def revive_simulation(rev_parameters, sim_functions):
print('\n[' + rev_parameters["simulation_name"].upper() + ' REVIVAL SIMULATION]')
Populations = {}
if "sim_folder" in rev_parameters:
print('Accessing simulation files directory...')
print('Excavating World entity: ' + rev_parameters['eco_file'] + '...')
World = excavate_world(rev_parameters['sim_folder'] + \
rev_parameters['eco_file'])
print('Updating parameters with World dimensions...')
rev_parameters["world_z"] = len(World.ecosystem[0][0][0])
rev_parameters["world_y"] = len(World.ecosystem[0][0])
rev_parameters["world_x"] = len(World.ecosystem[0])
for i in range(len(rev_parameters["pop_files"])):
print('\nReviving population file: ' + \
rev_parameters["pop_files"][i] + '...')
pop_file = rev_parameters["sim_folder"] + \
rev_parameters["pop_files"][i]
Populations[rev_parameters["population_names"][i]] = \
revive_population(pop_file)
print('\nUpdating revival generation start in simulation parameters...')
rev_parameters["rev_start"] = [Populations[pop_name].generation
for pop_name in Populations]
elif "database_source" in rev_parameters:
print('Constructing database directory...')
dbpath = os.sep.join([os.getcwd(),
'Simulations',
rev_parameters["database_source"]])
print('Connecting to database file: ' + \
rev_parameters["database_source"] + '...')
(con, cur) = connect_database(dbpath, None)
if rev_parameters["simulation_time"] == 'default':
print('Acquiring simulation starting time...')
rev_parameters["simulation_time"] = db_list_simulations(cur)[0][0]
print('Reconstructing old simulation parameters...')
temp_parameters = db_reconstruct_simulation_parameters(cur,
rev_parameters["simulation_time"])
print('Assimilating old simulation parameters with new simulation parameters...')
for key in temp_parameters:
if key not in rev_parameters:
rev_parameters[key] = temp_parameters[key]
print('Reconstructing World entity...')
World = db_reconstruct_world(cur, rev_parameters["simulation_time"],
rev_parameters["rev_start"][0])
print('\nUpdating population names parameter...')
for pop_name in rev_parameters["population_names"]:
print('Reconstructing population: ' + pop_name + '...')
Populations[pop_name] = db_reconstruct_population(cur,
rev_parameters["simulation_time"], pop_name,
rev_parameters["rev_start"][rev_parameters["population_names"].index(pop_name)])
print('Terminating database connection...')
con.close()
print('Updating last generation revival and population size simulation parameters...')
rev_parameters["rev_finish"] = [(Populations[pop_name].generation + \
rev_parameters["extend_gen"])
for pop_name in Populations]
rev_parameters["rev_pop_size"] = [len(Populations[pop_name].agents)
for pop_name in Populations]
print('\nStarting simulation core...')
simulation_core(sim_functions, rev_parameters, Populations, World)
def __init__(self, db_source, population_name, starting_time = 'default'):
print('\n[INITIALIZING ANALYSIS]')
self.db_source = db_source
self.population_name = population_name
print('Assembling database file directory...')
dbpath = os.getcwd().split(os.sep)
dbpath[-1] = 'examples'
dbpath = os.sep.join(dbpath)
dbpath = os.sep.join([dbpath, 'Simulations', db_source])
print('Connecting to database file: ' + db_source + '...')
(self.con, self.cur) = database_calls.connect_database(dbpath, None)
print('Acquiring simulation starting time...')
if starting_time == 'default':
self.starting_time = database_calls.db_list_simulations(self.cur)[0][0]
else:
self.starting_time = starting_time
def __init__(self, db_source, population_name, starting_time='default'):
print('\n[INITIALIZING ANALYSIS]')
self.db_source = db_source
self.population_name = population_name
print('Assembling database file directory...')
dbpath = os.getcwd().split(os.sep)
dbpath[-1] = 'examples'
dbpath = os.sep.join(dbpath)
dbpath = os.sep.join([dbpath, 'Simulations', db_source])
print('Connecting to database file: ' + db_source + '...')
