def plot_trajectory(trajec):
threshold_odor = 10
fig = plt.figure()
ax = fig.add_subplot(111)
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[3]]:
#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 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]]
if heading_prior_to_saccade < 0:
heading_prior_to_saccade += np.pi
else:
heading_prior_to_saccade -= np.pi
frame0 = np.max([next_sac[0]-20, 0])
frame1 = np.min([next_sac[0]+20, trajec.length-1])
frames = np.arange(frame0, frame1)
ax.plot(trajec.positions[frames,0], trajec.positions[frames,1])
ax.plot(trajec.positions[frames[0],0], trajec.positions[frames[0],1], '.', color='green')
#pos_before_sac = trajec.positions[next_sac[0], :]
#heading_vector = pos_before_sac
print 'raw heading prior: ', heading_prior_to_saccade*180/np.pi
print 'raw heading after: ', trajec.heading_smooth[next_sac[-1]]*180/np.pi
print 'raw angle of sac: ', angle_of_saccade*180/np.pi
ax.set_aspect('equal')
return next_sac
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_odor_heading_book(pp, threshold_odor, path, config, dataset, odor_stimulus, keys=None, axis='xy'):
fig = plt.figure(figsize=(4,4))
ax = fig.add_subplot(111)
saccade_angles_after_odor = []
heading_at_saccade_initiation = []
odor_at_saccade = []
saccade_number = []
if 1:
for key in keys:
trajec = dataset.trajecs[key]
#if trajec.positions[0,0] < 0.2:
# continue
frames_in_odor = np.where(trajec.odor > threshold_odor)[0]
odor_blocks = hf.find_continuous_blocks(frames_in_odor, 5, return_longest_only=False)
b = 0
for block in odor_blocks:
if len(block) < 5:
continue
first_sac = None
if axis == 'xy':
saccades = trajec.saccades
elif axis == 'altitude':
saccades = trajec.saccades_z
for sac in saccades:
if trajec.positions[sac[0],0] < -0.1 or trajec.positions[sac[0],0] > 0.9:
continue
if np.abs(trajec.positions[sac[0],1]) > 0.05:
continue
if trajec.positions[sac[0],2] > 0.05 or trajec.positions[sac[0],2] < -0.01:
continue
if sac[0] > block[0]:
if first_sac is None:
if trajec.time_fly[sac[0]] - trajec.time_fly[block[-1]] > 0.5:
break
first_sac = sac
break
if first_sac is not None:
next_sac = first_sac
if axis == 'xy':
angle_of_saccade = tac.get_angle_of_saccade(trajec, next_sac)
heading_prior_to_saccade = trajec.heading_smooth[next_sac[0]]
elif axis == 'altitude':
angle_of_saccade = tac.get_angle_of_saccade_z(trajec, next_sac)
heading_prior_to_saccade = trajec.heading_altitude_smooth[next_sac[0]]
saccade_angles_after_odor.append(angle_of_saccade)
heading_at_saccade_initiation.append(heading_prior_to_saccade)
odor_at_saccade.append(trajec.odor[next_sac[0]])
b += 1
saccade_number.append(b)
saccade_angles_after_odor = np.array(saccade_angles_after_odor)
heading_at_saccade_initiation = np.array(heading_at_saccade_initiation)
odor_at_saccade = np.array(odor_at_saccade)
saccade_number = np.array(saccade_number)
print odor_stimulus, saccade_angles_after_odor.shape
#ax.plot(heading_at_saccade_initiation*180./np.pi, saccade_angles_after_odor*180./np.pi, '.', markersize=3)
fpl.scatter(ax, heading_at_saccade_initiation*180./np.pi, saccade_angles_after_odor*180./np.pi, color='black', radius=3, colornorm=[0,5])
xpts = np.linspace(-180,180, 100)
ax.plot(xpts, -1*xpts, color='red', zorder=-10)
#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: ' + odor_stimulus + ' Visual Stim: ' + trajec.visual_stimulus
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')
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')
