// Create a 256 x 256 Secondary Capture Image Storage
static private void CreateSmallDICOM(string fileName)
{
using (var writer = new gdcm.PixmapWriter())
{
gdcm.Pixmap img = writer.GetImage();
img.SetNumberOfDimensions(3);
img.SetDimension(0, 512);
img.SetDimension(1, 512);
img.SetDimension(2, 2); // fake a 3d volume
PhotometricInterpretation pi = new PhotometricInterpretation(PhotometricInterpretation.PIType.MONOCHROME2);
img.SetPhotometricInterpretation(pi);
gdcm.DataElement pixeldata = new gdcm.DataElement(new gdcm.Tag(0x7fe0, 0x0010));
byte[] buffer = new byte[512 * 512 * 2];
pixeldata.SetByteValue(buffer, new gdcm.VL((uint)buffer.Length));
img.SetDataElement(pixeldata);
gdcm.File file = writer.GetFile();
gdcm.DataSet ds = file.GetDataSet();
gdcm.DataElement ms = new gdcm.DataElement(new gdcm.Tag(0x0008, 0x0016));
string mediastorage = "1.2.840.10008.5.1.4.1.1.7.2"; // Multi-frame Grayscale Byte Secondary Capture Image Storage
byte[] val = StrToByteArray(mediastorage);
ms.SetByteValue(val, new gdcm.VL((uint)val.Length));
ds.Insert(ms);
writer.SetFileName(fileName);
writer.Write();
}
}
static int Main(string[] args)
{
if (args.Length != 1)
{
Console.WriteLine("This program prints the patient name of a dicom file with gdcm");
Console.WriteLine("Usage: [input.dcm]");
return(1);
}
gdcm.Reader reader = new gdcm.Reader();
reader.SetFileName(args[0]);
bool ret = reader.Read();
//TagSetType tst = new TagSetType();
//tst.Add( new Tag(0x7fe0,0x10) );
//bool ret = reader.ReadUpToTag( new Tag(0x88,0x200), tst );
if (!ret)
{
return(1);
}
gdcm.File file = reader.GetFile();
gdcm.StringFilter filter = new gdcm.StringFilter();
filter.SetFile(file);
string value = filter.ToString(new gdcm.Tag(0x0010, 0x0010));
Console.WriteLine("Patient Name: " + value);
return(0);
}
public static int Main(string[] args)
{
string filename = args[0];
gdcm.StreamImageReader reader = new gdcm.StreamImageReader();
reader.SetFileName(filename);
if (!reader.ReadImageInformation())
{
return(1);
}
// Get file infos
gdcm.File f = reader.GetFile();
// get some info about image
UIntArrayType extent = ImageHelper.GetDimensionsValue(f);
//System.Console.WriteLine( extent[0] );
uint dimx = extent[0];
//System.Console.WriteLine( extent[1] );
uint dimy = extent[1];
//System.Console.WriteLine( extent[2] );
uint dimz = extent[2];
PixelFormat pf = ImageHelper.GetPixelFormatValue(f);
int pixelsize = pf.GetPixelSize();
//System.Console.WriteLine( pixelsize );
// buffer to get the pixels
byte[] buffer = new byte[dimx * dimy * pixelsize];
for (int i = 0; i < dimz; i++)
{
// Define that I want the image 0, full size (dimx x dimy pixels)
reader.DefinePixelExtent(0, (ushort)dimx, 0, (ushort)dimy, (ushort)i, (ushort)(i + 1));
uint buf_len = reader.DefineProperBufferLength(); // take into account pixel size
//System.Console.WriteLine( buf_len );
if (buf_len > buffer.Length)
{
throw new Exception("buffer is too small for target");
}
if (reader.Read(buffer, (uint)buffer.Length))
{
using (System.IO.Stream stream =
System.IO.File.Open(@"/tmp/frame.raw",
System.IO.FileMode.Create))
{
System.IO.BinaryWriter writer = new System.IO.BinaryWriter(stream);
writer.Write(buffer);
}
}
else
{
throw new Exception("can't read pixels error");
}
}
return(0);
}
public static int Main(string[] args)
{
string filename = args[0];
// instantiate the reader:
gdcm.ImageRegionReader reader = new gdcm.ImageRegionReader();
reader.SetFileName(filename);
// pull DICOM info:
if (!reader.ReadInformation())
{
return(1);
}
// Get file infos
gdcm.File f = reader.GetFile();
// get some info about image
UIntArrayType dims = ImageHelper.GetDimensionsValue(f);
PixelFormat pf = ImageHelper.GetPixelFormatValue(f);
int pixelsize = pf.GetPixelSize();
// buffer to get the pixels
byte[] buffer = new byte[dims[0] * dims[1] * pixelsize];
// define a simple box region.
