Python moose.exists函数代码示例

    def newModelDialogSlot(self):
        if self.popup is not None:
            self.popup.close()
        newModelDialog = DialogWidget()
        if newModelDialog.exec_():
            modelPath = str(newModelDialog.modelPathEdit.text()).strip()
            if len(modelPath) == 0:
                raise mexception.ElementNameError('Model path cannot be empty')
            if re.search('[ /]',modelPath) is not None:
                raise mexception.ElementNameError('Model path should not containe / or whitespace')
            plugin = str(newModelDialog.getcurrentRadioButton())
            if moose.exists(modelPath+'/model'):
                moose.delete(modelPath)

            modelContainer = moose.Neutral('%s' %(modelPath))
            modelRoot = moose.Neutral('%s/%s' %(modelContainer.path,"model"))
            if not moose.exists(modelRoot.path+'/info'):
                moose.Annotator(modelRoot.path+'/info')
            
            modelAnno = moose.element(modelRoot.path+'/info')
            modelAnno.modeltype = "new_kkit"
            modelAnno.dirpath = " "
            self.loadedModelsAction(modelRoot.path,plugin)
            self.setPlugin(plugin, modelRoot.path)
            self.objectEditSlot('/', False)

def create_population(container, netparams, name_soma):
    netpath = container.path
    proto=[]
    neurXclass={}
    locationlist=[]
    #determine total number of neurons
    size,numneurons,vol=count_neurons(netparams)
    pop_percent=[]
    for neurtype in netparams.pop_dict.keys():
        if moose.exists(neurtype):
            proto.append(moose.element(neurtype))
            neurXclass[neurtype]=[]
            pop_percent.append(netparams.pop_dict[neurtype].percent)
    #create cumulative array of probabilities for selecting neuron type
    choicearray=np.cumsum(pop_percent)
    if choicearray[-1]<1.0:
        log.info("Warning!!!! fractional populations sum to {}",choicearray[-1])
    #array of random numbers that will be used to select neuron type
    rannum = np.random.uniform(0,choicearray[-1],numneurons)
    #Error check for last element in choicearray equal to 1.0
    log.info("numneurons= {} {} choicarray={}", size, numneurons, choicearray)
    log.debug("rannum={}", rannum)
    for i,xloc in enumerate(np.linspace(netparams.grid[0]['xyzmin'], netparams.grid[0]['xyzmax'], size[0])):
        for j,yloc in enumerate(np.linspace(netparams.grid[1]['xyzmin'], netparams.grid[1]['xyzmax'], size[1])):
            for k,zloc in enumerate(np.linspace(netparams.grid[2]['xyzmin'], netparams.grid[2]['xyzmax'], size[2])):
                #for each location in grid, assign neuron type, update soma location, add in spike generator
                neurnumber=i*size[2]*size[1]+j*size[2]+k
                neurtypenum=np.min(np.where(rannum[neurnumber]<choicearray))
                log.debug("i,j,k {} {} {} neurnumber {} type {}", i,j,k, neurnumber, neurtypenum)
                typename = proto[neurtypenum].name
                tag = '{}_{}'.format(typename, neurnumber)
                new_neuron=moose.copy(proto[neurtypenum],netpath, tag)
                neurXclass[typename].append(container.path + '/' + tag)
                comp=moose.element(new_neuron.path + '/'+name_soma)
                comp.x=i*xloc
                comp.y=j*yloc
                comp.z=k*zloc
                log.debug("x,y,z={},{},{} {}", comp.x, comp.y, comp.z, new_neuron.path)
                locationlist.append([new_neuron.name,comp.x,comp.y,comp.z])
                #spike generator - can this be done to the neuron prototype?
                spikegen = moose.SpikeGen(comp.path + '/spikegen')
                #should these be parameters in netparams?
                spikegen.threshold = 0.0
                spikegen.refractT=1e-3
                m = moose.connect(comp, 'VmOut', spikegen, 'Vm')
    #Create variability in neurons of network
    for neurtype in netparams.chanvar.keys():
        for chan,var in netparams.chanvar[neurtype].items():
            #single multiplier for Gbar for all the channels compartments
            if var>0:
                log.debug('adding variability to {} soma {}, variance: {}', neurtype,chan, var)
                GbarArray=abs(np.random.normal(1.0, var, len(neurXclass[neurtype])))
                for ii,neurname in enumerate(neurXclass[neurtype]):
                    soma_chan_path=neurname+'/'+name_soma+'/'+chan
                    if moose.exists(soma_chan_path):
                        chancomp=moose.element(soma_chan_path)
                        chancomp.Gbar=chancomp.Gbar*GbarArray[ii]
    #
    return {'location': locationlist,
            'pop':neurXclass}

