public void GetCodec_KnownTransferSyntax_ShouldReturnCodecObject(DicomTransferSyntax transferSyntax, string expected)
{
var codec = DicomTranscoder.GetCodec(transferSyntax);
var actual = codec.Name;
Assert.Equal(expected, actual);
}
public static DicomFile ChangeTransferSyntax(this DicomFile file, DicomTransferSyntax syntax, DicomCodecParams parameters = null)
{
DicomTranscoder transcoder = new DicomTranscoder(file.FileMetaInfo.TransferSyntax, syntax);
transcoder.OutputCodecParams = parameters;
return(transcoder.Transcode(file));
}
public static DicomDataset ChangeTransferSyntax(this DicomDataset dataset, DicomTransferSyntax syntax, DicomCodecParams parameters = null)
{
DicomTranscoder transcoder = new DicomTranscoder(dataset.InternalTransferSyntax, syntax);
transcoder.OutputCodecParams = parameters;
return(transcoder.Transcode(dataset));
}
/// <summary>
/// Create a copy of the specified DICOM dataset with requested transfer syntax.
/// </summary>
/// <param name="dataset">DICOM dataset to copy.</param>
/// <param name="syntax">Requested transfer syntax for the created DICOM dataset.</param>
/// <param name="parameters">Codec parameters.</param>
/// <returns>DICOM dataset with modified transfer syntax.</returns>
public static DicomDataset Clone(
this DicomDataset dataset,
DicomTransferSyntax syntax,
DicomCodecParams parameters = null)
{
var transcoder = new DicomTranscoder(dataset.InternalTransferSyntax, syntax, null, parameters);
return(transcoder.Transcode(dataset));
}
/// <summary>
/// Create a copy of the specified DICOM file with requested transfer syntax.
/// </summary>
/// <param name="file">DICOM file to copy.</param>
/// <param name="syntax">Requested transfer syntax for the created DICOM file.</param>
/// <param name="parameters">Codec parameters.</param>
/// <returns>DICOM file with modified transfer syntax.</returns>
public static DicomFile Clone(
this DicomFile file,
DicomTransferSyntax syntax,
DicomCodecParams parameters = null)
{
var transcoder = new DicomTranscoder(file.FileMetaInfo.TransferSyntax, syntax, null, parameters);
return(transcoder.Transcode(file));
}
public static GrayscaleRenderOptions FromMinMax(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);
int padding = dataset.Get<int>(DicomTag.PixelPaddingValue, 0, Int32.MinValue);
var transcoder = new DicomTranscoder(dataset.InternalTransferSyntax, DicomTransferSyntax.ExplicitVRLittleEndian);
var pixels = transcoder.DecodePixelData(dataset, 0);
var range = pixels.GetMinMax(padding);
if (range.Minimum < bits.MinimumValue || range.Minimum == Double.MaxValue)
range.Minimum = bits.MinimumValue;
if (range.Maximum > bits.MaximumValue || range.Maximum == Double.MinValue)
range.Maximum = bits.MaximumValue;
options.WindowWidth = Math.Abs(range.Maximum - range.Minimum);
options.WindowCenter = range.Minimum + (options.WindowWidth / 2.0);
options.VOILUTFunction = dataset.Get<string>(DicomTag.VOILUTFunction, "LINEAR");
options.Monochrome1 = dataset.Get<PhotometricInterpretation>(DicomTag.PhotometricInterpretation) == PhotometricInterpretation.Monochrome1;
return options;
}
public static GrayscaleRenderOptions FromHistogram(DicomDataset dataset, int percent = 90)
{
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);
var transcoder = new DicomTranscoder(dataset.InternalTransferSyntax, DicomTransferSyntax.ExplicitVRLittleEndian);
var pixels = transcoder.DecodePixelData(dataset, 0);
var histogram = pixels.GetHistogram(0);
int padding = dataset.Get<int>(DicomTag.PixelPaddingValue, 0, Int32.MinValue);
if (padding != Int32.MinValue)
histogram.Clear(padding);
histogram.ApplyWindow(percent);
options.WindowWidth = histogram.WindowEnd - histogram.WindowStart;
options.WindowCenter = histogram.WindowStart + (options.WindowWidth / 2.0);
options.VOILUTFunction = dataset.Get<string>(DicomTag.VOILUTFunction, "LINEAR");
options.Monochrome1 = dataset.Get<PhotometricInterpretation>(DicomTag.PhotometricInterpretation) == PhotometricInterpretation.Monochrome1;
return options;
}
/// <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;
// temporary fix for JPEG 2000 Lossy images
if (pixelData.PhotometricInterpretation == PhotometricInterpretation.YbrIct || pixelData.PhotometricInterpretation == PhotometricInterpretation.YbrRct)
pixelData.PhotometricInterpretation = PhotometricInterpretation.Rgb;
_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;
CreatePipeline();
}
/// <summary>
/// Create grayscale render options based on pixel data histogram.
