trying with actual kernels (91616de2) · Commits · Elphel / imagej-elphel

src/main/java/EyesisCorrectionParameters.java

+59 −26

Original line number	Original line	Diff line number	Diff line
	@@ -1666,7 +1666,15 @@ public class EyesisCorrectionParameters {
	public double dbg_sigma =2.0;		public double dbg_sigma =2.0;
	public String dbg_mask = ".........:::::::::.........:::::::::........::::::::.........:::::::::.........";		public String dbg_mask = ".........:::::::::.........:::::::::........::::::::.........:::::::::.........";
	public int dbg_mode = 1; // 0 - old LMA, 1 - new LMA		public int dbg_mode = 1; // 0 - old LMA, 1 - new LMA
	public int dbg_window_mode = 2; // 0 - none, 1 - square, 2 - sin		public int dbg_window_mode = 2; // 0 - none, 1 - square, 2 - sin 3 - sin^2
			public boolean centerWindowToTarget = true;
			// parameters to extract a kernel from the kernel image file
			public int color_channel = 2; // green (<0 - use simulated kernel, also will use simulated if kernels are not set)
			public int decimation = 2; // decimate original kernel this much in each direction
			public double decimateSigma = 0.4; // what is the optimal value for each decimation?
			public int tileX = 82; // number of kernel tile (0..163)
			public int tileY = 62; // number of kernel tile (0..122)


	public DCTParameters(		public DCTParameters(
	int dct_size,		int dct_size,
	@@ -1697,7 +1705,6 @@ public class EyesisCorrectionParameters {
	properties.setProperty(prefix+"asym_tax_free", this.asym_tax_free+"");		properties.setProperty(prefix+"asym_tax_free", this.asym_tax_free+"");
	properties.setProperty(prefix+"seed_size", this.seed_size+"");		properties.setProperty(prefix+"seed_size", this.seed_size+"");
	properties.setProperty(prefix+"asym_random", this.asym_random+"");		properties.setProperty(prefix+"asym_random", this.asym_random+"");

	properties.setProperty(prefix+"LMA_steps", this.LMA_steps+"");		properties.setProperty(prefix+"LMA_steps", this.LMA_steps+"");
	properties.setProperty(prefix+"dbg_x", this.dbg_x+"");		properties.setProperty(prefix+"dbg_x", this.dbg_x+"");
	properties.setProperty(prefix+"dbg_y", this.dbg_y+"");		properties.setProperty(prefix+"dbg_y", this.dbg_y+"");
	@@ -1707,6 +1714,12 @@ public class EyesisCorrectionParameters {
	properties.setProperty(prefix+"dbg_mask", this.dbg_mask+"");		properties.setProperty(prefix+"dbg_mask", this.dbg_mask+"");
	properties.setProperty(prefix+"dbg_mode", this.dbg_mode+"");		properties.setProperty(prefix+"dbg_mode", this.dbg_mode+"");
	properties.setProperty(prefix+"dbg_window_mode", this.dbg_window_mode+"");		properties.setProperty(prefix+"dbg_window_mode", this.dbg_window_mode+"");
			properties.setProperty(prefix+"centerWindowToTarget", this.centerWindowToTarget+"");
			properties.setProperty(prefix+"color_channel", this.color_channel+"");
			properties.setProperty(prefix+"decimation", this.dbg_window_mode+"");
			properties.setProperty(prefix+"decimateSigma", this.decimateSigma+"");
			properties.setProperty(prefix+"tileX", this.tileX+"");
			properties.setProperty(prefix+"tileY", this.tileY+"");

	}		}
	public void getProperties(String prefix,Properties properties){		public void getProperties(String prefix,Properties properties){
	@@ -1728,32 +1741,46 @@ public class EyesisCorrectionParameters {
	if (properties.getProperty(prefix+"dbg_sigma")!=null) this.dbg_sigma=Double.parseDouble(properties.getProperty(prefix+"dbg_sigma"));		if (properties.getProperty(prefix+"dbg_sigma")!=null) this.dbg_sigma=Double.parseDouble(properties.getProperty(prefix+"dbg_sigma"));
	if (properties.getProperty(prefix+"dbg_mask")!=null) this.dbg_mask=properties.getProperty(prefix+"dbg_mask");		if (properties.getProperty(prefix+"dbg_mask")!=null) this.dbg_mask=properties.getProperty(prefix+"dbg_mask");
	if (properties.getProperty(prefix+"dbg_mode")!=null) this.dbg_mode=Integer.parseInt(properties.getProperty(prefix+"dbg_mode"));		if (properties.getProperty(prefix+"dbg_mode")!=null) this.dbg_mode=Integer.parseInt(properties.getProperty(prefix+"dbg_mode"));
			if (properties.getProperty(prefix+"tileY")!=null) this.tileY=Integer.parseInt(properties.getProperty(prefix+"tileY"));

