Stack.cc

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// -*- lsst-c++ -*-
 
/*
 * LSST Data Management System
 * Copyright 2008, 2009, 2010 LSST Corporation.
 *
 * This product includes software developed by the
 * LSST Project (http://www.lsst.org/).
 *
 * 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 LSST License Statement and
 * the GNU General Public License along with this program.  If not,
 * see <http://www.lsstcorp.org/LegalNotices/>.
 */
 
/*
 * Provide functions to stack images
 *
 */
#include <vector>
#include <cassert>
#include <memory>
 
#include "lsst/base.h"
#include "lsst/pex/exceptions.h"
#include "lsst/afw/math/Stack.h"
#include "lsst/afw/math/MaskedVector.h"
#include "lsst/log/Log.h"
 
namespace pexExcept = lsst::pex::exceptions;
 
namespace {
    LOG_LOGGER _log = LOG_GET("afw.math.Stack");
}
 
namespace lsst {
namespace afw {
namespace math {
 
namespace {
typedef std::vector<WeightPixel> WeightVector;  // vector of weights (yes, really)
int bitcount(unsigned int x) {
    int b;
    for (b = 0; x != 0; x >>= 1) {
        if (x & 01) {
            b++;
        }
    }
    return b;
}
 
void checkOnlyOneFlag(unsigned int flags) {
    if (bitcount(flags & ~ERRORS) != 1) {
        throw LSST_EXCEPT(pexExcept::InvalidParameterError,
                          "Requested more than one type of statistic to make the image stack.");
    }
}
 
template <typename ObjectVectorT, typename WeightVectorT>
void checkObjectsAndWeights(ObjectVectorT const &objects, WeightVectorT const &wvector) {
    if (objects.size() == 0) {
        throw LSST_EXCEPT(pexExcept::LengthError, "Please specify at least one object to stack");
    }
 
    if (!wvector.empty() && wvector.size() != objects.size()) {
        throw LSST_EXCEPT(pexExcept::InvalidParameterError,
                          str(boost::format("Weight vector has different length "
                                            "from number of objects to be stacked: %d v. %d") %
                              wvector.size() % objects.size()));
    }
}
 
template <typename ImageT>
void checkImageSizes(ImageT const &out, std::vector<std::shared_ptr<ImageT>> const &images) {
    lsst::geom::Extent2I const &dim = out.getDimensions();
    for (unsigned int i = 0; i < images.size(); ++i) {
        if (images[i]->getDimensions() != dim) {
            throw LSST_EXCEPT(pexExcept::InvalidParameterError,
                              (boost::format("Bad dimensions for image %d: %dx%d vs %dx%d") % i %
                               images[i]->getDimensions().getX() % images[i]->getDimensions().getY() %
                               dim.getX() % dim.getY())
                                      .str());
        }
    }
}
 
/* ************************************************************************** *
 *
 * stack MaskedImages
 *
 * ************************************************************************** */
 
 
template <typename PixelT, bool isWeighted, bool useVariance>
void computeMaskedImageStack(image::MaskedImage<PixelT> &imgStack,
                             std::vector<std::shared_ptr<image::MaskedImage<PixelT>>> const &images,
                             Property flags, StatisticsControl const &sctrl, image::MaskPixel const clipped,
                             std::vector<std::pair<image::MaskPixel, image::MaskPixel>> const &maskMap,
                             WeightVector const &wvector = WeightVector()) {
    // get a list of row_begin iterators
    typedef typename image::MaskedImage<PixelT>::x_iterator x_iterator;
    std::vector<x_iterator> rows;
    rows.reserve(images.size());
 
    MaskedVector<PixelT> pixelSet(images.size());  // a pixel from x,y for each image
    WeightVector weights;                          // weights; non-const version
    //
    StatisticsControl sctrlTmp(sctrl);
 
    if (useVariance) {  // weight using the variance image
        assert(isWeighted);
        assert(wvector.empty());
 
        weights.resize(images.size());
 
        sctrlTmp.setWeighted(true);
    } else if (isWeighted) {
        weights.assign(wvector.begin(), wvector.end());
 
        sctrlTmp.setWeighted(true);
    }
    assert(weights.empty() || weights.size() == images.size());
 
