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Rename scansDir

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This commit is contained in:
Bryan Roessler
2024-08-01 12:32:47 -04:00
parent 54f375face
commit e3f4c1ee9c
9 changed files with 58 additions and 56 deletions
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18
workflow/apps/matlab/easy/DgenResults.m
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@@ -1,7 +1,7 @@
%% CALLED BY EASYconsole.m %%
% Updated 240724 Bryan C Roessler to improve file operations and portability
%
global scansDir
global projectScansDir
global matFile
global defImParMat
global printResultsDir
@@ -46,16 +46,16 @@ for n=1:size(scan,2)
end
end
% if length(scansDir) == max(strfind(scansDir,'\'))
% localscansDir=scansDir(1:end-1);
% if length(projectScansDir) == max(strfind(projectScansDir,'\'))
% localprojectScansDir=projectScansDir(1:end-1);
% else
% localscansDir=scansDir;
% localprojectScansDir=projectScansDir;
% end
% TODO this seems weird
expNm=scansDir(max(strfind(scansDir,'/'))+1:end);
drivePos=min(strfind(scansDir,'/'));
drive=scansDir(1:(drivePos-1));
expNm=projectScansDir(max(strfind(projectScansDir,'/'))+1:end);
drivePos=min(strfind(projectScansDir,'/'));
drive=projectScansDir(1:(drivePos-1));
DBupload=fullfile(drive,'EZdbFiles','DBupLOADfiles');
% Added to allow backward compatability
@@ -75,7 +75,7 @@ if isequal(opt,'DB')||isequal(opt,'Both'),fid2=fopen(DBfilename,'w');end
if isequal(opt,'Res')||isequal(opt,'Both')
fprintf(fid,'%d\t',ln); % Results header
fprintf(fid,'%s\t\n',scansDir);
fprintf(fid,'%s\t\n',projectScansDir);
ln=ln+1;
fprintf(fid,'%d\t',ln);
end
@@ -383,7 +383,7 @@ try
if isequal(opt,'DB')||isequal(opt,'Both'),fid2=fopen(DBfilename,'w');end %121012 Combo
if isequal(opt,'Res')||isequal(opt,'Both') %print Results
fprintf(fid,'%d\t',ln); %Results header
fprintf(fid,'%s\t\n',scansDir);
fprintf(fid,'%s\t\n',projectScansDir);
ln=ln+1;
fprintf(fid,'%d\t',ln);
end

