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Mesh_3::Add handling of *.nii files in one example

This commit is contained in:
Andreas Fabri 2023-10-24 13:11:12 +01:00
parent d5c8582bd2
commit 1db8ff6e68
2 changed files with 39 additions and 15 deletions
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2
Mesh_3/doc/Mesh_3/Mesh_3.txt
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@ -693,7 +693,7 @@ View of a remeshed surface. (Left) input mesh (Right) output mesh. Code from sub
The following example produces a 3D mesh for a domain whose boundary surface The following example produces a 3D mesh for a domain whose boundary surface
is the isosurface associated to an isovalue inside the input gray-level is the isosurface associated to an isovalue inside the input gray-level
3D image. In the distribution you can also find the example \ref Mesh_3/mesh_3D_gray_vtk_image.cpp which can deal with DICOM files as input. 3D image. In the distribution you can also find the example \ref Mesh_3/mesh_3D_gray_vtk_image.cpp which can deal with `*.nii` as well as `DICOM` files as input.
\cgalExample{Mesh_3/mesh_3D_gray_image.cpp} \cgalExample{Mesh_3/mesh_3D_gray_image.cpp}

52
Mesh_3/examples/Mesh_3/mesh_3D_gray_vtk_image.cpp
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@ -1,6 +1,8 @@
#include <vtkNew.h>
#include <vtkImageData.h> #include <vtkImageData.h>
#include <vtkDICOMImageReader.h> #include <vtkDICOMImageReader.h>
#include <vtkNIFTIImageReader.h>
#include <vtkImageReader.h> #include <vtkImageReader.h>
#include <vtkImageGaussianSmooth.h> #include <vtkImageGaussianSmooth.h>
#include <vtkDemandDrivenPipeline.h> #include <vtkDemandDrivenPipeline.h>
@ -19,6 +21,8 @@
#include <boost/lexical_cast.hpp> #include <boost/lexical_cast.hpp>
#include <boost/functional.hpp> #include <boost/functional.hpp>
#include <filesystem>
typedef short Image_word_type; typedef short Image_word_type;
// Domain // Domain
@ -43,36 +47,56 @@ public:
} }
}; };
namespace fs = std::filesystem;
int main(int argc, char* argv[]) int main(int argc, char* argv[])
{ {
// Loads image // Loads image
if(argc == 1){ if(argc == 1){
std::cerr << "Usage: " << argv[0] << " <directory with dicom data> iso_level=1 facet_size=1 facet_distance=0.1 cell_size=1\n"; std::cerr << "Usage: " << argv[0] << " <nii file or dicom directory> iso_level=1 facet_size=1 facet_distance=0.1 cell_size=1\n";
return 0; return 0;
} }
vtkImageData* vtk_image;
Image_word_type iso = (argc>2)? boost::lexical_cast<Image_word_type>(argv[2]): 1; Image_word_type iso = (argc>2)? boost::lexical_cast<Image_word_type>(argv[2]): 1;
double fs = (argc>3)? boost::lexical_cast<double>(argv[3]): 1; double fs = (argc>3)? boost::lexical_cast<double>(argv[3]): 1;
double fd = (argc>4)? boost::lexical_cast<double>(argv[4]): 0.1; double fd = (argc>4)? boost::lexical_cast<double>(argv[4]): 0.1;
double cs = (argc>5)? boost::lexical_cast<double>(argv[5]): 1; double cs = (argc>5)? boost::lexical_cast<double>(argv[5]): 1;
vtkDICOMImageReader*dicom_reader = vtkDICOMImageReader::New(); fs::path path(argv[1]);
dicom_reader->SetDirectoryName(argv[1]);
vtkDemandDrivenPipeline*executive = if(fs::is_regular_file(path)){
vtkDemandDrivenPipeline::SafeDownCast(dicom_reader->GetExecutive()); std::cout << "regular file" << std::endl;
if (executive) if (path.has_extension()){
{ fs::path stem = path.stem();
executive->SetReleaseDataFlag(0, 0); // where 0 is the port index if ((path.extension() == "nii") || (stem.has_extension() && (stem.extension() == "nii") && (path.extension() == "gz"))) {
vtkNew<vtkNIFTIImageReader> reader;
reader->SetFileName(argv[1]);
reader->Update();
vtk_image = reader->GetOutput();
vtk_image->Print(std::cerr);
}
} }
}
else if (fs::is_directory(path)) {
vtkDICOMImageReader* dicom_reader = vtkDICOMImageReader::New();
dicom_reader->SetDirectoryName(argv[1]);
vtkImageGaussianSmooth* smoother = vtkImageGaussianSmooth::New(); vtkDemandDrivenPipeline* executive =
smoother->SetStandardDeviations(1., 1., 1.); vtkDemandDrivenPipeline::SafeDownCast(dicom_reader->GetExecutive());
smoother->SetInputConnection(dicom_reader->GetOutputPort()); if (executive)
smoother->Update(); {
vtkImageData* vtk_image = smoother->GetOutput(); executive->SetReleaseDataFlag(0, 0); // where 0 is the port index
vtk_image->Print(std::cerr); }
vtkImageGaussianSmooth* smoother = vtkImageGaussianSmooth::New();
smoother->SetStandardDeviations(1., 1., 1.);
smoother->SetInputConnection(dicom_reader->GetOutputPort());
smoother->Update();
vtkImageData* vtk_image = smoother->GetOutput();
vtk_image->Print(std::cerr);
}
CGAL::Image_3 image = CGAL::IO::read_vtk_image_data(vtk_image); CGAL::Image_3 image = CGAL::IO::read_vtk_image_data(vtk_image);
if(image.image() == nullptr){ if(image.image() == nullptr){
std::cerr << "could not create a CGAL::Image_3 from the vtk image\n"; std::cerr << "could not create a CGAL::Image_3 from the vtk image\n";