/**
* Test DataFilters
*/
void test_datafilters()
{
std::vector<std::string> datas;
datas.push_back("1");
datas.push_back("2");
datas.push_back("3");
DataVector datav;
datav.push_back(DataPoint(1,true));
datav.push_back(DataPoint(2,true));
datav.push_back(DataPoint(3,true));
DataFilters filters;
ASSERT(filters.isFiltered(datas), "DataFilters::isFiltered failed on string vector with no filter");
ASSERT(filters.isFiltered(datav), "DataFilters::isFiltered failed on data vector with no filter");
filters.addNumericFilter(0,1,1,true);
ASSERT(filters.isFiltered(datav), "DataFilters::isFiltered failed on data vector with numeric accepting filter on 0");
filters.addNumericFilter(1,4,4,false);
ASSERT(filters.isFiltered(datav), "DataFilters::isFiltered failed on data vector with numeric rejection filter on 1");
filters.addStringFilter(0,"1",true,true,true);
ASSERT(filters.isFiltered(datas), "DataFilters::isFiltered failed on data vector with string accepting filter on 0");
filters.addStringFilter(1,"4",true,true,false);
ASSERT(filters.isFiltered(datas), "DataFilters::isFiltered failed on data vector with string rejection filter on 1");
}
/**
* Test DataVector
*/
void test_datavector()
{
DataVector src;
src.push_back(DataPoint(1,true));
src.push_back(DataPoint(2,true));
src.push_back(DataPoint(3,true));
std::vector<bool> mask(3,true);
DataVector dst;
dst.copy(src,mask);
ASSERT_EQUAL(dst.at(0).value, 1, "DataVector::copy value failed on enabled data point at 0");
ASSERT(dst.at(0).active, "DataVector::copy active failed on enabled data point at 0");
ASSERT_EQUAL(dst.at(1).value, 2, "DataVector::copy value failed on enabled data point at 1");
ASSERT(dst.at(1).active, "DataVector::copy active failed on enabled data point at 1");
ASSERT_EQUAL(dst.at(2).value, 3, "DataVector::copy value failed on enabled data point at 2");
ASSERT(dst.at(2).active, "DataVector::copy active failed on enabled data point at 2");
src.deactivate();
dst.clear();
dst.copy(src,mask);
ASSERT_EXCEPTION(dst.at(0), "DataVector::copy failed on disabled data point at 0");
ASSERT_EXCEPTION(dst.at(1), "DataVector::copy failed on disabled data point at 1");
ASSERT_EXCEPTION(dst.at(2), "DataVector::copy failed on disabled data point at 2");
}
SimulResult Model::simulate(double sim_time) {
int nresults = int(ceil(sim_time / result_step));
std::vector<DataPoint> result;
result.reserve(nresults);
result.push_back(this->initial_cond);
DataPoint prev = this->initial_cond;
DataPoint curr = DataPoint();
while (prev.time < sim_time) {
double s_to_i = this->infect_prob * prev.S * prev.I;
double i_to_r = this->recovery_rate * prev.I;
curr.S = prev.S - s_to_i * sim_step;
curr.I = prev.I + (s_to_i - i_to_r) * sim_step;
curr.R = prev.R + i_to_r * sim_step;
curr.time = prev.time + sim_step;
curr.S = std::max(curr.S, 0.0);
curr.I = std::max(curr.I, 0.0);
if (int(curr.time / result_step) > int(prev.time / result_step)) {
result.push_back(curr);
}
prev = curr;
}
return SimulResult(std::move(result));
}
CrossSection calculateRelativeDiff(CrossSection a, CrossSection b)
{
CrossSection relative;
DataSet aData = a.getDataSet();
DataSet bData = b.getDataSet();
if(aData.getNumberOfPoints()!=bData.getNumberOfPoints())
{
cerr << "Error: can't calculate relative cross section from "
<< "data sets of different sizes. Returning empty cross section."
