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 simulation_core(sim_functions, sim_parameters, eb, populations, world):
'''
Sequential ecological cell DOSE simulator.
Performs the following operations:
- Creating simulation file directory for results text file, population
freeze, and world burial storage
- Generate a simulation start time to identify the current simulation
- Define active Ragaraja instructions
- Connecting to logging database (if needed)
- Writing simulation parameters into results text file
- Initialize World and Population
- Deploy population(s) onto the world
- Run the simulation and recording the results
- Writing final results into results text file
- Close logging database (if used)
- Copy simulation script into simulation file directory
Events available for subscription and data:
- SIMULATION_START:
- time_start: datetime = simulation start time
- directory: String = simulation file path directory
- max_generation: int = maximum generations
- generation: int = starting generation
- GENERATION_WORLD_UPDATE:
- world: dose_world.World = world object
- generation: int = current generation
- GENERATION_POPULATIONS_UPDATE:
- populations: dict = dictionary of population objects
- generation: int = current generation
- SIMULATION_END:
- time_end: datetime = simulation end time
@param sim_functions: implemented simulation functions (see
dose.dose_functions)
@param sim_parameters: simulation parameters dictionary (see Examples)
@param eb: An instance of dose.event_broker
@param populations: dictionary of population objects
@param world: dose_world.World object
'''
eb.log('Started simulation preparation')
time_start = datetime.utcnow()
time_start_str = '-'.join([str(time_start).split(' ')[0], str(time())])
eb.log('Creating simulation file directories')
directory = '_'.join([sim_parameters["simulation_name"], time_start_str])
directory = os.sep.join([os.getcwd(), 'Simulations', directory]) + os.sep
if not os.path.exists(directory):
os.makedirs(directory)
eb.log('Adding simulation directory to simulation parameters')
sim_parameters["directory"] = directory
eb.log('Adding starting time to simulation parameters')
sim_parameters["starting_time"] = time_start_str
sim_functions = sim_functions()
eb.log('Activating ragaraja version: ' + str(sim_parameters["ragaraja_version"]))
if sim_parameters["ragaraja_version"] == 0:
ragaraja.activate_version(sim_parameters["ragaraja_version"], sim_parameters["ragaraja_instructions"])
else:
ragaraja.activate_version(sim_parameters["ragaraja_version"])
con = None
cur = None
if "database_file" in sim_parameters and "database_logging_frequency" in sim_parameters:
eb.log('Connecting to database file: ' + sim_parameters["database_file"])
(con, cur) = connect_database(None, sim_parameters)
eb.log('Logging simulation parameters to database file')
(con, cur) = db_log_simulation_parameters(con, cur, sim_parameters)
max_generations = None
generation_count = None
for pop_name in populations:
eb.log('Preparing population: ' + pop_name + ' for simulation')
if 'sim_folder' in sim_parameters or 'database_source' in sim_parameters:
eb.log('Calculating final generation count')
max_generations = sim_parameters["rev_start"][sim_parameters["population_names"].index(pop_name)] + \
sim_parameters["extend_gen"]
eb.log('Updating generation count from previous simulation')
generation_count = sim_parameters["rev_start"][0]
else:
eb.log('Deploying population in World entity')
if sim_parameters["deployment_code"] == 0:
eb.log('Executing user defined deployment scheme')
deploy_0(sim_parameters, populations, pop_name, world)
elif sim_parameters["deployment_code"] == 1:
eb.log('Executing deployment code 1: Single eco-cell deployment')
deploy_1(sim_parameters, populations, pop_name, world)
elif sim_parameters["deployment_code"] == 2:
eb.log('Executing deployment code 2: Random eco-cell deployment')
deploy_2(sim_parameters, populations, pop_name, world)
elif sim_parameters["deployment_code"] == 3:
eb.log('Executing deployment code 3: Even eco-cell deployment')
deploy_3(sim_parameters, populations, pop_name, world)
elif sim_parameters["deployment_code"] == 4:
eb.log('Executing deployment code 4: Centralized eco-cell deployment')
deploy_4(sim_parameters, populations, pop_name, world)
max_generations = sim_parameters["maximum_generations"]
generation_count = 0
eb.log('Writing simulation parameters into txt file report')
write_parameters(sim_parameters, pop_name)
eb.log('Updating generation count')
populations[pop_name].generation = generation_count
eb.log('Simulation preparation complete')
eb.publish(events.SIMULATION_START, {
'time_start': time_start,
'directory': directory,
'max_generation': max_generations,
'generation': generation_count
})
while generation_count < max_generations:
generation_count += 1
sim_functions.ecoregulate(world)
eco_cell_iterator(world, sim_parameters, sim_functions.update_ecology)
eco_cell_iterator(world, sim_parameters, sim_functions.update_local)
eco_cell_iterator(world, sim_parameters, sim_functions.report)
eb.publish(events.GENERATION_WORLD_UPDATE, {
'world': world,
'generation': generation_count
})
