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In a matlab script, I use the shell escape character "!" to run other python scripts like external commands. All was running without any problem, excepted since the addition of a portion of code concerning the module Wand (I need this to convert images.pdf to images.png and crop margins). It's incredible, it is not working from matlab but is working very well if it is launched from a shell !

From the Python interpreter, it is working fine:

:~ $ python
Python 2.7.9 (v2.7.9:648dcafa7e5f, Dec 10 2014, 10:10:46) 
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

>>> from wand.image import Image as wandImage
>>> with wandImage(filename = '/Users/toto/test.pdf') as img:
...     img.save(filename = '/Users/toto/test.png')
... 
>>>

From a script, it is working fine:

-The script test.py:

$ pwd; ls -l test.py
/Users/toto
-rwxrwxrwx  1 toto  staff  326 22 sep 10:23 test.py
$
$ more test.py
#! /usr/bin/python
# -*- coding: utf-8 -*- # Character encoding, recommended
## -*- coding: iso-8859-1 -*- # Character encoding, old  (Latin-1)

from wand.image import Image as wandImage

with wandImage(filename = '/Users/toto/test.pdf') as img:
  img.save(filename = '/Users/toto/test.png')

-Call in a shell:

$ /Users/toto/test.py
$

From Matlab, not working !:

>> ! /Users/toto/test.py
Traceback (most recent call last):
  File "/Users/toto/test.py", line 9, in <module>
    img.save(filename = '/Users/toto/test.png')
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/wand/image.py", line 2719, in save
    self.raise_exception()
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/wand/resource.py", line 222, in raise_exception
    raise e
wand.exceptions.WandError: wand contains no images `MagickWand-1' @ error/magick-image.c/MagickWriteImage/13115
>>

Arghhh I feel like a caged lion. I guess I have forgotten something, but I do not find !! Any help / suggestion will be very appreciated !!!

Edit 1:

It seems that the problem comes from the "convert" function of ImageMagick.

-In a shell, work fine:

$ /usr/local/bin/convert /Users/toto/test.pdf -crop 510x613+42+64 /Users/toto/test-crop.png
$

-In Matlab, does not work:

>>! /usr/local/bin/convert /Users/toto/test.pdf -crop 510x613+42+64 /Users/toto/test-crop.png
convert: no images defined `/Users/toto/test-crop.png' @ error/convert.c/ConvertImageCommand/3230.
>>

:-(

servoz
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1 Answers1

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I just found the solution ! All was caused because the user $PATH is not the same in Matlab ......

Example, in a Shell:

$ echo $PATH
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/texbin:/usr/X11/bin:/usr/bin/IRMAGE_python_scripts
$

But in Matlab:

>> ! echo $PATH
/usr/bin:/bin:/usr/sbin:/sbin
>>

The solution is to define in Matlab the correct PATH (the same than the user $PATH, in the system) :

2 solutions:

-Starting from the current PATH in Matlab:

>> setenv('PATH', [getenv('PATH'),':','/usr/local/bin',':','/opt/X11/bin',':','/usr/texbin',':','/usr/X11/bin',':','/usr/bin/IRMAGE_python_scripts']);
>> ! echo $PATH
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/texbin:/usr/X11/bin:/usr/bin/IRMAGE_python_scripts
>>

-Or defining totally the PATH:

>> !echo $PATH
/usr/bin:/bin:/usr/sbin:/sbin
>> setenv('PATH', ['/usr/bin',':','/bin',':','/usr/sbin',':','/sbin',':','/usr/local/bin',':','/opt/X11/bin',':','/usr/texbin',':','/usr/X11/bin',':','/usr/bin/IRMAGE_python_scripts'])
>> !echo $PATH
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/texbin:/usr/X11/bin:/usr/bin/IRMAGE_python_scripts

All is working very well now. Hoping this will help somebody, I have worked around a long time before understanding !!!

servoz
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