def test_blosc_missing_time_step(self):
"""Test case when one of the cuboids at a time step is missing. This
happens when trying to load from the cache. Only keys in the cache
are passed to from_blosc().
"""
EXTENTS = [10, 20, 5]
cube_t0_1 = ImageCube8(EXTENTS, [0, 2])
cube_t3 = ImageCube8(EXTENTS)
exp_cube = ImageCube8(EXTENTS, [0, 4])
exp_cube.zeros()
exp_cube.overwrite(cube_t0_1.data, [0, 2])
exp_cube.overwrite(cube_t3.data, [3, 4])
cube_bytes_t0 = cube_t0_1.to_blosc_by_time_index(0)
cube_bytes_t1 = cube_t0_1.to_blosc_by_time_index(1)
cube_bytes_t3 = cube_t3.to_blosc_by_time_index(0)
cube_list = (cube_bytes_t0, cube_bytes_t1, cube_bytes_t3)
actual_cube = ImageCube8(EXTENTS, [0, 4])
missing_time_step = [2]
# Method under test.
actual_cube.from_blosc(cube_list, [0, 4], missing_time_step)
np.testing.assert_array_equal(exp_cube.data, actual_cube.data)
assert actual_cube.is_time_series is True
def test_add_data_no_time(self):
"""Test adding data from a smaller cube to a bigger one"""
c_base = ImageCube8([20, 15, 10])
c_base.zeros()
assert c_base.is_not_zeros() is False
c_add = ImageCube8([5, 5, 5])
c_add.zeros()
c_add.data += 1
assert c_add.is_not_zeros() is True
# Make sure c_base empty
assert c_base.data.sum() == 0
# Insert c_add into c_base
c_base.add_data(c_add, [0, 0, 0])
# Make sure insertion happened
assert c_base.data.sum() == 5 * 5 * 5
# Make sure it was in the right spot
assert c_base.data[0, 1, 2, 3] == 1
assert c_base.data[0, 4, 4, 4] == 1
assert c_base.data[0, 0, 0, 0] == 1
assert c_base.data[0, 4, 4, 6] == 0
assert c_base.data[0, 6, 4, 4] == 0
assert c_base.data[0, 4, 6, 4] == 0
# Try an offset in x insert
c_base.zeros()
c_base.add_data(c_add, [1, 0, 0])
# Make sure insertion happened
assert c_base.data.sum() == 5 * 5 * 5
# Make sure it was in the right spot (remember data is still stored in zyx under the hood)
assert c_base.data[0, 1, 1, 1] == 0
assert c_base.data[0, 4, 4, 6] == 1
# Try an offset in y insert
c_base.zeros()
c_base.add_data(c_add, [0, 1, 0])
# Make sure insertion happened
assert c_base.data.sum() == 5 * 5 * 5
# Make sure it was in the right spot (remember data is still stored in zyx under the hood)
assert c_base.data[0, 1, 1, 1] == 0
assert c_base.data[0, 4, 6, 4] == 1
# Try an offset in z insert
c_base.zeros()
c_base.add_data(c_add, [0, 0, 1])
# Make sure insertion happened
assert c_base.data.sum() == 5 * 5 * 5
# Make sure it was in the right spot (remember data is still stored in zyx under the hood)
assert c_base.data[0, 1, 1, 1] == 0
assert c_base.data[0, 6, 4, 4] == 1
def test_blosc_time_index_specific_time(self):
"""Test blosc compression of Cube data"""
c = ImageCube8([10, 20, 5], [0, 4])
c.random()
c2 = ImageCube8([10, 20, 5], [0, 4])
byte_array = c.to_blosc_by_time_index(2)
c2.from_blosc([byte_array])
np.testing.assert_array_equal(np.expand_dims(c.data[2, :, :, :], axis=0), c2.data)
assert c.cube_size == c2.cube_size
assert c.z_dim == c2.z_dim
assert c.y_dim == c2.y_dim
assert c.x_dim == c2.x_dim
def test_blosc_time_index_no_time(self):
"""Test blosc compression of Cube data"""
c = ImageCube8([10, 20, 5])
c.random()
c2 = ImageCube8([10, 20, 5])
byte_array = c.to_blosc_by_time_index()
c2.from_blosc([byte_array])
np.testing.assert_array_equal(c.data, c2.data)
assert c.cube_size == c2.cube_size
assert c.z_dim == c2.z_dim
assert c.y_dim == c2.y_dim
assert c.x_dim == c2.x_dim
def test_overwrite_simple(self):
"""Test overwriting data - for ImageCub8 this just does a copy."""
