void RddtClust::doHeatmap(){
using namespace Rcpp;
XmdvToolMainWnd* m_mwd = this->m_rddtOp->m_pm->getMainWnd();
RInside r = m_mwd->getRinstance();
int dims = this->m_selected.size();
if(dims==0)
return;
//m_colSelected.clear();
NumericVector nvSelected(dims);
for(int i = 0; i<dims; i++){
nvSelected[i] = m_selected[i];
//this->m_colSelected.push_back(false);
}
r["selected"] = nvSelected;
// for heatmap view; this applies to any similarity metrics
std::string clustOrdcmd =
"selected<-as.integer(selected)+1;\n" //R index starts from 1;
"seldist <- distances[selected,selected];\n"
//"sdist<-apply(seldist,1,sort);\n"
"seldist";
SEXP evals = r.parseEval(clustOrdcmd);
//NumericVector rClustOrd(evals);
//evals = r.parseEval(paramValCmd);
NumericMatrix rParamVal(evals);
m_paraMtx.clear();
for(int i = 0; i<dims; i++){
for(int j = 0; j<dims; j++){
double v = rParamVal(i,j);
this->m_paraMtx.push_back(v);
}
}
std::string ordcmd =
"ordidx <- apply(seldist,1,order);\n"
"ordidx-1";
evals = r.parseEval(ordcmd);
NumericMatrix rOrd(evals);
this->m_paraOrdMtx.clear();
for(int i = 0; i<dims; i++){
for(int j = 0; j<dims; j++){
int v = rOrd(i,j);
this->m_paraOrdMtx.push_back(v);
}
}
/*this->m_dimOrd.clear();
for(int i=0; i<dims; i++){
int ord = (int)(rClustOrd[i]);
m_dimOrd.push_back(ord);
}*/
}
void td_r_invoke1(td_val_t *out, char *fname, td_val_t *arg)
{
SEXP ans;
string arg_name =
r_env.parseEval("paste(sample(letters, 10, replace=TRUE), collapse='')");
r_env[arg_name] = from_td_val(arg);
r_env.parseEval( (string(fname) + "(" + arg_name + ")").c_str(), ans);
r_env.parseEvalQ(string("rm(") + arg_name + ")");
R_PreserveObject(ans);
to_td_val(out, ans);
}
void td_r_invokeGraph2(graph_t *out, char *fname, graph_t *arg, int k)
{
char str[255];
derived_graph_and_annotation_t ret;
SEXP ans;
r_env["m"] = graph_to_dgRMatrix(*arg);
r_env["k"] = k;
sprintf(str, "%s(m, k)", fname);
r_env.parseEval(str, ans);
r_env.parseEvalQ("rm(\"m\", \"k\")");
List l(ans);
ret.graph = SEXP_to_graph2(l["graph"], *out);
ret.cluster_assignments = copy_to_c_type<IntegerVector>(l["clusters"]);
}
void td_r_eval(td_val_t *out, char *str)
{
SEXP ans;
r_env.parseEval(str, ans);
// WS: I decree by general hack, for now this will be void
//to_td_val(out, ans);
}
// Propose, evaluate and accept based on temperature
// Returns 1 if accepted, 0 if rejected
int MLST::update(double temperature)
{
int accepted = 0;
// Proposal
int replace_idx = mlst_index(generator);
int replaced_gene = _mlst[replace_idx];
int new_gene = rand_gene(generator);
while (new_gene == replaced_gene)
{
new_gene = rand_gene(generator);
}
_mlst[replace_idx] = new_gene;
std::sort(_mlst.begin(), _mlst.end());
// Calculate distance
string mlst_genes
double new_dist = _R.parseEval("tree_metric()");
// Decide whether to accept
if (new_dist < _distance)
{
_distance = new_dist;
accepted = 1;
}
return accepted;
}
void RddtClust::getDimData(DoubleVector& dimData, int idx){
using namespace Rcpp;
XmdvToolMainWnd* m_mwd = this->m_rddtOp->m_pm->getMainWnd();
RInside r = m_mwd->getRinstance();
//qDebug()<<"idx qt "<<idx;
r["currentDim"] = idx;
std::string cmd = "currentDim <- as.integer(currentDim)+1;\n"
//"print(currentDim);\n"
"dimData <- M[,currentDim];\n"
"dimData";
SEXP evals = r.parseEval(cmd);
NumericVector rDimData(evals);
