1._The_MATLAB_server_running_in_MATLAB: 1. The MATLAB server running in MATLAB

In R.matlab: Read and Write MAT Files and Call MATLAB from Within R

1. The MATLAB server running in MATLAB

Description

This section gives addition details on the MATLAB server. At the end, the MatlabServer.m script and the InputStreamByteWrapper.java code is shown.

Starting the MATLAB server on Windows

Note that you "cannot prevent MATLAB from creating a window when starting on Windows systems, but you can force the window to be hidden, by using " the option -minimize. See https://www.mathworks.com/matlabcentral/answers/102082 for more information.

MatlabServer.m script

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% MatlabServer
%
% This scripts starts a minimalistic MATLAB "server".
%
% When started, the server listens for connections at port 9999 or the
% port number specified by the environment variable 'MATLABSERVER_PORT'.
%
% Troubleshooting: If not working out of the box, add this will to the
% MATLAB path. Make sure InputStreamByteWrapper.class is in the same
% directory as this file!
%
% Requirements:
% This requires MATLAB with Java support, i.e. MATLAB v6 or higher.
%
% Author: Henrik Bengtsson, 2002-2016
%
% References:
% [1] http://www.mathworks.com/access/helpdesk/help/techdoc/
%                                     matlab_external/ch_jav34.shtml#49439
% [2] http://staff.science.uva.nl/~horus/dox/horus2.0/user/
%                                                  html/n_installUnix.html
% [3] http://www.mathworks.com/access/helpdesk/help/toolbox/
%                                              modelsim/a1057689278b4.html
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
fprintf(2, 'Running MatlabServer v3.5.9-9000\n');

%  addpath R/R_LIBS/linux/library/R.matlab/misc/

% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% MATLAB version-dependent setup
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Identify major version of Matlab
MatlabServer_tmp_hasMajor = eval('length(regexp(version, ''^[0-9]'')) ~= 0', '0');
if (MatlabServer_tmp_hasMajor)
  MatlabServer_tmp_verParts = sscanf(version, '%d.');
  MatlabServer_tmp_verMajor = MatlabServer_tmp_verParts(1);
  clear MatlabServer_tmp_verParts;
else
  MatlabServer_tmp_verMajor = -1;
end
clear MatlabServer_tmp_hasMajor;

if (MatlabServer_tmp_verMajor < 6)
  % Java is not available/supported
  error('MATLAB v5.x and below is not supported.');
elseif (MatlabServer_tmp_verMajor == 6)
  fprintf(2, 'MATLAB v6.x detected.\n');
  % Default save option
  MatlabServer_saveOption = '';
  % In MATLAB v6 only the static Java CLASSPATH is supported. It is
  % specified by a 'classpath.txt' file. The default one can be found
  % by which('classpath.txt'). If a 'classpath.txt' exists in the
  % current(!) directory (that MATLAB is started from), it *replaces*
  % the global one. Thus, it is not possible to add additional paths;
  % the global ones has to be copied to the local 'classpath.txt' file.
  %
  % To do the above automatically from R, does not seem to be an option.
else
  fprintf(2, 'MATLAB v7.x or higher detected.\n');
  % MATLAB v7 and above saves compressed files, which is not recognized
  % by R.matlab's readMat(); force saving in old format.
  MatlabServer_saveOption = '-V6';
  fprintf(2, 'Saving with option -V6.\n');

  % In MATLAB v7 and above both static and dynamic Java CLASSPATH:s exist.
  % Using dynamic ones, it is possible to add the file
  % InputStreamByteWrapper.class to CLASSPATH, given it is
  % in the same directory as this script.
  javaaddpath({fileparts(which('MatlabServer'))});
  fprintf(2, 'Added InputStreamByteWrapper to dynamic Java CLASSPATH.\n');
end
clear MatlabServer_tmp_verMajor;


% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Import Java classes
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
import java.io.*;
import java.net.*;


% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% If an old MATLAB server is running, close it
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% If a server object exists from a previous run, close it.
if (exist('MatlabServer_server'))
  close(MatlabServer_server);
  clear MatlabServer_server;
end

% If an input stream exists from a previous run, close it.
if (exist('MatlabServer_is'))
  close(MatlabServer_is);
  clear MatlabServer_is;
end

% If an output stream exists from a previous run, close it.
if (exist('MatlabServer_os'))
  close(MatlabServer_os);
  clear MatlabServer_os;
end

fprintf(2, '----------------------\n');
fprintf(2, 'MATLAB server started!\n');
fprintf(2, '----------------------\n');

fprintf(2, 'MATLAB working directory: %s\n', pwd);


% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Initiate server socket to which clients may connect
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
MatlabServer_port = getenv('MATLABSERVER_PORT');
if (length(MatlabServer_port) > 0)
  MatlabServer_port = str2num(MatlabServer_port);
else
  % Try to open a server socket on port 9999
  MatlabServer_port = 9999;
end

% Ports 1-1023 are reserved for the Internet Assigned Numbers Authority.
% Ports 49152-65535 are dynamic ports for the OS. [3]
if (MatlabServer_port < 1023 | MatlabServer_port > 65535)
  error('Cannot not open connection. Port (''MATLABSERVER_PORT'') is out of range [1023,65535]: %d', MatlabServer_port);
end

fprintf(2, 'Trying to open server socket (port %d)...', MatlabServer_port);
MatlabServer_server = java.net.ServerSocket(MatlabServer_port);
fprintf(2, 'done.\n');


% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Wait for client to connect
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Create a socket object from the ServerSocket to listen and accept
% connections.
% Open input and output streams

% Wait for the client to connect
fprintf(2, 'Waiting for client to connect (port %d)...', MatlabServer_port);
MatlabServer_clientSocket = accept(MatlabServer_server);
fprintf(2, 'connected.\n');

% ...client connected.
MatlabServer_is = java.io.DataInputStream(getInputStream(MatlabServer_clientSocket));
MatlabServer_os = java.io.DataOutputStream(getOutputStream(MatlabServer_clientSocket));



% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% The MATLAB server state machine
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Commands
MatlabServer_commands = {'eval', 'send', 'receive', 'send-remote', 'receive-remote', 'echo', 'evalc'};

MatlabServer_lasterr = [];
MatlabServer_variables = [];

% As long as we receive data, echo that data back to the client.
MatlabServer_state = 0;
while (MatlabServer_state >= 0),
  if (MatlabServer_state == 0)
    MatlabServer_tmp_cmd = readByte(MatlabServer_is);
    fprintf(2, 'Received cmd: %d\n', MatlabServer_tmp_cmd);
    if (MatlabServer_tmp_cmd < -1 | MatlabServer_tmp_cmd > length(MatlabServer_commands))
      fprintf(2, 'Unknown command code: %d\n', MatlabServer_tmp_cmd);
    else
      MatlabServer_state = MatlabServer_tmp_cmd;
    end
    clear MatlabServer_tmp_cmd;

  %-------------------
  % 'evalc'
  %-------------------
  elseif (MatlabServer_state == strmatch('evalc', MatlabServer_commands, 'exact'))
    MatlabServer_tmp_bfr = char(readUTF(MatlabServer_is));
    fprintf(2, '"evalc" string: "%s"\n', MatlabServer_tmp_bfr);
    try
      MatlabServer_tmp_bfr = sprintf(MatlabServer_tmp_bfr);
      MatlabServer_tmp_result = evalc(MatlabServer_tmp_bfr);
      writeByte(MatlabServer_os, 0);
      fprintf(2, 'Sent byte: %d\n', 0);
      writeUTF(MatlabServer_os, MatlabServer_tmp_result);
      fprintf(2, 'Sent UTF: %s\n', MatlabServer_tmp_result);
      flush(MatlabServer_os);
      clear MatlabServer_tmp_result;
    catch
      MatlabServer_lasterr = sprintf('Failed to evaluate expression ''%s''.', MatlabServer_tmp_bfr);
      fprintf(2, 'EvaluationException: %s\n', MatlabServer_lasterr);
      writeByte(MatlabServer_os, -1);
      fprintf(2, 'Sent byte: %d\n', -1);
      writeUTF(MatlabServer_os, MatlabServer_lasterr);
      fprintf(2, 'Sent UTF: %s\n', MatlabServer_lasterr);
      flush(MatlabServer_os);
    end
    flush(MatlabServer_os);
    MatlabServer_state = 0;
    clear MatlabServer_tmp_bfr;

