From 1f69d192f3257d01614844bfbcbe385d1e60dc5c Mon Sep 17 00:00:00 2001
From: Jan Lemmer <jan.lemmer@fst.tu-darmstadt.de>
Date: Tue, 12 Oct 2021 14:56:49 +0200
Subject: [PATCH] clean commit

---
 {fcn_core => +PlotID}/CreateID.m              |   7 +-
 +PlotID/Publish.m                             | 190 +++++++++
 {fcn_core => +PlotID}/TagPlot.m               |  51 ++-
 +PlotID/createLinkedHDF5.m                    |  32 ++
 +PlotID/fileCompare.m                         |  56 +++
 fcn_help/FriendlyID.m => +PlotID/friendlyID.m |   2 +-
 {fcn_help => +PlotID}/removePltIdFiles.m      |   2 +-
 {fcn_help => +PlotID}/replaceLinkedHDF5.m     |   0
 .gitignore                                    |   8 +
 .gitlab-ci.yml                                |  10 +
 CI_files/default_test.m                       |  17 +-
 CI_files/runner_test.m                        |   7 +
 LICENSE                                       | 373 ------------------
 PlotID_Demo.m                                 |  74 ++++
 README.md                                     | 112 +++++-
 example-config.json                           |   5 +
 example.m                                     | 110 +++---
 fcn_core/Publish.m                            | 104 -----
 fcn_help/createFileCopy.m                     |  52 ---
 fcn_help/createLinkedHDF5.m                   |  20 -
 fcn_help/fileCompare.m                        |  49 ---
 21 files changed, 613 insertions(+), 668 deletions(-)
 rename {fcn_core => +PlotID}/CreateID.m (85%)
 create mode 100644 +PlotID/Publish.m
 rename {fcn_core => +PlotID}/TagPlot.m (59%)
 create mode 100644 +PlotID/createLinkedHDF5.m
 create mode 100644 +PlotID/fileCompare.m
 rename fcn_help/FriendlyID.m => +PlotID/friendlyID.m (91%)
 rename {fcn_help => +PlotID}/removePltIdFiles.m (86%)
 rename {fcn_help => +PlotID}/replaceLinkedHDF5.m (100%)
 create mode 100644 .gitlab-ci.yml
 create mode 100644 CI_files/runner_test.m
 delete mode 100644 LICENSE
 create mode 100644 PlotID_Demo.m
 create mode 100644 example-config.json
 delete mode 100644 fcn_core/Publish.m
 delete mode 100644 fcn_help/createFileCopy.m
 delete mode 100644 fcn_help/createLinkedHDF5.m
 delete mode 100644 fcn_help/fileCompare.m

