void BackProp::predict(const std::vector<double>& features, std::vector<double>& labels)
{
assert(labels.size() == 1);
assert(_nLayers > 0);
assert(features.size() == _layers[0].getNumUnits());
if(_loggingOn)
{
std::cout << "Input features: " << vectorToString(features) << std::endl;
}
std::vector<double> finalLayerOutput;
_layers[0].predict(features, finalLayerOutput);
if(_loggingOn)
{
std::cout << "Prediction: " << vectorToString(finalLayerOutput) << std::endl;
}
size_t maxLabel = 0;
double maxLabelOuput = -5.0;
for(size_t labelIndex = 0; labelIndex < finalLayerOutput.size(); labelIndex++)
{
if(finalLayerOutput[labelIndex] > maxLabelOuput)
{
maxLabel = labelIndex;
maxLabelOuput = finalLayerOutput[labelIndex];
}
}
labels[0] = maxLabel;
}
void Functions::toString(Aurora::NWScript::FunctionContext &ctx) {
ctx.getReturn() = "";
switch (ctx.getParams()[0].getType()) {
case Aurora::NWScript::kTypeInt:
intToString(ctx);
break;
case Aurora::NWScript::kTypeFloat:
floatToString(ctx);
break;
case Aurora::NWScript::kTypeString:
ctx.getReturn() = ctx.getParams()[0];
break;
case Aurora::NWScript::kTypeObject:
objectToString(ctx);
break;
case Aurora::NWScript::kTypeVector:
vectorToString(ctx);
break;
default:
break;
}
}
bool setOption(T &option, std::string flagStr,
const std::string &shortDescription, bool required = false) {
flag currentFlag = flag(option, flagStr, shortDescription, required);
bool found = false;
for (const auto &fTok : currentFlag.flags_) {
if (commands_.lookForOption(option, fTok)) {
currentFlag.setValue(option);
found = true;
break;
} else {
found = false;
}
}
if (required && !found) {
std::stringstream tempStream;
tempStream << bashCT::bold + bashCT::black << "Need to have "
<< bashCT::red << vectorToString(tokenizeString(flagStr, ","), " or ")
<< bashCT::black << " see " << bashCT::red
<< commands_["-program"] + " -help " << bashCT::black
<< "for more details" << bashCT::reset;
warnings_.emplace_back(tempStream.str());
failed_ = true;
}
flags_.addFlag(currentFlag);
return found;
}
string replaceWords(vector<string>& dict, string sentence) {
if (sentence.empty()) return sentence;
auto vec = stringToVector(sentence);
replaceByRoot(vec, dict);
return vectorToString(vec);
}
void ExtractionStator::outStatsPerName(std::ostream & out, const std::string & delim){
for(auto & mid : counts_){
uint32_t totalReads = mid.second[true].getTotal() + mid.second[false].getTotal();
uint32_t totalGoodReads = mid.second[true].good_ + mid.second[false].good_;
uint32_t totalBadReads = mid.second[true].bad_ + mid.second[false].bad_;
uint32_t totalContam = mid.second[true].contamination_ + mid.second[false].contamination_;
uint32_t totalBadRev = mid.second[true].badReverse_ + mid.second[false].badReverse_;
uint32_t totalConN = mid.second[true].containsNs_ + mid.second[false].containsNs_;
uint32_t totalMinLen = mid.second[true].minLenBad_ + mid.second[false].minLenBad_;
uint32_t totalMaxLen = mid.second[true].maxLenBad_ + mid.second[false].maxLenBad_;
uint32_t totalQualFail = mid.second[true].qualityFailed_ + mid.second[false].qualityFailed_;
out << vectorToString(toVecStr(mid.first, totalReads,
getPercentageString(totalGoodReads, totalReads),
getPercentageString(mid.second[false].good_, totalGoodReads),
getPercentageString(mid.second[true].good_, totalGoodReads),
getPercentageString(totalBadReads, totalReads),
getPercentageString(totalBadRev, totalBadReads),
getPercentageString(totalConN, totalBadReads),
getPercentageString(totalMinLen, totalBadReads),
getPercentageString(totalMaxLen, totalBadReads),
getPercentageString(totalQualFail, totalBadReads),
getPercentageString(totalContam, totalReads)), delim) << "\n";
}
}
void HighScoreComponentTest::testFull()
{
expectedScore.clear();
expectedScore.push_back(1000);
expectedScore.push_back(900);
expectedScore.push_back(800);
expectedScore.push_back(700);
expectedScore.push_back(600);
expectedScore.push_back(500);
expectedScore.push_back(400);
expectedScore.push_back(300);
expectedScore.push_back(200);
expectedScore.push_back(100);
_highScoreComponentFull->submitScore(200);
_highScoreComponentFull->submitScore(300);
_highScoreComponentFull->submitScore(400);
_highScoreComponentFull->submitScore(1000);
_highScoreComponentFull->submitScore(600);
_highScoreComponentFull->submitScore(100);
_highScoreComponentFull->submitScore(500);
_highScoreComponentFull->submitScore(700);
_highScoreComponentFull->submitScore(900);
_highScoreComponentFull->submitScore(800);
_highScoreComponentFull->submitScore(50);
CPPUNIT_ASSERT_MESSAGE(vectorToString(expectedScore, _highScoreComponentFull->scores()), expectedScore == _highScoreComponentFull->scores());
}
void OperatorControl()
{
float xJoy, yJoy, gyroVal, angle = 0, turn = 0, angleDiff, turnPower;
gyro.Reset();
gyro.SetSensitivity(9.7);
while (IsEnabled() && IsOperatorControl()) // loop as long as the robot is running
{
yJoy = xbox.getAxis(Xbox::L_STICK_V);
xJoy = xbox.getAxis(Xbox::R_STICK_H);
gyroVal = gyro.GetAngle()/0.242*360;
turn = 0.15;
angle = angle - xJoy * xJoy * xJoy * turn;
angleDiff = mod(angle - gyroVal, 360);
turnPower = - mod(angleDiff / 180.0 + 1.0, 2) + 1.0;