  %-------------------
  % 'eval'
  %-------------------
  elseif (MatlabServer_state == strmatch('eval', MatlabServer_commands, 'exact'))
    MatlabServer_tmp_bfr = char(readUTF(MatlabServer_is));
    fprintf(2, '"eval" string: "%s"\n', MatlabServer_tmp_bfr);
    try
      eval(MatlabServer_tmp_bfr);
      writeByte(MatlabServer_os, 0);
      fprintf(2, 'Sent byte: %d\n', 0);
      flush(MatlabServer_os);
    catch
      MatlabServer_lasterr = sprintf('Failed to evaluate expression ''%s''.', MatlabServer_tmp_bfr);
      fprintf(2, 'EvaluationException: %s\n', MatlabServer_lasterr);
      writeByte(MatlabServer_os, -1);
      fprintf(2, 'Sent byte: %d\n', -1);
      writeUTF(MatlabServer_os, MatlabServer_lasterr);
      fprintf(2, 'Sent UTF: %s\n', MatlabServer_lasterr);
      flush(MatlabServer_os);
    end
    flush(MatlabServer_os);
    MatlabServer_state = 0;
    clear MatlabServer_tmp_bfr;
 
  %-------------------
  % 'send'
  %-------------------
  elseif (MatlabServer_state == strmatch('send', MatlabServer_commands, 'exact'))
    MatlabServer_tmp_tmpname = sprintf('%s_%d.mat', tempname, MatlabServer_port);
    MatlabServer_tmp_expr = sprintf('save(MatlabServer_tmp_tmpname, ''%s''', MatlabServer_saveOption);
    MatlabServer_tmp_ok = 1;
    for MatlabServer_tmp_k=1:length(MatlabServer_variables),
      MatlabServer_tmp_variable = MatlabServer_variables{MatlabServer_tmp_k};
      if (exist(MatlabServer_tmp_variable) ~= 1)
        MatlabServer_lasterr = sprintf('Variable ''%s'' not found.', MatlabServer_tmp_variable);
        fprintf(2, '%s\n', MatlabServer_lasterr);
        MatlabServer_tmp_ok = 0;
        break;
      end;
      MatlabServer_tmp_expr = sprintf('%s, ''%s''', MatlabServer_tmp_expr, MatlabServer_tmp_variable);
    end;

    MatlabServer_tmp_expr = sprintf('%s)', MatlabServer_tmp_expr);
    if (~MatlabServer_tmp_ok)
      writeInt(MatlabServer_os, -1);
      writeUTF(MatlabServer_os, MatlabServer_lasterr);
    else
      fprintf(2, '%s\n', MatlabServer_tmp_expr);
      eval(MatlabServer_tmp_expr);
      writeInt(MatlabServer_os, 0); % Here anything but -1 means "success"
      writeUTF(MatlabServer_os, MatlabServer_tmp_tmpname);
    end
   
    MatlabServer_tmp_answer = readByte(MatlabServer_is);
    fprintf(2, 'answer=%d\n', MatlabServer_tmp_answer);
   
    MatlabServer_state = 0;
    clear MatlabServer_tmp_name MatlabServer_tmp_expr MatlabServer_tmp_ok MatlabServer_tmp_answer;

