def test_basic_resource_from_dict(self):
"""Test basic to dict deserialization method
Returns:
None
"""
setup_data = get_image_dict()
resource1 = BossResourceBasic(setup_data)
resource2 = BossResourceBasic()
resource2.from_dict(resource1.to_dict())
# Check Collection
col = resource2.get_collection()
assert col.name == setup_data['collection']['name']
assert col.description == setup_data['collection']['description']
# Check coord frame
coord = resource2.get_coord_frame()
assert coord.name == setup_data['coord_frame']['name']
assert coord.description == setup_data['coord_frame']['description']
assert coord.x_start == setup_data['coord_frame']['x_start']
assert coord.x_stop == setup_data['coord_frame']['x_stop']
assert coord.y_start == setup_data['coord_frame']['y_start']
assert coord.y_stop == setup_data['coord_frame']['y_stop']
assert coord.z_start == setup_data['coord_frame']['z_start']
assert coord.z_stop == setup_data['coord_frame']['z_stop']
assert coord.x_voxel_size == setup_data['coord_frame']['x_voxel_size']
assert coord.y_voxel_size == setup_data['coord_frame']['y_voxel_size']
assert coord.z_voxel_size == setup_data['coord_frame']['z_voxel_size']
assert coord.voxel_unit == setup_data['coord_frame']['voxel_unit']
# Check exp
exp = resource2.get_experiment()
assert exp.name == setup_data['experiment']['name']
assert exp.description == setup_data['experiment']['description']
assert exp.num_hierarchy_levels == setup_data['experiment']['num_hierarchy_levels']
assert exp.hierarchy_method == setup_data['experiment']['hierarchy_method']
assert exp.num_time_samples == setup_data['experiment']['num_time_samples']
assert exp.time_step == setup_data['experiment']['time_step']
assert exp.time_step_unit == setup_data['experiment']['time_step_unit']
# Check channel
channel = resource2.get_channel()
assert channel.is_image() is True
assert channel.name == setup_data['channel']['name']
assert channel.description == setup_data['channel']['description']
assert channel.datatype == setup_data['channel']['datatype']
assert channel.base_resolution == setup_data['channel']['base_resolution']
assert channel.sources == setup_data['channel']['sources']
assert channel.related == setup_data['channel']['related']
assert channel.default_time_sample == setup_data['channel']['default_time_sample']
# check keys
assert resource2.get_lookup_key() == setup_data['lookup_key']
assert resource2.get_boss_key() == setup_data['boss_key']
def test_basic_resource_from_dict(self):
"""Test basic to dict deserialization method
Returns:
None
"""
setup_data = get_image_dict()
resource1 = BossResourceBasic(setup_data)
resource2 = BossResourceBasic()
resource2.from_dict(resource1.to_dict())
# Check Collection
col = resource2.get_collection()
assert col.name == setup_data['collection']['name']
assert col.description == setup_data['collection']['description']
# Check coord frame
coord = resource2.get_coord_frame()
assert coord.name == setup_data['coord_frame']['name']
assert coord.description == setup_data['coord_frame']['description']
assert coord.x_start == setup_data['coord_frame']['x_start']
assert coord.x_stop == setup_data['coord_frame']['x_stop']
assert coord.y_start == setup_data['coord_frame']['y_start']
assert coord.y_stop == setup_data['coord_frame']['y_stop']
assert coord.z_start == setup_data['coord_frame']['z_start']
assert coord.z_stop == setup_data['coord_frame']['z_stop']
assert coord.x_voxel_size == setup_data['coord_frame']['x_voxel_size']
assert coord.y_voxel_size == setup_data['coord_frame']['y_voxel_size']
assert coord.z_voxel_size == setup_data['coord_frame']['z_voxel_size']
assert coord.voxel_unit == setup_data['coord_frame']['voxel_unit']
# Check exp
exp = resource2.get_experiment()
assert exp.name == setup_data['experiment']['name']
assert exp.description == setup_data['experiment']['description']
assert exp.num_hierarchy_levels == setup_data['experiment']['num_hierarchy_levels']
assert exp.hierarchy_method == setup_data['experiment']['hierarchy_method']
assert exp.num_time_samples == setup_data['experiment']['num_time_samples']
assert exp.time_step == setup_data['experiment']['time_step']
assert exp.time_step_unit == setup_data['experiment']['time_step_unit']
# Check channel
channel = resource2.get_channel()
assert channel.is_image() is True
assert channel.name == setup_data['channel']['name']
assert channel.description == setup_data['channel']['description']
