bryan/hartman-server
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

EASY refactor: First attempt

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

62
workflow/templates/easy/par4GblFnc8c.m
View File

@@ -2,11 +2,13 @@
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)
numRows,numCols,scLst,easyResultsDir,scansDir,~, Tmpsbdg)
global printResultsDir
selScan=selScanNumLst(scCount);
tptLength0=length(tifFileLstP4{scCount});
%tptLength=numFiles;
% tptLength=numFiles;
tifFileLst={tifFileLstP4(scCount)};
% Extract the Imaging time stamps from selected tif files
@@ -21,13 +23,13 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
scLst;
scLst(scCount)
char(scLst(scCount))
char(fullfile(expDir,char(scLst(scCount))))
expDir;
char(fullfile(scansDir,char(scLst(scCount))))
scansDir;
swCatch=0;
nndx=nndx+1;
tifFile=char(fullfile(expDir,char(scLst(scCount)), tifFileLstP4{scCount}(tPt)));
tifFile=char(fullfile(scansDir,char(scLst(scCount)), tifFileLstP4{scCount}(tPt)));
try
info=imfinfo(tifFile); %('D:\jwrDevel\DevelCurveFittingJWR\ImageScans\Scan2\020hr002.tif')
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
@@ -35,30 +37,31 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
% 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')));
fFail=((fullfile(printResultsDir,'ImageFileReadFailure.txt')));
fid=fopen(fFail,'a'); %create,open and append
%fprintf(fid,'%s \n',char(tifFile))
% 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:
% 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);
% newtifFileLst(nndx)=tifFileLst(tPt);
end
end
% clear tifFileLst;
% Clear tifFileLst;
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=[];
@@ -69,7 +72,7 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
t0Seriesv=((scTmNumv-scTmNumv(1))*24);
end
% added to jump over and fill data for invalid Sscan(plate runs
% Added to jump over and fill data for invalid Sscan(plate runs
if tptLength>=3
% Create blank scan
ImHeigth=2075;
@@ -83,7 +86,7 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
% 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);
tptLength,selScan,Empsc,TmpexpScanIntens,TmpFexpScanSpots,TmpFexpScanBMtp,TmpanlZoneRefs,easyResultsDir, Tmpsbdg);
TmpexpScanIntens3=TmpexpScanIntens2;
TmpFexpScanSpots3=TmpFexpScanSpots2;
@@ -100,25 +103,23 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
% 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'));
filename=fullfile(easyResultsDir,'PrintResults',(strcat('Plate',num2str(selScan),'_Intens.txt')));
fid=fopen(filename,'w');
end
if length(size(plate))==2 %Only two dims if only one image
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
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
@@ -148,10 +149,10 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
% for p=1:lastPlateOnScan
if SWprint==1
if SWgrowthArea==1
filename=(strcat('Plate',num2str(selScan),'_Areas.txt'));
filename=fullfile(printResultsDir,(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'));
filename=fullfile(printResultsDir,(strcat('ALTgrowthA_Scan',num2str(selScan),'_Plate',num2str(1),'_Areas.txt')));
filename=fullfile(printResultsDir,(strcat('ALTgrowthA_Plate',num2str(selScan),'_Plate','_Areas.txt')));
end
fid=fopen(filename,'w');
end
@@ -170,11 +171,7 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
if SWprint==1
fclose(fid);
end
if SWprint==1
cd(wkDir);
fclose('all');
% fclose('all'); % TODO do we need this?
end
% AutoImCF curveFit kickoff setup
@@ -186,7 +183,6 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
suffix=strcat('Scan', num2str(selScan),'_Plate', num2str(1)); % char(QspLst(n));
AUCfinalTime=96;
arrayFormat=384;
currDirResults=fullfile(resDir,'PrintResults');
% Version compatability fixes
%{
@@ -225,10 +221,10 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
% CFscanIntens
% 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;
% NCfitImCF(times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, printResultsDir, autoImCFlag, selScan,sols) %,scan)%, scPltList) outputDirectory;
% [scanTmp2]=NCfitImCFparforFailGbl(times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, printResultsDir, 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;
NCfitImCFparforFailGbl2(parMat,times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, printResultsDir, 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);