# -*- coding: utf-8 -*- ''' This module defines :class:`Epoch`, an array of epochs. :class:`Epoch` derives from :class:`BaseNeo`, from :module:`neo.core.baseneo`. ''' # needed for python 3 compatibility from __future__ import absolute_import, division, print_function import sys from copy import deepcopy import numpy as np import quantities as pq from neo.core.baseneo import BaseNeo, merge_annotations from neo.core.dataobject import DataObject, ArrayDict PY_VER = sys.version_info[0] def _new_epoch(cls, times=None, durations=None, labels=None, units=None, name=None, description=None, file_origin=None, array_annotations=None, annotations=None, segment=None): ''' A function to map epoch.__new__ to function that does not do the unit checking. This is needed for pickle to work. ''' e = Epoch(times=times, durations=durations, labels=labels, units=units, name=name, file_origin=file_origin, description=description, array_annotations=array_annotations, **annotations) e.segment = segment return e class Epoch(DataObject): ''' Array of epochs. *Usage*:: >>> from neo.core import Epoch >>> from quantities import s, ms >>> import numpy as np >>> >>> epc = Epoch(times=np.arange(0, 30, 10)*s, ... durations=[10, 5, 7]*ms, ... labels=np.array(['btn0', 'btn1', 'btn2'], dtype='S')) >>> >>> epc.times array([ 0., 10., 20.]) * s >>> epc.durations array([ 10., 5., 7.]) * ms >>> epc.labels array(['btn0', 'btn1', 'btn2'], dtype='|S4') *Required attributes/properties*: :times: (quantity array 1D) The start times of each time period. :durations: (quantity array 1D or quantity scalar) The length(s) of each time period. If a scalar, the same value is used for all time periods. :labels: (numpy.array 1D dtype='S') Names or labels for the time periods. *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. *Optional attributes/properties*: :array_annotations: (dict) Dict mapping strings to numpy arrays containing annotations \ for all data points Note: Any other additional arguments are assumed to be user-specific metadata and stored in :attr:`annotations`, ''' _single_parent_objects = ('Segment',) _quantity_attr = 'times' _necessary_attrs = (('times', pq.Quantity, 1), ('durations', pq.Quantity, 1), ('labels', np.ndarray, 1, np.dtype('S'))) def __new__(cls, times=None, durations=None, labels=None, units=None, name=None, description=None, file_origin=None, array_annotations=None, **annotations): if times is None: times = np.array([]) * pq.s if durations is None: durations = np.array([]) * pq.s elif durations.size != times.size: if durations.size == 1: durations = durations * np.ones_like(times.magnitude) else: raise ValueError("Durations array has different length to times") if labels is None: labels = np.array([], dtype='S') elif len(labels) != times.size: raise ValueError("Labels array has different length to times") if units is None: # No keyword units, so get from `times` try: units = times.units dim = 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) # check to make sure the units are time # this approach is much 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 %s has dimensions %s, not [time]" % (units, dim.simplified)) obj = pq.Quantity.__new__(cls, times, units=dim) obj.labels = labels obj.durations = durations obj.segment = None return obj def __init__(self, times=None, durations=None, labels=None, units=None, name=None, description=None, file_origin=None, array_annotations=None, **annotations): ''' Initialize a new :class:`Epoch` instance. ''' DataObject.__init__(self, name=name, file_origin=file_origin, description=description, array_annotations=array_annotations, **annotations) def __reduce__(self): ''' Map the __new__ function onto _new_epoch, so that pickle works ''' return _new_epoch, (self.__class__, self.times, self.durations, self.labels, self.units, self.name, self.file_origin, self.description, self.array_annotations, self.annotations, self.segment) def __array_finalize__(self, obj): super(Epoch, self).