From 8a408beb5261fe342749d6773625b66e8209d5bd Mon Sep 17 00:00:00 2001
From: Tiago Freitas Pereira <tiagofrepereira@gmail.com>
Date: Mon, 13 Jul 2015 18:01:15 +0200
Subject: [PATCH] Solved issue #2. Now it is possible to compute the likelihood
using 2D arrays
---
bob/learn/em/cpp/GMMMachine.cpp | 19 +++++++++++++++
bob/learn/em/gmm_machine.cpp | 24 ++++++++++++-------
.../em/include/bob.learn.em/GMMMachine.h | 9 +++++++
bob/learn/em/test/test_gmm.py | 23 ++++++++++++++++++
4 files changed, 67 insertions(+), 8 deletions(-)
diff --git a/bob/learn/em/cpp/GMMMachine.cpp b/bob/learn/em/cpp/GMMMachine.cpp
index a3cbe44..d2512b7 100644
--- a/bob/learn/em/cpp/GMMMachine.cpp
+++ b/bob/learn/em/cpp/GMMMachine.cpp
@@ -233,6 +233,7 @@ double bob::learn::em::GMMMachine::logLikelihood(const blitz::Array<double, 1> &
return logLikelihood_(x,log_weighted_gaussian_likelihoods);
}
+
double bob::learn::em::GMMMachine::logLikelihood_(const blitz::Array<double, 1> &x,
blitz::Array<double,1> &log_weighted_gaussian_likelihoods) const
{
@@ -250,6 +251,22 @@ double bob::learn::em::GMMMachine::logLikelihood_(const blitz::Array<double, 1>
return log_likelihood;
}
+
+double bob::learn::em::GMMMachine::logLikelihood(const blitz::Array<double, 2> &x) const {
+ // Check dimension
+ bob::core::array::assertSameDimensionLength(x.extent(1), m_n_inputs);
+ // Call the other logLikelihood_ (overloaded) function
+
+
+ double sum_ll = 0;
+ for (int i=0; i<x.extent(0); i++)
+ sum_ll+= logLikelihood_(x(i,blitz::Range::all()));
+
+ return sum_ll/x.extent(0);
+}
+
+
+
double bob::learn::em::GMMMachine::logLikelihood(const blitz::Array<double, 1> &x) const {
// Check dimension
bob::core::array::assertSameDimensionLength(x.extent(0), m_n_inputs);
@@ -258,6 +275,8 @@ double bob::learn::em::GMMMachine::logLikelihood(const blitz::Array<double, 1> &
return logLikelihood_(x,m_cache_log_weighted_gaussian_likelihoods);
}
+
+
double bob::learn::em::GMMMachine::logLikelihood_(const blitz::Array<double, 1> &x) const {
// Call the other logLikelihood (overloaded) function
// (log_weighted_gaussian_likelihoods will be discarded)
diff --git a/bob/learn/em/gmm_machine.cpp b/bob/learn/em/gmm_machine.cpp
index 4057bc5..86c965c 100644
--- a/bob/learn/em/gmm_machine.cpp
+++ b/bob/learn/em/gmm_machine.cpp
@@ -643,7 +643,8 @@ static PyObject* PyBobLearnEMGMMMachine_resize(PyBobLearnEMGMMMachineObject* sel
static auto log_likelihood = bob::extension::FunctionDoc(
"log_likelihood",
"Output the log likelihood of the sample, x, i.e. :math:`log(p(x|GMM))`. Inputs are checked.",
- ".. note:: The :py:meth:`__call__` function is an alias for this.",
+ ".. note:: The :py:meth:`__call__` function is an alias for this. \n "
+ "If `input` is 2D the average along the samples will be computed (:math:`\\frac{log(p(x|GMM))}{N}`) ",
true
)
.add_prototype("input","output")
@@ -667,21 +668,28 @@ static PyObject* PyBobLearnEMGMMMachine_loglikelihood(PyBobLearnEMGMMMachineObje
