[vtkusers] segfault with MarchingCubes

[Clément D.]

Hello all,

I am trying to use the Marching Cubes algorithm to show a 3D surface of a
3D image given by a Python (numpy array).
I thought I had it all mapped out, things were going great with arrays of
small size (generated and rendered 3D isosurfaces), but now that I'm
working with arrays of slightly bigger size, the programm crashes with
Python error 11 SIGSEGV which means seg fault. What worries me a bit is
that the array I'm using is not that big, 150*150*150, and I have a fairly
recent computer who shouldn't have any problem handling it.

Code MWE is below (in Python)

=========================================== Code snippet
=======================

import numpy as np
import vtk

# Creating a numpy array representing a 3D image
npa=np.zeros((150,150,150)).astype(np.uint8)
npa[100:102,100:102,100:102]=255

# Importing it as  object vtk (based on vtk example
http://www.vtk.org/Wiki/VTK/Examples/Python/vtkWithNumpy)
dataImporter = vtk.vtkImageImport()
dataString = npa.tostring()
[hh, ww, dd] = npa.shape
dataImporter.CopyImportVoidPointer(dataString, len(dataString))
dataImporter.SetDataScalarTypeToUnsignedChar()
dataImporter.SetNumberOfScalarComponents(3)
dataImporter.SetDataExtent(0, dd - 1, 0, ww - 1, 0, hh - 1)
dataImporter.SetWholeExtent(0, dd - 1, 0, ww - 1, 0, hh - 1)
dataImporter.Update()
vol = dataImporter.GetOutputPort()
# (print(dataImporter.GetOutput().GetClassName()) yields "vtk.ImageData")

# Use MarchingCubes to generate iso-surface
surface = vtk.vtkMarchingCubes();
surface.SetInputConnection(vol);
surface.ComputeNormalsOn();
surface.ComputeScalarsOn();
isoValue = 128
surface.SetValue(0, isoValue);

#This line causes segfault if npa is "too big"
surface.Update();

# .... rest of pipeline
# decimator = vtk.vtkDecimatePro(); ....
# smoother = vtk.vtkSmoothPolyDataFilter(); ....
# connectivityFilter = vtk.vtkPolyDataConnectivityFilter(); ....
# mesh = vtk.vtkPolyData(); ....
# mapper = vtk.vtkPolyDataMapper(); ....
# actor = vtk.vtkActor(); ....


=========================================== End of code snippet
=======================



So I have a couple of questions here :
1/ Is this a problem of input for MarchingCubes being too big ? Or is this
segfault indicating something else ?
- arguments for the former : Reducing the size of npa in this code makes it
work
- arguments for the latter : This code I'm showing is a MWE for my code
which is more complicated, and in my code, this code portion fails with a
large array, but succeeds if I reduce in size *another* array which has
nothing to do with MarchingCubes() (again, that other array is not that
big, so I don't think I'm reaching the limits of Python memory or anything
like that...)

2/ Am I doing the whole import numpy thing correctly ? I've based myself on
the vtk example, but I am unsure of whether it is the recommended way for
my case or if it was case specific


Thanks everyone,
Clément
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