private Point3d GetSpacing(DicomFile[] files)
{
Point3d spacing = new Point3d(0, 0, 0);
if (files.Length == 1)
{
return(GetSpacing(files[0]));
}
else
{
PixelDataInfo fileHeader = new PixelDataInfo(files[0]);
double thirdDimension = 0;
if (fileHeader.SliceThickness != 0)
{
thirdDimension = fileHeader.SliceThickness;
}
else if (fileHeader.GridFrameOffsetVector.Length > 1)
{
thirdDimension = fileHeader.GridFrameOffsetVector[1] - fileHeader.GridFrameOffsetVector[0];
}
spacing.X += Math.Abs(fileHeader.RowDir.X) * fileHeader.PixelSpacing[1] + Math.Abs(fileHeader.ColDir.X) * fileHeader.PixelSpacing[0];
spacing.Y += Math.Abs(fileHeader.RowDir.Y) * fileHeader.PixelSpacing[1] + Math.Abs(fileHeader.ColDir.Y) * fileHeader.PixelSpacing[0];
spacing.Z += Math.Abs(fileHeader.RowDir.Z) * fileHeader.PixelSpacing[1] + Math.Abs(fileHeader.ColDir.Z) * fileHeader.PixelSpacing[0];
spacing.X += (1 - Math.Abs(fileHeader.RowDir.X) - Math.Abs(fileHeader.ColDir.X)) * thirdDimension;
spacing.Y += (1 - Math.Abs(fileHeader.RowDir.Y) - Math.Abs(fileHeader.ColDir.Y)) * thirdDimension;
spacing.Z += (1 - Math.Abs(fileHeader.RowDir.Z) - Math.Abs(fileHeader.ColDir.Z)) * thirdDimension;
}
return(spacing);
}
private float[] GetCoords(DicomFile[] files, int size, double rowDir, double colDir, double position, int scale)
{
PixelDataInfo tempHeader = new PixelDataInfo(files[0]);
float[] coords = new float[size];
if (rowDir != 0 || colDir != 0)
{
for (int i = 0; i < size; i++)
{
coords[i] = (float)(position + i * rowDir * tempHeader.PixelSpacing[1] + i * colDir * tempHeader.PixelSpacing[0]);
}
}
else
{
if (tempHeader.GridFrameOffsetVector.Length > 1)
{
for (int i = 0; i < size; i++)
{
coords[i] = (float)(position + tempHeader.GridFrameOffsetVector[i]);
}
}
for (int i = 0; i < files.Length; i++)
{
coords[i] = (float)(position + i * tempHeader.SliceThickness);
}
}
return(coords);
}
private PixelDataInfo[] GetHeaderInfo(DicomFile[] files)
{
PixelDataInfo[] headerInfo = new PixelDataInfo[files.Length];
for (int i = 0; i < files.Length; i++)
{
headerInfo[i] = new PixelDataInfo(files[i]);
}
return(headerInfo);
}
private Point3d GetSize(DicomFile file)
{
PixelDataInfo fileHeader = new PixelDataInfo(file);
Point3d size = new Point3d();
size.X += Math.Abs(fileHeader.RowDir.X) * fileHeader.Columns + Math.Abs(fileHeader.ColDir.X) * fileHeader.Rows;
size.Y += Math.Abs(fileHeader.RowDir.Y) * fileHeader.Columns + Math.Abs(fileHeader.ColDir.Y) * fileHeader.Rows;
size.Z += Math.Abs(fileHeader.RowDir.Z) * fileHeader.Columns + Math.Abs(fileHeader.ColDir.Z) * fileHeader.Rows;
size.X += (1 - Math.Abs(fileHeader.RowDir.X) - Math.Abs(fileHeader.ColDir.X)) * fileHeader.GridFrameOffsetVector.Length;
size.Y += (1 - Math.Abs(fileHeader.RowDir.Y) - Math.Abs(fileHeader.ColDir.Y)) * fileHeader.GridFrameOffsetVector.Length;
size.Z += (1 - Math.Abs(fileHeader.RowDir.Z) - Math.Abs(fileHeader.ColDir.Z)) * fileHeader.GridFrameOffsetVector.Length;
return(size);
}
public GridBasedVoxelDataStructure Load(DicomFile[] dicomFiles)
{
GridBasedVoxelDataStructure grid = new GridBasedVoxelDataStructure();
DicomFile[] files = SortOnZIncreasing(dicomFiles);
PixelDataInfo DicomHeader = new PixelDataInfo(files[0]);
Point3d size = GetSize(files);
grid.ConstantGridSpacing = true;
grid.GridSpacing = GetSpacing(files);
grid.XCoords = GetCoords(files, (int)size.X, DicomHeader.RowDir.X, DicomHeader.ColDir.X, DicomHeader.ImagePositionPatient.X, 1);
grid.YCoords = GetCoords(files, (int)size.Y, DicomHeader.RowDir.Y, DicomHeader.ColDir.Y, DicomHeader.ImagePositionPatient.Y, 1);
