public static List <string> CreateVolume(string outputDirectory, string outputName, params string[] sortedInputSliceFilenames)
{
var volumeMetadata = new VolumeData();
var imageSerializer = new XmlSerializer(typeof(ImageData));
var volumeSerializer = new XmlSerializer(typeof(VolumeData));
Directory.CreateDirectory(outputDirectory);
var volumeRawFilename = Path.Combine(outputDirectory, outputName + ".raw");
var volumeRawStream = File.Create(volumeRawFilename);
var firstSlicePosition = new[] { 0.0, 0.0, 0.0 };
var lastSlicePosition = new[] { 0.0, 0.0, 0.0 };
var sliceCount = 0;
foreach (var inputFilename in sortedInputSliceFilenames)
{
try
{
using (var inputStream = File.OpenRead(inputFilename))
{
var imageData = (ImageData)imageSerializer.Deserialize(inputStream);
volumeRawStream.Write(imageData.PixelData, 0, imageData.PixelData.Length);
if (sliceCount == 0) // Use first slice as reference slice for volume.
{
firstSlicePosition = imageData.ImagePositionPatient;
volumeMetadata.FirstSliceLocation = imageData.SliceLocation;
volumeMetadata.Columns = imageData.Columns;
volumeMetadata.Rows = imageData.Rows;
volumeMetadata.Height = imageData.Height;
volumeMetadata.Width = imageData.Width;
volumeMetadata.ImageOrientationPatient = imageData.ImageOrientationPatient;
volumeMetadata.RescaleIntercept = imageData.RescaleIntercept;
volumeMetadata.RescaleSlope = imageData.RescaleSlope;
volumeMetadata.WindowCenter = imageData.WindowCenter;
volumeMetadata.WindowWidth = imageData.WindowWidth;
}
volumeMetadata.MinIntensity = Math.Min(volumeMetadata.MinIntensity, imageData.MinIntensity);
volumeMetadata.MaxIntensity = Math.Max(volumeMetadata.MaxIntensity, imageData.MaxIntensity);
volumeMetadata.LastSliceLocation = imageData.SliceLocation;
lastSlicePosition = imageData.ImagePositionPatient;
sliceCount++;
}
}
catch (Exception err)
{
Logger.Debug("Problem reading slice: " + inputFilename + ". " + err.Message);
}
}
volumeRawStream.Close();
volumeMetadata.Depth = Math.Abs(volumeMetadata.LastSliceLocation - volumeMetadata.FirstSliceLocation);
volumeMetadata.Slices = sliceCount;
volumeMetadata.ImagePositionPatient = new[]
{
(lastSlicePosition[0] + firstSlicePosition[0]) / 2.0,
(lastSlicePosition[1] + firstSlicePosition[1]) / 2.0,
(lastSlicePosition[2] + firstSlicePosition[2]) / 2.0
};
var volumeXmlFilename = Path.Combine(outputDirectory, outputName + ".xml");
var volumeXmlStream = File.Create(volumeXmlFilename);
volumeSerializer.Serialize(volumeXmlStream, volumeMetadata);
volumeXmlStream.Close();
return(new List <string> {
volumeXmlFilename, volumeRawFilename
});
}
public static List<string> CreateVolume(string outputDirectory, string outputName, params string[] sortedInputSliceFilenames)
{
var volumeMetadata = new VolumeData();
var imageSerializer = new XmlSerializer(typeof(ImageData));
var volumeSerializer = new XmlSerializer(typeof (VolumeData));
Directory.CreateDirectory(outputDirectory);
var volumeRawFilename = Path.Combine(outputDirectory, outputName + ".raw");
var volumeRawStream = File.Create(volumeRawFilename);
var firstSlicePosition = new[] { 0.0, 0.0, 0.0 };
var lastSlicePosition = new[] { 0.0, 0.0, 0.0 };
var sliceCount = 0;
foreach (var inputFilename in sortedInputSliceFilenames)
{
try
{
using (var inputStream = File.OpenRead(inputFilename))
{
var imageData = (ImageData) imageSerializer.Deserialize(inputStream);
volumeRawStream.Write(imageData.PixelData, 0, imageData.PixelData.Length);
if (sliceCount == 0) // Use first slice as reference slice for volume.
{
firstSlicePosition = imageData.ImagePositionPatient;
volumeMetadata.FirstSliceLocation = imageData.SliceLocation;
volumeMetadata.Columns = imageData.Columns;
volumeMetadata.Rows = imageData.Rows;
volumeMetadata.Height = imageData.Height;
volumeMetadata.Width = imageData.Width;
volumeMetadata.ImageOrientationPatient = imageData.ImageOrientationPatient;
volumeMetadata.RescaleIntercept = imageData.RescaleIntercept;
volumeMetadata.RescaleSlope = imageData.RescaleSlope;
volumeMetadata.WindowCenter = imageData.WindowCenter;
volumeMetadata.WindowWidth = imageData.WindowWidth;
}
volumeMetadata.MinIntensity = Math.Min(volumeMetadata.MinIntensity, imageData.MinIntensity);
volumeMetadata.MaxIntensity = Math.Max(volumeMetadata.MaxIntensity, imageData.MaxIntensity);
volumeMetadata.LastSliceLocation = imageData.SliceLocation;
lastSlicePosition = imageData.ImagePositionPatient;
sliceCount++;
}
}
catch (Exception err)
{
Logger.Debug("Problem reading slice: " + inputFilename + ". " + err.Message);
}
}
volumeRawStream.Close();
volumeMetadata.Depth = Math.Abs(volumeMetadata.LastSliceLocation - volumeMetadata.FirstSliceLocation);
volumeMetadata.Slices = sliceCount;
volumeMetadata.ImagePositionPatient = new[]
{
(lastSlicePosition[0] + firstSlicePosition[0]) / 2.0,
(lastSlicePosition[1] + firstSlicePosition[1]) / 2.0,
(lastSlicePosition[2] + firstSlicePosition[2]) / 2.0
};
var volumeXmlFilename = Path.Combine(outputDirectory, outputName + ".xml");
var volumeXmlStream = File.Create(volumeXmlFilename);
volumeSerializer.Serialize(volumeXmlStream, volumeMetadata);
volumeXmlStream.Close();
return new List<string> { volumeXmlFilename, volumeRawFilename };
}
