updated 16.12.2008 23:08

ij/CompositeImage.java

@@ -546,6 +546,16 @@ public void setChannelLut(LUT table) {
 		customLuts = true;
 	}
 
+	/* Sets the LUT of the specified channel using a clone of 'table'. */
+	public void setChannelLut(LUT table, int channel) {
+		int channels = getNChannels();
+		if (lut==null) setupLuts(channels);
+		if (channel<1 || channel>lut.length)
+			throw new IllegalArgumentException("Channel out of range");
+		lut[channel-1] = (LUT)table.clone();
+		cip = null;
+	}
+
 	/* Sets the IndexColorModel of the current channel. */
 	public void setChannelColorModel(IndexColorModel cm) {
 		byte[] reds = new byte[256];

ij/VirtualStack.java

@@ -5,12 +5,12 @@
 
 /** This class represents an array of disk-resident images. */
 public class VirtualStack extends ImageStack {
-	static final int INITIAL_SIZE = 100;
-	String path;
-	int nSlices;
-	String[] names;
-	String[] labels;
-	int bitDepth;
+	private static final int INITIAL_SIZE = 100;
+	private String path;
+	private int nSlices;
+	private String[] names;
+	private String[] labels;
+	private int bitDepth;
 
 	/** Default constructor. */
 	public VirtualStack() { }
@@ -167,6 +167,5 @@ public void setBitDepth(int bitDepth) {
 		this.bitDepth = bitDepth;
 	}
 
-
 } 
 

ij/io/TiffDecoder.java

@@ -431,7 +431,7 @@ else if (value==2) {
 					} else if (value==3)
 						fi.unit = "cm";
 					break;
-				case PLANAR_CONFIGURATION:
+				case PLANAR_CONFIGURATION:  // 1=chunky, 2=planar
 					if (value==2 && fi.fileType==FileInfo.RGB48)
 							 fi.fileType = FileInfo.GRAY16_UNSIGNED;
 					else if (value==2 && fi.fileType==FileInfo.RGB)
@@ -440,7 +440,6 @@ else if (value==1 && fi.samplesPerPixel==4)
 						fi.fileType = FileInfo.ARGB;
 					else if (value!=2 && !((fi.samplesPerPixel==1)||(fi.samplesPerPixel==3))) {
 						String msg = "Unsupported interleaved SamplesPerPixel: " + fi.samplesPerPixel;
-						//if (fi.samplesPerPixel==4) msg += " \n \n" + "ImageJ cannot open CMYK TIFFs";
 						error(msg);
 					}
 					break;

ij/plugin/FITS_Writer.java

@@ -8,9 +8,10 @@
 /**
  * This plugin saves a 16 or 32 bit image in FITS format. It is a stripped-down version of the SaveAs_FITS 
  *	plugin from the collection of astronomical image processing plugins by Jennifer West at
- *	http://www.umanitoba.ca/faculties/science/astronomy/jwest/plugins.html
+ *	http://www.umanitoba.ca/faculties/science/astronomy/jwest/plugins.html.
  *
- * Version 2008-09-07 : preserves non-minimal FITS header if already present (F.V. Hessman, Univ. Goettingen)
+ * <br>Version 2008-09-07 : preserves non-minimal FITS header if already present (F.V. Hessman, Univ. Goettingen).
+ * <br>Version 2008-12-15 : fixed END card recognition bug (F.V. Hessman, Univ. Goettingen).
  */
 public class FITS_Writer implements PlugIn {
 
@@ -68,7 +69,7 @@ else if (ip instanceof FloatProcessor)
 	void createHeader(String path, ImageProcessor ip, int numBytes) {
 		int numCards = 5;
 		String bitperpix = "";
-		if (numBytes==2) {bitperpix = "                  16";}
+		if      (numBytes==2) {bitperpix = "                  16";}
 		else if (numBytes==4) {bitperpix = "                 -32";}
 		else if (numBytes==1) {bitperpix = "                   8";}
  		appendFile(writeCard("SIMPLE", "                   T", "Created by ImageJ FITS_Writer 2008-09-07"), path);
@@ -202,7 +203,8 @@ else if (depth > 1) {
 
 		int iend = istart+1;
 		for (; iend < lines.length; iend++) {
-			if ( lines[iend].startsWith ("END ") ) break;
+			String s = lines[iend].trim();
+			if ( s.equals ("END") || s.startsWith ("END ") ) break;
 		}
 		if (iend >= lines.length) return null;
 
