Skip to content

Commit

Permalink
Merge pull request #148 from desihub/2.3.1-candidate
Browse files Browse the repository at this point in the history 
2.3.1 release candidate
  • Loading branch information
@moustakas
moustakas authored Aug 19, 2023
2 parents 2d72f73 + f7d0359 commit 87227fb
Show file tree
Hide file tree
Showing 20 changed files with 1,947 additions and 523 deletions.
4 changes: 2 additions & 2 deletions .github/workflows/python-package.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ jobs:
python-version: ['3.10']
fitsio-version: ['==1.1.7']
env:
DESIUTIL_VERSION: 3.2.6
DESIUTIL_VERSION: 3.3.1
FASTSPECFIT: ${GITHUB_WORKSPACE}/fastspecfit
DESI_ROOT: ${FASTSPECFIT}/desi

Expand Down Expand Up @@ -60,7 +60,7 @@ jobs:
python-version: ['3.10']
fitsio-version: ['==1.1.7']
env:
DESIUTIL_VERSION: 3.2.6
DESIUTIL_VERSION: 3.3.1
FASTSPECFIT: ${GITHUB_WORKSPACE}/fastspecfit
DESI_ROOT: ${FASTSPECFIT}/desi

Expand Down
62 changes: 27 additions & 35 deletions bin/build-fsps-templates
View file
Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,9 @@ import matplotlib.pyplot as plt

from desispec.interpolation import resample_flux
from fastspecfit.util import C_LIGHT
from fastspecfit.continuum import PIXKMS_BLU, PIXKMS_RED, PIXKMS_WAVESPLIT

irfactor = int(PIXKMS_RED / PIXKMS_BLU)

def smooth_continuum(wave, flux, medbin=1000, smooth_window=200,
smooth_step=50, png=None):
Expand Down Expand Up @@ -103,8 +106,8 @@ def smooth_continuum(wave, flux, medbin=1000, smooth_window=200,

return smooth

def build_templates(models, logages, agebins, imf='chabrier', pixkms=25.0,
wavesplit=1e4, irfactor=4, include_nebular=True):
def build_templates(models, logages, agebins, imf='chabrier',
include_nebular=True):

nsed = len(models)

Expand Down Expand Up @@ -187,10 +190,10 @@ def build_templates(models, logages, agebins, imf='chabrier', pixkms=25.0,
# Resample to constant log-lambda / velocity. In the IR (starting at ~1
# micron), take every fourth sampling, to save space.
if imodel == 0:
dlogwave = pixkms / C_LIGHT / np.log(10) # pixel size [log-lambda]
dlogwave = PIXKMS_BLU / C_LIGHT / np.log(10) # pixel size [log-lambda]
newwave = 10**np.arange(np.log10(np.min(wave)), np.log10(np.max(wave)), dlogwave)

isplit = np.argmin(np.abs(newwave-wavesplit)) + 1
isplit = np.argmin(np.abs(newwave-PIXKMS_WAVESPLIT)) + 1
newwave = np.hstack((newwave[:isplit], newwave[isplit:][::irfactor]))
npix = len(newwave)

Expand All @@ -217,17 +220,12 @@ def build_templates(models, logages, agebins, imf='chabrier', pixkms=25.0,

def main(args):

version = '1.0.0'

# pixel resampling choices
pixkms = 25.0 # pixel size [km/s]
irfactor = 4
wavesplit = 1e4 # [A]
version = '1.1.0'

# velocity dispersion grid
vdispmin = 100.0
vdispmax = 350.0
dvdisp = 25.0
vdispmin = 50.
vdispmax = 350.
dvdisp = 25.
nvdisp = int(np.ceil((vdispmax - vdispmin) / dvdisp)) + 1
vdisp = np.linspace(vdispmin, vdispmax, nvdisp)

Expand All @@ -239,14 +237,10 @@ def main(args):
#logages = np.linspace(minlogage, maxlogage, nages)

