openlifu.db.database.Database

class openlifu.db.database.Database(path: str | None = None)

Bases: object

delete_session(subject_id: str, session_id: str, on_conflict: OnConflictOpts | str = OnConflictOpts.ERROR)

Delete a session and its associated data from the database.

Parameters:

• subject_id – ID of the subject the session belongs to

• session_id – ID of the session to delete

• on_conflict – Behavior when session doesn’t exist (‘error’ or ‘skip’)

static get_default_path()

Get the default path for the database

Returns:

Default path for the database

static get_default_user_dir()

Get the default user directory for the database

Returns:

Default user directory

get_photocollection_absolute_filepaths(subject_id: str, session_id: str, reference_number: str) → List[Path]

get the absolute filepaths of all photos in a specific photocollection.

Parameters:

• subject_id (str) – The subject ID.

• session_id (str) – The session ID.

• reference_number (str) – The reference number of the photocollection.

Returns:

List of absolute file paths to the photos in the photocollection.

Return type:

List[Path]

get_photocollection_reference_numbers(subject_id: str, session_id: str) → List[str]

Get a list of reference numbers of the photocollections associated with the given session

get_photocollections_filename(subject_id, session_id) → Path

Get the path to the overall photocollections json file for the requested session

get_photoscan_absolute_filepaths_info(subject_id, session_id, photoscan_id)

Returns the photoscan information with absolute paths to any data

get_photoscan_ids(subject_id: str, session_id: str) → List[str]

Get a list of IDs of the photoscans associated with the given session

get_photoscans_filename(subject_id, session_id) → Path

Get the path to the overall photoscans json file for the requested session

get_solution_filepath(subject_id, session_id, solution_id) → Path

Get the solution json file for the solution with the given ID

get_solution_ids(subject_id: str, session_id: str) → List[str]

Get a list of IDs of the solutions associated with the given session

get_solutions_filename(subject_id, session_id) → Path

Get the path to the overall solutions json file for the requested session

get_transducer_absolute_filepaths(transducer_id: str) → Dict[str, str | None]

Returns the absolute filepaths to the model data files i.e. transducer body and registration surface model files affiliated with the transducer, with ID transducer_id. Unlike load_transducer, which specifies the relative paths to the model datafiles along with other transducer attributes, this function only returns the absolute filepaths to the datafiles based on the Database directory.

Parameters:

transducer_id – Transducer ID

Returns:

A dictionary containing the absolute filepaths to the affiliated transducer data files with the following possible keys:

• ”id” (str): transducer ID

• ”name” (str): transducer name

• ”registration_surface_abspath” (str or None): absolute path to the transducer registration surface (open-surface mesh used for transducer tracking registration). This key is only included if there is an affiliated registration surface. None if no registration surface is available.

• ”transducer_body_abspath” (str or None): absolute path to the transducer body model (closed-surface mesh for visualizing the transducer). This key is only included if there is an affiliated body model. None if no transducer body is available.

Return type:

dict

static initialize_empty_database(database_filepath: str | PathLike) → Database

Initializes an empty database at the given database_filepath

load_photoscan(subject_id, session_id, photoscan_id, load_data=False)

Returns a photoscan object and optionally, also returns the loaded model and texture data as Tuple[vtkPolyData, vtkImageData | None ] if load_data = True.

load_solution(session: Session, solution_id: str) → Solution

Load the Solution of the given ID that is associated with the given Session

load_transducer(transducer_id, convert_array: bool = True) → Transducer | TransducerArray

Given a transducer_id, reads the corresponding transducer file from database and returns a transducer object. Note: the transducer object includes the relative path to the affiliated transducer model data. get_transducer_absolute_filepaths, should be used to obtain the absolute data filepaths based on the Database directory path. :param transducer_id: Transducer ID :param convert_array: When enabled, if a TransducerArray is encountered then it is converted to a Transducer.

Returns:

Corresponding Transducer object

load_volume(subject, volume_id)

Load the volume with the given ID for the specified subject.

write_photocollection(subject_id, session_id, reference_number: str, photo_paths: List[str | PathLike], on_conflict: OnConflictOpts | str = OnConflictOpts.ERROR)

Writes a photocollection to database and copies the associated photos into the database, specified by the subject, session, and reference_number of the photocollection.

write_photoscan(subject_id, session_id, photoscan: Photoscan, model_data_filepath: str | None = None, texture_data_filepath: str | None = None, mtl_data_filepath: str | None = None, on_conflict: OnConflictOpts | str = OnConflictOpts.ERROR)

Writes a photoscan object to database and copies the associated data filepaths into the database. While the model data file is required, the associated texture and .mtl files are optional and can be provided if present. When a photoscan that is already present in the database is being re-written,the associated data files do not need to be specified

write_run(run: Run, session: Session = None, protocol: Protocol = None, on_conflict: OnConflictOpts | str = OnConflictOpts.ERROR)

Write a run with a snapshot of session and a snapshot of protocol if provided

Parameters:

• run – Run to be written

• session (optional) – the Session used in the Run, it will have a snapshot written alongside the Run

• protocol (optional) – the Protocol used in the Run, it will have a snapshot written alongside the Run

Returns:

This method does not return a value

Return type:

None

write_solution_ids(session: Session, solution_ids: List[str])

Write to the list of overall solution IDs

write_transducer(transducer, registration_surface_model_filepath: str | PathLike | None = None, transducer_body_model_filepath: str | PathLike | None = None, on_conflict: OnConflictOpts | str = OnConflictOpts.ERROR) → None

Writes a transducer object to database and copies the affiliated transducer data files to the database if provided. When a transducer that is already present in the database is being re-written, the associated model data files do not need to be provided if they have previously been added to the database. :param transducer: Transducer to be written :param transducer_body_model_filepath: Model file containing a mesh of transducer body mesh. This is a closed surface meant for visualization of the transducer. :type transducer_body_model_filepath: optional :param registration_surface_model_filepath: Model file containing an open-surface sub-mesh of the transducer body model. This model is meant to be used for registration during transducer tracking. :type registration_surface_model_filepath: optional

Returns:

This method does not return a value

Return type:

None