/// <summary>
/// Resize image depending on a reference image.
/// </summary>
/// <param name="toResize">image</param>
/// <param name="referenceImage">reference image</param>
/// <returns>resampled image</returns>
public static sitk.Image ResizeImage(sitk.Image toResize, sitk.Image referenceImage)
{
if (toResize.GetWidth() == referenceImage.GetWidth() && toResize.GetHeight() == referenceImage.GetHeight())
{
return(toResize);
}
uint width = toResize.GetWidth() < referenceImage.GetWidth() ? referenceImage.GetWidth() : toResize.GetWidth();
uint height = toResize.GetHeight() < referenceImage.GetHeight() ? referenceImage.GetHeight() : toResize.GetHeight();
sitk.VectorUInt32 vec = new sitk.VectorUInt32();
vec.Add(width);
vec.Add(height);
sitk.ResampleImageFilter resampleFilter = new sitk.ResampleImageFilter();
resampleFilter.SetSize(vec);
resampleFilter.SetOutputOrigin(toResize.GetOrigin());
resampleFilter.SetOutputDirection(toResize.GetDirection());
resampleFilter.SetOutputSpacing(toResize.GetSpacing());
resampleFilter.SetOutputPixelType(referenceImage.GetPixelID());
resampleFilter.SetDefaultPixelValue(255.0);
sitk.Image resultImage = resampleFilter.Execute(toResize);
return(resultImage);
}
/// <summary>
/// Resize image by new width and height.
/// </summary>
/// <param name="image">input image</param>
/// <param name="newWidth">width</param>
/// <param name="newHeight">height</param>
/// <returns>resized image</returns>
public static sitk.Image ResizeImage(sitk.Image image, uint newWidth, uint newHeight)
{
if (image.GetWidth() == newWidth && image.GetHeight() == newHeight)
{
return(image);
}
sitk.VectorUInt32 vec = new sitk.VectorUInt32();
vec.Add(newWidth);
vec.Add(newHeight);
sitk.ResampleImageFilter resampleFilter = new sitk.ResampleImageFilter();
resampleFilter.SetSize(vec);
resampleFilter.SetOutputOrigin(image.GetOrigin());
resampleFilter.SetOutputDirection(image.GetDirection());
resampleFilter.SetOutputSpacing(image.GetSpacing());
resampleFilter.SetOutputPixelType(image.GetPixelID());
resampleFilter.SetDefaultPixelValue(255.0);
sitk.Image resultImage = resampleFilter.Execute(image);
return(resultImage);
}
/// <summary>
/// Execute transformation of rgb image.
/// </summary>
public void Execute()
{
string outputDir = ReadWriteUtils.GetOutputDirectory(registrationParameters, registrationParameters.Iteration);
if (Directory.Exists(outputDir))
{
Directory.CreateDirectory(outputDir);
}
// split rgb channels
sitk.VectorIndexSelectionCastImageFilter rgbVector = new sitk.VectorIndexSelectionCastImageFilter();
sitk.Image redChannel = rgbVector.Execute(movingImage, 0, sitk.PixelIDValueEnum.sitkFloat32);
sitk.Image greenChannel = rgbVector.Execute(movingImage, 1, sitk.PixelIDValueEnum.sitkFloat32);
sitk.Image blueChannel = rgbVector.Execute(movingImage, 2, sitk.PixelIDValueEnum.sitkFloat32);
foreach (var parameter in parameterMaps[0])
{
parameter["DefaultPixelValue"][0] = "255.0";
parameter["ResultImagePixelType"][0] = "short";
if (parameter.ContainsKey("UseBinaryFormatForTransformationParameters"))
{
parameter.Remove("UseBinaryFormatForTransformationParameters");
}
if (interpolationOrder != -1)
{
parameter["FinalBSplineInterpolationOrder"][0] = interpolationOrder.ToString();
}
else
{
parameter["FinalBSplineInterpolationOrder"][0] = "3";
