Merge branch...

Merge branch '49-moglichkeit-datenvariablen-zu-ubergeben-anstelle-von-dateipfaden' into 'development'

Resolve "Möglichkeit Datenvariablen zu übergeben anstelle von Dateipfaden"

See merge request !51

+PlotID/@dataPath/dataPath.m

+classdef dataPath < handle
+    %DATAPATH stores the datapaths to the research data
+    %   usage of a class is neccessary to support variables, argument
+    %   validation and storing variables as tempory files
+    
+    properties (SetAccess = protected)
+        DataPaths (1,:) cell % dataPaths
+        tmpPath  % path to TMP files 
+        ID %ID
+    end
+    
+    methods
+        function obj = dataPath(inputPaths,ID)
+            %DATAPATH Construct an instance of this class
+            %   start with argument validation
+            obj.ID = ID;
+            %catch non cell inputs in inputPaths 
+            if ~iscell(inputPaths)
+                  inputPaths = {inputPaths}; %Cell array
+            end
+            
+            isStruct = false([1,numel(inputPaths)]);
+            % strings will cause problems, therefore chars are used 
+            for i=1:numel(inputPaths)
+                if isstring(inputPaths{i})
+                   inputPaths{i} = char(inputPaths{i});
+                end
+                % check for Variable inputs           
+                if isstruct(inputPaths{i})
+                    isStruct(i) = true;
+                elseif ~ischar(inputPaths{i})
+                    obj.throwError(); 
+                end
+            end
+                        
+            obj.DataPaths = inputPaths;
+            % create temporary file from all Variables
+            if any(isStruct)
+               obj.vars2file(isStruct); 
+            end
+
+            % final check if all paths are valid
+            mustBeDataPath(obj);
+        end
+
+         function mustBeDataPath(obj)
+            if ~isempty(obj.DataPaths)
+                %checks if input is a valid DataPath object
+                  tf = ~isfile(obj.DataPaths);
+                  if any(tf)
+                     dataPath.throwError();
+                  end
+            end
+        end 
+              
+        
+        function cleanTmpFile(obj)
+            if ~isempty(obj.tmpPath)
+                delete(obj.tmpPath); 
+            end
+        end
+
+        %% non local functions
+        vars2file(obj,isvar);
+    end
+    methods (Static)
+        function throwError()
+        %THROWERROR throws an error Dialog for invalid Data
+          eidType = 'mustBeDataPath:notaValidFilePath';
+          msgType = 'DataPaths must contain file-path(s) or Variables';
+          throwAsCaller(MException(eidType,msgType))
+        end 
+    end %static
+end %class
+

+PlotID/@dataPath/vars2file.m

+function obj = vars2file(obj,isStruct)
+%vars2file creates a temporary file for all variables in inputPaths
+% the number of inputPaths is reduced by the number of variables
+
+tmpEnv= getenv('TMP');
+tmpDir = fullfile(tmpEnv,'PlotID');
+if ~isfolder(tmpDir)
+    mkdir(tmpDir);
+end
+obj.tmpPath = fullfile(tmpDir,[obj.ID,'_vars.mat']); 
+
+% save only the first struct (intended) 
+struct = obj.DataPaths{isStruct};
+save(obj.tmpPath,'-struct','struct');
+
+% remove variable from Datapath
+obj.DataPaths(isStruct) = [];
+% add tmppath as Datapath
+
+obj.DataPaths{end+1} = obj.tmpPath;
+
+end
+

+PlotID/Publish.m

@@ -2,20 +2,21 @@ function Publish(DataPaths,scriptPath, figure, options)
 %%Publish(DataPaths,scriptPath, ID, figure, options) saves plot, data and measuring script 
 %
 %   DataPaths contains the path(s) to the research data, for multiple files
-%   use a cell array
+%   use a cell array or ONE struct of variables (only the first struct will
+%   be exported)
 %   scriptPath contains the path to the script, this can be provided with
 %   the simple call of scriptPath = [mfilename('fullpath'),'.m']
 %
 %   Options:
 %   Location sets the storage location. 'local' sets the storage location
 %   to the current folder (an export folder will be created), 'manual' opens
-%   a explorer window, where you can choose the folder. If you define a export
-%   path in the config file, this will used per defaul (exportPath).
+%   an explorer window, where you can choose the folder. If you define a export
+%   path in the config file, this will used per default (exportPath).
 %   remote path, that is defined in the config file.
 %   Two Methods are implemented 'individual' stores the data for
 %   each plot while 'centralized' uses a data folder and uses reference links
 %   to the original data (hdf5 only).
-%   'ParentFolder' is the folder Name where the exported data is stored if an
+%   'ParentFolder' is the folder name where the exported data is stored if an
 %   path is used, PlotId will use this path as storagePath
 %   'ConfigFileName' is needed for handling multiple config files (see example)
 %   'CSV' turns a summary table of all exports on or off 
@@ -26,7 +27,7 @@ function Publish(DataPaths,scriptPath, figure, options)
 %   'ForcePublish' will publish even if one step was not successful (not recommended) 
 
