XY transposable sim.plot() plots (issue1072) VERSION 2

tests/test_components/test_IO.py

@@ -73,19 +73,19 @@ def test_simulation_load_export(split_string, tmp_path):
     SIM.to_hdf5(path_hdf5)
     SIM2 = td.Simulation.from_file(path)
     SIM_HDF5 = td.Simulation.from_hdf5(path_hdf5)
-    assert set_datasets_to_none(SIM)._json_string == SIM2._json_string, (
-        "original and loaded simulations are not the same"
-    )
+    assert (
+        set_datasets_to_none(SIM)._json_string == SIM2._json_string
+    ), "original and loaded simulations are not the same"
     assert SIM == SIM_HDF5, "original and loaded from hdf5 simulations are not the same"
 
 
 def test_simulation_load_export_yaml(tmp_path):
     path = str(tmp_path / "simulation.yaml")
     SIM.to_file(path)
     SIM2 = td.Simulation.from_file(path)
-    assert set_datasets_to_none(SIM)._json_string == SIM2._json_string, (
-        "original and loaded simulations are not the same"
-    )
+    assert (
+        set_datasets_to_none(SIM)._json_string == SIM2._json_string
+    ), "original and loaded simulations are not the same"
 
 
 def test_component_load_export(tmp_path):

tests/test_components/test_autograd.py

@@ -1247,18 +1247,18 @@ def test_adjoint_src_width():
     adj_srcs_fwidth = td.SimulationData._adjoint_src_width_single(adj_srcs)
 
     for src in adj_srcs_fwidth:
-        assert np.isclose((src.source_time.freq0 - f0) / f0, 0.0), (
-            "f0 of adjoint source should be centered on original f0"
-        )
+        assert np.isclose(
+            (src.source_time.freq0 - f0) / f0, 0.0
+        ), "f0 of adjoint source should be centered on original f0"
 
         check_fwidth = (
             src.source_time.freq0
             - td.components.data.sim_data.NUM_ADJOINT_FWIDTH_TO_ZERO * src.source_time.fwidth
         ) / src.source_time.freq0
 
-        assert np.isclose(check_fwidth, 0.0) or (check_fwidth > 0.0), (
-            "fwidth of adjoint source should decay sufficiently before f=0"
-        )
+        assert np.isclose(check_fwidth, 0.0) or (
+            check_fwidth > 0.0
+        ), "fwidth of adjoint source should decay sufficiently before f=0"
 
 
 def test_broadband_adjoint_src_width():
@@ -1305,12 +1305,12 @@ def test_broadband_adjoint_src_width():
             f0_expected - np.min(f0_adj_all)
         ) / td.components.data.sim_data.NUM_ADJOINT_FWIDTH_TO_FMIN
 
-        assert np.isclose((f0_expected - broadband_f0) / f0_expected, 0.0), (
-            "Expected freq0 not matching for broadband source"
-        )
-        assert np.isclose((fwidth_expected - broadband_fwidth) / fwidth_expected, 0.0), (
-            "Expected fwidth not matching for broadband source"
-        )
+        assert np.isclose(
+            (f0_expected - broadband_f0) / f0_expected, 0.0
+        ), "Expected freq0 not matching for broadband source"
+        assert np.isclose(
+            (fwidth_expected - broadband_fwidth) / fwidth_expected, 0.0
+        ), "Expected fwidth not matching for broadband source"
 
     # Test the case where we need a wider pulse to cover all the adjoint frequencies than we would otherwise choose for
     # each individual adjoint source
@@ -1333,12 +1333,12 @@ def test_broadband_adjoint_src_width():
         f0_expected - np.min(f0_broadband)
     ) / td.components.data.sim_data.NUM_ADJOINT_FWIDTH_TO_FMIN
 
