class GanyScene(AppComponent):
"""Canvas for 3D surface mesh interactive plotting based on ipygany."""
name = '3D Scene'
def setup(self):
vertices, triangle_indices = self.dataset._widgets.to_unstructured_mesh()
elev_da = self.dataset._widgets.elevation
elev_min = elev_da.min()
elev_max = elev_da.max()
elev_arr = self.dataset._widgets.current_elevation.values
data = {
'color': [Component(name='value', array=elev_arr, min=elev_min, max=elev_max)],
'warp': [Component(name='value', array=elev_arr, min=elev_min, max=elev_max)],
}
self.polymesh = PolyMesh(vertices=vertices, triangle_indices=triangle_indices, data=data)
self.isocolor = IsoColor(
self.polymesh, input=('color', 'value'), min=elev_min, max=elev_max
)
self.warp = WarpByScalar(self.isocolor, input='warp', factor=1)
self.scene = Scene([self.warp])
return self.scene
def redraw_isocolor_warp(self):
"""Trigger scene redraw if data slice has been updated."""
new_warp_array = self.dataset._widgets.current_elevation.values
new_color_array = self.dataset._widgets.current_color.values
with self.scene.hold_sync():
self.polymesh[('color', 'value')].array = new_color_array
self.polymesh[('warp', 'value')].array = new_warp_array
def reset_isocolor_limits(self, step=False):
"""Resets color limits to data range.
Parameters
----------
step : bool
If true, resets the color range to the range of the data that is shown
in the current scene. Otherwise (default), resets the color range to the
whole data range.
"""
if step:
da = self.dataset._widgets.current_color
else:
da = self.dataset._widgets.color
with self.scene.hold_sync():
self.isocolor.min = da.min()
self.isocolor.max = da.max()
@property
def linkable_traits(self):
return [(self.scene, 'camera')]
def show_ipygany(plotter, return_viewer, height=None, width=None):
"""Show an ipygany scene."""
# convert each mesh in the plotter to an ipygany scene
actors = plotter.renderer._actors
meshes = []
for actor in actors.values():
ipygany_obj = ipygany_block_from_actor(actor)
if ipygany_obj is not None:
meshes.append(ipygany_obj)
bc_color = color_float_to_hex(*plotter.background_color)
scene = Scene(meshes,
background_color=bc_color,
camera=ipygany_camera_from_plotter(plotter))
# optionally size of the plotter
if height is not None:
scene.layout.height = f'{height}'
if width is not None:
scene.layout.width = f'{width}'
cbar = None
if len(plotter.scalar_bars):
for mesh in meshes:
if isinstance(mesh, ipygany.IsoColor):
cbar = ipygany.ColorBar(mesh)
colored_mesh = mesh
break
# Simply return the scene
if return_viewer:
return scene
if cbar is not None:
# Colormap choice widget
colormap_dd = Dropdown(options=colormaps, description='Colormap:')
jslink((colored_mesh, 'colormap'), (colormap_dd, 'index'))
# sensible colorbar maximum width, or else it looks bad when
# window is large.
cbar.layout.max_width = '500px'