dimData.clear();
for(int i = 0; i< rDimData.length(); i++){
dimData.push_back(rDimData[i]);
}
}
void RddtClust::doOutliers(){
using namespace Rcpp;
XmdvToolMainWnd* m_mwd = this->m_rddtOp->m_pm->getMainWnd();
RInside r = m_mwd->getRinstance();
int dims = this->m_selected.size();
if(dims<2)
return;
//int numSelected = this->m_selected.size();
NumericVector nvSelected(dims);
for(int i = 0; i<dims; i++){
nvSelected[i] = m_selected[i];
}
r["selected"] = nvSelected;
std::string rankcmd = "vars<-apply(M[,selected],2,sd);\n"
"vars<-as.matrix(vars);\n"
"rownames(vars)<-1:nrow(vars);\n"
"vars<-as.matrix(vars[order(vars[,1],decreasing=TRUE),]);\n"
"as.numeric(rownames(vars))-1"; //order in r starts from 0;
SEXP evals = r.parseEval(rankcmd);
NumericVector rDimRank(evals);
//ranking scores;
std::string scorecmd="as.numeric(vars[,1])";
evals = r.parseEval(scorecmd);
NumericVector rScoreMtx(evals);
//save dimension statistics: rank order, rank score and heatmap order;
this->m_order.clear();
// this->m_scores.clear();
for(int i=0; i<dims; i++){
int tmp = ((int)(rDimRank[i]));
//this->m_dimRank;
m_order.push_back(tmp);
// double score = rScoreMtx[i];
//m_scores.push_back(score);
}
}
void RddtClust::doCenter(){
using namespace Rcpp;
XmdvToolMainWnd* m_mwd = this->m_rddtOp->m_pm->getMainWnd();
RInside r = m_mwd->getRinstance();
int dims = this->m_selected.size();
int numSelected = this->m_selected.size();
//no need for single element reordering;
if(numSelected<2)
return;
NumericVector nvSelected(numSelected);
for(int i = 0; i<numSelected; i++){
nvSelected[i] = m_selected[i];
}
r["selected"] = nvSelected;
//cmd = ;
//r.parseEval(cmd);
if(m_selected.size()<=1){
assert(m_selected.size()>1);
}
std::string rcmd = "selected<-as.integer(selected)+1;\n" //R index starts from 1;
"seldist <- distances[selected,selected];\n"
//"print(distances);\n"
"centroid <- colSums(seldist);\n"
"ord<-as.vector(order(centroid));\n"
"ord-1";
SEXP evals = r.parseEval(rcmd);
NumericVector rCntrdOrder(evals);
this->m_order.clear();
//this->m_scores.clear();
for(int i=0; i<dims; i++){
int tmp = ((int)(rCntrdOrder[i]));
m_order.push_back(tmp);
}
rcmd = "max(as.dist(seldist));\n";
evals = r.parseEval(rcmd);
m_worstFit = Rcpp::as<double>(evals);
rcmd = "min(as.dist(seldist));\n";
evals = r.parseEval(rcmd);
m_bestFit = Rcpp::as<double>(evals);
rcmd = "mean(as.dist(seldist));\n";
evals = r.parseEval(rcmd);
m_fitConsistency = Rcpp::as<double>(evals);
rcmd = //"print(seldist);\n"
"max(seldist[,ord[1]]);\n";
evals = r.parseEval(rcmd);
m_fitRadius = Rcpp::as<double>(evals);
}
void td_r_invoke0(td_val_t *out, char *fname)
{
SEXP ans;
r_env.parseEval((string(fname) + "()").c_str(), ans);
to_td_val(out, ans);
}
BpdeMainWindow::BpdeMainWindow(RInside& R, const QString& sourceFile, QObject *parent)
: R(R),
sourceFile(sourceFile), x(), y(), H(), solver(NULL)
{
tempfile = QString::fromStdString(Rcpp::as<std::string>(R.parseEval("tfile <- tempfile()")));
svgfile = QString::fromStdString(Rcpp::as<std::string>(R.parseEval("sfile <- tempfile()")));
QWidget *window = new QWidget;
window->setWindowTitle("BpdeGUI");
setCentralWidget(window);
QGroupBox *runParameters = new QGroupBox("Параметры запуска");
openMPEnabled = new QRadioButton("&OpenMP");
openClEnabled = new QRadioButton("&OpenCL");
