def test_windowfunc_basics():
for window_name, params in window_funcs:
window = getattr(signal, window_name)
with warnings.catch_warnings(record=True): # window is not suitable...
w1 = window(7, *params, sym=True)
w2 = window(7, *params, sym=False)
assert_array_almost_equal(w1, w2)
# Check that functions run and output lengths are correct
assert_equal(len(window(6, *params, sym=True)), 6)
assert_equal(len(window(6, *params, sym=False)), 6)
assert_equal(len(window(7, *params, sym=True)), 7)
assert_equal(len(window(7, *params, sym=False)), 7)
# Check invalid lengths
assert_raises(ValueError, window, 5.5, *params)
assert_raises(ValueError, window, -7, *params)
# Check degenerate cases
assert_array_equal(window(0, *params, sym=True), [])
assert_array_equal(window(0, *params, sym=False), [])
assert_array_equal(window(1, *params, sym=True), [1])
assert_array_equal(window(1, *params, sym=False), [1])
# Check dtype
assert_(window(0, *params, sym=True).dtype == 'float')
assert_(window(0, *params, sym=False).dtype == 'float')
assert_(window(1, *params, sym=True).dtype == 'float')
assert_(window(1, *params, sym=False).dtype == 'float')
assert_(window(6, *params, sym=True).dtype == 'float')
assert_(window(6, *params, sym=False).dtype == 'float')
def test_array_richcompare_legacy_weirdness(self):
# It doesn't really work to use assert_deprecated here, b/c part of
# the point of assert_deprecated is to check that when warnings are
# set to "error" mode then the error is propagated -- which is good!
# But here we are testing a bunch of code that is deprecated *because*
# it has the habit of swallowing up errors and converting them into
# different warnings. So assert_warns will have to be sufficient.
assert_warns(FutureWarning, lambda: np.arange(2) == "a")
assert_warns(FutureWarning, lambda: np.arange(2) != "a")
# No warning for scalar comparisons
with warnings.catch_warnings():
warnings.filterwarnings("error")
assert_(not (np.array(0) == "a"))
assert_(np.array(0) != "a")
assert_(not (np.int16(0) == "a"))
assert_(np.int16(0) != "a")
for arg1 in [np.asarray(0), np.int16(0)]:
struct = np.zeros(2, dtype="i4,i4")
for arg2 in [struct, "a"]:
for f in [operator.lt, operator.le, operator.gt, operator.ge]:
if sys.version_info[0] >= 3:
# py3
with warnings.catch_warnings() as l:
warnings.filterwarnings("always")
assert_raises(TypeError, f, arg1, arg2)
assert_(not l)
else:
# py2
assert_warns(DeprecationWarning, f, arg1, arg2)
def test_corrupted_data():
import zlib
for exc, fname in [(ValueError, 'corrupted_zlib_data.mat'),
(zlib.error, 'corrupted_zlib_checksum.mat')]:
with open(pjoin(test_data_path, fname), 'rb') as fp:
rdr = MatFile5Reader(fp)
assert_raises(exc, rdr.get_variables)
def test_renn_sample_wt_fit():
"""Test either if an error is raised when sample is called before
fitting"""
# Create the object
renn = RepeatedEditedNearestNeighbours(random_state=RND_SEED)
assert_raises(RuntimeError, renn.sample, X, Y)
def test_TimeSeries():
"""Testing the initialization of the uniform time series object """
# Test initialization with duration:
tseries1 = ts.TimeSeries([1, 2, 3, 4, 5, 6, 7, 8, 9, 10], duration=10)
tseries2 = ts.TimeSeries([1, 2, 3, 4, 5, 6, 7, 8, 9, 10], sampling_interval=1)
npt.assert_equal(tseries1.time, tseries2.time)
# downsampling:
t1 = ts.UniformTime(length=8, sampling_rate=2)
# duration is the same, but we're downsampling to 1Hz
tseries1 = ts.TimeSeries(data=[1, 2, 3, 4], time=t1, sampling_rate=1)
# If you didn't explicitely provide the rate you want to downsample to, that
# is an error:
npt.assert_raises(ValueError, ts.TimeSeries, dict(data=[1, 2, 3, 4], time=t1))
tseries2 = ts.TimeSeries(data=[1, 2, 3, 4], sampling_rate=1)
tseries3 = ts.TimeSeries(data=[1, 2, 3, 4], sampling_rate=1000, time_unit="ms")
# you can specify the sampling_rate or the sampling_interval, to the same
# effect, where specificying the sampling_interval is in the units of that
# time-series:
tseries4 = ts.TimeSeries(data=[1, 2, 3, 4], sampling_interval=1, time_unit="ms")
npt.assert_equal(tseries4.time, tseries3.time)
# The units you use shouldn't matter - time is time:
tseries6 = ts.TimeSeries(data=[1, 2, 3, 4], sampling_interval=0.001, time_unit="s")
npt.assert_equal(tseries6.time, tseries3.time)
# And this too - perverse, but should be possible:
tseries5 = ts.TimeSeries(data=[1, 2, 3, 4], sampling_interval=ts.TimeArray(0.001, time_unit="s"), time_unit="ms")
npt.assert_equal(tseries5.time, tseries3.time)
# initializing with a UniformTime object:
t = ts.UniformTime(length=3, sampling_rate=3)
data = [1, 2, 3]
tseries7 = ts.TimeSeries(data=data, time=t)
npt.assert_equal(tseries7.data, data)
data = [1, 2, 3, 4]
# If the data is not the right length, that should throw an error:
npt.assert_raises(ValueError, ts.TimeSeries, dict(data=data, time=t))
# test basic arithmetics wiht TimeSeries
tseries1 = ts.TimeSeries([1, 2, 3, 4, 5, 6, 7, 8, 9, 10], sampling_rate=1)
tseries2 = tseries1 + 1
npt.assert_equal(tseries1.data + 1, tseries2.data)
npt.assert_equal(tseries1.time, tseries2.time)
tseries2 -= 1
npt.assert_equal(tseries1.data, tseries2.data)
npt.assert_equal(tseries1.time, tseries2.time)
tseries2 = tseries1 * 2
npt.assert_equal(tseries1.data * 2, tseries2.data)
npt.assert_equal(tseries1.time, tseries2.time)
tseries2 = tseries2 / 2
npt.assert_equal(tseries1.data, tseries2.data)
npt.assert_equal(tseries1.time, tseries2.time)
def test_invalid_seed():
seed = np.ones((5, 5))
mask = np.ones((5, 5))
assert_raises(ValueError, reconstruction, seed * 2, mask,
method='dilation')
assert_raises(ValueError, reconstruction, seed * 0.5, mask,
method='erosion')
def test_read_opts():
# tests if read is seeing option sets, at initialization and after
# initialization
arr = np.arange(6).reshape(1,6)
stream = BytesIO()
savemat(stream, {'a': arr})
rdr = MatFile5Reader(stream)
back_dict = rdr.get_variables()
rarr = back_dict['a']
assert_array_equal(rarr, arr)
rdr = MatFile5Reader(stream, squeeze_me=True)
assert_array_equal(rdr.get_variables()['a'], arr.reshape((6,)))
rdr.squeeze_me = False
assert_array_equal(rarr, arr)
rdr = MatFile5Reader(stream, byte_order=boc.native_code)
assert_array_equal(rdr.get_variables()['a'], arr)
# inverted byte code leads to error on read because of swapped
# header etc
rdr = MatFile5Reader(stream, byte_order=boc.swapped_code)
assert_raises(Exception, rdr.get_variables)
rdr.byte_order = boc.native_code
assert_array_equal(rdr.get_variables()['a'], arr)
arr = np.array(['a string'])
stream.truncate(0)
stream.seek(0)
savemat(stream, {'a': arr})
rdr = MatFile5Reader(stream)
assert_array_equal(rdr.get_variables()['a'], arr)
rdr = MatFile5Reader(stream, chars_as_strings=False)
carr = np.atleast_2d(np.array(list(arr.item()), dtype='U1'))
assert_array_equal(rdr.get_variables()['a'], carr)
rdr.chars_as_strings = True
assert_array_equal(rdr.get_variables()['a'], arr)
def test_wrong_dimensions(self):
x0 = 1.0
assert_raises(RuntimeError, approx_derivative,
self.wrong_dimensions_fun, x0)
f0 = self.wrong_dimensions_fun(np.atleast_1d(x0))
assert_raises(ValueError, approx_derivative,
self.wrong_dimensions_fun, x0, f0=f0)
def test_pad_too_many_axes(self):
arr = np.arange(30).reshape(5, 6)
# Attempt to pad using a 3D array equivalent
bad_shape = (((3,), (4,), (5,)), ((0,), (1,), (2,)))
assert_raises(ValueError, pad, arr, bad_shape,
mode='constant')
def test_ada_sample_wt_fit():
"""Test either if an error is raised when sample is called before
fitting"""
# Create the object
ada = ADASYN(random_state=RND_SEED)
assert_raises(RuntimeError, ada.sample, X, Y)
def test_ada_wrong_nn_obj():
"""Test either if an error is raised while passing a wrong NN object"""
# Resample the data
nn = 'rnd'
ada = ADASYN(random_state=RND_SEED, n_neighbors=nn)
assert_raises(ValueError, ada.fit_sample, X, Y)
def test_normalize_data():
sig = np.arange(1, 66)[::-1]
where_b0 = np.zeros(65, 'bool')
where_b0[0] = True
assert_raises(ValueError, normalize_data, sig, where_b0, out=sig)
norm_sig = normalize_data(sig, where_b0, min_signal=1)
assert_array_almost_equal(norm_sig, sig / 65.)
norm_sig = normalize_data(sig, where_b0, min_signal=5)
assert_array_almost_equal(norm_sig[-5:], 5 / 65.)
where_b0[[0, 1]] = [True, True]
norm_sig = normalize_data(sig, where_b0, min_signal=1)
assert_array_almost_equal(norm_sig, sig / 64.5)
norm_sig = normalize_data(sig, where_b0, min_signal=5)
assert_array_almost_equal(norm_sig[-5:], 5 / 64.5)
sig = sig * np.ones((2, 3, 1))
where_b0[[0, 1]] = [True, False]
norm_sig = normalize_data(sig, where_b0, min_signal=1)
assert_array_almost_equal(norm_sig, sig / 65.)
norm_sig = normalize_data(sig, where_b0, min_signal=5)
assert_array_almost_equal(norm_sig[..., -5:], 5 / 65.)
