diff --git a/+PlotID/@config/config.m b/+PlotID/@config/config.m
deleted file mode 100644
index e5366246dc0adb85837b6038864a26f72ec6fbd8..0000000000000000000000000000000000000000
--- a/+PlotID/@config/config.m
+++ /dev/null
@@ -1,78 +0,0 @@
-classdef config < handle
- %CONFIG class handles methoths and attributes related to the config
- %file
- % Detailed explanation goes here
- % handle class used for dynamicy property updates
-
- properties (SetAccess = private)
- mandatoryFields = {'Author', 'ProjectID'}
- optionFields
- end
-
- properties (SetAccess = protected)
- configData
- configFileName
- end
-
- methods
- function obj = config(configFileName)
- %CONFIG Construct an instance of this class
- % Detailed explanation goes here
- obj.configFileName = configFileName;
- try
- txt = fileread(obj.configFileName);
- obj.configData = jsondecode(txt);
- assert(checkConfig(obj));
-
- catch
- msg = ['no valid config File with the filename ',...
- obj.configFileName, ' found.' newline,...
- 'Please enter the required information manually'];
- disp(msg);
- obj.configData = obj.wizard('initilise');
- m = input('Do you want to save the config, Y/N [Y]:','s');
- if ismember(m,{'Y','y'})
- obj.writeConfig(fullfile(pwd));
- end
- end%try
-
- end
-
- function outputArg = checkConfig(obj)
- %checkConfig validates the config file
- % 1. Check if mandatory Fields are set
- check = isfield(obj.configData,obj.mandatoryFields);
- outputArg = all(check);
-
- end
-
- function writeConfig(obj,path)
- %writeConfig writes the config file to path
- % TODo;
- fid = fopen(fullfile(path,obj.configFileName),'w');
- txt = jsonencode(obj.configData,'PrettyPrint',true);
- %fprintf does not write paths correctly !!!
- fwrite(fid,txt);
- fclose(fid);
- end
-
- function configData = addPublishOptions(obj,mode)
- %writeConfig writes the config file to path
- % TODo;
- obj.configData.options = obj.plotID_options(mode);
- end
-
- function outputArg = method1(obj,inputArg)
- %METHOD1 Summary of this method goes here
- % Detailed explanation goes here
- outputArg = obj.Property1 + inputArg;
- end
-
- end
-
- methods (Static)
- configStruct = wizard(mode)
- optionStruct = plotID_options(input)
- end
-end
-
diff --git a/+PlotID/@config/plotID_options.m b/+PlotID/@config/plotID_options.m
deleted file mode 100644
index 235f1cb791ef0484873d32a2883aae5daf387406..0000000000000000000000000000000000000000
--- a/+PlotID/@config/plotID_options.m
+++ /dev/null
@@ -1,28 +0,0 @@
-function [options] = plotID_options(input)
-%PLOTID_OPTIONS Summary of this function goes here
-% Detailed explanation goes here
-
-options = struct();
-switch input
- case 'default' %same as Arguments Block
- options.Location = 'local'; % storage path
- options.Method = 'individual';
- options.ParentFolder = 'export';
- options.ConfigFileName = 'config.json';%individual config names possible
- options.CopyUserFCN = true;
- options.CSV = false;
- options.ShowMessages = true;
- options.ForcePublish = false; %publish anyway
- case 'debug'
- options.Location = 'local'; % storage path
- options.Method = 'individual';
- options.ParentFolder = 'export';
- options.ConfigFileName = 'config.json';%individual config names possible
- options.CopyUserFCN = true;
- options.CSV = true;
- options.ShowMessages = true;
- options.ForcePublish = true; %publish anyway
-end
-
-end
-
diff --git a/+PlotID/@config/wizard.m b/+PlotID/@config/wizard.m
deleted file mode 100644
index de66181d95c25c8d3efa4d06e2e693c28f8bdfbc..0000000000000000000000000000000000000000
--- a/+PlotID/@config/wizard.m
+++ /dev/null
@@ -1,39 +0,0 @@
-function config = wizard(mode)
-%wizard creates config files depending on the selected mode
-% initilise ask only for the input that is neccessary to run plotID
-
-config = struct();
-switch mode
- case 'initilise'
- config.Author = inputRequired('your Name');
- config.ProjectID = inputRequired('your Project Number');
-
- msg = ['Do you want to add a remote path?' newline,...
- 'Otherwise your files will be stored locally.' newline,...
- 'You can add this later by rerunning the initilisation.'];
- disp(msg);
- m = input('Do you want add a remothe path, Y/N [Y]:','s');
-
- if ismember(m,{'Y','y'})
- config.ServerPath = uigetdir();
- end
- otherwise
- error('wizard mode undefined in CLASS config');
-end %switch
-
-end
-
-function usrTxt = inputRequired(msg)
-%Input Dialog that repeats if left empty
-inputRequired = true;
-while inputRequired
- prompt = ['Please enter ', msg , ':'];
- inpt = input(prompt,'s');
- if isempty(inpt)
- disp('Input must not be empty!');
- else
- usrTxt = inpt;
- inputRequired = false;
- end
-end
-end
\ No newline at end of file
diff --git a/+PlotID/@userDLG/userDLG.m b/+PlotID/@userDLG/userDLG.m
deleted file mode 100644
index 3ec2b4b9f2af8d2833631b67a52cf9d0f1c1a8a0..0000000000000000000000000000000000000000
--- a/+PlotID/@userDLG/userDLG.m
+++ /dev/null
@@ -1,80 +0,0 @@
-classdef userDLG
- %userDLG the userDLG Class is responsible for the user dialog
- % error handeling, user messages and warnings will be provided from
- % this class, depending on the user options and error type.
