def plot_patch_clamp(experiment_key, picture_file='/tmp/voltage_trace_f-265_iclamp', picture_formats=['png']):
db = Database(
db_name='postgresql://hal08.g-node.pri/morphjongleur',
exec_role='morphjokey_admin',
exec_path='mitsubachi')
# must be mapped before Object is created
mapping = morphjongleur.orm.experiment.Mapper( db.engine )
mapping.orm_map()
e = db.load_experiment( experiment_key )
print e
print e.voltage_trace
e.voltage_trace.plot(picture_file=picture_file+str(e.morphology), picture_formats=picture_formats)
def generate(morphologies=[16,17,18,19]):
for m in morphologies:
# try:
db = Database(
db_name='postgresql://hal08.g-node.pri/morphjongleur',
exec_role='morphjokey_admin',
exec_path='mitsubachi')
# must be mapped before Object is created
#mapping = morphjongleur.orm.experiment.Mapper( db.engine )
mapping = morphjongleur.orm.morphology.Mapper( db.engine )
mapping.orm_map()
morphology = db.load_morphology( m )
print morphology
iclamp = morphjongleur.model.clamp.IClamp(morphology.biggest)
r = morphjongleur.model.experiment.RecordingPoint(morphology.compartments[len(morphology.compartments)-1])
experiment = morphjongleur.model.experiment.Experiment(
morphology,
clamps=[iclamp], recording_points=r,
neuron_passive_parameter=Neuron_passive_parameter(Ra=35.4,g=0.001)
)
db.store( experiment )
print experiment
experiment.run_simulation()
voltage_trace = experiment.get_voltage_trace()
db.store( voltage_trace )
print voltage_trace
