private DicomDirectoryRecord ParseDirectoryRecord(uint offset, List <uint> notFoundOffsets)
{
DicomDirectoryRecord record = null;
if (!_lookup.TryGetValue(offset, out var dataset))
{
if (offset != 0)
{
notFoundOffsets.Add(offset);
}
}
else
{
record = new DicomDirectoryRecord(dataset)
{
Offset = offset
};
_lookup.Remove(offset);
record.NextDirectoryRecord =
ParseDirectoryRecord(record.GetSingleValue <uint>(DicomTag.OffsetOfTheNextDirectoryRecord), notFoundOffsets);
record.LowerLevelDirectoryRecord =
ParseDirectoryRecord(record.GetSingleValue <uint>(DicomTag.OffsetOfReferencedLowerLevelDirectoryEntity), notFoundOffsets);
}
return(record);
}
public void Exact_Offsets_Should_All_Match()
{
var offsets = GenerateUniqueRandonmOffsets(155, 500000);
var root = new Container()
{
Sequence = new DicomDataset()
};
root.CreateChildren(offsets, 5, 3, 3, 2);
var allChildren = root.AllContainer.Skip(1).ToArray();
var sequence = new DicomSequence(DicomTag.DirectoryRecordSequence);
root.Sequence.AddOrUpdate(sequence);
var byteSource = new TestByteSource();
var observer = new DicomDirectoryReaderObserver(root.Sequence);
observer.OnBeginSequence(byteSource, DicomTag.DirectoryRecordSequence, 0);
foreach (var container in allChildren)
{
sequence.Items.Add(container.Sequence);
byteSource.Position = container.Offset + 8;
observer.OnBeginSequenceItem(byteSource, 0);
observer.OnEndSequenceItem();
}
observer.OnEndSequence();
var rootRecord = new DicomDirectoryRecord
{
LowerLevelDirectoryRecord = observer.BuildDirectoryRecords(),
};
root.AssertRecord(rootRecord);
}
private DicomDirectoryRecord ParseDirectoryRecord(DicomDirectoryRecord record, uint offset, uint[] offsets)
{
if (record == null)
{
// Find the best matching existing offset for the given offset
// The given offset should be in offsets and the following entry in that sorted array gives
// us the next used offset. That's the upper bound for the search
var index = Array.BinarySearch(offsets, offset);
if (index < 0)
{
return(null);
}
uint maxOffset;
int maxIndex = offsets.Length - 1;
// Deal with the rare possibility that offsets can contain duplicates
while (true)
{
if (index >= maxIndex)
{
maxOffset = uint.MaxValue;
break;
}
maxOffset = offsets[++index];
if (maxOffset != offset)
{
break;
}
}
offset = _lookup.Keys.FirstOrDefault(key => key >= offset && key < maxOffset);
if (!_lookup.TryGetValue(offset, out var dataset))
{
return(null);
}
record = new DicomDirectoryRecord(dataset)
{
Offset = offset
};
_lookup.Remove(offset);
}
var nextOffset = record.GetSingleValue <uint>(DicomTag.OffsetOfTheNextDirectoryRecord);
if (nextOffset > 0)
{
record.NextDirectoryRecord = ParseDirectoryRecord(record.NextDirectoryRecord, nextOffset, offsets);
}
var lowerLevelOffset = record.GetSingleValue <uint>(DicomTag.OffsetOfReferencedLowerLevelDirectoryEntity);
if (lowerLevelOffset > 0)
{
record.LowerLevelDirectoryRecord = ParseDirectoryRecord(record.LowerLevelDirectoryRecord, lowerLevelOffset, offsets);
}
return(record);
}
private DicomDirectoryRecord ParseDirectoryRecord(uint offset) {
DicomDirectoryRecord record = null;
if (_lookup.ContainsKey(offset)) {
record = new DicomDirectoryRecord(_lookup[offset]);
record.Offset = offset;
record.NextDirectoryRecord = ParseDirectoryRecord(record.Get<uint>(DicomTag.OffsetOfTheNextDirectoryRecord));
