Update tests to use XDMF mesh

KVSlab · Aug 29, 2023 · e46b777 · e46b777
1 parent 3ed480e
commit e46b777
Showing 1 changed file with 41 additions and 41 deletions.
diff --git a/tests/test_pre_processing.py b/tests/test_pre_processing.py
@@ -1,6 +1,6 @@
 import vtk
 from pathlib import Path
-from dolfin import Mesh, HDF5File
+from dolfin import Mesh, XDMFFile
 from vampy.automatedPreprocessing.preprocessing_common import read_polydata
 from fsipy.automatedPreprocessing.automated_preprocessing import read_command_line, \
     run_pre_processing
@@ -13,7 +13,7 @@ def test_mesh_model_with_one_inlet():
     # Define test data paths
     model_path = Path("tests/test_data/tube/tube.stl")
     mesh_path_vtu = model_path.with_suffix(".vtu")
-    mesh_path_hdf5 = model_path.with_suffix(".h5")
+    mesh_path_xdmf = model_path.with_suffix(".xdmf")
 
     # Define expected values
     expected_num_points = 3626
@@ -39,21 +39,21 @@ def test_mesh_model_with_one_inlet():
 
     # Check that mesh files are created
     assert mesh_path_vtu.is_file(), f"VTU mesh file not found at {mesh_path_vtu}"
-    assert mesh_path_hdf5.is_file(), f"HDF5 mesh file not found at {mesh_path_hdf5}"
+    assert mesh_path_xdmf.is_file(), f"XDMF mesh file not found at {mesh_path_xdmf}"
 
     # Check that mesh files are not empty and have expected sizes
     mesh_vtu = read_polydata(str(mesh_path_vtu))
-    mesh_hdf5 = Mesh()
+    mesh_xdmf = Mesh()
     try:
-        hdf5_file = HDF5File(mesh_hdf5.mpi_comm(), str(mesh_path_hdf5), "r")
-        hdf5_file.read(mesh_hdf5, "/mesh", False)
+        with XDMFFile(str(mesh_path_xdmf)) as xdmf_file:
+            xdmf_file.read(mesh_xdmf)
     except Exception as e:
-        print(f"Error reading HDF5 mesh: {e}")
+        print(f"Error reading XDMF mesh: {e}")
 
     assert mesh_vtu.GetNumberOfPoints() == expected_num_points, \
         f"VTU mesh has {mesh_vtu.GetNumberOfPoints()} points, expected {expected_num_points}"
-    assert mesh_hdf5.num_cells() == expected_num_cells, \
-        f"HDF5 mesh has {mesh_hdf5.num_cells()} cells, expected {expected_num_cells}"
+    assert mesh_xdmf.num_cells() == expected_num_cells, \
+        f"XDMF mesh has {mesh_xdmf.num_cells()} cells, expected {expected_num_cells}"
 
 
 def test_mesh_model_with_one_inlet_and_one_outlet():
@@ -63,7 +63,7 @@ def test_mesh_model_with_one_inlet_and_one_outlet():
     # Define test data paths
     model_path = Path("tests/test_data/cylinder/cylinder.vtp")
     mesh_path_vtu = model_path.with_suffix(".vtu")
-    mesh_path_hdf5 = model_path.with_suffix(".h5")
+    mesh_path_xdmf = model_path.with_suffix(".xdmf")
 
     # Define expected values
     expected_num_points = 2153
@@ -89,21 +89,21 @@ def test_mesh_model_with_one_inlet_and_one_outlet():
 
     # Check that mesh files are created
     assert mesh_path_vtu.is_file(), f"VTU mesh file not found at {mesh_path_vtu}"
-    assert mesh_path_hdf5.is_file(), f"HDF5 mesh file not found at {mesh_path_hdf5}"
+    assert mesh_path_xdmf.is_file(), f"XDMF mesh file not found at {mesh_path_xdmf}"
 
