def set_compartment_param(self, compartment, name, value, mechanismname):
""" Set the param for the compartment depending on name and mechanismname. """
if name == 'CM':
compartment.Cm = value*math.pi*compartment.diameter*compartment.length
elif name == 'RM':
compartment.Rm = value/(math.pi*compartment.diameter*compartment.length)
elif name == 'RA':
compartment.Ra = value*compartment.length/(math.pi*(compartment.diameter/2.0)**2)
elif name == 'Em':
compartment.Em = value
elif name == 'initVm':
compartment.initVm = value
elif name == 'inject':
# this reader converts to SI
_logger.info("Comparment %s inject %s A." % (compartment.name, value))
compartment.inject = value
elif name == 'v_reset':
compartment.vReset = value # compartment is a moose.LIF instance (intfire)
elif name == 'threshold':
compartment.thresh = value # compartment is a moose.LIF instance (intfire)
elif name == 't_refrac':
compartment.refractoryPeriod = value # compartment is a moose.LIF instance (intfire)
elif name == 'g_refrac':
_logger.info("SORRY, current moose.LIF doesn't support g_refrac.")
elif mechanismname is 'synapse': # synapse being added to the compartment
## these are potential locations, we do not actually make synapses,
## unless the user has explicitly asked for it
if self.createPotentialSynapses:
syn_name = value
if not moose.exists(compartment.path+'/'+syn_name):
make_new_synapse(syn_name, compartment, syn_name, self.nml_params)
## I assume below that compartment name has _segid at its end
segid = compartment.name.split('_')[-1] # get segment id from compartment name
self.segDict[segid][5].append(value)
elif mechanismname is 'spikegen': # spikegen being added to the compartment
## these are potential locations, we do not actually make the spikegens.
## spikegens for different synapses can have different thresholds,
## hence include synapse_type in its name
## value contains name of synapse i.e. synapse_type
#spikegen = moose.SpikeGen(compartment.path+'/'+value+'_spikegen')
#moose.connect(compartment,"VmSrc",spikegen,"Vm")
pass
## previous were mechanism that don't need a ChannelML definition
## including integrate_and_fire (I ignore the ChannelML definition)
## thus integrate_and_fire mechanism default values cannot be used
## i.e. nothing needed in /library, but below mechanisms need.
elif mechanismname is not None:
## if mechanism is not present in compartment, deep copy from library
## all mechanisms have been loaded into the library earlier
if not moose.exists(compartment.path+'/'+mechanismname):
neutralObj = moose.element("/library/"+mechanismname) # gives error if not present
if 'CaConc' == neutralObj.className: # Ion concentration pool
libcaconc = moose.CaConc("/library/"+mechanismname)
## deep copies the library caconc under the compartment
caconc = moose.copy(libcaconc,compartment,mechanismname)
caconc = moose.CaConc(caconc)
## CaConc connections are made later using connect_CaConc()
## Later, when calling connect_CaConc,
## B is set for caconc based on thickness of Ca shell and compartment l and dia
## OR based on the Mstring phi under CaConc path.
channel = None
elif 'HHChannel2D' == neutralObj.className : ## HHChannel2D
libchannel = moose.HHChannel2D("/library/"+mechanismname)
## deep copies the library channel under the compartment
channel = moose.copy(libchannel,compartment,mechanismname)
channel = moose.HHChannel2D(channel)
moose.connect(channel,'channel',compartment,'channel')
elif 'HHChannel' == neutralObj.className : ## HHChannel
libchannel = moose.HHChannel("/library/"+mechanismname)
## deep copies the library channel under the compartment
channel = moose.copy(libchannel,compartment,mechanismname)
channel = moose.HHChannel(channel)
moose.connect(channel,'channel',compartment,'channel')
## if mechanism is present in compartment, just wrap it
else:
neutralObj = moose.element(compartment.path+'/'+mechanismname)
if 'CaConc' == neutralObj.className: # Ion concentration pool
caconc = moose.CaConc(compartment.path+'/'+mechanismname) # wraps existing channel
channel = None
elif 'HHChannel2D' == neutralObj.className : ## HHChannel2D
channel = moose.HHChannel2D(compartment.path+'/'+mechanismname) # wraps existing channel
elif 'HHChannel' == neutralObj.className : ## HHChannel
channel = moose.HHChannel(compartment.path+'/'+mechanismname) # wraps existing channel
if name == 'Gbar':
if channel is None: # if CaConc, neuroConstruct uses gbar for thickness or phi
## If child Mstring 'phi' is present, set gbar as phi
## BUT, value has been multiplied by Gfactor as a Gbar,
## SI or physiological not known here,
## ignoring Gbar for CaConc, instead of passing units here
child = moose_utils.get_child_Mstring(caconc,'phi')
if child is not None:
#child.value = value
pass
else:
#caconc.thick = value
pass
else: # if ion channel, usual Gbar
channel.Gbar = value*math.pi*compartment.diameter*compartment.length
elif name == 'Ek':
channel.Ek = value
elif name == 'thick': # thick seems to be NEURON's extension to NeuroML level 2.
caconc.thick = value ## JUST THIS WILL NOT DO - HAVE TO SET B based on this thick!
## Later, when calling connect_CaConc,
## B is set for caconc based on thickness of Ca shell and compartment l and dia.
## OR based on the Mstring phi under CaConc path.
if neuroml_utils.neuroml_debug:
_logger.info("Setting %s for comparment %s to %s" % (name, compartment.path, value))
def connect(self, syn_name, pre_path, post_path, weight, threshold, delay):
postcomp = moose.Compartment(post_path)
## We usually try to reuse an existing SynChan & SynHandler -
## event based SynHandlers have an array of weights and delays and can represent multiple synapses,
## so a new element of the weights and delays array is created
## every time a 'synapse' message connects to the SynHandler (from 'event' of spikegen)
## BUT for a graded synapse with a lookup table output connected to 'activation' message,
## not to 'synapse' message, we make a new synapse everytime
## ALSO for a saturating synapse i.e. KinSynChan, we always make a new synapse
## as KinSynChan is not meant to represent multiple synapses
libsyn = moose.SynChan('/library/'+syn_name)
gradedchild = utils.get_child_Mstring(libsyn,'graded')
if libsyn.className == 'KinSynChan' or gradedchild.value == 'True': # create a new synapse
syn_name_full = syn_name+'_'+utils.underscorize(pre_path)
make_new_synapse(syn_name, postcomp, syn_name_full, self.nml_params)
else:
## if syn doesn't exist in this compartment, create it
syn_name_full = syn_name
if not moose.exists(post_path+'/'+syn_name_full):
make_new_synapse(syn_name, postcomp, syn_name_full, self.nml_params)
## moose.element is a function that checks if path exists,
## and returns the correct object, here SynChan
syn = moose.element(post_path+'/'+syn_name_full) # wrap the SynChan in this compartment
synhandler = moose.element(post_path+'/'+syn_name_full+'/handler') # wrap the SynHandler
gradedchild = utils.get_child_Mstring(syn,'graded')
#### weights are set at the end according to whether the synapse is graded or event-based
#### If graded, connect pre-comp Vm to the table which is connected to SynChan's activation
#### If event-based, connect spikegen/timetable's spikeOut to Simple/STDP SynHandler's addSpike
## I rely on second term below not being evaluated if first term is None;
## otherwise None.value gives error.
if gradedchild is not None and gradedchild.value=='True': # graded synapse
interpol = moose.element(syn.path+"/graded_table")
#### always connect source to input - else 'cannot create message' error.
precomp = moose.Compartment(pre_path)
moose.connect(precomp,"VmOut",interpol,"input")
try:
tau_table = moose.element(syn.path+'/tau_table')
tau_table_present = True
except ValueError:
tau_table_present = False
# if tau_table is not found, don't connect it
if tau_table_present:
moose.connect(precomp,'VmOut',tau_table,'input')
