multielectrode_grasp/code/python-neo/neo/io/nixio.py

# -*- coding: utf-8 -*-
# Copyright (c) 2016, German Neuroinformatics Node (G-Node)
#                     Achilleas Koutsou <achilleas.k@gmail.com>
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted under the terms of the BSD License. See
# LICENSE file in the root of the Project.
"""
Module for reading data from files in the NIX format.

Author: Achilleas Koutsou

This IO supports both writing and reading of NIX files. Reading is supported
only if the NIX file was created using this IO.
"""

from __future__ import absolute_import

import time
from datetime import datetime
from collections import Iterable
import itertools
from hashlib import md5
from uuid import uuid4

import quantities as pq
import numpy as np

from neo.io.baseio import BaseIO
from neo.core import (Block, Segment, ChannelIndex, AnalogSignal,
                      IrregularlySampledSignal, Epoch, Event, SpikeTrain, Unit)
from neo.io.tools import LazyList

try:
    import nixio as nix
    HAVE_NIX = True
except ImportError:
    HAVE_NIX = False

try:
    string_types = basestring
except NameError:
    string_types = str


def stringify(value):
    if value is None:
        return value
    if isinstance(value, bytes):
        value = value.decode()
    return str(value)


def calculate_timestamp(dt):
    if isinstance(dt, datetime):
        return int(time.mktime(dt.timetuple()))
    return int(dt)


class NixIO(BaseIO):
    """
    Class for reading and writing NIX files.
    """

    is_readable = True
    is_writable = True

    supported_objects = [Block, Segment, ChannelIndex,
                         AnalogSignal, IrregularlySampledSignal,
                         Epoch, Event, SpikeTrain, Unit]
    readable_objects = [Block]
    writeable_objects = [Block]

    name = "NIX"
    extensions = ["h5"]
    mode = "file"

    _container_map = {
        "segments": "groups",
        "analogsignals": "data_arrays",
        "irregularlysampledsignals": "data_arrays",
        "events": "multi_tags",
        "epochs": "multi_tags",
        "spiketrains": "multi_tags",
        "channel_indexes": "sources",
        "units": "sources"
    }

    def __init__(self, filename, mode="rw"):
        """
        Initialise IO instance and NIX file.

        :param filename: Full path to the file
        """

        if not HAVE_NIX:
            raise Exception("Failed to import NIX. "
                            "The NixIO requires the Python bindings for NIX "
                            "(nixio on PyPi). Try `pip install nixio`.")

        BaseIO.__init__(self, filename)
        self.filename = filename
        if mode == "ro":
            filemode = nix.FileMode.ReadOnly
        elif mode == "rw":
            filemode = nix.FileMode.ReadWrite
        elif mode == "ow":
            filemode = nix.FileMode.Overwrite
        else:
            raise ValueError("Invalid mode specified '{}'. "
                             "Valid modes: 'ro' (ReadOnly)', 'rw' (ReadWrite),"
                             " 'ow' (Overwrite).".format(mode))
        self.nix_file = nix.File.open(self.filename, filemode, backend="h5py")
        self._neo_map = dict()
        self._nix_map = dict()
        self._lazy_loaded = list()
        self._object_hashes = dict()
        self._block_read_counter = 0
        self._path_map = dict()

    def __enter__(self):
        return self

    def __exit__(self, *args):
        self.close()

    def read_all_blocks(self, cascade=True, lazy=False):
        blocks = list()
        for blk in self.nix_file.blocks:
            blocks.append(self.read_block("/" + blk.name, cascade, lazy))
        return blocks

    def read_block(self, path="/", cascade=True, lazy=False):
        if path == "/":
            try:
                nix_block = self.nix_file.blocks[self._block_read_counter]
                path += nix_block.name
                self._block_read_counter += 1
            except KeyError:
                return None
        else:
            nix_block = self._get_object_at(path)
        neo_block = self._block_to_neo(nix_block)
        neo_block.path = path
        if cascade:
            self._read_cascade(nix_block, path, cascade, lazy)
        self._update_maps(neo_block, lazy)
        return neo_block

    def read_segment(self, path, cascade=True, lazy=False):
        nix_group = self._get_object_at(path)
        neo_segment = self._group_to_neo(nix_group)
        neo_segment.path = path
        if cascade:
            self._read_cascade(nix_group, path, cascade, lazy)
        self._update_maps(neo_segment, lazy)
        nix_parent = self._get_parent(path)
        neo_parent = self._neo_map.get(nix_parent.name)
        if neo_parent:
            neo_segment.block = neo_parent
        return neo_segment

    def read_channelindex(self, path, cascade=True, lazy=False):
        nix_source = self._get_object_at(path)
        neo_rcg = self._source_chx_to_neo(nix_source)
        neo_rcg.path = path
        if cascade:
            self._read_cascade(nix_source, path, cascade, lazy)
        self._update_maps(neo_rcg, lazy)
        nix_parent = self._get_parent(path)
        neo_parent = self._neo_map.get(nix_parent.name)
        neo_rcg.block = neo_parent
        return neo_rcg

    def read_signal(self, path, lazy=False):
        nix_data_arrays = list()
        parent_group = self._get_parent(path)
        parent_container = parent_group.data_arrays
        signal_group_name = path.split("/")[-1]
        for idx in itertools.count():
            signal_name = "{}.{}".format(signal_group_name, idx)
            if signal_name in parent_container:
                nix_data_arrays.append(parent_container[signal_name])
            else:
                break
        # check metadata segment
        group_section = nix_data_arrays[0].metadata
        for da in nix_data_arrays:
            assert da.metadata == group_section,\
                "DataArray {} is not a member of signal group {}".format(
                    da.name, group_section.name
                )
        neo_signal = self._signal_da_to_neo(nix_data_arrays, lazy)
        neo_signal.path = path
        if self._find_lazy_loaded(neo_signal) is None:
            self._update_maps(neo_signal, lazy)
            nix_parent = self._get_parent(path)
            neo_parent = self._neo_map.get(nix_parent.name)
            neo_signal.segment = neo_parent
        return neo_signal

