From c0fc27c586fb5b7aee41dbde4edddcfe17734176 Mon Sep 17 00:00:00 2001
From: "Hock, Martin" <martin.hock@fst.tu-darmstadt.de>
Date: Tue, 24 Aug 2021 07:14:39 +0200
Subject: [PATCH] Add Link-replacement feature
---
.gitignore | 6 +++
CI_files/default_test.m | 66 ++++++++++++++++++++++++++
copiedFile.h5 | Bin 896 -> 0 bytes
example.m | 58 ++++++++++++++++++-----
example_fcn.m | 6 +++
fcn_core/CreateID.m | 7 ++-
fcn_core/Publish.m | 87 +++++++++++++++++------------------
fcn_core/TagPlot.m | 42 +++++++++++++++--
fcn_help/FileCompare.m | 29 ------------
fcn_help/createFileCopy.m | 52 +++++++++++++++++++++
fcn_help/createLinkedHDF5.m | 22 ++++-----
fcn_help/fileCompare.m | 49 ++++++++++++++++++++
fcn_help/removePltIdFiles.m | 19 ++++++++
fcn_help/replaceLinkedHDF5.m | 61 ++++++++++++++++++++++++
test_data.mat | Bin 1526 -> 0 bytes
testdata_2.h5 | Bin 3064 -> 0 bytes
16 files changed, 403 insertions(+), 101 deletions(-)
create mode 100644 CI_files/default_test.m
delete mode 100644 copiedFile.h5
create mode 100644 example_fcn.m
delete mode 100644 fcn_help/FileCompare.m
create mode 100644 fcn_help/createFileCopy.m
create mode 100644 fcn_help/fileCompare.m
create mode 100644 fcn_help/removePltIdFiles.m
create mode 100644 fcn_help/replaceLinkedHDF5.m
delete mode 100644 test_data.mat
delete mode 100644 testdata_2.h5
diff --git a/.gitignore b/.gitignore
index b0afd48..3d5fc69 100644
--- a/.gitignore
+++ b/.gitignore
@@ -26,7 +26,13 @@ codegen/
# Personal test files
test*.m
+test123_data.h5
+
+# files that are created in example.m
+testdata_2.h5
+test_data.mat
export/*
# Octave session info
octave-workspace
+test_data.mat
diff --git a/CI_files/default_test.m b/CI_files/default_test.m
new file mode 100644
index 0000000..515ad37
--- /dev/null
+++ b/CI_files/default_test.m
@@ -0,0 +1,66 @@
+function [result] = default_test()
+%UNTITLED2 This is a simple test if Plot ID works for the default settings
+% Detailed explanation goes here
+
+clear; clc; close all;
+addpath('./fcn_core','./fcn_help');
+
+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] = TagPlot(fig, ProjectID);
+
+ %% call a dummy function
+ a=1;
+ a = example_fcn(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
+
+ % file name of the data
+ path.rdata = {dataset1,dataset2} ; % don't forget the extension
+
+ Publish(path, ID, figs, 'Location', 'CI-Test')
+
+ % clean up
+ delete CI_files/export/* CI_files/*.mat CI_files/*.h5
+ rmdir('CI_files/export','s');
+ result = true;
+ clc;
+catch
+ result = false;
+ warning('simple_test failed');
+end
+
+end
+
diff --git a/copiedFile.h5 b/copiedFile.h5
deleted file mode 100644
index 4ddca81c276e204d2476b044f5a2fda057105080..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001
literal 896
zcmeD5aB<`1lHy_j0S*oZ76t(j3y%LoK?5^H2+I8r;W02Iz!*4aMg|rJMg|5338=gP
z)O-b~c`*GUL9VVKB{1`0G)Qa|kA{GUt78Bt6e2(b0|NsGls>@(Wk4xVS_3h`ia`tt
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Pk{EBKmto4F4^jvKGyFnS
diff --git a/example.m b/example.m
index e25950d..f208097 100644
--- a/example.m
+++ b/example.m
@@ -1,14 +1,28 @@
-% test skript
+%% Example Script
+% This Script is meant to demonstrate the capabilities of the PlotID tool.
+
+%% Clear Environment
clear; clc; close all;
addpath('fcn_core','fcn_help');
+addpath('CI_files'); % Test scripts
try
delete testdata_2.h5;
end
+
+%% Set ProjectID
+% ProjectID
+
+% TODO: decide how projectID and optionally ORCID will be implemented
+% ORCID placed on startup (alternative?) - projectID as persistent
+% otherwise dialogue?
