Viewing file:  timer_comparison.py (17.05 KB) -rw-r--r--
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import timeit
import numpy as np
from numpy import float_
import np.core.fromnumeric as fromnumeric
from np.testing.utils import build_err_msg
np.seterr(all='ignore')
pi = np.pi
class moduletester:
#-----------------------------------
def __init__(self, module):
self.module = module
self.allequal = module.allequal
self.arange = module.arange
self.array = module.array
# self.average = module.average
self.concatenate = module.concatenate
self.count = module.count
self.equal = module.equal
self.filled = module.filled
self.getmask = module.getmask
self.getmaskarray = module.getmaskarray
self.id = id
self.inner = module.inner
self.make_mask = module.make_mask
self.masked = module.masked
self.masked_array = module.masked_array
self.masked_values = module.masked_values
self.mask_or = module.mask_or
self.nomask = module.nomask
self.ones = module.ones
self.outer = module.outer
self.repeat = module.repeat
self.resize = module.resize
self.sort = module.sort
self.take = module.take
self.transpose = module.transpose
self.zeros = module.zeros
self.MaskType = module.MaskType
try:
self.umath = module.umath
except AttributeError:
self.umath = module.core.umath
self.testnames = []
#........................
def assert_array_compare(self, comparison, x, y, err_msg='', header='',
fill_value=True):
"""Asserts that a comparison relation between two masked arrays is satisfied
elementwise."""
xf = self.filled(x)
yf = self.filled(y)
m = self.mask_or(self.getmask(x), self.getmask(y))
x = self.filled(self.masked_array(xf, mask=m), fill_value)
y = self.filled(self.masked_array(yf, mask=m), fill_value)
if (x.dtype.char != "O"):
x = x.astype(float_)
if isinstance(x, np.ndarray) and x.size > 1:
x[np.isnan(x)] = 0
elif np.isnan(x):
x = 0
if (y.dtype.char != "O"):
y = y.astype(float_)
if isinstance(y, np.ndarray) and y.size > 1:
y[np.isnan(y)] = 0
elif np.isnan(y):
y = 0
try:
cond = (x.shape==() or y.shape==()) or x.shape == y.shape
if not cond:
msg = build_err_msg([x, y],
err_msg
+ '\n(shapes %s, %s mismatch)' % (x.shape,
y.shape),
header=header,
names=('x', 'y'))
assert cond, msg
val = comparison(x,y)
if m is not self.nomask and fill_value:
val = self.masked_array(val, mask=m)
if isinstance(val, bool):
cond = val
reduced = [0]
else:
reduced = val.ravel()
cond = reduced.all()
reduced = reduced.tolist()
if not cond:
match = 100-100.0*reduced.count(1)/len(reduced)
msg = build_err_msg([x, y],
err_msg
+ '\n(mismatch %s%%)' % (match,),
header=header,
names=('x', 'y'))
assert cond, msg
except ValueError:
msg = build_err_msg([x, y], err_msg, header=header, names=('x', 'y'))
raise ValueError(msg)
#............................
def assert_array_equal(self, x, y, err_msg=''):
"""Checks the elementwise equality of two masked arrays."""
self.assert_array_compare(self.equal, x, y, err_msg=err_msg,
header='Arrays are not equal')
#----------------------------------
def test_0(self):
"Tests creation"
x = np.array([1.,1.,1.,-2., pi/2.0, 4., 5., -10., 10., 1., 2., 3.])
m = [1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0]
xm = self.masked_array(x, mask=m)
xm[0]
#----------------------------------
def test_1(self):
"Tests creation"
x = np.array([1.,1.,1.,-2., pi/2.0, 4., 5., -10., 10., 1., 2., 3.])
y = np.array([5.,0.,3., 2., -1., -4., 0., -10., 10., 1., 0., 3.])
a10 = 10.
m1 = [1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0]
m2 = [0, 0, 1, 0, 0, 1, 1, 0, 0, 0 ,0, 1]
xm = self.masked_array(x, mask=m1)
ym = self.masked_array(y, mask=m2)
z = np.array([-.5, 0., .5, .8])
zm = self.masked_array(z, mask=[0,1,0,0])
xf = np.where(m1, 1.e+20, x)
xm.set_fill_value(1.e+20)
#.....
assert((xm-ym).filled(0).any())
#fail_if_equal(xm.mask.astype(int_), ym.mask.astype(int_))
s = x.shape
assert(xm.size == reduce(lambda x,y:x*y, s))
assert(self.count(xm) == len(m1) - reduce(lambda x,y:x+y, m1))
#.....
