implementing initial orientation estimation, full window for eo (8295add0) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/calibration/Aberration_Calibration.java

+40 −10

Original line number	Diff line number	Diff line
		@@ -2165,7 +2165,7 @@ if (MORE_BUTTONS) {
		);
		// set initial orientation of the cameras from the sensors that see mpst of the matching pointers
		// just for the LMA to start
		DISTORTION_CALIBRATION_DATA.setInitialOrientation(true);
		DISTORTION_CALIBRATION_DATA.setInitialOrientation(PATTERN_PARAMETERS, true);
		return;
		}

		@@ -5871,7 +5871,7 @@ if (MORE_BUTTONS) {
		DISTORTION_CALIBRATION_DATA.updateSetOrientation(null); // restore orientation from (enabled) image files
		if (DEBUG_LEVEL>0) System.out.println("Setting sets orientation from per-grid image data");
		}
		if (overwriteAll) DISTORTION_CALIBRATION_DATA.setInitialOrientation(overwriteAll); // needed here? modify?
		if (overwriteAll) DISTORTION_CALIBRATION_DATA.setInitialOrientation(PATTERN_PARAMETERS, overwriteAll); // needed here? modify?
		if ((DEBUG_LEVEL>0) && (DISTORTION_CALIBRATION_DATA.gIS!=null)){
		System.out.println("There are now "+DISTORTION_CALIBRATION_DATA.getNumberOfEstimated(true)+ "("+DISTORTION_CALIBRATION_DATA.getNumberOfEstimated(false)+") images with estimated orientation");
		}
		@@ -6255,7 +6255,7 @@ if (MORE_BUTTONS) {
		/* ======================================================================== */
		if (label.equals("Get Orientation")) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		if (DEBUG_LEVEL>0){
		if (DEBUG_LEVEL>10) { // 0){
		IJ.showMessage("disabled option");
		return;
		}
		@@ -6278,11 +6278,22 @@ if (MORE_BUTTONS) {
		System.out.println("GONIOMETER was initialized");
		}
		// initialize needed classes
		if (DISTORTION_CALIBRATION_DATA == null ) {
		System.out.println("Initiaslizing DISTORTION_CALIBRATION_DATA");
		DISTORTION_CALIBRATION_DATA=new DistortionCalibrationData( // images are not setup yet
		EYESIS_CAMERA_PARAMETERS, //EyesisCameraParameters eyesisCameraParameters
		GONIOMETER_PARAMETERS);

		} else if (DEBUG_LEVEL>1){
		System.out.println("DISTORTION_CALIBRATION_DATA was initialized");
		}
		if ((LENS_DISTORTIONS!=null) && (LENS_DISTORTIONS.fittingStrategy!=null)) {
		LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData=DISTORTION_CALIBRATION_DATA;
		if (DEBUG_LEVEL>0){
		System.out.println("Setting LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData=DISTORTION_CALIBRATION_DATA");
		}
		} else if (DEBUG_LEVEL>0){
		System.out.println("Was already set: LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData=DISTORTION_CALIBRATION_DATA");
		}

		if (DEBUG_LEVEL>1){
		@@ -6301,9 +6312,10 @@ if (MORE_BUTTONS) {
		IJ.showMessage("Error",msg);
		return;
		}

		LENS_DISTORTIONS=new Distortions(LENS_DISTORTION_PARAMETERS,PATTERN_PARAMETERS,REFINE_PARAMETERS,this.SYNC_COMMAND.stopRequested);
		if (DEBUG_LEVEL>1){
		System.out.println("Initiaslizing Distortions class");
		System.out.println("Initiaslizing Distortions class (LENS_DISTORTIONS)");
		}
		} else if (DEBUG_LEVEL>1){
		System.out.println("LENS_DISTORTIONS was initialized");
		@@ -6324,6 +6336,9 @@ if (MORE_BUTTONS) {
		return;
		}
		GONIOMETER_PARAMETERS.gridGeometryFile=gridPathname;
		if (DEBUG_LEVEL > 0){
		System.out.println("Using pattern file: "+gridPathname);
		}

