def calcMagNorm(self,
objectMags,
sedObj,
bandpassDict,
mag_error=None,
redshift=None,
filtRange=None):
"""
This will find the magNorm value that gives the closest match to the magnitudes of the object
using the matched SED. Uses scipy.optimize.leastsq to find the values of fluxNorm that minimizes
the function: ((flux_obs - (fluxNorm*flux_model))/flux_error)**2.
@param [in] objectMags are the magnitude values for the object with extinction matching that of
the SED object. In the normal case using the selectSED routines above it will be dereddened mags.
@param [in] sedObj is an Sed class instance that is set with the wavelength and flux of the
matched SED
@param [in] bandpassDict is a BandpassDict class instance with the Bandpasses set to those
for the magnitudes given for the catalog object
@param [in] mag_error are provided error values for magnitudes in objectMags. If none provided
then this defaults to 1.0. This should be an array of the same length as objectMags.
@param [in] redshift is the redshift of the object if the magnitude is observed
@param [in] filtRange is a selected range of filters specified by their indices in the bandpassList
to match up against. Used when missing data in some magnitude bands.
@param [out] bestMagNorm is the magnitude normalization for the given magnitudes and SED
"""
import scipy.optimize as opt
sedTest = Sed()
sedTest.setSED(sedObj.wavelen, flambda=sedObj.flambda)
if redshift is not None:
sedTest.redshiftSED(redshift)
imSimBand = Bandpass()
imSimBand.imsimBandpass()
zp = -2.5 * np.log10(3631) #Note using default AB zeropoint
flux_obs = np.power(10, (objectMags + zp) / (-2.5))
sedTest.resampleSED(wavelen_match=bandpassDict.values()[0].wavelen)
sedTest.flambdaTofnu()
flux_model = sedTest.manyFluxCalc(bandpassDict.phiArray,
bandpassDict.wavelenStep)
if filtRange is not None:
flux_obs = flux_obs[filtRange]
flux_model = flux_model[filtRange]
if mag_error is None:
flux_error = np.ones(len(flux_obs))
else:
flux_error = np.abs(flux_obs * (np.log(10) / (-2.5)) * mag_error)
bestFluxNorm = opt.leastsq(
lambda x: ((flux_obs - (x * flux_model)) / flux_error), 1.0)[0][0]
sedTest.multiplyFluxNorm(bestFluxNorm)
bestMagNorm = sedTest.calcMag(imSimBand)
return bestMagNorm
def testMatchToRestFrame(self):
"""Test that Galaxies with no effects added into catalog mags are matched correctly."""
rng = np.random.RandomState(42)
galPhot = BandpassDict.loadTotalBandpassesFromFiles()
imSimBand = Bandpass()
imSimBand.imsimBandpass()
testMatching = selectGalaxySED(galDir=self.testSpecDir)
testSEDList = testMatching.loadBC03()
testSEDNames = []
testMags = []
testMagNormList = []
magNormStep = 1
for testSED in testSEDList:
getSEDMags = Sed()
testSEDNames.append(testSED.name)
getSEDMags.setSED(wavelen=testSED.wavelen, flambda=testSED.flambda)
testMagNorm = np.round(rng.uniform(20.0, 22.0), magNormStep)
testMagNormList.append(testMagNorm)
fluxNorm = getSEDMags.calcFluxNorm(testMagNorm, imSimBand)
getSEDMags.multiplyFluxNorm(fluxNorm)
testMags.append(galPhot.magListForSed(getSEDMags))
# Also testing to make sure passing in non-default bandpasses works
# Substitute in nan values to simulate incomplete data.
testMags[0][1] = np.nan
testMags[0][2] = np.nan
testMags[0][4] = np.nan
testMags[1][1] = np.nan
testMatchingResults = testMatching.matchToRestFrame(
testSEDList, testMags, bandpassDict=galPhot)
self.assertEqual(None, testMatchingResults[0][0])
self.assertEqual(testSEDNames[1:], testMatchingResults[0][1:])
self.assertEqual(None, testMatchingResults[1][0])
np.testing.assert_almost_equal(testMagNormList[1:],
testMatchingResults[1][1:],
decimal=magNormStep)
# Test Match Errors
errMags = np.array(
(testMags[2], testMags[2], testMags[2], testMags[2]))
errMags[1, 1] += 1. # Total MSE will be 2/(5 colors) = 0.4
errMags[2, 0:2] = np.nan
errMags[2, 3] += 1. # Total MSE will be 2/(3 colors) = 0.667
errMags[3, :] = None
errSED = testSEDList[2]
testMatchingResultsErrors = testMatching.matchToRestFrame(
[errSED], errMags, bandpassDict=galPhot)
np.testing.assert_almost_equal(np.array((0.0, 0.4, 2. / 3.)),
testMatchingResultsErrors[2][0:3],
decimal=3)
self.assertEqual(None, testMatchingResultsErrors[2][3])
def setUp(self):
starName = os.path.join(lsst.utils.getPackageDir("sims_sed_library"), defaultSpecMap["km20_5750.fits_g40_5790"])
self.starSED = Sed()
self.starSED.readSED_flambda(starName)
imsimband = Bandpass()
imsimband.imsimBandpass()
fNorm = self.starSED.calcFluxNorm(22.0, imsimband)
self.starSED.multiplyFluxNorm(fNorm)
self.totalBandpasses = []
self.hardwareBandpasses = []
componentList = ["detector.dat", "m1.dat", "m2.dat", "m3.dat", "lens1.dat", "lens2.dat", "lens3.dat"]
hardwareComponents = []
for c in componentList:
hardwareComponents.append(os.path.join(lsst.utils.getPackageDir("throughputs"), "baseline", c))
self.bandpasses = ["u", "g", "r", "i", "z", "y"]
for b in self.bandpasses:
filterName = os.path.join(lsst.utils.getPackageDir("throughputs"), "baseline", "filter_%s.dat" % b)
components = hardwareComponents + [filterName]
bandpassDummy = Bandpass()
bandpassDummy.readThroughputList(components)
self.hardwareBandpasses.append(bandpassDummy)
components = components + [os.path.join(lsst.utils.getPackageDir("throughputs"), "baseline", "atmos.dat")]
bandpassDummy = Bandpass()
bandpassDummy.readThroughputList(components)
self.totalBandpasses.append(bandpassDummy)
def setUp(self):
starName = os.path.join(lsst.utils.getPackageDir('sims_sed_library'),defaultSpecMap['km20_5750.fits_g40_5790'])
self.starSED = Sed()
self.starSED.readSED_flambda(starName)
imsimband = Bandpass()
imsimband.imsimBandpass()
fNorm = self.starSED.calcFluxNorm(22.0, imsimband)
self.starSED.multiplyFluxNorm(fNorm)
self.totalBandpasses = []
self.hardwareBandpasses = []
componentList = ['detector.dat', 'm1.dat', 'm2.dat', 'm3.dat',
'lens1.dat', 'lens2.dat', 'lens3.dat']
hardwareComponents = []
for c in componentList:
hardwareComponents.append(os.path.join(lsst.utils.getPackageDir('throughputs'),'baseline',c))
self.bandpasses = ['u', 'g', 'r', 'i', 'z', 'y']
for b in self.bandpasses:
filterName = os.path.join(lsst.utils.getPackageDir('throughputs'),'baseline','filter_%s.dat' % b)
components = hardwareComponents + [filterName]
bandpassDummy = Bandpass()
bandpassDummy.readThroughputList(components)
self.hardwareBandpasses.append(bandpassDummy)
components = components + [os.path.join(lsst.utils.getPackageDir('throughputs'),'baseline','atmos.dat')]
bandpassDummy = Bandpass()
bandpassDummy.readThroughputList(components)
self.totalBandpasses.append(bandpassDummy)
def testAlternateBandpassesStars(self):
"""
This will test our ability to do photometry using non-LSST bandpasses.
It will first calculate the magnitudes using the getters in cartoonPhotometryStars.
It will then load the alternate bandpass files 'by hand' and re-calculate the magnitudes
and make sure that the magnitude values agree. This is guarding against the possibility
that some default value did not change and the code actually ended up loading the
LSST bandpasses.
"""
obs_metadata_pointed = ObservationMetaData(
mjd=2013.23, boundType="circle", unrefractedRA=200.0, unrefractedDec=-30.0, boundLength=1.0
)
bandpassDir = os.path.join(lsst.utils.getPackageDir("sims_photUtils"), "tests", "cartoonSedTestData")
cartoon_dict = BandpassDict.loadTotalBandpassesFromFiles(
["u", "g", "r", "i", "z"], bandpassDir=bandpassDir, bandpassRoot="test_bandpass_"
)
testBandPasses = {}
keys = ["u", "g", "r", "i", "z"]
bplist = []
for kk in keys:
testBandPasses[kk] = Bandpass()
testBandPasses[kk].readThroughput(os.path.join(bandpassDir, "test_bandpass_%s.dat" % kk))
bplist.append(testBandPasses[kk])
sedObj = Sed()
phiArray, waveLenStep = sedObj.setupPhiArray(bplist)
sedFileName = os.path.join(lsst.utils.getPackageDir("sims_sed_library"), "starSED", "kurucz")
sedFileName = os.path.join(sedFileName, "km20_5750.fits_g40_5790.gz")
ss = Sed()
ss.readSED_flambda(sedFileName)
controlBandpass = Bandpass()
controlBandpass.imsimBandpass()
ff = ss.calcFluxNorm(22.0, controlBandpass)
ss.multiplyFluxNorm(ff)
testMags = cartoon_dict.magListForSed(ss)
ss.resampleSED(wavelen_match=bplist[0].wavelen)
ss.flambdaTofnu()
mags = -2.5 * numpy.log10(numpy.sum(phiArray * ss.fnu, axis=1) * waveLenStep) - ss.zp
self.assertTrue(len(mags) == len(testMags))
self.assertTrue(len(mags) > 0)
for j in range(len(mags)):
self.assertAlmostEqual(mags[j], testMags[j], 10)
def testMatchToRestFrame(self):
"""Test that Galaxies with no effects added into catalog mags are matched correctly."""
np.random.seed(42)
galPhot = BandpassDict.loadTotalBandpassesFromFiles()
imSimBand = Bandpass()
imSimBand.imsimBandpass()
testMatching = selectGalaxySED(galDir = self.testSpecDir)
testSEDList = testMatching.loadBC03()
testSEDNames = []
testMags = []
testMagNormList = []
magNormStep = 1
for testSED in testSEDList:
getSEDMags = Sed()
testSEDNames.append(testSED.name)
getSEDMags.setSED(wavelen = testSED.wavelen, flambda = testSED.flambda)
testMagNorm = np.round(np.random.uniform(20.0,22.0),magNormStep)
testMagNormList.append(testMagNorm)
fluxNorm = getSEDMags.calcFluxNorm(testMagNorm, imSimBand)
getSEDMags.multiplyFluxNorm(fluxNorm)
testMags.append(galPhot.magListForSed(getSEDMags))
#Also testing to make sure passing in non-default bandpasses works
#Substitute in nan values to simulate incomplete data.
