def __init__(self,
index=0,
coordinate=None,
name=None,
description=None,
file_origin=None,
**annotations):
'''
Initialize a new :class:`RecordingChannel` instance.
'''
# Inherited initialization
# Sets universally recommended attributes, and places all others
# in annotations
BaseNeo.__init__(self,
name=name,
file_origin=file_origin,
description=description,
**annotations)
# Store required and recommended attributes
self.index = index
self.coordinate = coordinate
# Initialize contianers
self.analogsignals = []
self.irregularlysampledsignals = []
# Many to many relationship
self.recordingchannelgroups = []
def __init__(self,
time=0 * pq.s,
waveform=None,
sampling_rate=None,
left_sweep=None,
name=None,
description=None,
file_origin=None,
**annotations):
'''
Initialize a new :class:`Spike` instance.
'''
BaseNeo.__init__(self,
name=name,
file_origin=file_origin,
description=description,
**annotations)
self.time = time
self.waveform = waveform
self.left_sweep = left_sweep
self.sampling_rate = sampling_rate
self.segment = None
self.unit = None
def __init__(self, times=None, durations=None, labels=None, units=None,
name=None, description=None, file_origin=None, **annotations):
'''
Initialize a new :class:`Epoch` instance.
'''
BaseNeo.__init__(self, name=name, file_origin=file_origin,
description=description, **annotations)
def __init__(self, array_annotations=None, **annotations):
# this for py27 str vs py3 str in neo attributes ompatibility
annotations = check_annotations(annotations)
if 'file_origin' not in annotations:
# the str is to make compatible with neo_py27 where attribute
# used to be str so raw bytes
annotations['file_origin'] = str(self._rawio.source_name())
if array_annotations is None:
array_annotations = {}
for k, v in array_annotations.items():
array_annotations[k] = np.asarray(v)
# clean array annotations that are not 1D
# TODO remove this once multi-dimensional array_annotations are possible
array_annotations = {
k: v
for k, v in array_annotations.items() if v.ndim == 1
}
# this mock the array annotations to avoid inherits DataObject
self.array_annotations = ArrayDict(self.shape[-1])
self.array_annotations.update(array_annotations)
BaseNeo.__init__(self, **annotations)
def __init__(self,
times=None,
durations=None,
labels=None,
name=None,
description=None,
file_origin=None,
**annotations):
'''
Initialize a new :class:`EpochArray` instance.
'''
BaseNeo.__init__(self,
name=name,
file_origin=file_origin,
description=description,
**annotations)
if times is None:
times = np.array([]) * pq.s
if durations is None:
durations = np.array([]) * pq.s
if labels is None:
labels = np.array([], dtype='S')
self.times = times
self.durations = durations
self.labels = labels
self.segment = None
def __init__(self,
channel_names=None,
channel_indexes=None,
name=None,
description=None,
file_origin=None,
**annotations):
"""Initialize a new RecordingChannelGroup."""
# Inherited initialization
# Sets universally recommended attributes, and places all others
# in annotations
BaseNeo.__init__(self,
name=name,
file_origin=file_origin,
description=description,
**annotations)
# Defaults
if channel_indexes is None:
channel_indexes = np.array([])
if channel_names is None:
channel_names = np.array([])
# Store recommended attributes
self.channel_names = channel_names
self.channel_indexes = channel_indexes
# Initialize containers for child objects
self.analogsignalarrays = []
self.units = []
# Many to many relationship
self.recordingchannels = []
self.block = None
def __init__(self,
name=None,
description=None,
file_origin=None,
file_datetime=None,
rec_datetime=None,
index=None,
**annotations):
BaseNeo.__init__(self,
name=name,
file_origin=file_origin,
description=description,
**annotations)
self.file_datetime = file_datetime
self.rec_datetime = rec_datetime
self.index = index
self.epochs = []
self.epocharrays = []
self.events = []
self.eventarrays = []
self.analogsignals = []
self.analogsignalarrays = []
self.irregularlysampledsignals = []
self.spikes = []
self.spiketrains = []
self.block = None
def __init__(self, channel_names=None, channel_indexes=None, name=None,
description=None, file_origin=None, **annotations):
"""Initialize a new RecordingChannelGroup."""
