Merge pull request #28 from lsst/tickets/DM-20566-meas_extensions_sha…

…peHSM

DM-20566: Replace afwGeom with geom where appropriate

include/lsst/meas/extensions/shapeHSM/HsmAdapter.h

@@ -1,7 +1,7 @@
 #ifndef LSST_MEAS_EXTENSIONS_SHAPEHSM_HSMADAPTER_H
 #define LSST_MEAS_EXTENSIONS_SHAPEHSM_HSMADAPTER_H
 
-#include "lsst/afw/geom/Box.h"
+#include "lsst/geom/Box.h"
 #include "lsst/afw/image/Image.h"
 #include "galsim/Image.h"
 
@@ -19,7 +19,7 @@ class ImageConverter
     /// doesn't allow us to access a shared_ptr to the pixels.  Instead, we use a
     /// dummy shared ptr to a single (new) pixel.  The ImageConverter is holding
     /// on to this too (RAII) so we shouldn't have any memory worries.
-    ImageConverter(PTR(afw::image::Image<PixelT>) image, afw::geom::Box2I box) :
+    ImageConverter(PTR(afw::image::Image<PixelT>) image, geom::Box2I box) :
         _image(image), _owner(new PixelT), _box(box) {}
     ImageConverter(PTR(afw::image::Image<PixelT>) image) :
         _image(image), _owner(new PixelT), _box(image->getBBox(afw::image::LOCAL)) {}
@@ -63,7 +63,7 @@ class ImageConverter
 private:
     PTR(afw::image::Image<PixelT>) _image;
     std::shared_ptr<PixelT> _owner;
-    afw::geom::Box2I _box;
+    geom::Box2I _box;
 };
 
 
@@ -73,7 +73,7 @@ class ImageConverter
 inline
 PTR(afw::image::Image<int>) convertMask(
     afw::image::Mask<afw::image::MaskPixel> const& afwMask, ///< Traditional afw Mask using mask planes
-    afw::geom::Box2I const& bbox,            ///< Bounding box of interest
+    geom::Box2I const& bbox,            ///< Bounding box of interest
     afw::image::MaskPixel const badPixelMask ///< Mask for selecting bad pixels
     )
 {

include/lsst/meas/extensions/shapeHSM/HsmMomentsControl.h

@@ -109,8 +109,8 @@ class HsmMomentsAlgorithm : public base::SimpleAlgorithm {
         afw::table::SourceRecord& source, // Source for recording moments
         PTR(afw::image::Image<PixelT>) const& afwImage, // Image on which to measure moments
         PTR(afw::image::Mask<afw::image::MaskPixel>) const& afwMask, // Mask for image
-        afw::geom::Box2I const& bbox,     // Bounding box
-        afw::geom::Point2D const& center, // Starting center for measuring moments
+        geom::Box2I const& bbox,     // Bounding box
+        geom::Point2D const& center, // Starting center for measuring moments
         afw::image::MaskPixel const badPixelMask, // Bitmask for bad pixels
         float const width,            // PSF width estimate, for starting moments
         bool roundMoments=false, // Use round weight function

src/HsmMoments.cc

@@ -55,8 +55,8 @@ void HsmMomentsAlgorithm::calculate(
     afw::table::SourceRecord& source,
     PTR(afw::image::Image<PixelT>) const& afwImage,
     PTR(afw::image::Mask<afw::image::MaskPixel>) const& afwMask,
-    afw::geom::Box2I const& bbox,
-    afw::geom::Point2D const& center,
+    geom::Box2I const& bbox,
+    geom::Point2D const& center,
     afw::image::MaskPixel const badPixelMask,
     float const width,
     bool roundMoments,
@@ -108,20 +108,20 @@ void HsmSourceMomentsAlgorithm::measure(
     afw::image::Exposure<float> const & exposure
 ) const {
 
-    afw::geom::Point2D center = _centroidExtractor(source, _flagHandler);
+    geom::Point2D center = _centroidExtractor(source, _flagHandler);
 
     std::vector<std::string> const & badMaskPlanes = _ctrl.badMaskPlanes;
     afw::image::MaskPixel badPixelMask = exposure.getMaskedImage().getMask()->getPlaneBitMask(badMaskPlanes);
 
