Python moose.vec函数代码示例

def find_max_voxel(): #added by Chaitanya
    spineCa = len(moose.vec( '/model/chem/spine/Ca' ))
    dendCa = len(moose.vec( '/model/chem/dend/DEND/Ca' ))
    Ca = len([ x.Ca * 0.0001 for x in moose.wildcardFind( '/model/elec/##[ISA=CaConcBase]') ])
    spineCaM = len(moose.vec( '/model/chem/spine/Ca_CaM' ))
    psdCaM = len(moose.vec( '/model/chem/psd/Ca_CaM' ))
    return max(spineCa, dendCa, Ca, spineCaM, psdCaM)

def create_population(container, size):
    """Create a population of `size` single compartmental neurons with Na+
    and K+ channels. Also create SpikeGen objects and SynChan objects
    connected to these which can act as plug points for setting up
    synapses later.

    This uses ..ref::`ionchannel.create_1comp_neuron`.

    """
    path = container.path
    print((path, size, type(path)))
    comps = create_1comp_neuron('{}/neuron'.format(path), number=size)
    synpath = path+'/synchan'
    print((synpath, size, type(size)))
    synchan = moose.vec(synpath, n=size, dtype='SynChan')
    synchan.Gbar = 1e-8
    synchan.tau1 = 2e-3
    synchan.tau2 = 2e-3
    m = moose.connect(comps, 'channel', synchan, 'channel', 'OneToOne')
    synhandler = moose.vec('{}/synhandler'.format(path), n=size,
                           dtype='SimpleSynHandler')
    moose.connect(synhandler, 'activationOut', synchan, 'activation', 'OneToOne')
    spikegen = moose.vec('{}/spikegen'.format(path), n=size, dtype='SpikeGen')
    spikegen.threshold = 0.0
    m = moose.connect(comps, 'VmOut', spikegen, 'Vm', 'OneToOne')
    return {'compartment': comps, 'spikegen': spikegen, 'synchan':
            synchan, 'synhandler': synhandler}

def create_population(container, size):
    """Create a population of `size` single compartmental neurons with Na+
    and K+ channels. Also create SpikeGen objects and SynChan objects
    connected to these which can act as plug points for setting up
    synapses later.

    This uses ..ref::`ionchannel.create_1comp_neuron`.

    """
    path = container.path
    print path, size, type(path)
    comps = create_1comp_neuron("{}/neuron".format(path), number=size)
    synpath = path + "/synchan"
    print synpath, size, type(size)
    synchan = moose.vec(synpath, n=size, dtype="SynChan")
    synchan.Gbar = 1e-8
    synchan.tau1 = 2e-3
    synchan.tau2 = 2e-3
    m = moose.connect(comps, "channel", synchan, "channel", "OneToOne")
    synhandler = moose.vec("{}/synhandler".format(path), n=size, dtype="SimpleSynHandler")
    moose.connect(synhandler, "activationOut", synchan, "activation", "OneToOne")
    spikegen = moose.vec("{}/spikegen".format(path), n=size, dtype="SpikeGen")
    spikegen.threshold = 0.0
    m = moose.connect(comps, "VmOut", spikegen, "Vm", "OneToOne")
    return {"compartment": comps, "spikegen": spikegen, "synchan": synchan, "synhandler": synhandler}

def showVisualization():
    makeModel()
    elec = moose.element( '/model/elec' )
    elec.setSpineAndPsdMesh( moose.element('/model/chem/spine'), moose.element('/model/chem/psd') )

