protected override byte[] CreateNormalizedPixelData()
{
string photometricInterpretation;
byte[] pixelData = _framePixelData.GetUncompressedPixelData(out photometricInterpretation);
string photometricInterpretationCode = photometricInterpretation ?? Parent[DicomTags.PhotometricInterpretation].ToString();
PhotometricInterpretation pi = PhotometricInterpretation.FromCodeString(photometricInterpretationCode);
if (pi.IsColor)
{
pixelData = ToArgb(this.Parent, pixelData, pi);
}
else
{
var overlayPlaneModuleIod = new OverlayPlaneModuleIod(Parent);
foreach (var overlayPlane in overlayPlaneModuleIod)
{
if (!overlayPlane.HasOverlayData && _overlayData[overlayPlane.Index] == null)
{
// if the overlay is embedded in pixel data and we haven't cached it yet, extract it now before we normalize the frame pixel data
var overlayData = OverlayData.UnpackFromPixelData(overlayPlane.OverlayBitPosition, Parent[DicomTags.BitsAllocated].GetInt32(0, 0), false, pixelData);
_overlayData[overlayPlane.Index] = overlayData;
}
}
NormalizeGrayscalePixels(this.Parent, pixelData);
}
return(pixelData);
}
public void TestUnpackFromPixelData_16BitsAllocated()
{
// 1 frame, 7x3
// 1111111
// 1001011
// 0000011
// continuous bit stream: 11111111 00101100 00011xxx xxxxxxxx
const string expectedResult = "111111110010110000011";
// 16 bits allocated
// some pixel data: 1st col is a random "pixel", 2nd col creates room for overlay bit, 3rd col is the overlay
// 4th col moves the overlay to bit position 14, 5th col is the lower byte of the random pixel
var pixelData = SwapBytes(new byte[] // written in big endian form for ease of reading :P
{
(0xC5 & 0x0F) | (1 << 6), 0x93,
(0x2D & 0x0F) | (1 << 6), 0x9C,
(0x5B & 0x0F) | (1 << 6), 0x78,
(0xB3 & 0x0F) | (1 << 6), 0x17,
(0xFC & 0x0F) | (1 << 6), 0x0c,
(0xBC & 0x0F) | (1 << 6), 0xc4,
(0x0B & 0x0F) | (1 << 6), 0x4c,
(0x74 & 0x0F) | (1 << 6), 0xe5,
(0x4d & 0x0F) | (0 << 6), 0x45,
(0xbf & 0x0F) | (0 << 6), 0xcd,
(0x86 & 0x0F) | (1 << 6), 0xAE,
(0x75 & 0x0F) | (0 << 6), 0xA9,
(0x51 & 0x0F) | (1 << 6), 0xbe,
(0x71 & 0x0F) | (1 << 6), 0x7e,
(0xA8 & 0x0F) | (0 << 6), 0x29,
(0x19 & 0x0F) | (0 << 6), 0x11,
(0xAC & 0x0F) | (0 << 6), 0xDD,
(0xD4 & 0x0F) | (0 << 6), 0x01,
(0x79 & 0x0F) | (0 << 6), 0xF0,
(0xA0 & 0x0F) | (1 << 6), 0xe2,
(0xBA & 0x0F) | (1 << 6), 0x98
});
// little endian
{
var extractedBits = OverlayData.UnpackFromPixelData(14, 16, false, pixelData);
var actualResult = FormatNonZeroBytes(extractedBits);
Assert.AreEqual(expectedResult, actualResult, "Error in extracted bits from pixel data (16-bit pixels, little endian)");
}
// big endian
{
var extractedBits = OverlayData.UnpackFromPixelData(14, 16, true, SwapBytes(pixelData));
var actualResult = FormatNonZeroBytes(extractedBits);
Assert.AreEqual(expectedResult, actualResult, "Error in extracted bits from pixel data (16-bit pixels, big endian)");
}
}
private void ExtractOverlayFrames(byte[] rawPixelData, int bitsAllocated)
{
// if any overlays have embedded pixel data, extract them now or forever hold your peace
var overlayPlaneModuleIod = new OverlayPlaneModuleIod(Parent);
foreach (var overlayPlane in overlayPlaneModuleIod)
{
if (!overlayPlane.HasOverlayData && _overlayCache[overlayPlane.Index] == null)
{
// if the overlay is embedded in pixel data and we haven't cached it yet, extract it now before we normalize the frame pixel data
var overlayData = OverlayData.UnpackFromPixelData(overlayPlane.OverlayBitPosition, bitsAllocated, false, rawPixelData);
_overlayCache[overlayPlane.Index] = overlayData;
}
}
}
protected override byte[] CreateNormalizedPixelData()
{
