def test_write_griddata_ascii():
x0 = np.array([0., 1.])
x1 = np.array([0., 1., 2.])
y = np.zeros((2, 3))
f = StringIO()
sncosmo.write_griddata_ascii(x0, x1, y, f)
# Read it back
f.seek(0)
x0_in, x1_in, y_in = sncosmo.read_griddata_ascii(f)
f.close()
assert_allclose(x0_in, x0)
assert_allclose(x1_in, x1)
assert_allclose(y_in, y)
# with a filename:
dirname = mkdtemp()
fname = os.path.join(dirname, 'griddata.dat')
sncosmo.write_griddata_ascii(x0, x1, y, fname)
x0_in, x1_in, y_in = sncosmo.read_griddata_ascii(fname)
assert_allclose(x0_in, x0)
assert_allclose(x1_in, x1)
assert_allclose(y_in, y)
os.remove(fname)
os.rmdir(dirname)
def test_write_griddata_ascii():
x0 = np.array([0., 1.])
x1 = np.array([0., 1., 2.])
y = np.zeros((2, 3))
f = six.StringIO()
sncosmo.write_griddata_ascii(x0, x1, y, f)
# Read it back
f.seek(0)
x0_in, x1_in, y_in = sncosmo.read_griddata_ascii(f)
f.close()
assert_allclose(x0_in, x0)
assert_allclose(x1_in, x1)
assert_allclose(y_in, y)
# with a filename:
dirname = mkdtemp()
fname = os.path.join(dirname, 'griddata.dat')
sncosmo.write_griddata_ascii(x0, x1, y, fname)
x0_in, x1_in, y_in = sncosmo.read_griddata_ascii(fname)
assert_allclose(x0_in, x0)
assert_allclose(x1_in, x1)
assert_allclose(y_in, y)
os.remove(fname)
os.rmdir(dirname)
def setup_class(self):
"""Create a SALT2 model with a lot of components set to 1."""
phase = np.linspace(0., 100., 10)
wave = np.linspace(1000., 10000., 100)
vals1d = np.zeros(len(phase), dtype=np.float64)
vals = np.ones([len(phase), len(wave)], dtype=np.float64)
# Create some 2-d grid files
files = []
for i in [0, 1]:
f = StringIO()
sncosmo.write_griddata_ascii(phase, wave, vals, f)
f.seek(0) # return to start of file.
files.append(f)
# CL file. The CL in magnitudes will be
# CL(wave) = -(wave - B) / (V - B) [B = 4302.57, V = 5428.55]
# and transmission will be 10^(-0.4 * CL(wave))^c
clfile = StringIO()
clfile.write("1\n"
"0.0\n"
"Salt2ExtinctionLaw.version 1\n"
"Salt2ExtinctionLaw.min_lambda 3000\n"
"Salt2ExtinctionLaw.max_lambda 7000\n")
clfile.seek(0)
# Create some more 2-d grid files
for factor in [1., 0.01, 0.01, 0.01]:
f = StringIO()
sncosmo.write_griddata_ascii(phase, wave, factor * vals, f)
f.seek(0) # return to start of file.
files.append(f)
# Create a 1-d grid file (color dispersion)
cdfile = StringIO()
for w in wave:
cdfile.write("{0:f} {1:f}\n".format(w, 0.2))
cdfile.seek(0) # return to start of file.
# Create a SALT2Source
self.source = sncosmo.SALT2Source(m0file=files[0],
m1file=files[1],
clfile=clfile,
errscalefile=files[2],
lcrv00file=files[3],
lcrv11file=files[4],
lcrv01file=files[5],
cdfile=cdfile)
for f in files:
f.close()
cdfile.close()
clfile.close()
def test_write_griddata_ascii():
x0 = np.array([0., 1.])
x1 = np.array([0., 1., 2.])
