void GridDomain::global_to_local(
blitz::Array<double,1> const &global,
std::vector<blitz::Array<double,1>> &olocal)
{
if (olocal.size() != this->num_local_indices) {
fprintf(stderr, "MatrixDomainer::get_rows() had bad dimension 1 = %d (expected %ld)\n", olocal.extent(1), this->num_local_indices);
throw std::exception();
}
for (auto ii = olocal.begin(); ii != olocal.end(); ++ii) {
// Make sure it has the right dimensions
if (olocal[i].extent(0) != global.extent(0)) {
fprintf(stderr, "MatrixDomainer::get_rows() had bad dimension 0 = %d (expected %ld)\n", olocal.extent(0), global.extent(0));
throw std::exception();
}
}
// Copy out data, translating to local coordinates
for (int j=0; j < global.extent(0); ++j) {
int lindex[this->num_local_indices];
this->global_to_local(global(j), lindex);
for (int i=0; i<this->num_local_indices; ++i)
olocal[i](j) = lindex[i];
}
}
double bob::learn::em::GMMMachine::logLikelihood(const blitz::Array<double, 1> &x,
blitz::Array<double,1> &log_weighted_gaussian_likelihoods) const
{
// Check dimension
bob::core::array::assertSameDimensionLength(log_weighted_gaussian_likelihoods.extent(0), m_n_gaussians);
bob::core::array::assertSameDimensionLength(x.extent(0), m_n_inputs);
return logLikelihood_(x,log_weighted_gaussian_likelihoods);
}
void Machine::setInputDivision (const blitz::Array<double,1>& v) {
if (m_weight.extent(0) != v.extent(0)) {
boost::format m("mismatch on the input division shape: expected a vector of size %d, but you input one with size = %d instead");
m % m_weight.extent(0) % v.extent(0);
throw std::runtime_error(m.str());
}
m_input_div.reference(bob::core::array::ccopy(v));
}
blitz::Array<double,1> bob::example::library::reverse (const blitz::Array<double,1>& array){
// create new array in the desired shape
blitz::Array<double,1> retval(array.shape());
// copy data
for (int i = 0, j = array.extent(0)-1; i < array.extent(0); ++i, --j){
retval(j) = array(i);
}
// return the copied data
return retval;
}
void Machine::setBiases (const blitz::Array<double,1>& bias) {
if (m_weight.extent(1) != bias.extent(0)) {
boost::format m("mismatch on the bias shape: expected a vector of size %d, but you input one with size = %d instead");
m % m_weight.extent(1) % bias.extent(0);
throw std::runtime_error(m.str());
}
m_bias.reference(bob::core::array::ccopy(bias));
}
Machine::Machine(const blitz::Array<double,2>& weight)
: m_input_sub(weight.extent(0)),
m_input_div(weight.extent(0)),
m_bias(weight.extent(1)),
m_activation(boost::make_shared<bob::learn::activation::IdentityActivation>()),
m_buffer(weight.extent(0))
{
m_input_sub = 0.0;
m_input_div = 1.0;
m_bias = 0.0;
m_weight.reference(bob::core::array::ccopy(weight));
}
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);
}
void check_dimensions(
std::string const &vname,
blitz::Array<T, rank> const &arr,
std::vector<int> const &dims)
{
for (int i=0; i<rank; ++i) {
if (dims[i] >= 0 && arr.extent(i) != dims[i]) {
fprintf(stderr,
"Error in %s: expected dimension #%d = %d (is %d instead)\n",
vname.c_str(), i, dims[i], arr.extent(i));
throw std::exception();
}
}
}
void Machine::forward (const blitz::Array<double,1>& input, blitz::Array<double,1>& output) const {
if (m_weight.extent(0) != input.extent(0)) { //checks input dimension
