EASY refactor: First attempt

2024-07-27 02:58:49 -04:00
parent 5269962927
commit bce30095aa
11 changed files with 340 additions and 301 deletions
--- a/workflow/script-run-workflow
+++ b/workflow/script-run-workflow
@@ -357,10 +357,6 @@ init_project() {
  
  ask "Initialize a project at $SCANS_DIR?" || return 1

-  [[ -d $SCANS_DIR/MasterPlateFiles ]] || mkdir -p "$SCANS_DIR/MasterPlateFiles"
-
-  DRUG_MEDIA_FILE="$SCANS_DIR/MasterPlateFiles/DrugMedia_$PROJECT.xls"
-  MASTER_PLATE_FILE="$SCANS_DIR/MasterPlateFiles/MasterPlate_$PROJECT.xls"

  # Write skeleton files in csv
  # If we have to convert to xlsx later, so be it
@@ -379,17 +375,7 @@ init_project() {
  # TODO here we'll copy scan from robot but for now let's pause and wait for transfer
  read -r -p "Hit <Enter> to continue: "

-  # Refactor some of the EASY fs code into here
-  # Make EASY directories
-  results_dir="Results$DATE-$PROJECT_SUFFIX"
-  mkdir "$results_dir"
-  dirs=('PrintResults' 'CFfigs' 'Fotos' 'Fotos/BkUp' 'matResults')
-  for d in "${dirs[@]}"; do
-    mkdir "$results_dir/$d"
-  done

-  # Copy templates
-  rsync -a "$EASY_TEMPLATE_DIR"/{figs,Ptmats} "$results_dir"


 }
@@ -533,19 +519,57 @@ easy() {
 		'NoGrowth_.txt', and 'GrowthOnly_.txt' files will be generated in the 'PrintResults' folder. 
 	EOF

-  script="$EASY_TEMPLATE_DIR/EASYConsole.m"
+  script="$EASY_DIR/EASYConsole.m"
+
+  # Copy templates
  
  # Add EASY directory to the Matlab path
  # If this does not work we can try changing the -sd argument and if that fails then pushing/popping
  debug "Adding EASY directory to the Matlab path"
  hash matlab &>/dev/null && 
-    matlab -nodisplay -nosplash -nodesktop -nojvm -batch "addpath('$EASY_TEMPLATE_DIR')"
+    matlab -nodisplay -nosplash -nodesktop -nojvm -batch "addpath('$EASY_DIR')"

  # Ask the user to launch EASYconsole.m in MATLAB
  # MATLAB doesn't support passing args to scripts se we have to use ENV VARS instead
-  # These are proably already set in our scope but be explicit just in case
-  ! ((YES)) && ask "Start EASY in MATLAB? This requires a GUI." &&
-    SCANS_DIR="$SCANS_DIR" matlab -nosplash -sd "$SCANS_DIR" -r "run $script"
+  # These are proably already set in our scope but be explicit just in case so we don't have to export?
+  # TODO will need to play with the -sd startup option to see what works (well)
+  # Skip this step altogether in auto mode since it requires graphical interaction
+  if ! ((YES)) && ask "Start EASY in MATLAB? This requires a GUI."; then
+    export SCANS_DIR PROJECT_DATE EASY_DIR PROJECT_USER PROJECT_PREFIX EASY_SUFFIX EASY_RESULTS_DIR MASTER_PLATE_FILE DRUG_MEDIA_FILE
+    echo "Hit enter to use the default EASY results directory $SCANS_DIR/Results_${PROJECT_PREFIX}_($PROJECT_SUFFIX)"
+    (( YES )) || read -r -p "Or enter a custom suffix: " suffix
+    EASY_RESULTS_DIR="$SCANS_DIR/Results_${PROJECT_PREFIX}_${Ssuffix:-$PROJECT_SUFFIX}"
+    while [[ -d $EASY_RESULTS_DIR ]]; do
+      count=1
+      if [[ $count -eq 1 ]] && ask "$EASY_RESULTS_DIR already exists, increment dir name (y) or overwrite (N)?"; then
+        EASY_SUFFIX="${Ssuffix:-$PROJECT_SUFFIX}.$((count++))"
+        EASY_RESULTS_DIR="$SCANS_DIR/Results_${PROJECT_PREFIX}_${EASY_SUFFIX}"
+      else
+        EASY_SUFFIX=${suffix:-$PROJECT_SUFFIX}
+      fi
+    done
+    EASY_SUFFIX=${EASY_SUFFIX:-$suffix:-$PROJECT_SUFFIX}
+    EASY_RESULTS_DIR="$SCANS_DIR/Results_${PROJECT_PREFIX}_${EASY_SUFFIX}"
+    [[ -d $SCANS_DIR/MasterPlateFiles ]] || mkdir -p "$SCANS_DIR/MasterPlateFiles"
+    DRUG_MEDIA_FILE="$SCANS_DIR/MasterPlateFiles/DrugMedia_$PROJECT.xls"
+    MASTER_PLATE_FILE="$SCANS_DIR/MasterPlateFiles/MasterPlate_$PROJECT.xls"
+
+    # Make EASY dirs
+    debug "mkdir -p $EASY_RESULTS_DIR"
+    mkdir -p "$EASY_RESULTS_DIR"
+    dirs=('PrintResults' 'CFfigs' 'Fotos' 'Fotos/BkUp' 'matResults')
+    for d in "${dirs[@]}"; do
+      mkdir "$EASY_RESULTS_DIR/$d"
+    done
+
+    # Copy templates
+    rsync -a "$EASY_DIR"/{figs,Ptmats} "$EASY_RESULTS_DIR"
+
+    # Launch matlab
+    matlab -nosplash -r "run $script"
+    # matlab -nosplash -sd "$SCANS_DIR" -r "run $script"
+  
+  fi

  # Use the function return code see if we succeeded
  get_easy_results "$SCANS_DIR" || return 1
@@ -1379,14 +1403,15 @@ main() {
  # Templates
  QHTCP_TEMPLATE_DIR="$SCRIPT_DIR/templates/qhtcp"
  STUDY_TEMPLATE_DIR="$QHTCP_TEMPLATE_DIR/ExpTemplate"
-  EASY_TEMPLATE_DIR="$SCRIPT_DIR/templates/easy"
+  EASY_DIR="$SCRIPT_DIR/templates/easy"
  IMAGES="${IMAGES:-"/mnt/data/ExpJobs"}" 

-  DATE="$(date +%y_%m%d)"
+  DATE="$(date +%Y%m%d)" # change general date format here 

