Bug in primatologist -> Basic Mixture Fitting

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Olivier Coulon
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Bug in primatologist -> Basic Mixture Fitting

Postby Olivier Coulon » Mon Feb 19, 2018 5:05 pm

Hello,
Moving on with Primatologist, I encountered the following bug in the "Basic Mixture Fitting" sub-process. It crashes because on lines 73, 84, 106, and 116 there is a call for the function numpy.random.choice().
This function is available in numpy from version 1.7 and above, and BrainVisa comes with numpy 1.6.2 (at least the version I installed on my Ubuntu 14.04).

Olivier
Olivier Coulon
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org

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Olivier Coulon
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Location: MeCA research group, Institut de Neurosciences de La Timone, Marseille, France
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Re: Bug in primatologist -> Basic Mixture Fitting

Postby Olivier Coulon » Tue Feb 20, 2018 3:43 pm

About this bug. On my debian system, we installed the Mandriva 2008 version, and it comes with a newer numpy version, so the bug is not there. On my Ubuntu, I had installed the Ubuntu 12.04 version...
Olivier Coulon
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org

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riviere
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Re: Bug in primatologist -> Basic Mixture Fitting

Postby riviere » Tue Feb 20, 2018 5:32 pm

Hi,
I probably forgot to upgrade numpy on this machine...
Denis

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riviere
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Re: Bug in primatologist -> Basic Mixture Fitting

Postby riviere » Tue Feb 20, 2018 5:58 pm

Can you try to upgrade directly in the brainvisa install directory ?

Code: Select all

<brainvisa_dir>/bin/pip install -U --prefix <brainvisa_dir> numpy scipy

just in case it works ;) (I haven't tried and the pip version here has problems, I had to reinstall it manually)
Denis

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Olivier Coulon
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Re: Bug in primatologist -> Basic Mixture Fitting

Postby Olivier Coulon » Tue Feb 20, 2018 6:34 pm

OK, I'll try tomorrow and will let you know.

Olivier
Olivier Coulon
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org

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Olivier Coulon
Posts: 176
Joined: Fri Feb 27, 2004 11:48 am
Location: MeCA research group, Institut de Neurosciences de La Timone, Marseille, France
Contact:

Re: Bug in primatologist -> Basic Mixture Fitting

Postby Olivier Coulon » Thu Feb 22, 2018 8:00 am

Hello Denis,
pip install does not have any --prefix option.

Olivier
Olivier Coulon
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org

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riviere
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Re: Bug in primatologist -> Basic Mixture Fitting

Postby riviere » Fri Feb 23, 2018 11:06 am

Hi Olivier,
So it's an old pip. You can try to upgrade pip first, using easy_install:

Code: Select all

<brainvisa_dir>/bin/easy_install -U --prefix <brainvisa_dir> pip

then retry the pip command
Denis


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