I have the following code:
r = numpy.zeros(shape = (width, height, 9))
It creates a width x height x 9 matrix filled with zero
As said, numpy.empty() is the way to go. However, for objects, fill() might not do exactly what you think it does:
In[36]: a = numpy.empty(5,dtype=object)
In[37]: a.fill([])
In[38]: a
Out[38]: array([[], [], [], [], []], dtype=object)
In[39]: a[0].append(4)
In[40]: a
Out[40]: array([[4], [4], [4], [4], [4]], dtype=object)
One way around can be e.g.:
In[41]: a = numpy.empty(5,dtype=object)
In[42]: a[:]= [ [] for x in range(5)]
In[43]: a[0].append(4)
In[44]: a
Out[44]: array([[4], [], [], [], []], dtype=object)