////////////////////////////////////////////////////////////////////////////////
// 'processFeatureVector' reads a feature vector and modifies the classifier's
// data members accordingly
////////////////////////////////////////////////////////////////////////////////
void
MaxEnt::processFeatureVector(const FeatureVector& features){
// Class=2; // what does this do? Need to be there?
en.f.resize(C);
en.fs.resize(C);
en.Ny.resize(C);
size_t c=0; // class
en.Ny[c]=0.0; // strength of class (first num after @)
// for each feature
for (FeatureVector::const_iterator feat = features.begin();
feat!=features.end();feat++)
{
// these loops may have to be reversed !!
// the classes may need to be looped over first, and features within
// instead of classes within feature loop
StringXML feature;
double value = feat->getValue();
// for each class
for (unsigned int i=0;i<C;i++){
stringstream ss;
ss << "cat" << i << "_" << feat->getFeature();
feature = ss.str();
if (value!=0) {
// set values
if (f2s.count(feature)!=0) { // check whether feature exists
(s2f)[f2s[feature]].second+=(en.Ny[i]!=0);
en.f[i].push_back(make_pair(f2s[feature], value));
en.fs[i]+=value;
F=max(F, en.fs[i]);
}
}
}
}
}
inline
Tp1 dot_product(const FeatureVector<Tp1, Alloc1>& x, const WeightVector<Tp, Alloc>& w, const FeatureVector<Tp2, Alloc2>& y)
{
typedef FeatureVector<Tp1, Alloc1> feature_vector1_type;
typedef WeightVector<Tp, Alloc> weight_vector_type;
typedef FeatureVector<Tp2, Alloc2> feature_vector2_type;
if (x.empty() || y.empty()) return Tp1();
if (static_cast<const void*>(&x) == static_cast<const void*>(&y))
return details::__inner_product(x.begin(), x.end(), w, Tp1());
if (x.size() < y.size())
return dot_product(x.begin(), x.end(), w, y, Tp1());
else
return dot_product(x, w, y.begin(), y.end(), Tp1());
}
inline
Tp1 dot_product(const FeatureVector<Tp1, Alloc1>& x, const FeatureVector<Tp2, Alloc2>& y)
{
typedef FeatureVector<Tp1, Alloc1> feature_vector1_type;
typedef FeatureVector<Tp2, Alloc2> feature_vector2_type;
if (x.empty() || y.empty()) return Tp1();
// if the same address, we are identical!
if (static_cast<const void*>(&x) == static_cast<const void*>(&y))
return details::__inner_product(x.begin(), x.end(), Tp1());
if (x.size() < y.size())
return dot_product(x.begin(), x.end(), y, Tp1());
else
return dot_product(x, y.begin(), y.end(), Tp1());
}
inline
Tp dot_product(const FeatureVector<Tp1, Alloc1>& x, Iterator first, Iterator last, Tp __dot)
{
typedef FeatureVector<Tp1, Alloc1> feature_vector1_type;
for (/**/; first != last; ++ first) {
typename feature_vector1_type::const_iterator iter = x.find(first->first);
if (iter != x.end())
__dot += iter->second * first->second;
}
return __dot;
}
inline
Tp dot_product(Iterator first, Iterator last, const FeatureVector<Tp2, Alloc2>& y, Tp __dot)
{
typedef FeatureVector<Tp2, Alloc2> feature_vector2_type;
for (/**/; first != last; ++ first) {
typename feature_vector2_type::const_iterator iter = y.find(first->first);
if (iter != y.end())
__dot += first->second * iter->second;
}
return __dot;
}
inline
Tp1 dot_product(const WeightVector<Tp1, Alloc1>& x, const FeatureVector<Tp2, Alloc2>& y)
{
return dot_product(x, y.begin(), y.end(), Tp1());
}
void ClassifySvmSharedCommand::processSharedAndDesignData(vector<SharedRAbundVector*> lookup) {
try {
OutputFilter outputFilter(verbosity);
LabeledObservationVector labeledObservationVector;
FeatureVector featureVector;
readSharedRAbundVectors(lookup, designMap, labeledObservationVector, featureVector);
// optionally remove features with low standard deviation
if ( stdthreshold > 0.0 ) {
