      this.noise.scale_fpn+"");	
+		properties.setProperty(prefix+"noise.initial_offset", this.noise.initial_offset+"");	
+		properties.setProperty(prefix+"noise.used_sensors",   this.noise.used_sensors+"");	
+		properties.setProperty(prefix+"ref_only",             this.ref_only+"");	
+		properties.setProperty(prefix+"show_final_2d",        this.show_final_2d+"");	
+		properties.setProperty(prefix+"noise_debug_level",    this.noise_debug_level+"");	
 	}
 	public void getProperties(String prefix,Properties properties){
-		if (properties.getProperty(prefix+"noise_sigma")!=null)       this.noise_sigma=Double.parseDouble(properties.getProperty(prefix+"noise_sigma"));
-		if (properties.getProperty(prefix+"noise_scale")!=null)       this.noise_scale=Double.parseDouble(properties.getProperty(prefix+"noise_scale"));
-		if (properties.getProperty(prefix+"initial_offset")!=null)    this.initial_offset=Double.parseDouble(properties.getProperty(prefix+"initial_offset"));
+		if (properties.getProperty(prefix+"noise.sigma")!=null) {
+			this.noise.sigma=Double.parseDouble(properties.getProperty(prefix+"noise.sigma"));
+		} else if (properties.getProperty(prefix+"noise_sigma")!=null) { // old format
+			this.noise.sigma=Double.parseDouble(properties.getProperty(prefix+"noise_sigma"));
+		}
+		if (properties.getProperty(prefix+"noise.scale_random")!=null) {
+			this.noise.scale_random=Double.parseDouble(properties.getProperty(prefix+"noise.scale_random"));
+		} else if (properties.getProperty(prefix+"noise_scale")!=null) {
+			this.noise.scale_random=Double.parseDouble(properties.getProperty(prefix+"noise_scale"));
+		}
+		if (properties.getProperty(prefix+"noise.scale_fpn")!=null) this.noise.scale_fpn=Double.parseDouble(properties.getProperty(prefix+"noise.scale_fpn"));
+		
+		if (properties.getProperty(prefix+"noise.initial_offset")!=null) {
+			this.noise.initial_offset=Double.parseDouble(properties.getProperty(prefix+"noise.initial_offset"));
+		} else if (properties.getProperty(prefix+"initial_offset")!=null) {
+			this.noise.initial_offset=Double.parseDouble(properties.getProperty(prefix+"initial_offset"));
+		}
+		if (properties.getProperty(prefix+"noise.used_sensors")!=null) this.noise.used_sensors=Integer.parseInt(properties.getProperty(prefix+"noise.used_sensors"));
+
 		if (properties.getProperty(prefix+"ref_only")!=null)          this.ref_only=Boolean.parseBoolean(properties.getProperty(prefix+"ref_only"));
+		
+		if (properties.getProperty(prefix+"show_final_2d")!=null)     this.show_final_2d=Boolean.parseBoolean(properties.getProperty(prefix+"show_final_2d"));
+		
 		if (properties.getProperty(prefix+"noise_debug_level")!=null) this.noise_debug_level=Integer.parseInt(properties.getProperty(prefix+"noise_debug_level"));
 	}
 	@Override
 	public InterNoiseParameters clone() throws CloneNotSupportedException {
-		InterNoiseParameters inp =     new InterNoiseParameters();
-		inp.noise_sigma =          this.noise_sigma;
-		inp.noise_scale =          this.noise_scale;
-		inp.initial_offset =       this.initial_offset;
+		InterNoiseParameters inp = new InterNoiseParameters();
+		inp.noise =                this.noise.clone();
 		inp.ref_only =             this.ref_only;
+		inp.show_final_2d =        this.show_final_2d;
 		inp.noise_debug_level =    this.noise_debug_level;
 		return inp;
 	}	
-	
-	
-	
 }

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

+package com.elphel.imagej.tileprocessor;
+
+import com.elphel.imagej.cameras.InterNoiseParameters;
+
+public class NoiseParameters {
+	public double scale_random =   0.1;
+	public double scale_fpn    =   0.0;
+	public double sigma        =   1.5;
+	public double initial_offset = 1.0;
+	public int    used_sensors =   16; // 2/4/8/16
+	
+	public NoiseParameters (
+			double scale_random,
+			double scale_fpn,
+			double sigma,
+			double initial_offset,
+			int used_sensors) {
+		this.scale_random = scale_random;
+		this.scale_fpn = scale_fpn;
+		this.sigma = sigma;
+		this.initial_offset= initial_offset;
+		this.used_sensors = used_sensors;
+	}
+	@Override
+	public NoiseParameters clone() throws CloneNotSupportedException {
+		return  new NoiseParameters(
+				scale_random,
+				scale_fpn,
+				sigma,
+				initial_offset,
+				used_sensors);
+	}	
+	
+}