  # Set the automatic project directory prefix
-  PROJECT_PREFIX="${DATE}_$(whoami)_" # reversed these so easier to sort and parse date
-  san() { [[ $1 =~ [0-9][0-9]_[0-9][0-9]_[0-9][0-9]_.+_.+ ]]; } # sanitizer regex for prefix
+  PROJECT_USER="$(whoami)"
+  PROJECT_PREFIX="${DATE}_${PROJECT_USER}_" # reversed these so easier to sort and parse date
+  san() { [[ $1 =~ [0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9]_.+_.+ ]]; } # sanitizer regex for prefix
  
  declare -ag PROJECTS=() # this array will hold all of the projects for this run

@@ -1441,9 +1466,9 @@ main() {
  # Loop over projects
  for PROJECT in "${PROJECTS[@]}"; do 
    SCANS_DIR="$IMAGES/$PROJECT"
-    PROJECT_DATE="${PROJECT%"${PROJECT#??_????}"}" # e.g. 24_0723
-    PROJECT_SUFFIX="${PROJECT#??_????_*_}"
-    PROJECT_USER="${PROJECT#??_????_}"
+    PROJECT_DATE="${PROJECT%"${PROJECT#????????}"}" # e.g. 20240723
+    PROJECT_SUFFIX="${PROJECT#????????_*_}"
+    PROJECT_USER="${PROJECT#????????_}"
    PROJECT_USER="${PROJECT_USER%%_*}"
    # Run selected modules
    for m in "${MODULES[@]}"; do
--- a/workflow/templates/easy/DMPexcel2mat.m
+++ b/workflow/templates/easy/DMPexcel2mat.m
@@ -26,7 +26,7 @@ if ~exist(masterPlateFile, 'file') || isempty(masterPlateFile)
      sortedFiles=mpFiles(sortedIndices);
      masterPlateFile=sortedFiles{1};
      disp('Using newest MasterPlate file: ', masterPlateFile, ', skipping directory selection');
-    catch Me
+    catch ME
      % This can be silent, not really an error
    end

@@ -157,7 +157,7 @@ try
        MP(numb).specifics= ' ';
      end
      excLnNum=excLnNum+385;
-      msg=strcat('NumberOfMP = ',num2str(numb), 'lastLineNo. = ',num2str(excLnNum))
+      msg=strcat('NumberOfMP = ',num2str(numb), 'lastLineNo. = ',num2str(excLnNum));
    end
  end
 catch ME
@@ -173,7 +173,7 @@ numOfMedias=0;

 % Grabbing the bare filename from the MasterPlate file to see if we can automatically
 % find a matching DrugMedia file
-[mpFile, mpPath]=fullfile(masterPlateFile)
+[mpFile, mpPath]=fullfile(masterPlateFile);
 mpFileParts=strsplit(mpFile, '_');
 mpBareFileName=strjoin(parts(2:end-1), '_');

@@ -261,7 +261,7 @@ if isequal(Linked,1) % Drugs and Media are linked 1 to 1; else they are combinat
      DM.mod2(numb) = {raw(excLnNum,7)};
      DM.conc2(numb) = {raw(excLnNum,8)};
      excLnNum=excLnNum+1;
-      msg=strcat('NumberOf1:1DrugMediaPlates = ',num2str(numb), '   lastLineNo. = ',num2str(excLnNum))
+      msg=strcat('NumberOf1:1DrugMediaPlates = ',num2str(numb), '   lastLineNo. = ',num2str(excLnNum));
    end
  else
    clear DM
@@ -283,7 +283,7 @@ if isequal(Linked,1) % Drugs and Media are linked 1 to 1; else they are combinat
      DM.conc2(numb) = {DMtbl(excLnNum,8)};
      DM.conc2(numb)= table2cell(DM.conc2{numb});
      excLnNum=excLnNum+1;
-      msg=strcat('NumberOf1:1DrugMediaPlates = ',num2str(numb), '   lastLineNo. = ',num2str(excLnNum))
+      msg=strcat('NumberOf1:1DrugMediaPlates = ',num2str(numb), '   lastLineNo. = ',num2str(excLnNum));
    end
  end
 end
@@ -321,7 +321,7 @@ if isequal(Linked,0) % 0 indicates Drugs and Media are combinatorial
      excLnNum=excLnNum+1;
    end
  end
-  msg=strcat('NumberOfDrugs = ',num2str(drgCnt), '     NumberOfMedias = ',num2str(medCnt)  )
+  msg=strcat('NumberOfDrugs = ',num2str(drgCnt), '     NumberOfMedias = ',num2str(medCnt)  );
 end

 save(mpdmFile, 'fields','MP','DM','Linked');
--- a/workflow/templates/easy/EASYconsole.m
+++ b/workflow/templates/easy/EASYconsole.m
@@ -3,18 +3,25 @@
 % 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 fotosResultsDir
+  global figsResultsDir
+  global pointMapsResultsDir
+  global pointMapsFile
+  global printResultsDir
  global matDir
  global matFile
+  global drugMediaFile
+  global masterPlateFile
+  global mpdmFile
  global userName
+  global srchRange

  % Initialize some variables from matlab
-  startDir=pwd;
  easyPath=which(mfilename);
  [easyDir,easyFileName]=fileparts(easyPath);
  easyDir=fullfile(easyDir);
@@ -27,22 +34,27 @@ function varargout = EASYconsole(varargin)
  % 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')
+  if exist('PROJECT', 'env') && ~isempty(getenv('PROJECT'))
    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')
+  elseif exist('SCANS_DIR', 'env') && ~isempty(getenv('SCANS_DIR'))
    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
+    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 standalone mode');
+    disp('This usually indicates that we are in stand-alone mode');
  end

-  % If we don't have the EASY_SUFFIX from the module, generate it from scanDir
-  if exist('EASY_SUFFIX', 'env')
+  % If we don't have the EASY_SUFFIX from the module, generate it from scansDir
+  if exist('EASY_SUFFIX', 'env') && ~isempty(getenv('EASY_SUFFIX'))
    easySuffix=get_env('EASY_SUFFIX');
  else
    [dirName, ~]=fileparts(scansDir);
@@ -69,10 +81,11 @@ function varargout = EASYconsole(varargin)
  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')
+  if exist('EASY_DIR','env') && ~isempty(getenv('EASY_DIR'))
    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");
+      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
    disp(strcat('Using EASY script directory: ', easyDir, ' from environment variable EASY_DIR'));
@@ -80,12 +93,7 @@ function varargout = EASYconsole(varargin)
    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')
+  if exist('EASY_RESULTS_DIR', 'env') && ~isempty(getenv('EASY_RESULTS_DIR'))
    easyResultsDir=fullfile(get_env('EASY_RESULTS_DIR'));
    disp(strcat('Using project prefix: ', easyResultsDir, ' from environment variable EASY_RESULTS_DIR'))
  else
@@ -95,21 +103,73 @@ function varargout = EASYconsole(varargin)
    disp(strcat('Using project prefix: ', PROJECT_PREFIX, ' from environment variable PROJECT_PREFIX'))
  end

-  if exist('PROJECT_USER', 'env')
+  if exist('PROJECT_USER', 'env') && ~isempty(getenv('PROJECT_USER'))
    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'));
+  if exist('MASTER_PLATE_FILE', 'env') && ~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'))
+  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'))
+    else
+      disp("WARNING: Have you created a MasterPlate_ file?")
+    end
+  end

