def writeTreatments(self, sSim):
lj = self.lJust1
trtList = sSim.network.chemSyns
self.treatmentFile = "treatments.hoc"
trtFileName = os.path.join(self.nrnDirPath, self.nrnDirName,
self.treatmentFile)
print "TRTFilename: ", trtFileName
with open(trtFileName, "w") as tf:
tf.write("// create stim objects\n")
iClamps = sSim.treatemts.currentInjList
nIC = len(iClamps)
if nIC == 0:
return
tf.write("objref stim[" + str(nIC) + "]\n\n")
for i in range(len(iClamps)):
ic = iClamps[i]
stimID = "stim[" + str(i) + "]"
tf.write((ic.neuronName + " " + stimID).ljust(lj) +
"= new IClamp(0.5)\n")
# convert seconds to miliseconds
st = float(ic.start) * 1000.0
stop = float(ic.stop) * 1000.0
# duration of the IClamp
dur = stop - st
tf.write(
util.formatedObjectVar(stimID, "del") + "= " +
str(st).ljust(lj) + "// (ms)\n")
tf.write(
util.formatedObjectVar(stimID, "dur") + "= " +
str(dur).ljust(lj) + "// (ms)\n")
# in SNNAP magnitude of current inject is in nA
mag = float(ic.magnitude)
tf.write(
util.formatedObjectVar(stimID, "amp") + "= " +
str(mag).ljust(lj) + "// (nA)\n\n")
return
def write_InActF_timeConstant(self, file, vdgObj, ivd):
lj = self.lJust1
inactfType = ivd.BType
if inactfType == "2":
#file.write(util.formatedObjectVar(vdgObj, "B_IV")+ "= "+ ivd.B_IV+ "\n")
tBType = ivd.tBType
file.write(util.formatedObjectVar(vdgObj, "tB_type")+ "= "+ tBType+ "\n")
# convert seconds to ms
tB_tx = float(ivd.tB_tx) * 1000.0
file.write(util.formatedObjectVar(vdgObj, "tB_tx")+ "= "+ str(tB_tx).ljust(lj)+ "// (ms)\n")
if tBType in ['2', '3']:
# convert seconds to ms
tB_tn = float(ivd.tB_tn) * 1000.0
file.write(util.formatedObjectVar(vdgObj, "tB_tn")+ "= "+ str(tB_tn).ljust(lj)+ "// (ms)\n")
file.write(util.formatedObjectVar(vdgObj, "tB_h1")+ "= "+ (ivd.tB_h1).ljust(lj)+ "// (mV)\n")
file.write(util.formatedObjectVar(vdgObj, "tB_s1")+ "= "+ (ivd.tB_s1).ljust(lj)+ "// (mV)\n")
file.write(util.formatedObjectVar(vdgObj, "tB_p1")+ "= "+ ivd.tB_p1+ "\n\n")
if tBType in ['3']:
file.write(util.formatedObjectVar(vdgObj, "tB_h2")+ "= "+ (ivd.tB_h2).ljust(lj)+ "// (mV)\n")
file.write(util.formatedObjectVar(vdgObj, "tB_s2")+ "= "+ (ivd.tB_s2).ljust(lj)+ "// (mV)\n")
file.write(util.formatedObjectVar(vdgObj, "tB_p2")+ "= "+ ivd.tB_p2+ "\n\n")
elif tBType != '1':
print "WARNING: Time constant forms other than 1, 2, or 3 are not supported yet!!!"
