Complex coherency
=================

This function may be called for data in the time domain or the frequency domain.

.. currentmodule:: sfc.td
.. autofunction:: run_cc

.. currentmodule:: sfc.fd
.. autofunction:: run_cc

The following code example shows how to calcualte complex coherency, a precurses to several connectivity metrics. 

.. code:: python
    
   import numpy as np

   import finn.sfc.td as td
   import finn.sfc.fd as fd

   import finn.sfc._misc as misc
   import demo_data.demo_data_paths as paths

   def main():
       data = np.load(paths.fct_sfc_data)
       frequency_sampling = 5500
       frequency_peak = 30
       
       noise_weight = 0.2
       
       phase_shift = 153
       
       nperseg = frequency_sampling
       nfft = frequency_sampling
       
       #Generate data
       offset = int(np.ceil(frequency_sampling/frequency_peak))
       loc_data = data[offset:]
       signal_1 = np.zeros((loc_data).shape)
       signal_1 += loc_data
       signal_1 += np.random.random(len(loc_data)) * noise_weight
       
       loc_offset = offset - int(np.ceil(frequency_sampling/frequency_peak * phase_shift/360))
       loc_data = data[(loc_offset):]
       signal_2 = np.zeros(loc_data.shape)
       signal_2 += loc_data
       signal_2 += np.random.random(len(loc_data)) * noise_weight
       
       (bins, cc_td) = calc_from_time_domain(signal_1, signal_2, frequency_sampling, nperseg, nfft)
       cc_fd = calc_from_frequency_domain(signal_1, signal_2, frequency_sampling, nperseg, nfft)
       
       if ((cc_fd == cc_td).all() == False):
           print("Error")
       
   def calc_from_time_domain(signal_1, signal_2, frequency_sampling, nperseg, nfft, window = "hann", pad_type = "zero"):
       return td.run_cc(signal_1, signal_2, nperseg, pad_type, frequency_sampling, nfft, window)

   def calc_from_frequency_domain(signal_1, signal_2, frequency_sampling, nperseg, nfft, window = "hann", pad_type = "zero"):
       seg_data_X = misc._segment_data(signal_1, nperseg, pad_type)
       seg_data_Y = misc._segment_data(signal_2, nperseg, pad_type)

       (bins, fd_signal_1) = misc._calc_FFT(seg_data_X, frequency_sampling, nfft)
       (_,    fd_signal_2) = misc._calc_FFT(seg_data_Y, frequency_sampling, nfft)
       
       return fd.run_cc(fd_signal_1, fd_signal_2)
       
       
   main()