Fixing sensor geometric corrections (f25142a1) · Commits · Elphel / imagej-elphel

src/main/java/ImageDtt.java

+14 −1

Original line number	Diff line number	Diff line
		@@ -4042,7 +4042,7 @@ public class ImageDtt {
		public double data_y = 0.0; // kernel data is relative to this displacement Y (0.5 pixel increments)
		public double center_x = 0.0; // actual center X (use to find derivatives)
		public double center_y = 0.0; // actual center X (use to find derivatives)
		public double dxc_dx = 0.0; // add this to data_x per each pixel X-shift relative to the kernel centger location
		public double dxc_dx = 0.0; // add this to data_x per each pixel X-shift relative to the kernel center location
		public double dxc_dy = 0.0; // same per each Y-shift pixel
		public double dyc_dx = 0.0;
		public double dyc_dy = 0.0;
		@@ -4075,6 +4075,17 @@ public class ImageDtt {
		}
		}

		public void offsetKernelSensor(
		double [][] clt_tile, // clt tile, including [4] - metadata
		double dx,
		double dy) {
		CltExtra ce = new CltExtra (clt_tile[4]);
		ce.center_x += dx;
		ce.center_y += dy;
		ce.data_x += dx;
		ce.data_y += dy;
		clt_tile[4] = ce.getArray();
		}
		public void clt_fill_coord_corr(
		final int kern_step, // distance between kernel centers, in pixels.
		final double [][][][][] clt_data,
		@@ -4201,6 +4212,8 @@ public class ImageDtt {
		// same with extra shift
		px = centerX - transform_size - (ce.data_x + ce.dxc_dx * kdx + ce.dxc_dy * kdy) ; // fractional left corner
		py = centerY - transform_size - (ce.data_y + ce.dyc_dx * kdx + ce.dyc_dy * kdy) ; // fractional top corner
		}else {
		System.out.println("Skipping kernels!!!");
		}
		if (bdebug0){
		System.out.print(px+"\t"+py+"\t");

src/main/java/PixelMapping.java

+960 −925

Original line number	Diff line number	Diff line
		@@ -37,9 +37,6 @@ import java.util.concurrent.atomic.AtomicInteger;

		import javax.swing.SwingUtilities;

		import loci.common.services.DependencyException;
		import loci.common.services.ServiceException;
		import loci.formats.FormatException;
		import Jama.Matrix;
		import ij.IJ;
		import ij.ImagePlus;
		@@ -50,6 +47,9 @@ import ij.io.FileSaver;
		import ij.io.Opener;
		import ij.process.ColorProcessor;
		import ij.text.TextWindow;
		import loci.common.services.DependencyException;
		import loci.common.services.ServiceException;
		import loci.formats.FormatException;


		public class PixelMapping {
		@@ -494,6 +494,7 @@ public class PixelMapping {
		IJ.showStatus("Warping image channel "+channel);
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		for (int opy=opyAtomic.getAndIncrement(); opy<erm.mapWOI.height;opy=opyAtomic.getAndIncrement()){

		@@ -561,6 +562,7 @@ public class PixelMapping {
		final int numFinished=opyDoneAtomic.getAndIncrement();
		// IJ.showProgress(progressValues[numFinished]);
		SwingUtilities.invokeLater(new Runnable() {
		@Override
		public void run() {
		// Here, we can safely update the GUI
		// because we'll be called from the
		@@ -618,6 +620,7 @@ public class PixelMapping {
		IJ.showStatus("Warping image channel "+channel);
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		for (int opy=opyAtomic.getAndIncrement(); opy<erm.mapWOI.height;opy=opyAtomic.getAndIncrement()){

		@@ -666,6 +669,7 @@ public class PixelMapping {
		final int numFinished=opyDoneAtomic.getAndIncrement();
		// IJ.showProgress(progressValues[numFinished]);
		SwingUtilities.invokeLater(new Runnable() {
		@Override
		public void run() {
		// Here, we can safely update the GUI
		// because we'll be called from the
		@@ -2499,6 +2503,7 @@ public class PixelMapping {

