multielectrode_grasp/code/python-neo/neo/core/spiketrain.py

# -*- coding: utf-8 -*-
'''
This module implements :class:`SpikeTrain`, an array of spike times.

:class:`SpikeTrain` derives from :class:`BaseNeo`, from
:module:`neo.core.baseneo`, and from :class:`quantites.Quantity`, which
inherits from :class:`numpy.array`.

Inheritance from :class:`numpy.array` is explained here:
http://docs.scipy.org/doc/numpy/user/basics.subclassing.html

In brief:
* Initialization of a new object from constructor happens in :meth:`__new__`.
This is where user-specified attributes are set.

* :meth:`__array_finalize__` is called for all new objects, including those
created by slicing. This is where attributes are copied over from
the old object.
'''

# needed for python 3 compatibility
from __future__ import absolute_import, division, print_function
import sys

import copy
import numpy as np
import quantities as pq
from neo.core.baseneo import BaseNeo, MergeError, merge_annotations


def check_has_dimensions_time(*values):
    '''
    Verify that all arguments have a dimensionality that is compatible
    with time.
    '''
    errmsgs = []
    for value in values:
        dim = value.dimensionality
        if (len(dim) != 1 or list(dim.values())[0] != 1 or
                not isinstance(list(dim.keys())[0], pq.UnitTime)):
            errmsgs.append("value %s has dimensions %s, not [time]" %
                           (value, dim.simplified))
    if errmsgs:
        raise ValueError("\n".join(errmsgs))


def _check_time_in_range(value, t_start, t_stop, view=False):
    '''
    Verify that all times in :attr:`value` are between :attr:`t_start`
    and :attr:`t_stop` (inclusive.

    If :attr:`view` is True, vies are used for the test.
    Using drastically increases the speed, but is only safe if you are
    certain that the dtype and units are the same
    '''

    if not value.size:
        return

    if view:
        value = value.view(np.ndarray)
        t_start = t_start.view(np.ndarray)
        t_stop = t_stop.view(np.ndarray)

    if value.min() < t_start:
        raise ValueError("The first spike (%s) is before t_start (%s)" %
                         (value, t_start))
    if value.max() > t_stop:
        raise ValueError("The last spike (%s) is after t_stop (%s)" %
                         (value, t_stop))


def _check_waveform_dimensions(spiketrain):
    '''
    Verify that waveform is compliant with the waveform definition as
    quantity array 3D (spike, channel_index, time)
    '''

    if not spiketrain.size:
        return

    waveforms = spiketrain.waveforms

    if (waveforms is None) or (not waveforms.size):
        return

    if waveforms.shape[0] != len(spiketrain):
        raise ValueError("Spiketrain length (%s) does not match to number of "
                         "waveforms present (%s)" % (len(spiketrain),
                                                     waveforms.shape[0]))


def _new_spiketrain(cls, signal, t_stop, units=None, dtype=None,
                    copy=True, sampling_rate=1.0 * pq.Hz,
                    t_start=0.0 * pq.s, waveforms=None, left_sweep=None,
                    name=None, file_origin=None, description=None,
                    annotations=None, segment=None, unit=None):
    '''
    A function to map :meth:`BaseAnalogSignal.__new__` to function that
    does not do the unit checking. This is needed for :module:`pickle` to work.
    '''
    if annotations is None:
        annotations = {}
    obj = SpikeTrain(signal, t_stop, units, dtype, copy, sampling_rate,
                     t_start, waveforms, left_sweep, name, file_origin,
                     description, **annotations)
    obj.segment = segment
    obj.unit = unit
    return obj


class SpikeTrain(BaseNeo, pq.Quantity):
    '''
    :class:`SpikeTrain` is a :class:`Quantity` array of spike times.

    It is an ensemble of action potentials (spikes) emitted by the same unit
    in a period of time.

