Standalone compiled with Matlab compiler doesn't work

I have compiled a .exe file of MRiLab (https://se.mathworks.com/matlabcentral/fileexchange/45456-mrilab-v1-2-1) using Matlab compiler.

The program is an excellent MRI-Simulator with which you can, for example, load different phantoms and image them with different MRI sequences and imaging parameters.However, the compiled exe from MRiLab does not work as it does in Matlab. Standalone application of program starts but does not work fully. For example, when I select an MRI sequence the program gives an error message (when the exe is started in Matlab):

Error using DoParseXML (line 60) 
Failed to read XML file C:\Users\sylisiur\AppData\Local\Temp\sylisiur\mcrCache9.9\MRiLab1\MRiLab\PSD\3D\FastSpinEcho\PSD_FSE3D\PSD_FSE3D.xml. 
 
Error in SeqList>Seq_listbox_Callback (line 272) 
 
Error in gui_mainfcn (line 95) 
 
Error in SeqList (line 94) 
 
Error in matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)SeqList('Seq_listbox_Callback',hObject,eventdata,guidata(hObject)) 
 
Error using waitforallfiguresclosed (line 16) 
Error while evaluating UIControl Callback. 

Sometimes the program lets you select some of a sequences, but when I then press the scan button it gives a new error message:

To correct the error, I have tried e.g. change the MCR_CACHE_ROOT to another path that also did not help or delete the mcrcache9.9 folder and run the program again. The versions of Matlab (R2020b) and Runtime (v9.9) also match. Apparently the problem, I think, is with the DoParseXML function (code below)?

I have been trying for a long time to solve the problem and I would be very grateful if someone could help?

BR: S.Y

function theStruct = DoParseXML(dnode)
%DoParseXML(XML_filename)
%convert XML file to a MATLAB structure.

try
   tree = xmlread(dnode);
catch me
   error('Failed to read XML file %s.',dnode);
end

% Recurse over child nodes. This could run into problems 
% with very deeply nested trees.

theStruct = parseChildNodes(tree);
theStruct.current=1;

% ----- Subfunction PARSECHILDNODES -----
function children = parseChildNodes(theNode)
% Recurse over node children.
children = [];
if theNode.hasChildNodes
   childNodes = theNode.getChildNodes;
   numChildNodes = childNodes.getLength;
   allocCell = cell(1, numChildNodes);
   children = struct('Name', allocCell,...
                     'Attributes', allocCell,...
                     'Data', allocCell,...
                     'Children', allocCell,...
                     'current', allocCell);
    i=0;
    for count = 1:numChildNodes
        theChild = childNodes.item(count-1);
        c = makeStructFromNode(theChild);
        if isempty(c)
            i=i+1;
        else
            children(count-i) = c;
        end
    end
    if i>0
        children(numChildNodes-i+1:numChildNodes)=[]; 
    end
end

% ----- Subfunction MAKESTRUCTFROMNODE -----
function nodeStruct = makeStructFromNode(theNode)
% Create structure of node info.

PC=parseChildNodes(theNode);
nodeStruct = struct('Name', char(theNode.getNodeName),...
                    'Attributes', parseAttributes(theNode),...
                    'Data', '',...
                    'Children', PC,...
                    'current',0);

if any(strcmp(methods(theNode), 'getData'))
   nodeStruct.Data = char(theNode.getData); 
else
   nodeStruct.Data = '';
end
if strcmp(nodeStruct.Name,'#text')
   nodeStruct=[];
end

% ----- Subfunction PARSEATTRIBUTES -----
function attributes = parseAttributes(theNode)
% Create attributes structure.
attributes = [];
if theNode.hasAttributes
   theAttributes = theNode.getAttributes;
   numAttributes = theAttributes.getLength;
   allocCell = cell(1, numAttributes);
   attributes = struct('Name', allocCell,...
                       'Value', allocCell);

   for count = 1:numAttributes
      attrib = theAttributes.item(count-1);
      attributes(count).Name = char(attrib.getName);
      attributes(count).Value = char(attrib.getValue);
   end
end

Answer 1

[Bruno Luong]

Have you include PSD_FSE3D.xml in the packaging?

Do you take into account the path of the file is different when you run in standalone mode?

Answer 2

[Sam Y.]

Yes, I added PSD_FSE3D.xml to the package. The path can be a problem. I've been wondering how to add a path to the code in terms of standalone so that it works on different computers. Now, the main file (MRiLab.m) reads the path as follows

[pathstr,name,ext]=fileparts(mfilename('fullpath'));

which is input to the SimuPanel function which opens the program's user interface

SimuPanel(pathstr);

Simupanel contains an opening function that reads the path to its own variable (MRiLabPath):

function varargout = SimuPanel(varargin)
% SIMUPANEL M-file for SimuPanel.fig
%      SIMUPANEL, by itself, creates a new SIMUPANEL or raises the existing
%      singleton*.
%
%      H = SIMUPANEL returns the handle to a new SIMUPANEL or the handle to
%      the existing singleton*.
%
%      SIMUPANEL('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in SIMUPANEL.M with the given input arguments.
%
%      SIMUPANEL('Property','Value',...) creates a new SIMUPANEL or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before SimuPanel_OpeningFcn gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to SimuPanel_OpeningFcn via varargin.
%
%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
%      instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES

% Edit the above text to modify the response to help SimuPanel

% Last Modified by GUIDE v2.5 26-Feb-2014 17:07:31

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @SimuPanel_OpeningFcn, ...
                   'gui_OutputFcn',  @SimuPanel_OutputFcn, ...
                   'gui_LayoutFcn',  [] , ...
                   'gui_Callback',   []);
if nargin && ischar(varargin{1})
    gui_State.gui_Callback = str2func(varargin{1});
end

if nargout
    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
    gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT


% --- Executes just before SimuPanel is made visible.
function SimuPanel_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
% varargin   command line arguments to SimuPanel (see VARARGIN)


%MALab('Welcome')
% clc;
disp( '                                               _______       ');
disp( '_________________________________________     / _____ \      ');
disp( '    .  .     |---- (OO)|       ___   |       | |     | |     ');
disp( '   /\  /\    |__ |  || |      /   \  |___    |_|     |_|     ');
disp( '  /  \/  \   |  \   || |      \___/  |   \   |S|     |N|     ');
disp( ' /   ||   \  |   \_ || |____|     \  |___/  MRI Simulator    ');
disp( '_________________________________________                    ');
disp( 'Version 1.2 - https://sourceforge.net/projects/mrilab/      ');
fprintf('\n');

%MRiLab path
handles.MRiLabPath=varargin{1};


% Check MEX existence
fpath = [handles.MRiLabPath filesep 'Lib' filesep 'bin'];
if exist([fpath filesep 'DoScanAtCPU.mexw64'], 'file')
    % MEX exist, do nothing
else
    try 
        fileUrl = ['http://mrilab.sourceforge.net/bin/MRiLab1.2Bin.zip'];
        zipFileName = fullfile(fpath,'MRiLab1.2Bin.zip');
        disp('Downloading core MEX files from MRiLab website http://sourceforge.net/projects/mrilab/');
        urlwrite(fileUrl,zipFileName);
        disp('Unzip files ...');
        unzip(zipFileName,fpath);
        rehash;
    catch me
        error_msg{1,1}='Some core MEX files for running MRiLab can not be configured.';
        error_msg{2,1}='Please download MRiLab full version with all MEX configured from';
        error_msg{3,1}='http://sourceforge.net/projects/mrilab/';
        errordlg(error_msg);
        return;
    end
end

%System Seperator
if isunix
     sep='/';
elseif ispc
     sep='\';
end
handles.Sep=sep;

%Output Dir
time=clock;
OutputDir=[handles.MRiLabPath handles.Sep 'Output' handles.Sep num2str(time(1)) num2str(time(2)) num2str(time(3)) '-' num2str(time(4)) '-' num2str(time(5))];
if ~isdir(OutputDir)
    mkdir(OutputDir);
    handles.OutputDir=OutputDir;
else
    handles.OutputDir=OutputDir;
end

%System Hardware Check
try
    handles.CPUInfo=DoCPUOSChk;
    if ~isempty(handles.CPUInfo)
        handles.CPU_uimenu=uimenu(handles.SelectPU_uimenu,'Label',handles.CPUInfo.Name);
        set(handles.CPU_uimenu,'Callback',{@Uimenu_ChkFunction, handles.CPU_uimenu});
        set(handles.CPU_uimenu,'Checked','on');
    end
catch me
    handles.CPUInfo.NumThreads = 8; % Open up to 8 threads as default if CPU model is unknown
    handles.CPU_uimenu=uimenu(handles.SelectPU_uimenu,'Label','unknown CPU model');
    set(handles.CPU_uimenu,'Callback',{@Uimenu_ChkFunction, handles.CPU_uimenu});
    set(handles.CPU_uimenu,'Checked','on');
    error_msg{1,1}='Detecting local CPU infomation failed!';
    error_msg{2,1}=me.message;
    warndlg(error_msg);
end

try
    handles.GPUCount=gpuDeviceCount;
    if handles.GPUCount~=0
        for i=1:handles.GPUCount
            handles.GPUInfo=gpuDevice(i);
            GPU_flag = ['GPU' num2str(i) '_uimenu'];
            handles.(GPU_flag)=uimenu(handles.SelectPU_uimenu,'Label',['nVIDIA(R) ' handles.GPUInfo.Name]);
            set(handles.(GPU_flag),'Callback',{@Uimenu_ChkFunction, handles.(GPU_flag)});
            set(handles.(GPU_flag),'Checked','on');
        end
        Uimenu_ChkFunction([],[],handles.GPU1_uimenu); % Set first GPU as default processing unit
    else
        handles.GPU1_uimenu=uimenu(handles.SelectPU_uimenu,'Label','No GPU or unknown GPU model');
        set(handles.GPU1_uimenu,'Callback',{@Uimenu_ChkFunction, handles.GPU1_uimenu});
        error_msg{1,1}='Detecting local GPU infomation failed!';
        warndlg(error_msg);
    end
%     handles.GPUInfo=gpuDevice;
%     if ~isempty(handles.GPUInfo)
% %         handles.GPU_uimenu=uimenu(handles.SelectPU_uimenu,'Label',['nVIDIA(R) ' handles.GPUInfo.Name ' GPU' char(ones(1,12)*32) '@ ' num2str(handles.GPUInfo.ClockRateKHz/1048576,'%3.2f') 'GHz']);
%         handles.GPU_uimenu=uimenu(handles.SelectPU_uimenu,'Label',['nVIDIA(R) ' handles.GPUInfo.Name]);
%         set(handles.GPU_uimenu,'Callback',{@Uimenu_ChkFunction, handles.GPU_uimenu});
%         set(handles.GPU_uimenu,'Checked','on');
%         Uimenu_ChkFunction([],[],handles.GPU_uimenu); % Set GPU as default processing unit
%     end
    
