Christopher Snyder | 1 Aug 15:15 2015
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ArraySource vs ScalarField produces different results

Specifically I can't get them to look the same by adjusting all the parameters I can find on the GUI.

Side question: I couldn't figure out how to synchronize the colormaps for each scene to get a rigorous comparison.

On the one hand I call mlab.pipeline.volume(scalar_field_object) and I get a very nice volume that is mostly translucent except for the main region of intensity.

On the other I have this ArraySource.add_module(mlab.modules.Volume()) #sudo code, don't actually try either of these things, and I get very opaque image volumes even from areas of low intensity.

Any thoughts ?

Chris
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Christopher Snyder | 29 Jul 01:02 2015
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volume rendering with anisotropic, but regularly spaced pixels, (delz=2*delz=2*dely)

Hi there,

My usual routine involves
ix,iy,iz=np.indices(Image)
s=mlab.pipeline.scalar_field(spacing[0]*ix,spacing[1]*iy,spacing[2]*iz,Image)
mlab.pipeline(volume(s))

However, I am strapped for memory. Actually forming the indices ix,iy,iz is putting a burden on my code. Is there some workaround, perhaps through the depths of vtk, that lets me specify this with just the scalar tuple (1,1,2) ??? 

Thanks in anticipation,
Chris Snyder
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Andrew Andrade | 23 Jul 01:02 2015
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Representing an additional scalar on barchart

Hello everyone,

Sorry for my noobness, I am somewhat new to Mayavi. I have 3d visualization working using the bar chart.  The data is discrete across all four variables (not a surface)

I have a 4th dimention of the same size and I wanted to represent that via color, effectively showing the relationship between the 4 variables.

Any idea how to do this? I found this post [1] , but my values are a list of scalars not a function. 

Where results is a pandas dataframe, if I put in barchart(results.var1, results.var2 ,results.var3, results.var4) it gives me incorrect plots, so I am confused what the S argument is for the function. Any ideas?


Thanks,

Andrew

http://gael-varoquaux.info/programming/mayavi-representing-an-additional-scalar-on-surfaces.html
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Felix Repp | 15 Jul 14:59 2015
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set_active_attribute returns error using vtk 6.x

Hello list,

I ran in to a problem running code on a Linux installation where vtk 6.0 
is used.

Adding two arrays to a dataset, mlab.pipeline.set_active_attribute does 
not recognize the name of the second array.

The problem can be reproduced using the atomic orital example:

http://docs.enthought.com/mayavi/mayavi/auto/example_atomic_orbital.html

The following error message is returned:
TraitError: The 'point_scalars_name' trait of a SetActiveAttribute 
instance must be one of ['scalar', ''], but a value of 'angle' <type 
'str'> was specified.

A colleague of mine ran into the same problem using the current Canopy 
installation under Windows where vtk 6.2 is used, so I guess it is 
related to vtk 6.x, as the code works well  using VTK 5.x

Did anyone else run into this Problem? Is there a workaround?

Thanks a lot,
Felix

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Christopher Snyder | 13 Jul 23:35 2015
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native multiresolution viewing in mayavi

Hi there,

I have a large image that I would like to visualize, and I would like users to be able to interact with pieces of it at full resolution.

The strategy seems to be to display a subsampled image at first and have higher resolution images displayed as the users zooms in.

It seems like such a common thing to want, I was wondering if anyone has already done this. I can't seem to find anything on it though.

Thanks,
Chris
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Christopher Snyder | 13 Jul 23:30 2015
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This email is a test

I would appreciate it if someone could respond to me telling me if they got this email.

I sent an email some time ago with no response. I also don't recall seeing any mailing list emails.

--Chris
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Christopher Snyder | 26 Jun 22:54 2015
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automatically setting the scalar opacity for vol image data

Hi there,

I would truly truly be grateful if someone could help me with this. It has caused me much strife.

I would like to change the opacity scaling to some default piecewise function when I first run my code -- without messing with the GUI or the pop up window: volume.edit_traits()

I've tried many related ways, but for sanity I'll stick to a prototypical example:
#########
volume=mlab.pipeline.volume(mlab.pipeline.scalar_field(sIzi,sIxi,sIyi,I))
from tvtk.util.ctf import PiecewiseFunction
otf = PiecewiseFunction()
otf.add_point(0.0,0.0)
#otf.add_point(0.25,0.0)
otf.add_point(0.35,0.15)
otf.add_point(1.0,.25)

volume.volume_property.set_scalar_opacity(otf)

#########

This code seems to edit the opacity, but it acts as if I had typed in 0.0025 (or maybe 0.025?) and 0.0035 instead of 0.35. For clarity, I would like slope of the opacity function to change at the 25% and 35% percentiles.

Thanks,
Chris


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Tom | 22 Jun 17:02 2015
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Problem with mayavi 4.4.0 - mlab.figure.scene.save() and mlab.text3d()

Hallo,
I'm using mayavi 4.4.0, Windows 8, python 2.7 on my PC & my laptop.
However, there are 2 issues with mayavi
1. On my laptop, I can call mlab.figure.scene.save() to save screen 
shot. But the same code doesn't work on my PC (error).