# Inherited initialization
# Sets universally recommended attributes, and places all others
# in annotations
BaseNeo.__init__(self, name=name, file_origin=file_origin,
description=description, **annotations)
# Defaults
if channel_indexes is None:
channel_indexes = np.array([])
if channel_names is None:
channel_names = np.array([])
# Store recommended attributes
self.channel_names = channel_names
self.channel_indexes = channel_indexes
# Initialize containers for child objects
self.analogsignalarrays = []
self.units = []
# Many to many relationship
self.recordingchannels = []
self.block = None
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 __init__(self,
signal,
units=None,
dtype=None,
copy=True,
t_start=0 * pq.s,
sampling_rate=None,
sampling_period=None,
name=None,
file_origin=None,
description=None,
**annotations):
'''
Initializes a newly constructed :class:`AnalogSignal` instance.
'''
# This method is only called when constructing a new AnalogSignal,
# 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 __init__(self, times=None, durations=None, labels=None, units=None,
name=None, description=None, file_origin=None, **annotations):
'''
Initialize a new :class:`Epoch` instance.
'''
BaseNeo.__init__(self, name=name, file_origin=file_origin,
description=description, **annotations)
def __init__(self, times, signal, units=None, time_units=None, dtype=None,
copy=True, name=None, file_origin=None, description=None,
**annotations):
'''
Initializes a newly constructed :class:`IrregularlySampledSignal`
instance.
'''
BaseNeo.__init__(self, name=name, file_origin=file_origin,
description=description, **annotations)
def __init__(self, signal, units=None, dtype=None, copy=True,
t_start=0 * pq.s, sampling_rate=None, sampling_period=None,
name=None, file_origin=None, description=None,
channel_index=None, **annotations):
'''
Initializes a newly constructed :class:`AnalogSignalArray` instance.
'''
BaseNeo.__init__(self, name=name, file_origin=file_origin,
description=description, **annotations)
def __init__(self, time, label, name=None, description=None,
file_origin=None, **annotations):
"""Initialize a new Event."""
BaseNeo.__init__(self, name=name, file_origin=file_origin,
description=description, **annotations)
self.time = time
self.label = label
self.segment =None
def __init__(self, signal, units=None, dtype=None, copy=True,
t_start=0 * pq.s, sampling_rate=None, sampling_period=None,
name=None, file_origin=None, description=None,
channel_index=None, **annotations):
'''
Initializes a newly constructed :class:`AnalogSignalArray` instance.
'''
BaseNeo.__init__(self, name=name, file_origin=file_origin,
description=description, **annotations)
def __init__(self, times, signal, units=None, time_units=None, dtype=None,
copy=True, name=None, description=None, file_origin=None,
**annotations):
'''
Initializes a newly constructed :class:`IrregularlySampledSignal`
instance.
'''
BaseNeo.__init__(self, name=name, file_origin=file_origin,
description=description, **annotations)
def __init__(self, times=np.array([]) * pq.s,
labels=np.array([], dtype='S'), name=None, description=None,
file_origin=None, **annotations):
"""Initialize a new EventArray."""
BaseNeo.__init__(self, name=name, file_origin=file_origin,
description=description, **annotations)
self.times = times
self.labels = labels
self.segment = None
def __init__(self, time, label, name=None, description=None,
file_origin=None, **annotations):
'''
Initialize a new :class:`Event` instance.
'''
BaseNeo.__init__(self, name=name, file_origin=file_origin,
description=description, **annotations)
self.time = time
self.label = label
self.segment = None
def __init__(self, name=None, description=None, file_origin=None,
channel_indexes = None, **annotations):
"""Initialize a new neuronal Unit (spike source)"""
BaseNeo.__init__(self, name=name, file_origin=file_origin,
description=description, **annotations)
self.channel_indexes = channel_indexes
self.spiketrains = [ ]
self.spikes = [ ]
self.recordingchannelgroup = None
def __init__(self, times, values,
name=None, description=None,
file_origin=None, **annotations):
"""Initalize a new IrregularlySampledSignal."""
BaseNeo.__init__(self, name=name, file_origin=file_origin,
description=description, **annotations)
self.times = times
self.values = values
self.segment = None
self.recordingchannel = None
def __init__(self, name=None, description=None, file_origin=None,
file_datetime=None, rec_datetime=None, index=None,
**annotations):
"""Initalize a new Block."""
