285 lines
9.1 KiB
Matlab
Executable File
285 lines
9.1 KiB
Matlab
Executable File
%% CALLED BY EASYconsole.m %%
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w=pwd;
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%function NImStartupImCF02par4Gbl
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Fflg=1; %0;
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fclose('all'); %close all open files
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clear ('plate2', 'scanIntens','Scanfiles','pathname','tifFileLstP4')
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%global SWsingleSc
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global SWgrowthArea
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global scLst
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global ImParMat
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%global CSearchRange
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%global CSrchRng
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global expDir
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global SWnewExp
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global openExpfile
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global openExppath
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global newExpfile
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global newExppath
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global ExpOutmat
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global fhconsole
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global ExpPath
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global resDir
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global wCodeDir
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global matDir
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global ImWidth
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global ImHeigth
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global numRows;
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global numCols;
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%global SWprintLeg
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global scan
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%global scanSize
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global scanMax
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global tptLength
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%global scanPar4x
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%global sols
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%global CFmeth
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numRows=24; %for Single Vertical
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numCols=16; %for Single Vertical
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%*************CIRCLE related*************************
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doCircle=1; %use Circle area analysis 14_0807
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radius=14;
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ImParMat(10)=radius;
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ImParMat(11)=doCircle;
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try
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clf(fhconsole,'reset')
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catch ME
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end
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close
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%******************************************
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EASYconsole
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%******************************************
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try
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load(ExpOutmat)
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copyfile(ExpOutmat,(fullfile(matDir,'BkUp',strcat((num2str(datenum(now))),'.mat'))))
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catch
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end
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try
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load(fullfile(resDir,'Fotos','Nbdg')) %Modified to load from 'Fotos' 20_0819
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catch
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%Reloacated from 'PTmats' to prevent potential overwrite when PTmats is
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%copied into new job when the PT template is about the same. We also
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%now have a default template if one is not made. i.e., when the images
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%from the new experiment are too sketchy to make a good pintool
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%template. By moving it to 'Fotos' we avoid possible issues due to
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%copying the Nbdg.mat file along with the default template '.mat' files.
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%A copy of Ndbg.mat is placed also saved to the 'PTmats' directory
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%after each run to allow previous version of EASY to access data made
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%by EASY versions after 20_0819.
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load(fullfile(resDir,'PTmats','Nbdg')) %Left in to accomodate loads of work before 20_0819
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end
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%++++++++++++++Load Fotos stored data++++++++++++++++++++
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try
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load(fullfile(resDir,'Fotos','Coordinates'))
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catch
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end
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try
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load(fullfile(resDir,'Fotos','BGatTpts'))
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catch
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end
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try
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load(fullfile(resDir,'Fotos','anlZones'))
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catch
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end
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%******autoImCF*******************
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try
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load(fullfile(resDir,'PTmats','NCFparms'))
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catch ME
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load parameters
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end
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%************Get Print Times*******************************
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PrintTimes=[];
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if ispc
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expDir=fullfile(ExpPath,'\');
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elseif (isunix || ismac)
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expDir=ExpPath
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end
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scLst={};
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%**************Parameter Entry******************
