Refactor kWaveGrid initialization in at_circular_piston_3D example

- Updated the grid creation process to utilize the new `from_domain` method for better clarity and efficiency.
- Adjusted sensor mask and data reshaping to align with the new grid structure.
- Ensured consistent usage of grid properties throughout the example for improved readability and maintainability.

Author: waltsims

examples/at_circular_piston_3D/at_circular_piston_3D.py

@@ -48,20 +48,9 @@
 # GRID
 # --------------------
 
-# calculate the grid spacing based on the PPW and F0
-dx: float = c0 / (ppw * source_f0)  # [m]
-
-# compute the size of the grid
-# is round_even needed?
-Nx: int = round_even(axial_size / dx)
-Ny: int = round_even(lateral_size / dx)
-Nz: int = Ny
-
-grid_size_points = Vector([Nx, Ny, Nz])
-grid_spacing_meters = Vector([dx, dx, dx])
-
-# create the k-space grid
-kgrid = kWaveGrid(grid_size_points, grid_spacing_meters)
+kgrid = kWaveGrid.from_domain(
+    dimensions=np.array([axial_size, lateral_size, lateral_size]), frequency=source_f0, sound_speed_min=c0, points_per_wavelength=ppw
+)
 
 # compute points per temporal period
 ppp: int = round(ppw / cfl)
@@ -113,8 +102,8 @@
 sensor = kSensor()
 
 # set sensor mask to record central plane, not including the source point
-sensor.mask = np.zeros((Nx, Ny, Nz), dtype=bool)
-sensor.mask[1:, :, Nz // 2] = True
+sensor.mask = np.zeros(kgrid.N, dtype=bool)
+sensor.mask[1:, :, kgrid.Nz // 2] = True
 
 # record the pressure
 sensor.record = ["p"]
@@ -143,10 +132,10 @@
 amp, _, _ = extract_amp_phase(sensor_data["p"].T, 1.0 / kgrid.dt, source_f0, dim=1, fft_padding=1, window="Rectangular")
 
 # reshape data
-amp = np.reshape(amp, (Nx - 1, Ny), order="F")
+amp = np.reshape(amp, (kgrid.Nx - 1, kgrid.Ny), order="F")
 
 # extract pressure on axis
-amp_on_axis = amp[:, Ny // 2]
+amp_on_axis = amp[:, kgrid.Ny // 2]
 
 # define axis vectors for plotting
 x_vec = kgrid.x_vec[1:, :] - kgrid.x_vec[0]
@@ -161,7 +150,7 @@
 
 # define radius and axis
 a: float = source_diam / 2.0
-x_max: float = (Nx - 1) * dx
+x_max: float = (kgrid.Nx - 1) * kgrid.dx
 delta_x: float = x_max / 10000.0
 x_ref: float = np.arange(0.0, x_max + delta_x, delta_x, dtype=float)
 
@@ -194,7 +183,7 @@
 # plot the source mask (pml is outside the grid in this example)
 fig2, ax2 = plt.subplots(1, 1)
 ax2.pcolormesh(
-    1e3 * np.squeeze(kgrid.y_vec), 1e3 * np.squeeze(kgrid.x_vec), np.flip(source.p_mask[:, :, Nz // 2], axis=0), shading="nearest"
+    1e3 * np.squeeze(kgrid.y_vec), 1e3 * np.squeeze(kgrid.x_vec), np.flip(source.p_mask[:, :, kgrid.Nz // 2], axis=0), shading="nearest"
 )
 ax2.set(xlabel="y [mm]", ylabel="x [mm]", title="Source Mask")
 

kwave/kgrid.py

@@ -37,6 +37,8 @@ def __init__(self, N, spacing):
         N, spacing = np.atleast_1d(N), np.atleast_1d(spacing)  # if inputs are lists
         assert N.ndim == 1 and spacing.ndim == 1  # ensure no multidimensional lists
         assert (1 <= N.size <= 3) and (1 <= spacing.size <= 3)  # ensure valid dimensionality
+        if spacing.size == 1:
+            spacing = spacing * np.ones(N.size)
         assert N.size == spacing.size, "Size list N and spacing list do not have the same size."
 
         self.N = N.astype(int)  #: grid size in each dimension [grid points]
@@ -725,11 +727,14 @@ def from_geometry(cls, domain_size, min_element_width, points_per_wavelength=10,
         # Ensure at least points_per_wavelength points across the smallest element
         grid_spacing = min_element_width / points_per_wavelength
 
+        # Create a list of grid spacings with the same length as domain_size
+        grid_spacing_list = [grid_spacing] * domain_size.size
+
         # Calculate grid size
         N = np.ceil(domain_size / grid_spacing).astype(int)
 
         # Create grid instance
-        grid = cls(N=N, spacing=grid_spacing)
+        grid = cls(N=N, spacing=grid_spacing_list)
 
         # Note: Time parameters are left as "auto"
         # The user can set them later using makeTime method
@@ -764,7 +769,7 @@ def from_domain(cls, dimensions, frequency, sound_speed_min, sound_speed_max=Non
         # Use sound_speed_min for sound_speed_max if not provided
         if sound_speed_max is None:
             sound_speed_max = sound_speed_min
-        if sound_speed_max > 0:
+        if not sound_speed_max > 0:
             raise ValueError("Sound speed must be positive")
 
         # Calculate wavelength