package com.elphel.imagej.correction;
/**
 ** -----------------------------------------------------------------------------**
 ** EyesisCorrections.java
 **
 ** Aberration correction for Eyesis4pi
 **
 **
 ** Copyright (C) 2012 Elphel, Inc.
 **
 ** -----------------------------------------------------------------------------**
 **
 **  EyesisCorrections.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.io.IOException;
import java.util.concurrent.atomic.AtomicInteger;

import javax.swing.SwingUtilities;

import com.elphel.imagej.calibration.DebayerScissorsClass;
import com.elphel.imagej.calibration.PixelMapping;
import com.elphel.imagej.cameras.ColorProcParameters;
import com.elphel.imagej.cameras.EyesisCorrectionParameters;
import com.elphel.imagej.common.DoubleFHT;
import com.elphel.imagej.common.DoubleGaussianBlur;
import com.elphel.imagej.common.ShowDoubleFloatArrays;
import com.elphel.imagej.jp4.JP46_Reader_camera;
import com.elphel.imagej.readers.EyesisTiff;
import com.elphel.imagej.readers.ImagejJp4Tiff;
import com.elphel.imagej.tileprocessor.ImageDtt;

import ij.CompositeImage;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.Prefs;
import ij.io.FileInfo;
import ij.io.FileSaver;
import ij.process.ColorProcessor;
import ij.process.FloatProcessor;
import ij.process.ImageProcessor;
import loci.common.services.DependencyException;
import loci.common.services.ServiceException;
import loci.formats.FormatException;


public class EyesisCorrections {
	public JP46_Reader_camera JP4_INSTANCE=   new JP46_Reader_camera(false);
	DebayerScissorsClass debayerScissors=null;
	public AtomicInteger stopRequested=null; // 1 - stop now, 2 - when convenient
	public PixelMapping pixelMapping=null;
	public EyesisCorrectionParameters.CorrectionParameters correctionsParameters=null;
	public boolean [] usedChannels;
	public float [][] channelVignettingCorrection=null;
	public int [][][] defectsXY=null; // per each channel: pixel defects coordinates list (starting with worst)
	public double [][] defectsDiff=null; // per each channel: pixel defects value (diff from average of neighbors), matching defectsXY

	///	public int   [][] channelWidthHeight=null;
	public ImagePlus [] imageNoiseGains=null;
	public String [] sharpKernelPaths=null;
	public String [] smoothKernelPaths=null;
	public int debugLevel;
	public String [] stackColorNames= {"Red","Green","Blue"};
	public int psfSubpixelShouldBe4=4;         // sub-pixel decimation
	public long   startTime=0;

	public boolean ALL_AS_JP4 = true; // all w/o 10359mux - treat tiff as JP4

	//	public boolean BUG_subchannel=true; // top channel - 1, middle - 0, bottom - 2 (should be -0-1-2)
	//	public boolean BUG_subchannel=false; // top channel - 1, middle - 0, bottom - 2 (should be -0-1-2)



	public EyesisCorrections (
			AtomicInteger stopRequested,
			EyesisCorrectionParameters.CorrectionParameters correctionsParameters
			){
		this.correctionsParameters=correctionsParameters;
		this.stopRequested=stopRequested;
//		setDebug(-2);
	}
	/*
	public void setDebug(int debugLevel){
		this.debugLevel=debugLevel;
		String LOG_LEVEL = "OFF";
		switch (this.debugLevel) {
		case -2: LOG_LEVEL = "FATAL"; break;
		case -1: LOG_LEVEL = "ERROR"; break;
		case  0: LOG_LEVEL = "WARN";  break;
		case  1: LOG_LEVEL = "INFO";  break;
		case  2: LOG_LEVEL = "DEBUG"; break;
		default: LOG_LEVEL = "OFF";
		}
		
		System.out.println("Method disabled: EyesisCorrections.setDebug("+debugLevel+"), LOG_LEVEL="+LOG_LEVEL);
		return;
		/*
//		LOG_LEVEL = "ERROR"; // overwrite for testing
		boolean LOG_LEVEL_SET = loci.common.DebugTools.enableLogging(LOG_LEVEL);
//		if (!LOG_LEVEL_SET) { // only first time true
			loci.common.DebugTools.setRootLevel(LOG_LEVEL);
//		}
		System.out.println("EyesisCorrections.setDebug("+debugLevel+"), LOG_LEVEL_SET="+LOG_LEVEL_SET+" LOG_LEVEL="+LOG_LEVEL);
	}
*/	
	/*
	public void setDebugOnce(int debugLevel){
		this.debugLevel=debugLevel;
		String LOG_LEVEL = "OFF";
		switch (this.debugLevel) {
		case -2: LOG_LEVEL = "FATAL"; break;
		case -1: LOG_LEVEL = "ERROR"; break;
		case  0: LOG_LEVEL = "WARN";  break;
		case  1: LOG_LEVEL = "INFO";  break;
		case  2: LOG_LEVEL = "DEBUG"; break;
		default: LOG_LEVEL = "OFF";
		}
		boolean LOG_LEVEL_SET = loci.common.DebugTools.enableLogging(LOG_LEVEL);
		if (!LOG_LEVEL_SET) { // only first time true
			loci.common.DebugTools.setRootLevel(LOG_LEVEL);
		}
		System.out.println("EyesisCorrections.setDebug("+debugLevel+"), LOG_LEVEL_SET="+LOG_LEVEL_SET+" LOG_LEVEL="+LOG_LEVEL);
		return;
	}
	*/
	public static String stringLogLevel(int ilev) {
		String LOG_LEVEL = "OFF";
		switch (ilev) {
		case -2: LOG_LEVEL = "FATAL"; break;
		case -1: LOG_LEVEL = "ERROR"; break;
		case  0: LOG_LEVEL = "WARN";  break;
		case  1: LOG_LEVEL = "INFO";  break;
		case  2: LOG_LEVEL = "DEBUG"; break;
		default: LOG_LEVEL = "OFF";
		}
		return LOG_LEVEL;
	}
	

	public int getNumChannels(){return (this.usedChannels!=null)?this.usedChannels.length:0;}


	// TODO: preserve some data when re-running with new source files
	// FIXME: Make forgiving alien files
	public void initSensorFiles(int debugLevel){
		initSensorFiles(
				debugLevel,
				false,
				false,
				false);
	}

	public void initPixelMapping(
			int debugLevel) {
		String [] sensorPaths=correctionsParameters.selectSensorFiles(this.debugLevel);
		this.pixelMapping=new PixelMapping(
				sensorPaths,
				correctionsParameters.firstSubCameraConfig, // 	int first_channel, // 0 - old way
				correctionsParameters.numSubCameras,        // int num_channels,  // 0 - any
				true, // boolean update_channel, // false (replace file channel with effective channel (subtract first_channel)
				debugLevel);
	}

	public void initSensorFiles(
			int debugLevel,
			boolean missing_ok,
			boolean all_sensors,
			boolean correct_vignetting
			){
		this.sharpKernelPaths=null;
		this.smoothKernelPaths=null;
		if (this.pixelMapping == null) { // NOTE: will not notice switching sensor files !
			initPixelMapping(debugLevel);
		}
		/*
		String [] sensorPaths=correctionsParameters.selectSensorFiles(this.debugLevel);
		this.pixelMapping=new PixelMapping(
				sensorPaths,
				correctionsParameters.firstSubCameraConfig, // 	int first_channel, // 0 - old way
				correctionsParameters.numSubCameras,        // int num_channels,  // 0 - any
				true, // boolean update_channel, // false (replace file channel with effective channel (subtract first_channel)
				debugLevel);
        */
		if (all_sensors) {
			this.usedChannels = new boolean [this.pixelMapping.sensors.length];
			for (int i = 0; i < this.usedChannels.length; i++) {
				this.usedChannels[i] = true;
			}
		} else {
			this.usedChannels= usedChannels(correctionsParameters.getSourcePaths(),missing_ok);
		}
		// TODO: Combine with additional channel map to be able to select single image (of all 3)
		if (correctionsParameters.removeUnusedSensorData){
			for (int nChn=0;nChn< this.usedChannels.length; nChn++) {
				if (!this.usedChannels[nChn]) this.pixelMapping.removeChannel(nChn);
			}
		}
		int numUsedChannels=00;
		for (int nChn=0;nChn< this.usedChannels.length; nChn++) if (this.usedChannels[nChn]) numUsedChannels++;
		if (this.debugLevel>0) {
			String sChannels="";
			for (int nChn=0;nChn< this.usedChannels.length; nChn++) if (this.usedChannels[nChn]) sChannels+=" "+nChn;
			System.out.println ("Number of used channels: "+numUsedChannels+" ("+sChannels+" )");
		}
		createChannelVignetting(correct_vignetting); // *** THIS READS ALL SOURCE FILES !  Need to clean up (03.27.2023)***
		if ((this.debugLevel>101) && (correctionsParameters.sourcePaths!=null) && (correctionsParameters.sourcePaths.length>0)) {
			testFF(correctionsParameters.sourcePaths[0]);
		}
		if (debugLevel > -2) {
			System.out.println();
		}
	}

	// Never used !
	public void initSensorFilesAux(int debugLevel, // what is different from initSensorFiles()? Never used !
			boolean missing_ok,
			boolean all_sensors,
			boolean no_vignetting
			){
		//		this.sharpKernelPaths=null;
		//		this.smoothKernelPaths=null;
		String [] sensorPaths=correctionsParameters.selectSensorFiles(this.debugLevel);

		//		this.pixelMapping=new PixelMapping(sensorPaths,debugLevel);

		this.pixelMapping=new PixelMapping(
				sensorPaths,
				correctionsParameters.firstSubCameraConfig, // 	int first_channel, // 0 - old way
				correctionsParameters.numSubCameras,        // int num_channels,  // 0 - any
				true, // boolean update_channel, // false (replace file channel with effective channel (subtract first_channel)
				debugLevel);
		if (all_sensors) {
			this.usedChannels = new boolean [this.pixelMapping.sensors.length];
			for (int i = 0; i < this.usedChannels.length; i++) {
				this.usedChannels[i] = true;
			}
		} else {
			this.usedChannels= usedChannels(correctionsParameters.getSourcePaths(),missing_ok);
		}
		// TODO: Combine with additional channel map to be able to select single image (of all 3)
		if (correctionsParameters.removeUnusedSensorData){
			for (int nChn=0;nChn< this.usedChannels.length; nChn++) if (!this.usedChannels[nChn]) this.pixelMapping.removeChannel(nChn);
		}
		int numUsedChannels=0;
		for (int nChn=0;nChn< this.usedChannels.length; nChn++) if (this.usedChannels[nChn]) numUsedChannels++;
		if (this.debugLevel>0) {
			String sChannels="";
			for (int nChn=0;nChn< this.usedChannels.length; nChn++) if (this.usedChannels[nChn]) sChannels+=" "+nChn;
			System.out.println ("Number of used channels: "+numUsedChannels+" ("+sChannels+" )");
		}
		createChannelVignetting(true);
		//java.lang.ClassCastException: [B cannot be cast to [F
		//if ((this.debugLevel>1) && (correctionsParameters.sourcePaths!=null) && (correctionsParameters.sourcePaths.length>0)) {
		if ((this.debugLevel>101) && (correctionsParameters.sourcePaths!=null) && (correctionsParameters.sourcePaths.length>0)) {
			testFF(correctionsParameters.sourcePaths[0]);
		}
	}

	public ImagePlus getJp4Tiff(
			String path,
			int [] woi_tops,
			int [] camera_heights
			) {
		return getJp4Tiff(path, false, woi_tops, camera_heights);
	}
	public ImagePlus getJp4Tiff(
			String path) {
		return getJp4Tiff(path, false, null, null);
	}

	public ImagePlus getJp4Tiff(
			String path,
			boolean ignore_alien, // open image even if it does not belong to the current camera
			int [] woi_tops,
			int [] camera_heights
			) {
		// get source file channel
		int src_channel = correctionsParameters.getChannelFromSourceTiff(path);
		int sub_camera = src_channel - correctionsParameters.firstSubCamera;
		int subchannel=  pixelMapping.getSubChannelSilent(sub_camera); // only used for demux
		ImagejJp4Tiff      imagejJp4Tiff =  new ImagejJp4Tiff(); // override global
		ImagePlus imp = null;
		try {
			imp = imagejJp4Tiff.readTiffJp4(
					path,
					true); // scale);
		} catch (IOException | FormatException e) {
			e.printStackTrace();
			return null;
		}
		if ((subchannel >=0) && correctionsParameters.isJP4()) {
			if (this.correctionsParameters.swapSubchannels01) {
				switch (subchannel){
				case 0: subchannel=1; break;
				case 1: subchannel=0; break;
				}
			}
			ImagePlus imp_demux=JP4_INSTANCE.demuxImage(imp, subchannel);
			if (imp_demux != null) imp = imp_demux;
		}
		int [] wh = null;
		if (!this.pixelMapping.subcamerasUsed()) { // non-eyesis, single sensor file per input channel
			int [] channels = this.pixelMapping.channelsForSubCamera(src_channel - correctionsParameters.firstSubCameraConfig);
			if (channels != null) {
				int sensor_number = channels[0];
				wh = pixelMapping.getSensorWH(sensor_number);
				if ((woi_tops != null) && (imp.getProperty("WOI_TOP") != null) && (sensor_number< woi_tops.length)) {
					if (imp.getProperty("WOI_TOP") != null)
						woi_tops[sensor_number] = Integer.parseInt((String) imp.getProperty("WOI_TOP"));
				}
				if ((camera_heights != null) && (sensor_number< camera_heights.length)) { // actually acquired height (not padded)
					camera_heights[sensor_number] = imp.getHeight();
				}
			} else if (!ignore_alien) {
				return null;
			}
		}
		imp =  ShowDoubleFloatArrays.padBayerToFullSize(
				imp, // ImagePlus imp_src,
				wh, // null OK
				true); // boolean replicate);
		return imp;
	}


