added saving dct kernel files (271830ae) · Commits · Elphel / imagej-elphel

src/main/java/EyesisCorrectionParameters.java

+22 −22

src/main/java/EyesisDCT.java

+47 −29

Original line number	Original line	Diff line number	Diff line
	@@ -29,6 +29,7 @@ import ij.IJ;
	import ij.ImagePlus;		import ij.ImagePlus;
	import ij.ImageStack;		import ij.ImageStack;
	import ij.Prefs;		import ij.Prefs;
			import ij.io.FileSaver;
	import ij.process.FloatProcessor;		import ij.process.FloatProcessor;
	import ij.process.ImageProcessor;		import ij.process.ImageProcessor;

	@@ -107,31 +108,10 @@ public class EyesisDCT {
	}		}
	}		}
	showDoubleFloatArrays sdfa_instance = new showDoubleFloatArrays(); // just for debugging?		showDoubleFloatArrays sdfa_instance = new showDoubleFloatArrays(); // just for debugging?
	// String [] sensor_files = correctionsParameters.selectSensorFiles(eyesisCorrections.debugLevel);


	for (int chn=0;chn<eyesisCorrections.usedChannels.length;chn++){		for (int chn=0;chn<eyesisCorrections.usedChannels.length;chn++){
	if (eyesisCorrections.usedChannels[chn] && (sharpKernelPaths[chn]!=null) && (kernels[chn]==null)){		if (eyesisCorrections.usedChannels[chn] && (sharpKernelPaths[chn]!=null) && (kernels[chn]==null)){
	// if ((sensor_files!= null) && (sensor_files.length > chn) && (sensor_files[chn]!=null)){
	/*
	double [][] vignetting = null;
	int vign_width = 0;
	int vign_height = 0;
	int vign_decimation = 1;
	if ((pixelMapping != null) &&
	(pixelMapping.sensors != null) &&
	(pixelMapping.sensors[chn] != null) &&
	(pixelMapping.sensors[chn].pixelCorrection != null) &&
	(pixelMapping.sensors[chn].pixelCorrection.length >=6)){
	vignetting = new double[3][];
	vignetting[0] = pixelMapping.sensors[chn].pixelCorrection[3]; // red
	vignetting[2] = pixelMapping.sensors[chn].pixelCorrection[4]; // green
	vignetting[1] = pixelMapping.sensors[chn].pixelCorrection[5]; // blue
	vign_width = pixelMapping.sensors[chn].pixelCorrectionWidth;
	vign_height = pixelMapping.sensors[chn].pixelCorrectionHeight;
	vign_decimation = pixelMapping.sensors[chn].pixelCorrectionDecimation;
	}
	*/
	ImagePlus imp_kernel_sharp=new ImagePlus(sharpKernelPaths[chn]);		ImagePlus imp_kernel_sharp=new ImagePlus(sharpKernelPaths[chn]);
	if (imp_kernel_sharp.getStackSize()<3) {		if (imp_kernel_sharp.getStackSize()<3) {
	System.out.println("Need a 3-layer stack with kernels");		System.out.println("Need a 3-layer stack with kernels");
	@@ -145,22 +125,60 @@ public class EyesisDCT {
	kernel_sharp_stack, // final ImageStack kernelStack, // first stack with 3 colors/slices convolution kernels		kernel_sharp_stack, // final ImageStack kernelStack, // first stack with 3 colors/slices convolution kernels
	srcKernelSize, // final int kernelSize, // 64		srcKernelSize, // final int kernelSize, // 64
	dct_parameters, // final double blurSigma,		dct_parameters, // final double blurSigma,
	/*
	vignetting,
	vign_width,
	vign_height,
	vign_decimation,
	*/
	threadsMax, // maximal number of threads to launch		threadsMax, // maximal number of threads to launch
	updateStatus,		updateStatus,
	debugLevel); // update status info		debugLevel); // update status info
	int sym_width = kernels.numHor * kernels.dct_size;		int sym_width = kernels.numHor * kernels.dct_size;
	int sym_height = kernels.sym_kernels[0].length /sym_width;		int sym_height = kernels.sym_kernels[0].length /sym_width;
	sdfa_instance.showArrays(kernels.sym_kernels, sym_width, sym_height, true, imp_kernel_sharp.getTitle()+"-sym");		// save files
			String [] symNames = {"red_sym","blue_sym","green_sym"};
			String [] asymNames = {"red_asym","blue_asym","green_asym"};
			ImageStack symStack = sdfa_instance.makeStack(
			kernels.sym_kernels,
			sym_width,
			sym_height,
			symNames);
			String symPath=correctionsParameters.dctKernelDirectory+
			Prefs.getFileSeparator()+
			correctionsParameters.dctKernelPrefix+
			String.format("%02d",chn)+
			correctionsParameters.dctSymSuffix;
			String msg="Saving symmetrical convolution kernels to "+symPath;
			IJ.showStatus(msg);
			if (debugLevel>0) System.out.println(msg);
			ImagePlus imp_sym=new ImagePlus(imp_kernel_sharp.getTitle()+"-sym",symStack);
			if (debugLevel > 1) {
			imp_sym.getProcessor().resetMinAndMax();
			imp_sym.show();
			}
			FileSaver fs=new FileSaver(imp_sym);
			fs.saveAsTiffStack(symPath);

