====== Loading Amplipex data into fieldtrip ======

Note: as of Jan/2014, make sure you use the APX_devel branch on GitHub to get the latest version. At some point this will be merged back into master.

Eric's Note (Jan 12/2014):  Use session R041-2013-08-06 as a test since it contains an events file within the directory. If you are using another session be sure to run the AMPX_getEvetns script in the util/amplipex/loading folder.  

To load data:

<code matlab>
channels_to_load = [10:13]; % specify channels in the APX data file to load
data = AMPX_loadData('R041-2013-08-06.dat',channels_to_load,20); % note decimation factor of 20
</code>

To convert into a fieldtrip data structure:

<code matlab>
data_ft = AMPX_makeft(data);
</code>

Make trials (note, this will require an event file to have been created previously, Eric to update explanation of this):

<code matlab>
%% trl
cfg = [];
cfg.trialfun = 'ft_trialfun_AMPXsquareTrack';
cfg.trialdef.hdr = data.hdr;
cfg.trialdef.pre = 2;    % time before the event to be included (It would take roughly 3 seconds to get from one feeder to the next)
cfg.trialdef.post = 3;   % time after the event to be included (The rats would typically stay for at least 2 seconds while eating)
 
cfg.trialdef.eventtype = 'nose_in_nofires'; % could be 'fires', 'no_fires', 'nose_in_fires', 'nose_in_nofires'
 
[trl, event] = ft_trialfun_AMPXsquareTrack(cfg);
cfg.trl = trl;
 
data_trl = ft_redefinetrial(cfg,data_ft);
</code>

Now you can do the usual ft analysis stuff:

<code matlab>
%%
cfg              = []; % start with empty cfg
cfg.output       = 'pow';
cfg.channel      = '10';
cfg.method       = 'mtmconvol';
cfg.taper        = 'hanning';
cfg.foi          = 1:1:100; % frequencies of interest
cfg.t_ftimwin    = ones(size(cfg.foi)).*0.5;  % window size: fixed at 0.5s
cfg.toi          = -1.5:0.05:2.5; % times of interest

</code>