private sitk.VectorOfParameterMap InvertTransformParameters(string parameterFilename)
{
sitk.Image fixedImage = ReadWriteUtils.ReadITKImageFromFile(registrationParameters.FixedImageFilename, sitk.PixelIDValueEnum.sitkFloat32);
sitk.ElastixImageFilter elastix = null;
try
{
// elastix manual 6.1.6: DisplacementMagnitudePenalty
elastix = new sitk.ElastixImageFilter();
elastix.SetInitialTransformParameterFileName(parameterFilename);
elastix.SetParameterMap(sitk.SimpleITK.GetDefaultParameterMap("rigid"));
elastix.SetFixedImage(fixedImage);
elastix.SetMovingImage(fixedImage);
elastix.SetParameter("HowToCombineTransforms", "Compose");
elastix.SetParameter("Metric", "DisplacementMagnitudePenalty");
elastix.SetParameter("NumberOfResolutions", "1");
elastix.Execute();
return(elastix.GetTransformParameterMap());
/*sitk.TransformixImageFilter transformix = new sitk.TransformixImageFilter();
* transformix.SetTransformParameterMap(elastix.GetTransformParameterMap());
* transformix.SetTransformParameter("InitialTransformParametersFileName", "NoInitialTransform");
* transformix.Execute();*/
}
catch (Exception ex)
{
Console.WriteLine(ex);
return(null);
} finally
{
elastix.Dispose();
fixedImage.Dispose();
}
}
/// <summary>
/// Start transformation process.
/// </summary>
public void StartTransformation()
{
sitk.VectorOfParameterMap parameterMaps = PrepareTransformationParameters();
foreach (string imageFilename in TransformImages)
{
using (sitk.Image img = ReadWriteUtils.ReadITKImageFromFile(imageFilename))
{
List <sitk.Image> channels = TransformationUtils.SplitColorChannels(img);
List <sitk.Image> transformedChannels = new List <sitk.Image>();
foreach (sitk.Image channel in channels)
{
transformedChannels.Add(ExecuteTransform(parameterMaps, channel));
channel.Dispose();
}
sitk.VectorOfImage vectorImages = new sitk.VectorOfImage();
foreach (sitk.Image tChannel in transformedChannels)
{
vectorImages.Add(TransformationUtils.InterpolateImage(tChannel, GetInterpolatorEnum(), sitk.PixelIDValueEnum.sitkUInt8));
}
sitk.ComposeImageFilter composeImageFilter = new sitk.ComposeImageFilter();
sitk.Image composedImage = composeImageFilter.Execute(vectorImages);
TransformationUtils.WriteTransformedImage(composedImage, ApplicationContext.OutputPath + "\\" + Path.GetFileNameWithoutExtension(imageFilename) + "_transformed.png");
}
}
}
/// <summary>
/// Get the coefficient map of inner structures of tissue for the transform rigidity penalty term.
/// </summary>
/// <param name="filename">image filename</param>
/// <returns>return coefficient map filename</returns>
private string GetInnerStructureSegmentationsAsCoefficientMap(string filename)
{
InnerTissueSegmentation innerSegImage = GetInnerStructureSegmentation(filename);
string filenameCoefficientMap = ReadWriteUtils.GetOutputDirectory(_parameters, _parameters.Iteration) + Constants.cCoefficientFilename;
ReadWriteUtils.WriteUMatToFile(filenameCoefficientMap, innerSegImage.GetOutput().FirstOrDefault());
innerSegImage.Dispose();
// rescale image
sitk.Image img = ReadWriteUtils.ReadITKImageFromFile(filenameCoefficientMap);
sitk.CastImageFilter castFilter = new sitk.CastImageFilter();
castFilter.SetOutputPixelType(sitk.PixelIDValueEnum.sitkFloat32);
img = castFilter.Execute(img);
sitk.RescaleIntensityImageFilter filter = new sitk.RescaleIntensityImageFilter();
filter.SetOutputMinimum(0.0);
filter.SetOutputMaximum(1.0);
sitk.Image coefficientMap = filter.Execute(img);
// save as mhd
filenameCoefficientMap = ReadWriteUtils.GetOutputDirectory(_parameters, _parameters.Iteration) + Constants.cCoefficientFilename;
ReadWriteUtils.WriteSitkImage(coefficientMap, filenameCoefficientMap);
coefficientMap.Dispose();
return(filenameCoefficientMap);
}
/// <summary>
/// Write transformed image and deformation field to disk
/// </summary>
/// <param name="filename"></param>
/// <param name="transformparams"></param>
private void WriteTransform(string filename, List <sitk.VectorOfParameterMap> transformparams)
{
string resultFilename = ReadWriteUtils.GetOutputDirectory(_parameters) + "\\" + Path.GetFileNameWithoutExtension(filename) + ".png";
// add transform parameter map to registration parameters
if (_parameters.TransformationParameterMap.ContainsKey(resultFilename))
{
_parameters.TransformationParameterMap.Remove(resultFilename);
}
_parameters.TransformationParameterMap.Add(resultFilename, transformparams);