    def read_analogsignal(self, path, cascade=True, lazy=False):
        return self.read_signal(path, lazy)

    def read_irregularlysampledsignal(self, path, cascade=True, lazy=False):
        return self.read_signal(path, lazy)

    def read_eest(self, path, lazy=False):
        nix_mtag = self._get_object_at(path)
        neo_eest = self._mtag_eest_to_neo(nix_mtag, lazy)
        neo_eest.path = path
        self._update_maps(neo_eest, lazy)
        nix_parent = self._get_parent(path)
        neo_parent = self._neo_map.get(nix_parent.name)
        neo_eest.segment = neo_parent
        return neo_eest

    def read_epoch(self, path, cascade=True, lazy=False):
        return self.read_eest(path, lazy)

    def read_event(self, path, cascade=True, lazy=False):
        return self.read_eest(path, lazy)

    def read_spiketrain(self, path, cascade=True, lazy=False):
        return self.read_eest(path, lazy)

    def read_unit(self, path, cascade=True, lazy=False):
        nix_source = self._get_object_at(path)
        neo_unit = self._source_unit_to_neo(nix_source)
        neo_unit.path = path
        if cascade:
            self._read_cascade(nix_source, path, cascade, lazy)
        self._update_maps(neo_unit, lazy)
        nix_parent = self._get_parent(path)
        neo_parent = self._neo_map.get(nix_parent.name)
        neo_unit.channel_index = neo_parent
        return neo_unit

    def _block_to_neo(self, nix_block):
        neo_attrs = self._nix_attr_to_neo(nix_block)
        neo_block = Block(**neo_attrs)
        neo_block.rec_datetime = datetime.fromtimestamp(
            nix_block.created_at
        )
        self._neo_map[nix_block.name] = neo_block
        return neo_block

    def _group_to_neo(self, nix_group):
        neo_attrs = self._nix_attr_to_neo(nix_group)
        neo_segment = Segment(**neo_attrs)
        neo_segment.rec_datetime = datetime.fromtimestamp(
            nix_group.created_at
        )
        self._neo_map[nix_group.name] = neo_segment
        return neo_segment

    def _source_chx_to_neo(self, nix_source):
        neo_attrs = self._nix_attr_to_neo(nix_source)
        chx = list(self._nix_attr_to_neo(c)
                   for c in nix_source.sources
                   if c.type == "neo.channelindex")
        chan_names = list(c["neo_name"] for c in chx if "neo_name" in c)
        chan_ids = list(c["channel_id"] for c in chx if "channel_id" in c)
        if chan_names:
            neo_attrs["channel_names"] = chan_names
        if chan_ids:
            neo_attrs["channel_ids"] = chan_ids
        neo_attrs["index"] = np.array([c["index"] for c in chx])
        if "coordinates" in chx[0]:
            coord_units = chx[0]["coordinates.units"]
            coord_values = list(c["coordinates"] for c in chx)
            neo_attrs["coordinates"] = pq.Quantity(coord_values, coord_units)
        rcg = ChannelIndex(**neo_attrs)
        self._neo_map[nix_source.name] = rcg
        return rcg

    def _source_unit_to_neo(self, nix_unit):
        neo_attrs = self._nix_attr_to_neo(nix_unit)
        neo_unit = Unit(**neo_attrs)
        self._neo_map[nix_unit.name] = neo_unit
        return neo_unit

    def _signal_da_to_neo(self, nix_da_group, lazy):
        """
        Convert a group of NIX DataArrays to a Neo signal. This method expects
        a list of data arrays that all represent the same, multidimensional
        Neo Signal object.
        This returns either an AnalogSignal or IrregularlySampledSignal.

        :param nix_da_group: a list of NIX DataArray objects
        :return: a Neo Signal object
        """
        nix_da_group = sorted(nix_da_group, key=lambda d: d.name)
        neo_attrs = self._nix_attr_to_neo(nix_da_group[0])
        metadata = nix_da_group[0].metadata
        neo_type = nix_da_group[0].type
        neo_attrs["nix_name"] = metadata.name  # use the common base name

        unit = nix_da_group[0].unit
        if lazy:
            signaldata = pq.Quantity(np.empty(0), unit)
            lazy_shape = (len(nix_da_group[0]), len(nix_da_group))
        else:
            signaldata = np.array([d[:] for d in nix_da_group]).transpose()
            signaldata = pq.Quantity(signaldata, unit)
            lazy_shape = None
        timedim = self._get_time_dimension(nix_da_group[0])
        if (neo_type == "neo.analogsignal" or
                timedim.dimension_type == nix.DimensionType.Sample):
            if lazy:
                sampling_period = pq.Quantity(1, timedim.unit)
                t_start = pq.Quantity(0, timedim.unit)
            else:
                if "sampling_interval.units" in metadata.props:
                    sample_units = metadata["sampling_interval.units"]
                else:
                    sample_units = timedim.unit
                sampling_period = pq.Quantity(timedim.sampling_interval,
                                              sample_units)
                if "t_start.units" in metadata.props:
                    tsunits = metadata["t_start.units"]
                else:
                    tsunits = timedim.unit
                t_start = pq.Quantity(timedim.offset, tsunits)
            neo_signal = AnalogSignal(
                signal=signaldata, sampling_period=sampling_period,
                t_start=t_start, **neo_attrs
            )
        elif (neo_type == "neo.irregularlysampledsignal"
              or timedim.dimension_type == nix.DimensionType.Range):
            if lazy:
                times = pq.Quantity(np.empty(0), timedim.unit)
            else:
                times = pq.Quantity(timedim.ticks, timedim.unit)
            neo_signal = IrregularlySampledSignal(
                signal=signaldata, times=times, **neo_attrs
            )
        else:
            return None
        for da in nix_da_group:
            self._neo_map[da.name] = neo_signal
        if lazy_shape:
            neo_signal.lazy_shape = lazy_shape
        return neo_signal

