def __init__(self, **kwargs):
# get the inputs
electrodes, description, times, features = popargs(
'electrodes', 'description', 'times', 'features', kwargs)
# Validate the shape of the inputs
# Validate event times compared to features
shape_validators = []
shape_validators.append(
assertEqualShape(data1=features,
data2=times,
axes1=0,
axes2=0,
name1='feature_shape',
name2='times',
ignore_undetermined=True))
# Validate electrodes compared to features
shape_validators.append(
assertEqualShape(data1=features,
data2=electrodes,
axes1=1,
axes2=0,
name1='feature_shape',
name2='electrodes',
ignore_undetermined=True))
# Valided description compared to features
shape_validators.append(
assertEqualShape(data1=features,
data2=description,
axes1=2,
axes2=0,
name1='feature_shape',
name2='description',
ignore_undetermined=True))
# Raise an error if any of the shapes do not match
raise_error = False
error_msg = ""
for sv in shape_validators:
raise_error |= not sv.result
if not sv.result:
error_msg += sv.message + "\n"
if raise_error:
raise ValueError(error_msg)
# Initialize the object
super(FeatureExtraction, self).__init__(**kwargs)
self.electrodes = electrodes
self.description = description
self.times = list(times)
self.features = features
def test_DynamicTableRegion_shape_validation(self):
# Create a test DynamicTable
dt_spec = [
{
'name': 'foo',
'description': 'foo column'
},
{
'name': 'bar',
'description': 'bar column'
},
{
'name': 'baz',
'description': 'baz column'
},
]
dt_data = [[1, 2, 3, 4, 5], [10.0, 20.0, 30.0, 40.0, 50.0],
['cat', 'dog', 'bird', 'fish', 'lizard']]
columns = [
VectorData(name=s['name'], description=s['description'], data=d)
for s, d in zip(dt_spec, dt_data)
]
dt = DynamicTable("with_columns_and_data",
"a test table",
columns=columns)
# Create test DynamicTableRegion
dtr = DynamicTableRegion('dtr', [1, 2, 2], 'desc', table=dt)
# Confirm that the shapes match
res = assertEqualShape(dtr, np.arange(9).reshape(3, 3))
self.assertTrue(res.result)
def test_array_axis_index_out_of_bounds_single_axis(self):
# Test too large frist axis
d1 = np.arange(10).reshape(2, 5)
d2 = np.arange(20).reshape(5, 2, 2)
res = assertEqualShape(d1, d2, 4, 1)
self.assertFalse(res.result)
self.assertEqual(res.error, 'AXIS_OUT_OF_BOUNDS')
self.assertTupleEqual(res.ignored, ())
self.assertTupleEqual(res.unmatched, ())
self.assertTupleEqual(res.shape1, (2, 5))
self.assertTupleEqual(res.shape2, (5, 2, 2))
self.assertTupleEqual(res.axes1, (4,))
self.assertTupleEqual(res.axes2, (1,))
def test_array_unequal_number_of_axes_for_comparison(self):
# Test unequal num axes for comparison
d1 = np.arange(10).reshape(2, 5)
d2 = np.arange(20).reshape(5, 2, 2)
res = assertEqualShape(d1, d2, [0, 1], 1)
self.assertFalse(res.result)
self.assertEqual(res.error, "NUM_AXES_ERROR")
self.assertTupleEqual(res.ignored, ())
self.assertTupleEqual(res.unmatched, ())
self.assertTupleEqual(res.shape1, (2, 5))
self.assertTupleEqual(res.shape2, (5, 2, 2))
self.assertTupleEqual(res.axes1, (0, 1))
self.assertTupleEqual(res.axes2, (1,))
def test_array_unequal_number_of_dimensions_check_multiple_axesy(self):
# Test unequal num dims compare multiple axes
d1 = np.arange(10).reshape(2, 5)
d2 = np.arange(20).reshape(5, 2, 2)
res = assertEqualShape(d1, d2, [0, 1], [1, 0])
self.assertTrue(res.result)
self.assertIsNone(res.error)
self.assertTupleEqual(res.ignored, ())
self.assertTupleEqual(res.unmatched, ())
self.assertTupleEqual(res.shape1, (2, 5))
self.assertTupleEqual(res.shape2, (5, 2, 2))
self.assertTupleEqual(res.axes1, (0, 1))
self.assertTupleEqual(res.axes2, (1, 0))
def test_array_unequal_number_of_dimensions_check_one_axis_only(self):
# Test unequal num dims compare one axis
d1 = np.arange(10).reshape(2, 5)
d2 = np.arange(20).reshape(2, 5, 2)
res = assertEqualShape(d1, d2, 0, 0)
self.assertTrue(res.result)
self.assertIsNone(res.error)
self.assertTupleEqual(res.ignored, ())
self.assertTupleEqual(res.unmatched, ())
