private DicomObject doNCreate(DicomObject rq, DicomObject data, DicomObject rsp)
throws DicomServiceException {
String iuid = rq.getString(Tag.AffectedSOPInstanceUID);
if (iuid == null) iuid = rsp.getString(Tag.AffectedSOPInstanceUID);
File f = mkFile(iuid);
if (f.exists()) {
throw new DicomServiceException(rq, Status.DuplicateSOPinstance);
}
data.initFileMetaInformation(
UID.ModalityPerformedProcedureStepSOPClass, iuid, UID.ExplicitVRLittleEndian);
try {
store(f, data);
try {
Context.openSession();
DicomUtils.updateStudyPerformedStatusByMpps(data);
} catch (Exception e) {
debug("Can not update database with");
debug(data.toString());
e.printStackTrace();
} finally {
Context.closeSession();
}
} catch (Exception e) {
throw new DicomServiceException(rq, Status.ProcessingFailure);
}
return null;
}
public static TCDocumentObject create(TCReferencedInstance ref) throws Exception {
Instance instance =
((TCQueryLocal) JNDIUtils.lookup(TCQueryLocal.JNDI_NAME))
.findInstanceByUID(ref.getInstanceUID());
if (instance == null) {
return null;
}
DicomObject attrs = instance.getAttributes(false);
MimeType mimeType = null;
String mimeTypeStr = attrs.getString(Tag.MIMETypeOfEncapsulatedDocument);
if (mimeTypeStr != null) {
mimeType = MimeType.get(mimeTypeStr);
}
if (mimeType == null) {
mimeType = getDocumentMimeTypeFromLabel(attrs.getString(Tag.ContentLabel));
}
if (mimeType != null) {
DocumentType docType = mimeType.getDocumentType();
if (TCImageDocument.DOC_TYPES.contains(docType)) {
return TCImageDocument.create(ref);
} else if (TCEncapsulatedDocument.DOC_TYPES.contains(docType)) {
return TCEncapsulatedDocument.create(ref);
}
}
throw new Exception(
"Unable to create TC encapsulated object: Mime type not supported (" + mimeTypeStr + ")");
}
public static TCEncapsulatedDocument create(TCReferencedInstance ref) throws Exception {
Instance instance =
((TCQueryLocal) JNDIUtils.lookup(TCQueryLocal.JNDI_NAME))
.findInstanceByUID(ref.getInstanceUID());
List<org.dcm4chee.archive.entity.File> files = instance.getFiles();
DicomObject attrs = instance.getAttributes(false);
attrs.remove(Tag.EncapsulatedDocument);
MimeType mimeType = null;
String mimeTypeStr = attrs.getString(Tag.MIMETypeOfEncapsulatedDocument);
if (mimeTypeStr != null) {
mimeType = MimeType.get(mimeTypeStr);
}
if (mimeType == null) {
mimeType = getDocumentMimeTypeFromLabel(attrs.getString(Tag.ContentLabel));
}
String fsId = files.get(0).getFileSystem().getDirectoryPath();
String fileId = files.get(0).getFilePath();
File file =
fsId.startsWith("tar:")
? TarRetrieveDelegate.getInstance().retrieveFileFromTar(fsId, fileId)
: FileUtils.resolve(new File(fsId, fileId));
return new TCEncapsulatedDocument(mimeType, ref, attrs, file);
}
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 DicomObject toSCN(DicomObject ian) {
DicomObject scn = new BasicDicomObject();
scn.putString(Tag.PatientID, VR.LO, ian.getString(Tag.PatientID));
scn.putString(Tag.PatientName, VR.PN, ian.getString(Tag.PatientName));
scn.putString(Tag.StudyID, VR.SH, ian.getString(Tag.StudyID));
scn.putString(Tag.StudyInstanceUID, VR.UI, ian.getString(Tag.StudyInstanceUID));