    def _mtag_eest_to_neo(self, nix_mtag, lazy):
        neo_attrs = self._nix_attr_to_neo(nix_mtag)
        neo_type = nix_mtag.type

        time_unit = nix_mtag.positions.unit
        if lazy:
            times = pq.Quantity(np.empty(0), time_unit)
            lazy_shape = np.shape(nix_mtag.positions)
        else:
            times = pq.Quantity(nix_mtag.positions, time_unit)
            lazy_shape = None
        if neo_type == "neo.epoch":
            if lazy:
                durations = pq.Quantity(np.empty(0), nix_mtag.extents.unit)
                labels = np.empty(0, dtype='S')
            else:
                durations = pq.Quantity(nix_mtag.extents,
                                        nix_mtag.extents.unit)
                labels = np.array(nix_mtag.positions.dimensions[0].labels,
                                  dtype="S")
            eest = Epoch(times=times, durations=durations, labels=labels,
                         **neo_attrs)
        elif neo_type == "neo.event":
            if lazy:
                labels = np.empty(0, dtype='S')
            else:
                labels = np.array(nix_mtag.positions.dimensions[0].labels,
                                  dtype="S")
            eest = Event(times=times, labels=labels, **neo_attrs)
        elif neo_type == "neo.spiketrain":
            if "t_start" in neo_attrs:
                if "t_start.units" in neo_attrs:
                    t_start_units = neo_attrs["t_start.units"]
                    del neo_attrs["t_start.units"]
                else:
                    t_start_units = time_unit
                t_start = pq.Quantity(neo_attrs["t_start"], t_start_units)
                del neo_attrs["t_start"]
            else:
                t_start = None
            if "t_stop" in neo_attrs:
                if "t_stop.units" in neo_attrs:
                    t_stop_units = neo_attrs["t_stop.units"]
                    del neo_attrs["t_stop.units"]
                else:
                    t_stop_units = time_unit
                t_stop = pq.Quantity(neo_attrs["t_stop"], t_stop_units)
                del neo_attrs["t_stop"]
            else:
                t_stop = None
            if "sampling_interval.units" in neo_attrs:
                interval_units = neo_attrs["sampling_interval.units"]
                del neo_attrs["sampling_interval.units"]
            else:
                interval_units = None
            if "left_sweep.units" in neo_attrs:
                left_sweep_units = neo_attrs["left_sweep.units"]
                del neo_attrs["left_sweep.units"]
            else:
                left_sweep_units = None
            eest = SpikeTrain(times=times, t_start=t_start,
                              t_stop=t_stop, **neo_attrs)
            if len(nix_mtag.features):
                wfda = nix_mtag.features[0].data
                wftime = self._get_time_dimension(wfda)
                if lazy:
                    eest.waveforms = pq.Quantity(np.empty((0, 0, 0)),
                                                 wfda.unit)
                    eest.sampling_period = pq.Quantity(1, wftime.unit)
                    eest.left_sweep = pq.Quantity(0, wftime.unit)
                else:
                    eest.waveforms = pq.Quantity(wfda, wfda.unit)
                    if interval_units is None:
                        interval_units = wftime.unit
                    eest.sampling_period = pq.Quantity(
                        wftime.sampling_interval, interval_units
                    )
                    if left_sweep_units is None:
                        left_sweep_units = wftime.unit
                    if "left_sweep" in wfda.metadata:
                        eest.left_sweep = pq.Quantity(
                            wfda.metadata["left_sweep"], left_sweep_units
                        )
        else:
            return None
        self._neo_map[nix_mtag.name] = eest
        if lazy_shape:
            eest.lazy_shape = lazy_shape
        return eest

    def _read_cascade(self, nix_obj, path, cascade, lazy):
        neo_obj = self._neo_map[nix_obj.name]
        for neocontainer in getattr(neo_obj, "_child_containers", []):
            nixcontainer = self._container_map[neocontainer]
            if not hasattr(nix_obj, nixcontainer):
                continue
            if neocontainer == "channel_indexes":
                neotype = "channelindex"
            else:
                neotype = neocontainer[:-1]
            chpaths = list(path + "/" + neocontainer + "/" + c.name
                           for c in getattr(nix_obj, nixcontainer)
                           if c.type == "neo." + neotype)
            if neocontainer in ("analogsignals",
                                "irregularlysampledsignals"):
                chpaths = self._group_signals(chpaths)
            if cascade != "lazy":
                read_func = getattr(self, "read_" + neotype)
                children = list(read_func(cp, cascade, lazy)
                                for cp in chpaths)
            else:
                children = LazyList(self, lazy, chpaths)
            setattr(neo_obj, neocontainer, children)

        if isinstance(neo_obj, ChannelIndex):
            # set references to signals
            parent_block_path = "/" + path.split("/")[1]
            parent_block = self._get_object_at(parent_block_path)
            ref_das = self._get_referers(nix_obj, parent_block.data_arrays)
            ref_signals = list(self._neo_map[da.name] for da in ref_das)
            # deduplicate by name
            ref_signals = list(dict((s.annotations["nix_name"], s)
                                    for s in ref_signals).values())
            for sig in ref_signals:
                if isinstance(sig, AnalogSignal):
                    neo_obj.analogsignals.append(sig)
                elif isinstance(sig, IrregularlySampledSignal):
                    neo_obj.irregularlysampledsignals.append(sig)
                sig.channel_index = neo_obj

