lsst.pipe.tasks
13.0-66-gfbf2f2ce+5
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Assemble a coadded image from a set of warps (coadded temporary exposures). More...
Public Member Functions | |
def | __init__ (self, args, kwargs) |
Initialize the task. More... | |
def | run (self, dataRef, selectDataList=[]) |
Assemble a coadd from a set of Warps. More... | |
def | makeSupplementaryData (self, dataRef, selectDataList) |
Make additional inputs to assemble() specific to subclasses. 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 | assemble (self, skyInfo, tempExpRefList, imageScalerList, weightList, bgInfoList=None, altMaskList=None, mask=None, supplementaryData=None) |
Assemble a coadd from input warps. 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 = AssembleCoaddConfig | |
RunnerClass = CoaddTaskRunner | |
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. By default, each Warp has backgrounds and hence will require config.doMatchBackgrounds=True. When background matching is enabled, the task may be configured to automatically select a reference exposure (config.autoReference=True). If this is not done, we require that the input dataRef provides access to a Warp (dataset type coaddName + 'Coadd' + warpType + 'Warp') which is used as the reference exposure. 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
You can retarget these subtasks if you wish.
Initialize the task. Create the interpImage, matchBackgrounds, & scaleZeroPoint subtasks.
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. |
The command line task 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 documetation for the subtasks for further information.
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 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 Warps 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 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
We can perform all of these steps by running
This will produce warped exposures for each visit. To coadd the warped data, we call assembleCoadd.py as follows:
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:
to generate the coadd for the HSC-R band if you are interested in following multiBand Coadd processing as discussed in High-level Overview of Multi-Band Coadd Processing (but note that normally, one would use the SafeClipAssembleCoaddTask rather than AssembleCoaddTask to make the coadd.
Definition at line 196 of file assembleCoadd.py.
def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.__init__ | ( | self, | |
args, | |||
kwargs | |||
) |
Initialize the task.
Create the interpImage, matchBackgrounds, & scaleZeroPoint subtasks.
Definition at line 320 of file assembleCoadd.py.
def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.addBackgroundMatchingMetadata | ( | self, | |
coaddExposure, | |||
tempExpRefList, | |||
backgroundInfoList | |||
) |
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.AssembleCoaddTask.assemble | ( | self, | |
skyInfo, | |||
tempExpRefList, | |||
imageScalerList, | |||
weightList, | |||
bgInfoList = None , |
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altMaskList = None , |
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mask = None , |
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supplementaryData = None |
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) |
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.
[in] | skyInfo | Patch geometry information, from getSkyInfo |
[in] | tempExpRefList | List of data references to Warps (previously called CoaddTempExps) |
[in] | imageScalerList | List of image scalers |
[in] | weightList | List of weights |
[in] | bgInfoList | List of background data from background matching, or None |
[in] | altMaskList | List of alternate masks to use rather than those stored with tempExp, or None |
[in] | mask | Mask to ignore when coadding |
[in] | supplementaryData | pipeBase.Struct with additional data products needed to assemble coadd. Only used by subclasses that implement makeSupplementaryData and override assemble. |
Definition at line 603 of file assembleCoadd.py.
def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.assembleMetadata | ( | self, | |
coaddExposure, | |||
tempExpRefList, | |||
weightList | |||
) |
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.
def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.assembleSubregion | ( | self, | |
coaddExposure, | |||
bbox, | |||
tempExpRefList, | |||
imageScalerList, | |||
weightList, | |||
bgInfoList, | |||
altMaskList, | |||
statsFlags, | |||
statsCtrl, | |||
nImage = None |
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) |
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.
def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.backgroundMatching | ( | self, | |
inputData, | |||
refExpDataRef = None , |
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refImageScaler = None |
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) |
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.AssembleCoaddTask.getBackgroundReferenceScaler | ( | self, | |
dataRef | |||
) |
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.
def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.getTempExpRefList | ( | self, | |
patchRef, | |||
calExpRefList | |||
) |
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.AssembleCoaddTask.makeSupplementaryData | ( | self, | |
dataRef, | |||
selectDataList | |||
) |
Make additional inputs to assemble() specific to subclasses.
Available to be implemented by subclasses only if they need the coadd dataRef for performing preliminary processing before assembling the coadd.
Definition at line 415 of file assembleCoadd.py.
def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.prepareInputs | ( | self, | |
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.
[in] | refList | List of data references to tempExp |
Definition at line 470 of file assembleCoadd.py.
def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.readBrightObjectMasks | ( | self, | |
dataRef | |||
) |
Returns None on failure
Definition at line 810 of file assembleCoadd.py.
def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.run | ( | self, | |
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. 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.
def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.setBrightObjectMasks | ( | self, | |
exposure, | |||
dataId, | |||
brightObjectMasks | |||
) |
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.
lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.brightObjectBitmask |
Definition at line 333 of file assembleCoadd.py.
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static |
Definition at line 317 of file assembleCoadd.py.
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staticinherited |
Definition at line 96 of file coaddBase.py.
lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.warpType |
Definition at line 339 of file assembleCoadd.py.