			if (properties.getProperty(prefix+"centerWindowToTarget")!=null) this.centerWindowToTarget=Boolean.parseBoolean(properties.getProperty(prefix+"centerWindowToTarget"));
			if (properties.getProperty(prefix+"color_channel")!=null) this.color_channel=Integer.parseInt(properties.getProperty(prefix+"color_channel"));
			if (properties.getProperty(prefix+"decimation")!=null) this.decimation=Integer.parseInt(properties.getProperty(prefix+"decimation"));
			if (properties.getProperty(prefix+"decimateSigma")!=null) this.decimateSigma=Double.parseDouble(properties.getProperty(prefix+"decimateSigma"));
			if (properties.getProperty(prefix+"tileX")!=null) this.tileX=Integer.parseInt(properties.getProperty(prefix+"tileX"));
	if (properties.getProperty(prefix+"dbg_window_mode")!=null) this.dbg_window_mode=Integer.parseInt(properties.getProperty(prefix+"dbg_window_mode"));		if (properties.getProperty(prefix+"dbg_window_mode")!=null) this.dbg_window_mode=Integer.parseInt(properties.getProperty(prefix+"dbg_window_mode"));


	}		}
	public boolean showDialog() {		public boolean showDialog() {
	GenericDialog gd = new GenericDialog("Set DCT parameters");		GenericDialog gd = new GenericDialog("Set DCT parameters");
	gd.addNumericField("DCT size", this.dct_size, 0); //32		gd.addNumericField("DCT size", this.dct_size, 0);
	gd.addNumericField("Size of asymmetrical (non-DCT) kernel", this.asym_size, 0); //6		gd.addNumericField("Size of asymmetrical (non-DCT) kernel", this.asym_size, 0);
	gd.addNumericField("Maximal number of non-zero pixels in direct convolution kernel", this.asym_pixels, 0); //6		gd.addNumericField("Maximal number of non-zero pixels in direct convolution kernel", this.asym_pixels, 0);
	gd.addNumericField("How far to try a new asym kernel pixel from existing ones", this.asym_distance, 0); //6		gd.addNumericField("How far to try a new asym kernel pixel from existing ones", this.asym_distance, 0);
	gd.addNumericField("MDCT window type (0,1,2)", this.dct_window, 0); //0..2		gd.addNumericField("MDCT window type (0,1,2)", this.dct_window, 0);
	gd.addNumericField("LMA_steps", this.LMA_steps, 0); //0..2		gd.addNumericField("LMA_steps", this.LMA_steps, 0);
	gd.addNumericField("Compactness (punish off-center asym_kernel pixels (proportional to r^2)", this.compactness, 2); //0..2		gd.addNumericField("Compactness (punish off-center asym_kernel pixels (proportional to r^2)", this.compactness,2);
	gd.addNumericField("Factorization target precision (stop if achieved)", this.fact_precision, 4); //0..2		gd.addNumericField("Factorization target precision (stop if achieved)", this.fact_precision, 4);
	gd.addNumericField("Do not punish pixels in the square around center", this.asym_tax_free, 0); //0..2		gd.addNumericField("Do not punish pixels in the square around center", this.asym_tax_free, 0);
	gd.addNumericField("Start asym_kernel with this number of pixels (0 - single, 4n+0 (X between cells), 4*n+1 - x around center cell", this.seed_size, 0); //0..2		gd.addNumericField("Start asym_kernel with this number of pixels (0 - single, 4n+0 (X between cells), 4*n+1 - x around center cell", this.seed_size, 0); //0..2
	gd.addNumericField("Initialize asym_kernel with random numbers (amplitude)", this.asym_random, 2); //0..2		gd.addNumericField("Initialize asym_kernel with random numbers (amplitude)", this.asym_random, 2);
	gd.addNumericField("dbg_x", this.dbg_x, 2); //0..2		gd.addNumericField("dbg_x", this.dbg_x, 2);
	gd.addNumericField("dbg_y", this.dbg_y, 2); //0..2		gd.addNumericField("dbg_y", this.dbg_y, 2);
	gd.addNumericField("dbg_x1", this.dbg_x1, 2); //0..2		gd.addNumericField("dbg_x1", this.dbg_x1, 2);
	gd.addNumericField("dbg_y1", this.dbg_y1, 2); //0..2		gd.addNumericField("dbg_y1", this.dbg_y1, 2);
	gd.addNumericField("dbg_sigma", this.dbg_sigma, 3); //0..2		gd.addNumericField("dbg_sigma", this.dbg_sigma, 3);
	gd.addStringField ("Debug mask (anything but * is false)", this.dbg_mask, 100);		gd.addStringField ("Debug mask (anything but * is false)", this.dbg_mask, 100);
	gd.addNumericField("LMA implementation: 0 - old, 1 - new", this.dbg_mode, 0); //32		gd.addNumericField("LMA implementation: 0 - old, 1 - new", this.dbg_mode, 0);
	gd.addNumericField("Convolution window: 0 - none, 1 - square, 2 - sin, 3 - sin^2", this.dbg_window_mode, 0); //32		gd.addNumericField("Convolution window: 0 - none, 1 - square, 2 - sin, 3 - sin^2", this.dbg_window_mode, 0);
			gd.addCheckbox ("Center convolution window around target kernel center", this.centerWindowToTarget);
	// gd.addNumericField("Debug Level:", MASTER_DEBUG_LEVEL, 0);		gd.addNumericField("Color channel to extract kernel (<0 - use synthetic)", this.color_channel, 0);
			gd.addNumericField("Convolution kernel decimation (original is normally 2x)", this.decimation, 0);
			gd.addNumericField("Smooth convolution kernel before decimation", this.decimateSigma, 3);
			gd.addNumericField("Tile X to extract (0..163)", this.tileX, 0);
			gd.addNumericField("Tile Y to extract (0..122)", this.tileY, 0);
	gd.showDialog();		gd.showDialog();