 arguments
-   DataPaths {mustBeDataPath} % location of the data-file(s)
+   DataPaths % location of the data-file(s) and/or ONE struct of variables
    scriptPath (1,:) {mustBeText} % location of the matlab script
    figure (1,:) {mustBeFigure} % Checks if figure is a figure object
    options.Location {mustBeMember(options.Location ,{'local','exportPath','manual','CI-Test'})} = 'local' % storage path
@@ -37,22 +38,10 @@ arguments
    options.CSV (1,1) {mustBeNumericOrLogical} = true
    options.ShowMessages(1,1) {mustBeNumericOrLogical} = false 
    options.ForcePublish (1,1) {mustBeNumericOrLogical} = false %publish anyway
-   
 end
 
 %% argument validation 
-%catch string and non cell inputs in DataPaths 
-if ~iscell(DataPaths)
-      DataPaths = {DataPaths}; %Cell array
-end
-
 % strings will cause problems, therefore chars are used 
-for i=1:numel(DataPaths)
-    if isstring(DataPaths{i})
-       DataPaths{i} = char(DataPaths{i});
-    end
-end
-
 if isstring(scriptPath)
    scriptPath = char(scriptPath);
 end
@@ -95,6 +84,9 @@ if isempty(ID)
    warning(msg);
 end
 
+%% Create a Datapath object from Input
+dataObj = PlotID.dataPath(DataPaths,ID);
+
 %% read config file
 % there is only one config Object (handleClass)
 configObj = PlotID.config(options.ConfigFileName);
@@ -124,7 +116,7 @@ switch options.Location
         if isfolder(configObj.exportPath)
            storPath = configObj.exportPath;
         else
-           msg = ['Your Export folder ', storPath, newline,...
+           msg = ['Your Export folder ', configObj.exportPath, newline,...
                 'does not exist, check the config file - publishing  not possible!'];         
            dlgObj.error(msg);
         end
@@ -197,9 +189,9 @@ switch options.Method
                 
         % Check if the new plot is based on the original data-set    
             % copy the data(once)
-        for i=1:numel(DataPaths)            
+        for i=1:numel(dataObj.DataPaths)            
             % check if identical file exists (status = 1)
-            [~, idx] = PlotID.fileCompare(DataPaths{i},fList);
+            [~, idx] = PlotID.fileCompare(dataObj.DataPaths{i},fList);
             % create Linked HDF5 files for identical files
             if any(idx)
                 fList.path = fullfile(fList.folder,fList.name);
@@ -215,10 +207,10 @@ switch options.Method
                 end
             else % no identical file exists
                 %Copy the file in data and create the links (if hdf5)
-                [dataPath, status, msg] = PlotID.createFileCopy(DataPaths{i},'data',storPath,ID,'dataCentral');
+                [dataPath, status, msg] = PlotID.createFileCopy(dataObj.DataPaths{i},'data',storPath,ID,'dataCentral');
                 pathToData = strrep(dataPath,currentPath,'');
                 %WIP
-                if contains(DataPaths{i},{'.h5','.hdf5'}) % Linking only for HDF5
+                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);
@@ -228,7 +220,7 @@ switch options.Method
         clear DataFolderName 
     case 'individual'
         % Create a copy of the research data    
-        [~, status, msg] = PlotID.createFileCopy(DataPaths,folderName,storPath,ID, 'data');
+        [~, status, msg] = PlotID.createFileCopy(dataObj.DataPaths,folderName,storPath,ID, 'data');
 end
 %temporary:
 dlgObj.rdFilesPublished = status;
@@ -282,11 +274,13 @@ if dlgObj.success || options.ForcePublish
     end
     status = movefile(oldPath,newPath); %rename directory
 end
+% delete tmp data
+dataObj.cleanTmpFile();
 
 %% CSV export
 if options.CSV
   T = table();
-  T.research_Data = DataPaths'; T.PlotID(:) = {ID};
+  T.research_Data = dataObj.DataPaths'; T.PlotID(:) = {ID};
   T.Author(:) = {configObj.configData.Author};
   T.Script_Name(:) = {scriptPath};
   T.Storage_Location(:) = {newPath};
@@ -310,21 +304,5 @@ function tf = mustBeFigure(h)
   tf = strcmp(get(h, 'type'), 'figure') & isa(h, 'matlab.ui.Figure');  
 end
 
-function mustBeDataPath(DataPaths)
-%checks if input is a valid DataPath object
-  if ~iscell(DataPaths)
-      DataPaths = {DataPaths};
-  end
-  tf = zeros(1,numel(DataPaths)); 
-  
-  for i=1:numel(DataPaths) 
-    tf(i) = ~isfile(DataPaths{i});
-  end
-  
-  if any(tf)
-     eidType = 'mustBeDataPath:notaValidFilePath';
-     msgType = 'DataPaths must contain file-path(s)';
-     throwAsCaller(MException(eidType,msgType))
-  end
-end
+
 

