def populate(self, channel_name, resolution, start_values, end_values, time_limit, neariso=False):
proj = self.resource_interface.getProject()
ch = NDChannel.fromName(proj, channel_name)
cubedim = proj.datasetcfg.get_cubedim(resolution)
image_size = proj.datasetcfg.get_imagesize(resolution)
if time_limit is None:
time_limit = ch.time_range[1]
if end_values == [0,0,0]:
end_values = image_size
[x_start, y_start, z_start] = map(div, start_values, cubedim)
x_end = (end_values[0] - 1) / cubedim[0] + 1
y_end = (end_values[1] - 1) / cubedim[1] + 1
z_end = (end_values[2] - 1) / cubedim[2] + 1
db = SpatialDB(proj)
for time_index in range(ch.time_range[0], time_limit, 1):
for z_index in range(z_start, z_end, 1):
for y_index in range(y_start, y_end, 1):
for x_index in range(x_start, x_end, 1):
print("Populating Cache with T:{},X:{},Y:{},Z:{}".format(time_index, x_index*cubedim[0], y_index*cubedim[1], z_index*cubedim[2]))
zidx = XYZMorton([x_index, y_index, z_index])
db.getCubes(ch, [time_index], [zidx], resolution, neariso=neariso)
def test_page_in_multi_cuboids_y_dir(self):
# Generate random data
cube1 = Cube.create_cube(self.resource, [self.x_dim, self.y_dim * 2, self.z_dim])
cube1.random()
cube1.morton_id = 0
sp = SpatialDB(self.kvio_config, self.state_config, self.object_store_config)
sp.write_cuboid(self.resource, (0, 0, 0), 0, cube1.data)
cube2 = sp.cutout(self.resource, (0, 0, 0), (self.x_dim, self.y_dim * 2, self.z_dim), 0)
np.testing.assert_array_equal(cube1.data, cube2.data)
# Make sure data is the same
np.testing.assert_array_equal(cube1.data, cube2.data)
# Delete everything in the cache
sp.kvio.cache_client.flushdb()
# Force use of lambda function.
sp.read_lambda_threshold = 0
# Get the data again, which should trigger lambda page in.
cube3 = sp.cutout(self.resource, (0, 0, 0), (self.x_dim, self.y_dim * 2, self.z_dim), 0)
# Make sure the data is the same
np.testing.assert_array_equal(cube1.data, cube3.data)
def test_delayed_write_daemon_simple(self):
"""Test handling delayed writes"""
sp = SpatialDB(self.kvio_config,
self.state_config,
self.object_store_config)
dwd = DelayedWriteDaemon("boss-delayedwrited-test.pid")
# Create some a single delayed write
cube1 = Cube.create_cube(self.resource, [512, 512, 16])
cube1.random()
cube1.morton_id = 0
res = 0
time_sample = 0
write_cuboid_base = "WRITE-CUBOID&{}&{}".format(self.resource.get_lookup_key(), 0)
write_cuboid_key = sp.kvio.insert_cube_in_write_buffer(write_cuboid_base, res, cube1.morton_id,
cube1.to_blosc_by_time_index(time_sample))
sp.cache_state.add_to_delayed_write(write_cuboid_key,
self.resource.get_lookup_key(),
res,
cube1.morton_id,
time_sample,
self.resource.to_json())
# Use Daemon To handle writes
dwd.process(sp)
time.sleep(30)
# Make sure they went through
cube2 = sp.cutout(self.resource, (0, 0, 0), (512, 512, 16), 0)
np.testing.assert_array_equal(cube1.data, cube2.data)
# Make sure delay key got deleted
keys = sp.cache_state.get_all_delayed_write_keys()
assert not keys
def setUp(self):
# Get data from nose2 layer based setup
# Setup Data
self.data = self.layer.setup_helper.get_image8_dict()
self.resource = BossResourceBasic(self.data)
# Setup config
self.kvio_config = self.layer.kvio_config
self.state_config = self.layer.state_config
self.object_store_config = self.layer.object_store_config
client = redis.StrictRedis(host=self.kvio_config['cache_host'],
port=6379, db=1, decode_responses=False)
client.flushdb()
client = redis.StrictRedis(host=self.state_config['cache_state_host'],
port=6379, db=1, decode_responses=False)
client.flushdb()
self.cache_miss = CacheMissDaemon('foo')
self.sp = SpatialDB(self.kvio_config, self.state_config, self.object_store_config)
self.cache_miss.set_spatialdb(self.sp)
def setUp(self):
# Setup Data
self.data = self.layer.setup_helper.get_image8_dict()
self.resource = BossResourceBasic(self.data)
# Setup config
self.kvio_config = self.layer.kvio_config
self.state_config = self.layer.state_config
self.object_store_config = self.layer.object_store_config
client = redis.StrictRedis(host=self.kvio_config['cache_host'],
port=6379, db=1, decode_responses=False)
client.flushdb()
client = redis.StrictRedis(host=self.state_config['cache_state_host'],
port=6379, db=1, decode_responses=False)
client.flushdb()
# Suppress ResourceWarning messages about unclosed connections.
warnings.simplefilter('ignore')
self.prefetch = PrefetchDaemon('foo')
self.sp = SpatialDB(self.kvio_config, self.state_config, self.object_store_config)
self.prefetch.set_spatialdb(self.sp)
def handler(event, context):
# Load settings
SETTINGS = BossSettings.load()
# Used as a guard against trying to delete the SQS message when lambda is
# triggered by SQS.
sqs_triggered = 'Records' in event and len(event['Records']) > 0
if sqs_triggered :
# Lambda invoked by an SQS trigger.
msg_data = json.loads(event['Records'][0]['body'])
# Load the project info from the chunk key you are processing
chunk_key = msg_data['chunk_key']
proj_info = BossIngestProj.fromSupercuboidKey(chunk_key)
proj_info.job_id = msg_data['ingest_job']
else:
# Standard async invoke of this lambda.
# Load the project info from the chunk key you are processing
proj_info = BossIngestProj.fromSupercuboidKey(event["chunk_key"])
proj_info.job_id = event["ingest_job"]
# Get message from SQS ingest queue, try for ~2 seconds
rx_cnt = 0
msg_data = None
msg_id = None
msg_rx_handle = None
while rx_cnt < 6:
ingest_queue = IngestQueue(proj_info)
try:
msg = [x for x in ingest_queue.receiveMessage()]
# StopIteration may be converted to a RunTimeError.
except (StopIteration, RuntimeError):
msg = None
if msg:
msg = msg[0]
print("MESSAGE: {}".format(msg))
print(len(msg))
msg_id = msg[0]
msg_rx_handle = msg[1]
msg_data = json.loads(msg[2])
print("MESSAGE DATA: {}".format(msg_data))
break
else:
rx_cnt += 1
print("No message found. Try {} of 6".format(rx_cnt))
time.sleep(1)
if not msg_id:
# No tiles ready to ingest.
print("No ingest message available")
