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/20260625T093605

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 0x79721784e700>,
 <lephare._lephare.flt at 0x79723069bc90>,
 <lephare._lephare.flt at 0x79723069bec0>,
 <lephare._lephare.flt at 0x79723069bf10>,
 <lephare._lephare.flt at 0x79723069bf60>,
 <lephare._lephare.flt at 0x79723069bfb0>,
 <lephare._lephare.flt at 0x7972306b0040>,
 <lephare._lephare.flt at 0x7972306b0090>,
 <lephare._lephare.flt at 0x7972306b00e0>,
 <lephare._lephare.flt at 0x7972306b0130>,
 <lephare._lephare.flt at 0x7972306b0180>,
 <lephare._lephare.flt at 0x7972306b01d0>,
 <lephare._lephare.flt at 0x7972306b0220>,
 <lephare._lephare.flt at 0x7972306b0270>,
 <lephare._lephare.flt at 0x7972306b02c0>,
 <lephare._lephare.flt at 0x7972306b0310>,
 <lephare._lephare.flt at 0x7972306b0360>,
 <lephare._lephare.flt at 0x7972306b03b0>,
 <lephare._lephare.flt at 0x7972306b0400>,
 <lephare._lephare.flt at 0x7972306b0450>,
 <lephare._lephare.flt at 0x7972306b04a0>,
 <lephare._lephare.flt at 0x7972306b04f0>,
 <lephare._lephare.flt at 0x7972306b0540>,
 <lephare._lephare.flt at 0x7972306b0590>,
 <lephare._lephare.flt at 0x7972306b05e0>,
 <lephare._lephare.flt at 0x7972306b0630>,
 <lephare._lephare.flt at 0x7972306b0680>,
 <lephare._lephare.flt at 0x7972306b06d0>,
 <lephare._lephare.flt at 0x7972306b0720>,
 <lephare._lephare.flt at 0x7972306b0770>]

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 0x797217877010>]

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 0x7972178c76a0>]

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,
)