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 = mrj.orm.experiment.Mapper( db.engine )
mapping = mrj.orm.morphology.Mapper( db.engine )
mapping.orm_map()
morphology = db.load_morphology( m )
print morphology
iclamp = mrj.model.clamp.IClamp(morphology.biggest)
r = mrj.model.experiment.RecordingPoint(morphology.compartments[len(morphology.compartments)-1])
experiment = mrj.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
def import_swc(swcs):
db = Database(db_name="postgresql://hal08.g-node.pri/lehmann", exec_role="morphjokey_admin", exec_path="morphjokey")
swc_parser = SwcParser()
for swc in swcs:
print(swc)
m_swc = swc_parser.parse(swc)
db.store(m_swc)
print("start to commit data according to '%s'." % (swc))
tic = time.time()
db.session.commit()
toc = time.time()
print("Done. It took %s seconds." % (toc - tic))
# -*- coding: utf-8 -*-
from mrj.io.swc import SwcParser
from mrj.io.database import Database
db = Database(
db_name='postgresql://hal08.g-node.pri/lehmann',
exec_role='morphjokey_admin',
exec_path='morphjokey')
swc_parser = SwcParser(db)
m = swc_parser.parse('../../../Data/example_morph.swc')
#print( m )
#print( m._compartments[0])
db.store( m )
#db.create_subtree( m )
# morphology_key mapped via sqlalchemy:
print m.morphology_key
m = db.load_morphology( m.morphology_key )
print( m ) # contains ALL auto calculated data from database
#print( m._compartments[0])
#print "\n\n\ncompartments as dicts:"
#for c in m._compartments:
# print c.info.__dict__
#a = db.session.execute("SELECT compartment_id,compartment_parent_id,children FROM morphjokey.mrj_v_compartments_children WHERE morphology_key = 150;")
#b = a.fetchall()
return mrj.model.sinusresult.SinusResult(voltage_trace, compartment, frequency, amplitude)
if __name__ == '__main__':
import mrj.io.swc
from mrj.io.database import Database
db = Database(
db_name='postgresql://hal08.g-node.pri/morphjongleur',
exec_role='morphjokey_admin',
exec_path='mitsubachi'
)
# must be mapped before Object is created
import mrj.orm.sinusresult
import mrj.model.morphology
mapping = mrj.orm.sinusresult.Mapper( db )
mapping.orm_map()
for swc in ['../../../data/H060602DB_10_2_zentai_.swc','../../../data/H060602VB_10_2_zentai_.swc','../../../data/H060607DB_10_2(zentai).swc','../../../data/H060607VB_10_2(zentai).swc']:#['../../../data/test.swc']:
print swc
morphology = mrj.model.morphology.swc_parse(swc)
cs = []#morphology.biggest
cs.extend( morphology.terminal_tips )
for f in range(10,1001,15):
print "%i Hz" % (f)
i = 0
for c in cs:
i = i + 1
print "%i/%i\t\r" % (cs.index(c)+1, len(cs)),
sinusresult = experiment(morphology=morphology, compartment=c, frequency=f, amplitude=-1e-9)
#sinusresult.save()
db.store(sinusresult)
for f in fs:
for gn in gns:
run_start = start_time
print "(%i,%i,%f,%i,%f,%s)\t" % (i,m,r,n,f,gn) ,
if resumepoint != None:
if resumepoint == (i,m,r,n,f,gn):
morphology = db.load_morphology( m )
resumepoint = None
else:
print "skipped"
continue
mso_neuron = Neuron_MSO( morphology )
experiment = Experiment_MSO(mso_neuron, f=f, r=r, n=n, group_name=gn, duration=duration, description=description)
#print experiment
db.store( experiment )
experiment.neuron_create()
end_time = time.time()
print "%f" %(end_time-start_time) ,
start_time = end_time
experiment.run_simulation()
end_time = time.time()
experiment.calc_time = end_time-start_time
print "+ %f" %(experiment.calc_time) ,
start_time = end_time
result = experiment.get_result()
#print result
