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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 ...@@ -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 ...@@ -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 ...@@ -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 ...@@ -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
View file @ f19a4557
...@@ -37,6 +37,7 @@ import ij.gui.GenericDialog; ...@@ -37,6 +37,7 @@ import ij.gui.GenericDialog;
public class EyesisCorrectionParameters { public class EyesisCorrectionParameters {
public static class CorrectionParameters{ public static class CorrectionParameters{
public static final String AUX_PREFIX = "AUX-";
public boolean swapSubchannels01= true; // false; // (false: 0-1-2, true - 1-0-2) public boolean swapSubchannels01= true; // false; // (false: 0-1-2, true - 1-0-2)
public boolean split= true; public boolean split= true;
public boolean vignetting= true; public boolean vignetting= true;
...@@ -75,46 +76,46 @@ public class EyesisCorrectionParameters { ...@@ -75,46 +76,46 @@ public class EyesisCorrectionParameters {
public boolean zcorrect= true; public boolean zcorrect= true;
public boolean saveSettings = true; public boolean saveSettings = true;
public String [] sourcePaths={}; public String [] sourcePaths= {};
public String sourceDirectory=""; public String sourceDirectory= "";
public String sourcePrefix=""; public String sourcePrefix= "";
public String sourceSuffix=".tiff"; //".jp4" public String sourceSuffix= ".tiff"; //".jp4"
public int firstSubCamera=1; // 0 or 1 public int firstSubCamera= 1; // channel index in source file names
public String sensorDirectory=""; public int numSubCameras= 4; // channel index in source file names
public String sensorPrefix="sensor-"; public String sensorDirectory= "";
public String sensorSuffix=".calib-tiff"; // fixed in PixelMapping public String sensorPrefix= "sensor-";
public String sensorSuffix= ".calib-tiff"; // fixed in PixelMapping
public String sharpKernelDirectory="";
public String sharpKernelPrefix="sharpKernel-"; public String sharpKernelDirectory= "";
public String sharpKernelSuffix=".kernel-tiff"; public String sharpKernelPrefix= "sharpKernel-";
public String smoothKernelDirectory=""; public String sharpKernelSuffix= ".kernel-tiff";
public String smoothKernelPrefix="smoothKernel-"; public String smoothKernelDirectory= "";
public String smoothKernelSuffix=".kernel-tiff"; public String smoothKernelPrefix= "smoothKernel-";
public String dctKernelDirectory=""; public String smoothKernelSuffix= ".kernel-tiff";
public String dctKernelPrefix="dct-"; public String dctKernelDirectory= "";
public String dctSymSuffix=".sym-tiff"; public String dctKernelPrefix= "dct-";
public String dctAsymSuffix=".asym-tiff"; public String dctSymSuffix= ".sym-tiff";
public String dctAsymSuffix= ".asym-tiff";
public String equirectangularDirectory=""; public String equirectangularDirectory="";
public String equirectangularPrefix=""; public String equirectangularPrefix= "";
public String equirectangularSuffix=".eqr-tiff"; public String equirectangularSuffix= ".eqr-tiff";
public boolean equirectangularCut=true; public boolean equirectangularCut= true;
public String planeMapPrefix=""; public String planeMapPrefix= "";
public String planeMapSuffix=".plane-proj-tiff"; public String planeMapSuffix= ".plane-proj-tiff";
public boolean usePlaneProjection=false; // public boolean usePlaneProjection= false; //
public boolean planeAsJPEG= true; // save de-warped image as JPEG (only if equirectangularFormat==0) public boolean planeAsJPEG= true; // save de-warped image as JPEG (only if equirectangularFormat==0)
// public String equirectangularSuffixA="A.eqr-tiff"; // or the roll-over part public String resultsDirectory= "";
public String resultsDirectory=""; public boolean removeUnusedSensorData= false;
public boolean removeUnusedSensorData=false; public int exposureCorrectionMode= 2; // - 0 - none, 1 - absolute, 2 - relative
public int exposureCorrectionMode=2; // - 0 - none, 1 - absolute, 2 - relative public double referenceExposure= 0.0003; // 3/10000 sec, used in absolute mode only
public double referenceExposure=0.0003; // 3/10000 sec, used in absolute mode only public double relativeExposure= 0.5; // 0.0 - use shortest (darken), 1.0 - use longest (brighten)
public double relativeExposure=0.5; // 0.0 - use shortest (darken), 1.0 - use longest (brighten)
public String cltKernelDirectory= "";
public String cltKernelDirectory=""; public String cltKernelPrefix= "clt-";
public String cltKernelPrefix="clt-"; public String cltSuffix= ".clt-tiff";
public String cltSuffix=".clt-tiff";
public boolean use_x3d_subdirs = true; public boolean use_x3d_subdirs = true;
public String x3dSubdirPrefix=""; public String x3dSubdirPrefix= "";
public String x3dSubdirSuffix=""; public String x3dSubdirSuffix= "";
// CLT 3d batch parameters // CLT 3d batch parameters
...@@ -133,6 +134,141 @@ public class EyesisCorrectionParameters { ...@@ -133,6 +134,141 @@ public class EyesisCorrectionParameters {
public String x3dModelVersion="v01"; public String x3dModelVersion="v01";
public String x3dDirectory=""; public String x3dDirectory="";
public CorrectionParameters getAux() {
return aux_camera;
}
public CorrectionParameters aux_camera = null; // auxiliarry camera parameters
// public boolean use_aux = true; // Generate debug images if a single set is selected
public void updateAuxFromMain() { // from master to aux
if (aux_camera == null) {
aux_camera = new CorrectionParameters();
initAuxFromMain(aux_camera);
} else {
updateAuxFromMain(aux_camera);
}
}
public void updateAuxFromMain(CorrectionParameters cp) { // from master to aux
cp.split = this.split;
cp.vignetting= this.vignetting;
cp.pixelDefects= this.pixelDefects;
cp.pixelDefectsThreshold= this.pixelDefectsThreshold;
cp.debayer= this.debayer;
cp.showDebayerEnergy = this.showDebayerEnergy;
cp.saveDebayerEnergy= this.saveDebayerEnergy;
cp.deconvolve= this.deconvolve;
cp.combine= this.combine;
cp.showDenoiseMask= this.showDenoiseMask;
cp.saveDenoiseMask= this.saveDenoiseMask;
cp.showChromaDenoiseMask= this.showChromaDenoiseMask;
cp.saveChromaDenoiseMask= this.saveChromaDenoiseMask;
cp.showNoiseGains= this.showNoiseGains;
cp.saveNoiseGains= this.saveNoiseGains;
cp.colorProc= this.colorProc;
cp.blueProc= this.blueProc;
cp.toRGB= this.toRGB;
cp.rotate= this.rotate;
cp.crop= this.crop;
cp.equirectangularFormat= this.equirectangularFormat;
cp.outputRangeInt= this.outputRangeInt;
cp.outputRangeFP= this.outputRangeFP;
cp.imageJTags= this.imageJTags;
cp.jpeg= this.jpeg;
cp.png= this.png;
cp.save= this.save;
cp.save16= this.save16;
cp.save32= this.save32;
cp.show= this.show;
cp.JPEG_quality= this.JPEG_quality;
cp.JPEG_scale= this.JPEG_scale;
cp.equirectangular= this.equirectangular;
cp.zcorrect= this.zcorrect;
cp.saveSettings= this.saveSettings;
cp.sourceDirectory= this.sourceDirectory;
cp.sourcePrefix= this.sourcePrefix;
cp.sourceSuffix= this.sourceSuffix;
// cp.firstSubCamera= this.firstSubCamera;
// cp.numSubCameras= this.numSubCameras;
// cp.sensorDirectory= this.sensorDirectory;
// cp.sensorPrefix= this.sensorPrefix;
// cp.sensorSuffix= this.sensorSuffix;
cp.sharpKernelDirectory= this.sharpKernelDirectory;
cp.sharpKernelPrefix= this.sharpKernelPrefix;
cp.sharpKernelSuffix= this.sharpKernelSuffix;
cp.smoothKernelDirectory= this.smoothKernelDirectory;
cp.smoothKernelPrefix= this.smoothKernelPrefix;
cp.smoothKernelSuffix= this.smoothKernelSuffix;
cp.dctKernelDirectory= this.dctKernelDirectory;
cp.dctKernelPrefix= this.dctKernelPrefix;
cp.dctSymSuffix= this.dctSymSuffix;
cp.dctAsymSuffix= this.dctAsymSuffix;
cp.equirectangularDirectory=this.equirectangularDirectory;
cp.equirectangularPrefix= this.equirectangularPrefix;
cp.equirectangularSuffix= this.equirectangularSuffix;
cp.equirectangularCut= this.equirectangularCut;
cp.planeMapPrefix= this.planeMapPrefix;
cp.planeMapSuffix= this.planeMapSuffix;
cp.usePlaneProjection= this.usePlaneProjection;
cp.planeAsJPEG= this.planeAsJPEG;
// cp.resultsDirectory= this.resultsDirectory;
cp.removeUnusedSensorData= this.removeUnusedSensorData;
if (this.sourcePaths!=null) {
cp.sourcePaths=new String[this.sourcePaths.length];
for (int i=0;i<this.sourcePaths.length;i++){
cp.sourcePaths[i] = this.sourcePaths[i];
}
}
cp.exposureCorrectionMode= this.exposureCorrectionMode;
cp.referenceExposure= this.referenceExposure;
cp.relativeExposure= this.relativeExposure;
cp.swapSubchannels01= this.swapSubchannels01;
// cp.cltKernelDirectory= this.cltKernelDirectory;
// cp.cltKernelPrefix= this.cltKernelPrefix;
// cp.cltSuffix= this.cltSuffix;
cp.x3dDirectory= this.x3dDirectory;
cp.use_x3d_subdirs= this.use_x3d_subdirs;
cp.x3dSubdirPrefix= this.x3dSubdirPrefix;
cp.x3dSubdirSuffix= this.x3dSubdirSuffix;
cp.x3dModelVersion= this.x3dModelVersion;
cp.clt_batch_apply_man= this.clt_batch_apply_man;
cp.clt_batch_extrinsic= this.clt_batch_extrinsic;
cp.clt_batch_poly= this.clt_batch_poly;
cp.clt_batch_4img= this.clt_batch_4img;
cp.clt_batch_explore= this.clt_batch_explore;
cp.clt_batch_surf= this.clt_batch_surf;