		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		DoubleFHT doubleFHT=new DoubleFHT();
		for (int row=rowNum.getAndIncrement(); row<numTileRows;row=rowNum.getAndIncrement()) {
		@@ -2523,6 +2528,7 @@ public class PixelMapping {
		debugLevel);
		final int numFinished=rowsFinished.getAndIncrement();
		SwingUtilities.invokeLater(new Runnable() {
		@Override
		public void run() {
		IJ.showProgress(numFinished,numTileRows);
		}
		@@ -3649,6 +3655,7 @@ public class PixelMapping {
		final AtomicInteger numNonEmpty = new AtomicInteger(0);
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		DoubleFHT doubleFHT=new DoubleFHT();
		double [] tilePlot;
		@@ -3706,6 +3713,7 @@ public class PixelMapping {
		}
		final int numFinished=tilesFinished.getAndIncrement();
		SwingUtilities.invokeLater(new Runnable() {
		@Override
		public void run() {
		IJ.showProgress(numFinished,numTiles);
		}
		@@ -3951,6 +3959,7 @@ public class PixelMapping {
		final double [][][] result=new double[numTileRows][numTileColumns][];
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		DoubleFHT doubleFHT=new DoubleFHT();
		for (int tile=tileNum.getAndIncrement(); tile<numTiles;tile=tileNum.getAndIncrement()) {
		@@ -3980,6 +3989,7 @@ public class PixelMapping {
		debugLevel);
		final int numFinished=tilesFinished.getAndIncrement();
		SwingUtilities.invokeLater(new Runnable() {
		@Override
		public void run() {
		IJ.showProgress(numFinished,numTiles);
		}
		@@ -5206,6 +5216,7 @@ public class PixelMapping {
		if (showProgress) IJ.showStatus("Centering correlation data...");
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		// common for the tread
		double [][] partial=new double [imagePairIndices.length][];
		@@ -5254,6 +5265,7 @@ public class PixelMapping {
		if (showProgress){
		final int fTile=tile;
		SwingUtilities.invokeLater(new Runnable() {
		@Override
		public void run() {
		// Here, we can safely update the GUI
		// because we'll be called from the
		@@ -5313,6 +5325,7 @@ public class PixelMapping {
		if (showProgress) IJ.showStatus("Re-centering correlation data...");
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		for (int tile=tileIndexAtomic.getAndIncrement(); tile<tiles;tile=tileIndexAtomic.getAndIncrement()){
		int nImage=tile/tilesPerImage;
		@@ -5342,6 +5355,7 @@ public class PixelMapping {
		if (showProgress){
		final int fTile=tile;
		SwingUtilities.invokeLater(new Runnable() {
		@Override
		public void run() {
		// Here, we can safely update the GUI
		// because we'll be called from the
		@@ -5765,6 +5779,7 @@ public class PixelMapping {
		final AtomicInteger numberUpdated = new AtomicInteger(0);
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		for (int tile=tileIndexAtomic.getAndIncrement(); tile<tiles;tile=tileIndexAtomic.getAndIncrement()){
		if (fillForegroundTile(
		@@ -5778,6 +5793,7 @@ public class PixelMapping {
		if (showProgress){
		final int finalTile=tile;
		SwingUtilities.invokeLater(new Runnable() {
		@Override
		public void run() {
		IJ.showProgress(finalTile,tiles);
		}
		@@ -5938,6 +5954,7 @@ public class PixelMapping {
		refineWindow[0]=Double.NaN;
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		DoubleFHT doubleFHT = new DoubleFHT();
		DoubleFHT refineFHT= new DoubleFHT();
		@@ -5980,6 +5997,7 @@ public class PixelMapping {
		if (showProgress){
		final int finalTile=tile;
		SwingUtilities.invokeLater(new Runnable() {
		@Override
		public void run() {
		IJ.showProgress(finalTile,tiles);
		}
		@@ -6613,6 +6631,7 @@ public class PixelMapping {
