@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);
 }
Example #2
0
 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);
 }
Example #3
0
 @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);
   }
 }