     # Check that mesh files are not empty and have expected sizes
     mesh_vtu = read_polydata(str(mesh_path_vtu))
-    mesh_hdf5 = Mesh()
+    mesh_xdmf = Mesh()
     try:
-        hdf5_file = HDF5File(mesh_hdf5.mpi_comm(), str(mesh_path_hdf5), "r")
-        hdf5_file.read(mesh_hdf5, "/mesh", False)
+        with XDMFFile(str(mesh_path_xdmf)) as xdmf_file:
+            xdmf_file.read(mesh_xdmf)
     except Exception as e:
-        print(f"Error reading HDF5 mesh: {e}")
+        print(f"Error reading XDMF mesh: {e}")
 
     assert mesh_vtu.GetNumberOfPoints() == expected_num_points, \
         f"VTU mesh has {mesh_vtu.GetNumberOfPoints()} points, expected {expected_num_points}"
-    assert mesh_hdf5.num_cells() == expected_num_cells, \
-        f"HDF5 mesh has {mesh_hdf5.num_cells()} cells, expected {expected_num_cells}"
+    assert mesh_xdmf.num_cells() == expected_num_cells, \
+        f"XDMF mesh has {mesh_xdmf.num_cells()} cells, expected {expected_num_cells}"
 
 
 def test_mesh_model_with_one_inlet_and_two_outlets():
@@ -113,7 +113,7 @@ def test_mesh_model_with_one_inlet_and_two_outlets():
     # Define test data paths
     model_path = Path("tests/test_data/artery/artery.stl")
     mesh_path_vtu = model_path.with_suffix(".vtu")
-    mesh_path_hdf5 = model_path.with_suffix(".h5")
+    mesh_path_xdmf = model_path.with_suffix(".xdmf")
 
     # Define expected values
     expected_num_points = 5860
@@ -139,21 +139,21 @@ def test_mesh_model_with_one_inlet_and_two_outlets():
 
     # Check that mesh files are created
     assert mesh_path_vtu.is_file(), f"VTU mesh file not found at {mesh_path_vtu}"
-    assert mesh_path_hdf5.is_file(), f"HDF5 mesh file not found at {mesh_path_hdf5}"
+    assert mesh_path_xdmf.is_file(), f"XDMF mesh file not found at {mesh_path_xdmf}"
 
     # Check that mesh files are not empty and have expected sizes
     mesh_vtu = read_polydata(str(mesh_path_vtu))
-    mesh_hdf5 = Mesh()
+    mesh_xdmf = Mesh()
     try:
-        hdf5_file = HDF5File(mesh_hdf5.mpi_comm(), str(mesh_path_hdf5), "r")
-        hdf5_file.read(mesh_hdf5, "/mesh", False)
+        with XDMFFile(str(mesh_path_xdmf)) as xdmf_file:
+            xdmf_file.read(mesh_xdmf)
     except Exception as e:
-        print(f"Error reading HDF5 mesh: {e}")
+        print(f"Error reading XDMF mesh: {e}")
 
     assert mesh_vtu.GetNumberOfPoints() == expected_num_points, \
         f"VTU mesh has {mesh_vtu.GetNumberOfPoints()} points, expected {expected_num_points}"
-    assert mesh_hdf5.num_cells() == expected_num_cells, \
-        f"HDF5 mesh has {mesh_hdf5.num_cells()} cells, expected {expected_num_cells}"
+    assert mesh_xdmf.num_cells() == expected_num_cells, \
+        f"XDMF mesh has {mesh_xdmf.num_cells()} cells, expected {expected_num_cells}"
 
 
 def test_mesh_model_with_variable_mesh_density():
@@ -167,7 +167,7 @@ def test_mesh_model_with_variable_mesh_density():
     copied_sphere_file_path = sphere_file_path.with_name(model_path.stem + "_distance_to_sphere_spheres.vtp")
 
     mesh_path_vtu = model_path.with_suffix(".vtu")
-    mesh_path_hdf5 = model_path.with_suffix(".h5")
+    mesh_path_xdmf = model_path.with_suffix(".xdmf")
 
     # Make copies of the original model and sphere files using pathlib
     model_path.write_text(original_model_path.read_text())
@@ -197,21 +197,21 @@ def test_mesh_model_with_variable_mesh_density():
 