    eHead = moose.wildcardFind( '/model/elec/#head#' )
    oldDia = [ i.diameter for i in eHead ]
    graphs = moose.Neutral( '/graphs' )
    #makePlot( 'psd_x', moose.vec( '/model/chem/psd/x' ), 'getN' )
    #makePlot( 'head_x', moose.vec( '/model/chem/spine/x' ), 'getN' )
    makePlot( 'dend_x', moose.vec( '/model/chem/dend/x' ), 'getN' )
    dendZ = makePlot( 'dend_z', moose.vec( '/model/chem/dend/z' ), 'getN' )
    makePlot( 'head_z', moose.vec( '/model/chem/spine/z' ), 'getN' )
    psdZ = makePlot( 'psd_z', moose.vec( '/model/chem/psd/z' ), 'getN' )
    diaTab = makePlot( 'headDia', eHead, 'getDiameter' )
    # print diaTab[0].vector[-1]
    # return
    dendrite = moose.element("/model/elec/dend")
    dendrites = [dendrite.path + "/" + str(i) for i in range(len(dendZ))]
    # print dendrites
    moose.reinit()

    spineHeads = moose.wildcardFind( '/model/elec/#head#')
    # print moose.wildcardFind( '/model/elec/##')

    # print "dendZ", readValues(dendZ)
    # print dendrite

    app = QtGui.QApplication(sys.argv)
    viewer = create_viewer("/model/elec", dendrite, dendZ, diaTab, psdZ)
    viewer.showMaximized()
    viewer.start()
    return app.exec_()

def saveNeuronPlots( fig, rdes ):
    #fig = plt.figure( figsize=(12, 10), facecolor='white' )
    #fig.subplots_adjust( left = 0.18 )
    plt.figure(1)

    ax = plt.subplot(222)
    cleanAx( ax, 'C' )
    plt.ylabel( 'Vm (mV)', fontsize = 16 )
    vtab = moose.element( '/graphs/vtab' )
    t = np.arange( 0, len( vtab.vector ), 1 ) * vtab.dt
    plt.plot( t, vtab.vector * 1000, label="Vm" )
    #plt.legend()
    
    ax = plt.subplot(223)
    cleanAx( ax, 'D', showXlabel = True )
    pcatab = list( moose.vec( '/graphs/pcatab' ) )[0::50]
    t = np.arange( 0, len( pcatab[0].vector ), 1 ) * pcatab[0].dt
    for i in pcatab:
        plt.plot( t, i.vector * 1000 )
    plt.ylabel( '[Ca] (uM)', fontsize = 16 )
    plt.xlabel( 'Time (s)', fontsize = 16 )

    ax = plt.subplot(224)
    cleanAx( ax, 'E', showXlabel = True )
    rtab = list( moose.vec( '/graphs/rtab' ) )[0::50]
    t = np.arange( 0, len( rtab[0].vector ), 1 ) * rtab[0].dt
    for i in rtab:
        plt.plot( t, i.vector )
    plt.ylabel( '# of inserted GluRs', fontsize = 16 )
    plt.xlabel( 'Time (s)', fontsize = 16 )
    '''

def makeGraphics( cPlotDt, ePlotDt ):
        plt.ion()
        fig = plt.figure( figsize=(10,16) )
        chem = fig.add_subplot( 411 )
        chem.set_ylim( 0, 0.006 )
        plt.ylabel( 'Conc (mM)' )
        plt.xlabel( 'time (seconds)' )
        for x in moose.wildcardFind( '/graphs/chem/#[ISA=Table]' ):
            pos = numpy.arange( 0, x.vector.size, 1 ) * cPlotDt
            line1, = chem.plot( pos, x.vector, label=x.name )
        plt.legend()

        elec = fig.add_subplot( 412 )
        plt.ylabel( 'Vm (V)' )
        plt.xlabel( 'time (seconds)' )
        for x in moose.wildcardFind( '/graphs/elec/#[ISA=Table]' ):
            pos = numpy.arange( 0, x.vector.size, 1 ) * ePlotDt
            line1, = elec.plot( pos, x.vector, label=x.name )
        plt.legend()