record.LowerLevelDirectoryRecord = ParseDirectoryRecord(record.Get<uint>(DicomTag.OffsetOfReferencedLowerLevelDirectoryEntity));
}
return record;
}
public void Duplicate_Offsets_Should_Not_Throw()
{
var offsets = new List <uint>(GenerateUniqueRandonmOffsets(155, 100000).Select(o => o * 5));
for (int i = 0; i < offsets.Count - 2; i += 2)
{
offsets[i + 1] = offsets[i];
}
var root = new Container()
{
Sequence = new DicomDataset()
};
root.CreateChildren(offsets, 5, 3, 3, 2);
var allChildren = root.AllContainer.Skip(1).ToArray();
var sequence = new DicomSequence(DicomTag.DirectoryRecordSequence);
root.Sequence.AddOrUpdate(sequence);
var byteSource = new TestByteSource();
var observer = new DicomDirectoryReaderObserver(root.Sequence);
observer.OnBeginSequence(byteSource, DicomTag.DirectoryRecordSequence, 0);
uint lastPosition = 0;
foreach (var container in allChildren)
{
sequence.Items.Add(container.Sequence);
var position = container.Offset + 8;
if (position == lastPosition)
{
position += 1;
}
lastPosition = position;
byteSource.Position = position;
observer.OnBeginSequenceItem(byteSource, 0);
observer.OnEndSequenceItem();
}
observer.OnEndSequence();
var rootRecord = new DicomDirectoryRecord
{
LowerLevelDirectoryRecord = observer.BuildDirectoryRecords(),
};
// Cannot assert all records when duplicate offsets exist.
// root.AssertRecord(rootRecord);
}
public DicomDirectoryRecord BuildDirectoryRecords()
{
var notFoundOffsets = new List <uint>();
var offset = _dataset.GetSingleValue <uint>(DicomTag.OffsetOfTheFirstDirectoryRecordOfTheRootDirectoryEntity);
DicomDirectoryRecord root = ParseDirectoryRecord(offset, notFoundOffsets);
if (_lookup.Count > 0)
{
// There are unresolved sequences. Try to resolve them with non exact offset match
root = ParseDirectoryRecordNotExact(root, offset, notFoundOffsets);
}
return(root);
}
private DicomDirectoryRecord ParseDirectoryRecord(uint offset)
{
DicomDirectoryRecord record = null;
if (_lookup.ContainsKey(offset))
{
record = new DicomDirectoryRecord(_lookup[offset]);
record.Offset = offset;
record.NextDirectoryRecord = ParseDirectoryRecord(record.Get <uint>(DicomTag.OffsetOfTheNextDirectoryRecord));
record.LowerLevelDirectoryRecord = ParseDirectoryRecord(record.Get <uint>(DicomTag.OffsetOfReferencedLowerLevelDirectoryEntity));
}
return(record);
}
public void AssertRecord(DicomDirectoryRecord record)
{
if (Id != 0)
{
Assert.Equal(Id.ToString(), record.GetSingleValue <string>(DicomTag.SOPInstanceUID));
}
DicomDirectoryRecord current = record.LowerLevelDirectoryRecord;
foreach (var child in Children)
{
Assert.NotNull(current);
child.AssertRecord(current);
current = current.NextDirectoryRecord;
}
Assert.Null(current);
}
private void CreateImageRecord(
DicomFileMetaInformation metaFileInfo,
DicomDataset dataset,
DicomDirectoryRecord seriesRecord,
string referencedFileId)
{
var currentImage = seriesRecord.LowerLevelDirectoryRecord;
var imageInstanceUid = dataset.Get <string>(DicomTag.SOPInstanceUID);
while (currentImage != null)
{
if (currentImage.Get <string>(DicomTag.ReferencedSOPInstanceUIDInFile) == imageInstanceUid)
{
return;
}
if (currentImage.NextDirectoryRecord != null)
{
currentImage = currentImage.NextDirectoryRecord;
}
else
{
//no more patient records, break the loop
break;
}
}
var newImage = CreateRecordSequenceItem(DicomDirectoryRecordType.Image, dataset);
