public bool IsPixelDataProcessable()
{
// The 'DICONDE Viewer' can only process the pixel data, if:
// a) the IOD is a CT Slice (SOPClassName: 'Computed Tomography Image', SOPClassUID: '1.2.840.10008.5.1.4.1.1.2')
if (!this.SOPClassUID.Equals("1.2.840.10008.5.1.4.1.1.2"))
{
return(false);
}
// b) the Transfer Syntax of the IOD does not indicate a compression of the pixel data. Supported Transfer Syntaxes are:
// - Explicit VR Encoding, little endian: '1.2.840.10008.1.2.1'
// - Implicit VR Encoding, little endian: '1.2.840.10008.1.2'
// - Explicit VR Encoding, big endian: '1.2.840.10008.1.2.2'
//
// Compressed pixel data is not supported by the 'DICONDE Viewer'
//
if (!(this.TransferSyntaxUID.Equals("1.2.840.10008.1.2.1") ||
this.TransferSyntaxUID.Equals("1.2.840.10008.1.2") ||
this.TransferSyntaxUID.Equals("1.2.840.10008.1.2.2")))
{
return(false);
}
// c) the IOD must contain pixel data (DICONDE attribute (7FE0,0010) has to be present)
if (!DICONDEParserUtility.DoesDICONDEAttributeExist(this.XDocument, "(7FE0,0010)"))
{
return(false);
}
// All above criterias are fullfilled, return true
return(true);
}
public IOD(string theFileName)
{
DICONDEParser aDICONDEParser = new DICONDEParser(theFileName);
this.XDocument = aDICONDEParser.GetXDocument();
this.FileName = theFileName;
this.StudyInstanceUID = DICONDEParserUtility.GetDICONDEAttributeAsString(this.XDocument, "(0020,000D)");
this.SeriesInstanceUID = DICONDEParserUtility.GetDICONDEAttributeAsString(this.XDocument, "(0020,000E)");
this.SOPInstanceUID = DICONDEParserUtility.GetDICONDEAttributeAsString(this.XDocument, "(0008,0018)");
this.SOPClassUID = DICONDEParserUtility.GetDICONDEAttributeAsString(this.XDocument, "(0008,0016)");
this.SOPClassName = SOPClassDictionary.GetSOPClassName(this.SOPClassUID);
//DICONDE:Component
this.ComponentName = DICONDEParserUtility.GetDICONDEAttributeAsString(this.XDocument, "(0010,0010)");
this.TransferSyntaxUID = DICONDEParserUtility.GetDICONDEAttributeAsString(this.XDocument, "(0002,0010)");
// The SortOrder attribute is used for sorting the CT Slices within one series.
// For all other IOD's, the SortOrder attribute has no meaning.
// For sorting the CT Slices, the Z-Value is used.
// The Z-Value is tried to be determined either from
// - 'Image Position Component' attribute (0020,0032) or from
// - 'Slice Location' attribute (0020,1041)
if (DICONDEParserUtility.DoesDICONDEAttributeExist(this.XDocument, "(0020,0032)")) //"(0020,0032)", "Image Position (Component)"
// 'Image Position Component' attribute will be encoded as "x\y\z"
{
string aImagePositionComponent = DICONDEParserUtility.GetDICONDEAttributeAsString(this.XDocument, "(0020,0032)");
string[] split = aImagePositionComponent.Split(new Char[] { '\\' });
this.SortOrder = Convert.ToDouble(split[2], CultureInfo.InvariantCulture);
}
else
{
if (DICONDEParserUtility.DoesDICONDEAttributeExist(this.XDocument, "(0020,1041)"))
{
this.SortOrder = DICONDEParserUtility.GetDICONDEAttributeAsDouble(this.XDocument, "(0020,1041)");
}
}
}
public static void µReadDICONDEFile(µImage destination, string fileName)
{
string aFileName = fileName;
var mIOD = (new IOD(aFileName));