        elif isinstance(neo_obj, Unit):
            # set references to spiketrains
            parent_block_path = "/" + path.split("/")[1]
            parent_block = self._get_object_at(parent_block_path)
            ref_mtags = self._get_referers(nix_obj, parent_block.multi_tags)
            ref_sts = list(self._neo_map[mt.name] for mt in ref_mtags)
            for st in ref_sts:
                neo_obj.spiketrains.append(st)
                st.unit = neo_obj

    def get(self, path, cascade, lazy):
        parts = path.split("/")
        if len(parts) > 2:
            neotype = parts[-2][:-1]
        else:
            neotype = "block"
        if neotype == "channel_indexe":
            neotype = "channelindex"
        read_func = getattr(self, "read_" + neotype)
        return read_func(path, cascade, lazy)

    def load_lazy_object(self, obj):
        return self.get(obj.path, cascade=False, lazy=False)

    def load_lazy_cascade(self, path, lazy):
        """
        Loads the object at the location specified by the path and all
        children. Data is loaded if lazy is False.

        :param path: Location of object in file
        :param lazy: Do not load data if True
        :return: The loaded object
        """
        neoobj = self.get(path, cascade=True, lazy=lazy)
        return neoobj

    def write_all_blocks(self, neo_blocks):
        """
        Convert all ``neo_blocks`` to the NIX equivalent and write them to the
        file.

        :param neo_blocks: List (or iterable) containing Neo blocks
        :return: A list containing the new NIX Blocks
        """
        for bl in neo_blocks:
            self.write_block(bl)

    def _write_object(self, obj, loc=""):
        objtype = type(obj).__name__.lower()
        if isinstance(obj, Block):
            containerstr = "/"
        else:
            if objtype == "channelindex":
                containerstr = "/channel_indexes/"
            else:
                containerstr = "/" + type(obj).__name__.lower() + "s/"
        if "nix_name" in obj.annotations:
            nix_name = obj.annotations["nix_name"]
        else:
            nix_name = "neo.{}.{}".format(objtype, self._generate_nix_name())
            obj.annotate(nix_name=nix_name)
        objpath = loc + containerstr + nix_name
        oldhash = self._object_hashes.get(nix_name)
        if oldhash is None:
            try:
                oldobj = self.get(objpath, cascade=False, lazy=False)
                oldhash = self._hash_object(oldobj)
            except (KeyError, IndexError):
                oldhash = None
        newhash = self._hash_object(obj)
        if oldhash != newhash:
            attr = self._neo_attr_to_nix(obj)
            attr["name"] = nix_name
            if isinstance(obj, pq.Quantity):
                attr.update(self._neo_data_to_nix(obj))
            if oldhash is None:
                nixobj = self._create_nix_obj(loc, attr)
            else:
                nixobj = self._get_object_at(objpath)
            self._write_attr_annotations(nixobj, attr, objpath)
            if isinstance(obj, pq.Quantity):
                self._write_data(nixobj, attr, objpath)
        else:
            nixobj = self._nix_map.get(nix_name)
            if nixobj is None:
                nixobj = self._get_object_at(objpath)
            else:
                # object is already in file but may not be linked at objpath
                objat = self._get_object_at(objpath)
                if not objat:
                    self._link_nix_obj(nixobj, loc, containerstr)
        self._nix_map[nix_name] = nixobj
        self._object_hashes[nix_name] = newhash
        self._write_cascade(obj, objpath)

    def _create_nix_obj(self, loc, attr):
        parentobj = self._get_object_at(loc)
        if attr["type"] == "block":
            nixobj = parentobj.create_block(attr["name"], "neo.block")
            nixobj.metadata = self.nix_file.create_section(
                attr["name"], "neo.block.metadata"
            )
        elif attr["type"] == "segment":
            nixobj = parentobj.create_group(attr["name"], "neo.segment")
            nixobj.metadata = parentobj.metadata.create_section(
                attr["name"], "neo.segment.metadata"
            )
        elif attr["type"] == "channelindex":
            nixobj = parentobj.create_source(attr["name"],
                                             "neo.channelindex")
            nixobj.metadata = parentobj.metadata.create_section(
                attr["name"], "neo.channelindex.metadata"
            )
        elif attr["type"] in ("analogsignal", "irregularlysampledsignal"):
            blockpath = "/" + loc.split("/")[1]
            parentblock = self._get_object_at(blockpath)
            nixobj = list()
            typestr = "neo.{}".format(attr["type"])
            sigmd = parentobj.metadata.create_section(
                attr["name"], "{}.metadata".format(typestr)
            )
            for idx, datarow in enumerate(attr["data"]):
                name = "{}.{}".format(attr["name"], idx)
                da = parentblock.create_data_array(name, typestr, data=datarow)
                da.metadata = sigmd
                nixobj.append(da)
            parentobj.data_arrays.extend(nixobj)
        elif attr["type"] in ("epoch", "event", "spiketrain"):
            blockpath = "/" + loc.split("/")[1]
            parentblock = self._get_object_at(blockpath)
            typestr = "neo.{}".format(attr["type"])
            timesda = parentblock.create_data_array(
                "{}.times".format(attr["name"]), "{}.times".format(typestr),
                data=attr["data"]
            )
            nixobj = parentblock.create_multi_tag(
                attr["name"], typestr, timesda
            )
            nixobj.metadata = parentobj.metadata.create_section(
                attr["name"], "{}.metadata".format(typestr)
            )
            parentobj.multi_tags.append(nixobj)
        elif attr["type"] == "unit":
            nixobj = parentobj.create_source(attr["name"], "neo.unit")
            nixobj.metadata = parentobj.metadata.create_section(
                attr["name"], "neo.unit.metadata"
            )
        else:
            raise ValueError("Unable to create NIX object. Invalid type.")
        return nixobj

    def _link_nix_obj(self, obj, loc, neocontainer):
        parentobj = self._get_object_at(loc)
        container = getattr(parentobj,
                            self._container_map[neocontainer.strip("/")])
        if isinstance(obj, list):
            container.extend(obj)
        else:
            container.append(obj)

    def write_block(self, bl, loc=""):
        """
        Convert ``bl`` to the NIX equivalent and write it to the file.

        :param bl: Neo block to be written
        :param loc: Unused for blocks
        """
        self._write_object(bl, loc)
        self._create_references(bl)

    def write_channelindex(self, chx, loc=""):
        """
        Convert the provided ``chx`` (ChannelIndex) to a NIX Source and write
        it to the NIX file at the location defined by ``loc``.

        :param chx: The Neo ChannelIndex to be written
        :param loc: Path to the parent of the new CHX
        """
        self._write_object(chx, loc)

    def write_segment(self, seg, loc=""):
        """
        Convert the provided ``seg`` to a NIX Group and write it to the NIX
        file at the location defined by ``loc``.

        :param seg: Neo seg to be written
        :param loc: Path to the parent of the new Segment
        """
        self._write_object(seg, loc)

    def write_indices(self, chx, loc=""):
        """
        Create NIX Source objects to represent individual indices based on the
        provided ``chx`` (ChannelIndex) write them to the NIX file at
        the parent ChannelIndex object.

        :param chx: The Neo ChannelIndex
        :param loc: Path to the CHX
        """
        nixsource = self._nix_map[chx.annotations["nix_name"]]
        for idx, channel in enumerate(chx.index):
            channame = "{}.ChannelIndex{}".format(chx.annotations["nix_name"],
                                                  idx)
            if channame in nixsource.sources:
                nixchan = nixsource.sources[channame]
            else:
                nixchan = nixsource.create_source(channame,
                                                  "neo.channelindex")
                nixchan.metadata = nixsource.metadata.create_section(
                    nixchan.name, "neo.channelindex.metadata"
                )
            nixchan.definition = nixsource.definition
            chanmd = nixchan.metadata
            chanmd["index"] = nix.Value(int(channel))
            if len(chx.channel_names):
                neochanname = stringify(chx.channel_names[idx])
                chanmd["neo_name"] = nix.Value(neochanname)
            if len(chx.channel_ids):
                chanid = chx.channel_ids[idx]
                chanmd["channel_id"] = nix.Value(chanid)
            if chx.coordinates is not None:
                coords = chx.coordinates[idx]
                coordunits = stringify(coords[0].dimensionality)
                nixcoords = tuple(
                    nix.Value(c.rescale(coordunits).magnitude.item())
                    for c in coords
                )
                if "coordinates" in chanmd:
                    del chanmd["coordinates"]
                chanprop = chanmd.create_property("coordinates", nixcoords)
                chanprop.unit = coordunits

    def write_analogsignal(self, anasig, loc=""):
        """
        Convert the provided ``anasig`` (AnalogSignal) to a list of NIX
        DataArray objects and write them to the NIX file at the location
        defined by ``loc``. All DataArray objects created from the same
        AnalogSignal have their metadata section point to the same object.

        :param anasig: The Neo AnalogSignal to be written
        :param loc: Path to the parent of the new AnalogSignal
        """
        self._write_object(anasig, loc)

    def write_irregularlysampledsignal(self, irsig, loc=""):
        """
        Convert the provided ``irsig`` (IrregularlySampledSignal) to a list of
        NIX DataArray objects and write them to the NIX file at the location
        defined by ``loc``. All DataArray objects created from the same
        IrregularlySampledSignal have their metadata section point to the same
        object.

        :param irsig: The Neo IrregularlySampledSignal to be written
        :param loc: Path to the parent of the new
        :return: The newly created NIX DataArray
        """
        self._write_object(irsig, loc)

    def write_epoch(self, ep, loc=""):
        """
        Convert the provided ``ep`` (Epoch) to a NIX MultiTag and write it to
        the NIX file at the location defined by ``loc``.

        :param ep: The Neo Epoch to be written
        :param loc: Path to the parent of the new MultiTag
        """
        self._write_object(ep, loc)

    def write_event(self, ev, loc=""):
        """
        Convert the provided ``ev`` (Event) to a NIX MultiTag and write it to
        the NIX file at the location defined by ``loc``.

        :param ev: The Neo Event to be written
        :param loc: Path to the parent of the new MultiTag
        """
        self._write_object(ev, loc)

    def write_spiketrain(self, sptr, loc=""):
        """
        Convert the provided ``sptr`` (SpikeTrain) to a NIX MultiTag and write
        it to the NIX file at the location defined by ``loc``.

        :param sptr: The Neo SpikeTrain to be written
        :param loc: Path to the parent of the new MultiTag
        """
        self._write_object(sptr, loc)

    def write_unit(self, ut, loc=""):
        """
        Convert the provided ``ut`` (Unit) to a NIX Source and write it to the
        NIX file at the parent RCG.