		refineWindow[0]=Double.NaN;
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		DoubleFHT doubleFHT = new DoubleFHT();
		DoubleFHT refineFHT= new DoubleFHT();
		@@ -6654,6 +6673,7 @@ public class PixelMapping {
		if (showProgress){
		final int finalTile=tile;
		SwingUtilities.invokeLater(new Runnable() {
		@Override
		public void run() {
		IJ.showProgress(finalTile,tiles);
		}
		@@ -7052,6 +7072,7 @@ public class PixelMapping {
		final int size=2*this.overlapStep;
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		DoubleFHT doubleFHT = new DoubleFHT();
		final double [] window=new double [size*size];
		@@ -7106,6 +7127,7 @@ public class PixelMapping {
		if (showProgress){
		final int finalTile=tile;
		SwingUtilities.invokeLater(new Runnable() {
		@Override
		public void run() {
		IJ.showProgress(finalTile,tiles);
		}
		@@ -7706,6 +7728,7 @@ public class PixelMapping {
		final int size=2*this.overlapStep;
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		DoubleFHT doubleFHT = new DoubleFHT();
		final double [] window=new double [size*size];
		@@ -7766,6 +7789,7 @@ public class PixelMapping {
		if (showProgress){
		final int finalTile=tile;
		SwingUtilities.invokeLater(new Runnable() {
		@Override
		public void run() {
		IJ.showProgress(finalTile,tiles);
		}
		@@ -9147,7 +9171,7 @@ public class PixelMapping {
		if (debugLevel>2) System.out.println("setupZMap() zMapWOI.x="+zMapWOI.x+" zMapWOI.y="+zMapWOI.y+
		" zMapWOI.width="+zMapWOI.width+" zMapWOI.height="+zMapWOI.height);
		this.paddedSize=this.overlapStep+2*overlap;
		this.innerMask=(BitSet) new BitSet(this.paddedSize*this.paddedSize);
		this.innerMask=new BitSet(this.paddedSize*this.paddedSize);
		for (int i=0;i<this.overlapStep;i++) for (int j=0;j<this.overlapStep;j++){
		this.innerMask.set((overlap+i)*this.paddedSize+overlap+j);
		}
		@@ -9165,6 +9189,7 @@ public class PixelMapping {
		if (showProgress) IJ.showStatus("Setting up zMap for image "+nImg+" ("+(nImg+1)+" of "+this.disparityScales.length+") ...");
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		for (int tile=tileIndexAtomic.getAndIncrement(); tile<tiles;tile=tileIndexAtomic.getAndIncrement()){
		setupZMapTile(
		@@ -9183,6 +9208,7 @@ public class PixelMapping {
		if (showProgress){
		final int finalTile=tile;
		SwingUtilities.invokeLater(new Runnable() {
		@Override
		public void run() {
		IJ.showProgress(finalTile,tiles);
		}
		@@ -10502,6 +10528,7 @@ public class PixelMapping {
		final AtomicInteger rsltTileAtomic = new AtomicInteger(0);
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		DoubleFHT doubleFHT=new DoubleFHT();
		DoubleFHT interpolationFHT=null; // will be initialized if needed
		@@ -10959,6 +10986,7 @@ public class PixelMapping {
		final AtomicInteger tileXAtomic = new AtomicInteger(tileXMin);
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		double [] alphaSlice=new double[length];
		double [] channelSlice=new double[length];
		@@ -12533,14 +12561,14 @@ public class PixelMapping {
		int index=pixelX[i]+pixelY[i]*imageWidth;
		dbgImage[0][index]=(float) speed[i]; // same as source image, just masked
		dbgImage[1][index]=(float) timeToReach[i]; //
		dbgImage[2][index]=(float) pathArea[i]; //
		dbgImage[3][index]=(float) pathLength[i]; //
		dbgImage[2][index]=pathArea[i]; //
		dbgImage[3][index]=pathLength[i]; //
		if (node[i]!=null){
		int numParents=0;
		for (int dir=0;dir<8;dir++) if ((parents[i]& (1<<dir))!=0) numParents++;
		dbgImage[4][index]=numParents;
		}
		dbgImage[6][index]=(float) parents[i]; //
		dbgImage[6][index]=parents[i]; //


