lsst.pipe.tasks gcb98b56dc4+7edcf6d93f
Loading...
Searching...
No Matches
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

Public Member Functions

def __init__ (self, *args, **kwargs)
 
def runQuantum (self, butlerQC, inputRefs, outputRefs)
 
def processResults (self, coaddExposure, brightObjectMasks=None, dataId=None)
 
def makeSupplementaryDataGen3 (self, butlerQC, inputRefs, outputRefs)
 
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 assembleOnlineMeanCoadd (self, coaddExposure, tempExpRefList, imageScalerList, weightList, altMaskList, statsCtrl, nImage=None)
 
def removeMaskPlanes (self, maskedImage)
 
def applyAltMaskPlanes (self, mask, altMaskSpans)
 
def shrinkValidPolygons (self, coaddInputs)
 
def setBrightObjectMasks (self, exposure, brightObjectMasks, dataId=None)
 
def setInexactPsf (self, mask)
 
def filterWarps (self, inputs, goodVisits)
 

Static Public Member Functions

def setRejectedMaskMapping (statsCtrl)
 

Public Attributes

 brightObjectBitmask
 
 warpType
 

Static Public Attributes

 ConfigClass = AssembleCoaddConfig
 

Detailed Description

Assemble a coadded image from a set of warps.

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

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

You can retarget these subtasks if you wish.

Raises
------
RuntimeError
    Raised if unable to define mask plane for bright objects.

Notes
-----
Debugging:
`AssembleCoaddTask` has no debug variables of its own. Some of the
subtasks may support `~lsst.base.lsstDebug` 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 run:

- 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 267 of file assembleCoadd.py.

Constructor & Destructor Documentation

◆ __init__()

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

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 985 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.

Raises
------
AssertionError
    Raised if there is a length mismatch.

Definition at line 724 of file assembleCoadd.py.

◆ assembleOnlineMeanCoadd()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.assembleOnlineMeanCoadd (   self,
  coaddExposure,
  tempExpRefList,
  imageScalerList,
  weightList,
  altMaskList,
  statsCtrl,
  nImage = None 
)
Assemble the coadd using the "online" method.

This method takes a running sum of images and weights to save memory.
It only works for MEAN statistics.

Parameters
----------
coaddExposure : `lsst.afw.image.Exposure`
    The target exposure for the 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.
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 865 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.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 789 of file assembleCoadd.py.

◆ filterWarps()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.filterWarps (   self,
  inputs,
  goodVisits 
)
Return list of only inputRefs with visitId in goodVisits ordered by goodVisit.

Parameters
----------
inputs : `list` of `~lsst.pipe.base.connections.DeferredDatasetRef`
    List of `lsst.pipe.base.connections.DeferredDatasetRef` with dataId containing visit.
goodVisit : `dict`
    Dictionary with good visitIds as the keys. Value ignored.

Returns
-------
filteredInputs : `list` of `~lsst.pipe.base.connections.DeferredDatasetRef`
    Filtered and sorted list of inputRefs with visitId in goodVisits ordered by goodVisit.

Definition at line 1140 of file assembleCoadd.py.

◆ makeSupplementaryDataGen3()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.makeSupplementaryDataGen3 (   self,
  butlerQC,
  inputRefs,
  outputRefs 
)

Definition at line 498 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`
    Results as a struct with attributes:

    ``tempExprefList``
        `list` of data references to tempExp.
    ``weightList``
        `list` of weightings.
    ``imageScalerList``
        `list` of image scalers.

Definition at line 501 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 as a struct with attributes:

    ``statsCtrl``
        Statistics control object for coadd (`~lsst.afw.math.StatisticsControl`).
    ``statsFlags``
        Statistic for coadd (`~lsst.afw.math.Property`).

Definition at line 572 of file assembleCoadd.py.

◆ processResults()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.processResults (   self,
  coaddExposure,
  brightObjectMasks = None,
  dataId = None 
)
Interpolate over missing data and mask bright stars.

Parameters
----------
coaddExposure : `lsst.afw.image.Exposure`
    The coadded exposure to process.
brightObjectMasks : `lsst.afw.table` or `None`, optional
    Table of bright objects to mask.
dataId : `lsst.daf.butler.DataId` or `None`, optional
    Data identification.

Definition at line 447 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.

Raises
------
InvalidParameterError
    Raised if no mask plane with that name was found.

Definition at line 935 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 : `int`, optional
    Bit mask value to exclude from coaddition.
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`
    Results as a struct with attributes:

    ``coaddExposure``
        Coadded exposure (``lsst.afw.image.Exposure``).
    ``nImage``
        Exposure count image (``lsst.afw.image.Image``), if requested.
    ``inputMap``
        Bit-wise map of inputs, if requested.
    ``warpRefList``
        Input list of refs to the warps (``lsst.daf.butler.DeferredDatasetHandle``)
        (unmodified).
    ``imageScalerList``
        Input list of image scalers (`list`) (unmodified).
    ``weightList``
        Input list of weights (`list`) (unmodified).

Raises
------
lsst.pipe.base.NoWorkFound
    Raised if no data references are provided.

Reimplemented in lsst.pipe.tasks.assembleCoadd.CompareWarpAssembleCoaddTask.

Definition at line 606 of file assembleCoadd.py.

◆ runQuantum()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.runQuantum (   self,
  butlerQC,
  inputRefs,
  outputRefs 
)

Definition at line 411 of file assembleCoadd.py.

◆ setBrightObjectMasks()

def lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.setBrightObjectMasks (   self,
  exposure,
  brightObjectMasks,
  dataId = None 
)
Set the bright object masks.

Parameters
----------
exposure : `lsst.afw.image.Exposure`
    Exposure under consideration.
brightObjectMasks : `lsst.afw.table`
    Table of bright objects to mask.
dataId : `lsst.daf.butler.DataId`, optional
    Data identifier dict for patch.

Definition at line 1038 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 1079 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 957 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 1017 of file assembleCoadd.py.

Member Data Documentation

◆ brightObjectBitmask

lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.brightObjectBitmask

Definition at line 399 of file assembleCoadd.py.

◆ ConfigClass

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

Definition at line 380 of file assembleCoadd.py.

◆ warpType

lsst.pipe.tasks.assembleCoadd.AssembleCoaddTask.warpType

Definition at line 408 of file assembleCoadd.py.


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