Exemple #1
0
 ImagePlus openDicomStack(ZipInputStream zis, ZipEntry entry) throws IOException {
   ImagePlus imp = null;
   int count = 0;
   ImageStack stack = null;
   while (true) {
     if (count > 0) entry = zis.getNextEntry();
     if (entry == null) break;
     String name = entry.getName();
     ImagePlus imp2 = null;
     if (name.endsWith(".dcm")) {
       ByteArrayOutputStream out = new ByteArrayOutputStream();
       byte[] buf = new byte[4096];
       int len, byteCount = 0, progress = 0;
       while (true) {
         len = zis.read(buf);
         if (len < 0) break;
         out.write(buf, 0, len);
         byteCount += len;
         // IJ.showProgress((double)(byteCount%fileSize)/fileSize);
       }
       byte[] bytes = out.toByteArray();
       out.close();
       InputStream is = new ByteArrayInputStream(bytes);
       DICOM dcm = new DICOM(is);
       dcm.run(name);
       imp2 = dcm;
       is.close();
     }
     zis.closeEntry();
     if (imp2 == null) continue;
     count++;
     String label = imp2.getTitle();
     String info = (String) imp2.getProperty("Info");
     if (info != null) label += "\n" + info;
     if (count == 1) {
       imp = imp2;
       imp.getStack().setSliceLabel(label, 1);
     } else {
       stack = imp.getStack();
       stack.addSlice(label, imp2.getProcessor());
       imp.setStack(stack);
     }
   }
   zis.close();
   IJ.showProgress(1.0);
   if (count == 0)
     throw new IOException("This ZIP archive does not appear to contain any .dcm files");
   return imp;
 }
Exemple #2
0
 /**
  * Opens a single TIFF or DICOM contained in a ZIP archive, or a ZIPed collection of ".roi" files
  * created by the ROI manager.
  */
 public ImagePlus openZip(String path) {
   ImagePlus imp = null;
   try {
     ZipInputStream zis = new ZipInputStream(new FileInputStream(path));
     ZipEntry entry = zis.getNextEntry();
     if (entry == null) {
       zis.close();
       return null;
     }
     String name = entry.getName();
     if (name.endsWith(".roi")) {
       zis.close();
       if (!silentMode)
         if (IJ.isMacro() && Interpreter.isBatchMode() && RoiManager.getInstance() == null)
           IJ.log(
               "Use roiManager(\"Open\", path) instead of open(path)\nto open ROI sets in batch mode macros.");
         else IJ.runMacro("roiManager(\"Open\", getArgument());", path);
       return null;
     }
     if (name.endsWith(".tif")) {
       imp = openTiff(zis, name);
     } else if (name.endsWith(".dcm")) {
       DICOM dcm = new DICOM(zis);
       dcm.run(name);
       imp = dcm;
     } else {
       zis.close();
       IJ.error(
           "Opener",
           "This ZIP archive does not appear to contain a \nTIFF (\".tif\") or DICOM (\".dcm\") file, or ROIs (\".roi\").");
       return null;
     }
     zis.close();
   } catch (Exception e) {
     IJ.error("Opener", "" + e);
     return null;
   }
   File f = new File(path);
   FileInfo fi = imp.getOriginalFileInfo();
   if (fi != null) {
     fi.fileFormat = FileInfo.ZIP_ARCHIVE;
     fi.fileName = f.getName();
     fi.directory = f.getParent() + File.separator;
   }
   return imp;
 }