Exemple #1
0
  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 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;
 }
  private BufferedImage windowMonochrome(
      ImageListViewCell displayedCell,
      BufferedImage srcImg,
      float windowLocation,
      float windowWidth) {
    BufferedImage destImg =
        new BufferedImage(srcImg.getWidth(), srcImg.getHeight(), BufferedImage.TYPE_INT_RGB);

    boolean isSigned = false;
    int minValue = 0;
    {
      // hack: try to determine signedness and minValue from DICOM metadata if available --
      // the BufferedImage's metadata don't contain that information reliably.
      // Only works for some special cases
      ImageListViewModelElement elt = displayedCell.getDisplayedModelElement();
      if (elt instanceof DicomImageListViewModelElement) {
        DicomImageListViewModelElement delt = (DicomImageListViewModelElement) elt;
        DicomObject imgMetadata = delt.getDicomImageMetaData();
        int bitsAllocated = imgMetadata.getInt(Tag.BitsAllocated);
        isSigned = (1 == imgMetadata.getInt(Tag.PixelRepresentation));
        if (isSigned && (bitsAllocated > 0)) {
          minValue = -(1 << (bitsAllocated - 1));
        }
      }
    }

    final int windowedImageGrayscalesCount = 256; // for BufferedImage.TYPE_INT_RGB
    float scale = windowedImageGrayscalesCount / windowWidth;
    float offset = (windowWidth / 2 - windowLocation) * scale;
    if (!(srcImg.getColorModel().getColorSpace().getType() == ColorSpace.TYPE_GRAY)) {
      throw new IllegalArgumentException("source image must be grayscales");
    }
    Raster srcRaster = srcImg.getRaster();
    if (srcRaster.getNumBands() != 1) {
      throw new IllegalArgumentException(
          "grayscale source image must have one color band, but has "
              + srcRaster.getNumBands()
              + "??");
    }
    WritableRaster resultRaster = destImg.getRaster();
    for (int x = 0; x < srcImg.getWidth(); x++) {
      for (int y = 0; y < srcImg.getHeight(); y++) {
        int srcGrayValue = srcRaster.getSample(x, y, 0);
        if (isSigned) {
          srcGrayValue = (int) (short) srcGrayValue; // will only work for 16-bit signed...
        }
        float destGrayValue = scale * srcGrayValue + offset;
        // clamp
        if (destGrayValue < 0) {
          destGrayValue = 0;
        } else if (destGrayValue >= windowedImageGrayscalesCount) {
          destGrayValue = windowedImageGrayscalesCount - 1;
        }
        resultRaster.setSample(x, y, 0, destGrayValue);
        resultRaster.setSample(x, y, 1, destGrayValue);
        resultRaster.setSample(x, y, 2, destGrayValue);
      }
    }
    return destImg;
  }
    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);
    }
  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 + ")");
  }
    @SuppressWarnings("restriction")
    public static TCImageDocument create(
        TCObject tc, MimeType mimeType, String filename, InputStream in, String description)
        throws Exception {

      mimeType = checkMimeType(mimeType);

      ByteArrayOutputStream out = null;

      try {
        BufferedImage image = null;

        if (MimeType.ImageJPEG.equals(mimeType)) {
          try {
            com.sun.image.codec.jpeg.JPEGImageDecoder decoder =
                com.sun.image.codec.jpeg.JPEGCodec.createJPEGDecoder(in);
            image = decoder.decodeAsBufferedImage();
          } catch (Exception e) {
            log.warn(null, e);
          }
        }

        if (image == null) {
          image = ImageIO.read(in);
        }

        TCReferencedInstance ref =
            createReferencedInstance(
                tc, UID.MultiFrameTrueColorSecondaryCaptureImageStorage, MODALITY);

        DicomObject metaData =
            TCDocumentObject.createDicomMetaData(
                mimeType,
                filename,
                description,
                ref,
                tc.getPatientId(),
                tc.getPatientIdIssuer(),
                tc.getPatientName(),
                MODALITY);

        metaData.putInt(Tag.NumberOfFrames, VR.IS, 1);

        return new TCImageDocument(mimeType, ref, metaData, image);
      } finally {
        if (in != null) {
          try {
            in.close();
          } catch (Exception e) {
          }
        }
        if (out != null) {
          try {
            out.close();
          } catch (Exception e) {
          }
        }
      }
    }
 private DicomStreamMetaData copyMeta(DicomImageReader reader, String tsuid) throws IOException {
   DicomStreamMetaData oldMeta = (DicomStreamMetaData) reader.getStreamMetadata();
   DicomStreamMetaData ret = new DicomStreamMetaData();
   DicomObject ds = oldMeta.getDicomObject();
   DicomObject newDs = new BasicDicomObject();
   ds.copyTo(newDs);
   newDs.putString(Tag.TransferSyntaxUID, VR.UI, tsuid);
   ret.setDicomObject(newDs);
   return ret;
 }
  private void insertDicomTags(
      int dcmobject_id, DicomObject obj, Integer parentId, PreparedStatement stmt)
      throws Exception {

    for (Iterator<DicomElement> it = obj.iterator(); it.hasNext(); ) {
      DicomElement e = it.next();

