def overscanCorrection(self, exposure, amp):
"""Apply overscan correction in place
If the input exposure is on the readout backplanes listed in
config.overscanBiasJumpBKP, cut the amplifier in two vertically
and correct each piece separately.
@param[in,out] exposure: exposure to process; must include both
DataSec and BiasSec pixels
@param[in] amp: amplifier device data
"""
if not (
exposure.getMetadata().exists("FPA")
and exposure.getMetadata().get("FPA") in self.config.overscanBiasJumpBKP
):
IsrTask.overscanCorrection(self, exposure, amp)
return
dataBox = amp.getRawDataBBox()
overscanBox = amp.getRawHorizontalOverscanBBox()
if amp.getReadoutCorner() in (afwTable.LL, afwTable.LR):
yLower = self.config.overscanBiasJumpLocation
yUpper = dataBox.getHeight() - yLower
else:
yUpper = self.config.overscanBiasJumpLocation
yLower = dataBox.getHeight() - yUpper
lowerDataBBox = afwGeom.Box2I(dataBox.getBegin(), afwGeom.Extent2I(dataBox.getWidth(), yLower))
upperDataBBox = afwGeom.Box2I(
dataBox.getBegin() + afwGeom.Extent2I(0, yLower), afwGeom.Extent2I(dataBox.getWidth(), yUpper)
)
lowerOverscanBBox = afwGeom.Box2I(overscanBox.getBegin(), afwGeom.Extent2I(overscanBox.getWidth(), yLower))
upperOverscanBBox = afwGeom.Box2I(
overscanBox.getBegin() + afwGeom.Extent2I(0, yLower), afwGeom.Extent2I(overscanBox.getWidth(), yUpper)
)
maskedImage = exposure.getMaskedImage()
lowerDataView = maskedImage.Factory(maskedImage, lowerDataBBox)
upperDataView = maskedImage.Factory(maskedImage, upperDataBBox)
expImage = exposure.getMaskedImage().getImage()
lowerOverscanImage = expImage.Factory(expImage, lowerOverscanBBox)
upperOverscanImage = expImage.Factory(expImage, upperOverscanBBox)
overscanCorrection(
ampMaskedImage=lowerDataView,
overscanImage=lowerOverscanImage,
fitType=self.config.overscanFitType,
order=self.config.overscanOrder,
collapseRej=self.config.overscanRej,
)
overscanCorrection(
ampMaskedImage=upperDataView,
overscanImage=upperOverscanImage,
fitType=self.config.overscanFitType,
order=self.config.overscanOrder,
collapseRej=self.config.overscanRej,
)
def run(self, exposure, crosstalkSources=None):
"""Perform crosstalk correction on a DECam exposure and its corresponding dataRef.
Parameters
----------
exposure : `lsst.afw.image.Exposure`
Exposure to correct.
dataRef : `lsst.daf.persistence.butlerSubset.ButlerDataRef`
DataRef of exposure to correct which must include a dataId
with at least one visit and ccdnum.
crosstalkSources : `defaultdict`
Must contain image data and corresponding crosstalk coefficients for
each crosstalk source of the given dataRef victim. This is returned
by prepCrosstalk.
Returns
-------
`lsst.pipe.base.Struct`
Struct with components:
- ``exposure``: The exposure after crosstalk correction has been
applied (`lsst.afw.image.Exposure`).
"""
self.log.info('Applying crosstalk correction')
assert crosstalkSources is not None, "Sources are required for DECam crosstalk correction; \
you must run CrosstalkTask via IsrTask which will \
call prepCrosstalk to get the sources."
# Load data from crosstalk 'victim' exposure we want to correct
det = exposure.getDetector()
for amp in det:
ccdnum = det.getId()
ccdnum_str = '%02d' % ccdnum
victim = ccdnum_str + amp.getName()
