"""
import numpy
import mozaik
from mozaik.core import BaseComponent
from mozaik import load_component
from mozaik.tools.distribution_parametrization import PyNNDistribution
from parameters import ParameterSet, UniformDist
from pyNN import space
from pyNN.errors import NothingToWriteError
from string import Template
from neo.core.spiketrain import SpikeTrain
import quantities as pq
logger = mozaik.getMozaikLogger()
class Sheet(BaseComponent):
"""
Sheet is an abstraction of a 2D continuouse sheet of neurons, roughly
corresponding to the PyNN Population class with the added spatial structure.
The spatial position of all cells is kept within the PyNN Population object.
Each sheet is assumed to be centered around (0,0) origin, corresponding to
whatever excentricity the model is looking at. The internal representation
of space is degrees of visual field. Thus x,y coordinates of a cell in all
sheets correspond to the degrees of visual field this cell is away from the
origin. However, the sheet and derived classes/methods are supposed to
accept parameters in units that are most natural for the given parameter and
recalculate these into the internal degrees of visual field representation.
"""
This module contains wrapper for the neo Segment, that add extra functionality to the class.
Within mozaik the data are stored and passed in this format.
Most of the included functionality should in future be provided directly by neo.
When this happens most of this code should become irrelevant and the rest should be
merged into the :mod:`.datastore` module.
"""
from neo.core.segment import Segment
import numpy
import cPickle
import quantities as qt
import mozaik
logger = mozaik.getMozaikLogger()
class MozaikSegment(Segment):
"""
This class extends Neo segment with several convenience functions.
The most important function is that it allows lazy loading of the data.
It should be moved to datastore.py once the NeoNeurotoolsWrapper is
obsolete and this file should be discarded.
"""
def __init__(self, segment, identifier,null=False):
"""
"""
self.init = True
Segment.__init__(self, name=segment.name,
import matplotlib
import time
import pylab
from mozaik.experiment import *
from pyNN import nest as sim
from model import VogelsAbbott
from mozaik.controller import run_experiments, setup_experiments, setup_logging
from mozaik.framework.population_selector import RCRandomPercentage
from mozaik.visualization.plotting import *
from mozaik.analysis.technical import NeuronAnnotationsToPerNeuronValues
from mozaik.storage.datastore import Hdf5DataStore,PickledDataStore
from NeuroTools.parameters import ParameterSet
from mozaik.storage.queries import *
import mozaik
logger = mozaik.getMozaikLogger("Mozaik")
if True:
params = setup_experiments('FFI',sim)
jens_model = VogelsAbbott(sim,params)
l4exc_kick = RCRandomPercentage(jens_model.sheets["V1_Exc_L4"],ParameterSet({'percentage': 20.0}))
l4inh_kick = RCRandomPercentage(jens_model.sheets["V1_Inh_L4"],ParameterSet({'percentage': 20.0}))
experiment_list = [
#Lets kick the network up into activation
PoissonNetworkKick(jens_model,duration=70*7,sheet_list=["V1_Exc_L4","V1_Inh_L4"],recording_configuration_list=[l4exc_kick,l4inh_kick],lambda_list=[100,100]),
#Spontaneous Activity
NoStimulation(jens_model,duration=70*7),
]
data_store = run_experiments(jens_model,experiment_list)
#jens_model.connectors['V1L4ExcL4ExcConnection'].store_connections(data_store)
