From 674ceb3fa4776679c14bd399d73eda17b382b45c Mon Sep 17 00:00:00 2001
From: Tiago Freitas Pereira <tiagofrepereira@gmail.com>
Date: Wed, 15 Jul 2015 12:08:35 +0200
Subject: [PATCH] A couple of fixes on bob.learn.em.EMPCATrainer: - Issue #9
- Bug in the bindings - Fixed documentation
---
bob/learn/em/cpp/EMPCATrainer.cpp | 6 ++-
bob/learn/em/empca_trainer.cpp | 81 ++++++++++++++++++-------------
bob/learn/em/test/test_em.py | 43 ++++++++++++++++
doc/index.rst | 4 ++
4 files changed, 97 insertions(+), 37 deletions(-)
diff --git a/bob/learn/em/cpp/EMPCATrainer.cpp b/bob/learn/em/cpp/EMPCATrainer.cpp
index c27a010..1217be2 100644
--- a/bob/learn/em/cpp/EMPCATrainer.cpp
+++ b/bob/learn/em/cpp/EMPCATrainer.cpp
@@ -16,6 +16,7 @@
#include <bob.math/linear.h>
#include <bob.math/det.h>
#include <bob.math/inv.h>
+#include <bob.math/pinv.h>
#include <bob.math/stats.h>
bob::learn::em::EMPCATrainer::EMPCATrainer(bool compute_likelihood):
@@ -172,6 +173,7 @@ void bob::learn::em::EMPCATrainer::initMembers(
m_tmp_dxf.resize(n_outputs, n_features);
m_tmp_d.resize(n_outputs);
m_tmp_f.resize(n_features);
+
m_tmp_dxd_1.resize(n_outputs, n_outputs);
m_tmp_dxd_2.resize(n_outputs, n_outputs);
m_tmp_fxd_1.resize(n_features, n_outputs);
@@ -240,8 +242,8 @@ void bob::learn::em::EMPCATrainer::computeInvM()
{
// Compute inverse(M), where M = W^T * W + sigma2 * Id
bob::math::eye(m_tmp_dxd_1); // m_tmp_dxd_1 = Id
- m_tmp_dxd_1 *= m_sigma2; // m_tmp_dxd_1 = sigma2 * Id
- m_tmp_dxd_1 += m_inW; // m_tmp_dxd_1 = M = W^T * W + sigma2 * Id
+ m_tmp_dxd_1 *= m_sigma2; // m_tmp_dxd_1 = sigma2 * Id
+ m_tmp_dxd_1 += m_inW; // m_tmp_dxd_1 = M = W^T * W + sigma2 * Id
bob::math::inv(m_tmp_dxd_1, m_invM); // m_invM = inv(M)
}
diff --git a/bob/learn/em/empca_trainer.cpp b/bob/learn/em/empca_trainer.cpp
index 0b42bca..dae075f 100644
--- a/bob/learn/em/empca_trainer.cpp
+++ b/bob/learn/em/empca_trainer.cpp
@@ -15,21 +15,28 @@
static auto EMPCATrainer_doc = bob::extension::ClassDoc(
BOB_EXT_MODULE_PREFIX ".EMPCATrainer",
- ""
+ "Trains a :py:class:`bob.learn.linear.Machine` using an Expectation-Maximization algorithm on the given dataset [Bishop1999]_ [Roweis1998]_ \n\n"
+ "Notations used are the ones from [Bishop1999]_\n\n"
+ "The probabilistic model is given by: :math:`t = Wx + \\mu + \\epsilon`\n\n"
+ " - :math:`t` is the observed data (dimension :math:`f`)\n"
+ " - :math:`W` is a projection matrix (dimension :math:`f \\times d`)\n"
+ " - :math:`x` is the projected data (dimension :math:`d < f`)\n"
+ " - :math:`\\mu` is the mean of the data (dimension :math:`f`)\n"
+ " - :math:`\\epsilon` is the noise of the data (dimension :math:`f`) \n"
+ " - Gaussian with zero-mean and covariance matrix :math:`\\sigma^2 Id`"
).add_constructor(
bob::extension::FunctionDoc(
"__init__",
+
"Creates a EMPCATrainer",
"",
true
)
- .add_prototype("convergence_threshold","")
.add_prototype("other","")
.add_prototype("","")
.add_parameter("other", ":py:class:`bob.learn.em.EMPCATrainer`", "A EMPCATrainer object to be copied.")
