Blendedness.cc

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// -*- LSST-C++ -*-
/*
 * This file is part of meas_base.
 *
 * Developed for the LSST Data Management System.
 * This product includes software developed by the LSST Project
 * (https://www.lsst.org).
 * See the COPYRIGHT file at the top-level directory of this distribution
 * for details of code ownership.
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <https://www.gnu.org/licenses/>.
 */
 
#include <cmath>
 
#include "boost/math/constants/constants.hpp"
 
#include "lsst/meas/base/Blendedness.h"
#include "lsst/afw/detection/HeavyFootprint.h"
#include "lsst/meas/base/exceptions.h"
#include "lsst/afw/geom/ellipses/Ellipse.h"
#include "lsst/afw/geom/ellipses/PixelRegion.h"
#include "lsst/afw/geom/ellipses/GridTransform.h"
 
namespace lsst {
namespace meas {
namespace base {
namespace {
FlagDefinitionList flagDefinitions;
}  // namespace
 
FlagDefinition const BlendednessAlgorithm::FAILURE = flagDefinitions.addFailureFlag();
FlagDefinition const BlendednessAlgorithm::NO_CENTROID =
        flagDefinitions.add("flag_noCentroid", "Object has no centroid");
FlagDefinition const BlendednessAlgorithm::NO_SHAPE =
        flagDefinitions.add("flag_noShape", "Object has no shape");
 
FlagDefinitionList const& BlendednessAlgorithm::getFlagDefinitions() { return flagDefinitions; }
 
namespace {
 
double computeOldBlendedness(std::shared_ptr<afw::detection::Footprint const> childFootprint,
                             afw::image::Image<float> const& parentImage) {
    if (!childFootprint) {
        throw LSST_EXCEPT(pex::exceptions::LogicError, "blendedness_old requires a Footprint.");
    }
 
    std::shared_ptr<afw::detection::HeavyFootprint<float> const>
    childHeavy = std::dynamic_pointer_cast<afw::detection::HeavyFootprint<float> const>(childFootprint);
 
    if (!childHeavy) {
        return 0.0;  // if it's not a HeavyFootprint, it's not blended.
    }
 
    if (!parentImage.getBBox(afw::image::PARENT).contains(childHeavy->getBBox())) {
        throw LSST_EXCEPT(pex::exceptions::LogicError, "Child footprint extends beyond image.");
    }
 
    // Iterate over all the spans in the child HeavyFootprint,
    // along with iterators for the child pixels (from the HeavyFootprint)
    // and parent pixels (from the Exposure).
    typedef afw::image::Image<float>::const_x_iterator ParentPixIter;
    typedef ndarray::Array<float const, 1, 1>::Iterator ChildPixIter;
    auto spanIter = childHeavy->getSpans()->begin();
    auto const spanEnd = childHeavy->getSpans()->end();
    ChildPixIter childPixIter = childHeavy->getImageArray().begin();
    double cp = 0.0;  // child.dot(parent)
    double cc = 0.0;  // child.dot(child)
    while (spanIter != spanEnd) {
        afw::geom::Span const& span = *spanIter;
        ParentPixIter parentPixIter =
                parentImage.x_at(span.getBeginX() - parentImage.getX0(), span.getY() - parentImage.getY0());
        int const width = span.getWidth();
        // Iterate over the pixels within the span, updating the dot products.
        for (int x = 0; x < width; ++parentPixIter, ++childPixIter, ++x) {
            cp += (*childPixIter) * ((*parentPixIter) - (*childPixIter));
            cc += (*childPixIter) * (*childPixIter);
        }
        ++spanIter;
    }
    if (cc > 0.0) {
        return cp / cc;
    }
    return 0.0;
}
 
class FluxAccumulator {
public:
    FluxAccumulator() : _w(0.0), _ww(0.0), _wd(0.0) {}
 
    void operator()(double, double, float weight, float data) {
        _w += weight;
        _ww += weight * weight;
        _wd += weight * data;
    }
 
    double getFlux() const { return _w * _wd / _ww; }
 
protected:
    double _w;
    double _ww;
    double _wd;
};
 
class ShapeAccumulator : public FluxAccumulator {
public:
    ShapeAccumulator() : FluxAccumulator(), _wdxx(0.0), _wdyy(0.0), _wdxy(0.0) {}
 
    void operator()(double x, double y, float weight, float data) {
        FluxAccumulator::operator()(x, y, weight, data);
        _wdxx += x * x * weight * data;
        _wdyy += y * y * weight * data;
        _wdxy += x * y * weight * data;
    }
 
