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DM-20163: Use PixelAreaBoundedField in fgcmcal calibration outputs #22

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Jan 10, 2020
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DM-20163: Use PixelAreaBoundedField in fgcmcal calibration outputs #22

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96341cd
Add ability to factor out wcs jacobian distortions from photom. calib…
erykoff Nov 1, 2019
f5d8d20
Post-review cleanup.
erykoff Jan 10, 2020
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50 changes: 36 additions & 14 deletions python/lsst/fgcmcal/fgcmBuildStars.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@
from lsst.meas.algorithms.sourceSelector import sourceSelectorRegistry

from .fgcmLoadReferenceCatalog import FgcmLoadReferenceCatalogTask
from .utilities import computeApproxPixelAreaFields

import fgcm

Expand Down Expand Up @@ -136,13 +137,22 @@ class FgcmBuildStarsConfig(pexConfig.Config):
applyJacobian = pexConfig.Field(
doc="Apply Jacobian correction?",
dtype=bool,
deprecated=("This field is no longer used, and has been deprecated by DM-20163. "
"It will be removed after v20."),
default=False
)
jacobianName = pexConfig.Field(
doc="Name of field with jacobian correction",
dtype=str,
deprecated=("This field is no longer used, and has been deprecated by DM-20163. "
"It will be removed after v20."),
default="base_Jacobian_value"
)
doApplyWcsJacobian = pexConfig.Field(
doc="Apply the jacobian of the WCS to the star observations prior to fit?",
dtype=bool,
default=True
)
psfCandidateName = pexConfig.Field(
doc="Name of field with psf candidate flag for propagation",
dtype=str,
Expand Down Expand Up @@ -340,17 +350,20 @@ def runDataRef(self, butler, dataRefs):

groupedDataRefs = self.findAndGroupDataRefs(butler, dataRefs)

camera = butler.get('camera')

# Make the visit catalog if necessary
if not butler.datasetExists('fgcmVisitCatalog'):
# we need to build visitCat
visitCat = self.fgcmMakeVisitCatalog(butler, groupedDataRefs)
visitCat = self.fgcmMakeVisitCatalog(camera, groupedDataRefs)
else:
self.log.info("Found fgcmVisitCatalog.")
visitCat = butler.get('fgcmVisitCatalog')

# Compile all the stars
if not butler.datasetExists('fgcmStarObservations'):
fgcmStarObservationCat = self.fgcmMakeAllStarObservations(groupedDataRefs, visitCat)
fgcmStarObservationCat = self.fgcmMakeAllStarObservations(groupedDataRefs,
visitCat)
else:
self.log.info("Found fgcmStarObservations")
fgcmStarObservationCat = butler.get('fgcmStarObservations')
Expand All @@ -370,28 +383,29 @@ def runDataRef(self, butler, dataRefs):
if fgcmRefCat is not None:
butler.put(fgcmRefCat, 'fgcmReferenceStars')

def fgcmMakeVisitCatalog(self, butler, groupedDataRefs):
def fgcmMakeVisitCatalog(self, camera, groupedDataRefs):
"""
Make a visit catalog with all the keys from each visit

Parameters
----------
butler: `lsst.daf.persistence.Butler`
camera: `lsst.afw.cameraGeom.Camera`
Camera from the butler
groupedDataRefs: `dict`
Dictionary with visit keys, and `list`s of `lsst.daf.persistence.ButlerDataRef`
Dictionary with visit keys, and `list`s of
`lsst.daf.persistence.ButlerDataRef`

Returns
-------
visitCat: `afw.table.BaseCatalog`
"""

camera = butler.get('camera')
nCcd = len(camera)

schema = self._makeFgcmVisitSchema(nCcd)

visitCat = afwTable.BaseCatalog(schema)
visitCat.table.preallocate(len(groupedDataRefs))
visitCat.reserve(len(groupedDataRefs))

self._fillVisitCatalog(visitCat, groupedDataRefs)