cp.clt_batch_assign= this.clt_batch_assign;
cp.clt_batch_gen3d= this.clt_batch_gen3d;
cp.clt_batch_dbg1= this.clt_batch_dbg1;
}
public void initAuxFromMain(CorrectionParameters cp) { // from master to aux
updateAuxFromMain(cp); // common parameters
// empty to prevent accidental use of the wrong kernels/sesnor calibration files
cp.sensorDirectory= ""; // this.sensorDirectory;
cp.cltKernelDirectory= ""; // this.cltKernelDirectory;
cp.resultsDirectory= this.resultsDirectory+"/aux";
cp.firstSubCamera= this.firstSubCamera + this.numSubCameras;
cp.numSubCameras= this.numSubCameras;
cp.sensorPrefix= ""; // this.sensorPrefix;
cp.sensorSuffix= this.sensorSuffix;
cp.cltKernelPrefix= this.cltKernelPrefix;
cp.cltSuffix= this.cltSuffix;
}
public void auxFromExternal(CorrectionParameters ecp) { // from master to aux
this.aux_camera.sensorDirectory= ecp.sensorDirectory;
this.aux_camera.cltKernelDirectory= ecp.cltKernelDirectory;
this.aux_camera.resultsDirectory= ecp.resultsDirectory+"/aux";
this.aux_camera.firstSubCamera= ecp.firstSubCamera;
this.aux_camera.numSubCameras= ecp.numSubCameras;
this.aux_camera.sensorPrefix= ecp.sensorPrefix;
this.aux_camera.sensorSuffix= ecp.sensorSuffix;
this.aux_camera.cltKernelPrefix= ecp.cltKernelPrefix;
this.aux_camera.cltSuffix= ecp.cltSuffix;
}
public void setProperties(String prefix,Properties properties){ public void setProperties(String prefix,Properties properties){
properties.setProperty(prefix+"split",this.split+""); properties.setProperty(prefix+"split",this.split+"");
properties.setProperty(prefix+"vignetting",this.vignetting+""); properties.setProperty(prefix+"vignetting",this.vignetting+"");
...@@ -174,6 +310,7 @@ public class EyesisCorrectionParameters { ...@@ -174,6 +310,7 @@ public class EyesisCorrectionParameters {
properties.setProperty(prefix+"sourcePrefix",this.sourcePrefix); properties.setProperty(prefix+"sourcePrefix",this.sourcePrefix);
properties.setProperty(prefix+"sourceSuffix",this.sourceSuffix); properties.setProperty(prefix+"sourceSuffix",this.sourceSuffix);
properties.setProperty(prefix+"firstSubCamera",this.firstSubCamera+""); properties.setProperty(prefix+"firstSubCamera",this.firstSubCamera+"");
properties.setProperty(prefix+"numSubCameras", this.numSubCameras+"");
properties.setProperty(prefix+"sensorDirectory",this.sensorDirectory); properties.setProperty(prefix+"sensorDirectory",this.sensorDirectory);
properties.setProperty(prefix+"sensorPrefix",this.sensorPrefix); properties.setProperty(prefix+"sensorPrefix",this.sensorPrefix);
...@@ -210,6 +347,7 @@ public class EyesisCorrectionParameters { ...@@ -210,6 +347,7 @@ public class EyesisCorrectionParameters {
properties.setProperty(prefix+"sourcePath"+i,this.sourcePaths[i]); properties.setProperty(prefix+"sourcePath"+i,this.sourcePaths[i]);
} }
} }
properties.setProperty(prefix+"exposureCorrectionMode",this.exposureCorrectionMode+""); properties.setProperty(prefix+"exposureCorrectionMode",this.exposureCorrectionMode+"");
properties.setProperty(prefix+"referenceExposure", this.referenceExposure+""); properties.setProperty(prefix+"referenceExposure", this.referenceExposure+"");
properties.setProperty(prefix+"relativeExposure", this.relativeExposure+""); properties.setProperty(prefix+"relativeExposure", this.relativeExposure+"");
...@@ -237,6 +375,20 @@ public class EyesisCorrectionParameters { ...@@ -237,6 +375,20 @@ public class EyesisCorrectionParameters {
properties.setProperty(prefix+"clt_batch_assign", this.clt_batch_assign+""); properties.setProperty(prefix+"clt_batch_assign", this.clt_batch_assign+"");
properties.setProperty(prefix+"clt_batch_gen3d", this.clt_batch_gen3d+""); properties.setProperty(prefix+"clt_batch_gen3d", this.clt_batch_gen3d+"");
properties.setProperty(prefix+"clt_batch_dbg1", this.clt_batch_dbg1+""); properties.setProperty(prefix+"clt_batch_dbg1", this.clt_batch_dbg1+"");
if (aux_camera != null) { // always
updateAuxFromMain();
String aux_prefix = prefix + AUX_PREFIX;
properties.setProperty(aux_prefix+"sensorDirectory", this.aux_camera.sensorDirectory);
properties.setProperty(aux_prefix+"cltKernelDirectory", this.aux_camera.cltKernelDirectory);
properties.setProperty(aux_prefix+"resultsDirectory", this.aux_camera.resultsDirectory);
properties.setProperty(aux_prefix+"firstSubCamera", this.aux_camera.firstSubCamera+"");
properties.setProperty(aux_prefix+"numSubCameras", this.aux_camera.numSubCameras+"");
properties.setProperty(aux_prefix+"sensorPrefix", this.aux_camera.sensorPrefix);
properties.setProperty(aux_prefix+"sensorSuffix", this.aux_camera.sensorSuffix);
properties.setProperty(aux_prefix+"cltKernelPrefix", this.aux_camera.cltKernelPrefix);
properties.setProperty(aux_prefix+"cltSuffix", this.aux_camera.cltSuffix);
}
} }
public void getProperties(String prefix,Properties properties){ public void getProperties(String prefix,Properties properties){
...@@ -278,7 +430,8 @@ public class EyesisCorrectionParameters { ...@@ -278,7 +430,8 @@ public class EyesisCorrectionParameters {
if (properties.getProperty(prefix+"sourceDirectory")!= null) this.sourceDirectory=properties.getProperty(prefix+"sourceDirectory"); if (properties.getProperty(prefix+"sourceDirectory")!= null) this.sourceDirectory=properties.getProperty(prefix+"sourceDirectory");
if (properties.getProperty(prefix+"sourcePrefix")!= null) this.sourcePrefix=properties.getProperty(prefix+"sourcePrefix"); if (properties.getProperty(prefix+"sourcePrefix")!= null) this.sourcePrefix=properties.getProperty(prefix+"sourcePrefix");
if (properties.getProperty(prefix+"sourceSuffix")!= null) this.sourceSuffix=properties.getProperty(prefix+"sourceSuffix"); if (properties.getProperty(prefix+"sourceSuffix")!= null) this.sourceSuffix=properties.getProperty(prefix+"sourceSuffix");
if (properties.getProperty(prefix+"firstSubCamera")!=null) this.firstSubCamera=Integer.parseInt(properties.getProperty(prefix+"firstSubCamera")); if (properties.getProperty(prefix+"firstSubCamera")!= null) this.firstSubCamera=Integer.parseInt(properties.getProperty(prefix+"firstSubCamera"));
if (properties.getProperty(prefix+"numSubCameras")!= null) this.numSubCameras=Integer.parseInt(properties.getProperty(prefix+"numSubCameras"));
if (properties.getProperty(prefix+"sensorDirectory")!= null) this.sensorDirectory=properties.getProperty(prefix+"sensorDirectory"); if (properties.getProperty(prefix+"sensorDirectory")!= null) this.sensorDirectory=properties.getProperty(prefix+"sensorDirectory");
if (properties.getProperty(prefix+"sensorPrefix")!= null) this.sensorPrefix=properties.getProperty(prefix+"sensorPrefix"); if (properties.getProperty(prefix+"sensorPrefix")!= null) this.sensorPrefix=properties.getProperty(prefix+"sensorPrefix");
if (properties.getProperty(prefix+"sensorSuffix")!= null) this.sensorSuffix=properties.getProperty(prefix+"sensorSuffix"); if (properties.getProperty(prefix+"sensorSuffix")!= null) this.sensorSuffix=properties.getProperty(prefix+"sensorSuffix");
...@@ -346,203 +499,21 @@ public class EyesisCorrectionParameters { ...@@ -346,203 +499,21 @@ public class EyesisCorrectionParameters {
if (properties.getProperty(prefix+"clt_batch_assign")!= null) this.clt_batch_assign=Boolean.parseBoolean(properties.getProperty(prefix+"clt_batch_assign")); if (properties.getProperty(prefix+"clt_batch_assign")!= null) this.clt_batch_assign=Boolean.parseBoolean(properties.getProperty(prefix+"clt_batch_assign"));
if (properties.getProperty(prefix+"clt_batch_gen3d")!= null) this.clt_batch_gen3d=Boolean.parseBoolean(properties.getProperty(prefix+"clt_batch_gen3d")); if (properties.getProperty(prefix+"clt_batch_gen3d")!= null) this.clt_batch_gen3d=Boolean.parseBoolean(properties.getProperty(prefix+"clt_batch_gen3d"));
if (properties.getProperty(prefix+"clt_batch_dbg1")!= null) this.clt_batch_dbg1=Boolean.parseBoolean(properties.getProperty(prefix+"clt_batch_dbg1")); if (properties.getProperty(prefix+"clt_batch_dbg1")!= null) this.clt_batch_dbg1=Boolean.parseBoolean(properties.getProperty(prefix+"clt_batch_dbg1"));
}
public boolean showDialog(String title) {
GenericDialog gd = new GenericDialog(title);
gd.addCheckbox ("Splt into Bayer stack (if false will exit)", this.split);
gd.addCheckbox ("Apply vignetting/color correction to source files",this.vignetting);
gd.addCheckbox ("Replace hot/warm/cold pixels with average of neighbors",this.pixelDefects);
gd.addNumericField("Pixel difference thershold to consider it \"bad\" on 255.0 scale (0 - use all)", this.pixelDefectsThreshold, 2,6,"8.0");
String [] choices={"none","absolute","relative"};
if (this.exposureCorrectionMode<0) this.exposureCorrectionMode=0;
else if (this.exposureCorrectionMode>=choices.length) this.exposureCorrectionMode=choices.length-1;
gd.addChoice ("Exposure correction",choices, choices[this.exposureCorrectionMode]);
gd.addNumericField("Reference exposure (effective only in \"absolute\" mode)", 1000.0*this.referenceExposure, 2,6,"ms");
gd.addNumericField("Exposure scale (effective only in \"relative\" mode) 0 - darken, 1 - lighten", this.relativeExposure, 3,5,"");
gd.addCheckbox ("De-mosaic (if false will exit)", this.debayer);
