% Launch the MATLAB EASY console
%
% Updated 240724 Bryan C Roessler to improve file operations and portability
% 
function varargout = EASYconsole(varargin)
  global startDir
  global easyDir
  global easySuffix
  global scansDir
  global easyResultsDir
  global easyResultsDirName
  global matDir
  global matFile
  global userName

  % Initialize some variables from matlab
  startDir=pwd;
  easyPath=which(mfilename);
  [easyDir,easyFileName]=fileparts(easyPath);
  easyDir=fullfile(easyDir)
  [parentDir, ~]=fileparts(easyDir);
  userName=system('whoami');

  disp(strcat('This script name: ', 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', 'env')
    scansDir=get_env('PROJECT');
    disp(strcat('Using project path: ', scansDir, ' from environment variable PROJECT'));
    disp('This usually indicates that we are in standalone mode');
  elseif exist('SCANS_DIR', 'env')
    scansDir=get_env('SCANS_DIR');
    disp(strcat('Using scans directory: ', scansDir, ' from environment variable SCANS_DIR'));
    disp('This usually indicates that we are in module mode');
  else
    scansDir=fullfile(parentDir,'ExpJobs'); % relative to easy script dir
    disp(strcat('Using scans directory: ', scansDir, ' from hardcoded default'));
    disp('This usually indicates that we are in standalone mode');
  end

  % If we don't have the EASY_SUFFIX from the module, generate it from scanDir
  if exist('EASY_SUFFIX', 'env')
    easySuffix=get_env('EASY_SUFFIX');
  else
    [dirName, ~]=fileparts(scansDir);
    [date, userNameScans, 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 ~= userNameScans
      disp('WARNING: userName does not match userNameScans');
      disp("This usually means that you are attempting to run an EASY analysis on another user's project data scans");
    end
    % For happiness
    if datestr(now, 'yyyymmdd') == date
      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','env')
    EASY_DIR=fullfile(get_env('EASY_DIR'))
    if easyDir ~= EASY_DIR % sanity check
      disp("WARNING: EASY_DIR does not match this script's default EASY location");
      easyDir=EASY_DIR
    end
    disp(strcat('Using EASY script directory: ', easyDir, ' from environment variable EASY_DIR'));
  else
    disp(strcat('Using EASY script directory: ', easyDir, ' from hardcoded default'));
  end

  % Now that we have easyDir let's add it to the path just to be safe
  % TODO I have no idea if this is necessary or effective but we'll see
  % I could image it would reduce some weird matlab errors?
  addpath(easyDir);

  if exist('EASY_RESULTS_DIR', 'env')
    easyResultsDir=fullfile(get_env('EASY_RESULTS_DIR'));
    disp(strcat('Using project prefix: ', easyResultsDir, ' from environment variable EASY_RESULTS_DIR'))
  else
    easyResultsDirName=strcat('Results_',datestr(now, 'yyyymmdd'),'_',easySuffix);
    easyResultsDir=fullfile(scansDir,easyResultsDirName);
    scansDir=fullfile(parent_dir,'ExpJobs') % relative to easy script dir
    disp(strcat('Using project prefix: ', PROJECT_PREFIX, ' from environment variable PROJECT_PREFIX'))
  end

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

  matDir=fullfile(easyResultsDir,'matResults');
  matFile=fullfile(matDir,strcat(easyResultsDirName,'.mat'));

  % Play around with making some common variables from our input data
  % resDirName=fullfile(SCANS_DIR,'Results',strcat(datestr(now, 'yyyymmdd'),'_', PROJECT_SUFFIX);
  % resDir=fullfile(SCANS_DIR,resDirName);
  % ExpOutmat=fullfile(matDir,strcat(datestr(now,29),newExpfile));
  % ExpPath=fullfile(newExppath);
  % ExpFile=fullfile(matDir,)

  % 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
  global easyResultsDir

  % 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;

  % BCR this is set in the global function so I think we're good here 
  % easyResultsDirName=strcat('Results',datestr(now, 'yyyymmdd'),newExpfilePref); 

  if exist('easyResultsDir','var') && ~isempty(easyResultsDir)
    set(fhconsole,'Name',strcat('EASYconsole- ',char(easyResultsDir)));
  else
    set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.')
  end
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 SWnewExp
  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');
    SWnewExp=1;

    inputFileName=strrep(inputFile,'.mat','');
    easyResultsDirName=strcat('Results_',datestr(now,'yyyymmdd'),'_',userName,'_',inputFileName);

    % Set paths
    scansDir=fullfile(inputPath);
    easyResultsDir=fullfile(scansDir,easyResultsDirName);
    matDir=fullfile(easyResultsDir,'matResults');
    matFile=fullfile(matDir,strcat(datestr(now,'yyyymmdd'),'_',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
    % returnStartDir
    disp('Error Creating a New Experiment')
  end

  % set the title for fhconsole depending on existence
  if exist('easyResultsDir','var')&&~isempty(easyResultsDir)
    set(fhconsole,'Name',strcat('EASYconsole- ',char(easyResultsDir)))
  else
    set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.')
  end
end


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

  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');
    SWnewExp=0;
    matDir=fullfile(inputPath)
    matFile=fullfile(inputPath,inputFile);
    load(matFile);
    easyResultsDir=fullfile(matDir,'..')
    scansDir=fullfile(matDir,'..', '..')

    if isfolder(fullfile(matDir, '..','..','1')) % If Inovation Vrobot Then
      if exist(fullfile(easyResultsDir,'PTmats','NImParameters.mat'), 'file')
        load(fullfile(easyResultsDir,'PTmats','NImParameters.mat'));
      else
        load(fullfile(easyPath,'NImParameters.mat'));
      end
    else % If Epson 10Plate Scans Then>
      if exist(fullfile(easyResultsDir,'PTmats','ImParameters.mat'), 'file')
        load(fullfile(easyResultsDir,'PTmats','ImParameters.mat'));
      else
        load(fullfile(easyPath,'ImParameters.mat'));
      end  
    end

    mkdir(fullfile(matDir,'BkUp'));

    % 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',strcat('EASYconsole- ',char(easyResultsDir)))
  else
    set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.')
  end
end

%% CALLBACKS %% 
% callback for the 'Run' in the dropdown menu
function run_Callback(~, ~, ~)
end

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

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

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

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

function GenPrintouts_Callback(~, ~, ~)
end

function uploadExcelMP2DB_Callback(~, ~, ~)
end

function runDMPexcel_Callback(~, ~, ~)
  try
    % DMPexcel2mat_2024winLinix %DMPexcel2mat_2023winLinix
    DMPexcel2mat % TODO Can't find above so using what I have available
  catch ME
    EASYconsole
  end
end

function runResults_DBcombo_Callback(~, ~, ~)
  try
    DgenResults240430 %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(strcat('Error in DgenResults240430: ', ME.message))
    EASYconsole
  end
end

function Tools_Callback(~, ~, ~)
end

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

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

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

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

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

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