CopickRoot

copick.models.CopickRoot

Root of a copick project. Contains references to the runs and pickable objects.

Attributes:

config (CopickConfig) –

Configuration of the copick project.
user_id (str) –

Unique identifier for the user.
session_id (str) –

Unique identifier for the session.
runs (List[CopickRun]) –

References to the runs for this project. Lazy loaded upon access.
pickable_objects (List[CopickObject]) –

References to the pickable objects for this project.

init

__init__(config: CopickConfig)

Parameters:

config (CopickConfig) –

Configuration of the copick project.

query

query() -> List[CopickRun]

Override this method to query for runs.

get_run

get_run(name: str, **kwargs) -> Union[CopickRun, None]

Get run by name.

Parameters:

name (str) –

Name of the run to retrieve.
**kwargs –

Additional keyword arguments for the run metadata.

Returns:

CopickRun ( Union[CopickRun, None] ) –

The run with the given name, or None if not found.

get_object

get_object(name: str) -> Union[CopickObject, None]

Get object by name.

Parameters:

name (str) –

Name of the object to retrieve.

Returns:

CopickObject ( Union[CopickObject, None] ) –

The object with the given name, or None if not found.

refresh

refresh() -> None

Refresh the list of runs.

reconnect

reconnect() -> None

Reconnect to the storage backend and invalidate all caches.

Override in subclasses that use remote filesystems (e.g. SSH, S3). No-op for local filesystem backends.

save_config

save_config(config_path: str) -> None

Save the configuration to a JSON file.

Parameters:

config_path (str) –

Path to the configuration file to save.

new_run

new_run(name: str, exist_ok: bool = False, **kwargs) -> CopickRun

Create a new run.

Parameters:

name (str) –

Name of the run to create.
exist_ok (bool, default: False ) –

Whether to raise an error if the run already exists.
**kwargs –

Additional keyword arguments for the run metadata.

Returns:

CopickRun ( CopickRun ) –

The newly created run.

Raises:

ValueError –

If a run with the given name already exists.

delete_run

delete_run(name: str) -> None

Delete a run by name.

Parameters:

name (str) –

Name of the run to delete.

new_object

new_object(name: str, is_particle: bool, label: Optional[int] = None, color: Optional[Tuple[int, int, int, int]] = None, emdb_id: Optional[str] = None, pdb_id: Optional[str] = None, identifier: Optional[str] = None, map_threshold: Optional[float] = None, radius: Optional[float] = None, metadata: Optional[Dict[str, Any]] = None, exist_ok: bool = False) -> CopickObject

Create a new pickable object and add it to the configuration.

Parameters:

name (str) –

Name of the object.
is_particle (bool) –

Whether this object should be represented by points (True) or segmentation masks (False).
label (Optional[int], default: None ) –

Numeric label/id for the object. If None, will use the next available label.
color (Optional[Tuple[int, int, int, int]], default: None ) –

RGBA color for the object. If None, will use a default color.
emdb_id (Optional[str], default: None ) –

EMDB ID for the object.
pdb_id (Optional[str], default: None ) –

PDB ID for the object.
identifier (Optional[str], default: None ) –

Identifier for the object (e.g. Gene Ontology ID or UniProtKB accession).
map_threshold (Optional[float], default: None ) –

Threshold to apply to the map when rendering the isosurface.
radius (Optional[float], default: None ) –

Radius of the particle, when displaying as a sphere.
metadata (Optional[Dict[str, Any]], default: None ) –

Additional metadata for the object (user-defined contents).
exist_ok (bool, default: False ) –

Whether existing objects with the same name should be overwritten..

Returns:

CopickObject ( CopickObject ) –

The newly created object.

Raises:

ValueError –

If an object with the given name already exists and exist_ok is False.