more tests

tests/test_expectation_maximization.py

@@ -90,7 +90,7 @@ def test_grid_SO3_uniform(test_ir, n_particles):
 def test_generate_xy_plane(test_ir, n_pix):
     """Test generation of xy plane."""
     xy_plane = test_ir.generate_xy_plane(n_pix)
-    assert xy_plane.shape == (n_pix**2, 3)
+    assert xy_plane.shape == (n_pix ** 2, 3)
 
 
 def test_generate_slices(test_ir, n_particles, n_pix):
@@ -101,9 +101,9 @@ def test_generate_slices(test_ir, n_particles, n_pix):
 
     slices, xyz_rotated = test_ir.generate_slices(map_3d, xy_plane, n_pix, rots)
 
-    assert xy_plane.shape == (n_pix**2, 3)
+    assert xy_plane.shape == (n_pix ** 2, 3)
     assert slices.shape == (n_particles, n_pix, n_pix)
-    assert xyz_rotated.shape == (n_pix**2, 3)
+    assert xyz_rotated.shape == (n_pix ** 2, 3)
 
 
 def test_apply_ctf_to_slice(test_ir, n_pix):
@@ -201,10 +201,15 @@ def test_compute_fsc(test_ir, n_pix):
 def test_binary_mask_3d(test_ir):
     """Test binary_mask_3d.
 
-    Sums shell through an axis, then converts to circle,
+    Tests the limit of infinite n_pix. Use high n_pix so good approx.
+    1. Sums shell through an axis, then converts to circle,
     then checks if circle/square ratio agrees with largest
-    circle inscribed in square. Should be pi/4 by trigonometry,
-    in the limit of infinite n_pix. Use high n_pix so good approx.
+    circle inscribed in square. Should be pi/4.
+
+    2. Make shells at sizes r and r/2 and check ratios of perimeter
+    of circle (mid slice) and surface area of sphere.
+
+    3. Make filled sphere of sizes r and r/2 and check ratio of volume.
     """
     n_pix = 512
 
@@ -221,6 +226,41 @@ def test_binary_mask_3d(test_ir):
             circle_to_square_ratio = circle.mean()
             assert np.isclose(circle_to_square_ratio, np.pi / 4, atol=1e-3)
 
+    mask = test_ir.binary_mask_3d(center, radius, shape, fill=True, shell_thickness=1)
+    circle = mask[n_pix // 2]
+    circle_to_square_ratio = circle.mean()
+    assert np.isclose(circle_to_square_ratio, np.pi / 4, atol=1e-3)
+
+    r_half = radius / 2
+    for shell_thickness in [1, 2]:
+        mask_r = test_ir.binary_mask_3d(
+            center, radius, shape, fill=False, shell_thickness=1
+        )
+        mask_r_half = test_ir.binary_mask_3d(
+            center, r_half, shape, fill=False, shell_thickness=1
+        )
+        perimeter_ratio = mask_r[n_pix // 2].sum() / mask_r_half[n_pix // 2].sum()
+        assert np.isclose(2, perimeter_ratio, atol=0.1)
+        if shell_thickness == 1:
+            assert np.isclose(
+                mask_r[n_pix // 2].sum() / (2 * np.pi * radius), 1, atol=0.1
+            )
+            assert np.isclose(
+                mask_r_half[n_pix // 2].sum() / (2 * np.pi * r_half), 1, atol=0.1
+            )
+
+        surface_area_ratio = mask_r.sum() / mask_r_half.sum()
+        surface_area_ratio_analytic = (radius / r_half) ** 2
+        assert np.isclose(surface_area_ratio, surface_area_ratio_analytic, atol=0.1)
+
+    mask_r = test_ir.binary_mask_3d(center, radius, shape, fill=True, shell_thickness=1)
+    mask_r_half = test_ir.binary_mask_3d(
+        center, r_half, shape, fill=True, shell_thickness=1
+    )
+    volume_ratio = mask_r.sum() / mask_r_half.sum()
+    volume_ratio_analytic = (radius / r_half) ** 3
+    assert np.isclose(volume_ratio, volume_ratio_analytic, atol=0.005)
+
 
 def test_expand_1d_to_3d(test_ir, n_pix):
     """Test expansion of 1D array into spherical shell."""