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make_norm_spec_plots.py
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import os
if os.environ['HOST'] == 'pummelo.stsci.edu':
base_dir = '/Users/bostroem/science'
elif os.environ['HOST'] == 'satsuma.stsci.edu':
base_dir = '/user/bostroem/science'
else:
print 'Computer not recognized, paths will need to be manually updated, HOST = %s' %(os.environ['HOST'])
import sys
sys.path.append(os.path.join(base_dir, 'programs'))
import normalize_spec
import pyfits
from matplotlib import pyplot
from stsci.convolve import boxcar
import pdb
import numpy as np
from optparse import OptionParser
def make_plots(fuv, ccd1, ccd2, ccd3, ccd4, reject_cr_flag, norm_spec_flag, ax1_ylim, ax2_ylim, title, base_dir, bin_flag = None):
check_existance_of_files(ccd1, ccd2, ccd3, ccd4, fuv)
if norm_spec_flag == True:
tbdata5 = pyfits.getdata(fuv, 1)
wl5 = tbdata5['wavelength'].ravel()
net5 = tbdata5['flux'].ravel()
#dq = tbdata5['dq'].ravel()
#wl5 = wl5[dq&512 != 512]
#net5 = net5[dq&512 != 512]
#cr_reject
if reject_cr_flag:
#Open data files
tbdata1 = pyfits.getdata(ccd1, 1)
tbdata2 = pyfits.getdata(ccd2, 1)
tbdata3 = pyfits.getdata(ccd3, 1)
tbdata4 = pyfits.getdata(ccd4, 1)
wl1 = tbdata1['wavelength'].ravel()
net1 = tbdata1['net'].ravel()
dq = tbdata1['dq'].ravel()
wl1 = wl1[dq&512 != 512]
net1 = net1[dq&512 != 512]
wl2 = tbdata2['wavelength'].ravel()
net2 = tbdata2['net'].ravel()
dq = tbdata2['dq'].ravel()
wl2 = wl2[dq&512 != 512]
net2 = net2[dq&512 != 512]
wl3 = tbdata3['wavelength'].ravel()
net3 = tbdata3['net'].ravel()
dq = tbdata3['dq'].ravel()
wl3 = wl3[dq&512 != 512]
net3 = net3[dq&512 != 512]
wl4 = tbdata4['wavelength'].ravel()
net4 = tbdata4['net'].ravel()
dq = tbdata4['dq'].ravel()
wl4 = wl4[dq&512 != 512]
net4 = net4[dq&512 != 512]
else:
tbdata1 = pyfits.getdata(ccd1.replace('.fits', '_crj.fits'), 1)
wl1 = tbdata1['wavelength'].ravel()
net1 = tbdata1['net'].ravel()
tbdata2 = pyfits.getdata(ccd2.replace('.fits', '_crj.fits'), 1)
wl2 = tbdata2['wavelength'].ravel()
net2 = tbdata2['net'].ravel()
tbdata3 = pyfits.getdata(ccd3.replace('.fits', '_crj.fits'), 1)
wl3 = tbdata3['wavelength'].ravel()
net3 = tbdata3['net'].ravel()
tbdata4 = pyfits.getdata(ccd4.replace('.fits', '_crj.fits'), 1)
wl4 = tbdata4['wavelength'].ravel()
net4 = tbdata4['net'].ravel()
net1 = normalize_spec.manually_remove_CR(wl1, net1, flt = os.path.join(base_dir, 'combined_dithered_images/%s_%i_combined_img.fits' %(pyfits.getval(ccd1, 'targname', 0)[5:], pyfits.getval(ccd1, 'cenwave', 0))))
write_fits_file(ccd1.replace('.fits', '_crj.fits'), wl1, net1, pyfits.getheader(ccd1, 0), spec_name = 'net')
norm_spec2 = normalize_spec.manually_remove_CR(wl2, net2, flt = os.path.join(base_dir, 'combined_dithered_images/%s_%i_combined_img.fits' %(pyfits.getval(ccd2, 'targname', 0)[5:], pyfits.getval(ccd2, 'cenwave', 0))))
