Coverage for src/bob/bio/base/database/file.py: 61%
33 statements
« prev ^ index » next coverage.py v7.6.5, created at 2024-11-14 21:41 +0100
1import bob.io.base
3from bob.bio.base.utils.annotations import read_annotation_file
4from bob.pipelines.sample import _ReprMixin
6from .legacy import File as LegacyFile
9class BioFile(LegacyFile, _ReprMixin):
10 """
11 A simple base class that defines basic properties of File object for the use
12 in verification experiments
14 Attributes
15 ----------
16 client_id : str or int
17 The id of the client this file belongs to.
18 Its type depends on your implementation.
19 If you use an SQL database, this should be an SQL type like Integer or
20 String.
21 path : object
22 see :py:class:`bob.bio.base.database.legacy.File` constructor
23 file_id : object
24 see :py:class:`bob.bio.base.database.legacy.File` constructor
25 original_directory : str or None
26 The path to the original directory of the file
27 original_extension : str or None
28 The extension of the original files. This attribute is deprecated.
29 Please try to include the extension in the ``path`` attribute
30 annotation_directory : str or None
31 The path to the directory of the annotations
32 annotation_extension : str or None
33 The extension of annotation files. Default is ``.json``
34 annotation_type : str or None
35 The type of the annotation file, see
36 :`bob.bio.base.utils.read_annotation_file`. Default is
37 ``json``.
38 """
40 def __init__(
41 self,
42 client_id,
43 path,
44 file_id=None,
45 original_directory=None,
46 original_extension=None,
47 annotation_directory=None,
48 annotation_extension=None,
49 annotation_type=None,
50 **kwargs,
51 ):
52 super(BioFile, self).__init__(path, file_id, **kwargs)
54 # just copy the information
55 self.client_id = client_id
56 """The id of the client, to which this file belongs to."""
57 self.original_directory = original_directory
58 self.original_extension = original_extension
59 self.annotation_directory = annotation_directory
60 self.annotation_extension = annotation_extension or ".json"
61 self.annotation_type = annotation_type or "json"
63 def load(self, original_directory=None, original_extension=None):
64 """Loads the data at the specified location and using the given extension.
65 Override it if you need to load differently.
67 Parameters
68 ----------
70 original_directory: :obj:`str` (optional)
71 The path to the root of the dataset structure.
72 If `None`, will try to use `self.original_directory`.
74 original_extension: :obj:`str` (optional)
75 The filename extension of every files in the dataset.
76 If `None`, will try to use `self.original_extension`.
78 Returns
79 -------
80 object
81 The loaded data (normally :py:class:`numpy.ndarray`).
82 """
84 if original_directory is None:
85 original_directory = self.original_directory
86 if original_extension is None:
87 original_extension = self.original_extension
88 # get the path
89 path = self.make_path(
90 original_directory or "", original_extension or ""
91 )
92 return bob.io.base.load(path)
94 @property
95 def annotations(self):
96 path = self.make_path(
97 self.annotation_directory or "", self.annotation_extension or ""
98 )
99 return read_annotation_file(path, annotation_type=self.annotation_type)
102class BioFileSet(BioFile):
103 """This class defines the minimum interface of a set of database files that needs to be exported.
104 Use this class, whenever the database provides several files that belong to the same probe.
105 Each file set has an id, and a list of associated files, which are of
106 type :py:class:`bob.bio.base.database.BioFile` of the same client.
107 The file set id can be anything hashable, but needs to be unique all over the database.
109 Parameters
110 ----------
112 file_set_id : str or int
113 A unique ID that identifies the file set.
115 files : [:py:class:`bob.bio.base.database.BioFile`]
116 A non-empty list of BioFile objects that should be stored inside this file.
117 All files of that list need to have the same client ID.
118 """
120 def __init__(self, file_set_id, files, path=None, **kwargs):
121 # don't accept empty file lists
122 assert len(files), "Cannot create an empty BioFileSet"
124 # call base class constructor
125 super(BioFileSet, self).__init__(
126 files[0].client_id,
127 "+".join(f.path for f in files) if path is None else path,
128 file_set_id,
129 **kwargs,
130 )
132 # check that all files come from the same client
133 assert all(f.client_id == self.client_id for f in files)
135 # The list of files contained in this set
136 self.files = files
138 def __lt__(self, other):
139 """Defines an order between file sets by using the order of the file set ids."""
140 # compare two BioFile set objects by comparing their IDs
141 return self.id < other.id