Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment

[Dan Davison]

[cc'ing list who were accidentally omitted]

Torsten Wagner <address@hidden> writes:

> Hi Dan,
>  
>
>
>     > 1. Hiding of the source code blocks for export
>     > I like to export the results of the source code block to LaTeX only.
>     However,
>
>     Using ':exports results' specifies that only the results should appear
>     in the exported document. This
>
>     #+begin_src python :exports results
>      6 + 6
>     #+end_src
>
>

Hi Torsten

> I tried this but the result is first the source code block followed by the
> result:

If it's not working, could you provide the exact example and tell us
your operating system, git version etc?

> Furthermore, I tried to create some LaTeX code as result of the code block

You need to use the ':results latex' header if you want the result to be
output as latex.

<...>

> In general I could try to use org-mode as much as possible. However, in that
> special case I like to merge three (or more) documents together.
> 1. The source code (e.g. python)
> 2. A laboratory journal (this would use org-mode magic)
> 3. An official report e.g. a manuscript to be submitted to a journal (this
> would be a LaTeX file)
>
> The idea is to be able to merge all this together to make sure data
> manipulation and calculus (source code) are as close as possible to the
> specific journal entry, which may supply additional important information and
> the final manuscript snippets which presents officially the particular result.
> A short example would be (without real headers)
>
> --8<-------------------------------------------------------------->8---
> * 23.10.09
> Measurement this morning was performed as usual but this time without warm up
> of device foo.
> Measurement file is saved under _link_.
> TODO: Don't forget to prepare for meeting tomorrow
>
> <<Python>>
> for foo import *
> a = load("data.csv")
> b = apply_filter(a,lp)
> plot(b)
> saveplot(bar.pdf)
> <<Python>>

OK, currently, the way to do that is something like

#+srcname: pyplot(file="bar.pdf")
#+begin_src python :results file
  plot(outfile=file)
  file
#+end_src
 
#+resname: pyplot
[[file:bar.pdf]]


Note that for a generalist language like python (which does not always
create output to file) you currently need to

1. specify that it outputs a file with ':results file'
2. explicitly send output to the file in your python code
3. explicitly return the filepath as a string at the end of the
   block. it will get inserted as a link.

You have the option of not hard-wiring the filepath in the python code
by using a variable as I did there.

[We may want to change this so that (3) happens automatically when
':file filepath' or ':results file' is provided]

>
> First low pass filter was applied then a plot is generated
> This plot will be used in publication for journal foo
> DEADLINE: <2009-12-14 Mo>
> <<LaTeX>>
> \begin{figure}
>   \includegraphics{bar.pdf}
> \end{figure}
> <<LaTeX>>

To avoid hard-wiring the filename into the latex block you could use the
org-babel-latex.el that Eric has posted.

>  --8<-------------------------------------------------------------->8---
>
> Text outside should be org-mode text.
> Now I like to export with three scenarios
> 1. Only the LaTeX part (e.g. by using tangle) resulting in a pure native
> LaTeX-file ready for submission

See emails in the concurrent main thread on this topic.

> Above example will result in
>
> \begin{figure}
>   \includegraphics{bar.pdf}
> \end{figure}
>
> 2. The LaTeX part and the org-mode parts whereas the LaTeX blocks should be
> somehow verbatim
> or in a some way marked inline. Above example should result in a LaTeX export
> like 

'begin_src latex' blocks are exported as code blocks with appropriate
fontification under org-mode.

I hope this is getting clearer now :)

Dan

>
> \section{23.10.09}
> Measurement this morning was performed as usual but this time without warm up
> time.
> Measurement file is saved under \footnote[/home/foo/data.csv]{link}.
> First low pass filter was applied then a plot is generated
> This plot will be used in publication for journal foo
> \begin{minipage}
> \begin{figure}
>   \includegraphics{bar.pdf}
> \end{figure}
> \end{minipage}
>
> 3. Export of all which will include the python blocks in a inline form as 
> well.
>
> First of all I would be happy if I could avoid to have the source code blocks
> in the export file.
> I simply like to generate LaTeX-snipplets in python and export a LaTeX file
> finally.
>
> Thus,
>
> #+srcname: LaTeX
> #+begin_src python :session :exports results
>   plot([1,2,3,4,5],[2,4,6,8,10])
>  savefig(file,f-acecolor='w', edgecolor='w',format=None)
>  param1 = 19.7
>  perf = 77
> #+end_src