lsst.pipe.tasks
15.0-15-gc15de322
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Public Member Functions | |
def | __init__ (self, args, kwargs) |
def | makeSupplementaryData (self, dataRef, selectDataList) |
def | assemble (self, skyInfo, tempExpRefList, imageScalerList, weightList, supplementaryData, args, kwargs) |
def | applyAltEdgeMask (self, mask, altMaskList) |
def | findArtifacts (self, templateCoadd, tempExpRefList, imageScalerList) |
def | prefilterArtifacts (self, spanSetList, exp) |
def | filterArtifacts (self, spanSetList, epochCountImage, nImage, footprintsToExclude=None) |
def | run (self, dataRef, selectDataList=[]) |
def | getTempExpRefList (self, patchRef, calExpRefList) |
def | prepareInputs (self, refList) |
def | assembleMetadata (self, coaddExposure, tempExpRefList, weightList) |
def | assembleSubregion (self, coaddExposure, bbox, tempExpRefList, imageScalerList, weightList, altMaskList, statsFlags, statsCtrl, nImage=None) |
def | applyAltMaskPlanes (self, mask, altMaskSpans) |
def | shrinkValidPolygons (self, coaddInputs) |
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 = 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). Notes ----- The `lsst.pipe.base.cmdLineTask.CmdLineTask` interface supports a flag ``-d`` to import ``debug.py`` from your ``PYTHONPATH``; see ``baseDebug`` for more about ``debug.py`` files. This task supports the following debug variables: - ``saveCountIm`` If True then save the Epoch Count Image as a fits file in the `figPath` - ``figPath`` Path to save the debug fits images and figures For example, put something like: .. code-block:: python import lsstDebug def DebugInfo(name): di = lsstDebug.getInfo(name) if name == "lsst.pipe.tasks.assembleCoadd": di.saveCountIm = True di.figPath = "/desired/path/to/debugging/output/images" return di lsstDebug.Info = DebugInfo 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. Examples -------- ``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: .. code-block:: none assembleCoadd.py --help To demonstrate usage of the ``CompareWarpAssembleCoaddTask`` in the larger context of multi-band processing, we will generate the HSC-I & -R band oadds 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 - 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 .. code-block:: none $CI_HSC_DIR scons warp-903986 warp-904014 warp-903990 warp-904010 warp-903988 This will produce warped ``coaddTempExps`` for each visit. To coadd the warped data, we call ``assembleCoadd.py`` as follows: .. code-block:: none assembleCoadd.py --compareWarpCoadd $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I \ --selectId visit=903986 ccd=16 --selectId visit=903986 ccd=22 --selectId visit=903986 ccd=23 \ --selectId visit=903986 ccd=100 --selectId visit=904014 ccd=1 --selectId visit=904014 ccd=6 \ --selectId visit=904014 ccd=12 --selectId visit=903990 ccd=18 --selectId visit=903990 ccd=25 \ --selectId visit=904010 ccd=4 --selectId visit=904010 ccd=10 --selectId visit=904010 ccd=100 \ --selectId visit=903988 ccd=16 --selectId visit=903988 ccd=17 --selectId visit=903988 ccd=23 \ --selectId visit=903988 ccd=24 This will process the HSC-I band data. The results are written in ``$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I``.
Definition at line 1584 of file assembleCoadd.py.
def lsst.pipe.tasks.assembleCoadd.CompareWarpAssembleCoaddTask.__init__ | ( | self, | |
args, | |||
kwargs | |||
) |
Definition at line 1708 of file assembleCoadd.py.
def lsst.pipe.tasks.assembleCoadd.CompareWarpAssembleCoaddTask.applyAltEdgeMask | ( | self, | |
mask, | |||
altMaskList | |||
) |
Propagate alt EDGE mask to SENSOR_EDGE AND INEXACT_PSF planes. Parameters ---------- mask : `lsst.afw.image.Mask` Original mask. altMaskList : `list` List of Dicts containing ``spanSet`` lists. 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 1803 of file assembleCoadd.py.
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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.
Definition at line 718 of file assembleCoadd.py.
def lsst.pipe.tasks.assembleCoadd.CompareWarpAssembleCoaddTask.assemble | ( | self, | |
skyInfo, | |||
tempExpRefList, | |||
imageScalerList, | |||
weightList, | |||
supplementaryData, | |||
args, | |||
kwargs | |||
) |
Assemble the coadd. 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. Parameters ---------- skyInfo : `lsst.pipe.base.Struct` Patch geometry information. tempExpRefList : `list` List of data references to warps. imageScalerList : `list` List of image scalers. weightList : `list` List of weights. supplementaryData : `lsst.pipe.base.Struct` This Struct must contain a ``templateCoadd`` that serves as the model of the static sky. 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``), if requested.