	if (gd.wasCanceled()) return false;		if (gd.wasCanceled()) return false;
	this.dct_size= (int) gd.getNextNumber();		this.dct_size= (int) gd.getNextNumber();
	this.asym_size= (int) gd.getNextNumber();		this.asym_size= (int) gd.getNextNumber();
	@@ -1774,6 +1801,12 @@ public class EyesisCorrectionParameters {
	this.dbg_mask= gd.getNextString();		this.dbg_mask= gd.getNextString();
	this.dbg_mode= (int) gd.getNextNumber();		this.dbg_mode= (int) gd.getNextNumber();
	this.dbg_window_mode= (int) gd.getNextNumber();		this.dbg_window_mode= (int) gd.getNextNumber();
			this.centerWindowToTarget= gd.getNextBoolean();
			this.color_channel= (int) gd.getNextNumber();
			this.decimation= (int) gd.getNextNumber();
			this.decimateSigma= gd.getNextNumber();
			this.tileX= (int) gd.getNextNumber();
			this.tileY= (int) gd.getNextNumber();

	// MASTER_DEBUG_LEVEL= (int) gd.getNextNumber();		// MASTER_DEBUG_LEVEL= (int) gd.getNextNumber();
	return true;		return true;

src/main/java/EyesisDCT.java

+228 −35

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/Eyesis_Correction.java

+172 −128

Original line number	Original line	Diff line number	Diff line
	@@ -456,6 +456,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
	addButton("DCT test 4", panelDct1, color_process);		addButton("DCT test 4", panelDct1, color_process);
	addButton("Test Kernel Factorization", panelDct1, color_process);		addButton("Test Kernel Factorization", panelDct1, color_process);
	addButton("Min Kernel Factorization", panelDct1, color_process);		addButton("Min Kernel Factorization", panelDct1, color_process);
			addButton("Select kernels image", panelDct1, color_configure);
	addButton("Create DCT kernels", panelDct1, color_process);		addButton("Create DCT kernels", panelDct1, color_process);
	add(panelDct1);		add(panelDct1);
	}		}
	@@ -2838,14 +2839,33 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
	if (!DCT_PARAMETERS.showDialog()) return;		if (!DCT_PARAMETERS.showDialog()) return;
	FactorConvKernel factorConvKernel = new FactorConvKernel(DCT_PARAMETERS.dbg_mode == 1);		FactorConvKernel factorConvKernel = new FactorConvKernel(DCT_PARAMETERS.dbg_mode == 1);
	factorConvKernel.setDebugLevel(DEBUG_LEVEL);		factorConvKernel.setDebugLevel(DEBUG_LEVEL);
	factorConvKernel.setTargetWindowMode(DCT_PARAMETERS.dbg_window_mode);		factorConvKernel.setTargetWindowMode(DCT_PARAMETERS.dbg_window_mode, DCT_PARAMETERS.centerWindowToTarget);