newImage.AddOrUpdate(DicomTag.ReferencedFileID, referencedFileId);
newImage.AddOrUpdate(DicomTag.ReferencedSOPClassUIDInFile, metaFileInfo.MediaStorageSOPClassUID.UID);
newImage.AddOrUpdate(DicomTag.ReferencedSOPInstanceUIDInFile, metaFileInfo.MediaStorageSOPInstanceUID.UID);
newImage.AddOrUpdate(DicomTag.ReferencedTransferSyntaxUIDInFile, metaFileInfo.TransferSyntax.UID);
if (currentImage != null)
{
//study not found under patient record
currentImage.NextDirectoryRecord = newImage;
}
else
{
//no studies record found under patient record
seriesRecord.LowerLevelDirectoryRecord = newImage;
}
}
private void AddDirectoryRecordsToSequenceItem(DicomDirectoryRecord recordItem)
{
if (recordItem == null)
{
return;
}
_directoryRecordSequence.Items.Add(recordItem);
if (recordItem.LowerLevelDirectoryRecord != null)
{
AddDirectoryRecordsToSequenceItem(recordItem.LowerLevelDirectoryRecord);
}
if (recordItem.NextDirectoryRecord != null)
{
AddDirectoryRecordsToSequenceItem(recordItem.NextDirectoryRecord);
}
}
private DicomDirectoryRecord ParseDirectoryRecordNotExact(DicomDirectoryRecord root, uint rootOffset, List <uint> offsets)
{
// Collect all used offsets, and sort them (they can contain duplicates)
foreach (var dataset in _lookup.Values)
{
var offset = dataset.GetSingleValue <uint>(DicomTag.OffsetOfTheNextDirectoryRecord);
if (offset > 0)
{
offsets.Add(offset);
}
offset = dataset.GetSingleValue <uint>(DicomTag.OffsetOfReferencedLowerLevelDirectoryEntity);
if (offset > 0)
{
offsets.Add(offset);
}
}
var offsetArray = offsets.ToArray();
Array.Sort(offsetArray);
return(ParseDirectoryRecord(root, rootOffset, offsetArray));
}
private void SetOffsets(DicomDirectoryRecord record)
{
if (record.NextDirectoryRecord != null)
{
record.Add <uint>(DicomTag.OffsetOfTheNextDirectoryRecord, record.NextDirectoryRecord.Offset);
SetOffsets(record.NextDirectoryRecord);
}
else
{
record.Add <uint>(DicomTag.OffsetOfTheNextDirectoryRecord, 0);
}
if (record.LowerLevelDirectoryRecord != null)
{
record.Add <uint>(DicomTag.OffsetOfReferencedLowerLevelDirectoryEntity, record.LowerLevelDirectoryRecord.Offset);
SetOffsets(record.LowerLevelDirectoryRecord);
}
else
{
record.Add <uint>(DicomTag.OffsetOfReferencedLowerLevelDirectoryEntity, 0);
}
}
private DicomDirectoryRecord CreateSeriesRecord(DicomDataset dataset, DicomDirectoryRecord studyRecord)
{
var currentSeries = studyRecord.LowerLevelDirectoryRecord;
var seriesInstanceUid = dataset.Get <string>(DicomTag.SeriesInstanceUID);
while (currentSeries != null)
{
if (currentSeries.Get <string>(DicomTag.SeriesInstanceUID) == seriesInstanceUid)
{
return(currentSeries);
}
if (currentSeries.NextDirectoryRecord != null)
{
currentSeries = currentSeries.NextDirectoryRecord;
}
else
{
//no more patient records, break the loop
break;
}
}
var newSeries = CreateRecordSequenceItem(DicomDirectoryRecordType.Series, dataset);
if (currentSeries != null)
{
//series not found under study record
currentSeries.NextDirectoryRecord = newSeries;
}
else
{
//no series record found under study record
studyRecord.LowerLevelDirectoryRecord = newSeries;
}
return(newSeries);
}
private DicomDirectoryRecord CreateStudyRecord(DicomDataset dataset, DicomDirectoryRecord patientRecord)
{
var currentStudy = patientRecord.LowerLevelDirectoryRecord;
var studyInstanceUid = dataset.Get <string>(DicomTag.StudyInstanceUID);
while (currentStudy != null)
{
if (currentStudy.Get <string>(DicomTag.StudyInstanceUID) == studyInstanceUid)
{
return(currentStudy);
}
if (currentStudy.NextDirectoryRecord != null)
{
currentStudy = currentStudy.NextDirectoryRecord;
}
else
{
//no more patient records, break the loop
break;
}
}
var newStudy = CreateRecordSequenceItem(DicomDirectoryRecordType.Study, dataset);
if (currentStudy != null)
{
//study not found under patient record
currentStudy.NextDirectoryRecord = newStudy;
}
else
{
//no studies record found under patient record
patientRecord.LowerLevelDirectoryRecord = newStudy;
}
return(newStudy);
}
private DicomDirectoryRecord CreateRecordSequenceItem(DicomDirectoryRecordType recordType, DicomDataset dataset)
{
if (recordType == null)
{
throw new ArgumentNullException("recordType");
}
if (dataset == null)
{
throw new ArgumentNullException("dataset");
}
var sequenceItem = new DicomDirectoryRecord();
//add record item attributes
sequenceItem.Add <uint>(DicomTag.OffsetOfTheNextDirectoryRecord, 0);
sequenceItem.Add <ushort>(DicomTag.RecordInUseFlag, 0xFFFF);
sequenceItem.Add <uint>(DicomTag.OffsetOfReferencedLowerLevelDirectoryEntity, 0);
sequenceItem.Add <string>(DicomTag.DirectoryRecordType, recordType.ToString());
//copy the current dataset character set
sequenceItem.Add(dataset.FirstOrDefault(d => d.Tag == DicomTag.SpecificCharacterSet));
foreach (var tag in recordType.Tags)
{
if (dataset.Contains(tag))
{
sequenceItem.Add(dataset.Get <DicomItem>(tag));
}
else
{
System.Diagnostics.Debug.WriteLine("Cannot find tag {0} for record type {1}", tag, recordType);
}
}
return(sequenceItem);
}
private DicomDirectoryRecord CreateRecordSequenceItem(DicomDirectoryRecordType recordType, DicomDataset dataset) {
if (recordType == null)
throw new ArgumentNullException("recordType");
if (dataset == null)
throw new ArgumentNullException("dataset");
var sequenceItem = new DicomDirectoryRecord();
//add record item attributes
sequenceItem.Add<uint>(DicomTag.OffsetOfTheNextDirectoryRecord, 0);
sequenceItem.Add<ushort>(DicomTag.RecordInUseFlag, 0xFFFF);
sequenceItem.Add<uint>(DicomTag.OffsetOfReferencedLowerLevelDirectoryEntity, 0);
sequenceItem.Add<string>(DicomTag.DirectoryRecordType, recordType.ToString());
//copy the current dataset character set
sequenceItem.Add(dataset.FirstOrDefault(d => d.Tag == DicomTag.SpecificCharacterSet));
foreach (var tag in recordType.Tags) {
if (dataset.Contains(tag)) {
sequenceItem.Add(dataset.Get<DicomItem>(tag));
} else {
System.Diagnostics.Debug.WriteLine("Cannot find tag {0} for record type {1}", tag, recordType);
}
}
return sequenceItem;
}
private DicomDirectoryRecord CreateStudyRecord(DicomDataset dataset, DicomDirectoryRecord patientRecord) {
var currentStudy = patientRecord.LowerLevelDirectoryRecord;
var studyInstanceUid = dataset.Get<string>(DicomTag.StudyInstanceUID);
while (currentStudy != null) {
if (currentStudy.Get<string>(DicomTag.StudyInstanceUID) == studyInstanceUid) {
return currentStudy;
}
if (currentStudy.NextDirectoryRecord != null) {
currentStudy = currentStudy.NextDirectoryRecord;
} else {
//no more patient records, break the loop
break;
}
}
var newStudy = CreateRecordSequenceItem(DicomDirectoryRecordType.Study, dataset);
