bm_experiments.bm_ANTsPy module¶
Benchmark for ANTs
See references:
- http://stnava.github.io/ANTs
- https://sourceforge.net/projects/advants/
- https://github.com/ANTsX/ANTsPy
- https://github.com/ANTsX/ANTsPy/issues/85
Installation¶
Install it as python package:
pip install git+https://github.com/ANTsX/ANTsPy.git
Usage¶
Run the basic ANTs registration with original parameters:
python bm_experiments/bm_ANTsPy.py -t ./data_images/pairs-imgs-lnds_histol.csv -d ./data_images -o ./results -py python3 -script ./scripts/Python/run_ANTsPy.py
Note
required to use own compiled last version since some previous releases do not contain ants.apply_transforms_to_points
Copyright (C) 2017-2019 Jiri Borovec <jiri.borovec@fel.cvut.cz>
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class
bm_experiments.bm_ANTsPy.
BmANTsPy
(params)[source]¶ Bases:
birl.benchmark.ImRegBenchmark
Benchmark for ANTs wrapper in Python no run test while this method requires manual installation of ANTsPy package
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_table': path_csv, ... 'path_out': path_out, ... 'nb_workers': 2, ... 'unique': False, ... 'exec_Python': 'python', ... 'path_script': '.'} >>> benchmark = BmANTsPy(params) >>> benchmark.run() # doctest: +SKIP >>> del benchmark >>> shutil.rmtree(path_out, ignore_errors=True)
initialise benchmark
Parameters: params (dict) – parameters -
_extract_execution_time
(item)[source]¶ if needed update the execution time
Parameters: item (dict) – dictionary with registration params Return float|None: time in minutes
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_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
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_generate_regist_command
(item)[source]¶ generate the registration command(s)
Parameters: item (dict) – dictionary with registration params Return str|list(str): the execution commands
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static
extend_parse
(arg_parser)[source]¶ extent the basic arg parses by some extra required parameters
Return object:
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