% setup.m   Accepts data and organizes it.  

% Most "mother" programs start with the following:
clear  % removes all previously defined variables
before = 0; after = 1;  % assing numerical values to these strings
type = before;  % enter the data you want to analyze
if type < after
    disp('before data'); % prints this to the main window
    beforedata; % reads beforedata.m 
    flowmult = -1; % "before" flow readings are in the wrong direction (use later)
else
    disp('after data'); % prints this to the main window
    afterdata; % reads afterdata.m 
    flowmult = 1;  %"after" flow readings are fine
    indexBic = 18;
    indexBS = 26;
end
 
[nimages nvalues] = size(DATA);
    %size(matrix) returns [number of rows, number of columns] 
    %nimages now is the number of time frames = 397
    %nvalues is the number of data points at each frame = 52
    %DATA is a 397 x 52 Matrix

n = 120; % this assigns the number of time frames to investigate

% Break up the data into Time,Ap,Vp,Af,

% For some reason, the flow meter was calibrated for the opposite direction in the 
%  before data.  So we will multiply flow by negative one if data is before and by one 
%  if the data is after. 

% Furthermore, Af lags actual flow across the valve so we step ahead 3 time frames. 
%  I estimated this 3 from the animpfplots results.  It may not be the best choice.
for i=1:n
    Time(i) = DATA(i,1);
    Ap(i) = DATA(i,50);
    Vp(i) = DATA(i,51);
    Af(i) = flowmult * DATA(i+3,52);
end


% Break up the (X,Y,Z) data into x,y,z matrices. 
% i will count the rows (time frame index) 
% j will be the crystal number (data element index)
% subtracting the apex crystal locations guarantees that all 
%   plots will have an apex at (0,0,0). 
for i=1:n
    ooo = [DATA(i,47) DATA(i,48) DATA(i,49)]; %the apex will always be (0,0,0) 
    for j=1:16
        x(i,j) = DATA(i,2+3*(j-1))-ooo(1);
        y(i,j) = DATA(i,3+3*(j-1))-ooo(2);
        z(i,j) = DATA(i,4+3*(j-1))-ooo(3);
    end
end


% Now call the plotting file of your choice by uncommenting one of the following
% crystalplot %plots the 11 crystals 
% pressflowplots  %plots pressures and flows for the number of time frames indicated by n
% animpfplots  % this will help find index numbers of important points in the cycle
deltaVplot