DicomElement ianSeriesSeq = ian.get(Tag.ReferencedSeriesSequence);
DicomElement scnSeriesSeq = scn.putSequence(Tag.ReferencedSeriesSequence);
DicomObject ianSeriesItem, scnSeriesItem, scnSOPItem;
DicomElement ianSOPSeq, scnSOPSeq;
for (int i = 0, n = ianSeriesSeq.countItems(); i < n; ++i) {
ianSeriesItem = ianSeriesSeq.getDicomObject(i);
scnSeriesItem = new BasicDicomObject();
scnSeriesItem.putString(
Tag.SeriesInstanceUID, VR.UI, ianSeriesItem.getString(Tag.SeriesInstanceUID));
scnSeriesSeq.addDicomObject(scnSeriesItem);
ianSOPSeq = ianSeriesItem.get(Tag.ReferencedSOPSequence);
scnSOPSeq = scnSeriesItem.putSequence(Tag.ReferencedImageSequence);
for (int j = 0, m = ianSOPSeq.countItems(); j < m; ++j) {
scnSOPItem = new BasicDicomObject();
ianSOPSeq.getDicomObject(j).exclude(INSTANCE_AVAILABILITY).copyTo(scnSOPItem);
scnSOPSeq.addDicomObject(scnSOPItem);
}
}
return scn;
}
private DicomObject mkStgCmtResult(Association as, DicomObject rqdata) {
DicomObject result = new BasicDicomObject();
result.putString(Tag.TransactionUID, VR.UI, rqdata.getString(Tag.TransactionUID));
DicomElement rqsq = rqdata.get(Tag.ReferencedSOPSequence);
DicomElement resultsq = result.putSequence(Tag.ReferencedSOPSequence);
if (stgcmtRetrieveAET != null) {
result.putString(Tag.RetrieveAETitle, VR.AE, stgcmtRetrieveAET);
}
DicomElement failedsq = null;
File dir = getDir(as);
for (int i = 0, n = rqsq.countItems(); i < n; i++) {
DicomObject rqItem = rqsq.getDicomObject(i);
String uid = rqItem.getString(Tag.ReferencedSOPInstanceUID);
DicomObject resultItem = new BasicDicomObject();
rqItem.copyTo(resultItem);
if (stgcmtRetrieveAETs != null) {
resultItem.putString(Tag.RetrieveAETitle, VR.AE, stgcmtRetrieveAETs);
}
File f = new File(dir, uid);
if (f.isFile()) {
resultsq.addDicomObject(resultItem);
} else {
resultItem.putInt(Tag.FailureReason, VR.US, NO_SUCH_OBJECT_INSTANCE);
if (failedsq == null) {
failedsq = result.putSequence(Tag.FailedSOPSequence);
}
failedsq.addDicomObject(resultItem);
}
}
return result;
}
@Override
public void onDimseRSP(Association as, DicomObject cmd, DicomObject data) {
int status = cmd.getInt(Tag.Status);
switch (status) {
case 0:
{
LOG.debug("Dataset stored at {}", as.getCalledAET());
break;
}
case 0xA700:
{
LOG.error(
"Failed to store dataset - Out Of Resources! (status: {}H, calledAET:{}, comment:{})",
new Object[] {
StringUtils.shortToHex(status), as.getCalledAET(), cmd.getString(Tag.ErrorComment)
});
break;
}
case 0xA900:
{
LOG.error(
"Failed to store dataset - Dataset doesn't match SOP class! (status: {}H, calledAET:{}, comment:{})",
new Object[] {
StringUtils.shortToHex(status), as.getCalledAET(), cmd.getString(Tag.ErrorComment)
});
break;
}
case 0xC000:
{
LOG.error(
"Failed to store dataset - Can't understand! (status: {}H, calledAET:{}, comment:{})",
new Object[] {
StringUtils.shortToHex(status), as.getCalledAET(), cmd.getString(Tag.ErrorComment)
});
break;
}
case 0xB000:
case 0xB006:
case 0xB007:
LOG.warn(
"Dataset stored at {} with status {}H",
as.getCalledAET(),
StringUtils.shortToHex(status));
break;
