def test_non_unique_arg_member(self):
"""
test how the non-unique membership operation performs
"""
arr1 = numpy.array([[1, 1, 1], [1, 1, -1], [0, 0, 0]])
las2 = lexarrayset.create([[0, 1], [0, 1], [0, 0]])
members = lexarrayset.nonunique_member(arr1, las2.data)
assert_array_equal(members, [True,
True,
False])
arr1 = numpy.array([[1, 3, 3, 1, 1, 1, 1],
[2, 2, 2, 2, 1, 1, -1],
[3, 1, 1, 3, 0, 0, 0]])
las2 = lexarrayset.create([[0, 1, -1, 1],
[0, 1, -1, 2],
[0, 0, -1, 3]])
members = lexarrayset.nonunique_member(arr1, las2.data)
assert_array_equal(members, [True,
False,
False,
True,
True,
True,
False, ])
def test_non_unique_indices_query_offset(self):
states = [[0, 0, 1, 1, 2, 7, 2],
[0, 1, 0, 1, 1, 0, 2]]
goal_order = [0, 2, 5, 1, 3, 4, 6]
assert_array_equal(numpy.lexsort(states),
goal_order)
enum = state_enum.create(states)
# apply offset
offset = 42
enum.offset = offset
# verify that looking up the indices
# for a collection of non-unique query states
# returns a correctly sized index array with the correct
# corresponding indices
query_states = [[7, 2, 1, 2, 1, 7, 7, 2, 1],
[0, 1, 0, 2, 0, 0, 0, 2, 1]]
indices = enum.indices(query_states)
assert_array_equal(indices - offset,
[2, 5, 1, 6, 1, 2, 2, 6, 4])
def _mask_tester(norm_instance, vals):
"""
Checks mask handling
"""
masked_array = np.ma.array(vals)
masked_array[0] = np.ma.masked
assert_array_equal(masked_array.mask, norm_instance(masked_array).mask)
def test_non_unique_contains_query(self):
states = [[0, 0, 1, 1, 2, 7, 2],
[0, 1, 0, 1, 1, 0, 2]]
enum = state_enum.create(states)
query_states = [[-1, 7, 2, 1, 2, 9, 1, 7, 7, 2, -1, 1],
[-1, 0, 1, 0, 2, 9, 0, 0, 0, 2, -1, 1]]
member_flags = enum.contains(query_states)
goal_member_flags = [False,
True,
True,
True,
True,
False,
True,
True,
True,
True,
False,
True]
assert_array_equal(member_flags,
goal_member_flags)
def test_cmap_and_norm_from_levels_and_colors2():
levels = [-1, 2, 2.5, 3]
colors = ["red", (0, 1, 0), "blue", (0.5, 0.5, 0.5), (0.0, 0.0, 0.0, 1.0)]
clr = mcolors.colorConverter.to_rgba_array(colors)
bad = (0.1, 0.1, 0.1, 0.1)
no_color = (0.0, 0.0, 0.0, 0.0)
masked_value = "masked_value"
# Define the test values which are of interest.
# Note: levels are lev[i] <= v < lev[i+1]
tests = [
("both", None, {-2: clr[0], -1: clr[1], 2: clr[2], 2.25: clr[2], 3: clr[4], 3.5: clr[4], masked_value: bad}),
("min", -1, {-2: clr[0], -1: clr[1], 2: clr[2], 2.25: clr[2], 3: no_color, 3.5: no_color, masked_value: bad}),
("max", -1, {-2: no_color, -1: clr[0], 2: clr[1], 2.25: clr[1], 3: clr[3], 3.5: clr[3], masked_value: bad}),
(
"neither",
-2,
{-2: no_color, -1: clr[0], 2: clr[1], 2.25: clr[1], 3: no_color, 3.5: no_color, masked_value: bad},
),
]
for extend, i1, cases in tests:
cmap, norm = mcolors.from_levels_and_colors(levels, colors[0:i1], extend=extend)
cmap.set_bad(bad)
for d_val, expected_color in cases.items():
if d_val == masked_value:
d_val = np.ma.array([1], mask=True)
else:
d_val = [d_val]
assert_array_equal(
expected_color, cmap(norm(d_val))[0], "Wih extend={0!r} and data " "value={1!r}".format(extend, d_val)
)
assert_raises(ValueError, mcolors.from_levels_and_colors, levels, colors)
def test_MRData_clean_nans():
data = np.array([[1, 2, 3, np.nan], [np.nan, 4, 5, 6]])
result = MRData()._clean_nans(data)
expected_result = np.array([[1, 2, 3, 6], [1, 4, 5, 6]])
assert_array_equal(result, expected_result)
def test_strictly_decreasing_but_less_than_threshold(self):
data = np.linspace(1.05, 1.0, 10)
result = zigzag.peak_valley_pivots(data, 0.1, -0.1)
expected_result = np.zeros_like(data)
expected_result[0], expected_result[-1] = PEAK, VALLEY
assert_array_equal(result, expected_result)
def test_strictly_increasing(self):
data = np.linspace(1, 10, 10)
result = zigzag.peak_valley_pivots(data, 0.1, -0.1)
expected_result = np.zeros_like(data)
expected_result[0], expected_result[-1] = VALLEY, PEAK
assert_array_equal(result, expected_result)
def test_rgba(self):
actual = dmp(self.arr3, self.arr_rgba)
ind = [0, 1, 5]
expected = (self.arr3.take(ind).compressed(),
self.arr_rgba.take(ind, axis=0))
assert_array_equal(actual[0], expected[0])
assert_array_equal(actual[1], expected[1])
def test_set_density_simulator():
scen, control = test_ctm.small_scenario()
set_densities = {1: [.5] * scen.T}
sim = ctm_admm.ControlledCtmSimulator(set_densities)
state = sim.simulate(scen, control)
state.plot()
assert_array_equal(state.density[set_densities.keys(), :-1], set_densities.values())
def test_meg_field_interpolation_helmet():
"""Test interpolation of MEG field onto helmet
"""
evoked = read_evoked(evoked_fname, setno='Left Auditory')
info = evoked.info
surf = get_meg_helmet_surf(info)
# let's reduce the number of channels by a bunch to speed it up
info['bads'] = info['ch_names'][:200]
# bad ch_type
assert_raises(ValueError, make_surface_mapping, info, surf, 'foo')
# bad mode
assert_raises(ValueError, make_surface_mapping, info, surf, 'meg',
mode='foo')
# no picks
evoked_eeg = pick_types_evoked(evoked, meg=False, eeg=True)
assert_raises(RuntimeError, make_surface_mapping, evoked_eeg.info,
surf, 'meg')
# bad surface def
nn = surf['nn']
del surf['nn']
assert_raises(KeyError, make_surface_mapping, info, surf, 'meg')
surf['nn'] = nn
cf = surf['coord_frame']
del surf['coord_frame']
assert_raises(KeyError, make_surface_mapping, info, surf, 'meg')
surf['coord_frame'] = cf
# now do it
data = make_surface_mapping(info, surf, 'meg', mode='fast')
assert_array_equal(data.shape, (304, 106)) # data onto surf
def compare_wcs(w1, w2, exclude_keywords=None):
"""
Compare two WCSs.
