MarcCote

import resource
import numpy as np
from scipy import weave

x = np.ones(1e6, dtype=np.float32)

# There is no memory leak, when we let PyArray_CumSum creates the output array, i.e. when out=NULL.
code_good = r"""
npy_intp shape[1] = { PyArray_SIZE(x_array) };
int dtype = PyArray_DTYPE(x_array)->type_num;

MarcCote

import numpy as np
import theano
import theano.tensor as T
print "Version:", theano.version.version

print "=Theano="
A = T.zeros((2,10))
B = T.zeros((30, 10))

print "Shape of A:", A.eval().shape

MarcCote

import numpy as np
from nibabel import trackvis as tv
from dipy.segment.quickbundles import QuickBundles
from dipy.data import get_data

fname = get_data('fornix')

streams, hdr = tv.read(fname)
streamlines = [i[0] for i in streams]
qb = QuickBundles(streamlines, dist_thr=10., pts=12)

MarcCote

from dipy.viz import fvtk

import numpy as np

from numpy.testing import measure
from nose.tools import assert_equal, assert_almost_equal
from numpy.testing import assert_array_equal, assert_array_almost_equal

norm = lambda x: np.sqrt(np.sum(x**2))

MarcCote

ctypedef float[:,:] float2d
ctypedef double[:,:] double2d

ctypedef fused Line:
    float2d
    double2d

cdef class Metric:
    cdef float dist(Metric self, Line line) nogil:
        pass

MarcCote

import numpy as np
import resource

import metric


def test_memory_leak():
    NB_LOOPS = 20
    NB_LINES = 10000
    NB_POINTS = 100

MarcCote

import theano
import numpy as np
from theano.sandbox.rng_mrg import MRG_RandomStreams as RandomStreams
theano_rng = RandomStreams(42)

# This one works fine
print np.sum(theano_rng.uniform(size=(10000, 784), dtype=theano.config.floatX, nstreams=10000).eval(), 1)

# This one produces NaN at the end
print np.sum(theano_rng.uniform(size=(10000, 784), dtype=theano.config.floatX, nstreams=10000*400).eval(), 1)

MarcCote

import theano
import theano.tensor as T
import numpy as np

A = theano.shared(np.array([1, 2, 3, 4, 5]))

print "Theano"
print T.sum(T.stack(A, A), axis=0).eval()
print T.sum(T.stack(A, A), axis=1).eval()

MarcCote

import os
import argparse

import nibabel as nib
from nibabel.streamlines import Field
from nibabel.orientations import aff2axcodes


def build_argparser():
    DESCRIPTION = "Convert tractograms (TCK -> TRK)."

MarcCote

import os
import argparse
import nibabel as nib


def build_argparser():
    DESCRIPTION = "Convert tractograms (TRK -> TCK)."
    p = argparse.ArgumentParser(description=DESCRIPTION)
    p.add_argument('tractograms', metavar='bundle', nargs="+", help='list of tractograms.')
    p.add_argument('-f', '--force', action="store_true", help='overwrite existing output files.')