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EASY rewrite

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This commit is contained in:
Bryan Roessler
2024-07-23 10:54:58 -04:00
parent 0440912859
commit 811a1c2dc4
26 changed files with 5472 additions and 167 deletions
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246
workflow/templates/easy/DMPexcel2mat.m Executable file
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%% CALLED BY EASYconsole.m %%
w = pwd;
%{
cd ..
if exist('ExpJobs/')
cd('ExpJobs/');
else
pwd
end
%}
try
cd(ExpPath)
catch
cd(w)
end
pwd
numOfMPs=0;
%GUI input for selecting a MasterPlate Excel file
questdlg('\fontsize{20} Select Master Plate File','File Selection','OK', struct('Default','OK','Interpreter','tex'))
[Scanfiles, pathname]=uigetfile('*.*','MultiSelect','off');
if ispc
MPdir= fullfile(pathname,'\');
else
MPdir=fullfile(pathname,'/');
end
infile= Scanfiles(1,:);
cd(MPdir)
%fid=fopen(infile)%('exp23PrintTimes.xls'); % textread puts date and time sequentially into vector
if ispc
[num, txt, raw] = xlsread(infile); %,'Yor1HitsMPsetFinal');
fields= {txt(2,1:15)}; %or 1:17 for later but dont wish to exceed and cause error ? if used
else
clear MPtbl
opts = detectImportOptions(infile);
MPtbl = readtable(infile,opts);
MPtbl= readtable(infile);
fields= {opts.VariableNames}; %? if used anywhere although 'saved' to MPDMmat
MPcell= readcell(infile);
end
cd(w)
numb= 0;
clear MP;
try
if ispc
excLnNum=3;
while (isequal(txt{excLnNum,1},'###'))
numb=numb+1;
MP(numb).head = {raw(excLnNum,2:6)};
MP(numb).recNum = {raw((excLnNum+1):(excLnNum+384),1)};
MP(numb).orf = {raw((excLnNum+1):(excLnNum+384),2)};
MP(numb).strain = {raw((excLnNum+1):(excLnNum+384),3)};
MP(numb).genename= {raw((excLnNum+1):(excLnNum+384),12)};
MP(numb).drug= {raw((excLnNum+1):(excLnNum+384),8)};
MP(numb).media= {raw((excLnNum+1):(excLnNum+384),7)};
if size(raw,2)>15
MP(numb).orfRep= {raw((excLnNum+1):(excLnNum+384),16)}; %added 12_1005 to specify replicates Orfs in MP
MP(numb).specifics= {raw((excLnNum+1):(excLnNum+384),17)}; %added 12_1008 to specify replicates Specific details in MP
else
MP(numb).orfRep= ' ';
MP(numb).specifics= ' ';
end
%{
if size(raw,2)>17 ; Future MP field
MP(numb).specifics2= {raw((excLnNum+1):(excLnNum+384),18)}; %added 12_1008 to specify strain Bkground in MP
else
MP(numb).specifics2= ' ';
end
%}
excLnNum=excLnNum+385;
msg=strcat('NumberOfMP = ',num2str(numb), ' lastLineNo. = ',num2str(excLnNum));
end % end if ispc
else %if not ispc
excLnNum=1;
while (isequal(MPcell{(excLnNum+2),1},'###'))
numb=numb+1;
MP(numb).head = {MPtbl(excLnNum,2:6)};
MP(numb).head{1}= table2cell(MP(numb).head{1});
MP(numb).recNum = {MPtbl((excLnNum+1):(excLnNum+384),1)};
MP(numb).recNum{1}= table2cell(MP(numb).recNum{1});
MP(numb).orf = {MPtbl((excLnNum+1):(excLnNum+384),2)};
MP(numb).orf{1}= table2cell(MP(numb).orf{1});
MP(numb).strain = {MPtbl((excLnNum+1):(excLnNum+384),3)};
MP(numb).strain{1}= table2cell(MP(numb).strain{1});
MP(numb).genename= {MPtbl((excLnNum+1):(excLnNum+384),12)};
MP(numb).genename{1}= table2cell(MP(numb).genename{1});
MP(numb).media= {MPtbl((excLnNum+1):(excLnNum+384),7)};
MP(numb).media{1}= table2cell(MP(numb).media{1});
if size(MPtbl,2)>15
MP(numb).orfRep= {MPtbl((excLnNum+1):(excLnNum+384),16)}; %added 12_1005 to specify replicates Orfs in MP
MP(numb).orfRep{1}= table2cell(MP(numb).orfRep{1});
MP(numb).specifics= {MPtbl((excLnNum+1):(excLnNum+384),17)}; %added 12_1008 to specify replicates Specific details in MP
MP(numb).specifics{1}= table2cell(MP(numb).specifics{1});
else
MP(numb).orfRep= ' ';
MP(numb).specifics= ' ';
end
excLnNum=excLnNum+385;
msg=strcat('NumberOfMP = ',num2str(numb), 'lastLineNo. = ',num2str(excLnNum))
end
end %end of if ispc for MP while loop choice PC or Linux-other (ln~48)
catch ME
h = msgbox(msg,'Check Number of Master Plates and Excel Lines')
uiwait(h);
end %end for try MP excel sheet input
%*********************************************************************
%DMupload
%Drug and Media Plate setup Upload from Excel
%scan().plate().LocInd().gene
cd(MPdir);
excLnNum=1;
%w=pwd
%cd('D:\EASY\Experiments\'); %cd(ExpPath); %
numOfDrugs=0;
numOfMedias=0;
%GUI input for selecting a MasterPlate Excel file
questdlg('\fontsize{20} Select DrugMedia File','File Selection','OK', struct('Default','OK','Interpreter','tex'));
[Scanfiles, pathname]=uigetfile('*.*', 'MultiSelect','off');
if ispc
DMdir= fullfile(pathname,'\');
else
DMdir=fullfile(pathname,'/');
end
clear infile;
infile= Scanfiles(1,:);
cd(DMdir)
%fid=fopen(infile)%('exp23PrintTimes.xls'); % textread puts date and time sequentially into vector
if ispc
[num, txt, raw] = xlsread(infile); %,'Yor1HitsMPsetFinal');
fields= {txt(2,1:5)};
Linked= num(1,1);
else
opts = detectImportOptions(infile);
DMtbl= readtable(infile,opts);
fields= opts.VariableOptions;
Linked= DMtbl{1,1};
DMcell= readcell(infile);
end
cd(w)
numb=0;
%fields= {txt(2,1:5)};
%Linked= num(1,1);
if isequal(Linked,1) %Drugs and Media are linked 1 to 1; else they are combinatorial
clear DM;
%try
excLnNum=2;
if ispc
while (~isequal(txt{excLnNum,2},'###'))
numb=numb+1;
DM.drug(numb) = {raw(excLnNum,2)};
DM.conc(numb) = {raw(excLnNum,3)};
DM.media(numb) = {raw(excLnNum,4)};
DM.mod1(numb) = {raw(excLnNum,5)};
DM.conc1(numb) = {raw(excLnNum,6)};
DM.mod2(numb) = {raw(excLnNum,7)};
DM.conc2(numb) = {raw(excLnNum,8)};
excLnNum=excLnNum+1;
msg=strcat('NumberOf1:1DrugMediaPlates = ',num2str(numb), ' lastLineNo. = ',num2str(excLnNum))
end
else
clear DM
excLnNum=1;
while (~isequal(DMcell{excLnNum+1,2},'###'))
numb=numb+1;
DM.drug(numb) = {DMtbl(excLnNum,2)};
DM.drug(numb)= table2cell(DM.drug{numb});
DM.conc(numb) = {DMtbl(excLnNum,3)};
DM.conc(numb)= table2cell(DM.conc{numb});
DM.media(numb) = {DMtbl(excLnNum,4)};
DM.media(numb)= table2cell(DM.media{numb});
DM.mod1(numb) = {DMtbl(excLnNum,5)};
DM.mod1(numb)= table2cell(DM.mod1{numb});
DM.conc1(numb) = {DMtbl(excLnNum,6)};
DM.conc1(numb)= table2cell(DM.conc1{numb});
DM.mod2(numb) = {DMtbl(excLnNum,7)};
DM.mod2(numb)= table2cell(DM.mod2{numb});
DM.conc2(numb) = {DMtbl(excLnNum,8)};
DM.conc2(numb)= table2cell(DM.conc2{numb});
excLnNum=excLnNum+1;
msg=strcat('NumberOf1:1DrugMediaPlates = ',num2str(numb), ' lastLineNo. = ',num2str(excLnNum))
end
end
end
%Legacy contengency -Not ever used!!
if isequal(Linked,0) %0 indicates Drugs and Media are combinatorial
clear DM;
excLnNum=2;
drgCnt=0;
medCnt=0;
if ispc
while (~isequal(txt{excLnNum,2},'###'))
drgCnt=drgCnt+1;
DM.drug(drgCnt) = {raw(excLnNum,2)};
DM.conc(drgCnt) = {raw(excLnNum,3)};
excLnNum=excLnNum+1;
end
while (~isequal(txt{excLnNum,4},'###'))
medCnt=medCnt+1;
DM.media(medCnt) = {raw(excLnNum,4)};
excLnNum=excLnNum+1;
end
else %else if not PC (Then linux or other)
excLnNum=1;
while (~isequal(DMcell{excLnNum+1,2},'###'))
drgCnt=drgCnt+1;
DM.drug(drgCnt) = {DMtbl(excLnNum,2)};
DM.conc(drgCnt) = {DMtbl(excLnNum,3)};
excLnNum=excLnNum+1;
end
while (~isequal(DMcel{excLnNum+1,4},'###'))
medCnt=medCnt+1;
DM.media(medCnt) = {DMtbl(excLnNum,4)};
excLnNum=excLnNum+1;
end
end
msg=strcat('NumberOfDrugs = ',num2str(drgCnt), ' NumberOfMedias = ',num2str(medCnt) )
end
save (fullfile(MPdir,'MPDMmat'), 'fields','MP','DM','Linked');
cd(w)
msgbox(['Drug-Media-MasterPlate Annotation File Generation Complete'])

