working on calculating grids for low frequency pattern (4ffb8a32) · Commits · Elphel / imagej-elphel

src/main/java/JP46_Reader_camera0.java

+6 −2

Original line number	Original line	Diff line number	Diff line
	@@ -1413,9 +1413,13 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970
	NodeList allNodes=doc.getDocumentElement().getElementsByTagName("*");		NodeList allNodes=doc.getDocumentElement().getElementsByTagName("*");
	for (int i=0;i<allNodes.getLength();i++) {		for (int i=0;i<allNodes.getLength();i++) {
	String name= allNodes.item(i).getNodeName();		String name= allNodes.item(i).getNodeName();
	String value=allNodes.item(i).getFirstChild().getNodeValue();		String value="";
	imp.setProperty(name, value);		try {
			value=allNodes.item(i).getFirstChild().getNodeValue();
			} catch(Exception e) {

			}
			imp.setProperty(name, value);
	}		}

	return true;		return true;

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

+338 −131

File changed.

Preview size limit exceeded, changes collapsed.

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

+37 −15

Original line number	Original line	Diff line number	Diff line
	@@ -23,15 +23,16 @@ package com.elphel.imagej.calibration;
	**		**
	*/		*/

	import ij.IJ;
	import ij.Prefs;
	import ij.gui.GenericDialog;

	import java.io.File;		import java.io.File;
			import java.io.FilenameFilter;
	import java.util.Properties;		import java.util.Properties;

	import com.elphel.imagej.common.WindowTools;		import com.elphel.imagej.common.WindowTools;

			import ij.IJ;
			import ij.Prefs;
			import ij.gui.GenericDialog;


	public class DistortionProcessConfiguration{		public class DistortionProcessConfiguration{
	public String sourceDirectory="";		public String sourceDirectory="";
	@@ -207,4 +208,25 @@ import com.elphel.imagej.common.WindowTools;
	return sourceFiles;		return sourceFiles;
	}		}

			public String[] selectSourceSets() {
			File dir= new File (this.sourceDirectory);
			if (this.debugLevel>1) System.out.println("selectSourceSets, dir="+this.sourceDirectory);
			if (!dir.exists()) {
			String error="Source directory "+this.sourceDirectory+" does not exist.";
			IJ.showMessage("No files selected");
			if (this.debugLevel>1) System.out.println("selectSourceFiles() ERROR:"+error);
			return null;
			}
			File [] sourceFileSets = dir.listFiles(new FilenameFilter() {
			@Override
			public boolean accept(File current, String name) {
			return new File(current, name).isDirectory();
	}		}
			});
			String [] sourceSets = new String[sourceFileSets.length];
			for (int i=0;i<sourceSets.length;i++) sourceSets[i]=sourceFileSets[i].getPath();
			return sourceSets;
			}

			}

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

+267 −260

Original line number	Original line	Diff line number	Diff line
	package com.elphel.imagej.calibration;		package com.elphel.imagej.calibration;
	import ij.IJ;
	import ij.ImagePlus;
	import ij.ImageStack;
	import ij.Prefs;
	import ij.gui.GenericDialog;
	import ij.io.FileSaver;
	import ij.io.Opener;
	import ij.process.FloatProcessor;
	import ij.process.ImageProcessor;

	import java.awt.Rectangle;		import java.awt.Rectangle;
	import java.io.File;		import java.io.File;
	import java.util.ArrayList;		import java.util.ArrayList;
	@@ -19,14 +9,22 @@ import java.util.concurrent.atomic.AtomicInteger;

	import javax.swing.SwingUtilities;		import javax.swing.SwingUtilities;

	import com.elphel.imagej.calibration.CalibrationFileManagement.MultipleExtensionsFileFilter;
	import com.elphel.imagej.calibration.SimulationPattern.SimulParameters;
	import com.elphel.imagej.common.DoubleFHT;		import com.elphel.imagej.common.DoubleFHT;
	import com.elphel.imagej.common.DoubleGaussianBlur;		import com.elphel.imagej.common.DoubleGaussianBlur;
	import com.elphel.imagej.common.ShowDoubleFloatArrays;		import com.elphel.imagej.common.ShowDoubleFloatArrays;
	import com.elphel.imagej.common.WindowTools;		import com.elphel.imagej.common.WindowTools;
	import com.elphel.imagej.jp4.JP46_Reader_camera;		import com.elphel.imagej.jp4.JP46_Reader_camera;

