pyVertexModel 1.0.3.dev0__tar.gz → 1.0.5__tar.gz

{pyvertexmodel-1.0.3.dev0 → pyvertexmodel-1.0.5}/.github/workflows/python-publish.yml

@@ -28,8 +28,8 @@ jobs:
 
       - name: Build release distributions
         run: |
-          python -m pip install build
-          python -m build
+          python -m pip install --upgrade pip build twine setuptools setuptools-scm
+          python -m build --sdist -o dist
 
       - name: Upload distributions
         uses: actions/upload-artifact@v4

{pyvertexmodel-1.0.3.dev0 → pyvertexmodel-1.0.5}/.gitignore

@@ -192,3 +192,7 @@ data/
 Input
 
 *.xlsx
+
+src/pyVertexModel/_version.py
+
+Temp/

{pyvertexmodel-1.0.3.dev0 → pyvertexmodel-1.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyVertexModel
-Version: 1.0.3.dev0
+Version: 1.0.5
 License-File: LICENSE
 Requires-Dist: cython
 Requires-Dist: numpy
@@ -14,4 +14,5 @@ Requires-Dist: networkx
 Requires-Dist: pyvista
 Requires-Dist: scikit-learn
 Requires-Dist: matplotlib
+Requires-Dist: seaborn
 Dynamic: license-file

{pyvertexmodel-1.0.3.dev0 → pyvertexmodel-1.0.5}/Tests/test_vertexModel.py

@@ -12,9 +12,9 @@ from src.pyVertexModel.algorithm.newtonRaphson import newton_raphson
 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 @@ class TestVertexModel(Tests):
         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"
+
+

{pyvertexmodel-1.0.3.dev0 → pyvertexmodel-1.0.5}/pyVertexModel.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyVertexModel
-Version: 1.0.3.dev0
+Version: 1.0.5
 License-File: LICENSE
 Requires-Dist: cython
 Requires-Dist: numpy
@@ -14,4 +14,5 @@ Requires-Dist: networkx
 Requires-Dist: pyvista
 Requires-Dist: scikit-learn
 Requires-Dist: matplotlib
+Requires-Dist: seaborn
 Dynamic: license-file

{pyvertexmodel-1.0.3.dev0 → pyvertexmodel-1.0.5}/pyVertexModel.egg-info/SOURCES.txt

@@ -23,6 +23,7 @@ uv.lock
 .idea/vcs.xml
 .idea/inspectionProfiles/profiles_settings.xml
 .run/analyse_simulations.run.xml
+Input/wing_disc_150.mat
 Tests/__init__.py
 Tests/test_cell.py
 Tests/test_degreesOfFreedom.py
@@ -110,16 +111,4 @@ src/pyVertexModel/parameters/set.py
 src/pyVertexModel/util/__init__.py
 src/pyVertexModel/util/add_to_pythonpath.sh
 src/pyVertexModel/util/space_exploration.py
-src/pyVertexModel/util/utils.py
-tests/test_cell.py
-tests/test_degreesOfFreedom.py
-tests/test_face.py
-tests/test_flip.py
-tests/test_geo.py
-tests/test_kg.py
-tests/test_newtonRaphson.py
-tests/test_remodelling.py
-tests/test_tris.py
-tests/test_utils.py
-tests/test_vertexModel.py
-tests/tests.py
+src/pyVertexModel/util/utils.py

{pyvertexmodel-1.0.3.dev0 → pyvertexmodel-1.0.5}/pyVertexModel.egg-info/requires.txt

@@ -10,3 +10,4 @@ networkx
 pyvista
 scikit-learn
 matplotlib
+seaborn

{pyvertexmodel-1.0.3.dev0 → pyvertexmodel-1.0.5}/pyproject.toml

@@ -26,6 +26,7 @@ dependencies = [
     "pyvista",
     "scikit-learn",
     "matplotlib",
+    "seaborn",
 ]
 
 [tool.setuptools_scm]