Пример #1
0
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))
Пример #2
0
# -*- 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()
Пример #3
0
# -*- coding: utf-8 -*-
'''
@author: stransky
'''

from mrj.io.swc import SwcParser
from mp.model.synapse import Synapse
from mp.model.synapse import getSynapticActivity
from mrj.model.experiment import IClamp
from mrj.model.experiment import Experiment
from mrj.model.experiment import Neuron_passive_parameter
from mrj.model.experiment import plot

swc_parser  = SwcParser()
m_swc   = swc_parser.parse("../../../Data/test.swc") #slow swc_parser.parse("../../Data/MSO_Neurone/P09/ohne_axon_SkeletonTree_0015_2-1G.swc")
m_swc.neuron_create() # initialisiert die Synapse in NEURON
compartment = m_swc.compartments[5]

s = Synapse(compartment, 0.5, syntimes=getSynapticActivity(f=200, duration=5, sigma=0, fireing_rate=1, delay=0))#TODO: ??delta_time > 5
s.neuron_create()

clamp = IClamp(compartment=compartment, position=0.5, delay=1,amplitude=0,duration=3)#VClamp
neuron_passive_parameter = \
    Neuron_passive_parameter(Ra=1, g=0.004, e=-60, nseg=10)

f = Experiment(m_swc, clamp, neuron_passive_parameter, 
               description='passive channels')

f.neuron_create()
r_in, tau_eff = f.run_simulation(duration=20,dt=0.001)
tau_eff_fit     = f.tau_fit()