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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, PipelineTaskConfig, InitInputDatasetField, 

InitOutputDatasetField, InputDatasetField, OutputDatasetField) 

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

from lsst.meas.algorithms import DynamicDetectionTask, ReferenceObjectLoader 

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(PipelineTaskConfig): 

"""! 

@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", 

nameTemplate="{outputCoaddName}Coadd_det_schema", 

storageClass="SourceCatalog", 

) 

exposure = InputDatasetField( 

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

nameTemplate="{inputCoaddName}Coadd", 

scalar=True, 

storageClass="ExposureF", 

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

) 

outputBackgrounds = OutputDatasetField( 

doc="Output Backgrounds used in detection", 

nameTemplate="{outputCoaddName}Coadd_calexp_background", 

scalar=True, 

storageClass="Background", 

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

) 

outputSources = OutputDatasetField( 

doc="Detected sources catalog", 

nameTemplate="{outputCoaddName}Coadd_det", 

scalar=True, 

storageClass="SourceCatalog", 

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

) 

outputExposure = OutputDatasetField( 

doc="Exposure post detection", 

nameTemplate="{outputCoaddName}Coadd_calexp", 

scalar=True, 

storageClass="ExposureF", 

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

) 

 

def setDefaults(self): 

super().setDefaults() 

self.quantum.dimensions = ("Tract", "Patch", "AbstractFilter", "SkyMap") 

self.formatTemplateNames({"inputCoaddName": "deep", "outputCoaddName": "deep"}) 

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 

 

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) 

254 ↛ 256line 254 didn't jump to line 256, because the condition on line 254 was never false if schema is None: 

schema = afwTable.SourceTable.makeMinimalSchema() 

256 ↛ 257line 256 didn't jump to line 257, because the condition on line 256 was never true if self.config.doInsertFakes: 

self.makeSubtask("insertFakes") 

self.schema = schema 

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

260 ↛ exitline 260 didn't return from function '__init__', because the condition on line 260 was never false 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): 

packedId, maxBits = butler.registry.packDataId("TractPatchAbstractFilter", 

inputDataIds["exposure"], 

returnMaxBits=True) 

inputData["idFactory"] = afwTable.IdFactory.makeSource(packedId, 64 - maxBits) 

inputData["expId"] = packedId 

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 

""" 

306 ↛ 309line 306 didn't jump to line 309, because the condition on line 306 was never false if self.config.doScaleVariance: 

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

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

backgrounds = afwMath.BackgroundList() 

310 ↛ 311line 310 didn't jump to line 311, because the condition on line 310 was never true 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 

316 ↛ 319line 316 didn't jump to line 319, because the condition on line 316 was never false 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) 

424 ↛ 427line 424 didn't jump to line 427, because the condition on line 424 was never false 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() 

430 ↛ 434line 430 didn't jump to line 434, because the condition on line 430 was never false 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 

 

434 ↛ 435line 434 didn't jump to line 435, because the condition on line 434 was never true 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 

""" 

465 ↛ 467line 465 didn't jump to line 467, because the condition on line 465 was never true 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 

534 ↛ 540line 534 didn't jump to line 540, because the condition on line 534 was never false 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 

540 ↛ 541line 540 didn't jump to line 541, because the condition on line 540 was never true 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(PipelineTaskConfig): 

"""! 

@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") 

psfCache = Field(dtype=int, default=100, doc="Size of psfCache") 

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" 

) 

inputSchema = InitInputDatasetField( 

doc="Input schema for measure merged task produced by a deblender or detection task", 

nameTemplate="{inputCoaddName}Coadd_deblendedFlux_schema", 

storageClass="SourceCatalog" 

) 

outputSchema = InitOutputDatasetField( 

doc="Output schema after all new fields are added by task", 

nameTemplate="{inputCoaddName}Coadd_meas_schema", 

storageClass="SourceCatalog" 

) 

refCat = InputDatasetField( 

doc="Reference catalog used to match measured sources against known sources", 

name="ref_cat", 

storageClass="SimpleCatalog", 

dimensions=("SkyPix",), 

manualLoad=True 

) 

exposure = InputDatasetField( 

doc="Input coadd image", 

nameTemplate="{inputCoaddName}Coadd_calexp", 

scalar=True, 

storageClass="ExposureF", 

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

) 

skyMap = InputDatasetField( 

doc="SkyMap to use in processing", 

nameTemplate="{inputCoaddName}Coadd_skyMap", 

storageClass="SkyMap", 

dimensions=("SkyMap",), 

scalar=True 

) 

visitCatalogs = InputDatasetField( 

doc="Source catalogs for visits which overlap input tract, patch, abstract_filter. Will be " 

"further filtered in the task for the purpose of propagating flags from image calibration " 

"and characterization to codd objects", 

name="src", 

dimensions=("Instrument", "Visit", "Detector"), 

storageClass="SourceCatalog" 

) 

intakeCatalog = InputDatasetField( 

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, " 

