use image edge flip function

src/gnomon_package_tissueimagemesh/algorithm/meshFilter/surfaceCellMeshFlipOptimization.py

@@ -13,7 +13,7 @@ from copy import deepcopy
 
 import numpy as np
 
-from cellcomplex.property_topomesh.optimization import property_topomesh_edge_flip_optimization
+from timagetk_geometry.image_surface.tissue_image_mesh import surface_tissue_mesh_image_edge_flip_optimization
 
 
 # {# gnomon, plugin.class
@@ -46,37 +46,12 @@ class surfaceCellMeshFlipOptimization(gnomon.core.gnomonAbstractMeshFilter):
             # implement the run method
 
             if self['iterations']>0:
-                vertex_cells = surface_topomesh.wisp_property('label', 0)
-                unique_cells = np.unique(vertex_cells.values())
-                cell_vertices = {c: [] for c in unique_cells}
-                for v, c in vertex_cells.items():
-                    cell_vertices[c] += [v]
-    
                 seg_img = self.seg_img[time]
-                image_cell_edges = np.array([w for w in seg_img.wall_ids()])
-                image_edges = []
-                for c1, c2 in image_cell_edges:
-                    if c1 in cell_vertices and c2 in cell_vertices:
-                        image_edges += [
-                            (v1, v2)
-                            for v1 in cell_vertices[c1] for v2 in cell_vertices[c2]
-                        ]
-                        image_edges += [
-                            (v2, v1)
-                            for v1 in cell_vertices[c1] for v2 in cell_vertices[c2]
-                        ]
-                image_edges = np.array(image_edges)
-    
-                omega_energies = {'image': 1}
-                if self['regularization'] > 0:
-                    omega_energies.update({'regularization': self['regularization']})
-    
-                property_topomesh_edge_flip_optimization(
+                surface_topomesh = surface_tissue_mesh_image_edge_flip_optimization(
                     surface_topomesh,
+                    seg_img,
                     iterations=self['iterations'],
-                    omega_energies=omega_energies,
-                    simulated_annealing=False,
-                    image_edges=image_edges
+                    regularization_weight=self['regularization']
                 )
 
             self.surface_topomesh[time] = surface_topomesh

src/gnomon_package_tissueimagemesh/algorithm/meshFilter/surfaceMeshCellProjection.py

@@ -53,7 +53,9 @@ class surfaceMeshCellProjection(gnomon.core.gnomonAbstractMeshFilter):
                 method=self['method']
             )
 
-            if self['remove_isolated_labels']:
-                surface_vertex_remove_isolated_labels(surface_topomesh)
+            surface_vertex_remove_isolated_labels(
+                surface_topomesh,
+                background_only=not self['remove_isolated_labels']
+            )
 
             self.surface_topomesh[time] = surface_topomesh