// 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);
}
static internal unsafe void Start(string[] args)
{
DicomFile file = new DicomFile();
var z = file.Dataset.InternalTransferSyntax;
string sourceDirectory = Environment.GetEnvironmentVariable("SOURCE_DIRECTORY");
string fontDirectory = Environment.GetEnvironmentVariable("FONT_DIRECTORY");
System.Drawing.Bitmap w = new System.Drawing.Bitmap(100, 100, System.Drawing.Imaging.PixelFormat.Format24bppRgb);
w.Save(System.IO.Path.Combine(sourceDirectory, "image.png"));
var d = System.Drawing.Image.FromFile(System.IO.Path.Combine(sourceDirectory, "image.png"), false);
// string filePath = System.IO.Path.Combine(sourceDirectory, "DICOM/SikorskayaN.M/1.2.840.113681.3232266507.1433317480.4724.262");
// string filePath = System.IO.Path.Combine(sourceDirectory, "DICOM/Topina V A/1.2.840.113681.169869557.1534493190.4808.47144");
// string filePath = System.IO.Path.Combine(sourceDirectory, "DICOM/!Test/ИС Флюорография/ФЛЮ для показа/Пациент001/Пациент001.dcm");
// string filePath = System.IO.Path.Combine(sourceDirectory, "1");
// string filePath = System.IO.Path.Combine(sourceDirectory, "DICOM/Fluorography/Emias Compressed/1.871.3.2050448135.34720.20335.72851334.2248937210.1.1.1");
// string filePath = System.IO.Path.Combine(sourceDirectory, "DICOM/Fluorography/Emias Compressed/1.871.3.1778880733.53108.19741.3386264761.3888045999.1.1.1");
// string filePath = System.IO.Path.Combine(sourceDirectory, "DICOM/Fluorography/Emias Compressed/1.871.3.3958735481.62656.17963.4096047274.351950500.1.1.1");
string filePath = System.IO.Path.Combine(sourceDirectory, "/media/nikolaev_ov/CEFE3C54FE3C36D5/DICOM/ComputerTomography/Covid/SE0 (3)/IM0");
// string filePath = System.IO.Path.Combine(sourceDirectory, "SE000001/IM000000");
// string filePath = System.IO.Path.Combine(sourceDirectory, "SC_R_CC.dcm");
// string[] files = Directory.GetFiles("/media/nikolaev_ov/CEFE3C54FE3C36D5/DICOM/ComputerTomography/3000566.000000-03192/");
DicomFile dicomFile = DicomFile.Open(filePath);
DicomDataset dataset = dicomFile.Dataset;
// var t = dataset.InternalTransferSyntax;
// dataset = Compress(dataset, DicomTransferSyntax.JPEGProcess1, new DicomJpegProcess1Codec());
// dicomFile = new DicomFile(dataset);
// dicomFile.Save(System.IO.Path.Combine(sourceDirectory, "1"));
// dataset.AddOrUpdate(DicomTag.WindowCenter, 32767.0);
// dataset.AddOrUpdate(DicomTag.WindowWidth, 65534.0);
// dicomFile.Save(System.IO.Path.Combine(sourceDirectory, "1"));
// PullDicom(dataset);
// GetAverageValue(dataset, out double average, out double dispersion, out ushort min, out ushort max);
// GetAverageValue(dataset, new DicomJpegLsLosslessCodec(), out double average, out double dispersion, out ushort min, out ushort max);
// GetAverageValue(dataset, new JpegLosslessDecoderWrapperProcess14SV1(), out double average, out double dispersion, out ushort min, out ushort max);
var bitsAllocated = dataset.GetSingleValue <string>(DicomTag.BitsAllocated);
var BitsStored = dataset.GetSingleValue <string>(DicomTag.BitsStored);