	factorConvKernel.numIterations = DCT_PARAMETERS.LMA_steps;		factorConvKernel.numIterations = DCT_PARAMETERS.LMA_steps;
	factorConvKernel.setAsymCompactness(		factorConvKernel.setAsymCompactness(
	DCT_PARAMETERS.compactness,		DCT_PARAMETERS.compactness,
	DCT_PARAMETERS.asym_tax_free);		DCT_PARAMETERS.asym_tax_free);

	int target_kernel_size = 2*DCT_PARAMETERS.dct_size - 1;		int target_kernel_size = 2*DCT_PARAMETERS.dct_size - 1;
			int target_expanded_size = 2*DCT_PARAMETERS.dct_size + DCT_PARAMETERS.asym_size -2;
			double [] target_expanded = null;
			if ((EYESIS_DCT != null) && EYESIS_DCT.kernelImageSet() && (DCT_PARAMETERS.color_channel >= 0)){
			System.out.println("Using extracted target kernel");
			double [] src_kernel = EYESIS_DCT.extractOneKernelFromStack(
			CONVOLVE_FFT_SIZE/2 , // 64
			DCT_PARAMETERS.color_channel, // 0..2
			DCT_PARAMETERS.tileX, // horizontal number of kernel to extract
			DCT_PARAMETERS.tileY); // vertical number of kernel to extract
			target_expanded = EYESIS_DCT.reformatKernel(
			src_kernel,// will be blured in-place
			CONVOLVE_FFT_SIZE/2, // typical 64
			target_expanded_size, // typical 15
			DCT_PARAMETERS.decimation,// typical 2
			DCT_PARAMETERS.decimateSigma);
			} else {
			System.out.println("Using synthesized target kernel");

	double [] target_kernel = new double [target_kernel_size * target_kernel_size];		double [] target_kernel = new double [target_kernel_size * target_kernel_size];

	for (int ii=0; ii < target_kernel.length; ii++) target_kernel[ii]=0.0;		for (int ii=0; ii < target_kernel.length; ii++) target_kernel[ii]=0.0;
	double dist = Math.sqrt((DCT_PARAMETERS.dbg_x1-DCT_PARAMETERS.dbg_x)*(DCT_PARAMETERS.dbg_x1-DCT_PARAMETERS.dbg_x)+		double dist = Math.sqrt((DCT_PARAMETERS.dbg_x1-DCT_PARAMETERS.dbg_x)*(DCT_PARAMETERS.dbg_x1-DCT_PARAMETERS.dbg_x)+
	(DCT_PARAMETERS.dbg_y1-DCT_PARAMETERS.dbg_y)*(DCT_PARAMETERS.dbg_y1-DCT_PARAMETERS.dbg_y));		(DCT_PARAMETERS.dbg_y1-DCT_PARAMETERS.dbg_y)*(DCT_PARAMETERS.dbg_y1-DCT_PARAMETERS.dbg_y));
	@@ -2880,10 +2900,8 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
	target_kernel[target_kernel_sizeii+jj] = target_kernel[target_kernel_sizeii1+jj1];		target_kernel[target_kernel_sizeii+jj] = target_kernel[target_kernel_sizeii1+jj1];
	}		}
	}		}
			target_expanded = new double [target_expanded_size * target_expanded_size];


