def makeChemProto(name='hydra'):
chem = moose.Neutral('/library/' + name)
compt = moose.CubeMesh('/library/' + name + '/' + name)
A = moose.Pool(compt.path + '/A')
B = moose.Pool(compt.path + '/B')
C = moose.Pool(compt.path + '/C')
D = moose.Pool(compt.path + '/D')
E = moose.Pool(compt.path + '/E')
F = moose.Pool(compt.path + '/F')
Z1 = moose.Pool(compt.path + '/Z1')
Z2 = moose.Pool(compt.path + '/Z2')
#A.diffConst=params['diffA']
#B.diffConst=params['diffB']
Adot = moose.Function(A.path + '/Adot')
Bdot = moose.Function(B.path + '/Bdot')
Cdot = moose.Function(C.path + '/Cdot')
Ddot = moose.Function(D.path + '/Ddot')
Edot = moose.Function(E.path + '/Edot')
Fdot = moose.Function(F.path + '/Fdot')
#Zdot = moose.Function( Z.path + '/Zdot' )
#Adot.expr="x6*(1+x7)*(-x0+(5/(1+x1^3))*(2-x0-x3))"
#Bdot.expr="x6*(1+x7)*(0*x0-x1+(3+2*(x2^3/(1+x1^3)))*(1/(1+x0^3))*(2-x1-x4))"
#Cdot.expr="x6*(1+x7)*(0*x0+0*x1-0*x2+0.1*((0.2+0.3*(x0^3/(0.85^3+x0^3)))-x2^2*(0.2+1*x1^3/(0.85^3+x1^3))))"
Adot.expr = "x6*(1+x7)*(-x0+(4.5/(1+x1^3))*(2-x0-x3))"
Bdot.expr = "x6*(1+x7)*(0*x0-x1+(3+0.5*(x2^3/(1+x2^3)))*(1/(1+x0^3))*(2-x1-x4))"
Cdot.expr = "x6*(1+x7)*(0*x0+0*x1-0*x2+0.5*((0.2+0.3*(x0^3/(0.85^3+x0^3)))-x2^2*(0.2+1*x1^3/(0.85^3+x1^3))))"
#Ddot.expr="(1+x6)*x7*(0*x0+0*x1+0*x2-x3+(5/(1+x4^3))*(2-x0-x3))"
#Edot.expr="(1+x6)*x7*(0*x0+0*x1+0*x2+0*x3-x4+(3+2*(x5^3/(1+x4^3)))*(1/(1+x3^3))*(2-x1-x4))"
#Fdot.expr="(1+x6)*x7*(0*x0+0*x1+0*x2+0*x3+0*x4-0*x5+0.1*((0.2+0.3*(x3^3/(0.85^3+x3^3)))-x5^2*(0.2+1*x4^3/(0.85^3+x4^3))))"
Ddot.expr = "(1+x6)*x7*(0*x0+0*x1+0*x2-x3+(4.5/(1+x4^3))*(2-x0-x3))"
Edot.expr = "(1+x6)*x7*(0*x0+0*x1+0*x2+0*x3-x4+(3+0.5*(x5^3/(1+x5^3)))*(1/(1+x3^3))*(2-x1-x4))"
Fdot.expr = "(1+x6)*x7*(0*x0+0*x1+0*x2+0*x3+0*x4-0*x5+0.5*((0.2+0.3*(x3^3/(0.85^3+x3^3)))-x5^2*(0.2+1*x4^3/(0.85^3+x4^3))))"
print moose.showmsg(Adot)
Adot.x.num = 8 #2
Bdot.x.num = 8 #2
Cdot.x.num = 8 #2
Ddot.x.num = 8 #2
Edot.x.num = 8 #2
Fdot.x.num = 8 #2
#A.nInit=10
#B.nInit=5
moose.connect(A, 'nOut', Adot.x[0], 'input')
moose.connect(B, 'nOut', Adot.x[1], 'input')
moose.connect(C, 'nOut', Adot.x[2], 'input')
moose.connect(D, 'nOut', Adot.x[3], 'input')
moose.connect(E, 'nOut', Adot.x[4], 'input')
moose.connect(F, 'nOut', Adot.x[5], 'input')
moose.connect(Z1, 'nOut', Adot.x[6], 'input')
moose.connect(Z2, 'nOut', Adot.x[7], 'input')
moose.connect(Adot, 'valueOut', A, 'increment')
moose.connect(A, 'nOut', Bdot.x[0], 'input')
moose.connect(B, 'nOut', Bdot.x[1], 'input')
moose.connect(C, 'nOut', Bdot.x[2], 'input')
moose.connect(D, 'nOut', Bdot.x[3], 'input')
moose.connect(E, 'nOut', Bdot.x[4], 'input')
moose.connect(F, 'nOut', Bdot.x[5], 'input')
moose.connect(Z1, 'nOut', Bdot.x[6], 'input')
moose.connect(Z2, 'nOut', Bdot.x[7], 'input')
moose.connect(Bdot, 'valueOut', B, 'increment')
moose.connect(A, 'nOut', Cdot.x[0], 'input')
moose.connect(B, 'nOut', Cdot.x[1], 'input')
moose.connect(C, 'nOut', Cdot.x[2], 'input')
moose.connect(D, 'nOut', Cdot.x[3], 'input')
moose.connect(E, 'nOut', Cdot.x[4], 'input')
moose.connect(F, 'nOut', Cdot.x[5], 'input')
moose.connect(Z1, 'nOut', Cdot.x[6], 'input')
moose.connect(Z2, 'nOut', Cdot.x[7], 'input')
moose.connect(Cdot, 'valueOut', C, 'increment')
moose.connect(A, 'nOut', Ddot.x[0], 'input')
moose.connect(B, 'nOut', Ddot.x[1], 'input')
moose.connect(C, 'nOut', Ddot.x[2], 'input')
moose.connect(D, 'nOut', Ddot.x[3], 'input')
moose.connect(E, 'nOut', Ddot.x[4], 'input')
moose.connect(F, 'nOut', Ddot.x[5], 'input')
moose.connect(Z1, 'nOut', Ddot.x[6], 'input')
moose.connect(Z2, 'nOut', Ddot.x[7], 'input')
moose.connect(Ddot, 'valueOut', D, 'increment')
moose.connect(A, 'nOut', Edot.x[0], 'input')
moose.connect(B, 'nOut', Edot.x[1], 'input')
moose.connect(C, 'nOut', Edot.x[2], 'input')
moose.connect(D, 'nOut', Edot.x[3], 'input')
moose.connect(E, 'nOut', Edot.x[4], 'input')
moose.connect(F, 'nOut', Edot.x[5], 'input')
moose.connect(Z1, 'nOut', Edot.x[6], 'input')
moose.connect(Z2, 'nOut', Edot.x[7], 'input')
moose.connect(Edot, 'valueOut', E, 'increment')
moose.connect(A, 'nOut', Fdot.x[0], 'input')
moose.connect(B, 'nOut', Fdot.x[1], 'input')
moose.connect(C, 'nOut', Fdot.x[2], 'input')
moose.connect(D, 'nOut', Fdot.x[3], 'input')
moose.connect(E, 'nOut', Fdot.x[4], 'input')
moose.connect(F, 'nOut', Fdot.x[5], 'input')
moose.connect(Z1, 'nOut', Fdot.x[6], 'input')
moose.connect(Z2, 'nOut', Fdot.x[7], 'input')
moose.connect(Fdot, 'valueOut', F, 'increment')
return compt
import moose
import util as u
import pylab as plt
import numpy as np
neuron = moose.Neutral('/neuron')
spikegen = moose.SpikeGen('/neuron/spikegen')
spikegen.threshold = 0.0
spikegen.refractT = 1e-3
soma_l = 30e-6
soma_rad = 10e-6
dend_l = 100e-6
dend_rad = 1e-6
RM = 2
CM = 0.01
RA = 10
Em = -65e-3
pulse_dur = 100e-3
pulse_amp = 0.1e-9
pulse_delay = 50e-3
pulse_delay2 = 1e9
soma = u.createCompartment(neuron, 'swagginSoma', soma_l, soma_rad, RM, CM, RA,
Em, Em)
dend = u.createCompartment(neuron, 'swagginDend', dend_l, dend_rad, RM, CM, RA,
Em, Em)
moose.connect(soma, 'axialOut', dend, 'handleAxial')
# Create data tables to store the voltage for the soma and each compartment
# making up the dendritic branch
data = moose.Neutral('/data')
soma_pulse = u.createPulse(soma, 'rollingWave', pulse_dur, pulse_amp,
def makeElecPlots():
graphs = moose.Neutral('/graphs')
elec = moose.Neutral('/graphs/elec')
addPlot('/model/elec/soma', 'getVm', 'elec/somaVm')
addPlot('/model/elec/spine_head_14_4', 'getVm', 'elec/spineVm')
filemode='w')
# logging.basicConfig(level=LOG_LEVEL, format='%(asctime)s %(levelname)s %(name)s %(filename)s %(funcName)s: %(message)s', filemode='w')
logger = logging.getLogger('traub2005')
# Add a logging handler to print messages to stderr
ch = logging.StreamHandler()
ch.setLevel(logging.ERROR)
# create formatter and add it to the handlers
formatter = logging.Formatter(
'%(asctime)s %(name)s %(levelname)s %(filename)s %(funcName)s: %(message)s'
)
ch.setFormatter(formatter)
# add the handlers to logger
logger.addHandler(ch)
import os
os.environ['NUMPTHREADS'] = '1'
import sys
sys.path.append('../../../python')
import moose
############################################################
# Initialize library and other containers.
############################################################
library = moose.Neutral(modelSettings.libpath)
#
# config.py ends here
def readMorphML(self, cell, params={}, lengthUnits="micrometer"):
"""
returns cellDict = { cellname: (segDict, cableDict) } # note: single cell only
where segDict = { segid1 : [ segname,(proximalx,proximaly,proximalz),
(distalx,distaly,distalz),diameter,length,[potential_syn1, ... ] ] , ... }
segname is "<name>_<segid>" because 1) guarantees uniqueness,
& 2) later scripts obtain segid from the compartment's name!
and cableDict = { cablegroupname : [campartment1name, compartment2name, ... ], ... }
"""
if lengthUnits in ['micrometer', 'micron']:
self.length_factor = 1e-6
else:
self.length_factor = 1.0
cellname = cell.attrib["name"]
moose.Neutral(
'/library') # creates /library in MOOSE tree; elif present, wraps
pu.info("Loading cell %s into /library ." % cellname)
#~ moosecell = moose.Cell('/library/'+cellname)
#using moose Neuron class - in previous version 'Cell' class Chaitanya
moosecell = moose.Neuron('/library/' + cellname)
self.cellDictBySegmentId[cellname] = [moosecell, {}]
self.cellDictByCableId[cellname] = [moosecell, {}]
self.segDict = {}
if 'combineSegments' in list(params.keys()):
self.combineSegments = params['combineSegments']
else:
self.combineSegments = False
if 'createPotentialSynapses' in list(params.keys()):
self.createPotentialSynapses = params['createPotentialSynapses']
else:
self.createPotentialSynapses = False
pu.info("readMorphML using combineSegments = %s" %
self.combineSegments)
###############################################
#### load cablegroups into a dictionary
self.cablegroupsDict = {}
## Two ways of specifying cablegroups in neuroml 1.x
## <cablegroup>s with list of <cable>s
cablegroups = cell.findall(".//{" + self.mml + "}cablegroup")
for cablegroup in cablegroups:
cablegroupname = cablegroup.attrib['name']
self.cablegroupsDict[cablegroupname] = []
for cable in cablegroup.findall(".//{" + self.mml + "}cable"):
cableid = cable.attrib['id']
self.cablegroupsDict[cablegroupname].append(cableid)
## <cable>s with list of <meta:group>s
cables = cell.findall(".//{" + self.mml + "}cable")
for cable in cables:
cableid = cable.attrib['id']
cablegroups = cable.findall(".//{" + self.meta + "}group")
for cablegroup in cablegroups:
cablegroupname = cablegroup.text
if cablegroupname in list(self.cablegroupsDict.keys()):
self.cablegroupsDict[cablegroupname].append(cableid)
else:
self.cablegroupsDict[cablegroupname] = [cableid]
###################################################
## load all mechanisms in this cell into /library for later copying
## set which compartments have integrate_and_fire mechanism
self.intFireCableIds = {
} # dict with keys as Compartments/cableIds which are IntFire
# with mechanismnames as values
for mechanism in cell.findall(".//{" + self.bio + "}mechanism"):
mechanismname = mechanism.attrib["name"]
passive = False
if "passive_conductance" in mechanism.attrib:
if mechanism.attrib['passive_conductance'] in [
"true", 'True', 'TRUE'
]:
passive = True
if not passive:
## if channel does not exist in library load it from xml file
if not moose.exists("/library/" + mechanismname):
pu.info("Loading mechanism %s into library." %
mechanismname)
cmlR = ChannelML(self.nml_params)
model_filename = mechanismname + '.xml'
model_path = neuroml_utils.find_first_file(
model_filename, self.model_dir)
if model_path is not None:
cmlR.readChannelMLFromFile(model_path)
else:
raise IOError(
'For mechanism {0}: files {1} not found under {2}.'
