public void Render(int[] pixels, int width, int height)
{
byte[] data = null;
if (_scaledData == null) _scaledData = _originalData.Rescale(_scale);
data = (_scaledData as GrayscalePixelDataU8).Data;
int ox = (int)(_offsetX * _scale);
int oy = (int)(_offsetY * _scale);
#if NET35
for (var y = 0; y < _scaledData.Height; ++y)
#else
Parallel.For(0, _scaledData.Height, y =>
#endif
{
if ((oy + y) >= height) return;
for (int i = _scaledData.Width * y, e = i + _scaledData.Width, x = 0; i < e; i++, x++)
{
if (data[i] > 0)
{
//this is wrong, when scaling is active
//if ((ox + x) >= width) break;
int p = (oy * width) + ox + i;
pixels[p] = _color;
}
}
}
#if !NET35
);
#endif
}
public void Render(int[] pixels, int width, int height)
{
byte[] data = null;
if (_scaledData == null) _scaledData = _originalData.Rescale(_scale);
data = (_scaledData as GrayscalePixelDataU8).Data;
int ox = (int)(_offsetX * _scale);
int oy = (int)(_offsetY * _scale);
Parallel.For(
0,
_scaledData.Height,
y =>
{
if ((oy + y) >= height) return;
for (int i = _scaledData.Width * y, e = i + _scaledData.Width, x = 0; i < e; i++, x++)
{
if (data[i] > 0)
{
if ((ox + x) >= width) break;
int p = (oy * width) + ox + i;
pixels[p] = _color;
}
}
});
}
public void Render(int[] pixels, int width, int height)
{
byte[] data = null;
if (_scaledData == null) _scaledData = _originalData.Rescale(_scale);
data = (_scaledData as GrayscalePixelDataU8).Data;
int ox = (int)(_offsetX * _scale);
int oy = (int)(_offsetY * _scale);
#if NET35
for (var y = 0; y < _scaledData.Height; ++y)
#else
Parallel.For(0, _scaledData.Height, y =>
#endif
{
if ((oy + y) >= height) return;
for (int i = _scaledData.Width * y, e = i + _scaledData.Width, x = 0; i < e; i++, x++)
{
if (data[i] > 0)
{
//this is wrong, when scaling is active
//if ((ox + x) >= width) break;
int p = (oy * width) + ox + i;
pixels[p] = _color;
}
}
}
#if !NET35
);
#endif
}
public override DICOMImage Parse()
{
// Read the pixel data from the image, frame 0
IPixelData pixelData = PixelDataFactory.Create(image.PixelData, 0);
// Get the pixels from the pixel data
ushort[] pixels = ((GrayscalePixelDataU16)pixelData).Data;
// Get the multiplier
int min = image.PixelData.BitDepth.MinimumValue;
int max = image.PixelData.BitDepth.MaximumValue;
if (min != 0)
{
throw new FormatException("Error in the minimum value of the pixel data");
}
float multiplier = ushort.MaxValue / max;
// Apply the multiplier to the pixels
for (int i = 0; i < pixels.Length; i++)
{
pixels[i] = (ushort)(pixels[i] * multiplier);
}
return(DICOMImage.FromData(image.Width, image.Height, pixels));
}
public void Render(int[] pixels, int width, int height)
{
byte[] data = null;
if (_scaledData == null)
{
_scaledData = _originalData.Rescale(_scale);
}
data = (_scaledData as GrayscalePixelDataU8).Data;
int ox = (int)(_offsetX * _scale);
int oy = (int)(_offsetY * _scale);
Parallel.For(0, _scaledData.Height, y => {
if ((oy + y) >= height)
{
return;
}
for (int i = _scaledData.Width * y, e = i + _scaledData.Width, x = 0; i < e; i++, x++)
{
if (data[i] > 0)
{
if ((ox + x) >= width)
{
break;
}
int p = (oy * width) + ox + i;
pixels[p] = _color;
}
}
});
}
public ImageGraphic(IPixelData pixelData)
{
_originalData = pixelData;
