def testInitialization(self):
"""
Test that all of the member variables of BandpassDict are set
to the correct value upon construction.
"""
for nBp in range(3,10,1):
nameList, bpList = self.getListOfBandpasses(nBp)
testDict = BandpassDict(bpList, nameList)
self.assertEqual(len(testDict), nBp)
for controlName, testName in zip(nameList, testDict):
self.assertEqual(controlName, testName)
for controlName, testName in zip(nameList, testDict.keys()):
self.assertEqual(controlName, testName)
for name, bp in zip(nameList, bpList):
numpy.testing.assert_array_almost_equal(bp.wavelen, testDict[name].wavelen, 19)
numpy.testing.assert_array_almost_equal(bp.sb, testDict[name].sb, 19)
for bpControl, bpTest in zip(bpList, testDict.values()):
numpy.testing.assert_array_almost_equal(bpControl.wavelen, bpTest.wavelen, 19)
numpy.testing.assert_array_almost_equal(bpControl.sb, bpTest.sb, 19)
def testInitialization(self):
"""
Test that all of the member variables of BandpassDict are set
to the correct value upon construction.
"""
for nBp in range(3,10,1):
nameList, bpList = self.getListOfBandpasses(nBp)
testDict = BandpassDict(bpList, nameList)
self.assertEqual(len(testDict), nBp)
for controlName, testName in zip(nameList, testDict):
self.assertEqual(controlName, testName)
for controlName, testName in zip(nameList, testDict.keys()):
self.assertEqual(controlName, testName)
for name, bp in zip(nameList, bpList):
numpy.testing.assert_array_almost_equal(bp.wavelen, testDict[name].wavelen, 10)
numpy.testing.assert_array_almost_equal(bp.sb, testDict[name].sb, 10)
for bpControl, bpTest in zip(bpList, testDict.values()):
numpy.testing.assert_array_almost_equal(bpControl.wavelen, bpTest.wavelen, 10)
numpy.testing.assert_array_almost_equal(bpControl.sb, bpTest.sb, 10)
def testExceptions(self):
"""
Test that the correct exceptions are thrown by BandpassDict
"""
nameList, bpList = self.getListOfBandpasses(4)
dummyNameList = copy.deepcopy(nameList)
dummyNameList[1] = dummyNameList[0]
with self.assertRaises(RuntimeError) as context:
testDict = BandpassDict(bpList, dummyNameList)
self.assertTrue('occurs twice' in context.exception.message)
testDict = BandpassDict(bpList, nameList)
with self.assertRaises(AttributeError) as context:
testDict.phiArray = None
with self.assertRaises(AttributeError) as context:
testDict.wavelenStep = 0.9
with self.assertRaises(AttributeError) as context:
testDict.wavelenMatch = numpy.arange(10.0,100.0,1.0)
def testWavelenMatch(self):
"""
Test that when you load bandpasses sampled over different
wavelength grids, they all get sampled to the same wavelength
grid.
"""
dwavList = numpy.arange(5.0,25.0,5.0)
bpList = []
bpNameList = []
for ix, dwav in enumerate(dwavList):
name = 'bp_%d' % ix
wavelen = numpy.arange(10.0, 1500.0, dwav)
sb = numpy.exp(-0.5*(numpy.power((wavelen-100.0*ix)/100.0,2)))
bp = Bandpass(wavelen=wavelen, sb=sb)
bpList.append(bp)
bpNameList.append(name)
# First make sure that we have created distinct wavelength grids
for ix in range(len(bpList)):
for iy in range(ix+1,len(bpList)):
self.assertTrue(len(bpList[ix].wavelen)!=len(bpList[iy].wavelen))
testDict = BandpassDict(bpList, bpNameList)
# Now make sure that the wavelength grids in the dict were resampled, but that
# the original wavelength grids were not changed
for ix in range(len(bpList)):
numpy.testing.assert_array_almost_equal(testDict.values()[ix].wavelen, testDict.wavelenMatch, 19)
if ix!=0:
self.assertTrue(len(testDict.wavelenMatch)!=len(bpList[ix].wavelen))
def testWavelenMatch(self):
"""
Test that when you load bandpasses sampled over different
wavelength grids, they all get sampled to the same wavelength
grid.
"""
dwavList = numpy.arange(5.0,25.0,5.0)
bpList = []
bpNameList = []
for ix, dwav in enumerate(dwavList):
name = 'bp_%d' % ix
wavelen = numpy.arange(10.0, 1500.0, dwav)
sb = numpy.exp(-0.5*(numpy.power((wavelen-100.0*ix)/100.0,2)))
bp = Bandpass(wavelen=wavelen, sb=sb)
bpList.append(bp)
bpNameList.append(name)
# First make sure that we have created distinct wavelength grids
for ix in range(len(bpList)):
for iy in range(ix+1,len(bpList)):
self.assertTrue(len(bpList[ix].wavelen)!=len(bpList[iy].wavelen))
testDict = BandpassDict(bpList, bpNameList)
# Now make sure that the wavelength grids in the dict were resampled, but that
# the original wavelength grids were not changed
for ix in range(len(bpList)):
numpy.testing.assert_array_almost_equal(testDict.values()[ix].wavelen, testDict.wavelenMatch, 19)
if ix!=0:
self.assertTrue(len(testDict.wavelenMatch)!=len(bpList[ix].wavelen))
def _get_sed_mags_and_cosmology(catalog_name):
"""
Returns 3 numpy arrays: sed_names, sed_mag_list, sed_mag_norm
and a dictionary for cosmology
sed_names is 1d str array, with length = number of SED files in the library
sed_mag_list is MxN float array, with M = number of SED files in the library,
and N = number of top hat filters in the catalog
sed_mag_norm is 1d float array, with length = number of SED files in the library
cosmology = {'H0': H0, 'Om0': Om0}
"""
gc = GCRCatalogs.load_catalog(catalog_name,
config_overwrite=dict(md5=False))
cosmo = dict(H0=gc.cosmology.H0.value, Om0=gc.cosmology.Om0)
bp_params_raw = {'disk': set(), 'bulge': set()}
for q in gc.list_all_quantities():
m = _gcr_sed_re.match(q)
if m:
wav0, width, tag = m.groups()
bp_params_raw[tag].add((int(wav0), int(width)))
assert bp_params_raw['disk'] == bp_params_raw[
'bulge'], 'SEDs for disk and bulge do not match'
assert bp_params_raw['disk'], 'No SED found'
bp_params_sorted = sorted(bp_params_raw['disk'], key=lambda p: p[0])
# SED labels in GCR specify the band pass in angstrom, but CatSim uses nm
# Hence the conversion factor 0.1 in the code below
wav_min = bp_params_sorted[0][0] * 0.1
wav_max = max((0.1 * (wav0 + width) for wav0, width in bp_params_sorted))
wav_grid = np.arange(wav_min, wav_max, 0.1)
bp_name_list = list()
bp_list = list()
for wav0, width in bp_params_sorted:
sb_grid = ((wav_grid >= wav0 * 0.1) &
(wav_grid <= (wav0 + width) * 0.1)).astype(float)
bp_list.append(Bandpass(wavelen=wav_grid, sb=sb_grid))
bp_name_list.append('%d_%d' % (wav0, width))
bandpass_dict = BandpassDict(bp_list, bp_name_list)
sed_names = list()
sed_mag_list = list()