-  % Play around with making some common variables from our input data
-  % resDirName=fullfile(SCANS_DIR,'Results',dateStr,'_', PROJECT_SUFFIX);
-  % resDir=fullfile(SCANS_DIR,resDirName);
-  % ExpOutmat=fullfile(matDir,strcat(datestr(now,29),newExpfile));
-  % ExpPath=fullfile(newExppath);
-  % ExpFile=fullfile(matDir,)
+  if exist('DRUG_MEDIA_FILE', 'env') && ~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'))
+  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'))
+    else
+      disp("WARNING: Have you created a DrugMedia_ file?")
+    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')
+  CSearchRangeFile=fullfile(fotosResultsDir,'CSearchRange.mat');
+  mpdmFile=fullfile(matDir,'MPDM.mat');
+
+  % 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(CSearchRangeFile, 'file')
+    searchRangeNum=load(CSearchRangeFile);
+  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);
+
+  % 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)));
+  else
+    set(fhconsole,'Name','EASYconsole - No Active Experiment.')
+  end

  % GUI interface design
  gui_Singleton=1;
@@ -164,15 +224,6 @@ function EASYconsole_OpeningFcn(hObject, ~, handles, varargin)
  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',todayStr,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


@@ -200,7 +251,6 @@ end

 % New Experiment Button Interface
 function NewExpDat_Callback(~, ~, ~)
-  global SWnewExp
  global matDir
  global matFile
  global easyResultsDir
@@ -213,8 +263,6 @@ function NewExpDat_Callback(~, ~, ~)
  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_',todayStr,'_',userName,'_',inputFileName);

@@ -263,8 +311,7 @@ function NewExpDat_Callback(~, ~, ~)
    sbdg= cell(1,scanMax); 
    save((fullfile(easyResultsDir,'Fotos','Nbdg')),'sbdg'); 
  catch ME
-    % returnStartDir
-    disp('Error Creating a New Experiment')
+    disp(strcat('ERROR: ', ME.message))
  end

  % set the title for fhconsole depending on existence
@@ -278,39 +325,50 @@ 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,'..', '..');
+    point

+    % TODO this is pretty hacky and needs something more explicit
    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'));
+      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(easyResultsDir,'PTmats','ImParameters.mat'), 'file')
-        load(fullfile(easyResultsDir,'PTmats','ImParameters.mat'));
+      if exist(fullfile(pointMapsResultsDir,'ImParameters.mat'), 'file')
+        load(fullfile(pointMapsResultsDir,'ImParameters.mat'));
      else
-        load(fullfile(easyPath,'ImParameters.mat'));
+        try
+          load(fullfile(easyPath,'ImParameters.mat'));
+        catch
+          disp("Could not load the ImParameters.mat file")
+        end
      end  
    end

-    mkdir(fullfile(matDir,'BkUp'));
+    bkupDir=fullfile(matDir,'BkUp');
+    if ~exist(bkupDir, 'dir')
+      mkkdir(bkupDir);
+    end

    % Create supporting dirs
    dirs={'PrintResults', 'figs', 'CFfigs', 'PTmats', 'Fotos'}
@@ -333,8 +391,8 @@ function LoadDatFile_Callback(~, ~, ~)
  end
 end

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

@@ -378,8 +436,7 @@ end

 function runDMPexcel_Callback(~, ~, ~)
  try
-    % DMPexcel2mat_2024winLinix %DMPexcel2mat_2023winLinix
-    DMPexcel2mat % TODO Can't find above so using what I have available
+    DMPexcel2mat
  catch
    EASYconsole
  end
@@ -387,7 +444,7 @@ end

 function runResults_DBcombo_Callback(~, ~, ~)
  try
-    DgenResults240430 %similar but semicolons removed to restore so cmdLine display info.
+    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))
--- a/workflow/templates/easy/NCdisplayGui.m
+++ b/workflow/templates/easy/NCdisplayGui.m
@@ -1,5 +1,5 @@
 %% CALLED WHEN ACCESSING 'CurveFit Display' %%
-function [scLst, row, col] = NCdisplayGui(eDir)  %(ExpPath)
+function [scLst, row, col] = NCdisplayGui(scansDir)
  xPos=0.05;
  btnWid=0.10;
  btnHt=0.05;
@@ -49,7 +49,7 @@ function [scLst, row, col] = NCdisplayGui(eDir)  %(ExpPath)
  end

  % Read in numeric folder names
-  nlist=dir(fullfile(eDir,'*')); %(ExpPath,'*'));
+  nlist=dir(fullfile(scansDir,'*'));
  nnn=0;
  for n=1:size(nlist,1)
    if (~isempty(str2num(nlist(n).name)))
@@ -344,28 +344,28 @@ btnNumber=7;
   yPos=0.85-(btnNumber-1)*(btnHt+spacing);
   btnPos=[xPos yPos-spacing btnWid btnHt];
   try
-   CSrchRange=ImParMat(12);
-   CSrchRng=ImParMat(12)
+   srchRange=ImParMat(12);
+   searchRangeNum=ImParMat(12)
   catch  %Legacy default value was 18 before being made a user input variable (ImParMat(12)). A preferable value now might be 12 or 14.
-       CSrchRange=18;
+       srchRange=18;
       ImParMat(12)=18
-       CSrchRng=ImParMat(12)
+       searchRangeNum=ImParMat(12)
   end
   
   %{
   if size(scLst)>1
-      CSrchRange=ImParMat(12);
+      srchRange=ImParMat(12);
   else
      try
-         CSrchRange=CSearchRange(str2double(scLst))
+         srchRange=CSearchRange(str2double(scLst))
      catch
-          CSrchRange=ImParMat(12); 
+          srchRange=ImParMat(12); 
       end
   end
   %}
 hSearchRange = uicontrol(...
      'Style', 'edit',...
-      'String',CSrchRange,...
+      'String',srchRange,...
      'Units','normalized',...   
   	 'Position', btnPos,... 
     'callback',{@CsearchRange});  
@@ -376,7 +376,7 @@ hSearchRange = uicontrol(...
 	errordlg('You must enter a numeric value between 1 and 18 12->18 recommended. (ImParMat(12)))','Bad Input','modal')
 	return
    end
-    CSrchRng=user_entry
+    searchRangeNum=user_entry
        
 end

@@ -455,18 +455,4 @@ hedit = uicontrol(...
         end
 end
 %}
-%global SWsingleSc
-%global SWgrowthArea
-%global selScan
-%global scan
-%global scLst
-%global ImParMat
-%global CSearchRange
-%global CSrchRng
-%global defImParMat
-%global fhImRun
-%global fhconsole
-%global resDir
-%global ExpOutmat
-%global numRows;
-%global numCols;
+
--- a/workflow/templates/easy/NCfitImCFparforFailGbl2.m
+++ b/workflow/templates/easy/NCfitImCFparforFailGbl2.m
@@ -1,6 +1,6 @@
 %% CALLED BY par4GblFnc8c.m %%
 function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanIntensELr,par4scanCFparameters,par4scanCFdate,outC,outCstd]= ...
-  NCfitImCFparforFailGbl2(parMat,times, values, timeOffsets, fileSuffix, AUCfinalTime, ~, spotAreas, outputDirectory, ~,~, sols, ~)  %,scan)
+  NCfitImCFparforFailGbl2(parMat,times, values, timeOffsets, fileSuffix, AUCfinalTime, ~, spotAreas, printResultsDir, ~,~, sols, ~)  %,scan)

  % Preallocation for parfor loop
  st(1,1:size(times,2))=1111;
@@ -223,7 +223,7 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
  fileExt='.txt';
  filePrefix='FitResultsComplete_';
  fileNamePlate=[filePrefix fileSuffix fileExt];
-  fileName=fullfile(outputDirectory, fileNamePlate);  %[outputDirectory fileNamePlate];
+  fileName=fullfile(printResultsDir, fileNamePlate);  %[printResultsDir fileNamePlate];
  fid=fopen(fileName,'w');
  fprintf(fid, 'Fit Results Complete\n');
  %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');
--- a/workflow/templates/easy/NCsingleDisplay.m
+++ b/workflow/templates/easy/NCsingleDisplay.m
@@ -1,13 +1,10 @@
 %% CALLED WHEN ACCESSING 'CurveFit Display' %%
-global expDir
 global scLst
-global ExpPath
 global scan

-eDir=ExpPath;
 hf=figure;
 % Parameter Entry
-[scLst, row, col]=NCdisplayGui(eDir);  %(ExpPath); %Ncode 122111replaced removed  ,numOfPrtTimes)
+[scLst, row, col]=NCdisplayGui(scansDir);
 close(hf)
 selSpot=(row-1)*24 + col;
 for iPlate=1:length(scLst)
--- a/workflow/templates/easy/NImParamRadiusGui.m
+++ b/workflow/templates/easy/NImParamRadiusGui.m
@@ -1,29 +1,35 @@
 %% CALLED BY par4Gbl_Main8c.m %%
-function NImParamRadiusGui(expDir)
+% TODO Should some of these vars be pulled out higher so they are easier to change?
+%
+
+function NImParamRadiusGui(scansDir)
  global SWsingleSc
  global SWgrowthArea
-  %global selScan
  global scan
  global scLst
  global ImParMat
-  %global CSearchRange
-  global CSrchRng
+  global searchRangeNum
  global defImParMat
  global fhImRun
  global fhconsole
-  global resDir
-  global ExpOutmat
-  global numRows;
-  global numCols;
+  global easyResultsDir
+  global fotosResultsDir
+  global pointMapsResultsDir
+  global pointMapsFile
+  global matFile
+  global numRows
+  global numCols
  global scanSize
  global scanMax

-  defImParMat=[1, 1, 15, 34, 24, 1,0,0,1,14,1,18];  %Ncode ImRobot adaptation
+  % Ncode ImRobot adaptation
+  % TODO this code block and variables needs explanation
+  defImParMat=[1,1,15,34,24,1,0,0,1,14,1,18];  
  if ImParMat(3)==0 || ImParMat(4)==0 ||ImParMat(5)==0 || ImParMat(10)==0 ||ImParMat(11)==0 
    ImParMat=defImParMat;
  end
  if size(ImParMat,2)<12
-    ImParMat(12)=18; %Default before user input CsearchRange value
+    ImParMat(12)=18; % default before user input CsearchRange value
    msg='Data made before SearchRange user entry added (ImParMat(12). 18 was the set value and the current default.)';
  end
  % ImParMat=defImParMat; %Activate for INITIAL USE only
@@ -31,15 +37,17 @@ function NImParamRadiusGui(expDir)
  destPerMP=1;
  selScan=1;
  SWgrowthArea=1;
-  if exist(fullfile(resDir,'PTmats','NImParameters.mat'))
-    load(fullfile(resDir,'PTmats','NImParameters'));
+
+  if exist(pointMapsFile)
+    load(pointMapsFile);
  else
-    load NImParameters
+    load(fullfile(PTmats,'NImParameters')) % hardcoded default
+    disp('WARNING: Using hardcoded NImParameters.mat')
  end
-  ImParMat;
-  %if ~exist('CSearchRange','var') || isempty(CSearchRange)
-  if ~isequal(exist(fullfile(resDir,'Fotos','CSearchRange.mat')),0)
-    load(fullfile(resDir,'Fotos','CSearchRange'))
+  ImParMat
+  % if ~exist('searchRangeNum','var') || isempty(searchRangeNum)
+  if exist(CSearchRangeFile), 'file')
+    load(CSearchRangeFile);
    CSearchRange;
  end
      
@@ -54,9 +62,9 @@ function NImParamRadiusGui(expDir)
  yPos=0.85-(btnNumber-1)*(btnHt+spacing);
  btnPos=[xPos yPos-spacing btnWid btnHt];
  fhImParm=gcf;
-  if exist('resDir','var')&& ~isempty(resDir)
+  if exist('easyResultsDir','var')&& ~isempty(easyResultsDir)
    set(fhImParm,'NumberTitle','off')
-    set(fhImParm,'Name',strcat('ImageAnalysis- ',char(resDir)))
+    set(fhImParm,'Name',strcat('ImageAnalysis- ',char(easyResultsDir)))
  else
    set(fhImParm,'NumberTitle','off')
    set(fhImParm,'Name','EASYconsole -Exp. Analysis NOT selected.')
@@ -110,32 +118,30 @@ function NImParamRadiusGui(expDir)
  yPos=0.85-(btnNumber-1)*(btnHt+spacing);
  btnPos=[xPos yPos-spacing btnWid btnHt];
  try
-    CSrchRange=ImParMat(12);
-    CSrchRng=ImParMat(12);
-  catch  %Legacy default value was 18 before being made a user input variable (ImParMat(12)). A preferable value now might be 12 or 14.
-    CSrchRange=18;
+    srchRange=ImParMat(12);
+  catch  % Legacy default value was 18 before being made a user input variable (ImParMat(12)). A preferable value now might be 12 or 14.
+    srchRange=18;
    ImParMat(12)=18;
-    CSrchRng=ImParMat(12);
  end
    
  hSearchRange=uicontrol(...
    'Style', 'edit',...
-    'String',CSrchRange,...
+    'Value',searchRangeNum,...
    'Units','normalized',...   
    'Position', btnPos,... 
-    'callback',{@CsearchRange});  
+    'callback',{@searchRangeCallback});  

-  function CsearchRange(source,~)
+  function searchRangeCallback(source,~)
    user_entry=str2double(get(source,'string'));
    if (isnan(user_entry)||(user_entry<1)||(user_entry>50))  %originally 18; 19_0729 increased
      errordlg('You must enter a numeric value between 1 and 18 12->18 recommended. (ImParMat(12)))','Bad Input','modal')
      return
    end
-    CSrchRng=user_entry;      
+    searchRangeNum=user_entry;  
  end

  % Ncode 12_0120 for reading in numeric folder names
-  nlist=dir(fullfile(expDir,'*'));
+  nlist=dir(fullfile(scansDir,'*'));
  nnn=0;
  for n=1:size(nlist,1)
    if (~isempty(str2num(nlist(n).name)))
@@ -158,8 +164,7 @@ function NImParamRadiusGui(expDir)
    'callback',{@load_listbox});  %'uiresume(gcbf)'); 'Position', [5 100 60 20])
  
  function load_listbox(source,~)
-    %global CSrchRng
-    %global CSrearchRange
+    global 
    userIndx=(get(source,'value'));
    userStr=(get(source,'string'));
    %scLstIndx=str2num(char(strrep(userStr(userIndx), 'Scan', '')))
@@ -167,11 +172,11 @@ function NImParamRadiusGui(expDir)
    user_entry=userStr(userIndx);
    scLst=user_entry;
    if size(scLst,1)>1
-      %CSrchRng=num2str(ImParMat(12))
+      % searchRangeNum=num2str(ImParMat(12))
      set(hSearchRange,'string',num2str(ImParMat(12)))
    else
      try
-        CSrchRng=CSearchRange(str2double(scLst));
+        searchRangeNum=CSearchRange(str2double(scLst));
        set(hSearchRange,'string',CSearchRange(str2double(scLst)))
      catch
        % CSrchRng=num2str(ImParMat(12))
@@ -231,16 +236,10 @@ function NImParamRadiusGui(expDir)
  end    
    
