EASY passing linter checks

workflow/script-run-workflow

@@ -538,11 +538,11 @@ easy() {
     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:-$PROJECT_SUFFIX}"
+    EASY_RESULTS_DIR="$SCANS_DIR/Results_${PROJECT_PREFIX}_${suffix:-$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}.$((count++))"
+        EASY_SUFFIX="${suffix:-$PROJECT_SUFFIX}.$((count++))"
         EASY_RESULTS_DIR="$SCANS_DIR/Results_${PROJECT_PREFIX}_${EASY_SUFFIX}"
       else
         EASY_SUFFIX=${suffix:-$PROJECT_SUFFIX}

workflow/templates/easy/DMPexcel2mat.m

@@ -253,13 +253,13 @@ if isequal(Linked,1) % Drugs and Media are linked 1 to 1; else they are combinat
   if ispc
     while (~isequal(txt{excLnNum,2},'###'))
       numb=numb+1;    
-      DM.drug(numb) = {raw(excLnNum,2)};
+      DM.drug(numb)={raw(excLnNum,2)};
-      DM.conc(numb) = {raw(excLnNum,3)};
+      DM.conc(numb)={raw(excLnNum,3)};
-      DM.media(numb) = {raw(excLnNum,4)};
+      DM.media(numb)={raw(excLnNum,4)};
-      DM.mod1(numb) = {raw(excLnNum,5)};
+      DM.mod1(numb)={raw(excLnNum,5)};
-      DM.conc1(numb) = {raw(excLnNum,6)};
+      DM.conc1(numb)={raw(excLnNum,6)};
-      DM.mod2(numb) = {raw(excLnNum,7)};
+      DM.mod2(numb)={raw(excLnNum,7)};
-      DM.conc2(numb) = {raw(excLnNum,8)};
+      DM.conc2(numb)={raw(excLnNum,8)};
       excLnNum=excLnNum+1;
       msg=strcat('NumberOf1:1DrugMediaPlates = ',num2str(numb), '   lastLineNo. = ',num2str(excLnNum));
     end
@@ -268,20 +268,20 @@ if isequal(Linked,1) % Drugs and Media are linked 1 to 1; else they are combinat
     excLnNum=1;
     while (~isequal(DMcell{excLnNum+1,2},'###'))
       numb=numb+1;    
-      DM.drug(numb) = {DMtbl(excLnNum,2)};
+      DM.drug(numb)={DMtbl(excLnNum,2)};
-      DM.drug(numb)= table2cell(DM.drug{numb});
+      DM.drug(numb)=table2cell(DM.drug{numb});
-      DM.conc(numb) = {DMtbl(excLnNum,3)};
+      DM.conc(numb)={DMtbl(excLnNum,3)};
-      DM.conc(numb)= table2cell(DM.conc{numb});
+      DM.conc(numb)=table2cell(DM.conc{numb});
-      DM.media(numb) = {DMtbl(excLnNum,4)};
+      DM.media(numb)={DMtbl(excLnNum,4)};
-      DM.media(numb)= table2cell(DM.media{numb});
+      DM.media(numb)=table2cell(DM.media{numb});
-      DM.mod1(numb) = {DMtbl(excLnNum,5)};
+      DM.mod1(numb)={DMtbl(excLnNum,5)};
-      DM.mod1(numb)= table2cell(DM.mod1{numb});
+      DM.mod1(numb)=table2cell(DM.mod1{numb});
-      DM.conc1(numb) = {DMtbl(excLnNum,6)};
+      DM.conc1(numb)={DMtbl(excLnNum,6)};
-      DM.conc1(numb)= table2cell(DM.conc1{numb});
+      DM.conc1(numb)=table2cell(DM.conc1{numb});
-      DM.mod2(numb) = {DMtbl(excLnNum,7)};
+      DM.mod2(numb)={DMtbl(excLnNum,7)};
-      DM.mod2(numb)= table2cell(DM.mod2{numb});
+      DM.mod2(numb)=table2cell(DM.mod2{numb});
-      DM.conc2(numb) = {DMtbl(excLnNum,8)};
+      DM.conc2(numb)={DMtbl(excLnNum,8)};
-      DM.conc2(numb)= table2cell(DM.conc2{numb});
+      DM.conc2(numb)=table2cell(DM.conc2{numb});
       excLnNum=excLnNum+1;
       msg=strcat('NumberOf1:1DrugMediaPlates = ',num2str(numb), '   lastLineNo. = ',num2str(excLnNum));
     end
@@ -296,28 +296,28 @@ if isequal(Linked,0) % 0 indicates Drugs and Media are combinatorial
   if ispc
     while (~isequal(txt{excLnNum,2},'###'))
       drgCnt=drgCnt+1;    
-      DM.drug(drgCnt) = {raw(excLnNum,2)};
+      DM.drug(drgCnt)={raw(excLnNum,2)};
-      DM.conc(drgCnt) = {raw(excLnNum,3)};
+      DM.conc(drgCnt)={raw(excLnNum,3)};
       excLnNum=excLnNum+1;
     end
 