<< endl;
return relative;
}
DataSet relativeDataSet;
// for each point, calculate the relative cross section, including error
for(int i=0; i<aData.getNumberOfPoints(); i++)
{
DataPoint aPoint = aData.getPoint(i);
DataPoint bPoint = bData.getPoint(i);
double aXValue = aPoint.getXValue();
double bXValue = bPoint.getXValue();
if(aXValue != bXValue)
{
cerr << "Error: can't calculate relative cross section from "
<< "data points with different x values. Returning cross section."
<< endl;
return relative;
}
double aYValue = aPoint.getYValue();
double bYValue = bPoint.getYValue();
double yValue = (aYValue-bYValue)/(aYValue+bYValue);
// calculate cross section error
double aError = getPartialError(aPoint, bPoint, a.getArealDensity());
double bError = getPartialError(bPoint, aPoint, b.getArealDensity());
double totalError = pow(pow(aError,2)+pow(bError,2),0.5);
relativeDataSet.addPoint(
DataPoint(aXValue, aPoint.getXError(), 100*yValue, 100*totalError, /* convert to % */
aPoint.getBlankMonitorCounts()+bPoint.getBlankMonitorCounts(),
aPoint.getTargetMonitorCounts()+bPoint.getTargetMonitorCounts(),
aPoint.getBlankDetCounts()+bPoint.getBlankDetCounts(),
aPoint.getTargetDetCounts()+bPoint.getTargetDetCounts()));
}
relative.addDataSet(relativeDataSet);
return relative;
}
vector<DataPoint> getDataPoints(path p, size_t label, string catname){
vector<DataPoint> dps;
directory_iterator end_itr;
for ( directory_iterator sitr(p); sitr != end_itr; ++sitr){
if(is_image(sitr->path().extension().string())){
string filename = (string) sitr->path().filename().c_str();
string fileurl = (string) sitr->path().string().c_str();
dps.push_back(DataPoint(label, filename, fileurl, catname));
}
}
return dps;
}
DataSet::DataSet(double min, double max, double step)
{
m_numPts = 0;
double x = min;
while(x < max)
{
m_data.push_back(DataPoint(x, sin(x) / x));
x += step;
m_numPts++;
}
}
void DataSet::compute(double min, double max, double step, computeFunc f)
{
m_data.clear();
m_numPts = 0;
double x = min;
while(x < max)
{
m_data.push_back(DataPoint(x, f(x)));
x += step;
++m_numPts;
}
}
/**
* Test MultivariateTracker
*/
void test_multivariatetracker()
{
DataVector data1, data2, data3;
data1.push_back(DataPoint(1,true));
data1.push_back(DataPoint(3,true));
data2.push_back(DataPoint(2,true));
data2.push_back(DataPoint(2,true));
data3.push_back(DataPoint(3,true));
data3.push_back(DataPoint(1,true));
StatisticsTrackerOptions options;
options.doCov = options.doMax = options.doMean = options.doMin = options.doVar = true;
MultivariateTracker tracker(2, options);
tracker.update(data1);
tracker.update(data2);
tracker.update(data3);
double cov = 2.0/3.0;
ASSERT_EQUAL(tracker.getCovariance(0,0), cov, "StatisticsTracker::getCovariance failed on (0,0)");
ASSERT_EQUAL(tracker.getCovariance(0,1), -cov, "StatisticsTracker::getCovariance failed on (0,1)");
ASSERT_EQUAL(tracker.getCovariance(1,0), -cov, "StatisticsTracker::getCovariance failed on (1,0)");
ASSERT_EQUAL(tracker.getCovariance(1,1), cov, "StatisticsTracker::getCovariance failed on (1,1)");
}
void Reporter::AddLocation(location::GpsInfo const & info)
