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 get_time_to_saccade(dataset, keys, threshold_odor=25):
time_to_saccade = []
for key in keys:
trajec = dataset.trajecs[key]
frames_in_odor = np.where(trajec.odor > threshold_odor)[0].tolist()
if len(frames_in_odor) <= 0:
continue
odor_blocks = hf.find_continuous_blocks(frames_in_odor, 5)
for block in odor_blocks:
if len(block) < 1:
continue
for sac in trajec.saccades:
if sac[0] > block[-1]:
t_to_sac = (sac[0] - block[-1])/trajec.fps
time_to_saccade.append(t_to_sac)
break
return time_to_saccade
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_saccade_positions(pp, threshold_odor, path, config, dataset, odor_stimulus, keys=None):
ax_xy, ax_xz, ax_yz = xyz_axis_grid.get_axes()
if odor_stimulus is 'on':
n = 0
for key in keys:
if n > 1000:
break
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:
if len(block) < 5:
continue
first_sac = None
for sac in trajec.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:
first_sac = sac
break
if first_sac is not None:
sac = first_sac
n += 1
f = np.argmax(np.abs(trajec.heading_smooth_diff[sac])) + sac[0]
ax_xy.plot(trajec.positions[f,0], trajec.positions[f,1], '.', color='black')
ax_xz.plot(trajec.positions[f,0], trajec.positions[f,2], '.', color='black')
ax_yz.plot(trajec.positions[f,1], trajec.positions[f,2], '.', color='black')
if odor_stimulus is 'none':
n = 0
for key in keys:
if n > 1000:
break
trajec = dataset.trajecs[key]
for sac in trajec.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
n += 1
f = np.argmax(np.abs(trajec.heading_smooth_diff[sac])) + sac[0]
ax_xy.plot(trajec.positions[f,0], trajec.positions[f,1], '.', color='black')
ax_xz.plot(trajec.positions[f,0], trajec.positions[f,2], '.', color='black')
ax_yz.plot(trajec.positions[f,1], trajec.positions[f,2], '.', color='black')
xyz_axis_grid.set_spines_and_labels(ax_xy, ax_xz, ax_yz)
pp.savefig()
plt.close('all')
def plot_odor_heading_book(pp, threshold_odor, path, config, dataset, odor_stimulus, keys=None):
fig = plt.figure(figsize=(8,5))
fig.subplots_adjust(wspace=0.2, hspace=0.3)
ax_odor = fig.add_subplot(511)
ax_wall = fig.add_subplot(512)
ax_z = fig.add_subplot(513)
ax_heading = fig.add_subplot(514)
ax_speed = fig.add_subplot(515)
axes = [ax_odor, ax_wall, ax_z, ax_heading, ax_speed]
if odor_stimulus is 'pulsing':
return
if 1: #odor_stimulus is 'on':
n = 0
for key in keys:
if n > 1000:
break
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:
if len(block) < 5:
continue
first_sac = None
for sac in trajec.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[-1] and trajec.odor[sac[0]] < threshold_odor:
if first_sac is None:
first_sac = sac
break
if first_sac is not None:
sac = first_sac
n += 1
heading_prior_to_saccade = trajec.heading_smooth[sac[0]]
#if np.abs(heading_prior_to_saccade) > 45*np.pi/180. and np.abs(heading_prior_to_saccade) < 135*np.pi/180.:
if np.abs(heading_prior_to_saccade) < 15*np.pi/180.:# and np.abs(heading_prior_to_saccade) < 135*np.pi/180.:
if 0:
frame_of_saccade_middle = np.argmax(np.abs(trajec.heading_smooth_diff[sac])) + sac[0]
time_of_sac = trajec.time_fly[frame_of_saccade_middle]
if 1:
frame_of_max_odor = np.argmax(trajec.odor[block])+block[0]
time_of_sac = trajec.time_fly[frame_of_max_odor]
frame0 = np.max([0,sac[0]-60])
frame1 = np.min([trajec.length-1,sac[-1]+100])
if frame0 > 0:
frames = np.arange(frame0, frame1)
