How to write code from c++ to python using itk

Question

I'm new in programming with Python and I need to translate code from c++ to python using the itk library, but I'm encountering many difficulties. I show you an example, in the c++ code I have :

typedef itk::PasteImageFilter <Image3D, Image3D, Image3D> PasteImageFilterType;

with:

typedef itk::Image <unsigned char, 3> BinaryImageType3D;

I translate it in Python in this way:

PasteImageFilterType = itk.PasteImageFilter[itk.Image[itk.UC, 3], itk.Image[itk.UC, 3], itk.Image[itk.UC, 3]]

But I obtain the following error:

To limit the size of the package, only a limited number of
types are available in ITK Python. To print the supported
types, run the following command in your python environment:

    itk.PasteImageFilter.GetTypes()

Possible solutions:
* If you are an application user:
** Convert your input image into a supported format (see below).
** Contact developer to report the issue.
* If you are an application developer, force input images to be
loaded in a supported pixel type.

    e.g.: instance = itk.PasteImageFilter[itk.Image[itk.SS,2]].New(my_input)

* (Advanced) If you are an application developer, build ITK Python yourself and
turned to `ON` the corresponding CMake option to wrap the pixel type or image
dimension you need. When configuring ITK with CMake, you can set
`ITK_WRAP_${type}` (replace ${type} with appropriate pixel type such as
`double`). If you need to support images with 4 or 5 dimensions, you can add
these dimensions to the list of dimensions in the CMake variable
`ITK_WRAP_IMAGE_DIMS`.

Can someone explain how I can deal with this problem? Consider that it's not only for this function that I have this problem, but for many others; I don't find any documentation of itk for python; and I haven't understood very well the solution proposed by python. In your opinion which is the best strategy to deal with this error.

Thank you very much for the help

Trying to translate code directly from one language to another is usually a mistake. Better to learn both languages well, learn what the original program does, then write a *new* program doing the same in the second language, using its idioms and conventions. — Jesper Juhl, Jul 28 '22 at 11:03

score 1 · Answer 1 · answered Jul 28 '22 at 13:07

tl;dr: PasteImageFilterType = itk.PasteImageFilter[itk.Image[itk.UC, 3]]

Full answer:

A more direct way to translate those two lines of C++ into Python are:

BinaryImageType3D= itk.Image[itk.UC, 3]
PasteImageFilterType = itk.PasteImageFilter[BinaryImageType3D, BinaryImageType3D, BinaryImageType3D]

But you probably already knew that.

The error message also yields a list:

Supported input types:

itk.Image[itk.SS,2]
itk.Image[itk.SS,3]
itk.Image[itk.UC,2]
itk.Image[itk.UC,3]
itk.Image[itk.US,2]
itk.Image[itk.US,3]
itk.Image[itk.F,2]
itk.Image[itk.F,3]

And itk.Image[itk.UC,3] is on the list, so that causes confusion, understandably. You probably also took a look at the documentation of PasteImageFilter and saw that it has 3 template parameters, so providing 3 template parameters in Python was a logical choice.

It so happens that we are trying to make Python version of ITK simpler than C++ when we can, and PasteImageFilter was one of those places. As it is usually invoked with all 3 template parameters being the same, class' Python wrapping asks for just one template parameter. This is enough, as C++ declaration specifies default values for second and third template parameter equal to the first one.

So a declaration which works is: PasteImageFilterType = itk.PasteImageFilter[BinaryImageType3D].

Finally, ITK forum has more ITK experts paying attention, and is a better place to ask an ITK-related question.

How to write code from c++ to python using itk

1 Answers1