-    afw::geom::Box2I bbox = source.getFootprint()->getBBox();
+    geom::Box2I bbox = source.getFootprint()->getBBox();
     if (bbox.getArea() == 0) {
         throw LSST_EXCEPT(
             base::MeasurementError,
             NO_PIXELS.doc,
             NO_PIXELS.number
         );
     }
-    if (!bbox.contains(afw::geom::Point2I(center))) {
+    if (!bbox.contains(geom::Point2I(center))) {
         throw LSST_EXCEPT(
             base::MeasurementError,
             NOT_CONTAINED.doc,
@@ -142,7 +142,7 @@ void HsmPsfMomentsAlgorithm::measure(
     afw::image::Exposure<float> const & exposure
 ) const {
 
-    afw::geom::Point2D center = _centroidExtractor(source, _flagHandler);
+    geom::Point2D center = _centroidExtractor(source, _flagHandler);
 
     typedef afw::image::Mask<afw::image::MaskPixel> Mask;
     PTR(afw::detection::Psf::Image) image = exposure.getPsf()->computeKernelImage(center);
@@ -154,7 +154,7 @@ void HsmPsfMomentsAlgorithm::measure(
 
     double const psfSigma = exposure.getPsf()->computeShape(center).getTraceRadius();
     HsmMomentsAlgorithm::calculate(source, image, mask, image->getBBox(afw::image::PARENT),
-                                   afw::geom::Point2D(0, 0), 0, psfSigma);
+                                   geom::Point2D(0, 0), 0, psfSigma);
 }
 
 }}}} // namespace lsst::meas::extensions::shapeHSM

src/HsmShape.cc

@@ -22,7 +22,7 @@
  */
 
 #include "lsst/pex/exceptions.h"
-#include "lsst/afw/geom/Box.h"
+#include "lsst/geom/Box.h"
 #include "lsst/afw/image.h"
 #include "lsst/afw/detection/Psf.h"
 #include "lsst/afw/math/Statistics.h"
@@ -138,7 +138,7 @@ void HsmShapeAlgorithm::measure(
     afw::table::SourceRecord & source,
     afw::image::Exposure<float> const & exposure
 ) const {
-    afw::geom::Point2D center = _centroidExtractor(source, _flagHandler);
+    geom::Point2D center = _centroidExtractor(source, _flagHandler);
     if (_hasDeblendKey && source.get(_deblendKey) > 0) {
         throw LSST_EXCEPT(base::MeasurementError, "Ignoring parent source", PARENT_SOURCE.number);
     }
@@ -147,15 +147,15 @@ void HsmShapeAlgorithm::measure(
 
     afw::image::MaskPixel badPixelMask = exposure.getMaskedImage().getMask()->getPlaneBitMask(badMaskPlanes);
 
-    afw::geom::Box2I bbox = source.getFootprint()->getBBox();
+    geom::Box2I bbox = source.getFootprint()->getBBox();
     if (bbox.getArea() == 0) {
         throw LSST_EXCEPT(
             base::MeasurementError,
             NO_PIXELS.doc,
             NO_PIXELS.number
         );
     }
-    if (!bbox.contains(afw::geom::Point2I(center))) {
+    if (!bbox.contains(geom::Point2I(center))) {
         throw LSST_EXCEPT(
             base::MeasurementError,
             NOT_CONTAINED.doc,

tests/test_hsm.py

@@ -34,6 +34,7 @@
 import lsst.afw.detection as afwDetection
 import lsst.afw.table as afwTable
 import lsst.afw.geom as afwGeom
+import lsst.geom as geom
 import lsst.afw.geom.ellipses as afwEll
 import lsst.utils.tests
 import lsst.meas.extensions.shapeHSM
@@ -157,8 +158,8 @@ def setUp(self):
         # load the known values
         self.dataDir = os.path.join(os.getenv('MEAS_EXTENSIONS_SHAPEHSM_DIR'), "tests", "data")
         self.bkgd = 1000.0  # standard for atlas image
-        self.offset = afwGeom.Extent2I(1234, 1234)
-        self.xy0 = afwGeom.Point2I(5678, 9876)
+        self.offset = geom.Extent2I(1234, 1234)
+        self.xy0 = geom.Point2I(5678, 9876)
 