727
workflow/templates/easy/DgenResults.m Executable file
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%% CALLED BY EASYconsole.m %%
%to 'Fotos' from 'PTmaps'
%Console globals*******
global ExpPath
global resDir
global ExpOutmat
global ImParMat
w=pwd;
ln=1;
%******Version compatability fixes*******assoc'd with diff and solve v11a='7.12.0.635 (R2011a)';
if verLessThan('matlab','8.3') %original work 23_0227 updated 23_0525 (8.4 changed to 8.3)
fd4=diff(sym('K / (1 + exp(-r* (t - l )))'),4);
sols= solve(fd4);
else %accomodate new matlab changes after 2014a fix 2nd update 23_0227
syms t K r l;
fd4= diff(K / (1 + exp(-r* (t - l ))),t,4);
sols= solve(fd4);
tmpswap= sols(1);
sols(1)= sols(3);
sols(3)= tmpswap;
end
%MPnum=ImParMat(1);
%opt = questdlg('Print Results Only (RES), DB Only (DB), or Both','Results Printout Options','Res','DB','Both','Both');
opt='Res';
if ~exist('ImParMat','var') || isempty(ImParMat)
load ImParameters
end
destPerMP=ImParMat(2);
load (ExpOutmat);
load (fullfile(ExpPath,'MasterPlateFiles','MPDMmat.mat'))
numOfDrgs= length(DM.drug);
numOfMeds= length(DM.media);
destPerMP=numOfDrgs;
%Determine the longest set of intensity(tPts) for the Experiment Data Set
maxNumIntens=0;
for n=1:size(scan,2)
for m=1:size(scan(n).plate,2)
maxNumIntens= max(maxNumIntens,size(scan(n).plate(m).intens,2));
end
end
if length(ExpPath)== max(strfind(ExpPath,'\'))
localExpPath=ExpPath(1:end-1);
else
localExpPath=ExpPath;
end
if ispc %Linux accommodation
expNm=localExpPath(max(strfind(localExpPath,'\'))+1:end);
else
if isunix,expNm=localExpPath(max(strfind(localExpPath,'/'))+1:end);end
if ismac,expNm=localExpPath(max(strfind(localExpPath,'/'))+1:end);end
end
if ispc
drivePos=min(strfind(localExpPath,'\'));
else
drivePos= min(strfind(localExpPath,'/'));
end
drive= localExpPath(1:(drivePos-1));
DBupload=fullfile(drive,'EZdbFiles','DBupLOADfiles');
%DBupload=['G:\EZdbFiles\DBupLOADfiles']
%resultsFilename= strcat(resDir,'\PrintResults\!!Results_Output.txt') %'\PrintResults\zDevelCFitOutIndxSelectedRawDatTimesDrugMedia.txt'
%DBfilename= strcat(resDir,'\PrintResults\!!Dbase_Output.txt') % Print !Dbase file in PrintResults dir
%resultsFilename= strcat(resDir,'\PrintResults\!!Results_',expNm,'.txt')
%DBfilename= strcat(resDir,'\PrintResults\!!Dbase_',expNm,'.txt')
%Added to allow backward compatability************************************
%Test for CFoutStd as indication of 2018version with r_refined fit code;If
%earlier version with only a standard composite fite, Print results to
%!!ResultsStd_...txt only
%***********************
try
scan(1).plate(1).CFoutStd(1,1);
resultsFilename= fullfile(resDir,'PrintResults', strcat('!!ResultsELr_',expNm,'.txt'));
DBfilename= fullfile(resDir,'PrintResults', strcat('!!DbaseELr_',expNm,'.txt'));
catch
resultsFilename= fullfile(resDir,'PrintResults', strcat('!!ResultsStd_',expNm,'.txt'));
DBfilename= fullfile(resDir,'PrintResults', strcat('!!DbaseStd_',expNm,'.txt'));
end
%**************************************************************************
if isequal(opt,'Res')||isequal(opt,'Both'),fid = fopen(resultsFilename,'w');end
if isequal(opt,'DB')||isequal(opt,'Both'),fid2 = fopen(DBfilename,'w');end %121012 Combo
if isequal(opt,'Res')||isequal(opt,'Both') %print Results
fprintf(fid,'%d\t',ln); %Results header
fprintf(fid,'%s\t\n',localExpPath);
ln=ln+1;
fprintf(fid,'%d\t',ln);
end
mpCnt=0;
totPlCnt=0;
drgCnt=0;
medCnt=0;
%load(fullfile(resDir,'PTmats','Nbdg')) %Convolute scan array data into plates
try
load(fullfile(resDir,'Fotos','Nbdg')) %Convolute scan array data into plates
catch
load(fullfile(resDir,'PTmats','Nbdg')) %Convolute scan array data into plates
end
for s=1:size(scan,2)
%Convolute scan array data into plates DconB for DBcombo
clear Diag
try
Diag(:,:,:,1)= sbdg{s}(1:1:24,16:-1:1,:);
catch
sbdg{s};
end
%*****************************************************
for p=1:size((scan(s).plate),2)
totPlCnt=totPlCnt+1;
if destPerMP>1 &&rem(totPlCnt,destPerMP)==1, mpCnt=mpCnt+1; end
if destPerMP==1,mpCnt=mpCnt+1; end
pertCnt= rem(totPlCnt,destPerMP);
if pertCnt==0, pertCnt= destPerMP;end
pert= strcat('Perturb_',num2str(pertCnt));
s
p
clear outCmat
outCmat=scan(s).plate(p).CFout;
%Print Time Point HEADER for each plate for newly added intensity data
if isequal(opt,'Res')||isequal(opt,'Both')
fprintf(fid, '\n');
ln=ln+1;
fprintf(fid,'%d\t',ln);
fprintf(fid,'Scan\tPlate\tRow\tCol\t');
try
asd=cell2mat(scan(s).plate(1).CFparameters(1));
aucEndPt= strcat('AUC',num2str(asd(9)));
catch
asd=cell2mat(scan(s).plate(1).CFparameters{1,1}(1,384));
aucEndPt= strcat('AUC',num2str(asd(9)));
end
fprintf(fid, 'Num.\tDiagnostics\tDrug\tConc\tMedia\tModifier1\tConc1\tModifier2\tConc2\tORF\tGene');
fprintf(fid, '\t %s',aucEndPt);
fprintf(fid, '\triseTm\tK\tr\tl\tR-squared\tK-lower\tK-upper\tr-lower\tr-upper\tl-lower\tl-upper\tArea\tLastInten\tSplineMaxRateTm\tLastFitTm\t1stFitTm\tMedianBase\tFitBase\tMinTm\tThreshTm');
if size(outCmat,2)==27
fprintf(fid, '\ttc11Cut\ttc12Cut\ttc21Cut\ttc22Cut'); %'\tEarly1\tEarly2\tLate1\tLate2'); 17_0629 MinBaseIntens update for MedianBase label
end
fprintf(fid, '\tTotFitPts\tPostThreshFitPts\t1stBackgrd\tLstBackgrd\t1stMeanTotBackgrd\tLstMeanTotBackgrd');
end
clear outTseries
outTseries=[];
outTseries=scan(s).plate(p).tSeries;
TseriesSize= size(outTseries,1);
%***************************************************************
%clear outCmat
%outCmat=scan(s).plate(p).CFout;
clear outIntens
outIntens=[];
RawIntens=[];
RawIntens=scan(s).plate(p).intens;
RawIntensSize= size(RawIntens,2)
clear Ag; %Ag is Growth Area
Ag=scan(s).plate(p).Ag;
AgSize= size(Ag);
%***************************************
dataLength= min(TseriesSize,RawIntensSize);
%for j=1:length(outTseries)%(size(outTseries,2)
if isequal(opt,'Res')||isequal(opt,'Both')
for j=1:dataLength
fprintf(fid, '\t%.5f', outTseries(j));
end
end
%numBlkColTm=(maxNumIntens - size(outTseries,1));
numBlkCol=(maxNumIntens - dataLength); %size(outTseries,1));
%for nn=1:numBlkColTm %extend to col beyond longest rawDataSet
if isequal(opt,'Res')||isequal(opt,'Both')
for nn=1:numBlkCol %extend to col beyond longest rawDataSet
fprintf(fid, '\t');
end
fprintf(fid,'\tOrfRep');
fprintf(fid,'\tSpecifics');
fprintf(fid,'\tStrainBkGrd');
fprintf(fid, '\n');
ln=ln+1;
fprintf(fid,'%d\t',ln);
end
%*****************************************Begin Data Section
n=0;
for r=1:16
for c=1:24
n=n+1;
clear selcode;
Kval=outCmat(n,3);
rSq=outCmat(n,6);
lval=outCmat(n,5);
if Kval>160, selcode='K_Hi'; else selcode=' ';end
if Kval<40, selcode=strcat(selcode,' K_Lo'); end %12_1030
if rSq<.97 && rSq>0, selcode=strcat(selcode,' rSqLo'); end
if lval>(0.85*(max(outTseries))), selcode=strcat(selcode,' late');end
if isnan(outCmat(n,7))||isnan(outCmat(n,8))||isnan(outCmat(n,9))...
||isnan(outCmat(n,10))||isnan(outCmat(n,11))...
||isnan(outCmat(n,12)), selcode=strcat(selcode,' NaN');
end
%*************RiseTime Calculation*****************************************
K= (outCmat(n,3));
R= (outCmat(n,4));
L= (outCmat(n,5));
if R>0 && L>0 && K>0
rr=R; ll=L;
tc1= eval(sols(2));
tc2= eval(sols(3));
LL= eval(sols(1));
riseTm= LL-tc1;
else
riseTm=0;
end
%*************************************************************************
if Ag(n)< .30*(scan(s).Awindow),selcode=strcat(selcode,' smArea'); end %12_1030
if outCmat(n,3)==0,selcode=strcat('0 ',selcode); end
orf=cell2mat(MP(mpCnt).orf{1}(n));
gene=cell2mat(MP(mpCnt).genename{1}(n));
orfRep=cell2mat(MP(mpCnt).orfRep{1}(n));
specifics=cell2mat(MP(mpCnt).specifics{1}(n));
strain=cell2mat(MP(mpCnt).strain{1}(n));
drug= char(DM.drug{pertCnt});
conc= char(DM.conc{pertCnt});
media= char(DM.media{pertCnt});
try
mod1= char(DM.mod1{pertCnt});
conc1= char(DM.conc1{pertCnt});
catch
mod1= ' ';
conc1= ' ';
end
try
mod2= char(DM.mod2{pertCnt});
conc2= char(DM.conc2{pertCnt});
catch
mod2= ' ';
conc2= ' ';
end
if ~isempty(outCmat)
if isequal(opt,'Res')||isequal(opt,'Both')
fprintf(fid,'%d\t %d\t %d\t %d\t %d\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t',s,p,r,c,n,selcode,drug,conc,media,mod1,conc1,mod2,conc2,orf,gene);
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',...
outCmat(n,1),riseTm,outCmat(n,3),outCmat(n,4),...
outCmat(n,5),outCmat(n,6),outCmat(n,7),outCmat(n,8),...
outCmat(n,9),outCmat(n,10),outCmat(n,11),outCmat(n,12),...
outCmat(n,13),outCmat(n,14),outCmat(n,15),outCmat(n,16));
fprintf(fid, '\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f',...
outCmat(n,17),outCmat(n,18),outCmat(n,19),...
outCmat(n,20),outCmat(n,21));
%failPt= [s n r c]
%Added for data cut times used in 'r'optomized method 06/14/2018
if size(outCmat,2)==27
fprintf(fid, '\t%.5f\t%.5f\t%.5f\t%.5f',...
outCmat(n,24),outCmat(n,25),outCmat(n,26),outCmat(n,27));
end
fprintf(fid, '\t%d\t%d\t%d\t%d\t%d\t%d',...
outCmat(n,22),outCmat(n,23),Diag(c,r,1,p),Diag(c,r,2,p),Diag(c,r,3,p),Diag(c,r,4,p)); %,Diag(r,c,3,p),Diag(r,c,4,p));
end %Results print
%DBfile*******************************************
%riseTm calc*****
if isequal(opt,'DB')||isequal(opt,'Both')
dbRsq= 0;dbKup= 0; dbKlo= 0; dbrup= 0; dbrlo= 0; dbLlo= 0; dbLup= 0;
if isnumeric(outCmat(n,6)), dbRsq= outCmat(n,6);end
if isnumeric(outCmat(n,7)), dbKup= outCmat(n,7);end
if isnumeric(outCmat(n,8)), dbKlo= outCmat(n,8);end
if isnumeric(outCmat(n,9)), dbrup= outCmat(n,9);end
if isnumeric(outCmat(n,10)), dbrlo= outCmat(n,10);end
if isnumeric(outCmat(n,11)), dbLlo= outCmat(n,11);end
if isnumeric(outCmat(n,12)), dbLup= outCmat(n,12);end
end
%****************
if isequal(opt,'DB')||isequal(opt,'Both')
fprintf(fid2,'%s\t %d\t %d\t %d\t %d\t %d\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t',expNm,s,p,r,c,n,selcode,drug,conc,media,mod1,conc1,mod2,conc2,orf,gene);
fprintf(fid2, '%.5f\t %.5f\t %.5f\t %.5f\t %.5f\t %.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f',...
outCmat(n,1),riseTm,outCmat(n,3),outCmat(n,4),...
outCmat(n,5),dbRsq,dbKup,dbKlo,...
dbrup,dbrlo,dbLlo,dbLup); %\t%.5f\t%.5f\t%.5f\t%.5f
%... outCmat(n,13),outCmat(n,14),outCmat(n,15),outCmat(n,16));
end
%*****DB analysis data end************************************************
%Add Intensities series to end of curve fit data
outIntens=[];
outIntens=zeros(384,dataLength);
intensBlob='';
tmBlob ='';
for j=1:dataLength %size(RawIntens,2) %size(outTseries,1)
if Ag(n)==0,Ag(n)=scan(s).Awindow;end
outIntens(n,j)= RawIntens(n,j)/Ag(n);
if isequal(opt,'Res')||isequal(opt,'Both')
fprintf(fid, '\t%.5f', outIntens(n,j)); % Results print Intens
end
if isequal(opt,'DB')||isequal(opt,'Both')
if j<dataLength
intensBlob= strcat(intensBlob,num2str(outIntens(n,j)),';');
else
intensBlob= strcat(intensBlob,num2str(outIntens(n,j)));
end
if outTseries(j)<.0001,outTseries(j)=0;end
if j<dataLength
tmBlob= strcat(tmBlob,num2str(outTseries(j)),';');
else
tmBlob= strcat(tmBlob,num2str(outTseries(j)));
end
end %if DB
end %j
%***************************
% Results fprint***********
if isequal(opt,'Res')||isequal(opt,'Both')
for nn=1:numBlkCol %extend to col beyond longest rawDataSet
fprintf(fid, '\t');
end
%-----------------------------------------------
% UPDATE 14_0626 to writein ' ' if personnel fail to in their
% Masterplate sheet
if ~isnan(orfRep)
fprintf(fid, '\t%s', orfRep); %print OrfRep
else
fprintf(fid, '\t%s', ' ');
end
if ~isnan(specifics)
fprintf(fid, '\t%s', specifics);
else
fprintf(fid, '\t%s', ' ');
end
if ~isnan(strain)
fprintf(fid, '\t%s', strain);
else
fprintf(fid, '\t%s', ' ');
end
%-----------------------------------------------
%****************************
fprintf(fid, '\n');
ln=ln+1;
fprintf(fid,'%d\t',ln);
end
%****************************
%DB Raw Intensities and Timepoints
if isequal(opt,'DB')||isequal(opt,'Both')
fprintf(fid2, '\t%s\t%s',intensBlob,tmBlob );
%-------------------------------
% UPDATE 14_0626 to writein ' ' if personnel fail to in their
% Masterplate sheet
if ~isnan(orfRep)
fprintf(fid2, '\t%s',orfRep );
else
fprintf(fid2, '\t%s', ' ');
end
if ~isnan(specifics)
fprintf(fid2, '\t%s',specifics );
else
fprintf(fid2, '\t%s', ' ');
end
if ~isnan(strain)
fprintf(fid2, '\t%s',strain );
else
fprintf(fid2, '\t%s', ' ');
end
%---------------------------------
fprintf(fid2, '\n');
end %DB print
end %if ~isempty(outCmat)
end %c
end %r
end %p
end %s
if isequal(opt,'Res')||isequal(opt,'Both')
fclose(fid);
end
if isequal(opt,'DB')||isequal(opt,'Both')
fclose(fid2);
try
copyfile(DBfilename,DBupload)
catch ME
rep = getReport(ME, 'basic');
rep=strcat('Failed copyfile to ',DBupload,' -', rep);
errordlg(rep)
end
end %if DB
ln;
cd(w)
%***********************************************************************
%BEGIN PRINT RESULTS ROUTINE FOR STANDARD METHOD
%***********************************************************************
try
scan(1).plate(1).CFoutStd(1,1) %Test for 2018 r_refined version
ln=1;
resultsFilename= fullfile(resDir,'PrintResults', strcat('!!ResultsStd_',expNm,'.txt'));
DBfilename= fullfile(resDir,'PrintResults', strcat('!!DbaseStd_',expNm,'.txt'));
if isequal(opt,'Res')||isequal(opt,'Both'),fid = fopen(resultsFilename,'w');end
if isequal(opt,'DB')||isequal(opt,'Both'),fid2 = fopen(DBfilename,'w');end %121012 Combo
if isequal(opt,'Res')||isequal(opt,'Both') %print Results
fprintf(fid,'%d\t',ln); %Results header
fprintf(fid,'%s\t\n',localExpPath);
ln=ln+1;
fprintf(fid,'%d\t',ln);
end
mpCnt=0;
totPlCnt=0;
drgCnt=0;
medCnt=0;
for s=1:size(scan,2)
%Convolute scan array data into plates DconB for DBcombo
clear Diag
try
Diag(:,:,:,1)= sbdg{s}(1:1:24,16:-1:1,:);
catch
sbdg{s};
end
%*****************************************************
for p=1:size((scan(s).plate),2)
totPlCnt=totPlCnt+1;
if destPerMP>1 &&rem(totPlCnt,destPerMP)==1, mpCnt=mpCnt+1; end
if destPerMP==1,mpCnt=mpCnt+1; end
pertCnt= rem(totPlCnt,destPerMP);
if pertCnt==0, pertCnt= destPerMP;end
pert= strcat('Perturb_',num2str(pertCnt));
s
%Print Time Point HEADER for each plate for newly added intensity data
if isequal(opt,'Res')||isequal(opt,'Both')
fprintf(fid, '\n');
ln=ln+1;
fprintf(fid,'%d\t',ln);
fprintf(fid,'Scan\tPlate\tRow\tCol\t');
try
asd=cell2mat(scan(s).plate(1).CFparameters(1));
aucEndPt= strcat('AUC',num2str(asd(9)));
catch
asd=cell2mat(scan(s).plate(1).CFparameters{1,1}(1,384));
aucEndPt= strcat('AUC',num2str(asd(9)));
end
fprintf(fid, 'Num.\tDiagnostics\tDrug\tConc\tMedia\tModifier1\tConc1\tModifier2\tConc2\tORF\tGene')
fprintf(fid, '\t %s',aucEndPt)
fprintf(fid, '\triseTm\tK\tr\tl\tR-squared\tK-lower\tK-upper\tr-lower\tr-upper\tl-lower\tl-upper\tArea\tLastInten\tSplineMaxRateTm\tLastFitTm\t1stFitTm\tMedianBase\tFitBase\tMinTm\tThreshTm\tTotFitPts\tPostThreshFitPts\t1stBackgrd\tLstBackgrd\t1stMeanTotBackgrd\tLstMeanTotBackgrd'); %17_0629 MinBaseIntens update for MedianBase label
end
clear outTseries
outTseries=[];
outTseries=scan(s).plate(p).tSeries;
TseriesSize= size(outTseries,1);
%***************************************************************
clear outCmat
outCmat=scan(s).plate(p).CFoutStd;
clear outIntens
outIntens=[];
RawIntens=[];
RawIntens=scan(s).plate(p).intens;
RawIntensSize= size(RawIntens,2)
clear Ag; %Ag is Growth Area
Ag=scan(s).plate(p).Ag;
AgSize= size(Ag);
%***************************************
dataLength= min(TseriesSize,RawIntensSize);
if isequal(opt,'Res')||isequal(opt,'Both')
for j=1:dataLength
fprintf(fid, '\t%.5f', outTseries(j));
end
end
numBlkCol=(maxNumIntens - dataLength); %size(outTseries,1));
if isequal(opt,'Res')||isequal(opt,'Both')
for nn=1:numBlkCol %extend to col beyond longest rawDataSet
fprintf(fid, '\t');
end
fprintf(fid,'\tOrfRep');
fprintf(fid,'\tSpecifics');
fprintf(fid,'\tStrainBkGrd');
fprintf(fid, '\n');
ln=ln+1;
fprintf(fid,'%d\t',ln);
end
%*****************************************Begin Data Section
n=0;
for r=1:16
for c=1:24
n=n+1;
clear selcode;
Kval=outCmat(n,3);
rSq=outCmat(n,6);
lval=outCmat(n,5);
if Kval>160, selcode='K_Hi'; else selcode=' ';end
if Kval<40, selcode=strcat(selcode,' K_Lo'); end %12_1030
if rSq<.97 && rSq>0, selcode=strcat(selcode,' rSqLo'); end
if lval>(0.85*(max(outTseries))), selcode=strcat(selcode,' late');end
if isnan(outCmat(n,7))||isnan(outCmat(n,8))||isnan(outCmat(n,9))...
||isnan(outCmat(n,10))||isnan(outCmat(n,11))...
||isnan(outCmat(n,12)), selcode=strcat(selcode,' NaN');
end
%*************RiseTime Calculation*****************************************
K= (outCmat(n,3));
R= (outCmat(n,4));
L= (outCmat(n,5));
if R>0 && L>0 && K>0
rr=R; ll=L;
tc1= eval(sols(2));
tc2= eval(sols(3));
LL= eval(sols(1));
riseTm= LL-tc1;
else
riseTm=0;
end
%*************************************************************************
if Ag(n)< .30*(scan(s).Awindow),selcode=strcat(selcode,' smArea'); end %12_1030
if outCmat(n,3)==0,selcode=strcat('0 ',selcode); end
orf=cell2mat(MP(mpCnt).orf{1}(n));
gene=cell2mat(MP(mpCnt).genename{1}(n));
orfRep=cell2mat(MP(mpCnt).orfRep{1}(n));
specifics=cell2mat(MP(mpCnt).specifics{1}(n));
strain=cell2mat(MP(mpCnt).strain{1}(n));
drug= char(DM.drug{pertCnt});
conc= char(DM.conc{pertCnt});
media= char(DM.media{pertCnt});
try
mod1= char(DM.mod1{pertCnt});
conc1= char(DM.conc1{pertCnt});
catch
mod1= ' ';
conc1= ' ';
end
try
mod2= char(DM.mod2{pertCnt});
conc2= char(DM.conc2{pertCnt});
catch
mod2= ' ';
conc2= ' ';
end
if ~isempty(outCmat)
if isequal(opt,'Res')||isequal(opt,'Both')
fprintf(fid,'%d\t %d\t %d\t %d\t %d\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t',s,p,r,c,n,selcode,drug,conc,media,mod1,conc1,mod2,conc2,orf,gene);
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',...
outCmat(n,1),riseTm,outCmat(n,3),outCmat(n,4),...
outCmat(n,5),outCmat(n,6),outCmat(n,7),outCmat(n,8),...
outCmat(n,9),outCmat(n,10),outCmat(n,11),outCmat(n,12),...
outCmat(n,13),outCmat(n,14),outCmat(n,15),outCmat(n,16));
fprintf(fid, '\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%d\t%d',...
outCmat(n,17),outCmat(n,18),outCmat(n,19),...
outCmat(n,20),outCmat(n,21),outCmat(n,22),outCmat(n,23));
fprintf(fid, '\t%d\t%d\t%d\t%d',...
Diag(c,r,1,p),Diag(c,r,2,p),Diag(c,r,3,p),Diag(c,r,4,p)); %,Diag(r,c,3,p),Diag(r,c,4,p));
end %Results print
%DBfile*******************************************
%riseTm calc*****
if isequal(opt,'DB')||isequal(opt,'Both')
dbRsq= 0;dbKup= 0; dbKlo= 0; dbrup= 0; dbrlo= 0; dbLlo= 0; dbLup= 0;
if isnumeric(outCmat(n,6)), dbRsq= outCmat(n,6);end
if isnumeric(outCmat(n,7)), dbKup= outCmat(n,7);end
if isnumeric(outCmat(n,8)), dbKlo= outCmat(n,8);end
if isnumeric(outCmat(n,9)), dbrup= outCmat(n,9);end
if isnumeric(outCmat(n,10)), dbrlo= outCmat(n,10);end
if isnumeric(outCmat(n,11)), dbLlo= outCmat(n,11);end
if isnumeric(outCmat(n,12)), dbLup= outCmat(n,12);end
end
%****************
if isequal(opt,'DB')||isequal(opt,'Both')
fprintf(fid2,'%s\t %d\t %d\t %d\t %d\t %d\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t',expNm,s,p,r,c,n,selcode,drug,conc,media,mod1,conc1,mod2,conc2,orf,gene);
fprintf(fid2, '%.5f\t %.5f\t %.5f\t %.5f\t %.5f\t %.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f',...
outCmat(n,1),riseTm,outCmat(n,3),outCmat(n,4),...
outCmat(n,5),dbRsq,dbKup,dbKlo,...
dbrup,dbrlo,dbLlo,dbLup); %\t%.5f\t%.5f\t%.5f\t%.5f
%... outCmat(n,13),outCmat(n,14),outCmat(n,15),outCmat(n,16));
end
%*****DB analysis data end************************************************
%Add Intensities series to end of curve fit data
outIntens=[];
outIntens=zeros(384,dataLength);
intensBlob='';
tmBlob ='';
for j=1:dataLength %size(RawIntens,2) %size(outTseries,1)
if Ag(n)==0,Ag(n)=scan(s).Awindow;end
outIntens(n,j)= RawIntens(n,j)/Ag(n);
if isequal(opt,'Res')||isequal(opt,'Both')
fprintf(fid, '\t%.5f', outIntens(n,j)); % Results print Intens
end
if isequal(opt,'DB')||isequal(opt,'Both')
if j<dataLength
intensBlob= strcat(intensBlob,num2str(outIntens(n,j)),';');
else
intensBlob= strcat(intensBlob,num2str(outIntens(n,j)));
end
if outTseries(j)<.0001,outTseries(j)=0;end
if j<dataLength
tmBlob= strcat(tmBlob,num2str(outTseries(j)),';');
else
tmBlob= strcat(tmBlob,num2str(outTseries(j)));
end
end %if DB
end %j
%***************************
% Results fprint***********
if isequal(opt,'Res')||isequal(opt,'Both')
for nn=1:numBlkCol %extend to col beyond longest rawDataSet
fprintf(fid, '\t');
end
%-----------------------------------------------
% UPDATE 14_0626 to writein ' ' if personnel fail to in their
% Masterplate sheet
if ~isnan(orfRep)
fprintf(fid, '\t%s', orfRep); %print OrfRep
else
fprintf(fid, '\t%s', ' ');
end
if ~isnan(specifics)
fprintf(fid, '\t%s', specifics);
else
fprintf(fid, '\t%s', ' ');
end
if ~isnan(strain)
fprintf(fid, '\t%s', strain);
else
fprintf(fid, '\t%s', ' ');
end
%-----------------------------------------------
%****************************
fprintf(fid, '\n');
ln=ln+1;
fprintf(fid,'%d\t',ln);
end
%****************************
%DB Raw Intensities and Timepoints
if isequal(opt,'DB')||isequal(opt,'Both')
fprintf(fid2, '\t%s\t%s',intensBlob,tmBlob );
%-------------------------------
% UPDATE 14_0626 to writein ' ' if personnel fail to in their
% Masterplate sheet
if ~isnan(orfRep)
fprintf(fid2, '\t%s',orfRep );
else
fprintf(fid2, '\t%s', ' ');
end
if ~isnan(specifics)
fprintf(fid2, '\t%s',specifics );
else
fprintf(fid2, '\t%s', ' ');
end
if ~isnan(strain)
fprintf(fid2, '\t%s',strain );
else
fprintf(fid2, '\t%s', ' ');
end
%---------------------------------
fprintf(fid2, '\n');
end %DB print
end %if ~isempty(outCmat)
end %c
end %r
end %p
end %s
if isequal(opt,'Res')||isequal(opt,'Both')
fclose(fid);
end
if isequal(opt,'DB')||isequal(opt,'Both')
fclose(fid2);
try
copyfile(DBfilename,DBupload)
catch ME
rep = getReport(ME, 'basic');
rep=strcat('Failed copyfile to ',DBupload,' -', rep);
errordlg(rep)
end
end %if DB
ln;
catch
errorNstdResults='Catch at line720 for printing ResultsStd'
end %try scan(1).plate(1).CFoutStd(1,1) to test for 2018 r_refined version
cd(w)
scriptComplete= "line724 "
msgbox(['Printing Script complete. Check !!Results sheets in ../PrintResults folder.'])

