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strcat to sprintf

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This commit is contained in:
Bryan Roessler
2024-07-27 13:39:18 -04:00
parent 5a4bb8c90a
commit bb103a6f9a
6 changed files with 99 additions and 99 deletions
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13
workflow/templates/easy/DMPexcel2mat.m
View File

@@ -7,7 +7,7 @@ global matDir
% If we already have mpdmFile, don't recreate
if (exist(mpdmFile, 'file') && ~isempty(mpdmFile))
disp(strcat('The Drug Media/MasterPlate Annotation File: ', mpdmFile, ' exists, skipping DMPexcel2mat.m'));
disp(sprintf('The Drug Media/MasterPlate Annotation File: %s exists, skipping DMPexcel2mat.m\n', mpdmFile));
return
end
@@ -82,7 +82,7 @@ if ~exist(masterPlateFile, 'file') || isempty(masterPlateFile)
end
end
else
disp(strcat('Using MasterPlate file: ', masterPlateFile, ', skipping directory selection'));
disp(sprintf('Using MasterPlate file: %s skipping directory selection\n', masterPlateFile));
end
% fid=fopen(masterPlateFile)%('exp23PrintTimes.xls'); % textread puts date and time sequentially into vector
@@ -183,7 +183,7 @@ if ~exist(drugMediaFile, 'file') || isempty(drugMediaFile)
dmFileToTest=fullfile(mpPath, 'DrugMedia_', mpBareFileName, '.xlsx');
if exist(dmFileToTest, 'file') % Try to find a matching drug media file
drugMediaFile=dmFileToTest;
disp(strcat('Using matching DrugMedia file: ', drugMediaFile, ', skipping directory selection'));
disp(sprintf('Using matching DrugMedia file: %s, skipping directory selection\n', drugMediaFile));
else
% Try to find the DrugMedia file automatically (newest created first)
files=dir(matDir);
@@ -195,7 +195,8 @@ if ~exist(drugMediaFile, 'file') || isempty(drugMediaFile)
[~, sortedIndices]=sort(datenum({files(strncmp(dmFiles.name, 'DrugMedia_', 10)).date}), 'descend');
sortedFiles=dmFiles{sortedIndices};
drugMediaFile=sortedFiles{1};
disp(strcat('Using newest DrugMedia file: ', drugMediaFile, ', skipping directory selection'));
disp(sprintf('Using newest DrugMedia file: %s, skipping directory selection\n', drugMediaFile));
end
catch Me
% This can be silent, not really an error
@@ -228,7 +229,7 @@ if ~exist(drugMediaFile, 'file') || isempty(drugMediaFile)
end
end
else
disp(strcat('Using drugMediaFile: ', drugMediaFile, ', skipping directory selection'));
disp(sprintf('Using drugMediaFile: %s, skipping directory selection\n', drugMediaFile));
end
% Drug and Media Plate setup
@@ -325,4 +326,4 @@ if isequal(Linked,0) % 0 indicates Drugs and Media are combinatorial
end
save(mpdmFile, 'fields','MP','DM','Linked');
msgbox([strcat('Drug-Media-MasterPlate Annotation File', mpdmFile,'Generation Complete')])
msgbox(sprintf('Drug-Media-MasterPlate Annotation File %s Generation Complete', mpdmFile))

