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