aberration correction with clt (3e7f255e) · Commits · Elphel / imagej-elphel

src/main/java/EyesisCorrectionParameters.java

+104 −52

Original line number	Diff line number	Diff line
		@@ -1881,9 +1881,18 @@ public class EyesisCorrectionParameters {
		public int ishift_y = 0; // debug feature - shift source image by this pixels down
		public double fat_zero = 0.0; // modify phase correlation to prevent division by very small numbers
		public double corr_sigma = 0.8; // LPF correlarion sigma

		public boolean norm_kern = true; // normalize kernels

		public double novignetting_r = 0.2644; // reg gain in the center of sensor calibration R (instead of vignetting)
		public double novignetting_g = 0.3733; // green gain in the center of sensor calibration G
		public double novignetting_b = 0.2034; // blue gain in the center of sensor calibration B
		public double scale_r = 1.0; // extra gain correction after vignetting or nonvignetting, before other processing
		public double scale_g = 1.0;
		public double scale_b = 1.0;
		public double vignetting_max = 0.4; // value in vignetting data to correspond to 1x in the kernel
		public double vignetting_range = 5.0; // do not try to correct vignetting less than vignetting_max/vignetting_range
		public int kernel_step = 16; // source kernels step in pixels (have 1 kernel margin on each side)

		public CLTParameters(){}
		public void setProperties(String prefix,Properties properties){
		properties.setProperty(prefix+"transform_size", this.transform_size+"");
		@@ -1898,6 +1907,17 @@ public class EyesisCorrectionParameters {
		properties.setProperty(prefix+"ishift_y", this.ishift_y+"");
		properties.setProperty(prefix+"fat_zero", this.fat_zero+"");
		properties.setProperty(prefix+"corr_sigma", this.corr_sigma+"");
		properties.setProperty(prefix+"norm_kern", this.norm_kern+"");
		properties.setProperty(prefix+"novignetting_r", this.novignetting_r+"");
		properties.setProperty(prefix+"novignetting_g", this.novignetting_g+"");
		properties.setProperty(prefix+"novignetting_b", this.novignetting_b+"");
		properties.setProperty(prefix+"scale_r", this.scale_r+"");
		properties.setProperty(prefix+"scale_g", this.scale_g+"");
		properties.setProperty(prefix+"scale_b", this.scale_b+"");
		properties.setProperty(prefix+"vignetting_max", this.vignetting_max+"");
		properties.setProperty(prefix+"vignetting_range", this.vignetting_range+"");
		properties.setProperty(prefix+"kernel_step", this.kernel_step+"");

		}
		public void getProperties(String prefix,Properties properties){
		if (properties.getProperty(prefix+"transform_size")!=null) this.transform_size=Integer.parseInt(properties.getProperty(prefix+"transform_size"));
		@@ -1912,10 +1932,21 @@ public class EyesisCorrectionParameters {
		if (properties.getProperty(prefix+"ishift_y")!=null) this.ishift_y=Integer.parseInt(properties.getProperty(prefix+"ishift_y"));
		if (properties.getProperty(prefix+"fat_zero")!=null) this.fat_zero=Double.parseDouble(properties.getProperty(prefix+"fat_zero"));
		if (properties.getProperty(prefix+"corr_sigma")!=null) this.corr_sigma=Double.parseDouble(properties.getProperty(prefix+"corr_sigma"));
		if (properties.getProperty(prefix+"norm_kern")!=null) this.norm_kern=Boolean.parseBoolean(properties.getProperty(prefix+"norm_kern"));
		if (properties.getProperty(prefix+"novignetting_r")!=null) this.novignetting_r=Double.parseDouble(properties.getProperty(prefix+"novignetting_r"));
		if (properties.getProperty(prefix+"novignetting_g")!=null) this.novignetting_g=Double.parseDouble(properties.getProperty(prefix+"novignetting_g"));
		if (properties.getProperty(prefix+"novignetting_b")!=null) this.novignetting_b=Double.parseDouble(properties.getProperty(prefix+"novignetting_b"));
		if (properties.getProperty(prefix+"scale_r")!=null) this.scale_r=Double.parseDouble(properties.getProperty(prefix+"scale_r"));
		if (properties.getProperty(prefix+"scale_g")!=null) this.scale_g=Double.parseDouble(properties.getProperty(prefix+"scale_g"));
		if (properties.getProperty(prefix+"scale_b")!=null) this.scale_b=Double.parseDouble(properties.getProperty(prefix+"scale_b"));
		if (properties.getProperty(prefix+"vignetting_max")!=null) this.vignetting_max=Double.parseDouble(properties.getProperty(prefix+"vignetting_max"));
		if (properties.getProperty(prefix+"vignetting_range")!=null) this.vignetting_range=Double.parseDouble(properties.getProperty(prefix+"vignetting_range"));
		if (properties.getProperty(prefix+"kernel_step")!=null) this.kernel_step=Integer.parseInt(properties.getProperty(prefix+"kernel_step"));
		}