      StringBuffer sb = new StringBuffer();
      try {
        String[] values = e.getStrings(obj.getSpecificCharacterSet(), false);
        sb.append(values[0].replaceAll("\0", ""));
        int i;
        for (i = 1; i < values.length; i++) {
          sb.append("/").append(values[i].replaceAll("\0", ""));
        }

      } catch (Exception ee) {
        try {
          sb.append(e.getString(obj.getSpecificCharacterSet(), false));
        } catch (Exception e2) {

        }
      }
      stmt.setInt(1, dcmobject_id);
      stmt.setString(2, DicomHeader.toTagString(e.tag()));
      stmt.setString(3, e.vr().toString());

      // only the first 150 chars are saved if the tag-value is longer
      if (sb.length() > 150) {
        stmt.setString(
            4, sb.toString().substring(0, 150).concat("*** end of tag-value not applicable ***"));
      } else {
        stmt.setString(4, sb.toString());
      }

      stmt.setInt(5, itemOrder);
      if (parentId == null) {
        stmt.setNull(6, Types.INTEGER);
      } else {
        stmt.setInt(6, parentId);
      }
      stmt.addBatch();
      // System.out.println( stmt );

      itemOrder++;
      if (e.countItems() > 0) {
        if (e.hasDicomObjects()) {
          for (int i = 0; i < e.countItems(); i++) {
            insertDicomTags(dcmobject_id, e.getDicomObject(i), itemOrder - 1, stmt);
          }
        }
      }
    }
  }
    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);
    }
Exemple #10
0
 @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)
           });
   }
 }
Exemple #11
0
 @Override
 public void addMedia(MediaElement media) {
   if (media instanceof DicomVideoElement) {
     if (media.getMediaReader() instanceof DicomMediaIO) {
       DicomMediaIO dicomImageLoader = (DicomMediaIO) media.getMediaReader();
       frames = dicomImageLoader.getMediaElementNumber();
       byte[] mpeg = null;
       try {
         width = dicomImageLoader.getWidth(0);
         height = dicomImageLoader.getHeight(0);
         DicomObject pixData = dicomImageLoader.readPixelData();
         mpeg = pixData.get(TagW.PixelData.getId()).getFragment(1);
       } catch (Exception e) {
         e.printStackTrace();
       }
       if (mpeg != null) {
         OutputStream tempFileStream = null;
         try {
           File videoFile =
               File.createTempFile(
                   "video_", ".mpg", AbstractProperties.APP_TEMP_DIR); // $NON-NLS-1$ //$NON-NLS-2$
           tempFileStream = new BufferedOutputStream(new FileOutputStream(videoFile));
           tempFileStream.write(mpeg);
           DicomVideoElement dicom = (DicomVideoElement) media;
           dicom.setVideoFile(videoFile);
           this.add(dicom);
         } catch (Exception e) {
           e.printStackTrace();
         } finally {
           // Close file.
           if (tempFileStream != null) {
             try {
               tempFileStream.close();
             } catch (Exception e) {
             }
           }
         }
       }
       // DataExplorerModel model = (DataExplorerModel) getTagValue(TagW.ExplorerModel);
       // if (model != null) {
       // model.firePropertyChange(new ObservableEvent(ObservableEvent.BasicAction.Add, model,
       // null,
       // new SeriesEvent(SeriesEvent.Action.AddImage, this, insertIndex + frames)));
       // }
     }
   }
 }
Exemple #12
0
 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, "*");
   }
 }
Exemple #13
0
 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();
 }
Exemple #14
0
  public Date getDocumentAddedDate() {
    Date date = metaData.getDate(Tag.ContentDate);
    Date time = metaData.getDate(Tag.ContentTime);

    if (date != null && time != null) {
      return DateUtils.toDateTime(date, time);
    } else if (date != null) {
      return date;
    }

    return null;
  }
 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;
 }
 /**
  * Set query attributes for C-Move
  *
  * @return DicomObject contains initial set of attributes for query
  */
 private DicomObject setCmoveAttributes() {
   DicomObject returnObject = new BasicDicomObject();
   returnObject.putString(Tag.SOPClassUID, VR.UI, UID.RTPlanStorage);
   returnObject.putString(Tag.SOPInstanceUID, VR.UI, "1.2.34.56");
   returnObject.putString(Tag.QueryRetrieveLevel, VR.CS, "IMAGE");
   returnObject.putString(Tag.PatientID, VR.LO, "");
   returnObject.putString(Tag.StudyInstanceUID, VR.UI, "1.2.1.1");
   returnObject.putString(Tag.SeriesInstanceUID, VR.UI, "1.2.1.2");
   return returnObject;
 }
Exemple #17
0
    @Override
    public void onDimseRSP(Association as, DicomObject cmd, DicomObject data) {
      int status = cmd.getInt(Tag.Status);

