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3D visualization of scientific data in Python

Home Page: http://docs.enthought.com/mayavi/mayavi/

License: Other

Python 98.29% CSS 0.24% G-code 1.29% Cython 0.18%

mayavi's Introduction

Mayavi: 3D visualization of scientific data in Python

Mayavi docs: http://docs.enthought.com/mayavi/mayavi/ TVTK docs: http://docs.enthought.com/mayavi/tvtk

Vision

Mayavi seeks to provide easy and interactive visualization of 3D data. It does this by the following:

an (optional) rich user interface with dialogs to interact with all data and objects in the visualization.

a simple and clean scripting interface in Python, including one-liners, a-la mlab, or object-oriented programming interface.

harnesses the power of the VTK toolkit without forcing you to learn it.

Additionally Mayavi strives to be a reusable tool that can be embedded in your applications in different ways or combined with the envisage application-building framework to assemble domain-specific tools.

Mayavi is part of the Enthought Tool Suite (ETS).

Features

Mayavi is a general purpose, cross-platform tool for 2-D and 3-D scientific data visualization. Its features include:

Visualization of scalar, vector and tensor data in 2 and 3 dimensions

Easy scriptability using Python

Easy extendability via custom sources, modules, and data filters

Reading several file formats: VTK (legacy and XML), PLOT3D, etc.

Saving of visualizations

Saving rendered visualization in a variety of image formats

Convenient functionality for rapid scientific plotting via mlab (see mlab documentation)

See the Mayavi Users Guide for more information.

Unlike its predecessor MayaVi1, Mayavi has been designed with scriptability and extensibility in mind from the ground up. While the mayavi2 application is usable by itself, it may be used as an Envisage plugin which allows it to be embedded in user applications natively. Alternatively, it may be used as a visualization engine for any application.

Quick start

If you are new to Mayavi it is a good idea to read the online user manual which should introduce you to how to install and use it.

If you have installed Mayavi as described in the next section, you should be able to launch the mayavi2 application and also run any of the examples in the examples directory.

Installation

By itself Mayavi is not a difficult package to install but its dependencies are unfortunately rather heavy. However, many of these dependencies are now available as wheels on PyPI. The two critical dependencies are,

VTK

A GUI toolkit, either PyQt4, PySide, PySide2, PyQt5 or wxPython.

The latest VTK wheels are available on all the major platforms (Windows, MacOS, and Linux), but only for 64 bit machines. Python 3.x is fully supported on all these operating systems and Python 2.7.x on MacOS and Linux. If you are out of luck, and your platform is not supported then you will need to install VTK yourself using your particular distribution as discussed in the General Build and Installation instructions

On Python 3.x you will need to install PyQt5 and wheels are available for this. On 2.7.x you have more options, and can use PySide, PyQt4, and wxPython. These can be installed from pip or from your package manager.

Currently, Mayavi itself should work with the new wxPython 4.x. However, traitsui, pyface, and other ETS packages do not yet support it so the UI will not work correctly. Older versions should work. PyQt/PySide/PySide2 should work largely out of the box.

Latest stable release

As of the latest release, i.e. 4.6.0 and above, if you are using Python 3.x and are on a 64 bit machine, installation via pip is the easiest and is as follows:

$ pip install mayavi

$ pip install PyQt5

Thats it!

If you are unable to do this, read the documentation above and find a way to install VTK and a suitable UI toolkit and then repeat the above.

If you are interested in the jupyter notebook support as well, do the following (after ensuring that you have jupyter installed of course. Note, the Jupyter notebook function is only supported starting mayavi version 4.5.0):

$ jupyter nbextension install --py mayavi --user
$ jupyter nbextension enable --py mayavi --user

You will also need to have ipywidgets and ipyevents installed. These can be installed via pip or your favorite package manager.

Bleeding edge

If you want to install the latest version of Mayavi from github, you can simply do the following:

$ git clone https://github.com/enthought/mayavi.git
$ cd mayavi
$ pip install -r requirements.txt
$ pip install PyQt5  # replace this with any supported toolkit
$ python setup.py install  # or develop

Add the jupyter nbextensions using the instructions in the section above and you should be good to go.

Documentation

More documentation is available in the online user manual or in docs directory of the sources. This includes a man page for the mayavi2 application, a users guide in HTML and PDF format and documentation for mlab.

More documentation in the form of workshop/tutorial material is available here:

Tutorial Videos

Here are some tutorial videos that you can watch to learn Mayavi:

SciPy 2018 Mayavi tutorial (3 hrs):
- Video: https://www.youtube.com/watch?v=r6OD07Qq2mw
- Material: https://github.com/prabhuramachandran/mayavi-tutorial

Examples

Examples are all in the examples directory of the source or the git clone. The docs and examples do not ship with the binary eggs. The examples directory also contains some sample data.

Test suite

The basic test suites for tvtk and mayavi can be run using nose:

nosetests -v tvtk/tests
nosetests -v mayavi

The integration tests:

cd integrationtests/mayavi
python run.py

Bug tracker, mailing list etc.

The bug tracker is available in github Please provide info and details on platform, python, vtk and gui backends and their versions. If possible, a small example replicating the the problem.

If you have questions you could ask on the Mayavi-users mailing list. This is used by some folks and is not too active. Another mailing list that may be of use is the ETS Users mailing list. This is a more general list where a lot of folks experienced with the Enthought Tool Suite are available.

Authors and Contributors

Core contributors:

Prabhu Ramachandran: primary author.
Previous contributors:

Gaël Varoquaux: mlab, icons, many general improvements and maintenance.

Deepak Surti: Upgrade to VTK 5.10.1, VTK 6.x with new pipeline.
Support and code contributions from Enthought Inc.
Patches from many people (see the release notes), including K K Rai and R A Ambareesha for tensor support, parametric source and image data.

Many thanks to all those who have submitted bug reports and suggestions for further enhancements.

mayavi's People

Contributors

Stargazers

Watchers

Forkers

gaelvaroquaux nellev demianw chrisidefix kristoformaynard rajnishs91 mattions mluessi rosoba prabhuramachandran adamreeve mounte joonro wecacuee healthonrails bergtholdt aestrivex jtaylor mindw tradottb renjiec apollo2030 certik indranilsinharoy senganal chrismit dmsurti jenshnielsen cherry-wb gram003 victorliun bmnn moubachiryounes arung014 inclement b-rich frankzhao66 paulourio tedchengy coquer matk86 demosgill deamk seddikw pblocz maheshpj giapdangle mwilmer tmylt imclab alexandreleroux liulion sayiho planets09 tvern23 zaherabdulazeez u20024804 pariahofdarkness opoplawski ruwan2 princeofdarkness76 fish2000 heathckliff iceseismic wangxiong2015 simudream hassyma kitchoi mabl neuroidss coroner4817 grlee77 siggyf peterzhousz daytonb eventual arkyac patricksnape emmanuelle alizezhu darrenabramson zilongzhong souravsingh zyex1108 fayazr jabooth henfee bhavesh2109 gt-master minrk jakirkham fedemiorelli radovankavicky gapdata christianbrodbeck tiandiao123 isaomatsunami jayden11 webming solarjoe

mayavi's Issues

3D Visualizer / TVTK Window (Not Responding) on Windows 7 64-Bit

I am working to install Mayavi2 on my Windows 7 (64 Bit), but am not able to fully interact with the visualizer or TVTK window. They freeze immediately upon first opening. I have tried to install Mayavi2 using both the Enthought (64 Bit & 32 Bit) and Python(x,y) distributions with full system cleans before the installation to ensure that all Python materials are removed. Each installation allows me to interact with Python with no noticeable trouble and I am able to "import mayavi" to my shell. The problem comes when calling a mayavi function (e.g., mlab.plot3d) or simply running the Mayavi2 GUI. Immediately the window freezes and shows a (Not Responding) message. I have tried to install the package on another Windows 7 (64 Bit) machine with no problem. Thanks for the help. I am very interested to see if there is a machine-specific solution to my problem or what I might try to get around this window crash.

Spelling error in the enthought.mayavi.mlab.surf documentation

There seems to be a spelling error (marked in bold) in the enthought.mayavi.mlab.surf documentation, under "Keyword arguments":

line_width: The with of the lines, if any used. Must be a float. Default: 2.0

On a side note, just began learning Mayavi - you're the Django of Python data visualization :)

SetSize problem in wxVTKRenderWindowInteractor

when calling mlab.draw()

I get the following exception

TypeError Traceback (most recent call last)

/Library/Frameworks/EPD64.framework/Versions/7.0/lib/python2.7/site-packages/tvtk/pyface/ui/wx/scene.pyc in OnPaint(self, event)
526
527 # Call the original handler (this will Show the widget)

--> 528 self._vtk_control.OnPaint(event)
529 if len(self.renderer.lights) == 0:
530 # The renderer is not ready yet, we do not do anything, and

/Library/Frameworks/EPD64.framework/Versions/7.0/lib/python2.7/site-packages/tvtk/pyface/ui/wx/wxVTKRenderWindowInteractor.pyc in OnPaint(self, event)
391
392 # make sure the RenderWindow is sized correctly

--> 393 rw.SetSize(self.GetSizeTuple())
394
395 # Tell the RenderWindow to render inside the wx.Window.

Seems that rw.SetSize needs to be called with *self.GetSizeTuple()

VTK Qt

I updated VTK from 5.8.0 to 5.10.1 and there was now VTK with Qt bindings which I thought to try.
I had to rebuild mayavi but soon witness that it's not possible to use VTK-Qt with mayavi. For example I get error like:

QWidget: Must construct a QApplication before a QPaintDevice

I read in closed issues, that mayavi is ported to Qt, so why I'm getting this error?
FYI, I build current mayavi git version on Windows with Python 2.7

Sporadic Build Failure on Win32

The following error shows up when building mayai2 on windows.

running build
----------------------------------------------------------------------
Building TVTK classes... SyntaxError: ('invalid syntax', ('tvtk_classes\\ls_dyna_reader.py', 100, 11, '        Get/Set the directory containing the LS-Dyna database and determine\n'))

error: tvtk_classes\ls_dyna_reader.pyc: The system cannot find the file specified

I've tracked down the issue to an uninitialized variable, and the following fixes this:

Bus error when calling mlab.show() twice from script

Create a python script that shows an image plot using mlab.imshow. Call mlab.show() twice, and a bus error will result when the image window is closed.

Although this is a user error, it should not leave the realm of python. The error should either be ignored or raise an exception. It should not cause a bus error.

Fix masking in mlab to make copies

The current implementation of masking in mlab changes the data the user has supplied and this can be surprising. This should be fixed to copy the data and then mask it. If the user really wants to save on the copy they can send the masked arrays in directly as the scalars.

Allow Volume module to work with cell data

The volume module (and some others...) don't seem to work with cell data, only point data. The volume module is hard coded to look for point data when setting the data range. If you just simply change the input to cell data instead, everything seems to work. Of course this isn't a fix, just perhaps some evidence that more flexibility is required?

e.g.

--- old_volume.py   2012-08-22 14:31:39.000000000 -0700
+++ volume.py   2012-08-22 14:30:35.000000000 -0700
@@ -426,7 +426,7 @@

         # Set the current range.
         input = mm.source.outputs[0]
-        sc = input.point_data.scalars
+        sc = input.cell_data.scalars
         if sc is not None:
             rng = sc.range
         else:

Picking issue in mlab

I am trying to convert the picking examples to a more object oriented approach, with the mlabscenemodel embedded in a traited class.

However, trying to register picking callback functions does not work very well. It appears the mouse_pick_dispatcher of the scene object is not well-formed somehow.

Perhaps I am making some elementary mistake here; for instance, I am not sure of the order of initialization I should follow. Also, the (currently commented) exception handler at the top of the code appears to influence WHICH line causes an exception which strikes me as odd.

Here is a minimal example:

import numpy as np


from traits.api import HasTraits, Instance, Button, \
    on_trait_change, Range
from traitsui.api import View, Item, HSplit, Group

from mayavi import mlab
from mayavi.core.ui.api import MlabSceneModel, SceneEditor
from mayavi.core.ui.mayavi_scene import MayaviScene

##from enthought.traits.api import push_exception_handler
##push_exception_handler( handler = lambda o,t,ov,nv: None,
##                        reraise_exceptions = True,
##                        main = True,
##                        locked = True )


class RenderLock():
    def __init__(self, scene):
        self.scene = scene
    def __enter__(self):
        self.scene.disable_render = True
        return self.scene
    def __exit__(self, type, value, traceback):
        self.scene.disable_render = False



class MainInterface(HasTraits):
    """
    main app
    """
    scene = Instance(MlabSceneModel, args=())


    def __init__(self, datamodel):
        super(MainInterface, self).__init__()
        self.datamodel = datamodel
        self.draw_scene()
        #self.postinit()        #call inside or outside constructor, does not matter


    def draw_scene(self):
        with RenderLock(self.scene):
            figure = self.scene.mayavi_scene

            #figure = mlab.gcf()

 #           mlab.clf()


            #create cortex plots
            self.cortex_plots = [
                (p, mlab.points3d(
                    *p.T,
                    mode='sphere',
                    color=tuple(np.random.random(3)),
                    figure=figure))
                        for p in np.random.random((2,10,3))]


            #cursor
            self.outline = mlab.outline(line_width=3)
            self.outline.outline_mode = 'cornered'
            self.outline.bounds = (0-0.1, 0+0.1,
                                  0-0.1, 0+0.1,
                                  0-0.1, 0+0.1)
    def postinit(self):
        def picker_callback(picker):
            print 'never getting here...'