_zorder = 255;
_applyLut = true;
Scale(1.0);
}
public ImageGraphic(IPixelData pixelData)
{
_originalData = pixelData;
_zorder = 255;
_applyLut = true;
Scale(1.0);
}
private static ImageData CreateImageData(IPixelData pixelData)
{
ImageData image = null;
if (pixelData.Components != 1)
{
return(null);
}
if (pixelData is GrayscalePixelDataU16 grayscalePixelDataU16)
{
image = new ImageData(grayscalePixelDataU16.Data);
}
else if (pixelData is GrayscalePixelDataS16 grayscalePixelDataS16)
{
image = new ImageData(grayscalePixelDataS16.Data);
}
else if (pixelData is GrayscalePixelDataU8 grayscalePixelDataU8)
{
image = new ImageData(grayscalePixelDataU8.Data);
}
image.Width = pixelData.Width;
image.Height = pixelData.Height;
var minMax = pixelData.GetMinMax();
image.MinValue = minMax.Minimum;
image.MaxValue = minMax.Maximum;
return(image);
}
public void Scale(double scale)
{
if (Math.Abs(scale - _scale) <= Double.Epsilon) return;
_scale = scale;
_scaledData = null;
}
public void Scale(double scale)
{
if (Math.Abs(scale - _scale) <= Double.Epsilon) return;
_scale = scale;
_scaledData = null;
}
/// <summary>Renders DICOM image to <see cref="IImage"/>.</summary>
/// <param name="frame">Zero indexed frame number.</param>
/// <returns>Rendered image</returns>
public virtual IImage RenderImage(int frame = 0)
{
IPixelData pixels;
lock (_lock)
{
var load = frame >= 0 && (frame != CurrentFrame || _rerender);
CurrentFrame = frame;
_rerender = false;
if (load)
{
var frameIndex = GetFrameIndex(frame);
pixels = PixelDataFactory.Create(_pixelData, frameIndex).Rescale(_scale);
_pixels = pixels;
}
else
{
pixels = _pixels;
}
}
if (ShowOverlays)
{
EstablishGraphicsOverlays();
}
IImage image;
var graphic = new ImageGraphic(pixels);
if (ShowOverlays)
{
foreach (var overlay in _overlays)
{
if (overlay.Data is EmptyBuffer)//fixed overlay.data is null, exception thrown
{
continue;
}
if (frame + 1 < overlay.OriginFrame ||
frame + 1 > overlay.OriginFrame + overlay.NumberOfFrames - 1)
{
continue;
}
var og = new OverlayGraphic(
PixelDataFactory.Create(overlay),
overlay.OriginX - 1,
overlay.OriginY - 1,
OverlayColor);
graphic.AddOverlay(og);
og.Scale(_scale);
}
}
image = graphic.RenderImage(_pipeline.LUT);
return(image);
}
/// <summary>
/// Initialize new instance of <seealso cref="OverlayGraphic"/>
/// </summary>
/// <param name="pixelData">Overlay pixel data</param>
/// <param name="offsetx">X offset</param>
/// <param name="offsety">Y offset</param>
/// <param name="color">The color of the resulting overlay</param>
public OverlayGraphic(SingleBitPixelData pixelData, int offsetx, int offsety, int color) {
_originalData = pixelData;
_scaledData = _originalData;
_offsetX = offsetx;
_offsetY = offsety;
_color = color;
_scale = 1.0;
}
/// <summary>Renders DICOM image to <see cref="IImage"/>.</summary>
/// <param name="frame">Zero indexed frame number.</param>
/// <returns>Rendered image</returns>
public virtual IImage RenderImage(int frame = 0)
{
bool load;
lock (_lock)
{
load = frame >= 0 && (frame != CurrentFrame || _rerender);
_currentFrame = frame;
_rerender = false;
}
var frameIndex = GetFrameIndex(frame);
if (load)
{
lock (_lock)
{