sed_mag_norm = list()
imsim_bp = Bandpass()
imsim_bp.imsimBandpass()
for sed_file_name in os.listdir(_galaxy_sed_dir):
spec = Sed()
spec.readSED_flambda(os.path.join(_galaxy_sed_dir, sed_file_name))
sed_names.append(sed_file_name)
sed_mag_list.append(tuple(bandpass_dict.magListForSed(spec)))
sed_mag_norm.append(spec.calcMag(imsim_bp))
return np.array(sed_names), np.array(sed_mag_list), np.array(
sed_mag_norm), cosmo
def testManyMagSystems(self):
"""
Test that the SSM photometry mixin can simultaneously calculate magnitudes
in multiple bandpass systems
"""
catName = os.path.join(getPackageDir('sims_catUtils'), 'tests',
'scratchSpace', 'compoundSsmPhotCat.txt')
cat = Compound_SSM_photCat(self.photDB)
cat.write_catalog(catName)
dtype = np.dtype([('id', np.int), ('lsst_u', np.float),
('lsst_g', np.float), ('lsst_r', np.float),
('lsst_i', np.float), ('lsst_z', np.float),
('lsst_y', np.float), ('cartoon_u', np.float),
('cartoon_g', np.float), ('cartoon_r', np.float),
('cartoon_i', np.float), ('cartoon_z', np.float)])
testData = np.genfromtxt(catName, dtype=dtype, delimiter=',')
self.assertGreater(len(testData), 0)
controlData = np.genfromtxt(self.dbFile, dtype=self.dtype)
self.assertGreater(len(controlData), 0)
LSSTbandpasses = BandpassDict.loadTotalBandpassesFromFiles()
bandpassDir = os.path.join(getPackageDir('sims_photUtils'), 'tests',
'cartoonSedTestData')
cartoonBandpasses = BandpassDict.loadTotalBandpassesFromFiles(
['u', 'g', 'r', 'i', 'z'],
bandpassDir=bandpassDir,
bandpassRoot='test_bandpass_')
controlSedList = SedList(controlData['sedFilename'],
controlData['magNorm'],
wavelenMatch=LSSTbandpasses.wavelenMatch)
controlLsstMags = LSSTbandpasses.magListForSedList(controlSedList)
controlCartoonMags = cartoonBandpasses.magListForSedList(
controlSedList)
for ii in range(len(controlLsstMags)):
for jj, bpName in enumerate(
['lsst_u', 'lsst_g', 'lsst_r', 'lsst_i', 'lsst_z', 'lsst_y']):
self.assertAlmostEqual(controlLsstMags[ii][jj],
testData[bpName][ii], 10)
for jj, bpName in enumerate([
'cartoon_u', 'cartoon_g', 'cartoon_r', 'cartoon_i',
'cartoon_z'
]):
self.assertAlmostEqual(controlCartoonMags[ii][jj],
testData[bpName][ii], 10)
if os.path.exists(catName):
os.unlink(catName)
def testFluxListForSedList(self):
"""
Test that fluxListForSedList calculates the correct fluxes
"""
nBandpasses = 7
bpNameList, bpList = self.getListOfBandpasses(nBandpasses)
testBpDict = BandpassDict(bpList, bpNameList)
nSed = 20
sedNameList = self.getListOfSedNames(nSed)
magNormList = self.rng.random_sample(nSed)*5.0 + 15.0
internalAvList = self.rng.random_sample(nSed)*0.3 + 0.1
redshiftList = self.rng.random_sample(nSed)*5.0
galacticAvList = self.rng.random_sample(nSed)*0.3 + 0.1
# first, test on an SedList without a wavelenMatch
testSedList = SedList(sedNameList, magNormList,
fileDir=self.sedDir,
internalAvList=internalAvList,
redshiftList=redshiftList,
galacticAvList=galacticAvList)
fluxList = testBpDict.fluxListForSedList(testSedList)
self.assertEqual(fluxList.shape[0], nSed)
self.assertEqual(fluxList.shape[1], nBandpasses)
for ix, sedObj in enumerate(testSedList):
dummySed = Sed(wavelen=copy.deepcopy(sedObj.wavelen),
flambda=copy.deepcopy(sedObj.flambda))
for iy, bp in enumerate(testBpDict):
flux = dummySed.calcFlux(bpList[iy])
self.assertAlmostEqual(flux/fluxList[ix][iy], 1.0, 2)
# now use wavelenMatch
testSedList = SedList(sedNameList, magNormList,
fileDir=self.sedDir,
internalAvList=internalAvList,
redshiftList=redshiftList,
galacticAvList=galacticAvList,
wavelenMatch=testBpDict.wavelenMatch)
fluxList = testBpDict.fluxListForSedList(testSedList)
self.assertEqual(fluxList.shape[0], nSed)
self.assertEqual(fluxList.shape[1], nBandpasses)
for ix, sedObj in enumerate(testSedList):
dummySed = Sed(wavelen=copy.deepcopy(sedObj.wavelen),
flambda=copy.deepcopy(sedObj.flambda))
for iy, bp in enumerate(testBpDict):
flux = dummySed.calcFlux(bpList[iy])
self.assertAlmostEqual(flux/fluxList[ix][iy], 1.0, 2)
def testMagArrayForSedList(self):
"""
Test that magArrayForSedList calculates the correct magnitude
"""
nBandpasses = 7
bpNameList, bpList = self.getListOfBandpasses(nBandpasses)
testBpDict = BandpassDict(bpList, bpNameList)
nSed = 20
sedNameList = self.getListOfSedNames(nSed)
magNormList = self.rng.random_sample(nSed)*5.0 + 15.0
internalAvList = self.rng.random_sample(nSed)*0.3 + 0.1
redshiftList = self.rng.random_sample(nSed)*5.0
galacticAvList = self.rng.random_sample(nSed)*0.3 + 0.1
# first, test on an SedList without a wavelenMatch
testSedList = SedList(sedNameList, magNormList,
fileDir=self.sedDir,
internalAvList=internalAvList,
redshiftList=redshiftList,
galacticAvList=galacticAvList)
magArray = testBpDict.magArrayForSedList(testSedList)
for ix, sedObj in enumerate(testSedList):
dummySed = Sed(wavelen=copy.deepcopy(sedObj.wavelen),
flambda=copy.deepcopy(sedObj.flambda))
for iy, bp in enumerate(bpNameList):
mag = dummySed.calcMag(bpList[iy])
self.assertAlmostEqual(mag, magArray[bp][ix], 2)
# now use wavelenMatch
testSedList = SedList(sedNameList, magNormList,
fileDir=self.sedDir,
internalAvList=internalAvList,
redshiftList=redshiftList,
galacticAvList=galacticAvList,
wavelenMatch=testBpDict.wavelenMatch)
magArray = testBpDict.magArrayForSedList(testSedList)
for ix, sedObj in enumerate(testSedList):
dummySed = Sed(wavelen=copy.deepcopy(sedObj.wavelen),
flambda=copy.deepcopy(sedObj.flambda))
for iy, bp in enumerate(bpNameList):
mag = dummySed.calcMag(bpList[iy])
self.assertAlmostEqual(mag, magArray[bp][ix], 2)
def _create_sed_library_mags(wav_min, wav_width):
"""
Calculate the magnitudes of the SEDs in sims_sed_library dir in the
tophat filters specified by wav_min, wav_width
Parameters
----------
wav_min is a numpy array of the minimum wavelengths of the tophat
filters (in nm)
wav_width is a numpy array of the widths of the tophat filters (in nm)
Returns
-------
sed_names is an array containing the names of the SED files
sed_mag_list is MxN float array, with M = number of SED files in the library,
and N = number of top hat filters in the catalog
sed_mag_norm is 1d float array, with length = number of SED files in the library
"""
wav_max = max((wav0 + width for wav0, width in zip(wav_min, wav_width)))
