Megha's changes

.github/workflows/tests.yaml

@@ -1,6 +1,7 @@
 name: Run Python Tests
 
 on:
+  workflow_dispatch:
   push:
     branches: [ main megha]
   pull_request:

.gitignore

@@ -8,7 +8,7 @@ __pycache__/
 
 # Distribution / packaging
 .Python
-build/
+src/pyVertexModel/Kg/build/
 develop-eggs/
 dist/
 downloads/
@@ -186,3 +186,5 @@ data/
 .idea/misc.xml
 
 *.db
+
+*.o

Tests/test_cell.py

@@ -4,7 +4,6 @@
 from Tests.tests import Tests, load_data
 from src.pyVertexModel.geometry.cell import Cell
 
-
 class TestCell(Tests):
     def test_compute_cell_area(self):
         geo_test, _, _ = load_data('Geo_var_3x3_stretch.mat')
@@ -78,3 +77,17 @@ def test_copy(self):
         self.assertEqual(original_cell.ID, copied_cell.ID)
         self.assertTrue(np.array_equal(original_cell.X, copied_cell.X))
         self.assertTrue(np.array_equal(original_cell.T, copied_cell.T))
+
+    def test_compute_cell_area_edge_cases(self):
+        geo_test, _, _ = load_data('Geo_var_3x3_stretch.mat')
+
+        # Test with zero-area cells
+        geo_test.Cells[0].X = np.array([[0, 0], [0, 0], [0, 0]])  # Degenerate cell
+        geo_test.Cells[0].compute_area()
+        self.assertEqual(geo_test.Cells[0].Area, 0)
+
+        # Test with very large area
+        geo_test.Cells[1].X = np.array([[1e6, 1e6], [1e7, 1e7], [1e8, 1e8]])  # Extreme values
+        geo_test.Cells[1].compute_area()
+        self.assertTrue(geo_test.Cells[1].Area > 0)  # a non-zero area
+

Tests/test_geo.py

@@ -5,6 +5,7 @@
 from src.pyVertexModel.algorithm.vertexModelVoronoiFromTimeImage import VertexModelVoronoiFromTimeImage
 from src.pyVertexModel.geometry.geo import Geo, get_node_neighbours_per_domain
 from src.pyVertexModel.util.utils import load_state, ismember_rows
+from Tests.tests import Tests, load_data, assert_matrix
 
 
 def check_if_cells_are_the_same(geo_expected, geo_test):

Tests/test_vertexModel.py

@@ -8,10 +8,11 @@
 from Tests.tests import Tests, assert_matrix, load_data, assert_array1D
 from src.pyVertexModel.algorithm import newtonRaphson
 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, create_tetrahedra, add_tetrahedral_intercalations, build_2d_voronoi_from_image, \
+    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.geometry.degreesOfFreedom import DegreesOfFreedom
 from src.pyVertexModel.util.utils import save_backup_vars
@@ -296,7 +297,7 @@ def test_create_tetrahedra(self):
 
         # Test if initialize geometry function does not change anything
         Twg_test = create_tetrahedra(traingles_connectivity, neighbours_network, edges_of_vertices, x_internal,
-                                     x_face_ids, x_vertices_ids, x)
+                                     x_face_ids, x_vertices_ids)
 
         # Check if the test and expected are the same
         assert_matrix(Twg_test, mat_info['Twg'])

Tests/tests.py

@@ -1,15 +1,14 @@
 import unittest
-from os.path import exists
-
+import scipy.io
 import numpy as np
-import scipy
+from os.path import exists, abspath
 
 from src.pyVertexModel.geometry.geo import Geo
 from src.pyVertexModel.parameters.set import Set
-
+from src.pyVertexModel.Kg import kg_functions
 
 def load_data(file_name, return_geo=True):
-    test_dir = 'Tests/data/%s' % file_name
+    test_dir = abspath('Tests/data/%s' % file_name)
     if exists(test_dir):
         mat_info = scipy.io.loadmat(test_dir)
     else:
@@ -23,10 +22,8 @@ def load_data(file_name, return_geo=True):
 
         if 'Set' in mat_info.keys():
             set_test = Set(mat_info['Set'])
-            # Set the output folder to the test directory if it is not set
             if set_test.OutputFolder.__eq__(b'') or set_test.OutputFolder is None:
                 set_test.OutputFolder = '../Result/Test'
-
         else:
             set_test = None
     else:
@@ -40,9 +37,27 @@ def assert_matrix(k_expected, k):
     np.testing.assert_allclose(k_expected, k, rtol=1e-3, atol=1e-1)
 
