Added option to deconvolve patterns using projected (not extracted) grid (9e7ad476) · Commits · Elphel / imagej-elphel

src/main/java/Distortions.java

+24 −20

Original line number	Original line	Diff line number	Diff line
	@@ -2486,7 +2486,8 @@ For each point in the image
	subCam,		subCam,
	goniometerTilt, // Tilt, goniometerHorizontal		goniometerTilt, // Tilt, goniometerHorizontal
	goniometerAxial, // Axial,goniometerAxial		goniometerAxial, // Axial,goniometerAxial
	-1 // use camera parameters, not imageSet		-1, // use camera parameters, not imageSet
			true // filter border
	);		);
	if (hintGrid==null){		if (hintGrid==null){
	String msg="Grid is not visible for subcamera="+subCam+", tilt="+goniometerTilt+", axial="+goniometerAxial;		String msg="Grid is not visible for subcamera="+subCam+", tilt="+goniometerTilt+", axial="+goniometerAxial;
	@@ -2664,7 +2665,8 @@ For each point in the image
	dcd.gIP[numGridImage].channel,		dcd.gIP[numGridImage].channel,
	goniometerTiltAxial[0], // Tilt, goniometerHorizontal		goniometerTiltAxial[0], // Tilt, goniometerHorizontal
	goniometerTiltAxial[1], // Axial,goniometerAxial		goniometerTiltAxial[1], // Axial,goniometerAxial
	setNumber // -1 or specific image set		setNumber, // -1 or specific image set
			true // filter border
	);		);
	if (global_debug_level>0){		if (global_debug_level>0){
	System.out.println("\n**** applyHintedGrids(): processing grid image # "+numGridImage+", path="+dcd.gIP[numGridImage].path);		System.out.println("\n**** applyHintedGrids(): processing grid image # "+numGridImage+", path="+dcd.gIP[numGridImage].path);
	@@ -2859,7 +2861,6 @@ For each point in the image
	pixels[4][index]=1000.0;		pixels[4][index]=1000.0;
	}		}
	(new showDoubleFloatArrays()).showArrays(pixels, width, height, true, "grid-"+numGridImage, titles);		(new showDoubleFloatArrays()).showArrays(pixels, width, height, true, "grid-"+numGridImage, titles);

	}		}
	public void showGridAndHint(){		public void showGridAndHint(){
	GenericDialog gd=new GenericDialog("Show selected grid and/or hint grid");		GenericDialog gd=new GenericDialog("Show selected grid and/or hint grid");
	@@ -2903,7 +2904,8 @@ For each point in the image
	fittingStrategy.distortionCalibrationData.gIP[numGridImage].channel,		fittingStrategy.distortionCalibrationData.gIP[numGridImage].channel,
	goniometerTiltAxial[0], // Tilt, goniometerHorizontal		goniometerTiltAxial[0], // Tilt, goniometerHorizontal
	goniometerTiltAxial[1], // Axial,goniometerAxial		goniometerTiltAxial[1], // Axial,goniometerAxial
	useSetData?fittingStrategy.distortionCalibrationData.gIP[numGridImage].setNumber:-1		(useSetData?fittingStrategy.distortionCalibrationData.gIP[numGridImage].setNumber:-1),
			true // filter border
	);		);
	showHintGrid(hintGrid,"hint-"+numGridImage);		showHintGrid(hintGrid,"hint-"+numGridImage);

