Problem loading data file

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Re: Problem loading data file

david wende wrote:
> I am using mayavi2 on Linux platform.
[...]
> "/usr/lib/python2.6/site-packages/enthought/mayavi/sources/vtk_xml_file_reader.py", 
> line 236, in update_data
> pnt_attr, cell_attr = get_all_attributes(self.reader.output)
> File 
> "/usr/lib/python2.6/site-packages/enthought/mayavi/sources/vtk_xml_file_reader.py", 
> line 82, in get_all_attributes
> point_attr = get_attribute_list(obj.point_data)
> AttributeError: 'NoneType' object has no attribute 'point_data'

This is strange.  Can you give us more information on the version of 
mayavi2 you have installed and details on the OS?  My guess is that 
there is a Python-2.6 specific issue here but I am not sure.  I haven't 
tested mayavi with python-2.6 yet.

cheers,
prabhu

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Re: mayavi module

Håkan Jakobsson wrote:
> Hi,
> 
> I read on the mayavi website that it is possible to write own modules  
> to mayavi. My research group is looking to write a simple graphical  
> tool used to apply boundary conditions etc to geometries defined  
> by .poly files. The data would be saved in an xml file, read by our  
> solvers. Is it possible to write such a module to mayavi?

Yes, I think it is possible to do so.  I would recommend doing this with 
mayavi2 (and posting questions on enthought-dev <at> mail.enthought.com in 
addition).  Your strategy would be to learn a little of traits and TraitsUI

  http://code.enthought.com/projects/traits/

Then understand how to create a simple module with mayavi2.  The mayavi2 
user guide should give you a reasonable start:

  http://code.enthought.com/projects/mayavi

Then you should have a good idea of what kind of UI you want to provide 
for your module and how you want people to interact with your module to 
provide the boundary condition information and then implement it.  At 
this point you'll also need to learn a little VTK to understand things a 
little better.

HTH.

cheers,
prabhu

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Re: Problem loading data file

> On Sun, May 3, 2009 at 12:57 PM, Prabhu Ramachandran 
> <prabhu <at> aero.iitb.ac.in <mailto:prabhu <at> aero.iitb.ac.in>> wrote:
> 
>     david wende wrote:
> 
>         I am using mayavi2 on Linux platform.
> 
>     [...]
> 
>         "/usr/lib/python2.6/site-packages/enthought/mayavi/sources/vtk_xml_file_reader.py",
>         line 236, in update_data
>         pnt_attr, cell_attr = get_all_attributes(self.reader.output)
>         File
>         "/usr/lib/python2.6/site-packages/enthought/mayavi/sources/vtk_xml_file_reader.py",
>         line 82, in get_all_attributes
>         point_attr = get_attribute_list(obj.point_data)
>         AttributeError: 'NoneType' object has no attribute 'point_data'
> 
> 
>     This is strange.  Can you give us more information on the version of
>     mayavi2 you have installed and details on the OS?  My guess is that
>     there is a Python-2.6 specific issue here but I am not sure.  I
>     haven't tested mayavi with python-2.6 yet.

On 05/04/09 08:52, david wende wrote:
 > OS is archlinux.
 > Compling from sources in package called python-enthought-mayavi-3.2.0-1
 > from www.enthought.com/repo/ETS/Mayavi-3.2.0.aar.gz
 > <http://www.enthought.com/repo/ETS/Mayavi-3.2.0.aar.gz>

Can you try this:

  1. Drag the reader object on your tree view and drop it on the Python 
shell on the application.

  2. type the following:

  s = _
  s.reader.update()
  print s.reader.output

And tell us what you get?

prabhu

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weird behavior of warp_scale='auto' in mlabs surf() function

Hi everyone.

I hope this is the right place for my question. As far as I understood this,
the warp_scale='auto' option in mlab's surf() function is supposed to scale
the z-axis to a reasonable ratio. Following is a script that demonstrates a
problem I have found:

from numpy import *
from enthought.mayavi.mlab import *

epsilon = 100
x, y = mgrid[-10.05:10.05:0.1,-10.05:10.05:0.1]
U = epsilon / sqrt(x**2+y**2)
s = surf(x,y,U,warp_scale='auto')
show()

Now if you change the value of epsilon the image acts in a very weird way. If
epsilon is 1 or 10 it seems to be ok (ratio of ~2/3). If it's 100 the peak is
very low. If it's higher than that (1 000, 10 000), the peak is starting to
rise again. is this a numerical problem I'm experiencing here, or is this
indeed a bug in mayavi? Help would be very much apprecheated.

Jakob

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How to plot triangular mesh without the GUI coming up?

I got past the installation and am now trying
batch generation of images, in particular of
a triangular mesh.  At the top of my script,
following the nongui.py example, I have

import tables
import numpy
from enthought.mayavi import mlab
from enthought.mayavi.plugins.app import Mayavi, get_non_gui_plugins

class CrabCavity(Mayavi):

  def run(self):

# Then generate points and triangles

# Then at the bottom I have

# Create script and add triangles
    script = self.script
    script.new_scene()
    tmesh = mlab.triangular_mesh(points[:, 0], points[:, 1],
        points[:, 2], triangles)
    script.add_module(tmesh)

# Set the view
    s = script.engine.current_scene
    cam = s.scene.camera
    cam.azimuth(45)
    cam.elevation(15)
    s.render()
    s.scene.save("crabcav.png", size=(640,480))

if __name__ == '__main__':
  m = CrabCavity()
# Get the default non GUI plugins.
  plugins = get_non_gui_plugins()
# Start the app with these plugins.
  m.main(plugins=plugins)

which I run with python.