where_b0[[0, 1]] = [True, True]
norm_sig = normalize_data(sig, where_b0, min_signal=1)
assert_array_almost_equal(norm_sig, sig / 64.5)
norm_sig = normalize_data(sig, where_b0, min_signal=5)
assert_array_almost_equal(norm_sig[..., -5:], 5 / 64.5)
def test_sph_harm_ind_list():
m_list, n_list = sph_harm_ind_list(8)
assert_equal(m_list.shape, n_list.shape)
assert_equal(m_list.shape, (45,))
assert_true(np.all(np.abs(m_list) <= n_list))
assert_array_equal(n_list % 2, 0)
assert_raises(ValueError, sph_harm_ind_list, 1)
def test_SeedCoherenceAnalyzer():
""" Test the SeedCoherenceAnalyzer """
methods = (None,
{"this_method": 'welch', "NFFT": 256},
{"this_method": 'multi_taper_csd'},
{"this_method": 'periodogram_csd', "NFFT": 256})
Fs = np.pi
t = np.arange(256)
seed1 = np.sin(10 * t) + np.random.rand(t.shape[-1])
seed2 = np.sin(10 * t) + np.random.rand(t.shape[-1])
target = np.sin(10 * t) + np.random.rand(t.shape[-1])
T = ts.TimeSeries(np.vstack([seed1, target]), sampling_rate=Fs)
T_seed1 = ts.TimeSeries(seed1, sampling_rate=Fs)
T_seed2 = ts.TimeSeries(np.vstack([seed1, seed2]), sampling_rate=Fs)
T_target = ts.TimeSeries(np.vstack([seed1, target]), sampling_rate=Fs)
for this_method in methods:
if this_method is None or this_method['this_method']=='welch':
C1 = nta.CoherenceAnalyzer(T, method=this_method)
C2 = nta.SeedCoherenceAnalyzer(T_seed1, T_target,
method=this_method)
C3 = nta.SeedCoherenceAnalyzer(T_seed2, T_target,
method=this_method)
npt.assert_almost_equal(C1.coherence[0, 1], C2.coherence[1])
npt.assert_almost_equal(C2.coherence[1], C3.coherence[0, 1])
npt.assert_almost_equal(C1.phase[0, 1], C2.relative_phases[1])
npt.assert_almost_equal(C1.delay[0, 1], C2.delay[1])
else:
npt.assert_raises(ValueError,nta.SeedCoherenceAnalyzer, T_seed1,
T_target, this_method)
def test_SparseCoherenceAnalyzer():
Fs = np.pi
t = np.arange(256)
x = np.sin(10 * t) + np.random.rand(t.shape[-1])
y = np.sin(10 * t) + np.random.rand(t.shape[-1])
T = ts.TimeSeries(np.vstack([x, y]), sampling_rate=Fs)
C1 = nta.SparseCoherenceAnalyzer(T, ij=((0, 1), (1, 0)))
C2 = nta.CoherenceAnalyzer(T)
# Coherence symmetry:
npt.assert_equal(np.abs(C1.coherence[0, 1]), np.abs(C1.coherence[1, 0]))
npt.assert_equal(np.abs(C1.coherency[0, 1]), np.abs(C1.coherency[1, 0]))
# Make sure you get the same answers as you would from the standard
# CoherenceAnalyzer:
npt.assert_almost_equal(C2.coherence[0, 1], C1.coherence[0, 1])
# This is the PSD (for the first time-series in the object):
npt.assert_almost_equal(C2.spectrum[0, 0], C1.spectrum[0])
# And the second (for good measure):
npt.assert_almost_equal(C2.spectrum[1, 1], C1.spectrum[1])
# The relative phases should be equal
npt.assert_almost_equal(C2.phase[0, 1], C1.relative_phases[0, 1])
# But not the absolute phases (which have the same shape):
npt.assert_equal(C1.phases[0].shape, C1.relative_phases[0, 1].shape)
# The delay is equal:
npt.assert_almost_equal(C2.delay[0, 1], C1.delay[0, 1])
# Make sure that you would get an error if you provided a method other than
# 'welch':
npt.assert_raises(ValueError, nta.SparseCoherenceAnalyzer, T,
method=dict(this_method='foo'))
def test_version_2_0_memmap():
# requires more than 2 byte for header
dt = [(("%d" % i) * 100, float) for i in range(500)]
d = np.ones(1000, dtype=dt)
tf = tempfile.mktemp('', 'mmap', dir=tempdir)
# 1.0 requested but data cannot be saved this way
assert_raises(ValueError, format.open_memmap, tf, mode='w+', dtype=d.dtype,
shape=d.shape, version=(1, 0))
ma = format.open_memmap(tf, mode='w+', dtype=d.dtype,
shape=d.shape, version=(2, 0))
ma[...] = d
del ma
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings('always', '', UserWarning)
ma = format.open_memmap(tf, mode='w+', dtype=d.dtype,
shape=d.shape, version=None)
assert_(w[0].category is UserWarning)
ma[...] = d
del ma
ma = format.open_memmap(tf, mode='r')
assert_array_equal(ma, d)
def test_bad_header():
# header of length less than 2 should fail
s = BytesIO()
assert_raises(ValueError, format.read_array_header_1_0, s)
s = BytesIO(asbytes('1'))
