problems running anything with mayavi2

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problems running anything with mayavi2

Simeon Nifos
HI all,
thanks for mayavi2. I have installed it through my package manager in Debian.

$ apt-get install mayavi2

I am trying to run 2 examples. The heart.vtk and mri.py.

For the heart.vtk which I downloaded by googling for it (I have no
idea why debian doesn't install examples),
I get strange errors which say that:

$ mayavi2 -d heart.vtk -m Outline -m GridPlane -m GridPlane -m
GridPlane -m ContourGridPlane -m ContourGridPlane -m IsoSurface -m
ScalarCutPlane

FBI: Frame Based Inspector opens saying:
Exception:: 'NonType' object has no attribute 'point_data'

This is the Traceback

 File "/usr/lib/python2.5/site-packages/enthought/traits/trait_notifiers.py",
line 331, in call_2
   self.handler( object, new )
 File "/usr/lib/python2.5/site-packages/enthought/mayavi/sources/vtk_file_reader.py",
line 69, in _file_path_changed
   self.update_data()
 File "/usr/lib/python2.5/site-packages/enthought/mayavi/sources/vtk_xml_file_reader.py",
line 229, in update_data
   pnt_attr, cell_attr = get_all_attributes(self.reader.output)
 File "/usr/lib/python2.5/site-packages/enthought/mayavi/sources/vtk_xml_file_reader.py",
line 80, in get_all_attributes
   point_attr = get_attribute_list(obj.point_data)
Exception: 'NoneType' object has no attribute 'point_data'

When I try to run mri.py by typing:

$ python mri.py

I get:

Traceback (most recent call last):
 File "mri.py", line 50, in <module>
   mlab.figure(bgcolor=(0, 0, 0), size=(400, 400))
TypeError: figure() got an unexpected keyword argument 'bgcolor'

Is there anything wrong with my installation or is it a bug?

Best,
Simeon.
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Re: problems running anything with mayavi2

Gael Varoquaux
On Wed, May 12, 2010 at 08:52:41AM -0400, Simeon Nifos wrote:
> thanks for mayavi2. I have installed it through my package manager in Debian.

> $ apt-get install mayavi2

> I am trying to run 2 examples. The heart.vtk and mri.py.

What's your mayavi2 version, and how did you install the examples?

I suspect that the mayavi version and the examples don't match.

Cheers,

Gaël
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Re: problems running anything with mayavi2

Simeon Nifos
$ mayavi2 --version
MayaVi 2.2.0


On Wed, May 12, 2010 at 8:57 AM, Gael Varoquaux
<[hidden email]> wrote:

> On Wed, May 12, 2010 at 08:52:41AM -0400, Simeon Nifos wrote:
>> thanks for mayavi2. I have installed it through my package manager in Debian.
>
>> $ apt-get install mayavi2
>
>> I am trying to run 2 examples. The heart.vtk and mri.py.
>
> What's your mayavi2 version, and how did you install the examples?
>
> I suspect that the mayavi version and the examples don't match.
>
> Cheers,
>
> Gaël
> _______________________________________________
> Enthought-Dev mailing list
> [hidden email]
> https://mail.enthought.com/mailman/listinfo/enthought-dev
>
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Re: problems running anything with mayavi2

Gael Varoquaux
On Wed, May 12, 2010 at 09:00:24AM -0400, Simeon Nifos wrote:
> $ mayavi2 --version
> MayaVi 2.2.0

OK, that's way too old. You'll need version 3.x at least to be able to
run the examples.

You'll be able to adapt some of the basic functionnality in the examples
using mlab by replacing

'from enthought.mayavi import mlab' to
'from enthought.mayavi.tools import mlab'

But really, you are going to be missing a lot of the functionnality.

Sorry for the bad news,

Gaël
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Re: problems running anything with mayavi2

Simeon Nifos
In Debian this is the only version that is provided. How can I install
the new version?

