def plot_demo_flyby(dataset, key):
trajec = dataset.trajecs[key]
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_ylim(-.15,.15)
ax.set_xlim(-.25, .25)
ax.set_autoscale_on(False)
ax.set_aspect('equal')
frames = np.arange(0,trajec.frames_of_flyby[-1]).tolist()
ax.plot(trajec.positions[:,0], trajec.positions[:,1], color='gray')
ax.plot(trajec.positions[frames,0], trajec.positions[frames,1], color='black')
if len(trajec.all_saccades) > 0:
for s in trajec.all_saccades:
if s < trajec.frame_nearest_to_post:
sac_range = fa.get_saccade_range(trajec, s)
ax.plot(trajec.positions[sac_range,0], trajec.positions[sac_range,1], '-', color='green', alpha=1, linewidth=1)
sac = patches.Circle( (trajec.positions[sac_range[0],0], trajec.positions[sac_range[0],1]), radius=0.002, facecolor='green', edgecolor='none', alpha=1, zorder=100)
ax.add_artist(sac)
post = patches.Circle( (0, 0), radius=0.009565, facecolor='black', edgecolor='none', alpha=1)
ax.add_artist(post)
fig.savefig('demo_flyby_flydra.pdf', format='pdf')
def get_slipangles(movie, behavior='straight'):
fa.prep_movie_trajec(movie)
trajec = movie.trajec
# look at all frames not in saccade range or within 1cm of post
closest_dist = 0.01
first_frame = sa1.get_frame_from_timestamp_flydra(movie, movie.timestamps[0])
last_frame = sa1.get_frame_from_timestamp_flydra(movie, movie.timestamps[-1])
last_frame = np.min([last_frame, len(trajec.speed)-1])
saccade_frames = []
if len(trajec.saccades) > 0:
for s in trajec.saccades:
sac_range = fa.get_saccade_range(trajec, s)
saccade_frames.extend(sac_range)
straight_frames = []
saccade_frames = []
landing_frames = []
print first_frame, last_frame
for f in range(first_frame, last_frame):
print f
if f in saccade_frames:
print 'x'
saccade_frames.append(f)
if trajec.dist_to_stim_r_normed[f] < closest_dist and trajec.behavior == 'landing':
print 'y'
landing_frames.append(f)
else:
straight_frames.append(f)
if behavior == 'straight':
frames = straight_frames
elif behavior == 'saccade':
frames = saccade_frames
elif behavior == 'landing':
frames = landing_frames
slipangles = []
for f in frames:
sa1f = sa1.get_frame_from_timestamp(movie, trajec.epoch_time[f])
slipangles.append(movie.scaled.slipangle[sa1f])
for i, s in enumerate(slipangles):
while slipangles[i] > np.pi:
slipangles[i] -= np.pi
while slipangles[i] < -np.pi:
slipangles[i] += np.pi
return slipangles
def plot_demo_trajectory_speed_vs_angle(movie_dataset=None, movie_landing=None, movie_flyby=None, filename=None):
if movie_dataset is not None:
movie_landing = movie_dataset.movies['20101110_C001H001S0038']
movie_flyby = movie_dataset.movies['20101101_C001H001S0024']
fig = plt.figure()
angleax = fig.add_subplot(111)
## landing
trajec = movie_landing.trajec
ftp = np.arange(trajec.frames[0]-25, trajec.frames[-1]).tolist()
angleax.plot( np.log(trajec.angle_subtended_by_post[ftp]), trajec.speed[ftp], color='black')
angleax.plot( np.log(trajec.angle_at_deceleration), trajec.speed_at_deceleration, '.', markerfacecolor='blue', markeredgecolor='blue')
movieinfo = movie_landing
legextensionframe = movieinfo.legextensionrange[0] - movieinfo.firstframe_ofinterest
time_of_leg_ext = movieinfo.timestamps[legextensionframe]
flydra_frame_of_leg_ext = fa.get_flydra_frame_at_timestamp(trajec, time_of_leg_ext)+1
angleax.plot( np.log(trajec.angle_subtended_by_post[flydra_frame_of_leg_ext]), trajec.speed[flydra_frame_of_leg_ext], '.', markerfacecolor='red', markeredgecolor='red')
## flyby
trajec = movie_flyby.trajec
ftp = np.arange(trajec.frames[0]-25, trajec.frames[-1]).tolist()
