Пример #1
0
def populate(infile, outfile):
    dbmodel.db.connect()
    dbmodel.create_db()
    from dbmodel import Cells, Synapses
    
    # load the individual neurons
    indata = pickle.load(open(infile, 'r'))
    neurons = indata['neurons']

    for neuron_name, nd in neurons.iterrows():
        nt = nd['neurotransmitters']
        if type(nt) == float:
            nt = None

        role = nd['role']
        if type(role)==float:
            role = None
        Cells.create(cell_name =neuron_name, 
                     cell_class= nd['class'], 
                     soma_pos = nd['soma_pos'], 
                     neurotransmitters=nt, 
                     role = role)
        
    connections = indata['connections']
    
    for n1 in neurons.index.values:
        for n2 in neurons.index.values:
            c1 = Cells.get(Cells.cell_name == n1)
            c2 = Cells.get(Cells.cell_name == n2)

            c = (n1, n2)
            if c in connections:
                for synapse_type, nbr in connections[c]:
                    code = synapse_type[0]
                    st_short = None
                    # note this dataset includes entries for both A sends to B (type S) and B receives from A (type R)
                    if code == "Sp" or code == 'S':
                        st_short = 'C'
                    elif code == 'E':
                        st_short = 'E'
                    elif code == 'R' or code == 'Rp':
                        pass
                    else:
                        raise Exception("code %s not understood" % code)
                    if st_short:
                        s = Synapses.select().where(Synapses.from_id == c1, 
                                                    Synapses.to_id == c2, 
                                                    Synapses.synapse_type == st_short).count()
                        if s == 0:

                            Synapses.create(from_id = c1,
                                            to_id = c2, 
                                            synapse_type = st_short,
                                            count = nbr)
                        else:
                            Synapses.update(count = Synapses.count + nbr).where(Synapses.from_id == c1, 
                                                                                Synapses.to_id == c2, 
                                                                                synapse_type == st_short)
    dbmodel.db.close()
Пример #2
0
def populate(infile, outfile):
    dbmodel.db.connect()
    dbmodel.create_db()
    from dbmodel import Cells, Synapses

    # load the individual neurons
    indata = pickle.load(open(infile, 'r'))
    neurons = indata['neurons']

    for neuron_name, nd in neurons.iterrows():
        nt = nd['neurotransmitters']
        if type(nt) == float:
            nt = None

        role = nd['role']
        if type(role) == float:
            role = None
        Cells.create(cell_name=neuron_name,
                     cell_class=nd['class'],
                     soma_pos=nd['soma_pos'],
                     neurotransmitters=nt,
                     role=role)

    connections = indata['connections']

    for n1 in neurons.index.values:
        for n2 in neurons.index.values:
            c1 = Cells.get(Cells.cell_name == n1)
            c2 = Cells.get(Cells.cell_name == n2)

            c = (n1, n2)
            if c in connections:
                for synapse_type, nbr in connections[c]:
                    code = synapse_type[0]
                    st_short = None
                    # note this dataset includes entries for both A sends to B (type S) and B receives from A (type R)
                    if code == "Sp" or code == 'S':
                        st_short = 'C'
                    elif code == 'E':
                        st_short = 'E'
                    elif code == 'R' or code == 'Rp':
                        pass
                    else:
                        raise Exception("code %s not understood" % code)
                    if st_short:
                        s = Synapses.select().where(
                            Synapses.from_id == c1, Synapses.to_id == c2,
                            Synapses.synapse_type == st_short).count()
                        if s == 0:

                            Synapses.create(from_id=c1,
                                            to_id=c2,
                                            synapse_type=st_short,
                                            count=nbr)
                        else:
                            Synapses.update(count=Synapses.count + nbr).where(
                                Synapses.from_id == c1, Synapses.to_id == c2,
                                synapse_type == st_short)
    dbmodel.db.close()
Пример #3
0
def create_db(_, outfile):

    dbmodel.db.connect()

    dbmodel.create_db()