def summarizeVisit(butler, *, exp=None, extendedSummary=False, **kwargs):
from astroquery.simbad import Simbad
import astropy.units as u
from astropy.time import Time
from astropy.coordinates import SkyCoord, EarthLocation, AltAz
def _airMassFromrRawMd(md):
auxTelLocation = EarthLocation(lat=-30.244639 * u.deg,
lon=-70.749417 * u.deg,
height=2663 * u.m)
time = Time(md['DATE-OBS'])
skyLocation = SkyCoord(md['RASTART'], md['DECSTART'], unit=u.deg)
altAz = AltAz(obstime=time, location=auxTelLocation)
observationAltAz = skyLocation.transform_to(altAz)
return observationAltAz.secz.value
items = ["OBJECT", "expTime", "FILTER", "imageType"]
obj, expTime, filterCompound, imageType = butler.queryMetadata(
'raw', items, **kwargs)[0]
filt, grating = filterCompound.split('~')
rawMd = butler.get('raw_md', **kwargs)
airmass = _airMassFromrRawMd(rawMd)
print(f"Object name: {obj}")
print(f"expTime: {expTime}s")
print(f"imageType: {imageType}")
print(f"Filter: {filt}")
print(f"Grating: {grating}")
print(f"Airmass: {airmass:.3f}")
if imageType not in ['BIAS', 'FLAT', 'DARK']:
simbadObj = Simbad.query_object(obj)
if simbadObj is None:
print(f"Failed to find {obj} in Simbad.")
else:
assert (len(simbadObj.as_array()) == 1)
raStr = simbadObj[0]['RA']
decStr = simbadObj[0]['DEC']
skyLocation = SkyCoord(raStr,
decStr,
unit=(u.hourangle, u.degree),
frame='icrs')
raRad, decRad = skyLocation.ra.rad, skyLocation.dec.rad
print(f"obj RA (str): {raStr}")
print(f"obj DEC (str): {decStr}")
print(f"obj RA (rad): {raRad:5f}")
print(f"obj DEC (rad): {decRad:5f}")
print(f"obj RA (deg): {raRad*180/math.pi:5f}")
print(f"obj DEC (deg): {decRad*180/math.pi:5f}")
if exp is not None: # calc source coords from exp wcs
ra = geom.Angle(raRad)
dec = geom.Angle(decRad)
targetLocation = geom.SpherePoint(ra, dec)
pixCoord = exp.getWcs().skyToPixel(targetLocation)
print(exp.getWcs())
print(f"Source location: {pixCoord} using exp provided")
else: # try to find one, but not too hard
datasetTypes = ['calexp', 'quickLookExp', 'postISRCCD']
for datasetType in datasetTypes:
wcs = None
typeUsed = None
try:
wcs = butler.get(datasetType + '_wcs', **kwargs)
typeUsed = datasetType
break
except butlerExcept.NoResults:
pass
if wcs is not None:
ra = geom.Angle(raRad)
dec = geom.Angle(decRad)
targetLocation = geom.SpherePoint(ra, dec)
pixCoord = wcs.skyToPixel(targetLocation)
print(wcs)
print(f"Source location: {pixCoord} using {typeUsed}")
if extendedSummary:
print('\n--- Extended Summary ---')
ranIsr = False
if exp is None:
print("Running isr to compute image stats...")
