GeneticAlgorithm::GeneticAlgorithm(double* dataSet, int dataSetLength, int nPopulation, double scaleFactor, double crossingProbability, int order, double xHL, double yHL, double zHL, double density, int nMissing){
totalTime = 0; // for timing things
QueryPerformanceFrequency(&freq);
_nPopulation = nPopulation;
initializeRandomNumberGenerators();
_nMissing = nMissing;
_order = order;
_R = 3 * (order+1) * (order+2) * (order+3) / 6;
_xHL = xHL;
_yHL = yHL;
_zHL = zHL;
_density = density;
_basisPop = new int[8];
for(int i = 0; i < 8; i++){
_basisPop[i] = 0;
}
_basis = createBasis(order, _basisPop);
initialiseMatrices();
initializeParameters(dataSet, dataSetLength, nPopulation, scaleFactor, crossingProbability);
}
OutputInfo FullyConnected::initialize(std::vector<double*>& parameterPointers,
std::vector<double*>& parameterDerivativePointers)
{
parameterPointers.reserve(parameterPointers.size() + J * (I + bias));
parameterDerivativePointers.reserve(parameterDerivativePointers.size() + J * (I + bias));
for(int j = 0; j < J; j++)
{
for(int i = 0; i < I; i++)
{
parameterPointers.push_back(&W(j, i));
parameterDerivativePointers.push_back(&Wd(j, i));
}
if(bias)
{
parameterPointers.push_back(&b(j));
parameterDerivativePointers.push_back(&bd(j));
}
}
initializeParameters();
OutputInfo info;
info.dimensions.push_back(J);
return info;
}
MSAGeneralTab::MSAGeneralTab(MSAEditor* _msa)
: msa(_msa), savableTab(this, GObjectViewUtils::findViewByName(_msa->getName()))
{
SAFE_POINT(NULL != msa, "MSA Editor not defined.", );
setupUi(this);
ShowHideSubgroupWidget* alignmentInfo = new ShowHideSubgroupWidget("ALIGNMENT_INFO", tr("Alignment info"), alignmentInfoWidget, true);
ShowHideSubgroupWidget* consensusMode = new ShowHideSubgroupWidget("CONSENSUS_MODE", tr("Consensus mode"), consensusModeWidget, true);
ShowHideSubgroupWidget* copyType = new ShowHideSubgroupWidget("COPY_TYPE", tr("Copy to clipboard"), copyTypeWidget, true);
Ui_GeneralTabOptionsPanelWidget::layout->addWidget(alignmentInfo);
Ui_GeneralTabOptionsPanelWidget::layout->addWidget(consensusMode);
Ui_GeneralTabOptionsPanelWidget::layout->addWidget(copyType);
initializeParameters();
connectSignals();
U2WidgetStateStorage::restoreWidgetState(savableTab);
#ifdef Q_OS_MAC
copyButton->setToolTip("Cmd+Shift+C");
#else
copyButton->setToolTip("Ctrl+Shift+C");
#endif
}
ScopLib::ScopLib(Scop *S) : PollyScop(S) {
scoplib = scoplib_scop_malloc();
initializeArrays();
initializeParameters();
initializeScattering();
initializeStatements();
}
returnValue OptimizationAlgorithmBase::initializeParameters( const char* fileName)
{
VariablesGrid tmp = fopen( fileName,"r" );
if ( tmp.isEmpty() == BT_TRUE )
return RET_FILE_CAN_NOT_BE_OPENED;
return initializeParameters(tmp);
}
void Master::_initializeParameters()
{
// Master::_initializeParameters(): local variables
/* The function \a _initializeLpParameters() initializes the LP solver
* specific Parameters. It is called after the parameter-file
* {\tt .abacus} was read and all general parameters were processed.
*
* This function is implemented in the file \a lpif.cc.
