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

Cleanup par4Gbl_Main8c.m

Browse Source
This commit is contained in:
Bryan Roessler
2024-07-25 10:26:37 -04:00
parent 359b936b45
commit adf507476d
5 changed files with 176 additions and 268 deletions
Download Patch File Download Diff File Expand all files Collapse all files

16
workflow/script-run-workflow
View File

@@ -533,13 +533,19 @@ easy() {
'NoGrowth_.txt', and 'GrowthOnly_.txt' files will be generated in the 'PrintResults' folder.
EOF
script="EASYConsole.m"
script="$EASY_TEMPLATE_DIR/EASYConsole.m"
pushd "$EASY_TEMPLATE_DIR" || return 1
# Launch graphical matlab if the user wants
# Add EASY directory to the Matlab path
# If this does not work we can try changing the -sd argument and if that fails then pushing/popping
debug "Adding EASY directory to the Matlab path"
hash matlab &>/dev/null &&
matlab -nodisplay -nosplash -nodesktop -nojvm -batch "addpath('$EASY_TEMPLATE_DIR')"
# Ask the user to launch EASYconsole.m in MATLAB
# MATLAB doesn't support passing args to scripts se we have to use ENV VARS instead
# These are proably already set in our scope but be explicit just in case
! ((YES)) && ask "Start EASY in MATLAB? This requires a GUI." &&
matlab -nosplash -sd ~/downloads -r "$script"
popd || return 1
SCANS_DIR="$SCANS_DIR" matlab -nosplash -sd "$SCANS_DIR" -r "run $script"
# Use the function return code see if we succeeded
get_easy_results "$SCANS_DIR" || return 1

19
workflow/templates/easy/DMPexcel2mat.m
View File

@@ -1,21 +1,5 @@
%% CALLED BY EASYconsole.m %%
w = pwd;
%{
cd ..
if exist('ExpJobs/')
cd('ExpJobs/');
else
pwd
end
%}
try
cd(ExpPath)
catch
cd(w)
end
pwd
w=pwd
numOfMPs=0;
%GUI input for selecting a MasterPlate Excel file
questdlg('\fontsize{20} Select Master Plate File','File Selection','OK', struct('Default','OK','Interpreter','tex'))
@@ -26,7 +10,6 @@ else
MPdir=fullfile(pathname,'/');
end
infile= Scanfiles(1,:);
cd(MPdir)
%fid=fopen(infile)%('exp23PrintTimes.xls'); % textread puts date and time sequentially into vector

6
workflow/templates/easy/DgenResults.m
View File

@@ -6,7 +6,6 @@ global resDir
global ExpOutmat
global ImParMat
w=pwd;
ln=1;
@@ -403,8 +402,8 @@ catch ME
errordlg(rep)
end
end %if DB
ln;
cd(w)
% ln; TODO removed by BCR, this doesn't seem necessary
%***********************************************************************
@@ -721,7 +720,6 @@ catch
errorNstdResults='Catch at line720 for printing ResultsStd'
end %try scan(1).plate(1).CFoutStd(1,1) to test for 2018 r_refined version
cd(w)
scriptComplete= "line724 "
msgbox(['Printing Script complete. Check !!Results sheets in ../PrintResults folder.'])

37
workflow/templates/easy/EASYconsole.m
View File

@@ -14,7 +14,9 @@ function varargout = EASYconsole(varargin)
wCodeDir=pwd;
% changing directory to wCodeDir
returnStartDir
% returnStartDir
disp(getenv('SCANS_DIR'));
%% GUI INTERFACE DESIGN %%
% beginning of GUI formation & design, see help GUI or help GUIDE in
@@ -102,12 +104,12 @@ end
%% CONSOLE BUTTON INTERFACES %%
% File Button Interface
function FileMenu_Callback(~, ~, ~)
returnStartDir
%returnStartDir
end
% Load Experiment Button Interface
function LoadExp_Callback(~, ~, ~)
returnStartDir
%returnStartDir
end
% New Experiment Button Interface
@@ -123,7 +125,7 @@ function NewExpDat_Callback(~, ~, ~)
global scan
% put all users on same working directory
returnStartDir
%returnStartDir
% Create a new experiment
try
@@ -177,7 +179,7 @@ function NewExpDat_Callback(~, ~, ~)
sbdg= cell(1,scanMax);
save((fullfile(resDir,'Fotos','Nbdg')),'sbdg');
catch ME
returnStartDir
% returnStartDir
disp('Error Creating a New Experiment')
end
@@ -202,8 +204,6 @@ function LoadDatFile_Callback(~, ~, ~)
global fhconsole
%global ImParMat
returnStartDir
% TODO this entire try block needs work
try
% TODO this whole block is highly questionable
@@ -265,11 +265,10 @@ end
% callback for the 'Run' in the dropdown menu
function run_Callback(~, ~, ~)
returnStartDir
end
function runPlateMapPintool_Callback(~, ~, ~)
returnStartDir
try
NImapPT
catch ME
@@ -279,7 +278,6 @@ function runPlateMapPintool_Callback(~, ~, ~)
end
function NImCFcombo_Callback(~, ~, ~)
returnStartDir
try
par4Gbl_Main8c
catch
@@ -289,7 +287,6 @@ function NImCFcombo_Callback(~, ~, ~)
end
function runPlateImAnal_Callback(~, ~, ~)
returnStartDir
try
NImStartupOnly
catch ME
@@ -300,7 +297,6 @@ end
function PlateCFit_Callback(~, ~, ~)
%global ExpOutmat
returnStartDir
try
NCstart
catch ME
@@ -340,10 +336,8 @@ function Tools_Callback(~, ~, ~)
end
function runOverlayPlots_Callback(~, ~, ~)
returnStartDir
try
DoverlayPlots2
returnStartDir
EASYconsole
catch ME
returnStartDir
@@ -352,10 +346,8 @@ function runOverlayPlots_Callback(~, ~, ~)
end
function runFotoStrip_Callback(~, ~, ~)
returnStartDir
try
F_NImStartup_CentCir
returnStartDir
EASYconsole
catch ME
returnStartDir
@@ -364,7 +356,6 @@ function runFotoStrip_Callback(~, ~, ~)
end
function runDisplayFig_Callback(~, ~, ~)
returnStartDir
try
UfigDisplay
catch ME
@@ -374,7 +365,6 @@ function runDisplayFig_Callback(~, ~, ~)
end
function runViewParameters_Callback(~, ~, ~)
returnStartDir
try
catch ME
returnStartDir
@@ -383,17 +373,7 @@ function runViewParameters_Callback(~, ~, ~)
end
function QkviewN_Callback(~, ~, ~)
returnStartDir
try
try
cd(fullfile(ExpPath))
catch
if ispc
cd('C:\')
else
cd(fullfile('~'));
end
end
QkviewImages
catch ME
returnStartDir
@@ -402,7 +382,6 @@ function QkviewN_Callback(~, ~, ~)
end
function CFdisplay_Callback(~, ~, ~)
returnStartDir
try
NCsingleDisplay
returnStartDir

