class TimeDataFRB:
"""
Benchmarks related to data FRB calculations
"""
def setup(self):
self.data = Data(x=np.random.random((64, 64, 64)))
self.bounds = [(10., 54., 128)] * 3
def time_3d_frb(self):
self.data.compute_fixed_resolution_buffer(bounds=self.bounds,
target_cid=self.data.id['x'])
class TestFixedResolutionBuffer():
def setup_method(self, method):
self.data_collection = DataCollection()
# The reference dataset. Shape is (6, 7, 8, 9).
self.data1 = Data(x=ARRAY)
self.data_collection.append(self.data1)
# A dataset with the same shape but not linked. Shape is (6, 7, 8, 9).
self.data2 = Data(x=ARRAY)
self.data_collection.append(self.data2)
# A dataset with the same number of dimensions but in a different
# order, linked to the first. Shape is (9, 7, 6, 8).
self.data3 = Data(x=np.moveaxis(ARRAY, (3, 1, 0, 2), (0, 1, 2, 3)))
self.data_collection.append(self.data3)
self.data_collection.add_link(LinkSame(self.data1.pixel_component_ids[0],
self.data3.pixel_component_ids[2]))
self.data_collection.add_link(LinkSame(self.data1.pixel_component_ids[1],
self.data3.pixel_component_ids[1]))
self.data_collection.add_link(LinkSame(self.data1.pixel_component_ids[2],
self.data3.pixel_component_ids[3]))
self.data_collection.add_link(LinkSame(self.data1.pixel_component_ids[3],
self.data3.pixel_component_ids[0]))
# A dataset with fewer dimensions, linked to the first one. Shape is
# (8, 7, 6)
self.data4 = Data(x=ARRAY[:, :, :, 0].transpose())
self.data_collection.append(self.data4)
self.data_collection.add_link(LinkSame(self.data1.pixel_component_ids[0],
self.data4.pixel_component_ids[2]))
self.data_collection.add_link(LinkSame(self.data1.pixel_component_ids[1],
self.data4.pixel_component_ids[1]))
self.data_collection.add_link(LinkSame(self.data1.pixel_component_ids[2],
self.data4.pixel_component_ids[0]))
# A dataset with even fewer dimensions, linked to the first one. Shape
# is (8, 6)
self.data5 = Data(x=ARRAY[:, 0, :, 0].transpose())
self.data_collection.append(self.data5)
self.data_collection.add_link(LinkSame(self.data1.pixel_component_ids[0],
self.data5.pixel_component_ids[1]))
self.data_collection.add_link(LinkSame(self.data1.pixel_component_ids[2],
self.data5.pixel_component_ids[0]))
# A dataset that is not on the same pixel grid and requires reprojection
# self.data6 = Data()
# self.data6.coords = SimpleCoordinates()
# self.array_nonaligned = np.arange(60).reshape((5, 3, 4))
# self.data6['x'] = np.array(self.array_nonaligned)
# self.data_collection.append(self.data6)
# self.data_collection.add_link(LinkSame(self.data1.world_component_ids[0],
# self.data6.world_component_ids[1]))
# self.data_collection.add_link(LinkSame(self.data1.world_component_ids[1],
# self.data6.world_component_ids[2]))
# self.data_collection.add_link(LinkSame(self.data1.world_component_ids[2],
# self.data6.world_component_ids[0]))
# Start off with the cases where the data is the target data. Enumerate
# the different cases for the bounds and the expected result.
DATA_IS_TARGET_CASES = [
# Bounds are full extent of data
([(0, 5, 6), (0, 6, 7), (0, 7, 8), (0, 8, 9)],
ARRAY),
# Bounds are inside data
([(2, 3, 2), (3, 3, 1), (0, 7, 8), (0, 7, 8)],
ARRAY[2:4, 3:4, :, :8]),
# Bounds are outside data along some dimensions
([(-5, 9, 15), (3, 5, 3), (0, 9, 10), (5, 6, 2)],
np.pad(ARRAY[:, 3:6, :, 5:7], [(5, 4), (0, 0), (0, 2), (0, 0)],
mode='constant', constant_values=-np.inf)),
# No overlap
([(2, 3, 2), (3, 3, 1), (-5, -4, 2), (0, 7, 8)],
-np.inf * np.ones((2, 1, 2, 8)))
]
@pytest.mark.parametrize(('bounds', 'expected'), DATA_IS_TARGET_CASES)
def test_data_is_target_full_bounds(self, bounds, expected):
buffer = self.data1.compute_fixed_resolution_buffer(target_data=self.data1, bounds=bounds,
target_cid=self.data1.id['x'])
assert_equal(buffer, expected)
buffer = self.data3.compute_fixed_resolution_buffer(target_data=self.data1, bounds=bounds,
target_cid=self.data3.id['x'])
assert_equal(buffer, expected)
class TestFixedResolutionBuffer():
def setup_method(self, method):
self.data_collection = DataCollection()