        ca = fig.add_subplot( 413 )
        plt.ylabel( '[Ca] (mM)' )
        plt.xlabel( 'time (seconds)' )
        for x in moose.wildcardFind( '/graphs/ca/#[ISA=Table]' ):
            pos = numpy.arange( 0, x.vector.size, 1 ) * ePlotDt
            line1, = ca.plot( pos, x.vector, label=x.name )
        plt.legend()

        lenplot = fig.add_subplot( 414 )
        plt.ylabel( 'Ca (mM )' )
        plt.xlabel( 'Voxel#)' )

	spineCa = moose.vec( '/model/chem/spine/Ca' )
	dendCa = moose.vec( '/model/chem/dend/DEND/Ca' )
        line1, = lenplot.plot( range( len( spineCa ) ), spineCa.conc, label='spine' )
        line2, = lenplot.plot( range( len( dendCa ) ), dendCa.conc, label='dend' )

        ca = [ x.Ca * 0.0001 for x in moose.wildcardFind( '/model/elec/##[ISA=CaConcBase]') ]
        line3, = lenplot.plot( range( len( ca ) ), ca, label='elec' )

	spineCaM = moose.vec( '/model/chem/spine/CaM_dash_Ca4' )
        line4, = lenplot.plot( range( len( spineCaM ) ), spineCaM.conc, label='spineCaM' )
	psdCaM = moose.vec( '/model/chem/psd/CaM_dash_Ca4' )
        line5, = lenplot.plot( range( len( psdCaM ) ), psdCaM.conc, label='psdCaM' )
        plt.legend()


        fig.canvas.draw()
        raw_input()
                
        '''
        for x in moose.wildcardFind( '/graphs/##[ISA=Table]' ):
            t = numpy.arange( 0, x.vector.size, 1 )
            pylab.plot( t, x.vector, label=x.name )
        pylab.legend()
        pylab.show()
        '''

	print 'All done'

def main():
    """
    transportBranchingNeuron:
    This example illustrates bidirectional transport 
    embedded in the branching pseudo 1-dimensional geometry of a neuron. 
    This means that diffusion and transport only happen along the axis of 
    dendritic segments, not radially from inside to outside a dendrite, 
    nor tangentially around the dendrite circumference. 
    In this model there is a molecule **a** starting at the soma, which is
    transported out to the dendrites. There is another molecule, **b**,
    which is initially present at the dendrite tips, and is transported
    toward the soma.
    This example uses an external model file to specify a binary branching 
    neuron. This model does not have any spines. The electrical model is 
    used here purely for the geometry and is not part of the computations.
    In this example we build trival chemical model just having
    molecules **a** and **b** throughout the neuronal geometry, using 
    the makeChemModel function.
    The model is set up to run using the Ksolve for integration and the
    Dsolve for handling diffusion.

    The display has three parts:

        a. Animated pseudo-3D plot of neuronal geometry, where each point
           represents a diffusive voxel and moves in the y-axis to show
           changes in concentration of molecule a.
        b. Similar animated pseudo-3D plot for molecule b.
        c. Time-series plot that appears after the simulation has 
           ended. The plots are for the first and last diffusive voxel,
           that is, the soma and the tip of one of the apical dendrites.

    """
    chemdt = 0.1 # Tested various dts, this is reasonable.
    diffdt = 0.01
    plotdt = 1
    animationdt = 5
    runtime = 600 

    makeModel()
    plotlist = makeDisplay()

    # Schedule the whole lot
    for i in range( 11, 17 ):
        moose.setClock( i, chemdt ) # for the chem objects
    moose.setClock( 10, diffdt ) # for the diffusion
    moose.setClock( 18, plotdt ) # for the output tables.
    moose.reinit()
    a = moose.vec( '/model/chem/compt0/a' )
    b = moose.vec( '/model/chem/compt0/b' )
    a0 = sum( a.n )
    b0 = sum( b.n )
    for i in range( 0, runtime, animationdt ):
        moose.start( animationdt )
        plotlist[4].set_text( "time = %d" % i )
        updateDisplay( plotlist )

    print 'mass consv a = ', a0, sum( a.n ), ', b = ', b0, sum( b.n )

    finalizeDisplay( plotlist, plotdt )

 def testRename(self):
     """Rename an element in a Id and check if that was effective. This
     tests for setting values also."""
     id1 = moose.vec(path='/alpha', n=1, dtype='Neutral')
     id2 = moose.vec('alpha')
     id1[0].name = 'bravo'
     self.assertEqual(id1.path, '/bravo')
     self.assertEqual(id2.path, '/bravo')

