clear all;
%To use this code, just enter your input file prefix here - 
filename = '081706 Blank Test Turned';
%and the path to where your data should be saved.  If you don't specify an
%output location, it will  use the current directory.
% outputpath = '~/Desktop/Chassis-System/Data/PlateReader/DedicatedTranslation/';


[TimeData, LabelData] = platereaderread2MG(filename);

%%
%============
%set smoothing parameters
%============
method = 'fb';
if method == 'fb' | method == 'ff'
    cutofffreq = 0.15;
    neighbors = [];
elseif method == 'co'
    cutofffreq = 0.15;
    neighbors = 9;
elseif method == 'ma'
    cutofffreq = [];
    neighbors = 9;
end
plotunsmooth = 0;
plotsmooth = 1; 

Absbackgroundsamples = [];
GFPbackgroundsamples = [];

experimentsamples = [1:32];
names = ['A 1:3   ';...
         'A 4:6   ';...
         'A 7:9   ';...
         'A 10:12 ';...
         'B 1:3   ';...
         'B 4:6   ';...
         'B 7:9   ';...
         'B 10:12 ';...    
         'C 1:3   ';...
         'C 4:6   ';...
         'C 7:9   ';...
         'C 10:12 ';...
         'D 1:3   ';...
         'D 4:6   ';...
         'D 7:9   ';...
         'D 10:12 ';...
         'E 1:3   ';...
         'E 4:6   ';...
         'E 7:9   ';...
         'E 10:12 ';...
         'F 1:3   ';...
         'F 4:6   ';...
         'F 7:9   ';...
         'F 10:12 ';...
         'G 1:3   ';...
         'G 4:6   ';...
         'G 7:9   ';...
         'G 10:12 ';...    
         'H 1:3   ';...
         'H 4:6   ';...
         'H 7:9   ';...
         'H 10:12 '];
wellnames = cellstr(names(experimentsamples,:));

replicates = 3;
samples = [experimentsamples,GFPbackgroundsamples,Absbackgroundsamples];
% Extract the data that we are interested in into three new variables.  By
% default, consider all timepoints and wells
% timepoints = [1:size(LabelData,1)-1];
wells = [1:size(LabelData,2)];
timepoints = [5];
% wells = [1:6];

% rawGFP = LabelData(timepoints,wells,2);
rawAbs = LabelData(timepoints,wells,1);
Time = TimeData(timepoints);

%If your data has a fixed number of replicates for each sample and control,
%and the replicates are in adjacent wells, use this code to reshape both 
%matrices so that the third dimension represents the different replicates
orderedAbs = reshape(rawAbs,[size(rawAbs,1),replicates,size(rawAbs,2)/replicates]);
% orderedGFP = reshape(rawGFP,[size(rawGFP,1),replicates,size(rawGFP,2)/replicates]);
%reorder the dimensions of the array so that the third dimension is the
%number of replicates.
orderedAbs = permute(orderedAbs,[1,3,2]);
% orderedGFP = permute(orderedGFP,[1,3,2]);
orderedAbs = orderedAbs(:,samples,:);
% orderedGFP = orderedGFP(:,samples,:);

%Background subtraction
%If you are subtracting one time course from another as a background
%subtraction, it would be better to wait until after the data has been
%filtered.  For now, we'll just subtract the mean of a media only well from
%the absorbance.
   
if ~isempty(Absbackgroundsamples)
    Absbackground = mean(orderedAbs(:,end,:),3);
    cellAbs = orderedAbs - repmat(Absbackground,[1,size(orderedAbs,2),size(orderedAbs,3)]);
   
else 
    cellAbs = orderedAbs;
    
end

cellOD = 3.113.*cellAbs-0.0158;

% cellOD = cellAbs;
%==============================
%Data Smoothing
%Put the data to be smoothed into a cell array so the function can handle
%arbitrary numbers of labels.
if ~isempty(method)
    timeseries{1} = cellOD;
%     timeseries{2} = orderedGFP;
    [smoothtimeseries] = platereadersmooth(timeseries,method,cutofffreq,neighbors);
    %now get the smoothed data back out into individual arrays.
    fOD = smoothtimeseries{1};
    OD = cellOD;
%     fGFP = smoothtimeseries{2};
%     GFP = orderedGFP;
else
    fOD = cellOD;
%     fGFP = orderedGFP;
end

smoothOD = mean(fOD,1);

smoothOD = squeeze(smoothOD);

smoothOD = smoothOD';

asmoothOD = mean(smoothOD,2);

%averagedplatelayout = [asmoothOD(1:4)';0,0,0,0;asmoothOD(5:8)';asmoothOD(9:12)';asmoothOD(13:16)';asmoothOD(17:20)';0,0,0,0;asmoothOD(21:24)'];

          
 
fullplatelayout = [smoothOD(1:12);smoothOD(13:24);smoothOD(25:36);smoothOD(37:48);smoothOD(49:60);smoothOD(61:72)
    smoothOD(73:84);smoothOD(85:96)];
               

%timeandreplicatesmeanOD = mean(asmoothOD)
%deviation = std(asmoothOD)

% newOD = mean(fOD,3)
% newOD2 = newOD(5,:)
% avOD = mean(newOD2)
% deviation = std(newOD2)

clims = [.01 .3]

figure(6)             
imagesc(fullplatelayout,clims)
 axis image
 colorbar
 title('081706 Media OD Turned TP 5');
% figure(5)
%  imagesc(averagedplatelayout([1 3 4 5 6 8],:))
%  axis image
% colorbar
%  
%  figure(6)
%  bar3(averagedplatelayout([1 3 4 5 6 8],:))
%  zlabel('OD')
%  xlabel('Row')
%  ylabel('Column')