Widefield_compressRawVideo.m

function Widefield_compressRawVideo(sPath)
% Code to compress raw video data off the server. 
% Finds Widefield data folders in all recordings and compresses mj2 files into
% mp4 which occupy much less space.

if ~exist('sPath','var') || isempty(sPath)
    sPath = '\\grid-hs\churchland_nlsas_data\data\BpodImager\Animals\';
end

if sPath(end) ~= filesep
    sPath(end + 1) = filesep;
end

fileName = 'Frames'; %standard name for imaging files

%%
recs = dir(sPath);
for iRecs = 1 : length(recs)
    
    if strcmp(recs(iRecs).name, '.') || strcmp(recs(iRecs).name, '..')
        rawVids = [];
    else
        rawVids = dir([sPath recs(iRecs).name filesep fileName '*mj2']); %get raw videos of current recording
        fprintf('Rec: %s\nCompressing %d video files\n', recs(iRecs).name, length(rawVids));
    end
    
    % search for behavior video folder
    for iVids = 1 : length(rawVids)
            
        cFile = [sPath recs(iRecs).name filesep rawVids(iVids).name];
        rawData = squeeze(importdata(cFile));
        if max(rawData(:)) > 255 %data is not int8
            if max(rawData(:)) > 65535 %data is not int16
                error('Unknown data type');
            else
                rawData = mat2gray(rawData,[0 65535]);
            end
        else
            rawData = mat2gray(rawData,[0 255]);
        end
        
        rawData = padarray(rawData, 8 - [rem(size(rawData,1),8), rem(size(rawData,2),8)], 0, 'post'); %pad array to be dividable by 8
        rawData = reshape(rawData, size(rawData,1),size(rawData,2),1,[]);
        
        v = VideoWriter(strrep(cFile, '.mj2', ''), 'MPEG-4'); %save as compressed video file
        v.Quality = 100;
        open(v); 
        if size(rawData,4) > 500
            for iFrames = 1 : size(rawData,4)
                writeVideo(v,rawData(:,:,:,iFrames));
            end
        else
            writeVideo(v,rawData);
        end
        close(v);
        delete(cFile);
        
    end
end