Buffer function for python 3+

Question

I'm trying to open a vtk window using vtk_show, but my Ipython console crashes every time i do this, apparently this is because Ipython can't display an external window, which is exactly what vtk_show does. I searched on google for a solution, but it's written for python2 (i'm using python 3.6.3). Here's the solution i found:

import vtk
from IPython.display import Image

def vtk_show(renderer, width=400, height=300):
    """
    Takes vtkRenderer instance and returns an IPython Image with the 
    rendering.
    """
    renderWindow = vtk.vtkRenderWindow()
    renderWindow.SetOffScreenRendering(1)
    renderWindow.AddRenderer(renderer)
    renderWindow.SetSize(width, height)
    renderWindow.Render()

    windowToImageFilter = vtk.vtkWindowToImageFilter()
    windowToImageFilter.SetInput(renderWindow)
    windowToImageFilter.Update()

    writer = vtk.vtkPNGWriter()
    writer.SetWriteToMemory(1)
    writer.SetInputConnection(windowToImageFilter.GetOutputPort())
    writer.Write()
    data = str(buffer(writer.GetResult()))

    return Image(data)

I'm getting an error while trying to use the buffer built-in function of python2, but as this function doesn't exist on python3+ i'm stuck.. If anyone could help me with this i would be very appreciated. Thanks in advance!

jcgiret · Accepted Answer · 2018-05-05 16:13:22Z

13

At least these two points must be modified on your code to have the same behavior with Python 3:

The buffer(...) built-in function in Python 2 has been replaced by memoryview(...) in Python 3: What is Python buffer type for?. Replace the buffer call by memoryview
the str(...) built-in function has to replaced by a bytes(...) call to get a bytes object: https://docs.python.org/2/howto/pyporting.html#text-versus-binary-data

So the data = ... line should read:

data = bytes(memoryview(writer.GetResult()))

edited May 5, 2018 at 16:13

answered May 3, 2018 at 21:04

jcgiret

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5 Comments

jcgiret Over a year ago

What do you mean by it didn’t work? Could you post the error message? Also, could you you precise that in your initial post?

jcgiret Over a year ago

I think it comes from the str call now. Try to change the line ‘data=...’ in ‘data = memoryview(writer.GetResults()).tobytes()’

tomas-silveira Over a year ago

Hey again and sorry for the very late response! i managed to fix the error i was getting and completely forgot to come here.

jcgiret Over a year ago

No worries! Note that you can answer your own question!

Mason Over a year ago

This worked for fixing the example code for pyzmq as well.

amandagb · Accepted Answer · 2018-10-04 23:28:08Z

To clarify, I believe this example was an adaptation of a very informative blog example showing how to extract surfaces from medical images using VTK's marching cubes algorithm. The accompanying Jupyter notebook was intended for Python 2.7, and as mentioned for it to be used in Python 3.6+, the data=... portion needs to be changed.

import vtk
from IPython.display import Image

def vtk_show(renderer, width=400, height=300):
    """
    Takes vtkRenderer instance and returns an IPython Image with the 
    rendering.
    """
    renderWindow = vtk.vtkRenderWindow()
    renderWindow.SetOffScreenRendering(1)
    renderWindow.AddRenderer(renderer)
    renderWindow.SetSize(width, height)
    renderWindow.Render()

    windowToImageFilter = vtk.vtkWindowToImageFilter()
    windowToImageFilter.SetInput(renderWindow)
    windowToImageFilter.Update()

    writer = vtk.vtkPNGWriter()
    writer.SetWriteToMemory(1)
    writer.SetInputConnection(windowToImageFilter.GetOutputPort())
    writer.Write()
    data = memoryview(writer.GetResults()).tobytes()

    return Image(data)

Credit for the solution definitely goes to @MafiaSkafia and @jcgiret, but I wanted to post a full and final solution.

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