.format(mechanismname, model_filename,
self.model_dir))
## set those compartments to be LIF for which
## any integrate_and_fire parameter is set
if not moose.exists("/library/" + mechanismname):
print "Mechanism doesn't exist: ", mechanismname
moose.le('/library')
moosemech = moose.element("/library/" + mechanismname)
if moose.exists(moosemech.path + "/integrate_and_fire"):
mooseIaF = moose.element(
moosemech.path + "/integrate_and_fire") # Mstring
if mooseIaF.value in ['true', 'True', 'TRUE']:
mech_params = mechanism.findall(".//{" + self.bio +
"}parameter")
for parameter in mech_params:
parametername = parameter.attrib['name']
## check for the integrate_and_fire parameters
if parametername in [
'threshold', 't_refrac', 'v_reset',
'g_refrac'
]:
for group in parameter.findall(".//{" +
self.bio +
"}group"):
cablegroupname = group.text
if cablegroupname == 'all':
self.intFireCableIds = {
'all': mechanismname
}
break
else:
for cableid in self.cablegroupsDict[
cablegroupname]:
## only one intfire mechanism is allowed in a cable
## the last one parsed will override others
self.intFireCableIds[
cableid] = mechanismname
if 'all' in list(self.intFireCableIds.keys()):
break
############################################################
#### load morphology and connections between compartments
## Many neurons exported from NEURON have multiple segments in a section
## If self.combineSegments = True,
## then combine those segments into one Compartment / section
## for combining, assume segments of a compartment/section are in increasing order
## and assume all segments of a compartment/section have the same cableid
## findall() returns elements in document order:
running_cableid = ''
running_segid = ''
running_comp = None
running_diameter = 0.0
running_dia_nums = 0
segments = cell.findall(".//{" + self.mml + "}segment")
segmentstotal = len(segments)
for segnum, segment in enumerate(segments):
segmentname = segment.attrib['name']
## cable is an optional attribute. WARNING: Here I assume it is always present.
cableid = segment.attrib['cable']
segmentid = segment.attrib['id']
## if old cableid still running AND self.combineSegments == True,
## then don't start a new compartment, skip to next segment
if cableid == running_cableid and self.combineSegments:
self.cellDictBySegmentId[cellname][1][segmentid] = running_comp
proximal = segment.find('./{' + self.mml + '}proximal')
if proximal is not None:
running_diameter += float(
proximal.attrib["diameter"]) * self.length_factor
running_dia_nums += 1
distal = segment.find('./{' + self.mml + '}distal')
if distal is not None:
running_diameter += float(
distal.attrib["diameter"]) * self.length_factor
running_dia_nums += 1
## if (self.combineSegments and new cableid starts) or if not self.combineSegments,
## then start a new compartment
else:
## Create a new compartment
## the moose "hsolve" method assumes compartments to be
## asymmetric compartments and symmetrizes them
## but that is not what we want when translating
## from Neuron which has only symcompartments -- so be careful!
## Check if integrate_and_fire mechanism is present,
## if so use LIF instead of Compartment
moosecompname = segmentname + '_' + segmentid # just segmentname is NOT unique
# eg: mitral bbmit exported from NEURON
moosecomppath = moosecell.path + '/' + moosecompname
IntFireIds = list(self.intFireCableIds.keys())
mechanismname = None
if 'all' in IntFireIds:
mechanismname = self.intFireCableIds['all']
if cableid in IntFireIds:
mechanismname = self.intFireCableIds[cableid]
if mechanismname is not None: # this cableid is an intfire
## create LIF (subclass of Compartment) and set to default values
moosecomp = moose.LIF(moosecomppath)
moosechannel = moose.Neutral('/library/' + mechanismname)
moosechannelval = moose.Mstring(moosechannel.path +
'/vReset')
moosecomp.vReset = moosechannelval.value
moosechannelval = moose.Mstring(moosechannel.path +
'/thresh')
moosecomp.thresh = moosechannelval.value
moosechannelval = moose.Mstring(moosechannel.path +
'/refracT')
moosecomp.refractoryPeriod = moosechannelval.value
## refracG is currently not supported by moose.LIF
## when you implement it, check if refracG or g_refrac
## is a conductance density or a conductance, I think the former
#moosechannelval = moose.Mstring(moosechannel.path+'/refracG')
else:
moosecomp = moose.Compartment(moosecomppath)
self.cellDictBySegmentId[cellname][1][segmentid] = moosecomp
## cables are grouped and mechanism densities are set for cablegroups later.
## hence I will need to refer to segment according to which cable it belongs to.
## if combineSegments is False, there can be multiple segments per cable,
## so make array of compartments for cellDictByCableId[cellname][1][cableid]
if cableid in list(self.cellDictByCableId[cellname][1].keys()):
self.cellDictByCableId[cellname][1][cableid].append(
moosecomp)
else:
self.cellDictByCableId[cellname][1][cableid] = [moosecomp]
running_cableid = cableid
running_segid = segmentid
running_comp = moosecomp
running_diameter = 0.0
running_dia_nums = 0
if 'parent' in segment.attrib:
parentid = segment.attrib[
'parent'] # I assume the parent is created before the child
# so that I can immediately connect the child.
parent = self.cellDictBySegmentId[cellname][1][parentid]
## It is always assumed that axial of parent is connected to raxial of moosesegment
## THIS IS WHAT GENESIS readcell() DOES!!! UNLIKE NEURON!
## THIS IS IRRESPECTIVE OF WHETHER PROXIMAL x,y,z OF PARENT = PROXIMAL x,y,z OF CHILD.
## THIS IS ALSO IRRESPECTIVE OF fraction_along_parent SPECIFIED IN CABLE!
## THUS THERE WILL BE NUMERICAL DIFFERENCES BETWEEN MOOSE/GENESIS and NEURON.
## moosesegment sends Ra and Vm to parent, parent sends only Vm
## actually for symmetric compartment, both parent and moosesegment require each other's Ra/2,
## but axial and raxial just serve to distinguish ends.
moose.connect(parent, 'axial', moosecomp, 'raxial')
else:
parent = None
proximal = segment.find('./{' + self.mml + '}proximal')
if proximal is None: # If proximal tag is not present,
# then parent attribute MUST be present in the segment tag!
## if proximal is not present, then
## by default the distal end of the parent is the proximal end of the child
moosecomp.x0 = parent.x
moosecomp.y0 = parent.y
moosecomp.z0 = parent.z
else:
moosecomp.x0 = float(
proximal.attrib["x"]) * self.length_factor
moosecomp.y0 = float(
proximal.attrib["y"]) * self.length_factor
moosecomp.z0 = float(
proximal.attrib["z"]) * self.length_factor
running_diameter += float(
proximal.attrib["diameter"]) * self.length_factor
running_dia_nums += 1
distal = segment.find('./{' + self.mml + '}distal')
if distal is not None:
running_diameter += float(
distal.attrib["diameter"]) * self.length_factor
running_dia_nums += 1
## finished creating new compartment
## Update the end position, diameter and length, and segDict of this comp/cable/section
## with each segment that is part of this cable (assumes contiguous segments in xml).
## This ensures that we don't have to do any 'closing ceremonies',
## if a new cable is encoutered in next iteration.
if distal is not None:
running_comp.x = float(distal.attrib["x"]) * self.length_factor
running_comp.y = float(distal.attrib["y"]) * self.length_factor
running_comp.z = float(distal.attrib["z"]) * self.length_factor
## Set the compartment diameter as the average diameter of all the segments in this section
running_comp.diameter = running_diameter / float(running_dia_nums)
## Set the compartment length
running_comp.length = math.sqrt((running_comp.x-running_comp.x0)**2+\
(running_comp.y-running_comp.y0)**2+(running_comp.z-running_comp.z0)**2)
## NeuroML specs say that if (x0,y0,z0)=(x,y,z), then round compartment e.g. soma.
## In Moose set length = dia to give same surface area as sphere of dia.
if running_comp.length == 0.0:
running_comp.length = running_comp.diameter
## Set the segDict
## the empty list at the end below will get populated
## with the potential synapses on this segment, in function set_compartment_param(..)
self.segDict[running_segid] = [running_comp.name,\
(running_comp.x0,running_comp.y0,running_comp.z0),\
(running_comp.x,running_comp.y,running_comp.z),\
running_comp.diameter,running_comp.length,[]]
if neuroml_utils.neuroml_debug:
pu.info('Set up compartment/section %s' % running_comp.name)
###############################################
#### load biophysics into the compartments
biophysics = cell.find(".//{" + self.neuroml + "}biophysics")
if biophysics is not None:
## see pg 219 (sec 13.2) of Book of Genesis for Physiological Units
if biophysics.attrib["units"] == 'Physiological Units':
CMfactor = 1e-2 # F/m^2 from microF/cm^2
Cfactor = 1e-6 # F from microF
RAfactor = 1e1 # Ohm*m from KOhm*cm
RMfactor = 1e-1 # Ohm*m^2 from KOhm*cm^2
Rfactor = 1e-3 # Ohm from KOhm
Efactor = 1e-3 # V from mV
Gfactor = 1e1 # S/m^2 from mS/cm^2
Ifactor = 1e-6 # A from microA
Tfactor = 1e-3 # s from ms
else:
CMfactor = 1.0
Cfactor = 1.0
RAfactor = 1.0
RMfactor = 1.0
Rfactor = 1.0
Efactor = 1.0
Gfactor = 1.0
Ifactor = 1.0
Tfactor = 1.0
spec_capacitance = cell.find(".//{" + self.bio +
"}spec_capacitance")
for parameter in spec_capacitance.findall(".//{" + self.bio +
"}parameter"):
self.set_group_compartment_param(cell, cellname, parameter,\
'CM', float(parameter.attrib["value"])*CMfactor, self.bio)
spec_axial_resitance = cell.find(".//{" + self.bio +
"}spec_axial_resistance")
for parameter in spec_axial_resitance.findall(".//{" + self.bio +
"}parameter"):
self.set_group_compartment_param(cell, cellname, parameter,\
'RA', float(parameter.attrib["value"])*RAfactor, self.bio)
init_memb_potential = cell.find(".//{" + self.bio +
"}init_memb_potential")
for parameter in init_memb_potential.findall(".//{" + self.bio +
"}parameter"):
self.set_group_compartment_param(cell, cellname, parameter,\
'initVm', float(parameter.attrib["value"])*Efactor, self.bio)
for mechanism in cell.findall(".//{" + self.bio + "}mechanism"):
mechanismname = mechanism.attrib["name"]
passive = False
if "passive_conductance" in mechanism.attrib:
if mechanism.attrib['passive_conductance'] in [
"true", 'True', 'TRUE'
]:
passive = True
pu.info("Loading mechanism %s " % mechanismname)
## ONLY creates channel if at least one parameter (like gmax) is specified in the xml
## Neuroml does not allow you to specify all default values.
## However, granule cell example in neuroconstruct has Ca ion pool without
## a parameter, applying default values to all compartments!
mech_params = mechanism.findall(".//{" + self.bio +
"}parameter")
## if no params, apply all default values to all compartments
if len(mech_params) == 0:
for compartment_list in list(
self.cellDictByCableId[cellname][1].values()):
for compartment in compartment_list:
self.set_compartment_param(compartment, None,
'default',
mechanismname)
## if params are present, apply params to specified cable/compartment groups
for parameter in mech_params:
parametername = parameter.attrib['name']
if passive:
if parametername in ['gmax']:
self.set_group_compartment_param(cell, cellname, parameter,\
'RM', RMfactor*1.0/float(parameter.attrib["value"]), self.bio)
elif parametername in ['e', 'erev']:
self.set_group_compartment_param(cell, cellname, parameter,\
'Em', Efactor*float(parameter.attrib["value"]), self.bio)
elif parametername in ['inject']:
self.set_group_compartment_param(cell, cellname, parameter,\
'inject', Ifactor*float(parameter.attrib["value"]), self.bio)
else:
pu.warn([
"Yo programmer of MorphML! You didn't",
" implement parameter %s " % parametername,
" in mechanism %s " % mechanismname
])
else:
if parametername in ['gmax']:
gmaxval = float(
eval(parameter.attrib["value"],
{"__builtins__": None}, {}))
self.set_group_compartment_param(cell, cellname, parameter,\
'Gbar', Gfactor*gmaxval, self.bio, mechanismname)
elif parametername in ['e', 'erev']:
self.set_group_compartment_param(cell, cellname, parameter,\
'Ek', Efactor*float(parameter.attrib["value"]), self.bio, mechanismname)
elif parametername in [
'depth'
]: # has to be type Ion Concentration!
