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DM-46693: Add ability to re-apply bgModel1 in SkyCorrectionTask #989

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DM-46693: Add ability to re-apply bgModel1 in SkyCorrectionTask #989

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c94974e
Add ability to undo bgModel1 in SkyCorrectionTask
aemerywatkins Oct 9, 2024
06403b1
Add skyFrameScale as a returned output
leeskelvin Dec 18, 2024
ebb20b8
Add unit test for SkyCorrectionTask
leeskelvin Dec 18, 2024
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109 changes: 83 additions & 26 deletions python/lsst/pipe/tasks/skyCorrection.py
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Original file line number Diff line number Diff line change
Expand Up @@ -178,6 +178,11 @@ class SkyCorrectionConfig(PipelineTaskConfig, pipelineConnections=SkyCorrectionC
dtype=FocalPlaneBackgroundConfig,
doc="Initial background model, prior to sky frame subtraction",
)
undoBgModel1 = Field(
dtype=bool,
default=False,
doc="If True, adds back initial background model after sky and removes bgModel1 from the list",
)
sky = ConfigurableField(
target=SkyMeasurementTask,
doc="Sky measurement",
Expand Down Expand Up @@ -210,6 +215,11 @@ def setDefaults(self):
self.bgModel2.ySize = 256
self.bgModel2.smoothScale = 1.0

def validate(self):
super().validate()
if self.undoBgModel1 and not self.doSky and not self.doBgModel2:
raise ValueError("If undoBgModel1 is True, task requires at least one of doSky or doBgModel2.")


class SkyCorrectionTask(PipelineTask):
"""Perform a full focal plane sky correction."""
Expand Down Expand Up @@ -278,37 +288,45 @@ def run(self, calExps, calBkgs, skyFrames, camera):

Parameters
----------
calExps : `list` [`lsst.afw.image.exposure.ExposureF`]
calExps : `list` [`lsst.afw.image.ExposureF`]
Detector calibrated exposure images for the visit.
calBkgs : `list` [`lsst.afw.math.BackgroundList`]
Detector background lists matching the calibrated exposures.
skyFrames : `list` [`lsst.afw.image.exposure.ExposureF`]
skyFrames : `list` [`lsst.afw.image.ExposureF`]
Sky frame calibration data for the input detectors.
camera : `lsst.afw.cameraGeom.Camera`
Camera matching the input data to process.

Returns
-------
results : `Struct` containing:
skyFrameScale : `float`
Scale factor applied to the sky frame.
skyCorr : `list` [`lsst.afw.math.BackgroundList`]
Detector-level sky correction background lists.
calExpMosaic : `lsst.afw.image.exposure.ExposureF`
calExpMosaic : `lsst.afw.image.ExposureF`
Visit-level mosaic of the sky corrected data, binned.
Analogous to `calexp - skyCorr`.
calBkgMosaic : `lsst.afw.image.exposure.ExposureF`
calBkgMosaic : `lsst.afw.image.ExposureF`
Visit-level mosaic of the sky correction background, binned.
Analogous to `calexpBackground + skyCorr`.
"""
# Restore original backgrounds in-place; optionally refine mask maps
numOrigBkgElements = [len(calBkg) for calBkg in calBkgs]
_ = self._restoreBackgroundRefineMask(calExps, calBkgs)
_ = self._restoreOriginalBackgroundRefineMask(calExps, calBkgs)

# Bin exposures, generate full-fp bg, map to CCDs and subtract in-place
_ = self._subtractVisitBackground(calExps, calBkgs, camera, self.config.bgModel1)
initialBackgroundIndex = len(calBkgs[0]._backgrounds) - 1

# Subtract a scaled sky frame from all input exposures
skyFrameScale = None
if self.config.doSky:
self._subtractSkyFrame(calExps, skyFrames, calBkgs)
skyFrameScale = self._subtractSkyFrame(calExps, skyFrames, calBkgs)

