This is a port from the original WrapITK PyBuffer to an ITKv4 module.

Differences from the original PyBuffer:

• Support for VectorImage's
• Option to not swap the axes (only for GetArrayFromImage)
• Tests
• Based on the Python Buffer Protocol -- does not require NumPy to build.

This module is available in the ITK source tree as a Remote module. To enable it, set:

ITK_WRAP_PYTHON:BOOL=ON
Module_BridgeNumPy:BOOL=ON

in ITK's CMake build configuration. In ITK 4.12 and later, this module is enabled by default when ITK_WRAP_PYTHON is enabled.

To convert an ITK image to a NumPy array:

import itk

PixelType = itk.ctype('float')
Dimension = 3
ImageType = itk.Image[PixelType, Dimension]

image = ImageType.New()
size = itk.Size[Dimension]()
size.Fill(100)
region = itk.ImageRegion[Dimension](size)
image.SetRegions(region)
image.Allocate()

arr = itk.PyBuffer[ImageType].GetArrayFromImage(image)

To convert a NumPy array to an ITK image:

import numpy as np
import itk

PixelType = itk.ctype('float')
Dimension = 3
ImageType = itk.Image[PixelType, Dimension]

arr = np.zeros((100, 100, 100), np.float32)
image = itk.PyBuffer[ImageType].GetImageFromArray(arr)

It is also possible to convert VNL matrices and arrays to NumPy arrays and back:

import numpy as np
import itk

ElementType = itk.ctype('float')
vector = itk.vnl_vector[ElementType]()
vector.set_size(8)
arr = itk.PyVnl[ElementType].GetArrayFromVnlVector(vector)

matrix = itk.vnl_matrix[ElementType]()
matrix.set_size(3, 4)
arr = itk.PyVnl[ElementType].GetArrayFromVnlMatrix(matrix)

arr = np.zeros((100,), np.float32)
vector = itk.PyVnl[ElementType].GetVnlVectorFromArray(arr)

arr = np.zeros((100, 100), np.float32)
matrix = itk.PyVnl[ElementType].GetVnlMatrixFromArray(arr)