# write steady state
ssBType = ivd.ssBType
file.write(util.formatedObjectVar(vdgObj, "ssB_type")+ "= "+ ssBType+ "\n")
file.write(util.formatedObjectVar(vdgObj, "ssB_h")+ "= "+ (ivd.ssB_h).ljust(lj)+ "// (mV)\n")
file.write(util.formatedObjectVar(vdgObj, "ssB_s")+ "= "+ (ivd.ssB_s).ljust(lj)+ "// (mV)\n")
file.write(util.formatedObjectVar(vdgObj, "ssB_p")+ "= "+ ivd.ssB_p+ "\n")
if ssBType == '2':
file.write(util.formatedObjectVar(vdgObj, "ssB_Bn")+ "= "+ ivd.ssB_Bn+ "\n")
def write_InActF_rateConstant(self, file, vdgObj, ivd):
lj = self.lJust1
inactfType = ivd.hType
if inactfType == "2":
file.write(util.formatedObjectVar(vdgObj, "h_L")+ "= 0.001\n")
if inactfType == "3":
h_L = float(ivd.h_L) / 1000.0
file.write(util.formatedObjectVar(vdgObj, "h_L")+ "= "+str(h_L)+"\n")
#file.write(util.formatedObjectVar(vdgObj, "h_L")+ "= "+ ivd.h_L+ "\n")
ahType = ivd.ahType
file.write(util.formatedObjectVar(vdgObj, "ah_type")+ "= "+ ivd.ahType+ "\n")
file.write(util.formatedObjectVar(vdgObj, "ah_A")+ "= "+ ivd.ah_A + "\n")
if ahType != '1':
file.write(util.formatedObjectVar(vdgObj, "ah_B")+ "= "+ (ivd.ah_B).ljust(lj)+ "// (mV)\n")
if ahType != '4' and ahType != '8' and ahType != '9':
file.write(util.formatedObjectVar(vdgObj, "ah_C")+ "= "+ (ivd.ah_C).ljust(lj)+ "// (mV)\n")
if ahType != '5' and ahType != '6' and ahType != '7':
file.write(util.formatedObjectVar(vdgObj, "ah_D")+ "= "+ (ivd.ah_D).ljust(lj)+ "// (mV)\n")
bhType = ivd.bhType
file.write("\n")
file.write(util.formatedObjectVar(vdgObj, "bh_type")+ "= "+ bhType+ "\n")
file.write(util.formatedObjectVar(vdgObj, "bh_A")+ "= "+ ivd.bh_A+ "\n")
if bhType != '1':
file.write(util.formatedObjectVar(vdgObj, "bh_B")+ "= "+ (ivd.bh_B).ljust(lj)+ "// (mV)\n")
if bhType != '4' and bhType != '8' and bhType != '9':
file.write(util.formatedObjectVar(vdgObj, "bh_C")+ "= "+ (ivd.bh_C).ljust(lj)+ "// (mV)\n")
if bhType != '5' and bhType != '6' and bhType != '7':
file.write(util.formatedObjectVar(vdgObj, "bh_D")+ "= "+ (ivd.bh_D).ljust(lj)+ "// (mV)\n")
file.write("\n")
def write_ActF_rateConstant(self, file, vdgObj, ivd):
# in SNNAP time derivatives are also in seconds. to convert them to Neuron time derivatives
# must be divided by 1000.0
lj = self.lJust1
afType = ivd.mType
if afType == "2":
file.write(util.formatedObjectVar(vdgObj, "m_L")+ "= 0.001\n")
if afType == "3":
#m_L = float(ivd.m_L) / 3000.0 * 3.23
m_L = float(ivd.m_L) /1000.0
file.write(util.formatedObjectVar(vdgObj, "m_L")+ "= "+ str(m_L)+"\n")
#file.write(util.formatedObjectVar(vdgObj, "m_L")+ "= "+ ivd.m_L+ "\n")
amType = ivd.amType
file.write(util.formatedObjectVar(vdgObj, "am_type")+ "= "+ ivd.amType+ "\n")
file.write(util.formatedObjectVar(vdgObj, "am_A")+ "= "+ ivd.am_A+ "\n")
if amType != '1':
file.write(util.formatedObjectVar(vdgObj, "am_B")+ "= "+ (ivd.am_B).ljust(lj)+ "// (mV)\n")
if amType != '4' and amType != '8' and amType != '9':
file.write(util.formatedObjectVar(vdgObj, "am_C")+ "= "+ (ivd.am_C).ljust(lj)+ "// (mV)\n")
