Merge pull request #1 from fusion-energy/numpy_refactor

Numpy refactor

examples/one_volume_cadquery_tesselation.py

@@ -0,0 +1,16 @@
+import cadquery as cq
+
+result = cq.Workplane("front").box(2.0, 2.0, 0.5)
+
+vertices, triangles = result.val().tessellate(tolerance=0.1)
+
+vertices_to_h5m(
+    vertices=vertices,
+    triangles=triangles,
+    material_tags=["mat1"],
+    h5m_filename="one_cadquery_volume.h5m",
+)
+
+import os
+
+os.system("mbconvert one_cadquery_volume.h5m one_cadquery_volume.vtk")

tests/test_package.py

@@ -31,7 +31,9 @@ def transport_particles_on_h5m_geometry(
 
         materials.append(mat_dag_material_tag)
 
-    # materials.cross_sections='/home/jshim/brep_to_h5m/examples/h5m_from_coords/cross_sections.xml'
+    materials.cross_sections = (
+        "/home/jshim/brep_to_h5m/examples/h5m_from_coords/cross_sections.xml"
+    )
     # downloads the nuclear data and sets the openmc_cross_sections environmental variable
     odd.just_in_time_library_generator(libraries="ENDFB-7.1-NNDC", materials=materials)
 
@@ -98,18 +100,52 @@ def transport_particles_on_h5m_geometry(
     my_model.run()
 
 
-def test_h5m_production_with_single_volume():
+def test_h5m_production_with_single_volume_list():
+    """The simplest geometry, a single 4 sided shape with lists instead of np arrays"""
+
+    test_h5m_filename = "single_tet.h5m"
+
+    # a list of xyz coordinates
+    vertices = [
+        [0.0, 0.0, 0.0],
+        [1.0, 0.0, 0.0],
+        [0.0, 1.0, 0.0],
+        [0.0, 0.0, 1.0],
+    ]
+
+    # the index of the coordinate that make up the corner of a tet, normals need fixing
+    triangles = [[[0, 1, 2], [3, 1, 2], [0, 2, 3], [0, 1, 3]]]
+
+    vertices_to_h5m(
+        vertices=vertices,
+        triangles=triangles,
+        material_tags=["mat1"],
+        h5m_filename=test_h5m_filename,
+    )
+
+    transport_particles_on_h5m_geometry(
+        h5m_filename=test_h5m_filename,
+        material_tags=["mat1"],
+    )
+
+    assert Path(test_h5m_filename).is_file()
+    assert di.get_volumes_from_h5m(test_h5m_filename) == [1]
+    assert di.get_materials_from_h5m(test_h5m_filename) == ["mat1"]
+    assert di.get_volumes_and_materials_from_h5m(test_h5m_filename) == {1: "mat1"}
+
+
+def test_h5m_production_with_single_volume_numpy():
     """The simplest geometry, a single 4 sided shape"""
 
     test_h5m_filename = "single_tet.h5m"
 
     # a list of xyz coordinates
     vertices = np.array(
         [
-            [0, 0, 0],
-            [1, 0, 0],
-            [0, 1, 0],
-            [0, 0, 1],
+            [0.0, 0.0, 0.0],
+            [1.0, 0.0, 0.0],
+            [0.0, 1.0, 0.0],
+            [0.0, 0.0, 1.0],
         ],
         dtype="float64",
     )
@@ -135,20 +171,20 @@ def test_h5m_production_with_single_volume():
     assert di.get_volumes_and_materials_from_h5m(test_h5m_filename) == {1: "mat1"}
 
 
-def test_h5m_production_with_two_touching_volumes():
+def test_h5m_production_with_two_touching_volumes_numpy():
     """Two 4 sided shapes that share and edge"""
 
     test_h5m_filename = "double_tet.h5m"
 