# Choose lookback time bins.
nages = 7
tuniv = 13.7 # [Gyr]
tbinmax = (tuniv * 0.85) * 1e9
lim1, lim2 = 7.4772, 8.0
agelims = np.hstack(((0, lim1), np.linspace(lim2, np.log10(tbinmax), nages-2), np.log10(tuniv*1e9)))
agelims = 10**agelims / 1e9
agebins = np.array([agelims[:-1], agelims[1:]]).T # [Gyr]
agelims = np.array([0., 0.01, 0.03, 0.1, 0.33, 1.1, 3.6, 12., 14.]) # [Gyr]
nages = len(agelims) - 1

agebins = np.array([agelims[:-1], agelims[1:]]).T # [Gyr]
logages = np.log10(1e9*np.sum(agebins, axis=1) / 2) # mean age [yr] in each bin

#logmets = np.array([-1.0, -0.3, 0.0, 0.3])
Expand Down Expand Up @@ -325,12 +319,8 @@ def main(args):
models = models.flatten()

# Build models with and without line-emission.
meta, wave, flux = build_templates(models, logages, agebins, pixkms=pixkms,
wavesplit=wavesplit, include_nebular=True,
imf=args.imf)
_, _, fluxnolines = build_templates(models, logages, agebins, pixkms=pixkms,
wavesplit=wavesplit, include_nebular=False,
imf=args.imf)
meta, wave, flux = build_templates(models, logages, agebins, include_nebular=True, imf=args.imf)
_, _, fluxnolines = build_templates(models, logages, agebins, include_nebular=False, imf=args.imf)
lineflux = flux - fluxnolines

#I = (wave > 3500) * (wave < 9000)
Expand All @@ -345,7 +335,7 @@ def main(args):

# Select just the line-free models trimmed to the 1200-10000 A wavelength
# range.
I = np.where((wave > 1200) * (wave < wavesplit))[0]
I = np.where((wave > 1200) * (wave < PIXKMS_WAVESPLIT))[0]
#J = np.where(meta['fagn'] == 0)[0]
vdispwave = wave[I]
#nvdispmodel = len(J)
Expand All @@ -358,18 +348,18 @@ def main(args):
# normflux[:, imodel] = fluxnolines[I, J[imodel]] / smooth

vdispflux = []
for sigma in vdisp / pixkms:
for sigma in vdisp / PIXKMS_BLU:
vdispflux.append(gaussian_filter1d(fluxnolines[I, :], sigma=sigma, axis=0))
vdispflux = np.stack(vdispflux, axis=-1) # [npix,nvdispmodel,nvdisp]

#vdispflux = []
#for sigma in vdisp / pixkms:
#for sigma in vdisp / PIXKMS_BLU:
# vdispflux.append(gaussian_filter1d(fluxnolines[I, :][:, J], sigma=sigma, axis=0))
# #vdispflux.append(gaussian_filter1d(normflux, sigma=sigma, axis=0))
#vdispflux = np.stack(vdispflux, axis=-1) # [npix,nvdispmodel,nvdisp]

#vdispflux = []
#for sigma in vdisp / pixkms:
#for sigma in vdisp / PIXKMS_BLU:
# vdispflux.append(gaussian_filter1d(fluxnolines, sigma=sigma, axis=0))
#vdispflux = np.stack(vdispflux, axis=-1) # [npix,nvdispmodel,nvdisp]

Expand All @@ -381,7 +371,9 @@ def main(args):
#pdb.set_trace()