  %-------------------
  % 'send-remote'
  %-------------------
  elseif (MatlabServer_state == strmatch('send-remote', MatlabServer_commands, 'exact'))
    MatlabServer_tmp_tmpname = sprintf('%s_%d.mat', tempname, MatlabServer_port);
    MatlabServer_tmp_expr = sprintf('save(MatlabServer_tmp_tmpname, ''%s''', MatlabServer_saveOption);
    MatlabServer_tmp_ok = 1;
    for MatlabServer_tmp_k=1:length(MatlabServer_variables),
      MatlabServer_tmp_variable = MatlabServer_variables{MatlabServer_tmp_k};
      if (exist(MatlabServer_tmp_variable) ~= 1)
        MatlabServer_lasterr = sprintf('Variable ''%s'' not found.', MatlabServer_tmp_variable);
        fprintf(2, '%s\n', MatlabServer_lasterr);
        MatlabServer_tmp_ok = 0;
        break;
      end;
      MatlabServer_tmp_expr = sprintf('%s, ''%s''', MatlabServer_tmp_expr, MatlabServer_tmp_variable);
    end;
    clear MatlabServer_tmp_k MatlabServer_tmp_variable;

    MatlabServer_tmp_expr = sprintf('%s)', MatlabServer_tmp_expr);
    if (~MatlabServer_tmp_ok)
      writeInt(MatlabServer_os, -1);
      writeUTF(MatlabServer_os, MatlabServer_lasterr);
    else
      fprintf(2, '%s\n', MatlabServer_tmp_expr);
      eval(MatlabServer_tmp_expr);
      MatlabServer_tmp_file = java.io.File(MatlabServer_tmp_tmpname);
      MatlabServer_tmp_maxLength = length(MatlabServer_tmp_file);
      clear MatlabServer_tmp_file;
      writeInt(MatlabServer_os, MatlabServer_tmp_maxLength); % Here anything but -1 means "success"
      fprintf(2, 'Send int: %d (maxLength)\n', MatlabServer_tmp_maxLength);
      MatlabServer_tmp_fid = fopen(MatlabServer_tmp_tmpname, 'r');
      MatlabServer_tmp_count = 1;
      while (MatlabServer_tmp_count ~= 0)
        [MatlabServer_tmp_bfr, MatlabServer_tmp_count] = fread(MatlabServer_tmp_fid, 65536, 'int8');
        if (MatlabServer_tmp_count > 0)
          write(MatlabServer_os, MatlabServer_tmp_bfr);
        end;
      end;
      fclose(MatlabServer_tmp_fid);
      fprintf(2, 'Send buffer: %d bytes.\n', MatlabServer_tmp_maxLength);
      delete(MatlabServer_tmp_tmpname);
      clear MatlabServer_tmp_bfr MatlabServer_tmp_count MatlabServer_tmp_maxLength MatlabServer_tmp_fid MatlabServer_tmp_tmpname;
    end
    flush(MatlabServer_os);
   
    MatlabServer_tmp_answer = readByte(MatlabServer_is);
    fprintf(2, 'answer=%d\n', MatlabServer_tmp_answer);
   
    MatlabServer_state = 0;
    clear MatlabServer_tmp_name MatlabServer_tmp_expr MatlabServer_tmp_ok MatlabServer_tmp_answer; 

  %-------------------
  % 'receive-remote'
  %-------------------
  elseif (MatlabServer_state == strmatch('receive-remote', MatlabServer_commands, 'exact'))
    MatlabServer_tmp_len = readInt(MatlabServer_is);
    fprintf(2, 'Will read MAT file structure of length: %d bytes.\n', MatlabServer_tmp_len);