diff --git a/fcn_core/CreateID.m b/+PlotID/CreateID.m
similarity index 85%
rename from fcn_core/CreateID.m
rename to +PlotID/CreateID.m
index 42ec2b2..2579717 100644
--- a/fcn_core/CreateID.m
+++ b/+PlotID/CreateID.m
@@ -1,5 +1,5 @@
 function [ID] = CreateID(method)
-%CreateID Creates an Identifier (char)
+%CreateID Creates an identifier (char)
 %   Creates an (sometimes unique) identifier based on the selected method
 %   if no method is selected method 1 will be the default method
 arguments
@@ -10,10 +10,11 @@ switch method
     case 1 % UNIX Time in seconds as HEX
         ID = posixtime(datetime('now')); %get current Unix time
         ID = dec2hex(int32(ID)); % get it as Hex
-        pause(0.5); %Pausing for unique IDs
+        pause(1); %Pausing for unique IDs
     case 2 % random UUID from Java 128 bit
         %Static factory to retrieve a type 4 (pseudo randomly generated) UUID.
-        % The UUID is generated using a cryptographically strong pseudo random number generator.
+        % The UUID is generated using a cryptographically strong pseudo
+        % random number generator.
         temp =  java.util.UUID.randomUUID;
         ID = temp.toString;           
      otherwise
diff --git a/+PlotID/Publish.m b/+PlotID/Publish.m
new file mode 100644
index 0000000..fcd7772
--- /dev/null
+++ b/+PlotID/Publish.m
@@ -0,0 +1,190 @@
+function Publish(DataPaths, ID, figure, options)
+%Publishes saves plot, data and measuring script 
+%   Location sets the storage location. 'local' sets the storage location
+%   to the current folder (an export folder will be created), 'server' is a
+%   remote path, that is defined in the config file.
+%   Two Methods are implemented 'individual' stores the data for
+%   each plot while 'centralized' uses a data folder and uses reference links
+%   to the original data (hdf5 only).
+%   ParentFolder is the folder Name where the exported data is stored if an
+%   path is used, PlotId will use this path a storagePath
+
+arguments
+   DataPaths
+   ID (1,:) {mustBeNonzeroLengthText} % ID must be provided
+   figure (1,:) {mustBeFigure} % Checks if figure is a figure object
+   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.CopyUserFCN (1,1) {mustBeNumericOrLogical} = true 
+   options.CSV (1,1) {mustBeNumericOrLogical} = false
+end
+
+%catch multiple figures in fig
+if numel(figure) > 1
+    figure = figure(1);
+    msg = ['Publish is designed for handeling one figure at once' newline,...
+        '- publishes uses only the first figure.' newline , ...
+        'Consider an external for loop for multi figure export as provided in example.m'];
+    warning(msg);
+end
+
+%% 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;
+end
+
+%% storage location
+switch options.Location 
+    case 'local'
+        if contains(options.ParentFolder, {'/','\'})
+            storPath = options.ParentFolder;
+        else
+            % use the script path as export path
+            scriptPath = fileparts(DataPaths.script);
+            storPath = fullfile(scriptPath,options.ParentFolder);
+        end
+    case 'server' %from config File
+         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
+if isfolder(fullfile(storPath,folderName))
+   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');
+end
+disp(['publishing of ', ID, ' started']);
+
+%% Create a Copy of the script and user functions(optional)
+% script
+PlotID.createFileCopy({[DataPaths.script,'.m']},folderName,storPath,ID, 'script');
+
+% user functions
+[fList,pList] = matlab.codetools.requiredFilesAndProducts(DataPaths.script);
+if options.CopyUserFCN 
+   fList = fList(~ismember(fList,[DataPaths.script,'.m'])); % rmv script from list
+   fList = fList(~contains(fList,'config.json')); % rmv config.json from list
+   fList = PlotID.removePltIdFiles(fList); % Do not copy files that are part of plot ID
+   if ~isempty(fList)
+       PlotID.createFileCopy(fList,folderName,storPath,ID,'userFcn');
+   end
+end
+
+%% Research data handeling
+switch options.Method
+    case 'centralized' 
+        DataFolderName = 'data';
+        % check if data folder exists
+        if ~isfolder(fullfile(storPath,DataFolderName))
+            mkdir(fullfile(storPath,DataFolderName));
+        end
+        % to get relative Paths
+        currentPath = fullfile(storPath);
+        
+        %list all files
+        fList = dir(fullfile(storPath,DataFolderName, '**\*.*'));
+        %get list of files and folders in any subfolder
+        fList = fList(~[fList.isdir]);  %remove folders from list
+        fList = struct2table(fList);
+                
+        % Check if the new plot is based on the original data-set    
+            % copy the data(once)
+        for i=1:numel(DataPaths.rdata)            
+            % check if identical file exists (status = 1)
+            [~, idx] = PlotID.fileCompare(DataPaths.rdata{i},fList);
+            % create Linked HDF5 files for identical files
+            if any(idx)
+                fList.path = fullfile(fList.folder,fList.name);
+                sourcePath = fList{idx,'path'};
+                relativeSourcePath = strrep(sourcePath,currentPath,'');
+                                
+                if contains(sourcePath,{'.h5','.hdf5'}) % Linking only for HDF5
+                    PlotID.createLinkedHDF5(relativeSourcePath{1,1},storPath,ID);
+                end
+            else % no identical file exists
+                %Copy the file in data and create the links (if hdf5)
+                [dataPath] = PlotID.createFileCopy(DataPaths.rdata{i},'data',storPath,ID,'dataCentral');
+                relativeDataPath = strrep(dataPath,currentPath,'');
+                %WIP
+                if contains(DataPaths.rdata{i},{'.h5','.hdf5'}) % Linking only for HDF5
+                   % and create also linked files in the plot folder 
+                   PlotID.createLinkedHDF5(relativeDataPath,storPath,ID);
+                end  %if
+            end %if
+        end %for
+        clear DataFolderName 
+    case 'individual'
+        % Create a copy of the research data    
+        PlotID.createFileCopy(DataPaths.rdata,folderName,storPath,ID, 'data');
+end
+%% Write Config File
+
+if ~configError %config File must exist
+   % copy config file 
+   configPath = PlotID.createFileCopy('config.json',folderName,...
+       storPath,ID, 'data');
+else
+   configPath = fullpath(storPath,folderName, 'config.json');
+   config = struct(); 
+   if ispc
+    config.author = getenv('USERNAME');
+   end
+end
+% add further Metadata
+config.ProjectID = ID;
+config.CreationDate = datestr(now);
+config.MatlabVersion = version;
+config.ToolboxVersions = pList;
+
+%write config 
+fid = fopen(char(configPath),'w');
+txt = jsonencode(config,'PrettyPrint',true);
+fprintf(fid,txt); 
+fclose(fid);
+
+
+%% Export the Plot
+try 
+       PlotName = [ID,'_plot']; % plotname
+       RemotePath = fullfile(storPath ,folderName, PlotName);
+       % Matlab figure
+       savefig(figure,RemotePath);
+       % the png should only be a preview
+       exportgraphics(figure,[RemotePath,'.png'],'Resolution',300);
+catch 
+    warning('Plot export was not successful')
+end
+
+disp(['publishing of ', ID , ' done']);
+
+% CSV EXport
+if options.CSV
+  T = table();
+  T.research_Data = DataPaths.rdata'; T.PlotID(:) = {ID};
+  T.Script_Name(:) = {[DataPaths.script,'.m']};
+  T.Storage_Location(:) = {storPath};
+  T.Date(:) = {datestr(now)};
+  T = movevars(T,'PlotID','before',1);
+  writetable(T, fullfile(storPath, 'overview_table.csv'),'WriteMode','append');
+end
+
+end %function
+
+function tf = mustBeFigure(h)
+%checks if input is a figure object
+  tf = strcmp(get(h, 'type'), 'figure') & isa(h, 'matlab.ui.Figure');  
+end
diff --git a/fcn_core/TagPlot.m b/+PlotID/TagPlot.m
similarity index 59%
rename from fcn_core/TagPlot.m
rename to +PlotID/TagPlot.m
index 4fac128..4a59658 100644
--- a/fcn_core/TagPlot.m
+++ b/+PlotID/TagPlot.m
@@ -1,8 +1,11 @@
-function [figs, ID] = TagPlot(figs, prefix, options)
+function [figs, IDs] = TagPlot(figs, options)
 %TagPlot adds IDs to figures
-%   The ID is placed visual on the figure window and as Tag (Property of figure)
-%   TagPlot can tag multiple figures at once
-%   prefix is the project number (string or char)
+%   The ID is placed visual on the figure window and as Tag (property of figure)
+%   TagPlot can tag multiple figures at once.
+%   If a single Plot is taged IDs is a char, otherwise it is a cell array of
+%   chars 
+%   options.ProjectID is the project number (string or char), if empty the ID from the
+%   config file is used
 %   
 %   The ID is placed on the 'east' per default, if you want it somwhere
 %   else, use the 'Location' option. 'north','east','south','west' are
@@ -10,15 +13,29 @@ function [figs, ID] = TagPlot(figs, prefix, options)
 %   'Position' (relative to your x- and y-axis limits)
 arguments
     figs (1,:) {mustBeFigure}
-    prefix (1,:) {mustBeText}= ''
+    options.ProjectID (1,:) {mustBeText}= ''
     options.Fontsize (1,1) {mustBeInteger} = 8 
     options.Location (1,:) {mustBeText} = 'east'
     options.Position (1,2) {mustBeVector} = [1,0.4] % default for east
     options.Rotation (1,1) {mustBeInteger} = 0  
 end
 
-if isempty(prefix)
-    warning('no project prefix defined')
+if isempty(options.ProjectID)
+    try
+        txt = fileread('config.json');
+        config = jsondecode(txt);
+    catch
+        config =struct;
+        config.ProjectID = '';
+        warning("No ProjectID was definded and no config.json could be found");
+        
+    end
+   
+   if ~isempty(config.ProjectID)
+       options.ProjectID = config.ProjectID;
+   else
+       warning('no project options.ProjectID defined')
+   end
 end
 
 switch options.Location
@@ -38,27 +55,33 @@ switch options.Location
         % Check if Position is valid
         if ~all(0 <= options.Position & options.Position <= 1)
            options.Position = [1,0.4];
-           warning('options.Position is not valid, TagPlot default values instead');
+           warning('options.Position is not valid, TagPlot uses default values instead');
         end
     otherwise % set default position
         warning([options.Location, ' is not a defined location, TagPlot uses location east instead']);
         options.Location = 'east'; options.Position = [1,0.4];
 end
-    
+
+IDs = cell(numel(figs),1);
+
 for n = 1:numel(figs)
-    ID = CreateID; % Create ID
-    ID = [prefix,'-',ID]; % add Prefix
+    IDs{n} = PlotID.CreateID; % Create ID
+    IDs{n} = [options.ProjectID,'-',IDs{n}]; % add options.ProjectID
     axes = get(figs(n),'CurrentAxes'); % Axes object for text annotation
     % Limits for relative Positioning
     ylim =get(axes,'YLim');
     xlim =get(axes,'XLim');
     %ID
     position = [options.Position(1)*xlim(2), options.Position(2)*ylim(2)];
-    text(axes,position(1),position(2), ID,'Fontsize',options.Fontsize,...
+    text(axes,position(1),position(2), IDs{n},'Fontsize',options.Fontsize,...
     'Rotation',options.Rotation, 'VerticalAlignment','bottom','Color',...
         0.65*[1 1 1],'BackgroundColor','w');
-    set(figs(n),'Tag', ID);
-    
+    set(figs(n),'Tag', IDs{n});    
+end
+
+if numel(figs) == 1
+   % use char instead of a cell arry for a single ID
+   IDs = IDs{1}; 
 end
 
