public GrayscalePixelDataS16(int width, int height, BitDepth bitDepth, IByteBuffer data)
{
_bits = bitDepth;
_width = width;
_height = height;
_data = ByteBufferEnumerator <short> .Create(data).ToArray();
if (bitDepth.BitsStored != 16)
{
int sign = 1 << bitDepth.HighBit;
int mask = (UInt16.MaxValue >> (bitDepth.BitsAllocated - bitDepth.BitsStored));
Parallel.For(0, _data.Length, (int i) => {
short d = _data[i];
if ((d & sign) != 0)
{
_data[i] = (short)-(((-d) & mask) + 1);
}
else
{
_data[i] = (short)(d & mask);
}
});
}
}
internal void Add(IByteBuffer fragment)
{
if (_offsetTable == null)
{
var en = ByteBufferEnumerator <uint> .Create(fragment);
_offsetTable = new List <uint>(en);
return;
}
_fragments.Add(fragment);
}
public GrayscalePixelDataU16(int width, int height, BitDepth bitDepth, IByteBuffer data)
{
_width = width;
_height = height;
_data = ByteBufferEnumerator <ushort> .Create(data).ToArray();
if (bitDepth.BitsStored != 16)
{
int mask = (1 << (bitDepth.HighBit + 1)) - 1;
Parallel.For(0, _data.Length, (int i) => {
_data[i] = (ushort)(_data[i] & mask);
});
}
}
public override T Get <T>(int item = -1)
{
if (!typeof(T).IsArray && item == -1)
{
item = 0;
}
if (typeof(T) == typeof(short))
{
return((T)(object)ByteBufferEnumerator <short> .Create(Buffer).ToArray().GetValue(item));
}
if (typeof(T) == typeof(short[]))
{
return((T)(object)ByteBufferEnumerator <short> .Create(Buffer).ToArray());
}
if (typeof(T) == typeof(ushort))
{
return((T)(object)ByteBufferEnumerator <ushort> .Create(Buffer).ToArray().GetValue(item));
}
if (typeof(T) == typeof(ushort[]))
{
return((T)(object)ByteBufferEnumerator <ushort> .Create(Buffer).ToArray());
}
if (typeof(T) == typeof(int))
{
return((T)(object)ByteBufferEnumerator <int> .Create(Buffer).ToArray().GetValue(item));
}
if (typeof(T) == typeof(int[]))
{
return((T)(object)ByteBufferEnumerator <int> .Create(Buffer).ToArray());
}
if (typeof(T) == typeof(uint))
{
return((T)(object)ByteBufferEnumerator <uint> .Create(Buffer).ToArray().GetValue(item));
}
if (typeof(T) == typeof(uint[]))
{
return((T)(object)ByteBufferEnumerator <uint> .Create(Buffer).ToArray());
}
if (typeof(T) == typeof(float))
{
return((T)(object)ByteBufferEnumerator <float> .Create(Buffer).ToArray().GetValue(item));
}
if (typeof(T) == typeof(float[]))
{
return((T)(object)ByteBufferEnumerator <float> .Create(Buffer).ToArray());
}
if (typeof(T) == typeof(double))
{
return((T)(object)ByteBufferEnumerator <double> .Create(Buffer).ToArray().GetValue(item));
}
if (typeof(T) == typeof(double[]))
{
return((T)(object)ByteBufferEnumerator <double> .Create(Buffer).ToArray());
}
return(base.Get <T>(item));
}
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 IByteBuffer Load()
{
var tag = OverlayTag(DicomTag.OverlayData);
if (Dataset.Contains(tag))
{
var elem = Dataset.FirstOrDefault(x => x.Tag == tag) as DicomElement;
return(elem.Buffer);
}
else
{
// overlay embedded in high bits of pixel data
if (Dataset.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(Dataset);
// (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);
var bits = new BitList();
bits.Capacity = Rows * Columns;
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.");
}
return(new MemoryByteBuffer(bits.Array));
}
}