     def tearDown(self):
         del self.offset
@@ -171,8 +172,8 @@ def runMeasurement(self, algorithmName, imageid, x, y, v):
         img = afwImage.ImageF(imgFile)
         img -= self.bkgd
         nx, ny = img.getWidth(), img.getHeight()
-        msk = afwImage.Mask(afwGeom.Extent2I(nx, ny), 0x0)
-        var = afwImage.ImageF(afwGeom.Extent2I(nx, ny), v)
+        msk = afwImage.Mask(geom.Extent2I(nx, ny), 0x0)
+        var = afwImage.ImageF(geom.Extent2I(nx, ny), v)
         mimg = afwImage.MaskedImageF(img, msk, var)
         msk.getArray()[:] = np.where(np.fabs(img.getArray()) < 1.0e-8, msk.getPlaneBitMask("BAD"), 0)
 
@@ -181,16 +182,16 @@ def runMeasurement(self, algorithmName, imageid, x, y, v):
         big.getImage().set(0)
         big.getMask().set(0)
         big.getVariance().set(v)
-        subBig = afwImage.MaskedImageF(big, afwGeom.Box2I(big.getXY0() + self.offset, mimg.getDimensions()))
+        subBig = afwImage.MaskedImageF(big, geom.Box2I(big.getXY0() + self.offset, mimg.getDimensions()))
         subBig <<= mimg
         mimg = big
         mimg.setXY0(self.xy0)
 
         exposure = afwImage.makeExposure(mimg)
         cdMatrix = np.array([1.0/(2.53*3600.0), 0.0, 0.0, 1.0/(2.53*3600.0)])
         cdMatrix.shape = (2, 2)
-        exposure.setWcs(afwGeom.makeSkyWcs(crpix=afwGeom.Point2D(1.0, 1.0),
-                                           crval=afwGeom.SpherePoint(0, 0, afwGeom.degrees),
+        exposure.setWcs(afwGeom.makeSkyWcs(crpix=geom.Point2D(1.0, 1.0),
+                                           crval=geom.SpherePoint(0, 0, geom.degrees),
                                            cdMatrix=cdMatrix))
 
         # load the corresponding test psf
@@ -211,7 +212,7 @@ def runMeasurement(self, algorithmName, imageid, x, y, v):
         # Algorithm._apply.  Otherwise, when the PSF is realised it will have been warped
         # to account for the sub-pixel offset and we won't get *exactly* this PSF.
         plugin, table = makePluginAndCat(alg, algorithmName, control, centroid="centroid")
-        center = afwGeom.Point2D(int(x), int(y)) + afwGeom.Extent2D(self.offset + afwGeom.Extent2I(self.xy0))
+        center = geom.Point2D(int(x), int(y)) + geom.Extent2D(self.offset + geom.Extent2I(self.xy0))
         source = table.makeRecord()
         source.set("centroid_x", center.getX())
         source.set("centroid_y", center.getY())
@@ -340,7 +341,7 @@ def testHsmPsfMoments(self):
             source = cat.addNew()
             source.set("centroid_x", 23)
             source.set("centroid_y", 34)
-            offset = afwGeom.Point2I(23, 34)
+            offset = geom.Point2I(23, 34)
             tmpSpans = afwGeom.SpanSet.fromShape(int(width), offset=offset)
             source.setFootprint(afwDetection.Footprint(tmpSpans))
             plugin.measure(source, exposure)

ups/meas_extensions_shapeHSM.table

@@ -2,6 +2,7 @@ setupRequired(meas_base)
 setupRequired(meas_algorithms)
 setupRequired(galsim)
 
+setupRequired(geom)
 setupRequired(afw)
 setupRequired(daf_base)
 setupRequired(numpy)