 end
diff --git a/+PlotID/createLinkedHDF5.m b/+PlotID/createLinkedHDF5.m
new file mode 100644
index 0000000..8fecfae
--- /dev/null
+++ b/+PlotID/createLinkedHDF5.m
@@ -0,0 +1,32 @@
+function [status] = createLinkedHDF5(SourceFile,TargetPath,ID)
+%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
+
+plist_id = 'H5P_DEFAULT';
+
+%catches error of wrong file type
+if iscell(SourceFile)
+    SourceFile = SourceFile{1};
+end
+
+[~,filename,ext] = fileparts(SourceFile);
+
+% try
+    %old
+    %fid = H5F.create(fullfile(TargetPath,ID,[ID,'_data.h5']));
+    
+    fid = H5F.create(fullfile(TargetPath,ID,[filename,ext]));
+    %create External Link to Sourcefile in the Group linkToExternal
+    H5L.create_external(['..\',SourceFile],'/',fid, SourceFile ,plist_id,plist_id);
+    %H5L.create_external(['..\data\',SourceFile],'/',fid, SourceFile ,plist_id,plist_id); %original
+    H5F.close(fid);
+    disp([fullfile(TargetPath,ID,[filename,ext]),' created']);
+    status = 1;
+% catch
+%     warning('No linked HDF file was created');
+%     status = 0;
+% end
+
+end
+
diff --git a/+PlotID/fileCompare.m b/+PlotID/fileCompare.m
new file mode 100644
index 0000000..9d0f969
--- /dev/null
+++ b/+PlotID/fileCompare.m
@@ -0,0 +1,56 @@
+function [status, id] = fileCompare(filename,fileList)
+%% fileCompare checks if file1 is (binary) identical to a file in filelist
+% it returns a status and the id of the identical file
+% the functions uses the java libraries from matlab for windows systems 
+% or the unix function diff 
+% because of performance issues with windows system calls in matlab
+
+if isempty(fileList)
+   % no comparison necessary
+    status =false;
+    id = 0;
+    return
+end
+
+[~,~,ext1] = fileparts(filename); 
+id = zeros(height(fileList),1);
+
+for i=1:height(fileList)
+    [~,~,ext2] = fileparts(fileList{i,'name'});
+
+    if ~isequal(ext1,ext2)
+        %warning('File extension are not identical');
+        status = false;
+        continue
+    end
+
+    filepath = fullfile(fileList{i,'folder'},fileList{i,'name'});
+    
+    %% comparison with java function
+    % TODO test paths with spaces
+    status = comparejava(filename, char(filepath));
+    
+    if status == 1        
+        id(i) = 1;
+        id =logical(id); %bugfix
+        return;
+    else 
+        % Status can also be any other number e.g. 2 
+        id(i) = 0;
+    end
+    
+    id =logical(id); %bugfix
+end
+
+end
+
+function is_equal =  comparejava(file1, file2)
+%% Utilizing java functionalities for inter-os comparison of binary files
+% file1 and file2 should be full filepaths
+
+file1 = javaObject('java.io.File',file1);
+file2 = javaObject('java.io.File',file2);
+is_equal = javaMethod('contentEquals','org.apache.commons.io.FileUtils',file1,file2);
+
+is_equal = double(is_equal); % Conversion for compatibility reasons
+end
diff --git a/fcn_help/FriendlyID.m b/+PlotID/friendlyID.m
similarity index 91%
rename from fcn_help/FriendlyID.m
rename to +PlotID/friendlyID.m
index e18834b..cdac106 100644
--- a/fcn_help/FriendlyID.m
+++ b/+PlotID/friendlyID.m
@@ -1,4 +1,4 @@
-function [IDf,PrjID, Str] = FriendlyID(ID)
+function [IDf,PrjID, Str] = friendlyID(ID)
 %FriendlyID Changes the Hex Number to a human friendly datetime and dateStr
 % IDf ID as DateTime Object, PrjID returns the ProjectID, Str returns the
 % timestamp as String
diff --git a/fcn_help/removePltIdFiles.m b/+PlotID/removePltIdFiles.m
similarity index 86%
rename from fcn_help/removePltIdFiles.m
rename to +PlotID/removePltIdFiles.m
index 3080c22..37ef182 100644
--- a/fcn_help/removePltIdFiles.m
+++ b/+PlotID/removePltIdFiles.m
@@ -7,7 +7,7 @@ function [fListClean] = removePltIdFiles(fList)
 names = strcat(names, ext); % add ext for comparison
 
 % Get a list of all .m files that are part of Plot id
-PltID_flist = struct2table([dir('fcn_help'); dir('fcn_core')]); %get list of files 
+PltID_flist = struct2table(dir('+PlotID')); %get list of files 
 [~,~,PltID_flist.ext(:)] = fileparts(PltID_flist.name(:)); % add ext column
 
 PltID_flist = PltID_flist(strcmp(PltID_flist.ext,'.m'),:);
diff --git a/fcn_help/replaceLinkedHDF5.m b/+PlotID/replaceLinkedHDF5.m
similarity index 100%
rename from fcn_help/replaceLinkedHDF5.m
rename to +PlotID/replaceLinkedHDF5.m
diff --git a/.gitignore b/.gitignore
index 3d5fc69..708bea6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,6 @@
+# config file changes
+config.json
+
 # Windows default autosave extension
 *.asv
 
@@ -28,11 +31,16 @@ codegen/
 test*.m
 test123_data.h5
 
+
 # files that are created in example.m
 testdata_2.h5
+testdata2.h5
 test_data.mat
 export/*
 
 # Octave session info
 octave-workspace
 test_data.mat 
+
+#logs
+log.txt
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000..7901609
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,10 @@
+#Based on STFS Workshop
+stages:
+    - Run
+Test Code:
+    stage: Run
+    tags:
+        - matlab
+    script:
+        - ./CI_files/runtest.ps1
+        - cat log2.txt
diff --git a/CI_files/default_test.m b/CI_files/default_test.m
index 515ad37..505c360 100644
--- a/CI_files/default_test.m
+++ b/CI_files/default_test.m
@@ -3,7 +3,12 @@ function [result] = default_test()
 %   Detailed explanation goes here
 
 clear; clc; close all;
-addpath('./fcn_core','./fcn_help');
+
+% clean up, if previous run failed
+try
+    delete CI_files/export/* CI_files/*.mat CI_files/*.h5
+    rmdir('CI_files/export','s');
+end
 
 ProjectID = 'Test01';
 %% Data
@@ -35,7 +40,7 @@ plot(x1,y1,'-r');
 
 %% Tag the plot
 try
-    [figs, ID] = TagPlot(fig, ProjectID);
+    [figs, ID] = PlotID.TagPlot(fig,'ProjectID', ProjectID);
 
     %% call a dummy function
     a=1;
@@ -50,13 +55,15 @@ try
     % file name of the data
     path.rdata =  {dataset1,dataset2} ; % don't forget the extension
 
-    Publish(path, ID, figs, 'Location', 'CI-Test')
+    PlotID.Publish(path, ID, figs, 'Location', 'CI-Test')
+    result = true;
     