_pixels = PixelDataFactory.Create(_pixelData, frameIndex).Rescale(_scale);
}
}
if (ShowOverlays)
{
EstablishGraphicsOverlays();
}
IImage image;
lock (_lock)
{
var graphic = new ImageGraphic(_pixels);
if (ShowOverlays)
{
foreach (var overlay in _overlays)
{
if (frame + 1 < overlay.OriginFrame ||
frame + 1 > overlay.OriginFrame + overlay.NumberOfFrames - 1)
{
continue;
}
var og = new OverlayGraphic(
PixelDataFactory.Create(overlay),
overlay.OriginX - 1,
overlay.OriginY - 1,
OverlayColor);
graphic.AddOverlay(og);
og.Scale(_scale);
}
}
image = graphic.RenderImage(_pipeline.LUT);
}
return(image);
}
public OverlayGraphic(IPixelData pixelData, int offsetx, int offsety)
{
_originalData = pixelData;
_offsetX = offsetx;
_offsetY = offsety;
_zorder = 128;
_applyLut = false;
Scale(1.0f);
}
public OverlayGraphic(IPixelData pixelData, int offsetx, int offsety)
{
_originalData = pixelData;
_offsetX = offsetx;
_offsetY = offsety;
_zorder = 128;
_applyLut = false;
Scale(1.0f);
}
/// <summary>
/// Initialize new instance of <seealso cref="OverlayGraphic"/>
/// </summary>
/// <param name="pixelData">Overlay pixel data</param>
/// <param name="offsetx">X offset</param>
/// <param name="offsety">Y offset</param>
/// <param name="color">The color of the resulting overlay</param>
public OverlayGraphic(SingleBitPixelData pixelData, int offsetx, int offsety, int color)
{
_originalData = pixelData;
_scaledData = _originalData;
_offsetX = offsetx;
_offsetY = offsety;
_color = color;
_scale = 1.0;
}
/// <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();
}
private void Load(DcmDataset dataset) {
Dataset = dataset;
if (Dataset.InternalTransferSyntax.IsEncapsulated)
Dataset.ChangeTransferSyntax(DicomTransferSyntax.ExplicitVRLittleEndian, null);
DcmPixelData pixelData = new DcmPixelData(Dataset);
_pixelData = PixelDataFactory.Create(pixelData, 0);
_pipeline = PipelineFactory.Create(Dataset, pixelData);
pixelData.Unload();
_overlays = DcmOverlayData.FromDataset(Dataset);
}
private static int[] GetGrayPixelData(DicomDataset dataset)
{
DicomPixelData pixelData = DicomPixelData.Create(dataset);
IByteBuffer buffer = pixelData.GetFrame(0);
IPixelData data = PixelDataFactory.Create(pixelData, 0);
var renderOptions = GrayscaleRenderOptions.FromDataset(dataset);
int[] output = new int[pixelData.Width * pixelData.Height];
data.Render(new ModalityLUT(renderOptions), output);
return(output);
}
/// <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 ImageGraphic(IPixelData pixelData, Double scaleVal = 0)
: this()
{
_originalData = pixelData;
if (scaleVal > 0 && _originalData.Components == 1)
{
Scale(scaleVal);
}
else
{
Scale(1.0);
}
}
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);
}
/// <inheritdoc />
public void Scale(double scale)
{
if ((scale - _scaleFactor).IsNearlyZero())
{
return;
}
_scaleFactor = scale;
_scaledData = null;
foreach (var overlay in _overlays)
{
overlay.Scale(scale);
}
}
public void Scale(double scale)
{
if (Math.Abs(scale - _scaleFactor) <= Double.Epsilon)
{
return;
}
_scaleFactor = scale;
_scaledData = null;
foreach (var overlay in _overlays)
{
overlay.Scale(scale);
}
}
public void Scale(double scale)
{
if (Math.Abs(scale - _scaleFactor) <= Double.Epsilon)
{
return;
}
_scaleFactor = scale;
if (_bitmap != null)
{
_scaledData = null;
_pixels.Dispose();
_pixels = null;
_bitmap = null;
}
}
private double?Interpolate(IPixelData pixels, Point2D imgSpace)
{
if ((imgSpace.X >= 0.0) && (imgSpace.X < pixels.Width - 1) && (imgSpace.Y >= 0.0) && (imgSpace.Y < pixels.Height - 1))
{
var posX = (int)Math.Floor(imgSpace.X);
double alphaX = imgSpace.X - posX;
var posY = (int)Math.Floor(imgSpace.Y);
double alphaY = imgSpace.Y - posY;
return((1 - alphaX) * ((1 - alphaY) * pixels.GetPixel(posX, posY)
+ alphaY * pixels.GetPixel(posX, posY + 1))
+ alphaX * ((1 - alphaY) * pixels.GetPixel(posX + 1, posY)
+ alphaY * pixels.GetPixel(posX + 1, posY + 1)));
}
return(null);
}
public void Scale(double scale)
{
if (Math.Abs(scale - _scaleFactor) <= Double.Epsilon)
{
return;
}
_scaleFactor = scale;
if (_bitmap != null)
{
_scaledData = null;
_pixels.Dispose();
_pixels = null;
_bitmap = null;
}
foreach (var overlay in _overlays)
{
overlay.Scale(scale);
}
}
public string DicomToGraphicalJSON(string filePathToDir)
{
string[] allFilePaths = System.IO.Directory.GetFiles(filePathToDir);
// store all of the dicoms as a list of dicom files
List <DicomFile> dicoms = new List <DicomFile>();
// get the amount of data
DicomFileData dicomFile = null;
ArrayList data = new ArrayList();
// loop though all of the files and open them
foreach (string filePath in allFilePaths)
{
try
{
dicoms.Add(DicomFile.Open(filePath));
}
catch (Exception)
{
Console.WriteLine("file at \"" + filePath + "\" readable as a dicom file");
}
}
// sort the order of all the dicom objects so they work in the correct order
dicoms.Sort((d1, d2) => d1.Dataset.GetSingleValue <int>(DicomTag.InstanceNumber).CompareTo(d2.Dataset.GetSingleValue <int>(DicomTag.InstanceNumber)));
// sort out the intial values based on the first dicom in the list
// get the pixel data out as much as possible
DicomPixelData header = DicomPixelData.Create(dicoms[0].Dataset);
IPixelData pixelData = PixelDataFactory.Create(header, 0);
// Build the correct file for this data depending on what is stored in the dicom files
if (pixelData is GrayscalePixelDataU16)
{
data.AddRange(((GrayscalePixelDataU16)pixelData).Data);
dicomFile = new U16DicomFileData();
}
else if (pixelData is GrayscalePixelDataS16)
{
data.AddRange(((GrayscalePixelDataS16)pixelData).Data);
dicomFile = new S16DicomFileData();
}
else if (pixelData is GrayscalePixelDataU8)
{
data.AddRange(((GrayscalePixelDataU8)pixelData).Data);
dicomFile = new U8bitDicomFileData();
}
else if (pixelData is GrayscalePixelDataS32)
{
data.AddRange(((GrayscalePixelDataS32)pixelData).Data);
dicomFile = new S32DicomDataFile();
}
else if (pixelData is GrayscalePixelDataU32)
{
data.AddRange(((GrayscalePixelDataU32)pixelData).Data);
dicomFile = new U32DicomDataFile();
}
else if (pixelData is ColorPixelData24)
{
// note that this one will take some work
// 0 == red, 1 == Green, 2 == Blue and so on
data.AddRange(((ColorPixelData24)pixelData).Data);
dicomFile = new RGBColourDicomFileData();
}
else if (pixelData is SingleBitPixelData)
{
data.AddRange(((SingleBitPixelData)pixelData).Data);
dicomFile = new U8bitDicomFileData();
}
// get the amount of rows the image data set has out of the dicom file.
