Merge pull request #2 from luxigo/master (01246a62) · Commits · Elphel / imagej-elphel

src/main/java/EyesisCorrectionParameters.java

+6 −0

Original line number	Diff line number	Diff line
		@@ -61,6 +61,7 @@ public class EyesisCorrectionParameters {
		public double outputRangeFP= 255.0; // 1.0 intensity will be saved as 255.0 (in float 32-bit mode)
		public boolean imageJTags= false; // encode ImageJ info data to the TIFF output header

		public String tiffCompression = "UNCOMPRESSED"; // tiff compression codec
		public boolean jpeg = true; // convert to RGB and save JPEG (if save is true)
		public boolean save = true;
		public boolean save16 = false; // save 16-bit tiff also if the end result is 8 bit
		@@ -201,6 +202,7 @@ public class EyesisCorrectionParameters {
		if (properties.getProperty(prefix+"equirectangularFormat")!=null) this.equirectangularFormat=Integer.parseInt(properties.getProperty(prefix+"equirectangularFormat"));
		if (properties.getProperty(prefix+"outputRangeInt")!=null) this.outputRangeInt=Double.parseDouble(properties.getProperty(prefix+"outputRangeInt"));
		if (properties.getProperty(prefix+"outputRangeFP")!=null) this.outputRangeFP=Double.parseDouble(properties.getProperty(prefix+"outputRangeFP"));
		if (properties.getProperty(prefix+"tiffCompression")!=null) this.tiffCompression=properties.getProperty(prefix+"tiffCompression");
		if (properties.getProperty(prefix+"imageJTags")!=null) this.imageJTags=Boolean.parseBoolean(properties.getProperty(prefix+"imageJTags"));
		if (properties.getProperty(prefix+"jpeg")!=null) this.jpeg=Boolean.parseBoolean(properties.getProperty(prefix+"jpeg")); // convert to RGB and save jpeg (if save is true)
		if (properties.getProperty(prefix+"save")!=null) this.save=Boolean.parseBoolean(properties.getProperty(prefix+"save"));
		@@ -283,6 +285,8 @@ public class EyesisCorrectionParameters {
		gd.addCheckbox ("Save chroma denoise mask (white - use hi-res, black - low-res)", this.saveChromaDenoiseMask);
		gd.addCheckbox ("Rotate result image", this.rotate);
		gd.addCheckbox ("Crop result image to the original size", this.crop);
		String [] tiffCompressionChoices={"UNCOMPRESSED","LZW","JPEG", "JPEG_2000","ALT_JPEG2000"};
		int tiffCompressionIndex=0;
		String [] equirectangularFormatChoices={"RGBA 8-bit","RGBA 16-bit","RGBA 32-bit integer","RGBA 32-bit float","ImageJ stack"};
		int [] equirectangularFormats={0,1,2,3,4};
		int equirectangularFormatIndex=0;
		@@ -294,6 +298,7 @@ public class EyesisCorrectionParameters {
		gd.addNumericField("Map 1.0 intensity to this fraction of the full range 8/16/32-bit integer mode output", 100*this.outputRangeInt, 2,6,"%");
		gd.addNumericField("Map 1.0 intensity to this value in 32-bit floating point output mode", this.outputRangeFP, 2,6,"");
		gd.addCheckbox ("Encode ImageJ specific Info metadata to the output file TIFF header", this.imageJTags);
		gd.addChoice("TIFF lossless compression codec",tiffCompressionChoices,tiffCompressionChoices[tiffCompressionIndex]);

		gd.addCheckbox ("Convert to RGB48", this.toRGB);
		gd.addCheckbox ("Convert to 8 bit RGB (and save JPEG if save is enabled)", this.jpeg);
		@@ -372,6 +377,7 @@ public class EyesisCorrectionParameters {
		this.outputRangeInt=0.01*gd.getNextNumber();
		this.outputRangeFP= gd.getNextNumber();
		this.imageJTags= gd.getNextBoolean();
		this.tiffCompression= tiffCompressionChoices[gd.getNextChoiceIndex()];
		this.toRGB= gd.getNextBoolean();
		this.jpeg= gd.getNextBoolean();
		this.save= gd.getNextBoolean();