			import ij.IJ;
			import ij.ImagePlus;
			import ij.ImageStack;
			import ij.Prefs;
			import ij.gui.GenericDialog;
			import ij.io.FileSaver;
			import ij.io.Opener;
			import ij.process.FloatProcessor;
			import ij.process.ImageProcessor;

	public class EyesisAberrations {		public class EyesisAberrations {
	public double [][][][] pdfKernelMap=null;		public double [][][][] pdfKernelMap=null;
	JP46_Reader_camera JP4_INSTANCE= new JP46_Reader_camera(false);		JP46_Reader_camera JP4_INSTANCE= new JP46_Reader_camera(false);
	@@ -181,6 +179,7 @@ public class EyesisAberrations {
	final int numberOfKernelsInChn=tilesY*tilesX;		final int numberOfKernelsInChn=tilesY*tilesX;
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	float [] pixels=null;		float [] pixels=null;
	double [] kernel= new double[inverseParameters.dSize*inverseParameters.dSize];		double [] kernel= new double[inverseParameters.dSize*inverseParameters.dSize];
	@@ -555,7 +554,7 @@ public class EyesisAberrations {
	iy=-iy;		iy=-iy;
	}		}
	ix= (ix+size) % size;		ix= (ix+size) % size;
	floatPixels[i]=(float) clusterMap[iy][ix];		floatPixels[i]=clusterMap[iy][ix];
	}		}
	ip.setPixels(floatPixels);		ip.setPixels(floatPixels);
	ip.resetMinAndMax();		ip.resetMinAndMax();
	@@ -639,8 +638,8 @@ public class EyesisAberrations {
	row2=(fftsize-row1) %fftsize;		row2=(fftsize-row1) %fftsize;
	for (col1=0;col1 < fftsize;col1++) {		for (col1=0;col1 < fftsize;col1++) {
	col2=(fftsize-col1) %fftsize;		col2=(fftsize-col1) %fftsize;
	fht_pixels[row1*fftsize+col1]=(double) (fft[row1][col1][0]-fft[row1][col1][1]);		fht_pixels[row1*fftsize+col1]=fft[row1][col1][0]-fft[row1][col1][1];
	fht_pixels[row2*fftsize+col2]=(double) (fft[row1][col1][0]+fft[row1][col1][1]);		fht_pixels[row2*fftsize+col2]=fft[row1][col1][0]+fft[row1][col1][1];
	}		}
	}		}
	return fht_pixels;		return fht_pixels;
	@@ -1281,6 +1280,8 @@ public class EyesisAberrations {
	int rslt=matchSimulatedPattern.calculateDistortions(		int rslt=matchSimulatedPattern.calculateDistortions(
	distortionParameters, //		distortionParameters, //
	patternDetectParameters,		patternDetectParameters,
			patternDetectParameters.minGridPeriod/2,
			patternDetectParameters.maxGridPeriod/2,
	simulParameters,		simulParameters,
	colorComponents.equalizeGreens,		colorComponents.equalizeGreens,
	imp,		imp,
	@@ -2313,6 +2314,7 @@ public class EyesisAberrations {
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	// Concurrently run in as many threads as CPUs		// Concurrently run in as many threads as CPUs
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {

	// Each thread processes a few items in the total list		// Each thread processes a few items in the total list
	@@ -2399,6 +2401,7 @@ public class EyesisAberrations {
	}		}
	final int numFinished=tilesFinishedAtomic.getAndIncrement();		final int numFinished=tilesFinishedAtomic.getAndIncrement();
	SwingUtilities.invokeLater(new Runnable() {		SwingUtilities.invokeLater(new Runnable() {
			@Override
	public void run() {		public void run() {
	IJ.showProgress(numFinished,patternCells);		IJ.showProgress(numFinished,patternCells);
	}		}
	@@ -2679,6 +2682,8 @@ public class EyesisAberrations {
	if (matchSimulatedPattern.PATTERN_GRID==null) {		if (matchSimulatedPattern.PATTERN_GRID==null) {
	double[][] distortedPattern= matchSimulatedPattern.findPatternDistorted(input_bayer, // pixel array to process (no windowing!)		double[][] distortedPattern= matchSimulatedPattern.findPatternDistorted(input_bayer, // pixel array to process (no windowing!)
	patternDetectParameters,		patternDetectParameters,
			patternDetectParameters.minGridPeriod/2,
			patternDetectParameters.maxGridPeriod/2,
	true, //(greensToProcess==4), // boolean greens, // this is a pattern for combined greens (diagonal), adjust results accordingly		true, //(greensToProcess==4), // boolean greens, // this is a pattern for combined greens (diagonal), adjust results accordingly
	title); // title prefix to use for debug images		title); // title prefix to use for debug images

