private void buttonSave_Click(object sender, EventArgs e)
{
if (filename == null)
{
string[] parameters = richTextBox1.Text.Split('\n');
foreach (var param in parameters)
{
string[] splitted = param.Split(' ');
sitk.VectorString vec = GetVectorFromString(param);
if (vec != null)
{
if (Parametermap.ContainsKey(splitted[0]))
{
Parametermap[splitted[0]] = vec;
}
else
{
Parametermap.Add(splitted[0], vec);
}
}
}
this.DialogResult = DialogResult.OK;
this.Close();
}
else
{
sitk.ElastixImageFilter elx = new sitk.ElastixImageFilter();
elx.WriteParameterFile(Parametermap, filename);
elx.Dispose();
}
}
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();
}
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();
}
}
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();
}
public EditParametersForm(string parameterFilename)
{
InitializeComponent();
filename = parameterFilename;
sitk.ElastixImageFilter elx = new sitk.ElastixImageFilter();
Parametermap = elx.ReadParameterFile(filename);
elx.Dispose();
}
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>
/// Get default parameter map from elastix image filter for registration type.
/// </summary>
/// <param name="registrationType">registration type</param>
/// <returns>default params</returns>
private static sitk.ParameterMap GetDefaultRigidParameterMap(RegistrationDefaultParameters registrationType)
{
using (sitk.ElastixImageFilter elastix = new sitk.ElastixImageFilter())
{
sitk.ParameterMap map = elastix.GetDefaultParameterMap(registrationType.ToString());
ChangeOrAddParamIfNotExist(ref map, "Interpolator", GetVectorString("BSplineInterpolator"));
ChangeOrAddParamIfNotExist(ref map, "ResampleInterpolator", GetVectorString("FinalBSplineInterpolator"));
ChangeOrAddParamIfNotExist(ref map, "FixedImagePyramid", GetVectorString("FixedRecursiveImagePyramid"));
ChangeOrAddParamIfNotExist(ref map, "MovingImagePyramid", GetVectorString("MovingRecursiveImagePyramid"));
ChangeOrAddParamIfNotExist(ref map, "AutomaticTransformInitialization", GetVectorString("true"));
ChangeOrAddParamIfNotExist(ref map, "NumberOfResolutions", GetVectorString("8"));
ChangeOrAddParamIfNotExist(ref map, "MaximumNumberOfIterations", GetVectorString("1024"));
ChangeOrAddParamIfNotExist(ref map, "NumberOfSpatialSamples", GetVectorString("4096"));
ChangeOrAddParamIfNotExist(ref map, "NumberOfSamplesForExactGradient", GetVectorString("4096"));
ChangeOrAddParamIfNotExist(ref map, "ImageSampler", GetVectorString("Random"));
ChangeOrAddParamIfNotExist(ref map, "BSplineInterpolationOrder", GetVectorString("1"));
ChangeOrAddParamIfNotExist(ref map, "FinalBSplineInterpolationOrder", GetVectorString("3"));
ChangeOrAddParamIfNotExist(ref map, "Metric", GetVectorString("AdvancedMeanSquares"));
return(map);
}
}
public RigidRegistration(RegistrationParameters parameters) : base(parameters)
{
elastix = new sitk.ElastixImageFilter();
parameterMap = RegistrationUtils.GetDefaultParameterMap(parameters.RegistrationDefaultParams);
}