catch me
    handles.GPU1_uimenu=uimenu(handles.SelectPU_uimenu,'Label','No GPU or unknown GPU model');
    set(handles.GPU1_uimenu,'Callback',{@Uimenu_ChkFunction, handles.GPU1_uimenu});
    error_msg{1,1}='Detecting local GPU infomation failed!';
    error_msg{2,1}=me.message;
    warndlg(error_msg);
end

%Global Variables
global VObj; VObj=[];
global VCtl; VCtl=[];
global VMag; VMag=[];
global VCoi; VCoi=[];
global VMot; VMot=[];
global VVar; VVar=[];

try
    handles.SimuAttrStruct=DoParseXML([handles.MRiLabPath handles.Sep 'PSD' handles.Sep '3D' handles.Sep 'SimuAttr.xml']);
catch ME
    DoUpdateInfo(handles,'SimuAttr.xml file is missing or can not be loaded.');
    % Choose default command line output for SimuPanel
    handles.output = hObject;
    % Update handles structure
    guidata(hObject, handles);
    close(hObject);
    return;
end
handles.Setting_tabgroup=uitabgroup(handles.Setting_uipanel);
guidata(hObject, handles);
for i=1:length(handles.SimuAttrStruct.Children)
    eval(['handles.' handles.SimuAttrStruct.Children(i).Name '_tab=uitab( handles.Setting_tabgroup,' '''title'',''' handles.SimuAttrStruct.Children(i).Name ''',''Units'',''normalized'');']);
    eval(['DoEditValue(handles,handles.' handles.SimuAttrStruct.Children(i).Name '_tab,handles.SimuAttrStruct.Children(' num2str(i) ').Attributes,1,[0.2,0.12,0.01,0.1,0.1,0.05]);']);
    handles=guidata(hObject);
end

% Disable scan button when change settings
fieldname=fieldnames(handles.Attrh1);
for i=1:length(fieldname)/2
    set(handles.Attrh1.(fieldname{i*2}),'Callback',{@DoDisableButton,handles});
end

% Turn off uitab warning
% warning('off', 'last');

handles.CoilSel_tabgroup=uitabgroup(handles.CoilSel_uipanel);
handles.CoilTx_tab=uitab( handles.CoilSel_tabgroup, 'title', 'Tx');
handles.CoilRx_tab=uitab( handles.CoilSel_tabgroup, 'title', 'Rx');

% Choose default command line output for SimuPanel
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);

Answer 3

[Sam Y.]

So currently the program reads the path according to the MRiLab folders.

Do I need to program standalone code for compilation with an absolute path reference that I know is located on the target machine?

[Bruno Luong]

Not necessary, you can store file with relative path to your exe file or mfile. It's up to you to organize where your file is located. I have this function that I put somewhere one level seeper than my main app, and I call to retrive the path of my main app.

function currentDir = getcurrentdir
% currentDir = getcurrentdir
if isdeployed % Stand-alone mode.
    [~, result] = system('set PATH');
    currentDir = char(regexpi(result, 'Path=(.*?);', 'tokens', 'once'));
else % MATLAB mode.
    thisfile = mfilename('fullpath');
    currentDir = fileparts(fileparts(thisfile)); % adjust accordingly to on your source folder structure
end

PS: Please do not post your comments as answers.

[Steven Lord]

Not necessary, you can store file with relative path to your exe file or mfile.

That I believe is true for data files, but if the app is looking to add directories containing executable code (MATLAB script, function, or class files) to the application at runtime that will not work in a standalone application. Only code included in the application when it is compiled can be called by the application.

[Bruno Luong]

OP has issue with xml file, which is a data file.

[Sam Y.]

Thank you very much Bruno! I now got a standalone to work on my two different computers. I took advantage of your getcurrentdir code and added the folders contained in the MRiLab program to the standalone folder, which the program utilizes (picture below). This was a great help to me!

BR, SY

Answer 4

[Image Analyst]

Have you exhausted all the suggestions in the FAQ:

https://matlab.fandom.com/wiki/FAQ#My_standalone_executable_won.27t_run_on_the_target_computer._What_can_I_try.3F