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Rename easyProjectDir

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This commit is contained in:
Bryan Roessler
2024-08-01 14:22:27 -04:00
parent e3f4c1ee9c
commit e2b399a34c
2 changed files with 80 additions and 69 deletions
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124
workflow/apps/matlab/easy/EASYconsole.m
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@@ -3,6 +3,7 @@
function varargout = EASYconsole(varargin)
global easyDir
global projectName
global projectScansDir
global easyResultsDir
global easyProjectName
@@ -40,23 +41,32 @@ function varargout = EASYconsole(varargin)
fprintf('This script name: %s\n', easyFileName);
% Set projectScansDir (project scans directory) intelligently
% Allow EASY_DIR env to override hardcoded default EASY directory
if ~isempty(getenv('EASY_DIR'))
ed=fullfile(getenv('EASY_DIR'));
if ~strcmp(easyDir, ed) % sanity check
disp("WARNING: EASY_DIR does not match this script's hardcoded EASY location");
disp("This is probably OK but this pathway is not well-tested");
easyDir=ed;
end
fprintf('Using EASY script directory: %s from environment variable EASY_DIR\n', easyDir);
else
fprintf('Using EASY script directory: %s from hardcoded default\n', easyDir);
end
% Set projectScansDir intelligently
if ~isempty(getenv('PROJECT_SCANS_DIR'))
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(projectScansDir);
project=dirInfo.name;
end
else
disp('WARNING: PROJECT_SCANS_DIR does not exist');
end
elseif ~isempty(getenv('PROJECT')) % for standalone mode
% projectScansDir=fullfile(parentDir, '..', '..', 'scans', getenv('PROJECT') 'out', 'easy', getenv('PROJECT'));
project=getenv('PROJECT');
projectScansDir=fullfile(parentDir, '..', '..', 'scans', project);
elseif ~isempty(getenv('PROJECT_NAME')) % for standalone mode
projectName=getenv('PROJECT_NAME');
projectScansDir=fullfile(parentDir, '..', '..', 'scans', projectName);
fprintf('Using project path: %s from environment variable PROJECT\n', projectScansDir);
disp('This usually indicates that we are in standalone mode');
else
@@ -85,18 +95,41 @@ function varargout = EASYconsole(varargin)
end
whos
if ~isempty(matchedDirs)
fprintf('Found a non-empty scans directory in our list: %s\n', d);
fprintf('Setting projectScansDir to %s\n', char(d));
projectScansDir=fullfile(d);
fprintf('Using scansDir %s\n', char(d));
end
fprintf('Scanning inside %s for a project directory\n', d);
sortedMatchedDirs=sortrows(matchedDirs);
project=sortedMatchedDirs{1}; % select the latest dir (by date prefix)
fprintf('Selected latest project directory %s\n', char(project));
projectScansDir=fullfile(sortedMatchedDirs{end}); % select the latest dir (by date prefix)
fprintf('Using project scans directory: %s\n', char(projectScansDir));
break
end
end
end
% Get the name of the project
projectName=basename(projectScansDir);
% Set the run-specific EASY output directory
if ~isempty(getenv('EASY_RESULTS_DIR'))
easyResultsDir=fullfile(getenv('EASY_RESULTS_DIR'));
fprintf('Using output directory: %s from environment variable EASY_RESULTS_DIR\n', easyResultsDir);
else
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')
fprintf('Using output directory: %s\n', easyResultsDir);
end
end
% Get the name of the EASY project
if ~isempty(getenv('EASY_PROJECT_NAME'))