-    assert np.isclose((f0_expected - broadband_f0) / f0_expected, 0.0), (
-        "Expected freq0 not matching for broadband source"
-    )
-    assert np.isclose((fwidth_expected - broadband_fwidth) / fwidth_expected, 0.0), (
-        "Expected fwidth not matching for broadband source"
-    )
+    assert np.isclose(
+        (f0_expected - broadband_f0) / f0_expected, 0.0
+    ), "Expected freq0 not matching for broadband source"
+    assert np.isclose(
+        (fwidth_expected - broadband_fwidth) / fwidth_expected, 0.0
+    ), "Expected fwidth not matching for broadband source"
 
     # Test the case where we have a narrow set of frequencies for the adjoint sources and so we can
     # choose a wider overall source than is needed for covering those frequencies. This larger pulse width
@@ -1360,12 +1360,12 @@ def test_broadband_adjoint_src_width():
     f0_expected = 0.5 * (np.max(f0_broadband) + np.min(f0_broadband))
     fwidth_expected = f0_expected / td.components.data.sim_data.NUM_ADJOINT_FWIDTH_TO_ZERO
 
-    assert np.isclose((f0_expected - broadband_f0) / f0_expected, 0.0), (
-        "Expected freq0 not matching for broadband source"
-    )
-    assert np.isclose((fwidth_expected - broadband_fwidth) / fwidth_expected, 0.0), (
-        "Expected fwidth not matching for broadband source"
-    )
+    assert np.isclose(
+        (f0_expected - broadband_f0) / f0_expected, 0.0
+    ), "Expected freq0 not matching for broadband source"
+    assert np.isclose(
+        (fwidth_expected - broadband_fwidth) / fwidth_expected, 0.0
+    ), "Expected fwidth not matching for broadband source"
 
 
 @pytest.mark.parametrize("colocate", [True, False])

tests/test_components/test_autograd_mode_polyslab_numerical.py

@@ -332,7 +332,9 @@ def test_finite_difference_mode_data_polyslab(
         "geometry_size_wvl",
         "polyslab_permittivity",
         "test_number",
-    )(mode_data_test_parameters)
+    )(
+        mode_data_test_parameters
+    )
 
     adj_freq = td.C_0 / adj_wvl_um
 
@@ -372,11 +374,7 @@ def eval_fn(sim_data):
     polyslab_height_um = POLYSLAB_HEIGHT_WVL * adj_wvl_um
 
     objective = create_objective_function(
-        lambda mesh_wvl_um=mesh_wvl_um,
-        adj_wvl_um=adj_wvl_um,
-        geometry_size_wvl=geometry_size_wvl,
-        polyslab_permittivity=polyslab_permittivity,
-        box_for_override=box_for_override: make_base_sim(
+        lambda mesh_wvl_um=mesh_wvl_um, adj_wvl_um=adj_wvl_um, geometry_size_wvl=geometry_size_wvl, polyslab_permittivity=polyslab_permittivity, box_for_override=box_for_override: make_base_sim(
             mesh_wvl_um=mesh_wvl_um,
             adj_wvl_um=adj_wvl_um,
             geometry_size_wvl=geometry_size_wvl,

tests/test_components/test_autograd_numerical.py

@@ -256,7 +256,9 @@ def test_finite_difference_field_data(field_data_test_parameters, rng, tmp_path,
         "eval_fn",
         "eval_fn_name",
         "test_number",
-    )(field_data_test_parameters)
+    )(
+        field_data_test_parameters
+    )
 
     dim_um = mesh_wvl_um
     dim_um = mesh_wvl_um
@@ -279,11 +281,7 @@ def test_finite_difference_field_data(field_data_test_parameters, rng, tmp_path,
 
     objective = create_objective_function(
         block,
-        lambda mesh_wvl_um=mesh_wvl_um,
-        adj_wvl_um=adj_wvl_um,
-        monitor_size_wvl=monitor_size_wvl,
-        box_for_override=box_for_override,
-        monitor_bg_index=monitor_bg_index: make_base_sim(
+        lambda mesh_wvl_um=mesh_wvl_um, adj_wvl_um=adj_wvl_um, monitor_size_wvl=monitor_size_wvl, box_for_override=box_for_override, monitor_bg_index=monitor_bg_index: make_base_sim(
             mesh_wvl_um=mesh_wvl_um,
             adj_wvl_um=adj_wvl_um,
             monitor_size_wvl=monitor_size_wvl,

tests/test_components/test_eme.py

@@ -283,21 +283,22 @@ def test_eme_monitor():
     )
 