On Wed, May 12, 2010 at 9:21 AM, Gael Varoquaux
<[hidden email]> wrote:

> On Wed, May 12, 2010 at 09:00:24AM -0400, Simeon Nifos wrote:
>> $ mayavi2 --version
>> MayaVi 2.2.0
>
> OK, that's way too old. You'll need version 3.x at least to be able to
> run the examples.
>
> You'll be able to adapt some of the basic functionnality in the examples
> using mlab by replacing
>
> 'from enthought.mayavi import mlab' to
> 'from enthought.mayavi.tools import mlab'
>
> But really, you are going to be missing a lot of the functionnality.
>
> Sorry for the bad news,
>
> Gaël
> _______________________________________________
> Enthought-Dev mailing list
> [hidden email]
> https://mail.enthought.com/mailman/listinfo/enthought-dev
>
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Re: problems running anything with mayavi2

Gael Varoquaux
On Wed, May 12, 2010 at 09:22:56AM -0400, Simeon Nifos wrote:
> In Debian this is the only version that is provided. How can I install
> the new version?

Debian is a slow mover.

Check out the instal instructions. The relevent bit for you is here:
http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/installation.html#installing-with-easy-install

One thing I should add to these instructions, is that you should remove
all the Debian enthought-related packages from your system. Also,
I advice you to run 'easy_install --prefix /usr/local' to avoid
overriding system files.

Finally, if you run into problems with error messages talking about a
'sandbox violation', just retry running the same thing, until the error
goes away. Its a non-important bug somewhere that happens only every once
in a while.

Hope this helps,

Gaël
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Re: problems running anything with mayavi2

Simeon Nifos
easy_install not found.

Where can I get that from?


On Wed, May 12, 2010 at 9:32 AM, Gael Varoquaux
<[hidden email]> wrote:

> On Wed, May 12, 2010 at 09:22:56AM -0400, Simeon Nifos wrote:
>> In Debian this is the only version that is provided. How can I install
>> the new version?
>
> Debian is a slow mover.
>
> Check out the instal instructions. The relevent bit for you is here:
> http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/installation.html#installing-with-easy-install
>
> One thing I should add to these instructions, is that you should remove
> all the Debian enthought-related packages from your system. Also,
> I advice you to run 'easy_install --prefix /usr/local' to avoid
> overriding system files.
>
> Finally, if you run into problems with error messages talking about a
> 'sandbox violation', just retry running the same thing, until the error
> goes away. Its a non-important bug somewhere that happens only every once
> in a while.
>
> Hope this helps,
>
> Gaël
> _______________________________________________
> Enthought-Dev mailing list
> [hidden email]
> https://mail.enthought.com/mailman/listinfo/enthought-dev
>
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Re: problems running anything with mayavi2

Gael Varoquaux
On Wed, May 12, 2010 at 09:47:20AM -0400, Simeon Nifos wrote:
> easy_install not found.

> Where can I get that from?

Install setuptools, as indicated in the requirements:
http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/installation.html#installing-with-easy-instal

Gaël
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Re: problems running anything with mayavi2

Simeon Nifos
OK Thanks,

by the way,

any thoughts to provide a C/C++ interface, the way xmgrace or Grace (I
assume you are aware of xmgrace) does? This could be quite handy
because python is quite messy especially if you are new to it. Several
times I tried to become familiar with it and it was impossible. Every
attempt failed with messages like:

this module not found the other module not found etc.

Sorry this is just a personal opinion you do not really need to take
it seriously. But I always find the C++/C interfaces to be much more
reliable and useful. You link to a library write code once and for all
and that's it.

As I said, that is just a suggestion! I understand how much involved
this would be, but once you have it, then you do not need python or
all that stuff, you just provide mayavi2 and a library and I strongly
believe that all people who generate scientific data are using some
language to do that mostly C/C++ and they can easy use this library. I
once again apologize in case you feel uncomfortable with this
suggestion, but it is just another viewpoint. This way you make your
maintenance life easier since you only need to care about a library
instead of so many tools that only few people know how to use.

