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imagej-elphel
Commit 7a838c63 authored by Andrey Filippov's avatar Andrey Filippov
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fixing empty stacks in partial kernels command

parent 08bb8d2d
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Showing with 67 additions and 49 deletions
src/main/java/Distortions.java
View file @ 7a838c63
......@@ -6979,6 +6979,13 @@ List calibration
this.startTime+=(System.nanoTime()-startDialogTime); // do not count time used by the User.
if (this.showThisImages) showDiff (this.currentfX, "fit-"+this.iterationStepNumber);
if (this.showNextImages) showDiff (this.nextfX, "fit-"+(this.iterationStepNumber+1));
} else if ((this.debugLevel>0) && ((this.debugLevel>1) || ((System.nanoTime()-this.startTime)>10000000000.0))){ // > 10 sec
System.out.println("--> LevenbergMarquardt(): series:step ="+this.seriesNumber+":"+this.iterationStepNumber+
", RMS="+IJ.d2s(this.currentRMS,8)+
" ("+IJ.d2s(this.firstRMS,8)+") "+
", RMSPure="+IJ.d2s(this.currentRMSPure,8)+
" ("+IJ.d2s(this.firstRMSPure,8)+
") at "+ IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3));
}
stepLevenbergMarquardtAction(); // apply step - in any case?
if (this.updateStatus){
......
src/main/java/EyesisAberrations.java
View file @ 7a838c63
......@@ -2157,6 +2157,10 @@ public class EyesisAberrations {
length=kernel[i].length;
break;
}
if (length==0){
System.out.println("mergeKernelsToStack(): no non-null kernels");
return null;
}
int [] channelsMask = new int [kernel.length];
for (i=0;i<kernel.length;i++) channelsMask[i]=0;
for (i=0;i<tilesY ;i++) for (j=0;j<tilesX;j++) if (kernels[i][j]!=null) {
......@@ -2178,6 +2182,7 @@ public class EyesisAberrations {
int outHeight=size*tilesY;
ImageStack stack=new ImageStack(outWidth,outHeight);
int numKernels=0;
float [] fpixels;
for (chn=0;chn<nChn;chn++) {
fpixels= new float [outWidth*outHeight];
......@@ -2190,10 +2195,16 @@ public class EyesisAberrations {
fpixels[index]= (float) kernels[i][j][k][y*size+x];
}
}
if ((kernels[i][j]!=null && (kernels[i][j][k]!=null))) numKernels++;
}
if (names==null) stack.addSlice("channel"+k, fpixels);
else stack.addSlice(names[chn], fpixels);
}
if (numKernels==0){
System.out.println("mergeKernelsToStack(): all kernels are empty");
return null;
}
System.out.println("mergeKernelsToStack(): got "+numKernels +" non-null kernels");
return stack;
}
......@@ -2687,6 +2698,7 @@ public class EyesisAberrations {
if (!colorComponents.colorsToCorrect[i]) simul_pixels[i]=null; // removed unused
}
simul_pixels= normalizeAndWindow (simul_pixels, fullHamming);
} else {
Rectangle PSFCellSim=new Rectangle (x0*subpixel/2,y0*subpixel/2,size*subpixel/2,size*subpixel/2);
......@@ -3256,8 +3268,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
// if ((globalDebugLevel>0) && (tileY==22) && (tileX==32) && (y>=0) && (x>=0) && (y<height) && (x<width))System.out.println(" uvIndex["+(y*width+x)+"]="+uvIndex[y*width+x]);
}
result[tileY][tileX]=(sum>absThresh);
if (debugLevel>1) System.out.println(" tileY="+tileY+" tileX="+tileX+" x0="+x0+" y0="+y0+" sum="+sum);
if (debugLevel>1) System.out.println(" tileY="+tileY+" tileX="+tileX+" x0="+x0+" y0="+y0+" sum="+sum+" threshold="+threshold+" absThresh="+absThresh+" rrsult="+result[tileY][tileX]);
}
return result;
}
......