// read moving image from file
sitk.Image movingImageToTransform = ReadWriteUtils.ReadITKImageFromFile(filename, sitk.PixelIDValueEnum.sitkVectorUInt8);
// initialize transform instance
TransformRGB trans = new TransformRGB(movingImageToTransform, transformparams, _parameters);
if (_parameters.IsBinaryTransform)
{
// for binary reg set interpolation order to zero
trans.SetInterpolationOrder(0);
}
trans.Execute();
trans.WriteTransformedImage(resultFilename);
// write deformation field
sitk.Image deformationField = trans.GetDeformationField();
string filenameDeformationField = ReadWriteUtils.GetOutputDirectory(_parameters, _parameters.Iteration) + "\\deformationField.mhd";
ReadWriteUtils.WriteSitkImage(deformationField, filenameDeformationField);
trans.Dispose();
movingImageToTransform.Dispose();
}
/// <summary>
/// Retrieve mask for a given filename.
/// </summary>
/// <param name="filename">filename</param>
/// <returns>mask of given image</returns>
private sitk.Image GetMask(string filename, bool isFixed)
{
if (isFixed && _parameters.UseFixedMaskFromDisk)
{
sitk.Image img = ReadWriteUtils.ReadITKImageFromFile(_parameters.FixedMaskFromDisk);
return(img);
}
else if (!isFixed && _parameters.UseMovingMasksFromDisk)
{
sitk.Image img = ReadWriteUtils.ReadITKImageFromFile(_parameters.MovingMasksFromDisk.FirstOrDefault());
return(img);
}
else
{
if (_parameters.UseInnerStructuresSegmentation)
{
// segmentation of the inner structures of the particle
return(GetInnerStructureMask(filename));
}
else
{
// segmentation of the whole particle
return(GetWholeParticleMask(filename));
}
}
}
public static List <sitk.VectorOfParameterMap> PerformMultipleRigidRegistrationForComponents(
string fixedSegmentedMask,
string movingSegmentedMask,
int numberOfComposedTransformations,
RegistrationParameters parameters)
{
// created corresponding masks
Image <Gray, byte> fixedSegments = new Image <Gray, byte>(fixedSegmentedMask);
Image <Gray, byte> movingSegments = new Image <Gray, byte>(movingSegmentedMask);
VectorOfVectorOfPoint contoursFixed = new VectorOfVectorOfPoint();
VectorOfVectorOfPoint contoursMoving = new VectorOfVectorOfPoint();
CvInvoke.FindContours(fixedSegments, contoursFixed, null, Emgu.CV.CvEnum.RetrType.Ccomp, Emgu.CV.CvEnum.ChainApproxMethod.ChainApproxSimple);
CvInvoke.FindContours(movingSegments, contoursMoving, null, Emgu.CV.CvEnum.RetrType.Ccomp, Emgu.CV.CvEnum.ChainApproxMethod.ChainApproxSimple);
// retireve dict with contour index and area size ordered by size
Dictionary <int, double> contoursFixedDict = GetContourAreaDict(ref contoursFixed);
Dictionary <int, double> contoursMovingDict = GetContourAreaDict(ref contoursMoving);
List <Tuple <string, string> > filenameOfMaskComponents = new List <Tuple <string, string> >();
for (int i = 0; i <= numberOfComposedTransformations; i++)
{
var contourFixed = contoursFixed[contoursFixedDict.ElementAt(i).Key];
var contourMoving = contoursMoving[contoursMovingDict.ElementAt(i).Key];
Image <Gray, byte> maskFixed = new Image <Gray, byte>(fixedSegments.Width, fixedSegments.Height, new Gray(0.0));
Image <Gray, byte> maskMoving = new Image <Gray, byte>(movingSegments.Width, movingSegments.Height, new Gray(0.0));
CvInvoke.DrawContours(maskFixed, contourFixed, -1, new MCvScalar(255.0), thickness: -1);
CvInvoke.DrawContours(maskMoving, contourMoving, -1, new MCvScalar(255.0), thickness: -1);
string filenameFixed = Path.GetTempPath() + "\\fixed_0" + i + ".png";
string filenameMoving = Path.GetTempPath() + "\\moving_0" + i + ".png";
maskFixed.Save(filenameFixed);
maskMoving.Save(filenameMoving);
Tuple <string, string> temp = new Tuple <string, string>(filenameFixed, filenameMoving);
filenameOfMaskComponents.Add(temp);
}
sitk.ParameterMap map = GetDefaultParameterMap(parameters.RegistrationDefaultParams);
List <sitk.VectorOfParameterMap> list = new List <sitk.VectorOfParameterMap>();
foreach (Tuple <string, string> tuple in filenameOfMaskComponents)
{
sitk.Image img01 = ReadWriteUtils.ReadITKImageFromFile(tuple.Item1);
sitk.Image img02 = ReadWriteUtils.ReadITKImageFromFile(tuple.Item2);
parameters.ParamMapToUse = map;
RigidRegistration reg = new RigidRegistration(img01, img02, parameters);
reg.Execute();
sitk.VectorOfParameterMap toAdd = new sitk.VectorOfParameterMap(reg.GetTransformationParameterMap());
list.Add(toAdd);
reg.Dispose();
}
return(list);
}
/// <summary>
/// Componentwise rigid registration.
