def test_spikecache_1():
nspikes = 100000
nclusters = 100
nchannels = 8
spike_clusters = np.random.randint(size=nspikes, low=0, high=nclusters)
sc = SpikeCache(spike_clusters=spike_clusters,
cache_fraction=.1,
features_masks=np.zeros((nspikes, 3*nchannels, 2)),
waveforms_raw=np.zeros((nspikes, 20, nchannels)),
waveforms_filtered=np.zeros((nspikes, 20, nchannels)))
ind, fm = sc.load_features_masks(.1)
assert len(ind) == nspikes // 100
assert fm.shape[0] == nspikes // 100
ind, fm = sc.load_features_masks(clusters=[10, 20])
assert len(ind) == fm.shape[0]
assert np.allclose(ind, np.nonzero(np.in1d(spike_clusters, (10, 20)))[0])
ind, fm = sc.load_features_masks(clusters=[1000])
assert len(ind) == 0
assert len(fm) == 0
class Spikes(Node):
def __init__(self, files, node=None, root=None):
super(Spikes, self).__init__(files, node, root=root)
self.time_samples = self._node.time_samples
self.time_fractional = self._node.time_fractional
self.recording = self._node.recording
self.clusters = Clusters(self._files,
self._node.clusters,
root=self._root)
# Add concatenated time samples
self.concatenated_time_samples = self._compute_concatenated_time_samples(
)
self.channel_group_id = self._node._v_parent._v_name
# Get large datasets, that may be in external files.
# self.features_masks = self._get_child('features_masks')
# self.waveforms_raw = self._get_child('waveforms_raw')
# self.waveforms_filtered = self._get_child('waveforms_filtered')
# Load features masks directly from KWX.
g = self.channel_group_id
path = '/channel_groups/{}/features_masks'.format(g)
if files['kwx']:
self.features_masks = files['kwx'].getNode(path)
else:
self.features_masks = None
# Load raw data directly from raw data.
traces = _read_traces(files)
b = self._root.application_data.spikedetekt._f_getAttr(
'extract_s_before')
a = self._root.application_data.spikedetekt._f_getAttr(
'extract_s_after')
order = self._root.application_data.spikedetekt._f_getAttr(
'filter_butter_order')
rate = self._root.application_data.spikedetekt._f_getAttr(
'sample_rate')
low = self._root.application_data.spikedetekt._f_getAttr('filter_low')
if 'filter_high_factor' in self._root.application_data.spikedetekt._v_attrs:
high = self._root.application_data.spikedetekt._f_getAttr(
'filter_high_factor') * rate
else:
# NOTE: old format
high = self._root.application_data.spikedetekt._f_getAttr(
'filter_high')
b_filter = bandpass_filter(rate=rate, low=low, high=high, order=order)
debug("Enable waveform filter.")
def the_filter(x, axis=0):
return apply_filter(x, b_filter, axis=axis)
filter_margin = order * 3
channels = self._root.channel_groups._f_getChild(
self.channel_group_id)._f_getAttr('channel_order')
_waveform_loader = WaveformLoader(
n_samples=(b + a),
traces=traces,
filter=the_filter,
filter_margin=filter_margin,
scale_factor=.01,
channels=channels,
)
self.waveforms_raw = SpikeLoader(_waveform_loader,
self.time_samples[:])
self.waveforms_filtered = self.waveforms_raw
nspikes = len(self.time_samples)
if self.waveforms_raw is not None:
self.nsamples, self.nchannels = self.waveforms_raw.shape[1:]
if self.features_masks is None:
self.features_masks = np.zeros((nspikes, 1, 1), dtype=np.float32)
if len(self.features_masks.shape) == 3:
self.features = ArrayProxy(self.features_masks, col=0)
self.masks = ArrayProxy(self.features_masks, col=1)
elif len(self.features_masks.shape) == 2:
self.features = self.features_masks
self.masks = None #np.ones_like(self.features)
self.nfeatures = self.features.shape[1]
def _compute_concatenated_time_samples(self):
t_rel = self.time_samples[:]
recordings = self.recording[:]
if len(recordings) == 0 and len(t_rel) > 0:
recordings = np.zeros_like(t_rel)
# Get list of recordings.
recs = self._root.recordings
recs = sorted([int(_._v_name) for _ in recs._f_listNodes()])
# Get their start times.
if not recs:
return t_rel
start_times = np.zeros(max(recs) + 1, dtype=np.uint64)
for r in recs:
recgrp = getattr(self._root.recordings, str(r))
sample_rate = recgrp._f_getAttr('sample_rate')
start_time = recgrp._f_getAttr('start_time') or 0.
