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#!/usr/bin/env python 

# 

# LSST Data Management System 

# Copyright 2008-2015 AURA/LSST. 

# 

# 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 <https://www.lsstcorp.org/LegalNotices/>. 

# 

from lsst.coadd.utils.coaddDataIdContainer import ExistingCoaddDataIdContainer 

from lsst.pipe.base import (CmdLineTask, Struct, ArgumentParser, ButlerInitializedTaskRunner, 

PipelineTask, InitOutputDatasetField, InputDatasetField, OutputDatasetField, 

QuantumConfig) 

from lsst.pex.config import Config, Field, ConfigurableField 

from lsst.meas.algorithms import DynamicDetectionTask 

from lsst.meas.base import SingleFrameMeasurementTask, ApplyApCorrTask, CatalogCalculationTask 

from lsst.meas.deblender import SourceDeblendTask, MultibandDeblendTask 

from lsst.pipe.tasks.coaddBase import getSkyInfo 

from lsst.pipe.tasks.scaleVariance import ScaleVarianceTask 

from lsst.meas.astrom import DirectMatchTask, denormalizeMatches 

from lsst.pipe.tasks.fakes import BaseFakeSourcesTask 

from lsst.pipe.tasks.setPrimaryFlags import SetPrimaryFlagsTask 

from lsst.pipe.tasks.propagateVisitFlags import PropagateVisitFlagsTask 

import lsst.afw.image as afwImage 

import lsst.afw.table as afwTable 

import lsst.afw.math as afwMath 

from lsst.daf.base import PropertyList 

 

from .mergeDetections import MergeDetectionsConfig, MergeDetectionsTask # noqa: F401 

from .mergeMeasurements import MergeMeasurementsConfig, MergeMeasurementsTask # noqa: F401 

from .multiBandUtils import MergeSourcesRunner, CullPeaksConfig, _makeGetSchemaCatalogs # noqa: F401 

from .multiBandUtils import getInputSchema, getShortFilterName, readCatalog, _makeMakeIdFactory # noqa: F401 

from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesSingleConfig # noqa: F401 

from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesSingleTask # noqa: F401 

from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesMultiConfig # noqa: F401 

from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesMultiTask # noqa: F401 

 

 

""" 

New set types: 

* deepCoadd_det: detections from what used to be processCoadd (tract, patch, filter) 

* deepCoadd_mergeDet: merged detections (tract, patch) 

* deepCoadd_meas: measurements of merged detections (tract, patch, filter) 

* deepCoadd_ref: reference sources (tract, patch) 

All of these have associated *_schema catalogs that require no data ID and hold no records. 

 

In addition, we have a schema-only dataset, which saves the schema for the PeakRecords in 

the mergeDet, meas, and ref dataset Footprints: 

* deepCoadd_peak_schema 

""" 

 

 

############################################################################################################## 

 

class DetectCoaddSourcesConfig(Config): 

"""! 

@anchor DetectCoaddSourcesConfig_ 

 

@brief Configuration parameters for the DetectCoaddSourcesTask 

""" 

doScaleVariance = Field(dtype=bool, default=True, doc="Scale variance plane using empirical noise?") 

scaleVariance = ConfigurableField(target=ScaleVarianceTask, doc="Variance rescaling") 

detection = ConfigurableField(target=DynamicDetectionTask, doc="Source detection") 

coaddName = Field(dtype=str, default="deep", doc="Name of coadd") 

doInsertFakes = Field(dtype=bool, default=False, 

doc="Run fake sources injection task") 

insertFakes = ConfigurableField(target=BaseFakeSourcesTask, 

doc="Injection of fake sources for testing " 

"purposes (must be retargeted)") 

detectionSchema = InitOutputDatasetField( 

doc="Schema of the detection catalog", 

name="{}Coadd_det_schema", 

storageClass="SourceCatalog", 

) 

exposure = InputDatasetField( 

doc="Exposure on which detections are to be performed", 

name="deepCoadd", 

scalar=True, 

storageClass="Exposure", 

dimensions=("Tract", "Patch", "AbstractFilter", "SkyMap") 

) 

outputBackgrounds = OutputDatasetField( 

doc="Output Backgrounds used in detection", 

name="{}Coadd_calexp_background", 

scalar=True, 

storageClass="Background", 

dimensions=("Tract", "Patch", "AbstractFilter", "SkyMap") 

) 

outputSources = OutputDatasetField( 

doc="Detected sources catalog", 

name="{}Coadd_det", 

scalar=True, 

storageClass="SourceCatalog", 

dimensions=("Tract", "Patch", "AbstractFilter", "SkyMap") 

) 

outputExposure = OutputDatasetField( 

doc="Exposure post detection", 

name="{}Coadd_calexp", 

scalar=True, 

storageClass="Exposure", 

dimensions=("Tract", "Patch", "AbstractFilter", "SkyMap") 

