Python API

This section includes information for using the Python API of bob.db.base.

This section contains the reference guide for bob.db.base.

The db package contains simplified APIs to access data for various databases that can be used in Biometry, Machine Learning or Pattern Classification.

bob.db.base.get_config()

Returns a string containing the configuration information.

class bob.db.base.Database

Bases: object

Low-level Database API to be used within bob.

check_parameter_for_validity(parameter, parameter_description, valid_parameters, default_parameter=None)

Checks the given parameter for validity

Ensures a given parameter is in the set of valid parameters. If the parameter is None or empty, the value in default_parameter will be returned, in case it is specified, otherwise a ValueError will be raised.

This function will return the parameter after the check tuple or list of parameters, or raise a ValueError.

Parameters:

parameter : str

The single parameter to be checked. Might be a string or None.

parameter_description : str

A short description of the parameter. This will be used to raise an exception in case the parameter is not valid.

valid_parameters : [str]

A list/tuple of valid values for the parameters.

default_parameters : [str] or None

The default parameter that will be returned in case parameter is None or empty. If omitted and parameter is empty, a ValueError is raised.

check_parameters_for_validity(parameters, parameter_description, valid_parameters, default_parameters=None)

Checks the given parameters for validity.

Checks a given parameter is in the set of valid parameters. It also assures that the parameters form a tuple or a list. If parameters is ‘None’ or empty, the default_parameters will be returned (if default_parameters is omitted, all valid_parameters are returned).

This function will return a tuple or list of parameters, or raise a ValueError.

Parameters:

parameters : str, [str] or None

The parameters to be checked. Might be a string, a list/tuple of strings, or None.

parameter_description : str

A short description of the parameter. This will be used to raise an exception in case the parameter is not valid.

valid_parameters : [str]

A list/tuple of valid values for the parameters.

default_parameters : [str] or None

The list/tuple of default parameters that will be returned in case parameters is None or empty. If omitted, all valid_parameters are used.

convert_names_to_highlevel(names, low_level_names, high_level_names)

Converts group names from a low level to high level API

This is useful for example when you want to return db.groups() for the bob.bio.base. Your instance of the database should already have low_level_names and high_level_names initialized.

convert_names_to_lowlevel(names, low_level_names, high_level_names)

Same as convert_names_to_highlevel but on reverse

class bob.db.base.File(path, file_id=None)

Bases: object

Abstract class that define basic properties of File objects. Your file instance should have at least the self.id and self.path properties.

Constructor Documentation

Initialize the File object with the minimum required data.

Parameters:

path : str

The path to this file, relative to the basic directory. If you use an SQL database, this should be the SQL type String. Please do not specify any file extensions.

file_id : various type

The id of the file. Its type depends on your implementation. If you use an SQL database, this should be an SQL type like Integer or String. If you are using an automatically determined file id, you don’t need to specify this parameter.

load(directory=None, extension='.hdf5')

Loads the data at the specified location and using the given extension. Override it if you need to load differently.

Keyword Parameters:

data

The data blob to be saved (normally a numpy.ndarray).

directory

[optional] If not empty or None, this directory is prefixed to the final file destination

extension

[optional] The extension of the filename - this will control the type of output and the codec for saving the input blob.

make_path(directory=None, extension=None)

Wraps the current path so that a complete path is formed

Keyword Parameters:

directory

An optional directory name that will be prefixed to the returned result.

extension

An optional extension that will be suffixed to the returned filename. The extension normally includes the leading . character as in .jpg or .hdf5.

Returns a string containing the newly generated file path.

save(data, directory=None, extension='.hdf5', create_directories=True)

Saves the input data at the specified location and using the given extension. Override it if you need to save differently.

Keyword Parameters:

data

The data blob to be saved (normally a numpy.ndarray).

directory

[optional] If not empty or None, this directory is prefixed to the final file destination

extension

[optional] The extension of the filename - this will control the type of output and the codec for saving the input blob.

class bob.db.base.SQLiteDatabase(sqlite_file, file_class)

Bases: bob.db.base.Database

This class can be used for handling SQL databases.

It opens an SQL database in a read-only mode and keeps it opened during the whole session.

