diff --git a/bob/bio/vein/config/database/protocol_utfvp/full.py b/bob/bio/vein/config/database/protocol_utfvp/full.py
deleted file mode 100644
index 5a94135aa2a32dde74a63a7e2b6548a957d0701e..0000000000000000000000000000000000000000
--- a/bob/bio/vein/config/database/protocol_utfvp/full.py
+++ /dev/null
@@ -1,26 +0,0 @@
-# author: Yannick Dayer <yannick.dayer@idiap.ch>
-# Wed 21 Oct 2020 10:32:56 UTC+02
-
-# This is a config file for bob.bio.vein
-# It defines the database protocol to use with the Database Interface for the
-# utfvp dataset, defined at bob.db.utfvp.
-
-# It is defined as a resource in the setup file of this package.
-
-# Usage:
-# $ bob bio pipelines vanilla-biometrics <pipeline> full utfvp
-# or:
-# $ bob bio pipelines vanilla-biometrics -p <pipeline> full utfvp
-
-# The protocol resource must be specified before the database resource.
-
-
-# Available protocols are (some require the creation of your own config file):
-# '1vsall', 'full', 'fullLeftIndex', 'fullLeftMiddle', 'fullLeftRing',
-# 'fullRightIndex', 'fullRightMiddle', 'fullRightRing', 'nom', 'nomLeftIndex',
-# 'nomLeftMiddle', 'nomLeftRing', 'nomRightIndex', 'nomRightMiddle',
-# 'nomRightRing'
-
-
-protocol = 'full'
-
diff --git a/bob/bio/vein/config/database/protocol_utfvp/nom.py b/bob/bio/vein/config/database/protocol_utfvp/nom.py
deleted file mode 100644
index 415379379f8c78f84dedbfec1396865f713db0c6..0000000000000000000000000000000000000000
--- a/bob/bio/vein/config/database/protocol_utfvp/nom.py
+++ /dev/null
@@ -1,28 +0,0 @@
-# author: Yannick Dayer <yannick.dayer@idiap.ch>
-# Wed 21 Oct 2020 10:30:22 UTC+02
-
-# This is a config file for bob.bio.vein
-# It defines the database protocol to use with the Database Interface for the
-# utfvp dataset, defined at bob.db.utfvp.
-
-# It is defined as a resource in the setup file of this package.
-
-# Usage:
-# $ bob bio pipelines vanilla-biometrics <pipeline> nom utfvp
-# or:
-# $ bob bio pipelines vanilla-biometrics -p <pipeline> nom utfvp
-
-# The protocol resource must be specified before the database resource.
-
-
-# Available protocols are (some require the creation of your own config file):
-# '1vsall', 'full', 'fullLeftIndex', 'fullLeftMiddle', 'fullLeftRing',
-# 'fullRightIndex', 'fullRightMiddle', 'fullRightRing', 'nom', 'nomLeftIndex',
-# 'nomLeftMiddle', 'nomLeftRing', 'nomRightIndex', 'nomRightMiddle',
-# 'nomRightRing'
-
-
-# This will be the default protocol if none is specified.
-
-protocol = 'nom'
-
diff --git a/bob/bio/vein/config/database/protocol_utfvp/one_vs_all.py b/bob/bio/vein/config/database/protocol_utfvp/one_vs_all.py
deleted file mode 100644
index d5cc70894a888fb1425bbc502bd607de0df11e0f..0000000000000000000000000000000000000000
--- a/bob/bio/vein/config/database/protocol_utfvp/one_vs_all.py
+++ /dev/null
@@ -1,26 +0,0 @@
-# author: Yannick Dayer <yannick.dayer@idiap.ch>
-# Wed 21 Oct 2020 10:34:41 UTC+02
-
-# This is a config file for bob.bio.vein
-# It defines the database protocol to use with the Database Interface for the
-# utfvp dataset, defined at bob.db.utfvp.
-
-# It is defined as a resource in the setup file of this package.
-
-# Usage:
-# $ bob bio pipelines vanilla-biometrics <pipeline> 1vsall utfvp
-# or:
-# $ bob bio pipelines vanilla-biometrics -p <pipeline> 1vsall utfvp
-
-# The protocol resource must be specified before the database resource.
