public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null)
{
dataset.CopyTo(modifiedAttributesSequenceItem, _tag);
var uid = dataset.GetSingleValue <DicomUID>(_tag);
dataset.AddOrUpdate(_tag, _generator.Generate(uid));
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null) {
var remove = dataset.EnumerateMasked(_mask).Select(x => x.Tag).ToList();
foreach (DicomTag tag in remove) {
dataset.CopyTo(modifiedAttributesSequenceItem, tag);
dataset.Remove(tag);
}
}
public PresentationLut(DicomUID sopInstance, DicomDataset dataset)
{
if (dataset == null)
{
throw new ArgumentNullException("dataset");
}
dataset.CopyTo(this);
}
public PresentationLut(DicomUID sopInstance, DicomDataset dataset)
{
if (dataset == null)
{
throw new ArgumentNullException("dataset");
}
dataset.CopyTo(this);
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null)
{
if (dataset.Contains(_src))
{
dataset.CopyTo(modifiedAttributesSequenceItem, _dst);
dataset.AddOrUpdate(_dst, dataset.GetDicomItem <DicomElement>(_src).Buffer);
}
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null)
{
if (_match.Match(dataset))
{
dataset.CopyTo(modifiedAttributesSequenceItem, _match.Tag);
dataset.AddOrUpdate(_match.Tag, _value);
}
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null)
{
if (dataset.Contains(_tag))
{
dataset.CopyTo(modifiedAttributesSequenceItem, _tag);
var value = dataset.GetString(_tag);
dataset.AddOrUpdate(_tag, value.ToLower());
}
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null)
{
if (dataset.Contains(_tag))
{
dataset.CopyTo(modifiedAttributesSequenceItem, _tag);
var value = dataset.GetString(_tag);
value = Regex.Replace(value, _pattern, _replacement);
dataset.AddOrUpdate(_tag, value);
}
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null)
{
var remove = dataset.EnumerateMasked(_mask).Select(x => x.Tag).ToList();
foreach (DicomTag tag in remove)
{
dataset.CopyTo(modifiedAttributesSequenceItem, tag);
dataset.Remove(tag);
}
}
/// <summary>
/// Add or updates a Dicom tag at the top level of Dicom tags.
/// </summary>
/// <param name="dicomDatasetDeAnonymized">The dicom dataset de anonymized.</param>
/// <param name="referenceDicomDataset">The reference dicom dataset.</param>
/// <param name="addOrUpdateTag">The tag to add or update.</param>
public static void SimpleTopLevelAddOrUpdate(DicomDataset dicomDatasetDeAnonymized, DicomDataset referenceDicomDataset, DicomTag addOrUpdateTag)
{
referenceDicomDataset = referenceDicomDataset ?? throw new ArgumentNullException(nameof(referenceDicomDataset));
dicomDatasetDeAnonymized = dicomDatasetDeAnonymized ?? throw new ArgumentNullException(nameof(dicomDatasetDeAnonymized));
if (referenceDicomDataset.Contains(addOrUpdateTag))
{
referenceDicomDataset.CopyTo(dicomDatasetDeAnonymized, addOrUpdateTag);
}
}
public static DicomDataset GetDefaultSeriesQuery( )
{
DicomDataset ds = new DicomDataset( )
{
AutoValidate = false
};
_seriesDs.CopyTo(ds);
return(ds);
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null)
{
if (dataset.Contains(_tag))
{
dataset.CopyTo(modifiedAttributesSequenceItem, _tag);
var value = dataset.GetString(_tag);
string[] parts = value.Split(_seperators);
value = string.Format(_format, parts);
dataset.AddOrUpdate(_tag, value);
}
}
public static DicomDataset GetDefaultInstanceQuery( )
{
DicomDataset ds = new DicomDataset( )
{
AutoValidate = false
};
_instanceDs.CopyTo(ds);
return(ds);
}
/// <summary>
/// Construct new film session for specified SOP instance UID
/// </summary>
/// <param name="sopClassUID">Film session SOP Class UID</param>
/// <param name="sopInstance">Film session SOP instance UID</param>
/// <param name="dataset">Film session dataset</param>
/// <param name="isColor">Color images?</param>
public FilmSession(DicomUID sopClassUID, DicomUID sopInstance, DicomDataset dataset, bool isColor = false)
