def save_image_sequence(npmovie, frames, filename):
# filename should be path + filename with initial number scheme + .extension desired, ie. jpg or png
# the path should exist prior to calling the function
imname = filename[filename.rfind("/") + 1 :]
impath = filename[0 : filename.rfind("/") + 1]
imname_no_extension = imname[0 : imname.rfind(".")]
imext = imname[imname.rfind(".") :]
imbasename = imname_no_extension.rstrip("0123456789")
imnumlen = len(imname_no_extension) - len(imbasename)
i = -1
for frame in frames:
i += 1
stri = str(i)
while len(stri) < imnumlen:
stri = "0" + stri
fname = impath + imbasename + stri + imext
strobe = strobe_from_npmovie(npmovie, 1, frames=[frame, frame + 1])
strobe = nim.rotate_image(strobe, np.array([[0, 1], [-1, 0]]))
plt.imsave(fname, strobe, origin="lower")
def plot_movie_data(npmovie, show_wings=False, figure=None, legthresh=50, show_vision=True):
calc_frame_of_landing(npmovie)
frames = get_active_frames(npmovie)
time = np.array(frames) * 1 / float(npmovie.fps)
cl = xy_kalman(npmovie, figure=figure, frames=frames, colormap="gray")
# get strobe image:
strobe_img = strobe_from_npmovie(npmovie, interval=210, frames=frames)
strobe_img = nim.rotate_image(strobe_img, np.array([[0, 1], [-1, 0]]))
cl.ax0.imshow(strobe_img, pyplot.get_cmap("gray"), origin="lower")
# axis parameters for subplots
nxticks = 5
nyticks = 3
# subplot parameters
n = 8
h = (0.7 - 0.05 * (n - 2)) / float(n)
subplots = []
for s in range(n):
ax = cl.fig.add_axes([0.47, 0.1 + (h + 0.05) * s, 0.2, h])
subplots.append(ax)
xticks = np.linspace(0, 1, num=nxticks, endpoint=True).tolist()
p = 0
subplots[p].plot(time, npmovie.flycoord.worldangle[frames])
subplots[p].set_xticks(xticks)
default_yticks = subplots[p].get_yticks()
yticks = np.linspace(default_yticks[0], default_yticks[-1], nyticks, endpoint=True).tolist()
subplots[p].set_yticks(yticks)
subplots[p].set_xlabel("time, seconds")
subplots[p].set_ylabel("world angle")
p += 1
subplots[p].plot(time, npmovie.flycoord.postangle[frames])
subplots[p].set_xticks(xticks)
default_yticks = subplots[p].get_yticks()
yticks = np.linspace(default_yticks[0], default_yticks[-1], nyticks, endpoint=True).tolist()
subplots[p].set_yticks(yticks)
subplots[p].set_xlabel("time, seconds")
subplots[p].set_ylabel("angle to post")
p += 1
subplots[p].plot(time, npmovie.flycoord.slipangle[frames])
subplots[p].set_xticks(xticks)
default_yticks = subplots[p].get_yticks()
yticks = np.linspace(default_yticks[0], default_yticks[-1], nyticks, endpoint=True).tolist()
subplots[p].set_yticks(yticks)
subplots[p].set_ylabel("slip angle")
p += 1
subplots[p].plot(time, npmovie.flycoord.velocities[frames, 0])
subplots[p].set_xticks(xticks)
default_yticks = subplots[p].get_yticks()
yticks = np.linspace(default_yticks[0], default_yticks[-1], nyticks, endpoint=True).tolist()
subplots[p].set_yticks(yticks)
subplots[p].set_ylabel("forward vel")
p += 1
subplots[p].plot(time, npmovie.flycoord.velocities[frames, 1])
subplots[p].set_xticks(xticks)
default_yticks = subplots[p].get_yticks()
yticks = np.linspace(default_yticks[0], default_yticks[-1], nyticks, endpoint=True).tolist()
subplots[p].set_yticks(yticks)
subplots[p].set_ylabel("sideways vel")
p += 1
subplots[p].plot(time, npmovie.flycoord.speed[frames])
subplots[p].set_xticks(xticks)
default_yticks = subplots[p].get_yticks()