# Adds full-fp bg back onto exposures, removes it from list
if self.config.undoBgModel1:
_ = self._undoInitialBackground(calExps, calBkgs, initialBackgroundIndex)

# Bin exposures, generate full-fp bg, map to CCDs and subtract in-place
if self.config.doBgModel2:
Expand All @@ -326,9 +344,11 @@ def run(self, calExps, calBkgs, skyFrames, camera):
skyCorrExtras, camera, self.config.binning, ids=calExpIds, refExps=calExps
)

return Struct(skyCorr=calBkgs, calExpMosaic=calExpMosaic, calBkgMosaic=calBkgMosaic)
return Struct(
skyFrameScale=skyFrameScale, skyCorr=calBkgs, calExpMosaic=calExpMosaic, calBkgMosaic=calBkgMosaic
)

def _restoreBackgroundRefineMask(self, calExps, calBkgs):
def _restoreOriginalBackgroundRefineMask(self, calExps, calBkgs):
"""Restore original background to each calexp and invert the related
background model; optionally refine the mask plane.

Expand All @@ -350,17 +370,17 @@ def _restoreBackgroundRefineMask(self, calExps, calBkgs):

Parameters
----------
calExps : `lsst.afw.image.exposure.ExposureF`
calExps : `lsst.afw.image.ExposureF`
Detector level calexp images to process.
calBkgs : `lsst.afw.math._backgroundList.BackgroundList`
calBkgs : `lsst.afw.math.BackgroundList`
Detector level background lists associated with the calexps.

Returns
-------
calExps : `lsst.afw.image.exposure.ExposureF`
The calexps with the initially subtracted background restored.
skyCorrBases : `lsst.afw.math._backgroundList.BackgroundList`
The inverted initial background models; the genesis for skyCorrs.
calExps : `lsst.afw.image.ExposureF`
The calexps with the originally subtracted background restored.
skyCorrBases : `lsst.afw.math.BackgroundList`
The inverted original background models; the genesis for skyCorrs.
"""
skyCorrBases = []
for calExp, calBkg in zip(calExps, calBkgs):
Expand All @@ -379,14 +399,45 @@ def _restoreBackgroundRefineMask(self, calExps, calBkgs):

stats = np.nanpercentile(skyCorrBase.array, [50, 75, 25])
self.log.info(
"Detector %d: Initial background restored; BG median = %.1f counts, BG IQR = %.1f counts",
"Detector %d: Original background restored; BG median = %.1f counts, BG IQR = %.1f counts",
calExp.getDetector().getId(),
-stats[0],
np.subtract(*stats[1:]),
)
skyCorrBases.append(skyCorrBase)
return calExps, skyCorrBases

def _undoInitialBackground(self, calExps, calBkgs, initialBackgroundIndex):
"""Undo the initial background subtraction (bgModel1) after sky frame
subtraction.

Parameters
----------
calExps : `list` [`lsst.afw.image.ExposureF`]
Calibrated exposures to be background subtracted.
calBkgs : `list` [`lsst.afw.math.BackgroundList`]
Background lists associated with the input calibrated exposures.
initialBackgroundIndex : `int`
Index of the initial background (bgModel1) in the background list.

Notes
-----
Inputs are modified in-place.
"""
for calExp, calBkg in zip(calExps, calBkgs):
image = calExp.getMaskedImage()

# Remove bgModel1 from the background list; restore in the image
initialBackground = calBkg[initialBackgroundIndex][0].getImageF()
image += initialBackground
calBkg._backgrounds.pop(initialBackgroundIndex)

self.log.info(
"Detector %d: The initial background model prior to sky frame subtraction (bgModel1) has "
"been removed from the background list",
calExp.getDetector().getId(),
)

def _subtractVisitBackground(self, calExps, calBkgs, camera, config):
"""Perform a full focal-plane background subtraction for a visit.

