Development

+PlotID/@userDLG/userDLG.m

+classdef userDLG
+    %userDLG the userDLG Class is responsible for the user dialog
+    %   error handeling, user messages and warnings will be provided from
+    %   this class, depending on the user options and error type.
+    %   This reduces messaging overhead and code length in PlotID.Publish()
+    
+    properties
+        configError = false
+        scriptPublished = false
+        rdFilesPublished = false
+        figurePublished = false
+        msg = ''        
+    end
+    
+    properties (SetAccess = protected)        
+        success = false
+        showMessages {mustBeNumericOrLogical}
+        forcePublish {mustBeNumericOrLogical}
+        ID %plotID
+    end
+        
+    methods
+        function obj = userDLG(ID,options)
+            %CATCHERROR Construct an instance of this class
+            if isempty(ID)
+                ID = '';
+            end
+            obj.ID = ID;
+            obj.showMessages = options.ShowMessages;
+            obj.forcePublish = options.ForcePublish;
+        end
+        
+        function output = get.success(obj)
+            %   checks if all publish operations are true
+            obj.success = all([obj.scriptPublished; obj.rdFilesPublished;...
+                obj.figurePublished]);
+            output = obj.success;
+        end
+        
+        function obj = set.msg(obj,message)
+            %setmsg Summary of this method goes here
+            %   Detailed explanation goes here
+            obj.msg = message;
+        end
+        
+       function [] = userMSG(obj,message)
+            %userMSG user message without priority
+            %   MSG will only be displaye if ShowMessages is true
+            if obj.showMessages
+                disp(message);
+            end
+       end
+       
+       function [] = error(obj,message)
+            %error handles critical errors
+            %   critical errors will always result in a matlab error 
+            
+            %ToDO: Add function(s) before termination
+            error(message);
+       end 
+        
+       function [] = softError(obj,message)
+            %softError handles soft errors
+            %   soft errors can be changed to warning if ForcePublish is
+            %   selected by the user
+            if obj.forcePublish
+                warning(message);
+            else
+                error(message);
+            end
+        end
+        
+        function outputArg = method1(obj,inputArg)
+            %METHOD1 Summary of this method goes here
+            %   Detailed explanation goes here
+            outputArg = obj.Property1 + inputArg;
+        end
+    end
+end
+

+PlotID/Publish.m

@@ -24,8 +24,12 @@ arguments
    options.Location {mustBeMember(options.Location ,{'local','server','manual','CI-Test'})} = 'local' % storage path
    options.Method {mustBeMember(options.Method ,{'individual','centralized'})} = 'individual'
    options.ParentFolder (1,:) {mustBeText} = 'export'
+   options.ConfigFileName (1,:) {mustBeText} = 'config.json' %individual config names possible
    options.CopyUserFCN (1,1) {mustBeNumericOrLogical} = true
    options.CSV (1,1) {mustBeNumericOrLogical} = false
+   options.ShowMessages(1,1) {mustBeNumericOrLogical} = true
+   options.ForcePublish (1,1) {mustBeNumericOrLogical} = false %publish anyway
+   
 end
 
 %% argument validation 
@@ -39,8 +43,8 @@ if numel(figure) > 1
 end
 
 %get ID from Figure
-
 ID = figure.Tag;
+
 if isempty(ID)  
    % no ID found, User dialog for Folder name 
    ID = inputdlg(['No ID defined- ' newline,...
@@ -51,17 +55,15 @@ if isempty(ID)
    warning(msg);
 end
 
+% Error and MSG handeling
+dlgObj = PlotID.userDLG(ID,options); 
 
 %% read config file
 try 
    txt = fileread('config.json');
    config = jsondecode(txt);
-   configError = false;
 catch
-   msg = ['Error while reading the config file' newline,...
-       ' publishing on server not possible'];
-   warning(msg);
-   configError = true;
+   dlgObj.configError = true; 
 end
 