angleax.plot( np.log(trajec.angle_subtended_by_post[ftp]), trajec.speed[ftp], '-', color='black')
sf = fa.get_saccade_range(trajec, trajec.saccades[-1])
angleax.plot( np.log(trajec.angle_subtended_by_post[sf[0]]), trajec.speed[sf[0]], '.', markerfacecolor='green', markeredgecolor='green')
angleax.plot( np.log(trajec.angle_subtended_by_post[sf]), trajec.speed[sf], '-', color='green')
angleax.plot( np.log(trajec.angle_at_deceleration), trajec.speed_at_deceleration, '.', markerfacecolor='blue', markeredgecolor='blue')
fa.fix_angle_log_spine(angleax, histograms=False)
if filename is not None:
fig.subplots_adjust(right=0.9, bottom=0.3)
fig.savefig(filename, format='pdf')
return angleax
def plot_demo_trajectory(movieinfo, nudge, filename=None):
trajec = movieinfo.trajec
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_autoscale_on(False)
ax.set_xlim(-0.02, 0.05)
ax.set_ylim(-0.02, 0.05)
ax.set_axis_off()
cl = colorline.Colorline( xlim=ax.get_xlim(), ylim=ax.get_ylim(), norm=(0,0.8), colormap = 'jet', hide_colorbar=True, ax0=ax)
# plot trajectory
frames = np.arange(50, trajec.frame_of_landing).tolist()
cl.colorline( trajec.positions[frames,0], trajec.positions[frames,1], trajec.speed[frames],linewidth=1, alpha=0.5)
# parameters
radius = trajec.radius_at_nearest
if trajec.behavior == 'landing':
# show pt of deceleration
f = trajec.frame_at_deceleration
x = trajec.positions[f,0]
y = trajec.positions[f,1]
pt_of_deceleration = patches.Circle( (x,y), radius=0.0005, facecolor='blue', edgecolor='none')
ax.add_artist(pt_of_deceleration)
# anotate deceleration point
string = 'deceleration initiation'
string_position = (x-0.005, y+.015)
arrow = {'facecolor':'blue', 'arrowstyle':"->", 'edgecolor':'blue', 'linewidth':1}
ax.annotate(string, (x-.0001,y+.0001),
xytext=string_position,
arrowprops=arrow,
horizontalalignment='right', verticalalignment='top', color='blue')
# show angle subtended
if trajec.behavior == 'landing':
f = trajec.frames[20]
x = np.mean(trajec.positions[f-1:f+1,0])
y = np.mean(trajec.positions[f-1:f+1,1])
else:
f = trajec.frames[17]
x = trajec.positions[f,0]
y = trajec.positions[f,1]
d = np.linalg.norm([x,y])
half_angle_to_post = np.arcsin( radius / d )
world_angle = np.arctan2(y,x)
a = half_angle_to_post - world_angle
visual_intercept_1 = [0+np.cos(np.pi/2.-a)*radius, 0+np.sin(np.pi/2.-a)*radius]
a = half_angle_to_post + world_angle
visual_intercept_2 = [0+np.cos(np.pi/2.-a)*radius, 0-np.sin(np.pi/2.-a)*radius]
xy = np.vstack( (visual_intercept_1, visual_intercept_2, [x,y]) )
triangle = patches.Polygon( xy, facecolor='purple', edgecolor='none', zorder=-10, alpha=0.2 )
ax.add_artist(triangle)
# dist to post
ox = np.cos(world_angle)*radius
oy = np.sin(world_angle)*radius
ax.plot([ox,x], [oy,y], color='brown', linewidth=1, alpha=0.5)
# angle arc
if trajec.behavior == 'landing':
arc = patches.Arc( (x,y), .03, .03, 180, np.abs((half_angle_to_post - world_angle))*180/np.pi, (half_angle_to_post + world_angle)*180/np.pi, edgecolor='purple', linewidth=0.5)
else:
arc = patches.Arc( (x,y), .05, .05, 180, (world_angle - half_angle_to_post)*180/np.pi, (half_angle_to_post + world_angle)*180/np.pi, edgecolor='purple', linewidth=1)
ax.add_artist(arc)
if trajec.behavior == 'landing':
ax.text(.02, .006, 'retinal size', color='purple', horizontalalignment='center', verticalalignment='center')
ax.text(.02, 0, 'distance\nto post', color='brown', horizontalalignment='center', verticalalignment='center')
else:
ax.text(.02, -0.01, 'retinal size', color='purple', horizontalalignment='center', verticalalignment='center')
