example.py

import numpy as np

from experiments import init_experiment, QuickParams
from observations import DataMatrix

###
### First follow the configuration directions in README.md. Then run the following:
###
###     python example.py
###     python experiments.py everything example
###

def read_array(fname):
    return np.array([map(float, line.split()) for line in open(fname)])

def read_list(fname):
    return map(str.strip, open(fname).readlines())

def init():
    X = read_array('example_data/animals-data.txt')
    row_labels = read_list('example_data/animals-names.txt')
    col_labels = read_list('example_data/animals-features.txt')

    # normalize to zero mean, unit variance
    X -= X.mean()
    X /= X.std()

    # since the data were binary, add a small amount of noise to prevent degeneracy
    X = np.random.normal(X, np.sqrt(0.1))

    data_matrix = DataMatrix.from_real_values(X, row_labels=row_labels, col_labels=col_labels)
    init_experiment('example', data_matrix, QuickParams(search_depth=2))
                                                           
if __name__ == '__main__':
    init()