It seems that the gui always comes up.  I just want to
create my scene and save it in a png without the GUI
coming up.

What am I doing wrong?

Thanks....John Cary

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Re: How to plot triangular mesh without the GUI coming up?

On Mon, May 25, 2009 at 09:53:08AM -0600, John R. Cary wrote:
> It seems that the gui always comes up.  I just want to
> create my scene and save it in a png without the GUI
> coming up.

You are looking for offscreen rendering. I have sketched modifications to
your script that should do it:

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
import tables
import numpy
from enthought.mayavi import mlab
mlab.options.offscreen = True

def run():

    # Then generate points and triangles

    # Then at the bottom I have

    # Create script and add triangles
    tmesh = mlab.triangular_mesh(points[:, 0], points[:, 1],
                                    points[:, 2], triangles)

    # Set the view
    mlab.view(45, 15)
    mlab.savefig("crabcav.png", size=(640,480))

if __name__ == '__main__':
    run()
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

You should also read 
http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/tips.html#off-screen-rendering
as to avoid having a window poping up, you may need to do more, depending
on your platform.

HTH,

Gaël

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Re: weird behavior of warp_scale='auto' in mlabs surf() function

On Tue, May 26, 2009 at 03:46:54PM +0200, Rohrhirsch, Jakob wrote:
> I hope this is the right place for my question.

It is. The enthought-dev mailing-list
(https://mail.enthought.com/mailman/listinfo/enthought-dev) may also be
useful, as it has more traffic, and thus more people to help you.

> As far as I understood this,
> the warp_scale='auto' option in mlab's surf() function is supposed to scale
> the z-axis to a reasonable ratio. Following is a script that demonstrates a
> problem I have found:

> from numpy import *
> from enthought.mayavi.mlab import *

> epsilon = 100
> x, y = mgrid[-10.05:10.05:0.1,-10.05:10.05:0.1]
> U = epsilon / sqrt(x**2+y**2)
> s = surf(x,y,U,warp_scale='auto')
> show()

> Now if you change the value of epsilon the image acts in a very weird way. If
> epsilon is 1 or 10 it seems to be ok (ratio of ~2/3). If it's 100 the peak is
> very low. If it's higher than that (1 000, 10 000), the peak is starting to
> rise again. is this a numerical problem I'm experiencing here, or is this
> indeed a bug in mayavi? Help would be very much apprecheated.

This is a bug! Thanks for reporting it. I have fixed it in svn,
https://svn.enthought.com/enthought/changeset/23682
You can work around it by using the extent keyword argument. It is not as
handy as setting warp_scale to 'auto', but if you don't want to install
svn or patch your local version, this is a way forward.

Cheers,

Gaël

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Offscreen/remote rendering: script access to gl2ps dialog or magnification

Hi all,

I want to produce high-res files for an academic poster in offscreen mode.
My problem is that Im stuck with VTK-5.0.4. (i.e. cant seem to use the
mlab offscreen
flag) and also, I cannot put off work until the file is written, i.e.
I need my screen during
(rather lengthy) rendering. So what I did is use xvfb-run, but there
are two problems:

For vector images, the gl2ps dialog seems to block mlab from writing the file.
So any hint on how to circumvent the dialog or sent an 'OK' to a xvfb session
would solve my problem.
In addition, the .pdf and .ps files do not seem to qualify as vector
output. .PS clearly
produces an embedded raster image and .pdf is of very poor quality. .EPS gets it
amazingly right, but at the expense of quite longer output times.

For raster images, i have the problem that the size option in savefig() does not
work. It does at least try if I put the savefig() command with size
option twice,
but what happens is the following: The resulting figure's size is
right, but everything
is blank except for the upper left corner in which the original. So if
I could write a,
say 5000x5000 raster image, that would solve too. But I dont even know
if there is
a limit to the xvfb screen sizes. So .eps would be much preferred.

Renderman etc. are not an option, since I cannot install conversion software.
I think mayavi was installed via  enthought.mayavi-2.2.0-py2.5.egg, I
would have
to talk to my admin to get something else.

I am really thankful for any hints on this - Matt

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Re: Offscreen/remote rendering: script access to gl2ps dialog or magnification

daspostloch <at> googlemail.com wrote:
> For vector images, the gl2ps dialog seems to block mlab from writing the file.
> So any hint on how to circumvent the dialog or sent an 'OK' to a xvfb session
> would solve my problem.

No problem.  Do the following (assuming 's' is your mayavi scene or any 
object that has a scene trait):

  from enthought.tvtk.api import tvtk
  exp = tvtk.GL2PSExporter(file_format='pdf', sort='bsp', compress=1)
  s.scene.save_gl2ps('/tmp/t.pdf', exp)

It should not pop-up a UI in this case.

> In addition, the .pdf and .ps files do not seem to qualify as vector
> output. .PS clearly
> produces an embedded raster image and .pdf is of very poor quality. .EPS gets it
> amazingly right, but at the expense of quite longer output times.
> 
> For raster images, i have the problem that the size option in savefig() does not
> work. It does at least try if I put the savefig() command with size
> option twice,
> but what happens is the following: The resulting figure's size is
> right, but everything
> is blank except for the upper left corner in which the original. So if
> I could write a,
> say 5000x5000 raster image, that would solve too. But I dont even know
> if there is
> a limit to the xvfb screen sizes. So .eps would be much preferred.

Try using the magnification of the scene. If 's' is your mayavi scene 
then you can do:

  s.scene.magnification = 2 # or 4

and VTK should magnify the rendered image.  Try it and see if that helps.

HTH,
cheers,
prabhu

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