default:
LOG.error(
"Failed to store dataset! (status: {}H, calledAET:{}, comment:{})",
new Object[] {
StringUtils.shortToHex(status), as.getCalledAET(), cmd.getString(Tag.ErrorComment)
});
}
}
public void setAttributes(DicomObject attrs) {
PersonName pn = new PersonName(attrs.getString(Tag.HumanPerformerName));
this.humanPerformerName = pn.componentGroupString(PersonName.SINGLE_BYTE, false).toUpperCase();
this.humanPerformerIdeographicName = pn.componentGroupString(PersonName.IDEOGRAPHIC, false);
this.humanPerformerPhoneticName = pn.componentGroupString(PersonName.PHONETIC, false);
if (AttributeFilter.isSoundexEnabled()) {
this.humanPerformerFamilyNameSoundex = AttributeFilter.toSoundex(pn, PersonName.FAMILY, "*");
this.humanPerformerGivenNameSoundex = AttributeFilter.toSoundex(pn, PersonName.GIVEN, "*");
}
}
public static TCImageDocument create(TCReferencedInstance ref) throws Exception {
DicomObject attrs =
((TCQueryLocal) JNDIUtils.lookup(TCQueryLocal.JNDI_NAME))
.findInstanceByUID(ref.getInstanceUID())
.getAttributes(false);
attrs.remove(Tag.PixelData);
return new TCImageDocument(
checkMimeType(getDocumentMimeTypeFromLabel(attrs.getString(Tag.ContentLabel))),
ref,
attrs);
}
private DicomObject doNSet(DicomObject rq, DicomObject data) throws DicomServiceException {
final String iuid = rq.getString(Tag.RequestedSOPInstanceUID);
File f = mkFile(iuid);
if (!f.exists()) {
throw new DicomServiceException(rq, Status.NoSuchObjectInstance, iuid);
}
try {
DicomObject mpps = dcmOF.load(f);
String status = mpps.getString(Tag.PerformedProcedureStepStatus);
if (!"IN PROGRESS".equals(status)) {
DicomServiceException ex =
new DicomServiceException(
rq,
Status.ProcessingFailure,
"Performed Procedure Step Object may no longer be updated");
ex.setErrorID(0xA710);
throw ex;
}
data.copyTo(mpps);
store(f, mpps);
try {
Context.openSession();
DicomUtils.updateStudyPerformedStatusByMpps(mpps);
} catch (Exception e) {
debug("Can not update database with");
debug(mpps.toString());
e.printStackTrace();
} finally {
Context.closeSession();
}
} catch (DicomServiceException e) {
throw e;
} catch (Exception e) {
throw new DicomServiceException(rq, Status.ProcessingFailure, e.getMessage());
}
return null;
}
public String getStudyInstanceUID() {
return metaData.getString(Tag.StudyInstanceUID);
}
public String getSeriesInstanceUID() {
return metaData.getString(Tag.SeriesInstanceUID);
}
public String getSOPClassUID() {
return metaData.getString(Tag.SOPClassUID);
}
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;
}
private String getStringFromObject(int tag, DicomObject dicomObject) {
String returnValue = dicomObject.getString(tag);
return returnValue == null ? "[ Unknown ]" : returnValue;
}
void onCStoreRQ(
Association as,
int pcid,
DicomObject rq,
PDVInputStream dataStream,
String tsuid,
DicomObject rsp)
throws IOException {
String cuid = rq.getString(Tag.AffectedSOPClassUID);
String iuid = rq.getString(Tag.AffectedSOPInstanceUID);
DicomObject data =
dataStream
.readDataset(); // You have one shot to get the data. You can't read twice with
// readDataset method.