start_times[r] = int(start_time * sample_rate)
return t_rel + start_times[recordings]
def add(self, **kwargs):
"""Add a spike. Only `time_samples` is mandatory."""
add_spikes(self._files,
channel_group_id=self.channel_group_id,
**kwargs)
def init_cache(self):
"""Initialize the cache for the features & masks."""
self._spikecache = SpikeCache(
# TODO: handle multiple clusterings in the spike cache here
spike_clusters=self.clusters.main,
features_masks=self.features_masks,
waveforms_raw=self.waveforms_raw,
waveforms_filtered=self.waveforms_filtered,
# TODO: put this value in the parameters
cache_fraction=1.,
)
def load_features_masks_bg(self, *args, **kwargs):
return self._spikecache.load_features_masks_bg(*args, **kwargs)
def load_features_masks(self, *args, **kwargs):
return self._spikecache.load_features_masks(*args, **kwargs)
def load_waveforms(self, *args, **kwargs):
return self._spikecache.load_waveforms(*args, **kwargs)
def __getitem__(self, item):
raise NotImplementedError("""It is not possible to select entire spikes
yet.""")
def __len__(self):
return self.time_samples.shape[0]
class Spikes(Node):
def __init__(self, files, node=None, root=None):
super(Spikes, self).__init__(files, node, root=root)
self.time_samples = self._node.time_samples
self.time_fractional = self._node.time_fractional
self.recording = self._node.recording
self.clusters = Clusters(self._files, self._node.clusters, root=self._root)
# Add concatenated time samples
self.concatenated_time_samples = self._compute_concatenated_time_samples()
self.channel_group_id = self._node._v_parent._v_name
# Get large datasets, that may be in external files.
self.features_masks = self._get_child('features_masks')
self.waveforms_raw = self._get_child('waveforms_raw')
self.waveforms_filtered = self._get_child('waveforms_filtered')
nspikes = len(self.time_samples)
if self.waveforms_raw is not None:
self.nsamples, self.nchannels = self.waveforms_raw.shape[1:]
if self.features_masks is None:
self.features_masks = np.zeros((nspikes, 1, 1), dtype=np.float32)
if len(self.features_masks.shape) == 3:
self.features = ArrayProxy(self.features_masks, col=0)
self.masks = ArrayProxy(self.features_masks, col=1)
elif len(self.features_masks.shape) == 2:
self.features = self.features_masks
self.masks = None #np.ones_like(self.features)
self.nfeatures = self.features.shape[1]
def _compute_concatenated_time_samples(self):
t_rel = self.time_samples[:]
recordings = self.recording[:]
if len(recordings) == 0 and len(t_rel) > 0:
recordings = np.zeros_like(t_rel)
# Get list of recordings.
recs = self._root.recordings
recs = sorted([int(_._v_name) for _ in recs._f_listNodes()])
# Get their start times.
if not recs:
return t_rel
start_times = np.zeros(max(recs)+1, dtype=np.uint64)
for r in recs:
recgrp = getattr(self._root.recordings, str(r))
sample_rate = recgrp._f_getAttr('sample_rate')
start_time = recgrp._f_getAttr('start_time') or 0.
start_times[r] = int(start_time * sample_rate)
return t_rel + start_times[recordings]
def add(self, **kwargs):
"""Add a spike. Only `time_samples` is mandatory."""
add_spikes(self._files, channel_group_id=self.channel_group_id, **kwargs)
def init_cache(self):
"""Initialize the cache for the features & masks."""
