diff --git a/bob/bio/base/database/database.py b/bob/bio/base/database/database.py
index 7d0445eaa6c35c2ed52f03fc85d8736b38802621..7620ef507ed1008c7224af6f04074883106d933f 100644
--- a/bob/bio/base/database/database.py
+++ b/bob/bio/base/database/database.py
@@ -151,9 +151,6 @@ class BioDatabase(six.with_metaclass(abc.ABCMeta, bob.db.base.Database)):
return "%s(%s)" % (str(self.__class__), params)
- ###########################################################################
- # Helper functions that you might want to use in derived classes
- ###########################################################################
def replace_directories(self, replacements=None):
"""This helper function replaces the ``original_directory`` and the ``annotation_directory`` of the database with the directories read from the given replacement file.
@@ -203,27 +200,9 @@ class BioDatabase(six.with_metaclass(abc.ABCMeta, bob.db.base.Database)):
except AttributeError:
pass
- def sort(self, files):
- """sort(files) -> sorted
-
- Returns a sorted version of the given list of File's (or other structures that define an 'id' data member).
- The files will be sorted according to their id, and duplicate entries will be removed.
-
- **Parameters:**
-
- files : [:py:class:`bob.bio.base.database.BioFile`]
- The list of files to be uniquified and sorted.
-
- **Returns:**
-
- sorted : [:py:class:`bob.bio.base.database.BioFile`]
- The sorted list of files, with duplicate `BioFile.id`\s being removed.
- """
- # sort files using their sort function
- sorted_files = sorted(files)
- # remove duplicates
- return [f for i, f in enumerate(sorted_files) if not i or sorted_files[i - 1].id != f.id]
-
+ ###########################################################################
+ # Helper functions that you might want to use in derived classes
+ ###########################################################################
def uses_probe_file_sets(self, protocol=None):
"""Defines if, for the current protocol, the database uses several probe files to generate a score.
Returns True if the given protocol specifies file sets for probes, instead of a single probe file.
@@ -258,31 +237,6 @@ class BioDatabase(six.with_metaclass(abc.ABCMeta, bob.db.base.Database)):
files_by_clients.append(client_files[client])
return files_by_clients
- def annotations(self, file):
- """
- Returns the annotations for the given File object, if available.
- It uses `bob.db.base.read_annotation_file` to load the annotations.
-
- **Parameters:**
-
- file : :py:class:`bob.bio.base.database.BioFile`
- The file for which annotations should be returned.
-
- **Returns:**
-
- annots : dict or None
- The annotations for the file, if available.
- """
- if self.annotation_directory:
- try:
- from bob.db.base.annotations import read_annotation_file
- annotation_path = os.path.join(self.annotation_directory, file.path + self.annotation_extension)
- return read_annotation_file(annotation_path, self.annotation_type)
- except ImportError as e:
- raise NotImplementedError(str(e) + " Annotations are not read." % e)
-
- return None
-
def file_names(self, files, directory, extension):
"""file_names(files, directory, extension) -> paths
@@ -313,26 +267,6 @@ class BioDatabase(six.with_metaclass(abc.ABCMeta, bob.db.base.Database)):
# List of files, do not remove duplicates
return [f.make_path(directory, extension) for f in files]
- def original_file_names(self, files):
- """original_file_names(files) -> paths
-
- Returns the full path of the original data of the given File objects.
-
- **Parameters:**
-
- files : [:py:class:`bob.bio.base.database.BioFile`]
- The list of file object to retrieve the original data file names for.
-
- **Returns:**
-
- paths : [str] or [[str]]
- The paths extracted for the files, in the same order.
- If this database provides file sets, a list of lists of file names is returned, one sub-list for each file set.
- """
- assert self.original_directory is not None
- assert self.original_extension is not None
- return self.file_names(files, self.original_directory, self.original_extension)
-
#################################################################
###### Methods to be overwritten by derived classes #############
#################################################################
@@ -356,23 +290,6 @@ class BioDatabase(six.with_metaclass(abc.ABCMeta, bob.db.base.Database)):
"""
raise NotImplementedError("Please implement this function in derived classes")
- def model_ids(self, groups='dev'):
- """model_ids(group = 'dev') -> ids
-
- Returns a list of model ids for the given group, respecting the current protocol.
-
- **Parameters:**
-
- group : one of ``('dev', 'eval')``
- The group to get the model ids for.
-
- **Returns:**
-
- ids : [int] or [str]
- The list of (unique) model ids for models of the given group.
- """
- return sorted(self.model_ids_with_protocol(groups=groups, protocol=self.protocol))
-
@abc.abstractmethod
def objects(self, groups=None, protocol=None, purposes=None, model_ids=None, **kwargs):
"""This function returns lists of File objects, which fulfill the given restrictions.
@@ -401,31 +318,44 @@ class BioDatabase(six.with_metaclass(abc.ABCMeta, bob.db.base.Database)):
"""
raise NotImplementedError("This function must be implemented in your derived class.")
+ @abc.abstractmethod
+ def annotations(self, file):
+ """
+ Returns the annotations for the given File object, if available.
+ It uses `bob.db.base.read_annotation_file` to load the annotations.
+
+ **Parameters:**
+
+ file : :py:class:`bob.bio.base.database.BioFile`
+ The file for which annotations should be returned.
+
+ **Returns:**
+
+ annots : dict or None
+ The annotations for the file, if available.
+ """
+ raise NotImplementedError("This function must be implemented in your derived class.")
+
#################################################################
######### Methods to provide common functionality ###############
#################################################################
- def original_file_name(self, file):
- """This function returns the original file name for the given File object.
+ def model_ids(self, groups='dev'):
+ """model_ids(group = 'dev') -> ids
- Keyword parameters:
+ Returns a list of model ids for the given group, respecting the current protocol.
