# with the following commands at the prompt in the OpenCOR Python console: # # In [1]: cd path/to/folder_this_file_is_in # In [2]: run Fig1_sim.py import opencor as oc import matplotlib.pyplot as plt import numpy as np # The prefix of the saved output file name V_var = 1; V_clmp = 1; if V_var: prefilename = 'Fig3' # Load the simulation file simfile = 'Tong_2011.sedml' simulation = oc.open_simulation(simfile) data = simulation.data() # Reset states variables and parameters # simulation.reset(True) # Set constant values start = 0 end = 10000 pointInterval = 0.1 data.set_starting_point(start) data.set_ending_point(end) data.set_point_interval(pointInterval) # simulation.reset(True) data.constants()['interface/membrane_potential/v_init'] = -80 data.constants() ['interface/parameters/kmca'] = 0.001 simulation.run() # Access simulation results results = simulation.results() # Data to save varName = np.array(["Time", "bss", "gss", "btc", "gtc", "icat", "v"]) vars = np.reshape(varName, (1,7)) rows = end * 10 + 1 print(rows) # Access simulation results results = simulation.results() # Grab a some algebraic variable results r = np.zeros((rows, len(varName))) r [ :, 0 ] = results.voi().values() r [ :, 1 ] = results.algebraic()['interface/I_CaT/bss'].values() r [ :, 2 ] = results.algebraic()['interface/I_CaT/gss'].values() r [ :, 3 ] = results.algebraic() [ 'interface/I_CaT/btc' ].values() r [ :, 4 ] = results.algebraic() [ 'interface/I_CaT/gtc' ].values() r [ :, 5 ] = results.algebraic() [ 'interface/I_CaT/icat' ].values() r [ :, 6 ] = results.states() [ 'interface/membrane_potential/v' ].values() filename = '%s.csv' % (prefilename) np.savetxt(filename, vars, fmt='%s', delimiter=",") with open(filename, "ab") as f: np.savetxt(f, r, delimiter=",") f.close elif V_clmp: prefilename = 'Fig3_4' # Load the simulation file simfile = 'VoltageVAR_Tong_2011.sedml' simulation = oc.open_simulation(simfile) data = simulation.data() simulation.reset(True) # Reset states variables and parameters #simulation.reset(True) # Set constant values start = 0 end = 100 pointInterval = 0.001 data.set_starting_point(start) data.set_ending_point(end) data.set_point_interval(pointInterval) time_clamp = 13 # v_clamp = [-65,-55.-45,-35,-25,-15,-5,-15,25] # v_clamp =[50, 40, 30, 25, 20, 10, 0,-10,-20,-30,-40,-50,-60, -70,-80] v_clamp = [-60, -50, -40, -30, -20, -10, 0, 10, 20] for i in range(len(v_clamp)): data.constants()['interface/membrane_potential/v_hold'] = -80 data.constants() [ 'interface/parameters/kmca' ] = 0.001 simulation.reset(True) data.constants() [ 'interface/membrane_potential/v_clamp' ] = v_clamp[i] data.constants() [ 'interface/membrane_potential/time_clamp' ] = time_clamp data.constants() [ 'interface/parameters/ecat' ] = 25 simulation.run() # Access simulation results results = simulation.results() # Data to save varName = np.array([ "Time", "icat", "v" ]) vars = np.reshape(varName, (1, 3)) rows = end * 1000 + 1 # Grab a some algebraic variable results r = np.zeros((rows, len(varName))) r [ :, 0 ] = results.voi().values() r [ :, 1 ] = results.algebraic() [ 'interface/I_CaT/icat' ].values() r [ :, 2 ] = results.algebraic() [ 'interface/membrane_potential/v' ].values() # r [ :, 7 ] = results.algebric() ['membrane_potential/v' ].values() # Save the simulation result of the last run filename = '%s_%s.csv' % (prefilename, i) np.savetxt(filename, vars, fmt='%s', delimiter=",") with open(filename, "ab") as f: np.savetxt(f, r, delimiter=",") f.close else: prefilename = 'Fig3_5' # Load the simulation file simfile = 'VoltageVAR_Tong_2011.sedml' simulation = oc.open_simulation(simfile) data = simulation.data() # Reset states variables and parameters simulation.reset(True) # Set constant values start = 0 end = 100 pointInterval = 0.001 data.set_starting_point(start) data.set_ending_point(end) data.set_point_interval(pointInterval) time_clamp = 13 v_clamp = [ 50, 40, 30, 25, 20, 10, 0, -10, -20, -30, -40, -50, -60, -70, -80 ] # v_clamp =[50, 40, 30, 20, 10, 0,-10,-20,-30,-40,-50] for i in range(len(v_clamp)): data.constants() [ 'interface/membrane_potential/v_hold' ] = -80 simulation.reset(True) data.constants() [ 'interface/parameters/kmca' ] = 0.001 data.constants() [ 'interface/membrane_potential/v_clamp' ] = v_clamp [ i ] data.constants() [ 'interface/membrane_potential/time_clamp' ] = time_clamp data.constants() [ 'interface/parameters/ecat' ] = 25 simulation.run() # Access simulation results results = simulation.results() # Data to save # Data to save varName = np.array([ "Time", "icat", "v" ]) vars = np.reshape(varName, (1, 3)) rows = end * 1000 + 1 # Grab a some algebraic variable results r = np.zeros((rows, len(varName))) r [ :, 0 ] = results.voi().values() r [ :, 1 ] = results.algebraic() [ 'interface/I_CaT/icat' ].values() r [ :, 2 ] = results.algebraic() [ 'interface/membrane_potential/v' ].values() # r [ :, 7 ] = results.algebric() ['membrane_potential/v' ].values() # Save the simulation result of the last run filename = '%s_%s.csv' % (prefilename, i) np.savetxt(filename, vars, fmt='%s', delimiter=",") with open(filename, "ab") as f: np.savetxt(f, r, delimiter=",") f.close # # # The prefix of the saved output file name # prefilename = 'Fig3_3' # # Load the simulation file # # simfile = 'Tong_2011.sedml' # simulation = oc.open_simulation(simfile) # data = simulation.data() # # # Reset states variables and parameters # simulation.reset(True) # # Set constant values # start = 0 # end = 100 # pointInterval = 0.001 # data.set_starting_point(start) # data.set_ending_point(end) # data.set_point_interval(pointInterval) # # # # # The prefix of the saved output file name # # prefilename = 'Fig2_3' # # # Load the simulation file # # # # v_clamp =[-60, -50, -40, -30, -20, -10, 0, 10, 20, 25] # # v_clamp = [-60]