SmartDashboard::PutString("Joy1", vectorToString(xJoy, yJoy));
SmartDashboard::PutNumber("Heading", mod(gyroVal, 360));
SmartDashboard::PutNumber("Turn Power", turnPower);
SmartDashboard::PutBoolean("Switch is ON:", dumperSwitch.Get());
if (!xbox.isButtonPressed(Xbox::R))
{
drive.ArcadeDrive(yJoy * yJoy * yJoy, turnPower * fabs(turnPower), false);
}
}
}
void HighScoreComponentTest::testZero()
{
expectedScore.clear();
_highScoreComponentZero->submitScore(0);
CPPUNIT_ASSERT_MESSAGE(vectorToString(expectedScore, _highScoreComponentZero->scores()), expectedScore == _highScoreComponentZero->scores());
}
std::string mismatch::outputInfoString() const {
std::stringstream out;
if (transition) {
out << "transition\t";
} else {
out << "transversion\t";
}
out << refBasePos << "\t" << refBase << "\t" << refQual << "\t"
<< vectorToString(refLeadingQual, ",") << "\t"
<< vectorToString(refTrailingQual, ",") << "\t" << seqBasePos << "\t"
<< seqBase << "\t" << seqQual << "\t"
<< vectorToString(seqLeadingQual, ",") << "\t"
<< vectorToString(seqTrailingQual, ",") << "\t" << kMerFreqByPos << "\t"
<< kMerFreq;
return out.str();
}
string
SearchSpace::
getNthTranslation(int nth){
if(nth<1)return "";
string result="";
if((int)_hypoHeaps.back().size()<nth)
return "";
return vectorToString(_hypoHeaps.back()[nth-1].translation);
}
string MistarParser::getHeaderNoDefline(string prefix){
vector<string> fields=allTokens(headerNoDefline,'\n');
vector<string> toreturn;
for(unsigned int i=0;i<fields.size();i++){
if(!fields[i].empty())
toreturn.push_back(prefix+fields[i]);
}
return vectorToString(toreturn,"\n");
}
string terShift::toString()
{
stringstream s;
s.str ( "" );
s << "[" << start << ", " << end << ", " << moveto << "/" << newloc << "]";
if ( ( int ) shifted.size() > 0 ) {
s << " (" << vectorToString ( shifted ) << ")";
}
return s.str();
}
void VelocityTracker::addMovement(nsecs_t eventTime, BitSet32 idBits, const Position* positions) {
while (idBits.count() > MAX_POINTERS) {
idBits.clearLastMarkedBit();
}
if ((mCurrentPointerIdBits.value & idBits.value)
&& eventTime >= mLastEventTime + ASSUME_POINTER_STOPPED_TIME) {
#if DEBUG_VELOCITY
ALOGD("VelocityTracker: stopped for %0.3f ms, clearing state.",
(eventTime - mLastEventTime) * 0.000001f);
#endif
// We have not received any movements for too long. Assume that all pointers
// have stopped.
mStrategy->clear();
}
mLastEventTime = eventTime;
mCurrentPointerIdBits = idBits;
if (mActivePointerId < 0 || !idBits.hasBit(mActivePointerId)) {
mActivePointerId = idBits.isEmpty() ? -1 : idBits.firstMarkedBit();
}
mStrategy->addMovement(eventTime, idBits, positions);
#if DEBUG_VELOCITY
ALOGD("VelocityTracker: addMovement eventTime=%" PRId64 ", idBits=0x%08x, activePointerId=%d",
eventTime, idBits.value, mActivePointerId);
for (BitSet32 iterBits(idBits); !iterBits.isEmpty(); ) {
uint32_t id = iterBits.firstMarkedBit();
uint32_t index = idBits.getIndexOfBit(id);
iterBits.clearBit(id);
Estimator estimator;
getEstimator(id, &estimator);
ALOGD(" %d: position (%0.3f, %0.3f), "
"estimator (degree=%d, xCoeff=%s, yCoeff=%s, confidence=%f)",
id, positions[index].x, positions[index].y,
int(estimator.degree),
vectorToString(estimator.xCoeff, estimator.degree + 1).c_str(),
vectorToString(estimator.yCoeff, estimator.degree + 1).c_str(),
estimator.confidence);
}
#endif
}
std::ostream& operator<< (std::ostream& os, const JointGoal& j) {
os << "time_since_start(" << j.time_since_start << "), " <<
"sub_goal_idx(" << j.sub_goal_idx << "), " <<
"joint_index_mapping(" << vectorToString(j.joint_index_mapping) << "), " <<
"goal_msg(" << j.goal_msg << "), " <<
"num_goal_joints(" << j.num_goal_joints << "), " <<
"use_cubic_interpolation(" << j.use_cubic_interpolation << "), " <<
"status(" << j.status << ")";
return os;
}
std::string polylineToString(Polyline const & polyline, Layout const & layout) const
{
Polyline shifted_polyline = polyline;
shifted_polyline.offset(Point(margin.width, margin.height));
std::vector<Circle> vertices;
for (unsigned i = 0; i < shifted_polyline.points.size(); ++i)
vertices.push_back(Circle(shifted_polyline.points[i], getDimensions()->height / 30.0, Color::Black));
return shifted_polyline.toString(layout) + vectorToString(vertices, layout);
}
std::string Scene::toString() const {
return tfm::format(
"Scene[\n"
" settings = %s,\n"
" camera = %s,\n"
" world = %s,\n"
" boxes = %s,\n"
" spheres = %s,\n"
" meshes = %s\n,"
" cameraKeyframes = %s\n"
"]",
indent(settings.json().dump()),
indent(camera.toString()),
indent(world.toString()),
indent(vectorToString(boxes)),
indent(vectorToString(spheres)),
indent(vectorToString(meshes)),
indent(vectorToString(cameraKeyframes))
);
}
void
Hypothesis::
print(ostream& os)
{
os<<represent<<" : "<<vectorToString(translation)<<" ||| "<<currentScore<<" "<<estimatedScore<<endl;
os<<"\t";features.print(os);os<<endl;
os<<"\t";
if(trace.p_prev!=NULL)
os<<trace.p_prev->represent;
os<<" ||| ";
if(trace.p_rule!=NULL)
os<<(*trace.p_rule).srcPhrase<<" => "<<(*trace.p_rule).tarPhrase<<" ||| "<<(*trace.p_rule);
os<<endl;
}
void HighScoreComponentTest::testSortDesc()
{
