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survey_paper.py
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survey_paper.py
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import os
#import pyfits
import astropy.io.fits as pyfits
import numpy as np
import glob
import shutil
import matplotlib.pyplot as plt
USE_PLOT_GUI=False
from matplotlib.figure import Figure
from matplotlib.backends.backend_agg import FigureCanvasAgg
import matplotlib
import threedhst
import threedhst.eazyPy as eazy
import threedhst.catIO as catIO
import unicorn
import re
root = None
def throughput():
os.chdir('/research/HST/GRISM/3DHST/ANALYSIS/SURVEY_PAPER')
xg141, yg141 = np.loadtxt('g141.dat', unpack=True)
xf140, yf140 = np.loadtxt('f140w.dat', unpack=True)
xf814, yf814 = np.loadtxt('f814w.dat', unpack=True)
xg800l, yg800l = np.loadtxt('g800l.dat', unpack=True)
plt.rcParams['text.usetex'] = True
plt.rcParams['font.family'] = 'serif'
plt.rcParams['font.serif'] = 'Times'
fig = unicorn.catalogs.plot_init(square=True, xs=8, aspect=1./3, left=0.105, bottom=0.08, top=0.01, right=0.01)
ax = fig.add_subplot(111)
ax.plot(xg141, yg141, color='black', linewidth=2, alpha=0.5)
ax.fill(xg141, yg141, color='red', linewidth=2, alpha=0.1)
ax.plot(xf140, yf140, color='black', linewidth=2, alpha=0.7)
ax.plot(xg800l, yg800l, color='black', linewidth=2, alpha=0.5)
ax.fill(xg800l, yg800l, color='blue', linewidth=2, alpha=0.1)
ax.plot(xf814, yf814, color='black', linewidth=2, alpha=0.7)
em_lines = [3727, 4861, 4959, 5007, 6563.]
offset = np.array([0,-0.05,0,0,0])
offset = 0.25+np.array([-0.2,-0.05,0,-0.01,-0.1])
xoffset = np.array([0,-120,200,150,0])
line_scale = np.array([1,1,1./2.98,1,1])
em_names = ['[OII]',r'H$\beta$','','[OIII]',r'H$\alpha$']
dlam = 30
zi = 1
show_spectra = True
colors=['blue','green','red']
if show_spectra:
for zi in [1,2,3]:
sedx, sedy = np.loadtxt('templates/EAZY_v1.0_lines/eazy_v1.0_sed4_nolines.dat', unpack=True)
sedy *= 1.*sedy.max()
dl = dlam/(1+zi)
#dl = dlam
for i,em_line in enumerate(em_lines):
em_gauss = 1./np.sqrt(2*np.pi*dl**2)*np.exp(-1*(sedx-em_line)**2/2/dl**2)
sedy += em_gauss/em_gauss.max()*0.6*line_scale[i]
ax.plot(sedx*(1+zi), sedy*0.4+0.5, color=colors[zi-1], alpha=0.7, linewidth=2)
ax.text(5500.,1.18-zi*0.13,r'$z=%d$' %(zi), color=colors[zi-1], fontsize=11)
for i in range(len(em_lines)):
ax.text(em_lines[i]*(1+1)+xoffset[i], 1+offset[i], em_names[i], horizontalalignment='center', fontsize=10)
show_continuous = False
if show_continuous:
em_lines = [3727, 5007, 6563.]
zgrid = np.arange(1000)/1000.*4
for line in em_lines:
ax.plot(line*(1+zgrid), zgrid/4.*0.8+0.5, linewidth=2, alpha=0.5, color='black')
for zi in [0,1,2,3]:
ax.plot([0.1,2.e4],np.array([zi,zi])/4.*0.8+0.5, linestyle='--', color='black', alpha=0.2)
ax.text(5800, 0.08,'G800L',rotation=33., color='black', alpha=0.7)
ax.text(5800, 0.08,'G800L',rotation=33., color='blue', alpha=0.4)
ax.text(7100, 0.03,'F814W',rotation=80., color='black', alpha=0.9)
ax.text(1.115e4, 0.17,'G141',rotation=15., color='black', alpha=0.7)
ax.text(1.115e4, 0.17,'G141',rotation=15., color='red', alpha=0.4)
ax.text(1.21e4, 0.03,'F140W',rotation=88., color='black', alpha=0.9)
ax.set_xlim(4500, 1.79e4)
ax.set_ylim(0,1.4)
ax.set_xlabel(r'$\lambda$ [\AA]')
ax.set_ylabel('throughput')
#ax.set_yticklabels([]);
ytick = ax.set_yticks([0,0.25,0.5,0.75,1.0])
fig.savefig('throughput.pdf')
plt.rcParams['text.usetex'] = False
#
def throughput_v2():
from matplotlib.ticker import MultipleLocator, FormatStrFormatter
#os.chdir('/research/HST/GRISM/3DHST/ANALYSIS/SURVEY_PAPER')
# xg141, yg141 = np.loadtxt('g141.dat', unpack=True)
# xf140, yf140 = np.loadtxt('f140w.dat', unpack=True)
# xf814, yf814 = np.loadtxt('f814w.dat', unpack=True)
# xg800l, yg800l = np.loadtxt('g800l.dat', unpack=True)
import pysynphot as S
bp = S.ObsBandpass('wfc3,ir,g141')
xg141, yg141 = bp.wave, bp.throughput
bp = S.ObsBandpass('wfc3,ir,g102')
xg102, yg102 = bp.wave, bp.throughput
bp = S.ObsBandpass('wfc3,ir,f140w')
xf140, yf140 = bp.wave, bp.throughput
bp = S.ObsBandpass('acs,wfc1,f814w')
xf814, yf814 = bp.wave, bp.throughput
bp = S.ObsBandpass('acs,wfc1,g800l')
xg800l, yg800l = bp.wave, bp.throughput
plt.rcParams['text.usetex'] = True
plt.rcParams['font.family'] = 'Serif'
plt.rcParams['font.serif'] = 'Times'
plt.ioff()
fig = unicorn.catalogs.plot_init(square=True, xs=8, aspect=1./3, left=0.095, bottom=0.1, top=0.095, right=0.01)
#ax = fig.add_subplot(111)