BoxRegion box = new BoxRegion();
for (uint z = 0; z < dims[2]; z++)
{
// Define that I want the image 0, full size (dimx x dimy pixels)
// and do that for each z:
box.SetDomain(0, dims[0] - 1, 0, dims[1] - 1, z, z);
//System.Console.WriteLine( box.toString() );
reader.SetRegion(box);
// reader will try to load the uncompressed image region into buffer.
// the call returns an error when buffer.Length is too small. For instance
// one can call:
// uint buf_len = reader.ComputeBufferLength(); // take into account pixel size
// to get the exact size of minimum buffer
if (reader.ReadIntoBuffer(buffer, (uint)buffer.Length))
{
using (System.IO.Stream stream =
System.IO.File.Open(@"/tmp/frame.raw",
System.IO.FileMode.Create))
{
System.IO.BinaryWriter writer = new System.IO.BinaryWriter(stream);
writer.Write(buffer);
}
}
else
{
throw new Exception("can't read pixels error");
}
}
return(0);
}
public static int Main(string[] args)
{
string filename = args[0];
gdcm.Reader reader = new gdcm.Reader();
reader.SetFileName(filename);
if (!reader.Read())
{
return(1);
}
gdcm.File f = reader.GetFile();
gdcm.DataSet ds = f.GetDataSet();
string[] expectedSiemensTags = new string[] { "B_value", "AcquisitionMatrixText" };
using (PrivateTag gtag = CSAHeader.GetCSAImageHeaderInfoTag())
{
if (ds.FindDataElement(gtag))
{
using (DataElement de = ds.GetDataElement(gtag))
{
if (de != null && !de.IsEmpty())
{
using (CSAHeader csa = new CSAHeader())
{
if (csa.LoadFromDataElement(de))
{
foreach (string str in expectedSiemensTags)
{
if (csa.FindCSAElementByName(str))
{
using (CSAElement elem = csa.GetCSAElementByName(str))
{
if (elem != null)
{
System.Console.WriteLine(elem.toString());
}
}
}
}
}
}
}
}
}
}
return(0);
}
private void FramesQuery(string PatientId)
{
gdcm.ERootType typ = gdcm.ERootType.ePatientRootType;
gdcm.EQueryLevel poziom = gdcm.EQueryLevel.ePatient; // zobacz inne
gdcm.KeyValuePairArrayType klucze = new gdcm.KeyValuePairArrayType();
gdcm.KeyValuePairType klucz1 = new gdcm.KeyValuePairType(new gdcm.Tag(0x0010, 0x0020), PatientId); // NIE WOLNO TU STOSOWAC *; tutaj PatientID="01"
klucze.Add(klucz1);
// skonstruuj zapytanie
gdcm.BaseRootQuery zapytanie = gdcm.CompositeNetworkFunctions.ConstructQuery(typ, poziom, klucze, true);
// sprawdź, czy zapytanie spełnia kryteria
if (!zapytanie.ValidateQuery())
{
MessageBox.Show("Wrong frames query.", "Error");
}
// przygotuj katalog na wyniki
String odebrane = System.IO.Path.Combine(".", "temporary");
if (!System.IO.Directory.Exists(odebrane))
{
System.IO.Directory.CreateDirectory(odebrane);
}
dane = System.IO.Path.Combine(odebrane, System.IO.Path.GetRandomFileName()); //katalog
System.IO.Directory.CreateDirectory(dane);
// wykonaj zapytanie - pobierz do katalogu _dane_
bool stan = gdcm.CompositeNetworkFunctions.CMove(ip, port, zapytanie, port, aet, call, dane);
// sprawdź stan
if (!stan)
{
MessageBox.Show("PACS server doesn't work.", "Error");
}
// skasowanie listy zdjęć