write_fits_file(ccd2.replace('.fits', '_crj.fits'), wl2, net2, pyfits.getheader(ccd2, 0), spec_name = 'net')
norm_spec3 = normalize_spec.manually_remove_CR(wl3, net3, flt = os.path.join(base_dir, 'combined_dithered_images/%s_%i_combined_img.fits' %(pyfits.getval(ccd3, 'targname', 0)[5:], pyfits.getval(ccd3, 'cenwave', 0))))
write_fits_file(ccd3.replace('.fits', '_crj.fits'), wl3, net3, pyfits.getheader(ccd3, 0), spec_name = 'net')
norm_spec4 = normalize_spec.manually_remove_CR(wl4, net4, flt = os.path.join(base_dir, 'combined_dithered_images/%s_%i_combined_img.fits' %(pyfits.getval(ccd4, 'targname', 0)[5:], pyfits.getval(ccd4, 'cenwave', 0))))
write_fits_file(ccd4.replace('.fits', '_crj.fits'), wl4, net4, pyfits.getheader(ccd4, 0), spec_name = 'net')
if bin_flag:
wl1, net1 = bin_data(wl1, net1, bin_size = 3)
wl2, net2 = bin_data(wl2, net2, bin_size = 3)
wl3, net3 = bin_data(wl3, net3, bin_size = 3)
wl4, net4 = bin_data(wl4, net4, bin_size = 3)
#normalize spectra
wl1, norm_spec1, cont1 = normalize_spec.normalize_spectrum(wl1, net1)
write_fits_file(ccd1.replace('.fits', '_norm.fits'), wl1, norm_spec1, pyfits.getheader(ccd1, 0), spec_name = 'net')
wl2, norm_spec2, cont2 = normalize_spec.normalize_spectrum(wl2, net2)
write_fits_file(ccd2.replace('.fits', '_norm.fits'), wl2, norm_spec2, pyfits.getheader(ccd2, 0), spec_name = 'net')
wl3, norm_spec3, cont3 = normalize_spec.normalize_spectrum(wl3, net3)
write_fits_file(ccd3.replace('.fits', '_norm.fits'), wl3, norm_spec3, pyfits.getheader(ccd3, 0), spec_name = 'net')
wl4, norm_spec4, cont4 = normalize_spec.normalize_spectrum(wl4, net4)
write_fits_file(ccd4.replace('.fits', '_norm.fits'), wl4, norm_spec4, pyfits.getheader(ccd4, 0), spec_name = 'net')
wl5, norm_spec5, cont5 = normalize_spec.normalize_spectrum(wl5, net5, kernel_size = 401)
write_fits_file(fuv .replace('.fits', '_norm.fits'), wl5, norm_spec5, pyfits.getheader(fuv, 0))
else:
tbdata1 = pyfits.getdata(ccd1.replace('.fits', '_norm.fits'), 1)
wl1 = tbdata1['wavelength']
norm_spec1 = tbdata1['net']
tbdata2 = pyfits.getdata(ccd2.replace('.fits', '_norm.fits'), 1)
wl2 = tbdata2['wavelength']
norm_spec2 = tbdata2['net']
tbdata3 = pyfits.getdata(ccd3.replace('.fits', '_norm.fits'), 1)
wl3 = tbdata3['wavelength']
norm_spec3 = tbdata3['net']
tbdata4 = pyfits.getdata(ccd4.replace('.fits', '_norm.fits'), 1)
wl4 = tbdata4['wavelength']
norm_spec4 = tbdata4['net']
tbdata5 = pyfits.getdata(fuv.replace('.fits', '_norm.fits'), 1)
wl5 = tbdata5['wavelength']
norm_spec5 = tbdata5['flux']
#create plotting objects
fig = pyplot.figure(6, figsize = [26, 15])
fig.clf()
ax1 = fig.add_subplot(3, 1, 1)
ax2 = fig.add_subplot(3, 1, 2)
ax3 = fig.add_subplot(3, 1, 3)
ax2.plot(wl1, norm_spec1, 'k')
ax2.plot(wl2, norm_spec2, 'b')
ax2.plot(wl3, norm_spec3, 'k')
ax2.plot(wl4, norm_spec4, 'b')
ax3.plot(wl1, boxcar(norm_spec1, (3,)), 'k')
ax3.plot(wl2, boxcar(norm_spec2, (3,)), 'b')