64
workflow/apps/matlab/easy/EASYconsole.m
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@@ -3,9 +3,9 @@
function varargout = EASYconsole(varargin)
global easyDir
global scansDir
global projectScansDir
global easyResultsDir
global easyProject
global easyProjectName
global fotosResultsDir
global figsResultsDir
global pointMapsResultsDir
@@ -28,7 +28,8 @@ function varargout = EASYconsole(varargin)
parentDir=fullfile(parentDir); % ../easy/apps
userName=getenv('USER');
dt=datetime;
todayStr=char(dt, 'yyyyMMdd'); % This should match the parent workflow script
todayStr=char(dt, 'yyyyMMdd'); % This should match the parent workflow script 'hardcode'
outDir=fullfile(parentDir, '..','..', 'out'); % This should match the parent workflow script 'hardcode'
debug=1;
if debug
@@ -39,27 +40,27 @@ function varargout = EASYconsole(varargin)
fprintf('This script name: %s\n', easyFileName);
% Set scansDir (project scans directory) intelligently
% Set projectScansDir (project scans directory) intelligently
if ~isempty(getenv('PROJECT_SCANS_DIR'))
scansDir=fullfile(getenv('PROJECT_SCANS_DIR'));
if exist(scansDir, 'dir')
fprintf('Using scans directory: %s from environment variable PROJECT_SCANS_DIR\n', scansDir);
projectScansDir=fullfile(getenv('PROJECT_SCANS_DIR'));
if exist(projectScansDir, 'dir')
fprintf('Using scans directory: %s from environment variable PROJECT_SCANS_DIR\n', projectScansDir);
disp('This usually indicates that we are in module mode');
if isempty(getenv('PROJECT'))
dirInfo=fileparts(scansDir);
dirInfo=fileparts(projectScansDir);
project=dirInfo.name;
end
else
disp('WARNING: PROJECT_SCANS_DIR does not exist');
end
elseif ~isempty(getenv('PROJECT')) % for standalone mode
% scansDir=fullfile(parentDir, '..', '..', 'scans', getenv('PROJECT') 'out', 'easy', getenv('PROJECT'));
scansDir=fullfile(parentDir, '..', '..', 'scans', getenv('PROJECT'));
% projectScansDir=fullfile(parentDir, '..', '..', 'scans', getenv('PROJECT') 'out', 'easy', getenv('PROJECT'));
project=getenv('PROJECT');
fprintf('Using project path: %s from environment variable PROJECT\n', scansDir);
projectScansDir=fullfile(parentDir, '..', '..', 'scans', project);
fprintf('Using project path: %s from environment variable PROJECT\n', projectScansDir);
disp('This usually indicates that we are in standalone mode');
else
% TODO Lots of this is hardcoded logic, this TODO is just a reminder to change this block
% TODO Lots of hardcoded logic, this TODO is just a reminder to change this block
% when changing EASY and other variables in the parent script
fprintf('WARNING: Running in standalone mode without PROJECT or PROJECT_SCANS_DIR environment variables (not recommended)\n');
fprintf('Beginning parent scans directory search\n');
@@ -85,8 +86,8 @@ function varargout = EASYconsole(varargin)
whos
if ~isempty(matchedDirs)
fprintf('Found a non-empty scans directory in our list: %s\n', d);
fprintf('Setting scansDir to %s\n', char(d));
scansDir=fullfile(d);
fprintf('Setting projectScansDir to %s\n', char(d));
projectScansDir=fullfile(d);
end
fprintf('Scanning inside %s for a project directory\n', d);
sortedMatchedDirs=sortrows(matchedDirs);
@@ -120,8 +121,8 @@ function varargout = EASYconsole(varargin)
easyResultsDir=fullfile(getenv('EASY_RESULTS_DIR'));
fprintf('Using output directory: %s from environment variable EASY_RESULTS_DIR\n', easyResultsDir);
else
easyProject=strcat(todayStr,'_',userName,'_', project);
easyResultsDir=fullfile(parentDir, '..', '..', 'out', project, 'easy', easyProject);
easyProjectName=strcat(todayStr,'_',userName,'_', project);
easyResultsDir=fullfile(parentDir, '..', '..', 'out', project, 'easy', easyProjectName);
if exist(easyResultsDir, 'dir')
fprintf('WARNING: EASY results dir %s already exists\n', easyResultsDir);
disp('Files in this directory may be overwritten')
@@ -129,17 +130,18 @@ function varargout = EASYconsole(varargin)
end
end
if ~isempty(getenv('MASTER_PLATE_FILE'))
masterPlateFile=fullfile(getenv('MASTER_PLATE_FILE'));
fprintf('Using drug media file: %s from environment variable MASTER_PLATE_FILE\n', masterPlateFile);
else
% Try to find MasterPlate_ file on our own
mp=fullfile(scansDir, strcat('MasterPlate_', project,'.xlsx'));
mp=fullfile(projectScansDir, strcat('MasterPlate_', project,'.xlsx'));
if exist(mp, 'file')
masterPlateFile=mp;
fprintf('Using drug media file: %s from internal logic\n', masterPlateFile);
else
fprintf('WARNING: Have you created a MasterPlate_ file in %s/easy_in/?\n', scansDir);
fprintf('WARNING: Have you created a MasterPlate_ file in %s/easy_in/?\n', projectScansDir);
end
end
@@ -147,12 +149,12 @@ function varargout = EASYconsole(varargin)
drugMediaFile=fullfile(getenv('DRUG_MEDIA_FILE'));
fprintf('Using drug media file: %s from environment variable DRUG_MEDIA_FILE\n', drugMediaFile);
else
dm=fullfile(scansDir,'easy_in',strcat('DrugMedia_', project,'.xlsx'));
dm=fullfile(projectScansDir,'easy_in',strcat('DrugMedia_', project,'.xlsx'));
if exist(mp, 'file')
drugMediaFile=dm;
fprintf('Using drug media file: %s from internal logic\n', drugMediaFile);
else
fprintf('WARNING: Have you created a DrugMedia_ file in %s/MasterPlateFiles/?\n', scansDir);
fprintf('WARNING: Have you created a DrugMedia_ file in %s/MasterPlateFiles/?\n', projectScansDir);
end
end
@@ -214,7 +216,7 @@ end
% varargin--input arguments to EASYconsole (see VARARGIN)
function EASYconsole_OpeningFcn(hObject, ~, handles, varargin)
global fhconsole
global scansDir
global projectScansDir
% Choose default command line output for EASYconsole
handles.output=hObject;
@@ -229,8 +231,8 @@ function EASYconsole_OpeningFcn(hObject, ~, handles, varargin)
% Pulled this out of the opening function
% Seems better to wait until we have our vars set though?
if exist('scansDir','var') && ~isempty(scansDir)
set(fhconsole,'Name', sprintf('EASYconsole - %s', scansDir));
if exist('projectScansDir','var') && ~isempty(projectScansDir)
set(fhconsole,'Name', sprintf('EASYconsole - %s', projectScansDir));
else
set(fhconsole,'Name','EASYconsole - No Active Experiment.')
end
@@ -267,22 +269,22 @@ function NewExpDat_Callback(~, ~, ~)
global fhconsole
global scan
global userName
global todayStr
% Create a new experiment
try
questdlg('\fontsize{20} NAME the file and NAVIGATE to the directory with the image folders.','File Creation','OK', struct('Default','OK','Interpreter','tex'));
[inputFile,inputPath]=uiputfile('.mat');
[matfile,easyResultsDir]=uiputfile('.mat');
inputFileName=strrep(inputFile,'.mat','');
% easyResultsDirName=strcat('Results_',todayStr,'_',userName,'_',inputFileName);
project=basename(easyResultsDir);
% Set paths
scansDir=fullfile(inputPath);
easyResultsDir=fullfile(scansDir,easyResultsDirName);
matDir=fullfile(easyResultsDir,'matResults');
easyProjectName=strcat(todayStr,'_',userName,'_', project);
matFile=fullfile(matDir,strcat(todayStr,'_',userName,'_',inputFile));
%***Added for 'parfor global' to preallocate 'scan' structure 20-0123*****
nlist=dir(fullfile(scansDir,'*'));
% Added for 'parfor global' to preallocate 'scan' structure
nlist=dir(fullfile(projectScansDir,'*'));
nnn=0;
for n=1:size(nlist,1)
if (~isempty(str2num(nlist(n).name)))
@@ -347,8 +349,8 @@ function LoadDatFile_Callback(~, ~, ~)
matFile=fullfile(inputPath,inputFile);
load(matFile);
easyResultsDir=fullfile(matDir,'..');
scansDir=fullfile(matDir,'..', '..');
point
project=basename(easyResultsDir);
projectScansDir=fullfile(easyResultsDir, '..', '..', 'scans', project);
% TODO this is pretty hacky and needs something more explicit
if isfolder(fullfile(matDir, '..','..','1')) % If Inovation Vrobot Then

