lsst.pipe.tasks
14.0-33-gee53dea0+3
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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, 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 | 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 | assembleMetadata (self, coaddExposure, tempExpRefList, weightList) |
Set the metadata for the coadd. More... | |
def | assembleSubregion (self, coaddExposure, bbox, tempExpRefList, imageScalerList, weightList, altMaskList, statsFlags, statsCtrl, nImage=None) |
Assemble the coadd for a sub-region. More... | |
def | readBrightObjectMasks (self, dataRef) |
def | setBrightObjectMasks (self, exposure, dataId, brightObjectMasks) |
def | setEdge (self, mask) |
def | setInexactPsf (self, mask) |
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 template coadd by more than config.detect.threshold 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, these pixels have the 'CLIPPED' bit set in the mask. 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. 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 Using lsstDebug to control debugging output for more about debug.py files.
This task supports the following debug variables:
saveCountIm
figPath
saveAltMask
figPath
figPath
For example, put something like:
into your debug.py
file and run assemebleCoadd.py
with the --debug
flag. Some subtasks may have their own debug variables; see individual Task documentation
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 1323 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 1461 of file assembleCoadd.py.
def lsst.pipe.tasks.assembleCoadd.CompareWarpAssembleCoaddTask.assemble | ( | self, | |
skyInfo, | |||
tempExpRefList, | |||
imageScalerList, | |||
weightList, | |||
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 |
supplementaryData | PipeBase.Struct containing a templateCoadd |
return pipeBase.Struct with coaddExposure, nImage if requested
Definition at line 1497 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 527 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. 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] | 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 573 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 1593 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 1526 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 377 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 1470 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 394 of file assembleCoadd.py.
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inherited |
Returns None on failure
Definition at line 631 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. 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 307 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 639 of file assembleCoadd.py.
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inherited |
Set EDGE bits as SENSOR_EDGE The EDGE pixels from the individual CCDs have printed through into the coadd, but EDGE means "we couldn't search for sources in this area because we couldn't convolve by the PSF near the edge of the image", so this mask plane needs to be converted to something else if we want to keep them. We do want to be able to identify pixels near the edge of the detector because they will have an inexact `CoaddPsf`. We rename EDGE pixels as SENSOR_EDGE. Parameters ---------- mask : `lsst.afw.image.Mask` Coadded exposure's mask, modified in-place.
Definition at line 686 of file assembleCoadd.py.
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inherited |
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.
Definition at line 710 of file assembleCoadd.py.
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inherited |
Definition at line 298 of file assembleCoadd.py.
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static |
Definition at line 1458 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 304 of file assembleCoadd.py.