CopickVoxelSpacing

copick.models.CopickVoxelSpacing

Encapsulates all data pertaining to a specific voxel spacing. This includes the tomograms and feature maps at this voxel spacing.

Attributes:

• run (CopickRun) –

  Reference to the run this voxel spacing belongs to.

• meta (CopickVoxelSpacingMeta) –

  Metadata for this voxel spacing.

• tomograms (List[CopickTomogram]) –

  Tomograms for this voxel spacing. Either populated from config or lazily loaded when CopickVoxelSpacing.tomograms is accessed for the first time.

__init__

__init__(run: CopickRun, meta: CopickVoxelSpacingMeta, config: Optional[CopickConfig] = None)

Parameters:

• run (CopickRun) –

  Reference to the run this voxel spacing belongs to.

• meta (CopickVoxelSpacingMeta) –

  Metadata for this voxel spacing.

• config (Optional[CopickConfig], default: None ) –

  Configuration of the copick project.

query_tomograms

query_tomograms() -> List[CopickTomogram]

Override this method to query for tomograms.

get_tomogram

get_tomogram(tomo_type: str) -> Union[CopickTomogram, None]

Get tomogram by type.

Parameters:

• tomo_type (str) –

  Type of the tomogram to retrieve.

Returns:

• CopickTomogram ( Union[CopickTomogram, None] ) –

  The tomogram with the given type, or None if not found.

get_tomograms

get_tomograms(tomo_type: str) -> List[CopickTomogram]

Get tomograms by type.

Parameters:

• tomo_type (str) –

  Type of the tomograms to retrieve.

Returns:

• List[CopickTomogram] –

  List[CopickTomogram]: The tomograms with the given type.

refresh_tomograms

refresh_tomograms() -> None

Refresh CopickVoxelSpacing.tomograms from storage.

refresh

refresh() -> None

Refresh CopickVoxelSpacing.tomograms from storage.

new_tomogram

new_tomogram(tomo_type: str, exist_ok: bool = False, **kwargs) -> CopickTomogram

Create a new tomogram object, also creates the Zarr-store in the storage backend.

Parameters:

• tomo_type (str) –

  Type of the tomogram to create.

• exist_ok (bool, default: False ) –

  Whether to raise an error if the tomogram already exists.

• **kwargs –

  Additional keyword arguments for the tomogram metadata.

Returns:

• CopickTomogram ( CopickTomogram ) –

  The newly created tomogram object.

Raises:

• ValueError –

  If a tomogram with the given type already exists for this voxel spacing.

ensure

ensure(create: bool = False) -> bool

Override to check if the voxel spacing record exists, optionally create it if it does not.

Parameters:

• create (bool, default: False ) –

  Whether to create the voxel spacing record if it does not exist.

Returns:

• bool ( bool ) –

  True if the voxel spacing record exists, False otherwise.

delete

delete() -> None

Delete the voxel spacing record.

delete_tomograms

delete_tomograms(tomo_type: str = None) -> None

Delete a tomogram by type.

Parameters:

• tomo_type (str, default: None ) –

  Type of the tomogram to delete.