self.set_group_compartment_param(cell, cellname, parameter,\
'thick', self.length_factor*float(parameter.attrib["value"]),\
self.bio, mechanismname)
elif parametername in ['v_reset']:
self.set_group_compartment_param(cell, cellname, parameter,\
'v_reset', Efactor*float(parameter.attrib["value"]),\
self.bio, mechanismname)
elif parametername in ['threshold']:
self.set_group_compartment_param(cell, cellname, parameter,\
'threshold', Efactor*float(parameter.attrib["value"]),\
self.bio, mechanismname)
elif parametername in ['t_refrac']:
self.set_group_compartment_param(cell, cellname, parameter,\
't_refrac', Tfactor*float(parameter.attrib["value"]),\
self.bio, mechanismname)
else:
pu.warn([
"Yo programmer of MorphML import! You didn't",
" implement parameter %s " % parametername,
" in mechanism %s " % mechanismname
])
#### Connect the Ca pools and channels
#### Am connecting these at the very end so that all channels and pools have been created
#### Note: this function is in moose.utils not moose.neuroml.utils !
for compartment_list in list(
self.cellDictByCableId[cellname][1].values()):
moose_utils.connect_CaConc(compartment_list,\
self.temperature+neuroml_utils.ZeroCKelvin) # temperature should be in Kelvin for Nernst
##########################################################
#### load connectivity / synapses into the compartments
connectivity = cell.find(".//{" + self.neuroml + "}connectivity")
if connectivity is not None:
for potential_syn_loc in cell.findall(".//{" + self.nml +
"}potential_syn_loc"):
if 'synapse_direction' in list(
potential_syn_loc.attrib.keys()):
if potential_syn_loc.attrib['synapse_direction'] in [
'post', 'preAndOrPost'
]:
self.set_group_compartment_param(cell, cellname, potential_syn_loc,\
'synapse_type', potential_syn_loc.attrib['synapse_type'],\
self.nml, mechanismname='synapse')
if potential_syn_loc.attrib['synapse_direction'] in [
'pre', 'preAndOrPost'
]:
self.set_group_compartment_param(cell, cellname, potential_syn_loc,\
'spikegen_type', potential_syn_loc.attrib['synapse_type'],\
self.nml, mechanismname='spikegen')
##########################################################
#### annotate each compartment with the cablegroups it belongs to
self.cableDict = {}
for cablegroupname in list(self.cablegroupsDict.keys()):
comp_list = []
for cableid in self.cablegroupsDict[cablegroupname]:
for compartment in self.cellDictByCableId[cellname][1][
cableid]:
cableStringPath = compartment.path + '/cable_groups'
cableString = moose.Mstring(cableStringPath)
if cableString.value == '':
cableString.value += cablegroupname
else:
cableString.value += ',' + cablegroupname
comp_list.append(compartment.name)
self.cableDict[cablegroupname] = comp_list
pu.info("Finished loading into library, cell: %s " % cellname)
return {cellname: (self.segDict, self.cableDict)}
os.mkdir(data_dir)
filename_suffix = '_%s_%d' % (timestamp.strftime('%Y%m%d_%H%M%S'), mypid)
DATA_FILENAME = os.path.join(data_dir, 'data%s.h5' % (filename_suffix))
MODEL_FILENAME = os.path.join(data_dir, 'network%s.h5' % (filename_suffix))
LOGGER = logging.getLogger('traub2005')
BENCHMARK_LOGGER = logging.getLogger('traub2005.benchmark')
BENCHMARK_LOGGER.setLevel(logging.DEBUG)
benchmarking = True # Dump benchmarking information
#---------------------------------------------------------------------
# moose components
#---------------------------------------------------------------------
context = moose.PyMooseBase.getContext()
lib = moose.Neutral('/library')
root = moose.Neutral("/")
clockjob = moose.ClockJob('sched/cj')
clockjob.autoschedule = 1
solver = 'hsolve'
simdt = 0.5e-4
plotdt = 1e-3
gldt = 1e-2
vmin = -120e-3
vmax = 40e-3
ndivs = 640
dv = (vmax - vmin) / ndivs
channel_name_list = [
'AR', 'CaPool', 'CaL', 'CaT', 'CaT_A', 'K2', 'KA', 'KA_IB', 'KAHP',
'KAHP_DP', 'KAHP_SLOWER', 'KC', 'KC_FAST', 'KDR', 'KDR_FS', 'KM', 'NaF',
'NaF2', 'NaF_TCR', 'NaP', 'NaPF', 'NaPF_SS', 'NaPF_TCR', 'NaF2_nRT'
def vclamp_demo(simtime=50.0, dt=1e-2):
## It is good practice to modularize test elements inside a
## container
container = moose.Neutral('/vClampDemo')
## Create a compartment with properties of a squid giant axon
comp = SquidAxon('/vClampDemo/axon')
# Create and setup the voltage clamp object
clamp = moose.VClamp('/vClampDemo/vclamp')
## The defaults should work fine
# clamp.mode = 2
# clamp.tau = 10*dt
# clamp.ti = dt
# clamp.td = 0
# clamp.gain = comp.Cm / dt
## Setup command voltage time course
command = moose.PulseGen('/vClampDemo/command')
command.delay[0] = 10.0
command.width[0] = 20.0
command.level[0] = 50.0
command.delay[1] = 1e9
moose.connect(command, 'output', clamp, 'commandIn')
## Connect the Voltage Clamp to the compartemnt
moose.connect(clamp, 'currentOut', comp, 'injectMsg')
moose.connect(comp, 'VmOut', clamp, 'sensedIn')
## setup stimulus recroding - this is the command pulse
stimtab = moose.Table('/vClampDemo/vclamp_command')
moose.connect(stimtab, 'requestOut', command, 'getOutputValue')
## Set up Vm recording
vmtab = moose.Table('/vClampDemo/vclamp_Vm')
moose.connect(vmtab, 'requestOut', comp, 'getVm')
## setup command potential recording - this is the filtered input
## to PID controller
commandtab = moose.Table('/vClampDemo/vclamp_filteredcommand')
moose.connect(commandtab, 'requestOut', clamp, 'getCommand')
## setup current recording
Imtab = moose.Table('/vClampDemo/vclamp_inject')
moose.connect(Imtab, 'requestOut', clamp, 'getCurrent')
# Scheduling
moose.setClock(0, dt)
moose.setClock(1, dt)
moose.setClock(2, dt)
moose.setClock(3, dt)
moose.useClock(0, '%s/##[TYPE=Compartment]' % (container.path), 'init')
moose.useClock(0, '%s/##[TYPE=PulseGen]' % (container.path), 'process')
moose.useClock(1, '%s/##[TYPE=Compartment]' % (container.path), 'process')
moose.useClock(2, '%s/##[TYPE=HHChannel]' % (container.path), 'process')
moose.useClock(2, '%s/##[TYPE=VClamp]' % (container.path), 'process')
moose.useClock(3, '%s/##[TYPE=Table]' % (container.path), 'process')
moose.reinit()
print 'RC filter in VClamp:: tau:', clamp.tau
print 'PID controller in VClamp:: ti:', clamp.ti, 'td:', clamp.td, 'gain:', clamp.gain
moose.start(simtime)
print 'Finished simulation for %g seconds' % (simtime)
tseries = linspace(0, simtime, len(vmtab.vector))
subplot(211)
title('Membrane potential and clamp voltage')
plot(tseries, vmtab.vector, 'g-', label='Vm (mV)')
plot(tseries, commandtab.vector, 'b-', label='Filtered command (mV)')
plot(tseries, stimtab.vector, 'r-', label='Command (mV)')
xlabel('Time (ms)')
ylabel('Voltage (mV)')
legend()
# print len(commandtab.vector)
subplot(212)
title('Current through clamp circuit')
# plot(tseries, stimtab.vector, label='stimulus (uA)')
plot(tseries, Imtab.vector, label='injected current (uA)')
xlabel('Time (ms)')
ylabel('Current (uA)')
legend()
show()
def create_output_table(table_element='/output', table_name='somaVm'):
''' Creates and returns a moose table element.
'''
output = moose.Neutral(table_element)
membrane_voltage_table = moose.Table('/'.join((table_element, table_name)))
return membrane_voltage_table
synH.synapse.weight = 1.0
synH.connect('activationOut', syn, 'activation')
print(('Synapses:', len(synH.synapse), 'w=', synH.synapse[0].weight ))
spikegen = moose.SpikeGen('%s/spike' % (syn.parent.path))
spikegen.edgeTriggered = False # Make it fire continuously when input is high
spikegen.refractT = 10.0 # With this setting it will fire at 1 s / 10 ms = 100 Hz
spikegen.threshold = 0.5
# This will send alternatind -1 and +1 to SpikeGen to make it fire
spike_stim = moose.PulseGen('%s/spike_stim' % (syn.parent.path))
spike_stim.delay[0] = 1.0
spike_stim.level[0] = 1.0
spike_stim.width[0] = 100.0
moose.connect(spike_stim, 'output', spikegen, 'Vm')
m = moose.connect(spikegen, 'spikeOut', synH.synapse.vec, 'addSpike', 'Sparse')
m.setRandomConnectivity(1.0, 1)
m = moose.connect(spikegen, 'spikeOut', synH.synapse[0], 'addSpike') # this causes segfault
return syn, spikegen
if __name__ == '__main__':
model = moose.Neutral('/model')
syn, spikegen = make_synapse('/model/synchan')
moose.setClock(0, 0.01)
moose.useClock(0, '/model/##', 'process')
moose.reinit()
moose.start(100)
#
# test_synchan.py ends here
# for debugging only
#
print 'PRINTING Synapse info'
config.LOGGER.debug('PRINTING Synapse info')
for celltype, count in config.runconfig.items('cellcount'):
if int(count) == 0:
continue
synchans = moose.context.getWildcardList('%s/%s_0/##[ISA=SynChan]' % (net.network_container.path, celltype), True)
nmdachans = moose.context.getWildcardList('%s/%s_0/##[TYPE=NMDAChan]' % (net.network_container.path, celltype), True)
config.LOGGER.debug('No. of synchans on SpinyStellate_0 : %d' % (len(synchans)))
config.LOGGER.debug('No. of nmdachans on SpinyStellate_0 : %d' % (len(nmdachans)))
syn_tabs = []
for synid in chain(synchans, nmdachans):
synapse = moose.SynChan(synid)
config.LOGGER.debug('Recording from %s' % (synapse.path))
comp = moose.Neutral(synapse.parent)
cell = moose.Neutral(comp.parent)
synapse_data = moose.Neutral('synapse', sim.data)
tab = moose.Table('gk_%s_%s_%s' % (cell.name, comp.name, synapse.name), synapse_data)
tab.stepMode = 3
config.LOGGER.info('Connected recording table %s: %s' % (tab.name, tab.connect('inputRequest', synapse, 'Gk')))
syn_tabs.append(tab)
tab = moose.Table('Ik_%s_%s_%s' % (cell.name, comp.name, synapse.name), synapse_data)
tab.stepMode = 3
config.LOGGER.info('Connected recording table %s: %s' % (tab.name, tab.connect('inputRequest', synapse, 'Ik')))
syn_tabs.append(tab)
config.LOGGER.debug('== start synapse info')
config.LOGGER.debug(synapse.path)
msg_list = pymoose.listmsg(synapse)
for msg in msg_list:
config.LOGGER.debug(msg)
def main(*argv):
"""-c cell-count-file
-g celltype-graph-file
-s synaptic-scaling-file
-v synaptic-conductance-values-file
-t simulationtime
-d simdt
-p plotdt
-r randomseed
-s -- do explicit scheduling
--reseed -- seed the rng with PID of current process
-x prelease_unknown -- default release probability in stochastic simulations.