expectedScore.clear();
expectedScore.push_back(500);
expectedScore.push_back(400);
expectedScore.push_back(300);
expectedScore.push_back(200);
_highScoreComponentSortDesc->submitScore(500);
_highScoreComponentSortDesc->submitScore(400);
_highScoreComponentSortDesc->submitScore(300);
_highScoreComponentSortDesc->submitScore(200);
CPPUNIT_ASSERT_MESSAGE(vectorToString(expectedScore, _highScoreComponentSortDesc->scores()), expectedScore == _highScoreComponentSortDesc->scores());
}
CCArray* GlobalData::getAllCardProfile(CardQueryCriteria *query)
{
arrayCards = CCArray::create();
sqlite3 *pDB = NULL;
char* errMsg = NULL;
#if (CC_TARGET_PLATFORM == CC_PLATFORM_ANDROID)
std::string dbPath = getWritablePath();
#else
std::string dbPath = CCFileUtils::sharedFileUtils()->fullPathForFilename("card.s3db");
#endif
int result = sqlite3_open_v2(dbPath.c_str(),&pDB,SQLITE_OPEN_READWRITE, NULL);
if (result!=SQLITE_OK) {
return NULL;
}
std::string szSql = "select c.cardHeadImg,c.cardBodyImg,c.cardProfileImg,c.game_group_id,r.roleName,r.starGrade,r.beginGrade,r.blood,r.attack,r.defence,r.crit,r.dodge,r.roleDescription from card c left join game_role r on c.cardProfileImg = r.roleImageId where r.starGrade is not null";
if (query != NULL)
{
if (query->groupid >= 0)
{
}
if (query->cardName.length()>0)
{
std::vector<std::string> slist = split(query->cardName,';');
if (slist.size()<=1)
{
szSql.append(" AND c.cardProfileImg = '");
szSql.append(slist[0]);
szSql.append("'");
} else {
szSql.append(" AND c.cardProfileImg in (\'");
std::string sresult = vectorToString(slist,"\',\'");
szSql.append(sresult);
szSql.append("\')");
}
}
}
const char *argc = QUERY_CARD_PROFILE_ALL;
result = sqlite3_exec(pDB,szSql.c_str(), sqliteExecCallBack, (void *)argc, &errMsg);
if (result != SQLITE_OK) {
return NULL;
}
return arrayCards;
}
double BackPropUnit::getOutput(const std::vector<double>& features) const
{
if(_loggingOn)
{
std::cout << "Unit weights: " << vectorToString(_weights) << std::endl;
}
double sum = 0.0;
assert(features.size() == _weights.size() - 1);
for(size_t i = 0; i < features.size(); i++)
sum += _weights[i] * features[i];
sum += _weights[_weights.size() - 1];
double output = 1 / (1 + exp(-sum));
return output;
}
////////////////////////////////////////////////////////////////////
// for debug
void CTree::dfs(CNode *x, std::ostream& out, int8_t depth) {
if(x == NULL) {
return;
}
char str[512];
memset(str, 0, 512);
string label(txt + x->id, x->len);
for (int i = 0; i < kmerLen; ++i) {
if(shape[i] == '1') {
int id = i - depth;
if(id > 0 && id < x->len) label[id] = '_';
}
}
if(x->leaf) {
string poss = vectorToString(((CLeaf *) x)->pos);
sprintf(str, "\t%d [label=\"%s (%s)\"];\n", x, label.c_str(),
poss.c_str());
out << str;
return;
} else {
sprintf(str, "\t%d [label=\"%s\"];\n", x, label.c_str());
out << str;
}
CInnerNode* inner = (CInnerNode*) x;
for (uint8_t i = 0; i < CNode::SIGMA; ++i) {
if(inner->children[i]) {
memset(str, 0, 512);
// edges
sprintf(str, "\t%d -- %d;\n", inner, inner->children[i]);
out << str;
}
}
for (uint8_t i = 0; i < 4; ++i) {
if(inner->children[i]) {
dfs(inner->children[i], out, depth + inner->len);
}
}
}
void ExtractionStator::outTotalStats(std::ostream & out, const std::string & delim) {
uint32_t totalBadReads = 0;
uint32_t totalGoodReads = 0;
uint32_t totalContam = 0;
uint32_t totalFailedForward = 0;
for(auto & ff : failedForward_){
totalFailedForward += ff.second[true] + ff.second[false];
}
for (auto & mid : counts_) {
totalGoodReads += mid.second[true].good_ + mid.second[false].good_;
totalBadReads += mid.second[true].bad_ + mid.second[false].bad_;
totalContam += mid.second[true].contamination_
+ mid.second[false].contamination_;
}
out << vectorToString(toVecStr(totalReadCount_,
getPercentageString(readsUnrecBarcode_, totalReadCount_),
getPercentageString(readsUnrecBarcodePosContamination_, totalReadCount_),
getPercentageString(smallFrags_, totalReadCount_),
getPercentageString(totalFailedForward, totalReadCount_),
getPercentageString(totalBadReads, totalReadCount_),
getPercentageString(totalGoodReads, totalReadCount_),
getPercentageString(totalContam, totalReadCount_)), delim) << "\n";
}
void multiTxtDocument::loadFile ( string fileName, bool caseOn, bool noPunct, bool debugMode, bool noTxtIds, bool tercomLike )
{
if ( multiTxtDocumentParams.debugMode )
{
cerr << "DEBUG tercpp : multiTxtDocument::loadFile : loading files " << endl << fileName << endl << "END DEBUG" << endl;
cerr << "DEBUG tercpp : multiTxtDocument::loadFile : testing params " << endl << Tools::printParams ( multiTxtDocumentParams ) << endl << "END DEBUG" << endl;
cerr << "DEBUG tercpp : multiTxtDocument::loadFile : testing others params " << endl << "caseOn : " << caseOn << endl << "noPunct : " << noPunct << endl << "debugMode : " << debugMode << endl << "noTxtIds : " << noTxtIds << endl << "tercomLike : " << tercomLike << endl << "END DEBUG" << endl;
}
ifstream fichierLoad ( fileName.c_str(), ios::in );
string line="";
documentStructure l_doc;
stringstream l_stream;
l_doc.setFileName(fileName);
l_stream.str ( "" );
l_stream << ( int ) documents.size();
