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imagej-elphel
Commit f19a4557 authored by Andrey Filippov's avatar Andrey Filippov
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Adding support for a dual-quad camera for CNN ground truth

parent 6db01aca
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Showing with 1712 additions and 1621 deletions
src/main/java/CorrectionColorProc.java
View file @ f19a4557
......@@ -521,6 +521,7 @@ G= Y +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
public static class ColorGainsParameters {
public static final String AUX_PREFIX = "AUX-";
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,
......@@ -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]+"");
}
}
public void getProperties(String prefix,Properties properties){
public boolean getProperties(String prefix,Properties properties){
if (properties.getProperty(prefix+"channels")!=null) {
int numChannels=Integer.parseInt(properties.getProperty(prefix+"channels"));
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.balanceBlue[i]=Double.parseDouble(properties.getProperty(prefix+"balanceBlue_"+i));
}
return true;
}
return false;
}
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;
}
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/EyesisCorrections.java
View file @ f19a4557
......@@ -25,6 +25,11 @@
**
*/
import java.io.IOException;
import java.util.concurrent.atomic.AtomicInteger;
import javax.swing.SwingUtilities;
import ij.CompositeImage;
import ij.IJ;
import ij.ImagePlus;
......@@ -35,12 +40,6 @@ import ij.io.FileSaver;
import ij.process.ColorProcessor;
import ij.process.FloatProcessor;
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.ServiceException;
import loci.formats.FormatException;
......@@ -84,14 +83,43 @@ public class EyesisCorrections {
}
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);
}
public void initSensorFiles(int debugLevel, boolean missing_ok){
this.sharpKernelPaths=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);
this.pixelMapping=new PixelMapping(sensorPaths,debugLevel);
this.usedChannels= usedChannels(correctionsParameters.getSourcePaths());
// TODO: Combine with additional channel map to be able to select single image (of all 3)
// 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);
}
......@@ -108,8 +136,8 @@ public class EyesisCorrections {
if ((this.debugLevel>101) && (correctionsParameters.sourcePaths!=null) && (correctionsParameters.sourcePaths.length>0)) {
testFF(correctionsParameters.sourcePaths[0]);
}
}
public double [] calcReferenceExposures(int debugLevel){
String [] paths=this.correctionsParameters.getSourcePaths();
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.imageNoiseGains[chn]==null) ||
(!this.sharpKernelPaths[chn].equals((String) this.imageNoiseGains[chn].getProperty("sharpKernelPath"))) ||
(!this.smoothKernelPaths[chn].equals((String) this.imageNoiseGains[chn].getProperty("smoothKernelPath")))){
(!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) {
......@@ -486,6 +514,10 @@ public class EyesisCorrections {
}
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];
......@@ -498,7 +530,9 @@ public class EyesisCorrections {
if (channels!=null) for (int j=0;j<channels.length;j++) usedChannels[channels[j]]=true;
} else {
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;
}
}
......@@ -1795,6 +1829,7 @@ public class EyesisCorrections {
// 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
......@@ -1880,6 +1915,7 @@ public class EyesisCorrections {
final int numFinished=tilesFinishedAtomic.getAndIncrement();
if (numFinished % (numberOfKernels/100+1) == 0) {
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
IJ.showProgress(numFinished,numberOfKernels);
}
......@@ -2210,6 +2246,7 @@ public class EyesisCorrections {
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();
......
src/main/java/Eyesis_Correction.java
View file @ f19a4557
This source diff could not be displayed because it is too large. You can view the blob instead.
src/main/java/PixelMapping.java
View file @ f19a4557
......@@ -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
//removeUnusedSensorData xshould be off!
public int [] channelsForSubCamera(int subCamera){
if (subCamera < 0) {
return null;
}
System.out.println("channelsForSubCamera("+subCamera+"),this.sensors.length="+this.sensors.length);
// ArrayList<ArrayList<ArrayList<Integer>>> camera_IPs = new ArrayList<ArrayList<ArrayList<Integer>>>();
ArrayList<Point> cam_port = new ArrayList<Point>();
......@@ -172,11 +175,11 @@ public class PixelMapping {
}
});
// 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) {
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;
}
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;
int numChannels=0;
for (int i=0;i<this.sensors.length;i++) if (this.sensors[i]!=null) {
......
src/main/java/QuadCLT.java
View file @ f19a4557
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