Changing image format from real/imaginary to amplitude/phase format in EMAN2 is a straightforward procedure. To illustrate the process start with a test image and perform an inplace Fourier transform on it as follows:

[someone@localhost]$ e2.py

Welcome to EMAN2
Prompt provided by IPython
Enter '?' for ipython help

In [3]:  e = EMData(32,32,32)

In [4]:  e.process_inplace("testimage.axes")

In [5]:  e.do_fft_inplace()

You now have an EMData object (e) in real/imaginary format. You can verify that the image is in this format by calling the function is_ri, for example try:

In [6]:  e.is_ri()
Out[6]:  True

To convert the image to amplitude/phase format simply do the following:

In [7]:  e.ri2ap()

In [8]:  e.is_ri()
Out[8]:  False

In [9]:  e.get(2,0,0)
Out[9]:  62.0

In [10]:  e.get(3,0,0)
Out[10]:  3.1415927410125732

Note that it's relatively straightforward to access values from the EMData object (e) using the get function call, and that we have verified the EMData object is in amplitude/phase format using the function is_ri, as demonstrated above. Finally, you can convert back to to real/imaginary format by doing:

In [11]:  e.ap2ri()

In [12]:  e.is_ri()
Out[12]:  True