FeatureVector removedFeatureVector = applyStdThreshold(stdthreshold, labeledObservationVector, featureVector);
if (removedFeatureVector.size() > 0) {
std::cout << removedFeatureVector.size() << " OTUs were below the stdthreshold of " << stdthreshold << " and were removed" << std::endl;
if ( outputFilter.debug() ) {
std::cout << "the following OTUs were below the standard deviation threshold of " << stdthreshold << std::endl;
for (FeatureVector::iterator i = removedFeatureVector.begin(); i != removedFeatureVector.end(); i++) {
std::cout << " " << i->getFeatureLabel() << std::endl;
}
}
}
}
// apply [0,1] standardization
if ( transformName == "zeroone") {
std::cout << "transforming data to lie within range [0,1]" << std::endl;
transformZeroOne(labeledObservationVector);
}
else {
std::cout << "transforming data to have zero mean and unit variance" << std::endl;
transformZeroMeanUnitVariance(labeledObservationVector);
}
SvmDataset svmDataset(labeledObservationVector, featureVector);
OneVsOneMultiClassSvmTrainer trainer(svmDataset, evaluationFoldCount, trainingFoldCount, *this, outputFilter);
if ( mode == "rfe" ) {
SvmRfe svmRfe;
ParameterRange& linearKernelConstantRange = kernelParameterRangeMap["linear"]["constant"];
ParameterRange& linearKernelSmoCRange = kernelParameterRangeMap["linear"]["smoc"];
RankedFeatureList rankedFeatureList = svmRfe.getOrderedFeatureList(svmDataset, trainer, linearKernelConstantRange, linearKernelSmoCRange);
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
variables["[distance]"] = lookup[0]->getLabel();
string filename = getOutputFileName("summary", variables);
outputNames.push_back(filename);
outputTypes["summary"].push_back(filename);
m->mothurOutEndLine();
std::ofstream outputFile(filename.c_str());
int n = 0;
int rfeRoundCount = rankedFeatureList.front().getRank();
std::cout << "ordered features:" << std::endl;
std::cout << setw(5) << "index"
<< setw(12) << "OTU"
<< setw(5) << "rank"
<< std::endl;
outputFile << setw(5) << "index"
<< setw(12) << "OTU"
<< setw(5) << "rank"
<< std::endl;
for (RankedFeatureList::iterator i = rankedFeatureList.begin(); i != rankedFeatureList.end(); i++) {
n++;
int rank = rfeRoundCount - i->getRank() + 1;
outputFile << setw(5) << n
<< setw(12) << i->getFeature().getFeatureLabel()
<< setw(5) << rank
<< std::endl;
if ( n <= 20 ) {
std::cout << setw(5) << n
<< setw(12) << i->getFeature().getFeatureLabel()
<< setw(5) << rank
<< std::endl;
}
}
outputFile.close();
}
else {
MultiClassSVM* mcsvm = trainer.train(kernelParameterRangeMap);
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
variables["[distance]"] = lookup[0]->getLabel();
string filename = getOutputFileName("summary", variables);
outputNames.push_back(filename);
outputTypes["summary"].push_back(filename);
m->mothurOutEndLine();
std::ofstream outputFile(filename.c_str());
printPerformanceSummary(mcsvm, std::cout);
printPerformanceSummary(mcsvm, outputFile);
outputFile << "actual predicted" << std::endl;
for ( LabeledObservationVector::const_iterator i = labeledObservationVector.begin(); i != labeledObservationVector.end(); i++ ) {
Label actualLabel = i->getLabel();
outputFile << i->getDatasetIndex() << " " << actualLabel << " ";
try {
Label predictedLabel = mcsvm->classify(*(i->getObservation()));
outputFile << predictedLabel << std::endl;
}
catch ( MultiClassSvmClassificationTie& m ) {
outputFile << "tie" << std::endl;
std::cout << "classification tie for observation " << i->datasetIndex << " with label " << i->first << std::endl;
}
}
outputFile.close();
delete mcsvm;
}
}
catch (exception& e) {
m->errorOut(e, "ClassifySvmSharedCommand", "processSharedAndDesignData");
exit(1);
}
}
