def test_mesh_data_creation():
vertices, triangles, data_1d, data_3d = get_test_assets()
poly = PolyMesh(vertices=vertices,
triangle_indices=triangles,
data={
'1d': [Component('x', np.array([0., 0., 0.]))],
'2d': [
Component('x', np.array([1., 1., 1.])),
Component('y', np.array([2., 2., 2.]))
]
})
assert np.all(np.equal(poly['1d', 'x'].array, np.array([0., 0., 0.])))
assert np.all(np.equal(poly['2d', 'x'].array, np.array([1., 1., 1.])))
assert np.all(np.equal(poly['2d', 'y'].array, np.array([2., 2., 2.])))
poly = PolyMesh(vertices=vertices,
triangle_indices=triangles,
data={
'1d': {
'x': np.array([0., 0., 0.])
},
'2d': {
'x': np.array([1., 1., 1.]),
'y': np.array([2., 2., 2.])
}
})
assert np.all(np.equal(poly['1d', 'x'].array, np.array([0., 0., 0.])))
assert np.all(np.equal(poly['2d', 'x'].array, np.array([1., 1., 1.])))
assert np.all(np.equal(poly['2d', 'y'].array, np.array([2., 2., 2.])))
def test_default_input():
vertices, triangles, data_1d, data_3d = get_test_assets()
poly = PolyMesh(vertices=vertices, triangle_indices=triangles, data=[data_1d, data_3d])
warped_mesh = Warp(poly)
assert warped_mesh.input == (('1d', 'x'), 0, 0)
poly = PolyMesh(vertices=vertices, triangle_indices=triangles, data=[data_3d])
warped_mesh = Warp(poly)
assert warped_mesh.input == '3d'
def test_data_access():
vertices, triangles, data_1d, data_3d = get_test_assets()
poly = PolyMesh(vertices=vertices, triangle_indices=triangles, data=[data_1d, data_3d])
assert np.all(np.equal(poly['1d', 'x'].array, np.array([0., 0., 0.])))
assert np.all(np.equal(poly['3d', 'y'].array, np.array([2., 2., 2.])))
def test_input():
vertices, triangles, data_1d, data_3d = get_test_assets()
poly = PolyMesh(vertices=vertices, triangle_indices=triangles, data=[data_1d, data_3d])
warped_mesh = Warp(poly)
with pytest.raises(TraitError):
warped_mesh.input = (('1d', 'x'), 0)
warped_mesh.input = ('1d', 0, 0)
assert warped_mesh.input == (('1d', 'x'), 0, 0)
warped_mesh.input = ('1d', 0, 32)
assert warped_mesh.input == (('1d', 'x'), 0, 32)
warped_mesh.input = (0, 0, '1d')
assert warped_mesh.input == (0, 0, ('1d', 'x'))
with pytest.raises(TraitError):
warped_mesh.input = ('3d', 0, 0)
warped_mesh = Warp(poly, input=('1d', 0, 0))
assert warped_mesh.input == (('1d', 'x'), 0, 0)
warped_mesh = Warp(poly, input=(0, 0, '1d'))
assert warped_mesh.input == (0, 0, ('1d', 'x'))
warped_mesh = Warp(warped_mesh, input=(0, '1d', 0))
assert warped_mesh.input == (0, ('1d', 'x'), 0)
def pyvista_polydata_to_polymesh(obj):
"""Import a mesh from ``pyvista`` or ``vtk``.
Copies over the active scalars and only the active scalars.
Parameters
----------
obj : pyvista compatible object
Any object compatible with pyvista. Includes most ``vtk``
objects.
Returns
-------
PolyMesh
``ipygany.PolyMesh`` object.
"""
# attempt to wrap non-pyvista objects
if not pv.is_pyvista_dataset(obj): # pragma: no cover
mesh = pv.wrap(obj)
if not pv.is_pyvista_dataset(mesh):
raise TypeError(f'Object type ({type(mesh)}) cannot be converted to '
'a pyvista dataset')
else:
mesh = obj
# PolyMesh requires vertices and triangles, so we need to
# convert the mesh to an all triangle polydata
if not isinstance(obj, pv.PolyData):
# unlikely case that mesh does not have extract_surface
if not hasattr(mesh, 'extract_surface'): # pragma: no cover
mesh = mesh.cast_to_unstructured_grid()
surf = mesh.extract_surface()
else:
surf = mesh
# convert to an all-triangular surface
if surf.is_all_triangles():
trimesh = surf
else:
trimesh = surf.triangulate()
# finally, pass the triangle vertices to PolyMesh
triangle_indices = trimesh.faces.reshape(-1, 4)[:, 1:]
if not triangle_indices.size:
warnings.warn('Unable to convert mesh to triangular PolyMesh')
# only copy active scalars
data = []
if trimesh.active_scalars is not None:
arr = array('f', trimesh.active_scalars)
components = [ipygany.Component('X1', arr)]
data = [ipygany.Data(trimesh.active_scalars_name, components)]
# for speed, only convert the active scalars later
return PolyMesh(
vertices=trimesh.points,
triangle_indices=triangle_indices,
data=data
)
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 test_default_input():
vertices, triangles, data_1d, data_3d = get_test_assets()
poly = PolyMesh(vertices=vertices,
triangle_indices=triangles,
data=[data_1d, data_3d])
colored_mesh = IsoColor(poly)
assert colored_mesh.input == '1d'
poly = PolyMesh(vertices=vertices,
triangle_indices=triangles,
data=[data_3d])
colored_mesh = IsoColor(poly)
assert colored_mesh.input == (('3d', 'x'), )
def test_colormaps():
vertices, triangles, data_1d, data_3d = get_test_assets()
poly = PolyMesh(vertices=vertices,
triangle_indices=triangles,
data=[data_1d, data_3d])
colored_mesh = IsoColor(poly, colormap='Turbo')
assert colored_mesh.colormap == colormaps.Turbo
colormap = colormaps.Cividis
colored_mesh.colormap = colormap
assert colored_mesh.colormap == colormap
with pytest.raises(ValueError):
colored_mesh.colormap = 'InvalidColor'
with pytest.raises(ValueError):
colored_mesh.colormap = -1
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 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
def mesh_from_arrays(vertices, faces):
return PolyMesh(vertices=vertices, triangle_indices=faces)