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));
 }
示例#2
0
 protected void setCurrentRemoteQuerySelection(
     AttributeList uniqueKeys, Attribute uniqueKey, AttributeList identifier) {
   currentRemoteQuerySelectionUniqueKeys = uniqueKeys;
   currentRemoteQuerySelectionUniqueKey = uniqueKey;
   currentRemoteQuerySelectionRetrieveAE = null;
   if (identifier != null) {
     Attribute aRetrieveAETitle = identifier.get(TagFromName.RetrieveAETitle);
     if (aRetrieveAETitle != null)
       currentRemoteQuerySelectionRetrieveAE = aRetrieveAETitle.getSingleStringValueOrNull();
   }
   if (currentRemoteQuerySelectionRetrieveAE == null) {
     // it is legal for RetrieveAETitle to be zero length at all but the lowest levels of
     // the query model :( (See PS 3.4 C.4.1.1.3.2)
     // (so far the Leonardo is the only one that doesn't send it at all levels)
     // we could recurse down to the lower levels and get the union of the value there
     // but lets just keep it simple and ...
     // default to whoever it was we queried in the first place ...
     if (currentRemoteQueryInformationModel != null) {
       currentRemoteQuerySelectionRetrieveAE =
           currentRemoteQueryInformationModel.getCalledAETitle();
     }
   }
   currentRemoteQuerySelectionLevel = null;
   if (identifier != null) {
     Attribute a = identifier.get(TagFromName.QueryRetrieveLevel);
     if (a != null) {
       currentRemoteQuerySelectionLevel = a.getSingleStringValueOrNull();
     }
   }
   if (currentRemoteQuerySelectionLevel == null) {
     // QueryRetrieveLevel must have been (erroneously) missing in query response ... see with Dave
     // Harvey's code on public server
     // so try to guess it from unique key in tree record
     // Fixes [bugs.mrmf] (000224) Missing query/retrieve level in C-FIND response causes tree
     // select and retrieve to fail
     if (uniqueKey != null) {
       AttributeTag tag = uniqueKey.getTag();
       if (tag != null) {
         if (tag.equals(TagFromName.PatientID)) {
           currentRemoteQuerySelectionLevel = "PATIENT";
         } else if (tag.equals(TagFromName.StudyInstanceUID)) {
           currentRemoteQuerySelectionLevel = "STUDY";
         } else if (tag.equals(TagFromName.SeriesInstanceUID)) {
           currentRemoteQuerySelectionLevel = "SERIES";
         } else if (tag.equals(TagFromName.SOPInstanceUID)) {
           currentRemoteQuerySelectionLevel = "IMAGE";
         }
       }
     }
     log.warning(
         "RemotePACs.setCurrentRemoteQuerySelection(): Guessed missing currentRemoteQuerySelectionLevel to be "
             + currentRemoteQuerySelectionLevel);
   }
 }
 public void TestSafePrivateGEPACSRelated_FromFile() throws Exception {
   AttributeList list = new AttributeList();
   String testFilePath = System.getProperty("com.pixelmed.test.filepath");
   // System.err.println("TestSafePrivateGEPACSRelated.TestSafePrivateGEPACSRelated_FromFile():
   // testFilePath = "+testFilePath);
   list.read(new java.io.File(testFilePath, "philipsctwithgepacsprivateattributes.dcm"));
   // System.err.print("TestSafePrivateGEPACSRelated.TestSafePrivateGEPACSRelated():\n"+list);
   list.removeUnsafePrivateAttributes();
   assertTrue(
       "Checking Creator is not removed", list.get(new AttributeTag(0x0903, 0x0010)) != null);
   assertTrue(
       "Checking Reject Image Flag is not removed",
       list.get(new AttributeTag(0x0903, 0x1010)) != null);
 }
 public void TestSafePrivatePhilipsPETRelated_ScaleFactors_FromFile() throws Exception {
   AttributeList list = new AttributeList();
   String testFilePath = System.getProperty("com.pixelmed.test.filepath");
   // System.err.println("TestSafePrivatePhilipsPETRelated.TestSafePrivatePhilipsPETRelated_ScaleFactors_FromFile(): testFilePath = "+testFilePath);
   list.read(new java.io.File(testFilePath, "philipssuvandactivityscalefactors.dcm"));
   // System.err.print("TestSafePrivatePhilipsPETRelated.TestSafePrivatePhilipsPETRelated_ScaleFactors():\n"+list);
   list.removeUnsafePrivateAttributes();
   assertTrue(
       "Checking Creator is not removed", list.get(new AttributeTag(0x7053, 0x0010)) != null);
   assertTrue(
       "Checking SUV Factor is not removed", list.get(new AttributeTag(0x7053, 0x1000)) != null);
   assertTrue(
       "Checking Activity Concentration Factor is not removed",
       list.get(new AttributeTag(0x7053, 0x1009)) != null);
 }
示例#5
0
 // should be extracted to a utility class ... also used in DoseUtility and
 // DoseReporterWithLegacyOCRAndAutoSendToRegistry :(
 public static String getQueryRetrieveLevel(AttributeList identifier, Attribute uniqueKey) {
   String level = null;
   if (identifier != null) {
     Attribute a = identifier.get(TagFromName.QueryRetrieveLevel);
     if (a != null) {
       level = a.getSingleStringValueOrNull();
     }
   }
   if (level == null) {
     // QueryRetrieveLevel must have been (erroneously) missing in query response ... see with Dave
