use function in mesh decimation

src/gnomon_package_tissueimagemesh/algorithm/meshFilter/surfaceCellMeshDecimation.py

@@ -9,20 +9,12 @@ from gnomon.utils.decorators import meshInput, meshOutput
 # #}
 # add your imports before the next gnomon tag
 
-from copy import deepcopy
+from timagetk_geometry.image_surface.tissue_image_mesh import surface_tissue_mesh_collapse_same_label_edges
 
-import numpy as np
-import scipy.ndimage as nd
-
-from cellcomplex.property_topomesh.analysis import compute_topomesh_property, compute_topomesh_vertex_property_from_faces
-from cellcomplex.property_topomesh.topological_operations import topomesh_collapse_edge
-from cellcomplex.property_topomesh.extraction import clean_topomesh_properties
-
-from cellcomplex.utils import array_dict
 
 # {# gnomon, plugin.class
 # do not modify, any code after the gnomon tag will be overwritten
-@algorithmPlugin(version='0.1.0', coreversion='0.81.0', name="Surface Cell Projection")
+@algorithmPlugin(version='0.1.0', coreversion='0.81.0', name="Surface cell mesh decimation")
 @meshInput(attr='in_surface_topomesh', data_plugin='gnomonMeshDataPropertyTopomesh')
 @meshOutput(attr='surface_topomesh', data_plugin='gnomonMeshDataPropertyTopomesh')
 class surfaceCellMeshDecimation(gnomon.core.gnomonAbstractMeshFilter):
@@ -35,57 +27,21 @@ class surfaceCellMeshDecimation(gnomon.core.gnomonAbstractMeshFilter):
 
         self._parameters = {}
 
-        # self.seg_img = {}
         self.in_surface_topomesh = {}
         self.surface_topomesh = {}
 
     def run(self):
         self.surface_topomesh = {}
         for time in self.in_surface_topomesh.keys():
-            surface_topomesh = deepcopy(self.in_surface_topomesh[time])
+            in_surface_topomesh = self.in_surface_topomesh[time]
             # #}
             # implement the run method
 
-            edges = np.array(list(surface_topomesh.wisps(1)))
-            edge_vertices = surface_topomesh.wisp_property('vertices', 1).values(edges)
-            edge_vertex_cells = surface_topomesh.wisp_property('label',  0).values(edge_vertices)
-
-            inner_edges = edges[edge_vertex_cells[:, 1] == edge_vertex_cells[:, 0]]
-            inner_edge_lengths = surface_topomesh.wisp_property('length', 1).values(inner_edges)
-
-            inner_edges = inner_edges[np.argsort(inner_edge_lengths)]
-            collapsed_edges = inner_edges
-
-            iteration = 0
-            while len(collapsed_edges)>0:
-                collapsed_edges = []
-                affected_edges = set()
-                for e in inner_edges:
-                    if not e in affected_edges:
-                        neighbor_edges = set(surface_topomesh.border_neighbors(1, e))
-                        collapsed = topomesh_collapse_edge(surface_topomesh, e)
-                        if collapsed:
-                            collapsed_edges += [e]
-                            affected_edges |= set(neighbor_edges)
-                iteration += 1
-                print(f"Collapsed {len(collapsed_edges)} edges")
-
-                clean_topomesh_properties(surface_topomesh)
-                compute_topomesh_property(surface_topomesh, 'vertices', 1)
-                compute_topomesh_property(surface_topomesh, 'length', 1)
-
-                edges = np.array(list(surface_topomesh.wisps(1)))
-                edge_vertices = surface_topomesh.wisp_property('vertices', 1).values(edges)
-                edge_vertex_cells = surface_topomesh.wisp_property('label',  0).values(edge_vertices)
-
-                inner_edges = edges[edge_vertex_cells[:, 1] == edge_vertex_cells[:, 0]]
-                inner_edge_lengths = surface_topomesh.wisp_property('length', 1).values(inner_edges)
-
-                inner_edges = inner_edges[np.argsort(inner_edge_lengths)]
+            surface_topomesh = surface_tissue_mesh_collapse_same_label_edges(
+                in_surface_topomesh
+            )
 
-                compute_topomesh_property(surface_topomesh, 'borders', 2)
-                compute_topomesh_property(surface_topomesh, 'vertices', 2)
-                compute_topomesh_property(surface_topomesh, 'oriented_vertices', 2)
-                compute_topomesh_property(surface_topomesh, 'oriented_borders', 3)
+            print(surface_topomesh.nb_wisps(0))
+            print(surface_topomesh.wisp_property('label', 0))
 
             self.surface_topomesh[time] = surface_topomesh