Parameters
----------
w1, w2 : `astropy.wcs.WCS` objects
exclude_keywords : list
List of keywords to excude from comparison.
"""
exclude_ctype = False
keywords = ['crval', 'crpix', 'cd']
if exclude_keywords is not None:
exclude_keywords = [kw.lower() for kw in exclude_keywords]
if 'ctype' in exclude_keywords:
exclude_ctype = True
exclude_keywords.remove('ctype')
for kw in exclude_keywords:
keywords.remove(kw)
for kw in keywords:
kw1 = getattr(w1.wcs, kw)
kw2 = getattr(w2.wcs, kw)
utils.assert_allclose(kw1, kw2, 1e-10)
#utils.assert_allclose(w1.wcs.crpix, w2.wcs.crpix, 1e-10)
#utils.assert_allclose(w1.wcs.cd, w2.wcs.cd, 1e-10)
if not exclude_ctype:
utils.assert_array_equal(np.array(w1.wcs.ctype), np.array(w2.wcs.ctype))
def testFileOpenAndPostProcess():
raw = rawpy.imread(rawTestPath)
assert_array_equal(raw.raw_image.shape, [2844, 4288])
rgb = raw.postprocess(no_auto_bright=True, user_wb=raw.daylight_whitebalance)
assert_array_equal(rgb.shape, [2844, 4284, 3])
print_stats(rgb)
save('test_8daylight.tiff', rgb)
print('daylight white balance multipliers:', raw.daylight_whitebalance)
rgb = raw.postprocess(no_auto_bright=True, user_wb=raw.daylight_whitebalance)
print_stats(rgb)
save('test_8daylight2.tiff', rgb)
rgb = raw.postprocess(no_auto_bright=True, user_wb=raw.daylight_whitebalance,
output_bps=16)
print_stats(rgb)
save('test_16daylight.tiff', rgb)
# linear images are more useful for science (=no gamma correction)
# see http://www.mit.edu/~kimo/blog/linear.html
rgb = raw.postprocess(no_auto_bright=True, user_wb=raw.daylight_whitebalance,
gamma=(1,1), output_bps=16)
print_stats(rgb)
save('test_16daylight_linear.tiff', rgb)
def test_rotation_matrix():
from ..angles import rotation_matrix
assert_array_equal(rotation_matrix(0*u.deg, 'x'), np.eye(3))
assert_allclose(rotation_matrix(90*u.deg, 'y'), [[ 0, 0,-1],
[ 0, 1, 0],
[ 1, 0, 0]], atol=1e-12)
assert_allclose(rotation_matrix(-90*u.deg, 'z'), [[ 0,-1, 0],
[ 1, 0, 0],
[ 0, 0, 1]], atol=1e-12)
assert_allclose(rotation_matrix(45*u.deg, 'x'),
rotation_matrix(45*u.deg, [1, 0, 0]))
assert_allclose(rotation_matrix(125*u.deg, 'y'),
rotation_matrix(125*u.deg, [0, 1, 0]))
assert_allclose(rotation_matrix(-30*u.deg, 'z'),
rotation_matrix(-30*u.deg, [0, 0, 1]))
assert_allclose(np.dot(rotation_matrix(180*u.deg, [1, 1, 0]).A, [1, 0, 0]),
[0, 1, 0], atol=1e-12)
#make sure it also works for very small angles
assert_allclose(rotation_matrix(0.000001*u.deg, 'x'),
rotation_matrix(0.000001*u.deg, [1, 0, 0]))
def testMargin(self):
graph = Graph()
vol = np.zeros((100, 110, 10), dtype=np.float32)
# draw a big plus sign
vol[50:70, :, :] = 1.0
vol[:, 60:80, :] = 1.0
vol = vigra.taggedView(vol, axistags="xyz").withAxes(*"txyzc")
labels = np.zeros((100, 110, 10), dtype=np.uint32)
labels[45:75, 55:85, 3:4] = 1
labels = vigra.taggedView(labels, axistags="xyz").withAxes(*"txyzc")
op = OpObjectsSegment(graph=graph)
piper = OpArrayPiper(graph=graph)
piper.Input.setValue(vol)
op.Prediction.connect(piper.Output)
op.LabelImage.setValue(labels)
# without margin
op.Margin.setValue(np.asarray((0, 0, 0)))
out = op.Output[...].wait()
out = vigra.taggedView(out, axistags=op.Output.meta.axistags)
out = out.withAxes(*"xyz")
vol = vol.withAxes(*"xyz")
assert_array_equal(out[50:70, 60:80, 3] > 0, vol[50:70, 60:80, 3] > 0.5)
assert np.all(out[:45, ...] == 0)
# with margin
op.Margin.setValue(np.asarray((5, 5, 0)))
out = op.Output[...].wait()
out = vigra.taggedView(out, axistags=op.Output.meta.axistags)
out = out.withAxes(*"xyz")
assert_array_equal(out[45:75, 55:85, 3] > 0, vol[45:75, 55:85, 3] > 0.5)
assert np.all(out[:40, ...] == 0)
def test_ndarray_subclass_norm(recwarn):
# Emulate an ndarray subclass that handles units
# which objects when adding or subtracting with other
# arrays. See #6622 and #8696
class MyArray(np.ndarray):
def __isub__(self, other):
raise RuntimeError
def __add__(self, other):
raise RuntimeError
data = np.arange(-10, 10, 1, dtype=float)
for norm in [mcolors.Normalize(), mcolors.LogNorm(),
mcolors.SymLogNorm(3, vmax=5, linscale=1),
mcolors.PowerNorm(1)]:
assert_array_equal(norm(data.view(MyArray)), norm(data))
if isinstance(norm, mcolors.PowerNorm):
assert len(recwarn) == 1
warn = recwarn.pop(UserWarning)
assert ('Power-law scaling on negative values is ill-defined'
in str(warn.message))
else:
assert len(recwarn) == 0
recwarn.clear()
def test_pims_images(image_uid):
header = db[image_uid]
images = get_images(header, 'img')
images[:5] # smoke test
assert images.pixel_type == np.float64
assert_array_equal(images.frame_shape, images[0].shape)
assert len(images) == image_and_scalar.num1
def test_read_allow_secondary(tickstore_lib):
data = [{'ASK': 1545.25,
'ASKSIZE': 1002.0,
'BID': 1545.0,
'BIDSIZE': 55.0,
'CUMVOL': 2187387.0,
'DELETED_TIME': 0,
'INSTRTYPE': 'FUT',
'PRICE': 1545.0,
'SIZE': 1.0,
'TICK_STATUS': 0,
'TRADEHIGH': 1561.75,
'TRADELOW': 1537.25,
'index': 1185076787070},
{'CUMVOL': 354.0,
'DELETED_TIME': 0,
'PRICE': 1543.75,
'SIZE': 354.0,
'TRADEHIGH': 1543.75,
'TRADELOW': 1543.75,
'index': 1185141600600}]
tickstore_lib.write('FEED::SYMBOL', data)
with patch('pymongo.collection.Collection.find', side_effect=tickstore_lib._collection.find) as find:
with patch('pymongo.collection.Collection.with_options', side_effect=tickstore_lib._collection.with_options) as with_options:
with patch.object(tickstore_lib, '_read_preference', side_effect=tickstore_lib._read_preference) as read_pref:
df = tickstore_lib.read('FEED::SYMBOL', columns=['BID', 'ASK', 'PRICE'], allow_secondary=True)