if amType != '5' and amType != '6' and amType != '7':
file.write(util.formatedObjectVar(vdgObj, "am_D")+ "= "+ (ivd.am_D).ljust(lj)+ "// (mV)\n")
bmType = ivd.bmType
file.write("\n")
file.write(util.formatedObjectVar(vdgObj, "bm_type")+ "= "+ bmType+ "\n")
file.write(util.formatedObjectVar(vdgObj, "bm_A")+ "= "+ ivd.bm_A+ "\n")
if bmType != '1':
file.write(util.formatedObjectVar(vdgObj, "bm_B")+ "= "+ (ivd.bm_B).ljust(lj)+ "// (mV)\n")
if bmType != '4' and bmType != '8' and bmType != '9':
file.write(util.formatedObjectVar(vdgObj, "bm_C")+ "= "+ (ivd.bm_C).ljust(lj)+ "// (mV)\n")
if bmType != '5' and bmType != '6' and bmType != '7':
file.write(util.formatedObjectVar(vdgObj, "bm_D")+ "= "+ (ivd.bm_D).ljust(lj)+ "// (mV)\n")
file.write("\n")
def writeNeurons(self, sSim):
"""
write neuron data into files
"""
lj = self.lJust1
for nName in sSim.network.neurons.keys():
nf_local = "create_"+nName+".hoc"
nFileName = os.path.join(self.nrnDirPath,self.nrnDirName,nf_local)
nrn = sSim.network.neurons[nName]
with open(nFileName, "w") as nf:
# append file name to the neuron filelist
self.neutonFiles.append(nf_local)
nf.write("create "+ nName+"\n")
nf.write(nName + " {\n")
nf.write("\tnseg = 1\t\t// single compartment\n")
nf.write("\tdiam = 1\t\t// (um)\n")
nf.write("\tL = 3.1831e7\t\t// (um)\n")
nf.write("\t// total area = pi*diam*L = 1e8 um2 = 1 cm2\n\n")
# write membrane capacitance
if nrn.memAreaType == "0" or nrn.memAreaType == "":
# membrane capacitance is in uF
cm = float(nrn.cm)
nf.write("\tcm = "+ str(cm).ljust(lj)+"// (uF/cm2)\n")
else:
print "WARNING: memAreas other than \"0\" are not supported yet!!!"
# insert leak current
vdgs = nrn.vdgs
if self.useNrnPas:
for vdgName in vdgs.keys():
ivdType = vdgs[vdgName].ivdType
if ivdType == '5':
nf.write("\tinsert pas\n")
nf.write("\te_pas = "******"// (mV)\n")
g = float(vdgs[vdgName].g)
# in SNNAP cm is given in uS,
# convert conductance from uS to S if not using mem_area
if nrn.memAreaType == '0' or nrn.memAreaType == "":
g = float(vdgs[vdgName].g) * 1.0e-6
nf.write("\tg_pas = "******"// (S/cm2)\n")
nf.write("}\n\n")
# write inital Vm
nf.write(nName+".v(0.5) = " + str(nrn.vmInit).ljust(lj) +" // (mV)\n\n")
# insert VDGs
for vdgName in vdgs.keys():
ivdType = vdgs[vdgName].ivdType
aType = vdgs[vdgName].AType
bType = vdgs[vdgName].BType
mType = vdgs[vdgName].mType
hType = vdgs[vdgName].hType
if nrn.memAreaType == '0'or nrn.memAreaType == "":
# in SNNAP, if not using memArea conductance is given in uS
try:
g = float(vdgs[vdgName].g)
except:
print "WARNING!: could not convert "+vdgName+ " conductance of neuron " + nName
print "Exited unexpectedly!"
sys.exit(-1)
if not self.useNrnPas:
if ivdType == '5':
nf.write("// passive current\n")
vdgObjName = nName+"_pas"
nf.write("objref "+vdgObjName+ "\n")
nf.write(nName+" "+vdgObjName+ " = new snnap_ionic_pas_ivd5(0.5)\n")
nf.write(util.formatedObjectVar(vdgObjName, "e")+ "= "+(vdgs[vdgName].E).ljust(lj) + "// (mV)\n")
