lsst.pipe.tasks  13.0-66-gfbf2f2ce+5
Public Member Functions | Public Attributes | Static Public Attributes | List of all members
lsst.pipe.tasks.assembleCoadd.CompareWarpAssembleCoaddTask Class Reference

Assemble a compareWarp coadded image from a set of warps by masking artifacts detected by comparing PSF-matched warps. More...

Inheritance diagram for lsst.pipe.tasks.assembleCoadd.CompareWarpAssembleCoaddTask:
lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask lsst.pipe.tasks.coaddBase.CoaddBaseTask

Public Member Functions

def __init__ (self, args, kwargs)
 Initialize the task and make the assembleStaticSkyModel subtask. More...
 
def makeSupplementaryData (self, dataRef, selectDataList)
 Make inputs specific to Subclass. More...
 
def assemble (self, skyInfo, tempExpRefList, imageScalerList, weightList, bgModelList, supplementaryData, args, kwargs)
 Assemble the coadd. More...
 
def findArtifacts (self, templateCoadd, tempExpRefList, imageScalerList)
 Find artifacts. More...
 
def computeAltMaskList (self, tempExpRefList, maskSpanSets)
 Apply artifact span set lists to masks. More...
 
def run (self, dataRef, selectDataList=[])
 Assemble a coadd from a set of Warps. More...
 
def getTempExpRefList (self, patchRef, calExpRefList)
 Generate list data references corresponding to warped exposures that lie within the patch to be coadded. More...
 
def getBackgroundReferenceScaler (self, dataRef)
 Construct an image scaler for the background reference frame. More...
 
def prepareInputs (self, refList)
 Prepare the input warps for coaddition by measuring the weight for each warp and the scaling for the photometric zero point. More...
 
def backgroundMatching (self, inputData, refExpDataRef=None, refImageScaler=None)
 Perform background matching on the prepared inputs. More...
 
def assembleMetadata (self, coaddExposure, tempExpRefList, weightList)
 Set the metadata for the coadd. More...
 
def assembleSubregion (self, coaddExposure, bbox, tempExpRefList, imageScalerList, weightList, bgInfoList, altMaskList, statsFlags, statsCtrl, nImage=None)
 Assemble the coadd for a sub-region. More...
 
def addBackgroundMatchingMetadata (self, coaddExposure, tempExpRefList, backgroundInfoList)
 Add metadata from the background matching to the coadd. More...
 
def readBrightObjectMasks (self, dataRef)
 
def setBrightObjectMasks (self, exposure, dataId, brightObjectMasks)
 
def selectExposures (self, patchRef, skyInfo=None, selectDataList=[])
 Select exposures to coadd. More...
 
def getSkyInfo (self, patchRef)
 Use getSkyinfo to return the skyMap, tract and patch information, wcs and the outer bbox of the patch. More...
 
def getCalExp (self, dataRef, bgSubtracted)
 Return one "calexp" calibrated exposure. More...
 
def getCoaddDatasetName (self, warpType="direct")
 
def getTempExpDatasetName (self, warpType="direct")
 
def getBadPixelMask (self)
 Convenience method to provide the bitmask from the mask plane names. More...
 

Public Attributes

 brightObjectBitmask
 
 warpType
 

Static Public Attributes

 ConfigClass = CompareWarpAssembleCoaddConfig
 
 RunnerClass = CoaddTaskRunner
 

Detailed Description

Assemble a compareWarp coadded image from a set of warps by masking artifacts detected by comparing PSF-matched warps.

Contents

Description

CompareWarpAssembleCoaddTask

In AssembleCoaddTask, we compute the coadd as an clipped mean (i.e. we clip outliers). The problem with doing this is that when computing the coadd PSF at a given location, individual visit PSFs from visits with outlier pixels contribute to the coadd PSF and cannot be treated correctly. In this task, we correct for this behavior by creating a new badMaskPlane 'CLIPPED' which marks pixels in the individual warps suspected to contain an artifact. We populate this plane on the input warps by comparing PSF-matched warps with a PSF-matched median coadd which serves as a model of the static sky. Any group of pixels that deviates from the PSF-matched median coadd by more than config.chiThreshold sigma, is an artifact candidate. The candidates are then filtered to remove variable sources and sources that are difficult to subtract such as bright stars. This filter is configured using the config parameters temporalThreshold and spatialThreshold. The temporalThreshold is the maximum fraction of epochs that the deviation can appear in and still be considered an artifact. The spatialThreshold is the maximum fraction of pixels in the footprint of the deviation that appear in other epochs (where other epochs is defined by the temporalThreshold). If the deviant region meets this criteria of having a significant percentage of pixels that deviate in only a few epochs, it is grown by growMaskBy and bits set in the 'CLIPPED' plane. These regions will not contribute to the final coadd. Furthermore, any routine to determine the coadd PSF can now be cognizant of clipped regions. Note that the algorithm implemented by this task is preliminary and works correctly for HSC data. Parameter modifications and or considerable redesigning of the algorithm is likley required for other surveys.

