def show_one_timestep(self, date):
# Visualize the exposed zones for one time step
date_to_vis = datetime.datetime.strptime(date, '%m/%d/%Y %H:%M:%S')
print("You are visualizing: ",
date_to_vis.strftime("%b %d %Y %H:%M:%S"))
ind_date_to_vis = np.where(
date_to_vis.strftime("%b %d %Y %H:%M:%S") == np.array(
self.timeline))[0][0]
ray_directions = self.directions[ind_date_to_vis]
ray_directions = -np.ones(
(self.posture.number_faces, 3)) * ray_directions
ray_origins = self.posture.get_triangles_center - \
ray_directions*self.posture.get_max_bounds
inf = self.posture.get_posture.ray.intersects_first(
ray_origins=ray_origins, ray_directions=ray_directions)
expo_mask = (inf == np.arange(self.posture.number_faces))
col = np.zeros((self.posture.number_faces, 3)) # Black color
col[expo_mask] = [255, 255, 255] #White color
vtkmeshes = trimesh2vtk(self.posture.get_posture)
vtkmeshes.cellColors(col, cmap='Greys_r')
show(vtkmeshes)
def plot_stl_vertices_curvature(struct_seg, num_segments, color_segmetns,
surface_seg, vertices, Cmin, Cmax, title):
"""Функция для прорисовки вершин stl объекта, основанных на цвете по кривизне"""
for j in range(struct_seg.shape[0]):
for i in range(num_segments.shape[0]):
faces = copy.deepcopy(surface_seg[j][i][0])
mesh = trimesh.Trimesh(vertices=vertices,
faces=faces,
process=False)
vtkmeshes = trimesh2vtk(mesh)
vtkmeshes1 = trimesh2vtk(mesh)
# vtkmeshes.pointColors(Cmin, cmap='jet')
Cmin1, Cmax1 = copy.deepcopy(Cmin), copy.deepcopy(Cmax)
min_max_Cmin = np.array(
[np.mean(Cmin) - np.std(Cmin),
np.mean(Cmin) + np.std(Cmin)])
min_max_Cmax = np.array(
[np.mean(Cmax) - np.std(Cmax),
np.mean(Cmax) + np.std(Cmax)])
for i in range(Cmin.shape[0]):
if Cmin1[i] > min_max_Cmin[1]:
Cmin1[i] = min_max_Cmin[1]
elif Cmin1[i] < min_max_Cmin[0]:
Cmin1[i] = min_max_Cmin[0]
if Cmax1[i] > min_max_Cmax[1]:
Cmax1[i] = min_max_Cmax[1]
elif Cmax1[i] < min_max_Cmax[0]:
Cmax1[i] = min_max_Cmax[0]
vtkmeshes.pointColors(Cmin1, cmap='jet')
vtkmeshes1.pointColors(Cmax1, cmap='jet')
vtkmeshes.addScalarBar(title="Cmin")
vtkmeshes1.addScalarBar(title="Cmax")
show([vtkmeshes, vtkmeshes1], N=2, bg='w', axes=1)
def plot_stl_vertices_klast(struct_seg, num_segments, color_segmetns,
surface_seg, vertices, y_kmeans, title):
"""Функция для прорисовки вершин stl объекта, основанных на цвете по кривизне"""
for j in range(struct_seg.shape[0]):
for i in range(num_segments.shape[0]):
faces = copy.deepcopy(surface_seg[j][i][0])
mesh = trimesh.Trimesh(vertices=vertices,
faces=faces,
process=False)
vtkmeshes = trimesh2vtk(mesh)
vtkmeshes.pointColors(y_kmeans, cmap='jet')
vtkmeshes.addScalarBar(title="Cmin-Cmax_k_means")
show(vtkmeshes)
def show_beta_coefficients(self, beta_coeff):
"""
beta_coeff can be diff or refl
"""
if (beta_coeff == 'diff'):
this_beta = self.beta_coeff[:, 0]
elif (beta_coeff == 'refl'):
this_beta = self.beta_coeff[:, 1]
else:
raise TypeErro("Value not recognise! It can be 'diff' or 'refl'")
this_beta = this_beta / pi
vtkmeshes = trimesh2vtk(self.my_file)
vtkmeshes.cellColors(this_beta, cmap='jet', vmin=0., vmax=1.)
