private int store(String aet, String cuid, DicomObject dataset)
throws IOException, InterruptedException, GeneralSecurityException {
if (cuid == null) {
cuid = dataset.getString(Tag.SOPClassUID);
}
setTransferCapability(
new TransferCapability[] {
new TransferCapability(cuid, NATIVE_LE_TS, TransferCapability.SCU)
});
Association assoc = open(aet);
TransferCapability tc = assoc.getTransferCapabilityAsSCU(cuid);
if (tc == null) {
throw new NoPresentationContextException(
UIDDictionary.getDictionary().prompt(UID.KeyObjectSelectionDocumentStorage));
}
String tsuid = tc.getTransferSyntax()[0];
LOG.debug("Send C-STORE request to {}:\n{}", aet, dataset);
RspHandler rspHandler = new RspHandler();
assoc.cstore(
cuid,
dataset.getString(Tag.SOPInstanceUID),
priority,
new DataWriterAdapter(dataset),
tsuid,
rspHandler);
assoc.waitForDimseRSP();
try {
assoc.release(true);
} catch (InterruptedException t) {
LOG.error("Failed to release association! aet:" + aet, t);
}
return rspHandler.getStatus();
}
private int sendIAN(String aet, DicomObject ian)
throws IOException, InterruptedException, GeneralSecurityException {
String iuid = UIDUtils.createUID();
Association assoc = open(aet);
TransferCapability tc =
assoc.getTransferCapabilityAsSCU(UID.InstanceAvailabilityNotificationSOPClass);
RspHandler rspHandler = new RspHandler();
if (tc == null) {
tc = assoc.getTransferCapabilityAsSCU(UID.BasicStudyContentNotificationSOPClassRetired);
if (tc == null) {
throw new NoPresentationContextException(
UIDDictionary.getDictionary()
.prompt(
isOfferStudyContentNotification()
? UID.BasicStudyContentNotificationSOPClassRetired
: UID.InstanceAvailabilityNotificationSOPClass));
}
String tsuid = tc.getTransferSyntax()[0];
DicomObject scn = toSCN(ian);
scn.putString(Tag.SOPInstanceUID, VR.UI, iuid);
scn.putString(Tag.SOPClassUID, VR.UI, UID.BasicStudyContentNotificationSOPClassRetired);
LOG.debug("Study Content Notification to {}:\n{}", aet, scn);
assoc.cstore(
UID.BasicStudyContentNotificationSOPClassRetired,
iuid,
priority,
new DataWriterAdapter(scn),
tsuid,
rspHandler);
} else {
String tsuid = tc.getTransferSyntax()[0];
LOG.debug("Instance Availability Notification to {}:\n{}", aet, ian);
assoc.ncreate(UID.InstanceAvailabilityNotificationSOPClass, iuid, ian, tsuid, rspHandler);
}
assoc.waitForDimseRSP();
try {
assoc.release(true);
} catch (InterruptedException t) {
LOG.error("Association release failed! aet:" + aet, t);
}
return rspHandler.getStatus();
}
/**
* @author Gunter Zeilinger <*****@*****.**>
* @version $Rev$ $Date:: 0000-00-00 $
* @since Oct 22, 2010
*/
public class FixJpegLS {
private static final String USAGE = "fixjpegls [Options] SOURCE DEST";
private static final String DESCRIPTION =
" or fixjpegls [Options] "
+ "SOURCE... DIRECTORY\n.\n"
+ "Patch faulty DICOM JPEG-LS images compressed by JAI-IMAGEIO "
+ "JPEG-LS encoder by inserting a LSE marker segment with "
+ "encoder parameter values T1, T2 and T3 actually used by "
+ "JAI-IMAGEIO JPEG-LS encoder.\n.\n"
+ "Options:";
private static final String NO_CHECK_IMPL_CUID =
"fix also DICOM files "
+ "with different Implementation Class UID than specified by "
+ "option --check-impl-cuid";
private static final String CHECK_IMPL_CUID =
"Implementation Class UID " + "of files to fix; default: `1.2.40.0.13.1.1'";
private static final String NO_NEW_IMPL_CUID =
"do not replace "
