private void testIsNotRemovedAndRetainsValue(
     String description,
     AttributeTag creatorTag,
     String creator,
     Attribute privateAttribute,
     String expectValue)
     throws DicomException {
   AttributeList list = new AttributeList();
   {
     Attribute a = new LongStringAttribute(creatorTag);
     a.addValue(creator);
     list.put(a);
   }
   list.put(privateAttribute);
   AttributeTag privateTag = privateAttribute.getTag();
   list.removeUnsafePrivateAttributes();
   assertTrue("Checking Creator is not removed", list.get(creatorTag) != null);
   assertEquals(
       "Checking Creator retains value",
       creator,
       Attribute.getDelimitedStringValuesOrEmptyString(list, creatorTag));
   assertTrue("Checking " + description + " is not removed", list.get(privateTag) != null);
   assertEquals(
       "Checking " + description + " retains value",
       expectValue,
       Attribute.getDelimitedStringValuesOrEmptyString(list, privateTag));
 }
 public void TestSafePrivateGEMRRelated_CreatorFromList() throws Exception {
   {
     AttributeList list = new AttributeList();
     {
       Attribute a = new LongStringAttribute(new AttributeTag(0x0019, 0x0010));
       a.addValue("GEMS_ACQU_01");
       list.put(a);
     }
     assertTrue(
         "Internal Pulse Sequence Name is safe",
         ClinicalTrialsAttributes.isSafePrivateAttribute(new AttributeTag(0x0019, 0x109E), list));
   }
   {
     AttributeList list = new AttributeList();
     {
       Attribute a = new LongStringAttribute(new AttributeTag(0x0025, 0x0010));
       a.addValue("GEMS_SERS_01");
       list.put(a);
     }
     assertTrue(
         "Images In Series is safe",
         ClinicalTrialsAttributes.isSafePrivateAttribute(new AttributeTag(0x0025, 0x1007), list));
   }
   {
     AttributeList list = new AttributeList();
     {
       Attribute a = new LongStringAttribute(new AttributeTag(0x0043, 0x0010));
       a.addValue("GEMS_PARM_01");
       list.put(a);
     }
     assertTrue(
         "Scanner Table Entry + Gradient Coil Selected",
         ClinicalTrialsAttributes.isSafePrivateAttribute(new AttributeTag(0x0043, 0x106F), list));
   }
 }
Ejemplo n.º 3
0
  /**
   * @exception IOException
   * @exception DicomException
   */
  public CEchoRequestCommandMessage() throws DicomException, IOException {

    commandField = MessageServiceElementCommand.C_ECHO_RQ;
    messageID = super.getNextAvailableMessageID();
    int dataSetType = 0x0101; // none

    // NB. The Affected SOP Class UID should have no extra trailing padding, otherwise the
    // SCP may fail and send an A-ABORT :) (Part 5 says one null (not space) is allowed)
    // This is taken care of by the Attribute.write()

    AttributeList list = new AttributeList();
    {
      AttributeTag t = groupLengthTag;
      Attribute a = new UnsignedLongAttribute(t);
      a.addValue(0);
      list.put(t, a);
    }
    {
      AttributeTag t = TagFromName.AffectedSOPClassUID;
      Attribute a = new UniqueIdentifierAttribute(t);
      a.addValue(SOPClass.Verification);
      list.put(t, a);
    }
    {
      AttributeTag t = TagFromName.CommandField;
      Attribute a = new UnsignedShortAttribute(t);
      a.addValue(commandField);
      list.put(t, a);
    }
    {
      AttributeTag t = TagFromName.MessageID;
      Attribute a = new UnsignedShortAttribute(t);
      a.addValue(messageID);
      list.put(t, a);
    }
    {
      AttributeTag t = TagFromName.CommandDataSetType;
      Attribute a = new UnsignedShortAttribute(t);
      a.addValue(dataSetType);
      list.put(t, a);
    }

