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))
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 = mrj.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 = 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()
vclamps=[vclamp], iclamps=[iclamp],
neuron_passive_parameter=neuron_passive_parameter,
duration=3./frequency,
dt=1e-4,
description = "SinusExperiment %s %i %f" % (morphology.name, compartment.compartment_id, frequency),
)
experiment.run_simulation()
voltage_trace = experiment.get_voltage_trace(delay=2./frequency)# nach Einschwinphase
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)
# -*- coding: utf-8 -*-
'''
@author: stransky
'''
from mrj.io.database import Database
from mp.model.experiment_mso import Experiment_MSO
from mp.model.neuron_mso import Neuron_MSO
import time
#from sqlalchemy.dialects.postgresql import ARRAY
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 mp.orm.experiment_mso
mapping = mp.orm.experiment_mso.Mapper( db.engine )
mapping.orm_map()
ms = [500, 501, 505, 506, 507, 512, 513, 514, 515, 516, 517, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532, 534, 535, 536, 537, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551] # range(500, 551+1) # range(392, 443+1) # [244] #
synapses = [10] # range(10, 51, 5)
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') #
# -*- coding: utf-8 -*-
"""
@author: stransky
"""
if __name__ == "__main__":
###DOES NOT WORK IN SAME CLASS
# test: 248 , smallest: 392, smallest w/ : 394 , biggest: 433, oldest: 434
from mrj.io.database import Database
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 mp.orm.experiment_mso
mapping = mp.orm.experiment_mso.Mapper(db.engine)
mapping.orm_map()
result = db.load_result_mso(13)
# result.experiment_mso.e=-70
# result.experiment_mso.e=0
result.plot() # picture_file='../../../doc/voltage_trace_r-0'
print result.experiment_mso # takes most of the time
# -*- 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)
@author: stransky
'''
import neuron
#import scipy
#from mrj.model.pydesignlib import MSO_Neuron, Simulation
from mrj.io.database import Database
from mrj.model.neuron_passive import *
from mrj.model.morphology import *
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
# -*- coding: utf-8 -*-
'''
@author: stransky
'''
from mrj.model.neuron_mso import Neuron_MSO
from mrj.model.experiment_mso import Experiment_MSO
if __name__ == "__main__":
###DOES NOT WORK IN SAME CLASS
#test: 248 , smallest: 392, smallest w/ : 394 , biggest: 433, oldest: 434, fastest: 424, slowest: 393
from mrj.io.database import Database
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')