openMPEnabled->setChecked(true);
connect(openMPEnabled, SIGNAL(clicked()), this, SLOT(loadSource()));
connect(openClEnabled, SIGNAL(clicked()), this, SLOT(loadSource()));
QVBoxLayout *vbox = new QVBoxLayout;
vbox->addWidget(openMPEnabled);
vbox->addWidget(openClEnabled);
QLabel *threadsLabel = new QLabel("Количество потоков");
threadsLineEdit = new QLineEdit("4");
QHBoxLayout *threadNumber = new QHBoxLayout;
threadNumber->addWidget(threadsLabel);
threadNumber->addWidget(threadsLineEdit);
QHBoxLayout *deviceLayout = new QHBoxLayout;
QLabel *deviceLabel = new QLabel("Устройство");
deviceComboBox = new QComboBox();
scanDevices();
for (std::vector<cl::Device>::iterator it = devices.begin(); it != devices.end(); it++)
deviceComboBox->addItem((*it).getInfo<CL_DEVICE_NAME>().c_str());
connect(deviceComboBox, SIGNAL(currentIndexChanged(int)), this, SLOT(loadSource()));
deviceLayout->addWidget(deviceLabel);
deviceLayout->addWidget(deviceComboBox);
QHBoxLayout* runLayout = new QHBoxLayout;
runButton = new QPushButton("Начать вычисления", this);
qDebug() << "Connect : " <<
connect(runButton, SIGNAL(clicked()), this, SLOT(solve()));
runLayout->addWidget(runButton);
QVBoxLayout* ulLayout = new QVBoxLayout;
ulLayout->addLayout(vbox);
ulLayout->addLayout(threadNumber);
ulLayout->addLayout(deviceLayout);
ulLayout->addLayout(runLayout);
runParameters->setSizePolicy(QSizePolicy::Fixed, QSizePolicy::Fixed);
runParameters->setLayout(ulLayout);
QButtonGroup *kernelGroup = new QButtonGroup;
kernelGroup->addButton(openMPEnabled, 0);
kernelGroup->addButton(openClEnabled, 1);
QGroupBox *solveParamBox = new QGroupBox("Настройки вычислительного метода");
QHBoxLayout *iterationsLayout = new QHBoxLayout;
QHBoxLayout *stepLayout = new QHBoxLayout;
QLabel *sourceFileLabel = new QLabel("SourceFile");
sourceFileEdit = new QLineEdit(sourceFile);
iterationsEdit = new QLineEdit("10000");
stepEdit = new QLineEdit("3600");
QLabel *iterationsLabel = new QLabel("Итерации");
QLabel *stepLabel = new QLabel("Шаг ");
QHBoxLayout *exportLayout = new QHBoxLayout;
exportImage = new QPushButton("Экспорт изотерм");
export3D = new QPushButton("Экспорт 3D модели");
connect(exportImage, SIGNAL(clicked()), this, SLOT(exportIsoterms()));
connect(export3D, SIGNAL(clicked()), this, SLOT(export3DModel()));
iterationsLayout->addWidget(iterationsLabel);
iterationsLayout->addWidget(iterationsEdit);
stepLayout->addWidget(stepLabel);
stepLayout->addWidget(stepEdit);
exportLayout->addWidget(exportImage);
exportLayout->addWidget(export3D);
svg = new QSvgWidget();
loadSource();
QVBoxLayout *solveParamLayout = new QVBoxLayout;
solveParamLayout->addWidget(sourceFileLabel);
solveParamLayout->addWidget(sourceFileEdit);
solveParamLayout->addLayout(iterationsLayout);
solveParamLayout->addLayout(stepLayout);
solveParamLayout->addLayout(exportLayout);
solveParamBox->setSizePolicy(QSizePolicy::Fixed, QSizePolicy::Fixed);
solveParamBox->setLayout(solveParamLayout);
QHBoxLayout *upperlayout = new QHBoxLayout;
upperlayout->addWidget(runParameters);
upperlayout->addWidget(solveParamBox);
QHBoxLayout *lowerlayout = new QHBoxLayout;
lowerlayout->addWidget(svg);
QVBoxLayout *outer = new QVBoxLayout;
outer->addLayout(upperlayout);
outer->addLayout(lowerlayout);
window->setLayout(outer);
}