/// Each corresponding masked components will be registrated discretly.
/// Transformation parameters will be composed befor image is transformed.
/// </summary>
/// <param name="fixedMask">reference mask</param>
/// <param name="movingMask">template mask</param>
/// <param name="v">number of corresponding components</param>
/// <param name="filename">moving image filename</param>
/// <returns></returns>
private List <sitk.VectorOfParameterMap> ComponentWiseRigidRegistration(sitk.Image fixedMask, sitk.Image movingMask, int v, string filename)
{
// convert from sitk to opencv
var fixedImage = ReadWriteUtils.ConvertSitkImageToOpenCv <Gray, byte>(fixedMask);
var movingImage = ReadWriteUtils.ConvertSitkImageToOpenCv <Gray, byte>(movingMask);
// find contours
VectorOfVectorOfPoint contoursFixed = new VectorOfVectorOfPoint();
VectorOfVectorOfPoint contoursMoving = new VectorOfVectorOfPoint();
CvInvoke.FindContours(fixedImage, contoursFixed, null, Emgu.CV.CvEnum.RetrType.Ccomp, Emgu.CV.CvEnum.ChainApproxMethod.ChainApproxSimple);
CvInvoke.FindContours(movingImage, contoursMoving, null, Emgu.CV.CvEnum.RetrType.Ccomp, Emgu.CV.CvEnum.ChainApproxMethod.ChainApproxSimple);
// retireve dict with contour index and area size ordered by size
var contoursFixedDict = RegistrationUtils.GetContourAreaDict(ref contoursFixed).OrderByDescending(it => it.Value);
var contoursMovingDict = RegistrationUtils.GetContourAreaDict(ref contoursMoving).OrderByDescending(it => it.Value);
List <Tuple <string, string> > filenameOfMaskComponents = new List <Tuple <string, string> >();
for (int i = 1; i < v; i++)
{
var contourFixed = contoursFixed[contoursFixedDict.ElementAt(i).Key].ToArray();
var contourMoving = contoursMoving[contoursMovingDict.ElementAt(i).Key].ToArray();
Image <Gray, byte> maskFixed = new Image <Gray, byte>(fixedImage.Width, fixedImage.Height, new Gray(0.0));
Image <Gray, byte> maskMoving = new Image <Gray, byte>(movingImage.Width, movingImage.Height, new Gray(0.0));
maskFixed.Draw(contourFixed, new Gray(255.0), -1);
maskMoving.Draw(contourMoving, new Gray(255.0), -1);
//CvInvoke.DrawContours(maskFixed, contourFixed, -1, new MCvScalar(255.0), thickness: -1);
//CvInvoke.DrawContours(maskMoving, contourMoving, -1, new MCvScalar(255.0), thickness: -1);
string filenameFixed = Path.GetTempPath() + "\\fixed_0" + i + ".png";
string filenameMoving = Path.GetTempPath() + "\\moving_0" + i + ".png";
maskFixed.Save(filenameFixed);
maskMoving.Save(filenameMoving);
Tuple <string, string> temp = new Tuple <string, string>(filenameFixed, filenameMoving);
filenameOfMaskComponents.Add(temp);
}
sitk.ParameterMap map = RegistrationUtils.GetDefaultParameterMap(_parameters.RegistrationDefaultParams);
List <sitk.VectorOfParameterMap> list = new List <sitk.VectorOfParameterMap>();
foreach (Tuple <string, string> tuple in filenameOfMaskComponents)
{
sitk.Image img01 = ReadWriteUtils.ReadITKImageFromFile(tuple.Item1, sitk.PixelIDValueEnum.sitkUInt8);
sitk.Image img02 = ReadWriteUtils.ReadITKImageFromFile(tuple.Item2, sitk.PixelIDValueEnum.sitkUInt8);
_parameters.ParamMapToUse = map;
RigidRegistration reg = new RigidRegistration(img01, img02, _parameters);
reg.Execute();
sitk.VectorOfParameterMap toAdd = new sitk.VectorOfParameterMap(reg.GetTransformationParameterMap());
list.Add(toAdd);
reg.Dispose();
}
return(list);
}
private static sitk.LabelOverlapMeasuresImageFilter GetOverlapImageFilter(string mask01iFn, string mask02iFn)
{
sitk.LabelOverlapMeasuresImageFilter overlapFilter;
sitk.Image sImg01 = ReadWriteUtils.ReadITKImageFromFile(mask01iFn);
sitk.Image sImg02 = ReadWriteUtils.ReadITKImageFromFile(mask02iFn);
overlapFilter = VisualizationEvaluationUtils.GetOverlapImageFilter(sImg01, sImg02);
sImg01.Dispose();
sImg02.Dispose();
return(overlapFilter);
}
/// <summary>
/// Get image of the inner structures mask of an image.