--stochastic -- synapses are stochastic
-i -- interstimulus interval
"""
print '******** Starting run _{timestamp}_{PID} :', config.filename_suffix
config.LOGGER.info('Running moose version: %s revision: %s' % (moose.version, moose.revision))
celltypegraph_file = None
cellcount_file = None
synscale_file = None
synval_file = None
notes = None
netfile = None
optlist, args = getopt(argv[0], 'i:m:n:ehc:s:v:t:d:p:r:g:lx:', ['reseed', 'stochastic', 'netfile='])
print 'Program arguments: '
print 'Options:', optlist
print 'Args:', args
for arg in optlist:
if arg[0] == '-c':
cellcount_file = arg[1]
elif arg[0] == '-n':
notes = arg[1]
elif arg[0] == '-m':
with open(arg[1], 'r') as notes_file:
notes = '\n'.join(notes_file.readlines())
elif arg[0] == '-s':
synscale_file = arg[1]
elif arg[0] == '-v':
synval_file = arg[1]
elif arg[0] == '-t':
config.simtime = float(arg[1])
elif arg[0] == '-d':
config.simdt = float(arg[1])
elif arg[0] == '-p':
config.plotdt = float(arg[1])
elif arg[0] == '-r':
config.rngseed = int(arg[1])
elif arg[0] == '-g':
celltypegraph_file = arg[1]
elif '--reseed' == arg[0]:
config.to_reseed = True
elif '--stochastic' == arg[0]:
config.stochastic = True
elif '--netfile' == arg[0]:
netfile = arg[1]
elif '-e' == arg[0]:
config.solver = 'ee'
elif arg[0] == '-l':
config.clockjob.autoschedule = 0
elif arg[0] == '-x':
config.default_releasep = float(arg[1])
assert((config.default_releasep < 1.0) and (config.default_releasep >= 0.0))
elif arg[0] == '-i':
config.runconfig.set('stimulus', 'isi', arg[1])
print 'Set isi to', arg[1]
elif '-h' == arg[0]:
print main.__doc__
sys.exit(0)
sim = Simulation('sim%s' % (config.filename_suffix))
net = TraubNet(container=sim.model, netfile=netfile)
if notes is not None:
net.tweaks_doc.append(notes)
if celltypegraph_file is None:
net._generate_celltype_graph()
else:
net.setup_from_celltype_file(celltype_file=celltypegraph_file)
net.set_populations()
net.set_conductances(synval_file)
net.tune_conductances(synscale_file)
scale_nmda = config.runconfig.get('NMDA', 'conductance_scale')
if scale_nmda:
net.scale_conductance('gnmda', {('*', '*'):float(scale_nmda)})
scale_ampa = config.runconfig.get('AMPA', 'conductance_scale')
if scale_ampa:
net.scale_conductance('gampa', {('*', '*'):float(scale_ampa)})
scale_gaba = config.runconfig.get('GABA', 'conductance_scale')
if scale_gaba:
net.scale_conductance('ggaba', {('*', '*'):float(scale_gaba)})
net.set_unknown_prelease(config.default_releasep)
net._generate_cell_graph()
net.create_network()
if config.runconfig.get('stimulus', 'ectopic_spike') in ['1', 'yes', 'Yes', 'YES', 'true', 'True', 'TRUE']:
net.setup_ectopic_input()
# Comment out the following line to use original K+ reversal potential.
# net.tweak_Ek(KChannel, 10e-3)
net.randomize_passive_properties()
net.randomize_active_conductances()
background_celltype = config.runconfig.get('stimulus', 'background')
probe_celltype = config.runconfig.get('stimulus', 'probe')
bg_count = int(config.runconfig.get('stimulus', 'bg_count'))
probe_count = int(config.runconfig.get('stimulus', 'probe_count'))
onset = float(config.runconfig.get('stimulus', 'onset'))
bg_interval = float(config.runconfig.get('stimulus', 'bg_interval'))
bg_interval_spread = float(config.runconfig.get('stimulus', 'bg_interval_spread'))
pulse_width = float(config.runconfig.get('stimulus', 'pulse_width'))
isi = float(config.runconfig.get('stimulus', 'isi'))
print 'trbsim - isi', isi
amp = float(config.runconfig.get('stimulus', 'amplitude'))
print bg_interval, pulse_width, isi
if bg_interval_spread > 0.0:
num_bg_pulses = (config.simtime - onset) / (bg_interval + bg_interval_spread/2)
else:
num_bg_pulses = 0
stim_dict = net.setup_stimulus(bg_cells=background_celltype,
probe_cells=probe_celltype,
bg_count=bg_count,
probe_count=probe_count,
stim_onset=onset,
bg_interval=bg_interval,
bg_interval_spread=bg_interval_spread,
num_bg_pulses=num_bg_pulses,
pulse_width=pulse_width,
isi=isi,
level=amp)
# Record post synaptic Vm for cells with highest convergent connections
pspfrac = float(config.runconfig.get('record', 'pspfrac'))
pspcontainer = moose.Neutral('%s/psp' % (sim.data.path))
if pspfrac > 0:
bg_target_cells = [comppath.rpartition('/')[0] for comppath in stim_dict['bg_targets']]
target_source_map = get_targets(bg_target_cells)
max_targets = get_max_targets(target_source_map, pspfrac)
for celltype, cells in max_targets.items():
config.LOGGER.debug('Recording Vm for 1 hop from stimulus for %s: %s' % (celltype, cells))
for cellpath, count in cells:
soma = MyCompartment(cellpath + '/comp_1')
if soma.className == 'Compartment':
soma.insertRecorder(cellpath.rpartition('/')[-1], 'Vm', pspcontainer)
# for cpath in stim_dict['bg_targets']:
# cell = cpath.rpartition('/')[0]
# comp = MyCompartment(cpath)
# comp.insertRecorder(
# , stim_dict['probe_targtes']):
if net.from_netfile is not None and synscale_file is not None:
net.scale_synapses(synscale_file)
net.save_network_model(config.MODEL_FILENAME)
net.verify_saved_model(config.MODEL_FILENAME)
net.save_cell_network(config.MODEL_FILENAME + '.new')
net.setup_spike_recording(sim.data)
# net.setup_current_injection_test([-0.9e-9, -0.3e-9, 0.0, 0.1e-9, 0.0, 0.3e-9, 0.0, 0.9e-9], 1.0, 1.0, sim.data)
# Setup the bias currents
bias_current_delays = defaultdict(dict)
bias_current_levels = defaultdict(dict)
bias_current_widths = defaultdict(dict)
for key, value in config.runconfig.items('bias_current'):
if not value:
continue
tokens = key.split('_')
celltype = tokens[0]
param = tokens[1]
index = int(tokens[2])
try:
if param == 'delay':
bias_current_delays[celltype][index] = float(value)
elif param == 'width':
bias_current_widths[celltype][index] = float(value)
elif param == 'level':
bias_current_levels[celltype][index] = float(value)
except ValueError, e:
print 'Value:"', value, '"'
raise(e)
SIMDT = 0.01*ms
PLOTDT = 0.01*ms
RUNTIME = 5*ms
EREST = -70.0*mV
VLEAK = EREST + 10.613*mV
RM = 424.4e3
#RA = 7639.44e3
CM = 0.007854e-6
INJECT = 0.1e-6
VK = -90*mV
VNa = 40*mV
GK = 0.282743e-3
GNa = 0.94248e-3
model = moose.Neutral("/model")
#data = moose.Neutral("/data")
comp = moose.Compartment("/model/compartment")
comp.Rm = RM
#comp.Ra = RA
comp.Cm = CM
comp.Em = VLEAK
comp.initVm = EREST
comp.inject = INJECT
na = moose.HHChannel("na", comp)
na.Ek = VNa
na.Gbar = GNa
na.Xpower = 3
na.Ypower = 1
# (A + Bv)/(C + exp(D/E))
dt, tplot, avec = runPanelDEFG( 'negFB', 5.0, 2.0, 5, seq, 1.0 )
xplot.append( avec )
t = np.arange( 0, len( tplot[0] ), 1.0 ) * dt
dt, tplot, avec = runPanelDEFG( 'negFF', 10.0, 1.0, 5, seq, 1.0 )
xplot.append( avec )
t = np.arange( 0, len( tplot[0] ), 1.0 ) * dt
dt, tplot, avec = runPanelDEFG( 'fhn', 5.0, 1.5, 5, seq, 0.4 )
xplot.append( avec )
t = np.arange( 0, len( tplot[0] ), 1.0 ) * dt
dt, tplot, avec = runPanelDEFG( 'bis', 15.0, 2.0, 5, seq, 1.0 )
xplot.append( avec )
t = np.arange( 0, len( tplot[0] ), 1.0 ) * dt
ref = np.array( [0.04840247926323106, 0.060446860947786119
, 0.047612129439079991, 0.081329604404641223, 0.050365470686926379] )
res = np.array( [ np.mean( x ) for x in tplot ] )
assert np.isclose( ref.all(), res.all() ), "Expected %s got %s" % (ref,res)
if __name__ == '__main__':
moose.Neutral( '/library' )
moose.Neutral( '/model' )
plotPanelC()
#if sys.version_info[0] == 2:
# plotPanelDEFG( [0,1,2,3,4], 3 )
# plotPanelDEFG( [4,1,0,3,2], 4 )
#else:
# print( 'TODO: Running any of the following two functions causes seg-fault' )
print( 'All done' )
gran_cell = u.createMultiCompCell(swcfile, container, libraryName, compType,
chan_set, cond_set, rateParams, RM, CM, RA,
initVm, Em)
moose.showfield('/gran_cell/soma')
# Re-create the python variable pointing to the gran_cell to limit results just to
# type compartment (excludes the spines and allows for createDataTables function to
# work properly)
gran_cell = moose.wildcardFind('/gran_cell/#[TYPE=Compartment]')
# Create the pulse and apply it to the granule cell's soma
g_soma_pulse = u.createPulse(gran_cell[0], 'rollingWave', pulse_dur, pulse_amp,
pulse_delay1, pulse_delay2)
# Create a neutral object to store the data in
gran_data = moose.Neutral('/gran_data')
gran_tables = []
for comp in gran_cell:
gran_tables.append(u.createDataTables(comp, gran_data, g_soma_pulse))
# Choose the soma and a representative dendrite to view how voltage changes
# for the granule cell
g_soma0_Vm = gran_tables[0][0]
g_soma0_Iex = gran_tables[0][1]
g_dend_5_00_Vm = gran_tables[-11][0]
g_dend_5_00_Iex = gran_tables[-11][1]
# Plot the simulation
simTime = 0.5
simdt = 0.25e-5
plotdt = 0.25e-3
def main():
"""
This illustrates the use of rdesigneur to build a simple dendrite with
spines, and then to resize them using spine fields. These are the
fields that would be changed dynamically in a simulation with reactions
that affect spine geometry.
