clear all;
close all;
%======================
% Barry Canton, March 2006
%
% This code reads a results text file that is output by the Victor 3
% plate reader.  It expects that there are only two labels being
% measured, the first of which is absorbance, the second is 
% fluorescence. the start of the text file should look like this - 
%Plate	Repeat	Well	Type	Time        OD600 (A)	Time            GFP-separated (Counts)
%1      1       F01     M	00:00:26.27     0.076       00:00:51.68     977
%1      1       F02     M	00:00:26.59     0.069       00:00:52.04     914
%
%There is extra data at the bottom of the results text file but once the format is
%no longer as that shown above, this code will stop reading.

%To use this code, just enter your input file prefix here - 
filename = 'E70102firstscreen';
%and the path to where your data should be saved - 
outputpath = '~/Desktop/Chassis-System/Data/PlateReader/DedicatedTranslation/';
%======================


fullname = strcat(filename,'.txt');
fid=fopen(fullname);
% C is a cell array that contains each of the data columns from the result
% file, it skips 1 header row.
C = textscan(fid, '%n %n %s %s %s %n %s %n','headerLines',1);
fclose(fid);

%Extract the useful information from the data - 
Repeats = C{2};
Time = C{5};
Absorbance = C{6}; 
Fluorescence = C{8};

%======================
%Wells
%======================
%Work out what the wells are called and store them in a string array
Wells = C{3};
WellNames = unique(Wells);
WellNames = cell2mat(WellNames);

%======================
%Time
%======================
%Process the time mins, starting from 0
TimeVec = datevec(Time);
TimeSerial = datenum(TimeVec); %change time format
TimeData = TimeSerial*24*60;%convert to mins
TimeData = TimeData-TimeData(1); %set the start time to 0mins
%find one time point for each repeat. This gets the last time point 
%recorded for each repeat, use that as the single time point for each label 
%and for each well.
[Steps, index, junk] = unique(Repeats);
TimeData = TimeData(index); 


%======================
%Absorbance & Fluorescence
%======================
%Rearrange both of the data arrays so that each well has its own column.
%This will fail if for some reason all wells don't have the same number of
%repeats, for example, if you terminate the plate reader while its
%measuring wells.  If so you should use the loop that is commented out
%below.
Repeats = max(Repeats); %find the number of repeats
AbsorbanceData = reshape(Absorbance,[length(Absorbance)/Repeats,Repeats])';
FluorescenceData = reshape(Fluorescence,[length(Fluorescence)/Repeats,Repeats])';

%for i = 1:length(WellNames)
%    indices = strmatch(WellNames{i},Wells);
%    AbsorbanceData(:,i) = Absorbance(indices);
%    FluorescenceData(:,i) = Fluorescence(indices);
%end

%======================
%Save data
%======================
%Save the processed data to a .mat file
location = strcat(outputpath,filename,'processed');
save(location,'TimeData','AbsorbanceData','FluorescenceData','Wells');