def test_as_quantity(self):
times = [2, 3, 4, 5]
durations = [0.1, 0.2, 0.3, 0.4]
epc = Epoch(times * pq.ms, durations=durations * pq.ms)
epc_as_q = epc.as_quantity()
self.assertIsInstance(epc_as_q, pq.Quantity)
assert_array_equal(times * pq.ms, epc_as_q)
def test_as_array(self):
times = [2, 3, 4, 5]
durations = [0.1, 0.2, 0.3, 0.4]
epc = Epoch(times * pq.ms, durations=durations * pq.ms)
epc_as_arr = epc.as_array(units='ms')
self.assertIsInstance(epc_as_arr, np.ndarray)
assert_array_equal(times, epc_as_arr)
def test__children(self):
params = {'test2': 'y1', 'test3': True}
epc = Epoch([1.1, 1.5, 1.7]*pq.ms, durations=[20, 40, 60]*pq.ns,
labels=np.array(['test epoch 1',
'test epoch 2',
'test epoch 3'], dtype='S'),
name='test', description='tester',
file_origin='test.file',
test1=1, **params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
segment = Segment(name='seg1')
segment.epochs = [epc]
segment.create_many_to_one_relationship()
self.assertEqual(epc._single_parent_objects, ('Segment',))
self.assertEqual(epc._multi_parent_objects, ())
self.assertEqual(epc._single_parent_containers, ('segment',))
self.assertEqual(epc._multi_parent_containers, ())
self.assertEqual(epc._parent_objects, ('Segment',))
self.assertEqual(epc._parent_containers, ('segment',))
self.assertEqual(len(epc.parents), 1)
self.assertEqual(epc.parents[0].name, 'seg1')
assert_neo_object_is_compliant(epc)
def test__time_slice(self):
epc = Epoch(times=[10, 20, 30] * pq.s, durations=[10, 5, 7] * pq.ms,
labels=np.array(['btn0', 'btn1', 'btn2'], dtype='S'),
foo='bar')
epc2 = epc.time_slice(10 * pq.s, 20 * pq.s)
assert_arrays_equal(epc2.times, [10, 20] * pq.s)
assert_arrays_equal(epc2.durations, [10, 5] * pq.ms)
assert_arrays_equal(epc2.labels, np.array(['btn0','btn1'], dtype='S'))
self.assertEqual(epc.annotations, epc2.annotations)
def test__pretty(self):
epc = Epoch(1.5*pq.ms, duration=20*pq.ns,
label='test epoch', name='test', description='tester',
file_origin='test.file')
epc.annotate(targ1=1.1, targ0=[1])
assert_neo_object_is_compliant(epc)
prepr = pretty(epc)
targ = ("Epoch\nname: '%s'\ndescription: '%s'\nannotations: %s" %
(epc.name, epc.description, pretty(epc.annotations)))
self.assertEqual(prepr, targ)
def test__pretty(self):
epc = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'),
name='test', description='tester', file_origin='test.file')
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
prepr = pretty(epc)
targ = ("Epoch\nname: '%s'\ndescription: '%s'\nannotations: %s"
"" % (epc.name, epc.description, pretty(epc.annotations)))
self.assertEqual(prepr, targ)
def test__time_slice(self):
arr_ann = {'index': np.arange(3), 'test': ['a', 'b', 'c']}
epc = Epoch(times=[10, 20, 30] * pq.s, durations=[10, 5, 7] * pq.ms,
labels=np.array(['btn0', 'btn1', 'btn2'], dtype='S'), foo='bar',
array_annotations=arr_ann)
epc2 = epc.time_slice(10 * pq.s, 20 * pq.s)
assert_arrays_equal(epc2.times, [10, 20] * pq.s)
assert_arrays_equal(epc2.durations, [10, 5] * pq.ms)
assert_arrays_equal(epc2.labels, np.array(['btn0', 'btn1'], dtype='S'))
self.assertEqual(epc.annotations, epc2.annotations)
assert_arrays_equal(epc2.array_annotations['index'], np.arange(2))
assert_arrays_equal(epc2.array_annotations['test'], np.array(['a', 'b']))
self.assertIsInstance(epc2.array_annotations, ArrayDict)
def test_time_slice_none_stop(self):
params = {'test2': 'y1', 'test3': True}
arr_ann = {'index': np.arange(3), 'test': ['a', 'b', 'c']}
epc = Epoch([1.1, 1.5, 1.7] * pq.ms,
durations=[20, 40, 60] * pq.ns,
labels=np.array(
['test epoch 1', 'test epoch 2', 'test epoch 3'],
dtype='S'),
name='test',
description='tester',
file_origin='test.file',
test1=1,
array_annotations=arr_ann,
**params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
targ = Epoch([1.5, 1.7] * pq.ms,
durations=[40, 60] * pq.ns,
labels=np.array(['test epoch 2', 'test epoch 3'],
dtype='S'),
name='test',
description='tester',
file_origin='test.file',
test1=1,
array_annotations={
'index': [1, 2],
'test': ['b', 'c']
},
**params)
targ.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(targ)
t_start = 1.2
t_stop = None
result = epc.time_slice(t_start, t_stop)
assert_arrays_equal(result.times, targ.times)
assert_arrays_equal(result.durations, targ.durations)
assert_arrays_equal(result.labels, targ.labels)
self.assertEqual(result.name, targ.name)
self.assertEqual(result.description, targ.description)
self.assertEqual(result.file_origin, targ.file_origin)
self.assertEqual(result.annotations['test0'],
targ.annotations['test0'])
self.assertEqual(result.annotations['test1'],
targ.annotations['test1'])
self.assertEqual(result.annotations['test2'],
targ.annotations['test2'])
assert_arrays_equal(result.array_annotations['index'], np.array([1,
2]))
assert_arrays_equal(result.array_annotations['test'],
np.array(['b', 'c']))
self.assertIsInstance(result.array_annotations, ArrayDict)
def test__pretty(self):
epc = Epoch([1.1, 1.5, 1.7]*pq.ms, durations=[20, 40, 60]*pq.ns,
labels=np.array(['test epoch 1',
'test epoch 2',
'test epoch 3'], dtype='S'),
name='test', description='tester',
file_origin='test.file')
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
prepr = pretty(epc)
targ = ("Epoch\nname: '%s'\ndescription: '%s'\nannotations: %s" %
(epc.name, epc.description, pretty(epc.annotations)))
self.assertEqual(prepr, targ)
def test_Epoch_repr(self):
params = {'test2': 'y1', 'test3': True}
epc = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'),
name='test', description='tester', file_origin='test.file', test1=1, **params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
targ = ('<Epoch: test epoch [email protected] ms for 20.0 ns, '
+ 'test epoch [email protected] ms for 40.0 ns, '
+ 'test epoch [email protected] ms for 60.0 ns>')
res = repr(epc)
self.assertEqual(targ, res)
def test_Epoch_repr(self):
params = {'test2': 'y1', 'test3': True}
epc = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'),
name='test', description='tester', file_origin='test.file', test1=1, **params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
targ = ('<Epoch: test epoch [email protected] ms for 20.0 ns, '
+ 'test epoch [email protected] ms for 40.0 ns, '
+ 'test epoch [email protected] ms for 60.0 ns>')
res = repr(epc)
self.assertEqual(targ, res)
def setUp(self):
self.data = np.array([0.1, 0.5, 1.2, 3.3, 6.4, 7])
self.durations = np.array([0.2, 0.4, 1.1, 2.4, 0.2, 2.0])
self.quant = pq.ms
self.arr_ann = {'index': np.arange(6), 'test': ['a', 'b', 'c', 'd', 'e', 'f']}
self.epoch = Epoch(self.data * self.quant, durations=self.durations * self.quant,
array_annotations=self.arr_ann)
def test__pickle(self):
arr_ann = {'index': np.arange(3), 'test': ['a', 'b', 'c']}
epoch1 = Epoch(np.arange(0, 30, 10) * pq.s, durations=[1, 2, 3] * pq.s,
labels=np.array(['t0', 't1', 't2'], dtype='S'), units='s',
annotation1="foo", annotation2="bar", array_annotations=arr_ann)
fobj = open('./pickle', 'wb')
pickle.dump(epoch1, fobj)
fobj.close()
fobj = open('./pickle', 'rb')
try:
epoch2 = pickle.load(fobj)
except ValueError:
epoch2 = None
fobj.close()
assert_array_equal(epoch1.times, epoch2.times)
self.assertEqual(epoch2.annotations, epoch1.annotations)
assert_arrays_equal(epoch2.array_annotations['index'], np.array(arr_ann['index']))
assert_arrays_equal(epoch2.array_annotations['test'], np.array(arr_ann['test']))
self.assertIsInstance(epoch2.array_annotations, ArrayDict)
# Make sure the dict can perform correct checks after unpickling
epoch2.array_annotations['anno3'] = list(range(3, 6))
with self.assertRaises(ValueError):
epoch2.array_annotations['anno4'] = [2, 1]
os.remove('./pickle')
def test__children(self):
params = {'testarg2': 'yes', 'testarg3': True}
epc = Epoch(1.5 * pq.ms,
duration=20 * pq.ns,
label='test epoch',
name='test',
description='tester',
file_origin='test.file',
testarg1=1,
**params)
epc.annotate(testarg1=1.1, testarg0=[1, 2, 3])
assert_neo_object_is_compliant(epc)
segment = Segment(name='seg1')
segment.epochs = [epc]
segment.create_many_to_one_relationship()
self.assertEqual(epc._container_child_objects, ())
self.assertEqual(epc._data_child_objects, ())
self.assertEqual(epc._single_parent_objects, ('Segment', ))
self.assertEqual(epc._multi_child_objects, ())
self.assertEqual(epc._multi_parent_objects, ())
self.assertEqual(epc._child_properties, ())
self.assertEqual(epc._single_child_objects, ())
self.assertEqual(epc._container_child_containers, ())
self.assertEqual(epc._data_child_containers, ())
self.assertEqual(epc._single_child_containers, ())
self.assertEqual(epc._single_parent_containers, ('segment', ))
self.assertEqual(epc._multi_child_containers, ())
self.assertEqual(epc._multi_parent_containers, ())
self.assertEqual(epc._child_objects, ())
self.assertEqual(epc._child_containers, ())
self.assertEqual(epc._parent_objects, ('Segment', ))
self.assertEqual(epc._parent_containers, ('segment', ))
self.assertEqual(epc.children, ())
self.assertEqual(len(epc.parents), 1)
self.assertEqual(epc.parents[0].name, 'seg1')
epc.create_many_to_one_relationship()
epc.create_many_to_many_relationship()
epc.create_relationship()
assert_neo_object_is_compliant(epc)
def test__time_slice(self):
arr_ann = {'index': np.arange(3), 'test': ['a', 'b', 'c']}
epc = Epoch(times=[10, 20, 30] * pq.s,
durations=[10, 5, 7] * pq.ms,
labels=np.array(['btn0', 'btn1', 'btn2'], dtype='U'),
foo='bar',
array_annotations=arr_ann)
epc2 = epc.time_slice(10 * pq.s, 20 * pq.s)
assert_arrays_equal(epc2.times, [10, 20] * pq.s)
assert_arrays_equal(epc2.durations, [10, 5] * pq.ms)
assert_arrays_equal(epc2.labels, np.array(['btn0', 'btn1'], dtype='U'))
self.assertEqual(epc.annotations, epc2.annotations)
assert_arrays_equal(epc2.array_annotations['index'], np.arange(2))
assert_arrays_equal(epc2.array_annotations['test'],
np.array(['a', 'b']))
self.assertIsInstance(epc2.array_annotations, ArrayDict)
def test_Epoch_merge(self):
params1 = {'test2': 'y1', 'test3': True}
params2 = {'test2': 'no', 'test4': False}
paramstarg = {'test2': 'yes;no', 'test3': True, 'test4': False}
epc1 = Epoch(
[1.1, 1.5, 1.7] * pq.ms,
durations=[20, 40, 60] * pq.us,
labels=np.array(
['test epoch 1 1', 'test epoch 1 2', 'test epoch 1 3'],
dtype='S'),
name='test',
description='tester 1',
file_origin='test.file',
test1=1,
**params1)
epc2 = Epoch(
[2.1, 2.5, 2.7] * pq.us,
durations=[3, 5, 7] * pq.ms,
labels=np.array(
['test epoch 2 1', 'test epoch 2 2', 'test epoch 2 3'],
dtype='S'),
name='test',
description='tester 2',
file_origin='test.file',
test1=1,
**params2)
epctarg = Epoch(
[1.1, 1.5, 1.7, .0021, .0025, .0027] * pq.ms,
durations=[20, 40, 60, 3000, 5000, 7000] * pq.ns,
labels=np.array([
'test epoch 1 1', 'test epoch 1 2', 'test epoch 1 3',
'test epoch 2 1', 'test epoch 2 2', 'test epoch 2 3'
],
dtype='S'),
name='test',
description='merge(tester 1, tester 2)',
file_origin='test.file',
test1=1,
**paramstarg)
assert_neo_object_is_compliant(epc1)
assert_neo_object_is_compliant(epc2)
assert_neo_object_is_compliant(epctarg)
epcres = epc1.merge(epc2)
assert_neo_object_is_compliant(epcres)
assert_same_sub_schema(epctarg, epcres)
def test_time_slice_none_both(self):
params = {'test2': 'y1', 'test3': True}
arr_ann = {'index': np.arange(3), 'test': ['a', 'b', 'c']}
epc = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'),
name='test', description='tester', file_origin='test.file', test1=1,
array_annotations=arr_ann, **params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
targ = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'),
name='test', description='tester', file_origin='test.file', test1=1,
array_annotations=arr_ann, **params)
targ.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(targ)
t_start = None
t_stop = None
result = epc.time_slice(t_start, t_stop)
assert_arrays_equal(result.times, targ.times)
assert_arrays_equal(result.durations, targ.durations)
assert_arrays_equal(result.labels, targ.labels)
self.assertEqual(result.name, targ.name)
self.assertEqual(result.description, targ.description)
self.assertEqual(result.file_origin, targ.file_origin)
self.assertEqual(result.annotations['test0'], targ.annotations['test0'])
self.assertEqual(result.annotations['test1'], targ.annotations['test1'])
self.assertEqual(result.annotations['test2'], targ.annotations['test2'])
assert_arrays_equal(result.array_annotations['index'], np.array([0, 1, 2]))
assert_arrays_equal(result.array_annotations['test'], np.array(['a', 'b', 'c']))
self.assertIsInstance(result.array_annotations, ArrayDict)
def test_time_slice_empty(self):
params = {'test2': 'y1', 'test3': True}
epc = Epoch([]*pq.ms, durations=[]*pq.ns,
labels=np.array([], dtype='S'),
name='test', description='tester',
file_origin='test.file',
test1=1, **params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
targ = Epoch([]*pq.ms, durations=[]*pq.ns,
labels=np.array([], dtype='S'),
name='test', description='tester',
file_origin='test.file',
test1=1, **params)
targ.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(targ)
t_start = 1.2
t_stop = 1.6
result = epc.time_slice(t_start, t_stop)
assert_arrays_equal(result.times, targ.times)
assert_arrays_equal(result.durations, targ.durations)
assert_arrays_equal(result.labels, targ.labels)
self.assertEqual(result.name, targ.name)
self.assertEqual(result.description, targ.description)
self.assertEqual(result.file_origin, targ.file_origin)
self.assertEqual(result.annotations['test0'], targ.annotations['test0'])
self.assertEqual(result.annotations['test1'], targ.annotations['test1'])
self.assertEqual(result.annotations['test2'], targ.annotations['test2'])
def test_time_slice_differnt_units(self):
params = {'test2': 'y1', 'test3': True}
epc = Epoch([1.1, 1.5, 1.7]*pq.ms, durations=[20, 40, 60]*pq.ns,