    ByteArrayOutputStream bout = new ByteArrayOutputStream();
    DicomOutputStream dout =
        new DicomOutputStream(
            bout, null /* no meta-header */, TransferSyntax.ImplicitVRLittleEndian);
    list.write(dout);
    bytes = bout.toByteArray();

    groupLength = bytes.length - 12;
    bytes[8] = (byte) groupLength; // little endian
    bytes[9] = (byte) (groupLength >> 8);
    bytes[10] = (byte) (groupLength >> 16);
    bytes[11] = (byte) (groupLength >> 24);
    // System.err.println("CEchoRequestCommandMessage: bytes="+HexDump.dump(bytes));
  }
Ejemplo n.º 4
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 public void TestSafePrivateGEPACSRelated_AddedToList() throws Exception {
   AttributeList list = new AttributeList();
   {
     Attribute a = new LongStringAttribute(new AttributeTag(0x0903, 0x0010));
     a.addValue("GEIIS PACS");
     list.put(a);
   }
   {
     Attribute a = new UnsignedShortAttribute(new AttributeTag(0x0903, 0x1010));
     a.addValue(0);
     list.put(a);
   }
   list.removeUnsafePrivateAttributes();
   assertTrue(
       "Checking Creator is not removed", list.get(new AttributeTag(0x0903, 0x0010)) != null);
   assertTrue(
       "Checking Reject Image Flag is not removed",
       ClinicalTrialsAttributes.isSafePrivateAttribute(new AttributeTag(0x0903, 0x1010), list));
 }
Ejemplo n.º 5
0
 public void TestSafePrivateGEPACSRelated_CreatorFromList() throws Exception {
   AttributeList list = new AttributeList();
   {
     Attribute a = new LongStringAttribute(new AttributeTag(0x0903, 0x0010));
     a.addValue("GEIIS PACS");
     list.put(a);
   }
   assertTrue(
       "Checking Reject Image Flag is safe",
       ClinicalTrialsAttributes.isSafePrivateAttribute(new AttributeTag(0x0903, 0x1010), list));
 }
 public void TestSafePrivatePhilipsPETRelated_ScaleFactors_FromList() throws Exception {
   AttributeList list = new AttributeList();
   {
     Attribute a = new LongStringAttribute(new AttributeTag(0x7053, 0x0010));
     a.addValue("Philips PET Private Group");
     list.put(a);
   }
   assertTrue(
       "Checking SUV Factor is safe",
       ClinicalTrialsAttributes.isSafePrivateAttribute(new AttributeTag(0x7053, 0x1000), list));
   assertTrue(
       "Checking Activity Concentration Factor is safe",
       ClinicalTrialsAttributes.isSafePrivateAttribute(new AttributeTag(0x7053, 0x1009), list));
 }
Ejemplo n.º 7
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 protected CompositeInstanceContext mergePatientContext(
     Group group, CompositeInstanceContext newContext) {
   if (group.context == null) {
     // System.err.println("mergePatientContext(): creating new context for group");
     group.context = newContext;
   } else {
     AttributeList groupList = group.context.getAttributeList();
     Iterator<Attribute> newListIterator = newContext.getAttributeList().values().iterator();
     while (newListIterator.hasNext()) {
       Attribute a = newListIterator.next();
       AttributeTag tag = a.getTag();
       String groupValue = Attribute.getSingleStringValueOrEmptyString(groupList, tag);
       String newValue = a.getSingleStringValueOrEmptyString();
       if (!newValue.equals(groupValue)) {
         String describeTag = tag + " " + groupList.getDictionary().getFullNameFromTag(tag);
         System.err.println(
             "mergePatientContext(): in group "
                 + group.identity
                 + " for "
                 + describeTag
                 + " values differ between existing group value <"
                 + groupValue
                 + "> and new value <"
                 + newValue
                 + ">");
         if (newValue.length() > 0
             && (groupValue.length() == 0 || isNonZeroLengthDummyValue(groupValue))) {
           System.err.println(
               "mergePatientContext(): in group "
                   + group.identity
                   + " for "
                   + describeTag
                   + " replacing absent/empty/dummy existing group value with new value <"
                   + newValue
                   + ">");
           groupList.put(a);
         }
       }
     }
   }
   return group.context;
 }
Ejemplo n.º 8
0
 protected void performRetrieve(
     AttributeList uniqueKeys, String selectionLevel, String retrieveAE) {
   try {
     AttributeList identifier = new AttributeList();
     if (uniqueKeys != null) {
       identifier.putAll(uniqueKeys);
       {
         AttributeTag t = TagFromName.QueryRetrieveLevel;
         Attribute a = new CodeStringAttribute(t);
         a.addValue(selectionLevel);
         identifier.put(t, a);
       }
       currentRemoteQueryInformationModel.performHierarchicalMoveFrom(identifier, retrieveAE);
     } else {
       // else do nothing, since no unique key to specify what to retrieve
       log.warning("UniqueKeys for retrieval are null");
     }
   } catch (Exception e) {
     e.printStackTrace(System.err);
   }
 }
  /**
   * Generate commomn attributes for converted images.
   *
   * <p>Does NOT add ManufacturerModelName ... that should be added by caller.
   *
   * <p>Does NOT call
   * CodingSchemeIdentification.replaceCodingSchemeIdentificationSequenceWithCodingSchemesUsedInAttributeList
   * ... that should be done by caller.
   *
   * @param list
   * @param patientName
   * @param patientID
   * @param studyID
   * @param seriesNumber
   * @param instanceNumber
   * @param modality may be null
   * @param sopClass may be null
   * @throws DicomException
   * @throws NumberFormatException
   */
  public static void generateCommonAttributes(
      AttributeList list,
      String patientName,
      String patientID,
      String studyID,
      String seriesNumber,
      String instanceNumber,
      String modality,
      String sopClass)
      throws DicomException {
    UIDGenerator u = new UIDGenerator();

