Merge branch 'annotations' into 'master'

Sample Loaders able to handle certain type of annotations...

See merge request !81

MANIFEST.in

 include README.rst bootstrap-buildout.py buildout.cfg develop.cfg LICENSE version.txt requirements.txt
 recursive-include doc *.py *.rst
-recursive-include bob/bio/face/test/data *.hdf5 *.jpg *.pos *.png *.json
+recursive-include bob/bio/face/test/data *.hdf5 *.jpg *.pos *.png *.json *.tar.gz

bob/bio/face/database/__init__.py

@@ -12,13 +12,13 @@ from .multipie import MultipieBioDatabase
 from .ijbc import IJBCBioDatabase
 from .replaymobile import ReplayMobileBioDatabase
 from .fargo import FargoBioDatabase
-
+from .meds import MEDSDatabase
 
 # gets sphinx autodoc done right - don't remove it
 
 
 def __appropriate__(*args):
-  """Says object was actually declared here, and not in the import module.
+    """Says object was actually declared here, and not in the import module.
   Fixing sphinx warnings of not being able to find classes, when path is shortened.
   Parameters:
 
@@ -28,20 +28,22 @@ def __appropriate__(*args):
   <https://github.com/sphinx-doc/sphinx/issues/3048>`
   """
 
-  for obj in args:
-    obj.__module__ = __name__
+    for obj in args:
+        obj.__module__ = __name__
+
 
 __appropriate__(
-  FaceBioFile,
-  MobioBioDatabase,
-  ReplayBioDatabase,
-  AtntBioDatabase,
-  GBUBioDatabase,
-  ARFaceBioDatabase,
-  LFWBioDatabase,
-  MultipieBioDatabase,
-  IJBCBioDatabase,
-  ReplayMobileBioDatabase,
-  FargoBioDatabase
+    FaceBioFile,
+    MobioBioDatabase,
+    ReplayBioDatabase,
+    AtntBioDatabase,
+    GBUBioDatabase,
+    ARFaceBioDatabase,
+    LFWBioDatabase,
+    MultipieBioDatabase,
+    IJBCBioDatabase,
+    ReplayMobileBioDatabase,
+    FargoBioDatabase,
+    MEDSDatabase,
 )
-__all__ = [_ for _ in dir() if not _.startswith('_')]
+__all__ = [_ for _ in dir() if not _.startswith("_")]

bob/bio/face/database/meds.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# Tiago de Freitas Pereira <tiago.pereira@idiap.ch>
+
+"""
+  MEDS database implementation 
+"""
+
+from bob.bio.base.database import (
+    CSVDatasetDevEval,
+    CSVDatasetDevEvalZTNorm,
+    CSVToSampleLoader,
+)
+from bob.extension import rc
+from bob.extension.download import get_file
+import bob.io.base
+from bob.bio.face.database.sample_loaders import eyes_annotations_loader
+import os
+
+
+cache_subdir = "datasets"
+filename = "meds.tar.gz"
+dataset_protocol_path = os.path.join(
+    os.path.expanduser("~"), "bob_data", cache_subdir, filename
+)
+
+
+class MEDSDatabase(CSVDatasetDevEvalZTNorm):
+    """
+    The MEDS-II (Multiple Encounter Data Set II) database interface
+
+    .. warning::
+        Use the command below to set the path of the real data::
+
+            $ bob config set bob.db.meds.directory [PATH-TO-MEDS-DATA]
+
+    Parameters
+    ----------
+
+    protocol: str
+        One of the database protocols. Options are `verification_fold1`, `verification_fold2` and `verification_fold3`
+
+    """
+
+    def __init__(self, protocol):
+
+        # Downloading model if not exists
+        urls = [
+            "https://www.idiap.ch/software/bob/databases/latest/meds.tar.gz",
+            "http://www.idiap.ch/software/bob/databases/latest/meds.tar.gz",
+        ]
+        get_file(filename, urls)
+
+        self.annotation_type = ("eyes-center",)
+        self.fixed_positions = None
+
+        database = CSVDatasetDevEval(
+            dataset_protocol_path,
+            protocol,
+            csv_to_sample_loader=CSVToSampleLoader(
+                data_loader=bob.io.base.load,
+                metadata_loader=eyes_annotations_loader,
+                dataset_original_directory=rc["bob.db.meds.directory"]
+                if rc["bob.db.meds.directory"]
+                else "",
+                extension=".jpg",
+            ),
+        )
+
+        super().__init__(database)

bob/bio/face/database/sample_loaders.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+
+"""  Sample and Metatada loaders"""
+
+
+def eyes_annotations_loader(row, header=None):
+    """
+    Convert  leye_x, leye_y, reye_x, reye_y attributes to `annotations = (leye, reye)`
+    """
+
+    def find_attribute(attribute):
+        for i, a in enumerate(header):
+            if a == attribute:
+                return i
+        else:
+            ValueError(f"Attribute not found in the dataset: {a}")
+
+    eyes = {
+        "leye": (row[find_attribute("leye_x")], row[find_attribute("leye_y")]),
+        "reye": (row[find_attribute("reye_x")], row[find_attribute("reye_y")]),
+    }
+
+    annotation = {"annotations": eyes}
+
+    return annotation

bob/bio/face/test/test_algorithms.py

@@ -96,8 +96,7 @@ def test_gabor_jet():
 
 def test_histogram():
     histogram = bob.bio.face.algorithm.Histogram(
-      distance_function = bob.math.histogram_intersection,
-      is_distance_function = False
+        distance_function=bob.math.histogram_intersection, is_distance_function=False
     )
 
     assert isinstance(histogram, bob.bio.face.algorithm.Histogram)
@@ -150,29 +149,3 @@ def test_histogram():
         )
         < 1e-5
     )
-
-
-def test_bic_jets():
-
-    similarity_function = bob.ip.gabor.Similarity("PhaseDiffPlusCanberra", bob.ip.gabor.Transform())
-
-    def gabor_jet_similarities(f1, f2):
-        """Computes the similarity vector between two Gabor graph features"""
-        assert len(f1) == len(f2)
-        return [similarity_function(f1[i], f2[i]) for i in range(len(f1))]
-
-    bic = bob.bio.base.algorithm.BIC(
-        # measure to compare two features in input space
-        comparison_function = gabor_jet_similarities,
-        # load and save functions
-        read_function = bob.ip.gabor.load_jets,
-        write_function = bob.ip.gabor.save_jets,
-        # Limit the number of training pairs
-        maximum_training_pair_count = 1000000,
-        # Dimensions of intrapersonal and extrapersonal subspaces
-        subspace_dimensions = (20, 20),
-        multiple_model_scoring = 'max'
-    )
-
-    assert isinstance(bic, bob.bio.base.algorithm.BIC)
-    assert isinstance(bic, bob.bio.base.algorithm.Algorithm)

bob/bio/face/test/test_baselines.py

@@ -42,7 +42,7 @@ def get_fake_sample_set(face_size=(160, 160), purpose="bioref"):
                 )
             ],
             key=key,
-            subject=key,
+            reference_id=key,
             references=["1"],
         )
     ]
@@ -54,7 +54,7 @@ def get_fake_samples_for_training():
     annotations = {"reye": (131, 176), "leye": (222, 170)}
 
     return [
-        Sample(x, key=str(i), subject=str(i), annotations=annotations)
+        Sample(x, key=str(i), reference_id=str(i), annotations=annotations)
         for i, x in enumerate(data)
     ]
 

bob/bio/face/test/test_databases.py

@@ -22,16 +22,23 @@ from nose.plugins.skip import SkipTest
 
 import bob.bio.base
 from bob.bio.base.test.utils import db_available
-from bob.bio.base.test.test_database_implementations import check_database, check_database_zt
+from bob.bio.base.test.test_database_implementations import (
+    check_database,
+    check_database_zt,
+)
 import bob.core
+
 logger = bob.core.log.setup("bob.bio.face")
 
 
-def _check_annotations(database, topleft=False, required=True, limit_files=None, framed=False):
+def _check_annotations(
+    database, topleft=False, required=True, limit_files=None, framed=False
+):
     database_legacy = database.database
     files = database_legacy.all_files()
     if limit_files is not None:
         import random
+
         files = random.sample(files, limit_files)
     found_none = False
 
@@ -45,118 +52,168 @@ def _check_annotations(database, topleft=False, required=True, limit_files=None,
                 # take one of the frames
                 annotations = annotations[list(annotations.keys())[0]]
             if topleft:
-                assert 'topleft' in annotations
-                assert 'bottomright' in annotations
+                assert "topleft" in annotations
+                assert "bottomright" in annotations
             else:
-                assert 'reye' in annotations
-                assert 'leye' in annotations
+                assert "reye" in annotations
+                assert "leye" in annotations
         else:
             found_none = True
     if found_none:
         logger.warn("Some annotations were None for {}".format(database_legacy.name))
 