l_doc.setDocId ( l_stream.str() );
if ( fichierLoad )
{
int l_ids = 1;
l_stream.str ( "" );
string l_key="";
string line_mod="";
while ( getline ( fichierLoad, line ) )
{
l_key="";
line_mod="";
l_stream.str ( "" );
if ( noTxtIds )
{
l_stream << l_ids;
l_key = l_stream.str();
line_mod = line;
l_ids++;
}
else
{
if ((int)line.rfind ( "(" )==-1)
{
cerr << "ERROR : multiTxtDocument::loadFile : Id not found, maybe you should use the --noTxtIds Option ? " << endl;
exit ( 0 );
}
l_key = line.substr ( line.rfind ( "(" ), line.size() - 1 );
line_mod = line.substr ( 0, line.rfind ( "(" ) - 1 );
}
if ( multiTxtDocumentParams.debugMode )
{
cerr << "DEBUG multiTxtDocument::loadFile : line NOT tokenized |" << line_mod << "|" << endl << "END DEBUG" << endl;
}
if ( !tercomLike )
{
if ( multiTxtDocumentParams.debugMode )
{
cerr << "DEBUG tercpp : multiTxtDocument::loadFile : " << endl << "TERCOM AT FALSE " << endl << "END DEBUG" << endl;
}
// line_mod = tokenizePunct ( line_mod );
}
if ( !caseOn )
{
if ( multiTxtDocumentParams.debugMode )
{
cerr << "DEBUG tercpp : multiTxtDocument::loadFile : " << endl << "CASEON AT FALSE " << endl << "END DEBUG" << endl;
}
line_mod = lowerCase ( line_mod );
}
if ( noPunct )
{
if ( multiTxtDocumentParams.debugMode )
{
cerr << "DEBUG tercpp : multiTxtDocument::loadFile : " << endl << "NOPUNCT AT TRUE " << endl << "END DEBUG" << endl;
}
if ( !tercomLike )
{
line_mod = removePunctTercom ( line_mod );
}
else
{
line_mod = removePunct ( line_mod );
}
}
if ( multiTxtDocumentParams.debugMode )
{
cerr << "DEBUG multiTxtDocument::loadFile : line tokenized |" << line_mod << "|" << endl << "END DEBUG" << endl;
}
vector<string> vecDocLine = stringToVector ( line_mod, " " );
// string l_key;
// hashHypothesis.addValue(l_key,vecDocLine);
// l_key=(string)vecDocLine.at((int)vecDocLine.size()-1);
// vecDocLine.pop_back();
if ( multiTxtDocumentParams.debugMode )
{
cerr << "DEBUG tercpp multiTxtDocument::loadFile : " << l_key << "|" << vectorToString ( vecDocLine ) << "|" << endl << "Vector Size : " << vecDocLine.size() << endl << "Line length : " << ( int ) line_mod.length() << endl << "END DEBUG" << endl;
}
// hashHypothesis.addValue(l_key,vecDocLine);
segmentStructure l_seg ( l_key, vecDocLine, l_doc.getDocId() );
l_doc.addSegments ( l_seg );
}
// Ref=line;
// getline ( fichierHyp, line );
// Hyp=line;
fichierLoad.close(); // on ferme le fichier
addDocument ( l_doc );
if ( multiTxtDocumentParams.debugMode )
{
cerr << "DEBUG multiTxtDocument::loadFile : document " << l_doc.getDocId() << " added !!!" << endl << "END DEBUG" << endl;
}
l_key.erase();
line_mod.erase();
l_stream.str("");
}
else // sinon
{
cerr << "ERROR : multiTxtDocument::loadFile : can't open file : " + fileName + " !" << endl;
exit ( 0 );
}
}
/**
* Solves a linear least squares problem to obtain a N degree polynomial that fits
* the specified input data as nearly as possible.
*
* Returns true if a solution is found, false otherwise.
*
* The input consists of two vectors of data points X and Y with indices 0..m-1
* along with a weight vector W of the same size.
*
* The output is a vector B with indices 0..n that describes a polynomial
* that fits the data, such the sum of W[i] * W[i] * abs(Y[i] - (B[0] + B[1] X[i]
* + B[2] X[i]^2 ... B[n] X[i]^n)) for all i between 0 and m-1 is minimized.
*
* Accordingly, the weight vector W should be initialized by the caller with the
* reciprocal square root of the variance of the error in each input data point.
* In other words, an ideal choice for W would be W[i] = 1 / var(Y[i]) = 1 / stddev(Y[i]).
* The weights express the relative importance of each data point. If the weights are
* all 1, then the data points are considered to be of equal importance when fitting
* the polynomial. It is a good idea to choose weights that diminish the importance
* of data points that may have higher than usual error margins.
*
* Errors among data points are assumed to be independent. W is represented here
* as a vector although in the literature it is typically taken to be a diagonal matrix.
*
* That is to say, the function that generated the input data can be approximated
* by y(x) ~= B[0] + B[1] x + B[2] x^2 + ... + B[n] x^n.
*
* The coefficient of determination (R^2) is also returned to describe the goodness
* of fit of the model for the given data. It is a value between 0 and 1, where 1
* indicates perfect correspondence.
*
* This function first expands the X vector to a m by n matrix A such that
* A[i][0] = 1, A[i][1] = X[i], A[i][2] = X[i]^2, ..., A[i][n] = X[i]^n, then
* multiplies it by w[i]./
*
* Then it calculates the QR decomposition of A yielding an m by m orthonormal matrix Q
* and an m by n upper triangular matrix R. Because R is upper triangular (lower
* part is all zeroes), we can simplify the decomposition into an m by n matrix
* Q1 and a n by n matrix R1 such that A = Q1 R1.
*
* Finally we solve the system of linear equations given by R1 B = (Qtranspose W Y)
* to find B.
*
* For efficiency, we lay out A and Q column-wise in memory because we frequently
* operate on the column vectors. Conversely, we lay out R row-wise.
