def make_new_synapse(syn_name, postcomp, syn_name_full, nml_params):
## if channel does not exist in library load it from xml file
if not moose.exists('/library/' + syn_name):
cmlR = ChannelML(nml_params)
model_filename = syn_name + '.xml'
model_path = utils.find_first_file(model_filename,
nml_params['model_dir'])
if model_path is not None:
cmlR.readChannelMLFromFile(model_path)
else:
raise IOError(
'For mechanism {0}: files {1} not found under {2}.'.format(
syn_name, model_filename, nml_params['model_dir']))
## deep copies the library SynChan and SynHandler
## to instances under postcomp named as <arg3>
synid = moose.copy(moose.element('/library/' + syn_name), postcomp,
syn_name_full)
#synhandlerid = moose.copy(moose.element('/library/'+syn_name+'/handler'), postcomp,syn_name_full+'/handler') This line was a bug: double handler
synhandler = moose.element(synid.path + '/handler')
syn = moose.SynChan(synid)
synhandler = moose.element(
synid.path + '/handler') # returns SimpleSynHandler or STDPSynHandler
## connect the SimpleSynHandler or the STDPSynHandler to the SynChan (double exp)
moose.connect(synhandler, 'activationOut', syn, 'activation')
# mgblock connections if required
childmgblock = mu.get_child_Mstring(syn, 'mgblockStr')
#### connect the post compartment to the synapse
if childmgblock.value == 'True': # If NMDA synapse based on mgblock, connect to mgblock
mgblock = moose.Mg_block(syn.path + '/mgblock')
moose.connect(postcomp, "channel", mgblock, "channel")
else: # if SynChan or even NMDAChan, connect normally
moose.connect(postcomp, "channel", syn, "channel")
def __init__(self, *args):
#### The Mg_block way
moose.KinSynChan.__init__(self, *args)
self.mgblock = moose.Mg_block(self.path + "/mgblock")
self.mgblock.CMg = mitral_granule_NMDA_MgConc
self.mgblock.KMg_A = mitral_granule_NMDA_KMg_A
#### KMg_B has not been wrapped properly in pymoose, needed to set it via setField available in every pymoose object
#mgblock.KMg_B = mitral_granule_NMDA_KMg_B
self.mgblock.setField('KMg_B', str(mitral_granule_NMDA_KMg_B))
#### connect source to destination. excsyn2 sends Gk and Ek to mgblock. other way around gives error.
self.connect("origChannel", self.mgblock, "origChannel")
self.addField('mgblock')
self.setField('mgblock', 'True')
#### The Mg_block way ends
##### The NMDAChan way
#moose.NMDAChan.__init__(self,*args)
#self.MgConc = mitral_granule_NMDA_MgConc
#connect this in the calling script in the usual way as below:
#granulecomp.connect("channel", excsyn2, "channel")
##### The NMDAChan way - ends
self.Ek = mitral_granule_NMDA_Ek
self.Gbar = mitral_granule_saturatingNMDA_Gbar
# KinSynChan is implemented from Destexhe, Mainen and Sejnowski, 1994
# pulseWidth is the time for which the neurotransmitter is on
self.pulseWidth = mitral_granule_saturatingNMDA_pulseWidth
# decay time after neurotransmitter is switched off 1/beta in Destexhe, Mainen and Sejnowski, 1994
self.tau1 = mitral_granule_saturatingNMDA_tau1
# the fraction of bound/open receptors in infinite time with one synaptic event.
# rise time tau2 or tau_r in the paper is calculated as tau_1*(1-rInf) and cannot be set.
self.rInf = mitral_granule_saturatingNMDA_rInf
self.addField('graded')
self.setField('graded', 'False')
def __init__(self, *args):
#### The Mg_block way
moose.SynChan.__init__(self, *args)
self.mgblock = moose.Mg_block(self.path + "/mgblock")
self.mgblock.CMg = mitral_granule_NMDA_MgConc
self.mgblock.KMg_A = mitral_granule_NMDA_KMg_A
## KMg_B has not been wrapped properly in pymoose,
## needed to set it via setField available in every pymoose object
#mgblock.KMg_B = mitral_granule_NMDA_KMg_B
self.mgblock.setField('KMg_B', str(mitral_granule_NMDA_KMg_B))
