/// <summary>
/// Gets the VOI data LUTs for specified frame.
/// </summary>
/// <param name="frameNumber"></param>
/// <returns></returns>
internal IList <VoiDataLut> GetFrameVoiDataLuts(int frameNumber)
{
Platform.CheckPositive(frameNumber, "frameNumber");
lock (_syncLock)
{
var cacheKey = VoiDataLutsCacheKey.RootKey;
var dataset = (IDicomAttributeProvider)DataSource;
// attempt to find the VOI LUT Sequence in a functional group pertaining to the requested frame
FunctionalGroupDescriptor functionalGroupDescriptor;
if (_functionalGroups != null && _functionalGroups.TryGetValue(DicomTags.VoiLutSequence, out functionalGroupDescriptor))
{
bool perFrame;
var functionalGroup = MultiFrameFunctionalGroupsModuleIod.GetFunctionalGroup(functionalGroupDescriptor, DataSource, frameNumber, out perFrame);
var item = functionalGroup != null ? functionalGroup.SingleItem : null;
DicomAttribute dicomAttribute;
if (item != null && item.TryGetAttribute(DicomTags.VoiLutSequence, out dicomAttribute))
{
cacheKey = perFrame ? VoiDataLutsCacheKey.GetFrameKey(frameNumber) : VoiDataLutsCacheKey.SharedKey;
dataset = item;
}
}
IList <VoiDataLut> dataLuts;
if (!_frameVoiDataLuts.TryGetValue(cacheKey, out dataLuts))
{
_frameVoiDataLuts.Add(cacheKey, dataLuts = CreateVoiDataLuts(dataset));
}
return(dataLuts);
}
}
/// <summary>
/// Directly gets Per Frame ReferencedSegmentNumber without creating the full PerFrameFunctionalGroupsSequence[] collection.
/// </summary>
/// <param name="multiFrameFunctionalGroupsModuleIod"><see cref="MultiFrameFunctionalGroupsModuleIod"/> of the segmentation IOD</param>
/// <param name="frameIndex">frame index (0-based)</param>
/// <returns>ReferencedSegmentNumber or -1</returns>
private static int GetPerFrameReferencedSegmentNumber(MultiFrameFunctionalGroupsModuleIod multiFrameFunctionalGroupsModuleIod, int frameIndex)
{
var dicomAttribute = multiFrameFunctionalGroupsModuleIod.DicomAttributeProvider[DicomTags.PerFrameFunctionalGroupsSequence];
if (dicomAttribute.IsNull || dicomAttribute.IsEmpty || frameIndex >= dicomAttribute.Count)
{
return(-1);
}
var perFrameFunctionalGroupsSequenceItem = ((DicomSequenceItem[])dicomAttribute.Values)[frameIndex];
if (perFrameFunctionalGroupsSequenceItem != null)
{
var dicomAttr1 = perFrameFunctionalGroupsSequenceItem.GetAttribute(DicomTags.SegmentIdentificationSequence);
if (!dicomAttr1.IsNull && !dicomAttr1.IsEmpty)
{
var segmentIdentificationSequenceItem = ((DicomSequenceItem[])dicomAttr1.Values)[0];
var dicomAttr2 = segmentIdentificationSequenceItem.GetAttribute(DicomTags.ReferencedSegmentNumber);
if (!dicomAttr2.IsNull && !dicomAttr2.IsEmpty)
{
return(dicomAttr2.GetInt32(0, -1));
}
}
}
return(-1);
}
/// <summary>
/// Directly gets Per Frame <see cref="FunctionalGroupsSequenceItem"/> count without creating the full PerFrameFunctionalGroupsSequence[] collection.
