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 bydataRef
). 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 configsconfig.makeDirect
andconfig.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 inAssembleCoaddConfig
. 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 areScaleZeroPointTask
- 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 importdebug.py
from yourPYTHONPATH
; seebaseDebug
for more aboutdebug.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. TheAssembleCoaddTask
can be invoked by runningassembleCoadd.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 theci_hsc
package. To begin, assuming that the lsst stack has been already set up, we must set up the obs_subaru andci_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 theSafeClipAssembleCoaddTask
rather thanAssembleCoaddTask
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.
- mask :
-
assembleMetadata
(coaddExposure, tempExpRefList, weightList)¶ Set the metadata for the coadd.
This basic implementation sets the filter from the first input.
Parameters:
-
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 usinglsst.afw.math.statisticsStack
with the statistic specified by statsFlags. Typically, the statsFlag will be one of lsst.afw.math.MEAN for a mean-stack orlsst.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.
- coaddExposure :
-
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.
- patchRef :
-
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.
- dataRef :
-
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:
- refList :
-
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
)
- mask :
-
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.
- coaddExposure :
-
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.
- dataRef :
-
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.
- maskedImage :
-
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 overriderun
.
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
).
- skyInfo :
-
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
).
- dataRef :
-
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.
- exposure :
-
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.
- mask :
-
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: - statsCtrl :
-
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.
- coaddInputs :