octave-dev — GNU Octave developers' list

Re: [OctDev] finishing up new release of image package

[Carnë D. <car...@gm...>]

On 12 October 2012 09:53, Kris Thielemans <kri...@gm...> wrote:
>> On 6 October 2012 20:17, Carnë Draug <car...@gm...>
>> wrote:
>> > On 1 October 2012 17:34, Kris Thielemans <kri...@gm...>
>> wrote:
>> >> From: Jordi Gutiérrez Hermoso
>> >>> Sent: 01 October 2012 15:27
>> >>>
>> >>> On 1 October 2012 10:18, Kris Thielemans < > wrote:
>> >>> > Why not use fall back to boost unordered_map for (old) clang? At
> least
>> the
>> >>> user can then install boost.
>> >>>
>> >>> Sure, this is fine too. I suppose I'll have to write an autoconf
>> >>> script now... Or would you do it?
>> >>
>> >>
>> >> You got me there :-;
>> >>
>> >> Unfortunately, my knowledge of autoconf is close to zero. I did find
>> >>
>> http://code.google.com/p/carve/source/browse/configure.ac?name=rev-
>> 1.6
>> >> which is from a GPL project. Maybe somebody can use this as starting
>> point...
>> >
>> > Hi Kris
>> >
>> > I also don't know autoconf to fix this. Are you able to submit a patch
>> > to fix this? Or able to convince someone to fix it for you?
>> >
>> > About all the other warnings they are all in Octave core and have
>> > already been fixed in dev. There's nothing I can do about them.
>> >
>> > Carnë
>>
>> Hi Kris
>>
>> are you planning on fixing this? I'll be releasing the new version
>> this weekend if not.
>>
>> Carnë
>
> Hi Carnë
>
> Apologies but I don't have the time for this at least until December,
> especially as it'd take me a lot of effort to learn enough about autoconf to
> get it to work.
>
> All the best
> Kris

Hi

thanks to Jordi for fixing this problem. It should install fine now
with other compilers. Could you please give it a go, see if it
installs and if there's any other problems?

The new dev version is at http://carandraug.no-ip.org/octave/image-1.9.93.tar.gz

Thanks in advance,
Carnë

Re: [OctDev] Website down

[Juan P. C. <aju...@gm...>]

On Tue, Oct 23, 2012 at 10:30 PM, Jordi Gutiérrez Hermoso
<jo...@oc...> wrote:
> On 23 October 2012 15:08, Alexander Hansen <ale...@gm...> wrote:
>> On 10/23/12 12:06 PM, Nir Krakauer wrote:
>>> Are others able to access http://octave.sourceforge.net/ ?
>>>
>>
>> Nope:
>>
>> http://sourceforge.net/blog/various-sourceforge-services-down/
>
> Btw, because I'm a little scared about losing the svn history, I have
> made an hg backup here:
>
>     http://hg.octave.org/forge
>
> This is a backup of all the OF history... it's not really meant to be
> used for production, just in case something horrible happens to
> Sourceforge, well, we have backups.
>
> - Jordi G. H.
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_sfd2d_oct
> _______________________________________________
> Octave-dev mailing list
> Oct...@li...
> https://lists.sourceforge.net/lists/listinfo/octave-dev

Well done jordi,
Thanks :D

SF was up and down today. I guess they are fixing they forums that
were full of bugs.

Re: [OctDev] Website down

[Jordi G. H. <jo...@oc...>]

On 23 October 2012 15:08, Alexander Hansen <ale...@gm...> wrote:
> On 10/23/12 12:06 PM, Nir Krakauer wrote:
>> Are others able to access http://octave.sourceforge.net/ ?
>>
>
> Nope:
>
> http://sourceforge.net/blog/various-sourceforge-services-down/

Btw, because I'm a little scared about losing the svn history, I have
made an hg backup here:

    http://hg.octave.org/forge

This is a backup of all the OF history... it's not really meant to be
used for production, just in case something horrible happens to
Sourceforge, well, we have backups.

- Jordi G. H.