"""
makeModel()
elec = moose.element('/model/elec')
elec.setSpineAndPsdMesh(moose.element('/model/chem/spine'),
moose.element('/model/chem/psd'))
caDend = moose.vec('/model/chem/dend/Ca')
caHead = moose.vec('/model/chem/spine/Ca')
caPsd = moose.vec('/model/chem/psd/Ca')
eHead = moose.wildcardFind('/model/elec/#head#')
graphs = moose.Neutral('/graphs')
psdTab = moose.Table2('/graphs/psdTab', len(caPsd)).vec
headTab = moose.Table2('/graphs/headTab', len(caHead)).vec
dendTab = moose.Table2('/graphs/dendTab', len(caDend)).vec
eTab = moose.Table('/graphs/eTab', len(eHead)).vec
stimtab = moose.StimulusTable('/stim')
stimtab.stopTime = 0.3
stimtab.loopTime = 0.3
stimtab.doLoop = True
stimtab.vector = [
1.0 + numpy.sin(x) for x in numpy.arange(0, 2 * PI, PI / 1000)
]
estimtab = moose.StimulusTable('/estim')
estimtab.stopTime = 0.001
estimtab.loopTime = 0.001
estimtab.doLoop = True
estimtab.vector = [
1e-9 * numpy.sin(x) for x in numpy.arange(0, 2 * PI, PI / 1000)
]
for i in range(len(caPsd)):
moose.connect(psdTab[i], 'requestOut', caPsd[i], 'getConc')
for i in range(len(caHead)):
moose.connect(headTab[i], 'requestOut', caHead[i], 'getConc')
for i in range(len(caDend)):
moose.connect(dendTab[i], 'requestOut', caDend[i], 'getConc')
for i in range(len(eHead)):
moose.connect(eTab[i], 'requestOut', eHead[i], 'getVm')
moose.connect(stimtab, 'output', caDend, 'setConc', 'OneToAll')
dend = moose.element('/model/elec/dend')
moose.connect(estimtab, 'output', dend, 'setInject')
moose.reinit()
moose.start(1)
head0 = moose.element('/model/elec/head0')
shaft1 = moose.element('/model/elec/shaft1')
head2 = moose.element('/model/elec/head2')
# Here we scale the spine head length while keeping all vols constt.
print("Spine 0: longer head, same vol\nSpine 1: longer shaft")
print("Spine 2: Bigger head, same diffScale\n")
elecParms = [(i.Rm, i.Cm, i.Ra) for i in (head0, shaft1, head2)]
chemParms = [
i.volume for i in (caHead[0], caPsd[0], caHead[1], caPsd[1], caHead[2],
caPsd[2])
]
elec.spine[0].headLength *= 4 # 4x length
print("############## {0} {1} {2}".format(elecParms[0][0], head0.Rm,
elec.spine[0].headLength))
elec.spine[0].headDiameter *= 0.5 # 1/2 x dia
# Here we scale the shaft length. Vols are not touched.
elec.spine[1].shaftLength *= 2 # 2 x length
#Here we scale the spine head vol while retaining diffScale = xArea/len
# This gives 4x vol.
hdia = elec.spine[2].headDiameter
sdsolve = moose.element('/model/chem/spine/dsolve')
elec.spine[2].headLength *= 2 # 2x length
elec.spine[2].headDiameter *= numpy.sqrt(2) # sqrt(2) x dia
hdia = elec.spine[2].headDiameter
print("Checking scaling assertions: ")
assertEq(elecParms[0][0] * 0.5, head0.Rm)
assertEq(elecParms[0][1] * 2, head0.Cm)
assertEq(elecParms[0][2] * 16, head0.Ra)
assertEq(chemParms[0], caHead[0].volume)
assertEq(chemParms[1] * 0.25, caPsd[0].volume)
assertEq(elecParms[1][0] * 0.5, shaft1.Rm)
assertEq(elecParms[1][1] * 2, shaft1.Cm)
assertEq(elecParms[1][2] * 2, shaft1.Ra)
assertEq(chemParms[2], caHead[1].volume)
assertEq(chemParms[3], caPsd[1].volume)
ratio = 2 * numpy.sqrt(2)
assertEq(elecParms[2][0] / ratio, head2.Rm)
assertEq(elecParms[2][1] * ratio, head2.Cm)
assertEq(elecParms[2][2], head2.Ra)
assertEq(chemParms[4] * 4, caHead[2].volume)
assertEq(chemParms[5] * 2, caPsd[2].volume)
print("\nAll assertions cleared")
moose.start(2)
for i in range(len(psdTab)):
pylab.plot(psdTab[i].vector, label='PSD' + str(i))
pylab.legend()
pylab.figure()
for i in range(len(headTab)):
pylab.plot(headTab[i].vector, label='head' + str(i))
pylab.legend()
pylab.figure()
for i in range(len(dendTab)):
pylab.plot(dendTab[i].vector, label='dendCa' + str(i))
pylab.legend()
pylab.figure()
for i in range(len(eTab)):
pylab.plot(eTab[i].vector, label='headVm' + str(i))
#print i, len( eTab[i].vector ), eTab[i].vector
pylab.legend()
pylab.show()
app = QtGui.QApplication(sys.argv)
#widget = mv.MoogliViewer( '/model' )
morphology = moogli.read_morphology_from_moose(name="", path='/model/elec')
widget = moogli.MorphologyViewerWidget(morphology)
widget.show()
return app.exec_()
quit()
def main():
"""
This illustrates the use of rdesigneur to build a simple dendrite with
spines, and to confirm that the chemical contents of the spines align
with the electrical. Just a single molecule Ca is involved.
It diffuses and we plot the distribution.
It causes 'inject' of the relevant compartment to rise.
"""
makeModel()
# Create the output tables
graphs = moose.Neutral('/graphs')
#dendVm = addPlot( 'model/elec/dend', 'getVm', 'dendVm', 8 )
addPlot('model/chem/dend/Ca[0]', 'getConc', 'dCa0', 18)
addPlot('model/chem/dend/Ca[25]', 'getConc', 'dCa25', 18)
addPlot('model/chem/dend/Ca[49]', 'getConc', 'dCa49', 18)
addPlot('model/chem/spine/Ca[0]', 'getN', 'sCa0', 18)
addPlot('model/chem/spine/Ca[25]', 'getN', 'sCa25', 18)
addPlot('model/chem/spine/Ca[49]', 'getN', 'sCa49', 18)
addPlot('model/chem/psd/Ca[0]', 'getConc', 'pCa0', 18)
addPlot('model/chem/psd/Ca[25]', 'getConc', 'pCa25', 18)
addPlot('model/chem/psd/Ca[49]', 'getConc', 'pCa49', 18)
d = moose.vec('/model/chem/dend/Ca')
s = moose.vec('/model/chem/spine/Ca')
p = moose.vec('/model/chem/psd/Ca')
s[5].nInit = 1000
s[40].nInit = 5000
moose.reinit()
moose.start(runtime)
fig = plt.figure(figsize=(13, 10))
p1 = fig.add_subplot(311)
plotVm(p1, 'dend')
plotVm(p1, 'head')
plotVm(p1, 'psd')
p1.legend()
#time = numpy.arange( 0, dendVm.vector.size, 1 ) * dendVm.dt
#p1.plot( time, dendVm.vector, label = 'dendVm' )
p2 = fig.add_subplot(312)
p2.plot(d.conc, label='idendCa')
p2.plot(s.conc, label='ispineCa')
p2.plot(p.conc, label='ipsdCa')
p2.legend()
'''
p2 = fig.add_subplot( 312 )
for i in moose.wildcardFind( '/graphs/#Ca#' ):
time = numpy.arange( 0, i.vector.size, 1 ) * i.dt
p2.plot( time, i.vector, label = i.name )
p2.legend()
'''
p3 = fig.add_subplot(313)
p3.plot(getMidpts('dend'), d.conc, label='dendCa')
#p3.plot( range( 0, len( d ) ), d.conc, label = 'dendCa' )
p3.plot(getMidpts('spine'), s.conc, label='spineCa')
p3.plot(getMidpts('psd'), p.conc, label='psdCa')
p3.legend()
plt.show()
app = QtGui.QApplication(sys.argv)
#widget = mv.MoogliViewer( '/model' )
morphology = moogli.read_morphology_from_moose(name="", path='/model/elec')
widget = moogli.MorphologyViewerWidget(morphology)
widget.show()
return app.exec_()
quit()
def makeSpineProto2(name):
spine = moose.Neutral('/library/' + name)
shaft = rd.buildCompt(spine, 'shaft', 0.5e-6, 0.4e-6, 0, RM, RA, CM)
head = rd.buildCompt(spine, 'head', 0.5e-6, 0.5e-6, 0.5e-6, RM, RA, CM)
moose.connect(shaft, 'axial', head, 'raxial')
def main():
library=moose.Neutral('/library')
#makePassiveSoma( 'cell', params['dendL'], params['dendDia'] )
makeDendProto()
makeChemProto()
rdes=rd.rdesigneur(
turnOffElec=True,
chemPlotDt = 0.1,
diffusionLength=params['diffusionL'],
#cellProto=[['cell','soma']],
cellProto=[['elec','dend']],
chemProto=[['hydra','hydra']],
chemDistrib=[['hydra', '#soma#,#dend#', 'install', '1']],
plotList=[
['soma', '1', 'dend/A', 'n', '# of A'],
['soma', '1', 'dend/B', 'n', '# of B']
],
# moogList = [['soma', '1', 'dend/A', 'n', 'num of A (number)']]
)
moose.le( '/library' )
moose.le( '/library/hydra' )
#moose.showfield( '/library/soma/soma' )
rdes.buildModel()
#moose.element('/model/chem/dend/B').vec[50].nInit=15.5
A = moose.element('/model/chem/dend/A')
B = moose.element('/model/chem/dend/B')
C = moose.element('/model/chem/dend/C')
A.diffConst=1e-13
B.diffConst=0
C.diffConst=0
B.motorConst=1e-06
C.motorConst=-1e-06
# A.concInit=1
# B.concInit=10
moose.element('/model/chem/dend/A').vec[200].nInit=1.2
moose.element('/model/chem/dend/A').vec[100].nInit=1.2
#moose.element('/model/chem/dend/A').vec[95].nInit=1.2
#moose.element('/model/chem/dend/A').vec[127].nInit=1.2
#moose.element('/model/chem/dend/B').vec[244].nInit=1.2
#moose.element('/model/chem/dend/C').vec[400].nInit=1.2
#moose.element('/model/chem/dend/A').vec[105].nInit=1.2
#moose.element('/model/chem/dend/B').vec[105].nInit=1.2
#moose.element('/model/chem/dend/B').vec[25].nInit=0
#A.nInit=1
#B.nInit=15
#for i in range(0,499):
#moose.element('/model/chem/dend/A').vec[i].diffConst=9.45e-12
#moose.element('/model/chem/dend/A').vec[i].diffConst=1e-13
#moose.element('/model/chem/dend/B').vec[i].diffConst=1e-13
#moose.element('/model/chem/dend/B').vec[i].diffConst=0.27e-09
#for i in range(500,999):
#moose.element('/model/chem/dend/A').vec[i].diffConst=9.45e-12
#moose.element('/model/chem/dend/A').vec[i].diffConst=1e-13
#moose.element('/model/chem/dend/B').vec[i].diffConst=1e-13
#moose.element('/model/chem/dend/B').vec[i].diffConst=0.27e-09
#for i in range(0,200):
#moose.element('/model/chem/dend/A').vec[i].diffConst=1e-13
#for i in range(700,999):
#moose.element('/model/chem/dend/A').vec[i].diffConst=1e-13
moose.reinit()
#moose.start(2)
for t in range(0,2000,200):
moose.start(200)
avec=moose.vec('/model/chem/dend/A').n
plt.plot(avec)
avec = moose.vec( '/model/chem/dend/A' ).n
bvec = moose.vec( '/model/chem/dend/B' ).n
cvec = moose.vec( '/model/chem/dend/C' ).n
#plt.plot(bvec)
return bvec,avec,cvec
def main():
library = moose.Neutral('/library')
#makePassiveSoma( 'cell', params['dendL'], params['dendDia'] )
makeDendProto()
makeChemProto()
rdes = rd.rdesigneur(
turnOffElec=True,
chemPlotDt=0.1,
diffusionLength=params['diffusionL'],
#cellProto=[['cell','soma']],
cellProto=[['elec', 'dend']],
chemProto=[['hydra', 'hydra']],
chemDistrib=[['hydra', '#soma#,#dend#', 'install', '1']],
#stimList=[['soma','1','.','inject','(t>0.01&&t<0.2)*1e-10']],
plotList=[['soma', '1', 'dend/A', 'n', '# of A'],
['soma', '1', 'dend/B', 'n', '# of B']],
)
moose.le('/library')
moose.le('/library/hydra')
rdes.buildModel()
A = moose.element('/model/chem/dend/A')
B = moose.element('/model/chem/dend/B')
S = moose.element('/model/chem/dend/S')
space = moose.element('/model/chem/dend/space')
A.diffConst = 1e-13
B.diffConst = 1e-11
S.diffConst = 0
space.diffConst = 0
#moose.element('/model/chem/dend/A').vec[50].nInit=1.2
#moose.element('/model/chem/dend/B').vec[50].nInit=1.2
totLen = len(moose.vec('/model/chem/dend/A').n)
sourceApply = range(int(totLen * 0.1) + 1)
xl = 0
for j in range(totLen):
moose.element('/model/chem/dend/A').vec[j].concInit = 0.268331
moose.element('/model/chem/dend/B').vec[j].concInit = 2.0
for i in sourceApply:
#moose.element('/model/chem/dend/A').vec[i].concInit=0.268331
#moose.element('/model/chem/dend/B').vec[i].concInit=2
moose.element('/model/chem/dend/S').vec[i].concInit = 1
moose.element('/model/chem/dend/space').vec[i].concInit = xl * 0.1
print moose.element('/model/chem/dend/space').vec[i].concInit, xl
print moose.element('/model/chem/dend/S').vec[i].concInit
xl = xl + 1
#randper=np.random.uniform(1,2,savec)
print 'simulation start'
dtSol = 0.01
moose.setClock(16, dtSol)
moose.setClock(10, dtSol)
moose.reinit()
#avec=moose.vec('/model/chem/dend/A').n
#bvec=moose.vec('/model/chem/dend/B').n
#source=moose.vec('/model/chem/dend/S').n
storeAvec = []
numSteps = 2500
time = 0
t1 = 20
t2 = 25
maxs = 0.05
space = moose.vec('/model/chem/dend/space').n
# print 'coordinates are', space, np.cos(np.pi)
for i in range(0, numSteps):
#if t<20:
# source = maxs/2
#elif t > 20 and t < 25:
# s = (maxs/4)*(1+np.cos(np.pi*(t-t1)/(t2-t1)))
#else:
# s = 0
avec = moose.vec('/model/chem/dend/A').conc
#print moose.vec('/model/chem/dend/S').n
bvec = moose.vec('/model/chem/dend/B').conc
source = moose.vec('/model/chem/dend/S').conc
space = moose.vec('/model/chem/dend/space').conc
moose.start(dtSol)
storeAvec.append(avec)
time = time + dtSol
print time
#plt.ion()
#fig = plt.figure(figsize=(6,6))
trialNum = '1'
fileName = 'Mori.xml'
writeXML(storeAvec, trialNum, fileName)
plt.plot(avec)
plt.show()
raw_input()
print 'press any key to exit'
return bvec, avec, source, space, storeAvec
def makeNeuroMeshModel():
makeSpinyCompt()
diffLength = moose.element('/n/compt').length
diffLength = diffLength / 10.0
elec = moose.element('/n')
elec.name = 'elec'
model = moose.Neutral('/model')
moose.move(elec, model)
synInput = moose.element('/model/elec/compt/synInput')
synInput.refractT = 47e-3
chem = moose.Neutral('/model/chem')
neuroCompt = moose.NeuroMesh('/model/chem/neuroMesh')
neuroCompt.separateSpines = 1
neuroCompt.diffLength = diffLength
neuroCompt.geometryPolicy = 'cylinder'
spineCompt = moose.SpineMesh('/model/chem/spineMesh')
moose.connect(neuroCompt, 'spineListOut', spineCompt, 'spineList',
'OneToOne')
psdCompt = moose.PsdMesh('/model/chem/psdMesh')
moose.connect(neuroCompt, 'psdListOut', psdCompt, 'psdList', 'OneToOne')
createChemModel(neuroCompt, spineCompt, psdCompt)
# Put in the solvers, see how they fare.
nmksolve = moose.GslStoich('/model/chem/neuroMesh/ksolve')
nmksolve.path = '/model/chem/neuroMesh/##'
nmksolve.compartment = moose.element('/model/chem/neuroMesh')
nmksolve.method = 'rk5'
nm = moose.element('/model/chem/neuroMesh/mesh')
moose.connect(nm, 'remesh', nmksolve, 'remesh')
#print "neuron: nv=", nmksolve.numLocalVoxels, ", nav=", nmksolve.numAllVoxels, nmksolve.numVarPools, nmksolve.numAllPools
#print 'setting up smksolve'
smksolve = moose.GslStoich('/model/chem/spineMesh/ksolve')
smksolve.path = '/model/chem/spineMesh/##'
smksolve.compartment = moose.element('/model/chem/spineMesh')
smksolve.method = 'rk5'
sm = moose.element('/model/chem/spineMesh/mesh')
moose.connect(sm, 'remesh', smksolve, 'remesh')
#print "spine: nv=", smksolve.numLocalVoxels, ", nav=", smksolve.numAllVoxels, smksolve.numVarPools, smksolve.numAllPools
#
#print 'setting up pmksolve'
pmksolve = moose.GslStoich('/model/chem/psdMesh/ksolve')
pmksolve.path = '/model/chem/psdMesh/##'
pmksolve.compartment = moose.element('/model/chem/psdMesh')
pmksolve.method = 'rk5'
pm = moose.element('/model/chem/psdMesh/mesh')
moose.connect(pm, 'remesh', pmksolve, 'remesh')
#print "psd: nv=", pmksolve.numLocalVoxels, ", nav=", pmksolve.numAllVoxels, pmksolve.numVarPools, pmksolve.numAllPools
#
#print 'Assigning the cell model'
# Now to set up the model.
neuroCompt.cell = elec
ns = neuroCompt.numSegments
#assert( ns == 11 ) # dend, 5x (shaft+head)
ndc = neuroCompt.numDiffCompts
assert (ndc == 10)
ndc = neuroCompt.mesh.num
assert (ndc == 10)
sdc = spineCompt.mesh.num
assert (sdc == 5)
pdc = psdCompt.mesh.num
assert (pdc == 5)
#
# We need to use the spine solver as the master for the purposes of
# these calculations. This will handle the diffusion calculations
# between head and dendrite, and between head and PSD.
smksolve.addJunction(nmksolve)
#print "spine: nv=", smksolve.numLocalVoxels, ", nav=", smksolve.numAllVoxels, smksolve.numVarPools, smksolve.numAllPools
smksolve.addJunction(pmksolve)
#print "psd: nv=", pmksolve.numLocalVoxels, ", nav=", pmksolve.numAllVoxels, pmksolve.numVarPools, pmksolve.numAllPools
# Have to pass a message between the various solvers.
foo = moose.vec('/model/chem/spineMesh/headGluR')
# oddly, numLocalFields does not work.
ca = moose.element('/model/chem/neuroMesh/Ca')
assert (ca.lastDimension == ndc)
moose.vec('/model/chem/spineMesh/headGluR').nInit = 100
moose.vec('/model/chem/psdMesh/psdGluR').nInit = 0
# set up adaptors
aCa = moose.Adaptor('/model/chem/spineMesh/adaptCa', 5)
adaptCa = moose.vec('/model/chem/spineMesh/adaptCa')
chemCa = moose.vec('/model/chem/spineMesh/Ca')
assert (len(adaptCa) == 5)
for i in range(5):
path = '/model/elec/head' + str(i) + '/ca'
elecCa = moose.element(path)
moose.connect(elecCa, 'concOut', adaptCa[i], 'input', 'Single')
moose.connect(adaptCa, 'outputSrc', chemCa, 'setConc', 'OneToOne')
adaptCa.outputOffset = 0.0001 # 100 nM offset in chem.
adaptCa.scale = 0.05 # 0.06 to 0.003 mM
aGluR = moose.Adaptor('/model/chem/psdMesh/adaptGluR', 5)
adaptGluR = moose.vec('/model/chem/psdMesh/adaptGluR')
chemR = moose.vec('/model/chem/psdMesh/psdGluR')
assert (len(adaptGluR) == 5)
for i in range(5):
path = '/model/elec/head' + str(i) + '/gluR'
elecR = moose.element(path)
moose.connect(adaptGluR[i], 'outputSrc', elecR, 'setGbar', 'Single')
#moose.connect( chemR, 'nOut', adaptGluR, 'input', 'OneToOne' )
# Ksolve isn't sending nOut. Not good. So have to use requestOut.
moose.connect(adaptGluR, 'requestOut', chemR, 'getN', 'OneToOne')
adaptGluR.outputOffset = 1e-7 # pS
adaptGluR.scale = 1e-6 / 100 # from n to pS
adaptK = moose.Adaptor('/model/chem/neuroMesh/adaptK')
chemK = moose.element('/model/chem/neuroMesh/kChan')
elecK = moose.element('/model/elec/compt/K')
moose.connect(adaptK, 'requestOut', chemK, 'getConc', 'OneToAll')
moose.connect(adaptK, 'outputSrc', elecK, 'setGbar', 'Single')
adaptK.scale = 0.3 # from mM to Siemens
"""
def makeModel():
# create container for model
num = 1 # number of compartments
model = moose.Neutral('/model')
compartment = moose.CylMesh('/model/compartment')
compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
# create molecules and reactions
s = moose.Pool('/model/compartment/s')
rXfer = moose.Reac('/model/compartment/rXfer')
#####################################################################
# Put in endo compartment. Add molecule s
endo = moose.EndoMesh('/model/endo')
endo.isMembraneBound = True
endo.surround = compartment
es = moose.Pool('/model/endo/s')
erXfer = moose.Reac('/model/compartment/erXfer')
#####################################################################
moose.connect(erXfer, 'sub', es, 'reac')
moose.connect(erXfer, 'prd', s, 'reac')
moose.connect(rXfer, 'sub', s, 'reac')
moose.connect(rXfer, 'prd', es, 'reac')
rXfer.Kf = 0.04 # 0.04/sec
rXfer.Kb = 0.0 # 0.02/sec
erXfer.Kf = 0.02 # 0.04/sec
erXfer.Kb = 0.0 # 0.02/sec
#####################################################################
fixXreacs.fixXreacs('/model')
fixXreacs.restoreXreacs('/model')
fixXreacs.fixXreacs('/model')
#####################################################################
rx = moose.element('/model/compartment/rXfer')
erx = moose.element('/model/compartment/erXfer')
# Make solvers
ksolve = moose.Ksolve('/model/compartment/ksolve')
dsolve = moose.Dsolve('/model/dsolve')
eksolve = moose.Ksolve('/model/endo/ksolve')
edsolve = moose.Dsolve('/model/endo/dsolve')
stoich = moose.Stoich('/model/compartment/stoich')
stoich.compartment = compartment
stoich.ksolve = ksolve
stoich.dsolve = dsolve
stoich.path = "/model/compartment/##"
assert (dsolve.numPools == 2)
s.vec.concInit = [1] * num
estoich = moose.Stoich('/model/endo/stoich')
estoich.compartment = endo
estoich.ksolve = eksolve
estoich.dsolve = edsolve
estoich.path = "/model/endo/##"
assert (edsolve.numPools == 1)
edsolve.buildMeshJunctions(dsolve)
plot1 = moose.Table2('/model/plot1')
plot2 = moose.Table2('/model/plot2')
moose.connect('/model/plot1', 'requestOut', s, 'getN')
moose.connect('/model/plot2', 'requestOut', es, 'getN')
plot3 = moose.Table2('/model/plot3')
plot4 = moose.Table2('/model/plot4')
moose.connect('/model/plot3', 'requestOut', s, 'getConc')
moose.connect('/model/plot4', 'requestOut', es, 'getConc')
def addOneChan(chanpath, gbar,comp):
SA = np.pi * comp.length * comp.diameter
proto = moose.element('/library/' + chanpath)
chan = moose.copy(proto, comp, chanpath)
chan.Gbar = gbar * SA
# If we are using GHK AND it is a calcium channel, connect it to GHK
moose.connect(comp, 'VmOut', chan, 'Vm')
moose.connect(chan, "channelOut", comp, "handleChannel")
return chan
if __name__ == '__main__':
lib = moose.Neutral('/library')
for tick in range(0, 7):
moose.setClock(tick, dt)
moose.setClock(8, 0.005) # set output clock
model = moose.Neutral('/model')
dend = moose.Compartment('/model/dend')
pulse = moose.PulseGen('/model/pulse')
data = moose.Neutral('/data')
vmtab = moose.Table('/data/dend_Vm')
gktab = moose.Table('/data/CaT_Gk')
iktab = moose.Table('/data/CaT_Ik')
dend.Cm = Cm
dend.Rm = Rm
dend.Em = Em
dend.initVm = Vm_0
def set_compartment_param(self, compartment, name, value, mechanismname):
""" Set the param for the compartment depending on name and mechanismname. """
if name == 'CM':
compartment.Cm = value * math.pi * compartment.diameter * compartment.length
elif name == 'RM':
compartment.Rm = value / (math.pi * compartment.diameter *
compartment.length)
elif name == 'RA':
compartment.Ra = value * compartment.length / (
math.pi * (compartment.diameter / 2.0)**2)
elif name == 'Em':
compartment.Em = value
elif name == 'initVm':
compartment.initVm = value
elif name == 'inject':
# this reader converts to SI
pu.info("Comparment %s inject %s A." % (compartment.name, value))
compartment.inject = value
elif name == 'v_reset':
compartment.vReset = value # compartment is a moose.LIF instance (intfire)
elif name == 'threshold':
compartment.thresh = value # compartment is a moose.LIF instance (intfire)
elif name == 't_refrac':
compartment.refractoryPeriod = value # compartment is a moose.LIF instance (intfire)
elif name == 'g_refrac':
pu.info("SORRY, current moose.LIF doesn't support g_refrac.")
elif mechanismname is 'synapse': # synapse being added to the compartment
## these are potential locations, we do not actually make synapses,
## unless the user has explicitly asked for it
if self.createPotentialSynapses:
syn_name = value
if not moose.exists(compartment.path + '/' + syn_name):
make_new_synapse(syn_name, compartment, syn_name,
self.nml_params)
## I assume below that compartment name has _segid at its end
segid = string.split(
compartment.name,
'_')[-1] # get segment id from compartment name
self.segDict[segid][5].append(value)
elif mechanismname is 'spikegen': # spikegen being added to the compartment
## these are potential locations, we do not actually make the spikegens.
## spikegens for different synapses can have different thresholds,
## hence include synapse_type in its name
## value contains name of synapse i.e. synapse_type
#spikegen = moose.SpikeGen(compartment.path+'/'+value+'_spikegen')
#moose.connect(compartment,"VmSrc",spikegen,"Vm")
pass
## previous were mechanism that don't need a ChannelML definition
## including integrate_and_fire (I ignore the ChannelML definition)
## thus integrate_and_fire mechanism default values cannot be used
## i.e. nothing needed in /library, but below mechanisms need.
elif mechanismname is not None:
## if mechanism is not present in compartment, deep copy from library
## all mechanisms have been loaded into the library earlier
if not moose.exists(compartment.path + '/' + mechanismname):
neutralObj = moose.element(
"/library/" + mechanismname) # gives error if not present
if 'CaConc' == neutralObj.className: # Ion concentration pool
libcaconc = moose.CaConc("/library/" + mechanismname)
## deep copies the library caconc under the compartment
caconc = moose.copy(libcaconc, compartment, mechanismname)
caconc = moose.CaConc(caconc)
## CaConc connections are made later using connect_CaConc()
## Later, when calling connect_CaConc,
## B is set for caconc based on thickness of Ca shell and compartment l and dia
## OR based on the Mstring phi under CaConc path.
channel = None
elif 'HHChannel2D' == neutralObj.className: ## HHChannel2D
libchannel = moose.HHChannel2D("/library/" + mechanismname)
## deep copies the library channel under the compartment
channel = moose.copy(libchannel, compartment,
mechanismname)
channel = moose.HHChannel2D(channel)
moose.connect(channel, 'channel', compartment, 'channel')
elif 'HHChannel' == neutralObj.className: ## HHChannel
libchannel = moose.HHChannel("/library/" + mechanismname)
## deep copies the library channel under the compartment
channel = moose.copy(libchannel, compartment,
mechanismname)
channel = moose.HHChannel(channel)
moose.connect(channel, 'channel', compartment, 'channel')
## if mechanism is present in compartment, just wrap it
else:
neutralObj = moose.Neutral(compartment.path + '/' +
mechanismname)
if 'CaConc' == neutralObj.className: # Ion concentration pool
caconc = moose.CaConc(
compartment.path + '/' +
mechanismname) # wraps existing channel
channel = None
elif 'HHChannel2D' == neutralObj.className: ## HHChannel2D
channel = moose.HHChannel2D(
compartment.path + '/' +
mechanismname) # wraps existing channel
elif 'HHChannel' == neutralObj.className: ## HHChannel
channel = moose.HHChannel(
compartment.path + '/' +
mechanismname) # wraps existing channel
if name == 'Gbar':
if channel is None: # if CaConc, neuroConstruct uses gbar for thickness or phi
## If child Mstring 'phi' is present, set gbar as phi
## BUT, value has been multiplied by Gfactor as a Gbar,
## SI or physiological not known here,
## ignoring Gbar for CaConc, instead of passing units here
child = moose_utils.get_child_Mstring(caconc, 'phi')
if child is not None:
#child.value = value
pass
else:
#caconc.thick = value
pass
else: # if ion channel, usual Gbar
channel.Gbar = value * math.pi * compartment.diameter * compartment.length
elif name == 'Ek':
channel.Ek = value
elif name == 'thick': # thick seems to be NEURON's extension to NeuroML level 2.
caconc.thick = value ## JUST THIS WILL NOT DO - HAVE TO SET B based on this thick!
## Later, when calling connect_CaConc,
## B is set for caconc based on thickness of Ca shell and compartment l and dia.
## OR based on the Mstring phi under CaConc path.
if neuroml_utils.neuroml_debug:
pu.info("Setting %s for comparment %s to %s" %
(name, compartment.path, value))
def main():
"""
This example illustrates loading a model from an SWC file, inserting
spines, and viewing it.
"""
PI = 3.14159265358979
frameRunTime = 0.0002
runtime = 1.0
inject = 5e-10
simdt = 5e-5
RM = 1.0
RA = 1.0
CM = 0.01
spineSpacing = 2.0e-6
minSpacing = 0.2e-6
spineSize = 1.0
spineSizeDistrib = 0.5
spineAngle = 0
spineAngleDistrib = 2 * PI
app = QtGui.QApplication(sys.argv)
filename = 'barrionuevo_cell1zr.CNG.swc'
#filename = 'h10.CNG.swc'
moose.Neutral('/library')
rdes = rd.rdesigneur( \
cellProto = [[ filename, 'elec' ] ],\
spineProto = [['makeSpineProto()', 'spine' ]] ,\
spineDistrib = [ \
['spine', '#apical#', \
'spacing', str( spineSpacing ), \
'spacingDistrib', str( minSpacing ), \
'angle', str( spineAngle ), \
'angleDistrib', str( spineAngleDistrib ), \
'size', str( spineSize ), \
'sizeDistrib', str( spineSizeDistrib ) ] \
] \
)
rdes.buildModel('/model')
moose.reinit()
# Now we set up the display
compts = moose.wildcardFind("/model/elec/#[ISA=CompartmentBase]")
compts[0].inject = inject
ecomptPath = [x.path for x in compts]
morphology = moogli.extensions.moose.read(path="/model/elec", vertices=15)
#morphology = moogli.read_morphology_from_moose(name = "", path = "/model/elec")
#morphology.create_group( "group_all", ecomptPath, -0.08, 0.02, \
# [0.0, 0.5, 1.0, 1.0], [1.0, 0.0, 0.0, 0.9] )
#morphology.create_group( "group_all", ecomptPath, -0.08, 0.02, gnuplot )
#viewer = moogli.DynamicMorphologyViewerWidget(morphology)
viewer = moogli.Viewer("Viewer")
viewer.attach_shapes(morphology.shapes.values())
view = moogli.View("main-view")
viewer.attach_view(view)
#viewer.set_background_color( 1.0, 1.0, 1.0, 1.0 )
def callback(morphology, viewer):
moose.start(frameRunTime)
Vm = [moose.element(x).Vm for x in compts]
morphology.set_color("group_all", Vm)
currTime = moose.element('/clock').currentTime
#print currTime, compts[0].Vm
if (currTime < runtime):
return True
return False
#viewer.set_callback( callback, idletime = 0 )
#viewer.showMaximized()
viewer.show()
app.exec_()
def test_function_chemsys():
moose.Neutral('/library')
moose.Neutral('/model')
run()
print('All done')
def makeModel():
model = moose.Neutral('/model')
# Make neuronal model. It has no channels, just for geometry
cell = moose.loadModel('./spinyNeuron.p', '/model/cell', 'Neutral')
# We don't want the cell to do any calculations. Disable everything.
for i in moose.wildcardFind('/model/cell/##'):
i.tick = -1
diffConst = 0.0
# create container for model
model = moose.element('/model')
chem = moose.Neutral('/model/chem')
# The naming of the compartments is dicated by the places that the
# chem model expects to be loaded.
compt0 = moose.NeuroMesh('/model/chem/compt0')
compt0.separateSpines = 1
compt0.geometryPolicy = 'cylinder'
compt1 = moose.SpineMesh('/model/chem/compt1')
moose.connect(compt0, 'spineListOut', compt1, 'spineList', 'OneToOne')
compt2 = moose.PsdMesh('/model/chem/compt2')
moose.connect(compt0, 'psdListOut', compt2, 'psdList', 'OneToOne')
#reacSystem = moose.loadModel( 'simpleOsc.g', '/model/chem', 'ee' )
makeChemModel(compt0) # Populate all 3 compts with the chem system.
makeChemModel(compt1)
makeChemModel(compt2)
compt0.diffLength = 2e-6 # This will be over 100 compartments.