- .add_parameter("convergence_threshold", "float", "")
);
@@ -47,22 +54,6 @@ static int PyBobLearnEMEMPCATrainer_init_copy(PyBobLearnEMEMPCATrainerObject* se
return 0;
}
-static int PyBobLearnEMEMPCATrainer_init_number(PyBobLearnEMEMPCATrainerObject* self, PyObject* args, PyObject* kwargs) {
-
- char** kwlist = EMPCATrainer_doc.kwlist(0);
- double convergence_threshold = 0.0001;
- //Parsing the input argments
- if (!PyArg_ParseTupleAndKeywords(args, kwargs, "d", kwlist, &convergence_threshold))
- return -1;
-
- if(convergence_threshold < 0){
- PyErr_Format(PyExc_TypeError, "convergence_threshold argument must be greater than to zero");
- return -1;
- }
-
- self->cxx.reset(new bob::learn::em::EMPCATrainer(convergence_threshold));
- return 0;
-}
static int PyBobLearnEMEMPCATrainer_init(PyBobLearnEMEMPCATrainerObject* self, PyObject* args, PyObject* kwargs) {
BOB_TRY
@@ -76,21 +67,7 @@ static int PyBobLearnEMEMPCATrainer_init(PyBobLearnEMEMPCATrainerObject* self, P
return 0;
}
case 1:{
- //Reading the input argument
- PyObject* arg = 0;
- if (PyTuple_Size(args))
- arg = PyTuple_GET_ITEM(args, 0);
- else {
- PyObject* tmp = PyDict_Values(kwargs);
- auto tmp_ = make_safe(tmp);
- arg = PyList_GET_ITEM(tmp, 0);
- }
-
- // If the constructor input is EMPCATrainer object
- if (PyBobLearnEMEMPCATrainer_Check(arg))
- return PyBobLearnEMEMPCATrainer_init_copy(self, args, kwargs);
- else if(PyString_Check(arg))
- return PyBobLearnEMEMPCATrainer_init_number(self, args, kwargs);
+ return PyBobLearnEMEMPCATrainer_init_copy(self, args, kwargs);
}
default:{
PyErr_Format(PyExc_RuntimeError, "number of arguments mismatch - %s requires 0 or 1 arguments, but you provided %d (see help)", Py_TYPE(self)->tp_name, nargs);
@@ -139,7 +116,41 @@ static PyObject* PyBobLearnEMEMPCATrainer_RichCompare(PyBobLearnEMEMPCATrainerOb
/************ Variables Section ***********************************/
/******************************************************************/
+
+/***** sigma_2 *****/
+static auto sigma2 = bob::extension::VariableDoc(
+ "sigma2",
+ "float",
+ "The noise sigma2 of the probabilistic model",
+ ""
+);
+PyObject* PyBobLearnEMEMPCATrainer_getSigma2(PyBobLearnEMEMPCATrainerObject* self, void*){
+ BOB_TRY
+ return Py_BuildValue("d",self->cxx->getSigma2());
+ BOB_CATCH_MEMBER("sigma2 could not be read", 0)
+}
+int PyBobLearnEMEMPCATrainer_setSigma2(PyBobLearnEMEMPCATrainerObject* self, PyObject* value, void*){
+ BOB_TRY
+
+ if(!PyBob_NumberCheck(value)){
+ PyErr_Format(PyExc_RuntimeError, "%s %s expects a float", Py_TYPE(self)->tp_name, sigma2.name());
+ return -1;
+ }
+
+ self->cxx->setSigma2(PyFloat_AS_DOUBLE(value));
+ return 0;
+ BOB_CATCH_MEMBER("sigma2 could not be set", -1)
+}
+
+
static PyGetSetDef PyBobLearnEMEMPCATrainer_getseters[] = {
+ {
+ sigma2.name(),
+ (getter)PyBobLearnEMEMPCATrainer_getSigma2,
+ (setter)PyBobLearnEMEMPCATrainer_setSigma2,
+ sigma2.doc(),
+ 0
+ },
{0} // Sentinel
};