 
-def test_eme_simulation():
+@pytest.mark.parametrize("transpose", [True, False])
+def test_eme_simulation(transpose):
     sim = make_eme_sim()
-    _ = sim.plot(x=0, ax=AX)
-    _ = sim.plot(y=0, ax=AX)
-    _ = sim.plot(z=0, ax=AX)
-    _ = sim.plot_grid(x=0, ax=AX)
-    _ = sim.plot_grid(y=0, ax=AX)
-    _ = sim.plot_grid(z=0, ax=AX)
-    _ = sim.plot_eps(x=0, ax=AX)
-    _ = sim.plot_eps(y=0, ax=AX)
-    _ = sim.plot_eps(z=0, ax=AX)
+    _ = sim.plot(x=0, ax=AX, transpose=transpose)
+    _ = sim.plot(y=0, ax=AX, transpose=transpose)
+    _ = sim.plot(z=0, ax=AX, transpose=transpose)
+    _ = sim.plot_grid(x=0, ax=AX, transpose=transpose)
+    _ = sim.plot_grid(y=0, ax=AX, transpose=transpose)
+    _ = sim.plot_grid(z=0, ax=AX, transpose=transpose)
+    _ = sim.plot_eps(x=0, ax=AX, transpose=transpose)
+    _ = sim.plot_eps(y=0, ax=AX, transpose=transpose)
+    _ = sim.plot_eps(z=0, ax=AX, transpose=transpose)
     sim2 = sim.updated_copy(axis=1)
-    _ = sim2.plot(x=0, ax=AX)
-    _ = sim2.plot(y=0, ax=AX)
-    _ = sim2.plot(z=0, ax=AX)
+    _ = sim2.plot(x=0, ax=AX, transpose=transpose)
+    _ = sim2.plot(y=0, ax=AX, transpose=transpose)
+    _ = sim2.plot(z=0, ax=AX, transpose=transpose)
 
     # need at least one freq
     with pytest.raises(pd.ValidationError):

tests/test_components/test_geometry.py

@@ -85,14 +85,15 @@
 _, AX = plt.subplots()
 
 
-@pytest.mark.parametrize("component", GEO_TYPES)
-def test_plot(component):
-    _ = component.plot(z=0, ax=AX)
+@pytest.mark.parametrize("component, transpose", zip(GEO_TYPES, [True, False]))
+def test_plot(component, transpose):
+    _ = component.plot(z=0, ax=AX, transpose=transpose)
     plt.close()
 
 
-def test_plot_with_units():
-    _ = BOX.plot(z=0, ax=AX, plot_length_units="nm")
+@pytest.mark.parametrize("transpose", [True, False])
+def test_plot_with_units(transpose):
+    _ = BOX.plot(z=0, ax=AX, plot_length_units="nm", transpose=transpose)
     plt.close()
 
 
@@ -204,11 +205,11 @@ def test_array_to_vertices():
     assert np.all(np.array(vertices) == np.array(vertices2))
 
 
-@pytest.mark.parametrize("component", GEO_TYPES)
-def test_intersections_plane(component):
-    assert len(component.intersections_plane(z=0.2)) > 0
-    assert len(component.intersections_plane(x=0.2)) > 0
-    assert len(component.intersections_plane(x=10000)) == 0
+@pytest.mark.parametrize("component, transpose", zip(GEO_TYPES, [True, False]))
+def test_intersections_plane(component, transpose):
+    assert len(component.intersections_plane(z=0.2, transpose=transpose)) > 0
+    assert len(component.intersections_plane(x=0.2, transpose=transpose)) > 0
+    assert len(component.intersections_plane(x=10000, transpose=transpose)) == 0
 
 
 def test_intersections_plane_inf():
@@ -329,15 +330,15 @@ def test_polyslab_inf_to_finite_bounds(axis):
         vertices=[[0, 0], [2.5, 1], [2, 3], [0.5, 4], [-1.5, 2.5]],
     )
 
