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Refactor based on pull request review, AEW
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@aemerywatkins
aemerywatkins committed Oct 11, 2024
1 parent a4066ff commit bfe1508
Showing 1 changed file with 47 additions and 48 deletions.
95 changes: 47 additions & 48 deletions python/lsst/pipe/tasks/skyCorrection.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,13 +28,14 @@
import lsst.pipe.base.connectionTypes as cT
import numpy as np
from lsst.pex.config import Config, ConfigField, ConfigurableField, Field
from lsst.pipe.base import (PipelineTask, PipelineTaskConfig,
PipelineTaskConnections, Struct)
from lsst.pipe.tasks.background import (FocalPlaneBackground,
FocalPlaneBackgroundConfig,
MaskObjectsTask, SkyMeasurementTask)
from lsst.pipe.tasks.visualizeVisit import (VisualizeMosaicExpConfig,
VisualizeMosaicExpTask)
from lsst.pipe.base import PipelineTask, PipelineTaskConfig, PipelineTaskConnections, Struct
from lsst.pipe.tasks.background import (
FocalPlaneBackground,
FocalPlaneBackgroundConfig,
MaskObjectsTask,
SkyMeasurementTask,
)
from lsst.pipe.tasks.visualizeVisit import VisualizeMosaicExpConfig, VisualizeMosaicExpTask


def _skyFrameLookup(datasetType, registry, quantumDataId, collections):
Expand Down Expand Up @@ -177,10 +178,10 @@ class SkyCorrectionConfig(PipelineTaskConfig, pipelineConnections=SkyCorrectionC
dtype=FocalPlaneBackgroundConfig,
doc="Initial background model, prior to sky frame subtraction",
)
doBgModel1 = Field(
undoBgModel1 = Field(
dtype=bool,
default=True,
doc="If False, adds back initial background model after sky",
default=False,
doc="If True, adds back initial background model after sky and removes bgModel1 from the list",
)
sky = ConfigurableField(
target=SkyMeasurementTask,
Expand Down Expand Up @@ -216,8 +217,8 @@ def setDefaults(self):

def validate(self):
super().validate()
if not self.doBgModel1 and not self.doSky and not self.doBgModel2:
raise ValueError("Task requires at least one of doBgModel1, doSky or doBgModel2 to be True.")
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):
Expand Down Expand Up @@ -287,11 +288,11 @@ 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.
Expand All @@ -301,16 +302,16 @@ def run(self, calExps, calBkgs, skyFrames, camera):
results : `Struct` containing:
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)
Expand All @@ -320,8 +321,8 @@ def run(self, calExps, calBkgs, skyFrames, camera):
self._subtractSkyFrame(calExps, skyFrames, calBkgs)

# Adds full-fp bg back onto exposures, removes it from list
if not self.config.doBgModel1:
_ = self._restoreVisitBackground(calExps, calBkgs)
if self.config.undoBgModel1:
_ = self._undoInitialBackground(calExps, calBkgs)

# Bin exposures, generate full-fp bg, map to CCDs and subtract in-place
if self.config.doBgModel2:
Expand All @@ -341,7 +342,7 @@ def run(self, calExps, calBkgs, skyFrames, camera):

return Struct(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 @@ -363,17 +364,17 @@ 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 @@ -392,31 +393,28 @@ 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 _restoreVisitBackground(self, calExps, calBkgs):
def _undoInitialBackground(self, calExps, calBkgs):
"""Restores the full focal-plane background to a visit.
Runs after _subtractSkyFrame() if doBgModel1=False.
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.
Returns
-------
calExps : `list` [`lsst.afw.image.maskedImage.MaskedImageF`]
Background subtracted exposures for creating a focal plane image.
calBkgs : `list` [`lsst.afw.math._backgroundList.BackgroundList`]
Updated background lists with a visit-level model removed.
Notes
-----
Inputs are modified in-place.
"""
for calExp, calBkg in zip(calExps, calBkgs):
image = calExp.getMaskedImage()
Expand All @@ -427,7 +425,8 @@ def _restoreVisitBackground(self, calExps, calBkgs):
calBkg._backgrounds.pop(-2)

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

Expand All @@ -444,9 +443,9 @@ 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 @@ -457,7 +456,7 @@ 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 @@ -522,16 +521,16 @@ 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 @@ -554,11 +553,11 @@ 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.
"""
skyFrameBgModels = []
Expand Down Expand Up @@ -593,11 +592,11 @@ 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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