self._spikecache = SpikeCache(
# TODO: handle multiple clusterings in the spike cache here
spike_clusters=self.clusters.main,
features_masks=self.features_masks,
waveforms_raw=self.waveforms_raw,
waveforms_filtered=self.waveforms_filtered,
# TODO: put this value in the parameters
cache_fraction=1.,)
def load_features_masks_bg(self, *args, **kwargs):
return self._spikecache.load_features_masks_bg(*args, **kwargs)
def load_features_masks(self, *args, **kwargs):
return self._spikecache.load_features_masks(*args, **kwargs)
def load_waveforms(self, *args, **kwargs):
return self._spikecache.load_waveforms(*args, **kwargs)
def __getitem__(self, item):
raise NotImplementedError("""It is not possible to select entire spikes
yet.""")
def __len__(self):
return self.time_samples.shape[0]
class Spikes(Node):
def __init__(self, files, node=None, root=None):
super(Spikes, self).__init__(files, node, root=root)
self.time_samples = self._node.time_samples
self.time_fractional = self._node.time_fractional
self.recording = self._node.recording
self.clusters = Clusters(self._files, self._node.clusters, root=self._root)
# Add concatenated time samples
self.concatenated_time_samples = self._compute_concatenated_time_samples()
self.channel_group_id = self._node._v_parent._v_name
# Get large datasets, that may be in external files.
# self.features_masks = self._get_child('features_masks')
# self.waveforms_raw = self._get_child('waveforms_raw')
# self.waveforms_filtered = self._get_child('waveforms_filtered')
# Load features masks directly from KWX.
g = self.channel_group_id
path = '/channel_groups/{}/features_masks'.format(g)
if files['kwx']:
self.features_masks = files['kwx'].getNode(path)
else:
self.features_masks = None
# Load raw data directly from raw data.
traces = _read_traces(files)
b = self._root.application_data.spikedetekt._f_getAttr('extract_s_before')
a = self._root.application_data.spikedetekt._f_getAttr('extract_s_after')
order = self._root.application_data.spikedetekt._f_getAttr('filter_butter_order')
rate = self._root.application_data.spikedetekt._f_getAttr('sample_rate')
low = self._root.application_data.spikedetekt._f_getAttr('filter_low')
if 'filter_high_factor' in self._root.application_data.spikedetekt._v_attrs:
high = self._root.application_data.spikedetekt._f_getAttr('filter_high_factor') * rate
else:
# NOTE: old format
high = self._root.application_data.spikedetekt._f_getAttr('filter_high')
b_filter = bandpass_filter(rate=rate,
low=low,
high=high,
order=order)
debug("Enable waveform filter.")
def the_filter(x, axis=0):
return apply_filter(x, b_filter, axis=axis)
filter_margin = order * 3
channels = self._root.channel_groups._f_getChild(self.channel_group_id)._f_getAttr('channel_order')
_waveform_loader = WaveformLoader(n_samples=(b, a),
traces=traces,
filter=the_filter,
filter_margin=filter_margin,
scale_factor=.01,
channels=channels,
)
self.waveforms_raw = SpikeLoader(_waveform_loader,
self.concatenated_time_samples)
self.waveforms_filtered = self.waveforms_raw
nspikes = len(self.time_samples)
if self.waveforms_raw is not None:
self.nsamples, self.nchannels = self.waveforms_raw.shape[1:]
if self.features_masks is None:
self.features_masks = np.zeros((nspikes, 1, 1), dtype=np.float32)
if len(self.features_masks.shape) == 3:
self.features = ArrayProxy(self.features_masks, col=0)
self.masks = ArrayProxy(self.features_masks, col=1)
elif len(self.features_masks.shape) == 2:
self.features = self.features_masks
self.masks = None #np.ones_like(self.features)
self.nfeatures = self.features.shape[1]
def _compute_concatenated_time_samples(self):
t_rel = self.time_samples[:]
recordings = self.recording[:]
if len(recordings) == 0 and len(t_rel) > 0:
recordings = np.zeros_like(t_rel)
# Get list of recordings.
recs = self._root.recordings
recs = sorted([int(_._v_name) for _ in recs._f_listNodes()])
# Get their start times.
if not recs:
return t_rel
start_times = np.zeros(max(recs)+1, dtype=np.uint64)
for r in recs:
recgrp = getattr(self._root.recordings, str(r))
sample_rate = recgrp._f_getAttr('sample_rate')
start_time = recgrp._f_getAttr('start_time') or 0.
