sync_funcs.find_nearest(
y_positions[position_sorted_indices] * const.POSITION_MULT, rp)[0])
region_lines = np.array(region_lines)
tns = tn[position_sorted_indices]
plt.imshow(np.flipud(tns), aspect='auto')
plt.hlines(y=len(t) - region_lines,
xmin=0,
xmax=len(tns[0]) - 1,
linewidth=3,
color='w')
plt.vlines(x=int(len(tns[0]) / 2), ymin=0, ymax=len(tns) - 1)
i = 0
sv.graph_pane(globals(), 'i', 'tn')
time_around_beam_break = 8
index = 0
fig1 = plt.figure(1)
fig2 = plt.figure(2)
output = None
all_indices = np.arange(len(avg_firing_rate_around_suc_trials))
frames_around_beam_break = 120 * time_around_beam_break
args = [
all_indices, avg_firing_rate_around_suc_trials, template_info, spike_info,
start_pokes_after_delay, frames_around_beam_break, fig1, fig2
]
show_rasters_decrease = fr_funcs.show_rasters_for_live_update
label='Template = {}'.format(str(n)))
#labels.append(label)
maxima.append((np.argmax(t_s) - 100) * 8.33)
avg = np.mean(maxima)
var = np.var(maxima)
pdf_x = np.linspace(np.min(maxima), np.max(maxima), 100)
pdf_y = 1.0 / np.sqrt(2 * np.pi * var) * np.exp(-0.5 * (pdf_x - avg)**2 / var)
plt.hist(maxima, 50, density=True)
plt.plot(pdf_x, pdf_y, 'k--')
plt.title('Mean = {}'.format(str(avg)))
ims = np.array(ims)
index = 0
x = np.arange(-100 * 8.33, 100 * 8.33, 8.33)
sv.graph_pane(globals(), 'index', 'ims', 'x')
# </editor-fold>
# -------------------------------------------------
# <editor-fold desc=CHECK IF DIFFERENT SETS OF NEURONS ARE CORRELATED WITH SPEED FOR SUCCESSFUL TRIALS VS OTHER PERIODS
time_points_of_trial_pokes = np.load(
join(poke_folder, 'time_points_of_trial_pokes.npy'))
time_points_of_non_trial_pokes = np.load(
join(poke_folder, 'time_points_of_non_trial_pokes.npy'))
time_points_of_touch_ball = np.load(
join(poke_folder, 'time_points_of_touch_ball.npy'))
event_dataframes = ns_funcs.load_events_dataframes(events_folder,
sync_funcs.event_types)
num_of_events, int(2 * window_timepoints / const.LFP_DOWNSAMPLE_FACTOR)))
for i in np.arange(num_of_events):
start_imfs = int((events[i] - window_timepoints) / const.LFP_DOWNSAMPLE_FACTOR)
end_imfs = int((events[i] + window_timepoints) / const.LFP_DOWNSAMPLE_FACTOR)
imfs_around_tp[:, :, i, :] = imfs[:, :, start_imfs:end_imfs]
avg_imfs_around_tp = np.mean(imfs_around_tp, axis=2)
avg_imfs_around_tp = np.swapaxes(avg_imfs_around_tp, 0, 1)
'''
def space(data):
return cdf.space_data_factor(data, 2)
imf = 0
sv.graph_pane(globals(), 'imf', 'avg_imfs_around_tp', transform_name='space')
_ = plt.plot(space(avg_lfps_around_event).T)
random_times = np.random.choice(
np.arange(2 * window_timepoints, lfps.shape[1] - 2 * window_timepoints, 1),
num_of_events)
random_triggered_lfps = []
for spike in random_times:
random_triggered_lfps.append(lfps[:, spike - window_timepoints:spike +
window_timepoints])
random_triggered_lfps = np.array(random_triggered_lfps)
random_triggered_lfps_mean = random_triggered_lfps.mean(axis=0)
random_triggered_lfps_std = random_triggered_lfps.std(axis=0)
# _ = plt.plot(space(random_triggered_lfps_std).T)
large_channels_full = np.arange(int(largest_channel - 30),
int(largest_channel + 30))
#plt.plot(mua_template_data[large_channels_full, :].T)
spike_data = np.swapaxes(
np.reshape(spike_data_one[large_channels_full, :],
(len(large_channels_full), spike_time_windows.shape[0],
spike_time_windows.shape[1])), 0, 1)
spike_data = np.array(spike_data)
spike_data_mean = np.mean(spike_data, axis=0)
plt.plot(spike_data_mean.transpose())
s = 0
seq_v.graph_pane(globals(), 's', 'spike_data')
c = 0
seq_v.graph_pane(globals(), 'c', 'spike_data_mean')
# TSNE The 10 PCs of all the channels that are within the group of largest channels according to Kilosort
# -------------------------------------------------------------
n_components = 10
principal_components = np.empty(
(spike_data.shape[0], spike_data.shape[1] * n_components))
pca = PCA(n_components=n_components)
i = 0
for index in range(len(spike_data)):
pca.fit(spike_data[index, :, :].transpose())
components = pca.components_.flatten()
def update_trajectory(f):
global traj_x
global traj_y
traj_x = body_positions[:f, 0]
traj_y = body_positions[:f, 1]
return body_positions[:f, :]
traj = None
tr.connect_repl_var(globals(), 'frame', 'traj', 'update_trajectory')
osv.graph(globals(), 'traj_y', 'traj_x')
# -------------------------------------------------
'''
# -------------------------------------------------
# FITTING THE MARKERS TO GET BETTER ESTIMATES OF THE LOW LIKELIHOOD ONES
# Fitting 2d surface using multiple markers
# DID NOT WORK
body_markers_positions = markers.loc[:, markers.columns.get_level_values(1).isin(body_parts)]
body_markers_positions = body_markers.loc[:, body_markers.columns.get_level_values(2).isin(['x', 'y'])]
t = np.reshape(body_markers_positions.loc[:3605*120-1, :].values, (3605, 120, 6))
sec = 0
im_lev = [0, 50]
cm = 'jet'
sv.graph_pane(globals(), 'sec', 't')
data1[i] += i
data2 = np.random.random(500)
# Have a look at them
position1 = 0
range1 = 1000
sequence_viewer.graph_range(globals(), 'position1', 'range1', 'data1')
position2 = 0
range2 = 10
sequence_viewer.graph_range(globals(), 'position2', 'range2', 'data2')
# Also you can view data in panes
pane = 0
sequence_viewer.graph_pane(globals(), 'pane', 'data1')
# The pane viewer shows te last one or two dimensions of a 2d or 3d data set and itterates over the first one.
# Connect two guis
def pos1_to_pos2(pos1):
if pos1 >= 0 and pos1 <= 4000:
return int(pos1 / 10)
elif pos1 < 0:
return 0
elif pos1 > 4000:
return 400
transform.connect_repl_var(globals(), 'position1', 'pos1_to_pos2', 'position2')
# Press the Transform to deactivate the function from running and so stop the connection