def display_matrices(filenames, target, hemi, surface):
from mayavi import mlab
from surfer import Brain
print '\n'.join(filenames)
for name in filenames:
try:
corrmat = sio.loadmat(name)['corrmat']
except:
try:
corrmat = np.load(name)['corrmat']
except:
try:
corrmat = np.load(name)['arr_0']
except:
try:
corrmat = np.load(name)['avgcorr']
except:
h5file = openFile(name, 'r')
corrmat = h5file.root.corrmat
corrmats.append(corrmat)
for idx, name in enumerate(filenames):
path, name = os.path.split(name)
br = Brain(target, hemi, surface, title=name + '-%d' % idx)
brains.append(br)
for brain in brains[:-1]:
mlab.sync_camera(br._f, brain._f)
mlab.sync_camera(brain._f, br._f)
br._f.on_mouse_pick(picker_callback)
mlab.show()
def display_matrices(filenames, target, hemi, surface):
from mayavi import mlab
from surfer import Brain
print '\n'.join(filenames)
for name in filenames:
try:
corrmat = sio.loadmat(name)['corrmat']
except:
try:
corrmat = np.load(name)['corrmat']
except:
try:
corrmat = np.load(name)['arr_0']
except:
try:
corrmat = np.load(name)['avgcorr']
except:
h5file = openFile(name, 'r')
corrmat = h5file.root.corrmat
corrmats.append(corrmat)
for idx, name in enumerate(filenames):
path, name = os.path.split(name)
br = Brain(target, hemi, surface, title=name+'-%d' % idx)
brains.append(br)
for brain in brains[:-1]:
mlab.sync_camera(br._f, brain._f)
mlab.sync_camera(brain._f, br._f)
br._f.on_mouse_pick(picker_callback)
mlab.show()
def reset_plane(self):
self.slicer.ipw.plane_orientation = "z_axes"
self.volume_scene.camera.position = [808.944540639155, 829.3458612118793, 775.2145331434656]
self.volume_scene.camera.focal_point = [240.5, 180.5, 1.0]
self.volume_scene.camera.view_angle = 30.0
self.volume_scene.camera.view_up = [-0.4774879890979074, -0.468564520936391, 0.7432714914396268]
self.volume_scene.camera.clipping_range = [712.7852412300919, 1723.7390002418533]
self.volume_scene.camera.compute_view_plane_normal()
self.volume_scene.render()
mlab.sync_camera(self.volume_scene, self.scatter_scene)
def init_camera(self):
all_activated = self.prediction.scene.interactor is not None and \
self.mse.scene.interactor is not None and \
self.truth.scene.interactor is not None
if not all_activated:
return
self.prediction.scene.interactor.interactor_style = \
RotateAroundZInteractor()
self.mse.scene.interactor.interactor_style = RotateAroundZInteractor()
self.truth.scene.interactor.interactor_style = \
RotateAroundZInteractor()
self.truth.scene.anti_aliasing_frames = 2
try:
self._plot_fit()
except:
traceback.print_exc()
self._plot_plume()
extent = [-150, 140, -140, 150, -85, 0]
#ax = mlab.axes(extent=extent, xlabel='', ylabel='', zlabel='')
#ax.axes.number_of_labels = 3
#ax.axes.corner_offset = 0.05
#ax.axes.label_format = '%2.0f'
#ax.label_text_property.italic = False
#ax.label_text_property.bold = False
#ax.axes.font_factor = 2
#ax.axes.ranges = [-140, 140, -140, 140, -80, 0]
#ax.axes.use_ranges = True
x, y = np.meshgrid([-140, 140], [-140, 140], indexing='ij')
mlab.surf(x, y, np.zeros_like(x, 'd'), color=(1.0, 1.0, 1.0))
mlab.sync_camera(self.prediction.mayavi_scene, self.mse.mayavi_scene)
mlab.sync_camera(self.mse.mayavi_scene, self.prediction.mayavi_scene)
mlab.sync_camera(self.mse.mayavi_scene, self.truth.mayavi_scene)