# Write out.
outdir = os.path.join(os.environ.get('DESI_ROOT'), 'science', 'gqp', 'templates', 'fastspecfit')
outdir = os.path.join(os.environ.get('DESI_ROOT'), 'science', 'gqp', 'templates', 'fastspecfit', version)
if not os.path.isdir(outdir):
os.makedirs(outdir, exist_ok=True)
outfile = os.path.join(outdir, 'ftemplates-{}-{}.fits'.format(args.imf, version))

hduflux1 = fits.PrimaryHDU(flux)
Expand All @@ -402,21 +394,21 @@ def main(args):
hduflux3.header['VDISPRES'] = (dvdisp, 'velocity dispersion spacing [km/s]')
hduflux3.header['BUNIT'] = 'erg/(s cm2 Angstrom)'

isplit = np.argmin(np.abs(wave-wavesplit)) + 1
isplit = np.argmin(np.abs(wave-PIXKMS_WAVESPLIT)) + 1

hduwave1 = fits.ImageHDU(wave)
hduwave1.header['EXTNAME'] = 'WAVE'
hduwave1.header['BUNIT'] = 'Angstrom'
hduwave1.header['AIRORVAC'] = ('vac', 'vacuum wavelengths')
hduwave1.header['PIXSZBLU'] = (pixkms, 'pixel size blueward of PIXSZSPT [km/s]')
hduwave1.header['PIXSZRED'] = (irfactor*pixkms, 'pixel size redward of PIXSZSPT [km/s]')
hduwave1.header['PIXSZBLU'] = (PIXKMS_BLU, 'pixel size blueward of PIXSZSPT [km/s]')
hduwave1.header['PIXSZRED'] = (PIXKMS_RED, 'pixel size redward of PIXSZSPT [km/s]')
hduwave1.header['PIXSZSPT'] = (wave[isplit], 'wavelength where pixel size changes [Angstrom]')

hduwave2 = fits.ImageHDU(vdispwave)
hduwave2.header['EXTNAME'] = 'VDISPWAVE'
hduwave2.header['BUNIT'] = 'Angstrom'
hduwave2.header['AIRORVAC'] = ('vac', 'vacuum wavelengths')
hduwave2.header['PIXSZ'] = (pixkms, 'pixel size [km/s]')
hduwave2.header['PIXSZ'] = (PIXKMS_BLU, 'pixel size [km/s]')

hdutable = fits.convenience.table_to_hdu(meta)
hdutable.header['EXTNAME'] = 'METADATA'
Expand Down
5 changes: 5 additions & 0 deletions bin/get-cutouts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -383,6 +383,11 @@ def main():
except ImportError:
comm = None

# https://docs.nersc.gov/development/languages/python/parallel-python/#use-the-spawn-start-method
if args.mp > 1 and 'NERSC_HOST' in os.environ:
import multiprocessing
multiprocessing.set_start_method('spawn')

if args.coadd_type == 'healpix':
args.survey = args.survey.split(',')
args.program = args.program.split(',')
Expand Down
10 changes: 9 additions & 1 deletion doc/changes.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,19 @@
Change Log
==========

2.3.1 (not released yet)
2.4.1 (not released yet)
------------------------

*

2.4.0 (2023-08-18)
------------------

* Bug fixes and miscellaneous feature requests for next VACs, including modified
SPS templates and a user-friendly refactor of the K-correction code [`PR #148`_].