labels=np.array(['test epoch 1',
'test epoch 2',
'test epoch 3'], dtype='S'),
name='test', description='tester',
file_origin='test.file',
test1=1, **params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
targ = Epoch([1.5]*pq.ms, durations=[40]*pq.ns,
labels=np.array(['test epoch 2'], dtype='S'),
name='test', description='tester',
file_origin='test.file',
test1=1, **params)
targ.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(targ)
t_start = 0.0012 * pq.s
t_stop = 0.0016 * pq.s
result = epc.time_slice(t_start, t_stop)
assert_arrays_equal(result.times, targ.times)
assert_arrays_equal(result.durations, targ.durations)
assert_arrays_equal(result.labels, targ.labels)
self.assertEqual(result.name, targ.name)
self.assertEqual(result.description, targ.description)
self.assertEqual(result.file_origin, targ.file_origin)
self.assertEqual(result.annotations['test0'], targ.annotations['test0'])
self.assertEqual(result.annotations['test1'], targ.annotations['test1'])
self.assertEqual(result.annotations['test2'], targ.annotations['test2'])
def test_Epoch_creation_from_lists(self):
epc = Epoch([1.1, 1.5, 1.7],
[20.0, 20.0, 20.0],
['test event 1', 'test event 2', 'test event 3'],
units=pq.ms)
assert_arrays_equal(epc.times, [1.1, 1.5, 1.7] * pq.ms)
assert_arrays_equal(epc.durations, [20.0, 20.0, 20.0] * pq.ms)
assert_arrays_equal(epc.labels,
np.array(['test event 1', 'test event 2', 'test event 3']))
def test_Epoch_merge(self):
params1 = {'test2': 'y1', 'test3': True}
params2 = {'test2': 'no', 'test4': False}
paramstarg = {'test2': 'yes;no', 'test3': True, 'test4': False}
arr_ann1 = {'index': np.arange(10, 13)}
arr_ann2 = {'index': np.arange(3), 'test': ['a', 'b', 'c']}
epc1 = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.us,
labels=np.array(['test epoch 1 1', 'test epoch 1 2', 'test epoch 1 3'],
dtype='S'), name='test', description='tester 1',
file_origin='test.file', test1=1, array_annotations=arr_ann1, **params1)
epc2 = Epoch([2.1, 2.5, 2.7] * pq.us, durations=[3, 5, 7] * pq.ms,
labels=np.array(['test epoch 2 1', 'test epoch 2 2', 'test epoch 2 3'],
dtype='S'), name='test', description='tester 2',
file_origin='test.file', test1=1, array_annotations=arr_ann2, **params2)
epctarg = Epoch([1.1, 1.5, 1.7, .0021, .0025, .0027] * pq.ms,
durations=[20, 40, 60, 3000, 5000, 7000] * pq.us,
labels=np.array(['test epoch 1 1', 'test epoch 1 2', 'test epoch 1 3',
'test epoch 2 1', 'test epoch 2 2', 'test epoch 2 3'],
dtype='S'),
name='test',
description='merge(tester 1, tester 2)', file_origin='test.file',
array_annotations={'index': [10, 11, 12, 0, 1, 2]}, test1=1, **paramstarg)
assert_neo_object_is_compliant(epc1)
assert_neo_object_is_compliant(epc2)
assert_neo_object_is_compliant(epctarg)
with warnings.catch_warnings(record=True) as w:
epcres = epc1.merge(epc2)
self.assertTrue(len(w), 1)
self.assertEqual(w[0].category, UserWarning)
self.assertSequenceEqual(str(w[0].message), "The following array annotations were "
"omitted, because they were only present"
" in one of the merged objects: "
"[] from the one that was merged "
"into and ['test'] from the one that "
"was merged into the other")
assert_neo_object_is_compliant(epcres)
assert_same_sub_schema(epctarg, epcres)
# Remove this, when array_annotations are added to assert_same_sub_schema
assert_arrays_equal(epcres.array_annotations['index'], np.array([10, 11, 12, 0, 1, 2]))
self.assertTrue('test' not in epcres.array_annotations)
self.assertIsInstance(epcres.array_annotations, ArrayDict)
def test_Epoch_merge(self):
params1 = {'test2': 'y1', 'test3': True}
params2 = {'test2': 'no', 'test4': False}
paramstarg = {'test2': 'yes;no', 'test3': True, 'test4': False}
arr_ann1 = {'index': np.arange(10, 13)}
arr_ann2 = {'index': np.arange(3), 'test': ['a', 'b', 'c']}
epc1 = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.us,
labels=np.array(['test epoch 1 1', 'test epoch 1 2', 'test epoch 1 3'],
dtype='S'), name='test', description='tester 1',
file_origin='test.file', test1=1, array_annotations=arr_ann1, **params1)
epc2 = Epoch([2.1, 2.5, 2.7] * pq.us, durations=[3, 5, 7] * pq.ms,
labels=np.array(['test epoch 2 1', 'test epoch 2 2', 'test epoch 2 3'],
dtype='S'), name='test', description='tester 2',
file_origin='test.file', test1=1, array_annotations=arr_ann2, **params2)
epctarg = Epoch([1.1, 1.5, 1.7, .0021, .0025, .0027] * pq.ms,
durations=[20, 40, 60, 3000, 5000, 7000] * pq.us,
labels=np.array(['test epoch 1 1', 'test epoch 1 2', 'test epoch 1 3',
'test epoch 2 1', 'test epoch 2 2', 'test epoch 2 3'],
dtype='S'),
name='test',
description='merge(tester 1, tester 2)', file_origin='test.file',
array_annotations={'index': [10, 11, 12, 0, 1, 2]}, test1=1, **paramstarg)
assert_neo_object_is_compliant(epc1)
assert_neo_object_is_compliant(epc2)
assert_neo_object_is_compliant(epctarg)
with warnings.catch_warnings(record=True) as w:
epcres = epc1.merge(epc2)
self.assertTrue(len(w), 1)
self.assertEqual(w[0].category, UserWarning)
self.assertSequenceEqual(str(w[0].message), "The following array annotations were "
"omitted, because they were only present"
" in one of the merged objects: "
"[] from the one that was merged "
"into and ['test'] from the one that "
"was merged into the other")
assert_neo_object_is_compliant(epcres)
assert_same_sub_schema(epctarg, epcres)
# Remove this, when array_annotations are added to assert_same_sub_schema
assert_arrays_equal(epcres.array_annotations['index'], np.array([10, 11, 12, 0, 1, 2]))
self.assertTrue('test' not in epcres.array_annotations)
self.assertIsInstance(epcres.array_annotations, ArrayDict)
def test_getitem_scalar(self):
times = [2, 3, 4, 5]
durations = [0.1, 0.2, 0.3, 0.4]
labels = ["A", "B", "C", "D"]
epc = Epoch(times * pq.ms, durations=durations * pq.ms, labels=labels)
single_epoch = epc[2]
self.assertIsInstance(single_epoch, pq.Quantity)
assert_array_equal(single_epoch.times, np.array([4.0]))
assert_array_equal(single_epoch.durations, np.array([0.3]))
assert_array_equal(single_epoch.labels, np.array(["C"]))
def test_epoch_creation(self):
params = {'test2': 'y1', 'test3': True}
epc = Epoch(1.5*pq.ms, duration=20*pq.ns,
label='test epoch', name='test', description='tester',
file_origin='test.file',
test1=1, **params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
self.assertEqual(epc.time, 1.5*pq.ms)
self.assertEqual(epc.duration, 20*pq.ns)
self.assertEqual(epc.label, 'test epoch')
self.assertEqual(epc.name, 'test')
self.assertEqual(epc.description, 'tester')
self.assertEqual(epc.file_origin, 'test.file')
self.assertEqual(epc.annotations['test0'], [1, 2])
self.assertEqual(epc.annotations['test1'], 1.1)
self.assertEqual(epc.annotations['test2'], 'y1')
self.assertTrue(epc.annotations['test3'])
def to_epoch(self, pairwise=False, durations=None):
"""
Returns a new Epoch object based on the times and labels in the Event object.
