AssembleCoaddTask

class lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask(*args, **kwargs)

Bases: lsst.pipe.tasks.coaddBase.CoaddBaseTask

Assemble a coadded image from a set of warps (coadded temporary exposures).

We want to assemble a coadded image from a set of Warps (also called coadded temporary exposures or coaddTempExps). Each input Warp covers a patch on the sky and corresponds to a single run/visit/exposure of the covered patch. We provide the task with a list of Warps (selectDataList) from which it selects Warps that cover the specified patch (pointed at by dataRef). Each Warp that goes into a coadd will typically have an independent photometric zero-point. Therefore, we must scale each Warp to set it to a common photometric zeropoint. WarpType may be one of ‘direct’ or ‘psfMatched’, and the boolean configs config.makeDirect and config.makePsfMatched set which of the warp types will be coadded. The coadd is computed as a mean with optional outlier rejection. Criteria for outlier rejection are set in AssembleCoaddConfig. Finally, Warps can have bad ‘NaN’ pixels which received no input from the source calExps. We interpolate over these bad (NaN) pixels.

AssembleCoaddTask uses several sub-tasks. These are

  • ScaleZeroPointTask
  • create and use an imageScaler object to scale the photometric zeropoint for each Warp
  • InterpImageTask
  • interpolate across bad pixels (NaN) in the final coadd

You can retarget these subtasks if you wish.

Notes

The lsst.pipe.base.CmdLineTask interface supports a flag -d to import debug.py from your PYTHONPATH; see baseDebug for more about debug.py files. AssembleCoaddTask has no debug variables of its own. Some of the subtasks may support debug variables. See the documentation for the subtasks for further information.

Examples

AssembleCoaddTask assembles a set of warped images into a coadded image. The AssembleCoaddTask can be invoked by running assembleCoadd.py with the flag ‘–legacyCoadd’. Usage of assembleCoadd.py expects two inputs: a data reference to the tract patch and filter to be coadded, and a list of Warps to attempt to coadd. These are specified using --id and --selectId, respectively:

--id = [KEY=VALUE1[^VALUE2[^VALUE3...] [KEY=VALUE1[^VALUE2[^VALUE3...] ...]]
--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 AssembleCoaddTask 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 exposures for each visit. To coadd the warped data, we call assembleCoadd.py as follows:

assembleCoadd.py --legacyCoadd $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

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

You may also choose to run:

scons warp-903334 warp-903336 warp-903338 warp-903342 warp-903344 warp-903346
assembleCoadd.py --legacyCoadd $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R        --selectId visit=903334 ccd=16 --selectId visit=903334 ccd=22 --selectId visit=903334 ccd=23        --selectId visit=903334 ccd=100 --selectId visit=903336 ccd=17 --selectId visit=903336 ccd=24        --selectId visit=903338 ccd=18 --selectId visit=903338 ccd=25 --selectId visit=903342 ccd=4        --selectId visit=903342 ccd=10 --selectId visit=903342 ccd=100 --selectId visit=903344 ccd=0        --selectId visit=903344 ccd=5 --selectId visit=903344 ccd=11 --selectId visit=903346 ccd=1        --selectId visit=903346 ccd=6 --selectId visit=903346 ccd=12

to generate the coadd for the HSC-R band if you are interested in following multiBand Coadd processing as discussed in pipeTasks_multiBand (but note that normally, one would use the SafeClipAssembleCoaddTask rather than AssembleCoaddTask to make the coadd.

Methods Summary

applyAltMaskPlanes(mask, altMaskSpans) Apply in place alt mask formatted as SpanSets to a mask.
assembleMetadata(coaddExposure, …) Set the metadata for the coadd.
assembleSubregion(coaddExposure, bbox, …) Assemble the coadd for a sub-region.
getTempExpRefList(patchRef, calExpRefList) Generate list data references corresponding to warped exposures that lie within the patch to be coadded.
makeSupplementaryData(dataRef, selectDataList) Make additional inputs to run() specific to subclasses.
prepareInputs(refList) Prepare the input warps for coaddition by measuring the weight for each warp and the scaling for the photometric zero point.
prepareStats([mask]) Prepare the statistics for coadding images.
processResults(coaddExposure, dataRef) Interpolate over missing data and mask bright stars.
readBrightObjectMasks(dataRef) Retrieve the bright object masks.
removeMaskPlanes(maskedImage) Unset the mask of an image for mask planes specified in the config.
run(skyInfo, tempExpRefList, …[, …]) Assemble a coadd from input warps
runDataRef(dataRef[, selectDataList]) Assemble a coadd from a set of Warps.
setBrightObjectMasks(exposure, dataId, …) Set the bright object masks.
setInexactPsf(mask) Set INEXACT_PSF mask plane.
setRejectedMaskMapping(statsCtrl) Map certain mask planes of the warps to new planes for the coadd.
shrinkValidPolygons(coaddInputs) Shrink coaddInputs’ ccds’ ValidPolygons in place.

