MayaVi installation on Qt4 leads to segmentation faults

I am trying to install MayaVi on my computer. I'm on a MacBook Air with OS X 10.6.8, 4 GB RAM.

My python and most of my stack is built through Homebrew or pip. In particular this is true for python2.7, ipython, Qt4, numpy, scipy, vtk, etc. VTK was installed with --python and --qt-extern flags in Homebrew, and all the builds were fine. I do not have wxPython installed, as I failed to get it working through pip, manual building, or the binaries.

If I run ipython -q4thread, I cannot successfully execute from mayavi import mlab as I get an error related to usage of two different APIs for PyQt: http://groups.google.com/group/spyderlib/browse_thread/thread/36a35baec74ca144

However, if I run ipython alone, I can successfully run from mayavi import mlab. Then I try to follow this example: http://github.enthought.com/mayavi/mayavi/example_using_with_scipy.html, which includes these commands:

import numpy as np

def V(x, y, z):
    """ A 3D sinusoidal lattice with a parabolic confinement. """
    return np.cos(10*x) + np.cos(10*y) + np.cos(10*z) + 2*(x**2 + y**2 + z**2)

X, Y, Z = np.mgrid[-2:2:100j, -2:2:100j, -2:2:100开发者_开发百科j]

from mayavi import mlab
mlab.contour3d(X, Y, Z, V)

This all works fine, and I get a window that pops up and I can rotate the 3d plot etc. However, then I click on the icon to open up the pipeline, which opens another window. The tutorial then says to double-click on the "isosurface" to change its properties. As soon as I do that, I get a reproducible segmentation fault.

I have no idea how to begin to figure out what the problem is.

Alternatively, I can run MayaVi from the command line: mayavi2, and the GUI pops up. When I do so I get the following output:

Warning: Unable to import the wx backend for pyface due to traceback: Traceback (most recent call last):
      File "/usr/local/Cellar/python/2.7.1/lib/python2.7/site-packages/pyface/toolkit.py", line 45, in _init_toolkit
        be = import_toolkit(tk)
      File "/usr/local/Cellar/python/2.7.1/lib/python2.7/site-packages/pyface/toolkit.py", line 31, in import_toolkit
        __import__(be + 'init')
      File "/usr/local/Cellar/python/2.7.1/lib/python2.7/site-packages/pyface/ui/wx/init.py", line 14, in <module>
        import wx
    ImportError: No module named wx

Although the GUI does pop up, if I try to do any operation, I get a segfault.

Please let me know if you have any thoughts on troubleshooting this, or perhaps guidance on reinstalling the package successfully.

Thanks!

Uri

---

I also have a MacBook Air with OS X 10.7.4 (Lion). I spent a lot of time back in February to get mayavi working, eventually succeeding to a point where I could produce scientific plots. That still means that some of the examples and tests wouldn't run correctly, and the GUI produced lots of error messages in the console, but didn't crash (most of the time). Now, I managed to break my Python installation (probably by upgrading numpy), so I needed to reinstall. Alas, it didn't get any easier 6 months later!

There is still no viable precompiled option. I tried the Enthought Python Distribution from here: http://www.enthought.com/repo/.epd_academic_installers. Still no 64 bit version with ETS for Mac, components are ancient, mayavi based on wxPython looks ugly and feels slow and unresponsive. So back to brew and pip. After a lot of trial and error, here is what worked more or less:

1. Prerequisites

Hide/uninstall the broken Homebrew Python installation:

mv /usr/local/lib/python2.7/site-packages /usr/local/lib/python2.7/site-packages-old 
mv /usr/local/share/python /usr/local/share/python-old
brew uninstall python pyqt pyside vtk

From Xcode (4.4.1), choose llvm-gcc as the compiler (I had less success with clang):

cd /usr/bin
sudo rm cc c++
sudo ln -s gcc cc
sudo ln -s g++ c++

2. Installation

2.1 Python

brew install python --framework --universal

Point to the new installation:

cd /System/Library/Frameworks/Python.framework/Versions
rm Current
ln -s /usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/Current .

If the EPD is installed, one needs to do the same in /Library/Frameworks/Python.framework/Versions, otherwise the EPD will take priority.

2.2 Numpy

Install numpy from source (pip 1.2 currently doesn't install npymath.ini correctly, which will make scipy fail to build):

git clone https://github.com/numpy/numpy.git
cd numpy
git checkout v1.6.2
python setup.py install

Since so many packages link against numpy, I really recommend checking out an official release, 1.6.2 as of today. Next make the numpy headers visible:

cd /usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7
ln -s /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy .

2.3 qt, pyqt, vtk

Install qt (4.8.2) and pyqt (4.9.4):

brew install qt
brew install pyqt

One can also install pyside (1.1.1)

brew install pyside

but this appears to produce more crashes with mayavi. In any case, append

export QT_API=pyqt

to .bashrc to avoid any mixups. Next install vtk (5.10.0; 5.8.0 works just as well)

brew install vtk --python --tcl --examples --qt

...and wait (compilation takes around 40 minutes). The --qt flag isn't strictly necessary, but it doesn't harm either.

Next, download vtk data from http://www.vtk.org/files/release/5.10/vtkdata-5.10.0.tar.gz, unpack somewhere and have the VTK_DATA_ROOT environment variable point to the VTKData directory. Run some examples in

/usr/local/share/vtk/Examples

Launch python examples with python <example>.py and TCL examples with vtk <example.tcl>. Works absolutely beautifully, right? So let's see how mayavi messes it all up next...

2.4 ETS and mayavi

Although

pip install mayavi

gets you somewhere, it appears to produce more crashes than installing the bleeding edge from github. Get https://github.com/enthought/ets/raw/master/ets.py and run

python ets.py clone

to clone the ETS git repository. You only need apptools, mayavi, pyface, traits and traitsui, possibly envisage if you want to run mayavi2 from the command line. So delete the other directories and do

python ets.py develop

This should allow you to run some of the examples in the repository in mayavi/examples/tvtk and mayavi/examples/mayavi by running python <example>.py and play around with the GUI. There are lots of console errors and lots of GUI features that don't work, like selecting a LUT table. But it hopefully doesn't crash.

2.5 scipy, matplotlib, ipython

I prefer to get the bleeding edge from github for scipy and matplotlib. First install all dependencies using brew. Then

git clone https://github.com/scipy/scipy.git
cd scipy
python setup.py install

git clone https://github.com/matplotlib/matplotlib.git
cd matplotlib
python setup.py install

Then install ipython (0.13) using pip. For the qtconsole install first:

pip install pygments
pip install pyzmq

then

pip install ipython

There are a few possible ways to launch ipython for use with mayavi, depending on who controls the QT event loop:

• ipython without mlab.show(): Hangs.
• ipython with mlab.show(): Works, but prompt may become unresponsive.
• ipython --gui=qt or ipython --pylab=qt: Works, but "Save" dialog closes immediately.
• ipython qtconsole without mlab.show(): Hangs.
• ipython qtconsole with mlab.show(): Works.
• ipython qtconsole --gui=qt or ipython qtconsole --pylab=qt: Works.

Good luck!