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workflow/templates/easy/EASYconsole.fig Executable file
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workflow/templates/easy/EASYconsole.m Executable file
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% Launch the MATLAB EASY console
% From EstartConsole.m
clear;
clc;
global openExpfile
global openExppath
global newExpfile
global newExppath
global SWnewExp
global ExpOutmat
global ExpPath
global matDir
global resDir
global wCodeDir
global fhconsole
global ImParMat
global scan
% Set working dir as the pwd
wCodeDir=pwd
% Try to enter WCodeDir
function returnHome
global wCodeDir
try
cd(wCodeDir)
catch
msgbox('Failed to enter selected default directory so starting search at root.');
if ispc
cd(fullfile('C:\'));
elseif (isunix | ismac)
cd(fullfile('/mnt/data'));
else
msgbox('Unknown platform')
end
end
% Init
function varargout = EASYconsole(varargin)
% initialize global variables for function EASYconsole
global ExpOutmat
global ExpPath
global fhconsole
global resDir
global wCodeDir
global ImParMat
% changing directory to wCodeDir
returnHome
%% GUI INTERFACE DESIGN %%
% beginning of GUI formation & design, see help GUI or help GUIDE in
% command window for more information
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @EASYconsole_OpeningFcn, ...
'gui_OutputFcn', @EASYconsole_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% GUI
% Easyconcole_OpeningFcn executes just before the EASYconsole GUI is made visible.
% This function has no output args, see OutputFcn.
% hObject--handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles--structure with handles and user data (see GUIDATA)
% varargin--input arguments to EASYconsole (see VARARGIN)
function EASYconsole_OpeningFcn(hObject, ~, handles, varargin)
global ExpOutmat
global ExpPath
global fhconsole
global resDir
global wCodeDir
global ImParMat
% Choose default command line output for EASYconsole
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
%Figure header, Toolbar, etc. Setup
fhconsole=gcf;
set(fhconsole,'Toolbar','none');
fhconsole=gcf;
if exist('resDir','var')&&~isempty(resDir)
set(fhconsole,'Name',strcat('EASYconsole- ',char(resDir)));
else
set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.')
end
% Output
% Outputs from this function are returned to the command line.
% varargout--cell array for returning output args (see VARARGOUT);
% hObject--handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles--structure with handles and user data (see GUIDATA)
function varargout = EASYconsole_OutputFcn(~, ~, handles)
% Get default command line output from handles structure
varargout{1} = handles.output;
%% CONSOLE BUTTON INTERFACES %%
% File Button Interface
function FileMenu_Callback(~, ~, ~)
returnHome
% Load Experiment Button Interface
function LoadExp_Callback(~, ~, ~)
returnHome
% New Experiment Button Interface
function NewExpDat_Callback(~, ~, ~)
global newExpfile
global newExppath
global SWnewExp
global ExpOutmat
global ExpPath
global matDir
global resDir
global wCodeDir
global fhconsole
global scan
% CREATE NEW EXPERIMENT %
try
questdlg('\fontsize{20} NAME the file and NAVIGATE to the directory with the image folders.','File Creation','OK', struct('Default','OK','Interpreter','tex'));
[newExpfile,newExppath] = uiputfile(' .mat');
SWnewExp=1;
returnHome
newExpfilePref= strrep(newExpfile,'.mat','');
resDirName=strcat('Results',datestr(now,29),newExpfilePref);
% creation of the Results file
if ~exist(fullfile(newExppath,resDirName,'matResults'))
mkdir (fullfile(newExppath,resDirName,'matResults'));
end
% assigning paths to global variables
resDir= fullfile(newExppath,resDirName);
matDir= fullfile(newExppath,resDirName,'matResults');
ExpOutmat=fullfile(matDir,strcat(datestr(now,29),newExpfile));
ExpPath= fullfile(newExppath);
% Added for 'parfor global' to preallocate 'scan' structure 20-0123
nlist=dir(fullfile(ExpPath,'*'));
nnn=0;
for n=1:size(nlist,1)
if (~isempty(str2num(nlist(n).name)))
nnn=nnn+1;
PnumLst(nnn)= (str2num(nlist(n).name));
sl(nnn,1)={(nlist(n).name)};
end
end
scanSize= size(sl,1);
scanMax= max(str2double(sl));
clear scan;
scan(scanMax)= struct(); %changed for parfor global 20_0118
save(ExpOutmat,'scan')
% create 'PrintResults' file
if ~exist(fullfile(ExpPath,resDirName,'PrintResults'))
mkdir(fullfile(ExpPath,resDirName,'PrintResults'));
end
% copy 'figs' file and place it in ExpPath Directory
if ~exist(fullfile(ExpPath,resDirName,'figs'))
copyfile((fullfile(wCodeDir,'figs')), (fullfile(ExpPath,resDirName,'figs')))
end
% create 'CFfigs' file
if ~exist(fullfile(ExpPath,resDirName,'CFfigs'))
mkdir(fullfile(ExpPath,resDirName,'CFfigs'));
end
% copy 'PTmats' file and place it in ExpPath Directory
if ~exist(fullfile(ExpPath,resDirName,'PTmats'))
copyfile((fullfile(wCodeDir,'PTmats')), (fullfile(ExpPath,resDirName,'PTmats')))
end
% create 'Fotos' file
if ~exist(fullfile(ExpPath,resDirName,'Fotos'))
mkdir(fullfile(ExpPath,resDirName,'Fotos'));
clear sbdg % reduce possible retention of a previous job sdbg
sbdg= cell(1,scanMax);
save((fullfile(resDir,'Fotos','Nbdg')),'sbdg');
end
% create backup 'Fotos' file
if ~exist(fullfile(ExpPath,resDirName,'Fotos','BkUp'))
mkdir(fullfile(ExpPath,resDirName,'Fotos','BkUp'));
end
catch ME
returnHome
disp('Error Creating a New Experiment. Loc: EASYconsole.m Lines 106-197')
end
% set the title for fhconsole depending on existence
if exist('resDir','var')&&~isempty(resDir)
set(fhconsole,'Name',strcat('EASYconsole- ',char(resDir)))
else
set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.')
end
% Load a previous experiment
% Load Experiment Analysis directory/file structure
function LoadDatFile_Callback(~, ~, ~)
global openExpfile
global openExppath
global SWnewExp
global ExpOutmat
global ExpPath
global matDir
global resDir
global wCodeDir
global fhconsole
global ImParMat
returnHome
questdlg('\fontsize{20} Load file from ExpJobs/YourJob/YourResults/matResults','File Creation','OK', struct('Default','OK','Interpreter','tex'));
[openExpfile,openExppath] = uigetfile('.mat','Open Experiment folder and data storage .mat file name','MultiSelect','off');
SWnewExp=0;
ExpOutmat= fullfile(openExppath,openExpfile);
load(ExpOutmat);
cd(openExppath)
cd ..;
resDir=pwd;
cd ..;
ExpPath=pwd;
cd (wCodeDir)
ExpPath= fullfile(ExpPath);
if isfolder(fullfile(openExppath, '..','..','1')) %If Inovation Vrobot Then
if exist(fullfile(resDir,'PTmats','NImParameters.mat'))
load(fullfile(resDir,'PTmats','NImParameters.mat'));
else
curDir=pwd;
returnHome
load NImParameters.mat
cd(curDir)
end
else %If Epson 10Plate Scans Then>
if exist(fullfile(resDir,'PTmats','ImParameters.mat'))
load(fullfile(resDir,'PTmats','ImParameters.mat'));
else
curDir=pwd;
returnHome
load ImParameters.mat
cd(curDir)
end
end
matDir= fullfile(openExppath,'\');
mkdir(fullfile(matDir,'BkUp'));
% create supporting files
if ~exist(fullfile(resDir,'PrintResults'))
mkdir(fullfile(resDir,'PrintResults'));
end
if ~exist(fullfile(resDir,'figs'))
mkdir(fullfile(resDir,'figs'));
end
if ~exist(fullfile(resDir,'CFfigs'))
mkdir(fullfile(resDir,'CFfigs'));
end
if ~exist(fullfile(resDir,'PTmats'))
mkdir(fullfile(resDir,'PTmats'));
end
if ~exist(fullfile(resDir,'Fotos'))
mkdir(fullfile(resDir,'Fotos'));
end
catch
returnHome
end
clear scan
if exist('resDir','var')&&~isempty(resDir)
fhconsole= gcf;
set(fhconsole,'Name',strcat('EASYconsole- ',char(resDir)))
else
set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.')
end
%% CALLBACKS %%
% callback for the 'Run' in the dropdown menu
function run_Callback(~, ~, ~)
returnHome
function runPlateMapPintool_Callback(~, ~, ~)
returnHome
try
NImapPT
catch ME
returnHome
EASYconsole
end
function NImCFcombo_Callback(~, ~, ~)
returnHome
try
par4Gbl_Main8c
catch
returnHome
EASYconsole
end
function runPlateImAnal_Callback(~, ~, ~)
returnHome
try
NImStartupOnly
catch ME
returnHome
EASYconsole
end
function PlateCFit_Callback(~, ~, ~)
returnHome
try
NCstart
catch ME
returnHome
end
function GenPrintouts_Callback(~, ~, ~)
function uploadExcelMP2DB_Callback(~, ~, ~)
function runDMPexcel_Callback(~, ~, ~)
try
DMPexcel2mat
catch ME
returnHome
EASYconsole
end
function runResults_DBcombo_Callback(~, ~, ~)
try
DgenResults %similar but semicolons removed to restore so cmdLine display info.
%DgenResults %par4global -convert 1x1cell of 384cells to be like previous 1x384 cells CFparameter
catch ME
disp('Error in DgenResults')
returnHome
EASYconsole
end
function Tools_Callback(~, ~, ~)
function runOverlayPlots_Callback(~, ~, ~)
returnHome
try
DoverlayPlots2
returnHome
EASYconsole
catch ME
returnHome
EASYconsole
end
function runFotoStrip_Callback(~, ~, ~)
returnHome
try
F_NImStartup_CentCir
returnHome
EASYconsole
catch ME
returnHome
EASYconsole
end
function runDisplayFig_Callback(~, ~, ~)
returnHome
try
UfigDisplay
catch ME
returnHome
EASYconsole
end
function runViewParameters_Callback(~, ~, ~)
returnHome
try
% This was blank in original
catch ME
returnHome
EASYconsole
end
function QkviewN_Callback(~, ~, ~)
global ExpPath
returnHome
try
try
cd fullfile(ExpPath)
catch
if ispc cd c:\
else
cd (fullfile('~'));
end
end
QkviewImages
catch ME
returnHome
EASYconsole
end
function CFdisplay_Callback(~, ~, ~)
returnHome
try
NCsingleDisplay
returnHome
EASYconsole
catch ME
returnHome
EASYconsole
end

