def draw_tree(robot_env, start, goal, tree, vertex=True, save_gif=True, fname='rrt_tree'):
"""Draw the tree built by the planner
Args:
robot_env (rl_planner.env.base_env.BaseEnv): the robot gym env
start (numpy.ndarray)
goal (numpy.ndarray)
tree (list): list of nodes
vertex (bool): nodes will be plotted if vertex is True
fname (str)
"""
fig, ax = plt.subplots(figsize=(6,6))
plt.axis([-22,22,-22,22])
plt.xticks([])
plt.yticks([])
collection_list = [] # each entry is a collection
tmp = plot_problem_definition(ax, robot_env.obs_list, robot_env.rigid_robot, start, goal)
collection_list.append(tmp)
for node in tree:
if node.parent:
tmp = tmp.copy()
path = np.array(node.path[:])
ax_path, = plt.plot(path[:,0], path[:,1], "-g", linewidth=0.6)
tmp.append(ax_path)
if vertex:
ax_node, = plt.plot(node.state[0], node.state[1], 'x', c='black', markersize=1.0)
tmp.append(ax_node)
collection_list.append(tmp)
# plt.pause(2)
plt.savefig(fname+'.png')
# plt.show()
gif = anim.ArtistAnimation(fig, collection_list, interval=50)
if save_gif:
gif.save(fname+'.gif', writer = anim.PillowWriter(fps=4))
def animate_frames(frames,
jupyter=True,
save_gif=False,
path='./tmp_results/animation.gif'):
""" Animate frames from array (with ipython HTML extension for jupyter) and optionally save as gif.
@param frames: list of frames
@param jupyter: (bool), for using jupyter notebook extension to display animation
@param save_gif: (bool), indicator if frames should be saved as gif
@param path: path to save gif to
"""
fig, ax = plt.subplots(figsize=(12, 10))
plt.axis('off')
cmap = None if len(frames[0].shape) == 3 else 'Greys'
patch = plt.imshow(frames[0], cmap=cmap)
anim = animation.FuncAnimation(plt.gcf(),
lambda x: patch.set_data(frames[x]),
frames=len(frames),
interval=30)
if save_gif:
writer = animation.PillowWriter(fps=25)
anim.save(path, writer=writer)
if jupyter:
display(HTML(anim.to_jshtml())) # ipython extension
else:
plt.show()
plt.close()
def scatter3d_module(x,
y,
z,
cs,
tag,
title=None,
vtx=None,
sym_z=True,
colorsMap='jet',
savegif=False):
cm = plt.get_cmap(colorsMap)
cNorm = matplotlib.colors.Normalize(vmin=min(cs), vmax=max(cs))
scalarMap = cmx.ScalarMappable(norm=cNorm, cmap=cm)
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.scatter(
x[1:-1],
y[1:-1],
z[1:-1],
s=1,
c=scalarMap.to_rgba(cs)[1:-1],
)
start = np.rint(np.array([x[0], y[0], z[0]]) * 2) / 2
end = np.rint(np.array([x[-1], y[-1], z[-1]]) * 2) / 2
# if vtx is None:
# ax.text(x[0], y[0], z[0], f'Start: {tuple(start)}', size=10, zorder=1, color='k')
# ax.text(x[-1], y[-1], z[-1], f'End: {tuple(end)}', size=10, zorder=1, color='k')
# ax.scatter(x[0], y[0], z[0], s=3, c='red',)
# ax.scatter(x[-1], y[-1], z[-1], s=3, c='red',)
# else:
# ax.text(vtx[0], vtx[1], vtx[2], f'Vertex: {tuple(vtx.astype(int))}', size=10, zorder=1, color='k')
# ax.scatter(x[0], y[0], z[0], s=3, c='red',)
ax.set_xlim(x_range[0], x_range[1])
ax.set_ylim(y_range[0], y_range[1])
ax.set_zlim(z_range[0], z_range[1])
ax.set_xlabel('X[cm]')
ax.set_ylabel('Y[cm]')
ax.set_zlabel('Z[cm]')
if title:
ax.set_title(title)
scalarMap.set_array(cs)
if not savegif:
plt.savefig(EVENT_WRITE_DIR + f"event{tag}.png")
plt.close()
return
def animate(frame):
ax.view_init(30, frame / 4)
return fig
anim = animation.FuncAnimation(fig, animate, frames=200, interval=50)
anim.save(EVENT_WRITE_DIR + f"event{tag}.gif",
