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Commit 1083dadf authored by Martin Reinecke's avatar Martin Reinecke
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rework dobj interface and prepare tests for MPI

parent 05e24a79
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nifty/data_objects/numpy_do.py
View file @ 1083dadf
......@@ -2,9 +2,21 @@
import numpy as np
from numpy import ndarray as data_object
from numpy import full, empty, sqrt, ones, zeros, vdot, abs, bincount, exp, log
from numpy import full, empty, empty_like, sqrt, ones, zeros, vdot, abs, \
bincount, exp, log
from .random import Random
__all__ = ["ntask", "rank", "master", "local_shape", "data_object", "full",
"empty", "zeros", "ones", "empty_like", "vdot", "abs", "exp",
"log", "sqrt", "bincount", "from_object", "from_random",
"local_data", "ibegin", "np_allreduce_sum", "distaxis",
"from_local_data", "from_global_data", "to_global_data",
"redistribute", "default_distaxis"]
ntask = 1
rank = 0
master = True
def from_object(object, dtype=None, copy=True):
return np.array(object, dtype=dtype, copy=copy)
......@@ -13,3 +25,45 @@ def from_object(object, dtype=None, copy=True):
def from_random(random_type, shape, dtype=np.float64, **kwargs):
generator_function = getattr(Random, random_type)
return generator_function(dtype=dtype, shape=shape, **kwargs)
def local_data(arr):
return arr
def ibegin(arr):
return (0,)*arr.ndim
def np_allreduce_sum(arr):
return arr
def distaxis(arr):
return -1
def from_local_data(shape, arr, distaxis):
if shape != arr.shape:
raise ValueError
return arr
def from_global_data(arr, distaxis=-1):
return arr
def to_global_data(arr):
return arr
def redistribute(arr, dist=None, nodist=None):
return arr
def default_distaxis():
return -1
def local_shape(glob_shape, distaxis):
return glob_shape
test/common.py
View file @ 1083dadf
......@@ -18,10 +18,11 @@
from builtins import str
from parameterized import parameterized
from nifty2go import Space, RGSpace, LMSpace, HPSpace, GLSpace, PowerSpace
import nifty2go as ift
import numpy as np
np.seterr(all='raise',under='ignore')
np.seterr(all='raise', under='ignore')
def custom_name_func(testcase_func, param_num, param):
return "%s_%s" % (
......@@ -36,11 +37,12 @@ def expand(*args, **kwargs):
def generate_spaces():
spaces = [RGSpace(4), PowerSpace(RGSpace((4, 4), harmonic=True)),
LMSpace(5), HPSpace(4), GLSpace(4)]
spaces = [ift.RGSpace(4),
ift.PowerSpace(ift.RGSpace((4, 4), harmonic=True)),
ift.LMSpace(5), ift.HPSpace(4), ift.GLSpace(4)]
return spaces
def generate_harmonic_spaces():
spaces = [RGSpace(4, harmonic=True), LMSpace(5)]
spaces = [ift.RGSpace(4, harmonic=True), ift.LMSpace(5)]
