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„XDAWN_Trainer/ovpCBoxAlgorithmXDAWNTrainer.cpp“ ändern

master
Tobias Baumann 2 years ago
parent
commit
6ebaea4961
1 changed files with 282 additions and 282 deletions
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    282
      XDAWN_Trainer/ovpCBoxAlgorithmXDAWNTrainer.cpp

ovpCBoxAlgorithmXDAWNTrainer.cpp → XDAWN_Trainer/ovpCBoxAlgorithmXDAWNTrainer.cpp View File

@@ -1,282 +1,282 @@
#include "ovpCBoxAlgorithmXDAWNTrainer.h"
#include "fs/Files.h"
#include <cstdio>
#include <iostream>
namespace OpenViBE {
namespace Plugins {
namespace SignalProcessing {
CBoxAlgorithmXDAWNTrainer::CBoxAlgorithmXDAWNTrainer() {}
bool CBoxAlgorithmXDAWNTrainer::initialize()
{
m_trainStimulationID = FSettingValueAutoCast(*this->getBoxAlgorithmContext(), 0);
m_filterFilename = FSettingValueAutoCast(*this->getBoxAlgorithmContext(), 1);
OV_ERROR_UNLESS_KRF(m_filterFilename.length() != 0, "The filter filename is empty.\n", Kernel::ErrorType::BadSetting);
if (FS::Files::fileExists(m_filterFilename))
{
FILE* file = FS::Files::open(m_filterFilename, "wt");
OV_ERROR_UNLESS_KRF(file != nullptr, "The filter file exists but cannot be used.\n", Kernel::ErrorType::BadFileRead);
fclose(file);
}
const int filterDimension = FSettingValueAutoCast(*this->getBoxAlgorithmContext(), 2);
OV_ERROR_UNLESS_KRF(filterDimension > 0, "The dimension of the filter must be strictly positive.\n", Kernel::ErrorType::OutOfBound);
m_filterDim = size_t(filterDimension);
m_saveAsBoxConfig = FSettingValueAutoCast(*this->getBoxAlgorithmContext(), 3);
m_stimDecoder.initialize(*this, 0);
m_signalDecoder[0].initialize(*this, 1);
m_signalDecoder[1].initialize(*this, 2);
m_stimEncoder.initialize(*this, 0);
return true;
}
bool CBoxAlgorithmXDAWNTrainer::uninitialize()
{
m_stimDecoder.uninitialize();
m_signalDecoder[0].uninitialize();
m_signalDecoder[1].uninitialize();
m_stimEncoder.uninitialize();
return true;
}
bool CBoxAlgorithmXDAWNTrainer::processInput(const size_t index)
{
if (index == 0) { this->getBoxAlgorithmContext()->markAlgorithmAsReadyToProcess(); }
return true;
}
bool CBoxAlgorithmXDAWNTrainer::process()
{
Kernel::IBoxIO& dynamicBoxContext = this->getDynamicBoxContext();
bool train = false;
for (size_t i = 0; i < dynamicBoxContext.getInputChunkCount(0); ++i)
{
m_stimEncoder.getInputStimulationSet()->clear();
m_stimDecoder.decode(i);
if (m_stimDecoder.isHeaderReceived()) { m_stimEncoder.encodeHeader(); }
if (m_stimDecoder.isBufferReceived())
{
for (size_t j = 0; j < m_stimDecoder.getOutputStimulationSet()->getStimulationCount(); ++j)
{
const uint64_t stimulationId = m_stimDecoder.getOutputStimulationSet()->getStimulationIdentifier(j);
if (stimulationId == m_trainStimulationID)
{
train = true;
m_stimEncoder.getInputStimulationSet()->appendStimulation(
OVTK_StimulationId_TrainCompleted, m_stimDecoder.getOutputStimulationSet()->getStimulationDate(j), 0);
}
}
m_stimEncoder.encodeBuffer();
}
if (m_stimDecoder.isEndReceived()) { m_stimEncoder.encodeEnd(); }
dynamicBoxContext.markOutputAsReadyToSend(0, dynamicBoxContext.getInputChunkStartTime(0, i), dynamicBoxContext.getInputChunkEndTime(0, i));
}
if (train)
{
std::vector<size_t> erpSampleIndexes;