testMags[0][1] = np.nan
testMags[0][2] = np.nan
testMags[0][4] = np.nan
testMags[1][1] = np.nan
testMatchingResults = testMatching.matchToRestFrame(testSEDList, testMags,
bandpassDict = galPhot)
self.assertEqual(None, testMatchingResults[0][0])
self.assertEqual(testSEDNames[1:], testMatchingResults[0][1:])
self.assertEqual(None, testMatchingResults[1][0])
np.testing.assert_almost_equal(testMagNormList[1:], testMatchingResults[1][1:], decimal = magNormStep)
#Test Match Errors
errMags = np.array((testMags[2], testMags[2], testMags[2], testMags[2]))
errMags[1,1] += 1. #Total MSE will be 2/(5 colors) = 0.4
errMags[2, 0:2] = np.nan
errMags[2, 3] += 1. #Total MSE will be 2/(3 colors) = 0.667
errMags[3, :] = None
errSED = testSEDList[2]
testMatchingResultsErrors = testMatching.matchToRestFrame([errSED], errMags,
bandpassDict = galPhot)
np.testing.assert_almost_equal(np.array((0.0, 0.4, 2./3.)), testMatchingResultsErrors[2][0:3],
decimal = 3)
self.assertEqual(None, testMatchingResultsErrors[2][3])
def calcMagNorm(self, objectMags, sedObj, bandpassDict, mag_error = None,
redshift = None, filtRange = None):
"""
This will find the magNorm value that gives the closest match to the magnitudes of the object
using the matched SED. Uses scipy.optimize.leastsq to find the values of fluxNorm that minimizes
the function: ((flux_obs - (fluxNorm*flux_model))/flux_error)**2.
@param [in] objectMags are the magnitude values for the object with extinction matching that of
the SED object. In the normal case using the selectSED routines above it will be dereddened mags.
@param [in] sedObj is an Sed class instance that is set with the wavelength and flux of the
matched SED
@param [in] bandpassDict is a BandpassDict class instance with the Bandpasses set to those
for the magnitudes given for the catalog object
@param [in] mag_error are provided error values for magnitudes in objectMags. If none provided
then this defaults to 1.0. This should be an array of the same length as objectMags.
@param [in] redshift is the redshift of the object if the magnitude is observed
@param [in] filtRange is a selected range of filters specified by their indices in the bandpassList
to match up against. Used when missing data in some magnitude bands.
@param [out] bestMagNorm is the magnitude normalization for the given magnitudes and SED
"""
import scipy.optimize as opt
sedTest = Sed()
sedTest.setSED(sedObj.wavelen, flambda = sedObj.flambda)
if redshift is not None:
sedTest.redshiftSED(redshift)
imSimBand = Bandpass()
imSimBand.imsimBandpass()
zp = -2.5*np.log10(3631) #Note using default AB zeropoint
flux_obs = np.power(10,(objectMags + zp)/(-2.5))
sedTest.resampleSED(wavelen_match=bandpassDict.values()[0].wavelen)
sedTest.flambdaTofnu()
flux_model = sedTest.manyFluxCalc(bandpassDict.phiArray, bandpassDict.wavelenStep)
if filtRange is not None:
flux_obs = flux_obs[filtRange]
flux_model = flux_model[filtRange]
if mag_error is None:
flux_error = np.ones(len(flux_obs))
else:
flux_error = np.abs(flux_obs*(np.log(10)/(-2.5))*mag_error)
bestFluxNorm = opt.leastsq(lambda x: ((flux_obs - (x*flux_model))/flux_error), 1.0)[0][0]
sedTest.multiplyFluxNorm(bestFluxNorm)
bestMagNorm = sedTest.calcMag(imSimBand)
return bestMagNorm
def testAlternateBandpassesStars(self):
"""
This will test our ability to do photometry using non-LSST bandpasses.
It will first calculate the magnitudes using the getters in cartoonPhotometryStars.
It will then load the alternate bandpass files 'by hand' and re-calculate the magnitudes
and make sure that the magnitude values agree. This is guarding against the possibility
that some default value did not change and the code actually ended up loading the
LSST bandpasses.
"""
bandpassDir = os.path.join(lsst.utils.getPackageDir('sims_photUtils'), 'tests', 'cartoonSedTestData')
cartoon_dict = BandpassDict.loadTotalBandpassesFromFiles(['u', 'g', 'r', 'i', 'z'],
bandpassDir=bandpassDir,
bandpassRoot='test_bandpass_')
testBandPasses = {}
keys = ['u', 'g', 'r', 'i', 'z']
bplist = []
for kk in keys:
testBandPasses[kk] = Bandpass()
testBandPasses[kk].readThroughput(os.path.join(bandpassDir, "test_bandpass_%s.dat" % kk))
bplist.append(testBandPasses[kk])
sedObj = Sed()
phiArray, waveLenStep = sedObj.setupPhiArray(bplist)
sedFileName = os.path.join(lsst.utils.getPackageDir('sims_photUtils'),
'tests/cartoonSedTestData/starSed/')
sedFileName = os.path.join(sedFileName, 'kurucz', 'km20_5750.fits_g40_5790.gz')
ss = Sed()
ss.readSED_flambda(sedFileName)
controlBandpass = Bandpass()
controlBandpass.imsimBandpass()
ff = ss.calcFluxNorm(22.0, controlBandpass)
ss.multiplyFluxNorm(ff)
testMags = cartoon_dict.magListForSed(ss)
ss.resampleSED(wavelen_match = bplist[0].wavelen)
ss.flambdaTofnu()
mags = -2.5*np.log10(np.sum(phiArray*ss.fnu, axis=1)*waveLenStep) - ss.zp
self.assertEqual(len(mags), len(testMags))
self.assertGreater(len(mags), 0)
for j in range(len(mags)):
self.assertAlmostEqual(mags[j], testMags[j], 10)
def testCalcMagNorm(self):
"""Tests the calculation of magnitude normalization for an SED with the given magnitudes
in the given bandpasses."""
testUtils = matchBase()
bandpassDir = os.path.join(lsst.utils.getPackageDir('throughputs'),
'sdss')
testPhot = BandpassDict.loadTotalBandpassesFromFiles(
self.filterList, bandpassDir=bandpassDir, bandpassRoot='sdss_')
unChangedSED = Sed()
unChangedSED.readSED_flambda(
str(self.galDir + os.listdir(self.galDir)[0]))
imSimBand = Bandpass()
imSimBand.imsimBandpass()
testSED = Sed()
testSED.setSED(unChangedSED.wavelen, flambda=unChangedSED.flambda)
magNorm = 20.0
redVal = 0.1
testSED.redshiftSED(redVal)
fluxNorm = testSED.calcFluxNorm(magNorm, imSimBand)
testSED.multiplyFluxNorm(fluxNorm)
sedMags = testPhot.magListForSed(testSED)
stepSize = 0.001
testMagNorm = testUtils.calcMagNorm(sedMags,
unChangedSED,
testPhot,
redshift=redVal)
# Test adding in mag_errors. If an array of np.ones is passed in we should get same result
testMagNormWithErr = testUtils.calcMagNorm(sedMags,
unChangedSED,
testPhot,
mag_error=np.ones(
len(sedMags)),
redshift=redVal)
# Also need to add in test for filtRange
sedMagsIncomp = sedMags
sedMagsIncomp[1] = None
filtRangeTest = [0, 2, 3, 4]
testMagNormFiltRange = testUtils.calcMagNorm(sedMagsIncomp,
unChangedSED,
testPhot,
redshift=redVal,
filtRange=filtRangeTest)
self.assertAlmostEqual(magNorm, testMagNorm, delta=stepSize)
self.assertAlmostEqual(magNorm, testMagNormWithErr, delta=stepSize)
self.assertAlmostEqual(magNorm, testMagNormFiltRange, delta=stepSize)
def calc_colors(ast):
fdir = os.getenv('LSST_THROUGHPUTS_DEFAULT')
lsst = {}
for f in filterlist:
lsst[f] = Bandpass()
lsst[f].readThroughput(os.path.join(fdir, 'total_' + f + '.dat'))
mags = {}
for f in filterlist:
mags[f] = {}
for a in ast.keys():
mags[f][a] = ast[a].calcMag(lsst[f])
colormags = {}
for i in range(0, len(filterlist) - 1):
c = colornames[i]
c1 = c[0]
c2 = c[1]
colormags[c] = {}
for a in ast.keys():
colormags[c][a] = mags[c1][a] - mags[c2][a]
writestring = '#Name '
for c in colornames:
writestring = writestring + ' %s ' % (c)
print writestring
for a in ast.keys():
writestring = '%s ' % (a.strip('.txt'))
for c in colornames:
writestring = writestring + '%.3f ' % (colormags[c][a])
print writestring
return mags, colormags
def testAlternateBandpassesStars(self):
"""
This will test our ability to do photometry using non-LSST bandpasses.
It will first calculate the magnitudes using the getters in cartoonPhotometryStars.
It will then load the alternate bandpass files 'by hand' and re-calculate the magnitudes
and make sure that the magnitude values agree. This is guarding against the possibility
that some default value did not change and the code actually ended up loading the
LSST bandpasses.