/// </summary>
/// <param name="multiFrameFunctionalGroupsModuleIod"><see cref="MultiFrameFunctionalGroupsModuleIod"/> of the segmentation IOD</param>
/// <returns></returns>
private static long GetNumberOfPerFrameFinctionalGroupsSequenceItems(MultiFrameFunctionalGroupsModuleIod multiFrameFunctionalGroupsModuleIod)
{
var dicomAttribute = multiFrameFunctionalGroupsModuleIod.DicomAttributeProvider[DicomTags.PerFrameFunctionalGroupsSequence];
if (dicomAttribute.IsNull || dicomAttribute.IsEmpty)
{
return(-1);
}
return(dicomAttribute.Count);
}
private DicomAttribute GetFrameAttributeCore(int frameNumber, uint tag)
{
FunctionalGroupDescriptor functionalGroupDescriptor;
if (frameNumber > 0 && _functionalGroups != null && _functionalGroups.TryGetValue(tag, out functionalGroupDescriptor))
{
DicomAttribute dicomAttribute;
var functionalGroup = MultiFrameFunctionalGroupsModuleIod.GetFunctionalGroup(functionalGroupDescriptor, DataSource, frameNumber);
var item = functionalGroup != null ? functionalGroup.SingleItem : null;
if (item != null && item.TryGetAttribute(tag, out dicomAttribute))
{
return(dicomAttribute);
}
}
return(null);
}
public SegmentationDocumentIod(IDicomAttributeProvider dicomAttributeProvider)
{
_dicomAttributeProvider = dicomAttributeProvider;
_patientModule = new PatientModuleIod(_dicomAttributeProvider);
_clinicalTrialSubjectModule = new ClinicalTrialSubjectModuleIod(_dicomAttributeProvider);
_generalStudyModule = new GeneralStudyModuleIod(_dicomAttributeProvider);
_patientStudyModule = new PatientStudyModuleIod(_dicomAttributeProvider);
_clinicalTrialStudyModule = new ClinicalTrialStudyModuleIod(_dicomAttributeProvider);
_generalSeriesModule = new GeneralSeriesModuleIod(_dicomAttributeProvider);
_segmentationSeriesModule = new SegmentationSeriesModuleIod(_dicomAttributeProvider);
_clinicalTrialSeriesModule = new ClinicalTrialSeriesModuleIod(_dicomAttributeProvider);
_frameOfReferenceModule = new FrameOfReferenceModuleIod(_dicomAttributeProvider);
_generalEquipmentModule = new GeneralEquipmentModuleIod(_dicomAttributeProvider);
//_enhanceGeneralEquipmentModule = new EnhanceGeneralEquipmentModuleIod(_dicomAttributeProvider);
_generalImageModule = new GeneralImageModuleIod(_dicomAttributeProvider);
_imagePixelModule = new ImagePixelMacroIod(_dicomAttributeProvider);
_segmentationImageModule = new SegmentationImageModuleIod(_dicomAttributeProvider);
_multiFrameFunctionalGroupsModule = new MultiFrameFunctionalGroupsModuleIod(_dicomAttributeProvider);
_multiFrameDimensionModule = new MultiFrameDimensionModuleIod(_dicomAttributeProvider);
_specimenModule = new SpecimenModuleIod(_dicomAttributeProvider);
_commonInstanceReferenceModule = new CommonInstanceReferenceModuleIod(_dicomAttributeProvider);
_sopCommonModule = new SopCommonModuleIod(_dicomAttributeProvider);
_frameExtractionModule = new FrameExtractionModuleIod(_dicomAttributeProvider);
}
public void TestSeriesSplittingEnhancedMREcho()
{
const int numberOfSeries = 2;
const int instancesPerSeries = 3;
const int framesPerInstance = 10;
List <TestDataSource> dataSources = CreateMRStudyDataSources(numberOfSeries, instancesPerSeries, "1.2.3");
foreach (var dicomFile in dataSources.Select(d => d.File))
{
dicomFile.DataSet[DicomTags.NumberOfFrames].SetInt32(0, framesPerInstance);
if (dicomFile.DataSet[DicomTags.SeriesNumber].GetInt32(0, 0) != 2)
{
continue;
}
var dimUid = "1.2.3.4.5";
var mfdModule = new MultiFrameDimensionModuleIod(dicomFile.DataSet);
mfdModule.DimensionOrganizationSequence = new[] { new DimensionOrganizationSequenceItem {
DimensionOrganizationUid = dimUid
} };
mfdModule.DimensionIndexSequence = new[]
{
new DimensionIndexSequenceItem {
DimensionIndexPointer = DicomTags.StackId, FunctionalGroupPointer = DicomTags.FrameContentSequence, DimensionOrganizationUid = dimUid
},
new DimensionIndexSequenceItem {
DimensionIndexPointer = DicomTags.InStackPositionNumber, FunctionalGroupPointer = DicomTags.FrameContentSequence, DimensionOrganizationUid = dimUid
},
