def plot_uncertainty(filename, img_path="/tmp/diss_explore", show=True):
"""Compute the sum of uncertainty and plot as function of time"""
with h5py.File(filename, 'r') as hf:
rv = hf['reconstructed_vertex']
rw = hf['reconstructed_weight']
# get all the keys for the groups
v_keys = np.array(utilities.sorted_nicely(list(rv.keys())))
w_keys = np.array(utilities.sorted_nicely(list(rw.keys())))
t_array = []
w_array = []
for ii, wk in enumerate(w_keys):
t_array.append(ii)
w_array.append(np.sum(rw[wk][()]))
t_array = np.array(t_array)
w_array = np.array(w_array)
print(w_array[-1])
# now call the plotting function
publication.plot_uncertainty(t_array, w_array, img_path=img_path, pgf_save=True,
show=show)
def exploration_generate_plots(data_path, img_path='/tmp/diss_explore',
magnification=4, step=1, show=True):
"""Given a HDF5 file generated by explore (C++) this will generate some plots
"""
if not os.path.exists(img_path):
os.makedirs(img_path)
with h5py.File(data_path, 'r') as hf:
rv = hf['reconstructed_vertex']
rw = hf['reconstructed_weight']
# get all the keys
v_keys = np.array(utilities.sorted_nicely(list(rv.keys())))
w_keys = np.array(utilities.sorted_nicely(list(rw.keys())))
v_initial = hf['initial_vertex'][()]
f_initial = hf['initial_faces'][()]
w_initial = np.squeeze(hf['initial_weight'][()])
# determine the maximum extents of the mesh and add some margin
scale = 1.25
max_x = scale*np.max(v_initial[:, 0])
min_x = scale*np.min(v_initial[:, 0])
max_y = scale*np.max(v_initial[:, 1])
min_y = scale*np.min(v_initial[:, 1])
max_z = scale*np.max(v_initial[:, 2])
min_z = scale*np.min(v_initial[:, 2])
"""Partial images during the reconstruction"""
mfig = graphics.mayavi_figure(offscreen=(not show))
mesh = graphics.mayavi_addMesh(mfig, v_initial, f_initial)
ms = mesh.mlab_source
graphics.mayavi_axes(mfig, [min_x, max_x, min_x, max_x, min_x, max_x], line_width=5, color=(1, 0, 0))
graphics.mayavi_view(fig=mfig)
partial_index = np.array([0, v_keys.shape[0]*1/4, v_keys.shape[0]*1/2,
v_keys.shape[0]*3/4, v_keys.shape[0]*4/4-1],
dtype=np.int)
for img_index, vk in enumerate(partial_index):
filename = os.path.join(img_path, 'partial_' + str(vk) + '.jpg')
v = rv[str(vk)][()]
# generate an image and save it
ms.reset(x=v[:, 0], y=v[:, 1], z=v[:,2], triangles=f_initial)
graphics.mlab.savefig(filename, magnification=magnification)
"""Plot the truth asteroid"""
v_true = hf['truth_vertex'][()]
f_true = hf['truth_faces'][()]
ms.reset(x=v_true[:, 0], y=v_true[:, 1], z=v_true[:,2], triangles=f_true)
graphics.mayavi_axes(mfig, [min_x, max_x, min_x, max_x, min_x, max_x], line_width=5, color=(1, 0, 0))
graphics.mayavi_view(fig=mfig)
graphics.mlab.savefig(os.path.join(img_path, 'truth.jpg' ), magnification=magnification)
def plot_state_trajectory(filename):
"""Plot the state trajectory
Plot state in 3D
Plot state in cartesian map project
"""
# load the hdf5
with h5py.File(filename, 'r') as hf:
state_group = hf['state']
# get all the keys for the groups
state_keys = np.array(utilities.sorted_nicely(list(state_group.keys())))
t_array = np.zeros(len(state_keys))
state_inertial_array = np.zeros((len(state_keys), 18))
state_asteroid_array = np.zeros((len(state_keys), 18))
for ii, sk in enumerate(state_keys):
t_array[ii] = ii
state_inertial_array[ii, :] = state_group[sk][()]
state_asteroid_array[ii, :] = state_group[sk][()]
