LSST Applications  21.0.0+04719a4bac,21.0.0-1-ga51b5d4+f5e6047307,21.0.0-11-g2b59f77+a9c1acf22d,21.0.0-11-ga42c5b2+86977b0b17,21.0.0-12-gf4ce030+76814010d2,21.0.0-13-g1721dae+760e7a6536,21.0.0-13-g3a573fe+768d78a30a,21.0.0-15-g5a7caf0+f21cbc5713,21.0.0-16-g0fb55c1+b60e2d390c,21.0.0-19-g4cded4ca+71a93a33c0,21.0.0-2-g103fe59+bb20972958,21.0.0-2-g45278ab+04719a4bac,21.0.0-2-g5242d73+3ad5d60fb1,21.0.0-2-g7f82c8f+8babb168e8,21.0.0-2-g8f08a60+06509c8b61,21.0.0-2-g8faa9b5+616205b9df,21.0.0-2-ga326454+8babb168e8,21.0.0-2-gde069b7+5e4aea9c2f,21.0.0-2-gecfae73+1d3a86e577,21.0.0-2-gfc62afb+3ad5d60fb1,21.0.0-25-g1d57be3cd+e73869a214,21.0.0-3-g357aad2+ed88757d29,21.0.0-3-g4a4ce7f+3ad5d60fb1,21.0.0-3-g4be5c26+3ad5d60fb1,21.0.0-3-g65f322c+e0b24896a3,21.0.0-3-g7d9da8d+616205b9df,21.0.0-3-ge02ed75+a9c1acf22d,21.0.0-4-g591bb35+a9c1acf22d,21.0.0-4-g65b4814+b60e2d390c,21.0.0-4-gccdca77+0de219a2bc,21.0.0-4-ge8a399c+6c55c39e83,21.0.0-5-gd00fb1e+05fce91b99,21.0.0-6-gc675373+3ad5d60fb1,21.0.0-64-g1122c245+4fb2b8f86e,21.0.0-7-g04766d7+cd19d05db2,21.0.0-7-gdf92d54+04719a4bac,21.0.0-8-g5674e7b+d1bd76f71f,master-gac4afde19b+a9c1acf22d,w.2021.13
LSST Data Management Base Package
LocalBackground.cc
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1 // -*- lsst-c++ -*-
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3  * LSST Data Management System
4  * Copyright 2008-2018 AURA/LSST.
5  *
6  * This product includes software developed by the
7  * LSST Project (http://www.lsst.org/).
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23 
24 #include <array>
25 #include <cmath>
26 
28 #include "lsst/afw/table/Source.h"
29 #include "lsst/log/Log.h"
30 #include "lsst/afw/geom/SpanSet.h"
31 #include "lsst/afw/detection/Psf.h"
33 
34 namespace lsst {
35 namespace meas {
36 namespace base {
37 namespace {
38 FlagDefinitionList flagDefinitions;
39 } // namespace
40 
41 FlagDefinition const LocalBackgroundAlgorithm::FAILURE = flagDefinitions.addFailureFlag();
42 FlagDefinition const LocalBackgroundAlgorithm::NO_GOOD_PIXELS =
43  flagDefinitions.add("flag_noGoodPixels", "no good pixels in the annulus");
44 FlagDefinition const LocalBackgroundAlgorithm::NO_PSF = flagDefinitions.add("flag_noPsf", "no PSF provided");
45 
47 
49  afw::table::Schema& schema, std::string const& logName)
50  : _ctrl(ctrl),
51  _resultKey(FluxResultKey::addFields(schema, name, "background in annulus around source")),
52  _flagHandler(FlagHandler::addFields(schema, name, getFlagDefinitions())),
53  _centroidExtractor(schema, name),
54  _stats(ctrl.bgRej, ctrl.bgIter) {
55  _logName = logName.size() ? logName : name;
56 }
57 
59  afw::image::Exposure<float> const& exposure) const {
60  geom::Point2D const center = _centroidExtractor(measRecord, _flagHandler);
63  afw::image::MaskPixel const badMask = mask.getPlaneBitMask(_ctrl.badMaskPlanes);
64 
65  // Define pixels in annulus
66  auto const psf = exposure.getPsf();
67  if (!psf) {
69  }
70  float const psfSigma = psf->computeShape().getDeterminantRadius();
71 
72  float const innerRadius = _ctrl.annulusInner * psfSigma;
73  afw::geom::ellipses::Axes const innerCircle{innerRadius, innerRadius};
74  auto const& inner = afw::geom::SpanSet::fromShape(afw::geom::ellipses::Ellipse(innerCircle, center));
75 
76  float const outerRadius = _ctrl.annulusOuter * psfSigma;
77  afw::geom::ellipses::Axes const outerCircle{outerRadius, outerRadius};
78  auto const& outer = afw::geom::SpanSet::fromShape(afw::geom::ellipses::Ellipse(outerCircle, center));
79 
80  auto const& annulus = outer->clippedTo(image.getBBox())->intersectNot(*inner);
81  auto const& imageValues = annulus->flatten(image.getImage()->getArray(), image.getXY0());
82  auto const& maskValues = annulus->flatten(image.getMask()->getArray(), image.getXY0());
83 
84  // Extract from ndarray::Array into std::vector because of limitations in afw::math::makeStatistics
85  std::vector<float> values;
86  values.reserve(imageValues.getNumElements());
87  assert(imageValues.getNumElements() == maskValues.getNumElements()); // constructed from the same spans
88  auto maskIter = maskValues.begin();
89  for (auto imageIter = imageValues.begin(); imageIter != imageValues.end(); ++imageIter, ++maskIter) {
90  if ((*maskIter & badMask) == 0) {
91  values.push_back(*imageIter);
92  }
93  }
94 
95  if (values.size() == 0) {
97  }
98 
99  // Measure the background
100  auto const stats = afw::math::makeStatistics(values, afw::math::MEANCLIP | afw::math::STDEVCLIP, _stats);
101  FluxResult const result(stats.getValue(afw::math::MEANCLIP), stats.getValue(afw::math::STDEVCLIP));
102  measRecord.set(_resultKey, result);
103 }
104 
106  _flagHandler.handleFailure(measRecord, error);
107 }
108 
114  if (flag == LocalBackgroundAlgorithm::FAILURE) continue;
115  if (mapper.getInputSchema().getNames().count(mapper.getInputSchema().join(name, flag.name)) == 0)
116  continue;
118  mapper.getInputSchema().find<afw::table::Flag>(name + "_" + flag.name).key;
119  mapper.addMapping(key);
120  }
121 }
122 
123 } // namespace base
124 } // namespace meas
125 } // namespace lsst
py::object result
Definition: _schema.cc:430
table::Key< std::string > name
Definition: Amplifier.cc:116
#define LSST_EXCEPT(type,...)