byte[] pixelData = _framePixelData.GetUncompressedPixelData();
string photometricInterpretationCode = this.Parent[DicomTags.PhotometricInterpretation].ToString();
PhotometricInterpretation pi = PhotometricInterpretation.FromCodeString(photometricInterpretationCode);
TransferSyntax ts = TransferSyntax.GetTransferSyntax(this.Parent.TransferSyntaxUid);
if (pi.IsColor)
{
if (ts == TransferSyntax.Jpeg2000ImageCompression ||
ts == TransferSyntax.Jpeg2000ImageCompressionLosslessOnly ||
ts == TransferSyntax.JpegExtendedProcess24 ||
ts == TransferSyntax.JpegBaselineProcess1)
{
pi = PhotometricInterpretation.Rgb;
}
pixelData = ToArgb(this.Parent, pixelData, pi);
}
else
{
OverlayPlaneModuleIod opmi = new OverlayPlaneModuleIod(this.Parent);
foreach (OverlayPlane overlayPlane in opmi)
{
if (IsOverlayEmbedded(overlayPlane) && _overlayData[overlayPlane.Index] == null)
{
byte[] overlayData = OverlayData.UnpackFromPixelData(overlayPlane.OverlayBitPosition, this.Parent[DicomTags.BitsAllocated].GetInt32(0, 0), false, pixelData);
_overlayData[overlayPlane.Index] = overlayData;
}
else if (!overlayPlane.HasOverlayData)
{
Platform.Log(LogLevel.Warn, "The image {0} appears to be missing OverlayData for group 0x{1:X4}.", this.Parent.SopInstanceUid, overlayPlane.Group);
}
}
NormalizeGrayscalePixels(this.Parent, pixelData);
}
return(pixelData);
}
protected override byte[] CreateNormalizedPixelData()
{
byte[] pixelData = _framePixelData.GetUncompressedPixelData();
string photometricInterpretationCode = this.Parent[DicomTags.PhotometricInterpretation].ToString();
PhotometricInterpretation pi = PhotometricInterpretation.FromCodeString(photometricInterpretationCode);
TransferSyntax ts = TransferSyntax.GetTransferSyntax(this.Parent.TransferSyntaxUid);
if (pi.IsColor)
{
if (ts == TransferSyntax.Jpeg2000ImageCompression ||
ts == TransferSyntax.Jpeg2000ImageCompressionLosslessOnly ||
ts == TransferSyntax.JpegExtendedProcess24 ||
ts == TransferSyntax.JpegBaselineProcess1)
{
pi = PhotometricInterpretation.Rgb;
}
pixelData = ToArgb(this.Parent, pixelData, pi);
}
else
{
var overlayPlaneModuleIod = new OverlayPlaneModuleIod(Parent);
foreach (var overlayPlane in overlayPlaneModuleIod)
{
if (!overlayPlane.HasOverlayData && _overlayData[overlayPlane.Index] == null)
{
// if the overlay is embedded in pixel data and we haven't cached it yet, extract it now before we normalize the frame pixel data
var overlayData = OverlayData.UnpackFromPixelData(overlayPlane.OverlayBitPosition, Parent[DicomTags.BitsAllocated].GetInt32(0, 0), false, pixelData);
_overlayData[overlayPlane.Index] = overlayData;
}
}
NormalizeGrayscalePixels(this.Parent, pixelData);
}
return(pixelData);
}
public void TestUnpackFromPixelData_8BitsAllocated()
{
// 1 frame, 5x3
// 11111
// 10010
// 00000
// continuous bit stream: 11111100 1000000x
// continuous LE byte stream: 00111111 x0000001
const string expectedResult = "111111001000000";
// 8 bits allocated
// some pixel data: 1st col is a random "pixel", 2nd col creates room for overlay bit, 3rd col is the overlay
var pixelData = new byte[]
{
(0xC5 & 0xFE) | 1,
(0x2D & 0xFE) | 1,
(0x5B & 0xFE) | 1,
(0xB3 & 0xFE) | 1,
(0xFC & 0xFE) | 1,
(0xBC & 0xFE) | 1,
(0x4d & 0xFE) | 0,
(0xbf & 0xFE) | 0,
(0x86 & 0xFE) | 1,
(0x75 & 0xFE) | 0,
(0xA8 & 0xFE) | 0,
(0x19 & 0xFE) | 0,
(0xAC & 0xFE) | 0,
(0xD4 & 0xFE) | 0,
(0x79 & 0xFE) | 0
};
var extractedBits = OverlayData.UnpackFromPixelData(0, 8, false, pixelData);
var actualResult = FormatNonZeroBytes(extractedBits);
Assert.AreEqual(expectedResult, actualResult, "Error in extracted bits from pixel data (8-bit pixels)");
}
