Manipulating an SED object

SED objects represent SED templates belonging to one of the three possible classes “STAR”, “QSO” (for AGN type of objects), and “GAL” for galaxies. SED templates available with LePhare can be found under the sed directory.

The notebook can be downloaded here.

import os
import lephare as lp
import numpy as np
from matplotlib import pylab as plt
import struct

%matplotlib inline
%load_ext wurlitzer

LEPHAREDIR is being set to the default cache directory:
/home/docs/.cache/lephare/data
More than 1Gb may be written there.
LEPHAREWORK is being set to the default cache directory:
/home/docs/.cache/lephare/work
Default work cache is already linked.
This is linked to the run directory:
/home/docs/.cache/lephare/runs/20260506T145844

keymap = lp.all_types_to_keymap(lp.default_cosmos_config)
# Get the auxiliary files required.
lp.data_retrieval.get_auxiliary_data(keymap=keymap, additional_files=["sed/STAR/PICKLES/f2ii.sed"])

Registry file downloaded and saved as data_registry.txt.

Downloading file 'sed/STAR/PICKLES/f2ii.sed' from 'https://raw.githubusercontent.com/lephare-photoz/lephare-data/main/sed/STAR/PICKLES/f2ii.sed' to '/home/docs/.cache/lephare/data'.

Checking/downloading 445 files...
445 completed.
All files downloaded successfully and are non-empty.
Checking/downloading 1 files...
1 completed.
All files downloaded successfully and are non-empty.

filter_name = "cosmos/u_cfht.lowres"
f1 = lp.flt(0, filter_name, 1, 0)
f1.read(os.path.join(lp.LEPHAREDIR, "filt", filter_name))
f1.plot_filter_curve()

# we can write the config to a file to keep a record
config_file = "./config_file.para"
lp.write_para_config(keymap, config_file)
# before running PhotoZ we must run filt, sedtolib and maggal
filter_driver = lp.Filter(config_file=config_file)
filter_driver.run()

[<lephare._lephare.flt at 0x7f849aa87b50>,
 <lephare._lephare.flt at 0x7f849aa852b0>,
 <lephare._lephare.flt at 0x7f849aa86d40>,
 <lephare._lephare.flt at 0x7f849aa86840>,
 <lephare._lephare.flt at 0x7f849aa86b10>,
 <lephare._lephare.flt at 0x7f849c103920>,
 <lephare._lephare.flt at 0x7f849c103ba0>,
 <lephare._lephare.flt at 0x7f849c103bf0>,
 <lephare._lephare.flt at 0x7f849c103c40>,
 <lephare._lephare.flt at 0x7f849c103c90>,
 <lephare._lephare.flt at 0x7f849c103ce0>,
 <lephare._lephare.flt at 0x7f849c103d30>,
 <lephare._lephare.flt at 0x7f849c103d80>,
 <lephare._lephare.flt at 0x7f849c103dd0>,
 <lephare._lephare.flt at 0x7f849c103e20>,
 <lephare._lephare.flt at 0x7f849c103e70>,
 <lephare._lephare.flt at 0x7f849c103ec0>,
 <lephare._lephare.flt at 0x7f849c103f10>,
 <lephare._lephare.flt at 0x7f849c103f60>,
 <lephare._lephare.flt at 0x7f849c103fb0>,
 <lephare._lephare.flt at 0x7f849c0f0040>,
 <lephare._lephare.flt at 0x7f849c0f0090>,
 <lephare._lephare.flt at 0x7f849c0f00e0>,
 <lephare._lephare.flt at 0x7f849c0f0130>,
 <lephare._lephare.flt at 0x7f849c0f0180>,
 <lephare._lephare.flt at 0x7f849c0f01d0>,
 <lephare._lephare.flt at 0x7f849c0f0220>,
 <lephare._lephare.flt at 0x7f849c0f0270>,
 <lephare._lephare.flt at 0x7f849c0f02c0>,
 <lephare._lephare.flt at 0x7f849c0f0310>]

filter_output = os.path.join(
    os.environ["LEPHAREWORK"], "filt", filter_driver.keymap["FILTER_FILE"].value + ".dat"
)
filters = np.loadtxt(filter_output, dtype={"names": ("lamb", "val", "bid"), "formats": (float, float, int)})
plt.loglog(filters["lamb"], filters["val"])
plt.xlabel("wavelength");

!ls $LEPHAREDIR/sed

GAL  QSO  STAR

Let’s start with the template of a star. A SED object is created most easily with 3 arguments: its name, an identifying integer, and the type it belongs to. Then calling the read function reads the ASCII file passed as argument.

