Commit 67a6a946 authored by Andrey Filippov's avatar Andrey Filippov
Browse files

simultaneously correcting a quad

parent 5578f549

src/main/java/EyesisCorrectionParameters.java

+5 −0
Original line number Original line Diff line number Diff line
@@ -1892,6 +1892,7 @@ public class EyesisCorrectionParameters { 
  		public double     vignetting_max    = 0.4; // value in vignetting data to correspond to 1x in the kernel

  		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 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 int        kernel_step =       16;  // source kernels step in pixels (have 1 kernel margin on each side)  

  		public double     disparity  =        0.0; // nominal disparity between side of square cameras (pix) 

  		

  		

  		public CLTParameters(){}

  		public CLTParameters(){}

  		public void setProperties(String prefix,Properties properties){

  		public void setProperties(String prefix,Properties properties){
@@ -1919,6 +1920,7 @@ public class EyesisCorrectionParameters { 
  			properties.setProperty(prefix+"vignetting_max",   this.vignetting_max+"");

  			properties.setProperty(prefix+"vignetting_max",   this.vignetting_max+"");

  			properties.setProperty(prefix+"vignetting_range", this.vignetting_range+"");

  			properties.setProperty(prefix+"vignetting_range", this.vignetting_range+"");

  			properties.setProperty(prefix+"kernel_step",      this.kernel_step+"");

  			properties.setProperty(prefix+"kernel_step",      this.kernel_step+"");

  			properties.setProperty(prefix+"disparity",        this.disparity +"");

  			

  			

  		}

  		}

  		public void getProperties(String prefix,Properties properties){

  		public void getProperties(String prefix,Properties properties){
@@ -1945,6 +1947,7 @@ public class EyesisCorrectionParameters { 
  			if (properties.getProperty(prefix+"vignetting_max")!=null) this.vignetting_max=Double.parseDouble(properties.getProperty(prefix+"vignetting_max"));

  			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+"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"));

  			if (properties.getProperty(prefix+"kernel_step")!=null)    this.kernel_step=Integer.parseInt(properties.getProperty(prefix+"kernel_step"));

  			if (properties.getProperty(prefix+"disparity")!=null)      this.disparity=Double.parseDouble(properties.getProperty(prefix+"disparity"));

  		}

  		}

  		

  		

  		public boolean showDialog() {

  		public boolean showDialog() {
@@ -1972,6 +1975,7 @@ public class EyesisCorrectionParameters { 
  			gd.addNumericField("Value (max) in vignetting data to correspond to 1x in the kernel",        this.vignetting_max,      3);

  			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("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);

  			gd.addNumericField("Kernel step in pixels (has 1 kernel margin on each side)",                this.kernel_step,            0);

  			gd.addNumericField("Nominal (rectilinear) disparity between side of square cameras (pix)",    this.disparity,  3);

   			

   			

  			WindowTools.addScrollBars(gd);

  			WindowTools.addScrollBars(gd);

  			gd.showDialog();

  			gd.showDialog();
@@ -2000,6 +2004,7 @@ public class EyesisCorrectionParameters { 
  			this.vignetting_max=        gd.getNextNumber();

  			this.vignetting_max=        gd.getNextNumber();

  			this.vignetting_range=      gd.getNextNumber();

  			this.vignetting_range=      gd.getNextNumber();

  			this.kernel_step=     (int) gd.getNextNumber();

  			this.kernel_step=     (int) gd.getNextNumber();

  			this.disparity=             gd.getNextNumber();

  			

  			

  			return true;

  			return true;

  		}

  		}

src/main/java/EyesisDCT.java

+715 −3

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/Eyesis_Correction.java

+104 −0
Original line number Original line Diff line number Diff line
@@ -495,6 +495,7 @@ private Panel panel1, 
			addButton("Reset CLT kernels",         panelClt1, color_stop);

			addButton("Reset CLT kernels",         panelClt1, color_stop);

			addButton("CLT process files",         panelClt1, color_process);

			addButton("CLT process files",         panelClt1, color_process);

			addButton("CLT process sets",          panelClt1, color_process);

			addButton("CLT process sets",          panelClt1, color_process);

			addButton("CLT process quads",         panelClt1, color_process);

			add(panelClt1);

			add(panelClt1);