*
* http://en.wikipedia.org/wiki/Numerical_methods_for_linear_least_squares
* http://en.wikipedia.org/wiki/Gram-Schmidt
*/
static bool solveLeastSquares(const float* x, const float* y,
const float* w, uint32_t m, uint32_t n, float* outB, float* outDet) {
#if DEBUG_STRATEGY
ALOGD("solveLeastSquares: m=%d, n=%d, x=%s, y=%s, w=%s", int(m), int(n),
vectorToString(x, m).c_str(), vectorToString(y, m).c_str(),
vectorToString(w, m).c_str());
#endif
// Expand the X vector to a matrix A, pre-multiplied by the weights.
float a[n][m]; // column-major order
for (uint32_t h = 0; h < m; h++) {
a[0][h] = w[h];
for (uint32_t i = 1; i < n; i++) {
a[i][h] = a[i - 1][h] * x[h];
}
}
#if DEBUG_STRATEGY
ALOGD(" - a=%s", matrixToString(&a[0][0], m, n, false /*rowMajor*/).c_str());
#endif
// Apply the Gram-Schmidt process to A to obtain its QR decomposition.
float q[n][m]; // orthonormal basis, column-major order
float r[n][n]; // upper triangular matrix, row-major order
for (uint32_t j = 0; j < n; j++) {
for (uint32_t h = 0; h < m; h++) {
q[j][h] = a[j][h];
}
for (uint32_t i = 0; i < j; i++) {
float dot = vectorDot(&q[j][0], &q[i][0], m);
for (uint32_t h = 0; h < m; h++) {
q[j][h] -= dot * q[i][h];
}
}
float norm = vectorNorm(&q[j][0], m);
if (norm < 0.000001f) {
// vectors are linearly dependent or zero so no solution
#if DEBUG_STRATEGY
ALOGD(" - no solution, norm=%f", norm);
#endif
return false;
}
float invNorm = 1.0f / norm;
for (uint32_t h = 0; h < m; h++) {
q[j][h] *= invNorm;
}
for (uint32_t i = 0; i < n; i++) {
r[j][i] = i < j ? 0 : vectorDot(&q[j][0], &a[i][0], m);
}
}
#if DEBUG_STRATEGY
ALOGD(" - q=%s", matrixToString(&q[0][0], m, n, false /*rowMajor*/).c_str());
ALOGD(" - r=%s", matrixToString(&r[0][0], n, n, true /*rowMajor*/).c_str());
// calculate QR, if we factored A correctly then QR should equal A
float qr[n][m];
for (uint32_t h = 0; h < m; h++) {
for (uint32_t i = 0; i < n; i++) {
qr[i][h] = 0;
for (uint32_t j = 0; j < n; j++) {
qr[i][h] += q[j][h] * r[j][i];
}
}
}
ALOGD(" - qr=%s", matrixToString(&qr[0][0], m, n, false /*rowMajor*/).c_str());
#endif
// Solve R B = Qt W Y to find B. This is easy because R is upper triangular.
// We just work from bottom-right to top-left calculating B's coefficients.
float wy[m];
for (uint32_t h = 0; h < m; h++) {
wy[h] = y[h] * w[h];
}
for (uint32_t i = n; i != 0; ) {
i--;
outB[i] = vectorDot(&q[i][0], wy, m);
for (uint32_t j = n - 1; j > i; j--) {
outB[i] -= r[i][j] * outB[j];
}
outB[i] /= r[i][i];
}
#if DEBUG_STRATEGY
ALOGD(" - b=%s", vectorToString(outB, n).c_str());
#endif
// Calculate the coefficient of determination as 1 - (SSerr / SStot) where
// SSerr is the residual sum of squares (variance of the error),
// and SStot is the total sum of squares (variance of the data) where each
// has been weighted.
float ymean = 0;
for (uint32_t h = 0; h < m; h++) {
ymean += y[h];
}
ymean /= m;
float sserr = 0;
float sstot = 0;
for (uint32_t h = 0; h < m; h++) {
float err = y[h] - outB[0];
float term = 1;
for (uint32_t i = 1; i < n; i++) {
term *= x[h];
err -= term * outB[i];
}
sserr += w[h] * w[h] * err * err;
float var = y[h] - ymean;
sstot += w[h] * w[h] * var * var;
}
*outDet = sstot > 0.000001f ? 1.0f - (sserr / sstot) : 1;
#if DEBUG_STRATEGY
ALOGD(" - sserr=%f", sserr);
ALOGD(" - sstot=%f", sstot);
ALOGD(" - det=%f", *outDet);
#endif
return true;
}
bool LeastSquaresVelocityTrackerStrategy::getEstimator(uint32_t id,
VelocityTracker::Estimator* outEstimator) const {
outEstimator->clear();
// Iterate over movement samples in reverse time order and collect samples.
float x[HISTORY_SIZE];
float y[HISTORY_SIZE];
float w[HISTORY_SIZE];
float time[HISTORY_SIZE];
uint32_t m = 0;
uint32_t index = mIndex;
const Movement& newestMovement = mMovements[mIndex];
do {
const Movement& movement = mMovements[index];
if (!movement.idBits.hasBit(id)) {
break;
}
nsecs_t age = newestMovement.eventTime - movement.eventTime;
if (age > HORIZON) {
break;
}
const VelocityTracker::Position& position = movement.getPosition(id);
x[m] = position.x;
y[m] = position.y;
w[m] = chooseWeight(index);
time[m] = -age * 0.000000001f;
index = (index == 0 ? HISTORY_SIZE : index) - 1;
} while (++m < HISTORY_SIZE);
if (m == 0) {
return false; // no data
}
// Calculate a least squares polynomial fit.
uint32_t degree = mDegree;
if (degree > m - 1) {
degree = m - 1;
}
if (degree >= 1) {
if (degree == 2 && mWeighting == WEIGHTING_NONE) { // optimize unweighted, degree=2 fit
outEstimator->time = newestMovement.eventTime;
outEstimator->degree = 2;
outEstimator->confidence = 1;
outEstimator->xCoeff[0] = 0; // only slope is calculated, set rest of coefficients = 0
outEstimator->yCoeff[0] = 0;
outEstimator->xCoeff[1] = solveUnweightedLeastSquaresDeg2(time, x, m);
outEstimator->yCoeff[1] = solveUnweightedLeastSquaresDeg2(time, y, m);
outEstimator->xCoeff[2] = 0;
outEstimator->yCoeff[2] = 0;
return true;
}
float xdet, ydet;
uint32_t n = degree + 1;
if (solveLeastSquares(time, x, w, m, n, outEstimator->xCoeff, &xdet)
&& solveLeastSquares(time, y, w, m, n, outEstimator->yCoeff, &ydet)) {
outEstimator->time = newestMovement.eventTime;
outEstimator->degree = degree;
outEstimator->confidence = xdet * ydet;
#if DEBUG_STRATEGY
ALOGD("estimate: degree=%d, xCoeff=%s, yCoeff=%s, confidence=%f",
int(outEstimator->degree),
vectorToString(outEstimator->xCoeff, n).c_str(),
vectorToString(outEstimator->yCoeff, n).c_str(),
outEstimator->confidence);
#endif
return true;
}
}
// No velocity data available for this pointer, but we do have its current position.
