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Use sky-subtracted warps for ref-image selection
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_defineWarps() now rejects any image with all NaNs along any image
edge, and creates the cost function using a sky-subtracted image.
This sky-subtraction fits a 1st order Chebyshev polynomial to the
masked image background.

Also fixed a bug from LSK refactor by inserting a blank sky model
into the background model list at the chosen reference image index.
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@aemerywatkins
aemerywatkins committed Jul 25, 2024
1 parent b0463a5 commit 7c1554f
Showing 1 changed file with 114 additions and 71 deletions.
185 changes: 114 additions & 71 deletions python/lsst/pipe/tasks/matchBackgrounds.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@

import lsstDebug
import numpy as np
from lsst.afw.image import LOCAL, PARENT, Mask, MaskedImageF
from lsst.afw.image import LOCAL, PARENT, ImageF, Mask, MaskedImageF
from lsst.afw.math import (
MEAN,
MEANCLIP,
Expand Down Expand Up @@ -250,12 +250,11 @@ def run(self, warps):
raise TaskError("No exposures to match")

# Define a reference warp; 'warps' is modified in-place to exclude it
refWarp = self._defineWarps(warps=warps, refWarpVisit=self.config.refWarpVisit)
breakpoint()
refWarp, refInd = self._defineWarps(warps=warps, refWarpVisit=self.config.refWarpVisit)

# Images must be scaled to a common ZP
# Converting everything to nJy to accomplish this
refExposure = refMatchedWarp.get()
refExposure = refWarp.get()
refMI = self._fluxScale(refExposure) # Also modifies refExposure

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F841 

local variable 'refMI' is assigned to but never used

# TODO: figure out what this was creating and why
Expand All @@ -270,7 +269,7 @@ def run(self, warps):

# TODO: refactor below to construct blank bg model
im = refExposure.getMaskedImage()
blankIm = im.Factory(im, True) # Don't do this
blankIm = im.Factory(im, True)
blankIm.image.array *= 0

width = blankIm.getWidth()
Expand All @@ -286,53 +285,43 @@ def run(self, warps):
bctrl.setUndersampleStyle(self.config.undersampleStyle)

bkgd = makeBackground(blankIm, bctrl)
blank = BackgroundList(
(
bkgd,
stringToInterpStyle(self.config.interpStyle),
stringToUndersampleStyle(self.config.undersampleStyle),
ApproximateControl.UNKNOWN,
0,
0,
False,
)
)

backgroundInfoList = []
for ind, exp in enumerate(warps):
if ind in refIndSet:
backgroundInfoStruct = BackgroundList(
(
bkgd,
stringToInterpStyle(self.config.interpStyle),
stringToUndersampleStyle(self.config.undersampleStyle),
ApproximateControl.UNKNOWN,
0,
0,
False,
)
# TODO: simplify this maybe, using only visit IDs?
self.log.info("Matching background of %s to %s", exp.dataId, refWarp.dataId)
toMatchExposure = exp.get()
try:
# TODO: adjust logic to avoid creating spurious MIs like this
toMatchMI = self._fluxScale(toMatchExposure)

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F841 

local variable 'toMatchMI' is assigned to but never used

# store a string specifying the visit to label debug plot
# self.debugDataIdString = ''.join([str(toMatchRef.dataId[vk]) for vk in debugIdKeyList])

backgroundInfoStruct = self.matchBackgrounds(
refExposure=refExposure,
sciExposure=toMatchExposure,
)
else:
# TODO: simplify this maybe, using only visit IDs?
self.log.info("Matching background of %s to %s", exp.dataId, refMatchedWarp.dataId)
toMatchExposure = exp.get()
try:
# Seems to require exposure, not masked exposure.
toMatchMI = self._fluxScale(toMatchExposure)

# store a string specifying the visit to label debug plot
# self.debugDataIdString = ''.join([str(toMatchRef.dataId[vk]) for vk in debugIdKeyList])

backgroundInfoStruct = self.matchBackgrounds(
refExposure=refExposure,
sciExposure=toMatchExposure,
)
backgroundInfoStruct.isReference = False
except Exception as e:
self.log.warning("Failed to fit background %s: %s", exp.dataId, e)
backgroundInfoStruct = BackgroundList(
(
bkgd,
stringToInterpStyle(self.config.interpStyle),
stringToUndersampleStyle(self.config.undersampleStyle),
ApproximateControl.UNKNOWN,
0,
0,
False,
)
)
backgroundInfoStruct.isReference = False
except Exception as e:
self.log.warning("Failed to fit background %s: %s", exp.dataId, e)
backgroundInfoStruct = blank

backgroundInfoList.append(backgroundInfoStruct)

# TODO: more elegant solution than inserting blank model at ref ind?
backgroundInfoList.insert(refInd, blank)
return Struct(backgroundInfoList=backgroundInfoList)

@timeMethod
Expand Down Expand Up @@ -377,15 +366,38 @@ def _defineWarps(self, warps, refWarpVisit=None):
warpNPoints = []
for warpDDH in warps:
warp = warpDDH.get()

# First check if any image edge is all NaN
# If so, don't use
leftBool = np.all(np.isnan(warp.image.array[:, 0]))
rightBool = np.all(np.isnan(warp.image.array[:, warp.image.getHeight() - 1]))
bottomBool = np.all(np.isnan(warp.image.array[0, :]))
topBool = np.all(np.isnan(warp.image.array[warp.image.getWidth() - 1, :]))
if np.any([leftBool, rightBool, bottomBool, topBool]):
continue

warp.image.array *= warp.getPhotoCalib().instFluxToNanojansky(1) # Convert image plane to nJy
warpStats = makeStatistics(warp.image, warp.mask, MEAN | VARIANCE | NPOINT, self.statsCtrl)