     while (~isequal(txt{excLnNum,4},'###'))
       medCnt=medCnt+1;    
-      DM.media(medCnt) = {raw(excLnNum,4)};
+      DM.media(medCnt)={raw(excLnNum,4)};
       excLnNum=excLnNum+1;
     end
   else
     excLnNum=1;
     while (~isequal(DMcell{excLnNum+1,2},'###'))
       drgCnt=drgCnt+1;    
-      DM.drug(drgCnt) = {DMtbl(excLnNum,2)};
+      DM.drug(drgCnt)={DMtbl(excLnNum,2)};
-      DM.conc(drgCnt) = {DMtbl(excLnNum,3)};
+      DM.conc(drgCnt)={DMtbl(excLnNum,3)};
       excLnNum=excLnNum+1;
     end
 
     while (~isequal(DMcel{excLnNum+1,4},'###'))
       medCnt=medCnt+1;    
-      DM.media(medCnt) = {DMtbl(excLnNum,4)};
+      DM.media(medCnt)={DMtbl(excLnNum,4)};
       excLnNum=excLnNum+1;
     end
   end

workflow/templates/easy/DgenResults.m

@@ -2,12 +2,12 @@
 % Updated 240724 Bryan C Roessler to improve file operations and portability
 %
 global scansDir
-global easyResultsDir
 global matFile
 global defImParMat
 global printResultsDir
 global fotosResultsDir
 global pointMapsFile
+global pointMapsResultsDir
 
 ln=1;
 
@@ -52,6 +52,7 @@ end
 %   localscansDir=scansDir;
 % end
 
+% TODO this seems weird
 expNm=scansDir(max(strfind(scansDir,'/'))+1:end);
 drivePos=min(strfind(scansDir,'/'));
 drive=scansDir(1:(drivePos-1));
@@ -85,9 +86,9 @@ drgCnt=0;
 medCnt=0;
 
 try
-  load(fullfile(easyResultsDir,'Fotos','Nbdg')) % Convolute scan array data into plates
+  load(fullfile(fotosResultsDir,'Nbdg')) % Convolute scan array data into plates
 catch
-  load(fullfile(easyResultsDir,'PTmats','Nbdg')) % Convolute scan array data into plates
+  load(fullfile(pointMapsResultsDir,'Nbdg')) % Convolute scan array data into plates
 end
 
