Question

I have two arrays and I take their logs. When I do that and try to plot their scatter plot, I get this error:

  File "/Library/Python/2.6/site-packages/matplotlib-1.0.svn_r7892-py2.6-macosx-10.6-universal.egg/matplotlib/pyplot.py", line 2192, in scatter
    ret = ax.scatter(x, y, s, c, marker, cmap, norm, vmin, vmax, alpha, linewidths, faceted, verts, **kwargs)
  File "/Library/Python/2.6/site-packages/matplotlib-1.0.svn_r7892-py2.6-macosx-10.6-universal.egg/matplotlib/axes.py", line 5384, in scatter
    self.add_collection(collection)
  File "/Library/Python/2.6/site-packages/matplotlib-1.0.svn_r7892-py2.6-macosx-10.6-universal.egg/matplotlib/axes.py", line 1391, in add_collection
    self.update_datalim(collection.get_datalim(self.transData))
  File "/Library/Python/2.6/site-packages/matplotlib-1.0.svn_r7892-py2.6-macosx-10.6-universal.egg/matplotlib/collections.py", line 153, in get_datalim
    offsets = transOffset.transform_non_affine(offsets)
  File "/Library/Python/2.6/site-packages/matplotlib-1.0.svn_r7892-py2.6-macosx-10.6-universal.egg/matplotlib/transforms.py", line 1924, in transform_non_affine
    self._a.transform(points))
 File "/Library/Python/2.6/site-packages/matplotlib-1.0.svn_r7892-py2.6-macosx-10.6-universal.egg/matplotlib/transforms.py", line 1420, in transform
    return affine_transform(points, mtx)
ValueError: Invalid vertices array.

the code is simply:

myarray_x = log(my_array[:, 0])
myarray_y = log(my_array[:, 1])
plt.scatter(myarray_x, myarray_y)

any idea what could be causing this? thanks.

Answer 1

New Answer:

From looking at the source, this error is thrown if the points array passed into affine_transform is of the wrong dimensions or if it is empty. Here are the relevant lines:

if (!vertices ||
        (PyArray_NDIM(vertices) == 2 && PyArray_DIM(vertices, 1) != 2) ||
        (PyArray_NDIM(vertices) == 1 && PyArray_DIM(vertices, 0) != 2))
         throw Py::ValueError("Invalid vertices array.");

Take a look at the dimensions of your myarray_x and myarray_y arrays before going ahead maybe.

Old Answer:

My best guess it that you are taking the log of values <= 0. This will either give you nan’s or -infs(in the case of being equal to 0) in your arrays which of course it can’t plot.

(wiso is right though – these points are just ignored)