Re: [OctDev] Website down

[Alexander H. <ale...@gm...>]

On 10/23/12 12:06 PM, Nir Krakauer wrote:
> Are others able to access http://octave.sourceforge.net/ ?
> 

Nope:

http://sourceforge.net/blog/various-sourceforge-services-down/


-- 
Alexander Hansen, Ph.D.
Fink User Liaison
My package updates: http://finkakh.wordpress.com/

[OctDev] Website down

[Nir K. <nkr...@cc...>]

Are others able to access http://octave.sourceforge.net/ ?

Re: [OctDev] new package releases: bim 1.1.0 and msh 1.0.5

[c. <kin...@ti...>]

On 23 Oct 2012, at 20:34, c. wrote:

> I just uploaded a new version of the package in the release forum, could you please check if the problem is solved there?
this is a direct link:
https://sourceforge.net/p/octave/package-releases/9/attachment/msh-1.0.5.tar.gz

c.

Re: [OctDev] new package releases: bim 1.1.0 and msh 1.0.5

[c. <car...@gm...>]

On 23 Oct 2012, at 17:27, Rafael Laboissiere wrote:

> * c. <car...@gm...> [2012-10-22 12:21]:
> 
>> New versions of the Forge packages bim (1.1.0) and msh (1.0.5) have been uploaded to the package release forum, and will soon be available for download from Octave-Forge.
>> 
>> [snip]
> 
> Thanks for this new release.  I noticed a problem in it: the unit testing in the file msh3m_structured_mesh.m does not work.  The patch attached below fixes the problem (there were two issues: tests were preceded by "%" instead of "%!" and there were spurious "=" signs after "assert").  However, the test fails with the following error message:
> 
>     octave:1> test msh3m_structured_mesh
>     ***** test
>      x = y = z = linspace (0,1,2);
>      [mesh] = msh3m_structured_mesh (x, y, z, 1, 1:6);
>      assert (columns (mesh.p), 8);
>      assert (columns (mesh.t), 6);
>      assert (columns (mesh.e), 12);
>     !!!!! test failed
>     `p' undefined near line 145 column 10
> 
> It seems that several variables (x, y, z, p, and sides) that used inside the subfunction __t6_connections__ are only locally defined in msh3m_structured_mesh.
Rafael,
Thank you very much for testing the package!

I just uploaded a new version of the package in the release forum, could you please check if the problem is solved there?

> This bug also affects the bim package.

is this because of the dependency or is there similar bugs in bim?

> Rafael

c.

Re: [OctDev] new package releases: bim 1.1.0 and msh 1.0.5

[Rafael L. <ra...@la...>]

* c. <car...@gm...> [2012-10-22 12:21]:

> New versions of the Forge packages bim (1.1.0) and msh (1.0.5) have 
> been uploaded to the package release forum, and will soon be available 
> for download from Octave-Forge.
>
> [snip]

Thanks for this new release.  I noticed a problem in it: the unit 
testing in the file msh3m_structured_mesh.m does not work.  The patch 
attached below fixes the problem (there were two issues: tests were 
preceded by "%" instead of "%!" and there were spurious "=" signs after 
"assert").  However, the test fails with the following error message:

      octave:1> test msh3m_structured_mesh
      ***** test
       x = y = z = linspace (0,1,2);
       [mesh] = msh3m_structured_mesh (x, y, z, 1, 1:6);
       assert (columns (mesh.p), 8);
       assert (columns (mesh.t), 6);
       assert (columns (mesh.e), 12);
      !!!!! test failed
      `p' undefined near line 145 column 10

It seems that several variables (x, y, z, p, and sides) that used inside 
the subfunction __t6_connections__ are only locally defined in 
msh3m_structured_mesh.

This bug also affects the bim package.