ax3.plot(wl3, boxcar(norm_spec3, (3,)), 'k')
ax3.plot(wl4, boxcar(norm_spec4, (3,)), 'b')
ax1.plot(wl5, norm_spec5, 'k')
ax2.set_xlim(3900, 4750)
ax3.set_xlim(3900, 4750)
ax1.set_xlim(1150, 1700)
ax1.set_ylim(ax1_ylim[0], ax1_ylim[1])
ax2.set_ylim(ax2_ylim[0], ax2_ylim[1])
ax3.set_ylim(ax2_ylim[0], ax2_ylim[1])
ax1_xticks = np.arange(1150, 1750, 50)
ax2_xticks = np.arange(3900, 4750, 50)
ax1.set_xticks(ax1_xticks)
ax2.set_xticks(ax2_xticks)
ax3.set_xticks(ax2_xticks)
ax1.grid(b = 'on', color = 'gray', ls = ':')
ax2.grid(b = 'on', color = 'gray', ls = ':')
ax3.grid(b = 'on', color = 'gray', ls = ':')
#Label Plots
ax2.set_title('Optical Spectrum %s' %(title))
ax1.set_title('FUV Spectrum %s' %(title))
ax3.set_title('Optical Spectrum %s R~4000' %(title))
ax3.set_xlabel('Wavelength')
ax2.set_ylabel('Relative Intensity')
pyplot.draw()
return ax1, ax2, ax3, fig
def check_existance_of_files(ccd1, ccd2, ccd3, ccd4, fuv):
if not os.path.exists(ccd1):
raise IOError('%s does not exist' %(ccd1))
if not os.path.exists(ccd2):
raise IOError('%s does not exist' %(ccd2))
if not os.path.exists(ccd3):
raise IOError('%s does not exist' %(ccd3))
if not os.path.exists(ccd4):
raise IOError('%s does not exist' %(ccd4))
if not os.path.exists(fuv):
raise IOError('%s does not exist' %(fuv))
def write_fits_file(filename, wl, spec, hdr, spec_name = 'flux'):
c1 = pyfits.Column(name = 'wavelength', format = 'D', unit = 'Ang', array = wl)
c2 = pyfits.Column(name = spec_name, format = 'D', array = spec)
tbhdu = pyfits.new_table([c1, c2])
hdu = pyfits.PrimaryHDU()
thdulist = pyfits.HDUList([hdu, tbhdu])
thdulist.writeto(filename, clobber = True)
def label_spectrum(ax1, ax2, ax3):
NII_dict = {'name':['N II 3995', 'N II 4041/44'],\
'rest_wavelength':[[3995], [4041, 4044]]}
NIII_dict = {'name':['N III 4097','N III 4379' ,'N III 4511/15','N III 4634/14/42','N III 4905'],\
'rest_wavelength':[[4097],[4379],[4511, 4515],[4634, 4641, 4642],[4905]]}
NIV_dict = {'name':['N IV 4058'], \
'rest_wavelength': [[4058]]}
NV_dict = {'name':['N V 1238/42','N V 4604/20'],\
'rest_wavelength':[[1238, 1242],[4604, 4620]]}
HeI_dict = {'name':['He I 4009' ,'He I 4121','He I 4144','He I 4388', 'He I 4471','He I 4713','He I 4921'],\
'rest_wavelength':[[4009], [4121],[4144], [4388],[4471],[4713],[4921]]}
HeI_II_dict = {'name':['He I+II 4026'],\
'rest_wavelength':[[4026]]}
HeII_dict = {'name':['He II 1640', 'He II 4200','He II 4542','He II 4686'],\
'rest_wavelength':[ [1640], [4200],[4542], [4686]]}
NiIV_dict = {'name':['Ni IV 4058'],\
'rest_wavelength':[[4058]]}
CIV_dict = {'name':['C IV 1548/51'], \
'rest_wavelength':[[1548, 1551]]}
CIII_dict = {'name':['C III 1176','C III 4068/69/70','C III 4187','C III 4647/50/51'],\
'rest_wavelength':[ [1176],[4068, 4069, 4070],[4187],[4647, 4650, 4651]]}
CII_dict = {'name':['C II 4267'],\
'rest_wavelength':[[4267]]}
