Closes #12 and prepare User function export

example.m

@@ -41,19 +41,22 @@ hold on
 %fig(2) =figure;
 plot(x1,y1,'-r');
 set(gca, 'TickDir', 'out', 'YLim', [0,4]);
-
-% Tag the plot
+%% Tag the plot
 [figs, ID] = TagPlot(fig, ProjectID);
 
+%% call dummy function
+% a=1;
+% a = test_2(a);
+
 %% publishing
 
 % The functions needs the file location, the location of the data and the
 % figure
-path.script = mfilename('fullpath') % filename of the m.script
+path.script = mfilename('fullpath'); % filename of the m.script
 
 % file name of the data (should be extended to handle arrays)
 path.rdata =  {dataset1,dataset2} ; % don't forget the extension
 
 
-Publish(path, ID, figs, 'Location', 'local','Method','individual')
+Publish(path, ID, figs, 'Location', 'local','Method','individual','CopyUserFCN',true)
 

fcn_core/Publish.m

@@ -13,6 +13,7 @@ arguments
    figures (1,:) {mustBeFigure} % Checks if Figures are figures
    options.Location {mustBeMember(options.Location ,['local','server'])} = 'local' % storage path
    options.Method {mustBeMember(options.Method ,['individual','centraliced'])} = 'individual'
+   options.CopyUserFCN (1,1) {mustBeNumericOrLogical} = 'false' % should be true in realease !
 end
 
 switch options.Location 
@@ -32,20 +33,15 @@ end
 
 disp('Publishing started');
 
-%% Create a Copy of the script
+%% Create a Copy of the script and User functions
+createFileCopy({[DataPaths.script,'.m']},folderName,storPath,ID, 'script');
 
-try
-    %FileNameAndLocation=['C:\Users\Lemmer\Documents\GitLab\plot_identifier\MATLAB\test'];
-    FileNameAndLocation= DataPaths.script;
-    newbackup=sprintf([ID,'_script.m']);
-    currentfile=strcat(FileNameAndLocation, '.m');
-    % Write a Copy of the Plotting Script 
-    RemotePath = fullfile(storPath,folderName, newbackup);
-    copyfile(currentfile,RemotePath);
-    disp('Script sucessfully published');
-catch
-   warning('Script export was not sucessful')
+if options.CopyUserFCN
+   [fList,pList] = matlab.codetools.requiredFilesAndProducts(DataPaths.script);
+   fList = fList(~ismember(fList,[DataPaths.script,'.m'])); % rmv script from list
+   fList = removePltIdFiles(fList); % Do not copy files that are part of plot ID
 end
+
 %% Research data handeling
 switch options.Method
     case 'centraliced' % Work in progresss!!!
@@ -55,14 +51,16 @@ switch options.Method
         end
         % Check if the new plot is based on the original data-set    
             % copy the data(once)
-            createFileCopy(DataPaths.rdata,'data',storPath,ID);
-        % create a linked (soft) copy
-            
-        
-               
+        for i=1:numel(DataPaths.rdata)
+            if fileCompare(filename1,filename2) % identical file exists
+               createLinkedHDF5(SourceFile,storPath,ID)
+            else % no identical file exists
+               createFileCopy(DataPaths.rdata{i},'data',storPath,ID,'data');
+            end
+        end
     case 'individual'
         % Create a copy of the research data    
-        createFileCopy(DataPaths.rdata,folderName,storPath,ID);
+        createFileCopy(DataPaths.rdata,folderName,storPath,ID, 'data');
 end
 %% Export the Plots
 %try 
@@ -83,23 +81,35 @@ disp(['Publishing of ', ID , ' done']);
 
 end %function
 
-function [] = createFileCopy(filePaths,folderName,storPath,ID)
+function [] = createFileCopy(filePaths,folderName,storPath,ID,type)
 % Creates a copy of the files (can used for multiple paths in a cell array)
 % folderName is the name of the exporting folder
-    disp('Start to copy research data ...');   
+    disp(['Start to copy ', type]);  
+    
+    switch type
+        case 'data'
+            sufix = '_data';
+        case 'script'
+            sufix = '_script';
+        case 'userFcn'
+            sufix = '';
+        otherwise 
+            error([type,' is not a valid type for createFileCopy'])
+    end %switch 
+            
     try        
         for i = 1:numel(filePaths)
             FileNameAndLocation = filePaths{i};
             [~,~,ext] = fileparts(filePaths{i}); % get the extension
-            newbackup = sprintf([ID,'_data',ext]);
+            newbackup = sprintf([ID, sufix ,ext]);
 
             % Write the copied file
             RemotePath = fullfile(storPath,folderName, newbackup);
             copyfile(FileNameAndLocation,RemotePath);
         end
-        disp('Research data sucessfully published');
+        disp([type, ' sucessfully published']);
     catch
-        warning('Research data export was not sucessful')
+        warning([type,' export was not sucessful'])
    end %try
 end
 

fcn_help/FileCompare.m

 function [status] = fileCompare(filename1,filename2)
-%UNTITLED2 Summary of this function goes here
-%   Detailed explanation goes here
+%fileCompare checks if file1 is (binary) identical to file 2
+% the functions uses the windows system function fc or the unix function
+% diff
 
 [~,~,ext1] = fileparts(filename1); 
 [~,~,ext2] = fileparts(filename2);
 
 if ~isequal(ext1,ext2)
-    warning('File extension are not identical');
+    %warning('File extension are not identical');
     status = false;
     return
 end
 
 if ispc
-    filename2 = 'export\JL01-60DB3572\JL01-60DB3572_data.h5';
-    filename1 = 'export\JL01-60DB3576\JL01-60DB3576_data.h5';
     [status,result] = system(['fc ' filename1 ' ' filename2]);
 
 elseif isunix %untested!
-    filename2 = 'export/JL01-60DB3572/JL01-60DB3572_data.h5';
-    filename1 = 'export/JL01-60DB3576/JL01-60DB3576_data.h5';
     [status,result] = system(['diff ' filename1 ' ' filename2]);
 else
     warning('Platform not supported')

fcn_help/createLinkedHDF5.m

@@ -6,15 +6,15 @@ plist_id = 'H5P_DEFAULT';
 
 % Work in Progress... Problem mit dem Pfad...
 
-try
+%try
     fid = H5F.create(fullfile(TargetPath,[ID,'_data.h5']));
     %create External Link to Sourcefile in the Group linkToExternal
-    H5L.create_external(SourceFile,'/',fid,'linkToExternal',plist_id,plist_id);
+    H5L.create_external(SourceFile,'/',fid, SourceFile ,plist_id,plist_id);
     H5F.close(fid);
     status = 1;
-catch
-    warning('No linked HDF file was created');
-    status = 0;
-end
+% catch
+%     warning('No linked HDF file was created');
+%     status = 0;
+% end
 end
 

fcn_help/removePltIdFiles.m

+function [fListClean] = removePltIdFiles(fList)
+%removePltIdFiles removes functions that are part of PlotID out of flist
+%   Detailed explanation goes here
+%addpath('..\fcn_core');
+
+[~,names,ext] = fileparts(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.ext(:)] = fileparts(PltID_flist.name(:)); % add ext column
+
+PltID_flist = PltID_flist(strcmp(PltID_flist.ext,'.m'),:);
+
+% Comparison and filter
+fListClean = fList(~ismember(names,PltID_flist.name));
+
+end
+