Commit f50a13e8 authored by JX's avatar JX 😵
Browse files

Merge remote-tracking branch 'origin/develop'

parents 96254a11 5e8554bd
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...@@ -12,7 +12,7 @@ from astropy.table import Table ...@@ -12,7 +12,7 @@ from astropy.table import Table
from scipy import interpolate from scipy import interpolate
from datetime import datetime from datetime import datetime
from observation_sim.mock_objects import CatalogBase, Star, Galaxy, Quasar from observation_sim.mock_objects import CatalogBase, Star, Galaxy, Quasar, ExtinctionMW
from observation_sim.mock_objects._util import tag_sed, getObservedSED, getABMAG, integrate_sed_bandpass, comoving_dist from observation_sim.mock_objects._util import tag_sed, getObservedSED, getABMAG, integrate_sed_bandpass, comoving_dist
from observation_sim.astrometry.Astrometry_util import on_orbit_obs_position from observation_sim.astrometry.Astrometry_util import on_orbit_obs_position
...@@ -110,6 +110,12 @@ class Catalog(CatalogBase): ...@@ -110,6 +110,12 @@ class Catalog(CatalogBase):
self.max_size = 0. self.max_size = 0.
# [TODO] Milky Way extinction
self.mw_ext = ExtinctionMW()
self.mw_ext.init_ext_model(model_name="odonnell")
self.mw_ext.load_Planck_ext(
file_path="/public/home/fangyuedong/project/ext_maps/planck/HFI_CompMap_ThermalDustModel_2048_R1.20.fits")
if "star_cat" in config["catalog_options"]["input_path"] and config["catalog_options"]["input_path"]["star_cat"] and not config["catalog_options"]["galaxy_only"]: if "star_cat" in config["catalog_options"]["input_path"] and config["catalog_options"]["input_path"]["star_cat"] and not config["catalog_options"]["galaxy_only"]:
# Get the cloest star catalog file # Get the cloest star catalog file
star_file_name = get_star_cat( star_file_name = get_star_cat(
...@@ -248,6 +254,9 @@ class Catalog(CatalogBase): ...@@ -248,6 +254,9 @@ class Catalog(CatalogBase):
input_time_str=time_str input_time_str=time_str
) )
# [TODO] get Milky Way extinction AVs
MW_Av_arr = self.mw_ext.Av_from_Planck(ra=ra_arr, dec=dec_arr)
for igals in range(ngals): for igals in range(ngals):
# # (TEST) # # (TEST)
# if igals > 100: # if igals > 100:
...@@ -259,6 +268,9 @@ class Catalog(CatalogBase): ...@@ -259,6 +268,9 @@ class Catalog(CatalogBase):
param['ra_orig'] = gals['ra'][igals] param['ra_orig'] = gals['ra'][igals]
param['dec_orig'] = gals['dec'][igals] param['dec_orig'] = gals['dec'][igals]
# [TODO] get Milky Way extinction AVs
param['mw_Av'] = MW_Av_arr[igals]
if not self.chip.isContainObj(ra_obj=param['ra'], dec_obj=param['dec'], margin=200): if not self.chip.isContainObj(ra_obj=param['ra'], dec_obj=param['dec'], margin=200):
continue continue
...@@ -530,6 +542,11 @@ class Catalog(CatalogBase): ...@@ -530,6 +542,11 @@ class Catalog(CatalogBase):
speci = interpolate.interp1d(wave, flux) speci = interpolate.interp1d(wave, flux)
lamb = np.arange(2000, 11001+0.5, 0.5) lamb = np.arange(2000, 11001+0.5, 0.5)
y = speci(lamb) y = speci(lamb)
# [TODO] Apply Milky Way extinction
if obj.type != 'star':
self.mw_ext.apply_extinction(y, Av=obj.mw_Av)
# erg/s/cm2/A --> photon/s/m2/A # erg/s/cm2/A --> photon/s/m2/A
all_sed = y * lamb / (cons.h.value * cons.c.value) * 1e-13 all_sed = y * lamb / (cons.h.value * cons.c.value) * 1e-13
sed = Table(np.array([lamb, all_sed]).T, names=('WAVELENGTH', 'FLUX')) sed = Table(np.array([lamb, all_sed]).T, names=('WAVELENGTH', 'FLUX'))
......
