lsst.meas.base 22.0.1-27-gd28f579+a595c17f73
applyApCorr.py
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21
22import math
23
24import numpy as np
25
26import lsst.pex.config
28import lsst.afw.image
29import lsst.pipe.base
30from .apCorrRegistry import getApCorrNameSet
31
32# If True then scale instFlux error by apCorr; if False then use a more complex computation
33# that over-estimates instFlux error (often grossly so) because it double-counts photon noise.
34# This flag is intended to be temporary until we figure out a better way to compute
35# the effects of aperture correction on instFlux uncertainty
36UseNaiveFluxErr = True
37
38__all__ = ("ApplyApCorrConfig", "ApplyApCorrTask")
39
40
42 """Catalog field names and keys needed to aperture correct a particular
43 instrument flux.
44
45 Parameters
46 ----------
47 schema : `lsst.afw.table`
48 Source catalog schema. Three fields are used to generate keys:
49 - ``{name}_instFlux``
50 - ``{name}_instFluxErr``
51 - ``{name}_flag``
52 Three fields are added:
53 - ``{name}_apCorr`` (only if not already added by proxy)
54 - ``{name}_apCorrErr`` (only if not already added by proxy)
55 - ``{name}_flag_apCorr``
56 model : `str`
57 Field name prefix for instFlux with aperture correction model, e.g.
58 "base_PsfFlux"
59 name : `str`
60 Field name prefix for instFlux needing aperture correction; may be
61 `None` if it is the same as ``model``
62
63 Notes
64 -----
65 The aperture correction can be derived from the meaasurements in the
66 column being aperture-corrected or from measurements in a different
67 column (a "proxy"). In the first case, we will add columns to contain
68 the aperture correction values; in the second case (using a proxy),
69 we will add an alias to the proxy's aperture correction values. In
70 all cases, we add a flag.
71 """
72
73 name = None
74 """Field name prefix for flux needing aperture correction (`str`).
75 """
76
77 modelName = None
78 """Field name for aperture correction model for flux (`str`).
79 """
80
81 modelSigmaName = None
82 """Field name for aperture correction model for fluxErr (`str`).
83 """
84
85 doApCorrColumn = None
86 """Should we write the aperture correction values (`bool`)?
87
88 They should not be written if they're already being written by a proxy.
89 """
90
91 instFluxName = None
92 """Name of ``instFlux`` field (`str`).
93 """
94
95 instFluxErrName = None
96 """Name of ``instFlux`` sigma field (`str`).
97 """
98
99 instFluxKey = None
100 """Key to ``instFlux`` field (`lsst.afw.table.schema.Key`).
101 """
102
103 instFluxErrKey = None
104 """Key to ``instFlux`` sigma field (`lsst.afw.table.schema.Key`).
105 """
106
107 fluxFlagKey = None
108 """Key to the flux flag field (`lsst.afw.table.schema.Key`).
109 """
110
111 apCorrKey = None
112 """Key to new aperture correction field (`lsst.afw.table.schema.Key`).
113 """
114
115 apCorrErrKey = None
116 """Key to new aperture correction sigma field (`lsst.afw.table.schema.Key`).
117 """
118
119 apCorrFlagKey = None
120 """Key to new aperture correction flag field (`lsst.afw.table.schema.Key`).