Rafael

Re: [OctDev] physicalconstants-1.0.0

[Claudio F. <kla...@gm...>]

On Mon, Oct 22, 2012 at 8:35 PM, Carnë Draug <car...@gm...> wrote:
>> We generate rpm dependencies from octave-forge's package information,
>> so until all packages stop referring to physicalconstants I don't
>> think we can drop the package. However, I've done a quick grep, and I
>> don't find any mention to physical-constants. Have all packages been
>> updated to refer directly to misc already?
>
> No package was dependent on the physicalconstants packages, none
> should be referring it. The new release, empty but dependent on
> miscellaneous is just to prevent problems in case people had scripts
> that load it. Now that I think about it, should have made a PKG_ADD
> script to warn the user when loading the package. Please note that the
> same is true for the combinatorics and time package.

Good to know... will blacklist them then. Thanks.

Re: [OctDev] physicalconstants-1.0.0

[Carnë D. <car...@gm...>]

On 22 October 2012 16:10, Claudio Freire <kla...@gm...> wrote:
> On Mon, Oct 22, 2012 at 11:54 AM, Carnë Draug <car...@gm...> wrote:
>> Anyway, this package has been removed. You will notice that
>> physical-constants is completely empty and only dependent on
>> miscellaneous. I'd recommend you remove it.
>
> We generate rpm dependencies from octave-forge's package information,
> so until all packages stop referring to physicalconstants I don't
> think we can drop the package. However, I've done a quick grep, and I
> don't find any mention to physical-constants. Have all packages been
> updated to refer directly to misc already?

No package was dependent on the physicalconstants packages, none
should be referring it. The new release, empty but dependent on
miscellaneous is just to prevent problems in case people had scripts
that load it. Now that I think about it, should have made a PKG_ADD
script to warn the user when loading the package. Please note that the
same is true for the combinatorics and time package.

Carnë

Re: [OctDev] wavwrite() with integer arguments

[Jordi G. H. <jo...@oc...>]

Hi,

On 22 October 2012 13:44, Froebe, Matej <Mat...@mu...> wrote:
> I need to write integer values to wav file, so I modified  the wavwrite
> function. Its behavior now depends on data input type (for floats the input
> data range is -1.0 to 1.0).
>
> Does it make sense, to include this small change in the package? If yes, how
> do I proceed?

You have found the Octave Forge mailing list which is for add-on
packages to Octave, not for Octave itself. The wavwrite function is in
core Octave, so its modifications should be discussed on the
maintainers' list itself, mai...@oc..., CC'ed here.

As to how to actually produce the changes, show us what they are
first. If you have the desire to undertake the necessary paperwork to
get it accepted, please read these:

    http://jordi.inversethought.com/blog/how-to-write-a-patch-for-octave/
    http://www.gnu.org/software/octave/doc/interpreter/Contributing-Guidelines.html

Re: [OctDev] wavwrite() with integer arguments

[Juan P. C. <car...@if...>]

On Mon, Oct 22, 2012 at 7:44 PM, Froebe, Matej
<Mat...@mu...> wrote:
> Hi everybody,
>
>
>
> I need to write integer values to wav file, so I modified  the wavwrite
> function. Its behavior now depends on data input type (for floats the input
> data range is -1.0 to 1.0).
>
>
>
> Does it make sense, to include this small change in the package? If yes, how
> do I proceed?
>
>
>
> Matlab also behaves in a similar way, but with a possibility for integer
> values only for 8-, 16- and 24-bit wav files.
>
>
>
> Matej
>
>
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_sfd2d_oct
> _______________________________________________
> Octave-dev mailing list
> Oct...@li...
> https://lists.sourceforge.net/lists/listinfo/octave-dev
>

Please upload your modified file here
https://sourceforge.net/p/octave/feature-requests/

or send a patch.

This will allow the interested to look at your code.

Cheers

-- 
M. Sc. Juan Pablo Carbajal
-----
PhD Student
University of Zürich
http://ailab.ifi.uzh.ch/carbajal/

[OctDev] wavwrite() with integer arguments

[Froebe, M. <Mat...@Mu...>]

Hi everybody,

 

I need to write integer values to wav file, so I modified  the wavwrite
function. Its behavior now depends on data input type (for floats the
input data range is -1.0 to 1.0).

