% Launch the MATLAB EASY console
% Updated 240727 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);
  parentDir=fullfile(parentDir); % ../easy/apps
  userName=getenv('USER');
  dt=datetime;
  todayStr=char(dt, 'yyyyMMdd'); % This should match the parent workflow script

  demo=1;
  if demo
    disp('Running in demo mode');
    disp('Initialized variables:');
    whos;
  end

  fprintf('This script name: %s\n', easyFileName);

  % Set scansDir (project scans directory) intelligently
  if exist('PROJECT', 'var') && ~isempty(getenv('PROJECT'))
    scansDir=getenv('PROJECT');
    fprintf('Using project path: %s from environment variable PROJECT\n', scansDir);
    disp('This usually indicates that we are in standalone mode');
  elseif exist('PROJECT_SCANS_DIR', 'var') && ~isempty(getenv('PROJECT_SCANS_DIR'))
    scansDir=getenv('PROJECT_SCANS_DIR');
    fprintf('Using scans directory: %s from environment variable PROJECT_SCANS_DIR\n', scansDir);
    disp('This usually indicates that we are in module mode');
  else
    % TODO Lots of this is hardcoded logic, this TODO is just a reminder to change this block
    % when changing EASY and other variables in the parent script
    fprintf('Beginning parent scans directory search\n');
    fprintf('This usually indicates that we are in stand-alone mode without PROJECT or PROJECT_SCANS_DIR environment variables\n');
    dirsToScan={
      fullfile(parentDir,'..', '..', 'scans'),
      fullfile(parentDir, '..', '..', 'ExpJobs'),
      fullfile('/mnt/data/scans'),
      fullfile('/mnt/data/ExpJobs'),
      fullfile(parentDir, '..', '..', 'templates', 'scans-demo')
    };
    for d=dirsToScan
      if exist(d, 'dir')
        subDirs=dir(d);
        if ~isempty(subDirs)
          fprintf('Found a non-empty parent scans directory in our list: %s\n', d);
          fprintf('Scanning inside for a project scan directory\n');
          [~, sortedIndices]=sort(datenum({dirs.date}), 'descend'); % sort by newest first
          sortedDirs=dirs{sortedIndices};
          scansDir=sortedDirs{1};
          fprintf('Selected newest project scans directory: %s\n', scansDir);
        end
      end
    end
  end

  % Sanity check and warning
  if exist('PROJECT_USER', 'var') && ~isempty(getenv('PROJECT_USER'))
    if ~equal(getenv('PROJECT_USER'), userName)
      disp("WARNING: PROJECT_USER does not match the current namespace");
    end
  end

  % Allow module to override hardcoded default EASY directory
  if exist('EASY_DIR','var') && ~isempty(getenv('EASY_DIR'))
    EASY_DIR=fullfile(getenv('EASY_DIR'));
    if ~strcmp(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
    fprintf('Using EASY script directory: %s from environment variable EASY_DIR\n', easyDir);
  else
    fprintf('Using EASY script directory: %s from hardcoded default\n', easyDir);
  end

  % If we don't have tan EASY_SUFFIX from the module, generate it from scansDir
  if exist('EASY_SUFFIX', 'var') && ~isempty(getenv('EASY_SUFFIX'))
    easySuffix=getenv('EASY_SUFFIX');
  else
    % The following is a way to parse the project name from the scansDir
    [ ~, dirName]=fileparts(scansDir);
    parts=strsplit(dirName, '_');
    scansDate=parts{1};
    scansUserName=parts{2};
    easySuffix=strjoin(parts(3:end), '_');
    % Might as well check this too for fun
    if ~strcmp(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 strcmp(todayStr, scansDate)
      disp("Early bird gets the worm");
    end
  end

  if (exist('EASY_RESULTS_DIR', 'var') && ~isempty(getenv('EASY_RESULTS_DIR')))
    easyResultsDir=fullfile(getenv('EASY_RESULTS_DIR'));
    if exist(easyResultsDir, 'dir')
      fprintf('WARNING: EASY results dir %s already exists\n', easyResultsDir);
      disp('Files in this directory may be overwritten');
    end
    fprintf('Using output directory: %s from environment variable EASY_RESULTS_DIR\n', easyResultsDir);
  else
    easyResultsDirName=strcat('Results_',todayStr,'_',userName,'_',easySuffix);
    easyResultsDir=fullfile(scansDir,easyResultsDirName);
    if exist(easyResultsDir, 'dir')
      fprintf('WARNING: EASY results dir %s already exists\n', easyResultsDir);
      disp('Files in this directory may be overwritten')
      fprintf('Using output directory: %s\n', easyResultsDir);
    end
  end

  if exist('MASTER_PLATE_FILE', 'var') && ~isempty(getenv('MASTER_PLATE_FILE'))
    masterPlateFile=fullfile(getenv('MASTER_PLATE_FILE'));
    fprintf('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;
      fprintf('Using drug media file: %s from internal logic\n', masterPlateFile);
    else
      fprintf('WARNING: Have you created a MasterPlate_ file in %s/MasterPlateFiles/?\n', scansDir);
    end
  end

  if exist('DRUG_MEDIA_FILE', 'var') && ~isempty(getenv('DRUG_MEDIA_FILE'))
    drugMediaFile=fullfile(getenv('DRUG_MEDIA_FILE'));
    fprintf('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;
      fprintf('Using drug media file: %s from internal logic\n', drugMediaFile);
    else
      fprintf('WARNING: Have you created a DrugMedia_ file in %s/MasterPlateFiles/?\n', scansDir);
    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');

  % Decent time to print some helpful vars
  if demo
    disp('Vars at end of main loop:')
    whos;
  end

  % 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);

  % 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

% 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
  global scansDir

  % 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;

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

% EASYconsole output
% 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
    fprintf('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('Load results .mat from ../ExpJobs/YourJob/Results/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
    else
      disp('WARNING: cannot find project scans');
    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
    EASYconsole
  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
    EASYconsole
  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
    fprintf('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