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Cleanup par4Gbl_Main8c.m

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This commit is contained in:
Bryan Roessler
2024-07-25 10:26:37 -04:00
parent 359b936b45
commit adf507476d
5 changed files with 176 additions and 268 deletions
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18
workflow/script-run-workflow
View File

@@ -533,13 +533,19 @@ easy() {
'NoGrowth_.txt', and 'GrowthOnly_.txt' files will be generated in the 'PrintResults' folder. 'NoGrowth_.txt', and 'GrowthOnly_.txt' files will be generated in the 'PrintResults' folder.
EOF EOF
script="EASYConsole.m" script="$EASY_TEMPLATE_DIR/EASYConsole.m"
pushd "$EASY_TEMPLATE_DIR" || return 1 # Add EASY directory to the Matlab path
# Launch graphical matlab if the user wants # If this does not work we can try changing the -sd argument and if that fails then pushing/popping
! ((YES)) && ask "Start EASY in MATLAB? This requires a GUI." && debug "Adding EASY directory to the Matlab path"
matlab -nosplash -sd ~/downloads -r "$script" hash matlab &>/dev/null &&
popd || return 1 matlab -nodisplay -nosplash -nodesktop -nojvm -batch "addpath('$EASY_TEMPLATE_DIR')"
# Ask the user to launch EASYconsole.m in MATLAB
# MATLAB doesn't support passing args to scripts se we have to use ENV VARS instead
# These are proably already set in our scope but be explicit just in case
! ((YES)) && ask "Start EASY in MATLAB? This requires a GUI." &&
SCANS_DIR="$SCANS_DIR" matlab -nosplash -sd "$SCANS_DIR" -r "run $script"
# Use the function return code see if we succeeded # Use the function return code see if we succeeded
get_easy_results "$SCANS_DIR" || return 1 get_easy_results "$SCANS_DIR" || return 1

19
workflow/templates/easy/DMPexcel2mat.m
View File

@@ -1,21 +1,5 @@
%% CALLED BY EASYconsole.m %% %% CALLED BY EASYconsole.m %%
w = pwd; w=pwd
%{
cd ..
if exist('ExpJobs/')
cd('ExpJobs/');
else
pwd
end
%}
try
cd(ExpPath)
catch
cd(w)
end
pwd
numOfMPs=0; numOfMPs=0;
%GUI input for selecting a MasterPlate Excel file %GUI input for selecting a MasterPlate Excel file
questdlg('\fontsize{20} Select Master Plate File','File Selection','OK', struct('Default','OK','Interpreter','tex')) questdlg('\fontsize{20} Select Master Plate File','File Selection','OK', struct('Default','OK','Interpreter','tex'))
@@ -26,7 +10,6 @@ else
MPdir=fullfile(pathname,'/'); MPdir=fullfile(pathname,'/');
end end
infile= Scanfiles(1,:); infile= Scanfiles(1,:);
cd(MPdir) cd(MPdir)
%fid=fopen(infile)%('exp23PrintTimes.xls'); % textread puts date and time sequentially into vector %fid=fopen(infile)%('exp23PrintTimes.xls'); % textread puts date and time sequentially into vector

6
workflow/templates/easy/DgenResults.m
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@@ -6,7 +6,6 @@ global resDir
global ExpOutmat global ExpOutmat
global ImParMat global ImParMat
w=pwd;
ln=1; ln=1;
@@ -403,8 +402,8 @@ catch ME
errordlg(rep) errordlg(rep)
end end
end %if DB end %if DB
ln; % ln; TODO removed by BCR, this doesn't seem necessary
cd(w)
%*********************************************************************** %***********************************************************************
@@ -721,7 +720,6 @@ catch
errorNstdResults='Catch at line720 for printing ResultsStd' errorNstdResults='Catch at line720 for printing ResultsStd'
end %try scan(1).plate(1).CFoutStd(1,1) to test for 2018 r_refined version end %try scan(1).plate(1).CFoutStd(1,1) to test for 2018 r_refined version
cd(w)
scriptComplete= "line724 " scriptComplete= "line724 "
msgbox(['Printing Script complete. Check !!Results sheets in ../PrintResults folder.']) msgbox(['Printing Script complete. Check !!Results sheets in ../PrintResults folder.'])