 
-@db_available('arface')
+@db_available("arface")
 def test_arface():
     database = bob.bio.base.load_resource(
-        'arface', 'database', preferred_package='bob.bio.face')
+        "arface", "database", preferred_package="bob.bio.face"
+    )
     try:
-        check_database(database, groups=('dev', 'eval'))
+        check_database(database, groups=("dev", "eval"))
     except IOError as e:
         raise SkipTest(
-            "The database could not queried; probably the db.sql3 file is missing. Here is the error: '%s'" % e)
+            "The database could not queried; probably the db.sql3 file is missing. Here is the error: '%s'"
+            % e
+        )
     try:
         _check_annotations(database)
     except IOError as e:
         raise SkipTest(
-            "The annotations could not be queried; probably the annotation files are missing. Here is the error: '%s'" % e)
+            "The annotations could not be queried; probably the annotation files are missing. Here is the error: '%s'"
+            % e
+        )
 
 
-@db_available('atnt')
+@db_available("atnt")
 def test_atnt():
     database = bob.bio.base.load_resource(
-        'atnt', 'database', preferred_package='bob.bio.face')
+        "atnt", "database", preferred_package="bob.bio.face"
+    )
     try:
         check_database(database)
     except IOError as e:
         raise SkipTest(
-            "The database could not queried; probably the db.sql3 file is missing. Here is the error: '%s'" % e)
+            "The database could not queried; probably the db.sql3 file is missing. Here is the error: '%s'"
+            % e
+        )
 
 
-@db_available('gbu')
+@db_available("gbu")
 def test_gbu():
     database = bob.bio.base.load_resource(
-        'gbu', 'database', preferred_package='bob.bio.face')
+        "gbu", "database", preferred_package="bob.bio.face"
+    )
     try:
         check_database(database, models_depend=True)
-        check_database(database, protocol='Bad', models_depend=True)
-        check_database(database, protocol='Ugly', models_depend=True)
+        check_database(database, protocol="Bad", models_depend=True)
+        check_database(database, protocol="Ugly", models_depend=True)
     except IOError as e:
         raise SkipTest(
-            "The database could not queried; probably the db.sql3 file is missing. Here is the error: '%s'" % e)
+            "The database could not queried; probably the db.sql3 file is missing. Here is the error: '%s'"
+            % e
+        )
     try:
         _check_annotations(database, limit_files=1000)
     except IOError as e:
         raise SkipTest(
-            "The annotations could not be queried; probably the annotation files are missing. Here is the error: '%s'" % e)
+            "The annotations could not be queried; probably the annotation files are missing. Here is the error: '%s'"
+            % e
+        )
 
 
-@db_available('lfw')
+@db_available("lfw")
 def test_lfw():
     database = bob.bio.base.load_resource(
-        'lfw-restricted', 'database', preferred_package='bob.bio.face')
+        "lfw-restricted", "database", preferred_package="bob.bio.face"
+    )
     try:
         check_database(database, training_depends=True, models_depend=True)
-        check_database(database, groups=('dev', 'eval'),
-                       protocol='fold1', training_depends=True, models_depend=True)
-        check_database(bob.bio.base.load_resource('lfw-unrestricted', 'database', preferred_package='bob.bio.face'),
-                       training_depends=True, models_depend=True)
+        check_database(
+            database,
+            groups=("dev", "eval"),
+            protocol="fold1",
+            training_depends=True,
+            models_depend=True,
+        )
+        check_database(
+            bob.bio.base.load_resource(
+                "lfw-unrestricted", "database", preferred_package="bob.bio.face"
+            ),
+            training_depends=True,
+            models_depend=True,
+        )
     except IOError as e:
         raise SkipTest(
-            "The database could not queried; probably the db.sql3 file is missing. Here is the error: '%s'" % e)
+            "The database could not queried; probably the db.sql3 file is missing. Here is the error: '%s'"
+            % e
+        )
     try:
         _check_annotations(database, limit_files=1000)
     except IOError as e:
         raise SkipTest(
-            "The annotations could not be queried; probably the annotation files are missing. Here is the error: '%s'" % e)
+            "The annotations could not be queried; probably the annotation files are missing. Here is the error: '%s'"
+            % e
+        )
 