ProjectID = 'JL01';
+
+
+
%% Data
-% some random data
+% Creating Random Data to use as data-file
x = linspace(0,7);
y = rand(1,100)+2;
@@ -30,30 +44,52 @@ h5create(fpath, "/y1", size(y1), "Datatype", class(y1))
h5write(fpath, "/x1", x1)
h5write(fpath, "/y1", y1)
-%% Plotting
-fig(1) =figure;
+%% 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;
plot(x,y,'-k');
box off
set(gca, 'TickDir', 'out', 'YLim', [0,4]);
hold on
-%fig(2) =figure;
+%fig(2) = figure;
plot(x1,y1,'-r');
set(gca, 'TickDir', 'out', 'YLim', [0,4]);
-% Tag the plot
+%% Tag the plot
+% PlotID Implementation starts here.
+
[figs, ID] = TagPlot(fig, ProjectID);
-%% publishing
+
+%% call a dummy function
+% Place for post-processing of the plot, or additional related code.
+a=1;
+a = example_fcn(a);
+
+%% Publishing
+% Second part of plotID
% The functions needs the file location, the location of the data and the
-% figure
-path.script = mfilename('fullpath') % filename of the m.script
+% figure and can take several options.
+% TODO add explanations for Options
+path.script = mfilename('fullpath'); % filename of the m.script
-% file name of the data (should be extended to handle arrays)
+% file name of the dataset
path.rdata = {dataset1,dataset2} ; % don't forget the extension
+Publish(path, ID, figs, 'Location', 'local','Method','centraliced')
+
+%% Second Plot with identical data to test centralized method
+%
+
+fig2 =figure;
+plot(x,y,'-k');
+hold on
+plot(x1,y1,'-r');
-Publish(path, ID, figs, 'Location', 'local','Method','individual')
+[fig2, ID] = TagPlot(fig2, ProjectID);
+Publish(path, ID, fig2, 'Location', 'local','Method','centraliced')
\ No newline at end of file
diff --git a/example_fcn.m b/example_fcn.m
new file mode 100644
index 0000000..418f15c
--- /dev/null
+++ b/example_fcn.m
@@ -0,0 +1,6 @@
+function [outputArg1] = example_fcn(inputArg1)
+%TEST_2 just a dummy function
+outputArg1 = inputArg1;
+
+end
+
diff --git a/fcn_core/CreateID.m b/fcn_core/CreateID.m
index 94d0df2..42ec2b2 100644
--- a/fcn_core/CreateID.m
+++ b/fcn_core/CreateID.m
@@ -11,7 +11,12 @@ switch method
ID = posixtime(datetime('now')); %get current Unix time
ID = dec2hex(int32(ID)); % get it as Hex
pause(0.5); %Pausing for unique IDs
- otherwise
+ case 2 % random UUID from Java 128 bit
+ %Static factory to retrieve a type 4 (pseudo randomly generated) UUID.
+ % The UUID is generated using a cryptographically strong pseudo random number generator.
+ temp = java.util.UUID.randomUUID;
+ ID = temp.toString;
+ otherwise
error('The requested method is not defined yet');
end
diff --git a/fcn_core/Publish.m b/fcn_core/Publish.m
index eb0c428..e6952d7 100644
--- a/fcn_core/Publish.m
+++ b/fcn_core/Publish.m
@@ -11,15 +11,18 @@ arguments
DataPaths
ID (1,:) {mustBeNonzeroLengthText} % ID must be provided
figures (1,:) {mustBeFigure} % Checks if Figures are figures
- options.Location {mustBeMember(options.Location ,['local','server'])} = 'local' % storage path
+ options.Location {mustBeMember(options.Location ,['local','server','CI-Test'])} = 'local' % storage path
options.Method {mustBeMember(options.Method ,['individual','centraliced'])} = 'individual'
+ options.CopyUserFCN (1,1) {mustBeNumericOrLogical} = true
end
switch options.Location
case 'local'
storPath = fullfile(pwd,'export');
case 'server'
- storPath = '\\FST-220\Jans-50GB-SMB\Lemmer';
+ storPath = '\\FST-220\Jans-50GB-SMB\Lemmer';
+ case 'CI-Test'
+ storPath = fullfile(pwd,'CI_files','export');
end
folderName = char(ID);
@@ -32,40 +35,52 @@ end
disp('Publishing started');
-%% Create a Copy of the script
+%% Create a Copy of the script and User functions(optional)
+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);
+ % plist contains the required MATLAB Toolboxes, maybe usefull in future
+ fList = fList(~ismember(fList,[DataPaths.script,'.m'])); % rmv script from list
+ fList = removePltIdFiles(fList); % Do not copy files that are part of plot ID
+ if ~isempty(fList)
+ createFileCopy(fList,folderName,storPath,ID,'userFcn');
+ end
end
+
%% Research data handeling
switch options.Method
case 'centraliced' % Work in progresss!!!
