% Launch the MATLAB EASY console
%
% Updated 240724 Bryan C Roessler to improve file operations and portability
% 
function varargout = EASYconsole(varargin)
  global easyDir
  global easySuffix
  global scansDir
  global easyResultsDir
  global easyResultsDirName
  global fotosResultsDir
  global figsResultsDir
  global pointMapsResultsDir
  global pointMapsFile
  global printResultsDir
  global matDir
  global matFile
  global drugMediaFile
  global masterPlateFile
  global mpdmFile
  global userName
  global srchRange
  global searchRangeFile

  % Initialize some variables from matlab
  easyPath=which(mfilename);
  [easyDir,easyFileName]=fileparts(easyPath);
  easyDir=fullfile(easyDir);
  [parentDir, ~]=fileparts(easyDir);
  userName=system('whoami');
  todayStr=datetime('now', 'Format', 'yyyyMMdd'); % This should match the parent workflow script

  disp(sprintf('This script name: %s\n', easyFileName))

  % Set scansDir intelligently (project scans directory)
  % Allow users to specify a PROJECT=/mnt/data/ExpJobs/Job directory to analyze with EASY
  % This better enables running the new EASY in standalone mode
  if exist('PROJECT', 'var') && ~isempty(getenv('PROJECT'))
    scansDir=getenv('PROJECT') 
    disp(sprintf('Using project path: %s from environment variable PROJECT\n', scansDir));
    disp('This usually indicates that we are in standalone mode');
  elseif exist('SCANS_DIR', 'var') && ~isempty(getenv('SCANS_DIR'))
    scansDir=getenv('SCANS_DIR');
    disp(sprintf('Using scans directory: %s from environment variable SCANS_DIR\n', scansDir));
    disp('This usually indicates that we are in module mode');
  else
    dirToScan = fullfile(parentDir,'ExpJobs'); % hardcoded relative to easy script dir TODO: if we change pj layout this will change
    if exist(dirToScan, 'dir')
      dirs=dir(fullfile(dirToScan, 'dir')); % filter for dirs only
      [~, sortedIndices]=sort(datenum({dirs.date}), 'descend'); % sort by newest first
      sortedDirs=dirs{sortedIndices};
      scansDir=sortedDirs{1};
      disp('Beginning in newest project scans directory');
      disp(sprintf('Using scans directory: %s from hardcoded relative path\n', scansDir));
      disp('This usually indicates that we are in stand-alone mode without PROJECT or SCANS_DIR environment variables');
    else
      scansDir=fullfile('/mnt/data/ExpJobs/demo')
      if exist(scansDir, 'dir')
        disp(sprintf('Using scans directory: %s from hardcoded absolute path to demo\n', scansDir));
      else
        disp(sprintf('Error: scansDir %s does not exist\n', scansDir));
      end
    end
  end

  % If we don't have the EASY_SUFFIX from the module, generate it from scansDir
  if exist('EASY_SUFFIX', 'var') && ~isempty(getenv('EASY_SUFFIX'))
    easySuffix=get_env('EASY_SUFFIX');
  else
    [dirName, ~]=fileparts(scansDir);
    [scansDate, scansUserName, easySuffix]=strsplit(dirName, '_');
    % The following is handled by the workflow script that calls this module
    % Reimplementing here for stand-alone mode
    % While the easySuffix directory exists, increment by one and try again
    if exist(easySuffix, 'dir')
      oldSuffix=easySuffix;
      while exist(easySuffix, 'dir')
        count=1;
        easySuffix=strcat(oldSuffix,'.',num2str(count));
      end
    end
    % Might as well check this too
    if userName ~= scansUserName
      disp('WARNING: userName does not match scansUserName');
      disp("This usually means that you are attempting to run an EASY analysis on another user's project data scans");
    end
    % For happiness
    if todayStr == scansDate
      disp("Early bird gets the worm");
    end
  end

  % Helpful variables for running in workflow mode that I'll probably have to reimplement in matlab anyways for standalone mode
  if exist('EASY_DIR','var') && ~isempty(getenv('EASY_DIR'))
    EASY_DIR=fullfile(get_env('EASY_DIR'));
    if easyDir ~= EASY_DIR % sanity check
      disp("WARNING: EASY_DIR does not match this script's hardcoded EASY location");
      disp("This is probably OK but if strange beahvior arises, we'll need to fix it in code");
      easyDir=EASY_DIR;
    end
    disp(sprintf('Using EASY script directory: %s from environment variable EASY_DIR\n', easyDir));
  else
    disp(sprintf('Using EASY script directory: %s from hardcoded default\n', easyDir));
  end

