def plot_odor_heading_book(pp, threshold_odor, path, config, dataset, keys=None):
fig = plt.figure(figsize=(4,4))
ax = fig.add_subplot(111)
saccades_odor = {'saccade_angles': [], 'heading_prior': []}
saccades_control = {'saccade_angles': [], 'heading_prior': []}
for key in keys:
trajec = dataset.trajecs[key]
frames_in_odor = np.where(trajec.odor > threshold_odor)[0]
odor_blocks = hf.find_continuous_blocks(frames_in_odor, 5, return_longest_only=False)
for block in odor_blocks:
#middle_of_block = int(np.mean(block))
if len(block) < 5:
continue
# find next saccade
first_sac = None
#second_sac = None
#third_sac = None
for sac in trajec.saccades:
if trajec.positions[sac[0],0] < -0.15 or trajec.positions[sac[0],0] > 0.9:
continue
if np.abs(trajec.positions[sac[0],1]) > 0.08:
continue
if np.abs(trajec.positions[sac[0],2]) > 0.08:
continue
if sac[0] > block[0]:
if first_sac is None:
first_sac = sac
break
#elif second_sac is None:
# if trajec.odor[sac[0]] < threshold_odor:
# second_sac = sac
#elif third_sac is None:
# if trajec.odor[sac[0]] < threshold_odor:
# third_sac = sac
# break
if first_sac is not None:
next_sac = first_sac
angle_of_saccade = tac.get_angle_of_saccade(trajec, next_sac)
heading_prior_to_saccade = trajec.heading_smooth[next_sac[0]]
# flip heading
if heading_prior_to_saccade < 0:
heading_prior_to_saccade += np.pi
else:
heading_prior_to_saccade -= np.pi
saccade_angles_after_odor.append(angle_of_saccade)
heading_at_saccade_initiation.append(heading_prior_to_saccade)
heading_after_saccade.append(heading_prior_to_saccade + angle_of_saccade)
speed_at_saccade.append(trajec.speed[next_sac[0]])
saccade_angles_after_odor = np.array(saccade_angles_after_odor)
heading_at_saccade_initiation = np.array(heading_at_saccade_initiation)
heading_after_saccade = np.array(heading_after_saccade)
speed_at_saccade = np.array(speed_at_saccade)
ax.plot(heading_at_saccade_initiation*180./np.pi, saccade_angles_after_odor*180./np.pi, '.', markersize=4)
#fpl.scatter(ax, heading_at_saccade_initiation*180./np.pi, saccade_angles_after_odor*180./np.pi, color=speed_at_saccade, radius=1)
#ax.plot(heading_at_saccade_initiation*180./np.pi, heading_after_saccade*180./np.pi, '.')
xticks = [-180, -90, 0, 90, 180]
yticks = [-180, -90, 0, 90, 180]
fpl.adjust_spines(ax, ['left', 'bottom'], xticks=xticks, yticks=yticks)
ax.set_xlabel('Heading before saccade')
ax.set_ylabel('Angle of saccade')
title_text = 'Odor: ' + trajec.odor_stimulus.title()
ax.set_title(title_text)
ax.text(0,-180, 'Upwind', horizontalalignment='center', verticalalignment='top')
ax.text(90,-180, 'Starboard', horizontalalignment='center', verticalalignment='top')
ax.text(-90,-180, 'Port', horizontalalignment='center', verticalalignment='top')
ax.text(-180,90, 'Starboard', horizontalalignment='left', verticalalignment='center', rotation='vertical')
ax.text(-180,-90, 'Port', horizontalalignment='left', verticalalignment='center', rotation='vertical')
pp.savefig()
plt.close('all')
# angle of saccade histogram
if 0:
fig = plt.figure(figsize=(4,4))
ax = fig.add_subplot(111)
fpl.histogram_stack(ax, [np.array(time_to_saccade_cast)], bins=40, bin_width_ratio=0.9, colors=['red'], edgecolor='none', normed=True)
ax.set_xlabel('Angle of Saccade')