y = np.zeros((2, 3))
f = six.StringIO()
sncosmo.write_griddata_ascii(x0, x1, y, f)
# Read it back
f.seek(0)
x0_in, x1_in, y_in = sncosmo.read_griddata_ascii(f)
assert_allclose(x0_in, x0)
assert_allclose(x1_in, x1)
assert_allclose(y_in, y)
def test_write_griddata_ascii():
x0 = np.array([0., 1.])
x1 = np.array([0., 1., 2.])
y = np.zeros((2, 3))
f = six.StringIO()
sncosmo.write_griddata_ascii(x0, x1, y, f)
# Read it back
f.seek(0)
x0_in, x1_in, y_in = sncosmo.read_griddata_ascii(f)
assert_allclose(x0_in, x0)
assert_allclose(x1_in, x1)
assert_allclose(y_in, y)
#!/usr/bin/env python
import os
import numpy as np
import sncosmo
# generate arrays to input to interpolator
x = np.array([-1., 0., 2., 4., 5., 6., 6.5, 7.])
y = np.array([1., 2., 3., 4., 5.])
z = np.sin(x)[:, None] * np.cos(0.25 * y)
fname = '../sncosmo/tests/data/interpolation_test_input.dat'
if os.path.exists(fname):
print(fname, "already exists; skipping.")
else:
sncosmo.write_griddata_ascii(x, y, z, fname)
print("wrote", fname)
# generate test x and y arrays
xs = np.array([-2., -1., 0.5, 2.4, 3.0, 4.0, 4.5, 6.5, 8.0])
ys = np.array([0., 0.5, 1.0, 1.5, 2.8, 3.5, 4.0, 4.5, 5.0, 6.0])
for arr, name in ((xs, 'x'), (ys, 'y')):
fname = '../sncosmo/tests/data/interpolation_test_eval{}.dat'.format(name)
if os.path.exists(fname):
print(fname, "already exists; skipping.")
else:
np.savetxt(fname, arr)
def _addCCSpec(snType, sedFile, oldWave, specList=None, specName=None):
phase, newWave, flux = sncosmo.read_griddata_ascii(sedFile)
wave = np.append(newWave[newWave < oldWave[0]],
newWave[newWave > oldWave[-1]])
if len(wave) == 0:
return (flux)
#flux=flux[:][newWave==wave]
if specList:
spec = createAveSpec(specList)
elif specName:
spec = os.path.join(__dir__, 'data', 'spectra', specName)
allSpec = _readSpec(spec)
else:
tempInd, tempVal = _find_nearest(phase, 0)
if snType == 'II':
snType = 'IIP'
allSpec, bestConst = _findBest(snType, newWave, flux[tempInd])
#spec=os.path.join(__dir__,'data','spectra',_defaultSpec[snType])
#allSpec=_readSpec(spec)
x = [float(x[2:]) for x in allSpec.colnames if x != 'wave']
y = allSpec['wave']
allSpec.remove_column('wave')
func = interp2d(x, y, np.array([list(r) for r in np.array(allSpec)]))
tempFlux = np.transpose(
func(phase[phase >= x[0]][phase[phase >= x[0]] <= x[-1]],
newWave[newWave > 4000][newWave[newWave > 4000] < 7500]))
finalFlux = np.transpose(
func(phase[phase >= x[0]][phase[phase >= x[0]] <= x[-1]],
wave[wave >= y[0]][wave[wave >= y[0]] <= y[-1]]))
if np.max(np.max(finalFlux)) == 0:
return
#if os.path.basename(sedFile)=='SDSS-015339.SED':
# print(finalFlux)
# print(wave[wave>=y[0]][wave[wave>=y[0]]<=y[-1]])
# sys.exit()
splines = []
for p in phase[phase >= x[0]][phase[phase >= x[0]] <= x[-1]]:
ind = np.where(phase == p)[0][0]
mySpline = spl(
newWave[newWave > 4000][newWave[newWave > 4000] < 7500],
flux[ind][newWave < 7500][newWave[newWave < 7500] > 4000],
k=5,
ext=1)
tempSpline = mySpline(