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

@@ -228,7 +228,8 @@ public class QuadCLTCPU {
 			String               set_name,
 			CLTParameters        clt_parameters,
 			ColorProcParameters  colorProcParameters,
-			double []            noise_sigma_level,
+			NoiseParameters		 noise_sigma_level,
+			QuadCLTCPU           ref_scene, // may be null if scale_fpn <= 0
 			int                  threadsMax,
 			int                  debugLevel)
 	{
@@ -238,6 +239,7 @@ public class QuadCLTCPU {
 				clt_parameters,
 				colorProcParameters,
 				noise_sigma_level, // double []            noise_sigma_level,
+				ref_scene,         // QuadCLTCPU     ref_scene, // may be null if scale_fpn <= 0
 				threadsMax,
 				debugLevel);
 		
@@ -282,7 +284,8 @@ public class QuadCLTCPU {
 		quadCLT.restoreFromModel(
 				clt_parameters,
 				colorProcParameters,
-				null,                 // double []    noise_sigma_level,				
+				null,                 // double []    noise_sigma_level,
+				null, // final QuadCLTCPU     ref_scene, // may be null if scale_fpn <= 0
 				threadsMax,
 				debugLevel);
 		
@@ -614,7 +617,9 @@ public class QuadCLTCPU {
 	public QuadCLTCPU restoreFromModel(
 			CLTParameters        clt_parameters,
 			ColorProcParameters  colorProcParameters,
-			double []            noise_sigma_level,
+//			double []
+			NoiseParameters	     noise_sigma_level,
+			QuadCLTCPU           ref_scene, // may be null if scale_fpn <= 0
 			int                  threadsMax,
 			int                  debugLevel)
 
@@ -654,6 +659,7 @@ public class QuadCLTCPU {
 		if (noise_sigma_level != null) {
 			generateAddNoise(
 					"-NOISE",
+					ref_scene, // final QuadCLTCPU ref_scene, // may be null if scale_fpn <= 0
 					noise_sigma_level,
 					threadsMax,
 					1); // debugLevel); // final int       debug_level)
@@ -686,12 +692,110 @@ public class QuadCLTCPU {
 	