Expand All @@ -404,9 +418,10 @@ def _fillVisitCatalog(self, visitCat, groupedDataRefs):
Parameters
----------
visitCat: `afw.table.BaseCatalog`
Catalog with schema from _createFgcmVisitSchema()
Catalog with schema from _makeFgcmVisitSchema()
groupedDataRefs: `dict`
Dictionary with visit keys, and `list`s of `lsst.daf.persistence.ButlerDataRef`
Dictionary with visit keys, and `list`s of
`lsst.daf.persistence.ButlerDataRef`
"""

bbox = geom.BoxI(geom.PointI(0, 0), geom.PointI(1, 1))
Expand Down Expand Up @@ -573,8 +588,7 @@ def fgcmMakeAllStarObservations(self, groupedDataRefs, visitCat):
Returns
-------
fgcmStarObservations: `afw.table.BaseCatalog`
Full catalog of good observations. Only returned if
returnCatalog is True.
Full catalog of good observations.
"""

startTime = time.time()
Expand All @@ -589,6 +603,8 @@ def fgcmMakeAllStarObservations(self, groupedDataRefs, visitCat):
for ccdIndex, detector in enumerate(camera):
ccdMapping[detector.getId()] = ccdIndex

approxPixelAreaFields = computeApproxPixelAreaFields(camera)

sourceMapper = self._makeSourceMapper(sourceSchema)

# We also have a temporary catalog that will accumulate aperture measurements
Expand Down Expand Up @@ -648,12 +664,18 @@ def fgcmMakeAllStarObservations(self, groupedDataRefs, visitCat):
tempCat[instMagErrKey][:] = k * (sources[instFluxErrKey][goodSrc.selected] /
sources[instFluxKey][goodSrc.selected])

if self.config.applyJacobian:
# Compute the jacobian from an approximate PixelAreaBoundedField
tempCat['jacobian'] = approxPixelAreaFields[ccdId].evaluate(tempCat['x'],
tempCat['y'])

# Apply the jacobian if configured
if self.config.doApplyWcsJacobian:
tempCat[instMagKey][:] -= 2.5 * np.log10(tempCat['jacobian'][:])

fullCatalog.extend(tempCat)

# And the aperture information
# This does not need the jacobian because it is all locally relative
tempAperCat = afwTable.BaseCatalog(aperVisitCatalog.schema)
tempAperCat.reserve(goodSrc.selected.sum())
tempAperCat.extend(sources[goodSrc.selected], mapper=aperMapper)
Expand Down Expand Up @@ -900,8 +922,6 @@ def _makeSourceMapper(self, sourceSchema):
# map to ra/dec
sourceMapper.addMapping(sourceSchema['coord_ra'].asKey(), 'ra')
sourceMapper.addMapping(sourceSchema['coord_dec'].asKey(), 'dec')
sourceMapper.addMapping(sourceSchema[self.config.jacobianName].asKey(),
'jacobian')
sourceMapper.addMapping(sourceSchema['slot_Centroid_x'].asKey(), 'x')
sourceMapper.addMapping(sourceSchema['slot_Centroid_y'].asKey(), 'y')
sourceMapper.addMapping(sourceSchema[self.config.psfCandidateName].asKey(),
Expand All @@ -916,6 +936,8 @@ def _makeSourceMapper(self, sourceSchema):
"instMag", type=np.float32, doc="Instrumental magnitude")
sourceMapper.editOutputSchema().addField(
"instMagErr", type=np.float32, doc="Instrumental magnitude error")
sourceMapper.editOutputSchema().addField(
"jacobian", type=np.float32, doc="Relative pixel scale from wcs jacobian")

return sourceMapper

Expand Down
13 changes: 6 additions & 7 deletions python/lsst/fgcmcal/fgcmCalibrateTract.py
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Expand Up @@ -239,7 +239,8 @@ def runDataRef(self, butler, dataRefs):

