def plot_retino_image(mesh_path, name, tf=None, tex=None, curv=None, mask=None,
vmin=0, vmax=0):
"""Custom function to plot mesh in the case of retinotopic mapping
Parameters
----------
mesh_path: string, path of the mesh to plot
name: string, object identifier
tf: (4, 4) array
affine transformation that has to be applied to the mesh
tex: array of shape (mes.n_vertices),
texture to plot on the surface
curv: array of shape (mes.n_vertices),
curvature texture to plot on the surface
mask: array of shape (mes.n_vertices),
A mask for functional regions of interest
vmin, vmax: bounds for color clipping
"""
vertices, triangles = mesh_arrays(mesh_path)
af_coord = np.hstack((vertices, np.ones((vertices.shape[0], 1))))
if tf is not None:
af_coord = np.dot(af_coord, tf.T)
vertices = af_coord[:, :3]
x, y, z = vertices.T
# it is expected that the curvature takes values between 0 and 1
if curv is not None:
cmin = 2 * curv.min() - curv.max()
cmax = 2 * curv.max() - curv.min()
mlab.triangular_mesh(x, y, z, triangles, transparent=False, opacity=1.,
name=name, scalars=curv, colormap="bone",
vmin=cmin, vmax=cmax)
else:
mlab.triangular_mesh(x, y, z, triangles, transparent=False, opacity=1.,
name=name)
if tex is not None:
if mask is not None:
tex[mask == 0] = vmin - 1
func_mesh = mlab.pipeline.triangular_mesh_source(x, y, z,
triangles,
scalars=tex)
thresh = mlab.pipeline.threshold(func_mesh, low=vmin)
mlab.pipeline.surface(thresh, colormap="jet", vmin=vmin,
vmax=vmax, transparent=True,
opacity=.8)
mlab.scalarbar(thresh)
def plot_mesh(mesh, name, tf=None, tex=None):
""" old version -- probably deprecated
"""
vertices, triangles = mesh_arrays(mesh)
af_coord = np.hstack((vertices, np.ones((vertices.shape[0], 1))))
if tf is not None:
af_coord = np.dot(af_coord, tf.T)
vertices = af_coord[:, :3]
x, y, z = vertices.T
# show with mayavi
if tex is None:
mlab.triangular_mesh(x, y, z, triangles, transparent=False, opacity=1.,
name=name, color=(0.5, 0.5, 0.))
else:
mlab.triangular_mesh(x, y, z, triangles, transparent=False, opacity=1.,
name=name, scalars=tex)
def find_fovea(mesh, side, mask, xy):
"""Small utility that returns the assumed fovea position on a mesh
of a certain hemisphere"""
from .group_analysis import resample_from_average
REF_LEFT = np.arange(163842) == 71785
REF_RIGHT = np.arange(163842) == 129181
binary_texture = REF_LEFT if side == 'left' else REF_RIGHT
binary_texture_path = '/tmp/fovea.gii'
save_texture(binary_texture_path, binary_texture, intent='none')
subject_path = op.join(op.dirname(mesh), '..')
# resample from the average to the individual space
resampled = resample_from_average(binary_texture_path, subject_path,
side, verbose=True)
# get the vertices of the mesh
vertices, _ = mep.mesh_arrays(mesh)
point = vertices[load_texture(resampled).argmax()]
sq_dist = ((vertices - point) ** 2). sum(1)
# find the point on the mask
fovea = xy[np.argmin(sq_dist[mask])]
return fovea
def retino_template(xy, ring, wedge, mesh, mask_, verbose=False, side='left'):
""""""
if ring is None:
center = find_fovea(mesh, side, mask_, xy)
else:
center = get_ring_minimum(xy, ring, 0) # - np.pi / 2)
ecc = np.sqrt(np.sum((xy - center) ** 2, 1))
angle = - np.arctan2(xy.T[1] - center[1], xy.T[0] - center[0])
radius = np.sqrt(np.mean(ecc ** 2)) * 1.2
def retino_polar(angle, ecc, radius, scale=1.):
""""""
a1, a2, a3 = scale * np.pi *.2, scale * np.pi *.3, scale * np.pi * .4
delta = .2 * 4. / radius ** 2
corr = angle * (radius ** 2 / 4 - (ecc - radius / 2) ** 2)
angle_ = angle - delta * corr
mask = (ecc < radius) * (np.abs(angle_) < a3)
polar = np.zeros_like(angle_)
slope = np.pi / (2 * a1)
b1 = 2 * slope * a1
polar = slope * angle_
polar[angle_ > a1] = b1 - slope * angle_[angle_ > a1]
polar[angle_ > a2] = slope * angle_[angle_ > a2] - 2 * slope * (a2 - a1)
polar[angle_ < - a1] = - b1 - slope * angle_[angle_ < - a1]
polar[angle_ < - a2] = slope * (angle_[angle_ < - a2] + 2 * (a2 - a1))
polar[mask == 0] = 0
maps = {'V1v': mask * (angle_ < 0) * (angle_ > - a1),
'V1d': mask * (angle_ > 0) * (angle_ < a1),
'V2v': mask * (angle_ < -a1) * (angle_ > - a2),
'V2d': mask * (angle_ > a1) * (angle_ < a2),
'V3v': mask * (angle_ < - a2) * (angle_ > - a3),
'V3d': mask * (angle_ > a2) * (angle_ < a3),
}
return mask, polar, maps
vmin, vmax = 0., np.pi
if side == 'left':
vmin, vmax = -np.pi, 0.
best_score = - np.inf
# 2-dimensional search of the best rotation/scaling
for scale in [1.]:
for theta in np.linspace(0, 2 * np.pi, 100):
angle_ = angle + theta
angle_[angle_ > np.pi] -= 2 * np.pi
mask, polar, maps = retino_polar(angle_, ecc, radius, scale)
if mask.sum() == 0:
continue
if side == 'left':
polar -= np.pi / 2
else:
polar += np.pi / 2
weight = mask * (polar > vmin) * (polar < vmax)
score = 1. - np.sum(
weight[mask] * (wedge[mask] - polar[mask]) ** 2)/\
np.sum(weight[mask] * (wedge[mask]) ** 2)
score = np.corrcoef(wedge[mask], polar[mask])[0, 1]
if score > best_score:
best_score = score
best_polar = polar
best_theta = theta
visual_maps = maps
best_mask = mask
best_corr = np.corrcoef(wedge[mask], polar[mask])[0, 1]
if verbose:
print best_theta, best_corr
import matplotlib.pyplot as plt
plt.figure(figsize = (10, 5))
coord, tri = mep.mesh_arrays(mesh)
coord, tri = coord[mask_], tri[mask_[tri].all(1)]
tri = np.hstack((0, np.cumsum(mask_)[:-1]))[tri]
plt.subplot(1, 3, 1)
plt.tripcolor(xy.T[0], xy.T[1], tri, best_polar * best_mask,
vmin=vmin, vmax=vmax)
plt.plot(center[0], center[1], '+k', linewidth=4)
plt.subplot(1, 3, 2)
plt.tripcolor(xy.T[0], xy.T[1], tri, wedge, vmin=vmin, vmax=vmax)
plt.plot(center[0], center[1], '+k', linewidth=4)
plt.subplot(1, 3, 3)
if ring is not None:
plt.tripcolor(xy.T[0], xy.T[1], tri, ring)
plt.plot(center[0], center[1], '+k', linewidth=4)
return mask, polar, visual_maps