	@@ -3061,7 +3063,8 @@ For each point in the image
	int subCamera,		int subCamera,
	double goniometerHorizontal, // Tilt		double goniometerHorizontal, // Tilt
	double goniometerAxial, // Axial		double goniometerAxial, // Axial
	int imageSet){		int imageSet,
			boolean filterBorder){
	int debugThreshold=2;		int debugThreshold=2;
	// Get parameter vector (22) for the selected sensor, current Eyesisparameters and specified orientation angles		// Get parameter vector (22) for the selected sensor, current Eyesisparameters and specified orientation angles
	double [] parVector=fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getParametersVector(stationNumber,subCamera);		double [] parVector=fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getParametersVector(stationNumber,subCamera);
	@@ -3139,6 +3142,7 @@ For each point in the image
	}		}
	}		}
	}		}
			if (filterBorder){
	// now filter border nodes		// now filter border nodes
	boolean [] mask= new boolean [patternGeometry.length*patternGeometry[0].length];		boolean [] mask= new boolean [patternGeometry.length*patternGeometry[0].length];
	int index=0;		int index=0;
	@@ -3153,7 +3157,7 @@ For each point in the image
	for (int v=0;v<result.length;v++) for (int u=0;u<result[v].length;u++){		for (int v=0;v<result.length;v++) for (int u=0;u<result[v].length;u++){
	if (!mask[index++]) result[v][u]=null;		if (!mask[index++]) result[v][u]=null;
	}		}
			}
	if (this.debugLevel>debugThreshold){		if (this.debugLevel>debugThreshold){
	for (int v=0;v<result.length;v++) for (int u=0;u<result[v].length;u++){		for (int v=0;v<result.length;v++) for (int u=0;u<result[v].length;u++){
	int uv=u+v*result[v].length;		int uv=u+v*result[v].length;

src/main/java/EyesisAberrations.java

+32 −4

Original line number	Original line	Diff line number	Diff line
	@@ -1073,6 +1073,8 @@ public class EyesisAberrations {
	int debugLevel		int debugLevel
	){		){
	Distortions.DistortionCalibrationData distortionCalibrationData= distortions.fittingStrategy.distortionCalibrationData;		Distortions.DistortionCalibrationData distortionCalibrationData= distortions.fittingStrategy.distortionCalibrationData;
			boolean partialToReprojected=this.aberrationParameters.partialToReprojected;
			// this.distortions is set to top level LENS_DISTORTIONS
	if (distortions==null){		if (distortions==null){
	String msg="Distortions instance does not exist, exiting";		String msg="Distortions instance does not exist, exiting";
	IJ.showMessage("Error",msg);		IJ.showMessage("Error",msg);
	@@ -1212,7 +1214,7 @@ public class EyesisAberrations {
	}		}
	// reorder in the ascending channel number order		// reorder in the ascending channel number order
	String [][] files=new String [numFiles][2]; // 0 - source, 1 - result		String [][] files=new String [numFiles][2]; // 0 - source, 1 - result
	int [] fileIndices =new int [numFiles]; // needed to mark bad kernels		int [] fileIndices =new int [numFiles]; // needed to mark bad kernels (and also to reference grid parameters to replace extracted)
	int numListedFiles=0;		int numListedFiles=0;
	int numChannel=0;		int numChannel=0;
	while (numListedFiles<numFiles) {		while (numListedFiles<numFiles) {
	@@ -1239,6 +1241,22 @@ public class EyesisAberrations {
	int iRetry=0;		int iRetry=0;
	for (iRetry=0;iRetry<MaxRetries;iRetry++){ // is this retry needed?		for (iRetry=0;iRetry<MaxRetries;iRetry++){ // is this retry needed?
	try {		try {

			double [][][] projectedGrid=null;
			double hintTolerance=0.0;
			if (partialToReprojected){ // replace px, py with projected values form the grid
			// this.distortions is set to the global LENS_DISTORTIONS
			int numGridImage=fileIndices[imgNum];
			projectedGrid=distortions.estimateGridOnSensor( // return grid array [v][u][0- x, 1 - y, 2 - u, 3 - v]
			distortions.fittingStrategy.distortionCalibrationData.getImageStation(numGridImage), // station number,
			distortions.fittingStrategy.distortionCalibrationData.gIP[numGridImage].channel, // subCamera,
			Double.NaN, // goniometerHorizontal, - not used
			Double.NaN, // goniometerAxial, - not used
			distortions.fittingStrategy.distortionCalibrationData.gIP[numGridImage].getSetNumber(), //imageSet,
			true); //filterBorder)
			hintTolerance=5.0; // TODO:set from configurable parameter
			}