- % This reduces messaging overhead and code length in PlotID.Publish()
-
- properties
- configError = false
- scriptPublished = false
- rdFilesPublished = false
- figurePublished = false
- msg = ''
- end
-
- properties (SetAccess = protected)
- success = false
- showMessages {mustBeNumericOrLogical}
- forcePublish {mustBeNumericOrLogical}
- ID %plotID
- end
-
- methods
- function obj = userDLG(ID,options)
- %CATCHERROR Construct an instance of this class
- if isempty(ID)
- ID = '';
- end
- obj.ID = ID;
- obj.showMessages = options.ShowMessages;
- obj.forcePublish = options.ForcePublish;
- end
-
- function output = get.success(obj)
- % checks if all publish operations are true
- obj.success = all([obj.scriptPublished; obj.rdFilesPublished;...
- obj.figurePublished]);
- output = obj.success;
- end
-
- function obj = set.msg(obj,message)
- %setmsg Summary of this method goes here
- % Detailed explanation goes here
- obj.msg = message;
- end
-
- function [] = userMSG(obj,message)
- %userMSG user message without priority
- % MSG will only be displaye if ShowMessages is true
- if obj.showMessages
- disp(message);
- end
- end
-
- function [] = error(obj,message)
- %error handles critical errors
- % critical errors will always result in a matlab error
-
- %ToDO: Add function(s) before termination
- error(message);
- end
-
- function [] = softError(obj,message)
- %softError handles soft errors
- % soft errors can be changed to warning if ForcePublish is
- % selected by the user
- if obj.forcePublish
- warning(message);
- else
- error(message);
- end
- end
-
- function outputArg = method1(obj,inputArg)
- %METHOD1 Summary of this method goes here
- % Detailed explanation goes here
- outputArg = obj.Property1 + inputArg;
- end
- end
-end
-
diff --git a/+PlotID/Publish.m b/+PlotID/Publish.m
index 231c185ab862f4e32daa5c97a263f1a49a5c1e02..79ecc2b1799132e3890d2924bf90ec8b46a64d01 100644
--- a/+PlotID/Publish.m
+++ b/+PlotID/Publish.m
@@ -1,13 +1,5 @@
-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
-% scriptPath contains the path to the script, this can be provided with
-% the simple call of scriptPath = [mfilename('fullpath'),'.m'], note that
-% the extension is mandatory
-%
-% Options:
+function Publish(DataPaths, ID, 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.
@@ -18,31 +10,14 @@ function Publish(DataPaths,scriptPath, figure, options)
% path is used, PlotId will use this path a storagePath
arguments
- DataPaths {mustBeDataPath} % location of the data-file(s)
- scriptPath (1,:) {mustBeFile} % location of the matlab script
+ DataPaths
+ ID (1,:) {mustBeNonzeroLengthText} % ID must be provided
figure (1,:) {mustBeFigure} % Checks if figure is a figure object
options.Location {mustBeMember(options.Location ,{'local','server','manual','CI-Test'})} = 'local' % storage path
options.Method {mustBeMember(options.Method ,{'individual','centralized'})} = 'individual'
options.ParentFolder (1,:) {mustBeText} = 'export'
- options.ConfigFileName (1,:) {mustBeText} = 'config.json' %individual config names possible
- options.CopyUserFCN (1,1) {mustBeNumericOrLogical} = true
+ options.CopyUserFCN (1,1) {mustBeNumericOrLogical} = true
options.CSV (1,1) {mustBeNumericOrLogical} = false
- options.ShowMessages(1,1) {mustBeNumericOrLogical} = true
- 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
-
-for i=1:numel(DataPaths)
- if isstring(DataPaths{i})
- % strings will cause problems
- DataPaths{i} = char(DataPaths{i});
- end
end
%catch multiple figures in fig
@@ -54,31 +29,18 @@ if numel(figure) > 1
warning(msg);
end
-%get ID from Figure
-ID = figure.Tag;
-
-if isempty(ID)
- % no ID found, User dialog for Folder name
- ID = inputdlg(['No ID defined- ' newline,...
- 'Please enter a folder name to continue:'],'Please enter a folder name');
- ID = ID{1};
- msg = ['No ID found - consider to use the TagPlot function before ',...
- 'you publish ', newline, 'your files will be stored in ' , ID];
- warning(msg);
-end
-
%% read config file
-% there is only one config Object (handleClass)
-configObj = PlotID.config(options.ConfigFileName);
-if isfield(configObj.configData, 'options')
- % is working but prune to user errors
- options = configObj.configData.options;
+try
+ txt = fileread('config.json');
+ config = jsondecode(txt);
+ configError = false;
+catch
+ msg = ['Error while reading the config file' newline,...
+ ' publishing on server not possible'];
+ warning(msg);
+ configError = true;
end
-% Error and MSG handeling
-dlgObj = PlotID.userDLG(ID,options);
-
-
%% storage location
switch options.Location
case 'local'
@@ -86,43 +48,35 @@ switch options.Location
storPath = options.ParentFolder;
else
% use the script path as export path
- scriptLocation = fileparts(scriptPath);
- storPath = fullfile(scriptLocation,options.ParentFolder);
+ scriptPath = fileparts(DataPaths.script);
+ storPath = fullfile(scriptPath,options.ParentFolder);
end
case 'server' %from config File
- if dlgObj.configError
- msg = ['Error while reading the config file' newline,...
