Merge branch 'refactoring_2016' into 'master'

Implements the annotations

See merge request !21

README.rst

 .. vim: set fileencoding=utf-8 :
 .. Fri 19 Aug 2016 13:32:51 CEST
 
-.. image:: http://img.shields.io/badge/docs-stable-yellow.png
+.. image:: http://img.shields.io/badge/docs-stable-yellow.svg
    :target: http://pythonhosted.org/bob.bio.vein/index.html
-.. image:: http://img.shields.io/badge/docs-latest-orange.png
+.. image:: http://img.shields.io/badge/docs-latest-orange.svg
    :target: https://www.idiap.ch/software/bob/docs/latest/bob/bob.bio.vein/master/index.html
 .. image:: https://gitlab.idiap.ch/bob/bob.bio.vein/badges/v2.1.0/build.svg
    :target: https://gitlab.idiap.ch/bob/bob.bio.vein/commits/v2.1.0
@@ -44,6 +44,6 @@ development `mailing list`_.
 
 .. Place your references here:
 .. _bob: https://www.idiap.ch/software/bob
-.. _installation: https://gitlab.idiap.ch/bob/bob/wikis/Installation
+.. _installation: https://www.idiap.ch/software/bob/install
 .. _mailing list: https://groups.google.com/forum/?fromgroups#!forum/bob-devel
 .. _bob.bio.base: https://pypi.python.org/pypi/bob.bio.base

bob/bio/vein/database/utfvp.py

@@ -19,7 +19,7 @@ class File(BioFile):
     def __init__(self, f):
 
         super(File, self).__init__(client_id=f.client_id, path=f.path,
-            file_id=f.id)
+                                   file_id=f.id)
         self.__f = f
 
 
@@ -32,18 +32,19 @@ class Database(BioDatabase):
 
         super(Database, self).__init__(name='utfvp', **kwargs)
         from bob.db.utfvp.query import Database as LowLevelDatabase
-        self.__db = 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)
-
+        return self._db.model_ids(groups=groups, protocol=protocol)
 
     def objects(self, groups=None, protocol=None, purposes=None,
-        model_ids=None, **kwargs):
+                model_ids=None, **kwargs):
 
-        retval = self.__db.objects(groups=groups, protocol=protocol,
-            purposes=purposes, model_ids=model_ids, **kwargs)
+        retval = self._db.objects(groups=groups, protocol=protocol,
+                                  purposes=purposes, model_ids=model_ids, **kwargs)
 
         return [File(f) for f in retval]
+
+    def annotations(self, file):
+        return None

bob/bio/vein/database/verafinger.py

@@ -7,81 +7,77 @@ from bob.bio.base.database import BioFile, BioDatabase
 
 
 class File(BioFile):
-  """
-  Implements extra properties of vein files for the Vera Fingervein database
+    """
+    Implements extra properties of vein files for the Vera Fingervein database
 
 
-  Parameters:
+    Parameters:
 
-    f (object): Low-level file (or sample) object that is kept inside
+        f (object): Low-level file (or sample) object that is kept inside
 
-  """
+    """
 
-  def __init__(self, f):
+    def __init__(self, f):
 
-    super(File, self).__init__(client_id=f.unique_finger_name, path=f.path,
-        file_id=f.id)
-    self.__f = f
+        super(File, self).__init__(client_id=f.unique_finger_name, path=f.path,
+                                   file_id=f.id)
+        self.__f = f
 
+    def mask(self):
+        """Returns the binary mask from the ROI annotations available"""
 
-  def mask(self):
-    """Returns the binary mask from the ROI annotations available"""
+        from ..preprocessor.utils import poly_to_mask
 
-    from ..preprocessor.utils import poly_to_mask
+        # The size of images in this database is (250, 665) pixels (h, w)
+        return poly_to_mask((250, 665), 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())
+    def load(self, *args, **kwargs):
+        """(Overrides base method) Loads both image and mask"""
 
+        image = super(File, self).load(*args, **kwargs)
 
-  def load(self, *args, **kwargs):
-    """(Overrides base method) Loads both image and mask"""
-
-    image = super(File, self).load(*args, **kwargs)
-
-    return image, self.mask()
-
+        return image, self.mask()
 
 
 class Database(BioDatabase):
-  """
-  Implements verification API for querying Vera Fingervein database.
-  """
-
-  def __init__(self, **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')
+    """
+    Implements verification API for querying Vera Fingervein database.
+    """
 
+    def __init__(self, **kwargs):
 
-  def groups(self):
+        super(Database, self).__init__(name='verafinger', **kwargs)
+        from bob.db.verafinger.query import Database as LowLevelDatabase
+        self._db = LowLevelDatabase()
 
-    return self.convert_names_to_highlevel(self.__db.groups(),
-        self.low_level_group_names, self.high_level_group_names)
+        self.low_level_group_names = ('train', 'dev')
+        self.high_level_group_names = ('world', 'dev')
 
+    def groups(self):
 
-  def client_id_from_model_id(self, model_id, group='dev'):
-    """Required as ``model_id != client_id`` on this database"""
+        return self.convert_names_to_highlevel(self._db.groups(),
+                                               self.low_level_group_names, self.high_level_group_names)
 
-    return self.__db.finger_name_from_model_id(model_id)
+    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):
+    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)
+        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):
 
-  def objects(self, groups=None, protocol=None, purposes=None,
-      model_ids=None, **kwargs):
+        groups = self.convert_names_to_lowlevel(groups,
+                                                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)
 
-    groups = self.convert_names_to_lowlevel(groups,
-        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 [File(f) for f in retval]
 
-    return [File(f) for f in retval]
+    def annotations(self, file):
+            return None

doc/extra-intersphinx.txt

+python
+bob.db.base

doc/links.rst

@@ -5,12 +5,7 @@
 .. This file contains all links we use for documentation in a centralized place
 
 .. _idiap: http://www.idiap.ch
-.. _github: http://www.github.com/idiap
 .. _bob: http://www.idiap.ch/software/bob
-.. _github bug reporting system: http://github.com/bioidiap/fingervein/issues
-.. _idiap at github: http://www.github.com/bioidiap
-.. _bob's github page: http://idiap.github.com/bob
-.. _gridtk: http://github.com/idiap/gridtk
 .. _buildout: http://www.buildout.org
 .. _nist: http://www.nist.gov/itl/iad/ig/focs.cfm
 .. _pypi: http://pypi.python.org
@@ -20,7 +15,7 @@
 .. _vera fingervein: https://www.idiap.ch/dataset/vera-fingervein
 .. _utfvp: http://scs.ewi.utwente.nl/downloads/show,Finger%20Vein/
 .. _put: http://biometrics.put.poznan.pl/vein-dataset/
-.. _installation: https://gitlab.idiap.ch/bob/bob/wikis/Installation
+.. _installation: https://www.idiap.ch/software/bob/install
 .. _dependencies: https://gitlab.idiap.ch/bob/bob/wikis/Dependencies
 .. _mailing list: https://groups.google.com/forum/?fromgroups#!forum/bob-devel
 .. _bob.bio.base: https://pypi.python.org/pypi/bob.bio.base