	int rslt=matchSimulatedPattern.calculateDistortions(		int rslt=matchSimulatedPattern.calculateDistortions(
	distortionParameters, //		distortionParameters, //
	patternDetectParameters,		patternDetectParameters,
	@@ -1247,9 +1265,8 @@ public class EyesisAberrations {
	imp,		imp,
	null, // LaserPointer laserPointer, // LaserPointer object or null		null, // LaserPointer laserPointer, // LaserPointer object or null
	true, // don't care -removeOutOfGridPointers		true, // don't care -removeOutOfGridPointers
	null, // double [][][] hintGrid, // predicted grid array (or null)		projectedGrid, // null, // double [][][] hintGrid, // predicted grid array (or null)
	0, // double hintGridTolerance, // allowed mismatch (fraction of period) or 0 - orientation only		hintTolerance, // 0, // double hintGridTolerance, // allowed mismatch (fraction of period) or 0 - orientation only

	threadsMax,		threadsMax,
	updateStatus,		updateStatus,
	debugLevel,		debugLevel,
	@@ -1259,6 +1276,11 @@ public class EyesisAberrations {
	if (debugLevel>0) System.out.println("calculateDistortions failed, returned error code "+rslt+" iRetry="+iRetry+" (of "+MaxRetries+")");		if (debugLevel>0) System.out.println("calculateDistortions failed, returned error code "+rslt+" iRetry="+iRetry+" (of "+MaxRetries+")");
	continue;		continue;
	}		}
			// now replace extracted grid X,Y with projected:
			if (projectedGrid!=null){
			int numReplaced= matchSimulatedPattern.replaceGridXYWithProjected(projectedGrid);
			if (debugLevel>0) System.out.println("Replaced extracted XY with projected ones for "+numReplaced+" nodes");
			}
	correlationSizesUsed=matchSimulatedPattern.getCorrelationSizesUsed();		correlationSizesUsed=matchSimulatedPattern.getCorrelationSizesUsed();
	simArray= (new SimulationPattern(simulParameters)).simulateGridAll (		simArray= (new SimulationPattern(simulParameters)).simulateGridAll (
	imp.getWidth(),		imp.getWidth(),
	@@ -4428,6 +4450,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	public boolean autoReCalibrateIgnoreLaser=false; // "Ignore laser pointers on recalibrate"		public boolean autoReCalibrateIgnoreLaser=false; // "Ignore laser pointers on recalibrate"
	public boolean noMessageBoxes=true;		public boolean noMessageBoxes=true;
	public boolean overwriteResultFiles=false;		public boolean overwriteResultFiles=false;
			public boolean partialToReprojected=true; // Use reprojected grid for partial kernel calculation (false - use extracted)
	public int seriesNumber=0;		public int seriesNumber=0;
	public boolean allImages;		public boolean allImages;
	public String sourcePrefix="";		public String sourcePrefix="";
	@@ -4460,6 +4483,8 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	properties.setProperty(prefix+"autoReCalibrateIgnoreLaser",this.autoReCalibrateIgnoreLaser+"");		properties.setProperty(prefix+"autoReCalibrateIgnoreLaser",this.autoReCalibrateIgnoreLaser+"");
	properties.setProperty(prefix+"noMessageBoxes",this.noMessageBoxes+"");		properties.setProperty(prefix+"noMessageBoxes",this.noMessageBoxes+"");
	properties.setProperty(prefix+"overwriteResultFiles",this.overwriteResultFiles+"");		properties.setProperty(prefix+"overwriteResultFiles",this.overwriteResultFiles+"");
			properties.setProperty(prefix+"partialToReprojected",this.partialToReprojected+"");

	properties.setProperty(prefix+"seriesNumber",this.seriesNumber+"");		properties.setProperty(prefix+"seriesNumber",this.seriesNumber+"");
	properties.setProperty(prefix+"allImages",this.allImages+"");		properties.setProperty(prefix+"allImages",this.allImages+"");

