From f41083f8e8fda7dd8310f1795e2ff30f8f5e38d6 Mon Sep 17 00:00:00 2001
From: Manuel Gunther <siebenkopf@googlemail.com>
Date: Thu, 11 Feb 2016 09:30:54 -0700
Subject: [PATCH] Added an algorithm that applies a simple distance function
---
bob/bio/base/algorithm/Distance.py | 110 ++++++++++++++++++
bob/bio/base/algorithm/__init__.py | 1 +
.../base/config/algorithm/distance_cosine.py | 9 ++
.../config/algorithm/distance_euclidean.py | 9 ++
bob/bio/base/test/test_algorithms.py | 38 +++---
setup.py | 2 +
version.txt | 2 +-
7 files changed, 156 insertions(+), 15 deletions(-)
create mode 100644 bob/bio/base/algorithm/Distance.py
create mode 100644 bob/bio/base/config/algorithm/distance_cosine.py
create mode 100644 bob/bio/base/config/algorithm/distance_euclidean.py
diff --git a/bob/bio/base/algorithm/Distance.py b/bob/bio/base/algorithm/Distance.py
new file mode 100644
index 00000000..10291337
--- /dev/null
+++ b/bob/bio/base/algorithm/Distance.py
@@ -0,0 +1,110 @@
+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# Manuel Gunther <siebenkopf@googlemail.com>
+
+import numpy
+import scipy.spatial
+
+from .Algorithm import Algorithm
+
+import logging
+logger = logging.getLogger("bob.bio.base")
+
+class Distance (Algorithm):
+ """This class defines a simple distance measure between two features.
+ Independent of the actual shape, each feature vector is treated as a one-dimensional vector, and the specified distance function is used to compute the distance between the two features.
+ If the given ``distance_function`` actually computes a distance, we simply return its negative value (as all :py:class:`Algorithm`'s are supposed to return similarity values).
+ If the ``distance_function`` computes similarities, the similarity value is returned unaltered.
+
+ **Parameters:**
+
+ ``distance_function`` : callable
+ A function taking two 1D arrays and returning a ``float``
+
+ ``is_distance_function`` : bool
+ Set this flag to ``False`` if the given ``distance_function`` computes a similarity value (i.e., higher values are better)
+
+ ``kwargs`` : ``key=value`` pairs
+ A list of keyword arguments directly passed to the :py:class:`Algorithm` base class constructor.
+ """
+
+ def __init__(
+ self,
+ distance_function = scipy.spatial.distance.euclidean,
+ is_distance_function = True,
+ **kwargs # parameters directly sent to the base class
+ ):
+
+ # call base class constructor and register that the algorithm performs a projection
+ Algorithm.__init__(
+ self,
+ distance_function = str(distance_function),
+ is_distance_function = is_distance_function,
+
+ **kwargs
+ )
+
+ self.distance_function = distance_function
+ self.factor = -1. if is_distance_function else 1.
+
+ def _check_feature(self, feature):
+ """Checks that the features are appropriate"""
+ if not isinstance(feature, numpy.ndarray):
+ raise ValueError("The given feature should be of type numpy.ndarray")
+
+ def enroll(self, enroll_features):
+ """enroll(enroll_features) -> model
+
+ Enrolls the model by storing all given input vectors.
+
+ **Parameters:**
+
+ ``enroll_features`` : [:py:class:`numpy.ndarray`]
+ The list of projected features to enroll the model from.
+
+ **Returns:**
+
+ ``model`` : 2D :py:class:`numpy.ndarray`
+ The enrolled model.
+ """
+ assert len(enroll_features)
+ [self._check_feature(feature) for feature in enroll_features]
+ # just store all the features
+ return numpy.vstack([f.flatten() for f in enroll_features])
+
+ def score(self, model, probe):
+ """score(model, probe) -> float
+
+ Computes the distance of the model to the probe using the distance function specified in the constructor.