18
workflow/templates/easy/DgenResults.m
View File

@@ -366,9 +366,9 @@ if isequal(opt,'DB')||isequal(opt,'Both')
try
copyfile(DBfilename,DBupload)
catch ME
rep=getReport(ME, 'basic');
rep=strcat('Failed copyfile to ',DBupload,' -', rep);
errordlg(rep)
disp(sprintf('DB upload failed with error: %s\n', getReport(ME, 'basic')));
rep=sprintf('Failed copyfile to %s - %s', DBupload, rep);
errordlg(rep);
end
end
@@ -475,7 +475,7 @@ try
rSq=outCmat(n,6);
lval=outCmat(n,5);
if Kval>160, selcode='K_Hi'; else selcode=' ';end
if Kval<40, selcode=strcat(selcode,' K_Lo'); end %12_1030
if Kval<40, selcode=strcat(selcode,' K_Lo');end % TODO sprintf if you want a space
if rSq<.97 && rSq>0, selcode=strcat(selcode,' rSqLo');end
if lval>(0.85*(max(outTseries))), selcode=strcat(selcode,' late');end
if isnan(outCmat(n,7))||isnan(outCmat(n,8))||isnan(outCmat(n,9))...
@@ -497,7 +497,7 @@ try
riseTm=0;
end
if Ag(n)< .30*(scan(s).Awindow),selcode=strcat(selcode,' smArea'); end
if Ag(n)< .30*(scan(s).Awindow),selcode=strcat(selcode,' smArea'); end % same, need sprintf for space
if outCmat(n,3)==0,selcode=strcat('0 ',selcode); end
orf=cell2mat(MP(mpCnt).orf{1}(n));
gene=cell2mat(MP(mpCnt).genename{1}(n));
@@ -654,15 +654,15 @@ try
try
copyfile(DBfilename,DBupload)
catch ME
rep = getReport(ME, 'basic');
rep=strcat('Failed copyfile to ',DBupload,' -', rep);
disp(sprintf('DB upload failed with error: %s\n', getReport(ME, 'basic')));
rep=sprintf('Failed copyfile to %s - %s\n', DBupload, rep);
errordlg(rep)
end
end
msgbox([strcat('Printing Script complete. Check !!Results sheets in ',printResultsDir,' for results.')])
msgbox([sprintf('Printing Script complete. Check !!Results sheets in %s for results.', printResultsDir)])
catch ME
disp(strcat("Results printing failed with error: ", getReport(ME, 'basic')))
disp(sprintf('Printing Script failed with error: %s\n', getReport(ME, 'basic')));
end

