LSSTApplications  19.0.0-14-gb0260a2+72efe9b372,20.0.0+7927753e06,20.0.0+8829bf0056,20.0.0+995114c5d2,20.0.0+b6f4b2abd1,20.0.0+bddc4f4cbe,20.0.0-1-g253301a+8829bf0056,20.0.0-1-g2b7511a+0d71a2d77f,20.0.0-1-g5b95a8c+7461dd0434,20.0.0-12-g321c96ea+23efe4bbff,20.0.0-16-gfab17e72e+fdf35455f6,20.0.0-2-g0070d88+ba3ffc8f0b,20.0.0-2-g4dae9ad+ee58a624b3,20.0.0-2-g61b8584+5d3db074ba,20.0.0-2-gb780d76+d529cf1a41,20.0.0-2-ged6426c+226a441f5f,20.0.0-2-gf072044+8829bf0056,20.0.0-2-gf1f7952+ee58a624b3,20.0.0-20-geae50cf+e37fec0aee,20.0.0-25-g3dcad98+544a109665,20.0.0-25-g5eafb0f+ee58a624b3,20.0.0-27-g64178ef+f1f297b00a,20.0.0-3-g4cc78c6+e0676b0dc8,20.0.0-3-g8f21e14+4fd2c12c9a,20.0.0-3-gbd60e8c+187b78b4b8,20.0.0-3-gbecbe05+48431fa087,20.0.0-38-ge4adf513+a12e1f8e37,20.0.0-4-g97dc21a+544a109665,20.0.0-4-gb4befbc+087873070b,20.0.0-4-gf910f65+5d3db074ba,20.0.0-5-gdfe0fee+199202a608,20.0.0-5-gfbfe500+d529cf1a41,20.0.0-6-g64f541c+d529cf1a41,20.0.0-6-g9a5b7a1+a1cd37312e,20.0.0-68-ga3f3dda+5fca18c6a4,20.0.0-9-g4aef684+e18322736b,w.2020.45
LSSTDataManagementBasePackage
LocalBackground.cc
Go to the documentation of this file.
1 // -*- lsst-c++ -*-
2 /*
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/).
8  *
9  * This program is free software: you can redistribute it and/or modify
10  * it under the terms of the GNU General Public License as published by
11  * the Free Software Foundation, either version 3 of the License, or
12  * (at your option) any later version.
13  *
14  * This program is distributed in the hope that it will be useful,
15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17  * GNU General Public License for more details.
18  *
19  * You should have received a copy of the LSST License Statement and
20  * the GNU General Public License along with this program. If not,
21  * see <http://www.lsstcorp.org/LegalNotices/>.
22  */
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
schema
table::Schema schema
Definition: Amplifier.cc:115
lsst::afw::image
Backwards-compatibility support for depersisting the old Calib (FluxMag0/FluxMag0Err) objects.
Definition: imageAlgorithm.dox:1
lsst::afw::image::Exposure::getPsf
std::shared_ptr< lsst::afw::detection::Psf const > getPsf() const
Return the Exposure's Psf object.
Definition: Exposure.h:307
lsst::meas::base::FlagDefinition::number
std::size_t number
Definition: FlagHandler.h:54
lsst::meas::base::LocalBackgroundAlgorithm::NO_GOOD_PIXELS
static FlagDefinition const NO_GOOD_PIXELS
Definition: LocalBackground.h:69
std::string
STL class.
lsst::afw::image::Mask
Represent a 2-dimensional array of bitmask pixels.
Definition: Mask.h:77
Psf.h
lsst::meas::base::FluxResult
A reusable result struct for instFlux measurements.
Definition: FluxUtilities.h:41
lsst::log.log.logContinued.error
def error(fmt, *args)
Definition: logContinued.py:213
lsst::meas::base::LocalBackgroundAlgorithm::measure
virtual void measure(afw::table::SourceRecord &measRecord, afw::image::Exposure< float > const &exposure) const
Called to measure a single child source in an image.
Definition: LocalBackground.cc:58
lsst::meas::base::FlagHandler::handleFailure
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
lsst::afw::table::SourceRecord
Record class that contains measurements made on a single exposure.
Definition: Source.h:80
lsst::afw::image::Exposure< float >
lsst::meas::base::LocalBackgroundTransform::LocalBackgroundTransform
LocalBackgroundTransform(Control const &ctrl, std::string const &name, afw::table::SchemaMapper &mapper)
Definition: LocalBackground.cc:109
std::vector::reserve
T reserve(T... args)
lsst::meas::base::LocalBackgroundControl::badMaskPlanes
std::vector< std::string > badMaskPlanes
"Mask planes that indicate pixels that should be excluded from the measurement" ;
Definition: LocalBackground.h:43
std::vector< float >
std::string::size
T size(T... args)
psf
Key< int > psf
Definition: Exposure.cc:65
lsst::meas::base::LocalBackgroundAlgorithm::LocalBackgroundAlgorithm
LocalBackgroundAlgorithm(Control const &ctrl, std::string const &name, afw::table::Schema &schema, std::string const &logName="")
Definition: LocalBackground.cc:48
lsst::meas::base::FlagDefinition::doc
std::string doc
Definition: FlagHandler.h:53
lsst::meas::base::LocalBackgroundAlgorithm::getFlagDefinitions
static FlagDefinitionList const & getFlagDefinitions()
Definition: LocalBackground.cc:46
lsst::meas::base::MeasurementError
Exception to be thrown when a measurement algorithm experiences a known failure mode.
