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Support for Fastspec PCA templates #260

Merged
merged 14 commits into from
Dec 4, 2023
Merged

Support for Fastspec PCA templates #260

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a90b12d
scan galaxies to z=7
moustakas Sep 12, 2023
f5fbb03
add DLA and LAF coefficient files needed for IGM attenuation model
moustakas Sep 21, 2023
b5a9aa3
add Inoue+14 IGM class to utils
moustakas Sep 21, 2023
8d8ebc5
Merge branch 'main' into fastspec-pca-templates
moustakas Sep 21, 2023
f014300
fix igm transmission bug
moustakas Sep 23, 2023
f1eaa9b
add --zscan-galaxy, --zscan-qso, and --zscan-star optional arguments
moustakas Sep 23, 2023
f939243
Rewrote IGM transmission:
craigwarner-ufastro Sep 25, 2023
e54890a
Merge branch 'fastspec-pca-templates' of https://github.com/desihub/r…
craigwarner-ufastro Sep 25, 2023
d0d8bc6
I believe this finishes the merge
craigwarner-ufastro Sep 25, 2023
80674b8
a little cleanup
moustakas Sep 27, 2023
e2e2296
restore Calura12 ias default IGM model
Dec 4, 2023
1af50ea
drop py3.8 support due to importlib.resources.files
Dec 4, 2023
40e018c
str vs. PosixPath
Dec 4, 2023
868f303
py3.10 not 3.12, create IGM on demand
Dec 4, 2023
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2 changes: 1 addition & 1 deletion .github/workflows/python-package.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ jobs:
fail-fast: true
matrix:
os: [ubuntu-latest]
python-version: ['3.8', '3.9'] # fitsio does not like Python < 3.7
python-version: ['3.9', '3.10'] # fitsio does not like Python < 3.7
# astropy-version: ['<3.0', '<4.1'] #, '<5.0']
env:
DESIUTIL_VERSION: 3.2.5
Expand Down
39 changes: 39 additions & 0 deletions py/redrock/data/DLAcoeff.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,39 @@
2 1215.670 1.61698E-04 5.38995E-05
3 1025.720 1.54539E-04 5.15129E-05
4 972.537 1.49767E-04 4.99222E-05
5 949.743 1.46031E-04 4.86769E-05
6 937.803 1.42893E-04 4.76312E-05
7 930.748 1.40159E-04 4.67196E-05
8 926.226 1.37714E-04 4.59048E-05
9 923.150 1.35495E-04 4.51650E-05
10 920.963 1.33452E-04 4.44841E-05
11 919.352 1.31561E-04 4.38536E-05
12 918.129 1.29785E-04 4.32617E-05
13 917.181 1.28117E-04 4.27056E-05
14 916.429 1.26540E-04 4.21799E-05
15 915.824 1.25041E-04 4.16804E-05
16 915.329 1.23614E-04 4.12046E-05
17 914.919 1.22248E-04 4.07494E-05
18 914.576 1.20938E-04 4.03127E-05
19 914.286 1.19681E-04 3.98938E-05
20 914.039 1.18469E-04 3.94896E-05
21 913.826 1.17298E-04 3.90995E-05
22 913.641 1.16167E-04 3.87225E-05
23 913.480 1.15071E-04 3.83572E-05
24 913.339 1.14011E-04 3.80037E-05
25 913.215 1.12983E-04 3.76609E-05
26 913.104 1.11972E-04 3.73241E-05
27 913.006 1.11002E-04 3.70005E-05