		}

		}

		pack();

		pack();
@@ -4283,6 +4284,15 @@ private Panel panel1, 
        	}

        	}

        }

        }





        if (!EYESIS_DCT.geometryCorrectionAvailable()){

        	if (DEBUG_LEVEL > 0){

        		System.out.println("Calculating geometryCorrection");

        	}

        	if (!EYESIS_DCT.initGeometryCorrection(DEBUG_LEVEL+2)){

        		return;

        	}

        }

        

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

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

        

        

        EYESIS_DCT.processCLTSets(

        EYESIS_DCT.processCLTSets(
@@ -4307,6 +4317,100 @@ private Panel panel1, 
        }

        }

        return;

        return;

        

        

    } else if (label.equals("CLT process quads")) {

    	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);

        	}

        }



        if (!EYESIS_DCT.geometryCorrectionAvailable()){

        	if (DEBUG_LEVEL > 0){

        		System.out.println("Calculating geometryCorrection");

        	}

        	if (!EYESIS_DCT.initGeometryCorrection(DEBUG_LEVEL+2)){

        		return;

        	}

        }

        

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

        

        EYESIS_DCT.processCLTQuads(

        		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;

src/main/java/GeometryCorrection.java

+66 −6
Original line number Original line Diff line number Diff line
@@ -114,6 +114,7 @@ public class GeometryCorrection { 
			double      heading,    // NaN - keep

			double      heading,    // NaN - keep

			double []   forward,    // null - keep all, NaN - keep individual

			double []   forward,    // null - keep all, NaN - keep individual

			double []   right,      // null - keep all, NaN - keep individual

			double []   right,      // null - keep all, NaN - keep individual

			double []   height,      // null - keep all, NaN - keep individual

			double []   roll,       // null - keep all, NaN - keep individual

			double []   roll,       // null - keep all, NaN - keep individual

			double [][] pXY0){      // null - keep all, [] null - keep individual

			double [][] pXY0){      // null - keep all, [] null - keep individual
@@ -136,6 +137,14 @@ public class GeometryCorrection { 
			for (int i = 0; i < numSensors; i++) if (!Double.isNaN(right[i]))      this.right[i] = right[i];

			for (int i = 0; i < numSensors; i++) if (!Double.isNaN(right[i]))      this.right[i] = right[i];

		}

		}





		if (height != null){

			if (height.length != numSensors){

				throw new IllegalArgumentException ("height.length ("+height.length+") != numSensors ("+numSensors+")");

			}

			if ((this.height == null) || (this.height.length != numSensors)) this.height = new double [numSensors];

			for (int i = 0; i < numSensors; i++) if (!Double.isNaN(height[i]))      this.height[i] = height[i];

		}



		if (roll != null){

		if (roll != null){

			if (roll.length != numSensors){

			if (roll.length != numSensors){

				throw new IllegalArgumentException ("roll.length ("+roll.length+") != numSensors ("+numSensors+")");

				throw new IllegalArgumentException ("roll.length ("+roll.length+") != numSensors ("+numSensors+")");
@@ -245,9 +254,60 @@ public class GeometryCorrection { 
		}

		}

	}

	}

	

	

	public void listGeometryCorrection(boolean showAll){

		System.out.println("'=== Constant parameters ===");

		System.out.println("pixelCorrectionWidth =\t"+  pixelCorrectionWidth+"\tpix");

		System.out.println("pixelCorrectionHeight =\t"+ pixelCorrectionHeight+"\tpix");

		System.out.println("pixelSize =\t"+             pixelSize+"\tum");