src/main/java/EyesisCorrections.java

+2 −2

Original line number	Diff line number	Diff line
		@@ -473,7 +473,7 @@ public class EyesisCorrections {
		this.defectsDiff[srcChannel]=this.pixelMapping.getDefectsDiff(srcChannel);
		if (this.debugLevel>0){
		if (this.defectsXY[srcChannel]==null){
		System.out.println("No pixel defects info is availabele for channel "+srcChannel);
		System.out.println("No pixel defects info is available for channel "+srcChannel);
		} else {
		System.out.println("Extracted "+this.defectsXY[srcChannel].length+" pixel outlayers for channel "+srcChannel+
		" (x:y:difference");
		@@ -701,7 +701,7 @@ public class EyesisCorrections {
		if (path!=null){
		path+=Prefs.getFileSeparator()+imp.getTitle()+".tiff";
		if (this.debugLevel>0) System.out.println("Saving equirectangular result to "+path);
		(new EyesisTiff()).saveTiff(
		(new EyesisTiff(correctionsParameters.tiffCompression)).saveTiff(
		imp,
		path,
		correctionsParameters.equirectangularFormat,

src/main/java/EyesisTiff.java

+15 −2

Original line number	Diff line number	Diff line
		@@ -34,6 +34,7 @@ import java.util.Arrays;

		//import org.apache.log4j.Logger;


		import ij.IJ;
		import ij.ImagePlus;
		import ij.WindowManager;
		@@ -42,20 +43,31 @@ import loci.common.RandomAccessInputStream;
		import loci.common.services.DependencyException;
		import loci.common.services.ServiceException;
		import loci.formats.FormatException;
		import loci.formats.codec.CodecOptions;
		import loci.formats.tiff.IFD;
		import loci.formats.tiff.IFDList;
		import loci.formats.tiff.TiffParser;
		import loci.formats.tiff.TiffRational;
		import loci.formats.tiff.TiffSaver;
		import loci.formats.tiff.TiffCompression;


		public class EyesisTiff {
		// private static org.apache.log4j.Logger log= Logger.getLogger(EyesisTiff.class);

		private String codec="UNCOMPRESSED";

		public EyesisTiff(){
		// Please initialize the log4j system properly


		}

		public EyesisTiff(String codec){
		// Please initialize the log4j system properly
		this.codec=codec;
		}

		public void saveTiff(
		ImagePlus imp,
		String path,
		@@ -175,7 +187,7 @@ public EyesisTiff(){
		ifd.putIFDValue(IFD.SOFTWARE, "Elphel Eyesis");
		ifd.putIFDValue(IFD.IMAGE_DESCRIPTION, description);
		// copy some other data?
		ifd.putIFDValue(IFD.COMPRESSION, 1); //TiffCompression.UNCOMPRESSED);
		ifd.putIFDValue(IFD.COMPRESSION, TiffCompression.valueOf(codec).getCode());
		ifd.putIFDValue(IFD.PHOTOMETRIC_INTERPRETATION,2); // RGB
		ifd.putIFDValue(IFD.EXTRA_SAMPLES,2); // 0 = Unspecified data 1 = Associated alpha data (with pre-multiplied color) 2 = Unassociated alpha data
		// int [] bpsArray={8,8,8,8};
		@@ -212,6 +224,7 @@ public EyesisTiff(){
		TiffSaver tiffSaver = new TiffSaver(path);
		tiffSaver.setWritingSequentially(true);
		tiffSaver.setLittleEndian(false);
		tiffSaver.setCodecOptions(TiffCompression.valueOf(codec).getCompressionCodecOptions(ifd));
		tiffSaver.writeHeader();
		// tiffSaver.writeIFD(ifd,0); //* SHould not write here, some fields are calculated during writeImage, that writes IFD too
		// System.out.println("bytes.length="+bytes.length);
		@@ -257,7 +270,7 @@ public EyesisTiff(){
		ifd.putIFDValue(IFD.SOFTWARE, "Elphel Eyesis");
		ifd.putIFDValue(IFD.IMAGE_DESCRIPTION, description);
		// copy some other data?
		ifd.putIFDValue(IFD.COMPRESSION, 1); //TiffCompression.UNCOMPRESSED);
		ifd.putIFDValue(IFD.COMPRESSION, TiffCompression.valueOf(codec).getCode());
		ifd.putIFDValue(IFD.PHOTOMETRIC_INTERPRETATION,2); // RGB
		ifd.putIFDValue(IFD.EXTRA_SAMPLES,2); // extra bytes (over 3) meaning Unassociated alpha data