 
-@db_available('mobio')
+@db_available("mobio")
 def test_mobio():
     database = bob.bio.base.load_resource(
-        'mobio-image', 'database', preferred_package='bob.bio.face')
+        "mobio-image", "database", preferred_package="bob.bio.face"
+    )
     try:
         check_database_zt(database, models_depend=True)
-        check_database_zt(database, protocol='female', models_depend=True)
-        check_database_zt(bob.bio.base.load_resource('mobio-male', 'database', preferred_package='bob.bio.face'),
-                          models_depend=True)
-        check_database_zt(bob.bio.base.load_resource('mobio-female', 'database', preferred_package='bob.bio.face'),
-                          models_depend=True)
+        check_database_zt(database, protocol="female", models_depend=True)
+        check_database_zt(
+            bob.bio.base.load_resource(
+                "mobio-male", "database", preferred_package="bob.bio.face"
+            ),
+            models_depend=True,
+        )
+        check_database_zt(
+            bob.bio.base.load_resource(
+                "mobio-female", "database", preferred_package="bob.bio.face"
+            ),
+            models_depend=True,
+        )
     except IOError as e:
         raise SkipTest(
-            "The database could not be queried; probably the db.sql3 file is missing. Here is the error: '%s'" % e)
+            "The database could not be queried; probably the db.sql3 file is missing. Here is the error: '%s'"
+            % e
+        )
 
     try:
         _check_annotations(database, limit_files=1000)
     except IOError as e:
         raise SkipTest(
-            "The annotations could not be queried; probably the annotation files are missing. Here is the error: '%s'" % e)
+            "The annotations could not be queried; probably the annotation files are missing. Here is the error: '%s'"
+            % e
+        )
 
 
-@db_available('multipie')
+@db_available("multipie")
 def test_multipie():
     database = bob.bio.base.load_resource(
-        'multipie', 'database', preferred_package='bob.bio.face')
+        "multipie", "database", preferred_package="bob.bio.face"
+    )
     try:
         check_database_zt(database, training_depends=True)
-        check_database_zt(bob.bio.base.load_resource('multipie-pose', 'database', preferred_package='bob.bio.face'),
-                          training_depends=True)
+        check_database_zt(
+            bob.bio.base.load_resource(
+                "multipie-pose", "database", preferred_package="bob.bio.face"
+            ),
+            training_depends=True,
+        )
     except IOError as e:
         raise SkipTest(
-            "The database could not queried; probably the db.sql3 file is missing. Here is the error: '%s'" % e)
+            "The database could not queried; probably the db.sql3 file is missing. Here is the error: '%s'"
+            % e
+        )
     except ValueError as e:
         raise SkipTest(
-            "The database could not queried; probably the protocol is missing inside the db.sql3 file. Here is the error: '%s'" % e)
+            "The database could not queried; probably the protocol is missing inside the db.sql3 file. Here is the error: '%s'"
+            % e
+        )
 
     try:
         if database.database.annotation_directory is None:
@@ -164,94 +221,136 @@ def test_multipie():
         _check_annotations(database)
     except IOError as e:
         raise SkipTest(
-            "The annotations could not be queried; probably the annotation files are missing. Here is the error: '%s'" % e)
+            "The annotations could not be queried; probably the annotation files are missing. Here is the error: '%s'"
+            % e
+        )
 
 
-@db_available('replay')
+@db_available("replay")
 def test_replay_licit():
     database = bob.bio.base.load_resource(
-        'replay-img-licit', 'database', preferred_package='bob.bio.face')
+        "replay-img-licit", "database", preferred_package="bob.bio.face"
+    )
     try:
-        check_database(database, groups=('dev', 'eval'))
+        check_database(database, groups=("dev", "eval"))
     except IOError as e:
         raise SkipTest(
-            "The database could not be queried; probably the db.sql3 file is missing. Here is the error: '%s'" % e)
+            "The database could not be queried; probably the db.sql3 file is missing. Here is the error: '%s'"
+            % e
+        )
     try:
         _check_annotations(database, topleft=True)
     except IOError as e:
         raise SkipTest(
-            "The annotations could not be queried; probably the annotation files are missing. Here is the error: '%s'" % e)
+            "The annotations could not be queried; probably the annotation files are missing. Here is the error: '%s'"
+            % e
+        )
 
