shapedna test cases

lapy/utils/tests/test_shape_DNA.py

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+import json
+
+import numpy as np
+import pytest
+
+from ...shapedna import *
+from ...tet_mesh import TetMesh
+from ...tria_mesh import TriaMesh
+
+tria = TriaMesh.read_vtk("data/cubeTria.vtk")
+tet = TetMesh.read_vtk("data/cubeTetra.vtk")
+
+ev = compute_shapedna(tria, k=3)
+ev["Eigenvectors"]
+ev["Eigenvalues"]
+
+
+@pytest.fixture
+def loaded_data():
+    """
+    Load expected outcomes data from a JSON file as a dictionary.
+    """
+    with open("lapy/utils/tests/expected_outcomes.json", "r") as f:
+        expected_outcomes = json.load(f)
+    return expected_outcomes
+
+
+def test_compute_shapedna(loaded_data):
+    """
+    Test compute_shapedna function for triangular mesh.
+
+    Args:
+        loaded_data (dict): Expected outcomes loaded from a JSON file.
+
+    Raises:
+        AssertionError: If computed eigenvalues don't match expected values within tolerance.
+        AssertionError: If eigenvalues' dtype isn't float32.
+    """
+    expected_Eigenvalues = np.array(
+        loaded_data["expected_outcomes"]["test_compute_shapedna"][
+            "expected_eigenvalues"
+        ]
+    )
+    tolerance = loaded_data["expected_outcomes"]["test_compute_shapedna"]["tolerance"]
+    assert np.allclose(ev["Eigenvalues"], expected_Eigenvalues, atol=tolerance)
+    assert ev["Eigenvalues"].dtype == np.float32
+
+
+def test_normalize_ev_geometry(loaded_data):
+    """
+    Test normalize_ev() using 'geometry' method for a triangular mesh.
+
+    Args:
+        loaded_data (dict): Expected outcomes from a JSON file.
+
+    Raises:
+        AssertionError: If normalized eigenvalues don't match expected values within tolerance.
+        AssertionError: If normalized eigenvalues' dtype isn't float32.
+    """
+    expected_normalized_values = np.array(
+        loaded_data["expected_outcomes"]["test_normalize_ev_geometry"][
+            "expected_normalized_values"
+        ]
+    )
+    tolerance = loaded_data["expected_outcomes"]["test_normalize_ev_geometry"][
+        "tolerance"
+    ]
+    normalized_eigenvalues = normalize_ev(tria, ev["Eigenvalues"], method="geometry")
+    assert np.allclose(
+        normalized_eigenvalues, expected_normalized_values, atol=tolerance
+    )
+    assert normalized_eigenvalues.dtype == np.float32
+
+
+def test_reweight_ev(loaded_data):
+    """
+    Test reweighted_ev() and validate reweighted eigenvalues' data type.
+
+    Args:
+        loaded_data (dict): Expected outcomes from a JSON file.
+
+    Raises:
+        AssertionError: If reweighted eigenvalues don't match expected values within tolerance.
+        AssertionError: If reweighted eigenvalues' dtype isn't float32.
+    """
+    expected_reweighted_values = np.array(
+        loaded_data["expected_outcomes"]["test_reweight_ev"][
+            "expected_reweighted_values"
+        ]
+    )
+    tolerance = loaded_data["expected_outcomes"]["test_reweight_ev"]["tolerance"]
+    reweighted_eigenvalues = reweight_ev(ev["Eigenvalues"])
+    tolerance = 1e-4
+    assert np.allclose(
+        reweighted_eigenvalues, expected_reweighted_values, atol=tolerance
+    )
+
+
+def test_compute_distance(loaded_data):
+    """
+    Test compute_distance() for eigenvalues and validate the computed distance.
+
+    Args:
+        loaded_data (dict): Expected outcomes from a JSON file.
+
+    Raises:
+        AssertionError: If computed distance doesn't match the expected value.