outEstimator->xCoeff[0] = x[0];
outEstimator->yCoeff[0] = y[0];
outEstimator->time = newestMovement.eventTime;
outEstimator->degree = 0;
outEstimator->confidence = 1;
return true;
}
void qsubMFT(JKArgs& args)
{
//"jkparser -qsubMFT -curDir=dir -stepLength=int -nStep=int -dConfig=trainConfig -o=ruleFile [-walltime=time] [-pmem=mem] [-queue=node]"
string curDir="";
int stepLength=5000;
int nStep=6;
string dConfig="";
int sleepTime=5;
if(!args.is_set("curDir")||!args.is_set("stepLength")||
!args.is_set("nStep")||!args.is_set("dConfig")||!args.is_set("o"))
usage();
curDir=args.value("curDir");
stepLength=atoi(args.value("stepLength").c_str());
nStep=atoi(args.value("nStep").c_str());
dConfig=args.value("dConfig");
string output=args.value("o");
int dlevel=atoi(args.value("debug").c_str());
if(args.is_set("sleepTime"))sleepTime=atoi(args.value("sleepTime").c_str());
JKArgs dArgs;
dArgs.init(dConfig.c_str());
string walltime="20:00:00";
string pmem="7g";
string queue="isi";
if(args.is_set("walltime"))
walltime=args.value("walltime");
if(args.is_set("pmem"))
pmem=args.value("pmem");
if(args.is_set("queue"))
queue=args.value("queue");
cerr<<"walltime="<<walltime<<endl;
string signal="mftsignal";
if(dArgs.is_set("signal"))signal=dArgs.value("signal");
string logerror=output+"-logerror";
vector<string> v_signal,v_logerror,v_log,v_sh;
CHDIR(curDir.c_str());
string cmd="";
cmd="cd "+curDir;
if(dlevel)cerr<<cmd<<endl;
else system(cmd.c_str());
for(int iter=0;iter<nStep;iter++)
{
int start=stepLength*iter+1;
int stop=start+stepLength-1;
string range=intToString(start)+"-"+intToString(stop);
string n_signal=signal+"."+range;
v_signal.push_back(n_signal);
string n_logerror=logerror+"."+range;
string n_log=output+"."+range;
v_logerror.push_back(n_logerror);
v_log.push_back(n_log);
string fd_cmd="( ./pbmt -config="+dConfig+" -range="+range+" -signal="+n_signal;
fd_cmd+=" > "+n_log+" ) >& "+n_logerror;
string fd_sh=curDir+"/mft."+range+".sh";
v_sh.push_back(fd_sh);
cmd="echo cd "+curDir+" > "+fd_sh;
if(dlevel)cerr<<cmd<<endl;
else system(cmd.c_str());
cmd="echo \""+fd_cmd+" \" >> "+fd_sh;
if(dlevel)cerr<<cmd<<endl;
else system(cmd.c_str());
cmd="qsub -l walltime="+walltime+" -l pmem="+pmem+" -q "+queue+" "+fd_sh;
if(dlevel)cerr<<cmd<<endl;
else system(cmd.c_str());
}
while(true)
{
bool allDone=true;
for(int iter=0;iter<nStep;iter++)
{
ifstream signalFile(v_signal[iter].c_str());
if(!signalFile.good())
allDone=false;
signalFile.close();
}
if(allDone)
break;
#ifndef WIN32
sleep(sleepTime);
#else
Sleep(sleepTime*100);
#endif
}
cmd="rm "+output+" "+logerror;
if(dlevel)cerr<<cmd<<endl;
else system(cmd.c_str());
cmd="cat "+vectorToString(v_log)+" > "+output;
if(dlevel)cerr<<cmd<<endl;
else system(cmd.c_str());
cmd="cat "+vectorToString(v_logerror)+" > "+logerror;
if(dlevel)cerr<<cmd<<endl;
else system(cmd.c_str());
string debugInfo=output+"-debugInfo";
cmd="mkdir "+debugInfo;
if(dlevel)cerr<<cmd<<endl;
else system(cmd.c_str());
cmd="mv "+vectorToString(v_log)+" "+vectorToString(v_logerror)+" "+vectorToString(v_sh)+" "+vectorToString(v_signal)\
+" *sh.e* *sh.o* "+debugInfo;
if(dlevel)cerr<<cmd<<endl;
else system(cmd.c_str());
}
void printVector(const std::vector<T>& vec, const std::string& delim = " ",
std::ostream& out = std::cout) {
out << vectorToString(vec, delim) << "\n";
}
void SimpleVCF::init(const vector<string> & fields, CoreVCF * corevcf_){ //string line){
unresolvedGT=false;
homozygousREF=false;
heterozygous=false;
homozygousALT=false;
indexGenotype=-1;
indexGenotypeQual=-1;
indexDepth=-1;
indexPL=-1;
typeOfData=1;
// fields=allTokens(line,'\t');
// corevcf = corevcf_;
int fieldIndex = corevcf->getFieldIndexAndIncrease();
// cerr<<"fieldIndex "<<fieldIndex<<endl;
//FORMAT FIELDS
rawFormatNames = fields[ corevcf->getFieldIndexINFO()+1 ];
rawFormatValues = fields[fieldIndex];
// cerr<<"rawFormatNames "<<rawFormatNames<<endl;
// cerr<<"rawFormatValues "<<rawFormatValues<<endl;
formatFieldNames = allTokens(rawFormatNames ,':');
formatFieldValues = allTokens(rawFormatValues,':');
if(rawFormatValues == "./."){
unresolvedGT=true;
observedPL=false;
observedGL=false;
haploidCall=false;
}else{
if(formatFieldNames.size() != formatFieldValues.size()){
cerr<<"SimpleVCF: for line "<<vectorToString(fields,"\t")<<" the format field does not have as many fields as the values"<<endl;
exit(1);
}
observedPL=false;
observedGL=false;
haploidCall=false;
for(unsigned int i=0;i<formatFieldNames.size();i++){
// cerr<<"formatFieldNames["<<i<<"] "<<formatFieldNames[i]<<" = "<<formatFieldValues[i]<<endl;
if(formatFieldNames[i] == "GT"){
indexGenotype =i;