        #assert(mlab.gcf() is self.scene.mayavi_scene)
        figure = self.scene.mayavi_scene
#        figure = mlab.gcf()

        print 'all goes down the drain here. seems the mouse picker event handler is not well formed somehow'
        picker = figure.on_mouse_pick(picker_callback)
        picker.tolerance = 0.01


    view = View(
        Item('scene', editor=SceneEditor(scene_class=MayaviScene),
            height=500, width=500, show_label=False),
        resizable=True
                )


def run(datamodel):
    m = MainInterface(datamodel)
    m.postinit()
    m.configure_traits()

if __name__=='__main__':
    run(None)

Using mask_points option in mlab.points3d crashes python

Plotting a list of points with points3d(x,y,z) works fine. Trying to plot the same points with the mask_points option gives a segfault.

This can be recreated within the gui by editing the pipeline. Clicking on Glyph->Glyph->Masking->"Mask input points" has the same effect.

Loading visualization with a "Text module" fails: Exception ...

Hi, anyone knows how to solve this:

After saving a visualization of a scene that includes a “Text module” in order to add a title to the image, if you try to load that visualization Mayavi2 shows the error: “Exception In /usr/lib/python2.7/dist-packages/traits/trait_handlers.py:168
TraitError: The 'y_position' trait of a Text instance must be a float, but a value of None <type 'NoneType'> was specified. (in error)”
I have try several things but it seems to be a bug. This text module is very useful when it is wanted to have the name of the images in the snapshots.

Saving/loading scene broken

I am not sure if it's a Mayavi problem, or a state pickler problem.

In [1]: from enthought.mayavi import mlab
mlab.test_surf()

In [2]: mlab.test_surf()
Out[2]: 

In [3]: e = mlab.get_engine()

In [4]: e.save_visualization('test.mv2')

In [5]: e.load_visualization('test.mv2')
/home/varoquau/dev/enthought/ets/apptools/enthought/persistence/state_pickler.py:197: DeprecationWarning: object.__init__() takes no parameters
  tuple.__init__(self, seq)
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
/home/varoquau/dev/enthought/ets/mayavi/examples/mayavi/interactive/ in ()
----> 1 e.load_visualization('test.mv2')

/home/varoquau/dev/enthought/ets/apptools/enthought/scripting/recordable.pyc in _wrapper(*args, **kw)
     43         if not record:
     44             # If the method was not recorded, just call it.

---> 45             result = func(*args, **kw)
     46 
     47         return result

/home/varoquau/dev/enthought/ets/mayavi/enthought/mayavi/core/engine.pyc in load_visualization(self, file_or_fname)
    264         try:
    265             # Get the state from the file.

--> 266             state = state_pickler.load_state(file_or_fname)
    267             state_pickler.update_state(state)
    268             # Add the new scenes.


/home/varoquau/dev/enthought/ets/apptools/enthought/persistence/state_pickler.pyc in load_state(file)
    929     f = _get_file_read(file)
    930     try:
--> 931         state = StateUnpickler().load_state(f)
    932     finally:
    933         if f is not file:

/home/varoquau/dev/enthought/ets/apptools/enthought/persistence/state_pickler.pyc in load_state(self, file)
    506             pass
    507         data = cPickle.load(file)
--> 508         result = self._process(data)
    509         return result
    510 

/home/varoquau/dev/enthought/ets/apptools/enthought/persistence/state_pickler.pyc in _process(self, data)
    550             for path in paths:
    551                 x = self._obj_cache[key]
--> 552                 exec('result%s = x'%path)
    553                 # if the reference is to an instance append its path.

    554                 if isinstance(x, State):

/home/varoquau/dev/enthought/ets/apptools/enthought/persistence/state_pickler.pyc in ()

TypeError: 'StateTuple' object does not support item assignment

In [6]:

segfaults in wxWindow::DoSetSize due to m_parent being NULL

http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=575536

The problem is hard to reproduce (I, Gael, cannot reproduce it). It seems to happen more often under VNC.

Relevant mailing list thread:
https://mail.enthought.com/pipermail/enthought-dev/2011-January/028113.html

If someone can reproduce the bug, it would be good to use gdb's Python helper to find what the calling code in Python is. See:
http://wiki.python.org/moin/DebuggingWithGdb and the mailing list thread mentionned above.

black mesh (software rendering issue)

Hello, people!
First of all, thank you for the great work! We use mayavi in our software and it's very useful :)

Second, about the issue. On some machines without 3D acceleration (or with minor OpenGL support i.e. on Intel integrated cards) we have found a bug: mesh (or StructuredGrid) with assigned data and colormap is colored black.

Seems like this bug was previously described in this mail-list post: https://mail.enthought.com/pipermail/enthought-dev/2009-January/019453.html

I was wondering why before turning black it appears colored for a second and decided to debug the scene building process.
While debugging, I found that it turns black after this bunch of code in tvtk/pyface/ui/qt4/scene.py:

   if scene.light_manager is None:
            scene.light_manager = light_manager.LightManager(scene)
            renwin = scene._renwin
            renwin.update_traits()
            vtk_rw = tvtk.to_vtk(renwin)
            renwin.add_observer('StartEvent', messenger.send)
            messenger.connect(vtk_rw, 'StartEvent', self._start_event_callback)
            renwin.add_observer('EndEvent', messenger.send)
            messenger.connect(vtk_rw, 'EndEvent', self._end_event_callback)
            self.created = True

If you comment/delete this lines everything starts working right, with and without opengl acceleration.
I'm not sure that this fix is the right way to do it but it works like a charm in my case.

I hope that this information will be useful and'll look forward for your comments about this issue :)

Countours in mlab.countour3d()

Hi,

If you don't mind my frequent posting...

I have array with this shape: (40, 40, 26)
When I do mlab.countour3d() I get 3D object with 5 contours. Then I open pipeline dialog and set contours to 26:

Are now these 26 contours interpolated or they represent exact data from the array?

CPU freeze with filled contours for array with nans

If I draw with mlab.surf(z), and change surface preferences to contours, I get line contours as expected. If I set filled contours CPU is maxed and process never finishes. z is array with nans, and I guess that's the reason for this behavior as otherwise filled contours works fine.

For example:

array([[ -2. ,   2. ,  -3.4,  -3.5,  -3.1,  -2.9,  -5.2,   0. ,  -0.7,
         -3. ,  -3. ,  -4.7,  -2.7,   1.8,   4.2,   6.6,   5.3,   1.9,
          7.1,  10.1,   8.2,  16.5,  10.3,  10.3,  10.2,  11.3,   6.6,
          8.2,   7.9,   4.7,   4.1],
       [  5.2,   8.1,  10.1,  17.4,  17. ,  12.1,  15.7,  13.1,   7.8,
          8.4,  12.1,   4.9,   2.8,   2.7,   2.3,   2.7,   3.3,   5.2,
          0.3,   0.9,   2.8,   2.3,   2.7,   5.4,   6.5,   6.8,   9.2,
          9.2,   nan,   nan,   nan],
       [ 14.7,  14.2,  10.7,  12.4,  12.4,  14. ,  11. ,   9.4,  13. ,
          9.2,  11.4,   7.3,  10.3,   8.4,  12.5,  11. ,   8.5,   8.7,
          8.9,   0. ,   1.2,   3.8,   6.8,   8. ,   1.7,   6.1,  12.5,
         15.1,  15.4,  18.4,  20.5],
       [ 19.7,  22.1,  17.7,  19.8,  21.6,  21.3,  20.9,  21.3,  22.4,
         22.6,  21.4,  20.8,  11.5,  10.7,  15.7,  21.2,  23.5,  18.3,
         17.7,  18.9,  18.4,  11.6,  16.8,  18.5,  19.9,  18. ,  18.2,
         15.2,  16.5,  15.1,   nan],
       [ 12. ,  19. ,  18.7,  21.2,  16.7,  20.3,  18.8,  22.7,  26. ,
         26.9,  27.2,  27.2,  27.9,  26. ,  28.1,  26.9,  27.6,  26. ,
         27.1,  28.5,  27.4,  28.7,  29.5,  30. ,  27.3,  25.4,  26.7,
         25. ,  13.3,  12.4,  22. ],
       [ 23.9,  25.7,  20.9,  24.6,  26.2,  27.8,  30. ,  28.8,  31.4,
         32.6,  31.4,  25.1,  24.6,  25.9,  29.1,  31.9,  29.1,  25. ,
         28.8,  31.5,  26. ,  21.3,  24. ,  18. ,  20.1,  24.9,  20. ,
         27.6,  27.9,  27.4,   nan],
       [ 27. ,  28.7,  28.5,  28.8,  28.8,  28.3,  27.9,  31.2,  27.9,
         24.7,  20.8,  23.2,  26.3,  29.5,  33. ,  33.7,  33. ,  34. ,
         26.6,  27.1,  28.7,  31.2,  32.9,  36.1,  37.4,  27.5,  29. ,
         30.7,  32.1,  32.1,  32.5],
       [ 32.8,  34.5,  34.6,  34.3,  28.6,  25.6,  21.1,  29.3,  28.1,
         29.5,  29. ,  23.7,  28.8,  30.5,  28.6,  29.5,  31.3,  31.6,
         31.9,  31.5,  31.5,  31.3,  30.8,  26.7,  26.5,  30.2,  31.2,
         32. ,  32.3,  27.2,  26.8],
       [ 28.2,  30.2,  31.6,  32.9,  33.3,  19.3,  18.4,  20.8,  24.3,
         26.6,  26.2,  20.4,  22.9,  23.8,  26.4,  28.5,  25.8,  26.9,
         23.4,  25.2,  24.6,  24.6,  25.1,  26.7,  21.5,  24.8,  25.1,
         24.7,  25.6,  26.6,   nan],
       [ 27.8,  23.4,  12.2,  18.8,  24.5,  24.3,  25.3,  25.4,  26. ,
         27.1,  25.6,  22.4,  11.7,  12.2,  12.8,   6.5,  11.4,   8.1,
          9.7,  12.4,  13.3,  15.7,  19. ,  16.1,  19.1,  20.9,  16.8,
         16.1,  16.7,  11.8,   9.5],
       [  9.8,   8. ,   4.7,  10.8,   7.7,  19.3,  17.9,  15.8,  12.7,
         13.2,  10.4,  13.4,  14. ,  13.3,  10.9,  13.9,  16.7,  13.4,
         13. ,  15.2,  13.6,  13. ,  12.3,  11.8,  15.1,  12.8,   9.1,
          8.9,   9. ,   4.9,   nan],
       [ 13.5,  14.3,  11.6,  10.7,  11. ,  10.2,  10.6,  11. ,   8.5,
          8.1,   7.4,   1.6,   4.5,   3.4,   5. ,   3.1,   5.2,  -0.6,
         -2.6,  -2.2,  -4.8,  -2.5,   5.3,   2.6,  14.4,  14.1,   9.9,
          6.8,   9.1,   5.7,  11.2]])

How does animate data work?

I thought to try simple animation, but can't get there. Executing for example mlab.test_simple_surf_anim() just displays the UI with a plane surface, and that's all. Same for other provided test animation functions. Is there some setting that needs to be set so that we can see object animate?

imshow clipped edges

Hi,

please consider this snippet:

import numpy as np
from mayavi import mlab

mlab.imshow(np.random.rand(10,20), interpolate=False)

As you can see edges are clipped, for some reason.
FYI, Matplotlib imshow() shows them correct

mayavi 4.0.0 fails to run tests in linux x86

I am on Arch Linux x86.

I installed using this AUR package which essentially downloads the tarball from github and runs setup.py

I try to run the test suite but I get this error:

----------------------------------------------------------------------
Running TVTK tests.
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/mayavi/tests/runtests.py", line 225, in <module>
    main()
  File "/usr/lib/python2.7/site-packages/mayavi/tests/runtests.py", line 217, in main
    status = m2_tests(verbose)
  File "/usr/lib/python2.7/site-packages/mayavi/tests/runtests.py", line 170, in m2_tests
    tests = find_tests(['tvtk'])
  File "/usr/lib/python2.7/site-packages/mayavi/tests/runtests.py", line 63, in find_tests
    mod = __import__(modname, globals(), locals(), [symbol])
ValueError: Empty module name

Please provide release source tarballs

This would help greatly with distribution packaging. Thanks.