    ShapeResult getShape() const {
        // Factor of 2 corrects for bias from weight function (correct is exact for an object
        // with a Gaussian profile.)
        ShapeResult result;
        result.xx = 2.0 * _wdxx / _wd;
        result.yy = 2.0 * _wdyy / _wd;
        result.xy = 2.0 * _wdxy / _wd;
        return result;
    }
 
private:
    double _wdxx;
    double _wdyy;
    double _wdxy;
};
 
template <typename Accumulator>
void computeMoments(afw::image::MaskedImage<float> const& image, geom::Point2D const& centroid,
                    afw::geom::ellipses::Quadrupole const& shape, double nSigmaWeightMax,
                    Accumulator& accumulatorRaw, Accumulator& accumulatorAbs) {
    geom::Box2I bbox = image.getBBox(afw::image::PARENT);
 
    afw::geom::ellipses::Ellipse ellipse(shape, centroid);
    ellipse.getCore().scale(nSigmaWeightMax);
 
    // To evaluate an elliptically-symmetric function, we transform points
    // by the following transform, then evaluate a circularly-symmetric function
    // at the transformed positions.
    geom::LinearTransform transform = shape.getGridTransform();
 
    typedef afw::geom::ellipses::PixelRegion::Iterator SpanIter;         // yields Spans
    typedef afw::geom::Span::Iterator PointIter;                         // yields Point2I positions
    typedef afw::image::MaskedImage<float>::const_x_iterator PixelIter;  // yields pixel values
 
    afw::geom::ellipses::PixelRegion region(ellipse);
    bool isContained = bbox.contains(region.getBBox());
    SpanIter const spanEnd = region.end();
    for (SpanIter spanIter = region.begin(); spanIter != spanEnd; ++spanIter) {
        afw::geom::Span span = *spanIter;
        if (!isContained) {
            if (span.getY() < bbox.getMinY() || span.getY() > bbox.getMaxY()) {
                continue;
            }
            span = afw::geom::Span(span.getY(), std::max(span.getMinX(), bbox.getMinX()),
                                   std::min(span.getMaxX(), bbox.getMaxX()));
            if (span.getMinX() > span.getMaxX()) {
                continue;
            }
        }
        PixelIter pixelIter = image.x_at(span.getBeginX() - image.getX0(), span.getY() - image.getY0());
        PointIter const pointEnd = span.end();
        for (PointIter pointIter = span.begin(); pointIter != pointEnd; ++pointIter, ++pixelIter) {
            geom::Extent2D d = geom::Point2D(*pointIter) - centroid;
            geom::Extent2D td = transform(d);
            // use single precision for faster exp, erf
            float weight = std::exp(static_cast<float>(-0.5 * td.computeSquaredNorm()));
            float data = pixelIter.image();
            accumulatorRaw(d.getX(), d.getY(), weight, data);
            float variance = pixelIter.variance();
            float mu = BlendednessAlgorithm::computeAbsExpectation(data, variance);
            float bias = BlendednessAlgorithm::computeAbsBias(mu, variance);
            accumulatorAbs(d.getX(), d.getY(), weight, std::abs(data) - bias);
        }
    }
}
 
}  // namespace
 
BlendednessAlgorithm::BlendednessAlgorithm(Control const& ctrl, std::string const& name,
                                           afw::table::Schema& schema)
        : _ctrl(ctrl) {
    if (_ctrl.doOld) {
        _old = schema.addField<double>(
                schema.join(name, "old"),
                "Blendedness from dot products: (child.dot(parent)/child.dot(child) - 1)");
    }
    if (_ctrl.doFlux) {
        _raw = schema.addField<double>(
                schema.join(name, "raw"),
                "Measure of how much the flux is affected by neighbors: "
                "(1 - child_instFlux/parent_instFlux).  Operates on the \"raw\" pixel values.");
        _instFluxChildRaw = schema.addField<double>(
                schema.join(name, "raw_child_instFlux"),
                "Instrumental flux of the child, measured with a Gaussian weight matched to the child.  "
                "Operates on the \"raw\" pixel values.", "count");
        _instFluxParentRaw = schema.addField<double>(
                schema.join(name, "raw_parent_instFlux"),
                "Instrumental flux of the parent, measured with a Gaussian weight matched to the child.  "
                "Operates on the \"raw\" pixel values.", "count");
        _abs = schema.addField<double>(
                schema.join(name, "abs"),
                "Measure of how much the flux is affected by neighbors: "
                "(1 - child_instFlux/parent_instFlux).  "
                "Operates on the absolute value of the pixels to try to obtain a \"de-noised\" value.  "
                "See section 4.9.11 of Bosch et al. 2018, PASJ, 70, S5 for details.");
        _instFluxChildAbs = schema.addField<double>(
                schema.join(name, "abs_child_instFlux"),
                "Instrumental flux of the child, measured with a Gaussian weight matched to the child.  "
                "Operates on the absolute value of the pixels to try to obtain a \"de-noised\" value.  "
                "See section 4.9.11 of Bosch et al. 2018, PASJ, 70, S5 for details.", "count");
        _instFluxParentAbs = schema.addField<double>(
                schema.join(name, "abs_parent_instFlux"),
                "Instrumental flux of the parent, measured with a Gaussian weight matched to the child.  "
                "Operates on the absolute value of the pixels to try to obtain a \"de-noised\" value.  "
                "See section 4.9.11 of Bosch et al. 2018, PASJ, 70, S5 for details.", "count");
    }
    if (_ctrl.doShape) {
        _shapeChildRaw = ShapeResultKey::addFields(
                schema, schema.join(name, "raw_child"),
                "Shape of the child, measured with a Gaussian weight matched to the child.  "
                "Operates on the \"raw\" pixel values.", NO_UNCERTAINTY);
        _shapeParentRaw = ShapeResultKey::addFields(
                schema, schema.join(name, "raw_parent"),
                "Shape of the parent, measured with a Gaussian weight matched to the child.  "
                "Operates on the \"raw\" pixel values.", NO_UNCERTAINTY);
        _shapeChildAbs = ShapeResultKey::addFields(
                schema, schema.join(name, "abs_child"),
                "Shape of the child, measured with a Gaussian weight matched to the child.  "
                "Operates on the absolute value of the pixels to try to obtain a \"de-noised\" value.  "
                "See section 4.9.11 of Bosch et al. 2018, PASJ, 70, S5 for details.",
                NO_UNCERTAINTY);
        _shapeParentAbs = ShapeResultKey::addFields(
                schema, schema.join(name, "abs_parent"),
                "Shape of the parent, measured with a Gaussian weight matched to the child.  "
                "Operates on the absolute value of the pixels to try to obtain a \"de-noised\" value.  "
                "See section 4.9.11 of Bosch et al. 2018, PASJ, 70, S5 for details.",
                NO_UNCERTAINTY);
    }
    if (_ctrl.doShape || _ctrl.doFlux) {
        _flagHandler = FlagHandler::addFields(schema, name, getFlagDefinitions());
    }
}
 
float BlendednessAlgorithm::computeAbsExpectation(float data, float variance) {
    float normalization = 0.5f * std::erfc(-data / std::sqrt(2.0f * variance));
    if (!(normalization > 0)) {
        // avoid division by zero; we know the limit at data << -sigma -> 0.
        return 0.0;
    }
    return data + (std::sqrt(0.5f * variance / boost::math::constants::pi<float>()) *
                   std::exp(-0.5f * (data * data) / variance) / normalization);
}
 
float BlendednessAlgorithm::computeAbsBias(float mu, float variance) {
    return (std::sqrt(2.0f * variance / boost::math::constants::pi<float>()) *
            std::exp(-0.5f * (mu * mu) / variance)) -
           mu * std::erfc(mu / std::sqrt(2.0f * variance));
}
 
void BlendednessAlgorithm::_measureMoments(afw::image::MaskedImage<float> const& image,
                                           afw::table::SourceRecord& child,
                                           afw::table::Key<double> const& instFluxRawKey,
                                           afw::table::Key<double> const& instFluxAbsKey,
                                           ShapeResultKey const& _shapeRawKey,
                                           ShapeResultKey const& _shapeAbsKey) const {
    if (_ctrl.doFlux || _ctrl.doShape) {
        if (!child.getTable()->getCentroidSlot().getMeasKey().isValid()) {
            throw LSST_EXCEPT(pex::exceptions::LogicError,
                              "Centroid Key must be defined to measure the blendedness instFlux");
        }
    }
    if (_ctrl.doShape) {
        if (!child.getTable()->getCentroidSlot().getMeasKey().isValid()) {
            throw LSST_EXCEPT(pex::exceptions::LogicError,
                              "Shape Key must be defined to measure the blendedness shape");
        }
    }
    if (_ctrl.doShape || _ctrl.doFlux) {
        bool fatal = false;
        if (child.getTable()->getCentroidSlot().getFlagKey().isValid()) {
            if (child.getCentroidFlag()) {
                // don't set general flag, because even a failed centroid should
                // just fall back to the peak, and that should be fine for this
                // measurement.
                _flagHandler.setValue(child, NO_CENTROID.number, true);
            }
        }
        if (child.getTable()->getShapeSlot().getFlagKey().isValid()) {
            if (child.getShapeFlag()) {
                _flagHandler.setValue(child, NO_SHAPE.number, true);
                _flagHandler.setValue(child, FAILURE.number, true);
            }
        }
        if (!(child.getShape().getDeterminant() >= 0.0)) {
            // shape flag should have been set already, but we're paranoid
            _flagHandler.setValue(child, NO_SHAPE.number, true);
            _flagHandler.setValue(child, FAILURE.number, true);
            fatal = true;
        }
        if (!(std::isfinite(child.getX()) && std::isfinite(child.getY()))) {
            // shape flag should have been set already, but we're paranoid
            _flagHandler.setValue(child, NO_CENTROID.number, true);
            _flagHandler.setValue(child, FAILURE.number, true);
            fatal = true;
        }
        if (fatal) return;
    }
 
    if (_ctrl.doShape) {
        ShapeAccumulator accumulatorRaw;
        ShapeAccumulator accumulatorAbs;
        computeMoments(image, child.getCentroid(), child.getShape(), _ctrl.nSigmaWeightMax, accumulatorRaw,
                       accumulatorAbs);
        if (_ctrl.doFlux) {
            child.set(instFluxRawKey, accumulatorRaw.getFlux());
            child.set(instFluxAbsKey, std::max(accumulatorAbs.getFlux(), 0.0));
        }
        _shapeRawKey.set(child, accumulatorRaw.getShape());
        _shapeAbsKey.set(child, accumulatorAbs.getShape());
    } else if (_ctrl.doFlux) {
        FluxAccumulator accumulatorRaw;
        FluxAccumulator accumulatorAbs;
        computeMoments(image, child.getCentroid(), child.getShape(), _ctrl.nSigmaWeightMax, accumulatorRaw,
                       accumulatorAbs);
        child.set(instFluxRawKey, accumulatorRaw.getFlux());
        child.set(instFluxAbsKey, std::max(accumulatorAbs.getFlux(), 0.0));
    }
}
 
void BlendednessAlgorithm::measureChildPixels(afw::image::MaskedImage<float> const& image,
                                              afw::table::SourceRecord& child) const {
    _measureMoments(image, child, _instFluxChildRaw, _instFluxChildAbs, _shapeChildRaw, _shapeChildAbs);
}
 
void BlendednessAlgorithm::measureParentPixels(afw::image::MaskedImage<float> const& image,
                                               afw::table::SourceRecord& child) const {
    if (_ctrl.doOld) {
        child.set(_old, computeOldBlendedness(child.getFootprint(), *image.getImage()));
    }
    _measureMoments(image, child, _instFluxParentRaw, _instFluxParentAbs, _shapeParentRaw, _shapeParentAbs);
    if (_ctrl.doFlux) {
        child.set(_raw, 1.0 - child.get(_instFluxChildRaw) / child.get(_instFluxParentRaw));
        child.set(_abs, 1.0 - child.get(_instFluxChildAbs) / child.get(_instFluxParentAbs));
        if (child.get(_instFluxParentAbs) == 0.0) {
            // We can get NaNs in the absolute measure if both parent and child have only negative
            // biased-corrected instFluxes (which we clip to zero).  We can't really recover from this,
            // so we should set the flag.
            _flagHandler.setValue(child, FAILURE.number, true);
        }
    }
}
 
}  // namespace base
}  // namespace meas
}  // namespace lsst