def run_environment_dynamics(TOTAL_TIME, task_index, task_defn_dict):
environment_creation_parameter_dict = make_parameter_dictionary(TOTAL_TIME, task_index, parameter_overrides=task_defn_dict)
an_environment = parameterorg.make_environment_given_user_cell_group_defns(**environment_creation_parameter_dict)
an_environment.execute_system_dynamics()
return an_environment.cells_in_environment[0]
def run_environment_dynamics(task_defn_dict):
an_environment = parameterorg.make_environment_given_user_cell_group_defns(
**task_defn_dict)
an_environment.execute_system_dynamics({},
produce_intermediate_visuals=False,
produce_final_visuals=False)
return an_environment.cells_in_environment[0]
def run_environment_dynamics(TOTAL_TIME, task_index, task_defn_dict,
invariant_parameter_overrides):
environment_creation_parameter_dict = make_parameter_dictionary(
TOTAL_TIME,
task_index,
parameter_overrides=task_defn_dict,
invariant_parameter_overrides=invariant_parameter_overrides)
an_environment = parameterorg.make_environment_given_user_cell_group_defns(
**environment_creation_parameter_dict)
an_environment.execute_system_dynamics(
{},
produce_intermediate_visuals=False,
produce_final_visuals=False,
elapsed_timesteps_before_producing_intermediate_visuals=0,
output_dir='')
return an_environment.cells_in_environment[0]
NUM_EXPERIMENT_REPEATS = 3
for x in xrange(NUM_EXPERIMENT_REPEATS):
environment_name = base_environment_name + '_NT={}_RPT={}'.format(
NUM_TIMESTEPS, x + 1)
corridor_height = 50e-6
corridor_length = 50e-6
space_physical_bdry_polygon = np.array([])
print "Creating environment..."
an_environment = parameterorg.make_environment_given_user_cell_group_defns(
environment_name,
NUM_TIMESTEPS,
user_cell_group_defns,
space_physical_bdry_polygon=space_physical_bdry_polygon,
parameter_overrides=candidate_po_set,
verbose=True,
environment_filepath=environment_dir)
print "Executing dynamics..."
an_environment.execute_system_dynamics_for_all_times()
a_cell = an_environment.cells_in_environment[0]
symmetry_output_labels, symmetry_output_values, symmetry_output_arrays = analysis.calculate_rgtpase_symmetries(
a_cell)
symmetry_results = dict(
zip(symmetry_output_labels, symmetry_output_values))
datavis.graph_important_cell_variables_over_time(