new DimensionIndexSequenceItem {
DimensionIndexPointer = DicomTags.EffectiveEchoTime, FunctionalGroupPointer = DicomTags.MrEchoSequence, DimensionOrganizationUid = dimUid
}
};
var mffgModule = new MultiFrameFunctionalGroupsModuleIod(dicomFile.DataSet);
mffgModule.PerFrameFunctionalGroupsSequence = Enumerable.Range(0, framesPerInstance).Select(i =>
{
var fg = new FunctionalGroupsSequenceItem();
ushort inStackPositionNumber = (ushort)(i % 5 + 1);
ushort echoNumber = (ushort)(i / 5 + 1);
fg.GetFunctionalGroup <FrameContentFunctionalGroup>().FrameContentSequence = new FrameContentSequenceItem {
InStackPositionNumber = inStackPositionNumber, StackId = "1", DimensionIndexValues = new uint[] { 1, inStackPositionNumber, echoNumber }
};
fg.GetFunctionalGroup <MrEchoFunctionalGroup>().MrEchoSequence = new MrEchoSequenceItem {
EffectiveEchoTime = echoNumber + 5 / 1000f
};
return(fg);
}).ToArray();
}
StudyTree studyTree = CreateStudyTree(ConvertToSops(dataSources));
MREchoDisplaySetFactory factory = new MREchoDisplaySetFactory();
factory.SetStudyTree(studyTree);
List <IDisplaySet> allDisplaySets = new List <IDisplaySet>();
try
{
Patient patient = studyTree.Patients[0];
Study study = patient.Studies[0];
Assert.AreEqual(numberOfSeries, study.Series.Count, "There should be exactly {0} series", numberOfSeries);
Series series2 = study.Series[1];
foreach (Series series in study.Series)
{
Assert.AreEqual(instancesPerSeries, series.Sops.Count, "There should be exactly {0} sops", instancesPerSeries);
List <IDisplaySet> displaySets = factory.CreateDisplaySets(series);
allDisplaySets.AddRange(displaySets);
if (series == series2)
{
Assert.AreEqual(2, displaySets.Count, "There should be exactly 4 display sets");
IDisplaySet displaySet = displaySets[0];
Assert.AreEqual(series.Sops.Count * framesPerInstance / 2, displaySet.PresentationImages.Count, "#presentation images should be #Sops/2");
Assert.AreNotEqual(series.SeriesInstanceUid, displaySet.Descriptor.Uid, "Series UID and Display Set UID don't match");
Assert.AreEqual(typeof(MREchoDisplaySetDescriptor), displaySet.Descriptor.GetType(), "Wrong display set descriptor type");
Assert.IsTrue(displaySet.Name.Contains("Echo"), "Display Set name not correct");
ValidateMultiframeEchoDisplaySet(displaySets[0], 1);
ValidateMultiframeEchoDisplaySet(displaySets[1], 2);
}
else
{
//Assert.AreEqual(0, displaySets.Count, "There should be no display sets");
}
}
}
finally
{
foreach (IDisplaySet displaySet in allDisplaySets)
{
displaySet.Dispose();
}
studyTree.Dispose();
}
}
public SegmentationDocumentIod(IDicomAttributeProvider dicomAttributeProvider)
{
_dicomAttributeProvider = dicomAttributeProvider;
_patientModule = new PatientModuleIod(_dicomAttributeProvider);
_clinicalTrialSubjectModule = new ClinicalTrialSubjectModuleIod(_dicomAttributeProvider);
_generalStudyModule = new GeneralStudyModuleIod(_dicomAttributeProvider);
_patientStudyModule = new PatientStudyModuleIod(_dicomAttributeProvider);
_clinicalTrialStudyModule = new ClinicalTrialStudyModuleIod(_dicomAttributeProvider);
_generalSeriesModule = new GeneralSeriesModuleIod(_dicomAttributeProvider);
_segmentationSeriesModule = new SegmentationSeriesModuleIod(_dicomAttributeProvider);
_clinicalTrialSeriesModule = new ClinicalTrialSeriesModuleIod(_dicomAttributeProvider);
_frameOfReferenceModule = new FrameOfReferenceModuleIod(_dicomAttributeProvider);
_generalEquipmentModule = new GeneralEquipmentModuleIod(_dicomAttributeProvider);
//_enhanceGeneralEquipmentModule = new EnhanceGeneralEquipmentModuleIod(_dicomAttributeProvider);
_generalImageModule = new GeneralImageModuleIod(_dicomAttributeProvider);
_imagePixelModule = new ImagePixelMacroIod(_dicomAttributeProvider);
_segmentationImageModule = new SegmentationImageModuleIod(_dicomAttributeProvider);
_multiFrameFunctionalGroupsModule = new MultiFrameFunctionalGroupsModuleIod(_dicomAttributeProvider);
_multiFrameDimensionModule = new MultiFrameDimensionModuleIod(_dicomAttributeProvider);
_specimenModule = new SpecimenModuleIod(_dicomAttributeProvider);