#ax = fig.add_axes(((x0+(dx+x0)*0), y0+0.5, dx, 0.5-top_panel-y0))
ysplit = 0.65
ax = fig.add_axes((0.06, 0.135, 0.935, (ysplit-0.135)))
ax.plot(xg141, yg141, color='black', linewidth=2, alpha=0.5)
ax.fill(xg141, yg141, color='red', linewidth=2, alpha=0.1)
ax.plot(xf140, yf140, color='black', linewidth=2, alpha=0.7)
ax.plot(xg102, yg102, color='black', linewidth=2, alpha=0.5)
ax.fill(xg102, yg102, color='orange', linewidth=2, alpha=0.1)
ax.plot(xg800l, yg800l, color='black', linewidth=2, alpha=0.5)
ax.fill(xg800l, yg800l, color='blue', linewidth=2, alpha=0.1)
ax.plot(xf814, yf814, color='black', linewidth=2, alpha=0.7)
em_names = ['[OII]',r'H$\beta$','','[OIII]',r'H$\alpha$']
dlam = 30
zi = 1
yy = 0.1
ax.text(5800, 0.12+yy,'G800L',rotation=48., color='black', alpha=0.7)
ax.text(5800, 0.12+yy,'G800L',rotation=48., color='blue', alpha=0.4)
ax.text(7100, 0.14+yy,'F814W',rotation=80., color='black', alpha=0.9)
# ax.text(1.115e4, 0.17+yy,'G141',rotation=15., color='black', alpha=0.7)
# ax.text(1.115e4, 0.17+yy,'G141',rotation=15., color='red', alpha=0.4)
ax.text(1.3e4, 0.29+yy,'G141',rotation=10., color='black', alpha=0.7)
ax.text(1.3e4, 0.29+yy,'G141',rotation=10., color='red', alpha=0.4)
ax.text(1.e4, 0.24+yy,'G102',rotation=15., color='black', alpha=0.7)
ax.text(1.e4, 0.24+yy,'G102',rotation=15., color='orange', alpha=0.4)
ax.text(1.21e4, 0.14+yy,'F140W',rotation=88., color='black', alpha=0.9)
#ax.set_yticklabels([]);
#ax2 = ax.twiny()
ax2 = fig.add_axes((0.06, ysplit+0.02, 0.935, (0.86-ysplit)))
ax2.xaxis.set_label_position('top')
ax2.xaxis.set_ticks_position('top')
### H-alpha
xbox = np.array([0,1,1,0,0])
dy= 0.333333
y0= 1.0
ybox = np.array([0,0,1,1,0])*dy
width_acs = np.array([6000.,9000.])
width_wfc3 = np.array([1.1e4,1.65e4])
width_g102 = np.array([0.82e4,1.13e4])
line_names = [r'H$\alpha$',r'H$\beta$ / [OIII]','[OII]']
for i, l0 in enumerate([6563.,4934.,3727]):
zline = width_acs/l0-1
ax2.fill(xbox*(zline[1]-zline[0])+zline[0],y0-ybox-i*dy, color='blue', alpha=0.1)
zline = width_wfc3/l0-1
ax2.fill(xbox*(zline[1]-zline[0])+zline[0],y0-ybox-i*dy, color='red', alpha=0.1)
zline = width_g102/l0-1
ax2.fill(xbox*(zline[1]-zline[0])+zline[0],y0-ybox-i*dy, color='orange', alpha=0.1)
ax2.plot([0,4],np.array([0,0])+y0-(i+1)*dy, color='black')
ax2.text(3.7,y0-(i+0.5)*dy, line_names[i], horizontalalignment='right', verticalalignment='center')
ax.set_xlim(4500, 1.79e4)
ax.set_ylim(0,0.65)
ytick = ax.set_yticks([0,0.2,0.4,0.6])
ax.set_xlabel(r'$\lambda$ [\AA]')
ax.set_ylabel('Throughput')
minorLocator = MultipleLocator(1000)
ax.xaxis.set_minor_locator(minorLocator)
minorLocator = MultipleLocator(0.1)
ax.yaxis.set_minor_locator(minorLocator)
ax2.set_xlim(0,3.8)
ytick = ax2.set_yticks([])
ax2.set_ylim(0,1)
minorLocator = MultipleLocator(0.1)
ax2.xaxis.set_minor_locator(minorLocator)
ax2.set_xlabel(r'$z_\mathrm{line}$')
#fig.savefig('throughput.eps')
fig.savefig('throughput.pdf')
plt.rcParams['text.usetex'] = False
def orbit_structure():
"""
Show the POSTARG offsets in WFC3 / ACS
"""
os.chdir('/research/HST/GRISM/3DHST/ANALYSIS/SURVEY_PAPER')
plt.rcParams['text.usetex'] = True
plt.rcParams['font.family'] = 'serif'
plt.rcParams['font.serif'] = 'Times'
wfc3_color, acs_color = 'red','blue'
wfc3_color, acs_color = 'blue','green'
fig = unicorn.catalogs.plot_init(square=True, xs=4.4, aspect=1, left=0.09, bottom=0.08)
ax = fig.add_subplot(111)
a11 = 0.1355
b10 = 0.1211 # arcsec / pix, from instrument HB
#dxs = np.array([0,-20,-13,7]) + np.int(np.round(xsh[0]))*0
#dys = np.array([0,-7,-20,-13]) + np.int(np.round(ysh[0]))*0
x3dhst = np.array([0, 1.355, 0.881, -0.474])/a11
y3dhst = np.array([0, 0.424, 1.212, 0.788])/b10
xgoodsn = np.array([0,0.6075, 0.270, -0.3375])/a11
ygoodsn = np.array([0,0.1815, 0.6655, 0.484])/b10
#### SN fields:
test = """
files=`ls ibfuw1*flt.fits.gz`
for file in $files; do result=`dfitsgz $file |fitsort FILTER APERTURE POSTARG1 POSTARG2 | grep -v POST`; echo "${file} ${result}"; done
"""
xmarshall = np.array([-0.34, -0.540, 0.0, 0.608, 0.273])/a11
ymarshall = np.array([-0.34, -0.243, 0.0, 0.244, 0.302])/b10
xgeorge = np.array([0.0, -0.608, 0.273, -0.340, 0.540])/a11
ygeorge = np.array([0.0, 0.244, 0.302, -0.340, -0.243])/b10
x41 = np.array([0.273, -0.608, 0.540, -0.340, -0.340, 0.540])/a11
y41 = np.array([0.302, 0.244, -0.243, -0.301, -0.301, -0.243])/b10
xprimo = np.array([0.0, 0.474, 0.290, 0.764, -0.290, 0.184])/a11
yprimo = np.array([0.0, 0.424, -0.290, 0.134, 0.290, 0.714])/b10