Images.Clear();
ImageNames.Clear();
Datas.Clear();
List <string> pliki = new List <string>(System.IO.Directory.EnumerateFiles(dane)); //nazwy plikow
foreach (String plik in pliki)
{
gdcm.Reader dataReader = new gdcm.Reader();
dataReader.SetFileName(plik);
if (!dataReader.Read())
{
continue;
}
gdcm.File file = dataReader.GetFile();
gdcm.DataSet dataSet = file.GetDataSet();
string data = dataSet.toString();
gdcm.Global g = gdcm.Global.GetInstance();
gdcm.Dicts dicts = g.GetDicts();
gdcm.Dict dict = dicts.GetPublicDict();
string[] dataArray = dataSet.toString().Split('\n');
Dictionary <string, string> dataValues = new Dictionary <string, string>();
String[] id = plik.Split('\\');
foreach (string s in dataArray)
{
string[] dataArrayRow = s.Split('\t');
if (dataArrayRow.Length > 1)
{
string[] tags = dataArrayRow[0].Remove(0, 1).Remove(dataArrayRow[0].Length - 2, 1).Split(',');
//Pobranie nazwy Tagu
//gdcm.Tag tag = new gdcm.Tag(Convert.ToUInt16(tags[0]),Convert.ToUInt16(tags[1]));
//string dictDorTag = dict.GetKeywordFromTag(tag);
//if (dictDorTag != null)
// dataValues.Add(dictDorTag, dataArrayRow[dataArrayRow.Length - 1]);
dataValues.Add(dataArrayRow[0], dataArrayRow[dataArrayRow.Length - 1]);
}
}
// przeczytaj pixele
gdcm.PixmapReader reader = new gdcm.PixmapReader();
reader.SetFileName(plik);
if (!reader.Read())
{
continue;
}
// przekonwertuj na "znany format"
gdcm.Bitmap bmjpeg2000 = PACS.ImageConverter.pxmap2jpeg2000(reader.GetPixmap());
// przekonwertuj na .NET bitmapy
System.Drawing.Bitmap[] X = PACS.ImageConverter.gdcmBitmap2Bitmap(bmjpeg2000);
// zapisz
for (int i = 0; i < X.Length; i++)
{
String name = "";
if (X.Length > 1)
{
name = String.Format("{0}_slice{1}.jpg", plik, i);
Images.Add(String.Format("{0}_slice{1}", id[id.Length - 1], i), X[i]);
ImageNames.Add(String.Format("{0}_slice{1}", id[id.Length - 1], i));
Datas.Add(String.Format("{0}_slice{1}", id[id.Length - 1], i), dataValues);
}
else
{
name = String.Format("{0}.jpg", plik);
Images.Add(String.Format("{0}", id[id.Length - 1]), X[i]);
ImageNames.Add(String.Format("{0}", id[id.Length - 1]));
Datas.Add(String.Format("{0}", id[id.Length - 1]), dataValues);
}
X[i].Save(name);
}
}
}
gdcm.DataSet GetDatasetFromFile(string path)
{
gdcm.Reader reader = CreateReader(path);
gdcm.File file = reader.GetFile();
return(file.GetDataSet());
}
private void FramesQuery(string PatientId, out string dane, out string name, out Dictionary <string, Dictionary <string, string> > Datas, out string segmentation_name)
{
gdcm.ERootType typ = gdcm.ERootType.ePatientRootType;
gdcm.EQueryLevel poziom = gdcm.EQueryLevel.ePatient; // zobacz inne
gdcm.KeyValuePairArrayType klucze = new gdcm.KeyValuePairArrayType();
gdcm.KeyValuePairType klucz1 = new gdcm.KeyValuePairType(new gdcm.Tag(0x0010, 0x0020), PatientId); // NIE WOLNO TU STOSOWAC *; tutaj PatientID="01"
klucze.Add(klucz1);
// skonstruuj zapytanie
gdcm.BaseRootQuery zapytanie = gdcm.CompositeNetworkFunctions.ConstructQuery(typ, poziom, klucze, true);
