public static RegistrationParameters GetMultipleRegistrationParameters()
{
RegistrationParameters parameters = new RegistrationParameters();
parameters.Type = RegistrationType.Multiple;
return(parameters);
}
public RigidRegistration(sitk.Image fixedImage, sitk.Image movingImage, RegistrationParameters parameters) : base(parameters)
{
this.fixedImage = ImageUtils.CastImageToFloat32(fixedImage);
this.movingImage = ImageUtils.CastImageToFloat32(movingImage);
this.registrationParameters = parameters;
elastix = new sitk.ElastixImageFilter();
if (parameterMap == null)
{
parameterMap = RegistrationUtils.GetDefaultParameterMap(parameters.RegistrationDefaultParams);
}
// set output dir
outputDirectory = Path.Combine(registrationParameters.OutputDirectory, registrationParameters.Iteration.ToString());
if (!Directory.Exists(outputDirectory))
{
Directory.CreateDirectory(outputDirectory);
}
elastix.SetOutputDirectory(outputDirectory);
//elastix.SetLogFileName(Path.Combine(outputDirectory, registrationParameters.ElastixLogFileName));
elastix.LogToFileOn();
//base.SetGeneralParameters();
}
public static RegistrationParameters GetRigidRegistrationParameters()
{
RegistrationParameters parameters = new RegistrationParameters();
parameters.Type = RegistrationType.Rigid;
parameters.RegistrationDefaultParams = RegistrationDefaultParameters.rigid;
return(parameters);
}
public static RegistrationParameters GetNonRigidRegistrationParameters()
{
RegistrationParameters parameters = new RegistrationParameters();
parameters.Type = RegistrationType.NonRigid;
parameters.RegistrationDefaultParams = RegistrationDefaultParameters.bspline;
return(parameters);
}
public TransformRGB(sitk.Image movingImage, List <sitk.VectorOfParameterMap> parameterMaps, RegistrationParameters parameters)
{
this.movingImage = movingImage;
this.parameterMaps = parameterMaps;
this.registrationParameters = parameters;
transformix = new sitk.TransformixImageFilter();
}
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);
}
public RegistrationController(RegistrationParameters parameters, BackgroundWorker worker)
{
_parameters = parameters;
_worker = worker;
// create output directory
if (!Directory.Exists(_parameters.OutputDirectory))
{
Directory.CreateDirectory(_parameters.OutputDirectory);
}
}
public NonRigidRegistration(sitk.Image fixedImage, sitk.Image movingImage, RegistrationParameters parameters) : base(parameters)
{
// cast images to from pixel type uint to vector of float
sitk.CastImageFilter castImageFilter = new sitk.CastImageFilter();
castImageFilter.SetOutputPixelType(sitk.PixelIDValueEnum.sitkVectorFloat32);
sitk.Image vector1 = castImageFilter.Execute(fixedImage);
sitk.Image vector2 = castImageFilter.Execute(movingImage);
sitk.Image tempImage1 = TransformationUtils.GetColorChannelAsImage(vector1, ColorChannel.R);
sitk.Image tempImage2 = TransformationUtils.GetColorChannelAsImage(vector2, ColorChannel.R);
this.fixedImage = tempImage1;
this.movingImage = tempImage2;
// initiate elastix and set default registration params
elastix = new sitk.ElastixImageFilter();
if (parameterMap == null)
{
parameterMap = RegistrationUtils.GetDefaultParameterMap(parameters.RegistrationDefaultParams);
}
// coefficient map is used for penalty term
if (parameters.CoefficientMapFilename != null && parameters.NonRigidOptions == MaskedNonRigidRegistrationOptions.BsplineWithPenaltyTermAndCoefficientMap)
{
RegistrationUtils.ChangeOrAddParamIfNotExist(ref parameterMap, "DilateRigidityImages", RegistrationUtils.GetVectorString("true"));
RegistrationUtils.ChangeOrAddParamIfNotExist(ref parameterMap, "FixedRigidityImageName", RegistrationUtils.GetVectorString(parameters.CoefficientMapFilename));
}
// coefficient map is used for diffuse registration
if (parameters.CoefficientMapFilename != null && parameters.NonRigidOptions == MaskedNonRigidRegistrationOptions.DiffuseRegistration)
{
RegistrationUtils.ChangeOrAddParamIfNotExist(ref parameterMap, "UseMovingSegmentation", RegistrationUtils.GetVectorString("true"));
RegistrationUtils.ChangeOrAddParamIfNotExist(ref parameterMap, "MovingSegmentationFileName", RegistrationUtils.GetVectorString(parameters.CoefficientMapFilename));
}
// set output dir and log file
outputDirectory = Path.Combine(registrationParameters.OutputDirectory, registrationParameters.Iteration.ToString());
if (!Directory.Exists(outputDirectory))
{
Directory.CreateDirectory(outputDirectory);
}
elastix.SetOutputDirectory(outputDirectory);
elastix.SetLogFileName(outputDirectory + registrationParameters.ElastixLogFileName);
elastix.LogToConsoleOn();
}
/// <summary>
/// Calculate a composite transform for a list of vector parameter maps.
/// </summary>
/// <param name="movingImage">moving image</param>
/// <param name="parameterMaps">list of vector of parameter maps</param>
/// <param name="parameters">registration params</param>
/// <param name="filename">filename of the result image</param>
public static void WriteCompositeTransformForMovingImage(
sitk.Image movingImage,
List <sitk.VectorOfParameterMap> parameterMaps,
RegistrationParameters parameters,
string filename)
{
sitk.VectorOfParameterMap initialTransform = parameterMaps.First();
parameterMaps.Remove(initialTransform);
TransformRGB transform = new TransformRGB(movingImage, parameterMaps, parameters);
foreach (sitk.VectorOfParameterMap vectorOfMaps in parameterMaps)
{
transform.AddVectorOfParameterMap(vectorOfMaps);
}
transform.Execute();
transform.WriteTransformedImage(filename);
}
public RigidRegistration(RegistrationParameters parameters) : base(parameters)
{
elastix = new sitk.ElastixImageFilter();
parameterMap = RegistrationUtils.GetDefaultParameterMap(parameters.RegistrationDefaultParams);
}
public MultipleParameterFileRegistration(sitk.Image fixedImage, sitk.Image movingImage, RegistrationParameters parameters) : base(parameters)
{
this.fixedImage = ImageUtils.CastImageToFloat32(fixedImage);
this.movingImage = ImageUtils.CastImageToFloat32(movingImage);
elastix = new sitk.ElastixImageFilter();
for (int i = 0; i < parameters.ParameterFiles.Count; i++)
{
if (i == 0)
{
elastix.SetParameterMap(elastix.ReadParameterFile(parameters.ParameterFiles[i]));
}
else
{
elastix.AddParameterMap(elastix.ReadParameterFile(parameters.ParameterFiles[i]));
}
}
// set output dir
outputDirectory = Path.Combine(registrationParameters.OutputDirectory, "multiple_" + DateTime.Now.ToShortDateString());
if (!Directory.Exists(outputDirectory))
{
Directory.CreateDirectory(outputDirectory);
}
elastix.SetOutputDirectory(outputDirectory);
//elastix.SetLogFileName(Path.Combine(outputDirectory, registrationParameters.ElastixLogFileName));
elastix.LogToFileOn();
}
protected RegInitialization(RegistrationParameters parameters)
{
this.registrationParameters = parameters;
this.parameterMap = parameters.ParamMapToUse;
}