  ImParMat;
-  CSearchRange;
-  try
-    save('NImParameters','ImParMat')
-    % save('CSearchRange','CSearchRange')
-  catch
-    save(fullfile('\','NImParameters'),'ImParMat')
-    % save(fullfile('\','CSearchRange'),'CSearchRange')
-  end
-  save((fullfile(resDir,'PTmats','NImParameters')), 'ImParMat');
-  save((fullfile(resDir,'Fotos','CSearchRange')),'CSearchRange');
+  searchRangeNum;
+
+  save(pointMapsFile, 'ImParMat');
+  save(CSearchRangeFile,'searchRangeNum');

  close
  return
--- a/workflow/templates/easy/NIscanIntensBGpar4GblFnc.m
+++ b/workflow/templates/easy/NIscanIntensBGpar4GblFnc.m
@@ -1,10 +1,12 @@
 %% CALLED BY par4GblFnc8c.m %%
 function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2, TmpFexpScanSpots2, TmpFexpScanBMtp2, TmpanlZoneRefs2,areaOfIntensAboveBG]= ...
    NIscanIntensBGpar4GblFnc(Fflg, tifFileLst, ImParMat,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,numRows,numCols,ImHeigth,ImWidth,cirMask, ...
-    tptLength,selScan,Empsc,~, ~, ~, ~,resDir, Tmpsbdg1)    
+    tptLength,selScan,Empsc,~, ~, ~, ~,easyResultsDir, Tmpsbdg1)    

-  global ExpOutmat
+  global matFile
  global CSrchRng
+  global figsResultsDir
+  global fotosResultsDir

  searchIntens=[]; intensMax=[]; detMaxPos=[]; scIntens=[]; areaOfIntensAboveBG=[]; BkgrdMat=[];

@@ -33,7 +35,8 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
        PTmapOnesDbl(PTrefPtR:(PTrefPtR+(diaExt-1)),PTrefPtC:(PTrefPtC+(diaExt-1)))=optCirMask; 
      end
    end
-  end  %if Fflg==1
+  end
+
  % Zeroth Initial Search Parameters
  rRangeUpper=-12; 
  rRangeLower=12;
@@ -73,11 +76,12 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
  intensPrev=zeros(24,16);
  cent=cell(24,16);
  BGTav=zeros(numRows,numCols);
-  BGthres(1:numRows,1:numCols)=95; %70;before incr.to95 to accommodate dark media %50forEpson;%Initialize for first tPt run *****************************************************<<
-  if length(tifFileLst) >2
-    %******Determine a good Plate Image from all the timepoints to use for Registration
-    %Plate Intensity curve over time points
-    %clear plateImage
+  % 7 0;before incr.to95 to accommodate dark media %50forEpson;%Initialize for first tPt run
+  BGthres(1:numRows,1:numCols)=95;
+  if length(tifFileLst)>2
+    % Determine a good Plate Image from all the timepoints to use for Registration
+    % Plate Intensity curve over time points
+    % clear plateImage
    plateImage={};
    %{
    % Version compatability fixes
@@ -517,8 +521,8 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
  % NIgenBkGrdDataPar4Fnc(ImParMat, tifFileLst, lastDetMaxPos, numRows, numCols, fullsc, tPt, BGthres, doCircle, cirPixA, diaExt, cirMask, BGTav)
  % Called by NIscanIntensBG.m
  
-  % global resDir
-  global ExpOutmat
+  % global easyResultsDir
+  global matFile
  % global pixsAboveBG
  MPnum=ImParMat(1);
  destPerMP=ImParMat(2);
@@ -1146,24 +1150,23 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
    title(strcat('Scan',num2str(selScan),'timePt-',num2str(tPt)));
    clf(hfscanIm,'reset');
    set(hfIm,'NumberTitle','off')
-    set(hfIm,'Name', char(ExpOutmat)) % strcat('EASYconsole- ',char(resDir)))
+    set(hfIm,'Name', char(matFile)) % strcat('EASYconsole- ',char(easyResultsDir)))
    if Fflg==1
-      resDir;  % for debugging
-      fullfile(resDir,'Fotos',strcat('Scan',num2str(selScan),'_timePt-',num2str(tPt)))  
-      hgsave(fullfile(resDir,'Fotos',strcat('Scan',num2str(selScan),'_timePt-',num2str(tPt)))); %F 14_0626 
+      fullfile(fotosResultsDir,strcat('Scan',num2str(selScan),'_timePt-',num2str(tPt)))  
+      hgsave(fullfile(fotosResultsDir,strcat('Scan',num2str(selScan),'_timePt-',num2str(tPt)))); %F 14_0626 
    else
-      hgsave(fullfile(resDir,'figs',strcat('Scan',num2str(selScan),'_timePt-',num2str(tPt))));
+      hgsave(fullfile(figsResultsDir,strcat('Scan',num2str(selScan),'_timePt-',num2str(tPt))));
    end
  else
    selScan;
-    %tifFile
+    % tifFile
  end

  BkgrdMat=totBkgrd; % BkgrdMat(:,:,tPt)=totBkgrd;  %debug parfor effort
  areaOfIntensAboveBG(:,:,tPt)=pixsAboveBG; % actual area of growth for each timepoint  (used for printout of grArea ?not used in previous analysis)
  scanIntens(:,:,tPt)=intens-BkgrdMat;

-  % capture first and last background values
+  % Capture first and last background values
  if tPt==1
    bdg(:,:,1)=bmm;  
    bdg(:,:,3)=rwm;
--- a/workflow/templates/easy/p4loop8c.m
+++ b/workflow/templates/easy/p4loop8c.m
@@ -3,7 +3,7 @@ function[p4L4,...
 TmpexpScanIntens4,TmpFexpScanSpots4,TmpFexpScanBMtp4,TmpanlZoneRefs4,Tmpsbdg4]= ...
    p4loop8c(parMat,tptLength,numScans,selScanNumLst,SWsingleSc,Fflg,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,cirMask,width, ... 
    TmpexpScanIntens00,TmpFexpScanSpots00,TmpFexpScanBMtp00,TmpanlZoneRefs00,~,tifFileLstP4,pathname,ImParMat, ...
-    numRows,numCols,scLst,resDir,expDir, p4L00,TmpexpScanIntens4,TmpFexpScanSpots4,TmpFexpScanBMtp4,TmpanlZoneRefs4, Tmpsbdg00, Tmpsbdg4)
+    numRows,numCols,scLst,easyResultsDir,scansDir, p4L00,TmpexpScanIntens4,TmpFexpScanSpots4,TmpFexpScanBMtp4,TmpanlZoneRefs4, Tmpsbdg00, Tmpsbdg4)
 p4L0=p4L00;
 TmpexpScanIntens0=TmpexpScanIntens00;
 TmpFexpScanSpots0=TmpFexpScanSpots00;
@@ -15,7 +15,7 @@ Tmpsbdg0= Tmpsbdg00;
 if SWsingleSc==1
  parforArg=0;
 else
-  parforArg= inf;
+  parforArg=inf;
 end