for s in [(4,3), (6,2)]:
x.shape = s
y.shape = s
xm.shape = s
ym.shape = s
xf.shape = s
assert(self.count(xm) == len(m1) - reduce(lambda x,y:x+y, m1))
#----------------------------------
def test_2(self):
"Tests conversions and indexing"
x1 = np.array([1,2,4,3])
x2 = self.array(x1, mask=[1,0,0,0])
x3 = self.array(x1, mask=[0,1,0,1])
x4 = self.array(x1)
# test conversion to strings
junk, garbage = str(x2), repr(x2)
# assert_equal(np.sort(x1), self.sort(x2, fill_value=0))
# tests of indexing
assert type(x2[1]) is type(x1[1])
assert x1[1] == x2[1]
# assert self.allequal(x1[2],x2[2])
# assert self.allequal(x1[2:5],x2[2:5])
# assert self.allequal(x1[:],x2[:])
# assert self.allequal(x1[1:], x3[1:])
x1[2] = 9
x2[2] = 9
self.assert_array_equal(x1,x2)
x1[1:3] = 99
x2[1:3] = 99
# assert self.allequal(x1,x2)
x2[1] = self.masked
# assert self.allequal(x1,x2)
x2[1:3] = self.masked
# assert self.allequal(x1,x2)
x2[:] = x1
x2[1] = self.masked
# assert self.allequal(self.getmask(x2),self.array([0,1,0,0]))
x3[:] = self.masked_array([1,2,3,4],[0,1,1,0])
# assert self.allequal(self.getmask(x3), self.array([0,1,1,0]))
x4[:] = self.masked_array([1,2,3,4],[0,1,1,0])
# assert self.allequal(self.getmask(x4), self.array([0,1,1,0]))
# assert self.allequal(x4, self.array([1,2,3,4]))
x1 = np.arange(5)*1.0
x2 = self.masked_values(x1, 3.0)
# assert self.allequal(x1,x2)
# assert self.allequal(self.array([0,0,0,1,0], self.MaskType), x2.mask)
x1 = self.array([1,'hello',2,3],object)
x2 = np.array([1,'hello',2,3],object)
s1 = x1[1]
s2 = x2[1]
assert x1[1:1].shape == (0,)
# Tests copy-size
n = [0,0,1,0,0]
m = self.make_mask(n)
m2 = self.make_mask(m)
assert(m is m2)
m3 = self.make_mask(m, copy=1)
assert(m is not m3)
#----------------------------------
def test_3(self):
"Tests resize/repeat"
x4 = self.arange(4)
x4[2] = self.masked
y4 = self.resize(x4, (8,))
assert self.allequal(self.concatenate([x4,x4]), y4)
assert self.allequal(self.getmask(y4),[0,0,1,0,0,0,1,0])
y5 = self.repeat(x4, (2,2,2,2), axis=0)
self.assert_array_equal(y5, [0,0,1,1,2,2,3,3])
y6 = self.repeat(x4, 2, axis=0)
assert self.allequal(y5, y6)
y7 = x4.repeat((2,2,2,2), axis=0)
assert self.allequal(y5,y7)
y8 = x4.repeat(2,0)
assert self.allequal(y5,y8)
#----------------------------------
def test_4(self):
"Test of take, transpose, inner, outer products"
x = self.arange(24)
y = np.arange(24)
x[5:6] = self.masked
x = x.reshape(2,3,4)
y = y.reshape(2,3,4)
assert self.allequal(np.transpose(y,(2,0,1)), self.transpose(x,(2,0,1)))
assert self.allequal(np.take(y, (2,0,1), 1), self.take(x, (2,0,1), 1))
assert self.allequal(np.inner(self.filled(x,0), self.filled(y,0)),
self.inner(x, y))
assert self.allequal(np.outer(self.filled(x,0), self.filled(y,0)),
self.outer(x, y))
y = self.array(['abc', 1, 'def', 2, 3], object)
y[2] = self.masked
t = self.take(y,[0,3,4])
assert t[0] == 'abc'
assert t[1] == 2
assert t[2] == 3
#----------------------------------
def test_5(self):
"Tests inplace w/ scalar"
x = self.arange(10)
y = self.arange(10)
xm = self.arange(10)
xm[2] = self.masked
x += 1
assert self.allequal(x, y+1)
xm += 1
assert self.allequal(xm, y+1)
x = self.arange(10)
xm = self.arange(10)
xm[2] = self.masked
x -= 1
assert self.allequal(x, y-1)
xm -= 1
assert self.allequal(xm, y-1)
x = self.arange(10)*1.0
xm = self.arange(10)*1.0
xm[2] = self.masked
x *= 2.0
assert self.allequal(x, y*2)
xm *= 2.0
assert self.allequal(xm, y*2)
x = self.arange(10)*2
xm = self.arange(10)*2
xm[2] = self.masked
x /= 2
assert self.allequal(x, y)
xm /= 2
assert self.allequal(xm, y)
x = self.arange(10)*1.0
xm = self.arange(10)*1.0
xm[2] = self.masked
x /= 2.0
assert self.allequal(x, y/2.0)
xm /= self.arange(10)
self.assert_array_equal(xm, self.ones((10,)))
x = self.arange(10).astype(float_)
xm = self.arange(10)
xm[2] = self.masked
id1 = self.id(x.raw_data())
x += 1.
