def prepare_simulation(prep_workspace=True):
""" Do the whole process of preparing a simulation """
# Prepare the necessary variables from the configuration files
if prep_workspace:
prepare_workspace()
# Shortenings
stimmethod = ws.settings["stimulation"]["method"]
nervemodel = ws.settings["nerve model"]
# Create the NERVE TOPOLOGY. Cross-section only
anatomy.create_nerve()
# BIOPHYSICS
# LOAD NEURON HOC CODE AND DEFINE FUNCTIONS
# Load NEURON code
h.load_file(os.path.join(ws.folders["src/hoc"], "ephap.hoc"))
h.load_file(os.path.join(ws.folders["src/hoc"], "wire.hoc"))
for m in ws.axonmodel_settings.values():
h.load_file(m['hoc file'])
# BUILD ALL THE WIRES with all their length
bio.build_cables()
# Finish setting up information for the fascicles
if nervemodel == "resistor network":
bio.finish_fascicles()
# Create electrodes
# This needs to be after the creation of the cables and before
# connecting the ephapses
if stimmethod == "from electrodes":
ws.log("Creating the electrodes")
electrodes.create_electrodes()
# elif stimmethod == "pre-computed":
# pass
# EPHAPSES
if ws.EC["presence"]:
if nervemodel == "resistor network":
# Create an instance of the Resistor Network
ws.log("Creating the Resistor Network")
ws.rnet = bio.ResistorNetwork()
# Get the resistances of the connections for each pair
ws.log("\tGetting resistor values")
ws.rnet.get_resistances()
# Connect resistors with ephapses in NEURON
ws.log("\tConnecting resistors")
ws.rnet.connect_resistors()
# OTHER CONNECTIONS
ws.log("Preparing connections to ground on the boundaries and xraxial")
# Prepare connections to ground in the system
if stimmethod == "from electrodes":
electrodes.prepare_ground_paths()
# Set xraxial and make the connections to ground
if nervemodel == "resistor network":
bio.electrics()
# STIMULATION
ws.log("Setting up stimulation")
# Inject currents from the cuff electrode
# Add injected currents, delays and durations
if stimmethod == "from electrodes":
# if nervemodel == "resistor network":
electrodes.set_stimulation()
elif stimmethod == "pre-computed":
bio.set_direct_extracellular_stimulation()
# RECORDINGS
ws.log("Setting up recordings")
# Time
als.set_time_recording()
# From electrodes
# Flag: presence of electrode recordings
# Set it to False by default; it will become True if a recording
# electrode is created
ws.settings["electrode recordings"] = False
if stimmethod == "from electrodes":
if nervemodel == "resistor network":
electrodes.set_recordings()
# Directly on the cables/axons
als.record_cables()
save=True,
xyzunits=r'$\rm \mu m$',
vunits='mV',
cmap=plt.cm.jet,
show_intp_points=False,
logscale=True,
zorder=zorder,
)
zorder += 1
# Include the contours
# Prepare the necessary stuff for the simulation
import simcontrol
# simcontrol.prepare_simulation()
simcontrol.prepare_workspace(remove_previous=False)
anatomy.create_nerve()
# Draw contours
if False:
ws.nvt.draw_axons_and_points(ax,
facecolor='none',
edgecolor='k',
zorder=zorder)
if False:
ws.nvt.draw_triangulation(
ax,
c='white',
lw=0.5,
alpha=0.4,
zorder=zorder,
)
zorder += 1