#########################################################################
# loadMorphology.py ---
#
# Filename: loadMorphology.py
# Author: Upinder S. Bhalla
# Maintainer:
# Created: Oct 12 16:26:05 2014 (+0530)
# Version:
# Last-Updated: May 16 2017
# By: Upinder S. Bhalla
# Update #:
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
# Change log: updated with current API
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2015 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2.1
## See the file COPYING.LIB for the full notice.
########################################################################
import moogli
import moose
from moose import neuroml
from PyQt4 import Qt, QtCore, QtGui
import sys
import os
frameRunTime = 0.0002
runtime = 1.0
inject = 5e-10
simdt = 5e-5
[docs]def main():
"""
Demonstrates how one can visualise morphology of a neuron using the MOOSE.
"""
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.extensions.moose.read(path="/model/testSwc", vertices=15)
viewer = moogli.Viewer("Viewer")
viewer.attach_shapes( morphology.shapes.values() )
view = moogli.View("main-view")
viewer.attach_view( view )
# 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_()
if __name__ == '__main__':
main()