Merge pull request #2 from luxigo/master

Allow running Eyesis_Correction and JP46_Reader_camera in headless mode

src/main/java/EyesisCorrectionParameters.java

@@ -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

@@ -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

@@ -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/JP46_Reader_camera.java

@@ -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);