bool CButtonMapXml::Serialize(const FeatureVector& features, TiXmlElement* pElement)
{
if (pElement == NULL)
return false;
for (FeatureVector::const_iterator it = features.begin(); it != features.end(); ++it)
{
const ADDON::JoystickFeature& feature = *it;
if (!IsValid(feature))
continue;
TiXmlElement featureElement(BUTTONMAP_XML_ELEM_FEATURE);
TiXmlNode* featureNode = pElement->InsertEndChild(featureElement);
if (featureNode == NULL)
return false;
TiXmlElement* featureElem = featureNode->ToElement();
if (featureElem == NULL)
return false;
featureElem->SetAttribute(BUTTONMAP_XML_ATTR_FEATURE_NAME, feature.Name());
switch (feature.Type())
{
case JOYSTICK_FEATURE_TYPE_SCALAR:
{
SerializePrimitive(featureElem, feature.Primitive());
break;
}
case JOYSTICK_FEATURE_TYPE_ANALOG_STICK:
{
if (!SerializePrimitiveTag(featureElem, feature.Up(), BUTTONMAP_XML_ELEM_UP))
return false;
if (!SerializePrimitiveTag(featureElem, feature.Down(), BUTTONMAP_XML_ELEM_DOWN))
return false;
if (!SerializePrimitiveTag(featureElem, feature.Right(), BUTTONMAP_XML_ELEM_RIGHT))
return false;
if (!SerializePrimitiveTag(featureElem, feature.Left(), BUTTONMAP_XML_ELEM_LEFT))
return false;
break;
}
case JOYSTICK_FEATURE_TYPE_ACCELEROMETER:
{
if (!SerializePrimitiveTag(featureElem, feature.PositiveX(), BUTTONMAP_XML_ELEM_POSITIVE_X))
return false;
if (!SerializePrimitiveTag(featureElem, feature.PositiveY(), BUTTONMAP_XML_ELEM_POSITIVE_Y))
return false;
if (!SerializePrimitiveTag(featureElem, feature.PositiveZ(), BUTTONMAP_XML_ELEM_POSITIVE_Z))
return false;
break;
}
default:
break;
}
}
return true;
}
void FaceTracking::track( FeatureVector &faces, double affWeightPos, double affWeightSize, double affThresh,
double cohWeightDir, double cohWeightVel, double cohWeightSize, double cohThresh, double tolDir, double tolVel, double tolSize,
double discardThresh, double damping, double cohRise,
const _2Real::Vec2 &minSizeFace,
double time )
{
std::set<_2Real::Space2D*> remainingDetections;
for( FeatureVector::iterator itF = faces.begin(); itF != faces.end(); ++itF )
remainingDetections.insert( &( *itF ) );
if( m_trackingInfoList.size() )
{
typedef std::multimap<double, std::pair<TrackingInfo*, _2Real::Space2D*> > PriorityMap; //ordered list of tracking results candidates, ordered by their coherence value
PriorityMap priorityMapAffinity;
PriorityMap priorityMapCoherence;
//STEP 1: create map of trajectory/detectiondata pairs
for( FeatureVector::iterator itF = faces.begin(); itF != faces.end(); ++itF )
{
for( TrackingInfoList::iterator itT = m_trackingInfoList.begin(); itT != m_trackingInfoList.end(); ++itT )
{
if( itT->getFaceTrajectory().canCalcAffinity() )
priorityMapAffinity.insert( std::make_pair( itT->getFaceTrajectory().calcAffinity( *itF, affWeightPos, affWeightSize, 1.0f, time ),
std::make_pair( &( *itT ), &( *itF ) ) ) );
if( itT->getFaceTrajectory().canCalcCoherence() )
priorityMapCoherence.insert( std::make_pair( itT->getFaceTrajectory().calcCoherence( *itF, cohWeightDir, cohWeightVel, cohWeightSize, time, tolDir, tolVel, tolSize ),
std::make_pair( &( *itT ), &( *itF ) ) ) );
}
}
std::set<TrackingInfo*> remainingTrajectories;
for( TrackingInfoList::iterator itT = m_trackingInfoList.begin(); itT != m_trackingInfoList.end(); ++itT )
remainingTrajectories.insert( &( *itT ) );
//STEP 2: get best face for each trajectory by coherence value (thresholded)
for( PriorityMap::const_iterator it = priorityMapCoherence.begin(); it != priorityMapCoherence.end(); ++it )
{
if( it->first > cohThresh )
break; //skip correlations with too high coherence value
std::set<TrackingInfo*>::const_iterator itT = remainingTrajectories.find( it->second.first );
if( itT == remainingTrajectories.end() )
