Merge branch 'casia_fasd' into 'master'

Add casia fasd and an optical flow extractor

See merge request !98

bob/pad/face/config/casiafasd.py

+#!/usr/bin/env python
+
+"""Config file for the CASIA FASD dataset.
+Please run ``bob config set bob.db.casia_fasd.directory /path/to/casia_fasd_files``
+in terminal to point to the original files of the dataset on your computer."""
+
+from bob.pad.face.database import CasiaFasdPadDatabase
+database = CasiaFasdPadDatabase()

bob/pad/face/config/extractor/optical_flow.py

+from bob.bio.base.extractor import CallableExtractor
+from bob.pad.face.extractor import OpticalFlow
+
+extractor = CallableExtractor(OpticalFlow())

bob/pad/face/config/preprocessor/optical_flow.py

+from bob.bio.base.preprocessor import CallablePreprocessor
+from bob.pad.face.extractor import OpticalFlow
+
+
+def _read_original_data(biofile, directory, extension):
+    return biofile.frames
+
+
+preprocessor = CallablePreprocessor(OpticalFlow(), accepts_annotations=False)
+preprocessor.read_original_data = _read_original_data

bob/pad/face/database/__init__.py

@@ -8,6 +8,8 @@ from .batl import BatlPadDatabase
 from .celeb_a import CELEBAPadDatabase
 from .maskattack import MaskAttackPadDatabase
 from .casiasurf import CasiaSurfPadDatabase
+from .casiafasd import CasiaFasdPadDatabase
+
 
 # gets sphinx autodoc done right - don't remove it
 def __appropriate__(*args):
@@ -35,7 +37,8 @@ __appropriate__(
     BatlPadDatabase,
     CELEBAPadDatabase,
     MaskAttackPadDatabase,
-    CasiaSurfPadDatabase
+    CasiaSurfPadDatabase,
+    CasiaFasdPadDatabase,
 )
 