# If doCrosstalkBeforeAssemble=True, then use getRawBBox(). Otherwise, getBBox().
dataBBox = amp.getRawBBox()
# Check to see if victim overscan has been corrected, and if not, correct it first
if not exposure.getMetadata().exists('OVERSCAN'):
decamisr = IsrTask()
decamisr.overscanCorrection(exposure, amp)
self.log.warn(
'Overscan correction did not happen prior to crosstalk correction'
)
self.log.info(
'Correcting victim %s overscan before crosstalk' % victim)
image = exposure.getMaskedImage().getImage()
victim_data = image.Factory(image, dataBBox)
# Load data from crosstalk 'source' exposures
for source in crosstalkSources[victim]:
source_data, source_coeff, source_idx = source
victim_idx = 0
if 'A' in victim:
victim_idx = 0
elif 'B' in victim:
victim_idx = 1
else:
self.log.fatal(
'DECam victim amp name does not contain A or B, cannot proceed'
)
if source_idx != victim_idx:
# Occurs with amp A and B mismatch; need to flip horizontally
source_data = afwMath.flipImage(source_data,
flipLR=True,
flipTB=False)
# Perform the linear crosstalk correction
try:
source_data *= source_coeff
victim_data -= source_data
except RuntimeError:
self.log.fatal(
'Crosstalk correction failed for victim %s from source %s'
% (victim, source))
return pipeBase.Struct(exposure=exposure, )
def prepCrosstalk(self, dataRef):
"""Retrieve source image data and coefficients to prepare for crosstalk correction.
This is called by readIsrData. The crosstalkSources land in isrData.
Parameters
----------
dataRef : `lsst.daf.persistence.butlerSubset.ButlerDataRef`
DataRef of exposure to correct which must include a dataId with
at least one visit and a ccdnum corresponding to the detector id.
Returns
-------
crosstalkSources : `defaultdict`
Contains image data and corresponding crosstalk coefficients for
each crosstalk source of the given dataRef victim.
"""
# Retrieve crosstalk sources and coefficients for the whole focal plane
sources, coeffs = self.config.getSourcesAndCoeffs()
# Define a butler to prepare for accessing crosstalk 'source' image data
try:
butler = dataRef.getButler()
except RuntimeError:
self.log.fatal('Cannot get a Butler from the dataRef provided')
# Retrieve visit and ccdnum from 'victim' so we can look up 'sources'
victim_exposure = dataRef.get()
det = victim_exposure.getDetector()
visit = dataRef.dataId['visit']
ccdnum = det.getId()
ccdnum_str = '%02d' % ccdnum
crosstalkSources = defaultdict(list)
decamisr = IsrTask() # needed for source_exposure overscan correction
for amp in det:
victim = ccdnum_str + amp.getName()
for source in sources[victim]:
source_ccdnum = int(source[:2])
try:
source_exposure = butler.get('raw',
dataId={
'visit': visit,
'ccdnum': source_ccdnum
})
except RuntimeError:
self.log.warn('Cannot access source %d, SKIPPING IT' %
source_ccdnum)
else:
self.log.info(
'Correcting victim %s from crosstalk source %s' %
(victim, source))
if 'A' in source:
amp_idx = 0
elif 'B' in source:
amp_idx = 1
else:
self.log.fatal(
'DECam source amp name does not contain A or B, cannot proceed'
)
source_amp = source_exposure.getDetector()[amp_idx]
# If doCrosstalkBeforeAssemble=True, then use getRawBBox(). Otherwise, getRawDataBBox().
source_dataBBox = source_amp.getRawBBox()
# Check to see if source overscan has been corrected, and if not, correct it first
if not source_exposure.getMetadata().exists('OVERSCAN'):
decamisr.overscanCorrection(source_exposure,
source_amp)
self.log.info(
'Correcting source %s overscan before using to correct crosstalk'
% source)
source_image = source_exposure.getMaskedImage().getImage()
source_data = source_image.Factory(source_image,
source_dataBBox,
deep=True)
crosstalkSources[victim].append(
(source_data, coeffs[(victim, source)], amp_idx))
return crosstalkSources
def overscanCorrection(self, exposure, amp):
"""Apply overscan correction in place
If the input exposure is on the readout backplanes listed in
config.overscanBiasJumpBKP, cut the amplifier in two vertically
and correct each piece separately.