star_sed = "f2ii.sed"
sed_filename = os.path.join(lp.LEPHAREDIR, "sed/STAR/PICKLES/", star_sed)
sed = lp.StarSED(star_sed, 1)
sed.read(sed_filename)

The python code exposes the templates vectors through the data method

x = sed.data()[0]
y = sed.data()[1]
plt.plot(x, y)

[<matplotlib.lines.Line2D at 0x7f849aa72320>]

In the context of LePhare, such a SED object is going to be written as a byte compressed file, and read back downstream to compute expected magnitudes and to perform the fit. Writing an reading this binary stored file goes as follows:

rootname = star_sed.split(".")[0]
sed.writeSED(rootname + ".bin", rootname + ".phys", rootname + ".doc")

We can read it back into a new SED object, and check that the values have been correctly read back

sed2 = lp.StarSED(star_sed, 2)
sed2.readSEDBin(rootname + ".bin")
x2 = sed.data()[0]
y2 = sed.data()[1]
assert np.all(x == x2)
assert np.all(y == y2)
print(sed.name, sed2.name)

f2ii.sed MOD_1

sed = lp.Sedtolib(config_file)
sed.run(typ="STAR", star_sed=f"{lp.LEPHAREDIR}/sed/STAR/STAR_MOD_ALL.list", star_fscale="1")

sed_output = os.path.join(os.environ["LEPHAREWORK"], "lib_bin", keymap["STAR_LIB"].value + ".bin")

sed_output

'/home/docs/.cache/lephare/work/lib_bin/LIB_STAR.bin'

# Code to unpack binary not running
# buf = open(sed_output, "rb").read()
# counter = 0
# off = 0
# while counter <= 0:
#     nrec, jtype, nbw = struct.unpack("iil", buf[off : off + 16])
#     wave = struct.unpack("d" * nbw, buf[off + 16 : off + 16 + 8 * nbw])
#     print(nrec, jtype, nbw)
#     off += 16 + 8 * nbw
#     nrec, jtype, nbw = struct.unpack("iil", buf[off : off + 16])
#     spec = struct.unpack("d" * nbw, buf[off + 16 : off + 16 + 8 * nbw])
#     print(nrec, jtype, nbw)
#     off += 16 + 8 * nbw
#     counter += 1
# plt.plot(wave, spec)
# # plt.xlim(1000,1.e4)
# # plt.ylim(1.e-10,1.e-6)

# n = 6973
# struct.unpack("d", buf[off + 16 + 8 * (n - 1) : off + 16 + 8 * n])

# nbw

# buf[38896 + 16 + 8 : 38896 + 16 + 16]

# struct.unpack("d", buf[38896 + 16 + 8 : 38896 + 16 + 16])

# print(4.2399775704000006e-08 / 1.23542470e01)

# struct.unpack("d" * 1, buf[off + 16 : off + 16 + 8])

# struct.calcsize("l")

# wave[1], spec[1]

d = np.loadtxt(f"{lp.LEPHAREDIR}/sed/STAR/PICKLES/o5v.sed.ext")
plt.plot(d[:, 0], d[:, 1])

[<matplotlib.lines.Line2D at 0x7f849aa88580>]

d[:, 1]

array([0.00000000e+00, 1.23542470e+01, 9.92826800e+00, ...,
       2.15824600e-65, 4.93845048e-66, 1.13000525e-66], shape=(4860,))

stream_buf = open(sed_output, "rb").read()

struct.unpack("iil", stream_buf[0:16])

(1, 4860, 0)

k = lp.keyword("TEST", "0.1,0.1,6")
print(k.split_double("0.03", 3))
print(k.split_double("0.03", 3))

[0.1, 0.1, 6.0]
[0.1, 0.1, 6.0]

mag = lp.MagGal(config_file)
mag.run(typ="STAR", lib_ascii="YES", star_lib_out="ALLSTAR_COSMOS")

sed.run(typ="QSO", qso_sed=f"{lp.LEPHAREDIR}/sed/QSO/SALVATO09/AGN_MOD.list")

sed.run(typ="GAL", gal_sed=f"{lp.LEPHAREDIR}/sed/GAL/COSMOS_SED/COSMOS_MOD.list", gal_lib="LIB_VISTA")

mag = lp.MagGal(config_file)
mag.run(
    typ="QSO",
    lib_ascii="NO",
    mod_extinc="0,1000",
    eb_v="0.,0.1,0.2,0.3",
    extinc_law="SB_calzetti.dat",
    z_step="0.04,0,6",
    verbose=True,
)