{
lock_guard<mutex> lg(m_mutex);
if (info.m_horizontalAccuracy > kRequiredHorizontalAccuracy)
return;
if (info.m_timestamp < m_lastGpsTime + kMinDelaySeconds)
return;
m_lastGpsTime = info.m_timestamp;
m_input.push_back(DataPoint(info.m_timestamp, ms::LatLon(info.m_latitude, info.m_longitude)));
}
//you will need to change
Communication::Communication(string comPort): q(),file("C:\\Users\\Megan Gardner\\GitHub\\490\\logOutput.log",ios::out){
mutex = false;
file<<"begin"<<endl;
io = new io_service();
port = new serial_port(*io,comPort);
//port->set_option(serial_port_base::baud_rate(9600));
port->set_option(serial_port_base::baud_rate(57600)); //to match baud rate of acc/gyro
data = new vector<DataPoint>();
data->push_back(DataPoint(QPoint(99,65),0)); //remove these when you have actual data
data->push_back(DataPoint(QPoint(115,117),0));
data->push_back(DataPoint(QPoint(35,158),0)); //remove these when you have actual data
data->push_back(DataPoint(QPoint(93,214),0));
data->push_back(DataPoint(QPoint(47,244),0)); //remove these when you have actual data
data->push_back(DataPoint(QPoint(85,324),0));
if(port->is_open())
cout<<"Opened "<<comPort<<endl;
}
void DataTable::addSample(std::vector<double> x, double y)
{
addSample(DataPoint(x, y));
}
void DataTable::addSample(double x, double y)
{
addSample(DataPoint(x, y));
}
//Default constructor
Headings::Headings()
{
DataPoint();
}
void BayesUnfoldingExample641()
{
#ifdef __CINT__ // Avoid CINT badness
Printf("Please compile this script (root BayesUnfoldingExample641.C+) "
"or use ROOT 6.");
gSystem->Exit(0);
#endif
if (!gROOT->IsBatch())
{
Printf("Several canvases coming...adding -b flag.");
gROOT->SetBatch();
}
gStyle->SetOptStat(0);
gStyle->SetPaintTextFormat(".2f");
if (gSystem->Getenv("TMPDIR"))
gSystem->SetBuildDir(gSystem->Getenv("TMPDIR"));
TRandom3 ran;
TStopwatch watch; // Watch starts here. A call to Start() would reset it.
TObjArray *cList = new TObjArray(); // List of drawn canvases --> PDF file
// Set up the problem
double bins[Nt+1] = {0};
for (int j=0; j<=Nt; j++)
bins[j] = 500*TMath::Exp(0.15*j);
TestProblem testprob = AtlasDiJetMass(Nt, Nr, bins, bins,
apar, bpar, nevts, evtWeight);
TH2D *hM = testprob.Response;
TH1D *hT = testprob.xTruth;
TH1D *hTmc = testprob.xTruthEst;
TH1D *hMt = testprob.xIni;
TH1D *hD = testprob.bNoisy;
TH1D *heff = testprob.eff;
SetHistProps(hT,kRed+2,kNone,kRed+2);
SetHistProps(hTmc,kRed,kNone,kRed);
SetHistProps(hD,kBlack,kNone,kBlack,kFullCircle,1.5);
TMatrixD M = MatrixUtils::Hist2Matrix(hM);
TVectorD T = MatrixUtils::Hist2Vec(hT); // \hat{T}
TVectorD Tmc = MatrixUtils::Hist2Vec(hTmc); // \tilde{T}
TVectorD D = MatrixUtils::Hist2Vec(hD);
TVectorD eff = MatrixUtils::Hist2Vec(heff);
TVectorD Pt = MatrixUtils::ElemDiv(MatrixUtils::Hist2Vec(hMt), eff); // P(t)
TMatrixD Prt = MatrixUtils::DivRowsByVector(M, Pt); // P(r|t)
// Compute initial sampling volume and do MCMC sampling
TGraphAsymmErrors *box = HyperBox(hTmc);
SetGraphProps(box, kGreen+2, kNone, kSpring, kFullSquare, 1.0);
// Likelihood functor
LogPoissonLikeFn llfunc(Prt, D);
// Curvature regularization.