vtkmeshes.addScalarBar(title="Beta coefficients")
show(vtkmeshes)
def show_one_timestep_received(self, one_timestep):
#row is timestep
#column is triangle
file_out_full = "output/{}_fullBody.txt".format(self.output_name)
total_body_output = np.loadtxt(file_out_full)
if (one_timestep < 0 or one_timestep > np.shape(total_body_output)[0]):
raise TypeError("Timestep must be smaller than {}".format(
np.shape(total_body_output)[0]))
col = total_body_output[one_timestep - 1, :]
vtkmeshes = trimesh2vtk(self.posture.get_posture)
vtkmeshes.cellColors(col, cmap='jet')
vtkmeshes.addScalarBar(title="J/m^2")
show(vtkmeshes)
def plot_stl_faces_color_curvature(struct_seg, num_segments, surface_seg,
vertices, curvature_face_klast, title):
"""Функция для прорисовки фасет stl объекта, основанных на цвете по кривизне для каждой фасеты"""
for j in range(struct_seg.shape[0]):
for i in range(num_segments.shape[0]):
faces = copy.deepcopy(surface_seg[j][i][0])
meshes = [
trimesh.Trimesh(vertices=vertices, faces=faces, process=False)
for i in range(2)
]
Cmin1, Cmax1 = copy.deepcopy(
curvature_face_klast[:, 0]), copy.deepcopy(
curvature_face_klast[:, 1])
#np.max(Cmin1)-np.min(Cmin1)
meshes[0].visual.face_colors = trimesh.visual.interpolate(
curvature_face_klast[:, 0], color_map='jet')
meshes[1].visual.face_colors = trimesh.visual.interpolate(
curvature_face_klast[:, 1], color_map='jet')
# create a scene containing the mesh and colorbar
# pyplot.pcolor(Cmin1)
#pyplot.colorbar()
#scene = trimesh.Scene([mesh])
# setup the normalization and the colormap
normalize = mcolors.Normalize(vmin=np.min(Cmin1),
vmax=np.max(Cmin1))
colormap = cm.jet
scalarmappaple = cm.ScalarMappable(norm=normalize, cmap=colormap)
scalarmappaple.set_array(Cmin1)
pyplot.colorbar(scalarmappaple)
vtkmeshes = [trimesh2vtk(m) for m in meshes]
vtkmeshes[0].addScalarBar(title="Cmin")
vtkmeshes[1].addScalarBar(title="Cmax")
#vp = Plotter(title="Cmin", interactive=0, axes=3)
#vp +=vtkmeshes
#vp.show(resetcam=0)
#vp.show()
show([vtkmeshes[0], vtkmeshes[1]],
interactive=0,
N=2,
bg='w',
axes=1) #bg2='wheat',
""" trimesh to vtkplotter interoperability """ # Install trimesh with: # sudo apt install python3-rtree # pip install rtree shapely # conda install trimesh import trimesh import vtkplotter from vtkplotter import trimesh2vtk, vtk2trimesh url = 'https://raw.githubusercontent.com/mikedh/trimesh/master/models/' filename = vtkplotter.download(url + 'machinist.XAML') mesh = trimesh.load(filename) vmesh = trimesh2vtk(mesh) # returns a Mesh(vtkActor) object from Trimesh vtkplotter.show(mesh) # vtkplotter visualizer (conversion is on the fly) trimsh_reconverted = vtk2trimesh(vmesh) trimsh_reconverted.show() # this is the trimesh built-in visualizer
def test_isocell_ray_casting():
# Create source to ray trace
# sphere = pv.Sphere(radius=0.85)
sphere1 = vp.Sphere(r=0.85, c="r", alpha=0.1).lw(0.1)
mesh = trimesh.Trimesh(vertices=sphere1.points(),
faces=sphere1.faces(),
process=False,
use_embree=True)
# mesh = trimesh.creation.icosphere()
# Create isocell rays
isocell = Isocell(rays=1000, div=5, isrand=0, draw_cells=True)
drays = ((
isocell.points @ r.vrrotvec2mat([0, 0, 1], [0, 0, 1]).T).T).reshape(
-1, 3)
# Define line segment
start = [0, 0, 0]
endPoints = drays
# intersects_location requires origins to be the same shape as vectors
origins = np.tile(np.expand_dims(start, 0), (len(drays), 1))
