/// <summary>
/// Returns the value of the tag within the given dataset. Throws an exception if the tag was not present or if the
/// tag value cannot be converted to type T.
/// </summary>
/// <typeparam name="T">The expected return type of the DICOM attribute.</typeparam>
/// <param name="dataset">The DICOM dataset you wish to extract the tag from</param>
/// <param name="tag">The tag you wish to extract from the dataset</param>
/// <param name="i">For multivalue tags, specify the ith element to return</param>
/// <returns>The required DICOM attribute as type T.</returns>
/// <exception cref="ArgumentException">The dataset did not contain the expected tag or the DICOM tag does not have a value at index 'i'.</exception>
/// <exception cref="ArgumentNullException">The DICOM dataset or DICOM tag provided was null.</exception>
/// <exception cref="InvalidCastException">The DICOM tag could not be converted into the expected type.</exception>
public static T GetRequiredDicomAttribute <T>(this DicomDataset dataset, DicomTag tag, uint i = 0)
{
dataset = dataset ?? throw new ArgumentNullException(nameof(dataset));
tag = tag ?? throw new ArgumentNullException(nameof(tag));
// Attempt to find the expected tag in the DICOM dataset.
if (!(dataset.FirstOrDefault(x => x.Tag == tag) is DicomElement dicomElement))
{
throw new ArgumentException($"The DICOM dataset does not contain the required attribute: {tag}.");
}
if (i >= dicomElement.Count)
{
throw new ArgumentException($"The DICOM tag {tag} only has {dicomElement.Count} parts. Expected to get value at index {i}.");
}
try
{
// Attempt to cast the i(th) element to the expected return type.
return(dicomElement.Get <T>((int)i));
}
catch (Exception)
{
throw new InvalidCastException($"The attribute: {tag} could not be converted to the expected type: {typeof(T)}.");
}
}
private void Load(DicomDataset ds)
{
_rows = ds.Get <ushort>(OverlayTag(DicomTag.OverlayRows));
_columns = ds.Get <ushort>(OverlayTag(DicomTag.OverlayColumns));
_type = ds.Get <string>(OverlayTag(DicomTag.OverlayType), "Unknown");
DicomTag tag = OverlayTag(DicomTag.OverlayOrigin);
if (ds.Contains(tag))
{
short[] xy = ds.Get <short[]>(tag);
if (xy != null && xy.Length == 2)
{
_originX = xy[0];
_originY = xy[1];
}
}
_bitsAllocated = ds.Get <ushort>(OverlayTag(DicomTag.OverlayBitsAllocated), 0, 1);
_bitPosition = ds.Get <ushort>(OverlayTag(DicomTag.OverlayBitPosition), 0, 0);
tag = OverlayTag(DicomTag.OverlayData);
if (ds.Contains(tag))
{
var elem = ds.FirstOrDefault(x => x.Tag == tag) as DicomElement;
_data = elem.Buffer;
}
_description = ds.Get <string>(OverlayTag(DicomTag.OverlayDescription), String.Empty);
_subtype = ds.Get <string>(OverlayTag(DicomTag.OverlaySubtype), String.Empty);
_label = ds.Get <string>(OverlayTag(DicomTag.OverlayLabel), String.Empty);
_frames = ds.Get <int>(OverlayTag(DicomTag.NumberOfFramesInOverlay), 0, 1);
_frameOrigin = ds.Get <ushort>(OverlayTag(DicomTag.ImageFrameOrigin), 0, 1);
//TODO: include ROI
}
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 void Load(DicomDataset ds) {
_rows = ds.Get<ushort>(OverlayTag(DicomTag.OverlayRows));
_columns = ds.Get<ushort>(OverlayTag(DicomTag.OverlayColumns));
var type = ds.Get<string>(OverlayTag(DicomTag.OverlayType), "Unknown");
if (type.StartsWith("R"))
_type = DicomOverlayType.ROI;
else
_type = DicomOverlayType.Graphics;
DicomTag tag = OverlayTag(DicomTag.OverlayOrigin);
if (ds.Contains(tag)) {
_originX = ds.Get<short>(tag, 0, 1);
_originY = ds.Get<short>(tag, 1, 1);
}
_bitsAllocated = ds.Get<ushort>(OverlayTag(DicomTag.OverlayBitsAllocated), 0, 1);
_bitPosition = ds.Get<ushort>(OverlayTag(DicomTag.OverlayBitPosition), 0, 0);
tag = OverlayTag(DicomTag.OverlayData);
if (ds.Contains(tag)) {
var elem = ds.FirstOrDefault(x => x.Tag == tag) as DicomElement;
_data = elem.Buffer;
} else {
// overlay embedded in high bits of pixel data
if (ds.InternalTransferSyntax.IsEncapsulated)
throw new DicomImagingException("Attempted to extract embedded overlay from compressed pixel data. Decompress pixel data before attempting this operation.");
var pixels = DicomPixelData.Create(ds);
// (1,1) indicates top left pixel of image
int ox = Math.Max(0, _originX - 1);
int oy = Math.Max(0, _originY - 1);
int ow = Math.Min(_rows, pixels.Width - _rows - ox);
int oh = Math.Min(_columns, pixels.Height - _columns - oy);
var frame = pixels.GetFrame(0);
// calculate length of output buffer
var count = (_rows * _columns) / 8;
if (((_rows * _columns) % 8) != 0)
count++;
if ((count & 1) != 0)
count++;
var bytes = new byte[count];
var bits = new BitArray(bytes);
int mask = 1 << _bitPosition;
if (pixels.BitsAllocated == 8) {
var data = ByteBufferEnumerator<byte>.Create(frame).ToArray();
for (int y = oy; y < oh; y++) {
int n = (y * pixels.Width) + ox;
int i = (y - oy) * _columns;
for (int x = ox; x < ow; x++) {
if ((data[n] & mask) != 0)
bits[i] = true;
n++;
i++;
}
}
} else if (pixels.BitsAllocated == 16) {
// we don't really care if the pixel data is signed or not
var data = ByteBufferEnumerator<ushort>.Create(frame).ToArray();
for (int y = oy; y < oh; y++) {
int n = (y * pixels.Width) + ox;
int i = (y - oy) * _columns;
for (int x = ox; x < ow; x++) {
if ((data[n] & mask) != 0)
bits[i] = true;
n++;
i++;
}
}
} else {
throw new DicomImagingException("Unable to extract embedded overlay from pixel data with bits stored greater than 16.");
}
_data = new MemoryByteBuffer(bytes);
}
_description = ds.Get<string>(OverlayTag(DicomTag.OverlayDescription), String.Empty);
_subtype = ds.Get<string>(OverlayTag(DicomTag.OverlaySubtype), String.Empty);
_label = ds.Get<string>(OverlayTag(DicomTag.OverlayLabel), String.Empty);
_frames = ds.Get<int>(OverlayTag(DicomTag.NumberOfFramesInOverlay), 0, 1);
_frameOrigin = ds.Get<ushort>(OverlayTag(DicomTag.ImageFrameOrigin), 0, 1);
//TODO: include ROI
}
private void Load(DicomDataset ds)
{
_rows = ds.Get <ushort>(OverlayTag(DicomTag.OverlayRows));
_columns = ds.Get <ushort>(OverlayTag(DicomTag.OverlayColumns));
var type = ds.Get <string>(OverlayTag(DicomTag.OverlayType), "Unknown");
if (type.StartsWith("R"))
{
_type = DicomOverlayType.ROI;
}
else
{
_type = DicomOverlayType.Graphics;
}
DicomTag tag = OverlayTag(DicomTag.OverlayOrigin);
if (ds.Contains(tag))
{
_originX = ds.Get <short>(tag, 0, 1);
_originY = ds.Get <short>(tag, 1, 1);
}
_bitsAllocated = ds.Get <ushort>(OverlayTag(DicomTag.OverlayBitsAllocated), 0, 1);
_bitPosition = ds.Get <ushort>(OverlayTag(DicomTag.OverlayBitPosition), 0, 0);
tag = OverlayTag(DicomTag.OverlayData);
