Commit f19a4557 authored by Andrey Filippov's avatar Andrey Filippov
Browse files

Adding support for a dual-quad camera for CNN ground truth

parent 6db01aca

src/main/java/CorrectionColorProc.java

+41 −1
Original line number Original line Diff line number Diff line
@@ -521,6 +521,7 @@ G= Y +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg 








    public static class ColorGainsParameters {

    public static class ColorGainsParameters {

    	public static final String AUX_PREFIX = "AUX-";

    	public double[] gain={

    	public double[] gain={

    			1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,

    			1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,

    			1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,

    			1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,
@@ -548,7 +549,7 @@ G= Y +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg 
    			properties.setProperty(prefix+"balanceBlue_"+i,this.balanceBlue[i]+"");

    			properties.setProperty(prefix+"balanceBlue_"+i,this.balanceBlue[i]+"");

    		}

    		}

    	}

    	}

    	public void getProperties(String prefix,Properties properties){

    	public boolean getProperties(String prefix,Properties properties){

    		if (properties.getProperty(prefix+"channels")!=null) {

    		if (properties.getProperty(prefix+"channels")!=null) {

        		int numChannels=Integer.parseInt(properties.getProperty(prefix+"channels"));

        		int numChannels=Integer.parseInt(properties.getProperty(prefix+"channels"));

        		this.gain=       new double[numChannels];

        		this.gain=       new double[numChannels];
@@ -559,7 +560,9 @@ G= Y +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg 
        			this.balanceRed[i]= Double.parseDouble(properties.getProperty(prefix+"balanceRed_"+i));

        			this.balanceRed[i]= Double.parseDouble(properties.getProperty(prefix+"balanceRed_"+i));

        			this.balanceBlue[i]=Double.parseDouble(properties.getProperty(prefix+"balanceBlue_"+i));

        			this.balanceBlue[i]=Double.parseDouble(properties.getProperty(prefix+"balanceBlue_"+i));

        		}

        		}

        		return true;

    		}

    		}

    		return false;

    	}

    	}





    	public void modifyNumChannels(int numChannels){

    	public void modifyNumChannels(int numChannels){
@@ -599,6 +602,43 @@ G= Y +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg 
    		return true;

    		return true;

    	}

    	}





    	public boolean showDialog(ColorGainsParameters aux) {



    		GenericJTabbedDialog gd = new GenericJTabbedDialog("Individual channels colors/gains", 600,1000);

    		if (aux != null) gd.addTab("Main camera");

    		for (int i =0; i<this.gain.length;i++){

    			gd.addMessage(String.format("=== CHANNEL %02d ===",i));

    			gd.addNumericField(String.format("%02d: Gain (brightness)",i), this.gain[i], 3);

    			gd.addNumericField(String.format("%02d: Balance Red/Green",i), this.balanceRed[i], 3);

    			gd.addNumericField(String.format("%02d: Balance Blue/Green",i), this.balanceBlue[i], 3);

    		}

    		if (aux != null) {

    			gd.addTab("Auxiliary camera");

        		for (int i =0; i<this.gain.length;i++){

        			gd.addMessage(String.format("=== CHANNEL %02d ===",i));

        			gd.addNumericField(String.format("%02d: Gain (brightness)",i), aux.gain[i], 3);

        			gd.addNumericField(String.format("%02d: Balance Red/Green",i), aux.balanceRed[i], 3);

        			gd.addNumericField(String.format("%02d: Balance Blue/Green",i), aux.balanceBlue[i], 3);

        		}



    		}

    		gd.showDialog();

    		if (gd.wasCanceled()) return false;

    		for (int i =0; i<this.gain.length;i++){

    			this.gain[i]=       gd.getNextNumber();

    			this.balanceRed[i]= gd.getNextNumber();

    			this.balanceBlue[i]=gd.getNextNumber();

    		}

       		if (aux != null) {

        		for (int i =0; i<this.gain.length;i++){

        			aux.gain[i]=       gd.getNextNumber();

        			aux.balanceRed[i]= gd.getNextNumber();

        			aux.balanceBlue[i]=gd.getNextNumber();

        		}

       		}

    		return true;

    	}







    }

    }

src/main/java/EyesisCorrectionParameters.java

+286 −286

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/EyesisCorrections.java

+197 −160
Original line number Original line Diff line number Diff line
@@ -25,6 +25,11 @@ 
**

**

*/

*/





import java.io.IOException;

import java.util.concurrent.atomic.AtomicInteger;



import javax.swing.SwingUtilities;



import ij.CompositeImage;

import ij.CompositeImage;

import ij.IJ;

import ij.IJ;

import ij.ImagePlus;

import ij.ImagePlus;
@@ -35,12 +40,6 @@ import ij.io.FileSaver; 
import ij.process.ColorProcessor;

import ij.process.ColorProcessor;

import ij.process.FloatProcessor;

import ij.process.FloatProcessor;

import ij.process.ImageProcessor;

import ij.process.ImageProcessor;



import java.io.IOException;

import java.util.concurrent.atomic.AtomicInteger;



import javax.swing.SwingUtilities;



import loci.common.services.DependencyException;

import loci.common.services.DependencyException;

import loci.common.services.ServiceException;

import loci.common.services.ServiceException;

import loci.formats.FormatException;

import loci.formats.FormatException;
@@ -84,10 +83,39 @@ public class EyesisCorrections { 
	}