     % clean up 
     delete CI_files/export/* CI_files/*.mat CI_files/*.h5 
     rmdir('CI_files/export','s'); 
-    result = true;
-    clc;
+    
+    clear; clc;
+     
 catch
     result = false;
     warning('simple_test failed');
diff --git a/CI_files/runner_test.m b/CI_files/runner_test.m
new file mode 100644
index 0000000..496afd8
--- /dev/null
+++ b/CI_files/runner_test.m
@@ -0,0 +1,7 @@
+function [result] = runner_test()
+%RUNNER_TEST testing function to test, if the runner is set up properly
+result = true;
+
+exit(result);
+end
+
diff --git a/LICENSE b/LICENSE
deleted file mode 100644
index a612ad9..0000000
--- a/LICENSE
+++ /dev/null
@@ -1,373 +0,0 @@
-Mozilla Public License Version 2.0
-==================================
-
-1. Definitions
---------------
-
-1.1. "Contributor"
-    means each individual or legal entity that creates, contributes to
-    the creation of, or owns Covered Software.
-
-1.2. "Contributor Version"
-    means the combination of the Contributions of others (if any) used
-    by a Contributor and that particular Contributor's Contribution.
-
-1.3. "Contribution"
-    means Covered Software of a particular Contributor.
-
-1.4. "Covered Software"
-    means Source Code Form to which the initial Contributor has attached
-    the notice in Exhibit A, the Executable Form of such Source Code
-    Form, and Modifications of such Source Code Form, in each case
-    including portions thereof.
-
-1.5. "Incompatible With Secondary Licenses"
-    means
-
-    (a) that the initial Contributor has attached the notice described
-        in Exhibit B to the Covered Software; or
-
-    (b) that the Covered Software was made available under the terms of
-        version 1.1 or earlier of the License, but not also under the
-        terms of a Secondary License.
-
-1.6. "Executable Form"
-    means any form of the work other than Source Code Form.
-
-1.7. "Larger Work"
-    means a work that combines Covered Software with other material, in
-    a separate file or files, that is not Covered Software.
-
-1.8. "License"
-    means this document.
-
-1.9. "Licensable"
-    means having the right to grant, to the maximum extent possible,
-    whether at the time of the initial grant or subsequently, any and
-    all of the rights conveyed by this License.
-
-1.10. "Modifications"
-    means any of the following:
-
-    (a) any file in Source Code Form that results from an addition to,
-        deletion from, or modification of the contents of Covered
-        Software; or
-
-    (b) any new file in Source Code Form that contains any Covered
-        Software.
-
-1.11. "Patent Claims" of a Contributor
-    means any patent claim(s), including without limitation, method,
-    process, and apparatus claims, in any patent Licensable by such
-    Contributor that would be infringed, but for the grant of the
-    License, by the making, using, selling, offering for sale, having
-    made, import, or transfer of either its Contributions or its
-    Contributor Version.
-
-1.12. "Secondary License"
-    means either the GNU General Public License, Version 2.0, the GNU
-    Lesser General Public License, Version 2.1, the GNU Affero General
-    Public License, Version 3.0, or any later versions of those
-    licenses.
-
-1.13. "Source Code Form"
-    means the form of the work preferred for making modifications.
-
-1.14. "You" (or "Your")
-    means an individual or a legal entity exercising rights under this
-    License. For legal entities, "You" includes any entity that
-    controls, is controlled by, or is under common control with You. For
-    purposes of this definition, "control" means (a) the power, direct
-    or indirect, to cause the direction or management of such entity,
-    whether by contract or otherwise, or (b) ownership of more than
-    fifty percent (50%) of the outstanding shares or beneficial
-    ownership of such entity.
-
-2. License Grants and Conditions
---------------------------------
-
-2.1. Grants
-
-Each Contributor hereby grants You a world-wide, royalty-free,
-non-exclusive license:
-
-(a) under intellectual property rights (other than patent or trademark)
-    Licensable by such Contributor to use, reproduce, make available,
-    modify, display, perform, distribute, and otherwise exploit its
-    Contributions, either on an unmodified basis, with Modifications, or
-    as part of a Larger Work; and
-
-(b) under Patent Claims of such Contributor to make, use, sell, offer
-    for sale, have made, import, and otherwise transfer either its
-    Contributions or its Contributor Version.
-
-2.2. Effective Date
-
-The licenses granted in Section 2.1 with respect to any Contribution
-become effective for each Contribution on the date the Contributor first
-distributes such Contribution.
-
-2.3. Limitations on Grant Scope
-
-The licenses granted in this Section 2 are the only rights granted under
-this License. No additional rights or licenses will be implied from the
-distribution or licensing of Covered Software under this License.
-Notwithstanding Section 2.1(b) above, no patent license is granted by a
-Contributor:
-
-(a) for any code that a Contributor has removed from Covered Software;
-    or
-
-(b) for infringements caused by: (i) Your and any other third party's
-    modifications of Covered Software, or (ii) the combination of its
-    Contributions with other software (except as part of its Contributor
-    Version); or
-
-(c) under Patent Claims infringed by Covered Software in the absence of
-    its Contributions.
-
-This License does not grant any rights in the trademarks, service marks,
-or logos of any Contributor (except as may be necessary to comply with
-the notice requirements in Section 3.4).
-
-2.4. Subsequent Licenses
-
-No Contributor makes additional grants as a result of Your choice to
-distribute the Covered Software under a subsequent version of this
-License (see Section 10.2) or under the terms of a Secondary License (if
-permitted under the terms of Section 3.3).
-
-2.5. Representation
-
-Each Contributor represents that the Contributor believes its
-Contributions are its original creation(s) or it has sufficient rights
-to grant the rights to its Contributions conveyed by this License.
-
-2.6. Fair Use
-
-This License is not intended to limit any rights You have under
-applicable copyright doctrines of fair use, fair dealing, or other
-equivalents.
-
-2.7. Conditions
-
-Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
-in Section 2.1.
-
-3. Responsibilities
--------------------
-
-3.1. Distribution of Source Form
-
-All distribution of Covered Software in Source Code Form, including any
-Modifications that You create or to which You contribute, must be under
-the terms of this License. You must inform recipients that the Source
-Code Form of the Covered Software is governed by the terms of this
-License, and how they can obtain a copy of this License. You may not
-attempt to alter or restrict the recipients' rights in the Source Code
-Form.
-
-3.2. Distribution of Executable Form
-
-If You distribute Covered Software in Executable Form then:
-
-(a) such Covered Software must also be made available in Source Code
-    Form, as described in Section 3.1, and You must inform recipients of
-    the Executable Form how they can obtain a copy of such Source Code
-    Form by reasonable means in a timely manner, at a charge no more
-    than the cost of distribution to the recipient; and
-
-(b) You may distribute such Executable Form under the terms of this
-    License, or sublicense it under different terms, provided that the
-    license for the Executable Form does not attempt to limit or alter
-    the recipients' rights in the Source Code Form under this License.
-
-3.3. Distribution of a Larger Work
-
-You may create and distribute a Larger Work under terms of Your choice,
-provided that You also comply with the requirements of this License for
-the Covered Software. If the Larger Work is a combination of Covered
-Software with a work governed by one or more Secondary Licenses, and the
-Covered Software is not Incompatible With Secondary Licenses, this
-License permits You to additionally distribute such Covered Software
-under the terms of such Secondary License(s), so that the recipient of
-the Larger Work may, at their option, further distribute the Covered
-Software under the terms of either this License or such Secondary
-License(s).
-
-3.4. Notices
-
-You may not remove or alter the substance of any license notices
-(including copyright notices, patent notices, disclaimers of warranty,
-or limitations of liability) contained within the Source Code Form of
