lsst.pipe.tasks
16.0-14-g9428de4d
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Public Member Functions | |
def | __init__ (self, args, kwargs) |
def | run (self, skyInfo, tempExpRefList, imageScalerList, weightList, args, kwargs) |
def | buildDifferenceImage (self, skyInfo, tempExpRefList, imageScalerList, weightList) |
def | detectClip (self, exp, tempExpRefList) |
def | detectClipBig (self, clipList, clipFootprints, clipIndices, detectionFootprints, maskClipValue, maskDetValue, coaddBBox) |
def | runDataRef (self, dataRef, selectDataList=[]) |
def | processResults (self, coaddExposure, dataRef) |
def | makeSupplementaryData (self, dataRef, selectDataList) |
def | getTempExpRefList (self, patchRef, calExpRefList) |
def | prepareInputs (self, refList) |
def | prepareStats (self, mask=None) |
def | run (self, skyInfo, tempExpRefList, imageScalerList, weightList, altMaskList=None, mask=None, supplementaryData=None) |
def | assembleMetadata (self, coaddExposure, tempExpRefList, weightList) |
def | assembleSubregion (self, coaddExposure, bbox, tempExpRefList, imageScalerList, weightList, altMaskList, statsFlags, statsCtrl, nImage=None) |
def | removeMaskPlanes (self, maskedImage) |
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... | |
Static Public Member Functions | |
def | setRejectedMaskMapping (statsCtrl) |
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. 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 ``SourceDetectionTask`` "clipDetection" subtask and also sub-classes ``AssembleCoaddTask``. You can retarget the ``SourceDetectionTask`` "clipDetection" subtask if you wish. 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. `SafeClipAssembleCoaddTask` has no debug variables of its own. The ``SourceDetectionTask`` "clipDetection" subtasks may support debug variables. See the documetation for `SourceDetectionTask` "clipDetection" for further information. Examples -------- `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: .. code-block:: none assembleCoadd.py --help 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 - ``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</DD> 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 $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I \ --selectId visit=903986 ccd=16 --selectId visit=903986 ccd=22 --selectId visit=903986 ccd=23 \ --selectId visit=903986 ccd=100--selectId visit=904014 ccd=1 --selectId visit=904014 ccd=6 \ --selectId visit=904014 ccd=12 --selectId visit=903990 ccd=18 --selectId visit=903990 ccd=25 \ --selectId visit=904010 ccd=4 --selectId visit=904010 ccd=10 --selectId visit=904010 ccd=100 \ --selectId visit=903988 ccd=16 --selectId visit=903988 ccd=17 --selectId visit=903988 ccd=23 \ --selectId visit=903988 ccd=24 This will process the HSC-I band data. The results are written in ``$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I``. You may also choose to run: .. code-block:: none scons warp-903334 warp-903336 warp-903338 warp-903342 warp-903344 warp-903346 nnn assembleCoadd.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R --selectId visit=903334 ccd=16 \ --selectId visit=903334 ccd=22 --selectId visit=903334 ccd=23 --selectId visit=903334 ccd=100 \ --selectId visit=903336 ccd=17 --selectId visit=903336 ccd=24 --selectId visit=903338 ccd=18 \ --selectId visit=903338 ccd=25 --selectId visit=903342 ccd=4 --selectId visit=903342 ccd=10 \ --selectId visit=903342 ccd=100 --selectId visit=903344 ccd=0 --selectId visit=903344 ccd=5 \ --selectId visit=903344 ccd=11 --selectId visit=903346 ccd=1 --selectId visit=903346 ccd=6 \ --selectId visit=903346 ccd=12 to generate the coadd for the HSC-R band if you are interested in following multiBand Coadd processing as discussed in ``pipeTasks_multiBand``.
Definition at line 1103 of file assembleCoadd.py.
def lsst.pipe.tasks.assembleCoadd.SafeClipAssembleCoaddTask.__init__ | ( | self, | |
args, | |||
kwargs | |||
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Definition at line 1215 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 776 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 607 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 663 of file assembleCoadd.py.
def lsst.pipe.tasks.assembleCoadd.SafeClipAssembleCoaddTask.buildDifferenceImage | ( | self, | |
skyInfo, | |||
tempExpRefList, | |||
imageScalerList, | |||
weightList | |||
) |
Return an exposure that contains the difference between 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. Parameters ---------- skyInfo : `lsst.pipe.base.Struct` Patch geometry information, from getSkyInfo tempExpRefList : `list` List of data reference to tempExp imageScalerList : `list` List of image scalers weightList : `list` List of weights Returns ------- exp : `lsst.afw.image.Exposure` Difference image of unclipped and clipped coadd wrapped in an Exposure
Definition at line 1295 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``. Parameters ---------- exp : `lsst.afw.image.Exposure` Exposure to run detection on. tempExpRefList : `list` List of data reference to tempExp. Returns ------- result : `lsst.pipe.base.Struct` Result struct with components: - ``clipFootprints``: list of clipped footprints. - ``clipIndices``: indices for each ``clippedFootprint`` in ``tempExpRefList``. - ``clipSpans``: List of dictionaries containing spanSet lists to clip. Each element contains the new maskplane name ("CLIPPED") as the key and list of ``SpanSets`` as the value. - ``detectionFootprints``: List of DETECTED/DETECTED_NEGATIVE plane compressed into footprints.