boost::format m("mismatch on the input dimension: expected a vector of size %d, but you input one with size = %d instead");
m % m_weight.extent(0) % input.extent(0);
throw std::runtime_error(m.str());
}
if (m_weight.extent(1) != output.extent(0)) { //checks output dimension
boost::format m("mismatch on the output dimension: expected a vector of size %d, but you input one with size = %d instead");
m % m_weight.extent(1) % output.extent(0);
throw std::runtime_error(m.str());
}
forward_(input, output);
}
void Machine::setWeights (const blitz::Array<double,2>& weight) {
if (weight.extent(0) != m_input_sub.extent(0)) { //checks 1st dimension
boost::format m("mismatch on the weight shape (number of rows): expected a weight matrix with %d row(s), but you input one with %d row(s) instead");
m % m_input_sub.extent(0) % weight.extent(0);
throw std::runtime_error(m.str());
}
if (weight.extent(1) != m_bias.extent(0)) { //checks 2nd dimension
boost::format m("mismatch on the weight shape (number of columns): expected a weight matrix with %d column(s), but you input one with %d column(s) instead");
m % m_bias.extent(0) % weight.extent(1);
throw std::runtime_error(m.str());
}
m_weight.reference(bob::core::array::ccopy(weight));
}
void bob::learn::boosting::LUTTrainer::weightedHistogram(const blitz::Array<uint16_t,1>& features, const blitz::Array<double,1>& weights) const{
bob::core::array::assertSameShape(features, weights);
_gradientHistogram = 0.;
for (int i = features.extent(0); i--;){
_gradientHistogram((int)features(i)) += weights(i);
}
}
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);
// Call the other logLikelihood_ (overloaded) function
// (log_weighted_gaussian_likelihoods will be discarded)
return logLikelihood_(x,m_cache_log_weighted_gaussian_likelihoods);
}
double bob::math::det_(const blitz::Array<double,2>& A)
{
// Size variable
int N = A.extent(0);
// Perform an LU decomposition
blitz::Array<double,2> L(N,N);
blitz::Array<double,2> U(N,N);
blitz::Array<double,2> P(N,N);
math::lu(A, L, U, P);
// Compute the determinant of A = det(P*L)*PI(diag(U))
// where det(P*L) = +- 1 (Number of permutation in P)
// and PI(diag(U)) is the product of the diagonal elements of U
blitz::Array<double,2> Lperm(N,N);
math::prod(P,L,Lperm);
int s = 1;
double Udiag=1.;
for (int i=0; i<N; ++i)
{
for (int j=i+1; j<N; ++j)
if (P(i,j) > 0)
{
s = -s;
break;
}
Udiag *= U(i,i);
}
return s*Udiag;
}
void bob::learn::em::GMMMachine::setVarianceThresholds(const blitz::Array<double, 2>& variance_thresholds) {
bob::core::array::assertSameDimensionLength(variance_thresholds.extent(0), m_n_gaussians);
bob::core::array::assertSameDimensionLength(variance_thresholds.extent(1), m_n_inputs);
for(size_t i=0; i<m_n_gaussians; ++i)
m_gaussians[i]->setVarianceThresholds(variance_thresholds(i,blitz::Range::all()));
m_cache_supervector = false;
}
double bob::math::slogdet_(const blitz::Array<double,2>& A, int& sign)
{
// Size variable
int N = A.extent(0);
// Perform an LU decomposition
blitz::Array<double,2> L(N,N);
blitz::Array<double,2> U(N,N);
blitz::Array<double,2> P(N,N);
math::lu(A, L, U, P);
// Compute the determinant of A = det(P*L)*SI(diag(U))
// where det(P*L) = +- 1 (Number of permutation in P)