cbar.layout.min_height = '50px' # stop from getting squished
# cbar.layout.height = '20%' # stop from getting squished
# cbar.layout.max_height = ''
# Create a slider that will dynamically change the boundaries of the colormap
# colormap_slider_range = FloatRangeSlider(value=[height_min, height_max],
# min=height_min, max=height_max,
# step=(height_max - height_min) / 100.)
# jslink((colored_mesh, 'range'), (colormap_slider_range, 'value'))
# create app
title = HTML(value=f'<h3>{list(plotter.scalar_bars.keys())[0]}</h3>')
legend = VBox((title, colormap_dd, cbar))
scene = AppLayout(center=scene,
footer=legend,
pane_heights=[0, 0, '150px'])
display.display_html(scene)
def show_dem3d(self, dem):
nr, nc = len(dem.y), len(dem.x)
triangle_indices = np.empty((nr - 1, nc - 1, 2, 3), dtype='uint32')
r = np.arange(nr * nc, dtype='uint32').reshape(nr, nc)
triangle_indices[:, :, 0, 0] = r[:-1, :-1]
triangle_indices[:, :, 1, 0] = r[:-1, 1:]
triangle_indices[:, :, 0, 1] = r[:-1, 1:]
triangle_indices[:, :, 1, 1] = r[1:, 1:]
triangle_indices[:, :, :, 2] = r[1:, :-1, None]
triangle_indices.shape = (-1, 3)
height_component = Component(name='value', array=self.alt)
mesh = PolyMesh(vertices=self.vertices,
triangle_indices=triangle_indices,
data={'height': [height_component]})
colored_mesh = IsoColor(mesh,
input='height',
min=np.min(self.alt),
max=np.max(self.alt))
warped_mesh = Warp(colored_mesh,
input=(0, 0, ('height', 'value')),
factor=0)
warp_slider = FloatSlider(min=0,
max=10,
value=0,
description='Vertical exaggeration',
style={'description_width': 'initial'})
jslink((warped_mesh, 'factor'), (warp_slider, 'value'))
self.dem3d.clear_output()
with self.dem3d:
display(VBox((Scene([warped_mesh]), warp_slider)))
def render_ipyany_scene(visualize: Visualize, off_screen_file=False):
from ipygany import Scene
meshes = []
for obj in visualize.objects:
meshes.append(obj.convert_to_ipygany_mesh())
return Scene(meshes)
def setup(self):
vertices, triangle_indices = self.dataset._widgets.to_unstructured_mesh()
elev_da = self.dataset._widgets.elevation
elev_min = elev_da.min()
elev_max = elev_da.max()
elev_arr = self.dataset._widgets.current_elevation.values
data = {
'color': [Component(name='value', array=elev_arr, min=elev_min, max=elev_max)],
'warp': [Component(name='value', array=elev_arr, min=elev_min, max=elev_max)],
}
self.polymesh = PolyMesh(vertices=vertices, triangle_indices=triangle_indices, data=data)
self.isocolor = IsoColor(
self.polymesh, input=('color', 'value'), min=elev_min, max=elev_max
)
self.warp = WarpByScalar(self.isocolor, input='warp', factor=1)
self.scene = Scene([self.warp])
return self.scene
colored_mesh = IsoColor(mesh,
input=('S', 'YY'),
min=sigmayy_min,
max=sigmayy_max)
# Create a slider that will dynamically change the boundaries of the colormap
colormap_slider_range = FloatRangeSlider(value=[sigmayy_min, sigmayy_max],
min=sigmayy_min,
max=sigmayy_max,
step=(sigmayy_max - sigmayy_min) /
100.)
jslink((colored_mesh, 'range'), (colormap_slider_range, 'value'))
# Create a colorbar widget
colorbar = ColorBar(colored_mesh)
# Colormap choice widget
colormap = Dropdown(options=colormaps, description='colormap:')
jslink((colored_mesh, 'colormap'), (colormap, 'index'))
AppLayout(
header=Scene([colored_mesh]),
left_sidebar=VBox((colormap, colormap_slider_range)),
right_sidebar=(colorbar),
pane_widths=[1, 0, 1],
pane_heights=['80%', '20%', 0],
footer=None,
)
#!/usr/bin/env python