start_times[r] = int(start_time * sample_rate)
return t_rel + start_times[recordings]
def add(self, **kwargs):
"""Add a spike. Only `time_samples` is mandatory."""
add_spikes(self._files, channel_group_id=self.channel_group_id, **kwargs)
def init_cache(self):
"""Initialize the cache for the features & masks."""
self._spikecache = SpikeCache(
# TODO: handle multiple clusterings in the spike cache here
spike_clusters=self.clusters.main,
features_masks=self.features_masks,
waveforms_raw=self.waveforms_raw,
waveforms_filtered=self.waveforms_filtered,
# TODO: put this value in the parameters
cache_fraction=1.,)
def load_features_masks_bg(self, *args, **kwargs):
return self._spikecache.load_features_masks_bg(*args, **kwargs)
def load_features_masks(self, *args, **kwargs):
return self._spikecache.load_features_masks(*args, **kwargs)
def load_waveforms(self, *args, **kwargs):
return self._spikecache.load_waveforms(*args, **kwargs)
def __getitem__(self, item):
raise NotImplementedError("""It is not possible to select entire spikes
yet.""")
def __len__(self):
return self.time_samples.shape[0]
class Spikes(Node):
def __init__(self, files, node=None, root=None):
super(Spikes, self).__init__(files, node, root=root)
self.time_samples = self._node.time_samples
self.time_fractional = self._node.time_fractional
self.recording = self._node.recording
self.clusters = Clusters(self._files, self._node.clusters, root=self._root)
# Add concatenated time samples
self.concatenated_time_samples = self._compute_concatenated_time_samples()
self.channel_group_id = self._node._v_parent._v_name
# Get large datasets, that may be in external files.
# self.features_masks = self._get_child('features_masks')
# self.waveforms_raw = self._get_child('waveforms_raw')
# self.waveforms_filtered = self._get_child('waveforms_filtered')
# Load features masks directly from KWX.
g = self.channel_group_id
path = '/channel_groups/{}/features_masks'.format(g)
self.features_masks = files['kwx'].getNode(path)
# Load raw data directly from raw data.
# path = '/recordings/{}/raw/dat_path'.format(0)
# traces_path = files['kwik'].getNode(path)
# TODO: include here
# from phy.traces.waveform import WaveformLoader, SpikeLoader
# b = self._root.application_data.spikedetekt.extract_s_before
# a = self._root.application_data.spikedetekt.extract_s_after
# _waveform_loader = WaveformLoader(n_samples=(b + a),
# # traces=traces,
# # filter=the_filter,
# # filter_margin=filter_margin,
# # dc_offset=dc_offset,
# # scale_factor=scale_factor,
# )
# self.waveforms_raw = SpikeLoader(_waveform_loader, self.time_samples)
# TODO
# self.waveforms_filtered = None
nspikes = len(self.time_samples)
if self.waveforms_raw is not None:
self.nsamples, self.nchannels = self.waveforms_raw.shape[1:]
if self.features_masks is None:
self.features_masks = np.zeros((nspikes, 1, 1), dtype=np.float32)
if len(self.features_masks.shape) == 3:
self.features = ArrayProxy(self.features_masks, col=0)
self.masks = ArrayProxy(self.features_masks, col=1)
elif len(self.features_masks.shape) == 2:
self.features = self.features_masks
self.masks = None #np.ones_like(self.features)
self.nfeatures = self.features.shape[1]
def _compute_concatenated_time_samples(self):
t_rel = self.time_samples[:]
recordings = self.recording[:]
if len(recordings) == 0 and len(t_rel) > 0:
recordings = np.zeros_like(t_rel)
# Get list of recordings.
recs = self._root.recordings
recs = sorted([int(_._v_name) for _ in recs._f_listNodes()])
# Get their start times.
if not recs:
return t_rel
start_times = np.zeros(max(recs)+1, dtype=np.uint64)
for r in recs:
recgrp = getattr(self._root.recordings, str(r))
sample_rate = recgrp._f_getAttr('sample_rate')
start_time = recgrp._f_getAttr('start_time') or 0.