: this(sopClassUID, sopInstance, isColor)
{
if (dataset == null)
{
throw new ArgumentNullException(nameof(dataset));
}
dataset.CopyTo(this);
InternalTransferSyntax = dataset.InternalTransferSyntax;
}
/// <summary>
/// Construct new film session for specified SOP instance UID
/// </summary>
/// <param name="sopInstance">Film session SOP instance UID</param>
/// <param name="dataset">Film session dataset</param>
public FilmSession(DicomUID sopClassUID, DicomUID sopInstance, DicomDataset dataset, bool isColor = false)
: this(sopClassUID, sopInstance)
{
if (dataset == null)
{
throw new ArgumentNullException("dataset");
}
dataset.CopyTo(this);
this.InternalTransferSyntax = dataset.InternalTransferSyntax;
IsColor = isColor;
}
static public unsafe void GetAverageValue(this DicomDataset original, IDicomCodec codec, out double average, out double dispersion, out ushort min, out ushort max)
{
DicomDataset dataset = new DicomDataset();
original.CopyTo(dataset);
DicomPixelData pixelData = DicomPixelData.Create(dataset, true);
DicomPixelData pixelDataSource = DicomPixelData.Create(original, false);
codec.Decode(pixelDataSource, pixelData, new DicomJpegParams {
});
GetAverageValue(dataset, out average, out dispersion, out min, out max);
}
static public unsafe void GetAverageValue(this DicomDataset original, byte[] bytes, int size, out double average, out double dispersion, out ushort min, out ushort max)
{
DicomDataset dataset = new DicomDataset();
original.CopyTo(dataset);
DicomPixelData pixelData = DicomPixelData.Create(dataset, true);
if (pixelData.BytesAllocated != 2 || pixelData.SamplesPerPixel != 1)
{
throw new Exception();
}
double sum = 0.0;
min = ushort.MaxValue;
max = ushort.MinValue;
fixed(byte *floorPointer = &bytes[0])
{
byte *roofPointer = floorPointer + size;
for (ushort *pointer = (ushort *)floorPointer; pointer != roofPointer; pointer++)
{
ushort value = *pointer;
sum += value;
if (value < min)
{
min = value;
}
if (value > max)
{
max = value;
}
}
}
average = sum / (pixelData.Width * pixelData.Height);
sum = 0.0;
fixed(byte *floorPointer = &bytes[0])
{
byte *roofPointer = floorPointer + size;
for (ushort *pointer = (ushort *)floorPointer; pointer != roofPointer; pointer++)
{
double temp = *pointer - average;
sum += temp * temp;
}
}
dispersion = Math.Sqrt(sum / (pixelData.Width * pixelData.Height - 1));
}
static public DicomDataset Compress(this DicomDataset original, DicomTransferSyntax dicomTransferSyntax, IDicomCodec codec, DicomCodecParams jpegParams)
{
DicomDataset dataset = new DicomDataset(dicomTransferSyntax);
original.CopyTo(dataset);
DicomPixelData pixelData = DicomPixelData.Create(dataset, true);
DicomPixelData pixelDataSource = DicomPixelData.Create(original, false);
codec.Encode(pixelDataSource, pixelData, jpegParams);
return(dataset);
}
public IList <TestInstanceInfo> Save(string destDir, string filenamePrefix, DicomTransferSyntax transferSyntax, int instancesToGenerate = 1, string sopClassUid = "1.2.840.10008.5.1.4.1.1.11.1")
{
Console.Write("Generating test files.");
if (!Directory.Exists(destDir))
{
Directory.CreateDirectory(destDir);
}
var dataset = new DicomDataset();
baseDataset.CopyTo(dataset);
dataset.AddOrUpdate(DicomTag.SOPClassUID, sopClassUid);
var dicomFile = new DicomFile(dataset);
if (transferSyntax != dicomFile.Dataset.InternalTransferSyntax)
{
var transcoder = new DicomTranscoder(dicomFile.Dataset.InternalTransferSyntax, transferSyntax, outputCodecParams: new DicomJpegParams()
{
Quality = 100, ConvertColorspaceToRGB = true
});
dicomFile = transcoder.Transcode(dicomFile);
}
var instancesCreated = new List <TestInstanceInfo>();
for (int i = 0; i < instancesToGenerate; i++)
{
Console.Write(".");
var sopInstanceUid = DicomUIDGenerator.GenerateDerivedFromUUID();