assert read_pref.call_args_list == [call(True)]
assert with_options.call_args_list == [call(read_preference=ReadPreference.NEAREST)]
assert find.call_args_list == [call({'sy': 'FEED::SYMBOL'}, sort=[('s', 1)], projection={'s': 1, '_id': 0}),
call({'sy': 'FEED::SYMBOL', 's': {'$lte': dt(2007, 8, 21, 3, 59, 47, 70000)}},
projection={'sy': 1, 'cs.PRICE': 1, 'i': 1, 'cs.BID': 1, 's': 1, 'im': 1, 'v': 1, 'cs.ASK': 1})]
assert_array_equal(df['ASK'].values, np.array([1545.25, np.nan]))
assert tickstore_lib._collection.find_one()['c'] == 2
def test_pims_images():
header = db[-1]
images = Images(header, 'img')
images[:5] # smoke test
assert_equal(images.pixel_type, np.float64)
assert_array_equal(images.frame_shape, images[0].shape)
assert_equal(len(images), image_and_scalar.num1)
def testBBMerge(self):
bb1 = BoundingBox(latSouth=-55, lonWest=95, latNorth=-45, lonEast=109)
bb2 = BoundingBox(latSouth=44, lonWest=-164, latNorth=74, lonEast=-35)
bb = BoundingBox.mergedBoundingBoxes([bb1,bb2])
assert_array_equal([bb.latSouth,bb.latNorth,bb.lonWest,bb.lonEast],
[bb1.latSouth,bb2.latNorth,bb1.lonWest,bb2.lonEast])
assert_array_almost_equal(bb.center, [21.136113246, -150])
def test_datetime(self):
actual = dmp(self.arr_dt, self.arr3)
ind = [0, 1, 5]
expected = (self.arr_dt2.take(ind),
self.arr3.take(ind).compressed())
assert_array_equal(actual[0], expected[0])
assert_array_equal(actual[1], expected[1])
def test_event_monitor_no_record():
# Check that you can switch off recording spike times/indices
G = NeuronGroup(3, '''dv/dt = rate : 1
rate: Hz''', events={'my_event': 'v>1'},
threshold='v>1', reset='v=0')
# We don't use 100 and 1000Hz, because then the membrane potential would
# be exactly at 1 after 10 resp. 100 timesteps. Due to floating point
# issues this will not be exact,
G.rate = [101, 0, 1001] * Hz
event_mon = EventMonitor(G, 'my_event', record=False)
event_mon2 = EventMonitor(G, 'my_event', variables='rate', record=False)
spike_mon = SpikeMonitor(G, record=False)
spike_mon2 = SpikeMonitor(G, variables='rate', record=False)
net = Network(G, event_mon, event_mon2, spike_mon, spike_mon2)
net.run(10*ms)
# i and t should not be there
assert 'i' not in event_mon.variables
assert 't' not in event_mon.variables
assert 'i' not in spike_mon.variables
assert 't' not in spike_mon.variables
assert_array_equal(event_mon.count, np.array([1, 0, 10]))
assert_array_equal(spike_mon.count, np.array([1, 0, 10]))
assert spike_mon.num_spikes == sum(spike_mon.count)
assert event_mon.num_events == sum(event_mon.count)
# Other variables should still have been recorded
assert len(spike_mon2.rate) == spike_mon.num_spikes
assert len(event_mon2.rate) == event_mon.num_events
def testBufferOpen():
with open(rawTestPath, 'rb') as rawfile:
with rawpy.imread(rawfile) as raw:
assert_array_equal(raw.raw_image.shape, [2844, 4288])
rgb = raw.postprocess()
print_stats(rgb)
save('test_buffer.tiff', rgb)
def test_cad_msip(self):
# collecting cad output
output_msip = cad.\
cell_assembly_detection(data=self.msip, maxlag=self.maxlag)
elements_msip = []
occ_msip = []
lags_msip = []
for out in output_msip:
elements_msip.append(out['neurons'])
occ_msip.append(out['times'])
lags_msip.append(list(out['lags']))
elements_msip = sorted(elements_msip, key=lambda d: len(d))
occ_msip = sorted(occ_msip, key=lambda d: len(d))
lags_msip = sorted(lags_msip, key=lambda d: len(d))
elements_msip = [sorted(e) for e in elements_msip]
# check neurons in the patterns
assert_array_equal(elements_msip, self.elements_msip)
# check the occurrences time of the patters
assert_array_equal(occ_msip[0], self.occ_msip[0])
assert_array_equal(occ_msip[1], self.occ_msip[1])
assert_array_equal(occ_msip[2], self.occ_msip[2])
lags_msip = [sorted(e) for e in lags_msip]
# check the lags
assert_array_equal(lags_msip, self.lags_msip)
def test_XOR(self):
ds = self._buildXORData()
self.nu.train(ds)
results, _ = self.nu.activate(ds)
assert_array_equal(results, [[2, 0, 100], [0, 2, 100]])
def test_volsurf_projections(self):
white = surf.generate_plane((0, 0, 0), (0, 1, 0), (0, 0, 1), 10, 10)
pial = white + np.asarray([[1, 0, 0]])
above = pial + np.asarray([[3, 0, 0]])
vg = volgeom.VolGeom((10, 10, 10), np.eye(4))
vs = volsurf.VolSurfMaximalMapping(vg, white, pial)
dx = pial.vertices - white.vertices
for s, w in ((white, 0), (pial, 1), (above, 4)):
xyz = s.vertices
ws = vs.surf_project_weights(True, xyz)
delta = vs.surf_unproject_weights_nodewise(ws) - xyz
assert_array_equal(delta, np.zeros((100, 3)))
assert_true(np.all(w == ws))
vs = volsurf.VolSurfMaximalMapping(vg, white, pial, nsteps=2)
n2vs = vs.get_node2voxels_mapping()
assert_equal(n2vs, dict((i, {i: 0.0, i + 100: 1.0}) for i in xrange(100)))
nd = 17
ds_mm_expected = np.sum((above.vertices - pial.vertices[nd, :]) ** 2, 1) ** 0.5
ds_mm = vs.coordinates_to_grey_distance_mm(nd, above.vertices)
assert_array_almost_equal(ds_mm_expected, ds_mm)
ds_mm_nodewise = vs.coordinates_to_grey_distance_mm(True, above.vertices)
assert_array_equal(ds_mm_nodewise, np.ones((100,)) * 3)
def test_poly1d_multiple_sets(self):
p1 = models.Polynomial1D(3, n_models=3)
utils.assert_equal(p1.parameters, [0.0, 0.0, 0.0, 0, 0, 0,
0, 0, 0, 0, 0, 0])
utils.assert_array_equal(p1.c0, [0, 0, 0])
p1.c0 = [10, 10, 10]
utils.assert_equal(p1.parameters, [10.0, 10.0, 10.0, 0, 0,
0, 0, 0, 0, 0, 0, 0])
def test_mixed_string_and_quantity():
a1 = Angle(['1d', 1. * u.deg])
assert_array_equal(a1.value, [1., 1.])
