double IIRNotch::processSample(double input){
bool v = false;
Eigen::Vector3d x_temp ( input , x(0), x(1) );
Eigen::Vector3d y_temp ( 0, y(0), y(1) );
if(v) std::cout << input << "\n";
if(v) std::cout << x_temp.transpose() << " x_temp\n";
if(v) std::cout << y_temp.transpose() << " y_temp\n";
if(v) std::cout << b.transpose() << " b\n";
if(v) std::cout << a.transpose() << " a\n";
if(v){
Eigen::Vector3d bit = x_temp.cross(b);
std::cout << bit.transpose() << " bit\n";
}
double output = (x_temp.dot(b)) - (y_temp.dot(a));
double temp_x = x(0);
x << input , temp_x ;
double temp_y = y(0);
y << output, temp_y ;
if(v) std::cout << x.transpose() << " x\n";
if(v) std::cout << y.transpose() << " y\n\n";
return output;
}
void Correlation::addResultCurve()
{
ApplicationWindow *app = dynamic_cast<ApplicationWindow *>(parent());
if (!app)
return;
QLocale locale = app->locale();
if (d_n > d_table->numRows())
d_table->setNumRows(d_n);
int cols = d_table->numCols();
int cols2 = cols+1;
d_table->addCol();
d_table->addCol();
int n = d_n/2;
QVarLengthArray<double> x_temp(d_n), y_temp(d_n);//double x_temp[d_n], y_temp[d_n];
for (int i = 0; i<d_n; i++){
double x = i - n;
x_temp[i] = x;
double y;
if(i < n)
y = d_x[n + i];
else
y = d_x[i - n];
y_temp[i] = y;
d_table->setText(i, cols, QString::number(x));
d_table->setText(i, cols2, locale.toString(y, 'g', app->d_decimal_digits));
}
QStringList l = d_table->colNames().grep(tr("Lag"));
QString id = QString::number((int)l.size()+1);
QString label = objectName() + id;
d_table->setColName(cols, tr("Lag") + id);
d_table->setColName(cols2, label);
d_table->setColPlotDesignation(cols, Table::X);
d_table->setHeaderColType();
if (d_graphics_display){
if (!d_output_graph)
d_output_graph = createOutputGraph()->activeGraph();
DataCurve *c = new DataCurve(d_table, d_table->colName(cols), d_table->colName(cols2));
c->setData(x_temp.data(), y_temp.data(), d_n);//c->setData(x_temp, y_temp, d_n);
c->setPen(QPen(ColorBox::color(d_curveColorIndex), 1));
d_output_graph->insertPlotItem(c, Graph::Line);
d_output_graph->updatePlot();
}
}
RcppExport SEXP readBeadFindMask(SEXP beadFindFile_in, SEXP x_in, SEXP y_in) {
SEXP rl = R_NilValue; // Use this when there is nothing to be returned.
char *exceptionMesg = NULL;
try {
// Recasting of input arguments
Rcpp::StringVector beadFindFile_temp(beadFindFile_in);
std::string *beadFindFile = new std::string(beadFindFile_temp(0));
// x
Rcpp::IntegerVector x_temp(x_in);
uint64_t nX = x_temp.size();
Rcpp::IntegerVector x(nX);
int xMin = INT_MAX;
int xMax = -1;
int newVal = 0;
for(uint64_t i=0; i<nX; i++) {
newVal = x_temp(i);
x(i) = newVal;
if(newVal < xMin)
xMin = newVal;
if(newVal > xMax)
xMax = newVal;
}
// y
Rcpp::IntegerVector y_temp(y_in);
uint64_t nY = y_temp.size();
Rcpp::IntegerVector y(nX);
int yMin = INT_MAX;
int yMax = -1;
for(uint64_t i=0; i<nY; i++) {
newVal = y_temp(i);
y(i) = newVal;
if(newVal < yMin)
yMin = newVal;
if(newVal > yMax)
yMax = newVal;
}
// Ensure lower bounds are positive and less than the upper bounds, then proceed to open the file
if(nX != nY) {
exceptionMesg = strdup("x and y should be of the same length");
} else if(nX < 0) {
exceptionMesg = strdup("x and y should be of positive length");
} else if(xMin < 0) {
exceptionMesg = strdup("xMin must be positive");
} else if(yMin < 0) {
exceptionMesg = strdup("yMin must be positive");
} else if(xMin > xMax) {
exceptionMesg = strdup("xMin must be less than xMax");
} else if(yMin > yMax) {
exceptionMesg = strdup("yMin must be less than yMax");
} else {
FILE *fp = NULL;
fp = fopen(beadFindFile->c_str(),"rb");
if(!fp) {
std::string exception = "unable to open beadFindFile " + *beadFindFile;
exceptionMesg = strdup(exception.c_str());
} else {
int32_t nRow = 0;
int32_t nCol = 0;
if ((fread (&nRow, sizeof(uint32_t), 1, fp )) != 1) {
// Read number of rows (aka "y" or "height")
std::string exception = "Problem reading nRow from beadFindFile" + *beadFindFile;
exceptionMesg = strdup(exception.c_str());
} else if ((fread (&nCol, sizeof(uint32_t), 1, fp )) != 1) {
// Read number of cols (aka "x" or "width")
std::string exception = "Problem reading nCol from beadFindFile" + *beadFindFile;
exceptionMesg = strdup(exception.c_str());
} else {
// Ensure upper bounds are within range before continuing
if(yMax >= nRow) {
exceptionMesg = strdup("yMax must be less than the number of rows");
} else if(xMax >= nCol) {
exceptionMesg = strdup("xMax must be less than the number of cols");
} else {
// Iterate over mask data and store out the encoded Boolean values
uint16_t mask = 0;
Rcpp::IntegerVector maskEmpty(nX);
Rcpp::IntegerVector maskBead(nX);
Rcpp::IntegerVector maskLive(nX);
Rcpp::IntegerVector maskDud(nX);
Rcpp::IntegerVector maskReference(nX);
Rcpp::IntegerVector maskTF(nX);
Rcpp::IntegerVector maskLib(nX);
Rcpp::IntegerVector maskPinned(nX);
Rcpp::IntegerVector maskIgnore(nX);
Rcpp::IntegerVector maskWashout(nX);
Rcpp::IntegerVector maskExclude(nX);
Rcpp::IntegerVector maskKeypass(nX);
Rcpp::IntegerVector maskFilteredBadKey(nX);
Rcpp::IntegerVector maskFilteredShort(nX);
Rcpp::IntegerVector maskFilteredBadPPF(nX);
Rcpp::IntegerVector maskFilteredBadResidual(nX);
int64_t headerSkipBytes = 2 * sizeof(uint32_t);
int64_t dataSkipBytes = sizeof(uint16_t);
int64_t offset;
for (uint64_t i=0; i < nX; i++) {
int col = x(i);
int row = y(i);
offset = headerSkipBytes + (row * nCol + col) * dataSkipBytes;
fseek(fp, offset, SEEK_SET);
if ((fread (&mask, sizeof(uint16_t), 1, fp)) != 1) {
std::string exception = "Problem reading mask values from " + *beadFindFile;
exceptionMesg = strdup(exception.c_str());
break;
} else {
maskEmpty(i) = (mask & MaskEmpty) > 0;
maskBead(i) = (mask & MaskBead) > 0;
maskLive(i) = (mask & MaskLive) > 0;
maskDud(i) = (mask & MaskDud) > 0;
maskReference(i) = (mask & MaskReference) > 0;
maskTF(i) = (mask & MaskTF) > 0;
maskLib(i) = (mask & MaskLib) > 0;
maskPinned(i) = (mask & MaskPinned) > 0;
maskIgnore(i) = (mask & MaskIgnore) > 0;
maskWashout(i) = (mask & MaskWashout) > 0;
maskExclude(i) = (mask & MaskExclude) > 0;
maskKeypass(i) = (mask & MaskKeypass) > 0;
maskFilteredBadKey(i) = (mask & MaskFilteredBadKey) > 0;
maskFilteredShort(i) = (mask & MaskFilteredShort) > 0;
maskFilteredBadPPF(i) = (mask & MaskFilteredBadPPF) > 0;
maskFilteredBadResidual(i) = (mask & MaskFilteredBadResidual) > 0;
}
}
// Check if there are any non-zero values for Keypass and Exclude and filtered data.
// If not then it is likely that this is a legacy bfmask.bin file and we won't return
// these fields.
//bool haveFiltered=0;
//for (uint64_t i=0; i < nX; i++) {
// if(maskKeypass(i) || maskExclude(i) || maskFilteredBadKey(i) || maskFilteredShort(i) ||
// maskFilteredBadPPF(i) || maskFilteredBadResidual(i)) {
// haveFiltered=1;
// break;
// }
//}
// Build result set to be returned as a list to R.
std::map<std::string,SEXP> map;
map["beadFindMaskFile"] = Rcpp::wrap( *beadFindFile );
map["nCol"] = Rcpp::wrap( nCol );
map["nRow"] = Rcpp::wrap( nRow );
map["col"] = Rcpp::wrap( x );
map["row"] = Rcpp::wrap( y );
map["maskEmpty"] = Rcpp::wrap( maskEmpty );
map["maskBead"] = Rcpp::wrap( maskBead );
map["maskLive"] = Rcpp::wrap( maskLive );
map["maskDud"] = Rcpp::wrap( maskDud );
map["maskReference"] = Rcpp::wrap( maskReference );
map["maskTF"] = Rcpp::wrap( maskTF );
map["maskLib"] = Rcpp::wrap( maskLib );
map["maskPinned"] = Rcpp::wrap( maskPinned );
map["maskIgnore"] = Rcpp::wrap( maskIgnore );
map["maskWashout"] = Rcpp::wrap( maskWashout );
//if(haveFiltered) {
map["maskExclude"] = Rcpp::wrap( maskExclude );
map["maskKeypass"] = Rcpp::wrap( maskKeypass );
map["maskFilteredBadKey"] = Rcpp::wrap( maskFilteredBadKey );
map["maskFilteredShort"] = Rcpp::wrap( maskFilteredShort );
map["maskFilteredBadPPF"] = Rcpp::wrap( maskFilteredBadPPF );
map["maskFilteredBadResidual"] = Rcpp::wrap( maskFilteredBadResidual );
//}
// Get the list to be returned to R.
rl = Rcpp::wrap( map ) ;
}
}
fclose(fp);
}
}
delete beadFindFile;
} catch(std::exception& ex) {
forward_exception_to_r(ex);
} catch(...) {
::Rf_error("c++ exception (unknown reason)");
}
if(exceptionMesg != NULL)
Rf_error(exceptionMesg);
return rl;
}