// and SI(diag(log|U|)) is the sum of the logarithm of the
// diagonal elements of U
blitz::Array<double,2> Lperm(N,N);
math::prod(P,L,Lperm);
sign = 1;
double Udiag=0.;
for (int i=0; i<N; ++i)
{
for (int j=i+1; j<N; ++j)
if (P(i,j) > 0)
{
sign = -sign;
break;
}
Udiag += log(fabs(U(i,i)));
}
// Check for infinity
if ((Udiag*-1) == std::numeric_limits<double>::infinity())
sign = 0;
return Udiag;
}
void bob::learn::em::GMMMachine::setMeans(const blitz::Array<double,2> &means) {
bob::core::array::assertSameDimensionLength(means.extent(0), m_n_gaussians);
bob::core::array::assertSameDimensionLength(means.extent(1), m_n_inputs);
for(size_t i=0; i<m_n_gaussians; ++i)
m_gaussians[i]->updateMean() = means(i,blitz::Range::all());
m_cache_supervector = false;
}
void netcdf_write_blitz(NcVar *nc_var, blitz::Array<T, rank> const &val)
{
long counts[rank];
for (int i=0; i<rank; ++i) counts[i] = val.extent(i);
//printf("netcdf_write_blitz: %p %p\n", nc_var, val.data());
nc_var->put(val.data(), counts);
}
void bob::learn::em::GMMMachine::setVarianceSupervector(const blitz::Array<double,1> &variance_supervector) {
bob::core::array::assertSameDimensionLength(variance_supervector.extent(0), m_n_gaussians*m_n_inputs);
for(size_t i=0; i<m_n_gaussians; ++i) {
m_gaussians[i]->updateVariance() = variance_supervector(blitz::Range(i*m_n_inputs, (i+1)*m_n_inputs-1));
m_gaussians[i]->applyVarianceThresholds();
}
m_cache_supervector = false;
}
void bob::learn::em::GMMMachine::accStatistics_(const blitz::Array<double,2>& input, bob::learn::em::GMMStats& stats) const {
// iterate over data
blitz::Range a = blitz::Range::all();
for(int i=0; i<input.extent(0); ++i) {
// Get example
blitz::Array<double,1> x(input(i, a));
// Accumulate statistics
accStatistics_(x,stats);
}
}
int32_t bob::learn::boosting::LUTTrainer::bestIndex(const blitz::Array<double,1>& array) const{
double min = std::numeric_limits<double>::max();
int32_t minIndex = -1;
for (int i = 0; i < array.extent(0); ++i){
if (array(i) < min){
min = array(i);
minIndex = i;
}
}
return minIndex;
}
void bob::ip::base::TanTriggs::performContrastEqualization(blitz::Array<double,2>& dst)
{
const double inv_alpha = 1./m_alpha;
const double wxh = dst.extent(0)*dst.extent(1);
// first step: I:=I/mean(abs(I)^a)^(1/a)
blitz::Range dst_y( dst.lbound(0), dst.ubound(0)),
dst_x( dst.lbound(1), dst.ubound(1));
double norm_fact =
pow( sum( pow( fabs(dst(dst_y,dst_x)), m_alpha)) / wxh, inv_alpha);
dst(dst_y,dst_x) /= norm_fact;
// Second step: I:=I/mean(min(threshold,abs(I))^a)^(1/a)
const double threshold_alpha = pow( m_threshold, m_alpha );
norm_fact = pow( sum( min( threshold_alpha,
pow( fabs(dst(dst_y,dst_x)), m_alpha))) / wxh, inv_alpha);
dst(dst_y,dst_x) /= norm_fact;
// Last step: I:= threshold * tanh( I / threshold )
dst(dst_y,dst_x) = m_threshold * tanh( dst(dst_y,dst_x) / m_threshold );
}
boost::function<void ()> netcdf_define(
NcFile &nc,
std::string const &vname,
blitz::Array<T,rank> const &val,
std::vector<NcDim *> const &ddims = {})
{
// Type-check for unit strides
int stride = 1;
for (int i=rank-1; i>=0; --i) {
if (val.stride(i) != stride) {
fprintf(stderr, "Unexpected stride of %d (should be %d) in dimension %d (extent=%d) of %s (rank=%d)\n", val.stride(i), stride, i, val.extent(i), vname.c_str(), rank);
