gias3 3.0.1

Geometry Image-Analysis Statistics version 3 (GIAS3)

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.

Modules

This meta-package includes the following modules:

• gias3.common

• gias3.fieldwork

• gias3.registration

• gias3.learning

• gias3.image-analysis

• gias3.mesh

• gias3.applications (optional)

• gias3.examples (optional)

• gias3.io (optional)

• gias3.testing (optional)

• gias3.visualisation (optional)

• gias3.mapclientpluginutilities (optional)

• gias3.musculoskeletal (optional - requires: OpenSIM)

See Installing optional modules for more information.

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

• OpenSIM (required for gias3.musculoskeletal)

Installation

Linux

1. If you would like to use in-built visualisation modules, first install Mayavi for your distribution, else you can skip this step.

   1. Install VTK and VTK python bindings (e.g., through your package manager). VTK 5.10 is the most stable in my experience with Mayavi.

   2. Install mayavi through your package manager (e.g. sudo apt-get install mayavi2) or pip (e.g., pip install –user mayavi)

2. If you would like to use the GIAS3 Musculoskeletal module, you must first install OpenSIM to your Python scripting environment. Otherwise, you may skip this step. See Installing OpenSIM for more information.

3. Install GIAS3

   pip install gias3

Windows

1. If you would like to use in-built visualisation modules, first install Mayavi, else you can skip this step.

   • If you are using Anaconda to manage your Python environment, use conda to install Mayavi (e.g., conda install mayavi), otherwise, use pip (e.g., pip install mayavi).

2. If you would like to use the GIAS3 Musculoskeletal module, you must first install OpenSIM to your Python scripting environment. Otherwise, you may skip this step. See Installing OpenSIM for more information.

3. Install GIAS3

   pip install gias3

Installing optional modules

Optional GIAS3 modules can be included in the installation by passing the corresponding keywords to pip:

• apps = gias3.applications

• examples = gias3.examples

• tests = gias3.testing

• vis = gias3.visualisation

• io = gias3.io

• mapclient = gias3.mapclientpluginutilities

• musculoskeletal = gias3.musculoskeletal

For example, if you want to include the modules gias3.applications and gias3.visualisation in addition to the default modules, use the command,

pip install gias3[apps,vis]

Installing OpenSIM

To be able to make use of the GIAS3 Musculoskeletal module, the user must first install OpenSIM to their Python scripting environment.

First, download OpenSIM from this page.

Then, follow the instructions here to install OpenSIM to your Python scripting environment.

Tutorials

• Using GIAS3 with MAP Client for lower limb model generation

• Using GIAS3 for statistical shape modelling

License

GIAS3 is under the Mozilla Public license 2.0.