Merge pull request #721 from cophus/tomography

Minor widget updates

Author: smribet

py4DSTEM/tomography/tomography.py

@@ -2056,9 +2056,16 @@ def _constraints(
 
             obj_6D = copy_to_device(self.object_6D, device="cpu")
 
-            obj_6D = gaussian_filter(
-                obj_6D, real_space_gaussian_filter, axes=(0, 1, 2)
-            )  # axes only supported in cpu
+            # obj_6D = gaussian_filter(
+            #     obj_6D, real_space_gaussian_filter, axes=(0, 1, 2)
+            # )  # axes only supported in cpu
+            for i in range(obj_6D.shape[3]):
+                for j in range(obj_6D.shape[4]):
+                    for k in range(obj_6D.shape[5]):
+                        obj_6D[:, :, :, i, j, k] = gaussian_filter(
+                            obj_6D[:, :, :, i, j, k], 
+                            sigma=real_space_gaussian_filter
+                        )
 
             self._object = copy_to_device(
                 obj_6D.reshape((s[0], s[1] * s[2], s[3] * s[4] * s[5])), device=storage
@@ -2255,7 +2262,7 @@ def widget(
         **kwargs,
     ):
         """ """
-        from ipywidgets import HBox, VBox, widgets, interact, Dropdown, Label, Layout
+        from ipywidgets import HBox, VBox, widgets, interact, Dropdown, Label, Layout, widgets
         from skimage.feature import peak_local_max
         from scipy.ndimage import gaussian_filter
         from py4DSTEM.visualize import return_scaled_histogram_ordering
@@ -2293,6 +2300,30 @@ def widget(
             vmax=vmax,
         )
 
+        # Buttons to set view angles
+        button_xy = widgets.Button(description="XY view", layout=Layout(width="100px"))
+        button_xz = widgets.Button(description="XZ view", layout=Layout(width="100px"))
+        button_yz = widgets.Button(description="YZ view", layout=Layout(width="100px"))
+
+        def on_click_xy(b):
+            ax2.view_init(elev=90, azim=-90)  # Top-down
+            fig.canvas.draw_idle()
+
+        def on_click_xz(b):
+            ax2.view_init(elev=0, azim=-90)   # Front-on
+            fig.canvas.draw_idle()
+
+        def on_click_yz(b):
+            ax2.view_init(elev=0, azim=0)     # Side-on
+            fig.canvas.draw_idle()
+
+        button_xy.on_click(on_click_xy)
+        button_xz.on_click(on_click_xz)
+        button_yz.on_click(on_click_yz)
+
+        view_buttons = widgets.HBox([button_xy, button_xz, button_yz])
+
+
         # %matplotlib ipympl
 
         with plt.ioff():
@@ -2301,6 +2332,10 @@ def widget(
             ax1 = fig.add_subplot(1, 3, 2)
             ax2 = fig.add_subplot(1, 3, 3, projection="3d")
 
+            from mpl_toolkits.mplot3d import Axes3D
+            from mpl_toolkits.mplot3d import axes3d
+            ax2.set_proj_type('ortho')
+
         x = obj_6D.shape[0] // 2
         y = obj_6D.shape[1] // 2
         z = obj_6D.shape[2] // 2
@@ -2370,6 +2405,7 @@ def widget(
         ax2.set_xlim([0, obj_6D.shape[3]])
         ax2.set_ylim([0, obj_6D.shape[4]])
         ax2.set_zlim([0, obj_6D.shape[5]])
+        set_axes_equal(ax2)
 
         plt.tight_layout()
 
@@ -2474,6 +2510,8 @@ def update_images(
             ax1.set_title("xz")
             ax2.set_title("Diffraction")
 
+            set_axes_equal(ax2)
+
             plt.tight_layout()
 
             fig.canvas.draw_idle()
@@ -2580,16 +2618,51 @@ def update_images(
         fig.canvas.layout.height = "400px"
         fig.canvas.toolbar_position = "bottom"
 
-        widget = widgets.VBox(
-            [
-                fig.canvas,
-                HBox([x, y]),
-                HBox([z, gaussian_filter_diffraction]),
-                HBox([minimum_threshold, scale_intensities]),
-                HBox([intensities_power, block_center]),
-            ],
-        )
+        widget = widgets.VBox([
+            fig.canvas,
+            view_buttons,
+            HBox([x, y]),
+            HBox([z, gaussian_filter_diffraction]),
+            HBox([minimum_threshold, scale_intensities]),
+            HBox([intensities_power, block_center]),
+        ])
+
+        # widget = widgets.VBox(
+        #     [
+        #         fig.canvas,
+        #         HBox([x, y]),
+        #         HBox([z, gaussian_filter_diffraction]),
+        #         HBox([minimum_threshold, scale_intensities]),
+        #         HBox([intensities_power, block_center]),
+        #     ],
+        # )
 
         display(widget)
 
         return self
+
+def set_axes_equal(ax):
+    """Set 3D plot axes to equal scale (for matplotlib >= 3.3)."""
+    xlim = ax.get_xlim3d()
+    ylim = ax.get_ylim3d()
+    zlim = ax.get_zlim3d()
+
+    # Calculate ranges and midpoints
+    x_range, x_middle = np.ptp(xlim), np.mean(xlim)
+    y_range, y_middle = np.ptp(ylim), np.mean(ylim)
+    z_range, z_middle = np.ptp(zlim), np.mean(zlim)
+
+    # Set max range
+    plot_radius = 0.5 * max([x_range, y_range, z_range])
+
+    ax.set_xlim3d([x_middle - plot_radius, x_middle + plot_radius])
+    ax.set_ylim3d([y_middle - plot_radius, y_middle + plot_radius])
+    ax.set_zlim3d([z_middle - plot_radius, z_middle + plot_radius])
+
+    # Force equal aspect
+    try:
+        ax.set_box_aspect([1, 1, 1])  # Requires matplotlib >= 3.3
+    except AttributeError:
+        pass
+
+