Squashed initial commit
This commit is contained in:
232
qhtcp-workflow/apps/matlab/easy/NCfitImCFparforFailGbl2.m
Executable file
232
qhtcp-workflow/apps/matlab/easy/NCfitImCFparforFailGbl2.m
Executable file
@@ -0,0 +1,232 @@
|
||||
%% CALLED BY par4GblFnc8c.m %%
|
||||
function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanIntensELr,par4scanCFparameters,par4scanCFdate,outC,outCstd]= ...
|
||||
NCfitImCFparforFailGbl2(parMat,times, values, timeOffsets, fileSuffix, AUCfinalTime, ~, spotAreas, printResultsDir, ~,~, 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);
|
||||
|
||||
% 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
|
||||
|
||||
% 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.m
|
||||
% Preallocate incase something bails in NCscurImCFparfor
|
||||
resMatStd=zeros(1,27);
|
||||
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;
|
||||
bl=0;
|
||||
Tpt1=0;numFitTpts=0;thresGT2=0;minTime=0;fitbl=0; % diagnostic outputs only
|
||||
|
||||
timepts=timepts; % timepts=currTimes; parfor
|
||||
normIntens=currNormIntens;
|
||||
|
||||
dataMatrix=[]; % arfor move clear from NCfitImCF...m
|
||||
loIntensThres=parMat(4);
|
||||
stdLoIntLim=parMat(5);
|
||||
|
||||
% Basic filtering
|
||||
% [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
|
||||
end
|
||||
end
|
||||
|
||||
% TODO repetitive code
|
||||
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);
|
||||
|
||||
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
|
||||
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
|
||||
|
||||
% TODO 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); %s elIntens(nn)=dataMatrix(4,n);
|
||||
|
||||
end
|
||||
end
|
||||
|
||||
selTimes=selTimes';
|
||||
selIntens=selIntens';
|
||||
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
|
||||
|
||||
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
|
||||
|
||||
outC(ii,:)=resMat; %{ii, par4resMat};
|
||||
outCstd(ii,:)=resMatStd; %{ii, par4resMatStd};
|
||||
end
|
||||
|
||||
% 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(printResultsDir, fileNamePlate); %[printResultsDir 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
|
||||
Reference in New Issue
Block a user