## connect source to destination.
## excsyn2 sends Gk and Ek to mgblock. other way around gives error.
self.connect("origChannel", self.mgblock, "origChannel")
self.addField('mgblock')
self.setField('mgblock', 'True')
#### The Mg_block way ends
##### The NMDAChan way
#moose.NMDAChan.__init__(self,*args)
#self.MgConc = mitral_granule_NMDA_MgConc
#connect this in the calling script in the usual way as below:
#granulecomp.connect("channel", excsyn2, "channel")
##### The NMDAChan way - ends
self.Ek = mitral_granule_NMDA_Ek
self.Gbar = mitral_granule_NMDA_Gbar
self.tau1 = mitral_granule_NMDA_tau1
self.tau2 = mitral_granule_NMDA_tau2
self.addField('graded')
self.setField('graded', 'False')
def connectSynapse(compartment, synname, gbar_factor):
"""
Creates a synname synapse under compartment, sets Gbar*gbar_factor, and attaches to compartment.
synname must be a synapse in /library of MOOSE.
"""
synapseid = moose.copy(moose.SynChan("/library/" + synname), compartment,
synname)
synapse = moose.SynChan(synapseid)
synapse.Gbar = synapse.Gbar * gbar_factor
synapse_mgblock = moose.Mstring(synapse.path + "/mgblockStr")
if (synapse_mgblock.value == "True"
): # If NMDA synapse based on mgblock, connect to mgblock
mgblock = moose.Mg_block(synapse.path + "/mgblock")
compartment.connect("channel", mgblock, "channel")
else:
compartment.connect("channel", synapse, "channel")
return synapse
def make_new_synapse(self, syn_name, postcomp, syn_name_full):
## if channel does not exist in library load it from xml file
if not self.context.exists('/library/' + syn_name):
cmlR = ChannelML(self.nml_params)
cmlR.readChannelMLFromFile(syn_name + '.xml')
synid = self.context.deepCopy(
self.context.pathToId('/library/' + syn_name), postcomp.id,
syn_name_full)
syn = moose.SynChan(synid)
#### connect the post compartment to the synapse
if syn.getField(
'mgblock'
) == 'True': # If NMDA synapse based on mgblock, connect to mgblock
mgblock = moose.Mg_block(syn.path + '/mgblock')
postcomp.connect("channel", mgblock, "channel")
else: # if SynChan or even NMDAChan, connect normally
postcomp.connect("channel", syn, "channel")
def makeNewSynapse(self, synName, postcomp, synNameFull):
'''This function creates a new synapses onto postcomp.
SpikeGen is spikeGenerator (presynaptic). SpikeGen connects to SynChan,
a synaptic channel which connects to post-synaptic compartment.
SpikeGen models the pre-synaptic events.