ax.text(.02, -0.015, 'distance\nto post', color='brown', horizontalalignment='center', verticalalignment='center')
if trajec.behavior == 'landing':
# show pt of leg extension
legextensionframe = movieinfo.legextensionrange[0] - movieinfo.firstframe_ofinterest
time_of_leg_ext = movieinfo.timestamps[legextensionframe]
flydra_frame_of_leg_ext = fa.get_flydra_frame_at_timestamp(trajec, time_of_leg_ext)+1
x = trajec.positions[flydra_frame_of_leg_ext, 0]
y = trajec.positions[flydra_frame_of_leg_ext, 1]
pt_of_leg_ext = patches.Circle( (x,y), radius=0.0005, facecolor='red', edgecolor='none')
ax.add_artist(pt_of_leg_ext)
# anotate leg extension point
string = 'leg extension'
string_position = (x, y+.01)
arrow = {'facecolor':'red', 'arrowstyle':"->", 'edgecolor':'red', 'linewidth':1}
ax.annotate(string, (x-.0001,y+.0001),
xytext=string_position,
arrowprops=arrow,
horizontalalignment='center', verticalalignment='top', color='red')
if trajec.behavior == 'flyby':
'''
s = trajec.saccades[0]
x = trajec.positions[s, 0]
y = trajec.positions[s, 1]
pt_of_saccade = patches.Circle( (x,y), radius=0.0005, facecolor='green', edgecolor='none')
ax.add_artist(pt_of_saccade)
'''
# show saccade duration
saccade_frames = fa.get_saccade_range(trajec, trajec.saccades[-1])
x = trajec.positions[saccade_frames, 0]
y = trajec.positions[saccade_frames, 1]
ax.plot(x,y,'-', color='green')
s = saccade_frames[0]
x = trajec.positions[s, 0]
y = trajec.positions[s, 1]
pt_of_saccade = patches.Circle( (x,y), radius=0.0005, facecolor='green', edgecolor='none')
ax.add_artist(pt_of_saccade)
# anotate saccade point
string = 'saccade initiation'
string_position = (x+0.01, y+.01)
arrow = {'facecolor':'green', 'arrowstyle':"->", 'edgecolor':'green', 'linewidth':1}
ax.annotate(string, (x-.0001,y+.0001),
xytext=string_position,
arrowprops=arrow,
horizontalalignment='right', verticalalignment='top', color='green')
if trajec.frame_at_deceleration is not None:
x = trajec.positions[trajec.frame_at_deceleration, 0]
y = trajec.positions[trajec.frame_at_deceleration, 1]
pt_of_deceleration = patches.Circle( (x,y), radius=0.0005, facecolor='blue', edgecolor='none')
ax.add_artist(pt_of_deceleration)
# anotate deceleration point
string = 'deceleration initiation'
string_position = (x-0.005, y+.015)
arrow = {'facecolor':'blue', 'arrowstyle':"->", 'edgecolor':'blue', 'linewidth':1}
ax.annotate(string, (x-.0001,y+.0001),
xytext=string_position,
arrowprops=arrow,
horizontalalignment='right', verticalalignment='top', color='blue')
post = patches.Circle( (0,0), radius=radius, facecolor='black', edgecolor='none')
ax.add_artist(post)
# annotate post
ax.text( 0,0, 'post\n(top view)', color='gray', verticalalignment='center', horizontalalignment='center', fontsize=9)
if movieinfo is not None:
strobe = sa1.strobe_from_movieinfo(movieinfo, interval=200)
ax.imshow(strobe.T, plt.get_cmap('gray'), origin='lower', extent = [-1*movieinfo.post_pos[0]*movieinfo.scale+nudge[0], (1024-movieinfo.post_pos[0])*movieinfo.scale+nudge[0], -1*movieinfo.post_pos[1]*movieinfo.scale+nudge[1], (1024-movieinfo.post_pos[1]+nudge[1])*movieinfo.scale], zorder=-20)
# scale bar
ax.hlines(-.012, -.005+.04, .005+.04, color='black')
ax.vlines(-.005+.04, -.012+.0005, -.012-.0005, color='black')
ax.vlines(.005+.04, -.012+.0005, -.012-.0005, color='black')
ax.text( .04, -.0125, '1 cm', horizontalalignment='center', verticalalignment='top', fontsize=9)
ax.set_aspect('equal')
fig.subplots_adjust(bottom=0., top=1, right=1, left=0)
#fig.set_size_inches(6.5,3.25)
fig.savefig(filename, format='pdf')
return