Question

I’m writing a program to read in data from a list, Fourier transform and shift it before plotting. So far, the code takes the spectroscopy data from the DICOM file and puts it into a list, with each element an array containing the values of each individual FID/spectra.

from pylab import *
import dicom

plan=dicom.read_file("")

all_points = array(plan.SpectroscopyData)
cmplx_data = all_points[0::2] + 1j*all_points[1::2]
frames = int(plan.NumberOfFrames)
fid_pts = len(cmplx_data)/frames

fid_list = []
for fidN in arange(frames):
    offset = fidN * fid_pts 
    current_fid = cmplx_data[offset:offset+fid_pts]
    fid_list.append(current_fid)

This works fine to group the data, but I encounter problems when trying to use the arrays generated. Firstly, when trying to display only the complex part of the data, for example:

plot(complex(fid_list[0]))

Returns

Traceback (most recent call last)
/home/dominicc/Desktop/<ipython-input-37-4146b7fbfd7c> in <module>()
----> 1 plot(complex(fid_list[0]))

TypeError: only length-1 arrays can be converted to Python scalars

Secondly, and most importantly though, I encounter infinite recursion when trying to plot the zero-frequency shift of the FFTed data:

plot(fftshift(fft(fid_list[0])))

Getting the following error

/home/dominicc/Desktop/New_Script.py in fftshift(fid_in)
     23 
     24 def fftshift(fid_in):
---> 25         fft_fid_in = fft(fid_in)
     26         plot(fftshift(fft_fid_in))
     27         show()

/usr/lib/python2.7/dist-packages/numpy/fft/fftpack.pyc in fft(a, n, axis)
    162     """
    163 
--> 164     return _raw_fft(a, n, axis, fftpack.cffti, fftpack.cfftf, _fft_cache)
    165 
    166 

/usr/lib/python2.7/dist-packages/numpy/fft/fftpack.pyc in _raw_fft(a, n, axis, init_function, work_function, fft_cache)
     43 def _raw_fft(a, n=None, axis=-1, init_function=fftpack.cffti,
     44              work_function=fftpack.cfftf, fft_cache = _fft_cache ):
---> 45     a = asarray(a)
     46 
     47     if n is None:

RuntimeError: maximum recursion depth exceeded

Can anyone suggest ways to improve my code so as to avoid these problems? Thanks.

Answer 1

Solved by adding another for loop that Fourier transformed the data before the fftshit:

fft_list = []
for i in range(0, frames):
    current_fid = fft(fid_list[i])
    fft_list.append(current_fid)