		}
		@@ -15498,6 +15526,7 @@ public class PixelMapping {
		IJ.showStatus("Warping image channel "+channel);
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		for (int opy=opyAtomic.getAndIncrement(); opy<mapHeight;opy=opyAtomic.getAndIncrement()){

		@@ -15546,6 +15575,7 @@ public class PixelMapping {
		final int numFinished=opyDoneAtomic.getAndIncrement();
		// IJ.showProgress(progressValues[numFinished]);
		SwingUtilities.invokeLater(new Runnable() {
		@Override
		public void run() {
		// Here, we can safely update the GUI
		// because we'll be called from the
		@@ -15805,6 +15835,7 @@ public class PixelMapping {

		/**
		* Interpolate (bi-linear) X/Y corrections and flat-field data for the sensor
		* @param rgbOnly - only flat field, no geometry
		* @param px - pixel X coordinate (non-decimated)
		* @param py - pixel Y coordinate (non-decimated)
		* @return - vector of {corrX, corrY, alpha, flatfield_red, flatfield_green, flatfield_blue}
		@@ -16540,6 +16571,7 @@ public class PixelMapping {
		// for (int iLat=0;iLat<equirectangularMap.pixelsVertical;iLat++){
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		for (int iLat=ipLatAtomic.getAndIncrement(); iLat<equirectangularMap.pixelsVertical;iLat=ipLatAtomic.getAndIncrement()){
		double [] a={distortionC,distortionB,distortionA,distortionA5,distortionA6,distortionA7,distortionA8};
		@@ -16657,6 +16689,7 @@ public class PixelMapping {
		final int numFinished=ipLatDoneAtomic.getAndIncrement();
		// IJ.showProgress(progressValues[numFinished]);
		SwingUtilities.invokeLater(new Runnable() {
		@Override
		public void run() {
		// Here, we can safely update the GUI
		// because we'll be called from the
		@@ -16734,6 +16767,7 @@ public class PixelMapping {
		// for (int iLat=0;iLat<equirectangularMap.pixelsVertical;iLat++){
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		for (int iLat=ipLatAtomic.getAndIncrement(); iLat<equirectangularMap.pixelsVertical;iLat=ipLatAtomic.getAndIncrement()){

		@@ -16826,6 +16860,7 @@ public class PixelMapping {
		final int numFinished=ipLatDoneAtomic.getAndIncrement();
		// IJ.showProgress(progressValues[numFinished]);
		SwingUtilities.invokeLater(new Runnable() {
		@Override
		public void run() {
		// Here, we can safely update the GUI
		// because we'll be called from the

src/main/java/QuadCLT.java

+758 −713

Original line number	Diff line number	Diff line
		@@ -250,6 +250,7 @@ public class QuadCLT {
		//GeometryCorrection

		public double [][][][][] calculateCLTKernel ( // per color/per tileY/ per tileX/per quadrant (plus offset as 5-th)/per pixel
		final PixelMapping.SensorData sensor, // to calculate extra shift
		final ImageStack kernelStack, // first stack with 3 colors/slices convolution kernels
		final int kernelSize, // 64
		final EyesisCorrectionParameters.CLTParameters clt_parameters,
		@@ -294,6 +295,7 @@ public class QuadCLT {
		System.out.println("calculateCLTKernel():numberOfKernels="+numberOfKernels);
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		float [] kernelPixels= null; // will be initialized at first use NOT yet?
		double [] kernel= new double[kernelSize*kernelSize];
		@@ -328,7 +330,7 @@ public class QuadCLT {
		double s =0.0;
		for (int i=0;i<kernel.length;i++) s+=kernel[i];
		System.out.println("calculateCLTKernel(): sum(kernel_raw)="+s);
		sdfa_instance.showArrays(
		if (globalDebugLevel > 1) sdfa_instance.showArrays(
		kernel,
		size,
		size,
		@@ -350,7 +352,7 @@ public class QuadCLT {
		int klen = (2dtt_size-1) (2*dtt_size-1);
		for (int i = 0; i < klen; i++) s += kernel_centered[i];
		System.out.println("calculateCLTKernel(): sum(kernel_centered)="+s);
		sdfa_instance.showArrays(
		if (globalDebugLevel > 1) sdfa_instance.showArrays(
		kernel_centered,
		size,
		size,
		@@ -370,7 +372,7 @@ public class QuadCLT {
		int klen = (2dtt_size-1) (2*dtt_size-1);
		for (int i = 0; i < klen; i++) s += kernel_centered[i];
		System.out.println("calculateCLTKernel(): sum(kernel_normalized)="+s);
		sdfa_instance.showArrays(
		if (globalDebugLevel > 1) sdfa_instance.showArrays(
		kernel_centered,
		size,
		size,
		@@ -394,7 +396,7 @@ public class QuadCLT {
		String [] titles = {"CC", "SC", "CS", "SS"};
		int length=dbg_clt[0].length;
		int size=(int) Math.sqrt(length);
		sdfa_instance.showArrays(
		if (globalDebugLevel > 1) sdfa_instance.showArrays(
		dbg_clt,
		size,
		size,
		@@ -406,6 +408,43 @@ public class QuadCLT {
		clt_kernels[chn][tileY][tileX], // double [][] kernels, // set of 4 SS, AS, SA, AA kdernels, each dtt_size * dtt_size (may have 5-th with center shift
		dtt_size, // 8
		dtt);

