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EASY refactor: First attempt

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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
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167
workflow/templates/easy/EASYconsole.m
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@@ -3,18 +3,25 @@
% Updated 240724 Bryan C Roessler to improve file operations and portability
%
function varargout = EASYconsole(varargin)
global startDir
global easyDir
global easySuffix
global scansDir
global easyResultsDir
global easyResultsDirName
global fotosResultsDir
global figsResultsDir
global pointMapsResultsDir
global pointMapsFile
global printResultsDir
global matDir
global matFile
global drugMediaFile
global masterPlateFile
global mpdmFile
global userName
global srchRange
% Initialize some variables from matlab
startDir=pwd;
easyPath=which(mfilename);
[easyDir,easyFileName]=fileparts(easyPath);
easyDir=fullfile(easyDir);
@@ -27,22 +34,27 @@ function varargout = EASYconsole(varargin)
% Set scansDir intelligently (project scans directory)
% Allow users to specify a PROJECT=/mnt/data/ExpJobs/Job directory to analyze with EASY
% This better enables running the new EASY in standalone mode
if exist('PROJECT', 'env')
if exist('PROJECT', 'env') && ~isempty(getenv('PROJECT'))
scansDir=get_env('PROJECT');
disp(strcat('Using project path: ', scansDir, ' from environment variable PROJECT'));
disp('This usually indicates that we are in standalone mode');
elseif exist('SCANS_DIR', 'env')
elseif exist('SCANS_DIR', 'env') && ~isempty(getenv('SCANS_DIR'))
scansDir=get_env('SCANS_DIR');
disp(strcat('Using scans directory: ', scansDir, ' from environment variable SCANS_DIR'));
disp('This usually indicates that we are in module mode');
else
scansDir=fullfile(parentDir,'ExpJobs'); % relative to easy script dir
dirToScan=fullfile(parentDir,'ExpJobs'); % hardcoded relative to easy script dir TODO: if we change pj layout this will change
dirs=dir(fullfile(dirToScan, 'dir')); % filter for dirs only
[~, sortedIndices] = sort(datenum({dirs.date}), 'descend'); % sort by newest first
sortedDirs=dirs{sortedIndices};
scansDir=sortedDirs{1};
disp('Beginning in newest project scans directory');
disp(strcat('Using scans directory: ', scansDir, ' from hardcoded default'));
disp('This usually indicates that we are in standalone mode');
disp('This usually indicates that we are in stand-alone mode');
end
% If we don't have the EASY_SUFFIX from the module, generate it from scanDir
if exist('EASY_SUFFIX', 'env')
% If we don't have the EASY_SUFFIX from the module, generate it from scansDir
if exist('EASY_SUFFIX', 'env') && ~isempty(getenv('EASY_SUFFIX'))
easySuffix=get_env('EASY_SUFFIX');
else
[dirName, ~]=fileparts(scansDir);
@@ -69,10 +81,11 @@ function varargout = EASYconsole(varargin)
end
% Helpful variables for running in workflow mode that I'll probably have to reimplement in matlab anyways for standalone mode
if exist('EASY_DIR','env')
if exist('EASY_DIR','env') && ~isempty(getenv('EASY_DIR'))
EASY_DIR=fullfile(get_env('EASY_DIR'));
if easyDir ~= EASY_DIR % sanity check
disp("WARNING: EASY_DIR does not match this script's default EASY location");
disp("WARNING: EASY_DIR does not match this script's hardcoded EASY location");
disp("This is probably OK but if strange beahvior arises, we'll need to fix it in code");
easyDir=EASY_DIR;
end
disp(strcat('Using EASY script directory: ', easyDir, ' from environment variable EASY_DIR'));
@@ -80,12 +93,7 @@ function varargout = EASYconsole(varargin)
disp(strcat('Using EASY script directory: ', easyDir, ' from hardcoded default'));
end
% Now that we have easyDir let's add it to the path just to be safe
% TODO I have no idea if this is necessary or effective but we'll see
% I could image it would reduce some weird matlab errors?