var filePath = Path.Combine(destDir, $"{filenamePrefix}-{i:00000}.dcm");
dicomFile.Dataset.AddOrUpdate(DicomTag.SOPInstanceUID, sopInstanceUid);
dicomFile.FileMetaInfo.AddOrUpdate(DicomTag.MediaStorageSOPInstanceUID, sopInstanceUid);
dicomFile.FileMetaInfo.AddOrUpdate(DicomTag.MediaStorageSOPClassUID, sopClassUid);
dicomFile.Clone().Save(filePath);
instancesCreated.Add(new TestInstanceInfo
{
PatientId = dicomFile.Dataset.GetSingleValue <string>(DicomTag.PatientID),
StudyInstanceUid = dicomFile.Dataset.GetSingleValue <string>(DicomTag.StudyInstanceUID),
SeriesInstanceUid = dicomFile.Dataset.GetSingleValue <string>(DicomTag.SeriesInstanceUID),
SopInstanceUid = dicomFile.Dataset.GetSingleValue <string>(DicomTag.SOPInstanceUID),
FilePath = filePath
});
}
Console.WriteLine(".");
return(instancesCreated);
}
static public DicomDataset Uncompress(this DicomDataset original, IDicomCodec codec)
{
DicomDataset dataset = new DicomDataset();
original.CopyTo(dataset);
DicomPixelData pixelData = DicomPixelData.Create(dataset, true);
DicomPixelData pixelDataSource = DicomPixelData.Create(original, false);
codec.Decode(pixelDataSource, pixelData, new DicomJpeg2000Params {
});
return(dataset);
}
/// <summary>
/// Initializes a new instance of the <see cref="PresentationLut"/> class.
/// </summary>
/// <param name="sopInstance">SOP Instance UID associated with the Presentation LUT information object. If <code>null</code>,
/// a UID will be automatically generated.</param>
/// <param name="dataset">Dataset presumed to contain Presentation LUT data.</param>
public PresentationLut(DicomUID sopInstance, DicomDataset dataset)
{
if (dataset == null)
{
throw new ArgumentNullException(nameof(dataset));
}
dataset.CopyTo(this);
if (!dataset.Contains(DicomTag.PresentationLUTSequence))
{
CreateLutSequence();
}
SopInstanceUid = string.IsNullOrEmpty(sopInstance?.UID) ? DicomUID.Generate() : sopInstance;
AddOrUpdate(DicomTag.SOPInstanceUID, SopInstanceUid);
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null)
{
if (dataset.Contains(_tag))
{
dataset.CopyTo(modifiedAttributesSequenceItem, _tag);
var value = dataset.GetString(_tag);
if (_totalLength < 0)
{
value = value.PadLeft(-_totalLength, _paddingChar);
}
else
{
value = value.PadRight(_totalLength, _paddingChar);
}
dataset.AddOrUpdate(_tag, value);
}
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null)
{
if (dataset.Contains(_tag))
{
dataset.CopyTo(modifiedAttributesSequenceItem, _tag);
var value = dataset.GetString(_tag);
string[] parts = value.Split('\\');
for (int i = 0; i < parts.Length; i++)
{
if (parts[i].Length > _length)
{
parts[i] = parts[i].Substring(0, _length);
}
}
value = string.Join("\\", parts);
dataset.AddOrUpdate(_tag, value);
}
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null)
{
if (dataset.Contains(_tag))
{
dataset.CopyTo(modifiedAttributesSequenceItem, _tag);
var value = dataset.GetString(_tag);
if (_position == DicomTrimPosition.Both)
{
if (_trim != null)
{
value = value.Trim(_trim);
}
else
{
value = value.Trim();
}
}
else if (_position == DicomTrimPosition.Start)
{
if (_trim != null)
{
value = value.TrimStart(_trim);
}
else
{
value = value.TrimStart();
}
}
else
{
if (_trim != null)
{
value = value.TrimEnd(_trim);
}
else
{
value = value.TrimEnd();
}
}
dataset.AddOrUpdate(_tag, value);
}
}
private void PopulateData()
{
var templateDS = DicomHelper.GetDicomDataset(0);
var modalities = new string[] { "CT", "MR", "XA" };
for (int studyIndex = 0; studyIndex < TotalNumberOfStudies; studyIndex++)
{
var studyDs = new DicomDataset( );
templateDS.CopyTo(studyDs);
studyDs.AddOrUpdate(DicomTag.StudyInstanceUID, string.Format("std.{0}", studyIndex));
for (int seriesIndex = 0; seriesIndex < NumberOfSeriesInStudy; seriesIndex++)
{
var seriesDs = new DicomDataset( );
studyDs.CopyTo(seriesDs);