wav_grid = np.arange(wav_min.min(), wav_max, 0.1)
bp_name_list = list()
bp_list = list()
for wav0, width in zip(wav_min, wav_width):
sb_grid = ((wav_grid >= wav0) & (wav_grid <=
(wav0 + width))).astype(float)
bp_list.append(Bandpass(wavelen=wav_grid, sb=sb_grid))
bp_name_list.append('%d_%d' % (wav0, width))
bandpass_dict = BandpassDict(bp_list, bp_name_list)
sed_names = list()
sed_mag_list = list()
sed_mag_norm = list()
imsim_bp = Bandpass()
imsim_bp.imsimBandpass()
for sed_file_name in os.listdir(_galaxy_sed_dir):
spec = Sed()
spec.readSED_flambda(os.path.join(_galaxy_sed_dir, sed_file_name))
sed_names.append(defaultSpecMap[sed_file_name])
sed_mag_list.append(tuple(bandpass_dict.magListForSed(spec)))
sed_mag_norm.append(spec.calcMag(imsim_bp))
return np.array(sed_names), np.array(sed_mag_list), np.array(sed_mag_norm)
def setUp(self):
"""
setup before tests
"""
throughputsDir = getPackageDir('throughputs')
self.approxBandPassDir = os.path.join(throughputsDir,
'approximate_baseline')
self.refBandPassDir = os.path.join(throughputsDir, 'baseline')
self.refBandPassDict = BandpassDict.loadTotalBandpassesFromFiles()
self.approxBandPassDict = \
BandpassDict.loadTotalBandpassesFromFiles(bandpassDir=self.approxBandPassDir)
self.errorMsg = "The failure of this test indicates that the"
" approximate bandpasses in the lsst throughputs directory do not"
"sync up with the baseline bandpasses is throughputs. This may require running"
" the script : throughputs.approximate_baseline/approximateBandpasses.py"
def testLoadTotalBandpassesFromFiles(self):
"""
Test that the class method loadTotalBandpassesFromFiles produces the
expected result
"""
bandpassDir = os.path.join(getPackageDir('sims_photUtils'), 'tests', 'cartoonSedTestData')
bandpassNames = ['g', 'r', 'u']
bandpassRoot = 'test_bandpass_'
bandpassDict = BandpassDict.loadTotalBandpassesFromFiles(bandpassNames=bandpassNames,
bandpassDir=bandpassDir,
bandpassRoot = bandpassRoot)
controlBandpassList = []
for bpn in bandpassNames:
dummyBp = Bandpass()
dummyBp.readThroughput(os.path.join(bandpassDir,bandpassRoot+bpn+'.dat'))
controlBandpassList.append(dummyBp)
wMin = controlBandpassList[0].wavelen[0]
wMax = controlBandpassList[0].wavelen[-1]
wStep = controlBandpassList[0].wavelen[1]-controlBandpassList[0].wavelen[0]
for bp in controlBandpassList:
bp.resampleBandpass(wavelen_min=wMin, wavelen_max=wMax, wavelen_step=wStep)
for test, control in zip(bandpassDict.values(), controlBandpassList):
numpy.testing.assert_array_almost_equal(test.wavelen, control.wavelen, 19)
numpy.testing.assert_array_almost_equal(test.sb, control.sb, 19)
def calculate_mags(sed_name, mag_norm, out_dict):
"""
Parameters
----------
sed_name is a numpy array of SED names
mag_norm is a numpy array of magNorms
out_dict is a multiprocessing.Manager.dict() that will
store the magnitudes calculated by this process.
"""
i_process = mp.current_process().pid
bp_dir = getPackageDir('throughputs')
bp_dir = os.path.join(bp_dir, 'imsim', 'goal')
bp_dict = BandpassDict.loadTotalBandpassesFromFiles(bandpassDir=bp_dir)
sed_dir = getPackageDir('sims_sed_library')
out_mags = np.zeros((len(sed_name), 6), dtype=float)
for i_star, (s_name, m_norm) in enumerate(zip(sed_name, mag_norm)):
spec = Sed()
spec.readSED_flambda(os.path.join(sed_dir, defaultSpecMap[s_name]))
fnorm = getImsimFluxNorm(spec, m_norm)
spec.multiplyFluxNorm(fnorm)
mags = bp_dict.magListForSed(spec)
out_mags[i_star] = mags
out_dict[i_process] = out_mags
def fromThroughputs(cls):
"""
instantiate class from the LSST throughputs in the throughputs
directory
"""
totalbpdict, hwbpdict = BandpassDict.loadBandpassesFromFiles()
return cls(hwBandpassDict=hwbpdict)
def testLSSTmags(self):
"""
Test that PhotometrySSM properly calculates LSST magnitudes
"""
catName = os.path.join(getPackageDir('sims_catUtils'), 'tests',
'scratchSpace', 'lsstSsmPhotCat.txt')
cat = LSST_SSM_photCat(self.photDB)
cat.write_catalog(catName)
dtype = np.dtype([('id', np.int), ('u', np.float), ('g', np.float),
('r', np.float), ('i', np.float), ('z', np.float),
('y', np.float)])
testData = np.genfromtxt(catName, dtype=dtype, delimiter=',')
self.assertGreater(len(testData), 0)
controlData = np.genfromtxt(self.dbFile, dtype=self.dtype)
self.assertGreater(len(controlData), 0)
LSSTbandpasses = BandpassDict.loadTotalBandpassesFromFiles()
controlSedList = SedList(controlData['sedFilename'],
controlData['magNorm'],
wavelenMatch=LSSTbandpasses.wavelenMatch)
controlMags = LSSTbandpasses.magListForSedList(controlSedList)
for ii in range(len(controlMags)):
for jj, bpName in enumerate(['u', 'g', 'r', 'i', 'z', 'y']):
self.assertAlmostEqual(controlMags[ii][jj],
testData[bpName][ii], 10)
if os.path.exists(catName):
os.unlink(catName)
def testLoadTotalBandpassesFromFiles(self):
"""
Test that the class method loadTotalBandpassesFromFiles produces the
expected result
"""
bandpassDir = os.path.join(getPackageDir('sims_photUtils'), 'tests', 'cartoonSedTestData')
bandpassNames = ['g', 'r', 'u']
bandpassRoot = 'test_bandpass_'
bandpassDict = BandpassDict.loadTotalBandpassesFromFiles(bandpassNames=bandpassNames,
bandpassDir=bandpassDir,
bandpassRoot = bandpassRoot)
controlBandpassList = []
for bpn in bandpassNames:
dummyBp = Bandpass()
dummyBp.readThroughput(os.path.join(bandpassDir,bandpassRoot+bpn+'.dat'))
controlBandpassList.append(dummyBp)
wMin = controlBandpassList[0].wavelen[0]
wMax = controlBandpassList[0].wavelen[-1]
wStep = controlBandpassList[0].wavelen[1]-controlBandpassList[0].wavelen[0]
for bp in controlBandpassList:
bp.resampleBandpass(wavelen_min=wMin, wavelen_max=wMax, wavelen_step=wStep)
for test, control in zip(bandpassDict.values(), controlBandpassList):
numpy.testing.assert_array_almost_equal(test.wavelen, control.wavelen, 19)
numpy.testing.assert_array_almost_equal(test.sb, control.sb, 19)
def _find_objects_on_chip(self, object_lines, chip_name):
num_lines = len(object_lines)
ra_phosim = np.zeros(num_lines, dtype=float)
dec_phosim = np.zeros(num_lines, dtype=float)
mag_norm = 55. * np.ones(num_lines, dtype=float)
for i, line in enumerate(object_lines):
if not line.startswith('object'):
raise RuntimeError('Trying to process non-object entry from '
'the instance catalog.')