		System.out.println("distortionRadius =\t"+      distortionRadius+"\tmm");

		System.out.println("'=== Common input parameters ===");

		System.out.println("focalLength =\t"+  focalLength + " mm");

		System.out.println("distortionA8 =\t"+ distortionA8);

		System.out.println("distortionA7 =\t"+ distortionA7);

		System.out.println("distortionA6 =\t"+ distortionA6);

		System.out.println("distortionA5 =\t"+ distortionA5);

		System.out.println("distortionA =\t"+  distortionA);

		System.out.println("distortionB =\t"+  distortionB);

		System.out.println("distortionC =\t"+  distortionC);

		System.out.println("elevation =\t"+    elevation+"\tdegrees");

		System.out.println("heading =\t"+      heading+"\tdegrees");

		System.out.println("numSensors =\t"+   numSensors);

		System.out.println("'=== Individual input parameters ===");

		System.out.print  ("forward = ");for (int i = 0; i < numSensors;i++) System.out.print("\t"+forward[i]); System.out.println("\tmm");

		System.out.print  ("right = ");  for (int i = 0; i < numSensors;i++) System.out.print("\t"+right[i]);   System.out.println("\tmm");

		System.out.print  ("height = "); for (int i = 0; i < numSensors;i++) System.out.print("\t"+height[i]);  System.out.println("\tmm");

		System.out.print  ("roll = ");   for (int i = 0; i < numSensors;i++) System.out.print("\t"+roll[i]);      System.out.println("\tdegrees");

		System.out.print  ("px0 = ");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+pXY0[i][0]);  System.out.println("\tpix");

		System.out.print  ("py0 = ");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+pXY0[i][1]);  System.out.println("\tpix");

		

		System.out.println("'=== Common calculated parameters ===");

		System.out.println("common_right =\t"+common_right + "\tmm");

		System.out.println("common_forward =\t"+common_forward + "\tmm");

		System.out.println("common_height =\t"+common_height + "\tmm");

		System.out.println("common_roll =\t"+common_roll + "\tdegrees");

		System.out.println("cameraRadius =\t"+cameraRadius + "\tmm");

		System.out.println("disparityRadius =\t"+disparityRadius + "\tmm");



		if (showAll){

			System.out.println("'=== Intermediate data: coordinates corrected for common elevation and heading ===");

			System.out.print  ("X_he =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+XYZ_he[i][0]);  System.out.println("\tmm");

			System.out.print  ("Y_he =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+XYZ_he[i][1]);  System.out.println("\tmm");

			System.out.print  ("Z_he =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+XYZ_he[i][2]);  System.out.println("\tmm");

			System.out.println("'=== Intermediate data: coordinates corrected for common elevation, heading and roll ===");

			System.out.print  ("X_her =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+XYZ_her[i][0]);  System.out.println("\tmm");

			System.out.print  ("Y_her =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+XYZ_her[i][1]);  System.out.println("\tmm");

			System.out.print  ("Z_her =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+XYZ_her[i][2]);  System.out.println("\tmm");

		}

		

		System.out.println("'=== Individual calculated parameters ===");

		System.out.print  ("residual_roll = ");   for (int i = 0; i < numSensors;i++) System.out.print("\t"+(roll[i]-common_roll));System.out.println("\tdegrees");

		System.out.print  ("X_rel =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+rXY[i][0]);  System.out.println("\trelative to disparityRadius");

		System.out.print  ("Y_rel =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+rXY[i][1]);  System.out.println("\trelative to disparityRadius");

	}



	// return distance from disparity (in pixel units) for the current camera geometry

	// return distance from disparity (in pixel units) for the current camera geometry

	public double getZFromDisparity(double disparity){

	public double getZFromDisparity(double disparity){

		return disparity * this.focalLength * this.pixelSize / this.disparityRadius;

		return disparity * this.focalLength * 0.001*this.pixelSize / this.disparityRadius;