continue; //trajectory already found it's best fitting face
std::set<_2Real::Space2D*>::const_iterator itF = remainingDetections.find( it->second.second );
if( itF == remainingDetections.end() )
continue; //face already used for another trajecotry
( *itT )->add( **itF, it->first, time );
remainingTrajectories.erase( itT );
remainingDetections.erase( itF );
}
//STEP 3: remaining short trajectories (size < 2) are filled with best faces by affinity value (thresholded)
for( PriorityMap::const_iterator it = priorityMapAffinity.begin(); it != priorityMapAffinity.end(); ++it )
{
if( it->first > affThresh )
break; //skip correllations with too high affinity value
if( it->second.first->getFaceTrajectory().canCalcCoherence() )
continue;
std::set<TrackingInfo*>::const_iterator itT = remainingTrajectories.find( it->second.first );
if( itT == remainingTrajectories.end() )
continue; //trajectory already found it's best fitting face
std::set<_2Real::Space2D*>::const_iterator itF = remainingDetections.find( it->second.second );
if( itF == remainingDetections.end() )
continue; //face already used for another trajecotry
( *itT )->add( **itF, 0.0, time );
remainingTrajectories.erase( itT );
remainingDetections.erase( itF );
}
//STEP 4: remaining trajectories are extrapolated (implement kalman, finally?) (if size is large enough, otherwise it does not make sense
for( std::set<TrackingInfo*>::const_iterator it = remainingTrajectories.begin(); it != remainingTrajectories.end(); ++it )
( *it )->extrapolate( time, damping, cohRise );
//STEP 5: discard all trajectories with too high coherence average
TrackingInfoList::iterator itT = m_trackingInfoList.begin();
while( itT != m_trackingInfoList.end() )
{
if( itT->getFaceTrajectory().getAvrgCoherence() > discardThresh )
{
remainingTrajectories.erase( &( *itT ) );
m_availableUserIDs.push_back( itT->getUserID() );
itT = m_trackingInfoList.erase( itT );
}
else
itT++;
}
for( std::set<TrackingInfo*>::iterator it = remainingTrajectories.begin(); it != remainingTrajectories.end(); ++it )
( *it )->prune();
//STEP 6: discard all trajectories which ran out of entries
itT = m_trackingInfoList.begin();
while( itT != m_trackingInfoList.end() )
{
if( !itT->getEntryCount() )
{
m_availableUserIDs.push_back( itT->getUserID() );
itT = m_trackingInfoList.erase( itT );
}
else
itT++;
}
}
//STEP 7: build new trajectories out of remaining faces (extrapolation not possible due to low number of entries)
if( m_availableUserIDs.size() )
{
for( std::set<_2Real::Space2D*>::const_iterator it = remainingDetections.begin(); it != remainingDetections.end(); ++it )
{
m_trackingInfoList.push_back( TrackingInfo( m_availableUserIDs.back(), minSizeFace ) );
m_availableUserIDs.pop_back();
m_trackingInfoList.back().add( **it, 0.0, time );
}
}
}
void TrackingInfo::addFromFeatureCandidates( const FeatureVector &eyesCandidates, const FeatureVector &noseCandidates, const FeatureVector &mouthCandidates, double time, double posAffWeight, double sizeAffWeight )
{
typedef std::multimap<double, const _2Real::Space2D*> PriorityMap;
if( eyesCandidates.size() )
{
PriorityMap mapLeft;
PriorityMap mapRight;
for( FeatureVector::const_iterator it = eyesCandidates.begin(); it != eyesCandidates.end(); ++it )
{
_2Real::Vec2 center( ( it->getP0() + it->getP1() ) * 0.5f );
if( center[0] > 0.5f )
{
if( m_eyeLeftTrajectory.canCalcAffinity() )
mapLeft.insert( std::make_pair( m_eyeLeftTrajectory.calcAffinity( *it, posAffWeight, sizeAffWeight, 1.0, time ), &( *it ) ) );
else
mapLeft.insert( std::make_pair( 0.0, &( *it ) ) );
}
else
{
if( m_eyeRightTrajectory.canCalcAffinity() )