     # Check that mesh files are created
     assert mesh_path_vtu.is_file(), f"VTU mesh file not found at {mesh_path_vtu}"
-    assert mesh_path_hdf5.is_file(), f"HDF5 mesh file not found at {mesh_path_hdf5}"
+    assert mesh_path_xdmf.is_file(), f"XDMF mesh file not found at {mesh_path_xdmf}"
 
     # Check that mesh files are not empty and have expected sizes
     mesh_vtu = read_polydata(str(mesh_path_vtu))
-    mesh_hdf5 = Mesh()
+    mesh_xdmf = Mesh()
     try:
-        hdf5_file = HDF5File(mesh_hdf5.mpi_comm(), str(mesh_path_hdf5), "r")
-        hdf5_file.read(mesh_hdf5, "/mesh", False)
+        with XDMFFile(str(mesh_path_xdmf)) as xdmf_file:
+            xdmf_file.read(mesh_xdmf)
     except Exception as e:
-        print(f"Error reading HDF5 mesh: {e}")
+        print(f"Error reading XDMF mesh: {e}")
 
     assert mesh_vtu.GetNumberOfPoints() == expected_num_points, \
         f"VTU mesh has {mesh_vtu.GetNumberOfPoints()} points, expected {expected_num_points} points"
-    assert mesh_hdf5.num_cells() == expected_num_cells, \
-        f"HDF5 mesh has {mesh_hdf5.num_cells()} cells, expected {expected_num_cells} cells"
+    assert mesh_xdmf.num_cells() == expected_num_cells, \
+        f"XDMF mesh has {mesh_xdmf.num_cells()} cells, expected {expected_num_cells} cells"
 
 
 def compute_cylinder_diameter_at_cut(mesh, point_coords, plane_normal):
@@ -252,7 +252,7 @@ def test_mesh_model_with_variable_solid_thickness():
     copied_sphere_file_path = sphere_file_path.with_name(model_path.stem + "_distance_to_sphere_solid_thickness.vtp")
 
     mesh_path_vtu = model_path.with_suffix(".vtu")
-    mesh_path_hdf5 = model_path.with_suffix(".h5")
+    mesh_path_xdmf = model_path.with_suffix(".xdmf")
 
     # Make copies of the original model and sphere files using pathlib
     model_path.write_text(original_model_path.read_text())
@@ -286,21 +286,21 @@ def test_mesh_model_with_variable_solid_thickness():
 
     # Check that mesh files are created
     assert mesh_path_vtu.is_file(), f"VTU mesh file not found at {mesh_path_vtu}"
-    assert mesh_path_hdf5.is_file(), f"HDF5 mesh file not found at {mesh_path_hdf5}"
+    assert mesh_path_xdmf.is_file(), f"XDMF mesh file not found at {mesh_path_xdmf}"
 
     # Check that mesh files are not empty and have expected sizes
     mesh_vtu = read_polydata(str(mesh_path_vtu))
-    mesh_hdf5 = Mesh()
+    mesh_xdmf = Mesh()
     try:
-        hdf5_file = HDF5File(mesh_hdf5.mpi_comm(), str(mesh_path_hdf5), "r")
-        hdf5_file.read(mesh_hdf5, "/mesh", False)
+        with XDMFFile(str(mesh_path_xdmf)) as xdmf_file:
+            xdmf_file.read(mesh_xdmf)
     except Exception as e:
-        print(f"Error reading HDF5 mesh: {e}")
+        print(f"Error reading XDMF mesh: {e}")
 
     assert mesh_vtu.GetNumberOfPoints() == expected_num_points, \
         f"VTU mesh has {mesh_vtu.GetNumberOfPoints()} points, expected {expected_num_points} points"
-    assert mesh_hdf5.num_cells() == expected_num_cells, \
-        f"HDF5 mesh has {mesh_hdf5.num_cells()} cells, expected {expected_num_cells} cells"
+    assert mesh_xdmf.num_cells() == expected_num_cells, \
+        f"XDMF mesh has {mesh_xdmf.num_cells()} cells, expected {expected_num_cells} cells"
 
     # Compute diameter at inlet and outlet
     diameter_at_inlet = compute_cylinder_diameter_at_cut(mesh_vtu, [0, -3.1, 0], [0, 1, 0])