OII_dict = {'name':['O II 4070/72/76','O II 4254','O II 4276/85','O II 4317/20', 'O II 4349','O II 4367','O II 4415/17','O II 4591/4596' ,'O II 4662/76' ,'O II 4699/705'],\
'rest_wavelength':[[4070, 4072, 4076],[4254],[4276, 4285], [4317, 4320],[4349], [4367], [4415, 4417],[4591, 4596],[4662, 4676],[4699, 4705]]}
OV_dict = {'name':['O V 1371'],\
'rest_wavelength':[[1371]]}
SiIV_dict = {'name':['Si IV 1393/402','Si IV 4089','Si IV 4116'],\
'rest_wavelength':[[1391, 1402], [4089], [4116]]}
SiIII_dict = {'name':['Si III 4553/68/75'],\
'rest_wavelength':[[4553, 4568, 4575]]}
SV_dict = {'name': ['SV 1502'], \
'rest_wavelength':[[1502]]}
MgII_dict = {'name':['Mg II 4481'],\
'rest_wavelength':[[4481]]}
SIV_dict = {'name':['S IV 4486','S IV 4504'],\
'rest_wavelength':[[4486],[4504]]}
balmer_dict = {'name':[r'H $\epsilon$ 3970', r'H $\delta$ 4102',r'H $\gamma$ 4340',r'H $\beta$ 4861'],\
'rest_wavelength':[[3970], [4102], [4340],[4861]]}
dib_dict = {'name':['DIB is 4429','DIB is 4502','DIB is 4727','DIB is 4762','DIB is 4780','DIB is 4881'],\
'rest_wavelength':[[4429], [4502], [4727],[4762], [4780],[4881]]}
ISM_dict = {'name': ['Ly $\\alpha$ 1215', 'Si II 1260', 'OI 1302', 'C II 1335', 'Si II 1526', 'Fe II 1608', 'Al II 1671', 'Ca II H 3968', 'Ca II K 3933'], \
'rest_wavelength': [[1215.6], [1260.4], [1302.2], [1334.5], [1526.7], [1608.5], [1670.8], [3968], [3933]]}
ISM_dict_shifted = {'name': ['Si II 1304'], \
'rest_wavelength': [[1304.4]]}
line_dict = normalize_spec.apply_redshift(HeI_dict, 268.0E3)
normalize_spec.mark_spectrum(HeI_dict, ax1, 'r')
normalize_spec.mark_spectrum(HeI_dict, ax2, 'r')
normalize_spec.mark_spectrum(HeI_dict, ax3, 'r')
line_dict = normalize_spec.apply_redshift(HeII_dict, 268.0E3)
normalize_spec.mark_spectrum(HeII_dict, ax1, 'r', offset = 10.0)
normalize_spec.mark_spectrum(HeII_dict, ax2, 'r', offset = 10.0)
normalize_spec.mark_spectrum(HeII_dict, ax3, 'r', offset = 10.0)
line_dict = normalize_spec.apply_redshift(HeI_II_dict, 268.0E3)
normalize_spec.mark_spectrum(HeI_II_dict, ax1, 'r')
normalize_spec.mark_spectrum(HeI_II_dict, ax2, 'r')
normalize_spec.mark_spectrum(HeI_II_dict, ax3, 'r')
line_dict = normalize_spec.apply_redshift(NIII_dict, 268.0E3)
normalize_spec.mark_spectrum(NIII_dict, ax1, 'purple')
normalize_spec.mark_spectrum(NIII_dict, ax2, 'purple')
normalize_spec.mark_spectrum(NIII_dict, ax3, 'purple')
line_dict = normalize_spec.apply_redshift(NV_dict, 268.0E3)
normalize_spec.mark_spectrum(NV_dict, ax1, 'purple')
normalize_spec.mark_spectrum(NV_dict, ax2, 'purple')
normalize_spec.mark_spectrum(NV_dict, ax3, 'purple')
line_dict = normalize_spec.apply_redshift(NIV_dict, 268.0E3)
normalize_spec.mark_spectrum(NIV_dict, ax1, 'purple')
normalize_spec.mark_spectrum(NIV_dict, ax2, 'purple')
normalize_spec.mark_spectrum(NIV_dict, ax3, 'purple')
line_dict = normalize_spec.apply_redshift(CIII_dict, 268.0E3)
normalize_spec.mark_spectrum(CIII_dict, ax1, 'g', offset = 10.0)
