fixing empty stacks in partial kernels command (7a838c63) · Commits · Elphel / imagej-elphel

src/main/java/Distortions.java

+7 −0

Original line number	Original line	Diff line number	Diff line
	@@ -6979,6 +6979,13 @@ List calibration
	this.startTime+=(System.nanoTime()-startDialogTime); // do not count time used by the User.		this.startTime+=(System.nanoTime()-startDialogTime); // do not count time used by the User.
	if (this.showThisImages) showDiff (this.currentfX, "fit-"+this.iterationStepNumber);		if (this.showThisImages) showDiff (this.currentfX, "fit-"+this.iterationStepNumber);
	if (this.showNextImages) showDiff (this.nextfX, "fit-"+(this.iterationStepNumber+1));		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?		stepLevenbergMarquardtAction(); // apply step - in any case?
	if (this.updateStatus){		if (this.updateStatus){

src/main/java/EyesisAberrations.java

+13 −2

Original line number	Original line	Diff line number	Diff line
	@@ -2157,6 +2157,10 @@ public class EyesisAberrations {
	length=kernel[i].length;		length=kernel[i].length;
	break;		break;
	}		}
			if (length==0){
			System.out.println("mergeKernelsToStack(): no non-null kernels");
			return null;
			}
	int [] channelsMask = new int [kernel.length];		int [] channelsMask = new int [kernel.length];
	for (i=0;i<kernel.length;i++) channelsMask[i]=0;		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) {		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;		int outHeight=size*tilesY;

	ImageStack stack=new ImageStack(outWidth,outHeight);		ImageStack stack=new ImageStack(outWidth,outHeight);
			int numKernels=0;
	float [] fpixels;		float [] fpixels;
	for (chn=0;chn<nChn;chn++) {		for (chn=0;chn<nChn;chn++) {
	fpixels= new float [outWidth*outHeight];		fpixels= new float [outWidth*outHeight];
	@@ -2190,10 +2195,16 @@ public class EyesisAberrations {
	fpixels[index]= (float) kernels[i][j][k][y*size+x];		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);		if (names==null) stack.addSlice("channel"+k, fpixels);
	else stack.addSlice(names[chn], 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;		return stack;
	}		}

	@@ -2687,6 +2698,7 @@ public class EyesisAberrations {
	if (!colorComponents.colorsToCorrect[i]) simul_pixels[i]=null; // removed unused		if (!colorComponents.colorsToCorrect[i]) simul_pixels[i]=null; // removed unused
	}		}
	simul_pixels= normalizeAndWindow (simul_pixels, fullHamming);		simul_pixels= normalizeAndWindow (simul_pixels, fullHamming);

	} else {		} else {
	Rectangle PSFCellSim=new Rectangle (x0subpixel/2,y0subpixel/2,sizesubpixel/2,sizesubpixel/2);		Rectangle PSFCellSim=new Rectangle (x0subpixel/2,y0subpixel/2,sizesubpixel/2,sizesubpixel/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["+(ywidth+x)+"]="+uvIndex[ywidth+x]);		// if ((globalDebugLevel>0) && (tileY==22) && (tileX==32) && (y>=0) && (x>=0) && (y<height) && (x<width))System.out.println(" uvIndex["+(ywidth+x)+"]="+uvIndex[ywidth+x]);
	}		}
	result[tileY][tileX]=(sum>absThresh);		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;		return result;
	}		}