tokens = line.split()
ra_phosim[i] = float(tokens[2])
dec_phosim[i] = float(tokens[3])
mag_norm[i] = float(tokens[4])
ra_appGeo, dec_appGeo \
= PhoSimAstrometryBase._appGeoFromPhoSim(np.radians(ra_phosim),
np.radians(dec_phosim),
self.obs_md)
ra_obs_rad, dec_obs_rad \
= _observedFromAppGeo(ra_appGeo, dec_appGeo,
obs_metadata=self.obs_md,
includeRefraction=True)
x_pupil, y_pupil = _pupilCoordsFromObserved(ra_obs_rad, dec_obs_rad,
self.obs_md)
on_chip_dict = _chip_downselect(mag_norm, x_pupil, y_pupil,
self.logger, [chip_name])
index = on_chip_dict[chip_name]
self.object_lines = []
for i in index[0]:
self.object_lines.append(object_lines[i])
self.x_pupil = list(x_pupil[index])
self.y_pupil = list(y_pupil[index])
self.bp_dict = BandpassDict.loadTotalBandpassesFromFiles()
def get_quiescent_lsst_magnitudes(self):
if not hasattr(self, 'lsstBandpassDict'):
self.lsstBandpassDict = BandpassDict.loadTotalBandpassesFromFiles()
return self._quiescentMagnitudeGetter(self.lsstBandpassDict,
self.get_quiescent_lsst_magnitudes._colnames)
def get_quiescent_lsst_magnitudes(self):
if not hasattr(self, 'lsstBandpassDict'):
self.lsstBandpassDict = BandpassDict.loadTotalBandpassesFromFiles()
return self._quiescentMagnitudeGetter(self.lsstBandpassDict,
self.get_quiescent_lsst_magnitudes._colnames)
def _fluxes(sed_name, mag_norm, redshift):
"""
Find the fluxes for a galaxy component
Parameters
----------
sed_name is an SED file name
mag_norm is a float
redshift is a float
Returns
-------
array of fluxes in ugrizy order
"""
if not hasattr(_fluxes, '_bp_dict'):
bp_dir = getPackageDir('throughputs')
bp_dir = os.path.join(bp_dir, 'imsim', 'goal')
_fluxes._bp_dict = BandpassDict.loadTotalBandpassesFromFiles(
bandpassDir=bp_dir)
_fluxes._sed_dir = getPackageDir('sims_sed_library')
spec = Sed()
full_sed_name = os.path.join(_fluxes._sed_dir, sed_name)
if not os.path.isfile(full_sed_name):
full_sed_name = os.path.join(_fluxes._sed_dir,
defaultSpecMap[sed_name])
spec.readSED_flambda(full_sed_name)
fnorm = getImsimFluxNorm(spec, mag_norm)
spec.multiplyFluxNorm(fnorm)
spec.redshiftSED(redshift, dimming=True)
return _fluxes._bp_dict.fluxListForSed(spec)
def testLSSTmags(self):
"""
Test that PhotometrySSM properly calculates LSST magnitudes
"""
catName = os.path.join(getPackageDir('sims_catUtils'), 'tests', 'scratchSpace', 'lsstSsmPhotCat.txt')
cat=LSST_SSM_photCat(self.photDB)
cat.write_catalog(catName)
dtype = np.dtype([('id', np.int), ('u', np.float), ('g', np.float),
('r', np.float), ('i', np.float), ('z', np.float),
('y', np.float)])
testData = np.genfromtxt(catName, dtype=dtype, delimiter=',')
self.assertGreater(len(testData), 0)
controlData = np.genfromtxt(self.dbFile, dtype=self.dtype)
self.assertGreater(len(controlData), 0)
LSSTbandpasses = BandpassDict.loadTotalBandpassesFromFiles()
controlSedList = SedList(controlData['sedFilename'], controlData['magNorm'],
wavelenMatch=LSSTbandpasses.wavelenMatch)
controlMags = LSSTbandpasses.magListForSedList(controlSedList)
for ii in range(len(controlMags)):
for jj, bpName in enumerate(['u', 'g', 'r', 'i', 'z', 'y']):
self.assertAlmostEqual(controlMags[ii][jj], testData[bpName][ii], 10)
if os.path.exists(catName):
os.unlink(catName)
def testLSSTmags(self):
"""
Test that PhotometrySSM properly calculates LSST magnitudes
"""
cat = LSST_SSM_photCat(self.photDB)
dtype = np.dtype([('id', np.int), ('u', np.float), ('g', np.float),
('r', np.float), ('i', np.float), ('z', np.float),
('y', np.float)])
with lsst.utils.tests.getTempFilePath('.txt') as catName:
cat.write_catalog(catName)
testData = np.genfromtxt(catName, dtype=dtype, delimiter=',')
self.assertGreater(len(testData), 0)
controlData = np.genfromtxt(self.dbFile, dtype=self.dtype)
self.assertGreater(len(controlData), 0)
LSSTbandpasses = BandpassDict.loadTotalBandpassesFromFiles()
controlSedList = SedList(controlData['sedFilename'],
controlData['magNorm'],
wavelenMatch=LSSTbandpasses.wavelenMatch,
fileDir=getPackageDir('sims_sed_library'),
specMap=defaultSpecMap)
controlMags = LSSTbandpasses.magListForSedList(controlSedList)
for ii in range(len(controlMags)):
for jj, bpName in enumerate(['u', 'g', 'r', 'i', 'z', 'y']):
self.assertAlmostEqual(controlMags[ii][jj],
testData[bpName][ii], 10)
def get_test_disk_mags(self):
if not hasattr(self, 'testBandpassDict'):
self.testBandpassDict = BandpassDict.loadTotalBandpassesFromFiles()
return self._magnitudeGetter('disk', self.testBandpassDict,
self.get_test_disk_mags._colnames)
def testLSSTmags(self):
"""
Test that PhotometrySSM properly calculates LSST magnitudes
"""
cat = LSST_SSM_photCat(self.photDB)
dtype = np.dtype([('id', np.int), ('u', np.float), ('g', np.float),
('r', np.float), ('i', np.float), ('z', np.float),
('y', np.float)])
with lsst.utils.tests.getTempFilePath('.txt') as catName:
cat.write_catalog(catName)
testData = np.genfromtxt(catName, dtype=dtype, delimiter=',')
self.assertGreater(len(testData), 0)
controlData = np.genfromtxt(self.dbFile, dtype=self.dtype)
self.assertGreater(len(controlData), 0)
LSSTbandpasses = BandpassDict.loadTotalBandpassesFromFiles()
controlSedList = SedList(controlData['sedFilename'], controlData['magNorm'],
wavelenMatch=LSSTbandpasses.wavelenMatch,
fileDir=getPackageDir('sims_sed_library'),
specMap=defaultSpecMap)
controlMags = LSSTbandpasses.magListForSedList(controlSedList)
for ii in range(len(controlMags)):
for jj, bpName in enumerate(['u', 'g', 'r', 'i', 'z', 'y']):
self.assertAlmostEqual(controlMags[ii][jj], testData[bpName][ii], 10)
def get_lsst_magnitudes(self):
"""
getter for LSST magnitudes of solar system objects
"""
if not hasattr(self, 'lsstBandpassDict'):
self.lsstBandpassDict = BandpassDict.loadTotalBandpassesFromFiles()
return self._quiescentMagnitudeGetter(self.lsstBandpassDict, self.get_lsst_magnitudes._colnames)
def get_lsst_magnitudes(self):
"""
getter for LSST magnitudes of solar system objects
"""
if not hasattr(self, 'lsstBandpassDict'):
self.lsstBandpassDict = BandpassDict.loadTotalBandpassesFromFiles()
return self._quiescentMagnitudeGetter(self.lsstBandpassDict, self.get_lsst_magnitudes._colnames)
def testExceptions(self):
"""
Test that the correct exceptions are thrown by BandpassDict
"""
nameList, bpList = self.getListOfBandpasses(4)
dummyNameList = copy.deepcopy(nameList)
dummyNameList[1] = dummyNameList[0]
