/// <summary>
/// Creates a DICOM overlay from a GDI+ Bitmap.
/// </summary>
/// <param name="ds">Dataset</param>
/// <param name="bitmap">Bitmap</param>
/// <param name="mask">Color mask for overlay</param>
/// <returns>DICOM overlay</returns>
public static DicomOverlayData FromBitmap(DicomDataset ds, Bitmap bitmap, Color mask)
{
ushort group = 0x6000;
while (ds.Contains(new DicomTag(group, DicomTag.OverlayBitPosition.Element))) group += 2;
var overlay = new DicomOverlayData(ds, group)
{
Type = DicomOverlayType.Graphics,
Rows = bitmap.Height,
Columns = bitmap.Width,
OriginX = 1,
OriginY = 1,
BitsAllocated = 1,
BitPosition = 1
};
var array = new BitList { Capacity = overlay.Rows * overlay.Columns };
int p = 0;
for (var y = 0; y < bitmap.Height; y++)
{
for (var x = 0; x < bitmap.Width; x++, p++)
{
if (bitmap.GetPixel(x, y).ToArgb() == mask.ToArgb()) array[p] = true;
}
}
overlay.Data = EvenLengthBuffer.Create(new MemoryByteBuffer(array.Array));
return overlay;
}
/// <summary>
/// Gets all overlays in a DICOM dataset.
/// </summary>
/// <param name="ds">Dataset</param>
/// <returns>Array of overlays</returns>
public static DicomOverlayData[] FromDataset(DicomDataset ds)
{
var groups = new List <ushort>();
groups.AddRange(
ds.Where(x => x.Tag.Group >= 0x6000 && x.Tag.Group <= 0x60FF && x.Tag.Element == 0x0010)
.Select(x => x.Tag.Group));
var overlays = new List <DicomOverlayData>();
foreach (var group in groups)
{
// ensure that 6000 group is actually an overlay group
if (ds.Get <DicomElement>(new DicomTag(group, 0x0010)).ValueRepresentation != DicomVR.US)
{
continue;
}
try
{
DicomOverlayData overlay = new DicomOverlayData(ds, group);
overlays.Add(overlay);
}
catch
{
// bail out if not an overlay group
}
}
return(overlays.ToArray());
}
/// <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 OverlayTypeGetter_TypeNotSet_ShouldThrow()
{
const ushort group = 0x6008;
var dataset = new DicomDataset();
var od = new DicomOverlayData(dataset, group);
var exception = Record.Exception(() => od.Type);
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 OverlayTypeGetter_TypeSetToOtherThanRAndG_ShouldThrow()
{
const ushort group = 0x6001;
var dataset = new DicomDataset();
var od = new DicomOverlayData(dataset, group);
dataset.AddOrUpdate(new DicomTag(group, 0x0040), "O");
var exception = Record.Exception(() => od.Type);
Assert.NotNull(exception);
}
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);
}
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);
}
public void OriginYGetter_ReturnsValueAtIndex0()
{
const int expected = 42;
const ushort group = 0x6012;
var dataset = new DicomDataset();
var od = new DicomOverlayData(dataset, group);
dataset.AddOrUpdate(new DicomTag(group, 0x0050), "42", "0");
var actual = od.OriginY;
Assert.Equal(expected, actual);
}
public void OriginYSetter_ReturnsValueAtIndex0()
{
const int expected = 96;
const ushort group = 0x6012;
DicomDataset dataset = new DicomDataset();
DicomOverlayData overlayData = new DicomOverlayData(dataset, group);
overlayData.OriginY = expected;
int originY = dataset.GetValueOrDefault <short>(new DicomTag(group, 0x0050), 0, 1);
Assert.Equal(expected, originY);
}
/// <summary>
/// Gets all overlays in a DICOM dataset.
/// </summary>
/// <param name="ds">Dataset</param>
/// <returns>Array of overlays</returns>
public static DicomOverlayData[] FromDataset(DicomDataset ds)
{
var groups = new List <ushort>();
groups.AddRange(ds.Where(x => x.Tag.Group >= 0x6000 && x.Tag.Group <= 0x60FF && x.Tag.Element == 0x0010).Select(x => x.Tag.Group));
var overlays = new List <DicomOverlayData>();
foreach (var group in groups)
{
DicomOverlayData overlay = new DicomOverlayData(ds, group);
overlays.Add(overlay);
}
return(overlays.ToArray());
}
public void OverlayTypeSetter_SetToROI_ReturnsR()
{
const string expected = "R";
const ushort group = 0x6011;
var dataset = new DicomDataset();
var od = new DicomOverlayData(dataset, group)
{
Type = DicomOverlayType.ROI
};
var actual = dataset.Get <string>(new DicomTag(group, 0x0040));
Assert.Equal(expected, actual);
}
public void Constructor_GroupSpecified_GroupTransferredToDescription()
{
const string expected = "Description 6002";
const ushort group = 0x6002;
var dataset = new DicomDataset();
var od = new DicomOverlayData(dataset, group)
{
Description = expected
};
var actual = dataset.Get <string>(new DicomTag(group, 0x0022));
Assert.Equal(expected, actual);
}
public void Constructor_GroupSpecified_GroupTransferredToSubtype()
{
const string expected = "Subtype 6005";
const ushort group = 0x6005;
var dataset = new DicomDataset();
var od = new DicomOverlayData(dataset, group)
{
Subtype = expected
};
var actual = dataset.Get <string>(new DicomTag(group, 0x0045));
Assert.Equal(expected, actual);
}
public void Constructor_GroupSpecified_GroupTransferredToLabel()
{
const string expected = "Label 6003";
const ushort group = 0x6003;
var dataset = new DicomDataset();
var od = new DicomOverlayData(dataset, group)
{
Label = expected
};
var actual = dataset.Get <string>(new DicomTag(group, 0x1500));
Assert.Equal(expected, actual);
}
/// <summary>
/// Creates a DICOM overlay from a GDI+ Bitmap.
