Geometry Image-Analysis Statistics version 3 (GIAS3)
Project description
A Python library for tools used in musculoskeletal modelling. Includes tools for parametric meshing, registration, image analysis, statistical shape modelling, and 3-D visualisation using Mayavi.
Installation order
gias3.common
gias3.fieldwork
gias3.registration
gias3.learning
gias3.image-analysis
gias3.mesh
gias3.io
gias3.examples
gias3.applications
gias3.mapclientpluginutilities
gias3.testing
gias3.musculoskeletal (requires: OpenSIM)
Optional dependencies
VTK and VTK Python bindings (for mesh processing)
Mayavi (for 3-D visualisation, requires Numpy, VTK, wxPython, configobj)
PyCSG (for generating constructive solids)
pydicom (for reading DICOM images)
Cython (speeds up active shape model and random forest segmentation)
matplotlib for some inbuilt plotting functions
Installation
Linux
If you would like to use in-built visualisation modules, first install Mayavi for you distribution, else you can skip this step.
Install VTK and VTK python bindings (e.g. through your package manager). VTK 5.10 is the most stable in my experience with Mayavi.
Install mayavi through your package manager (e.g. sudo apt-get install mayavi2) or pip (e.g. pip install –user mayavi)
Install GIAS 3
pip install gias3
Windows
The most painless way to install the python dependencies required by GIAS3 is to install the umbrella package Anaconda.
If you would like to use in-built visualisation modules, install Mayavi. In you installed Anaconda, from the Anaconda commandline,
conda install mayavi
Download the wheel and from the Anaconda commandline
pip install --user [path/to/wheel]
Examples
Example of some the capabilities of GIAS3 can be found in the gias3/examples/ directory. We are working to add more examples.
Tutorials
License
GIAS3 is under the Mozilla Public license 2.0.
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