"""
obs_metadata_pointed = ObservationMetaData(mjd=2013.23,
boundType='circle',
pointingRA=200.0,
pointingDec=-30.0,
boundLength=1.0)
test_cat = cartoonStars(self.star, obs_metadata=obs_metadata_pointed)
with lsst.utils.tests.getTempFilePath('.txt') as catName:
test_cat.write_catalog(catName)
with open(catName, 'r') as input_file:
lines = input_file.readlines()
self.assertGreater(len(lines), 1)
cartoonDir = os.path.join(getPackageDir('sims_photUtils'), 'tests',
'cartoonSedTestData')
testBandPasses = {}
keys = ['u', 'g', 'r', 'i', 'z']
bplist = []
for kk in keys:
testBandPasses[kk] = Bandpass()
testBandPasses[kk].readThroughput(
os.path.join(cartoonDir, "test_bandpass_%s.dat" % kk))
bplist.append(testBandPasses[kk])
sedObj = Sed()
phiArray, waveLenStep = sedObj.setupPhiArray(bplist)
i = 0
# since all of the SEDs in the cartoon database are the same, just test on the first
# if we ever include more SEDs, this can be something like
# for ss in test_cata.sedMasterList:
ss = test_cat.sedMasterList[0]
ss.resampleSED(wavelen_match=bplist[0].wavelen)
ss.flambdaTofnu()
mags = -2.5 * np.log10(
np.sum(phiArray * ss.fnu, axis=1) * waveLenStep) - ss.zp
self.assertEqual(len(mags), len(test_cat.cartoonBandpassDict))
self.assertGreater(len(mags), 0)
for j in range(len(mags)):
self.assertAlmostEqual(mags[j], test_cat.magnitudeMasterList[i][j],
4)
def testCalcMagNorm(self):
"""Tests the calculation of magnitude normalization for an SED with the given magnitudes
in the given bandpasses."""
testUtils = matchBase()
bandpassDir = os.path.join(lsst.utils.getPackageDir('throughputs'), 'sdss')
testPhot = BandpassDict.loadTotalBandpassesFromFiles(self.filterList,
bandpassDir = bandpassDir,
bandpassRoot = 'sdss_')
unChangedSED = Sed()
unChangedSED.readSED_flambda(str(self.galDir + os.listdir(self.galDir)[0]))
imSimBand = Bandpass()
imSimBand.imsimBandpass()
testSED = Sed()
testSED.setSED(unChangedSED.wavelen, flambda = unChangedSED.flambda)
magNorm = 20.0
redVal = 0.1
testSED.redshiftSED(redVal)
fluxNorm = testSED.calcFluxNorm(magNorm, imSimBand)
testSED.multiplyFluxNorm(fluxNorm)
sedMags = testPhot.magListForSed(testSED)
stepSize = 0.001
testMagNorm = testUtils.calcMagNorm(sedMags, unChangedSED, testPhot, redshift = redVal)
# Test adding in mag_errors. If an array of np.ones is passed in we should get same result
testMagNormWithErr = testUtils.calcMagNorm(sedMags, unChangedSED, testPhot,
mag_error = np.ones(len(sedMags)), redshift = redVal)
# Also need to add in test for filtRange
sedMagsIncomp = sedMags
sedMagsIncomp[1] = None
filtRangeTest = [0, 2, 3, 4]
testMagNormFiltRange = testUtils.calcMagNorm(sedMagsIncomp, unChangedSED, testPhot,
redshift = redVal, filtRange = filtRangeTest)
self.assertAlmostEqual(magNorm, testMagNorm, delta = stepSize)
self.assertAlmostEqual(magNorm, testMagNormWithErr, delta = stepSize)
self.assertAlmostEqual(magNorm, testMagNormFiltRange, delta = stepSize)
def testFindSED(self):
"""Pull SEDs from each type and make sure that each SED gets matched to itself.
Includes testing with extinction and passing in only colors."""
rng = np.random.RandomState(42)
bandpassDir = os.path.join(lsst.utils.getPackageDir('throughputs'), 'sdss')
starPhot = BandpassDict.loadTotalBandpassesFromFiles(('u', 'g', 'r', 'i', 'z'),
bandpassDir = bandpassDir,
bandpassRoot = 'sdss_')
imSimBand = Bandpass()
imSimBand.imsimBandpass()
testMatching = selectStarSED(kuruczDir=self.testKDir,
mltDir=self.testMLTDir,
wdDir=self.testWDDir)
testSEDList = []
testSEDList.append(testMatching.loadKuruczSEDs())
testSEDList.append(testMatching.loadmltSEDs())
testSEDListH, testSEDListHE = testMatching.loadwdSEDs()
testSEDList.append(testSEDListH)
testSEDList.append(testSEDListHE)
testSEDNames = []
testMags = []
testMagNormList = []
magNormStep = 1
for typeList in testSEDList:
if len(typeList) != 0:
typeSEDNames = []
typeMags = []
typeMagNorms = []
for testSED in typeList:
getSEDMags = Sed()
typeSEDNames.append(testSED.name)
getSEDMags.setSED(wavelen = testSED.wavelen, flambda = testSED.flambda)
testMagNorm = np.round(rng.uniform(20.0, 22.0), magNormStep)
typeMagNorms.append(testMagNorm)
fluxNorm = getSEDMags.calcFluxNorm(testMagNorm, imSimBand)
getSEDMags.multiplyFluxNorm(fluxNorm)
typeMags.append(starPhot.magListForSed(getSEDMags))
testSEDNames.append(typeSEDNames)
testMags.append(typeMags)
testMagNormList.append(typeMagNorms)
# Since default bandpassDict should be SDSS ugrizy shouldn't need to specify it
# Substitute in nan values to simulate incomplete data.
for typeList, names, mags, magNorms in zip(testSEDList, testSEDNames, testMags, testMagNormList):
if len(typeList) > 2:
nanMags = np.array(mags)
nanMags[0][0] = np.nan
nanMags[0][2] = np.nan
nanMags[0][3] = np.nan
nanMags[1][1] = np.nan
testMatchingResults = testMatching.findSED(typeList, nanMags, reddening = False)
self.assertEqual(None, testMatchingResults[0][0])
self.assertEqual(names[1:], testMatchingResults[0][1:])
self.assertEqual(None, testMatchingResults[1][0])
np.testing.assert_almost_equal(magNorms[1:], testMatchingResults[1][1:],
decimal = magNormStep)
else:
testMatchingResults = testMatching.findSED(typeList, mags, reddening = False)
self.assertEqual(names, testMatchingResults[0])
np.testing.assert_almost_equal(magNorms, testMatchingResults[1], decimal = magNormStep)
# Test Null Values option
nullMags = np.array(testMags[0])
nullMags[0][0] = -99.
nullMags[0][4] = -99.
nullMags[1][0] = -99.
nullMags[1][1] = -99.
testMatchingResultsNull = testMatching.findSED(testSEDList[0], nullMags,
nullValues = -99., reddening = False)
self.assertEqual(testSEDNames[0], testMatchingResultsNull[0])
np.testing.assert_almost_equal(testMagNormList[0], testMatchingResultsNull[1],
decimal = magNormStep)
# Test Error Output
errMags = np.array((testMags[0][0], testMags[0][0], testMags[0][0], testMags[0][0]))
errMags[1, 1] += 1. # Total MSE will be 2/(4 colors) = 0.5
errMags[2, 0:2] = np.nan
errMags[2, 3] += 1. # Total MSE will be 2/(2 colors) = 1.0
errMags[3, :] = None
errSED = testSEDList[0][0]
testMatchingResultsErrors = testMatching.findSED([errSED], errMags, reddening = False)
np.testing.assert_almost_equal(np.array((0.0, 0.5, 1.0)), testMatchingResultsErrors[2][0:3],
decimal = 3)
self.assertEqual(None, testMatchingResultsErrors[2][3])
# Now test what happens if we pass in a bandpassDict
testMatchingResultsNoDefault = testMatching.findSED(testSEDList[0], testMags[0],
bandpassDict = starPhot,
reddening = False)
self.assertEqual(testSEDNames[0], testMatchingResultsNoDefault[0])
np.testing.assert_almost_equal(testMagNormList[0], testMatchingResultsNoDefault[1],
decimal = magNormStep)
# Test Reddening
testRA = rng.uniform(10, 170, len(testSEDList[0]))
testDec = rng.uniform(10, 80, len(testSEDList[0]))
extFactor = .5
raDec = np.array((testRA, testDec))
ebvVals = ebv().calculateEbv(equatorialCoordinates = raDec)
extVals = ebvVals*extFactor
testRedMags = []
for extVal, testMagSet in zip(extVals, testMags[0]):
testRedMags.append(testMagSet + extVal)
testMatchingResultsRed = testMatching.findSED(testSEDList[0], testRedMags, catRA = testRA,
catDec = testDec, reddening = True,
extCoeffs = np.ones(5)*extFactor)
self.assertEqual(testSEDNames[0], testMatchingResultsRed[0])
np.testing.assert_almost_equal(testMagNormList[0], testMatchingResultsRed[1],
decimal = magNormStep)
# Finally, test color input
testColors = []
for testMagSet in testMags[0]:
testColorSet = []
for filtNum in range(0, len(starPhot)-1):
testColorSet.append(testMagSet[filtNum] - testMagSet[filtNum+1])
testColors.append(testColorSet)
testMatchingColorsInput = testMatching.findSED(testSEDList[0], testMags[0],
reddening = False, colors = testColors)
self.assertEqual(testSEDNames[0], testMatchingColorsInput[0])
np.testing.assert_almost_equal(testMagNormList[0], testMatchingColorsInput[1],
decimal = magNormStep)
def setUp(self):
starName = os.path.join(getPackageDir('sims_sed_library'),
defaultSpecMap['km20_5750.fits_g40_5790'])
self.starSED = Sed()
self.starSED.readSED_flambda(starName)
imsimband = Bandpass()
imsimband.imsimBandpass()
fNorm = self.starSED.calcFluxNorm(22.0, imsimband)
self.starSED.multiplyFluxNorm(fNorm)
self.totalBandpasses = []
self.hardwareBandpasses = []
componentList = [
'detector.dat', 'm1.dat', 'm2.dat', 'm3.dat', 'lens1.dat',
'lens2.dat', 'lens3.dat'
]
hardwareComponents = []
for c in componentList:
hardwareComponents.append(
os.path.join(getPackageDir('throughputs'), 'baseline', c))
self.bandpasses = ['u', 'g', 'r', 'i', 'z', 'y']
for b in self.bandpasses:
filterName = os.path.join(getPackageDir('throughputs'), 'baseline',
'filter_%s.dat' % b)
components = hardwareComponents + [filterName]
bandpassDummy = Bandpass()
bandpassDummy.readThroughputList(components)
self.hardwareBandpasses.append(bandpassDummy)
components = components + [
os.path.join(getPackageDir('throughputs'), 'baseline',
'atmos.dat')
]
bandpassDummy = Bandpass()
bandpassDummy.readThroughputList(components)
self.totalBandpasses.append(bandpassDummy)
def testMatchToObserved(self):
"""Test that Galaxy SEDs with extinction or redshift are matched correctly"""
rng = np.random.RandomState(42)
galPhot = BandpassDict.loadTotalBandpassesFromFiles()
imSimBand = Bandpass()
imSimBand.imsimBandpass()
testMatching = selectGalaxySED(galDir = self.testSpecDir)
testSEDList = testMatching.loadBC03()
testSEDNames = []
testRA = []
testDec = []
testRedshifts = []
testMagNormList = []
magNormStep = 1
extCoeffs = [1.8140, 1.4166, 0.9947, 0.7370, 0.5790, 0.4761]
testMags = []
testMagsRedshift = []
testMagsExt = []
for testSED in testSEDList:
# As a check make sure that it matches when no extinction and no redshift are present
getSEDMags = Sed()
testSEDNames.append(testSED.name)
getSEDMags.setSED(wavelen = testSED.wavelen, flambda = testSED.flambda)
testMags.append(galPhot.magListForSed(getSEDMags))
# Check Extinction corrections
sedRA = rng.uniform(10, 170)
sedDec = rng.uniform(10, 80)
testRA.append(sedRA)
testDec.append(sedDec)
raDec = np.array((sedRA, sedDec)).reshape((2, 1))
ebvVal = ebv().calculateEbv(equatorialCoordinates = raDec)
extVal = ebvVal*extCoeffs
testMagsExt.append(galPhot.magListForSed(getSEDMags) + extVal)
# Setup magnitudes for testing matching to redshifted values
getRedshiftMags = Sed()
testZ = np.round(rng.uniform(1.1, 1.3), 3)
testRedshifts.append(testZ)
testMagNorm = np.round(rng.uniform(20.0, 22.0), magNormStep)
testMagNormList.append(testMagNorm)
getRedshiftMags.setSED(wavelen = testSED.wavelen, flambda = testSED.flambda)
getRedshiftMags.redshiftSED(testZ)
fluxNorm = getRedshiftMags.calcFluxNorm(testMagNorm, imSimBand)
getRedshiftMags.multiplyFluxNorm(fluxNorm)
testMagsRedshift.append(galPhot.magListForSed(getRedshiftMags))
# Will also test in passing of non-default bandpass
testNoExtNoRedshift = testMatching.matchToObserved(testSEDList, testMags, np.zeros(8),
reddening = False,
bandpassDict = galPhot)
testMatchingEbvVals = testMatching.matchToObserved(testSEDList, testMagsExt, np.zeros(8),
catRA = testRA, catDec = testDec,
reddening = True, extCoeffs = extCoeffs,
bandpassDict = galPhot)