- ' publishing on server not possible'];
- dlgObj.error(msg);
- end
- storPath = config.ServerPath;
+ storPath = config.ServerPath;
case 'manual' %UI
storPath = uigetdir();
case 'CI-Test'
storPath = fullfile(pwd,'CI_files',options.ParentFolder);
end
+folderName = char(ID);
-folderName = ['.',char(ID)]; %hidden folder
-
-%% Create data directory
+%% Create Data-Directory
if isfolder(fullfile(storPath,folderName))
- dlgObj.error(['Folder ',folderName, ' exists - Plot was already published ']);
+ error(['Folder ',folderName, ' exists - Plot was already published ']);
elseif mkdir(fullfile(storPath,folderName))
else
- dlgObj.error('Directory could not be created - check remote path and permissions');
+ error('Directory could not be created - check remote path and permissions');
end
disp(['publishing of ', ID, ' started']);
-%% Create a copy of the script and user functions(optional)
+%% Create a Copy of the script and user functions(optional)
% script
-[~, status, msg] = PlotID.createFileCopy({scriptPath},folderName,storPath,ID, 'script');
-dlgObj.scriptPublished =status;
-dlgObj.userMSG(msg);
+PlotID.createFileCopy({[DataPaths.script,'.m']},folderName,storPath,ID, 'script');
% user functions
-[fList,pList] = matlab.codetools.requiredFilesAndProducts(scriptPath);
+[fList,pList] = matlab.codetools.requiredFilesAndProducts(DataPaths.script);
if options.CopyUserFCN
- fList = fList(~ismember(fList,scriptPath)); % rmv script from list
+ fList = fList(~ismember(fList,[DataPaths.script,'.m'])); % rmv script from list
fList = fList(~contains(fList,'config.json')); % rmv config.json from list
fList = PlotID.removePltIdFiles(fList); % Do not copy files that are part of plot ID
if ~isempty(fList)
@@ -142,16 +96,16 @@ switch options.Method
currentPath = fullfile(storPath);
%list all files
- fList = dir(fullfile(storPath,DataFolderName, ['**',filesep,'*.*']));
+ fList = dir(fullfile(storPath,DataFolderName, '**\*.*'));
%get list of files and folders in any subfolder
fList = fList(~[fList.isdir]); %remove folders from list
fList = struct2table(fList);
% 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(DataPaths.rdata)
% check if identical file exists (status = 1)
- [~, idx] = PlotID.fileCompare(DataPaths{i},fList);
+ [~, idx] = PlotID.fileCompare(DataPaths.rdata{i},fList);
% create Linked HDF5 files for identical files
if any(idx)
fList.path = fullfile(fList.folder,fList.name);
@@ -159,118 +113,78 @@ switch options.Method
relativeSourcePath = strrep(sourcePath,currentPath,'');
if contains(sourcePath,{'.h5','.hdf5'}) % Linking only for HDF5
- linkedHDFPath = fullfile(storPath,folderName);
- PlotID.createLinkedHDF5(relativeSourcePath{1,1},linkedHDFPath);
+ PlotID.createLinkedHDF5(relativeSourcePath{1,1},storPath,ID);
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');
- pathToData = strrep(dataPath,currentPath,'');
+ [dataPath] = PlotID.createFileCopy(DataPaths.rdata{i},'data',storPath,ID,'dataCentral');
+ relativeDataPath = strrep(dataPath,currentPath,'');
%WIP
- if contains(DataPaths{i},{'.h5','.hdf5'}) % Linking only for HDF5
+ if contains(DataPaths.rdata{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);
+ PlotID.createLinkedHDF5(relativeDataPath,storPath,ID);
end %if
end %if
end %for
clear DataFolderName
case 'individual'
% Create a copy of the research data
- [~, status, msg] = PlotID.createFileCopy(DataPaths,folderName,storPath,ID, 'data');
+ PlotID.createFileCopy(DataPaths.rdata,folderName,storPath,ID, 'data');
end
-%temporary:
-dlgObj.rdFilesPublished = status;
-dlgObj.userMSG(msg);
-
%% Write Config File
-exportPath = fullfile(storPath,folderName);
-configObj.writeConfig(exportPath);
-% add further Metadata
-meta =struct();
-if ispc
- meta.author = getenv('USERNAME');
+if ~configError %config File must exist
+ % copy config file
+ configPath = PlotID.createFileCopy('config.json',folderName,...
+ storPath,ID, 'data');
+else
+ configPath = fullfile(storPath,folderName,'config.json');
+ config = struct();
+ if ispc
+ config.author = getenv('USERNAME');
+ end
end
-meta.ProjectID = ID;
-meta.CreationDate = datestr(now);
-meta.MatlabVersion = version;
-meta.ToolboxVersions = pList;
-
-% write meta
-metaPath = fullfile(storPath,folderName,'plotID_data.json');
-fid = fopen(char(metaPath),'w');
-txt = jsonencode(meta,'PrettyPrint',true);
+% add further Metadata
+config.ProjectID = ID;
+config.CreationDate = datestr(now);
+config.MatlabVersion = version;
+config.ToolboxVersions = pList;
+
+%write config
+fid = fopen(char(configPath),'w');
+txt = jsonencode(config,'PrettyPrint',true);
fprintf(fid,txt);
fclose(fid);
%% Export the Plot
try
- PlotName = [ID,'_plot']; % plotname
- RemotePath = fullfile(storPath ,folderName, PlotName);
- % Matlab figure
- savefig(figure,RemotePath);
- % the png should only be a preview
- exportgraphics(figure,[RemotePath,'.png'],'Resolution',300);
- dlgObj.figurePublished = true;
+ PlotName = [ID,'_plot']; % plotname
+ RemotePath = fullfile(storPath ,folderName, PlotName);
+ % Matlab figure
+ savefig(figure,RemotePath);
+ % the png should only be a preview
+ exportgraphics(figure,[RemotePath,'.png'],'Resolution',300);
catch
- dlgObj.softError('Plot export was not successful');
+ warning('Plot export was not successful')
end
+disp(['publishing of ', ID , ' done']);
+
% CSV EXport
if options.CSV
T = table();
- T.research_Data = DataPaths'; T.PlotID(:) = {ID};
- T.Script_Name(:) = {scriptPath};
+ T.research_Data = DataPaths.rdata'; T.PlotID(:) = {ID};
+ T.Script_Name(:) = {[DataPaths.script,'.m']};
T.Storage_Location(:) = {storPath};
T.Date(:) = {datestr(now)};
T = movevars(T,'PlotID','before',1);
writetable(T, fullfile(storPath, 'overview_table.csv'),'WriteMode','append');
end
-%% final renaming and error/warning handeling
-% if no error orcurred or if force publish is activated, rename the hidden
-% folder to a non hidden one, otherwise delete it.
