def run():
"""
:return:
"""
persistent_globals = CompuCellSetup.persistent_globals
simulation_initialized = persistent_globals.simulation_initialized
if not simulation_initialized:
initialize_cc3d()
check_for_cpp_errors(CompuCellSetup.persistent_globals.simulator)
persistent_globals.steppable_registry.core_init()
check_for_cpp_errors(CompuCellSetup.persistent_globals.simulator)
# initializing extra visualization fields
field_registry = persistent_globals.field_registry
potts = persistent_globals.simulator.getPotts()
cell_field = potts.getCellFieldG()
dim = cell_field.getDim()
field_registry.dim = dim
field_registry.simthread = persistent_globals.simthread
field_registry.create_fields()
simulator = CompuCellSetup.persistent_globals.simulator
simthread = CompuCellSetup.persistent_globals.simthread
steppable_registry = CompuCellSetup.persistent_globals.steppable_registry
main_loop_fcn = determine_main_loop_fcn()
main_loop_fcn(simulator,
simthread=simthread,
steppable_registry=steppable_registry)
def initialize_cc3d():
"""
:return:
"""
CompuCellSetup.persistent_globals.simulator, \
CompuCellSetup.persistent_globals.simthread = get_core_simulation_objects()
check_for_cpp_errors(CompuCellSetup.persistent_globals.simulator)
simulator = CompuCellSetup.persistent_globals.simulator
# CompuCellSetup.persistent_globals.steppable_registry.simulator = simulator
CompuCellSetup.persistent_globals.steppable_registry.simulator = weakref.ref(
simulator)
CompuCellSetup.persistent_globals.simulation_initialized = True
def main_loop_player(sim, simthread=None, steppable_registry=None):
"""
main loop for GUI based simulations
:param sim:
:param simthread:
:param steppable_registry:
:return:
"""
t1 = time.time()
compiled_code_run_time = 0.0
pg = CompuCellSetup.persistent_globals
steppable_registry = pg.steppable_registry
simthread = pg.simthread
pg.restart_manager = RestartManager.RestartManager(sim)
restart_manager = pg.restart_manager
restart_manager.output_frequency = pg.restart_snapshot_frequency
restart_manager.allow_multiple_restart_directories = pg.restart_multiple_snapshots
init_using_restart_snapshot_enabled = restart_manager.restart_enabled()
# init_using_restart_snapshot_enabled = False
sim.setRestartEnabled(init_using_restart_snapshot_enabled)
check_nanohub_and_count()
if init_using_restart_snapshot_enabled:
print('WILL RESTART SIMULATION')
restart_manager.loadRestartFiles()
check_for_cpp_errors(CompuCellSetup.persistent_globals.simulator)
else:
print('WILL RUN SIMULATION FROM BEGINNING')
extra_init_simulation_objects(
sim,
simthread,
init_using_restart_snapshot_enabled=init_using_restart_snapshot_enabled
)
check_for_cpp_errors(CompuCellSetup.persistent_globals.simulator)
# simthread.waitForInitCompletion()
# simthread.waitForPlayerTaskToFinish()
if not steppable_registry is None:
steppable_registry.init(sim)
# called in extraInitSimulationObjects
# sim.start()
if not steppable_registry is None and not init_using_restart_snapshot_enabled:
steppable_registry.start()
simthread.steppablePostStartPrep()
run_finish_flag = True
restart_manager.prepare_restarter()
beginning_step = restart_manager.get_restart_step()
if init_using_restart_snapshot_enabled:
steppable_registry.restart_steering_panel()
cur_step = beginning_step
# initial drawing - we use mcs = -2 as a sentinel for mcs right after start function of steppables is completed
simthread.loopWork(-2)
simthread.loopWorkPostEvent(-2)
while cur_step < sim.getNumSteps():
simthread.beforeStep(_mcs=cur_step)
if simthread.getStopSimulation(
) or CompuCellSetup.persistent_globals.user_stop_simulation_flag:
run_finish_flag = False
break
if steppable_registry is not None:
steppable_registry.stepRunBeforeMCSSteppables(cur_step)
compiled_code_begin = time.time()
sim.step(cur_step) # steering using steppables
check_for_cpp_errors(CompuCellSetup.persistent_globals.simulator)
compiled_code_end = time.time()
compiled_code_run_time += (compiled_code_end -
compiled_code_begin) * 1000
# steering using GUI. GUI steering overrides steering done in the steppables
simthread.steerUsingGUI(sim)
if not steppable_registry is None:
steppable_registry.step(cur_step)
# restart manager will decide whether to output files or not based on its settings
restart_manager.output_restart_files(cur_step)
# passing Python-script-made changes in XML to C++ code
incorporate_script_steering_changes(simulator=sim)
# steer application will only update modules that uses requested using updateCC3DModule function from simulator
sim.steer()
check_for_cpp_errors(CompuCellSetup.persistent_globals.simulator)
