'''

    Parameters C:
        Cells:           Single compartment, conductance based cell models with HH like ion channels
        Chem Synapses:   Event based, ohmic; one rise & one decay constant
        Gap junctions:   Electrical connection; current linerly depends on difference in voltages 
        
    ASSESSMENT:
        May be possible to use this to generate oscilliatory behaviour, but use of event based synapses normally requires
        spiking in cells, so core neurons will have to have clear spikes.

'''

from neuroml import Cell
from neuroml import Morphology
from neuroml import Point3DWithDiam
from neuroml import Segment
from neuroml import BiophysicalProperties
from neuroml import IntracellularProperties
from neuroml import Resistivity
from neuroml import Species
from neuroml import MembraneProperties
from neuroml import InitMembPotential
from neuroml import SpecificCapacitance
from neuroml import ChannelDensity
from neuroml import SpikeThresh
from neuroml import FixedFactorConcentrationModel

from neuroml import ExpTwoSynapse
from neuroml import GapJunction
from neuroml import PulseGenerator

from bioparameters import c302ModelPrototype

class ParameterisedModel(c302ModelPrototype):

    def __init__(self):
        super(ParameterisedModel, self).__init__()
        self.level = "C"
        self.custom_component_types_definitions = 'cell_C.xml'
        
        self.set_default_bioparameters()
        self.print_("Set default parameters for %s"%self.level)

    def set_default_bioparameters(self):

        self.add_bioparameter("cell_diameter", "5", "BlindGuess", "0.1")
        self.add_bioparameter("muscle_length", "20", "BlindGuess", "0.1")

        self.add_bioparameter("initial_memb_pot", "-45 mV", "BlindGuess", "0.1")
        
        self.add_bioparameter("specific_capacitance", "1 uF_per_cm2", "BlindGuess", "0.1")

        self.add_bioparameter("muscle_spike_thresh", "-20 mV", "BlindGuess", "0.1")
        self.add_bioparameter("neuron_spike_thresh", "-20 mV", "BlindGuess", "0.1")

        self.add_bioparameter("muscle_leak_cond_density", "5e-7 S_per_cm2", "BlindGuess", "0.1")
        self.add_bioparameter("neuron_leak_cond_density", "0.005 mS_per_cm2", "BlindGuess", "0.1")
        self.add_bioparameter("leak_erev", "-50 mV", "BlindGuess", "0.1")

        self.add_bioparameter("muscle_k_slow_cond_density", "0.0006 S_per_cm2", "BlindGuess", "0.1")
        self.add_bioparameter("neuron_k_slow_cond_density", "3 mS_per_cm2", "BlindGuess", "0.1")
        self.add_bioparameter("k_slow_erev", "-60 mV", "BlindGuess", "0.1")

        self.add_bioparameter("muscle_k_fast_cond_density", "0.0001 S_per_cm2", "BlindGuess", "0.1")
        self.add_bioparameter("neuron_k_fast_cond_density", "0.0711643917483308 mS_per_cm2", "BlindGuess", "0.1")
        self.add_bioparameter("k_fast_erev", "-60 mV", "BlindGuess", "0.1")

        self.add_bioparameter("muscle_ca_boyle_cond_density", "0.0007 S_per_cm2", "BlindGuess", "0.1")
        self.add_bioparameter("neuron_ca_boyle_cond_density", "3 mS_per_cm2", "BlindGuess", "0.1")
        self.add_bioparameter("ca_boyle_erev", "40 mV", "BlindGuess", "0.1")
        
        self.add_bioparameter("ca_conc_decay_time", "11.5943 ms", "BlindGuess", "0.1")
        self.add_bioparameter("ca_conc_rho", "0.000238919 mol_per_m_per_A_per_s", "BlindGuess", "0.1")


        self.add_bioparameter("neuron_to_neuron_chem_exc_syn_gbase", ".1 nS", "BlindGuess", "0.1")
        self.add_bioparameter("neuron_to_muscle_chem_exc_syn_gbase", ".1 nS", "BlindGuess", "0.1")

        self.add_bioparameter("chem_exc_syn_erev", "0 mV", "BlindGuess", "0.1")
        self.add_bioparameter("chem_exc_syn_rise", "1 ms", "Bli ndGuess", "0.1")
        self.add_bioparameter("chem_exc_syn_decay", "5 ms", "BlindGuess", "0.1")

        self.add_bioparameter("neuron_to_neuron_chem_inh_syn_gbase", ".1 nS", "BlindGuess", "0.1")
        self.add_bioparameter("neuron_to_muscle_chem_inh_syn_gbase", ".1 nS", "BlindGuess", "0.1")

        self.add_bioparameter("chem_inh_syn_erev", "-60 mV", "BlindGuess", "0.1")
        self.add_bioparameter("chem_inh_syn_rise", "2 ms", "BlindGuess", "0.1")
        self.add_bioparameter("chem_inh_syn_decay", "40 ms", "BlindGuess", "0.1")

        self.add_bioparameter("neuron_to_neuron_elec_syn_gbase", "0.0005 nS", "BlindGuess", "0.1")
        self.add_bioparameter("neuron_to_muscle_elec_syn_gbase", "0.0005 nS", "BlindGuess", "0.1")

        self.add_bioparameter("unphysiological_offset_current", "6.076428433117039 pA", "KnownError", "0")
        self.add_bioparameter("unphysiological_offset_current_del", "0 ms", "KnownError", "0")
        self.add_bioparameter("unphysiological_offset_current_dur", "2000 ms", "KnownError", "0")





    def create_models(self):
        self.create_generic_muscle_cell()
        self.create_generic_neuron_cell()
        self.create_offsetcurrent_concentrationmodel()
        self.create_neuron_to_neuron_syn()
        self.create_neuron_to_muscle_syn()


    def create_generic_muscle_cell(self):

        self.generic_muscle_cell = Cell(id = "GenericMuscleCell")

        morphology = Morphology()
        morphology.id = "morphology_"+self.generic_muscle_cell.id

        self.generic_muscle_cell.morphology = morphology

        prox_point = Point3DWithDiam(x="0", y="0", z="0", diameter=self.get_bioparameter("cell_diameter").value)
        dist_point = Point3DWithDiam(x="0", y=self.get_bioparameter("muscle_length").value, z="0", diameter=self.get_bioparameter("cell_diameter").value)

        segment = Segment(id="0",
                          name="soma",
                          proximal = prox_point, 
                          distal = dist_point)

        morphology.segments.append(segment)

        self.generic_muscle_cell.biophysical_properties = BiophysicalProperties(id="biophys_"+self.generic_muscle_cell.id)

        mp = MembraneProperties()
        self.generic_muscle_cell.biophysical_properties.membrane_properties = mp

        mp.init_memb_potentials.append(InitMembPotential(value=self.get_bioparameter("initial_memb_pot").value))

        mp.specific_capacitances.append(SpecificCapacitance(value=self.get_bioparameter("specific_capacitance").value))

        mp.spike_threshes.append(SpikeThresh(value=self.get_bioparameter("muscle_spike_thresh").value))

        mp.channel_densities.append(ChannelDensity(cond_density=self.get_bioparameter("muscle_leak_cond_density").value, 
                                                   id="Leak_all", 
                                                   ion_channel="Leak", 
                                                   erev=self.get_bioparameter("leak_erev").value,
                                                   ion="non_specific"))

        mp.channel_densities.append(ChannelDensity(cond_density=self.get_bioparameter("muscle_k_slow_cond_density").value, 
                                                   id="k_slow_all", 
                                                   ion_channel="k_slow", 
                                                   erev=self.get_bioparameter("k_slow_erev").value,
                                                   ion="k"))

        mp.channel_densities.append(ChannelDensity(cond_density=self.get_bioparameter("muscle_k_fast_cond_density").value, 
                                                   id="k_fast_all", 
                                                   ion_channel="k_fast", 
                                                   erev=self.get_bioparameter("k_fast_erev").value,
                                                   ion="k"))

        mp.channel_densities.append(ChannelDensity(cond_density=self.get_bioparameter("muscle_ca_boyle_cond_density").value, 
                                                   id="ca_boyle_all", 
                                                   ion_channel="ca_boyle", 
                                                   erev=self.get_bioparameter("ca_boyle_erev").value,
                                                   ion="ca"))

        ip = IntracellularProperties()
        self.generic_muscle_cell.biophysical_properties.intracellular_properties = ip

        # NOTE: resistivity/axial resistance not used for single compartment cell models, so value irrelevant!
        ip.resistivities.append(Resistivity(value="0.1 kohm_cm"))


        # NOTE: Ca reversal potential not calculated by Nernst, so initial_ext_concentration value irrelevant!
        species = Species(id="ca", 
                          ion="ca",
                          concentration_model="CaPool",
                          initial_concentration="0 mM",
                          initial_ext_concentration="2E-6 mol_per_cm3")

        ip.species.append(species)  


    def create_generic_neuron_cell(self):

        self.generic_neuron_cell = Cell(id = "GenericNeuronCell")

        morphology = Morphology()
        morphology.id = "morphology_"+self.generic_neuron_cell.id

        self.generic_neuron_cell.morphology = morphology

        prox_point = Point3DWithDiam(x="0", y="0", z="0", diameter=self.get_bioparameter("cell_diameter").value)
        dist_point = Point3DWithDiam(x="0", y="0", z="0", diameter=self.get_bioparameter("cell_diameter").value)

        segment = Segment(id="0",
                          name="soma",
                          proximal = prox_point, 
                          distal = dist_point)

        morphology.segments.append(segment)

        self.generic_neuron_cell.biophysical_properties = BiophysicalProperties(id="biophys_"+self.generic_neuron_cell.id)

        mp = MembraneProperties()
        self.generic_neuron_cell.biophysical_properties.membrane_properties = mp

        mp.init_memb_potentials.append(InitMembPotential(value=self.get_bioparameter("initial_memb_pot").value))

        mp.specific_capacitances.append(SpecificCapacitance(value=self.get_bioparameter("specific_capacitance").value))

        mp.spike_threshes.append(SpikeThresh(value=self.get_bioparameter("neuron_spike_thresh").value))

        mp.channel_densities.append(ChannelDensity(cond_density=self.get_bioparameter("neuron_leak_cond_density").value, 
                                                   id="Leak_all", 
                                                   ion_channel="Leak", 
                                                   erev=self.get_bioparameter("leak_erev").value,
                                                   ion="non_specific"))

        mp.channel_densities.append(ChannelDensity(cond_density=self.get_bioparameter("neuron_k_slow_cond_density").value, 
                                                   id="k_slow_all", 
                                                   ion_channel="k_slow", 
                                                   erev=self.get_bioparameter("k_slow_erev").value,
                                                   ion="k"))

        mp.channel_densities.append(ChannelDensity(cond_density=self.get_bioparameter("neuron_k_fast_cond_density").value, 
                                                   id="k_fast_all", 
                                                   ion_channel="k_fast", 
                                                   erev=self.get_bioparameter("k_fast_erev").value,
                                                   ion="k"))

        mp.channel_densities.append(ChannelDensity(cond_density=self.get_bioparameter("neuron_ca_boyle_cond_density").value, 
                                                   id="ca_boyle_all", 
                                                   ion_channel="ca_boyle", 
                                                   erev=self.get_bioparameter("ca_boyle_erev").value,
                                                   ion="ca"))

        ip = IntracellularProperties()
        self.generic_neuron_cell.biophysical_properties.intracellular_properties = ip

        # NOTE: resistivity/axial resistance not used for single compartment cell models, so value irrelevant!
        ip.resistivities.append(Resistivity(value="0.1 kohm_cm"))


        # NOTE: Ca reversal potential not calculated by Nernst, so initial_ext_concentration value irrelevant!
        species = Species(id="ca", 
                          ion="ca",
                          concentration_model="CaPool",
                          initial_concentration="0 mM",
                          initial_ext_concentration="2E-6 mol_per_cm3")

        ip.species.append(species)


    def create_offsetcurrent_concentrationmodel(self):

        self.offset_current = PulseGenerator(id="offset_current",
                                delay=self.get_bioparameter("unphysiological_offset_current_del").value,
                                duration=self.get_bioparameter("unphysiological_offset_current_dur").value,
                                amplitude=self.get_bioparameter("unphysiological_offset_current").value)

    
        self.concentration_model = FixedFactorConcentrationModel(id="CaPool",
                                            ion="ca",
                                            resting_conc="0 mM",
                                            decay_constant=self.get_bioparameter("ca_conc_decay_time").value,
                                            rho=self.get_bioparameter("ca_conc_rho").value)

    def create_neuron_to_neuron_syn(self):
        self.neuron_to_neuron_exc_syn = ExpTwoSynapse(id="neuron_to_neuron_exc_syn",
                                gbase =         self.get_bioparameter("neuron_to_neuron_chem_exc_syn_gbase").value,
                                erev =          self.get_bioparameter("chem_exc_syn_erev").value,
                                tau_decay =     self.get_bioparameter("chem_exc_syn_decay").value,
                                tau_rise =      self.get_bioparameter("chem_exc_syn_rise").value)


        self.neuron_to_neuron_inh_syn = ExpTwoSynapse(id="neuron_to_neuron_inh_syn",
                                gbase =         self.get_bioparameter("neuron_to_neuron_chem_inh_syn_gbase").value,
                                erev =          self.get_bioparameter("chem_inh_syn_erev").value,
                                tau_decay =     self.get_bioparameter("chem_inh_syn_decay").value,
                                tau_rise =      self.get_bioparameter("chem_inh_syn_rise").value)

        self.neuron_to_neuron_elec_syn = GapJunction(id="neuron_to_neuron_elec_syn",
                               conductance =    self.get_bioparameter("neuron_to_neuron_elec_syn_gbase").value)


    def create_neuron_to_muscle_syn(self):
        self.neuron_to_muscle_exc_syn = ExpTwoSynapse(id="neuron_to_muscle_exc_syn",
                                gbase =         self.get_bioparameter("neuron_to_muscle_chem_exc_syn_gbase").value,
                                erev =          self.get_bioparameter("chem_exc_syn_erev").value,
                                tau_decay =     self.get_bioparameter("chem_exc_syn_decay").value,
                                tau_rise =      self.get_bioparameter("chem_exc_syn_rise").value)


        self.neuron_to_muscle_inh_syn = ExpTwoSynapse(id="neuron_to_muscle_inh_syn",
                                gbase =         self.get_bioparameter("neuron_to_muscle_chem_inh_syn_gbase").value,
                                erev =          self.get_bioparameter("chem_inh_syn_erev").value,
                                tau_decay =     self.get_bioparameter("chem_inh_syn_decay").value,
                                tau_rise =      self.get_bioparameter("chem_inh_syn_rise").value)

        self.neuron_to_muscle_elec_syn = GapJunction(id="neuron_to_muscle_elec_syn",
                               conductance =    self.get_bioparameter("neuron_to_muscle_elec_syn_gbase").value)



    def get_elec_syn(self, pre_cell, post_cell, type):
        self.found_specific_param = False
        if type == 'neuron_to_neuron':
            gbase = self.get_conn_param(pre_cell, post_cell, '%s_to_%s_elec_syn_%s', 'neuron_to_neuron_elec_syn_%s', 'gbase')
            conn_id = 'neuron_to_neuron_elec_syn'
        elif type == 'neuron_to_muscle':
            gbase = self.get_conn_param(pre_cell, post_cell, '%s_to_%s_elec_syn_%s', 'neuron_to_muscle_elec_syn_%s', 'gbase')
            conn_id = 'neuron_to_muscle_elec_syn'

        if self.found_specific_param:
            conn_id = '%s_to_%s_elec_syn' % (pre_cell, post_cell)

        return GapJunction(id=conn_id, conductance=gbase)



    def get_exc_syn(self, pre_cell, post_cell, type):
        self.found_specific_param = False

        specific_param_template = '%s_to_%s_chem_exc_syn_%s'
        if type == 'neuron_to_neuron':
            gbase = self.get_conn_param(pre_cell, post_cell, specific_param_template,
                                                              'neuron_to_neuron_chem_exc_syn_%s', 'gbase')
            erev = self.get_conn_param(pre_cell, post_cell, specific_param_template,
                                                             'chem_exc_syn_%s', 'erev')
            decay = self.get_conn_param(pre_cell, post_cell, specific_param_template,
                                                              'chem_exc_syn_%s', 'decay')
            rise = self.get_conn_param(pre_cell, post_cell, specific_param_template,
                                                             'chem_exc_syn_%s', 'rise')
            
            conn_id = 'neuron_to_neuron_exc_syn'

        elif type == 'neuron_to_muscle':
            gbase = self.get_conn_param(pre_cell, post_cell, specific_param_template,
                                                              'neuron_to_muscle_chem_exc_syn_%s', 'gbase')
            erev = self.get_conn_param(pre_cell, post_cell, specific_param_template,
                                                             'chem_exc_syn_%s', 'erev')
            decay = self.get_conn_param(pre_cell, post_cell, specific_param_template,
                                                              'chem_exc_syn_%s', 'decay')
            rise = self.get_conn_param(pre_cell, post_cell, specific_param_template,
                                                             'chem_exc_syn_%s', 'rise')
            conn_id = 'neuron_to_muscle_exc_syn'

        if self.found_specific_param:
            conn_id = '%s_to_%s_exc_syn' % (pre_cell, post_cell)

        return ExpTwoSynapse(id=conn_id,
                             gbase=gbase,
                             erev=erev,
                             tau_decay=decay,
                             tau_rise=rise)

    def get_inh_syn(self, pre_cell, post_cell, type):
        self.found_specific_param = False

        specific_param_template = '%s_to_%s_chem_inh_syn_%s'
        if type == 'neuron_to_neuron':
            gbase = self.get_conn_param(pre_cell, post_cell, specific_param_template,
                                                              'neuron_to_neuron_chem_inh_syn_%s', 'gbase')
            erev = self.get_conn_param(pre_cell, post_cell, specific_param_template,
                                                             'chem_inh_syn_%s', 'erev')
            decay = self.get_conn_param(pre_cell, post_cell, specific_param_template,
                                                              'chem_inh_syn_%s', 'decay')
            rise = self.get_conn_param(pre_cell, post_cell, specific_param_template,
                                                             'chem_inh_syn_%s', 'rise')
            
            conn_id = 'neuron_to_neuron_inh_syn'

        elif type == 'neuron_to_muscle':
            gbase = self.get_conn_param(pre_cell, post_cell, specific_param_template,
                                                              'neuron_to_muscle_chem_inh_syn_%s', 'gbase')
            erev = self.get_conn_param(pre_cell, post_cell, specific_param_template,
                                                             'chem_inh_syn_%s', 'erev')
            decay = self.get_conn_param(pre_cell, post_cell, specific_param_template,
                                                              'chem_inh_syn_%s', 'decay')
            rise = self.get_conn_param(pre_cell, post_cell, specific_param_template,
                                                             'chem_inh_syn_%s', 'rise')
            conn_id = 'neuron_to_muscle_inh_syn'

        if self.found_specific_param:
            conn_id = '%s_to_%s_inh_syn' % (pre_cell, post_cell)

        return ExpTwoSynapse(id=conn_id,
                             gbase=gbase,
                             erev=erev,
                             tau_decay=decay,
                             tau_rise=rise)