BaseNeo.__init__(self, name=name, file_origin=file_origin,
description=description, **annotations)
self.file_datetime = file_datetime
self.rec_datetime = rec_datetime
self.index = index
self.segments = []
self.recordingchannelgroups = []
def __init__(self, array_annotations=None, **annotations):
# this for py27 str vs py3 str in neo attributes ompatibility
annotations = check_annotations(annotations)
if 'file_origin' not in annotations:
# the str is to make compatible with neo_py27 where attribute
# used to be str so raw bytes
annotations['file_origin'] = str(self._rawio.source_name())
# this mock the array annotaions to avoid inherits DataObject
self.array_annotations = ArrayDict(self.shape[-1])
if array_annotations is not None:
self.array_annotations.update(array_annotations)
BaseNeo.__init__(self, **annotations)
def __init__(self, times=None, labels=None, name=None, description=None, file_origin=None, **annotations):
"""
Initialize a new :class:`EventArray` instance.
"""
BaseNeo.__init__(self, name=name, file_origin=file_origin, description=description, **annotations)
if times is None:
times = np.array([]) * pq.s
if labels is None:
labels = np.array([], dtype="S")
self.times = times
self.labels = labels
self.segment = None
def __init__(self, name=None, description=None, file_origin=None,
channel_indexes=None, **annotations):
'''
Initialize a new :clas:`Unit` instance (spike source)
'''
BaseNeo.__init__(self, name=name, file_origin=file_origin,
description=description, **annotations)
self.channel_indexes = channel_indexes
self.spiketrains = []
self.spikes = []
self.recordingchannelgroup = None
def __init__(self, array_annotations=None, **annotations):
# this for py27 str vs py3 str in neo attributes ompatibility
annotations = check_annotations(annotations)
if 'file_origin' not in annotations:
# the str is to make compatible with neo_py27 where attribute
# used to be str so raw bytes
annotations['file_origin'] = str(self._rawio.source_name())
# this mock the array annotaions to avoid inherits DataObject
self.array_annotations = ArrayDict(self.shape[-1])
if array_annotations is not None:
self.array_annotations.update(array_annotations)
BaseNeo.__init__(self, **annotations)
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 newly constructed SpikeTrain."""
# 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 __init__(self, name=None, description=None, file_origin=None, array_annotations=None,
**annotations):
"""
This method is called by each data object and initializes the newly created object by
adding array annotations and calling __init__ of the super class, where more annotations
and attributes are processed.
"""
if not hasattr(self, 'array_annotations') or not self.array_annotations:
self.array_annotations = ArrayDict(self._get_arr_ann_length())
if array_annotations is not None:
self.array_annotate(**array_annotations)
BaseNeo.__init__(self, name=name, description=description, file_origin=file_origin,
**annotations)
def __init__(self, name=None, description=None, file_origin=None, array_annotations=None,
**annotations):
"""
This method is called by each data object and initializes the newly created object by
adding array annotations and calling __init__ of the super class, where more annotations
and attributes are processed.
"""
if not hasattr(self, 'array_annotations') or not self.array_annotations:
self.array_annotations = ArrayDict(self._get_arr_ann_length())
if array_annotations is not None:
self.array_annotate(**array_annotations)
BaseNeo.__init__(self, name=name, description=description, file_origin=file_origin,
**annotations)
def __init__(self, time=0*pq.s, waveform=None, sampling_rate=None,
left_sweep=None, name=None, description=None,
file_origin=None, **annotations):
"""Initialize a new Spike."""
BaseNeo.__init__(self, name=name, file_origin=file_origin,
description=description, **annotations)
self.time = time
self.waveform = waveform
self.left_sweep = left_sweep
self.sampling_rate = sampling_rate
self.segment = None
self.unit = None
def __init__(self, signal, units=None, dtype=None, copy=True,
t_start=0 * pq.s, sampling_rate=None, sampling_period=None,
name=None, file_origin=None, description=None,
channel_index=None, **annotations):
'''
Initializes a newly constructed :class:`BaseAnalogSignal` instance.