# catch all the ISR chat
# logRedirection1 = LogRedirect(1, open(os.devnull, 'w'))
# logRedirection2 = LogRedirect(2, open(os.devnull, 'w'))
# import ipdb as pdb; pdb.set_trace()
from lsst.ip.isr.isrTask import IsrTask
isrConfig = IsrTask.ConfigClass()
isrConfig.doLinearize = False
isrConfig.doBias = False
isrConfig.doFlat = False
isrConfig.doDark = False
isrConfig.doFringe = False
isrConfig.doDefect = False
isrConfig.doWrite = False
isrTask = IsrTask(config=isrConfig)
dataRef = butler.dataRef('raw', **kwargs)
exp = isrTask.runDataRef(dataRef).exposure
wcs = exp.getWcs()
ranIsr = True
# logRedirection1.finish() # end re-direct
# logRedirection2.finish() # end re-direct
print(wcs)
if simbadObj and ranIsr:
ra = geom.Angle(raRad)
dec = geom.Angle(decRad)
targetLocation = geom.SpherePoint(ra, dec)
pixCoord = wcs.skyToPixel(targetLocation)
print(
f"Source location: {pixCoord} using postISR just-reconstructed wcs"
)
print(
f'\nImage stats from {"just-constructed" if ranIsr else "provided"} exp:\n'
)
print(f'Image mean: {np.mean(exp.image.array):.2f}')
print(f'Image median: {np.median(exp.image.array):.2f}')
print(f'Image min: {np.min(exp.image.array):.2f}')
print(f'Image max: {np.max(exp.image.array):.2f}')
# TODO: quartiles/percentiles here
# number of masked pixels, saturated pixels
print()
print(f'BAD pixels: {countPixels(exp.maskedImage, "BAD")}')
print(f'SAT pixels: {countPixels(exp.maskedImage, "SAT")}')
print(f'CR pixels: {countPixels(exp.maskedImage, "CR")}')
print(f'INTRP pixels: {countPixels(exp.maskedImage, "INTRP")}')
print(f'DETECTED pixels: {countPixels(exp.maskedImage, "DETECTED")}')
# detector = exp.getDetector()
visitInfo = exp.getInfo().getVisitInfo()
rotAngle = visitInfo.getBoresightRotAngle()
boresight = visitInfo.getBoresightRaDec()
md = butler.get('raw_md', **kwargs)
print("\n From VisitInfo:")
print(f"boresight: {boresight}")
print(f"rotAngle: {rotAngle}")
print(f" → {rotAngle.asDegrees():.4f} deg")
print("\n From raw_md:")
print(f"ROTPA: {md['ROTPA']} deg")
print(f" → {(md['ROTPA']*math.pi/180):.6f} rad")
class IsrTaskUnTrimmedTestCases(lsst.utils.tests.TestCase):
"""Test IsrTask methods using untrimmed raw data.
"""
def setUp(self):
self.config = IsrTaskConfig()
self.config.qa = IsrQaConfig()
self.task = IsrTask(config=self.config)
self.mockConfig = isrMock.IsrMockConfig()
self.mockConfig.isTrimmed = False
self.doGenerateImage = True
self.dataRef = isrMock.DataRefMock(config=self.mockConfig)
self.camera = isrMock.IsrMock(config=self.mockConfig).getCamera()
self.inputExp = isrMock.RawMock(config=self.mockConfig).run()
self.amp = self.inputExp.getDetector()[0]
self.mi = self.inputExp.getMaskedImage()
def batchSetConfiguration(self, value):
"""Set the configuration state to a consistent value.
Disable options we do not need as well.
Parameters
----------
value : `bool`
Value to switch common ISR configuration options to.
"""
self.config.qa.flatness.meshX = 20
self.config.qa.flatness.meshY = 20
self.config.doWrite = False
self.config.doLinearize = False
self.config.doCrosstalk = False
self.config.doConvertIntToFloat = value
self.config.doSaturation = value
self.config.doSuspect = value
self.config.doSetBadRegions = value
self.config.doOverscan = value
self.config.doBias = value
self.config.doVariance = value
self.config.doWidenSaturationTrails = value
self.config.doBrighterFatter = value
self.config.doDefect = value
self.config.doSaturationInterpolation = value
self.config.doDark = value
self.config.doStrayLight = value
self.config.doFlat = value
self.config.doFringe = value
self.config.doMeasureBackground = value
self.config.doVignette = value
self.config.doAttachTransmissionCurve = value
self.config.doUseOpticsTransmission = value
self.config.doUseFilterTransmission = value
self.config.doUseSensorTransmission = value
self.config.doUseAtmosphereTransmission = value
self.config.qa.saveStats = value
self.config.qa.doThumbnailOss = value
self.config.qa.doThumbnailFlattened = value
self.config.doApplyGains = not value
self.config.doCameraSpecificMasking = value
def validateIsrResults(self):
"""results should be a struct with components that are
not None if included in the configuration file.
Returns
-------
results : `pipeBase.Struct`
Results struct generated from the current ISR configuration.