*/
if(readParamFromFile_) {
// set up the name of the configuration file
// The location of the configuration file .abacus is given by the environment variable ABACUS_DIR.
char *abacusDir = getenv("ABACUS_DIR");
if (!abacusDir) {
Logger::ifout() << "environment variable ABACUS_DIR not found\n";
OGDF_THROW_PARAM(AlgorithmFailureException, ogdf::AlgorithmFailureCode::IllegalParameter);
}
#ifdef OGDF_SYSTEM_UNIX
string configFileName = string(abacusDir) + "/.abacus";
#else
string configFileName = string(abacusDir) + "\\.abacus";
#endif
readParameters(configFileName);
} else {
// set default values for abacus parameters
insertParameter("EnumerationStrategy","BestFirst");
insertParameter("BranchingStrategy","CloseHalfExpensive");
insertParameter("NBranchingVariableCandidates","1");
insertParameter("NStrongBranchingIterations","50");
insertParameter("Guarantee","0.0");
insertParameter("MaxLevel","999999");
insertParameter("MaxNSub","9999999");
insertParameter("MaxCpuTime","99999:59:59");
insertParameter("MaxCowTime","99999:59:59");
insertParameter("ObjInteger","false");
insertParameter("TailOffNLps","0");
insertParameter("TailOffPercent","0.0001");
insertParameter("DelayedBranchingThreshold","0");
insertParameter("MinDormantRounds","1");
insertParameter("PrimalBoundInitMode","None");
insertParameter("PricingFrequency","0");
insertParameter("SkipFactor","1");
insertParameter("SkippingMode","SkipByNode");
insertParameter("FixSetByRedCost","true");
insertParameter("PrintLP","false");
insertParameter("MaxConAdd","100");
insertParameter("MaxConBuffered","100");
insertParameter("MaxVarAdd","500");
insertParameter("MaxVarBuffered","500");
insertParameter("MaxIterations","-1");
insertParameter("EliminateFixedSet","false");
insertParameter("NewRootReOptimize","false");
insertParameter("ShowAverageCutDistance","false");
insertParameter("ConstraintEliminationMode","Basic");
insertParameter("ConElimEps","0.001");
insertParameter("ConElimAge","1");
insertParameter("VariableEliminationMode","ReducedCost");
insertParameter("VarElimEps","0.001");
insertParameter("VarElimAge","1");
insertParameter("VbcLog","None");
#if defined(COIN_OSI_CPX)
insertParameter("DefaultLpSolver","CPLEX");
#elif defined(COIN_OSI_SYM)
insertParameter("DefaultLpSolver","SYMPHONY");
#elif defined(COIN_OSI_GRB)
insertParameter("DefaultLpSolver","Gurobi");
#else
insertParameter("DefaultLpSolver","Clp");
#endif
insertParameter("SolveApprox","false");
_setDefaultLpParameters();
}
// let the user set/overwrite parameters in 4 steps.
// 1) Assign parameters that were read from the global abacus config file
assignParameters();
// 2) Allow user to read parameters from custom config file
initializeParameters();
// 3) Assign parameters from custom config file.
// this assigns all parameters that were read from the abacus config file
// in the abacus directory and those that the user read from a file
// in initializeParameters(). However, this will overwrite any parameter
// that was set directly.
assignParameters();
// 4) Allow user to set parameters directly
// call initializeParameters again so that parameters that were set directly
// (and not via a config file) can be set (undo the overwrite from step 2).
// Since we do *not* call assignParameters again, those parameters are not
// overwritten this time.
initializeParameters();
_initializeLpParameters();
}
GeneticAlgorithm2::GeneticAlgorithm2(double** dataSet, int dataSetLength, int nPopulation, double scaleFactor, double crossingProbability){
QueryPerformanceFrequency(&freq);
_nPopulation = nPopulation;
initializeRandomNumberGenerators();
initializeParameters(dataSet, dataSetLength, nPopulation, scaleFactor, crossingProbability);
}
OutputInfo Subsampling::initialize(std::vector<double*>& parameterPointers,
std::vector<double*>& parameterDerivativePointers)
{
OutputInfo info;
info.dimensions.push_back(fm);
outRows = inRows / kernelRows;
outCols = inCols / kernelCols;
fmOutSize = outRows * outCols;
