DM-20566: Replace afwGeom with geom

bin.src/psfex.py

@@ -4,7 +4,6 @@
 import sys
 from lsst.meas.extensions.psfex import psfex, readPrefs, makeitLsst, makeit, showPsf, dafBase
 
-#-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="Wrapper for Point Spread Function Extractor (PSFEX)")

include/lsst/meas/extensions/psfex/Field.hh

@@ -40,15 +40,15 @@ public:
          );
     ~Field();
     //
-    void finalize() { _finalize(true); }        
-    
+    void finalize() { _finalize(true); }
+
     void addExt(lsst::afw::geom::SkyWcs const& wcs, int const naxis1, int const naxis2, int const nobj=0);
-    
+
     /// Return the number of extensions
     int getNext() const { return impl->next; }
     /// Return the Psfs
     std::vector<Psf> getPsfs() const;
-    
+
 private:
    fieldstruct* impl;
    mutable std::vector<Psf> _psfs;

include/lsst/meas/extensions/psfex/PsfexPsf.h

@@ -24,7 +24,7 @@
 # if !defined(LSST_MEAS_EXTENSIONS_PSFEX_PSFEX_H)
 #define LSST_MEAS_EXTENSIONS_PSFEX_PSFEX_H 1
 
-#include "lsst/afw/geom/Box.h"
+#include "lsst/geom/Box.h"
 #include "lsst/meas/algorithms/ImagePsf.h"
 #include "lsst/meas/extensions/psfex/psf.hh"
 
@@ -45,7 +45,7 @@ class PsfexPsf : public lsst::afw::table::io::PersistableFacade<PsfexPsf>,
      */
     explicit PsfexPsf(
         lsst::meas::extensions::psfex::Psf const& psf, ///< [in] Psfex PSF model to be wrapped into an LSST Psf
-        lsst::afw::geom::Point2D const & averagePosition=lsst::afw::geom::Point2D()
+        lsst::geom::Point2D const & averagePosition=lsst::geom::Point2D()
                                         ///< [in] Average position of stars used to construct the Psf.
     );
     virtual ~PsfexPsf();
@@ -57,20 +57,20 @@ class PsfexPsf : public lsst::afw::table::io::PersistableFacade<PsfexPsf>,
     virtual PTR(afw::detection::Psf) resized(int width, int height) const;
 
     /// Return average position of stars; used as default position.
-    virtual lsst::afw::geom::Point2D getAveragePosition() const { return _averagePosition; }
-    
+    virtual lsst::geom::Point2D getAveragePosition() const { return _averagePosition; }
+
     /// Return the PSF's basis functions as a spatially-invariant LinearCombinationKernel
     /// with unit weights
     PTR(lsst::afw::math::LinearCombinationKernel const)
-    getKernel(lsst::afw::geom::Point2D =
-              lsst::afw::geom::Point2D(std::numeric_limits<double>::quiet_NaN())) const;
+    getKernel(lsst::geom::Point2D =
+              lsst::geom::Point2D(std::numeric_limits<double>::quiet_NaN())) const;
 
     /// Is this object persistable?
     virtual bool isPersistable() const noexcept override { return true; }
-    
+
     void write(lsst::afw::table::io::OutputArchiveHandle & handle) const;
 private:
-    lsst::afw::geom::Point2D _averagePosition;
+    lsst::geom::Point2D _averagePosition;
     // Here are the unpacked fields from the psfex psf struct
     struct poly *_poly;                 // Polynom describing the PSF variations
     float _pixstep;                     // Mask oversampling (pixel)
@@ -84,35 +84,35 @@ class PsfexPsf : public lsst::afw::table::io::PersistableFacade<PsfexPsf>,
 
     /// Compute an image of the Psf at the specified position/colour, at pixel position in the output image
     virtual PTR(lsst::afw::detection::Psf::Image) _doComputeImage(
-        lsst::afw::geom::Point2D const & position, ///< position within the chip
+        lsst::geom::Point2D const & position, ///< position within the chip
         lsst::afw::image::Color const& color,      ///< colour of object
-        lsst::afw::geom::Point2D const& center     ///< position of center of image in the output image
+        lsst::geom::Point2D const& center     ///< position of center of image in the output image
     ) const;
 