  if exist('PROJECT_USER', 'var') && ~isempty(getenv('PROJECT_USER'))
    if get_env('PROJECT_USER') ~= userName % sanity check
      disp("WARNING: PROJECT_USER does not match the current namespace");
    end
  end

  if exist('EASY_RESULTS_DIR', 'var') && ~isempty(getenv('EASY_RESULTS_DIR'))
    easyResultsDir=fullfile(get_env('EASY_RESULTS_DIR'));
    disp(sprintf('Using output directory: %s from environment variable EASY_RESULTS_DIR\n', easyResultsDir))
  else
    easyResultsDirName=strcat('Results_',todayStr,'_',userName,'_',easySuffix);
    easyResultsDir=fullfile(scansDir,easyResultsDirName);
    disp(sprintf('Using output directory: %s\n', PROJECT_PREFIX))
  end

  if exist('MASTER_PLATE_FILE', 'var') && ~isempty(getenv('MASTER_PLATE_FILE'))
    masterPlateFile=fullfile(get_env('MASTER_PLATE_FILE'));
    disp(sprintf('Using drug media file: %s from environment variable MASTER_PLATE_FILE\n', masterPlateFile))
  else
    % Try to find MasterPlate_ file on our own
    mp=fullfile(scansDir,'MasterPlateFiles',strcat('MasterPlate_', easySuffix,'.xlsx'));
    if exist(mp, 'file')
      masterPlateFile=mp;
      disp(sprintf('Using drug media file: %s from internal logic\n', masterPlateFile))
    else
      disp("WARNING: Have you created a MasterPlate_ file?")
    end
  end

  if exist('DRUG_MEDIA_FILE', 'var') && ~isempty(getenv('DRUG_MEDIA_FILE'))
    drugMediaFile=fullfile(get_env('DRUG_MEDIA_FILE'));
    disp(sprintf('Using drug media file: %s from environment variable DRUG_MEDIA_FILE\n', drugMediaFile))
  else
    % Try to find MasterPlate_ file on our own
    dm=fullfile(scansDir,'MasterPlateFiles',strcat('DrugMedia_', easySuffix,'.xlsx'));
    if exist(mp, 'file')
      drugMediaFile=dm;
      disp(sprintf('Using drug media file: %s from internal logic\n', drugMediaFile))
    else
      disp("WARNING: Have you created a DrugMedia_ file?")
    end
  end

  matDir=fullfile(easyResultsDir,'matResults');
  if ~exist(matDir, 'dir')
    mkdir(matDir);
  end
  matFile=fullfile(matDir,strcat(easyResultsDirName,'.mat'));
  % Pulled these out of par4GblFnc8c
  printResultsDir=fullfile(easyResultsDir,'PrintResults');
  fotosResultsDir=fullfile(easyResultsDir,'Fotos');
  figsResultsDir=fullfile(easyResultsDir,'figs');
  pointMapsResultsDir=fullfile(easyResultsDir,'PTmats');
  pointMapsFile=fullfile(pointMapsResultsDir,'NImParameters.mat');
  oldPointMapsFile=fullfile(pointMapsResultsDir,'ImParameters.mat');
  searchRangeFile=fullfile(fotosResultsDir,'CSearchRange.mat');
  mpdmFile=fullfile(matDir,'MPDM.mat');

  % This can be removed, I think it should add the previous search range?
  % Might be nice feature but can remove if it causes issues
  % We are using searchRangeNum to hold old CSrchRange value(s)
  if exist(searchRangeFile, 'file')
    searchRangeNum=load(searchRangeFile);
  end
  % Add easyDir to the MATLAB path
  % I have not idea if this is necessary or works but theoretically should
  % reduce directory scoping issues when calling scripts w/o a path
  addpath(easyDir);

  % Pulled this out of the opening function
  % Seems better to wait until we have our ars set
  if exist('scansDir','var') && ~isempty(scansDir)
    set(fhconsole,'Name',sprintf('EASYconsole - %s', scansDir));
  else
    set(fhconsole,'Name','EASYconsole - No Active Experiment.')
  end

  % GUI interface design
  gui_Singleton=1;
  gui_State=struct( 'gui_Name',       mfilename, ...
                    'gui_Singleton',  gui_Singleton, ...
                    'gui_OpeningFcn', @EASYconsole_OpeningFcn, ...
                    'gui_OutputFcn',  @EASYconsole_OutputFcn, ...
                    'gui_LayoutFcn',  [] , ...
                    'gui_Callback',   []);
  if nargin && ischar(varargin{1})
    gui_State.gui_Callback=str2func(varargin{1});
  end

  if nargout
    [varargout{1:nargout}]=gui_mainfcn(gui_State, varargin{:});
  else
    gui_mainfcn(gui_State, varargin{:});
  end
end

