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make_spectra_movie.py
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make_spectra_movie.py
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import trident
import numpy as np
import yt
import MISTY
import sys
import os
import matplotlib as mpl
import seaborn as sns
sns.set_style("whitegrid", {'axes.grid' : False})
mpl.rcParams['font.family'] = 'stixgeneral'
mpl.rcParams['font.size'] = 6.
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
from mpl_toolkits.axes_grid1 import AxesGrid
import matplotlib.ticker as ticker
from astropy.table import Table
from astropy.io import fits
from get_refine_box import get_refine_box
from get_proper_box_size import get_proper_box_size
from get_halo_center import get_halo_center
from consistency import *
def extract_spectra(ds, impact, **kwargs):
read_fits_file = kwargs.get('read_fits_file', False)
out_fits_name = kwargs.get('out_fits_name', "temp.fits")
xmin = kwargs.get("xmin", 0)
xmax = kwargs.get("xmax", 1)
halo_center = kwargs.get("halo_center", [0.5, 0.5, 0.5])
if read_fits_file:
print "opening ", out_fits_name
hdulist = fits.open(out_fits_name)
ray_start_str, ray_end_str = hdulist[0].header['RAYSTART'], hdulist[0].header['RAYEND']
ray_start = [float(ray_start_str.split(",")[0]), \
float(ray_start_str.split(",")[1]), \
float(ray_start_str.split(",")[2])]
ray_end = [float(ray_end_str.split(",")[0]), \
float(ray_end_str.split(",")[1]), \
float(ray_end_str.split(",")[2])]
return hdulist, ray_start, ray_end
else:
proper_box_size = get_proper_box_size(ds)
# line_list = ['H I 1216', 'Ly b', 'Ly c', 'Ly d', 'Ly 10', 'Si II 1260', 'C IV 1548', 'O VI 1032']
line_list = ['H I 1216', 'H I 1026', 'H I 973', 'H I 950', 'H I 919', 'Si II 1260', 'Si III 1207', 'C II 1335', 'C IV 1548', 'O VI 1032']
ray_start = np.zeros(3)
ray_end = np.zeros(3)
ray_start[0] = xmin
ray_end[0] = xmax
ray_start[1] = halo_center[1] - (impact/proper_box_size)
ray_end[1] = ray_start[1]
ray_start[2] = halo_center[2]
ray_end[2] = ray_start[2]
rs, re = np.array(ray_start), np.array(ray_end)
# out_fits_name = "hlsp_misty_foggie_"+haloname+"_"+ds.basename.lower()+"_i"+"{:05.1f}".format(impacts[i]) + \
# "_dx"+"{:4.2f}".format(dx[i])+"_v2_los.fits"
rs = ds.arr(rs, "code_length")
re = ds.arr(re, "code_length")
ray = ds.ray(rs, re)
triray = trident.make_simple_ray(ds, start_position=rs.copy(),
end_position=re.copy(),
data_filename="test.h5",
lines=line_list,
ftype='gas')
hdulist = MISTY.write_header(triray,start_pos=ray_start,end_pos=ray_end,
lines=line_list, impact=impact)
tmp = MISTY.write_parameter_file(ds,hdulist=hdulist)
for line in line_list:
sg = MISTY.generate_line(triray,line,write=True,use_spectacle=False,hdulist=hdulist)
MISTY.write_out(hdulist,filename=out_fits_name)
return hdulist, ray_start, ray_end
def make_movie():
# load the simulation
# ds = yt.load("/Users/molly/foggie/halo_008508/nref11n/nref11n_nref10f_refine200kpc_z4to2/RD0020/RD0020")
# track_name = "/Users/molly/foggie/halo_008508/nref11n/nref11n_nref10f_refine200kpc_z4to2/halo_track"
# output_dir = "/Users/molly/Dropbox/foggie-collab/plots_halo_008508/nref11n/nref11n_nref10f_refine200kpc_z4to2/spectra/"
ds = yt.load("/Users/molly/foggie/halo_008508/nref11n/natural/RD0020/RD0020")
track_name = "/Users/molly/foggie/halo_008508/nref11n/nref11n_nref10f_refine200kpc_z4to2/halo_track"
output_dir = "/Users/molly/Dropbox/foggie-collab/plots_halo_008508/nref11n/natural/spectra"
os.chdir(output_dir)
track = Table.read(track_name, format='ascii')
track.sort('col1')
zsnap = ds.get_parameter('CosmologyCurrentRedshift')
proper_box_size = get_proper_box_size(ds)
refine_box, refine_box_center, x_width = get_refine_box(ds, zsnap, track)
halo_center = get_halo_center(ds, refine_box_center)
# interpolate the center from the track
x_left = np.float(refine_box.left_edge[0].value)
x_right = np.float(refine_box.right_edge[0].value)
y_left = np.float(refine_box.left_edge[1].value)
y_right = np.float(refine_box.right_edge[1].value)
# slice will be repeated, so let's make it first
slc = yt.SlicePlot(ds,'z',('gas','density'),center=halo_center,width=x_width)
## slc = ds.r[xmin:xmax, ymin:ymax, halo_center[2]]
res = [1000,1000]
# frb = slc.frb(x_width, res)
frb = slc.frb['gas','density']
# image = np.array(frb['gas', 'density'])
image = np.array(frb)
print "min, max density = ", np.min(np.log10(image)), np.max(np.log10(image))
# extent = [float(x.in_units('code_length')) for x in (pro.xlim + pro.ylim)]
extent = [x_left, x_right, y_left, y_right]