# Substitute in nan values to simulate incomplete data and make sure magnorm works too.
testMagsRedshift[0][1] = np.nan
testMagsRedshift[0][3] = np.nan
testMagsRedshift[0][4] = np.nan
testMagsRedshift[1][1] = np.nan
testMatchingRedshift = testMatching.matchToObserved(testSEDList, testMagsRedshift, testRedshifts,
dzAcc = 3, reddening = False,
bandpassDict = galPhot)
self.assertEqual(testSEDNames, testNoExtNoRedshift[0])
self.assertEqual(testSEDNames, testMatchingEbvVals[0])
self.assertEqual(None, testMatchingRedshift[0][0])
self.assertEqual(testSEDNames[1:], testMatchingRedshift[0][1:])
self.assertEqual(None, testMatchingRedshift[1][0])
np.testing.assert_almost_equal(testMagNormList[1:], testMatchingRedshift[1][1:],
decimal = magNormStep)
# Test Match Errors
errMag = testMagsRedshift[2]
errRedshift = testRedshifts[2]
errMags = np.array((errMag, errMag, errMag, errMag))
errRedshifts = np.array((errRedshift, errRedshift, errRedshift, errRedshift))
errMags[1, 1] += 1. # Total MSE will be 2/(5 colors) = 0.4
errMags[2, 0:2] = np.nan
errMags[2, 3] += 1. # Total MSE will be 2/(3 colors) = 0.667
errMags[3, :] = None
errSED = testSEDList[2]
testMatchingResultsErrors = testMatching.matchToObserved([errSED], errMags, errRedshifts,
reddening = False,
bandpassDict = galPhot,
dzAcc = 3)
np.testing.assert_almost_equal(np.array((0.0, 0.4, 2./3.)), testMatchingResultsErrors[2][0:3],
decimal = 2) # Give a little more leeway due to redshifting effects
self.assertEqual(None, testMatchingResultsErrors[2][3])
def testMatchToObserved(self):
"""Test that Galaxy SEDs with extinction or redshift are matched correctly"""
np.random.seed(42)
galPhot = BandpassDict.loadTotalBandpassesFromFiles()
imSimBand = Bandpass()
imSimBand.imsimBandpass()
testMatching = selectGalaxySED(galDir = self.testSpecDir)
testSEDList = testMatching.loadBC03()
testSEDNames = []
testRA = []
testDec = []
testRedshifts = []
testMagNormList = []
magNormStep = 1
extCoeffs = [1.8140, 1.4166, 0.9947, 0.7370, 0.5790, 0.4761]
testMags = []
testMagsRedshift = []
testMagsExt = []
for testSED in testSEDList:
#As a check make sure that it matches when no extinction and no redshift are present
getSEDMags = Sed()
testSEDNames.append(testSED.name)
getSEDMags.setSED(wavelen = testSED.wavelen, flambda = testSED.flambda)
testMags.append(galPhot.magListForSed(getSEDMags))
#Check Extinction corrections
sedRA = np.random.uniform(10,170)
sedDec = np.random.uniform(10,80)
testRA.append(sedRA)
testDec.append(sedDec)
raDec = np.array((sedRA, sedDec)).reshape((2,1))
ebvVal = ebv().calculateEbv(equatorialCoordinates = raDec)
extVal = ebvVal*extCoeffs
testMagsExt.append(galPhot.magListForSed(getSEDMags) + extVal)
#Setup magnitudes for testing matching to redshifted values
getRedshiftMags = Sed()
testZ = np.round(np.random.uniform(1.1,1.3),3)
testRedshifts.append(testZ)
testMagNorm = np.round(np.random.uniform(20.0,22.0),magNormStep)
testMagNormList.append(testMagNorm)
getRedshiftMags.setSED(wavelen = testSED.wavelen, flambda = testSED.flambda)
getRedshiftMags.redshiftSED(testZ)
fluxNorm = getRedshiftMags.calcFluxNorm(testMagNorm, imSimBand)
getRedshiftMags.multiplyFluxNorm(fluxNorm)
testMagsRedshift.append(galPhot.magListForSed(getRedshiftMags))
#Will also test in passing of non-default bandpass
testNoExtNoRedshift = testMatching.matchToObserved(testSEDList, testMags, np.zeros(20),
reddening = False,
bandpassDict = galPhot)
testMatchingEbvVals = testMatching.matchToObserved(testSEDList, testMagsExt, np.zeros(20),
catRA = testRA, catDec = testDec,
reddening = True, extCoeffs = extCoeffs,
bandpassDict = galPhot)
#Substitute in nan values to simulate incomplete data and make sure magnorm works too.
testMagsRedshift[0][1] = np.nan
testMagsRedshift[0][3] = np.nan
testMagsRedshift[0][4] = np.nan
testMagsRedshift[1][1] = np.nan
testMatchingRedshift = testMatching.matchToObserved(testSEDList, testMagsRedshift, testRedshifts,
dzAcc = 3, reddening = False,
bandpassDict = galPhot)
self.assertEqual(testSEDNames, testNoExtNoRedshift[0])
self.assertEqual(testSEDNames, testMatchingEbvVals[0])
self.assertEqual(None, testMatchingRedshift[0][0])
self.assertEqual(testSEDNames[1:], testMatchingRedshift[0][1:])
self.assertEqual(None, testMatchingRedshift[1][0])
np.testing.assert_almost_equal(testMagNormList[1:], testMatchingRedshift[1][1:],
decimal = magNormStep)
#Test Match Errors
errMag = testMagsRedshift[2]
errRedshift = testRedshifts[2]
errMags = np.array((errMag, errMag, errMag, errMag))
errRedshifts = np.array((errRedshift, errRedshift, errRedshift, errRedshift))
errMags[1,1] += 1. #Total MSE will be 2/(5 colors) = 0.4
errMags[2, 0:2] = np.nan
errMags[2, 3] += 1. #Total MSE will be 2/(3 colors) = 0.667
errMags[3, :] = None
errSED = testSEDList[2]
testMatchingResultsErrors = testMatching.matchToObserved([errSED], errMags, errRedshifts,
reddening = False,
bandpassDict = galPhot,
dzAcc = 3)
np.testing.assert_almost_equal(np.array((0.0, 0.4, 2./3.)), testMatchingResultsErrors[2][0:3],
decimal = 2) #Give a little more leeway due to redshifting effects
self.assertEqual(None, testMatchingResultsErrors[2][3])
def testAlternateBandpassesGalaxies(self):
"""
the same as testAlternateBandpassesStars, but for galaxies
"""
obs_metadata_pointed = ObservationMetaData(mjd=50000.0,
boundType='circle',
pointingRA=0.0, pointingDec=0.0,
boundLength=10.0)
dtype = np.dtype([('galid', np.int),
('ra', np.float),
('dec', np.float),
('uTotal', np.float),
('gTotal', np.float),
('rTotal', np.float),
('iTotal', np.float),
('zTotal', np.float),
('uBulge', np.float),
('gBulge', np.float),
('rBulge', np.float),
('iBulge', np.float),
('zBulge', np.float),
('uDisk', np.float),
('gDisk', np.float),
('rDisk', np.float),
('iDisk', np.float),
('zDisk', np.float),
('uAgn', np.float),
('gAgn', np.float),
('rAgn', np.float),
('iAgn', np.float),
('zAgn', np.float),
('bulgeName', str, 200),
('bulgeNorm', np.float),
('bulgeAv', np.float),
('diskName', str, 200),
('diskNorm', np.float),
('diskAv', np.float),
('agnName', str, 200),
('agnNorm', np.float),
('redshift', np.float)])
test_cat = cartoonGalaxies(self.galaxy, obs_metadata=obs_metadata_pointed)
with lsst.utils.tests.getTempFilePath('.txt') as catName:
test_cat.write_catalog(catName)
catData = np.genfromtxt(catName, dtype=dtype, delimiter=', ')
self.assertGreater(len(catData), 0)
cartoonDir = getPackageDir('sims_photUtils')
cartoonDir = os.path.join(cartoonDir, 'tests', 'cartoonSedTestData')
sedDir = getPackageDir('sims_sed_library')
testBandpasses = {}
keys = ['u', 'g', 'r', 'i', 'z']
for kk in keys:
testBandpasses[kk] = Bandpass()
testBandpasses[kk].readThroughput(os.path.join(cartoonDir, "test_bandpass_%s.dat" % kk))
imsimBand = Bandpass()
imsimBand.imsimBandpass()
specMap = defaultSpecMap
ct = 0
for line in catData:
bulgeMagList = []
diskMagList = []
agnMagList = []
if line['bulgeName'] == 'None':
for bp in keys:
np.testing.assert_equal(line['%sBulge' % bp], np.NaN)
bulgeMagList.append(np.NaN)
else:
ct += 1
dummySed = Sed()
dummySed.readSED_flambda(os.path.join(sedDir, specMap[line['bulgeName']]))
fnorm = dummySed.calcFluxNorm(line['bulgeNorm'], imsimBand)
dummySed.multiplyFluxNorm(fnorm)
a_int, b_int = dummySed.setupCCM_ab()
dummySed.addDust(a_int, b_int, A_v=line['bulgeAv'])
dummySed.redshiftSED(line['redshift'], dimming=True)
dummySed.resampleSED(wavelen_match=testBandpasses['u'].wavelen)
for bpName in keys:
mag = dummySed.calcMag(testBandpasses[bpName])
self.assertAlmostEqual(mag, line['%sBulge' % bpName], 10)
bulgeMagList.append(mag)
if line['diskName'] == 'None':
for bp in keys:
np.assert_equal(line['%sDisk' % bp], np.NaN)
diskMagList.append(np.NaN)
else:
ct += 1
dummySed = Sed()
dummySed.readSED_flambda(os.path.join(sedDir, specMap[line['diskName']]))
fnorm = dummySed.calcFluxNorm(line['diskNorm'], imsimBand)
dummySed.multiplyFluxNorm(fnorm)
a_int, b_int = dummySed.setupCCM_ab()
dummySed.addDust(a_int, b_int, A_v=line['diskAv'])
dummySed.redshiftSED(line['redshift'], dimming=True)
dummySed.resampleSED(wavelen_match=testBandpasses['u'].wavelen)
for bpName in keys:
mag = dummySed.calcMag(testBandpasses[bpName])
self.assertAlmostEqual(mag, line['%sDisk' % bpName], 10)
diskMagList.append(mag)
if line['agnName'] == 'None':
for bp in keys:
np.testing.assert_true(line['%sAgn' % bp], np.NaN)
agnMagList.append(np.NaN)
else:
ct += 1
dummySed = Sed()
dummySed.readSED_flambda(os.path.join(sedDir, specMap[line['agnName']]))
fnorm = dummySed.calcFluxNorm(line['agnNorm'], imsimBand)
dummySed.multiplyFluxNorm(fnorm)
dummySed.redshiftSED(line['redshift'], dimming=True)
dummySed.resampleSED(wavelen_match=testBandpasses['u'].wavelen)
for bpName in keys:
mag = dummySed.calcMag(testBandpasses[bpName])
self.assertAlmostEqual(mag, line['%sAgn' % bpName], 10)
agnMagList.append(mag)
totalMags = PhotometryGalaxies().sum_magnitudes(bulge=np.array(bulgeMagList),
disk=np.array(diskMagList),
agn=np.array(agnMagList))
for testMag, bpName in zip(totalMags, keys):
if np.isnan(line['%sTotal' % bpName]):
np.testing.assert_equal(testMag, np.NaN)
else:
self.assertAlmostEqual(testMag, line['%sTotal' % bpName], 10)
self.assertGreater(ct, 0)
def testFindSED(self):
"""Pull SEDs from each type and make sure that each SED gets matched to itself.
