Small fix for non-orthogonal cells. Also shifted points to (0,0,0)

Author: jensj

ase/visualize/mlab.py

@@ -24,8 +24,6 @@ def plot(atoms, data, contours):
 
     # Delay slow imports:
     from mayavi import mlab
-    from tvtk.api import tvtk
-    import mayavi.tools.pipeline
 
     mlab.figure(1, bgcolor=(1, 1, 1))  # make a white figure
 
@@ -38,7 +36,6 @@ def plot(atoms, data, contours):
 
     # Draw the unit cell:
     A = atoms.cell
-    print('A=%s' % str(A))
     for i1, a in enumerate(A):
         i2 = (i1 + 1) % 3
         i3 = (i1 + 2) % 3
@@ -51,17 +48,18 @@ def plot(atoms, data, contours):
                             [p1[2], p2[2]],
                             tube_radius=0.1)
 
-    cp = mlab.contour3d(data, contours=contours)
-    # Do some tvtk magic in order to allow for non-orthogonal unit cells
+    cp = mlab.contour3d(data, contours=contours, transparent=True,
+                        opacity=0.5, colormap='hot')
+    # Do some tvtk magic in order to allow for non-orthogonal unit cells:
     polydata = cp.actor.actors[0].mapper.input
-    pts = np.array(polydata.points)
-    # Transform the points to the unit cell
-    polydata.points = np.dot(pts, A / data.shape)
+    pts = np.array(polydata.points) - 1
+    # Transform the points to the unit cell:
+    polydata.points = np.dot(pts, A / np.array(data.shape)[:, np.newaxis])
 
     # Apparently we need this to redraw the figure, maybe it can be done in
     # another way?
     mlab.view(azimuth=155, elevation=70, distance='auto')
-    # Show the 3d plot
+    # Show the 3d plot:
     mlab.show()