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
# -*- 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()
rs = [1,0.93,0.64,0.32,0] # [1,0]
fs = [500] # 500 Hz [1/s]
duration = 10e-3 # 50-100 ms
iterations = 10 # 10
gns = ['both', 'medial', 'lateral']
description = 'exitatory'
resumepoint = None # (0,424,1,10,500,'both') #
start_time = time.time()
#from neuron import gui
#print "morphology type r -> sigma synapsen minU[mV] at[ms] calc_time[s]"
print "resumepoint(iteration, morphology_key, r, #synapses, frequency, group_name)\tinit time + exp time + store time = run time [s]\tResult"
for m in ms:
for i in range(iterations):
if resumepoint == None:
morphology = db.load_morphology( m )
for r in rs:
for n in synapses:
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 )
# -*- coding: utf-8 -*-
from mrj.io.database import Database
from mrj.model.neuromorph import Morph
db = Database(
db_name='postgresql://hal08.g-node.pri/lehmann',
exec_role='morphjokey_admin',
exec_path='morphjokey')
# must be mapped before Object is created
import mrj.orm.morphology
mapping = mrj.orm.morphology.Mapper( db.engine )
mapping.orm_map()
m_db = db.load_morphology( 460 )
m = Morph(m_db)
print(m.get_surface_volume_ratio())
print(m.db_model.analysis['surface_volume_ratio'])
print(m.db_model.analysis)
print m
m.show_tree()
# -*- coding: utf-8 -*-
from mrj.io.database import Database
from mrj.model.morphology import *
import os
db = Database(
db_name='postgresql://hal08.g-node.pri/lehmann',
exec_role='morphjokey_admin',
exec_path='morphjokey')
m = db.load_morphology( 291 )
print( m )
print( m.compartments[2] )
mg = Morphology_groups()
mg.name = 'groupname'
mg.age = '23'
mg.description = 'cool'
m._groups.append( mg )
m.description += ' owner:'+str( os.environ['USER'] ) # use your name!
cg = Compartment_groups()
cg.name = 'primes'
cg.description = 'cool'
cg.type = 'axon'
print( m ) # key not available
print( m.compartments[2] )
#append OR store sufficient to get key
m.compartments[2]._groups.append(cg)
from mrj.model.clamp import *
from mrj.model.experiment import *
from mrj.model.experiment import plot
import mrj.orm.experiment
from neuron import gui; # For an overview (gui menu bar): Tools -> Model View -> 1 real cell -> root...
db = Database(
db_name='postgresql://hal08.g-node.pri/lehmann',
exec_role='morphjokey_admin',
exec_path='morphjokey')
# must be mapped before Object is created
mapping = mrj.orm.experiment.Mapper( db.engine )
mapping.orm_map()
morphology = db.load_morphology( 256 )
print morphology
#morphology.create_tree()
clamp = IClamp(morphology.root.children[0])
neuron_passive_parameter = Neuron_passive_parameter(Ra=80)
experiment = Experiment(morphology, clamp, neuron_passive_parameter)
print experiment
db.store( experiment )
#TODO: change compartments needs group group mapping
#c = m.getCompartment( 5 )
#c = m.getCompartment( 7 )
experiment.neuron_create()
import time
db = Database(
db_name='postgresql://hal08.g-node.pri/lehmann',
exec_role='morphjokey_admin',
exec_path='morphjokey'
)
# must be mapped before Object is created
import mrj.orm.experiment_mso
mapping = mrj.orm.experiment_mso.Mapper( db.engine )
mapping.orm_map()
# mapping.create_tables()
m = db.load_morphology( 424 )
#from mrj.io.swc import SwcParser
#swc_parser = SwcParser()
#m = swc_parser.parse('../../../Data/test.swc')
n = Neuron_MSO(m)#, exitatoric_medial_dendrits=[4], exitatoric_lateral_dendrits=[8]
s = Experiment_MSO(n, f=200, r=1.00, n=None, duration=10e-3, delay=1e-3, group_name=None, description='test')#, group_name='medial'
s.neuron_create()
#db.store( s )
#print s
start_time = time.time()
s.run_simulation()
end_time = time.time()
result = s.get_result()#Result(t=[0.001,0.002,0.003,0.004],v=[-60.0,-60.0,-60.0,-66.0],t_min=0.03,v_min=-66,experiment=experiment)#
