我如何在Python中使用ITK类

Question

I have written a class using ITK in CPP which reads all files in a directory and then averages them. I would like to use this class in a pipeline constructed using Python.

I had previously tried to use Swig to wrap template code but according to the swig documenation , it doesn't have template support and the type names need to explicitly specified. But when I use ITK in Python , the interface is very different to that I expect from Swig-generated template code (the type name is not specified in the function/class name at all, which is contrary to what Swig documentation says).

A small snippet from my code illustrating the usage of the class is shown below:

typedef unsigned char PixelType;
typedef itk::Image<PixelType, 2> ImageType;
typedef itk::NaryMeanImageFilter< ImageType, ImageType > FilterType; // custom class
typedef itk::ImageFileReader<ImageType> ReaderType;
typedef itk::ImageFileWriter<ImageType> WriterType;

ImageType::Pointer image = ImageType::New();
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
FilterType::Pointer filter = FilterType::New(); // custom class

for (unsigned int i = 0; i< fileNames.size(); ++i)
{
  reader->SetFileName(fileNames[i]);
  filter->SetInput(i, reader->GetOutput()); // custom class
}

writer->SetFileName(outName);
writer->SetInput(filter->GetOutput());
writer->Update();

The code for the class can be seen in the Git repository . I don't have an issue with increasing the dependencies of my project by using Boost::Python but I need a starting point to proceed. Any help would be extremely appreciated.

Thanks.

UPDATE:

Expected usage in Python would be,

readerType=itk.ImageFileReader[inputImageType]
reader=readerType.New()
filterType=itk.NaryMeanImageFilter[inputImageType,inputImageType]
filter=filterType.New()

for i in range(0, fileNames.size()):
    reader.SetFileName(fileNames[i])
    filter.SetInput(i, reader->GetOutput())

Answer 1

The main idea is to use the WrapITK module. It basically uses internal ITK wrapping and parsing mechanism (using GCCXML for C++ to XML parsing - to be moved to CastXML in the future) to generate the *.i files which SWIG uses to generate the Python wrapping code.

Basic idea:

• Say you have an ITK filter 'itkDummy.h' which want to use from a Python script
• Write a file 'itkDummy.wrap' giving the information about the pixel types and template initializations.
• Use the WrapITK module (which is along with the ITK Python bindings) - needs to be verified because every time I tried this, I kept getting an error
• Be happy that itkDummy can be called from Python

Reference: http://www.itk.org/Wiki/ITK/Release_4/Wrapping/BuildProcess

This is what I was looking for.

Answer 2

In Itk Software Guide vol. 1 ( http://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch3.html#x34-410003.7 ) they explain that they are using their own wrapping consisting of:

1. gccxml , that generates xml files from C++ program
2. a script called igenerator.py , which generates .i files for swig
3. swig

I've never done it before, but you could try to go through their wrapping pipeline to see how the generated *.i file looks like (or maybe even including your filter in your local ITK repository and see if the wrapping automatically works)