def run(db_name, save_fig_name=None):
"""If save_fig_name is not None, should be ex. '~/test.png' """
# Load the raw data
db = OE.open_db(url=('sqlite:///%s' % db_name))
id_blocks, = OE.sql(
'SELECT block.id FROM block WHERE block.name="Raw Data"')
id_block = id_blocks[0]
id_recordingpoints, rp_names = OE.sql("SELECT \
recordingpoint.id, recordingpoint.name \
FROM recordingpoint \
WHERE recordingpoint.id_block = :id_block",
id_block=id_block)
f = plt.figure(figsize=(10, 10))
# Process each recording point separately
for n, (id_rp, tt) in enumerate(zip(id_recordingpoints[:16],
rp_names[:16])):
# Load all signals from all segments with this recording point
id_sigs, = OE.sql('SELECT analogsignal.id FROM analogsignal ' + \
'WHERE analogsignal.id_recordingpoint = :id_recordingpoint',
id_recordingpoint=id_rp)
# Average the signal
avgsig = np.zeros(OE.AnalogSignal().load(id_sigs[0]).signal.shape)
for id_sig in id_sigs:
sig = OE.AnalogSignal().load(id_sig)
avgsig = avgsig + sig.signal
avgsig = old_div(avgsig, len(id_sigs))
# Plot the average signal of this recording point
ax = f.add_subplot(4, 4, n + 1)
ax.plot(
old_div(np.arange(len(avgsig)), sig.sampling_rate) * 1000, avgsig)
#ax.set_ylim((-250, 250))
ax.set_title(tt)
if save_fig_name is None:
plt.show()
else:
plt.savefig(save_fig_name)
plt.close()
def stuff(filename,
db_name,
TIMESTAMPS,
SHOVE_CHANNELS,
pre_slice_len,
post_slice_len,
db_type='sqlite'):
# Load the file and file header
l = ns5.Loader(filename=filename)
l.load_file()
# Audio channel numbers
AUDIO_CHANNELS = l.get_audio_channel_numbers()
# Open connection to OE db and create a block
if db_type is 'postgres':
OE.open_db(url=(
'postgresql://[email protected]/test')) # %s' % db_name))
print('post')
else:
OE.open_db(url=('sqlite:///%s' % db_name))
#OE.open_db(url=('mysql://*****:*****@localhost/%s' % db_name))
block = OE.Block(name='Raw Data',
info='Raw data sliced around trials',
fileOrigin=filename)
id_block = block.save() # need this later
# Convert requested slice lengths to samples
pre_slice_len_samples = int(pre_slice_len * l.header.f_samp)
post_slice_len_samples = int(post_slice_len * l.header.f_samp)
# Add RecordingPoint
ch2rpid = dict()
for ch in SHOVE_CHANNELS:
rp = OE.RecordingPoint(name=('RP%d' % ch),
id_block=id_block,
channel=float(ch))
rp_id = rp.save()
ch2rpid[ch] = rp_id
# Extract each trial as a segment
for tn, trial_start in enumerate(TIMESTAMPS):
# Create segment for this trial
segment = OE.Segment(id_block=id_block,
name=('trial%d' % tn),
info='raw data loaded from good channels')
id_segment = segment.save()
# Create AnalogSignal for each channel
for chn, ch in enumerate(SHOVE_CHANNELS):
# Load
x = np.array(l._get_channel(ch)[trial_start-pre_slice_len_samples:\
trial_start+post_slice_len_samples])
# Convert to uV
x = x * uV_QUANTUM
# Put in AnalogSignal and save to db
sig = OE.AnalogSignal(signal=x,
channel=float(ch),
sampling_rate=l.header.f_samp,
t_start=old_div(
(trial_start - pre_slice_len_samples),
l.header.f_samp),
id_segment=id_segment,
id_recordingpoint=ch2rpid[ch],
name=('Channel %d Trial %d' % (ch, tn)))
# Special processing for audio channels
if ch == AUDIO_CHANNELS[0]:
sig.name = ('L Speaker Trial %d' % tn)
elif ch == AUDIO_CHANNELS[1]:
sig.name = ('R Speaker Trial %d' % tn)
# Save signal to database
sig.save()
# Handle AUDIO CHANNELS only slightly differently
for ch in AUDIO_CHANNELS:
# Load
x = np.array(l._get_channel(ch)[trial_start-pre_slice_len_samples:\
trial_start+post_slice_len_samples])
# Special processing for audio channels
if ch == AUDIO_CHANNELS[0]:
sname = ('L Speaker Trial %d' % tn)
elif ch == AUDIO_CHANNELS[1]:
sname = ('R Speaker Trial %d' % tn)
# Put in AnalogSignal and save to db
sig = OE.AnalogSignal(signal=x,
channel=float(ch),
sampling_rate=l.header.f_samp,
t_start=old_div(
(trial_start - pre_slice_len_samples),
l.header.f_samp),
id_segment=id_segment,
name=sname)
# Save signal to database
sig.save()
# Save segment (with all analogsignals) to db
# Actually this may be unnecessary
# Does saving the signals link to the segment automatically?
segment.save()
return (id_segment, id_block)
def run(db_name, CAR=True, smooth_spikes=True):
"""Filters the data for spike extraction.
db_name: Name of the OpenElectrophy db file
CAR: If True, subtract the common-average of every channel.
smooth_spikes: If True, add an additional low-pass filtering step to
the spike filter.