Mayavi 4.0.0 fails to open with PySide 1.0.4

When opening Mayavi 4.0.0 (from ETS 4.0.0), I get the following:

Traceback (most recent call last):
  File "/usr/local/share/python/mayavi2", line 9, in <module>
    load_entry_point('mayavi==4.0.1', 'console_scripts', 'mayavi2')()
  File "/usr/local/lib/python2.7/site-packages/mayavi/scripts/mayavi2.py", line 649, in main
    mayavi.main(sys.argv[1:])
  File "/usr/local/lib/python2.7/site-packages/mayavi/plugins/app.py", line 195, in main
    app.run()
  File "/usr/local/lib/python2.7/site-packages/mayavi/plugins/mayavi_workbench_application.py", line 81, in run
    window.open()
  File "/usr/local/lib/python2.7/site-packages/pyface/workbench/workbench_window.py", line 144, in open
    self._create()
  File "/usr/local/lib/python2.7/site-packages/pyface/ui/qt4/application_window.py", line 122, in _create
    contents = self._create_contents(self.control)
  File "/usr/local/lib/python2.7/site-packages/pyface/workbench/workbench_window.py", line 217, in _create_contents
    contents = self.layout.create_initial_layout(parent)
  File "/usr/local/lib/python2.7/site-packages/pyface/ui/qt4/workbench/workbench_window_layout.py", line 141, in create_initial_layout
    self._qt4_editor_area = editor_area = SplitTabWidget(parent)
  File "/usr/local/lib/python2.7/site-packages/pyface/ui/qt4/workbench/split_tab_widget.py", line 48, in __init__
    self._focus_changed)
TypeError: 'PySide.QtCore.QObject.connect' called with wrong argument types:
  PySide.QtCore.QObject.connect(NoneType, str, instancemethod)
Supported signatures:
  PySide.QtCore.QObject.connect(PySide.QtCore.QObject, str, PyCallable, PySide.QtCore.Qt.ConnectionType = Qt.AutoConnection)
  PySide.QtCore.QObject.connect(PySide.QtCore.QObject, str, PySide.QtCore.QObject, str, PySide.QtCore.Qt.ConnectionType = Qt.AutoConnection)
  PySide.QtCore.QObject.connect(PySide.QtCore.QObject, str, str, PySide.QtCore.Qt.ConnectionType = Qt.AutoConnection)
  PySide.QtCore.QObject.connect(str, PyCallable, PySide.QtCore.Qt.ConnectionType = Qt.AutoConnection)
  PySide.QtCore.QObject.connect(str, PySide.QtCore.QObject, str, PySide.QtCore.Qt.ConnectionType = Qt.AutoConnection)

Using:

Python 2.7.2
Qt 4.7.3
PySide 1.0.4

On OS X 10.6.8

unable to launch mayavi on os x x64

(devpype)[satra@robinhill ~]$ export ETS_TOOLKIT=qt4
(devpype)[satra@robinhill ~]$ mayavi2
Traceback (most recent call last):
File "/Library/Frameworks/EPD64.framework/Versions/Current/bin/mayavi2", line 9, in
load_entry_point('Mayavi==3.4.2', 'console_scripts', 'mayavi2')()
File "/Library/Frameworks/EPD64.framework/Versions/7.0/lib/python2.7/site-packages/Mayavi-3.4.2-py2.7-macosx-10.5-x86_64.egg/enthought/mayavi/scripts/mayavi2.py", line 649, in main
mayavi.main(sys.argv[1:])
File "/Library/Frameworks/EPD64.framework/Versions/7.0/lib/python2.7/site-packages/Mayavi-3.4.2-py2.7-macosx-10.5-x86_64.egg/enthought/mayavi/plugins/app.py", line 195, in main
app.run()
File "/Library/Frameworks/EPD64.framework/Versions/7.0/lib/python2.7/site-packages/Mayavi-3.4.2-py2.7-macosx-10.5-x86_64.egg/enthought/mayavi/plugins/mayavi_workbench_application.py", line 76, in run
if self.start():
File "/Library/Frameworks/EPD64.framework/Versions/7.0/lib/python2.7/site-packages/EnvisageCore-3.2.1-py2.7.egg/enthought/envisage/application.py", line 277, in start
self.plugin_manager.start()
File "/Library/Frameworks/EPD64.framework/Versions/7.0/lib/python2.7/site-packages/EnvisageCore-3.2.1-py2.7.egg/enthought/envisage/plugin_manager.py", line 105, in start
map(lambda plugin: self.start_plugin(plugin), self._plugins)
File "/Library/Frameworks/EPD64.framework/Versions/7.0/lib/python2.7/site-packages/EnvisageCore-3.2.1-py2.7.egg/enthought/envisage/plugin_manager.py", line 105, in
map(lambda plugin: self.start_plugin(plugin), self._plugins)
File "/Library/Frameworks/EPD64.framework/Versions/7.0/lib/python2.7/site-packages/EnvisageCore-3.2.1-py2.7.egg/enthought/envisage/plugin_manager.py", line 115, in start_plugin
plugin.activator.start_plugin(plugin)
File "/Library/Frameworks/EPD64.framework/Versions/7.0/lib/python2.7/site-packages/EnvisageCore-3.2.1-py2.7.egg/enthought/envisage/plugin_activator.py", line 31, in start_plugin
plugin.start()
File "/Library/Frameworks/EPD64.framework/Versions/7.0/lib/python2.7/site-packages/EnvisageCore-3.2.1-py2.7.egg/enthought/envisage/core_plugin.py", line 145, in start
self._load_preferences(self.application.preferences)
File "/Library/Frameworks/EPD64.framework/Versions/7.0/lib/python2.7/site-packages/EnvisageCore-3.2.1-py2.7.egg/enthought/envisage/core_plugin.py", line 226, in _load_preferences
f = resource_manager.file(resource_name)
File "/Library/Frameworks/EPD64.framework/Versions/7.0/lib/python2.7/site-packages/EnvisageCore-3.2.1-py2.7.egg/enthought/envisage/resource/resource_manager.py", line 56, in file
return protocol.file(address)
File "/Library/Frameworks/EPD64.framework/Versions/7.0/lib/python2.7/site-packages/EnvisageCore-3.2.1-py2.7.egg/enthought/envisage/resource/package_resource_protocol.py", line 50, in file
raise NoSuchResourceError(address)
enthought.envisage.resource.no_such_resource_error.NoSuchResourceError: traits.logger/plugin/preferences.ini

mlab.test_imshow() fail

Mac OSX 10.8, current macports build of Python 2.7.3 and vtk 5.10, and mayavi++ built through ets.py cloned from github, gives me the following error:

In [2]: mlab.test_imshow()

TraitError Traceback (most recent call last)
in ()
----> 1 mlab.test_imshow()

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/mayavi-4.2.1-py2.7-macosx-10.8-x86_64.egg/mayavi/tools/helper_functions.pyc in test_imshow()
620 """
621 s = numpy.random.random((10, 10))
--> 622 return imshow(s, colormap='gist_earth')
623
624

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/mayavi-4.2.1-py2.7-macosx-10.8-x86_64.egg/mayavi/tools/helper_functions.pyc in the_function(_args, *_kwargs)
34
35 def the_function(_args, *_kwargs):
---> 36 return pipeline(_args, *_kwargs)
37
38 if hasattr(pipeline, 'doc'):

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/mayavi-4.2.1-py2.7-macosx-10.8-x86_64.egg/mayavi/tools/helper_functions.pyc in call(self, _args, *_kwargs)
79 scene.disable_render = True
80 # Then call the real logic
---> 81 output = self.call_internal(_args, *_kwargs)
82 # And re-enable the rendering, if needed.
83 if scene is not None:

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/mayavi-4.2.1-py2.7-macosx-10.8-x86_64.egg/mayavi/tools/helper_functions.pyc in call_internal(self, _args, *_kwargs)
92 # Copy the pipeline so as not to modify it for the next call
93 self.pipeline = self._pipeline[:]
---> 94 return self.build_pipeline()
95
96 def store_kwargs(self, kwargs):

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/mayavi-4.2.1-py2.7-macosx-10.8-x86_64.egg/mayavi/tools/helper_functions.pyc in build_pipeline(self)
120 if key in keywords:
121 this_kwargs[key] = value
--> 122 object = pipe(object, **this_kwargs)._target
123 return object
124

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/mayavi-4.2.1-py2.7-macosx-10.8-x86_64.egg/mayavi/tools/modules.pyc in init(self, _args, *_kwargs)
153
154 def init(self, _args, *_kwargs):
--> 155 super(DataModuleFactory, self).init(_args, *_kwargs)
156 # We are adding data to the scene, reset the zoom:
157 scene = self._scene.scene

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/mayavi-4.2.1-py2.7-macosx-10.8-x86_64.egg/mayavi/tools/pipe_base.pyc in init(self, parent, **kwargs)
161 # Now calling the traits setter, so that traits handlers are
162 # called
--> 163 self.set(**traits)
164 if scene is not None:
165 scene.disable_render = not self._do_redraw

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/mayavi-4.2.1-py2.7-macosx-10.8-x86_64.egg/mayavi/tools/pipe_base.pyc in set(self, trait_change_notify, **traits)
177 try:
178 if callback is not None:
--> 179 callback()
180 self._anytrait_changed(trait, value)
181 except TraitError:

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/mayavi-4.2.1-py2.7-macosx-10.8-x86_64.egg/mayavi/tools/modules.pyc in _line_width_changed(self)
73 def _line_width_changed(self):
74 try:
---> 75 self._target.actor.property.line_width = self.line_width
76 except AttributeError:
77 try:

TraitError: Cannot set the undefined 'line_width' attribute of a 'ImageProperty' object.

contour_surf contours argument is broken

The documentation for the contours argument to mlab.contour_surf says, "Specifying 0 shows no contours," but specifying 0 actually gives an error:

AssertionError: The contours argument must be positive

I also have many other problems with this argument but I've only been able to test them on 3.3, so I'm not sure if they still apply:

Passing a list to the contours parameter seems to have no effect, the resulting contours are the same no matter what I put in the list.
Passing an integer as the contours parameter actually gives me two less than that number of contour levels. So I have to pass 3 to get one set of contour lines.

Qt embedding example doesn't work

I've just installed the latest Mayavi and I found out that the Qt backend is misbehaving.

When I run the example application http://github.enthought.com/mayavi/mayavi/auto/example_qt_embedding.html, as soon you open the Envisage GUI, the application crash badly:

Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/traitsui/qt4/image_enum_editor.py", line 286, in sizeHint
    pixmap = self._get_pixmap(name)
  File "/usr/local/lib/python2.7/dist-packages/traitsui/qt4/image_enum_editor.py", line 292, in _get_pixmap
    return self._editor.get_pixmap(name)
  File "/usr/local/lib/python2.7/dist-packages/traitsui/qt4/image_enum_editor.py", line 51, in get_pixmap
    name = ''.join((factory.prefix, name, factory.suffix))
TypeError: sequence item 1: expected string or Unicode, NoneType found

This was not happening with mayavi 3.6.0.
Any idea how to fix it?

Random SIGSEGVs on Mac OS X 10.7 using Qt-based Interface

I'm running:
Python 2.7.2, VTK 5.8.0, Qt 4.7.4, on Mac OS X and ets develop as of Dec 20.

If I bring up Mayavi and begin working with it for some time (change DataSetClipper to ImplicitPlane, add some IsoSurfaces) eventually I seem to get a crash at some point that I haven't been able to tie to a particular action. I'm wondering if I can provide some better feedback or if there's some way to better track down the cause of the crash myself? I'm not terribly familiar with using qt or GUI programming, but I've done plenty of C and Python programming. What are the recommended methodologies for figuring out which component might be causing this? It looks like ultimately we're dropping into a C/C++ binding call through SIP which causes the meltdown, but I'm not sure what tool would be best to track this further.