    // loop over x,y ... the loop over the stack to fill pixelSet
    // - get the stats on pixelSet and put the value in the output image at x,y
    for (int y = 0; y != imgStack.getHeight(); ++y) {
        for (unsigned int i = 0; i < images.size(); ++i) {
            x_iterator ptr = images[i]->row_begin(y);
            if (y == 0) {
                rows.push_back(ptr);
            } else {
                rows[i] = ptr;
            }
        }
 
        for (x_iterator ptr = imgStack.row_begin(y), end = imgStack.row_end(y); ptr != end; ++ptr) {
            typename MaskedVector<PixelT>::iterator psPtr = pixelSet.begin();
            WeightVector::iterator wtPtr = weights.begin();
            for (unsigned int i = 0; i < images.size(); ++rows[i], ++i, ++psPtr, ++wtPtr) {
                *psPtr = *rows[i];
                if (useVariance) {  // we're weighting using the variance
                    *wtPtr = 1.0 / rows[i].variance();
                }
            }
 
            Property const eflags = static_cast<Property>(flags | NPOINT | ERRORS | NCLIPPED | NMASKED);
            Statistics stat = isWeighted ? makeStatistics(pixelSet, weights, eflags, sctrlTmp)
                                         : makeStatistics(pixelSet, eflags, sctrlTmp);
 
            PixelT variance = ::pow(stat.getError(flags), 2);
            image::MaskPixel msk(stat.getOrMask());
            int const npoint = stat.getValue(NPOINT);
            if (npoint == 0) {
                msk = sctrlTmp.getNoGoodPixelsMask();
            } else if (npoint == 1) {
                /*
                 * you should be using sctrl.setCalcErrorFromInputVariance(true) if you want to avoid
                 * getting a variance of NaN when you only have one input
                 */
            }
            // Check to see if any pixels were rejected due to clipping
            if (stat.getValue(NCLIPPED) > 0) {
                msk |= clipped;
            }
            // Check to see if any pixels were rejected by masking, and apply
            // any associated masks to the result.
            if (stat.getValue(NMASKED) > 0) {
                for (auto const &pair : maskMap) {
                    for (auto pp = pixelSet.begin(); pp != pixelSet.end(); ++pp) {
                        if ((*pp).mask() & pair.first) {
                            msk |= pair.second;
                            break;
                        }
                    }
                }
            }
 
            *ptr = typename image::MaskedImage<PixelT>::Pixel(stat.getValue(flags), msk, variance);
        }
    }
}
template <typename PixelT, bool isWeighted, bool useVariance>
void computeMaskedImageStack(image::MaskedImage<PixelT> &imgStack,
                             std::vector<std::shared_ptr<image::MaskedImage<PixelT>>> const &images,
                             Property flags, StatisticsControl const &sctrl, image::MaskPixel const clipped,
                             image::MaskPixel const excuse, WeightVector const &wvector = WeightVector()) {
    std::vector<std::pair<image::MaskPixel, image::MaskPixel>> maskMap;
    maskMap.push_back(std::make_pair(sctrl.getAndMask() & ~excuse, clipped));
    computeMaskedImageStack<PixelT, isWeighted, useVariance>(imgStack, images, flags, sctrl, clipped, maskMap,
                                                             wvector);
}
 
}  // end anonymous namespace
 
template <typename PixelT>
std::shared_ptr<image::MaskedImage<PixelT>> statisticsStack(
        std::vector<std::shared_ptr<image::MaskedImage<PixelT>>> &images, Property flags,
        StatisticsControl const &sctrl, WeightVector const &wvector, image::MaskPixel clipped,
        image::MaskPixel excuse) {
    if (images.size() == 0) {
        throw LSST_EXCEPT(pexExcept::LengthError, "Please specify at least one image to stack");
    }
    std::shared_ptr<image::MaskedImage<PixelT>> out(
            new image::MaskedImage<PixelT>(images[0]->getDimensions()));
    statisticsStack(*out, images, flags, sctrl, wvector, clipped, excuse);
    return out;
}
 