	int target_expanded_size = 2*DCT_PARAMETERS.dct_size + DCT_PARAMETERS.asym_size -2;
	double [] target_expanded = new double [target_expanded_size * target_expanded_size];
	for (int ii=0; ii < target_expanded.length; ii++) target_expanded[ii]=0.0;		for (int ii=0; ii < target_expanded.length; ii++) target_expanded[ii]=0.0;
	int left_top_margin = ((DCT_PARAMETERS.asym_size-1)/2);		int left_top_margin = ((DCT_PARAMETERS.asym_size-1)/2);
	for (int ii=0;ii < target_kernel_size; ii++){		for (int ii=0;ii < target_kernel_size; ii++){
	@@ -2892,6 +2910,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
	target_kernel[ii*target_kernel_size + jj];		target_kernel[ii*target_kernel_size + jj];
	}		}
	}		}
			}

	boolean [] mask = null;		boolean [] mask = null;
	if (!DCT_PARAMETERS.dbg_mask.equals("")){		if (!DCT_PARAMETERS.dbg_mask.equals("")){
	@@ -2901,7 +2920,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
	}		}

	}		}
			long startTime = System.nanoTime();
	boolean result = factorConvKernel.calcKernels(		boolean result = factorConvKernel.calcKernels(
	target_expanded,		target_expanded,
	DCT_PARAMETERS.asym_size,		DCT_PARAMETERS.asym_size,
	@@ -2911,6 +2930,11 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
	DCT_PARAMETERS.seed_size,		DCT_PARAMETERS.seed_size,
	DCT_PARAMETERS.asym_random);		DCT_PARAMETERS.asym_random);
	System.out.println("factorConvKernel.calcKernels() returned: >>> "+result+ " <<<");		System.out.println("factorConvKernel.calcKernels() returned: >>> "+result+ " <<<");
			System.out.println(
			"RMS = "+factorConvKernel.getRMSes()[0]+
			", RMSPure = "+factorConvKernel.getRMSes()[1]+
			", relRMSPure = "+(factorConvKernel.getRMSes()[1]/factorConvKernel.getTargetRMS())+
			", spent "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+" sec");
	double [] sym_kernel = factorConvKernel.getSymKernel();		double [] sym_kernel = factorConvKernel.getSymKernel();
	double [] asym_kernel = factorConvKernel.getAsymKernel();		double [] asym_kernel = factorConvKernel.getAsymKernel();
	double [] convolved = factorConvKernel.getConvolved();		double [] convolved = factorConvKernel.getConvolved();
	@@ -2923,11 +2947,12 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
	weighted_diff100[ii] = diff100[ii]* target_weights[ii];		weighted_diff100[ii] = diff100[ii]* target_weights[ii];
	}		}
	double [][] compare_kernels = {target_expanded, convolved, weighted_diff100,target_weights, diff100};		double [][] compare_kernels = {target_expanded, convolved, weighted_diff100,target_weights, diff100};
			if (DEBUG_LEVEL>0) {
	System.out.println("DCT_PARAMETERS.dct_size="+DCT_PARAMETERS.dct_size+" DCT_PARAMETERS.asym_size="+DCT_PARAMETERS.asym_size);		System.out.println("DCT_PARAMETERS.dct_size="+DCT_PARAMETERS.dct_size+" DCT_PARAMETERS.asym_size="+DCT_PARAMETERS.asym_size);
	System.out.println("sym_kernel.length="+ sym_kernel.length);		System.out.println("sym_kernel.length="+ sym_kernel.length);
	System.out.println("asym_kernel.length="+asym_kernel.length);		System.out.println("asym_kernel.length="+asym_kernel.length);
	System.out.println("convolved.length="+convolved.length);		System.out.println("convolved.length="+convolved.length);
			}
	SDFA_INSTANCE.showArrays(sym_kernel, DCT_PARAMETERS.dct_size, DCT_PARAMETERS.dct_size, "sym_kernel");		SDFA_INSTANCE.showArrays(sym_kernel, DCT_PARAMETERS.dct_size, DCT_PARAMETERS.dct_size, "sym_kernel");
	SDFA_INSTANCE.showArrays(asym_kernel, DCT_PARAMETERS.asym_size, DCT_PARAMETERS.asym_size, "asym_kernel");		SDFA_INSTANCE.showArrays(asym_kernel, DCT_PARAMETERS.asym_size, DCT_PARAMETERS.asym_size, "asym_kernel");
	SDFA_INSTANCE.showArrays(compare_kernels, target_expanded_size, target_expanded_size, true, "compare_kernels");		SDFA_INSTANCE.showArrays(compare_kernels, target_expanded_size, target_expanded_size, true, "compare_kernels");
	@@ -2938,13 +2963,29 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
	if (!DCT_PARAMETERS.showDialog()) return;		if (!DCT_PARAMETERS.showDialog()) return;
	FactorConvKernel factorConvKernel = new FactorConvKernel(DCT_PARAMETERS.dbg_mode == 1);		FactorConvKernel factorConvKernel = new FactorConvKernel(DCT_PARAMETERS.dbg_mode == 1);
	factorConvKernel.setDebugLevel(DEBUG_LEVEL);		factorConvKernel.setDebugLevel(DEBUG_LEVEL);
	factorConvKernel.setTargetWindowMode(DCT_PARAMETERS.dbg_window_mode);		factorConvKernel.setTargetWindowMode(DCT_PARAMETERS.dbg_window_mode, DCT_PARAMETERS.centerWindowToTarget);
	factorConvKernel.numIterations = DCT_PARAMETERS.LMA_steps;		factorConvKernel.numIterations = DCT_PARAMETERS.LMA_steps;
	factorConvKernel.setAsymCompactness(		factorConvKernel.setAsymCompactness(
	DCT_PARAMETERS.compactness,		DCT_PARAMETERS.compactness,
	DCT_PARAMETERS.asym_tax_free);		DCT_PARAMETERS.asym_tax_free);

