Merge pull request #72 from lsst/tickets/DM-9188

DM-9188: Cleanup pybind11 code in core meas and ip packages

python/lsst/meas/base/SConscript

@@ -20,4 +20,4 @@ scripts.BasicSConscript.pybind11(['algorithm',
                                   'sdssShape',
                                   'sincCoeffs',
                                   'shapeUtilities',
-                                  'transform',])
+                                  'transform',], addUnderscore=False)

python/lsst/meas/base/__init__.py

@@ -23,14 +23,38 @@
 """lsst..meas.base
 """
 from __future__ import absolute_import
+# Needed for pybind11-generated docstrings
+from lsst.afw.image import Calib, Wcs
+
+from .centroidUtilities import *
+from .fluxUtilities import *
+from .inputUtilities import *
+from .shapeUtilities import *
+from .algorithm import *
+from .apertureFlux import *
+from .blendedness import *
+from .circularApertureFlux import *
+from .exceptions import *
+from .flagHandler import *
+from .gaussianCentroid import *
+from .gaussianFlux import *
+from .naiveCentroid import *
+from .peakLikelihoodFlux import *
+from .pixelFlags import *
+from .psfFlux import *
+from .scaledApertureFlux import *
+from .sdssCentroid import *
+from .sdssShape import *
+from .sincCoeffs import *
+from .transform import *
+
 from .apCorrRegistry import *
 from .pluginRegistry import *
 from .baseMeasurement import *
 from .pluginsBase import *
 from .sfm import *
 from .plugins import *
 from .classification import *
-from .baseLib import *
 from .noiseReplacer import *
 from .baseMeasurement import *
 from .forcedMeasurement import *

python/lsst/meas/base/algorithm.cc

@@ -20,8 +20,7 @@
  * see <https://www.lsstcorp.org/LegalNotices/>.
  */
 
-#include <pybind11/pybind11.h>
-//#include <pybind11/stl.h>
+#include "pybind11/pybind11.h"
 
 #include "lsst/afw/image/Wcs.h"
 #include "lsst/afw/table/Source.h"
@@ -35,19 +34,13 @@ namespace lsst {
 namespace meas {
 namespace base {
 
-PYBIND11_PLUGIN(_algorithm) {
-    py::module mod("_algorithm", "Python wrapper for afw _algorithm library");
+PYBIND11_PLUGIN(algorithm) {
+    py::module mod("algorithm");
 
     /* Module level */
     py::class_<SingleFrameAlgorithm, std::shared_ptr<SingleFrameAlgorithm>> clsSingleFrameAlgorithm(mod, "SingleFrameAlgorithm");
     py::class_<SimpleAlgorithm, std::shared_ptr<SimpleAlgorithm>, SingleFrameAlgorithm> clsSimpleAlgorithm(mod, "SimpleAlgorithm");
 
-    /* Member types and enums */
-
-    /* Constructors */
-
-    /* Operators */
-
     /* Members */
     python::declareAlgorithm<SingleFrameAlgorithm>(clsSingleFrameAlgorithm);
 

python/lsst/meas/base/apertureFlux.cc

@@ -20,8 +20,8 @@
  * see <https://www.lsstcorp.org/LegalNotices/>.
  */
 
-#include <pybind11/pybind11.h>
-#include <pybind11/stl.h>
+#include "pybind11/pybind11.h"
+#include "pybind11/stl.h"
 
 #include "lsst/pex/config/python.h"
 #include "lsst/meas/base/python.h"
@@ -57,8 +57,8 @@ namespace {
     }
 }
 
-PYBIND11_PLUGIN(_apertureFlux) {
-    py::module mod("_apertureFlux", "Python wrapper for afw _apertureFlux library");
+PYBIND11_PLUGIN(apertureFlux) {
+    py::module mod("apertureFlux");
 
     /* Module level */
     py::class_<ApertureFluxAlgorithm, std::shared_ptr<ApertureFluxAlgorithm>, SimpleAlgorithm> clsApertureFluxAlgorithm(mod, "ApertureFluxAlgorithm");
@@ -67,6 +67,8 @@ PYBIND11_PLUGIN(_apertureFlux) {
     py::class_<ApertureFluxTransform> clsApertureFluxTransform(mod, "ApertureFluxTransform");
 