		public boolean showDialog() {
		GenericDialog gd = new GenericDialog("Set DCT parameters");
		gd.addNumericField("DCT size", this.transform_size, 0);
		gd.addNumericField("Transform size (default 8)", this.transform_size, 0);
		gd.addNumericField("Lapped transform window type (0- rectangular, 1 - sinus)", this.clt_window, 0);
		gd.addNumericField("shift_x", this.shift_x, 4);
		gd.addNumericField("shift_y", this.shift_y, 4);
		@@ -1927,6 +1958,17 @@ public class EyesisCorrectionParameters {
		gd.addNumericField("ishift_y: shift source image by this pixels down", this.ishift_y, 0);
		gd.addNumericField("Modify phase correlation to prevent division by very small numbers", this.fat_zero, 4);
		gd.addNumericField("LPF correlarion sigma ", this.corr_sigma, 3);
		gd.addCheckbox ("Normalize kernels ", this.norm_kern);
		gd.addNumericField("Reg gain in the center of sensor calibration R (instead of vignetting)", this.novignetting_r, 4);
		gd.addNumericField("Green gain in the center of sensor calibration G (instead of vignetting)",this.novignetting_g, 4);
		gd.addNumericField("Blue gain in the center of sensor calibration B (instead of vignetting)", this.novignetting_b, 4);
		gd.addNumericField("Extra red correction to compensate for light temperature", this.scale_r, 4);
		gd.addNumericField("Extra green correction to compensate for light temperature", this.scale_g, 4);
		gd.addNumericField("Extra blue correction to compensate for light temperature", this.scale_b, 4);
		gd.addNumericField("Value (max) in vignetting data to correspond to 1x in the kernel", this.vignetting_max, 3);
		gd.addNumericField("Do not try to correct vignetting smaller than this fraction of max", this.vignetting_range, 3);
		gd.addNumericField("Kernel step in pixels (has 1 kernel margin on each side)", this.kernel_step, 0);

		WindowTools.addScrollBars(gd);
		gd.showDialog();

		@@ -1943,6 +1985,17 @@ public class EyesisCorrectionParameters {
		this.ishift_y= (int) gd.getNextNumber();
		this.fat_zero = gd.getNextNumber();
		this.corr_sigma = gd.getNextNumber();
		this.norm_kern= gd.getNextBoolean();
		this.novignetting_r= gd.getNextNumber();
		this.novignetting_g= gd.getNextNumber();
		this.novignetting_b= gd.getNextNumber();
		this.scale_r= gd.getNextNumber();
		this.scale_g= gd.getNextNumber();
		this.scale_b= gd.getNextNumber();
		this.vignetting_max= gd.getNextNumber();
		this.vignetting_range= gd.getNextNumber();
		this.kernel_step= (int) gd.getNextNumber();

		return true;
		}
		}
		@@ -2272,17 +2325,16 @@ public class EyesisCorrectionParameters {
		this.antiwindow= gd.getNextBoolean();
		this.skip_sym= gd.getNextBoolean();
		this.convolve_direct= gd.getNextBoolean();

		this.novignetting_r= gd.getNextNumber();
		this.novignetting_g= gd.getNextNumber();
		this.novignetting_b= gd.getNextNumber();

		this.scale_r= gd.getNextNumber();
		this.scale_g= gd.getNextNumber();
		this.scale_b= gd.getNextNumber();


		this.vignetting_max= gd.getNextNumber();
		this.vignetting_range= gd.getNextNumber();

		this.post_debayer= gd.getNextBoolean();
		this.color_DCT= gd.getNextBoolean();
		this.sigma_rb= gd.getNextNumber();

src/main/java/EyesisCorrections.java

+46 −1

Original line number	Diff line number	Diff line
		@@ -2078,6 +2078,51 @@ public class EyesisCorrections {
		return outStack;
		}

