In [1]:
# Makes print and division act like Python 3
from __future__ import print_function, division
# Import the usual libraries
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
# Enable inline plotting
%matplotlib inline
from IPython.display import display, Latex, clear_output
from matplotlib.backends.backend_pdf import PdfPages
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import pynrc
from pynrc import nrc_utils
from pynrc.nrc_utils import S, source_spectrum
pynrc.setup_logging('WARNING', verbose=False)
In [3]:
# Observation Definitions
from pynrc.nb_funcs import make_key, obs_wfe, obs_optimize
from pynrc.nb_funcs import model_info, disk_rim_model
# Functions to run a series of operations
from pynrc.nb_funcs import do_opt, do_contrast, do_gen_hdus, do_sat_levels
# Plotting routines
from pynrc.nb_funcs import plot_contrasts, plot_contrasts_mjup, planet_mags, plot_planet_patches
from pynrc.nb_funcs import update_yscale, do_plot_contrasts, do_plot_contrasts2
from pynrc.nb_funcs import plot_hdulist, plot_images, plot_images_swlw
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# Various Bandpasses
bp_v = S.ObsBandpass('v')
bp_k = pynrc.bp_2mass('k')
bp_w1 = pynrc.bp_wise('w1')
bp_w2 = pynrc.bp_wise('w2')
In [5]:
# source, dist, age, sptype, vmag kmag W1 W2
args_sources = [('TW Hya', 60, 10, 'M0V', 11.0, 7.3, 7.0, 6.9)]
ref_sources = args_sources
In [6]:
# Directory housing VOTables
# http://vizier.u-strasbg.fr/vizier/sed/
votdir = 'votables/'
# Directory to save plots and figures
outdir = 'YSOs/'
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# List of filters
args_filter = [('F187N', None, None),
('F200W', None, None),
('F405N', None, None),
('F410M', None, None),]
filt_keys = []
for filt,mask,pupil in args_filter:
filt_keys.append(make_key(filt, mask=mask, pupil=pupil))
In [8]:
# Fit spectrum to SED photometry
i=0
name_sci, dist_sci, age_sci, spt_sci, vmag_sci, kmag_sci, w1_sci, w2_sci = args_sources[i]
vot = votdir + name_sci.replace(' ' ,'') + '.vot'
mag_sci, bp_sci = vmag_sci, bp_v
args = (name_sci, spt_sci, mag_sci, bp_sci, vot)
src = source_spectrum(*args)
src.fit_SED(use_err=False, robust=False, wlim=[1,30], IR_excess=True)
# Final source spectrum
sp_sci = src.sp_model
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# Do the same for the reference source
name_ref, spt_ref, sp_ref = name_sci, spt_sci, sp_sci
In [10]:
cols = plt.rcParams['axes.prop_cycle'].by_key()['color']
# Plot spectra
fig, axes = plt.subplots(1,2, figsize=(14,4.5))
ax = axes[0]
src.plot_SED(ax=axes[0], xr=[0.5,30])
ax.set_title('Science SED -- {} ({})'.format(name_sci, spt_sci))
# ax.set_xscale('linear')
# ax.xaxis.set_minor_locator(AutoMinorLocator())
ax = axes[1]
xr = [1,6]
bp = pynrc.read_filter(*args_filter[-1])
sp = sp_sci
w = sp.wave / 1e4
o = S.Observation(sp, bp, binset=bp.wave)
sp.convert('photlam')
f = sp.flux / sp.flux[(w>xr[0]) & (w<xr[1])].max()
ind = (w>=xr[0]) & (w<=xr[1])
ax.plot(w[ind], f[ind], lw=1, label=sp.name)
ax.set_ylabel('Normalized Flux (ph/s/wave)')
sp.convert('flam')
ax.set_xlim(xr)
ax.set_xlabel(r'Wavelength ($\mu m$)')
ax.set_title('{} Spectrum and Bandpasses'.format(sp_sci.name))
# Overplot Filter Bandpass
ax2 = ax.twinx()
for i, af in enumerate(args_filter):
bp = pynrc.read_filter(*af)
ax2.plot(bp.wave/1e4, bp.throughput, color=cols[i+1], label=bp.name+' Bandpass')
ax2.set_ylim([0,ax2.get_ylim()[1]])
ax2.set_xlim(xr)
ax2.set_ylabel('Bandpass Throughput')
ax.legend(loc='upper left')
ax2.legend(loc='upper right')
fig.tight_layout()
fig.savefig(outdir+'{}_SED.pdf'.format(name_sci.replace(' ','')))
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from astropy.io import fits