4
workflow/apps/matlab/easy/NCdisplayGui.m
View File

@@ -1,5 +1,5 @@
%% CALLED WHEN ACCESSING 'CurveFit Display' %%
function [scLst, row, col] = NCdisplayGui(scansDir)
function [scLst, row, col] = NCdisplayGui(projectScansDir)
xPos=0.05;
btnWid=0.10;
btnHt=0.05;
@@ -49,7 +49,7 @@ function [scLst, row, col] = NCdisplayGui(scansDir)
end
% Read in numeric folder names
nlist=dir(fullfile(scansDir,'*'));
nlist=dir(fullfile(projectScansDir,'*'));
nnn=0;
for n=1:size(nlist,1)
if (~isempty(str2num(nlist(n).name)))

2
workflow/apps/matlab/easy/NCsingleDisplay.m
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@@ -4,7 +4,7 @@ global scan
hf=figure;
% Parameter Entry
[scLst, row, col]=NCdisplayGui(scansDir);
[scLst, row, col]=NCdisplayGui(projectScansDir);
close(hf)
selSpot=(row-1)*24 + col;
for iPlate=1:length(scLst)

4
workflow/apps/matlab/easy/NImParamRadiusGui.m
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@@ -1,7 +1,7 @@
%% CALLED BY par4Gbl_Main8c.m %%
% TODO Should some of these vars be pulled out higher so they are easier to change?
%
function NImParamRadiusGui(scansDir)
function NImParamRadiusGui(projectScansDir)
global SWsingleSc
global SWgrowthArea
global scan
@@ -143,7 +143,7 @@ function NImParamRadiusGui(scansDir)
end
% Ncode 12_0120 for reading in numeric folder names
nlist=dir(fullfile(scansDir,'*'));
nlist=dir(fullfile(projectScansDir,'*'));
nnn=0;
for n=1:size(nlist,1)
if (~isempty(str2num(nlist(n).name)))