 __all__ = [_ for _ in dir() if not _.startswith('_')]

bob/pad/face/database/casiafasd.py

+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from bob.bio.video import FrameSelector
+from bob.extension import rc
+from bob.io.video import reader
+from bob.pad.base.database import PadDatabase
+from bob.pad.face.database import VideoPadFile
+from bob.db.base.utils import (
+    check_parameter_for_validity, check_parameters_for_validity)
+import numpy
+import os
+
+
+CASIA_FASD_FRAME_SHAPE = (3, 1280, 720)
+
+
+class CasiaFasdPadFile(VideoPadFile):
+    """
+    A high level implementation of the File class for the CASIA_FASD database.
+    """
+
+    def __init__(self, f, original_directory=None):
+        """
+        Parameters
+        ----------
+        f : object
+            An instance of the File class defined in the low level db interface
+            of the CasiaFasd database, in bob.db.casia_fasd.models
+        """
+
+        self.f = f
+        self.original_directory = original_directory
+
+        if f.is_real():
+            attack_type = None
+        else:
+            attack_type = 'attack/{}/{}'.format(f.get_type(), f.get_quality())
+
+        super(CasiaFasdPadFile, self).__init__(
+            client_id=str(f.get_clientid()),
+            path=f.filename,
+            attack_type=attack_type,
+            file_id=f.filename)
+
+    @property
+    def frames(self):
+        """Yields the frames of the biofile one by one.
+
+        Yields
+        ------
+        :any:`numpy.array`
+            A frame of the video. The size is :any:`CASIA_FASD_FRAME_SHAPE`.
+        """
+        vfilename = self.make_path(
+            directory=self.original_directory, extension='.avi')
+        for frame in reader(vfilename):
+            # pad frames to 1280 x 720 so they all have the same size
+            h, w = frame.shape[1:]
+            H, W = CASIA_FASD_FRAME_SHAPE[1:]
+            assert h <= H
+            assert w <= W
+            frame = numpy.pad(frame, ((0, 0), (0, H - h), (0, W - w)),
+                              mode='constant', constant_values=0)
+            yield frame
+
+    @property
+    def number_of_frames(self):
+        """Returns the number of frames in a video file.
+
+        Returns
+        -------
+        int
+            The number of frames.
+        """
+        vfilename = self.make_path(
+            directory=self.original_directory, extension='.avi')
+        return reader(vfilename).number_of_frames
+
+    @property
+    def frame_shape(self):
+        """Returns the size of each frame in this database.
+
+        Returns
+        -------
+        (int, int, int)
+            The (#Channels, Height, Width) which is
+            :any:`CASIA_FASD_FRAME_SHAPE`.
+        """
+        return CASIA_FASD_FRAME_SHAPE
+
+    @property
+    def annotations(self):
+        """Reads the annotations
+
+        Returns
+        -------
+        annotations : :py:class:`dict`
+            A dictionary containing the annotations for each frame in the
+            video. Dictionary structure:
+            ``annotations = {'1': frame1_dict, '2': frame1_dict, ...}``.Where
+            ``frameN_dict = {'topleft': (row, col), 'bottomright':(row, col)}``
+            is the dictionary defining the coordinates of the face bounding box
+            in frame N.
+        """
+        annots = self.f.bbx()
+        annotations = {}
+        for i, v in enumerate(annots):
+            topleft = (v[2], v[1])
+            bottomright = (v[2] + v[4], v[1] + v[3])
+            annotations[str(i)] = {'topleft': topleft,
+                                   'bottomright': bottomright}
+        return annotations
+
+    def load(self, directory=None, extension='.avi',
+             frame_selector=FrameSelector(selection_style='all')):
+        """Loads the video file and returns in a
+        :any:`bob.bio.video.FrameContainer`.
+
+        Parameters
+        ----------
+        directory : :obj:`str`, optional
+            The directory to load the data from.
+        extension : :obj:`str`, optional
+            The extension of the file to load.
+        frame_selector : :any:`bob.bio.video.FrameSelector`, optional
+            Which frames to select.
+
+        Returns
+        -------
+        :any:`bob.bio.video.FrameContainer`
+            The loaded frames inside a frame container.
+        """
+        directory = directory or self.original_directory
+        return frame_selector(self.make_path(directory, extension))
+
+
+class CasiaFasdPadDatabase(PadDatabase):
+    """
+    A high level implementation of the Database class for the CASIA_FASD
+    database. Please run ``bob config set bob.db.casia_fasd.directory
+    /path/to/casia_fasd_files`` in a terminal to point to the original files on
+    your computer. This interface is different from the one implemented in
+    ``bob.db.casia_fasd.Database``.
+    """
+
+    def __init__(
+            self,
+            # grandtest is the new modified protocol for this database
+            protocol='grandtest',
+            original_directory=rc['bob.db.casia_fasd.directory'],