	}

	}





	/*

	/*
@@ -263,8 +323,8 @@ public class GeometryCorrection { 
		double [][] pXY = new double [numSensors][2];

		double [][] pXY = new double [numSensors][2];

		double pXcd = px - 0.5 * this.pixelCorrectionWidth;

		double pXcd = px - 0.5 * this.pixelCorrectionWidth;

		double pYcd = py - 0.5 * this.pixelCorrectionHeight;

		double pYcd = py - 0.5 * this.pixelCorrectionHeight;

		double rD = Math.sqrt(pXcd*pXcd + pYcd*pYcd); // distorted radius in a virtual center camera

		double rD = Math.sqrt(pXcd*pXcd + pYcd*pYcd)*0.001*this.pixelSize; // distorted radius in a virtual center camera

		double rND2R=getRByRDist(rD/this.distortionRadius, (debugLevel > 1));

		double rND2R=getRByRDist(rD/this.distortionRadius, (debugLevel > -1));

		double pXc = pXcd * rND2R; // non-distorted coordinates relative to the (0.5 * this.pixelCorrectionWidth, 0.5 * this.pixelCorrectionHeight)

		double pXc = pXcd * rND2R; // non-distorted coordinates relative to the (0.5 * this.pixelCorrectionWidth, 0.5 * this.pixelCorrectionHeight)

		double pYc = pYcd * rND2R; // in pixels

		double pYc = pYcd * rND2R; // in pixels

		double [] a={this.distortionC,this.distortionB,this.distortionA,this.distortionA5,this.distortionA6,this.distortionA7,this.distortionA8};

		double [] a={this.distortionC,this.distortionB,this.distortionA,this.distortionA5,this.distortionA6,this.distortionA7,this.distortionA8};
@@ -275,7 +335,7 @@ public class GeometryCorrection { 
			// calculate back to distorted

			// calculate back to distorted

			double rNDi = Math.sqrt(pXci*pXci + pYci*pYci); // in pixels

			double rNDi = Math.sqrt(pXci*pXci + pYci*pYci); // in pixels

			//		Rdist/R=A8*R^7+A7*R^6+A6*R^5+A5*R^4+A*R^3+B*R^2+C*R+(1-A6-A7-A6-A5-A-B-C)");

			//		Rdist/R=A8*R^7+A7*R^6+A6*R^5+A5*R^4+A*R^3+B*R^2+C*R+(1-A6-A7-A6-A5-A-B-C)");

			double ri = rNDi* this.pixelSize / this.distortionRadius; // relative to distortion radius

			double ri = rNDi* 0.001 * this.pixelSize / this.distortionRadius; // relative to distortion radius

			//    		double rD2rND = (1.0 - distortionA8 - distortionA7 - distortionA6 - distortionA5 - distortionA - distortionB - distortionC);

			//    		double rD2rND = (1.0 - distortionA8 - distortionA7 - distortionA6 - distortionA5 - distortionA - distortionB - distortionC);

			double rD2rND = 1.0;

			double rD2rND = 1.0;

			double rri = 1.0;

			double rri = 1.0;
@@ -286,8 +346,8 @@ public class GeometryCorrection { 
			double pXid = pXci * rD2rND;  

			double pXid = pXci * rD2rND;  

			double pYid = pYci * rD2rND;

			double pYid = pYci * rD2rND;

			// individual rotate (check sign)

			// individual rotate (check sign)

			double c_roll = Math.cos(this.roll[i] * Math.PI/180.0);

			double c_roll = Math.cos((this.roll[i] - this.common_roll) * Math.PI/180.0);

			double s_roll = Math.sin(this.roll[i] * Math.PI/180.0);

			double s_roll = Math.sin((this.roll[i] - this.common_roll) * Math.PI/180.0);

			pXY[i][0] =  c_roll *  pXid + s_roll* pYid + this.pXY0[i][0];

			pXY[i][0] =  c_roll *  pXid + s_roll* pYid + this.pXY0[i][0];

			pXY[i][1] = -s_roll *  pXid + c_roll* pYid + this.pXY0[i][1];

			pXY[i][1] = -s_roll *  pXid + c_roll* pYid + this.pXY0[i][1];