    {
      Attribute a = new UniqueIdentifierAttribute(TagFromName.SOPInstanceUID);
      a.addValue(u.getAnotherNewUID());
      list.put(a);
    }
    {
      Attribute a = new UniqueIdentifierAttribute(TagFromName.SeriesInstanceUID);
      a.addValue(u.getAnotherNewUID());
      list.put(a);
    }
    {
      Attribute a = new UniqueIdentifierAttribute(TagFromName.StudyInstanceUID);
      a.addValue(u.getAnotherNewUID());
      list.put(a);
    }
    {
      Attribute a = new UniqueIdentifierAttribute(TagFromName.FrameOfReferenceUID);
      a.addValue(u.getAnotherNewUID());
      list.put(a);
    }

    {
      Attribute a = new PersonNameAttribute(TagFromName.PatientName);
      a.addValue(patientName);
      list.put(a);
    }
    {
      Attribute a = new LongStringAttribute(TagFromName.PatientID);
      a.addValue(patientID);
      list.put(a);
    }
    {
      Attribute a = new DateAttribute(TagFromName.PatientBirthDate);
      list.put(a);
    }
    {
      Attribute a = new CodeStringAttribute(TagFromName.PatientSex);
      list.put(a);
    }
    {
      Attribute a = new ShortStringAttribute(TagFromName.StudyID);
      a.addValue(studyID);
      list.put(a);
    }
    {
      Attribute a = new PersonNameAttribute(TagFromName.ReferringPhysicianName);
      a.addValue("^^^^");
      list.put(a);
    }
    {
      Attribute a = new ShortStringAttribute(TagFromName.AccessionNumber);
      list.put(a);
    }
    {
      Attribute a = new IntegerStringAttribute(TagFromName.SeriesNumber);
      a.addValue(seriesNumber);
      list.put(a);
    }
    {
      Attribute a = new IntegerStringAttribute(TagFromName.InstanceNumber);
      a.addValue(instanceNumber);
      list.put(a);
    }

    {
      Attribute a = new LongStringAttribute(TagFromName.Manufacturer);
      a.addValue("PixelMed");
      list.put(a);
    }
    {
      Attribute a = new LongStringAttribute(TagFromName.DeviceSerialNumber);
      a.addValue(new java.rmi.dgc.VMID().toString());
      list.put(a);
    }
    {
      Attribute a = new LongStringAttribute(TagFromName.SoftwareVersions);
      a.addValue(VersionAndConstants.getBuildDate());
      list.put(a);
    }

    {
      Attribute a = new CodeStringAttribute(TagFromName.PatientOrientation);
      list.put(a);
    }