106
workflow/templates/easy/par4Gbl_Main8c.m
View File

@@ -1,5 +1,7 @@
%% CALLED BY EASYconsole.m %%
w=pwd;
%function NImStartupImCF02par4Gbl
Fflg=1; %0;
@@ -14,7 +16,6 @@ global ImParMat
%global CSrchRng
global expDir
global SWnewExp
%Console globals*******
global openExpfile
global openExppath
global newExpfile
@@ -24,8 +25,7 @@ global fhconsole
global ExpPath
global resDir
global wCodeDir
global matDir %
global matDir
global ImWidth
global ImHeigth
global numRows;
@@ -35,15 +35,14 @@ global scan
%global scanSize
global scanMax
global tptLength
%global scanPar4x
%global sols
%global CFmeth
numRows=24; %for Single Vertical
numCols=16; %for Single Vertical
%global scanPar4x
%*************CIRCLE related*************************
doCircle=1; %use Circle area analysis 14_0807
radius=14;
ImParMat(10)=radius;
@@ -54,6 +53,7 @@ clf(fhconsole,'reset')
catch ME
end
close
%******************************************
EASYconsole
%******************************************
@@ -75,7 +75,6 @@ catch
%A copy of Ndbg.mat is placed also saved to the 'PTmats' directory
%after each run to allow previous version of EASY to access data made
%by EASY versions after 20_0819.
load(fullfile(resDir,'PTmats','Nbdg')) %Left in to accomodate loads of work before 20_0819
end
%++++++++++++++Load Fotos stored data++++++++++++++++++++
@@ -97,47 +96,41 @@ load(fullfile(resDir,'PTmats','NCFparms'))
catch ME
load parameters
end
%*******************************
%************Get Print Times*******************************
PrintTimes=[];
w= cd; %Capture current dir in w
if ispc %Linux accommodation
if ispc
expDir=fullfile(ExpPath,'\');
else
if isunix, expDir= ExpPath;end
if ismac , expDir=ExpPath;end
elseif (isunix || ismac)
expDir=ExpPath
end
scLst={};
%**************Parameter Entry******************
NImParamRadiusGui(expDir) %Ncode 122111replaced removed ,numOfPrtTimes)
%***********************************************
%width=ImParMat(5);
width=24;
widthEx=width-1; %width extention from reference point
dither=ImParMat(6);
radius=ImParMat(10);
%>>>>>>>>>>>>>>>>>>>>>>
NIcircle
%<<<<<<<<<<<<<<<<<<<<<<<
%***************** Load Stuff*************************
lastPlateOnLastScan=1; %Ncode
if size(scLst,1)==1,SWsingleSc=1;else SWsingleSc=0;end
%**************************????????????????????????
if size(scLst,1)==1
SWsingleSc=1
else
SWsingleSc=0
end
dvec=datevec(datestr(floor(now))); %method to get current offset year '01-Jan-"currentyr"'
dvec(2)=1;
dvec(3)=1;
%yrOffset=datenum('01-Jan-2012');%(dvec); %('01-Jan-2009'); %time num default is currentyear jan1
%******************+++++++++++++*****************+++++++++++++++***********
numScans=size(scLst,1);
if(isequal(SWsingleSc,1))
selScan=str2double(char(scLst(1)));
%numScans=selScan;
%startScan=selScan;
else
% startScan=1;
end
@@ -146,20 +139,10 @@ SWgrowthArea= ImParMat(9);
load(fullfile(resDir,'PTmats','NPTmapSearch'))
PTmapPos=detPos;
%**************************************************************************
selScanNumLst=[];
%++++++++++++++++++++++++++++++++++++++++++++++++++++++++
%**************************************************************************
%*********Preallocation for Scan Loop**************************************************
Scanfiles=[];
pathname=[];
%++++++++++++++++++++++++++++++++ SETUP FOR GLOBAL PARFOR LOOP+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
%if SWsingleSc == 1 %if single scan else do expMultiTseries to execute multiple scans
%******Gui Select Scan -> *.tif files for Analysis*****************
w= cd; %Capture current dir in w
if ispc
cd(char(strcat(expDir,scLst(1))))
end
@@ -169,14 +152,12 @@ end
Scanfiles=[];
pathname=[];
for ii=1:length(scLst)
if SWsingleSc == 1
if (SWsingleSc == 1)
[Scanfiles, pathname]=uigetfile('*.bmp', 'Select files','MultiSelect','on');% change '*hr*.bmp' 12/20/2011
if ischar(Scanfiles)
scd=imread(char(Scanfiles));
tptLength=1;
else
scd=imread(char(Scanfiles(1,1)));
tptLength=length(Scanfiles);
@@ -188,47 +169,28 @@ for ii= 1:length(scLst)
cd(w);
numFiles=size(Scanfiles,2);
%tifFileLst= Scanfiles;
% Initialize tifFilesLst for parfor loop
if ispc %Linux and mac accomodation
tifFileLst4MultiT = dir(fullfile(expDir, char(scLst(ii)), '\*.bmp'));
end
if isunix || ismac
tifFileLst4MultiT = dir(fullfile(expDir, char(scLst(ii)), '*.bmp'));
end
dir(fullfile(expDir, char(scLst(ii)), '*.bmp'));
numFiles=length(tifFileLst4MultiT);
tptLength=numFiles;
tifFileLstP4{ii}={tifFileLst4MultiT.name};
%{
dateTmStampP4{ii}= {tifFileLst4MultiT.date}