This method has three modes of action.
1. By default, an array of `n` event times will be transformed into
`n-1` epochs, where the end of one epoch is the beginning of the next.
This assumes that the events are ordered in time; it is the
responsibility of the caller to check this is the case.
2. If `pairwise` is True, then the event times will be taken as pairs
representing the start and end time of an epoch. The number of
events must be even, otherwise a ValueError is raised.
3. If `durations` is given, it should be a scalar Quantity or a
Quantity array of the same size as the Event.
Each event time is then taken as the start of an epoch of duration
given by `durations`.
`pairwise=True` and `durations` are mutually exclusive. A ValueError
will be raised if both are given.
If `durations` is given, epoch labels are set to the corresponding
labels of the events that indicate the epoch start
If `durations` is not given, then the event labels A and B bounding
the epoch are used to set the labels of the epochs in the form 'A-B'.
"""
if pairwise:
# Mode 2
if durations is not None:
raise ValueError("Inconsistent arguments. "
"Cannot give both `pairwise` and `durations`")
if self.size % 2 != 0:
raise ValueError("Pairwise conversion of events to epochs"
" requires an even number of events")
times = self.times[::2]
durations = self.times[1::2] - times
labels = np.array([
"{}-{}".format(a, b)
for a, b in zip(self.labels[::2], self.labels[1::2])
])
elif durations is None:
# Mode 1
times = self.times[:-1]
durations = np.diff(self.times)
labels = np.array([
"{}-{}".format(a, b)
for a, b in zip(self.labels[:-1], self.labels[1:])
])
else:
# Mode 3
times = self.times
labels = self.labels
return Epoch(times=times, durations=durations, labels=labels)
def test_Epoch_creation_scalar_duration(self):
# test with scalar for durations
epc = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=20 * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'))
assert_neo_object_is_compliant(epc)
assert_arrays_equal(epc.times, [1.1, 1.5, 1.7] * pq.ms)
assert_arrays_equal(epc.durations, [20, 20, 20] * pq.ns)
self.assertEqual(epc.durations.size, 3)
assert_arrays_equal(epc.labels,
np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'))
def test_Epoch_merge(self):
params1 = {'test2': 'y1', 'test3': True}
params2 = {'test2': 'no', 'test4': False}
paramstarg = {'test2': 'yes;no',
'test3': True,
'test4': False}
epc1 = Epoch([1.1, 1.5, 1.7]*pq.ms,
durations=[20, 40, 60]*pq.us,
labels=np.array(['test epoch 1 1',
'test epoch 1 2',
'test epoch 1 3'], dtype='S'),
name='test', description='tester 1',
file_origin='test.file',
test1=1, **params1)
epc2 = Epoch([2.1, 2.5, 2.7]*pq.us,
durations=[3, 5, 7]*pq.ms,
labels=np.array(['test epoch 2 1',
'test epoch 2 2',
'test epoch 2 3'], dtype='S'),
name='test', description='tester 2',
file_origin='test.file',
test1=1, **params2)
epctarg = Epoch([1.1, 1.5, 1.7, .0021, .0025, .0027]*pq.ms,
durations=[20, 40, 60, 3000, 5000, 7000]*pq.ns,
labels=np.array(['test epoch 1 1',
'test epoch 1 2',
'test epoch 1 3',
'test epoch 2 1',
'test epoch 2 2',
'test epoch 2 3'], dtype='S'),
name='test',
description='merge(tester 1, tester 2)',
file_origin='test.file',
test1=1, **paramstarg)
assert_neo_object_is_compliant(epc1)
assert_neo_object_is_compliant(epc2)
assert_neo_object_is_compliant(epctarg)
epcres = epc1.merge(epc2)
assert_neo_object_is_compliant(epcres)
assert_same_sub_schema(epctarg, epcres)
def test_time_slice_empty(self):
params = {'test2': 'y1', 'test3': True}
epc = Epoch([] * pq.ms,
durations=[] * pq.ns,
labels=np.array([], dtype='S'),
name='test',
description='tester',
file_origin='test.file',
test1=1,
**params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
targ = Epoch([] * pq.ms,
durations=[] * pq.ns,
labels=np.array([], dtype='S'),
name='test',
description='tester',
file_origin='test.file',
test1=1,
**params)
targ.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(targ)
t_start = 1.2
t_stop = 1.6
result = epc.time_slice(t_start, t_stop)
assert_arrays_equal(result.times, targ.times)
assert_arrays_equal(result.durations, targ.durations)
assert_arrays_equal(result.labels, targ.labels)
self.assertEqual(result.name, targ.name)
self.assertEqual(result.description, targ.description)
self.assertEqual(result.file_origin, targ.file_origin)
self.assertEqual(result.annotations['test0'],
targ.annotations['test0'])
self.assertEqual(result.annotations['test1'],
targ.annotations['test1'])
self.assertEqual(result.annotations['test2'],
targ.annotations['test2'])
assert_arrays_equal(result.array_annotations['durations'],
np.array([], dtype='float64') * pq.ns)
assert_arrays_equal(result.array_annotations['labels'],
np.array([], dtype='S'))
self.assertIsInstance(result.array_annotations, ArrayDict)
def test_time_slice_none_both(self):
params = {'test2': 'y1', 'test3': True}
epc = Epoch([1.1, 1.5, 1.7] * pq.ms,
durations=[20, 40, 60] * pq.ns,
labels=np.array(
['test epoch 1', 'test epoch 2', 'test epoch 3'],
dtype='S'),
name='test',
description='tester',
file_origin='test.file',
test1=1,
**params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
targ = Epoch([1.1, 1.5, 1.7] * pq.ms,
durations=[20, 40, 60] * pq.ns,
labels=np.array(
['test epoch 1', 'test epoch 2', 'test epoch 3'],
dtype='S'),
name='test',
description='tester',
file_origin='test.file',
test1=1,
**params)
targ.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(targ)
t_start = None
t_stop = None
result = epc.time_slice(t_start, t_stop)
assert_arrays_equal(result.times, targ.times)
assert_arrays_equal(result.durations, targ.durations)
assert_arrays_equal(result.labels, targ.labels)
self.assertEqual(result.name, targ.name)
self.assertEqual(result.description, targ.description)
self.assertEqual(result.file_origin, targ.file_origin)
self.assertEqual(result.annotations['test0'],
targ.annotations['test0'])
self.assertEqual(result.annotations['test1'],
targ.annotations['test1'])
self.assertEqual(result.annotations['test2'],
targ.annotations['test2'])
def test__children(self):
params = {'test2': 'y1', 'test3': True}
epc = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='U'),
name='test', description='tester', file_origin='test.file', test1=1, **params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
segment = Segment(name='seg1')
segment.epochs = [epc]
segment.create_many_to_one_relationship()
self.assertEqual(epc._parent_objects, ('Segment',))
self.assertEqual(epc._parent_containers, ('segment',))
self.assertEqual(epc._parent_objects, ('Segment',))
self.assertEqual(epc._parent_containers, ('segment',))
self.assertEqual(len(epc.parents), 1)
self.assertEqual(epc.parents[0].name, 'seg1')
assert_neo_object_is_compliant(epc)
def test__children(self):
params = {'testarg2': 'yes', 'testarg3': True}
epc = Epoch(1.5*pq.ms, duration=20*pq.ns,
label='test epoch', name='test', description='tester',
file_origin='test.file',
testarg1=1, **params)
epc.annotate(testarg1=1.1, testarg0=[1, 2, 3])
assert_neo_object_is_compliant(epc)
segment = Segment(name='seg1')
segment.epochs = [epc]
segment.create_many_to_one_relationship()
