def test_axis_ording_cvdb_channels(self):
data_xyz = array(
"bossdb://wildenberg2021/VTA_dat12a_saline_control_Dendrites_6nm_aligned/image",
axis_order="XYZ",
)
data_zyx = array(
"bossdb://wildenberg2021/VTA_dat12a_saline_control_Dendrites_6nm_aligned/image",
axis_order="ZYX",
)
self.assertTupleEqual(
data_xyz.shape,
(data_zyx.shape[2], data_zyx.shape[1], data_zyx.shape[0]))
def test_get_data_cvdb_channels(self):
data_boss = array(
"bossdb://wildenberg2021/VTA_dat12a_saline_control_Dendrites_6nm_aligned/image",
volume_provider=_BossDBVolumeProvider(),
)
data_cv = array(
"bossdb://wildenberg2021/VTA_dat12a_saline_control_Dendrites_6nm_aligned/image",
)
excerpt_boss = data_boss[40:50, 40:50, 40:50]
excerpt_cv = data_cv[40:50, 40:50, 40:50]
self.assertTrue(np.array_equal(excerpt_boss, excerpt_cv))
def test_get_data_cvdb_channels_rollaxes(self):
data_xyz = array(
"bossdb://wildenberg2021/VTA_dat12a_saline_control_Dendrites_6nm_aligned/image",
axis_order="XYZ",
)
data_zyx = array(
"bossdb://wildenberg2021/VTA_dat12a_saline_control_Dendrites_6nm_aligned/image",
axis_order="ZYX",
)
excerpt_xyz = data_xyz[40:50, 40:50, 40:50]
excerpt_zyx = data_zyx[40:50, 40:50, 40:50]
self.assertTrue(
np.array_equal(excerpt_xyz, np.rollaxis(excerpt_zyx, 0, 2)))
def test_array_instantiation_with_channel(self):
"""
Array can be instantiated.
.
"""
boss = BossRemote(_DEFAULT_BOSS_OPTIONS)
_ = array(boss.get_channel("cc", "kasthuri2015", "em"))
def test_array_instantiation_dtype(self):
"""
Array can be instantiated with type.
.
"""
boss = BossRemote(_DEFAULT_BOSS_OPTIONS)
test_array = array(boss.get_channel("cc", "kasthuri2015", "em"))
self.assertEqual(test_array.dtype, "uint8")
def test_can_retrieve_correct_u64_data(self):
data = array("bossdb://kasthuri2015/em/3cylneuron_v1")
boss = BossRemote(_DEFAULT_BOSS_OPTIONS)
get_cutout_data = boss.get_cutout(
boss.get_channel("3cylneuron_v1", "kasthuri2015", "em"),
0,
[6000, 6200],
[12000, 12500],
[923, 924],
)
self.assertTrue(
(get_cutout_data == data[923:924, 12000:12500, 6000:6200]).all()
)
def test_get_remote_type(self):
data = array("bossdb://kasthuri2015/em/3cylneuron_v1")
self.assertEqual(data.remote, "BossDB")
def test_can_guess_cvdb_channels(self):
data = array(
"bossdb://wildenberg2021/VTA_dat12a_saline_control_Dendrites_6nm_aligned/image"
)
self.assertEqual(data.remote, "CloudVolumeOpenData")
def test_precompute_inference_cvdb(self):
data = array(
"precomputed://s3://bossdb-open-data/wildenberg2021/VTA_dat12a_saline_control_Dendrites_6nm_aligned/image"
)
self.assertEqual(data.remote, "CloudVolumeOpenData")
def test_can_retrieve_data_with_XYZ_order_of_correct_shape(self):
data = array("bossdb://Kasthuri/em/images", resolution=1, axis_order="XYZ")
array_cutout = data[10000:10012, 10000:10011, 1000:1010]
self.assertEqual(array_cutout.shape, (12, 11, 10))
def test_can_retrieve_data_of_correct_shape(self):
data = array("bossdb://Kasthuri/em/images", resolution=1)
array_cutout = data[1000:1010, 10000:10011, 10000:10012]
self.assertEqual(array_cutout.shape, (10, 11, 12))
def test_can_get_shape_of_array_with_resolution(self):
res = 1
data = array("bossdb://Kasthuri/em/images", resolution=res)
self.assertEqual(data.shape, (1850, 26624 / (2 ** res), 21504 / (2 ** res)))
def test_can_get_shape_of_array(self):
data = array("bossdb://Kasthuri/em/images")
self.assertEqual(data.shape, (1850, 26624, 21504))
def test_can_initialize_array_without_checks(self):
array("bossdb://Kasthuri/em/images")
def __init__(self, cloud_path):
_check_intern_importable()
self._data = array(cloud_path)