		// Find curernt orientation
		double [] currentOrientation=GONIOMETER.estimateOrientation (
		@@ -9871,7 +9886,22 @@ if (MORE_BUTTONS) {

		PATTERN_PARAMETERS.debugLevel=MASTER_DEBUG_LEVEL;
		EYESIS_CAMERA_PARAMETERS.updateNumstations (numStations);
		DISTORTION_CALIBRATION_DATA=new DistortionCalibrationData( // new way for LWIR - initialize form dirs

		// Adding class here to use for orientation estimation - will not be needed?
		if (GONIOMETER==null) {
		GONIOMETER= new Goniometer(
		CAMERAS, // CalibrationHardwareInterface.CamerasInterface cameras,
		DISTORTION, //MatchSimulatedPattern.DistortionParameters distortion,
		PATTERN_DETECT, //MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
		EYESIS_CAMERA_PARAMETERS, //EyesisCameraParameters eyesisCameraParameters,
		LASER_POINTERS, // MatchSimulatedPattern.LaserPointer laserPointers
		SIMUL, //SimulationPattern.SimulParameters simulParametersDefault,
		GONIOMETER_PARAMETERS, //LensAdjustment.FocusMeasurementParameters focusMeasurementParameters,
		DISTORTION_PROCESS_CONFIGURATION
		);
		}

		DISTORTION_CALIBRATION_DATA=new DistortionCalibrationData( // new way for LWIR - initialize from dirs
		gridFileDirs,
		sourceStationDirs,
		gridFilter,
		@@ -9889,7 +9919,7 @@ if (MORE_BUTTONS) {
		);
		// set initial orientation of the cameras from the sensors that see most of the matching pointers
		// just for the LMA to start
		DISTORTION_CALIBRATION_DATA.setInitialOrientation(true);
		DISTORTION_CALIBRATION_DATA.setInitialOrientation(PATTERN_PARAMETERS, true);
		return true;

src/main/java/com/elphel/imagej/calibration/DistortionCalibrationData.java

+167 −9

Original line number	Diff line number	Diff line
		@@ -46,6 +46,7 @@ import com.elphel.imagej.common.ShowDoubleFloatArrays;
		import com.elphel.imagej.common.WindowTools;
		import com.elphel.imagej.jp4.JP46_Reader_camera;

