classdef (Abstract) CasesFinder < handle
  % The CasesFinder class is looking for data related to a ShoulderCase in a folder tree.
  % It has been designed to work with the datastructure found in lbovenus.epfl.ch/shoulder/.
  %
  % A concrete subclass of CasesFinder must implement the expression related to the
  % 'branch' of the datastructure it is looking at.
  % Then, the CasesFinder will list all the cases that can be found following a 
  % fullfile(dataRootPath,casesSpecificExpression) path.
  % The found cases are then filtered according to the dicom files found following their
  % path.


  properties (Access = protected)
    dataRootPath
    casesSpecificExpression
    casesDirectories
  end



  methods (Abstract)
    setCasesSpecificExpression(obj);
  end



  methods

    function obj = CasesFinder(dataRootPath)
      obj.dataRootPath = dataRootPath;
      obj.casesSpecificExpression = [];
      obj.casesDirectories = containers.Map;

      obj.setCasesSpecificExpression;
      obj.mapCasesDirectories;
      obj.removeCasesWithNoCTDirectory;
      obj.reachBestCTDirectory;
    end

  end



  methods (Access = protected)

    function mapCasesDirectories(obj)
      cases = dir(fullfile(obj.dataRootPath,obj.casesSpecificExpression));
      cases = obj.addSCaseIDToDirOutput(cases);
      obj.updateMapWithCases(cases);
    end

    function dirOutput = addSCaseIDToDirOutput(obj,dirOutput)
      for i = 1:length(dirOutput)
        dirOutput(i).SCaseID = regexp(dirOutput(i).name,'[NP]\d{1,3}','match','once');
      end
    end


    function updateMapWithCases(obj,cases)
      for i = 1:length(cases)
        if not(isempty(cases(i).SCaseID))
          obj.casesDirectories(cases(i).SCaseID) = fullfile(cases(i).folder,cases(i).name);
        end
      end
    end

    function removeCasesWithNoCTDirectory(obj)
      SCases = obj.casesDirectories.keys;
      for i = 1:length(SCases)
        SCase = SCases{i};
        if not(obj.containsCTDirectories(obj.casesDirectories(SCase)));
          obj.casesDirectories.remove(SCase);
        end
      end
    end

    function output = containsCTDirectories(obj,directory)
      if isempty(dir(fullfile(directory,'CT*')))
        output = false;
      else
        output = true;
      end
    end

    function reachBestCTDirectory(obj)
      SCases = obj.casesDirectories.keys;
      for i = 1:length(SCases)
        SCase = SCases{i};
        caseWithBestDirectory = obj.getBestCTDirectoryForSCase(SCase);
        caseWithBestDirectory = obj.addSCaseIDToDirOutput(caseWithBestDirectory);
        obj.updateMapWithCases(caseWithBestDirectory)
      end
    end

    function output = getBestCTDirectoryForSCase(obj,SCase)
      %  Each SCase directory should at least contain a
      %  directory with a name staring with 'CT' and ending with either
      %  '-1' : preop/shoulder/sharp/noPhantom
      %  '-2' : preop/shoulder/smooth/noPhantom
      %  '-3' : preop/shoulder/sharp/phantom
      %  '-4' : preop/shoulder/smooth/phantom
      %  and containing a 'dicom' subdirectory. The priority is '1', '2', '3', '4',
      %  unless there is a amira folder already present in one of these diretories.
      observedCTDirectories = dir(fullfile(obj.casesDirectories(SCase),'CT*'));
      for i = 1:length(observedCTDirectories)
        if obj.containsAmiraDirectory(observedCTDirectories(i))
          output = observedCTDirectories(i);
          return
        end
      end
      output = observedCTDirectories(1);
    end

    function output = containsAmiraDirectory(obj,directory)
      if isempty(dir(fullfile(directory.folder,directory.name,'amira')))
        output = false;
      else
        output = true;
      end
    end

  end



  methods

    function output = getPathTo(obj,SCase)
      if obj.containsCase(SCase)
        output = obj.casesDirectories(SCase);
      else
        output = [];
      end
    end

    function output = getAllCasesIDs(obj)
      output = obj.casesDirectories.keys;
    end

    function output = getNumberOfCases(obj)
      output = obj.casesDirectories.Count;
    end

    function output = containsCase(obj,SCase)
      output = obj.casesDirectories.isKey(SCase);
    end
  end



end