# coding: utf-8
# In[1]:
from ipygany import Scene, TetraMesh
mesh = TetraMesh.from_vtk('benchmarks/000-tuning-fork/fork.vtk')
scene = Scene([mesh])
scene
def getNotebookBackend(actors2show, zoom, viewup):
vp = settings.plotter_instance
if zoom == 'tight':
zoom=1 # disable it
if isinstance(vp.shape, str) or sum(vp.shape) > 2:
colors.printc("Multirendering is not supported in jupyter.", c=1)
return
####################################################################################
# https://github.com/InsightSoftwareConsortium/itkwidgets
# /blob/master/itkwidgets/widget_viewer.py
if 'itk' in settings.notebookBackend:
from itkwidgets import view
settings.notebook_plotter = view(actors=actors2show,
cmap='jet', ui_collapsed=True,
gradient_opacity=False)
####################################################################################
elif settings.notebookBackend == 'k3d':
try:
import k3d # https://github.com/K3D-tools/K3D-jupyter
except:
print("Cannot find k3d, install with: pip install k3d")
return
actors2show2 = []
for ia in actors2show:
if not ia:
continue
if isinstance(ia, vtk.vtkAssembly): #unpack assemblies
acass = ia.unpack()
actors2show2 += acass
else:
actors2show2.append(ia)
# vbb, sizes, _, _ = addons.computeVisibleBounds()
# kgrid = vbb[0], vbb[2], vbb[4], vbb[1], vbb[3], vbb[5]
settings.notebook_plotter = k3d.plot(axes=[vp.xtitle, vp.ytitle, vp.ztitle],
menu_visibility=settings.k3dMenuVisibility,
height=settings.k3dPlotHeight,
antialias=settings.k3dAntialias,
)
# settings.notebook_plotter.grid = kgrid
settings.notebook_plotter.lighting = settings.k3dLighting
# set k3d camera
settings.notebook_plotter.camera_auto_fit = settings.k3dCameraAutoFit
settings.notebook_plotter.grid_auto_fit = settings.k3dGridAutoFit
settings.notebook_plotter.axes_helper = settings.k3dAxesHelper
if settings.plotter_instance and settings.plotter_instance.camera:
k3dc = utils.vtkCameraToK3D(settings.plotter_instance.camera)
if zoom:
k3dc[0] /= zoom
k3dc[1] /= zoom
k3dc[2] /= zoom
settings.notebook_plotter.camera = k3dc
# else:
# vsx, vsy, vsz = vbb[0]-vbb[1], vbb[2]-vbb[3], vbb[4]-vbb[5]
# vss = numpy.linalg.norm([vsx, vsy, vsz])
# if zoom:
# vss /= zoom
# vfp = (vbb[0]+vbb[1])/2, (vbb[2]+vbb[3])/2, (vbb[4]+vbb[5])/2 # camera target
# if viewup == 'z':
# vup = (0,0,1) # camera up vector
# vpos= vfp[0] + vss/1.9, vfp[1] + vss/1.9, vfp[2]+vss*0.01 # camera position
# elif viewup == 'x':
# vup = (1,0,0)
# vpos= vfp[0]+vss*0.01, vfp[1] + vss/1.5, vfp[2] # camera position
# else:
# vup = (0,1,0)
# vpos= vfp[0]+vss*0.01, vfp[1]+vss*0.01, vfp[2] + vss/1.5 # camera position
# settings.notebook_plotter.camera = [vpos[0], vpos[1], vpos[2],
# vfp[0], vfp[1], vfp[2],
# vup[0], vup[1], vup[2] ]
if not vp.axes:
settings.notebook_plotter.grid_visible = False
for ia in actors2show2:
if isinstance(ia, (vtk.vtkCornerAnnotation, vtk.vtkAssembly)):
continue
kobj = None
kcmap= None
name = None
if hasattr(ia, 'filename'):
if ia.filename:
name = os.path.basename(ia.filename)
if ia.name:
name = os.path.basename(ia.name)
#####################################################################scalars
# work out scalars first, Points Lines are also Mesh objs
if isinstance(ia, (Mesh, shapes.Line, Points)):
# print('scalars', ia.name, ia.N())
iap = ia.GetProperty()
if isinstance(ia, (shapes.Line, Points)):
iapoly = ia.polydata()
else:
iapoly = ia.clone().clean().triangulate().computeNormals().polydata()