Parameters:

sqlite_file : str

The file name (including full path) of the SQLite file to read or generate.

file_class : a class instance

The File class, which needs to be derived from bob.db.base.File. This is required to be able to query() the databases later on.

all_files(**kwargs)

Returns the list of all File objects that satisfy your query.

For possible keyword arguments, please check the implemention’s objects() method.

assert_validity()

Raise a RuntimeError if the database back-end is not available.

check_parameter_for_validity(parameter, parameter_description, valid_parameters, default_parameter=None)

Checks the given parameter for validity

Ensures a given parameter is in the set of valid parameters. If the parameter is None or empty, the value in default_parameter will be returned, in case it is specified, otherwise a ValueError will be raised.

This function will return the parameter after the check tuple or list of parameters, or raise a ValueError.

Parameters:

parameter : str

The single parameter to be checked. Might be a string or None.

parameter_description : str

A short description of the parameter. This will be used to raise an exception in case the parameter is not valid.

valid_parameters : [str]

A list/tuple of valid values for the parameters.

default_parameters : [str] or None

The default parameter that will be returned in case parameter is None or empty. If omitted and parameter is empty, a ValueError is raised.

check_parameters_for_validity(parameters, parameter_description, valid_parameters, default_parameters=None)

Checks the given parameters for validity.

Checks a given parameter is in the set of valid parameters. It also assures that the parameters form a tuple or a list. If parameters is ‘None’ or empty, the default_parameters will be returned (if default_parameters is omitted, all valid_parameters are returned).

This function will return a tuple or list of parameters, or raise a ValueError.

Parameters:

parameters : str, [str] or None

The parameters to be checked. Might be a string, a list/tuple of strings, or None.

parameter_description : str

A short description of the parameter. This will be used to raise an exception in case the parameter is not valid.

valid_parameters : [str]

A list/tuple of valid values for the parameters.

default_parameters : [str] or None

The list/tuple of default parameters that will be returned in case parameters is None or empty. If omitted, all valid_parameters are used.

convert_names_to_highlevel(names, low_level_names, high_level_names)

Converts group names from a low level to high level API

This is useful for example when you want to return db.groups() for the bob.bio.base. Your instance of the database should already have low_level_names and high_level_names initialized.

convert_names_to_lowlevel(names, low_level_names, high_level_names)

Same as convert_names_to_highlevel but on reverse

files(ids, preserve_order=True)

Returns a list of File objects with the given file ids

Parameters:

ids : list, tuple

The ids of the object in the database table “file”. This object should be a python iterable (such as a tuple or list).

preserve_order : bool

If True (the default) the order of elements is preserved, but the execution time increases.

Returns:

list: a list (that may be empty) of File objects.

is_valid()

Returns if a valid session has been opened for reading the database.

paths(ids, prefix=None, suffix=None, preserve_order=True)

Returns a full file paths considering particular file ids

Parameters:

ids : list, tuple

The ids of the object in the database table “file”. This object should be a python iterable (such as a tuple or list).

prefix : str or None

The bit of path to be prepended to the filename stem

suffix : str or None

The extension determines the suffix that will be appended to the filename stem.

preserve_order : bool

If True (the default) the order of elements is preserved, but the execution time increases.

Returns:

list: A list (that may be empty) of the fully constructed paths given the file ids.

query(*args)

Creates a query to the database using the given arguments.

reverse(paths, preserve_order=True)

Reverses the lookup from certain paths, returns a list of File‘s

Parameters:

paths : [str]

The filename stems to query for. This object should be a python iterable (such as a tuple or list)

preserve_order : True

If True (the default) the order of elements is preserved, but the execution time increases.

Returns:

list: A list (that may be empty).

uniquify(file_list)

Sorts the given list of File objects and removes duplicates from it.

Parameters:

file_list: [File]

A list of File objects to be handled. Also other objects can be handled, as long as they are sortable.

Returns:

list: A sorted copy of the given file_list with the duplicates

removed.

bob.db.base.read_annotation_file(file_name, annotation_type)

This function provides default functionality to read annotation files.

