package com.elphel.imagej.correction;
/**
 **
 ** EyesisDCT - Process images with DTT-based methods (code specific to ImageJ plugin)
 **
 ** Copyright (C) 2016 Elphel, Inc.
 **
 ** -----------------------------------------------------------------------------**
 **
 **  EyesisDCT.java is free software: you can redistribute it and/or modify
 **  it under the terms of the GNU General Public License as published by
 **  the Free Software Foundation, either version 3 of the License, or
 **  (at your option) any later version.
 **
 **  This program is distributed in the hope that it will be useful,
 **  but WITHOUT ANY WARRANTY; without even the implied warranty of
 **  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 **  GNU General Public License for more details.
 **
 **  You should have received a copy of the GNU General Public License
 **  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 ** -----------------------------------------------------------------------------**
 **
 */

import java.util.Properties;
import java.util.concurrent.atomic.AtomicInteger;

import com.elphel.imagej.cameras.ColorProcParameters;
import com.elphel.imagej.cameras.EyesisCorrectionParameters;
import com.elphel.imagej.common.DoubleGaussianBlur;
import com.elphel.imagej.common.ShowDoubleFloatArrays;
import com.elphel.imagej.dct.FactorConvKernel;
import com.elphel.imagej.tileprocessor.DttRad2;
import com.elphel.imagej.tileprocessor.ImageDtt;

import ij.CompositeImage;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.Prefs;
import ij.io.FileSaver;
import ij.process.ImageProcessor;

public class EyesisDCT {
///	static String [] fine_corr_coeff_names = {"A","B","C","D","E","F"};
///	static String [] fine_corr_dir_names = {"X","Y"};
	static String    prefix = "EYESIS_DCT.";
	public Properties properties = null;
	public EyesisCorrections eyesisCorrections = null;
	public EyesisCorrectionParameters.CorrectionParameters correctionsParameters=null;
	public EyesisCorrectionParameters.DCTParameters dctParameters = null;
	public DCTKernels [] kernels = null;
///	double [][][][][][] clt_kernels = null;
///	GeometryCorrection geometryCorrection = null;
///	public int extra_items = 8; // number of extra items saved with kernels (center offset (partial, full, derivatives)
	public ImagePlus eyesisKernelImage = null;
	public long startTime;

	public EyesisDCT(
			Properties                                      properties,
			EyesisCorrections                               eyesisCorrections,
			EyesisCorrectionParameters.CorrectionParameters correctionsParameters,
			EyesisCorrectionParameters.DCTParameters        dctParameters
			){
		this.eyesisCorrections=      eyesisCorrections;
		this.correctionsParameters = correctionsParameters;
		this.dctParameters=          dctParameters;
		this.properties =            properties;
///		getProperties();
	}

	// TODO:Add saving just calibration
/***
	public void setProperties(){
		for (int n = 0; n < fine_corr.length; n++){
			for (int d = 0; d < fine_corr[n].length; d++){
				for (int i = 0; i < fine_corr[n][d].length; i++){
					String name = prefix+"fine_corr_"+n+fine_corr_dir_names[d]+fine_corr_coeff_names[i];
					properties.setProperty(name,   this.fine_corr[n][d][i]+"");
				}
			}
		}
	}

	public void getProperties(){
		for (int n = 0; n < fine_corr.length; n++){
			for (int d = 0; d < fine_corr[n].length; d++){
				for (int i = 0; i < fine_corr[n][d].length; i++){
					String name = prefix+"fine_corr_"+n+fine_corr_dir_names[d]+fine_corr_coeff_names[i];
		  			if (properties.getProperty(name)!=null) this.fine_corr[n][d][i]=Double.parseDouble(properties.getProperty(name));
				}
			}
		}
	}
*/
	public class DCTKernels{
		// -- old --
		public int           size = 32;     // kernel (DCT) size
		public int           img_step = 32; // pixel step in the image for each kernel
		public double [][][] offsets = null; // per color, per kernel,per coord
		public double [][]   kern = null;  // kernel image in linescan order
		// -- new --
		public int           numHor =        164; // number of kernel tiles in a row
		public int           dct_size =        8;  // DCT-II size, sym. kernel square side is 2*dct_size-1
		public int           asym_size =      15; // asymmetrical convolution limits, odd
		public int           asym_nonzero =   4; // maximal number of non-zero elements in the asymmetrical kernels
		public double [][]   sym_kernels =  null; // per-color channel, DCT kernels in linescan order
		public double [][]   sym_direct =   null; // per-color channel, DCT kernels in linescan order (direct, not dct-iii transformed) - debug feature
		public double [][]   asym_kernels = null; // per-color channel, asymmetrical kernels (all but asym_nonzero elements are strictly 0)
		public double [][][][] st_kernels = null; // [color][tileY][tileX][pixel]
		public double [][][][] st_direct =  null; // [color][tileY][tileX][pixel] - direct, not converted with DCT-III - debug feature
		public double [][][][] asym_val =   null; // [color][tileY][tileX][index] // value - asym kernel for elements
		public int    [][][][] asym_indx =  null; // [color][tileY][tileX][index] // value - index of non-zero elements in the list
	}

	public void setKernelImageFile(ImagePlus img_kernels){
		eyesisKernelImage = img_kernels;
	}

	public boolean kernelImageSet(){
		return eyesisKernelImage != null;
	}

	public boolean DCTKernelsAvailable(){
		return kernels != null;
	}

	  public DCTKernels calculateDCTKernel (
			  final ImageStack kernelStack,  // first stack with 3 colors/slices convolution kernels
			  final int          kernelSize, // 64
			  final EyesisCorrectionParameters.DCTParameters dct_parameters,
			  final int          threadsMax,  // maximal number of threads to launch
			  final boolean      updateStatus,
			  final int          globalDebugLevel) // update status info
	  {
		  if (kernelStack==null) return null;
		  final int kernelWidth=kernelStack.getWidth();
		  final int kernelNumHor=kernelWidth/kernelSize;
		  final int kernelNumVert=kernelStack.getHeight()/kernelSize;
		  final int nChn=kernelStack.getSize();
		  final DCTKernels dct_kernel = new DCTKernels();
		  dct_kernel.size = dct_parameters.dct_size;
		  dct_kernel.img_step = kernelSize/2/dct_parameters.decimation ; // May be wrong
		  dct_kernel.sym_kernels =  new double [nChn][kernelNumHor*kernelNumVert*dct_parameters.dct_size * dct_parameters.dct_size];
		  dct_kernel.asym_kernels = new double [nChn][kernelNumHor*kernelNumVert*dct_parameters.asym_size * dct_parameters.asym_size];
		  dct_kernel.asym_nonzero = dct_parameters.asym_pixels;
		  // currently each 64x64 kernel corresponds to 16x16 original pixels tile, 2 tiles margin each side
		  final Thread[] threads = ImageDtt.newThreadArray(threadsMax);
		  final AtomicInteger ai = new AtomicInteger(0);
		  final int numberOfKernels=     kernelNumHor*kernelNumVert*nChn;
		  final int numberOfKernelsInChn=kernelNumHor*kernelNumVert;
		  final int dct_size =      dct_parameters.dct_size;
		  final int preTargetSize = 4 * dct_size;
		  final int targetSize =    2 * dct_size; // normally 16
		  final double [] anitperiodic_window = createAntiperiodicWindow(dct_size);
		  final long startTime = System.nanoTime();
		  System.out.println("calculateDCTKernel():numberOfKernels="+numberOfKernels);
		  for (int ithread = 0; ithread < threads.length; ithread++) {
			  threads[ithread] = new Thread() {
				  @Override
				public void run() {
					  DoubleGaussianBlur gb=null;
					  if (dct_parameters.decimateSigma > 0)	 gb=new DoubleGaussianBlur();
					  float [] kernelPixels= null; // will be initialized at first use NOT yet?
					  double [] kernel=      new double[kernelSize*kernelSize];
					  double [] pre_target_kernel= new double [preTargetSize * preTargetSize]; // before made antiperiodic
					  double [] target_kernel = new double [targetSize * targetSize]; // strictly antiperiodic in both x and y directions

					  FactorConvKernel factorConvKernel = new FactorConvKernel();
					  factorConvKernel.setDebugLevel       (0); // globalDebugLevel);
					  factorConvKernel.setTargetWindowMode (dct_parameters.centerWindowToTarget);
					  factorConvKernel.numIterations =     dct_parameters.LMA_steps;
					  factorConvKernel.setAsymCompactness  (dct_parameters.compactness,	dct_parameters.asym_tax_free);
					  factorConvKernel.setSymCompactness   (dct_parameters.sym_compactness);
					  factorConvKernel.setDCWeight         (dct_parameters.dc_weight);

					  int chn,tileY,tileX;
					  for (int nTile = ai.getAndIncrement(); nTile < numberOfKernels; nTile = ai.getAndIncrement()) {
						  chn=nTile/numberOfKernelsInChn;
						  tileY =(nTile % numberOfKernelsInChn)/kernelNumHor;
						  tileX = nTile % kernelNumHor;
						  if (tileX==0) {
							  if (updateStatus) IJ.showStatus("Processing kernels, channel "+(chn+1)+" of "+nChn+", row "+(tileY+1)+" of "+kernelNumVert);
							  if (globalDebugLevel>2) System.out.println("Processing kernels, channel "+(chn+1)+" of "+nChn+", row "+(tileY+1)+" of "+kernelNumVert+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
						  }
						  kernelPixels=(float[]) kernelStack.getPixels(chn+1);

						  /* read convolution kernel */
						  extractOneKernel(
								  kernelPixels, //  array of combined square kernels, each
								  kernel, // will be filled, should have correct size before call
								  kernelNumHor, // number of kernels in a row
								  tileX, // horizontal number of kernel to extract
								  tileY); // vertical number of kernel to extract

						  if ((dct_parameters.decimation == 2) && (dct_parameters.decimateSigma<0)) {
							  reformatKernel2( // averages by exactly 2 (decimate==2)
									  kernel,
									  pre_target_kernel, // expand/crop, blur/decimate result (32x32)
									  kernelSize,
									  preTargetSize); // 32
						  } else {
							  reformatKernel(
									  kernel,        // will be blurred in-place
									  pre_target_kernel, // expand/crop, blur/decimate result (32x32)
									  kernelSize,
									  preTargetSize, // 32
									  dct_parameters.decimation,
									  dct_parameters.decimateSigma,
									  gb);
						  }
						  if (dct_parameters.normalize) { // or should it be normalized after antiperiodic?
							  double s =0.0;
							  for (int i = 0; i < pre_target_kernel.length; i++){
								  s+=pre_target_kernel[i];
							  }
							  s =  1.0 / s;
							  for (int i = 0; i < pre_target_kernel.length; i++){
								  pre_target_kernel[i] *= s;
							  }
							  if (globalDebugLevel > 1){ // was already close to 1.0
								  System.out.println(tileX+"/"+tileY+ " s="+s);
							  }
						  }
						  // make exactly anitperiodic
						  makeAntiperiodic(
								  dct_size,
								  pre_target_kernel,   // 16*dct_zize*dct_zize
								  anitperiodic_window, // 16*dct_zize*dct_zize
								  target_kernel);      //  4*dct_zize*dct_zize