 	public void generateAddNoise(
 			final String    suffix,
-			final double [] noise_sigma_level,
+			final QuadCLTCPU ref_scene, // may be null if scale_fpn <= 0
+//			final double [] 
+			final NoiseParameters noise_sigma_level,
+			final int       threadsMax,
+			final int       debug_level)
+	{
+		final double scale_random = noise_sigma_level.scale_random; // _sigma_level[0];
+		final double scale_fpn =    noise_sigma_level.scale_fpn;    // noise_sigma_level[0];
+		final double sigma =        noise_sigma_level.sigma; // [1];
+		ImagePlus imp = generateAddNoise(
+				suffix,       // final String    suffix,
+				sigma,        // final double    sigma,
+				threadsMax, // final int       threadsMax,
+				debug_level); // final int       debug_level) : null;
+		
+		ImagePlus imp_ref = null;
+		if (scale_fpn >0){
+			if (ref_scene !=null) {
+			imp_ref= ref_scene.generateAddNoise(
+					suffix,       // final String    suffix,
+					sigma,        // final double    sigma,
+					threadsMax, // final int       threadsMax,
+					debug_level); // final int       debug_level) : null;
+			} else {
+				imp_ref= imp; // when calculating ref_scene itself it is provided as null
+			}
+		}
+		
+		
+		final int num_cams = this.image_data.length;
+		final int num_cols = image_data[0].length;
+		final Thread[] threads = ImageDtt.newThreadArray(threadsMax);
+		final AtomicInteger ai = new AtomicInteger(0);
+		ImageStack imageStack = imp.getStack();
+		final float [][] fpixels = new float [num_cams][];
+		for (int q = 0; q < num_cams; q++) {
+			fpixels[q] = (float[]) imageStack.getPixels(q+1);
+		}
+		final float [][] fpixels_ref = (imp_ref != null) ? (new float [num_cams][]): null;
+		if (imp_ref != null) {
+			ImageStack imageStack_ref = imp_ref.getStack();
+			for (int q = 0; q < num_cams; q++) {
+				fpixels_ref[q] = (float[]) imageStack_ref.getPixels(q+1);
+			}
+		}
+		
+		
+		for (int q = 0; q < num_cams; q++) {
+			final int fq = q;
+			for (int c =0; c < num_cols; c++) {
+				final int fc = c;
+				ai.set(0);
+				for (int ithread = 0; ithread < threads.length; ithread++) {
+					threads[ithread] = new Thread() {
+						public void run() {
+							for (int i = ai.getAndIncrement(); i < image_data[fq][fc].length; i = ai.getAndIncrement()) {
+								if (image_data[fq][fc][i] != 0.0) {
+									image_data[fq][fc][i] += scale_random * fpixels[fq][i];
+									if (fpixels_ref != null) {
+										image_data[fq][fc][i] += scale_fpn * fpixels_ref[fq][i];
+									}
+								}
+							}
+						}
+					};
+				}		      
+				ImageDtt.startAndJoin(threads);
+			}			
+		}
+		if (debug_level > 100) {
+			double [][] dbg_data = new double [num_cams*num_cols][];
+			for (int q = 0; q < num_cams;q++) {
+				for (int c = 0; c < num_cols; c++) {
+					dbg_data[q*num_cols+c] = image_data[q][c];
+				}
+			}
+			int [] image_wh = geometryCorrection.getSensorWH();
+			String noise_suffix = suffix + sigma;
+			saveDoubleArrayInModelDirectory(
+					noise_suffix + "-MIXED-RND"+scale_random+"-FPN"+scale_fpn, // noise_sigma_level[0],  // String      suffix,
+					null,          // String []   labels, // or null
+					dbg_data,         // double [][] data,
+					image_wh[0],   // int         width,
+					image_wh[1]);  // int         height)
+		}
+	}
+	
+
+	
+	// May need to run twice - for both refscene and this one if fpn >=0
+	/**
+	 * Load existing noise image, generate if it did no exist 
+	 * @param suffix file name suffix (sigma will be added)
+	 * @param sigma blur sigma (in pixels), the amount of added noise will be used by caller, noise image only depends on sigma 
+	 * @param threadsMax
+	 * @param debug_level
+	 * @return Noise image, one slice per sensor (Bayer mosaic still use 1 slice per sensor)
+	 */
+	public ImagePlus generateAddNoise(
+			final String    suffix,
+			final double    sigma,
 			final int       threadsMax,
 			final int       debug_level)
 	{
-		final double scale =noise_sigma_level[0];
-		final double sigma =noise_sigma_level[1];
 		final int num_cams = this.image_data.length;
 		final int num_cols = image_data[0].length;
 		final int [] image_wh = geometryCorrection.getSensorWH();
@@ -815,45 +919,12 @@ public class QuadCLTCPU {
 					image_wh[0],   // int         width,
 					image_wh[1]);  // int         height)
 		}
-		ImageStack imageStack = imp.getStack();
-		float [][] fpixels = new float [num_cams][];
-		for (int q = 0; q < num_cams; q++) {
-			fpixels[q] = (float[]) imageStack.getPixels(q+1);
-		}
-		for (int q = 0; q < num_cams; q++) {
-			final int fq = q;
-			for (int c =0; c < num_cols; c++) {
-				final int fc = c;
-				ai.set(0);
-				for (int ithread = 0; ithread < threads.length; ithread++) {
-					threads[ithread] = new Thread() {
-						public void run() {
-							for (int i = ai.getAndIncrement(); i < image_data[fq][fc].length; i = ai.getAndIncrement()) {
-								if (image_data[fq][fc][i] != 0.0) {
-									image_data[fq][fc][i] += scale * fpixels[fq][i];
-								}
-							}
-						}
-					};
-				}		      
-				ImageDtt.startAndJoin(threads);
-			}			
-		}
-		if (debug_level > 100) {
-			double [][] dbg_data = new double [num_cams*num_cols][];
-			for (int q = 0; q < num_cams;q++) {
-				for (int c = 0; c < num_cols; c++) {
-					dbg_data[q*num_cols+c] = image_data[q][c];
-				}
-			}
-			saveDoubleArrayInModelDirectory(
-					noise_suffix + "-MIXED"+noise_sigma_level[0],  // String      suffix,
-					null,          // String []   labels, // or null
-					dbg_data,         // double [][] data,
-					image_wh[0],   // int         width,
-					image_wh[1]);  // int         height)
-		}
-	}
+		return imp;
+	}	
+	
+	
+	
+	
 	
 	
 	public ImagePlus saveDoubleArrayInModelDirectory(
@@ -874,6 +945,7 @@ public class QuadCLTCPU {
 		ImagePlus imp = new ImagePlus( file_name, imageStack);
 		FileSaver fs=new FileSaver(imp);
 		fs.saveAsTiff(file_path);
+		System.out.println("saveDoubleArrayInModelDirectory(): saved "+file_path);
 		return imp;
 	}
 	