## since there is no weight field for a graded synapse
## (no 'synapse' message connected),
## I set the Gbar to weight*Gbar
syn.Gbar = weight*syn.Gbar
else: # Event based synapse
## synapse could be connected to either spikegen at pre-compartment OR to a file!
if 'file' not in pre_path:
## element() can return either Compartment() or IzhikevichNrn(),
## since it queries and wraps the actual object
precomp = moose.element(pre_path)
## if spikegen for this synapse doesn't exist in this compartment, create it
## spikegens for different synapse_types can have different thresholds
## but an integrate and fire spikegen supercedes all other spikegens
if 'IF' in precomp.className: # intfire LIF
spikegen = precomp # LIF has a spikeOut message
else:
if not moose.exists(pre_path+'/'+syn_name+'_spikegen'):
## create new spikegen
spikegen = moose.SpikeGen(pre_path+'/'+syn_name+'_spikegen')
## connect the compartment Vm to the spikegen
moose.connect(precomp,"VmOut",spikegen,"Vm")
## spikegens for different synapse_types can have different thresholds
spikegen.threshold = threshold
spikegen.edgeTriggered = 1 # This ensures that spike is generated only on leading edge.
## usually events are raised at every time step that Vm > Threshold,
## can set either edgeTriggered as above or refractT
#spikegen.refractT = 0.25e-3
## wrap the existing or newly created spikegen in this compartment
spikegen = moose.SpikeGen(pre_path+'/'+syn_name+'_spikegen')
## connect the spikegen to the SynHandler
## note that you need to use Synapse (auto-created) under SynHandler
## to get/set weights , addSpike-s etc.
## wrap Synapse element by moose.Synapse(synhandler.path+'/synapse') or synhandler.synapse
## Synpase is an array element, first add to it, to addSpike-s, get/set weights, etc.
synhandler.numSynapses += 1
## see Demos/snippets/synapse.py for an example of
## how to connect multiple SpikeGens to the same SynChan
m = moose.connect(spikegen, 'spikeOut',
synhandler.synapse[-1], 'addSpike', 'Single')
else:
## if connected to a file, create a timetable,
## put in a field specifying the connected filenumbers to this segment,
## and leave it for simulation-time connection
## pre_path is 'file[+<glomnum>]_<filenum1>[_<filenum2>...]' i.e. glomnum could be present
## hack for my (Aditya's) OB model to use files in NeuroML, should not affect others
filesplit = pre_path.split('+')
if len(filesplit) == 2:
glomsplit = filesplit[1].split('_',1)
glomstr = '_'+glomsplit[0]
filenums = glomsplit[1]
else:
glomstr = ''
filenums = pre_path.split('_',1)[1]
tt_path = postcomp.path+'/'+syn_name_full+glomstr+'_tt'
if not moose.exists(tt_path):
## if timetable for this synapse doesn't exist in this compartment, create it,
## and add the field 'fileNumbers'
tt = moose.TimeTable(tt_path)
tt_filenums = moose.Mstring(tt_path+'/fileNumbers')
tt_filenums.value = filenums
## Be careful to connect the timetable only once while creating it as below:
## note that you need to use Synapse (auto-created) under SynChan
## to get/set weights , addSpike-s etc.
## wrap Synapse element by moose.Synapse(synhandler.path+'/synapse') or synhandler.synapse
## Synpase is an array element, first add to it, to addSpike-s, get/set weights, etc.
synhandler.numSynapses += 1
m = moose.connect(tt,"eventOut",synhandler.synapse[-1],"addSpike","Single")
else:
## if it exists, append file number to the field 'fileNumbers'
## append filenumbers from 'file[+<glomnum>]_<filenumber1>[_<filenumber2>...]'
tt_filenums = moose.Mstring(tt_path+'/fileNumbers')
tt_filenums.value += '_' + filenums
#### syn.Gbar remains the same, but we play with the weight which is a factor to Gbar
#### The delay and weight can be set only after connecting a spike event generator.
#### delay and weight are arrays: multiple event messages can be connected to a single synapse
## first argument below is the array index, we connect to the latest synapse created above
## But KinSynChan ignores weight of the synapse, so set the Gbar for it
if libsyn.className == 'KinSynChan':
syn.Gbar = weight*syn.Gbar
else:
## note that you need to use Synapse (auto-created) under SynHandler
## to get/set weights , addSpike-s etc.
## wrap Synpase element by moose.Synapse(synhandler.path+'/synapse') or synhandler.synapse
synhandler.synapse[-1].weight = weight
synhandler.synapse[-1].delay = delay # seconds
def connect(self, syn_name, pre_path, post_path, weight, threshold, delay):
postcomp = moose.Compartment(post_path)
## We usually try to reuse an existing SynChan & SynHandler -
## event based SynHandlers have an array of weights and delays and can represent multiple synapses,
## so a new element of the weights and delays array is created
## every time a 'synapse' message connects to the SynHandler (from 'event' of spikegen)
## BUT for a graded synapse with a lookup table output connected to 'activation' message,
## not to 'synapse' message, we make a new synapse everytime
## ALSO for a saturating synapse i.e. KinSynChan, we always make a new synapse
## as KinSynChan is not meant to represent multiple synapses
libsyn = moose.SynChan('/library/' + syn_name)
gradedchild = utils.get_child_Mstring(libsyn, 'graded')
if libsyn.className == 'KinSynChan' or gradedchild.value == 'True': # create a new synapse
syn_name_full = syn_name + '_' + utils.underscorize(pre_path)
make_new_synapse(syn_name, postcomp, syn_name_full,
self.nml_params)
else:
## if syn doesn't exist in this compartment, create it
syn_name_full = syn_name
if not moose.exists(post_path + '/' + syn_name_full):
make_new_synapse(syn_name, postcomp, syn_name_full,
self.nml_params)
## moose.element is a function that checks if path exists,
## and returns the correct object, here SynChan
syn = moose.element(
post_path + '/' +
syn_name_full) # wrap the SynChan in this compartment
synhandler = moose.element(post_path + '/' + syn_name_full +
'/handler') # wrap the SynHandler
gradedchild = utils.get_child_Mstring(syn, 'graded')
#### weights are set at the end according to whether the synapse is graded or event-based
#### If graded, connect pre-comp Vm to the table which is connected to SynChan's activation
#### If event-based, connect spikegen/timetable's spikeOut to Simple/STDP SynHandler's addSpike
## I rely on second term below not being evaluated if first term is None;
## otherwise None.value gives error.
if gradedchild is not None and gradedchild.value == 'True': # graded synapse
interpol = moose.element(syn.path + "/graded_table")
#### always connect source to input - else 'cannot create message' error.
precomp = moose.Compartment(pre_path)
moose.connect(precomp, "VmOut", interpol, "input")
try:
tau_table = moose.element(syn.path + '/tau_table')
tau_table_present = True
except ValueError:
tau_table_present = False
# if tau_table is not found, don't connect it
if tau_table_present:
moose.connect(precomp, 'VmOut', tau_table, 'input')
## since there is no weight field for a graded synapse
## (no 'synapse' message connected),
## I set the Gbar to weight*Gbar
syn.Gbar = weight * syn.Gbar
else: # Event based synapse
## synapse could be connected to either spikegen at pre-compartment OR to a file!
if 'file' not in pre_path:
## element() can return either Compartment() or IzhikevichNrn(),
## since it queries and wraps the actual object
precomp = moose.element(pre_path)
## if spikegen for this synapse doesn't exist in this compartment, create it
## spikegens for different synapse_types can have different thresholds
## but an integrate and fire spikegen supercedes all other spikegens
if 'IF' in precomp.className: # intfire LIF
spikegen = precomp # LIF has a spikeOut message
else:
if not moose.exists(pre_path + '/' + syn_name +
'_spikegen'):
## create new spikegen
spikegen = moose.SpikeGen(pre_path + '/' + syn_name +
'_spikegen')
## connect the compartment Vm to the spikegen
moose.connect(precomp, "VmOut", spikegen, "Vm")
## spikegens for different synapse_types can have different thresholds
spikegen.threshold = threshold
spikegen.edgeTriggered = 1 # This ensures that spike is generated only on leading edge.