						  factorConvKernel.calcKernels(
								  target_kernel,
								  dct_parameters.asym_size,
								  dct_parameters.dct_size,
								  dct_parameters.fact_precision,
								  dct_parameters.asym_pixels,         // maximal number of non-zero pixels in asymmmetrical kernel
								  dct_parameters.asym_distance,       // how far to seed a new pixel
								  dct_parameters.seed_size);
						  double [] sym_kernel =  factorConvKernel.getSymKernel();
						  double [] asym_kernel = factorConvKernel.getAsymKernel();
						  int sym_kernel_inc_index =   kernelNumHor * dct_parameters.dct_size;
						  int sym_kernel_start_index = (sym_kernel_inc_index * tileY + tileX) * dct_parameters.dct_size;
						  for (int i = 0; i<dct_parameters.dct_size;i++){
								System.arraycopy(
										sym_kernel,
										i * dct_parameters.dct_size,
										dct_kernel.sym_kernels[chn],
										sym_kernel_start_index + i * sym_kernel_inc_index,
										dct_parameters.dct_size);
						  }
						  int asym_kernel_inc_index =   kernelNumHor * dct_parameters.asym_size;
						  int asym_kernel_start_index = (asym_kernel_inc_index * tileY + tileX)* dct_parameters.asym_size;
						  for (int i = 0; i<dct_parameters.asym_size;i++){
								System.arraycopy(
										asym_kernel,
										i * dct_parameters.asym_size,
										dct_kernel.asym_kernels[chn],
										asym_kernel_start_index + i * asym_kernel_inc_index,
										dct_parameters.asym_size);
						  }
					  }
				  }
			  };
		  }
		  ImageDtt.startAndJoin(threads);
		  if (globalDebugLevel > 1) System.out.println("Threads done at "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
		  System.out.println("1.Threads done at "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
		  /* prepare result stack to return */
		  return dct_kernel;
	  }


	public boolean createDCTKernels(
			EyesisCorrectionParameters.DCTParameters dct_parameters,
			int          srcKernelSize,
			int          threadsMax,  // maximal number of threads to launch
			boolean      updateStatus,
			int          debugLevel
			){
		String [] sharpKernelPaths= correctionsParameters.selectKernelChannelFiles(
				0,  // 0 - sharp, 1 - smooth
				  correctionsParameters.firstSubCameraConfig,
//				  correctionsParameters.numSubCameras,
				eyesisCorrections.usedChannels.length, // numChannels, // number of channels
				eyesisCorrections.debugLevel);
		if (sharpKernelPaths==null) return false;
		for (int i=0;i<sharpKernelPaths.length;i++){
			System.out.println(i+":"+sharpKernelPaths[i]);
		}
		if (kernels == null){
			kernels = new DCTKernels[eyesisCorrections.usedChannels.length];
			for (int chn=0;chn<eyesisCorrections.usedChannels.length;chn++){
				kernels[chn] = null;
			}
		}
	    ShowDoubleFloatArrays sdfa_instance = new ShowDoubleFloatArrays(); // just for debugging?


		for (int chn=0;chn<eyesisCorrections.usedChannels.length;chn++){
			if (eyesisCorrections.usedChannels[chn] && (sharpKernelPaths[chn]!=null) && (kernels[chn]==null)){
				ImagePlus imp_kernel_sharp=new ImagePlus(sharpKernelPaths[chn]);
				if (imp_kernel_sharp.getStackSize()<3) {
					System.out.println("Need a 3-layer stack with kernels");
					sharpKernelPaths[chn]=null;
					continue;
				}
				ImageStack kernel_sharp_stack= imp_kernel_sharp.getStack();
				System.out.println("debugLevel = "+debugLevel+" kernel_sharp_stack.getWidth() = "+kernel_sharp_stack.getWidth()+
						" kernel_sharp_stack.getHeight() = "+kernel_sharp_stack.getHeight());
				DCTKernels kernels = calculateDCTKernel (
						kernel_sharp_stack,            // final ImageStack kernelStack,  // first stack with 3 colors/slices convolution kernels
						srcKernelSize,                 // final int          kernelSize, // 64
						dct_parameters,                // final double       blurSigma,
						threadsMax,  // maximal number of threads to launch
						updateStatus,
						debugLevel); // update status info
				int sym_width =  kernels.numHor * kernels.dct_size;
				int sym_height = kernels.sym_kernels[0].length /sym_width;
// 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_height = kernels.asym_kernels[0].length /asym_width;
				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;
	}

//eyesisKernelImage
	  public double [] extractOneKernelFromStack(
			  final int          kernelSize, // 64
			  final int chn,
			  final int xTile, // horizontal number of kernel to extract
			  final int yTile)  // vertical number of kernel to extract
	  {
		  if (eyesisKernelImage == null) return null;
		  final ImageStack kernelStack = eyesisKernelImage.getStack();
		  return extractOneKernelFromStack(
				  kernelStack,  // first stack with 3 colors/slices convolution kernels
				  kernelSize, // 64
				  chn,
				  xTile, // horizontal number of kernel to extract
				  yTile);  // vertical number of kernel to extract
	  }
	  private double [] extractOneKernelFromStack(
			  final ImageStack kernelStack,  // first stack with 3 colors/slices convolution kernels
			  final int          kernelSize, // 64
			  final int chn,
			  final int xTile, // horizontal number of kernel to extract
			  final int yTile)  // vertical number of kernel to extract
	  {

		  final int kernelWidth=kernelStack.getWidth();
		  final int kernelNumHor=kernelWidth/kernelSize;
		  double [] kernel = new double [kernelSize*kernelSize];
		  extractOneKernel((float[]) kernelStack.getPixels(chn+1), //  array of combined square kernels, each
				  kernel,        // will be filled, should have correct size before call
				  kernelNumHor,  // number of kernels in a row
				  xTile,         // horizontal number of kernel to extract
				  yTile);
		  return kernel;
	  }
	  // to be used in threaded method
	  private void extractOneKernel(float [] pixels, //  array of combined square kernels, each
			  double [] kernel, // will be filled, should have correct size before call
			  int numHor, // number of kernels in a row
			  int xTile, // horizontal number of kernel to extract
			  int yTile) { // vertical number of kernel to extract
		  int length=kernel.length;
		  int size=(int) Math.sqrt(length);
		  int i,j;
		  int pixelsWidth=numHor*size;
		  int pixelsHeight=pixels.length/pixelsWidth;
		  int numVert=pixelsHeight/size;
		  /* limit tile numbers - effectively add margins around the known kernels */
		  if (xTile<0) xTile=0;
		  else if (xTile>=numHor) xTile=numHor-1;
		  if (yTile<0) yTile=0;
		  else if (yTile>=numVert) yTile=numVert-1;
		  int base=(yTile*pixelsWidth+xTile)*size;
		  for (i=0;i<size;i++) for (j=0;j<size;j++) kernel [i*size+j]=pixels[base+i*pixelsWidth+j];
	  }
	  public double [] reformatKernel(
			  double [] src_kernel,// will be blured in-place
			  int       src_size,  // typical 64
			  int       dst_size,  // typical 15 // destination size
			  int       decimation,// typical 2
			  double    sigma)
	  {
		  double [] dst_kernel = new double [dst_size*dst_size];
		  DoubleGaussianBlur gb = null;
		  if (sigma > 0) gb = new DoubleGaussianBlur();
		  reformatKernel(
				  src_kernel,
				  dst_kernel,
				  src_size,
				  dst_size,
				  decimation,
				  sigma,
				  gb);
		  return dst_kernel;

	  }
	  // to be used in threaded method
	  public void reformatKernel(
			  double [] src_kernel, // will be blured in-place
			  double [] dst_kernel,
			  int src_size,
			  int dst_size,
			  int decimation,
			  double sigma,
			  DoubleGaussianBlur gb)
	  {
		  if (gb != null) gb.blurDouble(src_kernel, src_size, src_size, sigma, sigma, 0.01);
		  int src_center = src_size / 2; // 32
		  int dst_center = dst_size / 2; // 7
		  for (int i = 0; i< dst_size; i++){
			  int src_i = (i - dst_center)*decimation + src_center;
			  if ((src_i >= 0) && (src_i < src_size)) {
				  for (int j = 0; j< dst_size; j++) {
					  int src_j = (j - dst_center)*decimation + src_center;
					  if ((src_j >= 0) && (src_j < src_size)) {
						  dst_kernel[i*dst_size + j] = src_kernel[src_i*src_size + src_j];
					  } else {
						  dst_kernel[i*dst_size + j] = 0;
					  }
				  }
			  } else {
				  for (int j = 0; j< dst_size; j++) dst_kernel[i*dst_size + j] = 0;
			  }
		  }
	  }
	  public double []reformatKernel2( // averages by exactly 2 (decimate==2)
			  double [] src_kernel, //
			  int src_size,
			  int dst_size){
		  double [] dst_kernel = new double [dst_size*dst_size];
		  reformatKernel2(
				  src_kernel,
				  dst_kernel,
				  src_size,
				  dst_size);
		  return dst_kernel;
	  }

	  private void reformatKernel2( // averages by exactly 2 (decimate==2)
			  double [] src_kernel, //
			  double [] dst_kernel,
			  int src_size,
			  int dst_size)
	  {
		  int decimation = 2;
		  int [] indices = {0,-src_size,-1,1,src_size,-src_size-1,-src_size+1,src_size-1,src_size+1};
		  double [] weights = {0.25,0.125,0.125,0.125,0.125,0.0625,0.0625,0.0625,0.0625};
		  int src_center = src_size / 2; // 32
		  int dst_center = dst_size / 2; // 7
		  int src_len = src_size*src_size;
		  for (int i = 0; i< dst_size; i++){
			  int src_i = (i - dst_center)*decimation + src_center;
			  if ((src_i >= 0) && (src_i < src_size)) {
				  for (int j = 0; j< dst_size; j++) {
					  int src_j = (j - dst_center)*decimation + src_center;
					  int dst_index = i*dst_size + j;
					  dst_kernel[dst_index] = 0.0;
					  if ((src_j >= 0) && (src_j < src_size)) {
						  int src_index = src_i*src_size + src_j;
						  for (int k = 0; k < indices.length; k++){
							  int indx = src_index + indices[k]; // normally source kernel should be larger, these lines just to save from "out of bounds"
							  if      (indx < 0)        indx += src_len;
							  else if (indx >= src_len) indx -= src_len;
							  dst_kernel[dst_index] += weights[k]*src_kernel[indx];
						  }
					  }
				  }
			  } else {
				  for (int j = 0; j< dst_size; j++) dst_kernel[i*dst_size + j] = 0;
			  }
		  }
	  }

	  private double [] createAntiperiodicWindow(
			  int dct_size)
	  {
		  double [] wnd = new double[4*dct_size];
		  for (int i =0; i<dct_size; i++){
			  wnd[i]=                 0.5 * (1.0-Math.cos(Math.PI*i/dct_size));
			  wnd[i + 1 * dct_size] = 1.0;
			  wnd[i + 2 * dct_size] = 1.0;
			  wnd[i + 3 * dct_size] = 1.0 - wnd[i];
		  }
		  int n4 = dct_size*4;
		  double [] window = new double [n4 * n4];
		  for (int i =0; i < n4; i++){
			  for (int j =0; j < n4; j++){
				  window[i * n4 + j] = wnd[i]*wnd[j];
			  }
		  }
		  return window;
	  }

	  public double []makeAntiperiodic(
			  int       dct_size,
			  double [] src_kernel) // 16*dct_zize*dct_zize
	  {
		 double [] window =  createAntiperiodicWindow(dct_size);
		 double [] antiperiodic_kernel = new double [4*dct_size*dct_size];
		 makeAntiperiodic(
				  dct_size,
				  src_kernel, // 16*dct_zize*dct_zize
				  window,     // 16*dct_zize*dct_zize
				  antiperiodic_kernel); //  4*dct_zize*dct_zize

		 return antiperiodic_kernel;
	  }


	  private void makeAntiperiodic(
			  int       dct_size,
			  double [] src_kernel,          // 16*dct_zize*dct_zize
			  double [] window,              // 16*dct_zize*dct_zize
			  double [] antiperiodic_kernel) //  4*dct_zize*dct_zize
	  {
		  int n2 = dct_size * 2;
		  int n4 = dct_size * 4;
		  for (int i = 0; i < n2; i++){
			  for (int j = 0; j < n2; j++){
				  int dst_index = i*n2+j;
				  int isrc = i+dct_size;
				  int jsrc =  j+dct_size;
				  int isrcp = (isrc + n2) % n4;
				  int jsrcp = (jsrc + n2) % n4;
				  int src_index0= (isrc)  * n4 + jsrc;
				  int src_index1= (isrcp) * n4 + jsrc;
				  int src_index2= (isrc) *  n4 + jsrcp;
				  int src_index3= (isrcp) * n4 + jsrcp;

				  antiperiodic_kernel[dst_index] =
						    src_kernel[src_index0] * window[src_index0]
						  - src_kernel[src_index1] * window[src_index1]
						  - src_kernel[src_index2] * window[src_index2]
						  + src_kernel[src_index3] * window[src_index3];
			  }
		  }
	  }
	  public void resetDCTKernels()
	  {
		  kernels = null;
	  }

	  public boolean readDCTKernels(
			  EyesisCorrectionParameters.DCTParameters dct_parameters,
			  int          srcKernelSize,
			  int          threadsMax,  // maximal number of threads to launch
			  boolean      updateStatus,
			  int          debugLevel
			  ){
		  String [] symKernelPaths = correctionsParameters.selectDCTChannelFiles(
				  //					0,  // 0 - sharp, 1 - smooth
				  eyesisCorrections.usedChannels.length, // numChannels, // number of channels
				  eyesisCorrections.debugLevel);
		  if (symKernelPaths==null) return false;