CompareWarpAssembleCoaddTask sub-classes AssembleCoaddTask and instantiates AssembleCoaddTask as a subtask to generate the TemplateCoadd (the model of the static sky)

Task initialization

Initialize the task and make the assembleStaticSkyModel subtask.

Invoking the Task

Assemble a coadd from a set of Warps. Coadd a set of Warps. Compute weights to be applied to each Warp and find scalings to match the photometric zeropoint to a reference Warp. Optionally, match backgrounds across Warps if the background has not already been removed. Assemble the Warps using assemble. Interpolate over NaNs and optionally write the coadd to disk. Return the coadded exposure.

Parameters
[in]dataRefData reference defining the patch for coaddition and the reference Warp (if config.autoReference=False). Used to access the following data products:
  • [in] self.config.coaddName + "Coadd_skyMap"
  • [in] self.config.coaddName + "Coadd_ + <warpType> + "Warp" (optionally) - [out] self.config.coaddName + "Coadd"
[in]selectDataList[in]List of data references to Warps. Data to be coadded will be selected from this list based on overlap with the patch defined by dataRef.
Returns
a pipeBase.Struct with fields:
  • coaddExposure: coadded exposure
  • nImage: exposure count image

Configuration parameters

See CompareWarpAssembleCoaddConfig

Debug variables

The command line task interface supports a flag -d to import debug.py from your PYTHONPATH; see baseDebug for more about debug.py files. CompareWarpAssembleCoaddTask has no debug variables of its own.

A complete example of using

CompareWarpAssembleCoaddTask

CompareWarpAssembleCoaddTask assembles a set of warped images into a coadded image. The CompareWarpAssembleCoaddTask is invoked by running assembleCoadd.py with the flag '–compareWarpCoadd'. Usage of assembleCoadd.py expects a data reference to the tract patch and filter to be coadded (specified using '–id = [KEY=VALUE1[^VALUE2[^VALUE3...] [KEY=VALUE1[^VALUE2[^VALUE3...] ...]]') along with a list of coaddTempExps to attempt to coadd (specified using '–selectId [KEY=VALUE1[^VALUE2[^VALUE3...] [KEY=VALUE1[^VALUE2[^VALUE3...] ...]]'). Only the warps that cover the specified tract and patch will be coadded. A list of the available optional arguments can be obtained by calling assembleCoadd.py with the –help command line argument:

assembleCoadd.py --help

To demonstrate usage of the CompareWarpAssembleCoaddTask in the larger context of multi-band processing, we will generate the HSC-I & -R band coadds from HSC engineering test data provided in the ci_hsc package. To begin, assuming that the lsst stack has been already set up, we must set up the obs_subaru and ci_hsc packages. This defines the environment variable $CI_HSC_DIR and points at the location of the package. The raw HSC data live in the $CI_HSC_DIR/raw directory. To begin assembling the coadds, we must first

processCcd
process the individual ccds in $CI_HSC_RAW to produce calibrated exposures
makeSkyMap
create a skymap that covers the area of the sky present in the raw exposures
makeCoaddTempExp
warp the individual calibrated exposures to the tangent plane of the coadd

We can perform all of these steps by running

$CI_HSC_DIR scons warp-903986 warp-904014 warp-903990 warp-904010 warp-903988

This will produce warped coaddTempExps for each visit. To coadd the warped data, we call assembleCoadd.py as follows:

assembleCoadd.py --compareWarpCoadd $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I \
--selectId visit=903986 ccd=16 --selectId visit=903986 ccd=22 --selectId visit=903986 ccd=23 \
--selectId visit=903986 ccd=100 --selectId visit=904014 ccd=1 --selectId visit=904014 ccd=6 \
--selectId visit=904014 ccd=12 --selectId visit=903990 ccd=18 --selectId visit=903990 ccd=25 \
--selectId visit=904010 ccd=4 --selectId visit=904010 ccd=10 --selectId visit=904010 ccd=100 \
--selectId visit=903988 ccd=16 --selectId visit=903988 ccd=17 --selectId visit=903988 ccd=23 \
--selectId visit=903988 ccd=24

This will process the HSC-I band data. The results are written in $CI_HSC_DIR/DATA/deepCoadd-results/HSC-I.

