Re: org-mode and python pandas

[Dov Grobgeld <dov.grobgeld@gmail.com>]

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I returned to this issue recently and tried to get the ob-python to output
a table with a header, but didn't manage. Here is the code:

#+BEGIN_SRC python :colnames true
return [['','A','B','C'],
        [0,0.628365,0.424279,0.619791],
        [1,0.799666,0.527572,0.132928]]
#+END_SRC

#+RESULTS:
|   |        A |        B |        C |
| 0 | 0.628365 | 0.424279 | 0.619791 |
| 1 | 0.799666 | 0.527572 | 0.132928 |

What I want is:

|   |        A |        B |        C |
|---+----------+----------+----------|
| 0 | 0.628365 | 0.424279 | 0.619791 |
| 1 | 0.799666 | 0.527572 | 0.132928 |

Is there any way to do that besides using the :results raw option?

Thanks!
Dov


On Wed, Jul 3, 2013 at 5:09 PM, Eric Schulte <schulte.eric@gmail.com> wrote:

> Dov Grobgeld <dov.grobgeld@gmail.com> writes:
>
> > Thanks for the answers, but there is still something missing in order
> > to get it to work. Part of it seems to be connected to the python
> > parsing. E.g. the following translation of Eric's sh example doesn't
> > output correctly with python:
> >
> >
> > #+BEGIN_SRC python :results output
> > print """,A,B,C
> > 0,0.628365,0.424279,0.619791
> > 1,0.799666,0.527572,0.132928
> > 2,0.837255,0.138906,0.408233
> > 3,0.388080,0.146212,0.575346
> > """
> > #+END_SRC
> >
> > #+RESULTS:
> > : ,A,B,C
> > : 0,0.628365,0.424279,0.619791
> > : 1,0.799666,0.527572,0.132928
> > : 2,0.837255,0.138906,0.408233
> > : 3,0.388080,0.146212,0.575346
> >
> >
> > #+BEGIN_SRC python :results table
> > return """,A,B,C
> > 0,0.628365,0.424279,0.619791
> > 1,0.799666,0.527572,0.132928
> > 2,0.837255,0.138906,0.408233
> > 3,0.388080,0.146212,0.575346
> > """
> > #+END_SRC
> >
> > #+RESULTS:
> > |
> ,A,B,C\n\n0,0.628365,0.424279,0.619791\n\n1,0.799666,0.527572,0.132928\n\n2,0.837255,0.138906,0.408233\n\n3,0.388080,0.146212,0.575346
> > |
> >
> > It seems that the only way to get a table from python is by outputting
> > a two dimensional python structure:
> >
> > #+BEGIN_SRC python
> > return [[0,0.628365,0.424279,0.619791],
> >         [1,0.799666,0.527572,0.132928]]
> > #+END_SRC
> >
> > #+RESULTS:
> > | 0 | 0.628365 | 0.424279 | 0.619791 |
> > | 1 | 0.799666 | 0.527572 | 0.132928 |
> >
> > This seems quite limiting....
> >
>
> In most cases this is what one wants when returning data from python
> code.  The following elisp defined a "panda" code block, which is just
> like python, only it assumes that the results will be these sort of
> human readable strings instead of python code.
>
>     ;; -*- emacs-lisp -*-
>     (defun org-babel-execute:panda (body params)
>       (let ((results
>              (org-babel-execute:python
>               body (org-babel-merge-params '((:results . "scalar"))
> params))))
>         (org-babel-result-cond (cdr (assoc :result-params params))
>           results
>           (let ((tmp-file (org-babel-temp-file "sh-")))
>             (with-temp-file tmp-file (insert results))
>             (org-babel-import-elisp-from-file tmp-file)))))
>
> With the above evaluated the following works
>
>     #+BEGIN_SRC panda
>     return """,A,B,C
>     0,0.628365,0.424279,0.619791
>     1,0.799666,0.527572,0.132928
>     2,0.837255,0.138906,0.408233
>     3,0.388080,0.146212,0.575346
>     """
>     #+END_SRC
>
>     #+RESULTS:
>     |   |        A |        B |        C |
>     | 0 | 0.628365 | 0.424279 | 0.619791 |
>     | 1 | 0.799666 | 0.527572 | 0.132928 |
>     | 2 | 0.837255 | 0.138906 | 0.408233 |
>     | 3 |  0.38808 | 0.146212 | 0.575346 |
>
> >
> > Another related question is if there is any support for header tables?
> > I.e. instead of this:
> >
> > |   |        A |        B |        C |
> > | 0 | 0.827817 | 0.664009 | 0.089161 |
> > | 1 | 0.170031 | 0.729214 | 0.110918 |
> > | 2 | 0.575918 | 0.863924 | 0.757536 |
> > | 3 | 0.682722 | 0.774445 | 0.992041 |
> >
> > I want this:
> >
> > |   |        A |        B |        C |
> > |---+----------+----------+----------|
> > | 0 | 0.827817 | 0.664009 | 0.089161 |
> > | 1 | 0.170031 | 0.729214 | 0.110918 |
> > | 2 | 0.575918 | 0.863924 | 0.757536 |
> > | 3 | 0.682722 | 0.774445 | 0.992041 |
> >
> > I guess that if I start playing around with the python ob module, it
> > should be possible to get this working?
> >
>
> See the :colnames header argument in the manual.
>
> Best,
>
> >
> > Regards,
> > Dov
> >
> > On Mon, Jul 1, 2013 at 8:04 PM, Rasmus <rasmus@gmx.us> wrote:
> >> Achim Gratz <Stromeko@nexgo.de> writes:
> >>
> >>>>> 2. Add to pandas the option of globally influencing the text
> >>>>> formatting so that it outputs something more parsable by org-mode.
> >>>>
> >>>> This sounds promising, if pandas support csv output that will be
> >>>> correctly parsed by Org-mode.
> >>>
> >>> The package already has CSV export, so one could use that.  I don't
> know
> >>> if you could echo the result directly to the output, all examples
> >>> revolve around putting the CSV into a file.  For Org, TSV output would
> >>> be more natural.
> >>
> >> Something like:
> >>
> >> from pandas import DataFrame
> >> from numpy.random import rand
> >> from sys import stdout
> >> df = DataFrame(rand(10,3), columns = list('abc'))
> >> df
> >> df.to_csv(stdout, sep="\t", header = True, cols=(1,2))
> >>
> >> I was completely unable to get ob-python working this morning, so I
> >> haven't tested it.  I'm using python3, build in python mode and elpy.
> >>
> >> In any case, the csv route might be better, as Pandas doesn't print
> >> the table if it's too big (try changing 10 to 1000 above).
> >>
> >> --
> >> Powered by magic pixies!
> >>
> >>
> >
>
> --
> Eric Schulte
> http://cs.unm.edu/~eschulte
>

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