     # a list of xyz coordinates
     vertices = np.array(
         [
-            [0, 0, 0],
-            [1, 0, 0],
-            [0, 1, 0],
-            [0, 0, 1],
-            [1, 1, 1],
-            [1, 1, 0],
+            [0.0, 0.0, 0.0],
+            [1.0, 0.0, 0.0],
+            [0.0, 1.0, 0.0],
+            [0.0, 0.0, 1.0],
+            [1.0, 1.0, 1.0],
+            [1.0, 1.0, 0.0],
         ],
         dtype="float64",
     )
@@ -180,7 +216,49 @@ def test_h5m_production_with_two_touching_volumes():
     }
 
 
-def test_h5m_production_with_two_touching_vertex():
+def test_h5m_production_with_two_touching_volumes_lists():
+    """Two 4 sided shapes that share and edge"""
+
+    test_h5m_filename = "double_tet.h5m"
+
+    # a list of xyz coordinates
+    vertices = [
+        [0.0, 0.0, 0.0],
+        [1.0, 0.0, 0.0],
+        [0.0, 1.0, 0.0],
+        [0.0, 0.0, 1.0],
+        [1.0, 1.0, 1.0],
+        [1.0, 1.0, 0.0],
+    ]
+
+    # the index of the coordinate that make up the corner of a tet, normals need fixing
+    triangles = [
+        [[0, 1, 2], [3, 1, 2], [0, 2, 3], [0, 1, 3]],
+        [[4, 5, 1], [4, 5, 2], [4, 1, 2], [5, 1, 2]],
+    ]
+
+    vertices_to_h5m(
+        vertices=vertices,
+        triangles=triangles,
+        material_tags=["mat1", "mat2"],
+        h5m_filename=test_h5m_filename,
+    )
+
+    transport_particles_on_h5m_geometry(
+        h5m_filename=test_h5m_filename,
+        material_tags=["mat1", "mat2"],
+    )
+
+    assert Path(test_h5m_filename).is_file()
+    assert di.get_volumes_from_h5m(test_h5m_filename) == [1, 2]
+    assert di.get_materials_from_h5m(test_h5m_filename) == ["mat1", "mat2"]
+    assert di.get_volumes_and_materials_from_h5m(test_h5m_filename) == {
+        1: "mat1",
+        2: "mat2",
+    }
+
+
+def test_h5m_production_with_two_touching_vertex_numpy():
     """Two 4 sided shapes that share an single vertex"""
 
     test_h5m_filename = "touching_vertex_tets.h5m"
@@ -223,3 +301,45 @@ def test_h5m_production_with_two_touching_vertex():
         1: "mat1",
         2: "mat2",
     }
+
+
+def test_h5m_production_with_two_touching_vertex_list():
+    """Two 4 sided shapes that share an single vertex"""
+
+    test_h5m_filename = "touching_vertex_tets.h5m"
+
+    vertices = [
+        [0.0, 0.0, 0.0],
+        [1.0, 0.0, 0.0],
+        [0.0, 1.0, 0.0],
+        [0.0, 0.0, 1.0],
+        [-1.0, 0.0, 0.0],
+        [0.0, -1.0, 0.0],
+        [0.0, 0.0, -1.0],
+    ]
+
+    # the index of the coordinate that make up the corner of a tet, normals need fixing
+    triangles = [
+        [[0, 4, 5], [6, 4, 5], [0, 5, 6], [0, 4, 6]],
+        [[0, 1, 2], [3, 1, 2], [0, 2, 3], [0, 1, 3]],
+    ]
+
+    vertices_to_h5m(
+        vertices=vertices,
+        triangles=triangles,
+        material_tags=["mat1", "mat2"],
+        h5m_filename=test_h5m_filename,
+    )
+
+    transport_particles_on_h5m_geometry(
+        h5m_filename=test_h5m_filename,
+        material_tags=["mat1", "mat2"],
+    )
+
+    assert Path(test_h5m_filename).is_file()
+    assert di.get_volumes_from_h5m(test_h5m_filename) == [1, 2]
+    assert di.get_materials_from_h5m(test_h5m_filename) == ["mat1", "mat2"]
+    assert di.get_volumes_and_materials_from_h5m(test_h5m_filename) == {
+        1: "mat1",
+        2: "mat2",
+    }