"or deblendedFlux if the multiband deblender was configured to output " 

"deblended flux catalogs. If no deblending was performed this should " 

"be 'mergeDet'"), 

nameTemplate="{inputCoaddName}Coadd_deblendedFlux", 

storageClass="SourceCatalog", 

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

scalar=True 

) 

outputSources = OutputDatasetField( 

doc="Source catalog containing all the measurement information generated in this task", 

nameTemplate="{outputCoaddName}Coadd_meas", 

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

storageClass="SourceCatalog", 

scalar=True 

) 

matchResult = OutputDatasetField( 

doc="Match catalog produced by configured matcher, optional on doMatchSources", 

nameTemplate="{outputCoaddName}Coadd_measMatch", 

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

storageClass="Catalog", 

scalar=True 

) 

denormMatches = OutputDatasetField( 

doc="Denormalized Match catalog produced by configured matcher, optional on " 

"doWriteMatchesDenormalized", 

nameTemplate="{outputCoaddName}Coadd_measMatchFull", 

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

storageClass="Catalog", 

scalar=True 

) 

 

@property 

def refObjLoader(self): 

return self.match.refObjLoader 

 

def setDefaults(self): 

super().setDefaults() 

self.formatTemplateNames({"inputCoaddName": "deep", "outputCoaddName": "deep"}) 

self.quantum.dimensions = ("Tract", "Patch", "AbstractFilter", "SkyMap") 

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(PipelineTask, 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, initInputs=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. 

""" 

super().__init__(**kwargs) 

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

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

866 ↛ 867line 866 didn't jump to line 867, because the condition on line 866 was never true if initInputs is not None: 

schema = initInputs['inputSchema'].schema 

868 ↛ 871line 868 didn't jump to line 871, because the condition on line 868 was never false 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) 

877 ↛ 878line 877 didn't jump to line 878, because the condition on line 877 was never true if self.config.doMatchSources: 

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

879 ↛ 881line 879 didn't jump to line 881, because the condition on line 879 was never false if self.config.doPropagateFlags: 

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

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

882 ↛ 884line 882 didn't jump to line 884, because the condition on line 882 was never false if self.config.doApCorr: 

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

884 ↛ exitline 884 didn't return from function '__init__', because the condition on line 884 was never false if self.config.doRunCatalogCalculation: 

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

 

@classmethod 

def getInputDatasetTypes(cls, config): 

inputDatasetTypes = super().getInputDatasetTypes(config) 

if not config.doPropagateFlags: 

inputDatasetTypes.pop("visitCatalogs") 

return inputDatasetTypes 

 

@classmethod 

def getOutputDatasetTypes(cls, config): 

outputDatasetTypes = super().getOutputDatasetTypes(config) 

if config.doMatchSources is False: 

outputDatasetTypes.pop("matchResult") 

if config.doWriteMatchesDenormalized is False: 

outputDatasetTypes.pop("denormMatches") 

return outputDatasetTypes 

 

def getInitOutputDatasets(self): 

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

 

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

refObjLoader = ReferenceObjectLoader(inputDataIds['refCat'], butler, 

config=self.config.refObjLoader, log=self.log) 

self.match.setRefObjLoader(refObjLoader) 

 

# Set psfcache 

# move this to run after gen2 deprecation 

inputData['exposure'].getPsf().setCacheCapacity(self.config.psfCache) 

 

# Get unique integer ID for IdFactory and RNG seeds 

packedId, maxBits = butler.registry.packDataId("TractPatch", outputDataIds["outputSources"], 

returnMaxBits=True) 

inputData['exposureId'] = packedId 

idFactory = afwTable.IdFactory.makeSource(packedId, 64 - maxBits) 

# Transform inputCatalog 

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

sources = afwTable.SourceCatalog(table) 

sources.extend(inputData.pop('intakeCatalog'), self.schemaMapper) 

table = sources.getTable() 

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

inputData['sources'] = sources 

 

skyMap = inputData.pop('skyMap') 

tractNumber = inputDataIds['intakeCatalog']['tract'] 

tractInfo = skyMap[tractNumber] 

patchInfo = tractInfo.getPatchInfo(inputDataIds['intakeCatalog']['patch']) 

skyInfo = Struct( 

skyMap=skyMap, 

tractInfo=tractInfo, 

patchInfo=patchInfo, 

wcs=tractInfo.getWcs(), 

bbox=patchInfo.getOuterBBox() 

) 

inputData['skyInfo'] = skyInfo 

 

if self.config.doPropagateFlags: 

# Filter out any visit catalog that is not coadd inputs 

ccdInputs = inputData['exposure'].getInfo().getCoaddInputs().ccds 

visitKey = ccdInputs.schema.find("visit").key 

ccdKey = ccdInputs.schema.find("ccd").key 

inputVisitIds = set() 

ccdRecordsWcs = {} 

for ccdRecord in ccdInputs: 

visit = ccdRecord.get(visitKey) 

ccd = ccdRecord.get(ccdKey) 

inputVisitIds.add((visit, ccd)) 

ccdRecordsWcs[(visit, ccd)] = ccdRecord.getWcs() 