Below is Apple's "Problem Report" that gets generated when the crash occurs:

Process:         Python [3575]
Path:            /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier:      org.python.python
Version:         2.7.2 (2.7.2)
Code Type:       X86-64 (Native)
Parent Process:  ??? [1]

Date/Time:       2011-12-21 14:47:16.115 -0600
OS Version:      Mac OS X 10.7.2 (11C73)
Report Version:  9

Interval Since Last Report:          74660 sec
Crashes Since Last Report:           12
Per-App Interval Since Last Report:  69843 sec
Per-App Crashes Since Last Report:   12
Anonymous UUID:                      21C65421-D31F-4F37-A596-94EF9C347B88

Crashed Thread:  0  Dispatch queue: com.apple.main-thread

Exception Type:  EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000010

VM Regions Near 0x10:
--> 
    __TEXT                 0000000100000000-0000000100001000 [    4K] r-x/rwx SM=COW  /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python

Application Specific Information:
objc[3575]: garbage collection is OFF

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   sip.so                          0x00000001007e959c sip_api_is_py_method + 308
1   sip.so                          0x00000001007e96c1 sip_api_common_dtor + 95
2   QtGui.so                        0x00000001031c2a37 sipQLineEdit::~sipQLineEdit() + 57
3   QtCore                          0x000000010160e57f QObjectPrivate::deleteChildren() + 95
4   QtGui                           0x00000001039c57e9 QWidget::~QWidget() + 697
5   QtGui.so                        0x00000001031ff34f sipQGroupBox::~sipQGroupBox() + 65
6   QtCore                          0x000000010160e57f QObjectPrivate::deleteChildren() + 95
7   QtGui                           0x00000001039c57e9 QWidget::~QWidget() + 697
8   QtGui.so                        0x000000010336017f sipQWidget::~sipQWidget() + 65
9   QtCore                          0x0000000101703ebe QObject::event(QEvent*) + 1118
10  QtGui                           0x00000001039cc83e QWidget::event(QEvent*) + 78
11  QtGui.so                        0x000000010335cb7c sipQWidget::event(QEvent*) + 76
12  QtGui                           0x000000010397215d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 189
13  QtGui                           0x000000010397818d QApplication::notify(QObject*, QEvent*) + 349
14  QtGui.so                        0x0000000103319d62 sipQApplication::notify(QObject*, QEvent*) + 84
15  QtCore                          0x00000001016094dc QCoreApplication::notifyInternal(QObject*, QEvent*) + 124
16  QtCore                          0x00000001016f70cb QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 731
17  com.apple.CoreFoundation        0x00007fff923f0b51 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
18  com.apple.CoreFoundation        0x00007fff923f03bd __CFRunLoopDoSources0 + 253
19  com.apple.CoreFoundation        0x00007fff924171a9 __CFRunLoopRun + 905
20  com.apple.CoreFoundation        0x00007fff92416ae6 CFRunLoopRunSpecific + 230
21  com.apple.HIToolbox             0x00007fff8e27e3d3 RunCurrentEventLoopInMode + 277
22  com.apple.HIToolbox             0x00007fff8e28558f ReceiveNextEventCommon + 181
23  com.apple.HIToolbox             0x00007fff8e2854ca BlockUntilNextEventMatchingListInMode + 62
24  com.apple.AppKit                0x00007fff95cf13f1 _DPSNextEvent + 659
25  com.apple.AppKit                0x00007fff95cf0cf5 -[NSApplication nextEventMatchingMask:untilDate:inMode:dequeue:] + 135
26  com.apple.AppKit                0x00007fff95ced62d -[NSApplication run] + 470
27  QtGui                           0x000000010392d174 QEventDispatcherMac::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 1588
28  QtCore                          0x00000001016f5a34 QEventLoop::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 68
29  QtCore                          0x00000001016f5d54 QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 180
30  QtCore                          0x00000001016f737c QCoreApplication::exec() + 188
31  QtGui.so                        0x000000010331aa81 meth_QApplication_exec_ + 81
32  org.python.python               0x00000001000a357b PyEval_EvalFrameEx + 18011
33  org.python.python               0x00000001000a67d7 PyEval_EvalCodeEx + 2103
34  org.python.python               0x00000001000a6988 fast_function + 296
35  org.python.python               0x00000001000a362d PyEval_EvalFrameEx + 18189
36  org.python.python               0x00000001000a6913 fast_function + 179
37  org.python.python               0x00000001000a362d PyEval_EvalFrameEx + 18189
38  org.python.python               0x00000001000a6913 fast_function + 179
39  org.python.python               0x00000001000a362d PyEval_EvalFrameEx + 18189
40  org.python.python               0x00000001000a67d7 PyEval_EvalCodeEx + 2103
41  org.python.python               0x00000001000a6988 fast_function + 296
42  org.python.python               0x00000001000a362d PyEval_EvalFrameEx + 18189
43  org.python.python               0x00000001000a67d7 PyEval_EvalCodeEx + 2103
44  org.python.python               0x00000001000a6988 fast_function + 296
45  org.python.python               0x00000001000a362d PyEval_EvalFrameEx + 18189
46  org.python.python               0x00000001000a67d7 PyEval_EvalCodeEx + 2103
47  org.python.python               0x00000001000a6856 PyEval_EvalCode + 54
48  org.python.python               0x00000001000c4ae4 PyRun_FileExFlags + 164
49  org.python.python               0x00000001000c5d68 PyRun_SimpleFileExFlags + 392
50  org.python.python               0x00000001000d8b99 Py_Main + 2969
51  org.python.python               0x0000000100000f04 0x100000000 + 3844

Thread 1:: Dispatch queue: com.apple.libdispatch-manager
0   libsystem_kernel.dylib          0x00007fff8e14c7e6 kevent + 10
1   libdispatch.dylib               0x00007fff8c3015be _dispatch_mgr_invoke + 923
2   libdispatch.dylib               0x00007fff8c30014e _dispatch_mgr_thread + 54

Thread 2:
0   libsystem_kernel.dylib          0x00007fff8e14a67a mach_msg_trap + 10
1   libsystem_kernel.dylib          0x00007fff8e149d71 mach_msg + 73
2   com.apple.opengl                0x00007fff94eb1389 glcDebugListener + 500
3   libsystem_c.dylib               0x00007fff918228bf _pthread_start + 335
4   libsystem_c.dylib               0x00007fff91825b75 thread_start + 13

Thread 3:
0   libsystem_kernel.dylib          0x00007fff8e14c192 __workq_kernreturn + 10
1   libsystem_c.dylib               0x00007fff91824594 _pthread_wqthread + 758
2   libsystem_c.dylib               0x00007fff91825b85 start_wqthread + 13

Thread 4:
0   libsystem_kernel.dylib          0x00007fff8e14c192 __workq_kernreturn + 10
1   libsystem_c.dylib               0x00007fff91824594 _pthread_wqthread + 758
2   libsystem_c.dylib               0x00007fff91825b85 start_wqthread + 13

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000000  rbx: 0x000000011b1099c0  rcx: 0x0000000103515f00  rdx: 0x0000000114a154d0
  rdi: 0x0000000000000000  rsi: 0x00000001007f302b  rbp: 0x00007fff5fbfc500  rsp: 0x00007fff5fbfc4b0
   r8: 0x00007fff5fbfc40c   r9: 0x00007fff5fbfc408  r10: 0x0000000000000081  r11: 0x000000011b1099e4
  r12: 0x0000000000000000  r13: 0x0000000100147220  r14: 0x000000011bc9e570  r15: 0x0000000000000000
  rip: 0x00000001007e959c  rfl: 0x0000000000010246  cr2: 0x0000000000000010
Logical CPU: 2

Binary Images:
       0x100000000 -        0x100000ff7 +org.python.python (2.7.2 - 2.7.2) <FD6FC5BC-8E24-3F3E-A1BA-830E555F5927> /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
       0x100003000 -        0x100142fe7 +org.python.python (2.7.2, [c] 2004-2011 Python Software Foundation. - 2.7.2) <65B3A222-1EDE-3FBB-936E-D51018C646A3> /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/Python
       0x1002f4000 -        0x1002f6ff7 +time.so (??? - ???) <07716085-0826-3EA2-BBFD-37F3251840D6> /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/time.so
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       0x100500000 -        0x10050cfb1 +libgcc_s.1.dylib (??? - ???) <BBB4EAFF-D7EC-4B7A-9AED-C5BB3003BDE0> /usr/local/lib/libgcc_s.1.dylib
       0x100515000 -        0x100516ff7 +cStringIO.so (??? - ???) <9293CE21-2A99-3682-9DD0-D4548D77502D> /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/cStringIO.so
       0x10051b000 -        0x10051efff +_collections.so (??? - ???) <7871AD9A-021E-3603-9111-90902DD3B31C> /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_collections.so
       0x100524000 -        0x100528ff7 +operator.so (??? - ???) <486720C8-A397-3152-971F-F2ECC5BDD693> /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/operator.so
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    0x7fff925b3000 -     0x7fff925dcfff  com.apple.CoreServicesInternal (113.8 - 113.8) <C1A3CF1B-BC45-3FC6-82B3-1511EBBA9D51> /System/Library/PrivateFrameworks/CoreServicesInternal.framework/Versions/A/CoreServicesInternal
    0x7fff925eb000 -     0x7fff92907ff7  com.apple.CoreServices.CarbonCore (960.18 - 960.18) <6020C3FB-6125-3EAE-A55D-1E77E38BEDEA> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/CarbonCore
    0x7fff92908000 -     0x7fff9297dff7  libc++.1.dylib (19.0.0 - compatibility 1.0.0) <C0EFFF1B-0FEB-3F99-BE54-506B35B555A9> /usr/lib/libc++.1.dylib
    0x7fff92bcd000 -     0x7fff92bd3ff7  libunwind.dylib (30.0.0 - compatibility 1.0.0) <1E9C6C8C-CBE8-3F4B-A5B5-E03E3AB53231> /usr/lib/system/libunwind.dylib
    0x7fff92c1a000 -     0x7fff92c6cff7  libGLU.dylib (??? - ???) <3C9153A0-8499-3DC0-AAA4-9FA6E488BE13> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
    0x7fff92ee7000 -     0x7fff92ef4fff  libCSync.A.dylib (600.0.0 - compatibility 64.0.0) <931F40EB-CA75-3A90-AC97-4DB8E210BC76> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libCSync.A.dylib
    0x7fff93325000 -     0x7fff9333bff7  com.apple.ImageCapture (7.0 - 7.0) <69E6E2E1-777E-332E-8BCF-4F0611517DD0> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ImageCapture.framework/Versions/A/ImageCapture
    0x7fff9333c000 -     0x7fff9333cfff  com.apple.Cocoa (6.6 - ???) <021D4214-9C23-3CD8-AFB2-F331697A4508> /System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa
    0x7fff9333f000 -     0x7fff93345fff  libGFXShared.dylib (??? - ???) <343AE6C0-EB02-333C-8D35-DF6093B92758> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
    0x7fff933f8000 -     0x7fff93453ff7  com.apple.HIServices (1.10 - ???) <BAB8B422-7047-3D2D-8E0A-13FCF153E4E7> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices
    0x7fff93454000 -     0x7fff93b67587  com.apple.CoreGraphics (1.600.0 - ???) <A9F2451E-6F60-350E-A6E5-539669B53074> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics
    0x7fff93b69000 -     0x7fff93b69fff  com.apple.Accelerate (1.7 - Accelerate 1.7) <82DDF6F5-FBC3-323D-B71D-CF7ABC5CF568> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
    0x7fff93b6a000 -     0x7fff93d6cfff  libicucore.A.dylib (46.1.0 - compatibility 1.0.0) <38CD6ED3-C8E4-3CCD-89AC-9C3198803101> /usr/lib/libicucore.A.dylib
    0x7fff93d6d000 -     0x7fff93de0fff  libstdc++.6.dylib (52.0.0 - compatibility 7.0.0) <6BDD43E4-A4B1-379E-9ED5-8C713653DFF2> /usr/lib/libstdc++.6.dylib
    0x7fff93de1000 -     0x7fff93e85fef  com.apple.ink.framework (1.3.2 - 110) <F69DBD44-FEC8-3C14-8131-CC0245DBBD42> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink
    0x7fff942b0000 -     0x7fff942b4ff7  com.apple.CommonPanels (1.2.5 - 94) <0BB2C436-C9D5-380B-86B5-E355A7711259> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/Versions/A/CommonPanels
    0x7fff942b5000 -     0x7fff942dcfff  com.apple.PerformanceAnalysis (1.10 - 10) <2A058167-292E-3C3A-B1F8-49813336E068> /System/Library/PrivateFrameworks/PerformanceAnalysis.framework/Versions/A/PerformanceAnalysis
    0x7fff942dd000 -     0x7fff942faff7  libxpc.dylib (77.17.0 - compatibility 1.0.0) <72A16104-2F23-3C22-B474-1953F06F9376> /usr/lib/system/libxpc.dylib
    0x7fff94526000 -     0x7fff9467ffff  com.apple.audio.toolbox.AudioToolbox (1.7.1 - 1.7.1) <4877267E-F736-3019-85D3-40A32A042A80> /System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioToolbox
    0x7fff94e21000 -     0x7fff94e4efe7  libSystem.B.dylib (159.1.0 - compatibility 1.0.0) <C6EC2616-5A21-39AA-9DF7-8AFA390CDDF2> /usr/lib/libSystem.B.dylib
    0x7fff94e80000 -     0x7fff94eabff7  libxslt.1.dylib (3.24.0 - compatibility 3.0.0) <8051A3FC-7385-3EA9-9634-78FC616C3E94> /usr/lib/libxslt.1.dylib
    0x7fff94eac000 -     0x7fff94ebbff7  com.apple.opengl (1.7.5 - 1.7.5) <2945F1A6-910C-3596-9988-5701B04BD821> /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
    0x7fff95a35000 -     0x7fff95a37fff  libquarantine.dylib (36.0.0 - compatibility 1.0.0) <4C3BFBC7-E592-3939-B376-1C2E2D7C5389> /usr/lib/system/libquarantine.dylib
    0x7fff95acb000 -     0x7fff95b06ff7  libsystem_info.dylib (??? - ???) <9C8C2DCB-96DB-3471-9DCE-ADCC26BE2DD4> /usr/lib/system/libsystem_info.dylib
    0x7fff95b07000 -     0x7fff95b0cfff  com.apple.OpenDirectory (10.7 - 146) <91A87249-6A2F-3F89-A8DE-0E95C0B54A3A> /System/Library/Frameworks/OpenDirectory.framework/Versions/A/OpenDirectory
    0x7fff95b0d000 -     0x7fff95b10fff  com.apple.help (1.3.2 - 42) <AB67588E-7227-3993-927F-C9E6DAC507FD> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Help.framework/Versions/A/Help
    0x7fff95ce8000 -     0x7fff968e9ff7  com.apple.AppKit (6.7.2 - 1138.23) <5CD2C850-4F52-3BA2-BA11-3107DFD2D23C> /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit
    0x7fff9697a000 -     0x7fff9697afff  libkeymgr.dylib (23.0.0 - compatibility 1.0.0) <61EFED6A-A407-301E-B454-CD18314F0075> /usr/lib/system/libkeymgr.dylib
    0x7fff9697b000 -     0x7fff9698dff7  libz.1.dylib (1.2.5 - compatibility 1.0.0) <30CBEF15-4978-3DED-8629-7109880A19D4> /usr/lib/libz.1.dylib
    0x7fff9773c000 -     0x7fff9773cfff  com.apple.vecLib (3.7 - vecLib 3.7) <9A58105C-B36E-35B5-812C-4ED693F2618F> /System/Library/Frameworks/vecLib.framework/Versions/A/vecLib
    0x7fff97778000 -     0x7fff9778bff7  libCRFSuite.dylib (??? - ???) <034D4DAA-63F0-35E4-BCEF-338DD7A453DD> /usr/lib/libCRFSuite.dylib
    0x7fff977d6000 -     0x7fff977dfff7  libsystem_notify.dylib (80.1.0 - c