writer=animation.PillowWriter(fps=10))
plt.close()
def gif2Animation(gifPath, label="none"):
#pdb.set_trace()
# *png path
gifs = glob.glob(gifPath)
fig = plt.figure()
# animationの体裁を整える
ax = plt.subplot()
ax.spines['right'].set_color('None')
ax.spines['left'].set_color('None')
ax.spines['top'].set_color('None')
ax.spines['bottom'].set_color('None')
ax.tick_params(axis='x',
which='both',
top='off',
bottom='off',
labelbottom='off')
ax.tick_params(axis='y',
which='both',
left='off',
right='off',
labelleft='off')
imgs = []
for gif in gifs:
img = Image.open(gif)
imgs.append([plt.imshow(img)])
# making animation
myAnima = animation.ArtistAnimation(fig, imgs, repeat_delay=10000)
#plt.show()
pw = animation.PillowWriter(fps=20)
myAnima.save(os.path.join(imgPath, "animaPF", f"{label}.gif"), writer=pw)
def plotCcgPerf_anim(byCCG, map_df, timeperiod, column='quantity'):
fig, ax = plt.subplots(1, figsize=(10, 10))
def plotMap(i):
n = 0
while n < 5:
ax.clear()
ax.axis('off')
map_df[column] = map_df['ccgid'].map(lambda x: byCCG[x][i])
ax.set_title(str("CCG " + column + ' ' + timeperiod[i]))
map_df.plot(column=column,
cmap='Blues',
scheme='QUANTILES',
k=5,
linewidth=0.5,
ax=ax,
edgecolor='0.1',
legend=True)
n += 1
animator = ani.FuncAnimation(fig,
plotMap,
frames=len(timeperiod) * 5,
repeat=False)
writergif = ani.PillowWriter(fps=5)
save_path = '2 geographical variation/'
if not os.path.exists(save_path):
os.makedirs(save_path)
filename = os.path.join(save_path, str(column + '.gif'))
animator.save(filename, writer=writergif)
def tsne_3d(tsne_data, mpath, df):
fig = plt.figure(figsize=(10, 10))
ax = Axes3D(fig)
colors = 'g', 'r'
labels = '1', '0'
for i, mcolor, mlabel in zip(range(len(labels)), colors, labels):
ax.scatter(tsne_data[df[df.columns[-1]] == i, 0],
tsne_data[df[df.columns[-1]] == i, 1],
tsne_data[df[df.columns[-1]] == i, 2],
s=30,
c=mcolor,
label=mlabel,
alpha=0.5)
fig.legend()
def rotate(angle):
ax.view_init(azim=angle)
angle = 1
ani = animation.FuncAnimation(fig,
rotate,
frames=np.arange(0, 360, angle),
interval=100)
ani.save(mpath, writer=animation.PillowWriter(fps=20))
def Animation(self, filename):
x, y, z = self.Vr[0], self.Vr[1], self.Vr[2]
plt.close('All')
fig, ax = plt.figure(1), plt.axes(xlim=(0, 40), ylim=(-20, 10))
plt.grid(linestyle='-')
plt.xlabel('x')
plt.ylabel('z')
[line] = ax.plot([], [], 'ro', lw=30 * self.R)
def init():
line.set_data([], [])
return ([line])
def animate(i):
line.set_data([x[i - 1]], [y[i - 1]]) #(x[:i], y[:i])
return ([line])
animation = anim.FuncAnimation(fig,
animate,
init_func=init,
frames=len(x) + 1,
interval=1000,
blit=True)
animation.save(filename, writer=anim.PillowWriter(fps=10))
def saveDataAnimation(data):
fig = plt.figure()
data_size = len(data[0])
ax = plt.axes(xlim=(0, data_size),
ylim=(torch.min(data[1]) * 1.5, torch.max(data[1]) * 1.5))
scatter_plot = ax.scatter([], [], s=1)
def init():
print('Saving gifs')
scatter_plot.set_offsets([])
return scatter_plot,
def animate(i):
x = np.arange(data_size)
y = data[i].numpy()
offsets = np.stack((x, y)).T
scatter_plot.set_offsets(offsets)
if (i % 64 == 0):
print('{}%'.format(round(100 * i / len(data))))
return scatter_plot,
anim = animation.FuncAnimation(fig,
animate,
init_func=init,
frames=len(data),
interval=20,
blit=False)
writergif = animation.PillowWriter(fps=60)
anim.save('weights.gif', writer=writergif)
plt.close(fig)
def display_frames_as_gif(frames, episode):
try:
pylab.figure(figsize=(frames[0].shape[1] / 72.0,
frames[0].shape[0] / 72.0),
dpi=72)
patch = pylab.imshow(frames[0])
pylab.axis('off')
pylab.subplots_adjust(left=0, right=1, top=1, bottom=0)
def animate(i):
patch.set_data(frames[i])
anim = animation.FuncAnimation(pylab.gcf(),
animate,
frames=len(frames),
interval=33)
anim.save(str(episode) + '_gameplay.gif')
except:
pylab.figure(figsize=(frames[0].shape[1] / 72.0,
frames[0].shape[0] / 72.0),
dpi=72)
patch = pylab.imshow(frames[0])
pylab.axis('off')
pylab.subplots_adjust(left=0, right=1, top=1, bottom=0)
def animate(i):
patch.set_data(frames[i])
anim = animation.FuncAnimation(pylab.gcf(),
animate,
frames=len(frames),
interval=33)
anim.save(str(episode) + '_gameplay.gif',
writer=animation.PillowWriter(fps=40))
def _create_animation(self, i, outputarray):
fig = plt.figure()
ax = plt.axes(xlim=(np.nanmin(outputarray.real)-1, np.nanmax(outputarray.real)+1),
ylim=(np.nanmin(outputarray.imag)-1, np.nanmax(outputarray.imag)+1))
# ax.plot(inputarray.real, inputarray.imag)
function, = ax.plot([], [], lw=2)
arrows = []
def init():
function.set_data([], [])
for ii in range(i):
arrows.append(Arrow(0, 0, 0, 0))
ax.add_patch(arrows[ii])
return function,
def animate(n):
function.set_data(outputarray.real[:n:2, -1], outputarray.imag[:n:2, -1])
for ii in range(i):
arrows[ii].remove()
for ii in range(i):
if ii == 0:
arrows[ii] = Arrow(0, 0, outputarray.real[n, 0], outputarray.imag[n, 1], color='k', lw=1)
else:
arrows[ii] = Arrow(outputarray.real[n, ii-1], outputarray.imag[n, ii-1],
outputarray.real[n, ii], outputarray.imag[n, ii], color='k', lw=1)
ax.add_patch(arrows[ii])
return function,
anim = animation.FuncAnimation(fig, animate, init_func=init, frames=len(outputarray), blit=True,
interval=100)
gifwriter = animation.PillowWriter(fps=60)
anim.save(self.save_path + os.sep + 'fourier_series.gif', writer=gifwriter)
return
def plot_animal_attributes(self):
"""
Plot animal attributes
"""
#Create graph
self.animal_fig, self.animal_ax = plt.subplots(figsize=(5, 5))
#Set labels and axis for graph
self.animal_ax.set_xlabel("Speed")
self.animal_ax.set_ylabel("Range")
self.animal_ax.set_xlim(-1, 11)
self.animal_ax.set_ylim(-1, 11)
x_data = []
y_data = []
sizes = []
scatter = self.animal_ax.scatter(-2, -2, c="#ff0000")
#Create (x, y) coordinates
def create_coordinates(x, y):
coordinates = []
for n, x_coor in enumerate(x):
coor = (x_coor, y[n])
coordinates.append(coor)
return coordinates
#Create sizes for points
def create_sizes(coordinates):
sizes = []
for point in coordinates:
size = coordinates.count(point) * 80
sizes.append(size)
return sizes
def animate(i):
data = self.data[i]
x_data = data["animals"]["speed"]
y_data = data["animals"]["range"]
plt.title(f"Cycle: {data['cycle']} Population: {data['pop']}")
points = create_coordinates(x_data, y_data)
sizes = create_sizes(points)
#Update the graph
scatter.set_offsets(points)
scatter.set_sizes(sizes)
return scatter,
line_animation = animation.FuncAnimation(self.animal_fig,
animate,
frames=np.arange(
0, len(self.data), 1),
interval=0.05 * 1000,
blit=True,
save_count=len(self.data))
writergif = animation.PillowWriter(fps=5)
line_animation.save('animals.gif', writer=writergif)
plt.close(self.animal_fig)
def scatter_plot_animation_new(time_ani, frequency_ani, parameters):
