protected void ensureContentAvailable() {
if (!isContentAvailable()) {
DicomInputStream dis = null;
try {
List<org.dcm4chee.archive.entity.File> files =
((TCQueryLocal) JNDIUtils.lookup(TCQueryLocal.JNDI_NAME))
.findInstanceByUID(getSOPInstanceUID())
.getFiles();
String fsId = files.get(0).getFileSystem().getDirectoryPath();
String fileId = files.get(0).getFilePath();
dis =
new DicomInputStream(
fsId.startsWith("tar:")
? TarRetrieveDelegate.getInstance().retrieveFileFromTar(fsId, fileId)
: FileUtils.resolve(new File(fsId, fileId)));
metaData = dis.readDicomObject();
} catch (Exception e) {
log.error("Unable to retrieve instance!", e); // $NON-NLS-1$
} finally {
if (dis != null) {
try {
dis.close();
} catch (Exception e2) {
}
}
}
}
}
private void fixRecursive(File source, File target, int[] counts) {
if (!source.exists()) {
System.err.println("no such file or directory `" + source + "'");
} else if (source.isDirectory()) {
if (!target.exists()) {
if (!target.mkdir()) System.err.println("failed to create directory `" + target + "'");
}
if (target.isFile()) {
System.err.println(
"cannot overwrite non-directory `" + target + "' with directory `" + source + "'");
return;
}
String[] ss = source.list();
for (String s : ss) {
fixRecursive(new File(source, s), new File(target, s), counts);
}
} else if (target.isDirectory()) {
System.err.println(
"cannot overwrite directory `" + target + "' with non-directory `" + source + "'");
} else {
Replacements replacements = new Replacements();
try {
counts[0]++;
DicomInputStream din = new DicomInputStream(source);
try {
din.setHandler(replacements);
din.readDicomObject();
} finally {
try {
din.close();
} catch (IOException ignore) {
}
}
if (replacements.numItems == 0) throw new NoFixException("no Pixel Data Fragments");
replacements.applyTo(source, target);
counts[1]++;
System.out.println(
"PATCHED " + source + ": JPEG-LS " + replacements.bitsStored + "-bit -> " + target);
} catch (Exception e) {
System.out.println("skipped " + source + ": " + e.getMessage());
}
}
}
private byte[] getDocumentContent() {
if (data != null) {
return data;
} else if (dicomFile != null) {
DicomInputStream dis = null;
try {
dis = new DicomInputStream(dicomFile);
return dis.readDicomObject().getBytes(Tag.EncapsulatedDocument);
} catch (Exception e) {
log.error("Unable to get content of encapsulated document!", e);
} finally {
if (dis != null) {
try {
dis.close();
} catch (Exception e) {
log.error(null, e);
}
}
}
}
return null;
}