	// FIXME: Use only this PixelMappings's channels, do not mix exposures from main/aux!
	public double [] calcReferenceExposures(int debugLevel){
		String [] paths=this.correctionsParameters.getSourcePaths();
		return calcReferenceExposures(paths, debugLevel);
	}

	public double [] calcReferenceExposures(String [] paths,int debugLevel){
//		String [] paths=this.correctionsParameters.getSourcePaths();
		double [] exposures=new double [paths.length];
		if (this.correctionsParameters.exposureCorrectionMode<2){
			for (int nFile=0;nFile<paths.length;nFile++) {
				exposures[nFile]=(this.correctionsParameters.exposureCorrectionMode>0)?this.correctionsParameters.referenceExposure:Double.NaN;
			}
		} else {
			ImagePlus imp; // using that composite image has same exposure
			for (int nFile=0;nFile<paths.length;nFile++){
				imp = getJp4Tiff(paths[nFile]);
				/*
				try {
					imp = imagejJp4Tiff.readTiffJp4(
							paths[nFile],
							true); // scale);
				} catch (IOException | FormatException e) {
					e.printStackTrace();
					imp = null;
					exposures[nFile]=Double.NaN;
					continue;
				}
				if (this.correctionsParameters.isJP4()){
					imp=JP4_INSTANCE.open(
							"", // path,
							paths[nFile],
							"",  //arg - not used in JP46 reader
							true, // un-apply camera color gains
							null, // new window
							false); // do not show
				} else {
					imp=new ImagePlus(paths[nFile]);
					//				  JP46_Reader_camera.decodeProperiesFromInfo(imp_src); // decode existent properties from info
					JP46_Reader_camera.decodeProperiesFromInfo(imp); // decode existent properties from info
				}
				 */
				if ((imp != null) &&(imp.getProperty("EXPOSURE")!=null)){
					exposures[nFile]=Double.parseDouble((String)imp.getProperty("EXPOSURE"));
				} else {
					exposures[nFile]=Double.NaN;
				}
				if (debugLevel>1){
					System.out.println((nFile+1)+": "+paths[nFile]+" - exposure="+exposures[nFile]);
				}
			}
			String [] names=new String [paths.length];
			for (int nFile=0;nFile<paths.length;nFile++) names[nFile]=this.correctionsParameters.getNameFromSourceTiff(paths[nFile]);
			int [] firstImageIndex=new int [paths.length];
			for (int nFile=0;nFile<paths.length;nFile++) {
				firstImageIndex[nFile]=nFile;
				for (int j=0;j<nFile;j++) if (names[j].equals(names[nFile])){
					firstImageIndex[nFile]=j;
					break;
				}
			}
			double [][] minMaxExposure=new double[paths.length][2];
			for (int nFile=0;nFile<paths.length;nFile++) {
				minMaxExposure[nFile][0]=Double.NaN;
				minMaxExposure[nFile][1]=Double.NaN;
			}
			for (int nFile=0;nFile<paths.length;nFile++) if (!Double.isNaN(exposures[nFile])){
				int j=firstImageIndex[nFile];
				if (Double.isNaN(minMaxExposure[j][0]) || (minMaxExposure[j][0]>exposures[nFile])) minMaxExposure[j][0]=exposures[nFile];
				if (Double.isNaN(minMaxExposure[j][1]) || (minMaxExposure[j][1]<exposures[nFile])) minMaxExposure[j][1]=exposures[nFile];
			}
			for (int nFile=0;nFile<paths.length;nFile++) if (!Double.isNaN(exposures[nFile])){
				int j=firstImageIndex[nFile];
				exposures[nFile]=(1.0-this.correctionsParameters.relativeExposure)*minMaxExposure[j][0]+
						this.correctionsParameters.relativeExposure*minMaxExposure[j][1];
			}
		}
		// apply modes
		return exposures;
	}

	public void rebuildEquirectangularMaps(
			EyesisCorrectionParameters.EquirectangularParameters equirectangularParameters,
			int          threadsMax,  // maximal number of threads to launch
			boolean    updateStatus,
			int        debugLevel){
		this.sharpKernelPaths=null;
		this.smoothKernelPaths=null;
		String [] sensorPaths=correctionsParameters.selectSensorFiles(this.debugLevel);
		String directory= correctionsParameters.selectEquirectangularDirectory(true,true);
		if (directory==null) {
			System.out.println ("No directory selected for equirectangular maps to save");
			return;
		}
		//		boolean processPlaneProjection= equirectangularParameters.generateCommonPlane &&
		//			equirectangularParameters.selectChannelsToProcess("Select channels for plane projection", this.pixelMapping.sensors.length);

		this.pixelMapping=new PixelMapping(
				sensorPaths,
				0, // int first_channel, // 0 - old way
				0, // int num_channels,  // 0 - any
				false, // boolean update_channel, // false (replace file channel with effective channel (subtract first_channel)
				debugLevel);
		pixelMapping.generateAndSaveEquirectangularMaps(
				correctionsParameters.equirectangularDirectory+
				Prefs.getFileSeparator()+
				correctionsParameters.equirectangularPrefix+
				correctionsParameters.equirectangularSuffix,
				equirectangularParameters.longitudeLeft,
				equirectangularParameters.longitudeRight,
				equirectangularParameters.latitudeTop,
				equirectangularParameters.latitudeBottom,
				equirectangularParameters.pixelsHorizontal,
				equirectangularParameters.imageWidth, //int width,
				equirectangularParameters.imageHeight, //int height,
				equirectangularParameters.x0, //double x0,
				equirectangularParameters.y0, //double y0,
				1.0/equirectangularParameters.resolutionScale, //double pixelStep,
				equirectangularParameters.longitudeWidth,
				equirectangularParameters.clearFullMap,
				equirectangularParameters.clearAllMaps,
				threadsMax);
		boolean processPlaneProjection= equirectangularParameters.generateCommonPlane &&
				equirectangularParameters.selectChannelsToProcess("Select channels for plane projection", this.pixelMapping.sensors.length);

		if (processPlaneProjection){
			//			equirectangularParameters.projectionPixelSize=pixelMapping.degreesPerPixel*Math.PI/180.0;
			boolean [] channelMask= equirectangularParameters.getChannelsToProcess();
			int numUsedChannels=0;
			for (int i=0;i<channelMask.length;i++) if (channelMask[i]) numUsedChannels++;
			int [] channelList=new int [numUsedChannels];
			int iChannel=0;
			for (int i=0;i<channelMask.length;i++) if (channelMask[i]) channelList[iChannel++]=i;
			String sChannels="";
			for (int i=0;i<channelList.length;i++) sChannels+=" "+channelList[i];

			for (int i=0;i<channelList.length;i++) {
				int channel=channelList[i];
				if (!pixelMapping.isChannelAvailable(channel)){
					String msg="No sensor data for channel "+channel;
					System.out.println("Error "+msg);
					IJ.showMessage("Error",msg);
					return;
				}
				if (!pixelMapping.isEquirectangularMapAvailable(channel)){
					String path=correctionsParameters.selectEquirectangularMapFile(
							channel,
							debugLevel);

					if (path==null) {
						String msg="No equirectangular map found for channel "+channel;
						System.out.println("Error "+msg);
						IJ.showMessage("Error",msg);
						return;
					}
					if (debugLevel>1) System.out.println("rebuildEquirectangularMaps(): channel="+channel+" path="+path);

					pixelMapping.loadChannelEquirectangularMap(
							channel,
							path);

					if (!this.pixelMapping.isEquirectangularMapAvailable(channel)){
						String msg="Failed to load equirectangular map for channel "+channel;
						System.out.println("Error "+msg);
						IJ.showMessage("Error",msg);
						return;
					}
				}
			}



			String title="Projection_plane_map";
			ImagePlus imp_pixelmap= pixelMapping.getPlaneToSensorsMap( // need to re-load equirectangular maps?
					channelList, // int [] channels,
					equirectangularParameters.projectionElevation, // Latitude (in degrees) of the normal to the projection plane
					equirectangularParameters.projectionYaw,       // Longitude (in degrees) of the normal to the projection plane
					equirectangularParameters.projectionRoll,      // Rotation of the projection plane around the perpendicular from the lens centers
					equirectangularParameters.matchPixelSize?0.0:	equirectangularParameters.projectionPixelSize, // Ratio of the plane pixel size to the distance from the lens center to the projection plane
							equirectangularParameters.projectionWidth,     // Width of the projection rectangle
							equirectangularParameters.projectionHeight,    // Height of the projection rectangle
							equirectangularParameters.projectionCenterX,   // X-coordinate (along the projection plane X - right) of the intersection of the projection plane with the perpendicular from the lens center
							equirectangularParameters.projectionCenterY,   // Y-coordinate (along the projection plane Y - down) of the intersection of the projection plane with the perpendicular from the lens center
							equirectangularParameters.nominalHorizontalDisparity, // 60.0 - nominal distance between horizontal cameras, mm
							title,
							debugLevel
					);
			if (equirectangularParameters.matchPixelSize) {
				equirectangularParameters.projectionPixelSize=Math.PI/180.0*pixelMapping.panoDegreesPerPixel;
				if (debugLevel>0) System.out.println("rebuildEquirectangularMaps(): Setting  equirectangularParameters.projectionPixelSize="+equirectangularParameters.projectionPixelSize);
			}
			if (imp_pixelmap!=null) {
				if (debugLevel>2) {
					imp_pixelmap.getProcessor().resetMinAndMax(); // imp_psf will be reused
					imp_pixelmap.show();
				}
				FileSaver fs=new FileSaver(imp_pixelmap);
				String resultPath=correctionsParameters.equirectangularDirectory+
						Prefs.getFileSeparator()+correctionsParameters.planeMapPrefix+correctionsParameters.planeMapSuffix;
				String msg="Saving pixel map to a common plane for sensors "+sChannels+": "+resultPath;
				if (updateStatus) IJ.showStatus(msg);
				if (debugLevel>0) System.out.println(msg);
				fs.saveAsTiffStack(resultPath);
			} else {
				System.out.println("Failed to create pixel map for sensors "+sChannels);
			}

		}
	}


	public boolean updateImageNoiseGains(
			EyesisCorrectionParameters.NonlinParameters nonlinParameters,
			int          fftSize, // 128 - fft size, kernel size should be size/2
			int          threadsMax,  // maximal number of threads to launch
			boolean    updateStatus,
			int        globalDebugLevel){
		boolean removeUnused=this.correctionsParameters.removeUnusedSensorData;
		int numChannels=this.usedChannels.length;
		if (this.imageNoiseGains==null){
			this.imageNoiseGains= new ImagePlus[0];
		}
		if (this.imageNoiseGains.length!=numChannels){
			ImagePlus [] tmp=this.imageNoiseGains.clone();
			this.imageNoiseGains=new ImagePlus[numChannels];
			for (int chn=0;chn<numChannels;chn++) this.imageNoiseGains[chn]=(chn<tmp.length)?tmp[chn]:null;
		}
		this.sharpKernelPaths=correctionsParameters.selectKernelChannelFiles(
				0,  // 0 - sharp, 1 - smooth
				correctionsParameters.firstSubCameraConfig,
				//				  correctionsParameters.numSubCameras,
				numChannels, // number of channels
				this.debugLevel);
		if (this.sharpKernelPaths==null) return false;
		if (nonlinParameters.useDiffNoiseGains) {
			this.smoothKernelPaths=correctionsParameters.selectKernelChannelFiles(
					1,  // 0 - sharp, 1 - smooth
					correctionsParameters.firstSubCameraConfig,
					//					  correctionsParameters.numSubCameras,
					numChannels, // number of channels
					this.debugLevel);
			if (this.smoothKernelPaths==null) return false;
		}
		for (int chn=0;chn<this.usedChannels.length;chn++){
			if (this.usedChannels[chn] && (this.sharpKernelPaths[chn]!=null) && (!nonlinParameters.useDiffNoiseGains ||(this.smoothKernelPaths[chn]!=null))){
				if (
						(this.imageNoiseGains[chn]==null) ||
						(!this.sharpKernelPaths[chn].equals(this.imageNoiseGains[chn].getProperty("sharpKernelPath"))) ||
						(!this.smoothKernelPaths[chn].equals(this.imageNoiseGains[chn].getProperty("smoothKernelPath")))){

					ImagePlus imp_kernel_sharp=new ImagePlus(this.sharpKernelPaths[chn]);
					if (imp_kernel_sharp.getStackSize()<3) {
						System.out.println("Need a 3-layer stack with kernels");
						this.sharpKernelPaths[chn]=null;
						continue;
					}
					ImageStack kernel_sharp_stack= imp_kernel_sharp.getStack();
					ImageStack kernel_smooth_stack=null;
					if (nonlinParameters.useDiffNoiseGains) {
						ImagePlus imp_kernel_smooth=new ImagePlus(this.smoothKernelPaths[chn]);
						if (imp_kernel_smooth.getStackSize()<3) {
							System.out.println("Need a 3-layer stack with kernels");
							this.smoothKernelPaths[chn]=null;
							continue;
						}
						kernel_smooth_stack= imp_kernel_smooth.getStack();
					}
					ImageStack kernelsNoise=
							calculateKernelsNoiseGains (
									kernel_sharp_stack, //final ImageStack kernelStack1, // first stack with 3 colors/slices convolution kernels
									kernel_smooth_stack, //final ImageStack kernelStack2, // second stack with 3 colors/slices convolution kernels (or null)
									fftSize, //size, // 128 - fft size, kernel size should be size/2
									nonlinParameters.blurSigma,
									threadsMax,  // maximal number of threads to launch
									updateStatus,
									globalDebugLevel);
					kernel_sharp_stack= null; // TODO: - maybe keep one set to speed-up single-channel processing?
					kernel_smooth_stack=null;
					Runtime.getRuntime().gc();
					String title="noiseGains_"+(nonlinParameters.useDiffNoiseGains?"diff_":"")+String.format("%02d",chn);
					imageNoiseGains[chn]= new ImagePlus(title, kernelsNoise);
					imageNoiseGains[chn].setProperty("sharpKernelPath", this.sharpKernelPaths[chn]);
					imageNoiseGains[chn].setProperty("smoothKernelPath", nonlinParameters.useDiffNoiseGains?this.smoothKernelPaths[chn]:"");
					if (this.correctionsParameters.saveNoiseGains || this.correctionsParameters.showNoiseGains) {
						saveAndShow(this.imageNoiseGains[chn],
								this.correctionsParameters,
								this.correctionsParameters.saveNoiseGains,
								this.correctionsParameters.showNoiseGains
								);
					}
				}
			} else {
				if (removeUnused) this.imageNoiseGains[chn]=null;
			}
			if (this.stopRequested.get()>0) {
				System.out.println("User requested stop");
				return false;
			}