xers = np.array([-10.012, 9.988, 9.971, -9.958])/a11
yers = np.array([5.058, 5.050, -5.045, -5.045])/b10
xcooper = np.array([0, 0.6075, 0.270 ,-0.3375])/a11
ycooper = np.array([0, 0.1815, 0.6655, 0.484])/b10
xstanford = np.array([-0.169, 0.372, 0.169, -0.372])/a11
ystanford = np.array([-0.242, 0.06064, 0.242, 0.06064])/b10
xstanford += 0.2
xoff = x3dhst
yoff = y3dhst
print np.round(xoff*10)/10.*2
print np.round(yoff*10)/10.*2
plt.plot(np.round(xoff*10)/10. % 1, np.round(yoff*10)/10. % 1)
plt.xlim(-0.1,1.1); plt.ylim(-0.1,1.1)
ax.plot(xoff, yoff, marker='o', markersize=10, color=wfc3_color, alpha=0.8, zorder=10)
if 1 == 1:
for i in range(4):
ax.text(xoff[i], yoff[i]+0.5, 'F140W + G141', horizontalalignment='center', backgroundcolor='white', zorder=20)
ax.set_xlabel(r'$x$ offset [pix]')
ax.set_ylabel(r'$y$ offset [pix]')
scale = 4
x0 = -2.9
y0 = -5.5
ax.fill(np.array([0,1,1,0])*scale+x0, np.array([0,0,1,1])*scale+y0, color='white', zorder=10)
ax.fill(np.array([0,1,1,0])*scale+x0, np.array([0,0,1,1])*scale+y0, color='black', alpha=0.1, zorder=11)
ax.plot(np.array([0.5,0.5])*scale+x0, np.array([0,1])*scale+y0, color='black', alpha=0.2, zorder=12)
ax.plot(np.array([0,1])*scale+x0, np.array([0.5,0.5])*scale+y0, color='black', alpha=0.2, zorder=12)
ax.plot(np.abs(xoff-np.cast[int](xoff))*scale+x0, np.abs(yoff-np.cast[int](yoff))*scale+y0, marker='o', markersize=10, color=wfc3_color, alpha=0.8, zorder=13)
ax.text(x0+scale/2., y0-1, 'WFC3 Primary', horizontalalignment='center')
#plt.xlim(-5,11)
#plt.ylim(-5,11)
#### ACS:
# XPOS = x*a11 + y*a10
# YPOS = x*b11 + y*b10
#
# a10 a11 b10 b11
# WFC: 0.0000 0.0494 0.0494 0.0040
a10, a11, b10, b11 = 0.0000,0.0494,0.0494,0.0040
#xoff = np.cumsum(xpostarg)
#yoff = np.cumsum(ypostarg)
acsang = 45.
acsang = 92.16- -45.123
xpos_acs, ypos_acs = threedhst.utils.xyrot(xpostarg, ypostarg, acsang)
xpix_acs = xpos_acs / a11
ypix_acs = (ypos_acs-xpix_acs*b11)/b10
x0 = 5.5
#y0 = -4.5
ax.fill(np.array([0,1,1,0])*scale+x0, np.array([0,0,1,1])*scale+y0, color='white', zorder=10)
ax.fill(np.array([0,1,1,0])*scale+x0, np.array([0,0,1,1])*scale+y0, color='black', alpha=0.1, zorder=11)
ax.plot(np.array([0.5,0.5])*scale+x0, np.array([0,1])*scale+y0, color='black', alpha=0.2, zorder=12)
ax.plot(np.array([0,1])*scale+x0, np.array([0.5,0.5])*scale+y0, color='black', alpha=0.2, zorder=12)
ax.plot(np.abs(xpix_acs-np.cast[int](xpix_acs))*scale+x0, np.abs(ypix_acs-np.cast[int](ypix_acs))*scale+y0, marker='o', markersize=10, color=acs_color, alpha=0.8, zorder=13)
#ax.plot(np.array([0,0.5,1,0.5])*scale+x0, np.array([0,0.5,0.5,1])*scale+y0, marker='o', marker='None', color=acs_color, linestyle='--', alpha=0.6, zorder=13)
ax.plot(np.array([0,0.5,0.5,1])*scale+x0, np.array([0,1,0.5,0.5])*scale+y0, marker='o', color=acs_color, linestyle='--', alpha=0.6, zorder=13)
ax.text(x0+scale/2., y0-1, 'ACS Parallel', horizontalalignment='center')
#plt.grid(alpha=0.5, zorder=1, markevery=5)
from matplotlib.ticker import MultipleLocator, FormatStrFormatter
ax.set_xlim(-5.9,12.5)
#ax.set_ylim(-5.9,12.5)
ax.set_ylim(-6.9,11.5)
majorLocator = MultipleLocator(5)
majorFormatter = FormatStrFormatter('%d')
minorLocator = MultipleLocator(1)
ax.xaxis.set_major_locator(majorLocator)
ax.xaxis.set_minor_locator(minorLocator)
ax.xaxis.set_major_formatter(majorFormatter)
ax.xaxis.grid(alpha=0.5, zorder=1, which='major')
ax.xaxis.grid(alpha=0.2, zorder=1, which='minor')
ax.yaxis.set_major_locator(majorLocator)
ax.yaxis.set_minor_locator(minorLocator)
ax.yaxis.set_major_formatter(majorFormatter)
ax.yaxis.grid(alpha=0.5, zorder=1, which='major')
ax.yaxis.grid(alpha=0.2, zorder=1, which='minor')
fig.savefig('dither_box.pdf')
plt.rcParams['text.usetex'] = False
def exptimes():
"""
Extract the range of exposure times from the formatted Phase-II files
"""
os.system('grep F814W 12???.pro |grep " S " > f814w.exptime')
os.system('grep G800L 12???.pro |grep " S " > g800l.exptime')
os.system('grep F140W *.pro |grep MULTIAC |grep NSAMP > f140w.exptime')
os.system('grep G141 *.pro |grep MULTIAC |grep NSAMP > g141.exptime')
### G141
fp = open('g141.exptime')
lines = fp.readlines()
fp.close()
nsamp = []
object = []
for line in lines:
nsamp.append(line.split('NSAMP=')[1][0:2])
object.append(line.split()[1])
expsamp = np.zeros(17)
expsamp[12] = 1002.94
expsamp[13] = 1102.94
expsamp[14] = 1202.94
expsamp[15] = 1302.94
expsamp[16] = 1402.94
nsamp = np.cast[int](nsamp)
nsamp+=1 ### this seems to be the case for all actual observations !!
