""" Author(s): Matthew Loper See LICENCE.txt for licensing and contact information. """ import scipy.sparse as sp import numpy as np def row(A): return A.reshape((1, -1)) def col(A): return A.reshape((-1, 1)) class timer(object): def time(self): import time return time.time() def __init__(self): self._elapsed = 0 self._start = self.time() def __call__(self): if self._start is not None: return self._elapsed + self.time() - self._start else: return self._elapsed def pause(self): assert self._start is not None self._elapsed += self.time() - self._start self._start = None def resume(self): assert self._start is None self._start = self.time() def dfs_do_func_on_graph(node, func, *args, **kwargs): ''' invoke func on each node of the dr graph ''' for _node in node.tree_iterator(): func(_node, *args, **kwargs) def sparse_is_desireable(lhs, rhs): ''' Examines a pair of matrices and determines if the result of their multiplication should be sparse or not. ''' return False if len(lhs.shape) == 1: return False else: lhs_rows, lhs_cols = lhs.shape if len(rhs.shape) == 1: rhs_rows = 1 rhs_cols = rhs.size else: rhs_rows, rhs_cols = rhs.shape result_size = lhs_rows * rhs_cols if sp.issparse(lhs) and sp.issparse(rhs): return True elif sp.issparse(lhs): lhs_zero_rows = lhs_rows - np.unique(lhs.nonzero()[0]).size rhs_zero_cols = np.all(rhs==0, axis=0).sum() elif sp.issparse(rhs): lhs_zero_rows = np.all(lhs==0, axis=1).sum() rhs_zero_cols = rhs_cols- np.unique(rhs.nonzero()[1]).size else: lhs_zero_rows = np.all(lhs==0, axis=1).sum() rhs_zero_cols = np.all(rhs==0, axis=0).sum() num_zeros = lhs_zero_rows * rhs_cols + rhs_zero_cols * lhs_rows - lhs_zero_rows * rhs_zero_cols # A sparse matrix uses roughly 16 bytes per nonzero element (8 + 2 4-byte inds), while a dense matrix uses 8 bytes per element. So the break even point for sparsity is 50% nonzero. But in practice, it seems to be that the compression in a csc or csr matrix gets us break even at ~65% nonzero, which lets us say 50% is a conservative, worst cases cutoff. return (float(num_zeros) / float(size)) >= 0.5 def convert_inputs_to_sparse_if_necessary(lhs, rhs): ''' This function checks to see if a sparse output is desireable given the inputs and if so, casts the inputs to sparse in order to make it so. ''' if not sp.issparse(lhs) or not sp.issparse(rhs): if sparse_is_desireable(lhs, rhs): if not sp.issparse(lhs): lhs = sp.csc_matrix(lhs) #print "converting lhs into sparse matrix" if not sp.issparse(rhs): rhs = sp.csc_matrix(rhs) #print "converting rhs into sparse matrix" return lhs, rhs