+
+ **Parameters:**
+
+ ``model`` : 2D :py:class:`numpy.ndarray`
+ The model storing all enrollment features
+
+ ``probe`` : :py:class:`numpy.ndarray`
+ The probe feature vector
+
+ **Returns:**
+
+ ``score`` : float
+ A similarity value between ``model`` and ``probe``
+ """
+ self._check_feature(probe)
+ probe = probe.flatten()
+ # return the negative distance (as a similarity measure)
+ if model.ndim == 2:
+ # we have multiple models, so we use the multiple model scoring
+ return self.score_for_multiple_models(model, probe)
+ else:
+ # single model, single probe (multiple probes have already been handled)
+ return self.factor * self.distance_function(model, probe)
+
+ # re-define unused functions, just so that they do not get documented
+ def train_projector(*args,**kwargs): raise NotImplementedError()
+ def load_projector(*args,**kwargs): pass
+ def project(*args,**kwargs): raise NotImplementedError()
+ def write_feature(*args,**kwargs): raise NotImplementedError()
+ def read_feature(*args,**kwargs): raise NotImplementedError()
+ def train_enroller(*args,**kwargs): raise NotImplementedError()
+ def load_enroller(*args,**kwargs): pass
diff --git a/bob/bio/base/algorithm/__init__.py b/bob/bio/base/algorithm/__init__.py
index e1bc1ad9..015cf9e6 100644
--- a/bob/bio/base/algorithm/__init__.py
+++ b/bob/bio/base/algorithm/__init__.py
@@ -1,4 +1,5 @@
from .Algorithm import Algorithm
+from .Distance import Distance
from .PCA import PCA
from .LDA import LDA
from .PLDA import PLDA
diff --git a/bob/bio/base/config/algorithm/distance_cosine.py b/bob/bio/base/config/algorithm/distance_cosine.py
new file mode 100644
index 00000000..00d82ea8
--- /dev/null
+++ b/bob/bio/base/config/algorithm/distance_cosine.py
@@ -0,0 +1,9 @@
+#!/usr/bin/env python
+
+import bob.bio.base
+import scipy.spatial
+
+algorithm = bob.bio.base.algorithm.Distance(
+ distance_function = scipy.spatial.distance.cosine,
+ is_distance_function = True
+)
diff --git a/bob/bio/base/config/algorithm/distance_euclidean.py b/bob/bio/base/config/algorithm/distance_euclidean.py
new file mode 100644
index 00000000..3ab5422d
--- /dev/null
+++ b/bob/bio/base/config/algorithm/distance_euclidean.py
@@ -0,0 +1,9 @@
+#!/usr/bin/env python
+
+import bob.bio.base
+import scipy.spatial
+
+algorithm = bob.bio.base.algorithm.Distance(
+ distance_function = scipy.spatial.distance.euclidean,
+ is_distance_function = True
+)
diff --git a/bob/bio/base/test/test_algorithms.py b/bob/bio/base/test/test_algorithms.py
index ffb872a5..66fd5881 100644
--- a/bob/bio/base/test/test_algorithms.py
+++ b/bob/bio/base/test/test_algorithms.py
@@ -45,20 +45,30 @@ def _compare(data, reference, write_function = bob.bio.base.save, read_function
assert numpy.allclose(data, read_function(reference), atol=1e-5)
-def _gmm_stats(self, feature_file, count = 50, minimum = 0, maximum = 1):
- # generate a random sequence of GMM-Stats features
- numpy.random.seed(42)
- train_set = []
- f = bob.io.base.HDF5File(feature_file)
- for i in range(count):
- per_id = []
- for j in range(count):
- gmm_stats = bob.learn.em.GMMStats(f)
- gmm_stats.sum_px = numpy.random.random(gmm_stats.sum_px.shape) * (maximum - minimum) + minimum
- gmm_stats.sum_pxx = numpy.random.random(gmm_stats.sum_pxx.shape) * (maximum - minimum) + minimum
- per_id.append(gmm_stats)
- train_set.append(per_id)
- return train_set
+def test_distance():
+ # test the two registered distance functions
+
+ # euclidean distance
+ euclidean = bob.bio.base.load_resource("distance-euclidean", "algorithm", preferred_package = 'bob.bio.base')
+ assert isinstance(euclidean, bob.bio.base.algorithm.Distance)
+ assert isinstance(euclidean, bob.bio.base.algorithm.Algorithm)
+ assert not euclidean.performs_projection
+ assert not euclidean.requires_projector_training
+ assert not euclidean.use_projected_features_for_enrollment
+ assert not euclidean.split_training_features_by_client
+ assert not euclidean.requires_enroller_training
+
+ # test distance computation
+ f1 = numpy.ones((20,10), numpy.float64)
+ f2 = numpy.ones((20,10), numpy.float64) * 2.
+
+ model = euclidean.enroll([f1, f1])
+ assert abs(euclidean.score_for_multiple_probes(model, [f2, f2]) + math.sqrt(200.)) < 1e-6, euclidean.score_for_multiple_probes(model, [f2, f2])
+
+ # test cosine distance
+ cosine = bob.bio.base.load_resource("distance-cosine", "algorithm", preferred_package = 'bob.bio.base')
+ model = cosine.enroll([f1, f1])
+ assert abs(cosine.score_for_multiple_probes(model, [f2, f2])) < 1e-8, cosine.score_for_multiple_probes(model, [f2, f2])
def test_pca():
diff --git a/setup.py b/setup.py
index 26e9c57d..df866752 100644
--- a/setup.py
+++ b/setup.py
@@ -127,6 +127,8 @@ setup(
'bob.bio.algorithm': [
'dummy = bob.bio.base.test.dummy.algorithm:algorithm', # for test purposes only
+ 'distance-euclidean = bob.bio.base.config.algorithm.distance_euclidean:algorithm',
+ 'distance-cosine = bob.bio.base.config.algorithm.distance_cosine:algorithm',
'pca = bob.bio.base.config.algorithm.pca:algorithm',
'lda = bob.bio.base.config.algorithm.lda:algorithm',
'pca+lda = bob.bio.base.config.algorithm.pca_lda:algorithm',
diff --git a/version.txt b/version.txt
index 4b20305a..13cb7641 100644
--- a/version.txt
+++ b/version.txt
@@ -1 +1 @@
-2.0.5b0
\ No newline at end of file
+2.0.5b1
--
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