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Fix vedo api #88

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Fix vedo api #88

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c59f5e0
replaced `.points()` with `.vertices`
jo-mueller Nov 29, 2023
7060575
fixed call to deprecated `._data`
jo-mueller Nov 29, 2023
d409e92
replaced call to faces()`` with `cells`
jo-mueller Nov 29, 2023
723ae03
replaced deprecated `compute_connectivity`
jo-mueller Nov 29, 2023
747c9d5
update vedo version
jo-mueller Nov 30, 2023
bcdb609
removed `__main__`
jo-mueller Nov 30, 2023
5bf3823
re-introduced connected-components labelling
jo-mueller Dec 5, 2023
f4d2148
Introduced split-mesh function according to new vedo API
jo-mueller Dec 5, 2023
92cd994
Added mention of both functionality (connected components & split) to…
jo-mueller Dec 5, 2023
bc99d09
added test coverage for both
jo-mueller Dec 5, 2023
1d81b06
fixed test
jo-mueller Dec 5, 2023
4bcdd92
Changed connected components labelling function name to original
jo-mueller Dec 5, 2023
0826bb1
removed unused __main__
jo-mueller Dec 6, 2023
0ae5a7b
removed deprecated `origin` display
jo-mueller Dec 6, 2023
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153 changes: 112 additions & 41 deletions docs/connected_component_labeling.ipynb
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11 changes: 6 additions & 5 deletions napari_process_points_and_surfaces/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,8 @@
smooth_pointcloud_moving_least_squares_2d_radius,
smooth_pointcloud_moving_least_squares_2d,
reconstruct_surface_from_pointcloud,
connected_component_labeling
connected_component_labeling,
split_mesh
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This change seems unrelated to the PR title. Also does it break backwards compatibility?

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@haesleinhuepf Thanks for looking at this. I thought about it for a while and came to the conclusion that it really is a breaking change, already from the vedo side. The original compute_connectivity function allowed to retrieve a per-vertex label which indicated to which object it belonged, which we could then nicely display as the vertex color.

In the new version, the id of each vertex isn't public anymore and vedo just returns a list [mesh1, mesh2, ...] of the connected components :/

To answer your question: The function mesh.compute_connectivity() has been renamed in vedo to mesh.split() so I'd consider that as part of an API change, and it has been done so in a breaking way.

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But we could use the split function to implement what has been there before, correct? I'm asking because I'm using this stuff in projects. Removing it is no option

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But we could use the split function to implement what has been there before, correct? I'm asking because I'm using this stuff in projects. Removing it is no option

I'm not sure, tbh. The split function never exposes which vertex belongs to which object. -_-

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But it gives lists of vertices grouped, no?

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It returns a list of meshes. Each mesh consists of vertices [0, n_mesh_i]

)

from ._utils import isotropic_scale_surface
Expand Down Expand Up @@ -116,7 +117,7 @@ def gastruloid() -> "napari.types.SurfaceData":
def _vedo_ellipsoid() -> "napari.types.SurfaceData":
import vedo
shape = vedo.shapes.Ellipsoid().scale(10)
return (shape.points(), np.asarray(shape.faces()))
return (shape.vertices, np.asarray(shape.cells))


def _vedo_stanford_bunny() -> "napari.types.SurfaceData":
Expand Down Expand Up @@ -207,7 +208,7 @@ def surface_to_binary_volume(surface: "napari.types.SurfaceData", as_large_as_im
_init_viewer(viewer)

my_mesh = vedo.mesh.Mesh((surface[0], surface[1]))
vertices = my_mesh.points() # get coordinates of surface vertices
vertices = my_mesh.vertices # get coordinates of surface vertices