start_times[r] = int(start_time * sample_rate)
return t_rel + start_times[recordings]
def add(self, **kwargs):
"""Add a spike. Only `time_samples` is mandatory."""
add_spikes(self._files, channel_group_id=self.channel_group_id, **kwargs)
def init_cache(self):
"""Initialize the cache for the features & masks."""
self._spikecache = SpikeCache(
# TODO: handle multiple clusterings in the spike cache here
spike_clusters=self.clusters.main,
features_masks=self.features_masks,
waveforms_raw=self.waveforms_raw,
waveforms_filtered=self.waveforms_filtered,
# TODO: put this value in the parameters
cache_fraction=1.,)
def load_features_masks_bg(self, *args, **kwargs):
return self._spikecache.load_features_masks_bg(*args, **kwargs)
def load_features_masks(self, *args, **kwargs):
return self._spikecache.load_features_masks(*args, **kwargs)
def load_waveforms(self, *args, **kwargs):
return self._spikecache.load_waveforms(*args, **kwargs)
def __getitem__(self, item):
raise NotImplementedError("""It is not possible to select entire spikes
yet.""")
def __len__(self):
return self.time_samples.shape[0]
class Spikes(Node):
def __init__(self, files, node=None, root=None):
super(Spikes, self).__init__(files, node, root=root)
self.time_samples = self._node.time_samples
self.time_fractional = self._node.time_fractional
self.recording = self._node.recording
self.clusters = Clusters(self._files,
self._node.clusters,
root=self._root)
# Add concatenated time samples
self.concatenated_time_samples = self._compute_concatenated_time_samples(
)
self.channel_group_id = self._node._v_parent._v_name
# Get large datasets, that may be in external files.
self.features_masks = self._get_child('features_masks')
self.waveforms_raw = self._get_child('waveforms_raw')
self.waveforms_filtered = self._get_child('waveforms_filtered')
nspikes = len(self.time_samples)
if self.waveforms_raw is not None:
self.nsamples, self.nchannels = self.waveforms_raw.shape[1:]
if self.features_masks is None:
self.features_masks = np.zeros((nspikes, 1, 1), dtype=np.float32)
if len(self.features_masks.shape) == 3:
self.features = ArrayProxy(self.features_masks, col=0)
self.masks = ArrayProxy(self.features_masks, col=1)
elif len(self.features_masks.shape) == 2:
self.features = self.features_masks
self.masks = None #np.ones_like(self.features)
self.nfeatures = self.features.shape[1]
def _compute_concatenated_time_samples(self):
t_rel = self.time_samples[:]
recordings = self.recording[:]
if len(recordings) == 0 and len(t_rel) > 0:
recordings = np.zeros_like(t_rel)
# Get list of recordings.
recs = self._root.recordings
recs = sorted([int(_._v_name) for _ in recs._f_listNodes()])
# Get their start times.
if not recs:
return t_rel
start_times = np.zeros(max(recs) + 1, dtype=np.uint64)
for r in recs:
recgrp = getattr(self._root.recordings, str(r))
sample_rate = recgrp._f_getAttr('sample_rate')
start_time = recgrp._f_getAttr('start_time') or 0.
start_times[r] = int(start_time * sample_rate)
return t_rel + start_times[recordings]
def add(self, **kwargs):
"""Add a spike. Only `time_samples` is mandatory."""
add_spikes(self._files,
channel_group_id=self.channel_group_id,
**kwargs)
def init_cache(self):
"""Initialize the cache for the features & masks."""
self._spikecache = SpikeCache(
# TODO: handle multiple clusterings in the spike cache here
spike_clusters=self.clusters.main,
features_masks=self.features_masks,
waveforms_raw=self.waveforms_raw,
waveforms_filtered=self.waveforms_filtered,
# TODO: put this value in the parameters
cache_fraction=1.,
)
def load_features_masks_bg(self, *args, **kwargs):
return self._spikecache.load_features_masks_bg(*args, **kwargs)
def load_features_masks(self, *args, **kwargs):
return self._spikecache.load_features_masks(*args, **kwargs)
def load_waveforms(self, *args, **kwargs):
return self._spikecache.load_waveforms(*args, **kwargs)
def __getitem__(self, item):
raise NotImplementedError(
"""It is not possible to select entire spikes
yet.""")