with self.assertRaises(RuntimeError) as context:
testDict = BandpassDict(bpList, dummyNameList)
self.assertTrue('occurs twice' in context.exception.message)
testDict = BandpassDict(bpList, nameList)
with self.assertRaises(AttributeError) as context:
testDict.phiArray = None
with self.assertRaises(AttributeError) as context:
testDict.wavelenStep = 0.9
with self.assertRaises(AttributeError) as context:
testDict.wavelenMatch = numpy.arange(10.0,100.0,1.0)
def get_test_agn_mags(self):
if not hasattr(self, 'testBandpassDict'):
self.testBandpassDict = BandpassDict.loadTotalBandpassesFromFiles()
mag = self._quiescentMagnitudeGetter('agn', self.testBandpassDict,
self.get_test_agn_mags._colnames)
mag += self._variabilityGetter(self.get_test_agn_mags._colnames)
return mag
def testLoadBandpassesFromFiles(self):
"""
Test that running the classmethod loadBandpassesFromFiles produces
expected result
"""
fileDir = os.path.join(getPackageDir('sims_photUtils'),
'tests', 'cartoonSedTestData')
bandpassNames = ['g', 'z', 'i']
bandpassRoot = 'test_bandpass_'
componentList = ['toy_mirror.dat']
atmo = os.path.join(fileDir, 'toy_atmo.dat')
bandpassDict, hardwareDict = BandpassDict.loadBandpassesFromFiles(bandpassNames=bandpassNames,
filedir=fileDir,
bandpassRoot=bandpassRoot,
componentList=componentList,
atmoTransmission=atmo)
controlBandpassList = []
controlHardwareList = []
for bpn in bandpassNames:
componentList = [os.path.join(fileDir, bandpassRoot+bpn+'.dat'),
os.path.join(fileDir, 'toy_mirror.dat')]
dummyBp = Bandpass()
dummyBp.readThroughputList(componentList)
controlHardwareList.append(dummyBp)
componentList = [os.path.join(fileDir, bandpassRoot+bpn+'.dat'),
os.path.join(fileDir, 'toy_mirror.dat'),
os.path.join(fileDir, 'toy_atmo.dat')]
dummyBp = Bandpass()
dummyBp.readThroughputList(componentList)
controlBandpassList.append(dummyBp)
wMin = controlBandpassList[0].wavelen[0]
wMax = controlBandpassList[0].wavelen[-1]
wStep = controlBandpassList[0].wavelen[1]-controlBandpassList[0].wavelen[0]
for bp, hh in zip(controlBandpassList, controlHardwareList):
bp.resampleBandpass(wavelen_min=wMin, wavelen_max=wMax,
wavelen_step=wStep)
hh.resampleBandpass(wavelen_min=wMin, wavelen_max=wMax,
wavelen_step=wStep)
for test, control in zip(bandpassDict.values(), controlBandpassList):
np.testing.assert_array_almost_equal(test.wavelen,
control.wavelen, 19)
np.testing.assert_array_almost_equal(test.sb, control.sb, 19)
for test, control in zip(hardwareDict.values(), controlHardwareList):
np.testing.assert_array_almost_equal(test.wavelen,
control.wavelen, 19)
np.testing.assert_array_almost_equal(test.sb, control.sb, 19)
def get_test_agn_mags(self):
if not hasattr(self, 'testBandpassDict'):
self.testBandpassDict = BandpassDict.loadTotalBandpassesFromFiles()
mag = self._quiescentMagnitudeGetter('agn', self.testBandpassDict,
self.get_test_agn_mags._colnames)
mag += self._variabilityGetter(self.get_test_agn_mags._colnames)
return mag
def get_test_mags(self):
if not hasattr(self, 'variabilitybandpassDict'):
self.variabilityBandpassDict = BandpassDict.loadTotalBandpassesFromFiles()
self._loadSedList(self.variabilityBandpassDict.wavelenMatch)
if not hasattr(self, '_sedList'):
return numpy.ones((6,0))
return self._magnitudeGetter(self.variabilityBandpassDict, self.get_test_mags._colnames)
def testManyMagSystems(self):
"""
Test that the SSM photometry mixin can simultaneously calculate magnitudes
in multiple bandpass systems
"""
catName = os.path.join(getPackageDir('sims_catUtils'), 'tests', 'scratchSpace', 'compoundSsmPhotCat.txt')
cat=Compound_SSM_photCat(self.photDB)
cat.write_catalog(catName)
dtype = np.dtype([('id', np.int), ('lsst_u', np.float), ('lsst_g', np.float),
('lsst_r', np.float), ('lsst_i', np.float), ('lsst_z', np.float),
('lsst_y', np.float),
('cartoon_u', np.float), ('cartoon_g', np.float),
('cartoon_r', np.float), ('cartoon_i', np.float),
('cartoon_z', np.float)])
testData = np.genfromtxt(catName, dtype=dtype, delimiter=',')
self.assertGreater(len(testData), 0)
controlData = np.genfromtxt(self.dbFile, dtype=self.dtype)
self.assertGreater(len(controlData), 0)
LSSTbandpasses = BandpassDict.loadTotalBandpassesFromFiles()
cartoonBandpasses = BandpassDict.loadTotalBandpassesFromFiles(
['u', 'g', 'r', 'i', 'z'],
bandpassDir = os.path.join(getPackageDir('sims_photUtils'), 'tests', 'cartoonSedTestData'),
bandpassRoot = 'test_bandpass_'
)
controlSedList = SedList(controlData['sedFilename'], controlData['magNorm'],
wavelenMatch=LSSTbandpasses.wavelenMatch)
controlLsstMags = LSSTbandpasses.magListForSedList(controlSedList)
controlCartoonMags = cartoonBandpasses.magListForSedList(controlSedList)
for ii in range(len(controlLsstMags)):
for jj, bpName in enumerate(['lsst_u', 'lsst_g', 'lsst_r', 'lsst_i', 'lsst_z', 'lsst_y']):
self.assertAlmostEqual(controlLsstMags[ii][jj], testData[bpName][ii], 10)
for jj, bpName in enumerate(['cartoon_u', 'cartoon_g', 'cartoon_r', 'cartoon_i', 'cartoon_z']):
self.assertAlmostEqual(controlCartoonMags[ii][jj], testData[bpName][ii], 10)
if os.path.exists(catName):
os.unlink(catName)
def fromTwinklesData(cls,
tableName,
objectTypeID=42,
dbHostName=None,
idCol='snid',
columns=('snid', 'redshift', 'snra', 'sndec', 't0',
'x0', 'x1', 'c'),
idSequence=None):
"""
Simplified classmethod to construct this class from the Twinkles Run 1
perspective.
Parameters
----------
tableName : string, mandatory
case insensitive string name of table on database to connect to
for model parameters of astrophysical objects
idCol : string, optional, defaults to 'snid'
column name of Index on the table
columns : tuple of strings, optional, defaults to values for SN
tuple of strings that completely specify the truth values for
idSequence : sequence of one dimension, optional, defaults to None
sequence of unique ids in the catsim universe indexing the
astrophysical objects in the database.
dbHostName : string, optional, defaults to None
force the class to use this hostname. If not provided, the class
will set this to localhost, which is the desired hostname when
using an ssh tunnel. This parameter is useful when working from
whitelisted computers.
Returns
------
An instance of the class RefLightCurve class where the other parameters
have been defaulted to sensible values for Twinkles Run1 Analysis.
