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

"""
Module for reading and writing NSDF files

Author: Mieszko Grodzicki

This module support both reading and writing NDSF files.
Note: Read file must be written using this IO
"""


import numpy as np
import quantities as pq

from uuid import uuid1
import pickle
from datetime import datetime
import os

try:
    import nsdf
except ImportError as err:
    HAVE_NSDF = False
    NSDF_ERR = err
else:
    HAVE_NSDF = True
    NSDF_ERR = None

from neo.io.baseio import BaseIO
from neo.core import Block, Segment, AnalogSignal, ChannelIndex


class NSDFIO(BaseIO):
    """
    Class for reading and writing files in NSDF Format.

    It supports reading and writing: Block, Segment, AnalogSignal, ChannelIndex, with all relationships and metadata.
    """
    is_readable = True
    is_writable = False  # True - disabled pending update to Neo 0.9 API

    supported_objects = [Block, Segment, AnalogSignal, ChannelIndex]

    readable_objects = [Block, Segment]
    writeable_objects = []  # [Block, Segment] - disabled pending update to Neo 0.9 API

    has_header = False
    is_streameable = False

    name = 'NSDF'
    extensions = ['h5']
    mode = 'file'

    def __init__(self, filename=None):
        """
        Initialise NSDFIO instance

        :param filename: Path to the file
        """
        if not HAVE_NSDF:
            raise Exception("Failed to import NSDF.")

        if filename is None:
            raise ValueError("Must provide an input file.")

        BaseIO.__init__(self)

        self.filename = filename
        self.dt_format = '%d/%m/%Y %H:%M:%S'
        self.modeltree_path = '/model/modeltree/neo/'

    def write_all_blocks(self, blocks):
        """
        Write list of blocks to the file

        :param blocks: List of blocks to be written
        """
        raise NotImplementedError("Implementation not yet updated for Neo 0.9")
        writer = self._init_writing()
        neo_model, blocks_model, segments_model = self._prepare_model_tree(writer)

        name_pattern = self._name_pattern(len(blocks))
        for i, block in enumerate(blocks):
            self.write_block(block, name_pattern.format(i), writer, blocks_model)

    def write_block(self, block=None, name='0', writer=None, parent=None):
        """
        Write a Block to the file

        :param block: Block to be written
        :param name: Name for block representation in NSDF model tree (optional)
        :param writer: NSDFWriter instance (optional)
        :param parent: NSDF ModelComponent which will be the parent of block NSDF representation (optional)
        """
        raise NotImplementedError("Implementation not yet updated for Neo 0.9")
        if not isinstance(block, Block):
            raise ValueError("Must provide a Block to write.")

        if writer is None:
            writer = self._init_writing()

        if parent is None:
            neo_model, parent, segments_model = self._prepare_model_tree(writer)

        block_model = nsdf.ModelComponent(name, uid=uuid1().hex, parent=parent)
        self._write_container_metadata(block, block_model)
        self._write_model_component(block_model, writer)

        self._write_block_children(block, block_model, writer)

        self._clean_nsdfio_annotations(block)

    def _write_block_children(self, block, block_model, writer):
        segments_model = nsdf.ModelComponent(name='segments', uid=uuid1().hex, parent=block_model)
        self._write_model_component(segments_model, writer)
        name_pattern = self._name_pattern(len(block.segments))
        for i, segment in enumerate(block.segments):
            self.write_segment(segment=segment, name=name_pattern.format(i),
                               writer=writer, parent=segments_model)

        channel_indexes_model = nsdf.ModelComponent(
            name='channel_indexes', uid=uuid1().hex, parent=block_model)
        self._write_model_component(channel_indexes_model, writer)
        name_pattern = self._name_pattern(len(block.channel_indexes))
        for i, channelindex in enumerate(block.channel_indexes):
            self.write_channelindex(channelindex=channelindex, name=name_pattern.format(i),
                                    writer=writer, parent=channel_indexes_model)

    def write_segment(self, segment=None, name='0', writer=None, parent=None):
        """
        Write a Segment to the file

        :param segment: Segment to be written
        :param name: Name for segment representation in NSDF model tree (optional)
        :param writer: NSDFWriter instance (optional)
        :param parent: NSDF ModelComponent which will be the parent of segment NSDF representation (optional)
        """
        raise NotImplementedError("Implementation not yet updated for Neo 0.9")
        if not isinstance(segment, Segment):
            raise ValueError("Must provide a Segment to write.")