cut_time = [_.flatten()[:110] / _.max() for _ in time_ani]
cut_frequency = [_.flatten()[:110] / _.max() for _ in frequency_ani]
writer = ani.PillowWriter()
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_xlabel("Time domain cost")
ax.set_ylabel("Frequency domain cost")
ax.set_xlim(0, 1)
ax.set_ylim(0, 1)
sctr, = ax.plot(cut_time[0], cut_frequency[0], '.b')
def chart(i):
# time_data = (time_ani[i]) / (time_ani[i].max()).flatten()
# frequency_data = (frequency_ani[i] / frequency_ani[i].max()).flatten()
sctr.set_data(cut_time[i], cut_frequency[i])
ax.set_title(
"Comparision of frequency and time domain costs $a = {:.3f}$".
format(1 + (1 / 11) * i))
animator = ani.FuncAnimation(fig, chart, frames=100, repeat=False)
plt.show()
animator.save("./GridAnalysisData/ScatterAnimationExperiment" +
parameters + ".gif",
writer=writer)
plt.close(fig)
def animate_evolution(self):
try:
no_snaps = len([name for name in os.listdir(snap_dir) if os.path.isfile(os.path.join(snap_dir, name))])
plt.clf()
fig = plt.figure(figsize = (30,30))
images = []
print('Recomposing animation ({} snapshots found)'.format(no_snaps), flush = True)
files = glob.glob(snap_dir + '/*')
for file in files:
im = plt.imread(file)
images.append([plt.imshow(im)])
ani = animation.ArtistAnimation(fig, images, interval=100, repeat_delay=0)
plt.axis('off')
writergif = animation.PillowWriter(fps=5)
ani.save(gif_file, writer = writergif)
#plt.show()
except:
pass
def main():
U, F = load_problem(DEFAULT_FILE)
N = U.shape[0]
cycle = PoissonCycle(F, 1, 0, 1, 0)
ims = []
fig = plt.figure()
ax = fig.gca(projection="3d")
x = np.linspace(0, 1, 1024)
X, Y = np.meshgrid(x, x)
for i in range(100):
#im = plt.imshow(U, cmap='RdBu_r', interpolation='nearest')
im = ax.plot_surface(
X[1: -1, 1: -1],
Y[1: -1, 1: -1],
U[1: -1, 1: -1],
alpha=0.7, cmap='magma')
t = ax.annotate(i, (0.1, 0.1), xycoords='figure fraction')
norm = cycle.norm(U)
n = ax.annotate(norm, (0.7, 0.1), xycoords='figure fraction')
ims.append([im, t, n])
if norm <= 1e-6 * N * N:
break
U = cycle(U)
fig.colorbar(ims[0][0], shrink=0.5, aspect=10, pad=0.1)
ani = animation.ArtistAnimation(fig, ims, interval=1000, repeat=True)
writer = animation.PillowWriter(fps=2)
ani.save('../graphs/wave.gif', writer=writer)
def save_animation_as_gif_image(write_animation, animation_name):
"""
use animation.writers.list() to list writer current machine supported
"""
write_animation.save(''.join((animation_name, '.gif')),
writer=animation.PillowWriter(fps=40))
def animateSolution(x, time, sol_list, gif_name='pipe_flow_simulation'):
fig = plt.figure()
ax = plt.axes(xlim=(x[0], x[-1]),
ylim=(np.min(sol_list), np.max(sol_list)))
#ax = plt.axes(xlim=(x[0], x[-1]), ylim=(-1,1))
#ax = plt.axes(xlim=(x[0], x[-1]), ylim=(np.min(sol_list),1003))
plt.grid(True)
line, = ax.plot([], [], lw=2)
# initialization function: plot the background of each frame
def init():
line.set_data([], [])
return line,
def animate(i):
plt.title(str(time[i]))
y = sol_list[i]
line.set_data(x, y)
return line,
writergif = animation.PillowWriter(fps=5)
anim = animation.FuncAnimation(fig,
animate,
init_func=init,
frames=len(sol_list),
interval=20,
blit=True)
# save the animation as mp4 video file
anim.save(gif_name + '.gif', writer=writergif)
def draw_path(robot_env, start, goal, path, fname='rrt_path'):
"""Draw the planned path.
