Improve vertexModel.initialize efficacy

[Pablo1990]

It is taking too much. Here is the report:

Name | Call count | Time (ms) | own time (ms) VertexModelVoronoiFromTimeImage.calculate_vertices | 2 | 3298 | 3199 -- | -- | -- | -- Face.compute_face_area | 26973 | 26366 | 2495 VertexModelVoronoiFromTimeImage.calculate_neighbours | 4 | 34122 | 1074 Tris.compute_tri_length_measurements | 129456 | 4824 | 1030 copy_non_mutable_attributes | 40752 | 8698 | 866 Cell.compute_volume_fraction | 23976 | 3830 | 815 Geo.build_global_ids | 1 | 17585 | 814 Tris.ensure_consistent_order | 113274 | 1884 | 504 Face.build_edges | 2997 | 11580 | 442 Tris.is_degenerated | 129456 | 1210 | 366 compute_tri_aspect_ratio | 129456 | 1612 | 299 Geo.update_measures | 7 | 30001 | 278 build_edge_based_on_tetrahedra | 2997 | 2549 | 224 sorting_cells_based_on_distance | 1 | 297 | 175 get_interface | 84516 | 218 | 137   | 24273 | 98 | 98 Geo.ensure_consistent_tris_order | 7 | 1981 | 97 Geo.build_cells | 1 | 47420 | 86 Cell.compute_volume | 1200 | 4070 | 57 Face.build_face | 2997 | 14903 | 54 Tris.__init__ | 48546 | 53 | 53   | 13485 | 49 | 49   | 13485 | 49 | 49   | 8991 | 44 | 44 compute_y | 5394 | 492 | 41   | 151050 | 40 | 40 Geo.update_lmin0 | 2 | 8417 | 39 VertexModelVoronoiFromTimeImage.initialize | 1 | 117900 | 38   | 10788 | 36 | 36 Face.__init__ | 8991 | 45 | 35 Cell.compute_neighbours | 2592 | 78 | 34 Tris.copy | 32364 | 3143 | 33 Cell.compute_area | 2100 | 125 | 29 boundary_of_cell | 300 | 229 | 26 Face.copy | 5994 | 8589 | 24   | 8991 | 23 | 23 create_tetrahedra | 2 | 325 | 22 Geo.get_opposite_border_cell | 95 | 51 | 21   | 5844 | 18 | 18   | 5994 | 3160 | 17 Geo.init_reference_values_and_noise | 2 | 201 | 17   | 300 | 17 | 17 VertexModelVoronoiFromTimeImage.build_2d_voronoi_from_image | 2 | 37906 | 15 Face.build_face_centre | 2997 | 160 | 13 Face.build_interface_type | 2997 | 100 | 13 Cell.build_y_from_x | 150 | 505 | 12   | 5394 | 12 | 12 Cell.__init__ | 3588 | 20 | 11   | 5394 | 10 | 10 Geo.resize_tissue | 1 | 8435 | 9 VertexModelVoronoiFromTimeImage.obtain_initial_x_and_tetrahedra | 1 | 38707 | 7   | 300 | 24 | 7 Geo.update_barrier_tri0 | 2 | 9097 | 6 build_quartets_of_neighs_2d | 2 | 10 | 6 Cell.copy | 2392 | 8850 | 5 VertexModelVoronoiFromTimeImage.populate_vertices_info | 2 | 3627 | 5   | 2 | 136 | 5 add_tetrahedral_intercalations | 1 | 82 | 5 ismember_rows | 300 | 36 | 5   | 5994 | 5 | 5   | 2392 | 8593 | 4 build_triplets_of_neighs | 2 | 13 | 4 Geo.copy | 2 | 8856 | 3   | 1 | 46 | 3   | 994 | 14 | 3 DegreesOfFreedom.get_dofs | 1 | 7 | 3 Cell.is_scutoid | 1196 | 173 | 2 Geo.compute_average_3d_neighbours | 1 | 15 | 1 generate_neighbours_network | 2 | 5 | 1   | 1 | 131473 | 0 VertexModelVoronoiFromTimeImage.initialize_cells | 1 | 87091 | 0 Geo.init_reference_cell_values | 2 | 17725 | 0   | 1 | 13505 | 0   | 1 | 9450 | 0 save_state | 2 | 5093 | 0   | 1 | 4578 | 0   | 1 | 1585 | 0   | 1 | 1501 | 0   | 1 | 1472 | 0   | 1 | 754 | 0   | 1 | 752 | 0 generate_tetrahedra_from_information | 1 | 326 | 0 process_image | 1 | 297 | 0 VertexModelVoronoiFromTimeImage.adjust_percentage_of_scutoids | 1 | 190 | 0 Geo.compute_percentage_of_scutoids | 1 | 174 | 0   | 1 | 174 | 0 calculate_cell_height_on_model | 1 | 75 | 0 Geo.apply_periodic_boundary_conditions | 1 | 52 | 0   | 2 | 39 | 0   | 2 | 39 | 0   | 2 | 38 | 0   | 1 | 25 | 0   | 1 | 17 | 0 get_four_fold_vertices | 2 | 10 | 0 Geo.get_substrate_z | 2 | 4 | 0   | 2 | 2 | 0   | 2 | 2 | 0 VertexModelVoronoiFromTimeImage.renumber_tets_xs | 1 | 2 | 0 Geo.compute_edge_length_0 | 2 | 1 | 0   | 1 | 1 | 0 Cell.add_noise_to_parameters | 300 | 1 | 0 Set.redirect_output | 1 | 1 | 0   | 2 | 0 | 0   | 300 | 0 | 0 VertexModelVoronoiFromTimeImage.create_temporary_folder | 1 | 0 | 0   | 7 | 0 | 0 VertexModelVoronoiFromTimeImage.__init__ | 1 | 0 | 0 VertexModelVoronoiFromTimeImage.__init__ | 1 | 0 | 0 add_noise_to_parameter | 2400 | 0 | 0   | 300 | 0 | 0 Set.update_derived_parameters | 1 | 0 | 0   | 2 | 0 | 0   | 1 | 0 | 0   | 2 | 0 | 0   | 1 | 0 | 0   | 1 | 0 | 0   | 95 | 0 | 0 Geo.compute_centre_of_tissue | 1 | 0 | 0   | 1 | 0 | 0   | 2 | 0 | 0   | 2 | 0 | 0   | 1 | 0 | 0   | 514 | 0 | 0   | 2 | 0 | 0   | 2 | 0 | 0   | 1 | 0 | 0   | 1 | 0 | 0   | 1 | 0 | 0   | 1 | 0 | 0   | 1 | 0 | 0   | 1 | 0 | 0   | 1 | 0 | 0 add_faces_and_vertices_to_x | 2 | 0 | 0   | 1 | 0 | 0   | 2 | 0 | 0   | 1 | 0 | 0   | 1 | 0 | 0   | 2 | 0 | 0   | 1 | 0 | 0 Set.__init__ | 1 | 0 | 0   | 1 | 0 | 0   | 1 | 0 | 0   | 1 | 0 | 0   | 2 | 0 | 0 VertexModel | 1 | 0 | 0   | 2 | 0 | 0   | 2 | 0 | 0   | 2 | 0 | 0 Geo | 1 | 0 | 0 Set.define_if_not_defined | 17 | 0 | 0 Cell | 1 | 0 | 0 Geo.__init__ | 3 | 0 | 0 Set | 1 | 0 | 0 VertexModelVoronoiFromTimeImage | 1 | 0 | 0   | 1 | 0 | 0 Set.wing_disc_equilibrium | 1 | 0 | 0 KgVolume | 1 | 0 | 0 KgSurfaceCellBasedAdhesion | 1 | 0 | 0 Kg | 1 | 0 | 0 Remodelling | 1 | 0 | 0 Tris | 1 | 0 | 0 screenshot_ | 2 | 0 | 0 Face | 1 | 0 | 0 KgViscosity | 1 | 0 | 0 DegreesOfFreedom | 1 | 0 | 0 DegreesOfFreedom.__init__ | 1 | 0 | 0 Set.check_for_non_used_parameters | 1 | 0 | 0 KgContractility | 1 | 0 | 0   | 1 | 0 | 0 KgContractilityExternal | 1 | 0 | 0 KgSubstrate | 1 | 0 | 0 VertexModelVoronoiFromTimeImage.change_tissue_height | 1 | 0 | 0   | 1 | 0 | 0   | 1 | 0 | 0 KgTriEnergyBarrier | 1 | 0 | 0 KgTriAREnergyBarrier | 1 | 0 | 0   | 1 | 0 | 0   | 1 | 0 | 0   | 1 | 0 | 0   | 1 | 0 | 0   | 1 | 0 | 0 