src/main/java/EyesisCameraParameters.java
View file @ 7a838c63
......@@ -858,62 +858,62 @@ import org.apache.commons.configuration.XMLConfiguration;
if (subCam!=null) {
gd.addMessage("Channel weight "+subCam.channelWeightCurrent);
if (numStation==0){
gd.addNumericField("Channel "+numSubCam+" default weight", subCam.channelWeightDefault, 3,6,"");
gd.addNumericField("Channel "+numSubCam+" default weight", subCam.channelWeightDefault, 5,8,"");
}
if (this.numStations>1) gd.addMessage("--- Station number "+numStation+" ---");
gd.addNumericField("Subcamera azimuth", subCam.azimuth, 3,7,"degrees");
gd.addNumericField("Subcamera distance from the axis", subCam.radius, 3,7,"mm");
gd.addNumericField("Subcamera height from the 'equator'", subCam.height, 3,7,"mm");
gd.addNumericField("Optical axis heading (relative to azimuth)", subCam.phi, 3,7,"degrees");
gd.addNumericField("Optical axis elevation (up from equator)", subCam.theta, 3,7,"degrees");
gd.addNumericField("Camera roll, positive CW looking to the target",subCam.psi, 3,7,"degrees");
gd.addNumericField("Lens focal length", subCam.focalLength, 3,6,"mm");
gd.addNumericField("Sensor pixel period", subCam.pixelSize, 3,6,"um");
gd.addNumericField("Distortion radius (half width)", subCam.distortionRadius, 5,8,"mm");
gd.addNumericField("Distortion A8 (r^8)", subCam.distortionA8, 6,8,"");
gd.addNumericField("Distortion A7 (r^7)", subCam.distortionA7, 6,8,"");
gd.addNumericField("Distortion A6 (r^6)", subCam.distortionA6, 6,8,"");
gd.addNumericField("Distortion A5 (r^5)", subCam.distortionA5, 6,8,"");
gd.addNumericField("Distortion A (r^4)", subCam.distortionA, 6,8,"");
gd.addNumericField("Distortion B (r^3)", subCam.distortionB, 6,8,"");
gd.addNumericField("Distortion C (r^2)", subCam.distortionC, 6,8,"");
gd.addNumericField("Lens axis on the sensor (horizontal, from left edge)", subCam.px0, 2,7,"pixels");
gd.addNumericField("Lens axis on the sensor (vertical, from top edge)", subCam.py0, 2,7,"pixels");
gd.addNumericField("Subcamera azimuth", subCam.azimuth, 5,9,"degrees");
gd.addNumericField("Subcamera distance from the axis", subCam.radius, 5,9,"mm");
gd.addNumericField("Subcamera height from the 'equator'", subCam.height, 5,9,"mm");
gd.addNumericField("Optical axis heading (relative to azimuth)", subCam.phi, 5,9,"degrees");
gd.addNumericField("Optical axis elevation (up from equator)", subCam.theta, 5,9,"degrees");
gd.addNumericField("Camera roll, positive CW looking to the target",subCam.psi, 5,9,"degrees");
gd.addNumericField("Lens focal length", subCam.focalLength, 5,8,"mm");
gd.addNumericField("Sensor pixel period", subCam.pixelSize, 5,8,"um");
gd.addNumericField("Distortion radius (half width)", subCam.distortionRadius, 6,8,"mm");
gd.addNumericField("Distortion A8 (r^8)", subCam.distortionA8, 8,10,"");
gd.addNumericField("Distortion A7 (r^7)", subCam.distortionA7, 8,10,"");
gd.addNumericField("Distortion A6 (r^6)", subCam.distortionA6, 8,10,"");
gd.addNumericField("Distortion A5 (r^5)", subCam.distortionA5, 8,10,"");
gd.addNumericField("Distortion A (r^4)", subCam.distortionA, 8,10,"");