+ "Implementation Class UID in fixed files with UID specified by "
+ "option --new-impl-cuid";
private static final String NEW_IMPL_CUID =
"Implementation Class UID " + "inserted in fixed files; default: `1.2.40.0.13.1.1.1'";
private static final String EXAMPLE = null;
private static final int SOI = 0xffd8;
private static final int SOF55 = 0xfff7;
private static final int LSE = 0xfff8;
private static final int SOS = 0xffda;
private static final byte[] LSE_13 = {
(byte) 0xff,
(byte) 0xf8,
(byte) 0x00,
(byte) 0x0D,
(byte) 0x01,
(byte) 0x1f,
(byte) 0xff,
(byte) 0x00,
(byte) 0x22, // T1 = 34
(byte) 0x00,
(byte) 0x83, // T2 = 131
(byte) 0x02,
(byte) 0x24, // T3 = 548
(byte) 0x00,
(byte) 0x40
};
private static final byte[] LSE_14 = {
(byte) 0xff,
(byte) 0xf8,
(byte) 0x00,
(byte) 0x0D,
(byte) 0x01,
(byte) 0x3f,
(byte) 0xff,
(byte) 0x00,
(byte) 0x42, // T1 = 66
(byte) 0x01,
(byte) 0x03, // T2 = 259
(byte) 0x04,
(byte) 0x44, // T3 = 1092
(byte) 0x00,
(byte) 0x40
};
private static final byte[] LSE_15 = {
(byte) 0xff,
(byte) 0xf8,
(byte) 0x00,
(byte) 0x0D,
(byte) 0x01,
(byte) 0x7f,
(byte) 0xff,
(byte) 0x00,
(byte) 0x82, // T1 = 130
(byte) 0x02,
(byte) 0x03, // T2 = 515
(byte) 0x08,
(byte) 0x84, // T3 = 2180
(byte) 0x00,
(byte) 0x40
};
private static final byte[] LSE_16 = {
(byte) 0xff,
(byte) 0xf8,
(byte) 0x00,
(byte) 0x0D,
(byte) 0x01,
(byte) 0xff,
(byte) 0xff,
(byte) 0x01,
(byte) 0x02, // T1 = 258
(byte) 0x04,
(byte) 0x03, // T2 = 1027
(byte) 0x11,
(byte) 0x04, // T3 = 4356
(byte) 0x00,
(byte) 0x40
};
private static final byte[] PADDING_BYTE = {0};
private static final UIDDictionary DICT = UIDDictionary.getDictionary();
private String implClassUID = "1.2.40.0.13.1.1";
private String newImplClassUID = "1.2.40.0.13.1.1.1";
@SuppressWarnings("serial")
private static final class NoFixException extends IOException {
public NoFixException(String message) {
super(message);
}
}
private static final class Replacement {
final long pos;
final int len;
final byte[] val;
Replacement(long pos, int len, byte[] val) {
super();
this.pos = pos;
this.len = len;
this.val = val;
}
}
private final class Replacements implements DicomInputHandler {
boolean pixelData;
boolean fmi = true;
List<Replacement> replacements;
int numItems;
int bitsStored;
public boolean readValue(DicomInputStream in) throws IOException {
int tag = in.tag();
int len = in.valueLength();
long pos = in.getStreamPosition();
DicomObject attrs = in.getDicomObject();
String uid;
if (fmi && tag >= 0x00080000) {
if (replacements == null)
throw new NoFixException("File Meta Information (0002,eeee) is missing");
if (FixJpegLS.this.implClassUID != null) {
uid = attrs.getString(Tag.ImplementationClassUID);
if (!FixJpegLS.this.implClassUID.equals(uid))
throw new NoFixException("Implementation Class UID (0002,0012) = " + uid);
}
fmi = false;
}
switch (tag) {
case Tag.FileMetaInformationGroupLength:
case Tag.ItemDelimitationItem:
case Tag.SequenceDelimitationItem:
return in.readValue(in);
case Tag.TransferSyntaxUID:
in.readValue(in);
uid = attrs.getString(Tag.TransferSyntaxUID);
if (!UID.JPEGLSLossless.equals(uid))
throw new NoFixException("Transfer Syntax UID (0002,0010) = " + DICT.prompt(uid));
replacements = new ArrayList<Replacement>();
return true;
case Tag.ImplementationClassUID:
if (replacements == null)
throw new NoFixException("File Meta Information (0002,eeee) is missing");
in.readValue(in);
if (FixJpegLS.this.newImplClassUID != null)
