# -*- 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 >>> train2 *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 '' % ( 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)