assert_raises(ValueError, format.read_array_header_1_0, s)
# header shorter than indicated size should fail
s = BytesIO(asbytes('\x01\x00'))
assert_raises(ValueError, format.read_array_header_1_0, s)
# headers without the exact keys required should fail
d = {"shape": (1, 2),
"descr": "x"}
s = BytesIO()
format.write_array_header_1_0(s, d)
assert_raises(ValueError, format.read_array_header_1_0, s)
d = {"shape": (1, 2),
"fortran_order": False,
"descr": "x",
"extrakey": -1}
s = BytesIO()
format.write_array_header_1_0(s, d)
assert_raises(ValueError, format.read_array_header_1_0, s)
def test_diags_bad(self):
a = array([1, 2, 3, 4, 5])
b = array([6, 7, 8, 9, 10])
c = array([11, 12, 13, 14, 15])
cases = []
cases.append(([a[:0]], 0, (1, 1)))
cases.append(([a], [0], (1, 1)))
cases.append(([a[:3],b], [0,2], (3, 3)))
cases.append(([a[:4],b,c[:3]], [-1,0,1], (5, 5)))
cases.append(([a[:2],c,b[:3]], [-4,2,-1], (6, 5)))
cases.append(([a[:2],c,b[:3]], [-4,2,-1], None))
cases.append(([], [-4,2,-1], None))
cases.append(([1], [-4], (4, 4)))
cases.append(([a[:0]], [-1], (1, 2)))
cases.append(([a], 0, None))
for d, o, shape in cases:
try:
assert_raises(ValueError, construct.diags, d, o, shape)
except:
print("%r %r %r" % (d, o, shape))
raise
assert_raises(TypeError, construct.diags, [[None]], [0])
def test_random_sampling(self):
# Simple sanity checks for sparse random sampling.
for f in sprand, _sprandn:
for t in [np.float32, np.float64, np.longdouble]:
x = f(5, 10, density=0.1, dtype=t)
assert_equal(x.dtype, t)
assert_equal(x.shape, (5, 10))
assert_equal(x.nonzero()[0].size, 5)
x1 = f(5, 10, density=0.1, random_state=4321)
assert_equal(x1.dtype, np.double)
x2 = f(5, 10, density=0.1, random_state=np.random.RandomState(4321))
assert_array_equal(x1.data, x2.data)
assert_array_equal(x1.row, x2.row)
assert_array_equal(x1.col, x2.col)
for density in [0.0, 0.1, 0.5, 1.0]:
x = f(5, 10, density=density)
assert_equal(x.nnz, int(density * np.prod(x.shape)))
for fmt in ['coo', 'csc', 'csr', 'lil']:
x = f(5, 10, format=fmt)
assert_equal(x.format, fmt)
assert_raises(ValueError, lambda: f(5, 10, 1.1))
assert_raises(ValueError, lambda: f(5, 10, -0.1))
def test_config_parser():
_environ = dict(os.environ)
os.environ['BLOCKS_CONFIG'] = os.path.join(os.getcwd(),
'.test_blocksrc')
with open(os.environ['BLOCKS_CONFIG'], 'w') as f:
f.write('data_path: yaml_path')
if 'BLOCKS_DATA_PATH' in os.environ:
del os.environ['BLOCKS_DATA_PATH']
try:
config = Configuration()
config.add_config('data_path', str, env_var='BLOCKS_DATA_PATH')
config.add_config('config_with_default', int, default='1',
env_var='BLOCKS_CONFIG_TEST')
config.add_config('config_without_default', str)
assert config.data_path == 'yaml_path'
os.environ['BLOCKS_DATA_PATH'] = 'env_path'
assert config.data_path == 'env_path'
assert config.config_with_default == 1
os.environ['BLOCKS_CONFIG_TEST'] = '2'
assert config.config_with_default == 2
assert_raises(ConfigurationError, getattr, config,
'non_existing_config')
assert_raises(ConfigurationError, getattr, config,
'config_without_default')
finally:
os.remove(os.environ['BLOCKS_CONFIG'])
os.environ.clear()
os.environ.update(_environ)
def test_invalid_array(self):
# seed must be an unsigned 32 bit integer
assert_raises(TypeError, np.random.RandomState, [-0.5])
assert_raises(ValueError, np.random.RandomState, [-1])
assert_raises(ValueError, np.random.RandomState, [4294967296])
assert_raises(ValueError, np.random.RandomState, [1, 2, 4294967296])
assert_raises(ValueError, np.random.RandomState, [1, -2, 4294967296])
def test_plot_sparse_source_estimates():
"""Test plotting of (sparse) source estimates
"""
sample_src = read_source_spaces(op.join(data_dir, 'subjects', 'sample',
'bem', 'sample-oct-6-src.fif'))
# dense version
vertices = [s['vertno'] for s in sample_src]
n_time = 5
n_verts = sum(len(v) for v in vertices)
stc_data = np.zeros((n_verts * n_time))
stc_data[(np.random.rand(20) * n_verts * n_time).astype(int)] = 1
stc_data.shape = (n_verts, n_time)
stc = SourceEstimate(stc_data, vertices, 1, 1)
colormap = mne_analyze_colormap(format='matplotlib')
