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)

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()

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)

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

pymialsrtk.cli.mialsuperresolutiontoolkit_singularity.main()

Main function that creates and executes the BIDS App singularity 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}