Args:
robot_env (rl_planner.env.base_env.BaseEnv): the robot gym env
start (numpy.ndarray)
goal (numpy.ndarray)
path (list): the planned path
fname (str)
"""
fig, ax = plt.subplots(figsize=(6,6))
plt.axis([-22,22,-22,22])
plt.xticks([])
plt.yticks([])
collection_list = [] # each entry is a collection
tmp = plot_problem_definition(ax, robot_env.obs_list, robot_env.rigid_robot, start, goal)
array_path = np.array([state[:2] for state in path])
plt.plot(array_path[:,0], array_path[:,1], c='k', linewidth=1.0)
collection_list.append(tmp)
for state in path:
tmp_ = tmp.copy()
robot_marker = plot_robot(ax, robot_env.rigid_robot, state[:3])
tmp_ += robot_marker
collection_list.append(tmp_)
gif = anim.ArtistAnimation(fig, collection_list, interval=200)
gif.save(fname+'.gif', writer = anim.PillowWriter(fps=5))
def animate_sim(self, path, exited_maze, T):
" Animate a game and save as a GIF"
pathx = [path[i][0] for i in range(len(path))]
pathy = [path[i][1] for i in range(len(path))]
mino_pathx = [path[i][2] for i in range(len(path))]
mino_pathy = [path[i][3] for i in range(len(path))]
wall = [(6, 4)]
for i in range(4):
wall.append((i, 2))
for i in range(3):
wall.append((i + 1, 5))
wall.append((2, 5 + i))
for j in range(1, 7):
wall.append((5, j))
A = (0, 0)
B = (6, 5)
f = plt.figure(0)
plt.scatter(*zip(*[(s[1], s[0]) for s in wall]),
1000,
c="r",
marker="x")
plt.scatter(*A[::-1], c=0, cmap='winter', s=300, marker='o')
plt.scatter(*B[::-1], c='palegreen', s=300, marker='D')
plt.gca().invert_yaxis()
scat = plt.scatter(x=[pathx[0], mino_pathx[0]],
y=[pathy[0], mino_pathy[0]],
c=['b', 'r'],
s=[100, 200],
zorder=100)
def animationUpdate(t):
'''anim update function'''
plt.plot(mino_pathx[:t + 1],
mino_pathy[:t + 1],
c='r',
linewidth=3)
plt.plot(pathx[:t + 1], pathy[:t + 1], c='b')
x = [pathx[t], mino_pathx[t]]
y = [pathy[t], mino_pathy[t]]
scat.set_offsets(np.c_[x, y])
#plt.title(f'seed = {seed}; t = {t}; Win = {not dead}')
# plt.savefig(f'{seed}a{t}.png')
return scat,
anim = FuncAnimation(f,
animationUpdate,
frames=T + 1,
interval=100,
blit=False)
writergif = animation.PillowWriter(fps=5)
anim.save(f'p1_{self.seed}.gif', writer=writergif)
plt.clf()
print(f'Saved video as p1_{self.seed}.gif')
self.seed += 1
def exportFig(fig, updateFunc, frameNum, new_file_path):
anim = FuncAnimation(fig, updateFunc,
frames=frameNum, interval=50, blit=True)
fig.set_size_inches(16, 9, True)
anim.save(new_file_path, writer = animation.PillowWriter(fps = 30))
return new_file_path
def animate_trajectory(traj_file, action="play", filename=""):
def animation_init(): # only required for blitting to give a clean slate.