## usually events are raised at every time step that Vm > Threshold,
## can set either edgeTriggered as above or refractT
#spikegen.refractT = 0.25e-3
## wrap the existing or newly created spikegen in this compartment
spikegen = moose.SpikeGen(pre_path + '/' + syn_name +
'_spikegen')
## connect the spikegen to the SynHandler
## note that you need to use Synapse (auto-created) under SynHandler
## to get/set weights , addSpike-s etc.
## wrap Synapse element by moose.Synapse(synhandler.path+'/synapse') or synhandler.synapse
## Synpase is an array element, first add to it, to addSpike-s, get/set weights, etc.
synhandler.numSynapses += 1
## see Demos/snippets/synapse.py for an example of
## how to connect multiple SpikeGens to the same SynChan
m = moose.connect(spikegen, 'spikeOut', synhandler.synapse[-1],
'addSpike', 'Single')
else:
## if connected to a file, create a timetable,
## put in a field specifying the connected filenumbers to this segment,
## and leave it for simulation-time connection
## pre_path is 'file[+<glomnum>]_<filenum1>[_<filenum2>...]' i.e. glomnum could be present
## hack for my (Aditya's) OB model to use files in NeuroML, should not affect others
filesplit = pre_path.split('+')
if len(filesplit) == 2:
glomsplit = filesplit[1].split('_', 1)
glomstr = '_' + glomsplit[0]
filenums = glomsplit[1]
else:
glomstr = ''
filenums = pre_path.split('_', 1)[1]
tt_path = postcomp.path + '/' + syn_name_full + glomstr + '_tt'
if not moose.exists(tt_path):
## if timetable for this synapse doesn't exist in this compartment, create it,
## and add the field 'fileNumbers'
tt = moose.TimeTable(tt_path)
tt_filenums = moose.Mstring(tt_path + '/fileNumbers')
tt_filenums.value = filenums
## Be careful to connect the timetable only once while creating it as below:
## note that you need to use Synapse (auto-created) under SynChan
## to get/set weights , addSpike-s etc.
## wrap Synapse element by moose.Synapse(synhandler.path+'/synapse') or synhandler.synapse
## Synpase is an array element, first add to it, to addSpike-s, get/set weights, etc.
synhandler.numSynapses += 1
m = moose.connect(tt, "eventOut", synhandler.synapse[-1],
"addSpike", "Single")
else:
## if it exists, append file number to the field 'fileNumbers'
## append filenumbers from 'file[+<glomnum>]_<filenumber1>[_<filenumber2>...]'
tt_filenums = moose.Mstring(tt_path + '/fileNumbers')
tt_filenums.value += '_' + filenums
#### syn.Gbar remains the same, but we play with the weight which is a factor to Gbar
#### The delay and weight can be set only after connecting a spike event generator.
#### delay and weight are arrays: multiple event messages can be connected to a single synapse
## first argument below is the array index, we connect to the latest synapse created above
## But KinSynChan ignores weight of the synapse, so set the Gbar for it
if libsyn.className == 'KinSynChan':
syn.Gbar = weight * syn.Gbar
else:
## note that you need to use Synapse (auto-created) under SynHandler
## to get/set weights , addSpike-s etc.
## wrap Synpase element by moose.Synapse(synhandler.path+'/synapse') or synhandler.synapse
synhandler.synapse[-1].weight = weight
synhandler.synapse[-1].delay = delay # seconds
def set_compartment_param(self, compartment, name, value, mechanismname):
""" Set the param for the compartment depending on name and mechanismname. """
if name == 'CM':
compartment.Cm = value * math.pi * compartment.diameter * compartment.length
elif name == 'RM':
compartment.Rm = value / (math.pi * compartment.diameter *
compartment.length)
elif name == 'RA':
compartment.Ra = value * compartment.length / (
math.pi * (compartment.diameter / 2.0)**2)
elif name == 'Em':
compartment.Em = value
elif name == 'initVm':
compartment.initVm = value
elif name == 'inject':
# this reader converts to SI
_logger.info("Comparment %s inject %s A." %
(compartment.name, value))
compartment.inject = value
elif name == 'v_reset':
compartment.vReset = value # compartment is a moose.LIF instance (intfire)
elif name == 'threshold':
compartment.thresh = value # compartment is a moose.LIF instance (intfire)
elif name == 't_refrac':
compartment.refractoryPeriod = value # compartment is a moose.LIF instance (intfire)
elif name == 'g_refrac':
_logger.info("SORRY, current moose.LIF doesn't support g_refrac.")
