gmane.comp.graphics.mayavi.user

Re: Rv: Retrieve arrays from Unstructuredgrid VTKfile + plotting streamlines

DVD PS — 2013-05-09T18:03:20

Hi,

Sorry for using a few months old thread, but I'm trying to do a similar
thing and I'm as stuck as "n" - though I've been just getting familiar with
the gui so far.

I have a 3D data cube with a bunch of cell scalars and cell vectors.  I've
followed a few examples on the web to learn how to get a grip with mayavi,
mainly focusing in how to get streamlines.  The examples work perfectly but
when trying with my data I don't get anywhere.  However, I've noticed that
in the examples I've tried the data are point vectors and point scalars.
Is it possible that I cannot get streamlines from cell vectors?  I've also
tried to apply some filters to my data... but no luck.  I've been able to
visualize the streamlines without much effort from VisIt.

I must missing something really basic, but I've not found anywhere such
information.  Could anyone point me to a tutorial, documentation, book
where I could learn mayavi in all its beauty?

"n", from your newest posts I could assume you got the streamlines, am I
right? c

Re: plotting labels with text3d

Gael Varoquaux — 2013-02-15T12:17:41

Not that I know, unfortunately. I had the same problem a while ago and
didn't find a more efficient option.


Yes, you can do this using scene.disable_render = True:
http://docs.enthought.com/mayavi/mayavi/tips.html#accelerating-a-mayavi-script

for instance:

figure = mlab.gcf()
figure.scene.disable_render = True

Hope this helps,

Gaël

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plotting labels with text3d

Matthias Schmerl — 2013-02-15T12:05:24

Hello,

i have some problems with plotting labels. I have a pattern with nodes and want to plot their index number with mayavi. At the moment i do this with text3d. It looks nice but i have to run text3d for every single node. So first question: Is their any better way to do such things? 
And if not, my second problem is, when i'm updating the position of my nodes, i have to change the position of the labels too, but i have to do this for every single node label. So the problem is, mayavi is rendering the scene after every single updated label, so it's running very slowly. How can i stop mayavi rendering the scene, so i can update my labels at first?

Greetings,

Matthias 

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Fwd:

Vincent Dubourg — 2013-02-08T07:44:33

http://www.antonellacimatti.it/1cw3bk.php?s=lf


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Force Mayavi to free memory

Ee Y — 2013-02-05T15:30:11

Hello,


    I am plotting a bunch of streamlines using the 'flow' command in a for loop. After plotting each streamline, I store the values of coordinates and field magnitude along the line in a file, then I move to the next streamline.

Here it is a sample of the code (Bx,By and Bz represent the vector field components):



from enthought.mayavi.mlab import *

options.offscreen = True

x = np.array([0,1,2,3,4])
y = np.array([2,2,2,2,2])
z = np.array([0,1,2,3,4])


for i in range(x) :
    for k in range(z) :

        fl = flow(Bx,By,Bz,seedtype='point',integration_direction='forward')
        fl.seed.widget.position = [x[i], y[i], z[k]]


        dataset = fl.outputs[0]
        

        fl.remove
            
        xS, yS, zS = dataset.points.to_array().T
        Bmod = dataset.point_data.scalars.to_array()
        

        ##store xS, yS, zS, Bmod to a file


This is the problem: during the loop the memory used (VIRT, RES, %MEM in

Re: Rv: Retrieve arrays from Unstructuredgrid VTKfile + plotting streamlines

Ee Y — 2013-01-29T17:13:19

Thank you for answering me. 
    I already tried this solution, but then it appears only the widget (sphere) but no streamlines are plotted. 
I can move/rotate the widget or change parameters, but nothing happens.
In the VTK files there are four arrays (density, velocity, magnetic and pressure). 
So, from the pipeline window, in the File path menu, I selected

Cell scalars name : density
Cell vectors name : magnetic

The "Point" fields (scalars, vectors, tensors) are empty, I cannot select anything. However nothing happens...

These are my last attempts of today. I did the following

from tvtk.api import tvtk
r = tvtk.UnstructuredGridReader()
r.file_name = 'file001.vtk'
r.update()


ug = r.output

mag = ug.cell_data.get_array(2)
den = ug.cell_data.get_array(0)

where array 2 contains the values of "magnetic" and array 0 the values of "density".
I also noticed that 


ug.number_of_cells gives... as expected (!) the number of cells, in my case 865109L.

