def convert_2dpath_to_3dpath(self, z, zdir = 'z'):
'''
convert a path on flat surface
to 3d path
'''
#print("calling convert 2dpath to 3dpath")
x1 = []; y1 = []; z1 =[]; norms = []; idxset = []
idxbase = 0
if zdir == 'x':
norm = np.array([1., 0, 0.])
elif zdir == 'y':
norm = np.array([0., 1, 0.])
else:
norm = np.array([0., 0, 1.])
txs, tys, tzs, ones = self._vec
xyzlist = [(txs[si:ei], tys[si:ei], tzs[si:ei]) \
for si, ei in self._segis]
for v0, v1, v2 in xyzlist:
x1.append(v0)
y1.append(v1)
idxset.append(np.arange(len(v0))+idxbase)
z1.append(v2)
# norms.append(np.hstack([norm]*len(v0)))
idxbase = len(v0)+idxbase
x1 = np.hstack(x1)
y1 = np.hstack(y1)
z1 = np.hstack(z1)
# norms = np.hstack(norms).reshape(-1, 3)
X3D, Y3D, Z3D = juggle_axes(x1, y1, z1, zdir)
norms = np.array([norm]).reshape(-1, 3)
self._gl_3dpath = [X3D, Y3D, Z3D, norms, idxset]
def convert_2dpath_to_3dpath(self, z=None, zdir = 'z'):
x1 = []; y1 = []; z1 =[]; norms = []; idxset = []
idxbase = 0
if zdir == 'x':
norm = np.array([1., 0, 0.])
elif zdir == 'y':
norm = np.array([0., 1, 0.])
else:
norm = np.array([0., 0, 1.])
xyzlist = []
for points in self._segments3d:
points = np.vstack(points)
xyzlist.append((points[:,0], points[:, 1], points[:,2],))
# xyzlist = [(points[:,0], points[:, 1], points[:,2])
# for points in self._segments3d]
for v0, v1, v2 in xyzlist:
x1.append(v0)
y1.append(v1)
idxset.append(np.arange(len(v0))+idxbase)
z1.append(v2)
norms.append(np.hstack([norm]*len(v0)))
idxbase = len(v0)+idxbase
x1 = np.hstack(x1)
y1 = np.hstack(y1)
z1 = np.hstack(z1)
norms = np.hstack(norms).reshape(-1, 3)
X3D, Y3D, Z3D = juggle_axes(x1, y1, z1, zdir)
##does norm may mean anything, but let's leave it...
self._gl_3dpath = [X3D, Y3D, Z3D, norms, idxset]
def animate(i):
gamma = point_defects(self,snap_to_time(snap_start+i,self))
gamma_transited = gamma.transi(tran)
inter = gamma_transited['inter'][:]
vac = gamma_transited['vac'][:]
# 3 arrays containing the coordinates of the interstitials
xi,yi,zi = np.transpose(inter)
# 3 arrays containing the coordinates of the vacancies
xv,yv,zv = np.transpose(vac)
pi._offsets3d = juggle_axes(xi,yi,zi,'z')
pv._offsets3d = juggle_axes(xv,yv,zv,'z')
'''
ax.clear()
ax.scatter(xi,yi,zi, label='Interstitials', c='r', marker='^')
ax.scatter(xv,yv,zv, label='Vacancies', c='b', marker='o')
ax.set_title('Movie of the defects from '+str(t_start)+' ps to '+str(snap_to_time(snap_end,self))+' ps')
ax.set_xlabel('x axis[Angström]')
ax.set_ylabel('y axis[Angström]')
ax.set_zlabel('z axis[Angström]')
ax.set_xlim3d(0,self.box_dim[0])
ax.set_ylim3d(0,self.box_dim[0])
ax.set_zlim3d(0,self.box_dim[0])
ax.legend(frameon = True, fancybox = True, ncol = 1, fontsize = 'x-small', loc = 'lower right')
'''
# Display of the progression
if i % round(0.2*(snap_end-snap_start+1))==0 and i // round(0.2*(snap_end-snap_start+1)) != 0:
if i // round(0.2*(snap_end-snap_start+1)) == 1:
print('Progression of defects_movie:')
print(str(round(100*i/(snap_end-snap_start+1)))+'%')
def update(self, i):
""" Use new particle position for drawing next frame """
data = next(self.stream)
#data = np.transpose(data)
#print data
self.scat._offsets3d = juggle_axes(data[0,:],data[1,:],data[2,:], 'z')
self.ax.view_init(30,self.angle)
plt.draw()
return self.scat,
def set_3d_properties(self, zs=0, zdir='z'):
xs = self.get_xy()[:,0]
ys = self.get_xy()[:,1]
try:
# If *zs* is a list or array, then this will fail and
# just proceed to juggle_axes().
zs = float(zs)
zs = [zs for x in xs]
except TypeError:
pass
self._verts3d = juggle_axes(xs, ys, zs, zdir)
self._invalidz = True
def moveTarget(self, index, target, speed):
# Target circle
x = target[0, 3]
y = target[1, 3]
z = target[2, 3]
self.allTargetElements[index].circles._offsets3d = juggle_axes([x],
[y],
[z],
'z')
# Line along X
tmpVec = np.array([50, 0, 0, 1]).reshape(4, 1)
tmpVec = target * tmpVec
lx = tmpVec[0, 0]
ly = tmpVec[1, 0]
lz = tmpVec[2, 0]
self.allTargetElements[index].frameXLines.set_data([x, lx], [y, ly])
self.allTargetElements[index].frameXLines.set_3d_properties([z, lz],
'z')
# Line along Y
tmpVec = np.array([0, 50, 0, 1]).reshape(4, 1)
tmpVec = target * tmpVec
lx = tmpVec[0, 0]
ly = tmpVec[1, 0]
lz = tmpVec[2, 0]
self.allTargetElements[index].frameYLines.set_data([x, lx], [y, ly])
self.allTargetElements[index].frameYLines.set_3d_properties([z, lz],
'z')
# Line along Z
tmpVec = np.array([0, 0, 50, 1]).reshape(4, 1)
tmpVec = target * tmpVec
lx = tmpVec[0, 0]
ly = tmpVec[1, 0]
lz = tmpVec[2, 0]
self.allTargetElements[index].frameZLines.set_data([x, lx], [y, ly])
self.allTargetElements[index].frameZLines.set_3d_properties([z, lz],
'z')
# Speed vector
sx = speed[0]
sy = speed[1]
sz = speed[2]
# Arbitrary scaling, to make max. length of vector constant
k = 400.0 / Params.inputForceMax
self.allTargetElements[index].speedLines.set_data([x, x + sx * k],
[y, y + sy * k])
self.allTargetElements[index].speedLines.set_3d_properties(
[z, z + sz * k], 'z')
def update(t):
pts._offsets3d = juggle_axes(seq[t, :, 0], seq[t, :, 1], seq[t, :, 2],
'z')
for i, l in enumerate(lines):
if l is not None:
l.set_data(xline[t, i, :2])
l.set_3d_properties(xline[t, i, 2])
if ghost is not None:
pts_g._offsets3d = juggle_axes(ghost[t, :, 0], ghost[t, :, 1],
ghost[t, :, 2], 'z')
for i, l in enumerate(lines_g):
l.set_data(xline_g[t, i, :2])
l.set_3d_properties(xline_g[t, i, 2])
if pointer is not None:
ax.quiv.remove()
ax.quiv = ax.quiver(X[t],
Y[t],
Z[t],
dX[t],
dY[t],
0,
color=pointer_color)
def set_3d_properties(self, zs, zdir):
# Force the collection to initialize the face and edgecolors
# just in case it is a scalarmappable with a colormap.
self.update_scalarmappable()
offsets = self.get_offsets()
if len(offsets) > 0:
xs, ys = list(zip(*offsets))
else:
xs = []
ys = []
from mpl_toolkits.mplot3d.art3d import juggle_axes
self._offsets3d = juggle_axes(xs, ys, np.atleast_1d(zs), zdir)
self._facecolor3d = self.get_facecolor()
self._edgecolor3d = self.get_edgecolor()
def set_3d_properties(self, zs, zdir):