		}
		return true;
	}

	public void createChannelVignetting(
			final boolean correct_vignetting){
		final int threadsMax = 100;
		///		this.channelWidthHeight=new int [this.usedChannels.length][];
		this.channelVignettingCorrection=new float [this.usedChannels.length][];
		this.defectsXY=new int [this.usedChannels.length][][];
		this.defectsDiff=new double [this.usedChannels.length][];

		for (int nChn=0;nChn< this.usedChannels.length; nChn++){
			///			this.channelWidthHeight[nChn]=null;
			this.channelVignettingCorrection[nChn]=null;
			this.defectsXY[nChn]=null;
			this.defectsDiff[nChn]=null;
		}
		int [][] bayer={{1,0},{2,1}}; // GR/BG
// Assign static final Logger LOGGER here to prevent multi-hreaded races in new ImagejJp4Tiff();
//		ImagejJp4Tiff.setLogger();
//		ImagejJp4Tiff      imagejJp4Tiff = 
		new ImagejJp4Tiff(); // just to cause
// still not enough, as 		
		
		final Thread[] threads = ImageDtt.newThreadArray(threadsMax);
		final AtomicInteger ai = new AtomicInteger(0);
		for (int ithread = 0; ithread < threads.length; ithread++) {
			threads[ithread] = new Thread() {
				public void run() {
					ImagePlus imp=null,imp_composite=null;
					ImagejJp4Tiff      imagejJp4Tiff = new ImagejJp4Tiff(); // override instance-global
					//for (int nFile=0;nFile<correctionsParameters.getSourcePaths().length;nFile++){
					for (int nFile = ai.getAndIncrement(); nFile < correctionsParameters.getSourcePaths().length; nFile = ai.getAndIncrement()) {
						int [] channels={correctionsParameters.getChannelFromSourceTiff(correctionsParameters.getSourcePaths()[nFile])};
						if (!pixelMapping.subcamerasUsed()) {
							channels = pixelMapping.channelsForSubCamera(channels[0]-correctionsParameters.firstSubCameraConfig); // index in calibration files matching this source
						} else 	if (correctionsParameters.isJP4()){
							int subCamera= channels[0]- correctionsParameters.firstSubCamera; // to match those in the sensor files
							channels=pixelMapping.channelsForSubCamera(subCamera);
						}

						if (pixelMapping.isChannelAvailable(channels)) { //channels!=null) {
							imp=null;
							imp_composite=null;

							try {
								imp_composite = imagejJp4Tiff.readTiffJp4(
										correctionsParameters.getSourcePaths()[nFile],
										true); // scale);
							} catch (IOException | FormatException e) {
								// TODO Auto-generated catch block
								e.printStackTrace();
							} // throws IOException, FormatException { // std - include non-elphel properties with prefix std

							if ((imp==null) && (imp_composite==null)) {
								if (debugLevel>0) System.out.println("createChannelVignetting(): can not open "+correctionsParameters.getSourcePaths()[nFile]+
										" as "+(correctionsParameters.isJP4()?"JP4":"TIFF")+" file");
								continue;
							}
							for (int chn=0;chn<channels.length;chn++) {
								int srcChannel=channels[chn];
								///					if ((channelWidthHeight[srcChannel]==null) && pixelMapping.isChannelAvailable(srcChannel)){
								if (pixelMapping.isChannelAvailable(srcChannel)){
									int subChannel=pixelMapping.getSubChannel(srcChannel);
									if (correct_vignetting) {
										if (correctionsParameters.swapSubchannels01) {
											switch (subChannel){
											case 0: subChannel=1; break;
											case 1: subChannel=0; break;
											}
										}
										if ((channels.length > 1) && correctionsParameters.isJP4()) {
											if (subChannel<0){
												System.out.println("BUG in createChannelVignetting(): chn="+chn+
														" subChannel="+subChannel+
														" nFile="+nFile+" : "+correctionsParameters.getSourcePaths()[nFile]+
														" channels.length="+channels.length);
												for (int i=0;i<channels.length;i++) System.out.print(" "+channels[i]);
												System.out.println();
												for (int i=0;i<usedChannels.length;i++) if (usedChannels[i]) {
													System.out.println(i+": subCamera="+pixelMapping.sensors[i].subcamera);
												}

											}
											imp=JP4_INSTANCE.demuxImage(imp_composite, subChannel);
											if (imp==null) imp=imp_composite; // not a composite image
										} else {
											imp=imp_composite;
										}

										imp =  ShowDoubleFloatArrays.padBayerToFullSize(
												imp, // ImagePlus imp_src,
												pixelMapping.sensors[srcChannel].getSensorWH(),
												true); // boolean replicate);
										channelVignettingCorrection[srcChannel]=pixelMapping.getBayerFlatFieldFloat(
												srcChannel,
												bayer,
												1.5); // TODO: Make range configurable, improve FF interpolation in calibraion
									} else { // no vignetting correction
										int [] wh = pixelMapping.getSensorWH(srcChannel);
										channelVignettingCorrection[srcChannel] = new float [wh[0]*wh[1]];
										for (int i = 0; i < channelVignettingCorrection[srcChannel].length; i++) {
											channelVignettingCorrection[srcChannel][i] = 1.0f;
										}
									}
									if (debugLevel>0){
										ShowDoubleFloatArrays.showArrays(
												channelVignettingCorrection[srcChannel],
												pixelMapping.sensors[srcChannel].pixelCorrectionWidth,
												pixelMapping.sensors[srcChannel].pixelCorrectionHeight,
												"Vingetting-"+srcChannel
												);
									}
									if (debugLevel>0){
										System.out.println("Created vignetting info for channel "+srcChannel+
												" subchannel="+subChannel+" ("+
												correctionsParameters.getSourcePaths()[nFile]+")");
										///							System.out.println("imageWidth= "+channelWidthHeight[srcChannel][0]+" imageHeight="+channelWidthHeight[srcChannel][1]);
									}
									defectsXY[srcChannel]=pixelMapping.getDefectsXY(srcChannel);
									defectsDiff[srcChannel]=pixelMapping.getDefectsDiff(srcChannel);
									if (debugLevel>0){
										if (defectsXY[srcChannel]==null){
											System.out.println("No pixel defects info is available for channel "+srcChannel);
										} else {
											System.out.println("Extracted "+defectsXY[srcChannel].length+" pixel outliers for channel "+srcChannel+
													" (x:y:difference");
											int numInLine=8;
											for (int i=0;i<defectsXY[srcChannel].length;i++){
												System.out.print(defectsXY[srcChannel][0]+":"+defectsXY[srcChannel][1]);
												if ((defectsDiff[srcChannel]!=null) && (defectsDiff[srcChannel].length>i)){
													System.out.print(":"+IJ.d2s(defectsDiff[srcChannel][i],3)+" ");
												}
												if (((i%numInLine)==(numInLine-1)) || (i == (defectsXY[srcChannel].length-1))) System.out.println();
											}
										}
									}
								}
							}
						}
					}
				}
			};
		}		      
		ImageDtt.startAndJoin(threads);
		return;
	}

	boolean [] usedChannels(String [] paths){
		return usedChannels(paths, false);
	}

	boolean [] usedChannels(String [] paths, boolean missing_ok){
		if (paths==null) paths=new String[0];
		int numChannels=this.pixelMapping.getNumChannels();
		boolean [] usedChannels=new boolean[numChannels];
		for (int i=0;i<numChannels;i++) usedChannels[i]= false; // this.pixelMapping.isChannelAvailable(i);
		for (int i=0;i<paths.length;i++){
			int srcChannel=correctionsParameters.getChannelFromSourceTiff(paths[i]); // different for JP4
			int subCamera= srcChannel- correctionsParameters.firstSubCamera; // to match those in the sensor files
			if (correctionsParameters.isJP4() || ALL_AS_JP4){
				int [] channels=this.pixelMapping.channelsForSubCamera(subCamera);
				if (channels!=null) for (int j=0;j<channels.length;j++) usedChannels[channels[j]]=true;
			} else {
				if (!this.pixelMapping.isChannelAvailable(srcChannel)){
					if ((debugLevel>0) && !missing_ok) {
						System.out.println("No sensor data for channel "+srcChannel+", needed for source file "+paths[i]);
					}
				} else usedChannels[srcChannel] = true;
			}
		}
		return usedChannels;
	}

	public void testFF(String path){
		ImagePlus imp=new ImagePlus(path);
		imp.getProcessor().resetMinAndMax(); // imp_psf will be reused
		imp.show();
		int srcChannel=correctionsParameters.getChannelFromSourceTiff(path);
		int [] channels={srcChannel};
		if (correctionsParameters.isJP4()){
			int subCamera= srcChannel- correctionsParameters.firstSubCamera; // to match those in the sensor files
			channels=this.pixelMapping.channelsForSubCamera(subCamera);
		}
		/*		int [][] bayer={{1,0},{2,1}}; // GR/BG
//		double [] corrFF=this.pixelMapping.getBayerFlatField(
		float [] corrFF=this.pixelMapping.getBayerFlatFieldFloat(
				srcChannel,
				imp.getWidth(),
				imp.getHeight(),
				bayer);
		 */
		for (int chn=0;chn<channels.length;chn++){
			srcChannel=channels[chn];
			float [] corrFF=this.channelVignettingCorrection[srcChannel];
			if (corrFF==null) return;
			float [] pixels=(float[]) imp.getProcessor().getPixels();
			double [] pixelsFlat=new double [corrFF.length];
			for (int i=0;i<corrFF.length;i++) pixelsFlat[i]=pixels[i]*corrFF[i];
			ShowDoubleFloatArrays.showArrays(corrFF, imp.getWidth(), imp.getHeight(), srcChannel+"-FF-correction");
			ShowDoubleFloatArrays.showArrays(pixelsFlat, imp.getWidth(), imp.getHeight(), srcChannel+"-flat-"+imp.getTitle());
		}
	}

	public boolean isChannelEnabled(int channel){
		return ((channel>=0) && (channel<this.usedChannels.length) && this.usedChannels[channel]);
	}
	public void processChannelImages(
			EyesisCorrectionParameters.SplitParameters         splitParameters,
			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
					channels=this.pixelMapping.channelsForSubCamera(subCamera);
				}
				if (channels!=null){
					for (int i=0;i<channels.length;i++) if (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=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=this.pixelMapping.channelsForSubCamera(subCamera);
				}
				if (channels!=null){
					for (int i=0;i<channels.length;i++) if (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=this.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=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=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]);
				//				  JP46_Reader_camera.decodeProperiesFromInfo(imp_src); // decode existent properties from info
				JP46_Reader_camera.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
			processChannelImage( // returns ImagePlus, but it already should be saved/shown
					imp_src, // should have properties "name"(base for saving results), "channel","path"
					splitParameters,
					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) pixelMapping.deleteEquirectangularMapFull(srcChannel); // save memory? //removeUnusedSensorData - no, use equirectangular specific settings
				if (equirectangularParameters.clearAllMaps) pixelMapping.deleteEquirectangularMapAll(srcChannel); // save memory? //removeUnusedSensorData - no, use equirectangular specific settings
			}
			//pixelMapping
			Runtime.getRuntime().gc();
			if (debugLevel>0) 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 (this.stopRequested.get()>0) {
				System.out.println("User requested stop");
				return;
			}
		}
	}

	public void saveTiffWithAlpha(
			ImagePlus imp,
			EyesisCorrectionParameters.CorrectionParameters correctionsParameters)
					throws IOException, FormatException, ServiceException, DependencyException{
		int fullWidth,x0;
		boolean cutTile=!this.correctionsParameters.usePlaneProjection && correctionsParameters.equirectangularCut;
		if (cutTile){
			fullWidth=Integer.parseInt((String) imp.getProperty("ImageFullWidth"));
			x0=       Integer.parseInt((String) imp.getProperty("XPosition"));
			cutTile=(x0+imp.getWidth()>fullWidth) ;
		}
		if (cutTile  ) {
			if (this.debugLevel>0) System.out.println("Cutting result image in two parts to prevent roll-over");
			saveTiffWithAlpha(
					cropEquirectangular(imp, false),
					correctionsParameters);
			saveTiffWithAlpha(
					cropEquirectangular(imp, true),
					correctionsParameters);
			return;
		} else {
			String path= correctionsParameters.selectResultsDirectory(
					true,  // smart,
					true);  //newAllowed, // save
			if (path!=null){
				path+=Prefs.getFileSeparator()+imp.getTitle()+".tiff";
				if (this.debugLevel>0) System.out.println("Saving equirectangular result to "+path);
				(new EyesisTiff()).saveTiff(
						imp,
						path,
						correctionsParameters.equirectangularFormat,
						((correctionsParameters.equirectangularFormat==3)?correctionsParameters.outputRangeFP:correctionsParameters.outputRangeInt),
						correctionsParameters.imageJTags,
						debugLevel);
			}
		}
	}