// Note that this is not directly penalizing curvature of the solution.
// Instead it smooths the solution divided by the trial spectrum.
std::vector<double> regpars;
regpars.push_back(alpha); // Regularization strength
for (int i=0; i<box->GetN(); i++)
regpars.push_back(box->GetY()[i]);
CurvatureRegFn regfunc(regpars);
TTree *tmcmc = SampleMH(nMcmcSamples, 1e4, 0.01, box, llfunc, regfunc);
// Create marginal prob. distributions from MCMC
std::cout << Form("Marginalizing parameters from Markov chain...")
<< std::flush;
TH1D *hMCMC[Nt];
for (int t=0; t<Nt; t++)
{
double tlo = box->GetY()[t] - box->GetEYlow()[t];
double thi = box->GetY()[t] + box->GetEYhigh()[t];
hMCMC[t] = new TH1D(Form("hMCMC%d",t),"",nMcmcBins, tlo, thi);
hMCMC[t]->SetTitle(Form("MCMC - point %d;"
"entries;"
"Marginal posterior probability",t));
// Marginalize with unit weight when using MCMC, weight by
// likelihood if sampling was uniform.
tmcmc->Draw(Form("T%d >> hMCMC%d",t,t), "", "goff");
hMCMC[t]->Scale(1./hMCMC[t]->Integral(1, nMcmcBins));
SetHistProps(hMCMC[t], kBlack, kYellow, kBlack, kFullCircle, 1.0);
hMCMC[t]->GetYaxis()->SetTitleOffset(1.5);
}
Printf("Done marginalizing MCMC.");
// Now compute reduced sampling volume, and do uniform sampling
TGraphAsymmErrors *rbox = ReducedSamplingVolume(hMCMC, box);
SetGraphProps(rbox, kBlack, kNone, kNone, kFullSquare, 1.0);
TH1D *hFlat[Nt];
if (doUniformSampling)
{
TTree *tflat = SampleUniform(nFlatSamples, D, Prt, rbox);
std::cout << Form("Marginalizing parameters from uniform volume...")
<< std::flush;
for (int t=0; t<Nt; t++)
{
double tlo = rbox->GetY()[t] - rbox->GetEYlow()[t];
double thi = rbox->GetY()[t] + rbox->GetEYhigh()[t];
hFlat[t] = new TH1D(Form("hFlat%d",t),"",nFlatBins, tlo, thi);
hFlat[t]->SetTitle(Form("Uniform sampling - point %d;"
"dijet mass (GeV/c^{2});"
"Marginal posterior probability",t));
tflat->Draw(Form("T%d >> hFlat%d",t,t), "L", "goff");
hFlat[t]->Scale(1./hFlat[t]->Integral(1,nFlatBins));
SetHistProps(hFlat[t], kBlack, kOrange, kBlack, kFullCircle, 1.0);
}
Printf("Done marginalizing uniform volume.");
}
// Unfolded spectrum from MCMC
TGraphErrors *unf1 = new TGraphErrors();
SetGraphProps(unf1, kBlue, kNone, kBlue, kOpenSquare, 1.5);
unf1->SetLineWidth(2);
for (int t=0; t<Nt; t++)
{
MaxDensityInterval mdi = GetMDI(hMCMC[t], 0.68);
unf1->SetPoint(t, hD->GetBinCenter(t+1), mdi.u);
unf1->SetPointError(t, 0.48*hD->GetBinWidth(t+1), mdi.du);
}
// Unfolded spectrum from uniform sampling after volume reduction
TGraphErrors *unf2 = 0;
if (doUniformSampling)
{
unf2 = new TGraphErrors();
SetGraphProps(unf2, kRed, kNone, kRed, kOpenSquare, 1.5);
unf2->SetLineWidth(2);
for (int t=0; t<Nt; t++)
{
MaxDensityInterval mdi = GetMDI(hFlat[t], 0.68);
unf2->SetPoint(t, hD->GetBinCenter(t+1), mdi.u);