        if writer is None:
            writer = self._init_writing()

        single_segment = False
        if parent is None:
            neo_model, blocks_model, parent = self._prepare_model_tree(writer)
            single_segment = True

        model = nsdf.ModelComponent(name, uid=uuid1().hex, parent=parent)
        self._write_container_metadata(segment, model)
        self._write_model_component(model, writer)

        self._write_segment_children(model, segment, writer)

        if single_segment:
            self._clean_nsdfio_annotations(segment)

    def _write_segment_children(self, model, segment, writer):
        analogsignals_model = nsdf.ModelComponent(
            name='analogsignals', uid=uuid1().hex, parent=model)
        self._write_model_component(analogsignals_model, writer)
        name_pattern = self._name_pattern(len(segment.analogsignals))
        for i, signal in enumerate(segment.analogsignals):
            self.write_analogsignal(signal=signal, name=name_pattern.format(i),
                                    parent=analogsignals_model, writer=writer)

    def write_analogsignal(self, signal, name, writer, parent):
        """
        Write an AnalogSignal to the file

        :param signal: AnalogSignal to be written
        :param name: Name for signal representation in NSDF model tree
        :param writer: NSDFWriter instance
        :param parent: NSDF ModelComponent which will be the parent of signal NSDF representation
        """
        raise NotImplementedError("Implementation not yet updated for Neo 0.9")
        uid = uuid1().hex
        model = nsdf.ModelComponent(name, uid=uid, parent=parent)

        if signal.annotations.get('nsdfio_uid') is not None:
            model.attrs['reference_to'] = signal.annotations['nsdfio_uid']
            self._write_model_component(model, writer)
            return

        self._write_basic_metadata(model, signal)
        signal.annotations['nsdfio_uid'] = uid

        r_signal = np.swapaxes(signal, 0, 1)
        channels_model, channels, source_ds = self._create_signal_data_sources(
            model, r_signal, uid, writer)
        self._write_signal_data(model, channels, r_signal, signal, source_ds, writer)

        self._write_model_component(model, writer)
        self._write_model_component(channels_model, writer)
        for channel_model in channels:
            self._write_model_component(channel_model, writer)

    def write_channelindex(self, channelindex, name, writer, parent):
        """
        Write a ChannelIndex to the file

        :param channelindex: ChannelIndex to be written
        :param name: Name for channelindex representation in NSDF model tree
        :param writer: NSDFWriter instance
        :param parent: NSDF ModelComponent which will be the parent of channelindex NSDF representation
        """
        raise NotImplementedError("Implementation not yet updated for Neo 0.9")
        uid = uuid1().hex
        model = nsdf.ModelComponent(name, uid=uid, parent=parent)

        self._write_basic_metadata(model, channelindex)
        self._write_model_component(model, writer)

        self._write_channelindex_arrays(model, channelindex, writer)

        self._write_channelindex_children(channelindex, model, writer)

    def _write_channelindex_children(self, channelindex, model, writer):
        analogsignals_model = nsdf.ModelComponent(
            name='analogsignals', uid=uuid1().hex, parent=model)
        self._write_model_component(analogsignals_model, writer)
        name_pattern = self._name_pattern(len(channelindex.analogsignals))
        for i, signal in enumerate(channelindex.analogsignals):
            self.write_analogsignal(signal=signal, name=name_pattern.format(i),
                                    parent=analogsignals_model, writer=writer)

    def _init_writing(self):
        return nsdf.NSDFWriter(self.filename, mode='w')

    def _prepare_model_tree(self, writer):
        neo_model = nsdf.ModelComponent('neo', uid=uuid1().hex)
        self._write_model_component(neo_model, writer)

        blocks_model = nsdf.ModelComponent('blocks', uid=uuid1().hex, parent=neo_model)
        self._write_model_component(blocks_model, writer)

        segments_model = nsdf.ModelComponent('segments', uid=uuid1().hex, parent=neo_model)
        self._write_model_component(segments_model, writer)

        return neo_model, blocks_model, segments_model

    def _number_of_digits(self, n):
        return len(str(n))

    def _name_pattern(self, how_many_items):
        return '{{:0{}d}}'.format(self._number_of_digits(max(how_many_items - 1, 0)))

    def _clean_nsdfio_annotations(self, object):
        nsdfio_annotations = ('nsdfio_uid',)

        for key in nsdfio_annotations:
            object.annotations.pop(key, None)

        if hasattr(object, 'children'):
            for child in object.children:
                self._clean_nsdfio_annotations(child)

    def _write_model_component(self, model, writer):
        if model.parent is None:
            nsdf.add_model_component(model, writer.model['modeltree/'])
        else:
            nsdf.add_model_component(model, model.parent.hdfgroup)

    def _write_container_metadata(self, container, container_model):
        self._write_basic_metadata(container_model, container)

        self._write_datetime_attributes(container_model, container)
        self._write_index_attribute(container_model, container)

    def _write_basic_metadata(self, model, object):
        self._write_basic_attributes(model, object)
        self._write_annotations(model, object)

    def _write_basic_attributes(self, model, object):
        if object.name is not None:
            model.attrs['name'] = object.name
        if object.description is not None:
            model.attrs['description'] = object.description