 
-@db_available('replay')
+@db_available("replay")
 def test_replay_spoof():
     database = bob.bio.base.load_resource(
-        'replay-img-spoof', 'database', preferred_package='bob.bio.face')
+        "replay-img-spoof", "database", preferred_package="bob.bio.face"
+    )
     try:
-        check_database(database, groups=('dev', 'eval'))
+        check_database(database, groups=("dev", "eval"))
     except IOError as e:
         raise SkipTest(
-            "The database could not be queried; probably the db.sql3 file is missing. Here is the error: '%s'" % e)
+            "The database could not be queried; probably the db.sql3 file is missing. Here is the error: '%s'"
+            % e
+        )
     try:
         _check_annotations(database, topleft=True)
     except IOError as e:
         raise SkipTest(
-            "The annotations could not be queried; probably the annotation files are missing. Here is the error: '%s'" % e)
+            "The annotations could not be queried; probably the annotation files are missing. Here is the error: '%s'"
+            % e
+        )
 
 
-@db_available('replaymobile')
+@db_available("replaymobile")
 def test_replaymobile_licit():
     database = bob.bio.base.load_resource(
-        'replaymobile-img-licit', 'database', preferred_package='bob.bio.face')
+        "replaymobile-img-licit", "database", preferred_package="bob.bio.face"
+    )
     try:
-        check_database(database, groups=('dev', 'eval'))
+        check_database(database, groups=("dev", "eval"))
     except IOError as e:
         raise SkipTest(
-            "The database could not be queried; probably the db.sql3 file is missing. Here is the error: '%s'" % e)
+            "The database could not be queried; probably the db.sql3 file is missing. Here is the error: '%s'"
+            % e
+        )
     try:
         _check_annotations(database, topleft=True, limit_files=20)
     except IOError as e:
         raise SkipTest(
-            "The annotations could not be queried; probably the annotation files are missing. Here is the error: '%s'" % e)
+            "The annotations could not be queried; probably the annotation files are missing. Here is the error: '%s'"
+            % e
+        )
 
 
-@db_available('replaymobile')
+@db_available("replaymobile")
 def test_replaymobile_spoof():
     database = bob.bio.base.load_resource(
-        'replaymobile-img-spoof', 'database', preferred_package='bob.bio.face')
+        "replaymobile-img-spoof", "database", preferred_package="bob.bio.face"
+    )
     try:
-        check_database(database, groups=('dev', 'eval'))
+        check_database(database, groups=("dev", "eval"))
     except IOError as e:
         raise SkipTest(
-            "The database could not be queried; probably the db.sql3 file is missing. Here is the error: '%s'" % e)
+            "The database could not be queried; probably the db.sql3 file is missing. Here is the error: '%s'"
+            % e
+        )
     try:
         _check_annotations(database, topleft=True, limit_files=20)
     except IOError as e:
         raise SkipTest(
-            "The annotations could not be queried; probably the annotation files are missing. Here is the error: '%s'" % e)
+            "The annotations could not be queried; probably the annotation files are missing. Here is the error: '%s'"
+            % e
+        )
 
 
-@db_available('ijbc')
+@db_available("ijbc")
 def test_ijbc():
     database = bob.bio.base.load_resource(
-        'ijbc-11', 'database', preferred_package='bob.bio.face')
+        "ijbc-11", "database", preferred_package="bob.bio.face"
+    )
     try:
         check_database(database, models_depend=True, training_depends=True)
     except IOError as e:
-        raise SkipTest(
-            "The database could not queried; Here is the error: '%s'" % e)
+        raise SkipTest("The database could not queried; Here is the error: '%s'" % e)
     try:
         _check_annotations(database, topleft=True, limit_files=1000)
     except IOError as e:
         raise SkipTest(
-            "The annotations could not be queried; probably the annotation files are missing. Here is the error: '%s'" % e)
+            "The annotations could not be queried; probably the annotation files are missing. Here is the error: '%s'"
+            % e
+        )
 
-@db_available('fargo')
+
+@db_available("fargo")
 def test_fargo():
     database = bob.bio.base.load_resource(
-        'fargo', 'database', preferred_package='bob.bio.face')
+        "fargo", "database", preferred_package="bob.bio.face"
+    )
     try:
         check_database(database)
     except IOError as e:
-        raise SkipTest(
-            "The database could not queried; Here is the error: '%s'" % e)
+        raise SkipTest("The database could not queried; Here is the error: '%s'" % e)
+
+
+def test_meds():
+    from bob.bio.face.database import MEDSDatabase
+
+    database = MEDSDatabase("verification_fold1")
+