# pass to the plotting function
publication.plot_state(t_array, state_inertial_array, state_asteroid_array)
def inertial_asteroid_landing_cpp_save(time,
state,
filename,
mayavi_objects,
output_path,
move_cam=False,
mesh_weight=False,
magnification=1):
"""Animation for the landing portion
"""
mesh, com, time_text, weight_text = mayavi_objects
fig = mlab.gcf()
camera = fig.scene.camera
ms = mesh.mlab_source
ts = com.mlab_source
with h5py.File(filename, 'r') as hf:
v = hf['landing/vertices'][()]
f = hf['landing/faces'][()]
Ra_group = hf['landing/Ra']
keys = np.array(utilities.sorted_nicely(list(Ra_group.keys())))
ii = 0
for (t, pos, Rb2i, key) in zip(time, state[:, 0:3], state[:, 6:15],
keys):
mesh.scene.disable_render = True
Ra = Ra_group[key][()]
Rb2i = Rb2i.reshape((3, 3))
new_vertices = Ra.dot(v.T).T
new_faces = f
time_text.trait_set(text="t: {:8.1f}".format(t))
# option to change color of mesh_weight
ms.set(x=new_vertices[:, 0],
y=new_vertices[:, 1],
z=new_vertices[:, 2],
triangles=new_faces)
ts.set(x=pos[0], y=pos[1], z=pos[2])
if move_cam:
pos_sph = wavefront.cartesian2spherical(pos)
graphics.mayavi_view(fig,
azimuth=np.rad2deg(pos_sph[2]),
elevation=90 - np.rad2deg(pos_sph[1]),
distance=pos_sph[0] + 0.5,
focalpoint=[0, 0, 0])
filename = os.path.join(output_path, str(ii).zfill(7) + '.jpg')
mesh.scene.disable_render = False
graphics.mlab.savefig(filename, magnification=magnification)
ii += 1
def view_final_reconstruction(data_path):
"""View the final mesh after reconstruction"""
with h5py.File(data_path, 'r') as hf:
rv = hf['reconstructed_vertex']
v_keys = np.array(utilities.sorted_nicely(list(rv.keys())))
v = rv[v_keys[-1]][()]
f = hf['initial_faces'][()]
mfig = graphics.mayavi_figure()
graphics.mayavi_addMesh(mfig, v, f)
def plot_volume(filename, img_path="/tmp/diss_explore", show=True):
"""Compute the volume of the asteroid at each time step
"""
with h5py.File(filename, 'r') as hf:
rv_group = hf['reconstructed_vertex']
f_initial = hf['initial_faces'][()]
rv_keys = np.array(utilities.sorted_nicely(list(rv_group.keys())))
t_array = np.zeros(len(rv_keys))
vol_array = np.zeros(len(rv_keys))
for ii, key in enumerate(rv_keys):
t_array[ii] = ii
vol_array[ii] = stats.volume(rv_group[key][()], f_initial)
true_vertices = hf['truth_vertex'][()]
true_faces = hf['truth_faces'][()]
true_volume = stats.volume(true_vertices, true_faces)
publication.plot_volume(t_array, vol_array, true_volume, img_path=img_path, pgf_save=True,
show=show)
def asteroid_generate_plots(data_path,
img_path='/tmp/diss_reconstruct',
magnification=1,
step=10):
"""Given a HDF5 file this will read the data and create a bunch of plots/images
"""
# check and create output directory if not existed
if not os.path.exists(img_path):
os.makedirs(img_path)
with h5py.File(data_path, 'r') as hf:
rv = hf['reconstructed_vertex']
rw = hf['reconstructed_weight']
# get all the keys for the groups
v_keys = np.array(utilities.sorted_nicely(list(rv.keys())))
w_keys = np.array(utilities.sorted_nicely(list(rw.keys())))
v_initial = hf['initial_vertex'][()]
f_initial = hf['initial_faces'][()]
w_initial = hf['initial_weight'][()]
"""Partial images during the reconstruction"""
mfig = graphics.mayavi_figure(offscreen=True)
mesh = graphics.mayavi_addMesh(mfig, v_initial, f_initial)
ms = mesh.mlab_source
