def plot_speed(prm, speed_light, speed_nolight, param):
print('plotting speed...')
#plot continuous data
fig = plt.figure(figsize=(14, 8))
ax = fig.add_subplot(111)
ax.plot(np.arange(0, 20, 1), speed_light, label='light')
ax.plot(np.arange(0, 20, 1), speed_nolight, label='nolight')
vr_plot_utility.makelegend(fig, ax, 0.4)
ax.tick_params(axis='x',
pad=10,
top='off',
right='off',
direction='out',
width=2,
length=8,
labelsize=18)
ax.tick_params(axis='y',
pad=10,
top='off',
right='off',
direction='out',
width=2,
length=8,
labelsize=18)
ax.locator_params(axis='x', nbins=7) # set number of ticks on x axis
ax.locator_params(axis='y', nbins=7) # set number of ticks on y axis
ax.set_xlabel('Location (cm)', fontsize=18, labelpad=20)
ax.set_ylabel('Speed (cm/s)', fontsize=18, labelpad=20)
vr_plot_utility.adjust_spines(ax, ['left', 'bottom'])
vr_plot_utility.adjust_spine_thickness(ax)
plt.subplots_adjust(hspace=.35,
wspace=.35,
bottom=0.15,
left=0.15,
right=0.92,
top=0.92)
if param == 1:
fig.savefig(prm.get_filepath() + 'Behaviour/Analysis/Speed/' +
'Speed_light.png',
dpi=200)
plt.close()
if param == 2:
fig.savefig(prm.get_filepath() + 'Behaviour/Analysis/Speed/' +
'Speed_nolight.png',
dpi=200)
plt.close()
def plot_test_power_spectrum(prm, data):
print('Plotting and saving power spectra')
fig, ax = plt.subplots()
ax.spines['right'].set_visible(False)
ax.spines['top'].set_visible(False)
ax.xaxis.set_ticks_position('bottom')
ax.yaxis.set_ticks_position('left')
ax.tick_params(axis='y',
pad=10,
top='off',
right='off',
direction='out',
width=2,
length=8,
labelsize=18)
ax.tick_params(axis='x',
pad=10,
top='off',
right='off',
direction='out',
width=2,
length=8,
labelsize=18)
vr_plot_utility.adjust_spine_thickness(ax)
power_spectrum(prm, data, 30000, 'k')
fig.savefig(prm.get_filepath() +
'Electrophysiology/track_location_analysis/fft/CH' +
'_test.png',
dpi=200)
power_spectrum_log(prm,
data,
30000,
'k',
prm.get_filename(),
title="$Power spectrum$",
x_lim=10,
line_width=15,
legend='stationary')
fig.savefig(prm.get_filepath() +
'Electrophysiology/track_location_analysis/fft/CH' +
'_test2.png',
dpi=200)
plt.close()
def plot_continuous_filtered_data(prm, channel_data_all, channel):
start_time = 0 # in ms
end_time = (np.array((25,50,100,500,1000,5000)))+ start_time # in ms
for t, times in enumerate(end_time):
end_time = times
#plot continuous data
fig = plt.figure(figsize = (14,8))
ax = fig.add_subplot(111)
ax.plot(np.arange(start_time,end_time,(1/30)),channel_data_all[0,(start_time*30):(end_time*30)])
ax.tick_params(axis='x', pad = 10, top='off', right = 'off', direction = 'out',width = 2, length = 8,labelsize =18)
ax.tick_params(axis='y', pad = 10, top='off', right = 'off', direction = 'out',width = 2, length = 8, labelsize =18)
ax.locator_params(axis = 'x', nbins=7) # set number of ticks on x axis
ax.locator_params(axis = 'y', nbins=7) # set number of ticks on y axis
ax.set_xlabel('Time (ms)', fontsize=18, labelpad = 20)
ax.set_ylabel('Amplitude (uV)', fontsize=18, labelpad = 20)
vr_plot_utility.adjust_spines(ax, ['left','bottom'])
vr_plot_utility.adjust_spine_thickness(ax)
plt.subplots_adjust(hspace = .35, wspace = .35, bottom = 0.15, left = 0.15, right = 0.92, top = 0.92)
fig.savefig(prm.get_filepath() + 'Electrophysiology/continuous/raw/CH' + str(channel) + '_' + str(end_time) + 'ms_filtered.png', dpi=200)
plt.close()
def plot_continuous_opto_data(prm, data, channel, param):
print('plotting continuous data...')