fprintf(stderr, "Are you trying to write a Fortran-style array? Use f_to_c() in blitz.hpp first\n");
throw std::exception();
}
//printf("(stride=%d) *= (val.extent[%d]=%d)\n", stride, i, val.extent(i));
stride *= val.extent(i);
}
// Create the required dimensions
NcDim const *dims[rank];
for (int i=0; i<rank; ++i) {
if (i >= ddims.size()) {
char dim_name[200];
sprintf(dim_name, "%s.dim%d", vname.c_str(), i);
dims[i] = nc.add_dim(dim_name, val.extent(i));
} else {
dims[i] = ddims[i];
}
assert(dims[i] != NULL);
}
// Create the variable
NcVar *nc_var = nc.add_var(vname.c_str(), get_nc_type<T>(), rank, dims);
assert(nc_var != NULL);
// Write it out (later)
return boost::bind(&netcdf_write_blitz<T,rank>, nc_var, val);
}
void matmul_A_M_B( const blitz::Array<VAL,2> & A, blitz::Array<VAL,2> & M, const blitz::Array<VAL,2> & B ) {
assert (A.extent(0) == A.extent(1));
assert (B.extent(0) == B.extent(1));
assert (A.extent(1) == M.extent(0));
assert (B.extent(0) == M.extent(1));
blitz::Array<VAL,2> tmp(M.extent(0),B.extent(1), blitz::fortranArray);
matmul_lapack(M, B ,tmp);
matmul_lapack( A, tmp, M);
}
void bob::io::audio::Writer::append(const blitz::Array<double,1>& data) {
if (!m_opened) {
boost::format m("audio writer for file `%s' is closed and cannot be written to");
m % m_filename;
throw std::runtime_error(m.str());
}
if (!m_typeinfo.shape[0]) /* set for the first time */ {
m_file->signal.channels = data.extent(0);
m_typeinfo.shape[0] = data.extent(0);
m_typeinfo.update_strides();
}
//checks data specifications
if (m_typeinfo.shape[0] != (size_t)data.extent(0)) {
boost::format m("input sample size for file `%s' should be (%d,)");
m % m_filename % m_typeinfo.shape[0];
throw std::runtime_error(m.str());
}
for (int j=0; j<data.extent(0); ++j)
m_buffer[j] = (sox_sample_t)(data(j) * bob::io::audio::SOX_CONVERSION_COEF);
size_t written = sox_write(m_file.get(), m_buffer.get(), m_typeinfo.shape[0]);
// updates internal counters
m_file->signal.length += m_file->signal.channels;
m_typeinfo.shape[1] += 1;
m_typeinfo.update_strides();
if (written != 1) {
boost::format m("I was asked to append 1 sample to file `%s', but `sox_write()' failed miserably - this is not a definitive error, the stream is still sane");
m % m_filename;
throw std::runtime_error(m.str());
}
}
void bob::math::eigSym(const blitz::Array<double,2>& A, const blitz::Array<double,2>& B,
blitz::Array<double,2>& V, blitz::Array<double,1>& D)
{
// Size variable
const int N = A.extent(0);
const blitz::TinyVector<int,1> shape1(N);
const blitz::TinyVector<int,2> shape2(N,N);
bob::core::array::assertZeroBase(A);
bob::core::array::assertZeroBase(B);
bob::core::array::assertZeroBase(V);
bob::core::array::assertZeroBase(D);
bob::core::array::assertSameShape(A,shape2);
bob::core::array::assertSameShape(B,shape2);
bob::core::array::assertSameShape(V,shape2);
bob::core::array::assertSameShape(D,shape1);
bob::math::eigSym_(A, B, V, D);
}
boost::shared_ptr<bob::learn::boosting::LUTMachine> bob::learn::boosting::LUTTrainer::train(const blitz::Array<uint16_t,2>& trainingFeatures, const blitz::Array<double,2>& lossGradient) const{
int featureLength = trainingFeatures.extent(1);
_lossSum.resize(featureLength, m_numberOfOutputs);
// Compute the sum of the gradient based on the feature values or the loss associated with each feature index
// Compute the loss for each feature
for (int featureIndex = featureLength; featureIndex--;){
for (int outputIndex = m_numberOfOutputs; outputIndex--;){
weightedHistogram(trainingFeatures(blitz::Range::all(),featureIndex), lossGradient(blitz::Range::all(), outputIndex));
_lossSum(featureIndex,outputIndex) = - blitz::sum(blitz::abs(_gradientHistogram));
}
}
// Select the most discriminative index (or indices) for classification which minimizes the loss
// and compute the sum of gradient for that index
if (m_selectionType == independent){
// independent feature selection is used if all the dimension of output use different feature
// each of the selected feature minimize a dimension of the loss function
for (int outputIndex = m_numberOfOutputs; outputIndex--;){
_selectedIndices(outputIndex) = bestIndex(_lossSum(blitz::Range::all(),outputIndex));
}
} else {
// for 'shared' feature selection the loss function is summed over multiple dimensions and
// the feature that minimized this cumulative loss is used for all the outputs
blitz::secondIndex j;
const blitz::Array<double,1> sum(blitz::sum(_lossSum, j));
_selectedIndices = bestIndex(sum);
}
// compute the look-up-tables for the best index
for (int outputIndex = m_numberOfOutputs; outputIndex--;){
int selectedIndex = _selectedIndices(outputIndex);
weightedHistogram(trainingFeatures(blitz::Range::all(), selectedIndex), lossGradient(blitz::Range::all(), outputIndex));
for (int lutIndex = m_maximumFeatureValue; lutIndex--;){
_luts(lutIndex, outputIndex) = (_gradientHistogram(lutIndex) > 0) * 2. - 1.;
}
}
// create new weak machine
return boost::shared_ptr<LUTMachine>(new LUTMachine(_luts.copy(), _selectedIndices.copy()));
}
void bob::ap::Ceps::addDerivative(const blitz::Array<double,2>& input, blitz::Array<double,2>& output) const
{
// Initialize output to zero
output = 0.;
const int n_frames = input.extent(0);
blitz::Range rall = blitz::Range::all();
// Fill in the inner part as follows:
// \f$output[i] += \sum_{l=1}^{DW} l * (input[i+l] - input[i-l])\f$
for (int l=1; l<=(int)m_delta_win; ++l) {
blitz::Range rout(l,n_frames-l-1);
blitz::Range rp(2*l,n_frames-1);
blitz::Range rn(0,n_frames-2*l-1);
output(rout,rall) += l*(input(rp,rall) - input(rn,rall));
}
const double factor = m_delta_win*(m_delta_win+1)/2;
// Continue to fill the left boundary part as follows:
// \f$output[i] += (\sum_{l=1+i}^{DW} l*input[i+l]) - (\sum_{l=i+1}^{DW}l)*input[0])\f$
for (int i=0; i<(int)m_delta_win; ++i) {
output(i,rall) -= (factor - i*(i+1)/2) * input(0,rall);
for (int l=1+i; l<=(int)m_delta_win; ++l) {
output(i,rall) += l*(input(i+l,rall));
}
}
// Continue to fill the right boundary part as follows:
// \f$output[i] += (\sum_{l=Nframes-1-i}^{DW}l)*input[Nframes-1]) - (\sum_{l=Nframes-1-i}^{DW} l*input[i-l])\f$
for (int i=n_frames-(int)m_delta_win; i<n_frames; ++i) {
int ii = (n_frames-1)-i;
output(i,rall) += (factor - ii*(ii+1)/2) * input(n_frames-1,rall);
for (int l=1+ii; l<=(int)m_delta_win; ++l) {
output(i,rall) -= l*input(i-l,rall);
}
}
// Sum of the integer squared from 1 to delta_win