return
# Get the chunk key of the tiles to ingest.
chunk_key = msg_data['chunk_key']
tile_error_queue = TileErrorQueue(proj_info)
print("Ingesting Chunk {}".format(chunk_key))
tiles_in_chunk = int(chunk_key.split('&')[1])
# Setup SPDB instance
sp = SpatialDB(msg_data['parameters']["KVIO_SETTINGS"],
msg_data['parameters']["STATEIO_CONFIG"],
msg_data['parameters']["OBJECTIO_CONFIG"])
# Get tile list from Tile Index Table
tile_index_db = BossTileIndexDB(proj_info.project_name)
# tile_index_result (dict): keys are S3 object keys of the tiles comprising the chunk.
tile_index_result = tile_index_db.getCuboid(msg_data["chunk_key"], int(msg_data["ingest_job"]))
if tile_index_result is None:
# If chunk_key is gone, another lambda uploaded the cuboids and deleted the chunk_key afterwards.
if not sqs_triggered:
# Remove message so it's not redelivered.
ingest_queue.deleteMessage(msg_id, msg_rx_handle)
print("Aborting due to chunk key missing from tile index table")
return
# Sort the tile keys
print("Tile Keys: {}".format(tile_index_result["tile_uploaded_map"]))
tile_key_list = [x.rsplit("&", 2) for x in tile_index_result["tile_uploaded_map"].keys()]
if len(tile_key_list) < tiles_in_chunk:
print("Not a full set of 16 tiles. Assuming it has handled already, tiles: {}".format(len(tile_key_list)))
if not sqs_triggered:
ingest_queue.deleteMessage(msg_id, msg_rx_handle)
return
tile_key_list = sorted(tile_key_list, key=lambda x: int(x[1]))
tile_key_list = ["&".join(x) for x in tile_key_list]
print("Sorted Tile Keys: {}".format(tile_key_list))
# Augment Resource JSON data so it will instantiate properly that was pruned due to S3 metadata size limits
resource_dict = msg_data['parameters']['resource']
_, exp_name, ch_name = resource_dict["boss_key"].split("&")
resource_dict["channel"]["name"] = ch_name
resource_dict["channel"]["description"] = ""
resource_dict["channel"]["sources"] = []
resource_dict["channel"]["related"] = []
resource_dict["channel"]["default_time_sample"] = 0
resource_dict["channel"]["downsample_status"] = "NOT_DOWNSAMPLED"
resource_dict["experiment"]["name"] = exp_name
resource_dict["experiment"]["description"] = ""
resource_dict["experiment"]["num_time_samples"] = 1
resource_dict["experiment"]["time_step"] = None
resource_dict["experiment"]["time_step_unit"] = None
resource_dict["coord_frame"]["name"] = "cf"
resource_dict["coord_frame"]["name"] = ""
resource_dict["coord_frame"]["x_start"] = 0
resource_dict["coord_frame"]["x_stop"] = 100000
resource_dict["coord_frame"]["y_start"] = 0
resource_dict["coord_frame"]["y_stop"] = 100000
resource_dict["coord_frame"]["z_start"] = 0
resource_dict["coord_frame"]["z_stop"] = 100000
resource_dict["coord_frame"]["voxel_unit"] = "nanometers"
# Setup the resource
resource = BossResourceBasic()
resource.from_dict(resource_dict)
dtype = resource.get_numpy_data_type()
# read all tiles from bucket into a slab
tile_bucket = TileBucket(proj_info.project_name)
data = []
num_z_slices = 0
for tile_key in tile_key_list:
try:
image_data, message_id, receipt_handle, metadata = tile_bucket.getObjectByKey(tile_key)
except KeyError:
print('Key: {} not found in tile bucket, assuming redelivered SQS message and aborting.'.format(
tile_key))
if not sqs_triggered:
# Remove message so it's not redelivered.
ingest_queue.deleteMessage(msg_id, msg_rx_handle)
print("Aborting due to missing tile in bucket")
return
image_bytes = BytesIO(image_data)
image_size = image_bytes.getbuffer().nbytes
# Get tiles size from metadata, need to shape black tile if actual tile is corrupt.
if 'x_size' in metadata:
tile_size_x = metadata['x_size']
else:
print('MetadataMissing: x_size not in tile metadata: using 1024.')
tile_size_x = 1024
if 'y_size' in metadata:
tile_size_y = metadata['y_size']
else:
print('MetadataMissing: y_size not in tile metadata: using 1024.')
tile_size_y = 1024
if image_size == 0:
print('TileError: Zero length tile, using black instead: {}'.format(tile_key))
error_msg = 'Zero length tile'
enqueue_tile_error(tile_error_queue, tile_key, chunk_key, error_msg)
tile_img = np.zeros((tile_size_x, tile_size_y), dtype=dtype)
else:
try:
# DP NOTE: Issues when specifying dtype in the asarray function with Pillow ver 8.3.1.
# Fixed by separating array instantiation and dtype assignment.
tile_img = np.asarray(Image.open(image_bytes))
tile_img = tile_img.astype(dtype)
except TypeError as te:
print('TileError: Incomplete tile, using black instead (tile_size_in_bytes, tile_key): {}, {}'
.format(image_size, tile_key))
error_msg = 'Incomplete tile'
enqueue_tile_error(tile_error_queue, tile_key, chunk_key, error_msg)
tile_img = np.zeros((tile_size_x, tile_size_y), dtype=dtype)
except OSError as oe:
print('TileError: OSError, using black instead (tile_size_in_bytes, tile_key): {}, {} ErrorMessage: {}'
.format(image_size, tile_key, oe))
error_msg = 'OSError: {}'.format(oe)
enqueue_tile_error(tile_error_queue, tile_key, chunk_key, error_msg)
tile_img = np.zeros((tile_size_x, tile_size_y), dtype=dtype)
data.append(tile_img)
num_z_slices += 1
# Make 3D array of image data. It should be in XYZ at this point
chunk_data = np.array(data)
del data
tile_dims = chunk_data.shape
# Break into Cube instances
print("Tile Dims: {}".format(tile_dims))
print("Num Z Slices: {}".format(num_z_slices))
num_x_cuboids = int(math.ceil(tile_dims[2] / CUBOIDSIZE[proj_info.resolution][0]))
num_y_cuboids = int(math.ceil(tile_dims[1] / CUBOIDSIZE[proj_info.resolution][1]))
print("Num X Cuboids: {}".format(num_x_cuboids))
print("Num Y Cuboids: {}".format(num_y_cuboids))
chunk_key_parts = BossUtil.decode_chunk_key(chunk_key)
t_index = chunk_key_parts['t_index']
for x_idx in range(0, num_x_cuboids):
for y_idx in range(0, num_y_cuboids):
# TODO: check time series support
cube = Cube.create_cube(resource, CUBOIDSIZE[proj_info.resolution])
cube.zeros()
# Compute Morton ID
# TODO: verify Morton indices correct!
print(chunk_key_parts)
morton_x_ind = x_idx + (chunk_key_parts["x_index"] * num_x_cuboids)
morton_y_ind = y_idx + (chunk_key_parts["y_index"] * num_y_cuboids)
print("Morton X: {}".format(morton_x_ind))
print("Morton Y: {}".format(morton_y_ind))
morton_index = XYZMorton([morton_x_ind, morton_y_ind, int(chunk_key_parts['z_index'])])
# Insert sub-region from chunk_data into cuboid
x_start = x_idx * CUBOIDSIZE[proj_info.resolution][0]
x_end = x_start + CUBOIDSIZE[proj_info.resolution][0]
x_end = min(x_end, tile_dims[2])
y_start = y_idx * CUBOIDSIZE[proj_info.resolution][1]
y_end = y_start + CUBOIDSIZE[proj_info.resolution][1]
y_end = min(y_end, tile_dims[1])
z_end = CUBOIDSIZE[proj_info.resolution][2]
# TODO: get sub-array w/o making a copy.
print("Yrange: {}".format(y_end - y_start))
print("Xrange: {}".format(x_end - x_start))
print("X start: {}".format(x_start))
print("X stop: {}".format(x_end))
cube.data[0, 0:num_z_slices, 0:(y_end - y_start), 0:(x_end - x_start)] = chunk_data[0:num_z_slices,
y_start:y_end, x_start:x_end]
# Create object key
object_key = sp.objectio.generate_object_key(resource, proj_info.resolution, t_index, morton_index)
print("Object Key: {}".format(object_key))
# Put object in S3
sp.objectio.put_objects([object_key], [cube.to_blosc()])
# Add object to index
sp.objectio.add_cuboid_to_index(object_key, ingest_job=int(msg_data["ingest_job"]))
# Update id indices if this is an annotation channel
# We no longer index during ingest.
#if resource.data['channel']['type'] == 'annotation':
# try:
# sp.objectio.update_id_indices(
# resource, proj_info.resolution, [object_key], [cube.data])
# except SpdbError as ex:
# sns_client = boto3.client('sns')
# topic_arn = msg_data['parameters']["OBJECTIO_CONFIG"]["prod_mailing_list"]
# msg = 'During ingest:\n{}\nCollection: {}\nExperiment: {}\n Channel: {}\n'.format(
# ex.message,
# resource.data['collection']['name'],
# resource.data['experiment']['name'],
# resource.data['channel']['name'])
# sns_client.publish(
# TopicArn=topic_arn,
# Subject='Object services misuse',
# Message=msg)
lambda_client = boto3.client('lambda', region_name=SETTINGS.REGION_NAME)
names = AWSNames.from_lambda(context.function_name)
delete_tiles_data = {
'tile_key_list': tile_key_list,
'region': SETTINGS.REGION_NAME,
'bucket': tile_bucket.bucket.name
}
# Delete tiles from tile bucket.
lambda_client.invoke(
FunctionName=names.delete_tile_objs.lambda_,
InvocationType='Event',
Payload=json.dumps(delete_tiles_data).encode()
)
delete_tile_entry_data = {
'tile_index': tile_index_db.table.name,
'region': SETTINGS.REGION_NAME,
'chunk_key': chunk_key,
'task_id': msg_data['ingest_job']
}
# Delete entry from tile index.
lambda_client.invoke(
FunctionName=names.delete_tile_index_entry.lambda_,
InvocationType='Event',
Payload=json.dumps(delete_tile_entry_data).encode()
)
if not sqs_triggered:
# Delete message since it was processed successfully
ingest_queue.deleteMessage(msg_id, msg_rx_handle)
class IntegrationTestPrefetchDaemon(unittest.TestCase):
layer = AWSSetupLayer
def setUp(self):
# Setup Data
self.data = self.layer.setup_helper.get_image8_dict()
self.resource = BossResourceBasic(self.data)
# Setup config
self.kvio_config = self.layer.kvio_config
self.state_config = self.layer.state_config
self.object_store_config = self.layer.object_store_config
client = redis.StrictRedis(host=self.kvio_config['cache_host'],
port=6379, db=1, decode_responses=False)
client.flushdb()
client = redis.StrictRedis(host=self.state_config['cache_state_host'],
port=6379, db=1, decode_responses=False)
client.flushdb()
# Suppress ResourceWarning messages about unclosed connections.
warnings.simplefilter('ignore')
self.prefetch = PrefetchDaemon('foo')
self.sp = SpatialDB(self.kvio_config, self.state_config, self.object_store_config)
self.prefetch.set_spatialdb(self.sp)
def tearDown(self):
"""Clean kv store in between tests"""
client = redis.StrictRedis(host=self.kvio_config['cache_host'],
port=6379, db=1, decode_responses=False)
client.flushdb()
client = redis.StrictRedis(host=self.state_config['cache_state_host'],
port=6379, db=1, decode_responses=False)
client.flushdb()
def test_add_to_prefetch(self):
cuboid_dims = CUBOIDSIZE[0]
# Cuboid dimensions.
x_dim = cuboid_dims[0]
y_dim = cuboid_dims[1]
z_dim = cuboid_dims[2]
cube_above = Cube.create_cube(self.resource, [x_dim, y_dim, z_dim])
cube_above.random()
# Write cuboid that are stacked vertically.
self.sp.write_cuboid(self.resource, (0, 0, z_dim * 2), 0, cube_above.data)
cube_above.morton_id = ndlib.XYZMorton([0, 0, z_dim * 2 // z_dim])
cube_above_cache_key = self.sp.kvio.generate_cached_cuboid_keys(
self.resource, 0, [0], [cube_above.morton_id])
# Make sure cuboid saved.
cube_act = self.sp.cutout(self.resource, (0, 0, z_dim * 2), (x_dim, y_dim, z_dim), 0)
np.testing.assert_array_equal(cube_above.data, cube_act.data)
# Clear cache so we can test prefetch.
self.sp.kvio.cache_client.flushdb()
# Also clear cache state before running test.
self.sp.cache_state.status_client.flushdb()
obj_keys = self.sp.objectio.cached_cuboid_to_object_keys(
cube_above_cache_key)
# Place a cuboid in the pretch queue.
self.sp.cache_state.status_client.rpush('PRE-FETCH', obj_keys[0])
# This is the system under test.
self.prefetch.process()
# Wait for cube to be prefetched.
i = 0
while not self.sp.kvio.cube_exists(cube_above_cache_key[0]) and i < 30:
time.sleep(1)