normalize_spec.mark_spectrum(CIII_dict, ax2, 'g', offset = 10.0)
normalize_spec.mark_spectrum(CIII_dict, ax3, 'g', offset = 10.0)
line_dict = normalize_spec.apply_redshift(SiIV_dict, 268.0E3)
normalize_spec.mark_spectrum(SiIV_dict, ax1, 'c')
normalize_spec.mark_spectrum(SiIV_dict, ax2, 'c')
normalize_spec.mark_spectrum(SiIV_dict, ax3, 'c')
line_dict = normalize_spec.apply_redshift(balmer_dict, 268.0E3)
normalize_spec.mark_spectrum(balmer_dict, ax1, 'brown', offset = 9.0)
normalize_spec.mark_spectrum(balmer_dict, ax2, 'brown', offset = 9.0)
normalize_spec.mark_spectrum(balmer_dict, ax3, 'brown', offset = 9.0)
line_dict = normalize_spec.apply_redshift(CIV_dict, 268.0E3)
normalize_spec.mark_spectrum(CIV_dict, ax1, 'g')
normalize_spec.mark_spectrum(CIV_dict, ax2, 'g')
normalize_spec.mark_spectrum(CIV_dict, ax3, 'g')
line_dict = normalize_spec.apply_redshift(OV_dict, 268.0E3)
normalize_spec.mark_spectrum(OV_dict, ax1, '#FF66CC')
normalize_spec.mark_spectrum(OV_dict, ax2, '#FF66CC')
normalize_spec.mark_spectrum(OV_dict, ax3, '#FF66CC')
line_dict = normalize_spec.apply_redshift(ISM_dict, 268.0E3)
normalize_spec.mark_spectrum(ISM_dict, ax1, 'gray')
normalize_spec.mark_spectrum(ISM_dict, ax2, 'gray')
normalize_spec.mark_spectrum(ISM_dict, ax3, 'gray')
line_dict = normalize_spec.apply_redshift(ISM_dict_shifted, 268.0E3)
normalize_spec.mark_spectrum(ISM_dict_shifted, ax1, 'gray', offset = 5.0)
normalize_spec.mark_spectrum(ISM_dict_shifted, ax2, 'gray', offset = 5.0)
normalize_spec.mark_spectrum(ISM_dict_shifted, ax3, 'gray', offset = 5.0)
line_dict = normalize_spec.apply_redshift(SV_dict, 268.0E3)
normalize_spec.mark_spectrum(SV_dict, ax1, 'm')
normalize_spec.mark_spectrum(SV_dict, ax2, 'm')
normalize_spec.mark_spectrum(SV_dict, ax3, 'm')
return ax1, ax2, ax3
def bin_data(wl, net, bin_size = 3):
array_len = 3*len(wl[bin_size - 1::bin_size]) #In case the len(wl) is not evenly divisible by bin_size
bin_wl = wl[0:array_len:bin_size]
bin_net = net[0:array_len:bin_size]
for i in range(1, bin_size):
bin_wl += wl[i:array_len:bin_size]
bin_net += net[i:array_len:bin_size]
#pdb.set_trace()
bin_wl = bin_wl / float(bin_size)
return bin_wl, bin_net
def make_r136b_spec(options, base_dir):
ccd1 = os.path.join(base_dir, '12465_otfr20121109/ccd/SE8_3936_combined_img_loc545.fits')
ccd2 = os.path.join(base_dir, '12465_otfr20121109/ccd/SE8_4194_combined_img_loc496.fits')
ccd3 = os.path.join(base_dir, '12465_otfr20121109/ccd/SE8_4451_combined_img_loc546.fits')
ccd4 = os.path.join(base_dir, '12465_otfr20121109/ccd/SE8_4706_combined_img_loc543.fits')
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0005_G140L.fits')
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 2.3], [0.6, 2.1], 'H9, R136b', base_dir)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2013_greece/H9_R136b_cr_remove_spec.pdf'))
pyplot.close()
pyplot.close()
pyplot.close()
pyplot.close()
pyplot.close()
pyplot.close()
def make_H36_spec(options, base_dir):
#ccd1 = '/Users/bostroem/dropbox/R136/ccd/H36_3936SE3loc547.fits.gz'
#ccd2 = '/Users/bostroem/dropbox/R136/ccd/H36_4194SE3loc495.fits.gz'
#ccd3 = '/Users/bostroem/dropbox/R136/ccd/H36_4451SE3loc548.fits.gz'
#ccd4 = '/Users/bostroem/dropbox/R136/ccd/H36_4706SE3loc544.fits.gz'
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0015_G140L.fits')
ccd1 = os.path.join(base_dir, '12465_otfr20121109/ccd/SE3_3936_combined_img_loc546.fits')
ccd2 = os.path.join(base_dir, '12465_otfr20121109/ccd/SE3_4194_combined_img_loc494.fits')
ccd3 = os.path.join(base_dir, '12465_otfr20121109/ccd/SE3_4451_combined_img_loc547.fits')
ccd4 = os.path.join(base_dir, '12465_otfr20121109/ccd/SE3_4706_combined_img_loc544.fits')
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 2.3], [0.6, 1.4], 'H36', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2013_greece/H36_cr_remove_spec.pdf'))
def make_r136a7_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0007_G140L.fits')
ccd1 = '/Users/bostroem/dropbox/R136/ccd/R136a7_3936NW3loc517.fits.gz'
ccd2 = '/Users/bostroem/Dropbox/R136/ccd/R136a7_4194NW3loc526.fits.gz'
ccd3 = '/Users/bostroem/dropbox/R136/ccd/R136a7_4451NW3loc517.fits.gz'
ccd4 = '/Users/bostroem/dropbox/R136/ccd/R136a7_4706NW3loc515.fits.gz'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 2.3], [0.6, 1.4], 'R136a7', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2013_greece/r136a7_cr_remove_spec.pdf'))
def make_r136a6_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0004_G140L.fits')
ccd1 = '/Users/bostroem/dropbox/R136/ccd/R136a6_3936SE1loc506.fits.gz'
ccd2 = '/Users/bostroem/dropbox/R136/ccd/R136a6_4194SE1loc535.fits.gz'
ccd3 = '/Users/bostroem/dropbox/R136/ccd/R136a6_4451SE1loc507.fits.gz'
ccd4 = '/Users/bostroem/dropbox/R136/ccd/R136a6_4706SE1loc504.fits.gz'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 1.8], [0.6, 1.4], 'R136a6', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2013_greece/R136a6_cr_remove_spec.pdf'))
def make_H50_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0015_G140L.fits')
ccd1 = '/Users/bostroem/dropbox/R136/ccd/H50_3936SE3loc528.fits.gz'
ccd2 = '/Users/bostroem/dropbox/R136/ccd/H50_4194SE3loc514.fits.gz'
ccd3 = '/Users/bostroem/dropbox/R136/ccd/H50_4451SE3loc529.fits.gz'
ccd4 = '/Users/bostroem/dropbox/R136/ccd/H50_4706SE3loc525.fits.gz'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 1.8], [0.6, 1.4], 'H50', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2013_greece/H50_cr_remove_spec.pdf') )
def make_H40_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0020_G140L.fits')
ccd1 = '/Users/bostroem/dropbox/R136/ccd/H40_3936NW8loc500.fits.gz'
ccd2 = '/Users/bostroem/dropbox/R136/ccd/H40_4194NW8loc542.fits.gz'
ccd3 = '/Users/bostroem/dropbox/R136/ccd/H40_4451NW8loc500.fits.gz'