52
workflow/templates/easy/EASYconsole.m
View File

@@ -30,28 +30,37 @@ function varargout = EASYconsole(varargin)
userName=system('whoami');
todayStr=datetime('now', 'Format', 'yyyyMMdd'); % This should match the parent workflow script
disp(strcat('This script name: ', easyFileName))
disp(sprintf('This script name: %s\n', easyFileName))
% 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', 'var') && ~isempty(getenv('PROJECT'))
scansDir=get_env('PROJECT');
disp(strcat('Using project path: ', scansDir, ' from environment variable PROJECT'));
scansDir=getenv('PROJECT')
disp(sprintf('Using project path: %s from environment variable PROJECT\n', scansDir));
disp('This usually indicates that we are in standalone mode');
elseif exist('SCANS_DIR', 'var') && ~isempty(getenv('SCANS_DIR'))
scansDir=get_env('SCANS_DIR');
disp(strcat('Using scans directory: ', scansDir, ' from environment variable SCANS_DIR'));
scansDir=getenv('SCANS_DIR');
disp(sprintf('Using scans directory: %s from environment variable SCANS_DIR\n', scansDir));
disp('This usually indicates that we are in module mode');
else
dirToScan = fullfile(parentDir,'ExpJobs'); % hardcoded relative to easy script dir TODO: if we change pj layout this will change
if exist(dirToScan, 'dir')
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(sprintf('Using scans directory: %s from hardcoded relative path\n', scansDir));
disp('This usually indicates that we are in stand-alone mode without PROJECT or SCANS_DIR environment variables');
else
scansDir=fullfile('/mnt/data/ExpJobs/demo')
if exist(scansDir, 'dir')
disp(sprintf('Using scans directory: %s from hardcoded absolute path to demo\n', scansDir));
else
disp(sprintf('Error: scansDir %s does not exist\n', scansDir));
end
end
end
% If we don't have the EASY_SUFFIX from the module, generate it from scansDir
@@ -89,9 +98,9 @@ function varargout = EASYconsole(varargin)
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'));
disp(sprintf('Using EASY script directory: %s from environment variable EASY_DIR\n', easyDir));
else
disp(strcat('Using EASY script directory: ', easyDir, ' from hardcoded default'));
disp(sprintf('Using EASY script directory: %s from hardcoded default\n', easyDir));
end
if exist('PROJECT_USER', 'var') && ~isempty(getenv('PROJECT_USER'))
@@ -102,23 +111,22 @@ function varargout = EASYconsole(varargin)
if exist('EASY_RESULTS_DIR', 'var') && ~isempty(getenv('EASY_RESULTS_DIR'))
easyResultsDir=fullfile(get_env('EASY_RESULTS_DIR'));
disp(strcat('Using output directory: ', easyResultsDir, ' from environment variable EASY_RESULTS_DIR'))
disp(sprintf('Using output directory: %s from environment variable EASY_RESULTS_DIR\n', easyResultsDir))
else
easyResultsDirName=strcat('Results_',todayStr,'_',userName,'_',easySuffix);
easyResultsDir=fullfile(scansDir,easyResultsDirName);
disp(strcat('Using output directory: ', PROJECT_PREFIX, ' from environment variable PROJECT_PREFIX'))
disp(sprintf('Using output directory: %s\n', PROJECT_PREFIX))
end
if exist('MASTER_PLATE_FILE', 'var') && ~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'))
disp(sprintf('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,'MasterPlateFiles',strcat('MasterPlate_', easySuffix,'.xlsx'));
if exist(mp, 'file')
masterPlateFile=mp;
disp(strcat('Using drug media file: ', masterPlateFile, ' from internal logic'))
disp(sprintf('Using drug media file: %s from internal logic\n', masterPlateFile))
else
disp("WARNING: Have you created a MasterPlate_ file?")
end
@@ -126,13 +134,13 @@ function varargout = EASYconsole(varargin)
if exist('DRUG_MEDIA_FILE', 'var') && ~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'))
disp(sprintf('Using drug media file: %s from environment variable DRUG_MEDIA_FILE\n', drugMediaFile))
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'))
disp(sprintf('Using drug media file: %s from internal logic\n', drugMediaFile))
else
disp("WARNING: Have you created a DrugMedia_ file?")
end
@@ -167,7 +175,7 @@ function varargout = EASYconsole(varargin)
% 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)));
set(fhconsole,'Name',sprintf('EASYconsole - %s', scansDir));
else
set(fhconsole,'Name','EASYconsole - No Active Experiment.')
end
@@ -311,14 +319,14 @@ function NewExpDat_Callback(~, ~, ~)
sbdg= cell(1,scanMax);
save((fullfile(easyResultsDir,'Fotos','Nbdg')),'sbdg');
catch ME
disp(strcat('ERROR: ', ME.message))
disp(sprintf('ERROR: %s\n', ME.message));
end
% set the title for fhconsole depending on existence
if exist('easyResultsDir','var')&&~isempty(easyResultsDir)
set(fhconsole,'Name',strcat('EASYconsole- ',char(easyResultsDir)))
set(fhconsole,'Name',sprintf('EASYconsole - %s', easyResultsDir));
else
set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.')
set(fhconsole,'Name','EASYconsole - Master Plate directory not selected.');
end
end
@@ -385,9 +393,9 @@ function LoadDatFile_Callback(~, ~, ~)
if exist('easyResultsDir','var') && ~isempty(easyResultsDir)
fhconsole=gcf;
set(fhconsole,'Name',strcat('EASYconsole- ',char(easyResultsDir)))
set(fhconsole,'Name',sprintf('EASYconsole - %s', easyResultsDir));
else
set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.')
set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.');
end
end
@@ -447,7 +455,7 @@ function runResults_DBcombo_Callback(~, ~, ~)
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))
disp(sprintf('Error in DgenResults: %s\n', ME.message));
EASYconsole
end
end

2
workflow/templates/easy/NCsingleDisplay.m
View File

@@ -39,7 +39,7 @@ for iPlate=1:length(scLst)
catch
end
hold on;
title(strcat(filenameNoExt,''));
title(filenameNoExt); % this didn't make sense so changed
xlabel('Hours');
ylabel('Intensities Normalized by Area');
grid on;