...@@ -11,7 +11,7 @@ ...@@ -11,7 +11,7 @@
# can add some of the command-line arguments here as well; # can add some of the command-line arguments here as well;
# ok to pass either way or both, as long as they are consistent # ok to pass either way or both, as long as they are consistent
work_dir: "/public/home/fangyuedong/project/workplace/" work_dir: "/public/home/fangyuedong/project/workplace/"
run_name: "no_nonlinearity_test" run_name: "ext_test"
# Project cycle and run counter are used to name the outputs # Project cycle and run counter are used to name the outputs
project_cycle: 9 project_cycle: 9
...@@ -44,7 +44,7 @@ catalog_options: ...@@ -44,7 +44,7 @@ catalog_options:
star_only: NO star_only: NO
# Only simulate galaxies? # Only simulate galaxies?
galaxy_only: NO galaxy_only: YES
# rotate galaxy ellipticity # rotate galaxy ellipticity
rotateEll: 0. # [degree] rotateEll: 0. # [degree]
...@@ -65,7 +65,7 @@ obs_setting: ...@@ -65,7 +65,7 @@ obs_setting:
# - give a list of indexes of pointings: [ip_1, ip_2...] # - give a list of indexes of pointings: [ip_1, ip_2...]
# - run all pointings: null # - run all pointings: null
# Note: only valid when a pointing list is specified # Note: only valid when a pointing list is specified
run_pointings: [1] run_pointings: [0, 1, 2, 3, 4]
# Whether to enable astrometric modeling # Whether to enable astrometric modeling
enable_astrometric_model: True enable_astrometric_model: True
......
...@@ -16,7 +16,7 @@ obs_id: "00000001" # this setting will only be used if pointing list file is not ...@@ -16,7 +16,7 @@ obs_id: "00000001" # this setting will only be used if pointing list file is not
# Define list of chips # Define list of chips
# run_chips: [6,7,8,9,11,12,13,14,15,16,17,18,19,20,22,23,24,25] # Photometric chips # run_chips: [6,7,8,9,11,12,13,14,15,16,17,18,19,20,22,23,24,25] # Photometric chips
#run_chips: [1,2,3,4,5,10,21,26,27,28,29,30] # Spectroscopic chips #run_chips: [1,2,3,4,5,10,21,26,27,28,29,30] # Spectroscopic chips
run_chips: [1] run_chips: [17, 22]
# Define observation sequence # Define observation sequence
call_sequence: call_sequence:
......
import os
import numpy as np
import healpy as hp
from astropy.io import fits
from astropy import units as u
from astropy.coordinates import SkyCoord
class ExtinctionMW(object):
def __init__(self):
self.Rv = 3.1
self.lamb = np.arange(2000, 11001+0.5, 0.5)
@staticmethod
def radec2pix(ra, dec, NSIDE=2048):
return hp.pixelfunc.ang2pix(nside=NSIDE, theta=ra, phi=dec, lonlat=True)
def init_ext_model(self, model_name="odonnell", Av=1.0, Rv=3.1, lamb=None):
self.model_name = model_name
self.Av = Av
self.Rv = Rv
if lamb is not None:
self.lamb = lamb
if self.model_name == "odonnell":
alpha = np.zeros(self.lamb.shape)
beta = np.zeros(self.lamb.shape)
x = 1.e4 / self.lamb
def f_alpha_1(x): return 0.574 * (x**1.61)
def f_beta_1(x): return -0.527 * (x**1.61)
def f_alpha_2(x):
y = x - 1.82
return 1 + 0.104*y - 0.609*(y**2) + 0.701*(y**3) + \
1.137*(y**4) - 1.718*(y**5) - 0.827 * \
(y**6) + 1.647*(y**7) - 0.505*(y**8)
def f_beta_2(x):
y = x - 1.82
return 1.952*y + 2.908*(y**2) - 3.989*(y**3) - 7.985 * \
(y**4) + 11.102*(y**5) + 5.491 * \
(y**6) - 10.805*(y**7) + 3.347*(y**8)
def f_alpha_3(x): return 1.752 - 0.316*x - \