Methods Documentation

applyAltMaskPlanes(mask, altMaskSpans)

Apply in place alt mask formatted as SpanSets to a mask.

Parameters:
mask : lsst.afw.image.Mask

Original mask.

altMaskSpans : dict

SpanSet lists to apply. Each element contains the new mask plane name (e.g. “CLIPPED and/or “NO_DATA”) as the key, and list of SpanSets to apply to the mask.
Returns:
mask : lsst.afw.image.Mask

Updated mask.
assembleMetadata(coaddExposure, tempExpRefList, weightList)

Set the metadata for the coadd.

This basic implementation sets the filter from the first input.

Parameters:
coaddExposure : lsst.afw.image.Exposure

The target exposure for the coadd.

tempExpRefList : list

List of data references to tempExp.

weightList : list

List of weights.
assembleSubregion(coaddExposure, bbox, tempExpRefList, imageScalerList, weightList, altMaskList, statsFlags, statsCtrl, nImage=None)

Assemble the coadd for a sub-region.

For each coaddTempExp, check for (and swap in) an alternative mask if one is passed. Remove mask planes listed in config.removeMaskPlanes. Finally, stack the actual exposures using lsst.afw.math.statisticsStack with the statistic specified by statsFlags. Typically, the statsFlag will be one of lsst.afw.math.MEAN for a mean-stack or lsst.afw.math.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:
coaddExposure : lsst.afw.image.Exposure

The target exposure for the coadd.

bbox : lsst.afw.geom.Box

Sub-region to coadd.

tempExpRefList : list

List of data reference to tempExp.

imageScalerList : list

List of image scalers.

weightList : list

List of weights.

altMaskList : list

List of alternate masks to use rather than those stored with tempExp, or None. Each element is dict with keys = mask plane name to which to add the spans.

statsFlags : lsst.afw.math.Property

Property object for statistic for coadd.

statsCtrl : lsst.afw.math.StatisticsControl

Statistics control object for coadd.

nImage : lsst.afw.image.ImageU, optional

Keeps track of exposure count for each pixel.
getTempExpRefList(patchRef, calExpRefList)

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

Parameters:
patchRef : dataRef

Data reference for patch.

calExpRefList : list

List of data references for input calexps.
Returns:
tempExpRefList : list

List of Warp/CoaddTempExp data references.
makeSupplementaryData(dataRef, selectDataList)

Make additional inputs to run() specific to subclasses.

Available to be implemented by subclasses only if they need the coadd dataRef for performing preliminary processing before assembling the coadd.

Parameters:
dataRef : lsst.daf.persistence.ButlerDataRef

Butler data reference for supplementary data.

selectDataList : list

List of data references to Warps.
prepareInputs(refList)

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:
refList : list

List of data references to tempExp
Returns:
result : lsst.pipe.base.Struct

Result struct with components:

  • tempExprefList: list of data references to tempExp.
  • weightList: list of weightings.
  • imageScalerList: list of image scalers.
prepareStats(mask=None)

Prepare the statistics for coadding images.

Parameters:
mask : int, optional

Bit mask value to exclude from coaddition.
Returns:
stats : lsst.pipe.base.Struct

Statistics structure with the following fields:

  • statsCtrl: Statistics control object for coadd
    (lsst.afw.math.StatisticsControl)
  • statsFlags: Statistic for coadd (lsst.afw.math.Property)
processResults(coaddExposure, dataRef)

Interpolate over missing data and mask bright stars.

Parameters:
coaddExposure : lsst.afw.image.Exposure

The coadded exposure to process.

dataRef : lsst.daf.persistence.ButlerDataRef

Butler data reference for supplementary data.
readBrightObjectMasks(dataRef)

Retrieve the bright object masks.