+            **kwargs):
+        """
+        Parameters
+        ----------
+        protocol : str or None
+            The name of the protocol that defines the default experimental
+            setup for this database. Only grandtest is supported for now.
+
+        original_directory : str
+            The directory where the original data of the database are stored.
+
+        kwargs
+            The arguments of the :py:class:`bob.pad.base.database.PadDatabase`
+            base class constructor.
+        """
+        return super(CasiaFasdPadDatabase, self).__init__(
+            name='casiafasd',
+            protocol=protocol,
+            original_directory=original_directory,
+            original_extension='.avi',
+            training_depends_on_protocol=True,
+            **kwargs)
+
+    def objects(self,
+                groups=None,
+                protocol=None,
+                purposes=None,
+                model_ids=None,
+                **kwargs):
+        """
+        This function returns lists of CasiaFasdPadFile objects, which fulfill
+        the given restrictions.
+
+        Parameters
+        ----------
+        groups : :obj:`str` or [:obj:`str`]
+            The groups of which the clients should be returned.
+            Usually, groups are one or more elements of
+            ('train', 'dev', 'eval')
+
+        protocol : str
+            The protocol for which the clients should be retrieved.
+            Only 'grandtest' is supported for now. This protocol modifies the
+            'Overall Test' protocol and adds some ids to dev set.
+
+        purposes : :obj:`str` or [:obj:`str`]
+            The purposes for which File objects should be retrieved either
+            'real' or 'attack' or both.
+
+        model_ids
+            Ignored.
+
+        **kwargs
+            Ignored.
+
+        Returns
+        -------
+        files : [CasiaFasdPadFile]
+            A list of CasiaFasdPadFile objects.
+        """
+        groups = check_parameters_for_validity(
+            groups, 'groups', ('train', 'dev', 'eval'),
+            ('train', 'dev', 'eval'))
+        protocol = check_parameter_for_validity(
+            protocol, 'protocol', ('grandtest'), 'grandtest')
+        purposes = check_parameters_for_validity(
+            purposes, 'purposes', ('real', 'attack'), ('real', 'attack'))
+
+        qualities = ('low', 'normal', 'high')
+        types = ('warped', 'cut', 'video')
+        from bob.db.casia_fasd.models import File
+
+        files = []
+
+        db_mappings = {
+            'real_normal': '1',
+            'real_low': '2',
+            'real_high': 'HR_1',
+            'warped_normal': '3',
+            'warped_low': '4',
+            'warped_high': 'HR_2',
+            'cut_normal': '5',
+            'cut_low': '6',
+            'cut_high': 'HR_3',
+            'video_normal': '7',
+            'video_low': '8',
+            'video_high': 'HR_4'
+        }
+
+        # identitites 1-15 are for train, 16-20 are dev, and 21-50 for eval
+        grp_id_map = {
+            'train': list(range(1, 16)),
+            'dev': list(range(16, 21)),
+            'eval': list(range(21, 51)),
+        }
+        grp_map = {
+            'train': 'train',
+            'dev': 'train',
+            'eval': 'test',
+        }
+
+        for g in groups:
+            ids = grp_id_map[g]
+            for i in ids:
+                cur_id = i
+                if g == 'eval':
+                    cur_id = i - 20
+                    # the id within the group subset
+
+                # this group name (grp) is only train and test
+                grp = grp_map[g]
+
+                folder_name = grp + '_release'
+
+                for q in qualities:
+                    for c in purposes:
+                        # the class real doesn't have any different types, only
+                        # the attacks can be of different type
+                        if c == 'real':
+                            filename = os.path.join(folder_name, "%d" % cur_id,
+                                                    db_mappings['real_' + q])
+                            files.append(CasiaFasdPadFile(
+                                File(filename, c, grp),
+                                self.original_directory))
+                        else:
+                            for t in types:
+                                filename = os.path.join(
+                                    folder_name, "%d" % cur_id,
+                                    db_mappings[t + '_' + q])
+                                files.append(CasiaFasdPadFile(
+                                    File(filename, c, grp),
+                                    self.original_directory))
+        return files
+
+    def annotations(self, padfile):
+        return padfile.annotations
+
+    def frames(self, padfile):
+        return padfile.frames
+
+    def number_of_frames(self, padfile):
+        return padfile.number_of_frames
+
+    @property
+    def frame_shape(self):
+        return CASIA_FASD_FRAME_SHAPE

