CFC_wrapper.py
Directory ~/code/ contains the script “CFC_wrapper.py”. This script takes care of setting up parameters for “calculate_CFC.py” (e.g., which frequencies, bandwidths to use), handles data, and defines the category and comparison arrays.

You will want to change at least three variables:

1) Category array is an array of indicator variables which indicate trials that are independent of each other. For example, to do one CFC calculation for each stimulus_ID, set category_array = StimID.

2) Comparison array is an array of indicator variables which indicate which trials will be compared within each category. For example, to do 2nd half vs 1st half, set comparison_array = [0,0,0,…,1,1,1].

3) You will want to change “output_path” to the desired directory you wish to save the CFC calculations.

“CFC_wrapper.py” will then run “calculate_CFC.py”, which will output three variables to output_path:

1) e(phase_elec)_e(amp_elec)_groups: <frequencies, bandwidths, categories, comparisons>

2) e(phase_elec)_e(amp_elec)_diff: <frequencies, bandwidths, categories> (if two comparisons, e(phase_elec)_e(amp_elecs)_groups[:,:,:,1] - e(phase_elec)_e(amp_elecs)_groups[:,:,:,0])

3) e(phase_elec)_e(amp_elecs)_surrogate_diff <frequencies, bandwidths,categories,runs>


CFC_wrapper.py can be run in the command line:

python /home/jcase/code/CFC_wrapper.py SUBJ BLOCK PHASE_ELEC AMP_ELEC &

For example, if you are running only one block:
python /home/jcase/code/CFC_wrapper.py EC77 B26 100 100 &

Or if you are using two blocks:
python /home/jcase/code/CFC_wrapper.py EC77 [B26,B42] 100 100 &

doCFC_ALL:
If you would like to run CFC_wrapper more systematically, the bash script “/home/jcase/doCFC_all” will iterate through all subjects, blocks, and electrodes (running 4 CFC_wrapper jobs in parallel, one for each electrode pair). If you would like to adjust the electrodes run, you will need to change the “elec_start” and “elec_end” arrays. If you would like to adjust the subjects and blocks run, change the “subj” and “block” arrays.

If you need to kill this process, try “killall bash” and then “killall python”.

Running PAC from server:
Access my account via:

ssh -p 7777 jcase@dura.cin.ucsf.edu