assert channel.datatype == setup_data['channel']['datatype']
assert channel.base_resolution == setup_data['channel']['base_resolution']
assert channel.sources == setup_data['channel']['sources']
assert channel.related == setup_data['channel']['related']
assert channel.default_time_sample == setup_data['channel']['default_time_sample']
# check keys
assert resource2.get_lookup_key() == setup_data['lookup_key']
assert resource2.get_boss_key() == setup_data['boss_key']
def test_factory(self):
"""Test the Cube factory in Cube"""
data = get_image_dict()
resource = BossResourceBasic(data)
c = Cube.create_cube(resource, [30, 20, 13], [0, 15])
assert isinstance(c, ImageCube8) is True
assert c.cube_size == [13, 20, 30]
assert c.is_time_series is True
assert c.time_range == [0, 15]
def setUpClass(cls):
"""Setup the redis client at the start of the test"""
cls.data = get_image_dict()
cls.resource = BossResourceBasic(cls.data)
cls.config = configuration.BossConfig()
cls.state_client = redis.StrictRedis(host=cls.config["aws"]["cache-state"], port=6379, db=1,
decode_responses=False)
cls.config_data = {"state_client": cls.state_client}
def setUpClass(cls):
"""Setup the redis client at the start of the test"""
cls.data = get_image_dict()
cls.resource = BossResourceBasic(cls.data)
cls.config = configuration.BossConfig()
cls.cache_client = redis.StrictRedis(host=cls.config["aws"]["cache"], port=6379, db=1,
decode_responses=False)
cls.config_data = {"cache_client": cls.cache_client, "read_timeout": 86400}
def test_basic_resource_get_lookup_key(self):
"""Test basic get lookup key interface
Returns:
None
"""
setup_data = get_image_dict()
resource = BossResourceBasic(setup_data)
assert resource.get_lookup_key() == setup_data['lookup_key']
def test_basic_resource_get_bit_depth(self):
"""Test basic get bit depth interface
Returns:
None
"""
setup_data = get_image_dict()
resource = BossResourceBasic(setup_data)
assert resource.get_bit_depth() == 8
def test_factory(self):
"""Test the Cube factory in Cube"""
data = get_image_dict()
resource = BossResourceBasic(data)
c = Cube.create_cube(resource, [30, 20, 13], [0, 15])
assert isinstance(c, ImageCube8) is True
assert c.cube_size == [13, 20, 30]
assert c.is_time_series is True
assert c.time_range == [0, 15]
def test_basic_resource_get_data_type(self):
"""Test basic get datatype interface
Returns:
None
"""
setup_data = get_image_dict()
resource = BossResourceBasic(setup_data)
assert resource.get_data_type() == setup_data['channel']['datatype']
def test_basic_resource_get_bit_depth(self):
"""Test basic get bit depth interface
Returns:
None
"""
setup_data = get_image_dict()
resource = BossResourceBasic(setup_data)
assert resource.get_bit_depth() == 8
def test_basic_resource_numpy_data_type(self):
"""Test basic get bit depth interface
Returns:
None
"""
setup_data = get_image_dict()
resource = BossResourceBasic(setup_data)
assert resource.get_numpy_data_type() == np.uint8
def test_basic_resource_get_data_type(self):
"""Test basic get datatype interface
Returns:
None
"""
setup_data = get_image_dict()
resource = BossResourceBasic(setup_data)
assert resource.get_data_type() == setup_data['channel']['datatype']
def test_basic_resource_get_lookup_key(self):
"""Test basic get lookup key interface
Returns:
None
"""
setup_data = get_image_dict()
resource = BossResourceBasic(setup_data)
assert resource.get_lookup_key() == setup_data['lookup_key']
def test_basic_resource_numpy_data_type(self):
"""Test basic get bit depth interface
Returns:
None
"""
setup_data = get_image_dict()
resource = BossResourceBasic(setup_data)
assert resource.get_numpy_data_type() == np.uint8
def setUpClass(cls):
"""Setup the redis client at the start of the test"""
cls.data = get_image_dict()
cls.resource = BossResourceBasic(cls.data)
cls.state_client = redis.StrictRedis(host='localhost',
port=6379,
db=1,
decode_responses=False)
cls.config_data = {"state_client": cls.state_client}
def test_factory_no_time(self):
"""Test the Cube factory in Cube"""
data = get_image_dict()
data['channel']['datatype'] = 'uint16'
resource = BossResourceBasic(data)
c = Cube.create_cube(resource, [30, 20, 13])
assert isinstance(c, ImageCube16) is True
assert c.cube_size == [13, 20, 30]
assert c.is_time_series is False
assert c.time_range == [0, 1]
def test_factory_no_time(self):
"""Test the Cube factory in Cube"""
data = get_image_dict()
data['channel']['datatype'] = 'uint16'
