EASYconsole.m rewrite

2024-07-26 02:53:58 -04:00
parent 7d621c96ac
commit 3f1cd6ef0e
1 changed files with 323 additions and 271 deletions
--- a/workflow/templates/easy/EASYconsole.m
+++ b/workflow/templates/easy/EASYconsole.m
@@ -3,24 +3,107 @@
 % Updated 240724 Bryan C Roessler to improve file operations and portability
 % 
 function varargout = EASYconsole(varargin)
-    % initialize global variables for function EASYconsole
-    %global ExpOutmat
-    %global ExpPath
-    %global fhconsole
-    %global resDir
-    global wCodeDir
-    %global ImParMat
+  global startDir
+  global easyDir
+  global easySuffix
+  global scansDir
+  global easyResultsDir
+  global easyResultsDirName
+  global matDir
+  global matFile
+  global userName

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

-    % changing directory to wCodeDir
-    % returnStartDir
+  % 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

-    disp(getenv('SCANS_DIR'));
+  % 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

-    %% GUI INTERFACE DESIGN %%
-    % beginning of GUI formation & design, see help GUI or help GUIDE in
-    % command window for more information
+  % 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
+
+  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, ...
@@ -39,21 +122,15 @@ function varargout = EASYconsole(varargin)
  end
 end

-
-% Try to enter WCodeDir
+% To remove?
+% Try to enter 
 function returnStartDir
-	global wCodeDir
+	global 
 	try
-		cd(wCodeDir)
+		cd(SCANS_DIR)
 	catch
-		msgbox('Failed to enter selected default directory so starting search at root.');
-		if ispc
-			cd('C:\');
-		elseif (isunix || ismac)
-			cd('/mnt/data');
-		else
-			msgbox('Unknown platform')
-		end
+		msgbox('Failed to enter the project directory so starting search from where we started.');
+    cd(start_dir)
 	end
 end
  
@@ -65,11 +142,8 @@ end
 % handles--structure with handles and user data (see GUIDATA)
 % varargin--input arguments to EASYconsole (see VARARGIN)
 function EASYconsole_OpeningFcn(hObject, ~, handles, varargin)
-    %global ExpOutmat
-    %global ExpPath
  global fhconsole
-    global resDir
-    %global ImParMat
+  global easyResultsDir

  % Choose default command line output for EASYconsole
  handles.output = hObject;
@@ -82,15 +156,18 @@ function EASYconsole_OpeningFcn(hObject, ~, handles, varargin)
  set(fhconsole,'Toolbar','none');
  fhconsole=gcf;

-    if exist('resDir','var')&&~isempty(resDir)
-        set(fhconsole,'Name',strcat('EASYconsole- ',char(resDir)));
+  % 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 %%
+% 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
@@ -114,34 +191,32 @@ end

 % New Experiment Button Interface
 function NewExpDat_Callback(~, ~, ~)
-    global newExpfile
-    global newExppath
  global SWnewExp
-    global ExpOutmat
-    global ExpPath
  global matDir
-    global resDir
+  global matFile
+  global easyResultsDir
+  global easyResultsDirName
  global fhconsole
  global scan
-
-   % put all users on same working directory
-   %returnStartDir
+  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'));
-        [newExpfile,newExppath] = uiputfile(' .mat');
+    [inputFile,inputPath]=uiputfile('.mat');
    SWnewExp=1;

+    inputFileName=strrep(inputFile,'.mat','');
+    easyResultsDirName=strcat('Results_',datestr(now,'yyyymmdd'),'_',userName,'_',inputFileName);
+
    % Set paths
-        newExpfilePref= strrep(newExpfile,'.mat','');
-        resDir=fullfile(newExppath,resDirName);
-        matDir=fullfile(newExppath,resDirName,'matResults');
-        ExpOutmat=fullfile(matDir,strcat(datestr(now,29),newExpfile));
-        ExpPath=fullfile(newExppath);
+    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(ExpPath,'*'));
+    nlist=dir(fullfile(scansDir,'*'));
    nnn=0;
    for n=1:size(nlist,1)
      if (~isempty(str2num(nlist(n).name)))
@@ -154,38 +229,38 @@ function NewExpDat_Callback(~, ~, ~)
    scanMax=max(str2double(sl));
    clear scan;
    scan(scanMax)=struct(); % changed for parfor global 20_0118
-        save(ExpOutmat,'scan')
+    save(matFile,'scan')

-        % BCR rewrote these but moved the functionality into the main workflow script
-        % % create supporting dirs
-        % dirs = {'PrintResults', 'CFfigs', 'Fotos', 'Fotos/BkUp'};
-        % for i = 1:length(dirs)
-        %     d = dirs{i};
-        %     if ~exist(fullfile(ExpPath, resDirName, d), 'dir')
-        %         mkdir(fullfile(ExpPath, resDirName, d));
-        %     end
-        % end
+    % 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(ExpPath, resDirName, d), 'dir')
-        %         copyfile((fullfile(wCodeDir,d)), (fullfile(ExpPath,resDirName,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(,d)), (fullfile(easyResultsDir,d)));
+      end
+    end

    clear sbdg % reduce possible retention of a previous job sdbg
    sbdg= cell(1,scanMax); 
-        save((fullfile(resDir,'Fotos','Nbdg')),'sbdg'); 
+    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('resDir','var')&&~isempty(resDir)
-        set(fhconsole,'Name',strcat('EASYconsole- ',char(resDir)))
+  if exist('easyResultsDir','var')&&~isempty(easyResultsDir)
+    set(fhconsole,'Name',strcat('EASYconsole- ',char(easyResultsDir)))
  else
    set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.')
  end
@@ -194,78 +269,65 @@ end