 
-def assert_array1D(g_expected, g):
+def assert_array1D(array1, array2):
     np.testing.assert_allclose(g_expected, g, rtol=1e-3, atol=1e-1)
 
 
 class Tests(unittest.TestCase):
-    pass
+
+    def test_load_data_geo(self):
+        geo_test, set_test, mat_info = load_data('Geo_3x3_dofs_expected.mat')
+        self.assertIsNotNone(geo_test)
+        self.assertTrue('Geo' in mat_info)
+
+    def test_load_data_set(self):
+        geo_test, set_test, mat_info = load_data('Geo_var_3x3_stretch.mat')
+        self.assertIsNotNone(set_test)
+        self.assertTrue('Set' in mat_info)
+
+    def test_assert_matrix(self):
+        k_expected = np.array([[1, 2], [3, 4]])
+        k = np.array([[1, 2], [3, 4]])
+        assert_matrix(k_expected, k)
+
+    def test_load_data_invalid_file(self):
+        with self.assertRaises(FileNotFoundError):
+            load_data('invalid_file.mat')

pyproject.toml

@@ -15,14 +15,17 @@ dynamic = [
 ]
 dependencies = [
     "cython",
-    "numpy",
+    "numpy==1.26.4",
     "scipy",
     "pillow",
     "scikit-image",
     "cython",
     "vtk",
     "pandas",
-    "networkx"
+    "networkx",
+    "pyvista",
+    "scikit-learn",
+    "matplotlib",
 ]
 
 [tool.coverage]

src/pyVertexModel/Kg/kg_functions.pyx

@@ -4,6 +4,8 @@ import cython
 import numpy as np
 cimport numpy as np
 
+np.import_array()
+
 # RUN IT LIKE: python setup.py build_ext --inplace
 
 @cython.wraparound(False)

src/pyVertexModel/analysis/analyse_in_vivo_ablation_data.py

@@ -1,4 +1,3 @@
-from datetime import datetime
 import os
 
 import numpy as np

src/pyVertexModel/analysis/analyse_results_excel.py

@@ -1,8 +1,6 @@
-import numpy as np
+import matplotlib.pyplot as plt
 import pandas as pd
 import seaborn as sns
-import matplotlib.pyplot as plt
-from scipy.interpolate import griddata
 
 # Read excel into a pandas dataframe
 results_excel = pd.read_excel('data/simulations_results/all_files_features.xlsx')

src/pyVertexModel/analysis/analyse_simulation.py

@@ -1,7 +1,7 @@
 import os
 import pickle
-import cv2
 
+import cv2
 import numpy as np
 import pandas as pd
 from matplotlib import pyplot as plt

src/pyVertexModel/analysis/analyse_simulations.py

@@ -3,8 +3,7 @@
 import numpy as np
 import pandas as pd
 
-from src.pyVertexModel.analysis.analyse_simulation import analyse_simulation, analyse_edge_recoil, create_video
-from src.pyVertexModel.util.utils import save_variables, load_variables
+from src.pyVertexModel.analysis.analyse_simulation import analyse_simulation, create_video
 
 folder = '/media/pablo/d7c61090-024c-469a-930c-f5ada47fb049/PabloVicenteMunuera/VertexModel/pyVertexModel/Result/final_results'
 all_files_features = []

src/pyVertexModel/geometry/geo.py

@@ -3,9 +3,7 @@
 
 import numpy as np
 import vtk
-from numpy.ma.extras import setxor1d
 from scipy.spatial import ConvexHull
-from torch.fx.experimental.unification.unification_tools import get_in
 
 from src.pyVertexModel.Kg.kg import add_noise_to_parameter
 from src.pyVertexModel.geometry import face, cell
@@ -797,6 +795,8 @@ def check_ys_and_faces_have_not_changed(self, new_tets, old_tets, old_geo):
 
                     assert np.all(self.Cells[cell_id].Faces[id_with_new_index].Centre == c_face.Centre)
 