4
workflow/apps/matlab/easy/p4loop8c.m
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@@ -3,7 +3,7 @@ function[p4L4,...
TmpexpScanIntens4,TmpFexpScanSpots4,TmpFexpScanBMtp4,TmpanlZoneRefs4,Tmpsbdg4]= ...
p4loop8c(parMat,tptLength,numScans,selScanNumLst,SWsingleSc,Fflg,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,cirMask,width, ...
TmpexpScanIntens00,TmpFexpScanSpots00,TmpFexpScanBMtp00,TmpanlZoneRefs00,~,tifFileLstP4,pathname,ImParMat, ...
numRows,numCols,scLst,easyResultsDir,scansDir, p4L00,TmpexpScanIntens4,TmpFexpScanSpots4,TmpFexpScanBMtp4,TmpanlZoneRefs4, Tmpsbdg00, Tmpsbdg4)
numRows,numCols,scLst,easyResultsDir,projectScansDir, p4L00,TmpexpScanIntens4,TmpFexpScanSpots4,TmpFexpScanBMtp4,TmpanlZoneRefs4, Tmpsbdg00, Tmpsbdg4)
p4L0=p4L00;
TmpexpScanIntens0=TmpexpScanIntens00;
TmpFexpScanSpots0=TmpFexpScanSpots00;
@@ -25,7 +25,7 @@ parfor (scCount=1:numScans,parforArg)
[p4L3,TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneRefs3,Tmpsbdg3]= ...
par4GblFnc8c(parMat,tptLength,numScans,selScanNumLst,SWsingleSc,Fflg,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,cirMask,width, ...
TmpexpScanIntens0,TmpFexpScanSpots0,TmpFexpScanBMtp0,TmpanlZoneRefs0,scCount,tifFileLstP4,pathname,ImParMat, ...
numRows,numCols, scLst,easyResultsDir,scansDir, p4L0,Tmpsbdg0);
numRows,numCols, scLst,easyResultsDir,projectScansDir, p4L0,Tmpsbdg0);
p4L4(:,scCount)=p4L3; % (:,scCount);
TmpexpScanIntens4(scCount)=TmpexpScanIntens3;

8
workflow/apps/matlab/easy/par4GblFnc8c.m
View File

@@ -2,7 +2,7 @@
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,easyResultsDir,scansDir,~, Tmpsbdg)
numRows,numCols,scLst,easyResultsDir,projectScansDir,~, Tmpsbdg)
global printResultsDir
@@ -23,11 +23,11 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
scLst;
scLst(scCount)
char(scLst(scCount))
char(fullfile(scansDir,char(scLst(scCount))))
scansDir;
char(fullfile(projectScansDir,char(scLst(scCount))))
projectScansDir;
swCatch=0;
nndx=nndx+1;
tifFile=char(fullfile(scansDir,char(scLst(scCount)), tifFileLstP4{scCount}(tPt)));
tifFile=char(fullfile(projectScansDir,char(scLst(scCount)), tifFileLstP4{scCount}(tPt)));
try
info=imfinfo(tifFile); % D:\jwrDevel\DevelCurveFittingJWR\ImageScans\Scan2\020hr002.tif
catch ME

8
workflow/apps/matlab/easy/par4Gbl_Main8c.m
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@@ -3,7 +3,7 @@
global SWgrowthArea
global scLst
global ImParMat
global scansDir
global projectScansDir
global matFile
global fhconsole
global easyResultsDir
@@ -81,7 +81,7 @@ PrintTimes=[];
scLst={};
% Parameter Entry
NImParamRadiusGui(scansDir); % Ncode 122111replaced removed ,numOfPrtTimes)
NImParamRadiusGui(projectScansDir); % Ncode 122111replaced removed ,numOfPrtTimes)
width=24;
widthEx=width-1; % width extention from reference point
dither=ImParMat(6);
@@ -135,7 +135,7 @@ for ii=1:length(scLst)
numFiles=size(Scanfiles,2);
% Initialize tifFilesLst for parfor loop
dir(fullfile(scansDir, char(scLst(ii)), '*.bmp'));
dir(fullfile(projectScansDir, char(scLst(ii)), '*.bmp'));
numFiles=length(tifFileLst4MultiT);
tptLength=numFiles;
tifFileLstP4{ii}={tifFileLst4MultiT.name};
@@ -174,7 +174,7 @@ CFscanIntens=zeros(16,24);
[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,easyResultsDir,scansDir, p4L00,TmpexpScanIntens4,TmpFexpScanSpots4,TmpFexpScanBMtp4,TmpanlZoneRefs4, ...
numRows,numCols,scLst,easyResultsDir,projectScansDir, p4L00,TmpexpScanIntens4,TmpFexpScanSpots4,TmpFexpScanBMtp4,TmpanlZoneRefs4, ...
Tmpsbdg00,Tmpsbdg4);
for scanCnt=1:numScans

2
workflow/qhtcp-workflow
View File

@@ -593,7 +593,7 @@ easy() {
# Prompt user for suffix
echo "Default EASY results directory: $EASY_RESULTS_DIR"
read -r -p "Enter a custom suffix and/or hit enter to use the default (no suffix): " EASY_SUFFIX
((YES)) || read -r -p "Enter a custom suffix and/or hit enter to use the default (no suffix): " EASY_SUFFIX
[[ -n $EASY_SUFFIX ]] && EASY_RESULTS_DIR+="_$EASY_SUFFIX"
# Backup and create EASY results dirs