        :param ut: The Neo Unit to be written
        :param loc: Path to the parent of the new Source
        """
        self._write_object(ut, loc)

    def _write_cascade(self, neoobj, path=""):
        if isinstance(neoobj, ChannelIndex):
            containers = ["units"]
            self.write_indices(neoobj, path)
        elif isinstance(neoobj, Unit):
            containers = []
        else:
            containers = getattr(neoobj, "_child_containers", [])
        for neocontainer in containers:
            if neocontainer == "channel_indexes":
                neotype = "channelindex"
            else:
                neotype = neocontainer[:-1]
            children = getattr(neoobj, neocontainer)
            write_func = getattr(self, "write_" + neotype)
            for ch in children:
                write_func(ch, path)

    def _create_references(self, block):
        """
        Create references between NIX objects according to the supplied Neo
        Block.
        MultiTags reference DataArrays of the same Group.
        DataArrays reference ChannelIndexs as sources, based on Neo
         RCG -> Signal relationships.
        MultiTags (SpikeTrains) reference ChannelIndexs and Units as
         sources, based on Neo RCG -> Unit -> SpikeTrain relationships.

        :param block: A Neo Block that has already been converted and mapped to
         NIX objects.
        """
        for seg in block.segments:
            group = self._nix_map[seg.annotations["nix_name"]]
            group_signals = self._get_contained_signals(group)
            for mtag in group.multi_tags:
                if mtag.type in ("neo.epoch", "neo.event"):
                    mtag.references.extend([sig for sig in group_signals
                                            if sig not in mtag.references])
        for rcg in block.channel_indexes:
            chidxsrc = self._nix_map[rcg.annotations["nix_name"]]
            das = list(self._nix_map[sig.annotations["nix_name"]]
                       for sig in rcg.analogsignals +
                       rcg.irregularlysampledsignals)
            # flatten nested lists
            das = [da for dalist in das for da in dalist]
            for da in das:
                if chidxsrc not in da.sources:
                    da.sources.append(chidxsrc)
            for unit in rcg.units:
                unitsource = self._nix_map[unit.annotations["nix_name"]]
                for st in unit.spiketrains:
                    stmtag = self._nix_map[st.annotations["nix_name"]]
                    if chidxsrc not in stmtag.sources:
                        stmtag.sources.append(chidxsrc)
                    if unitsource not in stmtag.sources:
                        stmtag.sources.append(unitsource)

    def _get_object_at(self, path):
        """
        Returns the object at the location defined by the path.
        ``path`` is a '/' delimited string. Each part of the string alternates
        between an object name and a container.

        If the requested object is an AnalogSignal or IrregularlySampledSignal,
        identified by the second-to-last part of the path string, a list of
        (DataArray) objects is returned.

        Example path: /block_1/segments/segment_a/events/event_a1

        :param path: Path string
        :return: The object at the location defined by the path
        """
        if path in self._path_map:
            return self._path_map[path]
        if path in ("", "/"):
            return self.nix_file
        parts = path.split("/")
        if parts[0]:
            ValueError("Invalid object path: {}".format(path))
        if len(parts) == 2:  # root block
            return self.nix_file.blocks[parts[1]]
        parent_obj = self._get_parent(path)
        container_name = self._container_map[parts[-2]]
        parent_container = getattr(parent_obj, container_name)
        objname = parts[-1]
        if parts[-2] in ["analogsignals", "irregularlysampledsignals"]:
            obj = list()
            for idx in itertools.count():
                name = "{}.{}".format(objname, idx)
                if name in parent_container:
                    obj.append(parent_container[name])
                else:
                    break
        else:
            obj = parent_container[objname]
        self._path_map[path] = obj
        return obj

    def _get_parent(self, path):
        parts = path.split("/")
        parent_path = "/".join(parts[:-2])
        parent_obj = self._get_object_at(parent_path)
        return parent_obj

    def _write_attr_annotations(self, nixobj, attr, path):
        if isinstance(nixobj, list):
            metadata = nixobj[0].metadata
            for obj in nixobj:
                obj.definition = attr["definition"]
            self._write_attr_annotations(nixobj[0], attr, path)
            return
        else:
            metadata = nixobj.metadata
            nixobj.definition = attr["definition"]
        if "neo_name" in attr:
            metadata["neo_name"] = attr["neo_name"]
        if "created_at" in attr:
            nixobj.force_created_at(calculate_timestamp(attr["created_at"]))
        if "file_datetime" in attr:
            self._write_property(metadata,
                                 "file_datetime", attr["file_datetime"])
        if attr.get("rec_datetime"):
            self._write_property(metadata,
                                 "rec_datetime", attr["rec_datetime"])

        if "annotations" in attr:
            for k, v in attr["annotations"].items():
                self._write_property(metadata, k, v)

    def _write_data(self, nixobj, attr, path):
        if isinstance(nixobj, list):
            metadata = nixobj[0].metadata
            metadata["t_start.units"] = nix.Value(attr["t_start.units"])
            for obj in nixobj:
                obj.unit = attr["data.units"]
                if attr["type"] == "analogsignal":
                    timedim = obj.append_sampled_dimension(
                        attr["sampling_interval"]
                    )
                    timedim.unit = attr["sampling_interval.units"]
                elif attr["type"] == "irregularlysampledsignal":
                    timedim = obj.append_range_dimension(attr["times"])
                    timedim.unit = attr["times.units"]
                timedim.label = "time"
                timedim.offset = attr["t_start"]
        else:
            metadata = nixobj.metadata
            nixobj.positions.unit = attr["data.units"]
            blockpath = "/" + path.split("/")[1]
            parentblock = self._get_object_at(blockpath)
            if "extents" in attr:
                extname = nixobj.name + ".durations"
                exttype = nixobj.type + ".durations"
                if extname in parentblock.data_arrays:
                    del parentblock.data_arrays[extname]
                extents = parentblock.create_data_array(
                    extname,
                    exttype,
                    data=attr["extents"]
                )
                extents.unit = attr["extents.units"]
                nixobj.extents = extents
            if "labels" in attr:
                labeldim = nixobj.positions.append_set_dimension()
                labeldim.labels = attr["labels"]
            if "t_start" in attr:
                metadata["t_start"] = nix.Value(attr["t_start"])
                metadata["t_start.units"] = nix.Value(attr["t_start.units"])
            if "t_stop" in attr:
                metadata["t_stop"] = nix.Value(attr["t_stop"])
                metadata["t_stop.units"] = nix.Value(attr["t_stop.units"])
            if "waveforms" in attr:
                wfname = nixobj.name + ".waveforms"
                if wfname in parentblock.data_arrays:
                    del metadata.sections[wfname]
                    del parentblock.data_arrays[wfname]
                    del nixobj.features[0]
                wfda = parentblock.create_data_array(
                    wfname, "neo.waveforms",
                    data=attr["waveforms"]
                )
                wfda.metadata = nixobj.metadata.create_section(
                    wfda.name, "neo.waveforms.metadata"
                )
                wfda.unit = attr["waveforms.units"]
                nixobj.create_feature(wfda, nix.LinkType.Indexed)
                wfda.append_set_dimension()
                wfda.append_set_dimension()
                wftime = wfda.append_sampled_dimension(
                    attr["sampling_interval"]
                )
                metadata["sampling_interval.units"] =\
                    attr["sampling_interval.units"]
                wftime.unit = attr["times.units"]
                wftime.label = "time"
                if "left_sweep" in attr:
                    self._write_property(wfda.metadata, "left_sweep",
                                         attr["left_sweep"])