Definition at line 1498 of file assembleCoadd.py.

Constructor & Destructor Documentation

◆ __init__()

def lsst.pipe.tasks.assembleCoadd.CompareWarpAssembleCoaddTask.__init__ (   self,
  args,
  kwargs 
)

Initialize the task and make the assembleStaticSkyModel subtask.

Definition at line 1609 of file assembleCoadd.py.

Member Function Documentation

◆ addBackgroundMatchingMetadata()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.addBackgroundMatchingMetadata (   self,
  coaddExposure,
  tempExpRefList,
  backgroundInfoList 
)
inherited

Add metadata from the background matching to the coadd.

Parameters
[in]coaddExposureCoadd
[in]tempExpRefListList of data references for temp exps to go into coadd
[in]backgroundInfoListList of background info, results from background matching

Definition at line 787 of file assembleCoadd.py.

◆ assemble()

def lsst.pipe.tasks.assembleCoadd.CompareWarpAssembleCoaddTask.assemble (   self,
  skyInfo,
  tempExpRefList,
  imageScalerList,
  weightList,
  bgModelList,
  supplementaryData,
  args,
  kwargs 
)

Assemble the coadd.

Requires additional inputs Struct supplementaryData to contain a templateCoadd that serves as the model of the static sky.

Find artifacts and apply them to the warps' masks creating a list of alternative masks with a new "CLIPPED" plane and updated "NO_DATA" plane. Then pass these alternative masks to the base class's assemble method.

Parameters
skyInfoPatch geometry information
tempExpRefListList of data references to warps
imageScalerListList of image scalers
weightListList of weights
bgModelListList of background models from background matching
supplementaryDataPipeBase.Struct containing a templateCoadd

return pipeBase.Struct with coaddExposure, nImage if requested

Definition at line 1626 of file assembleCoadd.py.

◆ assembleMetadata()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.assembleMetadata (   self,
  coaddExposure,
  tempExpRefList,
  weightList 
)
inherited

Set the metadata for the coadd.

This basic implementation simply sets the filter from the first input.

Parameters
[in]coaddExposureThe target image for the coadd
[in]tempExpRefListList of data references to tempExp
[in]weightListList of weights

Definition at line 673 of file assembleCoadd.py.

◆ assembleSubregion()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.assembleSubregion (   self,
  coaddExposure,
  bbox,
  tempExpRefList,
  imageScalerList,
  weightList,
  bgInfoList,
  altMaskList,
  statsFlags,
  statsCtrl,
  nImage = None 
)
inherited

Assemble the coadd for a sub-region.

For each coaddTempExp, check for (and swap in) an alternative mask if one is passed. If background matching is enabled, add the background and background variance from each coaddTempExp. Remove mask planes listed in config.removeMaskPlanes, Finally, stack the actual exposures using statisticsStack with the statistic specified by statsFlags. Typically, the statsFlag will be one of afwMath.MEAN for a mean-stack or afwMath.MEANCLIP for outlier rejection using an N-sigma clipped mean where N and iterations are specified by statsCtrl. Assign the stacked subregion back to the coadd.

Parameters
[in]coaddExposureThe target image for the coadd
[in]bboxSub-region to coadd
[in]tempExpRefListList of data reference to tempExp
[in]imageScalerListList of image scalers
[in]weightListList of weights
[in]bgInfoListList of background data from background matching
[in]altMaskListList of alternate masks to use rather than those stored with tempExp, or None
[in]statsFlagsafwMath.Property object for statistic for coadd
[in]statsCtrlStatistics control object for coadd
[in]nImageoptional ImageU keeps track of exposure count for each pixel

Definition at line 719 of file assembleCoadd.py.

◆ backgroundMatching()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.backgroundMatching (   self,
  inputData,
  refExpDataRef = None,
  refImageScaler = None 
)
inherited

Perform background matching on the prepared inputs.

Each Warp has a different background level that must be normalized to a reference level before coaddition. If no reference is provided, the background matcher selects one. If the background matching is performed sucessfully, recompute the weight to be applied to the Warp (coaddTempExp) to be consistent with the scaled background.