# Force the collection to initialize the face and edgecolors
# just in case it is a scalarmappable with a colormap.
self.update_scalarmappable()
offsets = self.get_offsets()
if len(offsets) > 0:
xs, ys = list(zip(*offsets))
else:
xs = []
ys = []
from mpl_toolkits.mplot3d.art3d import juggle_axes
self._offsets3d = juggle_axes(xs, ys, np.atleast_1d(zs), zdir)
self._facecolor3d = self.get_facecolor()
self._edgecolor3d = self.get_edgecolor()
def update(tt):
tt = int(tt)
#update marker position
marker_pos.set_data(tt, self.mean_dist[tt])
#update coordinate positions
sc._offsets3d = juggle_axes(self.pos[tt][:, 0], self.pos[tt][:, 1],
self.pos[tt][:, 2], 'z')
#update marker sizes of coordinates
sc._sizes3d = 25 * self.std[tt]
#update title
ax_3d.set_title('Correlation at {}'.format(time_array[tt]))
#update color of markers: not working properly!
sc._faceolor3d = (self.mean[tt])
fig.canvas.draw_idle()
def convert_2dpath_to_3dpath(self, z, zdir='z'):
'''
convert a path on flat surface
to 3d path
'''
#print("calling convert 2dpath to 3dpath")
x1 = []
y1 = []
z1 = []
norms = []
idxset = []
idxbase = 0
if zdir == 'x':
norm = np.array([1., 0, 0.])
elif zdir == 'y':
norm = np.array([0., 1, 0.])
else:
norm = np.array([0., 0, 1.])
txs, tys, tzs, ones = self._vec
if hasattr(self, '_segis'):
xyzlist = [(txs[si:ei], tys[si:ei], tzs[si:ei])
for si, ei in self._segis]
else:
xyzlist = [(txs[sl], tys[sl], tzs[sl]) for sl in self._segslices]
for v0, v1, v2 in xyzlist:
x1.append(v0)
y1.append(v1)
idxset.append(np.arange(len(v0)) + idxbase)
z1.append(v2)
# norms.append(np.hstack([norm]*len(v0)))
idxbase = len(v0) + idxbase
x1 = np.hstack(x1)
y1 = np.hstack(y1)
z1 = np.hstack(z1)
# norms = np.hstack(norms).reshape(-1, 3)
X3D, Y3D, Z3D = juggle_axes(x1, y1, z1, zdir)
norms = np.array([norm]).reshape(-1, 3)
self._gl_3dpath = [X3D, Y3D, Z3D, norms, idxset]
def update_scatter(i, data, scat, acc=None, proj=None):
scat.set_label("{}".format(i))
if proj == '3d':
from mpl_toolkits.mplot3d import Axes3D
from mpl_toolkits.mplot3d.art3d import juggle_axes
xs = data[i,:,0]
ys = data[i,:,1]
zs = data[i,:,2]
scat._offsets3d = juggle_axes(xs, ys, zs, 'z')
else:
scat.set_offsets(data[i,:,:])
if acc is not None and proj is None:
scat.set_color(cm.RdYlGn(acc[i,:,0]))
#plt.legend()
return scat,
def _update_plot(i, scatters, worlds, species_list):
world = worlds[i]
for i, name in enumerate(species_list):
xs, ys, zs = [], [], []
particles = world.list_particles_exact(Species(name))
if max_count is not None and len(particles) > max_count:
particles = random.sample(particles, max_count)
for pid, p in particles:
pos = p.position()
xs.append(pos[0])
ys.append(pos[1])
zs.append(pos[2])
scatters[i]._offsets3d = juggle_axes(xs, ys, zs, 'z')
if rotate is not None:
ax.elev += rotate[0]
ax.azim += rotate[1]
fig.canvas.draw()
def convert_2dpath_to_3dpath(self, z=None, zdir='z'):
x1 = []
y1 = []
z1 = []
norms = []
idxset = []
idxbase = 0
if zdir == 'x':
norm = np.array([1., 0, 0.])
elif zdir == 'y':
norm = np.array([0., 1, 0.])
else:
norm = np.array([0., 0, 1.])
