[Orgmode] Re: [BABEL] Output with octave

[Dan Davison]

Hi,

d.tchin d.tc...@voila.fr writes:

 Hi,

 Dan Davison davison at stats.ox.ac.uk writes:

 
 Eric S Fraga ucecesf at ucl.ac.uk writes:
 
  On Fri, 23 Jul 2010 16:59:43 + (UTC), d.tchin d.tchin at voila.fr 
 wrote:
[...]
 So the current workaround is to say when using octave, you must end
 your block with a computation, rather than a simple statement of a
 variable name.
 
 Can someone suggest a better solution?
 
 Dan
 
 p.s. Or you could do this
 
 #+begin_src octave :session *out* :var vec=test
 vecb=vec;
 ans=vecb
 #+end_src
 
 #+begin_src octave :session *out* :var vec=test
 vecb=vec;
 ans=vecb
 ans
 #+end_src
 


 Thank you for the help. I will use it as it works clearly clearly well. 

 Following exchange you have with Juan Pechiar related to the way the output 
 is displayed, I would like to submit the following examples :

 First test :


 #+tblname: test
 | 1 | 2 | 3 |

 #+source: outtest
 #+begin_src octave  :session *out*   :var vec=test :results value vector
 vecb=[vec];
 ans=vecb;
 #+end_src


 The output is the following :


 #+results: outtest
 | 1.e+000 2.e+000 3.e+000 |


 It is considered as one character and each element are not clearly
 splitted in table. Certainly handled as string as Juan Pechiar.

Thanks for that. It should be fixed now.  I have changed octave and
matlab so that they now write their data to file using dlmwrite rather
than save -ascii.

Dan



 Second test :


 #+tblname: test
 | 1 | 2 | 3 |

 #+source: outtestb
 #+begin_src octave  :session *out*   :var vec=test :results value vector
 vecb=[vec;vec];
 ans=vecb;
 #+end_src


 The output is the following :

 #+results: outtestb
 | 1.e+000 | 2.e+000 | 3.e+000 |
 | 1.e+000 | 2.e+000 | 3.e+000 |

 This time output is splitted in a table as it should be ?






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[Orgmode] Re: [BABEL] Output with octave [PATCH]

[Dan Davison]

Hi Juan and d.tchin,

One thing I'd like to ask for advice about is the behaviour of tabular
data structures containing strings. For example

#+begin_src octave
ans = [['a','b'];['c','d']]
#+end_src

#+results:
: acbd

I don't know if my syntax above is correct, but it seems to me that this
is a 2x2 table of some sort and so it would seem natural to me for that
to return

| a | b |
| c | d |

however, if you look at the code we are using below, you'll see that
ischar() returns 1 for this object and so it gets written as a
string. Can you suggest how we should alter the octave/matlab code
below? Or perhaps people don't use tabular data structures containing
strings in these languages?

if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); 
fclose(fid);
else, dlmwrite('%s', ans, '\\t')
end

Dan


Juan Pechiar pech...@computer.org writes:

 Hi,

 Below is a single PATCH for the 3 issues:
- passing tables with EXP or complex notation to octave
- correct formatting of matrixes into octave
- interpretation of octave output as table

 Regards,
 .j.

 8

 diff --git a/lisp/ob-octave.el b/lisp/ob-octave.el
 index 8e99f86..bf7fdd3 100644
 --- a/lisp/ob-octave.el
 +++ b/lisp/ob-octave.el
 @@ -119,8 +119,9 @@ end)
  Converts an emacs-lisp variable into a string of octave code
  specifying a variable of the same value.
(if (listp var)
 -  (concat [ (mapconcat #'org-babel-octave-var-to-octave var ,
 ) ])
 -(format %S var)))
 +  (concat [ (mapconcat #'org-babel-octave-var-to-octave var
 +(if (listp (car var)) ;  ,)) ])
 +(format %s var)))

  (defun org-babel-prep-session:octave (session params optional
  matlabp)
Prepare SESSION according to the header arguments specified in
PARAMS.
 @@ -181,7 +182,7 @@ value of the last statement in BODY, as elisp.
(org-babel-eval
 cmd
 (format org-babel-octave-wrapper-method body tmp-file
 tmp-file))
 -  (org-babel-eval-read-file tmp-file))
 +  (org-babel-octave-import-elisp-from-file tmp-file))

  (defun org-babel-octave-evaluate-session
(session body result-type optional matlabp)

 8

 On Sun, Aug 01, 2010 at 05:07:27PM -0300, Juan wrote:
 I'm starting to work with ob-octave and found several problems:

 The first, for which I have a fix (see patch below) is that octave's
 output was passed on as a string instead of being interpreted as a table:


 The second problem is that if I use octave table output as input to
 another block, it gets interpreted as a string instead of a vector:


 This has to do with the EXP notation. The 'e+00' suffix makes the
 whole table into a string. The problem is with %S in the formatting
 inside org-babel-octave-var-to-octave.