) 

quantum = QuantumConfig( 

dimensions=("Tract", "Patch", "AbstractFilter", "SkyMap") 

) 

 

def setDefaults(self): 

Config.setDefaults(self) 

self.detection.thresholdType = "pixel_stdev" 

self.detection.isotropicGrow = True 

# Coadds are made from background-subtracted CCDs, so any background subtraction should be very basic 

self.detection.reEstimateBackground = False 

self.detection.background.useApprox = False 

self.detection.background.binSize = 4096 

self.detection.background.undersampleStyle = 'REDUCE_INTERP_ORDER' 

self.detection.doTempWideBackground = True # Suppress large footprints that overwhelm the deblender 

 

## @addtogroup LSST_task_documentation 

## @{ 

## @page DetectCoaddSourcesTask 

## @ref DetectCoaddSourcesTask_ "DetectCoaddSourcesTask" 

## @copybrief DetectCoaddSourcesTask 

## @} 

 

 

class DetectCoaddSourcesTask(PipelineTask, CmdLineTask): 

r"""! 

@anchor DetectCoaddSourcesTask_ 

 

@brief Detect sources on a coadd 

 

@section pipe_tasks_multiBand_Contents Contents 

 

- @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose 

- @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize 

- @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Run 

- @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Config 

- @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug 

- @ref pipe_tasks_multiband_DetectCoaddSourcesTask_Example 

 

@section pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose Description 

 

Command-line task that detects sources on a coadd of exposures obtained with a single filter. 

 

Coadding individual visits requires each exposure to be warped. This introduces covariance in the noise 

properties across pixels. Before detection, we correct the coadd variance by scaling the variance plane 

in the coadd to match the observed variance. This is an approximate approach -- strictly, we should 

propagate the full covariance matrix -- but it is simple and works well in practice. 

 

After scaling the variance plane, we detect sources and generate footprints by delegating to the @ref 

SourceDetectionTask_ "detection" subtask. 

 

@par Inputs: 

deepCoadd{tract,patch,filter}: ExposureF 

@par Outputs: 

deepCoadd_det{tract,patch,filter}: SourceCatalog (only parent Footprints) 

@n deepCoadd_calexp{tract,patch,filter}: Variance scaled, background-subtracted input 

exposure (ExposureF) 

@n deepCoadd_calexp_background{tract,patch,filter}: BackgroundList 

@par Data Unit: 

tract, patch, filter 

 

DetectCoaddSourcesTask delegates most of its work to the @ref SourceDetectionTask_ "detection" subtask. 

You can retarget this subtask if you wish. 

 

@section pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize Task initialization 

 

@copydoc \_\_init\_\_ 

 

@section pipe_tasks_multiBand_DetectCoaddSourcesTask_Run Invoking the Task 

 

@copydoc run 

 

@section pipe_tasks_multiBand_DetectCoaddSourcesTask_Config Configuration parameters 

 

See @ref DetectCoaddSourcesConfig_ "DetectSourcesConfig" 

 

@section pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug Debug variables 

 

The @link lsst.pipe.base.cmdLineTask.CmdLineTask command line task@endlink interface supports a 

flag @c -d to import @b debug.py from your @c PYTHONPATH; see @ref baseDebug for more about @b debug.py 

files. 

 

DetectCoaddSourcesTask has no debug variables of its own because it relegates all the work to 

@ref SourceDetectionTask_ "SourceDetectionTask"; see the documetation for 

@ref SourceDetectionTask_ "SourceDetectionTask" for further information. 

 

@section pipe_tasks_multiband_DetectCoaddSourcesTask_Example A complete example 

of using DetectCoaddSourcesTask 

 

DetectCoaddSourcesTask is meant to be run after assembling a coadded image in a given band. The purpose of 

the task is to update the background, detect all sources in a single band and generate a set of parent 

footprints. Subsequent tasks in the multi-band processing procedure will merge sources across bands and, 

eventually, perform forced photometry. Command-line usage of DetectCoaddSourcesTask expects a data 

reference to the coadd to be processed. A list of the available optional arguments can be obtained by 

calling detectCoaddSources.py with the `--help` command line argument: 

@code 

detectCoaddSources.py --help 

@endcode 

 

To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we 

will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has followed 

steps 1 - 4 at @ref pipeTasks_multiBand, one may detect all the sources in each coadd as follows: 

@code 

detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I 

@endcode 

that will process the HSC-I band data. The results are written to 

`$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I`. 

 

It is also necessary to run: 

@code 

detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R 

@endcode 

to generate the sources catalogs for the HSC-R band required by the next step in the multi-band 

processing procedure: @ref MergeDetectionsTask_ "MergeDetectionsTask". 