-if dlgObj.success || options.ForcePublish
- oldPath = fullfile(storPath,folderName);
- newPath = strrep(oldPath,'.',''); %remov dot
- status = movefile(oldPath,newPath); %rename directory
-else
- % error from userDlg class!
-end
-
-if status
- disp(['publishing of ', ID , ' done']); %always displayed onsucess
-else % publish was not sucessfull!
- %replace with error from userDLG Class
- dlgObj.error(['publishing of ', ID , ' failed'])
-end
-
-
end %function
-%% Argument Validation Functions
function tf = mustBeFigure(h)
%checks if input is a figure object
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
-
diff --git a/+PlotID/TagPlot.m b/+PlotID/TagPlot.m
index b925379f4a5a8a23f5b37d802d0edc61eda0bf4f..4a5965803f3f57eb5de1da8fce1ed84d070c5a0e 100644
--- a/+PlotID/TagPlot.m
+++ b/+PlotID/TagPlot.m
@@ -14,42 +14,43 @@ function [figs, IDs] = TagPlot(figs, options)
arguments
figs (1,:) {mustBeFigure}
options.ProjectID (1,:) {mustBeText}= ''
- options.Fontsize (1,1) {mustBeInteger} = 8
- options.Color (1,3) {mustBeNonnegative} = 0.65*[1 1 1] % grey
+ options.Fontsize (1,1) {mustBeInteger} = 8
options.Location (1,:) {mustBeText} = 'east'
- options.DistanceToAxis {mustBeReal} = .01 % relative distance
options.Position (1,2) {mustBeVector} = [1,0.4] % default for east
- options.Rotation (1,1) {mustBeReal} = NaN
- options.ConfigFileName (1,:) {mustBeText} = 'config.json'
+ options.Rotation (1,1) {mustBeInteger} = 0
end
if isempty(options.ProjectID)
- configObj = PlotID.config(options.ConfigFileName);
- configData = configObj.configData;
- options.ProjectID = configData.ProjectID;
+ try
+ txt = fileread('config.json');
+ config = jsondecode(txt);
+ catch
+ config =struct;
+ config.ProjectID = '';
+ warning("No ProjectID was definded and no config.json could be found");
+
+ end
+
+ if ~isempty(config.ProjectID)
+ options.ProjectID = config.ProjectID;
+ else
+ warning('no project options.ProjectID defined')
+ end
end
switch options.Location
case 'north'
- y = 1 - options.DistanceToAxis
- options.Position = [0.4,y];
- Rotation = 0;
+ options.Position = [0.4,0.95];
+ options.Rotation = 0;
case 'east'
- x = 1 - options.DistanceToAxis;
- options.Position = [x,0.4];
- Rotation = 90;
+ options.Position = [1,0.4];
+ options.Rotation = 90;
case 'south'
- y = 0 + options.DistanceToAxis;
- options.Position = [0.4,y];
- Rotation = 0;
+ options.Position = [0.4,.02];
+ options.Rotation = 0;
case 'west'
- x = 0 + options.DistanceToAxis;
- options.Position = [x,0.4];
- Rotation = 90;
- case 'southeast'
- y = 0 + options.DistanceToAxis;
- options.Position = [0.8, y];
- Rotation = 0;
+ options.Position = [.05,0.4];
+ options.Rotation = 90;
case 'custom'
% Check if Position is valid
if ~all(0 <= options.Position & options.Position <= 1)
@@ -61,10 +62,6 @@ switch options.Location
options.Location = 'east'; options.Position = [1,0.4];
end
-if ~isnan(options.Rotation)
- Rotation = options.Rotation;
-end
-
IDs = cell(numel(figs),1);
for n = 1:numel(figs)
@@ -75,11 +72,10 @@ for n = 1:numel(figs)
ylim =get(axes,'YLim');
xlim =get(axes,'XLim');
%ID
-
- position = [options.Position(1), options.Position(2)];
+ position = [options.Position(1)*xlim(2), options.Position(2)*ylim(2)];
text(axes,position(1),position(2), IDs{n},'Fontsize',options.Fontsize,...
- 'Rotation',Rotation, 'VerticalAlignment','bottom','Color',...
- options.Color,'BackgroundColor','w', 'Units', 'normalized');
+ 'Rotation',options.Rotation, 'VerticalAlignment','bottom','Color',...