 for s=1:size(scan,2)
@@ -102,14 +103,14 @@ for s=1:size(scan,2)
   for p=1:size((scan(s).plate),2)
     totPlCnt=totPlCnt+1;
     if destPerMP>1 && rem(totPlCnt,destPerMP)==1
-      mpCnt=mpCnt+1
+      mpCnt=mpCnt+1;
     end
     if destPerMP==1
-      mpCnt=mpCnt+1
+      mpCnt=mpCnt+1;
     end
     pertCnt=rem(totPlCnt,destPerMP);
     if pertCnt==0
-      pertCnt=destPerMP
+      pertCnt=destPerMP;
     end
     pert=strcat('Perturb_',num2str(pertCnt));
     s % TODO seems wrong
@@ -365,7 +366,7 @@ if isequal(opt,'DB')||isequal(opt,'Both')
   try
     copyfile(DBfilename,DBupload)
   catch ME
-    rep = getReport(ME, 'basic');
+    rep=getReport(ME, 'basic');
     rep=strcat('Failed copyfile to ',DBupload,' -', rep);
     errordlg(rep)
   end
@@ -424,8 +425,8 @@ try
           asd=cell2mat(scan(s).plate(1).CFparameters{1,1}(1,384));
           aucEndPt=  strcat('AUC',num2str(asd(9)));
         end
-        fprintf(fid, 'Num.\tDiagnostics\tDrug\tConc\tMedia\tModifier1\tConc1\tModifier2\tConc2\tORF\tGene')
+        fprintf(fid, 'Num.\tDiagnostics\tDrug\tConc\tMedia\tModifier1\tConc1\tModifier2\tConc2\tORF\tGene');
-        fprintf(fid, '\t %s',aucEndPt)
+        fprintf(fid, '\t %s',aucEndPt);
         fprintf(fid, '\triseTm\tK\tr\tl\tR-squared\tK-lower\tK-upper\tr-lower\tr-upper\tl-lower\tl-upper\tArea\tLastInten\tSplineMaxRateTm\tLastFitTm\t1stFitTm\tMedianBase\tFitBase\tMinTm\tThreshTm\tTotFitPts\tPostThreshFitPts\t1stBackgrd\tLstBackgrd\t1stMeanTotBackgrd\tLstMeanTotBackgrd'); %17_0629 MinBaseIntens update for MedianBase label
       end     
       clear outTseries
@@ -438,7 +439,7 @@ try
       outIntens=[];
       RawIntens=[];
       RawIntens=scan(s).plate(p).intens;
-      RawIntensSize= size(RawIntens,2)
+      RawIntensSize=size(RawIntens,2);
       clear Ag;  %Ag is Growth Area
       Ag=scan(s).plate(p).Ag;
       AgSize= size(Ag);

workflow/templates/easy/EASYconsole.m

@@ -20,6 +20,7 @@ function varargout = EASYconsole(varargin)
   global mpdmFile
   global userName
   global srchRange
+  global searchRangeFile
 
   % Initialize some variables from matlab
   easyPath=which(mfilename);
@@ -115,7 +116,7 @@ function varargout = EASYconsole(varargin)
   else
     % Try to find MasterPlate_ file on our own
     mp=fullfile(scansDir,'MasterPlateFiles',strcat('MasterPlate_', easySuffix,'.xlsx'));
-    if exist(mp, 'file'))
+    if exist(mp, 'file')
       masterPlateFile=mp;
       disp(strcat('Using drug media file: ', masterPlateFile, ' from internal logic'))
     else
@@ -129,7 +130,7 @@ function varargout = EASYconsole(varargin)
   else
     % Try to find MasterPlate_ file on our own
     dm=fullfile(scansDir,'MasterPlateFiles',strcat('DrugMedia_', easySuffix,'.xlsx'));
-    if exist(mp, 'file'))
+    if exist(mp, 'file')
       drugMediaFile=dm;
       disp(strcat('Using drug media file: ', drugMediaFile, ' from internal logic'))
     else
@@ -147,16 +148,16 @@ function varargout = EASYconsole(varargin)
   fotosResultsDir=fullfile(easyResultsDir,'Fotos');
   figsResultsDir=fullfile(easyResultsDir,'figs');
   pointMapsResultsDir=fullfile(easyResultsDir,'PTmats');
-  pointMapsFile=fullfile(pointMapsResultsDir,'NImParameters.mat')
+  pointMapsFile=fullfile(pointMapsResultsDir,'NImParameters.mat');
-  oldPointMapsFile=fullfile(pointMapsResultsDir,'ImParameters.mat')
+  oldPointMapsFile=fullfile(pointMapsResultsDir,'ImParameters.mat');
-  CSearchRangeFile=fullfile(fotosResultsDir,'CSearchRange.mat');
+  searchRangeFile=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')
+  if exist(searchRangeFile, 'file')
-    searchRangeNum=load(CSearchRangeFile);
+    searchRangeNum=load(searchRangeFile);
   end
   % Add easyDir to the MATLAB path
   % I have not idea if this is necessary or works but theoretically should
@@ -212,7 +213,6 @@ end
 % varargin--input arguments to EASYconsole (see VARARGIN)
 function EASYconsole_OpeningFcn(hObject, ~, handles, varargin)
   global fhconsole
-  global easyResultsDir
 