unf2->SetPointError(t, 0.47*hD->GetBinWidth(t+1), mdi.du);
}
}
Printf("Drawing results...");
DrawObject(hM, "colz", "matrix", cList, 550, 500);
gPad->SetLogx(); gPad->SetLogy(); gPad->SetLogz();
gPad->SetRightMargin(0.15);
DrawObject(heff, "", "efficiency", cList);
// Draw marginal dists. from MCMC
for (int t=0; t<Nt; t++)
{
DrawObject(hMCMC[t], "", Form("post_%d", t), cList);
gPad->SetLeftMargin(0.15);
if (doUniformSampling)
{
hFlat[t]->Scale(1./hFlat[t]->Integral(1, nFlatBins,"width"));
hFlat[t]->Draw("same");
}
double ymin = hMCMC[t]->GetMinimum();
double ymax = hMCMC[t]->GetMaximum();
double yDraw = 0.25*(ymax-ymin);
DataPoint(hD, hMCMC[t], t, 0.75*yDraw)->Draw("ep same");
TruePoint(hT, hMCMC[t], t, yDraw)->Draw("p same");
MD68Point(hMCMC[t], yDraw)->Draw("ep same");
}
// Result!
hT->GetYaxis()->SetRangeUser(0.002, 101*nevts*evtWeight);
DrawObject(hT, "ep", "result", cList);
gPad->SetLogy();
box->Draw("e5 same");
if (doUniformSampling || drawReducedVolume)
rbox->Draw("e5 same");
hT->Draw("same");
hD->Draw("ep same");
unf1->Draw("ep same");
if (unf2)
unf2->Draw("ep same");
if (printPDFs)
{
PrintPDFs(cList, "pdfs"); // Print individuals into ./pdfs dir
PrintPDF(cList, "pdfs/mcmc_unfold_example"); // Multipage PDF
}
Printf("All done.");
watch.Stop();
watch.Print();
return;
}
DataPoint DataPoint::clone()
{
return DataPoint(*this);
}
void DataTable::addSample(DenseVector x, double y)
{
addSample(DataPoint(x, y));
}
void Profile::loadDefaultProfile() {
QString defaultName = "default.json";
// Check if default profile exists on disk
QFile file(defaultName);
if(file.exists()) {
loadProfile(defaultName, false);
return;
}
// Default profile does not exist, we need to create one
profileName = "Default lead free";
// dataPoints.append(DataPoint(0,25)); // Starting temp
// dataPoints.append(DataPoint(90,150)); // Pre Heat
// dataPoints.append(DataPoint(180,217)); // End of soak
// dataPoints.append(DataPoint(225,245)); // Peak temp
// dataPoints.append(DataPoint(270,217)); // End of reflow zone
// dataPoints.append(DataPoint(337.5,25)); // End of profile
dataPoints.append(DataPoint(0,25)); // Starting temp
dataPoints.append(DataPoint(90,150)); // Pre Heat
dataPoints.append(DataPoint(112.5,200)); // End of soak
dataPoints.append(DataPoint(121.4,217)); // Ramp to 217
dataPoints.append(DataPoint(159.4,255)); // Ramp to 255
dataPoints.append(DataPoint(166.6,260)); // Peak
dataPoints.append(DataPoint(178.6,260)); // End of peak
dataPoints.append(DataPoint(185.8,255)); // Ramp down to 255
dataPoints.append(DataPoint(205,217)); // End of reflow zone
dataPoints.append(DataPoint(234.1,150)); // End of profile
dataPoints.append(DataPoint(290,25)); // Cool down
// Save the new default profiel
saveProfile(defaultName);
}
DataPoint::DataPoint(int x, int y, qint16 v){
DataPoint(QPoint(x,y),v);
}