objects = object[::4]
NOBJ = len(nsamp)/4
texp = np.zeros(NOBJ)
for i in range(NOBJ):
texp[i] = np.sum(expsamp[nsamp[i*4:(i+1)*4]])
print objects[i], texp[i]
print 'G141: %.1f - %.1f' %(texp.min(), texp.max())
def spectral_features():
wmin, wmax = 1.1e4, 1.65e4
print '%-8s %.1f -- %.1f' %('Halpha', wmin/6563.-1, wmax/6563.-1)
print '%-8s %.1f -- %.1f' %('OIII', wmin/5007.-1, wmax/5007.-1)
print '%-8s %.1f -- %.1f' %('OII', wmin/3727.-1, wmax/3727.-1)
print '%-8s %.1f -- %.1f' %('4000', wmin/4000.-1, wmax/4000.-1)
wmin, wmax = 0.55e4, 1.0e4
print '\n\nACS\n\n'
print '%-8s %.1f -- %.1f' %('Halpha', wmin/6563.-1, wmax/6563.-1)
print '%-8s %.1f -- %.1f' %('OIII', wmin/5007.-1, wmax/5007.-1)
print '%-8s %.1f -- %.1f' %('OII', wmin/3727.-1, wmax/3727.-1)
print '%-8s %.1f -- %.1f' %('4000', wmin/4000.-1, wmax/4000.-1)
def aXe_model():
import copy
import scipy.ndimage as nd
os.chdir('/research/HST/GRISM/3DHST/ANALYSIS/SURVEY_PAPER')
dir = pyfits.open('/research/HST/GRISM/3DHST/GOODS-S/PREP_FLT/UDF-F140W_drz.fits')
gri = pyfits.open('/research/HST/GRISM/3DHST/GOODS-S/PREP_FLT/UDF-FC-G141_drz.fits')
mod = pyfits.open('/research/HST/GRISM/3DHST/GOODS-S/PREP_FLT/UDF-FC-G141CONT_drz.fits')
#### rotate all the images so that dispersion axis is along X
angle = gri[1].header['PA_APER']#+180
direct = nd.rotate(dir[1].data, angle, reshape=False)
grism = nd.rotate(gri[1].data, angle, reshape=False)
model = nd.rotate(mod[1].data, angle, reshape=False)
xc, yc = 1877, 2175
NX, NY = 1270, 365
aspect = 3.*NY/NX
xc, yc = 1731, 977
NX, NY = 882, 467
aspect = 1.*NY/NX
plt.gray()
plt.rcParams['lines.linewidth'] = 2
plt.rcParams['text.usetex'] = True
plt.rcParams['font.family'] = 'serif'
plt.rcParams['font.serif'] = 'Times'
fig = unicorn.catalogs.plot_init(square=True, xs=8, aspect=aspect, left=0.12)
fig.subplots_adjust(wspace=0.0,hspace=0.0,left=0.01,
bottom=0.005,right=0.99,top=0.995)
fs1 = 12 ### Font size of label
xlab, ylab = 0.04*NX/3., NY-0.02*NY-0.02*NY
xd, yd = 65, 412 ### my direct images don't line up any more (deleted old ones?)