497
workflow/templates/easy/NCdisplayGui.m Executable file
View File

@@ -0,0 +1,497 @@
%% CALLED WHEN ACCESSING 'CurveFit Display' %%
function [scLst, row, col] = NCdisplayGui(eDir) %(ExpPath)
%global ExpPath
%global expDir
xPos=0.05;
btnWid=0.10;
btnHt=0.05;
spacing=0.02;% Spacing between the button and the next command's label
%hSpot= figure;
%figure
%====================================
% The ADD Groups button
btnNumber=1;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
%
row=1;
hedit = uicontrol(...
'Style', 'edit',...
'String',row,...
'Units','normalized',...
'Position', btnPos,... % [.002 .70 .08 .10],...
'callback',{@editRowNum}); % 'Position', [5 100 60 20])
function editRowNum(source,~)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<0)||(user_entry>17) )
errordlg('Enter a Row between 1 and 16','Bad Input','modal')
return
end
row= user_entry;
end
%-------------------222222-----------
%
btnNumber=2;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
col= 1;
hedit = uicontrol(...
'Style', 'edit',...
'String',col,...
'Units','normalized',...
'Position', btnPos,... % [.002 .70 .08 .10],...
'callback',{@entryColNum}); % 'Position', [5 100 60 20])
function entryColNum(source,~)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<0)||(user_entry>25))
errordlg('Enter a Column between 1 and 24','Bad Input','modal')
return
end
col= user_entry;
end
%}
%*************************************************************
%Ncode 12_0120 for reading in numeric folder names
nlist=dir(fullfile(eDir,'*')); %(ExpPath,'*'));
nnn=0;
for n=1:size(nlist,1)
if (~isempty(str2num(nlist(n).name)))
nnn=nnn+1;
PnumLst(nnn)= (str2num(nlist(n).name));
slst(nnn,1)={(nlist(n).name)};
end
end
hListbox = uicontrol(...
'Style', 'listbox',...
'String',sort(slst),...
'value',[],...
'max',1000,...
'min',1,...
'Units','normalized',...
'Position', [.40 .40 .10 .60],...
'callback',{@load_listbox}); %'uiresume(gcbf)'); 'Position', [5 100 60 20])
function load_listbox(source,~)
userIndx = (get(source,'value'));
userStr = (get(source,'string'));
%scLstIndx= str2num(char(strrep(userStr(userIndx), 'Scan', '')))
user_entry=userStr(userIndx);
scLst= user_entry;
end
%*****************************************************************
%-------------------10 10 10 10-----------
btnNumber=10;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
hedit8 = uicontrol(...
'Style', 'pushbutton',...
'String',{'Continue'},...
'Units','normalized',...
'Position', btnPos,...
'callback','uiresume(gcbf)');
%------------------------------
%***************************************************************
% {
%********LABELS******************************
% The Labels
xLPos=0.175;
yPos=0;
btnWid=0.20;
% Removed Not needed for Ncode ImRobot
lblNumber=1;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','Row',...
'Units','normalized',...
'Position', btnPos);
%-------------------222222-----------
lblNumber=2;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','Column',...
'Units','normalized',...
'Position', btnPos);
% Not needed for Ncode ImRobot
uiwait(gcf);
end %function end $$$$$
%}
%{
%-------------------333333-----------
lblNumber=3;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','BG Threshold (%above) Detection',...
'Units','normalized',...
'Position', btnPos);
%-------------------4-----------
lblNumber=4;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','SpotDetThres(1-60%)',...
'Units','normalized',...
'Position', btnPos);
%-------------------55555-----------
lblNumber=5;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','Radius',... %'String','Width',...
'Units','normalized',...
'Position', btnPos);
%-------------------66666-----------
lblNumber=6;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','Dither',...
'Units','normalized',...
'Position', btnPos);
%-------------------77777-----------
lblNumber=7;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','SearchRange',...
'Units','normalized',...
'Position', btnPos);
%-------------------88888-----------
%{
lblNumber=8;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','Blank2',...
'Units','normalized',...
'Position', btnPos);
%----------------------------------------
%}
%}
%{
%-------------------66666-----------
btnNumber=6;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
srcExtendFactor=ImParMat(7);
hedit = uicontrol(...
'Style', 'edit',...
'String',srcLoIntensThres,...
'Units','normalized',...
'Position', btnPos,...
'callback',{@entryExtendFactor});
function entryExtendFactor(source,eventdata)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<1.8)||(user_entry>4.0))
errordlg('You must enter a numeric value between 1.8 and 2.1','Bad Input','modal')
return
end
ExtendFactor=user_entry
ImParMat(7)= ExtendFactor
ExtendFactor
end
%}
%{
%-------------------333333-----------
btnNumber=3;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
srcBGthreshold=ImParMat(3);
hedit = uicontrol(...
'Style', 'edit',...
'String',srcBGthreshold,...
'Units','normalized',...
'Position', btnPos,... % [.002 .70 .08 .10],...
'callback',{@entryBGthreshold}); % 'Position', [5 100 60 20])
function entryBGthreshold(source,eventdata)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<1)||(user_entry>100))
errordlg('Enter a numeric value between 1 and 100 percent to produce a Background Threshold value as a percent above the time series average background for each spot.','Bad Input','modal')
return
end
BGthresInput=user_entry
ImParMat(3)= BGthresInput
BGthresInput
end
%-------------------444444-----------
btnNumber=4; %Enter spot detection threshold (lock-in Image frame)
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
srcSpotThres=ImParMat(4);
hedit = uicontrol(...
'Style', 'edit',...
'String',srcSpotThres,...
'Units','normalized',...
'Position', btnPos,...
'callback',{@entrySpotThres});
function entrySpotThres(source,eventdata)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<1)||(user_entry>60))
errordlg('You must enter a numeric value between 1 and 60','Bad Input','modal')
return
end
spotThres=user_entry
ImParMat(4)= spotThres
spotThres
end
%
%---------555555 Radius Entry After Sept.2014---------------------------------**
btnNumber=5;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
srcRadius=ImParMat(10);
hedit = uicontrol(...
'Style', 'edit',...
'String',srcRadius,...
'Units','normalized',...
'Position', btnPos,... % [.002 .70 .08 .10],...
'callback',{@entryRadius}); % 'Position', [5 100 60 20])
function entryRadius(source,eventdata)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<12)||(user_entry>17))
errordlg('You must enter a numeric value between 12 and 17','Bad Input','modal')
return
end
Radius=user_entry
ImParMat(10)= Radius
Radius
end
%---------555555 Width Entry prior the Sept.2014---------------------------------**
%{
btnNumber=5;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
srcWidth=ImParMat(5);
hedit = uicontrol(...
'Style', 'edit',...
'String',srcWidth,...
'Units','normalized',...
'Position', btnPos,... % [.002 .70 .08 .10],...
'callback',{@entryWidth}); % 'Position', [5 100 60 20])
function entryWidth(source,eventdata)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<5)||(user_entry>41))
errordlg('You must enter a numeric value between 5 and 40','Bad Input','modal')
return
end
Width=user_entry
ImParMat(5)= Width
Width
end
%}
%-------------------66666 Dither unnecessary after Sept.2014-----------
btnNumber=6;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
srcDither= ImParMat(6);
hedit = uicontrol(...
'Style', 'edit',...
'String',srcDither,...
'Units','normalized',...
'Position', btnPos,...
'callback',{@entryDither});
function entryDither(source,eventdata)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<0)||(user_entry>5))
errordlg('You must enter a numeric value between 1 and 4','Bad Input','modal')
return
end
Dither=user_entry
ImParMat(6)= Dither
Dither
end
%-------------------77777----------- Added July 7,2015 to allow Search Range constraint
btnNumber=7;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
try
CSrchRange=ImParMat(12);
CSrchRng=ImParMat(12)
catch %Legacy default value was 18 before being made a user input variable (ImParMat(12)). A preferable value now might be 12 or 14.
CSrchRange=18;
ImParMat(12)=18
CSrchRng=ImParMat(12)
end
%{
if size(scLst)>1
CSrchRange=ImParMat(12);
else
try
CSrchRange=CSearchRange(str2double(scLst))
catch
CSrchRange=ImParMat(12);
end
end
%}
hSearchRange = uicontrol(...
'Style', 'edit',...
'String',CSrchRange,...
'Units','normalized',...
'Position', btnPos,...
'callback',{@CsearchRange});
function CsearchRange(source,eventdata)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<1)||(user_entry>50)) %originally 18; 19_0729 increased
errordlg('You must enter a numeric value between 1 and 18 12->18 recommended. (ImParMat(12)))','Bad Input','modal')
return
end
CSrchRng=user_entry
end
%-------------------77777-----------
%{
btnNumber=7;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
srcExtend=ImParMat(7);
hedit = uicontrol(...
'Style', 'edit',...
'String',srcExtend,...
'Units','normalized',...
'Position', btnPos,...
'callback',{@entryExtend});
function entryExtend(source,eventdata)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<-0.10)||(user_entry>0.4))
errordlg('You must enter a numeric value between 0 and 0.4. 0.10 recommended','Bad Input','modal')
return
end
extend=user_entry
ImParMat(7)= extend
extend
end
%-------------------888888-----------
btnNumber=8;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
%ImParMat(8)=1;
srcpointExtend=ImParMat(8);
hedit = uicontrol(...
'Style', 'edit',...
'String',srcpointExtend,...
'Units','normalized',...
'Position', btnPos,...
'callback',{@entrypointExtend});
function entrypointExtend(source,eventdata)
user_entry = str2double(get(source,'string'));
user_entry= floor(user_entry);
if (isnan(user_entry)||(user_entry<-3)||(user_entry>5))
errordlg('You must enter an integer value between 0 and 5. 1 recommended','Bad Input','modal')
return
end
pointExtend=user_entry
ImParMat(8)= pointExtend
pointExtend
end
%}
%-------------------999999-----------
btnNumber=9;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
hedit = uicontrol(...
'Style', 'popupmenu',...
'String',{'GrowthArea','FixedArea'},...
'Units','normalized',...
'Position', btnPos,...
'callback',{@grwArea});
function grwArea(source,eventdata)
str = get(source, 'String');
val = get(source,'Value');
% Set current data to the selected data set.
switch str{val};
case 'GrowthArea' ;% User selects Peaks.
SWgrowthArea = 1
case 'FixedArea' % User selects Membrane.
SWgrowthArea = 0
end
end
%}
%global SWsingleSc
%global SWgrowthArea
%global selScan
%global scan
%global scLst
%global ImParMat
%global CSearchRange
%global CSrchRng
%global defImParMat
%global fhImRun
%global fhconsole
%global resDir
%global ExpOutmat
%global numRows;
%global numCols;

