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Format DgenResults.m

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This commit is contained in:
Bryan Roessler
2024-07-25 12:45:16 -04:00
parent adf507476d
commit 4d72a078b5
2 changed files with 560 additions and 613 deletions
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187
workflow/templates/easy/DgenResults.m
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@@ -1,5 +1,5 @@
%% CALLED BY EASYconsole.m %%
%to 'Fotos' from 'PTmaps'
% Updated 240724 Bryan C Roessler to improve file operations and portability
%Console globals*******
global ExpPath
global resDir
@@ -8,7 +8,6 @@ global ImParMat
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);
@@ -25,7 +24,6 @@ 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
@@ -50,29 +48,19 @@ else
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
elseif ((isunix) || (ismac))
expNm=localExpPath(max(strfind(localExpPath,'/'))+1:end)
drivePos=min(strfind(localExpPath,'/'));
end
drive= localExpPath(1:(drivePos-1));
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'));
@@ -81,7 +69,6 @@ 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
@@ -97,12 +84,13 @@ 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
@@ -111,19 +99,25 @@ for s=1:size(scan,2)
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
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
if pertCnt==0
pertCnt=destPerMP
end
pert=strcat('Perturb_',num2str(pertCnt));
s
p
s % TODO seems wrong
p % TODO seems wrong
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');
@@ -146,17 +140,13 @@ for s=1:size(scan,2)
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=[];
@@ -166,22 +156,19 @@ for s=1:size(scan,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');
@@ -189,11 +176,10 @@ dataLength= min(TseriesSize,RawIntensSize);
ln=ln+1;
fprintf(fid,'%d\t',ln);
end
%*****************************************Begin Data Section
% Data
n=0;
for r=1:16
for c=1:24
n=n+1;
clear selcode;
@@ -201,7 +187,7 @@ dataLength= min(TseriesSize,RawIntensSize);
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 Kval<40, selcode=strcat(selcode,' K_Lo');end
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))...
@@ -209,11 +195,10 @@ dataLength= min(TseriesSize,RawIntensSize);
||isnan(outCmat(n,12)), selcode=strcat(selcode,' NaN');
end
%*************RiseTime Calculation*****************************************
% 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));
@@ -223,9 +208,8 @@ dataLength= min(TseriesSize,RawIntensSize);
else
riseTm=0;
end
%*************************************************************************
if Ag(n)< .30*(scan(s).Awindow),selcode=strcat(selcode,' smArea'); end %12_1030
if Ag(n)< .30*(scan(s).Awindow),selcode=strcat(selcode,' smArea'); end
if outCmat(n,3)==0,selcode=strcat('0 ',selcode);end
orf=cell2mat(MP(mpCnt).orf{1}(n));
@@ -263,18 +247,18 @@ dataLength= min(TseriesSize,RawIntensSize);
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
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*****
end
% DBfile
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
@@ -286,17 +270,13 @@ dataLength= min(TseriesSize,RawIntensSize);
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));
outCmat(n,5),dbRsq,dbKup,dbKlo,dbrup,dbrlo,dbLlo,dbLup); %\t%.5f\t%.5f\t%.5f\t%.5f
end
%*****DB analysis data end************************************************
% Add Intensities series to end of curve fit data
outIntens=[];
outIntens=zeros(384,dataLength);
@@ -321,18 +301,14 @@ dataLength= min(TseriesSize,RawIntensSize);
else
tmBlob=strcat(tmBlob,num2str(outTseries(j)));
end
end %if DB
end %j
%***************************
end
end
% Results fprint***********
% Results
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
@@ -349,19 +325,14 @@ dataLength= min(TseriesSize,RawIntensSize);
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 );
@@ -378,11 +349,9 @@ dataLength= min(TseriesSize,RawIntensSize);
else
fprintf(fid2, '\t%s', ' ');
end
%---------------------------------
fprintf(fid2, '\n');
end %DB print
end
end %if ~isempty(outCmat)
end %c
end %r
end %p
@@ -391,9 +360,9 @@ 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
@@ -401,11 +370,9 @@ catch ME