i += 1
# Confirm cuboid now in cache.
self.assertTrue(self.sp.kvio.cube_exists(cube_above_cache_key[0]))
cube_act = self.sp.cutout(
self.resource, (0, 0, z_dim * 2), (x_dim, y_dim, z_dim), 0)
np.testing.assert_array_equal(cube_above.data, cube_act.data)
def test_delayed_write_daemon_multiple(self):
"""Test handling multiple delayed writes"""
sp = SpatialDB(self.kvio_config, self.state_config,
self.object_store_config)
dwd = DelayedWriteDaemon("boss-delayedwrited-test.pid")
# Create some a single delayed write
cube1 = Cube.create_cube(self.resource, [512, 512, 16])
cube1.random()
cube1.morton_id = 0
res = 0
time_sample = 0
cube1.data[0, 5, 100, 100] = 2
cube1.data[0, 5, 100, 101] = 2
cube1.data[0, 5, 100, 102] = 2
write_cuboid_base = "WRITE-CUBOID&{}&{}".format(
self.resource.get_lookup_key(), 0)
write_cuboid_key = sp.kvio.insert_cube_in_write_buffer(
write_cuboid_base, res, cube1.morton_id,
cube1.to_blosc_by_time_index(time_sample))
sp.cache_state.add_to_delayed_write(write_cuboid_key,
self.resource.get_lookup_key(),
res, cube1.morton_id, time_sample,
self.resource.to_json())
cube2 = Cube.create_cube(self.resource, [512, 512, 16])
cube2.random()
cube2.morton_id = 0
res = 0
time_sample = 0
cube2.data[0, 5, 100, 100] = 0
cube2.data[0, 5, 100, 101] = 1
cube2.data[0, 5, 100, 102] = 0
cube2.data[0, 5, 100, 103] = 0
write_cuboid_key = sp.kvio.insert_cube_in_write_buffer(
write_cuboid_base, res, cube2.morton_id,
cube2.to_blosc_by_time_index(time_sample))
sp.cache_state.add_to_delayed_write(write_cuboid_key,
self.resource.get_lookup_key(),
res, cube2.morton_id, time_sample,
self.resource.to_json())
# Use Daemon To handle writes
dwd.process(sp)
time.sleep(30)
# Make sure they went through
cube3 = sp.cutout(self.resource, (0, 0, 0), (512, 512, 16), 0)
cube2.data[0, 5, 100, 100] = 2
cube2.data[0, 5, 100, 101] = 1
cube2.data[0, 5, 100, 102] = 2
cube2.data[0, 5, 100, 103] = cube1.data[0, 5, 100, 103]
np.testing.assert_array_equal(cube3.data, cube2.data)
# Make sure delay key got deleted
keys = sp.cache_state.get_all_delayed_write_keys()
assert not keys
class MaxProjCatmaid:
"""Prefetch CATMAID tiles into MndcheDB"""
def __init__(self):
self.proj = None
self.db = None
self.token = None
self.tilesz = 512
def __del__(self):
pass
def getTileXY(self, ch, res, xtile, ytile, zslice, width):
"""Cutout, return the image"""
# figure out the cutout (limit to max image size)
xstart = xtile * self.tilesz
ystart = ytile * self.tilesz
xend = min((xtile + 1) * self.tilesz,
self.proj.datasetcfg.imageSize(res)[0][0])
yend = min((ytile + 1) * self.tilesz,
self.proj.datasetcfg.imageSize(res)[0][1])
zstart = max(zslice - width, 0)
zend = min(zslice + 1 + width, self.tilesz,
self.proj.datasetcfg.imageSize(res)[0][2])
# call the mcfc interface
imageargs = '{}/{},{}/{},{}/{},{}/'.format(res, xstart, xend, ystart,
yend, zstart, zend)
cutout = ndwsrest.cutout(imageargs, ch, self.proj, self.db)
tiledata = np.amax(cutout.data, axis=0)
tiledata = ndwsrest.window(tiledata, ch)
# turn into an 8-bit image and return
return Image.frombuffer('L', (tiledata.shape[1], tiledata.shape[0]),
tiledata.flatten(), 'raw', 'L', 0, 1)
def getTile(self, webargs):
"""Either fetch the file from mndche or get a mcfc image"""
try:
# arguments of format /token/channel/(?:width:3)/slice_type/z/x_y_res.png
m = re.match(
"(\w+)/([\w+,[:\w]*]*)(?:/width:([\d+]+))?/(xy|yz|xz)/(\d+)/(\d+)_(\d+)_(\d+).png",
webargs)
[self.token, channel, widthstr,
slice_type] = [i for i in m.groups()[:4]]
[ztile, ytile, xtile, res] = [int(i) for i in m.groups()[4:]]
# extract the width as an integer
width = int(widthstr)
except Exception, e:
logger.error("Incorrect arguments for getTile {}. {}".format(
webargs, e))
raise NDWSError("Incorrect arguments for getTile {}. {}".format(
webargs, e))
self.proj = NDProject.fromTokenName(self.token)
ch = self.proj.getChannelObj(channel)
with closing(SpatialDB(self.proj)) as self.db:
tile = None
if tile == None:
if slice_type == 'xy':
img = self.getTileXY(ch, res, xtile, ytile, ztile, width)
# elif slice_type == 'xz':
# img = self.getTileXZ(res, xtile, ytile, ztile, width)
# elif slice_type == 'yz':
# img = self.getTileYZ(res, xtile, ytile, ztile, width)
else:
logger.error(
"Requested illegal image plane {}. Should be xy, xz, yz."
.format(slice_type))
raise NDWSError(
"Requested illegal image plane {}. Should be xy, xz, yz."
.format(slice_type))
fobj = cStringIO.StringIO()
img.save(fobj, "PNG")
else:
fobj = cStringIO.StringIO(tile)
fobj.seek(0)
return fobj
time.sleep(.1)
if flush_msg_data:
# Got a message
# Get Message Receipt Handle
rx_handle = flush_msg_data['ReceiptHandle']
# Load the message body
flush_msg_data = json.loads(flush_msg_data['Body'])
print("Message: {}".format(flush_msg_data))
# Setup SPDB instance
sp = SpatialDB(flush_msg_data["config"]["kv_config"],
flush_msg_data["config"]["state_config"],
flush_msg_data["config"]["object_store_config"])
# Get the write-cuboid key to flush
write_cuboid_key = flush_msg_data['write_cuboid_key']
print("Flushing {} to S3".format(write_cuboid_key))
# Create resource instance
resource = BossResourceBasic()
resource.from_dict(flush_msg_data["resource"])
else:
# Nothing to flush. Exit.
print("No flush message available")
sys.exit(0)
# Check if cuboid is in S3
def test_get_tight_bounding_box_multi_cuboids_z_axis(self):
"""
Get the tight bounding box for an object that exists in two cuboids on the y axis.
"""
resolution = 0
[x_cube_dim, y_cube_dim, z_cube_dim] = CUBOIDSIZE[resolution]
id = 33333
# Customize resource with so it writes to its own channel and uses a
# coord frame large enough to encompass the data written. This is
# important for proper loose bounding box calculations.
data = get_anno_dict(boss_key='col1&exp1&ch100', lookup_key='1&1&100')
data['coord_frame']['x_stop'] = 10000
data['coord_frame']['y_stop'] = 10000
data['coord_frame']['z_stop'] = 10000
resource = BossResourceBasic(data)
time_sample = 0
version = 0
x_rng = [0, x_cube_dim]
y_rng = [0, y_cube_dim]
z_rng = [0, z_cube_dim]
t_rng = [0, 1]
cube_dim_tuple = (self.x_dim, self.y_dim, self.z_dim)
cube1 = Cube.create_cube(resource, [self.x_dim, self.y_dim, self.z_dim])
cube1.zeros()
cube1.data[0][14][509][508] = id
cube1.data[0][15][510][509] = id
cube1.data[0][15][510][510] = id
cube1.data[0][14][511][511] = id
pos1 = [10*self.x_dim, 15*self.y_dim, 2*self.z_dim]
cube1.morton_id = XYZMorton(pos1)
cube2 = Cube.create_cube(resource, [self.x_dim, self.y_dim, self.z_dim])
cube2.zeros()
cube2.data[0][0][509][508] = id
cube2.data[0][0][510][509] = id
cube2.data[0][1][510][510] = id
cube2.data[0][2][511][511] = id
pos2 = [10*self.x_dim, 15*self.y_dim, 3*self.z_dim]
cube2.morton_id = XYZMorton(pos2)
sp = SpatialDB(self.kvio_config, self.state_config, self.object_store_config)
sp.write_cuboid(resource, pos1, resolution, cube1.data, time_sample_start=0)
sp.write_cuboid(resource, pos2, resolution, cube2.data, time_sample_start=0)
