import matplotlib.pyplot as plt
import matplotlib.animation as animation
plt.rcParams[
'animation.ffmpeg_path'] = "C:\\Users\\IntelligentSystem\[email protected]\george\Code\Python\ExtraRequirements\\ffmpeg-20140618-git-7f52960-win64-static\\bin\\ffmpeg.exe"
fn_adc = "C:\George\Data\ECoG_Chronic_Recordings\\2014_08_06_Jpak65_Anesthesia_PawStimulation_Electrical\\2014_08_06_JPak65_PawStimulation_BackRight_200uA_2ms_ADC.bin"
fn_amp = "C:\George\Data\ECoG_Chronic_Recordings\\2014_08_06_Jpak65_Anesthesia_PawStimulation_Electrical\\2014_08_06_JPak65_PawStimulation_BackRight_200uA_2ms_Amp.bin"
sampling_freq = 20000
threshold = 10000
filt_cutoff_freq = None
minduration = 10
pick_out_or_in = True
data_raw_events = tl.load_raw_event_trace(fn_adc,
number_of_channels=1,
dtype=np.uint16)
event_times, event_values = tl.create_piezosensor_events(
data_raw_events.dataMatrix, threshold, sampling_freq, filt_cutoff_freq,
minduration, pick_out_or_in)
data_raw_amp = tl.load_raw_data(fn_amp, 128)
sub_tl_data, sub_tl_avg_data, sub_time_axis = tl.time_lock_raw_data(
data_raw_amp.dataMatrix,
event_times,
times_to_cut=[-2, 2],
sampling_freq=sampling_freq,
baseline_time=[-0.5, 0],
sub_sample_freq=1000)
#sub_tl_hp_data, sub_tl_hp_avg_data, sub_time_axis = tl.time_lock_raw_data(data_raw_amp.dataMatrix, event_times, times_to_cut=[-2, 2], sampling_freq=sampling_freq, baseline_time=[-0.5, 0], high_pass_cutoff=400, rectify=False, sub_sample_freq=1000)
#sub_tl_hpr_data, sub_tl_hpr_avg_data, sub_time_axis = tl.time_lock_raw_data(data_raw_amp.dataMatrix, event_times, times_to_cut=[-2, 2], sampling_freq=sampling_freq, baseline_time=[-0.5, 0], high_pass_cutoff=400, rectify=True, sub_sample_freq=1000)
import numpy as np import matplotlib.pyplot as plt import matplotlib.animation as animation plt.rcParams['animation.ffmpeg_path'] = "C:\\Users\\IntelligentSystem\[email protected]\george\Code\Python\ExtraRequirements\\ffmpeg-20140618-git-7f52960-win64-static\\bin\\ffmpeg.exe" import mne as mne sampling_freq = 30000 #Cell 1 fn_adc_c1 = "C:\\George\\Data\\ECoG_Juxta_Paired_Recordings\\2014_12_05_Jpak77\\2014_12_05_Jpak77_JuxtaCell1_ADC_Cell1.bin" fn_amp_c1 = "C:\\George\\Data\\ECoG_Juxta_Paired_Recordings\\2014_12_05_Jpak77\\2014_12_05_Jpak77_JuxtaCell1_Amp_Cell1.bin" threshold = 0.0003 cell_1_data_raw_spikes = tl.load_raw_event_trace(fn_adc_c1, number_of_channels=8, channel_used=0, dtype=np.uint16) cell_1_event_times, cell_1_eventdata_in_V = tl.create_spike_triggered_events(cell_1_data_raw_spikes.dataMatrix, threshold = threshold, inter_spike_time_distance=0.001, amp_gain=1000, sampling_freq=sampling_freq, amp_y_digitization=65536, amp_y_range=10) cell_1_event_times = cell_1_event_times[1:-120] cell_1_data_raw_amp = tl.load_raw_data(fn_amp_c1, 64) cell_1_tl_sub_reref_avg, sub_time_axis = tl.time_lock_raw_data(cell_1_data_raw_amp.dataMatrix, cell_1_event_times, times_to_cut=[-0.2, 0.2], sampling_freq=sampling_freq, baseline_time=[-0.2, -0.05], sub_sample_freq=2000, avg_reref = True, keep_trials=False) x_of_bad_channels = np.array([19, 136, 214, 87, 516]) #For 420 spikes average y_of_bad_channels = np.array([88, 68, 94, -119, 64]) cell_1_tl_sub_reref_avg_nbc, bad_channels_cell_1_tl_sub_reref_avg = bad_channel_removal(x_of_bad_channels, y_of_bad_channels, cell_1_tl_sub_reref_avg) pf.plot_video_topoplot(cell_1_tl_sub_reref_avg_nbc, sub_time_axis, pf.grid_layout_64channels(bad_channels_cell_1_tl_sub_reref_avg), times_to_plot = [-0.06, 0.1],