std::array<Eigen::MatrixXd, 2> X; // X[0] is session matrix, X[1] is averaged ERP
std::array<Eigen::MatrixXd, 2> C; // Covariance matrices
std::array<size_t, 2> n;
size_t nChannel = 0;
this->getLogManager() << Kernel::LogLevel_Info << "Received train stimulation...\n";
// Decodes input signals
for (size_t j = 0; j < 2; ++j)
{
n[j] = 0;
for (size_t i = 0; i < dynamicBoxContext.getInputChunkCount(j + 1); ++i)
{
Toolkit::TSignalDecoder<CBoxAlgorithmXDAWNTrainer>& decoder = m_signalDecoder[j];
decoder.decode(i);
CMatrix* matrix = decoder.getOutputMatrix();
nChannel = matrix->getDimensionSize(0);
const size_t nSample = matrix->getDimensionSize(1);
const size_t sampling = size_t(decoder.getOutputSamplingRate());
if (decoder.isHeaderReceived())
{
OV_ERROR_UNLESS_KRF(sampling > 0, "Input sampling frequency is equal to 0. Plugin can not process.\n", Kernel::ErrorType::OutOfBound);
OV_ERROR_UNLESS_KRF(nChannel > 0, "For condition " << j + 1 << " got no channel in signal stream.\n", Kernel::ErrorType::OutOfBound);
OV_ERROR_UNLESS_KRF(nSample > 0, "For condition " << j + 1 << " got no samples in signal stream.\n", Kernel::ErrorType::OutOfBound);
OV_ERROR_UNLESS_KRF(m_filterDim <= nChannel, "The filter dimension must not be superior than the channel count.\n", Kernel::ErrorType::OutOfBound);
if (!n[0]) // Initialize signal buffer (X[0]) only when receiving input signal header.
{
X[j].resize(nChannel, (dynamicBoxContext.getInputChunkCount(j + 1) - 1) * nSample);
}
else // otherwise, only ERP averaging buffer (X[1]) is reset
{
X[j] = Eigen::MatrixXd::Zero(nChannel, nSample);
}
}
if (decoder.isBufferReceived())
{
Eigen::MatrixXd A = Eigen::Map<Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor>>(
matrix->getBuffer(), nChannel, nSample);
switch (j)
{
case 0: // Session
X[j].block(0, n[j] * A.cols(), A.rows(), A.cols()) = A;
break;
case 1: // ERP
X[j] = X[j] + A; // Computes sumed ERP
// $$$ Assumes continuous session signal starting at date 0
{
size_t ERPSampleIndex = size_t(((dynamicBoxContext.getInputChunkStartTime(j + 1, i) >> 16) * sampling) >> 16);
erpSampleIndexes.push_back(ERPSampleIndex);
}
break;
default:
break;
}
n[j]++;
}
#if 0
if (decoder.isEndReceived())
{
}
#endif
}
OV_ERROR_UNLESS_KRF(n[j] != 0, "Did not have input signal for condition " << j + 1 << "\n", Kernel::ErrorType::BadValue);
switch (j)
{
case 0: // Session
break;
case 1: // ERP
X[j] = X[j] / double(n[j]); // Averages ERP
break;
default:
break;
}
}
// We need equal number of channels
OV_ERROR_UNLESS_KRF(X[0].rows() == X[1].rows(),
"Dimension mismatch, first input had " << size_t(X[0].rows()) << " channels while second input had " << size_t(X[1].rows()) <<
" channels\n",
Kernel::ErrorType::BadValue);
// Grabs usefull values
const size_t sampleCountSession = X[0].cols();
const size_t sampleCountERP = X[1].cols();
// Now we compute matrix D
const Eigen::MatrixXd DI = Eigen::MatrixXd::Identity(sampleCountERP, sampleCountERP);
Eigen::MatrixXd D = Eigen::MatrixXd::Zero(sampleCountERP, sampleCountSession);
for (size_t sampleIndex : erpSampleIndexes) { D.block(0, sampleIndex, sampleCountERP, sampleCountERP) += DI; }
// Computes covariance matrices
C[0] = X[0] * X[0].transpose();
C[1] = /*Y * Y.transpose();*/ X[1] * /* D.transpose() * */ (D * D.transpose()).fullPivLu().inverse() /* * D */ * X[1].transpose();