# get bounding box of mesh
boundaries_l = np.min(vertices + 0.5, axis=0).astype(int)
Expand Down Expand Up @@ -303,7 +304,7 @@ def all_labels_to_surface(labels: "napari.types.LabelsData", add_label_id_as_val
surface = set_vertex_values(surface, all_values)

return surface
#(mesh.points(), np.asarray(mesh.faces()), mesh.pointdata['OriginalMeshID'])
#(mesh.vertices, np.asarray(mesh.cells), mesh.pointdata['OriginalMeshID'])

# alias
marching_cubes = all_labels_to_surface
Expand Down Expand Up @@ -744,7 +745,7 @@ def fill_holes(surface: "napari.types.SurfaceData", size_limit: float = 100) ->
mesh = vedo.mesh.Mesh((surface[0], surface[1]))
mesh.fill_holes(size=size_limit)

return (mesh.points(), np.asarray(mesh.faces()))
return (mesh.vertices, np.asarray(mesh.cells))

def _check_open3d():
try:
Expand Down
12 changes: 6 additions & 6 deletions napari_process_points_and_surfaces/_quantification.py
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Original file line number Diff line number Diff line change
Expand Up @@ -124,8 +124,8 @@ def add_quality(surface: "napari.types.SurfaceData", quality_id: Quality = Quali
else:
raise NotImplementedError(f"Quality {quality_id} is not implemented.")

vertices = np.asarray(mesh2.points())
faces = np.asarray(mesh2.faces())
vertices = np.asarray(mesh2.vertices)
faces = np.asarray(mesh2.cells)

return SurfaceTuple((vertices, faces, values))

Expand Down Expand Up @@ -272,7 +272,7 @@ def add_curvature_scalars(surface: "napari.types.SurfaceData",
mesh.compute_curvature(method=used_method)
values = mesh.pointdata[curvature_id.name]

return SurfaceTuple((mesh.points(), np.asarray(mesh.faces()), values))
return SurfaceTuple((mesh.vertices, np.asarray(mesh.cells), values))

@register_function(menu="Measurement maps > Surface curvature (sphere-fitted, nppas)")
def add_spherefitted_curvature(surface: "napari.types.SurfaceData", radius: float = 1.0) -> List["napari.types.LayerDataTuple"]:
Expand Down Expand Up @@ -319,7 +319,7 @@ def _add_spherefitted_curvature(surface: "napari.types.SurfaceData", radius: flo
residues = np.zeros(mesh.npoints)
for idx in range(mesh.npoints):

patch = vedo.pointcloud.Points(mesh.closest_point(mesh.points()[idx], radius=radius))
patch = vedo.pointcloud.Points(mesh.closest_point(mesh.vertices[idx], radius=radius))

try:
s = vedo.pointcloud.fit_sphere(patch)
Expand All @@ -337,8 +337,8 @@ def _add_spherefitted_curvature(surface: "napari.types.SurfaceData", radius: flo
properties_curvature_layer = {'name': 'curvature', 'colormap': 'viridis'}
properties_residues_layer = {'name': 'fit residues', 'colormap': 'magma'}

layer1 = (SurfaceTuple((mesh.points(), np.asarray(mesh.faces()), curvature)), properties_curvature_layer, 'surface')
layer2 = (SurfaceTuple((mesh.points(), np.asarray(mesh.faces()), residues)), properties_residues_layer, 'surface')
layer1 = (SurfaceTuple((mesh.vertices, np.asarray(mesh.cells), curvature)), properties_curvature_layer, 'surface')
layer2 = (SurfaceTuple((mesh.vertices, np.asarray(mesh.cells), residues)), properties_residues_layer, 'surface')

return [layer1, layer2]