""" 

_DefaultName = "detectCoaddSources" 

ConfigClass = DetectCoaddSourcesConfig 

getSchemaCatalogs = _makeGetSchemaCatalogs("det") 

makeIdFactory = _makeMakeIdFactory("CoaddId") 

 

@classmethod 

def _makeArgumentParser(cls): 

parser = ArgumentParser(name=cls._DefaultName) 

parser.add_id_argument("--id", "deepCoadd", help="data ID, e.g. --id tract=12345 patch=1,2 filter=r", 

ContainerClass=ExistingCoaddDataIdContainer) 

return parser 

 

@classmethod 

def getOutputDatasetTypes(cls, config): 

coaddName = config.coaddName 

for name in ("outputBackgrounds", "outputSources", "outputExposure"): 

attr = getattr(config, name) 

setattr(attr, "name", attr.name.format(coaddName)) 

outputTypeDict = super().getOutputDatasetTypes(config) 

return outputTypeDict 

 

@classmethod 

def getInitOutputDatasetTypes(cls, config): 

coaddName = config.coaddName 

attr = config.detectionSchema 

setattr(attr, "name", attr.name.format(coaddName)) 

output = super().getInitOutputDatasetTypes(config) 

return output 

 

def __init__(self, schema=None, **kwargs): 

"""! 

@brief Initialize the task. Create the @ref SourceDetectionTask_ "detection" subtask. 

 

Keyword arguments (in addition to those forwarded to CmdLineTask.__init__): 

 

@param[in] schema: initial schema for the output catalog, modified-in place to include all 

fields set by this task. If None, the source minimal schema will be used. 

@param[in] **kwargs: keyword arguments to be passed to lsst.pipe.base.task.Task.__init__ 

""" 

# N.B. Super is used here to handle the multiple inheritance of PipelineTasks, the init tree 

# call structure has been reviewed carefully to be sure super will work as intended. 

super().__init__(**kwargs) 

if schema is None: 

schema = afwTable.SourceTable.makeMinimalSchema() 

if self.config.doInsertFakes: 

self.makeSubtask("insertFakes") 

self.schema = schema 

self.makeSubtask("detection", schema=self.schema) 

if self.config.doScaleVariance: 

self.makeSubtask("scaleVariance") 

 

def getInitOutputDatasets(self): 

return {"detectionSchema": afwTable.SourceCatalog(self.schema)} 

 

def runDataRef(self, patchRef): 

"""! 

@brief Run detection on a coadd. 

 

Invokes @ref run and then uses @ref write to output the 

results. 

 

@param[in] patchRef: data reference for patch 

""" 

exposure = patchRef.get(self.config.coaddName + "Coadd", immediate=True) 

expId = int(patchRef.get(self.config.coaddName + "CoaddId")) 

results = self.run(exposure, self.makeIdFactory(patchRef), expId=expId) 

self.write(results, patchRef) 

return results 

 

def adaptArgsAndRun(self, inputData, inputDataIds, outputDataIds, butler): 

# FINDME: DM-15843 needs to come back and address these next two lines with a final solution 

inputData["idFactory"] = afwTable.IdFactory.makeSimple() 

inputData["expId"] = 0 

return self.run(**inputData) 

 

def run(self, exposure, idFactory, expId): 

"""! 

@brief Run detection on an exposure. 

 

First scale the variance plane to match the observed variance 

using @ref ScaleVarianceTask. Then invoke the @ref SourceDetectionTask_ "detection" subtask to 

detect sources. 

 

@param[in,out] exposure: Exposure on which to detect (may be backround-subtracted and scaled, 

depending on configuration). 

@param[in] idFactory: IdFactory to set source identifiers 

@param[in] expId: Exposure identifier (integer) for RNG seed 

 

@return a pipe.base.Struct with fields 

- sources: catalog of detections 

- backgrounds: list of backgrounds 

""" 

if self.config.doScaleVariance: 

varScale = self.scaleVariance.run(exposure.maskedImage) 

exposure.getMetadata().add("variance_scale", varScale) 

backgrounds = afwMath.BackgroundList() 

if self.config.doInsertFakes: 

self.insertFakes.run(exposure, background=backgrounds) 

table = afwTable.SourceTable.make(self.schema, idFactory) 

detections = self.detection.makeSourceCatalog(table, exposure, expId=expId) 

sources = detections.sources 

fpSets = detections.fpSets 

if hasattr(fpSets, "background") and fpSets.background: 

for bg in fpSets.background: 

backgrounds.append(bg) 

return Struct(outputSources=sources, outputBackgrounds=backgrounds, outputExposure=exposure) 

 

def write(self, results, patchRef): 

"""! 

@brief Write out results from runDetection. 

