Fix vedo api

napari_process_points_and_surfaces/__init__.py

@@ -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
                     )
 
 from ._utils import isotropic_scale_surface
@@ -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":
@@ -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)
@@ -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
@@ -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:

napari_process_points_and_surfaces/_quantification.py

@@ -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))
 
@@ -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"]:
@@ -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)
@@ -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]
 

napari_process_points_and_surfaces/_tests/test_function.py

@@ -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)

napari_process_points_and_surfaces/_tests/test_vedo_functions.py

@@ -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
 
-    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
@@ -208,3 +210,6 @@ def test_create_convex_hull_from_points():
 #    gastruloid = nppas.gastruloid()
 #
 #    nppas.show(gastruloid)
+
+if __name__ == '__main__':
+    test_connected_components()

napari_process_points_and_surfaces/_vedo.py

@@ -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()
@@ -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 = ""
@@ -104,13 +105,13 @@ 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>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,
@@ -124,13 +125,13 @@ 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():
@@ -184,26 +185,83 @@ 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)")
@@ -411,7 +469,7 @@ 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)

setup.cfg

@@ -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