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# 

# LSST Data Management System 

# Copyright 2015 LSST Corporation. 

# 

# This product includes software developed by the 

# LSST Project (http://www.lsst.org/). 

# 

# This program is free software: you can redistribute it and/or modify 

# it under the terms of the GNU General Public License as published by 

# the Free Software Foundation, either version 3 of the License, or 

# (at your option) any later version. 

# 

# This program is distributed in the hope that it will be useful, 

# but WITHOUT ANY WARRANTY; without even the implied warranty of 

# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 

# GNU General Public License for more details. 

# 

# You should have received a copy of the LSST License Statement and 

# the GNU General Public License along with this program. If not, 

# see <http://www.lsstcorp.org/LegalNotices/>. 

# 

import math 

 

import numpy as np 

 

import lsst.pex.config 

import lsst.pex.exceptions 

import lsst.afw.image 

import lsst.pipe.base 

from .apCorrRegistry import getApCorrNameSet 

 

# If True then scale instFlux error by apCorr; if False then use a more complex computation 

# that over-estimates instFlux error (often grossly so) because it double-counts photon noise. 

# This flag is intended to be temporary until we figure out a better way to compute 

# the effects of aperture correction on instFlux uncertainty 

UseNaiveFluxErr = True 

 

__all__ = ("ApplyApCorrConfig", "ApplyApCorrTask") 

 

 

class ApCorrInfo: 

"""!Catalog field names and keys needed to aperture correct a particular instrument flux 

""" 

 

def __init__(self, schema, model, name=None): 

"""!Construct an ApCorrInfo and add fields to the schema 

 

The aperture correction can be derived from the meaasurements in the 

column being aperture-corrected or from measurements in a different 

column (a "proxy"). In the first case, we will add columns to contain 

the aperture correction values; in the second case (using a proxy), 

we will add an alias to the proxy's aperture correction values. In 

all cases, we add a flag. 

 

@param[in,out] schema source catalog schema; 

three fields are used to generate keys: 

- {name}_instFlux 

- {name}_instFluxErr 

- {name}_flag 

three fields are added: 

- {name}_apCorr (only if not already added by proxy) 

- {name}_apCorrErr (only if not already added by proxy) 

- {name}_flag_apCorr 

@param[in] model field name prefix for instFlux with aperture correction model, e.g. "base_PsfFlux" 

@param[in] name field name prefix for instFlux needing aperture correction; may be None if it's the 

same as for the 'model' parameter 

 

ApCorrInfo has the following attributes: 

- name: field name prefix for instFlux needing aperture correction 

- modelName: field name for aperture correction model for instFlux 

- modelSigmaName: field name for aperture correction model for instFluxErr 

- doApCorrColumn: should we write the aperture correction values? (not if they're already being 

written by a proxy) 

- instFluxName: name of instFlux field 

- instFluxErrName: name of instFlux sigma field 

- instFluxKey: key to instFlux field 

- instFluxErrKey: key to instFlux sigma field 

- fluxFlagKey: key to flux flag field 

- apCorrKey: key to new aperture correction field 

- apCorrErrKey: key to new aperture correction sigma field 

- apCorrFlagKey: key to new aperture correction flag field 

""" 

if name is None: 

name = model 

self.name = name 

self.modelName = model + "_instFlux" 

self.modelSigmaName = model + "_instFluxErr" 

self.instFluxName = name + "_instFlux" 

self.instFluxErrName = name + "_instFluxErr" 

self.instFluxKey = schema.find(self.instFluxName).key 

self.instFluxErrKey = schema.find(self.instFluxErrName).key 

self.fluxFlagKey = schema.find(name + "_flag").key 

 

# No need to write the same aperture corrections multiple times 

self.doApCorrColumn = (name == model or model + "_apCorr" not in schema) 

if self.doApCorrColumn: 

self.apCorrKey = schema.addField( 

name + "_apCorr", 

doc="aperture correction applied to %s" % (name,), 

type=np.float64, 

) 

self.apCorrErrKey = schema.addField( 

name + "_apCorrErr", 

doc="standard deviation of aperture correction applied to %s" % (name,), 

type=np.float64, 

) 

else: 

aliases = schema.getAliasMap() 

aliases.set(name + "_apCorr", model + "_apCorr") 

aliases.set(name + "_apCorrErr", model + "_apCorrErr") 

self.apCorrKey = schema.find(name + "_apCorr").key 

self.apCorrErrKey = schema.find(name + "_apCorrErr").key 

 

self.apCorrFlagKey = schema.addField( 

name + "_flag_apCorr", 

doc="set if unable to aperture correct %s" % (name,), 

type="Flag", 

) 

 

 

class ApplyApCorrConfig(lsst.pex.config.Config): 

ignoreList = lsst.pex.config.ListField( 

doc="flux measurement algorithms in getApCorrNameSet() to ignore; " 

"if a name is listed that does not appear in getApCorrNameSet() then a warning is logged", 

dtype=str, 

optional=False, 

default=(), 

) 

doFlagApCorrFailures = lsst.pex.config.Field( 

doc="set the general failure flag for a flux when it cannot be aperture-corrected?", 

dtype=bool, 

default=True, 

) 

proxies = lsst.pex.config.DictField( 

doc="flux measurement algorithms to be aperture-corrected by reference to another algorithm; " 