-the Covered Software, except that You may alter any license notices to
-the extent required to remedy known factual inaccuracies.
-
-3.5. Application of Additional Terms
-
-You may choose to offer, and to charge a fee for, warranty, support,
-indemnity or liability obligations to one or more recipients of Covered
-Software. However, You may do so only on Your own behalf, and not on
-behalf of any Contributor. You must make it absolutely clear that any
-such warranty, support, indemnity, or liability obligation is offered by
-You alone, and You hereby agree to indemnify every Contributor for any
-liability incurred by such Contributor as a result of warranty, support,
-indemnity or liability terms You offer. You may include additional
-disclaimers of warranty and limitations of liability specific to any
-jurisdiction.
-
-4. Inability to Comply Due to Statute or Regulation
----------------------------------------------------
-
-If it is impossible for You to comply with any of the terms of this
-License with respect to some or all of the Covered Software due to
-statute, judicial order, or regulation then You must: (a) comply with
-the terms of this License to the maximum extent possible; and (b)
-describe the limitations and the code they affect. Such description must
-be placed in a text file included with all distributions of the Covered
-Software under this License. Except to the extent prohibited by statute
-or regulation, such description must be sufficiently detailed for a
-recipient of ordinary skill to be able to understand it.
-
-5. Termination
---------------
-
-5.1. The rights granted under this License will terminate automatically
-if You fail to comply with any of its terms. However, if You become
-compliant, then the rights granted under this License from a particular
-Contributor are reinstated (a) provisionally, unless and until such
-Contributor explicitly and finally terminates Your grants, and (b) on an
-ongoing basis, if such Contributor fails to notify You of the
-non-compliance by some reasonable means prior to 60 days after You have
-come back into compliance. Moreover, Your grants from a particular
-Contributor are reinstated on an ongoing basis if such Contributor
-notifies You of the non-compliance by some reasonable means, this is the
-first time You have received notice of non-compliance with this License
-from such Contributor, and You become compliant prior to 30 days after
-Your receipt of the notice.
-
-5.2. If You initiate litigation against any entity by asserting a patent
-infringement claim (excluding declaratory judgment actions,
-counter-claims, and cross-claims) alleging that a Contributor Version
-directly or indirectly infringes any patent, then the rights granted to
-You by any and all Contributors for the Covered Software under Section
-2.1 of this License shall terminate.
-
-5.3. In the event of termination under Sections 5.1 or 5.2 above, all
-end user license agreements (excluding distributors and resellers) which
-have been validly granted by You or Your distributors under this License
-prior to termination shall survive termination.
-
-************************************************************************
-*                                                                      *
-*  6. Disclaimer of Warranty                                           *
-*  -------------------------                                           *
-*                                                                      *
-*  Covered Software is provided under this License on an "as is"       *
-*  basis, without warranty of any kind, either expressed, implied, or  *
-*  statutory, including, without limitation, warranties that the       *
-*  Covered Software is free of defects, merchantable, fit for a        *
-*  particular purpose or non-infringing. The entire risk as to the     *
-*  quality and performance of the Covered Software is with You.        *
-*  Should any Covered Software prove defective in any respect, You     *
-*  (not any Contributor) assume the cost of any necessary servicing,   *
-*  repair, or correction. This disclaimer of warranty constitutes an   *
-*  essential part of this License. No use of any Covered Software is   *
-*  authorized under this License except under this disclaimer.         *
-*                                                                      *
-************************************************************************
-
-************************************************************************
-*                                                                      *
-*  7. Limitation of Liability                                          *
-*  --------------------------                                          *
-*                                                                      *
-*  Under no circumstances and under no legal theory, whether tort      *
-*  (including negligence), contract, or otherwise, shall any           *
-*  Contributor, or anyone who distributes Covered Software as          *
-*  permitted above, be liable to You for any direct, indirect,         *
-*  special, incidental, or consequential damages of any character      *
-*  including, without limitation, damages for lost profits, loss of    *
-*  goodwill, work stoppage, computer failure or malfunction, or any    *
-*  and all other commercial damages or losses, even if such party      *
-*  shall have been informed of the possibility of such damages. This   *
-*  limitation of liability shall not apply to liability for death or   *
-*  personal injury resulting from such party's negligence to the       *
-*  extent applicable law prohibits such limitation. Some               *
-*  jurisdictions do not allow the exclusion or limitation of           *
-*  incidental or consequential damages, so this exclusion and          *
-*  limitation may not apply to You.                                    *
-*                                                                      *
-************************************************************************
-
-8. Litigation
--------------
-
-Any litigation relating to this License may be brought only in the
-courts of a jurisdiction where the defendant maintains its principal
-place of business and such litigation shall be governed by laws of that
-jurisdiction, without reference to its conflict-of-law provisions.
-Nothing in this Section shall prevent a party's ability to bring
-cross-claims or counter-claims.
-
-9. Miscellaneous
-----------------
-
-This License represents the complete agreement concerning the subject
-matter hereof. If any provision of this License is held to be
-unenforceable, such provision shall be reformed only to the extent
-necessary to make it enforceable. Any law or regulation which provides
-that the language of a contract shall be construed against the drafter
-shall not be used to construe this License against a Contributor.
-
-10. Versions of the License
----------------------------
-
-10.1. New Versions
-
-Mozilla Foundation is the license steward. Except as provided in Section
-10.3, no one other than the license steward has the right to modify or
-publish new versions of this License. Each version will be given a
-distinguishing version number.
-
-10.2. Effect of New Versions
-
-You may distribute the Covered Software under the terms of the version
-of the License under which You originally received the Covered Software,
-or under the terms of any subsequent version published by the license
-steward.
-
-10.3. Modified Versions
-
-If you create software not governed by this License, and you want to
-create a new license for such software, you may create and use a
-modified version of this License if you rename the license and remove
-any references to the name of the license steward (except to note that
-such modified license differs from this License).
-
-10.4. Distributing Source Code Form that is Incompatible With Secondary
-Licenses
-
-If You choose to distribute Source Code Form that is Incompatible With
-Secondary Licenses under the terms of this version of the License, the
-notice described in Exhibit B of this License must be attached.
-
-Exhibit A - Source Code Form License Notice
--------------------------------------------
-
-  This Source Code Form is subject to the terms of the Mozilla Public
-  License, v. 2.0. If a copy of the MPL was not distributed with this
-  file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-If it is not possible or desirable to put the notice in a particular
-file, then You may include the notice in a location (such as a LICENSE