if (ds.Contains(tag))
{
var elem = ds.FirstOrDefault(x => x.Tag == tag) as DicomElement;
_data = elem.Buffer;
}
else
{
// overlay embedded in high bits of pixel data
if (ds.InternalTransferSyntax.IsEncapsulated)
{
throw new DicomImagingException("Attempted to extract embedded overlay from compressed pixel data. Decompress pixel data before attempting this operation.");
}
var pixels = DicomPixelData.Create(ds);
// (1,1) indicates top left pixel of image
int ox = Math.Max(0, _originX - 1);
int oy = Math.Max(0, _originY - 1);
int ow = _rows - (pixels.Width - _rows - ox);
int oh = _columns - (pixels.Height - _columns - oy);
var frame = pixels.GetFrame(0);
// calculate length of output buffer
var count = (_rows * _columns) / 8;
if (((_rows * _columns) % 8) != 0)
{
count++;
}
if ((count & 1) != 0)
{
count++;
}
var bytes = new byte[count];
var bits = new BitArray(bytes);
int mask = 1 << _bitPosition;
if (pixels.BitsAllocated == 8)
{
var data = ByteBufferEnumerator <byte> .Create(frame).ToArray();
for (int y = oy; y < oh; y++)
{
int n = (y * pixels.Width) + ox;
int i = (y - oy) * _columns;
for (int x = ox; x < ow; x++)
{
if ((data[n] & mask) != 0)
{
bits[i] = true;
}
n++;
i++;
}
}
}
else if (pixels.BitsAllocated == 16)
{
// we don't really care if the pixel data is signed or not
var data = ByteBufferEnumerator <ushort> .Create(frame).ToArray();
for (int y = oy; y < oh; y++)
{
int n = (y * pixels.Width) + ox;
int i = (y - oy) * _columns;
for (int x = ox; x < ow; x++)
{
if ((data[n] & mask) != 0)
{
bits[i] = true;
}
n++;
i++;
}
}
}
else
{
throw new DicomImagingException("Unable to extract embedded overlay from pixel data with bits stored greater than 16.");
}
_data = new MemoryByteBuffer(bytes);
}
_description = ds.Get <string>(OverlayTag(DicomTag.OverlayDescription), String.Empty);
_subtype = ds.Get <string>(OverlayTag(DicomTag.OverlaySubtype), String.Empty);
_label = ds.Get <string>(OverlayTag(DicomTag.OverlayLabel), String.Empty);
_frames = ds.Get <int>(OverlayTag(DicomTag.NumberOfFramesInOverlay), 0, 1);
_frameOrigin = ds.Get <ushort>(OverlayTag(DicomTag.ImageFrameOrigin), 0, 1);
//TODO: include ROI
}
private void Load(DicomDataset ds)
{
_rows = ds.Get<ushort>(OverlayTag(DicomTag.OverlayRows));
_columns = ds.Get<ushort>(OverlayTag(DicomTag.OverlayColumns));
_type = ds.Get<string>(OverlayTag(DicomTag.OverlayType), "Unknown");
DicomTag tag = OverlayTag(DicomTag.OverlayOrigin);
if (ds.Contains(tag)) {
short[] xy = ds.Get<short[]>(tag);
if (xy != null && xy.Length == 2) {
_originX = xy[0];
_originY = xy[1];
}
}
_bitsAllocated = ds.Get<ushort>(OverlayTag(DicomTag.OverlayBitsAllocated), 0, 1);
_bitPosition = ds.Get<ushort>(OverlayTag(DicomTag.OverlayBitPosition), 0, 0);
tag = OverlayTag(DicomTag.OverlayData);
if (ds.Contains(tag)) {
var elem = ds.FirstOrDefault(x => x.Tag == tag) as DicomElement;
_data = elem.Buffer;
}
_description = ds.Get<string>(OverlayTag(DicomTag.OverlayDescription), String.Empty);
_subtype = ds.Get<string>(OverlayTag(DicomTag.OverlaySubtype), String.Empty);
_label = ds.Get<string>(OverlayTag(DicomTag.OverlayLabel), String.Empty);
_frames = ds.Get<int>(OverlayTag(DicomTag.NumberOfFramesInOverlay), 0, 1);
_frameOrigin = ds.Get<ushort>(OverlayTag(DicomTag.ImageFrameOrigin), 0, 1);
//TODO: include ROI
}