"this is a mapping alg1:alg2, where 'alg1' is the algorithm being corrected, and 'alg2' " 

"is the algorithm supplying the corrections", 

keytype=str, 

itemtype=str, 

default={}, 

) 

 

 

class ApplyApCorrTask(lsst.pipe.base.Task): 

"""!Apply aperture corrections 

""" 

ConfigClass = ApplyApCorrConfig 

_DefaultName = "applyApCorr" 

 

def __init__(self, schema, **kwds): 

"""Construct an instance of this task 

""" 

lsst.pipe.base.Task.__init__(self, **kwds) 

 

self.apCorrInfoDict = dict() 

apCorrNameSet = getApCorrNameSet() 

ignoreSet = set(self.config.ignoreList) 

missingNameSet = ignoreSet - set(apCorrNameSet) 

if missingNameSet: 

self.log.warn("Fields in ignoreList that are not in fluxCorrectList: %s", 

sorted(list(missingNameSet))) 

for name in sorted(list(apCorrNameSet - ignoreSet)): 

if name + "_instFlux" not in schema: 

# if a field in the registry is missing from the schema, silently ignore it. 

continue 

self.apCorrInfoDict[name] = ApCorrInfo(schema=schema, model=name) 

 

for name, model in self.config.proxies.items(): 

if name in apCorrNameSet: 

# Already done or ignored 

continue 

if name + "_instFlux" not in schema: 

# Silently ignore 

continue 

self.apCorrInfoDict[name] = ApCorrInfo(schema=schema, model=model, name=name) 

 

def run(self, catalog, apCorrMap): 

"""Apply aperture corrections to a catalog of sources 

 

@param[in,out] catalog catalog of sources 

@param[in] apCorrMap aperture correction map (an lsst.afw.image.ApCorrMap) 

 

If you show debug-level log messages then you will see statistics for the effects of 

aperture correction. 

""" 

self.log.info("Applying aperture corrections to %d instFlux fields", len(self.apCorrInfoDict)) 

if UseNaiveFluxErr: 

self.log.debug("Use naive instFlux sigma computation") 

else: 

self.log.debug("Use complex instFlux sigma computation that double-counts photon noise " 

"and thus over-estimates instFlux uncertainty") 

for apCorrInfo in self.apCorrInfoDict.values(): 

apCorrModel = apCorrMap.get(apCorrInfo.modelName) 

apCorrErrModel = apCorrMap.get(apCorrInfo.modelSigmaName) 

if None in (apCorrModel, apCorrErrModel): 

missingNames = [(apCorrInfo.modelName, apCorrInfo.modelSigmaName)[i] 

for i, model in enumerate((apCorrModel, apCorrErrModel)) if model is None] 

self.log.warn("Cannot aperture correct %s because could not find %s in apCorrMap" % 

(apCorrInfo.name, " or ".join(missingNames),)) 

for source in catalog: 

source.set(apCorrInfo.apCorrFlagKey, True) 

continue 

 

for source in catalog: 

center = source.getCentroid() 

# say we've failed when we start; we'll unset these flags when we succeed 

source.set(apCorrInfo.apCorrFlagKey, True) 

oldFluxFlagState = False 

if self.config.doFlagApCorrFailures: 

oldFluxFlagState = source.get(apCorrInfo.fluxFlagKey) 

source.set(apCorrInfo.fluxFlagKey, True) 

 

apCorr = 1.0 

apCorrErr = 0.0 

try: 

apCorr = apCorrModel.evaluate(center) 

if not UseNaiveFluxErr: 

apCorrErr = apCorrErrModel.evaluate(center) 

except lsst.pex.exceptions.DomainError: 

continue 

 

if apCorrInfo.doApCorrColumn: 

source.set(apCorrInfo.apCorrKey, apCorr) 

source.set(apCorrInfo.apCorrErrKey, apCorrErr) 

 

if apCorr <= 0.0 or apCorrErr < 0.0: 

continue 

 

instFlux = source.get(apCorrInfo.instFluxKey) 

instFluxErr = source.get(apCorrInfo.instFluxErrKey) 

source.set(apCorrInfo.instFluxKey, instFlux*apCorr) 

if UseNaiveFluxErr: 

source.set(apCorrInfo.instFluxErrKey, instFluxErr*apCorr) 

else: 

a = instFluxErr/instFlux 

b = apCorrErr/apCorr 

source.set(apCorrInfo.instFluxErrKey, abs(instFlux*apCorr)*math.sqrt(a*a + b*b)) 

source.set(apCorrInfo.apCorrFlagKey, False) 

if self.config.doFlagApCorrFailures: 

source.set(apCorrInfo.fluxFlagKey, oldFluxFlagState) 

 

if self.log.getLevel() <= self.log.DEBUG: 

# log statistics on the effects of aperture correction 

apCorrArr = np.array([s.get(apCorrInfo.apCorrKey) for s in catalog]) 

apCorrErrArr = np.array([s.get(apCorrInfo.apCorrErrKey) for s in catalog]) 

self.log.debug("For instFlux field %r: mean apCorr=%s, stdDev apCorr=%s, " 

"mean apCorrErr=%s, stdDev apCorrErr=%s for %s sources", 

apCorrInfo.name, apCorrArr.mean(), apCorrArr.std(), 

apCorrErrArr.mean(), apCorrErrArr.std(), len(catalog))