def __len__(self):
return self.time_samples.shape[0]
class Spikes(Node):
def __init__(self, files, node=None, root=None):
super(Spikes, self).__init__(files, node, root=root)
self.time_samples = self._node.time_samples
self.time_fractional = self._node.time_fractional
self.recording = self._node.recording
self.clusters = Clusters(self._files,
self._node.clusters,
root=self._root)
# Add concatenated time samples
self.concatenated_time_samples = self._compute_concatenated_time_samples(
)
self.channel_group_id = self._node._v_parent._v_name
# Get large datasets, that may be in external files.
# self.features_masks = self._get_child('features_masks')
# self.waveforms_raw = self._get_child('waveforms_raw')
# self.waveforms_filtered = self._get_child('waveforms_filtered')
# Load features masks directly from KWX.
g = self.channel_group_id
path = '/channel_groups/{}/features_masks'.format(g)
self.features_masks = files['kwx'].getNode(path)
# Load raw data directly from raw data.
# path = '/recordings/{}/raw/dat_path'.format(0)
# traces_path = files['kwik'].getNode(path)
# TODO: include here
# from phy.traces.waveform import WaveformLoader, SpikeLoader
# b = self._root.application_data.spikedetekt.extract_s_before
# a = self._root.application_data.spikedetekt.extract_s_after
# _waveform_loader = WaveformLoader(n_samples=(b + a),
# # traces=traces,
# # filter=the_filter,
# # filter_margin=filter_margin,
# # dc_offset=dc_offset,
# # scale_factor=scale_factor,
# )
# self.waveforms_raw = SpikeLoader(_waveform_loader, self.time_samples)
# TODO
# self.waveforms_filtered = None
nspikes = len(self.time_samples)
if self.waveforms_raw is not None:
self.nsamples, self.nchannels = self.waveforms_raw.shape[1:]
if self.features_masks is None:
self.features_masks = np.zeros((nspikes, 1, 1), dtype=np.float32)
if len(self.features_masks.shape) == 3:
self.features = ArrayProxy(self.features_masks, col=0)
self.masks = ArrayProxy(self.features_masks, col=1)
elif len(self.features_masks.shape) == 2:
self.features = self.features_masks
self.masks = None #np.ones_like(self.features)
self.nfeatures = self.features.shape[1]
def _compute_concatenated_time_samples(self):
t_rel = self.time_samples[:]
recordings = self.recording[:]
if len(recordings) == 0 and len(t_rel) > 0:
recordings = np.zeros_like(t_rel)
# Get list of recordings.
recs = self._root.recordings
recs = sorted([int(_._v_name) for _ in recs._f_listNodes()])
# Get their start times.
if not recs:
return t_rel
start_times = np.zeros(max(recs) + 1, dtype=np.uint64)
for r in recs:
recgrp = getattr(self._root.recordings, str(r))
sample_rate = recgrp._f_getAttr('sample_rate')
start_time = recgrp._f_getAttr('start_time') or 0.
start_times[r] = int(start_time * sample_rate)
return t_rel + start_times[recordings]
def add(self, **kwargs):
"""Add a spike. Only `time_samples` is mandatory."""
add_spikes(self._files,
channel_group_id=self.channel_group_id,
**kwargs)
def init_cache(self):
"""Initialize the cache for the features & masks."""
self._spikecache = SpikeCache(
# TODO: handle multiple clusterings in the spike cache here
spike_clusters=self.clusters.main,
features_masks=self.features_masks,
waveforms_raw=self.waveforms_raw,
waveforms_filtered=self.waveforms_filtered,
# TODO: put this value in the parameters
cache_fraction=1.,
)
def load_features_masks_bg(self, *args, **kwargs):
return self._spikecache.load_features_masks_bg(*args, **kwargs)
def load_features_masks(self, *args, **kwargs):
return self._spikecache.load_features_masks(*args, **kwargs)
def load_waveforms(self, *args, **kwargs):
return self._spikecache.load_waveforms(*args, **kwargs)
def __getitem__(self, item):
raise NotImplementedError("""It is not possible to select entire spikes
yet.""")
def __len__(self):
return self.time_samples.shape[0]