Re: [O] [Orgmode] Unable to capture the file name generated using matplotlib

[Dror Atariah]

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 <address@hidden> 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