	public ImagePlus cropEquirectangular(
			ImagePlus imp,
			boolean right){ // right - rolled over to the left of the result, adds "-LEFT", "-RIGHT" to the title
		int fullWidth=Integer.parseInt((String) imp.getProperty("ImageFullWidth"));
		int x0=       Integer.parseInt((String) imp.getProperty("XPosition"));
		int height=   imp.getHeight();
		int width=    imp.getWidth();
		int dx=(fullWidth-x0);
		int cropedWidth=right?(imp.getWidth()+-dx):dx;
		ImagePlus imp_croped;
		int addX=right?dx:0;
		if (imp.getType()==ImagePlus.COLOR_RGB) {
			int [] allPixels= (int []) imp.getProcessor().getPixels();
			int [] cropedPixels=new int[cropedWidth*height];
			for (int y=0;y<height;y++) for (int x=0;x< cropedWidth; x++){
				cropedPixels[y*cropedWidth+x] = allPixels[y*width+(x+addX)];
			}
			ColorProcessor colorProcessor=new ColorProcessor(cropedWidth,height);
			colorProcessor.setPixels(cropedPixels);
			imp_croped= new ImagePlus(imp.getTitle()+(right?"-RIGHT":"-LEFT"),colorProcessor);
		} else if (imp.getStackSize()==4) {
			float [][] allPixels= new float [4][];
			for (int c=0;c<allPixels.length;c++) allPixels[c]= (float []) imp.getStack().getPixels(c+1);
			float [][] cropedPixels=new float [4][];
			for (int c=0;c<cropedPixels.length;c++) cropedPixels[c]= new float [cropedWidth*height];
			for (int c=0;c<cropedPixels.length;c++) for (int y=0;y<height;y++) for (int x=0;x< cropedWidth; x++){
				cropedPixels[c][y*cropedWidth+x] = allPixels[c][y*width+(x+addX)];
			}
			ImageStack croppedStack=new ImageStack(cropedWidth,height);
			for (int c=0;c<allPixels.length;c++){
				croppedStack.addSlice(imp.getStack().getSliceLabel(c+1),  cropedPixels[c]);
			}
			imp_croped= new ImagePlus(imp.getTitle()+(right?"-RIGHT":"-LEFT"),croppedStack);
		} else{
			String msg="cropEquirectangular(): Unsupported image format";
			System.out.println("Error "+msg);
			IJ.showMessage("Error",msg);
			return null;
		}
		(new JP46_Reader_camera(false)).copyProperties (imp, imp_croped);
		if (right) imp_croped.setProperty("XPosition", "0");
		JP46_Reader_camera.encodeProperiesToInfo(imp_croped);
		return imp_croped;
	}


	public ImagePlus applyEquirectangular(
			int channel,
			ImagePlus imp,
			int threadsMax,
			int debugLevel){
		if (!pixelMapping.isChannelAvailable(channel)){
			String msg="No sensor data for channel "+channel;
			System.out.println("Error "+msg);
			IJ.showMessage("Error",msg);
			return null;
		}
		if (!pixelMapping.isEquirectangularMapAvailable(channel)){
			String path=correctionsParameters.selectEquirectangularMapFile(
					channel,
					debugLevel);

			if (path==null) {
				String msg="No equirectangular map found for channel "+channel;
				System.out.println("Error "+msg);
				IJ.showMessage("Error",msg);
				return null;
			}
			if (debugLevel>1) System.out.println("applyEquirectangular(): channel="+channel+" path="+path);

			pixelMapping.loadChannelEquirectangularMap(
					channel,
					path);

			if (!this.pixelMapping.isEquirectangularMapAvailable(channel)){
				String msg="Failed to load equirectangular map for channel "+channel;
				System.out.println("Error "+msg);
				IJ.showMessage("Error",msg);
				return null;
			}
		}
		// apply warping here
		//		  double sourceImageScale=2.0*this.correctionsParameters.JPEG_scale;
		int sourceImageScale=2; // *this.correctionsParameters.JPEG_scale;
		ImagePlus imp_warped= pixelMapping.resampleToEquirectangular( // will Add "_EQR"
				imp,
				channel,
				sourceImageScale,
				threadsMax);
		return 	imp_warped;
	}

	public ImagePlus applyCommonPlane(
			int channel,
			ImagePlus imp,
			int threadsMax,
			int debugLevel){
		if (!pixelMapping.isChannelAvailable(channel)){
			String msg="No sensor data for channel "+channel;
			System.out.println("Error "+msg);
			IJ.showMessage("Error",msg);
			return null;
		}
		if (!pixelMapping.isPlaneMapMapAvailable(channel)){
			String path=correctionsParameters.selectPlaneMapFile(
					//					channel,
					debugLevel);

			if (path==null) {
				String msg="No common plane projection map found";
				System.out.println("Error "+msg);
				IJ.showMessage("Error",msg);
				return null;
			}
			if (debugLevel>1) System.out.println("applyCommonPlane(): channel="+channel+" path="+path);
			pixelMapping.loadPlaneMap(
					//					channel,
					path,
					debugLevel);

			if (!this.pixelMapping.isPlaneMapMapAvailable(channel)){
				String msg="Failed to load a common plane projection map for channel "+channel+", or that file does not have this sensor data";
				System.out.println("Error "+msg);
				IJ.showMessage("Error",msg);
				return null;
			}
		}
		// apply warping here
		//		  double sourceImageScale=2.0*this.correctionsParameters.JPEG_scale;
		int sourceImageScale=2; // *this.correctionsParameters.JPEG_scale;
		ImagePlus imp_warped= pixelMapping.applyPlaneMap(
				imp, //ImagePlus impSrc,
				channel,
				sourceImageScale, // 2.0
				threadsMax,
				debugLevel
				);
		return 	imp_warped;
	}

	public int correctDefects(
			ImagePlus imp,
			int channel,
			int debugLevel){
		int numApplied=0;
		if (this.correctionsParameters.pixelDefects && (this.defectsXY!=null)&& (this.defectsXY[channel]!=null)){
			// apply pixel correction
			float [] pixels=(float []) imp.getProcessor().getPixels();
			int width=imp.getWidth();
			int height=pixels.length/width;
			int [] dirsRB={2,2*width,-2,-2*width};
			int [] dirsG={width+1,width-1,-width-1,-width+1};
			for (int i=0;i<this.defectsXY[channel].length;i++){
				if ( // difference provided and is smaller than threshold
						(this.defectsDiff != null) &&
						(this.defectsDiff[channel]!=null) &&
						(this.defectsDiff[channel].length>i) &&
						(Math.abs(this.defectsDiff[channel][i])<this.correctionsParameters.pixelDefectsThreshold)) break;
				int x=this.defectsXY[channel][i][0];
				int y=this.defectsXY[channel][i][1];
				int index=x+y*width;
				int [] dirs=(((x^y)&1)==0)?dirsG:dirsRB;
				// do not bother to correct border pixels
				if ((x<2) || (y<2) || (x>(width-3)) || (y>height-3)) continue;
				double s=0.0;
				for (int dir=0;dir<dirs.length;dir++) s+=pixels[index+dirs[dir]];
				pixels[index]=(float) (s/dirs.length);
				numApplied++;
			}
		}
		return numApplied;
	}


	public ImagePlus processChannelImage(
			ImagePlus imp_src, // should have properties "name"(base for saving results), "channel","path"
			EyesisCorrectionParameters.SplitParameters         splitParameters,
			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 && (this.defectsXY!=null)&& (this.defectsXY[channel]!=null)){
			// apply pixel correction
			int numApplied=	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 ((this.channelVignettingCorrection==null) || (channel<0) || (channel>=this.channelVignettingCorrection.length) || (this.channelVignettingCorrection[channel]==null)){
				System.out.println("No vignetting data for channel "+channel);
				return null;
			}
			float [] pixels=(float []) imp_src.getProcessor().getPixels();
			if (pixels.length!=this.channelVignettingCorrection[channel].length){
				System.out.println("Vignetting data for channel "+channel+" has "+this.channelVignettingCorrection[channel].length+" pixels, image "+path+" has "+pixels.length);
				return null;
			}
			for (int i=0;i<pixels.length;i++){
				pixels[i]*=this.channelVignettingCorrection[channel][i];
			}
		}
		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){
			saveAndShow(result, this.correctionsParameters);
			return result;
		}
		// Split into Bayer components, oversample, increase canvas
		ImageStack stack= bayerToStack(
				result, // source Bayer image, linearized, 32-bit (float))
				splitParameters);
		String titleFull=title+"-SPLIT";
		if (!this.correctionsParameters.debayer) {
			result= new ImagePlus(titleFull, stack);
			saveAndShow(result, this.correctionsParameters);
			return result;
		}
		// Demosaic image
		if (debayerScissors==null) debayerScissors=new DebayerScissorsClass(this.stopRequested);
		debayerScissors.setDebug(debugLevel);
		stack= debayerScissors.aliasScissorsStack(stack,  // stack with 3 colors/slices with the image
				debayerParameters,
				(this.correctionsParameters.saveDebayerEnergy || this.correctionsParameters.showDebayerEnergy),
				threadsMax, // number of image pixels/ sensor pixels (each direction) == 2
				updateStatus,// update status info
				debugLevel);
		if (this.correctionsParameters.saveDebayerEnergy || this.correctionsParameters.showDebayerEnergy) {
			if (debayerScissors.getDebayerEnergy()!=null) {
				ImagePlus debayerMask=ShowDoubleFloatArrays.makeArrays (debayerScissors.getDebayerEnergy(),
						debayerScissors.getDebayerEnergyWidth(),
						debayerScissors.getDebayerEnergy().length/debayerScissors.getDebayerEnergyWidth(),
						title+"-DEBAYER-ENERGY");
				saveAndShow(debayerMask,
						this.correctionsParameters,
						this.correctionsParameters.saveDebayerEnergy,
						this.correctionsParameters.showDebayerEnergy
						);
			}
		}
		titleFull=title+"-DEMOSAIC";
		CorrectionDenoise correctionDenoise=new CorrectionDenoise(stopRequested);
		CorrectionColorProc correctionColorProc=new CorrectionColorProc(stopRequested);
		result= new ImagePlus(titleFull, stack);
		if (this.correctionsParameters.deconvolve) {
			//Ask for the kernel directory if it is undefined
			if (this.sharpKernelPaths==null){ // make sure the paths list is reset after changing parameters
				this.sharpKernelPaths=correctionsParameters.selectKernelChannelFiles(
						0,  // 0 - sharp, 1 - smooth
						correctionsParameters.firstSubCameraConfig,
						correctionsParameters.numSubCameras,
						//						this.usedChannels.length, // number of channels
						this.debugLevel);
			}
			if ((this.sharpKernelPaths==null) || (this.sharpKernelPaths[channel]==null)){
				System.out.println("Sharp kernel path does not exist");
				return null;
			}
			// Read deconvolution kernels
			ImagePlus imp_sharp_kernels=new ImagePlus(this.sharpKernelPaths[channel]);
			if (imp_sharp_kernels.getStackSize()<3) {
				System.out.println("Need a 3-layer stack with kernels - file "+this.sharpKernelPaths[channel]);
				return null;
			}
			ImageStack convolutionSharpKernelStack=imp_sharp_kernels.getStack();
			if (debugLevel>1) System.out.println("Using kernel stack "+this.sharpKernelPaths[channel]+" for convolution with "+result.getTitle());
			ImageStack stackDeconvolvedSharp= convolveStackWithKernelStack( //  stack_d
					stack,  // stack with 3 colors/slices with the image
					convolutionSharpKernelStack, // stack with 3 colors/slices convolution kernels
					convolveFFTSize, // 128 - fft size, kernel size should be size/2
					threadsMax,
					updateStatus, // update status info
					debugLevel);
			imp_sharp_kernels=null; // free memory
			convolutionSharpKernelStack=null;
			Runtime.getRuntime().gc();
			titleFull=title+"-DECONV";
			if (this.correctionsParameters.combine) {
				// Read "smooth" kernels
				if (this.smoothKernelPaths==null){ // make sure the paths list is reset after changing parameters
					this.smoothKernelPaths=correctionsParameters.selectKernelChannelFiles(
							1,  // 0 - sharp, 1 - smooth
							correctionsParameters.firstSubCameraConfig,
							//							  correctionsParameters.numSubCameras,
							this.usedChannels.length, // number of channels
							this.debugLevel);
				}
				if ((this.smoothKernelPaths==null) || (this.smoothKernelPaths[channel]==null)){
					System.out.println("Smooth kernel path does not exist");
					return null;
				}
				ImagePlus imp_smooth_kernels=new ImagePlus(this.smoothKernelPaths[channel]);
				if (imp_smooth_kernels.getStackSize()<3) {
					System.out.println("Need a 3-layer stack with kernels - file "+this.smoothKernelPaths[channel]);
					return null;
				}
				ImageStack convolutionSmoothKernelStack=imp_smooth_kernels.getStack();
				if (debugLevel>1) System.out.println("Using smooth kernel stack "+this.smoothKernelPaths[channel]+" for convolution with "+result.getTitle());
				ImageStack stackDeconvolvedSmooth = convolveStackWithKernelStack( //stack_g
						stack,  // stack with 3 colors/slices with the image
						convolutionSmoothKernelStack, // stack with 3 colors/slices convolution kernels
						convolveFFTSize, // 128 - fft size, kernel size should be size/2
						threadsMax,
						updateStatus, // update status info
						debugLevel);
				imp_smooth_kernels=null; // free memory
				convolutionSmoothKernelStack=null;
				Runtime.getRuntime().gc();
				// Combine Smooth and Sharp images
				double [][] noiseMask= extractNoiseMask(
						this.imageNoiseGains[channel],// contains 3-slice stack (r,b,g)
						nonlinParameters.noiseGainWeights[0], // coefficient for slice 0 (r)
						nonlinParameters.noiseGainWeights[1], // coefficient for slice 1 (b)
						nonlinParameters.noiseGainWeights[2], // coefficient for slice 2 (g)
						1,     // decimate result (not yet supported)
						nonlinParameters.noiseGainPower
						);

