Hi,
I am trying to extend ImageJ so it can open up zipped dicom (.dcm) files via the URL open command. We are doing this so we can open a zipped-dicom using ImageJ api (from our applet) and not by using "File/Open" menu manually". The OpenURL class can open a zipped TIFF so I thought this wouldn't be too tricky :) . I was able to figure out how to modify the openURL class to handle zipped DCM. But I am confused about how to modify the ij.plugin.DICOM (
http://rsb.info.nih.gov/ij/developer/source/ij/plugin/DICOM.java.html) so it can handle an input stream as the TiffDecoder (
http://rsb.info.nih.gov/ij/developer/source/ij/io/TiffDecoder.java.html ) does for opening TIFFs via a URL.
Below is the class for opening a ZIP that I extended at the end to handle a zip that contains a .dcm file. Some advice/pointers greatly appreciated -- thanks in advance for your help!
/** Opens the ZIP compressed TIFF at the specified URL. */
ImagePlus openZip(URL url) throws IOException {
IJ.showProgress(0.01);
URLConnection uc = url.openConnection();
int fileSize = uc.getContentLength(); // compressed size
fileSize *=2; // estimate uncompressed size
InputStream in = uc.getInputStream();
ZipInputStream zin = new ZipInputStream(in);
ByteArrayOutputStream out = new ByteArrayOutputStream();
byte[] buf = new byte[4096];
ZipEntry entry = zin.getNextEntry();
if (entry==null)
return null;
String name = entry.getName();
//double fileSize = entry.getSize(); //returns -1
//If zip contains a TIF file
if (name.endsWith(".tif")) {
int len;
int byteCount = 0;
int progress = 0;
while (true) {
len = zin.read(buf);
if (len<0) break;
out.write(buf, 0, len);
byteCount += len;
IJ.showProgress((double)(byteCount%fileSize)/fileSize);
}
zin.close();
byte[] bytes = out.toByteArray();
IJ.showProgress(1.0);
return openTiff(new ByteArrayInputStream(bytes), name);
}
/* --------------------------------
Start for Zip contains a dcm file
---------------------------------- */
else if (name.endsWith(".dcm")) {
int len;
int byteCount = 0;
int progress = 0;
while (true) {
len = zin.read(buf);
if (len<0) break;
out.write(buf, 0, len);
byteCount += len;
IJ.showProgress((double)(byteCount%fileSize)/fileSize);
}
zin.close();
byte[] bytes = out.toByteArray();
IJ.showProgress(1.0);
return IJ.runPlugIn("ij.plugin.DICOM", name);
}
/* --------------------------------
End for Zip contains a dcm file
---------------------------------- */
else
throw new IOException("This ZIP archive does not appear to contain a TIFF or DCM file");
}
}
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