diff --git a/bob/bio/base/database/database.py b/bob/bio/base/database/database.py
index 4fe518172266864987031a87d092c895b2593fa8..7620ef507ed1008c7224af6f04074883106d933f 100644
--- a/bob/bio/base/database/database.py
+++ b/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
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()