int mColumnCount = DICONDEParserUtility.GetDICONDEAttributeAsInt(mIOD.XDocument, "(0028,0011)"); //width
int mRowCount = DICONDEParserUtility.GetDICONDEAttributeAsInt(mIOD.XDocument, "(0028,0010)"); //height
bool aPixelPaddingValueExist = DICONDEParserUtility.DoesDICONDEAttributeExist(mIOD.XDocument, "(0028,0120)");
int aPixelPaddingValue = DICONDEParserUtility.GetDICONDEAttributeAsInt(mIOD.XDocument, "(0028,0120)");
int aPixelBitsAllocated = DICONDEParserUtility.GetDICONDEAttributeAsInt(mIOD.XDocument, "(0028,0100)");
ushort aPixelPaddingValue16;
aPixelPaddingValue16 = 0;
int aWindowCenter = DICONDEParserUtility.GetDICONDEAttributeAsInt(mIOD.XDocument, "(0028,1050)");
int aWindowWidth = DICONDEParserUtility.GetDICONDEAttributeAsInt(mIOD.XDocument, "(0028,1051)");
var aPixelDataQuery = from Element in mIOD.XDocument.Descendants("DataElement")
where Element.Attribute("Tag").Value.Equals("(7FE0,0010)")
select Element;
// Get the start position of the stream for the pixel data attribute
long aStreamPosition = Convert.ToInt64(aPixelDataQuery.Last().Attribute("StreamPosition").Value);
BinaryReader aBinaryReader = new BinaryReader(File.Open(aFileName, FileMode.Open, FileAccess.Read, FileShare.Read));
// Set the stream position of the binary reader to first pixel
aBinaryReader.BaseStream.Position = aStreamPosition;
OpenCvSharp.Mat image = null;
var size = new OpenCvSharp.Size();
size.Width = mColumnCount;
size.Height = mRowCount;
long length = aBinaryReader.BaseStream.Length; //! Important to get length outside of the cycle, otherwise too sloooow
if (16 == aPixelBitsAllocated)
{
image = new OpenCvSharp.Mat(size, OpenCvSharp.MatType.CV_16U);
var mat16 = new OpenCvSharp.Mat <ushort>(image);
var indexer = mat16.GetIndexer();
for (int aRowIndex = 0; aRowIndex < mRowCount; aRowIndex++)
{
for (int aColumnIndex = 0; aColumnIndex < mColumnCount; aColumnIndex++)
{
// For some images, the pixel buffer is smaller than '2Byte * RowCount * ColumnCount'
// That's why we need the check...
if (aBinaryReader.BaseStream.Position - 2 < length)
{
byte aByte0 = aBinaryReader.ReadByte();
byte aByte1 = aBinaryReader.ReadByte();
ushort aPixelValue = Convert.ToUInt16((aByte1 << 8) + aByte0);
// Check for Pixel Padding Value
if ((aPixelPaddingValueExist) && (aPixelValue == aPixelPaddingValue16))
{
aPixelValue = UInt16.MinValue;
}
indexer[aRowIndex, aColumnIndex] = aPixelValue;
// Rescale handling
//aPixelValue = aPixelValue * aRescaleSlope + aRescaleIntercept;
// Value of the voxel is stored in Hounsfield Units
//mHounsfieldPixelBuffer[aRowIndex, aColumnIndex] = aPixelValue;
}
}
}
OpenCvSharp.Cv2.CopyTo(mat16, destination._image);
}
else
{
image = new OpenCvSharp.Mat(size, OpenCvSharp.MatType.CV_8U);
var mat8 = new OpenCvSharp.Mat <byte>(image);
var indexer = mat8.GetIndexer();
for (int aRowIndex = 0; aRowIndex < mRowCount; aRowIndex++)
{
for (int aColumnIndex = 0; aColumnIndex < mColumnCount; aColumnIndex++)
{
if (aBinaryReader.BaseStream.Position - 2 < length)
{
byte aPixelValue = aBinaryReader.ReadByte();
if ((aPixelPaddingValueExist) && (aPixelValue == aPixelPaddingValue16))
{
aPixelValue = 0;
}
indexer[aRowIndex, aColumnIndex] = aPixelValue;
}
}
}
OpenCvSharp.Cv2.CopyTo(mat8, destination._image);
}
}
