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_embeddings.py

@@ -40,7 +40,7 @@ def test_idiap_inceptionv2_msceleb_memory_demanding():
 
     reference = bob.io.base.load(
         pkg_resources.resource_filename(
-            "bob.bio.face.test", "data/inception_resnet_v2_rgb.hdf5"
+            "bob.bio.face.test", "data/inception_resnet_v2_msceleb_rgb.hdf5"
         )
     )
     np.random.seed(10)

bob/bio/face/test/test_scripts.py

@@ -4,36 +4,45 @@ import tempfile
 import shutil
 import os
 
+
 def test_display_annotations():
 
     from bob.bio.face.script.display_face_annotations import display_face_annotations
+
     try:
         tmp_dir = tempfile.mkdtemp(prefix="bobtest_")
         annotations_dir = pkg_resources.resource_filename(
-            "bob.bio.face.test",
-            "data/annotations/"
+            "bob.bio.face.test", "data/annotations/"
         )
         runner = CliRunner()
         result = runner.invoke(
             display_face_annotations,
             args=(
-                '--database', 'dummy',
-                '--groups', 'world', '--groups', 'dev',
-                '--annotations-dir', annotations_dir,
-                '--output-dir', tmp_dir, '--keep-all',
-                '--self-test',
-            )
+                "--database",
+                "dummy",
+                "--groups",
+                "train",
+                "--groups",
+                "dev",
+                "--annotations-dir",
+                annotations_dir,
+                "--output-dir",
+                tmp_dir,
+                "--keep-all",
+                "--self-test",
+            ),
         )
         assertion_error_message = (
-            'Command exited with this output: `{}\' \n'
-            'If the output is empty, you can run this script locally to see '
-            'what is wrong:\n'
-            '$ bob bio display_face_annotations -vvv -d dummy -g world -g dev -a ./annotations/ -o /tmp/temp_annotated'
-            ''.format(result.output))
+            "Command exited with this output: `{}' \n"
+            "If the output is empty, you can run this script locally to see "
+            "what is wrong:\n"
+            "$ bob bio display-face-annotations -vvv -d dummy -g train -g dev -a ./annotations/ -o /tmp/temp_annotated"
+            "".format(result.output)
+        )
         assert result.exit_code == 0, assertion_error_message
 
         # Checks if an annotated sample exists
-        sample_1_path = os.path.join(tmp_dir, "s1","1.png")
+        sample_1_path = os.path.join(tmp_dir, "s1", "1.png")
         assertion_error_message = "File '{}' not created.".format(sample_1_path)
         assert os.path.isfile(sample_1_path), assertion_error_message
 

doc/implemented.rst

@@ -20,6 +20,7 @@ Databases
    bob.bio.face.database.LFWBioDatabase
    bob.bio.face.database.MultipieBioDatabase
    bob.bio.face.database.FargoBioDatabase
+   bob.bio.face.database.meds.MEDSDatabase
 
 
 Face Image Annotators