37
workflow/templates/easy/EASYconsole.m
View File

@@ -14,7 +14,9 @@ function varargout = EASYconsole(varargin)
wCodeDir=pwd; wCodeDir=pwd;
% changing directory to wCodeDir % changing directory to wCodeDir
returnStartDir % returnStartDir
disp(getenv('SCANS_DIR'));
%% GUI INTERFACE DESIGN %% %% GUI INTERFACE DESIGN %%
% beginning of GUI formation & design, see help GUI or help GUIDE in % beginning of GUI formation & design, see help GUI or help GUIDE in
@@ -102,12 +104,12 @@ end
%% CONSOLE BUTTON INTERFACES %% %% CONSOLE BUTTON INTERFACES %%
% File Button Interface % File Button Interface
function FileMenu_Callback(~, ~, ~) function FileMenu_Callback(~, ~, ~)
returnStartDir %returnStartDir
end end
% Load Experiment Button Interface % Load Experiment Button Interface
function LoadExp_Callback(~, ~, ~) function LoadExp_Callback(~, ~, ~)
returnStartDir %returnStartDir
end end
% New Experiment Button Interface % New Experiment Button Interface
@@ -123,7 +125,7 @@ function NewExpDat_Callback(~, ~, ~)
global scan global scan
% put all users on same working directory % put all users on same working directory
returnStartDir %returnStartDir
% Create a new experiment % Create a new experiment
try try
@@ -177,7 +179,7 @@ function NewExpDat_Callback(~, ~, ~)
sbdg= cell(1,scanMax); sbdg= cell(1,scanMax);
save((fullfile(resDir,'Fotos','Nbdg')),'sbdg'); save((fullfile(resDir,'Fotos','Nbdg')),'sbdg');
catch ME catch ME
returnStartDir % returnStartDir
disp('Error Creating a New Experiment') disp('Error Creating a New Experiment')
end end
@@ -202,8 +204,6 @@ function LoadDatFile_Callback(~, ~, ~)
global fhconsole global fhconsole
%global ImParMat %global ImParMat
returnStartDir
% TODO this entire try block needs work % TODO this entire try block needs work
try try
% TODO this whole block is highly questionable % TODO this whole block is highly questionable
@@ -265,11 +265,10 @@ end
% callback for the 'Run' in the dropdown menu % callback for the 'Run' in the dropdown menu
function run_Callback(~, ~, ~) function run_Callback(~, ~, ~)
returnStartDir
end end
function runPlateMapPintool_Callback(~, ~, ~) function runPlateMapPintool_Callback(~, ~, ~)
returnStartDir
try try
NImapPT NImapPT
catch ME catch ME
@@ -279,7 +278,6 @@ function runPlateMapPintool_Callback(~, ~, ~)
end end
function NImCFcombo_Callback(~, ~, ~) function NImCFcombo_Callback(~, ~, ~)
returnStartDir
try try
par4Gbl_Main8c par4Gbl_Main8c
catch catch
@@ -289,7 +287,6 @@ function NImCFcombo_Callback(~, ~, ~)
end end
function runPlateImAnal_Callback(~, ~, ~) function runPlateImAnal_Callback(~, ~, ~)
returnStartDir
try try
NImStartupOnly NImStartupOnly
catch ME catch ME
@@ -300,7 +297,6 @@ end
function PlateCFit_Callback(~, ~, ~) function PlateCFit_Callback(~, ~, ~)
%global ExpOutmat %global ExpOutmat
returnStartDir
try try
NCstart NCstart
catch ME catch ME
@@ -340,10 +336,8 @@ function Tools_Callback(~, ~, ~)
end end
function runOverlayPlots_Callback(~, ~, ~) function runOverlayPlots_Callback(~, ~, ~)
returnStartDir
try try
DoverlayPlots2 DoverlayPlots2
returnStartDir
EASYconsole EASYconsole
catch ME catch ME
returnStartDir returnStartDir
@@ -352,10 +346,8 @@ function runOverlayPlots_Callback(~, ~, ~)
end end
function runFotoStrip_Callback(~, ~, ~) function runFotoStrip_Callback(~, ~, ~)
returnStartDir
try try
F_NImStartup_CentCir F_NImStartup_CentCir
returnStartDir
EASYconsole EASYconsole
catch ME catch ME
returnStartDir returnStartDir
@@ -364,7 +356,6 @@ function runFotoStrip_Callback(~, ~, ~)
end end
function runDisplayFig_Callback(~, ~, ~) function runDisplayFig_Callback(~, ~, ~)
returnStartDir
try try
UfigDisplay UfigDisplay
catch ME catch ME
@@ -374,7 +365,6 @@ function runDisplayFig_Callback(~, ~, ~)
end end
function runViewParameters_Callback(~, ~, ~) function runViewParameters_Callback(~, ~, ~)
returnStartDir
try try
catch ME catch ME
returnStartDir returnStartDir
@@ -383,17 +373,7 @@ function runViewParameters_Callback(~, ~, ~)
end end
function QkviewN_Callback(~, ~, ~) function QkviewN_Callback(~, ~, ~)
returnStartDir
try try
try
cd(fullfile(ExpPath))
catch
if ispc
cd('C:\')
else
cd(fullfile('~'));
end
end
QkviewImages QkviewImages
catch ME catch ME
returnStartDir returnStartDir
@@ -402,7 +382,6 @@ function QkviewN_Callback(~, ~, ~)
end end
function CFdisplay_Callback(~, ~, ~) function CFdisplay_Callback(~, ~, ~)
returnStartDir
try try
NCsingleDisplay NCsingleDisplay
returnStartDir returnStartDir