# Select reference based on BG of plane sky-subtracted images
bkgd, __, __, __ = self._setupBackground(warp)

weightByInverseVariance = self.config.approxWeighting
actrl = ApproximateControl(ApproximateControl.CHEBYSHEV, 1, 1, weightByInverseVariance)
undersampleStyle = stringToUndersampleStyle(self.config.undersampleStyle)
approx = bkgd.getApproximate(actrl, undersampleStyle)
bgSubImage = ImageF(warp.image.array - approx.getImage().array)

warpStats = makeStatistics(bgSubImage, warp.mask, MEAN | VARIANCE | NPOINT, self.statsCtrl)
warpMean, _ = warpStats.getResult(MEAN)
warpVar, _ = warpStats.getResult(VARIANCE)
warpNPoint, _ = warpStats.getResult(NPOINT)
warpMeans.append(warpMean)
warpVars.append(warpVar)
warpNPoints.append(int(warpNPoint))

if len(warpNPoints) == 0:
raise TaskError("No suitable reference visit found in list of warps.")

# Normalize mean/var/npoints to range from 0 to 1
warpMeansFrac = np.array(warpMeans) / np.nanmax(warpMeans)
warpVarsFrac = np.array(warpVars) / np.nanmax(warpVars)
Expand All @@ -396,21 +408,22 @@ def _defineWarps(self, warps, refWarpVisit=None):
costFunctionVals += self.config.bestRefWeightVariance * warpVarsFrac
costFunctionVals += self.config.bestRefWeightCoverage * warpNPointsFrac

refWarp = warps.pop(np.nanargmin(costFunctionVals))
ind = np.nanargmin(costFunctionVals)
refWarp = warps.pop(ind)
self.log.info("Using best reference visit %d", refWarp.dataId["visit"])
return refWarp
return refWarp, ind

def _fluxScale(self, exposure):
"""Scales image to nJy flux using photometric calibration.
Parameters
----------
exposure: ``
exposure: `lsst.afw.image._exposure.ExposureF`
Exposure to scale.
Returns
-------
maskedImage: ``
maskedImage: `lsst.afw.image._maskedImage.MaskedImageF`
Flux-scaled masked exposure.
"""
maskedImage = exposure.getMaskedImage()
Expand All @@ -419,6 +432,56 @@ def _fluxScale(self, exposure):

return maskedImage

def _setupBackground(self, warp):
"""Set up and return a background model container and associated images
and controllers.
Uses the following config parameters:
- ``gridStatistic``
- ``numSigmaClip``
- ``numIter``
- ``binSize``
- ``undersampleStyle``
Parameters
----------
warp: `lsst.afw.image._exposure.ExposureF`
Warped exposure or difference image for which to estimate
background.
Returns
-------
bkgd: `lsst.afw.math.BackgroundMI`
Background model container.
bctrl: `lsst.afw.math.BackgroundControl`
Background model control
warpMI: `lsst.afw.image._maskedImage.MaskedImageF`
Masked image associated with warp
statsFlag: `lsst.afw.math.Property`
Flag for grid statistic property (self.config.gridStatistic)
"""
statsFlag = stringToStatisticsProperty(self.config.gridStatistic)
self.statsCtrl.setNumSigmaClip(self.config.numSigmaClip)
self.statsCtrl.setNumIter(self.config.numIter)

warpMI = warp.getMaskedImage()

width = warpMI.getWidth()
height = warpMI.getHeight()
nx = width // self.config.binSize
if width % self.config.binSize != 0:
nx += 1
ny = height // self.config.binSize
if height % self.config.binSize != 0:
ny += 1

bctrl = BackgroundControl(nx, ny, self.statsCtrl, statsFlag)
bctrl.setUndersampleStyle(self.config.undersampleStyle)

bkgd = makeBackground(warpMI, bctrl)

return bkgd, bctrl, warpMI, statsFlag

@timeMethod
def matchBackgrounds(self, refExposure, sciExposure):
"""Match science exposure's background level to that of reference
Expand Down Expand Up @@ -489,27 +552,7 @@ def matchBackgrounds(self, refExposure, sciExposure):
"Exposures are different dimensions. sci:(%i, %i) vs. ref:(%i, %i)" % (wSci, hSci, wRef, hRef)
)

statsFlag = stringToStatisticsProperty(self.config.gridStatistic)
self.statsCtrl.setNumSigmaClip(self.config.numSigmaClip)
self.statsCtrl.setNumIter(self.config.numIter)

im = refExposure.getMaskedImage()
diffMI = im.Factory(im, True)
diffMI -= sciExposure.getMaskedImage()

width = diffMI.getWidth()
height = diffMI.getHeight()
nx = width // self.config.binSize
if width % self.config.binSize != 0:
nx += 1
ny = height // self.config.binSize
if height % self.config.binSize != 0:
ny += 1

bctrl = BackgroundControl(nx, ny, self.statsCtrl, statsFlag)
bctrl.setUndersampleStyle(self.config.undersampleStyle)

bkgd = makeBackground(diffMI, bctrl)
bkgd, bctrl, diffMI, statsFlag = self._setupBackground(refExposure)

# Some config and input checks if config.usePolynomial:
# 1) Check that order/bin size make sense:
Expand Down

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