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 a Fourier transform on it:
[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()