   % Choose default command line output for EASYconsole
   handles.output=hObject;
@@ -371,7 +371,7 @@ function LoadDatFile_Callback(~, ~, ~)
     end
 
     % Create supporting dirs
-    dirs={'PrintResults', 'figs', 'CFfigs', 'PTmats', 'Fotos'}
+    dirs={'PrintResults', 'figs', 'CFfigs', 'PTmats', 'Fotos'};
     for i=1:length(dirs)
       d=dirs{i};
       if ~exist(fullfile(easyResultsDir, d), 'dir')

workflow/templates/easy/NCfitImCFparforFailGbl2.m

@@ -20,18 +20,18 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
   par4resMat=zeros(384,27);
   par4resMatStd=zeros(384,27);
 
-  % Spot(cultures) loop
+  % Spot (cultures) loop
-  for ii=1:384   %startSpot:numCultures
+  for ii=1:384   % startSpot:numCultures
-    ii;  %%%db print out the culture number 
+    ii; % db print out the culture number 
     timepts=[];
     currValues=[];
     currSpotAreas=[];
     currSpotArea=[];
     dataMatrix=[];
-    selTimesStd=[];  %191024 parfor
+    selTimesStd=[]; % 191024 parfor
-    selIntensStd=[]; %191024 parfor
+    selIntensStd=[]; % 191024 parfor
-    FiltTimesELr=[]; %191024 parfor
+    FiltTimesELr=[]; % 191024 parfor
-    NormIntensELr=[]; %191024 parfor
+    NormIntensELr=[]; % 191024 parfor
     
     % add offset...1 offset PER PLATE
     timepts=times + timeOffsets;  % (floor((ii-1)/arrayFormat) + 1);    
@@ -48,7 +48,7 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
     currNormIntens=currValues/currSpotArea;
     tmpx=find(currNormIntens>5); %15jh % 2.3);
     validSpot=true;
-    if(isempty(tmpx) || (length(tmpx)<3)) 
+    if(isempty(tmpx) || length(tmpx)<3)
         validSpot=false;
         normIntens=currNormIntens;
         filterTimes=timepts; %filterTimes; %currTimes;
@@ -63,9 +63,9 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
       resMat=zeros(1,27);
       hold off;
       dataMatrix=[];
-      K=0;r=0;l=0;Klow=0;Kup=0;rlow=0;rup=0;llow=0;lup=0;AUC=0;MSR=0; rsquare=0; 
+      K=0;r=0;l=0;Klow=0;Kup=0;rlow=0;rup=0;llow=0;lup=0;AUC=0;MSR=0;rsquare=0; 
       bl=0;
-      Tpt1=0; numFitTpts =0;thresGT2=0;minTime=0;fitbl=0; %diagnostic outputs only 
+      Tpt1=0;numFitTpts=0;thresGT2=0;minTime=0;fitbl=0; % diagnostic outputs only 
       
       timepts=timepts; % timepts=currTimes; parfor
       normIntens=currNormIntens;
@@ -82,7 +82,7 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
         threshold=0;
       end
 