    def _update_maps(self, obj, lazy):
        objidx = self._find_lazy_loaded(obj)
        if lazy and objidx is None:
            self._lazy_loaded.append(obj)
        elif not lazy and objidx is not None:
            self._lazy_loaded.pop(objidx)
        if not lazy:
            nix_name = obj.annotations["nix_name"]
            self._object_hashes[nix_name] = self._hash_object(obj)

    def _find_lazy_loaded(self, obj):
        """
        Finds the index of an object in the _lazy_loaded list by comparing the
        path attribute. Returns None if the object is not in the list.

        :param obj: The object to find
        :return: The index of the object in the _lazy_loaded list or None if it
        was not added
        """
        for idx, llobj in enumerate(self._lazy_loaded):
            if llobj.path == obj.path:
                return idx
        else:
            return None

    @staticmethod
    def _generate_nix_name():
        return uuid4().hex

    @staticmethod
    def _neo_attr_to_nix(neoobj):
        neotype = type(neoobj).__name__
        attrs = dict()
        # NIX metadata does not support None values
        # The property will be excluded to signify 'name is None'
        if neoobj.name is not None:
            attrs["neo_name"] = neoobj.name
        attrs["type"] = neotype.lower()
        attrs["definition"] = neoobj.description
        if isinstance(neoobj, (Block, Segment)):
            attrs["rec_datetime"] = neoobj.rec_datetime
            if neoobj.rec_datetime:
                attrs["created_at"] = neoobj.rec_datetime
            if neoobj.file_datetime:
                attrs["file_datetime"] = neoobj.file_datetime
        if neoobj.annotations:
            attrs["annotations"] = neoobj.annotations
        return attrs

    @classmethod
    def _neo_data_to_nix(cls, neoobj):
        attr = dict()
        attr["data"] = np.transpose(neoobj.magnitude)
        attr["data.units"] = cls._get_units(neoobj)
        if isinstance(neoobj, IrregularlySampledSignal):
            attr["times"] = neoobj.times.magnitude
            attr["times.units"] = cls._get_units(neoobj.times)
        else:
            attr["times.units"] = cls._get_units(neoobj.times, True)
        if hasattr(neoobj, "t_start"):
            attr["t_start"] = neoobj.t_start.magnitude.item()
            attr["t_start.units"] = cls._get_units(neoobj.t_start)
        if hasattr(neoobj, "t_stop"):
            attr["t_stop"] = neoobj.t_stop.magnitude.item()
            attr["t_stop.units"] = cls._get_units(neoobj.t_stop)
        if hasattr(neoobj, "sampling_period"):
            attr["sampling_interval"] = neoobj.sampling_period.magnitude.item()
            attr["sampling_interval.units"] = cls._get_units(
                neoobj.sampling_period
            )
        if hasattr(neoobj, "durations"):
            attr["extents"] = neoobj.durations
            attr["extents.units"] = cls._get_units(neoobj.durations)
        if hasattr(neoobj, "labels"):
            attr["labels"] = neoobj.labels.tolist()
        if hasattr(neoobj, "waveforms") and neoobj.waveforms is not None:
            attr["waveforms"] = list(wf.magnitude for wf in
                                     list(wfgroup for wfgroup in
                                          neoobj.waveforms))
            attr["waveforms.units"] = cls._get_units(neoobj.waveforms)
        if hasattr(neoobj, "left_sweep") and neoobj.left_sweep is not None:
            attr["left_sweep"] = neoobj.left_sweep.magnitude
            attr["left_sweep.units"] = cls._get_units(neoobj.left_sweep)
        return attr

    def _write_property(self, section, name, v):
        """
        Create a metadata property with a given name and value on the provided
        metadata section.

