Add LinkReplace Feature

+PlotID/replaceLinkedHDF5.m

+function replaceLinkedHDF5(linkedFilepath)
+% replaceLinkedHDF5 replaces the HDF5, that contains only a link to another
+% HDF5 File with a file containing the actual Data, thus turning it into an
+% independent data file. It essentially turns the plotID option
+% 'centralized' into 'individual'.
+%   Filepath is the location of the File that contains the link. The
+%   filepath to the linked data has to be present in the file itself.
+
+
+
+%% Check whether the only Objects present are links
+h5inf = h5info(linkedFilepath);
+
+% default behaviour dont overwrite
+overwrite = false;
+
+if isempty([h5inf.Groups, h5inf.Datasets, h5inf.Datatypes, h5inf.Attributes]) && ...
+      all(size(h5inf.Links) == [1 1])  
+    % There are no other known objects present and
+    % there is only one linked file
+       overwrite = true;
+end
+
+%% Create Copies of files
+for i = 1:size(h5inf.Links, 2)
+    % This is the file with full data  
+    linkTargetPath = h5inf.Links(i).Value{1,1}; 
+    % This is the empty file
+    % TODO filename decision
+    linkSourcePath = strcat(linkedFilepath,'_',num2str(i)); 
+
+    % Create an absolute path from the relative linking path
+    absoluteTP = regexp(linkSourcePath, filesep, 'split');
+    TargetPathSplit = regexp(linkTargetPath, filesep, 'split');
+    % How many levels do we need to go up in the relative path
+    % This is merely counting the occurances of '..' within the path, but
+    % should not cause issues if the realtive path was created by the
+    % linking process
+    levelsUp = sum(contains(TargetPathSplit,'..'));
+    absoluteTP = absoluteTP(1:(end-(1+levelsUp)) ); %Remove filename + levels
+    linkTargetPath = strjoin([absoluteTP, TargetPathSplit(~contains(TargetPathSplit,'..'))],filesep);
+    
+    if ~isfile(linkTargetPath)
+        warning(strcat("Link destination """,linkTargetPath,""" does not exist or relative path does not fit, no copy created"))
+    end
+    
+    if overwrite % can only be for i=1, and size = 1
+    linkSourcePath = linkedFilepath;
+    end
+    disp('Copying file from ', linkSourcePath, ' to ', linkTargetPath)
+    copyfile(linkTargetPath,linkSourcePath);
+    
+end
+        
+        
+    
+end
+
+
+
+