formatFieldGT= formatFieldValues[i];
bool determinedGenotype=false;
//Taken from http://www.broadinstitute.org/gatk/guide/topic?name=intro
if(formatFieldGT == "./."){ determinedGenotype=true; unresolvedGT=true; }
if(formatFieldGT == "0"){ determinedGenotype=true; homozygousREF=true; haploidCall=true; }
if(formatFieldGT == "1"){ determinedGenotype=true; homozygousALT=true; haploidCall=true; }
if(formatFieldGT == "0/0"){ determinedGenotype=true; homozygousREF=true; }
if(formatFieldGT == "0|0"){ determinedGenotype=true; homozygousREF=true; }
if(formatFieldGT == "0/1"){ determinedGenotype=true; heterozygous=true; }
if(formatFieldGT == "0|1"){ determinedGenotype=true; heterozygous=true; }
if(formatFieldGT == "1|0"){ determinedGenotype=true; heterozygous=true; }
if(formatFieldGT == "1/1"){ determinedGenotype=true; homozygousALT=true; }
if(formatFieldGT == "1|1"){ determinedGenotype=true; homozygousALT=true; }
if(formatFieldGT == "1/2"){ determinedGenotype=true; heterozygousALT=true; } //has first alt and second alt
if(formatFieldGT == "1|2"){ determinedGenotype=true; heterozygousALT=true; } //has first alt and second alt
if(formatFieldGT == "2/1"){ determinedGenotype=true; heterozygousALT=true; } //has first alt and second alt
if(formatFieldGT == "2|1"){ determinedGenotype=true; heterozygousALT=true; } //has first alt and second alt
if(formatFieldGT == "0|2"){ determinedGenotype=true; heterozygous2ndALT=true; } //has ref and second alt
if(formatFieldGT == "0/2"){ determinedGenotype=true; heterozygous2ndALT=true; } //has ref and second alt
if(formatFieldGT == "2/0"){ determinedGenotype=true; heterozygous2ndALT=true; } //has ref and second alt
if(formatFieldGT == "2|0"){ determinedGenotype=true; heterozygous2ndALT=true; } //has ref and second alt
if(formatFieldGT == "2/2"){ determinedGenotype=true; homozygous2ndALT=true; } //twice the second alt
if(formatFieldGT == "2|2"){ determinedGenotype=true; homozygous2ndALT=true; } //twice the second alt
//for more than 3
if(!determinedGenotype){
vector<string> fieldsOfGT = allTokens(formatFieldGT ,'/');
if(fieldsOfGT.size() == 2){
// int alleleCFirst = destringify<int> (fieldsOfGT[0]);
// int alleleC2nd = destringify<int> (fieldsOfGT[1]);
if(isPositiveInt(fieldsOfGT[0]) &&
isPositiveInt(fieldsOfGT[1]) ){
determinedGenotype=true; unresolvedGT=true;
}
}else{
vector<string> fieldsOfGT = allTokens(formatFieldGT ,'|');
if(fieldsOfGT.size() == 2){
// int alleleCFirst = destringify<int> (fieldsOfGT[0]);
// int alleleC2nd = destringify<int> (fieldsOfGT[1]);
if(isPositiveInt(fieldsOfGT[0]) &&
isPositiveInt(fieldsOfGT[1]) ){
determinedGenotype=true; unresolvedGT=true;
}
}else{
}
}
}
// if(formatFieldGT == "0/3" ||
// formatFieldGT == "3/3" ||
// formatFieldGT == "3/3" ||
// ){ determinedGenotype=true; unresolvedGT=true;
if(!determinedGenotype){
cerr<<"SimpleVCF: unable to determine genotype for line "<<vectorToString(fields,"\t")<<" field=#"<<formatFieldGT<<"#"<<endl;
exit(1);
}
continue;
}
if(formatFieldNames[i] == "GQ"){
if(formatFieldValues[i] == "."){
indexGenotypeQual =i;
formatFieldGQ=0.0;
}else{
indexGenotypeQual =i;
formatFieldGQ=destringify<float>(formatFieldValues[i]);
}
continue; }
if(formatFieldNames[i] == "DP"){ indexDepth =i; formatFieldDP=destringify<int> (formatFieldValues[i]); continue;}
if(formatFieldNames[i] == "GL"){
observedGL=true;
if(observedPL){
cerr<<"SimpleVCF: cannot observed both GL and PL "<<vectorToString(fields,"\t")<<""<<endl;
exit(1);
}
indexPL = i;
formatFieldGL = formatFieldValues[i];
vector<string> glfields = allTokens(formatFieldGL,',');
if(glfields.size() == 2){ //haploid calls (e.g. X for a male)
if(!haploidCall){
cerr<<"SimpleVCF: cannot observed 2 GL fields for a non-haploid record "<<vectorToString(fields,"\t")<<""<<endl;
exit(1);
}
formatFieldPLHomoRef = int(-10.0*destringify<double>(glfields[0]));
formatFieldPLHetero = -1000000; //very unlikely
formatFieldPLHomoAlt = int(-10.0*destringify<double>(glfields[1]));
}else{
if(glfields.size() == 3){ //biallelic
formatFieldPLHomoRef = int(-10.0*destringify<double>(glfields[0]));
formatFieldPLHetero = int(-10.0*destringify<double>(glfields[1]));
formatFieldPLHomoAlt = int(-10.0*destringify<double>(glfields[2]));
}else{
if(glfields.size() == 6){ //triallelic
//according to VCF docs it has the following order AA,AB,BB,AC,BC,CC
formatFieldPLHomoRef = int(-10.0*destringify<double>(glfields[0])); //r-r
formatFieldPLHetero1 = int(-10.0*destringify<double>(glfields[1])); //r-a1
formatFieldPLHomoAlt1 = int(-10.0*destringify<double>(glfields[2])); //a1-a1
formatFieldPLHetero2 = int(-10.0*destringify<double>(glfields[3])); //r-a2
