AVGSUB_movs.m

function  bgsub_mov=AVGSUB_movs(filename,mov,goodframe,do_avg,subwidth,offset)
%% AVGSUB_tiffs
% updated BPI 3/10/18 This function does average (or median) subtraction
% of a movie.
%
% filename is the name of the movie to be subtracted, which will determine
% the name of the avgsub movie as 'filename_avgsub.mat'
%
% mov is the movie data as a 3D array where the third dimension is the
% frame number.
%
% do_avg is a Boolean. Set to true to use an average, or set to false to use a
% median. Note median is slightly slower than mean.
%
% subwidth is the length of temporal window that will be averaged.
%
% This function saves the AVGSUB movie as a .mat file at the original file
% location with the original file name, but with _avgsub appended to the
% name.

%%%% Dependencies %%%%

%     Copyright (C) 2018  Benjamin P Isaacoff
%
%     This program is free software: you can redistribute it and/or modify
%     it under the terms of the GNU General Public License as published by
%     the Free Software Foundation, either version 3 of the License, or
%     (at your option) any later version.
%
%     This program is distributed in the hope that it will be useful,
%     but WITHOUT ANY WARRANTY; without even the implied warranty of
%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
%     GNU General Public License for more details.
%
%     You should have received a copy of the GNU General Public License
%     along with this program.  If not, see <http://www.gnu.org/licenses/>.
%

%default offset
tic;%for measuring the time to run the entire program

%% Setup
[pathstr,fname] = fileparts(filename);
global verbose
if verbose
disp([char(datetime),'   Running AVGSUB for ',fname])
end
%change the bad frames as determined by the goodframe list to NaNs
mov(:,:,~goodframe)=NaN;

%% Do the avgsub
if do_avg
    bgsub_mov=mov-movmean(mov,subwidth,3,'omitnan')+offset;
else
    bgsub_mov=mov-movmedian(mov,subwidth,3,'omitnan')+offset;
end

%% Check and save

if any(bgsub_mov(:)<0)
    warning(['There are negative pixels in ',fname,'_avgsub, consider increasing the offset'])
end

tictoc=toc;%the time to do the calculations

%%%%Save the movie%%%%
% convert to int16 and rename for saving
mov=int16(bgsub_mov);
% save the movie and the parameters
save([pathstr,filesep,fname,'_avgsub.mat'],'mov','goodframe','do_avg','subwidth','offset','tictoc','-v7.3')

%this is the old tif saving code, commented out for now
% options.overwrite=true;
% %save using saveastiff
% saveastiff(uint16(bgsub_mov), [pathstr,filesep,fname,'_avgsub.tif'],options);

% %save a .txt file with the parameters
% fileID = fopen([pathstr,filesep,fname,'_avgsub_info.txt'],'w');
% if do_avg
%     fprintf(fileID,'Average of background was subtracted\n');
% else
%     fprintf(fileID,'Median of background was subtracted\n');
% end
% fprintf(fileID,['running average:\t',num2str(runningavg),'\n']);
% fprintf(fileID,['subwidth:\t',num2str(subwidth),'\n']);
% fprintf(fileID,['offset:\t',num2str(offset),'\n']);
% fprintf(fileID,['time to run:\t',num2str(tictoc)]);
% fclose(fileID);

end