String suid = data.getString(Tag.StudyInstanceUID);
// Calendar today = Calendar.getInstance();
// File struturedDestination = new File(destination.getAbsolutePath() + File.separator +
// today.get(Calendar.YEAR) + File.separator + today.get(Calendar.MONTH) + File.separator +
// today.get(Calendar.DATE) + File.separator + suid);
File struturedDestination =
new File(
destination.getAbsolutePath() + File.separator + "oviyam2" + File.separator + suid);
String child[] = struturedDestination.list();
if (child == null) {
struturedDestination.mkdirs();
}
File file = devnull != null ? struturedDestination : new File(struturedDestination, iuid);
// LOG.info("M-WRITE {}", file);
try {
DicomOutputStream dos =
new DicomOutputStream(
new BufferedOutputStream(new FileOutputStream(file), fileBufferSize));
try {
BasicDicomObject fmi = new BasicDicomObject();
fmi.initFileMetaInformation(cuid, iuid, tsuid);
dos.writeFileMetaInformation(fmi);
// dataStream.copyTo(dos);
dos.writeDataset(data, tsuid);
} finally {
CloseUtils.safeClose(dos);
}
} catch (IOException e) {
if (devnull == null && file != null) {
if (file.delete()) {
LOG.info("M-DELETE {}", file);
}
}
throw new DicomServiceException(rq, Status.ProcessingFailure, e.getMessage());
}
// Rename the file after it has been written. See DCM-279
/*if (devnull == null && file != null) {
File rename = new File(file.getParent(), iuid);
LOG.info("M-RENAME {} to {}", file, rename);
file.renameTo(rename);
if (cache.getJournalRootDir() != null) {
cache.record(rename);
}
}*/
// NetworkQueueUpdateDelegate networkQueueUpdateDelegate = new NetworkQueueUpdateDelegate();
// networkQueueUpdateDelegate.updateReceiveTable(file, as.getCallingAET());
}
public String getDocumentName() {
return getDocumentNameFromLabel(metaData.getString(Tag.ContentLabel), false);
}
public String getDocumentDescription() {
return metaData.containsValue(Tag.DocumentTitle)
? metaData.getString(Tag.DocumentTitle)
: metaData.getString(Tag.ContentDescription);
}
public void setAttributes(DicomObject attrs) {
AttributeFilter filter = AttributeFilter.getSeriesAttributeFilter();
this.seriesInstanceUID = attrs.getString(Tag.SeriesInstanceUID);
this.seriesNumber = attrs.getString(Tag.SeriesNumber, "");
this.seriesDescription =
filter.toUpperCase(attrs.getString(Tag.SeriesDescription, ""), Tag.SeriesDescription);
this.modality = filter.toUpperCase(attrs.getString(Tag.Modality, ""), Tag.Modality);
this.institutionalDepartmentName =
filter.toUpperCase(
attrs.getString(Tag.InstitutionalDepartmentName, ""), Tag.InstitutionalDepartmentName);
this.institutionName =
filter.toUpperCase(attrs.getString(Tag.InstitutionName, ""), Tag.InstitutionName);
this.stationName = filter.toUpperCase(attrs.getString(Tag.StationName, ""), Tag.StationName);
String srcAET = attrs.getString(attrs.resolveTag(PrivateTag.CallingAET, PrivateTag.CreatorID));
if (srcAET != null && srcAET.trim().length() > 1) this.sourceAET = srcAET;
this.bodyPartExamined =
filter.toUpperCase(attrs.getString(Tag.BodyPartExamined, ""), Tag.BodyPartExamined);
this.laterality = filter.toUpperCase(attrs.getString(Tag.Laterality, ""), Tag.Laterality);
PersonName pn = new PersonName(attrs.getString(Tag.PerformingPhysicianName));
this.performingPhysicianName =
pn.componentGroupString(PersonName.SINGLE_BYTE, false).toUpperCase();
this.performingPhysicianIdeographicName =
pn.componentGroupString(PersonName.IDEOGRAPHIC, false);
this.performingPhysicianPhoneticName = pn.componentGroupString(PersonName.PHONETIC, false);
if (AttributeFilter.isSoundexEnabled()) {
this.performingPhysicianFamilyNameSoundex =
AttributeFilter.toSoundex(pn, PersonName.FAMILY, "*");
this.performingPhysicianGivenNameSoundex =
AttributeFilter.toSoundex(pn, PersonName.GIVEN, "*");
}
this.performedProcedureStepStartDateTime =
attrs.getDate(Tag.PerformedProcedureStepStartDate, Tag.PerformedProcedureStepStartTime);
this.performedProcedureStepInstanceUID =
attrs.getString(
new int[] {
Tag.ReferencedPerformedProcedureStepSequence, 0, Tag.ReferencedSOPInstanceUID
});
int[] fieldTags = filter.getFieldTags();
for (int i = 0; i < fieldTags.length; i++) {
try {
setField(filter.getField(fieldTags[i]), attrs.getString(fieldTags[i], ""));
} catch (Exception e) {
throw new ConfigurationException(e);
}
}
this.encodedAttributes =
DicomObjectUtils.encode(filter.filter(attrs), filter.getTransferSyntaxUID());
}