Create an exception with a given type.
Definition: Exception.h:48
afw::table::Key< afw::table::Array< MaskPixelT > > mask
LSST DM logging module built on log4cxx.
Key< U > key
Definition: Schema.cc:281
SchemaMapper * mapper
Definition: SchemaMapper.cc:78
table::Schema schema
Definition: python.h:134
static std::shared_ptr< geom::SpanSet > fromShape(int r, Stencil s=Stencil::CIRCLE, lsst::geom::Point2I offset=lsst::geom::Point2I())
Factory function for creating SpanSets from a Stencil.
Definition: SpanSet.cc:689
An ellipse core for the semimajor/semiminor axis and position angle parametrization (a,...
Definition: Axes.h:47
An ellipse defined by an arbitrary BaseCore and a center point.
Definition: Ellipse.h:51
MaskedImageT getMaskedImage()
Return the MaskedImage.
Definition: Exposure.h:228
std::shared_ptr< lsst::afw::detection::Psf const > getPsf() const
Return the Exposure's Psf object.
Definition: Exposure.h:327
Represent a 2-dimensional array of bitmask pixels.
Definition: Mask.h:77
A class to manipulate images, masks, and variance as a single object.
Definition: MaskedImage.h:73
void set(Key< T > const &key, U const &value)
Set value of a field for the given key.
Definition: BaseRecord.h:164
Defines the fields and offsets for a table.
Definition: Schema.h:50
A mapping between the keys of two Schemas, used to copy data between them.
Definition: SchemaMapper.h:21
Record class that contains measurements made on a single exposure.
Definition: Source.h:80
vector-type utility class to build a collection of FlagDefinitions
Definition: FlagHandler.h:60
std::size_t size() const
return the current size (number of defined elements) of the collection
Definition: FlagHandler.h:125
Utility class for handling flag fields that indicate the failure modes of an algorithm.
Definition: FlagHandler.h:148
void handleFailure(afw::table::BaseRecord &record, MeasurementError const *error=nullptr) const
Handle an expected or unexpected Exception thrown by a measurement algorithm.
Definition: FlagHandler.cc:76
A FunctorKey for FluxResult.
Definition: FluxUtilities.h:59
Base for instFlux measurement transformations.
LocalBackgroundAlgorithm(Control const &ctrl, std::string const &name, afw::table::Schema &schema, std::string const &logName="")
virtual void measure(afw::table::SourceRecord &measRecord, afw::image::Exposure< float > const &exposure) const
Called to measure a single child source in an image.
virtual void fail(afw::table::SourceRecord &measRecord, MeasurementError *error=nullptr) const
Handle an exception thrown by the current algorithm by setting flags in the given record.
static FlagDefinitionList const & getFlagDefinitions()
static FlagDefinition const NO_GOOD_PIXELS
Configuration of LocalBackgroundAlgorithm.
std::vector< std::string > badMaskPlanes
"Mask planes that indicate pixels that should be excluded from the measurement" ;
float annulusInner
"Inner radius for background annulus as a multiple of the PSF sigma" ;
float annulusOuter
"Outer radius for background annulus as a multiple of the PSF sigma" ;
LocalBackgroundTransform(Control const &ctrl, std::string const &name, afw::table::SchemaMapper &mapper)
Exception to be thrown when a measurement algorithm experiences a known failure mode.
Definition: exceptions.h:48
Backwards-compatibility support for depersisting the old Calib (FluxMag0/FluxMag0Err) objects.
Statistics makeStatistics(lsst::afw::image::Image< Pixel > const &img, lsst::afw::image::Mask< image::MaskPixel > const &msk, int const flags, StatisticsControl const &sctrl=StatisticsControl())
Handle a watered-down front-end to the constructor (no variance)
Definition: Statistics.h:354
@ STDEVCLIP
estimate sample N-sigma clipped stdev (N set in StatisticsControl, default=3)
Definition: Statistics.h:73
@ MEANCLIP
estimate sample N-sigma clipped mean (N set in StatisticsControl, default=3)
Definition: Statistics.h:72
A base class for image defects.
T push_back(T... args)
T reserve(T... args)
T size(T... args)
Simple class used to define and document flags The name and doc constitute the identity of the FlagDe...
Definition: FlagHandler.h:40
A reusable result struct for instFlux measurements.
Definition: FluxUtilities.h:41
Key< int > psf
Definition: Exposure.cc:65