vtkscals = None
color_attribute = None
if ia.mapper().GetScalarVisibility():
vtkdata = iapoly.GetPointData()
vtkscals = vtkdata.GetScalars()
if vtkscals is None:
vtkdata = iapoly.GetCellData()
vtkscals = vtkdata.GetScalars()
if vtkscals is not None:
c2p = vtk.vtkCellDataToPointData()
c2p.SetInputData(iapoly)
c2p.Update()
iapoly = c2p.GetOutput()
vtkdata = iapoly.GetPointData()
vtkscals = vtkdata.GetScalars()
if vtkscals is not None:
if not vtkscals.GetName():
vtkscals.SetName('scalars')
scals_min, scals_max = ia.mapper().GetScalarRange()
color_attribute = (vtkscals.GetName(), scals_min, scals_max)
lut = ia.mapper().GetLookupTable()
lut.Build()
kcmap=[]
nlut = lut.GetNumberOfTableValues()
for i in range(nlut):
r,g,b,a = lut.GetTableValue(i)
kcmap += [i/(nlut-1), r,g,b]
#####################################################################Volume
if isinstance(ia, Volume):
# print('Volume', ia.name, ia.dimensions())
kx, ky, kz = ia.dimensions()
arr = ia.pointdata[0]
kimage = arr.reshape(-1, ky, kx)
colorTransferFunction = ia.GetProperty().GetRGBTransferFunction()
kcmap=[]
for i in range(128):
r,g,b = colorTransferFunction.GetColor(i/127)
kcmap += [i/127, r,g,b]
kbounds = numpy.array(ia.imagedata().GetBounds()) \
+ numpy.repeat(numpy.array(ia.imagedata().GetSpacing()) / 2.0, 2)\
* numpy.array([-1,1] * 3)
kobj = k3d.volume(kimage.astype(numpy.float32),
color_map=kcmap,
#color_range=ia.imagedata().GetScalarRange(),
alpha_coef=10,
bounds=kbounds,
name=name,
)
settings.notebook_plotter += kobj
#####################################################################text
elif hasattr(ia, 'info') and 'formula' in ia.info.keys():
pos = (ia.GetPosition()[0],ia.GetPosition()[1])
kobj = k3d.text2d(ia.info['formula'], position=pos)
settings.notebook_plotter += kobj
#####################################################################Mesh
elif isinstance(ia, Mesh) and ia.N() and len(ia.faces()):
# print('Mesh', ia.name, ia.N(), len(ia.faces()))
kobj = k3d.vtk_poly_data(iapoly,
name=name,
# color=_rgb2int(iap.GetColor()),
color_attribute=color_attribute,
color_map=kcmap,
opacity=iap.GetOpacity(),
wireframe=(iap.GetRepresentation()==1))
if iap.GetInterpolation() == 0:
kobj.flat_shading = True
settings.notebook_plotter += kobj
#####################################################################Points
elif isinstance(ia, Points):
# print('Points', ia.name, ia.N())
kcols=[]
if color_attribute is not None:
scals = utils.vtk2numpy(vtkscals)
kcols = k3d.helpers.map_colors(scals, kcmap,
[scals_min,scals_max]).astype(numpy.uint32)
# sqsize = numpy.sqrt(numpy.dot(sizes, sizes))
kobj = k3d.points(ia.points().astype(numpy.float32),
color=_rgb2int(iap.GetColor()),
colors=kcols,
opacity=iap.GetOpacity(),
shader=settings.k3dPointShader,
point_size=iap.GetPointSize(),
name=name,
)
settings.notebook_plotter += kobj
#####################################################################Lines
elif ia.polydata(False).GetNumberOfLines():
# print('Line', ia.name, ia.N(), len(ia.faces()),
# ia.polydata(False).GetNumberOfLines(), len(ia.lines()),
# color_attribute, [vtkscals])
# kcols=[]
# if color_attribute is not None:
# scals = utils.vtk2numpy(vtkscals)
# kcols = k3d.helpers.map_colors(scals, kcmap,
# [scals_min,scals_max]).astype(numpy.uint32)
# sqsize = numpy.sqrt(numpy.dot(sizes, sizes))
for i, ln_idx in enumerate(ia.lines()):
if i>200:
print('WARNING: K3D nr of line segments is limited to 200.')