ax.set_ylabel('Occurences, normalized')
#xticks = [-180, -90, 0, 90, 180]
fpl.adjust_spines(ax, ['left', 'bottom'])
ax.set_title(title_text)
pp.savefig()
plt.close('all')
def plot_odor_heading_book(pp, threshold_odor, path, config, dataset, keys=None):
fig = plt.figure(figsize=(4,4))
ax = fig.add_subplot(111)
saccade_angles_after_odor = []
heading_at_saccade_initiation = []
heading_after_saccade = []
for key in keys:
trajec = dataset.trajecs[key]
frames_in_odor = np.where(trajec.odor > threshold_odor)[0]
odor_blocks = hf.find_continuous_blocks(frames_in_odor, 5, return_longest_only=False)
for block in odor_blocks:
middle_of_block = int(np.mean(block))
# find next saccade
first_sac = None
second_sac = None
for sac in trajec.saccades:
if sac[0] > middle_of_block:
if first_sac is None:
first_sac = sac
elif second_sac is None:
if trajec.odor[sac[0]] < threshold_odor:
second_sac = sac
break
if first_sac is not None:
next_sac = first_sac
angle_of_saccade = tac.get_angle_of_saccade(trajec, next_sac)
heading_prior_to_saccade = trajec.heading_smooth[next_sac[0]]
# flip heading
if heading_prior_to_saccade < 0:
heading_prior_to_saccade += np.pi
else:
heading_prior_to_saccade -= np.pi
# flip saccade angle
if angle_of_saccade < 0:
angle_of_saccade += np.pi
else:
angle_of_saccade -= np.pi
saccade_angles_after_odor.append(angle_of_saccade)
heading_at_saccade_initiation.append(heading_prior_to_saccade)
heading_after_saccade.append(heading_prior_to_saccade + angle_of_saccade)
saccade_angles_after_odor = np.array(saccade_angles_after_odor)
heading_at_saccade_initiation = np.array(heading_at_saccade_initiation)
heading_after_saccade = np.array(heading_after_saccade)
ax.plot(heading_at_saccade_initiation*180./np.pi, saccade_angles_after_odor*180./np.pi, '.')
#ax.plot(heading_at_saccade_initiation*180./np.pi, heading_after_saccade*180./np.pi, '.')
xticks = [-180, -90, 0, 90, 180]
yticks = [-180, -90, 0, 90, 180]
fpl.adjust_spines(ax, ['left', 'bottom'], xticks=xticks, yticks=yticks)
ax.set_xlabel('Heading before saccade')
ax.set_ylabel('Angle of saccade')
title_text = 'Odor: ' + trajec.odor_stimulus.title()
ax.set_title(title_text)
ax.text(0,-180, 'Upwind', horizontalalignment='center', verticalalignment='top')
ax.text(90,-180, 'Starboard', horizontalalignment='center', verticalalignment='top')
ax.text(-90,-180, 'Port', horizontalalignment='center', verticalalignment='top')
ax.text(-180,90, 'Starboard', horizontalalignment='left', verticalalignment='center', rotation='vertical')
ax.text(-180,-90, 'Port', horizontalalignment='left', verticalalignment='center', rotation='vertical')
pp.savefig()
plt.close('all')
# angle of saccade histogram
fig = plt.figure()
ax = fig.add_subplot(111)
fpl.histogram_stack(ax, [saccade_angles_after_odor*180./np.pi], bins=20, bin_width_ratio=0.9, colors=['red'], edgecolor='none', normed=True)
ax.set_xlabel('Angle of Saccade')
ax.set_ylabel('Occurences, normalized')
xticks = [-180, -90, 0, 90, 180]
fpl.adjust_spines(ax, ['left', 'bottom'], xticks=xticks)
ax.set_title(title_text)
pp.savefig()
plt.close('all')
def plot_landing_histogram(config, dataset, save_figure_path=''):
keys = get_keys(dataset)
print 'number of keys: ', len(keys)
if len(keys) < 1:
print 'No data'
return