resource = BossResourceBasic(data)
c = Cube.create_cube(resource, [30, 20, 13])
assert isinstance(c, ImageCube16) is True
assert c.cube_size == [13, 20, 30]
assert c.is_time_series is False
assert c.time_range == [0, 1]
def test_basic_resource_col(self):
"""Test basic get collection interface
Returns:
None
"""
setup_data = get_image_dict()
resource = BossResourceBasic(setup_data)
col = resource.get_collection()
assert col.name == setup_data['collection']['name']
assert col.description == setup_data['collection']['description']
def setUpClass(cls):
"""Setup the redis client at the start of the test"""
cls.data = get_image_dict()
cls.resource = BossResourceBasic(cls.data)
cls.config = load_test_config_file()
cls.state_client = redis.StrictRedis(
host=cls.config["aws"]["cache-state"],
port=6379,
db=1,
decode_responses=False)
cls.config_data = {"state_client": cls.state_client}
def test_basic_resource_col(self):
"""Test basic get collection interface
Returns:
None
"""
setup_data = get_image_dict()
resource = BossResourceBasic(setup_data)
col = resource.get_collection()
assert col.name == setup_data['collection']['name']
assert col.description == setup_data['collection']['description']
def test_is_downsampled(self):
"""Test is downsampled method
Returns:
None
"""
setup_data = get_image_dict()
resource = BossResourceBasic(setup_data)
self.assertFalse(resource.is_downsampled())
setup_data['channel']['downsample_status'] = "DOWNSAMPLED"
resource = BossResourceBasic(setup_data)
self.assertTrue(resource.is_downsampled())
def test_is_downsampled(self):
"""Test is downsampled method
Returns:
None
"""
setup_data = get_image_dict()
resource = BossResourceBasic(setup_data)
self.assertFalse(resource.is_downsampled())
setup_data['channel']['downsample_status'] = "DOWNSAMPLED"
resource = BossResourceBasic(setup_data)
self.assertTrue(resource.is_downsampled())
def test_basic_resource_experiment(self):
"""Test basic get experiment interface
Returns:
None
"""
setup_data = get_image_dict()
resource = BossResourceBasic(setup_data)
exp = resource.get_experiment()
assert exp.name == setup_data['experiment']['name']
assert exp.description == setup_data['experiment']['description']
assert exp.num_hierarchy_levels == setup_data['experiment']['num_hierarchy_levels']
assert exp.hierarchy_method == setup_data['experiment']['hierarchy_method']
assert exp.num_time_samples == setup_data['experiment']['num_time_samples']
assert exp.time_step == setup_data['experiment']['time_step']
assert exp.time_step_unit == setup_data['experiment']['time_step_unit']
def test_basic_resource_experiment(self):
"""Test basic get experiment interface
Returns:
None
"""
setup_data = get_image_dict()
resource = BossResourceBasic(setup_data)
exp = resource.get_experiment()
assert exp.name == setup_data['experiment']['name']
assert exp.description == setup_data['experiment']['description']
assert exp.num_hierarchy_levels == setup_data['experiment']['num_hierarchy_levels']
assert exp.hierarchy_method == setup_data['experiment']['hierarchy_method']
assert exp.num_time_samples == setup_data['experiment']['num_time_samples']
assert exp.time_step == setup_data['experiment']['time_step']
assert exp.time_step_unit == setup_data['experiment']['time_step_unit']
def test_basic_resource_to_dict(self):
"""Test basic to dict serialization method
Returns:
None
"""
setup_data = get_image_dict()
resource = BossResourceBasic(setup_data)
data = resource.to_dict()
assert data['channel'] == setup_data['channel']
assert data['collection'] == setup_data['collection']
assert data['experiment'] == setup_data['experiment']
assert data['lookup_key'] == '4&3&2'
assert data['boss_key'] == 'col1&exp1&ch1'
def test_basic_resource_to_dict(self):
"""Test basic to dict serialization method
Returns:
None
"""
setup_data = get_image_dict()
resource = BossResourceBasic(setup_data)
data = resource.to_dict()
assert data['channel'] == setup_data['channel']
assert data['collection'] == setup_data['collection']
assert data['experiment'] == setup_data['experiment']
assert data['lookup_key'] == '4&3&2'
assert data['boss_key'] == 'col1&exp1&ch1'
def test_basic_resource_channel_no_time(self):
"""Test basic get channel interface
Returns:
None
"""
setup_data = get_image_dict()
resource = BossResourceBasic(setup_data)
channel = resource.get_channel()
assert channel.is_image() is True
assert channel.name == setup_data['channel']['name']