 

Does it make sense, to include this small change in the package? If yes,
how do I proceed?

 

Matlab also behaves in a similar way, but with a possibility for integer
values only for 8-, 16- and 24-bit wav files.

 

Matej

 

[OctDev] New package real2rgb

[Juan P. C. <aju...@gm...>]

Hi,

I got real2rgb under GPLv3. I will add it as a new package in Octave
Forge in three days, unless somebody has a better idea.

Cheers

--
JuanPi Carbajal
-----
"It is one thing not to be able to perform a certain feat, but quite
another to prove that it cannot be done." - Henry Ernest Dudeney
-----
http://ailab.ifi.uzh.ch/carbajal/

Re: [OctDev] new package releases: bim 1.1.0 and msh 1.0.5

[c. <car...@gm...>]

On 22 Oct 2012, at 16:39, luk...@gm... wrote:

>> BIM provides functions to solve Advection-Diffusion-Reaction Partial Differential Equations in 1, 2 and 3 
>> spatial dimensions on structured or unstructured triangular/tetrahedral meshes. 
> 
> Pointers to literature on the theory and implementation behind BIM
> would be very much appreciated.

The method used for the discretization of symmetric elliptic operators is a piecewise linear continuos 
Finite Element method with mass-lumpig, which is described in many elementary textbooks on numerical 
methods for PDEs as, for example, this one: http://www.springer.com/math/book/978-88-470-1070-3

For stabilization of Advection dominated problems the Exponential Fitting approach is used. 
The description of this method can be found in the same book mentioned above for the 1D case, 
for references to papers about the 2d and 3d case you can have a look at chapter 5 my PHD thesis 
(http://mox.polimi.it/it/progetti/pubblicazioni/tesi/de_falco.pdf).

For 3D there is also functions that implement the computation of the stiffness matrix with the 
Orthogonal Subdomain Collocation method described here: http://dx.doi.org/10.1137/S1064827595290711.


> This link
> 	http://agora.octave.org/snippet/1bqV
> to the example source code doesn't seem to work.

Thanks for noting this. 

That's probably because the Agora database 
was flushed during the latest update and all snippets were lost :(
Sorry for that, Agora is starting to look good but it is still work 
in progress.

I commented out that line on the wiki page for the moment.

c.

Re: [OctDev] physicalconstants-1.0.0

[Carnë D. <car...@gm...>]

On 20 October 2012 07:52, Dmitry Roshchin <dm...@ro...> wrote:
> physicalconstants-1.0.0 source archive now contains directory "physical-
> constants", not "physicalconstants". Please, use one variant of package name,
> it breaks our octave-forge update scrips.

Hi Dmitry

we can try to do this but pkg accepts it with no problem so it seems
it's a bug in your update scripts. The last version nof this package
even had the version number on the directory inside. That doesn't
happen anymore for example.

Anyway, this package has been removed. You will notice that
physical-constants is completely empty and only dependent on
miscellaneous. I'd recommend you remove it.

Carnë

Re: [OctDev] minmax

[Carnë D. <car...@gm...>]

On 21 October 2012 15:15,  <gio...@un...> wrote:
> Hi!
> there is a difference between matlab's minmax, and octave nnet pkg's min_max.
>
> In matlab:
> minmax([1 2 3 4 3 4 5 6 4 3 4 5])
> gives
> ans =
>      1     6
>
> In octave with nnet:
> min_max([1 2 3 4 3 4 5 6 4 3 4 5])
> gives
> error: Argument must be a matrix.
>
> Octave does not like the input image to be a single line.
>
> Best regards!
> Ciao
> Giorgio

Hi Giorgio

I'm sending this e-mail to the package maintainer, Michael Schmid, but
its last release was almost 2 years ago. Could you please report the
bug at https://sourceforge.net/p/octave/bugs/

And of course, if you are able to attach a patch too that would be
great. I just tok a look at its source and should not be too
difficult. And to create a patch (against the dev version), the
following command will do it:

svn diff > ~/bugfix.diff

Carnë

Re: [OctDev] minmax

[Jordi G. H. <jo...@oc...>]

On 21 October 2012 10:15,  <gio...@un...> wrote:
> there is a difference between matlab's minmax, and octave nnet pkg's min_max.