/// </summary>
/// <param name="filename">filename of the image</param>
/// <returns>masked image</returns>
private sitk.Image GetInnerStructureMask(string filename)
{
string outputFilename = ReadWriteUtils.GetOutputDirectory(_parameters, _parameters.Iteration) + "\\mask_" + Path.GetFileName(filename);
InnerTissueSegmentation seg = GetInnerStructureSegmentation(filename);
seg.GetOutput()[1].Save(outputFilename);
seg.Dispose();
sitk.Image mask = ReadWriteUtils.ReadITKImageFromFile(outputFilename);
return(mask);
}
/// <summary>
/// Retrieves the mask of the whole tissue.
/// </summary>
/// <param name="filename">filename of the image</param>
/// <returns>masked image</returns>
private sitk.Image GetWholeParticleMask(string filename)
{
string outputFilename = ReadWriteUtils.GetOutputDirectory(_parameters, _parameters.Iteration) + "\\mask_" + Path.GetFileName(filename);
Image <Bgr, byte> image = ReadWriteUtils.ReadOpenCVImageFromFile <Bgr, byte>(filename);
WholeTissueSegmentation segImage = new WholeTissueSegmentation(image, _parameters.WholeTissueSegParams);
segImage.Execute();
segImage.GetOutput().Save(outputFilename);
segImage.Dispose();
image.Dispose();
sitk.Image mask = ReadWriteUtils.ReadITKImageFromFile(outputFilename);
return(mask);
}
private void buttonDiffImage_Click(object sender, EventArgs e)
{
Cursor.Current = Cursors.WaitCursor;
string fixedImageFilename = registrationParameters.FixedImageFilename;
string movingImageFilename = comboBoxMovingImage.SelectedValue.ToString();
// read images
var img01 = ReadWriteUtils.ReadITKImageFromFile(fixedImageFilename);
var img02 = ReadWriteUtils.ReadITKImageFromFile(movingImageFilename);
var difference = VisualizationEvaluationUtils.GetTotalDifferenceImage(img01, img02);
ReadWriteUtils.WriteSitkImage(difference, registrationParameters.OutputDirectory + "\\difference.png");
img01.Dispose();
img02.Dispose();
difference.Dispose();
Cursor.Current = Cursors.Default;
}
/// <summary>
/// Load and resize image depending on the width and height of the largest image in stack.
/// </summary>
/// <param name="filename">filename of the image to load</param>
/// <param name="writeFilename">output filename if image should be written back to disk</param>
/// <returns>simpleitk image</returns>
private sitk.Image LoadAndResizeImage(string filename, string writeFilename = null)
{
sitk.Image refImage = ReadWriteUtils.ReadITKImageFromFile(filename, sitk.PixelIDValueEnum.sitkVectorUInt8);
if (refImage.GetWidth() == _parameters.LargestImageWidth && refImage.GetHeight() == _parameters.LargestImageHeight)
{
return(refImage);
}
else
{
sitk.Image refResized = ImageUtils.ResizeImage(refImage, _parameters.LargestImageWidth, _parameters.LargestImageHeight);
// write image if output filename is defined
if (writeFilename != null)
{
ReadWriteUtils.WriteSitkImage(refResized, Path.Combine(_parameters.OutputDirectory, Path.GetFileName(writeFilename)));
}
return(refResized);
}
}
