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EASY passing linter checks

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This commit is contained in:
Bryan Roessler
2024-07-27 12:09:09 -04:00
parent d77711acb7
commit 78d5e26d71
10 changed files with 810 additions and 772 deletions
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61
workflow/templates/easy/NCfitImCFparforFailGbl2.m
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@@ -20,18 +20,18 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
par4resMat=zeros(384,27);
par4resMatStd=zeros(384,27);
% Spot(cultures) loop
for ii=1:384 %startSpot:numCultures
ii; %%%db print out the culture number
% Spot (cultures) loop
for 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
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);
@@ -48,7 +48,7 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
currNormIntens=currValues/currSpotArea;
tmpx=find(currNormIntens>5); %15jh % 2.3);
validSpot=true;
if(isempty(tmpx) || (length(tmpx)<3))
if(isempty(tmpx) || length(tmpx)<3)
validSpot=false;
normIntens=currNormIntens;
filterTimes=timepts; %filterTimes; %currTimes;
@@ -63,9 +63,9 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
resMat=zeros(1,27);
hold off;
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;
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
Tpt1=0;numFitTpts=0;thresGT2=0;minTime=0;fitbl=0; % diagnostic outputs only
timepts=timepts; % timepts=currTimes; parfor
normIntens=currNormIntens;
@@ -82,7 +82,7 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
threshold=0;
end
dropThreshold=-0.0001* max(normIntens);
dropThreshold=-0.0001*max(normIntens);
% Initialize dataMatrix
dataMatrix(1,:)=timepts;
@@ -102,7 +102,7 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
% NCLoIntstdTrim
% NCLoSstdTrim.m called by NCfilImCF and NCfil.m
flg1=0;
loScurvLim=stdLoIntLim; %
loScurvLim=stdLoIntLim;
loStimeN=1;
last2n=1;
stdDev=[];
@@ -110,26 +110,27 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
for n=1:meanIntIndPt
if nrmIntens0(n)<=0
nrmIntens0(n)=0;
end
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;
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 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
flg1=1;
end
end
end
% TODO repetitive code
@@ -142,14 +143,14 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
qcutoff=2;
qind=find(normIntens>2); %,:,'first');
if ~isempty(qind(3))
qcutoff=qind(3)
qcutoff=qind(3);
end
[minInt,I]=min(normIntens(2:qcutoff));
bl=minInt;
minTime=dataMatrix(1,I); %diagnostic output only
minTime=dataMatrix(1,I);
if (length(qind)>5)&&I>1
dataMatrix(3,1:(I-1))=5
dataMatrix(3,1:(I-1))=5;
end
tGT2Flg=0;
@@ -157,7 +158,7 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
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
end
resMat(18)=bl;