/// </summary>
/// <param name="dataset">DICOM dataset from which render options should be obtained.</param>
/// <param name="percent">Percentage of histogram window to include.</param>
/// <returns>Grayscale render options based on pixel data histogram.</returns>
public static GrayscaleRenderOptions FromHistogram(DicomDataset dataset, int percent = 90)
{
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);
var transcoder = new DicomTranscoder(
dataset.InternalTransferSyntax,
DicomTransferSyntax.ExplicitVRLittleEndian);
var pixels = transcoder.DecodePixelData(dataset, 0);
var histogram = pixels.GetHistogram(0);
int padding = dataset.Get<int>(DicomTag.PixelPaddingValue, 0, Int32.MinValue);
if (padding != Int32.MinValue) histogram.Clear(padding);
histogram.ApplyWindow(percent);
var min = histogram.WindowStart * options.RescaleSlope + options.RescaleIntercept;
var max = histogram.WindowEnd * options.RescaleSlope + options.RescaleIntercept;
options.WindowWidth = Math.Abs(max - min);
options.WindowCenter = (max + min) / 2.0;
options.VOILUTFunction = dataset.Get<string>(DicomTag.VOILUTFunction, "LINEAR");
options.ColorMap = GetColorMap(dataset);
return options;
}
/// <summary>
/// Create grayscale render options based on identified minimum and maximum pixel values.
/// </summary>
/// <param name="dataset">DICOM dataset from which render options should be obtained.</param>
/// <returns>Grayscale render options based on identified minimum and maximum pixel values.</returns>
public static GrayscaleRenderOptions FromMinMax(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);
int padding = dataset.Get<int>(DicomTag.PixelPaddingValue, 0, Int32.MinValue);
var transcoder = new DicomTranscoder(
dataset.InternalTransferSyntax,
DicomTransferSyntax.ExplicitVRLittleEndian);
var pixels = transcoder.DecodePixelData(dataset, 0);
var range = pixels.GetMinMax(padding);
if (range.Minimum < bits.MinimumValue || range.Minimum == Double.MaxValue) range.Minimum = bits.MinimumValue;
if (range.Maximum > bits.MaximumValue || range.Maximum == Double.MinValue) range.Maximum = bits.MaximumValue;
var min = range.Minimum * options.RescaleSlope + options.RescaleIntercept;
var max = range.Maximum * options.RescaleSlope + options.RescaleIntercept;
options.WindowWidth = Math.Abs(max - min);
options.WindowCenter = (max + min) / 2.0;
options.VOILUTFunction = dataset.Get<string>(DicomTag.VOILUTFunction, "LINEAR");
options.ColorMap = GetColorMap(dataset);
return options;
}
public static DicomFile ChangeTransferSyntax(this DicomFile file, DicomTransferSyntax syntax, DicomCodecParams parameters = null) {
DicomTranscoder transcoder = new DicomTranscoder(file.FileMetaInfo.TransferSyntax, syntax);
transcoder.InputCodecParams = parameters;
transcoder.OutputCodecParams = parameters;
return transcoder.Transcode(file);
}
public static DicomDataset ChangeTransferSyntax(this DicomDataset dataset, DicomTransferSyntax syntax, DicomCodecParams parameters = null) {
DicomTranscoder transcoder = new DicomTranscoder(dataset.InternalTransferSyntax, syntax);
transcoder.InputCodecParams = parameters;
transcoder.OutputCodecParams = parameters;
return transcoder.Transcode(dataset);
}