formatFieldPLHetero12 = int(-10.0*destringify<double>(glfields[4])); //a1-a2
formatFieldPLHomoAlt2 = int(-10.0*destringify<double>(glfields[5])); //a2-a2
}else{
cerr<<"SimpleVCF: for line "<<vectorToString(fields,"\t")<<" the GL field does not have 3 or 6 fields"<<endl;
exit(1);
}
}
}
}
if(formatFieldNames[i] == "PL"){
observedPL=true;
if(observedGL){
cerr<<"SimpleVCF: cannot observed both GL and PL "<<vectorToString(fields,"\t")<<""<<endl;
exit(1);
}
indexPL = i;
if(formatFieldValues[i] == "."){
formatFieldPL = formatFieldValues[i];
unresolvedGT=true;
continue;
}
formatFieldPL = formatFieldValues[i];
vector<string> plfields = allTokens(formatFieldPL,',');
if(plfields.size() == 3){ //biallelic
formatFieldPLHomoRef = destringify<int>(plfields[0]);
formatFieldPLHetero = destringify<int>(plfields[1]);
formatFieldPLHomoAlt = destringify<int>(plfields[2]);
}else{
if(plfields.size() == 6){ //triallelic
//according to VCF docs it has the following order AA,AB,BB,AC,BC,CC
formatFieldPLHomoRef = destringify<int>(plfields[0]); //r-r
formatFieldPLHetero1 = destringify<int>(plfields[1]); //r-a1
formatFieldPLHomoAlt1 = destringify<int>(plfields[2]); //a1-a1
formatFieldPLHetero2 = destringify<int>(plfields[3]); //r-a2
formatFieldPLHetero12 = destringify<int>(plfields[4]); //a1-a2
formatFieldPLHomoAlt2 = destringify<int>(plfields[5]); //a2-a2
}else{
cerr<<"SimpleVCF: for line "<<vectorToString(fields,"\t")<<" the PL field does not have 3 or 6 fields"<<endl;
exit(1);
}
}
continue;
}
//To uncomment the fields to get these fields
if(formatFieldNames[i] == "A"){
vector<string> adfield = allTokens( formatFieldValues[i] ,',');
for(unsigned int j=0;j<adfield.size();j++){
countA.push_back( destringify<int>( adfield[j]) );
}
continue;
}
if(formatFieldNames[i] == "C"){
vector<string> adfield = allTokens( formatFieldValues[i] ,',');
for(unsigned int j=0;j<adfield.size();j++){
countC.push_back( destringify<int>( adfield[j]) );
}
continue;
}
if(formatFieldNames[i] == "G"){
vector<string> adfield = allTokens( formatFieldValues[i] ,',');
for(unsigned int j=0;j<adfield.size();j++){
countG.push_back( destringify<int>( adfield[j]) );
}
continue;
}
if(formatFieldNames[i] == "T"){
vector<string> adfield = allTokens( formatFieldValues[i] ,',');
for(unsigned int j=0;j<adfield.size();j++){
countT.push_back( destringify<int>( adfield[j]) );
}
continue;
}
}
}
// cout<<getADforA()<<endl;
// cout<<getADforC()<<endl;
// cout<<getADforG()<<endl;
// cout<<getADforT()<<endl;
// cerr<<"end"<<endl;
}
void slave(int rank, int comm_sz) {
Message msg;
int local_v[MAX_VECTOR];
int local_l;
MPI_Status status;
int q; // disposable index
char * strVector; // pointer for string representation of vector
char label[3]; // storage for local event label
// initialize vector
for (q = 0; q < comm_sz; q++)
local_v[q] = 0;
// initialize lamport
local_l = 0;
// initialize label
label[0] = '0' + rank - 1;
label[1] = '@'; // == 'A' - 1
label[2] = '\0';
while (1) {
MPI_Recv(&msg, 1, MESSAGE, MPI_ANY_SOURCE, MPI_ANY_TAG, MPI_COMM_WORLD, &status);
sleep(1);
// On finalize, MPI_TAG == 1
if (status.MPI_TAG == 1) {
strVector = vectorToString(local_v, comm_sz);
sprintf(msg.string, "Process %d report: Event %s - Logical: %d - Vector: %s",
rank - 1, label, local_l, strVector);
free(strVector);
MPI_Send(&msg, 1, MESSAGE, 0, 0, MPI_COMM_WORLD);
break;
}
local_l++;
local_v[rank]++;
label[1]++;
if (status.MPI_SOURCE == 0) {
if (msg.dest == 0) {
printf("Executing event %s in process %d.\n", label, rank - 1);
}
else {
printf("Message sent event %s from process %d to process %d: %s\n",
label, rank - 1, msg.dest - 1, msg.string);
for (q = 0; q < comm_sz; q++) {
msg.vector[q] = local_v[q];
}
msg.lamport = local_l;
MPI_Send(&msg, 1, MESSAGE, msg.dest, 0, MPI_COMM_WORLD);
}
sprintf(msg.string, "receievd");
MPI_Send(&msg, 1, MESSAGE, 0, 0, MPI_COMM_WORLD);
} else {
printf("Message received event %s from process %d by process %d: %s\n",
label, status.MPI_SOURCE - 1, rank - 1, msg.string);
mergeVectors(msg.vector, local_v, comm_sz);
local_l = (msg.lamport >= (local_l - 1)? msg.lamport + 1 : local_l);
}
// print status to stdout
strVector = vectorToString(local_v, comm_sz);
printf("The Logical/Vector time of event %s at process %d is: %d / %s\n\n",
label, rank - 1, local_l, strVector);
free(strVector);
}
}
/*!
\param input the input combination ("1" = true, "0" = false).
\return The outputs of the input combination in string form ("1" = true, "0" = false).
*/
wxString TruthTable::getOutput(wxString input)
{
vector<bool> vInput = stringToVector(input);
return vectorToString(getOutput(vInput));
}