+
+
     def add_and_rebuild_cells(self, old_geo, old_tets, new_tets, y_new, c_set, update_measurements):
         """
         Add and rebuild the cells

src/pyVertexModel/mesh_remodelling/remodelling.py

@@ -5,8 +5,7 @@
 import pandas as pd
 from numpy.ma.extras import setdiff1d
 
-from src.pyVertexModel.algorithm.newtonRaphson import gGlobal, newton_raphson_iteration_explicit
-from src.pyVertexModel.geometry.cell import face_centres_to_middle_of_neighbours_vertices
+from src.pyVertexModel.algorithm.newtonRaphson import gGlobal
 from src.pyVertexModel.geometry.face import get_interface
 from src.pyVertexModel.geometry.geo import edge_valence, get_node_neighbours_per_domain, get_node_neighbours
 from src.pyVertexModel.mesh_remodelling.flip import y_flip_nm, post_flip

src/pyVertexModel/parameters/set.py

@@ -220,15 +220,15 @@ def update_derived_parameters(self):
 
         current_datetime = datetime.now()
         new_outputFolder = ''.join([PROJECT_DIRECTORY, '/Result/', str(current_datetime.strftime("%m-%d_%H%M%S_")),
-                                    'noise_', '{:0.2e}'.format(self.noise_random), '_bNoise_', '{:0.2e}'.format(self.brownian_motion_scale),
-                                    '_lVol_', '{:0.2e}'.format(self.lambdaV), '_refV0_', '{:0.2e}'.format(self.ref_V0),
-                                    '_kSubs_', '{:0.2e}'.format(self.kSubstrate),
-                                    '_lt_', '{:0.2e}'.format(self.cLineTension),
-                                    '_refA0_', '{:0.2e}'.format(self.ref_A0),
-                                    '_eARBarrier_', '{:0.2e}'.format(self.lambdaR),
-                                    '_RemStiff_', str(self.RemodelStiffness), '_lS1_', '{:0.2e}'.format(self.lambdaS1),
-                                    '_lS2_', '{:0.2e}'.format(self.lambdaS2), '_lS3_', '{:0.2e}'.format(self.lambdaS3),
-                                    '_ps_', '{:0.2e}'.format(self.purseStringStrength), '_lc_', '{:0.2e}'.format(self.lateralCablesStrength)])
+                            'noise_', '{:0.2e}'.format(self.noise_random), '_bNoise_', '{:0.2e}'.format(self.brownian_motion_scale),
+                            '_lVol_', '{:0.2e}'.format(self.lambdaV), '_refV0_', '{:0.2e}'.format(self.ref_V0),
+                            '_kSubs_', '{:0.2e}'.format(self.kSubstrate),
+                            '_lt_', '{:0.2e}'.format(self.cLineTension),
+                            '_refA0_', '{:0.2e}'.format(self.ref_A0),
+                            '_eARBarrier_', '{:0.2e}'.format(self.lambdaR),
+                            '_RemStiff_', str(self.RemodelStiffness), '_lS1_', '{:0.2e}'.format(self.lambdaS1),
+                            '_lS2_', '{:0.2e}'.format(self.lambdaS2), '_lS3_', '{:0.2e}'.format(self.lambdaS3),
+                            '_ps_', '{:0.2e}'.format(self.purseStringStrength), '_lc_', '{:0.2e}'.format(self.lateralCablesStrength)])
         self.define_if_not_defined("OutputFolder", new_outputFolder)
 
     def stretch(self):
@@ -320,7 +320,7 @@ def wing_disc(self):
         self.lambdaS4 = self.lambdaS2
 
         # VTK
-        self.VTK = False
+        self.VTK = True
 
         # Implicit vs Explicit
         self.implicit_method = False
@@ -337,7 +337,7 @@ def wound_default(self):
         self.debris_contribution = np.finfo(float).eps
         # =========================== Contractility ==========================
         self.Contractility = True
-        self.TypeOfPurseString = 0
+        self.TypeOfPurseString = 2
         # 0: Intensity-based purse string
         # 1: Strain-based purse string (delayed)
         # 2: Fixed with linear increase purse string

src/pyVertexModel/util/space_exploration.py

@@ -12,6 +12,7 @@
 from src.pyVertexModel.parameters.set import Set
 from src.pyVertexModel.util.utils import load_state, load_variables, save_variables
 
+
 def objective(trial):
     """
     Objective function to minimize

src/pyVertexModel/util/utils.py

@@ -6,8 +6,8 @@
 import pickle
 
 import imageio
-import pyvista as pv
 import numpy as np
+import pyvista as pv
 from scipy.optimize import fsolve