yticks = np.linspace(default_yticks[0], default_yticks[-1], nyticks, endpoint=True).tolist()
subplots[p].set_yticks(yticks)
subplots[p].set_ylabel("speed")
p += 1
subplots[p].plot(time, npmovie.kalmanobj.legs[frames])
subplots[p].set_xticks(xticks)
default_yticks = subplots[p].get_yticks()
yticks = np.linspace(default_yticks[0], default_yticks[-1], nyticks, endpoint=True).tolist()
subplots[p].set_yticks(yticks)
subplots[p].set_ylabel("leg extension")
p += 1
subplots[p].plot(time, npmovie.flycoord.dist_to_post[frames])
subplots[p].set_xticks(xticks)
default_yticks = subplots[p].get_yticks()
yticks = np.linspace(default_yticks[0], default_yticks[-1], nyticks, endpoint=True).tolist()
subplots[p].set_yticks(yticks)
subplots[p].set_ylabel("dist to post")
interval = 70
i = frames[0]
while i < frames[-1]:
# plot body orientation vector
center = sa1_to_flydra_data_transform(npmovie.kalmanobj.positions[i], fix_sign=True)
long_axis = sa1_to_flydra_img_transform(npmovie.kalmanobj.long_axis[i], fix_sign=False) * -1
factor = npmovie.obj.axis_ratio[i][0] * 4.0
factor = min(15.0, factor)
dx = long_axis[1] * factor
dy = long_axis[0] * factor
legs = npmovie.kalmanobj.legs[i]
#### get color from kmeans clusters ###
colormap = plt.get_cmap("jet")
if npmovie.cluster is not None:
speed = np.interp(npmovie.timestamps[i], npmovie.trajec.epoch_time, npmovie.trajec.speed)
slipangle = npmovie.flycoord.slipangle[i]
print npmovie.id, i
dyaw = np.interp(
npmovie.timestamps[i],
npmovie.trajec.epoch_time[npmovie.sync2d3d.frames3d],
npmovie.sync2d3d.smoothyaw[:, 1],
)
obs = np.nan_to_num(np.array([np.abs(dyaw), speed, np.abs(slipangle)]))
cluster = kn.get_cluster_for_data(npmovie, obs)
color = colormap((cluster) / float(npmovie.cluster_means.shape[0]))
else:
speed = np.interp(npmovie.timestamps[i], npmovie.trajec.epoch_time, npmovie.trajec.speed)
color = colormap(speed)
print "color: ", color
arrow = Arrow(center[0], center[1], dx, dy, width=1.0, color=color)
cl.ax0.add_artist(arrow)
if show_wings:
# plot wing orientation vectors
wingR = npmovie.kalmanobj.wingcenterR[i]
if not np.isnan(wingR[0]):
arrow = Arrow(center[0], center[1], wingR[1] - 30, wingR[0] - 30, width=1.0, color="b")
cl.ax0.add_artist(arrow)
wingL = npmovie.kalmanobj.wingcenterL[i]
if not np.isnan(wingL[0]):
arrow = Arrow(center[0], center[1], wingL[1] - 30, wingL[0] - 30, width=1.0, color="b")
cl.ax0.add_artist(arrow)
i += interval
# plt.show()
try:
if npmovie.vision_timeseries is not None:
cl.vision_axes = [None for m in range(3)]
for m in range(3):
print
print m, len(npmovie.vision_timeseries)
cl.vision_axes[m] = cl.fig.add_axes([0.75, 0.1 + 0.25 * m, 0.2, 0.2])
cl.vision_axes[m].imshow(npmovie.vision_timeseries[m], pyplot.get_cmap("gray"), origin="lower")
cl.vision_axes[m].set_xticks([])
time_raw = npmovie.timestamps[npmovie.sync2d3d.frames2d] - npmovie.timestamps[0]
time = np.array([float(int(1000.0 * time_raw[i])) / 1000.0 for i in range(len(time_raw))])
cl.vision_axes[m].set_yticks(np.linspace(0, npmovie.vision_timeseries[m].shape[0], 5).tolist())
cl.vision_axes[m].set_yticklabels(np.linspace(time[0], time[-1], 5).tolist())
xlabel = "horizontal slice of fly eye at " + str((m - 1) * 45) + " deg"
cl.vision_axes[m].set_xlabel(xlabel)
cl.vision_axes[m].set_ylabel("time, sec")
except:
print "no vision timeseries"
return cl