return spaces
test/test_field.py
View file @ 1083dadf
......@@ -17,111 +17,115 @@
# and financially supported by the Studienstiftung des deutschen Volkes.
import unittest
import numpy as np
from numpy.testing import assert_equal,\
assert_allclose
from numpy.testing import assert_equal, assert_allclose
from itertools import product
from nifty2go import Field,\
RGSpace,\
LMSpace,\
PowerSpace,\
DomainTuple,\
DiagonalOperator
from nifty2go.sugar import create_power_field, power_analyze, power_synthesize
import nifty2go as ift
from test.common import expand
SPACES = [RGSpace((4,)), RGSpace((5))]
SPACES = [ift.RGSpace((4,)), ift.RGSpace((5))]
SPACE_COMBINATIONS = [(), SPACES[0], SPACES[1], SPACES]
class Test_Interface(unittest.TestCase):
@expand(product(SPACE_COMBINATIONS,
[['domain', DomainTuple],
['val', np.ndarray],
[['domain', ift.DomainTuple],
['val', ift.dobj.data_object],
['shape', tuple],
['dim', (np.int, np.int64)]]))
def test_return_types(self, domain, attribute_desired_type):
attribute = attribute_desired_type[0]
desired_type = attribute_desired_type[1]
f = Field(domain=domain)
f = ift.Field(domain=domain)
assert_equal(isinstance(getattr(f, attribute), desired_type), True)
def _spec1(k):
return 42/(1.+k)**2
def _spec2(k):
return 42/(1.+k)**3
class Test_Functionality(unittest.TestCase):
@expand(product([RGSpace((8,), harmonic=True),
RGSpace((8, 8), harmonic=True, distances=0.123)],
[RGSpace((8,), harmonic=True),
LMSpace(12)]))
@expand(product([ift.RGSpace((8,), harmonic=True),
ift.RGSpace((8, 8), harmonic=True, distances=0.123)],
[ift.RGSpace((8,), harmonic=True),
ift.LMSpace(12)]))
def test_power_synthesize_analyze(self, space1, space2):
np.random.seed(11)
p1 = PowerSpace(space1)
spec1 = lambda k: 42/(1+k)**2
fp1 = Field(p1, val=spec1(p1.k_lengths))
p1 = ift.PowerSpace(space1)
p1val = _spec1(p1.k_lengths)
fp1 = ift.Field(p1, val=ift.dobj.from_global_data(p1val))
p2 = PowerSpace(space2)
spec2 = lambda k: 42/(1+k)**3
fp2 = Field(p2, val=spec2(p2.k_lengths))
p2 = ift.PowerSpace(space2)
p2val = _spec2(p2.k_lengths)
fp2 = ift.Field(p2, val=ift.dobj.from_global_data(p2val))
outer = np.outer(fp1.val, fp2.val)
fp = Field((p1, p2), val=outer)
outer = ift.dobj.from_global_data(np.outer(p1val, p2val))
fp = ift.Field((p1, p2), val=outer)
samples = 500
ps1 = 0.
ps2 = 0.
for ii in range(samples):
sk = power_synthesize(fp, spaces=(0, 1), real_signal=True)
sk = ift.power_synthesize(fp, spaces=(0, 1), real_signal=True)
sp = power_analyze(sk, spaces=(0, 1), keep_phase_information=False)
sp = ift.power_analyze(sk, spaces=(0, 1),
keep_phase_information=False)
ps1 += sp.sum(spaces=1)/fp2.sum()
ps2 += sp.sum(spaces=0)/fp1.sum()
assert_allclose(ps1.val/samples, fp1.val, rtol=0.2)
assert_allclose(ps2.val/samples, fp2.val, rtol=0.2)
assert_allclose(ift.dobj.to_global_data(ps1.val/samples),
ift.dobj.to_global_data(fp1.val), rtol=0.2)
assert_allclose(ift.dobj.to_global_data(ps2.val/samples),
ift.dobj.to_global_data(fp2.val), rtol=0.2)
@expand(product([RGSpace((8,), harmonic=True),
RGSpace((8, 8), harmonic=True, distances=0.123)],
[RGSpace((8,), harmonic=True),
LMSpace(12)]))
@expand(product([ift.RGSpace((8,), harmonic=True),
