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/20260304T132506

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 0x732429db6bb0>,
 <lephare._lephare.flt at 0x732429db76a0>,
 <lephare._lephare.flt at 0x732429db62f0>,
 <lephare._lephare.flt at 0x732429df00e0>,
 <lephare._lephare.flt at 0x732429df0c70>,
 <lephare._lephare.flt at 0x732429df1cb0>,
 <lephare._lephare.flt at 0x732429df0bd0>,
 <lephare._lephare.flt at 0x732429df05e0>,
 <lephare._lephare.flt at 0x732429df0ae0>,
 <lephare._lephare.flt at 0x732429df07c0>,
 <lephare._lephare.flt at 0x732429df21b0>,
 <lephare._lephare.flt at 0x732429df1940>,
 <lephare._lephare.flt at 0x732429df02c0>,
 <lephare._lephare.flt at 0x732429df22a0>,
 <lephare._lephare.flt at 0x732429df06d0>,
 <lephare._lephare.flt at 0x732429df0b80>,
 <lephare._lephare.flt at 0x732429df1080>,
 <lephare._lephare.flt at 0x732429df2700>,
 <lephare._lephare.flt at 0x732429df0e00>,
 <lephare._lephare.flt at 0x73242b48cc70>,
 <lephare._lephare.flt at 0x73242b48cef0>,
 <lephare._lephare.flt at 0x73242b48cf40>,
 <lephare._lephare.flt at 0x73242b48cf90>,
 <lephare._lephare.flt at 0x73242b48cfe0>,
 <lephare._lephare.flt at 0x73242b48d030>,
 <lephare._lephare.flt at 0x73242b48d080>,
 <lephare._lephare.flt at 0x73242b48d0d0>,
 <lephare._lephare.flt at 0x73242b48d120>,
 <lephare._lephare.flt at 0x73242b48d170>,
 <lephare._lephare.flt at 0x73242b48d1c0>]

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 0x73242b0ca590>]

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 0x73242b263cd0>]

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,
)