def vectorization(N_theta=N_theta,
N_azimuth=N_azimuth,
N_eccentricity=N_eccentricity,
N_phase=N_phase,
N_X=N_X,
N_Y=N_Y,
rho=rho,
ecc_max=.8,
B_sf=.4,
B_theta=np.pi / N_theta / 2,
figure_type='',
save=False):
retina = np.zeros((N_theta, N_azimuth, N_eccentricity, N_phase, N_X * N_Y))
parameterfile = 'https://raw.githubusercontent.com/bicv/LogGabor/master/default_param.py'
lg = LogGabor(parameterfile)
lg.set_size((N_X, N_Y))
# params = {'sf_0': .1, 'B_sf': lg.pe.B_sf,
# 'theta': np.pi * 5 / 7., 'B_theta': lg.pe.B_theta}
# phase = np.pi/4
# edge = lg.normalize(lg.invert(lg.loggabor(
# N_X/3, 3*N_Y/4, **params)*np.exp(-1j*phase)))
for i_theta in range(N_theta):
for i_azimuth in range(N_azimuth):
for i_eccentricity in range(N_eccentricity):
ecc = ecc_max * (1 / rho)**(N_eccentricity - i_eccentricity)
r = np.sqrt(N_X**2 + N_Y**2) / 2 * ecc # radius
sf_0 = 0.5 * 0.03 / ecc
x = N_X/2 + r * \
np.cos((i_azimuth+(i_eccentricity % 2)*.5)*np.pi*2 / N_azimuth)
y = N_Y/2 + r * \
np.sin((i_azimuth+(i_eccentricity % 2)*.5)*np.pi*2 / N_azimuth)
for i_phase in range(N_phase):
params = {
'sf_0': sf_0,
'B_sf': B_sf,
'theta': i_theta * np.pi / N_theta,
'B_theta': B_theta
}
phase = i_phase * np.pi / 2
# print(r, x, y, phase, params)
retina[i_theta, i_azimuth, i_eccentricity,
i_phase, :] = lg.normalize(
lg.invert(
lg.loggabor(x, y, **params) *
np.exp(-1j * phase))).ravel()
if figure_type == 'retina':
FIG_WIDTH = 10
fig, ax = plt.subplots(figsize=(FIG_WIDTH, FIG_WIDTH))
for i_theta in range(N_theta):
for i_azimuth in range(N_azimuth):
for i_eccentricity in range(N_eccentricity):
env = np.sqrt(retina[i_theta, i_azimuth, i_eccentricity,
0, :]**2 +
retina[i_theta, i_azimuth, i_eccentricity,
1, :]**2).reshape((N_X, N_Y))
ax.contourf(env,
levels=[env.max() / 1.2,
env.max() / 1.00001],
lw=1,
colors=[plt.cm.viridis(i_theta / (N_theta))],
alpha=.1)
fig.suptitle('Tiling of visual space using the retinal filters')
ax.set_xlabel(r'$Y$')
ax.set_ylabel(r'$X$')
ax.axis('equal')
if save: plt.savefig('retina_filter.pdf')
plt.tight_layout()
return fig, ax
elif figure_type == 'colliculus':
FIG_WIDTH = 10
fig, ax = plt.subplots(figsize=(FIG_WIDTH, FIG_WIDTH))
for i_azimuth in range(N_azimuth):
for i_eccentricity in range(N_eccentricity):
env = np.sqrt(colliculus[i_azimuth,
i_eccentricity, :]**2.5).reshape(
(N_X, N_Y))
#ax.contour(colliculus[i_azimuth, i_eccentricity, :].reshape((N_X, N_Y)), levels=[env.max()/2], lw=1, colors=[plt.cm.viridis(i_theta/(N_theta))])
ax.contourf(
env,
levels=[env.max() / 1.2,
env.max() / 1.00001],
lw=1,
colors=[plt.cm.viridis(i_eccentricity / (N_eccentricity))],
alpha=.1)
fig.suptitle('Tiling of visual space using energy')
ax.set_xlabel(r'$Y$')
ax.set_ylabel(r'$X$')
ax.axis('equal')
plt.tight_layout()
if save: plt.savefig('colliculus_filter.pdf')
return fig, ax
else:
return retina
def generate_gabors_coordinates(theta, params, N_X, N_Y, centers_coordinates,
B_theta=15, sf_0=.05, B_sf=.5,
distrib_size=8, grid_res=3,
on_thresh=.1, off_thresh=-.1,
verbose=True):
'''
Given some gabor parameters, a set of coordinates for centering gabors, returns a set of
coordinates for filters belonging into the gabors
Params :
theta : gabor theta angle
params : the default parameters dictionnary for the gabor generation
N_X, N_Y : Gabor size, usually the same as the video
centers_coordinates : a 2D array giving the centers of each gabor
B_theta, sf_0, B_sf : Parameters for the LogGabor shape
B_theta is the opening of the gabor,
sf_0 is the spatial frequency
b_sf is the bandwidth frequency
distrib_size : the size of each group of filters, in image coordinates
grid_res : resolution of the group of filters, passed in a np.mgrid
on_thresh, off_thresh : threshold at which a filter is selected to
be on/off, by scanning the Gabor phi-space
verbose : display the filter size as a sanity check
'''
xs = centers_coordinates[0]
ys = centers_coordinates[1]
nbr_gabors = len(xs)
N_X = int(N_X)
N_Y = int(N_Y)
N_phase = 2
lg = LogGabor(params)
lg.set_size((N_X, N_Y))
B_theta = B_theta / 180 * np.pi
params = {'sf_0': sf_0, 'B_sf': B_sf, 'B_theta': B_theta}
params.update(theta=theta)
phi = np.zeros((1, N_phase, N_X, N_Y))
filters_per_gab = []
for gab in range(nbr_gabors):
x = xs[gab]
y = ys[gab]
for i_phase in range(N_phase):
phase = i_phase * np.pi/2
kernel = lg.invert(lg.loggabor(
x, y, **params)*np.exp(-1j*phase))
phi[0, i_phase, :] = lg.normalize(kernel)
fx_min = x - distrib_size
fx_max = x + distrib_size
fy_min = y - distrib_size
fy_max = y + distrib_size
filters_coordinates = np.mgrid[fx_min:fx_max:grid_res,
fy_min:fy_max:grid_res].reshape(2, -1).T
if verbose and gab == 0:
print('Thread started !\nFilter grid shape',
filters_coordinates.shape, '\n')
filters_in_gabor = gabor_connectivity(filters=filters_coordinates,
phi=phi, theta=0, threshold=on_thresh)
off_filters_in_gabor = gabor_connectivity(filters=filters_coordinates,
phi=phi, theta=0, threshold=off_thresh, on=False)
filters_per_gab.append((filters_in_gabor, off_filters_in_gabor))
return filters_per_gab