	@@ -4498,6 +4523,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	if (properties.getProperty(prefix+"autoReCalibrateIgnoreLaser")!=null) this.autoReCalibrateIgnoreLaser=Boolean.parseBoolean(properties.getProperty(prefix+"autoReCalibrateIgnoreLaser"));		if (properties.getProperty(prefix+"autoReCalibrateIgnoreLaser")!=null) this.autoReCalibrateIgnoreLaser=Boolean.parseBoolean(properties.getProperty(prefix+"autoReCalibrateIgnoreLaser"));
	if (properties.getProperty(prefix+"noMessageBoxes")!=null) this.noMessageBoxes=Boolean.parseBoolean(properties.getProperty(prefix+"noMessageBoxes"));		if (properties.getProperty(prefix+"noMessageBoxes")!=null) this.noMessageBoxes=Boolean.parseBoolean(properties.getProperty(prefix+"noMessageBoxes"));
	if (properties.getProperty(prefix+"overwriteResultFiles")!=null) this.overwriteResultFiles=Boolean.parseBoolean(properties.getProperty(prefix+"overwriteResultFiles"));		if (properties.getProperty(prefix+"overwriteResultFiles")!=null) this.overwriteResultFiles=Boolean.parseBoolean(properties.getProperty(prefix+"overwriteResultFiles"));
			if (properties.getProperty(prefix+"partialToReprojected")!=null) this.partialToReprojected=Boolean.parseBoolean(properties.getProperty(prefix+"partialToReprojected"));
	if (properties.getProperty(prefix+"seriesNumber")!=null) this.seriesNumber=Integer.parseInt(properties.getProperty(prefix+"seriesNumber"));		if (properties.getProperty(prefix+"seriesNumber")!=null) this.seriesNumber=Integer.parseInt(properties.getProperty(prefix+"seriesNumber"));
	if (properties.getProperty(prefix+"allImages")!=null) this.allImages=Boolean.parseBoolean(properties.getProperty(prefix+"allImages"));		if (properties.getProperty(prefix+"allImages")!=null) this.allImages=Boolean.parseBoolean(properties.getProperty(prefix+"allImages"));
	if (properties.getProperty(prefix+"sourcePrefix")!=null) this.sourcePrefix=properties.getProperty(prefix+"sourcePrefix");		if (properties.getProperty(prefix+"sourcePrefix")!=null) this.sourcePrefix=properties.getProperty(prefix+"sourcePrefix");
	@@ -4629,6 +4655,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	gd.addCheckbox("Select aberrations kernels directory", false);		gd.addCheckbox("Select aberrations kernels directory", false);
	gd.addCheckbox("Supress non-essential message boxes", this.noMessageBoxes);		gd.addCheckbox("Supress non-essential message boxes", this.noMessageBoxes);
	gd.addCheckbox("Overwrite result files if they exist", this.overwriteResultFiles);		gd.addCheckbox("Overwrite result files if they exist", this.overwriteResultFiles);
			gd.addCheckbox("Use reprojected grids for partial kernel calculation (false - extracted grids)", this.partialToReprojected);
	gd.addNumericField("Fitting series number to use for image selection", this.seriesNumber,0);		gd.addNumericField("Fitting series number to use for image selection", this.seriesNumber,0);
	gd.addCheckbox("Process all enabled image files (false - use selected fitting series)", this.allImages);		gd.addCheckbox("Process all enabled image files (false - use selected fitting series)", this.allImages);
	gd.addMessage("===== Autoload options (when restoring configuration) =====");		gd.addMessage("===== Autoload options (when restoring configuration) =====");
	@@ -4673,6 +4700,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	if (gd.getNextBoolean()) selectAberrationsKernelDirectory(false, this.aberrationsKernelDirectory, false);		if (gd.getNextBoolean()) selectAberrationsKernelDirectory(false, this.aberrationsKernelDirectory, false);
	this.noMessageBoxes= gd.getNextBoolean();		this.noMessageBoxes= gd.getNextBoolean();
	this.overwriteResultFiles= gd.getNextBoolean();		this.overwriteResultFiles= gd.getNextBoolean();
			this.partialToReprojected= gd.getNextBoolean();
	this.seriesNumber= (int) gd.getNextNumber();		this.seriesNumber= (int) gd.getNextNumber();
	this.allImages= gd.getNextBoolean();		this.allImages= gd.getNextBoolean();
	this.autoRestore= gd.getNextBoolean();		this.autoRestore= gd.getNextBoolean();

