/**Returns the unsorted files list in the given directory. This list is not filtered
* (that means that the list may have non-dicom files) nor sorted.*/
private gdcm.FilenamesType GetUnsortedFilenameList(string path)
{
gdcm.Directory dir = new gdcm.Directory();
dir.Load(path);
gdcm.FilenamesType unsortedFiles = dir.GetFilenames();
return(unsortedFiles);
}
public bool Store(string path)
{
gdcm.FilenamesType pliki = new gdcm.FilenamesType();
pliki.Add(path);
bool stan = gdcm.CompositeNetworkFunctions.CStore(ip, port, pliki, aet, call);
return(stan);
}
private gdcm.FilenamesType GetFilteredFiles(string path, Func <float, string, float> progressCallback)
{
gdcm.FilenamesType unsortedFiles = GetUnsortedFilenameList(path);
progressCallback(0.01f, "Aquired file list.");
gdcm.Scanner scanner = PrepareFileScanner();
gdcm.FilenamesType filteredFiles = ScanFiles(scanner, unsortedFiles);
progressCallback(0.05f, "Filtered files.");
return(filteredFiles);
}
/// <summary>
/// Scan the given directory with the given scanner returning the only the files that
/// have the tags on the given scanner.
/// </summary>
/// <param name="scanner">The scanner with the tags</param>
/// <param name="directory">The directory to be scanned</param>
/// <returns>The file list without the files that don't have the tags.</returns>
gdcm.FilenamesType ScanFiles(gdcm.Scanner scanner, gdcm.FilenamesType directory)
{
bool b = scanner.Scan(directory);
if (!b)
{
throw new FileScanException(directory.First());
}
return(scanner.GetKeys());
}
List <PathAndData> SortFilenames(gdcm.FilenamesType files, Func <float, string, float> progressCallback)
{
var currentFileCount = 0;
List <PathAndData> paths = files.Select(currFilePath =>
{
gdcm.DataSet ds1 = GetDatasetFromFile(currFilePath);
float percentage = (float)currentFileCount / (float)files.Count();
progressCallback(percentage, currFilePath);
Thread.Yield();
string p1Name = GetPatientName(ds1);
string p1Study = GetStudyUid(ds1);
string p1Series = GetSeriesUid(ds1);
float[] p1Position = GetImagePosition(ds1);
float[] image1OrientationPlane = GetDirectionCosines(ds1);
var pd = new PathAndData()
{
path = currFilePath, patient = p1Name, study = p1Study, series = p1Series, orientationPlane = image1OrientationPlane, position = p1Position
};
currentFileCount++;
return(pd);
}).ToList <PathAndData>();
paths.Sort((PathAndData file1, PathAndData file2) =>
{
int nameComparison = file1.patient.CompareTo(file2.patient);
int studyComparison = file1.study.CompareTo(file2.study);
int seriesComparison = file1.series.CompareTo(file2.series);
var image1OrientationPlane = file1.orientationPlane;
var p1Position = file1.position;
var p2Position = file2.position;
double[] normal = new double[3];
normal[0] = image1OrientationPlane[1] * image1OrientationPlane[5] - image1OrientationPlane[2] * image1OrientationPlane[4];
normal[1] = image1OrientationPlane[2] * image1OrientationPlane[3] - image1OrientationPlane[0] * image1OrientationPlane[5];
normal[2] = image1OrientationPlane[0] * image1OrientationPlane[4] - image1OrientationPlane[1] * image1OrientationPlane[3];
double dist1 = 0;
for (var i = 0; i < 3; ++i)
{
dist1 += normal[i] * p1Position[i];
}
double dist2 = 0;
for (var i = 0; i < 3; ++i)
{
dist2 += normal[i] * p2Position[i];
}
int imagePositionComparison = dist1.CompareTo(dist2);
if (nameComparison != 0)
{
return(nameComparison); //Se o nome é diferente retorna a comparacao do nome
}
if (studyComparison != 0)
{
return(studyComparison); //Se o nome é igual e o estudo é diferente retorna a comparação do estudo
}
if (seriesComparison != 0)
{
return(seriesComparison); //Se o nome e o estudo são iguais e a serie é diferente retorna a comparacao da serie.
}
//Se o nome, estudo e série são iguais retorna a comparação da image position
return(imagePositionComparison);
});
return(paths);
}
public static int Main(string[] args)
{
string directory = args[0];
gdcm.Directory dir = new gdcm.Directory();
uint nfiles = dir.Load(directory);
//System.Console.WriteLine(dir.toString());
gdcm.FilenamesType filenames = dir.GetFilenames();
Image image = new Image();
image.SetNumberOfDimensions(3); // important for now
DataElement pixeldata = new DataElement(new gdcm.Tag(0x7fe0, 0x0010));
// Create a new SequenceOfFragments C++ object, store it as a SmartPointer :
SmartPtrFrag sq = SequenceOfFragments.New();
// Yeah, the file are not garantee to be in order, please adapt...
for (uint i = 0; i < nfiles; ++i)
{
System.Console.WriteLine(filenames[(int)i]);
string file = filenames[(int)i];
System.IO.FileStream infile =
new System.IO.FileStream(file, System.IO.FileMode.Open, System.IO.FileAccess.Read);
uint fsize = gdcm.PosixEmulation.FileSize(file);
byte[] jstream = new byte[fsize];
infile.Read(jstream, 0, jstream.Length);
Fragment frag = new Fragment();
frag.SetByteValue(jstream, new gdcm.VL((uint)jstream.Length));
sq.AddFragment(frag);
}
// Pass by reference:
pixeldata.SetValue(sq.__ref__());
// insert:
image.SetDataElement(pixeldata);
// JPEG use YBR to achieve better compression ratio by default (not RGB)
// FIXME hardcoded:
PhotometricInterpretation pi = new PhotometricInterpretation(PhotometricInterpretation.PIType.MONOCHROME2);
image.SetPhotometricInterpretation(pi);
// FIXME hardcoded:
PixelFormat pixeltype = new PixelFormat(1, 8, 8, 7);
image.SetPixelFormat(pixeltype);
// FIXME hardcoded:
image.SetTransferSyntax(new TransferSyntax(TransferSyntax.TSType.JPEGLosslessProcess14_1));
image.SetDimension(0, 512);
image.SetDimension(1, 512);
image.SetDimension(2, 355);
// Decompress !
byte[] decompressedData = new byte[(int)image.GetBufferLength()];
image.GetBuffer(decompressedData);
// Write out the decompressed bytes
System.Console.WriteLine(image.toString());
using (System.IO.Stream stream =
System.IO.File.Open(@"/tmp/dd.raw",
System.IO.FileMode.Create))
{
System.IO.BinaryWriter writer = new System.IO.BinaryWriter(stream);
writer.Write(decompressedData);
}
return(0);
}