elif mechanismname is 'synapse': # synapse being added to the compartment
## these are potential locations, we do not actually make synapses,
## unless the user has explicitly asked for it
if self.createPotentialSynapses:
syn_name = value
if not moose.exists(compartment.path + '/' + syn_name):
make_new_synapse(syn_name, compartment, syn_name,
self.nml_params)
## I assume below that compartment name has _segid at its end
segid = compartment.name.split('_')[
-1] # get segment id from compartment name
self.segDict[segid][5].append(value)
elif mechanismname is 'spikegen': # spikegen being added to the compartment
## these are potential locations, we do not actually make the spikegens.
## spikegens for different synapses can have different thresholds,
## hence include synapse_type in its name
## value contains name of synapse i.e. synapse_type
#spikegen = moose.SpikeGen(compartment.path+'/'+value+'_spikegen')
#moose.connect(compartment,"VmSrc",spikegen,"Vm")
pass
## previous were mechanism that don't need a ChannelML definition
## including integrate_and_fire (I ignore the ChannelML definition)
## thus integrate_and_fire mechanism default values cannot be used
## i.e. nothing needed in /library, but below mechanisms need.
elif mechanismname is not None:
## if mechanism is not present in compartment, deep copy from library
## all mechanisms have been loaded into the library earlier
if not moose.exists(compartment.path + '/' + mechanismname):
neutralObj = moose.element(
"/library/" + mechanismname) # gives error if not present
if 'CaConc' == neutralObj.className: # Ion concentration pool
libcaconc = moose.CaConc("/library/" + mechanismname)
## deep copies the library caconc under the compartment
caconc = moose.copy(libcaconc, compartment, mechanismname)
caconc = moose.CaConc(caconc)
## CaConc connections are made later using connect_CaConc()
## Later, when calling connect_CaConc,
## B is set for caconc based on thickness of Ca shell and compartment l and dia
## OR based on the Mstring phi under CaConc path.
channel = None
elif 'HHChannel2D' == neutralObj.className: ## HHChannel2D
libchannel = moose.HHChannel2D("/library/" + mechanismname)
## deep copies the library channel under the compartment
channel = moose.copy(libchannel, compartment,
mechanismname)
channel = moose.HHChannel2D(channel)
moose.connect(channel, 'channel', compartment, 'channel')
elif 'HHChannel' == neutralObj.className: ## HHChannel
libchannel = moose.HHChannel("/library/" + mechanismname)
## deep copies the library channel under the compartment
channel = moose.copy(libchannel, compartment,
mechanismname)
channel = moose.HHChannel(channel)
moose.connect(channel, 'channel', compartment, 'channel')
## if mechanism is present in compartment, just wrap it
else:
neutralObj = moose.Neutral(compartment.path + '/' +
mechanismname)
if 'CaConc' == neutralObj.className: # Ion concentration pool
caconc = moose.CaConc(
compartment.path + '/' +
mechanismname) # wraps existing channel
channel = None
elif 'HHChannel2D' == neutralObj.className: ## HHChannel2D
channel = moose.HHChannel2D(
compartment.path + '/' +
mechanismname) # wraps existing channel
elif 'HHChannel' == neutralObj.className: ## HHChannel
channel = moose.HHChannel(
compartment.path + '/' +
mechanismname) # wraps existing channel
if name == 'Gbar':
if channel is None: # if CaConc, neuroConstruct uses gbar for thickness or phi
## If child Mstring 'phi' is present, set gbar as phi
## BUT, value has been multiplied by Gfactor as a Gbar,
## SI or physiological not known here,
## ignoring Gbar for CaConc, instead of passing units here
child = moose_utils.get_child_Mstring(caconc, 'phi')
if child is not None:
#child.value = value
pass
else:
#caconc.thick = value
pass
else: # if ion channel, usual Gbar
channel.Gbar = value * math.pi * compartment.diameter * compartment.length
elif name == 'Ek':
channel.Ek = value
elif name == 'thick': # thick seems to be NEURON's extension to NeuroML level 2.
caconc.thick = value ## JUST THIS WILL NOT DO - HAVE TO SET B based on this thick!
## Later, when calling connect_CaConc,
## B is set for caconc based on thickness of Ca shell and compartment l and dia.
## OR based on the Mstring phi under CaConc path.
if neuroml_utils.neuroml_debug:
_logger.info("Setting %s for comparment %s to %s" %
(name, compartment.path, value))
