Move code of the centralized method into an function

Reasons: Clearness, eliminate unwanted dependencies, improve readability

ID is also stored in dataObj so no need to pass it individually

+PlotID/@dataPath/dataPath.m

@@ -6,7 +6,8 @@ classdef dataPath < handle
     properties (SetAccess = protected)
         DataPaths (1,:) cell % dataPaths
         tmpPath  % path to TMP files 
-        ID %ID
+        ID %PlotID
+        dataFolderName = 'data' %name for the data folder when using centralized
     end
     
     methods

+PlotID/Publish.m

@@ -167,58 +167,8 @@ end
 %% Research data handling
 switch options.Method
     case 'centralized' 
-        DataFolderName = 'data';
-        warning(['Linked HDF5 can only be moved with their ',...
-            'respective master files in the ', DataFolderName, ' folder.']);
-        % check if data folder exists
-        if ~isfolder(fullfile(storPath,DataFolderName))
-            mkdir(fullfile(storPath,DataFolderName));
-        end
-        % to get relative Paths
-        currentPath = fullfile(storPath);
+        [status, msg] = PlotID.centralized(storPath, dataObj, folderName);
         
-        %list all files
-        fList = dir(fullfile(storPath,DataFolderName, ['**',filesep,'*.*']));
-        %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(dataObj.DataPaths)            
-            % check if identical file exists (status = 1)
-            [~, idx] = PlotID.fileCompare(dataObj.DataPaths{i},fList);
-            % create Linked HDF5 files for identical files
-            if any(idx)
-                fList.path = fullfile(fList.folder,fList.name);
-                sourcePath = fList{idx,'path'};
-                if ~iscell(sourcePath)
-                    sourcePath = {sourcePath};
-                end
-                relativeSourcePath = strrep(sourcePath,currentPath,'');
-                                
-                if contains(sourcePath,{'.h5','.hdf5'}) % Linking only for HDF5
-                    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, status, msg] = PlotID.createFileCopy(dataObj.DataPaths{i},'data',storPath,ID,'dataCentral');
-                pathToData = strrep(dataPath,currentPath,'');
-                %WIP
-                if contains(dataObj.DataPaths{i},{'.h5','.hdf5'}) % Linking only for HDF5
-                   % and create also linked files in the plot folder 
-                   linkedHDFPath = fullfile(storPath,folderName);
-                   [status] = PlotID.createLinkedHDF5(pathToData,linkedHDFPath);
-                end  %if
-            end %if
-            % add do not move message
-            doNotMove = ['do not move this folder without the ',...
-                DataFolderName, ' folder'];
-            fid = fopen(fullfile(storPath,folderName,[doNotMove,'.txt']),'w');
-            fprintf(fid,doNotMove); fclose(fid);
-        end %for
-        clear DataFolderName doNotmove
     case 'individual'
         % Create a copy of the research data    
         [~, status, msg] = PlotID.createFileCopy(dataObj.DataPaths,folderName,storPath,ID, 'data');

+PlotID/centralized.m

+function [status, msg] = centralized(storPath, dataObj, folderName)
+%centralized stores the research files in a centrelized folder. Linked
+%files are created for subsequent folders (HDF5 only).
+msg = '';
+warning(['Linked HDF5 can only be moved with their ',...
+    'respective master files in the ', dataObj.dataFolderName, ' folder.']);
+
+% check if data folder exists
+if ~isfolder(fullfile(storPath,dataObj.dataFolderName))
+    mkdir(fullfile(storPath,dataObj.dataFolderName));
+end
+% to get relative Paths
+currentPath = fullfile(storPath);
+
+%list all files
+fList = dir(fullfile(storPath,dataObj.dataFolderName, ['**',filesep,'*.*']));
+%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(dataObj.DataPaths)            
+    % check if identical file exists (status = 1)
+    [~, idx] = PlotID.fileCompare(dataObj.DataPaths{i},fList);
+    % create l inked HDF5 files for identical files
+    if any(idx)
+        fList.path = fullfile(fList.folder,fList.name);
+        sourcePath = fList{idx,'path'};
+        if ~iscell(sourcePath)
+            sourcePath = {sourcePath};
+        end
+        relativeSourcePath = strrep(sourcePath,currentPath,'');
+                        
+        if contains(sourcePath,{'.h5','.hdf5'}) % Linking only for HDF5
+            linkedHDFPath = fullfile(storPath,folderName);
+           [status] = PlotID.createLinkedHDF5(relativeSourcePath{1,1},linkedHDFPath);
+        end
+    else % no identical file exists
+        %Copy the file in data and create the links (if hdf5)
+        [dataPath, status, msg] = PlotID.createFileCopy(dataObj.DataPaths{i},...
+            'data',storPath,dataObj.ID,'dataCentral');
+        pathToData = strrep(dataPath,currentPath,'');
+        
+        if ~status
+           return; % an error orccured
+        end
+
+        %WIP
+        if contains(dataObj.DataPaths{i},{'.h5','.hdf5'}) % Linking only for HDF5
+           % and create also linked files in the plot folder 
+           linkedHDFPath = fullfile(storPath,folderName);
+           [status] = PlotID.createLinkedHDF5(pathToData,linkedHDFPath);
+        else
+            warning(['You use the centralized method for non hdf files,',...
+                newline, 'Your research files are located in the ',...
+                DataFolederName , 'folder.']);
+            status = true;
+        end  %if
+    end %if
+    % add do not move message
+    doNotMove = ['do not move this folder without the ',...
+        dataObj.dataFolderName, ' folder'];
+    fid = fopen(fullfile(storPath,folderName,[doNotMove,'.txt']),'w');
+    fprintf(fid,doNotMove); fclose(fid);
+end %for
+
+end
\ No newline at end of file

CHANGELOG.md

-# V0.3
+# V1.0 RC1
 - Add changelog 
 - Add support for file or function name as scriptPath 
 - Add support for  passing Variables in publish
+- Move centralized method in fuction
+- Improve usability
+- Improve documentation

Examples/PlotID_centralized.m

@@ -22,4 +22,12 @@ fig2 = figure;
 plot(x.^2,y,'-r'); 
 [fig2, ID] = PlotID.TagPlot(fig2);
 
-PlotID.Publish(datapath,scriptPath, fig2, 'Method','centralized')
\ No newline at end of file
+PlotID.Publish(datapath,scriptPath, fig2, 'Method','centralized')
+
+%% Note:
+% If you rerun this script PlotId will tell you that a identical named (but
+% not binary idetical) file exists in the data folder. This is intended,
+% due protect the user from overwritting non (binary) identical files. The
+% reason for this is that two hdf files with the same data are not idetical
+% when recreated (see line 11). Usually you would use an existing file
+% without changing it.
\ No newline at end of file