bm_experiments.bm_elastix module¶

Benchmark for Elastix.

See references:

Installation

Download compiled executables from https://github.com/SuperElastix/elastix/releases

Try to run both executables locally elastix –help and transformix –help

add path to the lib export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/Applications/elastix/lib

define permanent path or copy libraries cp /elastix/lib/* /usr/local/lib/

Example

Perform sample image registration:

$HOME/Applications/elastix/bin/elastix             -f ./data-images/images/artificial_reference.jpg             -m ./data-images/images/artificial_moving-affine.jpg             -out ./results/elastix             -p ./configs/elastix_affine.txt

Besides using transformix for deforming images, you can also use transformix
to evaluate the transformation at some points. This means that the input points are specified in the fixed image domain, since the transformation direction is from fixed to moving image. Perform image/points warping:
$HOME/Applications/elastix/bin/transformix -tp ./results/elastix/TransformParameters.0.txt -out ./results/elastix -in ./data-images/images/artificial_moving-affine.jpg -def ./data-images/landmarks/artificial_reference.pts

Usage¶

Run the basic ANTs registration with original parameters:

python bm_experiments/bm_elastix.py         -t ./data-images/pairs-imgs-lnds_histol.csv         -d ./data-images         -o ./results         -elastix $HOME/Applications/elastix/bin         -cfg ./configs/elastix_affine.txt

Note

The origin of VTK coordinate system is in left bottom corner of the image. Also the first dimension is horizontal (swapped to matplotlib)

Note

For proper confirmation see list of Elastix parameters: http://elastix.isi.uu.nl/doxygen/parameter.html

Note

If you have any complication with Elastix, see https://github.com/SuperElastix/elastix/wiki/FAQ

Klein, Stefan, et al. “Elastix: a toolbox for intensity-based medical image registration.”: IEEE transactions on medical imaging 29.1 (2009): 196-205. http://elastix.isi.uu.nl/marius/downloads/2010_j_TMI.pdf

class bm_experiments.bm_elastix.BmElastix(params)[source]¶

Bases: birl.benchmark.ImRegBenchmark

Benchmark for Elastix

For the app installation details, see module details.

Example

>>> from birl.utilities.data_io import create_folder, update_path
>>> path_out = create_folder('temp_results')
>>> fn_path_conf = lambda n: os.path.join(update_path('configs'), n)
>>> path_csv = os.path.join(update_path('data-images'), 'pairs-imgs-lnds_mix.csv')
>>> params = {'path_out': path_out,
...           'path_table': path_csv,
...           'nb_workers': 1,
...           'unique': False,
...           'path_elastix': '.',
...           'path_config': fn_path_conf('elastix_affine.txt')}
>>> benchmark = BmElastix(params)
>>> benchmark.run()  
>>> shutil.rmtree(path_out, ignore_errors=True)

initialise benchmark

Parameters: params (dict) – parameters

_clear_after_registration(item)[source]¶

clean unnecessarily files after the registration

Parameters: item (dict) – dictionary with regist. information
Return dict: the same or updated regist. info

_extract_warped_image_landmarks(item)[source]¶

get registration results - warped registered images and landmarks

Parameters: item (dict) – dictionary with registration params
Return dict: paths to warped images/landmarks

_generate_regist_command(item)[source]¶

generate the registration command(s)

Parameters: item (dict) – dictionary with registration params
Return str|list(str): the execution commands

_prepare()[source]¶: prepare BM - copy configurations

static extend_parse(arg_parser)[source]¶

extent the basic arg parses by some extra required parameters

Return object

static parse_warped_points(path_pts, col_name='OutputPoint')[source]¶

COMMAND_REGISTRATION = '%(exec_elastix)s -f %(target)s -m %(source)s -out %(output)s -p %(config)s'[source]¶: command template for image registration

COMMAND_TRANSFORMATION = '%(exec_transformix)s -tp %(output)s/TransformParameters.0.txt -out %(output)s -in %(source)s -def %(landmarks)s'[source]¶: command template for image/landmarks transformation

EXEC_ELASTIX = 'elastix'[source]¶: executable for performing image registration

EXEC_TRANSFX = 'transformix'[source]¶: executable for performing image/landmarks transformation

NAME_IMAGE_WARPED = 'result.*'[source]¶: default name of warped image (the image extension cam be changed in the config file)

NAME_LNDS_WARPED = 'outputpoints.txt'[source]¶: default name of warped landmarks

REQUIRED_PARAMS = ['path_out', 'path_table', 'path_config'][source]¶: required experiment parameters