global SWgrowthArea
global scLst
global ImParMat
global projectScansDir
global matFile
global fhconsole
global easyResultsDir
global printResultsDir
global pointMapsResultsDir
global fotosResultsDir
global matDir
global ImWidth
global ImHeigth
global numRows
global numCols
global scan
global scanMax
global tptLength
global easyDir

numRows=24; % for Single Vertical 
numCols=16; % for Single Vertical 

% CIRCLE related
doCircle=1; % use Circle area analysis 14_0807
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
end

% No idea why we're doing this so commenting out
% close
% EASYconsole

if exist(matFile, 'file')
  bkUpMatFile=fullfile(matFile, '.bk');
  copyfile(matFile,bkUpMatFile);
end

% Reloacated from 'PTmats' to prevent potential overwrite when PTmats is
% copied into new job when the PT template is about the same.  We also
% now have a default template if one is not made. i.e., when the images
% from the new experiment are too sketchy to make a good pintool
% template. By moving it to 'Fotos' we avoid possible issues due to
% copying the Nbdg.mat file along with the default template '.mat' files.
% A copy of Ndbg.mat is placed also saved to the 'PTmats' directory
% after each run to allow previous version of EASY to access data made
% by EASY versions after 20_0819.
try
  load(fullfile(fotosResultsDir,'Nbdg')); % modified to load from 'Fotos' 20_0819
catch
  load(fullfile(pointMapsResultsDir,'Nbdg')); % left in to accomodate loads of work before 20_0819
end
% Load Fotos stored data
fotosToLoad={'Coordinates', 'BGatTpts', 'anlZones', 'NCFparms'};
for i=1:length(fotosToLoad)
  try
    load(fullfile(fotosResultsDir, fotosToLoad{i}));
  catch
    load(fullfile(easyDir,'parameters'));
  end
end

% Get Print Times
PrintTimes=[];
scLst={};

% Parameter Entry
NImParamRadiusGui(projectScansDir); % Ncode 122111replaced removed  ,numOfPrtTimes)
width=24;
widthEx=width-1; % width extention from reference point
dither=ImParMat(6);
radius=ImParMat(10);
NIcircle;

% Load Stuff
lastPlateOnLastScan=1; % Ncode

if size(scLst,1)==1
  SWsingleSc=1;
else 
  SWsingleSc=0;
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
numScans=size(scLst,1);

if(isequal(SWsingleSc,1))
  selScan=str2double(char(scLst(1)));
else
  % startScan=1;
end

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

for ii=1:length(scLst)
  if (SWsingleSc == 1)
    % 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;
    else
      scd=imread(char(Scanfiles(1,1)));
      tptLength=length(Scanfiles);
    end
  ImHeigth=size(scd,1);
  ImWidth=size(scd,2);
  sc=scd(1:ImHeigth,1:ImWidth);
  end

  numFiles=size(Scanfiles,2);

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

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

% 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);
Tmpsbdg00=cell(1); 
TmpexpScanIntens4=cell(1,numScans);
TmpFexpScanSpots4=cell(1,numScans);
TmpFexpScanBMtp4=cell(1,numScans);
TmpanlZoneRefs4=cell(1,numScans);
Tmpsbdg4=cell(1,numScans);
TmpexpScanIntens5=cell(1,numScans);
TmpFexpScanSpots5=cell(1,numScans);
TmpFexpScanBMtp5=cell(1,numScans);
TmpanlZoneRefs5=cell(1,numScans);
Tmpsbdg5=cell(1,numScans);
p4L00=cell(18,1);
p4L0=p4L00;
p4L4=cell(18,numScans);
p4L5=p4L4;
Ag=ones(384);
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,easyResultsDir,projectScansDir, 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"
  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));
  scan(selScan).plate(1).intens=cell2mat(p4L4(4,scanCnt));
  scan(selScan).plate(1).rc=p4L4(5,scanCnt);
  scan(selScan).plate(1).pIndx=cell2mat(p4L4(6,scanCnt));
  scan(selScan).plate(1).Ag=cell2mat(p4L4(7,scanCnt));
  scan(selScan).plate(1).selIntens=p4L4(8,scanCnt); 
  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
  CFparm(1:384)=p4L4{12,scanCnt}(1:384);
  scan(selScan).plate(1).CFparameters=CFparm;
  scan(selScan).plate(1).CFdate=p4L4(13,scanCnt);
  scan(selScan).plate(1).CFout=cell2mat(p4L4(14,scanCnt)); 
  scan(selScan).plate(1).CFoutStd=cell2mat(p4L4(15,scanCnt));
  scan(selScan).Awindow=cell2mat(p4L4(17,scanCnt));
  scan(selScan).Idate=cell2mat(p4L4(18,scanCnt)); 
  expScanIntens(selScan)=TmpexpScanIntens5(scanCnt);
  FexpScanSpots(selScan)=TmpFexpScanSpots5(scanCnt);
  FexpScanBMtp(selScan)=TmpFexpScanBMtp5(scanCnt);
  anlZoneRefs(selScan)=TmpanlZoneRefs5(scanCnt);
  if ~isempty(Tmpsbdg5{scanCnt})
    sbdg(selScan)=Tmpsbdg5(scanCnt);
  else
    sbdg{selScan}=uint8(zeros(24,16,4));
  end
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(fotosResultsDir,'Nbdg')), 'sbdg');
save((fullfile(fotosResultsDir,'Coordinates')),'FexpScanSpots') % saves frames at each tPt
save((fullfile(fotosResultsDir,'BGatTpts')),'FexpScanBMtp')
save((fullfile(fotosResultsDir,'anlZones')),'anlZoneRefs') % saves anl Positions at each tPt

% Print FitResults
fileExt='.txt';
filePrefix='FitResults_';
for scanCnt=1:numScans
  selScan=p4L4{16,scanCnt}; % determine the actual scan in the scanCnt parfor distributed "id"
  fileSuffix=sprintf('Scan%d_Plate%d', selScan, 1);
  fileNamePlate=[filePrefix fileSuffix fileExt];
  fileName=fullfile(printResultsDir, fileNamePlate); % [outputDirectory fileNamePlate];

  % This,fprint for loop,is an very old legacy feature which slows processing. Could be
  % removed but allows easy observation of how a run is progressing and can be
  % 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
    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),...
    outCprint{14,scanCnt}(n,5),outCprint{14,scanCnt}(n,6),outCprint{14,scanCnt}(n,7),outCprint{14,scanCnt}(n,8),...
    outCprint{14,scanCnt}(n,9),outCprint{14,scanCnt}(n,10),outCprint{14,scanCnt}(n,11),outCprint{14,scanCnt}(n,12),...
    outCprint{14,scanCnt}(n,13),outCprint{14,scanCnt}(n,14),outCprint{14,scanCnt}(n,15),outCprint{14,scanCnt}(n,16));
  end
  fclose(fid);
end