if (!dicoms[0].Dataset.TryGetSingleValue(DicomTag.Rows, out dicomFile.width))
{
if (!dicoms[0].Dataset.TryGetSingleValue(DicomTag.NumberOfVerticalPixels, out dicomFile.width))
{
// if the value for rows dosn't exist mark the entry as -1
dicomFile.width = -1;
}
}
// get the amount of coloumns in the image
if (!dicoms[0].Dataset.TryGetSingleValue(DicomTag.Columns, out dicomFile.height))
{
// try getting this data another way then
if (!dicoms[0].Dataset.TryGetSingleValue(DicomTag.NumberOfHorizontalPixels, out dicomFile.height))
{
// if the value for rows dosn't exist mark the entry as -1
dicomFile.height = -1;
}
}
// Datastucture that will hold the final DS
float[] aspectOfPixel = new float[2];
// get the amount of coloumns in the image
if (!dicoms[0].Dataset.TryGetValues <float>(DicomTag.PixelSpacing, out aspectOfPixel))
{
// all these methods will try to do it until one works or this feild will be made invalid
if (!dicoms[0].Dataset.TryGetValues <float>(DicomTag.ImagerPixelSpacing, out aspectOfPixel))
{
if (!dicoms[0].Dataset.TryGetValues <float>(DicomTag.NominalScannedPixelSpacing, out aspectOfPixel))
{
if (!dicoms[0].Dataset.TryGetValues <float>(DicomTag.CompensatorPixelSpacing, out aspectOfPixel))
{
if (!dicoms[0].Dataset.TryGetValues <float>(DicomTag.DetectorElementSpacing, out aspectOfPixel))
{
if (!dicoms[0].Dataset.TryGetValues <float>(DicomTag.PresentationPixelSpacing, out aspectOfPixel))
{
if (!dicoms[0].Dataset.TryGetValues <float>(DicomTag.PrinterPixelSpacing, out aspectOfPixel))
{
if (!dicoms[0].Dataset.TryGetValues <float>(DicomTag.ObjectPixelSpacingInCenterOfBeam, out aspectOfPixel))
{
// if none of the above methods work mark the objects as invalid
aspectOfPixel[0] = -1;
aspectOfPixel[1] = -1;
// This could be valid in a case were only one row of data was colected
}
}
}
}
}
}
}
}
// TODO this dosn't take into account what will happen if the user only recorded one line of pixels since my work dosn't focus on it
// Save the data from pixel spacing
dicomFile.pixelSpacingX = aspectOfPixel[0];
dicomFile.pixelSpacingY = aspectOfPixel[1];
// try to get the thickness of the the slice or else set it to an invalid number
if (dicoms[0].Dataset.TryGetSingleValue(DicomTag.SliceThickness, out dicomFile.sliceThickness))
{
dicomFile.sliceThickness = -1;
}
// try to get how much room is between each slice
if (!dicoms[0].Dataset.TryGetSingleValue(DicomTag.SpacingBetweenSlices, out dicomFile.spacingBetweenSlices))
{
dicomFile.spacingBetweenSlices = -1;
}
dicomFile.breath = dicoms.Count;
// loop though all of the dicoms in order now
for (int index = 1; index < dicoms.Count; index++)
{
// get the pixel data out as much as possible
header = DicomPixelData.Create(dicoms[index].Dataset);
pixelData = PixelDataFactory.Create(header, 0);
// Build the correct file for this data depending on what is stored in the dicom files
if (pixelData is GrayscalePixelDataU16)
{
data.AddRange(((GrayscalePixelDataU16)pixelData).Data);
}
else if (pixelData is GrayscalePixelDataS16)
{
data.AddRange(((GrayscalePixelDataS16)pixelData).Data);
}
else if (pixelData is GrayscalePixelDataU8)
{
data.AddRange(((GrayscalePixelDataU8)pixelData).Data);
}
else if (pixelData is GrayscalePixelDataS32)
{
data.AddRange(((GrayscalePixelDataS32)pixelData).Data);
}
else if (pixelData is GrayscalePixelDataU32)
{
data.AddRange(((GrayscalePixelDataU32)pixelData).Data);
}
else if (pixelData is ColorPixelData24)
{
// note that this one will take some work
// 0 == red, 1 == Green, 2 == Blue and so on
data.AddRange(((ColorPixelData24)pixelData).Data);
}
else if (pixelData is SingleBitPixelData)
{
data.AddRange(((SingleBitPixelData)pixelData).Data);
}
int tempDicomRows = -1;
// get the amount of rows the image data set has out of the dicom file.