newWave[newWave < 7500][newWave[newWave < 7500] > 4000])
splines.append(
np.log10(
flux[ind][newWave < 7500][newWave[newWave < 7500] > 4000] /
tempSpline))
splines = np.array(splines)
waves = wave[wave >= y[0]][wave[wave >= y[0]] <= y[-1]]
for i in range(len(phase[phase >= x[0]][phase[phase >= x[0]] <= x[-1]])):
#const1=math.fabs(np.max(splines[i])/np.max(tempFlux[i]))
#const2=math.fabs(np.min(splines[i])/np.max(tempFlux[i]))
const = minimize(_specChi,
np.array([bestConst]),
args=(splines[i], tempFlux[i])).x
#const=np.nanmedian([math.fabs(k) for k in splines[i]/tempFlux[i]])
finalFlux[i] *= const
if i == 4:
final = const
#if tempFlux[i][0]>splines[i][0]:
# constMinus=tempFlux[i][0]-splines[i][0]
# finalFlux[i]-=constMinus
#else:
# constMinus=splines[i][0]-tempFlux[i][0]
# tempFlux[i]+=constMinus
#splines[i]+=finalFlux[i]
ind = np.where(phase == phase[phase >= x[0]][
phase[phase >= x[0]] <= x[-1]][i])[0][0]
for j in range(len(waves)):
ind2 = np.where(newWave == waves[j])[0][0]
flux[ind][ind2] = max(0, flux[ind][ind2] + finalFlux[i][j])
#fig=plt.figure()
#ax=fig.gca()
#ax.plot(newWave[newWave<7500][newWave[newWave<7500]>4000],tempFlux[4]*const)
#ax.plot(newWave[newWave<7500][newWave[newWave<7500]>4000],splines[4])
#plt.savefig('test_'+os.path.basename(sedFile[:-3])+'pdf',format='pdf',overwrite=True)
#plt.close()
sncosmo.write_griddata_ascii(phase, newWave, flux, sedFile)
return
def setup_class(self):
"""Create a SALT2 model with a lot of components set to 1."""
phase = np.linspace(0., 100., 10)
wave = np.linspace(1000., 10000., 100)
vals1d = np.zeros(len(phase), dtype=np.float64)
# Create some 2-d grid files
files = []
for i in [0, 1]:
f = six.StringIO()
sncosmo.write_griddata_ascii(phase, wave, vals, f)
f.seek(0) # return to start of file.
files.append(f)
# CL file. The CL in magnitudes will be
# CL(wave) = -(wave - B) / (V - B) [B = 4302.57, V = 5428.55]
# and transmission will be 10^(-0.4 * CL(wave))^c
clfile = six.StringIO()
clfile.write("1\n"
"0.0\n"
"Salt2ExtinctionLaw.version 1\n"
"Salt2ExtinctionLaw.min_lambda 3000\n"
"Salt2ExtinctionLaw.max_lambda 7000\n")
clfile.seek(0)
# Create some more 2-d grid files
for factor in [1., 0.01, 0.01, 0.01]:
f = six.StringIO()
sncosmo.write_griddata_ascii(phase, wave, factor * vals, f)
f.seek(0) # return to start of file.
files.append(f)
# Create a 1-d grid file (color dispersion)
cdfile = six.StringIO()
for w in wave:
cdfile.write("{0:f} {1:f}\n".format(w, 0.2))
cdfile.seek(0) # return to start of file.
# Create a SALT2Source
self.source = sncosmo.SALT2Source(m0file=files[0],
m1file=files[1],
clfile=clfile,
errscalefile=files[2],
lcrv00file=files[3],
lcrv11file=files[4],
lcrv01file=files[5],
cdfile=cdfile)
def test_bandflux_rcov(self):
# component 1:
# ans = (F0/F1)^2 S^2 (V00 + 2 x1 V01 + x1^2 V11)
# when x1=0, this reduces to S^2 V00 = 1^2 * 0.01 = 0.01
#
# component 2:
# cd^2 = 0.04
band = ['bessellb', 'bessellb', 'bessellr', 'bessellr', 'besselli']
phase = [10., 20., 30., 40., 50.]
self.source.set(x1=0.0)
result = self.source.bandflux_rcov(band, phase)
expected = np.array([[0.05, 0.04, 0., 0., 0.],
[0.04, 0.05, 0., 0., 0.],
[0., 0., 0.05, 0.04, 0.],
[0., 0., 0.04, 0.05, 0.],
[0., 0., 0., 0., 0.05]])
assert_allclose(result, expected)
def _extrapolatesed(sedfile,
newsedfile,
color,
table,
time,
modColor,
bands,
zpsys,
bandsDone,
UVoverwrite,
IRoverwrite,
niter=50):
"""
(Private)
Intermediate sed extrapolation function. Interpolate the given transmission function to the wavestep of the SED,
then get the area in the V band for color calculation and run the extrapolation algorithm.
"""
dlist, wlist, flist = _getsed(
sedfile) #first time this is read in, should be in ergs/s/cm^2/AA
i = 0
while dlist[i][0] < time[0]:
i += 1
dlist = dlist[i:]
wlist = wlist[i:]
flist = flist[i:]
i = -1
while dlist[i][0] > time[-1]:
i -= 1
if i != -1:
dlist = dlist[:i + 1]
wlist = wlist[:i + 1]
flist = flist[:i + 1]
blue = color[0]
red = color[-1]
bWave = bands[blue].wave
bTrans = bands[blue].trans
rWave = bands[red].wave
rTrans = bands[red].trans
bInterpFunc = scint.interp1d(bWave, bTrans)
rInterpFunc = scint.interp1d(rWave, rTrans)
cInterpFunc = scint.interp1d(time, modColor)
tempTime = [x[0] for x in dlist]
colorData = cInterpFunc(tempTime)
sed = createSNSED(
sedfile, rescale=False) #now the original sed is in ergs/s/cm^2/AA
model = sncosmo.Model(sed)
#out = open( newsedfile, 'wb' )
log = open('./error.log', 'wb')
def _extrap_helper(wave1, interpFunc1, wave2, interpFunc2, known,
currentPhase):
area = model.bandmag(bands[known], zpsys, currentPhase)
val = int(math.ceil(wave2[0] / wavestep)) * wavestep
val2 = int(math.floor(wave2[-1] / wavestep)) * wavestep
wave = arange(val, val2 + 1, wavestep)
trans = interpFunc2(wave)
return (wave, trans, area)
UV = False
IR = False
finalF = []
for i in range(len(dlist)):
d, w, f = dlist[i], wlist[i], flist[i]
wavestep = w[1] - w[0]
if bands[blue].wave_eff <= _UVrightBound:
bWave, bTrans, rArea = _extrap_helper(rWave, rInterpFunc, bWave,
bInterpFunc, red, d[0])
wnew, fnew = _extrapolate_uv(blue, rArea, colorData[i], bTrans,
bWave, f, w, niter, log, i, bands,
zpsys, UVoverwrite)
UV = True
elif bands[red].wave_eff >= _IRleftBound:
rWave, rTrans, bArea = _extrap_helper(bWave, bInterpFunc, rWave,
rInterpFunc, blue, d[0])
wnew, fnew = _extrapolate_ir(red, bArea, colorData[i], rTrans,
rWave, d, f, w, niter, log, i, IR,
bands, zpsys, model, bandsDone,
IRoverwrite)
IR = True
else:
raise RuntimeError(
"You supplied a color that does not support extrapolation to the IR or UV!"