@@ -257,7 +268,7 @@ static auto compute_likelihood = bob::extension::FunctionDoc(
0,
true
)
-.add_prototype("linear_machine,data")
+.add_prototype("linear_machine")
.add_parameter("linear_machine", ":py:class:`bob.learn.linear.Machine`", "LinearMachine Object");
static PyObject* PyBobLearnEMEMPCATrainer_compute_likelihood(PyBobLearnEMEMPCATrainerObject* self, PyObject* args, PyObject* kwargs) {
BOB_TRY
diff --git a/bob/learn/em/test/test_em.py b/bob/learn/em/test/test_em.py
index 97f1a2b..9acd5ce 100644
--- a/bob/learn/em/test/test_em.py
+++ b/bob/learn/em/test/test_em.py
@@ -253,3 +253,46 @@ def test_custom_trainer():
for i in range(0, 2):
assert (ar[i+1] == machine.means[i, :]).all()
+
+
+
+def test_EMPCA():
+
+ # Tests our Probabilistic PCA trainer for linear machines for a simple
+ # problem:
+ ar=numpy.array([
+ [1, 2, 3],
+ [2, 4, 19],
+ [3, 6, 5],
+ [4, 8, 13],
+ ], dtype='float64')
+
+ # Expected llh 1 and 2 (Reference values)
+ exp_llh1 = -32.8443
+ exp_llh2 = -30.8559
+
+ # Do two iterations of EM to check the training procedure
+ T = bob.learn.em.EMPCATrainer()
+ m = bob.learn.linear.Machine(3,2)
+ # Initialization of the trainer
+ T.initialize(m, ar)
+ # Sets ('random') initialization values for test purposes
+ w_init = numpy.array([1.62945, 0.270954, 1.81158, 1.67002, 0.253974,
+ 1.93774], 'float64').reshape(3,2)
+ sigma2_init = 1.82675
+ m.weights = w_init
+ T.sigma2 = sigma2_init
+ # Checks that the log likehood matches the reference one
+ # This should be sufficient to check everything as it requires to use
+ # the new value of W and sigma2
+ # This does an E-Step, M-Step, computes the likelihood, and compares it to
+ # the reference value obtained using matlab
+ T.e_step(m, ar)
+ T.m_step(m, ar)
+ llh1 = T.compute_likelihood(m)
+ assert abs(exp_llh1 - llh1) < 2e-4
+ T.e_step(m, ar)
+ T.m_step(m, ar)
+ llh2 = T.compute_likelihood(m)
+ assert abs(exp_llh2 - llh2) < 2e-4
+
diff --git a/doc/index.rst b/doc/index.rst
index a4b6ef0..d4b7062 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -42,6 +42,10 @@ References
.. [ElShafey2014] *Laurent El Shafey, Chris McCool, Roy Wallace, Sebastien Marcel*. **'A Scalable Formulation of Probabilistic Linear Discriminant Analysis: Applied to Face Recognition'**, TPAMI'2014
.. [PrinceElder2007] *Prince and Elder*. **'Probabilistic Linear Discriminant Analysis for Inference About Identity'**, ICCV'2007
.. [LiFu2012] *Li, Fu, Mohammed, Elder and Prince*. **'Probabilistic Models for Inference about Identity'**, TPAMI'2012
+
+.. [Bishop1999] Tipping, Michael E., and Christopher M. Bishop. "Probabilistic principal component analysis." Journal of the Royal Statistical Society: Series B (Statistical Methodology) 61.3 (1999): 611-622.
+.. [Roweis1998] Roweis, Sam. "EM algorithms for PCA and SPCA." Advances in neural information processing systems (1998): 626-632.
+
.. [WikiEM] `Expectation Maximization <http://en.wikipedia.org/wiki/Expectation%E2%80%93maximization_algorithm>`_
--
GitLab