var samplesPerPixel = dataset.GetSingleValue <string>(DicomTag.SamplesPerPixel);
var photometricInterpretation = dataset.GetSingleValue <string>(DicomTag.PhotometricInterpretation);
var PixelRepresentation = dataset.GetSingleValue <string>(DicomTag.PixelRepresentation);
double windowCenter = dataset.GetValue <double>(DicomTag.WindowCenter, 0);
double windowWidth = dataset.GetValue <double>(DicomTag.WindowWidth, 0);
byte[] pixelData;
using (FileStream readStream = new FileStream(filePath, FileMode.Open, FileAccess.Read))
pixelData = DicomDatasetExtensions.DecodeImage(readStream, out _).PixelData;
// using FileStream stream1 = new FileStream("/media/nikolaev_ov/CEFE3C54FE3C36D5/pixelData.bin", FileMode.OpenOrCreate, FileAccess.ReadWrite);
// pixelData = new byte[stream1.Length];
// stream1.Read(pixelData, 0, pixelData.Length);
// GetAverageValue(dataset, pixelData, pixelData.Length, out double average, out double dispersion, out ushort min, out ushort max);
DicomImage image = new DicomImage(dataset);
image.RenderImage().AsSharedBitmap().Save(System.IO.Path.Combine(sourceDirectory, "image.png"));
DicomPixelData sdsd = DicomPixelData.Create(dataset);
// pixelData = sdsd.GetFrame(0).Data;
fixed(byte *p = &pixelData[0])
{
// var bitmap2 = new System.Drawing.Bitmap(image.Width, image.Height, System.Drawing.Imaging.PixelFormat.Format24bppRgb);
// stream1.SetLength(0);
// for (int x = 0; x != bitmap2.Width; x++)
// for (int y = 0; y != bitmap2.Height; y++)
// {
// byte value = pixelData[y * bitmap2.Width + x];
// bitmap2.SetPixel(x, y, System.Drawing.Color.FromArgb(value));
// stream1.WriteByte(value);
// }
// stream1.Close();
// bitmap2.Save("/media/nikolaev_ov/CEFE3C54FE3C36D5/image.png");
// var img = new SixLabors.ImageSharp.Image<L8>(image.Width, image.Height);
// for (int y = 0; y < image.Height; y++)
// {
// Span<L8> span = img.GetPixelRowSpan(y);
// for (int x = 0; x < image.Width; x++)
// span[x] = new L8(pixelData[y * image.Width + x]);
// }
// var img = Image.LoadPixelData<L8>(new ReadOnlySpan<L8>(p, pixelData.Length), image.Width, image.Height);
var img = Image.LoadPixelData <L16>(new ReadOnlySpan <L16>(p, pixelData.Length / 2), image.Width, image.Height);
img.Mutate(a =>
{
// Color whiteColor = new Color(new Rgba64(ushort.MaxValue & 0x0FFF, ushort.MaxValue & 0x0FFF, ushort.MaxValue & 0x0FFF, ushort.MaxValue & 0x0FFF));
Color whiteColor = new Color(new Rgba64(ushort.MaxValue, ushort.MaxValue, ushort.MaxValue, ushort.MaxValue));
Color blackColor = new Color(new Rgba64(ushort.MinValue, ushort.MinValue, ushort.MinValue, ushort.MinValue));
a.Draw(Pens.Solid(whiteColor, 10), new EllipsePolygon(new PointF(image.Width * 0.5F, image.Height * 0.5F), 200F));
FontCollection fontCollection = new FontCollection();
fontCollection.Install(System.IO.Path.Combine(fontDirectory, "fonts/TIMES.TTF"));
string text = "ТОЛЬКО ДЛЯ ИССЛЕДОВАТЕЛЬСКИХ ЦЕЛЕЙ";
Font font = new Font(fontCollection.Families.First(), 64, FontStyle.Regular);
FontRectangle fontRectangle = TextMeasurer.Measure(text, new RendererOptions(font));
