From: Rainer M Krug <Rainer@krugs.de>
To: Eric Schulte <schulte.eric@gmail.com>
Cc: Andreas Leha <andreas.leha@med.uni-goettingen.de>, emacs-orgmode@gnu.org
Subject: Re: [babel] suggestion: wrap creation of graphics into try() block
Date: Mon, 20 Jan 2014 18:02:29 +0100 [thread overview]
Message-ID: <52DD56A5.4080901@krugs.de> (raw)
In-Reply-To: <87txcyy8dm.fsf@gmail.com>
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On 01/20/14, 16:28 , Eric Schulte wrote:
> Rainer M Krug <Rainer@krugs.de> writes:
>
>> On 01/20/14, 15:00 , Andreas Leha wrote:
>>> Rainer M Krug <Rainer@krugs.de> writes:
>>>
>>>> Hi
>>>>
>>>> I have two suggestions which are liked to each other. They
>>>> are based on R code blocks, but the should be useful for
>>>> other languages as well.
>>>>
>>>> I have a document in which I use :session for creating R
>>>> graphs. These look like:
>>>>
>>>> #+begin_src R :file Correlation_1.pdf :results graphics
>>>> IFN.mean <- load.IFN.mean() grid <-
>>>> load.grid.CASTANEA.average() image(IFN.mean) #+end_src
>>>>
>>>> Everything works fine, unless there is an error in one
>>>> graph.
>>>>
>>>> In this case, the device remains open, which leaves open
>>>> devices at the end of the export of the document.
>>>
>>> I experience the same problem. And would love to see that
>>> addressed.
>>
>> Just checked in the code from ob-R.el, and it should not be to
>> difficult:
>>
>> The functions org-babel-R-construct-graphics-device-call and
>> org-babel-expand-body:R
>>
>> would be affected.
>>
>> I changed :
>>
>>
>>
>> ... Trying it out ...
>>
>> This seems to be working - I just changed it and it closes the
>> device. But further tests are needed. I will leave it to see if
>> anything unexpected happens.
>>
>
> Sounds great. When you're confident that this is working please
> submit a patch and I'll be happy to apply it.
I will check it a little bit longer and see that I can display the
error message in the dummy graphic. Should have it by tomorrow.
I'll send you the patch then.
This is the first time I really work with patches - I assume "git
diff" will give me the patch you need?
Cheers,
Rainer
>
> Thanks,
>
>>
>> If somebody could look if this makes sense? (defun
>> org-babel-expand-body:R (body params &optional graphics-file)
>> "Expand BODY according to PARAMS, return the expanded body." (let
>> ((graphics-file (or graphics-file
>> (org-babel-R-graphical-output-file params)))) (mapconcat
>> #'identity (let ((inside (append (when (cdr (assoc :prologue
>> params)) (list (cdr (assoc :prologue params))))
>> (org-babel-variable-assignments:R params) (list body) (when (cdr
>> (assoc :epilogue params)) (list (cdr (assoc :epilogue
>> params))))))) (if graphics-file (append (list
>> (org-babel-R-construct-graphics-device-call graphics-file
>> params)) inside ;; my edits (list "},error=function(e){plot(-1:1,
>> -1:1, type='n'); text(0,0,'DUMMY')}); dev.off()")) inside)) ;;
>> end "\n")))
>>
>>
>>
>> and
>>
>> (format "%s(%s=\"%s\"%s%s%s); tryCatch({" device filearg out-file
>> args (if extra-args "," "") (or extra-args ""))))
>>
>> in org-babel-R-construct-graphics-device-call
>>
>> It is working with the Dummy.
>>
>> Could somebody please check if this is working?
>>
>> I am leaving my changes and will see during my work if it is
>> fine.
>>
>> Cheers,
>>
>> Rainer
>>
>>
>>>
>>>>
>>>> If the code block which should create the graph would be
>>>> wrapped into a try() block, so that it would look like the
>>>> following:
>>>>
>>>> try( { pdf("./Correlation_1.pdf") IFN.mean <-
>>>> load.IFN.mean() grid <- load.grid.CASTANEA.average()
>>>> image(IFN.mean) } ) dev.off()
>>>>
>>>> The device would be closed even if an error occurred during
>>>> the execution of the code.
>>>>
>>>> But still, when exporting to pdf, the call to pdflatex fails
>>>> as only a empty pdf is available. So it becomes necessary to
>>>> go through the pdf log to identify the graphs which failed.
>>>>
>>>> In this case it would be useful, to have a placeholder grah
>>>> in the final pdf, so that one can see which graphs did not
>>>> work.
>>>>
>>>> In addition, this could be used as placeholders (well - they
>>>> are placeholders) for to be created graphs, while the text
>>>> has already been written.
>>>>
>>>> So my second suggestion would be to include a placeholder
>>>> image, which would be used if the generation of the actual
>>>> graph fails. It would be great (but not necessary) if the
>>>> actual error message would be in the image.
>>>
>>> Such an place holder image would be great, indeed.
>>>
>>>
>>> Thanks for bringing this up!
>>>
>>> Regards, Andreas
>>>
>>>
>>
>> -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc
>> (Conservation Biology, UCT), Dipl. Phys. (Germany)
>>
>> Centre of Excellence for Invasion Biology Stellenbosch
>> University South Africa
>>
>> Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62
>> 59 98 Fax : +33 - (0)9 58 10 27 44
>>
>> Fax (D): +49 - (0)3 21 21 25 22 44
>>
>> email: Rainer@krugs.de
>>
>> Skype: RMkrug
>
- --
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)
Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa
Tel : +33 - (0)9 53 10 27 44
Cell: +33 - (0)6 85 62 59 98
Fax : +33 - (0)9 58 10 27 44
Fax (D): +49 - (0)3 21 21 25 22 44
email: Rainer@krugs.de
Skype: RMkrug
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next prev parent reply other threads:[~2014-01-20 17:02 UTC|newest]
Thread overview: 11+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-01-20 13:36 [babel] suggestion: wrap creation of graphics into try() block Rainer M Krug
2014-01-20 14:00 ` Andreas Leha
2014-01-20 15:13 ` Rainer M Krug
2014-01-20 15:28 ` Eric Schulte
2014-01-20 17:02 ` Rainer M Krug [this message]
2014-01-20 18:38 ` Eric Schulte
2014-01-21 9:52 ` Rainer M Krug
2014-01-21 10:03 ` Andreas Leha
2014-01-21 10:43 ` :draft header argument for source block evaluation - WAS: " Rainer M Krug
2014-01-26 18:07 ` Eric Schulte
2014-01-27 9:10 ` Rainer M Krug
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