Open Microscopy Environment

Hi,

I'm trying to use Malbwrap to call matlab function. Actually, I installed mlab on our server, which is newer than malbwrap.

Here is a link to the mlab project:
https://github.com/ewiger/mlab/blob/master/README.rst

However, I'm getting error:

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Traceback (most recent call last):
  File "./script", line 4, in <module>
    from mlab.releases import R2018a as matlab
  File "/usr/local/lib/python2.7/dist-packages/mlab/releases.py", line 125, in __getattr__
    return self.instances[name]
  File "/usr/local/lib/python2.7/dist-packages/mlab/releases.py", line 80, in __getitem__
    raise ImportError('Import failed, no MATLAB instance selected. Try import mlab.latest_release')
ImportError: Import failed, no MATLAB instance selected. Try import mlab.latest_release

Going into mlab's source code, in matlabcom.py, I found this:

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def find_available_releases():
    # report we have all versions
    return [('R%d%s' % (y,v), '')
        for y in range(2006,2015) for v in ('a','b')]


So, seems like mlab doesn't work with matlab R2018a.

What do you guys think? Is it because I didn't setup malb correctly? Or do I need to switch to an older version of Matlab?

Hang

Hi Hang,

thanks for reporting this issue.

Hang wrote:Here is a link to the mlab project:
https://github.com/ewiger/mlab/blob/master/README.rst

Yes it seems the original mlabwrap project is no longer maintained and mlab seems to have built on top of it although the latest activity dates from two years ago.

Going into mlab's source code, in matlabcom.py, I found this:

Code: Select all

def find_available_releases():
    # report we have all versions
    return [('R%d%s' % (y,v), '')
        for y in range(2006,2015) for v in ('a','b')]


Looking at the source code of `mlabraw.py` it seems that `matlabcom.py` defines the rules for Windows distributions which is probably not your case. For Unix-like systems, `matlabpipe.py` defines the list of releases and seems to be much more relaxed in terms of supported versions

What do you guys think? Is it because I didn't setup malb correctly? Or do I need to switch to an older version of Matlab?

On your server, what is the output of

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python -c 'import sys; print sys.platform'

?

From https://github.com/ewiger/mlab/blob/mas ... ipe.py#L50, the module is expecting MATLAB to be installed in standard locations (`/usr/local/MATLAB`). Does this match your deployment?

Best,
Sebastien

1. The output of

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python -c 'import sys; print sys.platform'

is: Linux2.

2. yea, so my Matlab location is not that. Instead, it's "/home/yuh5/Matlab2018a/bin".

So, I edited that line of code in matlabpipe.py:

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# base_path = '/usr/local/MATLAB/R%d%s/bin/matlab'
        base_path = '/home/yuh5/Matlab%d%s/bin/matlab'

But, now I'm getting error:

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Traceback (most recent call last):
  File "./testMlab.py", line 1, in <module>
    from mlab.releases import R2018a as matlab
  File "/usr/local/lib/python2.7/dist-packages/mlab/releases.py", line 125, in __getattr__
    return self.instances[name]
  File "/usr/local/lib/python2.7/dist-packages/mlab/releases.py", line 63, in __getitem__
    self[k] = self.get_mlab_instance(k)
  File "/usr/local/lib/python2.7/dist-packages/mlab/releases.py", line 87, in get_mlab_instance
    instance = MlabWrap()
  File "/usr/local/lib/python2.7/dist-packages/mlab/mlabwrap.py", line 405, in __init__
    self._session = mlabraw.open()
  File "/usr/local/lib/python2.7/dist-packages/mlab/mlabraw.py", line 60, in open
    raise MatlabReleaseNotFound('Could not open matlab, is it in %s?' % matlab_path)
mlab.matlabpipe.UnixMatlabReleaseNotFound: Could not open matlab, is it in /home/yuh5/Matlab2018a/bin/matlab?
Exception AssertionError: AssertionError() in <bound method MlabWrap.__del__ of <mlab.mlabwrap.MlabWrap object at 0x7f2ecf283450>> ignored

Any ideas?

Hi Hang,

Thanks for the update, seeing the non-standard location allowed the code to progress before the crash is positive.

Without a more detailed traceback, it is hard to know what causes your latest ImportError. It might be useful to uncomment this line and see which call is failing and why.

Also since this is effectively third-party code which is not maintained by OME, our expertise is limited. In addition to this thread, it might be worth double posting your configuration issues on GitHub.

Best,
Sebastien