line.set_ydata([np.nan] * len(x))
return line,
def animate(i):
if i < len(raw_points.x):
if raw_points.pressure[i] != 0:
xdata.append(raw_points.x[i])
ydata.append(raw_points.y[i])
line.set_data(xdata, ydata)
return line,
fields = ['x', 'y', 'pressure', 'time']
try:
raw_points = pd.read_csv(traj_file, usecols=fields)
except (IOError, FileNotFoundError):
QMessageBox().critical(
None, "Warning! file access error",
"WriTracker couldn't load the trajectory file.", QMessageBox.Ok)
return False
fig, ax = plt.subplots()
xmargin = 100
ymargin = 100
maxx = raw_points.x.max() + xmargin
minx = raw_points.x.min() - xmargin
maxy = raw_points.y.max() + ymargin
miny = raw_points.y.min() - ymargin
x = np.arange(0, max(maxx, maxy), 1)
y = np.arange(0, max(maxx, maxy), 1)
line, = ax.plot(x, y, 'o', markersize=1)
ax.set(xlim=(minx, maxx), ylim=(max(0, miny), maxy))
xdata, ydata = [], []
if action == "play":
# When using plt.show, 'interval' controls the speed of the animation
anim = animation.FuncAnimation(fig,
animate,
init_func=animation_init,
interval=10,
blit=True)
plt.show() # to display "live" the animation
return anim # required when calling from inside a function
elif action == "save":
print("WriTracker Plotter: Saving GIF, please wait")
f = filename + ".gif"
# save_count > 1000 might cause memory error.
ani = animation.FuncAnimation(fig,
animate,
init_func=animation_init,
blit=True,
save_count=1000)
writergif = animation.PillowWriter(
fps=40
) # fps > 60 | fps < 15 caused very very slow output. 30-40 fits.
ani.save(f, writer=writergif)
def export_frames_as_gif(frames, filename):
patch = plt.imshow(frames[0])
plt.axis('off')
def animate(i):
patch.set_data(frames[i])
anim = animation.FuncAnimation(plt.gcf(), animate, frames = len(frames), interval=3)
print('Saving gif...')
#anim.save('images/{}.gif'.format(filename), fps=30)
anim.save('images/{}.gif'.format(filename), writer=animation.PillowWriter(fps=30))
def main():
total_time = 20e-9
n_frames = 250
dx = 0.01
grid = Grid1D(dx, 2.0)
grid.set_material(1.0, 1.5, er=4.0, cond=0.0)
# grid = create_shield(0.25e-3, 1.0, 11.6e8)
print(grid)
src_z = 0.1
source = Gaussian(src_z, 'Gaussian', 1.0, 40 * grid.dt, 12 * grid.dt)
# source = Sinusoid(src_z, 'Sine', 1.0, 200e6)
# source = SinusoidalGauss(src_z, 'Sine-Gauss', 1e7, 1e9)
grid.add_source(source)
grid.add_probe(Probe(1.9, 'Transmitted'))
grid.solve(total_time, n_frames)
fig, axes = plt.subplots(2, 1, sharex=True)
axes[0].plot(grid.x, grid.ez)
axes[0].set_ylabel('Ez')
axes[1].plot(grid.x, grid.hy)
axes[1].set_ylabel('Hy')
axes[1].set_xlabel('x (m)')
fig2, ax2 = plt.subplots()
ax2.set_ylim(-2, 2)
eline, = ax2.plot(grid.x, grid.ez)
ax2.set_ylabel('Ez')
ax2.set_xlabel('x (m)')
collection = collections.BrokenBarHCollection.span_where(
grid.x,
ymin=-2,
ymax=2,
where=grid.cb < 0.5,
facecolor='red',
alpha=0.5)
ax2.add_collection(collection)
ani = animation.FuncAnimation(fig2,
animate,
fargs=(eline, grid.data),
interval=40,
blit=True,
frames=len(grid.data))
f = r"fdtd_1d.gif"
print('Saving', f, '...', end='')
writergif = animation.PillowWriter(fps=25)
ani.save(f, writer=writergif)
print(' done.')