xyzlist = []
for points in self._segments3d:
points = np.vstack(points)
xyzlist.append((
points[:, 0],
points[:, 1],
points[:, 2],
))
# xyzlist = [(points[:,0], points[:, 1], points[:,2])
# for points in self._segments3d]
for v0, v1, v2 in xyzlist:
x1.append(v0)
y1.append(v1)
idxset.append(np.arange(len(v0)) + idxbase)
z1.append(v2)
norms.append(np.hstack([norm] * len(v0)))
idxbase = len(v0) + idxbase
x1 = np.hstack(x1)
y1 = np.hstack(y1)
z1 = np.hstack(z1)
norms = np.hstack(norms).reshape(-1, 3)
X3D, Y3D, Z3D = juggle_axes(x1, y1, z1, zdir)
# does norm may mean anything, but let's leave it...
self._gl_3dpath = [X3D, Y3D, Z3D, norms, idxset]
def plot_object2(phys_obj, ax=None):
"""Takes an instance of the physical object class, and plots it's current
X, Y, and Z values such that a matplotlib figure can update whatever group
of particles in the figure that correspond to phys_obj. This function doesn't
return anything, rather it saves the particle data in <obj>.pdata. This
means that any time a matplotlib figure object needs data, just give it
<obj>.pdata.
"""
o = phys_obj
if (o.pdata == None) and (ax == None):
raise SyntaxError(
"Didn't supply an axis, but there is no particle data embedded in the "
+ "object to work off of. Please fix either issue.")
if (o.pdata != None) and (ax == None):
# the 3D way for doing <matplotlib_line>.set_data(...)
o.pdata._offsets3d = juggle_axes(o.X, o.Y, o.Z, 'z')
else:
# initialize matplotlib figure entity, and update <obj>.pdata with
# the returned particle data object.
o.pdata = ax.scatter(o.X,o.Y,o.Z,c='y')
def update(self, i):
xs, ys, zs = next(self.data)
self.scat._offsets3d = juggle_axes(xs, ys, zs, 'z')
return self.scat,
def render(particles, a, filename, cleanup=True):
global artist_particles, artist_text, ax_render
# Print out progress message
masterprint('Rendering and saving image "{}" ...'.format(filename))
# Switch to the render figure
plt.figure(fig_render_nr)
# Attach missing extension to filename
if not filename.endswith('.png'):
filename += '.png'
# Extract particle data
N = particles.N
N_local = particles.N_local
# Update particle positions on the figure
artist_particles._offsets3d = juggle_axes(particles.posx_mv[:N_local],
particles.posy_mv[:N_local],
particles.posz_mv[:N_local],
zdir='z')
# The particle size on the figure.
# The size is chosen such that the particles stand side by side in a
# homogeneous unvierse (more or less).
size = 1000*np.prod(fig_render.get_size_inches())/N**ℝ[2/3]
# The particle alpha on the figure.
# The alpha is chosen such that in a homogeneous unvierse, a column
# of particles have a collective alpha of 1 (more or less).
alpha = N**ℝ[-1/3]
# Alpha values lower than alpha_min appear completely invisible.
# Allow no alpha values lower than alpha_min. Shrink the size to
# make up for the large alpha.
alpha_min = 0.0059
if alpha < alpha_min:
size *= alpha/alpha_min
alpha = alpha_min
# Apply size and alpha
artist_particles.set_sizes([size])
artist_particles.set_alpha(alpha)
# Print the current scale factor on the figure
if master:
artist_text.set_text('')
a_str = significant_figures(a, 4, 'LaTeX')
artist_text = ax_render.text(+0.25*boxsize,
-0.3*boxsize,
0,
'$a = {}$'.format(a_str),
fontsize=16,
)
# Make the text color black or white, dependent on the bgcolor
if sum(bgcolor) < 1:
artist_text.set_color('white')
else:
artist_text.set_color('black')
# Update axis limits if a boxsize were explicitly passed
if boxsize:
ax_render.set_xlim(0, boxsize)
ax_render.set_ylim(0, boxsize)
ax_render.set_zlim(0, boxsize)
# If running with a single process, save the render, make a call to
# update the liverender and then return.
if nprocs == 1:
plt.savefig(filename, bbox_inches='tight', pad_inches=0)
masterprint('done')
update_liverender(filename)