+ 0.65*[1 1 1],'BackgroundColor','w');
set(figs(n),'Tag', IDs{n});
end
diff --git a/+PlotID/createFileCopy.m b/+PlotID/createFileCopy.m
index 03e394c2000633f015a48a9340889275dec54549..061f10903343ccde4ea33ea666f93b19f414cb79 100644
--- a/+PlotID/createFileCopy.m
+++ b/+PlotID/createFileCopy.m
@@ -1,4 +1,4 @@
-function [storagePaths, status, msg] = createFileCopy(filePaths,folderName,storPath,ID,type)
+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
@@ -68,10 +68,8 @@ try
copyfile(FileNameAndLocation,RemotePath);
storagePaths{i} = RemotePath;
end
- status = true;
- msg =([type, ' successfully published']);
+ disp([type, ' sucessfully published']);
catch
- status = false;
warning([type,' export was not sucessful'])
if exist('errorMSG')
error(errorMSG);
diff --git a/+PlotID/createLinkedHDF5.m b/+PlotID/createLinkedHDF5.m
index 8807977d929aed8af169a866c4ba4aa329fda8d4..8fecfaed42b86014895c16a9bdd9a03eb554bec5 100644
--- a/+PlotID/createLinkedHDF5.m
+++ b/+PlotID/createLinkedHDF5.m
@@ -1,4 +1,4 @@
-function [status] = createLinkedHDF5(SourceFile,TargetPath)
+function [status] = createLinkedHDF5(SourceFile,TargetPath,ID)
%createLinkedHDF5 creates a HDF file that references the Sourcefile
% TargetPath is the storage location, ID the foldername
% Status returns true if the function was sucessfull
@@ -16,12 +16,12 @@ end
%old
%fid = H5F.create(fullfile(TargetPath,ID,[ID,'_data.h5']));
- fid = H5F.create(fullfile(TargetPath,[filename,ext]));
+ fid = H5F.create(fullfile(TargetPath,ID,[filename,ext]));
%create External Link to Sourcefile in the Group linkToExternal
- H5L.create_external(['..',SourceFile],'/',fid, SourceFile ,plist_id,plist_id);
- %H5L.create_external(['..',filesep,'data',filesep,SourceFile],'/',fid, SourceFile ,plist_id,plist_id); %original
+ H5L.create_external(['..\',SourceFile],'/',fid, SourceFile ,plist_id,plist_id);
+ %H5L.create_external(['..\data\',SourceFile],'/',fid, SourceFile ,plist_id,plist_id); %original
H5F.close(fid);
- disp([fullfile(TargetPath,[filename,ext]),' created']);
+ disp([fullfile(TargetPath,ID,[filename,ext]),' created']);
status = 1;
% catch
% warning('No linked HDF file was created');
diff --git a/+PlotID/initilise.m b/+PlotID/initilise.m
deleted file mode 100644
index 4f893441299d085fa8f5a06fbd4dc36b105df04c..0000000000000000000000000000000000000000
--- a/+PlotID/initilise.m
+++ /dev/null
@@ -1,7 +0,0 @@
-function [status] = initilise()
-%INITILISE Initilisation for first time úsage
-
-
-
-end
-
diff --git a/+PlotID/removePltIdFiles.m b/+PlotID/removePltIdFiles.m
index 169990d0f7e6f6d99b73f1b5d91c8454b9cf9a65..37ef1827ad2049bd261780e4d190f05907a7b676 100644
--- a/+PlotID/removePltIdFiles.m
+++ b/+PlotID/removePltIdFiles.m
@@ -1,26 +1,19 @@
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
-packageContent = what('PlotID');
-% packageContent.classes has no extensions
-PltID_classlist = packageContent.classes;
+PltID_flist = struct2table(dir('+PlotID')); %get list of files
+[~,~,PltID_flist.ext(:)] = fileparts(PltID_flist.name(:)); % add ext column
+
+PltID_flist = PltID_flist(strcmp(PltID_flist.ext,'.m'),:);
-% Class Methods need to be listed in an additional function
-Class_flist = cell(1,numel(packageContent.classes)); %preallocate
-for i=1:numel(packageContent.classes)
- temp = what(['PlotID',filesep,'@',PltID_classlist{i}]);
- Class_flist{i} = temp.m;
-end
-
-Class_flist = vertcat(Class_flist{:});
-% all plotID .m files:
-PltID_flist = [packageContent.m; Class_flist];
% Comparison and filter
-fListClean = fList(~ismember(names,PltID_flist));
+fListClean = fList(~ismember(names,PltID_flist.name));
+
end
diff --git a/.gitignore b/.gitignore
index 32ea2493881e83b59a61c69dbd6ba01281a72d3b..708bea6b2032d70640c74a197d183a115ff0bdda 100644
--- a/.gitignore
+++ b/.gitignore
@@ -37,7 +37,6 @@ testdata_2.h5
testdata2.h5
test_data.mat
export/*
-unused*/*
# Octave session info
octave-workspace
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 938d8bc80d5bdeff95757803ef2d80a778269d1e..7901609ef3b830a97e409b23c51890ace703b737 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -5,16 +5,6 @@ Test Code:
stage: Run
tags:
- matlab
- - bash
script:
- - cd ./CI_files
- - chmod +x ./runner_linux.sh
- - ./runner_linux.sh
- - cat ./log.txt
- artifacts:
- paths:
- - ./CI_files/log.txt
- - ./CI_files/matlab_log.txt
-
- when: always
- expire_in: 1 week
+ - ./CI_files/runtest.ps1
+ - cat log2.txt
diff --git a/CITATION.cff b/CITATION.cff
deleted file mode 100644
index 6c8e17a380a65867c2de3888abcc23f8d09d4f8f..0000000000000000000000000000000000000000
--- a/CITATION.cff
+++ /dev/null
@@ -1,18 +0,0 @@
-cff-version: 1.2.0
-title: >-
- plotID a toolkit for connecting research data and
- figures
-message: >-
- developed at the Chair of Fluid System, Techische
- Universität Darmstadt within the framework of the NFDI4Ing consortium Funded by the German Research Foundation (DFG) - project number 442146713
-type: software
-authors:
- - given-names: Jan
- family-names: Lemmer
- email: jan.lemmer@fst.tu-darmstadt.de
- affiliation: 'Chair of Fluid Systems, TU Darmstadt'
- orcid: 'https://orcid.org/0000-0002-0638-1567'
- - given-names: Martin
- family-names: Hock
- email: martin.hock@fst.tu-darmstadt.de
- affiliation: 'Chair of Fluid Systems, TU Darmstadt'
diff --git a/CI_files/default_test.m b/CI_files/default_test.m
index f6c7309d399deaa2453cf51045d5970073da8ba8..505c360ea8fde4390434772eeece053120d15f0e 100644
--- a/CI_files/default_test.m
+++ b/CI_files/default_test.m
@@ -1,126 +1,72 @@
function [result] = default_test()
-%default_test() This is a simple test if Plot ID works for the default settings
+%UNTITLED2 This is a simple test if Plot ID works for the default settings
% Detailed explanation goes here
clear; clc; close all;
-% set path
-% starting path of gitlab runner is in CI_files
-if contains(pwd,'CI_files')
- cd .. % move one directory up
-end
-
-addpath('CI_files');
-
% clean up, if previous run failed
try
- delete(['CI_files' filesep 'export' filesep '*']);
- delete(['CI_files' filesep '*.mat']);
- delete(['CI_files' filesep '*.h5']);
- rmdir(['CI_files' filesep 'export'],'s');
+ delete CI_files/export/* CI_files/*.mat CI_files/*.h5
+ rmdir('CI_files/export','s');
end
-% initialise
-numberOfTests = 2;
-testResults = zeros(numberOfTests,1);
-
-%start log
-fid = fopen(fullfile('CI_files','log.txt'),'w');
-txt = ['default test started ' newline];
-fprintf(fid,txt);
-
-% create Config for CI-Tests
-fid1 = fopen(fullfile('CI_files','CI_config.json'),'w');
-configData.Author = 'CI-Test'; configData.ProjectID = 'CI-001';
-txt = jsonencode(configData,'PrettyPrint',true);
-%fprintf does not write paths correctly !!!
