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#include "baselineselector.h"
#include "../util/logger.h"
#include "../util/plot.h"
#include "../quality/defaultstatistics.h"
#include "thresholdtools.h"
#include <algorithm>
#include <map>
#include <memory>
namespace algorithms {
void BaselineSelector::Add(Mask2DCPtr mask,
TimeFrequencyMetaDataCPtr metaData) {
BaselineSelector::SingleBaselineInfo baseline;
baseline.length = metaData->Baseline().Distance();
if (baseline.length > 0) {
baseline.antenna1 = metaData->Antenna1().id;
baseline.antenna2 = metaData->Antenna2().id;
baseline.antenna1Name = metaData->Antenna1().name;
baseline.antenna2Name = metaData->Antenna2().name;
baseline.band = metaData->Band().windowIndex;
baseline.sequenceId = metaData->SequenceId();
baseline.rfiCount = mask->GetCount<true>();
baseline.totalCount = mask->Width() * mask->Height();
_baselines.push_back(baseline);
}
}
void BaselineSelector::Add(DefaultStatistics& baselineStat,
AntennaInfo& antenna1, AntennaInfo& antenna2) {
if (antenna1.id != antenna2.id) {
BaselineSelector::SingleBaselineInfo baseline;
baseline.length = Baseline(antenna1, antenna2).Distance();
baseline.antenna1 = antenna1.id;
baseline.antenna2 = antenna2.id;
baseline.antenna1Name = antenna1.name;
baseline.antenna2Name = antenna2.name;
baseline.band = 0;
baseline.sequenceId = 0;
const DefaultStatistics singleStat = baselineStat.ToSinglePolarization();
baseline.rfiCount = singleStat.rfiCount[0];
baseline.totalCount = singleStat.count[0] + singleStat.rfiCount[0];
_baselines.push_back(baseline);
}
}
void BaselineSelector::Search(
std::vector<BaselineSelector::SingleBaselineInfo>& markedBaselines) {
// Perform a first quick threshold to remove baselines which deviate a lot
// (e.g. 100% flagged baselines). Sometimes, there are a lot of them, causing
// instability if this would not be done.
for (int i = _baselines.size() - 1; i >= 0; --i) {
const double currentValue =
(double)_baselines[i].rfiCount / (double)_baselines[i].totalCount;
if (currentValue > _absThreshold ||
(_baselines[i].rfiCount == 0 && _baselines[i].totalCount >= 2500)) {
if (_useLog)
Logger::Info << "Baseline " << _baselines[i].antenna1Name << " x "
<< _baselines[i].antenna2Name
<< " looks bad: " << round(currentValue * 10000.0) / 100.0
<< "% rfi (zero or above " << (_absThreshold * 100.0)
<< "% abs threshold)\n";
_baselines[i].marked = true;
markedBaselines.push_back(_baselines[i]);
_baselines.erase(_baselines.begin() + i);
}
}
bool foundMoreBaselines;
do {
std::sort(_baselines.begin(), _baselines.end());
std::unique_ptr<Plot> plot;
if (_makePlot) {
plot.reset(new Plot("baselineSelection.pdf"));
plot->SetXAxisText("Baseline length (meters)");
plot->SetYAxisText("Percentage RFI");
}
const size_t unmarkedBaselineCount = _baselines.size();
std::vector<double> values(unmarkedBaselineCount);
// Calculate the smoothed values
if (_makePlot) plot->StartLine("Smoothed values");
size_t valueIndex = 0;
for (BaselineVector::const_iterator i = _baselines.begin();
i != _baselines.end(); ++i) {
const double smoothedVal = smoothedValue(*i);
if (_makePlot) plot->PushDataPoint(i->length, 100.0 * smoothedVal);
values[valueIndex] =
smoothedVal - (double)i->rfiCount / (double)i->totalCount;
++valueIndex;
}
// Calculate the std dev
double mean, stddev;
std::vector<double> valuesCopy;
for (size_t i = 0; i < unmarkedBaselineCount; ++i)
valuesCopy.push_back(values[i]);
ThresholdTools::TrimmedMeanAndStdDev(valuesCopy, mean, stddev);
if (_makePlot && _useLog)
Logger::Debug
<< "Estimated std dev for thresholding, in percentage of RFI: "
<< round(10000.0 * stddev) / 100.0 << "%\n";
// unselect already marked baselines
for (int i = markedBaselines.size() - 1; i >= 0; --i) {
