The code written during my Bachelor Thesis "Classification of Human Whole-Body Motion using Hidden Markov Models".
Python
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README.md

This code was written during the course of my Bachelor thesis Classification of Human Whole-Body Motion using Hidden Markov Models. Some things might be broken and I definitely don't recommend to use any of the code in any sort of production application. However, for research purposes this code might be useful so I decided to open-source it. Use at your own risk!

Requirements

Use pip to install most requriements (pip install -r requriements.txt). Sometimes this causes problems if Cython, numpy and scipy are not already installed, in which case this needs to be done manually.

Additionally, some packages must be installed that are not provided by pip.

pySimox and pyMMM

pySimox and pyMMM must be installed manually as well. To build them, perform the following steps:

git submodule update --init --recursive
cd vendor/pySimox/build
cmake ..
make
cp _pysimox.so ../../../lib/python2.7/site-packages/_pysimox.so
cp pysimox.py ../../../lib/python2.7/site-packages/pysimox.py
cd ../pyMMM/build
cmake ..
make
cp _pymmm.so ../../../lib/python2.7/site-packages/_pymmm.so
cp pymmm.py ../../../lib/python2.7/site-packages/pymmm.py

Note that the installation script may need some fine-tuning. Additionally, this assumes that all virtualenv is set up in the root of this git repo.

Basic Usage

This repo contains two main programs: dataset.py and evaluate_new.py. All of them are located in src and should be run from this directory. There are some additional files in there, some of them are out-dated and should be deleted (e.g. evaluate.py), some of them are really just scripts and should be moved to the scripts folder eventually.

The dataset tool

The dataset tool is concerened with handling everything related to datasets: plot plots features, export saves a dataset in a variety of formats, report prints details about a dataset and check performs a consistency check. Additionally, export-all can be used to create a dataset that contains all features (normalized and unnormalized) by merging Vicon C3D and MMM files into one giant file. A couple of examples:

  • python dataset.py ../data/dataset1.json plot --features root_pos plots the root_pos feature of all motions in the dataset; the dataset can be a JSON manifest or a pickled dataset
  • python dataset.py ../data/dataset1.json export --output ~/export.pkl exports dataset1 as a single pickled file; usually a JSON manifest is used
  • python dataset.py ../data/dataset1.json export-all --output ~/export_all.pkl exports dataset1 by combining vicon and MMM files and by computing both the normalized and unnormalized version of all features. It also performs normalization on the vicon data by using additional information from the MMM data (namely the root_pos and root_rot); the dataset has to be a JSON manifest
  • python dataset.py ../data/dataset1.json report prints details about a dataset; the dataset can be a JSON manifest or a pickled dataset
  • python dataset.py ../data/dataset1.json check performs a consistency check of a dataset; the manifest has to be a JSON manifest

Additional parameters are avaialble for most commands. Use dataset --help to get an overview.

The evaluate_new tool

The evaluate_new tool can be used to perform feature selection (using the feature command) or to evaluate different types of models with decision makers (by using the model command). It is important to note that the evaluate_new tool expects a pickled version of the dataset, hence export or export_all must be used to prepare a dataset. This is to avoid the computational complexity.

A couple of examples:

  • python evaluate_new.py model ../data/export_all.pkl --features normalized_joint_pos normalized_root_pos --decision-maker log-regression --n-states 5 --model fhmm-seq --output-dir ~/out trains a HMM ensemble with each HMM having 5 states on the normalized_joint_pos and normalized_root_pos features and uses logistic regression to perform the final predicition. The results are also saved in the directory ~/out
  • python evaluate_new.py features ../data/export_all.pkl --features normalized_joint_pos normalized_root_pos --measure wasserstein performs feature selection using the starting set normalized_joint_pos normalized_root_pos and the wasserstein measure

From dataset to result

First, define a JSON manifest dataset.json that links together the individual motions and pick labels. Next, export the dataset by using python dataset.py ../data/dataset.json export-all --output ../data/dataset_all.pkl. If you need smoothing, simply load the dataset (using pickle.load()), call smooth_features() on the Dataset object and dump it to a new file. There's currently no script for this but it can be done using three lines and the interactive python interpreter. Next, perform feature selection using python evaluate_new.py features ../data/dataset_all.pkl --features <list of features> --measure wasserstein --output-dir ~/features --transformers minmax-scaler. You'll want to use the minmax scaler transformer to avoid numerical problems during training. This will probably take a while. The results (at ~/features) will give you the best feature subsets that were found. Next, use those features to train an HMM ensemble: python evaluate_new model ../data/dataset_all.pkl --features <best features> --model fhmm-seq --n-chains 2 --n-states 10 --n-training-iter 30 -decision-maker log-regression --transformers minmax-scaler --output-dir ~/train (again, the minmax-scaler is almost always a good idea). The results will be in ~/output.