Examples
--------
"""
data_dir = os.path.join(os.environ['MONITOR_DIR'], 'data')
opsimCsv = os.path.join(data_dir, 'SelectedKrakenVisits.csv')
opsimdf = pd.read_csv(opsimCsv, index_col='obsHistID')
observations = opsimdf[['expMJD', 'filter', 'fiveSigmaDepth']].copy()
del opsimdf
# Obtain the tuple of total, HardWare bandPassDict and keep the total
lsstBP = BandpassDict.loadBandpassesFromFiles()[0]
cls = RefLightCurves(tableName=tableName,
objectTypeID=objectTypeID,
idCol=idCol,
dbHostName=dbHostName,
columns=columns,
observations=observations,
bandPassDict=lsstBP,
idSequence=idSequence)
return cls
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 testMagListForSed(self):
"""
Test that magListForSed calculates the correct magnitude
"""
wavelen = numpy.arange(10.0,2000.0,1.0)
flux = (wavelen*2.0-5.0)*1.0e-6
spectrum = Sed(wavelen=wavelen, flambda=flux)
for nBp in range(3, 10, 1):
nameList, bpList = self.getListOfBandpasses(nBp)
testDict = BandpassDict(bpList, nameList)
self.assertFalse(len(testDict.values()[0].wavelen)==len(spectrum.wavelen))
magList = testDict.magListForSed(spectrum)
for ix, (name, bp, magTest) in enumerate(zip(nameList, bpList, magList)):
magControl = spectrum.calcMag(bp)
self.assertAlmostEqual(magTest, magControl, 5)
def testFluxDictForSed(self):
"""
Test that fluxDictForSed calculates the correct fluxes
"""
wavelen = numpy.arange(10.0,2000.0,1.0)
flux = (wavelen*2.0-5.0)*1.0e-6
spectrum = Sed(wavelen=wavelen, flambda=flux)
for nBp in range(3, 10, 1):
nameList, bpList = self.getListOfBandpasses(nBp)
testDict = BandpassDict(bpList, nameList)
self.assertFalse(len(testDict.values()[0].wavelen)==len(spectrum.wavelen))
fluxDict = testDict.fluxDictForSed(spectrum)
for ix, (name, bp) in enumerate(zip(nameList, bpList)):
fluxControl = spectrum.calcFlux(bp)
self.assertAlmostEqual(fluxDict[name]/fluxControl, 1.0, 2)
def testMagListForSed(self):
"""
Test that magListForSed calculates the correct magnitude
"""
wavelen = numpy.arange(10.0,2000.0,1.0)
flux = (wavelen*2.0-5.0)*1.0e-6
spectrum = Sed(wavelen=wavelen, flambda=flux)
for nBp in range(3, 10, 1):
nameList, bpList = self.getListOfBandpasses(nBp)
testDict = BandpassDict(bpList, nameList)
self.assertFalse(len(testDict.values()[0].wavelen)==len(spectrum.wavelen))
magList = testDict.magListForSed(spectrum)
for ix, (name, bp, magTest) in enumerate(zip(nameList, bpList, magList)):
magControl = spectrum.calcMag(bp)
self.assertAlmostEqual(magTest, magControl, 5)
def testFluxDictForSed(self):
"""
Test that fluxDictForSed calculates the correct fluxes
"""
wavelen = numpy.arange(10.0,2000.0,1.0)
flux = (wavelen*2.0-5.0)*1.0e-6
spectrum = Sed(wavelen=wavelen, flambda=flux)
for nBp in range(3, 10, 1):
nameList, bpList = self.getListOfBandpasses(nBp)
testDict = BandpassDict(bpList, nameList)
self.assertFalse(len(testDict.values()[0].wavelen)==len(spectrum.wavelen))
fluxDict = testDict.fluxDictForSed(spectrum)
for ix, (name, bp) in enumerate(zip(nameList, bpList)):
fluxControl = spectrum.calcFlux(bp)
self.assertAlmostEqual(fluxDict[name]/fluxControl, 1.0, 2)
def _parallel_fitting(mag_array, redshift, redshift_true, H0, Om0, wav_min,
wav_width, lsst_mag_array, out_dict, tag):
pid = os.getpid()
(sed_names, mag_norms, av_arr,
rv_arr) = sed_from_galacticus_mags(mag_array, redshift, redshift_true, H0,
Om0, wav_min, wav_width,
lsst_mag_array)
tot_bp_dict = BandpassDict.loadTotalBandpassesFromFiles()
sed_dir = getPackageDir('sims_sed_library')
lsst_fit_fluxes = np.zeros((6, len(sed_names)), dtype=float)
t_start = time.time()
ccm_w = None
restframe_seds = {}
imsim_bp = Bandpass()
imsim_bp.imsimBandpass()
n04_ln10 = -0.4 * np.log(10)
for ii in range(len(sed_names)):
av_val = av_arr[ii]
rv_val = rv_arr[ii]
sed_tag = '%s_%.3f_%.3f' % (sed_names[ii], av_val, rv_val)
if sed_tag not in restframe_seds:
rest_sed = Sed()
rest_sed.readSED_flambda(os.path.join(sed_dir, sed_names[ii]))
mag = rest_sed.calcMag(imsim_bp)
if ccm_w is None or not np.array_equal(rest_sed.wavelen, ccm_w):
ccm_w = np.copy(rest_sed.wavelen)
ax, bx = rest_sed.setupCCM_ab()
rest_sed.addDust(ax, bx, A_v=av_val, R_v=rv_val)
restframe_seds[sed_tag] = (rest_sed, mag)
for i_bp, bp in enumerate('ugrizy'):
m_norm = mag_norms[i_bp][ii]
if m_norm > 0.0 and not np.isfinite(m_norm):
continue
spec = Sed(wavelen=restframe_seds[sed_tag][0].wavelen,
flambda=restframe_seds[sed_tag][0].flambda)
fnorm = np.exp(n04_ln10 * (m_norm - restframe_seds[sed_tag][1]))
try:
assert np.isfinite(fnorm)
assert fnorm > 0.0
except AssertionError:
print('\n\nmagnorm %e\n\n' % (m_norm))
raise
spec.multiplyFluxNorm(fnorm)
spec.redshiftSED(redshift[ii], dimming=True)
ff = spec.calcFlux(tot_bp_dict[bp])
lsst_fit_fluxes[i_bp][ii] = ff
out_dict[tag] = (sed_names, mag_norms, av_arr, rv_arr, lsst_fit_fluxes)
def testSignalToNoise(self):
"""
Test that calcSNR_m5 and calcSNR_sed give similar results
"""
defaults = LSSTdefaults()
photParams = PhotometricParameters()
totalDict, hardwareDict = BandpassDict.loadBandpassesFromFiles()
skySED = Sed()
skySED.readSED_flambda(
os.path.join(lsst.utils.getPackageDir('throughputs'), 'baseline',
'darksky.dat'))
m5 = []
for filt in totalDict:
m5.append(
calcM5(skySED,
totalDict[filt],
hardwareDict[filt],
photParams,
seeing=defaults.seeing(filt)))
sedDir = lsst.utils.getPackageDir('sims_sed_library')
sedDir = os.path.join(sedDir, 'starSED', 'kurucz')
fileNameList = os.listdir(sedDir)
numpy.random.seed(42)
offset = numpy.random.random_sample(len(fileNameList)) * 2.0
for ix, name in enumerate(fileNameList):
if ix > 100:
break
spectrum = Sed()
spectrum.readSED_flambda(os.path.join(sedDir, name))
ff = spectrum.calcFluxNorm(m5[2] - offset[ix],
totalDict.values()[2])
spectrum.multiplyFluxNorm(ff)
magList = []
controlList = []
magList = []
for filt in totalDict:
controlList.append(
calcSNR_sed(spectrum, totalDict[filt], skySED,
hardwareDict[filt], photParams,
defaults.seeing(filt)))
magList.append(spectrum.calcMag(totalDict[filt]))
testList, gammaList = calcSNR_m5(numpy.array(magList),
numpy.array(totalDict.values()),
numpy.array(m5), photParams)
for tt, cc in zip(controlList, testList):
msg = '%e != %e ' % (tt, cc)
self.assertTrue(numpy.abs(tt / cc - 1.0) < 0.001, msg=msg)
def _make_gs_interpreters(self, seed, sensor_list, file_id):
"""
Create a separate GalSimInterpreter for each sensor so that
they can be run in parallel and maintain separate checkpoint
files.
Also extract GsObjectLists from gs_obj_dict for only the
sensors in sensor_list so that the memory in the underlying
InstCatTrimmer object in gs_obj_dict can be recovered.