Expand Down
2 changes: 1 addition & 1 deletion napari_process_points_and_surfaces/_tests/test_function.py
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Original file line number Diff line number Diff line change
Expand Up @@ -109,7 +109,7 @@ def test_curvature():
import numpy as np

shape = vedo.shapes.Ellipsoid()
surface_data = (shape.points(), np.asarray(shape.faces()))
surface_data = (shape.vertices, np.asarray(shape.cells))

add_curvature_scalars(surface_data, Curvature.Gauss_Curvature)
add_curvature_scalars(surface_data, Curvature.Mean_Curvature)
Expand Down
6 changes: 4 additions & 2 deletions napari_process_points_and_surfaces/_tests/test_vedo_functions.py
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Expand Up @@ -32,9 +32,11 @@ def test_connected_components():
image[20:29, 20:29, 20:29] = 2

surface = nppas.all_labels_to_surface(image)
connected_components = nppas.connected_component_labeling(surface)
connected_components = nppas.split_mesh(surface)
assert len(connected_components) == 2
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assert len(np.unique(connected_components[2])) == 2
labelled_components = nppas.connected_component_labeling(surface)
assert len(np.unique((labelled_components[2]))) == 2

def test_decimate():
import napari_process_points_and_surfaces as nppas
Expand Down
93 changes: 75 additions & 18 deletions napari_process_points_and_surfaces/_vedo.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
from napari_tools_menu import register_function
import numpy as np
from typing import List

def to_vedo_mesh(surface):
_hide_vtk_warnings()
Expand Down Expand Up @@ -67,7 +68,7 @@ def _repr_html_(self):
# mesh statistics
bounds = "<br/>".join(["{min_x:.3f}...{max_x:.3f}".format(min_x=min_x, max_x=max_x) for min_x, max_x in zip(mesh.bounds()[::2], mesh.bounds()[1::2])])
average_size = "{size:.3f}".format(size=mesh.average_size())
center_of_mass = ",".join(["{size:.3f}".format(size=x) for x in mesh.centerOfMass()])
center_of_mass = ",".join(["{size:.3f}".format(size=x) for x in mesh.center_of_mass()])
scale = ",".join(["{size:.3f}".format(size=x) for x in mesh.scale()])
histogram = ""
min_max = ""
Expand Down Expand Up @@ -104,13 +105,12 @@ def _repr_html_(self):
"<td style=\"text-align: center; vertical-align: top;\">",
help_text,
"<table>",
"<tr><td>origin (z/y/x)</td><td>" + str(mesh.origin()).replace(" ", "&nbsp;") + "</td></tr>",
"<tr><td>center of mass(z/y/x)</td><td>" + center_of_mass.replace(" ", "&nbsp;") + "</td></tr>",
"<tr><td>scale(z/y/x)</td><td>" + scale.replace(" ", "&nbsp;") + "</td></tr>",
"<tr><td>bounds (z/y/x)</td><td>" + str(bounds).replace(" ", "&nbsp;") + "</td></tr>",
"<tr><td>average size</td><td>" + str(average_size) + "</td></tr>",
"<tr><td>number of vertices</td><td>" + str(mesh.npoints) + "</td></tr>",
"<tr><td>number of faces</td><td>" + str(len(mesh.faces())) + "</td></tr>",
"<tr><td>number of faces</td><td>" + str(len(mesh.cells)) + "</td></tr>",
min_max,
"</table>",
histogram,
Expand All @@ -124,13 +124,13 @@ def _repr_html_(self):

def to_napari_surface_data(vedo_mesh, values=None):
if values is None:
return SurfaceTuple((vedo_mesh.points(), np.asarray(vedo_mesh.faces())))
return SurfaceTuple((vedo_mesh.vertices, np.asarray(vedo_mesh.cells)))
else:
return SurfaceTuple((vedo_mesh.points(), np.asarray(vedo_mesh.faces()), values))
return SurfaceTuple((vedo_mesh.vertices, np.asarray(vedo_mesh.cells), values))


def to_napari_points_data(vedo_points):
return vedo_points.points()
return vedo_points.vertices


def _hide_vtk_warnings():
Expand Down Expand Up @@ -184,26 +184,83 @@ def remove_duplicate_vertices(surface: "napari.types.SurfaceData", viewer: "napa