source_data = source.solve(grid.t)
plot_time_freq(source_data, grid.t, grid.dt, 'Source')
for probe in grid.probes:
plot_time_freq(probe.data, grid.t, grid.dt, probe.label)
plot_response(source_data, probe.data, grid.t, grid.dt, 'Response')
plt.show()
def plot_trends_dynamically(name, countries=[]):
fig, ax = plt.subplots(figsize=(17, 9))
leg = ax.legend()
df_x_full = threshold_data(per_million(df_prevalence),
'cases',
'weekly',
countries,
reset=False)
df_y_full = threshold_data(per_million(df_incidence_weekly),
'cases',
'weekly',
countries,
reset=False)
def animate(i):
ax.clear()
ax.set_xscale('log')
ax.set_yscale('log')
ax.xaxis.set_major_formatter(
ticker.FuncFormatter(lambda y, pos: ('{{:.{:1d}f}}'.format(
int(np.maximum(-np.log10(y), 0)))).format(y)))
ax.yaxis.set_major_formatter(
ticker.FuncFormatter(lambda y, pos: ('{{:.{:1d}f}}'.format(
int(np.maximum(-np.log10(y), 0)))).format(y)))
ax.set_xlabel('Prevalence (Cases per Million)')
ax.set_ylabel('Incidence (New cases per million)')
i += 1
for country in countries:
x = df_x_full.iloc[:i][country]
y = df_y_full.iloc[:i][country]
line, = ax.plot(x, y, '-o', markevery=[-1], label=country)
plt.annotate(country, (x[-1], y[-1]),
textcoords="offset points",
xytext=(5, 10),
ha='right',
color=line.get_color())
if i > len(df_x_full) - 1:
i = len(df_x_full) - 1
ax.annotate(df_x_full.index[i].date(),
xy=(0.85, 0.05),
xycoords='axes fraction',
fontsize=15)
ax.legend(loc="upper left", frameon=False)
ax.set_title('Trends (steps per week)')
anim = animation.FuncAnimation(fig, animate, frames=20)
anim.save('dynamic-trends/' + name + '.gif',
writer=animation.PillowWriter(fps=2))
def animate(self):
plt.axis('off')
plt.tight_layout(pad=0)
im_ani = animation.FuncAnimation(self.fig,
self.update,
frames=self.i_number,
interval=200,
repeat_delay=1000,
blit=True)
writer_gif = animation.PillowWriter(fps=3)
im_ani.save('./assets/game-of-life.gif', writer=writer_gif)
def animate(self, f):
anim = animation.FuncAnimation(self.fig,
self._update,
frames=self.number_of_steps,
interval=1,
blit=True)
# If the keyword argument for show animation is true, show the plot
if self.show_anim:
plt.show()
if self.save:
writergif = animation.PillowWriter(fps=200)
anim.save(f, writer=writergif)
def save(animation, name, fps, ext=".gif"):
"""
Save animation as either a .gif or .mp4 file.
:param animation: matplotlib.animation.FuncAnimation object.
:param name: name of the saved file.
:param fps: frames per second.
:param ext: extension of the saved file, either .gif or .mp4.
"""
writer = anim.PillowWriter(fps) if ext == ".gif" else anim.FFMpegWriter(
fps)
animation.save("images/" + name + ext, writer)
def run(self, movie=False):
ani = animation.FuncAnimation(self.fig,
self.animate,
frames=269,
blit=True,
init_func=self.initAnimate,
repeat=False)
if movie:
pwriter = animation.PillowWriter(
fps=60, metadata=dict(artist='Dr. Ryan Clement'))
ani.save('../movies/pentagon_zombie_apocalypse.gif',
writer=pwriter)
def main(unused_argv):
if not FLAGS.rollout_path:
raise ValueError("A `rollout_path` must be passed.")
