Command-line interface (CLI) module¶
This module defines the mialsuperresolutiontoolkit_bidsapp_docker
script that wraps calls to the Docker BIDS APP image.
-
pymialsrtk.cli.mialsuperresolutiontoolkit_docker.
create_docker_cmd
(args)[source]¶ Function that creates and returns the BIDS App docker run command.
Parameters: args (dict) – Dictionary of parsed input argument in the form:
{ 'bids_dir': "/path/to/bids/dataset/directory", 'output_dir': "/path/to/output/directory", 'param_file': "/path/to/configuration/parameter/file", 'analysis_level': "participant", 'participant_label': ['01', '02', '03'], 'openmp_nb_of_cores': 1, 'nipype_nb_of_cores': 1, 'masks_derivatives_dir': 'manual_masks' }
Returns: cmd – String containing the command to be run via subprocess.run()
Return type: string
-
pymialsrtk.cli.mialsuperresolutiontoolkit_docker.
main
()[source]¶ Main function that creates and executes the BIDS App docker command.
Returns: exit_code – An exit code given to
sys.exit()
that can be:- ’0’ in case of successful completion
- ’1’ in case of an error
Return type: {0, 1}
This module defines the mialsuperresolutiontoolkit_bidsapp_singularity
script that wraps calls to the Singularity BIDS APP image.
-
pymialsrtk.cli.mialsuperresolutiontoolkit_singularity.
create_singularity_cmd
(args)[source]¶ Function that creates and returns the BIDS App singularity run command.
Parameters: args (dict) – Dictionary of parsed input argument in the form:
{ 'bids_dir': "/path/to/bids/dataset/directory", 'output_dir': "/path/to/output/directory", 'param_file': "/path/to/configuration/parameter/file", 'analysis_level': "participant", 'participant_label': ['01', '02', '03'], 'openmp_nb_of_cores': 1, 'nipype_nb_of_cores': 1, 'masks_derivatives_dir': 'manual_masks' }
Returns: cmd – String containing the command to be run via subprocess.run()
Return type: string