data = data[data[:, 3] > 3, :] # remove all data in black box
trials = np.unique(data[:, 1])
for tcount, trial in enumerate(trials[:20]):
array = data[data[:, 1] == trial, :]
trial_type = array[1, 2]
print(trial_type)
start_time = 900 # in ms
try:
end_time = (np.array((100, 500, 1000, 5000))) + start_time # in ms
for t, times in enumerate(end_time):
end_time = times
fig = plt.figure(figsize=(7.5, 12))
ax = fig.add_subplot(511)
ax.tick_params(axis='y',
pad=10,
top='off',
right='off',
direction='out',
width=2,
length=8,
labelsize=18)
ax.locator_params(axis='y',
nbins=3) # set number of ticks on y axis
ax.set_ylabel('Amplitude (uV)', fontsize=18, labelpad=20)
array_min = np.min(array[(start_time * 30):(end_time * 30), 5])
opto_ch = (array[(start_time * 30):(end_time * 30),
0]) + (array_min - 5)
ax.set_ylim(array_min - 10, array_min + 10)
ax.plot(np.arange(0, end_time - start_time, (1 / 30)), opto_ch,
'k')
vr_plot_utility.adjust_spines(ax, ['left'])
vr_plot_utility.adjust_spine_thickness(ax)
ax = fig.add_subplot(512)
ax.plot(np.arange(0, end_time - start_time, (1 / 30)),
array[(start_time * 30):(end_time * 30), 5])
ax.tick_params(axis='y',
pad=10,
top='off',
right='off',
direction='out',
width=2,
length=8,
labelsize=18)
ax.locator_params(axis='y',
nbins=3) # set number of ticks on y axis
ax.set_ylabel('Amplitude (uV)', fontsize=18, labelpad=20)
array_min = np.min(array[(start_time * 30):(end_time * 30), 5])
#opto_ch = (array[(start_time*30):(end_time*30),0])+(array_min-5)
ax.set_ylim(array_min - 10, )
vr_plot_utility.adjust_spines(ax, ['left'])
vr_plot_utility.adjust_spine_thickness(ax)
ax = fig.add_subplot(513)
ax.plot(np.arange(0, end_time - start_time, (1 / 30)),
array[(start_time * 30):(end_time * 30), 7])
ax.tick_params(axis='y',
pad=10,
top='off',
right='off',
direction='out',
width=2,
length=8,
labelsize=18)
ax.locator_params(axis='y',
nbins=3) # set number of ticks on y axis
ax.set_ylabel('Amplitude (uV)', fontsize=18, labelpad=20)
array_min = np.min(array[(start_time * 30):(end_time * 30), 6])
ax.set_ylim(-200, 200)
vr_plot_utility.adjust_spines(ax, ['left'])
vr_plot_utility.adjust_spine_thickness(ax)
ax = fig.add_subplot(514)
ax.plot(np.arange(0, end_time - start_time, (1 / 30)),
array[(start_time * 30):(end_time * 30), 9])
ax.plot(np.arange(0, end_time - start_time, (1 / 30)),
array[(start_time * 30):(end_time * 30), 8])
ax.tick_params(axis='y',
pad=10,
top='off',
right='off',
direction='out',
width=2,
length=8,
labelsize=18)
ax.locator_params(axis='y',
nbins=3) # set number of ticks on y axis
ax.set_ylabel('Amplitude (uV)', fontsize=18, labelpad=20)
array_min = np.min(array[(start_time * 30):(end_time * 30), 8])
opto_ch = (array[(start_time * 30):(end_time * 30),
0]) + (array_min - 5)
ax.set_ylim(-270, 270)
vr_plot_utility.adjust_spines(ax, ['left'])
vr_plot_utility.adjust_spine_thickness(ax)
ax = fig.add_subplot(515)
ax.plot(np.arange(0, end_time - start_time, (1 / 30)),
array[(start_time * 30):(end_time * 30), 3])
ax.tick_params(axis='x',
pad=10,
top='off',
right='off',
direction='out',
width=2,
length=8,
labelsize=18)
ax.tick_params(axis='y',
pad=10,
top='off',
right='off',
direction='out',
width=2,
length=8,
labelsize=18)
ax.locator_params(axis='x',
nbins=7) # set number of ticks on x axis
ax.locator_params(axis='y',
nbins=3) # set number of ticks on y axis
ax.set_xlabel('Time (ms)', fontsize=18, labelpad=20)
ax.set_ylabel('Location (cm)', fontsize=18, labelpad=20)
array_min = np.min(array[(start_time * 30):(end_time * 30), 4])
array_max = np.min(array[(start_time * 30):(end_time * 30), 4])
#ax.set_ylim(0,20)
vr_plot_utility.adjust_spines(ax, ['left', 'bottom'])