break
pts = ia.points()[ln_idx]
kobj = k3d.line(pts.astype(numpy.float32),
color=_rgb2int(iap.GetColor()),
opacity=iap.GetOpacity(),
shader=settings.k3dLineShader,
# width=iap.GetLineWidth()*sqsize/1000,
name=name,
)
settings.notebook_plotter += kobj
####################################################################################
elif settings.notebookBackend == 'panel' and hasattr(vp, 'window') and vp.window:
import panel # https://panel.pyviz.org/reference/panes/VTK.html
vp.renderer.ResetCamera()
settings.notebook_plotter = panel.pane.VTK(vp.window,
width=int(vp.size[0]/1.5),
height=int(vp.size[1]/2))
####################################################################################
elif 'ipyvtk' in settings.notebookBackend and hasattr(vp, 'window') and vp.window:
from ipyvtklink.viewer import ViewInteractiveWidget
vp.renderer.ResetCamera()
settings.notebook_plotter = ViewInteractiveWidget(vp.window)
####################################################################################
elif 'ipygany' in settings.notebookBackend:
from ipygany import PolyMesh, Scene, IsoColor, RGB, Component
from ipygany import Alpha, ColorBar, colormaps, PointCloud
from ipywidgets import FloatRangeSlider, Dropdown, VBox, AppLayout, jslink
bgcol = colors.rgb2hex(colors.getColor(vp.backgrcol))
actors2show2 = []
for ia in actors2show:
if not ia:
continue
if isinstance(ia, vedo.Assembly): #unpack assemblies
assacts = ia.unpack()
for ja in assacts:
if isinstance(ja, vedo.Assembly):
actors2show2 += ja.unpack()
else:
actors2show2.append(ja)
else:
actors2show2.append(ia)
pmeshes = []
colorbar = None
for obj in actors2show2:
# print("ipygany processing:", [obj], obj.name)
if isinstance(obj, vedo.shapes.Line):
lg = obj.diagonalSize()/1000 * obj.GetProperty().GetLineWidth()
vmesh = vedo.shapes.Tube(obj.points(), r=lg, res=4).triangulate()
vmesh.c(obj.c())
faces = vmesh.faces()
# todo: Lines
elif isinstance(obj, Mesh):
vmesh = obj.triangulate()
faces = vmesh.faces()
elif isinstance(obj, Points):
vmesh = obj
faces = []
elif isinstance(obj, Volume):
vmesh = obj.isosurface()
faces = vmesh.faces()
elif isinstance(obj, vedo.TetMesh):
vmesh = obj.tomesh(fill=False)
faces = vmesh.faces()
else:
print("ipygany backend: cannot process object type", [obj])
continue
vertices = vmesh.points()
scals = vmesh.inputdata().GetPointData().GetScalars()
if scals and not colorbar: # there is an active array, only pick the first
aname = scals.GetName()
arr = vmesh.pointdata[aname]
parr = Component(name=aname, array=arr)
if len(faces):
pmesh = PolyMesh(vertices=vertices, triangle_indices=faces, data={aname: [parr]})
else:
pmesh = PointCloud(vertices=vertices, data={aname: [parr]})
rng = scals.GetRange()
colored_pmesh = IsoColor(pmesh, input=aname, min=rng[0], max=rng[1])
if obj.scalarbar:
colorbar = ColorBar(colored_pmesh)
colormap_slider_range = FloatRangeSlider(value=rng,
min=rng[0], max=rng[1],
step=(rng[1] - rng[0]) / 100.)
jslink((colored_pmesh, 'range'), (colormap_slider_range, 'value'))
colormap = Dropdown(
options=colormaps,
description='Colormap:'
)
jslink((colored_pmesh, 'colormap'), (colormap, 'index'))
else:
if len(faces):
pmesh = PolyMesh(vertices=vertices, triangle_indices=faces)
else:
pmesh = PointCloud(vertices=vertices)
if vmesh.alpha() < 1:
colored_pmesh = Alpha(RGB(pmesh, input=tuple(vmesh.color())), input=vmesh.alpha())
else:
colored_pmesh = RGB(pmesh, input=tuple(vmesh.color()))
pmeshes.append(colored_pmesh)
if colorbar:
scene = AppLayout(
left_sidebar=Scene(pmeshes, background_color=bgcol),
right_sidebar=VBox((colormap_slider_range, #not working
colorbar,
colormap)),
pane_widths=[2, 0, 1],
)
else:
scene = Scene(pmeshes, background_color=bgcol)
settings.notebook_plotter = scene
####################################################################################
elif '2d' in settings.notebookBackend.lower() and hasattr(vp, 'window') and vp.window:
import PIL.Image
try:
import IPython
except ImportError:
raise Exception('IPython not available.')