-      dropThreshold=-0.0001* max(normIntens);
+      dropThreshold=-0.0001*max(normIntens);
 
       % Initialize dataMatrix
       dataMatrix(1,:)=timepts;
@@ -102,7 +102,7 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
       % NCLoIntstdTrim
       % NCLoSstdTrim.m called by NCfilImCF and NCfil.m
       flg1=0;
-      loScurvLim=stdLoIntLim;  %
+      loScurvLim=stdLoIntLim;
       loStimeN=1;
       last2n=1;
       stdDev=[];
@@ -115,7 +115,8 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
           if (loStimeN-2)>0
             dataMatrix(3,1:(n-2))=2; % add to lowIntensity cull flags, the pre S cull data
           else 
-            dataMatrix(3,1:n)=2;end
+            dataMatrix(3,1:n)=2;
+          end
           dataMatrix(3,1:(n-2))=2;
           last2n=n; 
         end
@@ -127,8 +128,8 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
             loStimeN=n;
           end
           if stdDev(n)>6
-            flg1=1
+            flg1=1;
-          end % detect S curve rise->stop stdLoInt detection
+          end
         end
       end
 
@@ -142,14 +143,14 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
       qcutoff=2;
       qind=find(normIntens>2);  %,:,'first');
       if ~isempty(qind(3))
-        qcutoff=qind(3)
+        qcutoff=qind(3);
       end
       [minInt,I]=min(normIntens(2:qcutoff));
       bl=minInt;
-      minTime=dataMatrix(1,I);  %diagnostic output only
+      minTime=dataMatrix(1,I);
 
       if (length(qind)>5)&&I>1
-        dataMatrix(3,1:(I-1))=5
+        dataMatrix(3,1:(I-1))=5;
       end
 
       tGT2Flg=0;
@@ -157,7 +158,7 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
         dataMatrix(4,n)=normIntens(n)-bl; 
         if n>I && dataMatrix(4,n)>=2 && tGT2Flg==0
           thresGT2=n;thresGT2Tm=dataMatrix(1,n);tGT2Flg=1;
-        end %diagnostic output only    
+        end   
       end
 
       resMat(18)=bl;

workflow/templates/easy/NCscurImCF_3parfor.m

@@ -86,7 +86,7 @@ function [resMatStd, resMat, selTimesStd, selIntensStd, FiltTimesELr, NormIntens
     if(isnan(Klow)||isnan(Kup)||isnan(llow)||isnan(lup)||isnan(rlow)||isnan(rup))
       NANcond=1; stdNANcond=1; % stdNANcond added to relay not to attempt ELr as there is no curve to find critical point
     end  
-  catch ME
+  catch
     % if no data is given, return zeros
     AUC=0;MSR=0;K=0;r=0;l=0;rsquare=0;Klow=0;Kup=0;
     rlow=0;rup=0;lup=0;llow=0; 
@@ -222,7 +222,7 @@ function [resMatStd, resMat, selTimesStd, selIntensStd, FiltTimesELr, NormIntens
         GrowthELr=K ./ (1 +  exp(-r.* (t - l )));
         fitblELr=min(GrowthELr);   %jh diag
       end
-    catch ME
+    catch
       % if no data is given, return zeros
       AUC=0;MSR=0;K=0;r=0;l=0;rsquare=0;Klow=0;Kup=0;
       rlow=0;rup=0;lup=0;llow=0; %normIntens=[];
@@ -290,7 +290,7 @@ function [resMatStd, resMat, selTimesStd, selIntensStd, FiltTimesELr, NormIntens
       resMat(19)=fitblStd; % only applicable to Std curve Fit; ELr superceeds and makes meaningless
       resMat(20)=minTime; % only applicable to Std curve Fit; ELr superceeds and makes meaningless
     end  % if r3>r1
-  catch ME
+  catch
     % if no data is given, return zeros
     AUC=0;MSR=0;K=0;r=0;l=0;rsquare=0;Klow=0;Kup=0;
     rlow=0;rup=0;lup=0;llow=0; % normIntens=[];

workflow/templates/easy/NImParamRadiusGui.m

@@ -21,6 +21,7 @@ function NImParamRadiusGui(scansDir)
   global numCols
   global scanSize
   global scanMax
+  global searchRangeFile
 