vr_plot_utility.adjust_spine_thickness(ax)
plt.subplots_adjust(hspace=.35,
wspace=.35,
bottom=0.15,
left=0.2,
right=0.92,
top=0.92)
if param == 1:
if trial_type == 0:
fig.savefig(
prm.get_filepath() +
'Electrophysiology/opto_stimulation/continuous/filtered/CH'
+ str(channel) + '_' + str(trial) + '_' +
str(end_time - start_time) + 'ms_light.png',
dpi=200)
plt.close()
if trial_type == 1:
fig.savefig(
prm.get_filepath() +
'Electrophysiology/opto_stimulation/continuous/filtered/CH'
+ str(channel) + '_' + str(trial) + '_' +
str(end_time - start_time) + 'ms_light.png',
dpi=200)
plt.close()
if trial_type == 2:
fig.savefig(
prm.get_filepath() +
'Electrophysiology/opto_stimulation/continuous/filtered/CH'
+ str(channel) + '_' + str(trial) + '_' +
str(end_time - start_time) + 'ms_light.png',
dpi=200)
plt.close()
if param == 2:
if trial_type == 0:
fig.savefig(
prm.get_filepath() +
'Electrophysiology/opto_stimulation/continuous/filtered/CH'
+ str(channel) + '_' + str(trial) + '_' +
str(end_time - start_time) + 'ms_nolight.png',
dpi=200)
plt.close()
if trial_type == 1:
fig.savefig(
prm.get_filepath() +
'Electrophysiology/opto_stimulation/continuous/filtered/CH'
+ str(channel) + '_' + str(trial) + '_' +
str(end_time - start_time) +
'ms_nonbeaconed_nolight.png',
dpi=200)
plt.close()
if trial_type == 2:
fig.savefig(
prm.get_filepath() +
'Electrophysiology/opto_stimulation/continuous/filtered/CH'
+ str(channel) + '_' + str(trial) + '_' +
str(end_time - start_time) +
'ms_probe_nolight.png',
dpi=200)
plt.close()
except ValueError:
continue
def plot_continuous_theta_opto_data(prm, theta, gamma, channel, param):
print('plotting continuous data...')
theta = theta[theta[:, 3] > 3, :] # remove all data in black box
trials = np.unique(theta[:, 1])
for tcount, trial in enumerate(trials[:10]):
theta = theta[theta[:, 1] == trial, :]
gamma = gamma[gamma[:, 1] == trial, :]
start_time = 0 # in ms
end_time = (np.array(
(25, 50, 100, 500, 1000, 5000))) + start_time # in ms
for t, times in enumerate(end_time):
end_time = times
#plot continuous data
fig = plt.figure(figsize=(14, 8))
ax = fig.add_subplot(111)
ax.plot(np.arange(start_time, end_time, (1 / 30)),
theta[(start_time * 30):(end_time * 30), 5])
ax.plot(np.arange(start_time, end_time, (1 / 30)),
gamma[(start_time * 30):(end_time * 30), 5], 'r')
array_min = np.min(theta[(start_time * 30):(end_time * 30), 5])
opto_ch = (theta[(start_time * 30):(end_time * 30),
0]) + (array_min - 5)
ax.set_ylim(array_min - 10, )
ax.plot(np.arange(start_time, end_time, (1 / 30)), opto_ch, 'k')
ax.tick_params(axis='x',
pad=10,
top='off',
right='off',
direction='out',
width=2,
length=8,
labelsize=18)
ax.tick_params(axis='y',
pad=10,
top='off',
right='off',
direction='out',
width=2,
length=8,
labelsize=18)
ax.locator_params(axis='x',
nbins=7) # set number of ticks on x axis
ax.locator_params(axis='y',
nbins=7) # set number of ticks on y axis
ax.set_xlabel('Time (ms)', fontsize=18, labelpad=20)
ax.set_ylabel('Amplitude (uV)', fontsize=18, labelpad=20)
vr_plot_utility.adjust_spines(ax, ['left', 'bottom'])
vr_plot_utility.adjust_spine_thickness(ax)
plt.subplots_adjust(hspace=.35,
wspace=.35,
bottom=0.15,
left=0.15,
right=0.92,
top=0.92)
if param == 1:
fig.savefig(prm.get_filepath() +
'Electrophysiology/opto_stimulation/theta/CH' +
str(channel) + '_' + str(trial) + '_' +
str(end_time - start_time) + 'ms_light.png',
dpi=200)
plt.close()
if param == 2:
fig.savefig(prm.get_filepath() +
'Electrophysiology/opto_stimulation/theta/CH' +
str(channel) + '_' + str(trial) + '_' +
str(end_time - start_time) + 'ms_nolight.png',
dpi=200)
plt.close()