_commonInstanceReferenceModule = new CommonInstanceReferenceModuleIod(_dicomAttributeProvider);
_sopCommonModule = new SopCommonModuleIod(_dicomAttributeProvider);
_frameExtractionModule = new FrameExtractionModuleIod(_dicomAttributeProvider);
}
public void TestSeriesSplittingEnhancedMREcho()
{
const int numberOfSeries = 2;
const int instancesPerSeries = 3;
const int framesPerInstance = 10;
List<TestDataSource> dataSources = CreateMRStudyDataSources(numberOfSeries, instancesPerSeries, "1.2.3");
foreach (var dicomFile in dataSources.Select(d => d.File))
{
dicomFile.DataSet[DicomTags.NumberOfFrames].SetInt32(0, framesPerInstance);
if (dicomFile.DataSet[DicomTags.SeriesNumber].GetInt32(0, 0) != 2) continue;
var dimUid = "1.2.3.4.5";
var mfdModule = new MultiFrameDimensionModuleIod(dicomFile.DataSet);
mfdModule.DimensionOrganizationSequence = new[] {new DimensionOrganizationSequenceItem {DimensionOrganizationUid = dimUid}};
mfdModule.DimensionIndexSequence = new[]
{
new DimensionIndexSequenceItem {DimensionIndexPointer = DicomTags.StackId, FunctionalGroupPointer = DicomTags.FrameContentSequence, DimensionOrganizationUid = dimUid},
new DimensionIndexSequenceItem {DimensionIndexPointer = DicomTags.InStackPositionNumber, FunctionalGroupPointer = DicomTags.FrameContentSequence, DimensionOrganizationUid = dimUid},
new DimensionIndexSequenceItem {DimensionIndexPointer = DicomTags.EffectiveEchoTime, FunctionalGroupPointer = DicomTags.MrEchoSequence, DimensionOrganizationUid = dimUid}
};
var mffgModule = new MultiFrameFunctionalGroupsModuleIod(dicomFile.DataSet);
mffgModule.PerFrameFunctionalGroupsSequence = Enumerable.Range(0, framesPerInstance).Select(i =>
{
var fg = new FunctionalGroupsSequenceItem();
ushort inStackPositionNumber = (ushort) (i%5 + 1);
ushort echoNumber = (ushort) (i/5 + 1);
fg.GetFunctionalGroup<FrameContentFunctionalGroup>().FrameContentSequence = new FrameContentSequenceItem {InStackPositionNumber = inStackPositionNumber, StackId = "1", DimensionIndexValues = new uint[] {1, inStackPositionNumber, echoNumber}};
fg.GetFunctionalGroup<MrEchoFunctionalGroup>().MrEchoSequence = new MrEchoSequenceItem {EffectiveEchoTime = echoNumber + 5/1000f};
return fg;
}).ToArray();
}
StudyTree studyTree = CreateStudyTree(ConvertToSops(dataSources));
MREchoDisplaySetFactory factory = new MREchoDisplaySetFactory();
factory.SetStudyTree(studyTree);
List<IDisplaySet> allDisplaySets = new List<IDisplaySet>();
try
{
Patient patient = studyTree.Patients[0];
Study study = patient.Studies[0];
Assert.AreEqual(numberOfSeries, study.Series.Count, "There should be exactly {0} series", numberOfSeries);
Series series2 = study.Series[1];
foreach (Series series in study.Series)
{
Assert.AreEqual(instancesPerSeries, series.Sops.Count, "There should be exactly {0} sops", instancesPerSeries);
List<IDisplaySet> displaySets = factory.CreateDisplaySets(series);
allDisplaySets.AddRange(displaySets);
if (series == series2)
{
Assert.AreEqual(2, displaySets.Count, "There should be exactly 4 display sets");
IDisplaySet displaySet = displaySets[0];
Assert.AreEqual(series.Sops.Count*framesPerInstance/2, displaySet.PresentationImages.Count, "#presentation images should be #Sops/2");
Assert.AreNotEqual(series.SeriesInstanceUid, displaySet.Descriptor.Uid, "Series UID and Display Set UID don't match");
Assert.AreEqual(typeof (MREchoDisplaySetDescriptor), displaySet.Descriptor.GetType(), "Wrong display set descriptor type");
Assert.IsTrue(displaySet.Name.Contains("Echo"), "Display Set name not correct");
ValidateMultiframeEchoDisplaySet(displaySets[0], 1);
ValidateMultiframeEchoDisplaySet(displaySets[1], 2);
}
else
{
//Assert.AreEqual(0, displaySets.Count, "There should be no display sets");
}
}
}
finally
{
foreach (IDisplaySet displaySet in allDisplaySets)
displaySet.Dispose();
studyTree.Dispose();
}
}
/// <summary>
/// Directly gets Per Frame <see cref="FunctionalGroupsSequenceItem"/> without creating the full PerFrameFunctionalGroupsSequence[] collection.