Definition: exceptions.h:48
lsst::meas::base::LocalBackgroundAlgorithm::FAILURE
static FlagDefinition const FAILURE
Definition: LocalBackground.h:68
lsst::afw::table::Schema
Defines the fields and offsets for a table.
Definition: Schema.h:50
LocalBackground.h
lsst::afw::geom::ellipses::Axes
An ellipse core for the semimajor/semiminor axis and position angle parametrization (a,...
Definition: Axes.h:47
lsst::afw::geom.transform.transformContinued.name
string name
Definition: transformContinued.py:32
mask
afw::table::Key< afw::table::Array< MaskPixelT > > mask
Definition: HeavyFootprint.cc:217
lsst::meas::base::FlagDefinition::name
std::string name
Definition: FlagHandler.h:52
lsst::meas::base::FluxResultKey
A FunctorKey for FluxResult.
Definition: FluxUtilities.h:59
lsst::afw::image::Exposure::getMaskedImage
MaskedImageT getMaskedImage()
Return the MaskedImage.
Definition: Exposure.h:228
lsst::meas::base::FlagDefinitionList
vector-type utility class to build a collection of FlagDefinitions
Definition: FlagHandler.h:60
std::vector::push_back
T push_back(T... args)
lsst::afw::math::makeStatistics
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
lsst::afw::math::MEANCLIP
@ MEANCLIP
estimate sample N-sigma clipped mean (N set in StatisticsControl, default=3)
Definition: Statistics.h:72
lsst::afw::image::MaskedImage
A class to manipulate images, masks, and variance as a single object.
Definition: MaskedImage.h:73
lsst::afw::math::STDEVCLIP
@ STDEVCLIP
estimate sample N-sigma clipped stdev (N set in StatisticsControl, default=3)
Definition: Statistics.h:73
lsst::meas::base::FlagHandler
Utility class for handling flag fields that indicate the failure modes of an algorithm.
Definition: FlagHandler.h:148
lsst::afw::table::SchemaMapper
A mapping between the keys of two Schemas, used to copy data between them.
Definition: SchemaMapper.h:21
lsst::afw::table::Key< afw::table::Flag >
lsst::meas::base::FluxTransform
Base for instFlux measurement transformations.
Definition: FluxUtilities.h:187
std::int32_t
result
py::object result
Definition: _schema.cc:429
Source.h
lsst
A base class for image defects.
Definition: imageAlgorithm.dox:1
SpanSet.h
LSST_EXCEPT
#define LSST_EXCEPT(type,...)
Create an exception with a given type.
Definition: Exception.h:48
lsst::afw::geom::ellipses::Ellipse
An ellipse defined by an arbitrary BaseCore and a center point.
Definition: Ellipse.h:51
lsst::meas::base::FlagDefinitionList::size
std::size_t size() const
return the current size (number of defined elements) of the collection
Definition: FlagHandler.h:125
lsst::meas::base::FlagDefinition
Simple class used to define and document flags The name and doc constitute the identity of the FlagDe...
Definition: FlagHandler.h:40
lsst::afw::geom::SpanSet::fromShape
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
lsst::meas::base::BaseAlgorithm::_logName
std::string _logName
Definition: Algorithm.h:69
Statistics.h
key
Key< U > key
Definition: Schema.cc:281
lsst::geom::Point< double, 2 >
lsst::meas::base::LocalBackgroundAlgorithm::NO_PSF
static FlagDefinition const NO_PSF
Definition: LocalBackground.h:70
mapper
SchemaMapper * mapper
Definition: SchemaMapper.cc:78
lsst::meas::base::LocalBackgroundControl
Configuration of LocalBackgroundAlgorithm.
Definition: LocalBackground.h:40
std::size_t
lsst::afw::table::BaseRecord::set
void set(Key< T > const &key, U const &value)
Set value of a field for the given key.
Definition: BaseRecord.h:164
lsst::meas::base::LocalBackgroundControl::annulusOuter
float annulusOuter
"Outer radius for background annulus as a multiple of the PSF sigma" ;
Definition: LocalBackground.h:47
lsst::meas::base::LocalBackgroundAlgorithm::fail
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.
Definition: LocalBackground.cc:105
lsst::meas::base::LocalBackgroundControl::annulusInner
float annulusInner
"Inner radius for background annulus as a multiple of the PSF sigma" ;
Definition: LocalBackground.h:45
Log.h
LSST DM logging module built on log4cxx.