		}

		}

src/main/java/ImageDtt.java

+135 −0
Original line number Original line Diff line number Diff line
@@ -757,6 +757,141 @@ public class ImageDtt { 
	}

	}









	public double [][][][][][] clt_aberrations_quad(

			final double              disparity,

			final double [][][]       imade_data, // first index - number of image in a quad

			final int                 width,

			final GeometryCorrection  geometryCorrection,

			final double [][][][][][] clt_kernels, // [channel_in_quad][color][tileY][tileX][band][pixel] , size should match image (have 1 tile around)

			final int                 kernel_step,

			final int                 transform_size,

			final int                 window_type,

			final double              shiftX, // shift image horizontally (positive - right) - just for testing

			final double              shiftY, // shift image vertically (positive - down)

			final int                 debug_tileX,

			final int                 debug_tileY,

			final boolean             no_fract_shift,

			final boolean             no_deconvolution,

			final boolean             transpose,

			final int                 threadsMax,  // maximal number of threads to launch                         

			final int                 globalDebugLevel)

	{

		final int quad = 4;

		final int nChn = imade_data[0].length;

		final int height=imade_data[0][0].length/width;

		final int tilesX=width/transform_size;

		final int tilesY=height/transform_size;

		final int nTilesInChn=tilesX*tilesY; 

		final int nTiles=tilesX*tilesY*nChn; 

		final double [][][][][][] clt_data = new double[quad][nChn][tilesY][tilesX][4][];

		final Thread[] threads = newThreadArray(threadsMax);

		final AtomicInteger ai = new AtomicInteger(0);

		

		double [][] centersXY_dbg = geometryCorrection.getPortsCoordinates(

				0.0, // centerX,

				0.0, // centerY,

				disparity);

		

		

		

		

		if (globalDebugLevel > 0) {

			System.out.println("clt_aberrations(): width="+width+" height="+height+" transform_size="+transform_size+

					" debug_tileX="+debug_tileX+" debug_tileY="+debug_tileY+" globalDebugLevel="+globalDebugLevel);

		}

		for (int ithread = 0; ithread < threads.length; ithread++) {

			threads[ithread] = new Thread() {

				public void run() {

					DttRad2 dtt = new DttRad2(transform_size);

					dtt.set_window(window_type);

					int tileY,tileX, chn;

					//						showDoubleFloatArrays sdfa_instance = new showDoubleFloatArrays(); // just for debugging?

					double centerX; // center of aberration-corrected (common model) tile, X

					double centerY; //

					double [][] fract_shiftsXY = new double[quad][];



					for (int nTile = ai.getAndIncrement(); nTile < nTiles; nTile = ai.getAndIncrement()) {

						// TODO: make all color channels to be processed here (atomically)

						chn=nTile/nTilesInChn;

						tileY =(nTile % nTilesInChn)/tilesX;

						tileX = nTile % tilesX;

						centerX = tileX * transform_size + transform_size/2 - shiftX;

						centerY = tileY * transform_size + transform_size/2 - shiftY;

						double [][] centersXY = geometryCorrection.getPortsCoordinates(

								centerX,

								centerY,

								disparity);

						if ((globalDebugLevel > -1) && (tileX >= debug_tileX - 2) && (tileX <= debug_tileX + 2) &&

								(tileY >= debug_tileY - 2) && (tileY <= debug_tileY+2)) {

							for (int i = 0; i < quad; i++) {

							System.out.println("clt_aberrations_quad(): color="+chn+", tileX="+tileX+", tileY="+tileY+

									" centerX="+centerX+" centerY="+centerY+" disparity="+disparity+

									" centersXY["+i+"][0]="+centersXY[i][0]+" centersXY["+i+"][1]="+centersXY[i][1]);