bob/pad/face/database/replay.py

-#!/usr/bin/env python2
+#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
 # Used in ReplayMobilePadFile class

bob/pad/face/extractor/OpticalFlow.py

+from bob.bio.base import vstack_features
+from bob.bio.video import FrameContainer
+from bob.io.base import HDF5File
+from bob.ip.optflow.liu.cg import flow
+from collections import Iterator
+from functools import partial
+import logging
+
+logger = logging.getLogger(__name__)
+
+
+def _check_frame(frame):
+    if frame.dtype == "uint8":
+        return frame.astype("float64") / 255.0
+    return frame.astype("float64")
+
+
+class _Reader:
+    def __init__(self, i1, flow_method):
+        self.i1 = _check_frame(i1)
+        self.flow_method = flow_method
+
+    def __call__(self, i2):
+        i2 = _check_frame(i2)
+        flows = self.flow_method(self.i1, i2)[:2]
+        self.i1 = i2
+        return flows
+
+
+class OpticalFlow(object):
+    """An optical flow extractor
+    For more information see :any:`bob.ip.optflow.liu.cg.flow`.
+
+    Attributes
+    ----------
+    alpha : float
+        Regularization weight
+    inner : int
+        The number of inner fixed point iterations
+    iterations : int
+        The number of conjugate-gradient (CG) iterations
+    min_width : int
+        Width of the coarsest level
+    outer : int
+        The number of outer fixed point iterations
+    ratio : float
+        Downsample ratio
+    """
+
+    def __init__(
+        self,
+        alpha=0.02,
+        ratio=0.75,
+        min_width=30,
+        outer=20,
+        inner=1,
+        iterations=50,
+        **kwargs
+    ):
+        super().__init__(**kwargs)
+        self.alpha = alpha
+        self.ratio = ratio
+        self.min_width = min_width
+        self.outer = outer
+        self.inner = inner
+        self.iterations = iterations
+
+    def __call__(self, video):
+        """Computes optical flows on a video
+        Please note that the video should either be uint8 or float64 with values from 0
+        to 1.
+
+        Parameters
+        ----------
+        video : numpy.ndarray
+            The video. Can be a FrameContainer, generator, bob.io.video.reader, or a
+            numpy array.
+
+        Returns
+        -------
+        numpy.ndarray
+            The flows calculated for each pixel. The output shape will be
+            [number_of_frames - 1, 2, height, width].
+        """
+        if isinstance(video, FrameContainer):
+            video = video.as_array()
+        if not isinstance(video, Iterator):
+            video = iter(video)
+
+        i1 = next(video)
+        reader = _Reader(
+            i1,
+            partial(
+                flow,
+                alpha=self.alpha,
+                ratio=self.ratio,
+                min_width=self.min_width,
+                n_outer_fp_iterations=self.outer,
+                n_inner_fp_iterations=self.inner,
+                n_cg_iterations=self.iterations,
+            ),
+        )
+        flows = vstack_features(reader, video)
+        shape = list(flows.shape)
+        shape[0] = 2
+        shape.insert(0, -1)
+        return flows.reshape(shape)
+
+    def write_feature(self, feature, feature_file):
+        if not isinstance(feature_file, HDF5File):
+            feature_file = HDF5File(feature_file, "w")
+
+        feature_file.set("uv", feature)
+        feature_file.set_attribute("method", "liu.cg", "uv")
+        feature_file.set_attribute("alpha", self.alpha, "uv")
+        feature_file.set_attribute("ratio", self.ratio, "uv")
+        feature_file.set_attribute("min_width", self.min_width, "uv")
+        feature_file.set_attribute("n_outer_fp_iterations", self.outer, "uv")
+        feature_file.set_attribute("n_inner_fp_iterations", self.inner, "uv")
+        feature_file.set_attribute("n_iterations", self.iterations, "uv")
+
+    def read_feature(self, feature_file):
+        if not isinstance(feature_file, HDF5File):
+            feature_file = HDF5File(feature_file, "r")
+
+        return feature_file["uv"]

conda/meta.yaml

@@ -47,6 +47,7 @@ requirements:
     - {{ pin_compatible('numpy') }}
     - {{ pin_compatible('scikit-learn') }}
     - {{ pin_compatible('scikit-image') }}
+    - {{ pin_compatible('opencv') }}
 
 test:
   imports:
@@ -67,6 +68,7 @@ test:
     - bob.db.replay
     - bob.db.replaymobile
     - bob.db.msu_mfsd_mod
+    - bob.db.casia_fasd
     - bob.db.mobio
     - bob.db.maskattack
     - bob.db.casiasurf

doc/installation.rst

 
-
 .. _bob.pad.face.installation:
 
