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WhiteDataReader

WhiteDataReader

Bases: ConnectomeDataset

Reader for datasets from White et al. 1986

Source code in cect/WhiteDataReader.py 
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class WhiteDataReader(ConnectomeDataset):
    """Reader for datasets from [White et al. 1986](../../White_1986.md)"""

    verbose = False

    def __init__(self, spreadsheet_filename):
        ConnectomeDataset.__init__(self)
        self.filename = spreadsheet_filename

        neurons, muscles, other_cells, conns = self.read_all_data()
        # neurons, conns = self.read_data()

        for conn in conns:
            self.add_connection_info(conn)

    def read_data(self):
        return self._read_data()

    def read_muscle_data(self):
        return self._read_muscle_data()

    def read_all_data(self):
        neurons = set([])
        muscles = set([])
        other_cells = set([])
        conns = []

        with open(self.filename, "r") as f:
            print_("Opened file: " + self.filename)
            f.readline()

            # known_nonconnected_cells = ["CANL", "CANR"]

            for line in f:
                pre, post, num, syntype, synclass = parse_line(line)

                pre = remove_leading_index_zero(pre)
                post = remove_leading_index_zero(post)

                if is_potential_muscle(pre):
                    pre = convert_to_preferred_muscle_name(pre)

                if is_potential_muscle(post):
                    post = convert_to_preferred_muscle_name(post)

                if synclass == "Generic_GJ":
                    conns.append(ConnectionInfo(post, pre, num, syntype, synclass))

                conns.append(ConnectionInfo(pre, post, num, syntype, synclass))

                for p in [pre, post]:
                    if is_herm_neuron(p):
                        neurons.add(pre)
                    elif is_known_muscle(p):
                        muscles.add(pre)
                    else:
                        other_cells.add(p)

        return list(neurons), list(muscles), list(other_cells), conns