lsst.pipe.tasks  16.0-13-g1e751bcc+1
Public Member Functions | Static Public Member Functions | Public Attributes | Static Public Attributes | List of all members
lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask Class Reference
Inheritance diagram for lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask:
lsst.pipe.tasks.coaddBase.CoaddBaseTask lsst.pipe.tasks.assembleCoadd.CompareWarpAssembleCoaddTask lsst.pipe.tasks.assembleCoadd.SafeClipAssembleCoaddTask lsst.pipe.tasks.dcrAssembleCoadd.DcrAssembleCoaddTask

Public Member Functions

def __init__ (self, args, kwargs)
 
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 = AssembleCoaddConfig
 
 RunnerClass = CoaddTaskRunner
 

Detailed Description

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. 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

- `ScaleZeroPointTask`
- create and use an ``imageScaler`` object to scale the photometric zeropoint for each Warp
- `InterpImageTask`
- interpolate across bad pixels (NaN) in the final coadd

You can retarget these subtasks 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. `AssembleCoaddTask` has
no debug variables of its own. Some of the subtasks may support debug
variables. See the documentation for the subtasks for further information.

Examples
--------
`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 two
inputs: a data reference to the tract patch and filter to be coadded, and
a list of Warps to attempt to coadd. These are specified using ``--id`` and
``--selectId``, respectively:

.. code-block:: none

   --id = [KEY=VALUE1[^VALUE2[^VALUE3...] [KEY=VALUE1[^VALUE2[^VALUE3...] ...]]
   --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 `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

- 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 exposures for each visit. To coadd the warped
data, we call assembleCoadd.py as follows:

.. code-block:: none

   assembleCoadd.py --legacyCoadd $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

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:

.. code-block:: none

   scons warp-903334 warp-903336 warp-903338 warp-903342 warp-903344 warp-903346
   assembleCoadd.py --legacyCoadd $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`
(but note that normally, one would use the `SafeClipAssembleCoaddTask`
rather than `AssembleCoaddTask` to make the coadd.

Definition at line 179 of file assembleCoadd.py.

Constructor & Destructor Documentation

◆ __init__()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.__init__ (   self,
  args,
  kwargs 
)

Definition at line 296 of file assembleCoadd.py.

Member Function Documentation

◆ applyAltMaskPlanes()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.applyAltMaskPlanes (   self,
  mask,
  altMaskSpans 
)
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.

◆ assembleMetadata()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.assembleMetadata (   self,
  coaddExposure,
  tempExpRefList,
  weightList 
)
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.

◆ assembleSubregion()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.assembleSubregion (   self,
  coaddExposure,
  bbox,
  tempExpRefList,
  imageScalerList,
  weightList,
  altMaskList,
  statsFlags,
  statsCtrl,
  nImage = None 
)
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.

◆ getBadPixelMask()

def lsst.pipe.tasks.coaddBase.CoaddBaseTask.getBadPixelMask (   self)
inherited

Convenience method to provide the bitmask from the mask plane names.

Definition at line 221 of file coaddBase.py.

◆ getCalExp()

def lsst.pipe.tasks.coaddBase.CoaddBaseTask.getCalExp (   self,
  dataRef,
  bgSubtracted 
)
inherited

Return one "calexp" calibrated exposure.

Parameters
[in]dataRefa sensor-level data reference
[in]bgSubtractedreturn calexp with background subtracted? If False get the calexp's background background model and add it to the calexp.
Returns
calibrated exposure

If config.doApplyUberCal, meas_mosaic calibrations will be applied to the returned exposure using applyMosaicResults.

Definition at line 143 of file coaddBase.py.

◆ getCoaddDatasetName()

def lsst.pipe.tasks.coaddBase.CoaddBaseTask.getCoaddDatasetName (   self,
  warpType = "direct" 
)
inherited
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.

◆ getSkyInfo()

def lsst.pipe.tasks.coaddBase.CoaddBaseTask.getSkyInfo (   self,
  patchRef 
)
inherited

Use getSkyinfo to return the skyMap, tract and patch information, wcs and the outer bbox of the patch.

Parameters
[in]patchRefdata reference for sky map. Must include keys "tract" and "patch"
Returns
pipe_base Struct containing:
  • skyMap: sky map
  • tractInfo: information for chosen tract of sky map
  • patchInfo: information about chosen patch of tract
  • wcs: WCS of tract
  • bbox: outer bbox of patch, as an afwGeom Box2I

Definition at line 127 of file coaddBase.py.

◆ getTempExpDatasetName()

def lsst.pipe.tasks.coaddBase.CoaddBaseTask.getTempExpDatasetName (   self,
  warpType = "direct" 
)
inherited
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.

◆ getTempExpRefList()

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.

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.

◆ makeSupplementaryData()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.makeSupplementaryData (   self,
  dataRef,
  selectDataList 
)
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.

◆ prepareInputs()

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.

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.

◆ prepareStats()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.prepareStats (   self,
  mask = None 
)
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.

◆ processResults()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.processResults (   self,
  coaddExposure,
  dataRef 
)
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.

◆ readBrightObjectMasks()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.readBrightObjectMasks (   self,
  dataRef 
)
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.

◆ removeMaskPlanes()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.removeMaskPlanes (   self,
  maskedImage 
)
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.

◆ run()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.run (   self,
  skyInfo,
  tempExpRefList,
  imageScalerList,
  weightList,
  altMaskList = None,
  mask = None,
  supplementaryData = None 
)
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.

◆ runDataRef()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.runDataRef (   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.
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.

◆ selectExposures()

def lsst.pipe.tasks.coaddBase.CoaddBaseTask.selectExposures (   self,
  patchRef,
  skyInfo = None,
  selectDataList = [] 
)
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.

Parameters
[in]patchRefdata reference for sky map patch. Must include keys "tract", "patch", plus the camera-specific filter key (e.g. "filter" or "band")
[in]skyInfogeometry for the patch; output from getSkyInfo
Returns
a list of science exposures to coadd, as butler data references

Definition at line 107 of file coaddBase.py.

◆ setBrightObjectMasks()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.setBrightObjectMasks (   self,
  exposure,
  dataId,
  brightObjectMasks 
)
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.

◆ setInexactPsf()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.setInexactPsf (   self,
  mask 
)
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.

◆ setRejectedMaskMapping()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.setRejectedMaskMapping (   statsCtrl)
static
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.

◆ shrinkValidPolygons()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.shrinkValidPolygons (   self,
  coaddInputs 
)
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.

Member Data Documentation

◆ brightObjectBitmask

lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.brightObjectBitmask

Definition at line 304 of file assembleCoadd.py.

◆ ConfigClass

lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.ConfigClass = AssembleCoaddConfig
static

Definition at line 293 of file assembleCoadd.py.

◆ RunnerClass

lsst.pipe.tasks.coaddBase.CoaddBaseTask.RunnerClass = CoaddTaskRunner
staticinherited

Definition at line 100 of file coaddBase.py.

◆ warpType

lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.warpType

Definition at line 310 of file assembleCoadd.py.


The documentation for this class was generated from the following file: