lsst.pipe.tasks
14.0-53-g87cac093+4
|
Assemble a coadded image from a set of coadded temporary exposures, being careful to clip & flag areas with potential artifacts. More...
Public Member Functions | |
def | __init__ (self, args, kwargs) |
Initialize the task and make the clipDetection subtask. More... | |
def | assemble (self, skyInfo, tempExpRefList, imageScalerList, weightList, args, kwargs) |
Assemble the coadd for a region. More... | |
def | buildDifferenceImage (self, skyInfo, tempExpRefList, imageScalerList, weightList) |
Return an exposure that contains the difference between and unclipped and clipped coadds. More... | |
def | detectClip (self, exp, tempExpRefList) |
Detect clipped regions on an exposure and set the mask on the individual tempExp masks. More... | |
def | detectClipBig (self, clipList, clipFootprints, clipIndices, detectionFootprints, maskClipValue, maskDetValue, coaddBBox) |
Return individual warp footprints for large artifacts and append them to clipList in place. 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 | 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 | assemble (self, skyInfo, tempExpRefList, imageScalerList, weightList, 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, altMaskList, statsFlags, statsCtrl, nImage=None) |
Assemble the coadd for a sub-region. More... | |
def | applyAltMaskPlanes (self, mask, altMaskSpans) |
Apply in place alt mask formatted as SpanSets to a mask. More... | |
def | shrinkValidPolygons (self, coaddInputs) |
Shrink coaddInputs' ccds' ValidPolygons in place. More... | |
def | readBrightObjectMasks (self, dataRef) |
def | setBrightObjectMasks (self, exposure, dataId, brightObjectMasks) |
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 = SafeClipAssembleCoaddConfig | |
RunnerClass = CoaddTaskRunner | |
Assemble a coadded image from a set of coadded temporary exposures, being careful to clip & flag areas with potential artifacts.
Read the documentation for AssembleCoaddTask first since SafeClipAssembleCoaddTask subtasks that task. 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'. We populate this plane on the input coaddTempExps and the final coadd where i. difference imaging suggests that there is an outlier and ii. this outlier appears on only one or two images. Such 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.
SafeClipAssembleCoaddTask uses a clipDetection subtask and also sub-classes AssembleCoaddTask. You can retarget the clipDetection subtask if you wish.
Initialize the task and make the clipDetection 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:
|
[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 SafeClipAssembleCoaddConfig
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. SafeClipAssembleCoaddTask has no debug variables of its own. The clipDetection subtasks may support debug variables. See the documetation for clipDetection for further information.
SafeClipAssembleCoaddTask assembles a set of warped coaddTempExp images into a coadded image. The SafeClipAssembleCoaddTask is invoked by running assembleCoadd.py without 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 coaddTempExps to attempt to coadd (specified using '–selectId [KEY=VALUE1[^VALUE2[^VALUE3...] [KEY=VALUE1[^VALUE2[^VALUE3...] ...]]'). Only the coaddTempExps 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 SafeClipAssembleCoaddTask 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
.
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.
Definition at line 952 of file assembleCoadd.py.
def lsst.pipe.tasks.assembleCoadd.SafeClipAssembleCoaddTask.__init__ | ( | self, | |
args, | |||
kwargs | |||
) |
Initialize the task and make the clipDetection subtask.
Definition at line 1072 of file assembleCoadd.py.
|
inherited |
Apply in place alt mask formatted as SpanSets to a mask.
mask | original mask |
altMaskSpans | Dict containing 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 |
Definition at line 668 of file assembleCoadd.py.
|
inherited |
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] | 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 475 of file assembleCoadd.py.
def lsst.pipe.tasks.assembleCoadd.SafeClipAssembleCoaddTask.assemble | ( | self, | |
skyInfo, | |||
tempExpRefList, | |||
imageScalerList, | |||
weightList, | |||
args, | |||
kwargs | |||
) |
Assemble the coadd for a region.
Compute the difference of coadds created with and without outlier rejection to identify coadd pixels that have outlier values in some individual visits. Detect clipped regions on the difference image and mark these regions on the one or two individual coaddTempExps where they occur if there is significant overlap between the clipped region and a source. This leaves us with a set of footprints from the difference image that have been identified as having occured on just one or two individual visits. However, these footprints were generated from a difference image. It is conceivable for a large diffuse source to have become broken up into multiple footprints acrosss the coadd difference in this process. Determine the clipped region from all overlapping footprints from the detected sources in each visit - these are big footprints. Combine the small and big clipped footprints and mark them on a new bad mask plane Generate the coadd using AssembleCoaddTask.assemble without outlier removal. Clipped footprints will no longer make it into the coadd because they are marked in the new bad mask plane.