xd, yd = 412, 65*2
ax = fig.add_subplot(221)
ax.imshow(0-direct[yc-NY/2+yd:yc+NY/2+yd, xc-NX/2+xd:xc+NX/2+xd], vmin=-0.2, vmax=0.02, interpolation='nearest')
ax.set_yticklabels([]); ax.set_xticklabels([])
xtick = ax.set_xticks([0,NX]); ytick = ax.set_yticks([0,NY])
ax.text(xlab, ylab, 'a) Direct F140W', fontsize=fs1, verticalalignment='top')
#ax.text(xlab, ylab, r'$%d\times\ $$%d^{\prime\prime}$' %(NX*0.06, NY*0.06), fontsize=18, backgroundcolor='white', verticalalignment='top')
ax = fig.add_subplot(222)
ax.imshow(0-grism[yc-NY/2:yc+NY/2, xc-NX/2:xc+NX/2], vmin=-0.04, vmax=0.004, interpolation='nearest')
ax.set_yticklabels([]); ax.set_xticklabels([])
xtick = ax.set_xticks([0,NX]); ytick = ax.set_yticks([0,NY])
ax.text(xlab, ylab, 'b) Grism G141', fontsize=fs1, verticalalignment='top')
ax = fig.add_subplot(224)
diff = grism-model
### Flag em lines and 0th order
dy0 = 20
emx, emy = [223, 272, 487, 754, 520, 850, 565, 558, 51, 834, 345, 495], [122, 189, 83, 240, 148, 124, 336, 418, 338, 225, 197, 268]
ax.plot(np.array(emx)+(xc-1731), np.array(emy)-dy0+(yc-977), marker='^', markersize=6, linestyle='None', color='blue', alpha=0.9)
zx, zy = [301, 393, 648], [183, 321, 446]
ax.plot(np.array(zx)+(xc-1731), np.array(zy)-dy0+(yc-977), marker='^', markersize=6, linestyle='None', markeredgecolor='black', markerfacecolor='None', alpha=0.9, markeredgewidth=1.2)
fonts = matplotlib.font_manager.FontProperties()
fonts.set_size(9)
ax.legend(['Emission',r'0th order'], numpoints=1, prop=fonts, handletextpad=0.001, borderaxespad=0.001)
# ax.text(0.04*NX/3., 0.02*NY, 'Em.', fontsize=fs1*0.8, backgroundcolor='white', verticalalignment='bottom', color='green')
# ax.text(0.3*NX/3., 0.02*NY, r'0th', fontsize=fs1*0.8, backgroundcolor='white', verticalalignment='bottom', color='red')
ax.imshow(0-diff[yc-NY/2:yc+NY/2, xc-NX/2:xc+NX/2], vmin=-0.02, vmax=0.002, interpolation='nearest')
ax.set_yticklabels([]); ax.set_xticklabels([])
xtick = ax.set_xticks([0,NX]); ytick = ax.set_yticks([0,NY])
ax.text(xlab, ylab, r'd) Model-subtracted grism', fontsize=fs1, verticalalignment='top')
ax = fig.add_subplot(223)
ax.imshow(0-model[yc-NY/2:yc+NY/2, xc-NX/2:xc+NX/2], vmin=-0.04, vmax=0.004, interpolation='nearest')
ax.set_yticklabels([]); ax.set_xticklabels([])
xtick = ax.set_xticks([0,NX]); ytick = ax.set_yticks([0,NY])
ax.text(xlab, ylab, r'c) aXe Model', fontsize=fs1, verticalalignment='top')
fig.savefig('grism_model.pdf')
plt.rcParams['text.usetex'] = False
def sync():
pass
"""
paths="RAW HTML/scripts PREP_FLT"
dirs="AEGIS COSMOS ERS GOODS-N GOODS-S SN-GEORGE SN-MARSHALL SN-PRIMO UDS"
for dir in $dirs; do
mkdir ${dir}
mkdir ${dir}/HTML
for path in $paths; do
# du -sh ${dir}/${path}
mkdir ${dir}/${path}
rsync -avz --progress $UNICORN:/3DHST/Spectra/Work/${dir}/${path} ${dir}/${path}
done
done
"""
def all_pointings():
pointings(ROOT='GOODS-SOUTH')
pointings(ROOT='COSMOS')
pointings(ROOT='AEGIS')
pointings(ROOT='UDS')
pointings(ROOT='GOODS-N')
def all_pointings_width():
"""
This is the mosaic figure from the paper. The individual fields are combined
manually with Adobe Illustrator.
"""
from unicorn.survey_paper import pointings
fs, left = 10, 0.22
fs, left = 12, 0.25
fs, left = 14, 0.28
fs, left = 16, 0.32
pointings(ROOT='GOODS-SOUTH', width=7, corner='ll', fontsize=fs, left=left)
pointings(ROOT='COSMOS', width=6, corner='lr', fontsize=fs, left=left, right=0.03, bottom=0.115)
pointings(ROOT='AEGIS', width=7, corner='ll', fontsize=fs, left=left, right=0.045)
pointings(ROOT='UDS', width=9, corner='lr', fontsize=fs, left=left-0.02, right=0.04, top=0.02)
pointings(ROOT='GOODS-N', width=6, corner='ur', fontsize=fs, left=left, bottom=0.115)
def pointings_with_status():
"""
Highlight pointings that have been observed (status == 'Archived')
"""
from unicorn.survey_paper import pointings
pointings(ROOT='GOODS-SOUTH', width=7, corner='ll', use_status=True)
pointings(ROOT='GOODS-SOUTH', width=7, corner='ll', use_status=True, show_acs=False)
pointings(ROOT='GOODS-SOUTH', width=7, corner='ll', use_status=True, show_wfc3=False)
pointings(ROOT='COSMOS', width=6, corner='lr', use_status=True)
pointings(ROOT='COSMOS', width=6, corner='lr', use_status=True, show_acs=False)
pointings(ROOT='COSMOS', width=6, corner='lr', use_status=True, show_wfc3=False)
pointings(ROOT='AEGIS', width=7, corner='ll', use_status=True)
pointings(ROOT='AEGIS', width=7, corner='ll', use_status=True, show_acs=False)
pointings(ROOT='AEGIS', width=7, corner='ll', use_status=True, show_wfc3=False)
pointings(ROOT='UDS', width=9, corner='lr', use_status=True)
