def makeChemProto(name):
chem = moose.Neutral('/library/' + name)
comptVol = diffLen * dendDia * dendDia * PI / 4.0
for i in (['dend', comptVol], ['spine', 1e-19], ['psd', 1e-20]):
print(('making ', i))
compt = moose.CubeMesh(chem.path + '/' + i[0])
compt.volume = i[1]
z = moose.Pool(compt.path + '/z')
z.concInit = 0.0
z.diffConst = diffConst
nInit = comptVol * 6e23 * concInit
nstr = str(1 / nInit)
x = moose.Pool(chem.path + '/dend/x')
x.diffConst = diffConst
func = moose.Function(x.path + '/func')
func.expr = "-x0 * (0.3 - " + nstr + " * x0) * ( 1 - " + nstr + " * x0)"
print((func.expr))
func.x.num = 1
moose.connect(x, 'nOut', func.x[0], 'input')
moose.connect(func, 'valueOut', x, 'increment')
z = moose.element('/library/' + name + '/dend/z')
reac = moose.Reac('/library/' + name + '/dend/reac')
reac.Kf = 1
reac.Kb = 10
moose.connect(reac, 'sub', x, 'reac')
moose.connect(reac, 'prd', z, 'reac')
def showVisualization():
makeModel()
elec = moose.element('/model/elec')
elec.setSpineAndPsdMesh(moose.element('/model/chem/spine'),
moose.element('/model/chem/psd'))
eHead = moose.wildcardFind('/model/elec/#head#')
oldDia = [i.diameter for i in eHead]
graphs = moose.Neutral('/graphs')
#makePlot( 'psd_x', moose.vec( '/model/chem/psd/x' ), 'getN' )
#makePlot( 'head_x', moose.vec( '/model/chem/spine/x' ), 'getN' )
makePlot('dend_x', moose.vec('/model/chem/dend/x'), 'getN')
dendZ = makePlot('dend_z', moose.vec('/model/chem/dend/z'), 'getN')
makePlot('head_z', moose.vec('/model/chem/spine/z'), 'getN')
psdZ = makePlot('psd_z', moose.vec('/model/chem/psd/z'), 'getN')
diaTab = makePlot('headDia', eHead, 'getDiameter')
dendrite = moose.element("/model/elec/dend")
dendrites = [dendrite.path + "/" + str(i) for i in range(len(dendZ))]
moose.reinit()
spineHeads = moose.wildcardFind('/model/elec/#head#')
if doMoo:
app = QtGui.QApplication(sys.argv)
viewer = create_viewer("/model/elec", dendrite, dendZ, diaTab, psdZ)
viewer.showMaximized()
viewer.start()
return app.exec_()
def makeModel():
moose.Neutral('/library')
makeCellProto('cellProto')
makeChemProto('cProto')
rdes = rd.rdesigneur(
useGssa=False,
turnOffElec=True,
chemDt=0.1,
diffDt=0.1,
combineSegments=False,
stealCellFromLibrary=True,
diffusionLength=1e-6,
cellProto=[['cellProto', 'elec']],
spineProto=[['makePassiveSpine()', 'spine']],
chemProto=[['cProto', 'chem']],
spineDistrib=[[
'spine', '#',
str(spineSpacing),
str(spineSpacingDistrib),
str(spineSize),
str(spineSizeDistrib),
str(spineAngle),
str(spineAngleDistrib)
]],
chemDistrib=[["chem", "#dend#,#psd#", "install", "1"]],
adaptorList=[
['psd/z', 'n', 'spine', 'psdArea', 50.0e-15, 500e-15],
])
moose.seed(1234)
rdes.buildModel('/model')
print('built model')
x = moose.vec('/model/chem/dend/x')
x.concInit = 0.0
for i in range(0, 20):
x[i].concInit = concInit
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.
In this simulation there is a propagating reaction wave using a
highly abstracted equation, whose product diffuses into the spines and
makes them bigger.
"""
makeModel()
elec = moose.element('/model/elec')
elec.setSpineAndPsdMesh(moose.element('/model/chem/spine'),
moose.element('/model/chem/psd'))
eHead = moose.wildcardFind('/model/elec/#head#')
oldDia = [i.diameter for i in eHead]
graphs = moose.Neutral('/graphs')
#makePlot( 'psd_x', moose.vec( '/model/chem/psd/x' ), 'getN' )
#makePlot( 'head_x', moose.vec( '/model/chem/spine/x' ), 'getN' )
makePlot('dend_x', moose.vec('/model/chem/dend/x'), 'getN')
makePlot('dend_z', moose.vec('/model/chem/dend/z'), 'getN')
makePlot('head_z', moose.vec('/model/chem/spine/z'), 'getN')
makePlot('psd_z', moose.vec('/model/chem/psd/z'), 'getN')
makePlot('headDia', eHead, 'getDiameter')
'''
debug = moose.PyRun( '/pyrun' )
debug.tick = 10
debug.runString = """print( "RUNNING: ", moose.element( '/model/chem/psd/z').n, moose.element( '/model/elec/head0' ).diameter)"""
'''
moose.reinit()
moose.start(runtime)
displayPlots()
pylab.plot(oldDia, label='old Diameter')
pylab.plot([i.diameter for i in eHead], label='new Diameter')
pylab.legend()
pylab.show()
if doMoo:
app = QtGui.QApplication(sys.argv)
morphology = moogli.read_morphology_from_moose(name="",
path='/model/elec')
widget = moogli.MorphologyViewerWidget(morphology)
widget.show()
return app.exec_()
quit()
