corrected z position of geometry

examples/plot_phir_slice_point_source.py

@@ -3,7 +3,7 @@
 # plotted using the openmc_cylindrical_plotter in the Phi R axis.
 
 import openmc
-from openmc_cylindrical_mesh_plotter import plot_mesh_tally_rz_slice
+from openmc_cylindrical_mesh_plotter import plot_mesh_tally_phir_slice
 from matplotlib.colors import LogNorm
 
 
@@ -48,7 +48,7 @@
 
 my_tally_result = statepoint.get_tally(name="my_tally")
 
-plot = plot_mesh_tally_rz_slice(
+plot = plot_mesh_tally_phir_slice(
     tally=my_tally_result,
     outline=True,
     geometry=my_geometry,

examples/plot_rz_slices_point_source.py

@@ -65,6 +65,6 @@
 
 for slice_index in range(1, len(mesh.phi_grid)):
     plot = plot_mesh_tally_rz_slice(
-        tally=my_tally_result, geometry=my_geometry, norm=LogNorm()
+        tally=my_tally_result, outline=True, geometry=my_geometry, norm=LogNorm()
     )
     plot.figure.savefig(f"rz_point_source_{slice_index}.png")

examples/plot_rz_slices_ring_source.py

@@ -10,26 +10,30 @@
 from matplotlib.colors import LogNorm
 
 mesh = openmc.CylindricalMesh(
-    phi_grid=np.linspace(0.0, 2 * pi, 3),
-    r_grid=np.linspace(0, 10, 50),
-    z_grid=np.linspace(0, 8, 50),
+    phi_grid=np.linspace(0.0, 2 * pi, 4),
+    r_grid=np.linspace(0,100, 50),
+    z_grid=np.linspace(-100, 50, 50),
 )
-tally = openmc.Tally(name="my_tally")
 mesh_filter = openmc.MeshFilter(mesh)
-tally.filters.append(mesh_filter)
-tally.scores.append("flux")
+
+tally = openmc.Tally(name="my_tally")
+tally.filters =[mesh_filter]
+tally.scores=["flux"]
 tallies = openmc.Tallies([tally])
 
-outer_surface = openmc.Sphere(r=100, boundary_type="vacuum")
-cell = openmc.Cell(region=-outer_surface)
+surf1=openmc.model.RectangularParallelepiped(-100,100,-100,100,-100,50, boundary_type="vacuum")
+surf2=openmc.model.RectangularParallelepiped(-95,95,-95,95,-95,45)
+surf3 = openmc.Sphere(r=40)
+cell1 = openmc.Cell(region=-surf3)
+cell2 = openmc.Cell(region=+surf2&-surf1)
+cell3 = openmc.Cell(region=+surf3&-surf2)
 
 material = openmc.Material()
 material.add_nuclide("Fe56", 1)
 material.set_density("g/cm3", 0.1)
 my_materials = openmc.Materials([material])
 
-universe = openmc.Universe(cells=[cell])
-my_geometry = openmc.Geometry(universe)
+my_geometry = openmc.Geometry([cell1, cell2, cell3])
 
 my_source = openmc.Source()
 
@@ -66,6 +70,7 @@
     plot = plot_mesh_tally_rz_slice(
         tally=my_tally_result,
         geometry=my_geometry,
+        outline=True,
         norm=LogNorm(),
         slice_index=slice_index,
     )

src/openmc_cylindrical_mesh_plotter/core.py

@@ -140,7 +140,15 @@ def plot_mesh_tally_rz_slice(
     xlabel, ylabel = f"r [{axis_units}]", f"z [{axis_units}]"
     axis_scaling_factor = {"km": 0.00001, "m": 0.01, "cm": 1, "mm": 10}[axis_units]
 
-    extent = [mesh.r_grid[0], mesh.r_grid[-1], mesh.z_grid[0], mesh.z_grid[-1]]
+    if mesh.origin[0] != 0. or mesh.origin[1] != 0.:
+        raise ValueError('Plotter only works for cylindrical meshes with x,y origins of 0,0')
+
+    extent = [
+        mesh.r_grid[0],
+        mesh.r_grid[-1],
+        mesh.origin[2] + mesh.z_grid[0],
+        mesh.origin[2] + mesh.z_grid[-1]
+    ]
 
     x_min, x_max, y_min, y_max = [i * axis_scaling_factor for i in extent]
 
@@ -157,22 +165,6 @@ def plot_mesh_tally_rz_slice(
     if outline and geometry is not None:
         import matplotlib.image as mpimg
 
-        # code to make sure geometry outline is in the middle of the mesh voxel
-        # two of the three dimensions are just in the center of the mesh
-        # but the slice can move one axis off the center so this needs calculating
-        # x1, y1, z1 = mesh.upper_right
-        # x_origin, y_origin, z_origin = mesh.origin
-
-        # # width_x = abs(x_origin + x1)/2
-        # # width_y = abs(y_origin + y1)/2
-        # # width_z = abs(z_origin + z1)
-
-        # width_x, width_y, width_z = mesh.bounding_box.width
-        # width_x=width_x/2
-        # width_y=width_y/2
-        # print('width_x,width_y,width_z')
-        # print(width_x,width_y,width_z)
-
         model = openmc.Model()
         model.geometry = geometry
         plot = openmc.Plot()
@@ -181,9 +173,9 @@ def plot_mesh_tally_rz_slice(
         width_y = abs(extent[1] - extent[0])  # same
         width_z = abs(extent[3] - extent[2])
 
-        x_center = abs(extent[0] + (width_x / 2))
-        y_center = abs(extent[0] + (width_y / 2))
-        z_center = abs(extent[2] + width_z * 0.5)
+        x_center = extent[0] + (width_x / 2)
+        y_center = extent[0] + (width_y / 2)
+        z_center = extent[2] + width_z * 0.5
 
         if geometry_basis == "xz":
             plot.origin = (x_center, 0, z_center)