openlifu.db.database.Database

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

Bases: object

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] 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.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.ERROR)

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

write_run(run: Run, session: Session | None = None, protocol: Protocol | None = None, on_conflict=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: PathLike | None = None, transducer_body_model_filepath: PathLike | None = None, on_conflict: OnConflictOpts = 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