static public unsafe DecodedDicomImageModel DecodeImage(Stream stream, out Dictionary <string, string> meta)
{
stream.Seek(0, SeekOrigin.Begin);
string filePath = System.IO.Path.Combine("memory", Thread.CurrentThread.ManagedThreadId.ToString());
itk.simple.Image image;
var tempStream = new FileStream(filePath, FileMode.OpenOrCreate, FileAccess.Write);
try
{
using (tempStream)
stream.CopyTo(tempStream);
var reader = new itk.simple.ImageFileReader();
reader.SetFileName(filePath);
image = reader.Execute();
var writer = new itk.simple.ImageFileWriter();
writer.SetFileName("/mnt/c/Users/nikol/Desktop/CR.1.871.3.1522049724.50292.18240.95439262.3570939512.1.1.dcm");
writer.KeepOriginalImageUIDOff();
writer.Execute(image);
reader.Dispose();
}
finally { File.Delete(filePath); }
var result = new DecodedDicomImageModel();
IntPtr intPtr;
var pixelId = image.GetPixelID();
if (pixelId == itk.simple.PixelIDValueEnum.sitkUInt8)
{
intPtr = image.GetBufferAsUInt8();
result.ChannelSize = 1;
result.Signed = false;
}
else if (pixelId == itk.simple.PixelIDValueEnum.sitkInt8)
{
intPtr = image.GetBufferAsInt8();
result.ChannelSize = 1;
result.Signed = true;
}
else if (pixelId == itk.simple.PixelIDValueEnum.sitkUInt16)
{
intPtr = image.GetBufferAsUInt16();
result.ChannelSize = 2;
result.Signed = false;
}
else if (pixelId == itk.simple.PixelIDValueEnum.sitkInt16)
{
intPtr = image.GetBufferAsInt16();
result.ChannelSize = 2;
result.Signed = true;
}
else if (pixelId == itk.simple.PixelIDValueEnum.sitkUInt32)
{
intPtr = image.GetBufferAsUInt32();
result.ChannelSize = 4;
result.Signed = false;
}
else if (pixelId == itk.simple.PixelIDValueEnum.sitkInt32)
{
intPtr = image.GetBufferAsInt32();
result.ChannelSize = 4;
result.Signed = true;
}
else
{
throw new Exception($"Неподдерживаемый формат изображения {image.GetPixelIDTypeAsString()}.");
}
result.ChannelCount = image.GetNumberOfComponentsPerPixel();
result.Width = (ushort)image.GetWidth();
result.Height = (ushort)image.GetHeight();
result.PixelCount = image.GetNumberOfPixels();
result.PixelData = new byte[result.ChannelCount * result.ChannelSize * result.PixelCount];
Marshal.Copy(intPtr, result.PixelData, 0, result.PixelData.Length);
meta = new Dictionary <string, string>();
var keys = image.GetMetaDataKeys();
foreach (var key in keys)
{
meta.Add(key, image.GetMetaData(key));
}
image.Dispose();
return(result);
}
// static private void StartGdcm()
// {
// var s = new gdcm.Reader();
// s.SetFileName("/mnt/c/Users/nikol/Desktop/CR.1.871.3.1522049724.50292.18240.95439262.3570939512.1.1.1");
// bool b = s.CanRead();
// bool d = s.Read();
// }
static private unsafe void Main(string[] args)
{
// ComparingDicomFiles.Start(args);
// return;
// StartGdcm();
Dicom.Imaging.Codec.TranscoderManager.SetImplementation(new NativeTranscoderManager());
ImageManager.SetImplementation(WinFormsImageManager.Instance);
const string filePath = "/mnt/d/DICOM/Fluorography/favorite/jpeg-process14-1/sources/1.871.3.2050448135.34720.20335.72851334.2248937210.1.1.1";
DicomFile dicomFile = DicomFile.Open(filePath);
DicomDataset dataset = dicomFile.Dataset;
DicomImage dicomImage = new DicomImage(dataset, 0);
var image = dicomImage.RenderImage(0);
var bitmap = image.AsSharedBitmap();
bitmap.Save("/mnt/c/Users/nikol/Desktop/image-new.png");
byte[] pixelData;
Dictionary <string, string> meta;
using (FileStream readStream = new FileStream(filePath, FileMode.Open, FileAccess.Read))
pixelData = DicomDatasetExtensions.DecodeImage(readStream, out meta).PixelData;
// using (FileStream readStream = new FileStream(sc, FileMode.Open, FileAccess.Read))
// pixelData = DicomDatasetExtensions.DecodeImage(readStream, out meta).PixelData;
ushort width = dataset.GetValue <ushort>(DicomTag.Columns, 0);
ushort height = dataset.GetValue <ushort>(DicomTag.Rows, 0);
byte[] pixelData2 = new byte[pixelData.Length / 2 * 3];
double windowCenter = dataset.GetValue <double>(DicomTag.WindowCenter, 0);
double windowWidth = dataset.GetValue <double>(DicomTag.WindowWidth, 0);
fixed(byte *pPixelData = &pixelData[0])
for (int pixelIndex = 0; pixelIndex != pixelData.Length / 2; pixelIndex++)
{
int rowIndex = pixelIndex / width;