	int target_kernel_size = 2*DCT_PARAMETERS.dct_size - 1;		int target_kernel_size = 2*DCT_PARAMETERS.dct_size - 1;
			int target_expanded_size = 2*DCT_PARAMETERS.dct_size + DCT_PARAMETERS.asym_size -2;
			double [] target_expanded = null;
			if ((EYESIS_DCT != null) && EYESIS_DCT.kernelImageSet() && (DCT_PARAMETERS.color_channel >= 0)){
			System.out.println("Using extracted target kernel");
			double [] src_kernel = EYESIS_DCT.extractOneKernelFromStack(
			CONVOLVE_FFT_SIZE/2 , // 64
			DCT_PARAMETERS.color_channel, // 0..2
			DCT_PARAMETERS.tileX, // horizontal number of kernel to extract
			DCT_PARAMETERS.tileY); // vertical number of kernel to extract
			target_expanded = EYESIS_DCT.reformatKernel(
			src_kernel,// will be blured in-place
			CONVOLVE_FFT_SIZE/2, // typical 64
			target_expanded_size, // typical 15
			DCT_PARAMETERS.decimation,// typical 2
			DCT_PARAMETERS.decimateSigma);
			} else {
			System.out.println("Using synthesized target kernel");
	double [] target_kernel = new double [target_kernel_size * target_kernel_size];		double [] target_kernel = new double [target_kernel_size * target_kernel_size];
	for (int ii=0; ii < target_kernel.length; ii++) target_kernel[ii]=0.0;		for (int ii=0; ii < target_kernel.length; ii++) target_kernel[ii]=0.0;
	double dist = Math.sqrt((DCT_PARAMETERS.dbg_x1-DCT_PARAMETERS.dbg_x)*(DCT_PARAMETERS.dbg_x1-DCT_PARAMETERS.dbg_x)+		double dist = Math.sqrt((DCT_PARAMETERS.dbg_x1-DCT_PARAMETERS.dbg_x)*(DCT_PARAMETERS.dbg_x1-DCT_PARAMETERS.dbg_x)+
	@@ -2959,17 +3000,13 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
	System.out.println(ii+": "+((DCT_PARAMETERS.dbg_x1-DCT_PARAMETERS.dbg_x)*ii/dist + DCT_PARAMETERS.dbg_x)+		System.out.println(ii+": "+((DCT_PARAMETERS.dbg_x1-DCT_PARAMETERS.dbg_x)*ii/dist + DCT_PARAMETERS.dbg_x)+
	" / "+ ((DCT_PARAMETERS.dbg_y1-DCT_PARAMETERS.dbg_y)*ii/dist + DCT_PARAMETERS.dbg_y)+" ("+dbg_x+":"+dbg_y+")");		" / "+ ((DCT_PARAMETERS.dbg_y1-DCT_PARAMETERS.dbg_y)*ii/dist + DCT_PARAMETERS.dbg_y)+" ("+dbg_x+":"+dbg_y+")");
	}		}