-    assert ps_low_inf.finite_length_axis == (LARGE_NUMBER + axis_bound), (
-        "Unexpected finite length for polyslab axis with -inf bound"
-    )
-    assert ps_high_inf.finite_length_axis == (LARGE_NUMBER + axis_bound), (
-        "Unexpected finite length for polyslab axis with inf bound"
-    )
-    assert ps_inf.finite_length_axis == 2 * LARGE_NUMBER, (
-        "Unexpected finite length for polyslab axis with two inf bounds"
-    )
+    assert ps_low_inf.finite_length_axis == (
+        LARGE_NUMBER + axis_bound
+    ), "Unexpected finite length for polyslab axis with -inf bound"
+    assert ps_high_inf.finite_length_axis == (
+        LARGE_NUMBER + axis_bound
+    ), "Unexpected finite length for polyslab axis with inf bound"
+    assert (
+        ps_inf.finite_length_axis == 2 * LARGE_NUMBER
+    ), "Unexpected finite length for polyslab axis with two inf bounds"
 
 
 def test_validate_polyslab_vertices_valid():
@@ -766,36 +767,49 @@ def test_geometry_touching_intersections_plane(x0):
 
 
 def test_pop_axis():
-    b = td.Box(size=(1, 1, 1))
     for axis in range(3):
         coords = (1, 2, 3)
-        Lz, (Lx, Ly) = b.pop_axis(coords, axis=axis)
-        _coords = b.unpop_axis(Lz, (Lx, Ly), axis=axis)
+        Lz, (Lx, Ly) = td.Box.pop_axis(coords, axis=axis)
+        _coords = td.Box.unpop_axis(Lz, (Lx, Ly), axis=axis)
         assert all(c == _c for (c, _c) in zip(coords, _coords))
-        _Lz, (_Lx, _Ly) = b.pop_axis(_coords, axis=axis)
+        _Lz, (_Lx, _Ly) = td.Box.pop_axis(_coords, axis=axis)
         assert Lz == _Lz
         assert Lx == _Lx
         assert Ly == _Ly
 
 
-def test_2b_box_intersections():
+@pytest.mark.parametrize("transpose", [True, False])
+def test_pop_axis_and_swap(transpose):
+    for axis in range(3):
+        coords = (1, 2, 3)
+        Lz, (Lx, Ly) = td.Box.pop_axis_and_swap(coords, axis=axis, transpose=transpose)
+        _coords = td.Box.unpop_axis_and_swap(Lz, (Lx, Ly), axis=axis, transpose=transpose)
+        assert all(c == _c for (c, _c) in zip(coords, _coords))
+        _Lz, (_Lx, _Ly) = td.Box.pop_axis_and_swap(_coords, axis=axis, transpose=transpose)
+        assert Lz == _Lz
+        assert Lx == _Lx
+        assert Ly == _Ly
+
+
+@pytest.mark.parametrize("transpose", [True, False])
+def test_2b_box_intersections(transpose):
     plane = td.Box(size=(1, 4, 0))
     box1 = td.Box(size=(1, 1, 1))
     box2 = td.Box(size=(1, 1, 1), center=(3, 0, 0))
 
-    result = plane.intersections_with(box1)
+    result = plane.intersections_with(box1, transpose=transpose)
     assert len(result) == 1
     assert result[0].geom_type == "Polygon"
-    assert len(plane.intersections_with(box2)) == 0
+    assert len(plane.intersections_with(box2, transpose=transpose)) == 0
 
     with pytest.raises(ValidationError):
-        _ = box1.intersections_with(box2)
+        _ = box1.intersections_with(box2, transpose=transpose)
 