# Make sure cube write complete and correct.
actual_cube = sp.cutout(resource, pos1, cube_dim_tuple, resolution)
np.testing.assert_array_equal(cube1.data, actual_cube.data)
actual_cube2 = sp.cutout(resource, pos2, cube_dim_tuple, resolution)
np.testing.assert_array_equal(cube2.data, actual_cube2.data)
del cube1
del actual_cube
del cube2
del actual_cube2
# Method under test.
actual = sp.get_bounding_box(resource, resolution, id, bb_type='tight')
expected = {
'x_range': [pos1[0]+508, pos2[0]+512],
'y_range': [pos1[1]+509, pos2[1]+512],
'z_range': [pos1[2]+14, pos2[2]+3],
't_range': t_rng
}
self.assertEqual(expected, actual)
def getHist(self):
with closing(NDProjectsDB()) as projdb:
proj = projdb.loadToken(self.token)
with closing(SpatialDB(proj)) as db:
ch = proj.getChannelObj(self.channel)
[xcubedim, ycubedim,
zcubedim] = cubedim = proj.datasetcfg.get_cubedim(self.res)
effcorner = self.roi_lower
effdim = self.roi_upper
# get starting and ending indices
zstart = (effcorner[2]) / zcubedim
ystart = (effcorner[1]) / ycubedim
xstart = (effcorner[0]) / xcubedim
zend = (effdim[2]) / zcubedim
yend = (effdim[1]) / ycubedim
xend = (effdim[0]) / xcubedim
hist_sum = np.zeros(self.numbins, dtype=np.uint32)
# sum the histogram
# we want to iterate over indices, checking for partial cubes
for z in range(zstart, zend + 1):
for y in range(ystart, yend + 1):
for x in range(xstart, xend + 1):
# cutout the data for the cube
cube = db.cutout(
ch, [x * xcubedim, y * ycubedim, z * zcubedim],
cubedim, self.res)
cubestart = [0, 0, 0]
cubeend = [xcubedim, ycubedim, zcubedim]
# check for partial cube
if x == xstart:
cubestart[0] = effcorner[0] - x * xcubedim
if y == ystart:
cubestart[1] = effcorner[1] - y * ycubedim
if z == zstart:
cubestart[2] = effcorner[2] - z * zcubedim
if x == xend:
cubeend[0] = effdim[0] - x * xcubedim
if y == yend:
cubeend[1] = effdim[1] - y * ycubedim
if z == zend:
cubeend[2] = effdim[2] - z * zcubedim
# trim cube if necessary
data = cube.data[cubestart[2]:cubeend[2],
cubestart[1]:cubeend[1],
cubestart[0]:cubeend[0]]
# compute the histogram and store it
(hist, bins) = np.histogram(data[data > 0],
bins=self.numbins,
range=(0, self.numbins))
hist_sum = np.add(hist_sum, hist)
logger.debug("Processed cube {} {} {}".format(x, y, z))
return (hist_sum, bins)
else:
rx_cnt += 1
print("No message found. Try {} of 6".format(rx_cnt))
time.sleep(1)
if not msg_id:
# Nothing to flush. Exit.
sys.exit("No ingest message available")
# Get the write-cuboid key to flush
chunk_key = msg_data['chunk_key']
print("Ingesting Chunk {}".format(chunk_key))
# Setup SPDB instance
sp = SpatialDB(msg_data['parameters']["KVIO_SETTINGS"],
msg_data['parameters']["STATEIO_CONFIG"],
msg_data['parameters']["OBJECTIO_CONFIG"])
# Get tile list from Tile Index Table
tile_index_db = BossTileIndexDB(proj_info.project_name)
# tile_index_result (dict): keys are S3 object keys of the tiles comprising the chunk.
tile_index_result = tile_index_db.getCuboid(msg_data["chunk_key"], int(msg_data["ingest_job"]))
if tile_index_result is None:
# Remove message so it's not redelivered.
ingest_queue.deleteMessage(msg_id, msg_rx_handle)
sys.exit("Aborting due to chunk key missing from tile index table")
# Sort the tile keys
print("Tile Keys: {}".format(tile_index_result["tile_uploaded_map"]))
tile_key_list = [x.rsplit("&", 2) for x in tile_index_result["tile_uploaded_map"].keys()]
tile_key_list = sorted(tile_key_list, key=lambda x: int(x[1]))
class IntegrationTestCacheMissDaemon(unittest.TestCase):
layer = AWSSetupLayer
def setUp(self):
# Get data from nose2 layer based setup
# Setup Data
self.data = self.layer.setup_helper.get_image8_dict()
self.resource = BossResourceBasic(self.data)
# Setup config
self.kvio_config = self.layer.kvio_config
self.state_config = self.layer.state_config
self.object_store_config = self.layer.object_store_config
client = redis.StrictRedis(host=self.kvio_config['cache_host'],
port=6379, db=1, decode_responses=False)
client.flushdb()
client = redis.StrictRedis(host=self.state_config['cache_state_host'],
port=6379, db=1, decode_responses=False)
client.flushdb()
self.cache_miss = CacheMissDaemon('foo')
self.sp = SpatialDB(self.kvio_config, self.state_config, self.object_store_config)
self.cache_miss.set_spatialdb(self.sp)
def tearDown(self):
"""Clean kv store in between tests"""
client = redis.StrictRedis(host=self.kvio_config['cache_host'],
port=6379, db=1, decode_responses=False)
client.flushdb()
client = redis.StrictRedis(host=self.state_config['cache_state_host'],
port=6379, db=1, decode_responses=False)
client.flushdb()
def test_add_to_prefetch(self):
cuboid_dims = CUBOIDSIZE[0]
# Cuboid dimensions.
x_dim = cuboid_dims[0]
y_dim = cuboid_dims[1]
z_dim = cuboid_dims[2]
cube = Cube.create_cube(self.resource, [x_dim, y_dim, z_dim])
cube.random()
cube_above = Cube.create_cube(self.resource, [x_dim, y_dim, z_dim])
cube_above.random()
cube_below = Cube.create_cube(self.resource, [x_dim, y_dim, z_dim])
cube_below.random()