(self.con, self.cur) = \
database_calls.connect_database(dbpath, None)
print('Acquiring simulation starting time...')
if starting_time == 'default':
self.starting_time = \
database_calls.db_list_simulations(self.cur)[0][0]
else:
self.starting_time = starting_time
def revive_simulation(rev_parameters, sim_functions, eb = event_broker()):
eb.log("[" + rev_parameters["simulation_name"].upper() + " REVIVAL SIMULATION]")
populations = {}
world = None
eb.log("Accessing simulation files directory")
if "sim_folder" in rev_parameters:
eb.log('Excavating World entity: ' + rev_parameters['eco_file'])
world = excavate_world(rev_parameters['sim_folder'] + rev_parameters['eco_file'])
eb.log('Updating parameters with World dimensions')
rev_parameters["world_z"] = len(world.ecosystem[0][0][0])
rev_parameters["world_y"] = len(world.ecosystem[0][0])
rev_parameters["world_x"] = len(world.ecosystem[0])
for i in range(len(rev_parameters["pop_files"])):
eb.log('Reviving population file: ' + rev_parameters["pop_files"][i])
pop_file = rev_parameters["sim_folder"] + rev_parameters["pop_files"][i]
populations[rev_parameters["population_names"][i]] = revive_population(pop_file)
eb.log('Updating revival generation start in simulation parameters')
rev_parameters["rev_start"] = [populations[pop_name].generation for pop_name in populations]
elif "database_source" in rev_parameters:
eb.log('Constructing database directory')
dbpath = os.sep.join([os.getcwd(), 'Simulations', rev_parameters["database_source"]])
eb.log('Connecting to database file: ' + rev_parameters["database_source"])
(con, cur) = connect_database(dbpath, None)
if rev_parameters["simulation_time"] == 'default':
eb.log('Acquiring simulation starting time')
rev_parameters["simulation_time"] = db_list_simulations(cur)[0][0]
eb.log('Reconstructing old simulation parameters')
temp_parameters = db_reconstruct_simulation_parameters(cur, rev_parameters["simulation_time"])
eb.log('Assimilating old simulation parameters with new simulation parameters')
for key in temp_parameters:
if key not in rev_parameters:
rev_parameters[key] = temp_parameters[key]
eb.log('Reconstructing World entity')
world = db_reconstruct_world(cur, rev_parameters["simulation_time"], rev_parameters["rev_start"][0])
eb.log('Updating population names parameter')
for pop_name in rev_parameters["population_names"]:
eb.log('Reconstructing population: ' + pop_name)
populations[pop_name] = db_reconstruct_population(cur, rev_parameters["simulation_time"], pop_name,
rev_parameters["rev_start"][rev_parameters
["population_names"].index(pop_name)])
eb.log('Terminating database connection')
con.close()
eb.log('Updating last generation revival and population size simulation parameters')
rev_parameters["rev_finish"] = [(populations[pop_name].generation + rev_parameters["extend_gen"])
for pop_name in populations]
rev_parameters["rev_pop_size"] = [len(populations[pop_name].agents) for pop_name in populations]
eb.log('Starting simulation core')
simulation_core(sim_functions, rev_parameters, populations, world)
import analytics
import database_calls
database_filename = "case_study_00.db"
outputfile = 'sim00_within_cell_analysis.csv'
print('Opening outputfile: ' + outputfile + '...')
outputfile = open(outputfile, 'w')
print('Assembling database file directory...')
dbpath = os.getcwd().split(os.sep)
dbpath[-1] = 'examples'
dbpath = os.sep.join(dbpath)
dbpath = os.sep.join([dbpath, 'Simulations', database_filename])
print('Connecting to database file: ' + database_filename + '...')
(con, cur) = database_calls.connect_database(dbpath, None)
print('Acquiring simulation starting time...')
starting_time = database_calls.db_list_simulations(cur)[0][0]
print('Constructing locations list...')
locations = []
for x in range(5):
for y in range(5):
locations.append((x, y, 0))
def get_chromosomes_by_location(starting_time, pop_name, generation):
organisms = database_calls.db_reconstruct_organisms(
cur, starting_time, pop_name, generation)
organism_chromosomes = {}
for location in locations:
organism_chromosomes[location] = []
for organism in organisms:
import analytics
import database_calls
database_filename = "case_study_00.db"
outputfile = 'sim00_within_cell_analysis.csv'
print('Opening outputfile: ' + outputfile + '...')
outputfile = open(outputfile, 'w')
print('Assembling database file directory...')
dbpath = os.getcwd().split(os.sep)
dbpath[-1] = 'examples'
dbpath = os.sep.join(dbpath)
dbpath = os.sep.join([dbpath, 'Simulations', database_filename])
print('Connecting to database file: ' + database_filename + '...')
(con, cur) = database_calls.connect_database(dbpath, None)
print('Acquiring simulation starting time...')
starting_time = database_calls.db_list_simulations(cur)[0][0]
print('Constructing locations list...')
locations = []
for x in range(5):
for y in range(5):
locations.append((x,y,0));
def get_chromosomes_by_location(starting_time, pop_name, generation):
organisms = database_calls.db_reconstruct_organisms(cur, starting_time, pop_name, generation)
organism_chromosomes = {}
for location in locations:
organism_chromosomes[location] = []
for organism in organisms:
if organism.status['location'] == location:
organism_chromosomes[location].append(organism.genome[0].sequence)