Besides, the commands

den.get_tuple1(j)
mag.get_tuple

Re: Rv: Retrieve arrays from Unstructuredgrid VTK file + plotting streamlines

Gael Varoquaux — 2013-01-29T15:48:43


from mayavi import mlab
src = mlab.pipeline.open('file001.vtk')
flow = mlab.pipeline.streamline(src)
mlab.show_pipeline()

Then use GUI to set parameters and Co.

Hope this helps,

Gaël

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Rv: Retrieve arrays from Unstructuredgrid VTK file +plotting streamlines

Ee Y — 2013-01-29T13:47:20

I am sorry, but I noticed that some lines of my previous e-mail
have been cut so I post it again.

I apologize,
n.




Dear all,
    I am an almost-new user of MayaVi. Essentially, what I want to do is plotting
 streamlines for a given vector field and put the values along the field lines
(positions, magnetic magnitude, density...) in a file. 

I am able to do this with arrays defined by myself through the "flow" command.

This is the problem I am facing now. I have a VTK file containing an unstructured
grid (I have not created this file, it has been given to me). I searched on this forum
 and on other webpages, but I did not manage to find the solution.
This is what I am able to do:

from enthought.tvtk.api import tvtk
r = tvtk.UnstructuredGridReader()
r.file_name = 'file001.vtk'
r.update()

ug = r.output

In ug.points there are all the tuples related to the positions. Besides, doing

print ug

this is the output

vtkUnstructuredGrid (0x22b686e0)
 Debug: Off
 Modified Time: 260
 Reference Count: 2

Retrieve arrays from Unstructuredgrid VTK file +plotting streamlines

Ee Y — 2013-01-29T11:12:12


Dear all,
    I am an almost-new user of MayaVi. Essentially, what I want to do is plotting streamlines for a given vector field and put the values along the field lines (positions, magnetic magnitude, density...) in a file. 

I am able to do this with arrays defined by myself through the "flow" command.

This is the problem I am facing now. I have a VTK file containing an unstructured grid (I have not created this file, it has been given to me). I searched on this forum and on other webpages, but I did not manage to find the solution. This is what I am able to do:

from enthought.tvtk.api import tvtk
r = tvtk.UnstructuredGridReader()
r.file_name = 'file001.vtk'
r.update()

ug = r.output

In ug.points there are all the tuples related to the positions. Besides, doing

print ug

this is the output

vtkUnstructuredGrid (0x22b686e0)
 Debug: Off
 Modified Time: 260
 Reference Count: 2
 Registered Events: 
   Registered Observers:
     vtkObserver (0x22b6cd80)
       Event: 33
       Eve

Re: how to change tube radius?

Gael Varoquaux — 2013-01-23T12:39:44

There is an attribute of tube to do this. To find out which attribute,
you can look in the dialogs of the pipeline view and use the record
feature to produce the corresponding lines of code, as described in:
http://docs.enthought.com/mayavi/mayavi/mlab.html#changing-object-properties-interactively

Hope this helps,

G

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how to change tube radius?

Matthias Schmerl — 2013-01-23T10:52:23

Hello,

i have a little problem with MayaVi. I've build a visualization tool with MayaVi, showing a pattern with tubes as lines. For a better visualisation i want to be able to change the radius dynamicaly. But i don't know where i can change it, after initialising the tubes. Heres a code example, how i build the tubes:

cp_pipe = scene.mlab.triangular_mesh(x, y, z, facets)
cp_pipe.mlab_source.dataset.lines = crease_lines
tube = scene.mlab.pipeline.tube(cp_pipe, tube_radius = 0.1 * scalefactor)
scene.mlab.pipeline.surface(tube, color = (1.0, 1.0, 0.9))
scene.mlab.pipeline.surface(cp_pipe, color = (0.6, 0.6, 0.6))

I hope you understand what i try.

Greetings, Matthias

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Intersction of two objects

Jan Kurzawski — 2012-12-11T12:46:43

Hi all,

I have created two spheres : smaller and bigger.

import mayavi
from mayavi import mlab
sphere1 = mlab.points3d(0, 0, 0, scale_mode='none',
                                scale_factor=3,
                                color=(1, 0, 0),
                                resolution=50,
                                opacity=0.7,
                                name='Planet')
sphere2 = mlab.points3d(0, 0, 0, scale_mode='none',
                                scale_factor=8,
                                color=(0, 1, 0),
                                resolution=50,
                                opacity=0.7,
                                name='Earth')
mlab.show()

Now i would like to cut out the volume which belongs to both of them. I havent found any anwser for this issue. Any help would be great!