Parameters
[in]inputDataStruct from prepareInputs() with tempExpRefList, weightList, imageScalerList
[in]refExpDataRefData reference for background reference Warp, or None
[in]refImageScalerImage scaler for background reference Warp, or None
Returns
Struct:
  • tempExprefList: List of data references to warped exposures (coaddTempExps)
  • weightList: List of weightings
  • imageScalerList: List of image scalers
  • backgroundInfoList: result from background matching

Definition at line 532 of file assembleCoadd.py.

◆ computeAltMaskList()

def lsst.pipe.tasks.assembleCoadd.CompareWarpAssembleCoaddTask.computeAltMaskList (   self,
  tempExpRefList,
  maskSpanSets 
)

Apply artifact span set lists to masks.

Parameters
tempExpRefListList of data references to warps
maskSpanSetsStruct containing artifact and noData spanSet lists to apply

return List of alternative masks

Add artifact span set list as "CLIPPED" plane and NaNs to existing "NO_DATA" plane

Definition at line 1717 of file assembleCoadd.py.

◆ findArtifacts()

def lsst.pipe.tasks.assembleCoadd.CompareWarpAssembleCoaddTask.findArtifacts (   self,
  templateCoadd,
  tempExpRefList,
  imageScalerList 
)

Find artifacts.

Loop through warps twice. The first loop builds a map with the count of how many epochs each pixel deviates from the templateCoadd by more than config.chiThreshold sigma. The second loop takes each difference image and filters the artifacts detected in each using count map to filter out variable sources and sources that are difficult to subtract cleanly.

Parameters
templateCoaddExposure to serve as model of static sky
tempExpRefListList of data references to warps
imageScalerListList of image scalers

Definition at line 1657 of file assembleCoadd.py.

◆ getBackgroundReferenceScaler()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.getBackgroundReferenceScaler (   self,
  dataRef 
)
inherited

Construct an image scaler for the background reference frame.

Each Warp has a different background level. A reference background level must be chosen before coaddition. If config.autoReference=True, backgroundMatching will pick the reference level and this routine is a no-op and None is returned. Otherwise, use the scaleZeroPoint subtask to compute an imageScaler object for the provided reference image and return it.

Parameters
[in]dataRefData reference for the background reference frame, or None
Returns
image scaler, or None

Definition at line 442 of file assembleCoadd.py.

◆ getBadPixelMask()

def lsst.pipe.tasks.coaddBase.CoaddBaseTask.getBadPixelMask (   self)
inherited

Convenience method to provide the bitmask from the mask plane names.

Definition at line 217 of file coaddBase.py.

◆ getCalExp()

def lsst.pipe.tasks.coaddBase.CoaddBaseTask.getCalExp (   self,
  dataRef,
  bgSubtracted 
)
inherited

Return one "calexp" calibrated exposure.

Parameters
[in]dataRefa sensor-level data reference
[in]bgSubtractedreturn calexp with background subtracted? If False get the calexp's background background model and add it to the calexp.
Returns
calibrated exposure

If config.doApplyUberCal, meas_mosaic calibrations will be applied to the returned exposure using applyMosaicResults.

Definition at line 139 of file coaddBase.py.

◆ getCoaddDatasetName()

def lsst.pipe.tasks.coaddBase.CoaddBaseTask.getCoaddDatasetName (   self,
  warpType = "direct" 
)
inherited
Return coadd name for given warpType and task config

Parameters
----------
warpType : string
    Either 'direct' or 'psfMatched'

Returns
-------
CoaddDatasetName : `string`

Definition at line 167 of file coaddBase.py.

◆ getSkyInfo()

def lsst.pipe.tasks.coaddBase.CoaddBaseTask.getSkyInfo (   self,
  patchRef 
)
inherited

Use getSkyinfo to return the skyMap, tract and patch information, wcs and the outer bbox of the patch.

Parameters
[in]patchRefdata reference for sky map. Must include keys "tract" and "patch"
Returns
pipe_base Struct containing:
  • skyMap: sky map
  • tractInfo: information for chosen tract of sky map
  • patchInfo: information about chosen patch of tract
  • wcs: WCS of tract
  • bbox: outer bbox of patch, as an afwGeom Box2I

Definition at line 123 of file coaddBase.py.

◆ getTempExpDatasetName()

def lsst.pipe.tasks.coaddBase.CoaddBaseTask.getTempExpDatasetName (   self,
  warpType = "direct" 
)
inherited
Return warp name for given warpType and task config

Parameters
----------
warpType : string
    Either 'direct' or 'psfMatched'

Returns
-------
WarpDatasetName : `string`

Definition at line 182 of file coaddBase.py.

