public void Create_TransferSyntaxExplicitLEBitsAllocatedLessThanOrEqualTo8_ReturnsOtherBytePixelDataObject(ushort bitsAllocated)
{
var dataset = new DicomDataset(DicomTransferSyntax.ExplicitVRLittleEndian);
dataset.Add(DicomTag.BitsAllocated, bitsAllocated);
var pixelData = DicomPixelData.Create(dataset, true);
Assert.Equal("OtherBytePixelData", pixelData.GetType().Name);
}
public void Create_TransferSyntaxExplicitLEBitsAllocatedGreaterThan16_ReturnsOtherWordPixelDataObject()
{
var dataset = new DicomDataset(DicomTransferSyntax.ExplicitVRLittleEndian);
dataset.Add(DicomTag.BitsAllocated, (ushort)32);
var pixelData = DicomPixelData.Create(dataset, true);
Assert.Equal("OtherWordPixelData", pixelData.GetType().Name);
}
public void Create_TransferSyntaxExplicitLEBitsAllocatedGreaterThan16_Throws()
{
var dataset = new DicomDataset(DicomTransferSyntax.ExplicitVRLittleEndian);
dataset.Add(DicomTag.BitsAllocated, (ushort)17);
var exception = Record.Exception(() => DicomPixelData.Create(dataset, true));
Assert.NotNull(exception);
}
/// <summary>
/// Loads the pixel data for specified frame and set the internal dataset
///
/// </summary>
/// <param name="dataset">dataset to load pixeldata from</param>
/// <param name="frame">The frame number to create pixeldata for</param>
private void Load(DicomDataset dataset, int frame)
{
Dataset = dataset;
if (PixelData == null)
{
PixelData = DicomPixelData.Create(Dataset);
PhotometricInterpretation = PixelData.PhotometricInterpretation;
}
if (Dataset.InternalTransferSyntax.IsEncapsulated)
{
// decompress single frame from source dataset
DicomCodecParams cparams = null;
if (Dataset.InternalTransferSyntax == DicomTransferSyntax.JPEGProcess1 || Dataset.InternalTransferSyntax == DicomTransferSyntax.JPEGProcess2_4)
{
cparams = new DicomJpegParams {
ConvertColorspaceToRGB = true
};
}
var transcoder = new DicomTranscoder(Dataset.InternalTransferSyntax, DicomTransferSyntax.ExplicitVRLittleEndian);
transcoder.InputCodecParams = cparams;
transcoder.OutputCodecParams = cparams;
var buffer = transcoder.DecodeFrame(Dataset, frame);
// clone the dataset because modifying the pixel data modifies the dataset
var clone = Dataset.Clone();
clone.InternalTransferSyntax = DicomTransferSyntax.ExplicitVRLittleEndian;
var pixelData = DicomPixelData.Create(clone, true);
pixelData.AddFrame(buffer);
// temporary fix for JPEG compressed YBR images
if ((Dataset.InternalTransferSyntax == DicomTransferSyntax.JPEGProcess1 || Dataset.InternalTransferSyntax == DicomTransferSyntax.JPEGProcess2_4) && pixelData.SamplesPerPixel == 3)
{
pixelData.PhotometricInterpretation = PhotometricInterpretation.Rgb;
}
_pixelData = PixelDataFactory.Create(pixelData, 0);
}
else
{
// pull uncompressed frame from source pixel data
_pixelData = PixelDataFactory.Create(PixelData, frame);
}
_pixelData.Rescale(_scale);
_overlays = DicomOverlayData.FromDataset(Dataset).Where(x => x.Type == DicomOverlayType.Graphics && x.Data != null).ToArray();
_currentFrame = frame;
CreatePipeline();
}
public void BitsStored_Setter_GreaterThanBitsAllocatedIsNotAllowed(ushort bitsAllocated, ushort bitsStored)
{
var dataset = new DicomDataset(DicomTransferSyntax.ExplicitVRLittleEndian);
dataset.Add(DicomTag.BitsAllocated, bitsAllocated);
var pixelData = DicomPixelData.Create(dataset, true);
var exception = Record.Exception(() => pixelData.BitsStored = bitsStored);
Assert.NotNull(exception);
}
/// <summary>
/// Loads the pixel data for specified frame and set the internal dataset
///
/// </summary>
/// <param name="dataset">dataset to load pixeldata from</param>
/// <param name="frame">The frame number to create pixeldata for</param>
private void Load(DicomDataset dataset, int frame)
{
Dataset = DicomTranscoder.ExtractOverlays(dataset);
if (PixelData == null)
{
PixelData = DicomPixelData.Create(Dataset);
PhotometricInterpretation = PixelData.PhotometricInterpretation;
}
if (frame < 0)
{
CurrentFrame = frame;
return;
}
if (Dataset.InternalTransferSyntax.IsEncapsulated)
{
// decompress single frame from source dataset
var transcoder = new DicomTranscoder(
this.Dataset.InternalTransferSyntax,
DicomTransferSyntax.ExplicitVRLittleEndian);
var buffer = transcoder.DecodeFrame(Dataset, frame);
// clone the dataset because modifying the pixel data modifies the dataset
var clone = Dataset.Clone();
clone.InternalTransferSyntax = DicomTransferSyntax.ExplicitVRLittleEndian;
var pixelData = DicomPixelData.Create(clone, true);
TrimDecodedPixelDataProperties(pixelData, Dataset.InternalTransferSyntax);
pixelData.AddFrame(buffer);
_pixelData = PixelDataFactory.Create(pixelData, 0);
}
else
{
// pull uncompressed frame from source pixel data
_pixelData = PixelDataFactory.Create(PixelData, frame);
}
_pixelData = _pixelData.Rescale(_scale);
_overlays =
DicomOverlayData.FromDataset(Dataset)
.Where(x => x.Type == DicomOverlayType.Graphics && x.Data != null)
.ToArray();
CurrentFrame = frame;
if (_pipeline == null)
{
CreatePipeline();
}
}
public void HighBit_Setter_SmallerThanBitsAllocatedIsAllowed(ushort bitsAllocated, ushort highBit)
{
var dataset = new DicomDataset(DicomTransferSyntax.ExplicitVRLittleEndian);
dataset.Add(DicomTag.BitsAllocated, bitsAllocated);
var pixelData = DicomPixelData.Create(dataset, true);
var exception = Record.Exception(() => pixelData.HighBit = highBit);
Assert.Null(exception);
Assert.Equal(highBit, pixelData.HighBit);
}
/// <summary>
/// Create <see cref="GrayscaleRenderOptions"/> from <paramref name="dataset"/> and populate the options properties with values:
/// Bit Depth
/// Rescale Slope
/// Rescale Intercept
/// Window Width
/// Window Center
/// </summary>
/// <param name="dataset">Dataset to extract <see cref="GrayscaleRenderOptions"/> from</param>
/// <returns>New grayscale render options instance</returns>
public static GrayscaleRenderOptions FromDataset(DicomDataset dataset)
{
var bits = BitDepth.FromDataset(dataset);
var options = new GrayscaleRenderOptions(bits);
options.RescaleSlope = dataset.Get <double>(DicomTag.RescaleSlope, 1.0);
options.RescaleIntercept = dataset.Get <double>(DicomTag.RescaleIntercept, 0.0);
if (dataset.Contains(DicomTag.WindowWidth) && dataset.Get <double>(DicomTag.WindowWidth) != 0.0)
{
//If dataset contains WindowWidth and WindowCenter valid attributes used initially for the grayscale options
options.WindowWidth = dataset.Get <double>(DicomTag.WindowWidth);
options.WindowCenter = dataset.Get <double>(DicomTag.WindowCenter);
}
else if (dataset.Contains(DicomTag.SmallestImagePixelValue) && dataset.Contains(DicomTag.LargestImagePixelValue))
{
//If dataset contains valid SmallesImagePixelValue and LargesImagePixelValue attributes, use range to calculage
//WindowWidth and WindowCenter
int smallValue = dataset.Get <int>(DicomTag.SmallestImagePixelValue, 0);
int largeValue = dataset.Get <int>(DicomTag.LargestImagePixelValue, 0);
largeValue = (int)((largeValue * options.RescaleSlope) + options.RescaleIntercept);
smallValue = (int)((smallValue * options.RescaleSlope) + options.RescaleIntercept);
if (smallValue != 0 || largeValue != 0)
{
options.WindowWidth = Math.Abs(largeValue - smallValue);
options.WindowCenter = (largeValue + smallValue) / 2.0;
}
}
else
{
//If reached here, minimum and maximum pixel values calculated from pixels data to calculate
//WindowWidth and WindowCenter
int padding = dataset.Get <int>(DicomTag.PixelPaddingValue, 0, bits.MinimumValue);
var pixelData = DicomPixelData.Create(dataset);
var pixels = PixelDataFactory.Create(pixelData, 0);
var range = pixels.GetMinMax(padding);
range.Maximum = (int)((range.Maximum * options.RescaleSlope) + options.RescaleIntercept);
range.Minimum = (int)((range.Minimum * options.RescaleSlope) + options.RescaleIntercept);
options.WindowWidth = Math.Abs(range.Maximum - range.Minimum);
options.WindowCenter = (range.Maximum + range.Minimum) / 2.0;
}
options.VOILUTFunction = dataset.Get <string>(DicomTag.VOILUTFunction, "LINEAR");
options.Monochrome1 = dataset.Get <PhotometricInterpretation>(DicomTag.PhotometricInterpretation) == PhotometricInterpretation.Monochrome1;
return(options);
}
private void Load(DicomDataset dataset)
{
Dataset = dataset;
if (Dataset.InternalTransferSyntax.IsEncapsulated)
{
Dataset = Dataset.ChangeTransferSyntax(DicomTransferSyntax.ExplicitVRLittleEndian, null);
}
DicomPixelData pixelData = DicomPixelData.Create(Dataset);
_pixelData = PixelDataFactory.Create(pixelData, 0);
_overlays = DicomOverlayData.FromDataset(Dataset);
}
/// <summary>
/// Create pixel data object based on <paramref name="dataset"/>.
/// </summary>
/// <param name="dataset">Dataset containing pixel data.</param>
/// <returns>For non-encapsulated dataset, create pixel data object from original pixel data. For encapsulated dataset,
/// create "empty" pixel data object to subsequentially be filled with uncompressed data for each frame.</returns>
private static DicomPixelData CreateDicomPixelData(DicomDataset dataset)
{
var inputTransferSyntax = dataset.InternalTransferSyntax;
if (!inputTransferSyntax.IsEncapsulated)
{
return(DicomPixelData.Create(dataset));
}
// Clone the encapsulated dataset because modifying the pixel data modifies the dataset
var clone = dataset.Clone();
clone.InternalTransferSyntax = DicomTransferSyntax.ExplicitVRLittleEndian;
var pixelData = DicomPixelData.Create(clone, true);
// temporary fix for JPEG compressed YBR images, according to enforcement above
if ((inputTransferSyntax == DicomTransferSyntax.JPEGProcess1 ||
inputTransferSyntax == DicomTransferSyntax.JPEGProcess2_4) && pixelData.SamplesPerPixel == 3)
{
// When converting to RGB in Dicom.Imaging.Codec.Jpeg.i, PlanarConfiguration is set to Interleaved
pixelData.PhotometricInterpretation = PhotometricInterpretation.Rgb;
pixelData.PlanarConfiguration = PlanarConfiguration.Interleaved;
}
// temporary fix for JPEG 2000 Lossy images
if ((inputTransferSyntax == DicomTransferSyntax.JPEG2000Lossy &&
pixelData.PhotometricInterpretation == PhotometricInterpretation.YbrIct) ||
(inputTransferSyntax == DicomTransferSyntax.JPEG2000Lossless &&
pixelData.PhotometricInterpretation == PhotometricInterpretation.YbrRct))
{
// Converted to RGB in Dicom.Imaging.Codec.Jpeg2000.cpp
pixelData.PhotometricInterpretation = PhotometricInterpretation.Rgb;
}
// temporary fix for JPEG2000 compressed YBR images
if ((inputTransferSyntax == DicomTransferSyntax.JPEG2000Lossless ||
inputTransferSyntax == DicomTransferSyntax.JPEG2000Lossy) &&
(pixelData.PhotometricInterpretation == PhotometricInterpretation.YbrFull ||
pixelData.PhotometricInterpretation == PhotometricInterpretation.YbrFull422 ||
pixelData.PhotometricInterpretation == PhotometricInterpretation.YbrPartial422))
{
// For JPEG2000 YBR type images in Dicom.Imaging.Codec.Jpeg2000.cpp,
// YBR_FULL is applied and PlanarConfiguration is set to Planar
pixelData.PhotometricInterpretation = PhotometricInterpretation.YbrFull;
pixelData.PlanarConfiguration = PlanarConfiguration.Planar;
}
return(pixelData);
}
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 = Columns;
int oh = Rows;
var frame = pixels.GetFrame(0);
var bits = new BitList();
bits.Capacity = Rows * Columns;
int mask = 1 << BitPosition;
// Sanity check: do not collect overlay data if Overlay Bit Position is within the used pixel range. (#110)
if (this.BitPosition <= pixels.HighBit && this.BitPosition > pixels.HighBit - pixels.BitsStored)
{
// Do nothing
}
else if (pixels.BitsAllocated == 8)
{
var data = IO.ByteConverter.ToArray <byte>(frame);
for (int y = 0; y < oh; y++)
{
int n = (y + oy) * pixels.Width + ox;
int i = y * Columns;
for (int x = 0; 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 = IO.ByteConverter.ToArray <ushort>(frame);
for (int y = 0; y < oh; y++)
{
int n = (y + oy) * pixels.Width + ox;
int i = y * Columns;
for (int x = 0; 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));
}
}
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));
}
}