Main

%% High Throughput analysis of NTA data 
% Using the Script it is possible to analyse a whole data set of any number
% of NTA experiments. NTA Particle tracking data
% has to be saved in one folder. The data name of the single measurements
% need to fit to the ones defined bellow. Also the data is tailored to use
% NTA data given by the NTA 3.2 software export options. 
clc, clear  
% Number of Measurements which need to be analyzed and output name?
prompt = {'How many measurements need to be analysed?',...
    'How should the data be called?',...
    'What is the mode size of a single particle[nm]?'};
dlgtitle = 'User input';
definput = {'25','any name','Please enter diameter in nanometer'};
opts.Interpreter = 'tex';
answer = inputdlg(prompt,dlgtitle,[1 75],definput,opts);
NoM = str2double(answer{1,1});
output = answer{2,1}; 
maximalval = str2double(answer{3,1});

% Where are the measurement files?
setInPath = uigetdir('C:\Users\Christoph\Documents\Promotion\LM-10\Messungen','Choose IMPORT FOLDER');
filesAllT = dir(fullfile(setInPath, '*AllTracks.csv'));
filesPaDa = dir(fullfile(setInPath, '*ParticleData.csv'));
filesExSum = dir(fullfile(setInPath, '*ExperimentSummary.csv'));
IFolder = [filesAllT(1).folder '\'];
% Where shall the evaluated data be saved?
setOutPath = uigetdir('C:\Users\Christoph\Documents\MATLAB\ParticleTracker\Exportdata','Choose EXPORT FOLDER');

% What should be analysed?
% list = {'Data Fusion','Import Alltracks and ParticleData','Tracklength Data',...
%     'Intensity Data','Size & Dt Distributions','Histograms','Interactions'};
% [indx,~] = listdlg('PromptString',{'Select what evaluations have to be done.',...
%     'Multiple selections possible.',''},...
%     'ListString',list);
% Eval = ismember(1:length(list),indx);
Eval = logical([0 1 0 0 1 1 1]);

% What type of data willbe analysed?
% choice = questdlg('Choose data type','Is this a interaction dataset?', ...
% 'It is a Monomer Sample(exclude unnecessary data)','A ggregation dataset','Aggregation dataset');
% % Handle response
% switch choice
% case 'It is a Monomer Sample(exclude unnecessary data)' 
%     fil = 1;    
% case 'Aggregation dataset'
%     fil = 0;
% end
fil = 0;

% Exclusion of unusable data 
if fil == 0 
    lowlim = maximalval - (maximalval* 0.101);
    highlim =  2.1 * maximalval; 
elseif fil == 1
    lowlim = maximalval - (maximalval* 0.101);
    highlim =  1.2 * maximalval;
end

% Script for analysis:
OverallPerc = zeros(NoM,5);
OverallEvents = zeros(NoM,3);
for NN =1:NoM
    OFolder = [setOutPath '\M' num2str(NN)];
    mkdir (OFolder)
    OFolder = [OFolder '\'];
    AllFile = filesAllT(NN).name;
    PartFile = filesPaDa(NN).name;
    if NN == 1 % For the first measurement some data has to be generated:
        ExSumFile = filesExSum.name;
        [MeasurementTimes,Conc,MeanConc,Temperature] = PlotExSumHT(output,OFolder,NoM,IFolder,ExSumFile);
    end
%     Temperature = [23,23.1,23.1,23.1];
    outputNN = [output '-' num2str(NN)];
    [Allspecies,OvPer,Events] =  Search4Interact_v2(Temperature(NN),Eval,AllFile,IFolder,PartFile,OFolder,outputNN,highlim,lowlim,maximalval);
    OverallPerc(NN,:) = OvPer;
    OverallEvents (NN,:) = Events;
    disp([datestr(now) '-' ' Evaluated measurement: ' num2str(NN) ' of ' num2str(NoM)]);
end
foldname = strcat(setOutPath,'\',output,'_Results');
Results = array2table(OverallPerc);
headers = {'Monomer [%]' 'Dimer [%]' 'Trimer [%]' 'Tetramer [%]' 'Unknown [%]'};
Results.Properties.VariableNames = headers;
writetable(Results,foldname);

foldname = strcat(setOutPath,'\',output,'_Events');
Events = array2table(OverallEvents);
headers = {'Aggregation [counts]' 'Separation [counts]' 'Number of particles [counts]'};
Events.Properties.VariableNames = headers;
writetable(Events,foldname);