# don't really need to test matplotlib method since it's not used now...
colormap = mne_analyze_colormap()
plot_source_estimates(stc, 'sample', colormap=colormap,
config_opts={'background': (1, 1, 0)},
subjects_dir=subjects_dir, colorbar=True)
assert_raises(TypeError, plot_source_estimates, stc, 'sample',
figure='foo', hemi='both')
# now do sparse version
vertices = sample_src[0]['vertno']
n_verts = len(vertices)
stc_data = np.zeros((n_verts * n_time))
stc_data[(np.random.rand(20) * n_verts * n_time).astype(int)] = 1
stc_data.shape = (n_verts, n_time)
inds = np.where(np.any(stc_data, axis=1))[0]
stc_data = stc_data[inds]
vertices = [vertices[inds], np.empty(0, dtype=np.int)]
stc = SourceEstimate(stc_data, vertices, 1, 1)
plot_sparse_source_estimates(sample_src, stc, bgcolor=(1, 1, 1),
opacity=0.5, high_resolution=True)
def test_set_item_index_error(self):
code = """
py::tuple a(3);
a[4] = 1;
return_val = a;
"""
assert_raises(IndexError, inline_tools.inline, code)
def test_rag_error():
img = np.zeros((10, 10, 3), dtype='uint8')
labels = np.zeros((10, 10), dtype='uint8')
labels[:5, :] = 0
labels[5:, :] = 1
testing.assert_raises(ValueError, graph.rag_mean_color, img, labels,
2, 'non existant mode')
def test_neighbors_badargs():
"""Test bad argument values: these should all raise ValueErrors"""
assert_raises(ValueError,
neighbors.NearestNeighbors,
algorithm='blah')
X = rng.random_sample((10, 2))
for cls in (neighbors.KNeighborsClassifier,
neighbors.RadiusNeighborsClassifier,
neighbors.KNeighborsRegressor,
neighbors.RadiusNeighborsRegressor):
assert_raises(ValueError,
cls,
weights='blah')
nbrs = cls()
assert_raises(ValueError,
nbrs.predict,
X)
nbrs = neighbors.NearestNeighbors().fit(X)
assert_raises(ValueError,
nbrs.kneighbors_graph,
X, mode='blah')
assert_raises(ValueError,
nbrs.radius_neighbors_graph,
X, mode='blah')
def test_roll_evals():
"""
"""
# Just making sure this never passes through
weird_evals = np.array([1, 0.5])
npt.assert_raises(ValueError, dti._roll_evals, weird_evals)
def test_representation():
# Test an invalid number of states
def zero_kstates():
mod = Representation(1, 0)
assert_raises(ValueError, zero_kstates)
# Test an invalid endogenous array
def empty_endog():
endog = np.zeros((0,0))
mod = Representation(endog, k_states=2)
assert_raises(ValueError, empty_endog)
# Test a Fortran-ordered endogenous array (which will be assumed to be in
# wide format: k_endog x nobs)
nobs = 10
k_endog = 2
endog = np.asfortranarray(np.arange(nobs*k_endog).reshape(k_endog,nobs)*1.)
mod = Representation(endog, k_states=2)
assert_equal(mod.nobs, nobs)
assert_equal(mod.k_endog, k_endog)
# Test a C-ordered endogenous array (which will be assumed to be in
# tall format: nobs x k_endog)
nobs = 10
k_endog = 2
endog = np.arange(nobs*k_endog).reshape(nobs,k_endog)*1.
mod = Representation(endog, k_states=2)
assert_equal(mod.nobs, nobs)
assert_equal(mod.k_endog, k_endog)
# Test getting the statespace representation
assert_equal(mod._statespace, None)
mod._initialize_representation()
assert(mod._statespace is not None)
def test_fetch_data():
symmetric362 = SPHERE_FILES['symmetric362']
with TemporaryDirectory() as tmpdir:
md5 = fetcher._get_file_md5(symmetric362)
bad_md5 = '8' * len(md5)
newfile = path.join(tmpdir, "testfile.txt")
# Test that the fetcher can get a file
testfile_url = pathname2url(symmetric362)
testfile_url = urljoin("file:", testfile_url)
files = {"testfile.txt" : (testfile_url, md5)}
fetcher.fetch_data(files, tmpdir)
npt.assert_(path.exists(newfile))
# Test that the file is replaced when the md5 doesn't match
with open(newfile, 'a') as f:
f.write("some junk")
fetcher.fetch_data(files, tmpdir)
npt.assert_(path.exists(newfile))
npt.assert_equal(fetcher._get_file_md5(newfile), md5)
# Test that an error is raised when the md5 checksum of the download
# file does not match the expected value
files = {"testfile.txt" : (testfile_url, bad_md5)}
npt.assert_raises(fetcher.FetcherError,
fetcher.fetch_data, files, tmpdir)
def test_roots_hermite():
rootf = sc.roots_hermite
evalf = orth.eval_hermite