addpath(easyDir);
if exist('EASY_RESULTS_DIR', 'env')
if exist('EASY_RESULTS_DIR', 'env') && ~isempty(getenv('EASY_RESULTS_DIR'))
easyResultsDir=fullfile(get_env('EASY_RESULTS_DIR'));
disp(strcat('Using project prefix: ', easyResultsDir, ' from environment variable EASY_RESULTS_DIR'))
else
@@ -95,21 +103,73 @@ function varargout = EASYconsole(varargin)
disp(strcat('Using project prefix: ', PROJECT_PREFIX, ' from environment variable PROJECT_PREFIX'))
end
if exist('PROJECT_USER', 'env')
if exist('PROJECT_USER', 'env') && ~isempty(getenv('PROJECT_USER'))
if get_env('PROJECT_USER') ~= userName % sanity check
disp("WARNING: PROJECT_USER does not match the current namespace");
end
end
matDir=fullfile(easyResultsDir,'matResults');
matFile=fullfile(matDir,strcat(easyResultsDirName,'.mat'));
if exist('MASTER_PLATE_FILE', 'env') && ~isempty(getenv('MASTER_PLATE_FILE'))
masterPlateFile=fullfile(get_env('MASTER_PLATE_FILE'));
disp(strcat('Using drug media file: ', masterPlateFile, ' from environment variable MASTER_PLATE_FILE'))
else
% Try to find MasterPlate_ file on our own
mp=fullfile(scansDir,'MasterPlateFiles',strcat('MasterPlate_', easySuffix,'.xlsx'));
if exist(mp, 'file'))
masterPlateFile=mp;
disp(strcat('Using drug media file: ', masterPlateFile, ' from internal logic'))
else
disp("WARNING: Have you created a MasterPlate_ file?")
end
end
% Play around with making some common variables from our input data
% resDirName=fullfile(SCANS_DIR,'Results',dateStr,'_', PROJECT_SUFFIX);
% resDir=fullfile(SCANS_DIR,resDirName);
% ExpOutmat=fullfile(matDir,strcat(datestr(now,29),newExpfile));
% ExpPath=fullfile(newExppath);
% ExpFile=fullfile(matDir,)
if exist('DRUG_MEDIA_FILE', 'env') && ~isempty(getenv('DRUG_MEDIA_FILE'))
drugMediaFile=fullfile(get_env('DRUG_MEDIA_FILE'));
disp(strcat('Using drug media file: ', drugMediaFile, ' from environment variable DRUG_MEDIA_FILE'))
else
% Try to find MasterPlate_ file on our own
dm=fullfile(scansDir,'MasterPlateFiles',strcat('DrugMedia_', easySuffix,'.xlsx'));
if exist(mp, 'file'))
drugMediaFile=dm;
disp(strcat('Using drug media file: ', drugMediaFile, ' from internal logic'))
else
disp("WARNING: Have you created a DrugMedia_ file?")
end
end
matDir=fullfile(easyResultsDir,'matResults');
if ~exist(matDir, 'dir')
mkdir(matDir);
end
matFile=fullfile(matDir,strcat(easyResultsDirName,'.mat'));
% Pulled these out of par4GblFnc8c
printResultsDir=fullfile(easyResultsDir,'PrintResults');
fotosResultsDir=fullfile(easyResultsDir,'Fotos');
figsResultsDir=fullfile(easyResultsDir,'figs');
pointMapsResultsDir=fullfile(easyResultsDir,'PTmats');
pointMapsFile=fullfile(pointMapsResultsDir,'NImParameters.mat')
oldPointMapsFile=fullfile(pointMapsResultsDir,'ImParameters.mat')
CSearchRangeFile=fullfile(fotosResultsDir,'CSearchRange.mat');
mpdmFile=fullfile(matDir,'MPDM.mat');
% This can be removed, I think it should add the previous search range?
% Might be nice feature but can remove if it causes issues
% We are using searchRangeNum to hold old CSrchRange value(s)
if exist(CSearchRangeFile, 'file')
searchRangeNum=load(CSearchRangeFile);
end
% Add easyDir to the MATLAB path
% I have not idea if this is necessary or works but theoretically should
% reduce directory scoping issues when calling scripts w/o a path
addpath(easyDir);
% Pulled this out of the opening function
% Seems better to wait until we have our ars set
if exist('scansDir','var') && ~isempty(scansDir)
set(fhconsole,'Name',strcat('EASYconsole - ',char(scansDir)));
else
set(fhconsole,'Name','EASYconsole - No Active Experiment.')
end
% GUI interface design
gui_Singleton=1;
@@ -164,15 +224,6 @@ function EASYconsole_OpeningFcn(hObject, ~, handles, varargin)
fhconsole=gcf;
set(fhconsole,'Toolbar','none');
fhconsole=gcf;
% BCR this is set in the global function so I think we're good here
% easyResultsDirName=strcat('Results',todayStr,newExpfilePref);
if exist('easyResultsDir','var') && ~isempty(easyResultsDir)
set(fhconsole,'Name',strcat('EASYconsole- ',char(easyResultsDir)));
else
set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.')