def mooseAddChemSolver(modelRoot, solver):
    """
    Add the solvers only if all are Chemical compartment
    """
    compts = moose.wildcardFind(modelRoot + '/##[ISA=ChemCompt]')
    if all(isinstance(x, (moose.CubeMesh,moose.CylMesh)) for x in compts):
        if not compts:
            return ("Atleast one compartment is required ")
        elif ( len(compts) > 3 ):
            return ("Warning: setSolverOnCompt Cannot handle " ,  len(compts) , " chemical compartments\n")

        else:
            comptinfo = moose.Annotator(moose.element(compts[0]).path + '/info')

            previousSolver = stdSolvertype(comptinfo.solver)
            currentSolver = stdSolvertype(solver)

            if previousSolver != currentSolver:
                comptinfo.solver = currentSolver
                if (moose.exists(compts[0].path + '/stoich')):
                    # "A: and stoich exists then delete the stoich add solver"
                    mooseDeleteChemSolver(modelRoot)
                setCompartmentSolver(modelRoot, currentSolver)
                return True
            else:
                if not moose.exists(compts[0].path + '/stoich'):
                    # " stoich exist, doing nothing"
                    setCompartmentSolver(modelRoot, currentSolver)
                    return True
    else:
        
        return ("mooseAddChemSolver is only for adding Chemical Model which has to be `CubeMesh` or `CylMesh` found ",list(set([x.className for x in compts]) - set(['CubeMesh',"CylMesh"])))

    def createRecordingTable(self, element, field):
        """Create table to record `field` from element `element`

        Tables are created under `dataRoot`, the names are generally
        created by removing `/model` in the beginning of `elementPath`
        and replacing `/` with `_`. If this conflicts with an existing
        table, the id value of the target element (elementPath) is
        appended to the name.

        """
        if len(field) == 0 or ((element, field) in self._recordingDict):            
            return
        # The table path is not foolproof - conflict is
        # possible: e.g. /model/test_object and
        # /model/test/object will map to same table. So we
        # check for existing table without element field
        # path in recording dict.
        relativePath = element.path.partition('/model/')[-1]
        if relativePath.startswith('/'):
            relativePath = relativePath[1:]
        tablePath = self.dataRoot.path + '/' + relativePath.replace('/', '_') + '.' + field
        if moose.exists(tablePath):
            tablePath = '%s_%d' % (tablePath, element.id_.value)
        if not moose.exists(tablePath):            
            table = moose.Table(tablePath)
            print 'Created', table.path, 'for plotting', '%s.%s' % (element.path, field)
            target = element
            moose.connect(table, 'requestData', target, 'get_%s' % (field))
            self._recordingDict[(target, field)] = table
            self._reverseDict[table] = (target, field)

def creaetHHComp(parent='/library', name='hhcomp', diameter=1e-6, length=1e-6):
    """Create a compartment with Hodgkin-Huxley type ion channels (Na and
    K).

    Returns a 3-tuple: (compartment, nachannel, kchannel)

    """
    compPath = '{}/{}'.format(parent, name)
    mc = MooseCompartment( compPath, length, diameter, {})
    c = mc.mc_
    sarea = mc.surfaceArea

    if moose.exists('/library/na'):
        moose.copy('/library/na', c.path, 'na')
    else:
        create_na_chan(parent = c.path)

    na = moose.element('%s/na' % (c.path))