 

@param[in] exposure: Exposure to write out 

@param[in] results: Struct returned from runDetection 

@param[in] patchRef: data reference for patch 

""" 

coaddName = self.config.coaddName + "Coadd" 

patchRef.put(results.outputBackgrounds, coaddName + "_calexp_background") 

patchRef.put(results.outputSources, coaddName + "_det") 

patchRef.put(results.outputExposure, coaddName + "_calexp") 

 

############################################################################################################## 

 

 

class DeblendCoaddSourcesConfig(Config): 

"""DeblendCoaddSourcesConfig 

 

Configuration parameters for the `DeblendCoaddSourcesTask`. 

""" 

singleBandDeblend = ConfigurableField(target=SourceDeblendTask, 

doc="Deblend sources separately in each band") 

multiBandDeblend = ConfigurableField(target=MultibandDeblendTask, 

doc="Deblend sources simultaneously across bands") 

simultaneous = Field(dtype=bool, default=False, doc="Simultaneously deblend all bands?") 

coaddName = Field(dtype=str, default="deep", doc="Name of coadd") 

 

def setDefaults(self): 

Config.setDefaults(self) 

self.singleBandDeblend.propagateAllPeaks = True 

 

 

class DeblendCoaddSourcesRunner(MergeSourcesRunner): 

"""Task runner for the `MergeSourcesTask` 

 

Required because the run method requires a list of 

dataRefs rather than a single dataRef. 

""" 

@staticmethod 

def getTargetList(parsedCmd, **kwargs): 

"""Provide a list of patch references for each patch, tract, filter combo. 

 

Parameters 

---------- 

parsedCmd: 

The parsed command 

kwargs: 

Keyword arguments passed to the task 

 

Returns 

------- 

targetList: list 

List of tuples, where each tuple is a (dataRef, kwargs) pair. 

""" 

refDict = MergeSourcesRunner.buildRefDict(parsedCmd) 

kwargs["psfCache"] = parsedCmd.psfCache 

return [(list(p.values()), kwargs) for t in refDict.values() for p in t.values()] 

 

 

class DeblendCoaddSourcesTask(CmdLineTask): 

"""Deblend the sources in a merged catalog 

 

Deblend sources from master catalog in each coadd. 

This can either be done separately in each band using the HSC-SDSS deblender 

(`DeblendCoaddSourcesTask.config.simultaneous==False`) 

or use SCARLET to simultaneously fit the blend in all bands 

(`DeblendCoaddSourcesTask.config.simultaneous==True`). 

The task will set its own `self.schema` atribute to the `Schema` of the 

output deblended catalog. 

This will include all fields from the input `Schema`, as well as additional fields 

from the deblender. 

 

`pipe.tasks.multiband.DeblendCoaddSourcesTask Description 

--------------------------------------------------------- 

` 

 

Parameters 

---------- 

butler: `Butler` 

Butler used to read the input schemas from disk or 

construct the reference catalog loader, if `schema` or `peakSchema` or 

schema: `Schema` 

The schema of the merged detection catalog as an input to this task. 

peakSchema: `Schema` 

The schema of the `PeakRecord`s in the `Footprint`s in the merged detection catalog 

""" 

ConfigClass = DeblendCoaddSourcesConfig 

RunnerClass = DeblendCoaddSourcesRunner 

_DefaultName = "deblendCoaddSources" 

makeIdFactory = _makeMakeIdFactory("MergedCoaddId") 

 

@classmethod 

def _makeArgumentParser(cls): 

parser = ArgumentParser(name=cls._DefaultName) 

parser.add_id_argument("--id", "deepCoadd_calexp", 

help="data ID, e.g. --id tract=12345 patch=1,2 filter=g^r^i", 

ContainerClass=ExistingCoaddDataIdContainer) 

parser.add_argument("--psfCache", type=int, default=100, help="Size of CoaddPsf cache") 

return parser 

 

def __init__(self, butler=None, schema=None, peakSchema=None, **kwargs): 

CmdLineTask.__init__(self, **kwargs) 

if schema is None: 

assert butler is not None, "Neither butler nor schema is defined" 

schema = butler.get(self.config.coaddName + "Coadd_mergeDet_schema", immediate=True).schema 

self.schemaMapper = afwTable.SchemaMapper(schema) 

self.schemaMapper.addMinimalSchema(schema) 

self.schema = self.schemaMapper.getOutputSchema() 

if peakSchema is None: 

assert butler is not None, "Neither butler nor peakSchema is defined" 

peakSchema = butler.get(self.config.coaddName + "Coadd_peak_schema", immediate=True).schema 

 

if self.config.simultaneous: 

self.makeSubtask("multiBandDeblend", schema=self.schema, peakSchema=peakSchema) 

else: 

self.makeSubtask("singleBandDeblend", schema=self.schema, peakSchema=peakSchema) 

 

def getSchemaCatalogs(self): 

"""Return a dict of empty catalogs for each catalog dataset produced by this task. 

