reenable some gmytool regression tests; the cylinder clipping is wrong

geometry-tool/tests/Model/test_OutputGeneration.py

@@ -27,13 +27,15 @@
 
 dataDir = os.path.join(os.path.split(__file__)[0], "data")
 
+
 def vec2np(v):
     ans = np.empty(3, dtype=float)
     ans[0] = v.x
     ans[1] = v.y
     ans[2] = v.z
     return ans
 
+
 class TestPolyDataGenerator:
     def test_regression(self, tmpdir):
         """Generate a gmy from a stored profile and check that the output is
@@ -65,7 +67,9 @@ def test_regression(self, tmpdir):
         test_dom = test_ldr.Domain
 
         # Per-block data length must be identical
-        assert np.all(ref_ldr.BlockUncompressedDataLength == test_ldr.BlockUncompressedDataLength)
+        assert np.all(
+            ref_ldr.BlockUncompressedDataLength == test_ldr.BlockUncompressedDataLength
+        )
         # Same for fluid site counts
         assert np.all(ref_dom.BlockFluidSiteCounts == test_dom.BlockFluidSiteCounts)
         nblocks = len(ref_dom.BlockFluidSiteCounts)
@@ -90,7 +94,12 @@ def test_regression(self, tmpdir):
                 if rs.IntersectionDistance is None:
                     assert ts.IntersectionDistance is None
                 else:
-                    assert np.allclose(rs.IntersectionDistance, ts.IntersectionDistance, rtol=0, atol=5e-5)
+                    assert np.allclose(
+                        rs.IntersectionDistance,
+                        ts.IntersectionDistance,
+                        rtol=0,
+                        atol=5e-5,
+                    )
 
                 assert np.all(rs.IOletIndex == ts.IOletIndex)
                 assert rs.WallNormalAvailable == ts.WallNormalAvailable
@@ -104,21 +113,21 @@ def test_regression(self, tmpdir):
     def test_cube(self, tmpdir):
         """Generate a gmy from a simple cubic profile and check the output"""
         cube = fixtures.cube(tmpdir)
-        cube.VoxelSize = 0.23
         cube.StlFileUnitId = 0
+        cube.VoxelSize = 0.11
         generator = OutputGeneration.GmyPolyDataGenerator(cube)
         generator.Execute()
         # Load back the resulting geometry file and assert things are as
         # expected
         checker = CubeTestingGmyParser(cube.OutputXmlFile, cube.VoxelSize)
         checker.Load()
 
-        fluid_sites = sum(checker.Domain.BlockFluidSiteCounts)
+        fluid_sites = checker.Domain.BlockFluidSiteCounts.sum()
         block_count = len(checker.Domain.Blocks)
         block_size = checker.Domain.BlockSize
         sites = block_count * block_size**3
-        # assert(sites==4096)
-        # assert(fluid_sites==729)
+        assert sites == 4096
+        assert fluid_sites == 729
         assert sites != fluid_sites
         # # Now, turn on the skip-non-intersecting-blocks optimisation, and
         # # assert same result
@@ -168,47 +177,52 @@ def test_cube_normals(self, tmpdir):
         checker.Load()
 
     def test_cylinder(self, tmpdir):
-        """Generate a gmy from a simple cylinder profile and check the output"""
-        cylinder = fixtures.cylinder(tmpdir)
-        cylinder.VoxelSize = 0.23
-        cylinder.StlFileUnitId = 0
+        """Generate a gmy from a cylinder and check the output.
 
-        """ The default VTK cylinder is 1 length unit long, aligned with the 
+        The cylinder is 1 length unit long, radius 0.5, aligned with the
         y-axis, and centred at the origin of coordinates.
         """
+        dx = 0.11
+        cylinder = fixtures.cylinder(tmpdir)
+        cylinder.VoxelSize = dx
+        cylinder.StlFileUnitId = 0
+
         inlet = Iolet(
             Name="inlet",
-            Centre=Vector(0.0, -0.5, 0.0),
+            Centre=Vector(0.0, -0.45, 0.0),
             Normal=Vector(0.0, -1.0, 0.0),
-            Radius=1,
+            Radius=1.0,
         )
         outlet = Iolet(
             Name="outlet",
-            Centre=Vector(0.0, 0.5, 0.0),
+            Centre=Vector(0.0, 0.45, 0.0),
             Normal=Vector(0.0, 1.0, 0.0),
-            Radius=1,
+            Radius=1.0,
         )
         cylinder.Iolets = [inlet, outlet]
+        L = 0.9
+        R = 0.5
 
         generator = OutputGeneration.GmyPolyDataGenerator(cylinder)
+
         generator.Execute()
         # Load back the resulting geometry file and assert things are as
         # expected
         checker = CylinderTestingGmyParser(
             cylinder.OutputXmlFile,
             cylinder.VoxelSize,
             np.array([0.0, 1.0, 0.0]),
-            1.0,
-            0.5,
+            L,
+            R,
         )
         checker.Load()
 
-        fluid_sites = sum(checker.Domain.BlockFluidSiteCounts)
+        fluid_sites = checker.Domain.BlockFluidSiteCounts.sum()
         block_count = len(checker.Domain.Blocks)
         block_size = checker.Domain.BlockSize
         sites = block_count * block_size**3
         # assert(sites==4096)
-        # assert(fluid_sites==621)
+        assert fluid_sites == 621
         assert sites != fluid_sites
         # # Now, turn on the skip-non-intersecting-blocks optimisation, and
         # # assert same result