- %check if data folder exists
+ % check if data folder exists
if ~isfolder(fullfile(storPath,'data'))
mkdir(fullfile(storPath,'data'));
end
+ %list all files
+ fList = dir(fullfile(storPath,'data', '**\*.*')); %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)
- createFileCopy(DataPaths.rdata,'data',storPath,ID);
- % create a linked (soft) copy
-
-
-
+ for i=1:numel(DataPaths.rdata)
+ % check if identical file exists (status = 1)
+ [~, idx] = fileCompare(DataPaths.rdata{i},fList);
+ % create Linked HDF5 files for identical files
+ if any(idx)
+ sourcePath = fList.name{idx}; % If there are multiple copies already, this only picks the last entry
+ if contains(sourcePath,{'.h5','.hdf5'}) % Linking only for HDF5
+ createLinkedHDF5(sourcePath,storPath,ID);
+ end
+ else % no identical file exists
+ createFileCopy(DataPaths.rdata{i},'data',storPath,ID,'dataCentral');
+ 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
+try
for i=1:numel(figures)
fig = figures(i);
PlotName = [ID,'_plot',num2str(i)]; % Der Plotnamen
@@ -75,34 +90,14 @@ end
exportgraphics(fig,[RemotePath,'.png'],'Resolution',300);
disp([num2str(i),' of ',num2str(numel(figures)),' figures exported']);
end
-%catch
- %warning('Plot export was not sucessful')
-%end
+catch
+ warning('Plot export was not successful')
+end
-disp(['Publishing of ', ID , ' done']);
+disp(['publishing of ', ID , ' done']);
end %function
-function [] = createFileCopy(filePaths,folderName,storPath,ID)
-% 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 ...');
- try
- for i = 1:numel(filePaths)
- FileNameAndLocation = filePaths{i};
- [~,~,ext] = fileparts(filePaths{i}); % get the extension
- newbackup = sprintf([ID,'_data',ext]);
-
- % Write the copied file
- RemotePath = fullfile(storPath,folderName, newbackup);
- copyfile(FileNameAndLocation,RemotePath);
- end
- disp('Research data sucessfully published');
- catch
- warning('Research data export was not sucessful')
- end %try
-end
-
function tf = mustBeFigure(h)
%checks if input is a figure object
tf = strcmp(get(h, 'type'), 'figure') & isa(h, 'matlab.ui.Figure');
diff --git a/fcn_core/TagPlot.m b/fcn_core/TagPlot.m
index 3c42626..4fac128 100644
--- a/fcn_core/TagPlot.m
+++ b/fcn_core/TagPlot.m
@@ -1,16 +1,50 @@
-function [figs, ID] = TagPlot(figs, prefix)
+function [figs, ID] = TagPlot(figs, prefix, options)
%TagPlot adds IDs to figures
% The ID is placed visual on the figure window and as Tag (Property of figure)
% TagPlot can tag multiple figures at once
+% prefix is the project number (string or char)
+%
+% The ID is placed on the 'east' per default, if you want it somwhere
+% else, use the 'Location' option. 'north','east','south','west' are
+% predefined, otherwise use the 'custom' option and provide the desired
+% 'Position' (relative to your x- and y-axis limits)
arguments
figs (1,:) {mustBeFigure}
prefix (1,:) {mustBeText}= ''
+ options.Fontsize (1,1) {mustBeInteger} = 8
+ options.Location (1,:) {mustBeText} = 'east'
+ options.Position (1,2) {mustBeVector} = [1,0.4] % default for east
+ options.Rotation (1,1) {mustBeInteger} = 0
end
if isempty(prefix)
warning('no project prefix defined')
end
+switch options.Location
+ case 'north'
+ options.Position = [0.4,0.95];
+ options.Rotation = 0;
+ case 'east'
+ options.Position = [1,0.4];
+ options.Rotation = 90;
+ case 'south'
+ options.Position = [0.4,.02];
+ options.Rotation = 0;
+ case 'west'
+ options.Position = [.05,0.4];
+ options.Rotation = 90;
+ case 'custom'
+ % Check if Position is valid
+ if ~all(0 <= options.Position & options.Position <= 1)
+ options.Position = [1,0.4];
+ warning('options.Position is not valid, TagPlot default values instead');
+ end
+ otherwise % set default position
+ warning([options.Location, ' is not a defined location, TagPlot uses location east instead']);
+ options.Location = 'east'; options.Position = [1,0.4];
+end
+
for n = 1:numel(figs)
ID = CreateID; % Create ID
ID = [prefix,'-',ID]; % add Prefix
@@ -19,8 +53,10 @@ for n = 1:numel(figs)
ylim =get(axes,'YLim');
xlim =get(axes,'XLim');
%ID
- text(axes,xlim(2),0.4*ylim(2), ID,'Fontsize',8,'Rotation',90,'VerticalAlignment','bottom',...