"""
self.task = IsrTask(config=self.config)
results = self.task.run(
self.inputExp,
camera=self.camera,
bias=self.dataRef.get("bias"),
dark=self.dataRef.get("dark"),
flat=self.dataRef.get("flat"),
bfKernel=self.dataRef.get("bfKernel"),
defects=self.dataRef.get("defects"),
fringes=Struct(fringes=self.dataRef.get("fringe"), seed=1234),
opticsTransmission=self.dataRef.get("transmission_"),
filterTransmission=self.dataRef.get("transmission_"),
sensorTransmission=self.dataRef.get("transmission_"),
atmosphereTransmission=self.dataRef.get("transmission_"))
self.assertIsInstance(results, Struct)
self.assertIsInstance(results.exposure, afwImage.Exposure)
return results
def test_overscanCorrection(self):
"""Expect that this should reduce the image variance with a full fit.
The default fitType of MEDIAN will reduce the median value.
This needs to operate on a RawMock() to have overscan data to use.
The output types may be different when fitType != MEDIAN.
"""
statBefore = computeImageMedianAndStd(
self.inputExp.image[self.amp.getRawDataBBox()])
oscanResults = self.task.overscanCorrection(self.inputExp, self.amp)
self.assertIsInstance(oscanResults, Struct)
self.assertIsInstance(oscanResults.imageFit, float)
self.assertIsInstance(oscanResults.overscanFit, float)
self.assertIsInstance(oscanResults.overscanImage,
afwImage.MaskedImageF)
statAfter = computeImageMedianAndStd(
self.inputExp.image[self.amp.getRawDataBBox()])
self.assertLess(statAfter[0], statBefore[0])
def test_overscanCorrectionMedianPerRow(self):
"""Expect that this should reduce the image variance with a full fit.
fitType of MEDIAN_PER_ROW will reduce the median value.
This needs to operate on a RawMock() to have overscan data to use.
The output types may be different when fitType != MEDIAN_PER_ROW.
"""
self.config.overscan.fitType = 'MEDIAN_PER_ROW'
statBefore = computeImageMedianAndStd(
self.inputExp.image[self.amp.getRawDataBBox()])
oscanResults = self.task.overscanCorrection(self.inputExp, self.amp)
self.assertIsInstance(oscanResults, Struct)
self.assertIsInstance(oscanResults.imageFit, afwImage.ImageF)
self.assertIsInstance(oscanResults.overscanFit, afwImage.ImageF)
self.assertIsInstance(oscanResults.overscanImage,
afwImage.MaskedImageF)
statAfter = computeImageMedianAndStd(
self.inputExp.image[self.amp.getRawDataBBox()])
self.assertLess(statAfter[0], statBefore[0])
def test_runDataRef(self):
"""Expect a dataRef to be handled correctly.
"""
self.config.doLinearize = False
self.config.doWrite = False
self.task = IsrTask(config=self.config)
results = self.task.runDataRef(self.dataRef)
self.assertIsInstance(results, Struct)
self.assertIsInstance(results.exposure, afwImage.Exposure)
def test_run_allTrue(self):
"""Expect successful run with expected outputs when all non-exclusive
configuration options are on.
Output results should be tested more precisely by the
individual function tests.
"""
self.batchSetConfiguration(True)
self.validateIsrResults()
def test_run_allFalse(self):
"""Expect successful run with expected outputs when all non-exclusive
configuration options are off.
Output results should be tested more precisely by the
individual function tests.
"""
self.batchSetConfiguration(False)
self.validateIsrResults()
def test_failCases(self):
"""Expect failure with crosstalk enabled.
Output results should be tested more precisely by the
individual function tests.
"""
self.batchSetConfiguration(True)
# This breaks it
self.config.doCrosstalk = True
with self.assertRaises(RuntimeError):
self.validateIsrResults()
def test_maskingCase_negativeVariance(self):
"""Test masking cases of configuration parameters.
"""
self.batchSetConfiguration(True)
self.config.overscanFitType = "POLY"
self.config.overscanOrder = 1
self.config.doSaturation = False
self.config.doWidenSaturationTrails = False
self.config.doSaturationInterpolation = False
self.config.doSuspect = False
self.config.doSetBadRegions = False
self.config.doDefect = False
self.config.doBrighterFatter = False
self.config.maskNegativeVariance = True
self.config.doInterpolate = False
results = self.validateIsrResults()
self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 40800)
def test_maskingCase_noMasking(self):
"""Test masking cases of configuration parameters.
