Add comments, remove some commandline outputs

+PlotID/Publish.m

@@ -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

@@ -2,7 +2,6 @@ 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
@@ -74,6 +73,7 @@ function [storagePaths] = createFileCopy(filePaths,folderName,storPath,ID,type)
     warning([type,' export was not sucessful'])
     if exist('errorMSG')
         error(errorMSG);
-   end %try
     end 
+end %try
+end %function
 

example.m

@@ -3,38 +3,30 @@
 
 %% 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 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 filepath & name
 dataset2 = 'testdata2.h5';
@@ -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');