 

Returns 

------- 

result: dict 

Dictionary of empty catalogs, with catalog names as keys. 

""" 

catalog = afwTable.SourceCatalog(self.schema) 

return {self.config.coaddName + "Coadd_deblendedFlux": catalog, 

self.config.coaddName + "Coadd_deblendedModel": catalog} 

 

def runDataRef(self, patchRefList, psfCache=100): 

"""Deblend the patch 

 

Deblend each source simultaneously or separately 

(depending on `DeblendCoaddSourcesTask.config.simultaneous`). 

Set `is-primary` and related flags. 

Propagate flags from individual visits. 

Write the deblended sources out. 

 

Parameters 

---------- 

patchRefList: list 

List of data references for each filter 

""" 

if self.config.simultaneous: 

# Use SCARLET to simultaneously deblend across filters 

filters = [] 

exposures = [] 

for patchRef in patchRefList: 

exposure = patchRef.get(self.config.coaddName + "Coadd_calexp", immediate=True) 

filters.append(patchRef.dataId["filter"]) 

exposures.append(exposure) 

# The input sources are the same for all bands, since it is a merged catalog 

sources = self.readSources(patchRef) 

exposure = afwImage.MultibandExposure.fromExposures(filters, exposures) 

fluxCatalogs, templateCatalogs = self.multiBandDeblend.run(exposure, sources) 

for n in range(len(patchRefList)): 

self.write(patchRefList[n], fluxCatalogs[filters[n]], templateCatalogs[filters[n]]) 

else: 

# Use the singeband deblender to deblend each band separately 

for patchRef in patchRefList: 

exposure = patchRef.get(self.config.coaddName + "Coadd_calexp", immediate=True) 

exposure.getPsf().setCacheCapacity(psfCache) 

sources = self.readSources(patchRef) 

self.singleBandDeblend.run(exposure, sources) 

self.write(patchRef, sources) 

 

def readSources(self, dataRef): 

"""Read merged catalog 

 

Read the catalog of merged detections and create a catalog 

in a single band. 

 

Parameters 

---------- 

dataRef: data reference 

Data reference for catalog of merged detections 

 

Returns 

------- 

sources: `SourceCatalog` 

List of sources in merged catalog 

 

We also need to add columns to hold the measurements we're about to make 

so we can measure in-place. 

""" 

merged = dataRef.get(self.config.coaddName + "Coadd_mergeDet", immediate=True) 

self.log.info("Read %d detections: %s" % (len(merged), dataRef.dataId)) 

idFactory = self.makeIdFactory(dataRef) 

for s in merged: 

idFactory.notify(s.getId()) 

table = afwTable.SourceTable.make(self.schema, idFactory) 

sources = afwTable.SourceCatalog(table) 

sources.extend(merged, self.schemaMapper) 

return sources 

 

def write(self, dataRef, flux_sources, template_sources=None): 

"""Write the source catalog(s) 

 

Parameters 

---------- 

dataRef: Data Reference 

Reference to the output catalog. 

flux_sources: `SourceCatalog` 

Flux conserved sources to write to file. 

If using the single band deblender, this is the catalog 

generated. 

template_sources: `SourceCatalog` 

Source catalog using the multiband template models 

as footprints. 

""" 

# The multiband deblender does not have to conserve flux, 

# so only write the flux conserved catalog if it exists 

if flux_sources is not None: 

assert not self.config.simultaneous or self.config.multiBandDeblend.conserveFlux 

dataRef.put(flux_sources, self.config.coaddName + "Coadd_deblendedFlux") 

# Only the multiband deblender has the option to output the 

# template model catalog, which can optionally be used 

# in MeasureMergedCoaddSources 

if template_sources is not None: 

assert self.config.multiBandDeblend.saveTemplates 

dataRef.put(template_sources, self.config.coaddName + "Coadd_deblendedModel") 

self.log.info("Wrote %d sources: %s" % (len(flux_sources), dataRef.dataId)) 

 

def writeMetadata(self, dataRefList): 

"""Write the metadata produced from processing the data. 

Parameters 

---------- 

dataRefList 

List of Butler data references used to write the metadata. 

The metadata is written to dataset type `CmdLineTask._getMetadataName`. 

""" 

for dataRef in dataRefList: 

try: 

metadataName = self._getMetadataName() 

if metadataName is not None: 

dataRef.put(self.getFullMetadata(), metadataName) 

except Exception as e: 

self.log.warn("Could not persist metadata for dataId=%s: %s", dataRef.dataId, e) 

 

def getExposureId(self, dataRef): 

"""Get the ExposureId from a data reference 

""" 

return int(dataRef.get(self.config.coaddName + "CoaddId")) 

 

 

class MeasureMergedCoaddSourcesConfig(Config): 

"""! 

