Workflow.m

%% Info:
% Once a set of sessions has been kilosorted and tracked with DLC, define 
% the two inputs below and run this script in one of the bonsai experiment
% folders to process them all together:

%% Inputs:
LocalDataRoot = '\\ion-nas.uoregon.edu\wehrlab\Rig2\maddie\'; %your local path to where all the experiment folders are
Rig = 'Rig2old'; %string indicating the rig these experiments were run on

%% Load the paths of the experiment folders:
load('Bdirs.mat'); %This file contains the paths to all the experiment folders that were kilosorted together

%% Process the spikes:
for idx = 1:length(Bdirs) %For each bonsai folder

    EphysPath = replace(dirs{idx},DataRoot,LocalDataRoot); %path to Ephys folder
    [SortedUnitsFile] = ProcessSpikes(EphysPath,LocalDataRoot); %Process the spikes

end

%% Process the cameras:
for idx = 1:length(Bdirs) %For each bonsai folder

    cd(replace(Bdirs{idx},DataRoot,LocalDataRoot)) %Go to the bonsai folder

    [BehaviorFile] = ProcessCams(Rig); %And run ProcessCams.

    if isequal(Rig,'Rig2old')
        load(BehaviorFile); %Now load the behaviorfile
        [Reye] = ProcessPupil(Reye,0.8); %Calculate the pupil diameter
        save(BehaviorFile, 'Head', 'Reye', 'Sky'); %And save the info back into the behaviorfile
    end

end

%% Example plot of spiketimes and corresponding pupil traces:
%(overlaying the pupil traces like this is not really an informative plot,
%but should be a decent example at least...)
BonsaiDir = replace(Bdirs{2},DataRoot,LocalDataRoot);
EphysDir = replace(dirs{2},DataRoot,LocalDataRoot);
[fig] = PlotPupil(BonsaiDir,EphysDir);

% Pre-processing Workflow:
% 1) DLC tracking:
%   You can use v_files4DLC('Reye') in matlab to select many videos to input
%   into a python terminal for DLC tracking.
% 
% 2) Kilosort:
%   Run master_16TT in matlab in the first bonsai directory, and then choose 
%   all the trial folders a mouse did that day. Once kilosort has completed,
%   then load up the data in Phy to sort and save the spikes.