28 912.918 1.10051E-04 3.66836E-05
29 912.839 1.09125E-04 3.63749E-05
30 912.768 1.08220E-04 3.60734E-05
31 912.703 1.07337E-04 3.57789E-05
32 912.645 1.06473E-04 3.54909E-05
33 912.592 1.05629E-04 3.52096E-05
34 912.543 1.04802E-04 3.49340E-05
35 912.499 1.03991E-04 3.46636E-05
36 912.458 1.03198E-04 3.43994E-05
37 912.420 1.02420E-04 3.41402E-05
38 912.385 1.01657E-04 3.38856E-05
39 912.353 1.00908E-04 3.36359E-05
40 912.324 1.00168E-04 3.33895E-05
39 changes: 39 additions & 0 deletions py/redrock/data/LAFcoeff.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,39 @@
2 1215.670 1.68976E-02 2.35379E-03 1.02611E-04
3 1025.720 4.69229E-03 6.53625E-04 2.84940E-05
4 972.537 2.23898E-03 3.11884E-04 1.35962E-05
5 949.743 1.31901E-03 1.83735E-04 8.00974E-06
6 937.803 8.70656E-04 1.21280E-04 5.28707E-06
7 930.748 6.17843E-04 8.60640E-05 3.75186E-06
8 926.226 4.60924E-04 6.42055E-05 2.79897E-06
9 923.150 3.56887E-04 4.97135E-05 2.16720E-06
10 920.963 2.84278E-04 3.95992E-05 1.72628E-06
11 919.352 2.31771E-04 3.22851E-05 1.40743E-06
12 918.129 1.92348E-04 2.67936E-05 1.16804E-06
13 917.181 1.62155E-04 2.25878E-05 9.84689E-07
14 916.429 1.38498E-04 1.92925E-05 8.41033E-07
15 915.824 1.19611E-04 1.66615E-05 7.26340E-07
16 915.329 1.04314E-04 1.45306E-05 6.33446E-07
17 914.919 9.17397E-05 1.27791E-05 5.57091E-07
18 914.576 8.12784E-05 1.13219E-05 4.93564E-07
19 914.286 7.25069E-05 1.01000E-05 4.40299E-07
20 914.039 6.50549E-05 9.06198E-06 3.95047E-07
21 913.826 5.86816E-05 8.17421E-06 3.56345E-07
22 913.641 5.31918E-05 7.40949E-06 3.23008E-07
23 913.480 4.84261E-05 6.74563E-06 2.94068E-07
24 913.339 4.42740E-05 6.16726E-06 2.68854E-07
25 913.215 4.06311E-05 5.65981E-06 2.46733E-07
26 913.104 3.73821E-05 5.20723E-06 2.27003E-07
27 913.006 3.45377E-05 4.81102E-06 2.09731E-07
28 912.918 3.19891E-05 4.45601E-06 1.94255E-07
29 912.839 2.97110E-05 4.13867E-06 1.80421E-07
30 912.768 2.76635E-05 3.85346E-06 1.67987E-07
31 912.703 2.58178E-05 3.59636E-06 1.56779E-07
32 912.645 2.41479E-05 3.36374E-06 1.46638E-07
33 912.592 2.26347E-05 3.15296E-06 1.37450E-07
34 912.543 2.12567E-05 2.96100E-06 1.29081E-07
35 912.499 1.99967E-05 2.78549E-06 1.21430E-07
36 912.458 1.88476E-05 2.62543E-06 1.14452E-07
37 912.420 1.77928E-05 2.47850E-06 1.08047E-07
38 912.385 1.68222E-05 2.34330E-06 1.02153E-07
39 912.353 1.59286E-05 2.21882E-06 9.67268E-08
40 912.324 1.50996E-05 2.10334E-06 9.16925E-08
16 changes: 15 additions & 1 deletion py/redrock/external/desi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -575,6 +575,15 @@ def rrdesi(options=None, comm=None):
parser.add_argument("--chi2-scan", type=str, default=None,
required=False, help="Load the chi2-scan from the input file")

