Java Programming

Hello

I have a java application that opens and reads a SINGLE file. There is no problem reading small to medium sized files (1 - 100s Megabytes). However once the file get "Large" (>1Gig) i get the following exception:

java.io.FileNotFoundException: /nrims/home3/jconnell/data/MESTER/EXP1_090902/090909-5-1-4x999.nrrd (Too many open files)
	at java.io.FileInputStream.open(Native Method)
	at java.io.FileInputStream.<init>(FileInputStream.java:137)
	at ij.io.FileOpener.createInputStream(FileOpener.java:437)
	at ij.io.FileOpener.readPixels(FileOpener.java:490)
	at ij.io.FileOpener.open(FileOpener.java:76)
	at com.nrims.data.Nrrd_Reader.getPixels(Nrrd_Reader.java:293)
	at com.nrims.MimsPlus.appendImage(MimsPlus.java:415)
	at com.nrims.UI.loadMIMSFile(UI.java:529)
	at com.nrims.UI.openFiles(UI.java:340)
	at com.nrims.UI.loadMIMSFile(UI.java:325)
	at com.nrims.UI.openMIMSImageMenuItemActionPerformed(UI.java:1685)
	at com.nrims.UI.access$400(UI.java:58)
	at com.nrims.UI$5.actionPerformed(UI.java:1222)
	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2012)
	at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2335)
	at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:404)
	at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
	at javax.swing.AbstractButton.doClick(AbstractButton.java:374)
	at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1688)
	at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1732)

I do not trust the "Too many files open" error because I am only dealing with 1 file. And the exception only occurs if the file is large (> 1 Gig)

Here is the code for the methods i have access to that are referenced in the Exception...

The createInputStream method in the ij.io.FileOpener class:

/** Returns an InputStream for the image described by this FileInfo. */
	public InputStream createInputStream(FileInfo fi) throws IOException, MalformedURLException {
		InputStream is = null;
		boolean gzip = fi.fileName!=null && (fi.fileName.endsWith(".gz")||fi.fileName.endsWith(".GZ"));
		if (fi.inputStream!=null)
			is = fi.inputStream;
		else if (fi.url!=null && !fi.url.equals(""))
			is = new URL(fi.url+fi.fileName).openStream();
		else {
			if (fi.directory.length()>0 && !fi.directory.endsWith(Prefs.separator))
				fi.directory += Prefs.separator;
		    File f = new File(fi.directory + fi.fileName);
		    if (gzip) fi.compression = FileInfo.COMPRESSION_UNKNOWN;
		    if (f==null || f.isDirectory() || !validateFileInfo(f, fi))
		    	is = null;
		    else
				is = new FileInputStream(f);
		}
		if (is!=null) {
		    if (fi.compression>=FileInfo.LZW)
				is = new RandomAccessStream(is);
			else if (gzip)
				is = new GZIPInputStream(is, 50000);
		}
		return is;
	}

The getPixels method in the com.nrims.data.Nrrd_Reader class:

public short[] getPixels(int index) throws IndexOutOfBoundsException, IOException {

        // Set up a temporary header to read the pixels from the file.
		NrrdFileInfo fi;
		try {
			fi=getHeaderInfo();
		} catch (IOException e) {
			IJ.write("readHeader: "+ e.getMessage());
			return null;
		}

        // Calculate offset
        long offset = fi.longOffset + // move down header
                      (2 * index * fi.width * fi.height * fi.nImages) + // move down to correct channel
                      (2 * fi.width * fi.height * currentIndex); // move down to correct image within that channel
        fi.longOffset = offset;
        fi.nImages=1; // only going to read 1 image.
        FileOpener fo = new FileOpener(fi);


        // Get image from file.
        ImagePlus imp = fo.open(false);
		if(imp==null) return null;

        return (short[])imp.getProcessor().getPixels();
    }

Any idea on how to get around this error? Is there a fundamental limit in the java.io.FileInputStream.open() method?
Any input appreciated. Thanks.