grid.ZCoords = GetCoords(files, (int)size.Z, DicomHeader.RowDir.Z, DicomHeader.ColDir.Z, DicomHeader.ImagePositionPatient.Z, 1);
grid.Data = new float[(int)size.X / 1, (int)size.Y / 1, (int)size.Z / 1];
int currYIndex = 0;
int currZIndex = 0;
int currXIndex = 0;
for (int i = 0; i < files.Length; i++)
{
DicomPixelData dicomPixelData = DicomPixelData.Create(files[i].Dataset);
PixelDataInfo tempHeaderInfo = new PixelDataInfo(files[i]);
for (int j = 0; j < tempHeaderInfo.GridFrameOffsetVector.Length; j++)
{
byte[] framePixelData = dicomPixelData.GetFrame(j).Data;
float[] dataArray = GetDataArray(framePixelData, tempHeaderInfo.BitsAllocated, tempHeaderInfo.PixelRepresentation);
for (int k = 0; k < dataArray.Length; k++)
{
int currRow = k % tempHeaderInfo.Columns;
int currCol = (int)Math.Floor((double)(k / (tempHeaderInfo.Columns)));
currXIndex = (int)Math.Abs(tempHeaderInfo.RowDir.X) * currRow + (int)Math.Abs(tempHeaderInfo.ColDir.X) * currCol
+ (1 - (int)Math.Abs(tempHeaderInfo.RowDir.X) - (int)Math.Abs(tempHeaderInfo.ColDir.X)) * (i + j);;
currYIndex = (int)Math.Abs(tempHeaderInfo.RowDir.Y) * currRow + (int)Math.Abs(tempHeaderInfo.ColDir.Y) * currCol
+ (1 - (int)Math.Abs(tempHeaderInfo.RowDir.Y) - (int)Math.Abs(tempHeaderInfo.ColDir.Y)) * (i + j);;
currZIndex = (int)Math.Abs(tempHeaderInfo.RowDir.Z) * currRow + (int)Math.Abs(tempHeaderInfo.ColDir.Z) * currCol
+ (1 - (int)Math.Abs(tempHeaderInfo.RowDir.Z) - (int)Math.Abs(tempHeaderInfo.ColDir.Z)) * (i + j);
//Rescale back to actual values
dataArray[k] = dataArray[k] * tempHeaderInfo.RescaleSlope + tempHeaderInfo.RescaleSlope;
grid.Data[currXIndex, currYIndex, currZIndex] = dataArray[k];
}
}
}
return(grid);
//setGlobalMax();
}
public SliceBasedVoxelDataStructure Load(DicomFile[] files)
{
SliceBasedVoxelDataStructure grid = new SliceBasedVoxelDataStructure();
files = sort(files);
PixelDataInfo[] headerInfos = GetHeaderInfo(files);
if (files.Length > 1)
{
grid.MatrixA = getMatrixA(files.First(), files.Last(), files.Length);
}
else
{
grid.MatrixA = getSingleMatrixA(files[0]);
}
for (int i = 0; i < files.Length; i++)
{
PixelDataInfo headerInfo = headerInfos[i];
DicomPixelData dicomPixelData = DicomPixelData.Create(files[i].Dataset);
for (int j = 0; j < headerInfo.GridFrameOffsetVector.Length; j++)
{
byte[] framePixelData = dicomPixelData.GetFrame(j).Data;
float[] dataArray = GetDataArray(framePixelData, dicomPixelData.BitsAllocated, headerInfo.PixelRepresentation);
//rescale to proper values
for (int k = 0; k < dataArray.Length; k++)
{
dataArray[k] = dataArray[k] * headerInfo.RescaleSlope + headerInfo.RescaleIntercept;
}
grid.AddSlice(dataArray, headerInfo.Rows, headerInfo.Columns, headerInfo.PixelSpacing[0], headerInfo.PixelSpacing[1], headerInfo.ImagePositionPatient.X, headerInfo.ImagePositionPatient.Y, headerInfo.ImagePositionPatient.Z + headerInfo.GridFrameOffsetVector[j], headerInfo.RowDir.X, headerInfo.RowDir.Y, headerInfo.RowDir.Z, headerInfo.ColDir.X, headerInfo.ColDir.Y, headerInfo.ColDir.Z);
}
files[i] = null;
}
//grid.Window = (int)grid.GlobalMax.Value ;
//grid.Level = (int)(grid.GlobalMax.Value / 2);
return(grid);
}
private Point3d GetSize(DicomFile[] files)
{
Point3d size = new Point3d(0, 0, 0);
if (files.Length == 1)
{
return(GetSize(files[0]));
}
else
{
PixelDataInfo fileHeader = new PixelDataInfo(files[0]);
size.X += Math.Abs(fileHeader.RowDir.X) * fileHeader.Columns + Math.Abs(fileHeader.ColDir.X) * fileHeader.Rows;
size.Y += Math.Abs(fileHeader.RowDir.Y) * fileHeader.Columns + Math.Abs(fileHeader.ColDir.Y) * fileHeader.Rows;
