Thin wrapper around elastix - a toolbox for rigid and nonrigid registration of images
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README.md

PyElastix - Python wrapper for the Elastix nonrigid registration toolkit

This Python module wraps the Elastix registration toolkit, which is a powerful tool, suitable for 2D and 3D images, capable of rigid as well as non-rigid (i.e. elastic) image registration.

For an overview of other image registration projects in Python, see http://pyimreg.github.io.

Installation

Install this library using conda install elastix or pip install pyelastix. This module depends on numpy.

Further, the Elastix command line application needs to be installed on your computer. You can obtain a copy at http://elastix.isi.uu.nl/.

This module tries to detect the Elastix executable in a series of common locations, such as program directories, the user directory, and next to this module. The executable (or the directory that contains it) can also be provided by setting the ELASTIX_PATH environment variable.

How it works

This module writes the images to register to disk, calls Elastix to do the registration and reads the resulting data. The temporary data is automatically cleaned up. This approach keeps this module relatively easy, while providing the full power of the awesome Elastix registration toolkit.

Example

# Given im1 and im2 images stored as numpy arrays ...

import pyelastix

# Get params and change a few values
params = pyelastix.get_default_params()
params.MaximumNumberOfIterations = 200
params.FinalGridSpacingInVoxels = 10

# Apply the registration (im1 and im2 can be 2D or 3D)
im1_deformed, field = pyelastix.register(im1, im2, params)

See example.py for a more complete example.

API


Parameters()

Struct object to represent the parameters for the Elastix registration toolkit. Sets of parameters can be combined by addition. (When adding p1 + p2, any parameters present in both objects will take the value that the parameter has in p2.)

Use get_default_params() to get a Parameters struct with sensible default values.

get_advanced_params()

Get Parameters struct with parameters that most users do not want to think about.

get_default_params(type='BSPLINE')

Get Parameters struct with parameters that users may want to tweak. The given type specifies the type of allowed transform, and can be 'RIGID', 'AFFINE', 'BSPLINE'.

For detail on what parameters are available and how they should be used, we refer to the Elastix documentation. Here is a description of the most common parameters:

  • Transform (str): Can be 'BSplineTransform', 'EulerTransform', or 'AffineTransform'. The transformation to apply. Chosen based on type.
  • FinalGridSpacingInPhysicalUnits (int): When using the BSplineTransform, the final spacing of the grid. This controls the smoothness of the final deformation.
  • AutomaticScalesEstimation (bool): When using a rigid or affine transform. Scales the affine matrix elements compared to the translations, to make sure they are in the same range. In general, it's best to use automatic scales estimation.
  • AutomaticTransformInitialization (bool): When using a rigid or affine transform. Automatically guess an initial translation by aligning the geometric centers of the fixed and moving.
  • NumberOfResolutions (int): Most registration algorithms adopt a multiresolution approach to direct the solution towards a global optimum and to speed up the process. This parameter specifies the number of scales to apply the registration at. (default 4)
  • MaximumNumberOfIterations (int): Maximum number of iterations in each resolution level. 200-2000 works usually fine for nonrigid registration. The more, the better, but the longer computation time. This is an important parameter! (default 500).

get_elastix_exes()

Get the executables for elastix and transformix. Raises an error if they cannot be found.

get_tempdir()

Get the temporary directory where pyelastix stores its temporary files. The directory is specific to the current process and the calling thread. Generally, the user does not need this; directories are automatically cleaned up. Though Elastix log files are also written here.

register(im1, im2, params, exact_params=False, verbose=1)

Perform the registration of im1 to im2, using the given parameters. Returns (im1_deformed, field), where field is a tuple with arrays describing the deformation for each dimension (x-y-z order, in world units).

Parameters:

  • im1 (ndarray or file location): The moving image (the one to deform).
  • im2 (ndarray or file location): The static (reference) image.
  • params (dict or Parameters): The parameters of the registration. Default parameters can be obtained using the get_default_params() method. Note that any parameter known to Elastix can be added to the parameter struct, which enables tuning the registration in great detail. See get_default_params() and the Elastix docs for more info.
  • exact_params (bool): If True, use the exact given parameters. If False (default) will process the parameters, checking for incompatible parameters, extending values to lists if a value needs to be given for each dimension.
  • verbose (int): Verbosity level. If 0, will not print any progress. If 1, will print the progress only. If 2, will print the full output produced by the Elastix executable. Note that error messages produced by Elastix will be printed regardless of the verbose level.

If im1 is a list of images, performs a groupwise registration. In this case the resulting field is a list of fields, each indicating the deformation to the "average" image.