[ENH] Add script that wraps the call to Singularity image

Merge pull request #61 from Medical-Image-Analysis-Laboratory/58_singularity_wrapper_v2.0.1-dev

pymialsrtk/cli/mialsuperresolutiontoolkit_bidsapp.py → pymialsrtk/cli/mialsuperresolutiontoolkit_bidsapp_docker.py

@@ -7,7 +7,7 @@
 #
 #  This software is distributed under the open-source license Modified BSD.
 
-"""This module defines the mialsuperresolutiontoolkit-bidsapp script that wraps calls to the BIDS APP."""
+"""This module defines the `mialsuperresolutiontoolkit_bidsapp_docker` script that wraps calls to the Docker BIDS APP image."""
 
 # General imports
 import sys

pymialsrtk/cli/mialsuperresolutiontoolkit_bidsapp_singularity.py

@@ -0,0 +1,103 @@
+#!/usr/bin/env python
+#
+# Copyright © 2016-2020
+# Medical Image Analysis Laboratory,
+# University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland,
+# and Contributors
+#
+#  This software is distributed under the open-source license Modified BSD.
+
+"""This module defines the `mialsuperresolutiontoolkit_bidsapp_singularity` script that wraps calls to the Singularity BIDS APP image."""
+
+# General imports
+import sys
+
+# Own imports
+from pymialsrtk.info import __version__
+from pymialsrtk.parser import get_parser
+from pymialsrtk.interfaces.utils import run
+
+
+def 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
+        String containing the command to be run via `subprocess.run()`
+    """
+    # Docker run command prelude
+    cmd = 'singularity run --containall '
+    cmd += f'--bind {args.bids_dir}:/bids_dir '
+    cmd += f'--bind {args.output_dir}:/output_dir '
+    cmd += f'--bind {args.param_file}:/bids_dir/code/participants_params.json '
+    cmd += f'library://tourbier/mialsuperresolutiontoolkit-bidsapp:v{__version__} '
+
+    # Standard BIDS App inputs
+    cmd += '/bids_dir '
+    cmd += '/output_dir '
+    cmd += f'{args.analysis_level} '
+    cmd += '--participant_label '
+    for label in args.participant_label:
+        cmd += f'{label} '
+
+    # MIALSRTK BIDS App inputs
+    cmd += '--param_file /bids_dir/code/participants_params.json '
+    if args.masks_derivatives_dir != '':
+        cmd += f'--masks_derivatives_dir {args.masks_derivatives_dir} '
+    cmd += f'--openmp_nb_of_cores {args.openmp_nb_of_cores} '
+    cmd += f'--nipype_nb_of_cores {args.nipype_nb_of_cores}'
+
+    return cmd
+
+
+def main():
+    """Main function that creates and executes the BIDS App singularity command.
+
+    Returns
+    -------
+    exit_code : {0, 1}
+        An exit code given to `sys.exit()` that can be:
+
+            * '0' in case of successful completion
+
+            * '1' in case of an error
+    """
+    # Create and parse arguments
+    parser = get_parser()
+    args = parser.parse_args()
+
+    # Create the singularity run command
+    cmd = create_singularity_cmd(args)
+
+    # Execute the singularity run command
+    try:
+        print(f'... cmd: {cmd}')
+        run(cmd)
+        exit_code = 0
+    except Exception as e:
+        print('Failed')
+        print(e)
+        exit_code = 1
+
+    return exit_code
+
+
+if __name__ == '__main__':
+    sys.exit(main())

setup.py

@@ -86,7 +86,8 @@ def main():
           url='https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit',
           entry_points={
                  "console_scripts": [
-                         'mialsuperresolutiontoolkit_bidsapp = pymialsrtk.cli.mialsuperresolutiontoolkit_bidsapp:main'
+                         'mialsuperresolutiontoolkit_bidsapp_docker = pymialsrtk.cli.mialsuperresolutiontoolkit_bidsapp_docker:main',
+                         'mialsuperresolutiontoolkit_bidsapp_singularity = pymialsrtk.cli.mialsuperresolutiontoolkit_bidsapp_singularity:main'
                  ]
           },
           license='BSD-3-Clause',

setup_pypi.py

@@ -80,9 +80,10 @@ def main():
           author_email='sebastien.tourbier@alumni.epfl.ch',
           url='https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit',
           entry_points={
-                 "console_scripts": [
-                         'mialsuperresolutiontoolkit_bidsapp = pymialsrtk.cli.mialsuperresolutiontoolkit_bidsapp:main'
-                 ]
+            "console_scripts": [
+              'mialsuperresolutiontoolkit_bidsapp_docker = pymialsrtk.cli.mialsuperresolutiontoolkit_bidsapp_docker:main',
+              'mialsuperresolutiontoolkit_bidsapp_singularity = pymialsrtk.cli.mialsuperresolutiontoolkit_bidsapp_singularity:main'
+            ]
           },
           license='BSD-3-Clause',
           classifiers=[