# This is the magic command that configures the diffusion compartments.
compt0.subTreePath = cell.path + "/#"
moose.showfields(compt0)
# Build the solvers. No need for diffusion in this version.
ksolve0 = moose.Ksolve('/model/chem/compt0/ksolve')
ksolve1 = moose.Ksolve('/model/chem/compt1/ksolve')
ksolve2 = moose.Ksolve('/model/chem/compt2/ksolve')
dsolve0 = moose.Dsolve('/model/chem/compt0/dsolve')
dsolve1 = moose.Dsolve('/model/chem/compt1/dsolve')
dsolve2 = moose.Dsolve('/model/chem/compt2/dsolve')
stoich0 = moose.Stoich('/model/chem/compt0/stoich')
stoich1 = moose.Stoich('/model/chem/compt1/stoich')
stoich2 = moose.Stoich('/model/chem/compt2/stoich')
# Configure solvers
stoich0.compartment = compt0
stoich1.compartment = compt1
stoich2.compartment = compt2
stoich0.ksolve = ksolve0
stoich1.ksolve = ksolve1
stoich2.ksolve = ksolve2
stoich0.dsolve = dsolve0
stoich1.dsolve = dsolve1
stoich2.dsolve = dsolve2
stoich0.path = '/model/chem/compt0/#'
stoich1.path = '/model/chem/compt1/#'
stoich2.path = '/model/chem/compt2/#'
assert (stoich0.numVarPools == 3)
assert (stoich0.numProxyPools == 0)
assert (stoich0.numRates == 4)
assert (stoich1.numVarPools == 3)
assert (stoich1.numProxyPools == 0)
assert (stoich1.numRates == 4)
assert (stoich2.numVarPools == 3)
assert (stoich2.numProxyPools == 0)
assert (stoich2.numRates == 4)
dsolve0.buildNeuroMeshJunctions(dsolve1, dsolve2)
stoich0.buildXreacs(stoich1)
stoich1.buildXreacs(stoich2)
stoich0.filterXreacs()
stoich1.filterXreacs()
stoich2.filterXreacs()
moose.element('/model/chem/compt2/a[0]').concInit *= 1.5
# Create the output tables
num = compt0.numDiffCompts - 1
graphs = moose.Neutral('/model/graphs')
moose.le('/model/chem/compt1')
a = moose.element('/model/chem/compt1')
print((a.voxelVolume))
makeTab('a_soma', '/model/chem/compt0/a[0]')
makeTab('b_soma', '/model/chem/compt0/b[0]')
makeTab('a_apical', '/model/chem/compt0/a[' + str(num) + ']')
makeTab('b_apical', '/model/chem/compt0/b[' + str(num) + ']')
makeTab('a_spine', '/model/chem/compt1/a[5]')
makeTab('b_spine', '/model/chem/compt1/b[5]')
makeTab('a_psd', '/model/chem/compt2/a[5]')
makeTab('b_psd', '/model/chem/compt2/b[5]')
import moose
from pylab import *
from moose.utils import *
import numpy as np
inputGiven = 1
moose.Neutral('/elec')
pg = moose.PulseGen('/elec/inPulGen')
pgTable = moose.Table('/elec/inPulGen/pgTable')
moose.connect(pgTable, 'requestOut', pg, 'getOutputValue')
pg.firstDelay = 10e-3
pg.firstWidth = 2e-03
pg.firstLevel = 3
pg.secondDelay = 1.0
cellPath = '/cell'
# cell = moose.LeakyIaF(cellPath)
# cell.setField('Cm',1e-6)
# cell.setField('Rm',1e4)
# cell.setField('Em',-0.07)
# cell.setField('initVm',-0.05)
# cell.setField('Vreset',-0.07)
# cell.setField('Vthreshold',0.0)
# cell.setField('refractoryPeriod',0.01)
cell = moose.IntFire(cellPath)
cell.setField('tau', 10e-3)
#cell.setField('Vm', 1.0)
cell.setField('refractoryPeriod', 5e-3)
def set_compartment_param(self, compartment, name, value, mechName):
""" Set the param for the compartment depending on name and mechName. """
if name == 'CM':
compartment.Cm = value * math.pi * compartment.diameter * compartment.length
elif name == 'RM':
compartment.Rm = value / (math.pi * compartment.diameter *
compartment.length)
elif name == 'RA':
compartment.Ra = value * compartment.length / \
(math.pi*(compartment.diameter/2.0)**2)
elif name == 'Em':
compartment.Em = value
elif name == 'initVm':
compartment.initVm = value
elif name == 'inject':
msg = " {0} inject {1} A.".format(compartment.name, value)
debug.printDebug("INFO", msg)
compartment.inject = value
elif mechName is 'synapse':
# synapse being added to the compartment
# these are potential locations, we do not actually make synapses.
# I assume below that compartment name has _segid at its end
# get segment id from compartment name
segid = moose_methods.getCompartmentId(compartment.name)
self.segDict[segid][5].append(value)
# spikegen being added to the compartment
elif mechName is 'spikegen':
# these are potential locations, we do not actually make the
# spikegens. spikegens for different synapses can have different
# thresholds, hence include synapse_type in its name value contains
# name of synapse i.e. synapse_type
#spikegen = moose.SpikeGen(compartment.path+'/'+value+'_spikegen')
#moose.connect(compartment,"VmSrc",spikegen,"Vm")
pass
elif mechName is not None:
# if mechanism is not present in compartment, deep copy from library
if not moose.exists(compartment.path + '/' + mechName):
# if channel does not exist in library load it from xml file
if not moose.exists(self.libraryPath + "/" + mechName):
cmlR = ChannelML(self.nml_params)
model_filename = mechName + '.xml'
model_path = neuroml_utils.find_first_file(
model_filename, self.model_dir)
if model_path is not None:
cmlR.readChannelMLFromFile(model_path)
else:
msg = 'Mechanism {0}: files {1} not found under {2}'\
.format( mechName
, model_filename
, self.model_dir
)
debug.printDebug("ERROR",
msg,
frame=inspect.currentframe())
sys.exit(0)
neutralObj = moose.Neutral(self.libraryPath + "/" + mechName)
# Ion concentration pool
if 'CaConc' == neutralObj.className:
libcaconc = moose.CaConc(self.libraryPath + "/" + mechName)
# deep copies the library caconc under the compartment
caconc = moose.copy(libcaconc, compartment, mechName)
caconc = moose.CaConc(caconc)
# CaConc connections are made later using connect_CaConc()
# Later, when calling connect_CaConc, B is set for caconc
# based on thickness of Ca shell and compartment l and dia
# OR based on the Mstring phi under CaConc path.
channel = None
elif 'HHChannel2D' == neutralObj.className: ## HHChannel2D
libchannel = moose.HHChannel2D(self.libraryPath + "/" +
mechName)
## deep copies the library channel under the compartment
channel = moose.copy(libchannel, compartment, mechName)
channel = moose.HHChannel2D(channel)
moose.connect(channel, 'channel', compartment, 'channel')
elif 'HHChannel' == neutralObj.className: ## HHChannel
libchannel = moose.HHChannel(self.libraryPath + "/" +
mechName)
# deep copies the library channel under the compartment
channel = moose.copy(libchannel, compartment, mechName)
channel = moose.HHChannel(channel)
moose.connect(channel, 'channel', compartment, 'channel')
# if mechanism is present in compartment, just wrap it
else:
neutralObj = moose.Neutral(compartment.path + '/' + mechName)
# Ion concentration pool
if 'CaConc' == neutralObj.className:
# wraps existing channel
caconc = moose.CaConc(compartment.path + '/' + mechName)
channel = None
elif 'HHChannel2D' == neutralObj.className: ## HHChannel2D
# wraps existing channel
channel = moose.HHChannel2D(compartment.path + '/' +
mechName)
elif 'HHChannel' == neutralObj.className: ## HHChannel
# wraps existing channel
channel = moose.HHChannel(compartment.path + '/' +
mechName)
if name == 'Gbar':
# if CaConc, neuroConstruct uses gbar for thickness or phi
if channel is None:
# If child Mstring 'phi' is present, set gbar as phi BUT,
# value has been multiplied by Gfactor as a Gbar, SI or
# physiological not known here, ignoring Gbar for CaConc,
# instead of passing units here
child = moose_utils.get_child_Mstring(caconc, 'phi')
if child is not None:
#child.value = value
pass
else:
#caconc.thick = value
pass
else: # if ion channel, usual Gbar
channel.Gbar = value * math.pi * compartment.diameter \
* compartment.length
elif name == 'Ek':
channel.Ek = value
# thick seems to be NEURON's extension to NeuroML level 2.
elif name == 'thick':
# JUST THIS WILL NOT DO - HAVE TO SET B based on this thick!
caconc.thick = value
# Later, when calling connect_CaConc, B is set for caconc based
# on thickness of Ca shell and compartment l and dia. OR based
# on the Mstring phi under CaConc path.
if neuroml_utils.neuroml_debug:
msg = "Setting {0} for {1} value {2}".format(
name, compartment.path, value)
debug.printDebug("DEBUG", msg, frame=inspect.currentframe())
def makeElecPlots():
graphs = moose.Neutral('/graphs')
elec = moose.Neutral('/graphs/elec')
addPlot('/model/elec/soma', 'getVm', 'elec/somaVm')
addPlot('/model/elec/spine_head', 'getVm', 'elec/spineVm')
addPlot('/model/elec/soma/Ca_conc', 'getCa', 'elec/somaCa')
def main():
library = moose.Neutral('/library')
#makePassiveSoma( 'cell', params['dendL'], params['dendDia'] )
makeDendProto()
makeChemProto()
rdes = rd.rdesigneur(
turnOffElec=True,
chemPlotDt=0.1,
diffusionLength=params['diffusionL'],
#cellProto=[['cell','soma']],
cellProto=[['elec', 'dend']],
chemProto=[['hydra', 'hydra']],
chemDistrib=[['hydra', '#soma#,#dend#', 'install', '1']],
plotList=[['soma', '1', 'dend/A', 'n', '# of A'],
['soma', '1', 'dend/B', 'n', '# of B'],
['soma', '1', 'dend/C', 'n', '# of C'],
['soma', '1', 'dend/D', 'n', '# of D'],
['soma', '1', 'dend/E', 'n', '# of E'],
['soma', '1', 'dend/F', 'n', '# of F']],
# moogList = [['soma', '1', 'dend/A', 'n', 'num of A (number)']]
)
moose.le('/library')
moose.le('/library/hydra')
#moose.showfield( '/library/soma/soma' )
rdes.buildModel()
#moose.element('/model/chem/dend/B').vec[50].nInit=15.5
A = moose.element('/model/chem/dend/A')
B = moose.element('/model/chem/dend/B')
C = moose.element('/model/chem/dend/C')
D = moose.element('/model/chem/dend/D')
E = moose.element('/model/chem/dend/E')
F = moose.element('/model/chem/dend/F')
Z1 = moose.element('/model/chem/dend/Z1')
Z2 = moose.element('/model/chem/dend/Z2')
A.diffConst = 1e-13
B.diffConst = 1e-13
C.diffConst = 1e-13
D.diffConst = 1e-13
E.diffConst = 1e-13
F.diffConst = 1e-13
Z1.diffConst = 0
Z2.diffConst = 0
#moose.element('/model/chem/dend/Z1').vec.nInit = 0
moose.element('/model/chem/dend/Z1').vec.nInit = 1
#moose.element('/model/chem/dend/Z2').vec.nInit = 0
moose.element('/model/chem/dend/Z2').vec.nInit = 1
#for i in range(50,55):
# moose.element('/model/chem/dend/Z1').vec[i].nInit = 1
# moose.element('/model/chem/dend/Z2').vec[i].nInit = 1
moose.element('/model/chem/dend/A').vec[20].nInit = 1
moose.element('/model/chem/dend/B').vec[20].nInit = 1
moose.element('/model/chem/dend/C').vec[20].nInit = 1
#moose.element('/model/chem/dend/D').vec[30].nInit=2
#moose.element('/model/chem/dend/E').vec[30].nInit=2
#moose.element('/model/chem/dend/F').vec[30].nInit=2
moose.element('/model/chem/dend/D').vec[60].nInit = 1
moose.element('/model/chem/dend/E').vec[60].nInit = 1
moose.element('/model/chem/dend/F').vec[60].nInit = 1
#moose.element('/model/chem/dend/A').vec[120].nInit=1
#moose.element('/model/chem/dend/B').vec[120].nInit=1
#moose.element('/model/chem/dend/C').vec[120].nInit=1
#moose.element('/model/chem/dend/D').vec[160].nInit=1
#moose.element('/model/chem/dend/E').vec[160].nInit=1
#moose.element('/model/chem/dend/F').vec[160].nInit=1
storeAvec = []
storeBvec = []
storeCvec = []
storeDvec = []
storeEvec = []
storeFvec = []
moose.reinit()
for i in range(1, 5000, 10):
moose.start(10)
avec = moose.vec('/model/chem/dend/A').n
bvec = moose.vec('/model/chem/dend/B').n
cvec = moose.vec('/model/chem/dend/C').n
dvec = moose.vec('/model/chem/dend/D').n
evec = moose.vec('/model/chem/dend/E').n
fvec = moose.vec('/model/chem/dend/F').n
storeAvec.append(avec)
storeBvec.append(bvec)
storeCvec.append(cvec)
storeDvec.append(dvec)
storeEvec.append(evec)
storeFvec.append(fvec)
return storeAvec, storeBvec, storeCvec, storeDvec, storeEvec, storeFvec