364
workflow/templates/easy/par4Gbl_Main8c.m
View File

@@ -1,7 +1,9 @@
%% CALLED BY EASYconsole.m %% %% CALLED BY EASYconsole.m %%
w=pwd;
%function NImStartupImCF02par4Gbl %function NImStartupImCF02par4Gbl
Fflg= 1; %0; Fflg=1; %0;
fclose('all'); %close all open files fclose('all'); %close all open files
clear ('plate2', 'scanIntens','Scanfiles','pathname','tifFileLstP4') clear ('plate2', 'scanIntens','Scanfiles','pathname','tifFileLstP4')
@@ -14,7 +16,6 @@ global ImParMat
%global CSrchRng %global CSrchRng
global expDir global expDir
global SWnewExp global SWnewExp
%Console globals*******
global openExpfile global openExpfile
global openExppath global openExppath
global newExpfile global newExpfile
@@ -24,8 +25,7 @@ global fhconsole
global ExpPath global ExpPath
global resDir global resDir
global wCodeDir global wCodeDir
global matDir % global matDir
global ImWidth global ImWidth
global ImHeigth global ImHeigth
global numRows; global numRows;
@@ -35,48 +35,47 @@ global scan
%global scanSize %global scanSize
global scanMax global scanMax
global tptLength global tptLength
%global scanPar4x
%global sols %global sols
%global CFmeth %global CFmeth
numRows=24; %for Single Vertical numRows=24; %for Single Vertical
numCols=16; %for Single Vertical numCols=16; %for Single Vertical
%global scanPar4x
%*************CIRCLE related************************* %*************CIRCLE related*************************
doCircle=1; %use Circle area analysis 14_0807 doCircle=1; %use Circle area analysis 14_0807
radius=14; radius=14;
ImParMat(10)=radius; ImParMat(10)=radius;
ImParMat(11)=doCircle; ImParMat(11)=doCircle;
try try
clf(fhconsole,'reset') clf(fhconsole,'reset')
catch ME catch ME
end end
close close
%****************************************** %******************************************
EASYconsole EASYconsole
%****************************************** %******************************************
try try
load(ExpOutmat) load(ExpOutmat)
copyfile(ExpOutmat,(fullfile(matDir,'BkUp',strcat((num2str(datenum(now))),'.mat')))) copyfile(ExpOutmat,(fullfile(matDir,'BkUp',strcat((num2str(datenum(now))),'.mat'))))
catch catch
end end
try 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 catch
%Reloacated from 'PTmats' to prevent potential overwrite when PTmats is %Reloacated from 'PTmats' to prevent potential overwrite when PTmats is
%copied into new job when the PT template is about the same. We also %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 %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 %from the new experiment are too sketchy to make a good pintool
%template. By moving it to 'Fotos' we avoid possible issues due to %template. By moving it to 'Fotos' we avoid possible issues due to
%copying the Nbdg.mat file along with the default template '.mat' files. %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 %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 %after each run to allow previous version of EASY to access data made
%by EASY versions after 20_0819. %by EASY versions after 20_0819.