To give you an idea, in my department we are all developing a high-end
simulator and we are all using C++ and know very well C++. This
involves many post-docs research associates and PhD and master
students. Imagine how hard it would be to convince them to learn a new
language hardly to be installed and mastered like Python, and how easy
it would be to give them a source code written in C/C++ which they
have to link to a library and they have what they want. Mayavi2 would
become much more popular if you could provide that.

But, needless to say, you have done an excellent job, even if it is python.

Thanks for the support, I really appreciate, and sorry if my comments
are not that python encouraging.

Archwn.




On Wed, May 12, 2010 at 9:50 AM, Gael Varoquaux
<[hidden email]> wrote:

> On Wed, May 12, 2010 at 09:47:20AM -0400, Simeon Nifos wrote:
>> easy_install not found.
>
>> Where can I get that from?
>
> Install setuptools, as indicated in the requirements:
> http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/installation.html#installing-with-easy-instal
>
> Gaël
> _______________________________________________
> Enthought-Dev mailing list
> [hidden email]
> https://mail.enthought.com/mailman/listinfo/enthought-dev
>
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Re: problems running anything with mayavi2

Simeon Nifos
Here is the output of the attempt to install it.


easy_install --prefix=/usr/local "Mayavi[app]"
Searching for Mayavi[app]
Best match: Mayavi 3.3.1
Processing Mayavi-3.3.1-py2.5-linux-i686.egg
Mayavi 3.3.1 is already the active version in easy-install.pth
Installing tvtk_doc script to /usr/local/bin
Installing mayavi2 script to /usr/local/bin

Using /usr/lib/python2.5/site-packages/Mayavi-3.3.1-py2.5-linux-i686.egg
Processing dependencies for Mayavi[app]
Searching for TraitsGUI>=3.3.0.dev
Reading http://pypi.python.org/simple/TraitsGUI/
Reading http://code.enthought.com/projects/traits_gui
Best match: TraitsGUI 3.3.0
Downloading http://enthought.com/repo/ets/TraitsGUI-3.3.0.tar.gz
Processing TraitsGUI-3.3.0.tar.gz
Running TraitsGUI-3.3.0/setup.py -q bdist_egg --dist-dir
/tmp/easy_install-W3LDvC/TraitsGUI-3.3.0/egg-dist-tmp-bMb5wH
Checking .pth file support in .
/usr/bin/python -E -c pass
Searching for setupdocs>=1.0
Reading http://pypi.python.org/simple/setupdocs/
Best match: SetupDocs 1.0.4
Downloading http://pypi.python.org/packages/source/S/SetupDocs/SetupDocs-1.0.4.tar.gz#md5=824bcf896b7e4e7c610d65544e28bdd1
Processing SetupDocs-1.0.4.tar.gz
Running SetupDocs-1.0.4/setup.py -q bdist_egg --dist-dir
/tmp/easy_install-W3LDvC/TraitsGUI-3.3.0/temp/easy_install-caOaR4/SetupDocs-1.0.4/egg-dist-tmp-hzRPdt
zip_safe flag not set; analyzing archive contents...
setupdocs.setupdocs: module references __file__

Installed /tmp/easy_install-W3LDvC/TraitsGUI-3.3.0/SetupDocs-1.0.4-py2.5.egg
Adding TraitsGUI 3.3.0 to easy-install.pth file

Installed /usr/local/lib/python2.5/site-packages/TraitsGUI-3.3.0-py2.5.egg
Searching for EnthoughtBase>=3.0.4.dev
Reading http://pypi.python.org/simple/EnthoughtBase/
Reading http://code.enthought.com/projects/enthought_base.php
Best match: EnthoughtBase 3.0.4
Downloading http://pypi.python.org/packages/source/E/EnthoughtBase/EnthoughtBase-3.0.4.tar.gz#md5=0e62eddfa37995a1956c648e06213132
Processing EnthoughtBase-3.0.4.tar.gz
Running EnthoughtBase-3.0.4/setup.py -q bdist_egg --dist-dir
/tmp/easy_install-fWdmAl/EnthoughtBase-3.0.4/egg-dist-tmp-ao4oLi
error: Setup script exited with error:
/tmp/easy_install-W3LDvC/TraitsGUI-3.3.0/docs/html.zip: No such file
or directory
[root /home/drosos/ETSProjectTools]#