		import Jama.Matrix;
		import ij.IJ;
		import ij.ImagePlus;
		import ij.ImageStack;
		@@ -122,7 +123,7 @@ import ij.text.TextWindow;
		public String source_path = null; // Full path of the source image this grid was calculated from
		public double [][] laserPixelCoordinates=null; // first index - absolute number of pointer. Each element may be either null or {x,y} pair
		// moving for new files to have laser UV contained in the file
		public double [][] laserUVCoordinates=null; // first index - absolute number of pointer. Each element may be either null or {u,v} pair
		public double [][] laserUVCoordinates=null; // first index - absolute number of pointer. Each element may be either null or {u,v} pair - never used??????
		public int matchedPointers=0;
		public int hintedMatch=-1; // -1 - not tried, 0 - no real grid (i.e. double reflection), applied orientation, applied orientation and shift
		public boolean enabled=true; //false; // to mask out some images from all strategy steps (i.e w/o reliable absolute calibration)
		@@ -153,6 +154,7 @@ import ij.text.TextWindow;
		public double getGridPeriod() { return gridPeriod;}
		public void setGridPeriod(double v) {gridPeriod = v;}
		public int getSetNumber(){return this.setNumber;}
		public int getImageNumber() {return this.imgNumber;}
		public GridImageParameters(int index){
		this.imgNumber=index;
		}
		@@ -2259,7 +2261,7 @@ import ij.text.TextWindow;
		((this.gIP[i].matchedPointers>0) && (this.gIP[i].hintedMatch>0)) \|\| // orientation and one pointer
		((this.gIP[i].hintedMatch>1) && enableNoLaser)) { // do not use bottom images w/o matched pointers
		// before enabling - copy orientation from gIS
		if (!this.gIP[i].enabled && (gIS_index[i]>=0)){
		if (!this.gIP[i].enabled && (gIS_index[i]>=0)){ // FIXME - is it correct to use set index 0?
		if (!Double.isNaN(this.gIS[gIS_index[i]].goniometerTilt)) setGH(i,this.gIS[gIS_index[i]].goniometerTilt );
		if (!Double.isNaN(this.gIS[gIS_index[i]].goniometerAxial)) setGA(i,this.gIS[gIS_index[i]].goniometerAxial );
		}
		@@ -2407,9 +2409,11 @@ import ij.text.TextWindow;
		/**
		* Set goniometer initial orientation from the image with maximal number of laser pointers (make averaging later?)
		* Needed before LMA to have some reasonable initial orientation
		* @param overwriteAll if true, overwrite orientation data even if it is alredy not NaN, false -skipp those that have orientation set
		* @param overwriteAll if true, overwrite orientation data even if it is already not NaN, false -skip those that have orientation set
		*/
		public void setInitialOrientation(boolean overwriteAll){
		public void setInitialOrientation(
		PatternParameters patternParameters,
		boolean overwriteAll) {
		if (this.debugLevel>0) {
		System.out.println("setInitialOrientation("+overwriteAll+"), debugLevel= "+this.debugLevel);
		}
		@@ -2427,6 +2431,70 @@ import ij.text.TextWindow;
		}
		if (bestRating>0){
		EyesisSubCameraParameters esp = this.eyesisCameraParameters.eyesisSubCameras[stationNumber][bestChannel];
		double [] uv_center = getGridUVfromXY(
		esp.px0, // final double px,
		esp.py0, // final double py,
		this.gIS[i].imageSet[bestChannel].getImageNumber(), // final int fileNumber,
		true); // boolean use_extra)
		// find UV of the center of the image getImageNumber
		if (uv_center == null) {
		if (this.debugLevel>0) {
		System.out.println("Center UV = NULL");
		}
		} else {
		if (this.debugLevel>0) {
		System.out.println("Center UV = "+uv_center[0]+","+uv_center[1]);
		}
		double [] patt_xyz = patternParameters.getXYZ(
		uv_center, // double [] uv,
		false, // boolean verbose,
		this.gIS[i].getStationNumber()); // int station); // u=0,v=0 - center!

		if (patt_xyz == null) {
		if (this.debugLevel>0) {
		System.out.println("Center UV = NULL");
		}
		} else {
		if (this.debugLevel>0) {
		System.out.println("Center XYZ = "+patt_xyz[0]+","+patt_xyz[1]+","+patt_xyz[2]);
		}
		// Calculate position relative to the view point on the target
		double [] aview = {
		patt_xyz[0]- this.gIS[i].GXYZ[0],
		-patt_xyz[1]+ (this.gIS[i].GXYZ[1] - this.gIS[i].centerAboveHorizontal),
		-patt_xyz[2]+ this.gIS[i].GXYZ[2]
		};
		Matrix mview = new Matrix(aview,3);
		double phi = -Math.PI/180.0*this.gIS[i].horAxisErrPhi;
		double cp = Math.cos(phi);
		double sp = Math.sin(phi);
		double [][] aphi = {
		{ cp, 0.0, sp},
		{0.0, 1.0, 0.0},
		{-sp, 0.0, cp}};
		Matrix mphi = new Matrix(aphi);
		Matrix mview_gon = mphi.times(mview); // view point on the target from the goniometer
		double tilt = -Math.atan2(mview_gon.get(1, 0), mview_gon.get(2, 0)); // y pointed up
		double ct = Math.cos(tilt);
		double st = Math.sin(tilt);

		double [][] atilt = {
		{1.0, 0.0, 0.0},
		{0.0, ct, st},
		{0.0, -st, ct}};
		Matrix mtilt = new Matrix(atilt);
		Matrix mview_tilt = mtilt.times(mview_gon); // view point on the target from the tilted goniometer
		double az = Math.atan2(mview_tilt.get(0, 0), mview_tilt.get(2, 0)); // x pointed right

		double tilt_deg = tilt/Math.PI*180;
		double az_deg = az/Math.PI*180;
		if (this.debugLevel>0) {
		System.out.println("Tilt = "+tilt_deg+", az = "+az_deg);
		System.out.print("");
		}
		}
		}

		if (overwriteAll \|\| Double.isNaN(this.gIS[i].goniometerAxial)){
		// System.out.println("setInitialOrientation("+overwriteAll+"), Double.isNaN(this.gIS["+i+"].goniometerAxial)="+Double.isNaN(this.gIS[i].goniometerAxial));