if (!dicoms[index].Dataset.TryGetSingleValue(DicomTag.Rows, out tempDicomRows))
{
if (!dicoms[index].Dataset.TryGetSingleValue(DicomTag.NumberOfVerticalPixels, out tempDicomRows))
{
if (dicomFile.height != tempDicomRows)
{
throw new NonConsistantDicomDirectoryException("The number of rows at index" + index);
}
}
}
else if (dicomFile.width != tempDicomRows)
{
throw new NonConsistantDicomDirectoryException("The number of rows at index" + index);
}
// get the amount of coloumns in the image and ensure it stays the same
int tempDicomCols = -1;
if (!dicoms[index].Dataset.TryGetSingleValue(DicomTag.Columns, out tempDicomCols))
{
// try getting this data another way then
if (dicoms[index].Dataset.TryGetSingleValue(DicomTag.NumberOfHorizontalPixels, out tempDicomCols))
{
if (dicomFile.height != tempDicomCols)
{
throw new NonConsistantDicomDirectoryException("The number of columns at index" + index);
}
}
}
else if (dicomFile.height != tempDicomCols)
{
throw new NonConsistantDicomDirectoryException("The number of columns at index" + index);
}
// TODO Maybe change how this works going forward
aspectOfPixel = new float[2];
// get the amount of coloumns in the image
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.PixelSpacing, out aspectOfPixel))
{
// all these methods will try to do it until one works or this feild will be made invalid
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.ImagerPixelSpacing, out aspectOfPixel))
{
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.NominalScannedPixelSpacing, out aspectOfPixel))
{
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.CompensatorPixelSpacing, out aspectOfPixel))
{
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.DetectorElementSpacing, out aspectOfPixel))
{
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.PresentationPixelSpacing, out aspectOfPixel))
{
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.PrinterPixelSpacing, out aspectOfPixel))
{
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.ObjectPixelSpacingInCenterOfBeam, out aspectOfPixel))
{
// if none of the above methods work mark the objects as invalid
aspectOfPixel[0] = -1;
aspectOfPixel[1] = -1;
// This could be valid in a case were only one row of data was colected
}
}
}
}
}
}
}
}
// check input data against the old data and throw an exception if the file isn't exact
if (dicomFile.pixelSpacingX != aspectOfPixel[0] || dicomFile.pixelSpacingY != aspectOfPixel[1])
{
throw new NonConsistantDicomDirectoryException("Pixel Spacing Dicom Tag at index " + index);
}
// check the slice thickness is constisant
if (dicoms[index].Dataset.TryGetSingleValue(DicomTag.SliceThickness, out float tempSliceThickness))
{
if (dicomFile.sliceThickness == -1)
{
dicomFile.sliceThickness = tempSliceThickness;
}
else if (tempSliceThickness != dicomFile.sliceThickness)
{
throw new NonConsistantDicomDirectoryException("Slice Thickness at index" + index);
}
}
// try to get how much room is between each slice
if (!dicoms[index].Dataset.TryGetSingleValue(DicomTag.SpacingBetweenSlices, out float tempSliceSpacing))
{
if (dicomFile.spacingBetweenSlices == -1)
{
dicomFile.spacingBetweenSlices = tempSliceSpacing;
}
else if (tempSliceThickness != dicomFile.sliceThickness)
{
throw new NonConsistantDicomDirectoryException("Spacing between slices at index" + index);
}
}
}
dicomFile.SetPixelBuffer(data);
// return the json strings here
return(Newtonsoft.Json.JsonConvert.SerializeObject(dicomFile));
}
/// <summary>
/// Initialize new instance of <seealso cref="ImageGraphic"/>
/// </summary>
/// <param name="pixelData">Pixel data</param>
public ImageGraphic(IPixelData pixelData) : this()
{
_originalData = pixelData;
Scale(1.0);
}
/// <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>
/// Initialize new instance of <seealso cref="ImageGraphic"/>
/// </summary>
/// <param name="pixelData">Pixel data</param>
public ImageGraphic(IPixelData pixelData)
: this()
{
_originalData = pixelData;
Scale(1.0);
}
public void Scale(double scale)
{
if (Math.Abs(scale - _scaleFactor) <= Double.Epsilon) return;
_scaleFactor = scale;
_scaledData = null;
foreach (var overlay in _overlays)
{
overlay.Scale(scale);
}
}
public void Scale(double scale)
{
if (Math.Abs(scale - _scaleFactor) <= Double.Epsilon)
return;
_scaleFactor = scale;
if (_bitmap != null) {
_scaledData = null;
_pixels.Dispose();
_pixels = null;
_bitmap = null;
}
}