# speed
# in saccade:
ax_speed.plot(trajec.time_fly[sac]-time_of_sac, trajec.speed[sac], 'crimson', linewidth=0.5, alpha=0.25)
# before saccade
frames_before_sac = np.arange(frames[0], sac[1])
ax_speed.plot(trajec.time_fly[frames_before_sac]-time_of_sac, trajec.speed[frames_before_sac], 'black', linewidth=0.5, alpha=0.25)
# after saccade
frames_after_sac = np.arange(sac[-2],frames[-1])
ax_speed.plot(trajec.time_fly[frames_after_sac]-time_of_sac, trajec.speed[frames_after_sac], 'black', linewidth=0.5, alpha=0.25)
# wall
# in saccade:
ax_wall.plot(trajec.time_fly[sac]-time_of_sac, np.abs(trajec.positions[sac,1]), 'crimson', linewidth=0.5, alpha=0.25)
# before saccade
ax_wall.plot(trajec.time_fly[frames_before_sac]-time_of_sac, np.abs(trajec.positions[frames_before_sac,1]), 'black', linewidth=0.5, alpha=0.25)
# after saccade
ax_wall.plot(trajec.time_fly[frames_after_sac]-time_of_sac, np.abs(trajec.positions[frames_after_sac,1]), 'black', linewidth=0.5, alpha=0.25)
# z
# in saccade:
ax_z.plot(trajec.time_fly[sac]-time_of_sac, (trajec.positions[sac,2]), 'crimson', linewidth=0.5, alpha=0.25)
# before saccade
ax_z.plot(trajec.time_fly[frames_before_sac]-time_of_sac, (trajec.positions[frames_before_sac,2]), 'black', linewidth=0.5, alpha=0.25)
# after saccade
ax_z.plot(trajec.time_fly[frames_after_sac]-time_of_sac, (trajec.positions[frames_after_sac,2]), 'black', linewidth=0.5, alpha=0.25)
# heading
heading = copy.copy(trajec.heading_smooth)
for i, h in enumerate(heading):
if h < 0:
heading[i] += np.pi
else:
heading[i] -= np.pi
#heading = floris_math.remove_angular_rollover(heading, np.pi)
# in saccade:
ax_heading.plot(trajec.time_fly[sac]-time_of_sac, np.abs(heading[sac]), 'crimson', linewidth=0.5, alpha=0.25)
# before saccade
ax_heading.plot(trajec.time_fly[frames_before_sac]-time_of_sac, np.abs(heading[frames_before_sac]), 'black', linewidth=0.5, alpha=0.25)
# after saccade
ax_heading.plot(trajec.time_fly[frames_after_sac]-time_of_sac, np.abs(heading[frames_after_sac]), 'black', linewidth=0.5, alpha=0.25)
# odor
# in saccade:
ax_odor.plot(trajec.time_fly[sac]-time_of_sac, trajec.odor[sac], 'crimson', linewidth=0.5, alpha=0.25)
# before saccade
ax_odor.plot(trajec.time_fly[frames_before_sac]-time_of_sac, trajec.odor[frames_before_sac], 'black', linewidth=0.5, alpha=0.25)
# after saccade
ax_odor.plot(trajec.time_fly[frames_after_sac]-time_of_sac, trajec.odor[frames_after_sac], 'black', linewidth=0.5, alpha=0.25)
######################################3
for ax in axes:
ax.set_xlim(-1,2)
ax_speed.set_ylim(0,.8)
yticks = [0,.4,.8]
fpl.adjust_spines(ax_speed, ['left', 'bottom'], yticks=yticks)
ax_speed.set_xlabel('time relative to saccade, sec')
ax_speed.set_ylabel('speed, m/s')
yticks = [0,125,250]
fpl.adjust_spines(ax_odor, ['left'], yticks=yticks)
ax_odor.set_ylabel('est. odor', horizontalalignment='center')
yticks = [-.15, 0, .15]
ax_wall.set_ylim(-.15, 0, .15)
fpl.adjust_spines(ax_wall, ['left'], yticks=yticks)
ax_wall.set_ylabel('y pos, m', horizontalalignment='center')
yticks = [-.15, 0, .15]
ax_z.set_ylim(-.15,0.15)
fpl.adjust_spines(ax_z, ['left'], yticks=yticks)
ax_z.set_ylabel('altitude, m')
ax_heading.set_ylim(0, np.pi+np.pi/6.)
yticks = [0, np.pi/2., np.pi]
fpl.adjust_spines(ax_heading, ['left'], yticks=yticks)
ax_heading.set_yticklabels(['upwind', 'crosswind', 'downwind'])
ax_heading.set_ylabel('heading')
title_str = 'Odor Stimulus: ' + odor_stimulus
fig.suptitle(title_str)
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')