Includes testing with extinction and passing in only colors."""
np.random.seed(42)
starPhot = BandpassDict.loadTotalBandpassesFromFiles(('u','g','r','i','z'),
bandpassDir = os.path.join(lsst.utils.getPackageDir('throughputs'),'sdss'),
bandpassRoot = 'sdss_')
imSimBand = Bandpass()
imSimBand.imsimBandpass()
testMatching = selectStarSED(sEDDir = self.testSpecDir, kuruczDir = self.testKDir,
mltDir = self.testMLTDir, wdDir = self.testWDDir)
testSEDList = []
testSEDList.append(testMatching.loadKuruczSEDs())
testSEDList.append(testMatching.loadmltSEDs())
testSEDListH, testSEDListHE = testMatching.loadwdSEDs()
testSEDList.append(testSEDListH)
testSEDList.append(testSEDListHE)
testSEDNames = []
testMags = []
testMagNormList = []
magNormStep = 1
for typeList in testSEDList:
if len(typeList) != 0:
typeSEDNames = []
typeMags = []
typeMagNorms = []
for testSED in typeList:
getSEDMags = Sed()
typeSEDNames.append(testSED.name)
getSEDMags.setSED(wavelen = testSED.wavelen, flambda = testSED.flambda)
testMagNorm = np.round(np.random.uniform(20.0,22.0),magNormStep)
typeMagNorms.append(testMagNorm)
fluxNorm = getSEDMags.calcFluxNorm(testMagNorm, imSimBand)
getSEDMags.multiplyFluxNorm(fluxNorm)
typeMags.append(starPhot.magListForSed(getSEDMags))
testSEDNames.append(typeSEDNames)
testMags.append(typeMags)
testMagNormList.append(typeMagNorms)
fakeRA = np.ones(len(testSEDList[0]))
fakeDec = np.ones(len(testSEDList[0]))
#Since default bandpassDict should be SDSS ugrizy shouldn't need to specify it
#Substitute in nan values to simulate incomplete data.
for typeList, names, mags, magNorms in zip(testSEDList, testSEDNames, testMags, testMagNormList):
if len(typeList) > 2:
nanMags = np.array(mags)
nanMags[0][0] = np.nan
nanMags[0][2] = np.nan
nanMags[0][3] = np.nan
nanMags[1][1] = np.nan
testMatchingResults = testMatching.findSED(typeList, nanMags, reddening = False)
self.assertEqual(None, testMatchingResults[0][0])
self.assertEqual(names[1:], testMatchingResults[0][1:])
self.assertEqual(None, testMatchingResults[1][0])
np.testing.assert_almost_equal(magNorms[1:], testMatchingResults[1][1:],
decimal = magNormStep)
else:
testMatchingResults = testMatching.findSED(typeList, mags, reddening = False)
self.assertEqual(names, testMatchingResults[0])
np.testing.assert_almost_equal(magNorms, testMatchingResults[1], decimal = magNormStep)
#Test Null Values option
nullMags = np.array(testMags[0])
nullMags[0][0] = -99.
nullMags[0][4] = -99.
nullMags[1][0] = -99.
nullMags[1][1] = -99.
testMatchingResultsNull = testMatching.findSED(testSEDList[0], nullMags,
nullValues = -99., reddening = False)
self.assertEqual(testSEDNames[0], testMatchingResultsNull[0])
np.testing.assert_almost_equal(testMagNormList[0], testMatchingResultsNull[1],
decimal = magNormStep)
#Test Error Output
errMags = np.array((testMags[0][0], testMags[0][0], testMags[0][0], testMags[0][0]))
errMags[1,1] += 1. #Total MSE will be 2/(4 colors) = 0.5
errMags[2, 0:2] = np.nan
errMags[2, 3] += 1. #Total MSE will be 2/(2 colors) = 1.0
errMags[3, :] = None
errSED = testSEDList[0][0]
testMatchingResultsErrors = testMatching.findSED([errSED], errMags, reddening = False)
np.testing.assert_almost_equal(np.array((0.0, 0.5, 1.0)), testMatchingResultsErrors[2][0:3],
decimal = 3)
self.assertEqual(None, testMatchingResultsErrors[2][3])
#Now test what happens if we pass in a bandpassDict
testMatchingResultsNoDefault = testMatching.findSED(testSEDList[0], testMags[0],
bandpassDict = starPhot,
reddening = False)
self.assertEqual(testSEDNames[0], testMatchingResultsNoDefault[0])
np.testing.assert_almost_equal(testMagNormList[0], testMatchingResultsNoDefault[1],
decimal = magNormStep)
#Test Reddening
testRA = np.random.uniform(10,170,len(testSEDList[0]))
testDec = np.random.uniform(10,80,len(testSEDList[0]))
extFactor = .5
raDec = np.array((testRA, testDec))
ebvVals = ebv().calculateEbv(equatorialCoordinates = raDec)
extVals = ebvVals*extFactor
testRedMags = []
for extVal, testMagSet in zip(extVals, testMags[0]):
testRedMags.append(testMagSet + extVal)
testMatchingResultsRed = testMatching.findSED(testSEDList[0], testRedMags, catRA = testRA,
catDec = testDec, reddening = True,
extCoeffs = np.ones(5)*extFactor)
self.assertEqual(testSEDNames[0], testMatchingResultsRed[0])
np.testing.assert_almost_equal(testMagNormList[0], testMatchingResultsRed[1],
decimal = magNormStep)
#Finally, test color input
testColors = []
for testMagSet in testMags[0]:
testColorSet = []
for filtNum in range(0, len(starPhot)-1):
testColorSet.append(testMagSet[filtNum] - testMagSet[filtNum+1])
testColors.append(testColorSet)
testMatchingColorsInput = testMatching.findSED(testSEDList[0], testMags[0],
reddening = False, colors = testColors)
self.assertEqual(testSEDNames[0], testMatchingColorsInput[0])
np.testing.assert_almost_equal(testMagNormList[0], testMatchingColorsInput[1],
decimal = magNormStep)
def loadGalfast(self, filenameList, outFileList, sEDPath = None, kuruczPath = None,
mltPath = None, wdPath = None, kuruczSubset = None,
mltSubset = None, wdSubset = None, chunkSize = 10000):
"""
This is customized for the outputs we currently need for the purposes of consistent output
It will read in a galfast output file and output desired values for database input into a file
@param [in] filenameList is a list of the galfast output files that will be loaded and processed.
Can process fits, gzipped, or txt output from galfast.
@param [in] outFileList is a list of the names of the output files that will be created. If gzipped
output is desired simply write the filenames with .gz at the end.
@param [in] kuruczPath is a place to specify a path to kurucz SED files
@param [in] mltPath is the same as kuruczPath except that it specifies a directory for the
mlt SEDs
@param [in] wdPath is the same as the previous two except that it specifies a path to a
white dwarf SED directory.
@param [in] kuruczSubset is a list which provides a subset of the kurucz files within the
kurucz folder that one wants to use
@param [in] mltSubset is a list which provides a subset of the mlt files within the
mlt folder that one wants to use
@param [in] wdSubset is a list which provides a subset of the wd files within the
wd folder that one wants to use
@param [in] chunkSize is the size of chunks of lines to be read from the catalog at one time.