// sprawdź, czy zapytanie spełnia kryteria
if (!zapytanie.ValidateQuery())
{
MessageBox.Show("Wrong frames query.", "Error");
}
// przygotuj katalog na wyniki
String odebrane = System.IO.Path.Combine(".", "temporary");
if (!System.IO.Directory.Exists(odebrane))
{
System.IO.Directory.CreateDirectory(odebrane);
}
dane = System.IO.Path.Combine(odebrane, System.IO.Path.GetRandomFileName()); //katalog
System.IO.Directory.CreateDirectory(dane);
// wykonaj zapytanie - pobierz do katalogu _dane_
bool stan = gdcm.CompositeNetworkFunctions.CMove(ip, port, zapytanie, 10104, aet, call, dane);
// sprawdź stan
if (!stan)
{
MessageBox.Show("PACS server doesn't work.", "Error");
}
// skasowanie listy zdjęć
name = "";
segmentation_name = "";
Datas = new Dictionary <string, Dictionary <string, string> >();
List <string> pliki = new List <string>(System.IO.Directory.EnumerateFiles(dane)); //nazwy plikow
//OBRAZ ORYGINALNY
gdcm.Reader dataReader = new gdcm.Reader();
dataReader.SetFileName(pliki[0]);
if (!dataReader.Read())
{
}
gdcm.File file = dataReader.GetFile();
gdcm.DataSet dataSet = file.GetDataSet();
string data = dataSet.toString();
gdcm.Global g = gdcm.Global.GetInstance();
gdcm.Dicts dicts = g.GetDicts();
gdcm.Dict dict = dicts.GetPublicDict();
string[] dataArray = dataSet.toString().Split('\n');
Dictionary <string, string> dataValues = new Dictionary <string, string>();
String[] id = pliki[0].Split('\\');
bool first_exp = true;
bool first_original = true;
foreach (string plik in pliki)
{
dataValues.Clear();
foreach (string s in dataArray)
{
string[] dataArrayRow = s.Split('\t');
if (dataArrayRow.Length > 1)
{
string[] tags = dataArrayRow[0].Remove(0, 1).Remove(dataArrayRow[0].Length - 2, 1).Split(',');
//Pobranie nazwy Tagu
//gdcm.Tag tag = new gdcm.Tag(Convert.ToUInt16(tags[0]),Convert.ToUInt16(tags[1]));
//string dictDorTag = dict.GetKeywordFromTag(tag);
//if (dictDorTag != null)
// dataValues.Add(dictDorTag, dataArrayRow[dataArrayRow.Length - 1]);
dataValues.Add(dataArrayRow[0], dataArrayRow[dataArrayRow.Length - 1]);
}
}
if (dataValues.Count > 0)
{
if (dataValues["(0020,000d)"].Substring(0, 1) == "E" && first_exp == true)
{//OBRAZ SEGMENTACJI
gdcm.Reader dataReader2 = new gdcm.Reader();
dataReader2.SetFileName(plik);
if (!dataReader2.Read())
{
}
gdcm.File file2 = dataReader2.GetFile();
// przeczytaj pixele
gdcm.PixmapReader reader2 = new gdcm.PixmapReader();
string temp = plik;
if (plik.Substring(plik.Length - 4, 4) != ".dcm")
{
temp = pliki[1] + ".dcm";
}
reader2.SetFileName(plik);
if (!reader2.Read())
{
}
segmentation_name = String.Format("{0}", plik.Substring(0, plik.Length - 4));
first_exp = false;
}
else
{
if (first_original == true)
{
// przeczytaj pixele
gdcm.PixmapReader reader = new gdcm.PixmapReader();
string temp = plik;
if (plik.Substring(plik.Length - 4, 4) != ".dcm")
{
temp = plik + ".dcm";
}
reader.SetFileName(plik);
if (!reader.Read())
{
}