        :param section: The metadata section to hold the new property
        :param name: The name of the property
        :param v: The value to write
        :return: The newly created property
        """

        if isinstance(v, pq.Quantity):
            if len(v.shape):
                section[name] = list(nix.Value(vv) for vv in v.magnitude)
            else:
                section[name] = nix.Value(v.magnitude.item())
            section.props[name].unit = str(v.dimensionality)
        elif isinstance(v, datetime):
            section[name] = nix.Value(calculate_timestamp(v))
        elif isinstance(v, string_types):
            section[name] = nix.Value(v)
        elif isinstance(v, bytes):
            section[name] = nix.Value(v.decode())
        elif isinstance(v, Iterable):
            values = []
            unit = None
            for item in v:
                if isinstance(item, pq.Quantity):
                    unit = str(item.dimensionality)
                    item = nix.Value(item.magnitude.item())
                elif isinstance(item, Iterable):
                    self.logger.warn("Multidimensional arrays and nested "
                                     "containers are not currently supported "
                                     "when writing to NIX.")
                    return None
                elif type(item).__module__ == "numpy":
                    item = nix.Value(item.item())
                else:
                    item = nix.Value(item)
                values.append(item)
            section[name] = values
            section.props[name].unit = unit
        elif type(v).__module__ == "numpy":
            section[name] = nix.Value(v.item())
        else:
            section[name] = nix.Value(v)
        return section.props[name]

    @staticmethod
    def _get_contained_signals(obj):
        return list(
             da for da in obj.data_arrays
             if da.type in ["neo.analogsignal", "neo.irregularlysampledsignal"]
        )

    @staticmethod
    def _get_units(quantity, simplify=False):
        """
        Returns the units of a quantity value or array as a string, or None if
        it is dimensionless.

        :param quantity: Quantity scalar or array
        :param simplify: True/False Simplify units
        :return: Units of the quantity or None if dimensionless
        """
        units = quantity.units.dimensionality
        if simplify:
            units = units.simplified
        units = stringify(units)
        if units == "dimensionless":
            units = None
        return units

    @staticmethod
    def _nix_attr_to_neo(nix_obj):
        neo_attrs = dict()
        neo_attrs["nix_name"] = nix_obj.name
        neo_attrs["description"] = stringify(nix_obj.definition)
        if nix_obj.metadata:
            for prop in nix_obj.metadata.props:
                values = prop.values
                values = list(v.value for v in values)
                if prop.unit:
                    values = pq.Quantity(values, prop.unit)
                if len(values) == 1:
                    neo_attrs[prop.name] = values[0]
                else:
                    neo_attrs[prop.name] = values
        neo_attrs["name"] = neo_attrs.get("neo_name")

        if "file_datetime" in neo_attrs:
            neo_attrs["file_datetime"] = datetime.fromtimestamp(
                neo_attrs["file_datetime"]
            )
        return neo_attrs

    @staticmethod
    def _group_signals(paths):
        """
        Groups data arrays that were generated by the same Neo Signal object.

        :param paths: A list of paths (strings) of all the signals to be
        grouped :return: A list of paths (strings) of signal groups. The last
        part of each path is the common name of the signals in the group.
        """
        grouppaths = list(".".join(p.split(".")[:-1])
                          for p in paths)
        # deduplicating paths
        uniquepaths = []
        for path in grouppaths:
            if path not in uniquepaths:
                uniquepaths.append(path)
        return uniquepaths

    @staticmethod
    def _get_referers(nix_obj, obj_list):
        ref_list = list()
        for ref in obj_list:
            if nix_obj.name in list(src.name for src in ref.sources):
                ref_list.append(ref)
        return ref_list

    @staticmethod
    def _get_time_dimension(obj):
        for dim in obj.dimensions:
            if hasattr(dim, "label") and dim.label == "time":
                return dim
        return None

    @staticmethod
    def _hash_object(obj):
        """
        Computes an MD5 hash of a Neo object based on its attribute values and
        data objects. Child objects are not counted.

        :param obj: A Neo object
        :return: MD5 sum
        """
        objhash = md5()

        def strupdate(a):
            objhash.update(str(a).encode())

        def dupdate(d):
            if isinstance(d, np.ndarray) and not d.flags["C_CONTIGUOUS"]:
                d = d.copy(order="C")
            objhash.update(d)

        # attributes
        strupdate(obj.name)
        strupdate(obj.description)

        # annotations
        for k, v in sorted(obj.annotations.items()):
            strupdate(k)
            strupdate(v)

        # data objects and type-specific attributes
        if isinstance(obj, (Block, Segment)):
            strupdate(obj.rec_datetime)
            strupdate(obj.file_datetime)
        elif isinstance(obj, ChannelIndex):
            for idx in obj.index:
                strupdate(idx)
            for n in obj.channel_names:
                strupdate(n)
            if obj.coordinates is not None:
                for coord in obj.coordinates:
                    for c in coord:
                        strupdate(c)
        elif isinstance(obj, AnalogSignal):
            dupdate(obj)
            dupdate(obj.units)
            dupdate(obj.t_start)
            dupdate(obj.sampling_rate)
            dupdate(obj.t_stop)
        elif isinstance(obj, IrregularlySampledSignal):
            dupdate(obj)
            dupdate(obj.times)
            dupdate(obj.units)
        elif isinstance(obj, Event):
            dupdate(obj.times)
            for l in obj.labels:
                strupdate(l)
        elif isinstance(obj, Epoch):
            dupdate(obj.times)
            dupdate(obj.durations)
            for l in obj.labels:
                strupdate(l)
        elif isinstance(obj, SpikeTrain):
            dupdate(obj.times)
            dupdate(obj.units)
            dupdate(obj.t_stop)
            dupdate(obj.t_start)
            if obj.waveforms is not None:
                dupdate(obj.waveforms)
            dupdate(obj.sampling_rate)
            if obj.left_sweep is not None:
                strupdate(obj.left_sweep)

        # type
        strupdate(type(obj).__name__)

        return objhash.hexdigest()

    def close(self):
        """
        Closes the open nix file and resets maps.
        """
        if (hasattr(self, "nix_file") and
                self.nix_file and self.nix_file.is_open()):
            self.nix_file.close()
            self.nix_file = None
            self._lazy_loaded = None
            self._object_hashes = None
            self._block_read_counter = None

    def __del__(self):
        self.close()