   % Ncode ImRobot adaptation
   % TODO this code block and variables needs explanation
@@ -38,17 +39,17 @@ function NImParamRadiusGui(scansDir)
   selScan=1;
   SWgrowthArea=1;
 
-  if exist(pointMapsFile)
+  if exist(pointMapsFile, 'file')
     load(pointMapsFile);
   else
     load(fullfile(PTmats,'NImParameters')) % hardcoded default
     disp('WARNING: Using hardcoded NImParameters.mat')
   end
-  ImParMat
+  ImParMat;
   % if ~exist('searchRangeNum','var') || isempty(searchRangeNum)
-  if exist(CSearchRangeFile), 'file')
+  if exist(searchRangeFile, 'file')
-    load(CSearchRangeFile);
+    load(searchRangeFile);
-    CSearchRange;
+    CSearchRange; % TODO, might be an issue, figure out what this is doing
   end
       
   % yInitPos=0.30;
@@ -117,6 +118,8 @@ function NImParamRadiusGui(scansDir)
   btnNumber=7;
   yPos=0.85-(btnNumber-1)*(btnHt+spacing);
   btnPos=[xPos yPos-spacing btnWid btnHt];
+
+  % TODO, I don't think these are defined?
   try
     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.
@@ -164,7 +167,6 @@ function NImParamRadiusGui(scansDir)
     'callback',{@load_listbox});  %'uiresume(gcbf)'); 'Position', [5 100 60 20])
   
   function load_listbox(source,~)
-    global 
     userIndx=(get(source,'value'));
     userStr=(get(source,'string'));
     %scLstIndx=str2num(char(strrep(userStr(userIndx), 'Scan', '')))
@@ -239,7 +241,7 @@ function NImParamRadiusGui(scansDir)
   searchRangeNum;
 
   save(pointMapsFile, 'ImParMat');
-  save(CSearchRangeFile,'searchRangeNum');
+  save(searchRangeFile,'searchRangeNum');
 
   close
   return

workflow/templates/easy/NIscanIntensBGpar4GblFnc.m

@@ -8,8 +8,9 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
   global figsResultsDir
   global fotosResultsDir
 
-  searchIntens=[]; intensMax=[]; detMaxPos=[]; scIntens=[]; areaOfIntensAboveBG=[]; BkgrdMat=[];
+  searchIntens=[];intensMax=[];detMaxPos=[];scIntens=[];areaOfIntensAboveBG=[];BkgrdMat=[];
 
+  % TODO needs explanation
   if Fflg==1
     % Preallocation
     tPtLength=length(tifFileLst);
@@ -169,7 +170,7 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
             testPosC=PTrefPt(2) + shiftPosC;         
             a=[testPosR,testPosC];   %testPos(r,c)={testPosR,testPosC};
             testPos(r,c)={a};
-            doCircle
+            doCircle;
             TestmapOnesDbl(testPosR:(testPosR+(diaExt-1)),testPosC:(testPosC+(diaExt-1)))=cirMask;  %optCirMask;
           end
         end
@@ -299,11 +300,11 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
     if ANDValCent>=MaxANDVal 
       MaxPosDbl=lastDetMaxCentDbl; 
       MaxPos=lastDetMaxPos;
-      %detPos=lastDetMaxPos;
+      % detPos=lastDetMaxPos;
     end
-    %detPos=lastDetMaxPos;
+    % detPos=lastDetMaxPos;
     detPos=MaxPos;
-  end  %if length(tifFileLst) >2
+  end
 
