run_examples.py

# -*- coding: utf-8 -*-
import os
import sys
from shutil import rmtree
from multiprocessing import cpu_count


def run_examples(example, pipelines, data_path, plugin=None, rm_base_dir=True):
    from nipype import config
    from nipype.interfaces.base import CommandLine

    if plugin is None:
        plugin = "MultiProc"

    print("running example: %s with plugin: %s" % (example, plugin))
    config.enable_debug_mode()
    config.enable_provenance()
    CommandLine.set_default_terminal_output("stream")

    plugin_args = {}
    if plugin == "MultiProc":
        plugin_args["n_procs"] = int(os.getenv("NIPYPE_NUMBER_OF_CPUS", cpu_count()))

    __import__(example)
    for pipeline in pipelines:
        wf = getattr(sys.modules[example], pipeline)
        wf.base_dir = os.path.join(os.getcwd(), "output", example, plugin)

        results_dir = os.path.join(wf.base_dir, wf.name)
        if rm_base_dir and os.path.exists(results_dir):
            rmtree(results_dir)

        # Handle a logging directory
        log_dir = os.path.join(os.getcwd(), "logs", example)
        if not os.path.exists(log_dir):
            os.makedirs(log_dir)
        wf.config = {
            "execution": {
                "hash_method": "timestamp",
                "stop_on_first_rerun": "true",
                "write_provenance": "true",
                "poll_sleep_duration": 2,
            },
            "logging": {"log_directory": log_dir, "log_to_file": True},
        }
        try:
            wf.inputs.inputnode.in_data = os.path.abspath(data_path)
        except AttributeError:
            pass  # the workflow does not have inputnode.in_data

        wf.run(plugin=plugin, plugin_args=plugin_args)
        # run twice to check if nothing is rerunning
        wf.run(plugin=plugin)


if __name__ == "__main__":
    path, file = os.path.split(__file__)
    sys.path.insert(0, os.path.realpath(os.path.join(path, "..", "examples")))
    examples = {
        "fmri_fsl_reuse": ["level1_workflow"],
        "fmri_spm_nested": ["level1", "l2pipeline"],
        # 'fmri_spm_dartel':['level1','l2pipeline'],
        # 'fmri_fsl_feeds':['l1pipeline']
    }
    example = sys.argv[1]
    plugin = sys.argv[2]
    data_path = sys.argv[3]
    pipelines = sys.argv[4:]
    run_examples(example, pipelines, data_path, plugin)