template.txt

import os
import sys
import glob
import shutil
import XCore
import time, datetime
import s4l_v1.document as doc
import s4l_v1.simulation.emlf as emlf

from s4l_v1 import analysis
from s4l_v1._api.application import run_application, get_app_safe


if get_app_safe() is None:
    run_application(disable_ui_plugins=True)
app = get_app_safe()

# In o²S²PARC, INPUT_FOLDER and OUTPUT_FOLDER are environment variables 
# that map to the Service input/output ports, respectively
input_dir = os.environ["INPUT_FOLDER"] 
output_dir = os.environ["OUTPUT_FOLDER"]


if __name__ == '__main__':
    start_time = time.time()
    root =  input_dir
    model_name = "$smashfile".rstrip(".smash")
    model_path = os.path.join(root, model_name+'.smash')
    config_path = os.path.join(root, 'emconfig_'+model_name+'.json')
    # set which tissues are active in the config file --> Bones and Discs are inactivated

    # intialize app and open project
    app = XCore.GetOrCreateConsoleApp()
    doc.New()
    doc.Open(model_path)
    analysis.ResetAnalysis()

    ## your code goes here
    os.makedirs(os.path.join(input_dir, "Results_EM"), exist_ok=True)
    list_active_sites = ["E" + str(int("$electrode_index")).zfill(2)]
    
    for active_site in list_active_sites:
        sim_mock = emlf.ElectroQsOhmicSimulation()
        sim_mock.Name = f"Subject_Anisotropy_{active_site}"
        doc.AllSimulations.Add(sim_mock)

    print("Total time of execution: ", datetime.timedelta(seconds=(time.time() - start_time)))
    print("Simulation DONE")

    # write data to outputfile_0_name, etc.
    for result in glob.glob(os.path.join(input_dir, "$smashfile"+"_Results", "*_Output.h5")):
        fn = os.path.basename(result)
        shutil.copy(result, os.path.join(output_dir, fn))

    source_dir = os.path.join(input_dir, "Results_EM")    
    dest_dir = os.path.join(output_dir, "Results_EM")
    if os.path.exists(dest_dir):
        shutil.rmtree(dest_dir)
    shutil.copytree(source_dir, dest_dir)