)
finalF.append(fnew)
sncosmo.write_griddata_ascii(array([x[0] for x in dlist]), array(wnew),
array(finalF), newsedfile)
#for j in range( len( wnew ) ) :
# fout.write("%5.1f %10i %12.7e \n"%( d[0], wnew[j], fnew[j] ))
#fout.close()
#log.close()
return (UV, IR)
def setup_class(self):
"""Create a SALT2 model with a lot of components set to 1."""
phase = np.linspace(0.0, 100.0, 10)
wave = np.linspace(1000.0, 10000.0, 100)
vals1d = np.zeros(len(phase), dtype=np.float64)
# Create some 2-d grid files
files = []
for i in [0, 1]:
f = six.StringIO()
sncosmo.write_griddata_ascii(phase, wave, vals, f)
f.seek(0) # return to start of file.
files.append(f)
# CL file. The CL in magnitudes will be
# CL(wave) = -(wave - B) / (V - B) [B = 4302.57, V = 5428.55]
# and transmission will be 10^(-0.4 * CL(wave))^c
clfile = six.StringIO()
clfile.write(
"1\n"
"0.0\n"
"Salt2ExtinctionLaw.version 1\n"
"Salt2ExtinctionLaw.min_lambda 3000\n"
"Salt2ExtinctionLaw.max_lambda 7000\n"
)
clfile.seek(0)
# Create some more 2-d grid files
for factor in [1.0, 0.01, 0.01, 0.01]:
f = six.StringIO()
sncosmo.write_griddata_ascii(phase, wave, factor * vals, f)
f.seek(0) # return to start of file.
files.append(f)
# Create a 1-d grid file (color dispersion)
cdfile = six.StringIO()
for w in wave:
cdfile.write("{0:f} {1:f}\n".format(w, 0.2))
cdfile.seek(0) # return to start of file.
# Create a SALT2Source
self.source = sncosmo.SALT2Source(
m0file=files[0],
m1file=files[1],
clfile=clfile,
errscalefile=files[2],
lcrv00file=files[3],
lcrv11file=files[4],
lcrv01file=files[5],
cdfile=cdfile,
)
def test_bandflux_rcov(self):
# component 1:
# ans = (F0/F1)^2 S^2 (V00 + 2 x1 V01 + x1^2 V11)
# when x1=0, this reduces to S^2 V00 = 1^2 * 0.01 = 0.01
#
# component 2:
# cd^2 = 0.04
band = ["bessellb", "bessellb", "bessellr", "bessellr", "besselli"]
phase = [10.0, 20.0, 30.0, 40.0, 50.0]
self.source.set(x1=0.0)
result = self.source.bandflux_rcov(band, phase)
expected = np.array(
[
[0.05, 0.04, 0.0, 0.0, 0.0],
[0.04, 0.05, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.05, 0.04, 0.0],
[0.0, 0.0, 0.04, 0.05, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.05],
]
)
assert_allclose(result, expected)
def sed_to_perturber(perturber_in,
base_sed,
perturber_var='Theta',
scale_band='bessellb',
rescale=True,
outname='my_perturber.dat',
phase_wave_source='perturber',
diff_limit=np.inf,
ave_spec=None):
if isinstance(perturber_in, dict):
perturber_dict = perturber_in
out_perturber_dict = {e: {} for e in perturber_in.keys()}
single = False
else:
perturber_dict = {'single': perturber_in}
single = True
base_phase = base_sed._phase
base_wave = base_sed._wave
overall_min_phase = -np.inf
overall_max_phase = np.inf
overall_max_wave = np.inf
overall_min_wave = -np.inf
for e in perturber_dict.keys():
perturber_sed = perturber_dict[e]
perturber_phase = perturber_sed._phase
perturber_wave = perturber_sed._wave
if np.min(perturber_wave) > overall_min_wave:
overall_min_wave = np.min(perturber_wave)
if np.max(perturber_wave) < overall_max_wave:
overall_max_wave = np.max(perturber_wave)
if np.min(perturber_phase) > overall_min_phase:
overall_min_phase = np.min(perturber_phase)
if np.max(perturber_phase) < overall_max_phase:
overall_max_phase = np.max(perturber_phase)
fluxes = []
for phase in base_phase:
base_flux = base_sed._flux(phase, base_wave).flatten()
if phase >= np.min(perturber_phase) and phase <= np.max(
perturber_phase
): # and ((e=='single' or float(e)<10.7001) or perturber_var!='hostmass'):
scale_factor = perturber_sed.bandflux(
scale_band, phase) / base_sed.bandflux(scale_band, phase)
try:
perturber_flux = perturber_sed._flux(phase,
base_wave).flatten()
except:
perturber_flux = base_sed._flux(
phase, base_wave
) #/np.max(base_sed._flux(phase,base_wave))#np.zeros(len(base_wave))
inds = base_wave[np.where(
np.logical_and(
base_wave >= np.min(perturber_wave),
base_wave <= np.max(perturber_wave)))[0]]
perturber_flux[inds] = perturber_sed._flux(
phase, base_wave[inds])
if not rescale:
scale_factor = 1.