		// return 2-d double array instead of the stack
		public double [][]bayerToDoubleStack(ImagePlus imp, // source bayer image, linearized, 32-bit (float))
		EyesisCorrectionParameters.SplitParameters splitParameters){ // if null - no margins, no oversample
		if (imp==null) return null;
		boolean adv = splitParameters != null;
		int oversample = adv? splitParameters.oversample : 1;
		int addTop= adv?splitParameters.addTop: 0;
		int addLeft= adv?splitParameters.addLeft: 0;
		int addBottom= adv?splitParameters.addBottom: 0;
		int addRight= adv?splitParameters.addRight: 0;
		String [] chnNames={"Red","Blue","Green"}; //Different sequence than RGB!!
		int nChn=chnNames.length;
		ImageProcessor ip=imp.getProcessor();
		int inWidth=imp.getWidth();
		int inHeight=imp.getHeight();
		int outHeight=inHeight*oversample + addTop + addBottom;
		int outWidth= inWidth* oversample + addLeft + addRight;
		int outLength=outWidth*outHeight;

		double [][] outPixels=new double[nChn][outLength];
		float [] pixels = (float[]) ip.getPixels();
		int chn,y,x,i,index;
		int bayerPeriod=2*oversample;
		int ovrWidth= inWidth * oversample;
		int ovrHeight= inHeight * oversample;
		for (chn=0;chn<nChn;chn++) for (i=0;i<outPixels[chn].length;i++) outPixels[chn][i]=0.0f;
		/* Can be optimized - now it calculate input address for all those 0-es */
		for (index=0; index<outLength; index++) {
		y=(index / outWidth) - addTop;
		x=(index % outWidth) - addLeft;
		if (y<0) y= (bayerPeriod-((-y) % bayerPeriod))%bayerPeriod;
		else if (y>=ovrHeight) y= ovrHeight-bayerPeriod +((y-ovrHeight) % bayerPeriod);
		if (x<0) x= (bayerPeriod-((-x) % bayerPeriod))%bayerPeriod;
		else if (x>=ovrWidth) x= ovrWidth-bayerPeriod +((x-ovrWidth) % bayerPeriod);
		if (((y% oversample)==0) && ((x% oversample)==0)) {
		x/=oversample;
		y/=oversample;
		chn=((x&1)==(y&1))?2:(((x&1)!=0)?0:1);
		outPixels[chn][index]=pixels[y*inWidth+x];
		}
		}
		return outPixels;
		}



		//double [] DENOISE_MASK=null;

src/main/java/EyesisDCT.java

+702 −29

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src/main/java/Eyesis_Correction.java

+88 −14

Original line number	Diff line number	Diff line
		@@ -2890,16 +2890,7 @@ private Panel panel1,
		int numChannels=EYESIS_CORRECTIONS.getNumChannels();
		NONLIN_PARAMETERS.modifyNumChannels(numChannels);
		CHANNEL_GAINS_PARAMETERS.modifyNumChannels(numChannels);
		/*
		if (CORRECTION_PARAMETERS.deconvolve && (NONLIN_PARAMETERS.noiseGainPower!=0)) {
		EYESIS_CORRECTIONS.updateImageNoiseGains(
		NONLIN_PARAMETERS, //EyesisCorrectionParameters.NonlinParameters nonlinParameters,
		CONVOLVE_FFT_SIZE, //int fftSize, // 128 - fft size, kernel size should be size/2
		THREADS_MAX, // int threadsMax, // maximal number of threads to launch
		UPDATE_STATUS, // boolean updateStatus,
		DEBUG_LEVEL); //int globalDebugLevel){
		}
		*/

		if (!EYESIS_DCT.DCTKernelsAvailable()){
		if (DEBUG_LEVEL > 0){
		System.out.println("Reading/converting DCT kernels");
		@@ -2914,11 +2905,7 @@ private Panel panel1,
		EYESIS_DCT.showKernels(); // show restored kernels
		}
		}