	}		}

	double blurSigma = DCT_PARAMETERS.dbg_sigma;		double blurSigma = DCT_PARAMETERS.dbg_sigma;
	DoubleGaussianBlur gb=null;		DoubleGaussianBlur gb=null;
	if (blurSigma>0) gb=new DoubleGaussianBlur();		if (blurSigma>0) gb=new DoubleGaussianBlur();
	if (blurSigma>0) gb.blurDouble(target_kernel, target_kernel_size, target_kernel_size, blurSigma, blurSigma, 0.01);		if (blurSigma>0) gb.blurDouble(target_kernel, target_kernel_size, target_kernel_size, blurSigma, blurSigma, 0.01);
	// SDFA_INSTANCE.showArrays(target_kernel, target_kernel_size, target_kernel_size, "target_kernel");		target_expanded = new double [target_expanded_size * target_expanded_size];

	int target_expanded_size = 2*DCT_PARAMETERS.dct_size + DCT_PARAMETERS.asym_size -2;
	double [] target_expanded = new double [target_expanded_size * target_expanded_size];
	for (int ii=0; ii < target_expanded.length; ii++) target_expanded[ii]=0.0;		for (int ii=0; ii < target_expanded.length; ii++) target_expanded[ii]=0.0;
	int left_top_margin = ((DCT_PARAMETERS.asym_size-1)/2);		int left_top_margin = ((DCT_PARAMETERS.asym_size-1)/2);
	for (int ii=0;ii < target_kernel_size; ii++){		for (int ii=0;ii < target_kernel_size; ii++){
	@@ -2978,7 +3015,8 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
	target_kernel[ii*target_kernel_size + jj];		target_kernel[ii*target_kernel_size + jj];
	}		}
	}		}
			}
			long startTime = System.nanoTime();
	int numPixels = factorConvKernel.calcKernels(		int numPixels = factorConvKernel.calcKernels(
	target_expanded,		target_expanded,
	DCT_PARAMETERS.asym_size,		DCT_PARAMETERS.asym_size,
	@@ -2987,21 +3025,14 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
	DCT_PARAMETERS.asym_pixels,		DCT_PARAMETERS.asym_pixels,
	DCT_PARAMETERS.asym_distance,		DCT_PARAMETERS.asym_distance,
	DCT_PARAMETERS.seed_size);		DCT_PARAMETERS.seed_size);
	/*		System.out.println(
	public int calcKernels(		"calcKernels() number of asym pixels = "+numPixels+
	double []target_kernel,		" RMS = "+factorConvKernel.getRMSes()[0]+
	int asym_size,		", RMSPure = "+factorConvKernel.getRMSes()[1]+
	int sym_radius,		", relRMSPure = "+(factorConvKernel.getRMSes()[1]/factorConvKernel.getTargetRMS())+
	double fact_precision,		", number of LMA runs = "+factorConvKernel.getLMARuns()+
	int asym_pixels, // maximal number of non-zero pixels in asymmmetrical kernel		", spent "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+" sec");
	int asym_distance){ // how far to seed a new pixel