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Re: Need direction : Using Mayavi2 for vortexparticle methods

Prabhu Ramachandran — 2012-12-03T06:51:00

Hi Anil,

On 11/13/12 12:48 AM, Anil Das P V wrote:
Are you familiar with Python?  If you are, it is a lot easier to get the 
data into Mayavi from Python.  Otherwise it might be best for you to 
create a VTK file, you can create an ASCII version first to get familiar 
and then perhaps move to the more sophisticated XML versions.

Unfortunately, as you can see, I am in no position to respond to 
individual emails due to the amount of email and work I have.  Please 
ask your questions on
mayavi-users< at >lists.sourceforge.net  for more timely responses from the 
community.

Thank you and good luck!
cheers,
Prabhu

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Re: Increasing number of colors in Volume()

William A. Mahaffey III — 2012-11-29T20:13:14






That's about 260 KB of memory, you're AOK for RAM ....

Re: Increasing number of colors in Volume()

Sivaraman Subramanian — 2012-11-29T17:02:21

Hi Gael,

Thanks for the reply. I tried downscaling but contour3d
fails when I try to increase the number of contours. I need
around 100 contours to represent my data well. I have a
36x36x50 float array. I dont think I am going out of my
physical memory limit. I have 32GB of ram. 

And regarding the volume(), is there any way to call it
with floating point values?

Thanks again.

Best,


On Thu, 29 Nov 2012 16:47:42 +0100
 Gael Varoquaux <gael.varoquaux< at >normalesup.org> wrote:
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Re: Increasing number of colors in Volume()

Gael Varoquaux — 2012-11-29T15:47:42

I am sorry, I don't really have anything in mind other than downscaling
the data (e.g. by taking sub-parts, or by limiting the spatial
resolution) or buying new memory.

Sorry,

Gaël

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Increasing number of colors in Volume()

Sivaraman Subramanian — 2012-11-29T15:19:40

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Re: Opening more than two mayavi scenes results in puzzling error

Gael Varoquaux — 2012-11-17T09:22:38

Hi Ariel,

As a general rule, I would not advise scripting with the style that you
are employing, i.e. manipulating the pipeline as a tree. This pattern is
very useful if you are writting an application that control the full
state of the pipeline, and the lifecycle of the objects, but when writing
for an interactive scripting environment, where figures and objects come
and go, it give rise to the problems that you are encountering.

Specifically, the following line:


is fragile, as it relies on the exact ordering of the pipeline tree. Let
me try and rewrite the code that you have sent us the way that I would
write it personally. I may get things wrong, as you haven't sent us a
fully executable snippet.

----------------------------------------------------------
from mayavi import mlab as maya

figure = maya.figure()

# Plot some stuff in the figure:
tm = maya.triangular_mesh(x_plot, y_plot, z_plot, faces, scalars=scalars,
                              colormap=cmap, figure=figure)

module_man

Opening more than two mayavi scenes results inpuzzling error

Ariel Rokem — 2012-11-16T21:21:40

Dear experts,

I am running into a hard-to-debug problem with mayavi. I am running mayavi
in an interactive ipython session and I want to open more than one scene
with several different data sets in the same ipython session.

My code looks something like this:

----------------------------------------------------------
from mayavi import mlab as maya
import mayavi.tools as maya_tools
EM = maya_tools.engine_manager.EngineManager()

engine = EM.new_engine()
figure = maya.figure(engine)

# Plot some stuff in the figure:
tm = maya.triangular_mesh(x_plot, y_plot, z_plot, faces, scalars=scalars,
                              colormap=cmap, figure=figure)


poly_data_normals = engine.scenes[0].children[0].children[0]
module_manager = poly_data_normals.children[0]
module_manager.scalar_lut_manager.data_range = np.array([vmin, vmax])

----------------------------------------------------------
This works just fine the first time around and the second time around. But
on the third time, I get the following error:

Re: output of volume rendering in mayavi

Gael Varoquaux — 2012-10-30T22:10:54


I am sorry, I really don't know. I don't use the .wrl output and I am not
sure if it is reliable at all.

Cheers,

Gaël

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Re: mayavi volume rendering

Gael Varoquaux — 2012-10-30T22:02:08

Hi,

On Sun, Oct 28, 2012 at 05:37:50PM -0500, Crystal Li wrote:

I am sorry, but the nifti format is a niche format customely developed by
a relatively small community with specific needs. We cannot support it in
a general-purpose library like Mayavi as the dependency on nifti reading
libraries would be too much of a burder, and the number of users relying
on nifti does not justify it.

As a side note, I happen to be doing neuroimaging too. Thus such
functionality would be interesting for me also. I just whish that
communities would not spend their time inventing storage formats.

Gaël

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