def readFits(cls, path):
"""Read an external detrended image and create an LSST Exposure object
from it.
Any significant processing (e.g. pixel interpolation) should probably
be done in a ExternalIsrTask instead of here so it can be done once and
saved, instead of being done every time the image is loaded.
THIS METHOD IS INCOMPLETE; IT MUST BE MODIFIED ACCORDING TO THE
FORMAT OF THE DATA BEING LOADED.
"""
directory, filename = os.path.split(path)
match = cls.EXTERNAL_REGEX.match(filename)
camera = cls.getCameraFromVisit(match.group("visit"))
# Customize the code below based on the camera determined above.
# To support more than one camera it may be useful to delegate
# to other methods that are specific to certain cameras.
# Read the actual image in from the given path using e.g. astropy,
# and use it to fill in various arrays below.
bbox = Box2I(Point2I(0, 0), Extent2I(..., ...)) # width, height
result = ExposureF(bbox)
# main image, as a [y, x] numpy.float32 array
result.image.array = ...
# variance image, as a [y, x] numpy.float32 array
result.variance.array = ...
# This example includes masking NaN pixels as NO_DATA and pixels above
# 1E5 counts as SAT. External information about where bad pixels
# should be preferred when available, and obviously that saturation
# threshold is just an example (saturation should actually be
# determined before flat-fielding, of course).
# Interpolating these bad pixels is handled by ExternalIsrTask.
noDataBitMask = result.mask.getPlaneBitMask("NO_DATA")
satBitMask = result.mask.getPlaneBitMask("SAT")
result.mask.array |= noDataBitMask * np.isnan(result.image.array)
result.mask.array |= satBitMask * (result.image.array > 1E5)
# If you have a better guess at the PSF, we can find a way to use it.
# But it'd be a good idea to at least put this in with a guess at the
# seeing (RMS in pixels).
result.setPsf(SingleGaussianPsf(seeingRMS))
# Add a guess for the WCS, in this case assuming it's in the FITS
# header of the first HDU. Need to have something here, even if it
# isn't very good (e.g. whatever comes from the telescope).
metadata = readMetadata(filename)
wcs = SkyWcs(metadata)
result.setWcs(wcs)
return result
class FilterFractionTest(lsst.utils.tests.TestCase):
def setUp(self):
# Set up a Coadd with CoaddInputs tables that have blank filter columns to be filled
# in by later test code.
self.coadd = ExposureF(30, 90)
# WCS is arbitrary, since it'll be the same for all images
wcs = makeSkyWcs(crpix=Point2D(0, 0),
crval=SpherePoint(45.0, 45.0, degrees),
cdMatrix=makeCdMatrix(scale=0.17 * degrees))
self.coadd.setWcs(wcs)
schema = ExposureCatalog.Table.makeMinimalSchema()
self.filterKey = schema.addField("filter", type=str, doc="", size=16)
weightKey = schema.addField("weight", type=float, doc="")
# First input image covers the first 2/3, second covers the last 2/3, so they
# overlap in the middle 1/3.
inputs = ExposureCatalog(schema)
self.input1 = inputs.addNew()
self.input1.setId(1)
self.input1.setBBox(Box2I(Point2I(0, 0), Point2I(29, 59)))
self.input1.setWcs(wcs)
self.input1.set(weightKey, 2.0)
self.input2 = inputs.addNew()
self.input2.setId(2)
self.input2.setBBox(Box2I(Point2I(0, 30), Point2I(29, 89)))
self.input2.setWcs(wcs)
self.input2.set(weightKey, 3.0)
# Use the same catalog for visits and CCDs since the algorithm we're testing only cares
# about CCDs.
self.coadd.getInfo().setCoaddInputs(CoaddInputs(inputs, inputs))
# Set up a catalog with centroids and a FilterFraction plugin.
# We have one record in each region (first input only, both inputs, second input only)
schema = SourceCatalog.Table.makeMinimalSchema()
centroidKey = Point2DKey.addFields(schema,
"centroid",
doc="position",
unit="pixel")
schema.getAliasMap().set("slot_Centroid", "centroid")
self.plugin = FilterFractionPlugin(
config=FilterFractionPlugin.ConfigClass(),
schema=schema,
name="subaru_FilterFraction",
metadata=PropertyList())
catalog = SourceCatalog(schema)
self.record1 = catalog.addNew()
self.record1.set(centroidKey, Point2D(14.0, 14.0))
self.record12 = catalog.addNew()
self.record12.set(centroidKey, Point2D(14.0, 44.0))
self.record2 = catalog.addNew()
self.record2.set(centroidKey, Point2D(14.0, 74.0))
def tearDown(self):
del self.coadd
del self.input1
del self.input2
del self.record1
del self.record2
del self.record12
del self.plugin
def testSingleFilter(self):
"""Test that we get FilterFraction=1 for filters with only one version."""
