From bb103a6f9a3a455e8c46a81b6496490b88727f3a Mon Sep 17 00:00:00 2001
From: Bryan Roessler <bryanroessler@gmail.com>
Date: Sat, 27 Jul 2024 13:39:18 -0400
Subject: [PATCH] strcat to sprintf

---
 workflow/templates/easy/DMPexcel2mat.m      | 13 ++--
 workflow/templates/easy/DgenResults.m       | 36 +++++-----
 workflow/templates/easy/EASYconsole.m       | 68 ++++++++++--------
 workflow/templates/easy/NCsingleDisplay.m   |  4 +-
 workflow/templates/easy/NImParamRadiusGui.m |  1 -
 workflow/templates/easy/par4Gbl_Main8c.m    | 76 +++++++++------------
 6 files changed, 99 insertions(+), 99 deletions(-)

diff --git a/workflow/templates/easy/DMPexcel2mat.m b/workflow/templates/easy/DMPexcel2mat.m
index a1c834b5..4fddde53 100755
--- a/workflow/templates/easy/DMPexcel2mat.m
+++ b/workflow/templates/easy/DMPexcel2mat.m
@@ -7,7 +7,7 @@ global matDir
 
 % If we already have mpdmFile, don't recreate
 if (exist(mpdmFile, 'file') && ~isempty(mpdmFile))
-  disp(strcat('The Drug Media/MasterPlate Annotation File: ', mpdmFile, ' exists, skipping DMPexcel2mat.m'));
+  disp(sprintf('The Drug Media/MasterPlate Annotation File: %s exists, skipping DMPexcel2mat.m\n', mpdmFile));
   return
 end
 
@@ -82,7 +82,7 @@ if ~exist(masterPlateFile, 'file') || isempty(masterPlateFile)
     end
   end
 else
-  disp(strcat('Using MasterPlate file: ', masterPlateFile, ', skipping directory selection'));
+  disp(sprintf('Using MasterPlate file: %s skipping directory selection\n', masterPlateFile));
 end
 
 % fid=fopen(masterPlateFile)%('exp23PrintTimes.xls'); % textread puts date and time sequentially into vector
@@ -183,7 +183,7 @@ if ~exist(drugMediaFile, 'file') || isempty(drugMediaFile)
       dmFileToTest=fullfile(mpPath, 'DrugMedia_', mpBareFileName, '.xlsx');
       if exist(dmFileToTest, 'file') % Try to find a matching drug media file
         drugMediaFile=dmFileToTest;
-        disp(strcat('Using matching DrugMedia file: ', drugMediaFile, ', skipping directory selection'));
+        disp(sprintf('Using matching DrugMedia file: %s, skipping directory selection\n', drugMediaFile));
       else
         % Try to find the DrugMedia file automatically (newest created first)
         files=dir(matDir);
@@ -195,7 +195,8 @@ if ~exist(drugMediaFile, 'file') || isempty(drugMediaFile)
         [~, sortedIndices]=sort(datenum({files(strncmp(dmFiles.name, 'DrugMedia_', 10)).date}), 'descend');
         sortedFiles=dmFiles{sortedIndices};
         drugMediaFile=sortedFiles{1};
-        disp(strcat('Using newest DrugMedia file: ', drugMediaFile, ', skipping directory selection'));
+        disp(sprintf('Using newest DrugMedia file: %s, skipping directory selection\n', drugMediaFile));
+
       end
     catch Me
       % This can be silent, not really an error
@@ -228,7 +229,7 @@ if ~exist(drugMediaFile, 'file') || isempty(drugMediaFile)
     end
   end
 else
-  disp(strcat('Using drugMediaFile: ', drugMediaFile, ', skipping directory selection'));
+  disp(sprintf('Using drugMediaFile: %s, skipping directory selection\n', drugMediaFile));
 end
 