@param[in,out] exposure: exposure to process; must include both
DataSec and BiasSec pixels
@param[in] amp: amplifier device data
"""
if not (exposure.getMetadata().exists('FPA')
and exposure.getMetadata().get('FPA')
in self.config.overscanBiasJumpBKP):
IsrTask.overscanCorrection(self, exposure, amp)
return
dataBox = amp.getRawDataBBox()
overscanBox = amp.getRawHorizontalOverscanBBox()
if amp.getReadoutCorner() in (afwTable.LL, afwTable.LR):
yLower = self.config.overscanBiasJumpLocation
yUpper = dataBox.getHeight() - yLower
else:
yUpper = self.config.overscanBiasJumpLocation
yLower = dataBox.getHeight() - yUpper
lowerDataBBox = afwGeom.Box2I(
dataBox.getBegin(), afwGeom.Extent2I(dataBox.getWidth(), yLower))
upperDataBBox = afwGeom.Box2I(
dataBox.getBegin() + afwGeom.Extent2I(0, yLower),
afwGeom.Extent2I(dataBox.getWidth(), yUpper))
lowerOverscanBBox = afwGeom.Box2I(
overscanBox.getBegin(),
afwGeom.Extent2I(overscanBox.getWidth(), yLower))
upperOverscanBBox = afwGeom.Box2I(
overscanBox.getBegin() + afwGeom.Extent2I(0, yLower),
afwGeom.Extent2I(overscanBox.getWidth(), yUpper))
maskedImage = exposure.getMaskedImage()
lowerDataView = maskedImage.Factory(maskedImage, lowerDataBBox)
upperDataView = maskedImage.Factory(maskedImage, upperDataBBox)
expImage = exposure.getMaskedImage().getImage()
lowerOverscanImage = expImage.Factory(expImage, lowerOverscanBBox)
upperOverscanImage = expImage.Factory(expImage, upperOverscanBBox)
overscanCorrection(
ampMaskedImage=lowerDataView,
overscanImage=lowerOverscanImage,
fitType=self.config.overscanFitType,
order=self.config.overscanOrder,
collapseRej=self.config.overscanRej,
)
overscanCorrection(
ampMaskedImage=upperDataView,
overscanImage=upperOverscanImage,
fitType=self.config.overscanFitType,
order=self.config.overscanOrder,
collapseRej=self.config.overscanRej,
)
def overscanCorrection(self, exposure, amp):
"""Apply overscan correction in place
If the input exposure is on the readout backplanes listed in
config.overscanBiasJumpBKP, cut the amplifier in two vertically
and correct each piece separately.
Parameters
----------
exposure: `lsst.afw.image.Exposure`
exposure to process; must include both DataSec and BiasSec pixels
amp: `lsst.afw.table.AmpInfoRecord`
amplifier device data
Returns
-------
exposure: `lsst.afw.image.Exposure`
exposure corrected in place with updated metadata
"""
if not (exposure.getMetadata().exists('FPA')
and exposure.getMetadata().get('FPA')
in self.config.overscanBiasJumpBKP):
IsrTask.overscanCorrection(self, exposure, amp)
return
dataBox = amp.getRawDataBBox()
overscanBox = amp.getRawHorizontalOverscanBBox()
if amp.getReadoutCorner() in (afwTable.LL, afwTable.LR):
yLower = self.config.overscanBiasJumpLocation
yUpper = dataBox.getHeight() - yLower
else:
yUpper = self.config.overscanBiasJumpLocation
yLower = dataBox.getHeight() - yUpper
lowerDataBBox = afwGeom.Box2I(
dataBox.getBegin(), afwGeom.Extent2I(dataBox.getWidth(), yLower))
upperDataBBox = afwGeom.Box2I(
dataBox.getBegin() + afwGeom.Extent2I(0, yLower),
afwGeom.Extent2I(dataBox.getWidth(), yUpper))
lowerOverscanBBox = afwGeom.Box2I(
overscanBox.getBegin(),
afwGeom.Extent2I(overscanBox.getWidth(), yLower))
upperOverscanBBox = afwGeom.Box2I(
overscanBox.getBegin() + afwGeom.Extent2I(0, yLower),
afwGeom.Extent2I(overscanBox.getWidth(), yUpper))
maskedImage = exposure.getMaskedImage()
lowerDataView = maskedImage.Factory(maskedImage, lowerDataBBox)
upperDataView = maskedImage.Factory(maskedImage, upperDataBBox)
expImage = exposure.getMaskedImage().getImage()
lowerOverscanImage = expImage.Factory(expImage, lowerOverscanBBox)
upperOverscanImage = expImage.Factory(expImage, upperOverscanBBox)
overscanCorrection(
ampMaskedImage=lowerDataView,
overscanImage=lowerOverscanImage,
fitType=self.config.overscanFitType,
order=self.config.overscanOrder,
collapseRej=self.config.overscanRej,
)
overscanCorrection(
ampMaskedImage=upperDataView,
overscanImage=upperOverscanImage,
fitType=self.config.overscanFitType,
order=self.config.overscanOrder,
collapseRej=self.config.overscanRej,
)
# Note that overscan correction has been done in exposure metadata
metadata = exposure.getMetadata()
metadata.set(
'OVERSCAN', 'Overscan corrected on {0}'.format(
dt.datetime.now().strftime("%Y-%m-%dT%H:%M:%S")))
exposure.setMetadata(metadata)