-file in a relevant directory) where a recipient would be likely to look
-for such a notice.
-
-You may add additional accurate notices of copyright ownership.
-
-Exhibit B - "Incompatible With Secondary Licenses" Notice
----------------------------------------------------------
-
-  This Source Code Form is "Incompatible With Secondary Licenses", as
-  defined by the Mozilla Public License, v. 2.0.
diff --git a/PlotID_Demo.m b/PlotID_Demo.m
new file mode 100644
index 0000000..766ad17
--- /dev/null
+++ b/PlotID_Demo.m
@@ -0,0 +1,74 @@
+%% Example Script
+% This Script is meant to demonstrate the capabilities of the PlotID tool.
+
+%% Clear Environment
+clear; clc; close all;
+addpath('CI_files'); % Test scripts
+try
+    delete testdata2.h5;
+end
+
+%% Set ProjectID
+% ProjectID can also be set in the config file 
+% Leave empty for using the ID from the config file
+ProjectID = 'FST01';
+
+%% Data
+% Creating Random Data to use as data-file
+x = linspace(0,7);
+y = rand(1,100)+2;
+dataset1 = 'test_data.mat';
+% use absolute paths for good practise
+dataset1 = fullfile(pwd, dataset1);
+save(dataset1,'x','y');
+
+% some data as .h5
+x1 = linspace(0,2*pi);
+y1 = sin(x1)+.5*sin(2*x1)+2;
+
+% define file path & name
+
+fpath = fullfile(pwd,"./testdata2.h5");
+dataset2 = fullfile(pwd,'testdata2.h5');
+
+% create hdf5 file and dataset > write data to hdf5 file / dataset
+h5create(fpath, "/x1", size(x1), "Datatype", class(x1))
+h5create(fpath, "/y1", size(y1), "Datatype", class(y1))
+h5write(fpath, "/x1", x1)
+h5write(fpath, "/y1", y1)
+
+%% Plotting
+% This is still part of a normal script to produce plots.
+% Make sure to save each figure in a variable to pass to PlotID-functions.
+fig(1) = figure;
+set(gcf,'Units','centimeters','PaperUnits','centimeters','PaperSize',[9 7],...
+'Position',[5 5 9 7]);
+plot(x,y,'Color',0.5*[1 1 1]);
+box off; hold on;
+plot(x1,y1,'-k');
+set(gca, 'TickDir', 'out', 'YLim', [0,4],'YTick',[0:1:4],'XLim',[0,6]);
+%fstplt.setfiguresize('1/2ppt16:9');
+%fstplt.pimpplot;
+
+%% Example 1: single plot based on two data-sets
+
+%% Tag the plot
+% PlotID Implementation starts here.
+% TagPlot adds a visible ID to the figure(s) and to the figures property
+% 'Tag'
+[fig, ID] = PlotID.TagPlot(fig, 'ProjectID', ProjectID);
+
+%% Publishing
+% Second part of plotID 
+% The functions needs the file location, the location of the data and the
+% figure and can take several options.
+path.script = mfilename('fullpath'); % filename of the m.script
+% file names of the datasets
+path.rdata =  {dataset1,dataset2} ; % don't forget the extension
+
+PlotID.Publish(path, ID, fig(1), 'Location', 'local' ,'Method','individual')
+
+
+
+%% End 
+
diff --git a/README.md b/README.md
index 7ee43f2..a9e8270 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,111 @@
-# Plot_Identifier
+**PlotID**
+
+`PlotID` is a toolkit that labels your plots and figures and copies all associated data (research data, plotting script, user-functions and a copy of the figure) to the desired location.
+
+This version of  `PlotID` is build for `MATLAB`.
+
+`PlotID` provides two core functions **TagPlot** and **Publish** which are described in detail below.
+
+Feel free to give feedback and feature requests or to take part in the development process.
+
+ [TOC]
+
+# Quick User Guide
+`PlotID` works in two Steps:
+
+1. tagging the plot
+`[figs, IDs] = plotId.TagPlot(figs, options)`
+
+
+2. publishing the plot and the associated data
+`plotID.Publish(DataPaths, ID, figure, options)`
+
+`DataPaths.script = mfilename('fullpath');` contains the filename of the m.script
+
+`DataPaths.rdata =  {dataset1, dataset2};`  file names of the datasets (they most be at the path)
+
+# PlotID.TagPlot()
+`[figs, IDs] = TagPlot(figs, options)`
+**TagPlot** adds IDs to figures
+The ID is placed visual on the figure window and as Tag (property of the figure)
+**TagPlot** can tag multiple figures at once. If a single Plot is tagged, IDs is a char, otherwise it is a cell array of chars .
+
+<details><summary>detailed description</summary>
+
+_options_ \
+you find the options for TagPlot below. The data type is in curled braces and the default value follows the equal sign.
+
+- ProjectID  {mustBeText}= '' 
+- Fontsize {mustBeInteger} = 8 
+- Location  {mustBeText} = 'east'
+- Position  {mustBeVector} = [1,0.4] 
+-  Rotation  {mustBeInteger} = 0  
+
+`options.ProjectID` is the project number (string or char), if empty the ID from the config file is used
+The ID is placed on the 'east' of the figure per default, if you want it somwhere else, use the `'Location'` option. 'north', 'east', 'south', 'west' are predefined, otherwise use the `'custom'` option and provide the desired 'Position'  as a vector relative to your x- and y-axis limits `[relX, relY]` .
+</details>
+
+## CreateID()
+`function [ID] = CreateID(method)` \
+CreateID Creates an identifier (char). It creates an (sometimes unique) identifier based on the selected method, if no method is selected method 1 will be the default method.
+
+1. **UNIX Time in seconds as HEX** \
+This is used by default due to its simplicity and it is human readable. 
+2. **random UUID from Java 128 bit.**\
+Static factory to retrieve a type 4 (pseudo randomly generated) UUID. The UUID is generated using a cryptographically strong pseudo random number generator.
+
+## friendlyID() 
+`[IDf,PrjID, Str] = friendlyID(ID)` \
+FriendlyID Changes the Hex Number to a human friendly *datetime* and *dateStr*. `IDf` returns the ID as DateTime Object, `PrjID` returns the ProjectID, `Str` returns the timestamp as String. \
+**This only works with ID method 1.**
+
+
+# PlotID.Publish() 
+`Publish(DataPaths, ID, figure, options)` \
+Publishes saves plot, data and measuring script 
+Location sets the storage location. 'local' sets the storage location  to the current folder (an export folder will be created), 'server' is a remote path, that is defined in the config file. Two Methods are implemented 'individual' stores the data for each plot while 'centralized' uses a data folder and uses reference links to the original data (hdf5 only). ParentFolder is the folder Name where the exported data is stored if a path is used, PlotId will use this path a storagePath
+
+<details><summary>detailed description</summary>
+
+_options_ \
+you find the options for publish below. The data is in curled braces and the default value follows the equal sign.
+
+- Location {mustBeMember(options.Location ,{'local','server','manual','CI-Test'})} = 'local' \
+'local' creates the folder in your current working path, 'server' on a remote path that needs to be specified in the config file. 'manual' opens an UI Window where the path must be choosen, 'CI-Test' is for CI testing only.
+- Method {mustBeMember(options.Method ,{'individual','centraliced'})} = 'individual'\
+'individual' each folder contains the assigned data files. (recommended for small file sizes and for sharing).
+'centralized' one central data folder is used for saving the research data files, the subfolders contain linked hdf5-files (if hdf5 is used). This is recommended, if many plots are made from the same data set.  Attention, the linked HDF5 will not work when a subfolder was moved or the data folder was deleted.
+- ParentFolder  {mustBeText} = 'export'\
+An individual folden name can be set with this option.
+- CopyUserFCN  {mustBeNumericOrLogical} = true \
+All user functions that are used by script that calls publish will be exported per default as well. Set this to false (not recommended) to prevent this.
+- CSV {mustBeNumericOrLogical} = false \
+An overview of all published plots and the associated data will be stored in a csv file.
+</details>
+
+## createFileCopy ()
+`[] = 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
+## createLinkedHDF ()
+`[status] = createLinkedHDF5(SourceFile,TargetPath,ID)` \
+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.
+## fileCompare()
+`[status, id] = fileCompare(filename,fileList)`  \
+fileCompare checks if file1 is (binary) identical to a file in filelist, it returns a sttus and the id of the identical file. The function uses the windows system function fc or the unix function diff (not tested).
+## removePltIdFiles()
+`[fListClean] = removePltIdFiles(fList)` \
+removePltIdFiles removes functions that are part of PlotID out of flist.
+
+# How to use the .config file
+The config file is a JSON-File. At the moment two options can be set in the config file, the project ID and the remote Path.
+
+```
+{
+    "ProjectID": "your ProjectID", 
+    "ServerPath": "\\\\Server\\Folder1\\Subfolder"
+}
+```
+
+# Known Issues
+# FAQs
 
