ConvGeNCode/library/NNSearch.py

import math

import tensorflow as tf
import numpy as np
from sklearn.neighbors import NearestNeighbors
from library.timing import timing


class NNSearch:
    def __init__(self, nebSize=5, timingDict=None):
        self.nebSize = nebSize
        self.neighbourhoods = []
        self.timingDict = timingDict


    def timerStart(self, name):
        if self.timingDict is not None:
            if name not in self.timingDict:
                self.timingDict[name] = timing(name)

            self.timingDict[name].start()

    def timerStop(self, name):
        if self.timingDict is not None:
            if name in self.timingDict:
                self.timingDict[name].stop()

    def neighbourhoodOfItem(self, i):
        return self.neighbourhoods[i]


    def fit(self, X, nebSize=None):
        self.timerStart("NN_fit_chained_init")
        if nebSize == None:
            nebSize = self.nebSize

        nPoints = len(X)
        nFeatures = len(X[0])

        neigh = NearestNeighbors(n_neighbors=nebSize)
        neigh.fit(X)
        self.timerStop("NN_fit_chained_init")
        self.timerStart("NN_fit_chained_toList")
        self.neighbourhoods = [
                (neigh.kneighbors([x], nebSize, return_distance=False))[0]
                for (i, x) in enumerate(X)
                ]
        self.timerStop("NN_fit_chained_toList")