gd.addCheckbox ("Show de-mosaic middle-frequency 'energy", this.showDebayerEnergy);
gd.addCheckbox ("Save de-mosaic middle-frequency 'energy", this.saveDebayerEnergy);
gd.addCheckbox ("Sharpen (convolve with calibration kernels)", this.deconvolve);
gd.addCheckbox ("Denoise (convolve with Gaussian in smooth areas)", this.combine);
gd.addCheckbox ("Show denoise mask (white - use hi-res, black - low-res)", this.showDenoiseMask);
gd.addCheckbox ("Save denoise mask (white - use hi-res, black - low-res)", this.saveDenoiseMask);
gd.addCheckbox ("Show kernel noise gains", this.showNoiseGains);
gd.addCheckbox ("Save kernel noise gains", this.saveNoiseGains);
gd.addCheckbox ("Convert colors", this.colorProc);
gd.addCheckbox ("Fix blue leak", this.blueProc);
gd.addCheckbox ("Show chroma denoise mask (white - use hi-res, black - low-res)", this.showChromaDenoiseMask);
gd.addCheckbox ("Save chroma denoise mask (white - use hi-res, black - low-res)", this.saveChromaDenoiseMask);
gd.addCheckbox ("Rotate result image", this.rotate);
gd.addCheckbox ("Crop result image to the original size", this.crop);
String [] equirectangularFormatChoices={"RGBA 8-bit","RGBA 16-bit","RGBA 32-bit integer","RGBA 32-bit float","ImageJ stack"};
int [] equirectangularFormats={0,1,2,3,4};
int equirectangularFormatIndex=0;
for ( int i=0;i<equirectangularFormats.length;i++) if (equirectangularFormats[i]==this.equirectangularFormat){
equirectangularFormatIndex=i;
break;
}
gd.addChoice ("Equirectangular output format",equirectangularFormatChoices, equirectangularFormatChoices[equirectangularFormatIndex]);
gd.addNumericField("Map 1.0 intensity to this fraction of the full range 8/16/32-bit integer mode output", 100*this.outputRangeInt, 2,6,"%");
gd.addNumericField("Map 1.0 intensity to this value in 32-bit floating point output mode", this.outputRangeFP, 2,6,"");
gd.addCheckbox ("Encode ImageJ specific Info metadata to the output file TIFF header", this.imageJTags);
gd.addCheckbox ("Convert to RGB48", this.toRGB);
gd.addCheckbox ("Convert to 8 bit RGB (and save JPEG if save is enabled)", this.jpeg);
gd.addCheckbox ("Use PNG instead of TIFF for 32 bit (8 per color) RGBA", this.png);
gd.addCheckbox ("Save the result to file system", this.save);
gd.addCheckbox ("Save 16-bit tiff if the result is 8 bit", this.save16);
gd.addCheckbox ("Save 32-bit tiff if the result is 8 or 16 bit", this.save32);
gd.addCheckbox ("Show the result image", this.show);
gd.addNumericField("JPEG quality (%)", this.JPEG_quality,0);
gd.addNumericField("JPEG scale (%)", 100* this.JPEG_scale,0);
gd.addCheckbox ("Warp results to equirectangular", this.equirectangular);
gd.addCheckbox ("Calculate distances in overlapping areas", this.zcorrect);
gd.addCheckbox ("Save current settings with results", this.saveSettings);
gd.addStringField ("Source files directory", this.sourceDirectory, 60);
gd.addCheckbox ("Select source directory", false);
gd.addStringField ("Sensor calibration directory", this.sensorDirectory, 60);
gd.addCheckbox ("Select sensor calibration directory", false);
gd.addStringField ("Aberration kernels (sharp) directory", this.sharpKernelDirectory, 60);
gd.addCheckbox ("Select aberration kernels (sharp) directory", false);
gd.addStringField ("Aberration kernels (smooth) directory", this.smoothKernelDirectory, 60);
gd.addCheckbox ("Select aberration kernels (smooth) directory", false);
gd.addStringField ("Aberration kernels for DCT directory", this.dctKernelDirectory, 60);
gd.addCheckbox ("Select aberration kernels for DCT directory", false);
gd.addStringField ("Aberration kernels for CLT directory", this.cltKernelDirectory, 60);
gd.addCheckbox ("Select aberration kernels for CLT directory", false);
gd.addStringField ("x3d model version", this.x3dModelVersion, 20); // 10a
gd.addStringField ("x3d output directory", this.x3dDirectory, 60);
gd.addCheckbox ("Select x3d output directory", false);
gd.addCheckbox ("Use individual subdirectory for each 3d model (timestamp as name)", this.use_x3d_subdirs);
gd.addStringField ("x3d subdirectory prefix", this.x3dSubdirPrefix, 10);
gd.addStringField ("x3d subdirectory suffix", this.x3dSubdirSuffix, 10);
gd.addStringField("Equirectangular maps directory (may be empty)", this.equirectangularDirectory, 60);
gd.addCheckbox("Select equirectangular maps directory", false);
gd.addStringField("Results directory", this.resultsDirectory, 60);
gd.addCheckbox("Select results directory", false);
gd.addStringField("Source files prefix", this.sourcePrefix, 60);
gd.addStringField("Source files suffix", this.sourceSuffix, 60);
gd.addNumericField("First subcamera (in the source filename)", this.firstSubCamera, 0);
gd.addStringField("Sensor files prefix", this.sensorPrefix, 40);
gd.addStringField("Sensor files suffix", this.sensorSuffix, 40);
gd.addStringField("Kernel files (sharp) prefix", this.sharpKernelPrefix, 40);
gd.addStringField("Kernel files (sharp) suffix", this.sharpKernelSuffix, 40);
gd.addStringField("Kernel files (smooth) prefix", this.smoothKernelPrefix, 40);
gd.addStringField("Kernel files (smooth) suffix", this.smoothKernelSuffix, 40);
gd.addStringField("DCT kernel files prefix", this.dctKernelPrefix, 40);
gd.addStringField("DCT symmetical kernel files", this.dctSymSuffix, 40);
gd.addStringField("DCT asymmetrical kernel files suffix", this.dctAsymSuffix, 40);
gd.addStringField("CLT kernel files prefix", this.cltKernelPrefix, 40);
gd.addStringField("CLT kernel files suffix", this.cltSuffix, 40);
gd.addStringField("Equirectangular maps prefix", this.equirectangularPrefix, 40);
gd.addStringField("Equirectangular maps suffix", this.equirectangularSuffix, 40);
gd.addCheckbox("Cut rolling-over equirectangular images in two", this.equirectangularCut);
gd.addStringField("Plane projection map prefix", this.planeMapPrefix, 40);
gd.addStringField("Plane projection map suffix", this.planeMapSuffix, 40);
gd.addCheckbox("Use projection to a common plane instead of the equirectangular", this.usePlaneProjection);
gd.addCheckbox("Save de-warped images as JPEG instead of TIFF", this.planeAsJPEG);
// gd.addStringField("Suffix for the second part of rolled-over equirectangular images", this.equirectangularSuffixA, 40);
gd.addCheckbox ("Remove unused sensor data", this.removeUnusedSensorData);
gd.addCheckbox ("Swap top and equator images", this.swapSubchannels01);
WindowTools.addScrollBars(gd);
gd.showDialog();
if (gd.wasCanceled()) return false;
this.split= gd.getNextBoolean();
this.vignetting= gd.getNextBoolean();
this.pixelDefects= gd.getNextBoolean();
this.pixelDefectsThreshold= gd.getNextNumber();
this.exposureCorrectionMode= gd.getNextChoiceIndex();
this.referenceExposure=0.001*gd.getNextNumber();
this.relativeExposure= gd.getNextNumber();
this.debayer= gd.getNextBoolean();
this.showDebayerEnergy= gd.getNextBoolean();
this.saveDebayerEnergy= gd.getNextBoolean();
this.deconvolve= gd.getNextBoolean();
this.combine= gd.getNextBoolean();
this.showDenoiseMask= gd.getNextBoolean();
this.saveDenoiseMask= gd.getNextBoolean();
this.showNoiseGains= gd.getNextBoolean();
this.saveNoiseGains= gd.getNextBoolean();
this.colorProc= gd.getNextBoolean();
this.blueProc= gd.getNextBoolean();
this.showChromaDenoiseMask= gd.getNextBoolean();
this.saveChromaDenoiseMask= gd.getNextBoolean();
this.rotate= gd.getNextBoolean();
this.crop= gd.getNextBoolean();
this.equirectangularFormat= equirectangularFormats[gd.getNextChoiceIndex()];
this.outputRangeInt=0.01*gd.getNextNumber();
this.outputRangeFP= gd.getNextNumber();
this.imageJTags= gd.getNextBoolean();
this.toRGB= gd.getNextBoolean();
this.jpeg= gd.getNextBoolean();
this.png= gd.getNextBoolean();
this.save= gd.getNextBoolean();
this.save16= gd.getNextBoolean();
this.save32= gd.getNextBoolean();
this.show= gd.getNextBoolean();
this.JPEG_quality=(int) gd.getNextNumber();
this.JPEG_scale= 0.01*gd.getNextNumber();
this.equirectangular= gd.getNextBoolean();
this.zcorrect= gd.getNextBoolean();
this.saveSettings= gd.getNextBoolean();
this.sourceDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectSourceDirectory(false, false); // copy common parameters to the auxiliary camera ones
this.sensorDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectSensorDirectory(false, false); updateAuxFromMain();
this.sharpKernelDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectSharpKernelDirectory(false, false); String aux_prefix = prefix + AUX_PREFIX;
this.smoothKernelDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectSmoothKernelDirectory(false, true); if (properties.getProperty(aux_prefix+"sensorDirectory")!= null) this.aux_camera.sensorDirectory=properties.getProperty(aux_prefix+"sensorDirectory");
this.dctKernelDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectDCTKernelDirectory(false, true); if (properties.getProperty(aux_prefix+"cltKernelDirectory")!= null) this.aux_camera.cltKernelDirectory=properties.getProperty(aux_prefix+"cltKernelDirectory");
this.cltKernelDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectCLTKernelDirectory(false, true); if (properties.getProperty(aux_prefix+"resultsDirectory")!= null) this.aux_camera.resultsDirectory=properties.getProperty(aux_prefix+"resultsDirectory");