name = String.Format("{0}", plik.Substring(0, plik.Length - 4));
Datas.Add(String.Format("{0}", plik.Substring(0, plik.Length - 4)).Replace("\\", "\\\\"), dataValues);
first_original = false;
}
else
{
gdcm.Reader dataReader2 = new gdcm.Reader();
dataReader2.SetFileName(plik);
if (!dataReader2.Read())
{
}
gdcm.File file2 = dataReader2.GetFile();
// przeczytaj pixele
gdcm.PixmapReader reader2 = new gdcm.PixmapReader();
string temp = plik;
if (plik.Substring(plik.Length - 4, 4) != ".dcm")
{
temp = pliki[1] + ".dcm";
}
reader2.SetFileName(plik);
if (!reader2.Read())
{
}
segmentation_name = String.Format("{0}", plik.Substring(0, plik.Length - 4));
first_exp = false;
}
}
}
}
}
public static int Main(string[] args)
{
string file1 = args[0];
Mpeg2VideoInfo info = new Mpeg2VideoInfo(file1);
System.Console.WriteLine(info.StartTime);
System.Console.WriteLine(info.EndTime);
System.Console.WriteLine(info.Duration);
System.Console.WriteLine(info.AspectRatio);
System.Console.WriteLine(info.FrameRate);
System.Console.WriteLine(info.PictureWidth);
System.Console.WriteLine(info.PictureHeight);
ImageReader r = new ImageReader();
//Image image = new Image();
Image image = r.GetImage();
image.SetNumberOfDimensions(3);
DataElement pixeldata = new DataElement(new gdcm.Tag(0x7fe0, 0x0010));
System.IO.FileStream infile =
new System.IO.FileStream(file1, System.IO.FileMode.Open, System.IO.FileAccess.Read);
uint fsize = gdcm.PosixEmulation.FileSize(file1);
byte[] jstream = new byte[fsize];
infile.Read(jstream, 0, jstream.Length);
SmartPtrFrag sq = SequenceOfFragments.New();
Fragment frag = new Fragment();
frag.SetByteValue(jstream, new gdcm.VL((uint)jstream.Length));
sq.AddFragment(frag);
pixeldata.SetValue(sq.__ref__());
// insert:
image.SetDataElement(pixeldata);
PhotometricInterpretation pi = new PhotometricInterpretation(PhotometricInterpretation.PIType.YBR_PARTIAL_420);
image.SetPhotometricInterpretation(pi);
// FIXME hardcoded:
PixelFormat pixeltype = new PixelFormat(3, 8, 8, 7);
image.SetPixelFormat(pixeltype);
// FIXME hardcoded:
TransferSyntax ts = new TransferSyntax(TransferSyntax.TSType.MPEG2MainProfile);
image.SetTransferSyntax(ts);
image.SetDimension(0, (uint)info.PictureWidth);
image.SetDimension(1, (uint)info.PictureHeight);
image.SetDimension(2, 721);
ImageWriter writer = new ImageWriter();
gdcm.File file = writer.GetFile();
file.GetHeader().SetDataSetTransferSyntax(ts);
Anonymizer anon = new Anonymizer();
anon.SetFile(file);
MediaStorage ms = new MediaStorage(MediaStorage.MSType.VideoEndoscopicImageStorage);
UIDGenerator gen = new UIDGenerator();
anon.Replace(new Tag(0x0008, 0x16), ms.GetString());
anon.Replace(new Tag(0x0018, 0x40), "25");
anon.Replace(new Tag(0x0018, 0x1063), "40.000000");
anon.Replace(new Tag(0x0028, 0x34), "4\\3");
anon.Replace(new Tag(0x0028, 0x2110), "01");
writer.SetImage(image);
writer.SetFileName("dummy.dcm");
if (!writer.Write())
{
System.Console.WriteLine("Could not write");
return(1);
}
return(0);
}