-Organisation und Beispiele aus den beiden Pilotprojekten zu Plotidentifiern
diff --git a/example-config.json b/example-config.json
new file mode 100644
index 0000000..9df3f40
--- /dev/null
+++ b/example-config.json
@@ -0,0 +1,5 @@
+{   
+    "Author": "Example Author"
+    "ProjectID": "AB01", 
+    "ServerPath": "\\\\Server\\path\\folder"
+}
\ No newline at end of file
diff --git a/example.m b/example.m
index f208097..04aa8c1 100644
--- a/example.m
+++ b/example.m
@@ -3,40 +3,35 @@
 
 %% Clear Environment
 clear; clc; close all;
-addpath('fcn_core','fcn_help');
-addpath('CI_files'); % Test scripts
 
 try
-    delete testdata_2.h5;
+    delete testdata2.h5;
 end
 
-
 %% Set ProjectID
-% ProjectID 
-
-% TODO:  decide how projectID and optionally ORCID will be implemented
-% ORCID placed on startup (alternative?) - projectID as persistent
-% otherwise dialogue?
-ProjectID = 'JL01';
-
+% ProjectID can also be set in the config file 
 
+% Leave empty for using the ID from the config file
+ProjectID = 'Example';
 
 %% Data
-% Creating Random Data to use as data-file
+% only necessary for this example
 
-x = linspace(0,7);
-y = rand(1,100)+2;
+% Creating Random Data to use as data-file
+x = linspace(0,7); y = rand(1,100)+2;
 dataset1 = 'test_data.mat';
-save('test_data.mat','x','y');
 
+% Use absolute paths for good practise
+dataset1 = fullfile(pwd,dataset1);
+save(dataset1,'x','y');
 
-% some data as .h5
-x1 = linspace(0,2*pi);
-y1 = sin(x1)+2;
+% some data for the .h5 file
+x1 = linspace(0,2*pi); y1 = sin(x1)+2;
 
-% define file path & name
-fpath = "./testdata_2.h5";
-dataset2 = 'testdata_2.h5';
+% define filepath & name
+dataset2 = 'testdata2.h5';
+dataset2 = fullfile(pwd,dataset2);
+fpath = dataset2;
 
 % create hdf5 file and dataset > write data to hdf5 file / dataset
 h5create(fpath, "/x1", size(x1), "Datatype", class(x1))
@@ -44,52 +39,79 @@ h5create(fpath, "/y1", size(y1), "Datatype", class(y1))
 h5write(fpath, "/x1", x1)
 h5write(fpath, "/y1", y1)
 
+%% function calls
+% 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
 
 %% Plotting
 % This is still part of a normal script to produce plots.
-% Make sure to save each figure in a variable to pass to PlotID-functions.
+% Make sure to save each figure in a variable
+% to pass it to PlotID-functions.
 fig(1) = figure;
 plot(x,y,'-k');
-box off
-set(gca, 'TickDir', 'out', 'YLim', [0,4]);
-
-hold on
-%fig(2) = figure;
+box off; hold on;
 plot(x1,y1,'-r');
 set(gca, 'TickDir', 'out', 'YLim', [0,4]);
 
+%% Example 1: single plot based on two data-sets
+
 %% Tag the plot
 % PlotID Implementation starts here.
- 
-[figs, ID] = TagPlot(fig, ProjectID);
-
-
-
-%% call a dummy function
-% Place for post-processing of the plot, or additional related code.
-a=1;
-a = example_fcn(a);
+% TagPlot adds a visible ID to the figure(s) and to the figures property
+% 'Tag'
+[fig, ID] = PlotID.TagPlot(fig, 'ProjectID', ProjectID);
 
 %% Publishing
 % Second part of plotID 
-% The functions needs the file location, the location of the data and the
-% figure and can take several options.
-% TODO add explanations for Options
+% The functions needs the file location of the script, the location of the
+% data and the figure and can take several options (see readme). 
+
 path.script = mfilename('fullpath'); % filename of the m.script
+% file names of the datasets
 
-% file name of the dataset
+%(defined above:) dataset1 = 'test_data.mat'; dataset2 = 'testdata2.h5'
 path.rdata =  {dataset1,dataset2} ; % don't forget the extension
 
-Publish(path, ID, figs, 'Location', 'local','Method','centraliced')
+%call publishing
+PlotID.Publish(path, ID, fig(1), 'Location', 'local' ,'Method','individual')
+
+%% Example 2: multiple plots plot, all based on dataset2 (hdf5)
+% for individual data-sets, use an appropriate array
+
+fig(2) = figure;
+plot(x,y,'-b');
+box off; hold on;
+plot(x1,y1,'--k');
+set(gca, 'TickDir', 'out', 'YLim', [0,4]);
+
+% tag both plots 
+[fig, IDs] = PlotID.TagPlot(fig,'ProjectID', ProjectID);
+
+% data locations
+path.script = mfilename('fullpath'); % filename of the m.script
+% file names of the datasets
+path.rdata =  {dataset2} ; % don't forget the extension
+
+% publsihing via a for-loop
+for i=1: numel(fig)
+    PlotID.Publish(path, IDs{i}, fig(i), 'Location', 'local',...
+        'Method','individual');
+end
 
 %% Second Plot with identical data to test centralized method
-% 
+% A central data folder is used for saving the research data files, the
+% subfolders contain linked hdf5-files (if hdf5 is used). This is
+% recommended, if many plots are made from the same data set.  Attention,
+% the linked HDF5 will not work when a subfolder was moved or the data
+% folder was deleted
 
 fig2 =figure;
 plot(x,y,'-k');
 hold on
 plot(x1,y1,'-r');
 
-[fig2, ID] = TagPlot(fig2, ProjectID);
+[fig2, ID] = PlotID.TagPlot(fig2,'ProjectID', ProjectID);
 