load(fullfile(resDir,'PTmats','Nbdg')) %Left in to accomodate loads of work before 20_0819
load(fullfile(resDir,'PTmats','Nbdg')) %Left in to accomodate loads of work before 20_0819
end end
%++++++++++++++Load Fotos stored data++++++++++++++++++++ %++++++++++++++Load Fotos stored data++++++++++++++++++++
try try
@@ -93,250 +92,193 @@ catch
end end
%******autoImCF******************* %******autoImCF*******************
try try
load(fullfile(resDir,'PTmats','NCFparms')) load(fullfile(resDir,'PTmats','NCFparms'))
catch ME catch ME
load parameters load parameters
end end
%*******************************
%************Get Print Times******************************* %************Get Print Times*******************************
PrintTimes=[]; PrintTimes=[];
w= cd; %Capture current dir in w if ispc
if ispc %Linux accommodation expDir=fullfile(ExpPath,'\');
expDir=fullfile(ExpPath,'\'); elseif (isunix || ismac)
else expDir=ExpPath
if isunix, expDir= ExpPath;end end
if ismac , expDir=ExpPath;end
end
scLst={}; scLst={};
%**************Parameter Entry****************** %**************Parameter Entry******************
NImParamRadiusGui(expDir) %Ncode 122111replaced removed ,numOfPrtTimes) NImParamRadiusGui(expDir) %Ncode 122111replaced removed ,numOfPrtTimes)
%***********************************************
%width=ImParMat(5);
width=24; width=24;
widthEx=width-1; %width extention from reference point widthEx=width-1; %width extention from reference point
dither=ImParMat(6); dither=ImParMat(6);
radius=ImParMat(10); radius=ImParMat(10);
%>>>>>>>>>>>>>>>>>>>>>>
NIcircle NIcircle
%<<<<<<<<<<<<<<<<<<<<<<<
%***************** Load Stuff************************* %***************** Load Stuff*************************
lastPlateOnLastScan=1; %Ncode lastPlateOnLastScan=1; %Ncode
if size(scLst,1)==1,SWsingleSc=1;else SWsingleSc=0;end 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=datevec(datestr(floor(now))); %method to get current offset year '01-Jan-"currentyr"'
dvec(2)=1; dvec(2)=1;
dvec(3)=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); numScans=size(scLst,1);
if(isequal(SWsingleSc,1)) if(isequal(SWsingleSc,1))
selScan=str2double(char(scLst(1))); selScan=str2double(char(scLst(1)));
%numScans=selScan;
%startScan=selScan;
else else
%startScan=1; % startScan=1;
end end
SWgrowthArea= ImParMat(9); SWgrowthArea=ImParMat(9);
load(fullfile(resDir,'PTmats','NPTmapSearch')) load(fullfile(resDir,'PTmats','NPTmapSearch'))
PTmapPos= detPos; PTmapPos=detPos;
%**************************************************************************
selScanNumLst= [];
%++++++++++++++++++++++++++++++++++++++++++++++++++++++++
%**************************************************************************
%*********Preallocation for Scan Loop**************************************************
selScanNumLst=[];
Scanfiles=[]; Scanfiles=[];
pathname=[]; 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 if ispc
cd(char(strcat(expDir,scLst(1)))) cd(char(strcat(expDir,scLst(1))))
end end
if isunix if isunix
cd (fullfile(expDir,cell2mat(scLst(1)))); cd(fullfile(expDir,cell2mat(scLst(1))));
end end
Scanfiles=[]; Scanfiles=[];