hdul = fits.open(outdir + 'model_TWHya.fits')
# Data is in million Jy per Steradian
data = hdul[0].data
data_wave = 2.2 # micons
pa_offset = 0
# Arcsec/pixel
pix_asec = 0.010
# Steradians to square arcsec
sr_to_asec2 = (3600*180/np.pi)**2
# Data in Jy/arcsec^2
data *= (1e9 * pix_asec**2 / sr_to_asec2) # mJy / pixel
# Mask inner disk region
rho = nrc_utils.dist_image(data, pixscale=pix_asec)
data[rho<=0.075] = 0
hdul[0].data = nrc_utils.rotate_offset(data, pa_offset, reshape=False)
args_disk = (hdul, pix_asec, dist_sci, data_wave, 'mJy/pixel')
#hdul_out = pynrc.obs_nircam.model_to_hdulist(args_disk, sp_sci, bp)
extent = np.array([-1,1,-1,1]) * hdul[0].data.shape[0] * pix_asec / 2
plt.imshow(hdul[0].data*rho**2, extent=extent)
#plt.xlim([-1,1])
#plt.ylim([-1,1])
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In [11]:
subsize = 400
# Create a dictionary that holds the obs_hci class for each filter
wfe_drift = 0
obs_dict = obs_wfe(wfe_drift, args_filter, sp_sci, dist_sci, sp_ref=sp_ref, args_disk=args_disk,
wind_mode='WINDOW', subsize=subsize, verbose=False)
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# if there's a disk input, then we want to remove disk
# contributions from stellar flux and recompute to make
# sure total flux counts matches what we computed for
# sp_sci in previous section to match real photometry
if args_disk is not None:
for key in filt_keys:
obs = obs_dict[key]
star_flux = obs.star_flux(sp=sp_sci) # Pass original input spectrum
disk_flux = obs.disk_hdulist[0].data.sum()
obs.sp_sci = sp_sci * (1 - disk_flux / star_flux)
obs.sp_sci.name = sp_sci.name
print(disk_flux, star_flux, obs.star_flux())
obs.sp_ref = obs.sp_sci
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# Update detector readout
for i, key in enumerate(filt_keys):
obs = obs_dict[key]
if 'none' in key:
pattern, ng, nint_sci, nint_ref = ('RAPID',5,160,160)
elif ('MASK210R' in key) or ('MASKSWB' in key):
pattern, ng, nint_sci, nint_ref = ('BRIGHT2',10,20,20)
else:
pattern, ng, nint_sci, nint_ref = ('MEDIUM8',10,15,15)
obs.update_detectors(read_mode=pattern, ngroup=ng, nint=nint_sci)
obs.nrc_ref.update_detectors(read_mode=pattern, ngroup=ng, nint=nint_ref)
# print(key)
# print(obs.multiaccum_times)
# _ = obs.sensitivity(nsig=5, units='vegamag', verbose=True)
# print('')
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sat_dict = {}
for k in filt_keys:
print('\n{}'.format(k))
obs = obs_dict[k]
dsat_asec = do_sat_levels(obs, satval=0.9, plot=False)
sat_dict[k] = dsat_asec
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# Determine contrast curves for various WFE drift values
wfe_list = [0, 1, 2, 5]
nsig = 5
roll = 10
# fk_contrast = ['F444W_none_none', 'F410M_none_none']
curves_dict = do_contrast(obs_dict, wfe_list, filt_keys,
nsig=nsig, roll_angle=roll, opt_diff=False, no_ref=True)
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lin_vals = np.linspace(0.2,0.8,len(wfe_list))
c1 = plt.cm.Reds_r(lin_vals)
c2 = plt.cm.Blues_r(lin_vals)
key1, key2 = ('F410M_none_none', 'F200W_none_none') #filt_keys[-2:][::-1]
lab1 = '{}'.format(obs_dict[key1].filter)
lab2 = '' if key2 is None else '{}'.format(obs_dict[key2].filter)
fig, axes_all = do_plot_contrasts2(key1, key2, curves_dict, nsig, obs_dict, wfe_list, age_sci,
sat_dict=sat_dict, label1=lab1, label2=lab2, c1=c1, c2=c2,
xr=[0,5], yr=[25,10], yscale2='log', yr2=[3e-2, 100])
fig.subplots_adjust(top=0.8, bottom=0.1 , left=0.05, right=0.95)
fname = "{}_contrast.pdf".format(name_sci.replace(" ", ""))
fig.savefig(outdir+fname)
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# Place 1MJup planets at 0.4" and 1.5"
# Maybe renormalize to lower mass COND planets?
rth_arr = [(0.4,45), (1.5,135)] # sep (asec), PA
mass_arr = [1, 1]
mdot_arr = [0e-8, 0e-8]
av_arr = [0, 0]
for key in filt_keys:
obs = obs_dict[key]
obs.kill_planets()
for i in range(len(rth_arr)):
obs.add_planet(rtheta=rth_arr[i], runits='asec', age=age_sci, mass=mass_arr[i], entropy=13,
accr=False, mdot=mdot_arr[i], Av=av_arr[i],
renorm_args=None)#(Lmag,'vegamag',Lbp))
pl_mags = []
for pl in obs.planets:
sp = obs.planet_spec(**pl)
#renorm_args = pl['renorm_args']
#sp_norm = sp.renorm(*renorm_args)
#sp_norm.name = sp.name
#sp = sp_norm
o = S.Observation(sp, obs.bandpass, binset=obs.bandpass.wave)
pl_mags.append(o.effstim('vegamag'))
print('Planet Mags:', key, pl_mags)
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# Ideal
wfe_ref = 0
wfe_roll = 0
hdul_dict_ideal = do_gen_hdus(obs_dict, filt_keys, wfe_ref, wfe_roll, no_ref=False, opt_diff=False,
oversample=4, PA1=0, PA2=0, exclude_noise=True)
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# Roll Subtracted
wfe_ref = 0
wfe_roll = 1
hdul_dict = do_gen_hdus(obs_dict, filt_keys, wfe_ref, wfe_roll, no_ref=True, opt_diff=False,
oversample=4, PA1=-5, PA2=5)
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fk_images = filt_keys
In [25]:
from copy import deepcopy
fig, axes_arr = plt.subplots(2,4, figsize=(14,6.3))
xylim = 2
xr = yr = np.array([-1,1])*xylim
axes = axes_arr[0]
for i, k in enumerate(fk_images):
ax = axes[i]
hdul = deepcopy(hdul_dict_ideal[k])
# Mask out inner region
mask_rad = 0.2
rho = nrc_utils.dist_image(hdul[0].data, pixscale=hdul[0].header['PIXELSCL'])
# hdul[0].data[rho<=mask_rad] = 0
hdul[0].data = hdul[0].data * rho**2
vmax = np.nanmax(hdul[0].data[(rho>mask_rad) & (rho<xylim)])
plot_hdulist(hdul, ax=ax, xr=xr, yr=yr, vmax=vmax, cb_label='')
ax.set_title('Ideal -- {} ($r^2$)'.format(obs_dict[k].filter))
axes = axes_arr[1]
for i, k in enumerate(fk_images):
ax = axes[i]
hdul = deepcopy(hdul_dict[k])
# Saturation radius
sat_rad = sat_dict[k]
# Mask out inner region
mask_rad = np.max([sat_rad, 0.25])
rho = nrc_utils.dist_image(hdul[0].data, pixscale=hdul[0].header['PIXELSCL'])
vmax = np.nanmax(hdul[0].data[(rho>mask_rad) & (rho<xylim)])
hdul[0].data[rho<=mask_rad] = 0
plot_hdulist(hdul, ax=ax, xr=xr, yr=yr, vmin=0, vmax=vmax, cb_label='')
ax.set_title('Roll Sub (' + '$\Delta$' + 'WFE = {} nm)'.format(wfe_roll))
# Location of planet
for pl in obs.planets:
loc = (np.array(pl['xyoff_pix'])) * obs.pix_scale
for ax in axes_arr.flatten():
circle = matplotlib.patches.Circle(loc, radius=xylim/15., lw=1, edgecolor='red', facecolor='none')
ax.add_artist(circle);
for axes in axes_arr:
for i, ax in enumerate(axes):
if i>0: ax.set_ylabel('')
major_ticks = np.arange(-xylim, xylim+1, 1)
minor_ticks = np.arange(-xylim, xylim+0.1, 0.1)
ax.set_xticks(major_ticks)
ax.set_yticks(major_ticks)
ax.set_xticks(minor_ticks, minor=True)
ax.set_yticks(minor_ticks, minor=True)
for ax in axes_arr[0]:
ax.set_xlabel('')
# Title
dist = obs.distance
age_str = 'Age = {:.0f} Myr'.format(age_sci)
dist_str = 'Distance = {:.1f} pc'.format(dist)
title_str = '{} ({}, {})'.format(name_sci,age_str,dist_str)
fig.suptitle(title_str, fontsize=16);
fig.tight_layout()
fig.subplots_adjust(top=0.92)
fname = "{}_images.pdf".format(name_sci.replace(" ", ""))
fig.savefig(outdir+fname)
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