this.x3dModelVersion= gd.getNextString(); // 10a if (properties.getProperty(aux_prefix+"firstSubCamera")!= null) this.aux_camera.firstSubCamera=Integer.parseInt(properties.getProperty(aux_prefix+"firstSubCamera"));
this.x3dDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectX3dDirectory(false, true); if (properties.getProperty(aux_prefix+"numSubCameras")!= null) this.aux_camera.numSubCameras=Integer.parseInt(properties.getProperty(aux_prefix+"numSubCameras"));
this.use_x3d_subdirs= gd.getNextBoolean(); if (properties.getProperty(aux_prefix+"sensorPrefix")!= null) this.aux_camera.sensorPrefix=properties.getProperty(aux_prefix+"sensorPrefix");
if (properties.getProperty(aux_prefix+"sensorSuffix")!= null) this.aux_camera.sensorSuffix=properties.getProperty(aux_prefix+"sensorSuffix");
this.x3dSubdirPrefix= gd.getNextString(); if (properties.getProperty(aux_prefix+"cltKernelPrefix")!= null) this.aux_camera.cltKernelPrefix=properties.getProperty(aux_prefix+"cltKernelPrefix");
this.x3dSubdirSuffix= gd.getNextString(); if (properties.getProperty(aux_prefix+"cltSuffix")!= null) this.aux_camera.cltSuffix=properties.getProperty(aux_prefix+"cltSuffix");
this.equirectangularDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectEquirectangularDirectory(false, false);
this.resultsDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectResultsDirectory(false, true);
this.sourcePrefix= gd.getNextString();
this.sourceSuffix= gd.getNextString();
this.firstSubCamera= (int) gd.getNextNumber();
this.sensorPrefix= gd.getNextString();
this.sensorSuffix= gd.getNextString();
this.sharpKernelPrefix= gd.getNextString();
this.sharpKernelSuffix= gd.getNextString();
this.smoothKernelPrefix= gd.getNextString();
this.smoothKernelSuffix= gd.getNextString();
this.dctKernelPrefix= gd.getNextString();
this.dctSymSuffix= gd.getNextString();
this.dctAsymSuffix= gd.getNextString();
this.cltKernelPrefix= gd.getNextString();
this.cltSuffix= gd.getNextString();
this.equirectangularPrefix= gd.getNextString();
this.equirectangularSuffix= gd.getNextString();
this.equirectangularCut= gd.getNextBoolean();
this.planeMapPrefix= gd.getNextString();
this.planeMapSuffix= gd.getNextString();
this.usePlaneProjection= gd.getNextBoolean();
this.planeAsJPEG= gd.getNextBoolean();
// this.equirectangularSuffixA= gd.getNextString();
this.removeUnusedSensorData= gd.getNextBoolean();
this.swapSubchannels01= gd.getNextBoolean();
return true;
} }
public boolean showJDialog(String title) { public boolean showJDialog(String title) {
// GenericDialog gd = new GenericDialog(title); // GenericDialog gd = new GenericDialog(title);
GenericJTabbedDialog gd = new GenericJTabbedDialog(title ,1000, 900); GenericJTabbedDialog gd = new GenericJTabbedDialog(title ,1000, 900);
...@@ -632,7 +603,8 @@ public class EyesisCorrectionParameters { ...@@ -632,7 +603,8 @@ public class EyesisCorrectionParameters {
gd.addTab("Prefix/suffix","Prefixes and suffixes for various file types"); gd.addTab("Prefix/suffix","Prefixes and suffixes for various file types");
gd.addStringField("Source files prefix", this.sourcePrefix, 60); gd.addStringField("Source files prefix", this.sourcePrefix, 60);
gd.addStringField("Source files suffix", this.sourceSuffix, 60); gd.addStringField("Source files suffix", this.sourceSuffix, 60);
gd.addNumericField("First subcamera (in the source filename)", this.firstSubCamera, 0); gd.addNumericField("First subcamera (in the source filenames)", this.firstSubCamera, 0);
gd.addNumericField("Number of subcameras in this camera (in the source filenames)", this.numSubCameras, 0);
gd.addStringField("Sensor files prefix", this.sensorPrefix, 40); gd.addStringField("Sensor files prefix", this.sensorPrefix, 40);
gd.addStringField("Sensor files suffix", this.sensorSuffix, 40); gd.addStringField("Sensor files suffix", this.sensorSuffix, 40);
...@@ -721,6 +693,7 @@ public class EyesisCorrectionParameters { ...@@ -721,6 +693,7 @@ public class EyesisCorrectionParameters {
this.sourcePrefix= gd.getNextString(); this.sourcePrefix= gd.getNextString();
this.sourceSuffix= gd.getNextString(); this.sourceSuffix= gd.getNextString();
this.firstSubCamera= (int) gd.getNextNumber(); this.firstSubCamera= (int) gd.getNextNumber();
this.numSubCameras= (int) gd.getNextNumber();
this.sensorPrefix= gd.getNextString(); this.sensorPrefix= gd.getNextString();
this.sensorSuffix= gd.getNextString(); this.sensorSuffix= gd.getNextString();
this.sharpKernelPrefix= gd.getNextString(); this.sharpKernelPrefix= gd.getNextString();
...@@ -746,20 +719,18 @@ public class EyesisCorrectionParameters { ...@@ -746,20 +719,18 @@ public class EyesisCorrectionParameters {
} }
public boolean showCLTDialog(String title, public boolean showCLTBatchDialog(String title,
CLTParameters clt_parameters) { CLTParameters clt_parameters) {
GenericJTabbedDialog gd = new GenericJTabbedDialog(title,1000,800); GenericJTabbedDialog gd = new GenericJTabbedDialog(title,1000,1000);
updateAuxFromMain();
gd.addTab ("File paths", "Select files and directories paths (common to main and optional auxilliary)");
gd.addMessage ("============ Common to the main and optional auxiliary camera============");
gd.addTab ("File paths", "Select files and directories pahs");
gd.addCheckbox ("Save current settings with results", this.saveSettings); // 1 gd.addCheckbox ("Save current settings with results", this.saveSettings); // 1
gd.addStringField ("Source files directory", this.sourceDirectory, 60); // 2 gd.addStringField ("Source files directory", this.sourceDirectory, 60); // 2
gd.addCheckbox ("Select source directory", false); // 3 gd.addCheckbox ("Select source directory", false); // 3
gd.addStringField ("Sensor calibration directory", this.sensorDirectory, 60); // 4
gd.addCheckbox ("Select sensor calibration directory", false); // 5
gd.addStringField ("Aberration kernels for CLT directory", this.cltKernelDirectory, 60); // 6
gd.addCheckbox ("Select aberration kernels for CLT directory", false); // 7
gd.addStringField ("x3d model version", this.x3dModelVersion, 60); // 10a gd.addStringField ("x3d model version", this.x3dModelVersion, 60); // 10a
gd.addStringField ("x3d output directory", this.x3dDirectory, 60); // 8 gd.addStringField ("x3d output directory", this.x3dDirectory, 60); // 8
...@@ -767,30 +738,53 @@ public class EyesisCorrectionParameters { ...@@ -767,30 +738,53 @@ public class EyesisCorrectionParameters {
gd.addCheckbox ("Use individual subdirectory for each 3d model (timestamp as name)", this.use_x3d_subdirs); //10 gd.addCheckbox ("Use individual subdirectory for each 3d model (timestamp as name)", this.use_x3d_subdirs); //10
gd.addStringField ("Source files prefix", this.sourcePrefix, 60); // 13
gd.addStringField ("Source files suffix", this.sourceSuffix, 60); // 14
gd.addMessage ("============ Main camera============");
gd.addStringField ("Sensor calibration directory", this.sensorDirectory, 60); // 4
gd.addCheckbox ("Select sensor calibration directory", false); // 5
gd.addStringField ("Aberration kernels for CLT directory", this.cltKernelDirectory, 60); // 6
gd.addCheckbox ("Select aberration kernels for CLT directory", false); // 7
gd.addStringField ("Results directory", this.resultsDirectory, 60); // 11 gd.addStringField ("Results directory", this.resultsDirectory, 60); // 11
gd.addCheckbox ("Select results directory", false); // 12 gd.addCheckbox ("Select results directory", false); // 12
gd.addStringField ("Source files prefix", this.sourcePrefix, 60); // 13
gd.addStringField ("Source files suffix", this.sourceSuffix, 60); // 14
gd.addNumericField("First subcamera (in the source filename)", this.firstSubCamera, 0); // 15 gd.addNumericField("First subcamera (in the source filename)", this.firstSubCamera, 0); // 15
gd.addNumericField("Number of subcameras in this camera (in the source filenames)", this.numSubCameras, 0); // 16
gd.addStringField ("Sensor files prefix", this.sensorPrefix, 40); // 17
gd.addStringField ("Sensor files suffix", this.sensorSuffix, 40); // 18
gd.addStringField ("CLT kernel files prefix", this.cltKernelPrefix, 40); // 19
gd.addStringField ("CLT kernel files suffix", this.cltSuffix, 40); // 20
gd.addMessage ("============ Auxiliary camera============");
gd.addStringField ("Aux sensor calibration directory", this.aux_camera.sensorDirectory, 60); // 4b
gd.addCheckbox ("Select aux sensor calibration directory", false); // 5b
gd.addStringField ("Aberration kernels for aux CLT directory", this.aux_camera.cltKernelDirectory, 60); // 6b
gd.addCheckbox ("Select aberration kernels for aux CLT directory", false); // 7b
gd.addStringField ("Aux results directory", this.aux_camera.resultsDirectory, 60); // 11b
gd.addCheckbox ("Select aux results directory", false); // 12b
gd.addNumericField("First aux subcamera (in the source filename)", this.aux_camera.firstSubCamera, 0); // 15b
gd.addNumericField("Number of aux subcameras in this camera (in the source filenames)", this.aux_camera.numSubCameras, 0); // 16b
