Merge pull request #372 from lsst/tickets/DM-14864

DM-14864: Make afw pybind11 wrappers compatible with pybind11 2.2

examples/simpleStacker.cc

@@ -37,7 +37,6 @@ namespace math = lsst::afw::math;
 typedef image::Image<float> ImageF;
 typedef image::MaskedImage<float> MImageF;
 typedef std::vector<float> VecF;
-typedef std::shared_ptr<VecF> VecFPtr;
 
 int main(int argc, char **argv) {
     int const nImg = 10;
@@ -85,13 +84,13 @@ int main(int argc, char **argv) {
     std::cout << "MaskedImage (const weight): " << (*wmimgStack->getImage())(nX / 2, nY / 2) << std::endl;
 
     // std::vector, and also with a constant weight vector
-    std::vector<VecFPtr> vecList;
+    std::vector<VecF> vecList;
     for (int iImg = 0; iImg < nImg; ++iImg) {
-        VecFPtr v = VecFPtr(new VecF(nX * nY, iImg));
+        VecF v(nX * nY, iImg);
         vecList.push_back(v);
     }
-    VecFPtr vecStack = math::statisticsStack<float>(vecList, math::MEAN);
-    std::cout << "Vector:                     " << (*vecStack)[nX * nY / 2] << std::endl;
-    VecFPtr wvecStack = math::statisticsStack<float>(vecList, math::MEAN, sctrl, wvec);
-    std::cout << "Vector (const weight):      " << (*wvecStack)[nX * nY / 2] << std::endl;
+    VecF vecStack = math::statisticsStack<float>(vecList, math::MEAN);
+    std::cout << "Vector:                     " << (vecStack)[nX * nY / 2] << std::endl;
+    VecF wvecStack = math::statisticsStack<float>(vecList, math::MEAN, sctrl, wvec);
+    std::cout << "Vector (const weight):      " << (wvecStack)[nX * nY / 2] << std::endl;
 }

include/lsst/afw/math/Stack.h

@@ -158,8 +158,8 @@ void statisticsStack(lsst::afw::image::MaskedImage<PixelT>& out,  ///< Output im
  * A function to compute some statistics of a stack of std::vectors
  */
 template <typename PixelT>
-std::shared_ptr<std::vector<PixelT>> statisticsStack(
-        std::vector<std::shared_ptr<std::vector<PixelT>>>& vectors,  ///< Vectors to process
+std::vector<PixelT> statisticsStack(
+        std::vector<std::vector<PixelT>>& vectors,  ///< Vectors to process
         Property flags,                                              ///< statistics requested
         StatisticsControl const& sctrl = StatisticsControl(),        ///< control structure
         std::vector<lsst::afw::image::VariancePixel> const& wvector =

python/lsst/afw/cameraGeom/SConscript

@@ -1,17 +1,7 @@
 ## -*- python -*-
 from lsst.sconsUtils import scripts
 scripts.BasicSConscript.pybind11(['cameraSys',
-                                  'detector',
+                                  'detector/detector',
                                   'orientation',
-                                  'transformMap'])
-
-#from lsst.sconsUtils import env, targets
-#
-## We can't use BasicSConscript here because the circular dependency requires the -D option in SWIGFLAGS
-#targets["python"].extend(
-#    env.SwigLoadableModule(
-#        "_cameraGeomLib", ["cameraGeomLib.i"],
-#        SWIGFLAGS=(env["SWIGFLAGS"] + ["-DIMPORT_IMAGE_I"]),
-#        LIBS=env.getLibs("main python")
-#    )
-#)
+                                  'transformMap'],
+                                 addUnderscore=False)

python/lsst/afw/cameraGeom/cameraGeomLib.py

@@ -1,5 +1,5 @@
 from lsst.afw.geom import Point2D
-from ._cameraSys import *
+from .cameraSys import *
 from .detector import *
-from ._orientation import *
-from ._transformMap import *
+from .orientation import *
+from .transformMap import *

python/lsst/afw/cameraGeom/cameraSys.cc

@@ -59,8 +59,8 @@ void declareCommonSysMethods(PyClass &cls) {
 }
 }
 
-PYBIND11_PLUGIN(_cameraSys) {
-    py::module mod("_cameraSys", "Python wrapper for afw _cameraSys library");
+PYBIND11_PLUGIN(cameraSys) {
+    py::module mod("cameraSys");
 