		@@ -2435,7 +2503,9 @@ import ij.text.TextWindow;
		for (int j=0;j<this.gIS[i].imageSet.length;j++) if (this.gIS[i].imageSet[j]!=null) setGA(this.gIS[i].imageSet[j].imgNumber,this.gIS[i].goniometerAxial);
		this.gIS[i].orientationEstimated=true;
		if (this.debugLevel>1) {
		System.out.println("Setting goniometerAxial for the image set #"+i+" ("+this.gIS[i].timeStamp+") to "+this.gIS[i].goniometerAxial+" +++++ orientationEstimated==true +++++");
		System.out.print(String.format("Setting goniometerAxial for the image set #%4d (%18.6f) to ", i, this.gIS[i].timeStamp));
		System.out.println(""+this.gIS[i].goniometerAxial+" +++++ orientationEstimated==true +++++");
		// System.out.println("Setting goniometerAxial for the image set #"+i+" ("+this.gIS[i].timeStamp+") to "+this.gIS[i].goniometerAxial+" +++++ orientationEstimated==true +++++");
		}
		}
		if (overwriteAll \|\| Double.isNaN(this.gIS[i].goniometerTilt )){
		@@ -2444,7 +2514,8 @@ import ij.text.TextWindow;
		for (int j=0;j<this.gIS[i].imageSet.length;j++) if (this.gIS[i].imageSet[j]!=null) setGH(this.gIS[i].imageSet[j].imgNumber,this.gIS[i].goniometerTilt);
		this.gIS[i].orientationEstimated=true;
		if (this.debugLevel>1) {
		System.out.println("Setting goniometerTilt for the image set #"+i+" ("+this.gIS[i].timeStamp+") to "+this.gIS[i].goniometerTilt+" ===== orientationEstimated==true =====");
		System.out.print(String.format("Setting goniometerTilt for the image set #%4d (%18.6f) to ", i, this.gIS[i].timeStamp));
		System.out.println(""+this.gIS[i].goniometerTilt+" ===== orientationEstimated==true =====");
		}
		}
		}
		@@ -3334,7 +3405,7 @@ import ij.text.TextWindow;
		len += this.gIP[fileNumber].pixelsXY_extra.length;
		}
		if (len<3) {
		this.gIP[fileNumber].gridPeriod=Double.NaN;
		this.gIP[fileNumber].setGridPeriod(Double.NaN);
		} else {
		// double [][][] data =new double [this.gIP[fileNumber].pixelsXY.length][2][2];
		double [][][] data =new double [len][2][2];
		@@ -3359,12 +3430,12 @@ import ij.text.TextWindow;
		}
		double [][] coeff=new PolynomialApproximation(this.debugLevel).quadraticApproximation(data, true); // force linear
		if (coeff!=null) {
		this.gIP[fileNumber].gridPeriod=2.0/Math.sqrt(coeff[0][0]coeff[0][0]+coeff[0][1]coeff[0][1]+coeff[1][0]coeff[1][0]+coeff[1][1]coeff[1][1]);
		this.gIP[fileNumber].setGridPeriod(2.0/Math.sqrt(coeff[0][0]coeff[0][0]+coeff[0][1]coeff[0][1]+coeff[1][0]coeff[1][0]+coeff[1][1]coeff[1][1]));
		if (this.debugLevel>3) {
		System.out.println("coeff[][]={{"+coeff[0][0]+","+coeff[0][1]+"},{"+coeff[1][0]+","+coeff[1][1]+"}}");
		}
		} else {
		this.gIP[fileNumber].gridPeriod=Double.NaN;
		this.gIP[fileNumber].setGridPeriod(Double.NaN);
		}
		}
		if (this.debugLevel>3) {
		@@ -3374,6 +3445,93 @@ import ij.text.TextWindow;

