From 7d621c96ac85bfbae33cbb851d6aa0ef2c90f0c9 Mon Sep 17 00:00:00 2001
From: Bryan Roessler <bryanroessler@gmail.com>
Date: Thu, 25 Jul 2024 18:41:24 -0400
Subject: [PATCH] Format par4Gbl_Main8c.m

---
 workflow/templates/easy/par4Gbl_Main8c.m | 71 +++++++++++-------------
 1 file changed, 33 insertions(+), 38 deletions(-)

diff --git a/workflow/templates/easy/par4Gbl_Main8c.m b/workflow/templates/easy/par4Gbl_Main8c.m
index cd8e3d41..22e53a46 100755
--- a/workflow/templates/easy/par4Gbl_Main8c.m
+++ b/workflow/templates/easy/par4Gbl_Main8c.m
@@ -6,7 +6,7 @@ w=pwd;
 Fflg=1; %0;
 
 fclose('all');  %close all open files
-clear ('plate2', 'scanIntens','Scanfiles','pathname','tifFileLstP4')
+clear('plate2', 'scanIntens','Scanfiles','pathname','tifFileLstP4')
 
 %global SWsingleSc
 global SWgrowthArea
@@ -39,11 +39,11 @@ global tptLength
 %global sols
 %global CFmeth
 
-numRows=24; %for Single Vertical 
-numCols=16; %for Single Vertical 
+numRows=24; % for Single Vertical 
+numCols=16; % for Single Vertical 
 
-%*************CIRCLE related*************************
-doCircle=1;  %use Circle area analysis  14_0807
+% CIRCLE related
+doCircle=1; % use Circle area analysis 14_0807
 radius=14;
 ImParMat(10)=radius;
 ImParMat(11)=doCircle;
@@ -52,11 +52,10 @@ try
   clf(fhconsole,'reset')
 catch ME
 end
-close
 
-%******************************************
+close
 EASYconsole
-%******************************************
+
 try
   load(ExpOutmat)
   copyfile(ExpOutmat,(fullfile(matDir,'BkUp',strcat((num2str(datenum(now))),'.mat'))))
@@ -64,58 +63,54 @@ catch
 end
 
 try
- load(fullfile(resDir,'Fotos','Nbdg')) %Modified to load from 'Fotos' 20_0819
+  load(fullfile(resDir,'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
-  %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.
+  % 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(resDir,'PTmats','Nbdg')) %Left in to accomodate loads of work before 20_0819
 end
-%++++++++++++++Load Fotos stored data++++++++++++++++++++
+% Load Fotos stored data
 try
-    load(fullfile(resDir,'Fotos','Coordinates'))
+  load(fullfile(resDir,'Fotos','Coordinates'))
 catch
 end
 try
-    load(fullfile(resDir,'Fotos','BGatTpts'))
+  load(fullfile(resDir,'Fotos','BGatTpts'))
 catch
 end
 try
-    load(fullfile(resDir,'Fotos','anlZones'))
+  load(fullfile(resDir,'Fotos','anlZones'))
 catch
 end
-%******autoImCF*******************
+% autoImCF
 try
   load(fullfile(resDir,'PTmats','NCFparms'))    
 catch ME
-    load parameters   
+  load parameters   
 end
 
-%************Get Print Times*******************************
+% Get Print Times
 PrintTimes=[];
-if ispc
-  expDir=fullfile(ExpPath,'\');
-elseif (isunix || ismac)
-   expDir=ExpPath
-end 
+expDir=fullfile(ExpPath);
 scLst={};
 
-%**************Parameter Entry******************
-NImParamRadiusGui(expDir) %Ncode 122111replaced removed  ,numOfPrtTimes)
+% Parameter Entry
+NImParamRadiusGui(expDir) % Ncode 122111replaced removed  ,numOfPrtTimes)
 width=24;
-widthEx=width-1;  %width extention from reference point
+widthEx=width-1; % width extention from reference point
 dither=ImParMat(6);
 radius=ImParMat(10);
 NIcircle
 
-%***************** Load Stuff************************* 
-lastPlateOnLastScan=1;  %Ncode
+% Load Stuff
+lastPlateOnLastScan=1; % Ncode
 
 if size(scLst,1)==1
   SWsingleSc=1
@@ -126,7 +121,7 @@ end
 dvec=datevec(datestr(floor(now))); %method to get current offset year '01-Jan-"currentyr"'
 dvec(2)=1;
 dvec(3)=1;
-%yrOffset=datenum('01-Jan-2012');%(dvec); %('01-Jan-2009'); %time num default is currentyear jan1
+% yrOffset=datenum('01-Jan-2012');%(dvec); %('01-Jan-2009'); %time num default is currentyear jan1
 numScans=size(scLst,1);
 
 if(isequal(SWsingleSc,1))
@@ -143,10 +138,10 @@ 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))))
-end
-if isunix
+elseif (isunix || ismac)
   cd(fullfile(expDir,cell2mat(scLst(1))));
 end
 Scanfiles=[];