return 0;
}
- if (input->ndim != 1){
- PyErr_Format(PyExc_TypeError, "`%s' only processes 1D arrays of float64", Py_TYPE(self)->tp_name);
+ if (input->ndim > 2){
+ PyErr_Format(PyExc_TypeError, "`%s' only processes 1D or 2D arrays of float64", Py_TYPE(self)->tp_name);
log_likelihood.print_usage();
return 0;
}
-
- if (input->shape[0] != (Py_ssize_t)self->cxx->getNInputs()){
+
+ int shape_index = input->ndim - 1; //Getting the index of the dimensionality (0 for 1D arrays, 1 for 2D arrays)
+
+ if (input->shape[shape_index] != (Py_ssize_t)self->cxx->getNInputs()){
PyErr_Format(PyExc_TypeError, "`%s' 1D `input` array should have %" PY_FORMAT_SIZE_T "d elements, not %" PY_FORMAT_SIZE_T "d", Py_TYPE(self)->tp_name, self->cxx->getNInputs(), input->shape[0]);
log_likelihood.print_usage();
return 0;
}
-
- double value = self->cxx->logLikelihood(*PyBlitzArrayCxx_AsBlitz<double,1>(input));
+
+ double value = 0;
+ if (input->ndim == 1)
+ value = self->cxx->logLikelihood(*PyBlitzArrayCxx_AsBlitz<double,1>(input));
+ else
+ value = self->cxx->logLikelihood(*PyBlitzArrayCxx_AsBlitz<double,2>(input));
+
+
return Py_BuildValue("d", value);
-
BOB_CATCH_MEMBER("cannot compute the likelihood", 0)
}
diff --git a/bob/learn/em/include/bob.learn.em/GMMMachine.h b/bob/learn/em/include/bob.learn.em/GMMMachine.h
index c3b1246..0a46f82 100644
--- a/bob/learn/em/include/bob.learn.em/GMMMachine.h
+++ b/bob/learn/em/include/bob.learn.em/GMMMachine.h
@@ -231,6 +231,15 @@ class GMMMachine
*/
double logLikelihood(const blitz::Array<double, 1> &x) const;
+
+ /**
+ * Output the averaged log likelihood of a set of samples, x, i.e. log(p(x|GMM))
+ * @param[in] x The sample
+ * Dimension of the input is checked
+ */
+ double logLikelihood(const blitz::Array<double, 2> &x) const;
+
+
/**
* Output the log likelihood of the sample, x, i.e. log(p(x|GMM))
* @param[in] x The sample
diff --git a/bob/learn/em/test/test_gmm.py b/bob/learn/em/test/test_gmm.py
index cc678c1..1733c66 100644
--- a/bob/learn/em/test/test_gmm.py
+++ b/bob/learn/em/test/test_gmm.py
@@ -238,3 +238,26 @@ def test_GMMMachine_3():
# implementation
matlab_ll_ref = -2.361583051672024e+02
assert abs(gmm(data) - matlab_ll_ref) < 1e-10
+
+
+def test_GMMMachine_4():
+
+ import numpy
+ numpy.random.seed(3) # FIXING A SEED
+
+ data = numpy.random.rand(100,50) #Doesn't matter if it is ramdom. The average of 1D array (in python) MUST output the same result for the 2D array (in C++)
+
+ gmm = GMMMachine(2, 50)
+ gmm.weights = bob.io.base.load(datafile('weights.hdf5', __name__, path="../data/"))
+ gmm.means = bob.io.base.load(datafile('means.hdf5', __name__, path="../data/"))
+ gmm.variances = bob.io.base.load(datafile('variances.hdf5', __name__, path="../data/"))
+
+
+ ll = 0
+ for i in range(data.shape[0]):
+ ll += gmm(data[i,:])
+ ll /= data.shape[0]
+
+ assert ll==gmm(data)
+
+
--
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