2. On my PC, mlab.text3d() works well, but on my laptop, the code show 
nothing (but there is no error).

Could somebody help me?
Thanks
Tom

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Prabhu Ramachandran | 3 Jun 16:37 2015
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[ANN] Mayavi-4.4.1 release

Hello,

Enthought is pleased to announce Mayavi-4.4.1.  Mayavi is a general purpose,
cross-platform Python package for 2-D and 3-D scientific data visualization.
Mayavi integrates seamlessly with numpy and provides a convenient Pythonic
wrapper for the VTK API.  It provides a high-level visualization API that sits
on top of the powerful VTK (http://www.vtk.org) library. It provides a
stand-alone UI to help visualize your data. Mayavi is easy to extend and embed
in your own dialogs and UIs.

For more information see here:

  http://docs.enthought.com/mayavi/mayavi/index.html

Mayavi-4.4.0 is available as part of the free Canopy
(https://store.enthought.com/downloads/) packages.  4.4.1 will be available soon.

This is a major public release as this is the first public version of Mayavi to
support VTK-6.x and also support VTK-5.x.  Mayavi-4.4.1 (and 4.4.0) should work
with all VTK 6.x releases as well as the latest development version. We did have
a 4.4.0 release but did not announce it widely. For more details on the
enhancements and fixes please see here:

http://docs.enthought.com/mayavi/mayavi/auto/changes.html#mayavi-4-4-1

and here:

http://docs.enthought.com/mayavi/mayavi/auto/changes.html#mayavi-4-4-0

This release is important as this will allow us to track major improvements that
are part of the VTK-6.x releases.

We are thankful to the following for their contributions towards this release:

Deepak Surti, Prabhu Ramachandran, Robert Kern, Mark Kness, Ioannis Tziakos,
Mark Dickinson, Paul Müller, Gael Varoquaux

cheers,
Mayavi Developers

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Stuart Mumford | 9 Feb 12:27 2015
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Mayavi 4.4 with VTK 6 and Setting Inputs

Hello,

I have just upgraded to 4.4 using VTK 6, and some of my more detailed TVTK code has exploded. I have managed to fix some of it but I am so far unable to find a solution to this problem:

the input to this code is 'bfield' which is a mayavi.sources.array_source.ArraySource.

Old code:

#Make a streamline instance with the bfield

surf_field_lines = tvtk.StreamTracer()

surf_field_lines.input = bfield


surf_field_lines.source = surf_seeds

surf_field_lines.integrator = tvtk.RungeKutta4()

surf_field_lines.maximum_propagation = 1000

surf_field_lines.integration_direction = 'backward'

surf_field_lines.update()


which raises an 'input is read only error' and presumably will do the same on 'source' once it gets there.


I have tried a few different things, including `input_connection` which does this:
surf_field_lines.input_connection = bfield.outputs[0]
--------------------------------------------------------------------------- TypeError Traceback (most recent call last) <ipython-input-38-a2fc63178a31> in <module>() ----> 1 surf_field_lines.input_connection = bfield.outputs[0] /usr/lib/python2.7/site-packages/tvtk/tvtk_classes.zip/tvtk_classes/algorithm.pyc in _set_input_connection(self, obj) 191 def _set_input_connection(self, obj): 192 old_val = self._get_input_connection() --> 193 self._wrap_call(self._vtk_obj.SetInputConnection, deref_vtk(obj)) 194 self.trait_property_changed('input_connection', old_val, obj) 195 input_connection = traits.Property(_get_input_connection, /usr/lib/python2.7/site-packages/tvtk/tvtk_base.pyc in _wrap_call(self, vtk_method, *args) 521 self._in_set += 1 522 mtime = self._wrapped_mtime(vtk_obj) + 1 --> 523 ret = vtk_method(*args) 524 self._in_set -= 1 525 if self._wrapped_mtime(vtk_obj) > mtime: TypeError: SetInputConnection argument 1: method requires a vtkAlgorithmOutput, a vtkImageData was provided.

I also tried this:

import tvtk.common as tvtk_commontvtk_common.configure_input(surf_field_lines, bfield.outputs[0])
--------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-37-2ac55d369a09> in <module>() 1 import tvtk.common as tvtk_common ----> 2 tvtk_common.configure_input(surf_field_lines, bfield.outputs[0]) /usr/lib/python2.7/site-packages/tvtk/common.pyc in configure_input(inp, op) 83 inp.input_connection = op 84 elif op.is_a('vtkDataSet'): ---> 85 inp.set_input_data(op) 86 else: 87 raise ValueError('Unknown input type for object %s'%op) AttributeError: 'StreamTracer' object has no attribute 'set_input_data'
With a very similar error happening for tvtk_common.configure_connection.

So what is the correct idiom for connecting the input and source data on these objects?

Thanks
Stuart

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Sushilkumar | 3 Jan 05:02 2015
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Mayavi query

Hello 

I am trying to use Mayavi to develop a magnetic dipole field in Cartesian coordinate system. 

However when I run the python script I get the following errors

Generic Warning: In /build/buildd/vtk-5.8.0/
Filtering/vtkPolyLine.cxx, line 199
Coincident points in polyline...can't compute normals

I am using the same python script as in the link below. The difference being the formula used for calculating the field components (Please let me know if you would like me to email you my python script). Could you suggest ways to overcome the above error? 

http://docs.enthought.com/mayavi/mayavi/auto/example_magnetic_field_lines.html#example-magnetic-field-lines

Thanks in advance and appreciate your help

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