nf.write(util.formatedObjectVar(vdgObjName, "gmax") + "= " + str(g).ljust(lj) + "// (uS)\n\n\n")
continue
# create object reference for this vdg
vdgObjName = nName+"_"+vdgName
nf.write("objref "+vdgObjName+ "\n")
if ivdType == '1' or ivdType == '3':
nf.write("//_A"+aType+"_B"+bType+"\n")
nf.write(nName+" "+vdgObjName+ " = new snnap_ionic_tc_ivd"+ivdType+"(0.5)\n")
nf.write(util.formatedObjectVar(vdgObjName, "e")+ "= "+(vdgs[vdgName].E).ljust(lj) + "// (mV)\n")
nf.write(util.formatedObjectVar(vdgObjName, "gmax") + "= " + str(g).ljust(lj) + "// (uS)\n")
nf.write(util.formatedObjectVar(vdgObjName, "p")+ "= "+vdgs[vdgName].P + "\n\n")
self.write_ActF_timeConstant(nf, vdgObjName, vdgs[vdgName])
if ivdType == '1':
self.write_InActF_timeConstant(nf, vdgObjName, vdgs[vdgName])
if ivdType == '2' or ivdType == '4':
nf.write("//_m"+mType+"_h"+hType+"\n")
nf.write(nName+" "+vdgObjName+ " = new snnap_ionic_rc_ivd"+ivdType+"(0.5)\n")
nf.write(util.formatedObjectVar(vdgObjName, "e")+ "= "+(vdgs[vdgName].E).ljust(lj) + "// (mV)\n")
nf.write(util.formatedObjectVar(vdgObjName, "gmax") + "= " + str(g).ljust(lj) + "// (uS)\n")
nf.write(util.formatedObjectVar(vdgObjName, "p")+ "= "+vdgs[vdgName].P + "\n\n")
self.write_ActF_rateConstant(nf, vdgObjName, vdgs[vdgName])
if ivdType == '2':
self.write_InActF_rateConstant(nf, vdgObjName, vdgs[vdgName])
nf.write("\n")
def writeChemSyns(self, sSim):
lj = self.lJust1
csList = sSim.network.chemSyns
neurons = sSim.network.neurons
i = 0
for cs in csList:
csf_local = "cs_"+cs.preSyn+"_to_" + cs.postSyn + "_" + cs.synType +".hoc"
csFileName = os.path.join(self.nrnDirPath,self.nrnDirName,csf_local)
with open(csFileName, "w") as csf:
# append file name to the chemical synapse filelist
self.chemSynFiles.append(csf_local)
AtType = cs.ATType
XtType = cs.XtType
csf.write("// presyn: "+ cs.preSyn+ " postSyn: " + cs.postSyn+"\n")
csf.write("//cs_ fATType:"+ cs.fATType+ " ATType:" + AtType +" XtType:"+ XtType+"\n\n")
csf.write("threshold".ljust(lj)+ "= "+neurons[cs.preSyn].treshold.ljust(lj)+ "// (mV)\n")
csf.write("delay".ljust(lj)+"= "+ "0.0".ljust(lj)+ "// (ms)\n")
csf.write("weight".ljust(lj)+ "= "+"1".ljust(lj)+ "\n\n")
#csf.write(("objref cs_"+str(i)).ljust()+"\n")
csObjName = "cs_"+str(i)
csf.write("objref "+ csObjName +"\n")
if AtType == '1' or AtType == '2':
csf.write(cs.postSyn+" "+ csObjName +" = new snnap_cs2_At12(0.5)\n\n")
if AtType == '3' or AtType == '4':
if XtType == '1':
csf.write(cs.postSyn+" "+ csObjName +" = new snnap_cs2_At34_Xt1(0.5)\n\n")
elif XtType == '3':
csf.write(cs.postSyn+" "+ csObjName +" = new snnap_cs2_At34_Xt3(0.5)\n\n")
else:
print "WARNING: Xt types other than \"1\" or \"3\" are not supported yet!!!"
if AtType == '5':
if XtType == '1':
csf.write(cs.postSyn+" "+ csObjName +" = new snnap_cs2_At5_Xt_1(0.5)\n\n")
elif XtType == '3':
csf.write(cs.postSyn+" "+ csObjName +" = new snnap_cs2_At5_Xt_3(0.5)\n\n")
else:
print "WARNING: Xt types other than \"1\" or \"3\" are not supported yet!!!"
