[BUG] Fix alpha bug on 3D PathCollection plots. (matplotlib#25478)

* Fix alpha bug on 3D PathCollection plots.

* Fix flake8 linting errors

* Handle RGB instead of RGBA case.

* Clean main if clause.

* linting

* Add tests for scatter alpha conversion

* Simplify logic for depth shading alpha correction

* linting

* linting

* linting

* Comments

* restore missing line

* linting

* Fix logic

* Apply suggestion from @timhoffm

* Fix alpha not having z_marker_idx sorting when applicable

---------

Co-authored-by: Scott Shambaugh <14363975+scottshambaugh@users.noreply.github.com>
Co-authored-by: Tim Hoffmann <2836374+timhoffm@users.noreply.github.com>
Co-authored-by: Scott Shambaugh <scottshambaugh@users.noreply.github.com>

Author: 3 people

lib/mpl_toolkits/mplot3d/art3d.py

@@ -819,18 +819,26 @@ def do_3d_projection(self):
             return np.nan
 
     def _maybe_depth_shade_and_sort_colors(self, color_array):
-        color_array = (
-            _zalpha(
+        # Adjust the color_array alpha values if point depths are defined
+        # and depth shading is active
+        alpha = self._alpha
+        if self._vzs is not None and self._depthshade:
+            color_array = _zalpha(
                 color_array,
                 self._vzs,
                 min_alpha=self._depthshade_minalpha,
             )
-            if self._vzs is not None and self._depthshade
-            else color_array
-        )
+            if alpha is not None and color_array.shape[1] == 4:  # RGBA, not RGB
+                alpha = alpha * color_array[:, 3]
+
+        # Adjust the order of the color_array using the _z_markers_idx,
+        # which has been sorted by z-depth
         if len(color_array) > 1:
             color_array = color_array[self._z_markers_idx]
-        return mcolors.to_rgba_array(color_array, self._alpha)
+            if np.ndim(alpha) > 0:
+                alpha = np.asarray(alpha)[self._z_markers_idx]
+
+        return mcolors.to_rgba_array(color_array, alpha)
 
     def get_facecolor(self):
         return self._maybe_depth_shade_and_sort_colors(super().get_facecolor())
@@ -1070,20 +1078,25 @@ def _use_zordered_offset(self):
     def _maybe_depth_shade_and_sort_colors(self, color_array):
         # Adjust the color_array alpha values if point depths are defined
         # and depth shading is active
+        alpha = self._alpha
         if self._vzs is not None and self._depthshade:
             color_array = _zalpha(
                 color_array,
                 self._vzs,
                 min_alpha=self._depthshade_minalpha,
                 _data_scale=self._data_scale,
             )
+            if alpha is not None and color_array.shape[1] == 4:  # RGBA, not RGB
+                alpha = alpha * color_array[:, 3]
 
         # Adjust the order of the color_array using the _z_markers_idx,
         # which has been sorted by z-depth
         if len(color_array) > 1:
             color_array = color_array[self._z_markers_idx]
+            if np.ndim(alpha) > 0:
+                alpha = np.asarray(alpha)[self._z_markers_idx]
 
-        return mcolors.to_rgba_array(color_array)
+        return mcolors.to_rgba_array(color_array, alpha)
 
     def get_facecolor(self):
         return self._maybe_depth_shade_and_sort_colors(super().get_facecolor())

lib/mpl_toolkits/mplot3d/tests/test_axes3d.py

@@ -440,6 +440,19 @@ def test_scatter3d_linewidth():
                marker='o', linewidth=np.arange(10))
 
 
+@check_figures_equal()
+def test_scatter3d_cmap_alpha(fig_ref, fig_test):
+    # Check that alpha is applied correctly with colormapped scatter.
+    # Regression test for https://github.com/matplotlib/matplotlib/issues/25468
+    x, y, z = np.arange(5), np.zeros(5), np.arange(5)
+    c = np.array([0, 1, np.nan, 3, 4])
+
+    ax_test = fig_test.add_subplot(projection='3d')
+    ax_test.scatter(x, y, z, c=c)
+    ax_ref = fig_ref.add_subplot(projection='3d')
+    ax_ref.scatter(x, y, z, c=c, alpha=1)
+
+
 @check_figures_equal()
 def test_scatter3d_linewidth_modification(fig_ref, fig_test):
     # Changing Path3DCollection linewidths with array-like post-creation