     /* Module level */
     py::class_<CameraSysPrefix> clsCameraSysPrefix(mod, "CameraSysPrefix");

python/lsst/afw/cameraGeom/detector/__init__.py

@@ -0,0 +1,2 @@
+from .detector import *
+from .detectorContinued import *

python/lsst/afw/cameraGeom/detector.cc → python/lsst/afw/cameraGeom/detector/detector.cc

@@ -74,8 +74,8 @@ void declare2SysMethods(PyClass &cls) {
             "points"_a, "fromSys"_a, "toSys"_a);
 }
 
-PYBIND11_PLUGIN(_detector) {
-    py::module mod("_detector", "Python wrapper for afw _detector library");
+PYBIND11_PLUGIN(detector) {
+    py::module mod("detector");
 
     /* Module level */
     py::class_<Detector, std::shared_ptr<Detector>> cls(mod, "Detector");

python/lsst/afw/cameraGeom/detector.py → python/lsst/afw/cameraGeom/detector/detectorContinued.py

@@ -20,11 +20,12 @@
 # see <http://www.lsstcorp.org/LegalNotices/>.
 #
 
-from ._detector import Detector, DetectorType
-
 __all__ = ["Detector", "DetectorType",
            "SCIENCE", "FOCUS", "GUIDER", "WAVEFRONT"]
 
+from lsst.utils import continueClass
+from .detector import Detector, DetectorType
+
 # export DetectorType enums as module globals for SWIG compatibility;
 # @TODO update our code to stop using these globals and remove this code
 SCIENCE = DetectorType.SCIENCE
@@ -33,8 +34,7 @@
 WAVEFRONT = DetectorType.WAVEFRONT
 
 
-def __iter__(self):
-    return (self[i] for i in range(len(self)))
-
-
-Detector.__iter__ = __iter__
+@continueClass  # noqa F811
+class Detector:
+    def __iter__(self):
+        return (self[i] for i in range(len(self)))

python/lsst/afw/cameraGeom/orientation.cc

@@ -33,8 +33,10 @@ namespace lsst {
 namespace afw {
 namespace cameraGeom {
 
-PYBIND11_PLUGIN(_orientation) {
-    py::module mod("_orientation", "Python wrapper for afw _orientation library");
+PYBIND11_PLUGIN(orientation) {
+    py::module mod("orientation");
+
+    py::module::import("lsst.geom");
 
     /* Module level */
     py::class_<Orientation> cls(mod, "Orientation");

python/lsst/afw/cameraGeom/transformMap.cc

@@ -35,8 +35,8 @@ namespace lsst {
 namespace afw {
 namespace cameraGeom {
 
-PYBIND11_PLUGIN(_transformMap) {
-    py::module mod("_transformMap");
+PYBIND11_PLUGIN(transformMap) {
+    py::module mod("transformMap");
 
     /* Module level */
     py::class_<TransformMap, std::shared_ptr<TransformMap>> cls(mod, "TransformMap");

python/lsst/afw/coord/SConscript

@@ -1,4 +1,5 @@
 ## -*- python -*-
 from lsst.sconsUtils import scripts
 scripts.BasicSConscript.pybind11(['observatory',
-                                  'weather'])
+                                  'weather'],
+                                 addUnderscore=False)

python/lsst/afw/coord/__init__.py

@@ -21,5 +21,5 @@
 #
 import lsst.afw.geom
 
-from ._observatory import *
-from ._weather import *
+from .observatory import *
+from .weather import *

python/lsst/afw/coord/observatory.cc

@@ -31,8 +31,8 @@ namespace lsst {
 namespace afw {
 namespace coord {
 
-PYBIND11_PLUGIN(_observatory) {
-    py::module mod("_observatory", "Python wrapper for afw _observatory library");
+PYBIND11_PLUGIN(observatory) {
+    py::module mod("observatory");
 
     py::class_<Observatory, std::shared_ptr<Observatory>> cls(mod, "Observatory");
 