self.assertEqual(epc._container_child_objects, ())
self.assertEqual(epc._data_child_objects, ())
self.assertEqual(epc._single_parent_objects, ('Segment',))
self.assertEqual(epc._multi_child_objects, ())
self.assertEqual(epc._multi_parent_objects, ())
self.assertEqual(epc._child_properties, ())
self.assertEqual(epc._single_child_objects, ())
self.assertEqual(epc._container_child_containers, ())
self.assertEqual(epc._data_child_containers, ())
self.assertEqual(epc._single_child_containers, ())
self.assertEqual(epc._single_parent_containers, ('segment',))
self.assertEqual(epc._multi_child_containers, ())
self.assertEqual(epc._multi_parent_containers, ())
self.assertEqual(epc._child_objects, ())
self.assertEqual(epc._child_containers, ())
self.assertEqual(epc._parent_objects, ('Segment',))
self.assertEqual(epc._parent_containers, ('segment',))
self.assertEqual(epc.children, ())
self.assertEqual(len(epc.parents), 1)
self.assertEqual(epc.parents[0].name, 'seg1')
epc.create_many_to_one_relationship()
epc.create_many_to_many_relationship()
epc.create_relationship()
assert_neo_object_is_compliant(epc)
def test_Epoch_creation(self):
params = {'test2': 'y1', 'test3': True}
epc = Epoch([1.1, 1.5, 1.7]*pq.ms, durations=[20, 40, 60]*pq.ns,
labels=np.array(['test epoch 1',
'test epoch 2',
'test epoch 3'], dtype='S'),
name='test', description='tester',
file_origin='test.file',
test1=1, **params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
assert_arrays_equal(epc.times, [1.1, 1.5, 1.7]*pq.ms)
assert_arrays_equal(epc.durations, [20, 40, 60]*pq.ns)
assert_arrays_equal(epc.labels, np.array(['test epoch 1',
'test epoch 2',
'test epoch 3'], dtype='S'))
self.assertEqual(epc.name, 'test')
self.assertEqual(epc.description, 'tester')
self.assertEqual(epc.file_origin, 'test.file')
self.assertEqual(epc.annotations['test0'], [1, 2])
self.assertEqual(epc.annotations['test1'], 1.1)
self.assertEqual(epc.annotations['test2'], 'y1')
self.assertTrue(epc.annotations['test3'])
def test_slice(self):
times = [2, 3, 4, 5]
durations = [0.1, 0.2, 0.3, 0.4]
labels = ["A", "B", "C", "D"]
arr_ann = {'index': np.arange(4), 'test': ['a', 'b', 'c', 'd']}
epc = Epoch(times * pq.ms, durations=durations * pq.ms, labels=labels,
array_annotations=arr_ann)
single_epoch = epc[1:3]
self.assertIsInstance(single_epoch, Epoch)
assert_array_equal(single_epoch.times, np.array([3.0, 4.0]))
assert_array_equal(single_epoch.durations, np.array([0.2, 0.3]))
assert_array_equal(single_epoch.labels, np.array(["B", "C"]))
assert_arrays_equal(single_epoch.array_annotations['index'], np.arange(1, 3))
assert_arrays_equal(single_epoch.array_annotations['test'], np.array(['b', 'c']))
self.assertIsInstance(single_epoch.array_annotations, ArrayDict)
def test_Epoch_creation(self):
params = {'test2': 'y1', 'test3': True}
arr_ann = {'names': ['a', 'b', 'c'], 'index': np.arange(10, 13)}
epc = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'),
name='test', description='tester', file_origin='test.file', test1=1,
array_annotations=arr_ann, **params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
assert_arrays_equal(epc.times, [1.1, 1.5, 1.7] * pq.ms)
assert_arrays_equal(epc.durations, [20, 40, 60] * pq.ns)
assert_arrays_equal(epc.labels,
np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'))
self.assertEqual(epc.name, 'test')
self.assertEqual(epc.description, 'tester')
self.assertEqual(epc.file_origin, 'test.file')
self.assertEqual(epc.annotations['test0'], [1, 2])
self.assertEqual(epc.annotations['test1'], 1.1)
self.assertEqual(epc.annotations['test2'], 'y1')
self.assertTrue(epc.annotations['test3'])
assert_arrays_equal(epc.array_annotations['names'], np.array(['a', 'b', 'c']))
assert_arrays_equal(epc.array_annotations['index'], np.arange(10, 13))
self.assertIsInstance(epc.array_annotations, ArrayDict)
def test__pickle(self):
epoch1 = Epoch(np.arange(0, 30, 10)*pq.s, labels=np.array(['t0', 't1', 't2'], dtype='S'),
units='s')
fobj = open('./pickle', 'wb')
pickle.dump(epoch1, fobj)
fobj.close()
fobj = open('./pickle', 'rb')
try:
epoch2 = pickle.load(fobj)
except ValueError:
epoch2 = None
fobj.close()
assert_array_equal(epoch1.times, epoch2.times)
os.remove('./pickle')
def test_Epoch_creation_scalar_duration(self):
# test with scalar for durations
epc = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=20 * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'))
assert_neo_object_is_compliant(epc)
def setUp(self):
self.params = {'test0': 'y1', 'test1': ['deeptest'], 'test2': True}
self.epc = Epoch(times=[10, 20, 30, 40, 50] * pq.s, durations=[10, 5, 7, 14, 9] * pq.ms,
labels=np.array(['btn0', 'btn1', 'btn2', 'btn0', 'btn3'], dtype='S'), **self.params)
def setUp(self):
self.data = np.array([0.1, 0.5, 1.2, 3.3, 6.4, 7])
self.durations = np.array([0.2, 0.4, 1.1, 2.4, 0.2, 2.0])
self.quant = pq.ms
self.epoch = Epoch(self.data * self.quant,
durations=self.durations * self.quant)
class TestEpoch(unittest.TestCase):
def setUp(self):
self.params = {'test0': 'y1', 'test1': ['deeptest'], 'test2': True}
self.seg = Segment()
self.epc = Epoch(times=[10, 20, 30, 40, 50] * pq.s, durations=[10, 5, 7, 14, 9] * pq.ms,
labels=np.array(['btn0', 'btn1', 'btn2', 'btn0', 'btn3'], dtype='S'),
**self.params)
self.epc.segment = self.seg
def test_Epoch_creation(self):
params = {'test2': 'y1', 'test3': True}
arr_ann = {'names': ['a', 'b', 'c'], 'index': np.arange(10, 13)}
epc = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'),
name='test', description='tester', file_origin='test.file', test1=1,
array_annotations=arr_ann, **params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
assert_arrays_equal(epc.times, [1.1, 1.5, 1.7] * pq.ms)
assert_arrays_equal(epc.durations, [20, 40, 60] * pq.ns)
assert_arrays_equal(epc.labels,
np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'))
self.assertEqual(epc.name, 'test')
self.assertEqual(epc.description, 'tester')
self.assertEqual(epc.file_origin, 'test.file')
self.assertEqual(epc.annotations['test0'], [1, 2])
self.assertEqual(epc.annotations['test1'], 1.1)
self.assertEqual(epc.annotations['test2'], 'y1')
self.assertTrue(epc.annotations['test3'])
assert_arrays_equal(epc.array_annotations['names'], np.array(['a', 'b', 'c']))
assert_arrays_equal(epc.array_annotations['index'], np.arange(10, 13))
self.assertIsInstance(epc.array_annotations, ArrayDict)
def test_Epoch_creation_invalid_durations_labels(self):
self.assertRaises(ValueError, Epoch, [1.1, 1.5, 1.7] * pq.ms,
durations=[20, 40, 60, 80] * pq.ns)
self.assertRaises(ValueError, Epoch, [1.1, 1.5, 1.7] * pq.ms,
durations=[20, 40, 60] * pq.ns,
labels=["A", "B"])
def test_Epoch_creation_scalar_duration(self):
# test with scalar for durations
epc = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=20 * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'))
assert_neo_object_is_compliant(epc)
assert_arrays_equal(epc.times, [1.1, 1.5, 1.7] * pq.ms)
assert_arrays_equal(epc.durations, [20, 20, 20] * pq.ns)
self.assertEqual(epc.durations.size, 3)
assert_arrays_equal(epc.labels,
np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'))
