Add numpy array support to initialize_cells for napari integration

Tests/test_vertexModel.py

@@ -12,9 +12,9 @@
 from src.pyVertexModel.algorithm.vertexModel import create_tetrahedra
 from src.pyVertexModel.algorithm.vertexModelBubbles import build_topo, SeedWithBoundingBox, generate_first_ghost_nodes, \
     delaunay_compute_entities, VertexModelBubbles
-from src.pyVertexModel.algorithm.vertexModelVoronoiFromTimeImage import build_triplets_of_neighs, calculate_neighbours, \
-    VertexModelVoronoiFromTimeImage, add_tetrahedral_intercalations, build_2d_voronoi_from_image, \
-    populate_vertices_info, calculate_vertices, get_four_fold_vertices, divide_quartets_neighbours, process_image
+from src.pyVertexModel.algorithm.vertexModelVoronoiFromTimeImage import build_triplets_of_neighs, \
+    VertexModelVoronoiFromTimeImage, add_tetrahedral_intercalations, \
+    get_four_fold_vertices, divide_quartets_neighbours, process_image
 from src.pyVertexModel.geometry.degreesOfFreedom import DegreesOfFreedom
 from src.pyVertexModel.util.utils import save_backup_vars
 
@@ -496,3 +496,84 @@ def test_initialize_voronoi_from_time_image(self):
         assert_array1D(g_test, mat_info['g'])
         assert_matrix(K_test, mat_info['K'])
 
+    def test_initialize_cells_with_numpy_array(self):
+        """
+        Test that initialize_cells can accept a numpy array directly.
+        :return:
+        """
+        import scipy.io
+        from src.pyVertexModel.parameters.set import Set
+
+        # Load an existing image as a numpy array
+        mat_data = scipy.io.loadmat('resources/LblImg_imageSequence.mat')
+        img_array = mat_data['imgStackLabelled']
+
+        # Create a simple 2D labeled image for testing
+        # Using a subset to make it faster
+        img_2d = img_array[:, :, 0]
+
+        # Create settings
+        set_test = Set(set_option='voronoi_from_image')
+        set_test.TotalCells = 50  # Use fewer cells for faster testing
+        set_test.CellHeight = 10
+
+        # Test with numpy array input
+        vModel_test = VertexModelVoronoiFromTimeImage(set_option='voronoi_from_image', set_test=set_test, 
+                                                      create_output_folder=False)
+        vModel_test.initialize_cells(img_2d)
+
+        # Verify that the geometry was created
+        assert vModel_test.geo is not None, "Geometry should be initialized"
+        assert vModel_test.geo.nCells > 0, "Should have cells"
+        assert len(vModel_test.geo.Cells) > 0, "Should have Cell objects"
+
+    def test_process_image_with_numpy_array(self):
+        """
+        Test that process_image can handle numpy array input.
+        :return:
+        """
+        # Create a simple labeled image
+        test_img = np.zeros((100, 100), dtype=np.uint16)
+        # Create some labeled regions
+        test_img[10:30, 10:30] = 1
+        test_img[40:60, 40:60] = 2
+        test_img[70:90, 70:90] = 3
+
+        # Test process_image with numpy array
+        img2d, img_stack = process_image(test_img)
+
+        # Verify the output
+        assert img2d is not None, "2D image should be returned"
+        assert img_stack is not None, "Image stack should be returned"
+        assert img2d.shape == test_img.shape, "2D image should have same shape as input"
+
+    def test_initialize_with_numpy_array(self):
+        """
+        Test that initialize method can accept a numpy array.
+        :return:
+        """
+        import scipy.io
+        from src.pyVertexModel.parameters.set import Set
+
+        # Load an existing image as a numpy array
+        mat_data = scipy.io.loadmat('resources/LblImg_imageSequence.mat')
+        img_array = mat_data['imgStackLabelled']
+
+        # Use a 2D slice for faster testing
+        img_2d = img_array[:, :, 0]
+
+        # Create settings
+        set_test = Set(set_option='voronoi_from_image')
+        set_test.TotalCells = 50
+        set_test.CellHeight = 10
+
+        # Test initialize with numpy array input
+        vModel_test = VertexModelVoronoiFromTimeImage(set_option='voronoi_from_image', set_test=set_test,
+                                                      create_output_folder=False)
+        vModel_test.initialize(img_2d)
+
+        # Verify that the geometry was created
+        assert vModel_test.geo is not None, "Geometry should be initialized"
+        assert vModel_test.geo.nCells > 0, "Should have cells"
+
+

src/pyVertexModel/algorithm/vertexModel.py

@@ -251,9 +251,11 @@ def __init__(self, set_option='wing_disc', c_set=None, create_output_folder=True
         self.tr = 0
         self.numStep = 1
 
-    def  initialize(self):
+    def  initialize(self, img_input=None):
         """
         Initialize the geometry and the topology of the model.
+        :param img_input: Optional. Either a filename (str) or a numpy array containing the image. 
+                         If None, uses the filename from settings.
         """
         filename = os.path.join(PROJECT_DIRECTORY, self.set.initial_filename_state)
 
@@ -285,7 +287,10 @@ def  initialize(self):
                 self.geo = Geo(mat_info['Geo'])
                 self.geo.update_measures()
             else:
-                self.initialize_cells(filename)
+                if img_input is None:
+                    self.initialize_cells(filename)
+                else:
+                    self.initialize_cells(img_input)
 
             # Resize the geometry to a given cell volume average
             self.geo.resize_tissue()