#assert id1 == self.id(x.raw_data())
assert self.allequal(x, y+1.)
def test_6(self):
"Tests inplace w/ array"
x = self.arange(10, dtype=float_)
y = self.arange(10)
xm = self.arange(10, dtype=float_)
xm[2] = self.masked
m = xm.mask
a = self.arange(10, dtype=float_)
a[-1] = self.masked
x += a
xm += a
assert self.allequal(x,y+a)
assert self.allequal(xm,y+a)
assert self.allequal(xm.mask, self.mask_or(m,a.mask))
x = self.arange(10, dtype=float_)
xm = self.arange(10, dtype=float_)
xm[2] = self.masked
m = xm.mask
a = self.arange(10, dtype=float_)
a[-1] = self.masked
x -= a
xm -= a
assert self.allequal(x,y-a)
assert self.allequal(xm,y-a)
assert self.allequal(xm.mask, self.mask_or(m,a.mask))
x = self.arange(10, dtype=float_)
xm = self.arange(10, dtype=float_)
xm[2] = self.masked
m = xm.mask
a = self.arange(10, dtype=float_)
a[-1] = self.masked
x *= a
xm *= a
assert self.allequal(x,y*a)
assert self.allequal(xm,y*a)
assert self.allequal(xm.mask, self.mask_or(m,a.mask))
x = self.arange(10, dtype=float_)
xm = self.arange(10, dtype=float_)
xm[2] = self.masked
m = xm.mask
a = self.arange(10, dtype=float_)
a[-1] = self.masked
x /= a
xm /= a
#----------------------------------
def test_7(self):
"Tests ufunc"
d = (self.array([1.0, 0, -1, pi/2]*2, mask=[0,1]+[0]*6),
self.array([1.0, 0, -1, pi/2]*2, mask=[1,0]+[0]*6),)
for f in ['sqrt', 'log', 'log10', 'exp', 'conjugate',
# 'sin', 'cos', 'tan',
# 'arcsin', 'arccos', 'arctan',
# 'sinh', 'cosh', 'tanh',
# 'arcsinh',
# 'arccosh',
# 'arctanh',
# 'absolute', 'fabs', 'negative',
# # 'nonzero', 'around',
# 'floor', 'ceil',
# # 'sometrue', 'alltrue',
# 'logical_not',
# 'add', 'subtract', 'multiply',
# 'divide', 'true_divide', 'floor_divide',
# 'remainder', 'fmod', 'hypot', 'arctan2',
# 'equal', 'not_equal', 'less_equal', 'greater_equal',
# 'less', 'greater',
# 'logical_and', 'logical_or', 'logical_xor',
]:
#print f
try:
uf = getattr(self.umath, f)
except AttributeError:
uf = getattr(fromnumeric, f)
mf = getattr(self.module, f)
args = d[:uf.nin]
ur = uf(*args)
mr = mf(*args)
self.assert_array_equal(ur.filled(0), mr.filled(0), f)
self.assert_array_equal(ur._mask, mr._mask)
#----------------------------------
def test_99(self):
# test average
ott = self.array([0.,1.,2.,3.], mask=[1,0,0,0])
self.assert_array_equal(2.0, self.average(ott,axis=0))
self.assert_array_equal(2.0, self.average(ott, weights=[1., 1., 2., 1.]))
