Step1ExtractMetrics.m

function MetricsMatrix = Step1ExtractMetrics(path, StudyType)
% NAStep1ExtractMetricsME - this main function extract all metrics from the path root directory and recursively explore any subsequent folders that contain all DICOM files.
%
% Syntax:  [output1,output2] = function_name(input1,input2,input3)
%
% Inputs:
%    	path 			- the root directory where all DICOM files are located.
%
% Outputs:
%    	MetricsMatrix			- aggregated matrix containing all metrics extracted in a 2D array for ML
%    	Output			- structure contain all indiviudal humanly readable metrics for data storage purposes.
%
% Example:
%    	Line 1 of example
%    	Line 2 of example
%    	Line 3 of example
%
% Other m-files required: 		RecursivelyLoadDICOM.m, LoadConfigVariables.m
% MAT-files required: 			   none
%
% See also: OTHER_FUNCTION_NAME1,  OTHER_FUNCTION_NAME2
% Author: Yang Ding
% All works sponsored by Dr. Gregory Lodygensky and the Canadian Neonatal Brain Platform
% Saint. Justine Hospital, Montreal, Quebec,
% email address: it@cnbp.ca
% Website: http://cnbp.ca
% 2017; Last revision: 2017-08-14 22:45:37 Eastern Time

%------------- BEGIN CODE --------------

  % Read in the setting files
  Settings = LoadConfigVariables();

  % Get current path of current script.
  scriptName = mfilename('fullpath');

  % Ensure dependencies are properly referred to by recursively add the folder and subdirectories.
  addpath(genpath(Settings.Folder.Root));
  addpath(genpath(Settings.Folder.Result));
  addpath(genpath(Settings.Folder.NSSMetrics));
  addpath(genpath(Settings.Folder.FocusMetrics));
  addpath(genpath(Settings.Folder.General));
  addpath(genpath(Settings.Folder.SNRMetrics));
  addpath(genpath(Settings.Folder.TextureMetrics));
  addpath(genpath(Settings.Folder.DICOM));
  addpath(genpath(Settings.Folder.General));

  %Update Windows System environment variables to ensure that the SVM-predict etc can be utilized.
  setenv('SVMLib',Settings.Folder.SVMLib);



  tic;

  % Use GUI to get path to the folder that contained all the DICOM files.
  % path = uigetdir;

  % Get output.
  Output = ParRecursivelyLoadDICOM(path);

  % Put everything in a gigantic matrix for further analyses.
  MetricsMatrix = cat (2, ...
    Output.FocusMetrics, ...
    Output.SNRMetrics, ...
    Output.TextureMetrics, ...
    Output.NSSMetrics, ...
    Output.DICOMMetrics ...
  );

  %Save EXTRA copy of the data in the final folder AS WELL as the regular output folder.
  cd(Settings.Folder.Result);
  if (exist(StudyType))
    if (StudyType == 'ASP')
      Output.Dir = Settings.Folder.ASPMetrics;
      % Enter the output folder
      mkdir (Output.Dir)
      cd (Output.Dir)
      % Save the various output
      save('MetricsDataStructure.mat','Output')
      save('MetricsMatrix.mat','MetricsMatrix')
      csvwrite('UnlabledMatrix.csv','MetricsMatrix');
      OutputTable = array2table(MetricsMatrix,'VariableNames',Output.LabelAggregate);
      writetable(OutputTable,'LabeledMatrix.csv');

    elseif (StudyType == 'BDP')
      Output.Dir = Settings.Folder.BDPMetrics;
      % Enter the output folder
      mkdir (Output.Dir)
      cd (Output.Dir)
      % Save the various output
      save('MetricsDataStructure.mat','Output')
      save('MetricsMatrix.mat','MetricsMatrix')
      csvwrite('UnlabledMatrix.csv','MetricsMatrix');
      OutputTable = array2table(MetricsMatrix,'VariableNames',Output.LabelAggregate);
      writetable(OutputTable,'LabeledMatrix.csv');
    end
  end

  %Regular saving process flow.

  %Enter Results directory, save the metrics computed.
  cd(Settings.Folder.Result);
  % Record and enter the specific directory
  Output.Dir = mkdirNowPrefix('MetricsComputation');

  % Enter the output folder
  cd (Output.Dir)
  % Save the various output
  save('MetricsDataStructure.mat','Output');
  save('MetricsMatrix.mat','MetricsMatrix');


  csvwrite('UnlabledMatrix.csv',MetricsMatrix);

  OutputTable = array2table(MetricsMatrix,'VariableNames',Output.LabelAggregate);
  writetable(OutputTable,'LabeledMatrix.csv');

  % Return to root.
  cd(Settings.Folder.Root);
  disp('Step 1 Completed:')
  toc
%------------- END OF CODE --------------
end