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 = map( lambda x : x.path, 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 testCompareId(self):
     """Test the rich comparison between ids"""
     id1 = moose.vec('A', n=2, dtype='Neutral')
     id2 = moose.vec('B', n=4, dtype='Neutral')
     id3 = moose.vec('A')
     self.assertTrue(id1 < id2)
     self.assertEqual(id1, id3)
     self.assertTrue(id2 > id1)
     self.assertTrue(id2 >= id1)
     self.assertTrue(id1 <= id2)

def updatePlots( plotlist, time ):
    a = moose.vec( '/model/compartment/a' )
    b = moose.vec( '/model/compartment/b' )
    c = moose.vec( '/model/compartment/c' )
    d = moose.vec( '/model/compartment/d' )

    plotlist[2].set_text( "time = %g" % time )
    plotlist[3].set_ydata( a.conc )
    plotlist[4].set_ydata( b.conc )
    plotlist[5].set_ydata( c.conc )
    plotlist[6].set_ydata( d.conc )

def updateGraphics( plotlist ):
	spineCa = moose.vec( '/model/chem/spine/Ca' )
	dendCa = moose.vec( '/model/chem/dend/DEND/Ca' )
        plotlist[5].set_ydata( spineCa.conc )
        plotlist[6].set_ydata( dendCa.conc )

        ca = [ x.Ca * 0.0001 for x in moose.wildcardFind( '/model/elec/##[ISA=CaConcBase]') ]
        plotlist[7].set_ydata( ca )
	spineCaM = moose.vec( '/model/chem/spine/Ca_CaM' )
        plotlist[8].set_ydata( spineCaM.conc )
	psdCaM = moose.vec( '/model/chem/psd/Ca_CaM' )
        plotlist[9].set_ydata( psdCaM.conc )
        plotlist[4].canvas.draw()

def updateDisplay( plotlist ):
    Ca = moose.vec( '/model/chem/compt0/Ca' )
    Ca_input = moose.vec( '/model/chem/compt0/Ca_input' )
    plotlist[5].set_ydata( Ca.conc )
    plotlist[6].set_ydata( Ca_input.conc )

    Ca = moose.vec( '/model/chem/compt1/Ca' )
    plotlist[7].set_ydata( Ca.conc )

    Ca = moose.vec( '/model/chem/compt2/Ca' )
    Ca_input = moose.vec( '/model/chem/compt2/Ca_input' )
    plotlist[8].set_ydata( Ca.conc )
    plotlist[9].set_ydata( Ca_input.conc )
    plotlist[4].canvas.draw()

def loadChem( neuroCompt, spineCompt, psdCompt ):
	# We need the compartments to come in with a volume of 1 to match the
	# original CubeMesh.
	assert( neuroCompt.volume == 1.0 )
	assert( spineCompt.volume == 1.0 )
	assert( psdCompt.volume == 1.0 )
	assert( neuroCompt.mesh.num == 1 )
	print 'volume = ', neuroCompt.mesh[0].volume
	#assert( neuroCompt.mesh[0].volume == 1.0 ) 
	#an unfortunate mismatch
	# So we'll have to resize the volumes of the current compartments to the
	# new ones.