// Solves generalized eigen decomposition
const Eigen::GeneralizedSelfAdjointEigenSolver<Eigen::MatrixXd> eigenSolver(C[0].selfadjointView<Eigen::Lower>(), C[1].selfadjointView<Eigen::Lower>());
if (eigenSolver.info() != Eigen::Success)
{
const enum Eigen::ComputationInfo error = eigenSolver.info();
const char* errorMessage = "unknown";
switch (error)
{
case Eigen::NumericalIssue: errorMessage = "Numerical issue";
break;
case Eigen::NoConvergence: errorMessage = "No convergence";
break;
// case Eigen::InvalidInput: errorMessage="Invalid input"; break; // FIXME
default: break;
}
OV_ERROR_KRF("Could not solve generalized eigen decomposition, got error[" << CString(errorMessage) << "]\n",
Kernel::ErrorType::BadProcessing);
}
// Create a CMatrix mapper that can spool the filters to a file
CMatrix eigenVectors;
eigenVectors.resize(m_filterDim, nChannel);
Eigen::Map<MatrixXdRowMajor> vectorsMapper(eigenVectors.getBuffer(), m_filterDim, nChannel);
vectorsMapper.block(0, 0, m_filterDim, nChannel) = eigenSolver.eigenvectors().block(0, 0, nChannel, m_filterDim).transpose();
// Saves filters
FILE* file = FS::Files::open(m_filterFilename.toASCIIString(), "wt");
OV_ERROR_UNLESS_KRF(file != nullptr, "Could not open file [" << m_filterFilename << "] for writing.\n", Kernel::ErrorType::BadFileWrite);
if (m_saveAsBoxConfig)
{
fprintf(file, "<OpenViBE-SettingsOverride>\n");
fprintf(file, "\t<SettingValue>");
for (size_t i = 0; i < eigenVectors.getBufferElementCount(); ++i) { fprintf(file, "%e ", eigenVectors.getBuffer()[i]); }
fprintf(file, "</SettingValue>\n");
fprintf(file, "\t<SettingValue>%u</SettingValue>\n", (unsigned int)m_filterDim);
fprintf(file, "\t<SettingValue>%u</SettingValue>\n", (unsigned int)nChannel);
fprintf(file, "\t<SettingValue></SettingValue>\n");
fprintf(file, "</OpenViBE-SettingsOverride>");
}
else
{
OV_ERROR_UNLESS_KRF(Toolkit::Matrix::saveToTextFile(eigenVectors, m_filterFilename),
"Unable to save to [" << m_filterFilename << "]\n", Kernel::ErrorType::BadFileWrite);
}
OV_WARNING_UNLESS_K(fclose(file) == 0, "Could not close file[" << m_filterFilename << "].\n");
this->getLogManager() << Kernel::LogLevel_Info << "Training finished and saved to [" << m_filterFilename << "]!\n";
}
return true;
}
} // namespace SignalProcessing
} // namespace Plugins
} // namespace OpenViBE
#include "ovpCBoxAlgorithmXDAWNTrainer.h"
#include "fs/Files.h"
#include <cstdio>
#include <iostream>
namespace OpenViBE {
namespace Plugins {
namespace SignalProcessing {
CBoxAlgorithmXDAWNTrainer::CBoxAlgorithmXDAWNTrainer() {}
bool CBoxAlgorithmXDAWNTrainer::initialize()
{
m_trainStimulationID = FSettingValueAutoCast(*this->getBoxAlgorithmContext(), 0);
m_filterFilename = FSettingValueAutoCast(*this->getBoxAlgorithmContext(), 1);
OV_ERROR_UNLESS_KRF(m_filterFilename.length() != 0, "The filter filename is empty.\n", Kernel::ErrorType::BadSetting);
if (FS::Files::fileExists(m_filterFilename))
{
FILE* file = FS::Files::open(m_filterFilename, "wt");
OV_ERROR_UNLESS_KRF(file != nullptr, "The filter file exists but cannot be used.\n", Kernel::ErrorType::BadFileRead);
fclose(file);
}
const int filterDimension = FSettingValueAutoCast(*this->getBoxAlgorithmContext(), 2);