PointF textPoint = new PointF(image.Width * 0.5F - fontRectangle.Width * 0.5F, image.Height * 0.5F - 200F - fontRectangle.Height);
a.DrawText(text, font, blackColor, new PointF(textPoint.X + 5, textPoint.Y + 5));
a.DrawText(text, font, whiteColor, textPoint);
});
using FileStream stream = new FileStream(System.IO.Path.Combine(sourceDirectory, "image.jpg"), FileMode.OpenOrCreate, FileAccess.Write);
img.Save(stream, new JpegEncoder()
{
Quality = 100, Subsample = JpegSubsample.Ratio444
});
for (int y = 0; y < image.Height; y++)
{
Span <L16> span = img.GetPixelRowSpan(y);
fixed(L16 *p2 = &span[0])
Buffer.MemoryCopy(p2, p + y * image.Width * 2, image.Width * 2, image.Width * 2);
}
}
DicomDataset dataset2 = new DicomDataset();
dataset.CopyTo(dataset2);
dataset = dataset2;
dicomFile = new DicomFile(dataset);
DicomPixelData dicomPixelData = DicomPixelData.Create(dataset, true);
dicomPixelData.AddFrame(new MemoryByteBuffer(pixelData));
// dicomFile.Save(Path.Combine(sourceDirectory, "1");
// GetAverageValue(dataset, out average, out dispersion, out min, out max);
windowCenter = dataset.GetSingleValue <double>(DicomTag.WindowCenter);
windowWidth = dataset.GetSingleValue <double>(DicomTag.WindowWidth);
// string VOILUTFunction = dataset.GetSingleValue<string>(DicomTag.VOILUTFunction);
// dataset = GenerateUncompressedDicomDataset(dataset);
dataset = dataset.Compress(DicomTransferSyntax.JPEGLSLossless, new DicomJpegLsLosslessCodec(), new DicomJpegParams {
});
// GetAverageValue(dataset, new DicomJpegLsLosslessCodec(), out average, out dispersion, out min, out max);
// dataset = Uncompress(dataset, new DicomJpegLsLosslessCodec());
// GetAverageValue(dataset, out average, out dispersion, out min, out max);
dicomFile = new DicomFile(dataset);
// dataset.AddOrUpdate(DicomTag.WindowCenter, 255.0 * 0.5);
// dataset.AddOrUpdate(DicomTag.WindowWidth, 255.0);
dataset.Remove(DicomTag.WindowCenter);
dataset.Remove(DicomTag.WindowWidth);
// CheckDicomTransferSyntax(dataset);
// PullDicom(dataset);
dicomFile.Save(System.IO.Path.Combine(sourceDirectory, "1"));
}
static internal unsafe void Start(string[] args)
{
string sourceDirectory = "/media/nikolaev_ov/CEFE3C54FE3C36D5/DICOM/Fluorography/favorite/invalid-window";
ProcessDicomFile(sourceDirectory);
// using var readStream = new FileStream("/media/nikolaev_ov/CEFE3C54FE3C36D5/DICOM/Mammography/favorite/presentation-lut-shape-inverse/sources/MG_1.2.276.0.7230010.3.1.4.50143260.1368.1571935817.381.dcm", FileMode.Open, FileAccess.ReadWrite);
return;
foreach (var fileName in new[] { "IDENTITY&MONOCHROME1.dcm", "IDENTITY&MONOCHROME2.dcm", "INVERSE&MONOCHROME1.dcm", "INVERSE&MONOCHROME2.dcm", "REMOVED&MONOCHROME1.dcm", "REMOVED&MONOCHROME2.dcm", "IDENTITY&REMOVED.dcm", "INVERSE&REMOVED.dcm", "REMOVED&REMOVED.dcm" })
{
using var readStream = new FileStream(System.IO.Path.Combine(sourceDirectory, fileName), FileMode.Open, FileAccess.ReadWrite);
var decodedDicomImage = DicomDatasetExtensions.DecodeImage(readStream, out _);