     /* Member types and enums */
+    clsApertureFluxAlgorithm.attr("Control") = clsApertureFluxControl;
+
     // ApertureFluxAlgorithm::Control wrapped in apertureFlux.py
     py::enum_<ApertureFluxAlgorithm::FlagBits>(clsApertureFluxAlgorithm, "FlagBits")
         .value("FAILURE", ApertureFluxAlgorithm::FlagBits::FAILURE)
@@ -75,10 +77,6 @@ PYBIND11_PLUGIN(_apertureFlux) {
         .value("N_FLAGS", ApertureFluxAlgorithm::FlagBits::N_FLAGS)
         .export_values();
 
-    /* Constructors */
-
-    /* Operators */
-
     /* Members */
     python::declareAlgorithm<ApertureFluxAlgorithm,
                              ApertureFluxControl,

python/lsst/meas/base/baseMeasurement.py

@@ -26,7 +26,7 @@
 import lsst.pex.config
 
 from .pluginRegistry import PluginMap
-from .baseLib import FatalAlgorithmError, MeasurementError
+from .exceptions import FatalAlgorithmError, MeasurementError
 from .pluginsBase import BasePluginConfig, BasePlugin
 from .noiseReplacer import NoiseReplacerConfig
 

python/lsst/meas/base/blendedness.cc

@@ -20,8 +20,7 @@
  * see <https://www.lsstcorp.org/LegalNotices/>.
  */
 
-#include <pybind11/pybind11.h>
-//#include <pybind11/stl.h>
+#include "pybind11/pybind11.h"
 
 #include "lsst/pex/config/python.h"
 #include "lsst/meas/base/python.h"
@@ -35,10 +34,8 @@ namespace lsst {
 namespace meas {
 namespace base {
 
-PYBIND11_PLUGIN(_blendedness) {
-    py::module mod("_blendedness", "Python wrapper for afw _blendedness library");
-
-    /* Module level */
+PYBIND11_PLUGIN(blendedness) {
+    py::module mod("blendedness");
 
     /* Member types and enums */
     py::class_<BlendednessAlgorithm, std::shared_ptr<BlendednessAlgorithm>, SimpleAlgorithm> clsBlendednessAlgorithm(mod, "BlendednessAlgorithm");
@@ -52,8 +49,6 @@ PYBIND11_PLUGIN(_blendedness) {
 
     clsBlendednessControl.def(py::init<>());
 
-    /* Operators */
-
     /* Members */
     python::declareAlgorithm<BlendednessAlgorithm, BlendednessControl>(
         clsBlendednessAlgorithm, clsBlendednessControl);

python/lsst/meas/base/catalogCalculation.py

@@ -8,7 +8,7 @@
 
 from .pluginsBase import BasePlugin, BasePluginConfig
 from .pluginRegistry import PluginRegistry, PluginMap
-from .baseLib import FatalAlgorithmError, MeasurementError
+from . import FatalAlgorithmError, MeasurementError
 
 # Exceptions that the measurement tasks should always propagate up to their callers
 FATAL_EXCEPTIONS = (MemoryError, FatalAlgorithmError)

python/lsst/meas/base/centroidUtilities.cc

@@ -20,12 +20,10 @@
  * see <https://www.lsstcorp.org/LegalNotices/>.
  */
 
-#include <pybind11/pybind11.h>
-//#include <pybind11/stl.h>
+#include "pybind11/pybind11.h"
 
 #include "numpy/arrayobject.h"
 #include "ndarray/pybind11.h"
-#include "ndarray/converter.h"
 
 #include "lsst/meas/base/CentroidUtilities.h"
 
@@ -36,8 +34,8 @@ namespace lsst {
 namespace meas {
 namespace base {
 
-PYBIND11_PLUGIN(_centroidUtilities) {
-    py::module mod("_centroidUtilities", "Python wrapper for afw _centroidUtilities library");
+PYBIND11_PLUGIN(centroidUtilities) {
+    py::module mod("centroidUtilities");
 
     if (_import_array() < 0) {
         PyErr_SetString(PyExc_ImportError, "numpy.core.multiarray failed to import");
@@ -49,8 +47,6 @@ PYBIND11_PLUGIN(_centroidUtilities) {
     py::class_<CentroidResult> clsCentroidResult(mod, "CentroidResult");
     py::class_<CentroidResultKey> clsCentroidResultKey(mod, "CentroidResultKey");
 