    def _write_datetime_attributes(self, model, object):
        if object.rec_datetime is not None:
            model.attrs['rec_datetime'] = object.rec_datetime.strftime(self.dt_format)

    def _write_index_attribute(self, model, object):
        if object.index is not None:
            model.attrs['index'] = object.index

    def _write_annotations(self, model, object):
        if object.annotations is not None:
            model.attrs['annotations'] = pickle.dumps(object.annotations)

    def _write_signal_data(self, model, channels, r_signal, signal, source_ds, writer):
        dataobj = nsdf.UniformData('signal', unit=str(signal.units.dimensionality))
        dataobj.dtype = signal.dtype
        for i in range(len(channels)):
            dataobj.put_data(channels[i].uid, r_signal[i])

        dataobj.set_dt(float(signal.sampling_period.magnitude),
                       str(signal.sampling_period.dimensionality))

        rescaled_tstart = signal.t_start.rescale(signal.sampling_period.dimensionality)
        writer.add_uniform_data(source_ds, dataobj,
                                tstart=float(rescaled_tstart.magnitude))
        model.attrs['t_start_unit'] = str(signal.t_start.dimensionality)

    def _create_signal_data_sources(self, model, r_signal, uid, writer):
        channels = []
        channels_model = nsdf.ModelComponent(name='channels', uid=uuid1().hex, parent=model)
        name_pattern = '{{:0{}d}}'.format(self._number_of_digits(max(len(r_signal) - 1, 0)))
        for i in range(len(r_signal)):
            channels.append(nsdf.ModelComponent(name_pattern.format(i),
                                                uid=uuid1().hex,
                                                parent=channels_model))

        source_ds = writer.add_uniform_ds(uid, [channel.uid for channel in channels])
        return channels_model, channels, source_ds

    def _write_channelindex_arrays(self, model, channelindex, writer):
        group = model.hdfgroup

        self._write_array(group, 'index', channelindex.index)
        if channelindex.channel_names is not None:
            self._write_array(group, 'channel_names', channelindex.channel_names)
        if channelindex.channel_ids is not None:
            self._write_array(group, 'channel_ids', channelindex.channel_ids)
        if channelindex.coordinates is not None:
            self._write_array(group, 'coordinates', channelindex.coordinates)

    def _write_array(self, group, name, array):
        if isinstance(array, pq.Quantity):
            group.create_dataset(name, data=array.magnitude)
            group[name].attrs['dimensionality'] = str(array.dimensionality)
        else:
            group.create_dataset(name, data=array)

    def read_all_blocks(self, lazy=False):
        """
        Read all blocks from the file

        :param lazy: Enables lazy reading
        :return: List of read blocks
        """
        assert not lazy, 'Do not support lazy'

        reader = self._init_reading()
        blocks = []

        blocks_path = self.modeltree_path + 'blocks/'
        for block in reader.model[blocks_path].values():
            blocks.append(self.read_block(group=block, reader=reader))

        return blocks

    def read_block(self, lazy=False, group=None, reader=None):
        """
        Read a Block from the file

        :param lazy: Enables lazy reading
        :param group: HDF5 Group representing the block in NSDF model tree (optional)
        :param reader: NSDFReader instance (optional)
        :return: Read block
        """
        assert not lazy, 'Do not support lazy'

        block = Block()
        group, reader = self._select_first_container(group, reader, 'block')

        if group is None:
            return None

        attrs = group.attrs

        self._read_block_children(block, group, reader)
        block.create_many_to_one_relationship()

        self._read_container_metadata(attrs, block)

        return block

    def _read_block_children(self, block, group, reader):
        for child in group['segments/'].values():
            block.segments.append(self.read_segment(group=child, reader=reader))
        for child in group['channel_indexes/'].values():
            block.channel_indexes.append(self.read_channelindex(group=child, reader=reader))

    def read_segment(self, lazy=False, group=None, reader=None):
        """
        Read a Segment from the file

        :param lazy: Enables lazy reading
        :param group: HDF5 Group representing the segment in NSDF model tree (optional)
        :param reader: NSDFReader instance (optional)
        :return: Read segment
        """
        assert not lazy, 'Do not support lazy'

        segment = Segment()
        group, reader = self._select_first_container(group, reader, 'segment')

        if group is None:
            return None

        attrs = group.attrs

        self._read_segment_children(group, reader, segment)

        self._read_container_metadata(attrs, segment)

        return segment

    def _read_segment_children(self, group, reader, segment):
        for child in group['analogsignals/'].values():
            segment.analogsignals.append(self.read_analogsignal(group=child, reader=reader))

    def read_analogsignal(self, lazy=False, group=None, reader=None):
        """
        Read an AnalogSignal from the file (must be child of a Segment)