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

@@ -8619,6 +8619,7 @@ if (debugLevel > -100) return true; // temporarily !
 				clt_parameters,
 				colorProcParameters, //
 				null, // noise_sigma_level,   // double []            noise_sigma_level,
+				null, // final QuadCLTCPU     ref_scene, // may be null if scale_fpn <= 0
 				threadsMax,
 				debugLevel);
 		// temporarily fix wrong sign:
@@ -8664,12 +8665,16 @@ if (debugLevel > -100) return true; // temporarily !
 //		double []            noise_sigma_level = {1.0, 1.5, 1.0};  // amount, sigma, offset
 //		double []            noise_sigma_level = {3.0, 1.5, 1.0};  // amount, sigma, offset
 //		double []            noise_sigma_level = {5.0, 1.5, 1.0};  // amount, sigma, offset
-		double []            noise_sigma_level = null;
-		if (clt_parameters.inp.noise_scale > 0.0) {
-			noise_sigma_level = new double[] {
+//		double []            noise_sigma_level = null;
+		NoiseParameters      noise_sigma_level = null;
+		if ((clt_parameters.inp.noise.scale_random  > 0.0) || (clt_parameters.inp.noise.scale_fpn  > 0.0)){
+			noise_sigma_level = clt_parameters.inp.noise.clone();
+			/*		
+					new double[] {
 					clt_parameters.inp.noise_scale,
 					clt_parameters.inp.noise_sigma,
 					clt_parameters.inp.initial_offset};  // amount, sigma, offset
+					*/
 		}
 		
 		boolean ref_only =  clt_parameters.inp.ref_only; //  true; // process only reference frame (false - inter-scene)
@@ -8692,6 +8697,7 @@ if (debugLevel > -100) return true; // temporarily !
 				clt_parameters,
 				colorProcParameters, //
 				noise_sigma_level,   // double []            noise_sigma_level,
+				null,                // QuadCLTCPU           ref_scene, // may be null if scale_fpn <= 0
 				threadsMax,
 				clt_parameters.inp.noise_debug_level); // debugLevel);
 		/**/
@@ -8722,12 +8728,16 @@ if (debugLevel > -100) return true; // temporarily !
 //		double []            noise_sigma_level = {1.0, 1.5, 1.0};  // amount, sigma, offset
 //		double []            noise_sigma_level = {3.0, 1.5, 1.0};  // amount, sigma, offset
 //		double []            noise_sigma_level = {5.0, 1.5, 1.0};  // amount, sigma, offset
-		double []            noise_sigma_level = null;
-		if (clt_parameters.inp.noise_scale >= 0.0) {// <0 - will generate no-noise data
-			noise_sigma_level = new double[] {
+//		double []            noise_sigma_level = null;
+		NoiseParameters            noise_sigma_level = null;
+		if ((clt_parameters.inp.noise.scale_random >= 0.0) || (clt_parameters.inp.noise.scale_fpn >= 0.0)) {// <0 - will generate no-noise data
+			noise_sigma_level = clt_parameters.inp.noise.clone();
+					/*
+					noise_sigma_level = new double[] {
 					clt_parameters.inp.noise_scale,
 					clt_parameters.inp.noise_sigma,
-					clt_parameters.inp.initial_offset};  // amount, sigma, offset
+					clt_parameters.inp.initial_offset};  // amount, sigma, offset\
+        */					
 		}
 		
 		boolean ref_only =  clt_parameters.inp.ref_only; //  true; // process only reference frame (false - inter-scene)
@@ -8750,6 +8760,7 @@ if (debugLevel > -100) return true; // temporarily !
 				clt_parameters,
 				colorProcParameters, //
 				noise_sigma_level,   // double []            noise_sigma_level,
+				null, // final QuadCLTCPU     ref_scene, // may be null if scale_fpn <= 0
 				threadsMax,
 				clt_parameters.inp.noise_debug_level); // debugLevel);
 		/*
@@ -8760,7 +8771,10 @@ if (debugLevel > -100) return true; // temporarily !
 		*/
 		// Create 4-slice image with noise from the current data
 		if (noise_sigma_level != null) {
-			String noisy_4slice_suffix = "-noise-level_"+ noise_sigma_level[0]+"-sigma_"+noise_sigma_level[1];
+			String noisy_4slice_suffix =
+					"-noise-random_"+ noise_sigma_level.scale_random+
+					"-noise-fpn_"+    noise_sigma_level.scale_fpn+
+					"-sigma_"+noise_sigma_level.sigma;
 			ref_quadCLT.genSave4sliceImage(
 					clt_parameters,        // CLTParameters                                   clt_parameters,
 					noisy_4slice_suffix,   // String                                          suffix,