csf.write(util.formatedObjectVar(csObjName, "e")+"= "+ cs.E.ljust(lj) + "// (mV)\n")
# in SNNAP synaptic conductance is in uS
g = float(cs.g)
csf.write(util.formatedObjectVar(csObjName, "g")+"= "+ str(g).ljust(lj) + "// (uS)\n")
# convert spike duration to ms
spDur = float(neurons[cs.preSyn].spikeDur) *1000
csf.write(util.formatedObjectVar(csObjName, "dur")+"= "+ str(spDur).ljust(lj) + "// (ms)\n\n")
if cs.fATType in ['3', '5', '6']:
csf.write(util.formatedObjectVar(csObjName, "fAt_a")+"= "+ cs.fAT_a + "\n")
if cs.fATType in ['3', '4', '5']:
csf.write(util.formatedObjectVar(csObjName, "fAt_b")+"= "+ cs.fAT_b + "\n")
csf.write(util.formatedObjectVar(csObjName, "Ics_type")+"= "+ cs.iCSType + "\n")
csf.write(util.formatedObjectVar(csObjName, "fAt_type")+"= "+ cs.fATType + "\n")
csf.write(util.formatedObjectVar(csObjName, "At_type")+"= "+ cs.ATType + "\n")
if AtType in ['3', '4', '5']:
csf.write(util.formatedObjectVar(csObjName, "Xt_type")+"= "+ cs.XtType + "\n\n")
if cs.ATType in ['1', '3', '4']:
# convert seconds to milliseconds
At_u1 = float(cs.At_u1) *1000.0
csf.write(util.formatedObjectVar(csObjName, "taucs1")+"= "+ str(At_u1).ljust(lj) + "// (ms)\n")
if cs.ATType in ['2', '4']:
# convert seconds to milliseconds
At_u2 = float(cs.At_u2) *1000.0
csf.write(util.formatedObjectVar(csObjName, "taucs2")+"= "+ str(At_u2).ljust(lj) + "// (ms)\n")
if cs.XtType == "3" or cs.XtType == "4":
# convert seconds to milliseconds
PSM_ud = float(cs.PSM_ud) *1000.0
PSM_ur = float(cs.PSM_ur) *1000.0
csf.write(util.formatedObjectVar(csObjName, "tauXt1")+"= "+ str(PSM_ud).ljust(lj) + "// (ms)\n")
csf.write(util.formatedObjectVar(csObjName, "tauXt2")+"= "+ str(PSM_ur).ljust(lj) + "// (ms)\n")
# setup netCon object
csncObjName = "cs_nc"+str(i)
csf.write("\nobjref "+ csncObjName +"\n")
csf.write(cs.preSyn+" "+ csncObjName +" = new NetCon(&v(0.5), "+ csObjName+ ", threshold, delay, weight)\n\n")
i = i+1
return
def write_ActF_timeConstant(self, file, vdgObj, ivd):
lj = self.lJust1
afType = ivd.AType
if afType == "2":
#file.write(util.formatedObjectVar(vdgObj, "A_IV")+ "= "+ ivd.A_IV+ "\n")
tAType = ivd.tAType
file.write(util.formatedObjectVar(vdgObj, "tA_type")+ "= "+ tAType+ "\n")
# convert seconds to ms
tA_tx = float(ivd.tA_tx) * 1000.0
file.write(util.formatedObjectVar(vdgObj, "tA_tx") + "= "+ str(tA_tx).ljust(lj)+ "// (ms)\n")
if tAType in ['2', '3', '6']:
file.write(util.formatedObjectVar(vdgObj, "tA_h1") + "= "+ (ivd.tA_h1).ljust(lj)+ "// (mV)\n")
file.write(util.formatedObjectVar(vdgObj, "tA_s1") + "= "+ (ivd.tA_s1).ljust(lj)+ "// (mV)\n")
if tAType != '6':
# convert seconds to ms
tA_tn = float(ivd.tA_tn) * 1000.0
file.write(util.formatedObjectVar(vdgObj, "tA_tn") + "= "+ str(tA_tn).ljust(lj)+ "// (ms)\n")
file.write(util.formatedObjectVar(vdgObj, "tA_p1") + "= "+ (ivd.tA_p1).ljust(lj)+ "\n\n")
if tAType in ['3', '6']:
file.write(util.formatedObjectVar(vdgObj, "tA_h2") + "= "+ (ivd.tA_h2).ljust(lj)+ "// (mV)\n")
file.write(util.formatedObjectVar(vdgObj, "tA_s2") + "= "+ (ivd.tA_s2).ljust(lj)+ "// (mV)\n")
if tAType != '6':
file.write(util.formatedObjectVar(vdgObj, "tA_p2") + "= "+ (ivd.tA_p2).ljust(lj)+ "\n\n")
elif tAType != '1':
print "WARNING: Time constant forms other than 1, 2, 3 or 6 are not supported yet!!!"
# write steady state
ssAType = ivd.ssAType
file.write(util.formatedObjectVar(vdgObj, "ssA_type") + "= "+ ssAType+ "\n")
file.write(util.formatedObjectVar(vdgObj, "ssA_h") + "= "+ (ivd.ssA_h).ljust(lj)+ "// (mV)\n")
file.write(util.formatedObjectVar(vdgObj, "ssA_s") + "= "+ (ivd.ssA_s).ljust(lj)+ "// (mV)\n")
file.write(util.formatedObjectVar(vdgObj, "ssA_p") + "= "+ ivd.ssA_p+ "\n")
if ssAType == '2':
file.write(util.formatedObjectVar(vdgObj, "ssA_An") + "= "+ ivd.ssA_An+ "\n")
file.write("\n")