dateTmNum{ii}= datenum(dateTmStampP4{1});
info{ii} = imfinfo(tifFileLstP4{ii});
scTmNumericP4(ii)=datenum(info{ii}.FileModDate);
%}
end
%**************************************************************************
%**************************************************************************
for jj=1:numScans %startScan:numScans
selScan=str2double(char(scLst(jj)));
selScanNumLst(jj)=selScan;
end
selScanNumLst2=selScanNumLst; %function passthrough, passback to par4gbl_Main 20_0205
%++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
%PREALLOCATION PREALLOCATION PREALLOCATION PREALLOCATION PREALLOCATION
%******************************************************************************
scCount= [];
% PREALLOCATION
scCount=[];
TmpexpScanIntens00=cell(1); %cell(1,scanMax);
TmpFexpScanSpots00=cell(1); %cell(1,scanMax);
TmpFexpScanBMtp00=cell(1); %cell(1,scanMax);
TmpanlZoneRefs00=cell(1); %cell(1,scanMax);
Tmpsbdg00=cell(1);
TmpexpScanIntens4=cell(1,numScans);
TmpFexpScanSpots4=cell(1,numScans);
TmpFexpScanBMtp4=cell(1,numScans);
@@ -239,26 +201,19 @@ TmpFexpScanSpots5= cell(1,numScans);
TmpFexpScanBMtp5=cell(1,numScans);
TmpanlZoneRefs5=cell(1,numScans);
Tmpsbdg5=cell(1,numScans);
p4L00=cell(18,1);
p4L0=p4L00;
p4L4=cell(18,numScans);
p4L5=p4L4;
Ag=ones(384);
CFscanIntens=zeros(16,24);
[p4L4,...
TmpexpScanIntens5,TmpFexpScanSpots5,TmpFexpScanBMtp5,TmpanlZoneRefs5,Tmpsbdg5]= ...
[p4L4,TmpexpScanIntens5,TmpFexpScanSpots5,TmpFexpScanBMtp5,TmpanlZoneRefs5,Tmpsbdg5]= ...
p4loop8c(parMat,tptLength,numScans,selScanNumLst,SWsingleSc,Fflg,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,cirMask,width, ...
TmpexpScanIntens00,TmpFexpScanSpots00,TmpFexpScanBMtp00,TmpanlZoneRefs00,scCount,tifFileLstP4,pathname,ImParMat, ...
numRows,numCols,scLst,resDir,expDir, p4L00,TmpexpScanIntens4,TmpFexpScanSpots4,TmpFexpScanBMtp4,TmpanlZoneRefs4, ...
Tmpsbdg00,Tmpsbdg4);
for scanCnt=1:numScans
selScan=p4L4{16,scanCnt}; %determine the actual scan in the scanCnt parfor distributed "id"
scan(selScan).plate(1).tSeries=cell2mat(p4L4(1,scanCnt));
@@ -268,24 +223,18 @@ selScan= p4L4{16,scanCnt}; %determine the actual scan in the scanCnt parfor dist
scan(selScan).plate(1).rc=p4L4(5,scanCnt);
scan(selScan).plate(1).pIndx=cell2mat(p4L4(6,scanCnt));
scan(selScan).plate(1).Ag=cell2mat(p4L4(7,scanCnt));
scan(selScan).plate(1).selIntens=p4L4(8,scanCnt);
scan(selScan).plate(1).selTimes=p4L4(9,scanCnt);
scan(selScan).plate(1).filterTimes=p4L4(10,scanCnt);
scan(selScan).plate(1).normIntens=p4L4(11,scanCnt);
%scan(selScan).plate(1).CFparameters=p4L4(12,scanCnt); %Need to convert to a matrix form like Old versions
CFparm(1:384)=p4L4{12,scanCnt}(1:384);
scan(selScan).plate(1).CFparameters=CFparm;
scan(selScan).plate(1).CFdate=p4L4(13,scanCnt);
scan(selScan).plate(1).CFout=cell2mat(p4L4(14,scanCnt));
scan(selScan).plate(1).CFoutStd=cell2mat(p4L4(15,scanCnt));
scan(selScan).Awindow=cell2mat(p4L4(17,scanCnt));
scan(selScan).Idate=cell2mat(p4L4(18,scanCnt));
expScanIntens(selScan)=TmpexpScanIntens5(scanCnt);
FexpScanSpots(selScan)=TmpFexpScanSpots5(scanCnt);
FexpScanBMtp(selScan)=TmpFexpScanBMtp5(scanCnt);
@@ -299,9 +248,8 @@ end
%SAVE DATA in .mat files
save(ExpOutmat,'scan');
save((fullfile(resDir,'PTmats','Nbdg')), 'sbdg'); %legacy location can probably get rid of in time
% save((fullfile(resDir,'PTmats','Nbdg')), 'sbdg'); %legacy location can probably get rid of in time
save((fullfile(resDir,'Fotos','Nbdg')), 'sbdg');
save((fullfile(resDir,'Fotos','Coordinates')),'FexpScanSpots') %Saves frames at each tPt
save((fullfile(resDir,'Fotos','BGatTpts')),'FexpScanBMtp')
save((fullfile(resDir,'Fotos','anlZones')),'anlZoneRefs')%Saves anl Positions at each tPt
@@ -311,7 +259,6 @@ fileExt = '.txt';
filePrefix='FitResults_';
for scanCnt=1:numScans
selScan=p4L4{16,scanCnt}; %determine the actual scan in the scanCnt parfor distributed "id"
fileSuffix=strcat('Scan', num2str(selScan),'_Plate', num2str(1));
fileNamePlate=[filePrefix fileSuffix fileExt];
fileName=fullfile(resDir,'PrintResults', fileNamePlate); %[outputDirectory fileNamePlate];
@@ -319,8 +266,6 @@ fileName= fullfile(resDir,'PrintResults', fileNamePlate); %[outputDirectory fil
%This,fprint for loop,is an very old legacy feature which slows processing. Could be
%removed but allows easy observation of how a run is progressing and can be
%used as a diagnostic tool.
outCprint=p4L4;
fid=fopen(fileName,'w');
@@ -337,6 +282,3 @@ fclose(fid);
end
EASYconsole;
%+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++