    *Usage*::

        >>> from neo.core import SpikeTrain
        >>> from quantities import s
        >>>
        >>> train = SpikeTrain([3, 4, 5]*s, t_stop=10.0)
        >>> train2 = train[1:3]
        >>>
        >>> train.t_start
        array(0.0) * s
        >>> train.t_stop
        array(10.0) * s
        >>> train
        <SpikeTrain(array([ 3.,  4.,  5.]) * s, [0.0 s, 10.0 s])>
        >>> train2
        <SpikeTrain(array([ 4.,  5.]) * s, [0.0 s, 10.0 s])>


    *Required attributes/properties*:
        :times: (quantity array 1D, numpy array 1D, or list) The times of
            each spike.
        :units: (quantity units) Required if :attr:`times` is a list or
                :class:`~numpy.ndarray`, not if it is a
                :class:`~quantites.Quantity`.
        :t_stop: (quantity scalar, numpy scalar, or float) Time at which
            :class:`SpikeTrain` ended. This will be converted to the
            same units as :attr:`times`. This argument is required because it
            specifies the period of time over which spikes could have occurred.
            Note that :attr:`t_start` is highly recommended for the same
            reason.

    Note: If :attr:`times` contains values outside of the
    range [t_start, t_stop], an Exception is raised.

    *Recommended attributes/properties*:
        :name: (str) A label for the dataset.
        :description: (str) Text description.
        :file_origin: (str) Filesystem path or URL of the original data file.
        :t_start: (quantity scalar, numpy scalar, or float) Time at which
            :class:`SpikeTrain` began. This will be converted to the
            same units as :attr:`times`.
            Default: 0.0 seconds.
        :waveforms: (quantity array 3D (spike, channel_index, time))
            The waveforms of each spike.
        :sampling_rate: (quantity scalar) Number of samples per unit time
            for the waveforms.
        :left_sweep: (quantity array 1D) Time from the beginning
            of the waveform to the trigger time of the spike.
        :sort: (bool) If True, the spike train will be sorted by time.

    *Optional attributes/properties*:
        :dtype: (numpy dtype or str) Override the dtype of the signal array.
        :copy: (bool) Whether to copy the times array.  True by default.
            Must be True when you request a change of units or dtype.

    Note: Any other additional arguments are assumed to be user-specific
    metadata and stored in :attr:`annotations`.

    *Properties available on this object*:
        :sampling_period: (quantity scalar) Interval between two samples.
            (1/:attr:`sampling_rate`)
        :duration: (quantity scalar) Duration over which spikes can occur,
            read-only.
            (:attr:`t_stop` - :attr:`t_start`)
        :spike_duration: (quantity scalar) Duration of a waveform, read-only.
            (:attr:`waveform`.shape[2] * :attr:`sampling_period`)
        :right_sweep: (quantity scalar) Time from the trigger times of the
            spikes to the end of the waveforms, read-only.
            (:attr:`left_sweep` + :attr:`spike_duration`)
        :times: (:class:`SpikeTrain`) Returns the :class:`SpikeTrain` without
            modification or copying.

    *Slicing*:
        :class:`SpikeTrain` objects can be sliced. When this occurs, a new
        :class:`SpikeTrain` (actually a view) is returned, with the same
        metadata, except that :attr:`waveforms` is also sliced in the same way
        (along dimension 0). Note that t_start and t_stop are not changed
        automatically, although you can still manually change them.

    '''

    _single_parent_objects = ('Segment', 'Unit')
    _quantity_attr = 'times'
    _necessary_attrs = (('times', pq.Quantity, 1),
                        ('t_start', pq.Quantity, 0),
                        ('t_stop', pq.Quantity, 0))
    _recommended_attrs = ((('waveforms', pq.Quantity, 3),
                           ('left_sweep', pq.Quantity, 0),
                           ('sampling_rate', pq.Quantity, 0)) +
                          BaseNeo._recommended_attrs)

    def __new__(cls, times, t_stop, units=None, dtype=None, copy=True,
                sampling_rate=1.0 * pq.Hz, t_start=0.0 * pq.s, waveforms=None,
                left_sweep=None, name=None, file_origin=None, description=None,
                **annotations):
        '''
        Constructs a new :clas:`Spiketrain` instance from data.

