Cleanup EASY startup

workflow/apps/matlab/easy/EASYconsole.m

@@ -3,10 +3,9 @@
 
 function varargout = EASYconsole(varargin)
   global easyDir
-  global easySuffix
   global scansDir
   global easyResultsDir
-  global easyResultsDirName
+  global easyProject
   global fotosResultsDir
   global figsResultsDir
   global pointMapsResultsDir
@@ -41,38 +40,52 @@ function varargout = EASYconsole(varargin)
   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');
+
+  if exist('PROJECT_SCANS_DIR', 'var') && ~isempty(getenv('PROJECT_SCANS_DIR'))
+    scansDir=fullfile(getenv('PROJECT_SCANS_DIR'));
+    if exist(scansDir, 'dir')
       fprintf('Using scans directory: %s from environment variable PROJECT_SCANS_DIR\n', scansDir);
       disp('This usually indicates that we are in module mode');
+      if ~exist('PROJECT', 'var') || isempty(getenv('PROJECT'))
+        dirInfo=fileparts(scansDir);
+        project=dirInfo.name;
+      end
+    else
+      disp('WARNING: PROJECT_SCANS_DIR does not exist');
+    end
+  elseif exist('PROJECT', 'var') && ~isempty(getenv('PROJECT')) % for standalone mode
+    % scansDir=fullfile(parentDir, '..', '..', 'scans', getenv('PROJECT') 'out', 'easy', getenv('PROJECT'));
+    scansDir=fullfile(parentDir, '..', '..', 'scans', getenv('PROJECT'));
+    project=getenv('PROJECT');
+    fprintf('Using project path: %s from environment variable PROJECT\n', scansDir);
+    disp('This usually indicates that we are in standalone 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('WARNING: Running in standalone mode without PROJECT or PROJECT_SCANS_DIR environment variables (not recommended)\n');
     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, '..', '..', 'scans'),
       fullfile(parentDir, '..', '..', 'ExpJobs'),
-      fullfile('/mnt/data/scans'),
-      fullfile('/mnt/data/ExpJobs'),
+      fullfile('mnt','data','scans'),
+      fullfile('mnt','data', 'ExpJobs'),
       fullfile(parentDir, '..', '..', 'templates', 'scans-demo')
     };
     for i=1:length(dirsToScan)
       d=dirsToScan(i);
       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);
+        pattern='^\d{6}_.*_.*';
+        matchedDirs={dirs(regexp(subDirs.name, pattern)).name};
+        if ~isempty(matchedDirs)
+          fprintf('Found a non-empty scans directory in our list: %s\n', char(d);
+          fprintf('Setting scansDir to %s\n', char(d));
+          scansDir=fullfile(d);
         end
+        fprintf('Scanning inside %s for a project directory\n', char(d));
+        sortedMatchedDirs=sortrows(matchedDirs);
+        project=sortedMatchedDirs{0}; % select the latest dir (by date prefix)
+        fprintf('Selected latest project directory %s\n', char(project));
       end
     end
   end
@@ -97,37 +110,12 @@ function varargout = EASYconsole(varargin)
     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);
+    easyProject=strcat(todayStr,'_',userName,'_', project);
+    easyResultsDir=fullfile(parentDir, '..', '..', 'out', project, 'easy', easyProject);
     if exist(easyResultsDir, 'dir')
       fprintf('WARNING: EASY results dir %s already exists\n', easyResultsDir);
       disp('Files in this directory may be overwritten')
@@ -140,12 +128,12 @@ function varargout = EASYconsole(varargin)
     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'));
+    mp=fullfile(scansDir, strcat('MasterPlate_', project,'.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);
+      fprintf('WARNING: Have you created a MasterPlate_ file in %s/easy_in/?\n', scansDir);
     end
   end
 
@@ -153,8 +141,7 @@ function varargout = EASYconsole(varargin)
     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'));
+    dm=fullfile(scansDir,'easy_in',strcat('DrugMedia_', project,'.xlsx'));
     if exist(mp, 'file')
       drugMediaFile=dm;
       fprintf('Using drug media file: %s from internal logic\n', drugMediaFile);
@@ -163,12 +150,9 @@ function varargout = EASYconsole(varargin)
     end
   end
 
-  matDir=fullfile(easyResultsDir,'matResults');
-  if ~exist(matDir, 'dir')
-    mkdir(matDir);
-  end
-  matFile=fullfile(matDir,strcat(easyResultsDirName,'.mat'));
-  % Pulled these out of par4GblFnc8c
+  matDir=fullfile(easyResultsDir);
+  matFile=fullfile(matDir,easyResultsDirName,'.mat');
+  mpdmFile=fullfile(matDir,'MPDM.mat');
   printResultsDir=fullfile(easyResultsDir,'PrintResults');
   fotosResultsDir=fullfile(easyResultsDir,'Fotos');
   figsResultsDir=fullfile(easyResultsDir,'figs');
@@ -176,7 +160,6 @@ function varargout = EASYconsole(varargin)
   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 debug
@@ -190,6 +173,7 @@ function varargout = EASYconsole(varargin)
   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
@@ -197,7 +181,8 @@ function varargout = EASYconsole(varargin)
 
   % GUI interface design
   gui_Singleton=1;
-  gui_State=struct( 'gui_Name',       mfilename, ...
+  gui_State=struct(...
+    'gui_Name',       mfilename, ...
     'gui_Singleton',  gui_Singleton, ...
     'gui_OpeningFcn', @EASYconsole_OpeningFcn, ...
     'gui_OutputFcn',  @EASYconsole_OutputFcn, ...
@@ -256,15 +241,15 @@ function varargout = EASYconsole_OutputFcn(~, ~, handles)
   varargout{1}=handles.output;
 end
 
-%% CONSOLE BUTTON INTERFACES %%
+% Console button interfaces
 % File Button Interface
 function FileMenu_Callback(~, ~, ~)
-    %returnStartDir
+  % returnStartDir
 end
 
 % Load Experiment Button Interface
 function LoadExp_Callback(~, ~, ~)
-    %returnStartDir
+  % returnStartDir
 end
 
 % New Experiment Button Interface
@@ -333,7 +318,7 @@ function NewExpDat_Callback(~, ~, ~)
   end
 
   % set the title for fhconsole depending on existence
-  if exist('easyResultsDir','var')&&~isempty(easyResultsDir)
+  if exist('easyResultsDir','var') && ~isempty(easyResultsDir)
     set(fhconsole,'Name',sprintf('EASYconsole - %s', easyResultsDir));
   else
     set(fhconsole,'Name','EASYconsole - Master Plate directory not selected.');