On Wed, May 12, 2010 at 10:07 AM, Simeon Nifos <[hidden email]> wrote:

> OK Thanks,
>
> by the way,
>
> any thoughts to provide a C/C++ interface, the way xmgrace or Grace (I
> assume you are aware of xmgrace) does? This could be quite handy
> because python is quite messy especially if you are new to it. Several
> times I tried to become familiar with it and it was impossible. Every
> attempt failed with messages like:
>
> this module not found the other module not found etc.
>
> Sorry this is just a personal opinion you do not really need to take
> it seriously. But I always find the C++/C interfaces to be much more
> reliable and useful. You link to a library write code once and for all
> and that's it.
>
> As I said, that is just a suggestion! I understand how much involved
> this would be, but once you have it, then you do not need python or
> all that stuff, you just provide mayavi2 and a library and I strongly
> believe that all people who generate scientific data are using some
> language to do that mostly C/C++ and they can easy use this library. I
> once again apologize in case you feel uncomfortable with this
> suggestion, but it is just another viewpoint. This way you make your
> maintenance life easier since you only need to care about a library
> instead of so many tools that only few people know how to use.
>
> To give you an idea, in my department we are all developing a high-end
> simulator and we are all using C++ and know very well C++. This
> involves many post-docs research associates and PhD and master
> students. Imagine how hard it would be to convince them to learn a new
> language hardly to be installed and mastered like Python, and how easy
> it would be to give them a source code written in C/C++ which they
> have to link to a library and they have what they want. Mayavi2 would
> become much more popular if you could provide that.
>
> But, needless to say, you have done an excellent job, even if it is python.
>
> Thanks for the support, I really appreciate, and sorry if my comments
> are not that python encouraging.
>
> Archwn.
>
>
>
>
> On Wed, May 12, 2010 at 9:50 AM, Gael Varoquaux
> <[hidden email]> wrote:
>> On Wed, May 12, 2010 at 09:47:20AM -0400, Simeon Nifos wrote:
>>> easy_install not found.
>>
>>> Where can I get that from?
>>
>> Install setuptools, as indicated in the requirements:
>> http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/installation.html#installing-with-easy-instal
>>
>> Gaël
>> _______________________________________________
>> Enthought-Dev mailing list
>> [hidden email]
>> https://mail.enthought.com/mailman/listinfo/enthought-dev
>>
>
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Re: problems running anything with mayavi2

Gael Varoquaux
In reply to this post by Simeon Nifos

Interesting point of view.

I happen to have the opposite, but it just shows that different
environments have different cultures. Around me, people mostly know
Matlab. I have had really bad experiences in my research with people
coding in C/C++ while they clearly didn't understand what they where
doing. Around me, most people can't code decent C++. Maybe it's because
you and I are talking about different crowds. I am interested in working
with many different people, and most of them never had a training in
computing (medical doctors, physicists, mechanical engineers, financial
annalists). They can learn and use Python fairly quickly. Teaching them
C/C++ requires a lot of time, and can actually lead to 'interesting'
code. As some one said last year at euroscipy 'debugging crappy Python
code is easier than debugging crappy C code'.

I see that their is some truth in your comments. First of all, the
current packaging situation in Python is a mess. Second, dynamic
languages are more 'unstable', because of lack of static linking, and
thus the 'unreliability' you mention. And finally, best practices are
less known and less established.

Anyhow, I believe that the real value of Mayavi is that it is exposing
a 3D plotting library in Python, and in a Pythonic way. If you like C++,
I suggest that you study VTK. Mayavi is based on it, and it's an
excellent library. The only issue I have with it, is that it's in C++ :).