-    assert len(box1.intersections_2dbox(plane)) == 1
-    assert len(box2.intersections_2dbox(plane)) == 0
+    assert len(box1.intersections_2dbox(plane, transpose=transpose)) == 1
+    assert len(box2.intersections_2dbox(plane, transpose=transpose)) == 0
 
     with pytest.raises(ValidationError):
-        _ = box2.intersections_2dbox(box1)
+        _ = box2.intersections_2dbox(box1, transpose=transpose)
 
 
 def test_polyslab_merge():
@@ -937,7 +951,8 @@ def test_to_gds(geometry, tmp_path):
     assert len(cell.polygons) == 0
 
 
-def test_custom_surface_geometry(tmp_path):
+@pytest.mark.parametrize("transpose", [True, False])
+def test_custom_surface_geometry(transpose, tmp_path):
     # create tetrahedron STL
     vertices = np.array([[0, 0, 0], [1, 0, 0], [0, 1, 0], [0, 0, 1]])
     faces = np.array([[1, 2, 3], [0, 3, 2], [0, 1, 3], [0, 2, 1]])
@@ -970,9 +985,13 @@ def test_custom_surface_geometry(tmp_path):
     assert np.isclose(geom.volume(), 1 / 6)
 
     # test intersections
-    assert shapely.equals(geom.intersections_plane(x=0), shapely.Polygon([[0, 0], [0, 1], [1, 0]]))
     assert shapely.equals(
-        geom.intersections_plane(z=0.5), shapely.Polygon([[0, 0], [0, 0.5], [0.5, 0]])
+        geom.intersections_plane(x=0, transpose=transpose),
+        shapely.Polygon([[0, 0], [0, 1], [1, 0]]),
+    )
+    assert shapely.equals(
+        geom.intersections_plane(z=0.5, transpose=transpose),
+        shapely.Polygon([[0, 0], [0, 0.5], [0.5, 0]]),
     )
 
     # test inside
@@ -981,7 +1000,7 @@ def test_custom_surface_geometry(tmp_path):
 
     # test plot
     _, ax = plt.subplots()
-    _ = geom.plot(z=0.1, ax=ax)
+    _ = geom.plot(z=0.1, ax=ax, transpose=transpose)
     plt.close()
 
     # test inconsistent winding
@@ -1031,7 +1050,7 @@ def test_custom_surface_geometry(tmp_path):
         boundary_spec=td.BoundarySpec.all_sides(td.PML()),
     )
     _, ax = plt.subplots()
-    _ = sim.plot(y=0, ax=ax)
+    _ = sim.plot(y=0, ax=ax, transpose=transpose)
     plt.close()
 
     # allow small triangles

tests/test_components/test_heat.py

@@ -335,11 +335,12 @@ def make_heat_sim(include_custom_source: bool = True):
     return heat_sim
 
 
-def test_heat_sim():
+@pytest.mark.parametrize("transpose", [True, False])
+def test_heat_sim(transpose):
     bc_temp, bc_flux, bc_conv = make_heat_bcs()
     heat_sim = make_heat_sim()
 
-    _ = heat_sim.plot(x=0)
+    _ = heat_sim.plot(x=0, transpose=transpose)
 
     # wrong names given
     for pl in [
@@ -373,14 +374,14 @@ def test_heat_sim():
     with pytest.raises(pd.ValidationError):
         heat_sim.updated_copy(monitors=[temp_mnt, temp_mnt])
 
-    _ = heat_sim.plot(x=0)
+    _ = heat_sim.plot(x=0, transpose=transpose)
     plt.close()
 
-    _ = heat_sim.plot_heat_conductivity(y=0)
+    _ = heat_sim.plot_heat_conductivity(y=0, transpose=transpose)
     plt.close()
 
     heat_sim_sym = heat_sim.updated_copy(symmetry=(0, 1, 1))
-    _ = heat_sim_sym.plot_heat_conductivity(z=0, colorbar="source")
+    _ = heat_sim_sym.plot_heat_conductivity(z=0, colorbar="source", transpose=transpose)
     plt.close()
 
     # no negative symmetry