% To remove?
% Try to enter 
% function returnStartDir
% 	global scansDir
%   global startDir
% 	try
% 		cd(scansDir)
% 	catch
% 		msgbox('Failed to enter the project directory so starting search from where we started.');
%     cd(startDir)
% 	end
% end
  
% GUI
% Easyconcole_OpeningFcn executes just before the EASYconsole GUI is made visible.
% This function has no output args, see OutputFcn.
% hObject--handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles--structure with handles and user data (see GUIDATA)
% varargin--input arguments to EASYconsole (see VARARGIN)
function EASYconsole_OpeningFcn(hObject, ~, handles, varargin)
  global fhconsole

  % Choose default command line output for EASYconsole
  handles.output=hObject;

  % Update handles structure
  guidata(hObject, handles);

  %Figure header, Toolbar, etc. Setup
  fhconsole=gcf;
  set(fhconsole,'Toolbar','none');
  fhconsole=gcf;
end


% EASYconsole OUTPUT FUNCTION %%
% Outputs from this function are returned to the command line.
% varargout--cell array for returning output args (see VARARGOUT);
% hObject--handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles--structure with handles and user data (see GUIDATA)
function varargout = EASYconsole_OutputFcn(~, ~, handles) 
  % Get default command line output from handles structure
  varargout{1}=handles.output;
end

%% CONSOLE BUTTON INTERFACES %%
% File Button Interface
function FileMenu_Callback(~, ~, ~)
    %returnStartDir
end

% Load Experiment Button Interface
function LoadExp_Callback(~, ~, ~)
    %returnStartDir
end

% New Experiment Button Interface
function NewExpDat_Callback(~, ~, ~)
  global matDir
  global matFile
  global easyResultsDir
  global easyResultsDirName
  global fhconsole
  global scan
  global userName

  % Create a new experiment
  try
    questdlg('\fontsize{20} NAME the file and NAVIGATE to the directory with the image folders.','File Creation','OK', struct('Default','OK','Interpreter','tex'));
    [inputFile,inputPath]=uiputfile('.mat');
    inputFileName=strrep(inputFile,'.mat','');
    easyResultsDirName=strcat('Results_',todayStr,'_',userName,'_',inputFileName);

    % Set paths
    scansDir=fullfile(inputPath);
    easyResultsDir=fullfile(scansDir,easyResultsDirName);
    matDir=fullfile(easyResultsDir,'matResults');
    matFile=fullfile(matDir,strcat(todayStr,'_',userName,'_',inputFile));
    
    %***Added for 'parfor global' to preallocate 'scan' structure 20-0123***** 
    nlist=dir(fullfile(scansDir,'*'));
    nnn=0;
    for n=1:size(nlist,1)
      if (~isempty(str2num(nlist(n).name)))
        nnn=nnn+1;
        PnumLst(nnn)= (str2num(nlist(n).name));
        sl(nnn,1)={(nlist(n).name)};
      end
    end
    scanSize=size(sl,1);
    scanMax=max(str2double(sl));
    clear scan;
    scan(scanMax)=struct(); % changed for parfor global 20_0118
    save(matFile,'scan')

    % create supporting dirs
    % this is also in the workflow script but here for standalone mode
    dirs={'PrintResults', 'CFfigs', 'Fotos', 'Fotos/BkUp'};
    for i=1:length(dirs)
      d=dirs{i};
      if ~exist(fullfile(easyResultsDir, d), 'dir')
        mkdir(fullfile(easyResultsDir, d));
      end
    end

    % templateDirs are stored in the easy template directory
    templates={'figs', 'PTmats'};
    for i=1:length(templates)
      d=dirs{i};
      if ~exist(fullfile(easyResultsDir, d), 'dir')
        copyfile((fullfile(easyDir,d)), (fullfile(easyResultsDir,d)));
      end
    end

    clear sbdg % reduce possible retention of a previous job sdbg
    sbdg= cell(1,scanMax); 
    save((fullfile(easyResultsDir,'Fotos','Nbdg')),'sbdg'); 
  catch ME
    disp(sprintf('ERROR: %s\n', ME.message));
  end

  % set the title for fhconsole depending on existence
  if exist('easyResultsDir','var')&&~isempty(easyResultsDir)
    set(fhconsole,'Name',sprintf('EASYconsole - %s', easyResultsDir));
  else
    set(fhconsole,'Name','EASYconsole - Master Plate directory not selected.');
  end
end