◆ getTempExpRefList()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.getTempExpRefList (   self,
  patchRef,
  calExpRefList 
)
inherited

Generate list data references corresponding to warped exposures that lie within the patch to be coadded.

Parameters
[in]patchRefData reference for patch
[in]calExpRefListList of data references for input calexps
Returns
List of Warp/CoaddTempExp data references

Definition at line 425 of file assembleCoadd.py.

◆ makeSupplementaryData()

def lsst.pipe.tasks.assembleCoadd.CompareWarpAssembleCoaddTask.makeSupplementaryData (   self,
  dataRef,
  selectDataList 
)

Make inputs specific to Subclass.

Generate a templateCoadd to use as a native model of static sky to subtract from warps.

Definition at line 1616 of file assembleCoadd.py.

◆ prepareInputs()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.prepareInputs (   self,
  refList 
)
inherited

Prepare the input warps for coaddition by measuring the weight for each warp and the scaling for the photometric zero point.

Each Warp has its own photometric zeropoint and background variance. Before coadding these Warps together, compute a scale factor to normalize the photometric zeropoint and compute the weight for each Warp.

Parameters
[in]refListList of data references to tempExp
Returns
Struct:
  • tempExprefList: List of data references to tempExp
  • weightList: List of weightings
  • imageScalerList: List of image scalers

Definition at line 470 of file assembleCoadd.py.

◆ readBrightObjectMasks()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.readBrightObjectMasks (   self,
  dataRef 
)
inherited
Returns None on failure

Definition at line 810 of file assembleCoadd.py.

◆ run()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.run (   self,
  dataRef,
  selectDataList = [] 
)
inherited

Assemble a coadd from a set of Warps.

Coadd a set of Warps. Compute weights to be applied to each Warp and find scalings to match the photometric zeropoint to a reference Warp. Optionally, match backgrounds across Warps if the background has not already been removed. Assemble the Warps using assemble. Interpolate over NaNs and optionally write the coadd to disk. Return the coadded exposure.

Parameters
[in]dataRefData reference defining the patch for coaddition and the reference Warp (if config.autoReference=False). Used to access the following data products:
  • [in] self.config.coaddName + "Coadd_skyMap"
  • [in] self.config.coaddName + "Coadd_ + <warpType> + "Warp" (optionally) - [out] self.config.coaddName + "Coadd"
[in]selectDataList[in]List of data references to Warps. Data to be coadded will be selected from this list based on overlap with the patch defined by dataRef.
Returns
a pipeBase.Struct with fields:
  • coaddExposure: coadded exposure
  • nImage: exposure count image

Definition at line 342 of file assembleCoadd.py.

◆ selectExposures()

def lsst.pipe.tasks.coaddBase.CoaddBaseTask.selectExposures (   self,
  patchRef,
  skyInfo = None,
  selectDataList = [] 
)
inherited

Select exposures to coadd.

Get the corners of the bbox supplied in skyInfo using afwGeom.Box2D and convert the pixel positions of the bbox corners to sky coordinates using skyInfo.wcs.pixelToSky. Use the WcsSelectImagesTask to select exposures that lie inside the patch indicated by the dataRef.

Parameters
[in]patchRefdata reference for sky map patch. Must include keys "tract", "patch", plus the camera-specific filter key (e.g. "filter" or "band")
[in]skyInfogeometry for the patch; output from getSkyInfo
Returns
a list of science exposures to coadd, as butler data references

Definition at line 103 of file coaddBase.py.

◆ setBrightObjectMasks()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.setBrightObjectMasks (   self,
  exposure,
  dataId,
  brightObjectMasks 
)
inherited
Set the bright object masks

exposure:          Exposure under consideration
dataId:            Data identifier dict for patch
brightObjectMasks: afwTable of bright objects to mask

Definition at line 818 of file assembleCoadd.py.

Member Data Documentation

◆ brightObjectBitmask

lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.brightObjectBitmask
inherited

Definition at line 333 of file assembleCoadd.py.

◆ ConfigClass

lsst.pipe.tasks.assembleCoadd.CompareWarpAssembleCoaddTask.ConfigClass = CompareWarpAssembleCoaddConfig
static

Definition at line 1606 of file assembleCoadd.py.

◆ RunnerClass

lsst.pipe.tasks.coaddBase.CoaddBaseTask.RunnerClass = CoaddTaskRunner
staticinherited

Definition at line 96 of file coaddBase.py.

◆ warpType

lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.warpType
inherited

Definition at line 339 of file assembleCoadd.py.


The documentation for this class was generated from the following file: