def build3dDisplay(rdes):
print "building 3d Display"
app = QtGui.QApplication(sys.argv)
compts = moose.wildcardFind(rdes.elecid.path + "/#[ISA=CompartmentBase]")
caElements = []
for i in compts:
if moose.exists(i.path + '/Ca_conc'):
caElements.append(moose.element(i.path + '/Ca_conc'))
else:
caElements.append(moose.element('/library/Ca_conc'))
eComptPath = map(lambda x: x.path, compts)
morphology1 = moogli.read_morphology_from_moose( name = "", \
path = rdes.elecid.path )
morphology1.create_group( "group_all", eComptPath, -0.08, 0.02, \
[0.0, 0.0, 1.0, 1.0], [1.0, 1.0, 0.0, 0.1] )
viewer1 = moogli.DynamicMorphologyViewerWidget(morphology1)
def callback1(morphology, viewer1):
moose.start(frameRunTime)
Vm = map(lambda x: moose.element(x).Vm, compts)
morphology.set_color("group_all", Vm)
currTime = moose.element('/clock').currentTime
viewer1.yaw(0.01, 0)
if (currTime < runtime):
deliverStim(currTime)
return True
displayPlots()
return False
viewer1.set_callback(callback1, idletime=0)
viewer1.pitch(PI / 2, 0)
viewer1.zoom(0.4, 0)
viewer1.resize(900, 900)
#viewer1.showMaximized()
viewer1.show()
morphology2 = moogli.read_morphology_from_moose( name = "", \
path = rdes.elecid.path )
morphology2.create_group( "group_all", eComptPath, 0.0, 0.002, \
[1.0, 0.0, 0.0, 1.0], [0.0, 1.0, 1.0, 0.1] )
viewer2 = moogli.DynamicMorphologyViewerWidget(morphology2)
def callback2(morphology, viewer2):
Ca = map(lambda x: moose.element(x).Ca, caElements)
morphology.set_color("group_all", Ca)
viewer2.yaw(0.01, 0)
return True
viewer2.set_callback(callback2, idletime=0)
viewer2.pitch(PI / 2, 0)
viewer2.zoom(0.4, 0)
viewer2.resize(900, 900)
#viewer1.showMaximized()
viewer2.show()
app.exec_()
def main():
numpy.random.seed(1234)
rdes = buildRdesigneur()
rdes.buildModel('/model')
assert (moose.exists('/model'))
moose.element('/model/elec/hsolve').tick = -1
for i in range(0, 10):
moose.setClock(i, 100)
for i in range(10, 18):
moose.setClock(i, dt)
moose.setClock(18, plotdt)
moose.reinit()
buildPlots()
# Run for baseline, tetanus, and post-tetanic settling time
print('starting...')
t1 = time.time()
moose.start(baselineTime)
caPsd = moose.vec('/model/chem/psd/Ca_input')
caDend = moose.vec('/model/chem/dend/DEND/Ca_input')
castim = (numpy.random.rand(len(caPsd.concInit)) * 0.8 + 0.2) * psdTetCa
caPsd.concInit = castim
caDend.concInit = numpy.random.rand(len(caDend.concInit)) * dendTetCa
moose.start(tetTime)
caPsd.concInit = basalCa
caDend.concInit = basalCa
moose.start(interTetTime)
caPsd.concInit = castim
caDend.concInit = numpy.random.rand(len(caDend.concInit)) * dendTetCa
moose.start(tetTime)
caPsd.concInit = basalCa
caDend.concInit = basalCa
moose.start(postTetTime)
caPsd.concInit = ltdCa
caDend.concInit = ltdCa
moose.start(ltdTime)
caPsd.concInit = basalCa
caDend.concInit = basalCa
moose.start(postLtdTime)
print(('real time = ', time.time() - t1))
if do3D:
app = QtGui.QApplication(sys.argv)
compts = moose.wildcardFind("/model/elec/#[ISA=compartmentBase]")
ecomptPath = [x.path for x in compts]
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] )
viewer = moogli.DynamicMorphologyViewerWidget(morphology)
def callback(morphology, viewer):
moose.start(0.1)
return True
viewer.set_callback(callback, idletime=0)
viewer.showMaximized()
viewer.show()
app.exec_()
displayPlots()
def create_vm_visualizer():
# Moogli requires a morphology object. Create a morphology object
# by reading the geometry details from all objects of type CompartmentBase
# inside /cells[0]
vm_morphology = moogli.read_morphology_from_moose(name = "", path = "/cells[0]")
# Create a named group of compartments called 'group-all'
# which will contain all the compartments of the model.
# Each group has a strict upper and lower limit for the
# variable which is being visualized.
# Both limits map to colors provided to the api.
# The value of the variable is linearly mapped to a color value
# lying between the upper and lower color values.
vm_morphology.create_group( "group-all" # group name
, ALL_COMPARTMENTS # sequence of compartments belonging to this group
, BASE_VM_VALUE # base value of variable
, PEAK_VM_VALUE # peak value of variable
, BASE_VM_COLOR # color corresponding to base value
, PEAK_VM_COLOR # color corresponding to peak value
)
# set initial color of all compartments in accordance with their vm
vm_morphology.set_color( "group-all"
, [moose.element(x).Vm for x in ALL_COMPARTMENTS]
)
# instantiate the visualizer with the morphology object created earlier
vm_viewer = moogli.DynamicMorphologyViewerWidget(vm_morphology)
# Callback function will be called by the visualizer at regular intervals.
# The callback can modify both the morphology and viewer object's properties
# since they are passed as arguments.
def callback(morphology, viewer):
# run simulation for 1 ms
moose.start(SIMULATION_DELTA)
# change color of all the compartments according to their vm values.
# a value higher than peak value will be clamped to peak value
# a value lower than base value will be clamped to base value.
morphology.set_color( "group-all"
, [moose.element(x).Vm for x in ALL_COMPARTMENTS]
)
# if the callback returns true, it will be called again.
# if it returns false it will not be called again.
# the condition below ensures that simulation runs for 1 sec
if moose.element("/clock").currentTime < SIMULATION_TIME : return True
else : return False
# set the callback function to be called after every idletime milliseconds
vm_viewer.set_callback(callback, idletime = 0)
# make sure that entire model is visible
vm_viewer.pitch(math.pi / 2)
vm_viewer.zoom(0.25)
vm_viewer.setWindowTitle("Vm Visualization")
return vm_viewer
def main():
"""
This example illustrates loading a model from an SWC file, inserting
spines, and viewing it.
"""
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.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.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 main():
"""
This snippet illustrates how the Neuron class does the spine
specification, without the rdesigneur intermediate.
"""
app = QtGui.QApplication(sys.argv)
moose.Neutral('/library')
makeSpineProto()
model = moose.loadModel(filename, '/model')
model[0].buildSegmentTree()
model[0].spineDistribution = [ \
'spine', '#apical#', \
'spacing', str( spineSpacing ), \
'spacingDistrib', str( minSpacing ), \
'angle', str( spineAngle ), \
'angleDistrib', str( spineAngleDistrib ), \
'size', str( spineSize ), \
'sizeDistrib', str( spineSizeDistrib ), \
'' \
]
moose.reinit()
# Now we set up the display
compts = moose.wildcardFind("/model/#[ISA=CompartmentBase]")
compts[0].inject = inject
ecomptPath = [x.path for x in compts]
morphology = moogli.read_morphology_from_moose(name="", path="/model")
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] )
viewer = moogli.DynamicMorphologyViewerWidget(morphology)
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 main():
app = QtGui.QApplication(sys.argv)
filename = 'barrionuevo_cell1zr.CNG.swc'
moose.Neutral('/library')
moose.Neutral('/model')
cell = moose.loadModel(filename, '/model/testSwc')
for i in range(8):
moose.setClock(i, simdt)
hsolve = moose.HSolve('/model/testSwc/hsolve')
hsolve.dt = simdt
hsolve.target = '/model/testSwc/soma'
moose.le(cell)
moose.reinit()
# Now we set up the display
compts = moose.wildcardFind("/model/testSwc/#[ISA=CompartmentBase]")
compts[0].inject = inject
ecomptPath = [x.path for x in compts]
morphology = moogli.read_morphology_from_moose(name="",
path="/model/testSwc")
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] )
viewer = moogli.DynamicMorphologyViewerWidget(morphology)
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 create_rm_visualizer():
# Moogli requires a morphology object. Create a morphology object
# by reading the geometry details from all objects of type CompartmentBase
# inside /cells[0]
morphology = moogli.read_morphology_from_moose(name = "", path = "/cells[0]")
# Create a named group of compartments called 'group-all'
# which will contain all the compartments of the model.
# Each group has a strict upper and lower limit for the
# variable which is being visualized.
# Both limits map to colors provided to the api.
# The value of the variable is linearly mapped to a color value
# lying between the upper and lower color values.
morphology.create_group( "group-all" # group name
, ALL_COMPARTMENTS # sequence of compartments belonging to this group
, BASE_RM_VALUE # base value of variable
, PEAK_RM_VALUE # peak value of variable
, BASE_RM_COLOR # color corresponding to base value
, PEAK_RM_COLOR # color corresponding to peak value
)
# set initial color of all compartments in accordance with their rm
morphology.set_color( "group-all"
, map( lambda x : moose.element(x).Rm
, ALL_COMPARTMENTS
)
)
# instantiate the visualizer with the morphology object created earlier
rm_viewer = moogli.DynamicMorphologyViewerWidget(morphology)
# make sure that entire model is visible
rm_viewer.pitch(math.pi / 2)
rm_viewer.zoom(0.25)
rm_viewer.setWindowTitle("Rm")
return rm_viewer
, "/cells[0]/BigCellCML_0[0]/Seg0_dend_390_391[0]"
, "/cells[0]/BigCellCML_0[0]/Seg0_dend_389_390[0]"
, "/cells[0]/BigCellCML_0[0]/Seg0_dend_1079_1080[0]"
]
, 0.0
, 1.0
, [0.0, 1.0, 0.0, 1.0]
, [0.0, 0.0, 1.0, 1.0]
)
def callback(morphology, viewer):
morphology.set_color( "group-1"
, np.random.random_sample((24,)) * (100.0 - 20.0) + 20.0
)
morphology.set_color( "group-2"
, np.random.random_sample((34,))
)
viewer.roll(0.05, 0)
viewer.pitch(0.05, 1)
viewer.yaw(0.05, 2)
return True
viewer = moogli.DynamicMorphologyViewerWidget(morphology)
viewer.showMaximized()
viewer.split_horizontally(0)
viewer.split_vertically(1)
viewer.zoom(0.5, 0)
viewer.zoom(0.5, 1)
viewer.zoom(0.5, 2)
viewer.set_callback(callback)
app.exec_()
