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. 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 that EMData 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