weightf = orth.hermite(5).weight_func
verify_gauss_quad(rootf, evalf, weightf, -np.inf, np.inf, 5)
verify_gauss_quad(rootf, evalf, weightf, -np.inf, np.inf, 25, atol=1e-13)
verify_gauss_quad(rootf, evalf, weightf, -np.inf, np.inf, 100, atol=1e-12)
# Golub-Welsch branch
x, w = sc.roots_hermite(5, False)
y, v, m = sc.roots_hermite(5, True)
assert_allclose(x, y, 1e-14, 1e-14)
assert_allclose(w, v, 1e-14, 1e-14)
muI, muI_err = integrate.quad(weightf, -np.inf, np.inf)
assert_allclose(m, muI, rtol=muI_err)
# Asymptotic branch (switch over at n >= 150)
x, w = sc.roots_hermite(200, False)
y, v, m = sc.roots_hermite(200, True)
assert_allclose(x, y, 1e-14, 1e-14)
assert_allclose(w, v, 1e-14, 1e-14)
assert_allclose(sum(v), m, 1e-14, 1e-14)
assert_raises(ValueError, sc.roots_hermite, 0)
assert_raises(ValueError, sc.roots_hermite, 3.3)
def test_GradientTable():
gradients = np.array([[0, 0, 0],
[1, 0, 0],
[0, 0, 1],
[3, 4, 0],
[5, 0, 12]], 'float')
expected_bvals = np.array([0, 1, 1, 5, 13])
expected_b0s_mask = expected_bvals == 0
expected_bvecs = gradients / (expected_bvals + expected_b0s_mask)[:, None]
gt = GradientTable(gradients, b0_threshold=0)
npt.assert_array_almost_equal(gt.bvals, expected_bvals)
npt.assert_array_equal(gt.b0s_mask, expected_b0s_mask)
npt.assert_array_almost_equal(gt.bvecs, expected_bvecs)
npt.assert_array_almost_equal(gt.gradients, gradients)
gt = GradientTable(gradients, b0_threshold=1)
npt.assert_array_equal(gt.b0s_mask, [1, 1, 1, 0, 0])
npt.assert_array_equal(gt.bvals, expected_bvals)
npt.assert_array_equal(gt.bvecs, expected_bvecs)
npt.assert_raises(ValueError, GradientTable, np.ones((6, 2)))
npt.assert_raises(ValueError, GradientTable, np.ones((6,)))
def test_index_no_floats(self):
a = np.array([[[5]]])
assert_raises(IndexError, lambda: a[0.0])
assert_raises(IndexError, lambda: a[0, 0.0])
assert_raises(IndexError, lambda: a[0.0, 0])
assert_raises(IndexError, lambda: a[0.0,:])
assert_raises(IndexError, lambda: a[:, 0.0])
assert_raises(IndexError, lambda: a[:, 0.0,:])
assert_raises(IndexError, lambda: a[0.0,:,:])
assert_raises(IndexError, lambda: a[0, 0, 0.0])
assert_raises(IndexError, lambda: a[0.0, 0, 0])
assert_raises(IndexError, lambda: a[0, 0.0, 0])
assert_raises(IndexError, lambda: a[-1.4])
assert_raises(IndexError, lambda: a[0, -1.4])
assert_raises(IndexError, lambda: a[-1.4, 0])
assert_raises(IndexError, lambda: a[-1.4,:])
assert_raises(IndexError, lambda: a[:, -1.4])
assert_raises(IndexError, lambda: a[:, -1.4,:])
assert_raises(IndexError, lambda: a[-1.4,:,:])
assert_raises(IndexError, lambda: a[0, 0, -1.4])
assert_raises(IndexError, lambda: a[-1.4, 0, 0])
assert_raises(IndexError, lambda: a[0, -1.4, 0])
assert_raises(IndexError, lambda: a[0.0:, 0.0])
assert_raises(IndexError, lambda: a[0.0:, 0.0,:])
def test_otsu_one_color_image():
img = np.ones((10, 10), dtype=np.uint8)
assert_raises(ValueError, threshold_otsu, img)
def test_invalid_mlags():
data = dt.data.double_well_discrete().dtraj
est = dt.markov.msm.MaximumLikelihoodMSM()
est.fit(data, lagtime=1)
with assert_raises(ValueError):
est.chapman_kolmogorov_validator(2, mlags=[0, 1, -10])
def test_index_no_array_to_index(self):
# No non-scalar arrays.
a = np.array([[[1]]])
assert_raises(TypeError, lambda: a[a:a:a])
def test_slicing_no_floats(self):
a = np.array([[5]])
# start as float.
assert_raises(TypeError, lambda: a[0.0:])
assert_raises(TypeError, lambda: a[0:, 0.0:2])
assert_raises(TypeError, lambda: a[0.0::2, :0])
assert_raises(TypeError, lambda: a[0.0:1:2,:])
assert_raises(TypeError, lambda: a[:, 0.0:])
# stop as float.
assert_raises(TypeError, lambda: a[:0.0])
assert_raises(TypeError, lambda: a[:0, 1:2.0])
assert_raises(TypeError, lambda: a[:0.0:2, :0])
assert_raises(TypeError, lambda: a[:0.0,:])
assert_raises(TypeError, lambda: a[:, 0:4.0:2])
# step as float.
assert_raises(TypeError, lambda: a[::1.0])
assert_raises(TypeError, lambda: a[0:, :2:2.0])
assert_raises(TypeError, lambda: a[1::4.0, :0])
assert_raises(TypeError, lambda: a[::5.0,:])
assert_raises(TypeError, lambda: a[:, 0:4:2.0])