@@ -235,10 +237,10 @@ void copyHeader(String[] hdr, String path, ImageProcessor ip, int numBytes) {
 		String bitperpix = "";
 
 		// THIS STUFF NEEDS TO BE MADE CONFORMAL WITH THE PRESENT IMAGE
-		if (numBytes==2) {bitperpix = "                  16";}
+		if      (numBytes==2) {bitperpix = "                  16";}
 		else if (numBytes==4) {bitperpix = "                 -32";}
 		else if (numBytes==1) {bitperpix = "                   8";}
- 		appendFile(writeCard("SIMPLE", "                   T", "Created by ImageJ FITS_Writer 2008-09-07"), path);
+ 		appendFile(writeCard("SIMPLE", "                   T", "Created by ImageJ FITS_Writer 2008-12-15"), path);
  		appendFile(writeCard("BITPIX", bitperpix, ""), path);
  		appendFile(writeCard("NAXIS", "                   2", ""), path);
 		appendFile(writeCard("NAXIS1", "                 "+ip.getWidth(), "image width"), path);
@@ -269,6 +271,6 @@ void copyHeader(String[] hdr, String path, ImageProcessor ip, int numBytes) {
 		appendFile(end, path);
 		appendFile(filler, path);
 	}
-	
+
 }
 

ij/plugin/HyperStackConverter.java

@@ -16,6 +16,7 @@ public class HyperStackConverter implements PlugIn {
 	static final int CZT=0, CTZ=1, ZCT=2, ZTC=3, TCZ=4, TZC=5;
     static final String[] orders = {"xyczt(default)", "xyctz", "xyzct", "xyztc", "xytcz", "xytzc"};
     static int order = CZT;
+    static boolean splitRGB = true;
 
 	public void run(String arg) {
 		if (arg.equals("new"))
@@ -38,24 +39,35 @@ void convertStackToHS(ImagePlus imp) {
 			IJ.error("Stack to HyperStack", "Stack required");
 			return;
 		}
-		if (imp.getBitDepth()==24) {
-			new CompositeConverter().run("color");
-			return;
-		}
+		boolean rgb = imp.getBitDepth()==24;
 		String[] modes = {"Composite", "Color", "Grayscale"};
 		GenericDialog gd = new GenericDialog("Convert to HyperStack");
 		gd.addChoice("Order:", orders, orders[order]);
 		gd.addNumericField("Channels (c):", nChannels, 0);
 		gd.addNumericField("Slices (z):", nSlices, 0);
 		gd.addNumericField("Frames (t):", nFrames, 0);
 		gd.addChoice("Display Mode:", modes, modes[1]);
+		if (rgb) {
+			gd.setInsets(15, 0, 0);
+			gd.addCheckbox("Convert RGB to 3 Channel Hyperstack", splitRGB);
+		}
 		gd.showDialog();
 		if (gd.wasCanceled()) return;
 		order = gd.getNextChoiceIndex();
 		nChannels = (int) gd.getNextNumber();
 		nSlices = (int) gd.getNextNumber();
 		nFrames = (int) gd.getNextNumber();
 		int mode = gd.getNextChoiceIndex();
+		if (rgb)
+			splitRGB = gd.getNextBoolean();
+		if (rgb && splitRGB==true) {
+			new CompositeConverter().run(mode==0?"composite":"color");
+			return;
+		}
+		if (rgb && nChannels>1) {
+			IJ.error("HyperStack Converter", "RGB stacks are limited to one channel");
+			return;
+		}
 		if (nChannels*nSlices*nFrames!=stackSize) {
 			IJ.error("HyperStack Converter", "channels x slices x frames <> stack size");
 			return;