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: Sat, 23 May 2015 20:49:52 +0200 [thread overview]
Message-ID: <CANfRcg0PRW9dop5V+3f7b4fXGd97VsmPQPWOeDWa84OMkOeBGw@mail.gmail.com> (raw)
In-Reply-To: <CANfRcg0CguKRXkE+4LC=stRo9ET+KRCny=L==wA+QjiMNoMBGw@mail.gmail.com>
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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!
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next prev parent reply other threads:[~2015-05-23 18:49 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 [this message]
2015-05-25 17:25 ` Dror Atariah
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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