    # Na-conductance 120 mS/cm^2
    na.Gbar = 120e-3 * sarea * 1e4
    na.Ek = 115e-3 + EREST_ACT

    moose.connect(c, 'channel', na, 'channel')
    if moose.exists('/library/k'):
        moose.copy('/library/k', c.path, 'k')
    else:
        create_k_chan(parent = c.path)

    k = moose.element('%s/k' % (c.path))
    # K-conductance 36 mS/cm^2
    k.Gbar = 36e-3 * sarea * 1e4
    k.Ek = -12e-3 + EREST_ACT
    moose.connect(c, 'channel', k, 'channel')
    return (c, na, k)

def create_compartment(path):
    comp = moose.Compartment(path)
    comp.diameter = soma_dia
    comp.Em = EREST_ACT + 10.613e-3
    comp.initVm = EREST_ACT
    sarea = np.pi * soma_dia * soma_dia
    comp.Rm = 1/(0.3e-3 * 1e4 * sarea)
    comp.Cm = 1e-6 * 1e4 * sarea
    if moose.exists('/library/na'):
        nachan = moose.element(moose.copy('/library/na', comp, 'na'))
    else:
        nachan = create_na_chan(comp.path)
    nachan.Gbar = 120e-3 * sarea * 1e4
    moose.showfield(nachan)
    moose.connect(nachan, 'channel', comp, 'channel')
    if moose.exists('/library/k'):
        kchan = moose.element(moose.copy('/library/k', comp, 'k'))
    else:
        kchan = create_k_chan(comp.path)
    kchan.Gbar = 36e-3 * sarea * 1e4
    moose.connect(kchan, 'channel', comp, 'channel')
    synchan = moose.SynChan(comp.path + '/synchan')
    synchan.Gbar = 1e-8
    synchan.tau1 = 2e-3
    synchan.tau2 = 2e-3
    synchan.Ek = 0.0
    m = moose.connect(comp, 'channel', synchan, 'channel')
    spikegen = moose.SpikeGen(comp.path + '/spikegen')
    spikegen.threshold = 0.0
    m = moose.connect(comp, 'VmOut', spikegen, 'Vm')
    return comp

    def buildModel( self, modelPath ):
        if not moose.exists( '/library' ):
            library = moose.Neutral( '/library' )
        if moose.exists( modelPath ):
            print "rdesigneur::buildModel: Build failed. Model '", \
                modelPath, "' already exists."
            return
        self.model = moose.Neutral( modelPath )
        try:
            self.buildCellProto()
            self.buildChanProto()
            self.buildSpineProto()
            self.buildChemProto()
            # Protos made. Now install the elec and chem protos on model.
            self.installCellFromProtos()
            # Now assign all the distributions
            self.buildPassiveDistrib()
            self.buildChanDistrib()
            self.buildSpineDistrib()
            self.buildChemDistrib()
            self._configureSolvers()
            self.buildAdaptors()
            self._configureClocks()
            self._printModelStats()

        except BuildError, msg:
            print "Error: rdesigneur: model build failed: ", msg
            moose.delete( self.model )

def checkFile_Obj_str(file_Obj_str):
    model = moose.element('/')
    loaded = False
    found = False
    if isinstance(file_Obj_str, str):
        if os.path.isfile(file_Obj_str) == True:
            model,loaded = loadModels(file_Obj_str)
            found = True
        elif file_Obj_str.find('/') != -1 :
            if not isinstance(file_Obj_str,moose.Neutral):
                if moose.exists(file_Obj_str):
                    model = file_Obj_str
                    loaded = True
                    found = True
        elif isinstance(file_Obj_str, moose.Neutral):
            if moose.exists(file_Obj_str.path):
                model = file_Obj_str.path
                loaded = True
                found = True
    elif isinstance(file_Obj_str, moose.Neutral):
        if moose.exists(file_Obj_str.path):
            model = file_Obj_str.path
            loaded = True
            found = True
    if not found:
        print ("%s path or filename doesnot exist. " % (file_Obj_str))
    return model,loaded

def create_hhcomp(parent='/library', name='hhcomp', diameter=-30e-6, length=0.0):
    """Create a compartment with Hodgkin-Huxley type ion channels (Na and
    K).

    Returns a 3-tuple: (compartment, nachannel, kchannel)