    MatlabServer_tmp_reader = InputStreamByteWrapper(4096);
    MatlabServer_tmp_bfr = [];
    MatlabServer_tmp_count = 1;
    while (MatlabServer_tmp_len > 0 & MatlabServer_tmp_count > 0)
      MatlabServer_tmp_count = MatlabServer_tmp_reader.read(MatlabServer_is, min(4096, MatlabServer_tmp_len));
      if (MatlabServer_tmp_count > 0)
        MatlabServer_tmp_bfr = [MatlabServer_tmp_bfr; MatlabServer_tmp_reader.bfr(1:MatlabServer_tmp_count)];
        MatlabServer_tmp_len = MatlabServer_tmp_len - MatlabServer_tmp_count;
      end;
    end;

    clear MatlabServer_tmp_reader MatlabServer_tmp_count MatlabServer_tmp_len;

    MatlabServer_tmp_tmpfile = sprintf('%s_%d.mat', tempname, MatlabServer_port);
    MatlabServer_tmp_fh = fopen(MatlabServer_tmp_tmpfile, 'wb');
    fwrite(MatlabServer_tmp_fh, MatlabServer_tmp_bfr, 'int8');
    fclose(MatlabServer_tmp_fh);

    clear MatlabServer_tmp_fh MatlabServer_tmp_bfr;
   
    load(MatlabServer_tmp_tmpfile);
   
    delete(MatlabServer_tmp_tmpfile);
    clear MatlabServer_tmp_tmpfile;
    writeByte(MatlabServer_os, 0);

    MatlabServer_state = 0;
   
  %-------------------
  % 'receive'
  %-------------------
  elseif (MatlabServer_state == strmatch('receive', MatlabServer_commands, 'exact'))
    MatlabServer_tmp_filename = char(readUTF(MatlabServer_is));
    fprintf(2, 'Will read MAT file: "%s"\n', MatlabServer_tmp_filename);
    load(MatlabServer_tmp_filename);
    clear MatlabServer_tmp_filename;
    writeByte(MatlabServer_os, 0);
    MatlabServer_state = 0;
    clear MatlabServer_tmp_filename;
  end
end


% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Shutting down the MATLAB server
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

fprintf(2, '-----------------------\n');
fprintf(2, 'MATLAB server shutdown!\n');
fprintf(2, '-----------------------\n');
writeByte(MatlabServer_os, 0);
close(MatlabServer_os);
close(MatlabServer_is);
close(MatlabServer_server);
quit;

