function signal_average

%    November 4, 2015
%  This code is to get averaged signal 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 "qdot_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 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,'*vs_traj*.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 iii=1:size(New_Time_Position,1)
    New_Time_Position(iii, 3)=New_Time_Position(iii, 2)*0.27;
end

for k=5:size(New_Time_Position,1)-5
    New_Time_Position(k, 4)=(New_Time_Position(k-4, 3)+New_Time_Position(k-3, 3)+New_Time_Position(k-2, 3)+....
                  New_Time_Position(k-1, 3)+New_Time_Position(k, 3)+New_Time_Position(k+1, 3)+....
                  New_Time_Position(k+2, 3)+New_Time_Position(k+3, 3)+New_Time_Position(k+4, 3)+...
                  New_Time_Position(k+5, 3))/10;
end


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

    close all
    
end