src/main/java/Eyesis_Correction.java

+119 −99

Original line number	Diff line number	Diff line
		@@ -33,6 +33,7 @@ import ij.io.FileSaver;
		import ij.io.OpenDialog;
		import ij.io.Opener;
		import ij.plugin.frame.*;
		import ij.plugin.PlugIn;

		import java.awt.*;
		import java.awt.event.*;
		@@ -60,10 +61,14 @@ import loci.formats.FormatException;
		//import javax.swing.SwingUtilities;
		//import javax.swing.UIManager;

		public class Eyesis_Correction extends PlugInFrame implements ActionListener {
		public class Eyesis_Correction implements PlugIn, ActionListener {
		/**
		*
		*/
		private Boolean headless=GraphicsEnvironment.getLocalGraphicsEnvironment().isHeadlessInstance();
		private PlugInFrame plugInFrame;
		String prefsPath;

		private static final long serialVersionUID = -1507307664341265263L;
		private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPostProcessing1,panelPostProcessing2,panelPostProcessing3;
		JP46_Reader_camera JP4_INSTANCE=null;
		@@ -310,9 +315,13 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
		public String buttonLabel="";
		}


		public Eyesis_Correction() {
		super("Eyesis_Correction");
		public void run(String arg) {
		String options=Macro.getOptions();
		try {
		prefsPath=Macro.getValue(options, "prefs", Prefs.getPrefsDir()+Prefs.getFileSeparator()+"Eyesis_Correction.xml");
		} catch(Exception e) {
		prefsPath=Prefs.getPrefsDir()+Prefs.getFileSeparator()+"Eyesis_Correction.xml";
		}
		if (IJ.versionLessThan("1.43q")) return;
		if (instance!=null) {
		instance.toFront();
		@@ -322,21 +331,36 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
		loadPrefs();
		} catch (IOException e1) {
		System.out.println("failed to load preferences");
		// e1.printStackTrace();
		e1.printStackTrace();
		}
		EYESIS_CORRECTIONS = new EyesisCorrections(SYNC_COMMAND.stopRequested,CORRECTION_PARAMETERS);
		if (options!=null \|\| headless) {
		processFiles();
		} else {
		initGui();
		}
		}

		public void initGui() {
		Color color_configure= new Color(200, 200,160);
		Color color_process= new Color(180, 180, 240);
		Color color_conf_process= new Color(180, 240, 240);
		Color color_restore= new Color(180, 240, 180);
		Color color_stop= new Color(255, 160, 160);


		instance = this;
		addKeyListener(IJ.getInstance());
		plugInFrame=new PlugInFrame("Eyesis_Correction") {
		private static final long serialVersionUID = -4138832568507690332L;
		@Override
		public void processWindowEvent(WindowEvent e) {
		super.processWindowEvent(e);
		if (e.getID()==WindowEvent.WINDOW_CLOSING) {
		instance = null;
		}
		}
		};
		instance=(Frame)plugInFrame;
		plugInFrame.addKeyListener(IJ.getInstance());
		int menuRows=4 + (ADVANCED_MODE?4:0) + (MODE_3D?3:0);
		setLayout(new GridLayout(menuRows, 1));