     // Harvey's code on public server
     // so try to guess it from unique key in tree record
     // Fixes [bugs.mrmf] (000224) Missing query/retrieve level in C-FIND response causes tree
     // select and retrieve to fail
     if (uniqueKey != null) {
       AttributeTag tag = uniqueKey.getTag();
       if (tag != null) {
         if (tag.equals(TagFromName.PatientID)) {
           level = "PATIENT";
         } else if (tag.equals(TagFromName.StudyInstanceUID)) {
           level = "STUDY";
         } else if (tag.equals(TagFromName.SeriesInstanceUID)) {
           level = "SERIES";
         } else if (tag.equals(TagFromName.SOPInstanceUID)) {
           level = "IMAGE";
         }
       }
     }
     log.warning(
         "DownloadOrTransmit.getQueryRetrieveLevel(): Guessed missing Query Retrieve Level to be "
             + level);
   }
   return level;
 }
示例#6
0
 /**
  * @param list
  * @return array of two String values, row then column orientation, else array of two nulls if
  *     cannot be obtained
  */
 private static String[] getPatientOrientation(AttributeList list) {
   String[] vPatientOrientation = null;
   Attribute aPatientOrientation = list.get(TagFromName.PatientOrientation);
   if (aPatientOrientation != null && aPatientOrientation.getVM() == 2) {
     try {
       vPatientOrientation = aPatientOrientation.getStringValues();
       if (vPatientOrientation != null && vPatientOrientation.length != 2) {
         vPatientOrientation = null;
       }
     } catch (DicomException e) {
       vPatientOrientation = null;
     }
   }
   if (vPatientOrientation == null) {
     vPatientOrientation = new String[2];
   }
   return vPatientOrientation;
 }
 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));
 }
  /**
   * 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);
    }
  }
示例#9
0
  /** @param list */
  private void doCommonConstructorStuff(AttributeList list) throws DicomException {
    String sopClassUID = Attribute.getSingleStringValueOrEmptyString(list, TagFromName.SOPClassUID);
    if (SOPClass.isImageStorage(sopClassUID)) {
      // System.err.println("SuperimposedDicomSegments.doCommonConstructorStuff(): is an image");
      SourceImage allFramesImage = new SourceImage(list);
      Attribute aSegmentSequence = list.get(TagFromName.SegmentSequence);
      Attribute aSharedFunctionalGroupsSequence =
          list.get(TagFromName.SharedFunctionalGroupsSequence);
      Attribute aPerFrameFunctionalGroupsSequence =
          list.get(TagFromName.PerFrameFunctionalGroupsSequence);
      int numberOfFrames = allFramesImage.getNumberOfBufferedImages();
      if (allFramesImage != null
          && numberOfFrames > 0
          && aSegmentSequence != null
          && aSegmentSequence instanceof SequenceAttribute
          && aSharedFunctionalGroupsSequence != null
          && aSharedFunctionalGroupsSequence instanceof SequenceAttribute
          && aPerFrameFunctionalGroupsSequence != null
          && aPerFrameFunctionalGroupsSequence instanceof SequenceAttribute) {
        System.err.println(
            "SuperimposedDicomSegments.doCommonConstructorStuff(): have a segmentation object with one or more frames");
        SequenceAttribute saSegmentSequence = (SequenceAttribute) aSegmentSequence;
        int numberOfSegments = saSegmentSequence.getNumberOfItems();
        if (numberOfSegments > 0) {
          for (int i = 0; i < numberOfSegments; ++i) {
            AttributeList itemList = saSegmentSequence.getItem(i).getAttributeList();
            String segmentNumber =
                Attribute.getSingleStringValueOrEmptyString(
                    itemList,
                    TagFromName
                        .SegmentNumber); // theoretically supposed to start at 1 and increase by 1,
                                         // but don't trust it
            if (segmentNumber.length() > 0) {
              int[] recommendedDisplayCIELabValues =
                  Attribute.getIntegerValues(itemList, TagFromName.RecommendedDisplayCIELabValue);
              SegmentInformation si = segmentInformationBySegmentNumber.get(segmentNumber);
              if (si == null) {
                si = new SegmentInformation(segmentNumber, recommendedDisplayCIELabValues);
                segmentInformationBySegmentNumber.put(segmentNumber, si);
              } else {
                throw new DicomException("Duplicate segment number");
              }
            } else {
              throw new DicomException("Missing segment number");
            }
          }
        } else {
          System.err.println(
              "SuperimposedDicomSegments.doCommonConstructorStuff(): Error: No segments in segmentation object");
        }

        SequenceAttribute saSharedFunctionalGroupsSequence =
            (SequenceAttribute) aSharedFunctionalGroupsSequence;
        SequenceAttribute saPerFrameFunctionalGroupsSequence =