gd.addNumericField("Distortion B (r^3)", subCam.distortionB, 8,10,"");
gd.addNumericField("Distortion C (r^2)", subCam.distortionC, 8,10,"");
gd.addNumericField("Lens axis on the sensor (horizontal, from left edge)", subCam.px0, 4,9,"pixels");
gd.addNumericField("Lens axis on the sensor (vertical, from top edge)", subCam.py0, 4,9,"pixels");
gd.addMessage("=== non-radial model parameters ===");
gd.addMessage("For r^2 (Distortion C):");
gd.addNumericField("Orthogonal elongation for r^2", 100*subCam.r_od[0][0], 3,7,"%");
gd.addNumericField("Diagonal elongation for r^2", 100*subCam.r_od[0][1], 3,7,"%");
gd.addNumericField("Orthogonal elongation for r^2", 100*subCam.r_od[0][0], 8,10,"%");
gd.addNumericField("Diagonal elongation for r^2", 100*subCam.r_od[0][1], 8,10,"%");
gd.addMessage("For r^3 (Distortion B):");
gd.addNumericField("Distortion center shift X for r^3", 100*subCam.r_xy[0][0], 1,6,"%");
gd.addNumericField("Distortion center shift Y for r^3", 100*subCam.r_xy[0][1], 1,6,"%");
gd.addNumericField("Orthogonal elongation for r^3", 100*subCam.r_od[1][0], 3,7,"%");
gd.addNumericField("Diagonal elongation for r^3", 100*subCam.r_od[1][1], 3,7,"%");
gd.addNumericField("Distortion center shift X for r^3", 100*subCam.r_xy[0][0], 8,10,"%");
gd.addNumericField("Distortion center shift Y for r^3", 100*subCam.r_xy[0][1], 8,10,"%");
gd.addNumericField("Orthogonal elongation for r^3", 100*subCam.r_od[1][0], 8,10,"%");
gd.addNumericField("Diagonal elongation for r^3", 100*subCam.r_od[1][1], 8,10,"%");
gd.addMessage("For r^4 (Distortion A):");
gd.addNumericField("Distortion center shift X for r^4", 100*subCam.r_xy[1][0], 1,6,"%");
gd.addNumericField("Distortion center shift Y for r^4", 100*subCam.r_xy[1][1], 1,6,"%");
gd.addNumericField("Orthogonal elongation for r^4", 100*subCam.r_od[2][0], 3,7,"%");
gd.addNumericField("Diagonal elongation for r^4", 100*subCam.r_od[2][1], 3,7,"%");
gd.addNumericField("Distortion center shift X for r^4", 100*subCam.r_xy[1][0], 8,10,"%");
gd.addNumericField("Distortion center shift Y for r^4", 100*subCam.r_xy[1][1], 8,10,"%");
gd.addNumericField("Orthogonal elongation for r^4", 100*subCam.r_od[2][0], 8,10,"%");
gd.addNumericField("Diagonal elongation for r^4", 100*subCam.r_od[2][1], 8,10,"%");
gd.addMessage("For r^5 (Distortion A5):");
gd.addNumericField("Distortion center shift X for r^5", 100*subCam.r_xy[2][0], 1,6,"%");
gd.addNumericField("Distortion center shift Y for r^5", 100*subCam.r_xy[2][1], 1,6,"%");
gd.addNumericField("Orthogonal elongation for r^5", 100*subCam.r_od[3][0], 3,7,"%");
gd.addNumericField("Diagonal elongation for r^5", 100*subCam.r_od[3][1], 3,7,"%");
gd.addNumericField("Distortion center shift X for r^5", 100*subCam.r_xy[2][0], 8,10,"%");
gd.addNumericField("Distortion center shift Y for r^5", 100*subCam.r_xy[2][1], 8,10,"%");
gd.addNumericField("Orthogonal elongation for r^5", 100*subCam.r_od[3][0], 8,10,"%");
gd.addNumericField("Diagonal elongation for r^5", 100*subCam.r_od[3][1], 8,10,"%");
gd.addMessage("For r^6 (Distortion A6:");
gd.addNumericField("Distortion center shift X for r^6", 100*subCam.r_xy[3][0], 1,6,"%");
