Add comments, remove some commandline outputs

+PlotID/Publish.m

@@ -17,7 +17,7 @@ arguments
    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 
+   options.CSV (1,1) {mustBeNumericOrLogical} = false
 end
 
 %catch multiple figures in fig
@@ -29,7 +29,7 @@ if numel(figure) > 1
     warning(msg);
 end
 
-%read config file
+%% read config file
 try 
    txt = fileread('config.json');
    config = jsondecode(txt);
@@ -41,6 +41,7 @@ catch
    configError = true;
 end
 
+%% storage location
 switch options.Location 
     case 'local'
         if contains(options.ParentFolder, {'/','\'})
@@ -66,7 +67,7 @@ elseif mkdir(fullfile(storPath,folderName))
 else
     error('Directory could not be created - check remote path and permissions');
 end
-disp('Publishing started');
+disp(['publishing of ', ID, ' started']);
 
 %% Create a Copy of the script, config and user functions(optional)
 % script

+PlotID/createFileCopy.m

@@ -2,78 +2,78 @@ function [storagePaths] = 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
-    disp(['start to copy ', type]);  
     
-    if ~iscell(filePaths)
-        %fixes Issue if Filepath is a char and not a cell array
-        filePaths = {filePaths};
-    end
+if ~iscell(filePaths)
+    %fixes Issue if Filepath is a char and not a cell array
+    filePaths = {filePaths};
+end
         
-    try 
-        storagePaths = cell(numel(filePaths,1));
-        for i = 1:numel(filePaths)
-            FileNameAndLocation = filePaths{i};
-            [~,name,ext] = fileparts(filePaths{i}); % get the extension
-                          
-            switch type
-                case 'data'                    
-                      newfile = sprintf([name,ext]); %keep original name
-                      %old behaviour
-                      %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 
-            
-            RemotePath = fullfile(storPath,folderName, newfile);
-                        
+try 
+    storagePaths = cell(numel(filePaths,1));
+    for i = 1:numel(filePaths)
+        FileNameAndLocation = filePaths{i};
+        [~,name,ext] = fileparts(filePaths{i}); % get the extension
+
+        switch type
+            case 'data'                    
+                  newfile = sprintf([name,ext]); %keep original name
+                  %old behaviour
+                  %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 
+
+        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
-                % TODO add more inteligent way then a simple sufix
-                count = count + 1;
-                [~,name,ext] = fileparts(RemotePath);
-                if count < 2
-                    RemotePath = fullfile(storPath,folderName,...
-                        [name,'_',num2str(count),ext]);
-                else 
-                    RemotePath = fullfile(storPath,folderName,...
-                    [name(1:end-length(num2str(count))),num2str(count),ext]);
-                end
-                [~, name, ~] = fileparts(RemotePath);
-                
-                
-                msg = ['Filename ',name,...
-                    ' already exists in the data folder' newline,...
-                    ' PlotID will add an suffix if you continue.' newline,...
-                    ' This can cause serious confusions.'];
-                warning(msg);                
-                m = input('Do you want to continue, Y/N [Y]:','s');
-                
-                if ismember(m,{'N','n'})
-                   errorMSG = ['Filename already exists in data folder.' newline,...
-                       ' Rename the File and restart PlotID.'];
-                   error();
-                end
+        count = 0;
+        while isfile(RemotePath) && ismember(type,{'data','dataCentral'})
+            % Add a Sufix number to new file name
+            % TODO add more inteligent way then a simple sufix
+            count = count + 1;
+            [~,name,ext] = fileparts(RemotePath);
+            if count < 2
+                RemotePath = fullfile(storPath,folderName,...
+                    [name,'_',num2str(count),ext]);
+            else 
+                RemotePath = fullfile(storPath,folderName,...
+                [name(1:end-length(num2str(count))),num2str(count),ext]);
+            end
+            [~, name, ~] = fileparts(RemotePath);
+
+
+            msg = ['Filename ',name,...
+                ' already exists in the data folder' newline,...
+                ' PlotID will add an suffix if you continue.' newline,...
+                ' This can cause serious confusions.'];
+            warning(msg);                
+            m = input('Do you want to continue, Y/N [Y]:','s');
+
+            if ismember(m,{'N','n'})
+               errorMSG = ['Filename already exists in data folder.' newline,...
+                   ' Rename the File and restart PlotID.'];
+               error();
             end
-            copyfile(FileNameAndLocation,RemotePath);
-            storagePaths{i} = RemotePath; 
         end
-        disp([type, ' sucessfully published']);
-    catch
-        warning([type,' export was not sucessful'])
+        copyfile(FileNameAndLocation,RemotePath);
+        storagePaths{i} = RemotePath; 
+    end
+    disp([type, ' sucessfully published']);
+catch
+    warning([type,' export was not sucessful'])
     if exist('errorMSG')
         error(errorMSG);
-   end %try
-end
+    end 
+end %try
+end %function
 

example.m

@@ -3,40 +3,32 @@
 
 %% 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 
 
-% TODO:  decide how projectID and optionally ORCID will be implemented
-% ORCID placed on startup (alternative?) - projectID as persistent
-% otherwise dialogue?
-
 % Leave empty for using the ID from the config file
-ProjectID = 'FST03';
-
+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';
+
 % Use absolute paths for good practise
 dataset1 = fullfile(pwd,dataset1);
 save(dataset1,'x','y');
 
+% some data for the .h5 file
+x1 = linspace(0,2*pi); y1 = sin(x1)+2;
 
-% some data as .h5
-x1 = linspace(0,2*pi);
-y1 = sin(x1)+2;
-
-% define file path & name
+% define filepath & name
 dataset2 = 'testdata2.h5';
 dataset2 = fullfile(pwd,dataset2);
 fpath = dataset2;
@@ -49,14 +41,14 @@ h5write(fpath, "/y1", y1)
 
 %% function calls
 % Place for post-processing of the data, or additional related code.
-a = 1;
 % example_fcn is a dummy function to show the functionality
-a = example_fcn(a); 
-%p = betacdf(0.5,1,1); % to test Toolboxes
+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; hold on;
@@ -73,17 +65,19 @@ set(gca, 'TickDir', 'out', 'YLim', [0,4]);
 
 %% 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
+
+%(defined above:) dataset1 = 'test_data.mat'; dataset2 = 'testdata2.h5'
 path.rdata =  {dataset1,dataset2} ; % don't forget the extension
 
+%call publishing
 PlotID.Publish(path, ID, fig(1), 'Location', 'local' ,'Method','individual')
 
-%% Example 2: multiple plots plot, all based on data-set2 (hdf5)
+%% Example 2: multiple plots plot, all based on dataset2 (hdf5)
 % for individual data-sets, use an appropriate array
 
 fig(2) = figure;
@@ -100,13 +94,18 @@ path.script = mfilename('fullpath'); % filename of the m.script
 % file names of the datasets
 path.rdata =  {dataset2} ; % don't forget the extension
 
-% publsihing via for-loop
+% publsihing via a for-loop
 for i=1: numel(fig)
-    PlotID.Publish(path, IDs{i}, fig(i), 'Location', 'server','Method','individual');
+    PlotID.Publish(path, IDs{i}, fig(i), 'Location', 'local',...
+        'Method','individual');
 end
 
 %% Second Plot with identical data to test centralized method
-% ToDO Add better description
+% 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');