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import numpy as np
from hdmf.common.table import DynamicTable, DynamicTableRegion, VectorData
from hdmf.data_utils import ShapeValidatorResult, DataChunkIterator, assertEqualShape
from hdmf.testing import TestCase
class ShapeValidatorTests(TestCase):
def setUp(self):
pass
def tearDown(self):
pass
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_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_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_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_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_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_axis_index_out_of_bounds_single_axis(self):
# Test too large first 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_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))
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_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_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_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(name="with_columns_and_data", description="a test table", columns=columns)
# Create test DynamicTableRegion
dtr = DynamicTableRegion(name='dtr', data=[1, 2, 2], description='desc', table=dt)
# Confirm that the shapes match
res = assertEqualShape(dtr, np.arange(9).reshape(3, 3))
self.assertTrue(res.result)
class ShapeValidatorResultTests(TestCase):
def setUp(self):
pass
def tearDown(self):
pass
def test_default_message(self):
temp = ShapeValidatorResult()
temp.error = 'AXIS_LEN_ERROR'
self.assertEqual(temp.default_message, ShapeValidatorResult.SHAPE_ERROR[temp.error])
def test_set_error_to_illegal_type(self):
temp = ShapeValidatorResult()
with self.assertRaises(ValueError):
temp.error = 'MY_ILLEGAL_ERROR_TYPE'
def test_ensure_use_of_tuples_during_asignment(self):
temp = ShapeValidatorResult()
temp_d = [1, 2]
temp_cases = ['shape1', 'shape2', 'axes1', 'axes2', 'ignored', 'unmatched']
for var in temp_cases:
setattr(temp, var, temp_d)
self.assertIsInstance(getattr(temp, var), tuple, var)
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