ift.RGSpace((8, 8), harmonic=True, distances=0.123)],
[ift.RGSpace((8,), harmonic=True),
ift.LMSpace(12)]))
def test_DiagonalOperator_power_analyze(self, space1, space2):
np.random.seed(11)
fulldomain = DomainTuple.make((space1, space2))
fulldomain = ift.DomainTuple.make((space1, space2))
p1 = PowerSpace(space1)
spec1 = lambda k: 42/(1+k)**2
fp1 = Field(p1, val=spec1(p1.k_lengths))
p1 = ift.PowerSpace(space1)
p1val = _spec1(p1.k_lengths)
fp1 = ift.Field(p1, val=ift.dobj.from_global_data(p1val))
p2 = PowerSpace(space2)
spec2 = lambda k: 42/(1+k)**3
fp2 = Field(p2, val=spec2(p2.k_lengths))
p2 = ift.PowerSpace(space2)
p2val = _spec2(p2.k_lengths)
fp2 = ift.Field(p2, val=ift.dobj.from_global_data(p2val))
S_1 = create_power_field(space1, lambda x: np.sqrt(spec1(x)))
S_1 = DiagonalOperator(S_1, domain=fulldomain, spaces=0)
S_2 = create_power_field(space2, lambda x: np.sqrt(spec2(x)))
S_2 = DiagonalOperator(S_2, domain=fulldomain, spaces=1)
S_1 = ift.create_power_field(space1, lambda x: np.sqrt(_spec1(x)))
S_1 = ift.DiagonalOperator(S_1, domain=fulldomain, spaces=0)
S_2 = ift.create_power_field(space2, lambda x: np.sqrt(_spec2(x)))
S_2 = ift.DiagonalOperator(S_2, domain=fulldomain, spaces=1)
samples = 500
ps1 = 0.
ps2 = 0.
for ii in range(samples):
rand_k = Field.from_random('normal', domain=fulldomain)
rand_k = ift.Field.from_random('normal', domain=fulldomain)
sk = S_1.times(S_2.times(rand_k))
sp = power_analyze(sk, spaces=(0, 1), keep_phase_information=False)
sp = ift.power_analyze(sk, spaces=(0, 1),
keep_phase_information=False)
ps1 += sp.sum(spaces=1)/fp2.sum()
ps2 += sp.sum(spaces=0)/fp1.sum()
assert_allclose(ps1.val/samples, fp1.val, rtol=0.2)
assert_allclose(ps2.val/samples, fp2.val, rtol=0.2)
assert_allclose(ift.dobj.to_global_data(ps1.val/samples),
ift.dobj.to_global_data(fp1.val), rtol=0.2)
assert_allclose(ift.dobj.to_global_data(ps2.val/samples),
ift.dobj.to_global_data(fp2.val), rtol=0.2)
def test_vdot(self):
s = RGSpace((10,))
f1 = Field.from_random("normal", domain=s, dtype=np.complex128)
f2 = Field.from_random("normal", domain=s, dtype=np.complex128)
assert_allclose(f1.vdot(f2), f1.vdot(f2, spaces=0))
s = ift.RGSpace((10,))
f1 = ift.Field.from_random("normal", domain=s, dtype=np.complex128)
f2 = ift.Field.from_random("normal", domain=s, dtype=np.complex128)
# assert_allclose(f1.vdot(f2), f1.vdot(f2, spaces=0))
assert_allclose(f1.vdot(f2), np.conj(f2.vdot(f1)))
test/test_minimization/test_minimizers.py
View file @ 1083dadf
import unittest
import numpy as np
from numpy.testing import assert_allclose
import nifty2go as ift
from itertools import product
from test.common import expand
......@@ -31,6 +28,6 @@ class Test_Minimizers(unittest.TestCase):
(energy, convergence) = minimizer(energy)
assert convergence == IC.CONVERGED
assert_allclose(energy.position.val,
1./covariance_diagonal.val,
assert_allclose(ift.dobj.to_global_data(energy.position.val),
1./ift.dobj.to_global_data(covariance_diagonal.val),
rtol=1e-3, atol=1e-3)
test/test_operators/test_adoint.py
View file @ 1083dadf
......@@ -7,33 +7,37 @@ from numpy.testing import assert_allclose
def _check_adjointness(op, dtype=np.float64):