				// show noise mask here?
				nonlinParameters.showMask=this.correctionsParameters.showDenoiseMask;
				//		          if (DEBUG_LEVEL>1) System.out.println ( " noiseMask.length="+((noiseMask==null)?"null":(noiseMask.length+" noiseMask[0].length="+noiseMask[0].length)));
				//				CorrectionDenoise correctionDenoise=new CorrectionDenoise(stopRequested);
				correctionDenoise.setDebug(debugLevel); // not yet used
				stack=  correctionDenoise.combineLoHiStacks(
						stackDeconvolvedSharp, // ImageStack with the image, convolved with the reversed PSF (sharp but with high noise)
						stackDeconvolvedSmooth,  // ImageStack with the image, convolved with the Gaussian (just lateral compensated)  (blurred, but low noise)
						channel,
						nonlinParameters, // show mask generated and used
						noiseMask, // 2-d array of kernelsNoiseGain (divide mask by it)
						32,        // linear pixels per noiseMask pixels (32)
						threadsMax,
						updateStatus, // update status info
						debugLevel);
				if (this.correctionsParameters.saveDenoiseMask || this.correctionsParameters.showDenoiseMask) {
					ImagePlus denoiseMask=ShowDoubleFloatArrays.makeArrays (
							correctionDenoise.getDenoiseMask(),
							correctionDenoise.getDenoiseMaskWidth(),
							correctionDenoise.getDenoiseMask().length/correctionDenoise.getDenoiseMaskWidth(),
							title+"-MASK");
					if (this.correctionsParameters.jpeg) {
						//crop Mask to original image size
						if (this.correctionsParameters.crop){
							denoiseMask=cropImage32(denoiseMask,splitParameters);
						}
						//rotate the result
						if (this.correctionsParameters.rotate){
							denoiseMask=rotateImage32CW(denoiseMask);
						}
						//scale the result
						if (this.correctionsParameters.JPEG_scale!=1.0){
							ImageProcessor ip=denoiseMask.getProcessor();
							ip.setInterpolationMethod(ImageProcessor.BICUBIC);
							ip=ip.resize((int)(ip.getWidth()*this.correctionsParameters.JPEG_scale),(int) (ip.getHeight()*this.correctionsParameters.JPEG_scale));
							denoiseMask= new ImagePlus(denoiseMask.getTitle(),ip);
							denoiseMask.updateAndDraw();
						}
						if (this.correctionsParameters.showDenoiseMask) denoiseMask.show();
						//public ImagePlus Image32toGreyRGB24(ImagePlus imp);
						if (this.correctionsParameters.saveDenoiseMask) {
							ImagePlus denoiseMaskRGB24=Image32toGreyRGB24(denoiseMask);
							saveAndShow(denoiseMaskRGB24,
									this.correctionsParameters,
									this.correctionsParameters.saveDenoiseMask,
									false, //processParameters.showDenoiseMask,
									this.correctionsParameters.JPEG_quality);
							denoiseMaskRGB24=null;
						}
					} else {
						saveAndShow(denoiseMask,
								this.correctionsParameters,
								this.correctionsParameters.saveDenoiseMask,
								this.correctionsParameters.showDenoiseMask
								);
					}
				}

			} else { // end of if (this.correctionsParameters.combine)
				stack=stackDeconvolvedSharp;
			} // end of else if (this.correctionsParameters.combine)
		}  else if (this.correctionsParameters.combine) { // "combine" w/o "deconvolve" - just use convolution with smooth kernels
			// Read smooth kernels
			// Read "smooth" kernels
			if (this.smoothKernelPaths==null){ // make sure the paths list is reset after changing parameters
				this.smoothKernelPaths=correctionsParameters.selectKernelChannelFiles(
						1,  // 0 - sharp, 1 - smooth
						correctionsParameters.firstSubCameraConfig,
						//						  correctionsParameters.numSubCameras,
						this.usedChannels.length, // number of channels
						this.debugLevel);
			}
			if ((this.smoothKernelPaths==null) || (this.smoothKernelPaths[channel]==null)){
				System.out.println("Smooth kernel path does not exist");
				return null;
			}
			ImagePlus imp_smooth_kernels=new ImagePlus(this.smoothKernelPaths[channel]);
			if (imp_smooth_kernels.getStackSize()<3) {
				System.out.println("Need a 3-layer stack with kernels - file "+this.smoothKernelPaths[channel]);
				return null;
			}
			ImageStack convolutionSmoothKernelStack=imp_smooth_kernels.getStack();
			if (debugLevel>1) System.out.println("Using smooth kernel stack "+this.smoothKernelPaths[channel]+" for convolution with "+result.getTitle());
			ImageStack stackDeconvolvedSmooth = convolveStackWithKernelStack( // stack_g
					stack,  // stack with 3 colors/slices with the image
					convolutionSmoothKernelStack, // stack with 3 colors/slices convolution kernels
					convolveFFTSize, // 128 - fft size, kernel size should be size/2
					threadsMax,
					updateStatus, // update status info
					debugLevel);
			imp_smooth_kernels=null; // free memory
			stack=stackDeconvolvedSmooth;
			convolutionSmoothKernelStack=null;
			Runtime.getRuntime().gc();
			titleFull=title+"-LOWRES";
		}// end of if (this.correctionsParameters.deconvolve)
		//stack now has the result, titleFull - correct title for the image
		if (!this.correctionsParameters.colorProc){
			result= new ImagePlus(titleFull, stack);
			saveAndShow(
					result,
					this.correctionsParameters);
			return result;
		}
		//Processing colors - changing stack sequence to r-g-b (was r-b-g)
		if (!fixSliceSequence(
				stack,
				debugLevel)){
			if (debugLevel>0) System.out.println("fixSliceSequence() returned false");
			return null;
		}
		//		  if (debugLevel>2){
		if (debugLevel>1){
			ImagePlus imp_dbg=new ImagePlus(imp_src.getTitle()+"-"+channel+"-preColors",stack);
			saveAndShow(
					imp_dbg,
					this.correctionsParameters);
		}

		correctionColorProc.processColorsWeights(stack,
				//				  255.0/this.psfSubpixelShouldBe4/this.psfSubpixelShouldBe4, //  double scale,     // initial maximal pixel value (16))
				255.0/this.psfSubpixelShouldBe4/this.psfSubpixelShouldBe4/scaleExposure, //  double scale,     // initial maximal pixel value (16))
				colorProcParameters,
				channelGainParameters,
				channel,
				correctionDenoise.getDenoiseMask(),
				this.correctionsParameters.blueProc,
				debugLevel);
		if (debugLevel>1) System.out.println("Processed colors to YPbPr, total number of slices="+stack.getSize());
		if (debugLevel>2){
			ImagePlus imp_dbg=new ImagePlus("procColors",stack);
			saveAndShow(
					imp_dbg,
					this.correctionsParameters);
		}

		// Show/save color denoise mask
		if ((this.correctionsParameters.saveChromaDenoiseMask || this.correctionsParameters.showChromaDenoiseMask) && (correctionColorProc.getDenoiseMaskChroma()!=null)) {
			ImagePlus chromaDenoiseMask=ShowDoubleFloatArrays.makeArrays (correctionColorProc.getDenoiseMaskChroma(),
					correctionColorProc.getDenoiseMaskChromaWidth(),
					correctionColorProc.getDenoiseMaskChroma().length/correctionColorProc.getDenoiseMaskChromaWidth(),
					title+"-MASK_CHROMA");
			if (this.correctionsParameters.jpeg) {
				//crop Mask to original image size
				if (this.correctionsParameters.crop){
					chromaDenoiseMask=cropImage32(chromaDenoiseMask,splitParameters);
				}
				//rotate the result
				if (this.correctionsParameters.rotate){
					chromaDenoiseMask=rotateImage32CW(chromaDenoiseMask);
				}
				//scale the result
				if (this.correctionsParameters.JPEG_scale!=1.0){
					ImageProcessor ip=chromaDenoiseMask.getProcessor();
					ip.setInterpolationMethod(ImageProcessor.BICUBIC);
					ip=ip.resize((int)(ip.getWidth()*this.correctionsParameters.JPEG_scale),(int) (ip.getHeight()*this.correctionsParameters.JPEG_scale));
					chromaDenoiseMask= new ImagePlus(chromaDenoiseMask.getTitle(),ip);
					chromaDenoiseMask.updateAndDraw();
				}
				if (this.correctionsParameters.showChromaDenoiseMask) chromaDenoiseMask.show();
				//public ImagePlus Image32toGreyRGB24(ImagePlus imp);
				if (this.correctionsParameters.saveChromaDenoiseMask) {
					ImagePlus chromaDenoiseMaskRGB24=Image32toGreyRGB24(chromaDenoiseMask);
					saveAndShow(chromaDenoiseMaskRGB24,
							this.correctionsParameters,
							this.correctionsParameters.saveChromaDenoiseMask,
							false, //processParameters.showChromaDenoiseMask,
							this.correctionsParameters.JPEG_quality);
					chromaDenoiseMaskRGB24=null;
				}
			} else {
				saveAndShow(chromaDenoiseMask,
						this.correctionsParameters,
						this.correctionsParameters.saveChromaDenoiseMask,
						this.correctionsParameters.showChromaDenoiseMask
						);
			}
		}
		if (toRGB) {
			correctionColorProc.YPrPbToRGB(stack,
					colorProcParameters.kr,        // 0.299;
					colorProcParameters.kb,        // 0.114;
					colorProcParameters.useFirstY?9:8,        //  int sliceY,
							6, // int slicePr,
							7// int slicePb
					);
			title=titleFull; // including "-DECONV" or "-COMBO"
			titleFull=title+"-RGB-float";
			//Trim stack to just first 3 slices
			if (debugLevel>2){
				ImagePlus imp_dbg=new ImagePlus("YPrPbToRGB",stack);
				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
			stack=cropStack32(stack,splitParameters);
			if (debugLevel>2){
				ImagePlus imp_dbg=new ImagePlus("cropped",stack);
				saveAndShow(
						imp_dbg,
						this.correctionsParameters);
			}

		}
		// rotate the result
		if (rotate){ // never rotate for equirectangular
			stack=rotateStack32CW(stack);
		}
		if (!toRGB && !this.correctionsParameters.jpeg){ // toRGB set for equirectangular
			saveAndShow(result, this.correctionsParameters);
			return result;
		} else { // that's not the end result, save if required
			saveAndShow(result, this.correctionsParameters, this.correctionsParameters.save32, false,this.correctionsParameters.JPEG_quality); // save, no show
		}
		// convert to RGB48 (16 bits per color component)
		ImagePlus imp_RGB;
		if (this.correctionsParameters.equirectangularFormat==0){
			stack=convertRGB32toRGB16Stack(
					stack,
					rgbParameters);

			titleFull=title+"-RGB48";
			result= new ImagePlus(titleFull, stack);
			//			  ImagePlus imp_RGB24;
			CompositeImage compositeImage=convertToComposite(result);
			if (!this.correctionsParameters.jpeg && !advanced){ // RGB48 was the end result
				saveAndShow(compositeImage, this.correctionsParameters);
				return result;
			} else { // that's not the end result, save if required
				saveAndShow(compositeImage, this.correctionsParameters, this.correctionsParameters.save16, false); // save, no show
			}
			imp_RGB=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();
			}
		} else {
			switch (this.correctionsParameters.equirectangularFormat){
			case 0:
				titleFull=title+"-INT8";
				break;
			case 1:
				titleFull=title+"-INT16";
				break;
			case 2:
				titleFull=title+"-INT32";
				break;
			case 3:
				titleFull=title+"-FLOAT32";
				break;
			case 4:
				titleFull=title+"-IJSTACK";
				break;
			}
			result= new ImagePlus(titleFull, stack);
			imp_RGB=result;
		}
		if (advanced){
			if (this.correctionsParameters.zcorrect){ // save double resolution image for distance measurements
				saveAndShow(
						imp_RGB,
						this.correctionsParameters,
						true,  // save
						false, // show
						0);    // force Tiff
			}
			if (this.correctionsParameters.equirectangular) {
				ImagePlus impWarped=null;
				if (this.correctionsParameters.usePlaneProjection){
					impWarped=	applyCommonPlane(
							channel,
							imp_RGB,
							threadsMax,
							debugLevel);

				} else {
					impWarped=	applyEquirectangular(
							channel,
							imp_RGB,
							threadsMax,
							debugLevel);
				}
				if ((impWarped.getFileInfo().fileType== FileInfo.RGB) && // only for 8-bit RGB (this.correctionsParameters.equirectangularFormat==0)
						this.correctionsParameters.planeAsJPEG &&
						this.correctionsParameters.usePlaneProjection){ // equirectangular - always TIFF
					saveAndShow(
							impWarped,
							this.correctionsParameters,
							this.correctionsParameters.save,
							this.correctionsParameters.show,
							this.correctionsParameters.JPEG_quality);

				} else {
					if (this.correctionsParameters.equirectangularFormat<4){
						try {
							saveTiffWithAlpha(impWarped,this.correctionsParameters);
						} catch (IOException e) {
							// TODO Auto-generated catch block
							e.printStackTrace();
						} catch (FormatException e) {
							// TODO Auto-generated catch block
							e.printStackTrace();
						} catch (ServiceException e) {
							// TODO Auto-generated catch block
							e.printStackTrace();
						} catch (DependencyException e) {
							// TODO Auto-generated catch block
							e.printStackTrace();
						}
					} else { // temporarily
						saveAndShow(impWarped, this.correctionsParameters);
					}
				}
			}
		} else {
			saveAndShow(imp_RGB, this.correctionsParameters);
		}
		return result;
	}

	/* ======================================================================== */


	//	  private boolean fixSliceSequence (
	public boolean fixSliceSequence ( // for EyesisDCT
			ImageStack stack,
			int debugLevel){
		int i,j;
		int [] rgbNumbers= {0,0,0};
		for (j=0;j<3;j++) {
			for (i=1;i<=3;i++) if (stack.getSliceLabel(i).toLowerCase().equals(this.stackColorNames[j].toLowerCase())){
				// fix case (capitalized)
				//				  System.out.println ( "stack.getSliceLabel("+i+")="+stack.getSliceLabel(i));
				//				  System.out.println ( "stackColorNames["+j+"]="+stackColorNames[j]);
				stack.setSliceLabel(this.stackColorNames[j],i);
				rgbNumbers[j]=i;
				//				  System.out.println ( "rgbNumbers["+j+"]="+rgbNumbers[j]);
				break;
			}
		}
		if (debugLevel > 2) {
			System.out.println ( "Input file color slice numbers:");
			System.out.println ( "  Red -   slice "+((rgbNumbers[0]>0)?rgbNumbers[0]:"missing"));
			System.out.println ( "  Green - slice "+((rgbNumbers[1]>0)?rgbNumbers[1]:"missing"));
			System.out.println ( "  Blue -  slice "+((rgbNumbers[2]>0)?rgbNumbers[2]:"missing"));
		}

		for (i=0;i<3;i++) if (rgbNumbers[i]<=0) {
			System.out.println ( this.stackColorNames[i]+ "  slice is missing in the input file. Please check slice names");
			return false;
		}
		while ((rgbNumbers[0]!=1) || (rgbNumbers[1]!=2) ||(rgbNumbers[2]!=3)) {
			if      (rgbNumbers[0]==1) swapStackSlices(stack,2,3);
			else if (rgbNumbers[2]==3) swapStackSlices(stack,1,2);
			else                       swapStackSlices(stack,1,3);
			for (j=0;j<3;j++) {
				for (i=1;i<=3;i++) if (stack.getSliceLabel(i).equals(this.stackColorNames[j])){
					rgbNumbers[j]=i;
					break;
				}
			}
		}
		return true;
	}
	/* ======================================================================== */
	public void swapStackSlices(ImageStack stack,
			int slice1,
			int slice2) {
		String label=stack.getSliceLabel(slice1);
		stack.setSliceLabel(stack.getSliceLabel(slice2), slice1);
		stack.setSliceLabel(label,                       slice2);
		Object pixels=stack.getPixels(slice1);
		stack.setPixels   (stack.getPixels(slice2),      slice1);
		stack.setPixels   (pixels,                       slice2);
	}





