def main( args ):
mooseBegin = time.time()
cableLength = args['length']
compNons = args['ncomp']
compartmentSize = cableLength / compNons
cable = PasiveCable( args )
first = 0
last = args['x']
table1 = utils.recordTarget('/data/table1', cable.cable[first].mc_, 'vm' )
table2 = utils.recordTarget('/data/table2', cable.cable[last].mc_, 'vm' )
records = { 'comp0' : table1, 'comp1' : table2 }
simTime = args['run_time']
sim_dt = args['dt']
outputFile = args['output']
st = cable.simulate(simTime)
print("++++ MOOSE took %s sec" % st)
#utils.plotRecords(records)
mooseEnds = time.time() - mooseBegin
#utils.saveRecords(records, outfile="data/moose.dat")
_profile.insert(simulator = 'moose'
, no_of_compartment=args['ncomp']
, coretime = st
, runtime = mooseEnds
)
def main( args ):
cableLength = args['length']
compNons = args['ncomp']
compartmentSize = cableLength / compNons
cable = PasiveCable( args )
first = 0
last = args['x']
table1 = utils.recordTarget('/data/table1', cable.cable[first].mc_, 'vm' )
table2 = utils.recordTarget('/data/table2', cable.cable[last].mc_, 'vm' )
records = { 'comp0' : table1, 'comp1' : table2 }
simTime = args['run_time']
sim_dt = args['dt']
outputFile = args['output']
st = cable.simulate(simTime)
print("++++ MOOSE took %s sec" % st)
#utils.plotRecords(records)
utils.saveRecords(records, outfile="data/moose.dat")
stamp = datetime.datetime.now().isoformat()
with open('moose.log', 'a') as logF:
logF.write('<simulation time_stamp="{}">\n'.format(stamp))
logF.write("\t<elements>\n")
logF.write("\t\t<Compartment>{}</Compartment>\n".format(args['ncomp']))
logF.write("\t</elements>\n")
logF.write("\t<times>\n")
logF.write("\t\t<Simulation>{}</Simulation>\n".format(st))
logF.write("\t</times>\n")
logF.write("</simulation>\n")
def main():
utils.parser
nml.loadNeuroML_L123('./two_cells_nml_1.8/two_cells.nml')
#mumbl.loadMumbl("./two_cells_nml_1.8/mumbl.xml")
table1 = utils.recordTarget('/tableA', '/cells/purkinjeGroup_0/Dend_37_41', 'vm')
table2 = utils.recordTarget('/tableB', '/cells/granuleGroup_0/Soma_0', 'vm')
moose.setClock(0, 5e-6)
moose.useClock(0, '/##', 'process')
moose.useClock(0, '/##', 'init')
moose.reinit()
utils.run(0.1)
graphviz.writeGraphviz(__file__+".dot", ignore='/library')
def main():
utils.parser
p = os.path.join(modeldir, "two_cells_nml_1.8/two_cells.nml")
nml.loadNeuroML_L123(p)
# mumbl.loadMumbl("./two_cells_nml_1.8/mumbl.xml")
table1 = utils.recordTarget("/tableA", "/cells/purkinjeGroup_0/Dend_37_41", "vm")
table2 = utils.recordTarget("/tableB", "/cells/granuleGroup_0/Soma_0", "vm")
moose.setClock(0, 5e-6)
moose.useClock(0, "/##", "process")
moose.useClock(0, "/##", "init")
moose.reinit()
utils.run(0.1, verify=True)
graphviz.writeGraphviz("test_mumble.dot", ignore="/library")
utils.plotRecords({"Dend 37": table1, "Soma 0": table2}, outfile="%s.png" % sys.argv[0], subplot=True)
def main():
utils.parser
nml.loadNeuroML_L123('./two_cells_nml_1.8/two_cells.nml')
#mumbl.loadMumbl("./two_cells_nml_1.8/mumbl.xml")
table1 = utils.recordTarget('/tableA', '/cells/purkinjeGroup_0/Dend_37_41',
'vm')
table2 = utils.recordTarget('/tableB', '/cells/granuleGroup_0/Soma_0',
'vm')
moose.setClock(0, 5e-6)
moose.useClock(0, '/##', 'process')
moose.useClock(0, '/##', 'init')
moose.reinit()
utils.run(0.1, verify=True)
graphviz.writeGraphviz(__file__ + ".dot", ignore='/library')
utils.plotTables([table1, table2])
def main():
utils.parser
nml.loadNeuroML_L123('./two_cells_nml_1.8/two_cells.nml')
#mumbl.loadMumbl("./two_cells_nml_1.8/mumbl.xml")
table1 = utils.recordTarget('/tableA', '/cells/purkinjeGroup_0/Dend_37_41', 'vm')
table2 = utils.recordTarget('/tableB', '/cells/granuleGroup_0/Soma_0', 'vm')
moose.setClock(0, 5e-6)
moose.useClock(0, '/##', 'process')
moose.useClock(0, '/##', 'init')
moose.reinit()
utils.run(0.1, verify=True)
graphviz.writeGraphviz(__file__+".dot", ignore='/library')
utils.plotRecords({ 'Dend 37' : table1, 'Soma 0' : table2 }
, outfile = '%s.png' % sys.argv[0]
, subplot = True
)
def main(args):
cableLength = float(args['length'])
compNons = int(args['ncomp'])
compartmentSize = cableLength / compNons
cable = PasiveCable(args)
first = 0
last = int(int(args['x']) / compartmentSize) - 1
table1 = utils.recordTarget('/data/table1', cable.cable[first].mc_, 'vm')
table2 = utils.recordTarget('/data/table2', cable.cable[last].mc_, 'vm')
simTime = args['run_time']
sim_dt = args['dt']
outputFile = args['output']
cable.simulate(simTime, sim_dt)
utils.plotTables([table1, table2], xscale=sim_dt, file=outputFile)
utils.saveTables([table1, table2],
xscale=sim_dt,
file='data/rallpack2_moose.dat')
def main( args ):
cableLength = args['length']
compNons = args['ncomp']
compartmentSize = cableLength / compNons
cable = PasiveCable( args )
first = 0
last = args['x']
table1 = utils.recordTarget('/data/table1', cable.cable[first].mc_, 'vm' )
table2 = utils.recordTarget('/data/table2', cable.cable[last].mc_, 'vm' )
simTime = args['run_time']
sim_dt = args['dt']
outputFile = args['output']
cable.simulate( simTime, sim_dt )
utils.saveTables( [table1, table2 ]
, xscale = sim_dt
, file = 'data/moose.dat'
)
def main():
utils.parser
p = os.path.join(modeldir, 'two_cells_nml_1.8/two_cells.nml')
nml.loadNeuroML_L123(p)
#mumbl.loadMumbl("./two_cells_nml_1.8/mumbl.xml")
table1 = utils.recordTarget('/tableA', '/cells/purkinjeGroup_0/Dend_37_41',
'vm')
table2 = utils.recordTarget('/tableB', '/cells/granuleGroup_0/Soma_0',
'vm')
moose.setClock(0, 5e-6)
moose.useClock(0, '/##', 'process')
moose.useClock(0, '/##', 'init')
moose.reinit()
utils.run(0.1, verify=True)
graphviz.writeGraphviz('test_mumble.dot', ignore='/library')
utils.plotRecords({
'Dend 37': table1,
'Soma 0': table2
},
outfile='%s.png' % sys.argv[0],
subplot=True)