121 """
122
123 def __init__(self, schema, model, name=None):
124 if name is None:
125 name = model
126 self.namename = name
127 self.modelNamemodelName = model + "_instFlux"
128 self.modelSigmaNamemodelSigmaName = model + "_instFluxErr"
129 self.instFluxNameinstFluxName = name + "_instFlux"
130 self.instFluxErrNameinstFluxErrName = name + "_instFluxErr"
131 self.instFluxKeyinstFluxKey = schema.find(self.instFluxNameinstFluxName).key
132 self.instFluxErrKeyinstFluxErrKey = schema.find(self.instFluxErrNameinstFluxErrName).key
133 self.fluxFlagKeyfluxFlagKey = schema.find(name + "_flag").key
134
135 # No need to write the same aperture corrections multiple times
136 self.doApCorrColumndoApCorrColumn = (name == model or model + "_apCorr" not in schema)
137 if self.doApCorrColumndoApCorrColumn:
138 self.apCorrKeyapCorrKey = schema.addField(
139 name + "_apCorr",
140 doc="aperture correction applied to %s" % (name,),
141 type=np.float64,
142 )
143 self.apCorrErrKeyapCorrErrKey = schema.addField(
144 name + "_apCorrErr",
145 doc="standard deviation of aperture correction applied to %s" % (name,),
146 type=np.float64,
147 )
148 else:
149 aliases = schema.getAliasMap()
150 aliases.set(name + "_apCorr", model + "_apCorr")
151 aliases.set(name + "_apCorrErr", model + "_apCorrErr")
152 self.apCorrKeyapCorrKey = schema.find(name + "_apCorr").key
153 self.apCorrErrKeyapCorrErrKey = schema.find(name + "_apCorrErr").key
154
155 self.apCorrFlagKeyapCorrFlagKey = schema.addField(
156 name + "_flag_apCorr",
157 doc="set if unable to aperture correct %s" % (name,),
158 type="Flag",
159 )
160
161
162class ApplyApCorrConfig(lsst.pex.config.Config):
163 """Aperture correction configuration.
164 """
165
166 ignoreList = lsst.pex.config.ListField(
167 doc="flux measurement algorithms in getApCorrNameSet() to ignore; "
168 "if a name is listed that does not appear in getApCorrNameSet() then a warning is logged",
169 dtype=str,
170 optional=False,
171 default=(),
172 )
173 doFlagApCorrFailures = lsst.pex.config.Field(
174 doc="set the general failure flag for a flux when it cannot be aperture-corrected?",
175 dtype=bool,
176 default=True,
177 )
178 proxies = lsst.pex.config.DictField(
179 doc="flux measurement algorithms to be aperture-corrected by reference to another algorithm; "
180 "this is a mapping alg1:alg2, where 'alg1' is the algorithm being corrected, and 'alg2' "
181 "is the algorithm supplying the corrections",
182 keytype=str,
183 itemtype=str,
184 default={},
185 )
186
187
188class ApplyApCorrTask(lsst.pipe.base.Task):
189 """Apply aperture corrections.
190
191 Parameters
192 ----------
193 schema : `lsst.afw.table.Schema`
194 """
195 ConfigClass = ApplyApCorrConfig
196 _DefaultName = "applyApCorr"
197
198 def __init__(self, schema, **kwds):
199 lsst.pipe.base.Task.__init__(self, **kwds)
200
201 self.apCorrInfoDictapCorrInfoDict = dict()
202 apCorrNameSet = getApCorrNameSet()
203 ignoreSet = set(self.config.ignoreList)
204 missingNameSet = ignoreSet - set(apCorrNameSet)
205 if missingNameSet:
206 self.log.warning("Fields in ignoreList that are not in fluxCorrectList: %s",
207 sorted(missingNameSet))
208 for name in sorted(apCorrNameSet - ignoreSet):
209 if name + "_instFlux" not in schema:
210 # if a field in the registry is missing from the schema, silently ignore it.
211 continue
212 self.apCorrInfoDictapCorrInfoDict[name] = ApCorrInfo(schema=schema, model=name)
213
214 for name, model in self.config.proxies.items():
215 if name in apCorrNameSet:
216 # Already done or ignored
217 continue
218 if name + "_instFlux" not in schema:
219 # Silently ignore
220 continue
221 self.apCorrInfoDictapCorrInfoDict[name] = ApCorrInfo(schema=schema, model=model, name=name)
222
223 def run(self, catalog, apCorrMap):
224 """Apply aperture corrections to a catalog of sources.