N.b. *args and **kwargs are passed but ignored in order to match the call signature expected by the parent task.
skyInfo | Patch geometry information, from getSkyInfo |
tempExpRefList | List of data reference to tempExp |
imageScalerList | List of image scalers |
weightList | List of weights return pipeBase.Struct with coaddExposure, nImage |
Definition at line 1080 of file assembleCoadd.py.
|
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 544 of file assembleCoadd.py.
|
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 Each element is dict with keys = mask plane name to which to add the spans |
[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 597 of file assembleCoadd.py.
def lsst.pipe.tasks.assembleCoadd.SafeClipAssembleCoaddTask.buildDifferenceImage | ( | self, | |
skyInfo, | |||
tempExpRefList, | |||
imageScalerList, | |||
weightList | |||
) |
Return an exposure that contains the difference between and unclipped and clipped coadds.
Generate a difference image between clipped and unclipped coadds. Compute the difference image by subtracting an outlier-clipped coadd from an outlier-unclipped coadd. Return the difference image.
skyInfo | Patch geometry information, from getSkyInfo |
tempExpRefList | List of data reference to tempExp |
imageScalerList | List of image scalers |
weightList | List of weights |
Definition at line 1137 of file assembleCoadd.py.
def lsst.pipe.tasks.assembleCoadd.SafeClipAssembleCoaddTask.detectClip | ( | self, | |
exp, | |||
tempExpRefList | |||
) |
Detect clipped regions on an exposure and set the mask on the individual tempExp masks.
Detect footprints in the difference image after smoothing the difference image with a Gaussian kernal. Identify footprints that overlap with one or two input coaddTempExps by comparing the computed overlap fraction to thresholds set in the config. A different threshold is applied depending on the number of overlapping visits (restricted to one or two). If the overlap exceeds the thresholds, the footprint is considered "CLIPPED" and is marked as such on the coaddTempExp. Return a struct with the clipped footprints, the indices of the coaddTempExps that end up overlapping with the clipped footprints and a list of new masks for the coaddTempExps.
[in] | exp | Exposure to run detection on |
[in] | tempExpRefList | List of data reference to tempExp |
Definition at line 1173 of file assembleCoadd.py.
def lsst.pipe.tasks.assembleCoadd.SafeClipAssembleCoaddTask.detectClipBig | ( | self, | |
clipList, | |||
clipFootprints, | |||
clipIndices, | |||
detectionFootprints, | |||
maskClipValue, | |||
maskDetValue, | |||
coaddBBox | |||
) |
Return individual warp footprints for large artifacts and append them to clipList in place.
Identify big footprints composed of many sources in the coadd difference that may have originated in a large diffuse source in the coadd. We do this by indentifying all clipped footprints that overlap significantly with each source in all the coaddTempExps.
[in] | clipList | List of alt mask SpanSets with clipping information. Modified. |
[in] | clipFootprints | List of clipped footprints |
[in] | clipIndices | List of which entries in tempExpClipList each footprint belongs to |
[in] | maskClipValue | Mask value of clipped pixels |
[in] | maskDetValue | Mask value of detected pixels |
[in] | coaddBBox | BBox of the coadd and warps |
Definition at line 1287 of file assembleCoadd.py.
|
inherited |
Convenience method to provide the bitmask from the mask plane names.
Definition at line 224 of file coaddBase.py.
|
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 146 of file coaddBase.py.
|
inherited |
Return coadd name for given warpType and task config Parameters ---------- warpType : string Either 'direct' or 'psfMatched' Returns ------- CoaddDatasetName : `string`
Definition at line 174 of file coaddBase.py.
|
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 130 of file coaddBase.py.
|
inherited |
Return warp name for given warpType and task config Parameters ---------- warpType : string Either 'direct' or 'psfMatched' Returns ------- WarpDatasetName : `string`
Definition at line 189 of file coaddBase.py.
|
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 395 of file assembleCoadd.py.
|
inherited |
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 385 of file assembleCoadd.py.
|
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 412 of file assembleCoadd.py.
|
inherited |
Returns None on failure
Definition at line 712 of file assembleCoadd.py.
|
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:
|
[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 324 of file assembleCoadd.py.
|
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 110 of file coaddBase.py.
|
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 720 of file assembleCoadd.py.
|
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 767 of file assembleCoadd.py.
|
inherited |
Shrink coaddInputs' ccds' ValidPolygons in place.
coaddInputs | original mask |
Either modify each ccd's validPolygon in place, or if CoaddInputs does not have a validPolygon, create one from its bbox.
Definition at line 693 of file assembleCoadd.py.
|
inherited |
Definition at line 315 of file assembleCoadd.py.
|
static |
Definition at line 1069 of file assembleCoadd.py.
|
staticinherited |
Definition at line 103 of file coaddBase.py.
|
inherited |
Definition at line 321 of file assembleCoadd.py.