pixelData2[pixelIndex * 3 + (int)(rowIndex / (double)height * 3)] = (byte)(Math.Clamp((*(((ushort *)pPixelData) + pixelIndex) - windowCenter + windowWidth * 0.5), 0.0, windowWidth) / windowWidth * 255.0);
}
meta = new Dictionary <string, string>();
foreach (var item in dataset)
{
try
{
string value = dataset.GetValue <string>(item.Tag, 0);
int count = dataset.GetValueCount(item.Tag);
for (int valueIndex = 1; valueIndex != count; valueIndex++)
{
value += $"\\{dataset.GetValue<string>(item.Tag, valueIndex)}";
}
meta.Add(item.Tag.ToString().Replace("(", string.Empty).Replace(")", string.Empty).Replace(',', '|'), value);
}
catch
{
}
}
fixed(byte *p = &pixelData2[0])
{
var im = itk.simple.SimpleITK.ImportAsUInt8(new IntPtr(p), new itk.simple.VectorUInt32(new uint[] { width, height }), new itk.simple.VectorDouble(new double[] { 1, 1 }), new itk.simple.VectorDouble(new double[] { 0, 0 }), new itk.simple.VectorDouble(new double[] { 1, 0, 0, 1 }), 3);
itk.simple.ImageFileWriter writer = new itk.simple.ImageFileWriter();
writer.SetFileName("/mnt/c/Users/nikol/Desktop/rewritten.dcm");
writer.KeepOriginalImageUIDOff();
foreach (var pair in meta)
{
im.SetMetaData(pair.Key, pair.Value);
}
writer.SetImageIO("GDCMImageIO");
writer.UseCompressionOff();
writer.Execute(im);
writer.Dispose();
im.Dispose();
}
// dicomFile = DicomFile.Open("/mnt/c/Users/nikol/Desktop/CR.1.871.3.1522049724.50292.18240.95439262.3570939512.1.1.dcm");
// dicomFile.Dataset.AddOrUpdate<string>(DicomTag.StudyInstanceUID, dicomFile.Dataset.GetSingleValue<string>(DicomTag.StudyInstanceUID));
// dicomFile.Save("/mnt/c/Users/nikol/Desktop/CR.1.871.3.1522049724.50292.18240.95439262.3570939512.1.2.dcm");
DicomDataset dataset2 = new DicomDataset();
dataset.CopyTo(dataset2);
dataset = dataset2;
DicomPixelData dicomPixelData = DicomPixelData.Create(dataset, true);
dicomPixelData.AddFrame(new MemoryByteBuffer(pixelData2));
dataset.AddOrUpdate(DicomTag.StudyInstanceUID, DicomUIDGenerator.GenerateDerivedFromUUID());
dataset.AddOrUpdate(DicomTag.SeriesInstanceUID, DicomUIDGenerator.GenerateDerivedFromUUID());
dataset.AddOrUpdate(DicomTag.SOPInstanceUID, DicomUIDGenerator.GenerateDerivedFromUUID());
dataset.AddOrUpdate(DicomTag.BitsAllocated, (ushort)8);
dataset.AddOrUpdate(DicomTag.BitsStored, (ushort)8);
dataset.AddOrUpdate(DicomTag.HighBit, (ushort)7);
dataset.AddOrUpdate(DicomTag.PixelRepresentation, (ushort)0);
dataset.AddOrUpdate(DicomTag.SamplesPerPixel, (ushort)3);
dataset.AddOrUpdate(DicomTag.PlanarConfiguration, (ushort)0);
dataset.AddOrUpdate(DicomTag.PhotometricInterpretation, PhotometricInterpretation.Rgb.Value);
dataset.AddOrUpdate(DicomTag.WindowCenter, 127.5);
dataset.AddOrUpdate(DicomTag.WindowWidth, 255.0);
dicomFile = new DicomFile(dataset);
dicomFile.Save("/mnt/c/Users/nikol/Desktop/efferent-no-compression.dcm");
var j2000lossy = dataset.Compress(DicomTransferSyntax.JPEGLSLossless, new DicomJpegLsLosslessCodec(), new Dicom.Imaging.Codec.DicomJpegLsParams());
j2000lossy.AddOrUpdate(DicomTag.StudyInstanceUID, DicomUIDGenerator.GenerateDerivedFromUUID());
j2000lossy.AddOrUpdate(DicomTag.SeriesInstanceUID, DicomUIDGenerator.GenerateDerivedFromUUID());
j2000lossy.AddOrUpdate(DicomTag.SOPInstanceUID, DicomUIDGenerator.GenerateDerivedFromUUID());
dicomFile = new DicomFile(j2000lossy);
dicomFile.Save("/mnt/c/Users/nikol/Desktop/efferent-ls-lossless.dcm");
var j2000lossless = dataset.Compress(DicomTransferSyntax.JPEGLSNearLossless, new DicomJpegLsNearLosslessCodec(), new Dicom.Imaging.Codec.DicomJpegLsParams());
j2000lossless.AddOrUpdate(DicomTag.StudyInstanceUID, DicomUIDGenerator.GenerateDerivedFromUUID());
j2000lossless.AddOrUpdate(DicomTag.SeriesInstanceUID, DicomUIDGenerator.GenerateDerivedFromUUID());
j2000lossless.AddOrUpdate(DicomTag.SOPInstanceUID, DicomUIDGenerator.GenerateDerivedFromUUID());
dicomFile = new DicomFile(j2000lossless);
dicomFile.Save("/mnt/c/Users/nikol/Desktop/efferent-ls-near-lossless.dcm");
// RemovePixelDataProgram.Start(args);
// ItkSimpleTestProgram.Start(args);
// ImageTestProgram.Start(args);
// CheckImageAttributesProgram.Start(args);
// TestDicom48bpp.Start(args);
// Testing3D.Start(args);
// TestingWindowPresets.Start(args);
// TestingMultiImageDicom.Start(args);
// ComparingDicomFiles.Start(args);
// PresentationState.Start(args);
// PresentationStateAnalyzer.Start(args);
}