assert channel.description == setup_data['channel']['description']
assert channel.datatype == setup_data['channel']['datatype']
assert channel.base_resolution == setup_data['channel']['base_resolution']
assert channel.sources == setup_data['channel']['sources']
assert channel.related == setup_data['channel']['related']
assert channel.default_time_sample == setup_data['channel']['default_time_sample']
assert channel.downsample_status == setup_data['channel']['downsample_status']
def test_basic_resource_channel_no_time(self):
"""Test basic get channel interface
Returns:
None
"""
setup_data = get_image_dict()
resource = BossResourceBasic(setup_data)
channel = resource.get_channel()
assert channel.is_image() is True
assert channel.name == setup_data['channel']['name']
assert channel.description == setup_data['channel']['description']
assert channel.datatype == setup_data['channel']['datatype']
assert channel.base_resolution == setup_data['channel']['base_resolution']
assert channel.sources == setup_data['channel']['sources']
assert channel.related == setup_data['channel']['related']
assert channel.default_time_sample == setup_data['channel']['default_time_sample']
assert channel.downsample_status == setup_data['channel']['downsample_status']
def test_basic_resource_channel_cloudvolume_uint16(self):
"""Test basic get channel interface
Returns:
None
"""
setup_data = get_image_dict(datatype="uint16", storage_type='cloudvol')
resource = BossResourceBasic(setup_data)
channel = resource.get_channel()
assert channel.is_image() is True
assert channel.is_cloudvolume() is True
assert channel.name == setup_data['channel']['name']
assert channel.description == setup_data['channel']['description']
assert channel.datatype == setup_data['channel']['datatype']
assert channel.base_resolution == setup_data['channel']['base_resolution']
assert channel.sources == setup_data['channel']['sources']
assert channel.related == setup_data['channel']['related']
assert channel.default_time_sample == setup_data['channel']['default_time_sample']
assert channel.downsample_status == setup_data['channel']['downsample_status']
assert channel.storage_type == setup_data['channel']['storage_type']
assert channel.bucket == setup_data['channel']['bucket']
assert channel.cv_path == setup_data['channel']['cv_path']
def test_basic_resource_coord_frame(self):
"""Test basic get coordinate frame interface
Returns:
None
"""
setup_data = get_image_dict()
resource = BossResourceBasic(setup_data)
coord = resource.get_coord_frame()
assert coord.name == setup_data['coord_frame']['name']
assert coord.description == setup_data['coord_frame']['description']
assert coord.x_start == setup_data['coord_frame']['x_start']
assert coord.x_stop == setup_data['coord_frame']['x_stop']
assert coord.y_start == setup_data['coord_frame']['y_start']
assert coord.y_stop == setup_data['coord_frame']['y_stop']
assert coord.z_start == setup_data['coord_frame']['z_start']
assert coord.z_stop == setup_data['coord_frame']['z_stop']
assert coord.x_voxel_size == setup_data['coord_frame']['x_voxel_size']
assert coord.y_voxel_size == setup_data['coord_frame']['y_voxel_size']
assert coord.z_voxel_size == setup_data['coord_frame']['z_voxel_size']
assert coord.voxel_unit == setup_data['coord_frame']['voxel_unit']
def test_basic_resource_coord_frame(self):
"""Test basic get coordinate frame interface
Returns:
None
"""
setup_data = get_image_dict()
resource = BossResourceBasic(setup_data)
coord = resource.get_coord_frame()
assert coord.name == setup_data['coord_frame']['name']
assert coord.description == setup_data['coord_frame']['description']
assert coord.x_start == setup_data['coord_frame']['x_start']
assert coord.x_stop == setup_data['coord_frame']['x_stop']
assert coord.y_start == setup_data['coord_frame']['y_start']
assert coord.y_stop == setup_data['coord_frame']['y_stop']
assert coord.z_start == setup_data['coord_frame']['z_start']
assert coord.z_stop == setup_data['coord_frame']['z_stop']
assert coord.x_voxel_size == setup_data['coord_frame']['x_voxel_size']
assert coord.y_voxel_size == setup_data['coord_frame']['y_voxel_size']
assert coord.z_voxel_size == setup_data['coord_frame']['z_voxel_size']
assert coord.voxel_unit == setup_data['coord_frame']['voxel_unit']
def get_image8_dict(self):
"""Method to get the config dictionary for an image8 resource"""
data = get_image_dict()
return data
