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

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

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 you can always tell if an EMData object is in real/imag or amplitude/phase format by calling 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