if (currentStudy != null) {
//study not found under patient record
currentStudy.NextDirectoryRecord = newStudy;
} else {
//no studies record found under patient record
patientRecord.LowerLevelDirectoryRecord = newStudy;
}
return newStudy;
}
private DicomDirectoryRecord CreateSeriesRecord(DicomDataset dataset, DicomDirectoryRecord studyRecord) {
var currentSeries = studyRecord.LowerLevelDirectoryRecord;
var seriesInstanceUid = dataset.Get<string>(DicomTag.SeriesInstanceUID);
while (currentSeries != null) {
if (currentSeries.Get<string>(DicomTag.SeriesInstanceUID) == seriesInstanceUid) {
return currentSeries;
}
if (currentSeries.NextDirectoryRecord != null) {
currentSeries = currentSeries.NextDirectoryRecord;
} else {
//no more patient records, break the loop
break;
}
}
var newSeries = CreateRecordSequenceItem(DicomDirectoryRecordType.Series, dataset);
if (currentSeries != null) {
//series not found under study record
currentSeries.NextDirectoryRecord = newSeries;
} else {
//no series record found under study record
studyRecord.LowerLevelDirectoryRecord = newSeries;
}
return newSeries;
}
private void CreateImageRecord(DicomFileMetaInformation metaFileInfo, DicomDataset dataset, DicomDirectoryRecord seriesRecord, string referencedFileId) {
var currentImage = seriesRecord.LowerLevelDirectoryRecord;
var imageInstanceUid = dataset.Get<string>(DicomTag.SOPInstanceUID);
while (currentImage != null) {
if (currentImage.Get<string>(DicomTag.ReferencedSOPInstanceUIDInFile) == imageInstanceUid) {
return;
}
if (currentImage.NextDirectoryRecord != null) {
currentImage = currentImage.NextDirectoryRecord;
} else {
//no more patient records, break the loop
break;
}
}
var newImage = CreateRecordSequenceItem(DicomDirectoryRecordType.Image, dataset);
newImage.Add(DicomTag.ReferencedFileID, referencedFileId);
newImage.Add(DicomTag.ReferencedSOPClassUIDInFile, metaFileInfo.MediaStorageSOPClassUID.UID);
newImage.Add(DicomTag.ReferencedSOPInstanceUIDInFile, metaFileInfo.MediaStorageSOPInstanceUID.UID);
newImage.Add(DicomTag.ReferencedTransferSyntaxUIDInFile, metaFileInfo.TransferSyntax.UID);
if (currentImage != null) {
//study not found under patient record
currentImage.NextDirectoryRecord = newImage;
} else {
//no studies record found under patient record
seriesRecord.LowerLevelDirectoryRecord = newImage;
}
}
private void SetOffsets(DicomDirectoryRecord record) {
if (record.NextDirectoryRecord != null) {
record.Add<uint>(DicomTag.OffsetOfTheNextDirectoryRecord, record.NextDirectoryRecord.Offset);
SetOffsets(record.NextDirectoryRecord);
} else {
record.Add<uint>(DicomTag.OffsetOfTheNextDirectoryRecord, 0);
}
if (record.LowerLevelDirectoryRecord != null) {
record.Add<uint>(DicomTag.OffsetOfReferencedLowerLevelDirectoryEntity, record.LowerLevelDirectoryRecord.Offset);
SetOffsets(record.LowerLevelDirectoryRecord);
} else {
record.Add<uint>(DicomTag.OffsetOfReferencedLowerLevelDirectoryEntity, 0);
}
}
private void AddDirectoryRecordsToSequenceItem(DicomDirectoryRecord recordItem) {
if (recordItem == null)
return;
_directoryRecordSequence.Items.Add(recordItem);
if (recordItem.LowerLevelDirectoryRecord != null)
AddDirectoryRecordsToSequenceItem(recordItem.LowerLevelDirectoryRecord);
if (recordItem.NextDirectoryRecord != null)
AddDirectoryRecordsToSequenceItem(recordItem.NextDirectoryRecord);
}