 

inputCatalogsToKeep = [] 

inputCatalogWcsUpdate = [] 

for i, dataId in enumerate(inputDataIds['visitCatalogs']): 

key = (dataId['visit'], dataId['detector']) 

if key in inputVisitIds: 

inputCatalogsToKeep.append(inputData['visitCatalogs'][i]) 

inputCatalogWcsUpdate.append(ccdRecordsWcs[key]) 

inputData['visitCatalogs'] = inputCatalogsToKeep 

inputData['wcsUpdates'] = inputCatalogWcsUpdate 

inputData['ccdInputs'] = ccdInputs 

 

return self.run(**inputData) 

 

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. 

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

 

984 ↛ 987line 984 didn't jump to line 987, because the condition on line 984 was never false if self.config.doPropagateFlags: 

ccdInputs = self.propagateFlags.getCcdInputs(exposure) 

else: 

ccdInputs = None 

 

results = self.run(exposure=exposure, sources=sources, 

ccdInputs=ccdInputs, 

skyInfo=skyInfo, butler=patchRef.getButler(), 

exposureId=self.getExposureId(patchRef)) 

 

994 ↛ 995line 994 didn't jump to line 995, because the condition on line 994 was never true if self.config.doMatchSources: 

self.writeMatches(patchRef, results) 

self.write(patchRef, results.outputSources) 

 

def run(self, exposure, sources, skyInfo, exposureId, ccdInputs=None, visitCatalogs=None, wcsUpdates=None, 

butler=None): 

"""Run measurement algorithms on the input exposure, and optionally populate the 

resulting catalog with extra information. 

 

Parameters 

---------- 

exposure : `lsst.afw.exposure.Exposure` 

The input exposure on which measurements are to be performed 

sources : `lsst.afw.table.SourceCatalog` 

A catalog built from the results of merged detections, or 

deblender outputs. 

skyInfo : `lsst.pipe.base.Struct` 

A struct containing information about the position of the input exposure within 

a `SkyMap`, the `SkyMap`, its `Wcs`, and its bounding box 

exposureId : `int` or `bytes` 

packed unique number or bytes unique to the input exposure 

ccdInputs : `lsst.afw.table.ExposureCatalog` 

Catalog containing information on the individual visits which went into making 

the exposure 

visitCatalogs : list of `lsst.afw.table.SourceCatalogs` or `None` 

A list of source catalogs corresponding to measurements made on the individual 

visits which went into the input exposure. If None and butler is `None` then 

the task cannot propagate visit flags to the output catalog. 

wcsUpdates : list of `lsst.afw.geom.SkyWcs` or `None` 

If visitCatalogs is not `None` this should be a list of wcs objects which correspond 

to the input visits. Used to put all coordinates to common system. If `None` and 

butler is `None` then the task cannot propagate visit flags to the output catalog. 

butler : `lsst.daf.butler.Butler` or `lsst.daf.persistence.Butler` 

Either a gen2 or gen3 butler used to load visit catalogs 

 

Returns 

------- 

results : `lsst.pipe.base.Struct` 

Results of running measurement task. Will contain the catalog in the 

sources attribute. Optionally will have results of matching to a 

reference catalog in the matchResults attribute, and denormalized 

matches in the denormMatches attribute. 

""" 

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

 

1039 ↛ 1049line 1039 didn't jump to line 1049, because the condition on line 1039 was never false 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. 

1049 ↛ 1050line 1049 didn't jump to line 1050, because the condition on line 1049 was never true if not sources.isContiguous(): 

sources = sources.copy(deep=True) 

 

1052 ↛ 1055line 1052 didn't jump to line 1055, because the condition on line 1052 was never false if self.config.doRunCatalogCalculation: 

self.catalogCalculation.run(sources) 

 

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

includeDeblend=self.deblended) 

1057 ↛ 1060line 1057 didn't jump to line 1060, because the condition on line 1057 was never false if self.config.doPropagateFlags: 

self.propagateFlags.run(butler, sources, ccdInputs, exposure.getWcs(), visitCatalogs, wcsUpdates) 

 

results = Struct() 

 

1062 ↛ 1063line 1062 didn't jump to line 1063, because the condition on line 1062 was never true if self.config.doMatchSources: 

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

matches = afwTable.packMatches(matchResult.matches) 

matches.table.setMetadata(matchResult.matchMeta) 

results.matchResult = matches 

if self.config.doWriteMatchesDenormalized: 

results.denormMatches = denormalizeMatches(matchResult.matches, 

matchResult.matchMeta) 

 

results.outputSources = sources 

return results 

 

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, results): 

"""! 

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

 

@param[in] dataRef: data reference 

@param[in] results: results struct from run method 

""" 

if hasattr(results, "matchResult"): 

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

if hasattr(results, "denormMatches"): 

dataRef.put(results.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"))