From 513f531fa4a2f5b5eb0790dd3d8927f1e5a084f8 Mon Sep 17 00:00:00 2001
From: Bryan Roessler <bryanroessler@gmail.com>
Date: Thu, 25 Jul 2024 14:38:26 -0400
Subject: [PATCH] Tighten up formatting

---
 workflow/templates/easy/NCscurImCF_3parfor.m | 33 +++++++++-----------
 1 file changed, 15 insertions(+), 18 deletions(-)

diff --git a/workflow/templates/easy/NCscurImCF_3parfor.m b/workflow/templates/easy/NCscurImCF_3parfor.m
index 608cb46e..f557671b 100755
--- a/workflow/templates/easy/NCscurImCF_3parfor.m
+++ b/workflow/templates/easy/NCscurImCF_3parfor.m
@@ -5,6 +5,7 @@ function [resMatStd, resMat, selTimesStd, selIntensStd, FiltTimesELr, NormIntens
   % Preallocate
   resMatStd=zeros(1,27);
   resMat=zeros(1,27);
+
   % Set internal variables sent to matlab fit function 
   me=200;
   meL=750;
@@ -17,6 +18,7 @@ function [resMatStd, resMat, selTimesStd, selIntensStd, FiltTimesELr, NormIntens
   normIntens=[];
   nn=1;
   numFitTpts=0;
+
   % Build filterTimes and normIntens from spot dataMatrix selection codes produced in filter section  
   for n=1:size(dataMatrix,2)
     if (((dataMatrix(3,n)==1))||(dataMatrix(3,n)==3)||(dataMatrix(3,n)==2)...
@@ -114,32 +116,27 @@ function [resMatStd, resMat, selTimesStd, selIntensStd, FiltTimesELr, NormIntens
   resMatStd(12)=lup;
   resMatStd(13)=currSpotArea;
   resMatStd(14)=lastIntensUsedStd; % filtNormIntens(length(filtNormIntens));
-
   maxRateTime=0; %[];  %Std shows []; ELr shows 0;  %parfor
   resMatStd(15)=0; %maxRateTimestdMeth;
-
   resMatStd(16)=lastTptUsedStd;
   if isempty(Tpt1Std)
     Tpt1Std=777;
   end
   resMatStd(17)=Tpt1Std;
-  resMatStd(18)=bl; %perform in the filter section of NCfitImCFparfor
-  resMatStd(19)=fitblStd; %Taken from NCfil... and not affected by NCscur...changes
-  resMatStd(20)=minTime; %Not affected by changes made in NCscur...for refined 'r'
+  resMatStd(18)=bl; % perform in the filter section of NCfitImCFparfor
+  resMatStd(19)=fitblStd; % taken from NCfil... and not affected by NCscur...changes
+  resMatStd(20)=minTime; % not affected by changes made in NCscur...for refined 'r'
   resMatStd(21)=thresGT2TmStd;
   resMatStd(22)=numFitTptsStd;
   resMatStd(23)=numTptsGT2Std;
-  resMatStd(24)=999; %The Standard method has no cuts .:.no cutTm  
+  resMatStd(24)=999; % yhe Standard method has no cuts .:.no cutTm  
   resMatStd(25)=999;
   resMatStd(26)=999;
   resMatStd(27)=999;
 
-  %if SwitchEvsEL==3  %Remove 'SwitchEvsEL==...' temporary SWITCH when Hartman decides what he wants
-  %*********************************************************************************
-  %ELr         New Experimental data through L+deltaS Logistic fit for 'Improved r'  Fitting
-  %*********************************************************************************
-  FiltTimesELr=[];  %{ii}= filterTimes;
-  NormIntensELr=[];  %{ii}= normIntens;  
+  % ELr New Experimental data through L+deltaS Logistic fit for 'Improved r'  Fitting
+  FiltTimesELr=[];  %{ii}=filterTimes;
+  NormIntensELr=[];  %{ii}=normIntens;  
   normIntens=selIntensStd;
   filterTimes=selTimesStd;
   stdIntens=selIntensStd;
@@ -215,20 +212,20 @@ function [resMatStd, resMat, selTimesStd, selIntensStd, FiltTimesELr, NormIntens
     
       ftype=fittype('K / (1 +  exp(-r* (t - l )))','independent','t','dependent',['K','l','r'],'options',opts);
       fitObject=[]; errObj=[];
-       % carry out the curve fitting process
+      % carry out the curve fitting process
       [fitObject, errObj]=fit(Tms,Ints,ftype);
       coeffsArray=coeffvalues(fitObject);
-      r3=coeffsArray(3); %sDat(slps,4)=coeffsArray(3); % rateS
+      r3=coeffsArray(3); % sDat(slps,4)=coeffsArray(3); % rateS
     
       if (exist('K','var')&& exist('r','var') && exist('l','var'))
         t=(0:1:200);   
-        GrowthELr = K ./ (1 +  exp(-r.* (t - l )));
-        fitblELr= min(GrowthELr);   %jh diag
+        GrowthELr=K ./ (1 +  exp(-r.* (t - l )));
+        fitblELr=min(GrowthELr);   %jh diag
       end
     catch ME
       % 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=[];
+      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=[];
     end
   end