		plugInFrame.setLayout(new GridLayout(menuRows, 1));
		panel6 = new Panel();
		panel6.setLayout(new GridLayout(1, 0, 5, 5));
		addButton("Save",panel6);
		@@ -344,13 +368,13 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
		addButton("Stop",panel6,color_stop);
		addButton("Abort",panel6,color_stop);

		add(panel6);
		plugInFrame.add(panel6);

		panel5 = new Panel();
		panel5.setLayout(new GridLayout(1, 0, 5, 5));
		addButton("Configure spilt", panel5, color_configure);
		addButton("Configure demosaic", panel5, color_configure);
		add(panel5);
		plugInFrame.add(panel5);
		panel5a = new Panel();
		panel5a.setLayout(new GridLayout(1, 0, 5, 5));
		addButton("Configure convolution", panel5a, color_configure);
		@@ -358,7 +382,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
		addButton("Configure color", panel5a, color_configure);
		addButton("Channel gains", panel5a, color_configure);
		addButton("Configure RGB", panel5a, color_configure);
		add(panel5a);
		plugInFrame.add(panel5a);


		// Debug/development options
		@@ -368,13 +392,13 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
		panel1.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
		addButton("Split Image",panel1);
		addButton("Debayer Image",panel1);
		add(panel1);
		plugInFrame.add(panel1);

		panel2 = new Panel();
		panel2.setLayout(new GridLayout(1, 0, 5, 5));
		addButton("Select kernel stack",panel2);
		addButton("Convolve with stack",panel2);
		add(panel2);
		plugInFrame.add(panel2);

		panel3 = new Panel();
		panel3.setLayout(new GridLayout(1, 0, 5, 5));
		@@ -382,14 +406,14 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
		addButton("Combine pair",panel3);
		addButton("Colors",panel3);
		addButton("RGB",panel3);
		add(panel3);
		plugInFrame.add(panel3);


		panel4 = new Panel();
		panel4.setLayout(new GridLayout(1, 0, 5, 5));
		addButton("Test",panel4);
		addButton("Test Debayer",panel4);
		add(panel4);
		plugInFrame.add(panel4);
		}
		panel7 = new Panel();
		panel7.setLayout(new GridLayout(1, 0, 5, 5));
		@@ -402,7 +426,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
		addButton("Tiff Writer", panel7);
		addButton("Tiff Properties", panel7);
		}
		add(panel7);
		plugInFrame.add(panel7);

		if (MODE_3D){
		panelPostProcessing1 = new Panel();
		@@ -412,7 +436,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
		addButton("ConvertPP", panelPostProcessing1,color_process);
		addButton("Linear Features", panelPostProcessing1);
		addButton("Intercam correlations", panelPostProcessing1);
		add(panelPostProcessing1);
		plugInFrame.add(panelPostProcessing1);

		panelPostProcessing2 = new Panel();
		panelPostProcessing2.setLayout(new GridLayout(1, 0, 5, 5));
		@@ -423,19 +447,19 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
		addButton("Fill FG gaps", panelPostProcessing2);
		addButton("Filter Z-map", panelPostProcessing2);
		addButton("Occluding FG", panelPostProcessing2);
		add(panelPostProcessing2);
		plugInFrame.add(panelPostProcessing2);

		panelPostProcessing3 = new Panel();
		panelPostProcessing3.setLayout(new GridLayout(1, 0, 5, 5));
		addButton("Refine Disparities", panelPostProcessing3);
		addButton("Init Photometry", panelPostProcessing3);
		addButton("Plane Likely", panelPostProcessing3);
		add(panelPostProcessing3);
		plugInFrame.add(panelPostProcessing3);
		}
		pack();
		plugInFrame.pack();

		GUI.center(this);
		setVisible(true);
		GUI.center(plugInFrame);
		plugInFrame.setVisible(true);
		FHT_INSTANCE= new DoubleFHT();
		SDFA_INSTANCE= new showDoubleFloatArrays();
		// main loop
		@@ -464,7 +488,6 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
		}