"""
# Open connection to the database
OE.open_db(url=('sqlite:///%s' % db_name))
# Check that I haven't already run
id_blocks, = OE.sql(
"SELECT block.id FROM block WHERE block.name='CAR Tetrode Data'")
if len(id_blocks) > 0:
print("CAR Tetrode Data already exists, no need to recompute")
return
# Find the block
id_blocks, = OE.sql(
"SELECT block.id FROM block WHERE block.name='Raw Data'")
assert (len(id_blocks) == 1)
id_block = id_blocks[0]
raw_block = OE.Block().load(id_block)
# Define spike filter
# TODO: fix so that doesn't assume all sampling rates the same!
fixed_sampling_rate = OE.AnalogSignal().load(1).sampling_rate
FILTER_B, FILTER_A = define_spike_filter(fixed_sampling_rate)
# If requested, define second spike filter
if smooth_spikes is True:
FILTER_B2, FILTER_A2 = define_spike_filter_2(fixed_sampling_rate)
# Find TETRODE_CHANNELS file in data directory of db
data_dir = path.split(db_name)[0]
TETRODE_CHANNELS = get_tetrode_channels(
path.join(data_dir, 'TETRODE_CHANNELS'))
N_TET = len(TETRODE_CHANNELS)
# For convenience, flatten TETRODE_CHANNELS to just get worthwhile channels
GOOD_CHANNELS = [item for sublist in TETRODE_CHANNELS for item in sublist]
# Create a new block for referenced data, and save to db.
car_block = OE.Block(\
name='CAR Tetrode Data',
info='Raw neural data, now referenced and ordered by tetrode',
fileOrigin=db_name)
id_car_block = car_block.save()
# Make RecordingPoint for each channel, linked to tetrode number with `group`
# Also keep track of link between channel and RP with ch2rpid dict
ch2rpid = dict()
for tn, ch_list in enumerate(TETRODE_CHANNELS):
for ch in ch_list:
rp = OE.RecordingPoint(name=('RP%d' % ch),
id_block=id_car_block,
trodness=len(ch_list),
channel=float(ch),
group=tn)
rp_id = rp.save()
ch2rpid[ch] = rp_id
# Find all segments in the block of raw data
id_segments, = OE.sql('SELECT segment.id FROM segment ' + \
'WHERE segment.id_block = :id_block', id_block=id_block)
# For each segment in this block, load each AnalogSignal listed in
# TETRODE channels and average
# to compute CAR. Then subtract from each AnalogSignal.
for id_segment in id_segments:
# Create a new segment in the new block with the same name
old_seg = OE.Segment().load(id_segment)
car_seg = OE.Segment(
name=old_seg.name,
id_block=id_car_block,
)
id_car_seg = car_seg.save()
# Find all AnalogSignals in this segment
id_sigs, = OE.sql('SELECT analogsignal.id FROM analogsignal ' + \
'WHERE analogsignal.id_segment = :id_segment', id_segment=id_segment)
# Compute average of each
running_car = 0
n_summed = 0
for id_sig in id_sigs:
sig = OE.AnalogSignal().load(id_sig)
if sig.channel not in GOOD_CHANNELS:
continue
running_car = running_car + sig.signal
n_summed = n_summed + 1
# Zero out CAR if CAR is not wanted
# TODO: eliminate the actual calculation of CAR above in this case
# For now, just want to avoid weird bugs
if CAR is False:
running_car = np.zeros(running_car.shape)
# Put the CAR into the new block
# not assigning channel, t_start, sample_rate, maybe more?
car_sig = OE.AnalogSignal(
name='CAR',
signal=old_div(running_car, n_summed),
info='CAR calculated from good channels for this segment',
id_segment=id_segment)
car_sig.save()
# Put all the substractions in id_car_seg
for id_sig in id_sigs:
# Load the raw signal (skip bad channels)
sig = OE.AnalogSignal().load(id_sig)
if sig.channel not in GOOD_CHANNELS:
continue
# Subtract the CAR
referenced_signal = sig.signal - car_sig.signal
# Filter!
filtered_signal = scipy.signal.filtfilt(FILTER_B, FILTER_A,
referenced_signal)
if smooth_spikes is True:
filtered_signal = scipy.signal.filtfilt(
FILTER_B2, FILTER_A2, filtered_signal)
# Check for infs or nans
if np.isnan(filtered_signal).any():
print("ERROR: Filtered signal contains NaN!")
if np.isinf(filtered_signal).any():
print("ERROR: Filtered signal contains Inf!")
# Store in db
new_sig = OE.AnalogSignal(\
name=sig.name,
signal=filtered_signal,
info='CAR has been subtracted',
id_segment=id_car_seg,
id_recordingpoint=ch2rpid[sig.channel],
channel=sig.channel,
t_start=sig.t_start,
sampling_rate=sig.sampling_rate)
new_sig.save()
# Finally, copy the audio channel over from the old block
id_audio_sigs, = OE.sql('SELECT analogsignal.id FROM analogsignal ' + \
'WHERE analogsignal.id_segment = :id_segment AND ' + \
"analogsignal.name LIKE '% Speaker %'", id_segment=id_segment)
for id_audio_sig in id_audio_sigs:
old_sig = OE.AnalogSignal().load(id_audio_sig)
OE.AnalogSignal(\
name=old_sig.name,
signal=old_sig.signal,
id_segment=id_car_seg,
channel=old_sig.channel,
t_start=old_sig.t_start,
sampling_rate=old_sig.sampling_rate).save()