	/* ======================================================================== */
	public ImageStack cropStack32(
			ImageStack stack,
			EyesisCorrectionParameters.SplitParameters splitParameters) {
		int size=stack.getSize();
		int iWidth=stack.getWidth();
		int height=stack.getHeight()-splitParameters.addTop-splitParameters.addBottom;
		int width= stack.getWidth()-splitParameters.addLeft-splitParameters.addRight;
		int length=width*height;
		ImageStack stack_crop = new ImageStack(width,height);
		int i,x,y,index,base;
		float [] ipixels;
		float [] opixels;
		for (i=0;i<size;i++) {
			ipixels= (float[])stack.getPixels(i+1);
			opixels=new float [length];
			index=0;
			for (y=0;y< height;y++) {
				base=iWidth*(y+splitParameters.addTop)+splitParameters.addLeft;
				for (x=0;x<width;x++) opixels[index++]=ipixels[base++];
			}
			stack_crop.addSlice(stack.getSliceLabel(i+1), opixels);
		}
		return stack_crop;
	}

	/* ======================================================================== */
	public ImageStack rotateStack32CW(
			ImageStack stack) {
		int size=stack.getSize();
		int height=stack.getHeight();
		int width= stack.getWidth();
		int length=width*height;
		ImageStack stack_rot = new ImageStack(height, width);
		int i,x,y,index;
		float [] ipixels;
		float [] opixels;
		for (i=0;i<size;i++) {
			ipixels= (float[])stack.getPixels(i+1);
			opixels=new float [length];
			index=0;
			for (x=0;x<width;x++)for(y=height-1;y>=0;y--) opixels[index++]=ipixels[y*width+x];
			stack_rot.addSlice(stack.getSliceLabel(i+1), opixels);
		}
		return stack_rot;

	}
	/* ======================================================================== */
	public ImagePlus cropImage32(
			ImagePlus imp,
			EyesisCorrectionParameters.SplitParameters splitParameters) {
		int iWidth=imp.getWidth();
		int height=imp.getHeight()-splitParameters.addTop-splitParameters.addBottom;
		int width= imp.getWidth()-splitParameters.addLeft-splitParameters.addRight;
		int length=width*height;
		int x,y,index,base;
		float [] ipixels=(float[])imp.getProcessor().getPixels();
		float [] opixels=new float [length];
		index=0;
		for (y=0;y< height;y++) {
			base=iWidth*(y+splitParameters.addTop)+splitParameters.addLeft;
			for (x=0;x<width;x++) opixels[index++]=ipixels[base++];
		}
		ImageProcessor ip_crop=new FloatProcessor(width,height,opixels,null);
		ImagePlus imp_crop = new ImagePlus(imp.getTitle(),ip_crop); // same title?
		return imp_crop;
	}

	/* ======================================================================== */
	public ImagePlus rotateImage32CW(
			ImagePlus imp) {
		int width=imp.getWidth();
		int height=imp.getHeight();
		int length=width*height;
		int x,y,index;
		float [] ipixels=(float[])imp.getProcessor().getPixels();
		float [] opixels=new float [length];
		index=0;
		for (x=0;x<width;x++)for(y=height-1;y>=0;y--) opixels[index++]=ipixels[y*width+x];
		ImageProcessor ip_rot=new FloatProcessor(height,width,opixels,null);
		ImagePlus imp_rot = new ImagePlus(imp.getTitle(),ip_rot); // same title?
		return imp_rot;
	}


	/* ======================================================================== */
	public CompositeImage convertToComposite( ImagePlus imp) {
		if (imp.isComposite()) return null;
		if (imp.getNChannels()>1) {
			return null; // number of channels should be just 1
		}
		int c = imp.getStackSize();
		imp.setDimensions(c, 1, 1);
		CompositeImage ci = new CompositeImage(imp, CompositeImage.COMPOSITE);
		return ci;
	}

	/* ======================================================================== */
	public ImageStack convertRGB32toRGB16Stack(
			ImageStack stack32,
			EyesisCorrectionParameters.RGBParameters rgbParameters) {
		ImageStack stack16 = new ImageStack(stack32.getWidth(), stack32.getHeight());
		int length=stack32.getWidth()*stack32.getHeight();
		int i,j;
		float [] fpixels;
		short [] spixels;
		int numSlices  = stack32.getSize();
		if (numSlices > 4) numSlices = 4;
		if (numSlices < 3) return null;
		double [] mins= {rgbParameters.r_min, rgbParameters.g_min, rgbParameters.b_min, rgbParameters.alpha_min};
		double [] maxs= {rgbParameters.r_max, rgbParameters.g_max, rgbParameters.b_max, rgbParameters.alpha_max};
		double value;
		double scale;
		for (i = 0; i < numSlices; i++) {
			fpixels= (float[])stack32.getPixels(i + 1);
			scale=65535.0 / (maxs[i] - mins[i]);
			spixels=new short [length];
			for (j = 0; j < length; j++) {
				value=(fpixels[j]-mins[i])*scale;
				if      (value<0.0)     value = 0.0;
				else if (value>65535.0) value = 65535.0;
				spixels[j]=(short)(value+0.5);
			}
			stack16.addSlice(stack32.getSliceLabel(i+1), spixels);
		}
		return stack16;

	}

	public ImagePlus convertRGB48toRGB24(
			ImageStack stack16,
			String title,
			int r_min,
			int r_max,
			int g_min,
			int g_max,
			int b_min,
			int b_max,
			int alpha_min,
			int alpha_max){
		int [] mins= {r_min,g_min,b_min,alpha_min};
		int [] maxs= {r_max,g_max,b_max,alpha_max};
		int i;
		int length=stack16.getWidth()*stack16.getHeight();
		int numSlices  = stack16.getSize();
		if (numSlices > 4) numSlices = 4;
		short [][] spixels=new short[numSlices][];
		int [] sliceSeq = new int [numSlices];
		for (int j = 0; j < numSlices; j++) sliceSeq[j] = (j + ((numSlices > 3)? 3:0)) % 4;

		int [] pixels=new int[length];
		int c,d;

		double [] scale=new double[numSlices];
		for (c = 0; c < numSlices; c++) {
			scale[c]=256.0/(maxs[c]-mins[c]);
		}
		for (i = 0; i < numSlices; i++) spixels[i]= (short[])stack16.getPixels(i+1);
		for (i = 0; i < length; i++) {
			pixels[i]=0;
			for (int j=0; j < numSlices; j++) {
				c = sliceSeq[j];
				d=(int)(((spixels[c][i]& 0xffff)-mins[c])*scale[c]);
				if (d > 255) d=255;
				else if (d < 0) d=0;
				pixels[i]= d | (pixels[i] << 8);
			}
		}
		ColorProcessor cp=new ColorProcessor(stack16.getWidth(),stack16.getHeight());
		cp.setPixels(pixels);
		ImagePlus imp=new ImagePlus(title,cp);
		return imp;
	}

	public static ImagePlus convertRGBAFloatToRGBA32(
			ImageStack stackFloat, //r,g,b,a
			String title,
			double r_min,
			double r_max,
			double g_min,
			double g_max,
			double b_min,
			double b_max,
			double alpha_min,
			double alpha_max){
		double [] mins= {r_min,g_min,b_min,alpha_min};
		double [] maxs= {r_max,g_max,b_max,alpha_max};
		int i;
		int length=stackFloat.getWidth()*stackFloat.getHeight();
		int numSlices  = stackFloat.getSize();
		if (numSlices > 4) numSlices = 4;
		float [][] fpixels=new float[numSlices][];
		int [] sliceSeq = new int [numSlices];
		for (int j = 0; j < numSlices; j++) sliceSeq[j] = (j + ((numSlices > 3)? 3:0)) % 4;

		int [] pixels=new int[length];
		int c,d;

		double [] scale=new double[numSlices];
		for (c = 0; c < numSlices; c++) {
			scale[c]=256.0/(maxs[c]-mins[c]);
		}
		for (i = 0; i < numSlices; i++) {

			fpixels[i]= (float[])stackFloat.getPixels(i+1);
		}
		for (i = 0; i < length; i++) {
			pixels[i]=0;
			for (int j=0; j < numSlices; j++) {
				c = sliceSeq[j];
				d=(int)((fpixels[c][i]-mins[c])*scale[c]);
				if (d > 255) d=255;
				else if (d < 0) d=0;
				pixels[i]= d | (pixels[i] << 8);
			}
		}
		ColorProcessor cp=new ColorProcessor(stackFloat.getWidth(),stackFloat.getHeight());
		cp.setPixels(pixels);
		ImagePlus imp=new ImagePlus(title,cp);
		return imp;
	}




	public ImageStack convertRGB48toRGBA24Stack(
			ImageStack stack16,
			double [] dalpha, // alpha pixel array 0..1.0 or null
			//			  String title,
			int r_min,
			int r_max,
			int g_min,
			int g_max,
			int b_min,
			int b_max){
		ImageStack stack8 = new ImageStack(stack16.getWidth(), stack16.getHeight());
		int [] mins= {r_min,g_min,b_min};
		int [] maxs= {r_max,g_max,b_max};
		int i;
		int length=stack16.getWidth()*stack16.getHeight();
		short [][] spixels=new short[3][];
		byte [][] bpixels=new byte [(dalpha != null)? 4: 3][length];
		int c,d;
		double [] scale=new double[3];
		for (c=0;c<3;c++) {
			scale[c]=256.0/(maxs[c]-mins[c]);
		}
		for (i = 0; i <3; i++) spixels[i]= (short[])stack16.getPixels(i+1);
		for (c = 0; c <3; c++) {
			for (i = 0; i < length; i++){
				d=(int)(((spixels[c][i]& 0xffff)-mins[c])*scale[c]);
				if (d>255) d=255;
				else if (d<0) d=0;
				bpixels[c][i]= (byte) d;
			}
			stack8.addSlice(stack16.getSliceLabel(c+1), bpixels[c]);
		}
		if (dalpha != null) {
			for (i = 0; i < length; i++){
				bpixels[3][i] = (byte) (255*dalpha[i]);
			}
			stack8.addSlice("alpha", bpixels[3]);
		}
		return stack8;
	}

	/* ======================================================================== */
	public ImagePlus Image32toGreyRGB24(
			ImagePlus imp){
		int width=imp.getWidth();
		int height=imp.getHeight();
		int length=width*height;
		int i;
		float [] ipixels=(float[])imp.getProcessor().getPixels();
		int [] pixels=new int[length];
		float min=ipixels[0];
		float max=ipixels[0];
		for (i=0;i<length;i++) {
			if (min>ipixels[i])min=ipixels[i];
			if (max<ipixels[i])max=ipixels[i];
		}
		double d= 256.0/(max-min);
		int c;
		for (i=0;i<length;i++) {
			c=(int)((ipixels[i]-min)*d);
			if (c>255) c=255;
			pixels[i]=c | (c <<8) | (c<<16);
		}
		ColorProcessor cp=new ColorProcessor(width,height,pixels);
		ImagePlus imp_rgb=new ImagePlus(imp.getTitle(),cp);
		return imp_rgb;
	}
	/* ======================================================================== */


	/* Combine 2 stacks and a mask */
	public ImageStack combineStacksWithMask (ImageStack stack_bg,
			ImageStack stack_fg,
			//                                                 float [] mask ) {
			double [] mask ) {

		ImageStack stack=new ImageStack(stack_bg.getWidth(),stack_bg.getHeight());
		int slice,i;
		float [] fpixels;
		float [] fpixels_bg;
		float [] fpixels_fg;
		for (slice=1; slice <=stack_bg.getSize(); slice++) {
			fpixels_bg= (float[])stack_bg.getPixels(slice);
			fpixels_fg= (float[])stack_fg.getPixels(slice);
			fpixels=new float [fpixels_bg.length];
			for (i=0;i<fpixels_bg.length;i++) fpixels[i]= (float) (mask[i]*fpixels_fg[i]+(1.0f-mask[i])*fpixels_bg[i]);
			stack.addSlice(stack_fg.getSliceLabel(slice), fpixels);
		}
		return stack;
	}





	/* ======================================================================== */
	public double [] getSlidingMask(int size) { // duplicate with DebayerScissors
		double [] mask = new double [size*size];
		double [] maskLine=new double [size];
		double k=2*Math.PI/size;
		int i,j,index;
		for (i=0;i<size;i++) maskLine[i]= 0.5*(1.0-Math.cos(i*k));
		index=0;
		for (i=0;i<size;i++) for (j=0;j<size;j++) mask[index++]=maskLine[i]*maskLine[j];
		return mask;
	}

	/* ======================================================================== */
	/* convolve image stack with the kernel stack using FHT. kernels should be (size/2)*(size/2) - currently 64x64, then image will be split into same
	      (size/2)*(size/2) overlapping by step=size/4 segments. Both are zero-padded to size x size, so after convolution the result will not roll over, and
	      processed 128x128 result arrays are accumulated in the output stack.
	      The input image should be properly extended by size/4 in each direction (and so the kernel arrays should match it) - that would minimize border effects.*/