My 2 euro cents,

Gaël

On Wed, May 12, 2010 at 10:07:36AM -0400, Simeon Nifos wrote:
> OK Thanks,

> by the way,

> any thoughts to provide a C/C++ interface, the way xmgrace or Grace (I
> assume you are aware of xmgrace) does? This could be quite handy
> because python is quite messy especially if you are new to it. Several
> times I tried to become familiar with it and it was impossible. Every
> attempt failed with messages like:

> this module not found the other module not found etc.

> Sorry this is just a personal opinion you do not really need to take
> it seriously. But I always find the C++/C interfaces to be much more
> reliable and useful. You link to a library write code once and for all
> and that's it.

> As I said, that is just a suggestion! I understand how much involved
> this would be, but once you have it, then you do not need python or
> all that stuff, you just provide mayavi2 and a library and I strongly
> believe that all people who generate scientific data are using some
> language to do that mostly C/C++ and they can easy use this library. I
> once again apologize in case you feel uncomfortable with this
> suggestion, but it is just another viewpoint. This way you make your
> maintenance life easier since you only need to care about a library
> instead of so many tools that only few people know how to use.

> To give you an idea, in my department we are all developing a high-end
> simulator and we are all using C++ and know very well C++. This
> involves many post-docs research associates and PhD and master
> students. Imagine how hard it would be to convince them to learn a new
> language hardly to be installed and mastered like Python, and how easy
> it would be to give them a source code written in C/C++ which they
> have to link to a library and they have what they want. Mayavi2 would
> become much more popular if you could provide that.

> But, needless to say, you have done an excellent job, even if it is python.

> Thanks for the support, I really appreciate, and sorry if my comments
> are not that python encouraging.

> Archwn.




> On Wed, May 12, 2010 at 9:50 AM, Gael Varoquaux
> <[hidden email]> wrote:
> > On Wed, May 12, 2010 at 09:47:20AM -0400, Simeon Nifos wrote:
> >> easy_install not found.

> >> Where can I get that from?

> > Install setuptools, as indicated in the requirements:
> > http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/installation.html#installing-with-easy-instal

> > Gaël
> > _______________________________________________
> > Enthought-Dev mailing list
> > [hidden email]
> > https://mail.enthought.com/mailman/listinfo/enthought-dev

> _______________________________________________
> Enthought-Dev mailing list
> [hidden email]
> https://mail.enthought.com/mailman/listinfo/enthought-dev

--
    Gael Varoquaux
    Research Fellow, INRIA
    Laboratoire de Neuro-Imagerie Assistee par Ordinateur
    NeuroSpin/CEA Saclay , Bat 145, 91191 Gif-sur-Yvette France
    Phone:  ++ 33-1-69-08-78-35
    Mobile: ++ 33-6-28-25-64-62
    http://gael-varoquaux.info
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Re: problems running anything with mayavi2

Gael Varoquaux
In reply to this post by Simeon Nifos
On Wed, May 12, 2010 at 10:19:37AM -0400, Simeon Nifos wrote:
> Running EnthoughtBase-3.0.4/setup.py -q bdist_egg --dist-dir
> /tmp/easy_install-fWdmAl/EnthoughtBase-3.0.4/egg-dist-tmp-ao4oLi
> error: Setup script exited with error:
> /tmp/easy_install-W3LDvC/TraitsGUI-3.3.0/docs/html.zip: No such file
> or directory

That's new, AFAIK.

Does it go away if you run again (easy_install has 'moods')?

Gaël
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Re: problems running anything with mayavi2

Simeon Nifos
No it doesn't,
I have tried several times and it is still there.

any ideas?