- 'Color', 0.65*[1 1 1],'BackgroundColor','w');
+ position = [options.Position(1)*xlim(2), options.Position(2)*ylim(2)];
+ text(axes,position(1),position(2), ID,'Fontsize',options.Fontsize,...
+ 'Rotation',options.Rotation, 'VerticalAlignment','bottom','Color',...
+ 0.65*[1 1 1],'BackgroundColor','w');
set(figs(n),'Tag', ID);
end
diff --git a/fcn_help/FileCompare.m b/fcn_help/FileCompare.m
deleted file mode 100644
index aa5adfe..0000000
--- a/fcn_help/FileCompare.m
+++ /dev/null
@@ -1,29 +0,0 @@
-function [status] = fileCompare(filename1,filename2)
-%UNTITLED2 Summary of this function goes here
-% Detailed explanation goes here
-
-[~,~,ext1] = fileparts(filename1);
-[~,~,ext2] = fileparts(filename2);
-
-if ~isequal(ext1,ext2)
- 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')
-end
-
-
-end
-
diff --git a/fcn_help/createFileCopy.m b/fcn_help/createFileCopy.m
new file mode 100644
index 0000000..4bf198e
--- /dev/null
+++ b/fcn_help/createFileCopy.m
@@ -0,0 +1,52 @@
+function [] = 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
+ disp(['start to copy ', type]);
+
+ if ~iscell(filePaths)
+ %fixes Issue if Filepath is a char and not a cell array
+ filePaths = {filePaths};
+ end
+
+ try
+ for i = 1:numel(filePaths)
+ FileNameAndLocation = filePaths{i};
+ [~,name,ext] = fileparts(filePaths{i}); % get the extension
+
+ switch type
+ case 'data'
+ 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
+
+ % Write the file
+ 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
+ count = count + 1;
+ [~,name,ext] = fileparts(RemotePath);
+ RemotePath = fullfile(storPath,folderName,...
+ [name,'_',num2str(count),ext]);
+ end
+ copyfile(FileNameAndLocation,RemotePath);
+ end
+ disp([type, ' sucessfully published']);
+ catch
+ warning([type,' export was not sucessful'])
+ end %try
+end
+
diff --git a/fcn_help/createLinkedHDF5.m b/fcn_help/createLinkedHDF5.m
index 5b1e971..2738fd1 100644
--- a/fcn_help/createLinkedHDF5.m
+++ b/fcn_help/createLinkedHDF5.m
@@ -1,20 +1,20 @@
function [status] = createLinkedHDF5(SourceFile,TargetPath,ID)
-%UNTITLED4 Summary of this function goes here
-% Detailed explanation goes here
+%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
plist_id = 'H5P_DEFAULT';
-% Work in Progress... Problem mit dem Pfad...