# Write 3 cuboids that are stacked vertically.
self.sp.write_cuboid(self.resource, (0, 0, 0), 0, cube_below.data)
self.sp.write_cuboid(self.resource, (0, 0, z_dim), 0, cube.data)
self.sp.write_cuboid(self.resource, (0, 0, z_dim * 2), 0, cube_above.data)
cube.morton_id = ndlib.XYZMorton([0, 0, z_dim // z_dim])
cube_below.morton_id = ndlib.XYZMorton([0, 0, 0])
cube_above.morton_id = ndlib.XYZMorton([0, 0, z_dim * 2 // z_dim])
print('mortons: {}, {}, {}'.format(
cube_below.morton_id, cube.morton_id, cube_above.morton_id))
cube_below_cache_key, cube_cache_key, cube_above_cache_key = self.sp.kvio.generate_cached_cuboid_keys(
self.resource, 0, [0],
[cube_below.morton_id, cube.morton_id, cube_above.morton_id])
# Make sure cuboids saved.
cube_act = self.sp.cutout(self.resource, (0, 0, 0), (x_dim, y_dim, z_dim), 0)
np.testing.assert_array_equal(cube_below.data, cube_act.data)
cube_act = self.sp.cutout(self.resource, (0, 0, z_dim), (x_dim, y_dim, z_dim), 0)
np.testing.assert_array_equal(cube.data, cube_act.data)
cube_act = self.sp.cutout(self.resource, (0, 0, z_dim * 2), (x_dim, y_dim, z_dim), 0)
np.testing.assert_array_equal(cube_above.data, cube_act.data)
# Clear cache so we can get a cache miss.
self.sp.kvio.cache_client.flushdb()
# Also clear CACHE-MISS before running testing.
self.sp.cache_state.status_client.flushdb()
# Get middle cube again. This should trigger a cache miss.
cube_act = self.sp.cutout(self.resource, (0, 0, z_dim), (x_dim, y_dim, z_dim), 0)
# Confirm there is a cache miss.
misses = self.sp.cache_state.status_client.lrange('CACHE-MISS', 0, 10)
print('misses:')
print(misses)
miss_actual = self.sp.cache_state.status_client.lindex('CACHE-MISS', 0)
self.assertEqual(cube_cache_key, str(miss_actual, 'utf-8'))
# This is the system under test.
self.cache_miss.process()
# Confirm PRE-FETCH has the object keys for the cube above and below.
fetch_actual1 = self.sp.cache_state.status_client.lindex('PRE-FETCH', 0)
fetch_actual2 = self.sp.cache_state.status_client.lindex('PRE-FETCH', 1)
obj_keys = self.sp.objectio.cached_cuboid_to_object_keys(
[cube_above_cache_key, cube_below_cache_key])
self.assertEqual(obj_keys[0], str(fetch_actual1, 'utf-8'))
self.assertEqual(obj_keys[1], str(fetch_actual2, 'utf-8'))
class SimpleCatmaid:
""" Prefetch CATMAID tiles into MndcheDB """
def __init__(self):
""" Bind the mndche """
self.proj = None
self.channel = None
self.tilesz = 512
# make the memcache connection
self.mc = pylibmc.Client(["127.0.0.1"],
binary=True,
behaviors={
"tcp_nodelay": True,
"ketama": True
})
def __del__(self):
pass
def buildKey(self, res, slice_type, xtile, ytile, ztile, timetile,
filterlist):
return 'simple/{}/{}/{}/{}/{}/{}/{}/{}/{}'.format(
self.token, self.channel, slice_type, res, xtile, ytile, ztile,
timetile, filterlist)
def cacheMissXY(self, res, xtile, ytile, ztile, timetile, filterlist):
"""On a miss. Cutout, return the image and load the cache in a background thread"""
# make sure that the tile size is aligned with the cubedim
if self.tilesz % self.proj.datasetcfg.cubedim[res][
0] != 0 or self.tilesz % self.proj.datasetcfg.cubedim[res][1]:
logger.error("Illegal tile size. Not aligned")
raise NDWSError("Illegal tile size. Not aligned")
# figure out the cutout (limit to max image size)
xstart = xtile * self.tilesz
ystart = ytile * self.tilesz
xend = min((xtile + 1) * self.tilesz,
self.proj.datasetcfg.get_imagesize(res)[0])
yend = min((ytile + 1) * self.tilesz,
self.proj.datasetcfg.get_imagesize(res)[1])
# get an xy image slice
if timetile is None:
imageargs = '{}/{}/{}/{},{}/{},{}/{}/'.format(
self.channel, 'xy', res, xstart, xend, ystart, yend, ztile)
else:
imageargs = '{}/{}/{}/{},{}/{},{}/{}/{}/'.format(
self.channel, 'xy', res, xstart, xend, ystart, yend, ztile,
timetile)
# if filter list exists then add on for downstream processing
if filterlist:
imageargs = imageargs + 'filter/{}/'.format(filterlist)
cb = ndwsrest.imgSlice(imageargs, self.proj, self.db)
if cb.data.shape != (1, self.tilesz,
self.tilesz) and cb.data.shape != (
1, 1, self.tilesz, self.tilesz):
if timetile is None:
tiledata = np.zeros((1, self.tilesz, self.tilesz),
cb.data.dtype)
tiledata[0, 0:((yend - 1) % self.tilesz + 1),
0:((xend - 1) % self.tilesz + 1)] = cb.data[0, :, :]
else:
tiledata = np.zeros((1, 1, self.tilesz, self.tilesz),
cb.data.dtype)
tiledata[0, 0, 0:((yend - 1) % self.tilesz + 1),
0:((xend - 1) % self.tilesz + 1)] = cb.data[0,
0, :, :]
cb.data = tiledata
return cb.xyImage()
def cacheMissXZ(self, res, xtile, ytile, ztile, timetile, filterlist):
"""On a miss. Cutout, return the image and load the cache in a background thread"""
# make sure that the tile size is aligned with the cubedim
if self.tilesz % self.proj.datasetcfg.cubedim[res][
0] != 0 or self.tilesz % self.proj.datasetcfg.get_cubedim(
res)[2]:
raise ("Illegal tile size. Not aligned")
# figure out the cutout (limit to max image size)
xstart = xtile * self.tilesz
xend = min((xtile + 1) * self.tilesz,
self.proj.datasetcfg.get_imagesize(res)[0])
