public void Display(DicomDirectoryRecord record)
{
switch (record.DirectoryRecordType)
{
case "PATIENT":
ShowPatientLevelInfo(record);
break;
case "STUDY":
ShowStudyLevelInfo(record);
break;
case "SERIES":
ShowSeriesLevelInfo(record);
break;
case "IMAGE":
ShowImageLevelInfo(record);
break;
default:
_log($"Unknown directory record type: {record.DirectoryRecordType}. " +
$"Please check your inputs");
break;
}
;
}
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);
}
public byte[] DICOMSeriesToVolume(DicomDirectoryRecord series, out Int3 size)
{
size = GetSizeForRecord(series);
var voxels = new VolumeBuffer <Color32>(size);
var tex = new Texture2D(2, 2);
var instanceNumbers = series.LowerLevelDirectoryRecordCollection.Select(x => x.Get <int>(DicomTag.InstanceNumber)).OrderBy(x => x).ToArray();
for (var z = 0; z < instanceNumbers.Length; z++)
{
var frame = instanceNumbers[z];
tex = loadDicomInstance.GetTexture2DForRecord(series, frame);
var fromPixels = tex.GetPixels32();
for (var y = 0; y < size.y; y++)
{
for (var x = 0; x < size.x; x++)
{
var from = fromPixels[x * resolution + ((size.y - 1 - y) * size.x) * resolution * 2];
voxels.SetVoxel(new Int3(x, y, z), from);
}
}
}
voxels.ClearEdges(new Color32(0, 0, 0, 0));
return(VolumeTextureUtils.Color32ArrayToByteArray(voxels.DataArray));
}
private static ImageRecord ToImage(DicomDirectoryRecord record)
{
ImageRecord image = new ImageRecord();
image.SOPInstanceUID = record.GetSingleValue <string>(DicomTag.ReferencedSOPInstanceUIDInFile);
image.ImageNumber = record.GetSingleValueOrDefault <string>(DicomTag.InstanceNumber, null);
image.ReferencedFileID = record.GetValueOrDefault <string>(DicomTag.ReferencedFileID, 0, null);
return(image);
}
static DicomDirectoryRecord GetSeries(DicomDirectoryRecord record)
{
if (record.DirectoryRecordType == "IMAGE")
{
return(record);
}
while (record.DirectoryRecordType != "SERIES")
{
record = record.LowerLevelDirectoryRecord;
}
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 Texture2D GetTexture2DForRecord(DicomDirectoryRecord record, int frame = -1)
{
var tex = new Texture2D(1, 1);
try
{
var img = GetImageForRecord(record, frame);
//var s = Time.realtimeSinceStartup;
tex = DicomToTex2D(img);
//Debug.Log("DicomToText2D took " + (Time.realtimeSinceStartup - s));
}
catch
{
}
return(tex);
}
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);
}
public DicomImage GetImageForRecord(DicomDirectoryRecord record, int frame = -1)
{
var directory = rootDirectoryMap[record];
var series = GetSeries(record);
var absoluteFilename = "";
var instanceNumbers = series.LowerLevelDirectoryRecordCollection.Select(x => x.Get <int>(DicomTag.InstanceNumber)).OrderBy(x => x).ToArray();
if (frame == 0)
{
frame = instanceNumbers[0];
}
if (frame == -1) // get thumbnail - get midpoint image
{
frame = instanceNumbers[instanceNumbers.Length / 2];
}
if (frame == -2) // get last
{
frame = instanceNumbers[instanceNumbers.Length - 1];
}
try
{
var imageRecord = series.LowerLevelDirectoryRecordCollection.First(x => x.Get <int>(DicomTag.InstanceNumber) == frame);
var filename = Path.Combine(imageRecord.Get <string[]>(DicomTag.ReferencedFileID));
absoluteFilename = Path.Combine(directory, filename);
//Debug.Log("load image " + absoluteFilename);
var img = new DicomImage(absoluteFilename);
return(img);
}
catch (InvalidOperationException)
{
Debug.LogError("series does not contain an image of InstanceNumber=" + frame + "- valid instance numbers = " + string.Join(",", instanceNumbers));
return(null);
}
catch (System.Exception e)
{
Debug.LogError("Failed to load " + absoluteFilename + ":" + e);
return(null);
}
}
string GetDicomName(DicomDirectoryRecord r, string infoParent, int count = -1)
{
string name = "";
try
{
if (infoParent is null || infoParent.Length == 0)
{
name = r.Get <string>(DicomTag.PatientName, -1);
}
else if (infoParent.StartsWith("dicom:patient"))
{
try
{
name = r.Get <string>(DicomTag.StudyDescription, -1);
}
catch
{
}
name += " - " + r.Get <string>(DicomTag.StudyDate, -1) + " " + r.Get <string>(DicomTag.StudyTime, -1);
}
else if (infoParent.StartsWith("dicom:study"))
{
try
{
name = r.Get <string>(DicomTag.SeriesNumber, -1);
}
catch
{
}
name += " - " + r.Get <string>(DicomTag.SeriesDate, -1) + " " + r.Get <string>(DicomTag.SeriesTime, -1);
}
else if (infoParent.StartsWith("dicom:series"))
{
name = Path.GetFileName(r.Get <string>(DicomTag.ReferencedFileID, -1));
}
}
public string GetDicomTag(DicomDirectoryRecord record, DicomTag tag)
{
return(string.Join(",", record.Get <string[]>(tag, new string[] { "" })));
}
public Int3 GetSizeForRecord(DicomDirectoryRecord series)
{
var img = loadDicomInstance.GetImageForRecord(series);
return(new Int3(img.Width / resolution, img.Height / resolution, series.LowerLevelDirectoryRecordCollection.Count()));
}