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% HISTORY:
% 2016-04-05 [v3.6.0]
% o All verbose/debug messages are outputted to stream #2 ("stderr").
% 2015-09-11 [v3.3.0]
% o Now temporary files use format <tempname>_<port>.mat.
% o Add 'MatlabServer_' prefix to all variables.
% o Add 'evalc' command.  Thanks to Rohan Shah for this.
% 2015-01-08 [v3.1.2]
% o BUG FIX: Matlab$getVariable() for a non-existing variable would
%   crash the R-to-Matlab communication if remote=FALSE.
% 2014-06-23 [v3.0.2]
% o ROBUSTNESS: Variables 'lasterr' and 'variables' are now always
%   defined. Potential bug spotted by Steven Jaffe at Morgan Stanley.
% o Added more progress/verbose output, e.g. current working directory.
% 2014-01-21 [v2.2.0]
% o BUG FIX: The MatlabServer.m script would incorrectly consider
%   Matlab v8 and above as Matlab v6.  Thanks to Frank Stephen at NREL
%   for reporting on this and providing a patch.
% 2013-07-11 [v1.3.5]
% o Updated messages to use 'MATLAB' instead of 'Matlab'.
% 2010-10-25 [v1.3.4]
% o BUG FIX: The MatlabServer.m script incorrectly referred to the
%   InputStreamByteWrapper class as java.io.InputStreamByteWrapper.
%   Thanks Kenvor Cothey at GMO LCC for reporting on this.
% 2010-08-28
% o Now the MatlabServer script reports its version when started.
% 2010-08-27
% o BUG FIX: Now MatlabServer.m saves variables using the function form,
%   i.e. save().  This solves the problem of having single quotation marks
%   in the pathname. Thanks Michael Q. Fan at NC State University for
%   reporting this problem.
% 2009-08-25
% o BUG FIX: Started to get the error "Undefined function or method
%   'ServerSocket' for input arguments of type 'double'.".  It seems like
%   import java.net.* etc does not work. A workaround is to specify the
%   full path for all Java classes, e.g. java.net.ServerSocket.
%   Thanks Nicolas Stadler for reporting this issue.
% 2006-12-28
% o Extended the accepted range of ports from [1023,49151] to [1023,66535].
% 2006-05-08
% o BUG FIX: The error message string for reporting port out of range
%   was invalid and gave the error '... Line: 109 Column: 45 ")" expected,
%   "identifier" found.'.  Thanks Alexander Nervedi for reporting this.
% 2006-01-21
% o Now an error is thrown if port number is out of (safe) range.
% o Added option to specify the port number via the system environment
%   variable MATLABSERVER_PORT, after request by Wang Yu, Iowa State Univ.
% 2005-03-08
% o BUG FIX: substring() is not recognized by MATLAB v7. Using regexp()
%   which works in MATLAB 6.5 and 7. Workaround eval('try', 'catch').
%   Thanks Patrick Drechsler, University of Wuerzburg for the bug report.
% 2005-02-24
% o Now the dynamic Java classpath is set for MATLAB v7 or higher. This
%   will simplify life for MATLAB v7 users.
% 2005-02-22
% o Added javaaddpath() to include InputStreamByteWrapper.class.
%   Thanks Yichun Wei for feedback and great suggestions.
% 2005-02-11
% o If MATLAB v7 or higher is detected, all MAT structures are saved with
%   option '-V6' so readMat() in R.matlab can read them.
% 2002-09-02 [or maybe a little bit earlier]
% o Created.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

 

InputStreamByteWrapper.(class|java) script

The Java class InputStreamByteWrapper is needed in order for MATLAB to receive data via a data stream. R sends data via a data stream if, and only if, the connection was setup for "remote" communication, that is, with argument remote = TRUE).

 
import java.io.*;

/*********************************************************************
% Compile from within MATLAB with:
% !javac InputStreamByteWrapper.java

% MATLAB example that reads a file using Java code and writes it
% back to a temporary file using MATLAB code. Finally the contents
% of the new file is displayed.

reader = InputStreamByteWrapper;  % Default buffer size is 4096 bytes.

in = java.io.FileInputStream('InputStreamByteWrapper.java');

bfr = [];
len = 1;
while (len > 0)
  len = reader.read(in, 16);  % Read 16 bytes at the time (offset=0).
  if (len > 0)
    bfr = [bfr; reader.bfr(1:len)];  % Add bytes to my MATLAB buffer.
  end
end

close(in);
clear in, reader;

disp(bfr');

tmpfile = tempname;
fh = fopen(tmpfile, 'wb');
fwrite(fh, bfr, 'char');
fclose(fh);

type(tmpfile);
*********************************************************************/
public class InputStreamByteWrapper {
  public static byte[] bfr = null;

  public InputStreamByteWrapper(int capasity) {
    bfr = new byte[capasity];
  }

  public InputStreamByteWrapper() {
    this(4096);
  }

  public int read(InputStream in, int offset, int length) throws IOException {
    return in.read(bfr, offset, length);
  }

  public int read(InputStream in, int length) throws IOException {
    return read(in, 0, length);
  }

  public int read(InputStream in) throws IOException {
    return in.read(bfr);
  }
}

/*********************************************************************
 HISTORY:
2013-07-11
 o Updated comments to use 'MATLAB' instead of 'Matlab'.
2002-09-02 [or maybe a little bit earlier]
 o Created.
*********************************************************************/


 

R.matlab documentation built on Aug. 26, 2022, 1:07 a.m.