# OK this weird but we have to choose a convention. xtile ytile ztile refere to the URL request. So ztile is ydata
# but xstart, zstart..... etc. refer to ndstore coordinates for the cutout.
#
# z cutouts need to get rescaled
# we'll map to the closest pixel range and tolerate one pixel error at the boundary
# scalefactor = zvoxel / yvoxel
scalefactor = self.proj.datasetcfg.get_voxelres(
res)[2] / self.proj.datasetcfg.get_voxelres(res)[1]
zoffset = self.proj.datasetcfg.get_offset(res)[2]
ztilestart = int((ytile * self.tilesz) / scalefactor) + zoffset
zstart = max(ztilestart, zoffset)
ztileend = int(math.ceil(
(ytile + 1) * self.tilesz / scalefactor)) + zoffset
zend = min(ztileend, self.proj.datasetcfg.get_imagesize(res)[2] + 1)
# get an xz image slice
if timetile is None:
imageargs = '{}/{}/{}/{},{}/{}/{},{}/'.format(
self.channel, 'xz', res, xstart, xend, ztile, zstart, zend)
else:
imageargs = '{}/{}/{}/{},{}/{}/{},{}/{}/'.format(
self.channel, 'xz', res, xstart, xend, ztile, zstart, zend,
timetile)
if filterlist:
imageargs = imageargs + 'filter/{}/'.format(filterlist)
cb = ndwsrest.imgSlice(imageargs, self.proj, self.db)
# scale by the appropriate amount
if cb.data.shape != (ztileend - ztilestart, 1,
self.tilesz) and cb.data.shape != (
1, ztileend - ztilestart, 1, self.tilesz):
if timetile is None:
tiledata = np.zeros((ztileend - ztilestart, 1, self.tilesz),
cb.data.dtype)
tiledata[0:zend - zstart, 0,
0:((xend - 1) % self.tilesz + 1)] = cb.data[:, 0, :]
else:
tiledata = np.zeros((1, ztileend - ztilestart, 1, self.tilesz),
cb.data.dtype)
tiledata[0, 0:zend - zstart, 0,
0:((xend - 1) % self.tilesz + 1)] = cb.data[0, :,
0, :]
cb.data = tiledata
return cb.xzImage(scalefactor)
def cacheMissYZ(self, res, xtile, ytile, ztile, timetile, filterlist):
""" On a miss. Cutout, return the image and load the cache in a background thread """
# make sure that the tile size is aligned with the cubedim
if self.tilesz % self.proj.datasetcfg.get_cubedim(
res)[1] != 0 or self.tilesz % self.proj.datasetcfg.get_cubedim(
res)[2]:
raise ("Illegal tile size. Not aligned")
# figure out the cutout (limit to max image size)
ystart = ytile * self.tilesz
yend = min((ytile + 1) * self.tilesz,
self.proj.datasetcfg.get_imagesize(res)[1])
# z cutouts need to get rescaled
# we'll map to the closest pixel range and tolerate one pixel error at the boundary
# Scalefactor = zvoxel / xvoxel
scalefactor = self.proj.datasetcfg.get_voxelres(
res)[2] / self.proj.datasetcfg.get_voxelres(res)[0]
zoffset = self.proj.datasetcfg.get_offset(res)[2]
ztilestart = int((ztile * self.tilesz) / scalefactor) + zoffset
zstart = max(ztilestart, zoffset)
ztileend = int(math.ceil(
(ztile + 1) * self.tilesz / scalefactor)) + zoffset
zend = min(ztileend, self.proj.datasetcfg.get_imagesize(res)[2] + 1)
# get an yz image slice
if timetile is None:
imageargs = '{}/{}/{}/{}/{},{}/{},{}/'.format(
self.channel, 'yz', res, xtile, ystart, yend, zstart, zend)
else:
imageargs = '{}/{}/{}/{}/{},{}/{},{}/{}/'.format(
self.channel, 'yz', res, xtile, ystart, yend, zstart, zend,
timetile)
if filterlist:
imageargs = imageargs + 'filter/{}/'.format(filterlist)
cb = ndwsrest.imgSlice(imageargs, self.proj, self.db)
# scale by the appropriate amount
if cb.data.shape != (ztileend - ztilestart, self.tilesz,
1) and cb.data.shape != (1, ztileend - ztilestart,
self.tilesz, 1):
if timetile is None:
tiledata = np.zeros((ztileend - ztilestart, self.tilesz, 1),
cb.data.dtype)
tiledata[0:zend - zstart, 0:((yend - 1) % self.tilesz + 1),
0] = cb.data[:, :, 0]
else:
tiledata = np.zeros((1, ztileend - ztilestart, self.tilesz, 1),
cb.data.dtype)
tiledata[0, 0:zend - zstart, 0:((yend - 1) % self.tilesz + 1),
0] = cb.data[0, :, :, 0]
cb.data = tiledata
return cb.yzImage(scalefactor)
def getTile(self, webargs):
"""Fetch the file from mndche or get a cutout from the database"""
try:
# argument of format token/channel/slice_type/z/y_x_res.png
# p = re.compile("(\w+)/([\w+,]*?)/(xy|yz|xz|)/(\d+/)?(\d+)/(\d+)_(\d+)_(\d+).png")
p = re.compile(
"(\w+)/([\w+,]*?)/(xy|yz|xz|)/(?:filter/([\d,]+)/)?(?:(\d+)/)?(\d+)/(\d+)_(\d+)_(\d+).png"
)
m = p.match(webargs)
[self.token, self.channel, slice_type,
filterlist] = [i for i in m.groups()[:4]]
[timetile, ztile, ytile, xtile, res] = [
int(i.strip('/')) if i is not None else None
for i in m.groups()[4:]
]
except Exception, e:
logger.error("Incorrect arguments give for getTile {}. {}".format(
webargs, e))
raise NDWSError(
"Incorrect arguments given for getTile {}. {}".format(
webargs, e))
self.proj = NDProject.fromTokenName(self.token)
with closing(SpatialDB(self.proj)) as self.db:
# memcache key
mckey = self.buildKey(res, slice_type, xtile, ytile, ztile,
timetile, filterlist)
# if tile is in memcache, return it
tile = self.mc.get(mckey)
tile = None
if tile == None:
if slice_type == 'xy':
img = self.cacheMissXY(res, xtile, ytile, ztile, timetile,
filterlist)
elif slice_type == 'xz':
img = self.cacheMissXZ(res, xtile, ytile, ztile, timetile,
filterlist)
elif slice_type == 'yz':
img = self.cacheMissYZ(res, ztile, xtile, ytile, timetile,
filterlist)
else:
logger.error(
"Requested illegal image plance {}. Should be xy, xz, yz."
.format(slice_type))
raise NDWSError(
"Requested illegal image plance {}. Should be xy, xz, yz."
.format(slice_type))
fobj = cStringIO.StringIO()
img.save(fobj, "PNG")
self.mc.set(mckey, fobj.getvalue())
else:
print "Hit"
fobj = cStringIO.StringIO(tile)
fobj.seek(0)
return fobj
# Expects these keys from the events dictionary:
# {
# 'kv_config': {...},
# 'state_config': {...},
# 'object_store_config': {...},
# 'object_key': '...',
# 'page_in_channel': '...'
# }
print("in s3_to_cache lambda")
import json
import sys
from spdb.spatialdb import SpatialDB
# Parse input args passed as a JSON string from the lambda loader
json_event = sys.argv[1]
event = json.loads(json_event)
# Setup SPDB instance
sp = SpatialDB(event['kv_config'], event['state_config'],
event['object_store_config'])
object_key = event['object_key']
page_in_channel = event['page_in_channel']
cube_bytes = sp.objectio.get_single_object(object_key)
cache_keys = sp.objectio.object_to_cached_cuboid_keys([object_key])
sp.kvio.put_cubes(cache_keys[0], [cube_bytes])
if page_in_channel is not None:
sp.cache_state.notify_page_in_complete(page_in_channel, object_key)
def test_sqs_watcher_send_message(self):
"""Inject message into queue and test that SqsWatcher kicks off a lambda and writes cuboid to s3."""