# mixed.
assert_raises(TypeError, lambda: a[1.0:2:2.0])
assert_raises(TypeError, lambda: a[1.0::2.0])
assert_raises(TypeError, lambda: a[0:, :2.0:2.0])
assert_raises(TypeError, lambda: a[1.0:1:4.0, :0])
assert_raises(TypeError, lambda: a[1.0:5.0:5.0,:])
assert_raises(TypeError, lambda: a[:, 0.4:4.0:2.0])
# should still get the DeprecationWarning if step = 0.
assert_raises(TypeError, lambda: a[::0.0])
def test_broaderrors_indexing(self):
a = np.zeros((5, 5))
assert_raises(IndexError, a.__getitem__, ([0, 1], [0, 1, 2]))
assert_raises(IndexError, a.__setitem__, ([0, 1], [0, 1, 2]), 0)
def test_too_many_fancy_indices_special_case(self):
# Just documents behaviour, this is a small limitation.
a = np.ones((1,) * 32) # 32 is NPY_MAXDIMS
assert_raises(IndexError, a.__getitem__, (np.array([0]),) * 32)
def test_basic(self):
a = np.arange(10)
assert_raises(IndexError, lambda: a[..., ...])
assert_raises(IndexError, a.__getitem__, ((Ellipsis,) * 2,))
assert_raises(IndexError, a.__getitem__, ((Ellipsis,) * 3,))
def test_reduce_axis_float_index(self):
d = np.zeros((3,3,3))
assert_raises(TypeError, np.min, d, 0.5)
assert_raises(TypeError, np.min, d, (0.5, 1))
assert_raises(TypeError, np.min, d, (1, 2.2))
assert_raises(TypeError, np.min, d, (.2, 1.2))
def test_setitem(self):
assign = functools.partial(array_indexing, 1)
# Deletion is impossible:
assert_raises(ValueError, assign, np.ones(10), 0)
# 0-d arrays don't work:
assert_raises(IndexError, assign, np.ones(()), 0, 0)
# Out of bound values:
assert_raises(IndexError, assign, np.ones(10), 11, 0)
assert_raises(IndexError, assign, np.ones(10), -11, 0)
assert_raises(IndexError, assign, np.ones((10, 10)), 11, 0)
assert_raises(IndexError, assign, np.ones((10, 10)), -11, 0)
a = np.arange(10)
assign(a, 4, 10)
assert_(a[4] == 10)
a = a.reshape(5, 2)
assign(a, 4, 10)
assert_array_equal(a[-1], [10, 10])
def test_octave_error(self):
npt.assert_raises(octavemagic.OctaveMagicError, self.ip.run_cell_magic,
'octave', '', 'a = ones2(1)')
def test_boolean_indexing_weirdness(self):
# Weird boolean indexing things
a = np.ones((2, 3, 4))
a[False, True, ...].shape == (0, 2, 3, 4)
a[True, [0, 1], True, True, [1], [[2]]] == (1, 2)
assert_raises(IndexError, lambda: a[False, [0, 1], ...])
def test_non_unique_vocab():
vocab = ['a', 'b', 'c', 'a', 'a']
vect = CountVectorizer(vocabulary=vocab)
assert_raises(ValueError, vect.fit, [])
def test_precision_prior_wrong_nb():
with assert_raises(ValueError):
m = tm.THMM(n_unique=2)
m.precision_prior_ = np.array([0.7, 0.8, 0.9])
def test_duplicate_keys(self):
a = np.zeros(3, dtype=[('a', 'i4'), ('b', 'f4'), ('c', 'u1')])
b = np.ones(3, dtype=[('c', 'u1'), ('b', 'f4'), ('a', 'i4')])
assert_raises(ValueError, join_by, ['a', 'b', 'b'], a, b)
def test_exceptions(self):
assert_raises(ValueError, triu_indices_from, np.ones((2, )))
assert_raises(ValueError, triu_indices_from, np.ones((2, 2, 2)))
def test_switched_arguments():
image = np.ones((5, 5))
template = np.ones((3, 3))
assert_raises(ValueError, match_template, template, image)
def test_vectorizer():
# raw documents as an iterator
train_data = iter(ALL_FOOD_DOCS[:-1])
test_data = [ALL_FOOD_DOCS[-1]]
n_train = len(ALL_FOOD_DOCS) - 1
# test without vocabulary
v1 = CountVectorizer(max_df=0.5)
counts_train = v1.fit_transform(train_data)
if hasattr(counts_train, 'tocsr'):
counts_train = counts_train.tocsr()
assert_equal(counts_train[0, v1.vocabulary_["pizza"]], 2)
# build a vectorizer v1 with the same vocabulary as the one fitted by v1
v2 = CountVectorizer(vocabulary=v1.vocabulary_)
# compare that the two vectorizer give the same output on the test sample
for v in (v1, v2):
counts_test = v.transform(test_data)
if hasattr(counts_test, 'tocsr'):
counts_test = counts_test.tocsr()
vocabulary = v.vocabulary_
assert_equal(counts_test[0, vocabulary["salad"]], 1)
assert_equal(counts_test[0, vocabulary["tomato"]], 1)
assert_equal(counts_test[0, vocabulary["water"]], 1)
# stop word from the fixed list
assert_false("the" in vocabulary)
# stop word found automatically by the vectorizer DF thresholding
# words that are high frequent across the complete corpus are likely
# to be not informative (either real stop words of extraction
# artifacts)
assert_false("copyright" in vocabulary)
