statistics/write_a_metric.py

This simple example shows how to write an IMP.statistics.Metric in Python.

## \example statistics/write_a_metric.py
# This simple example shows how to write an IMP.statistics.Metric in Python.

import IMP.statistics
import math
import random
import sys

IMP.setup_from_argv(sys.argv, "write a metric")


class MyMetric(IMP.statistics.Metric):

    """Define a metric on a list of floating point numbers based on
       their difference"""

    def __init__(self, nums):
        """Store the list of numbers to measure distances between"""
        IMP.statistics.Metric.__init__(self, "MyMetric%1%")
        self._nums = nums

    def get_distance(self, i, j):
        "Return the magnitude of the distance between the ith and jth number"
        return math.fabs(self._nums[i] - self._nums[j])

    def get_number_of_items(self):
        return len(self._nums)


mm = MyMetric([random.uniform(0, 1) for i in range(0, 15)])

cc = IMP.statistics.create_centrality_clustering(mm, .1, 3)
print(cc.get_number_of_clusters())