from vedo.io import screenshot
settings.screeshotLargeImage = True
nn = screenshot(returnNumpy=True, scale=settings.screeshotScale+2)
pil_img = PIL.Image.fromarray(nn)
settings.notebook_plotter = IPython.display.display(pil_img)
return settings.notebook_plotter
def visualize_it(res_file, temp_dir=".temp", default_index=0):
import pathlib
import meshio
from ipygany import ColorBar, IsoColor, PolyMesh, Scene, Warp, colormaps
from IPython.display import clear_output, display
from ipywidgets import AppLayout, Dropdown, FloatSlider, VBox, jslink
from ada.core.vector_utils import vector_length
res_file = pathlib.Path(res_file).resolve().absolute()
suffix = res_file.suffix.lower()
suffix_map = {".rmed": "med", ".vtu": None}
imesh = meshio.read(res_file, file_format=suffix_map[suffix])
imesh.point_data = {
key.replace(" ", "_"): value
for key, value in imesh.point_data.items()
}
def filter_keys(var):
if suffix == ".vtu" and var != "U":
return False
if suffix == ".rmed" and var == "point_tags":
return False
return True
warp_data = [key for key in filter(filter_keys, imesh.point_data.keys())]
magn_data = []
for d in warp_data:
res = [vector_length(v[:3]) for v in imesh.point_data[d]]
res_norm = [r / max(res) for r in res]
magn_data_name = f"{d}_magn"
imesh.point_data[magn_data_name] = np.array(res_norm, dtype=np.float64)
magn_data.append(magn_data_name)
imesh.field_data = {
key: np.array(value)
for key, value in imesh.field_data.items()
}
tf = (pathlib.Path(temp_dir).resolve().absolute() /
res_file.name).with_suffix(".vtu")
if tf.exists():
os.remove(tf)
os.makedirs(tf.parent, exist_ok=True)
imesh.write(tf)
mesh = PolyMesh.from_vtk(str(tf))
mesh.default_color = "gray"
warp_vec = warp_data[default_index]
try:
colored_mesh = IsoColor(mesh,
input=magn_data[default_index],
min=0.0,
max=1.0)
except KeyError as e:
trace_str = traceback.format_exc()
logging.error(f'KeyError "{e}"\nTrace: "{trace_str}"')
colored_mesh = mesh
except ImportError as e:
trace_str = traceback.format_exc()
logging.error("This might be")
logging.error(f'ImportError "{e}"\nTrace: "{trace_str}"')
return
warped_mesh = Warp(colored_mesh, input=warp_vec, warp_factor=0.0)
warp_slider = FloatSlider(value=0.0, min=-1.0, max=1.0)
jslink((warped_mesh, "factor"), (warp_slider, "value"))
# Create a colorbar widget
colorbar = ColorBar(colored_mesh)
# Colormap choice widget
colormap = Dropdown(options=colormaps, description="colormap:")
jslink((colored_mesh, "colormap"), (colormap, "index"))
# EigenValue choice widget
eig_map = Dropdown(options=warp_data, description="Data Value:")
scene = Scene([warped_mesh])
app = AppLayout(left_sidebar=scene,
right_sidebar=VBox(
(eig_map, warp_slider, colormap, colorbar)),
pane_widths=[2, 0, 1])
def change_input(change):
vec_name = change["new"]
logging.info(vec_name)
colored_mesh.input = vec_name + "_magn"
warped_mesh.input = vec_name
# Highly inefficient but likely needed due to bug https://github.com/QuantStack/ipygany/issues/69
clear_output()
display(app)
eig_map.observe(change_input, names=["value"])
return app