 % Load a previous experiment
 function LoadDatFile_Callback(~, ~, ~)
-    global openExpfile
-    global openExppath
  global SWnewExp
-    global ExpOutmat
-    global ExpPath
  global matDir
-    global resDir
+  global matFile
+  global easyResultsDir
+  global easyPath
  global fhconsole
  %global ImParMat

-    % TODO this entire try block needs work
  try
-        % TODO this whole block is highly questionable
    questdlg('\fontsize{20} Load file from ExpJobs/YourJob/YourResults/matResults','File Creation','OK', struct('Default','OK','Interpreter','tex'));
-        [openExpfile,openExppath] = uigetfile('.mat','Open Experiment folder and data storage .mat file name','MultiSelect','off');
+    [inputFile,inputPath]=uigetfile('.mat','Open Experiment folder and data storage .mat file name','MultiSelect','off');
    SWnewExp=0;
-        ExpOutmat= fullfile(openExppath,openExpfile);
-        load(ExpOutmat);
-        resdir=fullfile('../',openExppath)
-        ExpPath=fullfile('../../',openExppath)
+    matDir=fullfile(inputPath)
+    matFile=fullfile(inputPath,inputFile);
+    load(matFile);
+    easyResultsDir=fullfile(matDir,'..')
+    scansDir=fullfile(matDir,'..', '..')

-        if isfolder(fullfile(openExppath, '..','..','1')) %If Inovation Vrobot Then
-            if exist(fullfile(resDir,'PTmats','NImParameters.mat'), 'file')
-                load(fullfile(resDir,'PTmats','NImParameters.mat'));
+    if isfolder(fullfile(matDir, '..','..','1')) % If Inovation Vrobot Then
+      if exist(fullfile(easyResultsDir,'PTmats','NImParameters.mat'), 'file')
+        load(fullfile(easyResultsDir,'PTmats','NImParameters.mat'));
      else
-                curDir=pwd;
-                returnStartDir
-                load NImParameters.mat
-                cd(curDir)
+        load(fullfile(easyPath,'NImParameters.mat'));
      end
    else % If Epson 10Plate Scans Then>
-            if exist(fullfile(resDir,'PTmats','ImParameters.mat'), 'file')
-                load(fullfile(resDir,'PTmats','ImParameters.mat'));
+      if exist(fullfile(easyResultsDir,'PTmats','ImParameters.mat'), 'file')
+        load(fullfile(easyResultsDir,'PTmats','ImParameters.mat'));
      else
-                curDir=pwd;
-                returnStartDir
-                load ImParameters.mat
-                cd(curDir)
+        load(fullfile(easyPath,'ImParameters.mat'));
      end  
    end

-        mkdir(fullfile(openExppath,'\BkUp'));
-
-        % create supporting dirs
-        % dirs = {'PrintResults', 'figs', 'CFfigs', 'PTmats', 'Fotos'}
-        % for i = 1:length(dirs)
-        %     d = dirs{i}
-        %     if ~exist(fullfile(resDir, d), 'dir')
-        %         mkdir(fullfile(resDir, d));
-        %     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
    returnStartDir
  end

  clear scan   

-    if exist('resDir','var')&&~isempty(resDir)
+  if exist('easyResultsDir','var') && ~isempty(easyResultsDir)
    fhconsole=gcf;
-    set(fhconsole,'Name',strcat('EASYconsole- ',char(resDir)))
+    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(~, ~, ~)
@@ -296,7 +358,7 @@ function runPlateImAnal_Callback(~, ~, ~)
 end

 function PlateCFit_Callback(~, ~, ~)
-    %global ExpOutmat
+  % global matFile % TODO BCR not sure if needed
  try
    NCstart  
  catch ME
@@ -311,7 +373,6 @@ function uploadExcelMP2DB_Callback(~, ~, ~)
 end

 function runDMPexcel_Callback(~, ~, ~)
-    global ExpPath
  try
    DMPexcel2mat_2024winLinix %DMPexcel2mat_2023winLinix
  catch ME
@@ -321,13 +382,11 @@ function runDMPexcel_Callback(~, ~, ~)
 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('Error in DgenResults240430')
-        returnStartDir
    EASYconsole
  end
 end
@@ -340,7 +399,6 @@ function runOverlayPlots_Callback(~, ~, ~)
    DoverlayPlots2
    EASYconsole
  catch ME
-        returnStartDir
    EASYconsole
  end
 end
@@ -350,7 +408,6 @@ function runFotoStrip_Callback(~, ~, ~)
    F_NImStartup_CentCir
    EASYconsole
  catch ME
-        returnStartDir 
    EASYconsole
  end
 end
@@ -359,7 +416,6 @@ function runDisplayFig_Callback(~, ~, ~)
  try 
    UfigDisplay 
  catch ME
-        returnStartDir 
    EASYconsole
  end
 end
@@ -367,7 +423,6 @@ end
 function runViewParameters_Callback(~, ~, ~)
  try
  catch ME
-        returnStartDir
    EASYconsole
  end
 end
@@ -376,7 +431,6 @@ function QkviewN_Callback(~, ~, ~)
  try 
    QkviewImages
  catch ME
-        returnStartDir
    EASYconsole
  end
 end
@@ -384,10 +438,8 @@ end
 function CFdisplay_Callback(~, ~, ~)
  try   
    NCsingleDisplay
-        returnStartDir
    EASYconsole
  catch ME
-        returnStartDir
    EASYconsole
  end
 end