lsst.pipe.tasks
13.0-66-gfbf2f2ce+5
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Assemble a compareWarp coadded image from a set of warps by masking artifacts detected by comparing PSF-matched warps. More...
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 | |
Assemble a compareWarp coadded image from a set of warps by masking artifacts detected by comparing PSF-matched warps.
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)
Initialize the task and make the assembleStaticSkyModel subtask.
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.
[in] | dataRef | Data reference defining the patch for coaddition and the reference Warp (if config.autoReference=False). Used to access the following data products:
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[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. |
See CompareWarpAssembleCoaddConfig
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.
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:
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
We can perform all of these steps by running
This will produce warped coaddTempExps for each visit. To coadd the warped data, we call assembleCoadd.py as follows:
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.
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.
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inherited |
Add metadata from the background matching to the coadd.
[in] | coaddExposure | Coadd |
[in] | tempExpRefList | List of data references for temp exps to go into coadd |
[in] | backgroundInfoList | List of background info, results from background matching |
Definition at line 787 of file assembleCoadd.py.
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.
skyInfo | Patch geometry information |
tempExpRefList | List of data references to warps |
imageScalerList | List of image scalers |
weightList | List of weights |
bgModelList | List of background models from background matching |
supplementaryData | PipeBase.Struct containing a templateCoadd |
return pipeBase.Struct with coaddExposure, nImage if requested
Definition at line 1626 of file assembleCoadd.py.
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inherited |
Set the metadata for the coadd.
This basic implementation simply sets the filter from the first input.
[in] | coaddExposure | The target image for the coadd |
[in] | tempExpRefList | List of data references to tempExp |
[in] | weightList | List of weights |
Definition at line 673 of file assembleCoadd.py.
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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.
[in] | coaddExposure | The target image for the coadd |
[in] | bbox | Sub-region to coadd |
[in] | tempExpRefList | List of data reference to tempExp |
[in] | imageScalerList | List of image scalers |
[in] | weightList | List of weights |
[in] | bgInfoList | List of background data from background matching |
[in] | altMaskList | List of alternate masks to use rather than those stored with tempExp, or None |
[in] | statsFlags | afwMath.Property object for statistic for coadd |
[in] | statsCtrl | Statistics control object for coadd |
[in] | nImage | optional ImageU keeps track of exposure count for each pixel |
Definition at line 719 of file assembleCoadd.py.
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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.
[in] | inputData | Struct from prepareInputs() with tempExpRefList, weightList, imageScalerList |
[in] | refExpDataRef | Data reference for background reference Warp, or None |
[in] | refImageScaler | Image scaler for background reference Warp, or None |
Definition at line 532 of file assembleCoadd.py.
def lsst.pipe.tasks.assembleCoadd.CompareWarpAssembleCoaddTask.computeAltMaskList | ( | self, | |
tempExpRefList, | |||
maskSpanSets | |||
) |
Apply artifact span set lists to masks.
tempExpRefList | List of data references to warps |
maskSpanSets | Struct 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.
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.
templateCoadd | Exposure to serve as model of static sky |
tempExpRefList | List of data references to warps |
imageScalerList | List of image scalers |
Definition at line 1657 of file assembleCoadd.py.
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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.
[in] | dataRef | Data reference for the background reference frame, or None |
Definition at line 442 of file assembleCoadd.py.
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inherited |
Convenience method to provide the bitmask from the mask plane names.
Definition at line 217 of file coaddBase.py.
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inherited |
Return one "calexp" calibrated exposure.
[in] | dataRef | a sensor-level data reference |
[in] | bgSubtracted | return calexp with background subtracted? If False get the calexp's background background model and add it to the calexp. |
If config.doApplyUberCal, meas_mosaic calibrations will be applied to the returned exposure using applyMosaicResults.
Definition at line 139 of file coaddBase.py.
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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.
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inherited |
Use getSkyinfo to return the skyMap, tract and patch information, wcs and the outer bbox of the patch.
[in] | patchRef | data reference for sky map. Must include keys "tract" and "patch" |
Definition at line 123 of file coaddBase.py.
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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.
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inherited |
Generate list data references corresponding to warped exposures that lie within the patch to be coadded.
[in] | patchRef | Data reference for patch |
[in] | calExpRefList | List of data references for input calexps |
Definition at line 425 of file assembleCoadd.py.
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.
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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.
[in] | refList | List of data references to tempExp |
Definition at line 470 of file assembleCoadd.py.
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inherited |
Returns None on failure
Definition at line 810 of file assembleCoadd.py.
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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.
[in] | dataRef | Data reference defining the patch for coaddition and the reference Warp (if config.autoReference=False). Used to access the following data products:
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[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. |
Definition at line 342 of file assembleCoadd.py.
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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.
[in] | patchRef | data reference for sky map patch. Must include keys "tract", "patch", plus the camera-specific filter key (e.g. "filter" or "band") |
[in] | skyInfo | geometry for the patch; output from getSkyInfo |
Definition at line 103 of file coaddBase.py.
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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.
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inherited |
Definition at line 333 of file assembleCoadd.py.
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static |
Definition at line 1606 of file assembleCoadd.py.
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staticinherited |
Definition at line 96 of file coaddBase.py.
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inherited |
Definition at line 339 of file assembleCoadd.py.