On Wed, May 12, 2010 at 10:27 AM, Gael Varoquaux
<[hidden email]> wrote:

> On Wed, May 12, 2010 at 10:19:37AM -0400, Simeon Nifos wrote:
>> Running EnthoughtBase-3.0.4/setup.py -q bdist_egg --dist-dir
>> /tmp/easy_install-fWdmAl/EnthoughtBase-3.0.4/egg-dist-tmp-ao4oLi
>> error: Setup script exited with error:
>> /tmp/easy_install-W3LDvC/TraitsGUI-3.3.0/docs/html.zip: No such file
>> or directory
>
> That's new, AFAIK.
>
> Does it go away if you run again (easy_install has 'moods')?
>
> Gaël
> _______________________________________________
> Enthought-Dev mailing list
> [hidden email]
> https://mail.enthought.com/mailman/listinfo/enthought-dev
>
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Re: problems running anything with mayavi2

Gael Varoquaux
On Wed, May 12, 2010 at 10:40:12AM -0400, Simeon Nifos wrote:
> I have tried several times and it is still there.

> any ideas?

Actually, no. I am a bit surprised by this.

It seems that it is in either Traits or EnthoughtBase rather than Mayavi.
Let's wait till the Texan guys wake up, they know this stuff better than
me.

> On Wed, May 12, 2010 at 10:27 AM, Gael Varoquaux
> <[hidden email]> wrote:
> > On Wed, May 12, 2010 at 10:19:37AM -0400, Simeon Nifos wrote:
> >> Running EnthoughtBase-3.0.4/setup.py -q bdist_egg --dist-dir
> >> /tmp/easy_install-fWdmAl/EnthoughtBase-3.0.4/egg-dist-tmp-ao4oLi
> >> error: Setup script exited with error:
> >> /tmp/easy_install-W3LDvC/TraitsGUI-3.3.0/docs/html.zip: No such file
> >> or directory

> > That's new, AFAIK.

> > Does it go away if you run again (easy_install has 'moods')?

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Re: problems running anything with mayavi2

Simeon Nifos
OK thanks.

Could I ask you something else,
which algorithm are you using for tracing the streamlines? I have seen
a couple of papers, some faster than others, I could send you one if
you like, but it is interesting from many aspects. There are even
papers of visualizing the uncertainty in streamlines doing some
amazing plots. Have you ever heard about these things?

Cheers,
Archwn.


On Wed, May 12, 2010 at 10:50 AM, Gael Varoquaux
<[hidden email]> wrote:

> On Wed, May 12, 2010 at 10:40:12AM -0400, Simeon Nifos wrote:
>> I have tried several times and it is still there.
>
>> any ideas?
>
> Actually, no. I am a bit surprised by this.
>
> It seems that it is in either Traits or EnthoughtBase rather than Mayavi.
> Let's wait till the Texan guys wake up, they know this stuff better than
> me.
>
>> On Wed, May 12, 2010 at 10:27 AM, Gael Varoquaux
>> <[hidden email]> wrote:
>> > On Wed, May 12, 2010 at 10:19:37AM -0400, Simeon Nifos wrote:
>> >> Running EnthoughtBase-3.0.4/setup.py -q bdist_egg --dist-dir
>> >> /tmp/easy_install-fWdmAl/EnthoughtBase-3.0.4/egg-dist-tmp-ao4oLi
>> >> error: Setup script exited with error:
>> >> /tmp/easy_install-W3LDvC/TraitsGUI-3.3.0/docs/html.zip: No such file
>> >> or directory
>
>> > That's new, AFAIK.
>
>> > Does it go away if you run again (easy_install has 'moods')?
>
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Re: problems running anything with mayavi2

Gael Varoquaux
On Wed, May 12, 2010 at 10:57:22AM -0400, Simeon Nifos wrote:
> which algorithm are you using for tracing the streamlines?

It is VTK does the streamlining. I believe it is a Runge Kutta
integration.

> I have seen a couple of papers, some faster than others, I could send
> you one if you like, but it is interesting from many aspects. There are
> even papers of visualizing the uncertainty in streamlines doing some
> amazing plots. Have you ever heard about these things?

I know of the work in tractography, in diffusion MRI. There is a lot of
work. What you might be refering to could be what is called
'probabilistic tractography' in this field. Mayavi doesn't implement this
(nor VTK, AFAIK).

Gaël
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