# $Id: geom.py,v 1.30 2011/01/02 19:56:14 samn Exp $

from pyinit import *

class Synapse:
    def __init__(self, sect, loc, tau1, tau2, e):
        self.syn                = h.MyExp2SynBB(loc, sec=sect)
        self.syn.tau1   = tau1
        self.syn.tau2   = tau2
        self.syn.e              = e

class SynapseNMDA:
    def __init__(self, sect, loc, tau1, tau2, tau1NMDA, tau2NMDA, r, e):
        self.syn                        = h.MyExp2SynNMDABB(loc, sec=sect)
        self.syn.tau1           = tau1
        self.syn.tau2           = tau2
        self.syn.tau1NMDA       = tau1NMDA
        self.syn.tau2NMDA       = tau2NMDA
        self.syn.r                      = r
        self.syn.e                      = e

###############################################################################
#
# General Cell
#
###############################################################################
class Cell:
    "General cell"

    def __init__(self,x,y,z,id):
        self.x=x
        self.y=y
        self.z=z
        self.id=id
        self.all_sec = []
        self.add_comp('soma',True)
        self.set_morphology()
        self.set_conductances()
        self.set_synapses()
        self.set_inj()
        self.calc_area()

    def set_morphology(self):
        pass

    def set_conductances(self):
        pass

    def set_synapses(self):
        pass

    def set_inj(self):
        self.somaInj = h.IClamp(0.5, sec=self.soma)

    def add_comp(self, name, rec):
        self.__dict__[name] = h.Section()
        self.all_sec.append(self.__dict__[name])
        # Record voltage
        if rec:
            self.__dict__[name+"_volt"] = h.Vector(int(h.tstop/h.dt)+1)
            self.__dict__[name+"_volt"].record(self.__dict__[name](0.5)._ref_v)

    def plot_volt(self, name, fig=1):
        figure(fig)
        volt = self.__dict__[name+"_volt"].to_python()
        plot(arange(len(volt))*h.dt, volt)

    def calc_area(self):
        self.total_area = 0
        self.n = 0
        for sect in self.all_sec:
            self.total_area += h.area(0.5,sec=sect)
            self.n+=1

###############################################################################
#
# Basket Cell -- Bwb
#
###############################################################################

class Bwb(Cell):
    "Basket cell"

    def set_morphology(self):
        total_area = 10000 # um2
        self.soma.nseg  = 1
        self.soma.cm    = 1      # uF/cm2
        diam = sqrt(total_area) # um
        L    = diam/pi  # um

        h.pt3dclear(sec=self.soma)
        h.pt3dadd(self.x, self.y, self.z,   diam, sec=self.soma)
        h.pt3dadd(self.x, self.y, self.z+L, diam, sec=self.soma)

    def set_conductances(self):
        self.soma.insert('pas')
        self.soma.e_pas = -65     # mV
        self.soma.g_pas = 0.1e-3  # S/cm2

        self.soma.insert('Nafbwb')
        self.soma.insert('Kdrbwb')

    def set_synapses(self):
        self.somaAMPAf  = Synapse(sect=self.soma, loc=0.5, tau1=0.05, tau2=5.3, e=0)
        self.somaGABAf  = Synapse(sect=self.soma, loc=0.5, tau1=0.07, tau2=9.1, e=-80)
        self.somaGABAss = Synapse(sect=self.soma, loc=0.5, tau1=20,   tau2=40, e=-80)#only for septal input
        self.somaNMDA   = SynapseNMDA(sect=self.soma, loc=0.5, tau1=0.05, tau2=5.3, tau1NMDA=15, tau2NMDA=150, r=1, e=0)

###############################################################################
#
# OLM Cell -- Ow
#
###############################################################################
class Ow(Cell):
    "OLM cell"

    def set_morphology(self):
        total_area = 10000 # um2
        self.soma.nseg  = 1
        self.soma.cm    = 1      # uF/cm2
        diam = sqrt(total_area) # um
        L    = diam/pi  # um

        h.pt3dclear(sec=self.soma)
        h.pt3dadd(self.x, self.y, self.z,   diam, sec=self.soma)
        h.pt3dadd(self.x, self.y, self.z+L, diam, sec=self.soma)

    def set_conductances(self):
        self.soma.insert('pas')
        self.soma.e_pas = -65     # mV
        self.soma.g_pas = 0.1e-3  # S/cm2

        self.soma.insert('Nafbwb')
        self.soma.insert('Kdrbwb')

        self.soma.insert('Iholmw')
        self.soma.insert('Caolmw')
        self.soma.insert('ICaolmw')
        self.soma.insert('KCaolmw')

    def set_synapses(self):
        self.somaGABAf  = Synapse(sect=self.soma, loc=0.5, tau1=0.07, tau2=9.1, e=-80)
        self.somaAMPAf  = Synapse(    sect=self.soma, loc=0.5, tau1=0.05, tau2=5.3, e=0)
        self.somaGABAss = Synapse(    sect=self.soma, loc=0.5, tau1=20,   tau2=40, e=-80)#only for septal input
        self.somaNMDA   = SynapseNMDA(sect=self.soma, loc=0.5, tau1=0.05, tau2=5.3, tau1NMDA=15, tau2NMDA=150, r=1, e=0)

