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DM-20566: Replace afwGeom with geom where appropriate #27

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Jul 19, 2019
Merged

DM-20566: Replace afwGeom with geom where appropriate #27

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fd9b5d9
Remove trailing whitespace
timj Jul 16, 2019
0d73ed4
Formally depend on geom
timj Jul 16, 2019
787ef2c
Replace afwGeom with geom where appropriate
timj Jul 16, 2019
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7 changes: 4 additions & 3 deletions include/lsst/meas/extensions/simpleShape.h
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Expand Up @@ -26,6 +26,7 @@
#include <bitset>

#include "lsst/pex/config.h"
#include "lsst/geom.h"
#include "lsst/afw/geom/ellipses.h"
#include "lsst/afw/table.h"
#include "lsst/afw/image.h"
Expand Down Expand Up @@ -150,7 +151,7 @@ class SimpleShape : public lsst::meas::base::SimpleAlgorithm {
static Eigen::Matrix<double,5,6> convertRawMoments(
Eigen::Matrix<double,6,1> const & q,
afw::geom::ellipses::Quadrupole & quadrupole,
afw::geom::Point2D & center
geom::Point2D & center
);

/**
Expand Down Expand Up @@ -178,7 +179,7 @@ class SimpleShape : public lsst::meas::base::SimpleAlgorithm {
static Eigen::Matrix<double, 5, 5> correctWeightedMoments(
afw::geom::ellipses::Quadrupole const & weight,
afw::geom::ellipses::Quadrupole & ellipse,
afw::geom::Point2D & center
geom::Point2D & center
);

virtual void measure(
Expand All @@ -203,7 +204,7 @@ class SimpleShape : public lsst::meas::base::SimpleAlgorithm {
class SimpleShapeResult {
public:
afw::geom::ellipses::Quadrupole ellipse; ///< Measured second moments.
afw::geom::Point2D center; ///< Measured first moments, or the input center if !recentroid
geom::Point2D center; ///< Measured first moments, or the input center if !recentroid
Eigen::Matrix<double,5,5> covariance; ///< Matrix of uncertainties; ordered Ixx, Iyy, Ixy, Ix, Iy.

#ifndef SWIG
Expand Down
24 changes: 12 additions & 12 deletions src/simpleShape.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ namespace {

using afw::geom::Span;

Span clipSpan(Span const & span, afw::geom::Box2I const & box) {
Span clipSpan(Span const & span, geom::Box2I const & box) {
if (span.getY() < box.getMinY() || span.getY() > box.getMaxY()) return Span();
return Span(span.getY(),
std::min(std::max(span.getMinX(), box.getMinX()), box.getMaxX()),
Expand All @@ -72,7 +72,7 @@ void iterateSpan(Function & function, Iterator pixIter, Span const & span) {

template <typename Function, typename Image, typename Region>
void iterateRegion(Function & function, Image const & image, Region const & region) {
afw::geom::Box2I bbox = image.getBBox(afw::image::PARENT);
geom::Box2I bbox = image.getBBox(afw::image::PARENT);
if (bbox.contains(region.getBBox())) {
// if the box contains the region, there's no need to check each span to make sure it's entirely
// within the image
Expand Down Expand Up @@ -127,9 +127,9 @@ typedef Eigen::Matrix<double,N_M,N_Q> MatrixMQ;
struct RawMomentAccumulator {

template <typename PixelT>
void operator()(afw::geom::Point2I const & pos, PixelT const & pixel) {
afw::geom::Extent2D d = afw::geom::Point2D(pos) - _center;
afw::geom::Extent2D gtd = _gt(d);
void operator()(geom::Point2I const & pos, PixelT const & pixel) {
geom::Extent2D d = geom::Point2D(pos) - _center;
geom::Extent2D gtd = _gt(d);
double w = std::exp(-0.5 * (gtd.getX()*gtd.getX() + gtd.getY()*gtd.getY()));
VectorQ q = VectorQ::Constant(w);
q[QXX] *= d.getX() * d.getX();
Expand All @@ -151,8 +151,8 @@ struct RawMomentAccumulator {
VectorQ moments;
MatrixQ covariance;
private:
afw::geom::Point2D _center;
afw::geom::LinearTransform _gt;
geom::Point2D _center;
geom::LinearTransform _gt;
};

} // anonymous
Expand Down Expand Up @@ -194,7 +194,7 @@ SimpleShapeResult SimpleShape::computeMoments(
result.covariance = dc_dm * mCov.selfadjointView<Eigen::Lower>() * dc_dm.adjoint();

// Finally, we switch back to the native image coordinate system.
result.center += afw::geom::Extent2D(weight.getCenter());
result.center += geom::Extent2D(weight.getCenter());