 A third problem is with org-babel-octave-var-to-octave.

 For example:

 : (org-babel-octave-var-to-octave '( ( 1 2 3 ) ( 4 5 6 ) ))
 : -  [[1, 2, 3], [4, 5, 6]]

 This is not a 2x3 matrix, but a 1x6 vector:

 : octave-3.2.3:1 [[1,2,3],[4,5,6]]
 : ans =
 :1   2   3   4   5   6

 a semicolon ';' or '\n' is needed between rows instead of a comma.

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[Orgmode] Re: [BABEL] Output with octave

[Dan Davison]

Eric S Fraga ucec...@ucl.ac.uk writes:

 On Fri, 23 Jul 2010 16:59:43 + (UTC), d.tchin d.tc...@voila.fr wrote:
 
 Hi
 
 I use babel to use with octave language. I use it and
 define a session so as to have interaction with
 octave process. 
 
 It is great to have interaction with octave and
 check the action of the code easily.
 
 I have problem to get output back in org mode file. 
 I try the following code :
 
 
 --8---cut here---start-8---
 #+tblname: test
 | 1 | 2 | 3 |
 
 #+source: outtest
 #+begin_src octave  :session *out*   :var vec=test :results output
 vecb=vec;
 vecb
 #+end_src
 
 --8---cut here---end---8---
 
 You will get following output
 
 #+results: outtest
 : vec =
 : 
 :1   2   3
 : octave.exe vecb =
 : 
 :1   2   3
 
 As you see I get two outputs : vec variable and vecb (with octave prompt).
 It is what I expected, excepted vec output.

The inclusion of the prompt is undesirable, and that is now on a to-fix
list.

But the :results value problems are more serious:

 
 With :results value 
 
 --8---cut here---start-8---
 #+tblname: test
 | 1 | 2 | 3 |
 
 
 
 #+source: outtest
 #+begin_src octave  :session *out*   :var vec=test :results value
 vecb=vec;
 vecb
 #+end_src
 
 --8---cut here---end---8---
 
 I get the following output 
 
 
 #+results: outtest
 : org_babel_eoe

OK, perhaps you or other octave users could advise us on how to proceed
here, as neither Eric Schulte nor I know octave. Note that this works:

#+begin_src octave :session *out* :var vec=test
vecb=vec;
vecb+0
#+end_src

#+results:
: 1.e+00 2.e+00 3.e+00

octave evaluation in org works as follows:
- The user code is evaluated
- The value of the variable 'ans' is written to disk and imported into
  org

And the octave manual tells us that 'ans' is:

,
| The most recently computed result that was not explicitly assigned to a 
variable
`

The trouble seems to be that the final expression 'vecb' doesn't count
as a computation, and so doesn't change the value of ans.

So the current workaround is to say when using octave, you must end
your block with a computation, rather than a simple statement of a
variable name.

Can someone suggest a better solution?

Dan

p.s. Or you could do this

#+begin_src octave :session *out* :var vec=test
vecb=vec;
ans=vecb
#+end_src

#+begin_src octave :session *out* :var vec=test
vecb=vec;
ans=vecb
ans
#+end_src


 
 In the octave process, I check that it the last intruction. But 
 what I would expect is to get last instruction vecb.
 
 I certainly miss something. Could someone help me on this ?

 I don't think you are missing anything obvious as for the :results
 value case, I get the same thing.  In fact, for :results output, I
 don't actually get any output!  I'm not sure why.  I wonder if there
 is a dependence on the version of Octave?  I'm using a fairly old
 version (3.0.x instead of 3.2.x).

 : Org-mode version 7.01trans (release_7.01g.24.g6b5cf)
 : GNU Emacs 23.2.1 (i486-pc-linux-gnu, GTK+ Version 2.20.0)
 :  of 2010-05-16 on raven, modified by Debian

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Re: [Orgmode] Re: [BABEL] Output with octave + [PATCH] x2

[Juan]

Hi,

I'm starting to work with ob-octave and found several problems:

The first, for which I have a fix (see patch below) is that octave's
output was passed on as a string instead of being interpreted as a table:

8
diff --git a/lisp/ob-octave.el b/lisp/ob-octave.el
index 8e99f86..d0d16fe 100644
--- a/lisp/ob-octave.el
+++ b/lisp/ob-octave.el
@@ -181,7 +181,7 @@ value of the last statement in BODY, as elisp.
   (org-babel-eval
cmd
(format org-babel-octave-wrapper-method body tmp-file
tmp-file))
-  (org-babel-eval-read-file tmp-file))
+  (org-babel-octave-import-elisp-from-file tmp-file))

 (defun org-babel-octave-evaluate-session
   (session body result-type optional matlabp)
8

Now this works:

8
#+source: test_output
#+begin_src octave :results value vector
[[1 2 3];[4 5 6]]
#+end_src

#+results: test_output
| 1.e+00 | 2.e+00 | 3.e+00 |
| 4.e+00 | 5.e+00 | 6.e+00 |
8

(before the patch you'd get a single table element with something like
1 2 3\n 4 5 6\n inside).