-==============
- Installation
-==============
-
-The installation of this package is divided in 2-parts. Installation of the
-package and its software dependencies and the installation of databases.
-
-
-Package Installation
---------------------
-
-To install this package, first follow our `installation`_ instructions. Then,
-using the buildout command provided by the distribution, bootstrap this package
-using buildout:
-
-
-.. code-block:: sh
-
-  $ buildout
-
-
-Sphinx Documentation Building
------------------------------
-
-Once the package is installed, you may re-build this documentation locally by
-running:
-
-.. code-block:: sh
+======================
+ Setting up Databases
+======================
 
-  $ sphinx-build doc html
-
-The resulting HTML documentation will be output inside the directory `html`.
-
-
-Setting up Databases
---------------------
-
-In order to run face PAD algorithms using this package, you'll need to
-make sure to download the raw files corresponding to the databases you'd like
-to process. The raw files are not distributed with Bob_ software as biometric
+In order to run face PAD algorithms using this package, you'll need to make
+sure to download the raw files corresponding to the databases you'd like to
+process. The raw files are **not** distributed with Bob_ software as biometric
 data is, to most countries, considered sensible data that cannot be obtained
 without explicit licensing from a data controller. You must visit the websites
 below, sign the license agreements and then download the data before trying out
@@ -52,7 +18,7 @@ to run the baselines.
    If you're at the Idiap Research Institute in Switzlerand, the datasets in
    the baselines mentioned in this guide are already downloaded and
    pre-installed on our shared file system. You don't need to re-download
-   databases or create a ``~/.bob_bio_databases.txt`` file.
+   databases.
 
 
 The current system readily supports the following freely available datasets:
@@ -67,30 +33,11 @@ are installed. Then, follow the instructions in
 :ref:`bob.pad.base.installation` to let this framework know where databases are
 located on your system.
 
+.. note::
 
-Development
------------
-
-If you're developing this package, you may automatically clone all necessary
-Bob_ repositories on your local package installation. This allows you to build
-against an environment which contains all of our dependencies_, but no
-previously installed Bob_ packages. To do so, use the buildout recipe in
-``develop.cfg`` just after bootstraping:
-
-.. code-block:: sh
-
-  $ buildout -c develop.cfg
-
-Database SQL support files
-==========================
-
-If you installed all packages from scratch like above, you'll need to download
-the SQL support files of some of the database front-ends available in this
-package. This operation can be easily done like this:
-
-.. code-block:: sh
-
-  $ bob_dbmanage.py all download
+    Some databases may need to be configured using a newer method explained in
+    :ref:`bob.extension.rc`. Refer to the documentation of the database for
+    further information.
 
 
 .. include:: links.rst

setup.py

@@ -66,6 +66,7 @@ setup(
             'replay-attack = bob.pad.face.config.replay_attack:database',
             'replay-mobile = bob.pad.face.config.replay_mobile:database',
             'msu-mfsd = bob.pad.face.config.msu_mfsd:database',
+            'casiafasd = bob.pad.face.config.casiafasd:database',
             'aggregated-db = bob.pad.face.config.aggregated_db:database',
             'mifs = bob.pad.face.config.mifs:database',
             'batl-db = bob.pad.face.config.database.batl.batl_db:database',
@@ -85,6 +86,7 @@ setup(
             'replay-attack = bob.pad.face.config.replay_attack',
             'replay-mobile = bob.pad.face.config.replay_mobile',
             'msu-mfsd = bob.pad.face.config.msu_mfsd',
+            'casiafasd = bob.pad.face.config.casiafasd',
             'aggregated-db = bob.pad.face.config.aggregated_db',
             'mifs = bob.pad.face.config.mifs',
             'batl-db = bob.pad.face.config.database.batl.batl_db',

test-requirements.txt

@@ -2,6 +2,7 @@ nose
 bob.db.replay
 bob.db.replaymobile
 bob.db.msu_mfsd_mod
+bob.db.casia_fasd
 bob.db.mobio
 bob.db.maskattack
 bob.db.casiasurf