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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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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);
@@ -120,26 +121,27 @@ 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')
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(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