 %% storage location
@@ -75,26 +77,34 @@ switch options.Location
             storPath = fullfile(scriptLocation,options.ParentFolder);
         end
     case 'server' %from config File
+        if dlgObj.configError
+            msg = ['Error while reading the config file' newline,...
+                ' publishing on server not possible'];         
+            dlgObj.error(msg);
+        end
         storPath = config.ServerPath;
     case 'manual' %UI
         storPath = uigetdir();
     case 'CI-Test'
         storPath = fullfile(pwd,'CI_files',options.ParentFolder);
 end
-folderName = char(ID);
 
-%% Create Data-Directory
+folderName = ['.',char(ID)]; %hidden folder
+
+%% Create data directory
 if isfolder(fullfile(storPath,folderName))
-   error(['Folder ',folderName, ' exists - Plot was already published ']);
+   dlgObj.error(['Folder ',folderName, ' exists - Plot was already published ']);
 elseif mkdir(fullfile(storPath,folderName))
 else
-    error('Directory could not be created - check remote path and permissions');
+    dlgObj.error('Directory could not be created - check remote path and permissions');
 end
 disp(['publishing of ', ID, ' started']);
 
-%% Create a Copy of the script and user functions(optional)
+%% Create a copy of the script and user functions(optional)
 % script
-PlotID.createFileCopy({scriptPath},folderName,storPath,ID, 'script');
+[~, status, msg] = PlotID.createFileCopy({scriptPath},folderName,storPath,ID, 'script');
+dlgObj.scriptPublished =status;
+dlgObj.userMSG(msg);
 
 % user functions
 [fList,pList] = matlab.codetools.requiredFilesAndProducts(scriptPath);
@@ -136,27 +146,32 @@ switch options.Method
                 relativeSourcePath = strrep(sourcePath,currentPath,'');
                                 
                 if contains(sourcePath,{'.h5','.hdf5'}) % Linking only for HDF5
-                    PlotID.createLinkedHDF5(relativeSourcePath{1,1},storPath,ID);
+                    linkedHDFPath = fullfile(storPath,folderName);
+                    PlotID.createLinkedHDF5(relativeSourcePath{1,1},linkedHDFPath);
                 end
             else % no identical file exists
                 %Copy the file in data and create the links (if hdf5)
-                [dataPath] = PlotID.createFileCopy(DataPaths{i},'data',storPath,ID,'dataCentral');
-                relativeDataPath = strrep(dataPath,currentPath,'');
+                [dataPath, status, msg] = PlotID.createFileCopy(DataPaths{i},'data',storPath,ID,'dataCentral');
+                pathToData = strrep(dataPath,currentPath,'');
                 %WIP
                 if contains(DataPaths{i},{'.h5','.hdf5'}) % Linking only for HDF5
                    % and create also linked files in the plot folder 
-                   PlotID.createLinkedHDF5(relativeDataPath,storPath,ID);
+                   linkedHDFPath = fullfile(storPath,folderName);
+                   [status] = PlotID.createLinkedHDF5(pathToData,linkedHDFPath);
                 end  %if
             end %if
         end %for
         clear DataFolderName 
     case 'individual'
         % Create a copy of the research data    
-        PlotID.createFileCopy(DataPaths,folderName,storPath,ID, 'data');
+        [~, status, msg] = PlotID.createFileCopy(DataPaths,folderName,storPath,ID, 'data');
 end
-%% Write Config File
+%temporary:
+dlgObj.rdFilesPublished = status;
+dlgObj.userMSG(msg);
 
-if ~configError %config File must exist
+%% Write Config File
+if ~dlgObj.configError %config File must exist
    % copy config file 
    configPath = PlotID.createFileCopy('config.json',folderName,...
        storPath,ID, 'data');
@@ -188,12 +203,11 @@ try
    savefig(figure,RemotePath);
    % the png should only be a preview
    exportgraphics(figure,[RemotePath,'.png'],'Resolution',300);
+   dlgObj.figurePublished = true; 
 catch 
-    warning('Plot export was not successful')
+   dlgObj.softError('Plot export was not successful');
 end
 
