The Virtual Brain Project

Source code for tvb.adapters.analyzers.matlab_worker

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#   CITATION:
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#   Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide,
#   Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
#       The Virtual Brain: a simulator of primate brain network dynamics.
#   Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)
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"""
This module implements a class for executing arbitray MATLAB code

Conversion between Python types and MATLAB types is handled and dependent
on scipy.io's loadmat and savemat function.

.. moduleauthor:: Marmaduke Woodman <Marmaduke@tvb.invalid>
.. moduleauthor:: Stuart A. Knock <Stuart@tvb.invalid>
"""

import os
import time
import random
import tempfile
from scipy.io import loadmat, savemat
from tvb.basic.profile import TvbProfile
from tvb.core.utils import MATLAB, OCTAVE, matlab_cmd



[docs]class MatlabWorker(object): """ MatlabAnalyzer is an helper class for calling arbitrary MATLAB code with arbitrary parameters. Specific analyzers should derive from this class and implement the interface and launch methods inherited from Asynchronous Adapter. """ matlab_paths = [] def __init__(self): self.mlab_exe = TvbProfile.current.MATLAB_EXECUTABLE self.hex = hex(random.randint(0, 2 ** 32)) self.script_name = "script%s" % self.hex self.script_fname = self.script_name + '.m' self.wkspc_name = "wkspc%s" % self.hex self.wkspc_fname = self.wkspc_name + '.mat' self.done_name = "done%s" % self.hex self.done_fname = self.done_name + '.mat' self.log_fname = "log%s" % self.hex def _matlab_pre(self): """ Called to obtain the pre operation code for MATLAB. Current, we 1. add paths to the MATLAB path 2. enter a try clause """ paths = "".join(["addpath('" + p + "');\n" for p in self.matlab_paths]) return paths + "\ntry\n" def _matlab_post(self): """ Called to obtain the post operation code for MATLAB. Currently, we 1. catch exception if one was raised 2. set the hexstamp variable in MATLAB 3. save all working files """ catch = "\ncatch e\nexception%s = e\nend\n" % self.hex save_clause = "" if MATLAB in self.mlab_exe: save_clause = "hexstamp = '%s'\nsave %s -V7\nsave %s -V7 hexstamp\nquit" if OCTAVE in self.mlab_exe: save_clause = "hexstamp = '%s'\nsave %s.mat -V7\nsave %s.mat -V7 hexstamp\nquit" return catch + save_clause % (self.hex, self.wkspc_name, self.done_name)
[docs] def cleanup(self): """ Make sure Matlab is closed after execution. """ time.sleep(0.5) # wait for MATLAB to close for file_ref in [self.script_fname, self.wkspc_fname, self.done_fname, self.log_fname]: try: os.remove(file_ref) except Exception: pass
[docs] def add_to_path(self, path_to_add): """ Add a path to the list of paths that will be added to the path in the MATLAB session """ self.matlab_paths.append(path_to_add)
[docs] def matlab(self, code, data=None, work_dir=None, cleanup=True): """ method matlab takes as arguments: code: MATLAB code in a string data: a dict of data that scipy.io.savemat knows how to deal with work_dir: working directory to be used by MATLAB cleanup: set to False to keep files and returns a tuple: [0] string of code exec'd by MATLAB [1] string of log produced by MATLAB [2] dict of data from MATLAB's workspace """ wdir = tempfile.tempdir or os.getcwd() os.chdir(wdir) os.chdir(work_dir or os.getcwd()) pre, post = self._matlab_pre(), self._matlab_post() code = ("\nsuccess%s = 0\n" + code + "\nsuccess%s = 1\n") % (self.hex, self.hex) if data: pre += "\nload %s\n" % self.wkspc_name savemat(self.wkspc_fname, data, format="5") with open(self.script_fname, 'w') as file_data: file_data.write(pre + code + post) matlab_cmd(self.mlab_exe, self.script_name, self.log_fname) while not os.path.exists(self.done_fname): time.sleep(0.1) with open(self.log_fname, 'r') as file_data: logtext = file_data.read() retdata = loadmat(self.wkspc_fname, squeeze_me=True) if cleanup: self.cleanup() return pre + code + post, logtext, retdata