	*/




	System.out.println("factorConvKernel.calcKernels() returned: >>> "+numPixels+ " <<<");
	double [] sym_kernel = factorConvKernel.getSymKernel();		double [] sym_kernel = factorConvKernel.getSymKernel();
	double [] asym_kernel = factorConvKernel.getAsymKernel();		double [] asym_kernel = factorConvKernel.getAsymKernel();
	double [] convolved = factorConvKernel.getConvolved();		double [] convolved = factorConvKernel.getConvolved();
	@@ -3013,11 +3044,12 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
	weighted_diff100[ii] = diff100[ii]* target_weights[ii];		weighted_diff100[ii] = diff100[ii]* target_weights[ii];
	}		}
	double [][] compare_kernels = {target_expanded, convolved, weighted_diff100,target_weights, diff100};		double [][] compare_kernels = {target_expanded, convolved, weighted_diff100,target_weights, diff100};
			if (DEBUG_LEVEL>0) {
	System.out.println("DCT_PARAMETERS.dct_size="+DCT_PARAMETERS.dct_size+" DCT_PARAMETERS.asym_size="+DCT_PARAMETERS.asym_size);		System.out.println("DCT_PARAMETERS.dct_size="+DCT_PARAMETERS.dct_size+" DCT_PARAMETERS.asym_size="+DCT_PARAMETERS.asym_size);
	System.out.println("sym_kernel.length="+ sym_kernel.length);		System.out.println("sym_kernel.length="+ sym_kernel.length);
	System.out.println("asym_kernel.length="+asym_kernel.length);		System.out.println("asym_kernel.length="+asym_kernel.length);
	System.out.println("convolved.length="+convolved.length);		System.out.println("convolved.length="+convolved.length);
			}
	SDFA_INSTANCE.showArrays(sym_kernel, DCT_PARAMETERS.dct_size, DCT_PARAMETERS.dct_size, "sym_kernel");		SDFA_INSTANCE.showArrays(sym_kernel, DCT_PARAMETERS.dct_size, DCT_PARAMETERS.dct_size, "sym_kernel");
	SDFA_INSTANCE.showArrays(asym_kernel, DCT_PARAMETERS.asym_size, DCT_PARAMETERS.asym_size, "asym_kernel");		SDFA_INSTANCE.showArrays(asym_kernel, DCT_PARAMETERS.asym_size, DCT_PARAMETERS.asym_size, "asym_kernel");
	SDFA_INSTANCE.showArrays(compare_kernels, target_expanded_size, target_expanded_size, true, "compare_kernels");		SDFA_INSTANCE.showArrays(compare_kernels, target_expanded_size, target_expanded_size, true, "compare_kernels");
	@@ -3068,6 +3100,22 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
	EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL);		EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL);
	int numChannels=EYESIS_CORRECTIONS.getNumChannels();		int numChannels=EYESIS_CORRECTIONS.getNumChannels();


			} else if (label.equals("Select kernels image")) {
			if (!DCT_PARAMETERS.showDialog()) return;
			if (EYESIS_DCT == null){
			EYESIS_DCT = new EyesisDCT (
			EYESIS_CORRECTIONS,
			CORRECTION_PARAMETERS,
			DCT_PARAMETERS);
			}
			ImagePlus imp_src = WindowManager.getCurrentImage();
			if (imp_src==null){
			IJ.showMessage("Error","3-layer files of deconvolution kernels is required");
			return;
			}
			EYESIS_DCT.setKernelImageFile( imp_src);

	} else if (label.equals("Create DCT kernels")) {		} else if (label.equals("Create DCT kernels")) {
	if (!DCT_PARAMETERS.showDialog()) return;		if (!DCT_PARAMETERS.showDialog()) return;
	if (EYESIS_DCT == null){		if (EYESIS_DCT == null){
	@@ -3105,18 +3153,14 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos

	EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL);		EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL);

	EYESIS_DCT.createDCTKernels();		EYESIS_DCT.createDCTKernels(
			DCT_PARAMETERS,
			CONVOLVE_FFT_SIZE/2,
	/*		THREADS_MAX,
	EYESIS_CORRECTIONS.updateImageNoiseGains(		UPDATE_STATUS, // update status info
	NONLIN_PARAMETERS, //EyesisCorrectionParameters.NonlinParameters nonlinParameters,		DEBUG_LEVEL);
	CONVOLVE_FFT_SIZE, //int fftSize, // 128 - fft size, kernel size should be size/2		// EyesisCorrectionParameters.DCTParameters dCTParameters,
	THREADS_MAX, // int threadsMax, // maximal number of threads to launch		// int srcKernelSize,
	UPDATE_STATUS, // boolean updateStatus,
	DEBUG_LEVEL); //int globalDebugLevel){

	*/

	}		}
	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;

src/main/java/FactorConvKernel.java

+49 −28

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