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)