    """
    comp, sarea = create_passive_comp(parent, name, diameter, length)
    if moose.exists('/library/na'):
        moose.copy('/library/na', comp.path, 'na')
    else:
        create_na_chan(parent=comp.path)
    na = moose.element('%s/na' % (comp.path))
    # Na-conductance 120 mS/cm^2
    na.Gbar = 120e-3 * sarea * 1e4 
    na.Ek = 115e-3 + EREST_ACT
    moose.connect(comp, 'channel', na, 'channel')
    if moose.exists('/library/k'):
        moose.copy('/library/k', comp.path, 'k')
    else:
        create_k_chan(parent=comp.path)
    k = moose.element('%s/k' % (comp.path))
    # K-conductance 36 mS/cm^2
    k.Gbar = 36e-3 * sarea * 1e4 
    k.Ek = -12e-3 + EREST_ACT
    moose.connect(comp, 'channel', k, 'channel')
    return comp, na, k

def deleteSolver(modelRoot):
	compts = moose.wildcardFind(modelRoot+'/##[ISA=ChemCompt]')
	for compt in compts:
		if moose.exists(compt.path+'/stoich'):
			st = moose.element(compt.path+'/stoich')
			st_ksolve = st.ksolve
			moose.delete(st)
			if moose.exists((st_ksolve).path):
				moose.delete(st_ksolve)

def deleteSolver(modelRoot):
	if moose.wildcardFind(modelRoot+'/##[ISA=ChemCompt]'):
		compt = moose.wildcardFind(modelRoot+'/##[ISA=ChemCompt]')
		if ( moose.exists( compt[0].path+'/stoich' ) ):
			st = moose.element(compt[0].path+'/stoich')
			if moose.exists((st.ksolve).path):
				moose.delete(st.ksolve)
			moose.delete( compt[0].path+'/stoich' )
	for x in moose.wildcardFind( modelRoot+'/data/graph#/#' ):
                x.tick = -1

 def dump_cell(self, file_path):
     """Dump the cell information compartment by compartment for
     comparison with NEURON in csv format. All parameters are
     converted to SI units."""
     with open(file_path, 'w') as dump_file:
         fieldnames = ["comp", "len", "dia", "sarea", "xarea", "Em", "Cm","Rm","Ra"]
         for chtype in channel_types:
             if chtype != 'cad':
                 fieldnames += ['e_' + chtype, 'gbar_' + chtype]
             else:
                 fieldnames += ['tau_' + chtype, 'beta_' + chtype]
         # print fieldnames
         writer = csv.DictWriter(dump_file, fieldnames=fieldnames, delimiter=',')
         writer.writeheader()
         comps = moose.wildcardFind('%s/##[TYPE=Compartment]' % (self.path))
         comps = sorted(comps, key=lambda x: int(x.name[0].rpartition('_')[-1]))            
         for comp_e in comps:
             comp = moose.element(comp_e)
             row = {}
             row['comp'] = comp.name
             row['len'] = comp.length
             row['dia'] = comp.diameter
             row['sarea'] = comp.length * comp.diameter * np.pi
             row['xarea'] = comp.diameter * comp.diameter * np.pi/4
             row['Em'] = comp.Em
             row['Cm'] = comp.Cm
             row['Rm'] = comp.Rm
             row['Ra'] = comp.Ra
             if moose.exists(comp.path + '/CaPool'):
                 ca_pool = moose.CaConc(comp.path + '/CaPool')
             for chtype in channel_types:
                 found = False
                 for chname in channel_type_dict[chtype]:
                     chpath = comp.path + '/' + chname
                     if moose.exists(chpath):
                         found = True
                         channel = moose.element(chpath)
                         if channel.className == 'HHChannel':
                             row['e_'+chtype] = channel.Ek
                             row['gbar_'+chtype] = channel.Gbar                        
                         elif channel.className == 'CaConc':
                             row['tau_cad'] = channel.tau
                             row['beta_cad'] = channel.B
                         break
                 if not found:
                     if chtype != 'cad':
                         row['e_'+chtype] = 0.0
                         row['gbar_'+chtype] = 0.0
                     else:
                         row['tau_cad'] = 0.0
                         row['beta_cad'] = 0.0
             writer.writerow(row)

