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)