Example 1: Organizing Simulation Parameters

Two versions of configuration processing are shown. The first one merely collects the simulation parameters into a dictionary. The Second version stores them additionally in a database.

Without the use of a database:

from cytoskeleton_analyser.inout import Paths     # simulation-specific paths
from cytoskeleton_analyser.config.drivers import process  # driver fuction
from sim_specs import cell, data_in, data_out, rinds

# Decide if this is a new analysis, or we merely want to import one.
new = True

if __name__ == '__main__':

   for ci in rinds:
      paths = Paths(data_in, data_out, cell, ci)
      process(new, paths, ci, cell)

Accumulate the settings in a database:

Similar to the above, but the database module is included (line 3). The data are collected in ‘cfs’ (lines 11,12) list before sending to the database (line 13).

from cytoskeleton_analyser.inout import Paths     # simulation-specific paths
from cytoskeleton_analyser.config.drivers import process  # driver fuction
import cytoskeleton_analyser.database.sqlite_alchemy_orm.db as db  # database
from sim_specs import cell, data_in, data_out, rinds

# Decide if this is a new analysis, or we merely want to import one.
new = True

if __name__ == '__main__':

   cfs = [process(new, Paths(data_in, data_out, cell, ci), ci, cell)
          for ci in rinds]
   db.update(cfs, cell, Paths(data_in, data_out, cell).data_out.parent)