pointings(ROOT='UDS', width=9, corner='lr', use_status=True, show_acs=False)
pointings(ROOT='UDS', width=9, corner='lr', use_status=True, show_wfc3=False)
pointings(ROOT='UDS', width=9, corner='lr', show_sn_fields=True, use_status=True)
pointings(ROOT='GOODS-SOUTH', width=7, corner='ll', show_sn_fields=True, use_status=True)
def pointings(ROOT='GOODS-SOUTH', width=None, corner='lr', use_status=False, show_acs=True, show_wfc3=True, show_sn_fields=False, fontsize=10, left=22, right=0.02, top=0.01, bottom=0.11):
"""
Make a figure showing the 3D-HST pointing poisitions, read from region files
"""
import unicorn.survey_paper as sup
plt.rcParams['lines.linewidth'] = 0.3
wfc3_color = 'blue'
acs_color = 'green'
os.chdir(unicorn.GRISM_HOME+'ANALYSIS/SURVEY_PAPER')
yticklab = None
dx_ref = (53.314005633802822-52.886197183098595)*np.cos(-27.983151830808076/360*2*np.pi)
CANDELS_PATH = '/research/HST/GRISM/3DHST/REGIONS/CANDELS/'
candels_files = []
candels_alpha = 0.3
candels_color = '0.1'
if use_status:
pointing_list, pointing_status = np.loadtxt('/research/HST/GRISM/3DHST/REGIONS/pointing_status.dat', dtype=np.str, unpack=True)
pointing_list, pointing_status = np.array(pointing_list), np.array(pointing_status)
else:
pointing_list, pointing_status = np.array([]), np.array([])
#### GOODS-S
if ROOT=='GOODS-SOUTH':
x0, x1 = 53.314005633802822, 52.886197183098595
y0, y1 = -27.983151830808076, -27.654474431818176
xticklab = [r'$3^\mathrm{h}33^\mathrm{m}00^\mathrm{s}$', r'$3^\mathrm{h}32^\mathrm{m}30^\mathrm{s}$', r'$3^\mathrm{h}32^\mathrm{m}00^\mathrm{s}$']
xtickv = [degrees(3,33,00, hours=True), degrees(3,32,30, hours=True), degrees(3,32,00, hours=True)]
yticklab = [r'$-27^\circ40^\prime00^{\prime\prime}$', r'$45^\prime00^{\prime\prime}$', r'$-27^\circ50^\prime00^{\prime\prime}$', r'$55^\prime00^{\prime\prime}$']
ytickv = [degrees(-27, 40, 00, hours=False), degrees(-27, 45, 00, hours=False), degrees(-27, 50, 00, hours=False), degrees(-27, 55, 00, hours=False)]
candels_files = glob.glob(CANDELS_PATH+'/GOODS-S*reg')
candels_files.extend(glob.glob(CANDELS_PATH+'/GOODS-W*reg'))
#### COSMOS
if ROOT=='COSMOS':
x1, x0 = 149.99120563380279, 150.23823661971829
y0, y1 = 2.1678109478476815, 2.5996973302980129
xticklab = [r'$10^\mathrm{h}00^\mathrm{m}30^\mathrm{s}$', r'$00^\mathrm{m}00^\mathrm{s}$']
xtickv = [degrees(10,00,30, hours=True), degrees(10,00,00, hours=True)]
yticklab = [r'$+2^\circ15^\prime00^{\prime\prime}$', r'$25^\prime00^{\prime\prime}$', r'$35^\prime00^{\prime\prime}$']
ytickv = [degrees(02, 15, 00, hours=False), degrees(02, 25, 00, hours=False), degrees(02, 35, 00, hours=False)]
candels_files = glob.glob(CANDELS_PATH+'/COSMOS*reg')
#### AEGIS
if ROOT=='AEGIS':
x1, x0 = 214.49707154104345, 215.12704734584406
y0, y1 = 52.680946433013482, 53.01597137966467
xticklab = [r'$18^\mathrm{m}00^\mathrm{s}$', r'$14^\mathrm{h}19^\mathrm{m}00^\mathrm{s}$', r'$20^\mathrm{m}00^\mathrm{s}$']
xticklab = [r'$18^\mathrm{m}$', r'$14^\mathrm{h}19^\mathrm{m}$', r'$20^\mathrm{m}$']
xtickv = [degrees(14,18,00, hours=True), degrees(14,19,00, hours=True), degrees(14,20,00, hours=True)]
yticklab = [r'$+52^\circ45^\prime00^{\prime\prime}$', r'$50^\prime00^{\prime\prime}$', r'$55^\prime00^{\prime\prime}$']
ytickv = [degrees(52, 45, 00, hours=False), degrees(52, 50, 00, hours=False), degrees(52, 55, 00, hours=False)]
candels_files = glob.glob(CANDELS_PATH+'/EGS*reg')
#### UDS
if ROOT=='UDS':
x1, x0 = 34.116935194128146, 34.51871547581829
y0, y1 = -5.2957542206957582, -5.0834327182123147+2./3600
xticklab = [r'$18^\mathrm{m}00^\mathrm{s}$', r'$2^\mathrm{h}17^\mathrm{m}30^\mathrm{s}$', r'$17^\mathrm{m}00^\mathrm{s}$', r'$16^\mathrm{m}30^\mathrm{s}$']
xtickv = [degrees(2,18,00, hours=True), degrees(2,17,30, hours=True), degrees(2,17,00, hours=True), degrees(2,16,30, hours=True)]
yticklab = [r'$05^\prime00^{\prime\prime}$', r'$-5^\circ10^\prime00^{\prime\prime}$', r'$15^\prime00^{\prime\prime}$']
ytickv = [degrees(-5, 05, 00, hours=False), degrees(-5, 10, 00, hours=False), degrees(-5, 15, 00, hours=False)]
candels_files = glob.glob(CANDELS_PATH+'/UDS*reg')
#### GOODS-N
if ROOT=='GOODS-N':
wfc3_color = 'orange'
acs_color = None
x1, x0 = 188.9139017749491, 189.44688055895648
y0, y1 = 62.093791549511998, 62.384068625281309
xticklab = [r'$12^\mathrm{h}37^\mathrm{m}30^\mathrm{s}$', r'$37^\mathrm{m}00^\mathrm{s}$', r'$36^\mathrm{m}30^\mathrm{s}$', r'$36^\mathrm{m}00^\mathrm{s}$']
xtickv = [degrees(12,37,30, hours=True), degrees(12,37,00, hours=True), degrees(12,36,30, hours=True), degrees(12,36,00, hours=True)]
yticklab = [r'$+62^\circ10^\prime00^{\prime\prime}$', r'$15^\prime00^{\prime\prime}$', r'$20^\prime00^{\prime\prime}$']