'''
# This method is only called when constructing a new BaseAnalogSignal,
# 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 __init__(self,
times,
signal,
units=None,
time_units=None,
dtype=None,
copy=True,
name=None,
description=None,
file_origin=None,
**annotations):
"""Initalize a new IrregularlySampledSignal."""
BaseNeo.__init__(self,
name=name,
file_origin=file_origin,
description=description,
**annotations)
def __init__(self,
times=np.array([]) * pq.s,
labels=np.array([], dtype='S'),
name=None,
description=None,
file_origin=None,
**annotations):
"""Initialize a new EventArray."""
BaseNeo.__init__(self,
name=name,
file_origin=file_origin,
description=description,
**annotations)
self.times = times
self.labels = labels
self.segment = None
def __init__(self,
time,
label,
name=None,
description=None,
file_origin=None,
**annotations):
"""Initialize a new Event."""
BaseNeo.__init__(self,
name=name,
file_origin=file_origin,
description=description,
**annotations)
self.time = time
self.label = label
self.segment = None
def __init__(self, index=0, coordinate=None, name=None, description=None,
file_origin=None, **annotations):
"""Initialize a new RecordingChannel."""
# Inherited initialization
# Sets universally recommended attributes, and places all others
# in annotations
BaseNeo.__init__(self, name=name, file_origin=file_origin,
description=description, **annotations)
# Store required and recommended attributes
self.index = index
self.coordinate = coordinate
# Initialize contianers
self.analogsignals = [ ]
self.irregularlysampledsignals = [ ]
# Many to many relationship
self.recordingchannelgroups = [ ]
def __init__(self, name=None, description=None, file_origin=None,
file_datetime=None, rec_datetime=None, index=None, **annotations):
BaseNeo.__init__(self, name=name, file_origin=file_origin,
description=description, **annotations)
self.file_datetime = file_datetime
self.rec_datetime = rec_datetime
self.index = index
self.epochs = [ ]
self.epocharrays = [ ]
self.events = [ ]
self.eventarrays = [ ]
self.analogsignals = [ ]
self.analogsignalarrays = [ ]
self.irregularlysampledsignals = [ ]
self.spikes = [ ]
self.spiketrains = [ ]
self.block = None
def __init__(self,
name=None,
description=None,
file_origin=None,
channel_indexes=None,
**annotations):
"""Initialize a new neuronal Unit (spike source)"""
BaseNeo.__init__(self,
name=name,
file_origin=file_origin,
description=description,
**annotations)
self.channel_indexes = channel_indexes
self.spiketrains = []
self.spikes = []
self.recordingchannelgroup = None
def __init__(self, times=None, durations=None, labels=None,
name=None, description=None, file_origin=None, **annotations):
'''
Initialize a new :class:`EpochArray` instance.
'''
BaseNeo.__init__(self, name=name, file_origin=file_origin,
description=description, **annotations)
if times is None:
times = np.array([]) * pq.s
if durations is None:
durations = np.array([]) * pq.s
if labels is None:
labels = np.array([], dtype='S')
self.times = times
self.durations = durations
self.labels = labels
self.segment = None
def __init__(self,
name=None,
description=None,
file_origin=None,
file_datetime=None,
rec_datetime=None,
index=None,
**annotations):
"""Initalize a new Block."""
BaseNeo.__init__(self,
name=name,
file_origin=file_origin,
description=description,
**annotations)
self.file_datetime = file_datetime
self.rec_datetime = rec_datetime
self.index = index
self.segments = []
self.recordingchannelgroups = []
def __init__(self,
name=None,
description=None,
file_origin=None,
channel_indexes=None,
**annotations):
'''
Initialize a new :clas:`Unit` instance (spike source)
'''
BaseNeo.__init__(self,
name=name,
file_origin=file_origin,
description=description,
**annotations)
self.channel_indexes = channel_indexes
self.spiketrains = []
self.spikes = []
self.recordingchannelgroup = None
def __init__(self, times, signal, units=None, time_units=None, dtype=None,
copy=True, name=None, description=None, file_origin=None,
**annotations):
"""Initalize a new IrregularlySampledSignal."""
BaseNeo.__init__(self, name=name, file_origin=file_origin,
description=description, **annotations)