        This is called whenever a new :class:`SpikeTrain` is created from the
        constructor, but not when slicing.
        '''
        if len(times) != 0 and waveforms is not None and len(times) != \
                waveforms.shape[
                    0]:  # len(times)!=0 has been used to workaround a bug occuring during neo import)
            raise ValueError(
                "the number of waveforms should be equal to the number of spikes")

        # Make sure units are consistent
        # also get the dimensionality now since it is much faster to feed
        # that to Quantity rather than a unit
        if units is None:
            # No keyword units, so get from `times`
            try:
                dim = times.units.dimensionality
            except AttributeError:
                raise ValueError('you must specify units')
        else:
            if hasattr(units, 'dimensionality'):
                dim = units.dimensionality
            else:
                dim = pq.quantity.validate_dimensionality(units)

            if hasattr(times, 'dimensionality'):
                if times.dimensionality.items() == dim.items():
                    units = None  # units will be taken from times, avoids copying
                else:
                    if not copy:
                        raise ValueError("cannot rescale and return view")
                    else:
                        # this is needed because of a bug in python-quantities
                        # see issue # 65 in python-quantities github
                        # remove this if it is fixed
                        times = times.rescale(dim)

        if dtype is None:
            if not hasattr(times, 'dtype'):
                dtype = np.float
        elif hasattr(times, 'dtype') and times.dtype != dtype:
            if not copy:
                raise ValueError("cannot change dtype and return view")

            # if t_start.dtype or t_stop.dtype != times.dtype != dtype,
            # _check_time_in_range can have problems, so we set the t_start
            # and t_stop dtypes to be the same as times before converting them
            # to dtype below
            # see ticket #38
            if hasattr(t_start, 'dtype') and t_start.dtype != times.dtype:
                t_start = t_start.astype(times.dtype)
            if hasattr(t_stop, 'dtype') and t_stop.dtype != times.dtype:
                t_stop = t_stop.astype(times.dtype)

        # check to make sure the units are time
        # this approach is orders of magnitude faster than comparing the
        # reference dimensionality
        if (len(dim) != 1 or list(dim.values())[0] != 1 or
                not isinstance(list(dim.keys())[0], pq.UnitTime)):
            ValueError("Unit has dimensions %s, not [time]" % dim.simplified)

        # Construct Quantity from data
        obj = pq.Quantity(times, units=units, dtype=dtype, copy=copy).view(cls)

        # if the dtype and units match, just copy the values here instead
        # of doing the much more expensive creation of a new Quantity
        # using items() is orders of magnitude faster
        if (hasattr(t_start, 'dtype') and t_start.dtype == obj.dtype and
                hasattr(t_start, 'dimensionality') and
                    t_start.dimensionality.items() == dim.items()):
            obj.t_start = t_start.copy()
        else:
            obj.t_start = pq.Quantity(t_start, units=dim, dtype=obj.dtype)

        if (hasattr(t_stop, 'dtype') and t_stop.dtype == obj.dtype and
                hasattr(t_stop, 'dimensionality') and
                    t_stop.dimensionality.items() == dim.items()):
            obj.t_stop = t_stop.copy()
        else:
            obj.t_stop = pq.Quantity(t_stop, units=dim, dtype=obj.dtype)

        # Store attributes
        obj.waveforms = waveforms
        obj.left_sweep = left_sweep
        obj.sampling_rate = sampling_rate

        # parents
        obj.segment = None
        obj.unit = None

        # Error checking (do earlier?)
        _check_time_in_range(obj, obj.t_start, obj.t_stop, view=True)

        return obj

    def __init__(self, times, t_stop, units=None, dtype=np.float,
                 copy=True, sampling_rate=1.0 * pq.Hz, t_start=0.0 * pq.s,
                 waveforms=None, left_sweep=None, name=None, file_origin=None,
                 description=None, **annotations):
        '''
        Initializes a newly constructed :class:`SpikeTrain` instance.
        '''
        # This method is only called when constructing a new SpikeTrain,
        # not when slicing or viewing. We use the same call signature
        # as __new__ for documentation purposes. Anything not in the call
        # signature is stored in annotations.