 % Drug and Media Plate setup
@@ -325,4 +326,4 @@ if isequal(Linked,0) % 0 indicates Drugs and Media are combinatorial
 end
 
 save(mpdmFile, 'fields','MP','DM','Linked');
-msgbox([strcat('Drug-Media-MasterPlate Annotation File', mpdmFile,'Generation Complete')])
+msgbox(sprintf('Drug-Media-MasterPlate Annotation File %s Generation Complete', mpdmFile))
diff --git a/workflow/templates/easy/DgenResults.m b/workflow/templates/easy/DgenResults.m
index 1c2d83d1..ba1e42a7 100755
--- a/workflow/templates/easy/DgenResults.m
+++ b/workflow/templates/easy/DgenResults.m
@@ -366,9 +366,9 @@ if isequal(opt,'DB')||isequal(opt,'Both')
   try
     copyfile(DBfilename,DBupload)
   catch ME
-    rep=getReport(ME, 'basic');
-    rep=strcat('Failed copyfile to ',DBupload,' -', rep);
-    errordlg(rep)
+    disp(sprintf('DB upload failed with error: %s\n', getReport(ME, 'basic')));
+    rep=sprintf('Failed copyfile to %s - %s', DBupload, rep);
+    errordlg(rep);
   end
 end
 
@@ -406,9 +406,9 @@ try
       totPlCnt=totPlCnt+1;
       if destPerMP>1 &&rem(totPlCnt,destPerMP)==1, mpCnt=mpCnt+1; end
       if destPerMP==1,mpCnt=mpCnt+1; end
-      pertCnt= rem(totPlCnt,destPerMP);
+      pertCnt=rem(totPlCnt,destPerMP);
       if pertCnt==0, pertCnt= destPerMP;end
-      pert= strcat('Perturb_',num2str(pertCnt));
+      pert=strcat('Perturb_',num2str(pertCnt));
       s % BCR seems wrong
         
       %Print Time Point HEADER for each plate for newly added intensity data
@@ -420,10 +420,10 @@ try
         
         try
           asd=cell2mat(scan(s).plate(1).CFparameters(1));
-          aucEndPt=  strcat('AUC',num2str(asd(9)));
+          aucEndPt=strcat('AUC',num2str(asd(9)));
         catch
           asd=cell2mat(scan(s).plate(1).CFparameters{1,1}(1,384));
-          aucEndPt=  strcat('AUC',num2str(asd(9)));
+          aucEndPt=strcat('AUC',num2str(asd(9)));
         end
         fprintf(fid, 'Num.\tDiagnostics\tDrug\tConc\tMedia\tModifier1\tConc1\tModifier2\tConc2\tORF\tGene');
         fprintf(fid, '\t %s',aucEndPt);
@@ -475,8 +475,8 @@ try
           rSq=outCmat(n,6);
           lval=outCmat(n,5);
           if Kval>160, selcode='K_Hi'; else selcode=' ';end
-          if Kval<40, selcode=strcat(selcode,' K_Lo'); end  %12_1030
-          if rSq<.97 && rSq>0, selcode=strcat(selcode,' rSqLo'); end
+          if Kval<40, selcode=strcat(selcode,' K_Lo');end  % TODO sprintf if you want a space
+          if rSq<.97 && rSq>0, selcode=strcat(selcode,' rSqLo');end
           if lval>(0.85*(max(outTseries))), selcode=strcat(selcode,' late');end
           if isnan(outCmat(n,7))||isnan(outCmat(n,8))||isnan(outCmat(n,9))...
             ||isnan(outCmat(n,10))||isnan(outCmat(n,11))...
@@ -497,7 +497,7 @@ try
             riseTm=0;    
           end
          