# do the actual ray- mesh queries
points, index_ray, index_tri = mesh.ray.intersects_location(
origins, drays, multiple_hits=False)
# for each hit, find the distance along its vector
# you could also do this against the single camera Z vector
depth = trimesh.util.diagonal_dot(points - start, drays[index_ray])
locs = trimesh.points.PointCloud(points)
# # stack rays into line segments for visualization as Path3D
# ray_visualize = trimesh.load_path(np.hstack((origins, origins + drays * 1.2)).reshape(-1, 2, 3))
# render the result with vtkplotter
axes = vp.addons.buildAxes(vp.trimesh2vtk(mesh), c='k', zxGrid2=True)
# vp.show(mesh, ray_visualize, axes, locs, axes=4)
lines = vp.Lines(origins, drays, c='b')
vp.show(vp.trimesh2vtk(mesh).alpha(0.1).lw(0.1), lines, axes, locs, axes=4)
# Render the result with pyvista
sphere = pv.PolyData(
mesh.vertices, np.hstack((np.full((len(mesh.faces), 1),
3), mesh.faces)))
p = pv.Plotter()
p.add_mesh(sphere,
show_edges=True,
opacity=0.5,
color="w",
lighting=False,
label="Test Mesh")
# p.add_arrows(origins[1,:], drays[1,:], mag=1, color=True, opacity=0.5, )
p.add_lines(np.hstack([origins, drays]).reshape(-1, 3), color='b')
# intersections = pv.PolyData(points)
# p.add_mesh(intersections, color="maroon", point_size=25, label="Intersection Points")
# for i, stop in enumerate(drays):
#
# # Perform ray trace
# points, ind = sphere.ray_trace(start, stop)
#
# # Create geometry to represent ray trace
# ray = pv.Line(start, stop)
# intersection = pv.PolyData(points)
#
#
#
# # pv.plot_arrows(np.array(start),np.array(stop))
# # pv.plot_arrows(np.array(start),np.array(stop))
# p.add_mesh(ray, color="blue", line_width=5, label="Ray Segment")
# p.add_mesh(intersection, color="maroon",
# point_size=25, label="Intersection Points")
# p.add_legend()
p.show()
calvis.calvis_clear()
calvis.mesh_path(meshpath)
calvis.load_trimesh()
calvis.fit_SMPL_model_to_mesh(SMPL_basicModel, gender=genders[i])
calvis.segmentation(N=N)
calvis.assemble_mesh_signatur(m=m)
calvis.assemble_slice_statistics()
cc = calvis.chest_circumference()
ccslice_2D, to_3D = cc.to_planar()
cc_actor = trimesh2vtk(cc).unpack()[0].lw(2)
wc = calvis.waist_circumference()
wcslice_2D, to_3D = wc.to_planar()
wc_actor = trimesh2vtk(wc).unpack()[0].lw(2)
pc = calvis.pelvis_circumference()
pcslice_2D, to_3D = pc.to_planar()
pc_actor = trimesh2vtk(pc).unpack()[0].lw(2)
text = Text2D("Subject no. %s" % (i + 1))
# Print info
#print("Chest circunference length is: %s" % ccslice_2D.length)
#print("Waist circunference length is: %s" % wcslice_2D.length)
#print("Pelvis circunference length is: %s" % pcslice_2D.length)
""" trimesh to vtkplotter interoperability """ # Install trimesh with: # sudo apt install python3-rtree # pip install rtree shapely # conda install trimesh import trimesh from vtkplotter import download, trimesh2vtk, show url = 'https://raw.githubusercontent.com/mikedh/trimesh/master/models/' filename = download(url + 'machinist.XAML') mesh = trimesh.load(filename) actor = trimesh2vtk(mesh) # returns a Actor(vtkActor) object from Trimesh # Any of these will work: show(mesh) # conversion is on the fly (don't need 'actor') # or #actor.show() # or #show(actor) # or mesh.show() # this is the trimesh built-in visualizer
def view_mesh(
meshes: list,
output_file: str,
mesh_names: list = [],
patient_data="",
plid="",
scan_path="",
):
logging.info("Opening mesh viewer.")