}
if (parameter["Transform"][0] == "SimilarityTransform" ||
registrationParameters.RegistrationDefaultParams == RegistrationDefaultParameters.similarity)
{
sitk.VectorString vec = new sitk.VectorString();
vec.Add((registrationParameters.LargestImageWidth / 2).ToString()); // fixed image width / 2
vec.Add((registrationParameters.LargestImageHeight / 2).ToString()); // fixed image height / 2
parameter.Add("CenterOfRotationPoint", vec);
}
}
// initialize transformix
transformix.SetOutputDirectory(outputDir);
transformix.SetTransformParameterMap(parameterMaps.First()[0]);
// add further transform parameters
if (parameterMaps[0].Count > 1)
{
for (int i = 1; i < parameterMaps[0].Count; i++)
{
var vectorParameterMap = parameterMaps[0][i];
transformix.AddTransformParameterMap(vectorParameterMap);
}
}
transformix.ComputeDeformationFieldOn();
transformix.LogToFileOn();
if (registrationParameters.ComputeJaccobian)
{
transformix.ComputeSpatialJacobianOn();
transformix.ComputeDeterminantOfSpatialJacobianOn();
}
transformix.PrintParameterMap();
// red
transformix.SetMovingImage(redChannel);
sitk.Image resultRedChannel = transformix.Execute();
resultRedChannel = TransformationUtils.InterpolateImage(resultRedChannel, sitk.InterpolatorEnum.sitkBSplineResamplerOrder3, sitk.PixelIDValueEnum.sitkUInt8);
//ReadWriteUtils.WriteSitkImageWithPreCast(resultRedChannel, registrationParameters.OutputDirectory + "\\red_channel.png");
// green
transformix.SetMovingImage(greenChannel);
sitk.Image resultGreenChannel = transformix.Execute();
resultGreenChannel = TransformationUtils.InterpolateImage(resultGreenChannel, sitk.InterpolatorEnum.sitkBSplineResamplerOrder3, sitk.PixelIDValueEnum.sitkUInt8);
//ReadWriteUtils.WriteSitkImageWithPreCast(resultGreenChannel, registrationParameters.OutputDirectory + "\\green_channel.png");
// blue
transformix.SetMovingImage(blueChannel);
sitk.Image resultBlueChannel = transformix.Execute();
resultBlueChannel = TransformationUtils.InterpolateImage(resultBlueChannel, sitk.InterpolatorEnum.sitkBSplineResamplerOrder3, sitk.PixelIDValueEnum.sitkUInt8);
//ReadWriteUtils.WriteSitkImageWithPreCast(resultBlueChannel, registrationParameters.OutputDirectory + "\\blue_channel.png");
// compose image channels
sitk.VectorOfImage vectorImages = new sitk.VectorOfImage();
vectorImages.Add(resultRedChannel);
vectorImages.Add(resultGreenChannel);
vectorImages.Add(resultBlueChannel);
sitk.ComposeImageFilter composeImageFilter = new sitk.ComposeImageFilter();
sitk.Image composedImage = composeImageFilter.Execute(vectorImages);
if (registrationParameters.Type == RegistrationType.NonRigid)
{
transformedImage = TransformationUtils.InterpolateImage(composedImage, sitk.InterpolatorEnum.sitkBSplineResamplerOrder5, composedImage.GetPixelID());
}
else
{
transformedImage = composedImage;
}
transformedImage = composedImage;
// interpolation of output image (needs to be improved -> currently theres a little loss in quality)
// possible solution: interpolate grayscale images and compose afterwards
/*sitk.ExpandImageFilter expandImageFilter = new sitk.ExpandImageFilter();
* expandImageFilter.SetInterpolator(sitk.InterpolatorEnum.sitkLinear);
* transformedImage = expandImageFilter.Execute(composedImage);*/
//transformedImage = composedImage;
}