    {
      Attribute a = new CodeStringAttribute(TagFromName.BurnedInAnnotation);
      a.addValue("NO");
      list.put(a);
    }
    {
      Attribute a = new CodeStringAttribute(TagFromName.RecognizableVisualFeatures);
      a.addValue("NO");
      list.put(a);
    }
    {
      Attribute a = new CodeStringAttribute(TagFromName.ContentQualification);
      a.addValue("RESEARCH");
      list.put(a);
    }

    {
      Attribute a = new CodeStringAttribute(TagFromName.LossyImageCompression);
      a.addValue("00");
      list.put(a);
    }

    {
      Attribute a = new LongStringAttribute(TagFromName.PositionReferenceIndicator);
      list.put(a);
    }

    {
      java.util.Date currentDateTime = new java.util.Date();
      String currentDate = new java.text.SimpleDateFormat("yyyyMMdd").format(currentDateTime);
      String currentTime = new java.text.SimpleDateFormat("HHmmss.SSS").format(currentDateTime);
      {
        Attribute a = new DateAttribute(TagFromName.StudyDate);
        a.addValue(currentDate);
        list.put(a);
      }
      {
        Attribute a = new TimeAttribute(TagFromName.StudyTime);
        a.addValue(currentTime);
        list.put(a);
      }
      {
        Attribute a = new DateAttribute(TagFromName.SeriesDate);
        a.addValue(currentDate);
        list.put(a);
      }
      {
        Attribute a = new TimeAttribute(TagFromName.SeriesTime);
        a.addValue(currentTime);
        list.put(a);
      }
      {
        Attribute a = new DateAttribute(TagFromName.ContentDate);
        a.addValue(currentDate);
        list.put(a);
      }
      {
        Attribute a = new TimeAttribute(TagFromName.ContentTime);
        a.addValue(currentTime);
        list.put(a);
      }
      {
        Attribute a = new DateAttribute(TagFromName.InstanceCreationDate);
        a.addValue(currentDate);
        list.put(a);
      }
      {
        Attribute a = new TimeAttribute(TagFromName.InstanceCreationTime);
        a.addValue(currentTime);
        list.put(a);
      }
      {
        Attribute a = new ShortStringAttribute(TagFromName.TimezoneOffsetFromUTC);
        a.addValue(DateTimeAttribute.getTimeZone(java.util.TimeZone.getDefault(), currentDateTime));
        list.put(a);
      }
    }
    {
      Attribute a = new UniqueIdentifierAttribute(TagFromName.InstanceCreatorUID);
      a.addValue(VersionAndConstants.instanceCreatorUID);
      list.put(a);
    }

    int numberOfFrames =
        Attribute.getSingleIntegerValueOrDefault(list, TagFromName.NumberOfFrames, 1);
    int samplesPerPixel =
        Attribute.getSingleIntegerValueOrDefault(list, TagFromName.SamplesPerPixel, 1);

    if (sopClass == null) {
      // if modality were not null, could actually attempt to guess SOP Class based on modality here
      // :(
      sopClass = SOPClass.SecondaryCaptureImageStorage;
      if (numberOfFrames > 1) {
        if (samplesPerPixel == 1) {
          int bitsAllocated =
              Attribute.getSingleIntegerValueOrDefault(list, TagFromName.BitsAllocated, 1);
          if (bitsAllocated == 8) {
            sopClass = SOPClass.MultiframeGrayscaleByteSecondaryCaptureImageStorage;
          } else if (bitsAllocated == 16) {
            sopClass = SOPClass.MultiframeGrayscaleWordSecondaryCaptureImageStorage;
          } else {
            Attribute aPixelData = list.getPixelData();
            if (aPixelData instanceof OtherFloatAttribute
                || aPixelData instanceof OtherDoubleAttribute) {
              sopClass = SOPClass.ParametricMapStorage;
            }
          }
        } else if (samplesPerPixel == 3) {
          sopClass = SOPClass.MultiframeTrueColorSecondaryCaptureImageStorage;
        }
      }
    }

    if (sopClass.equals(SOPClass.ParametricMapStorage)) {
      addParametricMapFrameTypeSharedFunctionalGroup(list);
      {
        Attribute a = new CodeStringAttribute(TagFromName.ContentLabel);
        a.addValue("LABEL1");
        list.put(a);
      }
      {
        Attribute a = new LongStringAttribute(TagFromName.ContentDescription);
        list.put(a);
      }
      {
        Attribute a = new PersonNameAttribute(TagFromName.ContentCreatorName);
        list.put(a);
      }
    }

