Formats#

The mosaic.formats module provides file I/O for the geometry, density, and session formats used throughout Mosaic. Most user code only needs the high-level entry points open_file(), open_session(), and write_session(); the lower-level container types are listed for completeness.

Reading#

open_file() dispatches to the right parser based on the file extension and returns a GeometryDataContainer of one or more entities.

open_file(filename, *args, **kwargs)

Open and parse a file based on its extension.

Writing#

`OrientationsWriter`(points, quaternions, entities)
`write_density`(data, filename[, ...])	Write 3D density data to file (typically in CCP4/MRC format).

Session Files#

Mosaic sessions are written in an indexed binary format that bundles the pickled application state with optional auxiliary sections (thumbnails, metadata, …). The helpers below read and write those archives.

`is_session_file`(filepath)	Return `True` if filepath has a recognised session extension.
`open_session`(filepath)	Read session state, handling both legacy and indexed formats.
`write_session`(filepath, state[, sections])	Write a session file in the indexed format.
`read_session_index`(filepath)	Read the session file index.
`read_session_meta`(filepath)	Read session metadata without loading geometry data.
`read_session_section`(filepath, section)	Read raw bytes for a named section without decoding.

Streaming#

Helpers for chunked, level-of-detail access to OME-Zarr volumes.

`open_omezarr`(url)	Open a remote OME-Zarr store and return a VTK streaming source.
`ZarrImageSource`(pyramid[, initial_level])	VTK pipeline source that serves image data from a `ZarrPyramid`.

Data Containers#

In-memory representations returned by the parsers. GeometryDataContainer groups one or more geometry entities, while VertexPropertyContainer carries per-vertex scalar fields alongside them.

`GeometryDataContainer`	Container for multiple geometry entities with automatic validation.
`VertexPropertyContainer`	Container for managing custom vertex properties with automatic synchronization.

Exceptions#

NotASegmentationError

Raised when a volume cannot be interpreted as a segmentation.