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;
}
/**
* 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;
}