-
-
-# Available protocols are (some require the creation of your own config file):
-# '1vsall', 'full', 'fullLeftIndex', 'fullLeftMiddle', 'fullLeftRing',
-# 'fullRightIndex', 'fullRightMiddle', 'fullRightRing', 'nom', 'nomLeftIndex',
-# 'nomLeftMiddle', 'nomLeftRing', 'nomRightIndex', 'nomRightMiddle',
-# 'nomRightRing'
-
-
-protocol = 'full'
-
diff --git a/bob/bio/vein/config/database/utfvp.py b/bob/bio/vein/config/database/utfvp.py
deleted file mode 100644
index fe3a7c8fc1e93d71417ad30392e56cde60add223..0000000000000000000000000000000000000000
--- a/bob/bio/vein/config/database/utfvp.py
+++ /dev/null
@@ -1,61 +0,0 @@
-#!/usr/bin/env python
-# vim: set fileencoding=utf-8 :
-# Tue 27 Sep 2016 16:47:45 CEST
-
-"""`UTFVP`_ is a database for biometric fingervein recognition
-
-The University of Twente Finger Vascular Pattern (UTFVP) Database is made
-publically available in order to support and stimulate research efforts in the
-area of developing, testing and evaluating algorithms for vascular patter
-recognition. The University of Twente, Enschede, The Netherlands (henceforth,
-UT) owns copyright of and serves as the source for the UTFVP database, which is
-now distributed to any research group approved by the UTFVP principal
-investigator. The reference citation is [TV13]_.
-
-You can download the raw data of the `UTFVP`_ database by following the link.
-
-.. include:: links.rst
-"""
-
-from bob.extension import rc
-from bob.bio.vein.database.utfvp import Database
-from bob.bio.base.pipelines.vanilla_biometrics import DatabaseConnector
-
-import logging
-
-logger = logging.getLogger("bob.bio.vein")
-
-_utfvp_directory = rc.get("bob.db.utfvp.directory", "")
-"""Value in ``~/.bobrc`` for this dataset directory"""
-
-# Set default protocol if not given via a config file
-if "protocol" not in locals():
- logger.info("protocol not specified, using default: 'nom'")
- protocol = "nom"
-
-legacy_database = Database(
- original_directory=_utfvp_directory, original_extension=".png", protocol=protocol,
-)
-"""The :py:class:`bob.bio.base.database.BioDatabase` derivative with UTFVP settings
-"""
-
-database = DatabaseConnector(
- legacy_database, annotation_type=None, fixed_positions=None
-)
-"""
-The database interface wrapped for vanilla-biometrics
-
-.. warning::
-
- This class only provides a programmatic interface to load data in an orderly
- manner, respecting usage protocols. It does **not** contain the raw
- datafiles. You should procure those yourself.
-
-Notice that ``original_directory`` is set to ``rc[bob.db.utfvp.directory]``.
-You must make sure to set this value with
-``bob config set bob.db.utfvp.directory`` to the place where you actually
-installed the `utfvp`_ dataset, as explained in the section
-:ref:`bob.bio.vein.baselines`.
-"""
-
-logger.debug(f"Loaded database utfvp config file, using protocol '{protocol}'.")
diff --git a/bob/bio/vein/config/database/utfvp_1vsall.py b/bob/bio/vein/config/database/utfvp_1vsall.py
new file mode 100644
index 0000000000000000000000000000000000000000..bfc8b7fa08f2259aa93f39643891854146637ee9
--- /dev/null
+++ b/bob/bio/vein/config/database/utfvp_1vsall.py
@@ -0,0 +1,3 @@
+from bob.bio.vein.database.utfvp import UtfvpDatabase
+
+database = UtfvpDatabase(protocol="1vsall")
diff --git a/bob/bio/vein/config/database/utfvp_full.py b/bob/bio/vein/config/database/utfvp_full.py