mapRight.insert( std::make_pair( m_eyeRightTrajectory.calcAffinity( *it, posAffWeight, sizeAffWeight, 1.0, time ), &( *it ) ) );
else
mapRight.insert( std::make_pair( 0.0, &( *it ) ) );
}
}
if( mapLeft.size() )
m_eyeLeftTrajectory.add( *( mapLeft.begin()->second ), 0.0, time );
else
{
//NOTE: there is no measure (yet?) to decide whether or not it would make sense to still extrapolate face feature, so this is not done at all,
// instead trajectories are pruned so entries don't last forever. (actually *duplicating* last entry would make more sense in context of
// face feature regions)
m_eyeLeftTrajectory.prune();
}
if( mapRight.size() )
m_eyeRightTrajectory.add( *( mapRight.begin()->second ), 0.0, time );
else
{
//NOTE: there is no measure (yet?) to decide whether or not it would make sense to still extrapolate face feature, so this is not done at all,
// instead trajectories are pruned so entries don't last forever. (actually *duplicating* last entry would make more sense in context of
// face feature regions)
m_eyeRightTrajectory.prune();
}
}
else
{
//NOTE: there is no measure (yet?) to decide whether or not it would make sense to still extrapolate face feature, so this is not done at all,
// instead trajectories are pruned so entries don't last forever. (actually *duplicating* last entry would make more sense in context of
// face feature regions)
m_eyeLeftTrajectory.prune();
m_eyeRightTrajectory.prune();
}
if( noseCandidates.size() )
{
double minAffinity = 0.0;
const _2Real::Space2D *bestCandidate = NULL;
if( !m_noseTrajectory.canCalcAffinity() )
bestCandidate = &( noseCandidates.front() ); //not enough regions in trajectory history in order to judge, just take first in candidate list
else
{
for( FeatureVector::const_iterator it = noseCandidates.begin(); it != noseCandidates.end(); ++it )
{
if( !bestCandidate )
{
bestCandidate = &( *it );
minAffinity = m_noseTrajectory.calcAffinity( *it, posAffWeight, sizeAffWeight, 1.0, time );
}
else
{
double affinity = m_noseTrajectory.calcAffinity( *it, posAffWeight, sizeAffWeight, 1.0, time );
if( affinity < minAffinity )
{
bestCandidate = &( *it );
minAffinity = affinity;
}
}
}
}
m_noseTrajectory.add( *bestCandidate, 0.0, time );
}
else
{
//NOTE: there is no measure (yet?) to decide whether or not it would make sense to still extrapolate face feature, so this is not done at all,
// instead trajectories are pruned so entries don't last forever. (actually *duplicating* last entry would make more sense in context of
// face feature regions)
m_noseTrajectory.prune();
}
if( mouthCandidates.size() )
{
double minAffinity = 0.0;
const _2Real::Space2D *bestCandidate = NULL;
if( !m_mouthTrajectory.canCalcAffinity() )
bestCandidate = &( mouthCandidates.front() ); //not enough regions in trajectory history in order to judge, just take first in candidate list
else
{
for( FeatureVector::const_iterator it = mouthCandidates.begin(); it != mouthCandidates.end(); ++it )
{
if( !bestCandidate )
{
bestCandidate = &( *it );
minAffinity = m_mouthTrajectory.calcAffinity( *it, posAffWeight, sizeAffWeight, 1.0, time );
}
else
{
double affinity = m_mouthTrajectory.calcAffinity( *it, posAffWeight, sizeAffWeight, 1.0, time );
if( affinity < minAffinity )
{
bestCandidate = &( *it );
minAffinity = affinity;
}
}
}
}
m_mouthTrajectory.add( *bestCandidate, 0.0, time );
}
else
{
//NOTE: there is no measure (yet?) to decide whether or not it would make sense to still extrapolate face feature, so this is not done at all,
// instead trajectories are pruned so entries don't last forever. (actually *duplicating* last entry would make more sense in context of
// face feature regions)
m_mouthTrajectory.prune();
}
}