def getModelAnnotation(obj, baseId, basepath):
    annotationNode = obj.getAnnotation()
    if annotationNode is not None:
        numchild = annotationNode.getNumChildren()
        for child_no in range(0, numchild):
            childNode = annotationNode.getChild(child_no)
            if (childNode.getPrefix() ==
                    "moose" and childNode.getName() == "ModelAnnotation"):
                num_gchildren = childNode.getNumChildren()
                for gchild_no in range(0, num_gchildren):
                    grandChildNode = childNode.getChild(gchild_no)
                    nodeName = grandChildNode.getName()
                    if (grandChildNode.getNumChildren() == 1):
                        baseinfo = moose.Annotator(baseId.path + '/info')
                        baseinfo.modeltype = "xml"
                        if nodeName == "runTime":
                            runtime = float(
                                (grandChildNode.getChild(0).toXMLString()))
                            baseinfo.runtime = runtime
                        if nodeName == "solver":
                            solver = (grandChildNode.getChild(0).toXMLString())
                            baseinfo.solver = solver
                        if(nodeName == "plots"):
                            plotValue = (
                                grandChildNode.getChild(0).toXMLString())
                            p = moose.element(baseId)
                            datapath = moose.element(baseId).path + "/data"
                            if not moose.exists(datapath):
                                datapath = moose.Neutral(baseId.path + "/data")
                                graph = moose.Neutral(
                                    datapath.path + "/graph_0")
                                plotlist = plotValue.split(";")
                                tablelistname = []
                                for plots in plotlist:
                                    plots = plots.replace(" ", "")
                                    plotorg = plots
                                    if( moose.exists(basepath.path + plotorg) and isinstance(moose.element(basepath.path+plotorg),moose.PoolBase)) :
                                        plotSId = moose.element(
                                            basepath.path + plotorg)
                                        # plotorg = convertSpecialChar(plotorg)
                                        plot2 = plots.replace('/', '_')
                                        plot3 = plot2.replace('[', '_')
                                        plotClean = plot3.replace(']', '_')
                                        plotName = plotClean + ".conc"
                                        fullPath = graph.path + '/' + \
                                            plotName.replace(" ", "")
                                        # If table exist with same name then
                                        # its not created
                                        if not fullPath in tablelistname:
                                            tab = moose.Table2(fullPath)
                                            tablelistname.append(fullPath)
                                            moose.connect(tab, "requestOut", plotSId, "getConc")

def moosedeleteChemSolver(modelRoot):
    """Delete solvers from Chemical Compartment

    """
    compts = moose.wildcardFind(modelRoot + '/##[ISA=ChemCompt]')
    for compt in compts:
        if moose.exists(compt.path + '/stoich'):
            st = moose.element(compt.path + '/stoich')
            st_ksolve = st.ksolve
            moose.delete(st)
            if moose.exists((st_ksolve).path):
                moose.delete(st_ksolve)
                print("Solver is deleted for modelpath %s " % modelRoot)

def addSpineProto(
    name="spine",
    parent="/library",
    RM=1.0,
    RA=1.0,
    CM=0.01,
    shaftLen=1.0e-6,
    shaftDia=0.2e-6,
    headLen=0.5e-6,
    headDia=0.5e-6,
    synList=(),
    chanList=(),
    caTau=0.0,
):
    assert moose.exists(parent), "%s must exist" % parent
    spine = moose.Neutral(parent + "/" + name)
    shaft = buildComptWrapper(spine, "shaft", shaftLen, shaftDia, 0.0, RM, RA, CM)
    head = buildComptWrapper(spine, "head", headLen, headDia, shaftLen, RM, RA, CM)
    moose.connect(shaft, "axial", head, "raxial")

    if caTau > 0.0:
        conc = moose.CaConc(head.path + "/Ca_conc")
        conc.tau = caTau
        conc.length = head.length
        conc.diameter = head.diameter
        conc.thick = 0.0
        # The 'B' field is deprecated.
        # B = 1/(ion_charge * Faraday * volume)
        # vol = head.length * head.diameter * head.diameter * PI / 4.0
        # conc.B = 1.0 / ( 2.0 * FaradayConst * vol )
        conc.Ca_base = 0.0
    for i in synList:
        syn = buildSyn(i[0], head, i[1], i[2], i[3], i[4], CM)
        if i[5] and caTau > 0.0:
            moose.connect(syn, "IkOut", conc, "current")
    for i in chanList:
        if moose.exists(parent + "/" + i[0]):
            chan = moose.copy(parent + "/" + i[0], head)
        else:
            moose.setCwe(head)
            chan = make_LCa()
            chan.name = i[0]
            moose.setCwe("/")
        chan.Gbar = i[1] * head.Cm / CM
        # print "CHAN = ", chan, chan.tick, chan.Gbar
        moose.connect(head, "channel", chan, "channel")
        if i[2] and caTau > 0.0:
            moose.connect(chan, "IkOut", conc, "current")
    transformNMDAR(parent + "/" + name)
    return spine