threshold_distance_min = 0.05
keys_tmp = dataset.trajecs.keys()
keys = []
keys_not_near_post = []
for key in keys_tmp:
trajec = dataset.trajecs[key]
if trajec.distance_to_post_min < threshold_distance_min:
keys.append(key)
else:
keys_not_near_post.append(key)
timestamps_not_landings = []
timestamps_landings = []
timestamps_not_near_post = []
for i, key in enumerate(keys):
trajec = dataset.trajecs[key]
if 'landing' in trajec.post_behavior:
timestamps_landings.append( trajec.timestamp_local_float )
else:
timestamps_not_landings.append( trajec.timestamp_local_float )
for key in keys_not_near_post:
trajec = dataset.trajecs[key]
timestamps_not_near_post.append(trajec.timestamp_local_float)
# shift so time continuous
for i, t in enumerate(timestamps_not_landings):
if t > 12: timestamps_not_landings[i] = t-24
for i, t in enumerate(timestamps_landings):
if t > 12: timestamps_landings[i] = t-24
for i, t in enumerate(timestamps_not_near_post):
if t > 12: timestamps_not_near_post[i] = t-24
timestamps_not_landings = np.array(timestamps_not_landings)
timestamps_landings = np.array(timestamps_landings)
timestamps_not_near_post = np.array(timestamps_not_near_post)
fig = plt.figure(figsize=(4,4))
ax = fig.add_subplot(111)
nbins = 36 # note: if show_smoothed=True with default butter filter, nbins needs to be > ~15
bins1 = np.linspace(-12,-0.21,int(nbins/2.),endpoint=True)
bins2 = np.linspace(-.21,12,int(nbins/2.),endpoint=True)
#bins = [16.05-24, 17.05-24, 18.05-24, 19.05-24, 20.05-24, 21.05-24, 22.05-24, 23.05-24, 0.05, 1.05, 2.05, 3.05, 4.05, 5.05, 6.05, 7.05, 8.05, 9.05, 10.05]
bins = np.arange(16.05-24,10.05, 0.5)
data = [timestamps_landings, timestamps_not_landings, timestamps_not_near_post]
if save_figure_path == '':
save_figure_path = os.path.join(config.path, config.figure_path, 'activity/')
colors = ['black', 'green']
fpl.histogram_stack(ax, data, bins=bins, bin_width_ratio=0.8, colors=['green', 'black', 'gray'], edgecolor='none', normed=True)
#fpl.histogram(ax, data, bins=bins, bin_width_ratio=0.8, colors=colors, edgecolor='none', bar_alpha=1, curve_fill_alpha=0.4, curve_line_alpha=0, curve_butter_filter=[3,0.3], return_vals=False, show_smoothed=False, normed=True, normed_occurences=False, bootstrap_std=False, exponential_histogram=False)
if 'on' in config.odor_stimulus.keys():
odor_on = config.odor_stimulus['on']
if type(odor_on[0]) is not list:
ax.fill_between(np.array(odor_on), -10, 10, color='red', alpha=0.25, zorder=-10, edgecolor='none')
else:
for vals in odor_on:
odor_start = vals[0]
odor_end = vals[-1]
if odor_start > 12:
odor_start -= 24
if odor_end > 12:
odor_end -= 24
print 'odor on for time ranges: '
print odor_start, odor_end
ax.fill_between(np.array([odor_start, odor_end]), -10, 10, color='red', alpha=0.25, zorder=-10, edgecolor='none')
#xticks = [0,6,12,18,24]
xticks = [-12,-6,0,6,12]
fpl.adjust_spines(ax, ['left', 'bottom'], xticks=xticks)
ax.set_xlabel('Time of day, hours')
ax.set_ylabel('Occurences, normalized')
ax.set_title('Landings: green -- Nonlandings: black')
fig.set_size_inches(4,4)
if save_figure_path == '':
save_figure_path = os.path.join(config.path, config.figure_path, 'activity/')
figname = save_figure_path + 'landing_histogram' + '.pdf'
fig.savefig(figname, format='pdf')