Returns None on failure.

Parameters:
dataRef : lsst.daf.persistence.butlerSubset.ButlerDataRef

A Butler dataRef.
Returns:
result : lsst.daf.persistence.butlerSubset.ButlerDataRef

Bright object mask from the Butler object, or None if it cannot be retrieved.
removeMaskPlanes(maskedImage)

Unset the mask of an image for mask planes specified in the config.

Parameters:
maskedImage : lsst.afw.image.MaskedImage

The masked image to be modified.
run(skyInfo, tempExpRefList, imageScalerList, weightList, altMaskList=None, mask=None, supplementaryData=None)

Assemble a coadd from input warps

Assemble the coadd using the provided list of coaddTempExps. Since the full coadd covers a patch (a large area), the assembly is performed over small areas on the image at a time in order to conserve memory usage. Iterate over subregions within the outer bbox of the patch using assembleSubregion to stack the corresponding subregions from the coaddTempExps with the statistic specified. Set the edge bits the coadd mask based on the weight map.

Parameters:
skyInfo : lsst.pipe.base.Struct

Struct with geometric information about the patch.

tempExpRefList : list

List of data references to Warps (previously called CoaddTempExps).

imageScalerList : list

List of image scalers.

weightList : list

List of weights

altMaskList : list, optional

List of alternate masks to use rather than those stored with tempExp.

mask : lsst.afw.image.Mask, optional

Mask to ignore when coadding

supplementaryData : lsst.pipe.base.Struct, optional

Struct with additional data products needed to assemble coadd. Only used by subclasses that implement makeSupplementaryData and override run.
Returns:
result : lsst.pipe.base.Struct

Result struct with components:

  • coaddExposure: coadded exposure (lsst.afw.image.Exposure).
  • nImage: exposure count image (lsst.afw.image.Image).
runDataRef(dataRef, selectDataList=[])

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. Assemble the Warps using run. Interpolate over NaNs and optionally write the coadd to disk. Return the coadded exposure.

Parameters:
dataRef : lsst.daf.persistence.butlerSubset.ButlerDataRef

Data reference defining the patch for coaddition and the reference Warp (if config.autoReference=False). Used to access the following data products: - self.config.coaddName + "Coadd_skyMap" - self.config.coaddName + "Coadd_ + <warpType> + "Warp" (optionally) - self.config.coaddName + "Coadd"

selectDataList : list

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:
retStruct : lsst.pipe.base.Struct

Result struct with components:

  • coaddExposure: coadded exposure (Exposure).
  • nImage: exposure count image (Image).
setBrightObjectMasks(exposure, dataId, brightObjectMasks)

Set the bright object masks.

Parameters:
exposure : lsst.afw.image.Exposure

Exposure under consideration.

dataId : lsst.daf.persistence.dataId

Data identifier dict for patch.

brightObjectMasks : lsst.afw.table

Table of bright objects to mask.
setInexactPsf(mask)

Set INEXACT_PSF mask plane.

If any of the input images isn’t represented in the coadd (due to clipped pixels or chip gaps), the CoaddPsf will be inexact. Flag these pixels.

Parameters:
mask : lsst.afw.image.Mask

Coadded exposure’s mask, modified in-place.
static setRejectedMaskMapping(statsCtrl)

Map certain mask planes of the warps to new planes for the coadd.

If a pixel is rejected due to a mask value other than EDGE, NO_DATA, or CLIPPED, set it to REJECTED on the coadd. If a pixel is rejected due to EDGE, set the coadd pixel to SENSOR_EDGE. If a pixel is rejected due to CLIPPED, set the coadd pixel to CLIPPED.

Parameters:
statsCtrl : lsst.afw.math.StatisticsControl

Statistics control object for coadd
Returns:
maskMap : list of tuple of int

A list of mappings of mask planes of the warped exposures to mask planes of the coadd.
shrinkValidPolygons(coaddInputs)

Shrink coaddInputs’ ccds’ ValidPolygons in place.

Either modify each ccd’s validPolygon in place, or if CoaddInputs does not have a validPolygon, create one from its bbox.

Parameters:
coaddInputs : lsst.afw.image.coaddInputs

Original mask.