@register_function(menu="Surfaces > Connected components labeling (vedo, nppas)")
def connected_component_labeling(surface: "napari.types.SurfaceData", viewer: "napari.Viewer" = None) -> "napari.types.SurfaceData":
def connected_component_labeling(
surface: "napari.types.SurfaceData",
viewer: "napari.Viewer" = None) -> 'napari.types.SurfaceData':
from ._utils import _init_viewer
import vtk
import vtk.util.numpy_support as vtk_to_np

_init_viewer(viewer)

mesh = to_vedo_mesh(surface)

# Set up connectivity filter
conn = vtk.vtkConnectivityFilter()
conn.SetInputData(mesh.dataset)
conn.SetExtractionModeToAllRegions()

# Enable coloring of regions
conn.ColorRegionsOn()
conn.Update()
result = conn.GetOutput()

region_ids = vtk_to_np.vtk_to_numpy(
result.GetCellData().GetArray("RegionId"))

vertex_labels = np.zeros(mesh.npoints, dtype=np.uint32)
vertex_labels[np.asarray(mesh.cells)[:, 0]] = region_ids
vertex_labels[np.asarray(mesh.cells)[:, 1]] = region_ids
vertex_labels[np.asarray(mesh.cells)[:, 2]] = region_ids

return SurfaceTuple((
surface[0],
np.asarray(surface[1]),
vertex_labels))


def split_mesh(
surface: "napari.types.SurfaceData"
) -> list:
"""
Split a mesh into its connected components.

See Also
--------
..[0] https://vedo.embl.es/docs/vedo/mesh.html#Mesh.split
"""
Determine the connected components of a surface mesh.
mesh = to_vedo_mesh(surface)
meshes = mesh.split()

meshes_out = [
SurfaceTuple(to_napari_surface_data(mesh)) for mesh in meshes
]

return meshes_out


@register_function(menu="Surfaces > Split mesh (vedo, nppas)")
def _split_mesh(
surface: "napari.types.SurfaceData",
viewer: "napari.Viewer" = None
) -> List["napari.types.LayerDataTuple"]:
"""
Split a mesh into its connected components.

See Also
--------
..[0] https://vedo.embl.es/docs/vedo/mesh.html#Mesh.compute_connectivity
..[0] https://vedo.embl.es/docs/vedo/mesh.html#Mesh.split

"""
from ._quantification import set_vertex_values
from ._utils import _init_viewer
_init_viewer(viewer)

mesh = to_vedo_mesh(surface)
mesh.compute_connectivity()
region_id = mesh.pointdata["RegionId"]

mesh_out = to_napari_surface_data(mesh)
mesh_out = set_vertex_values(mesh_out, region_id)
meshes = split_mesh(surface)

return mesh_out
return [(mesh,
{'colormap': 'hsv',
'name': 'Component ' + str(i)},
'surface') for i, mesh in enumerate(meshes)]


@register_function(menu="Surfaces > Smooth (moving least squares, vedo, nppas)")
Expand Down Expand Up @@ -411,7 +468,7 @@ def subdivide_adaptive(surface: "napari.types.SurfaceData",

if maximum_edge_length == 0:
maximum_edge_length = mesh_in.diagonal_size(
) / np.sqrt(mesh_in._data.GetNumberOfPoints()) / number_of_iterations
) / np.sqrt(mesh_in.npoints) / number_of_iterations

mesh_out = mesh_in.subdivide(
number_of_iterations, method=2, mel=maximum_edge_length)
Expand Down
2 changes: 1 addition & 1 deletion setup.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ install_requires =
napari-tools-menu>=0.1.14
napari-time-slicer>=0.4.5
napari-workflows>=0.2.3
vedo>=2022.4.1
vedo>=2022.5.0
napari-skimage-regionprops>=0.5.5
pandas
imageio!=2.22.1
Expand Down
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