-    /* Member types and enums */
-
     /* Constructors */
     clsCentroidChecker.def(py::init<afw::table::Schema &,
                                     std::string const &,

python/lsst/meas/base/circularApertureFlux.cc

@@ -20,8 +20,7 @@
  * see <https://www.lsstcorp.org/LegalNotices/>.
  */
 
-#include <pybind11/pybind11.h>
-//#include <pybind11/stl.h>
+#include "pybind11/pybind11.h"
 
 #include "lsst/meas/base/CircularApertureFlux.h"
 
@@ -32,25 +31,19 @@ namespace lsst {
 namespace meas {
 namespace base {
 
-PYBIND11_PLUGIN(_circularApertureFlux) {
-    py::module mod("_circularApertureFlux", "Python wrapper for afw _circularApertureFlux library");
+PYBIND11_PLUGIN(circularApertureFlux) {
+    py::module mod("circularApertureFlux");
 
     /* Module level */
     py::class_<CircularApertureFluxAlgorithm, std::shared_ptr<CircularApertureFluxAlgorithm>, ApertureFluxAlgorithm> cls(mod, "CircularApertureFluxAlgorithm");
 
-    /* Member types and enums */
-
     /* Constructors */
     cls.def(py::init<CircularApertureFluxAlgorithm::Control const &,
                      std::string const &,
                      afw::table::Schema &,
                      daf::base::PropertySet &>(),
             "ctrl"_a, "name"_a, "schema"_a, "metadata"_a);
 
-    /* Operators */
-
-    /* Members */
-
     return mod.ptr();
 }
 

python/lsst/meas/base/exceptions.cc

@@ -20,8 +20,7 @@
  * see <https://www.lsstcorp.org/LegalNotices/>.
  */
 
-#include <pybind11/pybind11.h>
-//#include <pybind11/stl.h>
+#include "pybind11/pybind11.h"
 
 #include "lsst/meas/base/exceptions.h"
 #include "lsst/pex/exceptions/Runtime.h"
@@ -34,11 +33,12 @@ namespace lsst {
 namespace meas {
 namespace base {
 
-PYBIND11_PLUGIN(_exceptions) {
+PYBIND11_PLUGIN(exceptions) {
     using lsst::pex::exceptions::python::declareException;
     using lsst::pex::exceptions::DomainError;
     using lsst::pex::exceptions::RuntimeError;
-    py::module mod("_exceptions", "Python wrapper for afw _exceptions library");
+
+    py::module mod("exceptions");
 
     /* Module level */
     auto clsFatalAlgorithmError = declareException<FatalAlgorithmError, RuntimeError>(
@@ -48,15 +48,11 @@ PYBIND11_PLUGIN(_exceptions) {
     auto clsPixelValueError = declareException<PixelValueError, DomainError>(
         mod, "PixelValueError", "DomainError");
 
-    /* Member types and enums */
-
     /* Constructors */
     clsMeasurementError.def(py::init<std::string const &,
                                      std::size_t>(),
                             "message"_a, "flagBit"_a);
 
-    /* Operators */
-
     /* Members */
     clsMeasurementError.def("getFlagBit", &MeasurementError::getFlagBit);
 

python/lsst/meas/base/flagHandler.cc

@@ -20,8 +20,8 @@
  * see <https://www.lsstcorp.org/LegalNotices/>.
  */
 
-#include <pybind11/pybind11.h>
-#include <pybind11/stl.h>
+#include "pybind11/pybind11.h"
+#include "pybind11/stl.h"
 
 #include "lsst/meas/base/FlagHandler.h"
 
@@ -32,8 +32,8 @@ namespace lsst {
 namespace meas {
 namespace base {
 
-PYBIND11_PLUGIN(_flagHandler) {
-    py::module mod("_flagHandler", "Python wrapper for afw _flagHandler library");
+PYBIND11_PLUGIN(flagHandler) {
+    py::module mod("flagHandler");
 
     /* Module level */
     py::class_<FlagDefinition> clsFlagDefinition(mod, "FlagDefinition");
@@ -47,8 +47,6 @@ PYBIND11_PLUGIN(_flagHandler) {
     clsFlagDefinition.def(py::init<>());
     clsFlagDefinition.def(py::init<std::string, std::string>(), "_name"_a, "_doc"_a);
 
-    /* Operators */
-
     /* Members */
     clsFlagDefinition.def_readwrite("doc", &FlagDefinition::doc);
     clsFlagDefinition.def_readwrite("name", &FlagDefinition::name);