def test_box_grid():
grid = np.zeros((30, 30, 30))
grid[13:18, 5:25, 13:18] = 1
elements, vertices, vert_manager = grid_to_tets(grid, 0.1)
mesh = examples.download_cow()
distances = mesh_select(vertices, mesh)
print("distances: ", distances)
print(elements, vertices)
constraints = [[0, [1, 1, 1]], [1, [1, 1, 1]], [2, [1, 1, 1]],
[3, [1, 1, 1]]]
loads = [[32, -10000., 0.0, 0]]
# [20, 1000., 0.0, 0],
#[34, 1000., 0.0, 0],
# [31, 10000., 0.0, 0]]
poisson = 0.3
youngs = 2000
displacements = solve_full(elements, vertices, poisson, youngs,
constraints, loads)
magnitudes = get_displacement_magnitudes(displacements)
print("magnitudes", magnitudes)
plotter = pv.Plotter()
#add_tets_to_display(vertices, elements, plotter, magnitudes)
surface = generate_unstructured_grid(elements, vertices)
voxels = pv.voxelize(surface, density=surface.length / 200)
plotter.add_mesh(voxels)
plotter.show()
def logo_atomized(density=0.05, scale=0.6, depth=0.05):
"""Generate a voxelized pyvista logo with intra-cell spacing."""
mesh_letters = logo_letters(depth=depth)
grids = []
for letter in mesh_letters.values():
grid = pyvista.voxelize(letter, density=density)
grids.append(atomize(grid, scale=scale))
return grids[0].merge(grids[1:])
def test_voxelize_throws_when_density_is_not_length_3():
with pytest.raises(ValueError) as e:
mesh = pyvista.PolyData(ex.load_uniform().points)
vox = pyvista.voxelize(mesh, [0.5, 0.3])
assert "not enough values to unpack" in str(e.value)
def test_voxelize_non_uniform_desnity():
mesh = pyvista.PolyData(ex.load_uniform().points)
vox = pyvista.voxelize(mesh, [0.5, 0.3, 0.2])
assert vox.n_cells
def test_voxelize():
mesh = pyvista.PolyData(ex.load_uniform().points)
vox = pyvista.voxelize(mesh, 0.5)
assert vox.n_cells
def filter(self):
voxelized_mesh = pyvista.voxelize(self.mesh.pyvista, **self.kwargs)
return self.mesh.mesh_class(offset=1)(voxelized_mesh,
parents=[self.mesh])
#-----------------------------
# voxelize each cell and merge it into an image pixel array
#-----------------------------
# create a blank image array sized by the extents vector (plus edge padding)
image = np.zeros(tuple(np.around(vrange / PIXEL_SIZE).astype(int) + 3),
'uint16')
# iterate through the cell files
for fname in flist:
print(fname)
surface = pv.read(fname)
surface.translate(trans) # translate to positive quadrant
# voxelize the surface mesh
voxels = pv.voxelize(surface, density=PIXEL_SIZE)
# get voxel centers mapped to indices into the image array
centers = np.around(voxels.cell_centers().points / PIXEL_SIZE).astype(int)
# color the image pixels for this cell by cell number
for row in centers:
image[tuple(row)] = 200 + int(fname[-7:-4])
# save the image
tif.imsave('stack.tif', np.swapaxes(image, 0, 2))
#voxels.plot(color=True, show_edges=True)
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
def logo_voxel(density=0.03):
"""Create a voxelized PyVista logo."""
return pyvista.voxelize(text_3d(LOGO_TITLE, depth=0.3), density)
def _for_landing_page(jupyter_backend='ipygany', **kwargs):
"""Plot the stylized PyVista logo for ipygany.
To be shown on the landing page at index.rst
"""
mesh_letters = logo_letters()
# letter 'P'
p_mesh = mesh_letters['P'].compute_normals(split_vertices=True)
# letter 'y'
y_mesh = mesh_letters['y'].compute_normals(split_vertices=True)
# letter 'V'
v_grid = pyvista.voxelize(mesh_letters['V'], density=0.08)
v_grid_atom = atomize(v_grid)
v_grid_atom['scalars'] = v_grid_atom.points[:, 0]
i_grid = pyvista.voxelize(mesh_letters['i'], density=0.1)
i_mesh = i_grid.extract_surface().triangulate().subdivide(2)
i_mesh = i_mesh.smooth(500)
old_center = np.array(i_mesh.center)
i_mesh.points *= 1.07
i_mesh.points += old_center - np.array(i_mesh.center)
# letter 's'
s_vox = pyvista.voxelize(mesh_letters['s'], density=0.04)
s_cent = s_vox.cell_centers()
pd = pyvista.PolyData(s_cent.points)
sphere = pyvista.Sphere(theta_resolution=9, phi_resolution=9)
s_grid = pd.glyph(factor=0.04, geom=sphere)
# letter 't'
# t_mesh = mesh_letters['t'].subdivide(5)
# t_mesh.flip_normals()
# t_mesh = t_mesh.compute_normals(consistent_normals=True)
# import pyacvd
# clus = pyacvd.Clustering(t_mesh)
# clus.cluster(140)
# t_cmesh = clus.create_mesh()
# import _ as fe
# src = fe.Surface(t_cmesh)
# tgt = fe.Surface(t_mesh)
# src.morph(tgt, settings={'local_with_centroid': True, 'local_steps': 300})
# src.morph(tgt, settings={'local_with_centroid': True, 'local_steps': 300})
# t_mesh = t_cmesh.extract_all_edges().tube(radius=0.005, n_sides=4)
# t_mesh.extract_surface().save(...)
t_mesh_filename = os.path.join(THIS_PATH, 't_mesh.ply')
t_mesh = pyvista.read(t_mesh_filename)
# letter 'a'
grid = examples.download_letter_a()
grid.points[:, 0] += (mesh_letters['a'].center[0] - grid.center[0])
# select some cells from grid
cells = grid.cells.reshape(-1, 5)
mask = grid.points[cells[:, 1:], 2] < 0.2
mask = mask.all(1)
a_part = grid.extract_cells(mask)
plotter = pyvista.Plotter()
plotter.add_mesh(p_mesh, color='#376fa0')
plotter.add_mesh(y_mesh, color='#ffd040')
vista = v_grid_atom.merge([i_mesh, s_grid, t_mesh, a_part])
vista['xdist'] = vista.points[:, 0]
plotter.add_mesh(vista, cmap='viridis')
# cpos = None
# cpos = [(-0.9785294154224577, 1.2712499319005408, 10.965733716449193),
# (2.553950615449191, 0.34145688392081264, 0.06127122762851659),
# (0.019308531920309947, 0.996708840795678, -0.07873161547192065)]
# cpos = [(0.9060226106040606, 0.7752122028710583, 5.148283455883558),
# (2.553950615449191, 0.34145688392081264, 0.06127122762851659),
# (0.019308531920309943, 0.9967088407956779, -0.07873161547192063)]
# cpos = [(0.6861237002108157, 0.7572283207509382, 5.078581054505883),
# (2.334051705055946, 0.3234730018006926, -0.008431173749159387),
# (0.019308531920309947, 0.996708840795678, -0.07873161547192065)]
if jupyter_backend == 'ipygany':
x = 2.7
cpos = [(x, 0.306, 5), (x, 0.306, 0.15), (0.0, 1.0, 0.0)]
text = text_3d("I'm interactive!", depth=0.1)
text.points *= 0.15
text.translate([4, -0.4, 0])
plotter.add_mesh(text, color='black')
else:
cpos = [(0.9060226106040606, 0.7752122028710583, 5.148283455883558),
(2.553950615449191, 0.34145688392081264, 0.06127122762851659),
(0.019308531920309943, 0.9967088407956779,
-0.07873161547192063)]
plotter.background_color = 'white'
plotter.remove_scalar_bar()
return plotter.show(cpos=cpos,
jupyter_backend=jupyter_backend,
jupyter_kwargs=kwargs)
def plot_logo(window_size=None,
off_screen=None,
screenshot=None,
cpos=None,
**kwargs):
"""Plot the stylized PyVista logo.
Examples
--------
>>> from pyvista import demos
>>> cpos = demos.plot_logo()
"""
# initialize plotter
if window_size is None:
window_size = [960, 400]
plotter = pyvista.Plotter(window_size=window_size, off_screen=off_screen)
mesh_letters = logo_letters()
# letter 'P'
p_mesh = mesh_letters['P'].compute_normals(split_vertices=True)
plotter.add_mesh(p_mesh, color='#376fa0', smooth_shading=True)
# letter 'y'
p_mesh = mesh_letters['y'].compute_normals(split_vertices=True)
plotter.add_mesh(p_mesh, color='#ffd040', smooth_shading=True)
# letter 'V'
v_grid = pyvista.voxelize(mesh_letters['V'], density=0.08)
v_grid_atom = atomize(v_grid)
v_grid_atom['scalars'] = v_grid_atom.points[:, 0]
plotter.add_mesh(v_grid_atom,
scalars='scalars',
show_edges=True,
cmap='winter',
show_scalar_bar=False)
# letter 'i'
i_grid = pyvista.voxelize(mesh_letters['i'], density=0.1)
plotter.add_mesh(i_grid.extract_surface(),
style='points',
color='r',
render_points_as_spheres=True,
point_size=8)
plotter.add_mesh(i_grid, style='wireframe', color='k', line_width=4)
# letter 's'
mesh = mesh_letters['s']
scalars = mesh.points[:, 0]
plotter.add_mesh(mesh,
scalars=scalars,
style='wireframe',
color='w',
show_edges=True,
line_width=2,
cmap='gist_heat',
backface_culling=True,
render_lines_as_tubes=True)
# letter 't'
mesh = mesh_letters['t']
scalars = mesh.points[:, 0]
plotter.add_mesh(mesh,
scalars=scalars,
show_edges=True,
cmap='autumn',
lighting=True)
# letter 'a'
grid = examples.download_letter_a()
grid.points[:, 0] += (mesh_letters['a'].center[0] - grid.center[0])
# select some cells from grid
cells = grid.cells.reshape(-1, 5)
mask = grid.points[cells[:, 1:], 2] < 0.2
mask = mask.all(1)
a_part = grid.extract_cells(mask)
cells = a_part.cells.reshape(-1, 5)
scalars = grid.points[cells[:, 1], 1]
plotter.add_mesh(a_part, scalars=scalars, show_edges=True, cmap='Greens')
# finalize plot and show it
plotter.set_background(kwargs.pop('background', 'white'))
if cpos is None:
cpos = [(0.9060226106040606, 0.7752122028710583, 5.148283455883558),
(2.553950615449191, 0.34145688392081264, 0.06127122762851659),
(0.019308531920309943, 0.9967088407956779,
-0.07873161547192063)]
plotter.camera_position = cpos
plotter.remove_scalar_bar()
if screenshot: # pragma: no cover
plotter.show(cpos=cpos, auto_close=False)
plotter.screenshot(screenshot, True)
cpos_final = plotter.camera_position
plotter.close()
return cpos_final
else:
return plotter.show(cpos=cpos, **kwargs)
def test_voxel_fem():
surface = examples.download_foot_bones()
voxels = pv.voxelize(surface, density=surface.length / 200)
import ipdb
ipdb.set_trace()
import numpy as np
# Load a surface to voxelize
surface = examples.download_foot_bones()
surface
###############################################################################
cpos = [(7.656346967151718, -9.802071079151158, -11.021236183314311),
(0.2224512272564101, -0.4594554282112895, 0.5549738359311297),
(-0.6279216753504941, -0.7513057097368635, 0.20311105371647392)]
surface.plot(cpos=cpos, opacity=0.75)
###############################################################################
# Create a voxel model of the bounding surface
voxels = pv.voxelize(surface, density=surface.length / 200)
p = pv.Plotter()
p.add_mesh(voxels, color=True, show_edges=True, opacity=0.5)
p.add_mesh(surface, color="lightblue", opacity=0.5)
p.show(cpos=cpos)
###############################################################################
# We could even add a scalar field to that new voxel model in case we
# wanted to create grids for modelling. In this case, let's add a scalar field
# for bone density noting:
voxels["density"] = np.full(voxels.n_cells, 3.65) # g/cc
voxels
###############################################################################
voxels.plot(scalars="density", cpos=cpos)
print(f"Points Array1 shape: {points_array1.shape}")
points_array2 = create_box_points(x_size=2.0,
y_size=2.0,
z_size=2.0,
step=0.04)
print(f"Points Array2 type: {type(points_array2)}")
print(f"Points Array2 shape: {points_array2.shape}")
points_array = np.concatenate((points_array1, points_array2), axis=0)
print(f"Points Array type: {type(points_array)}")
print(f"Points Array shape: {points_array.shape}")
# Create PyVista Meshes
point_cloud = pv.PolyData(points_array)
voxels = pv.voxelize(point_cloud, density=0.05)
p = pv.Plotter()
p.add_mesh(voxels, color=True, show_edges=True, opacity=0.5)
p.add_mesh(point_cloud, color="lightblue", opacity=0.5)
p.show()
# Get a Z component of the point array
#zData = points_array[:,-1]
xData = points_array[:, 0]
print(f"xData points Array type: {type(xData)}")
print(f"xData points Array shape: {xData.shape}")
# Add to mesh
#point_cloud["height"] = zData
point_cloud["distance"] = xData
# Plot PyVista mesh
def plot_logo(window_size=None,
off_screen=None,
screenshot=None,
cpos=None,
just_return_plotter=False,
show_note=False,
**kwargs):
"""Plot the stylized PyVista logo.
Examples
--------
>>> from pyvista import demos
>>> cpos = demos.plot_logo()
"""
# initialize plotter
if window_size is None:
window_size = [960, 400]
plotter = pyvista.Plotter(window_size=window_size, off_screen=off_screen)
mesh_letters = logo_letters()
# letter 'P'
p_mesh = mesh_letters['P'].compute_normals(split_vertices=True)
p_mesh.flip_normals()
plotter.add_mesh(p_mesh, color='#376fa0', smooth_shading=True)
# letter 'y'
y_mesh = mesh_letters['y'].compute_normals(split_vertices=True)
y_mesh.flip_normals()
plotter.add_mesh(y_mesh, color='#ffd040', smooth_shading=True)
# letter 'V'
v_grid = pyvista.voxelize(mesh_letters['V'], density=0.08)
v_grid_atom = atomize(v_grid)
v_grid_atom['scalars'] = v_grid_atom.points[:, 0]
v_grid_atom_surf = v_grid_atom.extract_surface()
faces = v_grid_atom_surf.faces.reshape(-1, 5)
faces[:, 1:] = faces[:, 1:][:, ::-1]
v_grid_atom_surf.faces = faces
plotter.add_mesh(v_grid_atom_surf,
scalars='scalars',
show_edges=True,
cmap='winter',
show_scalar_bar=False)
# letter 'i'
i_grid = pyvista.voxelize(mesh_letters['i'], density=0.1)
plotter.add_mesh(i_grid.extract_surface(),
style='points',
color='r',
render_points_as_spheres=True,
point_size=14)
plotter.add_mesh(i_grid, style='wireframe', color='k', line_width=4)
# letter 's'
mesh = mesh_letters['s']
mesh['scalars'] = mesh.points[:, 0]
plotter.add_mesh(mesh,
scalars='scalars',
style='wireframe',
show_edges=True,
line_width=2,
cmap='gist_heat',
backface_culling=True,
render_lines_as_tubes=True,
show_scalar_bar=False)
# letter 't'
mesh = mesh_letters['t'].clean().compute_normals()
# strange behavior with pythreejs
if pyvista.global_theme.jupyter_backend == 'pythreejs':
mesh.flip_normals()
scalars = mesh.points[:, 0]
plotter.add_mesh(mesh,
scalars=scalars,
show_edges=True,
cmap='autumn',
show_scalar_bar=False)
# letter 'a'
grid = examples.download_letter_a()
grid.points[:, 0] += (mesh_letters['a'].center[0] - grid.center[0])
# select some cells from grid
cells = grid.cells.reshape(-1, 5)
mask = grid.points[cells[:, 1:], 2] < 0.2
mask = mask.all(1)
a_part = grid.extract_cells(mask)
cells = a_part.cells.reshape(-1, 5)
scalars = grid.points[cells[:, 1], 1]
plotter.add_mesh(a_part,
scalars=scalars,
show_edges=True,
cmap='Greens',
show_scalar_bar=False)
if show_note:
text = text_3d("You can move me!", depth=0.1)
text.points *= 0.1
text.translate([4.0, -0.3, 0])
plotter.add_mesh(text, color='black')
# finalize plot and show it
plotter.set_background(kwargs.pop('background', 'white'))
plotter.camera_position = 'xy'
if 'zoom' in kwargs:
plotter.camera.zoom(kwargs.pop('zoom'))
# plotter.remove_scalar_bar()
plotter.enable_anti_aliasing()
if just_return_plotter:
return plotter
if screenshot: # pragma: no cover
plotter.show(cpos=cpos, auto_close=False)
plotter.screenshot(screenshot, True)
cpos_final = plotter.camera_position
plotter.close()
return cpos_final
else:
return plotter.show(cpos=cpos, **kwargs)