     /// Compute an image of the Psf at the specified position/colour, at pixel (0.0, 0.0) in the output image
     virtual PTR(lsst::afw::detection::Psf::Image) doComputeKernelImage(
-        lsst::afw::geom::Point2D const & position, ///< position within the chip
+        lsst::geom::Point2D const & position, ///< position within the chip
         lsst::afw::image::Color const& color       ///< colour of object
     ) const;
 
     /// Compute an image of the Psf at the specified position/colour, at pixel position in the output image
     virtual PTR(lsst::afw::detection::Psf::Image) doComputeImage(
-        lsst::afw::geom::Point2D const & position, ///< position within the chip
+        lsst::geom::Point2D const & position, ///< position within the chip
         lsst::afw::image::Color const& color       ///< colour of object
     ) const;
 
     /// Compute the bbox of the kernel image at the specified position/color
-    virtual lsst::afw::geom::Box2I doComputeBBox(
-        lsst::afw::geom::Point2D const & position,
+    virtual lsst::geom::Box2I doComputeBBox(
+        lsst::geom::Point2D const & position,
         lsst::afw::image::Color const & color
     ) const;
 
     /// Compute bbox of either image or kernel image, depending on provided center
     /// Does not depend on color, which is left out of parameter list to permit reuse
     /// by doComputeBBox, doCompute[Kernel]Image, and getKernel.
-    lsst::afw::geom::Box2I _doComputeBBox(
-        lsst::afw::geom::Point2D const & position, ///< position within the chip
-        lsst::afw::geom::Point2D const & center ///< center of output image. Use (0., 0.) for a kernel image
+    lsst::geom::Box2I _doComputeBBox(
+        lsst::geom::Point2D const & position, ///< position within the chip
+        lsst::geom::Point2D const & center ///< center of output image. Use (0., 0.) for a kernel image
     ) const;
 
     /// Name used in table persistence

include/lsst/meas/extensions/psfex/prefs.hh

@@ -87,7 +87,7 @@ public:
    int   getPhotfluxerrNum() const { return prefs.photfluxerr_num; }
    double getProfAccuracy() const { return prefs.prof_accuracy; }
    int   getVerboseType() const { return prefs.verbose_type; }
-   
+
    std::vector<std::string> const& getContextName() const { return _context_names; }
    std::vector<int> const& getContextGroup() const { return _context_groups; }
    std::vector<int> const& getGroupDeg() const { return _group_degs; }

include/lsst/meas/extensions/psfex/psf.hh

@@ -34,7 +34,7 @@ class Context {
     friend class Set;
 public:
     enum { KEEPHIDDEN=CONTEXT_KEEPHIDDEN, REMOVEHIDDEN=CONTEXT_REMOVEHIDDEN };
-        
+
     Context(std::vector<std::string> const& names, ///< names of fields to use
             std::vector<int> const& group,         ///< tags for each member of names
             std::vector<int> const& degree,        ///< polynomial degree for each group
@@ -77,7 +77,7 @@ public:
     ndarray::Array<float,2,2> getVigWeight() const;
     std::pair<double, double> getXY() const { return std::pair<double,double>(impl->x, impl->y); }
     float getNorm() const { return impl->norm; }
-    
+
 private:
     Sample(samplestruct *s, bool recentroid, int *vigsize) : impl(s), _recentroid(recentroid),
                                                              _fluxrad(0.0), _vigsize(vigsize) { }
@@ -89,7 +89,7 @@ private:
 };
 
 /************************************************************************************************************/
-    
+
 class Set {
     friend class Psf;
     friend void makeit(std::vector<std::shared_ptr<Field> > &fields,
@@ -163,7 +163,7 @@ public:
     Psf() : impl(0) {}
     explicit Psf(psfstruct *psf) : impl(psf) {}
     ~Psf();
-    
+
     ndarray::Array<float,2,2> getLoc() const;
     ndarray::Array<float,2,2> getResi() const;
 #if 0
@@ -179,7 +179,7 @@ public:
     void clip() {
 	psf_clip(impl);
     }
-    
+
 protected:
     psfstruct *impl;
 };

python/lsst/meas/extensions/psfex/field.cc

@@ -8,14 +8,14 @@
  * 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, 
+ *
+ * You should have received a copy of the LSST License Statement and
+ * the GNU General Public License along with this program.  If not,
  * see <https://www.lsstcorp.org/LegalNotices/>.
  */
 #include "pybind11/pybind11.h"