gd.addStringField ("Aux sensor files prefix", this.aux_camera.sensorPrefix, 40); // 17b
gd.addStringField ("Aux sensor files suffix", this.aux_camera.sensorSuffix, 40); // 18b
gd.addStringField ("Aux CLT kernel files prefix", this.aux_camera.cltKernelPrefix, 40); // 19b
gd.addStringField ("Aux CLT kernel files suffix", this.aux_camera.cltSuffix, 40); // 20b
gd.addStringField("Sensor files prefix", this.sensorPrefix, 40); // 16
gd.addStringField("Sensor files suffix", this.sensorSuffix, 40); // 17
gd.addStringField("CLT kernel files prefix", this.cltKernelPrefix, 40); // 18
gd.addStringField("CLT kernel files suffix", this.cltSuffix, 40); // 19
gd.addTab ("Batch", "Select Batch parameters"); gd.addTab ("Batch", "Select Batch parameters");
gd.addCheckbox ("Apply (and disable) manual pixel shift", this.clt_batch_apply_man); // 20 gd.addCheckbox ("Apply (and disable) manual pixel shift", this.clt_batch_apply_man); // 21
gd.addCheckbox ("Calibrate extrinsic parameters for each set", this.clt_batch_extrinsic); // 21 gd.addCheckbox ("Calibrate extrinsic parameters for each set", this.clt_batch_extrinsic); // 22
gd.addCheckbox ("Calculate fine polynomial correction for each set", this.clt_batch_poly); // 22 gd.addCheckbox ("Calculate fine polynomial correction for each set", this.clt_batch_poly); // 23
gd.addCheckbox ("Create a set of 4 images, usually for disparity = 0", this.clt_batch_4img); // 23 gd.addCheckbox ("Create a set of 4 images, usually for disparity = 0", this.clt_batch_4img); // 24
gd.addCheckbox ("1-st step of 3d reconstruction - explore disparities for each tile", this.clt_batch_explore); // 24 gd.addCheckbox ("1-st step of 3d reconstruction - explore disparities for each tile", this.clt_batch_explore); // 25
gd.addCheckbox ("Create super-tile 2.5d surfaces", this.clt_batch_surf); // 25 gd.addCheckbox ("Create super-tile 2.5d surfaces", this.clt_batch_surf); // 26
gd.addCheckbox ("Assign tiles to surfaces", this.clt_batch_assign); // 26 gd.addCheckbox ("Assign tiles to surfaces", this.clt_batch_assign); // 27
gd.addCheckbox ("Generate 3d output: x3d and/or obj+mtl", this.clt_batch_gen3d); // 27 gd.addCheckbox ("Generate 3d output: x3d and/or obj+mtl", this.clt_batch_gen3d); // 28
gd.addCheckbox ("Generate debug images if a single set is selected", this.clt_batch_dbg1); // 28 gd.addCheckbox ("Generate debug images if a single set is selected", this.clt_batch_dbg1); // 29
if (clt_parameters != null) { if (clt_parameters != null) {
// gd.addMessage ("============ selected CLT parameters ============"); // gd.addMessage ("============ selected CLT parameters ============");
gd.addTab ("CLT", "Modify selected CLT parameters"); gd.addTab ("CLT", "Modify selected CLT parameters");
...@@ -810,29 +804,43 @@ public class EyesisCorrectionParameters { ...@@ -810,29 +804,43 @@ public class EyesisCorrectionParameters {
this.saveSettings= gd.getNextBoolean(); // 1 this.saveSettings= gd.getNextBoolean(); // 1
this.sourceDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectSourceDirectory(false, false); // 3 this.sourceDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectSourceDirectory(false, false); // 3
this.sensorDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectSensorDirectory(false, false); // 5
this.cltKernelDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectCLTKernelDirectory(false, true); // 7
this.x3dModelVersion= gd.getNextString(); // 10a this.x3dModelVersion= gd.getNextString(); // 10a
this.x3dDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectX3dDirectory(false, true); // 9 this.x3dDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectX3dDirectory(false, true); // 9
this.use_x3d_subdirs= gd.getNextBoolean(); // 10 this.use_x3d_subdirs= gd.getNextBoolean(); // 10
this.resultsDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectResultsDirectory(false, true); // 12
this.sourcePrefix= gd.getNextString(); // 13 this.sourcePrefix= gd.getNextString(); // 13
this.sourceSuffix= gd.getNextString(); // 14 this.sourceSuffix= gd.getNextString(); // 14
// main camera
this.sensorDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectSensorDirectory(false, false); // 5
this.cltKernelDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectCLTKernelDirectory(false, true); // 7
this.resultsDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectResultsDirectory(false, true); // 12
this.firstSubCamera= (int) gd.getNextNumber(); // 15 this.firstSubCamera= (int) gd.getNextNumber(); // 15
this.sensorPrefix= gd.getNextString(); // 16 this.numSubCameras= (int) gd.getNextNumber(); // 16
this.sensorSuffix= gd.getNextString(); // 17 this.sensorPrefix= gd.getNextString(); // 17
this.cltKernelPrefix= gd.getNextString(); // 18 this.sensorSuffix= gd.getNextString(); // 18
this.cltSuffix= gd.getNextString(); // 19 this.cltKernelPrefix= gd.getNextString(); // 19
this.cltSuffix= gd.getNextString(); // 20
this.clt_batch_apply_man= gd.getNextBoolean(); // 20
this.clt_batch_extrinsic= gd.getNextBoolean(); // 21 // aux camera
this.clt_batch_poly= gd.getNextBoolean(); // 22 this.aux_camera.sensorDirectory= gd.getNextString(); if (gd.getNextBoolean()) aux_camera.selectSensorDirectory(false, false); // 5b
this.clt_batch_4img= gd.getNextBoolean(); // 23 this.aux_camera.cltKernelDirectory= gd.getNextString(); if (gd.getNextBoolean()) aux_camera.selectCLTKernelDirectory(false, true); // 7b
this.clt_batch_explore= gd.getNextBoolean(); // 24 this.aux_camera.resultsDirectory= gd.getNextString(); if (gd.getNextBoolean()) aux_camera.selectResultsDirectory(false, true); // 12b
this.clt_batch_surf= gd.getNextBoolean(); // 25 this.aux_camera.firstSubCamera= (int) gd.getNextNumber(); // 15b
this.clt_batch_assign= gd.getNextBoolean(); // 26 this.aux_camera.numSubCameras= (int) gd.getNextNumber(); // 16b
this.clt_batch_gen3d= gd.getNextBoolean(); // 27 this.aux_camera.sensorPrefix= gd.getNextString(); // 17b
this.clt_batch_dbg1= gd.getNextBoolean(); // 28 this.aux_camera.sensorSuffix= gd.getNextString(); // 18b
this.aux_camera.cltKernelPrefix= gd.getNextString(); // 19b
this.aux_camera.cltSuffix= gd.getNextString(); // 20b
this.clt_batch_apply_man= gd.getNextBoolean(); // 21
this.clt_batch_extrinsic= gd.getNextBoolean(); // 22
this.clt_batch_poly= gd.getNextBoolean(); // 23
this.clt_batch_4img= gd.getNextBoolean(); // 24
this.clt_batch_explore= gd.getNextBoolean(); // 25
this.clt_batch_surf= gd.getNextBoolean(); // 26
this.clt_batch_assign= gd.getNextBoolean(); // 27
this.clt_batch_gen3d= gd.getNextBoolean(); // 28
this.clt_batch_dbg1= gd.getNextBoolean(); // 29
if (clt_parameters != null) { if (clt_parameters != null) {
clt_parameters.grow_disp_max = gd.getNextNumber(); clt_parameters.grow_disp_max = gd.getNextNumber();
clt_parameters.gain_equalize = gd.getNextBoolean(); clt_parameters.gain_equalize = gd.getNextBoolean();
...@@ -1723,14 +1731,6 @@ public class EyesisCorrectionParameters { ...@@ -1723,14 +1731,6 @@ public class EyesisCorrectionParameters {
public double alpha_min = 0.0; public double alpha_min = 0.0;
public double alpha_max = 1.0; public double alpha_max = 1.0;
/* public RGBParameters(double r_min, double g_min, double b_min, double r_max, double g_max, double b_max) {
this.r_min = r_min;
this.g_min = g_min;
this.b_min = b_min;
this.r_max = r_max;
this.g_max = g_max;
this.b_max = b_max;
} */
public RGBParameters(double r_min, double g_min, double b_min, double r_max, double g_max, double b_max, double alpha_min, double alpha_max) { public RGBParameters(double r_min, double g_min, double b_min, double r_max, double g_max, double b_max, double alpha_min, double alpha_max) {
this.r_min = r_min; this.r_min = r_min;
this.g_min = g_min; this.g_min = g_min;
......
src/main/java/EyesisCorrections.java
View file @ f19a4557
...@@ -25,6 +25,11 @@ ...@@ -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; ...@@ -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;
...@@ -84,14 +83,43 @@ public class EyesisCorrections { ...@@ -84,14 +83,43 @@ 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());
// 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){ if (correctionsParameters.removeUnusedSensorData){
for (int nChn=0;nChn< this.usedChannels.length; nChn++) if (!this.usedChannels[nChn]) this.pixelMapping.removeChannel(nChn); for (int nChn=0;nChn< this.usedChannels.length; nChn++) if (!this.usedChannels[nChn]) this.pixelMapping.removeChannel(nChn);
} }
...@@ -108,8 +136,8 @@ public class EyesisCorrections { ...@@ -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 { ...@@ -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 { ...@@ -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 { ...@@ -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 { ...@@ -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 { ...@@ -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 { ...@@ -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
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 { ...@@ -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 { ...@@ -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) {
......
src/main/java/QuadCLT.java
View file @ f19a4557
...@@ -44,9 +44,11 @@ import ij.process.ImageProcessor; ...@@ -44,9 +44,11 @@ import ij.process.ImageProcessor;
public class QuadCLT { public class QuadCLT {
static String [] fine_corr_coeff_names = {"A","B","C","D","E","F"}; static String [] fine_corr_coeff_names = {"A","B","C","D","E","F"};
static String [] fine_corr_dir_names = {"X","Y"}; static String [] fine_corr_dir_names = {"X","Y"};
static String prefix = "EYESIS_DCT."; // change later (first on save) public static String PREFIX = "EYESIS_DCT."; // change later (first on save)
public static String PREFIX_AUX = "EYESIS_DCT_AUX."; // change later (first on save)
static int QUAD = 4; // number of cameras static int QUAD = 4; // number of cameras
public Properties properties = null; public Properties properties = null;
// public String properties_prefix = "EYESIS_DCT.";
public EyesisCorrections eyesisCorrections = null; public EyesisCorrections eyesisCorrections = null;
public EyesisCorrectionParameters.CorrectionParameters correctionsParameters=null; public EyesisCorrectionParameters.CorrectionParameters correctionsParameters=null;
double [][][][][][] clt_kernels = null; double [][][][][][] clt_kernels = null;
...@@ -86,6 +88,7 @@ public class QuadCLT { ...@@ -86,6 +88,7 @@ public class QuadCLT {
} }
public QuadCLT( public QuadCLT(
String prefix,
Properties properties, Properties properties,
EyesisCorrections eyesisCorrections, EyesisCorrections eyesisCorrections,
EyesisCorrectionParameters.CorrectionParameters correctionsParameters EyesisCorrectionParameters.CorrectionParameters correctionsParameters
...@@ -93,11 +96,18 @@ public class QuadCLT { ...@@ -93,11 +96,18 @@ public class QuadCLT {
this.eyesisCorrections= eyesisCorrections; this.eyesisCorrections= eyesisCorrections;
this.correctionsParameters = correctionsParameters; this.correctionsParameters = correctionsParameters;
this.properties = properties; this.properties = properties;
getProperties(); // this.properties_prefix = prefix;
// System.out.println("new QuadCLT(), prefix = "+prefix);
getProperties(prefix);
} }
// TODO:Add saving just calibration // TODO:Add saving just calibration
public void setProperties(){ // save
// public void setProperties(){
// setProperties(this.properties_prefix);
// }
public void setProperties(String prefix){ // save
// System.out.println("setProperties("+prefix+")");
for (int n = 0; n < fine_corr.length; n++){ for (int n = 0; n < fine_corr.length; n++){
for (int d = 0; d < fine_corr[n].length; d++){ for (int d = 0; d < fine_corr[n].length; d++){
for (int i = 0; i < fine_corr[n][d].length; i++){ for (int i = 0; i < fine_corr[n][d].length; i++){
...@@ -113,8 +123,44 @@ public class QuadCLT { ...@@ -113,8 +123,44 @@ public class QuadCLT {
for (int i = 0; i < GeometryCorrection.CORR_NAMES.length; i++){ for (int i = 0; i < GeometryCorrection.CORR_NAMES.length; i++){
String name = prefix+"extrinsic_corr_"+GeometryCorrection.CORR_NAMES[i]; String name = prefix+"extrinsic_corr_"+GeometryCorrection.CORR_NAMES[i];
properties.setProperty(name, gc.getCorrVector().toArray()[i]+""); properties.setProperty(name, gc.getCorrVector().toArray()[i]+"");
// System.out.println("setProperties():"+i+": setProperty("+name+","+gc.getCorrVector().toArray()[i]+"");
}
}
public void copyPropertiesFrom(Properties other_properties, String other_prefix, String this_prefix){ // save
// System.out.println("copyPropertiesFrom(other_properties, "+other_prefix+", this_prefix"+")");
for (int n = 0; n < fine_corr.length; n++){
for (int d = 0; d < fine_corr[n].length; d++){
for (int i = 0; i < fine_corr[n][d].length; i++){
String other_name = other_prefix+"fine_corr_"+n+fine_corr_dir_names[d]+fine_corr_coeff_names[i];
String this_name = this_prefix+"fine_corr_"+n+fine_corr_dir_names[d]+fine_corr_coeff_names[i];
if (other_properties.getProperty(other_name)!=null) {
this.fine_corr[n][d][i]=Double.parseDouble(other_properties.getProperty(other_name));
properties.setProperty(this_name, this.fine_corr[n][d][i]+"");
}
}
}
}
GeometryCorrection gc = geometryCorrection;
if (gc == null) { // if it was not yet created
gc = new GeometryCorrection(this.extrinsic_corr);
}
for (int i = 0; i < GeometryCorrection.CORR_NAMES.length; i++){
String other_name = other_prefix+"extrinsic_corr_"+GeometryCorrection.CORR_NAMES[i];
if (other_properties.getProperty(other_name)!=null) {
this.extrinsic_corr[i] = Double.parseDouble(other_properties.getProperty(other_name));
if (geometryCorrection != null){
geometryCorrection.getCorrVector().toArray()[i] = this.extrinsic_corr[i];
} }
} }
String this_name = this_prefix+"extrinsic_corr_"+GeometryCorrection.CORR_NAMES[i];
properties.setProperty(this_name, gc.getCorrVector().toArray()[i]+"");
// System.out.println("copyPropertiesFrom():"+i+": setProperty("+this_name+","+gc.getCorrVector().toArray()[i]+"");
}
// System.out.println("Done copyPropertiesFrom");
}
public void listGeometryCorrection(boolean full){ public void listGeometryCorrection(boolean full){
GeometryCorrection gc = geometryCorrection; GeometryCorrection gc = geometryCorrection;
...@@ -124,7 +170,8 @@ public class QuadCLT { ...@@ -124,7 +170,8 @@ public class QuadCLT {
gc.listGeometryCorrection(full); gc.listGeometryCorrection(full);
} }
public void getProperties(){ // restore public void getProperties(String prefix){ // restore
// System.out.println("getProperties("+prefix+")");
for (int n = 0; n < fine_corr.length; n++){ for (int n = 0; n < fine_corr.length; n++){
for (int d = 0; d < fine_corr[n].length; d++){ for (int d = 0; d < fine_corr[n].length; d++){
for (int i = 0; i < fine_corr[n][d].length; i++){ for (int i = 0; i < fine_corr[n][d].length; i++){
...@@ -138,6 +185,8 @@ public class QuadCLT { ...@@ -138,6 +185,8 @@ public class QuadCLT {
String name = prefix+"extrinsic_corr_"+GeometryCorrection.CORR_NAMES[i]; String name = prefix+"extrinsic_corr_"+GeometryCorrection.CORR_NAMES[i];
if (properties.getProperty(name)!=null) { if (properties.getProperty(name)!=null) {
this.extrinsic_corr[i] = Double.parseDouble(properties.getProperty(name)); this.extrinsic_corr[i] = Double.parseDouble(properties.getProperty(name));
// System.out.println("getProperties():"+i+": getProperty("+name+") -> "+properties.getProperty(name)+"");
if (geometryCorrection != null){ if (geometryCorrection != null){
geometryCorrection.getCorrVector().toArray()[i] = this.extrinsic_corr[i]; geometryCorrection.getCorrVector().toArray()[i] = this.extrinsic_corr[i];
} }
...@@ -1180,7 +1229,7 @@ public class QuadCLT { ...@@ -1180,7 +1229,7 @@ public class QuadCLT {
public void processCLTChannelImages( public void processCLTChannelImages(
EyesisCorrectionParameters.CLTParameters clt_parameters, EyesisCorrectionParameters.CLTParameters clt_parameters,
EyesisCorrectionParameters.DebayerParameters debayerParameters, EyesisCorrectionParameters.DebayerParameters debayerParameters,
EyesisCorrectionParameters.NonlinParameters nonlinParameters, // EyesisCorrectionParameters.NonlinParameters nonlinParameters,
EyesisCorrectionParameters.ColorProcParameters colorProcParameters, EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
CorrectionColorProc.ColorGainsParameters channelGainParameters, CorrectionColorProc.ColorGainsParameters channelGainParameters,
EyesisCorrectionParameters.RGBParameters rgbParameters, EyesisCorrectionParameters.RGBParameters rgbParameters,
...@@ -1282,7 +1331,7 @@ public class QuadCLT { ...@@ -1282,7 +1331,7 @@ public class QuadCLT {
imp_src, // should have properties "name"(base for saving results), "channel","path" imp_src, // should have properties "name"(base for saving results), "channel","path"
clt_parameters, clt_parameters,
debayerParameters, debayerParameters,
nonlinParameters, // nonlinParameters,
colorProcParameters, colorProcParameters,
channelGainParameters, channelGainParameters,
rgbParameters, rgbParameters,
...@@ -1314,7 +1363,7 @@ public class QuadCLT { ...@@ -1314,7 +1363,7 @@ public class QuadCLT {
// EyesisCorrectionParameters.DCTParameters dct_parameters, // EyesisCorrectionParameters.DCTParameters dct_parameters,
EyesisCorrectionParameters.CLTParameters clt_parameters, EyesisCorrectionParameters.CLTParameters clt_parameters,
EyesisCorrectionParameters.DebayerParameters debayerParameters, EyesisCorrectionParameters.DebayerParameters debayerParameters,
EyesisCorrectionParameters.NonlinParameters nonlinParameters, // EyesisCorrectionParameters.NonlinParameters nonlinParameters,
EyesisCorrectionParameters.ColorProcParameters colorProcParameters, EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
CorrectionColorProc.ColorGainsParameters channelGainParameters, CorrectionColorProc.ColorGainsParameters channelGainParameters,
EyesisCorrectionParameters.RGBParameters rgbParameters, EyesisCorrectionParameters.RGBParameters rgbParameters,
...@@ -1768,7 +1817,7 @@ public class QuadCLT { ...@@ -1768,7 +1817,7 @@ public class QuadCLT {
public void processCLTSets( public void processCLTSets(
EyesisCorrectionParameters.CLTParameters clt_parameters, EyesisCorrectionParameters.CLTParameters clt_parameters,
EyesisCorrectionParameters.DebayerParameters debayerParameters, EyesisCorrectionParameters.DebayerParameters debayerParameters,
EyesisCorrectionParameters.NonlinParameters nonlinParameters, // EyesisCorrectionParameters.NonlinParameters nonlinParameters,
EyesisCorrectionParameters.ColorProcParameters colorProcParameters, EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
CorrectionColorProc.ColorGainsParameters channelGainParameters, CorrectionColorProc.ColorGainsParameters channelGainParameters,
EyesisCorrectionParameters.RGBParameters rgbParameters, EyesisCorrectionParameters.RGBParameters rgbParameters,
...@@ -2008,7 +2057,7 @@ public class QuadCLT { ...@@ -2008,7 +2057,7 @@ public class QuadCLT {
imp_srcs[srcChannel], // should have properties "name"(base for saving results), "channel","path" imp_srcs[srcChannel], // should have properties "name"(base for saving results), "channel","path"
clt_parameters, clt_parameters,
debayerParameters, debayerParameters,
nonlinParameters, // nonlinParameters,
colorProcParameters, colorProcParameters,
channelGainParameters, channelGainParameters,
rgbParameters, rgbParameters,
...@@ -2042,7 +2091,7 @@ public class QuadCLT { ...@@ -2042,7 +2091,7 @@ public class QuadCLT {
ImagePlus imp_src, // should have properties "name"(base for saving results), "channel","path" ImagePlus imp_src, // should have properties "name"(base for saving results), "channel","path"
EyesisCorrectionParameters.CLTParameters clt_parameters, EyesisCorrectionParameters.CLTParameters clt_parameters,
EyesisCorrectionParameters.DebayerParameters debayerParameters, EyesisCorrectionParameters.DebayerParameters debayerParameters,
EyesisCorrectionParameters.NonlinParameters nonlinParameters, // EyesisCorrectionParameters.NonlinParameters nonlinParameters,
EyesisCorrectionParameters.ColorProcParameters colorProcParameters, EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
CorrectionColorProc.ColorGainsParameters channelGainParameters, CorrectionColorProc.ColorGainsParameters channelGainParameters,
EyesisCorrectionParameters.RGBParameters rgbParameters, EyesisCorrectionParameters.RGBParameters rgbParameters,
...@@ -2418,7 +2467,7 @@ public class QuadCLT { ...@@ -2418,7 +2467,7 @@ public class QuadCLT {
public void processCLTQuads( public void processCLTQuads(
EyesisCorrectionParameters.CLTParameters clt_parameters, EyesisCorrectionParameters.CLTParameters clt_parameters,
EyesisCorrectionParameters.DebayerParameters debayerParameters, EyesisCorrectionParameters.DebayerParameters debayerParameters,
EyesisCorrectionParameters.NonlinParameters nonlinParameters, // EyesisCorrectionParameters.NonlinParameters nonlinParameters,
EyesisCorrectionParameters.ColorProcParameters colorProcParameters, EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
CorrectionColorProc.ColorGainsParameters channelGainParameters, CorrectionColorProc.ColorGainsParameters channelGainParameters,
EyesisCorrectionParameters.RGBParameters rgbParameters, EyesisCorrectionParameters.RGBParameters rgbParameters,
...@@ -2655,7 +2704,7 @@ public class QuadCLT { ...@@ -2655,7 +2704,7 @@ public class QuadCLT {
imp_srcs, // [srcChannel], // should have properties "name"(base for saving results), "channel","path" imp_srcs, // [srcChannel], // should have properties "name"(base for saving results), "channel","path"
clt_parameters, clt_parameters,
debayerParameters, debayerParameters,
nonlinParameters, // nonlinParameters,
colorProcParameters, colorProcParameters,
channelGainParameters, channelGainParameters,
rgbParameters, rgbParameters,
...@@ -2680,7 +2729,7 @@ public class QuadCLT { ...@@ -2680,7 +2729,7 @@ public class QuadCLT {
ImagePlus [] imp_quad, // should have properties "name"(base for saving results), "channel","path" ImagePlus [] imp_quad, // should have properties "name"(base for saving results), "channel","path"
EyesisCorrectionParameters.CLTParameters clt_parameters, EyesisCorrectionParameters.CLTParameters clt_parameters,
EyesisCorrectionParameters.DebayerParameters debayerParameters, EyesisCorrectionParameters.DebayerParameters debayerParameters,
EyesisCorrectionParameters.NonlinParameters nonlinParameters, // EyesisCorrectionParameters.NonlinParameters nonlinParameters,
EyesisCorrectionParameters.ColorProcParameters colorProcParameters, EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
CorrectionColorProc.ColorGainsParameters channelGainParameters, CorrectionColorProc.ColorGainsParameters channelGainParameters,
EyesisCorrectionParameters.RGBParameters rgbParameters, EyesisCorrectionParameters.RGBParameters rgbParameters,
...@@ -2983,11 +3032,11 @@ public class QuadCLT { ...@@ -2983,11 +3032,11 @@ public class QuadCLT {
public void processCLTQuadCorrs( public void processCLTQuadCorrs(
EyesisCorrectionParameters.CLTParameters clt_parameters, EyesisCorrectionParameters.CLTParameters clt_parameters,
EyesisCorrectionParameters.DebayerParameters debayerParameters, EyesisCorrectionParameters.DebayerParameters debayerParameters,
EyesisCorrectionParameters.NonlinParameters nonlinParameters, // EyesisCorrectionParameters.NonlinParameters nonlinParameters,
EyesisCorrectionParameters.ColorProcParameters colorProcParameters, EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
CorrectionColorProc.ColorGainsParameters channelGainParameters, CorrectionColorProc.ColorGainsParameters channelGainParameters,
EyesisCorrectionParameters.RGBParameters rgbParameters, EyesisCorrectionParameters.RGBParameters rgbParameters,
EyesisCorrectionParameters.EquirectangularParameters equirectangularParameters, // EyesisCorrectionParameters.EquirectangularParameters equirectangularParameters,
int convolveFFTSize, // 128 - fft size, kernel size should be size/2 int convolveFFTSize, // 128 - fft size, kernel size should be size/2
final boolean apply_corr, // calculate and apply additional fine geometry correction final boolean apply_corr, // calculate and apply additional fine geometry correction
final boolean infinity_corr, // calculate and apply geometry correction at infinity final boolean infinity_corr, // calculate and apply geometry correction at infinity
...@@ -3015,7 +3064,7 @@ public class QuadCLT { ...@@ -3015,7 +3064,7 @@ public class QuadCLT {
if (correctionsParameters.isJP4()){ if (correctionsParameters.isJP4()){
int subCamera= channels[0]- correctionsParameters.firstSubCamera; // to match those in the sensor files int subCamera= channels[0]- correctionsParameters.firstSubCamera; // to match those in the sensor files
// removeUnusedSensorData should be off!? // removeUnusedSensorData should be off!?
channels=this.eyesisCorrections.pixelMapping.channelsForSubCamera(subCamera); channels=this.eyesisCorrections.pixelMapping.channelsForSubCamera(subCamera); // limit here or disable Error
} }
if (channels!=null){ if (channels!=null){
for (int i=0;i<channels.length;i++) if (eyesisCorrections.isChannelEnabled(channels[i])){ for (int i=0;i<channels.length;i++) if (eyesisCorrections.isChannelEnabled(channels[i])){
...@@ -3035,7 +3084,7 @@ public class QuadCLT { ...@@ -3035,7 +3084,7 @@ public class QuadCLT {
double [] referenceExposures=eyesisCorrections.calcReferenceExposures(debugLevel); // multiply each image by this and divide by individual (if not NaN) double [] referenceExposures=eyesisCorrections.calcReferenceExposures(debugLevel); // multiply each image by this and divide by individual (if not NaN)
int [][] fileIndices=new int [numImagesToProcess][2]; // file index, channel number int [][] fileIndices=new int [numImagesToProcess][2]; // file index, channel number
int index=0; int index=0;
for (int nFile=0;nFile<enabledFiles.length;nFile++){ for (int nFile=0;nFile<enabledFiles.length;nFile++){ // enabledFiles not used anymore?
if ((sourceFiles[nFile]!=null) && (sourceFiles[nFile].length()>1)) { if ((sourceFiles[nFile]!=null) && (sourceFiles[nFile].length()>1)) {
int [] channels={correctionsParameters.getChannelFromSourceTiff(sourceFiles[nFile])}; int [] channels={correctionsParameters.getChannelFromSourceTiff(sourceFiles[nFile])};
if (correctionsParameters.isJP4()){ if (correctionsParameters.isJP4()){
...@@ -3060,18 +3109,23 @@ public class QuadCLT { ...@@ -3060,18 +3109,23 @@ public class QuadCLT {
setNames.add(setName); setNames.add(setName);
setFiles.add(new ArrayList<Integer>()); setFiles.add(new ArrayList<Integer>());
} }
setFiles.get(setNames.indexOf(setName)).add(new Integer(nFile));
//FIXME - similar in other places, extract common code
// setFiles.get(setNames.indexOf(setName)).add(new Integer(nFile));
setFiles.get(setNames.indexOf(setName)).add(new Integer(iImage));
} }
for (int nSet = 0; nSet < setNames.size(); nSet++){ for (int nSet = 0; nSet < setNames.size(); nSet++){
int maxChn = 0; int maxChn = 0;
for (int i = 0; i < setFiles.get(nSet).size(); i++){ for (int i = 0; i < setFiles.get(nSet).size(); i++){
int chn = fileIndices[setFiles.get(nSet).get(i)][1]; int chn = fileIndices[setFiles.get(nSet).get(i)][1]; // wrong,
if (chn > maxChn) maxChn = chn; if (chn > maxChn) maxChn = chn;
} }
int [] channelFiles = new int[maxChn+1]; int [] channelFiles = new int[maxChn+1];
for (int i =0; i < channelFiles.length; i++) channelFiles[i] = -1; for (int i =0; i < channelFiles.length; i++) channelFiles[i] = -1;
for (int i = 0; i < setFiles.get(nSet).size(); i++){ for (int i = 0; i < setFiles.get(nSet).size(); i++){
channelFiles[fileIndices[setFiles.get(nSet).get(i)][1]] = setFiles.get(nSet).get(i); // channelFiles[fileIndices[setFiles.get(nSet).get(i)][1]] = setFiles.get(nSet).get(i);
channelFiles[fileIndices[setFiles.get(nSet).get(i)][1]] = fileIndices[setFiles.get(nSet).get(i)][0];
} }
ImagePlus [] imp_srcs = new ImagePlus[channelFiles.length]; ImagePlus [] imp_srcs = new ImagePlus[channelFiles.length];
...@@ -3311,7 +3365,7 @@ public class QuadCLT { ...@@ -3311,7 +3365,7 @@ public class QuadCLT {
saturation_imp, // boolean [][] saturation_imp, // (near) saturated pixels or null saturation_imp, // boolean [][] saturation_imp, // (near) saturated pixels or null
clt_parameters, clt_parameters,
debayerParameters, debayerParameters,
nonlinParameters, // nonlinParameters,
colorProcParameters, colorProcParameters,
channelGainParameters, channelGainParameters,
rgbParameters, rgbParameters,
...@@ -3557,7 +3611,7 @@ public class QuadCLT { ...@@ -3557,7 +3611,7 @@ public class QuadCLT {
boolean [][] saturation_imp, // (near) saturated pixels or null boolean [][] saturation_imp, // (near) saturated pixels or null
EyesisCorrectionParameters.CLTParameters clt_parameters, EyesisCorrectionParameters.CLTParameters clt_parameters,
EyesisCorrectionParameters.DebayerParameters debayerParameters, EyesisCorrectionParameters.DebayerParameters debayerParameters,
EyesisCorrectionParameters.NonlinParameters nonlinParameters, // EyesisCorrectionParameters.NonlinParameters nonlinParameters,
EyesisCorrectionParameters.ColorProcParameters colorProcParameters, EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
CorrectionColorProc.ColorGainsParameters channelGainParameters, CorrectionColorProc.ColorGainsParameters channelGainParameters,
EyesisCorrectionParameters.RGBParameters rgbParameters, EyesisCorrectionParameters.RGBParameters rgbParameters,
...@@ -4377,7 +4431,11 @@ public class QuadCLT { ...@@ -4377,7 +4431,11 @@ public class QuadCLT {
} }
public void show_fine_corr() public void show_fine_corr()
{ {
show_fine_corr( this.fine_corr, ""); show_fine_corr("");
}
public void show_fine_corr(String prefix)
{
show_fine_corr( this.fine_corr, prefix);
} }
public void show_fine_corr( public void show_fine_corr(
...@@ -4396,7 +4454,8 @@ public class QuadCLT { ...@@ -4396,7 +4454,8 @@ public class QuadCLT {
} }
} }
System.out.println(); System.out.println();
showExtrinsicCorr(); String name = (sadd.length() == 0)?"":("("+sadd+")");
showExtrinsicCorr(name);
} }
...@@ -4405,9 +4464,9 @@ public class QuadCLT { ...@@ -4405,9 +4464,9 @@ public class QuadCLT {
this.fine_corr = new double [4][2][6]; // reset all coefficients to 0 this.fine_corr = new double [4][2][6]; // reset all coefficients to 0
} }
public void showExtrinsicCorr() public void showExtrinsicCorr(String name)
{ {
System.out.println("Extrinsic corrections"); System.out.println("Extrinsic corrections "+name);