Wrong colors on Ubuntu default theme

On ubuntu mayavi2 looks too dark.

http://itmag.es/4GId4

Mayavi2 on Ubuntu 12.04 (64 Bit)

Hello,

I used to use Mayavi2 on my Ubuntu 10.04 (python 2.6) machine. After a new installation of Ubuntu 12.04 (and Python 2.7.3), mayavi2 does not work.

I get the following error:

The program 'python' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadRequest (invalid request code or no such operation)'.
(Details: serial 2610 error_code 1 request_code 154 minor_code 19)
(Note to programmers: normally, X errors are reported asynchronously;
that is, you will receive the error a while after causing it.
To debug your program, run it with the --sync command line
option to change this behavior. You can then get a meaningful
backtrace from your debugger if you break on the gdk_x_error() function.)

After running in the verbose mode, the error is:

INFO|2012-06-08 14:45:02,095|********************************************************************************
INFO|2012-06-08 14:45:02,095|logfile is: '/home/deniz/.enthought/mayavi_e3/mayavi.log'
INFO|2012-06-08 14:45:02,095|********************************************************************************
DEBUG|2012-06-08 14:45:02,095|---------- workbench application ----------
DEBUG|2012-06-08 14:45:02,095|---------- application starting ----------
DEBUG|2012-06-08 14:45:02,096|plugin envisage.core starting
DEBUG|2012-06-08 14:45:02,102|extensions to <envisage.preferences> <[[], ['pkgfile://envisage.ui.workbench/preferences.ini'], ['pkgfile://mayavi/preferences/preferences.ini'], ['pkgfile://tvtk.plugins.scene/preferences.ini'], ['pkgfile://apptools.logger/plugin/preferences.ini'], [], [], [], []]>
DEBUG|2012-06-08 14:45:02,103|loading preferences from <<open file '/usr/lib/python2.7/dist-packages/envisage/ui/workbench/preferences.ini', mode 'rb' at 0x50eb420>>
DEBUG|2012-06-08 14:45:02,103|loading preferences from <<open file '/usr/lib/python2.7/dist-packages/mayavi/preferences/preferences.ini', mode 'rb' at 0x50eb4b0>>
DEBUG|2012-06-08 14:45:02,104|loading preferences from <<open file '/usr/lib/python2.7/dist-packages/tvtk/plugins/scene/preferences.ini', mode 'rb' at 0x50eb420>>
DEBUG|2012-06-08 14:45:02,104|loading preferences from <<open file '/usr/lib/python2.7/dist-packages/apptools/logger/plugin/preferences.ini', mode 'rb' at 0x50eb4b0>>
DEBUG|2012-06-08 14:45:02,109|extensions to <envisage.class_load_hooks> <[[], [], [], [], [], [], [], [], []]>
DEBUG|2012-06-08 14:45:02,115|extensions to <envisage.categories> <[[], [], [], [], [], [], [], [], []]>
DEBUG|2012-06-08 14:45:02,120|extensions to <envisage.service_offers> <[[], [<envisage.service_offer.ServiceOffer object at 0x5342590>, <envisage.service_offer.ServiceOffer object at 0x5342bf0>], [], [], [], [], [], [], []]>
DEBUG|2012-06-08 14:45:02,120|service <1> registered apptools.preferences.ui.preferences_manager.PreferencesManager
DEBUG|2012-06-08 14:45:02,120|service <2> registered envisage.ui.workbench.workbench.Workbench
DEBUG|2012-06-08 14:45:02,120|plugin envisage.core started
DEBUG|2012-06-08 14:45:02,121|plugin envisage.ui.workbench starting
DEBUG|2012-06-08 14:45:02,121|plugin envisage.ui.workbench started
DEBUG|2012-06-08 14:45:02,121|plugin mayavi starting
DEBUG|2012-06-08 14:45:02,121|plugin mayavi started
DEBUG|2012-06-08 14:45:02,121|plugin tvtk.scene starting
DEBUG|2012-06-08 14:45:02,121|plugin tvtk.scene started
DEBUG|2012-06-08 14:45:02,121|plugin apptools.logger starting
WARNING|2012-06-08 14:45:02,122|plugin <envisage.plugins.text_editor.text_editor_plugin.TextEditorPlugin object at 0x53420b0> has no Id - using <envisage.plugins.text_editor.text_editor_plugin.TextEditorPlugin>
WARNING|2012-06-08 14:45:02,590|view <envisage.plugins.python_shell.view.namespace_view.NamespaceView object at 0x562a3b0> has no Id - using <envisage.plugins.python_shell.view.namespace_view.NamespaceView>
The program 'python' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadRequest (invalid request code or no such operation)'.
(Details: serial 2610 error_code 1 request_code 154 minor_code 19)
(Note to programmers: normally, X errors are reported asynchronously;
that is, you will receive the error a while after causing it.
To debug your program, run it with the --sync command line
option to change this behavior. You can then get a meaningful
backtrace from your debugger if you break on the gdk_x_error() function.)

Can you please help.

Build issues with sphinx 1.1.3

When building Mayavi 4.2.0 on Fedora rawhide with sphinx 1.1.3, I had to make the following change to setup.py:

--- enthought-mayavi-a1e562a/setup.py.sphinx    2012-05-16 13:08:48.000000000 -0600
+++ enthought-mayavi-a1e562a/setup.py   2012-05-25 11:08:03.848464103 -0600
@@ -81,7 +81,7 @@ from setuptools.command import develop,
 info = {}
 execfile(join('mayavi', '__init__.py'), info)

-DEFAULT_HTML_TARGET_DIR = join('build', 'docs', 'html')
+DEFAULT_HTML_TARGET_DIR = join('docs', 'build')
 DEFAULT_INPUT_DIR = join('docs', 'source',)

 class GenDocs(Command):
@@ -270,7 +270,7 @@ def list_docs_data_files(project):

         returns a list of (install_dir, [data_files, ]) tuples.
     """
-    project_target_dir = join(DEFAULT_HTML_TARGET_DIR, project)
+    project_target_dir = join(DEFAULT_HTML_TARGET_DIR, project, 'html')
     return_list = []
     for root, dirs, files in os.walk(project_target_dir, topdown=True):
         # Modify inplace the list of directories to walk

There are also many build errors and warning when building the docs. See here http://koji.fedoraproject.org/koji/getfile?taskID=4101079&name=build.log for a full build log.

Python crash while maximizing mayavi window

For the record, I run latest git mayavi on Windows XP, Python 2.7 with Qt enabled.

I was running this example code: http://gael-varoquaux.info/blog/wp-content/uploads/2009/04/delaunay_py and it shows fine. But if I try to maximize mayavi window or go fullscreen, python crashes - I get MS visual C++ runtime error about python.exe process. Terminal writes this:

Qt has caught an exception thrown from an event handler. Throwing
exceptions from an event handler is not supported in Qt. You must
reimplement QApplication::notify() and catch all exceptions there.

QWidget::repaint: Recursive repaint detected

VTK warnings when modifying pipeline

Reported by Maik Beckmann:

This code

from enthought.mayavi import mlab

pts = mlab.points3d([0,1], [0,1], [0,1])
pts.mlab_source.set(x=[0,2])

works, but gives

ERROR: In /build/src/VTK/Filtering/vtkExecutive.cxx, line 756
vtkStreamingDemandDrivenPipeline (0x59b4900): Algorithm
vtkAssignAttribute(0x59bd8a0) returned failure for request:
vtkInformation (0x5ad6c60)
  Debug: Off
  Modified Time: 818743
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_DATA_OBJECT
  ALGORITHM_AFTER_FORWARD:

where this is the emitting code in vtkExecutive.cxx in
vtkExecutive::CallAlgorithm(...)

   ...
  // If the algorithm failed report it now.
  if(!result)
    {
    vtkErrorMacro("Algorithm " << this->Algorithm->GetClassName()
                  << "(" << this->Algorithm
                  << ") returned failure for request: "
                  << *request);
    }
  ...

Though its reported as an error by vtk, it doesn't seem to break anything.

ImportError: cannot import name NodeTree with PyQt4 backend

I was trying to run mayavi2 on macosx 10.6 with pyqt4 backend and I get the following error:

Exception occurred in traits notification handler for object: <pyface.ui.qt4.gui.GUI object at 0x12178e590>, trait: started, old value: False, new value: True
Traceback (most recent call last):
File "/Library/Python/2.6/site-packages/traits/trait_notifiers.py", line 536, in rebind_call_4
object, trait_name, old, new )
File "/Library/Python/2.6/site-packages/traits/trait_notifiers.py", line 448, in dispatch
handler( *args )
File "/Library/Python/2.6/site-packages/mayavi-4.0.0-py2.6-macosx-10.6-universal.egg/mayavi/plugins/mayavi_ui_plugin.py", line 207, in _on_application_gui_started
from apptools.naming.ui.api import explore
File "/Library/Python/2.6/site-packages/apptools/naming/ui/api.py", line 16, in
from explorer import Explorer, explore
File "/Library/Python/2.6/site-packages/apptools/naming/ui/explorer.py", line 23, in
from naming_tree import NamingTree
File "/Library/Python/2.6/site-packages/apptools/naming/ui/naming_tree.py", line 19, in
from pyface.tree.api import NodeTree
ImportError: cannot import name NodeTree
ERROR|2011-08-25 11:54:49,237|Exception occurred in traits notification handler for object: <pyface.ui.qt4.gui.GUI object at 0x12178e590>, trait: started, old value: False, new value: True
Traceback (most recent call last):
File "/Library/Python/2.6/site-packages/traits/trait_notifiers.py", line 536, in rebind_call_4
object, trait_name, old, new )
File "/Library/Python/2.6/site-packages/traits/trait_notifiers.py", line 448, in dispatch
handler( *args )
File "/Library/Python/2.6/site-packages/mayavi-4.0.0-py2.6-macosx-10.6-universal.egg/mayavi/plugins/mayavi_ui_plugin.py", line 207, in _on_application_gui_started
from apptools.naming.ui.api import explore
File "/Library/Python/2.6/site-packages/apptools/naming/ui/api.py", line 16, in
from explorer import Explorer, explore
File "/Library/Python/2.6/site-packages/apptools/naming/ui/explorer.py", line 23, in
from naming_tree import NamingTree
File "/Library/Python/2.6/site-packages/apptools/naming/ui/naming_tree.py", line 19, in
from pyface.tree.api import NodeTree
ImportError: cannot import name NodeTree

problem installing Mayavi with pip - no module named vtk

I want to use Mayavi.

Situation

I use a MacBook Air, with OSX 10.7.3.
I use pyhton 2.7.2
I have virtualenv installed. But I have not used it for this installation.

I've manually installed all it's dependencies, including VTK.

For VTK, I followed its installation guide and installed the python wrapper.

Now if I open a new terminal window and open python, I can import vtk without any error.