new file mode 100644
index 0000000000000000000000000000000000000000..a8e01a7d77f23e71daa2980bc8ddf8e7f92402f3
--- /dev/null
+++ b/bob/bio/vein/config/database/utfvp_full.py
@@ -0,0 +1,3 @@
+from bob.bio.vein.database.utfvp import UtfvpDatabase
+
+database = UtfvpDatabase(protocol="full")
diff --git a/bob/bio/vein/config/database/utfvp_nom.py b/bob/bio/vein/config/database/utfvp_nom.py
new file mode 100644
index 0000000000000000000000000000000000000000..90a62ac4bd74f1ad075b66024bb0ebf02310afbc
--- /dev/null
+++ b/bob/bio/vein/config/database/utfvp_nom.py
@@ -0,0 +1,3 @@
+from bob.bio.vein.database.utfvp import UtfvpDatabase
+
+database = UtfvpDatabase(protocol="nom")
diff --git a/bob/bio/vein/database/utfvp.py b/bob/bio/vein/database/utfvp.py
index 8ed153abbce616ba8e41ab21fd0e7c20aa94046e..2b7552cb3883d9fb545617df766db9e78a9f1c95 100644
--- a/bob/bio/vein/database/utfvp.py
+++ b/bob/bio/vein/database/utfvp.py
@@ -1,83 +1,56 @@
#!/usr/bin/env python
# vim: set fileencoding=utf-8 :
-# Tue 27 Sep 2016 16:48:57 CEST
+# Victor <vbros@idiap.ch>
+"""
+ Utfvp database implementation
+"""
-from bob.bio.base.database import BioFile, BioDatabase
+from bob.bio.base.database import CSVDataset
+from bob.bio.base.database import CSVToSampleLoaderBiometrics
+from bob.extension import rc
+from bob.extension.download import get_file
+import bob.io.image
-from . import AnnotatedArray
-from ..preprocessor.utils import poly_to_mask
-
-class File(BioFile):
+class UtfvpDatabase(CSVDataset):
"""
- Implements extra properties of vein files for the UTFVP database
-
-
- Parameters:
-
- f (object): Low-level file (or sample) object that is kept inside
-
+ The University of Twente Finger Vascular Pattern dataset
"""
- def __init__(self, f):
-
- super(File, self).__init__(client_id=f.unique_finger_name, path=f.path,
- file_id=f.id)
- self.__f = f
-
-
- def load(self, *args, **kwargs):
- """(Overrides base method) Loads both image and mask"""
-
- image = super(File, self).load(*args, **kwargs)
- roi = self.__f.roi()
- return AnnotatedArray(image, metadata=dict(roi=roi))
-
-
-class Database(BioDatabase):
- """
- Implements verification API for querying UTFVP database.
- """
-
- def __init__(self, **kwargs):
-
- super(Database, self).__init__(name='utfvp', **kwargs)
- from bob.db.utfvp.query import Database as LowLevelDatabase
- self._db = LowLevelDatabase()
-
- self.low_level_group_names = ('train', 'dev', 'eval')
- self.high_level_group_names = ('world', 'dev', 'eval')
-
- 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):
-
- 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]
-
-
- def annotations(self, file):
- return None
+ def __init__(self, protocol):
+ # Downloading model if not exists
+ urls = UtfvpDatabase.urls()
+ filename = get_file(
+ "utfvp_csv.tar.gz",
+ urls,
+ file_hash="0b22a4ea6a78d54879dc3d866a22108b7513d169cd5c1bceb044854a871f200a",
+ )
+
+ super().__init__(
+ name="utfvp",
+ dataset_protocol_path=filename,
+ protocol=protocol,
+ csv_to_sample_loader=CSVToSampleLoaderBiometrics(
+ data_loader=bob.io.image.load,
+ dataset_original_directory=rc.get(
+ "bob.bio.vein.utfvp.directory", ""
+ ),
+ extension='',
+ reference_id_equal_subject_id=False
+ ),
+ allow_scoring_with_all_biometric_references=True,
+ )
+
+ @staticmethod
+ def protocols():
+ # TODO: Until we have (if we have) a function that dumps the protocols, let's use this one.
+ return ["nom", "full", "1vsall",
+ "nomLeftRing", "nomRightRing", "nomLeftMiddle", "nomRightMiddle", "nomLeftIndex", "nomRightIndex",
+ "fullLeftRing", "fullRightRing", "fullLeftMiddle", "fullRightMiddle", "fullLeftIndex", "fullRightIndex"]
+
+ @staticmethod
+ def urls():
+ return ["https://www.idiap.ch/software/bob/databases/latest/utfvp_csv-0b22a4ea.tar.gz",
+ "http://www.idiap.ch/software/bob/databases/latest/utfvp_csv-0b22a4ea.tar.gz",
+ ]
diff --git a/bob/bio/vein/tests/test_databases.py b/bob/bio/vein/tests/test_databases.py
index d665d2710d2c4a1b8589d9155b546a106b23be27..7e07010412fe80601a8d2085521fe28a371ccaef 100644
--- a/bob/bio/vein/tests/test_databases.py
+++ b/bob/bio/vein/tests/test_databases.py
@@ -7,27 +7,154 @@ 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
+import os
+from bob.extension.download import get_file
-@db_available('utfvp')
def test_utfvp():
- module = bob.bio.base.load_resource('utfvp', 'config',
- preferred_package='bob.bio.vein')
+ from bob.bio.vein.database.utfvp import UtfvpDatabase
+
+ # Getting the absolute path
+ urls = UtfvpDatabase.urls()
+ filename = get_file("utfvp_csv.tar.gz", urls)
+
+ # Removing the file before the test
try:
- check_database(module.database, protocol='nomLeftIndex', 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)
+ os.remove(filename)
+ except Exception:
+ pass
+
+ N_SUBJECTS, N_FINGERS, N_SESSIONS = 60, 6, 4
+ # nom
+ nom_parameters = {'N_train': 10,
+ 'N_dev': 18,
+ 'N_eval': 32,
+ 'N_session': N_SESSIONS // 2,
+ 'N_session_training': N_SESSIONS,
+ 'N_fingers': 6,
+ 'N_fingers_training': 6,
+ }
+ # full
+ full_parameters = {'N_train': 0,
+ 'N_dev': N_SUBJECTS,
+ 'N_eval': 0,
+ 'N_session': N_SESSIONS,
+ 'N_fingers': 6,
+ }
+
+ # 1vsall
+ onevsall_parameters = {'N_train': 35,
+ 'N_dev': 65,
+ 'N_eval': 0,
+ 'N_session': N_SESSIONS,
+ 'N_session_training': N_SESSIONS,
+ 'N_fingers': 5,
+ 'N_fingers_training': 1,
+ }
+ # subnom
+ subnom_parameters = {'N_train': 10,
+ 'N_dev': 18,
+ 'N_eval': 32,
+ 'N_session': N_SESSIONS // 2,
+ 'N_session_training': N_SESSIONS,
+ 'N_fingers': 1,
+ 'N_fingers_training': 1,
+ }
+
+ # subfull
+ subfull_parameters = {'N_train': 0,
+ 'N_dev': N_SUBJECTS,
+ 'N_eval': 0,
+ 'N_session': N_SESSIONS,
+ 'N_fingers': 1,
+ }
+
+ protocols_parameters = {'nom': nom_parameters,
+ 'full': full_parameters,
+ '1vsall': onevsall_parameters,
+ 'subnom': subnom_parameters,
+ 'subfull': subfull_parameters,
+ }
+
+ def _check_protocol(p, parameters, train=False, eval=False):
+ database = UtfvpDatabase(protocol=p)
+
+ if train:
+ assert len(database.background_model_samples()) == \
+ parameters['N_train'] * parameters['N_fingers_training'] * parameters['N_session_training']
+
+ assert len(database.references(group="dev")) == \
+ parameters['N_dev'] * parameters['N_fingers'] * parameters['N_session']
+ assert len(database.probes(group="dev")) == \
+ parameters['N_dev'] * parameters['N_fingers'] * parameters['N_session']
+
+ if eval:
+ assert len(database.references(group="eval")) == \
+ parameters['N_eval'] * parameters['N_fingers'] * parameters['N_session']
+ assert len(database.probes(group="eval")) == \
+ parameters['N_eval'] * parameters['N_fingers'] * parameters['N_session']
+
+ return p
+
+ checked_protocols = []
+
+ checked_protocols.append(
+ _check_protocol("nom", protocols_parameters['nom'], train=True, eval=True)
+ )
+ checked_protocols.append(
+ _check_protocol("full", protocols_parameters['full'], train=False, eval=False)
+ )
+ checked_protocols.append(
+ _check_protocol("1vsall", protocols_parameters['1vsall'], train=True, eval=False)
+ )
+ checked_protocols.append(
+ _check_protocol("nomLeftIndex", protocols_parameters['subnom'], train=True, eval=True)
+ )
+ checked_protocols.append(
+ _check_protocol("nomLeftMiddle", protocols_parameters['subnom'], train=True, eval=True)