info.dimensions.push_back(outRows);
info.dimensions.push_back(outCols);
fmInSize = inRows * inCols;
maxRow = inRows - kernelRows + 1;
maxCol = inCols - kernelCols + 1;
W.resize(fm, Eigen::MatrixXd(outRows, outCols));
Wd.resize(fm, Eigen::MatrixXd(outRows, outCols));
int numParams = fm * outRows * outCols * kernelRows * kernelCols;
if(bias)
{
Wb.resize(fm, Eigen::MatrixXd(outRows, outCols));
Wbd.resize(fm, Eigen::MatrixXd(outRows, outCols));
numParams += fm * outRows * outCols;
}
parameterPointers.reserve(parameterPointers.size() + numParams);
parameterDerivativePointers.reserve(parameterDerivativePointers.size() + numParams);
for(int fmo = 0; fmo < fm; fmo++)
{
for(int r = 0; r < outRows; r++)
{
for(int c = 0; c < outCols; c++)
{
parameterPointers.push_back(&W[fmo](r, c));
parameterDerivativePointers.push_back(&Wd[fmo](r, c));
if(bias)
{
parameterPointers.push_back(&Wb[fmo](r, c));
parameterDerivativePointers.push_back(&Wbd[fmo](r, c));
}
}
}
}
initializeParameters();
a.resize(1, info.outputs());
y.resize(1, info.outputs());
yd.resize(1, info.outputs());
deltas.resize(1, info.outputs());
if(info.outputs() < 1)
throw OpenANNException("Number of outputs in subsampling layer is below"
" 1. You should either choose a smaller filter"
" size or generate a bigger input.");
OPENANN_CHECK(fmInSize > 0);
OPENANN_CHECK(outRows > 0);
OPENANN_CHECK(outCols > 0);
OPENANN_CHECK(fmOutSize > 0);
OPENANN_CHECK(maxRow > 0);
OPENANN_CHECK(maxCol > 0);
return info;
}
bool Jpeg2000::load (const QString &filename,
QImage &imageResult) const
{
LOG4CPP_INFO_S ((*mainCat)) << "Jpeg2000::load"
<< " filename=" << filename.toLatin1().data();
if (invalidFileExtension (filename)) {
return false;
}
opj_dparameters_t parameters;
initializeParameters (parameters);
parameters.decod_format = inputFormat (filename.toLatin1().data());
opj_stream_t *inStream = opj_stream_create_default_file_stream (filename.toLatin1().data(), 1);
if (!inStream) {
LOG4CPP_ERROR_S ((*mainCat)) << "Jpeg2000::load encountered error opening stream";
return false;
}
// Create decoder
opj_codec_t *inCodec = decode (parameters.decod_format);
if (!inCodec) {
LOG4CPP_ERROR_S ((*mainCat)) << "Jpeg2000::load encountered error creating decoding stream";
opj_stream_destroy (inStream);
return false;
}
// Callbacks for local handling of errors
opj_set_info_handler (inCodec, infoCallback, 0);
opj_set_warning_handler (inCodec, warningCallback, 0);
opj_set_error_handler (inCodec, errorCallback, 0);
if (!opj_setup_decoder (inCodec,
¶meters)) {
LOG4CPP_ERROR_S ((*mainCat)) << "Jpeg2000::load encountered error decoding stream";
opj_stream_destroy (inStream);
opj_destroy_codec (inCodec);
return false;
}
// Read header and, if necessary, the JP2 boxes
opj_image_t *image;
if (!opj_read_header (inStream,
inCodec,
&image)) {
LOG4CPP_ERROR_S ((*mainCat)) << "Jpeg2000::load encountered error reading header";
opj_stream_destroy (inStream);
opj_destroy_codec (inCodec);
opj_image_destroy (image);
return false;
}
// Get the decoded image
if (!(opj_decode (inCodec,
inStream,
image) &&
opj_end_decompress (inCodec,
inStream))) {
LOG4CPP_ERROR_S ((*mainCat)) << "Jpeg2000::load failed to decode image";
opj_destroy_codec (inCodec);
opj_stream_destroy (inStream);
opj_image_destroy (image);
return false;
}
// Close the byte stream
opj_stream_destroy (inStream);
applyImageTweaks (image);
// Transform into ppm image in memory
bool success = true;
QBuffer buffer;
buffer.open (QBuffer::WriteOnly);
if (imagetopnm (image,
buffer)) {
LOG4CPP_ERROR_S ((*mainCat)) << "Jpeg2000::load failed to generate new image";
success = false;
} else {
// Intermediate file for debugging
// QFile file ("jpeg2000.ppm");
// file.open (QIODevice::WriteOnly);
// file.write (buffer.data());
// file.close ();
// Create output
imageResult.loadFromData(buffer.data());
}
// Deallocate
if (inCodec) {
opj_destroy_codec (inCodec);
}
opj_image_destroy (image);
return success;
}
void S2Controller::initializeS2(){
initializeParameters();
connectToS2();
}
