scanLevel.py

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import os
import sys
import argparse
import time

import Initialization.initialization as init
import Quality_Control.dashboard as dash
from workflows import Workflows

"""
.. module:: scanLevel
    :platform: Unix
    :synopsis: Module to launch scan level analysis.
.. moduleauthor:: Thomas Funck <tffunck@gmail.com>
"""
def run_scan_level(opts,args): 
    ###Define args with exiting subject and condition combinations
    sub_valid_args, task_valid_args=init.gen_args(opts, args)
    
    scan_level_workflow = Workflows(opts)

    scan_level_workflow.initialize(opts) 

    #vizualization graph of the workflow
    try :
        scan_level_workflow.workflow.write_graph(opts.targetDir+os.sep+"workflow_graph.dot", graph2use = 'colored', format='png')
    except RuntimeError :
        print("Could not create exec workflow.")
    
    #Run the work flow
    if opts.num_threads > 1 :
        scan_level_workflow.workflow.run(plugin='MultiProc', plugin_args={'n_procs': opts.num_threads})
    else : 
        scan_level_workflow.workflow.run()
    return 0