      switch (status) {
        case 0x0000:
        case 0x0001:
        case 0x0002:
        case 0x0003:
          break;
        case 0x0116:
          LOG.warn(
              "Received Warning Status 116H (=Attribute Value Out of Range) from remote AE {}",
              as.getCalledAET());
          break;
        default:
          LOG.error(
              "Sending IAN(SCN) failed with status {}H at calledAET:{}",
              StringUtils.shortToHex(status),
              as.getCalledAET());
      }
    }
Exemple #18
0
 public DicomObject getAttributes(boolean cfindrsp) {
   DicomObject dataset = DicomObjectUtils.decode(encodedAttributes);
   if (cfindrsp) {
     dataset.putInt(Tag.NumberOfSeriesRelatedInstances, VR.IS, numberOfSeriesRelatedInstances);
     if (fileSetUID != null && fileSetID != null) {
       dataset.putString(Tag.StorageMediaFileSetUID, VR.UI, fileSetUID);
       dataset.putString(Tag.StorageMediaFileSetID, VR.SH, fileSetID);
     }
     if (retrieveAETs != null || externalRetrieveAET != null) {
       dataset.putString(
           Tag.RetrieveAETitle,
           VR.AE,
           externalRetrieveAET == null
               ? retrieveAETs
               : retrieveAETs == null
                   ? externalRetrieveAET
                   : retrieveAETs + '\\' + externalRetrieveAET);
     }
     dataset.putString(Tag.InstanceAvailability, VR.CS, availability.name());
   }
   return dataset;
 }
Exemple #19
0
    public static TCEncapsulatedDocument create(
        TCObject tc, MimeType mimeType, String filename, InputStream in, String description)
        throws Exception {

      if (mimeType == null || !DOC_TYPES.contains(mimeType.getDocumentType())) {
        throw new Exception("Mime-Type is not supported (" + mimeType + ")");
      }

      TCReferencedInstance ref = createReferencedInstance(tc, UID.EncapsulatedPDFStorage, MODALITY);

      DicomObject metaData =
          TCDocumentObject.createDicomMetaData(
              mimeType,
              filename,
              description,
              ref,
              tc.getPatientId(),
              tc.getPatientIdIssuer(),
              tc.getPatientName(),
              MODALITY);
      metaData.putString(Tag.TransferSyntaxUID, VR.UI, UID.ExplicitVRLittleEndian);
      metaData.putString(
          Tag.DocumentTitle,
          VR.ST,
          description != null && !description.isEmpty() ? description : getFileName(filename));
      metaData.putString(Tag.MIMETypeOfEncapsulatedDocument, VR.LO, mimeType.getMimeTypeString());
      metaData.putString(Tag.BurnedInAnnotation, VR.CS, "NO"); // $NON-NLS-1$
      metaData.putSequence(Tag.ConceptNameCodeSequence, 0);

      try {
        return new TCEncapsulatedDocument(mimeType, ref, metaData, IOUtils.toByteArray(in));
      } finally {
        if (in != null) {
          in.close();
        }
      }
    }
Exemple #20
0
 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;
 }
Exemple #21
0
 public String getSeriesInstanceUID() {
   return metaData.getString(Tag.SeriesInstanceUID);
 }
Exemple #22
0
 private static int eventTypeIdOf(DicomObject result) {
   return result.contains(Tag.FailedSOPInstanceUIDList) ? 2 : 1;
 }
Exemple #23
0
 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;
 }
Exemple #24
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  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());
  }
Exemple #25
0
 public String getStudyInstanceUID() {
   return metaData.getString(Tag.StudyInstanceUID);
 }
Exemple #26
0
 public String getDocumentName() {
   return getDocumentNameFromLabel(metaData.getString(Tag.ContentLabel), false);
 }
Exemple #27
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 public String getDocumentDescription() {
   return metaData.containsValue(Tag.DocumentTitle)
       ? metaData.getString(Tag.DocumentTitle)
       : metaData.getString(Tag.ContentDescription);
 }
Exemple #28
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  protected static DicomObject createDicomMetaData(
      MimeType mimeType,
      String filename,
      String description,
      TCReferencedInstance ref,
      String patId,
      String issuerOfPatId,
      String patName,
      String modality) {
    Date now = new Date();

    DicomObject attrs = new BasicDicomObject();

