makes the annotations method implementation mandatory

bob/bio/base/database/database.py

@@ -151,6 +151,55 @@ class BioDatabase(six.with_metaclass(abc.ABCMeta, bob.db.base.Database)):
 
         return "%s(%s)" % (str(self.__class__), params)
 
+    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.
+
+        This function is provided for convenience, so that the database configuration files do not need to be modified.
+        Instead, this function uses the given dictionary of replacements to change the original directory and the original extension (if given).
+
+        The given ``replacements`` can be of type ``dict``, including all replacements, or a file name (as a ``str``), in which case the file is read.
+        The structure of the file should be:
+
+        .. code-block:: text
+
+           # Comments starting with # and empty lines are ignored
+
+           [YOUR_..._DATA_DIRECTORY] = /path/to/your/data
+           [YOUR_..._ANNOTATION_DIRECTORY] = /path/to/your/annotations
+
+        If no annotation files are available (e.g. when they are stored inside the ``database``), the annotation directory can be left out.
+
+        **Parameters:**
+
+        replacements : dict or str
+          A dictionary with replacements, or a name of a file to read the dictionary from.
+          If the file name does not exist, no directories are replaced.
+        """
+        if replacements is None:
+            return
+        if isinstance(replacements, str):
+            if not os.path.exists(replacements):
+                return
+            # Open the database replacement file and reads its content
+            with open(replacements) as f:
+                replacements = {}
+                for line in f:
+                    if line.strip() and not line.startswith("#"):
+                        splits = line.split("=")
+                        assert len(splits) == 2
+                        replacements[splits[0].strip()] = splits[1].strip()
+
+        assert isinstance(replacements, dict)
+
+        if self.original_directory in replacements:
+            self.original_directory = replacements[self.original_directory]
+
+        try:
+            if self.annotation_directory in replacements:
+                self.annotation_directory = replacements[self.annotation_directory]
+        except AttributeError:
+            pass
+
     ###########################################################################
     # Helper functions that you might want to use in derived classes
     ###########################################################################
@@ -188,31 +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
 
@@ -266,23 +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.
@@ -311,10 +318,45 @@ 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 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))
+
     def all_files(self, groups=None):
         """all_files(groups=None) -> files
 

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()

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()

bob/bio/base/test/dummy/preprocessor.py

 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()