		if ((globalDebugLevel > 0) && (tileY == clt_parameters.tileY/2) && (tileX == clt_parameters.tileX/2)) {
		System.out.println("calculateCLTKernel() - before corr: chn="+chn+" "+
		"tileX = "+clt_parameters.tileX+" ("+(clt_parameters.tileX/2)+") "+
		"tileY = "+clt_parameters.tileY+" ("+(clt_parameters.tileY/2)+") "+
		"center_x = "+clt_kernels[chn][tileY][tileX][4][0]+", "+
		"center_y = "+clt_kernels[chn][tileY][tileX][4][1]+", "+
		"full_dx = "+clt_kernels[chn][tileY][tileX][4][2]+", "+
		"full_dy = "+clt_kernels[chn][tileY][tileX][4][3]);
		}
		// Add sensor geometry correction (optional?)
		// Kernel center in pixels
		double kpx0 = (tileX -1 +0.5) * clt_parameters.kernel_step;
		double kpy0 = (tileY -1 +0.5) * clt_parameters.kernel_step;
		double [] corrPxPy = sensor.interpolateCorrectionVector(false, kpx0, kpy0);
		image_dtt.offsetKernelSensor(
		clt_kernels[chn][tileY][tileX], // double [][] clt_tile, // clt tile, including [4] - metadata
		// (corrPxPy[0] - kpx0), // double dx,
		// (corrPxPy[1] - kpy0)); // double dy)
		-corrPxPy[0], // double dx,
		-corrPxPy[1]); // double dy)

		if ((globalDebugLevel > 0) && (tileY == clt_parameters.tileY/2) && (tileX == clt_parameters.tileX/2)) {
		System.out.println("calculateCLTKernel() - after corr: chn="+chn+" "+
		"tileX = "+clt_parameters.tileX+" ("+(clt_parameters.tileX/2)+") "+
		"tileY = "+clt_parameters.tileY+" ("+(clt_parameters.tileY/2)+") "+
		"center_x = "+clt_kernels[chn][tileY][tileX][4][0]+", "+
		"center_y = "+clt_kernels[chn][tileY][tileX][4][1]+", "+
		"full_dx = "+clt_kernels[chn][tileY][tileX][4][2]+", "+
		"full_dy = "+clt_kernels[chn][tileY][tileX][4][3]);
		System.out.println("calculateCLTKernel() - after corr: chn="+chn+" "+
		"kpx0 = "+kpx0+
		"kpy0 = "+kpy0+
		"corrPxPy[0] = "+corrPxPy[0]+
		"corrPxPy[1] = "+corrPxPy[1]);
		}

		if ((globalDebugLevel > 0) && (tileY == clt_parameters.tileY/2) && (tileX == clt_parameters.tileX/2)) {
		double [][] dbg_clt = {
		clt_kernels[chn][tileY][tileX][0],
		@@ -415,7 +454,7 @@ public class QuadCLT {
		String [] titles = {"CC", "SC", "CS", "SS"};
		int length=dbg_clt[0].length;
		int size=(int) Math.sqrt(length);
		sdfa_instance.showArrays(
		if (globalDebugLevel > 1) sdfa_instance.showArrays(
		dbg_clt,
		size,
		size,
		@@ -474,6 +513,7 @@ public class QuadCLT {
		System.out.println("flattenCLTKernels():numberOfKernels="+numberOfKernels);
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		int chn,tileY,tileX;
		for (int nTile = ai.getAndIncrement(); nTile < numberOfKernels; nTile = ai.getAndIncrement()) {
		@@ -604,6 +644,7 @@ public class QuadCLT {
		System.out.println("flattenCLTKernels():numberOfKernels="+numberOfKernels);
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		int chn,tileY,tileX;
		for (int nTile = ai.getAndIncrement(); nTile < numberOfKernels; nTile = ai.getAndIncrement()) {
		@@ -642,6 +683,9 @@ public class QuadCLT {
		boolean updateStatus,
		int debugLevel
		){
		// get sensor geometry correction to apply to kernels as extra shifts
		PixelMapping.SensorData [] sensors = eyesisCorrections.pixelMapping.sensors;

		String [] sharpKernelPaths= correctionsParameters.selectKernelChannelFiles(
		0, // 0 - sharp, 1 - smooth
		eyesisCorrections.usedChannels.length, // numChannels, // number of channels
		@@ -671,6 +715,7 @@ public class QuadCLT {
		" kernel_sharp_stack.getHeight() = "+kernel_sharp_stack.getHeight());

		double [][][][][] kernels = calculateCLTKernel ( // per color/per tileY/ per tileX/per quadrant (plus offset as 5-th)/per pixel
		sensors[chn], // to calculate extra shift (kernels are centered around green)
		kernel_sharp_stack, // final ImageStack kernelStack, // first stack with 3 colors/slices convolution kernels
		srcKernelSize, // final int kernelSize, // 64
		clt_parameters, // final EyesisCorrectionParameters.CLTParameters clt_parameters,

Admin message