"""
self.batchSetConfiguration(True)
self.config.overscanFitType = "POLY"
self.config.overscanOrder = 1
self.config.doSaturation = False
self.config.doWidenSaturationTrails = False
self.config.doSaturationInterpolation = False
self.config.doSuspect = False
self.config.doSetBadRegions = False
self.config.doDefect = False
self.config.doBrighterFatter = False
self.config.maskNegativeVariance = False
self.config.doInterpolate = False
results = self.validateIsrResults()
self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 0)
def test_maskingCase_satMasking(self):
"""Test masking cases of configuration parameters.
"""
self.batchSetConfiguration(True)
self.config.overscanFitType = "POLY"
self.config.overscanOrder = 1
self.config.saturation = 20000.0
self.config.doSaturation = True
self.config.doWidenSaturationTrails = True
self.config.doSaturationInterpolation = False
self.config.doSuspect = False
self.config.doSetBadRegions = False
self.config.doDefect = False
self.config.doBrighterFatter = False
self.config.maskNegativeVariance = False # These are mock images.
results = self.validateIsrResults()
self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 0)
def test_maskingCase_satMaskingAndInterp(self):
"""Test masking cases of configuration parameters.
"""
self.batchSetConfiguration(True)
self.config.overscanFitType = "POLY"
self.config.overscanOrder = 1
self.config.saturation = 20000.0
self.config.doSaturation = True
self.config.doWidenSaturationTrails = True
self.config.doSaturationInterpolation = True
self.config.doSuspect = False
self.config.doSetBadRegions = False
self.config.doDefect = False
self.config.doBrighterFatter = False
self.config.maskNegativeVariance = False # These are mock images.
results = self.validateIsrResults()
self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 0)
def test_maskingCase_throughEdge(self):
"""Test masking cases of configuration parameters.
"""
self.batchSetConfiguration(True)
self.config.overscanFitType = "POLY"
self.config.overscanOrder = 1
self.config.saturation = 20000.0
self.config.doSaturation = True
self.config.doWidenSaturationTrails = True
self.config.doSaturationInterpolation = True
self.config.numEdgeSuspect = 5
self.config.doSuspect = True
self.config.doSetBadRegions = False
self.config.doDefect = False
self.config.doBrighterFatter = False
self.config.maskNegativeVariance = False # These are mock images.
results = self.validateIsrResults()
self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 0)
def test_maskingCase_throughDefects(self):
"""Test masking cases of configuration parameters.
"""
self.batchSetConfiguration(True)
self.config.overscanFitType = "POLY"
self.config.overscanOrder = 1
self.config.saturation = 20000.0
self.config.doSaturation = True
self.config.doWidenSaturationTrails = True
self.config.doSaturationInterpolation = True
self.config.numEdgeSuspect = 5
self.config.doSuspect = True
self.config.doDefect = True
self.config.doSetBadRegions = False
self.config.doBrighterFatter = False
self.config.maskNegativeVariance = False # These are mock images.
results = self.validateIsrResults()
self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 2000)
self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 3940)
self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 2000)
def test_maskingCase_throughDefectsAmpEdges(self):
"""Test masking cases of configuration parameters.
"""
self.batchSetConfiguration(True)
self.config.overscanFitType = "POLY"
self.config.overscanOrder = 1
self.config.saturation = 20000.0
self.config.doSaturation = True
self.config.doWidenSaturationTrails = True
self.config.doSaturationInterpolation = True
self.config.numEdgeSuspect = 5
self.config.doSuspect = True
self.config.doDefect = True
self.config.edgeMaskLevel = 'AMP'
self.config.doSetBadRegions = False
self.config.doBrighterFatter = False
self.config.maskNegativeVariance = False # These are mock images.
results = self.validateIsrResults()
self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 2000)
self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 11280)
self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 2000)
def test_maskingCase_throughBad(self):
"""Test masking cases of configuration parameters.
"""
self.batchSetConfiguration(True)
self.config.overscanFitType = "POLY"
self.config.overscanOrder = 1
self.config.saturation = 20000.0
self.config.doSaturation = True
self.config.doWidenSaturationTrails = True
self.config.doSaturationInterpolation = True
self.config.doSuspect = True
self.config.doDefect = True
self.config.doSetBadRegions = True
self.config.doBrighterFatter = False
self.config.maskNegativeVariance = False # These are mock images.
results = self.validateIsrResults()
self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 2000)
self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 2000)