rep=strcat('Failed copyfile to ',DBupload,' -', rep);
errordlg(rep)
end
end %if DB
end
% ln; TODO removed by BCR, this doesn't seem necessary
%***********************************************************************
%BEGIN PRINT RESULTS ROUTINE FOR STANDARD METHOD
%***********************************************************************
@@ -438,16 +405,15 @@ for s=1:size(scan,2)
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
s % BCR seems wrong
%Print Time Point HEADER for each plate for newly added intensity data
if isequal(opt,'Res')||isequal(opt,'Both')
@@ -471,8 +437,6 @@ for s=1:size(scan,2)
outTseries=[];
outTseries=scan(s).plate(p).tSeries;
TseriesSize= size(outTseries,1);
%***************************************************************
clear outCmat
outCmat=scan(s).plate(p).CFoutStd;
clear outIntens
@@ -483,7 +447,7 @@ for s=1:size(scan,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
@@ -497,7 +461,6 @@ dataLength= min(TseriesSize,RawIntensSize);
for nn=1:numBlkCol %extend to col beyond longest rawDataSet
fprintf(fid, '\t');
end
fprintf(fid,'\tOrfRep');
fprintf(fid,'\tSpecifics');
fprintf(fid,'\tStrainBkGrd');
@@ -505,11 +468,10 @@ dataLength= min(TseriesSize,RawIntensSize);
ln=ln+1;
fprintf(fid,'%d\t',ln);
end
%*****************************************Begin Data Section
% Data
n=0;
for r=1:16
for c=1:24
n=n+1;
clear selcode;
@@ -525,7 +487,7 @@ dataLength= min(TseriesSize,RawIntensSize);
||isnan(outCmat(n,12)), selcode=strcat(selcode,' NaN');
end
%*************RiseTime Calculation*****************************************
% RiseTime Calculation
K=(outCmat(n,3));
R=(outCmat(n,4));
L=(outCmat(n,5));
@@ -539,11 +501,8 @@ dataLength= min(TseriesSize,RawIntensSize);
riseTm=0;
end
%*************************************************************************
if Ag(n)< .30*(scan(s).Awindow),selcode=strcat(selcode,' smArea'); end %12_1030
if Ag(n)< .30*(scan(s).Awindow),selcode=strcat(selcode,' smArea'); end
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));
@@ -582,9 +541,10 @@ dataLength= min(TseriesSize,RawIntensSize);
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*****
end
% DBFile
% RiseTime calculation
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
@@ -596,17 +556,15 @@ dataLength= min(TseriesSize,RawIntensSize);
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));
dbrup,dbrlo,dbLlo,dbLup);
end
%*****DB analysis data end************************************************
% DB Analysis
% Add Intensities series to end of curve fit data
outIntens=[];
outIntens=zeros(384,dataLength);
@@ -631,19 +589,15 @@ dataLength= min(TseriesSize,RawIntensSize);
else
tmBlob= strcat(tmBlob,num2str(outTseries(j)));
end
end %if DB
end %j
%***************************
end
end
% Results fprint***********
% 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
@@ -660,19 +614,17 @@ dataLength= min(TseriesSize,RawIntensSize);
else
fprintf(fid, '\t%s', ' ');
end
%-----------------------------------------------
%****************************
fprintf(fid, '\n');
ln=ln+1;
fprintf(fid,'%d\t',ln);
end
%****************************
%DB Raw Intensities and Timepoints
% 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 );
@@ -689,12 +641,9 @@ dataLength= min(TseriesSize,RawIntensSize);
else
fprintf(fid2, '\t%s', ' ');
end
%---------------------------------
fprintf(fid2, '\n');
end %DB print
end %if ~isempty(outCmat)
end %c
end %r
end %p
@@ -703,9 +652,9 @@ 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
@@ -713,13 +662,11 @@ catch ME
rep=strcat('Failed copyfile to ',DBupload,' -', rep);
errordlg(rep)
end
end %if DB
ln;
end
catch
errorNstdResults='Catch at line720 for printing ResultsStd'
end %try scan(1).plate(1).CFoutStd(1,1) to test for 2018 r_refined version
scriptComplete= "line724 "
msgbox(['Printing Script complete. Check !!Results sheets in ../PrintResults folder.'])
catch ME
errorNstdResults='Catch at line720 for printing ResultsStd'
end

8
workflow/templates/easy/datatipp.m
View File

@@ -1,15 +1,15 @@
%% PART OF GUI FUNCTIONALITY %%
function output_txt = datatipp(~,event_obj)
% Display the position of the data cursor
function output_txt = datatipp(~,event_obj)
% 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)]};
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
end