-Publish(path, ID, fig2, 'Location', 'local','Method','centraliced')
\ No newline at end of file
+PlotID.Publish(path, ID, fig2, 'Location', 'local','Method','centralized')
diff --git a/fcn_core/Publish.m b/fcn_core/Publish.m
deleted file mode 100644
index e6952d7..0000000
--- a/fcn_core/Publish.m
+++ /dev/null
@@ -1,104 +0,0 @@
-function Publish(DataPaths, ID, figures, options)
-%Publishes Saves Plot, Data and Measuring script 
-%   Detailed explanation goes here
-%   Location sets the storage location. local is in the current folder (an
-%   export folder will be created), server is a remote Path
-%   two Methods are implemented individual stores the data for each plot
-%   while centralized uses a data folder and uses reference links to the
-%   original data
-
-arguments
-   DataPaths
-   ID (1,:) {mustBeNonzeroLengthText} % ID must be provided
-   figures (1,:) {mustBeFigure} % Checks if Figures are figures
-   options.Location {mustBeMember(options.Location ,['local','server','CI-Test'])} = 'local' % storage path
-   options.Method {mustBeMember(options.Method ,['individual','centraliced'])} = 'individual'
-   options.CopyUserFCN (1,1) {mustBeNumericOrLogical} = true 
-end
-
-switch options.Location 
-    case 'local'
-         storPath = fullfile(pwd,'export');
-    case 'server'
-        storPath = '\\FST-220\Jans-50GB-SMB\Lemmer';
-    case 'CI-Test'
-        storPath = fullfile(pwd,'CI_files','export');
-end
-folderName = char(ID);
-
-%% Create Data-Directory
-addpath(storPath);
-if mkdir(fullfile(storPath,folderName))
-else
-    error('Directory could not be created - check remote path and permissions');
-end
-
-disp('Publishing started');
-
-%% Create a Copy of the script and User functions(optional)
-createFileCopy({[DataPaths.script,'.m']},folderName,storPath,ID, 'script');
-
-if options.CopyUserFCN
-   [fList,pList] = matlab.codetools.requiredFilesAndProducts(DataPaths.script);
-   % plist contains the required MATLAB Toolboxes, maybe usefull in future
-   fList = fList(~ismember(fList,[DataPaths.script,'.m'])); % rmv script from list
-   fList = removePltIdFiles(fList); % Do not copy files that are part of plot ID
-   if ~isempty(fList)
-       createFileCopy(fList,folderName,storPath,ID,'userFcn');
-   end
-end
-
-%% Research data handeling
-switch options.Method
-    case 'centraliced' % Work in progresss!!!
-        % check if data folder exists
-        if ~isfolder(fullfile(storPath,'data'))
-            mkdir(fullfile(storPath,'data'));
-        end
-        %list all files
-        fList = dir(fullfile(storPath,'data', '**\*.*'));  %get list of files and folders in any subfolder
-        fList = fList(~[fList.isdir]);  %remove folders from list
-        fList = struct2table(fList);
-        
-        % Check if the new plot is based on the original data-set    
-            % copy the data(once)
-        for i=1:numel(DataPaths.rdata)            
-            % check if identical file exists (status = 1)
-            [~, idx] = fileCompare(DataPaths.rdata{i},fList);
-            % create Linked HDF5 files for identical files
-            if any(idx)
-            sourcePath = fList.name{idx}; % If there are multiple copies already, this only picks the last entry
-            if contains(sourcePath,{'.h5','.hdf5'}) % Linking only for HDF5
-                createLinkedHDF5(sourcePath,storPath,ID);
-            end
-            else % no identical file exists
-               createFileCopy(DataPaths.rdata{i},'data',storPath,ID,'dataCentral');
-            end
-        end
-    case 'individual'
-        % Create a copy of the research data    
-        createFileCopy(DataPaths.rdata,folderName,storPath,ID, 'data');
-end
-%% Export the Plots
-try 
-   for i=1:numel(figures)
-       fig = figures(i);
-       PlotName = [ID,'_plot',num2str(i)]; % Der Plotnamen
-       RemotePath = fullfile(storPath ,folderName, PlotName);
-       % Matlab figure
-       savefig(fig,RemotePath);
-       exportgraphics(fig,[RemotePath,'.png'],'Resolution',300);
-       disp([num2str(i),' of ',num2str(numel(figures)),' figures exported']);
-   end
-catch 
-    warning('Plot export was not successful')
-end
-
-disp(['publishing of ', ID , ' done']);
-
-end %function
-
-function tf = mustBeFigure(h)
-%checks if input is a figure object
-  tf = strcmp(get(h, 'type'), 'figure') & isa(h, 'matlab.ui.Figure');
-end
diff --git a/fcn_help/createFileCopy.m b/fcn_help/createFileCopy.m
deleted file mode 100644
index 4bf198e..0000000
--- a/fcn_help/createFileCopy.m
+++ /dev/null
@@ -1,52 +0,0 @@
-function [] = 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
-    disp(['start to copy ', type]);  
-    
-    if ~iscell(filePaths)
-        %fixes Issue if Filepath is a char and not a cell array
-        filePaths = {filePaths};
-    end
-        
-    try        
-        for i = 1:numel(filePaths)
-            FileNameAndLocation = filePaths{i};
-            [~,name,ext] = fileparts(filePaths{i}); % get the extension
-                          
-            switch type
-                case 'data'
-                    sufix = '_data';
-                    newfile = sprintf([ID, sufix, '_' , num2str(i) ,ext]);
-                case 'dataCentral'
-                    %keep original name
-                    newfile = sprintf([name,ext]);
-                case 'script'
-                    sufix = '_script';
-                    newfile = sprintf([ID, sufix ,ext]);
-                case 'userFcn'
-                    %keep original name
-                    newfile = sprintf([name,ext]);
-                otherwise 
-                    error([type,' is not a valid type for createFileCopy'])
-            end %switch 
-            
-            % Write the file
-            RemotePath = fullfile(storPath,folderName, newfile);
-            
-%           Check if remote file already exists
-            count = 0;
-            while isfile(RemotePath) && ismember(type,{'data','dataCentral'})
-                % Add a Sufix number to new file name
-                count = count + 1;
-                [~,name,ext] = fileparts(RemotePath);
-                RemotePath = fullfile(storPath,folderName,...
-                    [name,'_',num2str(count),ext]);
-            end
-            copyfile(FileNameAndLocation,RemotePath);
-        end
-        disp([type, ' sucessfully published']);
-    catch
-        warning([type,' export was not sucessful'])
-   end %try
-end
-
diff --git a/fcn_help/createLinkedHDF5.m b/fcn_help/createLinkedHDF5.m
deleted file mode 100644
index 2738fd1..0000000
--- a/fcn_help/createLinkedHDF5.m
+++ /dev/null
@@ -1,20 +0,0 @@
-function [status] = createLinkedHDF5(SourceFile,TargetPath,ID)
-%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
-
-plist_id = 'H5P_DEFAULT';
-
-% try
-    fid = H5F.create(fullfile(TargetPath,ID,[ID,'_data.h5']));
-    %create External Link to Sourcefile in the Group linkToExternal
-    H5L.create_external(['..\data\',SourceFile],'/',fid, SourceFile ,plist_id,plist_id);
-    H5F.close(fid);
-    status = 1;
-% catch
-%     warning('No linked HDF file was created');
-%     status = 0;
-% end
-
-end
-
diff --git a/fcn_help/fileCompare.m b/fcn_help/fileCompare.m
deleted file mode 100644
index c9007e7..0000000
--- a/fcn_help/fileCompare.m
+++ /dev/null
@@ -1,49 +0,0 @@
-function [status, id] = fileCompare(filename,fileList)
-%fileCompare checks if file1 is (binary) identical to a file in filelist
-% it returns a sttus and the id of the identical file
-% the functions uses the windows system function fc or the unix function
-% diff
-
-if isempty(fileList)
-   % no comparison necessary
-    status =false;
-    id = 0;
-    return
-end
-
-[~,~,ext1] = fileparts(filename); 
-id = zeros(height(fileList),1);
-
-for i=1:height(fileList)
-    [~,~,ext2] = fileparts(fileList.name{i});
-
-    if ~isequal(ext1,ext2)
-        %warning('File extension are not identical');
-        status = false;
-        continue
-    end
-
-    filepath = fullfile(fileList.folder{i},fileList.name{i});
-    if ispc
-        [status,~] = system(['fc ' filename ' ' filepath]);
-        % 0 -> identical, 1 -> not identical
-         status = ~status; % false (not identical), true(identical)
-                   
-    elseif isunix %untested!
-        [status,~] = system(['diff ' filename ' ' filepath]);
-    else
-        warning('Platform not supported')
-    end
-    
-    if status == 1        
-        id(i) = 1;
-    else 
-        % Status can also be any other number e.g. 2 
-        id(i) = 0;
-    end
-    
-    id =logical(id); %bugfix
-end
-
-end
-
-- 
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