size.Z += Math.Abs(fileHeader.RowDir.Z) * fileHeader.Columns + Math.Abs(fileHeader.ColDir.Z) * fileHeader.Rows;
size.X += (1 - Math.Abs(fileHeader.RowDir.X) - Math.Abs(fileHeader.ColDir.X)) * files.Length;
size.Y += (1 - Math.Abs(fileHeader.RowDir.Y) - Math.Abs(fileHeader.ColDir.Y)) * files.Length;
size.Z += (1 - Math.Abs(fileHeader.RowDir.Z) - Math.Abs(fileHeader.ColDir.Z)) * files.Length;
}
return(size);
}
public GridBasedVoxelDataStructure Load(DicomFile[] dicomFiles, IProgress <double> progress)
{
GridBasedVoxelDataStructure grid = new GridBasedVoxelDataStructure();
DicomFile[] files = SortOnZIncreasing(dicomFiles);
PixelDataInfo DicomHeader = new PixelDataInfo(files[0]);
Point3d size = GetSize(files);
grid.ConstantGridSpacing = true;
grid.GridSpacing = GetSpacing(files);
grid.XCoords = GetCoords(files, (int)size.X, DicomHeader.RowDir.X, DicomHeader.ColDir.X, DicomHeader.ImagePositionPatient.X, 1);
grid.YCoords = GetCoords(files, (int)size.Y, DicomHeader.RowDir.Y, DicomHeader.ColDir.Y, DicomHeader.ImagePositionPatient.Y, 1);
grid.ZCoords = GetCoords(files, (int)size.Z, DicomHeader.RowDir.Z, DicomHeader.ColDir.Z, DicomHeader.ImagePositionPatient.Z, 1);
grid.Data = new float[(int)size.X * (int)size.Y * (int)size.Z];
int currYIndex = 0;
int currZIndex = 0;
int currXIndex = 0;
for (int i = 0; i < files.Length; i++)
{
DicomPixelData dicomPixelData = DicomPixelData.Create(files[i].Dataset);
PixelDataInfo tempHeaderInfo = new PixelDataInfo(files[i]);
for (int j = 0; j < tempHeaderInfo.GridFrameOffsetVector.Length; j++)
{
byte[] framePixelData = dicomPixelData.GetFrame(j).Data;
float[] dataArray = GetDataArray(framePixelData, tempHeaderInfo.BitsAllocated, tempHeaderInfo.PixelRepresentation);
for (int k = 0; k < dataArray.Length; k++)
{
int currRow = k % tempHeaderInfo.Columns;
int currCol = (int)Math.Floor((double)(k / (tempHeaderInfo.Columns)));
currXIndex = (int)Math.Abs(tempHeaderInfo.RowDir.X) * currRow + (int)Math.Abs(tempHeaderInfo.ColDir.X) * currCol
+ (1 - (int)Math.Abs(tempHeaderInfo.RowDir.X) - (int)Math.Abs(tempHeaderInfo.ColDir.X)) * (i + j);;
currYIndex = (int)Math.Abs(tempHeaderInfo.RowDir.Y) * currRow + (int)Math.Abs(tempHeaderInfo.ColDir.Y) * currCol
+ (1 - (int)Math.Abs(tempHeaderInfo.RowDir.Y) - (int)Math.Abs(tempHeaderInfo.ColDir.Y)) * (i + j);;
currZIndex = (int)Math.Abs(tempHeaderInfo.RowDir.Z) * currRow + (int)Math.Abs(tempHeaderInfo.ColDir.Z) * currCol
+ (1 - (int)Math.Abs(tempHeaderInfo.RowDir.Z) - (int)Math.Abs(tempHeaderInfo.ColDir.Z)) * (i + j);
//Rescale back to actual HUs
dataArray[k] = dataArray[k] * tempHeaderInfo.RescaleSlope + tempHeaderInfo.RescaleIntercept;
grid.SetVoxelByIndices(currXIndex, currYIndex, currZIndex, dataArray[k]);
if (dataArray[k] > grid.MaxVoxel.Value)
{
grid.MaxVoxel.Value = dataArray[k];
grid.MaxVoxel.Position.X = grid.XCoords[currXIndex];
grid.MaxVoxel.Position.Y = grid.YCoords[currYIndex];
grid.MaxVoxel.Position.Z = grid.ZCoords[currZIndex];
}
if (dataArray[k] < grid.MinVoxel.Value)
{
grid.MinVoxel.Value = dataArray[k];
grid.MinVoxel.Position.X = grid.XCoords[currXIndex];
grid.MinVoxel.Position.Y = grid.YCoords[currYIndex];
grid.MinVoxel.Position.Z = grid.ZCoords[currZIndex];
}
}
progress.Report(100 * ((((double)j / (double)tempHeaderInfo.GridFrameOffsetVector.Length) / files.Length) + ((double)i / (double)files.Length)));
}
}
grid.XRange = new Range(grid.XCoords[0], grid.XCoords[grid.XCoords.Length - 1]);
grid.YRange = new Range(grid.YCoords[0], grid.YCoords[grid.YCoords.Length - 1]);
grid.ZRange = new Range(grid.ZCoords[0], grid.ZCoords[grid.ZCoords.Length - 1]);
//grid.ComputeMax();
return(grid);
}