@anchor MeasureMergedCoaddSourcesConfig_ 

 

@brief Configuration parameters for the MeasureMergedCoaddSourcesTask 

""" 

inputCatalog = Field(dtype=str, default="deblendedFlux", 

doc=("Name of the input catalog to use." 

"If the single band deblender was used this should be 'deblendedFlux." 

"If the multi-band deblender was used this should be 'deblendedModel." 

"If no deblending was performed this should be 'mergeDet'")) 

measurement = ConfigurableField(target=SingleFrameMeasurementTask, doc="Source measurement") 

setPrimaryFlags = ConfigurableField(target=SetPrimaryFlagsTask, doc="Set flags for primary tract/patch") 

doPropagateFlags = Field( 

dtype=bool, default=True, 

doc="Whether to match sources to CCD catalogs to propagate flags (to e.g. identify PSF stars)" 

) 

propagateFlags = ConfigurableField(target=PropagateVisitFlagsTask, doc="Propagate visit flags to coadd") 

doMatchSources = Field(dtype=bool, default=True, doc="Match sources to reference catalog?") 

match = ConfigurableField(target=DirectMatchTask, doc="Matching to reference catalog") 

doWriteMatchesDenormalized = Field( 

dtype=bool, 

default=False, 

doc=("Write reference matches in denormalized format? " 

"This format uses more disk space, but is more convenient to read."), 

) 

coaddName = Field(dtype=str, default="deep", doc="Name of coadd") 

checkUnitsParseStrict = Field( 

doc="Strictness of Astropy unit compatibility check, can be 'raise', 'warn' or 'silent'", 

dtype=str, 

default="raise", 

) 

doApCorr = Field( 

dtype=bool, 

default=True, 

doc="Apply aperture corrections" 

) 

applyApCorr = ConfigurableField( 

target=ApplyApCorrTask, 

doc="Subtask to apply aperture corrections" 

) 

doRunCatalogCalculation = Field( 

dtype=bool, 

default=True, 

doc='Run catalogCalculation task' 

) 

catalogCalculation = ConfigurableField( 

target=CatalogCalculationTask, 

doc="Subtask to run catalogCalculation plugins on catalog" 

) 

 

def setDefaults(self): 

Config.setDefaults(self) 

self.measurement.plugins.names |= ['base_InputCount', 'base_Variance'] 

self.measurement.plugins['base_PixelFlags'].masksFpAnywhere = ['CLIPPED', 'SENSOR_EDGE', 

'INEXACT_PSF'] 

self.measurement.plugins['base_PixelFlags'].masksFpCenter = ['CLIPPED', 'SENSOR_EDGE', 

'INEXACT_PSF'] 

 

## @addtogroup LSST_task_documentation 

## @{ 

## @page MeasureMergedCoaddSourcesTask 

## @ref MeasureMergedCoaddSourcesTask_ "MeasureMergedCoaddSourcesTask" 

## @copybrief MeasureMergedCoaddSourcesTask 

## @} 

 

 

class MeasureMergedCoaddSourcesRunner(ButlerInitializedTaskRunner): 

"""Get the psfCache setting into MeasureMergedCoaddSourcesTask""" 

@staticmethod 

def getTargetList(parsedCmd, **kwargs): 

return ButlerInitializedTaskRunner.getTargetList(parsedCmd, psfCache=parsedCmd.psfCache) 

 

 

class MeasureMergedCoaddSourcesTask(CmdLineTask): 

r"""! 

@anchor MeasureMergedCoaddSourcesTask_ 

 

@brief Deblend sources from master catalog in each coadd seperately and measure. 

 

@section pipe_tasks_multiBand_Contents Contents 

 

- @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose 

- @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize 

- @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run 

- @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config 

- @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug 

- @ref pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example 

 

@section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose Description 

 

Command-line task that uses peaks and footprints from a master catalog to perform deblending and 

measurement in each coadd. 

 

Given a master input catalog of sources (peaks and footprints) or deblender outputs 

(including a HeavyFootprint in each band), measure each source on the 

coadd. Repeating this procedure with the same master catalog across multiple coadds will generate a 

consistent set of child sources. 

 

The deblender retains all peaks and deblends any missing peaks (dropouts in that band) as PSFs. Source 

properties are measured and the @c is-primary flag (indicating sources with no children) is set. Visit 

flags are propagated to the coadd sources. 

 

Optionally, we can match the coadd sources to an external reference catalog. 