/// </summary>
/// <param name="multiFrameFunctionalGroupsModuleIod"><see cref="MultiFrameFunctionalGroupsModuleIod"/> of the segmentation IOD</param>
/// <param name="frameIndex">frame index (0-based)</param>
/// <returns>PerFrameFunctionalGroupsSequenceItem for the requested frame</returns>
private static FunctionalGroupsSequenceItem GetPerFrameFunctionalGroupsSequenceItem(MultiFrameFunctionalGroupsModuleIod multiFrameFunctionalGroupsModuleIod,
int frameIndex)
{
var dicomAttribute = multiFrameFunctionalGroupsModuleIod.DicomAttributeProvider[DicomTags.PerFrameFunctionalGroupsSequence];
if (dicomAttribute.IsNull || dicomAttribute.IsEmpty || frameIndex >= dicomAttribute.Count)
{
return(null);
}
var item = ((DicomSequenceItem[])dicomAttribute.Values)[frameIndex];
return(new FunctionalGroupsSequenceItem(item));
}
/// <summary>
/// Gets the functional group sequence item for a particular tag in the data set (i.e. the parent sequence item containing the requested tag).
/// </summary>
/// <remarks>
/// <para>
/// If the requested tag is the root sequence tag of a functional group (e.g. <see cref="DicomTags.PatientOrientationInFrameSequence"/>),
/// the returned sequence item will be the functional group sequence item for the frame in which the requested attribute can be found.
/// </para>
/// <para>
/// If the requested tag is a nested tag of a functional group and the root sequence tag allows only one sequence item
/// (e.g. <see cref="DicomTags.PatientOrientation"/> as a nested tag of <see cref="DicomTags.PatientOrientationInFrameSequence"/>),
/// the returned sequence item will be the single sequence item in the root sequence attribute.
/// </para>
/// <para>
/// It is not possible to directly access a nested tag of a functional group if the root sequence tag allows multiple sequence items
/// (e.g. <see cref="DicomTags.RadiopharmaceuticalAgentNumber"/> as a nested tag of <see cref="DicomTags.RadiopharmaceuticalUsageSequence"/>).
/// To do so, access the <see cref="DicomTags.RadiopharmaceuticalUsageSequence"/> and handle the sequence items individually.
/// </para>
/// </remarks>
/// <param name="frameNumber">DICOM frame number (first frame is 1).</param>
/// <param name="tag">DICOM tag of the attribute.</param>
/// <param name="isFrameSpecific">Indicates whether or not the returned functional group is specific to the requested frame.</param>
/// <returns>The requested functional group sequence item.</returns>
public DicomSequenceItem GetFrameFunctionalGroupItem(int frameNumber, uint tag, out bool isFrameSpecific)
{
FunctionalGroupDescriptor functionalGroupDescriptor;
if (frameNumber > 0 && _tagMap != null && _tagMap.TryGetValue(tag, out functionalGroupDescriptor))
{
FrameFunctionalGroupValue functionalGroupResult;
var key = new FrameFunctionalGroupKey(functionalGroupDescriptor, frameNumber);
if (!_cache.TryGetValue(key, out functionalGroupResult))
{
_cache[key] = functionalGroupResult = new FrameFunctionalGroupValue(MultiFrameFunctionalGroupsModuleIod.GetFunctionalGroup(functionalGroupDescriptor, _dataSet, frameNumber, out isFrameSpecific), isFrameSpecific);
}
else
{
isFrameSpecific = functionalGroupResult.IsFrameSpecific;
}
var functionalGroup = functionalGroupResult.FunctionalGroupMacro;
if (functionalGroup == null)
{
return(null);
}
// if the requested tag is the root sequence tag, return the entire per-frame/shared functional group sequence item as the result
// otherwise, return the singleton sequence item that contains the requested nested tag (or null if the containing sequence item is not a singleton)
return(functionalGroup.DefinedTags.Contains(tag) ? functionalGroup.DicomSequenceItem : functionalGroup.SingleItem);
}
isFrameSpecific = false;
return(null);
}
