%% 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 fhconsole
global ExpPath
global resDir
global wCodeDir
global matDir
global ImWidth
global ImHeigth
global numRows;
global numCols;
%global SWprintLeg
global scan
%global scanSize
global scanMax
global tptLength
%global scanPar4x
%global sols
%global CFmeth

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;

try
  clf(fhconsole,'reset')
catch ME
end

close
EASYconsole

try
  load(ExpOutmat)
  copyfile(ExpOutmat,(fullfile(matDir,'BkUp',strcat((num2str(datenum(now))),'.mat'))))
catch
end

try
  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.
  load(fullfile(resDir,'PTmats','Nbdg')) %Left in to accomodate loads of work before 20_0819
end
% Load Fotos stored data
try
  load(fullfile(resDir,'Fotos','Coordinates'))
catch
end
try
  load(fullfile(resDir,'Fotos','BGatTpts'))
catch
end
try
  load(fullfile(resDir,'Fotos','anlZones'))
catch
end
% autoImCF
try
  load(fullfile(resDir,'PTmats','NCFparms'))    
catch ME
  load parameters   
end

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

% Parameter Entry
NImParamRadiusGui(expDir) % 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(resDir,'PTmats','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
    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);   %?Not used RefOnly
  end

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

  % Initialize tifFilesLst for parfor loop
  dir(fullfile(expDir, 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,resDir,expDir, 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(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

%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=strcat('Scan', num2str(selScan),'_Plate', num2str(1));
  fileNamePlate=[filePrefix fileSuffix fileExt];
  fileName=fullfile(resDir,'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.
  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

EASYconsole;