ytickv = [degrees(62, 10, 00, hours=False), degrees(62, 15, 00, hours=False), degrees(62, 20, 00, hours=False)]
candels_files = glob.glob(CANDELS_PATH+'/GOODSN-OR*reg')
candels_files.extend(glob.glob(CANDELS_PATH+'/GOODSN-SK*reg'))
#### Make square for given plot dimensions
dx = np.abs(x1-x0)*np.cos(y0/360*2*np.pi)
dy = (y1-y0)
if width is None:
width = 7*dx/dx_ref
print '%s: plot width = %.2f\n' %(ROOT, width)
fig = unicorn.catalogs.plot_init(square=True, xs=width, aspect=dy/dx, fontsize=fontsize, left=left, right=right, top=top, bottom=bottom)
#fig = unicorn.catalogs.plot_init(square=True)
ax = fig.add_subplot(111)
polys = []
for file in candels_files:
fp = open(file)
lines = fp.readlines()
fp.close()
#
polys.append(sup.polysplit(lines[1], get_shapely=True))
#fi = ax.fill(wfcx, wfcy, alpha=candels_alpha, color=candels_color)
sup.polys = polys
un = polys[0]
for pp in polys[1:]:
un = un.union(pp)
if un.geometryType() is 'MultiPolygon':
for sub_poly in un.geoms:
x,y = sub_poly.exterior.xy
ax.plot(x,y, alpha=candels_alpha, color=candels_color, linewidth=1)
ax.fill(x,y, alpha=0.1, color='0.7')
else:
x,y = un.exterior.xy
ax.plot(x,y, alpha=candels_alpha, color=candels_color, linewidth=1)
ax.fill(x,y, alpha=0.1, color='0.7')
files=glob.glob(unicorn.GRISM_HOME+'REGIONS/'+ROOT+'-[0-9]*reg')
if ROOT == 'UDS':
p18 = files.pop(9)
print '\n\nPOP %s\n\n' %(p18)
if show_sn_fields:
files.extend(glob.glob(unicorn.GRISM_HOME+'REGIONS/SN*reg'))
files.extend(glob.glob(unicorn.GRISM_HOME+'REGIONS/ERS*reg'))
wfc3_polys = []
acs_polys = []
for file in files:
#
base = os.path.basename(file.split('.reg')[0])
#print base, base in pointing_list
if base in pointing_list:
status = pointing_status[pointing_list == base][0] == 'Archived'
else:
status = False
if not use_status:
status = True
field = re.split('-[0-9]', file)[0]
pointing = file.split(field+'-')[1].split('.reg')[0]
fp = open(file)
lines = fp.readlines()
fp.close()
if base.startswith('SN') | base.startswith('ERS'):
wfc3_color = 'purple'
acs_color = None
pointing = os.path.basename(field)
status = True
#
wfc3_polys.append(sup.polysplit(lines[1], get_shapely=True))
acs_polys.append(sup.polysplit(lines[2], get_shapely=True))
acs_polys.append(sup.polysplit(lines[3], get_shapely=True))
#
wfcx, wfcy = sup.polysplit(lines[1])
if show_wfc3:
if status:
fi = ax.fill(wfcx, wfcy, alpha=0.2, color=wfc3_color)
fi = ax.plot(wfcx, wfcy, alpha=0.8, color=wfc3_color)
else:
fi = ax.fill(wfcx, wfcy, alpha=0.05, color=wfc3_color)
fi = ax.plot(wfcx, wfcy, alpha=0.8, color=wfc3_color)
#
if acs_color is not None:
acsx1, acsy1 = sup.polysplit(lines[2])
acsx2, acsy2 = sup.polysplit(lines[3])
#
if show_acs:
if show_wfc3:
afact = 3
else:
afact = 3
if status:
fi = ax.fill(acsx1, acsy1, alpha=0.05*afact, color=acs_color)
fi = ax.fill(acsx2, acsy2, alpha=0.05*afact, color=acs_color)
#
pl = ax.plot(acsx1, acsy1, alpha=0.1*afact, color=acs_color)
pl = ax.plot(acsx2, acsy2, alpha=0.1*afact, color=acs_color)
else:
pl = ax.plot(acsx1, acsy1, alpha=0.3*afact, color=acs_color)
pl = ax.plot(acsx2, acsy2, alpha=0.3*afact, color=acs_color)
#
xoff, yoff = 0.0, 0.0
if ROOT=='GOODS-SOUTH':
#print pointing
if pointing == '36':
xoff, yoff = 0.002,0.0075
if pointing == '37':
xoff, yoff = -0.005,-0.007
if pointing == '38':
xoff, yoff = 0.007,-0.007
#
if show_wfc3:
te = ax.text(np.mean(wfcx[:-1])+xoff, np.mean(wfcy[:-1])+yoff, pointing, va='center', ha='center', fontsize=13)
#### Get field area from full WFC3 polygons
un_wfc3 = wfc3_polys[0]
for pp in wfc3_polys[1:]:
un_wfc3 = un_wfc3.union(pp)
#
wfc3_union= []
if un_wfc3.geometryType() is 'MultiPolygon':
total_area = 0
xavg, yavg, wht = 0, 0, 0
for sub_poly in un_wfc3.geoms:
area_i = sub_poly.area*np.cos(y0/360.*2*np.pi)
total_area += area_i
x,y = sub_poly.exterior.xy
wfc3_union.append(sub_poly)
xavg += np.mean(x)*area_i**2
yavg += np.mean(y)*area_i**2
wht += area_i**2
#ax.plot(x,y, alpha=0.8, color='orange', linewidth=1)
xavg, yavg = xavg/wht, yavg/wht
else:
total_area = un_wfc3.area*np.cos(y0/360.*2*np.pi)
x,y = un_wfc3.exterior.xy
wfc3_union.append(un_wfc3)
#ax.plot(x,y, alpha=0.8, color='orange', linewidth=1)
xavg, yavg = np.mean(x), np.mean(y)
#plt.plot([xavg,xavg],[yavg,yavg], marker='x', markersize=20)
#### Get ACS overlap fraction
if ROOT != 'GOODS-N':
un_acs = acs_polys[0]
for pp in acs_polys[1:]:
un_acs = un_acs.union(pp)
acs_union = []
if un_acs.geometryType() is 'MultiPolygon':
for sub_poly in un_acs.geoms:
x,y = sub_poly.exterior.xy
acs_union.append(sub_poly)
else:
x,y = un_acs.exterior.xy
acs_union.append(un_acs)
wfc3_area = 0.