python/lsst/afw/coord/weather.cc

@@ -35,8 +35,8 @@ namespace lsst {
 namespace afw {
 namespace coord {
 
-PYBIND11_PLUGIN(_weather) {
-    py::module mod("_weather", "Python wrapper for afw _weather library");
+PYBIND11_PLUGIN(weather) {
+    py::module mod("weather");
 
     py::class_<lsst::afw::coord::Weather> cls(mod, "Weather");
 

python/lsst/afw/detection/SConscript

@@ -4,8 +4,9 @@ scripts.BasicSConscript.pybind11(['psf',
                                   'footprint',
                                   'footprintSet',
                                   'threshold',
-                                  'peak',
+                                  'peak/peak',
                                   'footprintCtrl',
                                   'gaussianPsf',
-                                  'footprintMerge',
-                                  'heavyFootprint'])
+                                  'footprintMerge/footprintMerge',
+                                  'heavyFootprint'],
+                                 addUnderscore=False)

python/lsst/afw/detection/detectionLib.py

@@ -3,15 +3,14 @@
 import lsst.afw.image
 from lsst.afw.geom import Span
 
-from ._psf import *
-from ._footprint import *
-from ._footprintSet import *
-from ._threshold import *
-from ._peak import *
+from .psf import *
+from .footprint import *
+from .footprintSet import *
+from .threshold import *
 from .peak import *
-from ._footprintCtrl import *
-from ._gaussianPsf import *
-from ._footprintMerge import *
+from .peak import *
+from .footprintCtrl import *
+from .gaussianPsf import *
+from .footprintMerge import *
 from .footprintMerge import *
-from ._heavyFootprint import *
-from ._footprint import *
+from .heavyFootprint import *

python/lsst/afw/detection/footprint.cc

@@ -66,8 +66,8 @@ void declareMaskFromFootprintList(py::module &mod) {
 
 }  // end anonymous namespace
 
-PYBIND11_PLUGIN(_footprint) {
-    py::module mod("_footprint", "Python wrapper for afw Footprint library");
+PYBIND11_PLUGIN(footprint) {
+    py::module mod("footprint");
 
     /* Footprint Constructors */
     py::class_<Footprint, std::shared_ptr<Footprint>, daf::base::Citizen> clsFootprint(mod, "Footprint");

python/lsst/afw/detection/footprintCtrl.cc

@@ -34,8 +34,8 @@ namespace lsst {
 namespace afw {
 namespace detection {
 
-PYBIND11_PLUGIN(_footprintCtrl) {
-    py::module mod("_footprintCtrl", "Python wrapper for afw _footprintCtrl library");
+PYBIND11_PLUGIN(footprintCtrl) {
+    py::module mod("footprintCtrl");
 
     py::class_<FootprintControl> clsFootprintControl(mod, "FootprintControl");
 

python/lsst/afw/detection/footprintMerge/__init__.py

@@ -0,0 +1,2 @@
+from .footprintMerge import *
+from .footprintMergeContinued import *

python/lsst/afw/detection/footprintMerge.cc → python/lsst/afw/detection/footprintMerge/footprintMerge.cc

@@ -33,8 +33,8 @@ namespace lsst {
 namespace afw {
 namespace detection {
 
-PYBIND11_PLUGIN(_footprintMerge) {
-    py::module mod("_footprintMerge", "Python wrapper for afw _footprintMerge library");
+PYBIND11_PLUGIN(footprintMerge) {
+    py::module mod("footprintMerge");
 
     py::class_<FootprintMergeList> clsFootprintMergeList(mod, "FootprintMergeList");
 

python/lsst/afw/detection/footprintMerge/footprintMergeContinued.py

@@ -0,0 +1,45 @@
+__all__ = []  # only imported for side effects
+
+from lsst.utils import continueClass
+from .footprintMerge import FootprintMergeList
+
+
+@continueClass  # noqa F811
+class FootprintMergeList:
+    def getMergedSourceCatalog(self, catalogs, filters,
+                               peakDist, schema, idFactory, samePeakDist):
+        """Add multiple catalogs and get the SourceCatalog with merged Footprints"""
+        import lsst.afw.table as afwTable
+
+        table = afwTable.SourceTable.make(schema, idFactory)
+        mergedList = afwTable.SourceCatalog(table)
+
+        # if peak is not an array, create an array the size of catalogs
+        try:
+            len(samePeakDist)
+        except TypeError:
+            samePeakDist = [samePeakDist] * len(catalogs)
+
+        try:
+            len(peakDist)
+        except TypeError:
+            peakDist = [peakDist] * len(catalogs)
+
+        if len(peakDist) != len(catalogs):
+            raise ValueError("Number of catalogs (%d) does not match length of peakDist (%d)"
+                             % (len(catalogs), len(peakDist)))
+
+        if len(samePeakDist) != len(catalogs):
+            raise ValueError("Number of catalogs (%d) does not match length of samePeakDist (%d)"
+                             % (len(catalogs), len(samePeakDist)))
+
+        if len(filters) != len(catalogs):
+            raise ValueError("Number of catalogs (%d) does not match number of filters (%d)"
+                             % (len(catalogs), len(filters)))
+
+        self.clearCatalog()
+        for cat, filter, dist, sameDist in zip(catalogs, filters, peakDist, samePeakDist):
+            self.addCatalog(table, cat, filter, dist, True, sameDist)
+
+        self.getFinalSources(mergedList)
+        return mergedList

python/lsst/afw/detection/footprintSet.cc

@@ -34,6 +34,7 @@ namespace afw {
 namespace detection {
 
 namespace {
+
 template <typename PixelT, typename PyClass>
 void declareMakeHeavy(PyClass &cls) {
     //    cls.def("makeHeavy", [](FootprintSet & self, image::MaskedImage<PixelT, image::MaskPixel> const&
@@ -76,8 +77,10 @@ void declareTemplatedMembers(PyClass &cls) {
 }
 }  // namespace
 
-PYBIND11_PLUGIN(_footprintSet) {
-    py::module mod("_footprintSet", "Python wrapper for afw _footprintSet library");
+PYBIND11_PLUGIN(footprintSet) {
+    py::module mod("footprintSet");
+
+    py::module::import("lsst.afw.detection.footprint");
 
     py::class_<FootprintSet, std::shared_ptr<FootprintSet>, lsst::daf::base::Citizen> clsFootprintSet(
             mod, "FootprintSet");
@@ -100,22 +103,11 @@ PYBIND11_PLUGIN(_footprintSet) {
                         "footprints2"_a, "includePeaks"_a);
 
     clsFootprintSet.def("swap", &FootprintSet::swap);
-    //    clsFootprintSet.def("swapFootprintList", &FootprintSet::swapFootprintList);
-    // The pybind11 wrapped getFootprints dereferences the shared pointer to the std::vector of Footprints
-    // held by the FootprintSet when returning to python to work around an STL caster issue. However this
-    // creates a problem for the setter that now expects a shared pointer, making the setter unable to
-    // operate on the output from the getter. Below defines two overrides for the setter function, one
-    // that can handle a shared pointer (in case somewhere else in the stack has one somehow) and one
-    // that will accept a standard vector of Footprints, which will be internally placed in a shared
-    // pointer to match the underlying C++ function signature
-    clsFootprintSet.def("setFootprints",
-                            [](FootprintSet &self, std::shared_ptr<FootprintSet::FootprintList> footListPtr) {
-                                self.setFootprints(footListPtr);
-                            });
+    // setFootprints takes shared_ptr<FootprintList> and getFootprints returns it,
+    // but pybind11 can't handle that type, so use a custom getter and setter
     clsFootprintSet.def("setFootprints", [](FootprintSet &self, FootprintSet::FootprintList footList) {
-        self.setFootprints(std::make_shared<FootprintSet::FootprintList>(footList));
+        self.setFootprints(std::make_shared<FootprintSet::FootprintList>(std::move(footList)));
     });
-    // getFootprints returns shared_ptr<FootprintList>, but stl caster can't handle this
     clsFootprintSet.def("getFootprints", [](FootprintSet &self) { return *(self.getFootprints()); });
     clsFootprintSet.def("makeSources", &FootprintSet::makeSources);
     clsFootprintSet.def("setRegion", &FootprintSet::setRegion);