Problem

I try to install Mayavi with the following command:

pip install mayavi

But the following error occurs:

Downloading/unpacking mayavi
  Running setup.py egg_info for package mayavi
    build_src
    building extension "tvtk.array_ext" sources
    building data_files sources
    build_src: building npy-pkg config files

    no previously-included directories found matching 'artwork'
    no previously-included directories found matching 'docs/pdf'
Requirement already satisfied (use --upgrade to upgrade): apptools in /Library/Python/2.7/site-packages (from mayavi)
Requirement already satisfied (use --upgrade to upgrade): traits in /Library/Python/2.7/site-packages (from mayavi)
Requirement already satisfied (use --upgrade to upgrade): traitsui in /Library/Python/2.7/site-packages (from mayavi)
Requirement already satisfied (use --upgrade to upgrade): configobj in /Library/Python/2.7/site-packages (from apptools->mayavi)
Requirement already satisfied (use --upgrade to upgrade): pyface in /Library/Python/2.7/site-packages (from traitsui->mayavi)
Installing collected packages: mayavi
  Running setup.py install for mayavi
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/Users/Yasser/build/mayavi/setup.py", line 498, in <module>
        **config
      File "/Library/Python/2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.7-intel.egg/numpy/distutils/core.py", line 186, in setup
        return old_setup(**new_attr)
      File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 152, in setup
        dist.run_commands()
      File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 953, in run_commands
        self.run_command(cmd)
      File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command
        cmd_obj.run()
      File "/Library/Python/2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.7-intel.egg/numpy/distutils/command/install.py", line 57, in run
        r = self.setuptools_run()
      File "/Library/Python/2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.7-intel.egg/numpy/distutils/command/install.py", line 31, in setuptools_run
        return old_install_mod._install.run(self)
      File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/command/install.py", line 573, in run
        self.run_command('build')
      File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/cmd.py", line 326, in run_command
        self.distribution.run_command(command)
      File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command
        cmd_obj.run()
      File "/Users/Yasser/build/mayavi/setup.py", line 303, in run
        build_tvtk_classes_zip()
      File "/Users/Yasser/build/mayavi/setup.py", line 290, in build_tvtk_classes_zip
        gen_tvtk_classes_zip()
      File "tvtk/setup.py", line 46, in gen_tvtk_classes_zip
        from code_gen import TVTKGenerator
      File "tvtk/code_gen.py", line 10, in <module>
        import vtk
    ImportError: No module named vtk
    Complete output from command /usr/bin/python -c "import setuptools;__file__='/Users/Yasser/build/mayavi/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --single-version-externally-managed --record /var/folders/53/_trhc_0x0fb6kvx6bw_wrk500000gn/T/pip-Z4hpsW-record/install-record.txt:
    running install

running build

Traceback (most recent call last):

  File "<string>", line 1, in <module>

  File "/Users/Yasser/build/mayavi/setup.py", line 498, in <module>

    **config

  File "/Library/Python/2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.7-intel.egg/numpy/distutils/core.py", line 186, in setup

    return old_setup(**new_attr)

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 152, in setup

    dist.run_commands()

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 953, in run_commands

    self.run_command(cmd)

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command

    cmd_obj.run()

  File "/Library/Python/2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.7-intel.egg/numpy/distutils/command/install.py", line 57, in run

    r = self.setuptools_run()

  File "/Library/Python/2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.7-intel.egg/numpy/distutils/command/install.py", line 31, in setuptools_run

    return old_install_mod._install.run(self)

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/command/install.py", line 573, in run

    self.run_command('build')

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/cmd.py", line 326, in run_command

    self.distribution.run_command(command)

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command

    cmd_obj.run()

  File "/Users/Yasser/build/mayavi/setup.py", line 303, in run

    build_tvtk_classes_zip()

  File "/Users/Yasser/build/mayavi/setup.py", line 290, in build_tvtk_classes_zip

    gen_tvtk_classes_zip()

  File "tvtk/setup.py", line 46, in gen_tvtk_classes_zip

    from code_gen import TVTKGenerator

  File "tvtk/code_gen.py", line 10, in <module>

    import vtk

ImportError: No module named vtk

----------------------------------------
Command /usr/bin/python -c "import setuptools;__file__='/Users/Yasser/build/mayavi/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --single-version-externally-managed --record /var/folders/53/_trhc_0x0fb6kvx6bw_wrk500000gn/T/pip-Z4hpsW-record/install-record.txt failed with error code 1 in /Users/Yasser/build/mayavi
Storing complete log in /Users/Yasser/Library/Logs/pip.log
Traceback (most recent call last):
  File "/usr/local/bin/pip", line 8, in <module>
    load_entry_point('pip==1.1', 'console_scripts', 'pip')()
  File "/Library/Python/2.7/site-packages/pip-1.1-py2.7.egg/pip/__init__.py", line 116, in main
    return command.main(args[1:], options)
  File "/Library/Python/2.7/site-packages/pip-1.1-py2.7.egg/pip/basecommand.py", line 141, in main
    log_fp = open_logfile(log_fn, 'w')
  File "/Library/Python/2.7/site-packages/pip-1.1-py2.7.egg/pip/basecommand.py", line 168, in open_logfile
    log_fp = open(filename, mode)
IOError: [Errno 13] Permission denied: '/Users/Yasser/Library/Logs/pip.log'

I think the problem is with vtk.

Can anyone help me?

Other Details

Running sudo pip install mayavi does not solve the problem.

I thought this might help

› which python
/usr/local/bin/python

› python
Python 2.7.2 (default, Feb 17 2012, 13:57:55) 
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import vtk
>>> vtk
<module 'vtk' from '/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/VTK-5.10.0-py2.7.egg/vtk/__init__.pyc'>
>>>

My PYTHONPATH is empty.

mayavi2: segfaults as soon as a module is loaded from object editor

Hi,

Please check this bug report filed in Debian:
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=677421

""""
Steps to reproduce:

take some data to visualize and start mayavi2; for instance:

$ zcat /usr/share/doc/mayavi2/examples/mayavi/data/fire_ug.vtu.gz > fire_ug.vtu
$ zcat /usr/share/doc/mayavi2/examples/mayavi/data/room_vis.wrl.gz > room_vis.wrl
$ mayavi2 -d room_vis.wrl -d fire_ug.vtu

add a module; for instance: Streamline, or IsoSurface, or something else using the Mayavi Object Editor
In the tree-like view of the objects, click on "+Add module or filter" (under "VTK XML file (fire_ug.vtu)"), then in the Mayavi object editor ("Visualization modules" tab) double-click on "Streamline".
mayavi2 exits and the only output on the terminal is
"Segmentation fault"

""""

Thanks,
Varun

Refactor SetInput/GetOutput methods (that are removed in VTK 6)

As of 0dedbd9, when using VTK 6, mayavi builds fine, but we get runtime exceptions:

In [3]: from mayavi import mlab
No handlers could be found for logger "traits.has_traits"

In [4]: mlab.options.offscreen = True

In [5]: mlab.test_contour3d()
---------------------------------------------------------------------------
TraitError                                Traceback (most recent call last)
/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/mayavi/toug/lib/python2.7/site-packages/mayavi-4.3.0-py2.7-linux-x86_64.egg/tvtk/messenger.pyc in send(obj, event, *args, **kw_args)
    306 
    307 def send(obj, event, *args, **kw_args):
--> 308     _messenger.send(obj, event, *args, **kw_args)
    309 send.__doc__ = _messenger.send.__doc__
    310 

/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/mayavi/toug/lib/python2.7/site-packages/mayavi-4.3.0-py2.7-linux-x86_64.egg/tvtk/messenger.pyc in send(self, source, event, *args, **kw_args)
    247                         inst = obj()
    248                         if inst:
--> 249                             getattr(inst, meth)(source, event, *args, **kw_args)
    250                         else:
    251                             # Oops, dead reference.

/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/mayavi/toug/lib/python2.7/site-packages/mayavi-4.3.0-py2.7-linux-x86_64.egg/tvtk/tvtk_base.pyc in update_traits(self, obj, event)
    454                     setattr(self, name, warn)
    455                 else:
--> 456                     setattr(self, name, val)
    457         # Reset the warning state.
    458         vtk.vtkObject.SetGlobalWarningDisplay(warn)

/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/traits/mupe/lib/python2.7/site-packages/traits-4.3.0-py2.7-linux-x86_64.egg/traits/trait_handlers.pyc in error(self, object, name, value)
    167         """
    168         raise TraitError( object, name, self.full_info( object, name, value ),
--> 169                           value )
    170 
    171     def arg_error ( self, method, arg_num, object, name, value ):

TraitError: The 'alpha_bit_planes' trait of a RenderWindow instance must be 'f' or 'false' or 'n' or 'no' or 'off' or 'on' or 't' or 'true' or 'y' or 'yes' or 0 or 1, but a value of 8 <type 'int'> was specified.
---------------------------------------------------------------------------
TraitError                                Traceback (most recent call last)
<ipython-input-5-ba825038dacc> in <module>()
----> 1 mlab.test_contour3d()

/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/mayavi/toug/lib/python2.7/site-packages/mayavi-4.3.0-py2.7-linux-x86_64.egg/mayavi/tools/helper_functions.pyc in test_contour3d()
    492     scalars = x * x * 0.5 + y * y + z * z * 2.0
    493 
--> 494     obj = contour3d(scalars, contours=4, transparent=True)
    495     return obj
    496 

/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/mayavi/toug/lib/python2.7/site-packages/mayavi-4.3.0-py2.7-linux-x86_64.egg/mayavi/tools/helper_functions.pyc in the_function(*args, **kwargs)
     34 
     35     def the_function(*args, **kwargs):
---> 36         return pipeline(*args, **kwargs)
     37 
     38     if hasattr(pipeline, 'doc'):

/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/mayavi/toug/lib/python2.7/site-packages/mayavi-4.3.0-py2.7-linux-x86_64.egg/mayavi/tools/helper_functions.pyc in __call__(self, *args, **kwargs)
     74             scene = figure.scene
     75         else:
---> 76             scene = tools.gcf().scene
     77         if scene is not None:
     78             self._do_redraw = not scene.disable_render

/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/mayavi/toug/lib/python2.7/site-packages/mayavi-4.3.0-py2.7-linux-x86_64.egg/mayavi/tools/figure.pyc in gcf(engine)
    115     scene = engine.current_scene
    116     if scene is None:
--> 117         return figure(engine=engine)
    118     return scene
    119 

/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/mayavi/toug/lib/python2.7/site-packages/mayavi-4.3.0-py2.7-linux-x86_64.egg/mayavi/tools/figure.pyc in figure(figure, bgcolor, fgcolor, engine, size)
     67             __scene_number_list.update((name,))
     68             name = 'Mayavi Scene %d' % name
---> 69             engine.new_scene(name=name, size=size)
     70             engine.current_scene.name = name
     71         else:

/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/apptools/wm2g/lib/python2.7/site-packages/apptools-4.2.0-py2.7.egg/apptools/scripting/recordable.pyc in _wrapper(*args, **kw)
     43         if not record:
     44             # If the method was not recorded, just call it.
---> 45             result = func(*args, **kw)
     46 
     47         return result

/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/mayavi/toug/lib/python2.7/site-packages/mayavi-4.3.0-py2.7-linux-x86_64.egg/mayavi/core/engine.pyc in new_scene(self, viewer, name, **kwargs)
    432                     factory_kwargs[arg] = value
    433 
--> 434             viewer = self.scene_factory(**factory_kwargs)
    435             process_ui_events()
    436 

/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/mayavi/toug/lib/python2.7/site-packages/mayavi-4.3.0-py2.7-linux-x86_64.egg/mayavi/core/off_screen_engine.pyc in off_screen_viewer_factory(size)
     14 def off_screen_viewer_factory(size=(400, 350)):
     15     """A factory that creates an offscreen viewer."""
---> 16     win = TVTKWindow(off_screen_rendering=True)
     17     # Set all preferences.
     18     set_scene_preferences(win.scene)

/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/mayavi/toug/lib/python2.7/site-packages/mayavi-4.3.0-py2.7-linux-x86_64.egg/tvtk/pyface/tvtk_scene.pyc in __init__(self, **traits)
    917         """All the keyword arguments are passed on to the `TVTKScene`
    918         instance created."""
--> 919         self.scene = TVTKScene(**traits)

/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/mayavi/toug/lib/python2.7/site-packages/mayavi-4.3.0-py2.7-linux-x86_64.egg/tvtk/pyface/tvtk_scene.pyc in __init__(self, parent, **traits)
    199         self._def_pos = 1
    200 
--> 201         self.control = self._create_control(parent)
    202         self._renwin.update_traits()
    203 

/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/mayavi/toug/lib/python2.7/site-packages/mayavi-4.3.0-py2.7-linux-x86_64.egg/tvtk/pyface/tvtk_scene.pyc in _create_control(self, parent)
    803         self._interactor.initialize()
    804         self._interactor.render()
--> 805         self.light_manager = light_manager.LightManager(self)
    806 
    807         if self.off_screen_rendering:

/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/mayavi/toug/lib/python2.7/site-packages/mayavi-4.3.0-py2.7-linux-x86_64.egg/tvtk/pyface/light_manager.pyc in __init__(self, renwin, **traits)
    349         self.lights = []
    350         for i in range(self.number_of_lights):
--> 351             light = CameraLight(self.renwin)
    352             self.lights.append(light)
    353 

/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/mayavi/toug/lib/python2.7/site-packages/mayavi-4.3.0-py2.7-linux-x86_64.egg/tvtk/pyface/light_manager.pyc in __init__(self, renwin, **traits)
    165     #################################################################
    166     def __init__(self, renwin, **traits):
--> 167         self.glyph = LightGlyph()
    168         super(CameraLight, self).__init__(**traits)
    169         self.source.light_type = 'camera_light'

/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/mayavi/toug/lib/python2.7/site-packages/mayavi-4.3.0-py2.7-linux-x86_64.egg/tvtk/pyface/light_manager.pyc in __init__(self)
     57         t.rotate_y(90.0)
     58         t.translate((-2, 0, 0))
---> 59         tf.input = arrow.output
     60 
     61         mapper = tvtk.PolyDataMapper()

/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/traits/mupe/lib/python2.7/site-packages/traits-4.3.0-py2.7-linux-x86_64.egg/traits/trait_handlers.pyc in _read_only(object, name, value)
     99 def _read_only ( object, name, value ):
    100     raise TraitError, "The '%s' trait of %s instance is 'read only'." % (
--> 101                       name, class_of( object ) )
    102 
    103 def _undefined_get ( object, name ):

TraitError: The 'input' trait of a TransformFilter instance is 'read only'.

In [6]:

And the reason is that Mayavi still uses the old SetInput/GetOutput methods which are no longer available in VTK 6.

@prabhuramachandran, do you know what the right fix should be? I have run into exactly this issue before with some C++ examples and the fix turned out to be straightforward:

http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Replacement_of_SetInput

Pretty much, one just has to use either SetInputConnection or SetInputData depending on whether one is chaining filters or not. In Mayavi, should this be fixed in the TVTK module?

Configuration dialog can be improved

Hi,

I installed current development version under Windows, with latest stable VTK and Wx. Configuration dialog looks awful, like someone made it with hardcoded values that maybe look fine under some other backend and machine:

I think it shouldn't be like this.

Thanks

mayavi-4.0.0 failed on MacOSX 10.6

Hi all,

I first installed VTK from source, and then "easy_install" sphinx and pygments. Then, I built mayavi-4.0.0 from source.

mayavi2 fails on:

d8-30-62-5b-c4-8c:enthought-mayavi-69d7ab9 thomashaxton$ mayavi2 
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/Current//bin/mayavi2", line 9, in <module>
    load_entry_point('mayavi==4.0.0', 'console_scripts', 'mayavi2')()
  File "/Library/Frameworks/Python.framework/Versions/7.1/lib/python2.7/site-packages/pkg_resources.py", line 337, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/Library/Frameworks/Python.framework/Versions/7.1/lib/python2.7/site-packages/pkg_resources.py", line 2281, in load_entry_point
    return ep.load()
  File "/Library/Frameworks/Python.framework/Versions/7.1/lib/python2.7/site-packages/pkg_resources.py", line 1991, in load
    entry = __import__(self.module_name, globals(),globals(), ['__name__'])
  File "/Users/thomashaxton/ksong/mayavi/4.0.0/lib/python2.7/site-packages/mayavi-4.0.0-py2.7-macosx-10.5-i386.egg/mayavi/scripts/mayavi2.py", line 475, in <module>
    from mayavi.plugins.app import Mayavi, setup_logger
  File "/Users/thomashaxton/ksong/mayavi/4.0.0/lib/python2.7/site-packages/mayavi-4.0.0-py2.7-macosx-10.5-i386.egg/mayavi/plugins/app.py", line 19, in <module>
    from mayavi_workbench_application import MayaviWorkbenchApplication
  File "/Users/thomashaxton/ksong/mayavi/4.0.0/lib/python2.7/site-packages/mayavi-4.0.0-py2.7-macosx-10.5-i386.egg/mayavi/plugins/mayavi_workbench_application.py", line 17, in <module>
    import mayavi.api
  File "/Users/thomashaxton/ksong/mayavi/4.0.0/lib/python2.7/site-packages/mayavi-4.0.0-py2.7-macosx-10.5-i386.egg/mayavi/api.py", line 2, in <module>
    from mayavi.core.engine import Engine
  File "/Users/thomashaxton/ksong/mayavi/4.0.0/lib/python2.7/site-packages/mayavi-4.0.0-py2.7-macosx-10.5-i386.egg/mayavi/core/engine.py", line 27, in <module>
    from mayavi.core.base import Base
  File "/Users/thomashaxton/ksong/mayavi/4.0.0/lib/python2.7/site-packages/mayavi-4.0.0-py2.7-macosx-10.5-i386.egg/mayavi/core/base.py", line 19, in <module>
    from tvtk.pyface.tvtk_scene import TVTKScene
  File "/Users/thomashaxton/ksong/mayavi/4.0.0/lib/python2.7/site-packages/mayavi-4.0.0-py2.7-macosx-10.5-i386.egg/tvtk/pyface/tvtk_scene.py", line 24, in <module>
    from tvtk.pyface import light_manager
  File "/Users/thomashaxton/ksong/mayavi/4.0.0/lib/python2.7/site-packages/mayavi-4.0.0-py2.7-macosx-10.5-i386.egg/tvtk/pyface/light_manager.py", line 130, in <module>
    class CameraLight(HasTraits):
  File "/Users/thomashaxton/ksong/mayavi/4.0.0/lib/python2.7/site-packages/mayavi-4.0.0-py2.7-macosx-10.5-i386.egg/tvtk/pyface/light_manager.py", line 146, in CameraLight
    source = Instance(tvtk.Light, ())
AttributeError: 'TVTK' object has no attribute 'Light'

similarly, "mayavi2 -t" failed on this as well. And in addition, TVTK tests failed on vtkProperty missing:

....
Traceback (most recent call last):
  File "tvtk/tests/test_wrapper_gen.py", line 38, in test_sig_types
    meths = [vtk.vtkProperty.GetColor,
AttributeError: 'module' object has no attribute 'vtkProperty'
....

Is there anything wrong with my vtk build? Why TVTK object has no attribute 'Light'?

Any help will be really appreciated.

Thanks,

Kai

Force Mayavi to plot when figure embedded in a TraitsUI window

Hello,

I am having an issue where I cannot get Mayavi to render the window when embedded in a TraitsUI window. Specifically, if I run the following code (minimal representation of Mayavi scene in TraitsUI window), I get strange results:

# Enthought imports.
from traits.api import HasTraits, Instance
from traitsui.api import View, Item
from tvtk.pyface.scene_editor import SceneEditor
from mayavi.tools.mlab_scene_model import MlabSceneModel
from mayavi.sources.api import ParametricSurface
from mayavi import mlab
import pylab as pl
pl.ion()


class Mayavi(HasTraits):
    scene = Instance(MlabSceneModel, ())
    view = View(Item(name='scene', editor=SceneEditor(),
                     show_label=False, resizable=True, height=250,
                     width=500))

s = ParametricSurface()
m = Mayavi()
m.edit_traits()
mlab.pipeline.surface(s, figure=m.scene.mayavi_scene)

# this one comes up all black
img = mlab.screenshot(figure=m.scene.mayavi_scene)
pl.imshow(img)
# wait a second for the figure to appear, then it works correctly

The output of the first call to pl.imshow(img) is:

Once that pops up, the Mayavi screen then finally shows up on-screen, and renders correctly:

And after that has happened, re-running the two lines to get the screenshot and plot the image with pylab works:

So basically, I need a way to force Mayavi (and/or TraitsUI) to have the window 1) show up, and then 2) fully render before moving on to the screenshot() line. I've tried inserting mlab.draw() after the addition of the surface (immediately preceding mlab.screenshot() to no avail. It's possible this might be solvable by telling TraitsUI to draw the window and not return control until it has. If that's the case, it would be useful to add to the examples, since I've searched and not managed to find a workable solution to this...

Note that this is not an issue if the figure is created with mlab.figure() instead of being buried inside a TraitsUI window, but that is not a workable solution for my use case because I want to pull up several plots simultaneously (several Mayavi scenes) in the same window. This is part of a GUI that shows multiple views of the same object, and I need them to be rendered properly in order to determine certain useful properties (such as optimal camera distance) that, at the moment, is broken. I also can't for example, set the lighting properties, since after telling the windows to be created, the scenes aren't rendered immediately so the lights or light_manager property is None (whereas, again, if I wait a few seconds for the window to actually show up, those properties exist).

Running Mayavi 4.1.0 on Ubuntu Linux.

mayavi-4.3.0 current testsuite status;FAILED (errors=71, failures=4); Ran 142 tests

well I can see why the last lot gave up on it and just set testsuite to restrict.

After manually building and unzipping the absent tvtk_classes/ to mayavi-4.3.0/tvtk/
and getting past the myriad of errors stating tvtk wasn't built 'properly', now it's built properly;

mayavi-4.3.0 $ PYTHONPATH=. nosetests .

EEEEEE.....................EEEEEEEEE.....EEEEEEEEEEE....EEEEEEEEEEEEE.F....E..............EEEEEEEEEE.EEEEEEEEEEEEEEEEEEEE...........F.FFE....

======================================================================

theres now a myriad of errors stating
 "ImportError: No module named array_ext"

    k = getattr(tvtk, t_name)
AttributeError: 'TVTK' object has no attribute 'QVTKInteractor'

    doc = doc[:doc.find('\n\n')]
AttributeError: 'NoneType' object has no attribute 'find'

and so forth culminating with

----------------------------------------------------------------------
Ran 142 tests in 2.837s

FAILED (errors=71, failures=4)

tilt

Now which is shattered? The testsuite or mayavi-4.3.0?

Was picker type=cell ported to Mayavi 4.0.0?

I've just upgraded to Mayavi 4.0.0 and I've discovered that the picker type=cell doesn't work.
to be precise is the line:

    picker = figure.on_mouse_pick(picker_callback, type='cell')

For example, try to use it with the redball example:

# Author: Gael Varoquaux <gael dot varoquaux at normalesup.org>
# Copyright (c) 2009, Enthought, Inc.
# License: BSD style.

import numpy as np
from mayavi import mlab

################################################################################
# Disable the rendering, to get bring up the figure quicker:
figure = mlab.gcf()
mlab.clf()
figure.scene.disable_render = True

# Creates two set of points using mlab.points3d: red point and
# white points
x1, y1, z1 = np.random.random((3, 10))
red_glyphs = mlab.points3d(x1, y1, z1, color=(1, 0, 0),
                resolution=20)

x2, y2, z2 = np.random.random((3, 10))
white_glyphs = mlab.points3d(x2, y2, z2, color=(0.9, 0.9, 0.9),
                resolution=20)

# Add an outline to show the selected point and center it on the first
# data point.
outline = mlab.outline(line_width=3)
outline.outline_mode = 'cornered'
outline.bounds = (x1[0]-0.1, x1[0]+0.1,
                  y1[0]-0.1, y1[0]+0.1,
                  z1[0]-0.1, z1[0]+0.1)

# Every object has been created, we can reenable the rendering.
figure.scene.disable_render = False
################################################################################


# Here, we grab the points describing the individual glyph, to figure
# out how many points are in an individual glyph.
glyph_points = red_glyphs.glyph.glyph_source.glyph_source.output.points.to_array()


def picker_callback(picker):
    """ Picker callback: this get called when on pick events.
    """
    if picker.actor in red_glyphs.actor.actors:
        # Find which data point corresponds to the point picked:
        # we have to account for the fact that each data point is
        # represented by a glyph with several points
        point_id = picker.point_id/glyph_points.shape[0]
        # If the no points have been selected, we have '-1'
        if point_id != -1:
            # Retrieve the coordinnates coorresponding to that data
            # point
            x, y, z = x1[point_id], y1[point_id], z1[point_id]
            # Move the outline to the data point.
            outline.bounds = (x-0.1, x+0.1,
                              y-0.1, y+0.1,
                              z-0.1, z+0.1)


picker = figure.on_mouse_pick(picker_callback, type='cell')

# Decrease the tolerance, so that we can more easily select a precise
# point.
picker.tolerance = 0.01

mlab.title('Click on red balls')

mlab.show()

I'm getting this error:

mattions@triton:examples(master*)$ python select_red_balls.py 
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/mayavi/core/mouse_pick_dispatcher.py", line 168, in on_button_release
    picker.pick((x, y, 0), self.scene.scene.renderer)
  File "tvtk_classes/abstract_picker.py", line 153, in pick
  File "/usr/local/lib/python2.7/dist-packages/tvtk/tvtk_base.py", line 523, in _wrap_call
    ret = vtk_method(*args)
TypeError: function takes exactly 4 arguments (2 given)

It worked before with 3.6.0

savefig problem (software rendering issue)

Hello again!
This issue is about software rendering too.
On some machines without 3D acceleration (or with minor OpenGL support i.e. on Intel integrated cards) mlab's savefig function crashes the entire application somewhere inside vtk dll.
This issue applies to vtk 5.2, 5.4, and 5.6.