result, wts = self.average(ott, weights=[1.,1.,2.,1.], returned=1)
self.assert_array_equal(2.0, result)
assert(wts == 4.0)
ott[:] = self.masked
assert(self.average(ott,axis=0) is self.masked)
ott = self.array([0.,1.,2.,3.], mask=[1,0,0,0])
ott = ott.reshape(2,2)
ott[:,1] = self.masked
self.assert_array_equal(self.average(ott,axis=0), [2.0, 0.0])
assert(self.average(ott,axis=1)[0] is self.masked)
self.assert_array_equal([2.,0.], self.average(ott, axis=0))
result, wts = self.average(ott, axis=0, returned=1)
self.assert_array_equal(wts, [1., 0.])
w1 = [0,1,1,1,1,0]
w2 = [[0,1,1,1,1,0],[1,0,0,0,0,1]]
x = self.arange(6)
self.assert_array_equal(self.average(x, axis=0), 2.5)
self.assert_array_equal(self.average(x, axis=0, weights=w1), 2.5)
y = self.array([self.arange(6), 2.0*self.arange(6)])
self.assert_array_equal(self.average(y, None), np.add.reduce(np.arange(6))*3./12.)
self.assert_array_equal(self.average(y, axis=0), np.arange(6) * 3./2.)
self.assert_array_equal(self.average(y, axis=1), [self.average(x,axis=0), self.average(x,axis=0) * 2.0])
self.assert_array_equal(self.average(y, None, weights=w2), 20./6.)
self.assert_array_equal(self.average(y, axis=0, weights=w2), [0.,1.,2.,3.,4.,10.])
self.assert_array_equal(self.average(y, axis=1), [self.average(x,axis=0), self.average(x,axis=0) * 2.0])
m1 = self.zeros(6)
m2 = [0,0,1,1,0,0]
m3 = [[0,0,1,1,0,0],[0,1,1,1,1,0]]
m4 = self.ones(6)
m5 = [0, 1, 1, 1, 1, 1]
self.assert_array_equal(self.average(self.masked_array(x, m1),axis=0), 2.5)
self.assert_array_equal(self.average(self.masked_array(x, m2),axis=0), 2.5)
# assert(self.average(masked_array(x, m4),axis=0) is masked)
self.assert_array_equal(self.average(self.masked_array(x, m5),axis=0), 0.0)
self.assert_array_equal(self.count(self.average(self.masked_array(x, m4),axis=0)), 0)
z = self.masked_array(y, m3)
self.assert_array_equal(self.average(z, None), 20./6.)
self.assert_array_equal(self.average(z, axis=0), [0.,1.,99.,99.,4.0, 7.5])
self.assert_array_equal(self.average(z, axis=1), [2.5, 5.0])
self.assert_array_equal(self.average(z,axis=0, weights=w2), [0.,1., 99., 99., 4.0, 10.0])
#------------------------
def test_A(self):
x = self.arange(24)
y = np.arange(24)
x[5:6] = self.masked
x = x.reshape(2,3,4)
################################################################################
if __name__ == '__main__':
setup_base = "from __main__ import moduletester \n"\
"import numpy\n" \
"tester = moduletester(module)\n"
# setup_new = "import np.ma.core_ini as module\n"+setup_base
setup_cur = "import np.ma.core as module\n"+setup_base
# setup_alt = "import np.ma.core_alt as module\n"+setup_base
# setup_tmp = "import np.ma.core_tmp as module\n"+setup_base
(nrepeat, nloop) = (10, 10)
if 1:
for i in range(1,8):
func = 'tester.test_%i()' % i
# new = timeit.Timer(func, setup_new).repeat(nrepeat, nloop*10)
cur = timeit.Timer(func, setup_cur).repeat(nrepeat, nloop*10)
# alt = timeit.Timer(func, setup_alt).repeat(nrepeat, nloop*10)
# tmp = timeit.Timer(func, setup_tmp).repeat(nrepeat, nloop*10)
# new = np.sort(new)
cur = np.sort(cur)
# alt = np.sort(alt)
# tmp = np.sort(tmp)
print "#%i" % i +50*'.'
print eval("moduletester.test_%i.__doc__" % i)
# print "core_ini : %.3f - %.3f" % (new[0], new[1])
print "core_current : %.3f - %.3f" % (cur[0], cur[1])
# print "core_alt : %.3f - %.3f" % (alt[0], alt[1])
# print "core_tmp : %.3f - %.3f" % (tmp[0], tmp[1])
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