        # Calls parent __init__, which grabs universally recommended
        # attributes and sets up self.annotations
        BaseNeo.__init__(self, name=name, file_origin=file_origin,
                         description=description, **annotations)

    def rescale(self, units):
        '''
        Return a copy of the :class:`SpikeTrain` converted to the specified
        units
        '''
        if self.dimensionality == pq.quantity.validate_dimensionality(units):
            return self.copy()
        spikes = self.view(pq.Quantity)
        obj = SpikeTrain(times=spikes, t_stop=self.t_stop, units=units,
                         sampling_rate=self.sampling_rate,
                         t_start=self.t_start, waveforms=self.waveforms,
                         left_sweep=self.left_sweep, name=self.name,
                         file_origin=self.file_origin,
                         description=self.description, **self.annotations)
        obj.segment = self.segment
        obj.unit = self.unit
        return obj

    def __reduce__(self):
        '''
        Map the __new__ function onto _new_BaseAnalogSignal, so that pickle
        works
        '''
        import numpy
        return _new_spiketrain, (self.__class__, numpy.array(self),
                                 self.t_stop, self.units, self.dtype, True,
                                 self.sampling_rate, self.t_start,
                                 self.waveforms, self.left_sweep,
                                 self.name, self.file_origin, self.description,
                                 self.annotations, self.segment, self.unit)

    def __array_finalize__(self, obj):
        '''
        This is called every time a new :class:`SpikeTrain` is created.

        It is the appropriate place to set default values for attributes
        for :class:`SpikeTrain` constructed by slicing or viewing.

        User-specified values are only relevant for construction from
        constructor, and these are set in __new__. Then they are just
        copied over here.

        Note that the :attr:`waveforms` attibute is not sliced here. Nor is
        :attr:`t_start` or :attr:`t_stop` modified.
        '''
        # This calls Quantity.__array_finalize__ which deals with
        # dimensionality
        super(SpikeTrain, self).__array_finalize__(obj)

        # Supposedly, during initialization from constructor, obj is supposed
        # to be None, but this never happens. It must be something to do
        # with inheritance from Quantity.
        if obj is None:
            return

        # Set all attributes of the new object `self` from the attributes
        # of `obj`. For instance, when slicing, we want to copy over the
        # attributes of the original object.
        self.t_start = getattr(obj, 't_start', None)
        self.t_stop = getattr(obj, 't_stop', None)
        self.waveforms = getattr(obj, 'waveforms', None)
        self.left_sweep = getattr(obj, 'left_sweep', None)
        self.sampling_rate = getattr(obj, 'sampling_rate', None)
        self.segment = getattr(obj, 'segment', None)
        self.unit = getattr(obj, 'unit', None)

        # The additional arguments
        self.annotations = getattr(obj, 'annotations', {})

        # Globally recommended attributes
        self.name = getattr(obj, 'name', None)
        self.file_origin = getattr(obj, 'file_origin', None)
        self.description = getattr(obj, 'description', None)

        if hasattr(obj, 'lazy_shape'):
            self.lazy_shape = obj.lazy_shape

    def __repr__(self):
        '''
        Returns a string representing the :class:`SpikeTrain`.
        '''
        return '<SpikeTrain(%s, [%s, %s])>' % (
            super(SpikeTrain, self).__repr__(), self.t_start, self.t_stop)

    def sort(self):
        '''
        Sorts the :class:`SpikeTrain` and its :attr:`waveforms`, if any,
        by time.
        '''
        # sort the waveforms by the times
        sort_indices = np.argsort(self)
        if self.waveforms is not None and self.waveforms.any():
            self.waveforms = self.waveforms[sort_indices]

        # now sort the times
        # We have sorted twice, but `self = self[sort_indices]` introduces
        # a dependency on the slicing functionality of SpikeTrain.
        super(SpikeTrain, self).sort()

    def __getslice__(self, i, j):
        '''
        Get a slice from :attr:`i` to :attr:`j`.

        Doesn't get called in Python 3, :meth:`__getitem__` is called instead
        '''
        return self.__getitem__(slice(i, j))

    def __add__(self, time):
        '''
        Shifts the time point of all spikes by adding the amount in
        :attr:`time` (:class:`Quantity`)

        Raises an exception if new time points fall outside :attr:`t_start` or
        :attr:`t_stop`
        '''
        spikes = self.view(pq.Quantity)
        check_has_dimensions_time(time)
        _check_time_in_range(spikes + time, self.t_start, self.t_stop)
        return SpikeTrain(times=spikes + time, t_stop=self.t_stop,
                          units=self.units, sampling_rate=self.sampling_rate,
                          t_start=self.t_start, waveforms=self.waveforms,
                          left_sweep=self.left_sweep, name=self.name,
                          file_origin=self.file_origin,
                          description=self.description, **self.annotations)

    def __sub__(self, time):
        '''
        Shifts the time point of all spikes by subtracting the amount in
        :attr:`time` (:class:`Quantity`)

