merged with lwir (3f9c52b0) · Commits · Elphel / imagej-elphel

src/main/java/JP46_Reader_camera0.java

+68 −6

Original line number	Diff line number	Diff line
		@@ -55,6 +55,8 @@ import org.w3c.dom.NodeList;
		import org.xml.sax.InputSource;
		import org.xml.sax.SAXException;

		import com.elphel.imagej.readers.ImagejJp4Tiff;

		import ij.IJ;
		import ij.ImageJ;
		import ij.ImagePlus;
		@@ -69,6 +71,7 @@ import ij.plugin.frame.PlugInFrame;
		import ij.process.ImageConverter;
		import ij.process.ImageProcessor;
		import ij.text.TextWindow;
		import loci.formats.FormatException;



		@@ -87,6 +90,8 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {

		static File dir;

		ImagejJp4Tiff imagejJp4Tiff = new ImagejJp4Tiff();

		public String camera_url = "http://192.168.0.236:8081/";
		public String camera_img = "bimg";
		public String camera_img_new = "towp/wait/bimg"; // will always wait for the next image (repetitive acquisitions get new images)
		@@ -109,8 +114,9 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {

		panel1 = new Panel();

		panel1.setLayout(new GridLayout(6, 1, 50, 5));
		panel1.setLayout(new GridLayout(8, 1, 50, 5));

		addButton("Open JP4/Tiff...",panel1);
		addButton("Open JP4/JP46...",panel1);
		addButton("Open JP4/JP46 from camera",panel1);
		addButton("Configure...",panel1);
		@@ -137,8 +143,8 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {

		panel1 = new Panel();

		panel1.setLayout(new GridLayout(6, 1, 50, 5));

		panel1.setLayout(new GridLayout(8, 1, 50, 5));
		addButton("Open JP4/Tiff...",panel1);
		addButton("Open JP4/JP46...",panel1);
		addButton("Open JP4/JP46 from camera",panel1);
		addButton("Configure...",panel1);
		@@ -169,7 +175,11 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {
		if (label==null) return;

		/* button */
		if (label.equals("Open JP4/JP46...")) {
		if (label.equals("Open JP4/Tiff...")) {
		read_jp4Tiff(arg,true);
		}else if (label.equals("Open JP4/Tiff (no scale)...")) {
		read_jp4Tiff(arg,false);
		}else if (label.equals("Open JP4/JP46...")) {
		read_jp46(arg,true);
		}else if (label.equals("Open JP4/JP46 (no scale)...")) {
		read_jp46(arg,false);
		@@ -227,7 +237,54 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {
		imp_stack.getProcessor().resetMinAndMax();
		imp_stack.show();
		}
		public void read_jp4Tiff(String arg, // not used?
		boolean scale) {

		String LOG_LEVEL = ABSOLUTELY_SILENT? "OFF" : (IS_SILENT?"ERROR":"INFO");
		boolean LOG_LEVEL_SET = loci.common.DebugTools.enableLogging(LOG_LEVEL);
		if (!LOG_LEVEL_SET) { // only first time true
		loci.common.DebugTools.setRootLevel(LOG_LEVEL);
		}

		JFileChooser fc=null;
		//try {fc = new JFileChooser();}

		fc = new JFileChooser();

		//catch (Throwable e) {IJ.error("This plugin requires Java 2 or Swing."); return;}
		fc.setMultiSelectionEnabled(true);

		if (dir==null) {
		String sdir = OpenDialog.getDefaultDirectory();
		if (sdir!=null)
		dir = new File(sdir);
		}
		if (dir!=null)
		fc.setCurrentDirectory(dir);

		int returnVal = fc.showOpenDialog(IJ.getInstance());
		if (returnVal!=JFileChooser.APPROVE_OPTION)
		return;
		File[] files = fc.getSelectedFiles();
		if (files.length==0) { // getSelectedFiles does not work on some JVMs
		files = new File[1];
		files[0] = fc.getSelectedFile();
		}
		String path = fc.getCurrentDirectory().getPath()+Prefs.getFileSeparator();
		dir = fc.getCurrentDirectory();
		for (int i=0; i<files.length; i++) {
		try {
		ImagePlus imp = imagejJp4Tiff.readTiffJp4(path + files[i].getName(), scale);
		// imp.updateAndDraw();
		imp.show();
		} catch (IOException \| FormatException e) {
		// TODO Auto-generated catch block
		e.printStackTrace();
		} // throws IOException, FormatException { // std - include non-elphel properties with prefix std
		// open(path, files[i].getName(), arg, scale);
		}