end
end
@@ -200,7 +251,6 @@ end
% New Experiment Button Interface
function NewExpDat_Callback(~, ~, ~)
global SWnewExp
global matDir
global matFile
global easyResultsDir
@@ -213,8 +263,6 @@ function NewExpDat_Callback(~, ~, ~)
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');
SWnewExp=1;
inputFileName=strrep(inputFile,'.mat','');
easyResultsDirName=strcat('Results_',todayStr,'_',userName,'_',inputFileName);
@@ -263,8 +311,7 @@ function NewExpDat_Callback(~, ~, ~)
sbdg= cell(1,scanMax);
save((fullfile(easyResultsDir,'Fotos','Nbdg')),'sbdg');
catch ME
% returnStartDir
disp('Error Creating a New Experiment')
disp(strcat('ERROR: ', ME.message))
end
% set the title for fhconsole depending on existence
@@ -278,39 +325,50 @@ end
% Load a previous experiment
function LoadDatFile_Callback(~, ~, ~)
global SWnewExp
global matDir
global matFile
global easyResultsDir
global easyPath
global fhconsole
%global ImParMat
try
questdlg('\fontsize{20} Load file from ExpJobs/YourJob/YourResults/matResults','File Creation','OK', struct('Default','OK','Interpreter','tex'));
[inputFile,inputPath]=uigetfile('.mat','Open Experiment folder and data storage .mat file name','MultiSelect','off');
SWnewExp=0;
matDir=fullfile(inputPath);
matFile=fullfile(inputPath,inputFile);
load(matFile);
easyResultsDir=fullfile(matDir,'..');
scansDir=fullfile(matDir,'..', '..');
point
% TODO this is pretty hacky and needs something more explicit
if isfolder(fullfile(matDir, '..','..','1')) % If Inovation Vrobot Then
if exist(fullfile(easyResultsDir,'PTmats','NImParameters.mat'), 'file')
load(fullfile(easyResultsDir,'PTmats','NImParameters.mat'));
else
load(fullfile(easyPath,'NImParameters.mat'));
try
exist(pointMapsFile, 'file')
load(pointMapsFile);
catch
try
load(fullfile(easyPath,'NImParameters.mat')); % hardcoded default
catch
disp("Could not load the NImParameters.mat file")
end
end
else % If Epson 10Plate Scans Then>
if exist(fullfile(easyResultsDir,'PTmats','ImParameters.mat'), 'file')
load(fullfile(easyResultsDir,'PTmats','ImParameters.mat'));
if exist(fullfile(pointMapsResultsDir,'ImParameters.mat'), 'file')
load(fullfile(pointMapsResultsDir,'ImParameters.mat'));
else
load(fullfile(easyPath,'ImParameters.mat'));
try
load(fullfile(easyPath,'ImParameters.mat'));
catch
disp("Could not load the ImParameters.mat file")
end
end
end
mkdir(fullfile(matDir,'BkUp'));
bkupDir=fullfile(matDir,'BkUp');
if ~exist(bkupDir, 'dir')
mkkdir(bkupDir);
end
% Create supporting dirs
dirs={'PrintResults', 'figs', 'CFfigs', 'PTmats', 'Fotos'}
@@ -333,8 +391,8 @@ function LoadDatFile_Callback(~, ~, ~)
end
end
%% CALLBACKS %%
% callback for the 'Run' in the dropdown menu
% Callbacks
% 'Run' in the dropdown menu
function run_Callback(~, ~, ~)
end
@@ -378,8 +436,7 @@ end
function runDMPexcel_Callback(~, ~, ~)
try
% DMPexcel2mat_2024winLinix %DMPexcel2mat_2023winLinix
DMPexcel2mat % TODO Can't find above so using what I have available
DMPexcel2mat
catch
EASYconsole
end
@@ -387,7 +444,7 @@ end
function runResults_DBcombo_Callback(~, ~, ~)
try
DgenResults240430 %similar but semicolons removed to restore so cmdLine display info.
DgenResults %similar but semicolons removed to restore so cmdLine display info.
%Dgen241010qhtcp %par4global -convert 1x1cell of 384cells to be like previous 1x384 cells CFparameter
catch ME
disp(strcat('Error in DgenResults240430: ', ME.message))