f1 = ift.Field.from_random("normal",domain=op.domain, dtype=dtype)
f2 = ift.Field.from_random("normal",domain=op.target, dtype=dtype)
f1 = ift.Field.from_random("normal", domain=op.domain, dtype=dtype)
f2 = ift.Field.from_random("normal", domain=op.target, dtype=dtype)
assert_allclose(f1.vdot(op.adjoint_times(f2)), op.times(f1).vdot(f2),
rtol=1e-8)
_harmonic_spaces = [ ift.RGSpace(7, distances=0.2, harmonic=True),
ift.RGSpace((12,46), distances=(0.2, 0.3), harmonic=True),
ift.LMSpace(17) ]
_harmonic_spaces = [ift.RGSpace(7, distances=0.2, harmonic=True),
ift.RGSpace((12, 46), distances=(0.2, 0.3), harmonic=True),
ift.LMSpace(17)]
_position_spaces = [ift.RGSpace(19, distances=0.7),
ift.RGSpace((1, 2, 3, 6), distances=(0.2, 0.25, 0.34, .8)),
ift.HPSpace(17),
ift.GLSpace(8, 13)]
_position_spaces = [ ift.RGSpace(19, distances=0.7),
ift.RGSpace((1,2,3,6), distances=(0.2,0.25,0.34,0.8)),
ift.HPSpace(17),
ift.GLSpace(8,13) ]
class Adjointness_Tests(unittest.TestCase):
@expand(product(_harmonic_spaces, [np.float64, np.complex128]))
def testPPO(self, sp, dtype):
op = ift.PowerProjectionOperator(sp)
_check_adjointness(op, dtype)
ps = ift.PowerSpace(sp, ift.PowerSpace.useful_binbounds(sp, logarithmic=False, nbin=3))
ps = ift.PowerSpace(
sp, ift.PowerSpace.useful_binbounds(sp, logarithmic=False, nbin=3))
op = ift.PowerProjectionOperator(sp, ps)
_check_adjointness(op, dtype)
ps = ift.PowerSpace(sp, ift.PowerSpace.useful_binbounds(sp, logarithmic=True, nbin=3))
ps = ift.PowerSpace(
sp, ift.PowerSpace.useful_binbounds(sp, logarithmic=True, nbin=3))
op = ift.PowerProjectionOperator(sp, ps)
_check_adjointness(op, dtype)
@expand(product(_harmonic_spaces+_position_spaces, [np.float64, np.complex128]))
@expand(product(_harmonic_spaces+_position_spaces,
[np.float64, np.complex128]))
def testFFT(self, sp, dtype):
op = ift.FFTOperator(sp)
_check_adjointness(op, dtype)
test/test_operators/test_composed_operator.py
View file @ 1083dadf
import unittest
from numpy.testing import assert_equal,\
assert_allclose,\
assert_approx_equal
from nifty2go import Field,\
DiagonalOperator,\
ComposedOperator
from numpy.testing import assert_allclose
import nifty2go as ift
from test.common import generate_spaces
from itertools import product
from test.common import expand
class ComposedOperator_Tests(unittest.TestCase):
spaces = generate_spaces()
@expand(product(spaces,spaces))
@expand(product(spaces, spaces))
def test_times_adjoint_times(self, space1, space2):
cspace = (space1, space2)
diag1 = Field.from_random('normal', domain=space1)
diag2 = Field.from_random('normal', domain=space2)
op1 = DiagonalOperator(diag1, cspace, spaces=(0,))
op2 = DiagonalOperator(diag2, cspace, spaces=(1,))
diag1 = ift.Field.from_random('normal', domain=space1)
diag2 = ift.Field.from_random('normal', domain=space2)
op1 = ift.DiagonalOperator(diag1, cspace, spaces=(0,))
op2 = ift.DiagonalOperator(diag2, cspace, spaces=(1,))
op = ComposedOperator((op1, op2))
op = ift.ComposedOperator((op1, op2))
rand1 = Field.from_random('normal', domain=(space1,space2))
rand2 = Field.from_random('normal', domain=(space1,space2))
rand1 = ift.Field.from_random('normal', domain=(space1, space2))