"""
bp_dict = BandpassDict.loadTotalBandpassesFromFiles(bandpassNames=self.obs_md.bandpass)
disable_sky_model = self.config['sky_model']['disable_sky_model']
noise_and_background \
= make_sky_model(self.obs_md, self.phot_params, seed=seed,
apply_sensor_model=self.apply_sensor_model,
disable_sky_model=disable_sky_model)
self.gs_interpreters = dict()
for det in self.camera_wrapper.camera:
det_type = det.getType()
det_name = det.getName()
if sensor_list is not None and det_name not in sensor_list:
continue
if det_type in (DetectorType.WAVEFRONT, DetectorType.GUIDER):
continue
gs_det = make_galsim_detector(self.camera_wrapper, det_name,
self.phot_params, self.obs_md)
self.gs_interpreters[det_name] \
= make_gs_interpreter(self.obs_md, [gs_det], bp_dict,
noise_and_background,
epoch=2000.0, seed=seed,
apply_sensor_model=self.apply_sensor_model,
bf_strength=self.config['ccd']['bf_strength'])
self.gs_interpreters[det_name].sky_bg_per_pixel \
= noise_and_background.sky_counts(det_name)
self.gs_interpreters[det_name].setPSF(PSF=self.psf)
if self.apply_sensor_model:
add_treering_info(self.gs_interpreters[det_name].detectors)
if file_id is not None:
self.gs_interpreters[det_name].checkpoint_file \
= self.checkpoint_file(file_id, det_name)
self.gs_interpreters[det_name].nobj_checkpoint \
= self.config['checkpointing']['nobj']
self.gs_interpreters[det_name]\
.restore_checkpoint(self.camera_wrapper,
self.phot_params,
self.obs_md)
if self.create_centroid_file:
self.gs_interpreters[det_name].centroid_base_name = \
os.path.join(self.outdir,
self.config['persistence']['centroid_prefix'])
def __init__(self, population, model, pointings, rng, maxObsHistID,
pointingColumnDict, pruneWithRadius):
self.model = model
self.population = population
self._pointings = pointings
self._rng = rng
self.maxObsHistID = maxObsHistID
self.pointingColumnDict = pointingColumnDict
self.pruneWithRadius = pruneWithRadius
self.bandPasses = BandpassDict.loadTotalBandpassesFromFiles()
def get_magnitudes(self):
"""
Example photometry getter for alternative (i.e. non-LSST) bandpasses
"""
if not hasattr(self, 'cartoonBandpassDict'):
bandpassNames = ['u','g','r','i','z']
bandpassDir = os.path.join(getPackageDir('sims_photUtils'), 'tests', 'cartoonSedTestData')
self.cartoonBandpassDict = BandpassDict.loadTotalBandpassesFromFiles(bandpassNames,bandpassDir = bandpassDir,
bandpassRoot = 'test_bandpass_')
return self._quiescentMagnitudeGetter(self.cartoonBandpassDict, self.get_magnitudes._colnames)
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 get_cartoon_mags(self):
if not hasattr(self, 'cartoonBandpassDict'):
bandpassDir = os.path.join(getPackageDir('sims_photUtils'), 'tests', 'cartoonSedTestData')
self.cartoonBandpassDict = \
BandpassDict.loadTotalBandpassesFromFiles(bandpassNames = ['u', 'g', 'r', 'i', 'z'],
bandpassDir = bandpassDir,
bandpassRoot = 'test_bandpass_')
return self._quiescentMagnitudeGetter(self.cartoonBandpassDict, self.get_cartoon_mags._colnames)
def get_cartoon_mags(self):
if not hasattr(self, 'cartoonBandpassDict'):
bandpassDir = os.path.join(getPackageDir('sims_photUtils'), 'tests', 'cartoonSedTestData')
self.cartoonBandpassDict = \
BandpassDict.loadTotalBandpassesFromFiles(bandpassNames = ['u', 'g', 'r', 'i', 'z'],
bandpassDir = bandpassDir,
bandpassRoot = 'test_bandpass_')
return self._quiescentMagnitudeGetter(self.cartoonBandpassDict, self.get_cartoon_mags._colnames)
def __init__(self, idSequence, opsim_csv=None, db_config=None):
if opsim_csv is None:
opsim_csv = os.path.join(lsst.utils.getPackageDir('monitor'),
'data', 'SelectedKrakenVisits.csv')
df = pd.read_csv(opsim_csv, index_col='obsHistID')
opsim_df = df[['expMJD', 'filter', 'fiveSigmaDepth']]
lsstBP = BandpassDict.loadBandpassesFromFiles()[0]
self.reflc = RefLightCurves(idSequence=idSequence,
tableName='TwinkSN',
bandPassDict=lsstBP,
observations=opsim_df)
def setUpClass(cls):
cls.scratchDir = os.path.join(getPackageDir('sims_GalSimInterface'), 'tests', 'scratchSpace')
cls.obs = ObservationMetaData(pointingRA=122.0, pointingDec=-29.1,
mjd=57381.2, rotSkyPos=43.2)
cls.camera = camTestUtils.CameraWrapper().camera
cls.dbFileName = os.path.join(cls.scratchDir, 'allowed_chips_test_db.txt')
if os.path.exists(cls.dbFileName):
os.unlink(cls.dbFileName)
cls.controlSed = Sed()
cls.controlSed.readSED_flambda(os.path.join(getPackageDir('sims_sed_library'),
'flatSED','sed_flat.txt.gz'))
cls.magNorm = 18.1
imsim = Bandpass()
imsim.imsimBandpass()
ff = cls.controlSed.calcFluxNorm(cls.magNorm, imsim)
cls.controlSed.multiplyFluxNorm(ff)
a_x, b_x = cls.controlSed.setupCCMab()
cls.controlSed.addCCMDust(a_x, b_x, A_v=0.1, R_v=3.1)
bpd = BandpassDict.loadTotalBandpassesFromFiles()
pp = PhotometricParameters()
cls.controlADU = cls.controlSed.calcADU(bpd['u'], pp)
cls.countSigma = np.sqrt(cls.controlADU/pp.gain)
cls.x_pix = 50
cls.y_pix = 50
x_list = []
y_list = []
name_list = []
for dd in cls.camera:
x_list.append(cls.x_pix)
y_list.append(cls.y_pix)
name_list.append(dd.getName())
x_list = np.array(x_list)
y_list = np.array(y_list)
ra_list, dec_list = raDecFromPixelCoords(x_list, y_list, name_list,
camera=cls.camera, obs_metadata=cls.obs,
epoch=2000.0)
dra_list = 3600.0*(ra_list-cls.obs.pointingRA)
ddec_list = 3600.0*(dec_list-cls.obs.pointingDec)
create_text_catalog(cls.obs, cls.dbFileName, dra_list, ddec_list,
mag_norm=[cls.magNorm]*len(dra_list))
cls.db = allowedChipsFileDBObj(cls.dbFileName, runtable='test')
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 setUpClass(cls):
cls.scratchDir = tempfile.mkdtemp(dir=ROOT, prefix='allowedChipsTest-')
cls.obs = ObservationMetaData(pointingRA=122.0, pointingDec=-29.1,
mjd=57381.2, rotSkyPos=43.2,
bandpassName='r')
cls.camera = camTestUtils.CameraWrapper().camera
cls.dbFileName = os.path.join(cls.scratchDir, 'allowed_chips_test_db.txt')
if os.path.exists(cls.dbFileName):
os.unlink(cls.dbFileName)
cls.controlSed = Sed()
cls.controlSed.readSED_flambda(os.path.join(getPackageDir('sims_sed_library'),
'flatSED', 'sed_flat.txt.gz'))
cls.magNorm = 18.1
imsim = Bandpass()
imsim.imsimBandpass()
ff = cls.controlSed.calcFluxNorm(cls.magNorm, imsim)
cls.controlSed.multiplyFluxNorm(ff)
a_x, b_x = cls.controlSed.setupCCMab()
cls.controlSed.addCCMDust(a_x, b_x, A_v=0.1, R_v=3.1)
bpd = BandpassDict.loadTotalBandpassesFromFiles()
pp = PhotometricParameters()
cls.controlADU = cls.controlSed.calcADU(bpd['u'], pp)
cls.countSigma = np.sqrt(cls.controlADU/pp.gain)
cls.x_pix = 50
cls.y_pix = 50
x_list = []
y_list = []
name_list = []
for dd in cls.camera:
x_list.append(cls.x_pix)
y_list.append(cls.y_pix)
name_list.append(dd.getName())
x_list = np.array(x_list)
y_list = np.array(y_list)
ra_list, dec_list = raDecFromPixelCoords(x_list, y_list, name_list,
camera=cls.camera, obs_metadata=cls.obs,
epoch=2000.0)
dra_list = 3600.0*(ra_list-cls.obs.pointingRA)
ddec_list = 3600.0*(dec_list-cls.obs.pointingDec)
create_text_catalog(cls.obs, cls.dbFileName, dra_list, ddec_list,
mag_norm=[cls.magNorm]*len(dra_list))
cls.db = allowedChipsFileDBObj(cls.dbFileName, runtable='test')
def testPhiArray(self):
"""
Test that the phi array is correctly calculated by BandpassDict
upon construction.