-disp(['publishing of ', ID , ' done']);
-
 % CSV EXport
 if options.CSV
   T = table();
@@ -205,6 +219,25 @@ if options.CSV
   writetable(T, fullfile(storPath, 'overview_table.csv'),'WriteMode','append');
 end
 
+%% final renaming and error/warning handeling
+% if no error orcurred or if force publish is activated, rename the hidden
+% folder to a non hidden one, otherwise delete it.
+if dlgObj.success || options.ForcePublish
+    oldPath = fullfile(storPath,folderName);
+    newPath = strrep(oldPath,'.',''); %remov dot
+    status = movefile(oldPath,newPath); %rename directory
+else
+    % error from userDlg class!
+end
+
+if status 
+    disp(['publishing of ', ID , ' done']); %always displayed onsucess   
+else % publish was not sucessfull! 
+    %replace with error from userDLG Class
+    dlgObj.error(['publishing of ', ID , ' failed'])
+end
+
+
 end %function
 
 %% Argument Validation Functions
@@ -216,7 +249,7 @@ end
 function mustBeDataPath(DataPaths)
 %checks if input is a valid DataPath object
 
-  if iscellstr(DataPaths)
+  if isstring(DataPaths)
      tf = zeros(1,numel(DataPaths)); 
      for i=1:numel(DataPaths)
          tf(i) = ~isfile(DataPaths{i});

+PlotID/TagPlot.m

@@ -15,9 +15,10 @@ arguments
     figs (1,:) {mustBeFigure}
     options.ProjectID (1,:) {mustBeText}= ''
     options.Fontsize (1,1) {mustBeInteger} = 8
+    options.Color (1,3)  {mustBeNonnegative} = 0.65*[1 1 1] % grey
     options.Location (1,:) {mustBeText} = 'east'
     options.Position (1,2) {mustBeVector} = [1,0.4] % default for east
-    options.Rotation (1,1) {mustBeInteger} = 0  
+    options.Rotation (1,1) {mustBeReal} = NaN 
 end
 
 if isempty(options.ProjectID)
@@ -41,16 +42,19 @@ end
 switch options.Location
     case 'north'
         options.Position = [0.4,0.95];
-        options.Rotation = 0;
+        Rotation = 0;
     case 'east'
         options.Position = [1,0.4];
-        options.Rotation = 90;
+        Rotation = 90;
     case 'south'
         options.Position = [0.4,.02];
-        options.Rotation = 0;
+        Rotation = 0;
     case 'west'
         options.Position = [.05,0.4];
-        options.Rotation = 90;
+        Rotation = 90;
+    case 'southeast'
+        options.Position = [0.8,.02];
+        Rotation = 0;
     case 'custom'
         % Check if Position is valid
         if ~all(0 <= options.Position & options.Position <= 1)
@@ -62,6 +66,10 @@ switch options.Location
         options.Location = 'east'; options.Position = [1,0.4];
 end
 
+if ~isnan(options.Rotation)
+   Rotation = options.Rotation; 
+end
+
 IDs = cell(numel(figs),1);
 
 for n = 1:numel(figs)
@@ -72,10 +80,11 @@ for n = 1:numel(figs)
     ylim =get(axes,'YLim');
     xlim =get(axes,'XLim');
     %ID
-    position = [options.Position(1)*xlim(2), options.Position(2)*ylim(2)];
+    
+    position = [options.Position(1), options.Position(2)];
     text(axes,position(1),position(2), IDs{n},'Fontsize',options.Fontsize,...
-    'Rotation',options.Rotation, 'VerticalAlignment','bottom','Color',...
-        0.65*[1 1 1],'BackgroundColor','w');
+    'Rotation',Rotation, 'VerticalAlignment','bottom','Color',...
+        options.Color,'BackgroundColor','w', 'Units', 'normalized');
     set(figs(n),'Tag', IDs{n});    
 end
 

