fix plots and imports in scripts

examples/at_circular_piston_3D/at_circular_piston_3D.py

@@ -18,7 +18,6 @@
 from kwave.options.simulation_execution_options import SimulationExecutionOptions
 from kwave.options.simulation_options import SimulationOptions
 
-
 # material values
 c0: float       = 1500.0     # sound speed [m/s]
 rho0: float     = 1000.0     # density [kg/m^3]
@@ -209,10 +208,10 @@
 
 # plot the source mask (pml is outside the grid in this example)
 fig2, ax2 = plt.subplots(1, 1)
-ax2.pcolormesh(1e3 * np.squeeze(kgrid.x_vec),
-               1e3 * np.squeeze(kgrid.y_vec),
-               source.p_mask[:, :, int(np.ceil(Nz / 2))].T,
-               shading='gouraud')
+ax2.pcolormesh(1e3 * np.squeeze(kgrid.y_vec),
+               1e3 * np.squeeze(kgrid.x_vec),
+               np.flip(source.p_mask[:, :, int(np.ceil(Nz / 2))], axis=0),
+               shading='nearest')
 ax2.set(xlabel='y [mm]',
         ylabel='x [mm]',
         title='Source Mask')

examples/at_focused_annular_array_3D/at_focused_annular_array_3D.py

@@ -16,7 +16,8 @@
 
 from kwave.kspaceFirstOrder3D import kspaceFirstOrder3D
 
-from kwave.options import SimulationOptions, SimulationExecutionOptions
+from kwave.options.simulation_options import SimulationOptions
+from kwave.options.simulation_execution_options import SimulationExecutionOptions
 
 verbose: bool = False
 
@@ -199,20 +200,21 @@
 grid_weights = karray.get_array_grid_weights(kgrid)
 
 fig2, (ax2a, ax2b) = plt.subplots(1, 2)
-ax2a.pcolormesh(1e3 * np.squeeze(kgrid.x_vec),
-                1e3 * np.squeeze(kgrid.y_vec),
-                source.p_mask[:, :, int(np.ceil(Nz / 2))].T,
-                shading='gouraud')
+ax2a.pcolormesh(1e3 * np.squeeze(kgrid.y_vec),
+                1e3 * np.squeeze(kgrid.x_vec),
+                np.flip(source.p_mask[:, :, int(np.ceil(Nz / 2))], axis=0),
+                shading='nearest')
 ax2a.set(xlabel='y [mm]',
          ylabel='x [mm]',
          title='Source Mask')
-ax2b.pcolormesh(1e3 * np.squeeze(kgrid.x_vec),
-                1e3 * np.squeeze(kgrid.y_vec),
-                grid_weights[:, :, int(np.ceil(Nz / 2))].T,
-                shading='gouraud')
+ax2b.pcolormesh(1e3 * np.squeeze(kgrid.y_vec),
+                1e3 * np.squeeze(kgrid.x_vec),
+                np.flip(grid_weights[:, :, int(np.ceil(Nz / 2))], axis=0),
+                shading='nearest')
 ax2b.set(xlabel='y [mm]',
          ylabel='x [mm]',
          title='Off-Grid Source Weights')
+plt.tight_layout(pad=1.2)
 
 # plot the pressure field
 fig3, ax3 = plt.subplots(1, 1)

examples/at_focused_bowl_3D/at_focused_bowl_3D.py

@@ -16,7 +16,8 @@
 
 from kwave.kspaceFirstOrder3D import kspaceFirstOrder3D
 
-from kwave.options import SimulationOptions, SimulationExecutionOptions
+from kwave.options.simulation_options import SimulationOptions
+from kwave.options.simulation_execution_options import SimulationExecutionOptions
 
 
 def L2_error(x: np.ndarray, y: np.ndarray, ord=None) -> float:	
@@ -202,16 +203,16 @@ def L2_error(x: np.ndarray, y: np.ndarray, ord=None) -> float:
 
 # calculate analytical solution
 p_ref_axial, _, _ = focused_bowl_oneil(source_roc,
-                                 source_diameter,
-                                 source_amp / (c0 * rho0),
-                                 source_f0,
-                                 c0,
-                                 rho0,
-                                 axial_positions=x_ref)
+                                       source_diameter,
+                                       source_amp / (c0 * rho0),
+                                       source_f0,
+                                       c0,
+                                       rho0,
+                                       axial_positions=x_ref)
 
 # calculate analytical solution at exactly the same points as k-Wave
 p_ref_axial_kw, _, _ = focused_bowl_oneil(source_roc, source_diameter, source_amp / (c0 * rho0),
-                                    source_f0, c0, rho0, axial_positions=x_vec)
+                                          source_f0, c0, rho0, axial_positions=x_vec)
 
 # calculate errors
 L2 = L2_error(p_ref_axial_kw, amp_on_axis, ord=2)
@@ -240,20 +241,21 @@ def L2_error(x: np.ndarray, y: np.ndarray, ord=None) -> float:
 grid_weights = karray.get_array_grid_weights(kgrid)
 
 fig2, (ax2a, ax2b) = plt.subplots(1, 2)
-ax2a.pcolormesh(1e3 * np.squeeze(kgrid.x_vec),
-                1e3 * np.squeeze(kgrid.y_vec),
-                source.p_mask[:, :, int(np.ceil(Nz / 2))].T,
-                shading='gouraud')
+ax2a.pcolormesh(1e3 * np.squeeze(kgrid.y_vec),
+                1e3 * np.squeeze(kgrid.x_vec),
+                np.flip(source.p_mask[:, :, int(np.ceil(Nz / 2))], axis=0),
+                shading='nearest')
 ax2a.set(xlabel='y [mm]',
          ylabel='x [mm]',
          title='Source Mask')
-ax2b.pcolormesh(1e3 * np.squeeze(kgrid.x_vec),
-                1e3 * np.squeeze(kgrid.y_vec),
-                grid_weights[:, :, int(np.ceil(Nz / 2))].T,
-                shading='gouraud')
+ax2b.pcolormesh(1e3 * np.squeeze(kgrid.y_vec),
+                1e3 * np.squeeze(kgrid.x_vec),
+                np.flip(grid_weights[:, :, int(np.ceil(Nz / 2))], axis=0),
+                shading='nearest')
 ax2b.set(xlabel='y [mm]',
          ylabel='x [mm]',
          title='Off-Grid Source Weights')
+plt.tight_layout(pad=1.2)
 
 # plot the pressure field
 fig3, ax3 = plt.subplots(1, 1)