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#include "antsUtilities.h"
#include <algorithm>
#include "itkSurfaceCurvatureBase.h"
#include "itkSurfaceImageCurvature.h"
#include "ReadWriteData.h"
namespace ants
{
/*
void test1()
{
typedef itk::SurfaceCurvatureBase<ImageType> ParamType;
ParamType::Pointer Parameterizer=ParamType::New();
// Parameterizer->TestEstimateTangentPlane(p);
Parameterizer->FindNeighborhood();
// Parameterizer->WeightedEstimateTangentPlane( Parameterizer->GetOrigin() );
Parameterizer->EstimateTangentPlane(
Parameterizer->GetAveragePoint());
Parameterizer->PrintFrame();
// Parameterizer->SetOrigin(Parameterizer->GetAveragePoint());
for(int i=0; i<3; i++){
Parameterizer->ComputeWeightsAndDirectionalKappaAndAngles
(Parameterizer->GetOrigin());
Parameterizer->ComputeFrame(Parameterizer->GetOrigin());
Parameterizer->EstimateCurvature();
Parameterizer->PrintFrame();
}
Parameterizer->ComputeJoshiFrame(Parameterizer->GetOrigin()); Parameterizer->PrintFrame();
std::cout << " err 1 " << Parameterizer->ErrorEstimate(Parameterizer->GetOrigin()) <<
" err 2 " << Parameterizer->ErrorEstimate(Parameterizer->GetOrigin(),-1) << std::endl;
}
*/
// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int
SurfaceCurvature(std::vector<std::string> args, std::ostream * /*out_stream = nullptr */)
{
// put the arguments coming in as 'args' into standard (argc,argv) format;
// 'args' doesn't have the command name as first, argument, so add it manually;
// 'args' may have adjacent arguments concatenated into one argument,
// which the parser should handle
args.insert(args.begin(), "SurfaceCurvature");
int argc = args.size();
char ** argv = new char *[args.size() + 1];
for (unsigned int i = 0; i < args.size(); ++i)
{
// allocate space for the string plus a null character
argv[i] = new char[args[i].length() + 1];
std::strncpy(argv[i], args[i].c_str(), args[i].length());
// place the null character in the end
argv[i][args[i].length()] = '\0';
}
argv[argc] = nullptr;
// class to automatically cleanup argv upon destruction
class Cleanup_argv
{
public:
Cleanup_argv(char ** argv_, int argc_plus_one_)
: argv(argv_)
, argc_plus_one(argc_plus_one_)
{}
~Cleanup_argv()
{
for (unsigned int i = 0; i < argc_plus_one; ++i)
{
delete[] argv[i];
}
delete[] argv;
}
private:
char ** argv;
unsigned int argc_plus_one;
};
Cleanup_argv cleanup_argv(argv, argc + 1);
// antscout->set_stream( out_stream );
if (argc < 3)
{
std::cout << " This implements The Shape Operator for Differential Analysis of Images (google for the pdf)"
<< std::endl;
std::cout << " By B. Avants and J.C. Gee " << std::endl;
std::cout << " Documentation is on demand --- if there is enough interest, documentation will improve."
<< std::endl;
std::cout << " There are several modes of operation and you must try parameters and input either binary or gray "
"scale images to see the different effects ---- experimentation or reading the (minimal) "
"documentation / paper / code is needed to understand the program "
<< std::endl;
std::cout << " usage : SurfaceCurvature FileNameIn FileNameOut sigma option " << std::endl;
std::cout << " e.g : SurfaceCurvature BrainIn.nii BrainOut.nii 3 0 " << std::endl;
std::cout << " option 0 means just compute mean curvature from intensity " << std::endl;
std::cout << " option 5 means characterize surface from intensity " << std::endl;
std::cout << " option 6 means compute gaussian curvature " << std::endl;
std::cout << " option 7 means surface area " << std::endl;
std::cout << " ... " << std::endl;
std::cout << " for surface characterization " << std::endl;
std::cout << " 1 == (+) bowl " << std::endl;
std::cout << " 2 == (-) bowl " << std::endl;
std::cout << " 3 == (+) saddle " << std::endl;
std::cout << " 4 == (-) saddle " << std::endl;
std::cout << " 5 == (+) U " << std::endl;
std::cout << " 6 == (-) U " << std::endl;
std::cout << " 7 == flat " << std::endl;
std::cout << " 8 == a perfectly even saddle (rare) " << std::endl;
std::cout << " " << std::endl;
std::cout << " we add 128 to mean curvature results s.t. they are differentiated from background (zero) "
<< std::endl;
return 0;
}
using ImageType = itk::Image<float, 3>;
using floatImageType = itk::Image<float, 3>;
enum
{
ImageDimension = ImageType::ImageDimension
};
using ParamType = itk::SurfaceImageCurvature<ImageType>;
ParamType::Pointer Parameterizer = ParamType::New();
int opt = 0;
float sig = 1.0;
if (argc > 3)
{
sig = atof(argv[3]);
}
if (argc > 4)
{
opt = (int)std::stoi(argv[4]);
}
if (opt < 0)
{
std::cout << " error " << std::endl;
return 0;
}
ImageType::Pointer input;
ReadImage<ImageType>(input, argv[1]);
Parameterizer->SetInputImage(input);
// Parameterizer->ProcessLabelImage();
Parameterizer->SetNeighborhoodRadius(1.);
if (sig <= 0.5f)
{
sig = 1.66f;
}
Parameterizer->SetSigma(sig);
if (opt == 1)
{
Parameterizer->SetUseLabel(true);
Parameterizer->SetUseGeodesicNeighborhood(false);
}
else
{
Parameterizer->SetUseLabel(false);
Parameterizer->SetUseGeodesicNeighborhood(false);
float sign = 1.0;
if (opt == 3)
{
sign = -1.0;
}
Parameterizer->SetkSign(sign);
Parameterizer->SetThreshold(0);
}
// Parameterizer->ComputeSurfaceArea();
// Parameterizer->IntegrateFunctionOverSurface();
// Parameterizer->IntegrateFunctionOverSurface(true);
if (opt != 5 && opt != 6 && opt != 7)
{
Parameterizer->ComputeFrameOverDomain(3);
}
else
{
Parameterizer->ComputeFrameOverDomain(opt);
}
// Parameterizer->SetNeighborhoodRadius( 2 );
// Parameterizer->LevelSetMeanCurvature();
// Parameterizer->SetNeighborhoodRadius( 2.9 );
// Parameterizer->IntegrateFunctionOverSurface(false);
// Parameterizer->SetNeighborhoodRadius( 1.5 );
// Parameterizer->IntegrateFunctionOverSurface(true);
// for (int i=0; i<1; i++) Parameterizer->PostProcessGeometry();
ImageType::Pointer output = Parameterizer->GetFunctionImage();
// Parameterizer->GetFunctionImage()->SetSpacing( input->GetSpacing() );
// Parameterizer->GetFunctionImage()->SetDirection( input->GetDirection() );
// Parameterizer->GetFunctionImage()->SetOrigin( input->GetOrigin() );
// smooth->SetSpacing(reader->GetOutput()->GetSpacing());
// SmoothImage(Parameterizer->GetFunctionImage(),smooth,3);
// NormalizeImage(smooth,output,mn);
// NormalizeImage(Parameterizer->GetFunctionImage(),output,mn);
ANTs::WriteImage<floatImageType>(output, argv[2]);
return 0;
}
} // namespace ants
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