mlab.sync_camera(self.truth.mayavi_scene, self.mse.mayavi_scene)
mlab.view(
azimuth=135, elevation=135, distance=1200, roll=-120,
figure=self.prediction.mayavi_scene)
self.truth.scene.interactor.interactor_style.move(
self.truth.camera, [0, -20])
mlab.move(up=-30)
def create_graph(mesh, centroids, normals, robot_pos, traversal_tresh=35):
print("Creating Graph... num faces:", mesh.num_faces)
G = nx.Graph()
for face_idx in xrange(mesh.num_faces):
face_inclination = graph_search.MeshGraphSearch.calculate_traversal_angle(
normals[face_idx])
if traversal_tresh < face_inclination < 180 - traversal_tresh:
continue
G.add_node(face_idx)
for face_idx in list(G.nodes()):
face_vertexes = mesh.faces[face_idx]
for v in face_vertexes:
vertex_adj_faces = mesh.get_vertex_adjacent_faces(v)
for face_adjacent in vertex_adj_faces:
if face_adjacent != face_idx and G.has_node(face_adjacent):
G.add_edge(face_idx, face_adjacent, weight=1)
# print "G node_list:", len(list(G.nodes())), sorted(list(G.nodes()))
# print "G edge_list:", len(list(G.edges())), sorted(list(G.edges()))
g_centroids = [(centroids[v][0], centroids[v][1], centroids[v][2])
for v in sorted(G.nodes())]
centroid_g_dict = {i: v for i, v in enumerate(sorted(G.nodes()))}
closer_centroid_idx = mesh_planner.mesh_helper.find_closer_centroid(
g_centroids, robot_pos, force_return_closer=True)
conn_nodes = nx.node_connected_component(
G, centroid_g_dict[closer_centroid_idx])
Gconn = G.subgraph(conn_nodes).copy()
Gconn_original = Gconn.copy()
# estimate borders of the remainder graph
# border_nodes = [Gconn.info(v) for v in sorted(Gconn.nodes())]
border_centroids = []
for v in sorted(Gconn.nodes()):
if nx.degree(G, v) <= 9:
border_centroids.append(
(centroids[v][0], centroids[v][1], centroids[v][2]))
# remove nodes from graph that are near to the borders
# given a distance treshold
border_kdtree = spatial.KDTree(border_centroids)
border_tresh = 0.4
for v in list(Gconn.nodes()):
point = centroids[v]
distances, nearest_idx = border_kdtree.query([point])
obstacle_d = distances[0]
if obstacle_d <= border_tresh:
Gconn.remove_node(v)
# remove small connected components
for component in list(nx.connected_components(G)):
if len(component) < 3:
for node in component:
G.remove_node(node)
f1 = mlab.figure("Borderless graph", bgcolor=(0, 0, 0))
mlab.clf()
plot_points(Gconn, centroids, border_centroids)
f2 = mlab.figure("Original graph", bgcolor=(0, 0, 0))
mlab.clf()
plot_points(Gconn_original, centroids, border_centroids)
mlab.sync_camera(f1, f2)
mlab.show()
ctf = ColorTransferFunction()
ctf.add_rgb_point(0, 1, 1, 1)
ctf.add_rgb_point(1, 0, 0, 0.3)
vol._volume_property.set_color(ctf)
vol._ctf = ctf
vol.update_ctf = True
mlab.outline()
if args.show_cut:
cut_figure = mlab.figure(bgcolor=(1, 1, 1), fgcolor=(0, 0, 0))
mlab.pipeline.image_plane_widget(mlab.pipeline.scalar_field(data),
plane_orientation='x_axes',
slice_index=data.shape[0] / 2,
figure=cut_figure)
mlab.sync_camera(volume_figure, cut_figure)
mlab.outline()
if args.show_iso:
# downsample to get a somewhat smoother surface
downscaled = scipy.ndimage.zoom(data, 256.0 / data.shape[0])
# do some blurring to get smoother contours
scipy.ndimage.gaussian_filter(downscaled, 2.0, output=downscaled)
iso_figure = mlab.figure(bgcolor=(1, 1, 1), fgcolor=(0, 0, 0))
iso_surface = mlab.pipeline.iso_surface(
mlab.pipeline.scalar_field(downscaled),
contours=[args.show_iso],
figure=iso_figure)
iso_surface.compute_normals = False # seems to look better this way
mlab.outline(extent=(0, 255, 0, 255, 0, 255))
def update_plot(self):
print "-----------------------------------------------------------"
# Disable rendering for the duration of the update
self.scenea.disable_render = True
self.sceneb.disable_render = True
self.scenec.disable_render = True
# Read parameters from the UI
self.me.pars.phi1 = self._phi
self.me.pars.phi2 = self._phi
self.me.pars.varphi = self._varphi
self.me.pars.k0_1 = self._k0
self.me.pars.k0_2 = self._k0
self.me.pars.c0_A = self._c0
self.me.pars.c0_B = self._c0
self.me.pars.L0_A = self._L0_A
self.me.pars.L0_B = self._L0_B
self.me.pars.rho = self._rho
self.me.pars.xi = self._xi
self.me.pars.mu = self._mu
self.me.pars.zeta = self._zeta
self.me.pars.psi = self._psi
self.me.pars.chi = self._chi
self.me.pars.gamma0 = self._gamma0
self.me.pars.gamma1 = self._gamma1
self.me.pars.gamma2 = self._gamma2
self.me.pars.q0 = self._q0
self.me.pars.q1 = self._q1
self.me.pars.c_bar = self._c_bar;
self.me.pars.X1 = self._X1
k_fcl_ubound = self.me.find_k_fcl_global_ubound()
print "k_fcl_ubound = ", k_fcl_ubound,
print " => max fcl-% = ", self.me.N_star(k_fcl_ubound),
print "(baseline ", self.me.N_star(self.me.pars.k0_1), ")"
k_max = self.me.pars.k0_1
xdata, ydata, kAdata, kBdata, z0data, z1data = self.me.compute_Omega_data(self._mesh_d)
z2data = z1data + z0data
z0min = z0data.min()
z0max = z0data.max()
z0data = (z0data - z0min) / (z0max - z0min)
z1min = z1data.min()
z1max = z1data.max()
z1data = (z1data - z1min) / (z1max - z1min)
z2min = z2data.min()
z2max = z2data.max()
z2data = (z2data - z2min) / (z2max - z2min)
if self.first:
self.first = False
self.surfa = self.scenea.mlab.surf(xdata, ydata, z0data, figure=self.scenea.mayavi_scene)
self.surfb = self.sceneb.mlab.surf(xdata, ydata, z1data, figure=self.sceneb.mayavi_scene)
self.surfc = self.scenec.mlab.surf(xdata, ydata, z2data, figure=self.scenec.mayavi_scene)
self.axa = my.axes(self.surfa, nb_labels=5,
xlabel="%-A forecl.", ylabel="%-B forecl.", zlabel="Omega A",
ranges = [0, 1, 0, 1, z0min, z0max],
figure=self.scenea.mayavi_scene)
self.axb = my.axes(self.surfb, nb_labels=5,
xlabel="%-A forecl.", ylabel="%-B forecl.", zlabel="Omega B",
ranges = [0, 1, 0, 1, z1min, z1max],
figure=self.sceneb.mayavi_scene)
self.axc = my.axes(self.surfc, nb_labels=5,
xlabel="%-A forecl.", ylabel="%-B forecl.", zlabel="Omega A+B",
ranges = [0, 1, 0, 1, z2min, z2max],
figure=self.scenec.mayavi_scene)
my.sync_camera(self.scenea.mayavi_scene, self.sceneb.mayavi_scene)
my.sync_camera(self.scenea.mayavi_scene, self.scenec.mayavi_scene)
else:
self.surfa.mlab_source.set(x=xdata, y=ydata, scalars=z0data)
self.surfb.mlab_source.set(x=xdata, y=ydata, scalars=z1data)
self.surfc.mlab_source.set(x=xdata, y=ydata, scalars=z2data)
self.axa.axes.ranges = [0, 1, 0, 1, z0min, z0max]
self.axb.axes.ranges = [0, 1, 0, 1, z1min, z1max]
self.axc.axes.ranges = [0, 1, 0, 1, z2min, z2max]
# Resume rendering
self.scenea.disable_render = False
self.sceneb.disable_render = False
self.scenec.disable_render = False
print "."
def sync(self):
print 'sync'
for scene in self.sceneL:
mlab.sync_camera(self.sceneL[0],scene)
from mayavi import mlab
from surfer import Brain, io
subject = 'fsaverage' # SAD_017
surface = 'pial'
br1 = Brain(subject, 'rh', surface, title='lgroup')
l_surf_data = io.project_volume_data('/mindhive/scratch/satra/sadfigures/nipype_mem/nipype-interfaces-spm-model-EstimateContrast/cf535c8b3e6380c2c8512307f3c294ad/spmT_0001.img',
'rh', subject_id='fsaverage',
target_subject=subject)
br1.add_overlay(l_surf_data, min=2, max=3.7, sign='pos', name='lgroup')
br2 = Brain(subject, 'rh', surface, title='hgroup')
h_surf_data = io.project_volume_data('/mindhive/scratch/satra/sadfigures/nipype_mem/nipype-interfaces-spm-model-EstimateContrast/d1fbe9c9d24038d7d1e16b16936f52ed/spmT_0001.img',
'rh', subject_id='fsaverage',
target_subject=subject)
br2.add_overlay(h_surf_data, min=2, max=3.7, sign='pos', name='hgroup')
mlab.sync_camera(br1._f, br2._f)
mlab.sync_camera(br2._f, br1._f)
"""
br1.save_image('lgroup.png')
br2.save_image('hgroup.png')
"""
def update_plot(self):
print "-----------------------------------------------------------"
# Disable rendering for the duration of the update
self.scenea.disable_render = True
self.sceneb.disable_render = True
# Read parameters from the UI
self.me.pars.phi1 = self._phi
self.me.pars.phi2 = self._phi
self.me.pars.varphi = self._varphi
self.me.pars.k0_1 = self._k0
self.me.pars.k0_2 = self._k0
self.me.pars.c0_A = self._c0
self.me.pars.c0_B = self._c0
self.me.pars.L0_A = self._L0_A
self.me.pars.L0_B = self._L0_B
self.me.pars.rho = self._rho
self.me.pars.xi = self._xi
self.me.pars.mu = self._mu
self.me.pars.zeta = self._zeta
self.me.pars.psi = self._psi
self.me.pars.chi = self._chi
self.me.pars.gamma0 = self._gamma0
self.me.pars.gamma1 = self._gamma1
self.me.pars.gamma2 = self._gamma2
self.me.pars.q0 = self._q0
self.me.pars.q1 = self._q1
self.me.pars.c_bar = self._c_bar;
self.me.pars.X1 = self._X1
k_fcl_ubound = self.me.find_k_fcl_global_ubound()
print "k_fcl_ubound = ", k_fcl_ubound,
print " => max fcl-% = ", self.me.N_star(k_fcl_ubound),
print "(baseline ", self.me.N_star(self.me.pars.k0_1), ")"
d = self._mesh_d*1j
self.F = np.vectorize(lambda x, y, b, f, n:
self.me.cap2_pdf_cdf_p(b, f, x, y, self._ptilde_B)[n])
c2min = self.me.pars.c_bar - 0.01
c2max = self.me.pars.c0_A
C2min = c2min*self.me.pars.L0_A
C2max = c2max*self.me.pars.L0_A
x0data, y0data = np.mgrid[C2min:C2max:d, 0.01:0.99:d]
z0data = self.F(x0data, y0data, 0, 0, 0)
x1data, y1data = np.mgrid[c2min:c2max:d, 0.01:0.99:d]
z1data = self.F(x1data, y1data, 0, 1, 0)
xdata, ydata = np.mgrid[0.0:1.0:d, 0.0:1.0:d]
z0min = z0data.min()
z0max = z0data.max()
z0data = (z0data - z0min) / (z0max - z0min)
z1min = z1data.min()
z1max = z1data.max()
z1data = (z1data - z1min) / (z1max - z1min)
if self.first:
self.first = False
self.surfa = self.scenea.mlab.surf(xdata, ydata, z0data, figure=self.scenea.mayavi_scene)
self.surfb = self.sceneb.mlab.surf(xdata, ydata, z1data, figure=self.sceneb.mayavi_scene)
self.axa = my.axes(self.surfa, nb_labels=5,
xlabel="Level C2", ylabel="%-A forecl.", zlabel="Cap pdf.",
ranges=[C2min, C2max, 0, 1, 0, 1],
figure=self.scenea.mayavi_scene)
self.axb = my.axes(self.surfb, nb_labels=5,
xlabel="Ratio c2", ylabel="%-A forecl.", zlabel="Ratio pdf.",
ranges=[c2min, c2max, 0, 1, 0, 1],
figure=self.sceneb.mayavi_scene)
my.sync_camera(self.scenea.mayavi_scene, self.sceneb.mayavi_scene)
my.sync_camera(self.sceneb.mayavi_scene, self.scenea.mayavi_scene)
else:
self.surfa.mlab_source.set(x=xdata, y=ydata, scalars=z0data)
self.surfb.mlab_source.set(x=xdata, y=ydata, scalars=z1data)
self.axa.axes.ranges = [C2min, C2max, 0, 1, 0, 1]
self.axb.axes.ranges = [c2min, c2max, 0, 1, 0, 1]
# Resume rendering
self.scenea.disable_render = False
self.sceneb.disable_render = False
print "."
def update_plot(self):
print "-----------------------------------------------------------"
# Disable rendering for the duration of the update
self.scenea.disable_render = True
self.sceneb.disable_render = True
self.scenec.disable_render = True
# Read parameters from the UI
self.me.pars.phi1 = self._phi
self.me.pars.phi2 = self._phi
self.me.pars.varphi = self._varphi
self.me.pars.k0_1 = self._k0
self.me.pars.k0_2 = self._k0
self.me.pars.c0_A = self._c0
self.me.pars.c0_B = self._c0
self.me.pars.L0_A = self._L0_A
self.me.pars.L0_B = self._L0_B
self.me.pars.rho = self._rho
self.me.pars.xi = self._xi
self.me.pars.mu = self._mu
self.me.pars.zeta = self._zeta
self.me.pars.psi = self._psi
self.me.pars.chi = self._chi
self.me.pars.gamma0 = self._gamma0
self.me.pars.gamma1 = self._gamma1
self.me.pars.gamma2 = self._gamma2
self.me.pars.q0 = self._q0
self.me.pars.q1 = self._q1
self.me.pars.c_bar = self._c_bar
self.me.pars.X1 = self._X1
k_fcl_ubound = self.me.find_k_fcl_global_ubound()
print "k_fcl_ubound = ", k_fcl_ubound,
print " => max fcl-% = ", self.me.N_star(k_fcl_ubound),
print "(baseline ", self.me.N_star(self.me.pars.k0_1), ")"
k_max = self.me.pars.k0_1
xdata, ydata, kAdata, kBdata, z0data, z1data = self.me.compute_Omega_data(
self._mesh_d)
z2data = z1data + z0data
z0min = z0data.min()
z0max = z0data.max()
z0data = (z0data - z0min) / (z0max - z0min)
z1min = z1data.min()
z1max = z1data.max()
z1data = (z1data - z1min) / (z1max - z1min)
z2min = z2data.min()
z2max = z2data.max()
z2data = (z2data - z2min) / (z2max - z2min)
if self.first:
self.first = False
self.surfa = self.scenea.mlab.surf(xdata,
ydata,
z0data,
figure=self.scenea.mayavi_scene)
self.surfb = self.sceneb.mlab.surf(xdata,
ydata,
z1data,
figure=self.sceneb.mayavi_scene)
self.surfc = self.scenec.mlab.surf(xdata,
ydata,
z2data,
figure=self.scenec.mayavi_scene)
self.axa = my.axes(self.surfa,
nb_labels=5,
xlabel="%-A forecl.",
ylabel="%-B forecl.",
zlabel="Omega A",
ranges=[0, 1, 0, 1, z0min, z0max],
figure=self.scenea.mayavi_scene)
self.axb = my.axes(self.surfb,
nb_labels=5,
xlabel="%-A forecl.",
ylabel="%-B forecl.",
zlabel="Omega B",
ranges=[0, 1, 0, 1, z1min, z1max],
figure=self.sceneb.mayavi_scene)
self.axc = my.axes(self.surfc,
nb_labels=5,
xlabel="%-A forecl.",
ylabel="%-B forecl.",
zlabel="Omega A+B",
ranges=[0, 1, 0, 1, z2min, z2max],
figure=self.scenec.mayavi_scene)
my.sync_camera(self.scenea.mayavi_scene, self.sceneb.mayavi_scene)
my.sync_camera(self.scenea.mayavi_scene, self.scenec.mayavi_scene)
else:
self.surfa.mlab_source.set(x=xdata, y=ydata, scalars=z0data)
self.surfb.mlab_source.set(x=xdata, y=ydata, scalars=z1data)
self.surfc.mlab_source.set(x=xdata, y=ydata, scalars=z2data)
self.axa.axes.ranges = [0, 1, 0, 1, z0min, z0max]
self.axb.axes.ranges = [0, 1, 0, 1, z1min, z1max]
self.axc.axes.ranges = [0, 1, 0, 1, z2min, z2max]
# Resume rendering
self.scenea.disable_render = False
self.sceneb.disable_render = False
self.scenec.disable_render = False
print "."
tag_buf.append(float(all_units[i + 2]))
tag_buf.append(float(all_units[8]))
for i in range(3):
tag_buf.append(float(all_units[i + 5]))
pass
pos_array = np.frombuffer(pos_buf, dtype=np.float).reshape([-1, 7])
tag_array = np.frombuffer(tag_buf, dtype=np.float).reshape([-1, 7])
from PythoTools.TrajectoryVisualization3D import *
visualize_trajectory(pos_array, 'pos array', 1, 1)
visualize_trajectory(tag_array, 'tag', 2, 1)
mlab.sync_camera(mlab.figure(1), mlab.figure(2))
# mlab.draw()
from mpl_toolkits.mplot3d import Axes3D
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.plot(
pos_array[:, 0],
pos_array[:, 1],
pos_array[:, 2],
)
plt.figure()
plt.title('trace')
for i in range(3):
plt.plot(pos_array[:, i], label=str(i))
def sync(self):
print 'sync'
for scene in self.sceneL:
mlab.sync_camera(self.sceneL[0], scene)