+
+ **Parameters:**
- file : :py:class:`bob.bio.base.database.BioFile` or a derivative
- The File objects for which the file name should be retrieved
+ group : one of ``('dev', 'eval')``
+ The group to get the model ids for.
- Return value : str
- The original file name for the given File object
+ **Returns:**
+
+ ids : [int] or [str]
+ The list of (unique) model ids for models of the given group.
"""
- # check if directory is set
- if not self.original_directory or not self.original_extension:
- raise ValueError(
- "The original_directory and/or the original_extension were not specified in the constructor.")
- # extract file name
- file_name = file.make_path(self.original_directory, self.original_extension)
- if not self.check_existence or os.path.exists(file_name):
- return file_name
- raise ValueError("The file '%s' was not found. Please check the original directory '%s' and extension '%s'?" % (
- file_name, self.original_directory, self.original_extension))
+ return sorted(self.model_ids_with_protocol(groups=groups, protocol=self.protocol))
def all_files(self, groups=None):
"""all_files(groups=None) -> files
diff --git a/bob/bio/base/test/dummy/database.py b/bob/bio/base/test/dummy/database.py
index e8cfac92044055f84a343cae0a226b92a9fb94f8..9c84e23bdbb79f0caf9bd26d15cd8060419fb665 100644
--- a/bob/bio/base/test/dummy/database.py
+++ b/bob/bio/base/test/dummy/database.py
@@ -16,16 +16,16 @@ class DummyDatabase(ZTBioDatabase):
models_depend_on_protocol=False
)
import bob.db.atnt
- self.__db = bob.db.atnt.Database()
+ self._db = bob.db.atnt.Database()
def _make_bio(self, files):
return [BioFile(client_id=f.client_id, path=f.path, file_id=f.id) for f in files]
def model_ids_with_protocol(self, groups=None, protocol=None, **kwargs):
- return self.__db.model_ids(groups, protocol)
+ return self._db.model_ids(groups, protocol)
def objects(self, groups=None, protocol=None, purposes=None, model_ids=None, **kwargs):
- return self._make_bio(self.__db.objects(model_ids, groups, purposes, protocol, **kwargs))
+ return self._make_bio(self._db.objects(model_ids, groups, purposes, protocol, **kwargs))
def tobjects(self, groups=None, protocol=None, model_ids=None, **kwargs):
return []
@@ -34,7 +34,7 @@ class DummyDatabase(ZTBioDatabase):
return []
def tmodel_ids_with_protocol(self, protocol=None, groups=None, **kwargs):
- return self.__db.model_ids(groups)
+ return self._db.model_ids(groups)
def t_enroll_files(self, t_model_id, group='dev'):
return self.enroll_files(t_model_id, group)
@@ -42,4 +42,8 @@ class DummyDatabase(ZTBioDatabase):
def z_probe_files(self, group='dev'):
return self.probe_files(None, group)
+ def annotations(self, file):
+ return None
+
+
database = DummyDatabase()
diff --git a/bob/bio/base/test/dummy/fileset.py b/bob/bio/base/test/dummy/fileset.py
index 4f2c6461b09b5bd15b20975394848cc4918fa288..0d2a7faf489c369e627fd82921e7a8689c0e2639 100644
--- a/bob/bio/base/test/dummy/fileset.py
+++ b/bob/bio/base/test/dummy/fileset.py
@@ -15,7 +15,7 @@ class DummyDatabase(ZTBioDatabase):
models_depend_on_protocol=False
)
import bob.db.atnt
- self.__db = bob.db.atnt.Database()
+ self._db = bob.db.atnt.Database()
def uses_probe_file_sets(self):
return True
@@ -31,10 +31,10 @@ class DummyDatabase(ZTBioDatabase):
return file_sets
def model_ids_with_protocol(self, groups=None, protocol=None, **kwargs):
- return self.__db.model_ids(groups, protocol)
+ return self._db.model_ids(groups, protocol)
def objects(self, groups=None, protocol=None, purposes=None, model_ids=None, **kwargs):
- return self._make_bio(self.__db.objects(model_ids, groups, purposes, protocol, **kwargs))
+ return self._make_bio(self._db.objects(model_ids, groups, purposes, protocol, **kwargs))
def tobjects(self, groups=None, protocol=None, model_ids=None, **kwargs):
return []
@@ -43,7 +43,7 @@ class DummyDatabase(ZTBioDatabase):
return []
def tmodel_ids_with_protocol(self, protocol=None, groups=None, **kwargs):
- return self.__db.model_ids(groups)
+ return self._db.model_ids(groups)
def t_enroll_files(self, t_model_id, group='dev'):
return self.enroll_files(t_model_id, group)
@@ -54,4 +54,8 @@ class DummyDatabase(ZTBioDatabase):
def z_probe_file_sets(self, group='dev'):
return self.probe_file_sets(None, group)
+ def annotations(self, file):
+ return None
+
+
database = DummyDatabase()
diff --git a/bob/bio/base/test/dummy/preprocessor.py b/bob/bio/base/test/dummy/preprocessor.py
index fd32e3ce9776efa53e1b638070688b866094b376..7ccfcdcb7bd60750203bcf883b4d38ed1b973cb4 100644
--- a/bob/bio/base/test/dummy/preprocessor.py
+++ b/bob/bio/base/test/dummy/preprocessor.py
@@ -1,5 +1,6 @@
from bob.bio.base.preprocessor import Preprocessor
+
class DummyPreprocessor (Preprocessor):
def __init__(self, return_none=False, **kwargs):
Preprocessor.__init__(self)
@@ -11,4 +12,5 @@ class DummyPreprocessor (Preprocessor):
return None
return data
+
preprocessor = DummyPreprocessor()