seriesDs.AddOrUpdate(DicomTag.SeriesInstanceUID, string.Format("std.{0}.ser.{1}", studyIndex, seriesIndex));
seriesDs.AddOrUpdate(DicomTag.Modality, modalities[studyIndex % modalities.Length]);
for (int instanceIndex = 0; instanceIndex < NumberOfInstancesInSeries; instanceIndex++)
{
var instanceDs = new DicomDataset( );
seriesDs.CopyTo(instanceDs);
instanceDs.AddOrUpdate(DicomTag.SOPInstanceUID, string.Format("std.{0}.ser.{1}.inst.{2}", studyIndex, seriesIndex, instanceIndex));
StoreService.StoreDicom(instanceDs, new DataAccess.InstanceMetadata());
}
}
}
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null)
{
if (dataset.Contains(_tag))
{
dataset.CopyTo(modifiedAttributesSequenceItem, _tag);
var value = dataset.GetString(_tag);
if (_position == DicomTrimPosition.Start || _position == DicomTrimPosition.Both)
{
while (value.StartsWith(_trim))
{
value = value.Substring(_trim.Length);
}
}
if (_position == DicomTrimPosition.End || _position == DicomTrimPosition.Both)
{
while (value.EndsWith(_trim))
{
value = value.Substring(0, value.Length - _trim.Length);
}
}
dataset.AddOrUpdate(_tag, value);
}
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null) {
if (dataset.Contains(_tag)) {
dataset.CopyTo(modifiedAttributesSequenceItem, _tag);
var value = dataset.Get<string>(_tag, -1, String.Empty);
if (_totalLength < 0)
value = value.PadLeft(-_totalLength, _paddingChar);
else
value = value.PadRight(_totalLength, _paddingChar);
dataset.Add(_tag, value);
}
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null) {
if (dataset.Contains(_tag)) {
dataset.CopyTo(modifiedAttributesSequenceItem, _tag);
var value = dataset.Get<string>(_tag, -1, String.Empty);
value = Regex.Replace(value, _pattern, _replacement);
dataset.Add(_tag, value);
}
}
public virtual void ReadData(string tableName, string columnName, object value)
{
var column = SchemaProvider.GetColumn(tableName, columnName);
var dicomTags = column.Tags;
if (IsDBNullValue(value))
{
return;
}
if (column.IsKey)
{
CurrentData.KeyValue = value.ToString( );
}
if (column.IsForeign)
{
string keyString = value.ToString( );
KeyToDataSetCollection resultSet = null;
if (ResultSets.TryGetValue(column.Table.Parent, out resultSet))
{
DicomDataset foreignDs = (DicomDataset)resultSet[keyString];
if (QueryLevelTableName == column.Table.Name)
{
foreignDs.Merge(CurrentData.CurrentDs);
//resultSet[keyString] = CurrentData.CurrentDs ;
}
else
{
if (column.Table.IsSequence)
{
DicomSequence sq = (DicomSequence)CurrentData.ForeignDs.Get <DicomSequence> (CurrentData.ForeignTagValue);
DicomDataset item = new DicomDataset( );
sq.Items.Add(item);
CurrentData.CurrentDs.Merge(item);
CurrentData.CurrentDs = item;
}
else if (column.Table.IsMultiValue)
{
CurrentData.CurrentDs = foreignDs;
}
else
{
CurrentData.CurrentDs.Merge(foreignDs);
foreignDs.CopyTo(CurrentData.CurrentDs); //TODO: check if above merge is still necessary with this new CopyTo method
}
}
}
}
if (null == dicomTags)
{
return;
}
ReadTags(columnName, value, dicomTags);
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null)
{
IDbConnection connection = null;
try
{
if (_dbType == DatabaseType.Odbc) connection = new OdbcConnection(_connectionString);
else if (_dbType == DatabaseType.MsSql) connection = new SqlConnection(_connectionString);
using (IDbCommand command = connection.CreateCommand())
{
command.Connection = connection;
command.CommandText = _query;
for (int i = 0; i < _params.Count; i++)
{
var str = dataset.Get<string>(_params[i], -1, String.Empty);
SqlParameter prm = new SqlParameter(String.Format("@{0}", i), str);
command.Parameters.Add(prm);
}
connection.Open();
if (_output.Count == 0)
{
command.ExecuteNonQuery();
}
else
{
using (IDataReader reader = command.ExecuteReader())
{
if (reader.Read())
{
for (int i = 0; i < _output.Count; i++)
{
dataset.CopyTo(modifiedAttributesSequenceItem, _output[i]);