1
workflow/templates/easy/NImParamRadiusGui.m
View File

@@ -1,7 +1,6 @@
%% CALLED BY par4Gbl_Main8c.m %%
% TODO Should some of these vars be pulled out higher so they are easier to change?
%
function NImParamRadiusGui(scansDir)
global SWsingleSc
global SWgrowthArea

46
workflow/templates/easy/par4Gbl_Main8c.m
View File

@@ -7,6 +7,7 @@ global scansDir
global matFile
global fhconsole
global easyResultsDir
global printResultsDir
global pointMapsResultsDir
global fotosResultsDir
global matDir
@@ -17,6 +18,7 @@ global numCols
global scan
global scanMax
global tptLength
global easyDir
numRows=24; % for Single Vertical
numCols=16; % for Single Vertical
@@ -34,10 +36,10 @@ Fflg=1;
% fclose('all'); % close all open files
% Unset some vars just in case they are already set
clear('scanIntens','Scanfiles','pathname','tifFileLstP4')
clear('scanIntens','Scanfiles','pathname','tifFileLstP4');
try
clf(fhconsole,'reset')
clf(fhconsole,'reset');
catch
end
@@ -46,13 +48,10 @@ end
% EASYconsole
if exist(matFile, 'file')
bkUpMatFile=fullfile(matDir,'BkUp',matFile)
copyfile(matFile,(fullfile(matDir,'BkUp',matFile)))
bkUpMatFile=fullfile(matDir,'BkUp',matFile);
copyfile(matFile,bkUpMatFile);
end
try
load(fullfile(easyResultsDir,'Fotos','Nbdg')) %Modified to load from 'Fotos' 20_0819
catch
% Reloacated from 'PTmats' to prevent potential overwrite when PTmats is
% copied into new job when the PT template is about the same. We also
% now have a default template if one is not made. i.e., when the images
@@ -62,26 +61,19 @@ 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(easyResultsDir,'PTmats','Nbdg')) %Left in to accomodate loads of work before 20_0819
try
load(fullfile(fotosResultsDir,'Nbdg')); %Modified to load from 'Fotos' 20_0819
catch
load(fullfile(pointMapsResultsDir,'Nbdg')); %Left in to accomodate loads of work before 20_0819
end
% Load Fotos stored data
fotosToLoad = {'Coordinates', 'BGatTpts', 'anlZones', 'NCFparms'};
for i = 1:length(fotosToLoad)
try
load(fullfile(easyResultsDir,'Fotos','Coordinates'))
load(fullfile(fotosResultsDir, fotosToLoad{i}));
catch
load(fullfile(easyDir,'parameters'));
end
try
load(fullfile(easyResultsDir,'Fotos','BGatTpts'))
catch
end
try
load(fullfile(easyResultsDir,'Fotos','anlZones'))
catch
end
% autoImCF
try
load(fullfile(easyResultsDir,'PTmats','NCFparms'))
catch ME
load parameters
end
% Get Print Times
@@ -89,12 +81,12 @@ PrintTimes=[];
scLst={};
% Parameter Entry
NImParamRadiusGui(scansDir) % Ncode 122111replaced removed ,numOfPrtTimes)
NImParamRadiusGui(scansDir); % Ncode 122111replaced removed ,numOfPrtTimes)
width=24;
widthEx=width-1; % width extention from reference point
dither=ImParMat(6);
radius=ImParMat(10);
NIcircle
NIcircle;
% Load Stuff
lastPlateOnLastScan=1; % Ncode
@@ -118,7 +110,7 @@ else
end
SWgrowthArea=ImParMat(9);
load(fullfile(pointMapsResultsDir,'NPTmapSearch'))
load(fullfile(pointMapsResultsDir,'NPTmapSearch'));
PTmapPos=detPos;
selScanNumLst=[];
Scanfiles=[];
@@ -230,9 +222,9 @@ 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));
fileSuffix=sprintf('Scan%d_Plate%d', selScan, 1);
fileNamePlate=[filePrefix fileSuffix fileExt];
fileName=fullfile(easyResultsDir,'PrintResults', fileNamePlate); % [outputDirectory fileNamePlate];
fileName=fullfile(printResultsDir, fileNamePlate); % [outputDirectory fileNamePlate];
% 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