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EASY refactor: First attempt

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This commit is contained in:
Bryan Roessler
2024-07-27 02:58:49 -04:00
parent 5269962927
commit bce30095aa
11 changed files with 340 additions and 301 deletions
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39
workflow/templates/easy/NIscanIntensBGpar4GblFnc.m
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@@ -1,10 +1,12 @@
%% CALLED BY par4GblFnc8c.m %%
function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2, TmpFexpScanSpots2, TmpFexpScanBMtp2, TmpanlZoneRefs2,areaOfIntensAboveBG]= ...
NIscanIntensBGpar4GblFnc(Fflg, tifFileLst, ImParMat,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,numRows,numCols,ImHeigth,ImWidth,cirMask, ...
tptLength,selScan,Empsc,~, ~, ~, ~,resDir, Tmpsbdg1)
tptLength,selScan,Empsc,~, ~, ~, ~,easyResultsDir, Tmpsbdg1)
global ExpOutmat
global matFile
global CSrchRng
global figsResultsDir
global fotosResultsDir
searchIntens=[]; intensMax=[]; detMaxPos=[]; scIntens=[]; areaOfIntensAboveBG=[]; BkgrdMat=[];
@@ -33,7 +35,8 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
PTmapOnesDbl(PTrefPtR:(PTrefPtR+(diaExt-1)),PTrefPtC:(PTrefPtC+(diaExt-1)))=optCirMask;
end
end
end %if Fflg==1
end
% Zeroth Initial Search Parameters
rRangeUpper=-12;
rRangeLower=12;
@@ -73,11 +76,12 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
intensPrev=zeros(24,16);
cent=cell(24,16);
BGTav=zeros(numRows,numCols);
BGthres(1:numRows,1:numCols)=95; %70;before incr.to95 to accommodate dark media %50forEpson;%Initialize for first tPt run *****************************************************<<
if length(tifFileLst) >2
%******Determine a good Plate Image from all the timepoints to use for Registration
%Plate Intensity curve over time points
%clear plateImage
% 7 0;before incr.to95 to accommodate dark media %50forEpson;%Initialize for first tPt run
BGthres(1:numRows,1:numCols)=95;
if length(tifFileLst)>2
% Determine a good Plate Image from all the timepoints to use for Registration
% Plate Intensity curve over time points
% clear plateImage
plateImage={};
%{
% Version compatability fixes
@@ -517,8 +521,8 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
% NIgenBkGrdDataPar4Fnc(ImParMat, tifFileLst, lastDetMaxPos, numRows, numCols, fullsc, tPt, BGthres, doCircle, cirPixA, diaExt, cirMask, BGTav)
% Called by NIscanIntensBG.m
% global resDir
global ExpOutmat
% global easyResultsDir
global matFile
% global pixsAboveBG
MPnum=ImParMat(1);
destPerMP=ImParMat(2);
@@ -1146,24 +1150,23 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
title(strcat('Scan',num2str(selScan),'timePt-',num2str(tPt)));
clf(hfscanIm,'reset');
set(hfIm,'NumberTitle','off')
set(hfIm,'Name', char(ExpOutmat)) % strcat('EASYconsole- ',char(resDir)))
if Fflg==1
resDir; % for debugging
fullfile(resDir,'Fotos',strcat('Scan',num2str(selScan),'_timePt-',num2str(tPt)))
hgsave(fullfile(resDir,'Fotos',strcat('Scan',num2str(selScan),'_timePt-',num2str(tPt)))); %F 14_0626
set(hfIm,'Name', char(matFile)) % strcat('EASYconsole- ',char(easyResultsDir)))
if Fflg==1
fullfile(fotosResultsDir,strcat('Scan',num2str(selScan),'_timePt-',num2str(tPt)))
hgsave(fullfile(fotosResultsDir,strcat('Scan',num2str(selScan),'_timePt-',num2str(tPt)))); %F 14_0626
else
hgsave(fullfile(resDir,'figs',strcat('Scan',num2str(selScan),'_timePt-',num2str(tPt))));
hgsave(fullfile(figsResultsDir,strcat('Scan',num2str(selScan),'_timePt-',num2str(tPt))));
end
else
selScan;
%tifFile
% tifFile
end
BkgrdMat=totBkgrd; % BkgrdMat(:,:,tPt)=totBkgrd; %debug parfor effort
areaOfIntensAboveBG(:,:,tPt)=pixsAboveBG; % actual area of growth for each timepoint (used for printout of grArea ?not used in previous analysis)
scanIntens(:,:,tPt)=intens-BkgrdMat;
% capture first and last background values
% Capture first and last background values
if tPt==1
bdg(:,:,1)=bmm;
bdg(:,:,3)=rwm;