# get a spectrum!
# impact = 25.
# impacts = np.arange(25.,45.,0.5)
impacts = [25.]
for impact in impacts:
out_fits_name = "hlsp_misty_foggie_halo008508_"+ds.basename.lower()+"_i"+"{:05.1f}".format(impact) + \
"_dx"+"{:4.2f}".format(0.)+"_v2_los.fits"
out_plot_name = "slice_with_spectra_halo008508_"+ds.basename.lower()+"_i"+"{:05.1f}".format(impact) + \
"_dx"+"{:4.2f}".format(0.)+".png"
hdulist, ray_start, ray_end = extract_spectra(ds, impact, read_fits_file=False,
out_fits_name=out_fits_name,
xmin=x_left, xmax=x_right, halo_center=halo_center)
print "(impact/proper_box_size)/x_width = ", (impact/proper_box_size)/x_width
# start by setting up plots
fig = plt.figure(figsize=(12,6), dpi=100)
# creates grid on which the figure will be plotted
gs = gridspec.GridSpec(3, 2)
## this will be the slice
ax_slice = fig.add_subplot(gs[:,0])
cax = ax_slice.imshow(np.log10(image), extent=extent, cmap=density_color_map, \
vmin = -29.6, vmax=-23.5)
ax_slice.plot([ray_start[0], ray_end[0]], [ray_start[1], ray_end[1]], color="white", lw=2.)
ax_slice.set_aspect('equal')
ax_slice.xaxis.set_major_locator(ticker.NullLocator())
ax_slice.yaxis.set_major_locator(ticker.NullLocator())
cbar = fig.colorbar(cax, orientation='vertical', pad=0.01, shrink=0.8)
cbar.set_label(r'log density [cm$^{-3}$]')
## print ray_start, ray_end, extent
zmin, zmax = 1.998, 2.004
## these will be the spectra
ax_spec1 = fig.add_subplot(gs[0,1])
ax_spec1.plot(hdulist["H I 1216"].data['redshift'], hdulist["H I 1216"].data['flux'], color="#4575b4",lw=2)
ax_spec1.text(zmin+0.0003, 0, "H I 1216", fontsize=12.)
plt.xlim(zmin, zmax)
plt.ylim(-0.05, 1.05)
## these will be the spectra
ax_spec2 = fig.add_subplot(gs[1,1])
ax_spec2.plot(hdulist["C IV 1548"].data['redshift'], hdulist["C IV 1548"].data['flux'], color="#4575b4",lw=2)
ax_spec2.text(zmin+0.0003, 0, "C IV 1548", fontsize=12.)
plt.xlim(zmin, zmax)
plt.ylim(-0.05, 1.05)
## these will be the spectra
ax_spec3 = fig.add_subplot(gs[2,1])
ax_spec3.plot(hdulist["O VI 1032"].data['redshift'], hdulist["O VI 1032"].data['flux'], color="#4575b4",lw=2)
ax_spec3.text(zmin+0.0003, 0, "O VI 1032", fontsize=12.)
plt.xlim(zmin, zmax)
plt.ylim(-0.05, 1.05)
fig.tight_layout()
plt.savefig(out_plot_name)
plt.close()
if __name__ == "__main__":
make_movie()
sys.exit("~~~*~*~*~*~*~all done!!!! spectra are fun!")