		}
		public void read_jp46(String arg, boolean scale) {
		JFileChooser fc=null;
		//try {fc = new JFileChooser();}
		@@ -274,6 +331,7 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {

		confpanel = new Panel();
		gd.addPanel(confpanel);
		addButton("Open JP4/Tiff (no scale)...", confpanel);
		addButton("Open JP4/JP46 (no scale)...", confpanel);
		addButton("Open JP4/JP46 from camera (no scale)", confpanel);

		@@ -1413,9 +1471,13 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970
		NodeList allNodes=doc.getDocumentElement().getElementsByTagName("*");
		for (int i=0;i<allNodes.getLength();i++) {
		String name= allNodes.item(i).getNodeName();
		String value=allNodes.item(i).getFirstChild().getNodeValue();
		imp.setProperty(name, value);
		String value="";
		try {
		value=allNodes.item(i).getFirstChild().getNodeValue();
		} catch(Exception e) {

		}
		imp.setProperty(name, value);
		}

		return true;

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

+404 −177

File changed.

Preview size limit exceeded, changes collapsed.

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

+37 −15

Original line number	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.FilenameFilter;
		import java.util.Properties;

		import com.elphel.imagej.common.WindowTools;

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


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

+272 −262

Original line number	Diff line number	Diff line
		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.io.File;
		import java.util.ArrayList;
		@@ -19,14 +9,22 @@ import java.util.concurrent.atomic.AtomicInteger;

		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.DoubleGaussianBlur;
		import com.elphel.imagej.common.ShowDoubleFloatArrays;
		import com.elphel.imagej.common.WindowTools;
		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 double [][][][] pdfKernelMap=null;
		JP46_Reader_camera JP4_INSTANCE= new JP46_Reader_camera(false);
		@@ -181,6 +179,7 @@ public class EyesisAberrations {
		final int numberOfKernelsInChn=tilesY*tilesX;
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		float [] pixels=null;
		double [] kernel= new double[inverseParameters.dSize*inverseParameters.dSize];
		@@ -555,7 +554,7 @@ public class EyesisAberrations {
		iy=-iy;
		}
		ix= (ix+size) % size;
		floatPixels[i]=(float) clusterMap[iy][ix];
		floatPixels[i]=clusterMap[iy][ix];
		}
		ip.setPixels(floatPixels);
		ip.resetMinAndMax();
		@@ -639,8 +638,8 @@ public class EyesisAberrations {
		row2=(fftsize-row1) %fftsize;
		for (col1=0;col1 < fftsize;col1++) {
		col2=(fftsize-col1) %fftsize;
		fht_pixels[row1*fftsize+col1]=(double) (fft[row1][col1][0]-fft[row1][col1][1]);
		fht_pixels[row2*fftsize+col2]=(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]=fft[row1][col1][0]+fft[row1][col1][1];
		}
		}
		return fht_pixels;
		@@ -1279,8 +1278,11 @@ public class EyesisAberrations {
		}

		int rslt=matchSimulatedPattern.calculateDistortions(
		null, // LwirReaderParameters lwirReaderParameters, // null is OK
		distortionParameters, //
		patternDetectParameters,
		// patternDetectParameters.minGridPeriod/2,
		// patternDetectParameters.maxGridPeriod/2,
		simulParameters,
		colorComponents.equalizeGreens,
		imp,
		@@ -2313,6 +2315,7 @@ public class EyesisAberrations {
		for (int ithread = 0; ithread < threads.length; ithread++) {
		// Concurrently run in as many threads as CPUs
		threads[ithread] = new Thread() {
		@Override
		public void run() {