c_base = ImageCube8([10, 20, 5], [0, 10])
c_base.zeros()
data = np.zeros((3, 5, 20, 10), np.uint8)
data[0, 1, 2, 5] = 1
data[2, 3, 15, 7] = 3
# Make sure c_base empty
assert c_base.data.sum() == 0
assert c_base.data[0, 1, 2, 5] == 0
assert c_base.data[2, 3, 15, 7] == 0
# Insert c_add into c_base
c_base.overwrite(data, [4, 7])
# Make sure insertion happened
assert c_base.data.sum() == 4
# Make sure it was in the right spot
assert c_base.data[0, 1, 2, 5] == 0
assert c_base.data[2, 3, 15, 7] == 0
# Should insert starting at T=4
assert c_base.data[4, 1, 2, 5] == 1
assert c_base.data[6, 3, 15, 7] == 3
def test_random(self):
"""Test populating a default Cube instance with zeros"""
c = ImageCube8()
c.random()
size = c.data.shape
assert size == (1, self.cuboid_z_dim, self.cuboid_y_dim, self.cuboid_x_dim)
assert c.from_zeros() is False
assert c.data.size == self.cuboid_z_dim * self.cuboid_y_dim * self.cuboid_x_dim
assert c.data.dtype == np.uint8
assert c.data.sum() > 0
c2 = ImageCube8()
c2.random()
self.assertRaises(AssertionError, np.testing.assert_array_equal, c.data, c2.data)
def test_blosc_all_time_samples_single_array(self):
"""Test blosc compression of Cube data"""
c = ImageCube8([10, 20, 5], [0, 4])
c.random()
c2 = ImageCube8([10, 20, 5], [0, 4])
byte_array = c.to_blosc()
c2.from_blosc(byte_array, [0, 4])
np.testing.assert_array_equal(c.data, c2.data)
assert c.cube_size == c2.cube_size
assert c.z_dim == c2.z_dim
assert c.y_dim == c2.y_dim
assert c.x_dim == c2.x_dim
assert c.time_range == c2.time_range
assert c.is_time_series is True
assert c2.is_time_series is True
def test_tile_xz(self):
"""Test getting an xy tile."""
# Create base data
c_base = ImageCube8([128, 100, 16], [0, 1])
c_base.zeros()
c_base.data = np.random.randint(1, 254, (1, 16, 100, 128)).astype(np.uint8)
img = c_base.xz_image(y_index=1)
assert img.size == (128, 16)
def test_constructor_no_time(self):
"""Test the Cube class constructor"""
c = ImageCube8([128, 64, 16])
assert c.cube_size == [16, 64, 128]
assert c.x_dim == 128
assert c.y_dim == 64
assert c.z_dim == 16
assert c.from_zeros() is False
assert c.time_range == [0, 1]
assert c.is_time_series is False
def test_constructor_no_dim_no_time(self):
"""Test the Cube class constructor"""
c = ImageCube8()
assert c.cube_size == [self.cuboid_z_dim, self.cuboid_y_dim, self.cuboid_x_dim]
assert c.x_dim == self.cuboid_x_dim
assert c.y_dim == self.cuboid_y_dim
assert c.z_dim == self.cuboid_z_dim
assert c.from_zeros() is False
assert c.time_range == [0, 1]
assert c.is_time_series is False
def test_zeros_time_samples(self):
"""Test populating a default Cube instance with zeros"""
c = ImageCube8([128, 64, 16], [2, 10])
c.zeros()
size = c.data.shape
assert size == (8, 16, 64, 128)
assert c.from_zeros() is True
assert c.data.size == 8 * 16 * 64 * 128
assert c.data.dtype == np.uint8
assert c.data.sum() == 0