    // patient level
    if (patId != null) {
      attrs.putString(Tag.PatientID, VR.LO, patId);
    }
    if (issuerOfPatId != null) {
      attrs.putString(Tag.IssuerOfPatientID, VR.LO, issuerOfPatId);
    }
    if (patName != null) {
      attrs.putString(Tag.PatientName, VR.PN, patName);
    }

    // study level
    attrs.putString(Tag.StudyInstanceUID, VR.UI, ref.getStudyUID());

    // series level
    attrs.putString(Tag.SeriesInstanceUID, VR.UI, ref.getSeriesUID());
    attrs.putString(Tag.SeriesDescription, VR.LO, SERIES_DESCRIPTION);
    attrs.putString(Tag.Modality, VR.CS, modality);

    // instance level
    attrs.putString(Tag.SOPInstanceUID, VR.UI, ref.getInstanceUID());
    attrs.putString(Tag.SOPClassUID, VR.UI, ref.getClassUID());
    attrs.putInt(Tag.InstanceNumber, VR.IS, ref.getInstanceNumber());
    attrs.putDate(Tag.InstanceCreationDate, VR.DA, now);
    attrs.putDate(Tag.InstanceCreationTime, VR.TM, now);
    attrs.putDate(Tag.ContentDate, VR.DA, now);
    attrs.putDate(Tag.ContentTime, VR.TM, now);
    attrs.putString(Tag.ContentLabel, VR.CS, filename);
    attrs.putString(
        Tag.ContentDescription,
        VR.CS,
        description != null && !description.isEmpty() ? description : getFileName(filename));

    return attrs;
  }
Exemple #29
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    private static DicomObject toDicom(BufferedImage image) throws Exception {
      int numSamples = image.getColorModel().getNumComponents();
      if (numSamples == 4) {
        numSamples = 3;
      }
      String pmi = numSamples > 1 ? "RGB" : "MONOCHROME2";
      int bits = image.getColorModel().getComponentSize(0);
      int allocated = 8;
      if (bits > 8) {
        allocated = 16;
      }

      DicomObject attrs = new BasicDicomObject();
      attrs.putString(Tag.TransferSyntaxUID, VR.UI, UID.ImplicitVRLittleEndian);
      attrs.putInt(Tag.Rows, VR.US, image.getHeight());
      attrs.putInt(Tag.Columns, VR.US, image.getWidth());
      attrs.putInt(Tag.SamplesPerPixel, VR.US, numSamples);
      attrs.putInt(Tag.BitsStored, VR.US, bits);
      attrs.putInt(Tag.BitsAllocated, VR.US, allocated);
      attrs.putInt(Tag.PixelRepresentation, VR.US, 0);
      attrs.putString(Tag.PhotometricInterpretation, VR.CS, pmi);

      if (numSamples > 1) {
        attrs.putInt(Tag.PlanarConfiguration, VR.US, 0);
      }

      int biType =
          numSamples == 3
              ? BufferedImage.TYPE_INT_RGB
              : allocated > 8 ? BufferedImage.TYPE_USHORT_GRAY : BufferedImage.TYPE_BYTE_GRAY;

      BufferedImage tmpImage = image;
      if (image.getType() != biType) {
        tmpImage = new BufferedImage(image.getWidth(), image.getHeight(), biType);
        tmpImage.getGraphics().drawImage(image, 0, 0, null);
      }

      byte[] pixelData = null;
      DataBuffer dataBuffer = tmpImage.getRaster().getDataBuffer();
      if (dataBuffer instanceof DataBufferInt) {
        final int[] data = (int[]) ((DataBufferInt) dataBuffer).getData();
        pixelData = new byte[data.length * 3];
        int index = 0;
        for (final int i : data) {
          pixelData[index++] = (byte) ((i >>> 16) & 0xFF);
          pixelData[index++] = (byte) ((i >>> 8) & 0xFF);
          pixelData[index++] = (byte) (i & 0xFF);
        }
      } else if (dataBuffer instanceof DataBufferUShort) {
        final short[] data = (short[]) ((DataBufferUShort) dataBuffer).getData();
        pixelData = new byte[data.length * 2];
        int index = 0;
        for (final int i : data) {
          pixelData[index++] = (byte) ((i >>> 8) & 0xFF);
          pixelData[index++] = (byte) (i & 0xFF);
        }
      } else if (dataBuffer instanceof DataBufferByte) {
        pixelData = ((DataBufferByte) dataBuffer).getData();
      }

      attrs.putBytes(Tag.PixelData, allocated > 8 ? VR.OW : VR.OB, pixelData);

      return attrs;
    }
Exemple #30
0
 @Override
 public DicomObject toDataset() throws Exception {
   DicomObject attrs = super.toDataset();
   attrs.putBytes(Tag.EncapsulatedDocument, VR.OB, getDocumentContent());
   return attrs;
 }