Beispiel #1
0
def dumpPlots(fname):
    if (os.path.exists(fname)):
        os.remove(fname)
    records = {}
    for x in moose.wildcardFind('/graphs/##[TYPE=Table2]'):
        records[x.name] = x
    mu.plotRecords(records, subplot=True, outfile='%s.png' % fname)
def plot(numPlots):
    global records_
    toPlots = list(records_.keys())[0:numPlots]
    newPlots = {}
    for i in toPlots:
        newPlots[i] = records_[i]
    mu.plotRecords(newPlots, subplot=True)
def dumpPlots( fname ):
    if ( os.path.exists( fname ) ):
        os.remove( fname )
    records = {}
    for x in moose.wildcardFind( '/graphs/##[TYPE=Table2]' ):
        records[x.name] = x
    mu.plotRecords(records, subplot=True, outfile='%s.png' % fname)
def plot( numPlots ):
    global records_ 
    toPlots = list(records_.keys())[0:numPlots]
    newPlots = {}
    for i in toPlots:
        newPlots[i] = records_[i]
    mu.plotRecords(newPlots, subplot = True)
Beispiel #5
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def plots(filter='soma'):
    global _records
    global _args
    toPlot = []
    tables = {}
    for k in _records:
        if filter in k:
            toPlot.append(k)
    for k in toPlot:
        tables[k] = _records[k]
    mu.plotRecords(tables, subplot=True) #, outfile=_args.plots)
    plt.show()
Beispiel #6
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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)
Beispiel #7
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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
            )
Beispiel #8
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def main(args):
    global cable
    dt = args['dt']
    makeCable(args)
    setupDUT(dt)
    table0 = recordAt( '/table0', cable[0], 'Vm')
    table1 = recordAt( '/table1', cable[-1], 'Vm')
    st = simulate( args['run_time'], dt )
    _profile.insert( simulator='moose'
            , no_of_compartment=args['ncomp']
            , coretime=st
            )

    if args['output']:
        print("Plotting data")
        utils.plotRecords({ 'table0' : table0, 'table1' : table1 }
                , outfile = args['output']
                , title = 'MOOSE'
                )
Beispiel #9
0
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)
    t = moose.Table2("/table%s" % m)
    tables[m] = t
    moose.connect(t, 'requestOut', pools[m], 'getConc')

#pools['ca'] = moose.BufPool('/compt/ca')
pools['ca'].nInit = 20

r_p0_p1 = moose.Reac('/compt/reacA')
funA = moose.Function('/compt/funA')
funA.expr = "{0}*(y0/{1})^6/(1+(y0/{1})^3)^2".format("1.5", "0.7e-3")
moose.connect(funA, 'requestOut',  pools['ca'], 'getConc')
moose.connect(funA, 'valueOut', pools['S1'], 'setConc')
moose.connect(r_p0_p1, 'sub', pools['S'], 'reac')
moose.connect(r_p0_p1, 'prd', pools['S1'], 'reac')

r_p1_up = moose.Reac('/compt/reacB')
moose.connect(r_p1_up, 'sub', pools['S1'], 'reac')
moose.connect(r_p1_up, 'prd', pools['Sp'], 'reac')

# Disabling solver executes the model accurately.
k = moose.Ksolve('/compt/ksolve')
s = moose.Stoich('/compt/stoich')
s.compartment = compt
s.ksolve = k
s.path = '/compt/##'


moose.reinit()
moose.start(10)
mu.plotRecords(tables)