-
-try
- fid = H5F.create(fullfile(TargetPath,[ID,'_data.h5']));
+% try
+ fid = H5F.create(fullfile(TargetPath,ID,[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(['..\data\',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
diff --git a/fcn_help/fileCompare.m b/fcn_help/fileCompare.m
new file mode 100644
index 0000000..c9007e7
--- /dev/null
+++ b/fcn_help/fileCompare.m
@@ -0,0 +1,49 @@
+function [status, id] = fileCompare(filename,fileList)
+%fileCompare checks if file1 is (binary) identical to a file in filelist
+% it returns a sttus and the id of the identical file
+% the functions uses the windows system function fc or the unix function
+% diff
+
+if isempty(fileList)
+ % no comparison necessary
+ status =false;
+ id = 0;
+ return
+end
+
+[~,~,ext1] = fileparts(filename);
+id = zeros(height(fileList),1);
+
+for i=1:height(fileList)
+ [~,~,ext2] = fileparts(fileList.name{i});
+
+ if ~isequal(ext1,ext2)
+ %warning('File extension are not identical');
+ status = false;
+ continue
+ end
+
+ filepath = fullfile(fileList.folder{i},fileList.name{i});
+ if ispc
+ [status,~] = system(['fc ' filename ' ' filepath]);
+ % 0 -> identical, 1 -> not identical
+ status = ~status; % false (not identical), true(identical)
+
+ elseif isunix %untested!
+ [status,~] = system(['diff ' filename ' ' filepath]);
+ else
+ warning('Platform not supported')
+ end
+
+ if status == 1
+ id(i) = 1;
+ else
+ % Status can also be any other number e.g. 2
+ id(i) = 0;
+ end
+
+ id =logical(id); %bugfix
+end
+
+end
+
diff --git a/fcn_help/removePltIdFiles.m b/fcn_help/removePltIdFiles.m
new file mode 100644
index 0000000..3080c22
--- /dev/null
+++ b/fcn_help/removePltIdFiles.m
@@ -0,0 +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
+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
+
diff --git a/fcn_help/replaceLinkedHDF5.m b/fcn_help/replaceLinkedHDF5.m
new file mode 100644
index 0000000..e84e49f
--- /dev/null
+++ b/fcn_help/replaceLinkedHDF5.m
@@ -0,0 +1,61 @@
+function replaceLinkedHDF5(linkedFilepath)
+% replaceLinkedHDF5 replaces the HDF5, that contains only a link to another
+% HDF5 File with a file containing the actual Data, thus turning it into an
+% independent data file. It essentially turns the plotID option
+% 'centralized' into 'individual'.
+% Filepath is the location of the File that contains the link. The
+% filepath to the linked data has to be present in the file itself.
+
+
+
+%% Check whether the only Objects present are links
+h5inf = h5info(linkedFilepath);
+
+% default behaviour dont overwrite
+overwrite = false;
+
+if isempty([h5inf.Groups, h5inf.Datasets, h5inf.Datatypes, h5inf.Attributes]) && ...
+ all(size(h5inf.Links) == [1 1])
+ % There are no other known objects present and
+ % there is only one linked file
+ overwrite = true;
+end
+
+%% Create Copies of files
+for i = 1:size(h5inf.Links, 2)
+ % This is the file with full data
+ linkTargetPath = h5inf.Links(i).Value{1,1};
+ % This is the empty file
+ % TODO filename decision
+ linkSourcePath = strcat(linkedFilepath,'_',num2str(i));
+
+ % Create an absolute path from the relative linking path
+ absoluteTP = regexp(linkSourcePath, filesep, 'split');
+ TargetPathSplit = regexp(linkTargetPath, filesep, 'split');
+ % How many levels do we need to go up in the relative path
+ % This is merely counting the occurances of '..' within the path, but
+ % should not cause issues if the realtive path was created by the
+ % linking process
+ levelsUp = sum(contains(TargetPathSplit,'..'));
+ absoluteTP = absoluteTP(1:(end-(1+levelsUp)) ); %Remove filename + levels
+ linkTargetPath = strjoin([absoluteTP, TargetPathSplit(~contains(TargetPathSplit,'..'))],filesep);
+
+ if ~isfile(linkTargetPath)
+ warning(strcat("Link destination """,linkTargetPath,""" does not exist or relative path does not fit, no copy created"))
+ end
+
+ if overwrite % can only be for i=1, and size = 1
+ linkSourcePath = linkedFilepath;
+ end
+ disp('Copying file from ', linkSourcePath, ' to ', linkTargetPath)
+ copyfile(linkTargetPath,linkSourcePath);
+
+end
+
+
+
+end
+
+
+
+
diff --git a/test_data.mat b/test_data.mat
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--
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