Expand All @@ -400,9 +451,9 @@ def _subtractVisitBackground(self, calExps, calBkgs, camera, config):

Parameters
----------
calExps : `list` [`lsst.afw.image.exposure.ExposureF`]
calExps : `list` [`lsst.afw.image.ExposureF`]
Calibrated exposures to be background subtracted.
calBkgs : `list` [`lsst.afw.math._backgroundList.BackgroundList`]
calBkgs : `list` [`lsst.afw.math.BackgroundList`]
Background lists associated with the input calibrated exposures.
camera : `lsst.afw.cameraGeom.Camera`
Camera description.
Expand All @@ -413,7 +464,7 @@ def _subtractVisitBackground(self, calExps, calBkgs, camera, config):
-------
calExps : `list` [`lsst.afw.image.maskedImage.MaskedImageF`]
Background subtracted exposures for creating a focal plane image.
calBkgs : `list` [`lsst.afw.math._backgroundList.BackgroundList`]
calBkgs : `list` [`lsst.afw.math.BackgroundList`]
Updated background lists with a visit-level model appended.
"""
# Set up empty full focal plane background model object
Expand Down Expand Up @@ -478,16 +529,16 @@ def _subtractDetectorBackground(self, calExp, bgModel):

Parameters
----------
calExp : `lsst.afw.image.exposure.ExposureF`
calExp : `lsst.afw.image.ExposureF`
Exposure to subtract the background model from.
bgModel : `lsst.pipe.tasks.background.FocalPlaneBackground`
Full focal plane camera-level background model.

Returns
-------
calExp : `lsst.afw.image.exposure.ExposureF`
calExp : `lsst.afw.image.ExposureF`
Background subtracted input exposure.
calBkgElement : `lsst.afw.math._backgroundList.BackgroundList`
calBkgElement : `lsst.afw.math.BackgroundList`
Detector level realization of the full focal plane bg model.
"""
image = calExp.getMaskedImage()
Expand All @@ -510,12 +561,17 @@ def _subtractSkyFrame(self, calExps, skyFrames, calBkgs):

Parameters
----------
calExps : `list` [`lsst.afw.image.exposure.ExposureF`]
calExps : `list` [`lsst.afw.image.ExposureF`]
Calibrated exposures to be background subtracted.
skyFrames : `list` [`lsst.afw.image.exposure.ExposureF`]
skyFrames : `list` [`lsst.afw.image.ExposureF`]
Sky frame calibration data for the input detectors.
calBkgs : `list` [`lsst.afw.math._backgroundList.BackgroundList`]
calBkgs : `list` [`lsst.afw.math.BackgroundList`]
Background lists associated with the input calibrated exposures.

Returns
-------
scale : `float`
Scale factor applied to the sky frame.
"""
skyFrameBgModels = []
scales = []
Expand All @@ -531,6 +587,7 @@ def _subtractSkyFrame(self, calExps, skyFrames, calBkgs):
# also updating the calBkg list in-place
self.sky.subtractSkyFrame(calExp.getMaskedImage(), skyFrameBgModel, scale, calBkg)
self.log.info("Sky frame subtracted with a scale factor of %.5f", scale)
return scale

def _binAndMosaic(self, exposures, camera, binning, ids=None, refExps=None):
"""Bin input exposures and mosaic across the entire focal plane.
Expand All @@ -549,11 +606,11 @@ def _binAndMosaic(self, exposures, camera, binning, ids=None, refExps=None):
Binning size to be applied to input images.
ids : `list` [`int`], optional
List of detector ids to iterate over.
refExps : `list` [`lsst.afw.image.exposure.ExposureF`], optional
refExps : `list` [`lsst.afw.image.ExposureF`], optional
If supplied, mask planes from these reference images will be used.
Returns
-------
mosaicImage : `lsst.afw.image.exposure.ExposureF`
mosaicImage : `lsst.afw.image.ExposureF`
Mosaicked full focal plane image.
"""
refExps = np.resize(refExps, len(exposures)) # type: ignore
Expand Down
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