From: Dror Atariah <drorata@gmail.com>
To: Nick Dokos <ndokos@gmail.com>
Cc: "emacs-orgmode@gnu.org" <emacs-orgmode@gnu.org>
Subject: Re: [Orgmode] Unable to capture the file name generated using matplotlib
Date: Mon, 25 May 2015 19:25:15 +0200 [thread overview]
Message-ID: <CANfRcg2TvK4EgEH_xx6ppR-i2nusqeYJ5s+dXVu6iqxcODEPrA@mail.gmail.com> (raw)
In-Reply-To: <CANfRcg0PRW9dop5V+3f7b4fXGd97VsmPQPWOeDWa84OMkOeBGw@mail.gmail.com>
[-- Attachment #1: Type: text/plain, Size: 4728 bytes --]
I am sorry for reposting, but I'm still in the dark. Am I the only one who
experience this kind of issue? Did someone managed to reproduce the
problem? Does anyone see this message? :)
On Sat, May 23, 2015 at 8:49 PM, Dror Atariah <drorata@gmail.com> wrote:
> I am still helpless here. Any idea how to debug the problem? I would be
> happy to provide any kind of help, but I just cannot do it myself.
>
> Further findings:
> 1) I don't think that matplotlib changes Python's '_', since the tmp file
> that contains the content of '_' is correct.
> 2) Somehow, emacs/orgmode fails to extract the filename.
> 3) It doesn't work also when using emacs 24.5 and orgmode 8.2.10.
>
>
> Following is an org file that tries to summarize the issue:
>
> #+TITLE: Integrate matplotlib figures in an org mode buffer
> * Goal
> The ultimate goal is to use org-babel as a replacement of IPython. The
> first motivation is to enable an easier version controling of the
> document. The first challenge I faced is integration of plots returned
> by ~matplotlib~ in the org buffer.
> * Capturing filename
>
> I would like to use (babel) orgmode as an interactive python
> notebook. Therefore, in order to allow the various code blocks to
> "know" each other, it is important to use the ~:session~
> option. However, once ~:session~ is used, together with ~matplotlib~
> the desired behavior is no longer in place.
>
> * Clean testing, no Matplotlib
> For the sake of testing, the following merely suppose to return the
> filename
>
> #+BEGIN_SRC python :session no_matplotlib :results file :exports both
> x = 'hello '
> y = 'world'
> z = x + y
> 'foo.bar'
> #+END_SRC
>
> #+RESULTS:
> [[file:foo.bar]]
>
> *Passed* Indeed, the ~RESULTS~ block contains a link to the filename
> indicated by the last string.
>
> * Importing Matplotlib
>
> The following minimal example should generate a simple figure,
> ~myfig.png~, and orgmode should capture it and interpret it as a
> filename to be used by the following ~RESULTS~ block.
>
> #+BEGIN_SRC python :session with_matplotlib :results file :exports both
> import matplotlib
> matplotlib.use('Agg')
> import matplotlib.pyplot as plt
> fig=plt.figure(figsize=(3,2))
> plt.plot([1,3,2])
> plt.savefig('myfig.png')
> 'myfig.png'
> #+END_SRC
>
> #+RESULTS:
> [[file:]]
>
> *Failed!* This time, it doesn't work anymore. The file ~myfig.png~ is
> properly generated, but the last string is not captured by
> ~matplotlib~. Following is the content of the corresponding
> interactive python session:
>
> #+BEGIN_SRC
> Process with_matplotlib finished
> Python 3.4.3 (default, Mar 10 2015, 14:53:35)
> [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> >>> >>> ,
> '''/var/folders/kz/1c2cxn1x60n_t5p2j1p02b180000gn/T/py32771xVI''', 'exec'));
> import matplotlib
> >>> import matplotlib
> matplotlib.use('Agg')
> matplotlib.use('Agg')
> import matplotlib.pyplot as plt
> import matplotlib.pyplot as plt
> fig=plt.figure(figsize=(3,2))
> fig=plt.figure(figsize=(3,2))
> plt.plot([1,3,2])
> plt.plot([1,3,2])
> plt.savefig('myfig.png')
> plt.savefig('myfig.png')
> 'myfig.png'
> 'myfig.png'
>
>
> open('/var/folders/kz/1c2cxn1x60n_t5p2j1p02b180000gn/T/babel-32771x4j/python-32771-fO',
> 'w').write(str(_))
> open('/var/folders/kz/1c2cxn1x60n_t5p2j1p02b180000gn/T/babel-32771x4j/python-32771-fO',
> 'w').write(str(_))
>
>
>
>
> 'org_babel_python_eoe'
> 'org_babel_python_eoe'
> >>> [<matplotlib.lines.Line2D object at 0x108e01828>]
> >>> 'myfig.png'
> >>> >>> 9
> >>> >>> >>> 'org_babel_python_eoe'
> >>>
> #+END_SRC
>
> * Some background
>
> ** Python Version
> #+BEGIN_SRC python :session background :results raw
> import sys
> sys.version
> #+END_SRC
>
> #+RESULTS:
> 3.4.3 (default, Mar 10 2015, 14:53:35)
> [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)]
>
> ** Matplotlib version
> #+BEGIN_SRC python :session background :results raw
> import matplotlib
> matplotlib.__version__
> #+END_SRC
>
> #+RESULTS:
> 1.4.3
>
> ** System
> I am running Emacs version ~GNU Emacs 24.5.1 (x86_64-apple-darwin14.1.0,
> NS apple-appkit-1344.72) of 2015-04-19 on tenten-slave.macports.org~
>
> The orgmode version is: ~Org-mode version 8.2.10
> (8.2.10-40-gc763fa-elpaplus @
> /Users/drorata/.emacs.d/elpa/org-plus-contrib-20150518/)~
>
> ** Stackoverflow reference
> I also posted a question in the SE network:
> [[
> http://emacs.stackexchange.com/questions/11075/org-mode-python-session-does-not-return-a-file-name
> ]]
>
> * Question
> So, my question is how to tackle/debug this issue? Can someone give me
> a hand here? That would be really great! Thanks!
>
>
--
Dror Atariah, Ph.D.
de.linkedin.com/in/atariah
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next prev parent reply other threads:[~2015-05-25 17:25 UTC|newest]
Thread overview: 22+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-05-02 7:48 [Orgmode] Unable to capture the file name generated using matplotlib Dror Atariah
2015-05-02 17:09 ` Nick Dokos
2015-05-02 17:11 ` Nick Dokos
2015-05-05 20:20 ` Dror Atariah
2015-05-23 18:49 ` Dror Atariah
2015-05-25 17:25 ` Dror Atariah [this message]
2015-05-25 17:29 ` Ken Mankoff
2015-05-25 18:22 ` Dror Atariah
2015-05-25 18:30 ` John Kitchin
2015-05-26 13:11 ` Dror Atariah
2015-05-26 13:15 ` Ken Mankoff
2015-05-26 13:19 ` Dror Atariah
2015-05-26 13:26 ` Dror Atariah
2015-05-26 14:02 ` Ken Mankoff
2015-05-26 14:37 ` Dror Atariah
2015-05-26 18:39 ` Dror Atariah
2015-06-02 5:49 ` Dror Atariah
2015-06-02 12:21 ` Ken Mankoff
2015-06-02 18:01 ` Dror Atariah
2015-05-26 1:49 ` Ken Mankoff
2015-05-26 13:18 ` Dror Atariah
2015-05-26 14:05 ` Ken Mankoff
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