+PlotID/createFileCopy.m

@@ -8,7 +8,7 @@ if ~iscell(filePaths)
     filePaths = {filePaths};
 end
         
-try 
+%try 
     storagePaths = cell(numel(filePaths,1));
     for i = 1:numel(filePaths)
         FileNameAndLocation = filePaths{i};
@@ -70,12 +70,12 @@ try
     end
     status = true;
     msg =([type, ' successfully published']);
-catch
-    status = false;
-    warning([type,' export was not successful'])
-    if exist('errorMSG')
-        error(errorMSG);
-    end 
-end %try
+% catch
+%     status = false;
+%     warning([type,' export was not successful'])
+%     if exist('errorMSG')
+%         error(errorMSG);
+%     end 
+% end %try
 end %function
 

CHANGELOG.md

 # V0.3
 - Add changelog 
 - Add support for file or function name as scriptPath 
+- Add support for  passing Variables in publish

CI_files/CI_config.json

+{
+  "Author": "CI-Test",
+  "ProjectID": "CI-001"
+}
\ No newline at end of file

Examples/PlotID_variables.m

+clear; clc; close all;
+%% Example Script - How to pass Variables
+% This script how to pass variables instead or additional to the DataPaths
+
+%% Data (only necessary for this example)
+[x, y, datapath] = createExampleData('matlab');
+scriptPath = mfilename('fullpath');
+
+%% Plotting
+% This is still part of a normal script to produce plots.
+% Make sure to save each figure in a variable to pass it to PlotID-functions.
+fig1 = figure;
+plot(x,y,'-k'); box off; set(gca, 'TickDir', 'out', 'YLim', [0,4]);
+[fig1, ID] = PlotID.TagPlot(fig1);
+
+%%  ----  2. Publishing -----
+% You can pass an abitrary number of variables to Publish.
+% IMPORTANT: they must be collected and passed in ONE struct
+% if multiple structs are passed, only the first one will be stored!
+% You can additionally add datapaths and combine the methods.
+% Passing multiple structs
+
+%Example: Passing the variables x,y to publish
+
+s.x =x; s.y=y; % Save both variables in struct s
+
+% Build the locations cell with the struct and one path
+locations =  {s,'test_data.mat'}; 
+
+%call publish
+PlotID.Publish(locations,scriptPath, fig1)
+
+% Your plot, script, the variables x,y and the path that your provided
+% are now published.

PlotID_example.m

@@ -68,6 +68,7 @@ PlotID.Publish(locations,scriptPath, fig2)
 % ---------------------------------
 %% Further examples and help
 % You find more examples in the Examples folder:
+%   - Passing Variables 
 %   - Advanced usage 
 %   - Working with HDF5-files
 %   - Using a central data folder

README.md

@@ -29,8 +29,10 @@ The **ProjectID** is your custom project number, it well be the prefix of the ID
 `PlotID.Publish(DataPaths,scriptPath,  figure, options)`
 
 `scriptPath` contains either the path to the script, this can be provided with the simple call of `scriptPath = [mfilename('fullpath'),'.m']` or the script or function name that is used for creating your plot. \
-`DataPaths` contains the path(s) to the research data, for multiple files you can use a cell array (they must be at the path). \
+`DataPaths` contains the path(s) to the research data, for multiple files you can use a cell array (they must be at the path). It is also possible to pass an arbitrary number of variables. All variables **must be** passed in **one** struct. \
 `figure` is the figure that should be published.
+
+**Please take also a look on the examples provided in the Example folder**.
  
 
 # PlotID.TagPlot()
@@ -72,7 +74,9 @@ FriendlyID Changes the Hex Number to a human friendly *datetime* and *dateStr*.
 # PlotID.Publish() 
 `Publish(DataPaths,scriptPath, figure, options)` \
 Publishes saves plot, data and measuring script 
-Location sets the storage location. 'local' sets the storage location  to the current folder (an export folder will be created), 'server' is a remote path, that is defined in the config file. Two Methods are implemented 'individual' stores the data for each plot while 'centralized' uses a data folder and uses reference links to the original data (hdf5 only). ParentFolder is the folder Name where the exported data is stored if a path is used, PlotId will use this path a storagePath
+Location sets the storage location. 'local' sets the storage location to the current folder (an export folder will be created), 'manual' opens an explorer window, where you can choose the desired folder. If you define a export path in the config file, this will used per default (exportPath).
+
+Two Methods are implemented 'individual' stores the data for each plot while 'centralized' uses a data folder and uses reference links to the original data (hdf5 only). ParentFolder is the folder name where the exported data is stored if a path is used, PlotId will use this path a storagePath.
 
 <details><summary>detailed description</summary>