# not present in the sample
assert_equal(counts_test[0, vocabulary["coke"]], 0)
assert_equal(counts_test[0, vocabulary["burger"]], 0)
assert_equal(counts_test[0, vocabulary["beer"]], 0)
assert_equal(counts_test[0, vocabulary["pizza"]], 0)
# test tf-idf
t1 = TfidfTransformer(norm='l1')
tfidf = t1.fit(counts_train).transform(counts_train).toarray()
assert_equal(len(t1.idf_), len(v1.vocabulary_))
assert_equal(tfidf.shape, (n_train, len(v1.vocabulary_)))
# test tf-idf with new data
tfidf_test = t1.transform(counts_test).toarray()
assert_equal(tfidf_test.shape, (len(test_data), len(v1.vocabulary_)))
# test tf alone
t2 = TfidfTransformer(norm='l1', use_idf=False)
tf = t2.fit(counts_train).transform(counts_train).toarray()
assert_equal(t2.idf_, None)
# test idf transform with unlearned idf vector
t3 = TfidfTransformer(use_idf=True)
assert_raises(ValueError, t3.transform, counts_train)
# test idf transform with incompatible n_features
X = [[1, 1, 5], [1, 1, 0]]
t3.fit(X)
X_incompt = [[1, 3], [1, 3]]
assert_raises(ValueError, t3.transform, X_incompt)
# L1-normalized term frequencies sum to one
assert_array_almost_equal(np.sum(tf, axis=1), [1.0] * n_train)
# test the direct tfidf vectorizer
# (equivalent to term count vectorizer + tfidf transformer)
train_data = iter(ALL_FOOD_DOCS[:-1])
tv = TfidfVectorizer(norm='l1')
tv.max_df = v1.max_df
tfidf2 = tv.fit_transform(train_data).toarray()
assert_false(tv.fixed_vocabulary_)
assert_array_almost_equal(tfidf, tfidf2)
# test the direct tfidf vectorizer with new data
tfidf_test2 = tv.transform(test_data).toarray()
assert_array_almost_equal(tfidf_test, tfidf_test2)
# test transform on unfitted vectorizer with empty vocabulary
v3 = CountVectorizer(vocabulary=None)
assert_raises(ValueError, v3.transform, train_data)
# ascii preprocessor?
v3.set_params(strip_accents='ascii', lowercase=False)
assert_equal(v3.build_preprocessor(), strip_accents_ascii)
# error on bad strip_accents param
v3.set_params(strip_accents='_gabbledegook_', preprocessor=None)
assert_raises(ValueError, v3.build_preprocessor)
# error with bad analyzer type
v3.set_params = '_invalid_analyzer_type_'
assert_raises(ValueError, v3.build_analyzer)
def test_request_unknown_dimension():
brick = TestBrick()
assert_raises(ValueError, brick.get_dim, 'unknown')
def test_may_share_memory_bad_max_work():
x = np.zeros([1])
assert_raises(OverflowError, np.may_share_memory, x, x, max_work=10**100)
assert_raises(OverflowError, np.shares_memory, x, x, max_work=10**100)
def test_transform_error(self, X, y, expected):
enc = TargetEncoder(cols=['cat'], handle_unseen='error')
X = pd.DataFrame(X, columns=['cat'])
enc.fit(X, pd.Series(y))
X.iloc[0, 0] = 'foo'
assert_raises(ValueError, enc.transform, X)
def test_apply():
brick = TestBrick(0)
assert TestBrick.apply(brick, [0]) == [0, 1]
if six.PY2:
assert_raises(TypeError, TestBrick.apply, [0])
def test_init_wrong_input(self, handle_unseen):
assert_raises(ValueError, TargetEncoder, None, handle_unseen)
def test_apply_not_child():
child = TestBrick()
parent = ParentBrick(child)
parent.children = []
assert_raises(ValueError, parent.apply, tensor.matrix())
def test_error_lowsamples(self):
# raises error if samples are low (< 3)
x = np.arange(3)
y = np.arange(3)
assert_raises(ValueError, _CheckInputs(x, y))
def test_transform_before_fit(self):
enc = TargetEncoder()
assert_raises(ValueError, enc.transform, 1)
def test_error_notndarray(self):
# raises error if x or y is not a ndarray
x = np.arange(20)
y = [5] * 20
assert_raises(TypeError, _CheckInputs(x, y))
assert_raises(TypeError, _CheckInputs(y, x))
def test_error_reps(self, reps):
# raises error if reps is negative
x = np.arange(20)
assert_raises(ValueError, _CheckInputs(x, x, reps=reps))
def test_pairwise_distances_no_broadcast(self):
assert_allclose(pairwise_distances_no_broadcast(self.X, self.Y),
[1.41421356, 2.23606798, 4.58257569, 4.12310563])
with assert_raises(ValueError):
pairwise_distances_no_broadcast([1, 2, 3], [6])
def test_error_shape(self):
# raises error if number of samples different (n)
x = np.arange(100).reshape(25, 4)
y = x.reshape(10, 10)
assert_raises(ValueError, _CheckInputs(x, y))