def test_Epoch_creation_from_lists(self):
epc = Epoch([1.1, 1.5, 1.7],
[20.0, 20.0, 20.0],
['test event 1', 'test event 2', 'test event 3'],
units=pq.ms)
assert_arrays_equal(epc.times, [1.1, 1.5, 1.7] * pq.ms)
assert_arrays_equal(epc.durations, [20.0, 20.0, 20.0] * pq.ms)
assert_arrays_equal(epc.labels,
np.array(['test event 1', 'test event 2', 'test event 3']))
def test_Epoch_repr(self):
params = {'test2': 'y1', 'test3': True}
epc = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'),
name='test', description='tester', file_origin='test.file', test1=1, **params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
targ = ('<Epoch: test epoch [email protected] ms for 20.0 ns, '
+ 'test epoch [email protected] ms for 40.0 ns, '
+ 'test epoch [email protected] ms for 60.0 ns>')
res = repr(epc)
self.assertEqual(targ, res)
def test_Epoch_merge(self):
params1 = {'test2': 'y1', 'test3': True}
params2 = {'test2': 'no', 'test4': False}
paramstarg = {'test2': 'yes;no', 'test3': True, 'test4': False}
arr_ann1 = {'index': np.arange(10, 13)}
arr_ann2 = {'index': np.arange(3), 'test': ['a', 'b', 'c']}
epc1 = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.us,
labels=np.array(['test epoch 1 1', 'test epoch 1 2', 'test epoch 1 3'],
dtype='S'), name='test', description='tester 1',
file_origin='test.file', test1=1, array_annotations=arr_ann1, **params1)
epc2 = Epoch([2.1, 2.5, 2.7] * pq.us, durations=[3, 5, 7] * pq.ms,
labels=np.array(['test epoch 2 1', 'test epoch 2 2', 'test epoch 2 3'],
dtype='S'), name='test', description='tester 2',
file_origin='test.file', test1=1, array_annotations=arr_ann2, **params2)
epctarg = Epoch([1.1, 1.5, 1.7, .0021, .0025, .0027] * pq.ms,
durations=[20, 40, 60, 3000, 5000, 7000] * pq.us,
labels=np.array(['test epoch 1 1', 'test epoch 1 2', 'test epoch 1 3',
'test epoch 2 1', 'test epoch 2 2', 'test epoch 2 3'],
dtype='S'),
name='test',
description='merge(tester 1, tester 2)', file_origin='test.file',
array_annotations={'index': [10, 11, 12, 0, 1, 2]}, test1=1, **paramstarg)
assert_neo_object_is_compliant(epc1)
assert_neo_object_is_compliant(epc2)
assert_neo_object_is_compliant(epctarg)
with warnings.catch_warnings(record=True) as w:
epcres = epc1.merge(epc2)
self.assertTrue(len(w), 1)
self.assertEqual(w[0].category, UserWarning)
self.assertSequenceEqual(str(w[0].message), "The following array annotations were "
"omitted, because they were only present"
" in one of the merged objects: "
"[] from the one that was merged "
"into and ['test'] from the one that "
"was merged into the other")
assert_neo_object_is_compliant(epcres)
assert_same_sub_schema(epctarg, epcres)
# Remove this, when array_annotations are added to assert_same_sub_schema
assert_arrays_equal(epcres.array_annotations['index'], np.array([10, 11, 12, 0, 1, 2]))
self.assertTrue('test' not in epcres.array_annotations)
self.assertIsInstance(epcres.array_annotations, ArrayDict)
def test_set_labels_duration(self):
epc = Epoch([1.1, 1.5, 1.7] * pq.ms,
durations=20 * pq.ns,
labels=['A', 'B', 'C'])
assert_array_equal(epc.durations.magnitude, np.array([20, 20, 20]))
epc.durations = [20.0, 21.0, 22.0] * pq.ns
assert_array_equal(epc.durations.magnitude, np.array([20, 21, 22]))
self.assertRaises(ValueError, setattr, epc, "durations", [25.0, 26.0] * pq.ns)
assert_array_equal(epc.labels, np.array(['A', 'B', 'C']))
epc.labels = ['D', 'E', 'F']
assert_array_equal(epc.labels, np.array(['D', 'E', 'F']))
self.assertRaises(ValueError, setattr, epc, "labels", ['X', 'Y'])
def test__children(self):
params = {'test2': 'y1', 'test3': True}
epc = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'),
name='test', description='tester', file_origin='test.file', test1=1, **params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
segment = Segment(name='seg1')
segment.epochs = [epc]
segment.create_many_to_one_relationship()
self.assertEqual(epc._single_parent_objects, ('Segment',))
self.assertEqual(epc._multi_parent_objects, ())
self.assertEqual(epc._single_parent_containers, ('segment',))
self.assertEqual(epc._multi_parent_containers, ())
self.assertEqual(epc._parent_objects, ('Segment',))
self.assertEqual(epc._parent_containers, ('segment',))
self.assertEqual(len(epc.parents), 1)
self.assertEqual(epc.parents[0].name, 'seg1')
assert_neo_object_is_compliant(epc)
@unittest.skipUnless(HAVE_IPYTHON, "requires IPython")
def test__pretty(self):
epc = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'),
name='test', description='tester', file_origin='test.file')
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
prepr = pretty(epc)
targ = ("Epoch\nname: '%s'\ndescription: '%s'\nannotations: %s"
"" % (epc.name, epc.description, pretty(epc.annotations)))
self.assertEqual(prepr, targ)
def test__time_slice(self):
arr_ann = {'index': np.arange(3), 'test': ['a', 'b', 'c']}
epc = Epoch(times=[10, 20, 30] * pq.s, durations=[10, 5, 7] * pq.ms,
labels=np.array(['btn0', 'btn1', 'btn2'], dtype='S'), foo='bar',
array_annotations=arr_ann)
epc2 = epc.time_slice(10 * pq.s, 20 * pq.s)
assert_arrays_equal(epc2.times, [10, 20] * pq.s)
assert_arrays_equal(epc2.durations, [10, 5] * pq.ms)
assert_arrays_equal(epc2.labels, np.array(['btn0', 'btn1'], dtype='S'))
self.assertEqual(epc.annotations, epc2.annotations)
assert_arrays_equal(epc2.array_annotations['index'], np.arange(2))
assert_arrays_equal(epc2.array_annotations['test'], np.array(['a', 'b']))
self.assertIsInstance(epc2.array_annotations, ArrayDict)
def test_time_slice2(self):
params = {'test2': 'y1', 'test3': True}
arr_ann = {'index': np.arange(3), 'test': ['a', 'b', 'c']}
epc = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'),
name='test', description='tester', file_origin='test.file', test1=1,
array_annotations=arr_ann, **params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
targ = Epoch([1.5] * pq.ms, durations=[40] * pq.ns,
labels=np.array(['test epoch 2'], dtype='S'), name='test',
description='tester', file_origin='test.file', test1=1,
array_annotations={'index': [1], 'test': ['b']}, **params)
targ.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(targ)
t_start = 1.2
t_stop = 1.6
result = epc.time_slice(t_start, t_stop)
assert_arrays_equal(result.times, targ.times)
assert_arrays_equal(result.durations, targ.durations)
assert_arrays_equal(result.labels, targ.labels)
self.assertEqual(result.name, targ.name)
self.assertEqual(result.description, targ.description)
self.assertEqual(result.file_origin, targ.file_origin)
self.assertEqual(result.annotations['test0'], targ.annotations['test0'])
self.assertEqual(result.annotations['test1'], targ.annotations['test1'])
self.assertEqual(result.annotations['test2'], targ.annotations['test2'])
assert_arrays_equal(result.array_annotations['index'], np.array([1]))
assert_arrays_equal(result.array_annotations['test'], np.array(['b']))
self.assertIsInstance(result.array_annotations, ArrayDict)
def test__time_slice_deepcopy_annotations(self):
params1 = {'test0': 'y1', 'test1': ['deeptest'], 'test2': True}
self.epc.annotate(**params1)
# time_slice spike train, keep sliced spike times
t_start = 15 * pq.s
t_stop = 45 * pq.s