# Note that we will need visitCat at the end of the procedure for the outputs
groupedDataRefs = self.fgcmBuildStars.findAndGroupDataRefs(butler, dataRefs)
visitCat = self.fgcmBuildStars.fgcmMakeVisitCatalog(butler, groupedDataRefs)
camera = butler.get('camera')
visitCat = self.fgcmBuildStars.fgcmMakeVisitCatalog(camera, groupedDataRefs)
fgcmStarObservationCat = self.fgcmBuildStars.fgcmMakeAllStarObservations(groupedDataRefs,
visitCat)

Expand Down Expand Up @@ -420,14 +421,12 @@ def runDataRef(self, butler, dataRefs):
rep = fgcmFitCycle.fgcmPars.compReservedRawRepeatability[i] * 1000.0
self.log.info(" Band %s, repeatability: %.2f mmag" % (band, rep))

# Do the outputs. Need to keep track of tract, blah.
# Do the outputs. Need to keep track of tract.

if self.config.fgcmFitCycle.superStarSubCcd or self.config.fgcmFitCycle.ccdGraySubCcd:
chebSize = fgcmFitCycle.fgcmZpts.zpStruct['FGCM_FZPT_CHEB'].shape[1]
else:
chebSize = 0
superStarChebSize = fgcmFitCycle.fgcmZpts.zpStruct['FGCM_FZPT_SSTAR_CHEB'].shape[1]
zptChebSize = fgcmFitCycle.fgcmZpts.zpStruct['FGCM_FZPT_CHEB'].shape[1]

zptSchema = makeZptSchema(chebSize)
zptSchema = makeZptSchema(superStarChebSize, zptChebSize)
zptCat = makeZptCat(zptSchema, fgcmFitCycle.fgcmZpts.zpStruct)

atmSchema = makeAtmSchema()
Expand Down
25 changes: 20 additions & 5 deletions python/lsst/fgcmcal/fgcmFitCycle.py
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Original file line number Diff line number Diff line change
Expand Up @@ -432,6 +432,22 @@ class FgcmFitCycleConfig(pexConfig.Config):
dtype=bool,
default=False,
)
autoPhotometricCutNSig = pexConfig.Field(
doc=("Number of sigma for automatic computation of (low) photometric cut. "
"Cut is based on exposure gray width (per band), unless "
"useRepeatabilityForExpGrayCuts is set, in which case the star "
"repeatability is used (also per band)."),
dtype=float,
default=3.0,
)
autoHighCutNSig = pexConfig.Field(
doc=("Number of sigma for automatic computation of (high) outlier cut. "
"Cut is based on exposure gray width (per band), unless "
"useRepeatabilityForExpGrayCuts is set, in which case the star "
"repeatability is used (also per band)."),
dtype=float,
default=4.0,
)
quietMode = pexConfig.Field(
doc="Be less verbose with logging.",
dtype=bool,
Expand Down Expand Up @@ -1024,11 +1040,10 @@ def _persistFgcmDatasets(self, butler, fgcmFitCycle):

# Save the zeropoint information and atmospheres only if desired
if self.outputZeropoints:
if self.config.superStarSubCcd or self.config.ccdGraySubCcd:
chebSize = fgcmFitCycle.fgcmZpts.zpStruct['FGCM_FZPT_CHEB'].shape[1]
else:
chebSize = 0
zptSchema = makeZptSchema(chebSize)
superStarChebSize = fgcmFitCycle.fgcmZpts.zpStruct['FGCM_FZPT_SSTAR_CHEB'].shape[1]
zptChebSize = fgcmFitCycle.fgcmZpts.zpStruct['FGCM_FZPT_CHEB'].shape[1]

zptSchema = makeZptSchema(superStarChebSize, zptChebSize)
zptCat = makeZptCat(zptSchema, fgcmFitCycle.fgcmZpts.zpStruct)

butler.put(zptCat, 'fgcmZeropoints', fgcmcycle=self.config.cycleNumber)
Expand Down