From bd592d5a23c4e205a2f35eeb1ebcfd35d5811e84 Mon Sep 17 00:00:00 2001
From: Tiago Freitas Pereira <tiagofrepereira@gmail.com>
Date: Tue, 1 Dec 2020 20:14:37 +0100
Subject: [PATCH] [db] implementing MEDS database in the new interface
---
bob/bio/face/database/__init__.py | 33 ++--
bob/bio/face/database/meds.py | 35 ++++
bob/bio/face/database/sample_loaders.py | 94 ++--------
bob/bio/face/test/test_databases.py | 239 ++++++++++++++++--------
4 files changed, 233 insertions(+), 168 deletions(-)
create mode 100644 bob/bio/face/database/meds.py
diff --git a/bob/bio/face/database/__init__.py b/bob/bio/face/database/__init__.py
index 57877158..83d143eb 100644
--- a/bob/bio/face/database/__init__.py
+++ b/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 +28,21 @@ 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,
)
-__all__ = [_ for _ in dir() if not _.startswith('_')]
+__all__ = [_ for _ in dir() if not _.startswith("_")]
diff --git a/bob/bio/face/database/meds.py b/bob/bio/face/database/meds.py
new file mode 100644
index 00000000..0eafb170
--- /dev/null
+++ b/bob/bio/face/database/meds.py
@@ -0,0 +1,35 @@
+#!/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, CSVToSampleLoader
+from bob.extension import rc
+import bob.io.base
+from bob.bio.face.database.sample_loaders import EyesAnnotationsLoader
+
+
+# TODO: POINT TO THE `.bob/meds``
+dataset_protocol_path = "/idiap/user/tpereira/gitlab/bob/bob.nightlies/meds"
+
+
+class MEDSDatabase(CSVDatasetDevEval):
+ def __init__(
+ self,
+ protocol,
+ dataset_protocol_path=dataset_protocol_path,
+ csv_to_sample_loader=CSVToSampleLoader(
+ data_loader=bob.io.base.load,
+ metadata_loader=EyesAnnotationsLoader(),
+ dataset_original_directory=rc["bob.db.meds.directory"],
+ extension=".jpg",
+ ),
+ ):
+
+ # TODO: IMPLEMENT THE DOWNLOAD MECHANISM
+
+ super().__init__(dataset_protocol_path, protocol, csv_to_sample_loader)
+
diff --git a/bob/bio/face/database/sample_loaders.py b/bob/bio/face/database/sample_loaders.py
index f19f86e2..c4016ef3 100644
--- a/bob/bio/face/database/sample_loaders.py
+++ b/bob/bio/face/database/sample_loaders.py
@@ -1,91 +1,27 @@
#!/usr/bin/env python
# vim: set fileencoding=utf-8 :
-""" Sample loader"""
+""" Sample and Metatada loader"""
-from bob.bio.base.database import CSVToSampleLoader
-from bob.pipelines import Sample, DelayedSample, SampleSet
-import functools
-import os
-
-
-class CSVToSampleLoaderEyesAnnotations(CSVToSampleLoader):
+class EyesAnnotationsLoader:
"""
- Convert CSV files in the format below to either a list of
- :any:`bob.pipelines.DelayedSample` or :any:`bob.pipelines.SampleSet`
-
Convert leye_x, leye_y, reye_x, reye_y attributes to `annotations = (leye, reye)`
-
"""
- def convert_row_to_sample(self, row, header):
- path = row[0]
- subject = row[1]
- kwargs = dict([[h, r] for h, r in zip(header[2:], row[2:])])
-
- annotations = {
- "leye": (kwargs["leye_x"], kwargs["leye_y"]),
- "reye": (kwargs["reye_x"], kwargs["reye_y"]),
+ def __call__(self, row, header=None):
+ 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")]),
}
- kwargs.pop("leye_x")
- kwargs.pop("leye_y")
- kwargs.pop("reye_x")
- kwargs.pop("reye_y")
-
- return DelayedSample(
- functools.partial(
- self.data_loader,
- os.path.join(self.dataset_original_directory, path + self.extension),
- ),
- key=path,
- subject=subject,
- annotations=annotations,
- **kwargs,
- )
-
-
-"""
-class CSVToSampleLoaderEyesAnnotations(CSVToSampleLoader):
- def __call__(self, filename):
- import ipdb
-
- ipdb.set_trace()
- samples = super(CSVToSampleLoaderEyesAnnotations, self).__call__(filename)
-
- def generate_annotations(sample):
-
- Convert leye_x, leye_y, reye_x, reye_y attributes to
- `annotations = (leye, reye)`
-
-
-
- check_keys = [
- a in (sample.__dict__.keys())
- for a in ["leye_x", "leye_y", "reye_x", "reye_y"]
- ]
-
- if not check_keys:
- raise ValueError(
- "Sample needs to contain the following annotations: 'leye_x', 'leye_y', 'reye_x', 'reye_y'"
- )
-
- annotations = {
- "leye": (sample.leye_x, sample.leye_y),
- "reye": (sample.reye_x, sample.reye_y),
- }
-
- # Changing the state of samples for efficiency
- # We might have a gigantic amount of datasets
- sample.__dict__.pop("leye_x")
- sample.__dict__.pop("leye_y")
- sample.__dict__.pop("reye_x")
- sample.__dict__.pop("reye_y")
- sample.annotations = annotations
-
- for sample in samples:
- generate_annotations(sample)
+ annotation = {"annotations": eyes}
- return samples
-"""
+ return annotation
diff --git a/bob/bio/face/test/test_databases.py b/bob/bio/face/test/test_databases.py
index ee2c9651..1dba94ce 100644
--- a/bob/bio/face/test/test_databases.py
+++ b/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 +221,130 @@ 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")
+
+ assert len(database.background_model_samples()) == 234
+
+ assert len(database.references()) == 223 // 2
+ assert len(database.probes()) == 313
--
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