result = self.epc.time_slice(t_start, t_stop)
# Change annotations of original
params2 = {'test0': 'y2', 'test2': False}
self.epc.annotate(**params2)
self.epc.annotations['test1'][0] = 'shallowtest'
self.assertNotEqual(self.epc.annotations['test0'], result.annotations['test0'])
self.assertNotEqual(self.epc.annotations['test1'], result.annotations['test1'])
self.assertNotEqual(self.epc.annotations['test2'], result.annotations['test2'])
# Change annotations of result
params3 = {'test0': 'y3'}
result.annotate(**params3)
result.annotations['test1'][0] = 'shallowtest2'
self.assertNotEqual(self.epc.annotations['test0'], result.annotations['test0'])
self.assertNotEqual(self.epc.annotations['test1'], result.annotations['test1'])
self.assertNotEqual(self.epc.annotations['test2'], result.annotations['test2'])
def test__time_slice_deepcopy_array_annotations(self):
length = self.epc.shape[-1]
params1 = {'test0': ['y{}'.format(i) for i in range(length)],
'test1': ['deeptest' for i in range(length)],
'test2': [(-1)**i > 0 for i in range(length)]}
self.epc.array_annotate(**params1)
# time_slice spike train, keep sliced spike times
t_start = 15 * pq.s
t_stop = 45 * pq.s
result = self.epc.time_slice(t_start, t_stop)
# Change annotations of original
params2 = {'test0': ['x{}'.format(i) for i in range(length)],
'test2': [(-1) ** (i + 1) > 0 for i in range(length)]}
self.epc.array_annotate(**params2)
self.epc.array_annotations['test1'][2] = 'shallowtest'
self.assertFalse(all(self.epc.array_annotations['test0'][1:4]
== result.array_annotations['test0']))
self.assertFalse(all(self.epc.array_annotations['test1'][1:4]
== result.array_annotations['test1']))
self.assertFalse(all(self.epc.array_annotations['test2'][1:4]
== result.array_annotations['test2']))
# Change annotations of result
params3 = {'test0': ['z{}'.format(i) for i in range(1, 4)]}
result.array_annotate(**params3)
result.array_annotations['test1'][1] = 'shallow2'
self.assertFalse(all(self.epc.array_annotations['test0'][1:4]
== result.array_annotations['test0']))
self.assertFalse(all(self.epc.array_annotations['test1'][1:4]
== result.array_annotations['test1']))
self.assertFalse(all(self.epc.array_annotations['test2'][1:4]
== result.array_annotations['test2']))
def test__time_slice_deepcopy_data(self):
result = self.epc.time_slice(None, None)
# Change values of original array
self.epc[2] = 7.3*self.epc.units
self.assertFalse(all(self.epc == result))
# Change values of sliced array
result[3] = 9.5*result.units
self.assertFalse(all(self.epc == result))
def test_time_slice_out_of_boundries(self):
params = {'test2': 'y1', 'test3': True}
arr_ann = {'index': np.arange(3), 'test': ['a', 'b', 'c']}
epc = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'),
name='test', description='tester', file_origin='test.file', test1=1,
array_annotations=arr_ann, **params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
targ = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'),
name='test', description='tester', file_origin='test.file', test1=1,
array_annotations=arr_ann, **params)
targ.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(targ)
t_start = 0.0001
t_stop = 30
result = epc.time_slice(t_start, t_stop)
assert_arrays_equal(result.times, targ.times)
assert_arrays_equal(result.durations, targ.durations)
assert_arrays_equal(result.labels, targ.labels)
self.assertEqual(result.name, targ.name)
self.assertEqual(result.description, targ.description)
self.assertEqual(result.file_origin, targ.file_origin)
self.assertEqual(result.annotations['test0'], targ.annotations['test0'])
self.assertEqual(result.annotations['test1'], targ.annotations['test1'])
self.assertEqual(result.annotations['test2'], targ.annotations['test2'])
assert_arrays_equal(result.array_annotations['index'], np.array(arr_ann['index']))
assert_arrays_equal(result.array_annotations['test'], np.array(arr_ann['test']))
self.assertIsInstance(result.array_annotations, ArrayDict)
def test_time_slice_empty(self):
params = {'test2': 'y1', 'test3': True}
epc = Epoch([] * pq.ms, durations=[] * pq.ns, labels=np.array([], dtype='S'), name='test',
description='tester', file_origin='test.file', test1=1, **params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
targ = Epoch([] * pq.ms, durations=[] * pq.ns, labels=np.array([], dtype='S'), name='test',
description='tester', file_origin='test.file', test1=1, **params)
targ.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(targ)
t_start = 1.2
t_stop = 1.6
result = epc.time_slice(t_start, t_stop)
assert_arrays_equal(result.times, targ.times)
assert_arrays_equal(result.durations, targ.durations)
assert_arrays_equal(result.labels, targ.labels)
self.assertEqual(result.name, targ.name)
self.assertEqual(result.description, targ.description)
self.assertEqual(result.file_origin, targ.file_origin)
self.assertEqual(result.annotations['test0'], targ.annotations['test0'])
self.assertEqual(result.annotations['test1'], targ.annotations['test1'])
self.assertEqual(result.annotations['test2'], targ.annotations['test2'])
self.assertIsInstance(result.array_annotations, ArrayDict)
def test_time_slice_none_stop(self):
params = {'test2': 'y1', 'test3': True}
arr_ann = {'index': np.arange(3), 'test': ['a', 'b', 'c']}
epc = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'),
name='test', description='tester', file_origin='test.file', test1=1,
array_annotations=arr_ann, **params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
targ = Epoch([1.5, 1.7] * pq.ms, durations=[40, 60] * pq.ns,
labels=np.array(['test epoch 2', 'test epoch 3'], dtype='S'), name='test',
description='tester', file_origin='test.file', test1=1,
array_annotations={'index': [1, 2], 'test': ['b', 'c']}, **params)
targ.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(targ)
t_start = 1.2
t_stop = None
result = epc.time_slice(t_start, t_stop)
assert_arrays_equal(result.times, targ.times)
assert_arrays_equal(result.durations, targ.durations)
assert_arrays_equal(result.labels, targ.labels)
self.assertEqual(result.name, targ.name)
self.assertEqual(result.description, targ.description)
self.assertEqual(result.file_origin, targ.file_origin)
self.assertEqual(result.annotations['test0'], targ.annotations['test0'])
self.assertEqual(result.annotations['test1'], targ.annotations['test1'])
self.assertEqual(result.annotations['test2'], targ.annotations['test2'])
assert_arrays_equal(result.array_annotations['index'], np.array([1, 2]))
assert_arrays_equal(result.array_annotations['test'], np.array(['b', 'c']))
self.assertIsInstance(result.array_annotations, ArrayDict)
def test_time_slice_none_start(self):
params = {'test2': 'y1', 'test3': True}
arr_ann = {'index': np.arange(3), 'test': ['a', 'b', 'c']}
epc = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'),
name='test', description='tester', file_origin='test.file', test1=1,
array_annotations=arr_ann, **params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
targ = Epoch([1.1, 1.5] * pq.ms, durations=[20, 40] * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2'], dtype='S'), name='test',
description='tester', file_origin='test.file', test1=1,
