How to call OCRopus software, or any conflicting software, from Matlab? - matlab

Question

When calling the OCR software OCRopus directly from Matlab prompt, there is a series of errors that would not appear when the software is called directly from the shell prompt:
>> ! gnome-terminal -x bash ./sampleBash.sh
Traceback (most recent call last):
File "/usr/local/bin/ocropus-gpageseg", line 15, in <module>
from pylab import *
File "/usr/lib/pymodules/python2.7/pylab.py", line 1, in <module>
from matplotlib.pylab import *
File "/usr/lib/pymodules/python2.7/matplotlib/__init__.py", line 156, in <module>
from matplotlib.cbook import is_string_like
File "/usr/lib/pymodules/python2.7/matplotlib/cbook.py", line 28, in <module>
import numpy as np
File "/usr/lib/python2.7/dist-packages/numpy/__init__.py", line 153, in <module>
from . import add_newdocs
File "/usr/lib/python2.7/dist-packages/numpy/add_newdocs.py", line 13, in <module>
from numpy.lib import add_newdoc
File "/usr/lib/python2.7/dist-packages/numpy/lib/__init__.py", line 18, in <module>
from .polynomial import *
File "/usr/lib/python2.7/dist-packages/numpy/lib/polynomial.py", line 19, in <module>
from numpy.linalg import eigvals, lstsq, inv
File "/usr/lib/python2.7/dist-packages/numpy/linalg/__init__.py", line 50, in <module>
from .linalg import *
File "/usr/lib/python2.7/dist-packages/numpy/linalg/linalg.py", line 29, in <module>
from numpy.linalg import lapack_lite, _umath_linalg
ImportError: /opt/MATLAB/R2012b/sys/os/glnxa64/libgfortran.so.3: version `GFORTRAN_1.4' not found (required by /usr/lib/liblapack.so.3)
where sampleBash.sh is:
#!/bin/bash -e
FILENAME='testfile.png'
ocropus-gpageseg --usefilename "$FILENAME"
$SHELL
It seems that there is a clash between Matlab's environment variables and those of the system bash shell. Any idea on how to send a 'clean' shell environment to the OCRopus software (or any other similar software)?
This is not limited to the OCRopus calls, and any software that would conflict with the Matlab environment variables set during the shell call from within Matlab would face the same problem.
Thanks.

Answer 1

A not-so-clean solution could be to remove the clashing variables before calling the OCRopus software:
>> ! gnome-terminal -x bash unset OSG_LD_LIBRARY_PATH; unset XAPPLRESDIR; unset XKEYSYMDB; unset LD_LIBRARY_PATH; unset TOOLBOX; unset XFILESEARCHPATH; unset BASEMATLABPATH; ./sampleBash.sh
In this way, variables such as OSG_LD_LIBRARY_PATH are removed from the environment before calling the OCR software.