README.md

elastix-py

A Python wrapper for the Elastix image registration software package. This package allows you to call Elastix and Transformix from Python.

Installation

Using pip, you can install from this repository:

pip install git+https://github.com/tueimage/elastix-py

The package requires numpy and SimpleITK, which can be installed with pip as well:

pip install SimpleITK
pip install numpy

You will also need to install Elastix yourself from http://elastix.lumc.nl/download.php.

Set the elastix_path and transformix_path to the paths where you installed the binaries for elastix and transformix when using the ElastixInterface and TransformixInterface classes. For windows, these paths need to point to the .exe files.

Tutorial

A Python script that covers most the functionality is included in the example.py file.

Minimal working example

import elastix

el = elastix.ElastixInterface(elastix_path=ELASTIX_PATH)

el.register(
    fixed_image=fixed_image_path,
    moving_image=moving_image_path,
    parameters=[parameter_file_path],
    output_dir='results')

result_path = os.path.join('results', 'result.0.tiff')

Optional plotting:

fixed_image = imageio.imread(fixed_image_path)[:, :, 0]
moving_image = imageio.imread(moving_image_path)[:, :, 0]
transformed_moving_image = imageio.imread(result_path)

fig, ax = plt.subplots(1, 4, figsize=(20, 5))
ax[0].imshow(fixed_image, cmap='gray')
ax[0].set_title('Fixed image')
ax[1].imshow(moving_image, cmap='gray')
ax[1].set_title('Moving image')
ax[2].imshow(transformed_moving_image, cmap='gray')
ax[2].set_title('Transformed\nmoving image')

plt.show()