Commit 72c01c75 authored by Floris Berendsen's avatar Floris Berendsen
Browse files

ENH: commandline can run groupwise 2d+t float registration

parent 301e21ec
......@@ -24,6 +24,8 @@
#include "selxAnyFileWriter.h"
#include "selxDefaultComponents.h"
#include "selxTypeList.h"
#include <boost/algorithm/string.hpp>
......@@ -55,7 +57,17 @@ main( int ac, char * av[] )
{
typedef std::vector< std::string > VectorOfStringsType;
selx::SuperElastixFilter< selx::DefaultComponents >::Pointer superElastixFilter = selx::SuperElastixFilter< selx::DefaultComponents >::New();
using Elastix3DComponents = selx::TypeList <
selx::MonolithicElastixComponent< 3, float >,
selx::MonolithicTransformixComponent< 3, float >,
selx::ItkImageSourceFixedComponent< 3, float >,
selx::ItkImageSourceMovingComponent< 3, float >,
selx::ItkImageSinkComponent< 3, float >
>;
using RegisterComponents = selx::list_append<selx::DefaultComponents, Elastix3DComponents>::type;
selx::SuperElastixFilter< RegisterComponents >::Pointer superElastixFilter = selx::SuperElastixFilter< RegisterComponents >::New();
fs::path configurationPath;
VectorOfStringsType inputPairs;
......
{
"Component": {
"Name": "RegistrationMethod",
"NameOfClass": "MonolithicElastixComponent",
"FixedInternalImagePixelType":"float",
"MovingInternalImagePixelType":"float",
"FixedImageDimension":"3",
"MovingImageDimension":"3",
"UseDirectionCosines":"true",
"Registration":"MultiResolutionRegistration",
"Interpolator":"ReducedDimensionBSplineInterpolator",
"ResampleInterpolator":"FinalReducedDimensionBSplineInterpolator",
"Resampler":"DefaultResampler",
"BSplineInterpolationOrder":"1",
"FinalBSplineInterpolationOrder":"3",
"FixedImagePyramid":"FixedSmoothingImagePyramid",
"MovingImagePyramid":"MovingSmoothingImagePyramid",
"Optimizer":"AdaptiveStochasticGradientDescent",
"HowToCombineTransforms":"Compose",
"Transform":"BSplineStackTransform",
"Metric":"PCAMetric2",
"UseFastAndLowMemoryVersion":"true",
"NumberOfFixedHistogramBins":"32",
"NumberOfMovingHistogramBins":"32",
"NumEigenValues":"3",
"SubtractMean":"true",
"MovingImageDerivativeScales": ["1","1","0"],
"FinalGridSpacingInPhysicalUnits":"64",
"NumberOfResolutions":"1",
"AutomaticParameterEstimation":"true",
"ASGDParameterEstimationMethod":"Original",
"MaximumNumberOfIterations":"512",
"ImagePyramidSchedule":["1","1","0","1","1","0"],
"NumberOfSpatialSamples":"512",
"NewSamplesEveryIteration":"true",
"ImageSampler":"RandomCoordinate",
"CheckNumberOfSamples":"true",
"ErodeMask":"false",
"ErodeFixedMask":"false",
"DefaultPixelValue":"0",
"WriteResultImage":"true",
"ResultImagePixelType":"short",
"ResultImageFormat":"mhd"
},
"Component": {
"Name": "FixedImage",
"NameOfClass": "ItkImageSourceFixedComponent",
"Dimensionality": "3"
},
"Component": {
"Name": "MovingImage",
"NameOfClass": "ItkImageSourceMovingComponent"
},
"Component": {
"Name": "ResultImage",
"NameOfClass": "ItkImageSinkComponent"
},
"Component": {
"Name": "TransformDisplacementField",
"NameOfClass": "MonolithicTransformixComponent"
},
"Component": {
"Name": "Controller",
"NameOfClass": "RegistrationControllerComponent"
},
"Connection": {
"Out": "FixedImage",
"In": "RegistrationMethod",
"NameOfInterface": "itkImageFixedInterface"
},
"Connection": {
"Out": "MovingImage",
"In": "RegistrationMethod",
"NameOfInterface": "itkImageMovingInterface"
},
"Connection": {
"Out": "FixedImage",
"In": "TransformDisplacementField",
"NameOfInterface": "itkImageDomainFixedInterface"
},
"Connection": {
"Out": "MovingImage",
"In": "TransformDisplacementField",
"NameOfInterface": "itkImageMovingInterface"
},
"Connection": {
"Out": "RegistrationMethod",
"In": "TransformDisplacementField",
"NameOfInterface": "elastixTransformParameterObjectInterface"
},
"Connection": {
"Out": "TransformDisplacementField",
"In": "ResultImage",
"NameOfInterface": "itkImageInterface"
},
"Connection": {
"Out": "RegistrationMethod",
"In": "Controller",
"NameOfInterface": "RunRegistrationInterface"
},
"Connection": {
"Out": "TransformDisplacementField",
"In": "Controller",
"NameOfInterface": "ReconnectTransformInterface"
}
}
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