.. _`PR #148`: https://github.com/desihub/fastspecfit/pull/148

2.3.0 (2023-08-07)
------------------

Expand Down
34 changes: 34 additions & 0 deletions doc/fastspec.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -263,6 +263,40 @@ Name Type Units Descript
CIV_1549_EW_LIMIT float32 Angstrom One-sigma upper limit on the emission line equivalent width.
CIV_1549_CHI2 float32 Chi-squared of the line-fit.
CIV_1549_NPIX int32 Number of pixels attributed to the emission line.
HEII_1640_MODELAMP float32 1e-17 erg / (Angstrom cm2 s) Model emission line amplitude.
HEII_1640_AMP float32 1e-17 erg / (Angstrom cm2 s) Emission line amplitude.
HEII_1640_AMP_IVAR float32 1e+34 Angstrom2 cm4 s2 / erg2 Inverse variance of line-amplitude.
HEII_1640_FLUX float32 1e-17 erg / (cm2 s) Gaussian-integrated emission-line flux.
HEII_1640_FLUX_IVAR float32 1e+34 cm4 s2 / erg2 Inverse variance of integrated flux.
HEII_1640_BOXFLUX float32 1e-17 erg / (cm2 s) Boxcar-integrated emission-line flux.
HEII_1640_BOXFLUX_IVAR float32 1e+34 cm4 s2 / erg2 Inverse variance of boxcar-integrated flux.
HEII_1640_VSHIFT float32 km / s Velocity shift relative to Z.
HEII_1640_SIGMA float32 km / s Gaussian emission-line width.
HEII_1640_CONT float32 1e-17 erg / (Angstrom cm2 s) Continuum flux at line center.
HEII_1640_CONT_IVAR float32 1e+34 Angstrom2 cm4 s2 / erg2 Inverse variance of continuum flux.
HEII_1640_EW float32 Angstrom Rest-frame emission-line equivalent width.
HEII_1640_EW_IVAR float32 1 / Angstrom2 Inverse variance of equivalent width.
HEII_1640_FLUX_LIMIT float32 erg / (cm2 s) One-sigma upper limit on the emission line flux.
HEII_1640_EW_LIMIT float32 Angstrom One-sigma upper limit on the emission line equivalent width.
HEII_1640_CHI2 float32 Chi-squared of the line-fit.
HEII_1640_NPIX int32 Number of pixels attributed to the emission line.
AlIII_1857_MODELAMP float32 1e-17 erg / (Angstrom cm2 s) Model emission line amplitude.
AlIII_1857_AMP float32 1e-17 erg / (Angstrom cm2 s) Emission line amplitude.
AlIII_1857_AMP_IVAR float32 1e+34 Angstrom2 cm4 s2 / erg2 Inverse variance of line-amplitude.
AlIII_1857_FLUX float32 1e-17 erg / (cm2 s) Gaussian-integrated emission-line flux.
AlIII_1857_FLUX_IVAR float32 1e+34 cm4 s2 / erg2 Inverse variance of integrated flux.
AlIII_1857_BOXFLUX float32 1e-17 erg / (cm2 s) Boxcar-integrated emission-line flux.
AlIII_1857_BOXFLUX_IVAR float32 1e+34 cm4 s2 / erg2 Inverse variance of boxcar-integrated flux.
AlIII_1857_VSHIFT float32 km / s Velocity shift relative to Z.
AlIII_1857_SIGMA float32 km / s Gaussian emission-line width.
AlIII_1857_CONT float32 1e-17 erg / (Angstrom cm2 s) Continuum flux at line center.
AlIII_1857_CONT_IVAR float32 1e+34 Angstrom2 cm4 s2 / erg2 Inverse variance of continuum flux.
AlIII_1857_EW float32 Angstrom Rest-frame emission-line equivalent width.
AlIII_1857_EW_IVAR float32 1 / Angstrom2 Inverse variance of equivalent width.
AlIII_1857_FLUX_LIMIT float32 erg / (cm2 s) One-sigma upper limit on the emission line flux.
AlIII_1857_EW_LIMIT float32 Angstrom One-sigma upper limit on the emission line equivalent width.
AlIII_1857_CHI2 float32 Chi-squared of the line-fit.
AlIII_1857_NPIX int32 Number of pixels attributed to the emission line.
SILIII_1892_MODELAMP float32 1e-17 erg / (Angstrom cm2 s) Model emission line amplitude.
SILIII_1892_AMP float32 1e-17 erg / (Angstrom cm2 s) Emission line amplitude.
SILIII_1892_AMP_IVAR float32 1e+34 Angstrom2 cm4 s2 / erg2 Inverse variance of line-amplitude.
Expand Down
Loading

0 comments on commit 87227fb

Please sign in to comment.