		}
		private String prefsPath=Prefs.getPrefsDir()+Prefs.getFileSeparator()+"Eyesis_Correction.xml";
		private Properties prefsProperties=new Properties();

		public void loadPrefs() throws IOException{
		@@ -478,6 +501,8 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
		}
		try {
		prefsProperties.loadFromXML(is);
		getAllProperties(prefsProperties);
		if (DEBUG_LEVEL>0) System.out.println("Configuration parameters are restored from "+this.prefsPath);

		} catch (IOException e) {
		String msg="Failed to read XML configuration file: "+this.prefsPath;
		@@ -536,13 +561,6 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
		b.addKeyListener(IJ.getInstance());
		panel.add(b);
		}
		public void processWindowEvent(WindowEvent e) {
		super.processWindowEvent(e);
		if (e.getID()==WindowEvent.WINDOW_CLOSING) {
		instance = null;
		}
		}

		public void actionPerformed(ActionEvent e) {
		String label = e.getActionCommand();
		if (label.equals("Abort")) {
		@@ -569,6 +587,70 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
		}
		// matchSimulatedPattern.FFT_SIZE=FFT_SIZE;
		}

		public void processFiles() {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
		String configPath=null;
		if (!headless && EYESIS_CORRECTIONS.correctionsParameters.saveSettings) {
		configPath=EYESIS_CORRECTIONS.correctionsParameters.selectResultsDirectory(
		true,
		true);
		if (configPath==null){
		String msg="No results directory selected, command aborted";
		System.out.println("Warning: "+msg);
		IJ.showMessage("Warning",msg);
		return;
		}
		configPath+=Prefs.getFileSeparator()+"autoconfig";
		try {
		saveTimestampedProperties(
		configPath, // full path or null
		null, // use as default directory if path==null
		true,
		PROPERTIES);
		} catch (Exception e){
		String msg="Failed to save configuration to "+configPath+", command aborted";
		System.out.println("Error: "+msg);
		IJ.showMessage("Error",msg);
		return;
		}
		}
		EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL);
		int numChannels=EYESIS_CORRECTIONS.getNumChannels();
		NONLIN_PARAMETERS.modifyNumChannels(numChannels);
		CHANNEL_GAINS_PARAMETERS.modifyNumChannels(numChannels);

		if (CORRECTION_PARAMETERS.deconvolve && (NONLIN_PARAMETERS.noiseGainPower!=0)) {
		EYESIS_CORRECTIONS.updateImageNoiseGains(
		NONLIN_PARAMETERS, //EyesisCorrectionParameters.NonlinParameters nonlinParameters,
		CONVOLVE_FFT_SIZE, //int fftSize, // 128 - fft size, kernel size should be size/2
		THREADS_MAX, // int threadsMax, // maximal number of threads to launch
		UPDATE_STATUS, // boolean updateStatus,
		DEBUG_LEVEL); //int globalDebugLevel){
		}

		EYESIS_CORRECTIONS.processChannelImages(
		SPLIT_PARAMETERS, // EyesisCorrectionParameters.SplitParameters splitParameters,
		DEBAYER_PARAMETERS, //EyesisCorrectionParameters.DebayerParameters debayerParameters,
		NONLIN_PARAMETERS, //EyesisCorrectionParameters.NonlinParameters nonlinParameters,
		COLOR_PROC_PARAMETERS, //EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
		CHANNEL_GAINS_PARAMETERS, //CorrectionColorProc.ColorGainsParameters channelGainParameters,
		RGB_PARAMETERS, //EyesisCorrectionParameters.RGBParameters rgbParameters,
		EQUIRECTANGULAR_PARAMETERS, // EyesisCorrectionParameters.EquirectangularParameters equirectangularParameters,
		CONVOLVE_FFT_SIZE, //int convolveFFTSize, // 128 - fft size, kernel size should be size/2
		THREADS_MAX, //final int threadsMax, // maximal number of threads to launch
		UPDATE_STATUS, //final boolean updateStatus,
		DEBUG_LEVEL); //final int debugLevel);
		if (configPath!=null) {
		saveTimestampedProperties( // save config again
		configPath, // full path or null
		null, // use as default directory if path==null
		true,
		PROPERTIES);
		}
		}