/// </summary>
/// <param name="ds">Dataset</param>
/// <param name="bitmap">Bitmap</param>
/// <param name="mask">Color mask for overlay</param>
/// <returns>DICOM overlay</returns>
public static DicomOverlayData FromBitmap(DicomDataset ds, Bitmap bitmap, Color mask)
{
ushort group = 0x6000;
while (ds.Contains(new DicomTag(group, DicomTag.OverlayBitPosition.Element)))
{
group += 2;
}
var overlay = new DicomOverlayData(ds, group);
overlay.Type = DicomOverlayType.Graphics;
overlay.Rows = bitmap.Height;
overlay.Columns = bitmap.Width;
overlay.OriginX = 1;
overlay.OriginY = 1;
overlay.BitsAllocated = 1;
overlay.BitPosition = 1;
var count = overlay.Rows * overlay.Columns / 8;
if ((overlay.Rows * overlay.Columns) % 8 > 0)
{
count++;
}
var array = new BitList();
array.Capacity = overlay.Rows * overlay.Columns;
int p = 0;
for (int y = 0; y < bitmap.Height; y++)
{
for (int x = 0; x < bitmap.Width; x++, p++)
{
if (bitmap.GetPixel(x, y).ToArgb() == mask.ToArgb())
{
array[p] = true;
}
}
}
overlay.Data = EvenLengthBuffer.Create(
new MemoryByteBuffer(array.Array));
return(overlay);
}
/// <summary>
/// Create array of graphics overlays from dataset.
/// </summary>
/// <param name="dataset">Dataset potentially containing overlays.</param>
/// <returns>Array of overlays of type <see cref="DicomOverlayType.Graphics"/>.</returns>
private static DicomOverlayData[] CreateGraphicsOverlays(DicomDataset dataset)
{
return(DicomOverlayData.FromDataset(dataset)
.Where(x => x.Type == DicomOverlayType.Graphics && x.Data != null)
.ToArray());
}
/// <summary>
/// Gets all overlays in a DICOM dataset.
/// </summary>
/// <param name="ds">Dataset</param>
/// <returns>Array of overlays</returns>
public static DicomOverlayData[] FromDataset(DicomDataset ds) {
var groups = new List<ushort>();
groups.AddRange(ds.Where(x => x.Tag.Group >= 0x6000 && x.Tag.Group <= 0x60FF && x.Tag.Element == 0x0010).Select(x => x.Tag.Group));
var overlays = new List<DicomOverlayData>();
foreach (var group in groups) {
// ensure that 6000 group is actually an overlay group
if (ds.Get<DicomElement>(new DicomTag(group, 0x0010)).ValueRepresentation != DicomVR.US)
continue;
try {
DicomOverlayData overlay = new DicomOverlayData(ds, group);
overlays.Add(overlay);
} catch {
// bail out if not an overlay group
}
}
return overlays.ToArray();
}
/// <summary>
/// Gets all overlays in a DICOM dataset.
/// </summary>
/// <param name="ds">Dataset</param>
/// <returns>Array of overlays</returns>
public static DicomOverlayData[] FromDataset(DicomDataset ds)
{
var groups = new List<ushort>();
groups.AddRange(ds.Where(x => x.Tag.Group >= 0x6000 && x.Tag.Group <= 0x60FF && x.Tag.Element == 0x0010).Select(x => x.Tag.Group));
var overlays = new List<DicomOverlayData>();
foreach (var group in groups) {
DicomOverlayData overlay = new DicomOverlayData(ds, group);
overlays.Add(overlay);
}
return overlays.ToArray();
}
public static DicomOverlayData FromBitmap(DicomDataset ds, Bitmap bitmap, Color mask) {
#endif
ushort group = 0x6000;
while (ds.Contains(new DicomTag(group, DicomTag.OverlayBitPosition.Element)))
group += 2;
var overlay = new DicomOverlayData(ds, group);
overlay.Type = DicomOverlayType.Graphics;
#if NETFX_CORE || SILVERLIGHT
overlay.Rows = bitmap.PixelHeight;
overlay.Columns = bitmap.PixelWidth;
#else
overlay.Rows = bitmap.Height;
overlay.Columns = bitmap.Width;
#endif
overlay.OriginX = 1;
overlay.OriginY = 1;
overlay.BitsAllocated = 1;
overlay.BitPosition = 1;
var count = overlay.Rows * overlay.Columns / 8;
if ((overlay.Rows * overlay.Columns) % 8 > 0)
count++;
var array = new BitList();
array.Capacity = overlay.Rows * overlay.Columns;
#if NETFX_CORE || SILVERLIGHT
int p = 0;
for (int y = 0; y < bitmap.PixelHeight; y++)
{
for (int x = 0; x < bitmap.PixelWidth; x++, p++)
{
if (bitmap.GetPixel(x, y).ToArgb() == mask.ToArgb())
array[p] = true;
#else
int p = 0;
for (int y = 0; y < bitmap.Height; y++) {
for (int x = 0; x < bitmap.Width; x++, p++) {
if (bitmap.GetPixel(x, y).ToArgb() == mask.ToArgb())
array[p] = true;
#endif
}
}
overlay.Data = EvenLengthBuffer.Create(
new MemoryByteBuffer(array.Array));
return overlay;
}