pathname=[]; 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
for ii= 1:length(scLst) cd(w);
if SWsingleSc == 1 numFiles=size(Scanfiles,2);
[Scanfiles, pathname]=uigetfile('*.bmp', 'Select files','MultiSelect','on');% change '*hr*.bmp' 12/20/2011
if ischar(Scanfiles)
scd= imread(char(Scanfiles));
tptLength=1;
% 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 else
scd= imread(char(Scanfiles(1,1))); sbdg{selScan}=uint8(zeros(24,16,4));
tptLength= length(Scanfiles);
end 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 end
%SAVE DATA in .mat files %SAVE DATA in .mat files
save(ExpOutmat,'scan'); save(ExpOutmat,'scan');
save((fullfile(resDir,'PTmats','Nbdg')), 'sbdg'); %legacy location can probably get rid of in time % 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','Nbdg')), 'sbdg');
save((fullfile(resDir,'Fotos','Coordinates')),'FexpScanSpots') %Saves frames at each tPt save((fullfile(resDir,'Fotos','Coordinates')),'FexpScanSpots') %Saves frames at each tPt
save((fullfile(resDir,'Fotos','BGatTpts')),'FexpScanBMtp') save((fullfile(resDir,'Fotos','BGatTpts')),'FexpScanBMtp')
save((fullfile(resDir,'Fotos','anlZones')),'anlZoneRefs')%Saves anl Positions at each tPt save((fullfile(resDir,'Fotos','anlZones')),'anlZoneRefs')%Saves anl Positions at each tPt
%Print FitResults ******************************************************* %Print FitResults *******************************************************
fileExt = '.txt'; fileExt='.txt';
filePrefix = 'FitResults_'; filePrefix='FitResults_';
for scanCnt= 1:numScans for scanCnt=1:numScans
selScan= p4L4{16,scanCnt}; %determine the actual scan in the scanCnt parfor distributed "id" 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];
fileSuffix= strcat('Scan', num2str(selScan),'_Plate', num2str(1)); %This,fprint for loop,is an very old legacy feature which slows processing. Could be
fileNamePlate = [filePrefix fileSuffix fileExt]; %removed but allows easy observation of how a run is progressing and can be
fileName= fullfile(resDir,'PrintResults', fileNamePlate); %[outputDirectory fileNamePlate]; %used as a diagnostic tool.
outCprint=p4L4;
%This,fprint for loop,is an very old legacy feature which slows processing. Could be fid=fopen(fileName,'w');
%removed but allows easy observation of how a run is progressing and can be 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');
%used as a diagnostic tool. 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= p4L4; 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),...
fid = fopen(fileName,'w'); outCprint{14,scanCnt}(n,9),outCprint{14,scanCnt}(n,10),outCprint{14,scanCnt}(n,11),outCprint{14,scanCnt}(n,12),...
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'); outCprint{14,scanCnt}(n,13),outCprint{14,scanCnt}(n,14),outCprint{14,scanCnt}(n,15),outCprint{14,scanCnt}(n,16));
for n=1:384 %startCount:numCultures end
fprintf(fid,'%d\t',n); fclose(fid);
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 end
fclose(fid);
end
EASYconsole; EASYconsole;
%+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++