	}





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

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





	// TODO: preserve some data when re-running with new source files

	// TODO: preserve some data when re-running with new source files

	// FIXME: Make forgiving alien files

	public void initSensorFiles(int debugLevel){

	public void initSensorFiles(int debugLevel){

		initSensorFiles(debugLevel, false);

	}

	public void initSensorFiles(int debugLevel, boolean missing_ok){

		this.sharpKernelPaths=null;

		this.sharpKernelPaths=null;

		this.smoothKernelPaths=null;

		this.smoothKernelPaths=null;

		String [] sensorPaths=correctionsParameters.selectSensorFiles(this.debugLevel);

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

		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();

		if ((this.debugLevel>101) && (correctionsParameters.sourcePaths!=null) && (correctionsParameters.sourcePaths.length>0)) {

			testFF(correctionsParameters.sourcePaths[0]);

		}

	}



	public void initSensorFilesAux(int debugLevel){

//		this.sharpKernelPaths=null;

//		this.smoothKernelPaths=null;

		String [] sensorPaths=correctionsParameters.selectSensorFiles(this.debugLevel);

		String [] sensorPaths=correctionsParameters.selectSensorFiles(this.debugLevel);

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

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

		this.usedChannels= usedChannels(correctionsParameters.getSourcePaths());

		this.usedChannels= usedChannels(correctionsParameters.getSourcePaths());
@@ -108,8 +136,8 @@ public class EyesisCorrections { 
		if ((this.debugLevel>101) && (correctionsParameters.sourcePaths!=null) && (correctionsParameters.sourcePaths.length>0)) {

		if ((this.debugLevel>101) && (correctionsParameters.sourcePaths!=null) && (correctionsParameters.sourcePaths.length>0)) {

			testFF(correctionsParameters.sourcePaths[0]);

			testFF(correctionsParameters.sourcePaths[0]);

		}

		}

		

	}

	}



	public double [] calcReferenceExposures(int debugLevel){

	public double [] calcReferenceExposures(int debugLevel){

		String [] paths=this.correctionsParameters.getSourcePaths();

		String [] paths=this.correctionsParameters.getSourcePaths();

		double [] exposures=new double [paths.length];

		double [] exposures=new double [paths.length];
@@ -329,8 +357,8 @@ public class EyesisCorrections { 
			if (this.usedChannels[chn] && (this.sharpKernelPaths[chn]!=null) && (!nonlinParameters.useDiffNoiseGains ||(this.smoothKernelPaths[chn]!=null))){

			if (this.usedChannels[chn] && (this.sharpKernelPaths[chn]!=null) && (!nonlinParameters.useDiffNoiseGains ||(this.smoothKernelPaths[chn]!=null))){

				if (

				if (

						(this.imageNoiseGains[chn]==null) ||

						(this.imageNoiseGains[chn]==null) ||

						(!this.sharpKernelPaths[chn].equals((String) this.imageNoiseGains[chn].getProperty("sharpKernelPath"))) ||

						(!this.sharpKernelPaths[chn].equals(this.imageNoiseGains[chn].getProperty("sharpKernelPath"))) ||

						(!this.smoothKernelPaths[chn].equals((String) this.imageNoiseGains[chn].getProperty("smoothKernelPath")))){

						(!this.smoothKernelPaths[chn].equals(this.imageNoiseGains[chn].getProperty("smoothKernelPath")))){





					ImagePlus imp_kernel_sharp=new ImagePlus(this.sharpKernelPaths[chn]);

					ImagePlus imp_kernel_sharp=new ImagePlus(this.sharpKernelPaths[chn]);

					  if (imp_kernel_sharp.getStackSize()<3) {

					  if (imp_kernel_sharp.getStackSize()<3) {
@@ -486,6 +514,10 @@ public class EyesisCorrections { 
	}

	}





	boolean [] usedChannels(String [] paths){

	boolean [] usedChannels(String [] paths){

		return usedChannels(paths, false);

	}



	boolean [] usedChannels(String [] paths, boolean missing_ok){

		if (paths==null) paths=new String[0];

		if (paths==null) paths=new String[0];

		int numChannels=this.pixelMapping.getNumChannels();

		int numChannels=this.pixelMapping.getNumChannels();

		boolean [] usedChannels=new boolean[numChannels];

		boolean [] usedChannels=new boolean[numChannels];
@@ -498,7 +530,9 @@ public class EyesisCorrections { 
				if (channels!=null) for (int j=0;j<channels.length;j++) usedChannels[channels[j]]=true;

				if (channels!=null) for (int j=0;j<channels.length;j++) usedChannels[channels[j]]=true;