__array_finalize__(obj) self.annotations = getattr(obj, 'annotations', None) self.name = getattr(obj, 'name', None) self.file_origin = getattr(obj, 'file_origin', None) self.description = getattr(obj, 'description', None) self.segment = getattr(obj, 'segment', None) # Add empty array annotations, because they cannot always be copied, # but do not overwrite existing ones from slicing etc. # This ensures the attribute exists if not hasattr(self, 'array_annotations'): self.array_annotations = ArrayDict(self._get_arr_ann_length()) def __repr__(self): ''' Returns a string representing the :class:`Epoch`. ''' # need to convert labels to unicode for python 3 or repr is messed up if PY_VER == 3: labels = self.labels.astype('U') else: labels = self.labels objs = ['%s@%s for %s' % (label, time, dur) for label, time, dur in zip(labels, self.times, self.durations)] return '' % ', '.join(objs) def _repr_pretty_(self, pp, cycle): super(Epoch, self)._repr_pretty_(pp, cycle) def rescale(self, units): ''' Return a copy of the :class:`Epoch` converted to the specified units ''' obj = super(Epoch, self).rescale(units) obj.segment = self.segment return obj def __getitem__(self, i): ''' Get the item or slice :attr:`i`. ''' obj = Epoch(times=super(Epoch, self).__getitem__(i)) obj._copy_data_complement(self) try: # Array annotations need to be sliced accordingly obj.array_annotate(**deepcopy(self.array_annotations_at_index(i))) except AttributeError: # If Quantity was returned, not Epoch pass return obj def __getslice__(self, i, j): ''' Get a slice from :attr:`i` to :attr:`j`.attr[0] Doesn't get called in Python 3, :meth:`__getitem__` is called instead ''' return self.__getitem__(slice(i, j)) @property def times(self): return pq.Quantity(self) def merge(self, other): ''' Merge the another :class:`Epoch` into this one. The :class:`Epoch` objects are concatenated horizontally (column-wise), :func:`np.hstack`). If the attributes of the two :class:`Epoch` are not compatible, and Exception is raised. ''' othertimes = other.times.rescale(self.times.units) times = np.hstack([self.times, othertimes]) * self.times.units 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) kwargs['array_annotations'] = self._merge_array_annotations(other) labels = kwargs['array_annotations']['labels'] durations = kwargs['array_annotations']['durations'] return Epoch(times=times, durations=durations, labels=labels, **kwargs) def _copy_data_complement(self, other): ''' Copy the metadata from another :class:`Epoch`. Note: Array annotations can not be copied here because length of data can change ''' # Note: Array annotations cannot be copied because length of data could be changed # here which would cause inconsistencies. This is instead done locally. for attr in ("name", "file_origin", "description", "annotations"): setattr(self, attr, getattr(other, attr, None)) def __deepcopy__(self, memo): cls = self.__class__ new_ep = cls(times=self.times, durations=self.durations, labels=self.labels, units=self.units, name=self.name, description=self.description, file_origin=self.file_origin) new_ep.__dict__.update(self.__dict__) memo[id(self)] = new_ep for k, v in self.__dict__.items(): try: setattr(new_ep, k, deepcopy(v, memo)) except TypeError: setattr(new_ep, k, v) return new_ep def duplicate_with_new_data(self, signal, units=None): ''' Create a new :class:`Epoch` with the same metadata but different data (times, durations) Note: Array annotations can not be copied here because length of data can change ''' if units is None: units = self.units else: units = pq.quantity.validate_dimensionality(units) new = self.__class__(times=signal, units=units) new._copy_data_complement(self) # Note: Array annotations can not be copied here because length of data can change return new def time_slice(self, t_start, t_stop): ''' Creates a new :class:`Epoch` corresponding to the time slice of the original :class:`Epoch` 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_epc = self[indices] return new_epc def set_labels(self, labels): self.array_annotate(labels=labels) def get_labels(self): return self.array_annotations['labels'] labels = property(get_labels, set_labels) def set_durations(self, durations): self.array_annotate(durations=durations) def get_durations(self): return self.array_annotations['durations'] durations = property(get_durations, set_durations)