self.input1.set(self.filterKey, "g")
self.input2.set(self.filterKey, "g")
self.plugin.measure(self.record1, self.coadd)
self.plugin.measure(self.record12, self.coadd)
self.plugin.measure(self.record2, self.coadd)
self.assertEqual(self.record1.get("subaru_FilterFraction_unweighted"),
1.0)
self.assertEqual(self.record12.get("subaru_FilterFraction_unweighted"),
1.0)
self.assertEqual(self.record2.get("subaru_FilterFraction_unweighted"),
1.0)
self.assertEqual(self.record1.get("subaru_FilterFraction_weighted"),
1.0)
self.assertEqual(self.record12.get("subaru_FilterFraction_weighted"),
1.0)
self.assertEqual(self.record2.get("subaru_FilterFraction_weighted"),
1.0)
def testTwoFiltersI(self):
"""Test that we get the right answers for a mix of i and i2."""
self.input1.set(self.filterKey, "i")
self.input2.set(self.filterKey, "i2")
self.plugin.measure(self.record1, self.coadd)
self.plugin.measure(self.record12, self.coadd)
self.plugin.measure(self.record2, self.coadd)
self.assertEqual(self.record1.get("subaru_FilterFraction_unweighted"),
0.0)
self.assertEqual(self.record12.get("subaru_FilterFraction_unweighted"),
0.5)
self.assertEqual(self.record2.get("subaru_FilterFraction_unweighted"),
1.0)
self.assertEqual(self.record1.get("subaru_FilterFraction_weighted"),
0.0)
self.assertEqual(self.record12.get("subaru_FilterFraction_weighted"),
0.6)
self.assertEqual(self.record2.get("subaru_FilterFraction_weighted"),
1.0)
def testTwoFiltersR(self):
"""Test that we get the right answers for a mix of r and r2."""
self.input1.set(self.filterKey, "r")
self.input2.set(self.filterKey, "r2")
self.plugin.measure(self.record1, self.coadd)
self.plugin.measure(self.record12, self.coadd)
self.plugin.measure(self.record2, self.coadd)
self.assertEqual(self.record1.get("subaru_FilterFraction_unweighted"),
0.0)
self.assertEqual(self.record12.get("subaru_FilterFraction_unweighted"),
0.5)
self.assertEqual(self.record2.get("subaru_FilterFraction_unweighted"),
1.0)
self.assertEqual(self.record1.get("subaru_FilterFraction_weighted"),
0.0)
self.assertEqual(self.record12.get("subaru_FilterFraction_weighted"),
0.6)
self.assertEqual(self.record2.get("subaru_FilterFraction_weighted"),
1.0)
def testInvalidCombination(self):
"""Test that we get a fatal exception for weird combinations of filters."""
self.input1.set(self.filterKey, "i")
self.input2.set(self.filterKey, "r")
with self.assertRaises(FatalAlgorithmError):
self.plugin.measure(self.record12, self.coadd)
class joinMatchListWithCatalogTestCase(unittest.TestCase):
def setUp(self):
# Load sample input from disk
testDir = os.path.dirname(__file__)
self.srcSet = SourceCatalog.readFits(os.path.join(testDir, "v695833-e0-c000.xy.fits"))
self.bbox = afwGeom.Box2I(afwGeom.Point2I(0, 0), afwGeom.Extent2I(2048, 4612)) # approximate
# create an exposure with the right metadata; the closest thing we have is
# apparently v695833-e0-c000-a00.sci.fits, which is much too small
smallExposure = ExposureF(os.path.join(testDir, "v695833-e0-c000-a00.sci.fits"))
self.exposure = ExposureF(self.bbox)
self.exposure.setWcs(smallExposure.getWcs())
self.exposure.setFilter(smallExposure.getFilter())
# copy the pixels we can, in case the user wants a debug display
mi = self.exposure.getMaskedImage()
mi.assign(smallExposure.getMaskedImage(), smallExposure.getBBox())
logLevel = Log.INFO
refCatDir = os.path.join(testDir, "data", "sdssrefcat")
butler = Butler(refCatDir)
refObjLoader = LoadIndexedReferenceObjectsTask(butler=butler)
astrometryConfig = AstrometryTask.ConfigClass()
self.astrom = AstrometryTask(config=astrometryConfig, refObjLoader=refObjLoader)
self.astrom.log.setLevel(logLevel)