parser.add_argument("--zscan-galaxy", type=str, default='-0.005,1.7,3e-4',
required=False, help="Redshift scan parameters for galaxies: zmin,zmax,dz")

parser.add_argument("--zscan-qso", type=str, default='0.05,6.0,5e-4',
required=False, help="Redshift scan parameters for QSO: zmin,zmax,dz")

parser.add_argument("--zscan-star", type=str, default='-0.002,0.00201,4e-5',
required=False, help="Redshift scan parameters for stars: zmin,zmax,dz")

parser.add_argument("-n", "--ntargets", type=int,
required=False, help="the number of targets to process in each file")

Expand Down Expand Up @@ -813,7 +822,12 @@ def rrdesi(options=None, comm=None):
# Read the template data
# Pass both use_gpu (this proc) and args.gpu (if any proc is using GPU)
dtemplates = load_dist_templates(dwave, templates=args.templates,
comm=comm, mp_procs=mpprocs, redistribute=redistribute_templates, use_gpu=use_gpu, gpu_mode=args.gpu)
zscan_galaxy=args.zscan_galaxy,
zscan_qso=args.zscan_qso,
zscan_star=args.zscan_star,
comm=comm, mp_procs=mpprocs,
redistribute=redistribute_templates,
use_gpu=use_gpu, gpu_mode=args.gpu)

# Compute the redshifts, including both the coarse scan and the
# refinement. This function only returns data on the rank 0 process.
Expand Down
32 changes: 22 additions & 10 deletions py/redrock/templates.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,8 @@ class Template(object):

"""
def __init__(self, filename=None, spectype=None, redshifts=None,
wave=None, flux=None, subtype=None):
wave=None, flux=None, subtype=None,
zscan_galaxy=None, zscan_qso=None, zscan_star=None):

if filename is not None:
fx = None
Expand Down Expand Up @@ -73,15 +74,23 @@ def __init__(self, filename=None, spectype=None, redshifts=None,
self._rrtype = hdr['RRTYPE'].strip().upper()
if old_style_templates:
if self._rrtype == 'GALAXY':
# redshifts = 10**np.arange(np.log10(1+0.005),
# np.log10(1+2.0), 1.5e-4) - 1
self._redshifts = 10**np.arange(np.log10(1-0.005),
np.log10(1+1.7), 3e-4) - 1
if zscan_galaxy is not None:
zmin, zmax, dz = zscan_galaxy.split(',')
self._redshifts = 10**np.arange(np.log10(1+float(zmin)), np.log10(1+float(zmax)), float(dz)) - 1
else:
self._redshifts = 10**np.arange(np.log10(1-0.005), np.log10(1+1.7), 3e-4) - 1
elif self._rrtype == 'STAR':
self._redshifts = np.arange(-0.002, 0.00201, 4e-5)
if zscan_star is not None:
zmin, zmax, dz = zscan_star.split(',')
self._redshifts = np.arange(float(zmin), float(zmax), float(dz))
else:
self._redshifts = np.arange(-0.002, 0.00201, 4e-5)
elif self._rrtype == 'QSO':
self._redshifts = 10**np.arange(np.log10(1+0.05),
np.log10(1+6.0), 5e-4) - 1
if zscan_qso is not None:
zmin, zmax, dz = zscan_qso.split(',')
self._redshifts = 10**np.arange(np.log10(1+float(zmin)), np.log10(1+float(zmax)), float(dz)) - 1
else:
self._redshifts = 10**np.arange(np.log10(1+0.05), np.log10(1+6.0), 5e-4) - 1
else:
raise ValueError("Unknown redshift range to use for "
"template type {}".format(self._rrtype))
Expand Down Expand Up @@ -446,7 +455,9 @@ def cycle(self):
return True


def load_dist_templates(dwave, templates=None, comm=None, mp_procs=1, redistribute=False, use_gpu=False, gpu_mode=False):
def load_dist_templates(dwave, templates=None, comm=None, mp_procs=1,
zscan_galaxy=None, zscan_qso=None, zscan_star=None,
redistribute=False, use_gpu=False, gpu_mode=False):
"""Read and distribute templates from disk.

This reads one or more template files from disk and distributes them among
Expand Down Expand Up @@ -509,7 +520,8 @@ def load_dist_templates(dwave, templates=None, comm=None, mp_procs=1, redistribu
template_data = list()
if (comm is None) or (comm.rank == 0):
for t in template_files:
template_data.append(Template(filename=t))
template_data.append(Template(filename=t, zscan_galaxy=zscan_galaxy,
zscan_star=zscan_star, zscan_qso=zscan_qso))

if comm is not None:
template_data = comm.bcast(template_data, root=0)
Expand Down
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