275
workflow/templates/easy/NCfitImCFparforFailGbl2.m Executable file
View File

@@ -0,0 +1,275 @@
%% CALLED BY par4GblFnc8c.m %%
function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanIntensELr,par4scanCFparameters,par4scanCFdate,outC,outCstd]= ...
NCfitImCFparforFailGbl2(parMat,times, values, timeOffsets, fileSuffix, AUCfinalTime, ~, spotAreas, outputDirectory, ~,~, sols, ~) %,scan)
%Preallocation for parfor loop**********************************
st(1,1:size(times,2))= 1111;
resMat(1,1:27)= 0;
resMatStd= resMat;
outC= zeros(384,27);
outCstd= zeros(384,27);
for m=1:384
pa{m}= st;
par4scanCFparameters{m}= parMat;
par4scanCFdate{m}= datestr((now),31);
end
par4scanselTimesStd= pa;
par4scanselIntensStd= pa;
par4scanTimesELr= pa;
par4scanIntensELr= pa;
par4resMat= zeros(384,27);
par4resMatStd= zeros(384,27);
%****************************************************************
%*****************Begin the Spot(cultures) loop****************************
for ii= 1:384 %startSpot:numCultures
%parfor ii= 1:384 %startSpot:numCultures
ii; %%%db print out the culture number
timepts= [];
currValues=[];
currSpotAreas=[];
currSpotArea=[];
dataMatrix=[];
selTimesStd=[]; %191024 parfor
selIntensStd=[]; %191024 parfor
FiltTimesELr=[]; %191024 parfor
NormIntensELr=[]; %191024 parfor
% add offset...1 offset PER PLATE
timepts = times + timeOffsets; %(floor((ii-1)/arrayFormat) + 1);
currValues = values(ii,:); %change values(spotNum,:);
% get spot areas for this culture
currSpotArea = spotAreas(:,ii);
% just use the area at the last time point
%currSpotArea = currSpotAreas(1);
%--------------------------------------------------------------
%Preallocate to accomodate parfor loop **************************
resMatStd= zeros(1,27);
resMat= zeros(1,27);
currNormIntens = currValues/currSpotArea;
tmpx=find(currNormIntens>5); %15jh % 2.3);
validSpot=true;
if(isempty(tmpx) || (length(tmpx)<3))
validSpot= false;
normIntens= currNormIntens;
filterTimes= timepts; %filterTimes; %currTimes;
selTimesStd= timepts;
selIntensStd= currNormIntens;
FiltTimesELr= timepts;
NormIntensELr= currNormIntens;
else
%*******************************************************
%NCfilImCF
%NCfilImCF.m called from NCfitImCF.m line 119*******************
%Preallocate incase something bails in NCscurImCFparfor
resMatStd= zeros(1,27);
resMat= zeros(1,27);
hold off %09_0704
dataMatrix=[];
K=0;r=0;l=0;Klow=0;Kup=0;rlow=0;rup=0;llow=0;lup=0;AUC=0;MSR=0; rsquare=0;
bl=0;
Tpt1=0; numFitTpts =0;thresGT2=0;minTime=0;fitbl=0; %diagnostic outputs only
timepts= timepts; %timepts= currTimes; parfor
normIntens= currNormIntens;
dataMatrix= []; %parfor move clear from NCfitImCF...m
loIntensThres=parMat(4);
stdLoIntLim=parMat(5);
%******Begin basic filter**********
%[loInten Thres,stdbased Trim before Scurve start, and dropout detection]
if(max(normIntens) > 2.29)
threshold = loIntensThres; %1.9; %Increase this value to reduce low data point (flag=2)
else
threshold = 0;
end
dropThreshold= -0.0001* max(normIntens);
%Initialize dataMatrix**********************************
dataMatrix(1,:)=timepts;
dataMatrix(2,:)=normIntens;
dataMatrix(3,:)= ones;
dataMatrix(4,:)=normIntens;
%Determine a mean Intensity Index point and assoc'd TimePt
a= min(normIntens(normIntens>=0)); %(find(normIntens>=0)));
b= max(normIntens(normIntens>=0)); %(find(normIntens>=0)));
c= 0.5*(b-a);
d= b-c;
meanIntIndPt= find(normIntens>d,1);
meanInt= normIntens(meanIntIndPt);
meanTime= times(meanIntIndPt);
%**********************************************************
%**************************************************************************
% NCLoIntstdTrim
%NCLoSstdTrim.m called by NCfilImCF and NCfil.m
flg1=0;
loScurvLim=stdLoIntLim; %
loStimeN=1;
last2n=1;
stdDev= [];
nrmIntens0= normIntens;
for n=1:meanIntIndPt
if nrmIntens0(n)<=0
nrmIntens0(n)=0;
end
if(nrmIntens0(n)<threshold)
if (loStimeN-2)>0,dataMatrix(3,1:(n-2))= 2; %add to lowIntensity cull flags, the pre S cull data
else dataMatrix(3,1:n)= 2;end
dataMatrix(3,1:(n-2))= 2;
last2n=n;
end
if n<(length(nrmIntens0)-3)
x=nrmIntens0(n:(n+3));
stdDev(n)=std(x);
if (stdDev(n)<loScurvLim && flg1~=1)
loStime=timepts(n);
loStimeN=n;
end
if stdDev(n)>6 ,flg1=1;end %detect S curve rise->stop stdLoInt detection
end
end %end for
if (loStimeN-2)>0,dataMatrix(3,1:(loStimeN-2))= 2; %add to lowIntensity cull flags, the pre S cull data
else dataMatrix(3,1:(loStimeN-2))= 2;end
qcutoff=2;
qind=find(normIntens>2); %,:,'first');
if ~isempty(qind(3)), qcutoff=qind(3);end
[minInt,I]= min(normIntens(2:qcutoff));
bl=minInt;
minTime=dataMatrix(1,I); %diagnostic output only
if (length(qind)>5)&&I>1,dataMatrix(3,1:(I-1))=5; end
tGT2Flg=0;
for n=1:length(normIntens)
dataMatrix(4,n)=normIntens(n)-bl;
if n>I && dataMatrix(4,n)>=2 && tGT2Flg==0
thresGT2=n;thresGT2Tm=dataMatrix(1,n);tGT2Flg=1;
end %diagnostic output only
end
resMat(18)= bl;
resMatStd(18)= bl;
resMatStd(20)= minTime;
resMat(20)= minTime;
%&&&&&&&&&&&&&&&&&&&&&&& &&&&&&&&&&&&&&&&&&&&&&&&
%*********************************************************
%DropOut cull section(single drop points)*******************
DropOutStartPt=length(normIntens);
for n=1:length(normIntens)
if(n>1)
if(((normIntens(n)- normIntens(n-1))< dropThreshold))&& ...
(n > max(meanIntIndPt,thresGT2) )
dataMatrix(3,n)= 6;
end
end
end
%??????should/could this be removed as recreated in%NCscurImCF_3parfor.m????????????????????
%Post Stdtest cull for low intensities inclusion of additional low value points
%selTimes= [--,--] %don't know size before as it is a filtered output
tmpIndx= 0;
for n=1:length(normIntens)
if (dataMatrix(3,n)==1)
tmpIndx= tmpIndx+1;
selTimes(tmpIndx)= dataMatrix(1,n); %selTimes(nn)= dataMatrix(1,n);
selIntens(tmpIndx)= dataMatrix(4,n); %selIntens(nn)= dataMatrix(4,n);
end
end
selTimes=selTimes';
selIntens=selIntens';
%???????????????????????????????????????????????????
%**********End Basic filter******************
%******************************************************
filtNormIntens=normIntens;
dataMatrix0= dataMatrix;
filterTimes= timepts; %parfor
%_____________________________________________________________
%*******************************************
%NCscurImCF
%NCscurImCF_1
%NCscurImCF_2
%NCscurImCF_3
%NCscurImCF_3parfor
%NCscurImCF_3parfor(dataMatrix, AUCfinalTime)
%dataMatrix %debugging parfor gbl ok 85.7145; 126.4579,6, 124.5264 37tPt
%adsfj %debugging parfor gbl
[resMatStd, resMat, selTimesStd, selIntensStd, FiltTimesELr, NormIntensELr] =...
NCscurImCF_3parfor(dataMatrix0, AUCfinalTime, currSpotArea, sols, bl, minTime);
end % end JUMP OVER associated with if(find(intensities>1000)<5)
%resMatStd
%asdf
%To accommodate parfor can't use global 'scan' variable 191002================
% {
par4scanselTimesStd{ii}= selTimesStd; %timepts'; %filterTimes';
par4scanselIntensStd{ii}= selIntensStd; %normIntens';
par4scanTimesELr{ii}= FiltTimesELr; %19_1021 preserve for CurveDisplay and EZview
par4scanIntensELr{ii}= NormIntensELr; %19_1021 preserve for CurveDisplay and EZview
%}
%$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
%************* striped down OutCell code was put back into NCfitImCF
outC(ii,:)= resMat; %{ii, par4resMat};
outCstd(ii,:)= resMatStd; %{ii, par4resMatStd};
end %Multispot parfor ii loop end PARFOR LOOP END##############################################################################
%###############################################################################################################################
%###############################################################################################################################
%outC
%*********************************19_1001***********************************
%To accomodate parfor copy par4scan thru global p4 functions inside of
%parfor loop --then outside to par4Gbl_Main8b.m
%**************************************************************************
fileExt = '.txt';
filePrefix = 'FitResultsComplete_';
fileNamePlate = [filePrefix fileSuffix fileExt];
fileName= fullfile(outputDirectory, fileNamePlate); %[outputDirectory fileNamePlate];
fid = fopen(fileName,'w');
fprintf(fid, 'Fit Results Complete\n');
%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');
fclose(fid);
end %function end
%&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&
%##########################################################################