'''
synPath = "%s/%s" % (self.libraryPath, synName)
utils.dump(
"SYNAPSE", "Creating {} with path {} onto compartment {}".format(
synName, synPath, postcomp.path))
# if channel does not exist in library load it from xml file
if not moose.exists(synPath):
utils.dump(
"SYNAPSE", "Synaptic Channel {} does not exists. {}".format(
synPath, "Loading is from XML file"))
cmlR = ChannelML.ChannelML(self.nml_params)
cmlR.readChannelMLFromFile(synName + '.xml')
# deep copies the library synapse to an instance under postcomp named as
# <arg3>
if config.disbleCopyingOfObject:
utils.dump(
"WARN", "Copying existing SynChan ({}) to {}".format(
synPath, postcomp))
synid = moose.copy(moose.Neutral(synPath), postcomp, synNameFull)
else:
synid = synPath
syn = moose.SynChan(synid)
syn = self.configureSynChan(syn, synParams={})
childmgblock = utils.get_child_Mstring(syn, 'mgblock')
# connect the post compartment to the synapse
# If NMDA synapse based on mgblock, connect to mgblock
if childmgblock.value == 'True':
mgblock = moose.Mg_block(syn.path + '/mgblock')
self.connectWrapper(postcomp, "channel", mgblock, "channel")
# if SynChan or even NMDAChan, connect normally
else:
self.connectWrapper(postcomp, "channel", syn, "channel")
def printRecursiveTree(elementid, level):
""" Recursive helper function for printCellTree,
specify depth/'level' to recurse and print subelements under MOOSE 'elementid'. """
spacefill = " " * level
element = moose.Neutral(elementid)
for childid in element.children:
childobj = moose.Neutral(childid)
classname = childobj.className
if classname in ["SynChan", "KinSynChan"]:
childobj = moose.SynChan(childid)
print(
spacefill + "|--",
childobj.name,
childobj.className,
"Gbar=",
childobj.Gbar,
"numSynapses=",
childobj.numSynapses,
)
return # Have yet to figure out the children of SynChan, currently not going deeper
elif classname in ["HHChannel", "HHChannel2D"]:
childobj = moose.HHChannel(childid)
print(
spacefill + "|--",
childobj.name,
childobj.className,
"Gbar=",
childobj.Gbar,
"Ek=",
childobj.Ek,
)
elif classname in ["CaConc"]:
childobj = moose.CaConc(childid)
print(
spacefill + "|--",
childobj.name,
childobj.className,
"thick=",
childobj.thick,
"B=",
childobj.B,
)
elif classname in ["Mg_block"]:
childobj = moose.Mg_block(childid)
print(
spacefill + "|--",
childobj.name,
childobj.className,
"CMg",
childobj.CMg,
"KMg_A",
childobj.KMg_A,
"KMg_B",
childobj.KMg_B,
)
elif classname in ["SpikeGen"]:
childobj = moose.SpikeGen(childid)
print(
spacefill + "|--",
childobj.name,
childobj.className,
"threshold",
childobj.threshold,
)
elif classname in ["Func"]:
childobj = moose.Func(childid)
print(
spacefill + "|--",
childobj.name,
childobj.className,
"expr",
childobj.expr,
)
elif classname in [
"Table"
]: # Table gives segfault if printRecursiveTree is called on it
return # so go no deeper
# for inmsg in childobj.inMessages():
# print spacefill+" |---", inmsg
# for outmsg in childobj.outMessages():
# print spacefill+" |---", outmsg
if len(childobj.children) > 0:
printRecursiveTree(childid, level + 1)
syn_name = synapse_names[idx]
context = moose.PyMooseBase.getContext()
soma = moose.Compartment('/soma')
soma.length = 1e-6 # m
soma.diameter = 1e-6 # m
soma.Cm = 0.01 * 3.14159 * soma.length * soma.diameter
synid = context.deepCopy(context.pathToId('/library/' + syn_name), soma.id,
syn_name)
syn = moose.SynChan(synid)
#### connect the soma to the synapse
if syn.getField(
'mgblock'
) == 'True': # If NMDA synapse based on mgblock, connect to mgblock
mgblock = moose.Mg_block(syn.path + '/mgblock')
compartment_connection = mgblock
else: # if SynChan or even NMDAChan, connect normally
compartment_connection = syn
soma.connect("channel", compartment_connection, "channel")
tt = moose.TimeTable('/soma/tt')
tt.connect("event", syn, "synapse")
syn.setWeight(syn.numSynapses - 1, 1.0)
syn.setDelay(syn.numSynapses - 1, 0)
fn = 'temp_spikefile.txt'
f = open(fn, 'w')
f.write(str(SETTLETIME))
f.close()
tt.filename = fn
os.remove(fn)