+PlotID/createFileCopy.m

-function [storagePaths] = createFileCopy(filePaths,folderName,storPath,ID,type)
+function [storagePaths, status, msg] = createFileCopy(filePaths,folderName,storPath,ID,type)
 % Creates a copy of the files (can be used for multiple paths in a cell array)
 % folderName is the name of the exporting folder
 % returns the storage paths were files were stored
@@ -68,8 +68,10 @@ try
         copyfile(FileNameAndLocation,RemotePath);
         storagePaths{i} = RemotePath; 
     end
-    disp([type, ' successfully published']);
+    status = true;
+    msg =([type, ' successfully published']);
 catch
+    status = false;
     warning([type,' export was not sucessful'])
     if exist('errorMSG')
         error(errorMSG);

+PlotID/createLinkedHDF5.m

-function [status] = createLinkedHDF5(SourceFile,TargetPath,ID)
+function [status] = createLinkedHDF5(SourceFile,TargetPath)
 %createLinkedHDF5 creates a HDF file that references the Sourcefile
 %   TargetPath is the storage location, ID the foldername
 %   Status returns true if the function was sucessfull
@@ -16,12 +16,12 @@ end
     %old
     %fid = H5F.create(fullfile(TargetPath,ID,[ID,'_data.h5']));
     
-    fid = H5F.create(fullfile(TargetPath,ID,[filename,ext]));
+    fid = H5F.create(fullfile(TargetPath,[filename,ext]));
     %create External Link to Sourcefile in the Group linkToExternal
     H5L.create_external(['..',SourceFile],'/',fid, SourceFile ,plist_id,plist_id);
     %H5L.create_external(['..',filesep,'data',filesep,SourceFile],'/',fid, SourceFile ,plist_id,plist_id); %original
     H5F.close(fid);
-    disp([fullfile(TargetPath,ID,[filename,ext]),' created']);
+    disp([fullfile(TargetPath,[filename,ext]),' created']);
     status = 1;
 % catch
 %     warning('No linked HDF file was created');

+PlotID/removePltIdFiles.m

@@ -7,7 +7,8 @@ names = strcat(names, ext); % add ext for comparison
 
 % Get a list of all .m files that are part of Plot id
 packageContent = what('PlotID');
-PltID_flist = packageContent.m; %get list of files 
+% packageContent.classes has no extensions
+PltID_flist = [packageContent.m; strcat(packageContent.classes,'.m')]; 
 
 % Comparison and filter
 fListClean = fList(~ismember(names,PltID_flist));

.gitignore

@@ -37,6 +37,7 @@ testdata_2.h5
 testdata2.h5
 test_data.mat
 export/*
+unused*/*
 
 # Octave session info
 octave-workspace

CITATION.cff

+cff-version: 1.2.0
+title: >-
+  plotID a toolkit for connecting research data and
+  figures
+message: >-
+  developed at the Chair of Fluid System, Techische
+  Universität Darmstadt within the framework of the NFDI4Ing consortium  Funded by the German Research Foundation (DFG) - project number 442146713 
+type: software
+authors:
+  - given-names: Jan
+    family-names: Lemmer
+    email: jan.lemmer@fst.tu-darmstadt.de
+    affiliation: 'Chair of Fluid Systems, TU Darmstadt'
+    orcid: 'https://orcid.org/0000-0002-0638-1567'
+  - given-names: Martin
+    family-names: Hock
+    email: martin.hock@fst.tu-darmstadt.de
+    affiliation: 'Chair of Fluid Systems, TU Darmstadt'

example.m

@@ -43,7 +43,8 @@ h5write(fpath, "/y1", y1)
 % Place for post-processing of the data, or additional related code.
 % example_fcn is a dummy function to show the functionality
 a = 1; a = example_fcn(a); 
-p = betacdf(0.5,1,1); % to test toolboxes
+% Uncomment to include the Statistics and Machine learning Toolbox
+% p = betacdf(0.5,1,1); % to test toolboxes
 
 %% Plotting
 % This is still part of a normal script to produce plots.