src/main/java/Goniometer.java

+2 −1

Original line number	Original line	Diff line number	Diff line
	@@ -598,7 +598,8 @@ horizontal axis:
	subCam,		subCam,
	goniometerTiltAxial[0], // Tilt, goniometerHorizontal		goniometerTiltAxial[0], // Tilt, goniometerHorizontal
	goniometerTiltAxial[1], // Axial,goniometerAxial		goniometerTiltAxial[1], // Axial,goniometerAxial
	-1 // use camera parameters, not imageSet		-1, // use camera parameters, not imageSet
			true // filter border
	);		);
	if (hintGrid==null){		if (hintGrid==null){
	String msg= "Target is not visible";		String msg= "Target is not visible";

src/main/java/MatchSimulatedPattern.java

+45 −0

Original line number	Original line	Diff line number	Diff line
	@@ -6983,6 +6983,51 @@ y=xy0[1] + dUdeltaUV[0](xy1[1]-xy0[1])+dVdeltaUV[1](xy2[1]-xy0[1])

	}		}

			public int replaceGridXYWithProjected(double [][][] projectedGrid){
			int minU=0,minV=0,maxU=0,maxV=0;
			boolean notYetSet=true;
			for (double [][]row:projectedGrid) for (double [] cell:row) if (cell!=null){
			int u = (int) cell[2];
			int v = (int) cell[3];
			if (notYetSet){
			minU=u;
			maxU=u;
			minV=v;
			maxV=v;
			notYetSet=false;
			} else {
			if (minU>u) minU=u;
			if (maxU<u) maxU=u;
			if (minV>v) minV=v;
			if (maxV<v) maxV=v;
			}
			}
			double [][][] grid=new double [maxV-minV+1][maxU-minU+1][];
			// for (double [][]row:grid) for (double [] cell:row) cell=null; // See if this works with "enhanced for loop"
			for (double [][]row:grid) for (int u=0;u<row.length;u++) row[u]=null; // See if this works with "enhanced for loop"

			for (double [][] row:projectedGrid) for (double [] cell:row) if (cell!=null){
			int u = (int) cell[2];
			int v = (int) cell[3];
			double [] xy={cell[0],cell[1]};
			grid[v-minV][u-minU]=xy;
			}
			int numNewDefined=0;
			for (int v=0;v<this.PATTERN_GRID.length;v++) for (int u=0;u<this.PATTERN_GRID[v].length;u++) {
			double [][] cell=this.PATTERN_GRID[v][u];
			if ((cell !=null) && (cell.length>0) &&(cell[0] !=null) && (cell[0].length>1)){
			cell[0][0]=grid[this.targetUV[v][u][1]+minV][this.targetUV[v][u][0]+minU][0];
			cell[0][1]=grid[this.targetUV[v][u][1]+minV][this.targetUV[v][u][0]+minU][1];
			if (Double.isNaN(cell[0][0]) \|\| Double.isNaN(cell[0][1])){
			this.PATTERN_GRID[v][u]=null; // make it undefined
			} else {
			numNewDefined++;
			}
			}
			}
			return numNewDefined;
			}

	/* Get calibrated pattern as a 8-slice image (can be saved as TIFF)		/* Get calibrated pattern as a 8-slice image (can be saved as TIFF)
	* first slice - pixel X or -1 for undefined		* first slice - pixel X or -1 for undefined
	* second slice - pixel Y or -1 for undefined		* second slice - pixel Y or -1 for undefined

Admin message