437
workflow/templates/easy/NCscurImCF_3parfor.m Executable file
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%% CALLED BY NCfitImCFparforFailGbl2.m %%
function [resMatStd, resMat, selTimesStd, selIntensStd, FiltTimesELr, NormIntensELr] =...
NCscurImCF_3parfor(dataMatrix, AUCfinalTime, currSpotArea, sols, bl, minTime)
%Major revision for Early-Late data cuts to improve accuracof 'r'. Removed legacy iterative method.
%Significant Modification for Parfor
%***************************************************************
%##########################################################################
%******************************************* New Stage 1***************************************************************
%Preallocate
resMatStd= zeros(1,27);
resMat= zeros(1,27);
%Set internal variables sent to matlab fit function
me=200;
meL=750;
mi=25; %50
miL=250;
%***********************************
rmsStg1=0;
rmsStg1I(1)= 0;
slps=1;
filterTimes=[];
normIntens=[];
nn=1;
numFitTpts=0;
%Build filterTimes and normIntens from spot dataMatrix selection codes produced in filter section
for n=1:size(dataMatrix,2)
if (((dataMatrix(3,n)==1))||(dataMatrix(3,n)==3)||(dataMatrix(3,n)==2)...
||(dataMatrix(3,n)==0))
filterTimes(nn)= dataMatrix(1,n);
normIntens(nn)=dataMatrix(4,n);
nn=nn+1;
end
end
%------------------------------------------------------------------
%++++++++++++++++++++++++++++++++++++++++
filterTimes=filterTimes';
selTimesStd=filterTimes;
normIntens=normIntens';
selIntensStd=normIntens;
%normIntens %debugging parfor gbl 200330 good values
%afgj
lastTptUsed= 1;
lastIntensUsed= 1;
thresGT2TmStd=0;
try
lastTptUsed=max(filterTimes);
lastIntensUsed=normIntens(length(normIntens));
lastIntensUsedStd= lastIntensUsed;
lastTptUsedStd= lastTptUsed;
Tpt1Std= filterTimes(1);
numFitTptsStd=nnz((normIntens(:)>=0)==1);
thresGT2 = find(((normIntens(:)>2)==1), 1);
if isempty(thresGT2)
thresGT2TmStd=0;
else
thresGT2TmStd = filterTimes(thresGT2);
end
numTptsGT2Std = nnz((normIntens(:)>=2)==1); %nnz(filterTimes(find(filterTimes>=thresGT2Tm)));
K_Guess = max(normIntens);
numTimePts = length(filterTimes);
opts = fitoptions('Method','Nonlinear','Robust','On',...
'DiffMinChange',1.0E-11,'DiffMaxChange',0.001,...
'MaxFunEvals',me, 'MaxIter', mi, 'TolFun', 1.0E-12, 'TolX', 1.0E-10, 'Lower', [K_Guess*0.5,0,0], 'StartPoint', [K_Guess,filterTimes(floor(numTimePts/2)),0.30], 'Upper', [K_Guess*2.0,max(filterTimes),1.0],'Display','off');
ftype = fittype('K / (1 + exp(-r* (t - l )))','independent','t','dependent',['K','r','l'],'options',opts);
% carry out the curve fitting process
[fitObject, errObj] = fit(filterTimes,normIntens,ftype);
coeffsArray = coeffvalues(fitObject);
rmsStg1=errObj.rsquare;
rmsStg1I(slps)= errObj.rsquare;
sDat(slps,1)=errObj.rsquare;
K = coeffsArray(1); sDat(slps,2)= coeffsArray(1); % Carrying Capacity
l = coeffsArray(2); sDat(slps,3)= coeffsArray(2); %lag time
r = coeffsArray(3); sDat(slps,4)= coeffsArray(3); % rateS
% integrate (from first to last time point)
numVals = size(filterTimes);
numVals = numVals(1);
t_begin = 0;
t_end = AUCfinalTime;
AUC = (K/r*log(1+exp(-r*(t_end-l)))-K/r*log(exp(-r*(t_end-l)))) - (K/r*log(1+exp(-r*(t_begin-l)))-K/r*log(exp(-r*(t_begin-l))));
MSR = r;
rsquare = errObj.rsquare;
confObj = confint(fitObject,0.9); % get the 90% confidence
NANcond=0; stdNANcond=0; %stdNANcond added to relay not to attempt ELr as there is no curve to find critical point
confObj_filtered=confObj;
Klow = confObj(1,1); sDat(slps,5)=confObj(1,1);
Kup = confObj(2,1); sDat(slps,6)=confObj(2,1);
llow = confObj(1,2); sDat(slps,7)=confObj(1,2);
lup = confObj(2,2); sDat(slps,8)=confObj(2,2);
rlow = confObj(1,3); sDat(slps,9)=confObj(1,3);
rup = confObj(2,3); sDat(slps,10)=confObj(2,3);
if(isnan(Klow)||isnan(Kup)||isnan(llow)||isnan(lup)||isnan(rlow)||isnan(rup))
NANcond=1; stdNANcond=1; %stdNANcond added to relay not to attempt ELr as there is no curve to find critical point
end
%rup %debugging parfor gbl 200330
%Klow
%asdfjj114
% {
catch %ME
% if no data is given, return zeros
AUC = 0;MSR = 0;K = 0;r = 0;l = 0;rsquare = 0;Klow = 0;Kup = 0;
rlow = 0;rup = 0;lup = 0;llow = 0;
NANcond=1; stdNANcond=1; %stdNANcond added to relay not to attempt ELr as there is no curve to find critical point
end %end Try
%}
if (exist('K','var')&& exist('r','var') && exist('l','var'))
t = (0:1:200);
Growth = K ./ (1 + exp(-r.* (t - l )));
fitblStd= min(Growth); %jh diag
end
cutTm(1:4)= 1000; %-1 means cuts not used or NA
%{
l %debugging parfor
K
r
Klow
k
%}
%***Preserve for ResultsStd+++++++++++++++++++++++++++++
resMatStd(1)= AUC;
resMatStd(2)= MSR;
resMatStd(3)= K;
resMatStd(4)= r;
resMatStd(5)= l;
resMatStd(6)= rsquare;
resMatStd(7)= Klow;
resMatStd(8)= Kup;
resMatStd(9)= rlow;
resMatStd(10)= rup;
resMatStd(11)= llow;
resMatStd(12)= lup;
resMatStd(13)= currSpotArea;
resMatStd(14)= lastIntensUsedStd; %filtNormIntens(length(filtNormIntens));
%spline fit unneccessary and removed;therefore No maxRateTime assoc'd w/spline fit
%try
%resMatStd(15)= maxRateTime;
%catch
maxRateTime= 0; %[]; %Std shows []; ELr shows 0; %parfor
resMatStd(15)= 0; %maxRateTimestdMeth;
%end
resMatStd(16)= lastTptUsedStd; %filterTimes(length(filterTimes));
if isempty(Tpt1Std)
Tpt1Std= 777; %0.000002; %
end
resMatStd(17)= Tpt1Std;
resMatStd(18)= bl; %perform in the filter section of NCfitImCFparfor
resMatStd(19)= fitblStd; %Taken from NCfil... and not affected by NCscur...changes
resMatStd(20)= minTime; %Not affected by changes made in NCscur...for refined 'r'
resMatStd(21)= thresGT2TmStd;
resMatStd(22)= numFitTptsStd;
resMatStd(23)= numTptsGT2Std;
resMatStd(24)= 999; %The Standard method has no cuts .:.no cutTm
resMatStd(25)= 999;
resMatStd(26)= 999;
resMatStd(27)= 999;
%if SwitchEvsEL==3 %Remove 'SwitchEvsEL==...' temporary SWITCH when Hartman decides what he wants
%*********************************************************************************
%ELr New Experimental data through L+deltaS Logistic fit for 'Improved r' Fitting
%*********************************************************************************
FiltTimesELr= []; %{ii}= filterTimes;
NormIntensELr= []; %{ii}= normIntens;
normIntens= selIntensStd;
filterTimes= selTimesStd;
stdIntens= selIntensStd;
tmpIntens= selIntensStd;
stdTimes= selTimesStd;
if stdNANcond==0
%Determine critical points and offsets for selecting Core Data based on
%Standard curve fit run. Put diff into NImStartupImCF02.m calling source
%to reduce repeated execution since it doesn't change.
%fd4=diff(sym('K / (1 + exp(-r* (t - l )))'),4);
%sols=solve(fd4);
tc1= eval(sols(2));
tc2= eval(sols(3));
LL= l; %eval(sols(1)); %exactly the same as 'l' from std. fit method-Save time
rsTmStd= LL-tc1; %%riseTime (first critical point to L)
deltS= rsTmStd/2;
tc1Early= tc1-deltS; %AKA- tc1AdjTm %2*tc1 -LL
L_Late= LL+deltS;
tc1EdatPt= find(filterTimes>(tc1Early),1,'first');
cutTm(1)= filterTimes(2);
cutDatNum(1)= 2;
cutTm(2)= tc1Early;
cutDatNum(2)= tc1EdatPt-1;
L_LDatPt= find(filterTimes< L_Late,1,'last');
tc2LdatPt= find(filterTimes< tc2+rsTmStd,1,'last');
cutTm(3)= L_Late;
cutDatNum(3)= L_LDatPt;
%Select Core Data Set (Remove Early data before critical point)
ints=[];
ints(1:L_LDatPt-tc1EdatPt+2)= (tmpIntens(L_LDatPt));
ints(2:end)= tmpIntens(tc1EdatPt:L_LDatPt);
ints(1)= tmpIntens(1);
tms=[];
tms(1:L_LDatPt-tc1EdatPt+2)= (stdTimes(L_LDatPt));
tms(2:end)= stdTimes(tc1EdatPt:L_LDatPt);
tms(1)= stdTimes(1);
%-----------------------------------------------
%Include/Keep late data that define K *********
if length(tmpIntens(tc2LdatPt:end))> 4
KlastInts= tmpIntens(tc2LdatPt:end);
KlastTms= stdTimes(tc2LdatPt:end);
lengthKlast= length(tmpIntens(tc2LdatPt:end));
ints(end:(end+ lengthKlast-1))= KlastInts;
tms(end:(end+ lengthKlast-1 ))= KlastTms;
cutTm(4)= tc2+rsTmStd;
cutDatNum(4)= tc2LdatPt-1;
else
lengthKlast= length(tmpIntens(tc2LdatPt-1:end));
if lengthKlast>1
KlastInts= tmpIntens(end-(lengthKlast-1):end);
KlastTms= stdTimes(end-(lengthKlast-1):end);
ints(end:(end+ lengthKlast-1 ))= KlastInts;
tms(end:(end+ lengthKlast-1 ))= KlastTms;
end
cutTm(4)= stdTimes(tc2LdatPt-1);
cutDatNum(4)= tc2LdatPt-2; %length(stdTimes(end-(lengthKlast-1):end));
end
%************************************************
Ints=[];
Tms=[];
Ints= ints';
Tms= tms';
try
filterTimes= Tms; filterTimes4= Tms;
normIntens= Ints; normIntens4=Ints;
%----------------------------------------------------------------------------------------------
%classic symetric logistic curve fit setup restated as COMMENTS for reference convenience----------------------------
%opts= fitoptions is the same as for Std and so is redundant
%opts = fitoptions('Method','Nonlinear','Robust','On',...
% 'DiffMinChange',1.0E-11,'DiffMaxChange',0.001,...
% 'MaxFunEvals',me, 'MaxIter', mi, 'TolFun', 1.0E-12, 'TolX', 1.0E-10, 'Lower', [K_Guess*0.5,0,0], 'StartPoint', [K_Guess,filterTimes(floor(numTimePts/2)),0.30], 'Upper', [K_Guess*2.0,max(filterTimes),1.0]);
ftype = fittype('K / (1 + exp(-r* (t - l )))','independent','t','dependent',['K','l','r'],'options',opts);
fitObject=[]; errObj=[];
% carry out the curve fitting process
[fitObject, errObj] = fit(Tms,Ints,ftype);
coeffsArray = coeffvalues(fitObject);
r3 = coeffsArray(3); %sDat(slps,4)= coeffsArray(3); % rateS
if (exist('K','var')&& exist('r','var') && exist('l','var'))
t = (0:1:200);
GrowthELr = K ./ (1 + exp(-r.* (t - l )));
fitblELr= min(GrowthELr); %jh diag
end
catch ME
% if no data is given, return zeros
AUC = 0;MSR = 0;K = 0;r = 0;l = 0;rsquare = 0;Klow = 0;Kup = 0;
rlow = 0;rup = 0;lup = 0;llow = 0; %normIntens=[];
end %end Try
end %if stdNANcond=0
%++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
%Update values if r is better(higher) with removal of early data
try
if r3>r && stdNANcond==0
r = r3; sDat(slps,4)= sDat(slps,4); % rateS
K = coeffsArray(1); sDat(slps,2)= coeffsArray(1); % Carrying Capacity
l = coeffsArray(2); sDat(slps,3)= coeffsArray(2); %lag time
coeffsArray = coeffvalues(fitObject);
rmsStg1=errObj.rsquare;
rmsStg1I(slps)= errObj.rsquare;
sDat(slps,1)=errObj.rsquare;
%jh diagnostics*************
numFitTpts=nnz((normIntens(:)>=0)==1);
thresGT2 = find(((normIntens(:)>2)==1), 1);
thresGT2Tm = filterTimes(thresGT2);
numTptsGT2 = nnz((normIntens(:)>=2)==1);
numTimePts = length(filterTimes);
AUC = (K/r*log(1+exp(-r*(t_end-l)))-K/r*log(exp(-r*(t_end-l)))) - (K/r*log(1+exp(-r*(t_begin-l)))-K/r*log(exp(-r*(t_begin-l))));
MSR = r3;
%***************************
rsquare = errObj.rsquare;
confObj = confint(fitObject,0.9); % get the 90% confidence
NANcond=0;
confObj_filtered=confObj;
Klow = confObj(1,1); sDat(slps,5)=confObj(1,1);
Kup = confObj(2,1); sDat(slps,6)=confObj(2,1);
llow = confObj(1,2); sDat(slps,7)=confObj(1,2);
lup = confObj(2,2); sDat(slps,8)=confObj(2,2);
rlow = confObj(1,3); sDat(slps,9)=confObj(1,3);
rup = confObj(2,3); sDat(slps,10)=confObj(2,3);
if(isnan(Klow)||isnan(Kup)||isnan(llow)||isnan(lup)||isnan(rlow)||isnan(rup))
NANcond=1;
end
filterTimes= Tms;
normIntens= Ints;
resMat(17)= .00002;
resMat(18)= bl;
resMat(19)= fitblELr;
resMat(20)= minTime;
else % r is better than r3 so use the Std data in the ELr result sheet
filterTimes=selTimesStd;
normIntens=selIntensStd;
lastTptUsed= lastTptUsedStd; %Reinstall Std values for jh diags
Tpt1=filterTimes(1);
try
if isempty(Tpt1)
Tpt1= 0.00002; %777;
end
catch
Tpt1= 0.00002; %777;
end
resMat(17)= Tpt1;
numFitTpts= numFitTptsStd;
numTptsGT2= numTptsGT2Std;
thresGT2Tm = thresGT2TmStd;
cutTm(1:4)= 1000; %-1 means cuts not used or NA
resMat(18)= bl; %only applicable to Std curve Fit; ELr superceeds and makes meaningless
resMat(19)= fitblStd; %only applicable to Std curve Fit; ELr superceeds and makes meaningless
resMat(20)= minTime; %only applicable to Std curve Fit; ELr superceeds and makes meaningless
end %if r3>r1
%rup
%asdf352
% {
catch ME
% if no data is given, return zeros
AUC = 0;MSR = 0;K = 0;r = 0;l = 0;rsquare = 0;Klow = 0;Kup = 0;
rlow = 0;rup = 0;lup = 0;llow = 0; %normIntens=[];
end %end Try
%}
resMat(1)= AUC;
resMat(2)= MSR;
resMat(3)= K;
resMat(4)= r;
resMat(5)= l;
resMat(6)= rsquare;
resMat(7)= Klow;
resMat(8)= Kup;
resMat(9)= rlow;
resMat(10)= rup;
resMat(11)= llow;
resMat(12)= lup;
resMat(13)= currSpotArea;
resMat(14)= lastIntensUsed; %filtNormIntens(length(filtNormIntens));
%spline fit unneccessary and removed therfor no max spline rate time->set 0
maxRateTime=0; %ELr will show 0; Std will show []
resMat(15)= maxRateTime;
resMat(16)= lastTptUsed; %filterTimes(length(filterTimes));
try %if Std fit used no cuts .:. no cutTm
resMat(24)= cutTm(1);
resMat(25)= cutTm(2);
resMat(26)= cutTm(3);
resMat(27)= cutTm(4);
catch
resMat(24)= 999; %if Std fit used no cuts .:. no cutTm
resMat(25)= 999;
resMat(26)= 999;
resMat(27)= 999;
end
FiltTimesELr= filterTimes;
NormIntensELr= normIntens;
%**********************************************************************************
%##########################################################################
lastTptUsed=max(filterTimes);
lastIntensUsed=normIntens(length(normIntens));
if (exist('K','var')&& exist('r','var') && exist('l','var'))
t = (0:1:200);
Growth = K ./ (1 + exp(-r.* (t - l )));
fitbl= min(Growth); %jh diag
end
%}
try
if isempty(thresGT2Tm),thresGT2Tm=0;end %jh diag
catch
thresGT2Tm= 0;
numTptsGT2= 0;
end
resMat(21)= thresGT2Tm;
resMat(22)= numFitTpts;
resMat(23)= numTptsGT2;
end %function end