OV_ERROR_UNLESS_KRF(filterDimension > 0, "The dimension of the filter must be strictly positive.\n", Kernel::ErrorType::OutOfBound);
m_filterDim = size_t(filterDimension);
m_saveAsBoxConfig = FSettingValueAutoCast(*this->getBoxAlgorithmContext(), 3);
m_stimDecoder.initialize(*this, 0);
m_signalDecoder[0].initialize(*this, 1);
m_signalDecoder[1].initialize(*this, 2);
m_stimEncoder.initialize(*this, 0);
return true;
}
bool CBoxAlgorithmXDAWNTrainer::uninitialize()
{
m_stimDecoder.uninitialize();
m_signalDecoder[0].uninitialize();
m_signalDecoder[1].uninitialize();
m_stimEncoder.uninitialize();
return true;
}
bool CBoxAlgorithmXDAWNTrainer::processInput(const size_t index)
{
if (index == 0) { this->getBoxAlgorithmContext()->markAlgorithmAsReadyToProcess(); }
return true;
}
bool CBoxAlgorithmXDAWNTrainer::process()
{
Kernel::IBoxIO& dynamicBoxContext = this->getDynamicBoxContext();
bool train = false;
for (size_t i = 0; i < dynamicBoxContext.getInputChunkCount(0); ++i)
{
m_stimEncoder.getInputStimulationSet()->clear();
m_stimDecoder.decode(i);
if (m_stimDecoder.isHeaderReceived()) { m_stimEncoder.encodeHeader(); }
if (m_stimDecoder.isBufferReceived())
{
for (size_t j = 0; j < m_stimDecoder.getOutputStimulationSet()->getStimulationCount(); ++j)
{
const uint64_t stimulationId = m_stimDecoder.getOutputStimulationSet()->getStimulationIdentifier(j);
if (stimulationId == m_trainStimulationID)
{
train = true;
m_stimEncoder.getInputStimulationSet()->appendStimulation(
OVTK_StimulationId_TrainCompleted, m_stimDecoder.getOutputStimulationSet()->getStimulationDate(j), 0);
}
}
m_stimEncoder.encodeBuffer();
}
if (m_stimDecoder.isEndReceived()) { m_stimEncoder.encodeEnd(); }
dynamicBoxContext.markOutputAsReadyToSend(0, dynamicBoxContext.getInputChunkStartTime(0, i), dynamicBoxContext.getInputChunkEndTime(0, i));
}
if (train)
{
std::vector<size_t> erpSampleIndexes;
std::array<Eigen::MatrixXd, 2> X; // X[0] is session matrix, X[1] is averaged ERP
std::array<Eigen::MatrixXd, 2> C; // Covariance matrices
std::array<size_t, 2> n;
size_t nChannel = 0;
this->getLogManager() << Kernel::LogLevel_Info << "Received train stimulation...\n";
// Decodes input signals
for (size_t j = 0; j < 2; ++j)
{
n[j] = 0;
for (size_t i = 0; i < dynamicBoxContext.getInputChunkCount(j + 1); ++i)
{
Toolkit::TSignalDecoder<CBoxAlgorithmXDAWNTrainer>& decoder = m_signalDecoder[j];
decoder.decode(i);
CMatrix* matrix = decoder.getOutputMatrix();
nChannel = matrix->getDimensionSize(0);
const size_t nSample = matrix->getDimensionSize(1);
const size_t sampling = size_t(decoder.getOutputSamplingRate());
if (decoder.isHeaderReceived())
{
OV_ERROR_UNLESS_KRF(sampling > 0, "Input sampling frequency is equal to 0. Plugin can not process.\n", Kernel::ErrorType::OutOfBound);
OV_ERROR_UNLESS_KRF(nChannel > 0, "For condition " << j + 1 << " got no channel in signal stream.\n", Kernel::ErrorType::OutOfBound);
OV_ERROR_UNLESS_KRF(nSample > 0, "For condition " << j + 1 << " got no samples in signal stream.\n", Kernel::ErrorType::OutOfBound);
OV_ERROR_UNLESS_KRF(m_filterDim <= nChannel, "The filter dimension must not be superior than the channel count.\n", Kernel::ErrorType::OutOfBound);
if (!n[0]) // Initialize signal buffer (X[0]) only when receiving input signal header.