-fwrite(fid1,txt);
-fclose(fid1);
-
-try
- ProjectID = 'Test01';
- %% Data
- % some random data
- x = linspace(0,7);
- y = rand(1,100)+2;
- dataset1 = fullfile('CI_files','test_data.mat');
- save(dataset1,'x','y');
- % some data as .h5
- x1 = linspace(0,2*pi);
- y1 = sin(x1)+2;
-
- % define file path & name
- fpath = fullfile("CI_files","testdata2.h5");
- dataset2 = fullfile('CI_files','testdata2.h5');
-
- % create hdf5 file and dataset > write data to hdf5 file / dataset
- h5create(fpath, "/x1", size(x1), "Datatype", class(x1))
- h5create(fpath, "/y1", size(y1), "Datatype", class(y1))
- h5write(fpath, "/x1", x1)
- h5write(fpath, "/y1", y1)
-
- %% Plotting
-
- fig(1) =figure('visible','off');
- plot(x,y,'-k');
- hold on
- plot(x1,y1,'-r');
- msg = 'simple_test succeed stage 1';
-catch
- testResults(1) = 1; %test fails
- msg = 'simple_test failed in Stage 1';
- warning(msg);
-end
-
-fprintf(fid,[msg newline]);
+ProjectID = 'Test01';
+%% Data
+% some random data
+x = linspace(0,7);
+y = rand(1,100)+2;
+dataset1 = 'test_data.mat';
+save('CI_files/test_data.mat','x','y');
+% some data as .h5
+x1 = linspace(0,2*pi);
+y1 = sin(x1)+2;
+
+% define file path & name
+fpath = "CI_files/testdata_2.h5";
+dataset2 = 'testdata_2.h5';
+
+% create hdf5 file and dataset > write data to hdf5 file / dataset
+h5create(fpath, "/x1", size(x1), "Datatype", class(x1))
+h5create(fpath, "/y1", size(y1), "Datatype", class(y1))
+h5write(fpath, "/x1", x1)
+h5write(fpath, "/y1", y1)
+
+%% Plotting
+
+fig(1) =figure('visible','off');
+plot(x,y,'-k');
+hold on
+plot(x1,y1,'-r');
%% Tag the plot
try
- [figs, ID] = PlotID.TagPlot(fig,'ConfigFileName', 'CI_config.json');
+ [figs, ID] = PlotID.TagPlot(fig,'ProjectID', ProjectID);
%% call a dummy function
- %a=1;
- %a = example_fcn(a);
+ a=1;
+ a = example_fcn(a);
%% publishing
% The functions needs the file location, the location of the data and the
% figure
- script = [mfilename('fullpath'),'.m']; % filename of the m.script
+ path.script = mfilename('fullpath'); % filename of the m.script
% file name of the data
- rdata = {dataset1,dataset2} ; % don't forget the extension
+ path.rdata = {dataset1,dataset2} ; % don't forget the extension
- PlotID.Publish(rdata,script, figs, 'Location', 'CI-Test',...
- 'ConfigFileName', 'CI_config.json');
+ PlotID.Publish(path, ID, figs, 'Location', 'CI-Test')
+ result = true;
- msg = 'simple_test succeed Stage 2';
-
+ % clean up
+ delete CI_files/export/* CI_files/*.mat CI_files/*.h5
+ rmdir('CI_files/export','s');
+
+ clear; clc;
+
catch
- testResults(2) = 1; %fail
- msg = 'simple_test failed in Stage 2';
- warning(msg);
-end
-fprintf(fid,[msg newline]); %log
-
-%% Test result
-if any(testResults)
- result = 1; %fail
- warning('test failed');
-else
- result = 0; % pass
- disp('test succeed');
-end
-
-fclose(fid);
-
-% final clean up
-try
- delete(['CI_files' filesep 'export' filesep '*']);
- delete(['CI_files' filesep '*.mat']);
- delete(['CI_files' filesep '*.h5']);
- rmdir(['CI_files' filesep 'export'],'s');
- delete(fullfile('CI_files','CI_config.json'));
+ result = false;
+ warning('simple_test failed');
end
end
diff --git a/CI_files/fail_runner.m b/CI_files/fail_runner.m
deleted file mode 100644
index e9071dd65411802d16b925aca9ca35c5df933ea4..0000000000000000000000000000000000000000
--- a/CI_files/fail_runner.m
+++ /dev/null
@@ -1,8 +0,0 @@
-function [retVal] = fail_runner()
-%RUNNER_TESTING testing function to test, if the runner is set up properly
- retVal = 1; % test should fail !
- fid = fopen(fullfile('log.txt'),'w');
- txt = ['This is a test, Errorstate: ', num2str(retVal)];
- fprintf(fid,txt);
- fclose(fid);
-end
diff --git a/CI_files/pass_runner.m b/CI_files/pass_runner.m
deleted file mode 100644
index 957268576f9bd1f4bdc89fb2cbcb69428d8cd229..0000000000000000000000000000000000000000
--- a/CI_files/pass_runner.m
+++ /dev/null
@@ -1,8 +0,0 @@
-function [retVal] = pass_runner()
-%pass_runner testing function to test, if the runner is set up properly
- retVal = 0; % test should succeed !
