public VolumeDataset Import()
{
// Check that the file exists
if (!File.Exists(filePath))
{
Debug.LogError("The file does not exist: " + filePath);
return(null);
}
FileStream fs = new FileStream(filePath, FileMode.Open);
BinaryReader reader = new BinaryReader(fs);
// Check that the dimension does not exceed the file size
long expectedFileSize = (long)(dimX * dimY * dimZ) * GetSampleFormatSize(contentFormat) + skipBytes;
if (fs.Length < expectedFileSize)
{
Debug.LogError($"The dimension({dimX}, {dimY}, {dimZ}) exceeds the file size. Expected file size is {expectedFileSize} bytes, while the actual file size is {fs.Length} bytes");
reader.Close();
fs.Close();
return(null);
}
VolumeDataset dataset = new VolumeDataset();
dataset.datasetName = Path.GetFileName(filePath);
dataset.filePath = filePath;
dataset.dimX = dimX;
dataset.dimY = dimY;
dataset.dimZ = dimZ;
// Skip header (if any)
if (skipBytes > 0)
{
reader.ReadBytes(skipBytes);
}
int uDimension = dimX * dimY * dimZ;
dataset.data = new float[uDimension];
// Read the data/sample values
for (int i = 0; i < uDimension; i++)
{
dataset.data[i] = (float)ReadDataValue(reader);
}
Debug.Log("Loaded dataset in range: " + dataset.GetMinDataValue() + " - " + dataset.GetMaxDataValue());
reader.Close();
fs.Close();
dataset.FixDimensions();
return(dataset);
}
public VolumeDataset Import()
{
if (!Directory.Exists(directoryPath))
{
throw new NullReferenceException("No directory found: " + directoryPath);
}
List <string> imagePaths = GetSortedImagePaths();
Vector3Int dimensions = GetVolumeDimensions(imagePaths);
int[] data = FillSequentialData(dimensions, imagePaths);
VolumeDataset dataset = FillVolumeDataset(data, dimensions);
dataset.FixDimensions();
return(dataset);
}
public VolumeDataset ImportDICOMSeries(DICOMSeries series)
{
List <DICOMSliceFile> files = series.dicomFiles;
// Check if the series is missing the slice location tag
bool needsCalcLoc = false;
foreach (DICOMSliceFile file in files)
{
needsCalcLoc |= file.missingLocation;
}
// Calculate slice location from "Image Position" (0020,0032)
if (needsCalcLoc)
{
CalcSliceLocFromPos(files);
}
// Sort files by slice location
files.Sort((DICOMSliceFile a, DICOMSliceFile b) => { return(a.location.CompareTo(b.location)); });
Debug.Log($"Importing {files.Count} DICOM slices");
if (files.Count <= 1)
{
Debug.LogError("Insufficient number of slices.");
return(null);
}
// Create dataset
VolumeDataset dataset = new VolumeDataset();
dataset.datasetName = Path.GetFileName(datasetName);
dataset.dimX = files[0].file.PixelData.Columns;
dataset.dimY = files[0].file.PixelData.Rows;
dataset.dimZ = files.Count;
int dimension = dataset.dimX * dataset.dimY * dataset.dimZ;
dataset.data = new float[dimension];
for (int iSlice = 0; iSlice < files.Count; iSlice++)
{
DICOMSliceFile slice = files[iSlice];
PixelData pixelData = slice.file.PixelData;
int[] pixelArr = ToPixelArray(pixelData);
if (pixelArr == null) // This should not happen
{
pixelArr = new int[pixelData.Rows * pixelData.Columns];
}
for (int iRow = 0; iRow < pixelData.Rows; iRow++)
{
for (int iCol = 0; iCol < pixelData.Columns; iCol++)
{
int pixelIndex = (iRow * pixelData.Columns) + iCol;
int dataIndex = (iSlice * pixelData.Columns * pixelData.Rows) + (iRow * pixelData.Columns) + iCol;
int pixelValue = pixelArr[pixelIndex];
float hounsfieldValue = pixelValue * slice.slope + slice.intercept;
dataset.data[dataIndex] = Mathf.Clamp(hounsfieldValue, -1024.0f, 3071.0f);
}
}
}
if (files[0].pixelSpacing > 0.0f)
{
dataset.scaleX = files[0].pixelSpacing * dataset.dimX;
dataset.scaleY = files[0].pixelSpacing * dataset.dimY;
dataset.scaleZ = Mathf.Abs(files[files.Count - 1].location - files[0].location);
}
dataset.FixDimensions();
return(dataset);
}