# The reference dataset. Shape is (6, 7, 8, 9).
self.data1 = Data(x=ARRAY)
self.data_collection.append(self.data1)
# A dataset with the same shape but not linked. Shape is (6, 7, 8, 9).
self.data2 = Data(x=ARRAY)
self.data_collection.append(self.data2)
# A dataset with the same number of dimensions but in a different
# order, linked to the first. Shape is (9, 7, 6, 8).
self.data3 = Data(x=np.moveaxis(ARRAY, (3, 1, 0, 2), (0, 1, 2, 3)))
self.data_collection.append(self.data3)
self.data_collection.add_link(LinkSame(self.data1.pixel_component_ids[0],
self.data3.pixel_component_ids[2]))
self.data_collection.add_link(LinkSame(self.data1.pixel_component_ids[1],
self.data3.pixel_component_ids[1]))
self.data_collection.add_link(LinkSame(self.data1.pixel_component_ids[2],
self.data3.pixel_component_ids[3]))
self.data_collection.add_link(LinkSame(self.data1.pixel_component_ids[3],
self.data3.pixel_component_ids[0]))
# A dataset with fewer dimensions, linked to the first one. Shape is
# (8, 7, 6)
self.data4 = Data(x=ARRAY[:, :, :, 0].transpose())
self.data_collection.append(self.data4)
self.data_collection.add_link(LinkSame(self.data1.pixel_component_ids[0],
self.data4.pixel_component_ids[2]))
self.data_collection.add_link(LinkSame(self.data1.pixel_component_ids[1],
self.data4.pixel_component_ids[1]))
self.data_collection.add_link(LinkSame(self.data1.pixel_component_ids[2],
self.data4.pixel_component_ids[0]))
# A dataset with even fewer dimensions, linked to the first one. Shape
# is (8, 6)
self.data5 = Data(x=ARRAY[:, 0, :, 0].transpose())
self.data_collection.append(self.data5)
self.data_collection.add_link(LinkSame(self.data1.pixel_component_ids[0],
self.data5.pixel_component_ids[1]))
self.data_collection.add_link(LinkSame(self.data1.pixel_component_ids[2],
self.data5.pixel_component_ids[0]))
# A dataset that is not on the same pixel grid and requires reprojection
# self.data6 = Data()
# self.data6.coords = SimpleCoordinates()
# self.array_nonaligned = np.arange(60).reshape((5, 3, 4))
# self.data6['x'] = np.array(self.array_nonaligned)
# self.data_collection.append(self.data6)
# self.data_collection.add_link(LinkSame(self.data1.world_component_ids[0],
# self.data6.world_component_ids[1]))
# self.data_collection.add_link(LinkSame(self.data1.world_component_ids[1],
# self.data6.world_component_ids[2]))
# self.data_collection.add_link(LinkSame(self.data1.world_component_ids[2],
# self.data6.world_component_ids[0]))
# Start off with the cases where the data is the target data. Enumerate
# the different cases for the bounds and the expected result.
DATA_IS_TARGET_CASES = [
# Bounds are full extent of data
([(0, 5, 6), (0, 6, 7), (0, 7, 8), (0, 8, 9)],
ARRAY),
# Bounds are inside data
([(2, 3, 2), (3, 3, 1), (0, 7, 8), (0, 7, 8)],
ARRAY[2:4, 3:4, :, :8]),
# Bounds are outside data along some dimensions
([(-5, 9, 15), (3, 5, 3), (0, 9, 10), (5, 6, 2)],
np.pad(ARRAY[:, 3:6, :, 5:7], [(5, 4), (0, 0), (0, 2), (0, 0)],
mode='constant', constant_values=-np.inf)),
# No overlap
([(2, 3, 2), (3, 3, 1), (-5, -4, 2), (0, 7, 8)],
-np.inf * np.ones((2, 1, 2, 8)))
]
@pytest.mark.parametrize(('bounds', 'expected'), DATA_IS_TARGET_CASES)
def test_data_is_target_full_bounds(self, bounds, expected):
buffer = self.data1.compute_fixed_resolution_buffer(target_data=self.data1, bounds=bounds,
target_cid=self.data1.id['x'])
assert_equal(buffer, expected)
buffer = self.data3.compute_fixed_resolution_buffer(target_data=self.data1, bounds=bounds,
target_cid=self.data3.id['x'])
assert_equal(buffer, expected)
