public void OverlayTypeGetter_TypeSetToR_ReturnsROI()
{
const DicomOverlayType expected = DicomOverlayType.ROI;
const ushort group = 0x6012;
var dataset = new DicomDataset();
var od = new DicomOverlayData(dataset, group);
dataset.AddOrUpdate(new DicomTag(group, 0x0040), "R");
var actual = od.Type;
Assert.Equal(expected, actual);
}
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
}