addImplClassUIDReplacements(pos, len, (int) in.getEndOfFileMetaInfoPosition());
return true;
case Tag.PixelData:
if (in.level() == 0) {
if (len != -1)
throw new NoFixException("Pixel Data is not encapsulated into Data Fragments");
pixelData = true;
}
return in.readValue(in);
case Tag.Item:
if (pixelData) {
if (len == 0) return true;
byte[] jpegheader = new byte[17];
in.readFully(jpegheader);
byte[] lse = selectLSE(jpegheader);
in.skipFully(len - 18);
addItemReplacements(pos, len, lse, in.read() == 0);
numItems++;
return true;
}
}
pixelData = false;
if (len == -1) return in.readValue(in);
in.skipFully(len);
return true;
}
@SuppressWarnings("deprecation")
private void addImplClassUIDReplacements(long pos, int len, int eoffmipos) {
int uidlen = FixJpegLS.this.newImplClassUID.length();
int newlen = (uidlen + 1) & ~1;
if (eoffmipos > 0) {
byte[] newfmilen = new byte[4];
ByteUtils.int2bytesLE(eoffmipos - 144 - len + newlen, newfmilen, 0);
replacements.add(new Replacement(140, 4, newfmilen));
}
byte[] newval = new byte[newlen + 2];
ByteUtils.ushort2bytesLE(newlen, newval, 0);
FixJpegLS.this.newImplClassUID.getBytes(0, uidlen, newval, 2);
replacements.add(new Replacement(pos - 2, len + 2, newval));
}
private void addItemReplacements(long pos, int len, byte[] lse, boolean padded) {
int newlen = len + (padded ? 14 : 15);
replacements.add(
new Replacement(pos - 4, 4, ByteUtils.int2bytesLE((newlen + 1) & ~1, new byte[4], 0)));
replacements.add(new Replacement(pos + 15, 0, lse));
boolean newPadded = (newlen & 1) != 0;
if (newPadded != padded)
replacements.add(
newPadded
? new Replacement(pos + len, 0, PADDING_BYTE)
: new Replacement(pos + len - 1, 1, null));
}
public void applyTo(File source, File target) throws IOException {
boolean failed = true;
FileInputStream fin = new FileInputStream(source);
try {
FileChannel in = fin.getChannel();
FileOutputStream fos = new FileOutputStream(target);
try {
FileChannel out = fos.getChannel();
long pos = 0L;
for (Replacement replacement : replacements) {
in.transferTo(pos, replacement.pos - pos, out);
if (replacement.val != null) out.write(ByteBuffer.wrap(replacement.val));
pos = replacement.pos + replacement.len;
}
in.transferTo(pos, source.length() - pos, out);
failed = false;
} finally {
fos.close();
if (failed == true) target.delete();
}
} finally {
fin.close();
}
}
private byte[] selectLSE(byte[] jpegheader) throws NoFixException {
if (ByteUtils.bytesBE2ushort(jpegheader, 0) != SOI)
throw new NoFixException("SOI marker is missing");
if (ByteUtils.bytesBE2ushort(jpegheader, 2) != SOF55)
throw new NoFixException("SOI marker is not followed by JPEG-LS SOF marker");
if (ByteUtils.bytesBE2ushort(jpegheader, 4) != 11)
throw new NoFixException("unexpected length of JPEG-LS SOF marker segment");
int marker = ByteUtils.bytesBE2ushort(jpegheader, 15);
if (marker != SOS) {
throw new NoFixException(
marker == LSE
? "contains already LSE marker segment"
: "JPEG-LS SOF marker segment is not followed by SOS marker");
}
switch (bitsStored = jpegheader[6]) {
case 13:
return LSE_13;
case 14:
return LSE_14;
case 15:
return LSE_15;
case 16:
return LSE_16;
}
throw new NoFixException("JPEG-LS " + bitsStored + "-bit");
}
}
@SuppressWarnings("unchecked")
public static void main(String[] args) {
try {
CommandLine cl = parseCommandLine(args);
if (cl == null) return;
List<String> argList = cl.getArgList();