"""
for nBp in range(3, 10, 1):
nameList, bpList = self.getListOfBandpasses(nBp)
testDict = BandpassDict(bpList, nameList)
dummySed = Sed()
controlPhi, controlWavelenStep = dummySed.setupPhiArray(bpList)
numpy.testing.assert_array_almost_equal(controlPhi, testDict.phiArray, 19)
self.assertAlmostEqual(controlWavelenStep, testDict.wavelenStep, 10)
def testUncertaintyExceptions(self):
"""
Test that calcSNR_m5 raises exceptions when it needs to
"""
totalDict, hardwareDict = BandpassDict.loadBandpassesFromFiles()
magnitudes = numpy.array([22.0, 23.0, 24.0, 25.0, 26.0, 27.0])
shortMagnitudes = numpy.array([22.0])
photParams = PhotometricParameters()
shortGamma = numpy.array([1.0, 1.0])
self.assertRaises(RuntimeError, calcSNR_m5, magnitudes, totalDict.values(), shortMagnitudes, photParams)
self.assertRaises(RuntimeError, calcSNR_m5, shortMagnitudes, totalDict.values(), magnitudes, photParams)
self.assertRaises(
RuntimeError, calcSNR_m5, magnitudes, totalDict.values(), magnitudes, photParams, gamma=shortGamma
)
snr, gg = calcSNR_m5(magnitudes, totalDict.values(), magnitudes, photParams)
def get_lsst_agn_mags(self):
"""
Getter for AGN magnitudes in the LSST bandpasses
"""
# load a BandpassDict of LSST bandpasses, if not done already
if not hasattr(self, 'lsstBandpassDict'):
self.lsstBandpassDict = BandpassDict.loadTotalBandpassesFromFiles()
# actually calculate the magnitudes
mag = self._quiescentMagnitudeGetter('agn', self.lsstBandpassDict,
self.get_lsst_agn_mags._colnames)
mag += self._variabilityGetter(self.get_lsst_agn_mags._colnames)
return mag
def testSignalToNoise(self):
"""
Test that calcSNR_m5 and calcSNR_sed give similar results
"""
defaults = LSSTdefaults()
photParams = PhotometricParameters()
totalDict, hardwareDict = BandpassDict.loadBandpassesFromFiles()
skySED = Sed()
skySED.readSED_flambda(os.path.join(lsst.utils.getPackageDir("throughputs"), "baseline", "darksky.dat"))
m5 = []
for filt in totalDict:
m5.append(calcM5(skySED, totalDict[filt], hardwareDict[filt], photParams, seeing=defaults.seeing(filt)))
sedDir = lsst.utils.getPackageDir("sims_sed_library")
sedDir = os.path.join(sedDir, "starSED", "kurucz")
fileNameList = os.listdir(sedDir)
numpy.random.seed(42)
offset = numpy.random.random_sample(len(fileNameList)) * 2.0
for ix, name in enumerate(fileNameList):
if ix > 100:
break
spectrum = Sed()
spectrum.readSED_flambda(os.path.join(sedDir, name))
ff = spectrum.calcFluxNorm(m5[2] - offset[ix], totalDict.values()[2])
spectrum.multiplyFluxNorm(ff)
magList = []
controlList = []
magList = []
for filt in totalDict:
controlList.append(
calcSNR_sed(
spectrum, totalDict[filt], skySED, hardwareDict[filt], photParams, defaults.seeing(filt)
)
)
magList.append(spectrum.calcMag(totalDict[filt]))
testList, gammaList = calcSNR_m5(
numpy.array(magList), numpy.array(totalDict.values()), numpy.array(m5), photParams
)
for tt, cc in zip(controlList, testList):
msg = "%e != %e " % (tt, cc)
self.assertTrue(numpy.abs(tt / cc - 1.0) < 0.001, msg=msg)
def testSystematicUncertainty(self):
"""
Test that systematic uncertainty is added correctly.
"""
sigmaSys = 0.002
m5 = [23.5, 24.3, 22.1, 20.0, 19.5, 21.7]
photParams = PhotometricParameters(sigmaSys=sigmaSys)
bandpassDict = BandpassDict.loadTotalBandpassesFromFiles()
obs_metadata = ObservationMetaData(unrefractedRA=23.0, unrefractedDec=45.0, m5=m5, bandpassName=self.bandpasses)
magnitudes = bandpassDict.magListForSed(self.starSED)
skySeds = []
for i in range(len(self.bandpasses)):
skyDummy = Sed()
skyDummy.readSED_flambda(os.path.join(lsst.utils.getPackageDir("throughputs"), "baseline", "darksky.dat"))
normalizedSkyDummy = setM5(
obs_metadata.m5[self.bandpasses[i]],
skyDummy,
self.totalBandpasses[i],
self.hardwareBandpasses[i],
seeing=LSSTdefaults().seeing(self.bandpasses[i]),
photParams=PhotometricParameters(),
)
skySeds.append(normalizedSkyDummy)
for i in range(len(self.bandpasses)):
snr = calcSNR_sed(
self.starSED,
self.totalBandpasses[i],
skySeds[i],
self.hardwareBandpasses[i],
seeing=LSSTdefaults().seeing(self.bandpasses[i]),
photParams=PhotometricParameters(),
)
testSNR, gamma = calcSNR_m5(
numpy.array([magnitudes[i]]),
[self.totalBandpasses[i]],
numpy.array([m5[i]]),
photParams=PhotometricParameters(sigmaSys=0.0),
)
self.assertAlmostEqual(snr, testSNR[0], 10, msg="failed on calcSNR_m5 test %e != %e " % (snr, testSNR[0]))
control = numpy.sqrt(numpy.power(magErrorFromSNR(testSNR), 2) + numpy.power(sigmaSys, 2))
def get_magnitudes(self):
"""
Example photometry getter for alternative (i.e. non-LSST) bandpasses
"""
idNames = self.column_by_name('id')
columnNames = [name for name in self.get_magnitudes._colnames]
bandpassNames = ['u','g','r','i','z']
bandpassDir = os.path.join(getPackageDir('sims_photUtils'), 'tests', 'cartoonSedTestData')
if not hasattr(self, 'cartoonBandpassDict'):
self.cartoonBandpassDict = BandpassDict.loadTotalBandpassesFromFiles(bandpassNames,bandpassDir = bandpassDir,
bandpassRoot = 'test_bandpass_')
output = self._quiescentMagnitudeGetter(self.cartoonBandpassDict, self.get_magnitudes._colnames)
#############################################################################
#Everything below this comment exists solely for the purposes of the unit test
#if you need to write a customized getter for photometry that uses non-LSST
#bandpasses, you only need to emulate the code above this comment.
magNormList = self.column_by_name('magNorm')
sedNames = self.column_by_name('sedFilename')
av = self.column_by_name('galacticAv')
#the two variables below will allow us to get at the SED and magnitude
#data from within the unit test class, so that we can be sure
#that the mixin loaded the correct bandpasses
sublist = SedList(sedNames, magNormList, galacticAvList=av,
fileDir=getPackageDir('sims_sed_library'),
specMap=defaultSpecMap)
for ss in sublist:
self.sedMasterList.append(ss)
if len(output) > 0:
for i in range(len(output[0])):
subList = []
for j in range(len(output)):
subList.append(output[j][i])
self.magnitudeMasterList.append(subList)
return output
def get_sdss_magnitudes(self):
"""
An example getter for stellar magnitudes in SDSS bands
"""
# Load a BandpassDict of SDSS bandpasses, if not done already
if not hasattr(self, 'sdssBandpassDict'):
bandpassNames = ['u','g','r','i','z']
bandpassDir = os.path.join(getPackageDir('throughputs'),'sdss')
bandpassRoot = 'sdss_'
self.sdssBandpassDict = BandpassDict.loadTotalBandpassesFromFiles(bandpassNames,
bandpassRoot = bandpassRoot,
bandpassDir = bandpassDir)
# Actually calculate the magnitudes
return self._magnitudeGetter(self.sdssBandpassDict, self.get_sdss_magnitudes._colnames)