 % for (scCount=1:numScans)
@@ -25,7 +25,7 @@ parfor (scCount=1:numScans,parforArg)
  [p4L3,TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneRefs3,Tmpsbdg3]= ...
  par4GblFnc8c(parMat,tptLength,numScans,selScanNumLst,SWsingleSc,Fflg,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,cirMask,width, ... 
  TmpexpScanIntens0,TmpFexpScanSpots0,TmpFexpScanBMtp0,TmpanlZoneRefs0,scCount,tifFileLstP4,pathname,ImParMat, ...
-  numRows,numCols, scLst,resDir,expDir, p4L0,Tmpsbdg0);
+  numRows,numCols, scLst,easyResultsDir,scansDir, p4L0,Tmpsbdg0);

  p4L4(:,scCount)=p4L3; % (:,scCount);
  TmpexpScanIntens4(scCount)=TmpexpScanIntens3;
--- a/workflow/templates/easy/par4GblFnc8c.m
+++ b/workflow/templates/easy/par4GblFnc8c.m
@@ -2,11 +2,13 @@
 function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneRefs3,Tmpsbdg3]= ...
  par4GblFnc8c(parMat,tptLength,~,selScanNumLst,~,Fflg,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,cirMask,~,...
  TmpexpScanIntens,TmpFexpScanSpots,TmpFexpScanBMtp,TmpanlZoneRefs,scCount,tifFileLstP4,~,ImParMat, ...
-  numRows,numCols,scLst,resDir,expDir,~, Tmpsbdg)
+  numRows,numCols,scLst,easyResultsDir,scansDir,~, Tmpsbdg)
+
+  global printResultsDir

  selScan=selScanNumLst(scCount);
  tptLength0=length(tifFileLstP4{scCount});  
-  %tptLength=numFiles;
+  % tptLength=numFiles;
  tifFileLst={tifFileLstP4(scCount)}; 
      
  % Extract the Imaging time stamps from selected tif files
@@ -21,13 +23,13 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
    scLst;
    scLst(scCount)
    char(scLst(scCount))
-    char(fullfile(expDir,char(scLst(scCount))))
-    expDir;
+    char(fullfile(scansDir,char(scLst(scCount))))
+    scansDir;
    swCatch=0;
    nndx=nndx+1;
-    tifFile=char(fullfile(expDir,char(scLst(scCount)), tifFileLstP4{scCount}(tPt)));
+    tifFile=char(fullfile(scansDir,char(scLst(scCount)), tifFileLstP4{scCount}(tPt)));
    try
-      info=imfinfo(tifFile);  %('D:\jwrDevel\DevelCurveFittingJWR\ImageScans\Scan2\020hr002.tif')
+      info=imfinfo(tifFile);  % D:\jwrDevel\DevelCurveFittingJWR\ImageScans\Scan2\020hr002.tif
    catch ME 
      % Note: During parallel operation Matlab will not open file (fid)
      % etc. Therefore error message text will not be written.The only way
@@ -35,30 +37,31 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
      % the ..Main8c script outside the parfor loop and print to file from
      % there.  Consequently for now it only prints error to file when one
      % edits p4loop8c.m from 'parfor' to ordinary 'for' loop
-      fFail=((fullfile(resDir,'PrintResults','ImageFileReadFailure.txt')));  
+      fFail=((fullfile(printResultsDir,'ImageFileReadFailure.txt')));  
      fid=fopen(fFail,'a'); %create,open and append
-      %fprintf(fid,'%s \n',char(tifFile))
+      % fprintf(fid,'%s \n',char(tifFile))
      fclose(fid)
      nndx=nndx-1;
      swCatch=1;
      rep=getReport(ME, 'basic');
      rep=strcat('Read info failure for-',tifFile,' -', rep);
-      %fprintf(fid,'%s \n',rep) %See Note:    
+      % fprintf(fid,'%s \n',rep) %See Note:    
    end
    tptLength=nndx;
    scTmNumeric=1;  %initialize for parfor 
    if swCatch==0
      scTmNumeric(nndx)=datenum(info.FileModDate);
      e(nndx,:)={tifFile, scTmNumeric(nndx)};
-      %newtifFileLst(nndx)=tifFileLst(tPt);
+      % newtifFileLst(nndx)=tifFileLst(tPt);
    end
  end

-  % clear tifFileLst;
+  % Clear tifFileLst;
  tifFileLst=cell(nndx,1);
  f={sortrows(e,2)};
  tifFileLst=f{1,1}(:,1);
  areaOfIntensAboveBG=zeros(24,16,length(tifFileLst));
+
  % Calculate Time series for each Plate of Selected Scan
  lastPlateOnScan=1;  %Ncode
  tSeriesv=[]; t0Seriesv=[];
@@ -69,7 +72,7 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
    t0Seriesv=((scTmNumv-scTmNumv(1))*24);
  end  

-  % added to jump over and fill data for invalid Sscan(plate runs
+  % Added to jump over and fill data for invalid Sscan(plate runs
  if tptLength>=3 
    % Create blank scan
    ImHeigth=2075;
@@ -83,7 +86,7 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
    % Execute Image conversion into Intensity Data
    [Tmpsbdg2, scanIntens, ~, ~, ~, TmpexpScanIntens2, TmpFexpScanSpots2, TmpFexpScanBMtp2, TmpanlZoneRefs2,areaOfIntensAboveBG]= ... 
        NIscanIntensBGpar4GblFnc(Fflg,tifFileLst, ImParMat, PTmapPos,optCirMask,diaExt,doCircle,cirPixA,numRows,numCols,ImHeigth,ImWidth,cirMask, ...
-        tptLength,selScan,Empsc,TmpexpScanIntens,TmpFexpScanSpots,TmpFexpScanBMtp,TmpanlZoneRefs,resDir, Tmpsbdg);
+        tptLength,selScan,Empsc,TmpexpScanIntens,TmpFexpScanSpots,TmpFexpScanBMtp,TmpanlZoneRefs,easyResultsDir, Tmpsbdg);

    TmpexpScanIntens3=TmpexpScanIntens2;
    TmpFexpScanSpots3=TmpFexpScanSpots2;
@@ -100,25 +103,23 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
    % NIcheck: Check for bad scans at time points (swapped plates etc.)
    % Set up cell arrays for storing each plate in each Scan ..(scan,plate)
    SWprint=0;
-    if SWprint==1
-      wkDir=pwd;
-      cd (fullfile(resDir,'PrintResults'));
-    end