gd.addNumericField("Distortion center shift Y for r^6", 100*subCam.r_xy[3][1], 1,6,"%");
gd.addNumericField("Orthogonal elongation for r^6", 100*subCam.r_od[4][0], 3,7,"%");
gd.addNumericField("Diagonal elongation for r^6", 100*subCam.r_od[4][1], 3,7,"%");
gd.addNumericField("Distortion center shift X for r^6", 100*subCam.r_xy[3][0], 8,10,"%");
gd.addNumericField("Distortion center shift Y for r^6", 100*subCam.r_xy[3][1], 8,10,"%");
gd.addNumericField("Orthogonal elongation for r^6", 100*subCam.r_od[4][0], 8,10,"%");
gd.addNumericField("Diagonal elongation for r^6", 100*subCam.r_od[4][1], 8,10,"%");
gd.addMessage("For r^7 (Distortion A7):");
gd.addNumericField("Distortion center shift X for r^7", 100*subCam.r_xy[4][0], 1,6,"%");
gd.addNumericField("Distortion center shift Y for r^7", 100*subCam.r_xy[4][1], 1,6,"%");
gd.addNumericField("Orthogonal elongation for r^7", 100*subCam.r_od[5][0], 3,7,"%");
gd.addNumericField("Diagonal elongation for r^7", 100*subCam.r_od[5][1], 3,7,"%");
gd.addNumericField("Distortion center shift X for r^7", 100*subCam.r_xy[4][0], 8,10,"%");
gd.addNumericField("Distortion center shift Y for r^7", 100*subCam.r_xy[4][1], 8,10,"%");
gd.addNumericField("Orthogonal elongation for r^7", 100*subCam.r_od[5][0], 8,10,"%");
gd.addNumericField("Diagonal elongation for r^7", 100*subCam.r_od[5][1], 8,10,"%");
gd.addMessage("For r^8 (Distortion A8):");
gd.addNumericField("Distortion center shift X for r^8", 100*subCam.r_xy[5][0], 1,6,"%");
gd.addNumericField("Distortion center shift Y for r^8", 100*subCam.r_xy[5][1], 1,6,"%");
gd.addNumericField("Orthogonal elongation for r^8", 100*subCam.r_od[6][0], 3,7,"%");
gd.addNumericField("Diagonal elongation for r^8", 100*subCam.r_od[6][1], 3,7,"%");
gd.addNumericField("Distortion center shift X for r^8", 100*subCam.r_xy[5][0], 8,10,"%");
gd.addNumericField("Distortion center shift Y for r^8", 100*subCam.r_xy[5][1], 8,10,"%");
gd.addNumericField("Orthogonal elongation for r^8", 100*subCam.r_od[6][0], 8,10,"%");
gd.addNumericField("Diagonal elongation for r^8", 100*subCam.r_od[6][1], 8,10,"%");
}
}
......@@ -1368,7 +1368,7 @@ import org.apache.commons.configuration.XMLConfiguration;
968.0, // double py0=968.0; // center of the lens on the sensor, pixels
null, // eccentricity for b,a,a5,a6,a7,a8
null, // elongation for c,b,a,a5,a6,a7,a8
4.0); //channelWeightDefault
8.0); //channelWeightDefault (was 4)
if (25<numSubCameras) this.eyesisSubCameras[numStation][25]=new EyesisSubCameraParameters(
270, // double azimuth, // azimuth of the lens entrance pupil center, degrees, clockwise looking from top
12.025, // double radius, // mm, distance from the rotation axis
......@@ -1390,7 +1390,7 @@ import org.apache.commons.configuration.XMLConfiguration;
968.0, // double py0=968.0; // center of the lens on the sensor, pixels
null, // eccentricity for b,a,a5,a6,a7,a8
null, // elongation for c,b,a,a5,a6,a7,a8
4.0); //channelWeightDefault
8.0); //channelWeightDefault (was 4)
}
}
public void recenterVertically(boolean [] subcams, boolean [] stations){
......
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