perturber_flux /= scale_factor
if ave_spec is None:
perturber_flux = (perturber_flux - base_flux) / base_flux
else:
perturber_flux = (perturber_flux - ave_spec._flux(
phase, base_wave).flatten()) / base_flux
perturber_flux[np.abs(perturber_flux) == np.inf] = np.nan
perturber_flux[np.abs(perturber_flux) > diff_limit] = np.nan
if np.isnan(perturber_flux[0]):
perturber_flux[0] = 0
for i in range(1, len(perturber_flux)):
if np.isnan(perturber_flux[i]):
perturber_flux[i] = perturber_flux[i - 1]
else:
perturber_wave = base_wave
perturber_flux = np.zeros(len(base_wave))
if not single:
out_perturber_dict[e][phase] = {
base_wave[i]: perturber_flux[i]
for i in range(len(base_wave))
}
else:
fluxes.append(perturber_flux)
accept_phase_inds = np.where(
np.logical_and(base_phase >= overall_min_phase,
base_phase <= overall_max_phase))[0]
accept_wave_inds = np.where(
np.logical_and(base_wave >= overall_min_wave,
base_wave <= overall_max_wave))[0]
if single:
fluxes = np.array(fluxes).reshape((len(base_phase), len(base_wave)))
base_phase = base_phase[accept_phase_inds].astype(int)
base_wave = base_wave[accept_wave_inds].astype(int)
fluxes = fluxes[np.ix_(accept_phase_inds, accept_wave_inds)]
sncosmo.write_griddata_ascii(base_phase, base_wave, fluxes, outname)
line_prepender(outname, '# phase wavelength flux')
else:
base_phase = base_phase[accept_phase_inds].astype(int)
base_wave = base_wave[accept_wave_inds].astype(int)
def func(velocity, phase, wavelength):
flux = np.array([
out_perturber_dict[v][p][w]
for v, p, w in zip(velocity, phase, wavelength)
])
return flux
generate_ND_grids(func, outname,
[perturber_var, 'phase', 'wavelength', 'flux'],
np.sort(list(out_perturber_dict.keys())), base_phase,
base_wave)
#!/usr/bin/env python
import os
import numpy as np
import sncosmo
# generate arrays to input to interpolator
x = np.array([-1., 0., 2., 4., 5., 6., 6.5, 7.])
y = np.array([1., 2., 3., 4., 5.])
z = np.sin(x)[:, None] * np.cos(0.25 * y)
fname = '../sncosmo/tests/data/interpolation_test_input.dat'
if os.path.exists(fname):
print(fname, "already exists; skipping.")
else:
sncosmo.write_griddata_ascii(x, y, z, fname)
print("wrote", fname)
# generate test x and y arrays
xs = np.array([-2., -1., 0.5, 2.4, 3.0, 4.0, 4.5, 6.5, 8.0])
ys = np.array([0., 0.5, 1.0, 1.5, 2.8, 3.5, 4.0, 4.5, 5.0, 6.0])
for arr, name in ((xs, 'x'), (ys, 'y')):
fname = '../sncosmo/tests/data/interpolation_test_eval{}.dat'.format(name)
if os.path.exists(fname):
print(fname, "already exists; skipping.")
else:
np.savetxt(fname, arr)