Definition at line 1341 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. Parameters ---------- clipList : `list` List of alt mask SpanSets with clipping information. Modified. clipFootprints : `list` List of clipped footprints. clipIndices : `list` List of which entries in tempExpClipList each footprint belongs to. maskClipValue Mask value of clipped pixels. maskDetValue Mask value of detected pixels. coaddBBox : `lsst.afw.geom.Box` BBox of the coadd and warps. Returns ------- bigFootprintsCoadd : `list` List of big footprints
Definition at line 1468 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 409 of file assembleCoadd.py.
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Make additional inputs to run() specific to subclasses. Available to be implemented by subclasses only if they need the coadd dataRef for performing preliminary processing before assembling the coadd. Parameters ---------- dataRef : `lsst.daf.persistence.ButlerDataRef` Butler data reference for supplementary data. selectDataList : `list` List of data references to Warps.
Definition at line 393 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 433 of file assembleCoadd.py.
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Prepare the statistics for coadding images. Parameters ---------- mask : `int`, optional Bit mask value to exclude from coaddition. Returns ------- stats : `lsst.pipe.base.Struct` Statistics structure with the following fields: - ``statsCtrl``: Statistics control object for coadd (`lsst.afw.math.StatisticsControl`) - ``statsFlags``: Statistic for coadd (`lsst.afw.math.Property`)
Definition at line 502 of file assembleCoadd.py.
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Interpolate over missing data and mask bright stars. Parameters ---------- coaddExposure : `lsst.afw.image.Exposure` The coadded exposure to process. dataRef : `lsst.daf.persistence.ButlerDataRef` Butler data reference for supplementary data.
Definition at line 372 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 830 of file assembleCoadd.py.
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Unset the mask of an image for mask planes specified in the config. Parameters ---------- maskedImage : `lsst.afw.image.MaskedImage` The masked image to be modified.
Definition at line 732 of file assembleCoadd.py.
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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. Parameters ---------- skyInfo : `lsst.pipe.base.Struct` Struct with geometric information about the patch. tempExpRefList : `list` List of data references to Warps (previously called CoaddTempExps). imageScalerList : `list` List of image scalers. weightList : `list` List of weights altMaskList : `list`, optional List of alternate masks to use rather than those stored with tempExp. mask : `lsst.afw.image.Mask`, optional Mask to ignore when coadding supplementaryData : lsst.pipe.base.Struct, optional Struct with additional data products needed to assemble coadd. Only used by subclasses that implement `makeSupplementaryData` and override `run`. 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``).
Definition at line 535 of file assembleCoadd.py.
def lsst.pipe.tasks.assembleCoadd.SafeClipAssembleCoaddTask.run | ( | 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.run` without outlier removal. Clipped footprints will no longer make it into the coadd because they are marked in the new bad mask plane. Parameters ---------- skyInfo : `lsst.pipe.base.Struct` Patch geometry information, from getSkyInfo tempExpRefList : `list` List of data reference to tempExp imageScalerList : `list` List of image scalers weightList : `list` List of weights 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``). Notes ----- args and kwargs are passed but ignored in order to match the call signature expected by the parent task.
Definition at line 1220 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 `run`. 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 852 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 904 of file assembleCoadd.py.
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Map certain mask planes of the warps to new planes for the coadd. If a pixel is rejected due to a mask value other than EDGE, NO_DATA, or CLIPPED, set it to REJECTED on the coadd. If a pixel is rejected due to EDGE, set the coadd pixel to SENSOR_EDGE. If a pixel is rejected due to CLIPPED, set the coadd pixel to CLIPPED. Parameters ---------- statsCtrl : `lsst.afw.math.StatisticsControl` Statistics control object for coadd Returns ------- maskMap : `list` of `tuple` of `int` A list of mappings of mask planes of the warped exposures to mask planes of the coadd.
Definition at line 748 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 808 of file assembleCoadd.py.
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Definition at line 304 of file assembleCoadd.py.
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Definition at line 1212 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.