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HaspelODonovanDataReader

HaspelODonovanDataReader

Bases: ConnectomeDataset

Reader for HaspelODonovan connectivity dataset

Source code in cect/readers/HaspelODonovanDataReader.py 
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class HaspelODonovanDataReader(ConnectomeDataset):
    """Reader for HaspelODonovan connectivity dataset"""

    def __init__(self, full_or_one_seg):
        ConnectomeDataset.__init__(self)

        self.full_or_one_seg = full_or_one_seg

        cells, conns = self.read_all_data()

        for conn in conns:
            self.add_connection_info(
                conn,
                append_existing_connections=False,
                check_overwritten_connections=True,
                fail_on_any_repeated_connection=True,
            )

    def read_all_data(self):

        cells = set([])
        conns = []

        import scipy.io

        print_("Loading data from: %s" % filename)
        mat = scipy.io.loadmat(filename)

        names = [
            str(n[0]) for n in mat["Names_conn_%s" % self.full_or_one_seg].flatten()
        ]
        A = mat["A_conn_%s" % self.full_or_one_seg]
        J = mat["J_conn_%s" % self.full_or_one_seg]

        for i, pre in enumerate(names):
            pre = _standardise_cell_name(pre)[0]
            cells.add(pre)
            for j, post in enumerate(names):
                posts = _standardise_cell_name(post)
                for post in posts:
                    cells.add(post)
                    w = A[j, i]
                    if w != 0:
                        print_("%s -> %s: A=%d" % (pre, post, w))
                        conns.append(
                            ConnectionInfo(
                                pre,
                                post,
                                w if w > 0 else -w,
                                CHEMICAL_SYN_TYPE,
                                GENERIC_EXCITATORY_CHEM_SYN_CLASS
                                if w > 0
                                else GENERIC_INHIBITORY_CHEM_SYN_CLASS,
                            )
                        )

                    if J[j, i] != 0:
                        print_("%s -> %s: J=%d" % (pre, post, J[j, i]))
                        conns.append(
                            ConnectionInfo(
                                pre,
                                post,
                                J[j, i],
                                ELECTRICAL_SYN_TYPE,
                                GENERIC_ELEC_SYN_CLASS,
                            )
                        )

        print_("Loaded %d cells and %d connections" % (len(cells), len(conns)))

        return cells, conns

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

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