function int_average

%    November 4, 2015
%  This code is to get averaged background trajectory. When you get data
%points, you might want to get averaged data point trajectory. This code
%averages 10 data points. It must be run after "int_track.m" was excuted.

clear all
close all

% User Inputs
% select directory with files to convert to better form
filepath=uigetdir('','select directory that has time versus intensity trajectory file');
% change matlab "Current Folder" to the selected directory
cd(filepath)

% select time versus trajectory text file to convert
%roi_file=uigetfile('*time_versus_trajectory*.txt','select time versus trajectory file of interest.')

% load only txt files.
D=dir([filepath,filesep,'*BG_t_vs_I*.txt']);

% directory to save converted text file
outdir=uigetdir('','select directory to save converted text file');

for jjj=1:length(D)

% read initial text file data
Original_File=load(D(jjj).name);

j=0;
New_Time_Position=[];
for i=1:size(Original_File,1)
    if Original_File(i, 2)<=0
        j=j+1;
    else
    New_Time_Position(i-j, 1)=Original_File(i, 1);
    New_Time_Position(i-j, 2)=Original_File(i, 2);
    end
end

for k=3:size(New_Time_Position,1)-3
    New_Time_Position(k, 3)=(New_Time_Position(k-2, 2)+...
                  New_Time_Position(k-1, 2)+New_Time_Position(k, 2)+New_Time_Position(k+1, 2)+....
                  New_Time_Position(k+2, 2)+New_Time_Position(k+3, 2))/6;
end


    % save file
    save([outdir '\' D(jjj).name 'intAVG.txt'],'New_Time_Position','-ascii')

    close all
    
end