- fid = fopen(fullfile('log.txt'),'w');
- txt = ['This is a test, Errorstate: ', num2str(retVal)];
- fprintf(fid,txt);
- fclose(fid);
-end
diff --git a/CI_files/runner_linux.sh b/CI_files/runner_linux.sh
deleted file mode 100644
index f64784cf471314482b52f05ff6f80a39067a367a..0000000000000000000000000000000000000000
--- a/CI_files/runner_linux.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/bin/bash
-
-#matlab -r "disp(['Current folder: ' pwd])"
-matlab $@ -nodisplay -nodesktop -nosplash -logfile matlab_log.txt -r "default_test;exit(ans);"
-
-exitstatus=$?
-if [[ $exitstatus -eq '0' ]]
-then
- echo "matlab succeed. Exitstatus: $exitstatus"
- exit $exitstatus
-else
- echo "matlab failed. Exitstatus: $exitstatus"
- exit $exitstatus
-
-fi
diff --git a/CI_files/runner_test.m b/CI_files/runner_test.m
new file mode 100644
index 0000000000000000000000000000000000000000..496afd8558f128e08826f25e62472d6b3cb15f62
--- /dev/null
+++ b/CI_files/runner_test.m
@@ -0,0 +1,7 @@
+function [result] = runner_test()
+%RUNNER_TEST testing function to test, if the runner is set up properly
+result = true;
+
+exit(result);
+end
+
diff --git a/CI_files/runtest.ps1 b/CI_files/runtest.ps1
deleted file mode 100644
index 15d17374764ae708af434eabcfa372828f527be0..0000000000000000000000000000000000000000
--- a/CI_files/runtest.ps1
+++ /dev/null
@@ -1,17 +0,0 @@
-# runtest.ps1
-
-$LOGFILE='CI_log.txt'
-$wd = pwd;
-$LOGFILE = $("$wd" + "\" + "$LOGFILE")
-$CIfolder = "$wd" + "\" + "CI_files\"
-# $MFILE='"C:\git\NFDI4ing\plot_ID_matlab\CI_files\runner_test.m"'
-$arguments = "-nodesktop", "-nosplash","-minimize","-wait","-sd", "$wd", "-logfile", "$LOGFILE","-batch","CI_files\test_runner_STFS.m"
-$Returnvalue = & 'C:\Program Files\MATLAB\R2021b\bin\matlab.exe' $arguments
-
-#$CODE = $?
-# Returnvalue doesnt get anything useful from matlab
-# Write-Output($Returnvalue)
-Write-Output(Get-Content($LOGFILE))
-
-exit $CODE
-
diff --git a/Initialisation.m b/Initialisation.m
deleted file mode 100644
index 97835f3364ac842e857a021953fa2f2c632fd38e..0000000000000000000000000000000000000000
--- a/Initialisation.m
+++ /dev/null
@@ -1,29 +0,0 @@
-%% This is the PlotID Initialisation file
-% Please run this script before using PlotID
-
-%% Step 1: Add plotID location to you MATLAB path
-% This is necessary to use PlotID in your personal MATLAB Scripts
-addpath(pwd);
-savepath;
-
-%% Section 2 Config File
-% To make things easy, you should use the config file. The following wizard
-% will help you create one:
-writeConfig = true;
-
-% Ask User if current config should be overwritten
-if isfile('config.json')
- m = input('Do you want to overwrite the current config file, Y/N [Y]:','s');
- writeConfig = ismember(m,{'Y','y'});
-end
-
-if writeConfig
- config = PlotID.config.wizard('initilise');
- fid = fopen('config.json','w');
- txt = jsonencode(config,'PrettyPrint',true);
- fwrite(fid,txt);
- fclose(fid);
-end
-
-%%
-disp('Initialisition done.')
diff --git a/PlotID_Demo.m b/PlotID_Demo.m
new file mode 100644
index 0000000000000000000000000000000000000000..766ad17cfb60feb31820c5382e61b6f3cc7d413b
--- /dev/null
+++ b/PlotID_Demo.m
@@ -0,0 +1,74 @@
+%% Example Script
+% This Script is meant to demonstrate the capabilities of the PlotID tool.
+
+%% 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
+% Leave empty for using the ID from the config file
+ProjectID = 'FST01';
+
+%% Data
+% 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)+.5*sin(2*x1)+2;
+
+% define file path & name
+
+fpath = fullfile(pwd,"./testdata2.h5");
+dataset2 = fullfile(pwd,'testdata2.h5');
+
+% create hdf5 file and dataset > write data to hdf5 file / dataset
+h5create(fpath, "/x1", size(x1), "Datatype", class(x1))
+h5create(fpath, "/y1", size(y1), "Datatype", class(y1))
+h5write(fpath, "/x1", x1)
+h5write(fpath, "/y1", y1)
+
+%% 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.
+fig(1) = figure;
+set(gcf,'Units','centimeters','PaperUnits','centimeters','PaperSize',[9 7],...
+'Position',[5 5 9 7]);
+plot(x,y,'Color',0.5*[1 1 1]);
+box off; hold on;
+plot(x1,y1,'-k');
+set(gca, 'TickDir', 'out', 'YLim', [0,4],'YTick',[0:1:4],'XLim',[0,6]);
+%fstplt.setfiguresize('1/2ppt16:9');
+%fstplt.pimpplot;
+
+%% Example 1: single plot based on two data-sets
+
+%% Tag the plot
+% PlotID Implementation starts here.
+% TagPlot adds a visible ID to the figure(s) and to the figures property
+% 'Tag'
+[fig, ID] = PlotID.TagPlot(fig, 'ProjectID', ProjectID);
+
+%% Publishing
+% Second part of plotID
+% The functions needs the file location, the location of the data and the
+% figure and can take several options.