    if (SOPClass.isEnhancedMultiframeImageStorage(sopClass)) {
      if (samplesPerPixel == 1) {
        double windowWidth =
            Attribute.getSingleDoubleValueOrDefault(list, TagFromName.WindowWidth, 0);
        if (windowWidth > 0) {
          double windowCenter =
              Attribute.getSingleDoubleValueOrDefault(list, TagFromName.WindowCenter, 0);
          String voiLUTFunction =
              Attribute.getSingleStringValueOrDefault(list, TagFromName.VOILUTFunction, "LINEAR");
          FunctionalGroupUtilities.generateVOILUTFunctionalGroup(
              list, numberOfFrames, windowWidth, windowCenter, voiLUTFunction);
          list.remove(TagFromName.WindowCenter);
          list.remove(TagFromName.WindowWidth);
          list.remove(TagFromName.VOILUTFunction);
        }
      }

      double rescaleSlope =
          Attribute.getSingleDoubleValueOrDefault(list, TagFromName.RescaleSlope, 0);
      if (rescaleSlope > 0) {
        double rescaleIntercept =
            Attribute.getSingleDoubleValueOrDefault(list, TagFromName.RescaleIntercept, 0);
        String rescaleType =
            Attribute.getSingleStringValueOrDefault(list, TagFromName.RescaleType, "US");
        FunctionalGroupUtilities.generatePixelValueTransformationFunctionalGroup(
            list, numberOfFrames, rescaleSlope, rescaleIntercept, rescaleType);
        list.remove(TagFromName.RescaleSlope);
        list.remove(TagFromName.RescaleIntercept);
        list.remove(TagFromName.RescaleType);
      }

      // four values required
      {
        Attribute a = new CodeStringAttribute(TagFromName.ImageType);
        a.addValue("DERIVED");
        a.addValue("PRIMARY");
        a.addValue("");
        a.addValue("");
        list.put(a);
      }
    } else {
      // two values will usually do
      {
        Attribute a = new CodeStringAttribute(TagFromName.ImageType);
        a.addValue("DERIVED");
        a.addValue("PRIMARY");
        list.put(a);
      }
    }

    if (SOPClass.isMultiframeSecondaryCaptureImageStorage(sopClass)) {
      if (list.get(TagFromName.PerFrameFunctionalGroupsSequence) != null) {
        {
          AttributeTagAttribute a = new AttributeTagAttribute(TagFromName.FrameIncrementPointer);
          a.addValue(TagFromName.PerFrameFunctionalGroupsSequence);
          list.put(a);
        }
      } else {
        if (numberOfFrames > 1) {
          {
            AttributeTagAttribute a = new AttributeTagAttribute(TagFromName.FrameIncrementPointer);
            a.addValue(TagFromName.PageNumberVector);
            list.put(a);
          }
          {
            Attribute a = new IntegerStringAttribute(TagFromName.PageNumberVector);
            for (int page = 1; page <= numberOfFrames; ++page) {
              a.addValue(page);
            }
            list.put(a);
          }
        }
      }
    }

    System.err.println(
        "CommonConvertedAttributeGeneration.generateCommonAttributes(): SOP Class = " + sopClass);
    {
      Attribute a = new UniqueIdentifierAttribute(TagFromName.SOPClassUID);
      a.addValue(sopClass);
      list.put(a);
    }

    if (SOPClass.isSecondaryCaptureImageStorage(sopClass)) {
      {
        Attribute a = new CodeStringAttribute(TagFromName.ConversionType);
        a.addValue("WSD");
        list.put(a);
      }
    }

    if (modality == null) {
      // could actually attempt to guess modality based on SOP Class here :(
      modality = "OT";
    }
    {
      Attribute a = new CodeStringAttribute(TagFromName.Modality);
      a.addValue(modality);
      list.put(a);
    }

    {
      Attribute a = new SequenceAttribute(TagFromName.AcquisitionContextSequence);
      list.put(a);
    }
  }