def getComptParent(obj):
k = moose.element(obj)
while not k.isA["CompartmentBase"]:
if k == moose.element("/"):
return k.path
k = moose.element(k.parent)
return k.path
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 interlude2(view):
val = [moose.getField(i, view.mooField, "double") * view.mooScale for i in view.mooObj]
view.mooGroup.set("color", val, view.mapper)
view.yaw(rotation)
if moose.element("/clock").currentTime >= runtime:
view.stop()
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 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()
def interlude(view):
moose.start(moogliDt)
val = [moose.getField(i, view.mooField, "double") * view.mooScale for i in view.mooObj]
# print "LEN = ", len( val ), "field = ", view.mooField
view.mooGroup.set("color", val, view.mapper)
view.yaw(rotation)
# print moogliDt, len( val ), runtime
if moose.element("/clock").currentTime >= runtime:
view.stop()
def interlude(view):
moose.start(frameruntime)
network.groups["spine"].groups["head"].set("radius",
readValues(diaTab),
lambda x: x * 0.5e6)
network.groups["spine"].groups["head"].set("color", readValues(psdZ),
mapper)
chem_compt_group.set("color", readValues(dendZ), mapper)
if moose.element("/clock").currentTime >= runtime:
view.stop()
def makeMoogli(rd, mooObj, moogliEntry, fieldInfo):
mooField = moogliEntry[3]
numMoogli = len(mooObj)
network = moogli.extensions.moose.read(path=rd.elecid.path, vertices=15)
# print len( network.groups["spine"].shapes )
# print len( network.groups["dendrite"].shapes )
# print len( network.groups["soma"].shapes )
# soma = network.groups["soma"].shapes[ '/model/elec/soma']
# print network.groups["soma"].shapes
soma = network.groups["soma"].shapes[rd.elecid.path + "/soma[0]"]
if mooField == "n" or mooField == "conc":
updateGroup = soma.subdivide(numMoogli)
displayObj = mooObj
else:
shell = moose.element("/")
displayObj = [i for i in mooObj if i != shell]
cpa = [getComptParent(i) for i in displayObj]
updateGroup = moogli.Group("update")
updateShapes = [network.shapes[i] for i in cpa]
# print "########### Len( cpa, mooObj ) = ", len( cpa ), len( mooObj ), len( updateShapes )
updateGroup.attach_shapes(updateShapes)
normalizer = moogli.utilities.normalizer(moogliEntry[5], moogliEntry[6], clipleft=True, clipright=True)
colormap = moogli.colors.MatplotlibColorMap(matplotlib.cm.rainbow)
mapper = moogli.utilities.mapper(colormap, normalizer)
viewer = moogli.Viewer("Viewer")
if mooField == "n" or mooField == "conc":
viewer.attach_shapes(updateGroup.shapes.values())
viewer.detach_shape(soma)
else:
viewer.attach_shapes(network.shapes.values())
if len(rd.moogNames) == 0:
view = moogli.View("main-view", prelude=prelude, interlude=interlude, postlude=postlude)
else:
view = moogli.View("main-view", prelude=prelude, interlude=interlude2)
cb = moogli.widgets.ColorBar(
id="cb",
title=fieldInfo[3],
text_color=moogli.colors.BLACK,
position=moogli.geometry.Vec3f(0.975, 0.5, 0.0),
size=moogli.geometry.Vec3f(0.30, 0.05, 0.0),
text_font="/usr/share/fonts/truetype/ubuntu-font-family/Ubuntu-R.ttf",
orientation=math.pi / 2.0,
text_character_size=20,
label_formatting_precision=0,
colormap=moogli.colors.MatplotlibColorMap(matplotlib.cm.rainbow),
color_resolution=100,
scalar_range=moogli.geometry.Vec2f(moogliEntry[5], moogliEntry[6]),
)
view.attach_color_bar(cb)
view.rd = rd
view.mooObj = displayObj
view.mooGroup = updateGroup
view.mooField = mooField
view.mooScale = fieldInfo[2]
view.mapper = mapper
viewer.attach_view(view)
return viewer