-          if Ag(n)< .30*(scan(s).Awindow),selcode=strcat(selcode,' smArea'); end         
+          if Ag(n)< .30*(scan(s).Awindow),selcode=strcat(selcode,' smArea'); end  % same, need sprintf for space       
           if outCmat(n,3)==0,selcode=strcat('0 ',selcode); end
           orf=cell2mat(MP(mpCnt).orf{1}(n));
           gene=cell2mat(MP(mpCnt).genename{1}(n));
@@ -575,15 +575,15 @@ try
               end
               if isequal(opt,'DB')||isequal(opt,'Both') 
                 if j<dataLength
-                  intensBlob= strcat(intensBlob,num2str(outIntens(n,j)),';');  
+                  intensBlob=strcat(intensBlob,num2str(outIntens(n,j)),';');  
                 else
-                  intensBlob= strcat(intensBlob,num2str(outIntens(n,j)));
+                  intensBlob=strcat(intensBlob,num2str(outIntens(n,j)));
                 end
                 if outTseries(j)<.0001,outTseries(j)=0;end
                 if j<dataLength
-                  tmBlob= strcat(tmBlob,num2str(outTseries(j)),';');
+                  tmBlob=strcat(tmBlob,num2str(outTseries(j)),';');
                 else
-                  tmBlob= strcat(tmBlob,num2str(outTseries(j))); 
+                  tmBlob=strcat(tmBlob,num2str(outTseries(j))); 
                 end
               end
             end
@@ -654,15 +654,15 @@ try
     try
       copyfile(DBfilename,DBupload)
     catch ME
-      rep = getReport(ME, 'basic');
-      rep=strcat('Failed copyfile to ',DBupload,' -', rep);
+      disp(sprintf('DB upload failed with error: %s\n', getReport(ME, 'basic')));
+      rep=sprintf('Failed copyfile to %s - %s\n', DBupload, rep);
       errordlg(rep)
     end
   end
 
-  msgbox([strcat('Printing Script complete. Check !!Results sheets in ',printResultsDir,' for results.')])
+  msgbox([sprintf('Printing Script complete. Check !!Results sheets in %s for results.', printResultsDir)])
 
 catch ME
-  disp(strcat("Results printing failed with error: ", getReport(ME, 'basic')))
+  disp(sprintf('Printing Script failed with error: %s\n', getReport(ME, 'basic')));
 end
 
diff --git a/workflow/templates/easy/EASYconsole.m b/workflow/templates/easy/EASYconsole.m
index 6082fce2..4c47c498 100644
--- a/workflow/templates/easy/EASYconsole.m
+++ b/workflow/templates/easy/EASYconsole.m
@@ -30,28 +30,37 @@ function varargout = EASYconsole(varargin)
   userName=system('whoami');
   todayStr=datetime('now', 'Format', 'yyyyMMdd'); % This should match the parent workflow script
 
-  disp(strcat('This script name: ', easyFileName))
+  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=get_env('PROJECT');
-    disp(strcat('Using project path: ', scansDir, ' from environment variable 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=get_env('SCANS_DIR');
-    disp(strcat('Using scans directory: ', scansDir, ' from environment variable 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
-    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(strcat('Using scans directory: ', scansDir, ' from hardcoded default'));
-    disp('This usually indicates that we are in stand-alone mode without PROJECT or SCANS_DIR environment variables');
+    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
@@ -67,7 +76,7 @@ function varargout = EASYconsole(varargin)
       oldSuffix=easySuffix;
       while exist(easySuffix, 'dir')
         count=1;
-        easySuffix=strcat(oldSuffix,'.', num2str(count));
+        easySuffix=strcat(oldSuffix,'.',num2str(count));
       end
     end
     % Might as well check this too
@@ -89,9 +98,9 @@ function varargout = EASYconsole(varargin)
       disp("This is probably OK but if strange beahvior arises, we'll need to fix it in code");
       easyDir=EASY_DIR;
     end
-    disp(strcat('Using EASY script directory: ', easyDir, ' from environment variable EASY_DIR'));
+    disp(sprintf('Using EASY script directory: %s from environment variable EASY_DIR\n', easyDir));
   else
-    disp(strcat('Using EASY script directory: ', easyDir, ' from hardcoded default'));
+    disp(sprintf('Using EASY script directory: %s from hardcoded default\n', easyDir));
   end
 
   if exist('PROJECT_USER', 'var') && ~isempty(getenv('PROJECT_USER'))
@@ -102,23 +111,22 @@ function varargout = EASYconsole(varargin)
 
   if exist('EASY_RESULTS_DIR', 'var') && ~isempty(getenv('EASY_RESULTS_DIR'))
     easyResultsDir=fullfile(get_env('EASY_RESULTS_DIR'));
-    disp(strcat('Using output directory: ', easyResultsDir, ' from environment variable 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(strcat('Using output directory: ', PROJECT_PREFIX, ' from environment variable PROJECT_PREFIX'))
+    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(strcat('Using drug media file: ', masterPlateFile, ' from environment variable 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(strcat('Using drug media file: ', masterPlateFile, ' from internal logic'))
+      disp(sprintf('Using drug media file: %s from internal logic\n', masterPlateFile))
     else
       disp("WARNING: Have you created a MasterPlate_ file?")
     end
@@ -126,13 +134,13 @@ function varargout = EASYconsole(varargin)
 
   if exist('DRUG_MEDIA_FILE', 'var') && ~isempty(getenv('DRUG_MEDIA_FILE'))
     drugMediaFile=fullfile(get_env('DRUG_MEDIA_FILE'));
-    disp(strcat('Using drug media file: ', drugMediaFile, ' from environment variable 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(strcat('Using drug media file: ', drugMediaFile, ' from internal logic'))
+      disp(sprintf('Using drug media file: %s from internal logic\n', drugMediaFile))
     else
       disp("WARNING: Have you created a DrugMedia_ file?")
     end
@@ -167,7 +175,7 @@ function varargout = EASYconsole(varargin)
   % 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',strcat('EASYconsole - ',char(scansDir)));
+    set(fhconsole,'Name',sprintf('EASYconsole - %s', scansDir));
   else
     set(fhconsole,'Name','EASYconsole - No Active Experiment.')
   end
@@ -311,14 +319,14 @@ function NewExpDat_Callback(~, ~, ~)
     sbdg= cell(1,scanMax); 
     save((fullfile(easyResultsDir,'Fotos','Nbdg')),'sbdg'); 
   catch ME
-    disp(strcat('ERROR: ', ME.message))
+    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',strcat('EASYconsole- ',char(easyResultsDir)))
+    set(fhconsole,'Name',sprintf('EASYconsole - %s', easyResultsDir));
   else
-    set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.')
+    set(fhconsole,'Name','EASYconsole - Master Plate directory not selected.');
   end
 end
 
@@ -385,9 +393,9 @@ function LoadDatFile_Callback(~, ~, ~)
 
   if exist('easyResultsDir','var') && ~isempty(easyResultsDir)
     fhconsole=gcf;
-    set(fhconsole,'Name',strcat('EASYconsole- ',char(easyResultsDir)))
+    set(fhconsole,'Name',sprintf('EASYconsole - %s', easyResultsDir));
   else
-    set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.')
+    set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.');
   end
 end
 
@@ -447,7 +455,7 @@ function runResults_DBcombo_Callback(~, ~, ~)
     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(strcat('Error in DgenResults240430: ', ME.message))
+    disp(sprintf('Error in DgenResults: %s\n', ME.message));
     EASYconsole
   end
 end
diff --git a/workflow/templates/easy/NCsingleDisplay.m b/workflow/templates/easy/NCsingleDisplay.m
index eac3c845..e0e71aff 100755
--- a/workflow/templates/easy/NCsingleDisplay.m
+++ b/workflow/templates/easy/NCsingleDisplay.m
@@ -39,14 +39,14 @@ for iPlate=1:length(scLst)
   catch
   end
   hold on;
-  title(strcat(filenameNoExt,''));
+  title(filenameNoExt); % this didn't make sense so changed
   xlabel('Hours');
   ylabel('Intensities Normalized by Area');
   grid on;
   if (exist('K','var')&& exist('r','var') && exist('l','var'))
     plot(t, Growth,'b-');
     % Plot L on curvefit figure
-    grL=Growth(round(l)); %growthCurve timePT for l in hours 
+    grL=Growth(round(l)); % growthCurve timePT for l in hours 
     plot(l,0:grL,'-b') % to display position of l 
     plot(l,grL,'^b') % to display l position on curve as an arrowhead
 
diff --git a/workflow/templates/easy/NImParamRadiusGui.m b/workflow/templates/easy/NImParamRadiusGui.m
index 09a79b0a..a096e980 100755
--- a/workflow/templates/easy/NImParamRadiusGui.m
+++ b/workflow/templates/easy/NImParamRadiusGui.m
@@ -1,7 +1,6 @@
 %% CALLED BY par4Gbl_Main8c.m %%
 % TODO Should some of these vars be pulled out higher so they are easier to change?
 %
-
 function NImParamRadiusGui(scansDir)
   global SWsingleSc
   global SWgrowthArea
diff --git a/workflow/templates/easy/par4Gbl_Main8c.m b/workflow/templates/easy/par4Gbl_Main8c.m
index 02b5b2a4..ddcf85f9 100755
--- a/workflow/templates/easy/par4Gbl_Main8c.m
+++ b/workflow/templates/easy/par4Gbl_Main8c.m
@@ -7,6 +7,7 @@ global scansDir
 global matFile
 global fhconsole
 global easyResultsDir
+global printResultsDir
 global pointMapsResultsDir
 global fotosResultsDir
 global matDir
@@ -17,6 +18,7 @@ global numCols
 global scan
 global scanMax
 global tptLength
+global easyDir
 
 numRows=24; % for Single Vertical 
 numCols=16; % for Single Vertical 
@@ -34,10 +36,10 @@ Fflg=1;
 % fclose('all');  % close all open files
 
 % Unset some vars just in case they are already set
-clear('scanIntens','Scanfiles','pathname','tifFileLstP4')
+clear('scanIntens','Scanfiles','pathname','tifFileLstP4');
 
 try
-  clf(fhconsole,'reset')
+  clf(fhconsole,'reset');
 catch
 end
 
@@ -46,42 +48,32 @@ end
 % EASYconsole
 
 if exist(matFile, 'file')
-  bkUpMatFile=fullfile(matDir,'BkUp',matFile)
-  copyfile(matFile,(fullfile(matDir,'BkUp',matFile)))
+  bkUpMatFile=fullfile(matDir,'BkUp',matFile);
+  copyfile(matFile,bkUpMatFile);
 end
 
+% Reloacated from 'PTmats' to prevent potential overwrite when PTmats is
+% copied into new job when the PT template is about the same.  We also
+% now have a default template if one is not made. i.e., when the images
+% from the new experiment are too sketchy to make a good pintool
+% template. By moving it to 'Fotos' we avoid possible issues due to
+% copying the Nbdg.mat file along with the default template '.mat' files.
+% A copy of Ndbg.mat is placed also saved to the 'PTmats' directory
+% after each run to allow previous version of EASY to access data made
+% by EASY versions after 20_0819.
 try
-  load(fullfile(easyResultsDir,'Fotos','Nbdg')) %Modified to load from 'Fotos' 20_0819
+  load(fullfile(fotosResultsDir,'Nbdg')); %Modified to load from 'Fotos' 20_0819
 catch
-  % Reloacated from 'PTmats' to prevent potential overwrite when PTmats is
-  % copied into new job when the PT template is about the same.  We also
-  % now have a default template if one is not made. i.e., when the images
-  % from the new experiment are too sketchy to make a good pintool
-  % template. By moving it to 'Fotos' we avoid possible issues due to
-  % copying the Nbdg.mat file along with the default template '.mat' files.
-  % A copy of Ndbg.mat is placed also saved to the 'PTmats' directory
-  % after each run to allow previous version of EASY to access data made
-  % by EASY versions after 20_0819.
-  load(fullfile(easyResultsDir,'PTmats','Nbdg')) %Left in to accomodate loads of work before 20_0819
+  load(fullfile(pointMapsResultsDir,'Nbdg')); %Left in to accomodate loads of work before 20_0819
 end
 % Load Fotos stored data
-try
-  load(fullfile(easyResultsDir,'Fotos','Coordinates'))
-catch
-end
-try
-  load(fullfile(easyResultsDir,'Fotos','BGatTpts'))
-catch
-end
-try
-  load(fullfile(easyResultsDir,'Fotos','anlZones'))
-catch
-end
-% autoImCF
-try
-  load(fullfile(easyResultsDir,'PTmats','NCFparms'))    
-catch ME
-  load parameters   
+fotosToLoad = {'Coordinates', 'BGatTpts', 'anlZones', 'NCFparms'};
+for i = 1:length(fotosToLoad)
+  try
+    load(fullfile(fotosResultsDir, fotosToLoad{i}));
+  catch
+    load(fullfile(easyDir,'parameters'));
+  end
 end
 
 % Get Print Times
@@ -89,12 +81,12 @@ PrintTimes=[];
 scLst={};
 
 % Parameter Entry
-NImParamRadiusGui(scansDir) % Ncode 122111replaced removed  ,numOfPrtTimes)
+NImParamRadiusGui(scansDir); % Ncode 122111replaced removed  ,numOfPrtTimes)
 width=24;
 widthEx=width-1; % width extention from reference point
 dither=ImParMat(6);
 radius=ImParMat(10);
-NIcircle
+NIcircle;
 
 % Load Stuff
 lastPlateOnLastScan=1; % Ncode
@@ -118,7 +110,7 @@ else
 end
 
 SWgrowthArea=ImParMat(9);
-load(fullfile(pointMapsResultsDir,'NPTmapSearch'))
+load(fullfile(pointMapsResultsDir,'NPTmapSearch'));
 PTmapPos=detPos;
 selScanNumLst=[];
 Scanfiles=[];
@@ -157,10 +149,10 @@ selScanNumLst2=selScanNumLst; % function passthrough, passback to par4gbl_Main 2
 
 % Preallocation
 scCount=[];
-TmpexpScanIntens00=cell(1);  % cell(1,scanMax);
-TmpFexpScanSpots00=cell(1);  % cell(1,scanMax);
-TmpFexpScanBMtp00=cell(1);  % cell(1,scanMax);
-TmpanlZoneRefs00=cell(1);  % cell(1,scanMax);
+TmpexpScanIntens00=cell(1); % cell(1,scanMax);
+TmpFexpScanSpots00=cell(1); % cell(1,scanMax);
+TmpFexpScanBMtp00=cell(1); % cell(1,scanMax);
+TmpanlZoneRefs00=cell(1); % cell(1,scanMax);
 Tmpsbdg00=cell(1); 
 TmpexpScanIntens4=cell(1,numScans);
 TmpFexpScanSpots4=cell(1,numScans);
@@ -230,9 +222,9 @@ fileExt='.txt';
 filePrefix='FitResults_';
 for scanCnt=1:numScans
   selScan=p4L4{16,scanCnt}; % determine the actual scan in the scanCnt parfor distributed "id"
-  fileSuffix=strcat('Scan', num2str(selScan),'_Plate', num2str(1));
+  fileSuffix=sprintf('Scan%d_Plate%d', selScan, 1);
   fileNamePlate=[filePrefix fileSuffix fileExt];
-  fileName=fullfile(easyResultsDir,'PrintResults', fileNamePlate); % [outputDirectory fileNamePlate];
+  fileName=fullfile(printResultsDir, fileNamePlate); % [outputDirectory fileNamePlate];
 
   % This,fprint for loop,is an very old legacy feature which slows processing. Could be
   % removed but allows easy observation of how a run is progressing and can be
@@ -241,7 +233,7 @@ for scanCnt=1:numScans
 
   fid=fopen(fileName,'w');
   fprintf(fid, 'Num.\tAUC\tMSR\tK\tr\tl\tR-squared\tK-lower\tK-upper\tr-lower\tr-upper\tl-upper\tl-lower\tArea\tLastInten\tSpineMaxRateTimePt\tLastFitTimePt\n');
-  for n=1:384   % startCount:numCultures
+  for n=1:384 % startCount:numCultures
     fprintf(fid,'%d\t',n);
     fprintf(fid, '%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\n',...
     outCprint{14,scanCnt}(n,1),outCprint{14,scanCnt}(n,2),outCprint{14,scanCnt}(n,3),outCprint{14,scanCnt}(n,4),...