{
X[j].resize(nChannel, (dynamicBoxContext.getInputChunkCount(j + 1) - 1) * nSample);
}
else // otherwise, only ERP averaging buffer (X[1]) is reset
{
X[j] = Eigen::MatrixXd::Zero(nChannel, nSample);
}
}
if (decoder.isBufferReceived())
{
Eigen::MatrixXd A = Eigen::Map<Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor>>(
matrix->getBuffer(), nChannel, nSample);
switch (j)
{
case 0: // Session
X[j].block(0, n[j] * A.cols(), A.rows(), A.cols()) = A;
break;
case 1: // ERP
X[j] = X[j] + A; // Computes sumed ERP
// $$$ Assumes continuous session signal starting at date 0
{
size_t ERPSampleIndex = size_t(((dynamicBoxContext.getInputChunkStartTime(j + 1, i) >> 16) * sampling) >> 16);
erpSampleIndexes.push_back(ERPSampleIndex);
}
break;
default:
break;
}
n[j]++;
}
#if 0
if (decoder.isEndReceived())
{
}
#endif
}
OV_ERROR_UNLESS_KRF(n[j] != 0, "Did not have input signal for condition " << j + 1 << "\n", Kernel::ErrorType::BadValue);
switch (j)
{
case 0: // Session
break;
case 1: // ERP
X[j] = X[j] / double(n[j]); // Averages ERP
break;
default:
break;
}
}
// We need equal number of channels
OV_ERROR_UNLESS_KRF(X[0].rows() == X[1].rows(),
"Dimension mismatch, first input had " << size_t(X[0].rows()) << " channels while second input had " << size_t(X[1].rows()) <<
" channels\n",
Kernel::ErrorType::BadValue);
// Grabs usefull values
const size_t sampleCountSession = X[0].cols();
const size_t sampleCountERP = X[1].cols();
// Now we compute matrix D
const Eigen::MatrixXd DI = Eigen::MatrixXd::Identity(sampleCountERP, sampleCountERP);
Eigen::MatrixXd D = Eigen::MatrixXd::Zero(sampleCountERP, sampleCountSession);
for (size_t sampleIndex : erpSampleIndexes) { D.block(0, sampleIndex, sampleCountERP, sampleCountERP) += DI; }
// Computes covariance matrices
C[0] = X[0] * X[0].transpose();
C[1] = /*Y * Y.transpose();*/ X[1] * /* D.transpose() * */ (D * D.transpose()).fullPivLu().inverse() /* * D */ * X[1].transpose();
// Solves generalized eigen decomposition
const Eigen::GeneralizedSelfAdjointEigenSolver<Eigen::MatrixXd> eigenSolver(C[0].selfadjointView<Eigen::Lower>(), C[1].selfadjointView<Eigen::Lower>());
if (eigenSolver.info() != Eigen::Success)
{
const enum Eigen::ComputationInfo error = eigenSolver.info();
const char* errorMessage = "unknown";
switch (error)
{
case Eigen::NumericalIssue: errorMessage = "Numerical issue";
break;
case Eigen::NoConvergence: errorMessage = "No convergence";
break;
// case Eigen::InvalidInput: errorMessage="Invalid input"; break; // FIXME
default: break;
}
OV_ERROR_KRF("Could not solve generalized eigen decomposition, got error[" << CString(errorMessage) << "]\n",
Kernel::ErrorType::BadProcessing);
}
// Create a CMatrix mapper that can spool the filters to a file
CMatrix eigenVectors;
eigenVectors.resize(m_filterDim, nChannel);
Eigen::Map<MatrixXdRowMajor> vectorsMapper(eigenVectors.getBuffer(), m_filterDim, nChannel);
vectorsMapper.block(0, 0, m_filterDim, nChannel) = eigenSolver.eigenvectors().block(0, 0, nChannel, m_filterDim).transpose();
// Saves filters
FILE* file = FS::Files::open(m_filterFilename.toASCIIString(), "wt");
OV_ERROR_UNLESS_KRF(file != nullptr, "Could not open file [" << m_filterFilename << "] for writing.\n", Kernel::ErrorType::BadFileWrite);
if (m_saveAsBoxConfig)
{
fprintf(file, "<OpenViBE-SettingsOverride>\n");
fprintf(file, "\t<SettingValue>");
for (size_t i = 0; i < eigenVectors.getBufferElementCount(); ++i) { fprintf(file, "%e ", eigenVectors.getBuffer()[i]); }
fprintf(file, "</SettingValue>\n");
fprintf(file, "\t<SettingValue>%u</SettingValue>\n", (unsigned int)m_filterDim);
fprintf(file, "\t<SettingValue>%u</SettingValue>\n", (unsigned int)nChannel);
fprintf(file, "\t<SettingValue></SettingValue>\n");
fprintf(file, "</OpenViBE-SettingsOverride>");
}
else
{
OV_ERROR_UNLESS_KRF(Toolkit::Matrix::saveToTextFile(eigenVectors, m_filterFilename),
"Unable to save to [" << m_filterFilename << "]\n", Kernel::ErrorType::BadFileWrite);
}
OV_WARNING_UNLESS_K(fclose(file) == 0, "Could not close file[" << m_filterFilename << "].\n");
this->getLogManager() << Kernel::LogLevel_Info << "Training finished and saved to [" << m_filterFilename << "]!\n";
}
return true;
}
} // namespace SignalProcessing
} // namespace Plugins
} // namespace OpenViBE

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