with open(FLAGS.rollout_path, "rb") as file:
rollout_data = pickle.load(file)
writer = animation.PillowWriter(fps=30)
fig, axes = plt.subplots(1, 2, figsize=(10, 5))
plot_info = []
for ax_i, (label, rollout_field) in enumerate([
("Ground truth", "ground_truth_rollout"),
("Prediction", "predicted_rollout")
]):
# Append the initial positions to get the full trajectory.
trajectory = np.concatenate(
[rollout_data["initial_positions"], rollout_data[rollout_field]],
axis=0)
ax = axes[ax_i]
ax.set_title(label)
bounds = rollout_data["metadata"]["bounds"]
ax.set_xlim(bounds[0][0] - 0.2, bounds[0][1] + 0.2)
ax.set_ylim(bounds[1][0] - 0.2, bounds[1][1] + 0.2)
ax.set_xticks([])
ax.set_yticks([])
ax.set_aspect(1.)
points = {
particle_type: ax.plot([], [], "o", ms=2, color=color)[0]
for particle_type, color in TYPE_TO_COLOR.items()
}
plot_info.append((ax, trajectory, points))
num_steps = trajectory.shape[0]
def update(step_i):
outputs = []
for _, trajectory, points in plot_info:
for particle_type, line in points.items():
mask = rollout_data["particle_types"] == particle_type
line.set_data(trajectory[step_i, mask, 0], trajectory[step_i,
mask, 1])
outputs.append(line)
return outputs
unused_animation = animation.FuncAnimation(fig,
update,
frames=np.arange(
0, num_steps,
FLAGS.step_stride),
interval=10)
unused_animation.save("animation10000.gif", writer=writer)
def saveSifGif(sif, ylo=0, yhi=10000, xlo=0, xhi=10000, **options):
"""Convert kinetic series to animated gif
Saves files to <siffilebase>.gif
The color range is scaled from min to max of the complete series. Other
options will hopefully be implemented soon.
Parameters:
ylo/yhi: lower/higher row index
xlo/xhi: lower/higher coloumn index
Known keyword arguments:
path: directory wherer to write images, default sif location
fname: filename base to use <fname>_iii.png, default sif name
figsize: tuple (w,h) for plt.set_size_inches(), default (4,4)
norm: default is max in series; other options to be added
extent: To be implemented, (xmin,xmax,ymin,ymax) axis limits, default px indices
aspect: To be implemented, axis aspect ratio, default "auto" (->square image)
transpose: (boolean) flip axis, default False
reversex/reverssey: to be implemented
reversex/reverssey: (boolean) invert data in x/y, default False
-> Axis labelling is not inverted! (to be implemented)
--- Further options kw-args are passed on to plt.imshow ---
"""
try:
fname = options.pop("fname", os.path.basename(sif.path)[:-3] + "gif")
path = options.pop("path", os.path.dirname(sif.path))
sifdata = sif.data
if options.pop("transpose", False):
sifdata = sif.data.transpose([0, 2, 1])
yhi = np.min([yhi, sifdata.shape[-2]])
xhi = np.min([xhi, sifdata.shape[-1]])
sifdata = sifdata[:, ylo:yhi, xlo:xhi]
extent = options.pop(
"extent", (xlo, xhi, ylo, yhi)) # TODO: invert for reversexy
if options.pop("reversex", False):
sifdata = sifdata[:, :, ::-1]
if options.pop("reversey", False):
sifdata = sifdata[:, ::-1, :]
outpath = os.path.join(path, fname)
if not outpath.endswith(".gif"):
outpath += ".gif"
fig = plt.figure()
mx = np.max(sifdata)
mn = np.min(sifdata)
arts = [[
plt.imshow(sifdata[i, :, :], vmin=mn, vmax=mx, extent=extent)
] for i in range(sif.kineticlength)]
anima = anim.ArtistAnimation(fig, arts)
anima.save(outpath, writer=anim.PillowWriter())
except: # TODO
raise () # TODO
def display_frames_as_gif(frames, filename='animation.gif'):
plt.figure(figsize=(frames[0].shape[1] / 72, frames[0].shape[0] / 72),
dpi=72)
patch = plt.imshow(frames[0])
plt.axis('off')
anim = animation.FuncAnimation(plt.gcf(),
lambda x: patch.set_data(frames[x]),
frames=len(frames),
interval=50)
writer = animation.PillowWriter(fps=30)
anim.save(filename, writer=writer)