return result;
}
Expand All @@ -203,7 +203,7 @@ SimpleShapeResult SimpleShape::computeMoments(
MatrixMQ SimpleShape::convertRawMoments(
VectorQ const & q,
afw::geom::ellipses::Quadrupole & ellipse,
afw::geom::Point2D & center
geom::Point2D & center
) {
VectorM m = q.segment<N_M>(1) / q[Q0];
MatrixMQ dm_dq = MatrixMQ::Zero();;
Expand Down Expand Up @@ -234,7 +234,7 @@ MatrixMQ SimpleShape::convertRawMoments(
MatrixM SimpleShape::correctWeightedMoments(
afw::geom::ellipses::Quadrupole const & weight,
afw::geom::ellipses::Quadrupole & ellipse,
afw::geom::Point2D & center
geom::Point2D & center
) {
Eigen::Matrix2d wMat = weight.getMatrix();
Eigen::Vector2d mVec = center.asEigen();
Expand Down Expand Up @@ -325,7 +325,7 @@ SimpleShapeResultKey SimpleShapeResultKey::addFields(
name, "elliptical Gaussian moments");
r._centroidResult = lsst::afw::table::Point2DKey::addFields(schema,
name, "elliptical Gaussian moments", "pixel");
r._uncertantyResult = lsst::afw::table::CovarianceMatrixKey<double, 5>::addFields(schema,name,
r._uncertantyResult = lsst::afw::table::CovarianceMatrixKey<double, 5>::addFields(schema,name,
std::vector<std::string> ({"Ixx", "Iyy", "Ixy",
"Ix", "Iy"}), "pixel");
r._flagHandler = lsst::meas::base::FlagHandler::addFields(schema,
Expand Down Expand Up @@ -389,7 +389,7 @@ void SimpleShape::measure(
afw::table::SourceRecord & source,
afw::image::Exposure<float> const & exposure
) const {
afw::geom::Point2D center = _centroidExtractor(source, _resultKey.getFlagHandler());
geom::Point2D center = _centroidExtractor(source, _resultKey.getFlagHandler());
afw::geom::ellipses::Ellipse weight(afw::geom::ellipses::Axes(_ctrl.sigma), center);
// set flags so an exception throw produces a flagged source
SimpleShapeResult result = computeMoments(weight, exposure.getMaskedImage(), _ctrl.nSigmaRegion);
Expand Down
8 changes: 5 additions & 3 deletions tests/test_measurementFramework.py
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Expand Up @@ -22,6 +22,8 @@
#
import unittest

import lsst.geom
import lsst.afw.geom
import lsst.utils.tests
import lsst.meas.base.tests
from lsst.meas.base.tests import AlgorithmTestCase
Expand All @@ -31,10 +33,10 @@
class SimpleShapeMFTestCase(AlgorithmTestCase, lsst.utils.tests.TestCase):

def setUp(self):
self.bbox = lsst.afw.geom.Box2I(lsst.afw.geom.Point2I(-20, -30),
lsst.afw.geom.Extent2I(240, 160))
self.bbox = lsst.geom.Box2I(lsst.geom.Point2I(-20, -30),
lsst.geom.Extent2I(240, 160))
self.dataset = lsst.meas.base.tests.TestDataset(self.bbox)
self.dataset.addSource(100000.0, lsst.afw.geom.Point2D(149.9, 50.3),
self.dataset.addSource(100000.0, lsst.geom.Point2D(149.9, 50.3),
lsst.afw.geom.ellipses.Quadrupole(8, 9, 3))

self.expectedKeySet = set(['ext_simpleShape_SimpleShape_IxErr',
Expand Down
12 changes: 6 additions & 6 deletions tests/test_simpleShape.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@
import numpy as np

import lsst.utils.tests
import lsst.afw.geom
import lsst.geom
import lsst.afw.geom.ellipses as el
import lsst.afw.image
from lsst.meas.extensions.simpleShape import SimpleShape
Expand All @@ -40,13 +40,13 @@ def setUp(self):
el.Quadrupole(23.0, 28.0, 2.0),
]
self.centers = [
lsst.afw.geom.Point2D(0.0, 0.0),
lsst.afw.geom.Point2D(2.0, 3.0),
lsst.afw.geom.Point2D(-1.0, 2.5),
lsst.geom.Point2D(0.0, 0.0),
lsst.geom.Point2D(2.0, 3.0),
lsst.geom.Point2D(-1.0, 2.5),
]
for ellipseCore in self.ellipseCores:
ellipseCore.scale(2)
self.bbox = lsst.afw.geom.Box2I(lsst.afw.geom.Point2I(-500, -500), lsst.afw.geom.Point2I(50, 50))
self.bbox = lsst.geom.Box2I(lsst.geom.Point2I(-500, -500), lsst.geom.Point2I(50, 50))
self.xg, self.yg = np.meshgrid(
np.arange(self.bbox.getBeginX(), self.bbox.getEndX(), dtype=float),
np.arange(self.bbox.getBeginY(), self.bbox.getEndY(), dtype=float)
Expand Down Expand Up @@ -99,7 +99,7 @@ def testCorrectWeightedMoments(self):
iyy = np.sum(product * (self.yg - iy)**2) / i0
ixy = np.sum(product * (self.xg - ix) * (self.yg - iy)) / i0
mEllipseCore = el.Quadrupole(ixx, iyy, ixy)
mCenter = lsst.afw.geom.Point2D(ix, iy)
mCenter = lsst.geom.Point2D(ix, iy)
SimpleShape.correctWeightedMoments(wEllipseCore, mEllipseCore, mCenter)
self.assertFloatsAlmostEqual(mEllipseCore.getParameterVector(),
dEllipseCore.getParameterVector(),
Expand Down
1 change: 1 addition & 0 deletions ups/meas_extensions_simpleShape.table
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Expand Up @@ -8,6 +8,7 @@ setupRequired(meas_base)
setupRequired(utils)
setupRequired(pex_config)
setupRequired(pex_exceptions)
setupRequired(geom)

# The following is boilerplate for all packages.
# Pure-Python packages only need the last line.
Expand Down