graphics.mayavi_axes(mfig, [-1, 1, -1, 1, -1, 1],
line_width=5,
color=(1, 0, 0))
graphics.mayavi_view(fig=mfig)
partial_index = np.array([
0, v_keys.shape[0] * 1 / 4, v_keys.shape[0] * 1 / 2,
v_keys.shape[0] * 3 / 4, v_keys.shape[0] * 4 / 4 - 1
],
dtype=np.int)
for img_index, vk in enumerate(partial_index):
filename = os.path.join(img_path, 'partial_' + str(vk) + '.jpg')
v = rv[str(vk)][()]
# generate an image and save it
ms.reset(x=v[:, 0], y=v[:, 1], z=v[:, 2], triangles=f_initial)
graphics.mlab.savefig(filename, magnification=4)
"""Partial images using a colormap for the data"""
mfig = graphics.mayavi_figure(offscreen=True)
mesh = graphics.mayavi_addMesh(mfig,
v_initial,
f_initial,
color=None,
colormap='viridis',
scalars=w_initial)
ms = mesh.mlab_source
graphics.mayavi_axes(mfig, [-1, 1, -1, 1, -1, 1],
line_width=5,
color=(1, 0, 0))
graphics.mayavi_view(fig=mfig)
partial_index = np.array([
0, v_keys.shape[0] * 1 / 4, v_keys.shape[0] * 1 / 2,
v_keys.shape[0] * 3 / 4, v_keys.shape[0] * 4 / 4 - 1
],
dtype=np.int)
for img_index, vk in enumerate(partial_index):
filename = os.path.join(img_path,
'partial_weights_' + str(vk) + '.jpg')
v = rv[str(vk)][()]
w = rw[str(vk)][()]
# generate an image and save it
ms.reset(x=v[:, 0],
y=v[:, 1],
z=v[:, 2],
triangles=f_initial,
scalars=w)
graphics.mlab.savefig(filename, magnification=4)
"""Generate the completed shape at a variety of different angles"""
# change the mesh to the finished mesh
ms.reset(x=rv[v_keys[-1]][()][:, 0],
y=rv[v_keys[-1]][()][:, 1],
z=rv[v_keys[-1]][()][:, 2],
triangles=f_initial)
elevation = np.array([30, -30])
azimuth = np.array([0, 45, 135, 215, 315])
for az, el in itertools.product(azimuth, elevation):
filename = os.path.join(
img_path, 'final_az=' + str(az) + '_el=' + str(el) + '.jpg')
graphics.mayavi_view(fig=mfig, azimuth=az, elevation=el)
graphics.mlab.savefig(filename, magnification=4)
"""Create a bunch of images for animation"""
animation_path = os.path.join(img_path, 'animation')
if not os.path.exists(animation_path):
os.makedirs(animation_path)
ms.reset(x=v_initial[:, 0],
y=v_initial[:, 1],
z=v_initial[:, 2],
triangles=f_initial,
scalars=w_initial)
graphics.mayavi_view(mfig)
for ii, vk in enumerate(v_keys[::step]):
filename = os.path.join(animation_path, str(ii).zfill(7) + '.jpg')
v = rv[vk][()]
w = rw[str(vk)][()]
ms.reset(x=v[:, 0],
y=v[:, 1],
z=v[:, 2],
triangles=f_initial,
scalars=w)
graphics.mayavi_savefig(mfig,
filename,
magnification=magnification)
return 0
def inertial_asteroid_refinement_cpp_save(time,
state,
inertial_intersections,
hdf5_file,
mayavi_objects,
move_cam=False,
mesh_weight=False,
output_path="/tmp/refinement",
magnification=1):
"""Save the refinment process to a bunch of images"""
mesh, com, pc_points, time_text, weight_text = mayavi_objects
f = mlab.gcf()
camera = f.scene.camera
# get all the keys for the reconstructed vertices and faces
# animate the rotation fo the asteroid
ms = mesh.mlab_source
ts = com.mlab_source
# ast_xs = ast_axes[0].mlab_source
# ast_ys = ast_axes[1].mlab_source
# ast_zs = ast_axes[2].mlab_source
# dum_xs = dum_axes[0].mlab_source
# dum_ys = dum_axes[1].mlab_source
# dum_zs = dum_axes[2].mlab_source
pc_sources = pc_points.mlab_source
with h5py.File(hdf5_file, 'r') as hf:
# oriignal vertices
est_initial_vertices = hf[
'simulation_parameters/estimate_asteroid/initial_vertices'][()]
num_vert = est_initial_vertices.shape[0]
rv_group = hf['refinement/reconstructed_vertex']
rf_group = hf['refinement/reconstructed_face']
rw_group = hf['refinement/reconstructed_weight']
Ra_group = hf['refinement/Ra']
rv_keys = np.array(utilities.sorted_nicely(list(rv_group.keys())))
ii = 0
for (t, pos, Rb2i, ints, key) in zip(time, state[:, 0:3], state[:,
6:15],
inertial_intersections, rv_keys):
# rotate teh asteroid
# Ra = ast.rot_ast2int(t)
mesh.scene.disable_render = True
Ra = Ra_group[key][()]
Rb2i = Rb2i.reshape((3, 3))
# parse out the vertices x, y, z
# rotate the asteroid
new_vertices = Ra.dot(rv_group[key][()].T).T
new_faces = rf_group[key][()]
new_weight = np.squeeze(rw_group[key][()])
# store value for number of vertices
# add current time
time_text.trait_set(text="t: {:8.1f}".format(t))
weight_text.trait_set(text="w: {:8.1f}".format(np.sum(new_weight)))
# update asteroid
if mesh_weight:
# check if size is different than the last mesh
if num_vert != new_vertices.shape[0]:
ms.reset(x=new_vertices[:, 0],
y=new_vertices[:, 1],
z=new_vertices[:, 2],
triangles=new_faces,
scalars=new_weight)
num_vert = new_vertices.shape[0]
else:
ms.set(x=new_vertices[:, 0],
y=new_vertices[:, 1],
z=new_vertices[:, 2],
triangles=new_faces,
scalars=new_weight)
else:
if num_vert != new_vertices.shape[0]:
ms.reset(x=new_vertices[:, 0],
y=new_vertices[:, 1],
z=new_vertices[:, 2],
triangles=new_faces)
else:
ms.set(x=new_vertices[:, 0],
y=new_vertices[:, 1],
z=new_vertices[:, 2],
triangles=new_faces)
# update the satellite
ts.set(x=pos[0], y=pos[1], z=pos[2])
# update the camera view to be right behind the satellite
if move_cam:
pos_sph = wavefront.cartesian2spherical(pos)
graphics.mayavi_view(f,
azimuth=np.rad2deg(pos_sph[2]),
elevation=90 - np.rad2deg(pos_sph[1]),
distance=pos_sph[0] + 0.5,
focalpoint=[0, 0, 0])
pc_sources.set(x=ints[:, 0], y=ints[:, 1], z=ints[:, 2])
mesh.scene.disable_render = False
filename = os.path.join(output_path, str(ii).zfill(7) + '.jpg')
graphics.mlab.savefig(filename, magnification=magnification)
ii += 1
def inertial_asteroid_trajectory_cpp(time,
state,
inertial_intersections,
hdf5_file,
mayavi_objects,
move_cam=False,
mesh_weight=False):
"""Animate the rotation of an asteroid and the motion of SC
This assumes an asteroid object from C++ and using the exploration sim
"""
# pdb.set_trace()
# mesh, ast_axes, com, dum_axes, pc_lines = mayavi_objects
mesh, com, pc_points, time_text, weight_text = mayavi_objects
f = mlab.gcf()
camera = f.scene.camera
# get all the keys for the reconstructed vertices and faces
# animate the rotation fo the asteroid
ms = mesh.mlab_source
ts = com.mlab_source
# ast_xs = ast_axes[0].mlab_source
# ast_ys = ast_axes[1].mlab_source
# ast_zs = ast_axes[2].mlab_source
# dum_xs = dum_axes[0].mlab_source
# dum_ys = dum_axes[1].mlab_source
# dum_zs = dum_axes[2].mlab_source
pc_sources = pc_points.mlab_source
with h5py.File(hdf5_file, 'r') as hf:
# oriignal vertices
est_initial_vertices = hf[
'simulation_parameters/estimate_asteroid/initial_vertices'][()]
num_vert = est_initial_vertices.shape[0]
rv_group = hf['reconstructed_vertex']
rf_group = hf['reconstructed_face']
rw_group = hf['reconstructed_weight']
Ra_group = hf['Ra']
rv_keys = np.array(utilities.sorted_nicely(list(rv_group.keys())))
for (t, pos, Rb2i, ints, key) in zip(time, state[:, 0:3], state[:,
6:15],
inertial_intersections, rv_keys):
# rotate teh asteroid
# Ra = ast.rot_ast2int(t)
mesh.scene.disable_render = True
Ra = Ra_group[key][()]
Rb2i = Rb2i.reshape((3, 3))
# parse out the vertices x, y, z
# rotate the asteroid
new_vertices = Ra.dot(rv_group[key][()].T).T
new_faces = rf_group[key][()]
new_weight = np.squeeze(rw_group[key][()])
# store value for number of vertices
# add current time
time_text.trait_set(text="t: {:8.1f}".format(t))
weight_text.trait_set(text="w: {:8.1f}".format(np.sum(new_weight)))
# update asteroid
if mesh_weight:
# check if size is different than the last mesh
if num_vert != new_vertices.shape[0]:
ms.reset(x=new_vertices[:, 0],
y=new_vertices[:, 1],
z=new_vertices[:, 2],
triangles=new_faces,
scalars=new_weight)
num_vert = new_vertices.shape[0]
else:
ms.set(x=new_vertices[:, 0],
y=new_vertices[:, 1],
z=new_vertices[:, 2],
triangles=new_faces,
scalars=new_weight)
else:
if num_vert != new_vertices.shape[0]:
ms.reset(x=new_vertices[:, 0],
y=new_vertices[:, 1],
z=new_vertices[:, 2],
triangles=new_faces)
else:
ms.set(x=new_vertices[:, 0],
y=new_vertices[:, 1],
z=new_vertices[:, 2],
triangles=new_faces)
# update the satellite
ts.set(x=pos[0], y=pos[1], z=pos[2])
# update the camera view to be right behind the satellite
if move_cam:
pos_sph = wavefront.cartesian2spherical(pos)
graphics.mayavi_view(f,
azimuth=np.rad2deg(pos_sph[2]),
elevation=90 - np.rad2deg(pos_sph[1]),
distance=pos_sph[0] + 0.5,
focalpoint=[0, 0, 0])
# update the asteroid axes
# ast_xs.set(x=[0, Ra[0,0]], y=[0, Ra[1,0]], z=[0, Ra[2,0]])
# ast_ys.set(x=[0, Ra[0,1]], y=[0, Ra[1,1]], z=[0, Ra[2,1]])
# ast_zs.set(x=[0, Ra[0,2]], y=[0, Ra[1,2]], z=[0, Ra[2,2]])
# dum_xs.set(x=[pos[0], pos[0]+Rb2i[0,0]], y=[pos[1], pos[1]+Rb2i[1,0]],
# z=[pos[2], pos[2]+Rb2i[2,0]])
# dum_ys.set(x=[pos[0], pos[0]+Rb2i[0,1]], y=[pos[1], pos[1]+Rb2i[1,1]],
# z=[pos[2], pos[2]+Rb2i[2,1]])
# dum_zs.set(x=[pos[0], pos[0]+Rb2i[0,2]], y=[pos[1], pos[1]+Rb2i[1,2]],
# z=[pos[2], pos[2]+Rb2i[2,2]])
pc_sources.set(x=ints[:, 0], y=ints[:, 1], z=ints[:, 2])
# for pcs, inter in zip(pc_sources, ints):
# check if intersection is empty
# if inter.size > 2:
# pcs.set(x=inter[0], y=inter[1], z=inter[2])
# else:
# pcs.set(x=0, y=0, z=0)
# pcs.set(x=1, y=1, z=1)
mesh.scene.disable_render = False
yield
def read_mesh_reconstruct(filename, output_path='/tmp/reconstruct_images'):
"""Use H5PY to read the data back and plot
"""
logger = logging.getLogger(__name__)
logger.info('Starting the image generation')
# check if location exists
if not os.path.exists(output_path):
os.makedirs(output_path)
logger.info('Opening {}'.format(filename))
with h5py.File(filename, 'r') as hf:
rv = hf['reconstructed_vertex']
rf = hf['reconstructed_face']
rw = hf['reconstructed_weight']
# get all the keys for the groups
v_keys = np.array(utilities.sorted_nicely(list(rv.keys())))
f_keys = np.array(utilities.sorted_nicely(list(rf.keys())))
w_keys = np.array(utilities.sorted_nicely(list(rw.keys())))
v_initial = hf['initial_vertex'][()]
f_initial = hf['initial_faces'][()]
w_initial = hf['initial_weight'][()]
"""Partial images during the reconstruction"""
logger.info('Starting on partial reconstruction images')
mfig = graphics.mayavi_figure(offscreen=True)
mesh = graphics.mayavi_addMesh(mfig, v_initial, f_initial)
ms = mesh.mlab_source
graphics.mayavi_axes(mfig, [-1, 1, -1, 1, -1, 1],
line_width=5,
color=(1, 0, 0))
graphics.mayavi_view(fig=mfig)
partial_index = np.array([
0, v_keys.shape[0] * 1 / 4, v_keys.shape[0] * 1 / 2,
v_keys.shape[0] * 3 / 4, v_keys.shape[0] * 4 / 4 - 1
],
dtype=np.int)
for img_index, vk in enumerate(partial_index):
filename = os.path.join(output_path, 'partial_' + str(vk) + '.jpg')
v = rv[str(vk)][()]
# generate an image and save it
ms.reset(x=v[:, 0], y=v[:, 1], z=v[:, 2], triangles=f_initial)
graphics.mlab.savefig(filename, magnification=4)
"""Partial images using a colormap for the data"""
logger.info('Now using a colormap for the uncertainty')
mfig = graphics.mayavi_figure(offscreen=True)
mesh = graphics.mayavi_addMesh(mfig,
v_initial,
f_initial,
color=None,
colormap='viridis',
scalars=w_initial)
ms = mesh.mlab_source
graphics.mayavi_axes(mfig, [-1, 1, -1, 1, -1, 1],
line_width=5,
color=(1, 0, 0))
graphics.mayavi_view(fig=mfig)
partial_index = np.array([
0, v_keys.shape[0] * 1 / 4, v_keys.shape[0] * 1 / 2,
v_keys.shape[0] * 3 / 4, v_keys.shape[0] * 4 / 4 - 1
],
dtype=np.int)
for img_index, vk in enumerate(partial_index):
filename = os.path.join(output_path,
'partial_weights_' + str(vk) + '.jpg')
v = rv[str(vk)][()]
w = rw[str(vk)][()]
# generate an image and save it
ms.reset(x=v[:, 0],
y=v[:, 1],
z=v[:, 2],
triangles=f_initial,
scalars=w)
graphics.mlab.savefig(filename, magnification=4)
"""Generate the completed shape at a variety of different angles"""
logger.info('Now generating some views of the final shape')
# change the mesh to the finished mesh
ms.reset(x=rv[v_keys[-1]][()][:, 0],
y=rv[v_keys[-1]][()][:, 1],
z=rv[v_keys[-1]][()][:, 2],
triangles=f_initial)
elevation = np.array([30, -30])
azimuth = np.array([0, 45, 135, 215, 315])
for az, el in itertools.product(azimuth, elevation):
filename = os.path.join(
output_path, 'final_az=' + str(az) + '_el=' + str(el) + '.jpg')
graphics.mayavi_view(fig=mfig, azimuth=az, elevation=el)
graphics.mlab.savefig(filename, magnification=4)
"""Create a bunch of images for animation"""
logger.info('Now making images for a movie')
animation_path = os.path.join(output_path, 'animation')
if not os.path.exists(animation_path):
os.makedirs(animation_path)
ms.reset(x=v_initial[:, 0],
y=v_initial[:, 1],
z=v_initial[:, 2],
triangles=f_initial)
for ii, vk in enumerate(v_keys):
filename = os.path.join(animation_path, str(ii).zfill(7) + '.jpg')
v = rv[vk][()]
ms.reset(x=v[:, 0], y=v[:, 1], z=v[:, 2], triangles=f_initial)
graphics.mayavi_savefig(mfig, filename, magnification=4)
logger.info('Finished')
return mfig
def TestSortedNicely():
s = ['booklet', '4 sheets', '48 sheets', '12 sheets']
s_sorted = utilities.sorted_nicely(s)
s_sorted_exp = ['4 sheets', '12 sheets', '48 sheets', 'booklet']
np.testing.assert_allclose(s_sorted, s_sorted_exp)
def save_animation(filename, output_path, mesh_weight=False, magnification=4):
output_path = os.path.join(output_path, 'animation')
if not os.path.exists(output_path):
os.makedirs(output_path)
with h5py.File(filename, 'r') as hf:
rv = hf['reconstructed_vertex']
rw = hf['reconstructed_weight']
# get all the keys
v_keys = np.array(utilities.sorted_nicely(list(rv.keys())))
w_keys = np.array(utilities.sorted_nicely(list(rw.keys())))
v_initial = hf['initial_vertex'][()]
f_initial = hf['initial_faces'][()]
w_initial = np.squeeze(hf['initial_weight'][()])
# think about a black background as well
mfig = graphics.mayavi_figure(bg=(0, 0, 0), size=(800,600), offscreen=True)
if mesh_weight:
mesh = graphics.mayavi_addMesh(mfig, v_initial, f_initial,
scalars=w_initial,
color=None, colormap='viridis')
else:
mesh = graphics.mayavi_addMesh(mfig, v_initial, f_initial)
# xaxis = graphics.mayavi_addLine(mfig, np.array([0, 0, 0]), np.array([2, 0, 0]), color=(1, 0, 0))
# yaxis = graphics.mayavi_addLine(mfig, np.array([0, 0, 0]), np.array([0, 2, 0]), color=(0, 1, 0))
# zaxis = graphics.mayavi_addLine(mfig, np.array([0, 0, 0]), np.array([0, 0, 2]), color=(0, 0, 1))
# ast_axes = (xaxis, yaxis, zaxis)
print("Images will be saved to {}".format(output_path))
ms = mesh.mlab_source
# determine the maximum extents of the mesh and add some margin
scale = 1.25
max_x = scale*np.max(v_initial[:, 0])
min_x = scale*np.min(v_initial[:, 0])
max_y = scale*np.max(v_initial[:, 1])
min_y = scale*np.min(v_initial[:, 1])
max_z = scale*np.max(v_initial[:, 2])
min_z = scale*np.min(v_initial[:, 2])
graphics.mayavi_axes(mfig, [min_x, max_x, min_x, max_x, min_x, max_x], line_width=5, color=(1, 0, 0))
graphics.mayavi_view(fig=mfig)
# loop over keys and save images
for img_index, vk in enumerate(v_keys):
filename = os.path.join(output_path, str(vk).zfill(7) + '.jpg')
new_vertices = rv[str(vk)][()]
new_faces = f_initial
new_weight = rw[str(vk)][()]
# generate an image and save it
if mesh_weight:
ms.set(x=new_vertices[:, 0],y=new_vertices[:, 1],
z=new_vertices[:,2], triangles=new_faces,
scalars=new_weight)
else:
ms.set(x=new_vertices[:, 0],y=new_vertices[:, 1],
z=new_vertices[:,2], triangles=new_faces)
graphics.mlab.savefig(filename, magnification=magnification)
# now call ffmpeg
fps = 60
name_str = "reconstruction_" + datetime.datetime.now().strftime("%Y%m%dT%H%M%S") + ".mp4"
name = os.path.join(output_path, name_str)
ffmpeg_fname = os.path.join(output_path, '%07d.jpg')
cmd = "ffmpeg -framerate {} -i {} -c:v libx264 -profile:v high -crf 20 -pix_fmt yuv420p -vf 'scale=trunc(iw/2)*2:trunc(ih/2)*2' {}".format(fps, ffmpeg_fname, name)
print(cmd)
subprocess.check_output(['bash', '-c', cmd])
# remove folder now
for file in os.listdir(output_path):
file_path = os.path.join(output_path, file)
if file_path.endswith('.jpg'):
os.remove(file_path)
mfig = graphics.mayavi_figure(offscreen=False)
mesh = graphics.mayavi_addMesh(mfig, vb_true, fb_true)
graphics.mayavi_view(mfig, *view)
graphics.mayavi_savefig(mfig, '/tmp/castalia_bump_true.jpg', magnification=4)
# load the refinement final version
with h5py.File('./data/exploration/refine/20180619_castalia_refinement.hdf5',
'r') as hf:
# oriignal vertices
est_initial_vertices = hf[
'simulation_parameters/estimate_asteroid/initial_vertices'][()]
num_vert = est_initial_vertices.shape[0]
rv_group = hf['refinement/reconstructed_vertex']
rf_group = hf['refinement/reconstructed_face']
rw_group = hf['refinement/reconstructed_weight']
Ra_group = hf['refinement/Ra']
rv_keys = np.array(utilities.sorted_nicely(list(rv_group.keys())))
v = rv_group[rv_keys[-1]][()]
f = rf_group[rv_keys[-1]][()]
w = rw_group[rv_keys[-1]][()]
mfig_est = graphics.mayavi_figure(offscreen=False)
mesh = graphics.mayavi_addMesh(mfig_est, v, f)
graphics.mayavi_view(mfig_est, *view)
graphics.mayavi_savefig(mfig_est,
'/tmp/castalia_bump_est.jpg',
magnification=4)
