Exemple #1
0
    def fromSupercuboidKey(cls, supercuboid_key):
        """Create a BossIngestProject instance from a supercuboid_key aka the chunk key

        Note, the BossIngestProj returned will have None for its job_id and
        will have ids for collection, experiment,  and channel, instead of names.

        Args:
            supercuboid_key(str): The chunk key

        Returns:
            (BossIngestProj):
        """
        parts = BossUtil.decode_chunk_key(supercuboid_key)
        return cls(parts['collection'], parts['experiment'],
                   parts['channel_layer'], parts['resolution'], None)
Exemple #2
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    def cuboidReady(self, chunk_key, tile_uploaded_map):
        """Verify if we have all tiles for a given cuboid.

        Args:
            chunk_key (string): Key used to store the entry for the cuboid.
            tile_uploaded_map (dict): Dictionary with tile keys as the keys.  Presence of a tile indicates it's been uploaded.

        Returns:
            (bool)
        """

        key_parts = BossUtil.decode_chunk_key(chunk_key)
        num_tiles = key_parts["num_tiles"]

        if num_tiles < settings.SUPER_CUBOID_SIZE[2]:
            return len(tile_uploaded_map) >= num_tiles

        return len(tile_uploaded_map) >= settings.SUPER_CUBOID_SIZE[2]
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)
            msg = [x for x in ingest_queue.receiveMessage()]
            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:
                tile_img = np.asarray(Image.open(image_bytes), dtype=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.create_from_lambda_name(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)
Exemple #4
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    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))

    # Cuboid List
    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'])])
Exemple #5
0
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)