The nnet package is severely bitrotten. Can you maintain it?

- Jordi G. H.

[OctDev] new package releases: bim 1.1.0 and msh 1.0.5

[c. <car...@gm...>]

Hi all,

New versions of the Forge packages bim (1.1.0) and msh (1.0.5) have been uploaded to the package release forum, 
and will soon be available for download from Octave-Forge.

BIM provides functions to solve Advection-Diffusion-Reaction Partial Differential Equations in 1, 2 and 3 
spatial dimensions on structured or unstructured triangular/tetrahedral meshes. 

MSH provides functions to generate and manage triangular and tetrahetral meshes in Octave.

See this page http://wiki.octave.org/Bim_package on the wiki for usage examples.

Enjoy,
cdf.

Re: [OctDev] physicalconstants-1.0.0

[Juan P. C. <aju...@gm...>]

On Sat, Oct 20, 2012 at 8:52 AM, Dmitry Roshchin <dm...@ro...> wrote:
> physicalconstants-1.0.0 source archive now contains directory "physical-
> constants", not "physicalconstants". Please, use one variant of package name,
> it breaks our octave-forge update scrips.
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_sfd2d_oct
> _______________________________________________
> Octave-dev mailing list
> Oct...@li...
> https://lists.sourceforge.net/lists/listinfo/octave-dev

Dmitry,

physical constants was deprecated and merged into miscellaneous. It
shouldn't be packaged anymore
http://octave.sourceforge.net/physicalconstants/overview.html

Does this solve your problem?

Re: [OctDev] Implementation of importdata belonging to Octave Core or Octave-Forge?

[c. <car...@gm...>]

On 21 Oct 2012, at 15:47, Ben Abbott wrote:

> On Oct 19, 2012, at 1:35 PM, Erik Kjellson wrote:
> 
>> Hello,
>> 
>> Now I have uploaded my implementation here: https://sourceforge.net/p/octave/feature-requests/41/
>> 
>> I've noticed that a lot of function files have some kind of tests in the end of the file. I guess that you use them to check that you haven't introduced any logic error in the code when modifying it?
>> I did find this page: http://wiki.octave.org/Tests
>> But I guess I need to fake input from a fake file in some way, is there anywhere I can read more on how to do that?
>> 
>> regards,
>> Erik
> 
> I suggest you create a temporary file and use it for testing.   See "help tmpnam"
> 
> Ben

This fuction:
https://sourceforge.net/p/octave/code/11324/tree/trunk/octave-forge/extra/bim/inst/bim3a_osc_advection_diffusion.m

has an example of creating a temporary file to work with in a demo.

HTH,
c.

Re: [OctDev] Implementation of importdata belonging to Octave Core or Octave-Forge?

[Ben A. <bpa...@ma...>]

On Oct 19, 2012, at 1:35 PM, Erik Kjellson wrote:

> Hello,
> 
> Now I have uploaded my implementation here: https://sourceforge.net/p/octave/feature-requests/41/
> 
> I've noticed that a lot of function files have some kind of tests in the end of the file. I guess that you use them to check that you haven't introduced any logic error in the code when modifying it?
> I did find this page: http://wiki.octave.org/Tests
> But I guess I need to fake input from a fake file in some way, is there anywhere I can read more on how to do that?
> 
> regards,
> Erik

I suggest you create a temporary file and use it for testing.   See "help tmpnam"

Ben

[OctDev] minmax

[<gio...@un...>]

Hi!
there is a difference between matlab's minmax, and octave nnet pkg's min_max.

In matlab:
minmax([1 2 3 4 3 4 5 6 4 3 4 5])
gives
ans =
     1     6

In octave with nnet:
min_max([1 2 3 4 3 4 5 6 4 3 4 5])
gives
error: Argument must be a matrix.