easyProjectName=getenv('EASY_PROJECT_NAME');
else
easyProjectName=basename(easyResultsDir);
end
% User sanity check and warning
if ~isempty(getenv('PROJECT_USER'))
if ~strcmp(getenv('PROJECT_USER'), userName)
@@ -104,44 +137,18 @@ function varargout = EASYconsole(varargin)
end
end
% Allow module to override hardcoded default EASY directory
if ~isempty(getenv('EASY_DIR'))
ed=fullfile(getenv('EASY_DIR'));
if ~strcmp(easyDir, ed) % sanity check
disp("WARNING: EASY_DIR does not match this script's hardcoded EASY location");
disp("This is probably OK but this pathway is not well-tested");
easyDir=ed;
end
fprintf('Using EASY script directory: %s from environment variable EASY_DIR\n', easyDir);
else
fprintf('Using EASY script directory: %s from hardcoded default\n', easyDir);
end
if ~isempty(getenv('EASY_RESULTS_DIR'))
easyResultsDir=fullfile(getenv('EASY_RESULTS_DIR'));
fprintf('Using output directory: %s from environment variable EASY_RESULTS_DIR\n', easyResultsDir);
else
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')
fprintf('Using output directory: %s\n', easyResultsDir);
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(projectScansDir, strcat('MasterPlate_', project,'.xlsx'));
mp=fullfile(easyResultsDir, strcat('MasterPlate_', projectName,'.xlsx'));
if exist(mp, 'file')
masterPlateFile=mp;
fprintf('Using drug media file: %s from internal logic\n', masterPlateFile);
fprintf('Using master plate file: %s from internal logic\n', masterPlateFile);
else
fprintf('WARNING: Have you created a MasterPlate_ file in %s/easy_in/?\n', projectScansDir);
fprintf('WARNING: Could not find MasterPlate file: %s\n', mp);
fprintf('WARNING: Have you created a MasterPlate_ file in %s', easyResultsDir);
end
end
@@ -149,17 +156,17 @@ 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(projectScansDir,'easy_in',strcat('DrugMedia_', project,'.xlsx'));
if exist(mp, 'file')
dm=fullfile(easyResultsDir, strcat('DrugMedia_', projectName,'.xlsx'));
if exist(dm, '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', projectScansDir);
fprintf('WARNING: Have you created a DrugMedia_ file in %s?\n', easyResultsDir);
end
end
matDir=fullfile(easyResultsDir);
matFile=fullfile(matDir,easyResultsDirName,'.mat');
matDir=fullfile(easyResultsDir, 'matResults');
matFile=fullfile(matDir,easyProjectName,'.mat');
mpdmFile=fullfile(matDir,'MPDM.mat');
printResultsDir=fullfile(easyResultsDir,'PrintResults');
fotosResultsDir=fullfile(easyResultsDir,'Fotos');
@@ -265,7 +272,7 @@ function NewExpDat_Callback(~, ~, ~)
global matDir
global matFile
global easyResultsDir
global easyResultsDirName
global easyProjectName
global fhconsole
global scan
global userName
@@ -276,12 +283,11 @@ function NewExpDat_Callback(~, ~, ~)
questdlg('\fontsize{20} NAME the file and NAVIGATE to the directory with the image folders.','File Creation','OK', struct('Default','OK','Interpreter','tex'));
[matfile,easyResultsDir]=uiputfile('.mat');
inputFileName=strrep(inputFile,'.mat','');
% easyResultsDirName=strcat('Results_',todayStr,'_',userName,'_',inputFileName);
project=basename(easyResultsDir);
projectName=basename(easyResultsDir);
% Set paths
matDir=fullfile(easyResultsDir,'matResults');
easyProjectName=strcat(todayStr,'_',userName,'_', project);
matFile=fullfile(matDir,strcat(todayStr,'_',userName,'_',inputFile));