		public void runMenuCommand(String label){
		int i, j; //,l,iq;
		// String label = e.getActionCommand();
		@@ -982,69 +1064,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
		return;
		/* ======================================================================== */
		} else if (label.equals("Process files")) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
		String configPath=null;
		if (EYESIS_CORRECTIONS.correctionsParameters.saveSettings) {
		configPath=EYESIS_CORRECTIONS.correctionsParameters.selectResultsDirectory(
		true,
		true);
		if (configPath==null){
		String msg="No results directory selected, command aborted";
		System.out.println("Warning: "+msg);
		IJ.showMessage("Warning",msg);
		return;
		}
		configPath+=Prefs.getFileSeparator()+"autoconfig";
		try {
		saveTimestampedProperties(
		configPath, // full path or null
		null, // use as default directory if path==null
		true,
		PROPERTIES);

		} catch (Exception e){
		String msg="Failed to save configuration to "+configPath+", command aborted";
		System.out.println("Error: "+msg);
		IJ.showMessage("Error",msg);
		return;
		}
		}

		EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL);
		int numChannels=EYESIS_CORRECTIONS.getNumChannels();
		NONLIN_PARAMETERS.modifyNumChannels(numChannels);
		CHANNEL_GAINS_PARAMETERS.modifyNumChannels(numChannels);

		if (CORRECTION_PARAMETERS.deconvolve && (NONLIN_PARAMETERS.noiseGainPower!=0)) {
		EYESIS_CORRECTIONS.updateImageNoiseGains(
		NONLIN_PARAMETERS, //EyesisCorrectionParameters.NonlinParameters nonlinParameters,
		CONVOLVE_FFT_SIZE, //int fftSize, // 128 - fft size, kernel size should be size/2
		THREADS_MAX, // int threadsMax, // maximal number of threads to launch
		UPDATE_STATUS, // boolean updateStatus,
		DEBUG_LEVEL); //int globalDebugLevel){
		}

		EYESIS_CORRECTIONS.processChannelImages(
		SPLIT_PARAMETERS, // EyesisCorrectionParameters.SplitParameters splitParameters,
		DEBAYER_PARAMETERS, //EyesisCorrectionParameters.DebayerParameters debayerParameters,
		NONLIN_PARAMETERS, //EyesisCorrectionParameters.NonlinParameters nonlinParameters,
		COLOR_PROC_PARAMETERS, //EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
		CHANNEL_GAINS_PARAMETERS, //CorrectionColorProc.ColorGainsParameters channelGainParameters,
		RGB_PARAMETERS, //EyesisCorrectionParameters.RGBParameters rgbParameters,
		EQUIRECTANGULAR_PARAMETERS, // EyesisCorrectionParameters.EquirectangularParameters equirectangularParameters,
		CONVOLVE_FFT_SIZE, //int convolveFFTSize, // 128 - fft size, kernel size should be size/2
		THREADS_MAX, //final int threadsMax, // maximal number of threads to launch
		UPDATE_STATUS, //final boolean updateStatus,
		DEBUG_LEVEL); //final int debugLevel);
		if (configPath!=null) {
		saveTimestampedProperties( // save config again
		configPath, // full path or null
		null, // use as default directory if path==null
		true,
		PROPERTIES);
		}