 

@par Inputs: 

deepCoadd_mergeDet{tract,patch} or deepCoadd_deblend{tract,patch}: SourceCatalog 

@n deepCoadd_calexp{tract,patch,filter}: ExposureF 

@par Outputs: 

deepCoadd_meas{tract,patch,filter}: SourceCatalog 

@par Data Unit: 

tract, patch, filter 

 

MeasureMergedCoaddSourcesTask delegates most of its work to a set of sub-tasks: 

 

<DL> 

<DT> @ref SingleFrameMeasurementTask_ "measurement" 

<DD> Measure source properties of deblended sources.</DD> 

<DT> @ref SetPrimaryFlagsTask_ "setPrimaryFlags" 

<DD> Set flag 'is-primary' as well as related flags on sources. 'is-primary' is set for sources that are 

not at the edge of the field and that have either not been deblended or are the children of deblended 

sources</DD> 

<DT> @ref PropagateVisitFlagsTask_ "propagateFlags" 

<DD> Propagate flags set in individual visits to the coadd.</DD> 

<DT> @ref DirectMatchTask_ "match" 

<DD> Match input sources to a reference catalog (optional). 

</DD> 

</DL> 

These subtasks may be retargeted as required. 

 

@section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize Task initialization 

 

@copydoc \_\_init\_\_ 

 

@section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run Invoking the Task 

 

@copydoc run 

 

@section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config Configuration parameters 

 

See @ref MeasureMergedCoaddSourcesConfig_ 

 

@section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug Debug variables 

 

The @link lsst.pipe.base.cmdLineTask.CmdLineTask command line task@endlink interface supports a 

flag @c -d to import @b debug.py from your @c PYTHONPATH; see @ref baseDebug for more about @b debug.py 

files. 

 

MeasureMergedCoaddSourcesTask has no debug variables of its own because it delegates all the work to 

the various sub-tasks. See the documetation for individual sub-tasks for more information. 

 

@section pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example A complete example of using 

MeasureMergedCoaddSourcesTask 

 

After MeasureMergedCoaddSourcesTask has been run on multiple coadds, we have a set of per-band catalogs. 

The next stage in the multi-band processing procedure will merge these measurements into a suitable 

catalog for driving forced photometry. 

 

Command-line usage of MeasureMergedCoaddSourcesTask expects a data reference to the coadds 

to be processed. 

A list of the available optional arguments can be obtained by calling measureCoaddSources.py with the 

`--help` command line argument: 

@code 

measureCoaddSources.py --help 

@endcode 

 

To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we 

will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has finished 

step 6 at @ref pipeTasks_multiBand, one may perform deblending and measure sources in the HSC-I band 

coadd as follows: 

@code 

measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I 

@endcode 

This will process the HSC-I band data. The results are written in 

`$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I/0/5,4/meas-HSC-I-0-5,4.fits 

 

It is also necessary to run 

@code 

measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R 

@endcode 

to generate the sources catalogs for the HSC-R band required by the next step in the multi-band 

procedure: @ref MergeMeasurementsTask_ "MergeMeasurementsTask". 

""" 

_DefaultName = "measureCoaddSources" 

ConfigClass = MeasureMergedCoaddSourcesConfig 

RunnerClass = MeasureMergedCoaddSourcesRunner 

getSchemaCatalogs = _makeGetSchemaCatalogs("meas") 

makeIdFactory = _makeMakeIdFactory("MergedCoaddId") # The IDs we already have are of this type 

 

@classmethod 

def _makeArgumentParser(cls): 

parser = ArgumentParser(name=cls._DefaultName) 

parser.add_id_argument("--id", "deepCoadd_calexp", 

help="data ID, e.g. --id tract=12345 patch=1,2 filter=r", 

ContainerClass=ExistingCoaddDataIdContainer) 

parser.add_argument("--psfCache", type=int, default=100, help="Size of CoaddPsf cache") 

return parser 

 

def __init__(self, butler=None, schema=None, peakSchema=None, refObjLoader=None, **kwargs): 

"""! 

@brief Initialize the task. 

 

Keyword arguments (in addition to those forwarded to CmdLineTask.__init__): 

@param[in] schema: the schema of the merged detection catalog used as input to this one 

@param[in] peakSchema: the schema of the PeakRecords in the Footprints in the merged detection catalog 

@param[in] refObjLoader: an instance of LoadReferenceObjectsTasks that supplies an external reference 

catalog. May be None if the loader can be constructed from the butler argument or all steps 

requiring a reference catalog are disabled. 

@param[in] butler: a butler used to read the input schemas from disk or construct the reference 

catalog loader, if schema or peakSchema or refObjLoader is None 

 

The task will set its own self.schema attribute to the schema of the output measurement catalog. 

This will include all fields from the input schema, as well as additional fields for all the 

measurements. 

