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Copy pathSanjaCubeStokesISingle.py
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SanjaCubeStokesISingle.py
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import numpy as np
from astropy.io import fits
import matplotlib.pyplot as plt
import lightweaver.constants as Const
from lightweaver.rh_atoms import H_6_atom, H_6_CRD_atom, H_3_atom, C_atom, O_atom, OI_ord_atom, Si_atom, Al_atom, CaII_atom, Fe_atom, FeI_atom, He_9_atom, He_atom, He_large_atom, MgII_atom, N_atom, Na_atom, S_atom
from lightweaver.atmosphere import Atmosphere, ScaleType
from lightweaver.atomic_set import RadiativeSet
from lightweaver.atomic_table import get_global_atomic_table
from lightweaver.molecule import MolecularTable
from lightweaver.LwCompiled import LwContext
from lightweaver.utils import InitialSolution
from concurrent.futures import ProcessPoolExecutor, wait, as_completed
from tqdm import tqdm
from contextlib import redirect_stdout
import os
import pickle
def prep_atmos(data, xIdx, yIdx):
height = data[xIdx, yIdx, :, 0].astype('<f8') / 1e2
temp = data[xIdx, yIdx, :, 1].astype('<f8')
vlos = data[xIdx, yIdx, :, 3].astype('<f8') / 1e2
# pgasTop = data[xIdx, yIdx, 0, 2].astype('<f8') / (Const.CM_TO_M**2 / Const.G_TO_KG)
pgas = data[xIdx, yIdx, :, 2].astype('<f8') / (Const.CM_TO_M**2 / Const.G_TO_KG)
return {'height': height, 'temp': temp, 'vlos': vlos, 'pgas': pgas}
def iterate_ctx(ctx, prd=True, Nscatter=3, NmaxIter=10000):
for i in range(NmaxIter):
dJ = ctx.formal_sol_gamma_matrices()
if i < Nscatter:
continue
delta = ctx.stat_equil()
if prd:
dRho = ctx.prd_redistribute(maxIter=5)
if ctx.crswDone and dJ < 3e-3 and delta < 1e-3:
print(i)
print('----------')
return
wave = np.linspace(853.9444, 854.9444, 1001)
data = fits.getdata('better_eb_310400.fits')
# atmosData = prep_atmos(data, 10,10)
def crsw_factory(initVal=1e3):
val = initVal
def callback():
nonlocal val
val = max(1.0, val * 0.1**(1/val))
return val
return callback
def cmo_synth(atmosData, parallel=False, crsw=None):
def inner():
atmos = Atmosphere(ScaleType.Geometric, depthScale=atmosData['height'], temperature=atmosData['temp'], vlos=atmosData['vlos'], vturb=4000*np.ones_like(atmosData['height']))
aSet = RadiativeSet([H_3_atom(), C_atom(), O_atom(), Si_atom(), Al_atom(), CaII_atom(), Fe_atom(), He_atom(), MgII_atom(), N_atom(), Na_atom(), S_atom()])
aSet.set_active('H', 'Ca')
spect = aSet.compute_wavelength_grid()
atmos.convert_scales(Pgas=atmosData['pgas'])
atmos.quadrature(5)
mols = MolecularTable()
eqPops = aSet.iterate_lte_ne_eq_pops(mols, atmos)
ctx = LwContext(atmos, spect, eqPops, conserveCharge=True, initSol=InitialSolution.Lte, crswCallback=crsw)
iterate_ctx(ctx, prd=False)
eqPops.update_lte_atoms_Hmin_pops(atmos)
Iwave = ctx.compute_rays(wave, [1.0])
return Iwave
if parallel:
with open(os.devnull, 'w') as f:
with redirect_stdout(f):
return inner()
else:
return inner()
def cmo_synth_2(atmosData, parallel=False):
def inner():
atmos = Atmosphere(ScaleType.Geometric, depthScale=atmosData['height'], temperature=atmosData['temp'], vlos=atmosData['vlos'], vturb=4000*np.ones_like(atmosData['height']))