assert a1.unit == u.deg
a2 = Angle(['1d', 1 * u.rad * np.pi, '3d'])
assert_array_equal(a2.value, [1., 180., 3.])
assert a2.unit == u.deg
def test_LogNorm():
"""
LogNorm ignored clip, now it has the same
behavior as Normalize, e.g., values > vmax are bigger than 1
without clip, with clip they are 1.
"""
ln = mcolors.LogNorm(clip=True, vmax=5)
assert_array_equal(ln([1, 6]), [0, 1.0])
def test_scatter_gather_numpy(self):
import numpy
from numpy.testing.utils import assert_array_equal, assert_array_almost_equal
view = self.client[:]
a = numpy.arange(64)
view.scatter('a', a)
b = view.gather('a', block=True)
assert_array_equal(b, a)
def test_time_histogram_output(self):
# Normalization mean
histogram = statistics.time_histogram(self.spiketrains,
bin_size=pq.s,
output='mean')
targ = np.array([4, 2, 1, 1, 2, 2, 1, 0, 1, 0], dtype=float) / 2
assert_array_equal(targ.reshape(targ.size, 1), histogram.magnitude)
# Normalization rate
histogram = statistics.time_histogram(self.spiketrains,
bin_size=pq.s,
output='rate')
assert_array_equal(histogram.view(pq.Quantity),
targ.reshape(targ.size, 1) * 1 / pq.s)
# Normalization unspecified, raises error
self.assertRaises(ValueError,
statistics.time_histogram,
self.spiketrains,
bin_size=pq.s,
output=' ')
def test_spade_msip_3d(self):
output_msip = spade.spade(self.msip,
self.bin_size,
self.winlen,
approx_stab_pars=dict(
n_subsets=self.n_subset,
stability_thresh=self.stability_thresh),
n_surr=self.n_surr,
spectrum='3d#',
alpha=self.alpha,
psr_param=self.psr_param,
stat_corr='no',
output_format='patterns')['patterns']
elements_msip = []
occ_msip = []
lags_msip = []
# collecting spade output
for out in output_msip:
elements_msip.append(out['neurons'])
occ_msip.append(list(out['times'].magnitude))
lags_msip.append(list(out['lags'].magnitude))
elements_msip = sorted(elements_msip, key=len)
occ_msip = sorted(occ_msip, key=len)
lags_msip = sorted(lags_msip, key=len)
# check neurons in the patterns
assert_array_equal(elements_msip, self.elements_msip)
# check the occurrences time of the patters
assert_array_equal(occ_msip, self.occ_msip)
# check the lags
assert_array_equal(lags_msip, self.lags_msip)
def test_minimal_dataset(self):
vol_shape = (10, 10, 10, 3)
vol_affine = np.identity(4)
vg = volgeom.VolGeom(vol_shape, vol_affine)
data = np.random.normal(size=vol_shape)
msk = np.ones(vol_shape[:3])
msk[:, 1:-1:2, :] = 0
ni_data = nb.Nifti1Image(data, vol_affine)
ni_msk = nb.Nifti1Image(msk, vol_affine)
ds = fmri_dataset(ni_data, mask=ni_msk)
sphere_density = 20
outer = surf.generate_sphere(sphere_density) * 10. + 5
inner = surf.generate_sphere(sphere_density) * 7. + 5
radius = 10
sel = surf_voxel_selection.run_voxel_selection(radius, ds, inner,
outer)
sel_fids = set.union(*(set(sel[k]) for k in sel.keys()))
ds_vox = map(tuple, ds.fa.voxel_indices)
vg = sel.volgeom
sel_vox = map(tuple, vg.lin2ijk(np.asarray(list(sel_fids))))
fid_mask = np.asarray([v in sel_vox for v in ds_vox])
assert_array_equal(fid_mask, sel.get_dataset_feature_mask(ds))
# check if it raises errors
ni_neg_msk = nb.Nifti1Image(1 - msk, vol_affine)
neg_ds = fmri_dataset(ni_data, mask=ni_neg_msk) # inverted mask
assert_raises(ValueError, sel.get_dataset_feature_mask, neg_ds)
min_ds = sel.get_minimal_dataset(ds)
assert_array_equal(min_ds.samples, ds[:, fid_mask].samples)
def test_spade_msip(self):
output_msip = spade.spade(self.msip,
self.binsize,
self.winlen,
n_subsets=self.n_subset,
stability_thresh=self.stability_thresh,
n_surr=self.n_surr,
alpha=self.alpha,
psr_param=self.psr_param,
output_format='patterns')['patterns']
elements_msip = []
occ_msip = []
lags_msip = []
# collecting spade output
for out in output_msip:
elements_msip.append(out['neurons'])
occ_msip.append(list(out['times'].magnitude))
lags_msip.append(list(out['lags'].magnitude))
elements_msip = sorted(elements_msip, key=lambda d: len(d))
occ_msip = sorted(occ_msip, key=lambda d: len(d))
lags_msip = sorted(lags_msip, key=lambda d: len(d))
# check neurons in the patterns
assert_array_equal(elements_msip, self.elements_msip)
# check the occurrences time of the patters
assert_array_equal(occ_msip, self.occ_msip)
# check the lags
assert_array_equal(lags_msip, self.lags_msip)
def test_date_range_BST(tickstore_lib):
DUMMY_DATA = [
{'a': 1.,
'b': 2.,
'index': dt(2013, 6, 1, 12, 00, tzinfo=mktz('Europe/London'))
},
{'a': 3.,
'b': 4.,
'index': dt(2013, 6, 1, 13, 00, tzinfo=mktz('Europe/London'))
},
]
tickstore_lib._chunk_size = 1
tickstore_lib.write('SYM', DUMMY_DATA)
df = tickstore_lib.read('SYM', columns=None)
assert_array_equal(df['b'].values, np.array([2., 4.]))