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NImParamRadiusGui(expDir) %Ncode 122111replaced removed ,numOfPrtTimes)
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width=24;
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widthEx=width-1; %width extention from reference point
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dither=ImParMat(6);
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radius=ImParMat(10);
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NIcircle
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%***************** Load Stuff*************************
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lastPlateOnLastScan=1; %Ncode
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if size(scLst,1)==1
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SWsingleSc=1
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else
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SWsingleSc=0
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end
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dvec=datevec(datestr(floor(now))); %method to get current offset year '01-Jan-"currentyr"'
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dvec(2)=1;
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dvec(3)=1;
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%yrOffset=datenum('01-Jan-2012');%(dvec); %('01-Jan-2009'); %time num default is currentyear jan1
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numScans=size(scLst,1);
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if(isequal(SWsingleSc,1))
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selScan=str2double(char(scLst(1)));
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else
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% startScan=1;
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end
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SWgrowthArea=ImParMat(9);
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load(fullfile(resDir,'PTmats','NPTmapSearch'))
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PTmapPos=detPos;
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selScanNumLst=[];
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Scanfiles=[];
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pathname=[];
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if ispc
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cd(char(strcat(expDir,scLst(1))))
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end
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if isunix
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cd(fullfile(expDir,cell2mat(scLst(1))));
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end
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Scanfiles=[];
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pathname=[];
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for ii=1:length(scLst)
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if (SWsingleSc == 1)
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[Scanfiles, pathname]=uigetfile('*.bmp', 'Select files','MultiSelect','on');% change '*hr*.bmp' 12/20/2011
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if ischar(Scanfiles)
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scd=imread(char(Scanfiles));
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tptLength=1;
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else
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scd=imread(char(Scanfiles(1,1)));
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tptLength=length(Scanfiles);
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end
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ImHeigth=size(scd,1);
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ImWidth=size(scd,2);
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sc=scd(1:ImHeigth,1:ImWidth); %?Not used RefOnly
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end
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cd(w);
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numFiles=size(Scanfiles,2);
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% Initialize tifFilesLst for parfor loop
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dir(fullfile(expDir, char(scLst(ii)), '*.bmp'));
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numFiles=length(tifFileLst4MultiT);
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tptLength=numFiles;
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tifFileLstP4{ii}={tifFileLst4MultiT.name};
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end
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for jj=1:numScans %startScan:numScans
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selScan=str2double(char(scLst(jj)));
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selScanNumLst(jj)=selScan;
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end
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selScanNumLst2=selScanNumLst; %function passthrough, passback to par4gbl_Main 20_0205
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% PREALLOCATION
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scCount=[];
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TmpexpScanIntens00=cell(1); %cell(1,scanMax);
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TmpFexpScanSpots00=cell(1); %cell(1,scanMax);
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TmpFexpScanBMtp00=cell(1); %cell(1,scanMax);
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TmpanlZoneRefs00=cell(1); %cell(1,scanMax);
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Tmpsbdg00=cell(1);
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TmpexpScanIntens4=cell(1,numScans);
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TmpFexpScanSpots4=cell(1,numScans);
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TmpFexpScanBMtp4=cell(1,numScans);
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TmpanlZoneRefs4=cell(1,numScans);
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Tmpsbdg4=cell(1,numScans);
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TmpexpScanIntens5=cell(1,numScans);
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TmpFexpScanSpots5=cell(1,numScans);
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TmpFexpScanBMtp5=cell(1,numScans);
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TmpanlZoneRefs5=cell(1,numScans);
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Tmpsbdg5=cell(1,numScans);
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p4L00=cell(18,1);
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p4L0=p4L00;
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p4L4=cell(18,numScans);
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p4L5=p4L4;
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Ag=ones(384);
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CFscanIntens=zeros(16,24);
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[p4L4,TmpexpScanIntens5,TmpFexpScanSpots5,TmpFexpScanBMtp5,TmpanlZoneRefs5,Tmpsbdg5]= ...
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p4loop8c(parMat,tptLength,numScans,selScanNumLst,SWsingleSc,Fflg,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,cirMask,width, ...
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TmpexpScanIntens00,TmpFexpScanSpots00,TmpFexpScanBMtp00,TmpanlZoneRefs00,scCount,tifFileLstP4,pathname,ImParMat, ...
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numRows,numCols,scLst,resDir,expDir, p4L00,TmpexpScanIntens4,TmpFexpScanSpots4,TmpFexpScanBMtp4,TmpanlZoneRefs4, ...