		// EYESIS_CORRECTIONS.processChannelImages(
		EYESIS_DCT.processDCTChannelImages(
		// SPLIT_PARAMETERS, // EyesisCorrectionParameters.SplitParameters splitParameters,
		DCT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters,
		DEBAYER_PARAMETERS, //EyesisCorrectionParameters.DebayerParameters debayerParameters,
		NONLIN_PARAMETERS, //EyesisCorrectionParameters.NonlinParameters nonlinParameters,
		@@ -4096,6 +4083,7 @@ private Panel panel1,
		if (EYESIS_DCT != null){
		EYESIS_DCT.resetCLTKernels();
		}

		} else if (label.equals("Read CLT kernels")) {
		if (!CLT_PARAMETERS.showDialog()) return;
		if (EYESIS_DCT == null){
		@@ -4145,6 +4133,92 @@ private Panel panel1,
		DEBUG_LEVEL);
		}

		return;
		} else if (label.equals("CLT process files")) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
		if (EYESIS_DCT == null){
		EYESIS_DCT = new EyesisDCT (
		EYESIS_CORRECTIONS,
		CORRECTION_PARAMETERS,
		DCT_PARAMETERS);
		if (DEBUG_LEVEL > 0){
		System.out.println("Created new EyesisDCT instance, will need to read CLT kernels");
		}
		}
		String configPath=null;
		if (EYESIS_CORRECTIONS.correctionsParameters.saveSettings) {
		configPath=EYESIS_CORRECTIONS.correctionsParameters.selectResultsDirectory(
		true,
		true);
		if (configPath==null){
		String msg="No results directory selected, command aborted";
		System.out.println("Warning: "+msg);
		IJ.showMessage("Warning",msg);
		return;
		}
		configPath+=Prefs.getFileSeparator()+"autoconfig";
		try {
		saveTimestampedProperties(
		configPath, // full path or null
		null, // use as default directory if path==null
		true,
		PROPERTIES);

		} catch (Exception e){
		String msg="Failed to save configuration to "+configPath+", command aborted";
		System.out.println("Error: "+msg);
		IJ.showMessage("Error",msg);
		return;
		}
		}

		EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL);
		int numChannels=EYESIS_CORRECTIONS.getNumChannels();
		NONLIN_PARAMETERS.modifyNumChannels(numChannels);
		CHANNEL_GAINS_PARAMETERS.modifyNumChannels(numChannels);

		if (!EYESIS_DCT.CLTKernelsAvailable()){
		if (DEBUG_LEVEL > 0){
		System.out.println("Reading CLT kernels");
		}
		EYESIS_DCT.readCLTKernels(
		CLT_PARAMETERS,
		THREADS_MAX,
		UPDATE_STATUS, // update status info
		DEBUG_LEVEL);

		if (DEBUG_LEVEL > 1){
		EYESIS_DCT.showCLTKernels(
		THREADS_MAX,
		UPDATE_STATUS, // update status info
		DEBUG_LEVEL);
		}
		}

		///========================================

		EYESIS_DCT.processCLTChannelImages(
		CLT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters,
		DEBAYER_PARAMETERS, //EyesisCorrectionParameters.DebayerParameters debayerParameters,
		NONLIN_PARAMETERS, //EyesisCorrectionParameters.NonlinParameters nonlinParameters,
		COLOR_PROC_PARAMETERS, //EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
		CHANNEL_GAINS_PARAMETERS, //CorrectionColorProc.ColorGainsParameters channelGainParameters,
		RGB_PARAMETERS, //EyesisCorrectionParameters.RGBParameters rgbParameters,
		EQUIRECTANGULAR_PARAMETERS, // EyesisCorrectionParameters.EquirectangularParameters equirectangularParameters,
		CONVOLVE_FFT_SIZE, //int convolveFFTSize, // 128 - fft size, kernel size should be size/2
		THREADS_MAX, //final int threadsMax, // maximal number of threads to launch
		UPDATE_STATUS, //final boolean updateStatus,
		DEBUG_LEVEL); //final int debugLevel);

		if (configPath!=null) {
		saveTimestampedProperties( // save config again
		configPath, // full path or null
		null, // use as default directory if path==null
		true,
		PROPERTIES);
		}

		return;

		// End of buttons code

src/main/java/ImageDtt.java

+433 −27

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