# df = tickstore_lib.read('SYM', columns=None, date_range=DateRange(dt(2013, 6, 1, 12),
# dt(2013, 6, 1, 13)))
# assert_array_equal(df['b'].values, np.array([2., 4.]))
df = tickstore_lib.read('SYM', columns=None, date_range=DateRange(dt(2013, 6, 1, 12, tzinfo=mktz('Europe/London')),
dt(2013, 6, 1, 13, tzinfo=mktz('Europe/London'))))
assert_array_equal(df['b'].values, np.array([2., 4.]))
df = tickstore_lib.read('SYM', columns=None, date_range=DateRange(dt(2013, 6, 1, 12, tzinfo=mktz('UTC')),
dt(2013, 6, 1, 13, tzinfo=mktz('UTC'))))
assert_array_equal(df['b'].values, np.array([4., ]))
def test_push_pull_recarray(self):
"""push/pull recarrays"""
import numpy
from numpy.testing.utils import assert_array_equal
view = self.client[-1]
R = numpy.array([
(1, 'hi', 0.),
(2**30, 'there', 2.5),
(-99999, 'world', -12345.6789),
], [('n', int), ('s', '|S10'), ('f', float)])
view['RR'] = R
R2 = view['RR']
r_dtype, r_shape = view.apply_sync(interactive(lambda : (RR.dtype, RR.shape)))
self.assertEqual(r_dtype, R.dtype)
self.assertEqual(r_shape, R.shape)
self.assertEqual(R2.dtype, R.dtype)
self.assertEqual(R2.shape, R.shape)
assert_array_equal(R2, R)
def test_spade_cpp(self):
output_cpp = spade.spade(self.cpp,
self.bin_size,
1,
approx_stab_pars=dict(
n_subsets=self.n_subset,
stability_thresh=self.stability_thresh),
n_surr=self.n_surr,
alpha=self.alpha,
psr_param=self.psr_param,
stat_corr='no',
output_format='patterns')['patterns']
elements_cpp = []
lags_cpp = []
# collecting spade output
for out in output_cpp:
elements_cpp.append(sorted(out['neurons']))
lags_cpp.append(list(out['lags'].magnitude))
# check neurons in the patterns
assert_array_equal(elements_cpp, [range(self.n_neu)])
# check the lags
assert_array_equal(lags_cpp, [np.array([0] * (self.n_neu - 1))])
def test_numpy():
import numpy
from numpy.testing.utils import assert_array_equal
for shape in SHAPES:
for dtype in DTYPES:
A = numpy.empty(shape, dtype=dtype)
_scrub_nan(A)
bufs = serialize_object(A)
B, r = unserialize_object(bufs)
yield nt.assert_equals(r, [])
yield nt.assert_equals(A.shape, B.shape)
yield nt.assert_equals(A.dtype, B.dtype)
yield assert_array_equal(A,B)
def testComplete(self):
graph = Graph()
op = OpObjectsSegment(graph=graph)
piper = OpArrayPiper(graph=graph)
piper.Input.setValue(self.vol)
op.Prediction.connect(piper.Output)
piper = OpArrayPiper(graph=graph)
piper.Input.setValue(self.labels)
op.LabelImage.connect(piper.Output)
# get whole volume
out = op.CachedOutput[...].wait()
out = vigra.taggedView(out, axistags=op.Output.meta.axistags)
# check whether no new blocks introduced
mask = np.where(self.labels > 0, 0, 1)
masked = out * mask
assert_array_equal(masked, 0 * masked)
# check whether the interior was labeled 1
assert np.all(out[:, 22:38, 22:38, 22:38, :] > 0)
assert np.all(out[:, 62:78, 62:78, 62:78, :] > 0)
def test_Normalize():
norm = mcolors.Normalize()
vals = np.arange(-10, 10, 1, dtype=float)
_inverse_tester(norm, vals)
_scalar_tester(norm, vals)
_mask_tester(norm, vals)
# Handle integer input correctly (don't overflow when computing max-min,
# i.e. 127-(-128) here).
vals = np.array([-128, 127], dtype=np.int8)
norm = mcolors.Normalize(vals.min(), vals.max())
assert_array_equal(np.asarray(norm(vals)), [0, 1])
# Don't lose precision on longdoubles (float128 on Linux):
# for array inputs...
vals = np.array([1.2345678901, 9.8765432109], dtype=np.longdouble)
norm = mcolors.Normalize(vals.min(), vals.max())
assert_array_equal(np.asarray(norm(vals)), [0, 1])
# and for scalar ones.
eps = np.finfo(np.longdouble).resolution
norm = plt.Normalize(1, 1 + 100 * eps)
assert_equal(norm(1 + 50 * eps), .5)
def test_pattern_set_reduction(self):
output_msip = spade.spade(self.patt_psr, self.binsize, self.winlen,
n_subsets=self.n_subset,
stability_thresh=self.stability_thresh,
n_surr=self.n_surr, spectrum='3d#',
alpha=self.alpha, psr_param=self.psr_param,
output_format='patterns')['patterns']
elements_msip = []
occ_msip = []
lags_msip = []
# collecting spade output
for out in output_msip:
elements_msip.append(sorted(out['neurons']))
occ_msip.append(list(out['times'].magnitude))
lags_msip.append(list(out['lags'].magnitude))
elements_msip = sorted(elements_msip, key=lambda d: len(d))
occ_msip = sorted(occ_msip, key=lambda d: len(d))
lags_msip = sorted(lags_msip, key=lambda d: len(d))
# check neurons in the patterns
assert_array_equal(elements_msip, [range(len(self.lags3) + 1)])
# check the occurrences time of the patters
assert_array_equal(len(occ_msip[0]), self.n_occ3)
def test_make_field_map_eeg():
"""Test interpolation of EEG field onto head
"""
evoked = read_evokeds(evoked_fname, condition='Left Auditory')
evoked.info['bads'] = ['MEG 2443', 'EEG 053'] # add some bads
surf = get_head_surf('sample', subjects_dir=subjects_dir)
# we must have trans if surface is in MRI coords
assert_raises(ValueError, _make_surface_mapping, evoked.info, surf, 'eeg')
evoked.pick_types(meg=False, eeg=True)
fmd = make_field_map(evoked, trans_fname,
subject='sample', subjects_dir=subjects_dir)
# trans is necessary for EEG only
assert_raises(RuntimeError, make_field_map, evoked, None,
subject='sample', subjects_dir=subjects_dir)
fmd = make_field_map(evoked, trans_fname,
subject='sample', subjects_dir=subjects_dir)
assert_true(len(fmd) == 1)
assert_array_equal(fmd[0]['data'].shape, (642, 59)) # maps data onto surf
assert_true(len(fmd[0]['ch_names']), 59)
def testScatterGatherNumpy(self):
try:
import numpy
from numpy.testing.utils import assert_array_equal, assert_array_almost_equal
except:
return
else:
self.addEngine(4)
a = numpy.arange(16)
d = self.multiengine.scatter('a', a)
d.addCallback(lambda r: self.multiengine.gather('a'))
d.addCallback(lambda r: assert_array_equal(r, a))
return d
def test_event_monitor():
G = NeuronGroup(3,
'''dv/dt = rate : 1
rate: Hz''',
events={'my_event': 'v>1'})
G.run_on_event('my_event', 'v=0')
# We don't use 100 and 1000Hz, because then the membrane potential would
# be exactly at 1 after 10 resp. 100 timesteps. Due to floating point
# issues this will not be exact,
G.rate = [101, 0, 1001] * Hz
mon = EventMonitor(G, 'my_event')
net = Network(G, mon)
net.run(10 * ms)
event_trains = mon.event_trains()
assert_allclose(mon.t[mon.i == 0], [9.9] * ms)
assert len(mon.t[mon.i == 1]) == 0
assert_allclose(mon.t[mon.i == 2], np.arange(10) * ms + 0.9 * ms)
assert_allclose(mon.t_[mon.i == 0], np.array([9.9 * float(ms)]))
assert len(mon.t_[mon.i == 1]) == 0
assert_allclose(mon.t_[mon.i == 2], (np.arange(10) + 0.9) * float(ms))
assert_allclose(event_trains[0], [9.9] * ms)
assert len(event_trains[1]) == 0
assert_allclose(event_trains[2], np.arange(10) * ms + 0.9 * ms)
assert_array_equal(mon.count, np.array([1, 0, 10]))
i, t = mon.it
i_, t_ = mon.it_
assert_array_equal(i, mon.i)
assert_array_equal(i, i_)
assert_array_equal(t, mon.t)
assert_array_equal(t_, mon.t_)
assert_raises(KeyError, lambda: event_trains[3])
assert_raises(KeyError, lambda: event_trains[-1])
assert_raises(KeyError, lambda: event_trains['string'])
def test_writeStructredFile(self):
filePath = self.PATH + "test_structured.csv"
data = {
"A": {
"value": [1, 2, 3],
"quality": [-1, -1, -1]
},
"B": {
"value": [4, 5, 6],
"quality": [-2, -2, -2]
},
"C": {
"value": [7, 8, 9],
"quality": [-3, -3, -3]
}
}
self.reader.writeStructredFile(filePath, data)
if isfile(filePath):
read = self.reader.readEEGFile(filePath)
for key, values in data.iteritems():
assert_array_equal(values["value"], read.getColumn(key))
self.removeFile(filePath)
def test_non_unique_indices_query_offset(self):
states = [[0, 0, 1, 1, 2, 7, 2], [0, 1, 0, 1, 1, 0, 2]]
goal_order = [0, 2, 5, 1, 3, 4, 6]
assert_array_equal(numpy.lexsort(states), goal_order)
enum = state_enum.create(states)
# apply offset
offset = 42
enum.offset = offset
# verify that looking up the indices
# for a collection of non-unique query states
# returns a correctly sized index array with the correct
# corresponding indices
query_states = [[7, 2, 1, 2, 1, 7, 7, 2, 1],
[0, 1, 0, 2, 0, 0, 0, 2, 1]]
indices = enum.indices(query_states)
assert_array_equal(indices - offset, [2, 5, 1, 6, 1, 2, 2, 6, 4])
def test_non_unique_arg_member(self):
"""
test how the non-unique membership operation performs
"""
arr1 = numpy.array([[1, 1, 1], [1, 1, -1], [0, 0, 0]])
las2 = lexarrayset.create([[0, 1], [0, 1], [0, 0]])
members = lexarrayset.nonunique_member(arr1, las2.data)
assert_array_equal(members, [True, True, False])
arr1 = numpy.array([[1, 3, 3, 1, 1, 1, 1], [2, 2, 2, 2, 1, 1, -1],
[3, 1, 1, 3, 0, 0, 0]])
las2 = lexarrayset.create([[0, 1, -1, 1], [0, 1, -1, 2], [0, 0, -1,
3]])
members = lexarrayset.nonunique_member(arr1, las2.data)
assert_array_equal(members, [
True,
False,
False,
True,
True,
True,
False,
])
def test_cad_msip(self):
# collecting cad output
output_msip = cad.cell_assembly_detection(binned_spiketrain=self.msip,
max_lag=self.max_lag)
for i, out in enumerate(output_msip):
assert_array_equal(out['times'], self.occ_msip[i] * self.bin_size)
assert_array_equal(
sorted(out['lags']) * pq.s, self.lags_msip[i] * self.bin_size)
assert_array_equal(sorted(out['neurons']), self.elements_msip[i])
def test_spike_monitor():
G = NeuronGroup(3, '''dv/dt = rate : 1
rate: Hz''', threshold='v>1', reset='v=0')
# We don't use 100 and 1000Hz, because then the membrane potential would
# be exactly at 1 after 10 resp. 100 timesteps. Due to floating point
# issues this will not be exact,
G.rate = [101, 0, 1001] * Hz
mon = SpikeMonitor(G)
assert_raises(ValueError, lambda: SpikeMonitor(G, order=1)) # need to specify 'when' as well
run(10*ms)
spike_trains = mon.spike_trains()
assert_allclose(mon.t[mon.i == 0], [9.9]*ms)
assert len(mon.t[mon.i == 1]) == 0
assert_allclose(mon.t[mon.i == 2], np.arange(10)*ms + 0.9*ms)
assert_allclose(mon.t_[mon.i == 0], np.array([9.9*float(ms)]))
assert len(mon.t_[mon.i == 1]) == 0
assert_allclose(mon.t_[mon.i == 2], (np.arange(10) + 0.9)*float(ms))
assert_allclose(spike_trains[0], [9.9]*ms)
assert len(spike_trains[1]) == 0
assert_allclose(spike_trains[2], np.arange(10)*ms + 0.9*ms)
assert_array_equal(mon.count, np.array([1, 0, 10]))
i, t = mon.it
i_, t_ = mon.it_
assert_array_equal(i, mon.i)
assert_array_equal(i, i_)
assert_array_equal(t, mon.t)
assert_array_equal(t_, mon.t_)
assert_raises(KeyError, lambda: spike_trains[3])
assert_raises(KeyError, lambda: spike_trains[-1])
assert_raises(KeyError, lambda: spike_trains['string'])
def testMargin(self):
graph = Graph()
vol = np.zeros((100, 110, 10), dtype=np.float32)
# draw a big plus sign
vol[50:70, :, :] = 1.0
vol[:, 60:80, :] = 1.0
vol = vigra.taggedView(vol, axistags='zyx').withAxes(*'tzyxc')
labels = np.zeros((100, 110, 10), dtype=np.uint32)
labels[45:75, 55:85, 3:4] = 1
labels = vigra.taggedView(labels,
axistags='zyx').withAxes(*'tzyxc')
op = OpObjectsSegment(graph=graph)
piper = OpArrayPiper(graph=graph)
piper.Input.setValue(vol)
op.Prediction.connect(piper.Output)
op.LabelImage.setValue(labels)
# without margin
op.MarginZYX.setValue(np.asarray((0, 0, 0)))
out = op.Output[...].wait()
out = vigra.taggedView(out, axistags=op.Output.meta.axistags)
out = out.withAxes(*'zyx')
vol = vol.withAxes(*'zyx')
assert_array_equal(out[50:70, 60:80, 3] > 0,
vol[50:70, 60:80, 3] > .5)
assert np.all(out[:45, ...] == 0)
# with margin
op.MarginZYX.setValue(np.asarray((5, 5, 0)))
out = op.Output[...].wait()
out = vigra.taggedView(out, axistags=op.Output.meta.axistags)
out = out.withAxes(*'zyx')
assert_array_equal(out[45:75, 55:85, 3] > 0,
vol[45:75, 55:85, 3] > .5)
assert np.all(out[:40, ...] == 0)
def test_make_field_map_meg():
"""Test interpolation of MEG field onto helmet
"""
evoked = read_evoked(evoked_fname, setno='Left Auditory')
info = evoked.info
surf = get_meg_helmet_surf(info)
# let's reduce the number of channels by a bunch to speed it up
info['bads'] = info['ch_names'][:200]
# bad ch_type
assert_raises(ValueError, _make_surface_mapping, info, surf, 'foo')
# bad mode
assert_raises(ValueError, _make_surface_mapping, info, surf, 'meg',
mode='foo')
# no picks
evoked_eeg = pick_types_evoked(evoked, meg=False, eeg=True)
assert_raises(RuntimeError, _make_surface_mapping, evoked_eeg.info,
surf, 'meg')
# bad surface def
nn = surf['nn']
del surf['nn']
assert_raises(KeyError, _make_surface_mapping, info, surf, 'meg')
surf['nn'] = nn
cf = surf['coord_frame']
del surf['coord_frame']
assert_raises(KeyError, _make_surface_mapping, info, surf, 'meg')
surf['coord_frame'] = cf
# now do it with make_field_map
evoked = pick_types_evoked(evoked, meg=True, eeg=False)
fmd = make_field_map(evoked, trans_fname=None,
subject='sample', subjects_dir=subjects_dir)
assert_true(len(fmd) == 1)
assert_array_equal(fmd[0]['data'].shape, (304, 106)) # maps data onto surf
assert_true(len(fmd[0]['ch_names']), 106)
assert_raises(ValueError, make_field_map, evoked, ch_type='foobar')
def testScatterGatherNumpyNonblocking(self):
try:
import numpy
from numpy.testing.utils import assert_array_equal, assert_array_almost_equal
except:
return
else:
self.addEngine(4)
a = numpy.arange(16)
d = self.multiengine.scatter('a', a, block=False)
d.addCallback(lambda did: self.multiengine.get_pending_deferred(did, True))
d.addCallback(lambda r: self.multiengine.gather('a', block=False))
d.addCallback(lambda did: self.multiengine.get_pending_deferred(did, True))
d.addCallback(lambda r: assert_array_equal(r, a))
return d
def test_parameters_3d(self):
# test min_spikes parameter
output_msip_min_spikes = spade.spade(
self.msip,
self.bin_size,
self.winlen,
min_spikes=self.min_spikes,
approx_stab_pars=dict(
n_subsets=self.n_subset),
n_surr=self.n_surr,
spectrum='3d#',
alpha=self.alpha,
psr_param=self.psr_param,
stat_corr='no',
output_format='patterns')['patterns']
# collecting spade output
elements_msip_min_spikes = []
for out in output_msip_min_spikes:
elements_msip_min_spikes.append(out['neurons'])
elements_msip_min_spikes = sorted(
elements_msip_min_spikes, key=len)
lags_msip_min_spikes = []
for out in output_msip_min_spikes:
lags_msip_min_spikes.append(list(out['lags'].magnitude))
lags_msip_min_spikes = sorted(
lags_msip_min_spikes, key=len)
# check the lags
assert_array_equal(lags_msip_min_spikes, [
l for l in self.lags_msip if len(l) + 1 >= self.min_spikes])
# check the neurons in the patterns
assert_array_equal(elements_msip_min_spikes, [
el for el in self.elements_msip if len(el) >= self.min_neu and len(
el) >= self.min_spikes])
# test min_occ parameter
output_msip_min_occ = spade.spade(
self.msip,
self.bin_size,
self.winlen,
min_occ=self.min_occ,
approx_stab_pars=dict(
n_subsets=self.n_subset),
n_surr=self.n_surr,
spectrum='3d#',
alpha=self.alpha,
psr_param=self.psr_param,
stat_corr='no',
output_format='patterns')['patterns']
# collect spade output
occ_msip_min_occ = []
for out in output_msip_min_occ:
occ_msip_min_occ.append(list(out['times'].magnitude))
occ_msip_min_occ = sorted(occ_msip_min_occ, key=len)
# test occurrences time
assert_array_equal(occ_msip_min_occ, [
occ for occ in self.occ_msip if len(occ) >= self.min_occ])
def test_read_allow_secondary(tickstore_lib):
data = [{'ASK': 1545.25,
'ASKSIZE': 1002.0,
'BID': 1545.0,
'BIDSIZE': 55.0,
'CUMVOL': 2187387.0,
'DELETED_TIME': 0,
'INSTRTYPE': 'FUT',
'PRICE': 1545.0,
'SIZE': 1.0,
'TICK_STATUS': 0,
'TRADEHIGH': 1561.75,
'TRADELOW': 1537.25,
'index': 1185076787070},
{'CUMVOL': 354.0,
'DELETED_TIME': 0,
'PRICE': 1543.75,
'SIZE': 354.0,
'TRADEHIGH': 1543.75,
'TRADELOW': 1543.75,
'index': 1185141600600}]
tickstore_lib.write('FEED::SYMBOL', data)
with patch('pymongo.collection.Collection.find', side_effect=tickstore_lib._collection.find) as find:
with patch('pymongo.collection.Collection.with_options', side_effect=tickstore_lib._collection.with_options) as with_options:
with patch.object(tickstore_lib, '_read_preference', side_effect=tickstore_lib._read_preference) as read_pref:
df = tickstore_lib.read('FEED::SYMBOL', columns=['BID', 'ASK', 'PRICE'], allow_secondary=True)
assert read_pref.call_args_list == [call(True)]
assert with_options.call_args_list == [call(read_preference=ReadPreference.NEAREST)]
assert find.call_args_list == [call({'sy': 'FEED::SYMBOL'}, sort=[('s', 1)], projection={'s': 1, '_id': 0}),
call({'sy': 'FEED::SYMBOL', 's': {'$lte': dt(2007, 8, 21, 3, 59, 47, 70000)}},
projection={'sy': 1, 'cs.PRICE': 1, 'i': 1, 'cs.BID': 1, 's': 1, 'im': 1, 'v': 1, 'cs.ASK': 1})]
assert_array_equal(df['ASK'].values, np.array([1545.25, np.nan]))
assert tickstore_lib._collection.find_one()['c'] == 2
def test_simple_two_model_class_compose_1d():
"""
Shift and Scale are two of the simplest models to test model composition
with.
"""
S1 = Shift | Scale # First shift then scale
assert issubclass(S1, Model)
assert S1.n_inputs == 1
assert S1.n_outputs == 1
s1 = S1(2, 3) # Shift by 2 and scale by 3
assert s1(1) == 9.0
S2 = Scale | Shift # First scale then shift
assert issubclass(S2, Model)
assert S2.n_inputs == 1
assert S2.n_outputs == 1
s2 = S2(2, 3) # Scale by 2 then shift by 3
assert s2(1) == 5.0
# Test with array inputs
assert_array_equal(s2([1, 2, 3]), [5.0, 7.0, 9.0])
def test_getField(self):
self._fillDto(count=self.winSize)
assert_array_equal(self.dto.getValue("X"), range(self.winSize))
assert_array_equal(self.dto.getQuality("X"),
np.array(range(self.winSize)) * 2)
testVal = np.array([17]) * self.winSize
self.dto.addNewField("X", "test", testVal)
assert_array_equal(self.dto.getField("X", "test"), testVal)
def test_rate_monitor_get_states():
G = NeuronGroup(5, 'v : 1', threshold='v>1') # no reset
G.v = 1.1 # All neurons spike every time step
rate_mon = PopulationRateMonitor(G)
run(10*defaultclock.dt)
all_states = rate_mon.get_states()
assert set(all_states.keys()) == {'rate', 't', 'N'}
assert_array_equal(all_states['rate'], rate_mon.rate[:])
assert_array_equal(all_states['t'], rate_mon.t[:])
assert_array_equal(all_states['N'], rate_mon.N)
def test_cad_single_sip(self):
# collecting cad output
output_single = cad.cell_assembly_detection(
binned_spiketrain=self.bin_patt1, max_lag=self.max_lag)
# check neurons in the pattern
assert_array_equal(sorted(output_single[0]['neurons']), self.elements1)
# check the occurrences time of the patter
assert_array_equal(output_single[0]['times'], self.occ1)
# check the lags
assert_array_equal(sorted(output_single[0]['lags']), self.output_lags1)
def test_numpy_in_dict():
import numpy
from numpy.testing.utils import assert_array_equal
for shape in SHAPES:
for dtype in DTYPES:
A = numpy.empty(shape, dtype=dtype)
_scrub_nan(A)
bufs = serialize_object(dict(a=A,b=1,c=list(range(20))))
canned = pickle.loads(bufs[0])
yield nt.assert_true(canned['a'], CannedArray)
d, r = unserialize_object(bufs)
B = d['a']
yield nt.assert_equals(r, [])
yield nt.assert_equals(A.shape, B.shape)
yield nt.assert_equals(A.dtype, B.dtype)
yield assert_array_equal(A,B)
def test_read_multiple_symbols(tickstore_lib):
data1 = [
{
'ASK': 1545.25,
'ASKSIZE': 1002.0,
'BID': 1545.0,
'BIDSIZE': 55.0,
'CUMVOL': 2187387.0,
'DELETED_TIME': 0,
'INSTRTYPE': 'FUT',
'PRICE': 1545.0,
'SIZE': 1.0,
'TICK_STATUS': 0,
'TRADEHIGH': 1561.75,
'TRADELOW': 1537.25,
'index': 1185076787070
},
]
data2 = [{
'CUMVOL': 354.0,
'DELETED_TIME': 0,
'PRICE': 1543.75,
'SIZE': 354.0,
'TRADEHIGH': 1543.75,
'TRADELOW': 1543.75,
'index': 1185141600600
}]
tickstore_lib.write('BAR', data2)
tickstore_lib.write('FOO', data1)
df = tickstore_lib.read(['FOO', 'BAR'], columns=['BID', 'ASK', 'PRICE'])
assert all(df['SYMBOL'].values == ['FOO', 'BAR'])
assert_array_equal(df['ASK'].values, np.array([1545.25, np.nan]))
assert_array_equal(df['BID'].values, np.array([1545, np.nan]))
assert_array_equal(df['PRICE'].values, np.array([1545, 1543.75]))
assert_array_equal(
df.index.values,
np.array([
'2007-07-22T04:59:47.070000000+0100',
'2007-07-22T23:00:00.600000000+0100'
],
dtype='datetime64[ns]'))
assert tickstore_lib._collection.find_one()['c'] == 1