		processFiles();
		return;
		/* ======================================================================== */
		} else if (label.equals("Tiff Writer")) {
		@@ -5673,7 +5693,7 @@ G= Y +Pr(- 2Kr(1-Kr))/Kg + Pb(-2Kb(1-Kb))/Kg
		*/
		public static void main(String[] args) {
		// set the plugins.dir property to make the plugin appear in the Plugins menu
		Class<?> clazz = Aberration_Calibration.class;
		Class<?> clazz = Eyesis_Correction.class;
		String url = clazz.getResource("/" + clazz.getName().replace('.', '/') + ".class").toString();
		String pluginsDir = url.substring(5, url.length() - clazz.getName().length() - 6);
		System.setProperty("plugins.dir", pluginsDir);

src/main/java/JP46_Reader_camera.java

+28 −38

Original line number	Diff line number	Diff line
		@@ -30,6 +30,7 @@ import ij.process.*;
		import ij.gui.*;
		import ij.plugin.frame.*;
		import ij.text.*;
		import ij.plugin.PlugIn;

		import java.awt.*;
		import java.awt.event.*;
		@@ -50,9 +51,8 @@ import org.xml.sax.InputSource;
		import org.xml.sax.SAXException;



		/* This plugin opens images in Elphel JP4/JP46 format (opens as JPEG, reads MakerNote and converts). */
		public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
		public class JP46_Reader_camera implements PlugIn, ActionListener {

		/**
		*
		@@ -61,6 +61,7 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
		Panel panel1;
		Panel confpanel;
		Frame instance;
		PlugInFrame plugInFrame;

		String arg;

		@@ -75,44 +76,31 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
		public boolean demux=true;
		public String imageTitle="cameraImage";
		private int ExifOffset=0x0c;
		private Boolean headless=GraphicsEnvironment.getLocalGraphicsEnvironment().isHeadlessInstance();

		public JP46_Reader_camera() {
		super("JP46 Reader Camera");
		if (IJ.versionLessThan("1.39t")) return;
		if (instance!=null) {
		instance.toFront();
		return;
		public void run(String arg) {
		}
		instance = this;
		addKeyListener(IJ.getInstance());

		panel1 = new Panel();

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

		addButton("Open JP4/JP46...",panel1);
		addButton("Open JP4/JP46 from camera",panel1);
		addButton("Configure...",panel1);
		addButton("Show image properties",panel1);
		addButton("Decode image info to properties",panel1);
		addButton("Split Bayer",panel1);
		public JP46_Reader_camera(Boolean showGui) {
		if (showGui) initGui();
		}

		public JP46_Reader_camera() {
		initGui();
		}

		add(panel1);
		private void initGui() {
		if (headless) return;

		pack();
		GUI.center(this);
		setVisible(true);
		}
		public JP46_Reader_camera(boolean showGUI) {
		super("JP46 Reader Camera");
		if (IJ.versionLessThan("1.39t")) return;
		if (instance!=null) {
		instance.toFront();
		return;
		}
		instance = this;
		addKeyListener(IJ.getInstance());
		plugInFrame=new PlugInFrame("JP46 Reader Camera");
		instance = (Frame)plugInFrame;

		plugInFrame.addKeyListener(IJ.getInstance());

		panel1 = new Panel();

		@@ -124,12 +112,14 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
		addButton("Show image properties",panel1);
		addButton("Decode image info to properties",panel1);
		addButton("Split Bayer",panel1);
		add(panel1);
		pack();
		GUI.center(this);
		setVisible(showGUI);
		}


		plugInFrame.add(panel1);

		plugInFrame.pack();
		GUI.center(plugInFrame);
		plugInFrame.setVisible(true);
		}
		void addButton(String label, Panel panel) {
		Button b = new Button(label);
		b.addActionListener(this);
		@@ -1321,7 +1311,7 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970
		*/
		public static void main(String[] args) {
		// set the plugins.dir property to make the plugin appear in the Plugins menu
		Class<?> clazz = Aberration_Calibration.class;
		Class<?> clazz = JP46_Reader_camera.class;
		String url = clazz.getResource("/" + clazz.getName().replace('.', '/') + ".class").toString();
		String pluginsDir = url.substring(5, url.length() - clazz.getName().length() - 6);
		System.setProperty("plugins.dir", pluginsDir);

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