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base repository: MinaKh/Khoei_2017_PLoSCB
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head repository: laurentperrinet/Khoei_2017_PLoSCB
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Commits on Feb 9, 2021

  1. Update MotionParticlesFLE.py 

    adapting to changes in matplotlib etc
    @laurentperrinet
    laurentperrinet authored Feb 9, 2021
    Copy the full SHA
    1971e39 View commit details
Showing with 27 additions and 27 deletions.
  1. +27 −27 scripts/MotionParticlesFLE.py
54 changes: 27 additions & 27 deletions scripts/MotionParticlesFLE.py
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Original file line number Diff line number Diff line change
@@ -307,7 +307,7 @@ def prediction(particles, N_frame, D_V, D_x, width, v_prior):
"""
N = particles.shape[1]
particles_out = particles.copy()
if particles.ndim is 3:
if particles.ndim == 3:
for i_frame in range(particles.shape[2]):
particles_out[:, :, i_frame] = prediction(particles[:, :, i_frame], N_frame, D_V=D_V, D_x=D_x, width=width, v_prior=v_prior)
else:
@@ -467,8 +467,8 @@ def show_particles(particles, image=None, N_X=N_X, N_Y=N_Y, N_show=N_show, alpha
if fig is None: fig = pylab.figure(figsize=(fig_width, fig_width * np.float(N_Y) / N_X))
# Add an a axes with axes rect [left, bottom, width, height] where all quantities are in fractions of figure width and height.
# a = fig.add_axes((border, border * np.float(N_Y) / N_X, 1.-2*border, 1.-2*border * np.float(N_Y) / N_X))
if a is None: a = fig.add_axes((border, border, 1.-2*border, 1.-2*border))#, frameon=False, axisbg='w')
a.axis(c='b', lw=2)
if a is None: a = fig.add_axes((border, border, 1.-2*border, 1.-2*border))#, frameon=False, facecolor='w')
#a.axis(lw=2)

ywidth = width * np.float(N_Y) / N_X
opts = {'vmin':vmin, 'vmax':vmax, 'interpolation':'nearest', 'extent':(-width/2, width/2, -ywidth/2., ywidth/2.), 'aspect':'auto'} # 'origin':'lower',
@@ -552,14 +552,14 @@ def show_particles(particles, image=None, N_X=N_X, N_Y=N_Y, N_show=N_show, alpha
if axis_label : pylab.xlabel(r'X axis'); pylab.ylabel(r'Y axis')
# else: pylab.axis([-1, 1, -1, 1])
if inset and particles.ndim == 2:
# a_inset = fig.add_axes([.8, .8, .195, .195], axisbg='k', polar=True)
a_inset = fig.add_axes([0, 0, .3, .3], axisbg='k', polar=True)
# a_inset = fig.add_axes([.8, .8, .195, .195], facecolor='k', polar=True)
a_inset = fig.add_axes([0, 0, .3, .3], facecolor='k', polar=True)
v_hist, v_r_edges, v_theta_edges = vel_readout(particles_full, display=False)
N_v, N_theta, v_max = v_r_edges.size, v_theta_edges.size, v_r_edges.max()
[V_r_edges, V_theta_edges] = np.mgrid[v_max/N_v:v_max:1j*N_v,
(-np.pi+ np.pi/N_theta):(np.pi+ np.pi/N_theta):1j*N_theta]
a_inset.pcolormesh(V_theta_edges, V_r_edges, v_hist, cmap=pylab.bone(),
vmin=0., vmax=v_hist.max(), edgecolor='none')
vmin=0., vmax=v_hist.max(), edgecolor='none', shading='auto')
# draw a cross in the center
from matplotlib.collections import LineCollection
# sequence of r, theta segments (we are in polar coordinates)
@@ -774,7 +774,7 @@ def vel_readout(particles, N_v=N_v, N_theta=N_theta, v_max=v_max, display=True,

if display:
fig = pylab.figure(figsize=figsize)
a = pylab.axes([0.1, 0.1, 0.8, 0.8], polar=True, axisbg='w')
a = pylab.axes([0.1, 0.1, 0.8, 0.8], polar=True, facecolor='w')
if direction:
theta = .5*(v_theta_edges[:-1]+v_theta_edges[1:])
prob = v_hist.sum(axis=0)
@@ -785,7 +785,7 @@ def vel_readout(particles, N_v=N_v, N_theta=N_theta, v_max=v_max, display=True,
[V_r_edges, V_theta_edges] = np.mgrid[v_max/N_v:v_max:1j*N_v,
(-np.pi+ np.pi/N_theta):(np.pi+ np.pi/N_theta):1j*N_theta]
# [V_r_edges, V_theta_edges] = mgrid[v_max/N_v:v_max:1j*N_v, -pi:pi:1j*N_theta]
a.pcolormesh(V_theta_edges, V_r_edges, v_hist, cmap=pylab.bone(), vmin=0., vmax=v_hist.max())#, edgecolor='k')
a.pcolormesh(V_theta_edges, V_r_edges, v_hist, cmap=pylab.bone(), vmin=0., vmax=v_hist.max(), shading='auto')#, edgecolor='k')
return fig
else:
return v_hist, v_r_edges, v_theta_edges
@@ -818,7 +818,7 @@ def spatial_readout(particles, N_X=N_X, N_Y=N_Y, N_quant_X=N_quant_X, N_quant_Y=
N_quant_Y = int(N_quant_X * np.float(N_Y) / N_X) # quantisation for position histograms
N_frame = None
if particles.ndim == 3: N_frame = particles.shape[2]
if (N_quant_Y is 1) and not (N_frame is None) :
if (N_quant_Y == 1) and not (N_frame is None) :
v_hist = np.zeros((N_quant_X, N_quant_T))
v_hist_u = np.zeros((N_quant_X, N_quant_T))
x_edges = np.linspace(-width/2, width/2, N_quant_X+1)
@@ -841,7 +841,7 @@ def spatial_readout(particles, N_X=N_X, N_Y=N_Y, N_quant_X=N_quant_X, N_quant_Y=
# ywidth = width * np.float(N_Y) / N_X
x_edges = np.linspace(-width/2, width/2, N_quant_X+1)
y_edges = np.linspace(-width/2 * np.float(N_Y)/N_X, width/2 * np.float(N_Y)/N_X, N_quant_Y+1)
if hue and display and not (N_quant_Y is 1):
if hue and display and not (N_quant_Y == 1):
N_theta_=3 # the 3 RGB channels
u = particles[3, ...].ravel()
v = particles[2, ...].ravel()
@@ -860,30 +860,30 @@ def spatial_readout(particles, N_X=N_X, N_Y=N_Y, N_quant_X=N_quant_X, N_quant_Y=
v_hist /= v_hist.sum()

if display:
if N_quant_Y is 1 and (N_frame is None) : # PDF of x at some time
if (N_quant_Y == 1) and (N_frame is None) : # PDF of x at some time
if fig is None: fig = pylab.figure(figsize=(fig_width, fig_width * np.float(N_Y) / N_X))
if a is None:
a = fig.add_subplot(1, 1, 1)
a.axis(c='b', lw=2)
# a.axis(lw=2)
a.plot(.5*x_edges[:-1] + .5*x_edges[1:], v_hist.ravel())
a.set_ylim([0., v_hist.max()])
# a.axis([-width/2, width/2, -width/2 * np.float(N_Y)/N_X, width/2 * np.float(N_Y)/N_X])
elif N_quant_Y is 1 and not (N_frame is None) : # X-T plot
elif (N_quant_Y == 1) and not (N_frame is None) : # X-T plot
if fig is None: fig = pylab.figure(figsize=(fig_width * np.float(N_quant_T) / N_X, fig_width))
# if a is None: a = fig.add_subplot(1, 1, 1)
if a is None:
a = []
a.append(fig.add_axes([0.1, 0.07, .86, .41]))
a.append(fig.add_axes([0.1, 0.57, .86, .41]))
for ax in a: ax.axis(c='b', lw=2)
#for ax in a: ax.axis(lw=2)
# time, (.5*x_edges[:-1] + .5*x_edges[1:]), print (time[np.newaxis, :].shape)
x_middle = .5*(x_edges[1:] + x_edges[:-1])
v_hist /= v_hist.max(axis=0)[np.newaxis, :]
Time, X = np.meshgrid(np.linspace(0, 1, N_quant_T), x_edges_)# .5*(x_edges_[:-1]+x_edges_[1:]))
a[0].pcolormesh(Time, X, v_hist, cmap=pylab.cm.Blues, vmin=0., vmax=v_hist.max())#, edgecolor='k')#(.1, .1, .1, .6))
a[0].pcolormesh(Time, X, v_hist, cmap=pylab.cm.Blues, vmin=0., vmax=v_hist.max(), shading='auto')#, edgecolor='k')#(.1, .1, .1, .6))
Time, U = np.meshgrid(np.linspace(0, 1, N_quant_T), u_edges_)# .5*(u_edges_[:-1]+u_edges_[1:]))
v_hist_u /= v_hist_u.max(axis=0)[np.newaxis, :]
a[1].pcolormesh(Time, U, v_hist_u, cmap=pylab.cm.Reds, vmin=0., vmax=v_hist_u.max())#, edgecolor='k')#(.1, .1, .1, .6))
a[1].pcolormesh(Time, U, v_hist_u, cmap=pylab.cm.Reds, vmin=0., vmax=v_hist_u.max(), shading='auto')#, edgecolor='k')#(.1, .1, .1, .6))
if ruler:
a[0].plot([0, 1], [-1, 1], 'b--', lw=2)
for i, min_y, max_y in zip(range(2), [-1, -1.4], [1, 1.4]):
@@ -901,14 +901,14 @@ def spatial_readout(particles, N_X=N_X, N_Y=N_Y, N_quant_X=N_quant_X, N_quant_Y=
if fig is None: fig = pylab.figure(figsize=(fig_width, fig_width * np.float(N_quant_Y) / N_quant_X))
if a is None:
a = fig.add_axes([0., 0., 1., 1.])
a.axis(c='b', lw=2)
#a.axis(lw=2)

if hue :
# TODO : overlay image and use RGB(A) information
a.imshow(np.fliplr(np.rot90(v_hist/v_hist.max(),3)), interpolation='nearest', origin='lower',
extent=(-width/2, width/2, -width/2 * np.float(N_quant_Y)/N_quant_X, width/2 * np.float(N_quant_Y)/N_quant_X))#
else:
a.pcolormesh(x_edges, y_edges, v_hist.T, cmap=pylab.bone(), vmin=0., vmax=v_hist.max())#, edgecolor='k')
a.pcolormesh(x_edges, y_edges, v_hist.T, cmap=pylab.bone(), vmin=0., vmax=v_hist.max(), shading='auto')#, edgecolor='k')
a.axis([-width/2, width/2, -width/2 * np.float(N_quant_Y)/N_quant_X, width/2 * np.float(N_quant_Y)/N_quant_X])

return fig, a
@@ -1177,7 +1177,7 @@ def make_frames(z, particles, N_X=N_X, N_Y=N_Y, N_quant_X=N_quant_X, N_quant_Y=N
im_ = z[:, :, i_frame % N_frame]
im_ = np.fliplr(im_).T
# toimage(im_, cmin=0., cmax=1.).save(fname)
imageio.imwrite(fname, im_)
imageio.imwrite(fname, (im_*255).astype(np.uint8))

else: # TODO: use a switch to choose the type of visualization?
fig_width = 10
@@ -1809,16 +1809,16 @@ def figure_4panels(mat, titles):
vmin = mat[: , :, 0].min()
fig = pylab.figure(figsize=(12, 8))
a1 = fig.add_subplot(221)
mapable = a1.pcolormesh(mat[: , :, 0], vmin=vmin, vmax=vmax)#, edgecolors='k')
mapable = a1.pcolormesh(mat[: , :, 0], vmin=vmin, vmax=vmax, shading='auto')#, edgecolors='k')
pylab.axis('tight')
a2 = fig.add_subplot(222)
a2.pcolormesh(mat[: , :, 1], vmin=vmin, vmax=vmax)#, edgecolors='k')
a2.pcolormesh(mat[: , :, 1], vmin=vmin, vmax=vmax, shading='auto')#, edgecolors='k')
pylab.axis('tight')
a3 = fig.add_subplot(223)
a3.pcolormesh(mat[: , :, 2], vmin=vmin, vmax=vmax)#, edgecolors='k')
a3.pcolormesh(mat[: , :, 2], vmin=vmin, vmax=vmax, shading='auto')#, edgecolors='k')
pylab.axis('tight')
a4 = fig.add_subplot(224)
a4.pcolormesh(mat[: , :, 3], vmin=vmin, vmax=vmax)#, edgecolors='k')
a4.pcolormesh(mat[: , :, 3], vmin=vmin, vmax=vmax, shading='auto')#, edgecolors='k')
pylab.axis('tight')

for i_a, ax in enumerate([a1, a2, a3, a4]):
@@ -1844,7 +1844,7 @@ def figure_4panels(mat, titles):

height = pylab.rcParams['figure.subplot.top']-pylab.rcParams['figure.subplot.bottom']
# print [0.91, pylab.rcParams['figure.subplot.bottom'] + height/4., .025, height/2. ]
a5 = pylab.axes([0.91, pylab.rcParams['figure.subplot.bottom'] + height/4., .025, height/2. ], axisbg='w') # [l, b, w, h]
a5 = pylab.axes([0.91, pylab.rcParams['figure.subplot.bottom'] + height/4., .025, height/2. ], facecolor='w') # [l, b, w, h]
pylab.colorbar(mapable, cax=a5, ax=a1, format='%.2f')
return fig
# print tracking.min(), tracking.max(), tracking.mean()
@@ -1908,10 +1908,10 @@ def figure_4panels(mat, titles):

fig = pylab.figure(figsize=(5, 10))
a1 = fig.add_subplot(211)
mapable = a1.pcolormesh(tracking_vel)#, edgecolors='k')
mapable = a1.pcolormesh(tracking_vel, shading='auto')#, edgecolors='k')
pylab.axis('tight')
a2 = fig.add_subplot(212)
a2.pcolormesh(bias_vel)#, edgecolors='k')
a2.pcolormesh(bias_vel, shading='auto')#, edgecolors='k')
pylab.axis('tight')

for i_a, ax in enumerate([a1, a2]):
@@ -1937,7 +1937,7 @@ def figure_4panels(mat, titles):

height = pylab.rcParams['figure.subplot.top']-pylab.rcParams['figure.subplot.bottom']
# print [0.91, pylab.rcParams['figure.subplot.bottom'] + height/4., .025, height/2. ]
a5 = pylab.axes([0.91, pylab.rcParams['figure.subplot.bottom'] + height/4., .025, height/2. ], axisbg='w') # [l, b, w, h]
a5 = pylab.axes([0.91, pylab.rcParams['figure.subplot.bottom'] + height/4., .025, height/2. ], facecolor='w') # [l, b, w, h]
pylab.colorbar(mapable, cax=a5, ax=a1, format='%.2f')
pylab.savefig(figname_statespace_phases)