		  String [] asymKernelPaths = new String[symKernelPaths.length];
		  for (int chn = 0; chn <symKernelPaths.length; chn++ ) if (symKernelPaths[chn] != null){
			  int indexPeriod=symKernelPaths[chn].indexOf('.',symKernelPaths[chn].lastIndexOf(Prefs.getFileSeparator()));
			  asymKernelPaths[chn] = symKernelPaths[chn].substring(0, indexPeriod) + correctionsParameters.dctAsymSuffix;
		  }

		  for (int i=0;i<symKernelPaths.length;i++){
			  System.out.println(i+":"+symKernelPaths[i]+", "+asymKernelPaths[i]); // some may be null!
		  }
		  if (kernels == null){
			  kernels = new DCTKernels[eyesisCorrections.usedChannels.length];
			  for (int chn=0;chn<eyesisCorrections.usedChannels.length;chn++){
				  kernels[chn] = null;
			  }
		  }


		  ShowDoubleFloatArrays sdfa_instance = new ShowDoubleFloatArrays(); // just for debugging?
		  DttRad2 dtt = new DttRad2(dct_parameters.dct_size);

		  for (int chn=0;chn<eyesisCorrections.usedChannels.length;chn++){
			  //				if (eyesisCorrections.usedChannels[chn] && (symKernelPaths[chn]!=null) && (kernels[chn]==null)){
			  if (eyesisCorrections.usedChannels[chn] && (symKernelPaths[chn]!=null)){
				  ImagePlus imp_kernel_sym=new ImagePlus(symKernelPaths[chn]);
				  if (imp_kernel_sym.getStackSize()<3) {
					  System.out.println("Need a 3-layer stack with symmetrical DCT kernels");
					  symKernelPaths[chn]=null;
					  continue;
				  }
				  ImagePlus imp_kernel_asym=new ImagePlus(asymKernelPaths[chn]);
				  if (imp_kernel_sym.getStackSize()<3) {
					  System.out.println("Need a 3-layer stack with asymmetrical kernels");
					  asymKernelPaths[chn]=null;
					  continue;
				  }

				  ImageStack kernel_sym_stack=  imp_kernel_sym.getStack();
				  ImageStack kernel_asym_stack= imp_kernel_asym.getStack();
				  if (debugLevel>0){
					  System.out.println(" kernel_asym_stack.getWidth() = "+kernel_asym_stack.getWidth()+
							  " kernel_asym_stack.getHeight() = "+kernel_asym_stack.getHeight());
				  }
				  int nColors = kernel_sym_stack.getSize();
				  kernels[chn]=  new DCTKernels();
				  kernels[chn].size = dct_parameters.dct_size;
				  kernels[chn].img_step = srcKernelSize/2/dct_parameters.decimation ; // May be wrong
				  kernels[chn].asym_nonzero = dct_parameters.asym_pixels;

				  kernels[chn].sym_kernels =  new double [nColors][];
				  kernels[chn].asym_kernels = new double [nColors][];

				  for (int nc = 0; nc < nColors; nc++){
					  float [] pixels = (float[]) kernel_sym_stack.getPixels(nc + 1);
					  kernels[chn].sym_kernels[nc]= new double[pixels.length];
					  for (int i = 0; i<pixels.length; i++){
						  kernels[chn].sym_kernels[nc][i] = pixels[i];
					  }
					  pixels = (float[]) kernel_asym_stack.getPixels(nc + 1);
					  kernels[chn].asym_kernels[nc]= new double[pixels.length];
					  for (int i = 0; i<pixels.length; i++){
						  kernels[chn].asym_kernels[nc][i] = pixels[i];
					  }
				  }
				  int dct_size = kernels[chn].dct_size;
				  int asym_size= kernels[chn].asym_size;
				  int sym_width =  kernels[chn].numHor * dct_size;
				  int sym_height = kernels[chn].sym_kernels[0].length /sym_width;
				  int asym_nonzero =kernels[chn].asym_nonzero;

				  int asym_width =  kernels[chn].numHor * kernels[chn].asym_size;
				  int asym_height = kernels[chn].asym_kernels[0].length /asym_width;
				  int numHor =   kernels[chn].numHor;
				  int numVert =  kernels[chn].sym_kernels[0].length / (dct_size * dct_size * numHor);
				  kernels[chn].st_kernels = new double [nColors][numVert][numHor][dct_size * dct_size];
				  kernels[chn].st_direct =  new double [nColors][numVert][numHor][dct_size * dct_size];
				  kernels[chn].asym_val =   new double [nColors][numVert][numHor][asym_nonzero];
				  kernels[chn].asym_indx =  new int [nColors][numVert][numHor][asym_nonzero];
				  int sym_kernel_inc_index =   numHor * dct_size;
				  int asym_kernel_inc_index =   numHor * asym_size;
				  double [] norm_sym_weights = new double [dct_size*dct_size];
				  for (int i = 0; i < dct_size; i++){
					  for (int j = 0; j < dct_size; j++){
						  double d = 	Math.cos(Math.PI*i/(2*dct_size))*Math.cos(Math.PI*j/(2*dct_size));
						  if (i > 0) d*= 2.0;
						  if (j > 0) d*= 2.0;
						  norm_sym_weights[i*dct_size+j] = d;
					  }
				  }
				  double [] inv_window = new double [dct_size*dct_size];
				  for (int i = 0; i < dct_size; i++){
					  for (int j = 0; j < dct_size; j++){
						  double d = 	1.0 / (Math.cos(Math.PI*i/(2*dct_size))*Math.cos(Math.PI*j/(2*dct_size)));
						  inv_window[i*dct_size+j] = d;
					  }
				  }

				  if (debugLevel>0) {
					  System.out.println("readDCTKernels() debugLevel = "+debugLevel+
							  " kernels["+chn+"].size = "+kernels[chn].size+
							  " kernels["+chn+"].img_step = "+kernels[chn].img_step+
							  " kernels["+chn+"].asym_nonzero = "+kernels[chn].asym_nonzero+
							  " nColors = "+ nColors+
							  " numVert = "+ numVert+
							  " numHor =  "+ numHor);
				  }
				  for (int nc = 0; nc < nColors; nc++){
					  for (int tileY = 0; tileY < numVert; tileY++){
						  for (int tileX = 0; tileX < numHor; tileX++){
							  // extract asymmetrical kernel and convert it to list of values and indices (as arrays as the length is known)
							  int asym_kernel_start_index = (asym_kernel_inc_index * tileY + tileX)* asym_size;
							  int indx = 0;
							  for (int i = 0; (i < dct_parameters.asym_size) && (indx < asym_nonzero); i++){
								  for (int j = 0; (j < dct_parameters.asym_size) && (indx < asym_nonzero); j++){
									  double v = kernels[chn].asym_kernels[nc][asym_kernel_start_index + i * asym_kernel_inc_index +j];
									  if (v!=0.0){
										  if ((debugLevel>0) && (tileY==67) && (tileX==125)) {
											  System.out.println("i="+i+" j="+j+" v="+v+" indx="+indx+" i * asym_size + j="+(i * asym_size + j));
											  System.out.println("asym_kernel_start_index + i * asym_kernel_inc_index +j="+(asym_kernel_start_index + i * asym_kernel_inc_index +j));
										  }

										  kernels[chn].asym_val[nc][tileY][tileX][indx] =    v;
										  kernels[chn].asym_indx[nc][tileY][tileX][indx++] = i * asym_size + j;
									  }
								  }
							  }
							  if ((debugLevel>0) && (tileY==67) && (tileX==125)) {
								  for (int i=0; i<kernels[chn].asym_indx[nc][tileY][tileX].length; i++){
									  System.out.println("kernels["+chn+"].asym_val["+nc+"]["+tileY+"]["+tileX+"]["+i+"]="+kernels[chn].asym_val[nc][tileY][tileX][i]);
									  System.out.println("kernels["+chn+"].asym_indx["+nc+"]["+tileY+"]["+tileX+"]["+i+"]="+kernels[chn].asym_indx[nc][tileY][tileX][i]);
								  }
							  }

							  double scale_asym = 0.0;
							  if (dct_parameters.normalize) {
								  for (int i = 0; i < kernels[chn].asym_val[nc][tileY][tileX].length;i++){
									  scale_asym += kernels[chn].asym_val[nc][tileY][tileX][i];
									  if ((debugLevel>0) && (tileY==67) && (tileX==125)) {
										  System.out.println("i="+i+", sum="+scale_asym);
									  }
								  }
							  } else {
								  scale_asym = 1.0;
							  }
							  // Compensate for Bayer pattern where there are twice less R,B than G green red blue
							  double k = ((nc == 2)? 1.0:2.0) / scale_asym;
							  for (int i = 0; i < kernels[chn].asym_val[nc][tileY][tileX].length;i++){
								  //										kernels[chn].asym_val[nc][tileY][tileX][i] /= scale_asym;
								  kernels[chn].asym_val[nc][tileY][tileX][i] *= k; // includes correction for different number of pixels in r,b(1/4) and G (2/4)
							  }

							  if ((debugLevel > 0) && (tileY==67) && (tileX==125)) {
								  System.out.println("nc="+nc+" sum="+scale_asym+", k="+k +", k*scale_asym="+(k*scale_asym)+", normalized:");

								  for (int i=0; i<kernels[chn].asym_indx[nc][tileY][tileX].length; i++){
									  System.out.println("kernels["+chn+"].asym_val["+nc+"]["+tileY+"]["+tileX+"]["+i+"]="+kernels[chn].asym_val[nc][tileY][tileX][i]);
									  System.out.println("kernels["+chn+"].asym_indx["+nc+"]["+tileY+"]["+tileX+"]["+i+"]="+kernels[chn].asym_indx[nc][tileY][tileX][i]);
								  }
							  }

							  // extract DCT (symmetrical) kernels
							  int sym_kernel_start_index = (sym_kernel_inc_index * tileY + tileX) * dct_size;
							  for (int i = 0; i < dct_size;i++){
								  System.arraycopy( // copy one kernel line
										  kernels[chn].sym_kernels[nc],
										  sym_kernel_start_index + i * sym_kernel_inc_index,
										  kernels[chn].st_kernels[nc][tileY][tileX],
										  i * dct_size,
										  dct_size);
							  }


							  // sym_kernel pre-compensation for window function
							  if (dct_parameters.antiwindow) {
								  for (int i=0; i < kernels[chn].st_kernels[nc][tileY][tileX].length;i++) {
									  kernels[chn].st_kernels[nc][tileY][tileX][i] *= inv_window[i];
								  }
							  }

							  if (scale_asym != 1.0){
								  for (int i=0; i < kernels[chn].st_kernels[nc][tileY][tileX].length;i++) {
									  kernels[chn].st_kernels[nc][tileY][tileX][i] *= scale_asym;
								  }
							  }