0.104 / ((x - 4.67)**2 + 0.341)
def f_beta_3(x): return -3.090 + 1.825*x + \
1.206 / ((x - 4.62)**2 + 0.262)
def f_alpha_4(x): return f_alpha_3(x) + -0.04473 * \
(x - 5.9)**2 - 0.009779 * (x - 5.9)**3
def f_beta_4(x): return f_beta_3(x) + 0.2130 * \
(x - 5.9)**2 + 0.1207 * (x - 5.9)**3
def f_alpha_5(x): return -1.073 - 0.628*(x - 8) + \
0.137*(x - 8)**2 - 0.070*(x - 8)**3
def f_beta_5(x): return 13.670 + 4.257*(x - 8) - \
0.420*(x - 8)**2 + 0.374 * (x - 8)**3
alpha = np.piecewise(
x, [x <= 1.1, (x > 1.1)*(x <= 3.3), (x > 3.3)*(x <= 5.9), (x > 5.9)*(x <= 8.), (x > 8.)], [f_alpha_1, f_alpha_2, f_alpha_3, f_alpha_4, f_alpha_5])
beta = np.piecewise(
x, [x <= 1.1, (x > 1.1)*(x <= 3.3), (x > 3.3)*(x <= 5.9), (x > 5.9)*(x <= 8.), (x > 8.)], [f_beta_1, f_beta_2, f_beta_3, f_beta_4, f_beta_5])
self.ext = (alpha + beta / self.Rv) * self.Av
def load_Planck_ext(self, file_path):
hdu = fits.open(file_path)
self.ebv_planck = hdu[1].data["EBV"]
def Av_from_Planck(self, ra, dec):
if not hasattr(self, 'ebv_planck'):
raise ValueError(
"Need to load planck dust map first")
# Convert to galactic coordinates
c = SkyCoord(ra=ra * u.degree, dec=dec *
u.degree, frame='icrs').galactic
l, b = c.l.radian, c.b.radian
NSIDE = hp.pixelfunc.get_nside(self.ebv_planck)
pix = hp.pixelfunc.ang2pix(nside=NSIDE, theta=np.pi/2. - b, phi=l)
return self.ebv_planck[pix] * self.Rv
def apply_extinction(self, spec, Av=1.0):
if len(spec) != len(self.lamb):
raise ValueError(
"Dimension of spec do not match that of ExtinctionMW.lamb: try initilize (init_ext_model) by the actual size of spec which you want to apply the extinction to")
if not hasattr(self, 'ext'):
raise ValueError(
"Need to initialize the extinction model (init_ext_model) first")
scale = 10**(-.4 * self.ext * Av)
print("scale = ", scale)
spec *= scale
return spec
...@@ -5,3 +5,4 @@ from .Quasar import Quasar ...@@ -5,3 +5,4 @@ from .Quasar import Quasar
from .Star import Star from .Star import Star
from .Stamp import Stamp from .Stamp import Stamp
from .FlatLED import FlatLED from .FlatLED import FlatLED
from .ExtinctionMW import ExtinctionMW
#!/bin/bash #!/bin/bash
#SBATCH -J CSSTSim #SBATCH -J CSSTSim
#SBATCH -N 1 #SBATCH -N 2
#SBATCH --ntasks-per-node=6 #SBATCH --ntasks-per-node=6
#SBATCH -p debug #SBATCH -p debug
#SBATCH --mem=60G #SBATCH --mem=96G
module load mpi/hpcx/2.4.1/gcc-7.3.1 module load mpi/hpcx/2.4.1/gcc-7.3.1
date date
...@@ -12,4 +12,4 @@ date ...@@ -12,4 +12,4 @@ date
#限定单节点任务数 #限定单节点任务数
srun hostname -s | sort -n | awk -F"-" '{print $2}' | uniq > pnodes srun hostname -s | sort -n | awk -F"-" '{print $2}' | uniq > pnodes
mpirun -mca pml ucx -x UCX_NET_DEVICES=mlx5_0:1 -machinefile pnodes -np 6 --map-by node python3 /public/home/fangyuedong/project/csst_msc_sim/run_sim.py --config_file config_overall.yaml --catalog C9_Catalog -c /public/home/fangyuedong/project/csst_msc_sim/config mpirun -mca pml ucx -x UCX_NET_DEVICES=mlx5_0:1 -machinefile pnodes -np 12 --map-by node python3 /public/home/fangyuedong/project/csst_msc_sim/run_sim.py --config_file config_overall.yaml --catalog C9_Catalog -c /public/home/fangyuedong/project/csst_msc_sim/config
\ No newline at end of file \ No newline at end of file
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