return
# Running with multiple processes.
# Each process save its rendered part to disk.
# First, make a temporary directory to hold the render parts.
dirname = os.path.dirname(filename)
basename = os.path.basename(filename)
renderparts_dirname = '{}/.renderparts'.format(dirname)
renderpart_filename = '{}/{}.png'.format(renderparts_dirname, rank)
if master:
os.makedirs(renderparts_dirname, exist_ok=True)
# Now save the render parts, including transparency
Barrier()
plt.savefig(renderpart_filename,
bbox_inches='tight',
pad_inches=0,
transparent=True,
)
Barrier()
# The master process combines the parts using ImageMagick
if master:
# List of all newly created renderparts
renderpart_filenames = ['{}/{}.png'.format(renderparts_dirname, r) for r in range(nprocs)]
# Combine all render parts into one,
# with the correct background color and no transparency.
subprocess.call([paths['convert']] + renderpart_filenames
+ ['-background', 'rgb({}%, {}%, {}%)'.format(100*bgcolor[0],
100*bgcolor[1],
100*bgcolor[2]),
'-layers', 'flatten', '-alpha', 'remove', filename])
# Remove the temporary directory, if cleanup is requested
if cleanup:
shutil.rmtree(renderparts_dirname)
masterprint('done')
# Update the live render (local and remote)
update_liverender(filename)
def update_sctr(handle, newdata):
if is_3d:
handle._offsets3d = juggle_axes(*newdata.T, 'z')
else:
handle.set_offsets(newdata)
def plot_frame(i): plot._offsets3d = art3d.juggle_axes(*zip(*self.all_data[i]), "z")
def update(self, k, kObs, E=None, P=None, **kwargs):
"""Plot forecast state"""
if self.skip_plotting(): return
stats = self.stats
mu = stats.mu
m = self.xx.shape[1]
ii, wrap = setup_wrapping(m)
#####################
# Dashboard
#####################
if hasattr(self, 'fga') and plt.fignum_exists(self.fga.number):
plt.figure(self.fga.number)
t = self.setup.t.tt[k]
self.fga.suptitle('t[k]={:<5.2f}, k={:<d}'.format(t, k))
# --------------
# Amplitude plot
# --------------
if hasattr(self, 'ax'):
# Truth
self.lx.set_ydata(wrap(self.xx[k]))
# Analysis
self.lmu.set_ydata(wrap(mu[k]))
# Forecast
if kObs is None:
self.fcast.set_visible(False)
else:
self.fcast.set_ydata(wrap(mu.f[kObs]))
self.fcast.set_visible(True)
# Ensemble/Confidence
if hasattr(self, 'lE'):
w = stats.w[k]
wmax = w.max()
for i, l in enumerate(self.lE):
l.set_ydata(wrap(E[i]))
l.set_alpha((w[i] / wmax).clip(0.1))
else:
self.CI.remove()
self.CI = self.ax.fill_between(ii, \
wrap(mu[k] - self.ks*sqrt(stats.var[k])), \
wrap(mu[k] + self.ks*sqrt(stats.var[k])), alpha=0.4)
plt.sca(self.ax)
if hasattr(self, 'obs'):
try:
self.obs.remove()
except Exception:
pass
if kObs is not None:
self.obs = self.yplot(self.yy[kObs])
update_ylim([mu[k], self.xx[k]], self.ax)