src/main/java/EyesisCameraParameters.java

+47 −47

Original line number	Original line	Diff line number	Diff line
	@@ -858,62 +858,62 @@ import org.apache.commons.configuration.XMLConfiguration;
	if (subCam!=null) {		if (subCam!=null) {
	gd.addMessage("Channel weight "+subCam.channelWeightCurrent);		gd.addMessage("Channel weight "+subCam.channelWeightCurrent);
	if (numStation==0){		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+" ---");		if (this.numStations>1) gd.addMessage("--- Station number "+numStation+" ---");
	gd.addNumericField("Subcamera azimuth", subCam.azimuth, 3,7,"degrees");		gd.addNumericField("Subcamera azimuth", subCam.azimuth, 5,9,"degrees");
	gd.addNumericField("Subcamera distance from the axis", subCam.radius, 3,7,"mm");		gd.addNumericField("Subcamera distance from the axis", subCam.radius, 5,9,"mm");
	gd.addNumericField("Subcamera height from the 'equator'", subCam.height, 3,7,"mm");		gd.addNumericField("Subcamera height from the 'equator'", subCam.height, 5,9,"mm");
	gd.addNumericField("Optical axis heading (relative to azimuth)", subCam.phi, 3,7,"degrees");		gd.addNumericField("Optical axis heading (relative to azimuth)", subCam.phi, 5,9,"degrees");
	gd.addNumericField("Optical axis elevation (up from equator)", subCam.theta, 3,7,"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, 3,7,"degrees");		gd.addNumericField("Camera roll, positive CW looking to the target",subCam.psi, 5,9,"degrees");
	gd.addNumericField("Lens focal length", subCam.focalLength, 3,6,"mm");		gd.addNumericField("Lens focal length", subCam.focalLength, 5,8,"mm");
	gd.addNumericField("Sensor pixel period", subCam.pixelSize, 3,6,"um");		gd.addNumericField("Sensor pixel period", subCam.pixelSize, 5,8,"um");
	gd.addNumericField("Distortion radius (half width)", subCam.distortionRadius, 5,8,"mm");		gd.addNumericField("Distortion radius (half width)", subCam.distortionRadius, 6,8,"mm");
	gd.addNumericField("Distortion A8 (r^8)", subCam.distortionA8, 6,8,"");		gd.addNumericField("Distortion A8 (r^8)", subCam.distortionA8, 8,10,"");
	gd.addNumericField("Distortion A7 (r^7)", subCam.distortionA7, 6,8,"");		gd.addNumericField("Distortion A7 (r^7)", subCam.distortionA7, 8,10,"");
	gd.addNumericField("Distortion A6 (r^6)", subCam.distortionA6, 6,8,"");		gd.addNumericField("Distortion A6 (r^6)", subCam.distortionA6, 8,10,"");
	gd.addNumericField("Distortion A5 (r^5)", subCam.distortionA5, 6,8,"");		gd.addNumericField("Distortion A5 (r^5)", subCam.distortionA5, 8,10,"");
	gd.addNumericField("Distortion A (r^4)", subCam.distortionA, 6,8,"");		gd.addNumericField("Distortion A (r^4)", subCam.distortionA, 8,10,"");
	gd.addNumericField("Distortion B (r^3)", subCam.distortionB, 6,8,"");		gd.addNumericField("Distortion B (r^3)", subCam.distortionB, 8,10,"");
	gd.addNumericField("Distortion C (r^2)", subCam.distortionC, 6,8,"");		gd.addNumericField("Distortion C (r^2)", subCam.distortionC, 8,10,"");
	gd.addNumericField("Lens axis on the sensor (horizontal, from left edge)", subCam.px0, 2,7,"pixels");		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, 2,7,"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("=== non-radial model parameters ===");
	gd.addMessage("For r^2 (Distortion C):");		gd.addMessage("For r^2 (Distortion C):");
	gd.addNumericField("Orthogonal elongation for r^2", 100*subCam.r_od[0][0], 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], 3,7,"%");		gd.addNumericField("Diagonal elongation for r^2", 100*subCam.r_od[0][1], 8,10,"%");
	gd.addMessage("For r^3 (Distortion B):");		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 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], 1,6,"%");		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], 3,7,"%");		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], 3,7,"%");		gd.addNumericField("Diagonal elongation for r^3", 100*subCam.r_od[1][1], 8,10,"%");
	gd.addMessage("For r^4 (Distortion A):");		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 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], 1,6,"%");		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], 3,7,"%");		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], 3,7,"%");		gd.addNumericField("Diagonal elongation for r^4", 100*subCam.r_od[2][1], 8,10,"%");

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