	modelId = moose.loadModel( 'diffonly.g', '/model', 'ee' )
	#moose.le( '/model/model' )
	#moose.le( '/model/model/kinetics' )
	#moose.le( '/model/model/kinetics/PSD' )
	#moose.le( '/model/model/kinetics/SPINE' )
	moose.delete( moose.vec( '/model/model/kinetics/PSD/kreac' ) )
	moose.delete( moose.vec( '/model/model/kinetics/SPINE/kreac' ) )
	#moose.le( '/model/model/kinetics/PSD' )
	#moose.le( '/model/model/kinetics/SPINE' )
	pCaCaM = moose.element( '/model/model/kinetics/PSD/Ca_CaM' )
	pCaCaM.concInit = 0.001
	dCaCaM = moose.element( '/model/model/kinetics/PSD/Ca_CaM' )
	sCaCaM = moose.element( '/model/model/kinetics/SPINE/Ca_CaM' )
	print "CaCaM.concInit[p,s,d] = ", pCaCaM.concInit, sCaCaM.concInit, dCaCaM.concInit
	#moose.delete( moose.vec( '/model/model/kinetics/SPINE/Ca_CaM' ) )
	#CaCaM2 = moose.element( '/model/model/kinetics/SPINE/Ca_CaM' )
	#CaCaM2.concInit = 0.001
	chem = moose.element( '/model/model' )
	chem.name = 'chem'
	oldS = moose.element( '/model/chem/compartment_1' )
	oldP = moose.element( '/model/chem/compartment_2' )
	oldN = moose.element( '/model/chem/kinetics' )
	print 'oldvols[p,s,d] = ', oldP.volume, oldS.volume, oldN.volume
	print 'newvols[p,s,d] = ', psdCompt.mesh[0].volume, spineCompt.mesh[0].volume, neuroCompt.mesh[0].volume
	oldN.volume = neuroCompt.mesh[0].volume
	oldS.volume = spineCompt.mesh[0].volume
	oldP.volume = psdCompt.mesh[0].volume
	print 'after redoing vols'
	print "CaCaM.concInit[p,s,d] = ", pCaCaM.concInit, sCaCaM.concInit, dCaCaM.concInit
	moveCompt( '/model/chem/kinetics/SPINE', oldS, spineCompt )
	moveCompt( '/model/chem/kinetics/PSD', oldP, psdCompt )
	# Need to do the DEND last because the oldN is /kinetics, 
	# and it will be deleted.
	moveCompt( '/model/chem/kinetics/DEND', oldN, neuroCompt )
	print 'after moving to new compts'
	print "CaCaM.concInit[p,s,d] = ", pCaCaM.concInit, sCaCaM.concInit, dCaCaM.concInit

def printPsd( name ):
    # Print the vol, the path dist from soma, the electrotonic dist, and N
    psdR = moose.vec( '/model/chem/psd/tot_PSD_R' )
    neuronVoxel = moose.element( '/model/chem/spine' ).neuronVoxel
    elecComptMap = moose.element( '/model/chem/dend' ).elecComptMap
    print(("len( neuronVoxel = ", len( neuronVoxel), min( neuronVoxel), max( neuronVoxel)))
    print((len( elecComptMap), elecComptMap[0], elecComptMap[12]))
    neuron = moose.element( '/model/elec' )
    ncompts = neuron.compartments
    d = {}
    j = 0
    for i in ncompts:
        #print i
        d[i] = j
        j += 1

    f = open( name + ".txt", 'w' )
    for i in range( len( psdR ) ):
        n = psdR[i].n
        conc = psdR[i].conc
        vol = psdR[i].volume
        compt = elecComptMap[ neuronVoxel[i] ]
        #print compt
        segIndex = d[compt[0]]
        p = neuron.geometricalDistanceFromSoma[ segIndex ]
        L = neuron.electrotonicDistanceFromSoma[ segIndex ]
        s = str( i ) + "    " + str(n) + "  " + str( conc ) + "  " + str(p) + "  " + str(L) + "\n"
        f.write( s )
    f.close()