array_annotations={'index': [0, 1], 'test': ['a', 'b']}, **params)
targ.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(targ)
t_start = None
t_stop = 1.6
result = epc.time_slice(t_start, t_stop)
assert_arrays_equal(result.times, targ.times)
assert_arrays_equal(result.durations, targ.durations)
assert_arrays_equal(result.labels, targ.labels)
self.assertEqual(result.name, targ.name)
self.assertEqual(result.description, targ.description)
self.assertEqual(result.file_origin, targ.file_origin)
self.assertEqual(result.annotations['test0'], targ.annotations['test0'])
self.assertEqual(result.annotations['test1'], targ.annotations['test1'])
self.assertEqual(result.annotations['test2'], targ.annotations['test2'])
assert_arrays_equal(result.array_annotations['index'], np.array([0, 1]))
assert_arrays_equal(result.array_annotations['test'], np.array(['a', 'b']))
self.assertIsInstance(result.array_annotations, ArrayDict)
def test_time_slice_none_both(self):
params = {'test2': 'y1', 'test3': True}
arr_ann = {'index': np.arange(3), 'test': ['a', 'b', 'c']}
epc = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'),
name='test', description='tester', file_origin='test.file', test1=1,
array_annotations=arr_ann, **params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
targ = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'),
name='test', description='tester', file_origin='test.file', test1=1,
array_annotations=arr_ann, **params)
targ.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(targ)
t_start = None
t_stop = None
result = epc.time_slice(t_start, t_stop)
assert_arrays_equal(result.times, targ.times)
assert_arrays_equal(result.durations, targ.durations)
assert_arrays_equal(result.labels, targ.labels)
self.assertEqual(result.name, targ.name)
self.assertEqual(result.description, targ.description)
self.assertEqual(result.file_origin, targ.file_origin)
self.assertEqual(result.annotations['test0'], targ.annotations['test0'])
self.assertEqual(result.annotations['test1'], targ.annotations['test1'])
self.assertEqual(result.annotations['test2'], targ.annotations['test2'])
assert_arrays_equal(result.array_annotations['index'], np.array([0, 1, 2]))
assert_arrays_equal(result.array_annotations['test'], np.array(['a', 'b', 'c']))
self.assertIsInstance(result.array_annotations, ArrayDict)
def test_time_slice_differnt_units(self):
params = {'test2': 'y1', 'test3': True}
arr_ann = {'index': np.arange(3), 'test': ['a', 'b', 'c']}
epc = Epoch([1.1, 1.5, 1.7] * pq.ms, durations=[20, 40, 60] * pq.ns,
labels=np.array(['test epoch 1', 'test epoch 2', 'test epoch 3'], dtype='S'),
name='test', description='tester', file_origin='test.file', test1=1,
array_annotations=arr_ann, **params)
epc.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(epc)
targ = Epoch([1.5] * pq.ms, durations=[40] * pq.ns,
labels=np.array(['test epoch 2'], dtype='S'), name='test',
description='tester', file_origin='test.file', test1=1,
array_annotations={'index': [1], 'test': ['b']}, **params)
targ.annotate(test1=1.1, test0=[1, 2])
assert_neo_object_is_compliant(targ)
t_start = 0.0012 * pq.s
t_stop = 0.0016 * pq.s
result = epc.time_slice(t_start, t_stop)
assert_arrays_equal(result.times, targ.times)
assert_arrays_equal(result.durations, targ.durations)
assert_arrays_equal(result.labels, targ.labels)
self.assertEqual(result.name, targ.name)
self.assertEqual(result.description, targ.description)
self.assertEqual(result.file_origin, targ.file_origin)
self.assertEqual(result.annotations['test0'], targ.annotations['test0'])
self.assertEqual(result.annotations['test1'], targ.annotations['test1'])
self.assertEqual(result.annotations['test2'], targ.annotations['test2'])
assert_arrays_equal(result.array_annotations['index'], np.array([1]))
assert_arrays_equal(result.array_annotations['test'], np.array(['b']))
self.assertIsInstance(result.array_annotations, ArrayDict)
def test__time_slice_should_set_parents_to_None(self):
# When timeslicing, a deep copy is made,
# thus the reference to parent objects should be destroyed
result = self.epc.time_slice(1 * pq.ms, 3 * pq.ms)
self.assertEqual(result.segment, None)
def test__deepcopy_should_set_parents_objects_to_None(self):
# Deepcopy should destroy references to parents
result = deepcopy(self.epc)
self.assertEqual(result.segment, None)
def test__time_shift_same_attributes(self):
result = self.epc.time_shift(1 * pq.ms)
assert_same_attributes(result, self.epc, exclude=['times'])
def test__time_shift_same_annotations(self):
result = self.epc.time_shift(1 * pq.ms)
assert_same_annotations(result, self.epc)
def test__time_shift_same_array_annotations(self):
result = self.epc.time_shift(1 * pq.ms)
assert_same_array_annotations(result, self.epc)
def test__time_shift_should_set_parents_to_None(self):
# When time-shifting, a deep copy is made,
# thus the reference to parent objects should be destroyed
result = self.epc.time_shift(1 * pq.ms)
self.assertEqual(result.segment, None)
def test__time_shift_by_zero(self):
shifted = self.epc.time_shift(0 * pq.ms)
assert_arrays_equal(shifted.times, self.epc.times)
def test__time_shift_same_units(self):
shifted = self.epc.time_shift(10 * pq.ms)
assert_arrays_equal(shifted.times, self.epc.times + 10 * pq.ms)
def test__time_shift_different_units(self):
shifted = self.epc.time_shift(1 * pq.s)
assert_arrays_equal(shifted.times, self.epc.times + 1000 * pq.ms)
def test_as_array(self):
times = [2, 3, 4, 5]
durations = [0.1, 0.2, 0.3, 0.4]
epc = Epoch(times * pq.ms, durations=durations * pq.ms)
epc_as_arr = epc.as_array(units='ms')
self.assertIsInstance(epc_as_arr, np.ndarray)
assert_array_equal(times, epc_as_arr)
def test_as_quantity(self):
times = [2, 3, 4, 5]
durations = [0.1, 0.2, 0.3, 0.4]
epc = Epoch(times * pq.ms, durations=durations * pq.ms)
epc_as_q = epc.as_quantity()
self.assertIsInstance(epc_as_q, pq.Quantity)
assert_array_equal(times * pq.ms, epc_as_q)
def test_getitem_scalar(self):
times = [2, 3, 4, 5]
durations = [0.1, 0.2, 0.3, 0.4]
labels = ["A", "B", "C", "D"]
epc = Epoch(times * pq.ms, durations=durations * pq.ms, labels=labels)
single_epoch = epc[2]
self.assertIsInstance(single_epoch, pq.Quantity)
assert_array_equal(single_epoch.times, np.array([4.0]))
assert_array_equal(single_epoch.durations, np.array([0.3]))
assert_array_equal(single_epoch.labels, np.array(["C"]))
def test_slice(self):
times = [2, 3, 4, 5]
durations = [0.1, 0.2, 0.3, 0.4]
labels = ["A", "B", "C", "D"]
arr_ann = {'index': np.arange(4), 'test': ['a', 'b', 'c', 'd']}
epc = Epoch(times * pq.ms, durations=durations * pq.ms, labels=labels,
array_annotations=arr_ann)
single_epoch = epc[1:3]
self.assertIsInstance(single_epoch, Epoch)
assert_array_equal(single_epoch.times, np.array([3.0, 4.0]))
assert_array_equal(single_epoch.durations, np.array([0.2, 0.3]))
assert_array_equal(single_epoch.labels, np.array(["B", "C"]))
assert_arrays_equal(single_epoch.array_annotations['index'], np.arange(1, 3))
assert_arrays_equal(single_epoch.array_annotations['test'], np.array(['b', 'c']))
self.assertIsInstance(single_epoch.array_annotations, ArrayDict)