python/lsst/meas/extensions/psfex/prefs.cc

@@ -1,6 +1,6 @@
 /* 
  * LSST Data Management System
- * 
+ *
  * This product includes software developed by the
  * LSST Project (http://www.lsst.org/).
  * See the COPYRIGHT file
@@ -9,14 +9,14 @@
  * 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, 
+ *
+ * You should have received a copy of the LSST License Statement and
+ * the GNU General Public License along with this program.  If not,
  * see <https://www.lsstcorp.org/LegalNotices/>.
  */
 #include "pybind11/pybind11.h"

python/lsst/meas/extensions/psfex/psf.cc

@@ -1,6 +1,6 @@
 /* 
  * LSST Data Management System
- * 
+ *
  * This product includes software developed by the
  * LSST Project (http://www.lsst.org/).
  * See the COPYRIGHT file
@@ -9,14 +9,14 @@
  * 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, 
+ *
+ * You should have received a copy of the LSST License Statement and
+ * the GNU General Public License along with this program.  If not,
  * see <https://www.lsstcorp.org/LegalNotices/>.
  */
 #include "pybind11/pybind11.h"

python/lsst/meas/extensions/psfex/psfex.py

@@ -9,6 +9,7 @@
 except ImportError:
     plt = None
 
+import lsst.geom as geom
 import lsst.afw.geom as afwGeom
 from lsst.afw.fits import readMetadata
 import lsst.afw.image as afwImage
@@ -182,16 +183,17 @@ def read_samples(prefs, set, filename, frmin, frmax, ext, next, catindex, contex
 
                 n = prefs.getPhotfluxNum() - 1
                 if n:
-                    assert False, "Code to handle e.g. FLUX_APER(3) isn't yet converted"
-                    if key.naxis == 1 and n < key.naxisn[0]:
+                    raise RuntimeError("Code to handle e.g. FLUX_APER(3) isn't yet converted")
+                    if key.naxis == 1 and n < key.naxisn[0]:  # noqa: F821
                         flux += n
                     else:
                         print("Not enough apertures for %s in catalogue %s: using first aperture" %
                               (prefs.getPhotfluxRkey(), filename), file=sys.stderr)
 
                 n = prefs.getPhotfluxerrNum() - 1
                 if n:
-                    if key.naxis == 1 and n < key.naxisn[0]:
+                    raise RuntimeError("Code for getPhotfluxerrNum is broken")
+                    if key.naxis == 1 and n < key.naxisn[0]:  # noqa: F821
                         fluxerr += n
                     else:
                         print("Not enough apertures for %s in catalogue %s: using first aperture" %
@@ -238,7 +240,8 @@ def read_samples(prefs, set, filename, frmin, frmax, ext, next, catindex, contex
     # Insert the good candidates into the set
     #
     if not vignet.dtype.isnative:
-        # without the swap setVig fails with "ValueError: 'unaligned arrays cannot be converted to C++'"
+        # without the swap setVig fails with
+        # "ValueError: 'unaligned arrays cannot be converted to C++'"
         vignet = vignet.byteswap()
 
     for i in np.where(good)[0]:
@@ -395,7 +398,7 @@ class _LSST():
 
 
 def setDataType(t):
-    _dataType = _dataTypes[t]
+    _dataType = _dataTypes[t]  # noqa: F841
 
 
 def getFlags():
@@ -598,10 +601,10 @@ def showPsf(psf, set, ext=None, wcsData=None, trim=0, nspot=5,
             bbox = mos.getBBox(i)
             mosx = bbox.getMinX() + 0.5*(bbox.getWidth() - 1)
             mosy = bbox.getMinY() + 0.5*(bbox.getHeight() - 1)
-            pos.append([afwGeom.PointD(mosx, mosy), wcs.pixelToSky(afwGeom.PointD(x, y))])
+            pos.append([geom.PointD(mosx, mosy), wcs.pixelToSky(geom.PointD(x, y))])
     else:
-        pos.append([afwGeom.PointD(0, 0), wcs.pixelToSky(afwGeom.PointD(0, 0))])
-        pos.append([afwGeom.PointD(*mosaic.getDimensions()), wcs.pixelToSky(afwGeom.PointD(naxis1, naxis2))])
+        pos.append([geom.PointD(0, 0), wcs.pixelToSky(geom.PointD(0, 0))])
+        pos.append([geom.PointD(*mosaic.getDimensions()), wcs.pixelToSky(geom.PointD(naxis1, naxis2))])
 