110
workflow/templates/easy/NCsingleDisplay.m Executable file
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%% CALLED WHEN ACCESSING 'CurveFit Display' %%
global expDir
global scLst
global ExpPath
global scan
eDir= ExpPath;
hf= figure;
%**************Parameter Entry******************
[scLst, row, col] = NCdisplayGui(eDir); %(ExpPath); %Ncode 122111replaced removed ,numOfPrtTimes)
%***********************************************
close(hf)
selSpot= (row-1)*24 + col;
for iPlate=1:length(scLst)
scanPltNum= str2double(scLst(iPlate));
%scanPltNum(iPlate);
%-----------------------------------------------------------------------
K= scan(scanPltNum).plate(1).CFout((selSpot),3);
r= scan(scanPltNum).plate(1).CFout((selSpot),4);
l= scan(scanPltNum).plate(1).CFout((selSpot),5);
suffix= strcat('Scan-Plate', scLst(iPlate)); %char(QspLst(n));
%fileSpotSuffix = strcat('-Spot#',num2str(selSpot),'-Row=',selSpotRC(1),'-Col=',selSpotRC(2),'-FitData','-L=',num2str(l),'-r=',num2str(r),'-K=',num2str(K));
fileSpotSuffix = strcat('-Spot#',num2str(selSpot),'-Row=',num2str(row),'-Col=',num2str(col),'-FitData','-L=',num2str(l),'-r=',num2str(r),'-K=',num2str(K));
filenameNoExt= [suffix fileSpotSuffix];
timeArr= scan(scanPltNum).plate(1).tSeries;
rawIntens= scan(scanPltNum).plate(1).intens((selSpot),:)/scan(scanPltNum).plate(1).Ag((selSpot));
try
filterTms= scan(scanPltNum).plate(1).filterTimes{(selSpot)};
normInts= scan(scanPltNum).plate(1).normIntens{(selSpot)};
catch
end
%********************************
if (exist('K','var')&& exist('r','var') && exist('l','var'))
t = (0:1:200);
Growth = K ./ (1 + exp(-r.* (t - l )));
end
if length(scLst)>1
figure
else
cla
end
hold on
plot(timeArr,rawIntens,'g*');
try
plot(filterTms,normInts,'o');
catch
end
hold on;
title(strcat(filenameNoExt,''));
xlabel('Hours');
ylabel('Intensities Normalized by Area');
grid on;
if (exist('K','var')&& exist('r','var') && exist('l','var'))
plot(t, Growth,'b-');
%*********Plot L on curvefit figure***********
grL=Growth(round(l)); %growthCurve timePT for l in hours
plot(l,0:grL,'-b') %to display position of l
plot(l,grL,'^b') %to display l position on curve as an arrowhead
%***Plot Arbitrary User Entry AUC "finalTimePt"
% plot(finalTimePt,0,'+m')
% plot(0:finalTimePt,bl,'-m')
end
end
%end %end for SWsingle display/plot figure
%############################################################
%Spot entry form------------------------------------------------------
%{
prompt = {'Enter spot to analyse:'};
dlg_title = 'Input spot to curve fit';
num_lines = 1;
def = {'1'};
selSpot = inputdlg(prompt,dlg_title,num_lines,def);
K= scan(scanPltNum).plate(1).CFout(str2double(selSpot),3);
r= scan(scanPltNum).plate(1).CFout(str2double(selSpot),4);
l= scan(scanPltNum).plate(1).CFout(str2double(selSpot),5);
suffix= strcat('Scan-Plate', scLst); %char(QspLst(n));
fileSpotSuffix = strcat('-Spot#',selSpot,'-FitData','-L=',num2str(l),'-r=',num2str(r),'-K=',num2str(K));
filenameNoExt= [suffix fileSpotSuffix];
timeArr= scan(scanPltNum).plate(1).tSeries;
rawIntens= scan(scanPltNum).plate(1).intens(str2double(selSpot),:)/scan(scanPltNum).plate(1).Ag(str2double(selSpot));
filterTms= scan(scanPltNum).plate(1).filterTimes{str2double(selSpot)};
normInts= scan(scanPltNum).plate(1).normIntens{str2double(selSpot)};
%}
%-----------------------------------------------------------------------
%{
prompt = {'Enter Spot row:','Enter Spot column:'};
dlg_title = 'Input spot to curve fit';
num_lines = 2;
def = {'1','1'};
selSpotRC = inputdlg(prompt,dlg_title,num_lines,def);
row= str2double(selSpotRC(1)); col=str2double(selSpotRC(2));
%}
%row= cell2mat(row);

62
workflow/templates/easy/NIcircle.m Executable file
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%% CALLED BY par4Gbl_Main8c.m %%
%{
%Imaging ToolBox method
r=14;
A=zeros(70,70); %(fIntsc(refPtR:(refPtRExt),refPtC:(refPtCExt)))
m= {40,40};
A(m{:})=1;
B= imdilate(A,strel('disk',r,0) );
imshow(B)
area=pi*r^2
clear all
%}
%without Image Proc. Toolbox
%r=14;
%A=zeros(70,70);
%A=zeros(r,r);
%P=[40,40];
%center= [refPtR+ round(.5*width), refPtC+ round(.5*width)];
%A=zeros(70,70);
%---------------------------------------------------------------------
%radius=14;
diaExt=2*(radius+1);
circBoxA=zeros(diaExt,diaExt);
center= [radius+2, radius+2];
[m, n ]=size(circBoxA);
X = bsxfun(@plus,(1:m)', zeros(1,n));
Y = bsxfun(@plus,(1:n), zeros(m,1));
cirMask= sqrt(sum(bsxfun(@minus,cat(3,X,Y),reshape(center,1,1,[])) .^2,3))<=radius;
area=pi*radius^2;
cirPixA= nnz(cirMask);
optCirMask= double(cirMask);
optCirMask(optCirMask==0)= 0.8;
%+++++++++++Foto Circle Fram(e)+++++++++++++++++++++
expansion=2;
radExpan= radius+expansion;
FdiaExt=2*(radExpan);
circBoxA=zeros(FdiaExt,FdiaExt);
center= [radExpan+1, radExpan+1];
[m, n ]=size(circBoxA);
X = bsxfun(@plus,(1:m)', zeros(1,n));
Y = bsxfun(@plus,(1:n), zeros(m,1));
FcirMask= sqrt(sum(bsxfun(@minus,cat(3,X,Y),reshape(center,1,1,[])) .^2,3))<=radExpan;
%FcirPixA= nnz(cirMask);
FoptCirMask= double(FcirMask);
FoptCirMask(FoptCirMask==1)= 2;
%FoptCirMask(FoptCirMask==0)= 1;
%********Combine Masks to create circular boundry************
padOptCirMask= padarray(optCirMask,[expansion-1 expansion-1],0.8);
FoptCirMask= FoptCirMask .* padOptCirMask;
FoptCirMask(FoptCirMask==1.6)= 0.8;
FoptCirMask(FoptCirMask==0)= 1;
FoptCirMask(FoptCirMask==2)= 1;
%---------------------------------------------------
%imagesc(cirMask)

281
workflow/templates/easy/NImParamRadiusGui.m Executable file
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%% CALLED BY par4Gbl_Main8c.m %%
function NImParamRadiusGui(expDir) %, numOfPrtTimes) 122111replace removed
global SWsingleSc
global SWgrowthArea
%global selScan
global scan
global scLst
global ImParMat
%global CSearchRange
global CSrchRng
global defImParMat
global fhImRun
global fhconsole
global resDir
global ExpOutmat
global numRows;
global numCols;
global scanSize
global scanMax
defImParMat=[1, 1, 15, 34, 24, 1,0,0,1,14,1,18]; %Ncode ImRobot adaptation
if ImParMat(3)==0 || ImParMat(4)==0 ||ImParMat(5)==0 || ImParMat(10)==0 ||ImParMat(11)==0
ImParMat=defImParMat;
end
if size(ImParMat,2)<12
ImParMat(12)=18; %Default before user input CsearchRange value
msg= 'Data made before SearchRange user entry added (ImParMat(12). 18 was the set value and the current default.)';
end
%ImParMat=defImParMat; %Activate for INITIAL USE only
MPnum=1;
destPerMP=1;
selScan=1;
SWgrowthArea=1;
if exist(fullfile(resDir,'PTmats','NImParameters.mat'))
load(fullfile(resDir,'PTmats','NImParameters'));
else
load NImParameters
end
ImParMat;
%end
%if ~exist('CSearchRange','var') || isempty(CSearchRange)
if ~isequal(exist(fullfile(resDir,'Fotos','CSearchRange.mat')),0)
load(fullfile(resDir,'Fotos','CSearchRange'))
CSearchRange;
end
% yInitPos=0.30;
xPos=0.05;
btnWid=0.10;
btnHt=0.05;
spacing=0.02;% Spacing between the button and the next command's label
%====================================
% The ADD Groups button
btnNumber=1;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
fhImParm=gcf;
if exist('resDir','var')&& ~isempty(resDir)
set(fhImParm,'NumberTitle','off')
set(fhImParm,'Name',strcat('ImageAnalysis- ',char(resDir)))
else
set(fhImParm,'NumberTitle','off')
set(fhImParm,'Name','EASYconsole -Exp. Analysis NOT selected.')
end
btnNumber=5;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
srcRadius=ImParMat(10);
hedit = uicontrol(...
'Style', 'edit',...
'String',srcRadius,...
'Units','normalized',...
'Position', btnPos,... % [.002 .70 .08 .10],...
'callback',{@entryRadius}); % 'Position', [5 100 60 20])
function entryRadius(source,~)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<12)||(user_entry>17))
errordlg('You must enter a numeric value between 12 and 17','Bad Input','modal')
return
end
Radius=user_entry;
ImParMat(10)= Radius;
Radius;
end
btnNumber=6;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
srcDither= ImParMat(6);
hedit = uicontrol(...
'Style', 'edit',...
'String',srcDither,...
'Units','normalized',...
'Position', btnPos,...
'callback',{@entryDither});
function entryDither(source,~)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<0)||(user_entry>5))
errordlg('You must enter a numeric value between 1 and 4','Bad Input','modal')
return
end
Dither=user_entry;
ImParMat(6)= Dither;
Dither;
end
%-------------------77777----------- Added July 7,2015 to allow Search Range constraint
btnNumber=7;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
try
CSrchRange=ImParMat(12);
CSrchRng=ImParMat(12);
catch %Legacy default value was 18 before being made a user input variable (ImParMat(12)). A preferable value now might be 12 or 14.
CSrchRange=18;
ImParMat(12)=18;
CSrchRng=ImParMat(12);
end
hSearchRange = uicontrol(...
'Style', 'edit',...
'String',CSrchRange,...
'Units','normalized',...
'Position', btnPos,...
'callback',{@CsearchRange});
function CsearchRange(source,~)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<1)||(user_entry>50)) %originally 18; 19_0729 increased
errordlg('You must enter a numeric value between 1 and 18 12->18 recommended. (ImParMat(12)))','Bad Input','modal')
return
end
CSrchRng=user_entry;
end
%Ncode 12_0120 for reading in numeric folder names
nlist=dir(fullfile(expDir,'*'));
nnn=0;
for n=1:size(nlist,1)
if (~isempty(str2num(nlist(n).name)))
nnn=nnn+1;
PnumLst(nnn)= (str2num(nlist(n).name));
sl(nnn,1)={(nlist(n).name)};
end
end
scanSize= size(sl,1);
scanMax= max(str2double(sl));
hListbox = uicontrol(...
'Style', 'listbox',...
'String',sort(sl),...
'value',[],...
'max',1000,...
'min',1,...
'Units','normalized',...
'Position', [.70 .40 .10 .60],...
'callback',{@load_listbox}); %'uiresume(gcbf)'); 'Position', [5 100 60 20])
function load_listbox(source,~)
%global CSrchRng
%global CSrearchRange
userIndx = (get(source,'value'));
userStr = (get(source,'string'));
%scLstIndx= str2num(char(strrep(userStr(userIndx), 'Scan', '')))
user_entry=userStr(userIndx);
scLst=user_entry;
if size(scLst,1)>1
%CSrchRng=num2str(ImParMat(12))
set(hSearchRange,'string',num2str(ImParMat(12)))
else
try
CSrchRng=CSearchRange(str2double(scLst));
set(hSearchRange,'string',CSearchRange(str2double(scLst)))
catch
% CSrchRng=num2str(ImParMat(12))
% set(hSearchRange,'string',num2str(ImParMat(12)))
end
end
%ImParMat(7)=MPnum
end
scLst;
%*****************************************************************
%-------------------10 10 10 10-----------
btnNumber=10;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
hedit8 = uicontrol(...
'Style', 'pushbutton',...
'String',{'Continue'},...
'Units','normalized',...
'Position', btnPos,...
'callback','uiresume(gcbf)');
%------------------------------
%***************************************************************
%********LABELS******************************
% The Labels
xLPos=0.175;
yPos=0;
btnWid=0.20;
%-------------------55555-----------
lblNumber=5;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','Radius',... %'String','Width',...
'Units','normalized',...
'Position', btnPos);
%-------------------66666-----------
lblNumber=6;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','Dither',...
'Units','normalized',...
'Position', btnPos);
%-------------------77777-----------
lblNumber=7;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','SearchRange',...
'Units','normalized',...
'Position', btnPos);
uiwait(gcf);
for i=1:length(scLst)
CSearchRange(str2double(scLst(i)))= CSrchRng;
ImParMat(12)= CSrchRng;
end
ImParMat;
CSearchRange;
try
save('NImParameters','ImParMat')
% save('CSearchRange','CSearchRange')
catch
save(fullfile('\','NImParameters'),'ImParMat')
%save(fullfile('\','CSearchRange'),'CSearchRange')
end
save((fullfile(resDir,'PTmats','NImParameters')), 'ImParMat');
save((fullfile(resDir,'Fotos','CSearchRange')),'CSearchRange');
close
return
end

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workflow/templates/easy/NIscanIntensBGpar4GblFnc.m Executable file
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workflow/templates/easy/PTmats/NCFparms.mat Executable file
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workflow/templates/easy/PTmats/NImParameters.mat Executable file
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workflow/templates/easy/PTmats/NPTdirectParameters.mat Executable file
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workflow/templates/easy/PTmats/NPTmapDirect.mat Executable file
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workflow/templates/easy/PTmats/NPTmapSearch.mat Executable file
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workflow/templates/easy/PTmats/NPTsearchParameters.mat Executable file
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workflow/templates/easy/PTmats/Nbdg.mat Executable file
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workflow/templates/easy/datatipp.m Executable file
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%% PART OF GUI FUNCTIONALITY %%
function output_txt = datatipp(~,event_obj)
% Display the position of the data cursor
% obj Currently not used (empty)
% event_obj Handle to event object
% output_txt Data cursor text string (string or cell array of strings).
pos = get(event_obj,'Position');
output_txt = {['X: ',num2str(pos(1),4)],...
['Y: ',num2str(pos(2),4)]};
% If there is a Z-coordinate in the position, display it as well
if length(pos) > 2
output_txt{end+1} = ['Z: ',num2str(pos(3),4)];
end