acs_overlap_area = 0.
for wun in wfc3_union:
wfc3_area += wun.area*np.cos(y0/360.*2*np.pi)*3600.
for aun in acs_union:
overlap = wun.intersection(aun)
acs_overlap_area += overlap.area*np.cos(y0/360.*2*np.pi)*3600.
print '== Combined areas ==\nWFC3, ACS, frac: %.1f %.1f %.1f' %(wfc3_area, acs_overlap_area ,acs_overlap_area/wfc3_area*100)
dummy = """
wf = 147.3 + 122.2 + 121.9 + 114.0
ac = 134.6 + 112.7 + 102.4 + 102.8
print ac/wf*100.
"""
#
if yticklab is not None:
ax.set_xticklabels(xticklab)
xtick = ax.set_xticks(xtickv)
ax.set_yticklabels(yticklab)
ytick = ax.set_yticks(ytickv)
ax.set_xlabel(r'$\alpha$')
ax.set_ylabel(r'$\delta$')
fsi = '20'
if ROOT == 'GOODS-SOUTH':
field_label = 'GOODS-S'
else:
field_label = ROOT
if corner=='lr':
ax.text(0.95, 0.05,r'$\mathit{%s}$' %(field_label),
horizontalalignment='right',
verticalalignment='bottom',
transform = ax.transAxes, fontsize=fsi)
#
if corner=='ll':
ax.text(0.05, 0.05,r'$\mathit{%s}$' %(field_label),
horizontalalignment='left',
verticalalignment='bottom',
transform = ax.transAxes, fontsize=fsi)
#
if corner=='ur':
ax.text(0.95, 0.95,r'$\mathit{%s}$' %(field_label),
horizontalalignment='right',
verticalalignment='top',
transform = ax.transAxes, fontsize=fsi)
#
if corner=='ul':
ax.text(0.05, 0.95,r'$\mathit{%s}$' %(field_label),
horizontalalignment='left',
verticalalignment='top',
transform = ax.transAxes, fontsize=fsi)
ax.set_xlim(x0, x1)
ax.set_ylim(y0, y1)
# print 'RA - ', hexagesimal(x0), hexagesimal(x1)
# print 'Dec - ', hexagesimal(y0, hours=False), hexagesimal(y1, hours=False)
print 'RA - ', hexagesimal(xavg)
print 'Dec - ', hexagesimal(yavg, hours=False)
print 'Area: %.1f\n' %(total_area*3600.)
tag = ''
if not show_acs:
tag += '_noacs'
if not show_wfc3:
tag += '_nowfc3'
if show_sn_fields:
tag += '_sn'
if use_status:
plt.savefig('%s_pointings_status%s.pdf' %(ROOT, tag))
else:
plt.savefig('%s_pointings%s.pdf' %(ROOT, tag))
def get_UDF_center():
file='/research/HST/GRISM/3DHST/REGIONS/GOODS-SOUTH-38.reg'
field = re.split('-[0-9]', file)[0]
pointing = file.split(field+'-')[1].split('.reg')[0]
fp = open(file)
lines = fp.readlines()
fp.close()
#
px, py = sup.polysplit(lines[1], get_shapely=False)
print 'UDF: ', hexagesimal(np.mean(px[:-1]), hours=True), hexagesimal(np.mean(py[:-1]), hours=False)
def degrees(deg, min, sec, hours=True):
adeg = np.abs(deg)
degrees = adeg + min/60. + sec/3600.
if deg < 0:
degrees *= -1
if hours:
degrees *= 360./24
return degrees
def hexagesimal(degrees, hours=True, string=True):
if hours:
degrees *= 24/360.
if degrees < 0:
sign = -1
si = '-'
else:
sign = 1
si = ''
degrees = np.abs(degrees)
deg = np.int(degrees)
min = np.int((degrees-deg)*60)
sec = (degrees-deg-min/60.)*3600
if string:
return '%s%02d:%02d:%05.2f' %(si, deg, min, sec)
else:
return sign*deg, min, sec
def polysplit(region='polygon(150.099223,2.391097,150.086084,2.422515,150.050573,2.407277,150.064586,2.376241)', get_shapely=False):
spl = region[region.find('(')+1:region.find(')')].split(',')
px = spl[0::2]
py = spl[1::2]
px.append(px[0])
py.append(py[0])
px, py = np.cast[float](px), np.cast[float](py)
if get_shapely:
from shapely.geometry import Polygon
list = []
for i in range(len(px)):
list.append((px[i], py[i]))
poly = Polygon(tuple(list))
return poly
else:
return px, py
#
def demo_background_subtract(root='COSMOS-13'):
"""
Make a figure demonstrating the background subtraction of the grism images
"""
import threedhst
import threedhst.prep_flt_files
import threedhst.grism_sky as bg
import unicorn
import unicorn.survey_paper as sup
import pyfits
path = unicorn.analysis.get_grism_path(root)
os.chdir(path)
if not os.path.exists('EXAMPLE'):
os.system('mkdir EXAMPLE')
os.chdir('EXAMPLE')
files = glob.glob('../PREP_FLT/%s-G141*' %(root))
files.append('../PREP_FLT/%s-F140W_tweak.fits' %(root))
for file in files:
if 'drz.fits' not in file:
os.system('cp %s .' %(file))
print file