Fix errors on databases

bob/bio/vein/configurations/utfvp.py

@@ -17,12 +17,12 @@ You can download the raw data of the `UTFVP`_ database by following the link.
 .. include:: links.rst
 """
 
-from bob.bio.vein.database import UtfvpBioDatabase
+from bob.bio.vein.database.utfvp import Database
 
 utfvp_directory = "[YOUR_UTFVP_DIRECTORY]"
 """Value of ``~/.bob_bio_databases.txt`` for this database"""
 
-database = UtfvpBioDatabase(
+database = Database(
     original_directory = utfvp_directory,
     original_extension = '.png',
     )

bob/bio/vein/configurations/verafinger.py

@@ -15,12 +15,12 @@ the link.
 """
 
 
-from bob.bio.vein.database import VerafingerBioDatabase
+from bob.bio.vein.database.verafinger import Database
 
 verafinger_directory = "[YOUR_VERAFINGER_DIRECTORY]"
 """Value of ``~/.bob_bio_databases.txt`` for this database"""
 
-database = VerafingerBioDatabase(
+database = Database(
     original_directory = verafinger_directory,
     original_extension = '.png',
     )

bob/bio/vein/database/__init__.py

-#!/usr/bin/env python
-# vim: set fileencoding=utf-8 :
-
-from .database import VeinBioFile
-from .verafinger import VerafingerBioDatabase
-from .utfvp import UtfvpBioDatabase
-
-# gets sphinx autodoc done right - don't remove it
-__all__ = [_ for _ in dir() if not _.startswith('_')]

bob/bio/vein/database/utfvp.py

 #!/usr/bin/env python
 # vim: set fileencoding=utf-8 :
-# Tue 27 Sep 2016 16:49:05 CEST
+# Fri 04 Nov 2016 14:46:53 CET
 
-from .database import VeinBioFile
-from bob.bio.base.database import BioDatabase
+from bob.bio.base.database import BioFile, BioDatabase
 
 
-class UtfvpBioDatabase(BioDatabase):
+class File(BioFile):
+    """
+    Implements extra properties of vein files for the UTFVP Fingervein database
+
+
+    Parameters:
+
+      f (object): Low-level file (or sample) object that is kept inside
+
+    """
+
+    def __init__(self, f):
+
+        super(File, self).__init__(client_id=f.client_id, path=f.path,
+            file_id=f.id)
+        self.__f = f
+
+
+class Database(BioDatabase):
     """
     Implements verification API for querying UTFVP Fingervein database.
     """
 
     def __init__(self, **kwargs):
 
-        super(UtfvpBioDatabase, self).__init__(name='utfvp',
-            **kwargs)
+        super(Database, self).__init__(name='utfvp', **kwargs)
         from bob.db.utfvp.query import Database as LowLevelDatabase
         self.__db = LowLevelDatabase()
 
+
     def model_ids_with_protocol(self, groups=None, protocol=None, **kwargs):
         protocol = protocol if protocol is not None else self.protocol
         return self.__db.model_ids(groups=groups, protocol=protocol)
 
+
     def objects(self, groups=None, protocol=None, purposes=None,
         model_ids=None, **kwargs):
 
         retval = self.__db.objects(groups=groups, protocol=protocol,
             purposes=purposes, model_ids=model_ids, **kwargs)
-        return [VeinBioFile(client_id=f.client_id, path=f.path, file_id=f.id) for f in retval]
+
+        return [File(f) for f in retval]

bob/bio/vein/database/verafinger.py

@@ -4,12 +4,11 @@
 
 
 from bob.bio.base.database import BioFile, BioDatabase
-from bob.bio.base.database.file import BioFile
 
 
-class VerafingerBioFile(BioFile):
+class File(BioFile):
     """
-    Implements extra properties of vein files
+    Implements extra properties of vein files for the Vera Fingervein database
 
 
     Parameters:
@@ -20,52 +19,54 @@ class VerafingerBioFile(BioFile):
 
     def __init__(self, f):
 
-        super(VerafingerBioFile, self).__init__(
-            client_id=f.model_id,
-            path=f.path,
-            file_id=f.id,
-            )
-        self.f = f
+        super(File, self).__init__(client_id=f.model_id, path=f.path,
+            file_id=f.id)
+        self.__f = f
 
 
     def roi(self):
         """Returns the binary mask from the ROI annotations available"""
+        from ..preprocessor.utils import poly_to_mask
 
-        points = self.f.roi()
+        # The size of images in this database is (250, 665) pixels (h, w)
+        return poly_to_mask((250, 665), self.__f.roi())
 
 
 
-class VerafingerBioDatabase(BioDatabase):
+class Database(BioDatabase):
     """
     Implements verification API for querying Vera Fingervein database.
     """
 
     def __init__(self, **kwargs):
 
-        super(VerafingerBioDatabase, self).__init__(name='verafinger',
-            **kwargs)
+        super(Database, self).__init__(name='verafinger', **kwargs)
         from bob.db.verafinger.query import Database as LowLevelDatabase
         self.__db = LowLevelDatabase()
 
         self.low_level_group_names = ('train', 'dev')
         self.high_level_group_names = ('world', 'dev')
 
+
     def groups(self):
 
         return self.convert_names_to_highlevel(self.__db.groups(),
             self.low_level_group_names, self.high_level_group_names)
 
+
     def client_id_from_model_id(self, model_id, group='dev'):
         """Required as ``model_id != client_id`` on this database"""
 
         return self.__db.finger_name_from_model_id(model_id)
 
+
     def model_ids_with_protocol(self, groups=None, protocol=None, **kwargs):
 
         groups = self.convert_names_to_lowlevel(groups,
             self.low_level_group_names, self.high_level_group_names)
         return self.__db.model_ids(groups=groups, protocol=protocol)
 
+
     def objects(self, groups=None, protocol=None, purposes=None,
         model_ids=None, **kwargs):
 
@@ -73,4 +74,5 @@ class VerafingerBioDatabase(BioDatabase):
             self.low_level_group_names, self.high_level_group_names)
         retval = self.__db.objects(groups=groups, protocol=protocol,
             purposes=purposes, model_ids=model_ids, **kwargs)
-        return [VeinBioFile(f) for f in retval]
+
+        return [File(f) for f in retval]

doc/api.rst

@@ -15,7 +15,15 @@ which can be used for vein experiments.
 Database Interfaces
 -------------------
 
-.. automodule:: bob.bio.vein.database
+Vera Fingervein Database
+========================
+
+.. automodule:: bob.bio.vein.database.verafinger
+
+UTFVP Database
+==============
+
+.. automodule:: bob.bio.vein.database.utfvp
 
 
 Pre-processors