Octave does not like the input image to be a single line.

Best regards!
Ciao
Giorgio

Re: [OctDev] Hi all, and a first question about graycomatrix

[<gio...@un...>]

Hi Carlo, thank you very much! I did not know the existence of the demo
function!
graycomatrix has no demo, but your hint will be useful for me in the future!
Ciao!
Giorgio


>
> On 20 Oct 2012, at 17:50, gio...@un... wrote:
>
>> "try the demos": can someone suggest me where they are?
> many Octave and Octave-Forge functions contain embedded demos:
> http://www.gnu.org/software/octave/doc/interpreter/Demonstration-Functions.html#Demonstration-Functions
> to run them just type:
> demo function_name
> at the Octave prompt.
> HTH,
> c.

Re: [OctDev] Hi all, and a first question about graycomatrix

[<gio...@un...>]

Hi Carnë,
thanks for your kind reply! I'll immediately check the changes in the pkg.

I prefer to send my reply to the list too, because it might  be useful to
other people who are using or will use graycomatrix in octave (before it
gets aligned with matlab's).

As to the differences between matlab and octave versions of graycomatrix,
here are some (as far as I can see at present):

input parameters:
1) matlab wants vectors, one row for each distance/direction couple, and
the necessary  information is a vector with x- and y- components,
describing the particular relative-position vector(s) we are interested in
 ('Offset' parameter) (no idea if I was clear… perhaps it is better to try
matlab help :-)  ; octave wants distinct angles (degrees) and distances:
    offsets = [0 1; 0 -1;   -1 1; 1 -1;   -1 0; 1 0;   -1 -1; 1 1];       
        % matlab
    angles = [6 ; 2 ; 5 ; 1 ; 4 ; 0 ; 3 ; 7] * pi/4;   distances = [1];   
     % octave

2) matlab implicitly transforms the input-image bit depth ('NumLevels'
parameter), while octave needs that you change it beforehand; matlab wants
to know the limits of gray level values ('GrayLimits' parameter), octave
does not (I do not know if it assumes the whole range of possible values
in accordance with the bit depth, or it calculates min and max from the
image data (I suppose the former is correct, but I have not checked yet).
Octave just wants to know how many levels are there (not their values).
Anyway I still have to totally verify this. The output is also different
because octave gives a 4D matrix (numlevels x numlevels x distances x
angles, iirc), while matlab gives a 3D matrix:

    numlevels = 16;
    graylimits = [0, 65535];

    % matlab
    theglcm = graycomatrix(I ,'Offset', offsets, 'NumLevels', numlevels ,
'GrayLimits', graylimits);

    % octave
    IOct = uint16(floor(numlevels*(double(I)/graylimits(2))));    %
diminuish bit depth; I supposed graylimits(1) to be zero.
    theglcm = graycomatrix(IOct, numlevels, distances, angles);
    theglcm = squeeze(theglcm);  % This works only because I am working
with just one distance value! Now the output is numlevels x numlevels
x angles like in matlab

I hope I made no mistakes in what I wrote… If I did please be patient...

Thanks again for your work!
Best regards
Giorgio



> Hi Giorgio
>
> I'm the current maintainer of the image package. I'll be releasing a
> new version of the image package very soon there's only a standing
> issue with the Clang compiler (but moving to another country so
> haven't had much time).
>
> I didn't touch graycomatrix but many many functions had changes for
> increased matlab compatibility. Just take a look at the NEWS file:
>
> https://sourceforge.net/p/octave/code/11300/tree/trunk/octave-forge/main/image/NEWS
>
> Some of the fixes may mean no porting issues for you. And if you still
> find a compatibility issue, this is rarely by design and should be
> fixed. So please don't "fix" too much of your code if you can fix the
> function in Octave Forge instead, most of the times this actually
> really easy. Or at least report it.
>
> The new release will be sometime this week but if you can't make the
> package from the repository, you can get the beta version from
>
> http://carandraug.no-ip.org/octave/image-1.9.91.tar.gz
>
> Carnë
>