"""
for filename in filenameList:
#Make sure input file exists and is readable format before doing anything else
if os.path.isfile(filename) == False:
raise RuntimeError('*** File does not exist')
#Process various possible galfast outputs
if filename.endswith(('.txt', '.gz', '.fits')):
continue
else:
raise RuntimeError(str('*** Unsupported File Format in file: ' + str(filename)))
#If all files exist and are in proper formats then load seds
selectStarSED0 = selectStarSED(kuruczDir=kuruczPath,
mltDir=mltPath,
wdDir=wdPath)
if kuruczSubset is None:
kuruczList = selectStarSED0.loadKuruczSEDs()
else:
kuruczList = selectStarSED0.loadKuruczSEDs(subset = kuruczSubset)
#Only need one dictionary since none of the names overlap
positionDict = {}
for kNum, kuruczSED in enumerate(kuruczList):
positionDict[kuruczSED.name] = kNum
if mltSubset is None:
mltList = selectStarSED0.loadmltSEDs()
else:
mltList = selectStarSED0.loadmltSEDs(subset = mltSubset)
for mltNum, mltSED in enumerate(mltList):
positionDict[mltSED.name] = mltNum
if wdSubset is None:
wdListH, wdListHE = selectStarSED0.loadwdSEDs()
else:
wdListH, wdListHE = selectStarSED0.loadwdSEDs(subset = wdSubset)
for hNum, hSED in enumerate(wdListH):
positionDict[hSED.name] = hNum
for heNum, heSED in enumerate(wdListHE):
positionDict[heSED.name] = heNum
#For adding/subtracting extinction when calculating colors
#Numbers below come from Schlafly and Finkbeiner (2011) (ApJ, 737, 103)
#normalized by SDSS r mag value
sdssExtCoeffs = [1.8551, 1.4455, 1.0, 0.7431, 0.5527]
lsstExtCoeffs = [1.8140, 1.4166, 0.9947, 0.7370, 0.5790, 0.4761]
sdssPhot = BandpassDict.loadTotalBandpassesFromFiles(['u','g','r','i','z'],
bandpassDir = os.path.join(lsst.utils.getPackageDir('throughputs'),
'sdss'),
bandpassRoot = 'sdss_')
#Load Bandpasses for LSST colors to get colors from matched SEDs
lsstFilterList = ('u', 'g', 'r', 'i', 'z', 'y')
lsstPhot = BandpassDict.loadTotalBandpassesFromFiles(lsstFilterList)
imSimBand = Bandpass()
imSimBand.imsimBandpass()
#Calculate colors and add them to the SED objects
kuruczColors = selectStarSED0.calcBasicColors(kuruczList, sdssPhot)
mltColors = selectStarSED0.calcBasicColors(mltList, sdssPhot)
hColors = selectStarSED0.calcBasicColors(wdListH, sdssPhot)
heColors = selectStarSED0.calcBasicColors(wdListHE, sdssPhot)
listDict = {'kurucz':kuruczList, 'mlt':mltList, 'H':wdListH, 'HE':wdListHE}
colorDict = {'kurucz':kuruczColors, 'mlt':mltColors, 'H':hColors, 'HE':heColors}
for filename, outFile in zip(filenameList, outFileList):
if filename.endswith('.txt'):
galfastIn = open(filename, 'rt')
inFits = False
gzFile = False
num_lines = sum(1 for line in open(filename))
elif filename.endswith('.gz'):
galfastIn = gzip.open(filename, 'rt')
inFits = False
gzFile = True
num_lines = sum(1 for line in gzip.open(filename))
elif filename.endswith('fits'):
hdulist = fits.open(filename)
galfastIn = hdulist[1].data
num_lines = len(galfastIn)
gzFile = False
inFits = True
if outFile.endswith('.txt'):
fOut = open(outFile, 'wt')
elif outFile.endswith('.gz'):
fOut = gzip.open(outFile, 'wt')
fOut.write('#oID, ra, dec, gall, galb, coordX, coordY, coordZ, sEDName, magNorm, ' +\
'LSSTugrizy, SDSSugriz, absSDSSr, pmRA, pmDec, vRad, pml, pmb, vRadlb, ' +\
'vR, vPhi, vZ, FeH, pop, distKpc, ebv, ebvInf\n')
header_length = 0
numChunks = 0
if inFits == False:
galfastDict = self.parseGalfast(galfastIn.readline())
header_length += 1
header_status = True
while header_status == True:
newLine = galfastIn.readline()
if newLine[0] != '#':
header_status = False
else:
header_length += 1
print('Total objects = %i' % (num_lines - header_length))
numChunks = ((num_lines-header_length)//chunkSize) + 1
for chunk in range(0,numChunks):
if chunk == numChunks-1:
lastChunkSize = (num_lines - header_length) % chunkSize
readSize = lastChunkSize
else:
readSize = chunkSize
oID = np.arange(readSize*chunk, readSize*(chunk+1))
if inFits:
starData = galfastIn[readSize*chunk:(readSize*chunk + readSize)]
sDSS = starData.field('SDSSugriz')
gall, galb = np.transpose(starData.field('lb'))
ra, dec = np.transpose(starData.field('radec'))
coordX, coordY, coordZ = np.transpose(starData.field('XYZ'))
DM = starData.field('DM')
absSDSSr = starData.field('absSDSSr')
pop = starData.field('comp')
FeH = starData.field('FeH')
vR, vPhi, vZ = np.transpose(starData.field('vcyl'))
pml, pmb, vRadlb = np.transpose(starData.field('pmlb'))
pmRA, pmDec, vRad = np.transpose(starData.field('pmradec'))
am = starData.field('Am')
amInf = starData.field('AmInf')
sdssPhotoFlags = starData.field('SDSSugrizPhotoFlags')
else:
if gzFile == False:
with open(filename) as t_in:
starData = np.loadtxt(itertools.islice(t_in,((readSize*chunk)+header_length),
((readSize*(chunk+1))+header_length)))
else:
with gzip.open(filename) as t_in:
starData = np.loadtxt(itertools.islice(t_in,((readSize*chunk)+header_length),
((readSize*(chunk+1))+header_length)))
starData = np.transpose(starData)
gall = starData[galfastDict['l']]
galb = starData[galfastDict['b']]
ra = starData[galfastDict['ra']]
dec = starData[galfastDict['dec']]
coordX = starData[galfastDict['X']]
coordY = starData[galfastDict['Y']]
coordZ = starData[galfastDict['Z']]
DM = starData[galfastDict['DM']]
absSDSSr = starData[galfastDict['absSDSSr']]
pop = starData[galfastDict['comp']]
FeH = starData[galfastDict['FeH']]
vR = starData[galfastDict['Vr']]
vPhi = starData[galfastDict['Vphi']]
vZ = starData[galfastDict['Vz']]
pml = starData[galfastDict['pml']]
pmb = starData[galfastDict['pmb']]
vRadlb = starData[galfastDict['vRadlb']]
pmRA = starData[galfastDict['pmra']]
pmDec = starData[galfastDict['pmdec']]
vRad = starData[galfastDict['vRad']]
am = starData[galfastDict['Am']]
amInf = starData[galfastDict['AmInf']]
sDSS = np.transpose(starData[galfastDict['SDSSu']:galfastDict['SDSSz']+1])
sDSSPhotoFlags = starData[galfastDict['SDSSPhotoFlags']]
#End of input, now onto processing and output
sDSSunred = selectStarSED0.deReddenMags(am, sDSS, sdssExtCoeffs)
if readSize == 1:
ra = np.array([ra])
dec = np.array([dec])
"""
Info about the following population cuts:
From Zeljko: "This color corresponds to the temperature (roughly spectral type M0) where
Kurucz models become increasingly bad, and thus we switch to empirical SEDs (the problem
is that for M and later stars, the effective surface temperature is low enough for
molecules to form, and their opacity is too complex to easily model, especially TiO)."
"""
mIn = np.where(((pop < 10) | (pop >= 20)) & (sDSSunred[:,2] - sDSSunred[:,3] > 0.59))
kIn = np.where(((pop < 10) | (pop >= 20)) & (sDSSunred[:,2] - sDSSunred[:,3] <= 0.59))
hIn = np.where((pop >= 10) & (pop < 15))
heIn = np.where((pop >= 15) & (pop < 20))
sEDNameK, magNormK, matchErrorK = selectStarSED0.findSED(listDict['kurucz'],
sDSSunred[kIn], ra[kIn], dec[kIn],
reddening = False,
colors = colorDict['kurucz'])
sEDNameM, magNormM, matchErrorM = selectStarSED0.findSED(listDict['mlt'],
sDSSunred[mIn], ra[mIn], dec[mIn],
reddening = False,
colors = colorDict['mlt'])
sEDNameH, magNormH, matchErrorH = selectStarSED0.findSED(listDict['H'],
sDSSunred[hIn], ra[hIn], dec[hIn],
reddening = False,
colors = colorDict['H'])
sEDNameHE, magNormHE, matchErrorHE = selectStarSED0.findSED(listDict['HE'],
sDSSunred[heIn],
ra[heIn], dec[heIn],
reddening = False,
colors = colorDict['HE'])
chunkNames = np.empty(readSize, dtype = 'S32')
chunkTypes = np.empty(readSize, dtype = 'S8')
chunkMagNorms = np.zeros(readSize)
chunkMatchErrors = np.zeros(readSize)
chunkNames[kIn] = sEDNameK
chunkTypes[kIn] = 'kurucz'
chunkMagNorms[kIn] = magNormK
chunkMatchErrors[kIn] = matchErrorK
chunkNames[mIn] = sEDNameM
chunkTypes[mIn] = 'mlt'
chunkMagNorms[mIn] = magNormM
chunkMatchErrors[mIn] = matchErrorM
chunkNames[hIn] = sEDNameH
chunkTypes[hIn] = 'H'
chunkMagNorms[hIn] = magNormH
chunkMatchErrors[hIn] = matchErrorH
chunkNames[heIn] = sEDNameHE
chunkTypes[heIn] = 'HE'
chunkMagNorms[heIn] = magNormHE
chunkMatchErrors[heIn] = matchErrorHE
lsstMagsUnred = []
for sedName, sedType, magNorm, matchError in zip(chunkNames.astype(str),
chunkTypes.astype(str),
chunkMagNorms,
chunkMatchErrors):
testSED = Sed()
testSED.setSED(listDict[sedType][positionDict[sedName]].wavelen,
flambda = listDict[sedType][positionDict[sedName]].flambda)
fluxNorm = testSED.calcFluxNorm(magNorm, imSimBand)
testSED.multiplyFluxNorm(fluxNorm)
lsstMagsUnred.append(lsstPhot.magListForSed(testSED))
#If the extinction value is negative then it will add the reddening back in
lsstMags = selectStarSED0.deReddenMags((-1.0*am), lsstMagsUnred,
lsstExtCoeffs)
distKpc = self.convDMtoKpc(DM)
ebv = am / 2.285 #From Schlafly and Finkbeiner 2011, (ApJ, 737, 103) for sdssr
ebvInf = amInf / 2.285
for line in range(0, readSize):
outFmt = '%i,%3.7f,%3.7f,%3.7f,%3.7f,%3.7f,' +\
'%3.7f,%3.7f,%s,' +\
'%3.7f,%3.7f,' +\
'%3.7f,%3.7f,%3.7f,' +\
'%3.7f,%3.7f,%3.7f,' +\
'%3.7f,%3.7f,%3.7f,%3.7f,' +\
'%3.7f,%3.7f,%3.7f,%3.7f,%3.7f,' +\
'%3.7f,%3.7f,%3.7f,%3.7f,%3.7f,%3.7f,' +\
'%3.7f,%i,%3.7f,%3.7f,%3.7f\n'
if readSize == 1:
if inFits == True:
sDSS = sDSS[0]
outDat = (oID, ra[line], dec[line], gall, galb, coordX,
coordY, coordZ, chunkNames,
chunkMagNorms, chunkMatchErrors,
lsstMags[line][0], lsstMags[line][1], lsstMags[line][2],
lsstMags[line][3], lsstMags[line][4], lsstMags[line][5],
sDSS[0], sDSS[1], sDSS[2], sDSS[3],
sDSS[4], absSDSSr, pmRA, pmDec, vRad,
pml, pmb, vRadlb, vR, vPhi, vZ,
FeH, pop, distKpc, ebv, ebvInf)
else:
outDat = (oID[line], ra[line], dec[line], gall[line], galb[line], coordX[line],
coordY[line], coordZ[line], chunkNames[line],
chunkMagNorms[line], chunkMatchErrors[line],
lsstMags[line][0], lsstMags[line][1], lsstMags[line][2],
lsstMags[line][3], lsstMags[line][4], lsstMags[line][5],
sDSS[line][0], sDSS[line][1], sDSS[line][2], sDSS[line][3],
sDSS[line][4], absSDSSr[line], pmRA[line], pmDec[line], vRad[line],
pml[line], pmb[line], vRadlb[line], vR[line], vPhi[line], vZ[line],
FeH[line], pop[line], distKpc[line], ebv[line], ebvInf[line])
fOut.write(outFmt % outDat)
print('Chunk Num Done = %i out of %i' % (chunk+1, numChunks))
def loadGalfast(self,
filenameList,
outFileList,
sEDPath=None,
kuruczPath=None,
mltPath=None,
wdPath=None,
kuruczSubset=None,
mltSubset=None,
wdSubset=None,
chunkSize=10000):
"""
This is customized for the outputs we currently need for the purposes of consistent output
It will read in a galfast output file and output desired values for database input into a file
@param [in] filenameList is a list of the galfast output files that will be loaded and processed.