screen_update_frequency = simthread.getScreenUpdateFrequency()
screenshot_frequency = simthread.getScreenshotFrequency()
screenshot_output_flag = simthread.getImageOutputFlag()
if pg.screenshot_manager is not None and pg.screenshot_manager.has_ad_hoc_screenshots(
):
simthread.loopWork(cur_step)
simthread.loopWorkPostEvent(cur_step)
elif (screen_update_frequency > 0
and cur_step % screen_update_frequency
== 0) or (screenshot_output_flag and screenshot_frequency > 0
and cur_step % screenshot_frequency == 0):
simthread.loopWork(cur_step)
simthread.loopWorkPostEvent(cur_step)
cur_step += 1
if run_finish_flag:
# # we emit request to finish simulation
simthread.emitFinishRequest()
# # then we wait for GUI thread to unlock the finishMutex - it will only happen when all tasks
# in the GUI thread are completed (especially those that need simulator object to stay alive)
print("CALLING FINISH")
simthread.waitForFinishingTasksToConclude()
simthread.waitForPlayerTaskToFinish()
steppable_registry.finish()
sim.cleanAfterSimulation()
simthread.simulationFinishedPostEvent(True)
steppable_registry.clean_after_simulation()
else:
steppable_registry.on_stop()
sim.cleanAfterSimulation()
# # sim.unloadModules()
print("CALLING UNLOAD MODULES NEW PLAYER")
if simthread is not None:
simthread.sendStopSimulationRequest()
simthread.simulationFinishedPostEvent(True)
steppable_registry.clean_after_simulation()
t2 = time.time()
print_profiling_report(
py_steppable_profiler_report=steppable_registry.get_profiler_report(),
compiled_code_run_time=compiled_code_run_time,
total_run_time=(t2 - t1) * 1000.0)
def main_loop(sim, simthread, steppable_registry=None):
"""
main loop for CML simulation
:param sim:
:param simthread:
:param steppable_registry:
:return:
"""
t1 = time.time()
compiled_code_run_time = 0.0
pg = CompuCellSetup.persistent_globals
steppable_registry = pg.steppable_registry
pg.restart_manager = RestartManager.RestartManager(sim)
restart_manager = pg.restart_manager
restart_manager.output_frequency = pg.restart_snapshot_frequency
restart_manager.allow_multiple_restart_directories = pg.restart_multiple_snapshots
init_using_restart_snapshot_enabled = restart_manager.restart_enabled()
# init_using_restart_snapshot_enabled = False
sim.setRestartEnabled(init_using_restart_snapshot_enabled)
check_for_cpp_errors(CompuCellSetup.persistent_globals.simulator)
check_nanohub_and_count()
if init_using_restart_snapshot_enabled:
print('WILL RESTART SIMULATION')
restart_manager.loadRestartFiles()
check_for_cpp_errors(CompuCellSetup.persistent_globals.simulator)
else:
print('WILL RUN SIMULATION FROM BEGINNING')
extra_init_simulation_objects(
sim,
simthread,
init_using_restart_snapshot_enabled=init_using_restart_snapshot_enabled
)
check_for_cpp_errors(CompuCellSetup.persistent_globals.simulator)
if steppable_registry is not None:
steppable_registry.init(sim)
init_lattice_snapshot_objects()
init_screenshot_manager()
if steppable_registry is not None and not init_using_restart_snapshot_enabled:
steppable_registry.start()
run_finish_flag = True
restart_manager.prepare_restarter()
beginning_step = restart_manager.get_restart_step()
cur_step = beginning_step
while cur_step < sim.getNumSteps():
if CompuCellSetup.persistent_globals.user_stop_simulation_flag:
run_finish_flag = False
break
if steppable_registry is not None:
steppable_registry.stepRunBeforeMCSSteppables(cur_step)
compiled_code_begin = time.time()
sim.step(cur_step) # steering using steppables
check_for_cpp_errors(CompuCellSetup.persistent_globals.simulator)
compiled_code_end = time.time()
compiled_code_run_time += (compiled_code_end -
compiled_code_begin) * 1000
if steppable_registry is not None:
steppable_registry.step(cur_step)
# restart manager will decide whether to output files or not based on its settings
restart_manager.output_restart_files(cur_step)
store_lattice_snapshot(cur_step=cur_step)
store_screenshots(cur_step=cur_step)
# passing Python-script-made changes in XML to C++ code
incorporate_script_steering_changes(simulator=sim)
# steer application will only update modules that uses requested using updateCC3DModule function from simulator
sim.steer()
check_for_cpp_errors(CompuCellSetup.persistent_globals.simulator)
cur_step += 1
if run_finish_flag:
print("CALLING FINISH")
steppable_registry.finish()
else:
steppable_registry.on_stop()
t2 = time.time()
print_profiling_report(
py_steppable_profiler_report=steppable_registry.get_profiler_report(),
compiled_code_run_time=compiled_code_run_time,
total_run_time=(t2 - t1) * 1000.0)