Fix alpha handling for image saving.

skimage/viewer/viewers/core.py

@@ -10,6 +10,7 @@ except ImportError:
 
 from skimage import io, img_as_float
 from skimage.util.dtype import dtype_range
+from skimage.exposure import rescale_intensity
 import numpy as np
 from .. import utils
 from ..widgets import Slider
@@ -19,6 +20,18 @@ from ..utils import dialogs
 __all__ = ['ImageViewer', 'CollectionViewer']
 
 
+def mpl_image_to_rgba(mpl_image):
+    """Return RGB image from the given matplotlib image object.
+
+    Each image in a matplotlib figure has it's own colormap and normalization
+    function. Return RGBA (RGB + alpha channel) image with float dtype.
+    """
+    input_range = (mpl_image.norm.vmin, mpl_image.norm.vmax)
+    image = rescale_intensity(mpl_image.get_array(), in_range=input_range)
+    image = mpl_image.cmap(img_as_float(image)) # cmap complains on bool arrays
+    return img_as_float(image)
+
+
 class ImageViewer(QMainWindow):
     """Viewer for displaying images.
 
@@ -121,17 +134,18 @@ class ImageViewer(QMainWindow):
         if filename is None:
             return
         if len(self.ax.images) == 1:
-            io.imsave(self.image, filename)
+            io.imsave(filename, self.image)
         else:
-            im1 = self.ax.images[1]
-            overlay = im1.cmap(img_as_float(im1.get_array()))
-            overlay = img_as_float(overlay)
-            im0 = self.ax.images[0]
-            underlay = im0.cmap(img_as_float(im0.get_array()))
-            underlay = img_as_float(underlay)
+            underlay = mpl_image_to_rgba(self.ax.images[0])
+            overlay = mpl_image_to_rgba(self.ax.images[1])
             alpha = overlay[:, :, 3]
-            alpha = np.dstack((alpha, alpha, alpha))
-            alpha /= alpha.max()
+
+            # alpha can be set by channel of array or by a scalar value.
+            # Prefer the alpha channel, but fall back to scalar value.
+            if np.all(alpha == 1):
+                alpha = np.ones_like(alpha) * self.ax.images[1].get_alpha()
+
+            alpha = alpha[:, :, np.newaxis]
             composite = (overlay[:, :, :3] * alpha +
                          underlay[:, :, :3] * (1 - alpha))
             io.imsave(filename, composite)