225
226 Parameters
227 ----------
229 Catalog of sources. Will be updated in place.
230 apCorrMap : `lsst.afw.image.ApCorrMap`
231 Aperture correction map
232
233 Notes
234 -----
235 If you show debug-level log messages then you will see statistics for
236 the effects of aperture correction.
237 """
238 self.log.info("Applying aperture corrections to %d instFlux fields", len(self.apCorrInfoDictapCorrInfoDict))
239 if UseNaiveFluxErr:
240 self.log.debug("Use naive instFlux sigma computation")
241 else:
242 self.log.debug("Use complex instFlux sigma computation that double-counts photon noise "
243 "and thus over-estimates instFlux uncertainty")
244 for apCorrInfo in self.apCorrInfoDictapCorrInfoDict.values():
245 apCorrModel = apCorrMap.get(apCorrInfo.modelName)
246 apCorrErrModel = apCorrMap.get(apCorrInfo.modelSigmaName)
247 if None in (apCorrModel, apCorrErrModel):
248 missingNames = [(apCorrInfo.modelName, apCorrInfo.modelSigmaName)[i]
249 for i, model in enumerate((apCorrModel, apCorrErrModel)) if model is None]
250 self.log.warning("Cannot aperture correct %s because could not find %s in apCorrMap",
251 apCorrInfo.name, " or ".join(missingNames))
252 for source in catalog:
253 source.set(apCorrInfo.apCorrFlagKey, True)
254 continue
255
256 for source in catalog:
257 center = source.getCentroid()
258 # say we've failed when we start; we'll unset these flags when we succeed
259 source.set(apCorrInfo.apCorrFlagKey, True)
260 oldFluxFlagState = False
261 if self.config.doFlagApCorrFailures:
262 oldFluxFlagState = source.get(apCorrInfo.fluxFlagKey)
263 source.set(apCorrInfo.fluxFlagKey, True)
264
265 apCorr = 1.0
266 apCorrErr = 0.0
267 try:
268 apCorr = apCorrModel.evaluate(center)
269 if not UseNaiveFluxErr:
270 apCorrErr = apCorrErrModel.evaluate(center)
272 continue
273
274 if apCorrInfo.doApCorrColumn:
275 source.set(apCorrInfo.apCorrKey, apCorr)
276 source.set(apCorrInfo.apCorrErrKey, apCorrErr)
277
278 if apCorr <= 0.0 or apCorrErr < 0.0:
279 continue
280
281 instFlux = source.get(apCorrInfo.instFluxKey)
282 instFluxErr = source.get(apCorrInfo.instFluxErrKey)
283 source.set(apCorrInfo.instFluxKey, instFlux*apCorr)
284 if UseNaiveFluxErr:
285 source.set(apCorrInfo.instFluxErrKey, instFluxErr*apCorr)
286 else:
287 a = instFluxErr/instFlux
288 b = apCorrErr/apCorr
289 source.set(apCorrInfo.instFluxErrKey, abs(instFlux*apCorr)*math.sqrt(a*a + b*b))
290 source.set(apCorrInfo.apCorrFlagKey, False)
291 if self.config.doFlagApCorrFailures:
292 source.set(apCorrInfo.fluxFlagKey, oldFluxFlagState)
293
294 if self.log.isEnabledFor(self.log.DEBUG):
295 # log statistics on the effects of aperture correction
296 apCorrArr = np.array([s.get(apCorrInfo.apCorrKey) for s in catalog])
297 apCorrErrArr = np.array([s.get(apCorrInfo.apCorrErrKey) for s in catalog])
298 self.log.debug("For instFlux field %r: mean apCorr=%s, stdDev apCorr=%s, "
299 "mean apCorrErr=%s, stdDev apCorrErr=%s for %s sources",
300 apCorrInfo.name, apCorrArr.mean(), apCorrArr.std(),
301 apCorrErrArr.mean(), apCorrErrArr.std(), len(catalog))
def __init__(self, schema, model, name=None)
Definition: applyApCorr.py:123
def run(self, catalog, apCorrMap)
Definition: applyApCorr.py:223