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
plt.rcParams[
'animation.ffmpeg_path'] = "C:\\Users\\IntelligentSystem\[email protected]\george\Code\Python\ExtraRequirements\\ffmpeg-20140618-git-7f52960-win64-static\\bin\\ffmpeg.exe"
import mne as mne
sampling_freq = 30000
#Cell 1
fn_adc_c1 = "C:\\George\\Data\\ECoG_Juxta_Paired_Recordings\\2014_12_05_Jpak77\\2014_12_05_Jpak77_JuxtaCell1_ADC_Cell1.bin"
fn_amp_c1 = "C:\\George\\Data\\ECoG_Juxta_Paired_Recordings\\2014_12_05_Jpak77\\2014_12_05_Jpak77_JuxtaCell1_Amp_Cell1.bin"
threshold = 0.0003
cell_1_data_raw_spikes = tl.load_raw_event_trace(fn_adc_c1,
number_of_channels=8,
channel_used=0,
dtype=np.uint16)
cell_1_event_times, cell_1_eventdata_in_V = tl.create_spike_triggered_events(
cell_1_data_raw_spikes.dataMatrix,
threshold=threshold,
inter_spike_time_distance=0.001,
amp_gain=1000,
sampling_freq=sampling_freq,
amp_y_digitization=65536,
amp_y_range=10)
cell_1_event_times = cell_1_event_times[1:-120]
cell_1_data_raw_amp = tl.load_raw_data(fn_amp_c1, 64)
cell_1_tl_sub_reref_avg, sub_time_axis = tl.time_lock_raw_data(
cell_1_data_raw_amp.dataMatrix,
import matplotlib.animation as animation plt.rcParams['animation.ffmpeg_path'] = "C:\\Users\\IntelligentSystem\[email protected]\george\Code\Python\ExtraRequirements\\ffmpeg-20140618-git-7f52960-win64-static\\bin\\ffmpeg.exe" fn_adc = "C:\George\Data\ECoG_Chronic_Recordings\\2014_08_06_Jpak65_Anesthesia_PawStimulation_Electrical\\2014_08_06_JPak65_PawStimulation_BackRight_200uA_2ms_ADC.bin" fn_amp = "C:\George\Data\ECoG_Chronic_Recordings\\2014_08_06_Jpak65_Anesthesia_PawStimulation_Electrical\\2014_08_06_JPak65_PawStimulation_BackRight_200uA_2ms_Amp.bin" sampling_freq = 20000 threshold = 10000 filt_cutoff_freq = None minduration = 10 pick_out_or_in = True data_raw_events = tl.load_raw_event_trace(fn_adc, number_of_channels= 1, dtype=np.uint16) event_times, event_values = tl.create_piezosensor_events(data_raw_events.dataMatrix, threshold, sampling_freq, filt_cutoff_freq, minduration, pick_out_or_in) data_raw_amp = tl.load_raw_data(fn_amp, 128) sub_tl_data, sub_tl_avg_data, sub_time_axis = tl.time_lock_raw_data(data_raw_amp.dataMatrix, event_times, times_to_cut=[-2, 2], sampling_freq=sampling_freq, baseline_time=[-0.5, 0], sub_sample_freq=1000) #sub_tl_hp_data, sub_tl_hp_avg_data, sub_time_axis = tl.time_lock_raw_data(data_raw_amp.dataMatrix, event_times, times_to_cut=[-2, 2], sampling_freq=sampling_freq, baseline_time=[-0.5, 0], high_pass_cutoff=400, rectify=False, sub_sample_freq=1000) #sub_tl_hpr_data, sub_tl_hpr_avg_data, sub_time_axis = tl.time_lock_raw_data(data_raw_amp.dataMatrix, event_times, times_to_cut=[-2, 2], sampling_freq=sampling_freq, baseline_time=[-0.5, 0], high_pass_cutoff=400, rectify=True, sub_sample_freq=1000) fn_adc2 = "C:\George\Data\ECoG_Chronic_Recordings\\14_06_03_Jpak65_Anesthesia_Stimulations\\14_06_03_stimulation_manual_paw_qtip2\stim.bin" fn_amp2 = "C:\George\Data\ECoG_Chronic_Recordings\\14_06_03_Jpak65_Anesthesia_Stimulations\\14_06_03_stimulation_manual_paw_qtip2\\amplifier.bin" sampling_freq = 8000 threshold = 1e7 filt_cutoff_freq = 1000 minduration = 100