self.assertTupleEqual(res.shape1, (2, 5))
self.assertTupleEqual(res.shape2, (2, 5, 2))
self.assertTupleEqual(res.axes1, (0,))
self.assertTupleEqual(res.axes2, (0,))
def test_array_unequal_number_of_dimensions(self):
# Test unequal num dims
d1 = np.arange(10).reshape(2, 5)
d2 = np.arange(20).reshape(5, 2, 2)
res = assertEqualShape(d1, d2)
self.assertFalse(res.result)
self.assertEqual(res.error, 'NUM_AXES_ERROR')
self.assertTupleEqual(res.ignored, ())
self.assertTupleEqual(res.unmatched, ())
self.assertTupleEqual(res.shape1, (2, 5))
self.assertTupleEqual(res.shape2, (5, 2, 2))
self.assertTupleEqual(res.axes1, (0, 1))
self.assertTupleEqual(res.axes2, (0, 1, 2))
def test_array_dimensions_mismatch(self):
# Test unmatched
d1 = np.arange(10).reshape(2, 5)
d2 = np.arange(10).reshape(5, 2)
res = assertEqualShape(d1, d2)
self.assertFalse(res.result)
self.assertEqual(res.error, 'AXIS_LEN_ERROR')
self.assertTupleEqual(res.ignored, ())
self.assertTupleEqual(res.unmatched, ((0, 0), (1, 1)))
self.assertTupleEqual(res.shape1, (2, 5))
self.assertTupleEqual(res.shape2, (5, 2))
self.assertTupleEqual(res.axes1, (0, 1))
self.assertTupleEqual(res.axes2, (0, 1))
def test_DataChunkIterator_error_on_undetermined_axis(self):
# Compare data chunk iterators with undetermined axis (error on undetermined axis)
d1 = DataChunkIterator(data=np.arange(10).reshape(2, 5), maxshape=(None, 5))
d2 = DataChunkIterator(data=np.arange(10).reshape(2, 5))
res = assertEqualShape(d1, d2, ignore_undetermined=False)
self.assertFalse(res.result)
self.assertEqual(res.error, 'AXIS_LEN_ERROR')
self.assertTupleEqual(res.ignored, ())
self.assertTupleEqual(res.unmatched, ((0, 0),))
self.assertTupleEqual(res.shape1, (None, 5))
self.assertTupleEqual(res.shape2, (2, 5))
self.assertTupleEqual(res.axes1, (0, 1))
self.assertTupleEqual(res.axes2, (0, 1))
def test_DataChunkIterator_ignore_undetermined_axis(self):
# Compare data chunk iterators with undetermined axis (ignore axis)
d1 = DataChunkIterator(data=np.arange(10).reshape(2, 5), maxshape=(None, 5))
d2 = DataChunkIterator(data=np.arange(10).reshape(2, 5))
res = assertEqualShape(d1, d2, ignore_undetermined=True)
self.assertTrue(res.result)
self.assertIsNone(res.error)
self.assertTupleEqual(res.ignored, ((0, 0),))
self.assertTupleEqual(res.unmatched, ())
self.assertTupleEqual(res.shape1, (None, 5))
self.assertTupleEqual(res.shape2, (2, 5))
self.assertTupleEqual(res.axes1, (0, 1))
self.assertTupleEqual(res.axes2, (0, 1))
def test_array_all_dimensions_match(self):
# Test match
d1 = np.arange(10).reshape(2, 5)
d2 = np.arange(10).reshape(2, 5)
res = assertEqualShape(d1, d2)
self.assertTrue(res.result)
self.assertIsNone(res.error)
self.assertTupleEqual(res.ignored, ())
self.assertTupleEqual(res.unmatched, ())
self.assertTupleEqual(res.shape1, (2, 5))
self.assertTupleEqual(res.shape2, (2, 5))
self.assertTupleEqual(res.axes1, (0, 1))
self.assertTupleEqual(res.axes2, (0, 1))
def test_DataChunkIterators_match(self):
# Compare data chunk iterators
d1 = DataChunkIterator(data=np.arange(10).reshape(2, 5))
d2 = DataChunkIterator(data=np.arange(10).reshape(2, 5))
res = assertEqualShape(d1, d2)
self.assertTrue(res.result)
self.assertIsNone(res.error)
self.assertTupleEqual(res.ignored, ())
self.assertTupleEqual(res.unmatched, ())
self.assertTupleEqual(res.shape1, (2, 5))
self.assertTupleEqual(res.shape2, (2, 5))
self.assertTupleEqual(res.axes1, (0, 1))
self.assertTupleEqual(res.axes2, (0, 1))
def test_array_axis_index_out_of_bounds_mutilple_axis(self):
# Test too large second axis
d1 = np.arange(10).reshape(2, 5)
d2 = np.arange(20).reshape(5, 2, 2)
res = assertEqualShape(d1, d2, [0, 1], [5, 0])
self.assertFalse(res.result)
self.assertEqual(res.error, 'AXIS_OUT_OF_BOUNDS')
self.assertTupleEqual(res.ignored, ())
self.assertTupleEqual(res.unmatched, ())
self.assertTupleEqual(res.shape1, (2, 5))
self.assertTupleEqual(res.shape2, (5, 2, 2))
self.assertTupleEqual(res.axes1, (0, 1))
self.assertTupleEqual(res.axes2, (5, 0))
