%% CALLED BY EASYconsole.m %%

%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
%Console globals*******
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 sols
%global CFmeth
numRows=24; %for Single Vertical 
numCols=16; %for Single Vertical 

%global scanPar4x
%*************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=[];
 w= cd; %Capture current dir in w
 if ispc  %Linux accommodation
 expDir=fullfile(ExpPath,'\');
 else
    if isunix, expDir= ExpPath;end
    if ismac , expDir=ExpPath;end
 end 
scLst={};
%**************Parameter Entry******************
NImParamRadiusGui(expDir) %Ncode 122111replaced removed  ,numOfPrtTimes)
%***********************************************
%width=ImParMat(5);
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)));
    %numScans=selScan;
    %startScan=selScan;
else
    %startScan=1;
end

SWgrowthArea= ImParMat(9);
load(fullfile(resDir,'PTmats','NPTmapSearch'))
     PTmapPos= detPos;

%**************************************************************************
selScanNumLst= [];

%++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 

%**************************************************************************
%*********Preallocation for Scan Loop**************************************************

Scanfiles=[];
pathname=[];
%++++++++++++++++++++++++++++++++ SETUP FOR GLOBAL PARFOR LOOP+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
%if SWsingleSc == 1  %if single scan else do expMultiTseries to execute multiple scans 
%******Gui Select Scan -> *.tif files for Analysis*****************  
 w= cd; %Capture current dir in w
if ispc
cd(char(strcat(expDir,scLst(1))))
end
if isunix
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);
%tifFileLst= Scanfiles;

%Initialize tifFilesLst for parfor loop
        if ispc  %Linux and mac accomodation
          tifFileLst4MultiT = dir(fullfile(expDir, char(scLst(ii)), '\*.bmp'));
        end
        if isunix || ismac
        tifFileLst4MultiT = dir(fullfile(expDir, char(scLst(ii)), '*.bmp'));
        end
       numFiles=length(tifFileLst4MultiT);  
       tptLength= numFiles;
      tifFileLstP4{ii}={tifFileLst4MultiT.name};  
      %{
      dateTmStampP4{ii}= {tifFileLst4MultiT.date}
      dateTmNum{ii}= datenum(dateTmStampP4{1});
      info{ii} = imfinfo(tifFileLstP4{ii});
      scTmNumericP4(ii)=datenum(info{ii}.FileModDate);
      %}
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  PREALLOCATION  PREALLOCATION  PREALLOCATION  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;


         %+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++