aSet = RadiativeSet([H_3_atom(), C_atom(), O_atom(), Si_atom(), Al_atom(), CaII_atom(), Fe_atom(), He_atom(), MgII_atom(), N_atom(), Na_atom(), S_atom()])
aSet.set_active('Ca')
spect = aSet.compute_wavelength_grid()
atmos.convert_scales(Pgas=atmosData['pgas'])
atmos.quadrature(5)
mols = MolecularTable()
eqPops = aSet.iterate_lte_ne_eq_pops(mols, atmos)
ctx = LwContext(atmos, spect, eqPops, conserveCharge=True, initSol=InitialSolution.Lte)
iterate_ctx(ctx, prd=False)
aSet.set_active('H')
spect = aSet.compute_wavelength_grid()
ctx2 = LwContext(atmos, spect, eqPops, conserveCharge=True, initSol=InitialSolution.Lte)
iterate_ctx(ctx2, prd=False)
eqPops.update_lte_atoms_Hmin_pops(atmos)
Iwave = ctx.compute_rays(wave, [1.0])
return Iwave
if parallel:
with open(os.devnull, 'w') as f:
with redirect_stdout(f):
return inner()
else:
return inner()
def cmo_synth_lte(atmosData, parallel=False):
def inner():
atmos = Atmosphere(ScaleType.Geometric, depthScale=atmosData['height'], temperature=atmosData['temp'], vlos=atmosData['vlos'], vturb=4000*np.ones_like(atmosData['height']))
aSet = RadiativeSet([H_3_atom(), C_atom(), O_atom(), Si_atom(), Al_atom(), CaII_atom(), Fe_atom(), He_atom(), MgII_atom(), N_atom(), Na_atom(), S_atom()])
aSet.set_active('Ca')
spect = aSet.compute_wavelength_grid()
atmos.convert_scales(Pgas=atmosData['pgas'])
atmos.quadrature(5)
mols = MolecularTable()
eqPops = aSet.iterate_lte_ne_eq_pops(mols, atmos)
ctx = LwContext(atmos, spect, eqPops, conserveCharge=False)
iterate_ctx(ctx, prd=False)
eqPops.update_lte_atoms_Hmin_pops(atmos)
Iwave = ctx.compute_rays(wave, [1.0])
return Iwave
if parallel:
with open(os.devnull, 'w') as f:
with redirect_stdout(f):
return inner()
else:
return inner()
atmosData = prep_atmos(data,21,21)
Iwave = cmo_synth(atmosData, crsw=crsw_factory())
IwaveNoCrsw = cmo_synth(atmosData)
IwaveLte = cmo_synth_lte(atmosData)
# atmos.convert_scales(Pgas=atmosData['pgas'])
# atmos.quadrature(5)
# mols = MolecularTable()
# eqPops = aSet.iterate_lte_ne_eq_pops(mols, atmos)
# ctx = LwContext(atmos, spect, eqPops, conserveCharge=True, initSol=InitialSolution.Lte)
# iterate_ctx(ctx, prd=False)
# aSet.set_active('H')
# spect = aSet.compute_wavelength_grid()
# atmosHse = Atmosphere(ScaleType.Geometric, depthScale=atmosData['height'], temperature=atmosData['temp'], vlos=atmosData['vlos'], vturb=4000*np.ones_like(atmosData['height']))
# atmosHse.convert_scales(Ptop=atmosData['pgas'][0])
# atmosHse.quadrature(5)
# aSet = RadiativeSet([H_3_atom(), C_atom(), O_atom(), Si_atom(), Al_atom(), CaII_atom(), Fe_atom(), He_atom(), MgII_atom(), N_atom(), Na_atom(), S_atom()])
# aSet.set_active('Ca')
# spectHse = aSet.compute_wavelength_grid()
# eqPopsHse = aSet.iterate_lte_ne_eq_pops(mols, atmosHse)
# ctxHse = LwContext(atmosHse, spectHse, eqPopsHse, conserveCharge=False, initSol=InitialSolution.Lte)
# iterate_ctx(ctxHse, prd=False)
# eqPopsHse.update_lte_atoms_Hmin_pops(atmosHse)
# IwaveHse = ctxHse.compute_rays(wave, [1.0])
plt.ion()
plt.plot(wave, Iwave)
plt.plot(wave, IwaveLte)
# plt.plot(wave, IwaveHse)
plt.show()