The second problem is that if I use octave table output as input to
another block, it gets interpreted as a string instead of a vector:

8
#+results: test_output
| 1.2500e+00 |

#+source: check_input
#+begin_src octave :var input=test_output() :results output
ischar( input )
size( input )
#+end_src

#+results: check_input
: input = 1.2500e+00
: ans =  1
: ans =
: 1   14
8

This has to do with the EXP notation. The 'e+00' suffix makes the
whole table into a string. The problem is with %S in the formatting
inside org-babel-octave-var-to-octave.

The following patch seems to fix it (and makes it possible to work with
complex numbers inside the tables)::

8
diff --git a/lisp/ob-octave.el b/lisp/ob-octave.el
index 8e99f86..4329c7f 100644
--- a/lisp/ob-octave.el
+++ b/lisp/ob-octave.el
@@ -120,7 +120,7 @@ Converts an emacs-lisp variable into a string of
octave code
 specifying a variable of the same value.
   (if (listp var)
   (concat [ (mapconcat #'org-babel-octave-var-to-octave var ,
   ) ])
-(format %S var)))
+(format %s var)))

 (defun org-babel-prep-session:octave (session params optional
 matlabp)
   Prepare SESSION according to the header arguments specified in
   PARAMS.
8


A third problem is with org-babel-octave-var-to-octave.

For example:

: (org-babel-octave-var-to-octave '( ( 1 2 3 ) ( 4 5 6 ) ))
: -  [[1, 2, 3], [4, 5, 6]]

This is not a 2x3 matrix, but a 1x6 vector:

: octave-3.2.3:1 [[1,2,3],[4,5,6]]
: ans =
:1   2   3   4   5   6

a semicolon ';' or '\n' is needed between rows instead of a comma.



To sum up:
   - 2 patches for prepare-session and importing the results back as
   org-tables (I don't know if these patches break anything).

   - 1 problem with matrix notation in org-babel-octave-var-to-octave.
   I'll try to provide a patch for this today.


I'm not working with sessions, so I have not yet tested the original
problem reported with 'org_babel_eoe' showing up as result.

Regards,
.j.



On Sun, Aug 01, 2010 at 02:18:40PM -0400, Dan Davison wrote:
 Eric S Fraga ucec...@ucl.ac.uk writes:
  On Fri, 23 Jul 2010 16:59:43 + (UTC), d.tchin d.tc...@voila.fr wrote:
  I have problem to get output back in org mode file.

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[Orgmode] Re: [BABEL] Output with octave + [PATCH] x2

[Dan Davison]

Juan pech...@computer.org writes:

 Hi,

 I'm starting to work with ob-octave and found several problems:

Hi Juan,

Thanks very much. I've applied your patch with one minor change:

(format %s (or var nil))

However, is there a better way to receive an elisp nil value in octave?

 I'm not working with sessions, so I have not yet tested the original
 problem reported with 'org_babel_eoe' showing up as result.

Sorry to pursue you for more help, but that problem is not limited to
sessions. A very simple demonstration of it is

#+begin_src octave
x = 5
x
#+end_src

#+results:
: /usr/share/octave/packages/3.2

This happens because neither of these two lines of code alter the value
of 'ans' (I presume the value we are seeing is something from octave's
start-up sequence).

Contrast this with

#+begin_src octave
x = 5
x+0
#+end_src

#+results:
: 5.e+00

Any idea of the best way forward?

Dan


 Regards,
 .j.



 On Sun, Aug 01, 2010 at 02:18:40PM -0400, Dan Davison wrote:
 Eric S Fraga ucec...@ucl.ac.uk writes:
  On Fri, 23 Jul 2010 16:59:43 + (UTC), d.tchin d.tc...@voila.fr wrote:
  I have problem to get output back in org mode file.

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[Orgmode] Re: [BABEL] Output with octave

[d . tchin]

Eric S Fraga ucecesf at ucl.ac.uk writes:

 
 I don't think you are missing anything obvious as for the :results
 value case, I get the same thing.  In fact, for :results output, I
 don't actually get any output!  I'm not sure why.  I wonder if there
 is a dependence on the version of Octave?  I'm using a fairly old
 version (3.0.x instead of 3.2.x).
 

I use following version of Octave : 

GNU Octave, version 3.2.0
Copyright (C) 2009 John W. Eaton and others.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  For details, type `warranty'.

Octave was configured for i686-pc-mingw32.



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