							  // +++++++++++++++++++++++++++++++++++++++++


							  if (dct_parameters.normalize_sym){ // normalize sym kernel regardless of asym:
								  double scale_sym = 0.0;
								  for (int i = 0; i< norm_sym_weights.length; i++){
									  scale_sym += norm_sym_weights[i]*kernels[chn].st_kernels[nc][tileY][tileX][i];
								  }
								  for (int i=0; i < kernels[chn].st_kernels[nc][tileY][tileX].length;i++) {
									  kernels[chn].st_kernels[nc][tileY][tileX][i] /= scale_sym;
								  }
								  if ((debugLevel > 0) && (tileY== dct_parameters.tileY) && (tileX==dct_parameters.tileX)) {
									  System.out.println("chn="+chn+" tileY="+tileY+", tileX"+tileY+" scale_sym="+scale_sym);
								  }
							  }
							  // Make a copy of direct kernels (debug feature, may be removed later)
							  for (int i = 0; i < dct_size;i++){
								  System.arraycopy( // copy one kernel line
										  kernels[chn].st_kernels[nc][tileY][tileX],
										  i * dct_size,
										  kernels[chn].st_direct[nc][tileY][tileX],
										  i * dct_size,
										  dct_size);
							  }
							  // scale so multiplication will not change normalization
							  for (int i=0; i < kernels[chn].st_kernels[nc][tileY][tileX].length;i++) {
								  kernels[chn].st_kernels[nc][tileY][tileX][i] *= dct_size;
							  }

							  //								kernels[chn].st_kernels[nc][tileY][tileX]= dtt.dttt_iii(kernels[chn].st_kernels[nc][tileY][tileX]);
							  kernels[chn].st_kernels[nc][tileY][tileX]= dtt.dttt_iiie(kernels[chn].st_kernels[nc][tileY][tileX]); //, 0, dct_size)
						  }
						  //							System.out.println("tileY="+tileY);
					  }
				  }
				  // Debug will be removed later, the
				  if (debugLevel > 0) {
					  sdfa_instance.showArrays(kernels[chn].sym_kernels,  sym_width, sym_height, true, symKernelPaths[chn]);
					  sdfa_instance.showArrays(kernels[chn].asym_kernels,  asym_width, asym_height, true, asymKernelPaths[chn]);
				  }
				  kernels[chn].sym_kernels = null;  // not needed anymore
				  kernels[chn].asym_kernels = null; // not needed anymore
			  }
		  }
		  return true;
	  }

	  public void showKernels(){
		  //			System.out.println("showKernels(): kernels.length="+kernels.length);
		  for (int chn=0;chn < kernels.length; chn++){
			  if (kernels[chn]!=null){
				  //					System.out.println("showKernels("+chn+")");
				  showKernels(chn);
			  }
		  }
	  }

	  public void showKernels(int chn){
		  int nColors = kernels[chn].st_kernels.length;
		  int numVert = kernels[chn].st_kernels[0].length;
		  int numHor =  kernels[chn].st_kernels[0][0].length;
		  int dct_size = kernels[chn].dct_size;
		  int asym_size= kernels[chn].asym_size;
		  int sym_width =  numHor * dct_size;
		  int sym_height = numVert * dct_size;
		  //			int asym_nonzero =kernels[chn].asym_nonzero;
		  int asym_width =  numHor * kernels[chn].asym_size;
		  int asym_height = numVert * kernels[chn].asym_size;
		  kernels[chn].sym_kernels =  new double [nColors][sym_width*sym_height];
		  if (kernels[chn].st_direct != null) {
			  kernels[chn].sym_direct =   new double [nColors][sym_width*sym_height];
		  }
		  kernels[chn].asym_kernels = new double [nColors][asym_width*asym_height];
		  int sym_kernel_inc_index =   numHor * dct_size;
		  int asym_kernel_inc_index =   numHor * asym_size;
		  ShowDoubleFloatArrays sdfa_instance = new ShowDoubleFloatArrays(); // just for debugging?
		  for (int nc = 0; nc < nColors; nc++){
			  for (int tileY = 0; tileY < numVert; tileY++){
				  for (int tileX = 0; tileX < numHor; tileX++){
					  // set DCT (symmetrical) kernels
					  int sym_kernel_start_index = (sym_kernel_inc_index * tileY + tileX) * dct_size;
					  for (int i = 0; i < dct_size;i++){
						  System.arraycopy( // copy one kernel line
								  kernels[chn].st_kernels[nc][tileY][tileX],
								  i * dct_size,
								  kernels[chn].sym_kernels[nc],
								  sym_kernel_start_index + i * sym_kernel_inc_index,
								  dct_size);
					  }
					  if (kernels[chn].st_direct != null){
						  for (int i = 0; i < dct_size;i++){
							  System.arraycopy( // copy one kernel line
									  kernels[chn].st_direct[nc][tileY][tileX],
									  i * dct_size,
									  kernels[chn].sym_direct[nc],
									  sym_kernel_start_index + i * sym_kernel_inc_index,
									  dct_size);
						  }
					  }

					  // set asymmetrical kernel from the list of values and indices
					  double [] asym_kernel = new double[asym_size*asym_size];
					  for (int i=0;i<asym_kernel.length; i++) asym_kernel[i] = 0.0;
					  for (int i = 0; i<kernels[chn].asym_indx[nc][tileY][tileX].length; i++){
						  asym_kernel[kernels[chn].asym_indx[nc][tileY][tileX][i]] = kernels[chn].asym_val[nc][tileY][tileX][i];
						  /*
							if ((tileY==67) && (tileX==125)) {
								System.out.println("kernels["+chn+"].asym_val["+nc+"]["+tileY+"]["+tileX+"]["+i+"]="+kernels[chn].asym_val[nc][tileY][tileX][i]);
								System.out.println("kernels["+chn+"].asym_indx["+nc+"]["+tileY+"]["+tileX+"]["+i+"]="+kernels[chn].asym_indx[nc][tileY][tileX][i]);
								System.out.println("asym_kernel["+(kernels[chn].asym_indx[nc][tileY][tileX][i])+"]="+asym_kernel[kernels[chn].asym_indx[nc][tileY][tileX][i]]);
							}
						   */
					  }
					  int asym_kernel_start_index = (asym_kernel_inc_index * tileY + tileX)* asym_size;
					  for (int i = 0; i < asym_size;i++){
						  System.arraycopy( // copy one kernel line
								  asym_kernel,
								  i * asym_size,
								  kernels[chn].asym_kernels[nc],
								  asym_kernel_start_index + i * asym_kernel_inc_index,
								  asym_size);
					  }
				  }
			  }
		  }
		  System.out.println("sym_width="+sym_width+" sym_height="+sym_height);
		  System.out.println("kernels["+chn+"].sym_kernels.length="+kernels[chn].sym_kernels.length);
		  System.out.println("kernels["+chn+"][0].sym_kernels.length="+kernels[chn].sym_kernels[0].length);
		  System.out.println("asym_width="+asym_width+" asym_height="+asym_height);
		  System.out.println("kernels["+chn+"].asym_kernels.length="+kernels[chn].asym_kernels.length);
		  System.out.println("kernels["+chn+"][0].asym_kernels.length="+kernels[chn].asym_kernels[0].length);
		  sdfa_instance.showArrays(kernels[chn].sym_kernels,  sym_width, sym_height, true, "restored-sym-"+chn);
		  sdfa_instance.showArrays(kernels[chn].asym_kernels,  asym_width, asym_height, true, "restored-asym-"+chn);
		  if (kernels[chn].st_direct != null){
			  sdfa_instance.showArrays(kernels[chn].sym_direct,  sym_width, sym_height, true, "restored-direct-"+chn);
		  }
		  kernels[chn].sym_kernels = null;  // not needed anymore
		  kernels[chn].asym_kernels = null; // not needed anymore
		  kernels[chn].sym_direct = null;  // not needed anymore
	  }

	  //		public boolean isChannelEnabled(int channel){
	  //			return ((channel>=0) && (channel<this.usedChannels.length) && this.usedChannels[channel]);
	  //		}


	  public void processDCTChannelImages(
			  //				EyesisCorrectionParameters.SplitParameters         splitParameters,
			  EyesisCorrectionParameters.DCTParameters           dct_parameters,
			  EyesisCorrectionParameters.DebayerParameters     debayerParameters,
			  EyesisCorrectionParameters.NonlinParameters       nonlinParameters,
			  ColorProcParameters colorProcParameters,
			  CorrectionColorProc.ColorGainsParameters     channelGainParameters,
			  EyesisCorrectionParameters.RGBParameters             rgbParameters,
			  EyesisCorrectionParameters.EquirectangularParameters equirectangularParameters,
			  int          convolveFFTSize, // 128 - fft size, kernel size should be size/2
			  final int          threadsMax,  // maximal number of threads to launch
			  final boolean    updateStatus,
			  final int        debugLevel)
	  {
		  this.startTime=System.nanoTime();
		  String [] sourceFiles=correctionsParameters.getSourcePaths();
		  boolean [] enabledFiles=new boolean[sourceFiles.length];
		  for (int i=0;i<enabledFiles.length;i++) enabledFiles[i]=false;
		  int numFilesToProcess=0;
		  int numImagesToProcess=0;
		  for (int nFile=0;nFile<enabledFiles.length;nFile++){
			  if ((sourceFiles[nFile]!=null) && (sourceFiles[nFile].length()>1)) {
				  int [] channels={correctionsParameters.getChannelFromSourceTiff(sourceFiles[nFile])};
				  if (correctionsParameters.isJP4()){
					  int subCamera= channels[0]- correctionsParameters.firstSubCamera; // to match those in the sensor files
					  // removeUnusedSensorData should be off!?
					  channels=this.eyesisCorrections.pixelMapping.channelsForSubCamera(subCamera);
				  }
				  if (channels!=null){
					  for (int i=0;i<channels.length;i++) if (eyesisCorrections.isChannelEnabled(channels[i])){
						  if (!enabledFiles[nFile]) numFilesToProcess++;
						  enabledFiles[nFile]=true;
						  numImagesToProcess++;
					  }
				  }
			  }
		  }
		  if (numFilesToProcess==0){
			  System.out.println("No files to process (of "+sourceFiles.length+")");
			  return;
		  } else {
			  if (debugLevel>0) System.out.println(numFilesToProcess+ " files to process (of "+sourceFiles.length+"), "+numImagesToProcess+" images to process");
		  }
		  double [] referenceExposures=eyesisCorrections.calcReferenceExposures(debugLevel); // multiply each image by this and divide by individual (if not NaN)
		  int [][] fileIndices=new int [numImagesToProcess][2]; // file index, channel number
		  int index=0;
		  for (int nFile=0;nFile<enabledFiles.length;nFile++){
			  if ((sourceFiles[nFile]!=null) && (sourceFiles[nFile].length()>1)) {
				  int [] channels={correctionsParameters.getChannelFromSourceTiff(sourceFiles[nFile])};
				  if (correctionsParameters.isJP4()){
					  int subCamera= channels[0]- correctionsParameters.firstSubCamera; // to match those in the sensor files
					  channels=eyesisCorrections.pixelMapping.channelsForSubCamera(subCamera);
				  }
				  if (channels!=null){
					  for (int i=0;i<channels.length;i++) if (eyesisCorrections.isChannelEnabled(channels[i])){
						  fileIndices[index  ][0]=nFile;
						  fileIndices[index++][1]=channels[i];
					  }
				  }
			  }
		  }
		  for (int iImage=0;iImage<fileIndices.length;iImage++){
			  int nFile=fileIndices[iImage][0];
			  ImagePlus imp_src=null;
			  //				  int srcChannel=correctionsParameters.getChannelFromSourceTiff(sourceFiles[nFile]);
			  int srcChannel=fileIndices[iImage][1];
			  if (correctionsParameters.isJP4()){
				  int subchannel=eyesisCorrections.pixelMapping.getSubChannel(srcChannel);
				  if (this.correctionsParameters.swapSubchannels01) {
					  switch (subchannel){
					  case 0: subchannel=1; break;
					  case 1: subchannel=0; break;
					  }
				  }
				  if (debugLevel>0) System.out.println("Processing channel "+fileIndices[iImage][1]+" - subchannel "+subchannel+" of "+sourceFiles[nFile]);
				  ImagePlus imp_composite=eyesisCorrections.JP4_INSTANCE.open(
						  "", // path,
						  sourceFiles[nFile],
						  "",  //arg - not used in JP46 reader
						  true, // un-apply camera color gains
						  null, // new window
						  false); // do not show
				  imp_src=eyesisCorrections.JP4_INSTANCE.demuxImage(imp_composite, subchannel);
				  if (imp_src==null) imp_src=imp_composite; // not a composite image

				  // do we need to add any properties?
			  } else {
				  imp_src=new ImagePlus(sourceFiles[nFile]);
				  //					  (new JP46_Reader_camera(false)).decodeProperiesFromInfo(imp_src); // decode existent properties from info
				  eyesisCorrections.JP4_INSTANCE.decodeProperiesFromInfo(imp_src); // decode existent properties from info
				  if (debugLevel>0) System.out.println("Processing "+sourceFiles[nFile]);
			  }
			  double scaleExposure=1.0;
			  if (!Double.isNaN(referenceExposures[nFile]) && (imp_src.getProperty("EXPOSURE")!=null)){
				  scaleExposure=referenceExposures[nFile]/Double.parseDouble((String) imp_src.getProperty("EXPOSURE"));
				  //					  imp_src.setProperty("scaleExposure", scaleExposure); // it may already have channel
				  if (debugLevel>0) System.out.println("Will scale intensity (to compensate for exposure) by  "+scaleExposure);
			  }
			  imp_src.setProperty("name",    correctionsParameters.getNameFromSourceTiff(sourceFiles[nFile]));
			  imp_src.setProperty("channel", srcChannel); // it may already have channel
			  imp_src.setProperty("path",    sourceFiles[nFile]); // it may already have channel
			  //				  ImagePlus result=processChannelImage( // returns ImagePlus, but it already should be saved/shown
			  processDCTChannelImage( // returns ImagePlus, but it already should be saved/shown
					  imp_src, // should have properties "name"(base for saving results), "channel","path"
					  //						  splitParameters,
					  dct_parameters,
					  debayerParameters,
					  nonlinParameters,
					  colorProcParameters,
					  channelGainParameters,
					  rgbParameters,
					  convolveFFTSize, // 128 - fft size, kernel size should be size/2
					  scaleExposure,
					  threadsMax,  // maximal number of threads to launch
					  updateStatus,
					  debugLevel);
			  // warp result (add support for different color modes)
			  if (this.correctionsParameters.equirectangular){
				  if (equirectangularParameters.clearFullMap) eyesisCorrections.pixelMapping.deleteEquirectangularMapFull(srcChannel); // save memory? //removeUnusedSensorData - no, use equirectangular specific settings
				  if (equirectangularParameters.clearAllMaps) eyesisCorrections.pixelMapping.deleteEquirectangularMapAll(srcChannel); // save memory? //removeUnusedSensorData - no, use equirectangular specific settings
			  }
			  //pixelMapping
			  Runtime.getRuntime().gc();
			  if (debugLevel >-1) System.out.println("Processing image "+(iImage+1)+" (of "+fileIndices.length+") finished at "+
					  IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
			  if (eyesisCorrections.stopRequested.get()>0) {
				  System.out.println("User requested stop");
				  return;
			  }
		  }
		  System.out.println("Processing "+fileIndices.length+" files finished at "+
				  IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");


	  }

	  public ImagePlus processDCTChannelImage(
			  ImagePlus imp_src, // should have properties "name"(base for saving results), "channel","path"
			  //				EyesisCorrectionParameters.SplitParameters         splitParameters, // will not be used !
			  EyesisCorrectionParameters.DCTParameters           dct_parameters,
			  EyesisCorrectionParameters.DebayerParameters     debayerParameters,
			  EyesisCorrectionParameters.NonlinParameters       nonlinParameters,
			  ColorProcParameters colorProcParameters,
			  CorrectionColorProc.ColorGainsParameters     channelGainParameters,
			  EyesisCorrectionParameters.RGBParameters             rgbParameters,
			  int          convolveFFTSize, // 128 - fft size, kernel size should be size/2
			  double 		     scaleExposure,
			  final int        threadsMax,  // maximal number of threads to launch
			  final boolean    updateStatus,
			  final int        debugLevel){
		  boolean advanced=this.correctionsParameters.zcorrect || this.correctionsParameters.equirectangular;
		  boolean crop=      advanced? true: this.correctionsParameters.crop;
		  boolean rotate=    advanced? false: this.correctionsParameters.rotate;
		  double JPEG_scale= advanced? 1.0: this.correctionsParameters.JPEG_scale;
		  boolean toRGB=     advanced? true: this.correctionsParameters.toRGB;

		  // may use this.StartTime to report intermediate steps execution times
		  String name=(String) imp_src.getProperty("name");
		  //		int channel= Integer.parseInt((String) imp_src.getProperty("channel"));
		  int channel= (Integer) imp_src.getProperty("channel");
		  String path= (String) imp_src.getProperty("path");
		  if (this.correctionsParameters.pixelDefects && (eyesisCorrections.defectsXY!=null)&& (eyesisCorrections.defectsXY[channel]!=null)){
			  // apply pixel correction
			  int numApplied=	eyesisCorrections.correctDefects(
					  imp_src,
					  channel,
					  debugLevel);
			  if ((debugLevel>0) && (numApplied>0)) { // reduce verbosity after verified defect correction works
				  System.out.println("Corrected "+numApplied+" pixels in "+path);
			  }
		  }
		  if (this.correctionsParameters.vignetting){
			  if ((eyesisCorrections.channelVignettingCorrection==null) || (channel<0) || (channel>=eyesisCorrections.channelVignettingCorrection.length) || (eyesisCorrections.channelVignettingCorrection[channel]==null)){
				  System.out.println("No vignetting data for channel "+channel);
				  return null;
			  }
			  float [] pixels=(float []) imp_src.getProcessor().getPixels();
			  if (pixels.length!=eyesisCorrections.channelVignettingCorrection[channel].length){
				  System.out.println("Vignetting data for channel "+channel+" has "+eyesisCorrections.channelVignettingCorrection[channel].length+" pixels, image "+path+" has "+pixels.length);
				  return null;
			  }
			  // TODO: Move to do it once:
			  double min_non_zero = 0.0;
			  for (int i=0;i<pixels.length;i++){
				  double d = eyesisCorrections.channelVignettingCorrection[channel][i];
				  if ((d > 0.0) && ((min_non_zero == 0) || (min_non_zero > d))){
					  min_non_zero = d;
				  }
			  }
			  double max_vign_corr = dct_parameters.vignetting_range*min_non_zero;

			  System.out.println("Vignetting data: channel="+channel+", min = "+min_non_zero);
			  for (int i=0;i<pixels.length;i++){
				  double d = eyesisCorrections.channelVignettingCorrection[channel][i];
				  if (d > max_vign_corr) d = max_vign_corr;
				  pixels[i]*=d;
			  }
			  // Scale here, combine with vignetting later?
			  int width =  imp_src.getWidth();
			  int height = imp_src.getHeight();
			  for (int y = 0; y < height-1; y+=2){
				  for (int x = 0; x < width-1; x+=2){
					  pixels[y*width+x        ] *= dct_parameters.scale_g;
					  pixels[y*width+x+width+1] *= dct_parameters.scale_g;
					  pixels[y*width+x      +1] *= dct_parameters.scale_r;
					  pixels[y*width+x+width  ] *= dct_parameters.scale_b;
				  }
			  }

		  } else { // assuming GR/BG pattern
			  System.out.println("Applying fixed color gain correction parameters: Gr="+
					  dct_parameters.novignetting_r+", Gg="+dct_parameters.novignetting_g+", Gb="+dct_parameters.novignetting_b);
			  float [] pixels=(float []) imp_src.getProcessor().getPixels();
			  int width =  imp_src.getWidth();
			  int height = imp_src.getHeight();
			  double kr = dct_parameters.scale_r/dct_parameters.novignetting_r;
			  double kg = dct_parameters.scale_g/dct_parameters.novignetting_g;
			  double kb = dct_parameters.scale_b/dct_parameters.novignetting_b;
			  for (int y = 0; y < height-1; y+=2){
				  for (int x = 0; x < width-1; x+=2){
					  pixels[y*width+x        ] *= kg;
					  pixels[y*width+x+width+1] *= kg;
					  pixels[y*width+x      +1] *= kr;
					  pixels[y*width+x+width  ] *= kb;
				  }
			  }
		  }
		  String title=name+"-"+String.format("%02d", channel);
		  ImagePlus result=imp_src;
		  if (debugLevel>1) System.out.println("processing: "+path);
		  result.setTitle(title+"RAW");
		  if (!this.correctionsParameters.split){
			  eyesisCorrections.saveAndShow(result, this.correctionsParameters);
			  return result;
		  }
		  // Generate split parameters for DCT processing mode
		  EyesisCorrectionParameters.SplitParameters splitParameters = new EyesisCorrectionParameters.SplitParameters(
				  (dct_parameters.decimation == 2)?1:2,  // oversample; // currently source kernels are oversampled
						  dct_parameters.dct_size/2, // addLeft
						  dct_parameters.dct_size/2, // addTop
						  dct_parameters.dct_size/2, // addRight
						  dct_parameters.dct_size/2  // addBottom
				  );

		  // Split into Bayer components, oversample, increase canvas
		  ImageStack stack= eyesisCorrections.bayerToStack(
				  result, // source Bayer image, linearized, 32-bit (float))
				  splitParameters);
		  String titleFull=title+"-SPLIT";
		  if (debugLevel > -1){
			  double [] chn_avg = {0.0,0.0,0.0};
			  float [] pixels;
			  int width =  stack.getWidth();
			  int height = stack.getHeight();

			  for (int c = 0; c <3; c++){
				  pixels = (float[]) stack.getPixels(c+1);
				  for (int i = 0; i<pixels.length; i++){
					  chn_avg[c] += pixels[i];
				  }
			  }
			  chn_avg[0] /= width*height/4;
			  chn_avg[1] /= width*height/4;
			  chn_avg[2] /= width*height/2;
			  System.out.println("Split channels averages: R="+chn_avg[0]+", G="+chn_avg[2]+", B="+chn_avg[1]);
		  }

		  if (!this.correctionsParameters.debayer) {
			  result= new ImagePlus(titleFull, stack);
			  eyesisCorrections.saveAndShow(result, this.correctionsParameters);
			  return result;
		  }
		  // =================
		  ShowDoubleFloatArrays sdfa_instance = new ShowDoubleFloatArrays(); // just for debugging?
		  if (debugLevel > 0) {
			  System.out.println("Showing image BEFORE_PROC");
			  ImagePlus imp_dbg= new ImagePlus("BEFORE_PROC",stack);
		      imp_dbg.getProcessor().resetMinAndMax();
			  imp_dbg.updateAndDraw();
		      imp_dbg.show();
		  }

		  if (this.correctionsParameters.deconvolve) { // process with DCT, otherwise use simple debayer
			  ImageDtt image_dtt = new ImageDtt(
					  4, // 4 sensors, will not be used here
					  dctParameters.dct_size,
					  null, // FIXME: needs ImageDttParameters (clt_parameters.img_dtt),
					  false, // aux
					  false, // mono
					  false, // lwir
					  1.0); // Bayer( not monochrome), scale correlation strengths
			  double [][][][] dct_data = image_dtt.mdctStack(
					  stack,
					  channel,
					  dct_parameters,
					  this,
					  threadsMax,
					  debugLevel,
					  updateStatus);
			  System.out.println("dct_data.length="+dct_data.length+" dct_data[0].length="+dct_data[0].length
					  +" dct_data[0][0].length="+dct_data[0][0].length+" dct_data[0][0][0].length="+dct_data[0][0][0].length);
			  if (dct_parameters.color_DCT){ // convert RBG -> YPrPb
				  dct_data = image_dtt.dct_color_convert(
						  dct_data,
						  colorProcParameters.kr,
						  colorProcParameters.kb,
						  dct_parameters.sigma_rb,        // blur of channels 0,1 (r,b) in addition to 2 (g)
						  dct_parameters.sigma_y,         // blur of Y from G
						  dct_parameters.sigma_color,     // blur of Pr, Pb in addition to Y
						  threadsMax,
						  debugLevel);
			  } else { // just LPF RGB
				  if (dct_parameters.dbg_sigma > 0){ // no filter at all
					  for (int chn = 0; chn < dct_data.length; chn++) {
						  image_dtt.dct_lpf(
								  dct_parameters.dbg_sigma,
								  dct_data[chn],
								  threadsMax,
								  debugLevel);
					  }
				  }

			  }

			  int tilesY = stack.getHeight()/dct_parameters.dct_size - 1;
			  int tilesX = stack.getWidth()/dct_parameters.dct_size - 1;
			  if (debugLevel > 0){
				  System.out.println("--tilesX="+tilesX);
				  System.out.println("--tilesY="+tilesY);
			  }
			  if (debugLevel > 1){
				  double [][] dct = new double [dct_data.length][];
				  for (int chn = 0; chn < dct.length; chn++) {
					  dct[chn] = image_dtt.lapped_dct_dbg(
							  dct_data [chn],
							  threadsMax,
							  debugLevel);
				  }
				  //	        System.out.println("dct_dc.length="+dct_dc.length+" dct_ac.length="+dct_ac.length);
				  sdfa_instance.showArrays(dct,
						  tilesX*dct_parameters.dct_size,
						  tilesY*dct_parameters.dct_size,
						  true,
						  result.getTitle()+"-DCT");
			  }
			  double [][] idct_data = new double [dct_data.length][];
			  for (int chn=0; chn<idct_data.length;chn++){
				  idct_data[chn] = image_dtt.lapped_idct(
						  dct_data[chn],                  // scanline representation of dcd data, organized as dct_size x dct_size tiles
						  dct_parameters.dct_size,        // final int
						  dct_parameters.dct_window,      //window_type
						  threadsMax,
						  debugLevel);
			  }
			  if (dct_parameters.color_DCT){ // convert RBG -> YPrPb
				  if (debugLevel > 0) sdfa_instance.showArrays(
						  idct_data,
						  (tilesX + 1) * dct_parameters.dct_size,
						  (tilesY + 1) * dct_parameters.dct_size,
						  true,
						  result.getTitle()+"-IDCT-YPrPb");
				  if (dct_parameters.nonlin && ((dct_parameters.nonlin_y != 0.0) || (dct_parameters.nonlin_c != 0.0))) {
					  System.out.println("Applying edge emphasis, nonlin_y="+dct_parameters.nonlin_y+
							  ", nonlin_c="+dct_parameters.nonlin_c+", nonlin_corn="+dct_parameters.nonlin_corn);
					  idct_data = edge_emphasis(
							  idct_data,                              // final double [][] yPrPb,
							  (tilesX + 1) * dct_parameters.dct_size, // final int         width,
							  dct_parameters.dct_size,                // final int         step,  //(does not need to be this)            // just for multi-threading efficiency?
							  dct_parameters.nonlin_max_y,            // final double      nonlin_max_y =     1.0; // maximal amount of nonlinear line/edge emphasis for Y component
							  dct_parameters.nonlin_max_c,            // final double      nonlin_max_c =     1.0; // maximal amount of nonlinear line/edge emphasis for C component
							  dct_parameters.nonlin_y,                // final double      nonlin_y,         //  =        0.01; // amount of nonlinear line/edge emphasis for Y component
							  dct_parameters.nonlin_c,                // final double      nonlin_c,         //  =        0.01; // amount of nonlinear line/edge emphasis for C component
							  dct_parameters.nonlin_corn,             // final double      nonlin_corn,      // =     0.5;  // relative weight for nonlinear corner elements
							  (dct_parameters.denoise? dct_parameters.denoise_y:0.0), // final double      denoise_y,        // =        1.0;  // maximal total smoothing of the Y post-kernel (will compete with edge emphasis)
							  (dct_parameters.denoise? dct_parameters.denoise_c:0.0), // final double      denoise_c,        //  =        1.0;  // maximal total smoothing of the color differences post-kernel (will compete with edge emphasis)
							  dct_parameters.denoise_y_corn,          // final double      denoise_y_corn,   // =   0.5;  // weight of the 4 corner pixels during denoise y (relative to 4 straight)
							  dct_parameters.denoise_c_corn,          // final double      denoise_c_corn,   // =   0.5;  // weight of the 4 corner pixels during denoise y (relative to 4 straight)
							  dct_parameters.dct_size,                //,                             // final int         threadsMax,       // maximal number of threads to launch
							  debugLevel);                            // final int         globalDebugLevel)
					  if (debugLevel > 0) sdfa_instance.showArrays(
							  idct_data,
							  (tilesX + 1) * dct_parameters.dct_size,
							  (tilesY + 1) * dct_parameters.dct_size,
							  true,
							  result.getTitle()+"-EMPH-"+dct_parameters.nonlin_y+"_"+dct_parameters.nonlin_c+"_"+dct_parameters.nonlin_corn);
				  }

				  // temporary convert back to RGB
				  idct_data = YPrPbToRBG(idct_data,
						  colorProcParameters.kr,        // 0.299;
						  colorProcParameters.kb,        // 0.114;
						  (tilesX + 1) * dct_parameters.dct_size);

			  } else {
				  if (dct_parameters.post_debayer){ // post_debayer
					  if (debugLevel > -1) System.out.println("Applying post-debayer");
					  if (debugLevel > -1) sdfa_instance.showArrays(
							  idct_data,
							  (tilesX + 1) * dct_parameters.dct_size,
							  (tilesY + 1) * dct_parameters.dct_size,
							  true,
							  result.getTitle()+"-rbg_before");

					  idct_data = post_debayer( // debayer in pixel domain after aberration correction
							  idct_data, // final double [][] rbg,    // yPrPb,
							  (tilesX + 1) * dct_parameters.dct_size, // final int         width,
							  dct_parameters.dct_size,                // final int         step,             // just for multi-threading efficiency?
							  dct_parameters.dct_size,                // final int         threadsMax,       // maximal number of threads to launch
							  debugLevel);                            // final int         globalDebugLevel)
					  // add here YPrPb conversion, then edge_emphasis
					  if (debugLevel > -1) sdfa_instance.showArrays(
							  idct_data,
							  (tilesX + 1) * dct_parameters.dct_size,
							  (tilesY + 1) * dct_parameters.dct_size,
							  true,
							  result.getTitle()+"-rbg_after");
				  } else {
					  if (debugLevel > -1) System.out.println("Applyed LPF, sigma = "+dct_parameters.dbg_sigma);
					  if (debugLevel > -1) sdfa_instance.showArrays(
							  idct_data,
							  (tilesX + 1) * dct_parameters.dct_size,
							  (tilesY + 1) * dct_parameters.dct_size,
							  true,
							  result.getTitle()+"-rbg_sigma");
				  }
			  }

			  if (debugLevel > 0) sdfa_instance.showArrays(idct_data,
					  (tilesX + 1) * dct_parameters.dct_size,
					  (tilesY + 1) * dct_parameters.dct_size,
					  true,
					  result.getTitle()+"-IDCT-RGB");

			  // convert to ImageStack of 3 slices
			  String [] sliceNames = {"red", "blue", "green"};
			  stack = sdfa_instance.makeStack(
					  idct_data,
					  (tilesX + 1) * dct_parameters.dct_size,
					  (tilesY + 1) * dct_parameters.dct_size,
					  sliceNames); // or use null to get chn-nn slice names


		  } else { // if (this.correctionsParameters.deconvolve) - here use a simple debayer
			  System.out.println("Bypassing DCT-based aberration correction");
			  debayer_rbg(stack, 0.25); // simple standard 3x3 kernel debayer
		  }
		  if (debugLevel > -1){
			  double [] chn_avg = {0.0,0.0,0.0};
			  float [] pixels;
			  int width =  stack.getWidth();
			  int height = stack.getHeight();

			  for (int c = 0; c <3; c++){
				  pixels = (float[]) stack.getPixels(c+1);
				  for (int i = 0; i<pixels.length; i++){
					  chn_avg[c] += pixels[i];
				  }
			  }
			  chn_avg[0] /= width*height;
			  chn_avg[1] /= width*height;
			  chn_avg[2] /= width*height;
			  System.out.println("Processed channels averages: R="+chn_avg[0]+", G="+chn_avg[2]+", B="+chn_avg[1]);
		  }

		  if (!this.correctionsParameters.colorProc){
			  result= new ImagePlus(titleFull, stack);
			  eyesisCorrections.saveAndShow(
					  result,
					  this.correctionsParameters);
			  return result;
		  }
		  if (debugLevel > 1) System.out.println("before colors.1");
		  //Processing colors - changing stack sequence to r-g-b (was r-b-g)
		  if (!eyesisCorrections.fixSliceSequence(
				  stack,
				  debugLevel)){
			  if (debugLevel > -1) System.out.println("fixSliceSequence() returned false");
			  return null;
		  }
		  if (debugLevel > 1) System.out.println("before colors.2");
		  if (debugLevel > 1){
			  ImagePlus imp_dbg=new ImagePlus(imp_src.getTitle()+"-"+channel+"-preColors",stack);
			  eyesisCorrections.saveAndShow(
					  imp_dbg,
					  this.correctionsParameters);
		  }
		  if (debugLevel > 1) System.out.println("before colors.3, scaleExposure="+scaleExposure+" scale = "+(255.0/eyesisCorrections.psfSubpixelShouldBe4/eyesisCorrections.psfSubpixelShouldBe4/scaleExposure));
		  CorrectionColorProc correctionColorProc=new CorrectionColorProc(eyesisCorrections.stopRequested);
		  double [][] yPrPb=new double [3][];
		  //			if (dct_parameters.color_DCT){
		  // need to get YPbPr - not RGB here
		  //			} else {
		  correctionColorProc.processColorsWeights(stack, // just gamma convert? TODO: Cleanup? Convert directly form the linear YPrPb
				  //					  255.0/this.psfSubpixelShouldBe4/this.psfSubpixelShouldBe4, //  double scale,     // initial maximal pixel value (16))
				  //					  255.0/eyesisCorrections.psfSubpixelShouldBe4/eyesisCorrections.psfSubpixelShouldBe4/scaleExposure, //  double scale,     // initial maximal pixel value (16))
				  //					  255.0/2/2/scaleExposure, //  double scale,     // initial maximal pixel value (16))
				  255.0/scaleExposure, //  double scale,     // initial maximal pixel value (16))
				  colorProcParameters,
				  channelGainParameters,
				  channel,
				  null, //correctionDenoise.getDenoiseMask(),
				  this.correctionsParameters.blueProc,
				  debugLevel);
		  if (debugLevel > 1) System.out.println("Processed colors to YPbPr, total number of slices="+stack.getSize());
		  if (debugLevel > 1) {
			  ImagePlus imp_dbg=new ImagePlus("procColors",stack);
			  eyesisCorrections.saveAndShow(
					  imp_dbg,
					  this.correctionsParameters);
		  }
		  float [] fpixels;
		  int [] slices_YPrPb = {8,6,7};
		  yPrPb=new double [3][];
		  for (int n = 0; n < slices_YPrPb.length; n++){
			  fpixels = (float[]) stack.getPixels(slices_YPrPb[n]);
			  yPrPb[n] = new double [fpixels.length];
			  for (int i = 0; i < fpixels.length; i++) yPrPb[n][i] = fpixels[i];
		  }

		  if (toRGB) {
			  if (debugLevel > 0){
				  System.out.println("correctionColorProc.YPrPbToRGB");
			  }
			  stack =  YPrPbToRGB(yPrPb,
					  colorProcParameters.kr,        // 0.299;
					  colorProcParameters.kb,        // 0.114;
					  stack.getWidth());

			  title=titleFull; // including "-DECONV" or "-COMBO"
			  titleFull=title+"-RGB-float";
			  //Trim stack to just first 3 slices
			  if (debugLevel > 1){ // 2){
				  ImagePlus imp_dbg=new ImagePlus("YPrPbToRGB",stack);
				  eyesisCorrections.saveAndShow(
						  imp_dbg,
						  this.correctionsParameters);
			  }
			  while (stack.getSize() > 3) stack.deleteLastSlice();
			  if (debugLevel > 1) System.out.println("Trimming color stack");
		  } else {
			  title=titleFull; // including "-DECONV" or "-COMBO"
			  titleFull=title+"-YPrPb"; // including "-DECONV" or "-COMBO"
			  if (debugLevel > 1) System.out.println("Using full stack, including YPbPr");
		  }

		  result= new ImagePlus(titleFull, stack);
		  // Crop image to match original one (scaled to oversampling)
		  if (crop){ // always crop if equirectangular
			  if (debugLevel > 1) System.out.println("cropping");
			  stack = eyesisCorrections.cropStack32(stack,splitParameters);
			  if (debugLevel > 2) { // 2){
				  ImagePlus imp_dbg=new ImagePlus("cropped",stack);
				  eyesisCorrections.saveAndShow(
						  imp_dbg,
						  this.correctionsParameters);
			  }
		  }
		  // rotate the result
		  if (rotate){ // never rotate for equirectangular
			  stack=eyesisCorrections.rotateStack32CW(stack);
		  }
		  if (!toRGB && !this.correctionsParameters.jpeg){ // toRGB set for equirectangular
			  if (debugLevel > 1) System.out.println("!toRGB && !this.correctionsParameters.jpeg");
			  eyesisCorrections.saveAndShow(result, this.correctionsParameters);
			  return result;
		  } else { // that's not the end result, save if required
			  if (debugLevel > 1) System.out.println("!toRGB && !this.correctionsParameters.jpeg - else");
			  eyesisCorrections.saveAndShow(result,
					  eyesisCorrections.correctionsParameters,
					  eyesisCorrections.correctionsParameters.save32,
					  false,
					  eyesisCorrections.correctionsParameters.JPEG_quality); // save, no show
		  }
		  // convert to RGB48 (16 bits per color component)
		  ImagePlus imp_RGB;
		  stack=eyesisCorrections.convertRGB32toRGB16Stack(
				  stack,
				  rgbParameters);

		  titleFull=title+"-RGB48";
		  result= new ImagePlus(titleFull, stack);
		  //			  ImagePlus imp_RGB24;
		  result.updateAndDraw();
		  if (debugLevel > 1) System.out.println("result.updateAndDraw(), "+titleFull+"-RGB48");

		  CompositeImage compositeImage=eyesisCorrections.convertToComposite(result);

		  if (!this.correctionsParameters.jpeg && !advanced){ // RGB48 was the end result
			  if (debugLevel > 1) System.out.println("if (!this.correctionsParameters.jpeg && !advanced)");
			  eyesisCorrections.saveAndShow(compositeImage, this.correctionsParameters);
			  return result;
		  } else { // that's not the end result, save if required
			  if (debugLevel > 1) System.out.println("if (!this.correctionsParameters.jpeg && !advanced) - else");
			  eyesisCorrections.saveAndShow(compositeImage, this.correctionsParameters, this.correctionsParameters.save16, false); // save, no show
			  //				  eyesisCorrections.saveAndShow(compositeImage, this.correctionsParameters, this.correctionsParameters.save16, true); // save, no show
		  }

		  imp_RGB=eyesisCorrections.convertRGB48toRGB24(
				  stack,
				  title+"-RGB24",
				  0, 65536, // r range 0->0, 65536->256
				  0, 65536, // g range
				  0, 65536,// b range
				  0, 65536);// alpha range
		  if (JPEG_scale!=1.0){
			  ImageProcessor ip=imp_RGB.getProcessor();
			  ip.setInterpolationMethod(ImageProcessor.BICUBIC);
			  ip=ip.resize((int)(ip.getWidth()*JPEG_scale),(int) (ip.getHeight()*JPEG_scale));
			  imp_RGB= new ImagePlus(imp_RGB.getTitle(),ip);
			  imp_RGB.updateAndDraw();
		  }
		  eyesisCorrections.saveAndShow(imp_RGB, this.correctionsParameters);

		  return result;
	  }

	  public ImageStack  YPrPbToRGB(double [][] yPrPb,
			  double Kr,        // 0.299;
			  double Kb,        // 0.114;
			  int width
			  ) {
		  int length = yPrPb[0].length;
		  int height = length/width;

		  float [] fpixels_r= new float [length];
		  float [] fpixels_g= new float [length];
		  float [] fpixels_b= new float [length];
		  double Kg=1.0-Kr-Kb;
		  int i;
		  /**
	R= Y+ Pr*2.0*(1-Kr)
	B= Y+ Pb*2.0*(1-Kb)
	G= Y  +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg

		   */
		  double KPrR=  2.0*(1-Kr);
		  double KPbB=  2.0*(1-Kb);
		  double KPrG= -2.0*Kr*(1-Kr)/Kg;
		  double KPbG= -2.0*Kb*(1-Kb)/Kg;
		  double Y,Pr,Pb;
		  for (i=0;i<length;i++) {
			  Pb=yPrPb[2][i];
			  Pr=yPrPb[1][i];
			  Y =yPrPb[0][i];
			  fpixels_r[i]=(float) (Y+ Pr*KPrR);
			  fpixels_b[i]=(float) (Y+ Pb*KPbB);
			  fpixels_g[i]=(float) (Y+ Pr*KPrG + Pb*KPbG);
		  }
		  ImageStack stack=new ImageStack(width,height);
		  stack.addSlice("red",   fpixels_r);
		  stack.addSlice("green", fpixels_g);
		  stack.addSlice("blue",  fpixels_b);
		  return stack;

	  }

	  public double [][]  YPrPbToRBG(double [][] yPrPb,
			  double Kr,        // 0.299;
			  double Kb,        // 0.114;
			  int width
			  ) {
		  int length = yPrPb[0].length;
		  //			int height = length/width;

		  double [][]rbg = new double[3][length];
		  double Kg=1.0-Kr-Kb;
		  int i;
		  /**
	R= Y+ Pr*2.0*(1-Kr)
	B= Y+ Pb*2.0*(1-Kb)
	G= Y  +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg

		   */
		  double KPrR=  2.0*(1-Kr);
		  double KPbB=  2.0*(1-Kb);
		  double KPrG= -2.0*Kr*(1-Kr)/Kg;
		  double KPbG= -2.0*Kb*(1-Kb)/Kg;
		  double Y,Pr,Pb;
		  for (i=0;i<length;i++) {
			  Pb=yPrPb[2][i];
			  Pr=yPrPb[1][i];
			  Y =yPrPb[0][i];
			  rbg[0][i]=(float) (Y+ Pr*KPrR);
			  rbg[1][i]=(float) (Y+ Pb*KPbB);
			  rbg[2][i]=(float) (Y+ Pr*KPrG + Pb*KPbG);
		  }
		  return rbg;
	  }


	  public double [][] post_debayer( // debayer in pixel domain after aberration correction
			  final double [][] rbg, // yPrPb,
			  final int         width,
			  final int         step,             // just for multi-threading efficiency?
			  final int         threadsMax,       // maximal number of threads to launch
			  final int         globalDebugLevel)
	  {
		  final double [][] rbg_new = new double [rbg.length][rbg[0].length];
		  final int         height = rbg[0].length/width;
		  final int tilesY = (height + step - 1) / step;
		  final int tilesX = (width +  step - 1) / step;
		  final int nTiles=tilesX * tilesY;
		  final double [] kern_g={
				  0.0,   0.125,  0.0  ,
				  0.125, 0.5,    0.125,
				  0.0,   0.125,  0.0  };
		  final double [] kern_rb={
				  0.0625,  0.125, 0.0625,
				  0.125,   0.25,  0.125,
				  0.0625,  0.125, 0.0625};
		  final double [][] kerns = {kern_rb,kern_rb,kern_g};

		  final int    []   neib_indices = {-width-1,-width,-width+1,-1,0,1,width-1,width,width+1};

		  final Thread[] threads = ImageDtt.newThreadArray(threadsMax);
		  final AtomicInteger ai = new AtomicInteger(0);

		  for (int ithread = 0; ithread < threads.length; ithread++) {
			  threads[ithread] = new Thread() {
				  @Override
				public void run() {
					  int tileY,tileX;
					  double [] neibs =   new double[9]; // pixels around current, first Y, then each color diff
					  for (int nTile = ai.getAndIncrement(); nTile < nTiles; nTile = ai.getAndIncrement()) {
						  tileY = nTile/tilesX;
						  tileX = nTile - tileY * tilesX;
						  int y1 = (tileY +1) * step;
						  if (y1 > height) y1 = height;
						  int x1 = (tileX +1) * step;
						  if (x1 > width) x1 = width;
						  for (int y = tileY * step; y < y1; y++) {
							  for (int x = tileX * step; x < x1; x++) {
								  int indx = y*width + x;
								  for (int n  = 0; n < rbg.length; n++) {
									  rbg_new[n][indx] = rbg[n][indx]; // default - just copy old value
								  }
								  if ((y > 0) && (y < (height - 1)) && (x > 0) && (x < (width - 1))) { // only correct those not on the edge
									  for (int n  = 0; n < rbg.length; n++) {
										  rbg_new[n][indx] = 0.0;
										  for (int i = 0; i < neibs.length; i++){
											  rbg_new[n][indx] += kerns[n][i]*rbg[n][indx+neib_indices[i]];
										  }
									  }
								  }
							  }
						  }
					  }
				  }
			  };
		  }
		  ImageDtt.startAndJoin(threads);
		  return rbg_new;
	  }

	  public double [][] edge_emphasis(
			  final double [][] yPrPb,
			  final int         width,
			  final int         step,             // just for multi-threading efficiency?
			  final double      nonlin_max_y, // =     1.0; // maximal amount of nonlinear line/edge emphasis for Y component
			  final double      nonlin_max_c, // =     1.0; // maximal amount of nonlinear line/edge emphasis for C component
			  final double      nonlin_y,         //  =        0.01; // amount of nonlinear line/edge emphasis for Y component
			  final double      nonlin_c,         //  =        0.01; // amount of nonlinear line/edge emphasis for C component
			  final double      nonlin_corn,      // =     0.5;  // relative weight for nonlinear corner elements
			  final double      denoise_y,        // =        1.0;  // maximal total smoothing of the Y post-kernel (will compete with edge emphasis)
			  final double      denoise_c,        //  =        1.0;  // maximal total smoothing of the color differences post-kernel (will compete with edge emphasis)
			  final double      denoise_y_corn,   // =   0.3;  // weight of the 4 corner pixels during denoise y (relative to 4 straight)
			  final double      denoise_c_corn,   // =   0.3;  // weight of the 4 corner pixels during denoise y (relative to 4 straight)
			  final int         threadsMax,       // maximal number of threads to launch
			  final int         globalDebugLevel)
	  {
		  final double [][] yPrPb_new = new double [yPrPb.length][yPrPb[0].length];
		  final int         height = yPrPb[0].length/width;
		  final int tilesY = (height + step - 1) / step;
		  final int tilesX = (width +  step - 1) / step;
		  final int nTiles = tilesX * tilesY;
		  final int    [][] probes =  {{1,7},{3,5},{2,6},{0,8}}; // indices in [012/345/678] 3x3 square to calculate squared sums of differences
		  final int    [][] kerns =   {{ 1,  3,  5,   7},  {1,   3,   5,  7},  {0,   2,   6,  8},  {0,   2,  6,   8}};  // indices in [012/345/678] 3x3 square to convolve data
		  final double [][] kernsw =  {{-1.0,1.0,1.0,-1.0},{1.0,-1.0,-1.0,1.0},{1.0,-1.0,-1.0,1.0},{-1.0,1.0,1.0,-1.0}}; // weights of kern elements
		  final int    []   neib_indices = {-width-1,-width,-width+1,-1,0,1,width-1,width,width+1};
		  final double [][] kernsw_y = new double [kernsw.length][];
		  final double [][] kernsw_c = new double [kernsw.length][];
		  final double []   denoise_kern_y = {
				  0.125*denoise_y*denoise_y_corn,         0.125*denoise_y*(1.0-denoise_y_corn), 0.125*denoise_y*denoise_y_corn,
				  0.125*denoise_y*(1.0-denoise_y_corn),  -0.5*  denoise_y,                      0.125*denoise_y*(1.0-denoise_y_corn),
				  0.125*denoise_y*denoise_y_corn,         0.125*denoise_y*(1.0-denoise_y_corn), 0.125*denoise_y*denoise_y_corn};
		  final double []   denoise_kern_c = {
				  0.125*denoise_c*denoise_c_corn,         0.125*denoise_c*(1.0-denoise_c_corn), 0.125*denoise_c*denoise_c_corn,
				  0.125*denoise_c*(1.0-denoise_c_corn),  -0.5*  denoise_c,                      0.125*denoise_c*(1.0-denoise_c_corn),
				  0.125*denoise_c*denoise_c_corn,         0.125*denoise_c*(1.0-denoise_c_corn), 0.125*denoise_c*denoise_c_corn};

		  for (int n = 0; n < kernsw.length; n++){
			  kernsw_y[n] = new double [kernsw[n].length];
			  kernsw_c[n] = new double [kernsw[n].length];
			  for (int i = 0; i < kernsw[n].length; i++){
				  double dy = nonlin_y * ((n>=2)? nonlin_corn: 1.0);
				  double dc = nonlin_c * ((n>=2)? nonlin_corn: 1.0);
				  kernsw_y[n][i] = kernsw[n][i] * dy* dy;
				  kernsw_c[n][i] = kernsw[n][i] * dc* dc;
			  }
		  }
		  if (globalDebugLevel > 0){
			  System.out.println("edge_emphasis(): nonlin_y="+nonlin_y+
					  ", nonlin_c="+nonlin_c+", nonlin_corn="+nonlin_corn);
			  for (int n=0; n<kernsw_y.length; n++){
				  System.out.print("kernsw_y["+n+"={");
				  for (int i = 0; i < kernsw_y[n].length; i++){
					  System.out.print(kernsw_y[n][i]);
					  if (i == (kernsw_y[n].length - 1)){
						  System.out.println("}");
					  } else {
						  System.out.print(", ");
					  }

				  }
			  }
			  for (int n=0; n<kernsw_c.length; n++){
				  System.out.print("kernsw_c["+n+"={");
				  for (int i = 0; i < kernsw_c[n].length; i++){
					  System.out.print(kernsw_c[n][i]);
					  if (i == (kernsw_c[n].length - 1)){
						  System.out.println("}");
					  } else {
						  System.out.print(", ");
					  }
				  }
			  }
		  }

		  final Thread[] threads = ImageDtt.newThreadArray(threadsMax);
		  final AtomicInteger ai = new AtomicInteger(0);

		  for (int ithread = 0; ithread < threads.length; ithread++) {
			  threads[ithread] = new Thread() {
				  @Override
				public void run() {
					  int tileY,tileX;
					  double [] neibs =   new double[9]; // pixels around current, first Y, then each color diff
					  double [] kern_y =  new double[9]; // weights of neighbors to add to the current for Y
					  double [] kern_c =  new double[9]; // weights of neighbors to add to the current for colors diffs
					  int center_index = 4;
					  for (int nTile = ai.getAndIncrement(); nTile < nTiles; nTile = ai.getAndIncrement()) {
						  tileY = nTile / tilesX;
						  tileX = nTile - tileY * tilesX;
						  int y1 = (tileY +1) * step;
						  if (y1 > height) y1 = height;
						  int x1 = (tileX +1) * step;
						  if (x1 > width) x1 = width;
						  for (int y = tileY * step; y < y1; y++) {
							  for (int x = tileX * step; x < x1; x++) {
								  int indx = y*width + x;
								  for (int n  = 0; n < yPrPb.length; n++) {
									  yPrPb_new[n][indx] = yPrPb[n][indx]; // default - just copy old value
								  }
								  if ((y > 0) && (y < (height - 1)) && (x > 0) && (x < (width - 1))) { // only correct those not on the edge
									  // read Y pixels around current
									  for (int i = 0; i < neibs.length; i++){
										  neibs[i] = yPrPb[0][indx+neib_indices[i]];
									  }
									  for (int i = 0; i < kern_y.length; i++){
										  kern_y[i] = 0.0;
										  kern_c[i] = 0.0;
									  }
									  // calculate amount of each pattern
									  for (int n = 0; n < probes.length; n++){
										  double squared=0.0;
										  for (int i = 0; i < probes[n].length; i++){
											  squared += neibs[probes[n][i]];
										  }
										  squared -= probes[n].length * neibs[center_index];
										  squared *= squared; // Now it a square of the sum of differences from the center
										  for (int i = 0; i < kernsw[n].length; i++){
											  int ni = kerns[n][i];
											  kern_y[ni]+= squared*kernsw_y[n][i];
											  kern_c[ni]+= squared*kernsw_c[n][i];
										  }
									  }
									  if (denoise_y > 0.0){
										  for (int i = 0; i < kern_y.length; i++){
											  kern_y[i]+= denoise_kern_y[i];
										  }
									  }
									  if (denoise_c > 0.0){
										  for (int i = 0; i < kern_y.length; i++){
											  kern_c[i]+= denoise_kern_c[i];
										  }
									  }

									  if (nonlin_max_y != 0){
										  double sum = 0;
										  for (int i = 0; i < kern_y.length; i++){
											  // (i != 4) just increases denoise maximal value
											  if (i != 4) sum += Math.abs(kern_y[i]);
										  }
										  if (sum > nonlin_max_y){
											  sum = nonlin_max_y/sum;
											  for (int i = 0; i < kern_y.length; i++){
												  kern_y[i] *= sum;
											  }
										  }
									  }

									  if (nonlin_max_c != 0){
										  double sum = 0;
										  for (int i = 0; i < kern_c.length; i++){
											  sum += Math.abs(kern_c[i]);
										  }
										  if (sum > nonlin_max_c){
											  sum = nonlin_max_c/sum;
											  for (int i = 0; i < kern_c.length; i++){
												  kern_c[i] *= sum;
											  }
										  }
									  }

									  for (int i = 0; i<kern_y.length; i++){
										  yPrPb_new[0][indx] += neibs[i]*kern_y[i];
									  }
									  for (int n = 1;n < 3; n++){ //color components
										  for (int i = 0; i < neibs.length; i++){
											  yPrPb_new[n][indx] += yPrPb[0][indx+neib_indices[i]]*kern_c[i];
										  }
									  }
								  }
							  }
						  }
					  }
				  }
			  };
		  }
		  ImageDtt.startAndJoin(threads);
		  return yPrPb_new;
	  }



	  public void debayer_rbg(
			  ImageStack stack_rbg){
		  debayer_rbg(stack_rbg, 1.0);
	  }

	  // Simple in-place debayer by (bi) linear approximation, assumes [0R/00], [00/B0], [G0/0G] slices
	  public void debayer_rbg(
			  ImageStack stack_rbg,
			  double scale)
	  {
		  int width = stack_rbg.getWidth();
		  int height = stack_rbg.getHeight();
		  float [] fpixels_r = (float[]) stack_rbg.getPixels(1);
		  float [] fpixels_b = (float[]) stack_rbg.getPixels(2);
		  float [] fpixels_g = (float[]) stack_rbg.getPixels(3);
		  int [][][] av_row = {
				  {{1,1},{-1,1},{-1,-1}},
				  {{1,1},{-1,1},{-1,-1}},
				  {{1,1},{-1,1},{-1,-1}}};
		  int [][][] av_col =  {
				  {{ width, width},{ width, width},{ width, width}},
				  {{-width, width},{-width, width},{-width, width}},
				  {{-width,-width},{-width,-width},{-width,-width}}};

		  int [][][] av_xcross =  {
				  {{ width+1, width+1, width+1, width+1}, { width-1, width+1, width-1, width+1}, { width-1, width-1, width-1, width-1}},
				  {{-width+1, width+1,-width+1, width+1}, {-width-1,-width+1, width-1, width+1}, {-width-1,-width-1, width-1, width-1}},
				  {{-width+1,-width+1,-width+1,-width+1}, {-width-1,-width+1,-width-1,-width+1}, {-width-1,-width-1,-width-1,-width-1}}};
		  int [][][] av_plus =  {
				  {{ width,         1,       1, width},   { width,        -1,       1, width  }, { width,        -1,      -1, width  }},
				  {{-width,         1,       1, width},   {-width,        -1,       1, width  }, {-width,        -1,      -1, width  }},
				  {{-width,         1,       1,-width},   {-width,        -1,       1,-width  }, {-width,        -1,      -1,-width  }}};
		  for (int y = 0; y < height; y++){
			  boolean odd_row = (y & 1) != 0;
			  int row_type = (y==0)? 0: ((y==(height-1))?2:1);
			  for (int x = 0; x < width; x++){
				  int indx = y*width+x;
				  boolean odd_col =   (x & 1) != 0;
				  int col_type = (x==0)? 0: ((x==(width-1))?2:1);
				  if (odd_row){
					  if (odd_col){ // GB site
						  fpixels_r[indx] = 0.5f*(
								  fpixels_r[indx+av_col[row_type][col_type][0]]+
								  fpixels_r[indx+av_col[row_type][col_type][1]]);
						  fpixels_b[indx] = 0.5f*(
								  fpixels_b[indx+av_row[row_type][col_type][0]]+
								  fpixels_b[indx+av_row[row_type][col_type][1]]);
					  } else { // !odd col  // B site
						  fpixels_r[indx] = 0.25f*(
								  fpixels_r[indx+av_xcross[row_type][col_type][0]]+
								  fpixels_r[indx+av_xcross[row_type][col_type][1]]+
								  fpixels_r[indx+av_xcross[row_type][col_type][2]]+
								  fpixels_r[indx+av_xcross[row_type][col_type][3]]);
						  fpixels_g[indx] = 0.25f*(
								  fpixels_g[indx+av_plus[row_type][col_type][0]]+
								  fpixels_g[indx+av_plus[row_type][col_type][1]]+
								  fpixels_g[indx+av_plus[row_type][col_type][2]]+
								  fpixels_g[indx+av_plus[row_type][col_type][3]]);
					  }

				  } else { // !odd_row
					  if (odd_col){  // R site
						  fpixels_b[indx] = 0.25f*(
								  fpixels_b[indx+av_xcross[row_type][col_type][0]]+
								  fpixels_b[indx+av_xcross[row_type][col_type][1]]+
								  fpixels_b[indx+av_xcross[row_type][col_type][2]]+
								  fpixels_b[indx+av_xcross[row_type][col_type][3]]);
						  fpixels_g[indx] = 0.25f*(
								  fpixels_g[indx+av_plus[row_type][col_type][0]]+
								  fpixels_g[indx+av_plus[row_type][col_type][1]]+
								  fpixels_g[indx+av_plus[row_type][col_type][2]]+
								  fpixels_g[indx+av_plus[row_type][col_type][3]]);
					  } else { // !odd col  // G site
						  fpixels_r[indx] = 0.5f*(
								  fpixels_r[indx+av_row[row_type][col_type][0]]+
								  fpixels_r[indx+av_row[row_type][col_type][1]]);
						  fpixels_b[indx] = 0.5f*(
								  fpixels_b[indx+av_col[row_type][col_type][0]]+
								  fpixels_b[indx+av_col[row_type][col_type][1]]);
					  }
				  }
			  }
		  }
		  if (scale !=1.0){
			  for (int i = 0; i< fpixels_r.length; i++){
				  fpixels_r[i] *= scale;
				  fpixels_b[i] *= scale;
				  fpixels_g[i] *= scale;
			  }
		  }
	  }


}
