--- a +++ b/src/readImage.cxx @@ -0,0 +1,105 @@ +#include <nanobind/nanobind.h> +#include <nanobind/stl/vector.h> +#include <nanobind/stl/string.h> +#include <nanobind/stl/tuple.h> +#include <nanobind/ndarray.h> + +#include <tuple> +#include "itkImageFileWriter.h" +#include "itkImageIOBase.h" +#include "itkNiftiImageIOFactory.h" +#include "itkMetaImageIOFactory.h" +#include "itkImageFileReader.h" +#include "itkImage.h" +#include "itkPyBuffer.h" + +#include "readImage.h" +#include "antsImage.h" + + +namespace nb = nanobind; +using namespace nb::literals; + + +template <typename ImageType> +AntsImage<ImageType> imageRead( std::string filename ) +{ + typedef typename ImageType::Pointer ImagePointerType; + typedef itk::ImageFileReader< ImageType > ImageReaderType; + + typename ImageReaderType::Pointer image_reader = ImageReaderType::New() ; + image_reader->SetFileName( filename.c_str() ) ; + image_reader->Update(); + + ImagePointerType itkImage = image_reader->GetOutput(); + AntsImage<ImageType> myImage = { itkImage }; + return myImage; +} + +/** + * Create an ANTsImage from a numpy array + * + * The data array must be C-contiguous, and ordered correctly + * See "4.1.7 Importing Image Data from a Buffer" + * https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch4.html + */ +template <typename ImageType> +AntsImage<ImageType> fromNumpy( nb::ndarray<nb::numpy> data, nb::tuple datashape ) +{ + typedef typename ImageType::Pointer ImagePointerType; + ImagePointerType antsImage = ImageType::New(); + typedef itk::PyBuffer<ImageType> PyBufferType; + + nb::object o = nb::cast(data); + antsImage = PyBufferType::_GetImageViewFromArray(o.ptr(), datashape.ptr(), nb::make_tuple(1)[0].ptr()); + + AntsImage<ImageType> myImage = { antsImage }; + return myImage; +} + + +void local_readImage(nb::module_ &m) { + + m.def("imageReadUC2", &imageRead<itk::Image<unsigned char,2>>); + m.def("imageReadUC3", &imageRead<itk::Image<unsigned char,3>>); + m.def("imageReadUC4", &imageRead<itk::Image<unsigned char,4>>); + m.def("imageReadUI2", &imageRead<itk::Image<unsigned int,2>>); + m.def("imageReadUI3", &imageRead<itk::Image<unsigned int,3>>); + m.def("imageReadUI4", &imageRead<itk::Image<unsigned int,4>>); + m.def("imageReadF2", &imageRead<itk::Image<float,2>>); + m.def("imageReadF3", &imageRead<itk::Image<float,3>>); + m.def("imageReadF4", &imageRead<itk::Image<float,4>>); + m.def("imageReadD2", &imageRead<itk::Image<double,2>>); + m.def("imageReadD3", &imageRead<itk::Image<double,3>>); + m.def("imageReadD4", &imageRead<itk::Image<double,4>>); + m.def("imageReadVUC2", &imageRead<itk::VectorImage<unsigned char,2>>); + m.def("imageReadVUC3", &imageRead<itk::VectorImage<unsigned char,3>>); + m.def("imageReadVUC4", &imageRead<itk::VectorImage<unsigned char,4>>); + m.def("imageReadVUI2", &imageRead<itk::VectorImage<unsigned int,2>>); + m.def("imageReadVUI3", &imageRead<itk::VectorImage<unsigned int,3>>); + m.def("imageReadVUI4", &imageRead<itk::VectorImage<unsigned int,4>>); + m.def("imageReadVF2", &imageRead<itk::VectorImage<float,2>>); + m.def("imageReadVF3", &imageRead<itk::VectorImage<float,3>>); + m.def("imageReadVF4", &imageRead<itk::VectorImage<float,4>>); + m.def("imageReadVD2", &imageRead<itk::VectorImage<double,2>>); + m.def("imageReadVD3", &imageRead<itk::VectorImage<double,3>>); + m.def("imageReadVD4", &imageRead<itk::VectorImage<double,4>>); + m.def("imageReadRGBUC2", &imageRead<itk::Image<itk::RGBPixel<unsigned char>,2>>); + m.def("imageReadRGBUC3", &imageRead<itk::Image<itk::RGBPixel<unsigned char>,3>>); + m.def("imageReadRGBF2", &imageRead<itk::Image<itk::RGBPixel<float>,2>>); + m.def("imageReadRGBF3", &imageRead<itk::Image<itk::RGBPixel<float>,3>>); + + + m.def("fromNumpyUC2", &fromNumpy<itk::Image<unsigned char,2>>); + m.def("fromNumpyUC3", &fromNumpy<itk::Image<unsigned char,3>>); + m.def("fromNumpyUC4", &fromNumpy<itk::Image<unsigned char,4>>); + m.def("fromNumpyUI2", &fromNumpy<itk::Image<unsigned int,2>>); + m.def("fromNumpyUI3", &fromNumpy<itk::Image<unsigned int,3>>); + m.def("fromNumpyUI4", &fromNumpy<itk::Image<unsigned int,4>>); + m.def("fromNumpyF2", &fromNumpy<itk::Image<float,2>>); + m.def("fromNumpyF3", &fromNumpy<itk::Image<float,3>>); + m.def("fromNumpyF4", &fromNumpy<itk::Image<float,4>>); + m.def("fromNumpyD2", &fromNumpy<itk::Image<double,2>>); + m.def("fromNumpyD3", &fromNumpy<itk::Image<double,3>>); + m.def("fromNumpyD4", &fromNumpy<itk::Image<double,4>>); +} \ No newline at end of file