+    """
+    expected_compute_distance = loaded_data["expected_outcomes"][
+        "test_compute_distance"
+    ]["expected_compute_distance"]
+    # compute distance for tria eigenvalues (trivial case)
+    computed_distance = compute_distance(ev["Eigenvalues"], ev["Eigenvalues"])
+    assert computed_distance == expected_compute_distance
+
+
+# Repeat testing steps for a tetrahedral mesh
+# compute eigenvalues and eigenvectors for tet mesh
+evTet = compute_shapedna(tet, k=3)
+evTet["Eigenvectors"]
+evTet["Eigenvalues"]
+
+
+def test_compute_shapedna_tet(loaded_data):
+    """
+    Test compute_shapedna for a tetrahedral mesh.
+
+    Args:
+        loaded_data (dict): Expected outcomes from a JSON file.
+
+    Raises:
+        AssertionError: If computed eigenvalues don't match expected values within tolerance.
+        AssertionError: If eigenvalues' dtype isn't float32.
+    """
+    expected_eigen_values = np.array(
+        loaded_data["expected_outcomes"]["test_compute_shapedna_tet"][
+            "expected_eigen_values"
+        ]
+    )
+    tolerance = loaded_data["expected_outcomes"]["test_compute_shapedna_tet"][
+        "tolerance"
+    ]
+    evTet = compute_shapedna(tet, k=3)
+    assert np.allclose(evTet["Eigenvalues"], expected_eigen_values, atol=tolerance)
+    assert evTet["Eigenvalues"].dtype == np.float32
+
+
+def test_normalize_ev_geometry_tet(loaded_data):
+    """
+    Test normalize_ev() using 'geometry' method for a tetrahedral mesh.
+
+    Args:
+        loaded_data (dict): Expected outcomes from a JSON file.
+
+    Raises:
+        AssertionError: If normalized eigenvalues don't match expected values within tolerance.
+        AssertionError: If normalized eigenvalues' dtype isn't float32.
+    """
+    expected_normalized_values = np.array(
+        loaded_data["expected_outcomes"]["test_normalize_ev_geometry_tet"][
+            "expected_normalized_values"
+        ]
+    )
+    tolerance = loaded_data["expected_outcomes"]["test_normalize_ev_geometry_tet"][
+        "tolerance"
+    ]
+    # volume / surface / geometry normalization of tet eigenvalues
+    normalized_eigenvalues = normalize_ev(tet, evTet["Eigenvalues"], method="geometry")
+
+    assert np.allclose(
+        normalized_eigenvalues, expected_normalized_values, atol=tolerance
+    )
+    assert normalized_eigenvalues.dtype == np.float32
+
+
+def test_reweight_ev_tet(loaded_data):
+    """
+    Test reweighted_ev() for tetrahedral meshes and validate reweighted eigenvalues' data type.
+
+    Args:
+        loaded_data (dict): Expected outcomes from a JSON file.
+
+    Raises:
+        AssertionError: If reweighted eigenvalues don't match expected values within tolerance.
+    """
+    expected_reweighted_values = np.array(
+        loaded_data["expected_outcomes"]["test_reweight_ev_tet"][
+            "expected_reweighted_values"
+        ]
+    )
+    tolerance = loaded_data["expected_outcomes"]["test_reweight_ev_tet"]["tolerance"]
+    # Linear reweighting of tet eigenvalues
+    reweighted_eigenvalues = reweight_ev(evTet["Eigenvalues"])
+    assert np.allclose(
+        reweighted_eigenvalues, expected_reweighted_values, atol=tolerance
+    )
+
+
+def test_compute_distance_tet(loaded_data):
+    """
+    Test compute_distance() for eigenvalues of tetrahedral meshes and validate computed distance.
+
+    Args:
+        loaded_data (dict): Expected outcomes from a JSON file.
+
+    Raises:
+        AssertionError: If computed distance doesn't match the expected value.
+    """
+    # compute distance for tria eigenvalues (trivial case)
+    computed_distance = compute_distance(evTet["Eigenvalues"], evTet["Eigenvalues"])
+    expected_compute_distance = loaded_data["expected_outcomes"][
+        "test_compute_distance_tet"
+    ]["exp_compute_distance"]
+
+    # Compare the computed distance with the expected distance using a tolerance
+    assert computed_distance == expected_compute_distance