% Load a previous experiment
function LoadDatFile_Callback(~, ~, ~)
  global matDir
  global matFile
  global easyResultsDir
  global easyPath
  global fhconsole

  try
    questdlg('\fontsize{20} Load file from ExpJobs/YourJob/YourResults/matResults','File Creation','OK', struct('Default','OK','Interpreter','tex'));
    [inputFile,inputPath]=uigetfile('.mat','Open Experiment folder and data storage .mat file name','MultiSelect','off');
    matDir=fullfile(inputPath);
    matFile=fullfile(inputPath,inputFile);
    load(matFile);
    easyResultsDir=fullfile(matDir,'..');
    scansDir=fullfile(matDir,'..', '..');
    point

    % TODO this is pretty hacky and needs something more explicit
    if isfolder(fullfile(matDir, '..','..','1')) % If Inovation Vrobot Then
      try 
        exist(pointMapsFile, 'file')
        load(pointMapsFile);
      catch
        try 
          load(fullfile(easyPath,'NImParameters.mat')); % hardcoded default
        catch
          disp("Could not load the NImParameters.mat file")
        end
      end
    else % If Epson 10Plate Scans Then>
      if exist(fullfile(pointMapsResultsDir,'ImParameters.mat'), 'file')
        load(fullfile(pointMapsResultsDir,'ImParameters.mat'));
      else
        try
          load(fullfile(easyPath,'ImParameters.mat'));
        catch
          disp("Could not load the ImParameters.mat file")
        end
      end  
    end

    bkupDir=fullfile(matDir,'BkUp');
    if ~exist(bkupDir, 'dir')
      mkkdir(bkupDir);
    end

    % Create supporting dirs
    dirs={'PrintResults', 'figs', 'CFfigs', 'PTmats', 'Fotos'};
    for i=1:length(dirs)
      d=dirs{i};
      if ~exist(fullfile(easyResultsDir, d), 'dir')
        mkdir(fullfile(easyResultsDir, d));
      end
    end
  catch
  end

  clear scan   

  if exist('easyResultsDir','var') && ~isempty(easyResultsDir)
    fhconsole=gcf;
    set(fhconsole,'Name',sprintf('EASYconsole - %s', easyResultsDir));
  else
    set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.');
  end
end

% Callbacks
% 'Run' in the dropdown menu
function run_Callback(~, ~, ~)
end

function runPlateMapPintool_Callback(~, ~, ~)
  try   
    NImapPT
  catch
    EASYconsole
  end
end

function NImCFcombo_Callback(~, ~, ~)
  try   
    par4Gbl_Main8c
  catch 
    EASYconsole
  end
end

function runPlateImAnal_Callback(~, ~, ~)
  try   
    NImStartupOnly
  catch
    EASYconsole
  end
end

function PlateCFit_Callback(~, ~, ~)
  % global matFile % TODO BCR not sure if needed
  try
    NCstart  
  catch
  end
end

function GenPrintouts_Callback(~, ~, ~)
end

function uploadExcelMP2DB_Callback(~, ~, ~)
end

function runDMPexcel_Callback(~, ~, ~)
  try
    DMPexcel2mat
  catch
    EASYconsole
  end
end

function runResults_DBcombo_Callback(~, ~, ~)
  try
    DgenResults %similar but semicolons removed to restore so cmdLine display info.
    %Dgen241010qhtcp %par4global -convert 1x1cell of 384cells to be like previous 1x384 cells CFparameter
  catch ME
    disp(sprintf('Error in DgenResults: %s\n', ME.message));
    EASYconsole
  end
end

function Tools_Callback(~, ~, ~)
end

function runOverlayPlots_Callback(~, ~, ~)
  try   
    DoverlayPlots2
    EASYconsole
  catch 
    EASYconsole
  end
end

function runFotoStrip_Callback(~, ~, ~)
  try   
    F_NImStartup_CentCir
    EASYconsole
  catch
    EASYconsole
  end
end

function runDisplayFig_Callback(~, ~, ~)
  try 
    UfigDisplay 
  catch
    EASYconsole
  end
end

function runViewParameters_Callback(~, ~, ~)
  try
  catch
    EASYconsole
  end
end

function QkviewN_Callback(~, ~, ~)
  try 
    QkviewImages
  catch
    EASYconsole
  end
end

function CFdisplay_Callback(~, ~, ~)
  try   
    NCsingleDisplay
    EASYconsole
  catch
    EASYconsole
  end
end