def test_zeros(self):
"""Test populating a default Cube instance with zeros"""
c = ImageCube8()
c.zeros()
size = c.data.shape
assert size == (1, self.cuboid_z_dim, self.cuboid_y_dim, self.cuboid_x_dim)
assert c.from_zeros() is True
assert c.data.size == self.cuboid_z_dim * self.cuboid_y_dim * self.cuboid_x_dim
assert c.data.dtype == np.uint8
assert c.data.sum() == 0
def test_trim_no_time(self):
"""Test trimming off part of a cube"""
c = ImageCube8([10, 20, 5])
c.zeros()
c.data += 1
assert c.data.sum() == 10 * 20 * 5
c.data[0, 2, 7, 5] = 5
c.trim(5, 5, 7, 6, 2, 2)
assert c.data[0, 0, 0, 0] == 5
assert c.data.sum() == 5 * 6 * 2 + 4
def test_constructor(self):
"""Test the Cube class constructor"""
c = ImageCube8([128, 64, 16], [0, 10])
assert c.cube_size == [16, 64, 128]
assert c.x_dim == 128
assert c.y_dim == 64
assert c.z_dim == 16
assert c.from_zeros() is False
assert c.time_range == [0, 10]
assert c.is_time_series is True
assert c.data.dtype == np.uint8
def test_trim(self):
"""Test trimming off part of a cube"""
c = ImageCube8([10, 20, 5], [0, 4])
c.zeros()
c.data += 1
assert c.data.sum() == 10 * 20 * 5 * 4
c.data[0, 2, 7, 5] = 5
c.data[1, 3, 10, 7] = 2
c.trim(5, 5, 7, 6, 2, 2)
assert c.data[0, 0, 0, 0] == 5
assert c.data[0, 1, 3, 2] == 1
assert c.data[1, 1, 3, 2] == 2
assert c.data.sum() == 4 * 2 * 6 * 5 + 4 + 1
def test_overwrite_no_time(self):
"""Test overwriting data - for ImageCub8 this just does a copy."""
c_base = ImageCube8([10, 20, 5])
c_base.zeros()
data = np.zeros((1, 5, 20, 10), np.uint8)
data[0, 1, 2, 5] = 1
# Make sure c_base empty
assert c_base.data.sum() == 0
# Insert c_add into c_base
c_base.overwrite(data)
# Make sure insertion happened
assert c_base.data.sum() == 1
# Make sure it was in the right spot
assert c_base.data[0, 1, 2, 5] == 1
def test_overwrite(self):
"""Test overwriting data with existing data in place."""
# Create base data
c_base = ImageCube8([10, 20, 5], [0, 10])
c_base.zeros()
c_base.data[1, 1, 1, 1] = 1
c_base.data[2, 4, 4, 1] = 2
# Create overwrite data - all zero locations
data = np.zeros((2, 5, 20, 10), np.uint8)
data[0, 2, 2, 2] = 3
data[1, 4, 5, 6] = 4
# Insert c_add into c_base
c_base.overwrite(data, [1, 3])
# Make sure insertion happened
assert c_base.data.sum() == 1 + 2 + 3 + 4
# Make sure it was in the right spot
assert c_base.data[1, 1, 1, 1] == 1
assert c_base.data[2, 4, 4, 1] == 2
assert c_base.data[1, 2, 2, 2] == 3
assert c_base.data[2, 4, 5, 6] == 4
# Place data in existing voxel locations and re-do overwrite
data[0, 1, 1, 1] = 5
data[1, 4, 4, 1] = 6
# Insert into c_base
c_base.overwrite(data, [1, 3])
# Make sure insertion happened
assert c_base.data.sum() == 3 + 4 + 5 + 6
# Make sure it was in the right spot
assert c_base.data[1, 1, 1, 1] == 5
assert c_base.data[2, 4, 4, 1] == 6
assert c_base.data[1, 2, 2, 2] == 3
assert c_base.data[2, 4, 5, 6] == 4