def plot_trajectories_from_dataset(dataset, keys, interpolated_data='hide'):
'''
interpolated_data - if trajectories contain interpolated data, use 'hide' to hide that data, 'dotted' to show it as a dotted line, or 'show' to show it in its entirety
'''
import fly_plot_lib.plot as fpl # download at: https://github.com/florisvb/FlyPlotLib
from fly_plot_lib.colormaps import viridis as viridis
path = dataset.config.path
bgimg_filename = get_filename(path, 'bgimg_N1.png')
bgimg = plt.imread(bgimg_filename)
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_aspect('equal')
ax.imshow(bgimg, cmap='gray')
for key in keys:
trajec = dataset.trajec(key)
if 'interpolated' in trajec.__dict__.keys():
interpolated_indices = np.where(trajec.interpolated==1)[0]
if interpolated_data == 'dotted':
r = np.arange(0, len(interpolated_indices), 5)
interpolated_indices = interpolated_indices[r]
if interpolated_data != 'show':
trajec.position_x[interpolated_indices] = np.nan
trajec.position_y[interpolated_indices] = np.nan
l = -1
fpl.colorline(ax, trajec.position_x[0:l], trajec.position_y[0:l], trajec.time_epoch[0:l]-trajec.time_epoch[0:l][0], linewidth=2, colormap='none', norm=None, zorder=1, alpha=1, linestyle='solid', cmap=viridis)
fpl.adjust_spines(ax, [])
ax.set_frame_on(False)
def plot_trajectories_from_dataset(dataset, keys, interpolated_data='hide'):
'''
interpolated_data - if trajectories contain interpolated data, use 'hide' to hide that data, 'dotted' to show it as a dotted line, or 'show' to show it in its entirety
'''
import matplotlib.pyplot as plt
# download at: https://github.com/florisvb/FlyPlotLib
import fly_plot_lib.plot as fpl
from fly_plot_lib.colormaps import viridis as viridis
path = dataset.config.path
bgimg_filename = get_filename(path, 'bgimg_N1.png')
bgimg = plt.imread(bgimg_filename)
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_aspect('equal')
ax.imshow(bgimg, cmap='gray')
for key in keys:
trajec = dataset.trajec(key)
if 'interpolated' in trajec.__dict__.keys():
interpolated_indices = np.where(trajec.interpolated==1)[0]
if interpolated_data == 'dotted':
r = np.arange(0, len(interpolated_indices), 5)
interpolated_indices = interpolated_indices[r]
if interpolated_data != 'show':
trajec.position_x[interpolated_indices] = np.nan
trajec.position_y[interpolated_indices] = np.nan
l = -1
fpl.colorline(ax, trajec.position_x[0:l], trajec.position_y[0:l], trajec.time_epoch[0:l]-trajec.time_epoch[0:l][0], linewidth=2, colormap='none', norm=None, zorder=1, alpha=1, linestyle='solid', cmap=viridis)
fpl.adjust_spines(ax, [])
ax.set_frame_on(False)
def cartesian_spagetti(ax, dataset, axes=[0,1], keys=None, nkeys=300, start_key=0, show_saccades=False, keys_to_highlight=[], colormap='jet', color='gray', color_attribute=None, norm=None, show_start=True):
if keys is None:
keys = dataset.trajecs.keys()
else:
if type(keys) is not list:
keys = [keys]
if nkeys < len(keys):
last_key = np.min([len(keys), start_key+nkeys])
keys = keys[start_key:last_key]
keys.extend(keys_to_highlight)
for key in keys:
trajec = dataset.trajecs[key]
frames = np.arange(trajec.frame_range_roi[0], trajec.frame_range_roi[-1])
if key in keys_to_highlight:
alpha = 1
linewidth = 1
color = 'black'
zorder = 500
ax.plot(trajec.positions[frames,axes[0]], trajec.positions[frames,axes[1]], '-', color='black', alpha=1, linewidth=linewidth, zorder=zorder)
else:
alpha = 1
linewidth = 0.5
color = color
zorder = 100
if color_attribute is not None:
c = trajec.__getattribute__(color_attribute)
fpl.colorline(ax,trajec.positions[frames,axes[0]], trajec.positions[frames,axes[1]], c[frames], colormap=colormap, linewidth=linewidth, alpha=alpha, zorder=zorder, norm=norm)
else:
ax.plot(trajec.positions[frames,axes[0]], trajec.positions[frames,axes[1]], '-', color=color, alpha=1, linewidth=linewidth, zorder=zorder)
if show_saccades:
if len(trajec.sac_ranges) > 0:
for sac_range in trajec.sac_ranges:
angle_subtended = trajec.angle_subtended_by_post[sac_range[0]]
if sac_range[0] in frames and angle_subtended < 100.*np.pi/180.:
#if 1:
ax.plot(trajec.positions[sac_range,0], trajec.positions[sac_range,1], '-', color='red', alpha=1, linewidth=linewidth, zorder=zorder+1)
#sac = patches.Circle( (trajec.positions[sac_range[0],0], trajec.positions[sac_range[0],1]), radius=0.001, facecolor='red', edgecolor='none', alpha=alpha2, zorder=zorder+1)
#ax.add_artist(sac)
if show_start:
start = patches.Circle( (trajec.positions[frames[0],axes[0]], trajec.positions[frames[0],axes[1]]), radius=0.004, facecolor='green', edgecolor='none', linewidth=0, alpha=1, zorder=zorder+1)
ax.add_artist(start)
def calc_positions_normalized_by_speed(trajec, normspeed=0.2, plot=False):
distance_travelled = np.cumsum(trajec.speed)
distance_travelled_normalized = np.arange(distance_travelled[0], distance_travelled[-1], normspeed)
warped_time = np.interp(distance_travelled_normalized, distance_travelled, trajec.time_fly)
trajec.positions_normalized_by_speed = np.zeros([len(warped_time), 3])
for i in range(3):
trajec.positions_normalized_by_speed[:,i] = np.interp(warped_time, trajec.time_fly, trajec.positions[:,i])
trajec.time_normalized_by_speed = warped_time
if plot:
fig = plt.figure()
ax = fig.add_subplot(111)
x = trajec.positions[:,0]
y = trajec.positions[:,1]
speed = trajec.speed
fpl.colorline(ax,x,y,speed)
x_warped = trajec.positions_normalized_by_speed[:,0]
y_warped = trajec.positions_normalized_by_speed[:,1]
ax.plot(x_warped, y_warped, '.')