rand2 = ift.Field.from_random('normal', domain=(space1, space2))
tt1 = rand2.vdot(op.times(rand1))
tt2 = rand1.vdot(op.adjoint_times(rand2))
assert_approx_equal(tt1, tt2)
assert_allclose(tt1, tt2)
@expand(product(spaces, spaces))
def test_times_inverse_times(self, space1, space2):
cspace = (space1, space2)
diag1 = Field.from_random('normal', domain=space1)
diag2 = Field.from_random('normal', domain=space2)
op1 = DiagonalOperator(diag1, cspace, spaces=(0,))
op2 = DiagonalOperator(diag2, cspace, spaces=(1,))
diag1 = ift.Field.from_random('normal', domain=space1)
diag2 = ift.Field.from_random('normal', domain=space2)
op1 = ift.DiagonalOperator(diag1, cspace, spaces=(0,))
op2 = ift.DiagonalOperator(diag2, cspace, spaces=(1,))
op = ComposedOperator((op1, op2))
op = ift.ComposedOperator((op1, op2))
rand1 = Field.from_random('normal', domain=(space1, space2))
rand1 = ift.Field.from_random('normal', domain=(space1, space2))
tt1 = op.inverse_times(op.times(rand1))
assert_allclose(tt1.val, rand1.val)
assert_allclose(ift.dobj.to_global_data(tt1.val),
ift.dobj.to_global_data(rand1.val))
test/test_operators/test_diagonal_operator.py
View file @ 1083dadf
from __future__ import division
import unittest
import numpy as np
from numpy.testing import assert_equal,\
assert_allclose,\
assert_approx_equal
from nifty2go import Field,\
DiagonalOperator
from numpy.testing import assert_equal, assert_allclose
import nifty2go as ift
from test.common import generate_spaces
from itertools import product
from test.common import expand
class DiagonalOperator_Tests(unittest.TestCase):
spaces = generate_spaces()
@expand(product(spaces))
def test_property(self, space):
diag = Field.from_random('normal', domain=space)
D = DiagonalOperator(diag)
diag = ift.Field.from_random('normal', domain=space)
D = ift.DiagonalOperator(diag)
if D.domain[0] != space:
raise TypeError
if D.unitary != False:
if D.unitary:
raise TypeError
if D.self_adjoint != True:
if not D.self_adjoint:
raise TypeError
@expand(product(spaces))
def test_times_adjoint(self, space):
rand1 = Field.from_random('normal', domain=space)
rand2 = Field.from_random('normal', domain=space)
diag = Field.from_random('normal', domain=space)
D = DiagonalOperator(diag)
rand1 = ift.Field.from_random('normal', domain=space)
rand2 = ift.Field.from_random('normal', domain=space)
diag = ift.Field.from_random('normal', domain=space)
D = ift.DiagonalOperator(diag)
tt1 = rand1.vdot(D.times(rand2))
tt2 = rand2.vdot(D.times(rand1))
assert_approx_equal(tt1, tt2)
assert_allclose(tt1, tt2)
@expand(product(spaces))
def test_times_inverse(self, space):
rand1 = Field.from_random('normal', domain=space)
diag = Field.from_random('normal', domain=space)
D = DiagonalOperator(diag)
rand1 = ift.Field.from_random('normal', domain=space)
diag = ift.Field.from_random('normal', domain=space)
D = ift.DiagonalOperator(diag)
tt1 = D.times(D.inverse_times(rand1))
assert_allclose(rand1.val, tt1.val)
assert_allclose(ift.dobj.to_global_data(rand1.val),
ift.dobj.to_global_data(tt1.val))
@expand(product(spaces))
def test_times(self, space):
rand1 = Field.from_random('normal', domain=space)
