Gael Varoquaux GaelVaroquaux

Cython example of exposing C-computed arrays in Python without data copies

The goal of this example is to show how an existing C codebase for numerical computing (here c_code.c) can be wrapped in Cython to be exposed in Python.

The meat of the example is that the data is allocated in C, but exposed in Python without a copy using the PyArray_SimpleNewFromData numpy

Bootstrapping a SciPy-related community project

This document is a lightning talk: it only gives pointers, you need to Google and read references

	import time
	import sys

	import numpy as np
	from numpy.lib.stride_tricks import as_strided
	from math import sqrt
	from scipy import linalg
	from scikits.learn.linear_model import Lasso, lars_path
	from joblib import Parallel, delayed

	"""A helper node to concatenate images in nipype"""

	import os

	from nipype.interfaces.base import TraitedSpec, File, CommandLineInputSpec, CommandLine
	from nipype.utils.misc import isdefined

	class ConcatImgInputSpec(CommandLineInputSpec):
	in_file1 = File(exists=True, argstr="-append %s",
	position=1, mandatory=True)

	import numpy as np

	def _compute_bins(x, n_bins=10):
	""" Find optimal bins from a univariate distribution

	Parameters
	===========
	x: 1D array-like
	Samples
	n_bins: integer

	#!/usr/bin/env python
	# gvaroquaux (adapted from tdh.net gmail com)
	# 31.August.2011
	# try clustering module in scikits.learn
	import numpy as np
	from scipy import linalg

	from sklearn.metrics.pairwise import euclidean_distances
	from sklearn.cluster import SpectralClustering

	"""
	Benching I/O with joblib and other libraries. Comment and
	un-comment what you are interested in.

	Warning: this is slow, and the benchs are easily offset by other disk
	activity.
	"""
	import os
	import time
	import shutil

	# Licence : BSD
	# Author: Gael Varoquaux

	from time import time

	import numpy as np
	import pylab as pl
	from scipy import linalg, ndimage

	from sklearn import linear_model

	import numpy as np
	import sklearn.linear_model as lm

	X = np.array([[ -2.18252949e-01, -8.21949578e-02, -4.64055457e-02,
	-1.78405908e-01, -1.93863740e-01, 5.30667625e-02,
	1.83851107e-01, 1.23426449e-01, 1.97396315e-01,
	-2.12615837e-01, 7.06452283e-02, -1.94509405e-01,
	-9.77929516e-02, 2.07135018e-01, -3.40368338e-02,
	2.02970673e-01, -2.28669466e-01, 4.17398420e-02,
	1.80163132e-01, 3.24254938e-02, -2.41198452e-03,

Gael Varoquaux GaelVaroquaux

Cython example of exposing C-computed arrays in Python without data copies

Bootstrapping a SciPy-related community project

Goal