def test__consume(self, mocker, redis_client):
# pylint: disable=W0613
queue = 'multiplex'
storage = DummyStorage()
consumer = consumers.MesmerConsumer(redis_client, storage, queue)
empty_data = {'input_file_name': 'file.tiff'}
output_shape = (1, 256, 256, 2)
mock_app = Bunch(
predict=lambda *x, **y: np.random.randint(1, 5, size=output_shape),
model_mpp=1,
model=Bunch(get_batch_size=lambda *x: 1,
input_shape=(1, 32, 32, 1)))
mocker.patch.object(consumer, 'get_grpc_app', lambda *x, **_: mock_app)
mocker.patch.object(consumer, 'get_image_scale', lambda *x, **_: 1)
mocker.patch.object(consumer, 'validate_model_input',
lambda *x, **_: x[0])
mocker.patch.object(consumer, 'detect_dimension_order',
lambda *x, **_: 'YXC')
test_hash = 'some hash'
redis_client.hmset(test_hash, empty_data)
result = consumer._consume(test_hash)
assert result == consumer.final_status
result = redis_client.hget(test_hash, 'status')
assert result == consumer.final_status
def test_get_image_label(self, mocker, redis_client):
queue = 'q'
stg = DummyStorage()
consumer = consumers.SegmentationConsumer(redis_client, stg, queue)
image = _get_image(256, 256, 1)
# test no label provided
expected = 1
mocker.patch.object(consumer, 'detect_label', lambda *x: expected)
label = consumer.get_image_label(None, image, 'some hash')
assert label == expected
# test label provided
expected = 2
label = consumer.get_image_label(expected, image, 'some hash')
assert label == expected
# test label provided is invalid
with pytest.raises(ValueError):
label = -1
consumer.get_image_label(label, image, 'some hash')
# test label provided is bad type
with pytest.raises(ValueError):
label = 'badval'
consumer.get_image_label(label, image, 'some hash')
def test__consume(self, mocker, redis_client):
queue = 'track'
storage = DummyStorage()
test_hash = 0
dummy_results = {
'y_tracked': np.zeros((32, 32, 1)),
'tracks': []
}
mock_model = Bunch(
get_batch_size=lambda *x: 1,
input_shape=(1, 32, 32, 1)
)
mock_app = Bunch(
predict=lambda *x, **y: dummy_results,
track=lambda *x, **y: dummy_results,
model_mpp=1,
model=mock_model,
)
consumer = consumers.CalibanConsumer(redis_client, storage, queue)
mocker.patch.object(consumer, 'get_grpc_app',
lambda *x, **y: mock_app)
# mock get_model_wrapper for neighborhood encoder
mocker.patch.object(consumer, 'get_model_wrapper',
lambda *x, **y: mock_model)
frames = 3
dummy_data = {
'X': np.array([_get_image(21, 21) for _ in range(frames)]),
'y': np.random.randint(0, 9, size=(frames, 21, 21)),
}
mocker.patch.object(consumer, '_load_data', lambda *x: dummy_data)
# test finished statuses are returned
for status in (consumer.failed_status, consumer.final_status):
test_hash += 1
data = {'input_file_name': 'file.tiff', 'status': status}
redis_client.hmset(test_hash, data)
result = consumer._consume(test_hash)
assert result == status
# test new key is processed
test_hash += 1
data = {'input_file_name': 'file.tiff', 'status': 'new'}
redis_client.hmset(test_hash, data)
result = consumer._consume(test_hash)
assert result == consumer.final_status
assert redis_client.hget(test_hash, 'status') == consumer.final_status
def test_is_valid_hash(self, mocker, redis_client):
queue = 'track'
storage = DummyStorage()
consumer = consumers.CalibanConsumer(redis_client, storage, queue)
mocker.patch.object(redis_client, 'hget', lambda x, y: x.split(':')[-1])
assert consumer.is_valid_hash(None) is False
assert consumer.is_valid_hash('predict:123456789:file.png') is False
assert consumer.is_valid_hash('predict:1234567890:file.tiff') is True
assert consumer.is_valid_hash('predict:1234567890:file.png') is False
assert consumer.is_valid_hash('track:1234567890:file.ZIp') is False
assert consumer.is_valid_hash('track:123456789:file.zip') is False
assert consumer.is_valid_hash('track:1234567890:file.png') is False
assert consumer.is_valid_hash('track:1234567890:file.tiff') is True
assert consumer.is_valid_hash('track:1234567890:file.trk') is True
assert consumer.is_valid_hash('track:1234567890:file.trks') is True
def test__consume_finished_status(self, redis_client):
queue = 'q'
storage = DummyStorage()
consumer = consumers.MesmerConsumer(redis_client, storage, queue)
empty_data = {'input_file_name': 'file.tiff'}
test_hash = 0
# test finished statuses are returned
for status in (consumer.failed_status, consumer.final_status):
test_hash += 1
data = empty_data.copy()
data['status'] = status
redis_client.hmset(test_hash, data)
result = consumer._consume(test_hash)
assert result == status
result = redis_client.hget(test_hash, 'status')
assert result == status
test_hash += 1
def test__load_data(self, tmpdir, mocker, redis_client):
queue = 'track'
storage = DummyStorage()
consumer = consumers.CalibanConsumer(redis_client, storage, queue)
tmpdir = str(tmpdir)
exp = random.randint(0, 99)
# test load trk files
key = 'trk file test'
mocker.patch('redis_consumer.utils.load_track_file', lambda x: exp)
result = consumer._load_data(key, tmpdir, 'data.trk')
assert result == exp
result = consumer._load_data(key, tmpdir, 'data.trks')
assert result == exp
# test bad filetype
key = 'invalid filetype test'
with pytest.raises(ValueError):
consumer._load_data(key, tmpdir, 'data.npz')
# test bad ndim for tiffstack
fname = 'test.tiff'
filepath = os.path.join(tmpdir, fname)
tifffile.imsave(filepath, _get_image())
with pytest.raises(ValueError):
consumer._load_data(key, tmpdir, fname)
# test successful workflow
def hget_successful_status(*_):
return consumer.final_status
def hget_failed_status(*_):
return consumer.failed_status
def write_child_tiff(*_, **__):
letters = string.ascii_lowercase
name = ''.join(random.choice(letters) for i in range(12))
path = os.path.join(tmpdir, '{}.tiff'.format(name))
tifffile.imsave(path, _get_image(21, 21))
return [path]
mocker.patch.object(settings, 'INTERVAL', 0)
mocker.patch.object(redis_client, 'hget', hget_successful_status)
mocker.patch('redis_consumer.utils.iter_image_archive',
write_child_tiff)
for label_detect in (True, False):
mocker.patch.object(settings, 'SCALE_DETECT_ENABLED', label_detect)
mocker.patch.object(settings, 'LABEL_DETECT_ENABLED', label_detect)
tifffile.imsave(filepath, np.random.random((3, 21, 21)))
results = consumer._load_data(key, tmpdir, fname)
X, y = results.get('X'), results.get('y')
assert isinstance(X, np.ndarray)
assert isinstance(y, np.ndarray)
assert X.shape == y.shape
# test failed child
with pytest.raises(RuntimeError):
mocker.patch.object(redis_client, 'hget', hget_failed_status)
consumer._load_data(key, tmpdir, fname)
# test wrong number of images in the test file
with pytest.raises(RuntimeError):
mocker.patch.object(redis_client, 'hget', hget_successful_status)
mocker.patch('redis_consumer.utils.iter_image_archive',
lambda *x: range(1, 3))
consumer._load_data(key, tmpdir, fname)