            (SequenceAttribute) aPerFrameFunctionalGroupsSequence;
        SequenceAttribute sharedSegmentIdentificationSequence =
            (SequenceAttribute)
                (SequenceAttribute.getNamedAttributeFromWithinSequenceWithSingleItem(
                    saSharedFunctionalGroupsSequence, TagFromName.SegmentIdentificationSequence));
        int nPerFrameFunctionalGroupsSequence =
            saPerFrameFunctionalGroupsSequence.getNumberOfItems();
        if (nPerFrameFunctionalGroupsSequence == numberOfFrames) {
          for (int f = 0; f < numberOfFrames; ++f) {
            SequenceAttribute useSegmentIdentificationSequence =
                sharedSegmentIdentificationSequence;
            if (useSegmentIdentificationSequence == null) {
              useSegmentIdentificationSequence =
                  (SequenceAttribute)
                      (saPerFrameFunctionalGroupsSequence
                          .getItem(f)
                          .getAttributeList()
                          .get(TagFromName.SegmentIdentificationSequence));
            }
            if (useSegmentIdentificationSequence != null) {
              Attribute aReferencedSegmentNumber =
                  SequenceAttribute.getNamedAttributeFromWithinSequenceWithSingleItem(
                      useSegmentIdentificationSequence, TagFromName.ReferencedSegmentNumber);
              String referencedSegmentNumber =
                  aReferencedSegmentNumber == null
                      ? ""
                      : aReferencedSegmentNumber.getSingleStringValueOrEmptyString();
              if (referencedSegmentNumber.length() > 0) {
                SortedSet<Integer> framesForSegment =
                    framesForSegmentBySegmentNumber.get(referencedSegmentNumber);
                if (framesForSegment == null) {
                  framesForSegment = new TreeSet<Integer>();
                  framesForSegmentBySegmentNumber.put(referencedSegmentNumber, framesForSegment);
                }
                framesForSegment.add(new Integer(f));
              } else {
                throw new DicomException("Missing ReferencedSegmentNumber for frame " + f);
              }
            } else {
              throw new DicomException("Missing SegmentIdentificationSequence for frame " + f);
            }
          }
        } else {
          throw new DicomException(
              "Number of frames "
                  + numberOfFrames
                  + " does not match number of PerFrameFunctionalGroupsSequence items "
                  + nPerFrameFunctionalGroupsSequence);
        }

        // SortedMap<String,SortedSet<Integer>> framesForSegmentBySegmentNumber
        for (String segmentNumber : framesForSegmentBySegmentNumber.keySet()) {
          // System.err.println("SuperimposedDicomSegments.doCommonConstructorStuff(): Making
          // SourceImageSubset for segmentNumber "+segmentNumber);
          SortedSet<Integer> framesForSegment = framesForSegmentBySegmentNumber.get(segmentNumber);
          int[] parentFrameNumbers = new int[framesForSegment.size()];
          {
            int childFrameNumber = 0;
            for (Integer parentFrameNumber : framesForSegment) {
              // System.err.println("SuperimposedDicomSegments.doCommonConstructorStuff():
              // parentFrameNumber["+childFrameNumber+"] = "+parentFrameNumber);
              parentFrameNumbers[childFrameNumber++] = parentFrameNumber.intValue();
            }
          }
          SourceImage sourceImageForSegment =
              new SourceImageSubset(allFramesImage, parentFrameNumbers);
          GeometryOfVolume geometryForSegment =
              new GeometryOfVolumeFromAttributeList(list, parentFrameNumbers);
          if (!geometryForSegment.isVolumeSampledRegularlyAlongFrameDimension()) {
            System.err.println(
                "SuperimposedDicomSegments.doCommonConstructorStuff(): Warning: superimposed geometry is not a single regularly sampled volume for segment "
                    + segmentNumber);
          }
          superimposedImagesBySegmentNumber.put(
              segmentNumber,
              new SuperimposedImage(
                  sourceImageForSegment,
                  geometryForSegment,
                  segmentInformationBySegmentNumber.get(segmentNumber)
                      .recommendedDisplayCIELabValues));
        }

        // superimposedGeometry = new GeometryOfVolumeFromAttributeList(list);
        // if (!superimposedGeometry.isVolumeSampledRegularlyAlongFrameDimension()) {
        // System.err.println("SuperimposedDicomSegments.doCommonConstructorStuff(): Warning:
        // superimposed geometry is not a single regularly sampled volume");
        // }
      } else {
        System.err.println(
            "SuperimposedDicomSegments.doCommonConstructorStuff(): Error: Not a valid segmentation object");
      }
    }
  }