Parameters:

file_name : str

The full path of the annotation file to read

annotation_type : str

The type of the annotation file that should be read. The following annotation_types are supported:

• eyecenter: The file contains a single row with four entries: re_x re_y le_x le_y
• named: The file contains named annotations, one per line, e.g.: reye re_x re_y or pose 25.7
• idiap: The file contains enumerated annotations, one per line, e.g.: 1 key1_x key1_y, and maybe some additional annotations like gender, age, ...

Returns:

dict: A python dictionary with the keypoint name as key and the

position (y,x) as value, and maybe some additional annotations.

Database Handling Utilities

Some utilities shared by many of the databases.

class bob.db.base.utils.null

Bases: object

A look-alike stream that discards the input

write(s)

Writes contents of string s on this stream

flush()

Flushes the stream

bob.db.base.utils.apsw_is_available()

Checks lock-ability for SQLite on the current file system

class bob.db.base.utils.SQLiteConnector(filename, readonly=False, lock=None)

Bases: object

An object that handles the connection to SQLite databases.

Initializes the connector

Keyword arguments

filename

The name of the file containing the SQLite database

readonly

Should I try and open the database in read-only mode?

lock

Any vfs name as output by apsw.vfsnames()

static filesystem_is_lockable(database)

Checks if the filesystem is lockable

APSW_IS_AVAILABLE = False

create_engine(echo=False)

Returns an SQLAlchemy engine

session(echo=False)

Returns an SQLAlchemy session

bob.db.base.utils.session(dbtype, dbfile, echo=False)

Creates a session to an SQLite database

bob.db.base.utils.session_try_readonly(dbtype, dbfile, echo=False)

Creates a read-only session to an SQLite database. If read-only sessions are not supported by the underlying sqlite3 python DB driver, then a normal session is returned. A warning is emitted in case the underlying filesystem does not support locking properly.

Raises a NotImplementedError if the dbtype is not supported.

bob.db.base.utils.create_engine_try_nolock(dbtype, dbfile, echo=False)

Creates an engine connected to an SQLite database with no locks. If engines without locks are not supported by the underlying sqlite3 python DB driver, then a normal engine is returned. A warning is emitted if the underlying filesystem does not support locking properly in this case.

Raises a NotImplementedError if the dbtype is not supported.

bob.db.base.utils.session_try_nolock(dbtype, dbfile, echo=False)

Creates a session to an SQLite database with no locks. If sessions without locks are not supported by the underlying sqlite3 python DB driver, then a normal session is returned. A warning is emitted if the underlying filesystem does not support locking properly in this case.

Raises a NotImplementedError if the dbtype is not supported.

bob.db.base.utils.connection_string(dbtype, dbfile, opts={})

Returns a connection string for supported platforms

Keyword parameters

dbtype

The type of database (only ‘sqlite’ is supported for the time being)

dbfile

The location of the file to be used

Driver API

This module defines, among other less important constructions, a management interface that can be used by Bob to display information about the database and manage installed files.

class bob.db.base.driver.Interface

Bases: object

Base manager for Bob databases

name()

Returns a simple name for this database, w/o funny characters, spaces

files()

Returns a python iterable with all auxiliary files needed.

The values should be take w.r.t. where the python file that declares the database is sitting at.

version()

Returns the current version number defined in setup.py

type()

Returns the type of auxiliary files you have for this database

If you return ‘sqlite’, then we append special actions such as ‘dbshell’ on ‘bob_dbmanage.py’ automatically for you. Otherwise, we don’t.

If you use auxiliary text files, just return ‘text’. We may provide special services for those types in the future.

Use the special name ‘builtin’ if this database is an integral part of Bob.

setup_parser(parser, short_description, long_description)

Sets up the base parser for this database.

Keyword arguments:

short_description

A short description (one-liner) for this database

long_description

A more involved explanation of this database

Returns a subparser, ready to be added commands on

add_commands(parser)

Adds commands to a given (argparse) parser.

This method, effectively, allows you to define special commands that your database will be able to perform when called from the common driver like for example create or checkfiles.

You are not obliged to overwrite this method. If you do, you will have the chance to establish your own commands. You don’t have to worry about stock commands such as files() or version(). They will be automatically hooked-in depending on the values you return for type() and files().

Keyword arguments

parser

An instance of a argparse.ArgumentParser that you can customize, i.e., call argparse.ArgumentParser.add_argument() on.