if (geometryCorrection == null){ if (geometryCorrection == null){
System.out.println("are not set, will be:"); System.out.println("are not set, will be:");
System.out.println(new GeometryCorrection(this.extrinsic_corr).getCorrVector().toString()); System.out.println(new GeometryCorrection(this.extrinsic_corr).getCorrVector().toString());
...@@ -4430,7 +4489,7 @@ public class QuadCLT { ...@@ -4430,7 +4489,7 @@ public class QuadCLT {
public void cltDisparityScans( public void cltDisparityScans(
EyesisCorrectionParameters.CLTParameters clt_parameters, EyesisCorrectionParameters.CLTParameters clt_parameters,
EyesisCorrectionParameters.DebayerParameters debayerParameters, EyesisCorrectionParameters.DebayerParameters debayerParameters,
EyesisCorrectionParameters.NonlinParameters nonlinParameters, // EyesisCorrectionParameters.NonlinParameters nonlinParameters,
EyesisCorrectionParameters.ColorProcParameters colorProcParameters, EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
CorrectionColorProc.ColorGainsParameters channelGainParameters, CorrectionColorProc.ColorGainsParameters channelGainParameters,
EyesisCorrectionParameters.RGBParameters rgbParameters, EyesisCorrectionParameters.RGBParameters rgbParameters,
...@@ -4678,7 +4737,7 @@ public class QuadCLT { ...@@ -4678,7 +4737,7 @@ public class QuadCLT {
saturation_imp, // boolean [][] saturation_imp, // (near) saturated pixels or null saturation_imp, // boolean [][] saturation_imp, // (near) saturated pixels or null
clt_parameters, clt_parameters,
debayerParameters, debayerParameters,
nonlinParameters, // nonlinParameters,
colorProcParameters, colorProcParameters,
channelGainParameters, channelGainParameters,
rgbParameters, rgbParameters,
...@@ -4705,7 +4764,7 @@ public class QuadCLT { ...@@ -4705,7 +4764,7 @@ public class QuadCLT {
boolean [][] saturation_imp, // (near) saturated pixels or null boolean [][] saturation_imp, // (near) saturated pixels or null
EyesisCorrectionParameters.CLTParameters clt_parameters, EyesisCorrectionParameters.CLTParameters clt_parameters,
EyesisCorrectionParameters.DebayerParameters debayerParameters, EyesisCorrectionParameters.DebayerParameters debayerParameters,
EyesisCorrectionParameters.NonlinParameters nonlinParameters, // EyesisCorrectionParameters.NonlinParameters nonlinParameters,
EyesisCorrectionParameters.ColorProcParameters colorProcParameters, EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
CorrectionColorProc.ColorGainsParameters channelGainParameters, CorrectionColorProc.ColorGainsParameters channelGainParameters,
EyesisCorrectionParameters.RGBParameters rgbParameters, EyesisCorrectionParameters.RGBParameters rgbParameters,
...@@ -5319,7 +5378,7 @@ public class QuadCLT { ...@@ -5319,7 +5378,7 @@ public class QuadCLT {
boolean adjust_poly, boolean adjust_poly,
EyesisCorrectionParameters.CLTParameters clt_parameters, EyesisCorrectionParameters.CLTParameters clt_parameters,
EyesisCorrectionParameters.DebayerParameters debayerParameters, EyesisCorrectionParameters.DebayerParameters debayerParameters,
EyesisCorrectionParameters.NonlinParameters nonlinParameters, // EyesisCorrectionParameters.NonlinParameters nonlinParameters,
EyesisCorrectionParameters.ColorProcParameters colorProcParameters, EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
CorrectionColorProc.ColorGainsParameters channelGainParameters, CorrectionColorProc.ColorGainsParameters channelGainParameters,
EyesisCorrectionParameters.RGBParameters rgbParameters, EyesisCorrectionParameters.RGBParameters rgbParameters,
...@@ -5576,9 +5635,9 @@ public class QuadCLT { ...@@ -5576,9 +5635,9 @@ public class QuadCLT {
saturation_imp, // boolean [][] saturation_imp, // (near) saturated pixels or null saturation_imp, // boolean [][] saturation_imp, // (near) saturated pixels or null
clt_parameters, clt_parameters,
debayerParameters, debayerParameters,
nonlinParameters, // nonlinParameters,
colorProcParameters, colorProcParameters,
channelGainParameters, // channelGainParameters,
rgbParameters, rgbParameters,
threadsMax, // maximal number of threads to launch threadsMax, // maximal number of threads to launch
updateStatus, updateStatus,
...@@ -5602,7 +5661,7 @@ public class QuadCLT { ...@@ -5602,7 +5661,7 @@ public class QuadCLT {
imp_srcs, // [srcChannel], // should have properties "name"(base for saving results), "channel","path" imp_srcs, // [srcChannel], // should have properties "name"(base for saving results), "channel","path"
clt_parameters, clt_parameters,
debayerParameters, debayerParameters,
nonlinParameters, // nonlinParameters,
colorProcParameters, colorProcParameters,
channelGainParameters, channelGainParameters,
rgbParameters, rgbParameters,
...@@ -5629,9 +5688,9 @@ public class QuadCLT { ...@@ -5629,9 +5688,9 @@ public class QuadCLT {
boolean [][] saturation_imp, // (near) saturated pixels or null boolean [][] saturation_imp, // (near) saturated pixels or null
EyesisCorrectionParameters.CLTParameters clt_parameters, EyesisCorrectionParameters.CLTParameters clt_parameters,
EyesisCorrectionParameters.DebayerParameters debayerParameters, EyesisCorrectionParameters.DebayerParameters debayerParameters,
EyesisCorrectionParameters.NonlinParameters nonlinParameters, // EyesisCorrectionParameters.NonlinParameters nonlinParameters,
EyesisCorrectionParameters.ColorProcParameters colorProcParameters, EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
CorrectionColorProc.ColorGainsParameters channelGainParameters, // CorrectionColorProc.ColorGainsParameters channelGainParameters,
EyesisCorrectionParameters.RGBParameters rgbParameters, EyesisCorrectionParameters.RGBParameters rgbParameters,
final int threadsMax, // maximal number of threads to launch final int threadsMax, // maximal number of threads to launch
final boolean updateStatus, final boolean updateStatus,
...@@ -6381,7 +6440,7 @@ public class QuadCLT { ...@@ -6381,7 +6440,7 @@ public class QuadCLT {
ImagePlus [] imp_quad, // should have properties "name"(base for saving results), "channel","path" ImagePlus [] imp_quad, // should have properties "name"(base for saving results), "channel","path"
EyesisCorrectionParameters.CLTParameters clt_parameters, EyesisCorrectionParameters.CLTParameters clt_parameters,
EyesisCorrectionParameters.DebayerParameters debayerParameters, EyesisCorrectionParameters.DebayerParameters debayerParameters,
EyesisCorrectionParameters.NonlinParameters nonlinParameters, // EyesisCorrectionParameters.NonlinParameters nonlinParameters,
EyesisCorrectionParameters.ColorProcParameters colorProcParameters, EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
CorrectionColorProc.ColorGainsParameters channelGainParameters, CorrectionColorProc.ColorGainsParameters channelGainParameters,
EyesisCorrectionParameters.RGBParameters rgbParameters, EyesisCorrectionParameters.RGBParameters rgbParameters,
...@@ -8422,7 +8481,7 @@ public class QuadCLT { ...@@ -8422,7 +8481,7 @@ public class QuadCLT {
public void batchCLT3d( public void batchCLT3d(
EyesisCorrectionParameters.CLTParameters clt_parameters, EyesisCorrectionParameters.CLTParameters clt_parameters,
EyesisCorrectionParameters.DebayerParameters debayerParameters, EyesisCorrectionParameters.DebayerParameters debayerParameters,
EyesisCorrectionParameters.NonlinParameters nonlinParameters, // EyesisCorrectionParameters.NonlinParameters nonlinParameters,
EyesisCorrectionParameters.ColorProcParameters colorProcParameters, EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
CorrectionColorProc.ColorGainsParameters channelGainParameters, CorrectionColorProc.ColorGainsParameters channelGainParameters,
EyesisCorrectionParameters.RGBParameters rgbParameters, EyesisCorrectionParameters.RGBParameters rgbParameters,
...@@ -8585,9 +8644,9 @@ public class QuadCLT { ...@@ -8585,9 +8644,9 @@ public class QuadCLT {
saturation_imp, // boolean [][] saturation_imp, // (near) saturated pixels or null saturation_imp, // boolean [][] saturation_imp, // (near) saturated pixels or null
clt_parameters, clt_parameters,
debayerParameters, debayerParameters,
nonlinParameters, // nonlinParameters,
colorProcParameters, colorProcParameters,
channelGainParameters, // channelGainParameters,
rgbParameters, rgbParameters,
threadsMax, // maximal number of threads to launch threadsMax, // maximal number of threads to launch
updateStatus, updateStatus,
...@@ -8609,9 +8668,9 @@ public class QuadCLT { ...@@ -8609,9 +8668,9 @@ public class QuadCLT {
saturation_imp, // boolean [][] saturation_imp, // (near) saturated pixels or null saturation_imp, // boolean [][] saturation_imp, // (near) saturated pixels or null
clt_parameters, clt_parameters,
debayerParameters, debayerParameters,
nonlinParameters, // nonlinParameters,
colorProcParameters, colorProcParameters,
channelGainParameters, // channelGainParameters,
rgbParameters, rgbParameters,
threadsMax, // maximal number of threads to launch threadsMax, // maximal number of threads to launch
updateStatus, updateStatus,
...@@ -8633,7 +8692,7 @@ public class QuadCLT { ...@@ -8633,7 +8692,7 @@ public class QuadCLT {
saturation_imp, // boolean [][] saturation_imp, // (near) saturated pixels or null saturation_imp, // boolean [][] saturation_imp, // (near) saturated pixels or null
clt_parameters, clt_parameters,
debayerParameters, debayerParameters,
nonlinParameters, // nonlinParameters,
colorProcParameters, colorProcParameters,
channelGainParameters, channelGainParameters,
rgbParameters, rgbParameters,
...@@ -8652,9 +8711,9 @@ public class QuadCLT { ...@@ -8652,9 +8711,9 @@ public class QuadCLT {
saturation_imp, // boolean [][] saturation_imp, // (near) saturated pixels or null saturation_imp, // boolean [][] saturation_imp, // (near) saturated pixels or null
clt_parameters, clt_parameters,
debayerParameters, debayerParameters,
nonlinParameters, // nonlinParameters,
colorProcParameters, colorProcParameters,
channelGainParameters, // channelGainParameters,
rgbParameters, rgbParameters,
threadsMax, // maximal number of threads to launch threadsMax, // maximal number of threads to launch
updateStatus, updateStatus,
...@@ -8665,7 +8724,7 @@ public class QuadCLT { ...@@ -8665,7 +8724,7 @@ public class QuadCLT {
imp_srcs, // [srcChannel], // should have properties "name"(base for saving results), "channel","path" imp_srcs, // [srcChannel], // should have properties "name"(base for saving results), "channel","path"
clt_parameters, clt_parameters,
debayerParameters, debayerParameters,
nonlinParameters, // nonlinParameters,
colorProcParameters, colorProcParameters,
channelGainParameters, channelGainParameters,
rgbParameters, rgbParameters,
......
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