    % Construct Legacy ...Intens.txt file
    if SWprint==1
-      filename=(strcat('Plate',num2str(selScan),'_Intens.txt'));
+      filename=fullfile(easyResultsDir,'PrintResults',(strcat('Plate',num2str(selScan),'_Intens.txt')));
      fid=fopen(filename,'w');
    end
-    if length(size(plate))==2 %Only two dims if only one image
+
+    if length(size(plate))==2 % only two dims if only one image
      numOfImages=1;
    else
      numOfImages=size(plate,3);
    end
+
    CFscanIntens=zeros(384,numOfImages);        
    locIndx=0; pl=1;
-    for n=1:numCols     %Ncode changed to 16 for Vert
-      for m=1:numRows   %Ncode change to 24 for Vert
+    for n=1:numCols % Ncode changed to 16 for Vert
+      for m=1:numRows % Ncode change to 24 for Vert
        locIndx=locIndx+1;      
        for k=1:numOfImages
          if SWprint==1
@@ -148,10 +149,10 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
    % for p=1:lastPlateOnScan
    if SWprint==1    
      if SWgrowthArea==1
-        filename=(strcat('Plate',num2str(selScan),'_Areas.txt'));
+        filename=fullfile(printResultsDir,(strcat('Plate',num2str(selScan),'_Areas.txt')));
      else
-        filename=(strcat('ALTgrowthA_Scan',num2str(selScan),'_Plate',num2str(1),'_Areas.txt'));
-        filename=(strcat('ALTgrowthA_Plate',num2str(selScan),'_Plate','_Areas.txt'));
+        filename=fullfile(printResultsDir,(strcat('ALTgrowthA_Scan',num2str(selScan),'_Plate',num2str(1),'_Areas.txt')));
+        filename=fullfile(printResultsDir,(strcat('ALTgrowthA_Plate',num2str(selScan),'_Plate','_Areas.txt')));
      end
      fid=fopen(filename,'w');
    end
@@ -170,11 +171,7 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR

    if SWprint==1
      fclose(fid);
-    end
-
-    if SWprint==1
-      cd(wkDir);
-      fclose('all');
+      % fclose('all'); % TODO do we need this? 
    end

    % AutoImCF curveFit kickoff setup
@@ -186,7 +183,6 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
    suffix=strcat('Scan', num2str(selScan),'_Plate', num2str(1)); % char(QspLst(n));
    AUCfinalTime=96;
    arrayFormat=384;
-    currDirResults=fullfile(resDir,'PrintResults');
        
    % Version compatability fixes
    %{
@@ -225,10 +221,10 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR

    % CFscanIntens
    % Call CurveFit routine
-    % NCfitImCF(times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, currDirResults, autoImCFlag, selScan,sols) %,scan)%, scPltList) outputDirectory;   
-    % [scanTmp2]=NCfitImCFparforFailGbl(times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, currDirResults, autoImCFlag, selScan, sols, scanTmp); %,scan)%, scPltList) outputDirectory;
+    % NCfitImCF(times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, printResultsDir, autoImCFlag, selScan,sols) %,scan)%, scPltList) outputDirectory;   
+    % [scanTmp2]=NCfitImCFparforFailGbl(times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, printResultsDir, autoImCFlag, selScan, sols, scanTmp); %,scan)%, scPltList) outputDirectory;
    [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanIntensELr,par4scanCFparameters,par4scanCFdate,outC2,outCstd2]= ...
-        NCfitImCFparforFailGbl2(parMat,times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, currDirResults, autoImCFlag, selScan, sols); %,scan)%, scPltList) outputDirectory;
+        NCfitImCFparforFailGbl2(parMat,times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, printResultsDir, autoImCFlag, selScan, sols); %,scan)%, scPltList) outputDirectory;
  else  %fill with default values when an invalid plate scan occurs
    CFscanIntens=zeros(16,24);
    Ag=zeros(1,384);
--- a/workflow/templates/easy/par4Gbl_Main8c.m
+++ b/workflow/templates/easy/par4Gbl_Main8c.m
@@ -1,43 +1,22 @@
 %% CALLED BY EASYconsole.m %%

-w=pwd;
-
-%function NImStartupImCF02par4Gbl
-Fflg=1; %0;
-
-fclose('all');  %close all open files
-clear('plate2', 'scanIntens','Scanfiles','pathname','tifFileLstP4')
-
-%global SWsingleSc
 global SWgrowthArea
 global scLst
 global ImParMat
-%global CSearchRange
-%global CSrchRng
-global expDir
-global SWnewExp
-global openExpfile
-global openExppath
-global newExpfile
-global newExppath
-global ExpOutmat
+global scansDir
+global matFile
 global fhconsole
-global ExpPath
-global resDir
-global wCodeDir
+global easyResultsDir
+global pointMapsResultsDir
+global fotosResultsDir
 global matDir
 global ImWidth
 global ImHeigth
-global numRows;
-global numCols;
-%global SWprintLeg
+global numRows
+global numCols
 global scan
-%global scanSize
 global scanMax
 global tptLength
-%global scanPar4x
-%global sols
-%global CFmeth

 numRows=24; % for Single Vertical 
 numCols=16; % for Single Vertical 
@@ -48,22 +27,31 @@ radius=14;
 ImParMat(10)=radius;
 ImParMat(11)=doCircle;

+% TODO what is this for?
+Fflg=1;
+
+% Don't think we need this
+% fclose('all');  % close all open files
+
+% Unset some vars just in case they are already set
+clear('scanIntens','Scanfiles','pathname','tifFileLstP4')
+
 try
  clf(fhconsole,'reset')
-catch ME
-end
-
-close
-EASYconsole
-
-try
-  load(ExpOutmat)
-  copyfile(ExpOutmat,(fullfile(matDir,'BkUp',strcat((num2str(datenum(now))),'.mat'))))
 catch
 end

+% No idea why we're doing this so commenting out
+% close
+% EASYconsole
+
+if exist(matFile, 'file')
+  bkUpMatFile=fullfile(matDir,'BkUp',matFile)
+  copyfile(matFile,(fullfile(matDir,'BkUp',matFile)))
+end
+
 try
-  load(fullfile(resDir,'Fotos','Nbdg')) %Modified to load from 'Fotos' 20_0819
+  load(fullfile(easyResultsDir,'Fotos','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
@@ -74,35 +62,34 @@ catch
  % 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(resDir,'PTmats','Nbdg')) %Left in to accomodate loads of work before 20_0819
+  load(fullfile(easyResultsDir,'PTmats','Nbdg')) %Left in to accomodate loads of work before 20_0819
 end
 % Load Fotos stored data
 try
-  load(fullfile(resDir,'Fotos','Coordinates'))
+  load(fullfile(easyResultsDir,'Fotos','Coordinates'))
 catch
 end
 try
-  load(fullfile(resDir,'Fotos','BGatTpts'))
+  load(fullfile(easyResultsDir,'Fotos','BGatTpts'))
 catch
 end
 try
-  load(fullfile(resDir,'Fotos','anlZones'))
+  load(fullfile(easyResultsDir,'Fotos','anlZones'))
 catch
 end
 % autoImCF
 try
-  load(fullfile(resDir,'PTmats','NCFparms'))    
+  load(fullfile(easyResultsDir,'PTmats','NCFparms'))    
 catch ME
  load parameters   
 end

 % Get Print Times
 PrintTimes=[];
-expDir=fullfile(ExpPath);
 scLst={};