template <typename PixelT>
std::shared_ptr<image::MaskedImage<PixelT>> statisticsStack(
        std::vector<std::shared_ptr<image::MaskedImage<PixelT>>> &images, Property flags,
        StatisticsControl const &sctrl, WeightVector const &wvector, image::MaskPixel clipped,
        std::vector<std::pair<image::MaskPixel, image::MaskPixel>> const &maskMap) {
    if (images.size() == 0) {
        throw LSST_EXCEPT(pexExcept::LengthError, "Please specify at least one image to stack");
    }
    std::shared_ptr<image::MaskedImage<PixelT>> out(
            new image::MaskedImage<PixelT>(images[0]->getDimensions()));
    statisticsStack(*out, images, flags, sctrl, wvector, clipped, maskMap);
    return out;
}
 
template <typename PixelT>
void statisticsStack(image::MaskedImage<PixelT> &out,
                     std::vector<std::shared_ptr<image::MaskedImage<PixelT>>> &images, Property flags,
                     StatisticsControl const &sctrl, WeightVector const &wvector, image::MaskPixel clipped,
                     image::MaskPixel excuse) {
    checkObjectsAndWeights(images, wvector);
    checkOnlyOneFlag(flags);
    checkImageSizes(out, images);
 
    if (sctrl.getWeighted()) {
        if (wvector.empty()) {
            return computeMaskedImageStack<PixelT, true, true>(out, images, flags, sctrl, clipped,
                                                               excuse);  // use variance
        } else {
            return computeMaskedImageStack<PixelT, true, false>(out, images, flags, sctrl, clipped, excuse,
                                                                wvector);  // use wvector
        }
    } else {
        if (!wvector.empty()) {
            LOGL_WARN(_log,
               "Weights passed on to statisticsStack are ignored as sctrl.getWeighted() is False."
               "Set sctrl.setWeighted(True) for them to be used.");
        }
        return computeMaskedImageStack<PixelT, false, false>(out, images, flags, sctrl, clipped, excuse);
    }
}
 
template <typename PixelT>
void statisticsStack(image::MaskedImage<PixelT> &out,
                     std::vector<std::shared_ptr<image::MaskedImage<PixelT>>> &images, Property flags,
                     StatisticsControl const &sctrl, WeightVector const &wvector, image::MaskPixel clipped,
                     std::vector<std::pair<image::MaskPixel, image::MaskPixel>> const &maskMap) {
    checkObjectsAndWeights(images, wvector);
    checkOnlyOneFlag(flags);
    checkImageSizes(out, images);
 
    if (sctrl.getWeighted()) {
        if (wvector.empty()) {
            return computeMaskedImageStack<PixelT, true, true>(out, images, flags, sctrl, clipped,
                                                               maskMap);  // use variance
        } else {
            return computeMaskedImageStack<PixelT, true, false>(out, images, flags, sctrl, clipped, maskMap,
                                                                wvector);  // use wvector
        }
    } else {
        return computeMaskedImageStack<PixelT, false, false>(out, images, flags, sctrl, clipped, maskMap);
    }
}
 
namespace {
/* ************************************************************************** *
 *
 * stack Images
 *
 * All the work is done in the function comuteImageStack.
 * A boolean template variable has been used to allow the compiler to generate the different instantiations
 *   to handle cases when we are, or are not, weighting
 *
 * ************************************************************************** */
template <typename PixelT, bool isWeighted>
void computeImageStack(image::Image<PixelT> &imgStack,
                       std::vector<std::shared_ptr<image::Image<PixelT>>> &images, Property flags,
                       StatisticsControl const &sctrl, WeightVector const &weights = WeightVector()) {
    MaskedVector<PixelT> pixelSet(images.size());  // a pixel from x,y for each image
    StatisticsControl sctrlTmp(sctrl);
 