							}

						}

						

						for (int i = 0; i < quad; i++) {

							fract_shiftsXY[i] = extract_correct_tile( // return a pair of resudual offsets

									imade_data[i],

									width,       // image width

									clt_kernels[i], // [color][tileY][tileX][band][pixel]

									clt_data[i][chn][tileY][tileX], //double  [][]        clt_tile,    // should be double [4][];

									kernel_step,

									transform_size,

									dtt, 

									chn,                              

									centersXY[i][0], // centerX, // center of aberration-corrected (common model) tile, X

									centersXY[i][1], // centerY, //

									(globalDebugLevel > 0) && (tileX == debug_tileX) && (tileY == debug_tileY) && (chn == 2), // external tile compare

									no_deconvolution,

									transpose);

						}

						if ((globalDebugLevel > 0) && (debug_tileX == tileX) && (debug_tileY == tileY)  && (chn == 2)) {

							showDoubleFloatArrays sdfa_instance = new showDoubleFloatArrays(); // just for debugging?

							String [] titles = {"CC0","SC0","CS0","SS0","CC1","SC1","CS1","SS1","CC2","SC2","CS2","SS2","CC3","SC3","CS3","SS3"};

							double [][] dbg_tile = new double [16][];

							for (int i = 0; i < 16; i++) dbg_tile[i]=clt_data[i>>2][chn][tileY][tileX][i & 3];   

							sdfa_instance.showArrays(dbg_tile,  transform_size, transform_size, true, "pre-shifted_x"+tileX+"_y"+tileY, titles);

						}

						

						if ((globalDebugLevel > -1) && (tileX >= debug_tileX - 2) && (tileX <= debug_tileX + 2) &&

								(tileY >= debug_tileY - 2) && (tileY <= debug_tileY+2)) {

							for (int i = 0; i < quad; i++) {

							System.out.println("clt_aberrations_quad(): color="+chn+", tileX="+tileX+", tileY="+tileY+

									" fract_shiftsXY["+i+"][0]="+fract_shiftsXY[i][0]+" fract_shiftsXY["+i+"][1]="+fract_shiftsXY[i][1]);

							}

						}

						

						if (!no_fract_shift) {

							// apply residual shift

							for (int i = 0; i < quad; i++) {

								fract_shift(    // fractional shift in transform domain. Currently uses sin/cos - change to tables with 2? rotations

										clt_data[i][chn][tileY][tileX], // double  [][]  clt_tile,

										transform_size,

										fract_shiftsXY[i][0],            // double        shiftX,

										fract_shiftsXY[i][1],            // double        shiftY,

										//									(globalDebugLevel > 0) && (tileX == debug_tileX) && (tileY == debug_tileY)); // external tile compare

										((globalDebugLevel > 0) && (chn==0) && (tileX >= debug_tileX - 2) && (tileX <= debug_tileX + 2) &&

												(tileY >= debug_tileY - 2) && (tileY <= debug_tileY+2)));									

							}

							if ((globalDebugLevel > 0) && (debug_tileX == tileX) && (debug_tileY == tileY)) {

								showDoubleFloatArrays sdfa_instance = new showDoubleFloatArrays(); // just for debugging?

								String [] titles = {"CC0","SC0","CS0","SS0","CC1","SC1","CS1","SS1","CC2","SC2","CS2","SS2","CC3","SC3","CS3","SS3"};

								double [][] dbg_tile = new double [16][];

								for (int i = 0; i < 16; i++) dbg_tile[i]=clt_data[i>>2][chn][tileY][tileX][i & 3];   

								sdfa_instance.showArrays(dbg_tile,  transform_size, transform_size, true, "shifted_x"+tileX+"_y"+tileY, titles);

							}

						}

					}

				}

			};

		}		      

		startAndJoin(threads);

		return clt_data;

	}