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workflow/templates/easy/figs/NPTdirect.fig Executable file
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workflow/templates/easy/figs/searchNPTIm.fig Executable file
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workflow/templates/easy/p4loop8c.m Executable file
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%% CALLED BY par4Gbl_Main8c.m %%
function[p4L4,...
TmpexpScanIntens4,TmpFexpScanSpots4,TmpFexpScanBMtp4,TmpanlZoneRefs4,Tmpsbdg4]= ...
p4loop8c(parMat,tptLength,numScans,selScanNumLst,SWsingleSc,Fflg,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,cirMask,width, ...
TmpexpScanIntens00,TmpFexpScanSpots00,TmpFexpScanBMtp00,TmpanlZoneRefs00,~,tifFileLstP4,pathname,ImParMat, ...
numRows,numCols,scLst,resDir,expDir, p4L00,TmpexpScanIntens4,TmpFexpScanSpots4,TmpFexpScanBMtp4,TmpanlZoneRefs4, Tmpsbdg00, Tmpsbdg4)
p4L0=p4L00;
TmpexpScanIntens0= TmpexpScanIntens00;
TmpFexpScanSpots0= TmpFexpScanSpots00;
TmpFexpScanBMtp0= TmpFexpScanBMtp00;
TmpanlZoneRefs0= TmpanlZoneRefs00;
Tmpsbdg0= Tmpsbdg00;
%resDir %for debugging
%START PARFOR PARFOR PARFOR PARFOR PARFOR PARFOR PARFOR PARFOR PARFOR PARFOR
%************************************************************************************************************************
%---------------Global Parfor Loop-----------------------------------------
%for scCount=1:numScans
if SWsingleSc==1
parforArg=0;
else
parforArg= inf;
end
%for (scCount=1:numScans)
parfor (scCount=1:numScans,parforArg)
scCount %for debugging
p4L0= cell(18,1);
[p4L3,...
TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneRefs3,Tmpsbdg3]= ...
par4GblFnc8c(parMat,tptLength,numScans,selScanNumLst,SWsingleSc,Fflg,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,cirMask,width, ...
TmpexpScanIntens0,TmpFexpScanSpots0,TmpFexpScanBMtp0,TmpanlZoneRefs0,scCount,tifFileLstP4,pathname,ImParMat, ...
numRows,numCols, scLst,resDir,expDir, p4L0,Tmpsbdg0);
p4L4(:,scCount)= p4L3; %(:,scCount);
TmpexpScanIntens4(scCount)= TmpexpScanIntens3;
TmpFexpScanSpots4(scCount)= TmpFexpScanSpots3;
TmpFexpScanBMtp4(scCount)= TmpFexpScanBMtp3;
TmpanlZoneRefs4(scCount)= TmpanlZoneRefs3;
Tmpsbdg4(scCount)= Tmpsbdg3;
%End of Global Scan loop*******************************************************************************************
%**************************************************************************************************************************
end
%---------------END OF Global Parfor Loop-----------------------------------------%**************************************************************************************************************************

357
workflow/templates/easy/par4GblFnc8c.m Executable file
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%% CALLED By p4loop8c.m %%
function [p4L2, ...
TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneRefs3,Tmpsbdg3]= ...
par4GblFnc8c(parMat,tptLength,~,selScanNumLst,~,Fflg,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,cirMask,~,...
TmpexpScanIntens,TmpFexpScanSpots,TmpFexpScanBMtp,TmpanlZoneRefs,scCount,tifFileLstP4,~,ImParMat, ...
numRows,numCols,scLst,resDir,expDir,~, Tmpsbdg)
selScan= selScanNumLst(scCount);
tptLength0= length(tifFileLstP4{scCount});
%tptLength= numFiles;
tifFileLst={tifFileLstP4(scCount)};
% Extract the Imaging time stamps from selected tif files
%clear('e','f'); %can't use clear inside a parfor loop. Preallocation
%can be larger than useable .bmp files! Therefore must be small and
%increased during for loop to maintain cell size integrity between e & f
e= cell(1,2); f= cell(1,2); %(tptLength,2); f= cell(tptLength,2);
nndx=0;
for tPt=1:tptLength0 %size(tifFileLst,1) %length(tifFileLst)
tifFileLstP4{scCount}(tPt)
scLst;
scLst(scCount)
char(scLst(scCount))
char(fullfile(expDir,char(scLst(scCount))))
expDir;
swCatch=0;
nndx=nndx+1;
tifFile=char(fullfile(expDir,char(scLst(scCount)), tifFileLstP4{scCount}(tPt)));
try
info = imfinfo(tifFile); %('D:\jwrDevel\DevelCurveFittingJWR\ImageScans\Scan2\020hr002.tif')
catch ME
%Note: During parallel operation Matlab will not open file (fid)
%etc. Therefore error message text will not be written.The only way
%to get it out would be to pass variable through called function to
%the ..Main8c script outside the parfor loop and print to file from
%there. Consequently for now it only prints error to file when one
%edits p4loop8c.m from 'parfor' to ordinary 'for' loop
fFail=((fullfile(resDir,'PrintResults','ImageFileReadFailure.txt')));
fid = fopen(fFail,'a'); %create,open and append
%fprintf(fid,'%s \n',char(tifFile))
fclose(fid)
nndx=nndx-1;
swCatch=1;
rep = getReport(ME, 'basic');
rep=strcat('Read info failure for-',tifFile,' -', rep);
%fprintf(fid,'%s \n',rep) %See Note:
end
tptLength= nndx;
scTmNumeric= 1; %initialize for parfor
if swCatch==0
scTmNumeric(nndx)=datenum(info.FileModDate);
e(nndx,:)= {tifFile, scTmNumeric(nndx)};
%newtifFileLst(nndx)= tifFileLst(tPt);
end
end % end for tPt=1:length(tifFileLst) loop
%clear tifFileLst; %Can't use clear inside a parfor loop
tifFileLst= cell(nndx,1);
f= {sortrows(e,2)};
tifFileLst= f{1,1}(:,1);
areaOfIntensAboveBG= zeros(24,16,length(tifFileLst));
% *******Calculate Time series for each Plate of Selected Scan ********
lastPlateOnScan=1; %Ncode
tSeriesv=[]; t0Seriesv=[];
if tptLength>0 %added to jump over and fill data for invalid Sscan(plate runs
scTmNumv= cell2mat(f{1,1}(:,2)); %(:,2)) %120613 fix for variant length data
prtTmNumv=min(scTmNumv)-.000001;
tSeriesv=((scTmNumv-prtTmNumv)*24);
t0Seriesv=((scTmNumv-scTmNumv(1))*24);
end
%*********************
%-------------------------------------------------------
if tptLength>= 3 %added to jump over and fill data for invalid Sscan(plate runs
%*******Create Blank Scan*********************
ImHeigth=2075;
ImWidth=1400;
Empsc=zeros(ImHeigth,ImWidth); %Ncode
%**************************************************************************
%*********Start Scan Loop**************************************************
lastPlateOnScan=1; %Ncode
%**********************************************************************************************************************************
disp('Before call to NIscanIntens.....')
resDir; %debugging parfor
%>>>*******Execute Image conversion into Intensity Data******
[Tmpsbdg2, scanIntens, ~, ~, ~, TmpexpScanIntens2, TmpFexpScanSpots2, TmpFexpScanBMtp2, TmpanlZoneRefs2,areaOfIntensAboveBG]= ...
NIscanIntensBGpar4GblFnc(Fflg,tifFileLst, ImParMat, PTmapPos,optCirMask,diaExt,doCircle,cirPixA,numRows,numCols,ImHeigth,ImWidth,cirMask, ...
tptLength,selScan,Empsc,TmpexpScanIntens,TmpFexpScanSpots,TmpFexpScanBMtp,TmpanlZoneRefs,resDir, Tmpsbdg);
%<<<<*******************************************************************************************************************************
TmpexpScanIntens3= TmpexpScanIntens2;
TmpFexpScanSpots3= TmpFexpScanSpots2;
TmpFexpScanBMtp3= TmpFexpScanBMtp2;
TmpanlZoneRefs3= TmpanlZoneRefs2;
Tmpsbdg3= Tmpsbdg2;
%***********************************************************************************
%Package Image data ->for Legacy Printing
%clear plate %Can't use clear inside a parfor loop
CFscanIntens= zeros(384,1);%zeros(16,24);
plate= [];
plate= zeros(24,16,tptLength);
plate(:,:,:,1)= scanIntens(1:1:24,16:-1:1,:); %TmpexpScanIntens2(1:1:24,16:-1:1,:);%Ncode Dev3Vertical Similar to below
%*******************************
%NIcheck %Check for bad scans at time points (swapped plates etc.)
%*******************************
%set up cell arrays for storing each plate in each Scan ..(scan,plate)
SWprint=0;
if SWprint==1
wkDir=pwd;
cd (fullfile(resDir,'PrintResults'));
end
% Construct Legacy ...Intens.txt file
if SWprint==1
filename=(strcat('Plate',num2str(selScan),'_Intens.txt'));
fid = fopen(filename,'w');
end
if length(size(plate))==2 %Only two dims if only one image
numOfImages=1;
else
numOfImages= size(plate,3);
end
CFscanIntens= zeros(384,numOfImages);
locIndx=0; pl=1;
for n=1:numCols %Ncode changed to 16 for Vert
for m=1:numRows %Ncode change to 24 for Vert
locIndx=locIndx+1;
for k=1:numOfImages
if SWprint==1
if k==1 && numOfImages==1, fprintf(fid,'%.2f\n',plate(m,n,k,pl));end
if k==1 && numOfImages~=1, fprintf(fid,'%.2f',plate(m,n,k,pl));end
if k>1 && k<numOfImages, fprintf(fid,'\t%.2f',plate(m,n,k,pl));end %
if k~=1 && k==numOfImages,fprintf(fid,'\t%.2f\n',plate(m,n,k,pl));end
end
CFscanIntens(locIndx,k)= plate(m,n,k,pl);
end
%MatLab Cell storage
end
end %end row loop n
if SWprint==1
fclose(fid);
end
%++++++++++++++++++++++
%printGrwAreas
%Area as the max number of pixels with intensities greater than the Background
%grArea(row,col,tPt,Plate) Note that images r and c are 90 degrees shifted
%and then mirror imaged. Thus data must be inverted and rotated to get
%for the rows a-p and col 1-24 (and the EMS expected 1-384) orientation
%clear grArea
grArea= ones(24,16,tptLength);
grArea(:,:,:,1)= areaOfIntensAboveBG(1:1:24,16:-1:1,:); %for Ncode dev3vert
%for p=1:lastPlateOnScan
if SWprint==1
if SWgrowthArea==1
filename=(strcat('Plate',num2str(selScan),'_Areas.txt'));
else
filename=(strcat('ALTgrowthA_Scan',num2str(selScan),'_Plate',num2str(1),'_Areas.txt'));
filename=(strcat('ALTgrowthA_Plate',num2str(selScan),'_Plate','_Areas.txt'));
end
fid = fopen(filename,'w');
end
locIndx=0;
Ag= zeros(1,384);
for m=1:16 %Ncode change from 16 %Vert back to 16
for n=1:24 %Ncode change from 24 %Vert back to 24
growthArea=max(grArea(n,m,:,1));
if SWprint==1
fprintf(fid,'%3.f\n',growthArea);
end
locIndx=locIndx+1;
Ag(locIndx)= growthArea;
end
end
if SWprint==1
fclose(fid);
end
%end
%++++++++++++++++++++++++
if SWprint==1
cd(wkDir);
fclose('all');
end
%********AutoImCF curveFit kickoff setup***********************************************************
autoImCFlag=1;
if autoImCFlag==1, SWgrowthArea=1;end
times= tSeriesv;
scanAreas= Ag; %growthArea;
offsets=0;
suffix= strcat('Scan', num2str(selScan),'_Plate', num2str(1)); %char(QspLst(n));
AUCfinalTime=96;
arrayFormat=384;
currDirResults= fullfile(resDir,'PrintResults');
%******Version compatability fixes*******assoc'd with diff and solve
%{
v11a='7.12.0.635 (R2011a)';
v14a='8.3.0.532 (R2014a)';
%v14b='8.4.0.150421 (R2014b)';
v18a='9.4.0.813654 (R2018a)';
v18b='9.5.0.944444 (R2018b)';
%Fourth order derivative of logistic equation********************************
if isequal(v18a,version)||isequal(v18b,version)
syms t K r l;
fd4= diff(K / (1 + exp(-r* (t - l ))),t,4);
else
fd4=diff(sym('K / (1 + exp(-r* (t - l )))'),4);
end
sols= solve(fd4);
if isequal(v11a,version) || isequal(v14a,version)
else
tmpswap= sols(1);
sols(1)= sols(3);
sols(3)= tmpswap;
end
%}
if verLessThan('matlab','8.3') %original work 23_0227 updated 23_0525 (8.4 changed to 8.3)
fd4=diff(sym('K / (1 + exp(-r* (t - l )))'),4);
sols= solve(fd4);
else %accomodate new matlab changes after 2014a fix 2nd update 23_0227
syms t K r l;
fd4= diff(K / (1 + exp(-r* (t - l ))),t,4);
sols= solve(fd4);
tmpswap= sols(1);
sols(1)= sols(3);
sols(3)= tmpswap;
end
%********************************************************************************
%CFscanIntens
%adsd
%********************************************************************************
%>>>>>>>>>>>Call CurveFit routine >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%NCfitImCF(times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, currDirResults, autoImCFlag, selScan,sols) %,scan)%, scPltList) outputDirectory;
%[scanTmp2]= NCfitImCFparforFailGbl(times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, currDirResults, autoImCFlag, selScan, sols, scanTmp); %,scan)%, scPltList) outputDirectory;
[par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanIntensELr,par4scanCFparameters,par4scanCFdate,outC2,outCstd2]= ...
NCfitImCFparforFailGbl2(parMat,times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, currDirResults, autoImCFlag, selScan, sols); %,scan)%, scPltList) outputDirectory;
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
else %fill with default values when an invalid plate scan occurs
CFscanIntens= zeros(16,24);
Ag= zeros(1,384);
%Preallocation for parfor loop**********************************
times= tSeriesv;
st(1,1:size(times,2))= 1111;
resMat(1,1:27)= 0;
resMatStd= resMat;
outC2= zeros(384,27);
outCstd2= zeros(384,27);
for m=1:384
pa{m}= st;
par4scanCFparameters{m}= parMat;
par4scanCFdate{m}= datestr((now),31);
end
par4scanselTimesStd= pa;
par4scanselIntensStd= pa;
par4scanTimesELr= pa;
par4scanIntensELr= pa;
par4resMat= zeros(384,27);
par4resMatStd= zeros(384,27);
%{
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);
%}
TmpexpScanIntens3= cell(1); %TmpexpScanIntens2;
TmpFexpScanSpots3= cell(1); %TmpFexpScanSpots2;
TmpFexpScanBMtp3= cell(1); %TmpFexpScanBMtp2;
TmpanlZoneRefs3= cell(1); %TmpanlZoneRefs2;
Tmpsbdg3= cell(1); %Tmpsbdg2;
%****************************************************************
end %if tptLenth>=3 line19 20_0928
tSeriesv; %debuggin parfor
p4L1{1}= tSeriesv;
p4L1{2}= t0Seriesv;
p4L1{3}= datestr(prtTmNumv,31);
p4L1{4}= CFscanIntens;
locIndx=0;
for n=1:numCols %Ncode changed to 16 for Vert
for m=1:numRows %Ncode change to 24 for Vert
locIndx=locIndx+1;
rc=[n,m];
p4rcTmp(locIndx)={rc};
p4pIndxTmp(locIndx)=locIndx;
end
end
p4L1{5}= p4rcTmp;
p4L1{6}= p4pIndxTmp;
p4L1{7}= Ag;
p4L1{8}= par4scanselIntensStd;
p4L1{9}= par4scanselTimesStd;
p4L1{10}= par4scanTimesELr;
p4L1{11}= par4scanIntensELr;
p4L1{12}= par4scanCFparameters;
p4L1{13}= par4scanCFdate;
p4L1{14}= outC2;
p4L1{15}= outCstd2;
p4L1{16}= selScan;
p4L1{17}= cirPixA;
p4L1{18}= datestr((now),31);
p4L2= p4L1;
end

342
workflow/templates/easy/par4Gbl_Main8c.m Executable file
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%% 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;
%+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++