    // set the mask to be an infinite iterator
    MaskImposter<image::MaskPixel> msk;
 
    if (!weights.empty()) {
        sctrlTmp.setWeighted(true);
    }
 
    // get the desired statistic
    for (int y = 0; y != imgStack.getHeight(); ++y) {
        for (int x = 0; x != imgStack.getWidth(); ++x) {
            for (unsigned int i = 0; i != images.size(); ++i) {
                (*pixelSet.getImage())(i, 0) = (*images[i])(x, y);
            }
 
            if (isWeighted) {
                imgStack(x, y) = makeStatistics(pixelSet, weights, flags, sctrlTmp).getValue();
            } else {
                imgStack(x, y) = makeStatistics(pixelSet, weights, flags, sctrlTmp).getValue();
            }
        }
    }
}
 
}  // end anonymous namespace
 
template <typename PixelT>
std::shared_ptr<image::Image<PixelT>> statisticsStack(
        std::vector<std::shared_ptr<image::Image<PixelT>>> &images, Property flags,
        StatisticsControl const &sctrl, WeightVector const &wvector) {
    if (images.size() == 0) {
        throw LSST_EXCEPT(pexExcept::LengthError, "Please specify at least one image to stack");
    }
    std::shared_ptr<image::Image<PixelT>> out(new image::Image<PixelT>(images[0]->getDimensions()));
    statisticsStack(*out, images, flags, sctrl, wvector);
    return out;
}
 
template <typename PixelT>
void statisticsStack(image::Image<PixelT> &out, std::vector<std::shared_ptr<image::Image<PixelT>>> &images,
                     Property flags, StatisticsControl const &sctrl, WeightVector const &wvector) {
    checkObjectsAndWeights(images, wvector);
    checkOnlyOneFlag(flags);
    checkImageSizes(out, images);
 
    if (wvector.empty()) {
        return computeImageStack<PixelT, false>(out, images, flags, sctrl);
    } else {
        return computeImageStack<PixelT, true>(out, images, flags, sctrl, wvector);
    }
}
 
/* ************************************************************************** *
 *
 * stack VECTORS
 *
 * ************************************************************************** */
 
namespace {
 
template <typename PixelT, bool isWeighted>
std::vector<PixelT> computeVectorStack(
        std::vector<std::vector<PixelT>> &vectors, Property flags,
        StatisticsControl const &sctrl, WeightVector const &wvector = WeightVector()) {
    // create the image to be returned
    typedef std::vector<PixelT> Vect;
    Vect vecStack(vectors[0].size(), 0.0);
 
    MaskedVector<PixelT> pixelSet(vectors.size());  // values from a given pixel of each image
 
    StatisticsControl sctrlTmp(sctrl);
    // set the mask to be an infinite iterator
    MaskImposter<image::MaskPixel> msk;
 
    if (!wvector.empty()) {
        sctrlTmp.setWeighted(true);
    }
 
    // collect elements from the stack into the MaskedVector to do stats
    for (unsigned int x = 0; x < vectors[0].size(); ++x) {
        typename MaskedVector<PixelT>::iterator psPtr = pixelSet.begin();
        for (unsigned int i = 0; i < vectors.size(); ++i, ++psPtr) {
            psPtr.value() = (vectors[i])[x];
        }
 
        if (isWeighted) {
            (vecStack)[x] = makeStatistics(pixelSet, wvector, flags, sctrlTmp).getValue(flags);
        } else {
            (vecStack)[x] = makeStatistics(pixelSet, flags, sctrlTmp).getValue(flags);
        }
    }
 
    return vecStack;
}
 
}  // end anonymous namespace
 
template <typename PixelT>
std::vector<PixelT> statisticsStack(
        std::vector<std::vector<PixelT>> &vectors, Property flags,
        StatisticsControl const &sctrl, WeightVector const &wvector) {
    checkObjectsAndWeights(vectors, wvector);
    checkOnlyOneFlag(flags);
 
    if (wvector.empty()) {
        return computeVectorStack<PixelT, false>(vectors, flags, sctrl);
    } else {
        return computeVectorStack<PixelT, true>(vectors, flags, sctrl, wvector);
    }
}
 
/* ************************************************************************ *
 *
 * XY row column stacking
 *
 * ************************************************************************ */
 
template <typename PixelT>
std::shared_ptr<image::MaskedImage<PixelT>> statisticsStack(image::Image<PixelT> const &image, Property flags,
                                                            char dimension, StatisticsControl const &sctrl) {
    int x0 = image.getX0();
    int y0 = image.getY0();
    typedef image::MaskedImage<PixelT> MImage;
    std::shared_ptr<MImage> imgOut;
 
    // do each row or column, one at a time
    // - create a subimage with a bounding box, and get the stats and assign the value to the output image
    if (dimension == 'x') {
        imgOut = std::shared_ptr<MImage>(new MImage(lsst::geom::Extent2I(1, image.getHeight())));
        int y = y0;
        typename MImage::y_iterator oEnd = imgOut->col_end(0);
        for (typename MImage::y_iterator oPtr = imgOut->col_begin(0); oPtr != oEnd; ++oPtr, ++y) {
            lsst::geom::Box2I bbox =
                    lsst::geom::Box2I(lsst::geom::Point2I(x0, y), lsst::geom::Extent2I(image.getWidth(), 1));
            image::Image<PixelT> subImage(image, bbox);
            Statistics stat = makeStatistics(subImage, flags | ERRORS, sctrl);
            *oPtr = typename image::MaskedImage<PixelT>::Pixel(stat.getValue(), 0x0,
                                                               stat.getError() * stat.getError());
        }
 
    } else if (dimension == 'y') {
        imgOut = std::shared_ptr<MImage>(new MImage(lsst::geom::Extent2I(image.getWidth(), 1)));
        int x = x0;
        typename MImage::x_iterator oEnd = imgOut->row_end(0);
        for (typename MImage::x_iterator oPtr = imgOut->row_begin(0); oPtr != oEnd; ++oPtr, ++x) {
            lsst::geom::Box2I bbox =
                    lsst::geom::Box2I(lsst::geom::Point2I(x, y0), lsst::geom::Extent2I(1, image.getHeight()));
            image::Image<PixelT> subImage(image, bbox);
            Statistics stat = makeStatistics(subImage, flags | ERRORS, sctrl);
            *oPtr = typename image::MaskedImage<PixelT>::Pixel(stat.getValue(), 0x0,
                                                               stat.getError() * stat.getError());
        }
    } else {
        throw LSST_EXCEPT(pexExcept::InvalidParameterError,
                          "Can only run statisticsStack in x or y for single image.");
    }
 
    return imgOut;
}
 
template <typename PixelT>
std::shared_ptr<image::MaskedImage<PixelT>> statisticsStack(image::MaskedImage<PixelT> const &image,
                                                            Property flags, char dimension,
                                                            StatisticsControl const &sctrl) {
    int const x0 = image.getX0();
    int const y0 = image.getY0();
    typedef image::MaskedImage<PixelT> MImage;
    std::shared_ptr<MImage> imgOut;
 
    // do each row or column, one at a time
    // - create a subimage with a bounding box, and get the stats and assign the value to the output image
    if (dimension == 'x') {
        imgOut = std::shared_ptr<MImage>(new MImage(lsst::geom::Extent2I(1, image.getHeight())));
        int y = 0;
        typename MImage::y_iterator oEnd = imgOut->col_end(0);
        for (typename MImage::y_iterator oPtr = imgOut->col_begin(0); oPtr != oEnd; ++oPtr, ++y) {
            lsst::geom::Box2I bbox =
                    lsst::geom::Box2I(lsst::geom::Point2I(x0, y), lsst::geom::Extent2I(image.getWidth(), 1));
            image::MaskedImage<PixelT> subImage(image, bbox);
            Statistics stat = makeStatistics(subImage, flags | ERRORS, sctrl);
            *oPtr = typename image::MaskedImage<PixelT>::Pixel(stat.getValue(), 0x0,
                                                               stat.getError() * stat.getError());
        }
 
    } else if (dimension == 'y') {
        imgOut = std::shared_ptr<MImage>(new MImage(lsst::geom::Extent2I(image.getWidth(), 1)));
        int x = 0;
        typename MImage::x_iterator oEnd = imgOut->row_end(0);
        for (typename MImage::x_iterator oPtr = imgOut->row_begin(0); oPtr != oEnd; ++oPtr, ++x) {
            lsst::geom::Box2I bbox =
                    lsst::geom::Box2I(lsst::geom::Point2I(x, y0), lsst::geom::Extent2I(1, image.getHeight()));
            image::MaskedImage<PixelT> subImage(image, bbox);
            Statistics stat = makeStatistics(subImage, flags | ERRORS, sctrl);
            *oPtr = typename image::MaskedImage<PixelT>::Pixel(stat.getValue(), 0x0,
                                                               stat.getError() * stat.getError());
        }
    } else {
        throw LSST_EXCEPT(pexExcept::InvalidParameterError,
                          "Can only run statisticsStack in x or y for single image.");
    }
 
    return imgOut;
}
 
/*
 * Explicit Instantiations
 *
 */
#define INSTANTIATE_STACKS(TYPE)                                                                             \
    template std::shared_ptr<image::Image<TYPE>> statisticsStack<TYPE>(                                      \
            std::vector<std::shared_ptr<image::Image<TYPE>>> & images, Property flags,                       \
            StatisticsControl const &sctrl, WeightVector const &wvector);                                    \
    template void statisticsStack<TYPE>(                                                                     \
            image::Image<TYPE> & out, std::vector<std::shared_ptr<image::Image<TYPE>>> & images,             \
            Property flags, StatisticsControl const &sctrl, WeightVector const &wvector);                    \
    template std::shared_ptr<image::MaskedImage<TYPE>> statisticsStack<TYPE>(                                \
            std::vector<std::shared_ptr<image::MaskedImage<TYPE>>> & images, Property flags,                 \
            StatisticsControl const &sctrl, WeightVector const &wvector, image::MaskPixel,                   \
            image::MaskPixel);                                                                               \
    template std::shared_ptr<image::MaskedImage<TYPE>> statisticsStack<TYPE>(                                \
            std::vector<std::shared_ptr<image::MaskedImage<TYPE>>> & images, Property flags,                 \
            StatisticsControl const &sctrl, WeightVector const &wvector, image::MaskPixel,                   \
            std::vector<std::pair<image::MaskPixel, image::MaskPixel>> const &);                             \
    template void statisticsStack<TYPE>(image::MaskedImage<TYPE> & out,                                      \
                                        std::vector<std::shared_ptr<image::MaskedImage<TYPE>>> & images,     \
                                        Property flags, StatisticsControl const &sctrl,                      \
                                        WeightVector const &wvector, image::MaskPixel, image::MaskPixel);    \
    template void statisticsStack<TYPE>(                                                                     \
            image::MaskedImage<TYPE> & out, std::vector<std::shared_ptr<image::MaskedImage<TYPE>>> & images, \
            Property flags, StatisticsControl const &sctrl, WeightVector const &wvector, image::MaskPixel,   \
            std::vector<std::pair<image::MaskPixel, image::MaskPixel>> const &);                             \
    template std::vector<TYPE> statisticsStack<TYPE>(                                       \
            std::vector<std::vector<TYPE>> & vectors, Property flags,                       \
            StatisticsControl const &sctrl, WeightVector const &wvector);                                    \
    template std::shared_ptr<image::MaskedImage<TYPE>> statisticsStack(image::Image<TYPE> const &image,      \
                                                                       Property flags, char dimension,       \
                                                                       StatisticsControl const &sctrl);      \
    template std::shared_ptr<image::MaskedImage<TYPE>> statisticsStack(                                      \
            image::MaskedImage<TYPE> const &image, Property flags, char dimension,                           \
            StatisticsControl const &sctrl);
 
INSTANTIATE_STACKS(double)
INSTANTIATE_STACKS(float)
}  // namespace math
}  // namespace afw
}  // namespace lsst