        :param lazy: Enables lazy reading
        :param group: HDF5 Group representing the analogsignal in NSDF model tree
        :param reader: NSDFReader instance
        :return: Read AnalogSignal
        """
        assert not lazy, 'Do not support lazy'

        attrs = group.attrs

        if attrs.get('reference_to') is not None:
            return self.objects_dict[attrs['reference_to']]

        uid = attrs['uid']
        data_group = reader.data['uniform/{}/signal'.format(uid)]

        t_start = self._read_analogsignal_t_start(attrs, data_group)
        signal = self._create_analogsignal(data_group, group, t_start, uid, reader)

        self._read_basic_metadata(attrs, signal)

        self.objects_dict[uid] = signal
        return signal

    def read_channelindex(self, lazy=False, group=None, reader=None):
        """
        Read a ChannelIndex from the file (must be child of a Block)

        :param lazy: Enables lazy reading
        :param group: HDF5 Group representing the channelindex in NSDF model tree
        :param reader: NSDFReader instance
        :return: Read ChannelIndex
        """
        assert not lazy, 'Do not support lazy'

        attrs = group.attrs

        channelindex = self._create_channelindex(group)
        self._read_channelindex_children(group, reader, channelindex)

        self._read_basic_metadata(attrs, channelindex)

        return channelindex

    def _read_channelindex_children(self, group, reader, channelindex):
        for child in group['analogsignals/'].values():
            channelindex.analogsignals.append(self.read_analogsignal(group=child, reader=reader))

    def _init_reading(self):
        reader = nsdf.NSDFReader(self.filename)
        self.file_datetime = datetime.fromtimestamp(os.stat(self.filename).st_mtime)
        self.objects_dict = {}
        return reader

    def _select_first_container(self, group, reader, name):
        if reader is None:
            reader = self._init_reading()

        if group is None:
            path = self.modeltree_path + name + 's/'
            if len(reader.model[path].values()) > 0:
                group = reader.model[path].values()[0]

        return group, reader

    def _read_container_metadata(self, attrs, container):
        self._read_basic_metadata(attrs, container)

        self._read_datetime_attributes(attrs, container)
        self._read_index_attribute(attrs, container)

    def _read_basic_metadata(self, attrs, signal):
        self._read_basic_attributes(attrs, signal)
        self._read_annotations(attrs, signal)

    def _read_basic_attributes(self, attrs, object):
        if attrs.get('name') is not None:
            object.name = attrs['name']
        if attrs.get('description') is not None:
            object.description = attrs['description']
        object.file_origin = self.filename

    def _read_datetime_attributes(self, attrs, object):
        object.file_datetime = self.file_datetime
        if attrs.get('rec_datetime') is not None:
            object.rec_datetime = datetime.strptime(attrs['rec_datetime'], self.dt_format)

    def _read_annotations(self, attrs, object):
        if attrs.get('annotations') is not None:
            object.annotations = pickle.loads(attrs['annotations'])

    def _read_index_attribute(self, attrs, object):
        if attrs.get('index') is not None:
            object.index = attrs['index']

    def _create_analogsignal(self, data_group, group, t_start, uid, reader):
        # for lazy
        # data_shape = data_group.shape
        # data_shape = (data_shape[1], data_shape[0])
        dataobj = reader.get_uniform_data(uid, 'signal')
        data = self._read_signal_data(dataobj, group)
        signal = self._create_normal_analogsignal(data, dataobj, uid, t_start)
        return signal

    def _read_analogsignal_t_start(self, attrs, data_group):
        t_start = float(data_group.attrs['tstart']) * pq.Quantity(1, data_group.attrs['tunit'])
        t_start = t_start.rescale(attrs['t_start_unit'])
        return t_start

    def _read_signal_data(self, dataobj, group):
        data = []
        for channel in group['channels/'].values():
            channel_uid = channel.attrs['uid']
            data += [dataobj.get_data(channel_uid)]
        return data

    def _create_normal_analogsignal(self, data, dataobj, uid, t_start):
        return AnalogSignal(np.swapaxes(data, 0, 1), dtype=dataobj.dtype, units=dataobj.unit,
                            t_start=t_start, sampling_period=pq.Quantity(dataobj.dt, dataobj.tunit))

    def _create_channelindex(self, group):
        return ChannelIndex(index=self._read_array(group, 'index'),
                            channel_names=self._read_array(group, 'channel_names'),
                            channel_ids=self._read_array(group, 'channel_ids'),
                            coordinates=self._read_array(group, 'coordinates'))

    def _read_array(self, group, name):
        if group.__contains__(name) == False:
            return None
        array = group[name][:]

        if group[name].attrs.get('dimensionality') is not None:
            return pq.Quantity(array, group[name].attrs['dimensionality'])
        return array