Definition at line 1759 of file assembleCoadd.py.
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Set the metadata for the coadd. This basic implementation sets the filter from the first input. Parameters ---------- coaddExposure : `lsst.afw.image.Exposure` The target exposure for the coadd. tempExpRefList : `list` List of data references to tempExp. weightList : `list` List of weights.
Definition at line 578 of file assembleCoadd.py.
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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. Remove mask planes listed in `config.removeMaskPlanes`. Finally, stack the actual exposures using `lsst.afw.math.statisticsStack` with the statistic specified by statsFlags. Typically, the statsFlag will be one of lsst.afw.math.MEAN for a mean-stack or `lsst.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.
Definition at line 634 of file assembleCoadd.py.
def lsst.pipe.tasks.assembleCoadd.CompareWarpAssembleCoaddTask.filterArtifacts | ( | self, | |
spanSetList, | |||
epochCountImage, | |||
nImage, | |||
footprintsToExclude = None |
|||
) |
Filter artifact candidates. Parameters ---------- spanSetList : `list` List of SpanSets representing artifact candidates. epochCountImage : `lsst.afw.image.Image` Image of accumulated number of warpDiff detections. nImage : `lsst.afw.image.Image` Image of the accumulated number of total epochs contributing. Returns ------- maskSpanSetList : `list` List of SpanSets with artifacts.
Definition at line 1957 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. Parameters ---------- templateCoadd : `lsst.afw.image.Exposure` Exposure to serve as model of static sky. tempExpRefList : `list` List of data references to warps. imageScalerList : `list` List of image scalers. Returns ------- altMasks : `list` List of dicts containing information about CLIPPED (i.e., artifacts), NO_DATA, and EDGE pixels.
Definition at line 1822 of file assembleCoadd.py.
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Convenience method to provide the bitmask from the mask plane names.
Definition at line 221 of file coaddBase.py.
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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 143 of file coaddBase.py.
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Return coadd name for given warpType and task config Parameters ---------- warpType : string Either 'direct' or 'psfMatched' Returns ------- CoaddDatasetName : `string`
Definition at line 171 of file coaddBase.py.
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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 127 of file coaddBase.py.
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Return warp name for given warpType and task config Parameters ---------- warpType : string Either 'direct' or 'psfMatched' Returns ------- WarpDatasetName : `string`
Definition at line 186 of file coaddBase.py.
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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.
Definition at line 398 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. Parameters ---------- dataRef : `lsst.daf.persistence.butlerSubset.ButlerDataRef` Butler dataRef for supplementary data. selectDataList : `list` List of data references to Warps. Returns ------- result : `lsst.pipe.base.Struct` Result struct with components: - ``templateCoaddcoadd``: coadded exposure (``lsst.afw.image.Exposure``).
Definition at line 1718 of file assembleCoadd.py.
def lsst.pipe.tasks.assembleCoadd.CompareWarpAssembleCoaddTask.prefilterArtifacts | ( | self, | |
spanSetList, | |||
exp | |||
) |
Remove artifact candidates covered by bad mask plane. Any future editing of the candidate list that does not depend on temporal information should go in this method. Parameters ---------- spanSetList : `list` List of SpanSets representing artifact candidates. exp : `lsst.afw.image.Exposure` Exposure containing mask planes used to prefilter. Returns ------- returnSpanSetList : `list` List of SpanSets with artifacts.
Definition at line 1925 of file assembleCoadd.py.
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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: - ``tempExprefList``: `list` of data references to tempExp. - ``weightList``: `list` of weightings. - ``imageScalerList``: `list` of image scalers.
Definition at line 422 of file assembleCoadd.py.
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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.
Definition at line 772 of file assembleCoadd.py.
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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. 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``).
Definition at line 313 of file assembleCoadd.py.
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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 107 of file coaddBase.py.
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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.
Definition at line 794 of file assembleCoadd.py.
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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 846 of file assembleCoadd.py.
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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.
Definition at line 750 of file assembleCoadd.py.
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Definition at line 304 of file assembleCoadd.py.
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static |
Definition at line 1705 of file assembleCoadd.py.
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Definition at line 100 of file coaddBase.py.
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Definition at line 310 of file assembleCoadd.py.