   % Preallocation for speed on 2019_1121 ***
   scIntens=zeros(24,16,length(tifFileLst));
@@ -521,9 +522,6 @@ 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 easyResultsDir
-  global matFile
-  % global pixsAboveBG
     MPnum=ImParMat(1);
     destPerMP=ImParMat(2);
     spotThres=ImParMat(4)/100;  %selScan=ImParMat(4);
@@ -610,7 +608,11 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
           if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
           meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
           if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
-        if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end
+          if doCircle==1
+            totBkgrd(r,c)=meanBkgrd* cirPixA;
+          else 
+            totBkgrd(r,c)=meanBkgrd* width^2;
+          end
           %{
           lineSum(1)=sum((fullsc(refBG(1),refBG(2):refBG(4)-1))); %mean across top rt
           lineSum(2)=sum((fullsc(refBG(1):refBG(3)-1,refBG(2)))); %mean down lf
@@ -707,7 +709,11 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
           meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
           if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
           if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
-        if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end    
+          if doCircle==1
+            totBkgrd(r,c)=meanBkgrd* cirPixA;
+          else 
+            totBkgrd(r,c)=meanBkgrd* width^2;
+          end    
           %{          
           lineSum(1)=sum((fullsc(refBG(1),refBG(2):refBG(4)-1))); %mean across top rt
           lineSum(2)=sum((fullsc(refBG(1):refBG(3)-1,refBG(2)))); %mean down lf
@@ -753,7 +759,11 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
             if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
             % meanBkgrd=(lineSum(1)+lineSum(2)+lineSum(4))./ ...
             % ((2*(refBG(4)-refBG(2))+(refBG(3)-refBG(1))));  %divby 2*across+1*down
-          if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end   
+            if doCircle==1
+              totBkgrd(r,c)=meanBkgrd* cirPixA;
+            else
+              totBkgrd(r,c)=meanBkgrd* width^2;
+            end   
           else
             % clear('lineV')  %3
             lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); %mean down rt
@@ -763,7 +773,11 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
             meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
             if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
             % meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
-          if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end   
+            if doCircle==1
+              totBkgrd(r,c)=meanBkgrd* cirPixA;
+            else 
+              totBkgrd(r,c)=meanBkgrd* width^2;
+            end   
           end
           if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
         end
@@ -814,7 +828,11 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
             meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
             if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
             % meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
-          if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end
+            if doCircle==1
+              totBkgrd(r,c)=meanBkgrd* cirPixA;
+            else 
+              totBkgrd(r,c)=meanBkgrd* width^2;
+            end
           else
             meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
             if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end   
@@ -871,7 +889,11 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
             if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
             % meanBkgrd=(lineSum(1)+lineSum(2)+lineSum(4))./ ...
             % ((2*(refBG(4)-refBG(2))+(refBG(3)-refBG(1))));  % divby 2*across+1*down
-          if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end   
+            if doCircle==1
+              totBkgrd(r,c)=meanBkgrd* cirPixA;
+            else 
+              totBkgrd(r,c)=meanBkgrd* width^2;
+            end   
           elseif refBGrExt>(botLim-botNotchOffset) && ...
             refBGcExt>(rtLim-cushion)%if intens area too close to bottom edge only
             % clear('lineV')  %3
@@ -905,7 +927,11 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
             meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
             if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
               % meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
-          if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end   
+            if doCircle==1
+              totBkgrd(r,c)=meanBkgrd* cirPixA;
+            else 
+              totBkgrd(r,c)=meanBkgrd* width^2;
+            end   
           end
           if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
         end
@@ -1011,7 +1037,11 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
             meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
             if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
             % meanBkgrd=(sum(lineSum(1:4)))./ ((2*(refBG(4)-refBG(2))+ 2*(refBG(3)-refBG(1))));
-          if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end 
+            if doCircle==1
+              totBkgrd(r,c)=meanBkgrd* cirPixA;
+            else 
+              totBkgrd(r,c)=meanBkgrd* width^2;
+            end 
           end 
           if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
         end
@@ -1056,7 +1086,11 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
           meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
           if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
           if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
-        if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end
+          if doCircle==1
+            totBkgrd(r,c)=meanBkgrd* cirPixA;
+          else 
+            totBkgrd(r,c)=meanBkgrd* width^2;
+          end
         end
       