# --------------
# Correlation plot.
# --------------
if hasattr(self, 'axC'):
if E is not None:
C = np.cov(E, rowvar=False)
else:
assert P is not None
C = P.full if isinstance(P, CovMat) else P
C = C.copy()
std = sqrt(diag(C))
C /= std[:, None]
C /= std[None, :]
C2 = np.ma.masked_where(self.mask, C)[::-1]
self.mesh.set_array(C2.ravel())
# Auto-corr function
acf = circulant_ACF(C)
ac6 = circulant_ACF(C, do_abs=True)
self.l5.set_ydata(acf)
self.l6.set_ydata(ac6)
update_ylim([acf, ac6], self.ax5)
# --------------
# Spectral error plot
# --------------
if self.do_spectral_error:
msft = abs(stats.umisf[k])
sprd = stats.svals[k]
self.lew.set_ydata(sprd)
self.lmf.set_ydata(msft)
update_ylim(msft, self.ax2)
plot_pause(0.01)
#####################
# Diagnostics
#####################
if hasattr(self, 'fgd') and plt.fignum_exists(self.fgd.number):
plt.figure(self.fgd.number)
chrono = self.setup.t
# Indices with shift
kkU = arange(chrono.pK) + max(0, k - chrono.pK)
ttU = chrono.tt[kkU]
# Indices for Obs-times
kkA = kkU[0] <= chrono.kkObs
kkA &= chrono.kkObs <= kkU[-1]
def update_axd(ax, dict_of_dicts):
ax.set_xlim(ttU[0], ttU[0] + 1.1 * (ttU[-1] - ttU[0]))
for name, d in dict_of_dicts.items():
stat = getattr(stats, name)
if isinstance(stat, np.ndarray):
tt_ = chrono.ttObs[kkA]
d['data'] = stat[kkA]
if d.get('step', False):
# Creat "step"-style graph
d['data'] = d['data'].repeat(2)
tt_ = tt_.repeat(2)
right = tt_[
-1] # use ttU[-1] for continuous extrapolation
tt_ = np.hstack([ttU[0], tt_[0:-2], right])
elif stat.dtype == 'bool':
# Creat "impulse"-style graph
tt_ = tt_.repeat(3)
d['data'] = d['data'].repeat(3)
tt_[2::3] = nan
d['data'][::3] = False
else:
tt_ = ttU
if stat.store_u:
d['data'] = stat[kkU]
else: # store .u manually
tmp = stat[k]
if self.prev_k != (k - 1):
# Reset display
d['data'][:] = nan
if k >= chrono.pK:
# Rolling display
d['data'] = roll_n_sub(d['data'], tmp, -1)
else:
# Initial display: append
d['data'][k] = tmp
d['data'] = d['transf'](d['data'])
d['h'].set_data(tt_, d['data'])
def rm_absent(ax, dict_of_dicts):
for name in list(dict_of_dicts):
d = dict_of_dicts[name]
if not np.any(np.isfinite(d['data'])):
d['h'].remove()
del dict_of_dicts[name]
if dict_of_dicts:
ax.legend(loc='upper left')
update_axd(self.ax_d1, self.d1)
update_axd(self.ax_d2, self.d2)
#if k%(chrono.pK/5) <= 1:
update_ylim([d['data'] for d in self.d1.values()],
self.ax_d1,
bottom=0,
cC=0.2,
cE=0.9)
update_ylim([d['data'] for d in self.d2.values()],
self.ax_d2,
Max=4,
Min=-4,
cC=0.3,
cE=0.9)
# Check which diagnostics are present
if (not self.has_checked_presence) and (k >= chrono.kkObs[0]):
rm_absent(self.ax_d1, self.d1)
rm_absent(self.ax_d2, self.d2)
self.has_checked_presence = True
plot_pause(0.01)
#####################
# 3D phase space
#####################
if hasattr(self, 'fg3') and plt.fignum_exists(self.fg3.number):
plt.figure(self.fg3.number)
def update_tail(handle, newdata):
handle.set_data(newdata[:, 0], newdata[:, 1])
handle.set_3d_properties(newdata[:, 2])
# Reset
if self.prev_k != (k - 1):
self.tail_xx[:] = self.xx[k, :3]
if hasattr(self, 'sE'):
self.tail_E[:] = E[:, :3]
else:
self.tail_mu[:] = mu[k, :3]
# Truth
self.sx._offsets3d = juggle_axes(*tp(self.xx[k, :3]), 'z')
self.tail_xx = roll_n_sub(self.tail_xx, self.xx[k, :3])
update_tail(self.ltx, self.tail_xx)
if hasattr(self, 'sE'):
# Ensemble
self.sE._offsets3d = juggle_axes(*E.T[:3], 'z')
clrs = self.sE.get_facecolor()[:, :3]
w = stats.w[k]
alpha = (w / w.max()).clip(0.1, 0.4)
if len(clrs) == 1: clrs = clrs.repeat(len(w), axis=0)
self.sE.set_color(np.hstack([clrs, alpha[:, None]]))
self.tail_E = roll_n_sub(self.tail_E, E[:, :3])
for n in range(E.shape[0]):
update_tail(self.ltE[n], self.tail_E[:, n, :])
self.ltE[n].set_alpha(alpha[n])
else:
# Mean
self.smu._offsets3d = juggle_axes(*tp(mu[k, :3]), 'z')
self.tail_mu = roll_n_sub(self.tail_mu, mu[k, :3])
update_tail(self.ltmu, self.tail_mu)
plot_pause(0.01)
# For animation:
#self.fg3.savefig('figs/l63_' + str(k) + '.png',format='png',dpi=70)
#####################
# Weight histogram
#####################
if kObs and hasattr(self, 'fgh') and plt.fignum_exists(
self.fgh.number):
plt.figure(self.fgh.number)
axh = self.axh
_ = [b.remove() for b in self.hst]
w = stats.w[k]
N = len(w)
wmax = w.max()
bins = exp(linspace(log(1e-5 / N), log(1), int(N / 20)))
counted = w > bins[0]
nC = np.sum(counted)
nn, _, pp = axh.hist(w[counted], bins=bins, color='b')
self.hst = pp
#thresh = '#(w<$10^{'+ str(int(log10(bins[0]*N))) + '}/N$ )'
axh.set_title('N: {:d}. N_eff: {:.4g}. Not shown: {:d}. '.\
format(N, 1/(w@w), N-nC))
update_ylim([nn], axh, cC=True)
plot_pause(0.01)
#####################
# User-defined state
#####################
if hasattr(self, 'fgu') and plt.fignum_exists(self.fgu.number):
plt.figure(self.fgu.number)
self.setter_truth(self.xx[k])
self.setter_mean(mu[k])
plot_pause(0.01)
# Trackers
self.prev_k = k
def plot_frame(self, i=0):
f_data = self.data[i]
self.plot._offsets3d = art3d.juggle_axes(*zip(*f_data), "z")
bbox = BBox(*zip(*f_data))
bbox.equal_3d_axes(self.ax, zoom=2)
self._frame = i
def update_plot(num, positions, body_lines, ani_lines, sc):
for line, (sp, ep) in zip(ani_lines, body_lines):
line._verts3d = positions[[sp, ep], :, num].T.tolist()
sc._offsets3d = juggle_axes(positions[:, 0, num], positions[:, 1, num],
positions[:, 2, num], 'z')
return sc
def run(num, data, points):
# update the data
print num
print len(data[num][0])
points._offsets3d = juggle_axes(data[num][0],data[num][1],data[num][2], 'z')
return range(num-1)
def update(frame):
indicesdict = {}
alts = []
lons = []
lats = []
global annolist
i = 0
for i, plane in enumerate(time_slices[frame]):
lon, lat = mymap(plane.lon, plane.lat)
lons.append(int(lon))
lats.append(int(lat))
alts.append(int(plane.altitude))
indicesdict[plane.hex] = i
time_text.set_text(
time.strftime(
"%F %H:%M:%S",
time.localtime(first_time + (frame * args.sec_per_frame))))
#
# Remove old texts from matplotlib's internal state
#
for anno in annolist:
if anno:
ax.texts.remove(anno)
anno = None
annolist = []
if args.display_hex or args.display_flt:
for lastpoint in indicesdict:
plane = time_slices[frame][indicesdict[lastpoint]]
if args.display_hex and args.display_flt:
txt = plane.hex + "/" + plane.flight
elif args.display_hex:
txt = plane.hex
else:
txt = plane.flight
x, y = mymap(plane.lon, plane.lat)
z = plane.altitude
annolist.append(ax.text(x, y, z, txt, fontsize=8))
scat._offsets3d = juggle_axes(lons, lats, alts, 'z')
if args.rotate:
ax.view_init(30, (frame + 270) % 360)
drawableslst = []
drawableslst.append(scat)
drawableslst.append(time_text)
for anno in annolist:
if anno:
drawableslst.append(anno)
if args.debug:
print(
frame,
time.strftime(
"%F %H:%M:%S",
time.localtime(first_time + (frame * args.sec_per_frame))),
len(time_slices[frame]), len(indicesdict), len(annolist),
len(ax.texts))
return tuple(drawableslst)