        Raises an exception if new time points fall outside :attr:`t_start` or
        :attr:`t_stop`
        '''
        spikes = self.view(pq.Quantity)
        check_has_dimensions_time(time)
        _check_time_in_range(spikes - time, self.t_start, self.t_stop)
        return SpikeTrain(times=spikes - time, t_stop=self.t_stop,
                          units=self.units, sampling_rate=self.sampling_rate,
                          t_start=self.t_start, waveforms=self.waveforms,
                          left_sweep=self.left_sweep, name=self.name,
                          file_origin=self.file_origin,
                          description=self.description, **self.annotations)

    def __getitem__(self, i):
        '''
        Get the item or slice :attr:`i`.
        '''
        obj = super(SpikeTrain, self).__getitem__(i)
        if hasattr(obj, 'waveforms') and obj.waveforms is not None:
            obj.waveforms = obj.waveforms.__getitem__(i)
        return obj

    def __setitem__(self, i, value):
        '''
        Set the value the item or slice :attr:`i`.
        '''
        if not hasattr(value, "units"):
            value = pq.Quantity(value, units=self.units)
            # or should we be strict: raise ValueError("Setting a value
            # requires a quantity")?
        # check for values outside t_start, t_stop
        _check_time_in_range(value, self.t_start, self.t_stop)
        super(SpikeTrain, self).__setitem__(i, value)

    def __setslice__(self, i, j, value):
        if not hasattr(value, "units"):
            value = pq.Quantity(value, units=self.units)
        _check_time_in_range(value, self.t_start, self.t_stop)
        super(SpikeTrain, self).__setslice__(i, j, value)

    def _copy_data_complement(self, other, deep_copy=False):
        '''
        Copy the metadata from another :class:`SpikeTrain`.
        '''
        for attr in ("left_sweep", "sampling_rate", "name", "file_origin",
                     "description", "annotations"):
            attr_value = getattr(other, attr, None)
            if deep_copy:
                attr_value = copy.deepcopy(attr_value)
            setattr(self, attr, attr_value)

    def duplicate_with_new_data(self, signal, t_start=None, t_stop=None,
                                waveforms=None, deep_copy=True):
        '''
        Create a new :class:`SpikeTrain` with the same metadata
        but different data (times, t_start, t_stop)
        '''
        # using previous t_start and t_stop if no values are provided
        if t_start is None:
            t_start = self.t_start
        if t_stop is None:
            t_stop = self.t_stop
        if waveforms is None:
            waveforms = self.waveforms

        new_st = self.__class__(signal, t_start=t_start, t_stop=t_stop,
                                waveforms=waveforms, units=self.units)
        new_st._copy_data_complement(self, deep_copy=deep_copy)

        # overwriting t_start and t_stop with new values
        new_st.t_start = t_start
        new_st.t_stop = t_stop

        # consistency check
        _check_time_in_range(new_st, new_st.t_start, new_st.t_stop, view=False)
        _check_waveform_dimensions(new_st)
        return new_st

    def time_slice(self, t_start, t_stop):
        '''
        Creates a new :class:`SpikeTrain` corresponding to the time slice of
        the original :class:`SpikeTrain` between (and including) times
        :attr:`t_start` and :attr:`t_stop`. Either parameter can also be None
        to use infinite endpoints for the time interval.
        '''
        _t_start = t_start
        _t_stop = t_stop
        if t_start is None:
            _t_start = -np.inf
        if t_stop is None:
            _t_stop = np.inf
        indices = (self >= _t_start) & (self <= _t_stop)
        new_st = self[indices]

        new_st.t_start = max(_t_start, self.t_start)
        new_st.t_stop = min(_t_stop, self.t_stop)
        if self.waveforms is not None:
            new_st.waveforms = self.waveforms[indices]

        return new_st

    def merge(self, other):
        '''
        Merge another :class:`SpikeTrain` into this one.