diag = Field.from_random('normal', domain=space)
D = DiagonalOperator(diag)
rand1 = ift.Field.from_random('normal', domain=space)
diag = ift.Field.from_random('normal', domain=space)
D = ift.DiagonalOperator(diag)
tt = D.times(rand1)
assert_equal(tt.domain[0], space)
@expand(product(spaces))
def test_adjoint_times(self, space):
rand1 = Field.from_random('normal', domain=space)
diag = Field.from_random('normal', domain=space)
D = DiagonalOperator(diag)
rand1 = ift.Field.from_random('normal', domain=space)
diag = ift.Field.from_random('normal', domain=space)
D = ift.DiagonalOperator(diag)
tt = D.adjoint_times(rand1)
assert_equal(tt.domain[0], space)
@expand(product(spaces))
def test_inverse_times(self, space):
rand1 = Field.from_random('normal', domain=space)
diag = Field.from_random('normal', domain=space)
D = DiagonalOperator(diag)
rand1 = ift.Field.from_random('normal', domain=space)
diag = ift.Field.from_random('normal', domain=space)
D = ift.DiagonalOperator(diag)
tt = D.inverse_times(rand1)
assert_equal(tt.domain[0], space)
@expand(product(spaces))
def test_adjoint_inverse_times(self, space):
rand1 = Field.from_random('normal', domain=space)
diag = Field.from_random('normal', domain=space)
D = DiagonalOperator(diag)
rand1 = ift.Field.from_random('normal', domain=space)
diag = ift.Field.from_random('normal', domain=space)
D = ift.DiagonalOperator(diag)
tt = D.adjoint_inverse_times(rand1)
assert_equal(tt.domain[0], space)
@expand(product(spaces))
def test_diagonal(self, space):
diag = Field.from_random('normal', domain=space)
D = DiagonalOperator(diag)
diag = ift.Field.from_random('normal', domain=space)
D = ift.DiagonalOperator(diag)
diag_op = D.diagonal()
assert_allclose(diag.val, diag_op.val)
assert_allclose(ift.dobj.to_global_data(diag.val),
ift.dobj.to_global_data(diag_op.val))
test/test_operators/test_fft_operator.py
View file @ 1083dadf
......@@ -20,12 +20,7 @@ from __future__ import division
import unittest
import numpy as np
from numpy.testing import assert_allclose
from nifty2go import Field,\
RGSpace,\
LMSpace,\
HPSpace,\
GLSpace,\
FFTOperator
import nifty2go as ift
from itertools import product
from test.common import expand
......@@ -42,75 +37,81 @@ class FFTOperatorTests(unittest.TestCase):
[np.float64, np.float32, np.complex64, np.complex128]))
def test_fft1D(self, dim1, d, itp):
tol = _get_rtol(itp)
a = RGSpace(dim1, distances=d)
b = RGSpace(dim1, distances=1./(dim1*d), harmonic=True)
fft = FFTOperator(domain=a, target=b)
a = ift.RGSpace(dim1, distances=d)
b = ift.RGSpace(dim1, distances=1./(dim1*d), harmonic=True)
fft = ift.FFTOperator(domain=a, target=b)
np.random.seed(16)
inp = Field.from_random(domain=a, random_type='normal', std=7, mean=3,
dtype=itp)
inp = ift.Field.from_random(domain=a, random_type='normal',
std=7, mean=3, dtype=itp)
out = fft.adjoint_times(fft.times(inp))
assert_allclose(inp.val, out.val, rtol=tol, atol=tol)
assert_allclose(ift.dobj.to_global_data(inp.val),
ift.dobj.to_global_data(out.val), rtol=tol, atol=tol)
@expand(product([12, 15], [9, 12], [0.1, 1, 3.7],
[0.4, 1, 2.7],
[np.float64, np.float32, np.complex64, np.complex128]))
def test_fft2D(self, dim1, dim2, d1, d2, itp):