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Tmpsbdg00,Tmpsbdg4);
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for scanCnt=1:numScans
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selScan=p4L4{16,scanCnt}; %determine the actual scan in the scanCnt parfor distributed "id"
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scan(selScan).plate(1).tSeries=cell2mat(p4L4(1,scanCnt));
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scan(selScan).plate(1).t0Series=cell2mat(p4L4(2,scanCnt));
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scan(selScan).plate(1).printTm=cell2mat(p4L4(3,scanCnt));
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scan(selScan).plate(1).intens=cell2mat(p4L4(4,scanCnt));
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scan(selScan).plate(1).rc=p4L4(5,scanCnt);
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scan(selScan).plate(1).pIndx=cell2mat(p4L4(6,scanCnt));
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scan(selScan).plate(1).Ag=cell2mat(p4L4(7,scanCnt));
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scan(selScan).plate(1).selIntens=p4L4(8,scanCnt);
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scan(selScan).plate(1).selTimes=p4L4(9,scanCnt);
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scan(selScan).plate(1).filterTimes=p4L4(10,scanCnt);
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scan(selScan).plate(1).normIntens=p4L4(11,scanCnt);
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%scan(selScan).plate(1).CFparameters=p4L4(12,scanCnt); %Need to convert to a matrix form like Old versions
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CFparm(1:384)=p4L4{12,scanCnt}(1:384);
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scan(selScan).plate(1).CFparameters=CFparm;
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scan(selScan).plate(1).CFdate=p4L4(13,scanCnt);
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scan(selScan).plate(1).CFout=cell2mat(p4L4(14,scanCnt));
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scan(selScan).plate(1).CFoutStd=cell2mat(p4L4(15,scanCnt));
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scan(selScan).Awindow=cell2mat(p4L4(17,scanCnt));
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scan(selScan).Idate=cell2mat(p4L4(18,scanCnt));
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expScanIntens(selScan)=TmpexpScanIntens5(scanCnt);
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FexpScanSpots(selScan)=TmpFexpScanSpots5(scanCnt);
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FexpScanBMtp(selScan)=TmpFexpScanBMtp5(scanCnt);
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anlZoneRefs(selScan)=TmpanlZoneRefs5(scanCnt);
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if ~isempty(Tmpsbdg5{scanCnt})
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sbdg(selScan)=Tmpsbdg5(scanCnt);
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else
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sbdg{selScan}=uint8(zeros(24,16,4));
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end
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end
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%SAVE DATA in .mat files
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save(ExpOutmat,'scan');
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% save((fullfile(resDir,'PTmats','Nbdg')), 'sbdg'); %legacy location can probably get rid of in time
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save((fullfile(resDir,'Fotos','Nbdg')), 'sbdg');
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save((fullfile(resDir,'Fotos','Coordinates')),'FexpScanSpots') %Saves frames at each tPt
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save((fullfile(resDir,'Fotos','BGatTpts')),'FexpScanBMtp')
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save((fullfile(resDir,'Fotos','anlZones')),'anlZoneRefs')%Saves anl Positions at each tPt
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%Print FitResults *******************************************************
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fileExt='.txt';
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filePrefix='FitResults_';
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for scanCnt=1:numScans
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selScan=p4L4{16,scanCnt}; %determine the actual scan in the scanCnt parfor distributed "id"
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fileSuffix=strcat('Scan', num2str(selScan),'_Plate', num2str(1));
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fileNamePlate=[filePrefix fileSuffix fileExt];
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fileName=fullfile(resDir,'PrintResults', fileNamePlate); %[outputDirectory fileNamePlate];
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%This,fprint for loop,is an very old legacy feature which slows processing. Could be
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%removed but allows easy observation of how a run is progressing and can be
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%used as a diagnostic tool.
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outCprint=p4L4;
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fid=fopen(fileName,'w');
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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');
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for n=1:384 %startCount:numCultures
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fprintf(fid,'%d\t',n);
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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',...
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outCprint{14,scanCnt}(n,1),outCprint{14,scanCnt}(n,2),outCprint{14,scanCnt}(n,3),outCprint{14,scanCnt}(n,4),...
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outCprint{14,scanCnt}(n,5),outCprint{14,scanCnt}(n,6),outCprint{14,scanCnt}(n,7),outCprint{14,scanCnt}(n,8),...
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outCprint{14,scanCnt}(n,9),outCprint{14,scanCnt}(n,10),outCprint{14,scanCnt}(n,11),outCprint{14,scanCnt}(n,12),...
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outCprint{14,scanCnt}(n,13),outCprint{14,scanCnt}(n,14),outCprint{14,scanCnt}(n,15),outCprint{14,scanCnt}(n,16));
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end
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fclose(fid);
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end
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EASYconsole;
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