@Override
protected DataWriter createDataWriter(InstanceLocator inst, String tsuid) throws IOException {
Attributes attrs;
DicomInputStream in = new DicomInputStream(inst.getFile());
try {
if (withoutBulkData) {
in.setIncludeBulkData(false);
attrs = in.readDataset(-1, Tag.PixelData);
} else {
in.setIncludeBulkDataLocator(true);
attrs = in.readDataset(-1, -1);
}
} finally {
SafeClose.close(in);
}
attrs.addAll((Attributes) inst.getObject());
adjustPatientID(attrs);
adjustAccessionNumber(attrs);
ArchiveApplicationEntity ae = (ArchiveApplicationEntity) as.getApplicationEntity();
try {
Templates tpl =
ae.getAttributeCoercionTemplates(
inst.cuid, Dimse.C_STORE_RQ, Role.SCU, as.getRemoteAET());
if (tpl != null) attrs.update(SAXTransformer.transform(attrs, tpl, false, false), null);
} catch (Exception e) {
throw new IOException(e);
}
return new DataWriterAdapter(attrs);
}
private static String addStudyPOIsAndGetPatientID(
List<ParticipantObjectIdentification> studyPOIs, RetrieveDocumentSetResponseType rsp) {
Attributes attrs = null;
String studyIUID, classUID;
HashMap<String, HashMap<String, List<String>>> studySopClassMap =
new HashMap<String, HashMap<String, List<String>>>();
HashMap<String, List<String>> sopClassInstanceMap;
List<String> instances;
for (DocumentResponse doc : rsp.getDocumentResponse()) {
BufferedInputStream is = null;
DicomInputStream dis = null;
try {
DataHandler dh = doc.getDocument();
is = new BufferedInputStream(dh.getInputStream(), BUF_SIZE);
is.mark(BUF_SIZE);
dis = new DicomInputStream(new BufferedInputStream(is));
attrs = dis.readDataset(-1, Tag.SeriesInstanceUID);
is.reset();
doc.setDocument(new DataHandler(new InputStreamDataSource(is, dh.getContentType())));
studyIUID = attrs.getString(Tag.StudyInstanceUID);
classUID = attrs.getString(Tag.SOPClassUID);
sopClassInstanceMap = studySopClassMap.get(studyIUID);
if (sopClassInstanceMap == null) {
sopClassInstanceMap = new HashMap<String, List<String>>();
studySopClassMap.put(studyIUID, sopClassInstanceMap);
instances = null;
} else {
instances = sopClassInstanceMap.get(classUID);
}
if (instances == null) {
instances = new ArrayList<String>();
sopClassInstanceMap.put(classUID, instances);
}
instances.add(attrs.getString(Tag.SOPInstanceUID));
} catch (IOException x) {
log.warn("Failed to read DICOM attachment! instanceUID:" + doc.getDocumentUniqueId(), x);
}
}
for (Entry<String, HashMap<String, List<String>>> e : studySopClassMap.entrySet()) {
ParticipantObjectDescription pod = new ParticipantObjectDescription();
studyPOIs.add(createStudyPOI(e.getKey(), pod));
for (Entry<String, List<String>> e1 : e.getValue().entrySet()) {
SOPClass sc = new SOPClass();
sc.setUID(e1.getKey());
sc.setNumberOfInstances(e1.getValue().size());
for (String iuid : e1.getValue()) {
Instance inst = new Instance();
inst.setUID(iuid);
sc.getInstance().add(inst);
}
pod.getSOPClass().add(sc);
}
}
return attrs == null ? null : attrs.getString(Tag.PatientID);
}
@Override
public void write(OutputStream out) throws IOException, WebApplicationException {
log.info(
"{}@{} << {}: Content-Type={}, iuid={}",
new Object[] {
request.getRemoteUser(),
request.getRemoteHost(),
System.identityHashCode(request),
mediaType,
fileRef.sopInstanceUID
});
DicomInputStream dis = new DicomInputStream(fileRef.getFile());
dis.setURI(bulkDataURI);
try {
dis.setIncludeBulkData(IncludeBulkData.URI);
Attributes dataset = dis.readDataset(-1, -1);
dataset.addAll(attrs);
Object pixelData = dataset.getValue(Tag.PixelAspectRatio);
if (pixelData instanceof Fragments) {
Fragments frags = (Fragments) pixelData;
Object frag0 = frags.get(0);
BulkData frag1 = (BulkData) frags.get(1);
dataset.setValue(
Tag.PixelData,
VR.OB,
new BulkData(
frag1.uri,
frag1.transferSyntax,
frag0 == Value.NULL ? frag1.offset - 16 : ((BulkData) frag0).offset - 8,
-1));
}
SAXTransformer.getSAXWriter(new StreamResult(out)).write(dataset);
} catch (IOException e) {
throw e;
} catch (Exception e) {
throw new WebApplicationException(e);
} finally {
SafeClose.close(dis);
}
}