		}

		public double [] getGridUVfromXY(
		final double px,
		final double py,
		final int fileNumber,
		boolean use_extra){ // use out-of grid nodes (can be w/o absolute matching
		use_extra &= (this.gIP[fileNumber].pixelsXY_extra !=null);
		int len = (this.gIP[fileNumber].pixelsXY==null)? 0 : this.gIP[fileNumber].pixelsXY.length;
		final int len0 = len;
		if (use_extra ) {
		len += this.gIP[fileNumber].pixelsXY_extra.length;
		}
		if (len<3) {
		return null;
		}
		final double [][] all_xy = new double [len][2];
		final int [][] all_uv = new int [len][2];
		if (len0 > 0) {
		System.arraycopy(this.gIP[fileNumber].pixelsXY, 0, all_xy, 0, len0);
		System.arraycopy(this.gIP[fileNumber].pixelsUV, 0, all_uv, 0, len0);
		}
		if (len > len0) {
		System.arraycopy(this.gIP[fileNumber].pixelsXY_extra, 0, all_xy, len0, len-len0);
		System.arraycopy(this.gIP[fileNumber].pixelsUV_extra, 0, all_uv, len0, len-len0);
		}

		ArrayList<Integer> neibs = new ArrayList<Integer>();
		for (int i = 0; i < len; i++) neibs.add(i);
		Collections.sort(neibs, new Comparator<Integer>() {
		@Override
		public int compare(Integer lhs, Integer rhs) {
		// double [] xy_lhs = (lhs < len0)? gIP[fileNumber].pixelsXY[lhs] : gIP[fileNumber].pixelsXY_extra[lhs-len0];
		// double [] xy_rhs = (rhs < len0)? gIP[fileNumber].pixelsXY[rhs] : gIP[fileNumber].pixelsXY_extra[rhs-len0];
		double x_lhs = all_xy[lhs][0] - px;
		double y_lhs = all_xy[lhs][1] - py;
		double x_rhs = all_xy[rhs][0] - px;
		double y_rhs = all_xy[rhs][1] - py;
		double l2_lhs = x_lhsx_lhs + y_lhsy_lhs;
		double l2_rhs = x_rhsx_rhs + y_rhsy_rhs;
		return l2_rhs > l2_lhs ? -1 : (l2_rhs < l2_lhs) ? 1 : 0;
		}
		});
		// now list neibs start with closest to px,py node. Get first with non-collinearU,V
		int dlen = -1;
		int [] i01 = {neibs.get(0), neibs.get(1)};
		int [] duv0 = {all_uv[i01[1]][0]-all_uv[i01[0]][0], all_uv[i01[1]][1]-all_uv[i01[0]][1]};
		for (int ii = 2;ii < len; ii++) {
		int i = neibs.get(ii);
		// int [] duv = {all_uv[i][0]-all_uv[0][0], all_uv[i][1]-all_uv[0][1]};
		int idet = (duv0[0] * (all_uv[i][1]-all_uv[i01[0]][1]))
		- (duv0[1] * (all_uv[i][0]-all_uv[i01[0]][0]));
		if (idet != 0) {
		dlen = i + 1;
		break;
		}
		}
		if (dlen < 0) {
		return null;
		}
		double [][][] data =new double [dlen][2][2];
		// U(x,y), v(x,y)
		for (int i=0; i < dlen; i++){
		int indx = neibs.get(i);
		data[i][0][0]=all_xy[indx][0];
		data[i][0][1]=all_xy[indx][1];
		data[i][1][0]=all_uv[indx][0];
		data[i][1][1]=all_uv[indx][1];
		}
		double [][] coeff=new PolynomialApproximation(this.debugLevel).quadraticApproximation(data, true); // force linear
		if (coeff == null) {
		return null;
		}
		double [] uv0 =
		{ (coeff[0][0] * px + coeff[0][1] * py + coeff[0][2]),
		(coeff[1][0] * px + coeff[1][1] * py + coeff[1][2])};