	@@ -4148,7 +4153,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	ImageProcessor ip = new FloatProcessor(size,size);		ImageProcessor ip = new FloatProcessor(size,size);
	float [] floatPixels = new float [size*size];		float [] floatPixels = new float [size*size];
	for (i=0;i<floatPixels.length;i++) {		for (i=0;i<floatPixels.length;i++) {
	floatPixels[i]=(float) clusterMap[i/size][i%size];		floatPixels[i]=clusterMap[i/size][i%size];
	}		}
	ip.setPixels(floatPixels);		ip.setPixels(floatPixels);
	ip.resetMinAndMax();		ip.resetMinAndMax();
	@@ -4404,11 +4409,11 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	if (debug) {		if (debug) {
	SDFA_INSTANCE.showArrays(debugPixels, title+"_mask_PSF");		SDFA_INSTANCE.showArrays(debugPixels, title+"_mask_PSF");
	double [] doublePixelsPSFCount=new double [pixelsPSF.length];		double [] doublePixelsPSFCount=new double [pixelsPSF.length];
	for (j=0;j<doublePixelsPSFCount.length;j++) doublePixelsPSFCount[j]=(double)pixelsPSFCount[j];		for (j=0;j<doublePixelsPSFCount.length;j++) doublePixelsPSFCount[j]=pixelsPSFCount[j];
	SDFA_INSTANCE.showArrays(doublePixelsPSFCount, title+"_PSF_bin_count");		SDFA_INSTANCE.showArrays(doublePixelsPSFCount, title+"_PSF_bin_count");
	SDFA_INSTANCE.showArrays(pixelsPSFWeight, title+"_PSF_bin_weight");		SDFA_INSTANCE.showArrays(pixelsPSFWeight, title+"_PSF_bin_weight");
	double [] doubleContrastCache=new double [contrastCache.length];		double [] doubleContrastCache=new double [contrastCache.length];
	for (j=0;j<doubleContrastCache.length;j++) doubleContrastCache[j]=(double)((contrastCache[j]>=0.0)?contrastCache[j]:-0.00001);		for (j=0;j<doubleContrastCache.length;j++) doubleContrastCache[j]=(contrastCache[j]>=0.0)?contrastCache[j]:-0.00001;
	SDFA_INSTANCE.showArrays(doubleContrastCache, title+"_ContrastCache");		SDFA_INSTANCE.showArrays(doubleContrastCache, title+"_ContrastCache");
	}		}
	return pixelsPSF;		return pixelsPSF;
	@@ -4988,6 +4993,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	this.thresholdHigh = thresholdHigh;		this.thresholdHigh = thresholdHigh;
	this.thresholdLow = thresholdLow;		this.thresholdLow = thresholdLow;
	}		}
			@Override
	public OTFFilterParameters clone() {		public OTFFilterParameters clone() {
	return new OTFFilterParameters(		return new OTFFilterParameters(
	this.deconvInvert,		this.deconvInvert,
	@@ -5076,6 +5082,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************


	}		}
			@Override
	public PSFParameters clone(){		public PSFParameters clone(){
	return new PSFParameters(		return new PSFParameters(
	this.minContrast,		this.minContrast,

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

+4 −0

Original line number	Original line	Diff line number	Diff line
	@@ -668,6 +668,8 @@ horizontal axis:
	// allow more of grid around pointers?		// allow more of grid around pointers?
	distortionParameters, //		distortionParameters, //
	this.patternDetectParameters,		this.patternDetectParameters,
			this.patternDetectParameters.minGridPeriod/2,
			this.patternDetectParameters.maxGridPeriod/2,
	simulParameters,		simulParameters,
	equalizeGreens, imp_eq,		equalizeGreens, imp_eq,
	this.laserPointers, // null, //LASER_POINTERS, //		this.laserPointers, // null, //LASER_POINTERS, //
	@@ -841,6 +843,8 @@ horizontal axis:
	// allow more of grid around pointers?		// allow more of grid around pointers?
	distortionParameters, //		distortionParameters, //
	this.patternDetectParameters,		this.patternDetectParameters,
			this.patternDetectParameters.minGridPeriod/2,
			this.patternDetectParameters.maxGridPeriod/2,
	simulParameters,		simulParameters,
	equalizeGreens, imp_eq,		equalizeGreens, imp_eq,
	this.laserPointers, // null, //LASER_POINTERS, //		this.laserPointers, // null, //LASER_POINTERS, //

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