if generation_count % int(sim_parameters["eco_buried_frequency"]) == 0:
bury_world(sim_parameters, world, generation_count)
for pop_name in populations:
if sim_parameters["interpret_chromosome"]:
interpret_chromosome(sim_parameters, populations, pop_name, world)
report_generation(sim_parameters, populations, pop_name, sim_functions, generation_count)
sim_functions.organism_movement(populations, pop_name, world)
sim_functions.organism_location(populations, pop_name, world)
eb.publish(events.GENERATION_POPULATIONS_UPDATE, {
'populations': populations,
'generation': generation_count
})
if "database_file" in sim_parameters and "database_logging_frequency" in sim_parameters and \
generation_count % int(sim_parameters["database_logging_frequency"]) == 0:
(con, cur) = db_report(con, cur, sim_functions, sim_parameters["starting_time"], populations, world,
generation_count)
eb.log('Generation ' + str(generation_count) + ' complete')
eb.log('Closing simulation results')
for pop_name in populations:
close_results(sim_parameters, pop_name)
if "database_file" in sim_parameters and "database_logging_frequency" in sim_parameters:
eb.log('Committing logged data into database file and terminating database connection')
con.commit()
con.close()
eb.log('Copying simulation file script to simulation results directory')
# DV on my system, the inspect.stack()[2][1] value returns the full
# path to the file ('/home/douwe/scr/.../scriptname.py').
# The end result is an error for the original code, below, as the
# copyfile command is pointed to a wrong location: the directory
# is added twice. This might be Py3, or Windows functionality.
# With using the os.path module, this should give an OS-independent
# way of extracting the basename and linking to the directory.
sim_script_basename = os.path.basename(inspect.stack()[2][1])
copyfile(inspect.stack()[2][1],
# DV_original
# sim_parameters['directory'] + inspect.stack()[2][1])
os.path.join(sim_parameters['directory'], sim_script_basename))
eb.log('Simulation ended')
eb.publish(events.SIMULATION_END, {
'time_end': datetime.utcnow()
})
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)
# needed to run this example without prior
# installation of DOSE into Python site-packages
import run_examples_without_installation
# Example codes starts from here
import dose, genetic, random, os
import simulation_calls as helper
import database_calls
dbpath = os.sep.join([os.getcwd(),
'Simulations',
"case_study_01"])
(con, cur) = database_calls.connect_database(dbpath, None)
World = database_calls.db_reconstruct_world(cur, '2013-10-19-1382200534.1', 1000)
# needed to run this example without prior
# installation of DOSE into Python site-packages
import run_examples_without_installation
# Example codes starts from here
import dose, genetic, random, os
import simulation_calls as helper
import database_calls
dbpath = os.sep.join([os.getcwd(), 'Simulations', "case_study_01"])
(con, cur) = database_calls.connect_database(dbpath, None)
World = database_calls.db_reconstruct_world(cur, '2013-10-19-1382200534.1',
1000)
def simulation_core(sim_functions, sim_parameters, Populations, World):
'''
Sequential ecological cell DOSE simulator.
Performs the following operations:
- Creating simulation file directory for results text file, population
freeze, and world burial storage
- Generate a simulation start time to identify the current simulation
- Define active Ragaraja instructions
- Connecting to logging database (if needed)
- Writing simulation parameters into results text file
- Initialize World and Population
- Deploy population(s) onto the world
- Run the simulation and recording the results
- Writing final results into results text file
- Close logging database (if used)
- Copy simulation script into simulation file directory
@param sim_functions: implemented simulation functions (see
dose.dose_functions)
@param sim_parameters: simulation parameters dictionary (see Examples)
@param Populations: dictionary of population objects
@param World: dose_world.World object
'''
time_start = '-'.join([str(datetime.utcnow()).split(' ')[0],
str(time())])
print('Creating simulation file directories...')
directory ='_'.join([sim_parameters["simulation_name"],time_start])
directory = os.sep.join([os.getcwd(), 'Simulations', directory])
directory = directory + os.sep
if not os.path.exists(directory): os.makedirs(directory)
print('Adding simulation directory to simulation parameters...')
sim_parameters["directory"] = directory
print('Adding starting time to simulation parameters...')
sim_parameters["starting_time"] = time_start
sim_functions = sim_functions()
if sim_parameters["ragaraja_version"] == 0:
print('Activating ragaraja version: 0...')
ragaraja.activate_version(sim_parameters["ragaraja_version"],
sim_parameters["ragaraja_instructions"])
else:
print('Activating ragaraja version: ' + \
str(sim_parameters["ragaraja_version"]) + '...')
ragaraja.activate_version(sim_parameters["ragaraja_version"])
if "database_file" in sim_parameters and \
"database_logging_frequency" in sim_parameters:
print('Connecting to database file: ' + \
sim_parameters["database_file"] + '...')