###############################################################################
#
# Pyramidal Cell -- KopAdr
#
###############################################################################
class PyrAdr(Cell):
    "Pyramidal cell"

    def set_morphology(self):
        self.add_comp('Bdend',True)
        self.add_comp('Adend1',False)
        self.add_comp('Adend2',False)
        self.add_comp('Adend3',True)

        h.pt3dclear(sec=self.soma)
        h.pt3dadd(self.x, self.y, self.z,          20, sec=self.soma)
        h.pt3dadd(self.x, self.y, self.z+20,       20, sec=self.soma)

        h.pt3dclear(sec=self.Bdend)
        h.pt3dadd(self.x, self.y, self.z,          2, sec=self.Bdend)
        h.pt3dadd(self.x, self.y, self.z-200,      2, sec=self.Bdend)

        h.pt3dclear(sec=self.Adend1)
        h.pt3dadd(self.x, self.y, self.z+20,       2, sec=self.Adend1)
        h.pt3dadd(self.x, self.y, self.z+20+150,   2, sec=self.Adend1)

        h.pt3dclear(sec=self.Adend2)
        h.pt3dadd(self.x, self.y, self.z+20+150,   2, sec=self.Adend2)
        h.pt3dadd(self.x, self.y, self.z+20+150*2, 2, sec=self.Adend2)

        h.pt3dclear(sec=self.Adend3)
        h.pt3dadd(self.x, self.y, self.z+20+150*2, 2, sec=self.Adend3)
        h.pt3dadd(self.x, self.y, self.z+20+150*3, 2, sec=self.Adend3)

        self.Bdend.connect(self.soma,      0, 0)
        self.Adend1.connect(self.soma,   0.5, 0)
        self.Adend2.connect(self.Adend1,   1, 0)
        self.Adend3.connect(self.Adend2,   1, 0)

    def set_conductances(self):
        for sect in self.all_sec:
            sect.insert('pas')
            sect(0.5).pas.g = 0.0000357
            sect.insert('nacurrent')
            sect.insert('kacurrent')
            sect.insert('kdrcurrent')
            sect.insert('hcurrent')
            sect(0.5).pas.e = -70     # mV
            sect.cm = 1
            sect.Ra = 150

        self.Adend1(0.5).nacurrent.ki = 0.5
        self.Adend1(0.5).kacurrent.g  = 0.072
        self.Adend1(0.5).hcurrent.v50 = -82
        self.Adend1(0.5).hcurrent.g   = 0.0002

        self.Adend2(0.5).nacurrent.ki = 0.5
        self.Adend2(0.5).kacurrent.g  = 0
        self.Adend2(0.5).kacurrent.gd = 0.120
        self.Adend2(0.5).hcurrent.v50 = -90
        self.Adend2(0.5).hcurrent.g   = 0.0004

        self.Adend3(0.5).cm           = 2
        self.Adend3(0.5).pas.g        = 0.0000714
        self.Adend3(0.5).nacurrent.ki = 0.5
        self.Adend3(0.5).kacurrent.g  = 0
        self.Adend3(0.5).kacurrent.gd = 0.200
        self.Adend3(0.5).hcurrent.v50 = -90
        self.Adend3(0.5).hcurrent.g   = 0.0007

        self.Bdend(0.5).nacurrent.ki  = 1

    def set_synapses(self):
        self.somaGABAf   = Synapse(    sect=self.soma,   loc=0.5, tau1=0.07, tau2=9.1,    e=-80)
        self.somaAMPAf   = Synapse(    sect=self.soma,   loc=0.5, tau1=0.05, tau2=5.3,     e=0)
        self.BdendAMPA   = Synapse(    sect=self.Bdend,  loc=1.0, tau1=0.05, tau2=5.3,     e=0)
        self.BdendNMDA   = SynapseNMDA(sect=self.Bdend,  loc=1.0, tau1=0.05, tau2=5.3, tau1NMDA=15, tau2NMDA=150, r=1, e=0)
        self.Adend2GABAs = Synapse(        sect=self.Adend2, loc=0.5, tau1=0.2,  tau2=20,   e=-80)
        self.Adend3GABAf = Synapse(        sect=self.Adend3, loc=0.5, tau1=0.07, tau2=9.1,   e=-80)
        self.Adend3AMPAf = Synapse(        sect=self.Adend3, loc=0.5, tau1=0.05, tau2=5.3,    e=0)
        self.Adend3NMDA  = SynapseNMDA(sect=self.Adend3, loc=0.5, tau1=0.05, tau2=5.3, tau1NMDA=15, tau2NMDA=150, r=1, e=0)