https://github.com/drorata/org-babel-matplotlib-integration
https://github.com/drorata/org-babel-matplotlib-integration
Last synced: 4 months ago
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- Host: GitHub
- URL: https://github.com/drorata/org-babel-matplotlib-integration
- Owner: drorata
- Created: 2015-05-18T20:00:02.000Z (about 11 years ago)
- Default Branch: master
- Last Pushed: 2015-05-26T11:45:15.000Z (about 11 years ago)
- Last Synced: 2025-03-05T10:46:36.717Z (over 1 year ago)
- Size: 125 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: readme.org
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README
#+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 for
all relevant code blocks. However, once ~:session~ is used, together
with ~matplotlib~ the desired behavior is no longer in place under Mac
OS X.
* Clean testing, no Matplotlib
For the sake of testing, the following merely suppose to return the
filename in an orgmode'ish link format:
#+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/py44814koH''', '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-44814cA3/python-44814xyN', 'w').write(str(_))
open('/var/folders/kz/1c2cxn1x60n_t5p2j1p02b180000gn/T/babel-44814cA3/python-44814xyN', 'w').write(str(_))
'org_babel_python_eoe'
'org_babel_python_eoe'
>>> >>> >>> >>> []
>>> 'myfig.png'
>>> >>> 9
>>> >>> >>> 'org_babel_python_eoe'
>>>
#+END_SRC
It seems like ~ob-python.el~ manages to create the correct temp file,
but somehow it is not capturing the filename and doesn't plug it into
the right place in the results block.
* 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!