		int [][] reMap= MatchSimulatedPattern.getRemapMatrix(this.gIP[fileNumber].getUVShiftRot());
		// double [] uv = { reMap[0][0]uv0[0] + reMap[0][1] uv0[1] + reMap[0][2], // u
		// ( reMap[1][0]uv0[0] + reMap[1][1] uv0[1] + reMap[1][2])}; // v;
		// Sign?
		double [] uv = { reMap[0][0]uv0[0] + reMap[0][1] uv0[1] - reMap[0][2], // u
		( reMap[1][0]uv0[0] + reMap[1][1] uv0[1] - reMap[1][2])}; // v;

		return uv;
		}



		public int [] setGridsWithRemap(
		int fileNumber,
		int [][] reMap,

src/main/java/com/elphel/imagej/calibration/Goniometer.java

+5 −1

Original line number	Diff line number	Diff line
		@@ -771,7 +771,7 @@ horizontal axis:
		throw new IllegalArgumentException(msg);
		}

		// remove unneeded, copied from updateFocusGrid()
		// remove unneeded, copied from updateFocusGrid() Now it is not needed?
		SimulationPattern.SimulParameters simulParameters = modifySimulParameters();
		MatchSimulatedPattern.DistortionParameters distortionParameters = modifyDistortionParameters();

		@@ -1007,6 +1007,10 @@ horizontal axis:
		};
		return result;
		}




		public static class GoniometerParameters {
		public String gridGeometryFile="";
		public String initialCalibrationFile="";

src/main/java/com/elphel/imagej/calibration/MatchSimulatedPattern.java

+5 −2

Original line number	Diff line number	Diff line
		@@ -6818,8 +6818,11 @@ public class MatchSimulatedPattern {
		numPointerDetected++;
		}
		}
		if (numPointerDetected>0) return pointersXY;
		else return null;
		if (numPointerDetected>0) {
		return pointersXY;
		} else {
		return null;
		}
		}

		public static void setPointersXYUV(ImagePlus imp, double [][] pointersXYUV){

src/main/java/com/elphel/imagej/calibration/PatternParameters.java

+26 −0

Original line number	Diff line number	Diff line
		@@ -739,6 +739,7 @@ import ij.io.Opener;
		int [] iUV={u1-this.U0, v1-this.V0};
		return iUV;
		}

		public double[] getXYZM(int u, int v, boolean verbose, int station){ // u=0,v=0 - center!
		int u1=u+this.U0;
		int v1=v+this.V0;
		@@ -761,6 +762,31 @@ import ij.io.Opener;
		return result;
		// return this.gridGeometry[v1][u1];
		}
		public double[] getXYZ(
		double [] uv,
		boolean verbose,
		int station){ // u=0,v=0 - center!
		int iu = (int) Math.floor(uv[0]);
		int iv = (int) Math.floor(uv[1]);
		double fu = uv[0] - iu;
		double fv = uv[1] - iv;
		double [][] corn = new double [4][];
		corn[0] = getXYZM(iu, iv, verbose, station);
		corn[1] = getXYZM(iu + 1, iv, verbose, station);
		corn[2] = getXYZM(iu, iv + 1, verbose, station);
		corn[3] = getXYZM(iu + 1, iv + 1, verbose, station);
		if ((corn[0] == null) \|\| (corn[1] == null) \|\| (corn[2] == null) \|\| (corn[3] == null)) {
		System.out.println("Optical axis outside of te grid: TODO: modify getXYZM() to handle!");
		return null;
		}
		double [] rslt_xyz = new double[3];
		rslt_xyz[0] = (1-fu) * (1-fv) * corn[0][0] + fu * (1-fv) * corn[1][0] + (1-fu) * fv * corn[2][0] + fu * fv * corn[3][0];
		rslt_xyz[1] = (1-fu) * (1-fv) * corn[0][1] + fu * (1-fv) * corn[1][1] + (1-fu) * fv * corn[2][1] + fu * fv * corn[3][1];
		rslt_xyz[2] = (1-fu) * (1-fv) * corn[0][2] + fu * (1-fv) * corn[1][2] + (1-fu) * fv * corn[2][2] + fu * fv * corn[3][2];
		return rslt_xyz;
		}


		public int getGridIndex(int u, int v){ // u=0,v=0 - center!
		int u1=u+this.U0;
		int v1=v+this.V0;

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