// pavel - remove division for the sake of compitability with Matlab code of RFFC features comparison paper
//const double sum = m_delta_win*(m_delta_win+1)*(2*m_delta_win+1)/3;
//output /= sum;
}
void bob::learn::em::GMMMachine::setMeanSupervector(const blitz::Array<double,1> &mean_supervector) {
bob::core::array::assertSameDimensionLength(mean_supervector.extent(0), m_n_gaussians*m_n_inputs);
for(size_t i=0; i<m_n_gaussians; ++i)
m_gaussians[i]->updateMean() = mean_supervector(blitz::Range(i*m_n_inputs, (i+1)*m_n_inputs-1));
m_cache_supervector = false;
}
double bob::math::slogdet(const blitz::Array<double,2>& A, int& sign)
{
bob::core::array::assertSameDimensionLength(A.extent(0),A.extent(1));
return bob::math::slogdet_(A, sign);
}
void bob::math::eigSym_(const blitz::Array<double,2>& A, const blitz::Array<double,2>& B,
blitz::Array<double,2>& V, blitz::Array<double,1>& D)
{
// Size variable
const int N = A.extent(0);
// Prepares to call LAPACK function
// Initialises LAPACK variables
const int itype = 1;
const char jobz = 'V'; // Get both the eigenvalues and the eigenvectors
const char uplo = 'U';
int info = 0;
const int lda = N;
const int ldb = N;
// Initialises LAPACK arrays
blitz::Array<double,2> A_blitz_lapack;
// Tries to use V directly
blitz::Array<double,2> Vt = V.transpose(1,0);
const bool V_direct_use = bob::core::array::isCZeroBaseContiguous(Vt);
if (V_direct_use)
{
A_blitz_lapack.reference(Vt);
// Ugly fix for non-const transpose
A_blitz_lapack = const_cast<blitz::Array<double,2>&>(A).transpose(1,0);
}
else
// Ugly fix for non-const transpose
A_blitz_lapack.reference(
bob::core::array::ccopy(const_cast<blitz::Array<double,2>&>(A).transpose(1,0)));
double *A_lapack = A_blitz_lapack.data();
// Ugly fix for non-const transpose
blitz::Array<double,2> B_blitz_lapack(
bob::core::array::ccopy(const_cast<blitz::Array<double,2>&>(B).transpose(1,0)));
double *B_lapack = B_blitz_lapack.data();
blitz::Array<double,1> D_blitz_lapack;
const bool D_direct_use = bob::core::array::isCZeroBaseContiguous(D);
if (D_direct_use)
D_blitz_lapack.reference(D);
else
D_blitz_lapack.resize(D.shape());
double *D_lapack = D_blitz_lapack.data();
// Calls the LAPACK function
// A/ Queries the optimal size of the working arrays
const int lwork_query = -1;
double work_query;
const int liwork_query = -1;
int iwork_query;
dsygvd_( &itype, &jobz, &uplo, &N, A_lapack, &lda, B_lapack, &ldb, D_lapack,
&work_query, &lwork_query, &iwork_query, &liwork_query, &info);
// B/ Computes the generalized eigenvalue decomposition
const int lwork = static_cast<int>(work_query);
boost::shared_array<double> work(new double[lwork]);
const int liwork = static_cast<int>(iwork_query);
boost::shared_array<int> iwork(new int[liwork]);
dsygvd_( &itype, &jobz, &uplo, &N, A_lapack, &lda, B_lapack, &ldb, D_lapack,
work.get(), &lwork, iwork.get(), &liwork, &info);
// Checks info variable
if (info != 0)
throw std::runtime_error("The LAPACK function 'dsygvd' returned a non-zero value. This might be caused by a non-positive definite B matrix.");
// Copy singular vectors back to V if required
if (!V_direct_use)
V = A_blitz_lapack.transpose(1,0);
// Copy result back to sigma if required
if (!D_direct_use)
D = D_blitz_lapack;
}