I'll try to run it under debugger and retrive the callstack in DLL libraries later.

Update: forgot to mention that I'm using it with offscreen rendering enabled.

VRML file extension

If I use mlab.savefig() to output model to VRML file and set extension to WRL, file is written as PNG, as I guess extension is not recognized. But if I name extension as VRML than it's OK.

This probably may not be the right way, as VRML readers expect WRL extension which I can also backup with wiki article: http://en.wikipedia.org/wiki/VRML

Loading visualization fails: it shows hidden module legends

Hi, this could be a bug:

Given a scene with a module that has actived “Show legend” (Colour and Legend layer), if this module is hidden, the legend (colour bar in the image) disappears with the rest of the image. However, if you save and close this visualization and load it later, the image is still hidden but not the colour bar. When it is only one module it is not a big problem but with more than ten is a big one due to I have to turn off all the legends that should be hidden.

Mayvi plot3d gets glitchy with many significant digits

Reporting against 3.3.0-1 on Ubuntu, which is the latest deb I could find.

DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=10.04
DISTRIB_CODENAME=lucid
DISTRIB_DESCRIPTION="Ubuntu 10.04.4 LTS"

Compare the visualization of these two plot3d calls:

mlab.plot3d([ 600000.63287674,  600000.63697936,  600000.66607347,
        600000.67137776], [ 600000.4572601 ,  600000.56022494,  600000.68954629,
        600000.82019476], [1, 1, 1, 1], [1, 1, 1, 1])

vs.

mlab.plot3d([ 0.63287674,  0.63697936,  0.66607347,
        0.67137776], [ 0.4572601 ,  0.56022494,  0.68954629,
        0.82019476], [1, 1, 1, 1], [1, 1, 1, 1])

The first call produces something very broken visually -- jerky motion, wrong shapes, missing parts of the tubes.

The second call works as expected.

mlab.text() draws into wrong figure when using multiple figures

When using multiple mlab figures, mlab.text() always draws into the last figure instead of the figure specified via the parameter or using mlab.figure(). For example, when using

f1 = mlab.figure()
mlab.test_contour_surf()

f2 = mlab.figure()
mlab.test_surface()

mlab.text(0.5, 0.5, 'test', figure=f1)

The text appears in f2 instead of f1. The same thing happens when the last line is replaced with

mlab.figure(f1)
mlab.text(0.5, 0.5, 'test')

Build fails with "QWidget: Must construct a QApplication before a QPaintDevice"

Hi,

I am trying to compile mayavi 4.1.0 on Gentoo linux (amd64) and it fails to build the TVTK classes with the error "QWidget: Must construct a QApplication before a QPaintDevice" (see output below). There is also a Gentoo bug report for the same problem:

https://bugs.gentoo.org/show_bug.cgi?id=399537

I am using VTK 5.8.0 and Qt 4.7.4. Has anyone encountered this problem before, or any ideas what could be causing it? I am happy to help resolving this issue.

Best,

Martin

Build output:

Compiling source in /var/tmp/portage/sci-visualization/mayavi-4.1.0/work/mayavi-4.1.0 ...

Building of sci-visualization/mayavi-4.1.0 with CPython 2.7...
python2.7 setup.py build -b build-2.7
running build
Building TVTK classes... vtkSimple3DCirclesStrategy: Ignoring method: Get/SetMarkedValue
default: (invalid), range: None
vtkArrayNorm: Ignoring method: Get/SetWindow
default: [0, 9223372036854775807), range: None
vtkChart: Ignoring method: Get/SetSize
default: [0.0, 0.0, 0.0, 0.0], range: None
QWidget: Must construct a QApplication before a QPaintDevice
/var/tmp/portage/sci-visualization/mayavi-4.1.0/temp/environment: line 1368: 1461 Aborted "$(PYTHON)" "${setup_file#*|}" "${_DISTUTILS_GLOBAL_OPTIONS[@]}" build -b "$(_distutils_get_build_dir)" "$@"

Mayavi + VTK 6.0.0.rc2 fails to build

The error log is:

...
[mayavi] creating stub loader for tvtk/array_ext.so
[mayavi] byte-compiling build/bdist.linux-x86_64/egg/tvtk/array_ext.py to array_ext.pyc
[mayavi] installing package data to build/bdist.linux-x86_64/egg
[mayavi] running install_data
[mayavi] ----------------------------------------------------------------------
[mayavi] Traceback (most recent call last):
[mayavi]   File "setup.py", line 498, in <module>
[mayavi] Building TVTK classes... vtkIncrementalForceLayout: Ignoring method: Get/SetGravityPoint
[mayavi] default: [200.0, 200.0], range: None
[mayavi]     
[mayavi]   File "/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/numpy/yzh7/lib/python2.7/site-packages/numpy/distutils/core.py", line 186, in setup
b/python2.7/distutils/core.py", line 152, in setup
[mayavi]     dist.run_commands()
[mayavi]   File "/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/python/mdo3/lib/python2.7/distutils/dist.py", line 953, in run_commands
[mayavi]     self.run_command(cmd)
[mayavi]   File "/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/python/mdo3/lib/python2.7/distutils/dist.py", line 972, in run_command
[mayavi]     cmd_obj.run()
[mayavi]   File "/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/numpy/yzh7/lib/python2.7/site-packages/numpy/distutils/command/install.py", line 57, in run
[mayavi]     r = self.setuptools_run()
[mayavi]   File "/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/numpy/yzh7/lib/python2.7/site-packages/numpy/distutils/command/install.py", line 51, in setuptools_run
[mayavi]     self.do_egg_install()
[mayavi]   File "/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/distribute/y2j4/lib/python2.7/site-packages/distribute-0.6.36-py2.7.egg/setuptools/command/install.py", line 93, in do_egg_install
[mayavi]     self.run_command('bdist_egg')
[mayavi]   File "/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/python/mdo3/lib/python2.7/distutils/cmd.py", line 326, in run_command
[mayavi]     self.distribution.run_command(command)
[mayavi]   File "/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/python/mdo3/lib/python2.7/distutils/dist.py", line 972, in run_command
[mayavi]     cmd_obj.run()
[mayavi]   File "/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/distribute/y2j4/lib/python2.7/site-packages/distribute-0.6.36-py2.7.egg/setuptools/command/bdist_egg.py", line 200, in run
[mayavi]     self.do_install_data()
[mayavi]   File "/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/distribute/y2j4/lib/python2.7/site-packages/distribute-0.6.36-py2.7.egg/setuptools/command/bdist_egg.py", line 150, in do_install_data
[mayavi]     self.call_command('install_data', force=0, root=None)
[mayavi]   File "/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/distribute/y2j4/lib/python2.7/site-packages/distribute-0.6.36-py2.7.egg/setuptools/command/bdist_egg.py", line 166, in call_command
[mayavi]     self.run_command(cmdname)
[mayavi]   File "/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/python/mdo3/lib/python2.7/distutils/cmd.py", line 326, in run_command
[mayavi]     self.distribution.run_command(command)
[mayavi]   File "/auto/nest/nest/u/ondrej/repos/python-hpcmp2/opt/python/mdo3/lib/python2.7/distutils/dist.py", line 972, in run_command
[mayavi]     cmd_obj.run()
[mayavi]   File "setup.py", line 356, in run
[mayavi]     
[mayavi]   File "setup.py", line 290, in build_tvtk_classes_zip
[mayavi]     
[mayavi]   File "tvtk/setup.py", line 62, in gen_tvtk_classes_zip
[mayavi]     # numpy.distutils does the Wrong(TM) thing.
[mayavi]   File "tvtk/code_gen.py", line 101, in generate_code
[mayavi]   File "tvtk/code_gen.py", line 191, in _write_wrapper_class
[mayavi]   File "tvtk/wrapper_gen.py", line 80, in generate_code
[mayavi]   File "tvtk/wrapper_gen.py", line 161, in _gen_methods
[mayavi]   File "tvtk/vtk_parser.py", line 152, in parse
[mayavi]   File "tvtk/vtk_parser.py", line 451, in _organize_methods
[mayavi]   File "tvtk/vtk_parser.py", line 597, in _find_get_set_methods
[mayavi]   File "tvtk/vtk_parser.py", line 655, in _get_instance
[mayavi] NotImplementedError: no concrete implementation exists for this class
[mayavi ERROR] Command '['bash', '../bash_script']' returned non-zero exit status 1
[mayavi ERROR] command failed (code=1); raising

Do you think that VTK 6 has introduced a lot of changes, or should this be relatively easy to fix?
I am using mayavi commit 576b9ca.

'extent' argument in mlab.imshow raises exception

In [21]: mlab.imshow(np.random.rand(10,20), interpolate=False, extent=[-1,11,-1,21,0,0])
Exception occurred in traits notification handler for object: <mayavi.tools.modules.ImageActorFactory object at 0x1d4487b0>, trait: extent, old value: [0 0 0 0 0 0], new value: [-1 11 -1 21 0 0]
Traceback (most recent call last):
File "/Users/pberkes/egit/ETS/traits/traits/trait_notifiers.py", line 366, in call_1
self.handler( object )
File "/Users/pberkes/egit/ETS/mayavi/mayavi/tools/modules.py", line 96, in _extent_changed
tools.set_extent(self._target, self.extent)
File "/Users/pberkes/egit/ETS/mayavi/mayavi/tools/tools.py", line 294, in set_extent
xmin, xmax, ymin, ymax, zmin, zmax = module.actor.actor.bounds
AttributeError: 'ImageActor' object has no attribute 'actor'

mlab.text fails

from mayavi import mlab
mlab.text(0.1, 0.1, "test")

cause an error in MayaVi 4.2. (The code ran well before)

The error is pasted. Is it a bug?

/local_data/chenxing/capture/2012_06_05/ in ()
----> 1 mlab.text(0.1, 0.1, "asdfsf")

/usr/lib/python2.7/site-packages/mayavi/tools/pipe_base.py in the_function(_args, *_kwargs)
35 def make_function(factory_class):
36 def the_function(_args, *_kwargs):
---> 37 factory = factory_class(_args, *_kwargs)
38 return factory._target
39

/usr/lib/python2.7/site-packages/mayavi/tools/decorations.py in init(self, x, y, text, *_kwargs)
468 raise ValueError('Text positions should be in [0, 1] if no z'
469 'position is given')
--> 470 super(Text, self).init(None, *_kwargs)
471 self._target.text = text
472 self._target.x_position = x

/usr/lib/python2.7/site-packages/mayavi/tools/pipe_base.py in init(self, parent, **kwargs)
142 self._do_redraw = not scene.disable_render
143 scene.disable_render = True
--> 144 if issubclass(self._target.class, Filter):
145 self._engine.add_filter(self._target, obj=parent)
146 else:

/usr/lib/python2.7/site-packages/traits/trait_types.pyc in create_default_value(self, _args, *_kw)
2776 raise TraitError, 'Unable to locate class: ' + args[0]
2777
-> 2778 return klass( _args[1:], *_kw )
2779
2780 #: fixme: Do we still need this method using the new style?...

/usr/lib/python2.7/site-packages/mayavi/core/module.py in init(self, **traits)
56
57 # Let the module setup its pipeline.

---> 58 self.setup_pipeline()
59
60 def get_pure_state(self):

/usr/lib/python2.7/site-packages/mayavi/modules/text.py in setup_pipeline(self)
156 actor.set(text_scale_mode='prop', width=0.4, height=1.0)
157 else:
--> 158 actor.set(scaled_text=True, width=0.4, height=1.0)
159
160 c = actor.position_coordinate

/usr/lib/python2.7/site-packages/traits/has_traits.pyc in trait_set(self, trait_change_notify, **traits)
1950 else:
1951 for name, value in traits.items():
-> 1952 setattr( self, name, value )
1953
1954 return self

TraitError: Cannot set the undefined 'scaled_text' attribute of a 'TextActor' object.

VTK on Mac OS X 10.6: /usr/lib/libIOKit.dylib: not a directory

Hi, all. This is more a problem in the documentation then the software. Following the instructions on http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/installation.html , I ran unto the following error during the "make -j" step:

cc1plus: error: /usr/lib/libIOKit.dylib: not a directory
make: *** [all] Error 2

I found a solution from: http://vtk.1045678.n5.nabble.com/VTK-5-6-compilation-on-Mac-OS-X-10-6-7-td4388683.html . One has to change the IOKit:FILEPATH line to:
IOKit:FILEPATH=/System/Library/Frameworks/IOKit.framework

After this, it finishes compiling.

Thanks!