在ITK中阅读* .mhd / *。原始格式​​的3D图像

Question

如何在ITK中加载和编写 .mhd / .raw格式的3D图像？我尝试使用以下代码，但它没有加载，因为加载的图像的尺寸显示为0,0,0。

有人可以指出我犯的错误吗？

typedef float InputPixelType;
const unsigned int  DimensionOfRaw = 3;
typedef itk::Image< InputPixelType, DimensionOfRaw > InputImageType;

//typedef itk::RawImageIO<InputPixelType, DimensionOfRaw> ImageIOType;
typedef itk::ImageFileReader<InputImageType >   ReaderType;

/*
 * --------------------Loader and saver of Raws, as well the function that takes a resulting (from inference matrix/vector) and creates a Raw out of it.-----------------------
 */
InputImageType::Pointer loadRawImageItk( std::string RawFullFilepathname, ReaderType::Pointer & RawImageIO ) {
    //http://www.itk.org/Doxygen/html/classitk_1_1Image.html
    //http://www.itk.org/Doxygen/html/classitk_1_1ImageFileReader.html

    typedef itk::ImageFileReader<InputImageType> ReaderType;

    ReaderType::Pointer reader = ReaderType::New();
    reader->SetFileName(RawFullFilepathname);


    //ImageIOType::Pointer RawImageIO = ImageIOType::New();
    reader->SetImageIO( RawImageIO );

    try {
        reader->Update();
    } catch (itk::ExceptionObject& e) {
        std::cerr << e.GetDescription() << std::endl;
        exit(1);  // You can choose to do something else, of course.
    }

    //InputImageType::Pointer inputImage = reader->GetOutput();
    InputImageType::Pointer inputImage = reader->GetOutput();

    return inputImage;

}


int saveRawImageItk( std::string RawFullFilepathname, InputImageType::Pointer & outputImageItkType , ImageIOType::Pointer & RawImageIO) {
  std::cout << "Saving image to: " << RawFullFilepathname << "\n";

  typedef itk::ImageFileWriter< InputImageType >  Writer1Type;
  Writer1Type::Pointer writer1 = Writer1Type::New();

  writer1->SetInput( outputImageItkType );
  writer1->SetFileName( RawFullFilepathname );
  writer1->SetImageIO( RawImageIO ); //seems like this is useless.

  // Execution of the writer is triggered by invoking the \code{Update()} method.
  try
    {
    writer1->Update();
    }
  catch (itk::ExceptionObject & e)
    {
    std::cerr << "exception in file writer " << std::endl;
    std::cerr << e.GetDescription() << std::endl;
    std::cerr << e.GetLocation() << std::endl;
    return 1;
    }

  return 0;
}

Answer 1

我刚刚使用以下SimpleITK代码成功阅读了Python中的mhd和原始文件：

import SimpleITK as sitk
import numpy as np
def load_itk_image(filename):
    itkimage = sitk.ReadImage(filename)
    numpyImage = sitk.GetArrayFromImage(itkimage)
    return numpyImage

也许您可以将它作为参考。

是否应该使用ReadImage函数而不是ImageFileReader？你可以尝试一下。

Answer 2

这里有一些很好的文件阅读示例，具体取决于已知的格式。

reader->SetImageIO( RawImageIO );

如果你要同时加载.mhd和.raw文件，因为它们是单独的格式，MetaImage vs Raw格式，你做什么，不知道图像大小，原点，间距等基于缺席或表达头文。

你如何确定图像的大小并得到（0,0,0）？图像 - ＆GT;的getSize（）？

您能提供测试数据吗？

https://itk.org/Wiki/ITK/Examples/IO/ReadUnknownImageType

https://itk.org/ITKExamples/src/IO/ImageBase/RegisterIOFactories/Documentation.html