ccd4 = '/Users/bostroem/dropbox/R136/ccd/H40_4706NW8loc499.fits.gz'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 1.8], [0.6, 1.4], 'H40', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2013_greece/H40_cr_remove_spec.pdf') )
def make_H55_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0023_G140L.fits')
ccd1 = '/Users/bostroem/dropbox/R136/ccd/H55_3936SE9loc516.fits.gz'
ccd2 = '/Users/bostroem/dropbox/R136/ccd/H55_4194SE9loc525.fits.gz'
ccd3 = '/Users/bostroem/dropbox/R136/ccd/H55_4451SE9loc517.fits.gz'
ccd4 = '/Users/bostroem/dropbox/R136/ccd/H55_4706SE9loc514.fits.gz'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 1.8], [0.6, 1.4], 'H55', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2013_greece/H55_cr_remove_spec.pdf'))
def make_H62_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0024_G140L.fits')
ccd1 = '/Users/bostroem/dropbox/R136/ccd/H62_3936SE3loc513.fits.gz'
ccd2 = '/Users/bostroem/dropbox/R136/ccd/H62_4194SE3loc533.fits.gz'
ccd3 = '/Users/bostroem/dropbox/R136/ccd/H62_4451SE3loc514.fits.gz'
ccd4 = '/Users/bostroem/dropbox/R136/ccd/H62_4706SE3loc510.fits.gz'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 1.8], [0.6, 1.4], 'H62', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2013_greece/H62_cr_remove_spec.pdf'))
def make_H58_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0024_G140L.fits')
ccd1 = '/Users/bostroem/dropbox/R136/ccd/H58_3936NW1loc531.fits.gz'
ccd2 = '/Users/bostroem/dropbox/R136/ccd/H58_4194NW1loc510.fits.gz'
ccd3 = '/Users/bostroem/dropbox/R136/ccd/H58_4451NW1loc532.fits.gz'
ccd4 = '/Users/bostroem/dropbox/R136/ccd/H58_4706NW1loc529.fits'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 1.8], [0.6, 1.4], 'H58', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2013_greece/H58_cr_remove_spec.pdf') )
def make_H48_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0026_G140L.fits')
ccd1 = '/Users/bostroem/dropbox/R136/ccd/H48_3936SE2loc542.fits.gz'
ccd2 = '/Users/bostroem/dropbox/R136/ccd/H48_4194SE2loc500.fits.gz'
ccd3 = '/Users/bostroem/dropbox/R136/ccd/H48_4451SE2loc542.fits.gz'
ccd4 = '/Users/bostroem/dropbox/R136/ccd/H48_4706SE2loc539.fits.gz'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 1.8], [0.6, 1.4], 'H48', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2013_greece/H48_cr_remove_spec.pdf'))
def make_H47_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0027_G140L.fits')
ccd1 = '/Users/bostroem/dropbox/R136/ccd/H47_3936NW3loc489.fits.gz'
ccd2 = '/Users/bostroem/dropbox/R136/ccd/H47_4194NW3loc554.fits.gz'
ccd3 = '/Users/bostroem/dropbox/R136/ccd/H47_4451NW3loc489.fits.gz'
ccd4 = '/Users/bostroem/dropbox/R136/ccd/H47_4706NW3loc487.fits.gz'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 1.8], [0.6, 1.4], 'H47', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2013_greece/H47_cr_remove_spec.pdf') )
def make_H35_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0012_G140L.fits')
ccd1 = '/Users/bostroem/dropbox/R136/ccd/H35_3936NW5loc528.fits.gz'