string str = reader.GetString(i);
dataset.Add(_output[i], str);
}
}
}
}
connection.Close();
connection = null;
}
}
finally
{
if (connection != null)
{
if (connection.State == ConnectionState.Closed || connection.State == ConnectionState.Broken) connection.Close();
connection.Dispose();
}
}
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null) {
dataset.CopyTo(modifiedAttributesSequenceItem, _tag);
dataset.Add(_tag, _value);
}
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"));
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null) {
if (dataset.Contains(_src)) {
dataset.CopyTo(modifiedAttributesSequenceItem, _dst);
dataset.Add(_dst, dataset.Get<IByteBuffer>(_src));
}
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null) {
if (dataset.Contains(_tag)) {
dataset.CopyTo(modifiedAttributesSequenceItem, _tag);
var value = dataset.Get<string>(_tag, -1, String.Empty);
string[] parts = value.Split('\\');
for (int i = 0; i < parts.Length; i++) {
if (parts[i].Length > _length)
parts[i] = parts[i].Substring(0, _length);
}
value = String.Join("\\", parts);
dataset.Add(_tag, value);
}
}
// 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);
}
public FilmBox(FilmSession filmSession, DicomUID sopInstance, DicomDataset dataset)
: this(filmSession, sopInstance, dataset.InternalTransferSyntax)
{
dataset.CopyTo(this);
this.InternalTransferSyntax = dataset.InternalTransferSyntax;
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null) {
dataset.CopyTo(modifiedAttributesSequenceItem, _tag);
var uid = dataset.Get<DicomUID>(_tag);
dataset.Add(_tag, _generator.Generate(uid));
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null) {
if (dataset.Contains(_tag)) {
dataset.CopyTo(modifiedAttributesSequenceItem, _tag);
var value = dataset.Get<string>(_tag, -1, String.Empty);
dataset.Add(_tag, value.ToLower());
}
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null) {
if (dataset.Contains(_tag)) {
dataset.CopyTo(modifiedAttributesSequenceItem, _tag);
var value = dataset.Get<string>(_tag, -1, String.Empty);
string[] parts = value.Split(_seperators);
value = String.Format(_format, parts);
dataset.Add(_tag, value);
}
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null) {
if (dataset.Contains(_tag)) {
dataset.CopyTo(modifiedAttributesSequenceItem, _tag);
var value = dataset.Get<string>(_tag, -1, String.Empty);
if (_position == DicomTrimPosition.Start || _position == DicomTrimPosition.Both)
while (value.StartsWith(_trim))
value = value.Substring(_trim.Length);
if (_position == DicomTrimPosition.End || _position == DicomTrimPosition.Both)
while (value.EndsWith(_trim))
value = value.Substring(0, value.Length - _trim.Length);
dataset.Add(_tag, value);
}
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null) {
if (dataset.Contains(_tag) && dataset.Get<string>(_tag, -1, String.Empty) == _match) {
dataset.CopyTo(modifiedAttributesSequenceItem, _tag);
dataset.Add(_tag, _value);
}
}
public FilmBox(FilmSession filmSession, DicomUID sopInstance, DicomDataset dataset)
: this(filmSession, sopInstance, dataset.InternalTransferSyntax)
{
dataset.CopyTo(this);
this.InternalTransferSyntax = dataset.InternalTransferSyntax;
}
public void Transform(DicomDataset dataset, DicomDataset modifiedAttributesSequenceItem = null) {
if (dataset.Contains(_tag)) {
dataset.CopyTo(modifiedAttributesSequenceItem, _tag);
var value = dataset.Get<string>(_tag, -1, String.Empty);
if (_position == DicomTrimPosition.Both) {
if (_trim != null)
value = value.Trim(_trim);
else
value = value.Trim();
} else if (_position == DicomTrimPosition.Start) {
if (_trim != null)
value = value.TrimStart(_trim);
else
value = value.TrimStart();
} else {
if (_trim != null)
value = value.TrimEnd(_trim);
else
value = value.TrimEnd();
}
dataset.Add(_tag, value);
}
}
