function [returnVar,msg] = ReRefFilFile(fname,nbChan,refChan,rerefChan)

% USAGE:

% ReRefFilFile(fbasename, nbChan, refChan, rerefChan)

% This function substracts one channel or the median of a series of

% channels (the 'reference' channel) from other channels.

%

% Note: this uses 1-based indexing, not zero-based, so you have to take

% the channel number in neuroscope and add one to it, e.g. channel 72

% in neuroscope is channel 73 here.

%

% INPUTS:

% fname: fil file name. Could be also a file basename not finishing

% with '.fil' and the program will be then executed for all the fil

% files begining with this file basename.

% nbChan: total number of channels in fil file

% refChan: reference channel (could be a vector, in this case the median will be the new reference)

% rerefChan: vector of channels to rereference

%

% Adrien Peyrache 2013

if ~strcmp(fname(end-2:end),'fil')

datFiles = dir([fname '*.fil']);

for ii=1:length(datFiles)

ReRefFilFile(datFiles(ii).name,nbChan,refChan,rerefChan)

end

else

fprintf('ReReferencing %s\n',fname)

try

infoFile = dir(fname);

chunk = 1e6;

nbChunks = floor(infoFile.bytes/(nbChan*chunk*2));

warning off

if nbChunks==0

chunk = infoFile.bytes/(nbChan*2);

end

for ix=0:nbChunks-1

m = memmapfile(fname,'Format','int16','Offset',ix*chunk*nbChan*2,'Repeat',chunk*nbChan,'writable',true);

d = m.Data;

d = reshape(d,[nbChan chunk]);

ref = d(refChan,:);

if length(refChan)>1

ref = median(double(ref));

end

ref = repmat(ref,[length(rerefChan) 1]);

d(rerefChan,:) = d(rerefChan,:)-int16(ref);

m.Data = d(:);

clear d m

end

%close(h)

newchunk = infoFile.bytes/(2*nbChan)-nbChunks*chunk;

if newchunk

m = memmapfile(fname,'Format','int16','Offset',nbChunks*chunk*nbChan*2,'Repeat',newchunk*nbChan,'writable',true);

d = m.Data;

d = reshape(d,[nbChan newchunk]);

ref = d(refChan,:);

if length(refChan)>1

ref = median(ref);

end

ref = repmat(ref,[length(rerefChan) 1]);

d(rerefChan,:) = d(rerefChan,:)-int16(ref);

m.Data = d(:);

clear d m

end

warning on

returnVar = 1;

msg = '';

catch

fprintf(['Error occurred in processing ' fname '. File not rereferenced.\n']);

keyboard

returnVar = 0;

msg = lasterr;

end

clear m

end