matFile=fullfile(matDir, projectName, '.mat');
% Added for 'parfor global' to preallocate 'scan' structure
nlist=dir(fullfile(projectScansDir,'*'));
@@ -338,19 +344,19 @@ end
function LoadDatFile_Callback(~, ~, ~)
global matDir
global matFile
global projectName
global easyResultsDir
global easyProjectName
global easyPath
global fhconsole
try
questdlg('Load results .mat from ../out/project/','File Creation','OK', struct('Default','OK','Interpreter','tex'));
[inputFile,inputPath]=uigetfile('.mat','Open Experiment folder and data storage .mat file name','MultiSelect','off');
matDir=fullfile(inputPath);
matFile=fullfile(inputPath,inputFile);
[matDir,matFile]=uigetfile('.mat','Open Experiment folder and data storage .mat file name','MultiSelect','off');
load(matFile);
easyResultsDir=fullfile(matDir,'..');
project=basename(easyResultsDir);
projectScansDir=fullfile(easyResultsDir, '..', '..', 'scans', project);
projectName=basename(easyResultsDir);
projectScansDir=fullfile(easyResultsDir, '..', '..', 'scans', projectName);
% TODO this is pretty hacky and needs something more explicit
if isfolder(fullfile(matDir, '..','..','1')) % If Inovation Vrobot Then

25
workflow/qhtcp-workflow
View File

@@ -592,10 +592,14 @@ easy() {
script="$EASY_DIR/EASYconsole.m"
# Prompt user for suffix
echo "Default EASY results directory: $EASY_RESULTS_DIR"
echo "Using default EASY results directory: $EASY_RESULTS_DIR"
((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"
# This dirname is separate from the project's so multiple EASY results can be generated
declare -gx EASY_PROJECT_NAME="${EASY_RESULTS_DIR##*/}"
debug "EASY results output name: $EASY_PROJECT_NAME"
# Backup and create EASY results dirs
[[ -d $EASY_RESULTS_DIR ]] && backup "$EASY_RESULTS_DIR"
[[ -d $EASY_RESULTS_DIR ]] || mkdir -p "$EASY_RESULTS_DIR"
@@ -1566,22 +1570,23 @@ main() {
done
# Loop over projects
for PROJECT in "${PROJECTS[@]}"; do
declare -gx PROJECT_SCANS_DIR="$SCANS_DIR/$PROJECT"
declare -gx PROJECT_DATE="${PROJECT%"${PROJECT#????????}"}" # e.g. 20240723
declare -gx PROJECT_SUFFIX="${PROJECT#????????_*_}"
declare -gx PROJECT_USER="${PROJECT#????????_}"; PROJECT_USER="${PROJECT_USER%%_*}"
for PROJECT_NAME in "${PROJECTS[@]}"; do
declare -gx PROJECT_NAME
declare -gx PROJECT_SCANS_DIR="$SCANS_DIR/$PROJECT_NAME"
declare -gx PROJECT_DATE="${PROJECT_NAME%"${PROJECT_NAME#????????}"}" # e.g. 20240723
declare -gx PROJECT_SUFFIX="${PROJECT_NAME#????????_*_}"
declare -gx PROJECT_USER="${PROJECT_NAME#????????_}"; PROJECT_USER="${PROJECT_USER%%_*}"
declare -gx STUDIES_ARCHIVE_FILE="$OUT_DIR/StudiesDataArchive.txt"
declare -gx QHTCP_PROJECT_DIR="$OUT_DIR/$PROJECT"
declare -gx QHTCP_PROJECT_DIR="$OUT_DIR/$PROJECT_NAME"
declare -gx QHTCP_TEMPLATE_DIR="$TEMPLATES_DIR/qhtcp"
declare -gx STUDY_TEMPLATE_DIR="$TEMPLATES_DIR/exp"
declare -gx STUDY_INFO_FILE="$QHTCP_PROJECT_DIR/StudyInfo.csv"
declare -gx EASY_OUT_DIR="$QHTCP_PROJECT_DIR/easy"
if ((DEBUG)); then
declare -p SCANS_DIR OUT_DIR TEMPLATES_DIR APPS_DIR \
PROJECTS PROJECT \
PROJECT_SCANS_DIR PROJECT_DATE PROJECT_SUFFIX \
PROJECT_USER STUDIES_ARCHIVE_FILE QHTCP_PROJECT_DIR QHTCP_TEMPLATE_DIR \
PROJECTS PROJECT_NAME \
PROJECT_SCANS_DIR PROJECT_DATE PROJECT_SUFFIX PROJECT_USER \
STUDIES_ARCHIVE_FILE QHTCP_PROJECT_DIR QHTCP_TEMPLATE_DIR \
STUDY_TEMPLATE_DIR STUDY_INFO_FILE
fi