From mboxrd@z Thu Jan 1 00:00:00 1970 From: Dror Atariah Subject: Re: [Orgmode] Unable to capture the file name generated using matplotlib Date: Sat, 23 May 2015 20:49:52 +0200 Message-ID: References: <87wq0qsy4o.fsf@alphaville.usersys.redhat.com> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=f46d04428da2fce21a0516c43df6 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:47450) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YwEUe-0003p4-Ig for emacs-orgmode@gnu.org; Sat, 23 May 2015 14:49:58 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YwEUc-0005dL-SB for emacs-orgmode@gnu.org; Sat, 23 May 2015 14:49:56 -0400 Received: from mail-wi0-x235.google.com ([2a00:1450:400c:c05::235]:34509) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YwEUc-0005cp-GF for emacs-orgmode@gnu.org; Sat, 23 May 2015 14:49:54 -0400 Received: by wicmc15 with SMTP id mc15so14111603wic.1 for ; Sat, 23 May 2015 11:49:53 -0700 (PDT) In-Reply-To: List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: Nick Dokos Cc: "emacs-orgmode@gnu.org" --f46d04428da2fce21a0516c43df6 Content-Type: text/plain; charset=UTF-8 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' >>> [] >>> '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! --f46d04428da2fce21a0516c43df6 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
I am still helpless here. Any idea how to debug the proble= m? I would be happy to provide any kind of help, but I just cannot do it my= self.

Further findings:
1) I don't think t= hat matplotlib changes Python's '_', since the tmp file that co= ntains the content of '_' is correct.
2) Somehow, emacs/o= rgmode 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 con= troling of the
document. The first challenge I faced is integrati= on 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 ~:sessi= on~ is used, together with ~matplotlib~
the desired behavior is n= o longer in place.

* Clean testing, no Matplotlib<= /div>
For the sake of testing, the following merely suppose to return t= he filename

#+BEGIN_SRC python :session no_matplot= lib :results file :exports both
x =3D 'hello '
= y =3D 'world'
z =3D x + y
'foo.bar'
#+END_SRC

#+RESULTS:
[[file:foo.b= ar]]

*Passed* Indeed, the ~RESULTS~ block contains= a link to the filename
indicated by the last string.
<= br>
* Importing Matplotlib

The following= minimal example should generate a simple figure,
~myfig.png~, an= d 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
impo= rt matplotlib
matplotlib.use('Agg')
import matp= lotlib.pyplot as plt
fig=3Dplt.figure(figsize=3D(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
=C2=A0properly generated= , but the last string is not captured by
=C2=A0~matplotlib~. Foll= owing is the content of the corresponding
=C2=A0interactive pytho= n session:

#+BEGIN_SRC
Process with_matp= lotlib 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.
>>> >>&= gt; >>> , '''/var/folders/kz/1c2cxn1x60n_t5p2j1p02b180= 000gn/T/py32771xVI''', 'exec'));
import matpl= otlib
>>> import matplotlib
matplotlib.use(= 9;Agg')
matplotlib.use('Agg')
import matplo= tlib.pyplot as plt
import matplotlib.pyplot as plt
fig= =3Dplt.figure(figsize=3D(3,2))
fig=3Dplt.figure(figsize=3D(3,2))<= /div>
plt.plot([1,3,2])
plt.plot([1,3,2])
plt.savef= ig('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/p= ython-32771-fO', 'w').write(str(_))



'org_babel_python_eoe'
'org_babel_python_eoe'
>>> [<matplot= lib.lines.Line2D object at 0x108e01828>]
>>> 'myf= ig.png'
>>> >>> 9
>>> &g= t;>> >>> 'org_babel_python_eoe'
>>&g= t;
#+END_SRC

* Some background

** Python Version
#+BEGIN_SRC python :session bac= kground :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-60= 0.0.56)]

** Matplotlib version
#+BEGIN_S= RC 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 app= le-appkit-1344.72) of 2015-04-19 on tenten-slave.macports.org~

The orgmode v= ersion is: ~Org-mode version 8.2.10 (8.2.10-40-gc763fa-elpaplus @ /Users/dr= orata/.emacs.d/elpa/org-plus-contrib-20150518/)~

*= * Stackoverflow reference
I also posted a question in the SE netw= ork:

* Question
So, my question is ho= w to tackle/debug this issue? Can someone give me
a hand here? Th= at would be really great! Thanks!

--f46d04428da2fce21a0516c43df6--