Can process fits, gzipped, or txt output from galfast.
@param [in] outFileList is a list of the names of the output files that will be created. If gzipped
output is desired simply write the filenames with .gz at the end.
@param [in] kuruczPath is a place to specify a path to kurucz SED files
@param [in] mltPath is the same as kuruczPath except that it specifies a directory for the
mlt SEDs
@param [in] wdPath is the same as the previous two except that it specifies a path to a
white dwarf SED directory.
@param [in] kuruczSubset is a list which provides a subset of the kurucz files within the
kurucz folder that one wants to use
@param [in] mltSubset is a list which provides a subset of the mlt files within the
mlt folder that one wants to use
@param [in] wdSubset is a list which provides a subset of the wd files within the
wd folder that one wants to use
@param [in] chunkSize is the size of chunks of lines to be read from the catalog at one time.
"""
for filename in filenameList:
#Make sure input file exists and is readable format before doing anything else
if os.path.isfile(filename) == False:
raise RuntimeError('*** File does not exist')
#Process various possible galfast outputs
if filename.endswith(('.txt', '.gz', '.fits')):
continue
else:
raise RuntimeError(
str('*** Unsupported File Format in file: ' +
str(filename)))
#If all files exist and are in proper formats then load seds
selectStarSED0 = selectStarSED(kuruczDir=kuruczPath,
mltDir=mltPath,
wdDir=wdPath)
if kuruczSubset is None:
kuruczList = selectStarSED0.loadKuruczSEDs()
else:
kuruczList = selectStarSED0.loadKuruczSEDs(subset=kuruczSubset)
#Only need one dictionary since none of the names overlap
positionDict = {}
for kNum, kuruczSED in enumerate(kuruczList):
positionDict[kuruczSED.name] = kNum
if mltSubset is None:
mltList = selectStarSED0.loadmltSEDs()
else:
mltList = selectStarSED0.loadmltSEDs(subset=mltSubset)
for mltNum, mltSED in enumerate(mltList):
positionDict[mltSED.name] = mltNum
if wdSubset is None:
wdListH, wdListHE = selectStarSED0.loadwdSEDs()
else:
wdListH, wdListHE = selectStarSED0.loadwdSEDs(subset=wdSubset)
for hNum, hSED in enumerate(wdListH):
positionDict[hSED.name] = hNum
for heNum, heSED in enumerate(wdListHE):
positionDict[heSED.name] = heNum
#For adding/subtracting extinction when calculating colors
#Numbers below come from Schlafly and Finkbeiner (2011) (ApJ, 737, 103)
#normalized by SDSS r mag value
sdssExtCoeffs = [1.8551, 1.4455, 1.0, 0.7431, 0.5527]
lsstExtCoeffs = [1.8140, 1.4166, 0.9947, 0.7370, 0.5790, 0.4761]
sdssPhot = BandpassDict.loadTotalBandpassesFromFiles(
['u', 'g', 'r', 'i', 'z'],
bandpassDir=os.path.join(lsst.utils.getPackageDir('throughputs'),
'sdss'),
bandpassRoot='sdss_')
#Load Bandpasses for LSST colors to get colors from matched SEDs
lsstFilterList = ('u', 'g', 'r', 'i', 'z', 'y')
lsstPhot = BandpassDict.loadTotalBandpassesFromFiles(lsstFilterList)
imSimBand = Bandpass()
imSimBand.imsimBandpass()
#Calculate colors and add them to the SED objects
kuruczColors = selectStarSED0.calcBasicColors(kuruczList, sdssPhot)
mltColors = selectStarSED0.calcBasicColors(mltList, sdssPhot)
hColors = selectStarSED0.calcBasicColors(wdListH, sdssPhot)
heColors = selectStarSED0.calcBasicColors(wdListHE, sdssPhot)
listDict = {
'kurucz': kuruczList,
'mlt': mltList,
'H': wdListH,
'HE': wdListHE
}
colorDict = {
'kurucz': kuruczColors,
'mlt': mltColors,
'H': hColors,
'HE': heColors
}
for filename, outFile in zip(filenameList, outFileList):
if filename.endswith('.txt'):
galfastIn = open(filename, 'rt')
inFits = False
gzFile = False
num_lines = sum(1 for line in open(filename))
elif filename.endswith('.gz'):
galfastIn = gzip.open(filename, 'rt')
inFits = False
gzFile = True
num_lines = sum(1 for line in gzip.open(filename))
elif filename.endswith('fits'):
hdulist = fits.open(filename)
galfastIn = hdulist[1].data
num_lines = len(galfastIn)
gzFile = False
inFits = True
if outFile.endswith('.txt'):
fOut = open(outFile, 'wt')
elif outFile.endswith('.gz'):
fOut = gzip.open(outFile, 'wt')
fOut.write('#oID, ra, dec, gall, galb, coordX, coordY, coordZ, sEDName, magNorm, ' +\
'LSSTugrizy, SDSSugriz, absSDSSr, pmRA, pmDec, vRad, pml, pmb, vRadlb, ' +\
'vR, vPhi, vZ, FeH, pop, distKpc, ebv, ebvInf\n')
header_length = 0
numChunks = 0
if inFits == False:
galfastDict = self.parseGalfast(galfastIn.readline())
header_length += 1
header_status = True
while header_status == True:
newLine = galfastIn.readline()
if newLine[0] != '#':
header_status = False
else:
header_length += 1
print('Total objects = %i' % (num_lines - header_length))
numChunks = ((num_lines - header_length) // chunkSize) + 1
for chunk in range(0, numChunks):
if chunk == numChunks - 1:
lastChunkSize = (num_lines - header_length) % chunkSize
readSize = lastChunkSize
else:
readSize = chunkSize
oID = np.arange(readSize * chunk, readSize * (chunk + 1))
if inFits:
starData = galfastIn[readSize * chunk:(readSize * chunk +
readSize)]
sDSS = starData.field('SDSSugriz')
gall, galb = np.transpose(starData.field('lb'))
ra, dec = np.transpose(starData.field('radec'))
coordX, coordY, coordZ = np.transpose(
starData.field('XYZ'))
DM = starData.field('DM')
absSDSSr = starData.field('absSDSSr')
pop = starData.field('comp')
FeH = starData.field('FeH')
vR, vPhi, vZ = np.transpose(starData.field('vcyl'))
pml, pmb, vRadlb = np.transpose(starData.field('pmlb'))
pmRA, pmDec, vRad = np.transpose(starData.field('pmradec'))
am = starData.field('Am')
amInf = starData.field('AmInf')
sdssPhotoFlags = starData.field('SDSSugrizPhotoFlags')
else:
if gzFile == False:
with open(filename) as t_in:
starData = np.loadtxt(
itertools.islice(
t_in, ((readSize * chunk) + header_length),
((readSize *
(chunk + 1)) + header_length)))
else:
with gzip.open(filename) as t_in:
starData = np.loadtxt(
itertools.islice(
t_in, ((readSize * chunk) + header_length),
((readSize *
(chunk + 1)) + header_length)))
starData = np.transpose(starData)
gall = starData[galfastDict['l']]
galb = starData[galfastDict['b']]
ra = starData[galfastDict['ra']]
dec = starData[galfastDict['dec']]
coordX = starData[galfastDict['X']]
coordY = starData[galfastDict['Y']]
coordZ = starData[galfastDict['Z']]
DM = starData[galfastDict['DM']]
absSDSSr = starData[galfastDict['absSDSSr']]
pop = starData[galfastDict['comp']]
FeH = starData[galfastDict['FeH']]
vR = starData[galfastDict['Vr']]
vPhi = starData[galfastDict['Vphi']]
vZ = starData[galfastDict['Vz']]
pml = starData[galfastDict['pml']]
pmb = starData[galfastDict['pmb']]
vRadlb = starData[galfastDict['vRadlb']]
pmRA = starData[galfastDict['pmra']]
pmDec = starData[galfastDict['pmdec']]
vRad = starData[galfastDict['vRad']]
am = starData[galfastDict['Am']]
amInf = starData[galfastDict['AmInf']]
sDSS = np.transpose(
starData[galfastDict['SDSSu']:galfastDict['SDSSz'] +
1])
sDSSPhotoFlags = starData[galfastDict['SDSSPhotoFlags']]
#End of input, now onto processing and output
sDSSunred = selectStarSED0.deReddenMags(
am, sDSS, sdssExtCoeffs)
if readSize == 1:
ra = np.array([ra])
dec = np.array([dec])
"""
Info about the following population cuts:
From Zeljko: "This color corresponds to the temperature (roughly spectral type M0) where
Kurucz models become increasingly bad, and thus we switch to empirical SEDs (the problem
is that for M and later stars, the effective surface temperature is low enough for
molecules to form, and their opacity is too complex to easily model, especially TiO)."