	/* ======================================================================== */
	public ImageStack convolveStackWithKernelStack (
			final ImageStack  imageStack,  // stack with 3 colors/slices with the image
			final ImageStack kernelStack, // stack with 3 colors/slices convolution kernels
			final int               size, // 128 - fft size, kernel size should be size/2
			final int          threadsMax,  // maximal number of threads to launch
			final boolean    updateStatus, // update status info
			final int globalDebugLevel)
	{
		if ((imageStack==null) || (kernelStack==null)) return null;
		final int imgWidth=imageStack.getWidth();
		final int imgHeight=imageStack.getHeight();
		final int length=imgWidth*imgHeight;
		final int step=size/4;
		final int kernelSize=size/2;
		final int tilesX=imgWidth/step-1; // horizontal number of overlapping tiles in the source image (should be expanded from the registerd one by "step" in each direction)
		final int tilesY=imgHeight/step-1; // vertical number of overlapping tiles in the source image (should be expanded from the registerd one by "step" in each direction)
		final int kernelWidth=kernelStack.getWidth();
		final int kernelNumHor=kernelWidth/(size/2);

		final int nChn=imageStack.getSize();
		final float [][] outPixels=new float[nChn][length]; // GLOBAL same as input
		//	   float [][] outPixels=new float[nChn][length]; // same as input
		int i,j;
		for (i=0;i<nChn;i++) for (j=0;j<length;j++) outPixels[i][j]=0.0f;
		final double [] slidingWindow=getSlidingMask(kernelSize); // 64x64
		final Thread[] threads = newThreadArray(threadsMax);
		final AtomicInteger ai = new AtomicInteger(0);
		final int numberOfKernels=     tilesY*tilesX*nChn;
		final int numberOfKernelsInChn=tilesY*tilesX;

		int ichn,indx,dx,dy,tx,ty,li;
		final int [] nonOverlapSeq = new int[numberOfKernels];
		int [] nextFirstFindex=new int[16*nChn];
		indx = 0;
		li=0;
		for (ichn=0;ichn<nChn;ichn++) for (dy=0;dy<4;dy++) for (dx=0;dx<4;dx++) {
			for (ty=dy; ty < tilesY; ty+=4) for (tx=dx; tx < tilesX; tx+=4){
				nonOverlapSeq[indx++] = ichn*numberOfKernelsInChn+ ty*tilesX + tx;
			}
			nextFirstFindex[li++] = indx;
		}
		final AtomicInteger aStopIndex = new AtomicInteger(0);
		final AtomicInteger tilesFinishedAtomic = new AtomicInteger(1); // first finished will be 1

		if (globalDebugLevel>1)
			System.out.println("Eyesis_Corrections:convolveStackWithKernelStack :\n"+
					"globalDebugLevel="+globalDebugLevel+"\n"+
					"imgWidth="+imgWidth+"\n"+
					"imgHeight="+imgHeight+"\n"+
					"tilesX="+tilesX+"\n"+
					"tilesY="+tilesY+"\n"+
					"nChn="+nChn+"\n"+
					"step="+step+"\n"+
					"size="+size+"\n"+
					"kernelSize="+kernelSize+"\n"+
					"kernelWidth="+kernelWidth+"\n"+
					"kernelNumHor="+kernelNumHor+"\n"+
					"numberOfKernelsInChn="+numberOfKernelsInChn+"\n");

		if (updateStatus) IJ.showStatus("Convolving image with kernels, "+nChn+" channels, "+tilesY+" rows");
		final long startTime = System.nanoTime();
		for (li = 0; li < nextFirstFindex.length; li++){
			aStopIndex.set(nextFirstFindex[li]);
			if (li>0){
				ai.set(nextFirstFindex[li-1]);
			}
			//			  System.out.println("\n=== nextFirstFindex["+li+"] =" + nextFirstFindex[li]+" === ");
			for (int ithread = 0; ithread < threads.length; ithread++) {
				threads[ithread] = new Thread() {
					@Override
					public void run() {
						float [] pixels=null;       // will be initialized at first use
						float [] kernelPixels=null; // will be initialized at first use
						double [] kernel=       new double[kernelSize*kernelSize];
						double [] inTile=       new double[kernelSize*kernelSize];
						double [] outTile=      new double[size * size];
						double [] doubleKernel= new double[size * size];
						int chn,tileY,tileX;
						int chn0=-1;
						//					  double debug_sum;
						//					  int i;
						DoubleFHT fht_instance =new DoubleFHT(); // provide DoubleFHT instance to save on initializations (or null)
						//					  for (int nTile0 = ai.getAndIncrement(); nTile0 < numberOfKernels; nTile0 = ai.getAndIncrement()) {
						for (int nTile0 = ai.getAndIncrement(); nTile0 < aStopIndex.get(); nTile0 = ai.getAndIncrement()) {
							//aStopIndex
							int nTile = nonOverlapSeq[nTile0];
							chn=nTile/numberOfKernelsInChn;
							tileY =(nTile % numberOfKernelsInChn)/tilesX;
							tileX = nTile % tilesX;
							if (tileX < 4) {
								int trow=(tileY+ ((tileY & 3) * tilesY))/4;
								if (updateStatus) IJ.showStatus("Convolving image with kernels, channel "+(chn+1)+" of "+nChn+", row "+(trow+1)+" of "+tilesY);
								if (globalDebugLevel>2) System.out.println("Processing kernels, channel "+(chn+1)+" of "+nChn+", row "+(trow+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
							}

							if (chn!=chn0) {
								pixels=      (float[]) imageStack.getPixels(chn+1);
								kernelPixels=(float[]) kernelStack.getPixels(chn+1);
								chn0=chn;
							}
							/* Read source image tile */
							extractSquareTile( pixels, // source pixel array,
									inTile, // will be filled, should have correct size before call
									slidingWindow, // window (same size as the kernel)
									imgWidth, // width of pixels array
									tileX*step, // left corner X
									tileY*step); // top corner Y
							/* zero pad twice the original size*/
							outTile=extendFFTInputTo (inTile, size);
							/* FHT transform of the source image data*/
							fht_instance.swapQuadrants(outTile);
							fht_instance.transform(    outTile);
							/* 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*kernelSize, // horizontal number of kernel to extract
									//tileY*kernelSize); // vertical number of kernel to extract
									tileX, // horizontal number of kernel to extract
									tileY); // vertical number of kernel to extract
							/* zero pad twice the original size*/
							doubleKernel=extendFFTInputTo (kernel, size);
							//						  debug_sum=0;
							//						  for (i=0;i<doubleKernel.length;i++) debug_sum+=doubleKernel[i];
							//						  if (globalDebugLevel>1) System.out.println("kernel sum="+debug_sum);

							//if ((tileY==tilesY/2) && (tileX==tilesX/2))  ShowDoubleFloatArrays.showArrays(doubleKernel,size,size, "doubleKernel-"+chn);
							/* FHT transform of the kernel */
							fht_instance.swapQuadrants(doubleKernel);
							fht_instance.transform(    doubleKernel);
							/* multiply in frequency domain */
							outTile=     fht_instance.multiply(outTile, doubleKernel, false);
							/* FHT inverse transform of the product - back to space domain */
							fht_instance.inverseTransform(outTile);
							fht_instance.swapQuadrants(outTile);
							/* accumulate result */
							//if ((tileY==tilesY/2) && (tileX==tilesX/2))  ShowDoubleFloatArrays.showArrays(outTile,size,size, "out-"+chn);
							/*This is synchronized method. It is possible to make threads to write to non-overlapping regions of the outPixels, but as the accumulation
							 * takes just small fraction of several FHTs, it should be OK - reasonable number of threads will spread and not "stay in line"
							 */

							// Add smart synchronization - wait only if is too far ahead. First test - no synchronization at all

							//accumulateSquareTile(
							//							  System.out.print(tileY+":"+tileX+"/"+chn+"("+nTile0+"/"+nTile+") ");
							//							  if (tileX < 4)System.out.println();
							nonSyncAccumulateSquareTile(
									outPixels[chn], //  float pixels array to accumulate tile
									outTile, // data to accumulate to the pixels array
									imgWidth, // width of pixels array
									(tileX-1)*step, // left corner X
									(tileY-1)*step); // top corner Y
							final int numFinished=tilesFinishedAtomic.getAndIncrement();
							if (numFinished % (numberOfKernels/100+1) == 0) {
								SwingUtilities.invokeLater(new Runnable() {
									@Override
									public void run() {
										IJ.showProgress(numFinished,numberOfKernels);
									}
								});
							}

							//numberOfKernels
						}
					}
				};
			}
			startAndJoin(threads);
		}
		if (updateStatus) IJ.showStatus("Convolution DONE");
		if (globalDebugLevel > 1) System.out.println("Threads done in "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
		IJ.showProgress(1.0);
		/* prepare result stack to return */
		ImageStack outStack=new ImageStack(imgWidth,imgHeight);
		for (i=0;i<nChn;i++) {
			outStack.addSlice(imageStack.getSliceLabel(i+1), outPixels[i]);
		}
		if (globalDebugLevel > 0) System.out.println("Convolution done in "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
		return outStack;
	}
	/* Adds zero pixels around the image, "extending canvas" */

	public double [][] extendFFTInputTo (double[][] input_pixels,
			int newSize) {
		double [][] pixels=new double[input_pixels.length][];
		int i;
		for (i=0;i<pixels.length;i++) pixels[i]= extendFFTInputTo (input_pixels[i], newSize);
		return pixels;
	}
	public double [][] extendFFTInput (double[][] input_pixels,
			int subDivFreq) {
		double [][] pixels=new double[input_pixels.length][];
		int i;
		for (i=0;i<pixels.length;i++) pixels[i]= extendFFTInput (input_pixels[i], subDivFreq);
		return pixels;
	}
	public double [] extendFFTInputTo (double[] input_pixels,
			int newSize) {
		int subDivFreq=newSize/((int)Math.sqrt (input_pixels.length));
		return extendFFTInput (input_pixels,
				subDivFreq);

	}
	public double [] extendFFTInput (double[] input_pixels,
			int subDivFreq) {
		if (input_pixels==null) return null;
		int width=(int) Math.sqrt(input_pixels.length);
		return extendFFTInput (input_pixels,
				width,   // width of the image
				subDivFreq);
	}

	public double [] extendFFTInput (double[] input_pixels,
			int width,   // width of the image
			int subDivFreq) {
		if (input_pixels==null) return null;
		double [] pixels=new double[input_pixels.length*subDivFreq*subDivFreq];
		int j,base,x,y;
		int height=input_pixels.length/width;
		for (j=0;j<pixels.length;j++) pixels[j]=0.0;
		j=0;
		for (y=0;y<height;y++) {
			base=width*(subDivFreq-1)*(width*subDivFreq +1)/2+y*width*subDivFreq;
			for (x=0;x<width;x++) pixels[base+x]=input_pixels[j++];
		}
		return pixels;
	}



	// duplicates with DebayerScissors

	/* ======================================================================== */
	/**extract and multiply by window function (same size as kernel itself) */
	void extractSquareTile(float [] pixels, // source pixel array,
			double [] tile, // will be filled, should have correct size before call
			double [] window, // window (same size as the kernel)
			int width, // width of pixels array
			int x0, // left corner X
			int y0) { // top corner Y
		int length=tile.length;
		int size=(int) Math.sqrt(length);
		int i,j,x,y;
		int height=pixels.length/width;
		int index=0;
		for (i=0;i<size;i++) {
			y=y0+i;
			if ((y>=0) && (y<height)) {
				index=i*size;
				for (j=0;j<size;j++) {
					x=x0+j;
					if ((x>=0) && (x<width)) tile [index]=pixels[y*width+x]*window[index];
					index++;
				}
			}
		}
	}
	/* ======================================================================== */
	void extractSquareTile(double [] pixels, // source pixel array,
			double [] tile, // will be filled, should have correct size before call
			double [] window, // window (same size as the kernel)
			int width, // width of pixels array
			int x0, // left corner X
			int y0) { // top corner Y
		int length=tile.length;
		int size=(int) Math.sqrt(length);
		int i,j,x,y;
		int height=pixels.length/width;
		int index=0;
		for (i=0;i<size;i++) {
			y=y0+i;
			if ((y>=0) && (y<height)) {
				index=i*size;
				for (j=0;j<size;j++) {
					x=x0+j;
					if ((x>=0) && (x<width)) tile [index]=pixels[y*width+x]*window[index];
					index++;
				}
			}
		}
	}


	/* ======================================================================== */
	/* accumulate square tile to the pixel array (tile may extend beyond the array, will be cropped) */
	synchronized void  accumulateSquareTile(
			float [] pixels, //  float pixels array to accumulate tile
			double []  tile, // data to accumulate to the pixels array
			int       width, // width of pixels array
			int          x0, // left corner X
			int          y0) { // top corner Y
		int length=tile.length;
		int size=(int) Math.sqrt(length);
		int i,j,x,y;
		int height=pixels.length/width;
		int index=0;
		for (i=0;i<size;i++) {
			y=y0+i;
			if ((y>=0) && (y<height)) {
				index=i*size;
				for (j=0;j<size;j++) {
					x=x0+j;
					if ((x>=0) && (x<width)) pixels[y*width+x]+=tile [index];
					index++;
				}
			}
		}
	}

	void  nonSyncAccumulateSquareTile(
			float [] pixels, //  float pixels array to accumulate tile
			double []  tile, // data to accumulate to the pixels array
			int       width, // width of pixels array
			int          x0, // left corner X
			int          y0) { // top corner Y
		int length=tile.length;
		int size=(int) Math.sqrt(length);
		int i,j,x,y;
		int height=pixels.length/width;
		int index=0;
		for (i=0;i<size;i++) {
			y=y0+i;
			if ((y>=0) && (y<height)) {
				index=i*size;
				for (j=0;j<size;j++) {
					x=x0+j;
					if ((x>=0) && (x<width)) pixels[y*width+x]+=tile [index];
					index++;
				}
			}
		}
	}


	synchronized void  accumulateSquareTile(
			double [] pixels, //  float pixels array to accumulate tile
			double []  tile, // data to accumulate to the pixels array
			int       width, // width of pixels array
			int          x0, // left corner X
			int          y0) { // top corner Y
		int length=tile.length;
		int size=(int) Math.sqrt(length);
		int i,j,x,y;
		int height=pixels.length/width;
		int index=0;
		for (i=0;i<size;i++) {
			y=y0+i;
			if ((y>=0) && (y<height)) {
				index=i*size;
				for (j=0;j<size;j++) {
					x=x0+j;
					if ((x>=0) && (x<width)) pixels[y*width+x]+=tile [index];
					index++;
				}
			}
		}
	}