			} else {

			} else {

				if (!this.pixelMapping.isChannelAvailable(srcChannel)){

				if (!this.pixelMapping.isChannelAvailable(srcChannel)){

					if (debugLevel>0) System.out.println("No sensor data for channel "+srcChannel+", needed for source file "+paths[i]);

					if ((debugLevel>0) && !missing_ok) {

						System.out.println("No sensor data for channel "+srcChannel+", needed for source file "+paths[i]);

					}

				} else usedChannels[srcChannel] = true;

				} else usedChannels[srcChannel] = true;

			}

			}

		}

		}
@@ -1795,6 +1829,7 @@ public class EyesisCorrections { 
//			  System.out.println("\n=== nextFirstFindex["+li+"] =" + nextFirstFindex[li]+" === ");

//			  System.out.println("\n=== nextFirstFindex["+li+"] =" + nextFirstFindex[li]+" === ");

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

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

				  threads[ithread] = new Thread() {

				  threads[ithread] = new Thread() {

					  @Override

					public void run() {

					public void run() {

						  float [] pixels=null;       // will be initialized at first use

						  float [] pixels=null;       // will be initialized at first use

						  float [] kernelPixels=null; // will be initialized at first use

						  float [] kernelPixels=null; // will be initialized at first use
@@ -1880,6 +1915,7 @@ public class EyesisCorrections { 
							  final int numFinished=tilesFinishedAtomic.getAndIncrement();

							  final int numFinished=tilesFinishedAtomic.getAndIncrement();

							  if (numFinished % (numberOfKernels/100+1) == 0) {

							  if (numFinished % (numberOfKernels/100+1) == 0) {

								  SwingUtilities.invokeLater(new Runnable() {

								  SwingUtilities.invokeLater(new Runnable() {

									  @Override

									public void run() {

									public void run() {

										  IJ.showProgress(numFinished,numberOfKernels);

										  IJ.showProgress(numFinished,numberOfKernels);

									  }

									  }
@@ -2210,6 +2246,7 @@ public class EyesisCorrections { 
		  final long startTime = System.nanoTime();

		  final long startTime = System.nanoTime();

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

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

			  threads[ithread] = new Thread() {

			  threads[ithread] = new Thread() {

				  @Override

				public void run() {

				public void run() {

					  DoubleGaussianBlur gb=null;

					  DoubleGaussianBlur gb=null;

					  if (blurSigma>0)	 gb=new DoubleGaussianBlur();

					  if (blurSigma>0)	 gb=new DoubleGaussianBlur();

src/main/java/Eyesis_Correction.java

+1079 −1127

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/PixelMapping.java

+5 −2
Original line number Original line Diff line number Diff line
@@ -154,6 +154,9 @@ public class PixelMapping { 
    // as stored in "subcamera" field of the calibration file and "sensor_port". sensor_port may start from non-0, so we need to count all combinations

    // as stored in "subcamera" field of the calibration file and "sensor_port". sensor_port may start from non-0, so we need to count all combinations

    //removeUnusedSensorData xshould be off!

    //removeUnusedSensorData xshould be off!

    public int [] channelsForSubCamera(int subCamera){

    public int [] channelsForSubCamera(int subCamera){

    	if (subCamera < 0) {

    		return null;

    	}

		System.out.println("channelsForSubCamera("+subCamera+"),this.sensors.length="+this.sensors.length);

		System.out.println("channelsForSubCamera("+subCamera+"),this.sensors.length="+this.sensors.length);

//    	ArrayList<ArrayList<ArrayList<Integer>>> camera_IPs = new ArrayList<ArrayList<ArrayList<Integer>>>();

//    	ArrayList<ArrayList<ArrayList<Integer>>> camera_IPs = new ArrayList<ArrayList<ArrayList<Integer>>>();

    	ArrayList<Point> cam_port = new ArrayList<Point>();

    	ArrayList<Point> cam_port = new ArrayList<Point>();
@@ -172,11 +175,11 @@ public class PixelMapping { 
			}

			}

		});

		});

		// debugging:

		// debugging:

		System.out.println("----- This filename subcamera "+subCamera+": physical camera "+cam_port_arr[subCamera].x+", sensor_port "+cam_port_arr[subCamera].y);

		if (subCamera >= cam_port_arr.length) {

		if (subCamera >= cam_port_arr.length) {

			System.out.println("Error: Subcamera "+subCamera+" > that total namera of sensor ports in the system = "+cam_port_arr.length);

			System.out.println("Error: Subcamera "+subCamera+" > that total number of sensor ports in the system = "+cam_port_arr.length);

			return null;

			return null;

		}

		}

		System.out.println("----- This filename subcamera "+subCamera+": physical camera "+cam_port_arr[subCamera].x+", sensor_port "+cam_port_arr[subCamera].y);

    	if (this.sensors == null) return null;

    	if (this.sensors == null) return null;

    	int numChannels=0;

    	int numChannels=0;

    	for (int i=0;i<this.sensors.length;i++) if (this.sensors[i]!=null) {

    	for (int i=0;i<this.sensors.length;i++) if (this.sensors[i]!=null) {