File target = removeTarget(argList);
FixJpegLS fixJpegLS = new FixJpegLS();
if (cl.hasOption("no-check-impl-cuid")) fixJpegLS.setImplClassUID(null);
else if (cl.hasOption("check-impl-cuid"))
fixJpegLS.setImplClassUID(cl.getOptionValue("check-impl-cuid"));
if (cl.hasOption("no-new-impl-cuid")) fixJpegLS.setNewImplClassUID(null);
else if (cl.hasOption("new-impl-cuid"))
fixJpegLS.setNewImplClassUID(cl.getOptionValue("new-impl-cuid"));
int[] counts = new int[2];
long start = System.currentTimeMillis();
for (String arg : argList) fixJpegLS.fix(new File(arg), target, counts);
long end = System.currentTimeMillis();
System.out.println();
System.out.println(
"Fix "
+ counts[1]
+ " of "
+ counts[0]
+ " scanned files in "
+ ((end - start) / 1000.f)
+ " s.");
} catch (ParseException e) {
System.err.println("fixjpegls: " + e.getMessage());
System.err.println("Try `fixjpegls --help' for more information.");
System.exit(1);
} catch (Exception e) {
System.err.println("fixjpegls: " + e.getMessage());
System.exit(1);
}
}
@SuppressWarnings("static-access")
private static CommandLine parseCommandLine(String[] args) throws ParseException {
Options options = new Options();
options.addOption(
OptionBuilder.withLongOpt("no-check-impl-cuid")
.withDescription(NO_CHECK_IMPL_CUID)
.create());
options.addOption(
OptionBuilder.withLongOpt("check-impl-cuid")
.hasArg()
.withArgName("uid")
.withDescription(CHECK_IMPL_CUID)
.create());
options.addOption(
OptionBuilder.withLongOpt("no-new-impl-cuid").withDescription(NO_NEW_IMPL_CUID).create());
options.addOption(
OptionBuilder.withLongOpt("new-impl-cuid")
.hasArg()
.withArgName("uid")
.withDescription(NEW_IMPL_CUID)
.create());
options.addOption(
OptionBuilder.withLongOpt("help").withDescription("display this help and exit").create());
options.addOption(
OptionBuilder.withLongOpt("version")
.withDescription("output version information and exit")
.create());
CommandLineParser parser = new PosixParser();
CommandLine cl = parser.parse(options, args);
if (cl.hasOption("help")) {
HelpFormatter formatter = new HelpFormatter();
formatter.printHelp(USAGE, DESCRIPTION, options, EXAMPLE);
return null;
}
if (cl.hasOption("version")) {
System.out.println("fixjpegls " + FixJpegLS.class.getPackage().getImplementationVersion());
return null;
}
return cl;
}
private static File removeTarget(List<String> argList) throws ParseException, IOException {
int size = argList.size();
if (size < 2)
throw new ParseException(
size == 0
? "missing file operand"
: "missing destination file operand after `" + argList.get(0) + "'");
String targetName = argList.get(size - 1);
File target = new File(targetName);
if (size > 2 && !target.isDirectory()) {
throw new IOException("target `" + targetName + "' is not a directory");
}
argList.remove(size - 1);
return target;
}
public final String getImplClassUID() {
return implClassUID;
}
public final void setImplClassUID(String implClassUID) {
this.implClassUID = implClassUID;
}
public final String getNewImplClassUID() {
return newImplClassUID;
}
public final void setNewImplClassUID(String newImplClassUID) {
this.newImplClassUID = newImplClassUID;
}
public void fix(File source, File target, int[] counts) {
if (target.isDirectory() && source.isFile()) target = new File(target, source.getName());
fixRecursive(source, target, counts);
}
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());
}
}
}
}