settings.useDepthPeeling = True
vmeshes = []
def slider1(widget, event):
value = widget.GetRepresentation().GetValue()
vmeshes[index].color(value)
def slider2(widget, event):
value = widget.GetRepresentation().GetValue()
vmeshes[index].opacity(value)
def buttonfunc():
global index
bu.switch()
index = mesh_names.index(bu.status())
def background_swap():
bg_button.switch()
vp.backgroundRenderer.SetBackground(colors.getColor(
bg_button.status()))
def ar_view():
save()
holo_registration_wrapper.start_viewer(output_file, plid)
def save():
write_mesh_as_glb_with_colour(vmeshes, output_file)
def open_scan():
external_2d_viewer.start(scan_path)
vp = Plotter(
sharecam=False,
bg="./core/client/images/hologram_icon2.png",
bg2='black',
shape=[1, 1],
size=[640, 480],
interactive=False,
)
# pos = position corner number: horizontal [1-4] or vertical [11-14]
vp.addSlider2D(slider1, -9, 9, value=0, pos=4, title="color number")
left_side_x = 0.1
vp.addSlider2D(
slider2,
xmin=0.00,
xmax=1.00,
value=0.5,
pos=14,
c="blue",
title="alpha value (opacity)",
)
bu = vp.addButton(
buttonfunc,
pos=(0.5, 0.05), # x,y fraction from bottom left corner
states=mesh_names,
font=font_style, # arial, courier, times
size=25,
bold=True,
italic=False,
)
save_button = vp.addButton(
save,
pos=(left_side_x, 0.05), # x,y fraction from bottom left corner
states=["Save"],
font=font_style, # arial, courier, times
size=25,
bold=True,
italic=False,
)
if holo_registration_wrapper.is_supported(plid):
ar_button = vp.addButton(
ar_view,
pos=(left_side_x, 0.20),
states=["AR View"],
font=font_style,
size=25,
bold=True,
italic=False,
)
if scan_path != "":
scan_button = vp.addButton(
open_scan,
pos=(left_side_x, 0.15),
states=["2D View"],
font=font_style,
size=25,
bold=True,
italic=False,
)
bg_button = vp.addButton(
background_swap,
pos=(left_side_x, 0.10), # x,y fraction from bottom left corner
states=["black", "white"],
font=font_style,
size=25,
bold=True,
italic=False,
)
for i in range(0, len(meshes)):
vmeshes.append(trimesh2vtk(meshes[i], alphaPerCell=True))
doc = Text2D(patient_data, pos=4, c=(0, 113, 197))
vp.show(doc)
vp.backgroundRenderer.GetActiveCamera().Zoom(1.3)
vp.show(vmeshes)
interactive()
""" trimesh to vtkplotter interoperability """ # Install trimesh with: # sudo apt install python3-rtree # pip install rtree shapely # conda install trimesh import trimesh import vtkplotter from vtkplotter import trimesh2vtk, vtk2trimesh url = 'https://raw.githubusercontent.com/mikedh/trimesh/master/models/' filename = vtkplotter.download(url + 'machinist.XAML') mesh = trimesh.load(filename) vtkplotter.show(mesh) # vtkplotter visualizer (conversion is on the fly) # explicit conversion vmesh = trimesh2vtk(mesh) # returns a vtkplotter.Mesh(vtkActor) object trimsh_reconverted = vtk2trimesh(vmesh) trimsh_reconverted.show() # this is the trimesh built-in visualizer