		// Each thread processes a few items in the total list
		@@ -2399,6 +2402,7 @@ public class EyesisAberrations {
		}
		final int numFinished=tilesFinishedAtomic.getAndIncrement();
		SwingUtilities.invokeLater(new Runnable() {
		@Override
		public void run() {
		IJ.showProgress(numFinished,patternCells);
		}
		@@ -2679,6 +2683,8 @@ public class EyesisAberrations {
		if (matchSimulatedPattern.PATTERN_GRID==null) {
		double[][] distortedPattern= matchSimulatedPattern.findPatternDistorted(input_bayer, // pixel array to process (no windowing!)
		patternDetectParameters,
		patternDetectParameters.minGridPeriod/2,
		patternDetectParameters.maxGridPeriod/2,
		true, //(greensToProcess==4), // boolean greens, // this is a pattern for combined greens (diagonal), adjust results accordingly
		title); // title prefix to use for debug images

		@@ -2704,7 +2710,8 @@ public class EyesisAberrations {
		distortedPattern[2], //
		simulParameters.subdiv,
		fft_size,
		simulParameters.center_for_g2);
		simulParameters.center_for_g2,
		false);//boolean mono
		wVectors[0][0]=2.0*distortedPattern[0][0]/subpixel;
		wVectors[0][1]=2.0*distortedPattern[0][1]/subpixel;
		wVectors[1][0]=2.0*distortedPattern[1][0]/subpixel;
		@@ -2747,7 +2754,8 @@ public class EyesisAberrations {
		simCorr, //
		simulParameters.subdiv,
		fft_size,
		simulParameters.center_for_g2);
		simulParameters.center_for_g2,
		false);//boolean mono
		}
		// simul_pixels= simulationPattern.extractSimulPatterns (
		simul_pixels= simulationPattern.extractSimulPatterns (
		@@ -4148,7 +4156,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
		ImageProcessor ip = new FloatProcessor(size,size);
		float [] floatPixels = new float [size*size];
		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.resetMinAndMax();
		@@ -4404,11 +4412,11 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
		if (debug) {
		SDFA_INSTANCE.showArrays(debugPixels, title+"_mask_PSF");
		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(pixelsPSFWeight, title+"_PSF_bin_weight");
		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");
		}
		return pixelsPSF;
		@@ -4988,6 +4996,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
		this.thresholdHigh = thresholdHigh;
		this.thresholdLow = thresholdLow;
		}
		@Override
		public OTFFilterParameters clone() {
		return new OTFFilterParameters(
		this.deconvInvert,
		@@ -5076,6 +5085,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************


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

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

+23 −17

Original line number	Diff line number	Diff line
		@@ -665,9 +665,12 @@ horizontal axis:

		boolean noMessageBoxes=true;
		int numAbsolutePoints = matchSimulatedPattern.calculateDistortions(
		null, // LwirReaderParameters lwirReaderParameters, // null is OK
		// allow more of grid around pointers?
		distortionParameters, //
		this.patternDetectParameters,
		// this.patternDetectParameters.minGridPeriod/2,
		// this.patternDetectParameters.maxGridPeriod/2,
		simulParameters,
		equalizeGreens, imp_eq,
		this.laserPointers, // null, //LASER_POINTERS, //
		@@ -838,9 +841,12 @@ horizontal axis:
		// matchSimulatedPatterns[numSensor].getChannel(images[numSensor])+" ");

		int numAbsolutePoints = this.matchSimulatedPatterns[numSensor].calculateDistortions(
		null, // LwirReaderParameters lwirReaderParameters, // null is OK
		// allow more of grid around pointers?
		distortionParameters, //
		this.patternDetectParameters,
		// this.patternDetectParameters.minGridPeriod/2,
		// this.patternDetectParameters.maxGridPeriod/2,
		simulParameters,
		equalizeGreens, imp_eq,
		this.laserPointers, // null, //LASER_POINTERS, //