			// sdfa_instance.showArrays(kernels.sym_kernels, sym_width, sym_height, true, imp_kernel_sharp.getTitle()+"-sym");

	int asym_width = kernels.numHor * kernels.asym_size;		int asym_width = kernels.numHor * kernels.asym_size;
	int asym_height = kernels.asym_kernels[0].length /asym_width;		int asym_height = kernels.asym_kernels[0].length /asym_width;
	sdfa_instance.showArrays(kernels.asym_kernels, asym_width, asym_height, true, imp_kernel_sharp.getTitle()+"-asym");		ImageStack asymStack = sdfa_instance.makeStack(
			kernels.asym_kernels,
			asym_width,
			asym_height,
			asymNames);
			String asymPath=correctionsParameters.dctKernelDirectory+
			Prefs.getFileSeparator()+
			correctionsParameters.dctKernelPrefix+
			String.format("%02d",chn)+
			correctionsParameters.dctAsymSuffix;
			msg="Saving asymmetrical convolution kernels "+asymPath;
			IJ.showStatus(msg);
			if (debugLevel>0) System.out.println(msg);
			ImagePlus imp_asym=new ImagePlus(imp_kernel_sharp.getTitle()+"-asym",asymStack);
			if (debugLevel > 1) {
			imp_asym.getProcessor().resetMinAndMax();
			imp_asym.show();
			}
			fs=new FileSaver(imp_asym);
			fs.saveAsTiffStack(asymPath);
			// sdfa_instance.showArrays(kernels.asym_kernels, asym_width, asym_height, true, imp_kernel_sharp.getTitle()+"-asym");
	}		}
	}		}
	return true;		return true;

Original line number	Original line	Diff line number	Diff line
	@@ -1767,32 +1767,32 @@ public class EyesisCorrectionParameters {
	}		}
	}		}
	public static class DCTParameters {		public static class DCTParameters {
	public int dct_size = 32; //		public int dct_size = 8; //
	public int asym_size = 6; //		public int asym_size = 15; //
	public int asym_pixels = 10; // maximal number of non-zero pixels in direct convolution kernel		public int asym_pixels = 4; // maximal number of non-zero pixels in direct convolution kernel
	public int asym_distance = 2; // how far to try a new asym kernel pixel from existing ones		public int asym_distance = 1; // how far to try a new asym kernel pixel from existing ones
	public int dct_window = 1; // currently only 3 types of windows - 0 (none), 1 and 2		public int dct_window = 1; // currently only 3 types of windows - 0 (none), 1 and 2
	public int LMA_steps = 100;		public int LMA_steps = 100;
	public double fact_precision= 0.003; // stop iterations if error rms less than this part of target kernel rms		public double fact_precision= 0.003; // stop iterations if error rms less than this part of target kernel rms
	public double compactness = 0.02;		public double compactness = 0.0;
	public double sym_compactness = 0.01;		public double sym_compactness = 0.5;
	public double dc_weight = 10; // importance of dc realtive to rms_pure		public double dc_weight = 1.0; // importance of dc realtive to rms_pure
	public int asym_tax_free = 5; // "compactness" does not apply to pixels with \|x\|<=asym_tax_free and \|y\| <= asym_tax_free		public int asym_tax_free = 0; // "compactness" does not apply to pixels with \|x\|<=asym_tax_free and \|y\| <= asym_tax_free
	public int seed_size = 8; // number of initial cells in asym_kernel - should be 4b + 1 (X around center cell) or 4n + 0 (X around between cells)		public int seed_size = 1; // number of initial cells in asym_kernel - should be 4b + 1 (X around center cell) or 4n + 0 (X around between cells)
	public double asym_random; // initialize asym_kernel with random numbers		public double asym_random = -1; // initialize asym_kernel with random numbers
	public double dbg_x =0;		public double dbg_x = 2.7;
	public double dbg_y =0;		public double dbg_y = 0.0;
	public double dbg_x1 =0;		public double dbg_x1 = -1.3;
	public double dbg_y1 =0;		public double dbg_y1 = 2.0;
	public double dbg_sigma =2.0;		public double dbg_sigma = 0.8;
	public String dbg_mask = ".........:::::::::.........:::::::::........::::::::.........:::::::::.........";		public String dbg_mask = ".........:::::::::.........:::::::::........::::::::.........:::::::::.........";
	public int dbg_mode = 1; // 0 - old LMA, 1 - new LMA - * not used anymore *		public int dbg_mode = 1; // 0 - old LMA, 1 - new LMA - * not used anymore *
	public int dbg_window_mode = 2; // 0 - none, 1 - square, 2 - sin 3 - sin^2		public int dbg_window_mode = 1; // 0 - none, 1 - square, 2 - sin 3 - sin^2 Now _should_ be square !!!
	public boolean centerWindowToTarget = true;		public boolean centerWindowToTarget = true;
	// parameters to extract a kernel from the kernel image file		// 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 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 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 double decimateSigma = -1.0; // special mode for 2:1 deciamtion
	public int tileX = 82; // number of kernel tile (0..163)		public int tileX = 82; // number of kernel tile (0..163)
	public int tileY = 62; // number of kernel tile (0..122)		public int tileY = 62; // number of kernel tile (0..122)
	public boolean subtract_dc = false;//subtract/restore dc		public boolean subtract_dc = false;//subtract/restore dc

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