+ )
+ checked_protocols.append(
+ _check_protocol("nomLeftRing", protocols_parameters['subnom'], train=True, eval=True)
+ )
+ checked_protocols.append(
+ _check_protocol("nomRightIndex", protocols_parameters['subnom'], train=True, eval=True)
+ )
+ checked_protocols.append(
+ _check_protocol("nomRightMiddle", protocols_parameters['subnom'], train=True, eval=True)
+ )
+ checked_protocols.append(
+ _check_protocol("nomRightRing", protocols_parameters['subnom'], train=True, eval=True)
+ )
+ checked_protocols.append(
+ _check_protocol("fullLeftIndex", protocols_parameters['subfull'], train=False, eval=False)
+ )
+ checked_protocols.append(
+ _check_protocol("fullLeftMiddle", protocols_parameters['subfull'], train=False, eval=False)
+ )
+ checked_protocols.append(
+ _check_protocol("fullLeftRing", protocols_parameters['subfull'], train=False, eval=False)
+ )
+ checked_protocols.append(
+ _check_protocol("fullRightIndex", protocols_parameters['subfull'], train=False, eval=False)
+ )
+ checked_protocols.append(
+ _check_protocol("fullRightMiddle", protocols_parameters['subfull'], train=False, eval=False)
+ )
+ checked_protocols.append(
+ _check_protocol("fullRightRing", protocols_parameters['subfull'], train=False, eval=False)
+ )
+
+ for p in UtfvpDatabase.protocols():
+ assert p in checked_protocols, "Protocol {} untested".format(p)
@db_available('verafinger')
def test_verafinger():
module = bob.bio.base.load_resource('verafinger', 'config',
- preferred_package='bob.bio.vein')
+ preferred_package='bob.bio.vein')
try:
check_database(module.database, protocol='Fifty', groups=('dev',
- 'eval'))
+ '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)
@@ -36,7 +163,7 @@ def test_verafinger():
@db_available('fv3d')
def test_fv3d():
module = bob.bio.base.load_resource('fv3d', 'config',
- preferred_package='bob.bio.vein')
+ preferred_package='bob.bio.vein')
try:
check_database(module.database, protocol='central', groups=('dev',))
except IOError as e:
@@ -47,7 +174,7 @@ def test_fv3d():
@db_available('putvein')
def test_putvein():
module = bob.bio.base.load_resource('putvein', 'config',
- preferred_package='bob.bio.vein')
+ preferred_package='bob.bio.vein')
try:
check_database(module.database, protocol='wrist-LR_1', groups=('dev',))
except IOError as e:
diff --git a/setup.py b/setup.py
index fbbe5a436ac65f84cedbffc656f40a2860e7bd45..a31d06f586a5c933b6dfc705a8316cadd1c73475 100644
--- a/setup.py
+++ b/setup.py
@@ -32,9 +32,9 @@ setup(
"Full = bob.bio.vein.config.database.protocol_verafinger.full",
"Cropped-Full = bob.bio.vein.config.database.protocol_verafinger.cropped_full",
# utfvp
- "nom = bob.bio.vein.config.database.protocol_utfvp.nom",
- "full = bob.bio.vein.config.database.protocol_utfvp.full",
- "1vsall = bob.bio.vein.config.database.protocol_utfvp.one_vs_all",
+ "nom = bob.bio.vein.config.database.utfvp_nom",
+ "full = bob.bio.vein.config.database.utfvp_full",
+ "1vsall = bob.bio.vein.config.database.utfvp_1vsall",
# fv3d
"central = bob.bio.vein.config.database.protocol_fv3d.central",
"left = bob.bio.vein.config.database.protocol_fv3d.left",
@@ -47,7 +47,6 @@ setup(
"palm-LR-4 = bob.bio.vein.config.database.protocol_putvein.palm_lr_4",
# legacy databases
"verafinger = bob.bio.vein.config.database.verafinger",
- "utfvp = bob.bio.vein.config.database.utfvp",
"fv3d = bob.bio.vein.config.database.fv3d",
"putvein = bob.bio.vein.config.database.putvein",
# legacy baselines
@@ -57,7 +56,7 @@ setup(
],
"bob.bio.database": [
"verafinger = bob.bio.vein.config.database.verafinger:database",
- "utfvp = bob.bio.vein.config.database.utfvp:database",
+ "utfvp = bob.bio.vein.config.database.utfvp_nom:database",
"fv3d = bob.bio.vein.config.database.fv3d:database",
"putvein = bob.bio.vein.config.database.putvein:database",
],