 % Parameter Entry
-NImParamRadiusGui(expDir) % Ncode 122111replaced removed  ,numOfPrtTimes)
+NImParamRadiusGui(scansDir) % Ncode 122111replaced removed  ,numOfPrtTimes)
 width=24;
 widthEx=width-1; % width extention from reference point
 dither=ImParMat(6);
@@ -131,25 +118,16 @@ else
 end

 SWgrowthArea=ImParMat(9);
-load(fullfile(resDir,'PTmats','NPTmapSearch'))
+load(fullfile(pointMapsResultsDir,'NPTmapSearch'))
 PTmapPos=detPos;
-
 selScanNumLst=[];
 Scanfiles=[];
 pathname=[];

-% TODO BCR this probably doesn't need to be here but I'm leaving it for now
-if ispc
-  cd(char(strcat(expDir,scLst(1))))
-elseif (isunix || ismac)
-  cd(fullfile(expDir,cell2mat(scLst(1))));
-end
-Scanfiles=[];
-pathname=[];
-
 for ii=1:length(scLst)
  if (SWsingleSc == 1)
-    [Scanfiles, pathname]=uigetfile('*.bmp', 'Select files','MultiSelect','on');% change '*hr*.bmp' 12/20/2011
+    % TODO proably need to make this more explicit with paths
+    [Scanfiles, pathname]=uigetfile('*.bmp', 'Select files','MultiSelect','on'); % change '*hr*.bmp' 12/20/2011 
    if ischar(Scanfiles)    
      scd=imread(char(Scanfiles));
      tptLength=1;
@@ -159,32 +137,30 @@ for ii=1:length(scLst)
    end
  ImHeigth=size(scd,1);
  ImWidth=size(scd,2);
-  sc=scd(1:ImHeigth,1:ImWidth);   %?Not used RefOnly
+  sc=scd(1:ImHeigth,1:ImWidth);
  end

-  cd(w);
  numFiles=size(Scanfiles,2);

  % Initialize tifFilesLst for parfor loop
-  dir(fullfile(expDir, char(scLst(ii)), '*.bmp'));
-
+  dir(fullfile(scansDir, char(scLst(ii)), '*.bmp'));
  numFiles=length(tifFileLst4MultiT);  
  tptLength=numFiles;
  tifFileLstP4{ii}={tifFileLst4MultiT.name};
 end

-for jj=1:numScans  %startScan:numScans
+for jj=1:numScans % startScan:numScans
  selScan=str2double(char(scLst(jj)));
  selScanNumLst(jj)=selScan;
 end
-selScanNumLst2=selScanNumLst;  %function passthrough, passback to par4gbl_Main 20_0205
+selScanNumLst2=selScanNumLst; % function passthrough, passback to par4gbl_Main 20_0205

-% PREALLOCATION  
+% 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);
@@ -206,11 +182,11 @@ CFscanIntens=zeros(16,24);
 [p4L4,TmpexpScanIntens5,TmpFexpScanSpots5,TmpFexpScanBMtp5,TmpanlZoneRefs5,Tmpsbdg5]= ...
  p4loop8c(parMat,tptLength,numScans,selScanNumLst,SWsingleSc,Fflg,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,cirMask,width, ... 
  TmpexpScanIntens00,TmpFexpScanSpots00,TmpFexpScanBMtp00,TmpanlZoneRefs00,scCount,tifFileLstP4,pathname,ImParMat, ...
-  numRows,numCols,scLst,resDir,expDir, p4L00,TmpexpScanIntens4,TmpFexpScanSpots4,TmpFexpScanBMtp4,TmpanlZoneRefs4, ...
+  numRows,numCols,scLst,easyResultsDir,scansDir, p4L00,TmpexpScanIntens4,TmpFexpScanSpots4,TmpFexpScanBMtp4,TmpanlZoneRefs4, ...
  Tmpsbdg00,Tmpsbdg4);

 for scanCnt=1:numScans
-  selScan=p4L4{16,scanCnt}; %determine the actual scan in the scanCnt parfor distributed "id"
+  selScan=p4L4{16,scanCnt}; % determine the actual scan in the scanCnt parfor distributed "id"
  scan(selScan).plate(1).tSeries=cell2mat(p4L4(1,scanCnt));
  scan(selScan).plate(1).t0Series=cell2mat(p4L4(2,scanCnt));
  scan(selScan).plate(1).printTm=cell2mat(p4L4(3,scanCnt));
@@ -222,7 +198,7 @@ for scanCnt=1:numScans
  scan(selScan).plate(1).selTimes=p4L4(9,scanCnt); 
  scan(selScan).plate(1).filterTimes=p4L4(10,scanCnt); 
  scan(selScan).plate(1).normIntens=p4L4(11,scanCnt); 
-  %scan(selScan).plate(1).CFparameters=p4L4(12,scanCnt); %Need to convert to a matrix form like Old versions
+  % scan(selScan).plate(1).CFparameters=p4L4(12,scanCnt); %Need to convert to a matrix form like Old versions
  CFparm(1:384)=p4L4{12,scanCnt}(1:384);
  scan(selScan).plate(1).CFparameters=CFparm;
  scan(selScan).plate(1).CFdate=p4L4(13,scanCnt);
@@ -241,31 +217,31 @@ for scanCnt=1:numScans
  end
 end 

-%SAVE DATA in .mat files
-save(ExpOutmat,'scan');
-% save((fullfile(resDir,'PTmats','Nbdg')), 'sbdg'); %legacy location can probably get rid of in time
-save((fullfile(resDir,'Fotos','Nbdg')), 'sbdg');
-save((fullfile(resDir,'Fotos','Coordinates')),'FexpScanSpots') %Saves frames at each tPt
-save((fullfile(resDir,'Fotos','BGatTpts')),'FexpScanBMtp')
-save((fullfile(resDir,'Fotos','anlZones')),'anlZoneRefs')%Saves anl Positions at each tPt
+% Save data in .mat files
+save(matFile,'scan');
+% save((fullfile(easyResultsDir,'PTmats','Nbdg')), 'sbdg'); %legacy location can probably get rid of in time
+save((fullfile(easyResultsDir,'Fotos','Nbdg')), 'sbdg');
+save((fullfile(easyResultsDir,'Fotos','Coordinates')),'FexpScanSpots') %Saves frames at each tPt
+save((fullfile(easyResultsDir,'Fotos','BGatTpts')),'FexpScanBMtp')
+save((fullfile(easyResultsDir,'Fotos','anlZones')),'anlZoneRefs')%Saves anl Positions at each tPt

-%Print FitResults  *******************************************************
+% Print FitResults
 fileExt='.txt';
 filePrefix='FitResults_';
 for scanCnt=1:numScans
-  selScan=p4L4{16,scanCnt}; %determine the actual scan in the scanCnt parfor distributed "id"
+  selScan=p4L4{16,scanCnt}; % determine the actual scan in the scanCnt parfor distributed "id"
  fileSuffix=strcat('Scan', num2str(selScan),'_Plate', num2str(1));
  fileNamePlate=[filePrefix fileSuffix fileExt];
-  fileName=fullfile(resDir,'PrintResults', fileNamePlate);  %[outputDirectory fileNamePlate];
+  fileName=fullfile(easyResultsDir,'PrintResults', 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
-  %used as a diagnostic tool.
+  % 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
+  % used as a diagnostic tool.
  outCprint=p4L4;

  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),...