+path.script = mfilename('fullpath'); % filename of the m.script
+% file names of the datasets
+path.rdata = {dataset1,dataset2} ; % don't forget the extension
+
+PlotID.Publish(path, ID, fig(1), 'Location', 'local' ,'Method','individual')
+
+
+
+%% End
+
diff --git a/README.md b/README.md
index 342cf55fc3bc97c07fcf011bc7ef83f2b9744015..83e88a152b92188d60874df012febdad41e3bce5 100644
--- a/README.md
+++ b/README.md
@@ -11,23 +11,20 @@ Feel free to give feedback and feature requests or to take part in the developme
[TOC]
# Quick User Guide
-**Requirements:** MATLAB R2021a or newer
-
`PlotID` works in two Steps:
1. tagging the plot
`[figs, IDs] = plotId.TagPlot(figs, options)`
-You should either set a ProjectID in the config.json (copy & rename the 'example-config.json' to 'config.json'), or pass it as option 'ProjectID' to the TagPlot function.
-2. publish the plot and the associated data
-`plotID.Publish(DataPaths,scriptPath, figure, options)`
-`scriptPath` contains the path to the script, this can be provided with the simple call of `scriptPath = [mfilename('fullpath'),'.m']`, note that
- **the extension is mandatory.**
+2. publishing the plot and the associated data
+`plotID.Publish(DataPaths, ID, figure, options)`
+
+`DataPaths.script = mfilename('fullpath');` contains the filename of the m.script
-`DataPaths` contains the path(s) to the research data, for multiple files you can use a cell arrays (they must be at the path).
-`figure` is the figure that should be published.
-
+`DataPaths.rdata = {dataset1, dataset2};` file names of the datasets (they most be at the path)
+
+You should either set a ProjectID in the config.json (copy & rename the 'example-config.json' to 'config.json'), or pass it as option 'ProjectID' to the TagPlot function.
# PlotID.TagPlot()
`[figs, IDs] = TagPlot(figs, options)`
@@ -66,7 +63,7 @@ FriendlyID Changes the Hex Number to a human friendly *datetime* and *dateStr*.
# PlotID.Publish()
-`Publish(DataPaths,scriptPath, figure, options)` \
+`Publish(DataPaths, ID, 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
diff --git a/example-config.json b/example-config.json
new file mode 100644
index 0000000000000000000000000000000000000000..92b8621a1d43e5fc26290fa6acce3be448471d3e
--- /dev/null
+++ b/example-config.json
@@ -0,0 +1,5 @@
+{
+ "Author": "Example Author",
+ "ProjectID": "AB01",
+ "ServerPath": "\\\\Server\\path\\folder"
+}
diff --git a/example.m b/example.m
index b64044db476204bb46edce6332f08ddb80be7573..04aa8c11aebc102d0810c7e23681ad1ba473d943 100644
--- a/example.m
+++ b/example.m
@@ -43,8 +43,7 @@ h5write(fpath, "/y1", y1)
% Place for post-processing of the data, or additional related code.
% example_fcn is a dummy function to show the functionality
a = 1; a = example_fcn(a);
-% Uncomment to include the Statistics and Machine learning Toolbox
-% p = betacdf(0.5,1,1); % to test toolboxes
+p = betacdf(0.5,1,1); % to test toolboxes
%% Plotting
% This is still part of a normal script to produce plots.
@@ -62,24 +61,21 @@ set(gca, 'TickDir', 'out', 'YLim', [0,4]);
% PlotID Implementation starts here.
% TagPlot adds a visible ID to the figure(s) and to the figures property
% 'Tag'
-% [fig, ID] = PlotID.TagPlot(fig, 'ProjectID', ProjectID);
-[fig, ID] = PlotID.TagPlot(fig);
+[fig, ID] = PlotID.TagPlot(fig, 'ProjectID', ProjectID);
+
%% Publishing
% Second part of plotID
% The functions needs the file location of the script, the location of the
% data and the figure and can take several options (see readme).
-% filename of the m.script, extension must be added!
-scriptPath = [mfilename('fullpath'),'.m'];
-
+path.script = mfilename('fullpath'); % filename of the m.script
% file names of the datasets
%(defined above:) dataset1 = 'test_data.mat'; dataset2 = 'testdata2.h5'
-locations = {dataset1,dataset2} ; % don't forget the extension
-locations = {string(dataset1),dataset2};
+path.rdata = {dataset1,dataset2} ; % don't forget the extension
%call publishing
-PlotID.Publish(locations,scriptPath, fig(1), 'Location', 'local' ,'Method','individual')
+PlotID.Publish(path, ID, fig(1), 'Location', 'local' ,'Method','individual')
%% Example 2: multiple plots plot, all based on dataset2 (hdf5)
% for individual data-sets, use an appropriate array
@@ -94,13 +90,13 @@ set(gca, 'TickDir', 'out', 'YLim', [0,4]);
[fig, IDs] = PlotID.TagPlot(fig,'ProjectID', ProjectID);
% data locations
-script = [mfilename('fullpath'),'.m']; % filename of the m.script
+path.script = mfilename('fullpath'); % filename of the m.script
% file names of the datasets
-rdata = dataset2 ; % don't forget the extension
+path.rdata = {dataset2} ; % don't forget the extension
% publsihing via a for-loop
for i=1: numel(fig)
- PlotID.Publish(rdata, script, fig(i), 'Location', 'local',...
+ PlotID.Publish(path, IDs{i}, fig(i), 'Location', 'local',...
'Method','individual');
end
@@ -118,4 +114,4 @@ plot(x1,y1,'-r');
[fig2, ID] = PlotID.TagPlot(fig2,'ProjectID', ProjectID);
-PlotID.Publish(locations,scriptPath, fig2, 'Location', 'local','Method','centralized')
+PlotID.Publish(path, ID, fig2, 'Location', 'local','Method','centralized')