# Generate random data
cube1 = Cube.create_cube(self.resource, [512, 512, 16])
cube1.random()
cube1.morton_id = 0
sp = SpatialDB(self.kvio_config, self.state_config,
self.object_store_config)
base_write_cuboid_key = "WRITE-CUBOID&{}&{}".format(
self.resource.get_lookup_key(), 0)
morton_idx = ndlib.XYZMorton([0, 0, 0])
t = 0
write_cuboid_key = sp.kvio.insert_cube_in_write_buffer(
base_write_cuboid_key, t, morton_idx,
cube1.to_blosc_by_time_index(t))
# Put page out job on the queue
sqs = boto3.client('sqs', region_name=get_region())
msg_data = {
"config": self.config_data,
"write_cuboid_key": write_cuboid_key,
"lambda-name": "s3_flush",
"resource": self.resource.to_dict()
}
response = sqs.send_message(
QueueUrl=self.object_store_config["s3_flush_queue"],
MessageBody=json.dumps(msg_data))
assert response['ResponseMetadata']['HTTPStatusCode'] == 200
watcher = SqsWatcher(self.lambda_data)
# verify_queue() needs the be run multiple times to verify that the queue is not changing
# only then does it send off a lambda message.
time.sleep(5)
watcher.verify_queue()
time.sleep(5)
lambdas_invoked = watcher.verify_queue()
if lambdas_invoked < 1:
time.sleep(5)
watcher.verify_queue()
time.sleep(15)
client = boto3.client('sqs', region_name=get_region())
response = client.get_queue_attributes(
QueueUrl=self.object_store_config["s3_flush_queue"],
AttributeNames=[
'ApproximateNumberOfMessages',
'ApproximateNumberOfMessagesNotVisible'
])
https_status_code = response['ResponseMetadata']['HTTPStatusCode']
queue_count = int(
response['Attributes']['ApproximateNumberOfMessages'])
# test that the queue count is now 0
assert queue_count == 0
s3 = boto3.client('s3', region_name=get_region())
objects_list = s3.list_objects(
Bucket=self.object_store_config['cuboid_bucket'])
# tests that bucket has some Contents.
assert "Contents" in objects_list.keys()
def ingestImageStack(self):
"""Ingest a TIF image stack"""
# Load a database
with closing(NDProjectsDB()) as projdb:
proj = projdb.loadToken(self.token)
with closing(SpatialDB(proj)) as db:
s3_io = S3IO(db)
# cuboidindex_db = CuboidIndexDB(proj.project_name, endpoint_url=ndsettings.DYNAMO_ENDPOINT)
ch = proj.getChannelObj(self.channel)
# get the dataset configuration
[ximagesz, yimagesz,
zimagesz] = proj.datasetcfg.dataset_dim(self.resolution)
[starttime, endtime] = ch.time_range
[xcubedim, ycubedim,
zcubedim] = cubedim = proj.datasetcfg.get_cubedim(self.resolution)
[xsupercubedim, ysupercubedim,
zsupercubedim] = supercubedim = proj.datasetcfg.get_supercubedim(
self.resolution)
[xoffset, yoffset,
zoffset] = proj.datasetcfg.get_offset(self.resolution)
if ch.channel_type in TIMESERIES_CHANNELS and (starttime == 0
and endtime == 0):
logger.error("Timeseries Data cannot have timerange (0,0)")
raise NDWSError("Timeseries Data cannot have timerange (0,0)")
# Get a list of the files in the directories
for timestamp in range(starttime, endtime):
for slice_number in range(zoffset, zimagesz, zsupercubedim):
slab = np.zeros([1, zsupercubedim, yimagesz, ximagesz],
dtype=ND_dtypetonp.get(
ch.channel_datatype))
# fetch 16 slices at a time
if ch.channel_type in TIMESERIES_CHANNELS:
time_value = timestamp
else:
time_value = None
self.fetchData(
range(slice_number, slice_number + zsupercubedim)
if slice_number + zsupercubedim <= zimagesz else range(
slice_number, zimagesz),
time_value=time_value)
for b in range(zsupercubedim):
if (slice_number + b < zimagesz):
try:
# reading the raw data
file_name = "{}{}".format(
self.path,
self.generateFileName(slice_number + b))
# print "Open filename {}".format(file_name)
logger.info(
"Open filename {}".format(file_name))
if ch.channel_datatype in [UINT8, UINT16]:
try:
image_data = np.asarray(
Image.open(file_name, 'r'))
slab[0, b, :, :] = image_data
except Exception as e:
slab[0, b, :, :] = np.zeros(
(yimagesz, ximagesz),
dtype=ND_dtypetonp.get(
ch.channel_datatype))
logger.warning(
"File corrupted. Cannot open file. {}"
.format(e))
elif ch.channel_datatype in [UINT32]:
image_data = np.asarray(
Image.open(file_name,
'r').convert('RGBA'))
slab[0, b, :, :] = np.left_shift(
image_data[:, :, 3],
24,
dtype=np.uint32) | np.left_shift(
image_data[:, :, 2],
16,
dtype=np.uint32) | np.left_shift(
image_data[:, :, 1],
8,
dtype=np.uint32) | np.uint32(
image_data[:, :, 0])
elif ch.channel_type in ANNOTATION_CHANNELS:
image_data = np.asarray(
Image.open(file_name, 'r'))
slab[0, b, :, :] = image_data
else:
logger.error("Cannot ingest this data yet")
raise NDWSError(
"Cannot ingest this data yet")
except IOError, e:
logger.warning("IOError {}.".format(e))
slab[0, b, :, :] = np.zeros(
(yimagesz, ximagesz),
dtype=ND_dtypetonp.get(
ch.channel_datatype))
for y in range(0, yimagesz + 1, ysupercubedim):
for x in range(0, ximagesz + 1, xsupercubedim):
# Getting a Cube id and ingesting the data one cube at a time
zidx = XYZMorton([
x / xsupercubedim, y / ysupercubedim,
(slice_number - zoffset) / zsupercubedim
])
cube = Cube.CubeFactory(supercubedim,
ch.channel_type,
ch.channel_datatype)
cube.zeros()
xmin, ymin = x, y
xmax = min(ximagesz, x + xsupercubedim)
ymax = min(yimagesz, y + ysupercubedim)
zmin = 0
zmax = min(slice_number + zsupercubedim,
zimagesz + 1)
cube.data[0, 0:zmax - zmin, 0:ymax - ymin,
0:xmax - xmin] = slab[0, zmin:zmax,
ymin:ymax,
xmin:xmax]
if cube.isNotZeros():
# cuboidindex_db.putItem(ch.channel_name, self.resolution, x, y, slice_number, ch.time_range[0])
# s3_io.putCube(ch, self.resolution, zidx, blosc.pack_array(cube.data))
s3_io.putCube(ch,
timestamp,
zidx,
self.resolution,
blosc.pack_array(cube.data),
neariso=False)
# clean up the slices fetched
self.cleanData(
range(slice_number, slice_number +
zsupercubedim) if slice_number + zsupercubedim <=
zimagesz else range(slice_number, zimagesz))