        The times of the :class:`SpikeTrain` objects combined in one array
        and sorted.

        If the attributes of the two :class:`SpikeTrain` are not
        compatible, an Exception is raised.
        '''
        if self.sampling_rate != other.sampling_rate:
            raise MergeError("Cannot merge, different sampling rates")
        if self.t_start != other.t_start:
            raise MergeError("Cannot merge, different t_start")
        if self.t_stop != other.t_stop:
            raise MemoryError("Cannot merge, different t_stop")
        if self.left_sweep != other.left_sweep:
            raise MemoryError("Cannot merge, different left_sweep")
        if self.segment != other.segment:
            raise MergeError("Cannot merge these two signals as they belong to"
                             " different segments.")
        if hasattr(self, "lazy_shape"):
            if hasattr(other, "lazy_shape"):
                merged_lazy_shape = (self.lazy_shape[0] + other.lazy_shape[0])
            else:
                raise MergeError("Cannot merge a lazy object with a real"
                                 " object.")
        if other.units != self.units:
            other = other.rescale(self.units)
        wfs = [self.waveforms is not None, other.waveforms is not None]
        if any(wfs) and not all(wfs):
            raise MergeError("Cannot merge signal with waveform and signal "
                             "without waveform.")
        stack = np.concatenate((np.asarray(self), np.asarray(other)))
        sorting = np.argsort(stack)
        stack = stack[sorting]
        kwargs = {}
        for name in ("name", "description", "file_origin"):
            attr_self = getattr(self, name)
            attr_other = getattr(other, name)
            if attr_self == attr_other:
                kwargs[name] = attr_self
            else:
                kwargs[name] = "merge(%s, %s)" % (attr_self, attr_other)
        merged_annotations = merge_annotations(self.annotations,
                                               other.annotations)
        kwargs.update(merged_annotations)
        train = SpikeTrain(stack, units=self.units, dtype=self.dtype,
                           copy=False, t_start=self.t_start,
                           t_stop=self.t_stop,
                           sampling_rate=self.sampling_rate,
                           left_sweep=self.left_sweep, **kwargs)
        if all(wfs):
            wfs_stack = np.vstack((self.waveforms, other.waveforms))
            wfs_stack = wfs_stack[sorting]
            train.waveforms = wfs_stack
        train.segment = self.segment
        if train.segment is not None:
            self.segment.spiketrains.append(train)

        if hasattr(self, "lazy_shape"):
            train.lazy_shape = merged_lazy_shape
        return train

    @property
    def times(self):
        '''
        Returns the :class:`SpikeTrain` without modification or copying.
        '''
        return self

    @property
    def duration(self):
        '''
        Duration over which spikes can occur,

        (:attr:`t_stop` - :attr:`t_start`)
        '''
        if self.t_stop is None or self.t_start is None:
            return None
        return self.t_stop - self.t_start

    @property
    def spike_duration(self):
        '''
        Duration of a waveform.

        (:attr:`waveform`.shape[2] * :attr:`sampling_period`)
        '''
        if self.waveforms is None or self.sampling_rate is None:
            return None
        return self.waveforms.shape[2] / self.sampling_rate

    @property
    def sampling_period(self):
        '''
        Interval between two samples.

        (1/:attr:`sampling_rate`)
        '''
        if self.sampling_rate is None:
            return None
        return 1.0 / self.sampling_rate

    @sampling_period.setter
    def sampling_period(self, period):
        '''
        Setter for :attr:`sampling_period`
        '''
        if period is None:
            self.sampling_rate = None
        else:
            self.sampling_rate = 1.0 / period

    @property
    def right_sweep(self):
        '''
        Time from the trigger times of the spikes to the end of the waveforms.

        (:attr:`left_sweep` + :attr:`spike_duration`)
        '''
        dur = self.spike_duration
        if self.left_sweep is None or dur is None:
            return None
        return self.left_sweep + dur

    def as_array(self, units=None):
        """
        Return the spike times as a plain NumPy array.

        If `units` is specified, first rescale to those units.
        """
        if units:
            return self.rescale(units).magnitude
        else:
            return self.magnitude

    def as_quantity(self):
        """
        Return the spike times as a quantities array.
        """
        return self.view(pq.Quantity)