This repository contains the material for the tutorial at SciPy 2022 conducted by Prabhu Ramachandran and Matt McCormick.
This tutorial will introduce the participants to 3D visualization using tools that are written with rendering support from VTK library. We start the workshop with Mayavi then some itkwidgets Mayavi is an Open Source, Python package for general purpose 3D visualization and provides a very Python-friendly API. itkwidgets are interactive Jupyter widgets to visualize images, point sets, and meshes. Mayavi makes use of VTK, and itkwidgets supports VTK data structures and supports VTK-based rendering.
The tutorial will provide an overview of 3D visualization in Python. Then, we
will introduce Mayavi, itkwidgets, and VTK and what they can offer for the
scientist/researcher. The tutorial wil cover mechanisms, behavior, benefits,
and requirements of client-side and server-side rendering. We will then use
the mayavi.mlab module to quickly produce visualizations that are useful
for scientists and engineers with a minimum of effort. This will cover several
basic visualizations. We then move on to exploring VTK datasets and how they
may be easily created using NumPy arrays and quickly visualized with Mayavi.
We will then explore visualizing the data on a Jupyter notebook followed by the creation of custom ipywidget Jupyter applications for large images and meshes with the itkwidgets package along with Mayavi. We will explore the generation of graphical applications from Python dashboarding and Jupyter notebook system. We will learn how to use 3D visualization to improve deep learning model development.
Attendees should have a computer with any Python version > 3.6. We primarily require that you have Mayavi and itkwidgets installed.
You will need Python versions < 3.10 if you are intending to install via pip as VTK wheels do not exist for Python 3.10.x. You can also install via conda / mamba.
Installation should be relatively simple
$ pip install numpy vtk pyqt5
$ pip install mayavi
If for some reason pyqt5 gives you problems, you can also try the following:
$ pip install pyside2
We also require jupyter and itkwidgets for the workshop so please also install the following:
$ pip install jupyter ipywidgets ipyevents itkwidgets
To install Mayavi and itkwidgets with conda try the following:
conda create -n py3dviz python=3.8
conda activate py3dviz
conda install -c conda-forge numpy jupyter ipywidgets ipyevents mayavi itkwidgets
As of July 12th, 2022, this will install python-3.8.13, Mayavi-4.8.0 and itkwidgets-0.32.2.
In case we have a new release after these which may be necessary as the latest release will incorporate better interactions between Mayavi and itkwidgets. If the version on conda-forge is not updated in time before the tutorial, you can do the following to obtain the latest versions. We remove the mayavi from conda as it is an older version.
$ pip install -U mayavi itkwidgets
Try the following:
$ pip install ipython
$ ipython
In []: %gui qt
In []: from mayavi import mlab
In []: mlab.test_plot3d()
This should produce a window that is interactive and usable without any tracebacks or exceptions.