const BaselineSelector::SingleBaselineInfo baseline = markedBaselines[i];
const double currentValue =
(double)baseline.rfiCount / (double)baseline.totalCount;
const double baselineValue =
smoothedValue(baseline.length) - currentValue;
if (baselineValue >= mean - _threshold * stddev &&
baselineValue <= mean + _threshold * stddev &&
currentValue < _absThreshold &&
(baseline.rfiCount != 0 || baseline.totalCount < 2500)) {
markedBaselines.erase(markedBaselines.begin() + i);
_baselines.push_back(baseline);
if (_useLog)
Logger::Info << "Baseline " << baseline.antenna1Name << " x "
<< baseline.antenna2Name
<< " is now within baseline curve\n";
}
}
// (re)select baselines to be thrown away
foundMoreBaselines = false;
if (_makePlot) plot->StartScatter("Threshold");
double maxPlotY = 0.0;
for (int i = unmarkedBaselineCount - 1; i >= 0; --i) {
const double currentValue =
(double)_baselines[i].rfiCount / (double)_baselines[i].totalCount;
if (_makePlot) {
const double plotY =
100.0 * (values[i] + currentValue + mean + _threshold * stddev);
plot->PushDataPoint(_baselines[i].length, plotY);
plot->PushDataPoint(
_baselines[i].length,
100.0 * (values[i] + currentValue + mean - _threshold * stddev));
if (plotY > maxPlotY) maxPlotY = plotY;
}
if (values[i] < mean - _threshold * stddev ||
values[i] > mean + _threshold * stddev ||
currentValue > _absThreshold ||
(_baselines[i].rfiCount == 0 && _baselines[i].totalCount >= 2500)) {
if (_useLog)
Logger::Info << "Baseline " << _baselines[i].antenna1Name << " x "
<< _baselines[i].antenna2Name << " looks bad: "
<< round(currentValue * 10000.0) / 100.0 << "% rfi, "
<< round(10.0 * fabs((values[i] - mean) / stddev)) / 10.0
<< "*sigma away from est baseline curve\n";
if (!_baselines[i].marked) {
foundMoreBaselines = true;
_baselines[i].marked = true;
}
markedBaselines.push_back(_baselines[i]);
_baselines.erase(_baselines.begin() + i);
}
}
if (_makePlot) {
plot->SetYRange(0.0, maxPlotY * 1.5);
plot->StartScatter("Accepted baselines");
for (BaselineVector::const_iterator i = _baselines.begin();
i != _baselines.end(); ++i) {
plot->PushDataPoint(
i->length, 100.0 * (double)i->rfiCount / (double)i->totalCount);
}
plot->StartScatter("Rejected baselines");
for (BaselineVector::const_iterator i = markedBaselines.begin();
i != markedBaselines.end(); ++i) {
plot->PushDataPoint(
i->length, 100.0 * (double)i->rfiCount / (double)i->totalCount);
}
plot->Close();
}
} while (foundMoreBaselines);
}
void BaselineSelector::ImplyStations(
const std::vector<BaselineSelector::SingleBaselineInfo>& markedBaselines,
double maxRatio, std::set<unsigned>& badStations) const {
std::map<unsigned, unsigned> stations;
for (std::vector<BaselineSelector::SingleBaselineInfo>::const_iterator i =
markedBaselines.begin();
i != markedBaselines.end(); ++i) {
stations[i->antenna1]++;
stations[i->antenna2]++;
}
for (std::map<unsigned, unsigned>::const_iterator i = stations.begin();
i != stations.end(); ++i) {
const double ratio = (double)i->second / (double)stations.size();
if (ratio > maxRatio) {
badStations.insert(i->first);
}
}
}
double BaselineSelector::smoothedValue(double length) const {
const double logLength = log(length);
double sum = 0.0;
double weight = 0.0;
for (BaselineSelector::BaselineVector::const_iterator i = _baselines.begin();
i != _baselines.end(); ++i) {
const double otherLogLength = log(i->length);
const double otherValue = (double)i->rfiCount / (double)i->totalCount;
const double x = otherLogLength - logLength;
const double curWeight =
exp(-x * x / (2.0 * _smoothingSigma * _smoothingSigma));
sum += curWeight * otherValue;
weight += curWeight;
}
return sum / weight;
}
} // namespace algorithms
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