(con, cur) = connect_database(None, sim_parameters)
print('Logging simulation parameters to database file...')
(con, cur) = db_log_simulation_parameters(con, cur, sim_parameters)
for pop_name in Populations:
print('\nPreparing population: ' + pop_name + ' for simulation...')
if 'sim_folder' in sim_parameters or \
'database_source' in sim_parameters:
print('Calculating final generation count...')
max = sim_parameters["rev_start"] \
[sim_parameters["population_names"].index(pop_name)] + \
sim_parameters["extend_gen"]
print('Updating generation count from previous simulation...')
generation_count = sim_parameters["rev_start"][0]
else:
print('Deploying population in World entity...')
if sim_parameters["deployment_code"] == 0:
print('Executing user defined deployment scheme...')
deploy_0(sim_parameters, Populations, pop_name, World)
elif sim_parameters["deployment_code"] == 1:
print('Executing deployment code 1: Single eco-cell deployment...')
deploy_1(sim_parameters, Populations, pop_name, World)
elif sim_parameters["deployment_code"] == 2:
print('Executing deployment code 2: Random eco-cell deployment...')
deploy_2(sim_parameters, Populations, pop_name, World)
elif sim_parameters["deployment_code"] == 3:
print('Executing deployment code 3: Even eco-cell deployment...')
deploy_3(sim_parameters, Populations, pop_name, World)
elif sim_parameters["deployment_code"] == 4:
print('Executing deployment code 4: Centralized eco-cell deployment...')
deploy_4(sim_parameters, Populations, pop_name, World)
print('Adding maximum generations to simulation parameters...')
max = sim_parameters["maximum_generations"]
generation_count = 0
print('Writing simulation parameters into txt file report...')
write_parameters(sim_parameters, pop_name)
print('Updating generation count...')
Populations[pop_name].generation = generation_count
print('\nSimulation preparation complete...')
while generation_count < max:
generation_count = generation_count + 1
sim_functions.ecoregulate(World)
eco_cell_iterator(World, sim_parameters,
sim_functions.update_ecology)
eco_cell_iterator(World, sim_parameters,
sim_functions.update_local)
eco_cell_iterator(World, sim_parameters, sim_functions.report)
bury_world(sim_parameters, World, generation_count)
for pop_name in Populations:
if sim_parameters["interpret_chromosome"]:
interpret_chromosome(sim_parameters, Populations,
pop_name, World)
report_generation(sim_parameters, Populations, pop_name,
sim_functions, generation_count)
sim_functions.organism_movement(Populations, pop_name, World)
sim_functions.organism_location(Populations, pop_name, World)
if "database_file" in sim_parameters and \
"database_logging_frequency" in sim_parameters and \
generation_count % \
int(sim_parameters["database_logging_frequency"]) == 0:
(con, cur) = db_report(con, cur, sim_functions,
sim_parameters["starting_time"],
Populations, World, generation_count)
print('Generation ' + str(generation_count) + ' complete...')
print('\nClosing simulation results...')
for pop_name in Populations: close_results(sim_parameters, pop_name)
if "database_file" in sim_parameters and \
"database_logging_frequency" in sim_parameters:
print('Committing logged data into database file...')
con.commit()
print('Terminating database connection...')
con.close()
print('Copying simulation file script to simulation results directory...')
#DV on my system, the inspect.stack()[2][1] value returns the full
# path to the file ('/home/douwe/scr/.../scriptname.py').
# The end result is an error for the original code, below, as the
# copyfile command is pointed to a wrong location: the directory
# is added twice. This might be Py3, or Windows functionality.
# With using the os.path module, this should give an OS-independent
# way of extracting the basename and linking to the directory.
sim_script_basename = os.path.basename(inspect.stack()[2][1])
copyfile(inspect.stack()[2][1],
#DV_original# sim_parameters['directory'] + inspect.stack()[2][1])
os.path.join(sim_parameters['directory'], sim_script_basename))
print('\nSimulation ended...')