# Since our sourceSelector is a registry object we have to wait for it to be created
# before setting default values.
self.astrom.matcher.sourceSelector.config.minSnr = 0
def tearDown(self):
del self.srcSet
del self.bbox
del self.exposure
del self.astrom
def getAstrometrySolution(self):
return self.astrom.solve(exposure=self.exposure, sourceCat=self.srcSet)
def testJoin(self):
res = self.getAstrometrySolution()
matches = res.matches
matchmeta = res.matchMeta
normalized = packMatches(matches)
normalized.table.setMetadata(matchmeta)
matches2 = self.astrom.refObjLoader.joinMatchListWithCatalog(normalized, self.srcSet)
self.assertEqual(len(matches2), len(matches))
for i in range(len(matches)):
self.assertEqual(matches2[i].second.table, matches[i].second.table)
self.assertEqual(matches2[i].second.getId(), matches[i].second.getId())
self.assertEqual(matches2[i].second, matches[i].second) # no deep copying, so we can compare ptrs
self.assertEqual(matches2[i].first.getId(), matches[i].first.getId())
self.assertEqual(matches2[i].first.getRa().asDegrees(), matches[i].first.getRa().asDegrees())
self.assertEqual(matches2[i].first.getDec().asDegrees(), matches[i].first.getDec().asDegrees())
self.assertEqual(matches2[i].first.get("i_flux"), matches[i].first.get("i_flux"))
def testJoinAllFluxes(self):
"""Test that we can read all the fluxes back from an a.n.d catalogue"""
res = self.getAstrometrySolution()
matches = res.matches
matchmeta = res.matchMeta
normalized = packMatches(matches)
normalized.table.setMetadata(matchmeta)
matches2 = self.astrom.refObjLoader.joinMatchListWithCatalog(normalized, self.srcSet)
self.assertGreater(len(matches2), 0)
ref = matches2[0][0]
names = ref.getSchema().getNames()
for b in ("u", "g", "r", "i", "z"):
self.assertIn("%s_flux" % (b,), names)
self.assertIn("%s_fluxSigma" % (b,), names)
class JoinMatchListWithCatalogTestCase(unittest.TestCase):
def setUp(self):
# Load sample input from disk
testDir = os.path.dirname(__file__)
self.srcSet = SourceCatalog.readFits(os.path.join(testDir, "v695833-e0-c000.xy.fits"))
self.bbox = lsst.geom.Box2I(lsst.geom.Point2I(0, 0), lsst.geom.Extent2I(2048, 4612)) # approximate
# create an exposure with the right metadata; the closest thing we have is
# apparently v695833-e0-c000-a00.sci.fits, which is much too small
smallExposure = ExposureF(os.path.join(testDir, "v695833-e0-c000-a00.sci.fits"))
self.exposure = ExposureF(self.bbox)
self.exposure.setWcs(smallExposure.getWcs())
self.exposure.setFilter(smallExposure.getFilter())
# copy the pixels we can, in case the user wants a debug display
mi = self.exposure.getMaskedImage()
mi.assign(smallExposure.getMaskedImage(), smallExposure.getBBox())
logLevel = Log.INFO
refCatDir = os.path.join(testDir, "data", "sdssrefcat")
butler = Butler(refCatDir)
refObjLoader = LoadIndexedReferenceObjectsTask(butler=butler)
astrometryConfig = AstrometryTask.ConfigClass()
self.astrom = AstrometryTask(config=astrometryConfig, refObjLoader=refObjLoader)
self.astrom.log.setLevel(logLevel)
# Since our sourceSelector is a registry object we have to wait for it to be created
# before setting default values.
self.astrom.sourceSelector.config.minSnr = 0
def tearDown(self):
del self.srcSet
del self.bbox
del self.exposure
del self.astrom
def getAstrometrySolution(self):
return self.astrom.solve(exposure=self.exposure, sourceCat=self.srcSet)
def testJoin(self):
res = self.getAstrometrySolution()
matches = res.matches
matchmeta = res.matchMeta
normalized = packMatches(matches)
normalized.table.setMetadata(matchmeta)
matches2 = self.astrom.refObjLoader.joinMatchListWithCatalog(normalized, self.srcSet)
self.assertEqual(len(matches2), len(matches))
for i in range(len(matches)):
self.assertEqual(matches2[i].second.table, matches[i].second.table)
self.assertEqual(matches2[i].second.getId(), matches[i].second.getId())
self.assertEqual(matches2[i].second, matches[i].second) # no deep copying, so we can compare ptrs
self.assertEqual(matches2[i].first.getId(), matches[i].first.getId())
self.assertEqual(matches2[i].first.getRa().asDegrees(), matches[i].first.getRa().asDegrees())
self.assertEqual(matches2[i].first.getDec().asDegrees(), matches[i].first.getDec().asDegrees())
self.assertEqual(matches2[i].first.get("i_flux"), matches[i].first.get("i_flux"))
def testJoinAllFluxes(self):
"""Test that we can read all the fluxes from a reference catalog"""
res = self.getAstrometrySolution()
matches = res.matches
matchmeta = res.matchMeta
normalized = packMatches(matches)
normalized.table.setMetadata(matchmeta)
matches2 = self.astrom.refObjLoader.joinMatchListWithCatalog(normalized, self.srcSet)
self.assertGreater(len(matches2), 0)
ref = matches2[0][0]
refSchema = ref.getSchema()
for b in ("u", "g", "r", "i", "z"):
self.assertIn("%s_flux" % (b,), refSchema)
self.assertIn("%s_fluxErr" % (b,), refSchema)