""" 

CmdLineTask.__init__(self, **kwargs) 

self.deblended = self.config.inputCatalog.startswith("deblended") 

self.inputCatalog = "Coadd_" + self.config.inputCatalog 

if schema is None: 

assert butler is not None, "Neither butler nor schema is defined" 

schema = butler.get(self.config.coaddName + self.inputCatalog + "_schema", immediate=True).schema 

self.schemaMapper = afwTable.SchemaMapper(schema) 

self.schemaMapper.addMinimalSchema(schema) 

self.schema = self.schemaMapper.getOutputSchema() 

self.algMetadata = PropertyList() 

self.makeSubtask("measurement", schema=self.schema, algMetadata=self.algMetadata) 

self.makeSubtask("setPrimaryFlags", schema=self.schema) 

if self.config.doMatchSources: 

if refObjLoader is None: 

assert butler is not None, "Neither butler nor refObjLoader is defined" 

self.makeSubtask("match", butler=butler, refObjLoader=refObjLoader) 

if self.config.doPropagateFlags: 

self.makeSubtask("propagateFlags", schema=self.schema) 

self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict) 

if self.config.doApCorr: 

self.makeSubtask("applyApCorr", schema=self.schema) 

if self.config.doRunCatalogCalculation: 

self.makeSubtask("catalogCalculation", schema=self.schema) 

 

def runDataRef(self, patchRef, psfCache=100): 

"""! 

@brief Deblend and measure. 

 

@param[in] patchRef: Patch reference. 

 

Set 'is-primary' and related flags. Propagate flags 

from individual visits. Optionally match the sources to a reference catalog and write the matches. 

Finally, write the deblended sources and measurements out. 

""" 

exposure = patchRef.get(self.config.coaddName + "Coadd_calexp", immediate=True) 

exposure.getPsf().setCacheCapacity(psfCache) 

sources = self.readSources(patchRef) 

table = sources.getTable() 

table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog. 

 

self.measurement.run(sources, exposure, exposureId=self.getExposureId(patchRef)) 

 

if self.config.doApCorr: 

self.applyApCorr.run( 

catalog=sources, 

apCorrMap=exposure.getInfo().getApCorrMap() 

) 

 

# TODO DM-11568: this contiguous check-and-copy could go away if we 

# reserve enough space during SourceDetection and/or SourceDeblend. 

# NOTE: sourceSelectors require contiguous catalogs, so ensure 

# contiguity now, so views are preserved from here on. 

if not sources.isContiguous(): 

sources = sources.copy(deep=True) 

 

if self.config.doRunCatalogCalculation: 

self.catalogCalculation.run(sources) 

 

skyInfo = getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRef) 

self.setPrimaryFlags.run(sources, skyInfo.skyMap, skyInfo.tractInfo, skyInfo.patchInfo, 

includeDeblend=self.deblended) 

if self.config.doPropagateFlags: 

self.propagateFlags.run(patchRef.getButler(), sources, self.propagateFlags.getCcdInputs(exposure), 

exposure.getWcs()) 

if self.config.doMatchSources: 

self.writeMatches(patchRef, exposure, sources) 

self.write(patchRef, sources) 

 

def readSources(self, dataRef): 

"""! 

@brief Read input sources. 

 

@param[in] dataRef: Data reference for catalog of merged detections 

@return List of sources in merged catalog 

 

We also need to add columns to hold the measurements we're about to make 

so we can measure in-place. 

""" 

merged = dataRef.get(self.config.coaddName + self.inputCatalog, immediate=True) 

self.log.info("Read %d detections: %s" % (len(merged), dataRef.dataId)) 

idFactory = self.makeIdFactory(dataRef) 

for s in merged: 

idFactory.notify(s.getId()) 

table = afwTable.SourceTable.make(self.schema, idFactory) 

sources = afwTable.SourceCatalog(table) 

sources.extend(merged, self.schemaMapper) 

return sources 

 

def writeMatches(self, dataRef, exposure, sources): 

"""! 

@brief Write matches of the sources to the astrometric reference catalog. 

 

We use the Wcs in the exposure to match sources. 

 

@param[in] dataRef: data reference 

@param[in] exposure: exposure with Wcs 

@param[in] sources: source catalog 

""" 

result = self.match.run(sources, exposure.getInfo().getFilter().getName()) 

if result.matches: 

matches = afwTable.packMatches(result.matches) 

matches.table.setMetadata(result.matchMeta) 

dataRef.put(matches, self.config.coaddName + "Coadd_measMatch") 

if self.config.doWriteMatchesDenormalized: 

denormMatches = denormalizeMatches(result.matches, result.matchMeta) 

dataRef.put(denormMatches, self.config.coaddName + "Coadd_measMatchFull") 

 

def write(self, dataRef, sources): 

"""! 

@brief Write the source catalog. 

 

@param[in] dataRef: data reference 

@param[in] sources: source catalog 

""" 

dataRef.put(sources, self.config.coaddName + "Coadd_meas") 

self.log.info("Wrote %d sources: %s" % (len(sources), dataRef.dataId)) 

 

def getExposureId(self, dataRef): 

return int(dataRef.get(self.config.coaddName + "CoaddId"))