"""
mIn = np.where(((pop < 10) | (pop >= 20))
& (sDSSunred[:, 2] - sDSSunred[:, 3] > 0.59))
kIn = np.where(((pop < 10) | (pop >= 20))
& (sDSSunred[:, 2] - sDSSunred[:, 3] <= 0.59))
hIn = np.where((pop >= 10) & (pop < 15))
heIn = np.where((pop >= 15) & (pop < 20))
sEDNameK, magNormK, matchErrorK = selectStarSED0.findSED(
listDict['kurucz'],
sDSSunred[kIn],
ra[kIn],
dec[kIn],
reddening=False,
colors=colorDict['kurucz'])
sEDNameM, magNormM, matchErrorM = selectStarSED0.findSED(
listDict['mlt'],
sDSSunred[mIn],
ra[mIn],
dec[mIn],
reddening=False,
colors=colorDict['mlt'])
sEDNameH, magNormH, matchErrorH = selectStarSED0.findSED(
listDict['H'],
sDSSunred[hIn],
ra[hIn],
dec[hIn],
reddening=False,
colors=colorDict['H'])
sEDNameHE, magNormHE, matchErrorHE = selectStarSED0.findSED(
listDict['HE'],
sDSSunred[heIn],
ra[heIn],
dec[heIn],
reddening=False,
colors=colorDict['HE'])
chunkNames = np.empty(readSize, dtype='S32')
chunkTypes = np.empty(readSize, dtype='S8')
chunkMagNorms = np.zeros(readSize)
chunkMatchErrors = np.zeros(readSize)
chunkNames[kIn] = sEDNameK
chunkTypes[kIn] = 'kurucz'
chunkMagNorms[kIn] = magNormK
chunkMatchErrors[kIn] = matchErrorK
chunkNames[mIn] = sEDNameM
chunkTypes[mIn] = 'mlt'
chunkMagNorms[mIn] = magNormM
chunkMatchErrors[mIn] = matchErrorM
chunkNames[hIn] = sEDNameH
chunkTypes[hIn] = 'H'
chunkMagNorms[hIn] = magNormH
chunkMatchErrors[hIn] = matchErrorH
chunkNames[heIn] = sEDNameHE
chunkTypes[heIn] = 'HE'
chunkMagNorms[heIn] = magNormHE
chunkMatchErrors[heIn] = matchErrorHE
lsstMagsUnred = []
for sedName, sedType, magNorm, matchError in zip(
chunkNames.astype(str), chunkTypes.astype(str),
chunkMagNorms, chunkMatchErrors):
testSED = Sed()
testSED.setSED(
listDict[sedType][positionDict[sedName]].wavelen,
flambda=listDict[sedType][
positionDict[sedName]].flambda)
fluxNorm = testSED.calcFluxNorm(magNorm, imSimBand)
testSED.multiplyFluxNorm(fluxNorm)
lsstMagsUnred.append(lsstPhot.magListForSed(testSED))
#If the extinction value is negative then it will add the reddening back in
lsstMags = selectStarSED0.deReddenMags(
(-1.0 * am), lsstMagsUnred, lsstExtCoeffs)
distKpc = self.convDMtoKpc(DM)
ebv = am / 2.285 #From Schlafly and Finkbeiner 2011, (ApJ, 737, 103) for sdssr
ebvInf = amInf / 2.285
for line in range(0, readSize):
outFmt = '%i,%3.7f,%3.7f,%3.7f,%3.7f,%3.7f,' +\
'%3.7f,%3.7f,%s,' +\
'%3.7f,%3.7f,' +\
'%3.7f,%3.7f,%3.7f,' +\
'%3.7f,%3.7f,%3.7f,' +\
'%3.7f,%3.7f,%3.7f,%3.7f,' +\
'%3.7f,%3.7f,%3.7f,%3.7f,%3.7f,' +\
'%3.7f,%3.7f,%3.7f,%3.7f,%3.7f,%3.7f,' +\
'%3.7f,%i,%3.7f,%3.7f,%3.7f\n'
if readSize == 1:
if inFits == True:
sDSS = sDSS[0]
outDat = (oID, ra[line], dec[line], gall, galb, coordX,
coordY, coordZ, chunkNames, chunkMagNorms,
chunkMatchErrors, lsstMags[line][0],
lsstMags[line][1], lsstMags[line][2],
lsstMags[line][3], lsstMags[line][4],
lsstMags[line][5], sDSS[0], sDSS[1], sDSS[2],
sDSS[3], sDSS[4], absSDSSr, pmRA, pmDec,
vRad, pml, pmb, vRadlb, vR, vPhi, vZ, FeH,
pop, distKpc, ebv, ebvInf)
else:
outDat = (oID[line], ra[line], dec[line], gall[line],
galb[line], coordX[line], coordY[line],
coordZ[line], chunkNames[line],
chunkMagNorms[line], chunkMatchErrors[line],
lsstMags[line][0], lsstMags[line][1],
lsstMags[line][2], lsstMags[line][3],
lsstMags[line][4], lsstMags[line][5],
sDSS[line][0], sDSS[line][1], sDSS[line][2],
sDSS[line][3], sDSS[line][4], absSDSSr[line],
pmRA[line], pmDec[line], vRad[line],
pml[line], pmb[line], vRadlb[line], vR[line],
vPhi[line], vZ[line], FeH[line], pop[line],
distKpc[line], ebv[line], ebvInf[line])
fOut.write(outFmt % outDat)
print('Chunk Num Done = %i out of %i' % (chunk + 1, numChunks))
def testAlternateBandpassesGalaxies(self):
"""
the same as testAlternateBandpassesStars, but for galaxies
"""
obs_metadata_pointed = ObservationMetaData(mjd=50000.0,
boundType='circle',
pointingRA=0.0,
pointingDec=0.0,
boundLength=10.0)
dtype = np.dtype([('galid', np.int), ('ra', np.float),
('dec', np.float), ('uTotal', np.float),
('gTotal', np.float), ('rTotal', np.float),
('iTotal', np.float), ('zTotal', np.float),
('uBulge', np.float), ('gBulge', np.float),
('rBulge', np.float), ('iBulge', np.float),
('zBulge', np.float), ('uDisk', np.float),
('gDisk', np.float), ('rDisk', np.float),
('iDisk', np.float), ('zDisk', np.float),
('uAgn', np.float), ('gAgn', np.float),
('rAgn', np.float), ('iAgn', np.float),
('zAgn', np.float), ('bulgeName', str, 200),
('bulgeNorm', np.float), ('bulgeAv', np.float),
('diskName', str, 200), ('diskNorm', np.float),
('diskAv', np.float), ('agnName', str, 200),
('agnNorm', np.float), ('redshift', np.float)])
test_cat = cartoonGalaxies(self.galaxy,
obs_metadata=obs_metadata_pointed)
with lsst.utils.tests.getTempFilePath('.txt') as catName:
test_cat.write_catalog(catName)
catData = np.genfromtxt(catName, dtype=dtype, delimiter=', ')
self.assertGreater(len(catData), 0)
cartoonDir = getPackageDir('sims_photUtils')
cartoonDir = os.path.join(cartoonDir, 'tests', 'cartoonSedTestData')
sedDir = getPackageDir('sims_sed_library')
testBandpasses = {}
keys = ['u', 'g', 'r', 'i', 'z']
for kk in keys:
testBandpasses[kk] = Bandpass()
testBandpasses[kk].readThroughput(
os.path.join(cartoonDir, "test_bandpass_%s.dat" % kk))
imsimBand = Bandpass()
imsimBand.imsimBandpass()
specMap = defaultSpecMap
ct = 0
for line in catData:
bulgeMagList = []
diskMagList = []
agnMagList = []
if line['bulgeName'] == 'None':
for bp in keys:
np.testing.assert_equal(line['%sBulge' % bp], np.NaN)
bulgeMagList.append(np.NaN)
else:
ct += 1
dummySed = Sed()
dummySed.readSED_flambda(
os.path.join(sedDir, specMap[line['bulgeName']]))
fnorm = dummySed.calcFluxNorm(line['bulgeNorm'], imsimBand)
dummySed.multiplyFluxNorm(fnorm)
a_int, b_int = dummySed.setupCCM_ab()
dummySed.addDust(a_int, b_int, A_v=line['bulgeAv'])
dummySed.redshiftSED(line['redshift'], dimming=True)
dummySed.resampleSED(wavelen_match=testBandpasses['u'].wavelen)
for bpName in keys:
mag = dummySed.calcMag(testBandpasses[bpName])
self.assertAlmostEqual(mag, line['%sBulge' % bpName], 10)
bulgeMagList.append(mag)
if line['diskName'] == 'None':
for bp in keys:
np.assert_equal(line['%sDisk' % bp], np.NaN)
diskMagList.append(np.NaN)
else:
ct += 1
dummySed = Sed()
dummySed.readSED_flambda(
os.path.join(sedDir, specMap[line['diskName']]))
fnorm = dummySed.calcFluxNorm(line['diskNorm'], imsimBand)
dummySed.multiplyFluxNorm(fnorm)
a_int, b_int = dummySed.setupCCM_ab()
dummySed.addDust(a_int, b_int, A_v=line['diskAv'])
dummySed.redshiftSED(line['redshift'], dimming=True)
dummySed.resampleSED(wavelen_match=testBandpasses['u'].wavelen)
for bpName in keys:
mag = dummySed.calcMag(testBandpasses[bpName])
self.assertAlmostEqual(mag, line['%sDisk' % bpName], 10)
diskMagList.append(mag)
if line['agnName'] == 'None':
for bp in keys:
np.testing.assert_true(line['%sAgn' % bp], np.NaN)
agnMagList.append(np.NaN)
else:
ct += 1
dummySed = Sed()
dummySed.readSED_flambda(
os.path.join(sedDir, specMap[line['agnName']]))
fnorm = dummySed.calcFluxNorm(line['agnNorm'], imsimBand)
dummySed.multiplyFluxNorm(fnorm)
dummySed.redshiftSED(line['redshift'], dimming=True)
dummySed.resampleSED(wavelen_match=testBandpasses['u'].wavelen)
for bpName in keys:
mag = dummySed.calcMag(testBandpasses[bpName])
self.assertAlmostEqual(mag, line['%sAgn' % bpName], 10)
agnMagList.append(mag)
totalMags = PhotometryGalaxies().sum_magnitudes(
bulge=np.array(bulgeMagList),
disk=np.array(diskMagList),
agn=np.array(agnMagList))
for testMag, bpName in zip(totalMags, keys):
if np.isnan(line['%sTotal' % bpName]):
np.testing.assert_equal(testMag, np.NaN)
else:
self.assertAlmostEqual(testMag, line['%sTotal' % bpName],
10)
self.assertGreater(ct, 0)
