skeleton.rst

Skeleton format

A skeleton representation of some or all segmented objects may be specified as a directory tree consisting of the following files:

• :file:`info` file in JSON format specifying the :json:schema:`metadata<PrecomputedSkeleton>`.
• For each segment ID for which there is a skeleton representation, a segment data file specifying the :ref:`encoded skeleton<precomputed-skeleton-format-encoding>` for a single segment.

The actual storage of the manifest and mesh fragment data depends on whether the :ref:`unsharded<precomputed-skeleton-format-unsharded>` or :ref:`sharded<precomputed-skeleton-format-sharded>` format is used.

:file:`info` metadata file

The :file:`info` file is a JSON-format text file with the following schema:

.. json:schema:: PrecomputedSkeleton

Encoded skeleton file format

The skeleton representation for a single segment ID is a binary file with the following format:

• num_vertices: uint32le, specifies the number of vertices.
• num_edges: uint32le, specifies the number of edges.
• vertex_positions: 3*num_vertices float32le, as a C-order [num_vertices, 3] array specifying the x, y, and z vertex positions in "stored model" coordinates.
• edges: 2*num_edges uint32le, as a C-order [num_edges, 2] array specifying the source and target vertex index in the range [0, num_vertices).
• For each additional attribute in vertex_attributes:
  • attribute_data: num_vertices * num_components elements of the specified data_type in little-endian format.

Unsharded format

In the unsharded format, the encoded skeleton data is stored as a separate file within the same directory as the :file:`info` file under the name :file:`{<segment-id>}`, where :file:`{<segment-id>}` is the base-10 string representation of the segment ID.

Sharded format

In the :ref:`sharded format<precomputed-sharded-format>`, the encoded skeleton data is retrieved using the segment ID as the key. The shard files are stored in the same directory as the :file:`info` file.