// var decodedDicomImage = file.Dataset.ReadPixelData();
// var image = DicomPixelData.Create(file.Dataset, false);
// var decodedDicomImage = new DecodedDicomImageModel()
// {
// PixelData = image.GetFrame(0).Data,
// ChannelSize = (uint)(file.Dataset.GetSingleValue<ushort>(DicomTag.BitsAllocated) >> 3),
// Signed = file.Dataset.GetSingleValue<ushort>(DicomTag.PixelRepresentation) == 1,
// ChannelCount = file.Dataset.GetSingleValue<ushort>(DicomTag.SamplesPerPixel),
// Width = file.Dataset.GetSingleValue<ushort>(DicomTag.Columns),
// Height = file.Dataset.GetSingleValue<ushort>(DicomTag.Rows),
// };
// decodedDicomImage.PixelCount = decodedDicomImage.Width * decodedDicomImage.Height;
fixed(byte *p = &decodedDicomImage.PixelData[0])
{
var pixelData = new Span <L16>(p, (int)(decodedDicomImage.PixelData.Length / decodedDicomImage.ChannelSize));
var min = ushort.MaxValue;
var max = ushort.MinValue;
foreach (var pixel in pixelData)
{
if (pixel.PackedValue < min)
{
min = pixel.PackedValue;
}
if (pixel.PackedValue > max)
{
max = pixel.PackedValue;
}
}
for (int pixelIndex = 0; pixelIndex != pixelData.Length; pixelIndex++)
{
pixelData[pixelIndex] = new L16(checked ((ushort)(pixelData[pixelIndex].PackedValue * 64)));
}
var img = Image.LoadPixelData <L16>(pixelData, (int)decodedDicomImage.Width, (int)decodedDicomImage.Height);
// img.Mutate(a =>
// {
// // Color whiteColor = new Color(new Rgba64(ushort.MaxValue & 0x0FFF, ushort.MaxValue & 0x0FFF, ushort.MaxValue & 0x0FFF, ushort.MaxValue & 0x0FFF));
// Color whiteColor = new Color(new Rgba64(ushort.MaxValue, ushort.MaxValue, ushort.MaxValue, ushort.MaxValue));
// Color blackColor = new Color(new Rgba64(ushort.MinValue, ushort.MinValue, ushort.MinValue, ushort.MinValue));
// a.Draw(Pens.Solid(whiteColor, 10), new EllipsePolygon(new PointF(image.Width * 0.5F, image.Height * 0.5F), 200F));
// FontCollection fontCollection = new FontCollection();
// fontCollection.Install(System.IO.Path.Combine(fontDirectory, "fonts/TIMES.TTF"));
// string text = "ТОЛЬКО ДЛЯ ИССЛЕДОВАТЕЛЬСКИХ ЦЕЛЕЙ";
// Font font = new Font(fontCollection.Families.First(), 64, FontStyle.Regular);
// FontRectangle fontRectangle = TextMeasurer.Measure(text, new RendererOptions(font));
// PointF textPoint = new PointF(image.Width * 0.5F - fontRectangle.Width * 0.5F, image.Height * 0.5F - 200F - fontRectangle.Height);
// a.DrawText(text, font, blackColor, new PointF(textPoint.X + 5, textPoint.Y + 5));
// a.DrawText(text, font, whiteColor, textPoint);
// });
using var writeStream = new FileStream(System.IO.Path.Combine(sourceDirectory, System.IO.Path.GetFileNameWithoutExtension(fileName) + ".jpg"), FileMode.OpenOrCreate, FileAccess.Write);
img.Save(writeStream, new JpegEncoder()
{
Quality = 100, Subsample = JpegSubsample.Ratio444
});
for (int y = 0; y < img.Height; y++)
{
Span <L16> span = img.GetPixelRowSpan(y);
fixed(L16 *p2 = &span[0])
Buffer.MemoryCopy(p2, p + y * img.Width * decodedDicomImage.ChannelSize, img.Width * decodedDicomImage.ChannelSize, img.Width * decodedDicomImage.ChannelSize);
}
}
}
}