     CD = []
     for i in range(2):
@@ -716,16 +719,17 @@ def makeitLsst(prefs, context, saveWcs=False, plot=dict()):
         wcss = []
         wcssList.append(wcss)
         with fits.open(cat):
-            # Hack: I want the WCS so I'll guess where the calexp is to be found
+            # Hack: I want the WCS so I'll guess where the calexp is to be
+            # found
             calexpFile = guessCalexp(cat)
             md = readMetadata(calexpFile)
             wcs = afwGeom.makeSkyWcs(md)
 
             if not wcs:
                 cdMatrix = np.array([1.0, 0.0, 0.0, 1.0])
                 cdMatrix.shape = (2, 2)
-                wcs = afwGeom.makeSkyWcs(crpix=afwGeom.PointD(0, 0),
-                                         crval=afwGeom.SpherePoint(0.0, 0.0, afwGeom.degrees),
+                wcs = afwGeom.makeSkyWcs(crpix=geom.PointD(0, 0),
+                                         crval=geom.SpherePoint(0.0, 0.0, geom.degrees),
                                          cdMatrix=cdMatrix)
 
             naxis1, naxis2 = md.getScalar("NAXIS1"), md.getScalar("NAXIS2")
@@ -851,7 +855,8 @@ def read_samplesLsst(prefs, set, filename, frmin, frmax, ext, next, catindex, co
     # Insert the good candidates into the set
     #
     if not vignet.dtype.isnative:
-        # without the swap setVig fails with "ValueError: 'unaligned arrays cannot be converted to C++'"
+        # without the swap setVig fails with
+        # "ValueError: 'unaligned arrays cannot be converted to C++'"
         vignet = vignet.byteswap()
 
     for i in np.where(good)[0]:
@@ -1006,8 +1011,8 @@ def load_samplesLsst(prefs, context, ext=psfexLib.Prefs.ALL_EXTENSIONS, next=1,
 
 
 def makeit(prefs, context, saveWcs=False, plot=dict()):
-    """This is the python wrapper for the original psfex that reads SExtractor outputs
-    """
+    """This is the python wrapper for the original psfex that reads SExtractor
+    outputs"""
     # Create an array of PSFs (one PSF for each extension)
     if prefs.getVerboseType() != prefs.QUIET:
         print("----- %d input catalogues:" % prefs.getNcat())

python/lsst/meas/extensions/psfex/psfexPsf.cc

@@ -1,6 +1,6 @@
-/* 
+/*
  * LSST Data Management System
- * 
+ *
  * This product includes software developed by the
  * LSST Project (http://www.lsst.org/).
  * See the COPYRIGHT file
@@ -9,14 +9,14 @@
  * 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, 
+ *
+ * You should have received a copy of the LSST License Statement and
+ * the GNU General Public License along with this program.  If not,
  * see <https://www.lsstcorp.org/LegalNotices/>.
  */
 #include "pybind11/pybind11.h"
@@ -58,13 +58,13 @@ PYBIND11_MODULE(psfexPsf, mod) {
 
     py::class_<PsfexPsf, std::shared_ptr<PsfexPsf>, lsst::afw::table::io::PersistableFacade<PsfexPsf>, lsst::meas::algorithms::ImagePsf> clsPsfexPsf(mod, "PsfexPsf");
 
-    clsPsfexPsf.def(py::init<lsst::meas::extensions::psfex::Psf const&, lsst::afw::geom::Point2D const &>(),
-            "psf"_a, "averagePosition"_a=lsst::afw::geom::Point2D());
+    clsPsfexPsf.def(py::init<lsst::meas::extensions::psfex::Psf const&, lsst::geom::Point2D const &>(),
+            "psf"_a, "averagePosition"_a=lsst::geom::Point2D());
 
     clsPsfexPsf.def("clone", &PsfexPsf::clone);
     clsPsfexPsf.def("getAveragePosition", &PsfexPsf::getAveragePosition);
     clsPsfexPsf.def("getKernel", &PsfexPsf::getKernel,
-            "position"_a=lsst::afw::geom::Point2D(std::numeric_limits<double>::quiet_NaN()));
+            "position"_a=lsst::geom::Point2D(std::numeric_limits<double>::quiet_NaN()));
     clsPsfexPsf.def("isPersistable", &PsfexPsf::isPersistable);
     clsPsfexPsf.def("write", &PsfexPsf::write);
 }