         % Determine the actual number of pixels(area) of growth above the  background
@@ -1125,7 +1159,7 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
           refPtR=refPt(1);
           refPtC=refPt(2);
           if doCircle==1
-          %OptmapOnesDbl(refPtR:(refPtR+diaExt),refPtC:(refPtC+diaExt))=cirMask;
+            % OptmapOnesDbl(refPtR:(refPtR+diaExt),refPtC:(refPtC+diaExt))=cirMask;
             OptmapOnesDbl(refPtR:(refPtR+(diaExt-1)),refPtC:(refPtC+(diaExt-1)))=optCirMask;   
           else
             refPtRExt=refPtR+widthEx; 
@@ -1187,5 +1221,5 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
     TmpFexpScanBMtp2=TmpFexpScanBMtp1;
     TmpanlZoneRefs2=TmpanlZoneRefs1;
     Tmpsbdg2=Tmpsbdg1;
-  
+  end
 end

workflow/templates/easy/par4GblFnc8c.m

@@ -40,7 +40,7 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
       fFail=((fullfile(printResultsDir,'ImageFileReadFailure.txt')));  
       fid=fopen(fFail,'a'); %create,open and append
       % fprintf(fid,'%s \n',char(tifFile))
-      fclose(fid)
+      fclose(fid);
       nndx=nndx-1;
       swCatch=1;
       rep=getReport(ME, 'basic');
@@ -158,8 +158,8 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
     end
     locIndx=0;
     Ag=zeros(1,384);
-    for m=1:16 %N code change from 16  %Vert back to 16
+    for m=1:16 % Ncode change from 16  %Vert back to 16
-      for n=1:24     %Ncode change from  24 %Vert back to 24
+      for n=1:24 % Ncode change from  24 %Vert back to 24
         growthArea=max(grArea(n,m,:,1));
         if SWprint==1
           fprintf(fid,'%3.f\n',growthArea);
@@ -294,7 +294,7 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
   p4L1{16}=selScan; 
 
   p4L1{17}=cirPixA;
-  p4L1{18}=datestr((now),31);
+  p4L1{18}=datestr((now),31); % TODO this seems bad
 
   p4L2=p4L1;
 end

workflow/templates/easy/par4Gbl_Main8c.m

@@ -100,9 +100,9 @@ NIcircle
 lastPlateOnLastScan=1; % Ncode
 
 if size(scLst,1)==1
-  SWsingleSc=1
+  SWsingleSc=1;
 else 
-  SWsingleSc=0
+  SWsingleSc=0;
 end
 
 dvec=datevec(datestr(floor(now))); %method to get current offset year '01-Jan-"currentyr"'
@@ -220,10 +220,10 @@ end
 % 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(fotosResultsDir,'Nbdg')), 'sbdg');
-save((fullfile(easyResultsDir,'Fotos','Coordinates')),'FexpScanSpots') %Saves frames at each tPt
+save((fullfile(fotosResultsDir,'Coordinates')),'FexpScanSpots') %Saves frames at each tPt
-save((fullfile(easyResultsDir,'Fotos','BGatTpts')),'FexpScanBMtp')
+save((fullfile(fotosResultsDir,'BGatTpts')),'FexpScanBMtp')
-save((fullfile(easyResultsDir,'Fotos','anlZones')),'anlZoneRefs')%Saves anl Positions at each tPt
+save((fullfile(fotosResultsDir,'anlZones')),'anlZoneRefs')%Saves anl Positions at each tPt
 
 % Print FitResults
 fileExt='.txt';