	// end of duplicates with DebayerScissors
	/* Convert source Bayer pattern (GR/BG) image to higher resolution, add margins by duplicating pattern around */
	public ImageStack  bayerToStack(ImagePlus imp, // source bayer image, linearized, 32-bit (float))
			EyesisCorrectionParameters.SplitParameters splitParameters){

		if (imp==null) return null;
		//	    String [] chnNames={"red","blue","green"};
		String [] chnNames={"Red","Blue","Green"}; //Different sequence than RGB!!
		int nChn=chnNames.length;
		ImageProcessor ip=imp.getProcessor();
		int inWidth=imp.getWidth();
		int inHeight=imp.getHeight();
		int outHeight=inHeight*splitParameters.oversample+splitParameters.addTop+splitParameters.addBottom;
		int outWidth=inWidth*splitParameters.oversample+splitParameters.addLeft+splitParameters.addRight;
		int outLength=outWidth*outHeight;

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

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

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



	//double []  DENOISE_MASK=null;


	// TODO: do similar for JP4, using "subcamera" to "use" all channels for it
	/* ======================================================================== */
	/* Calculate deconvolution kernel (or difference of the two) noise gain
	 *  to be used when calculating mask that selects between deconvolved with
	 *  different kernels
	 */
	public ImageStack calculateKernelsNoiseGains (
			final ImageStack kernelStack1, // first stack with 3 colors/slices convolution kernels
			final ImageStack kernelStack2, // second stack with 3 colors/slices convolution kernels (or null)
			final int               size, // 128 - fft size, kernel size should be size/2
			final double       blurSigma,
			final int          threadsMax,  // maximal number of threads to launch
			final boolean    updateStatus,
			final int        globalDebugLevel) // update status info
	{
		if (kernelStack1==null) return null;
		final boolean useDiff= (kernelStack2 != null);
		final int kernelSize=size/2;
		final int kernelWidth=kernelStack1.getWidth();
		final int kernelNumHor=kernelWidth/(size/2);
		final int kernelNumVert=kernelStack1.getHeight()/(size/2);
		final int length=kernelNumHor*kernelNumVert;
		final int nChn=kernelStack1.getSize();
		final float [][] outPixles=new float[nChn][length]; // GLOBAL same as input
		int i,j;
		for (i=0;i<nChn;i++) for (j=0;j<length;j++) outPixles[i][j]=0.0f;
		final Thread[] threads = newThreadArray(threadsMax);
		final AtomicInteger ai = new AtomicInteger(0);
		final int numberOfKernels=     kernelNumHor*kernelNumVert*nChn;
		final int numberOfKernelsInChn=kernelNumHor*kernelNumVert;
		final long startTime = System.nanoTime();
		for (int ithread = 0; ithread < threads.length; ithread++) {
			threads[ithread] = new Thread() {
				@Override
				public void run() {
					DoubleGaussianBlur gb=null;
					if (blurSigma>0)	 gb=new DoubleGaussianBlur();
					float [] kernelPixels1= null; // will be initialized at first use
					float [] kernelPixels2= null; // will be initialized at first use
					double [] kernel1=      new double[kernelSize*kernelSize];
					double [] kernel2=      new double[kernelSize*kernelSize];
					int chn,tileY,tileX;
					int chn0=-1;
					int i;
					double sum;
					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));
						}

						if (chn!=chn0) {
							kernelPixels1=(float[]) kernelStack1.getPixels(chn+1);
							if (useDiff) kernelPixels2=(float[]) kernelStack2.getPixels(chn+1);
							chn0=chn;
						}
						/* read convolution kernel */
						extractOneKernel(kernelPixels1, //  array of combined square kernels, each
								kernel1, // 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
						/* optionally read the second convolution kernel */
						if (useDiff) {extractOneKernel(kernelPixels2, //  array of combined square kernels, each
								kernel2, // 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
						for (i=0; i<kernel1.length;i++) kernel1[i]-=kernel2[i];
						}
						if (blurSigma>0) gb.blurDouble(kernel1, kernelSize, kernelSize, blurSigma, blurSigma, 0.01);
						/* Calculate sum of squared kernel1  elements */
						sum=0.0;
						for (i=0; i<kernel1.length;i++) sum+=kernel1[i]*kernel1[i];
						outPixles[chn][tileY*kernelNumHor+tileX]= (float) (Math.sqrt(sum));
						//						  System.out.println("Processing kernels, channel "+(chn+1)+" of "+nChn+", row "+(tileY+1)+" of "+kernelNumVert+" sum="+sum);
					}
				}
			};
		}
		startAndJoin(threads);
		if (globalDebugLevel > 1) System.out.println("Threads done at "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
		/* prepare result stack to return */
		ImageStack outStack=new ImageStack(kernelNumHor,kernelNumVert);
		for (i=0;i<nChn;i++) {
			outStack.addSlice(kernelStack1.getSliceLabel(i+1), outPixles[i]);
		}
		return outStack;
	}

	public 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];
	}

	/* Extract noise mask (proportional to noise gain of the kernels), the denoise mask should be divided by this
	 *
	 */
	public double [][] extractNoiseMask(
			ImagePlus imp,// contains 3-slice stack (r,b,g)
			double k0,    // coefficient for slice 0 (r)
			double k1,    // coefficient for slice 1 (b)
			double k2,    // coefficient for slice 2 (g)
			int decim,     // decimate result (not yet supported)
			double gainPower
			){
		if (imp==null) return null;
		if (gainPower==0.0) return null; // do not use noise gain correction
		ImageStack stack=imp.getStack();
		int width=stack.getWidth();
		int height=stack.getHeight();
		double [][]mask=new double[height*decim][width*decim];
		float [][] pixels= new float [3][];
		pixels[0]=(float[]) stack.getPixels(1);
		pixels[1]=(float[]) stack.getPixels(2);
		pixels[2]=(float[]) stack.getPixels(3);
		int i,j,x,y,indx;
		for (y=0;y<height;y++) for (x=0;x<width;x++) {
			indx=x+y*width;
			for (i=0;i<decim;i++) for (j=0;j<decim;j++) {
				mask[y*decim+i][x*decim+j]=Math.pow(k0*pixels[0][indx]+k1*pixels[1][indx]+k2*pixels[2][indx],gainPower);
			}
		}
		return mask;
	}
	/* ======================================================================== */
	//	   private void saveAndShow(
	public void saveAndShow(
			ImagePlus             imp,
			EyesisCorrectionParameters.CorrectionParameters  correctionsParameters){
		saveAndShowEnable( imp,    correctionsParameters , true, true);
	}

	public void saveAndShowEnable(
			ImagePlus             imp,
			EyesisCorrectionParameters.CorrectionParameters  correctionsParameters,
			boolean               enableSave,
			boolean               enableShow){
		saveAndShow(
				imp,
				correctionsParameters,
				correctionsParameters.save && enableSave,
				correctionsParameters.show && enableShow,
				correctionsParameters.JPEG_quality);
	}

	public void saveAndShow(
			//	   public void saveAndShow(
			ImagePlus             imp,
			EyesisCorrectionParameters.CorrectionParameters  correctionsParameters,
			boolean               save,
			boolean               show){
		saveAndShow(imp, correctionsParameters,  save,  show, -1);
	}

	public void saveAndShow(
			ImagePlus             imp,
			EyesisCorrectionParameters.CorrectionParameters  correctionsParameters,
			boolean               save,
			boolean               show,
			int                   jpegQuality){//  <0 - keep current, 0 - force Tiff, >0 use for JPEG
		String path=null;
		if (save) path= correctionsParameters.selectResultsDirectory(
				true,  // smart,
				true);  //newAllowed, // save

		saveAndShow(
				imp,
				path,
				correctionsParameters.png,
				show,
				jpegQuality);
	}

	public void saveAndShow(
			ImagePlus             imp,
			String                path,
			boolean               png,
			boolean               show,
			int                   jpegQuality){//  <0 - keep current, 0 - force Tiff, >0 use for JPEG
		saveAndShow(
				imp,
				path,
				png,
				show,
				jpegQuality,//  <0 - keep current, 0 - force Tiff, >0 use for JPEG
				this.debugLevel+3);
	}


	public static void saveAndShow(
			ImagePlus             imp,
			String                path,
			boolean               png,
			boolean               show,
			int                   jpegQuality,//  <0 - keep current, 0 - force Tiff, >0 use for JPEG
			int                   debugLevel){
		if (path!=null) {
			FileInfo fi = new FileInfo();
			path+=Prefs.getFileSeparator()+imp.getTitle();
			boolean hasAlphaHighByte = false;
			if ((imp.getStackSize()==1) && (imp.getFileInfo().fileType== FileInfo.RGB)) {
				int [] pixels = (int []) imp.getProcessor().getPixels();
				for (int i = 0; i < pixels.length; i++){
					if ((pixels[i] & 0xff000000) != 0){
						hasAlphaHighByte = true;
						break;
					}
				}
			}

			if (hasAlphaHighByte && ((jpegQuality <= 0) || png)){
				if (png){
					if (debugLevel > 0) System.out.println("Saving RGBA result to "+path+".png");
					EyesisTiff.savePNG_ARGB32(
							imp,
							path +".png",
							debugLevel
							);
					fi.url = path+".png";
					fi.fileName = imp.getTitle()+".png";
				} else {
					if (debugLevel > 0) System.out.println("Saving RGBA result to "+path+".tiff");
					try {
						EyesisTiff.saveTiffARGB32(
								imp,
								path+".tiff", //path, // +".tiff",
								false, // correctionsParameters.imageJTags,
								debugLevel);
					} catch (IOException e) {
						e.printStackTrace();
					} catch (FormatException e) {
						e.printStackTrace();
					} catch (ServiceException e) {
						e.printStackTrace();
					} catch (DependencyException e) {
						e.printStackTrace();
					}
					fi.url = path+".tiff";
					fi.fileName = imp.getTitle()+".tiff";
				}

			} else if (((imp.getStackSize()==1)) && (jpegQuality!=0) && ((imp.getFileInfo().fileType== FileInfo.RGB) || (jpegQuality>0))) {
				if (debugLevel>0) System.out.println("Saving result to "+path+".jpeg");
				FileSaver fs=new FileSaver(imp);
				if (jpegQuality>0) FileSaver.setJpegQuality(jpegQuality);
				fs.saveAsJpeg(path+".jpeg");
				fi.url = path+".jpeg";
				fi.fileName = imp.getTitle()+".jpeg";
			} else {
				if (debugLevel>0) System.out.println("Saving result to "+path+".tiff");
				FileSaver fs=new FileSaver(imp);
				// Save as RGBA if it is RGBA
				int bytesPerPixel = imp.getBytesPerPixel();
				int mode = 0;
				if (bytesPerPixel > 1) mode = 1;
				if (bytesPerPixel > 3) mode = 3;// float, mode 2 not supported

				if ((imp.getStackSize() == 4) && imp.getStack().getSliceLabel(4).equals("alpha")){
					try {
						EyesisTiff.saveTiff(
								imp,
								path+".tiff",
								mode, //
								1.0, // full scale, absolute
								false, // correctionsParameters.imageJTags,
								debugLevel);
					} catch (IOException e) {
						e.printStackTrace();
					} catch (FormatException e) {
						e.printStackTrace();
					} catch (ServiceException e) {
						e.printStackTrace();
					} catch (DependencyException e) {
						e.printStackTrace();
					}
				} else if (imp.getStackSize()>1)  fs.saveAsTiffStack(path+".tiff");
				else fs.saveAsTiff(path+".tiff");
				fi.url = path+".tiff";
				fi.fileName = imp.getTitle()+".tiff";
			}
			imp.setFileInfo(fi); // only url
		}
		if (show) {
			imp.getProcessor().resetMinAndMax(); // probably not needed
			imp.show();
		}
	}

	private void saveAndShow(
			CompositeImage        compositeImage,
			EyesisCorrectionParameters.CorrectionParameters correctionsParameters,
			boolean               save,
			boolean               show){
		String path=null;
		if (save)  path= correctionsParameters.selectResultsDirectory(
				true,  // smart,
				true);  //newAllowed, // save

		if (path!=null) {
			path+=Prefs.getFileSeparator()+compositeImage.getTitle();
			if (debugLevel>0) System.out.println("Saving result to "+path+".tiff");
			FileSaver fs=new FileSaver(compositeImage);
			if (compositeImage.getStackSize()>1)  fs.saveAsTiffStack(path+".tiff");
			else fs.saveAsTiff(path+".tiff");
		}

		if (show) {
			compositeImage.show();
		}
	}


	/* ======================================================================== */
	/* Create a Thread[] array as large as the number of processors available.
	 * From Stephan Preibisch's Multithreading.java class. See:
	 * http://repo.or.cz/w/trakem2.git?a=blob;f=mpi/fruitfly/general/MultiThreading.java;hb=HEAD
	 */
	private Thread[] newThreadArray(int maxCPUs) {
		int n_cpus = Runtime.getRuntime().availableProcessors();
		if (n_cpus>maxCPUs)n_cpus=maxCPUs;
		return new Thread[n_cpus];
	}
	/* Start all given threads and wait on each of them until all are done.
	 * From Stephan Preibisch's Multithreading.java class. See:
	 * http://repo.or.cz/w/trakem2.git?a=blob;f=mpi/fruitfly/general/MultiThreading.java;hb=HEAD
	 */
	public static void startAndJoin(Thread[] threads)
	{
		for (int ithread = 0; ithread < threads.length; ++ithread)
		{
			threads[ithread].setPriority(Thread.NORM_PRIORITY);
			threads[ithread].start();
		}

		try
		{
			for (int ithread = 0; ithread < threads.length; ++ithread)
				threads[ithread].join();
		} catch (InterruptedException ie)
		{
			throw new RuntimeException(ie);
		}
	}


}