ccd2 = '/Users/bostroem/dropbox/R136/ccd/H35_4194NW5loc515.fits.gz'
ccd3 = '/Users/bostroem/dropbox/R136/ccd/H35_4451NW5loc528.fits.gz'
ccd4 = '/Users/bostroem/dropbox/R136/ccd/H35_4706NW5loc526.fits.gz'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 1.8], [0.6, 1.4], 'H35', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2013_greece/H35_cr_remove_spec.pdf') )
#----------------------------------------------
def make_H42_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0022_G140L.fits')
ccd1 = '/Users/bostroem/science/2014_dc_aas/H42_NW8_3936_combined_img_loc544.fits'
ccd2 = '/Users/bostroem/science/2014_dc_aas/H42_NW8_4194_combined_img_loc498.fits'
ccd3 = '/Users/bostroem/science/2014_dc_aas/H42_NW8_4451_combined_img_loc543.fits'
ccd4 = '/Users/bostroem/science/2014_dc_aas/H42_NW8_4706_combined_img_loc542.fits'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 1.8], [0.6, 1.5], 'H42', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2014_dc_aas/H42_cr_remove_spec.pdf') )
def make_H45_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0021_G140L.fits')
ccd1 = '/Users/bostroem/science/2014_dc_aas/H45_SE7_3936_combined_img_loc558.fits'
ccd2 = '/Users/bostroem/science/2014_dc_aas/H45_SE7_4194_combined_img_loc481.fits'
ccd3 = '/Users/bostroem/science/2014_dc_aas/H45_SE7_4451_combined_img_loc559.fits'
ccd4 = '/Users/bostroem/science/2014_dc_aas/H45_SE7_4706_combined_img_loc556.fits'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 1.8], [0.6, 1.5], 'H45', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2014_dc_aas/H45_cr_remove_spec.pdf') )
def make_H52_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0019_G140L.fits')
ccd1 = '/Users/bostroem/science/2014_dc_aas/H52_SE5_3936_combined_img_loc514.fits'
ccd2 = '/Users/bostroem/science/2014_dc_aas/H52_SE5_4194_combined_img_loc527.fits'
ccd3 = '/Users/bostroem/science/2014_dc_aas/H52_SE5_4451_combined_img_loc514.fits'
ccd4 = '/Users/bostroem/science/2014_dc_aas/H52_SE5_4706_combined_img_loc511.fits'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 1.8], [0.6, 1.5], 'H52', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2014_dc_aas/H52_cr_remove_spec.pdf') )
def make_H64_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0040_G140L.fits')
ccd1 = '/Users/bostroem/science/2014_dc_aas/H64_NW7_3936_combined_img_loc481.fits'
ccd2 = '/Users/bostroem/science/2014_dc_aas/H64_NW7_4194_combined_img_loc561.fits'
ccd3 = '/Users/bostroem/science/2014_dc_aas/H64_NW7_4451_combined_img_loc480.fits'
ccd4 = '/Users/bostroem/science/2014_dc_aas/H64_NW7_4706_combined_img_loc479.fits'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 1.8], [0.6, 1.6], 'H64', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2014_dc_aas/H64_cr_remove_spec.pdf') )
def make_H68_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0042_G140L.fits')
ccd1 = '/Users/bostroem/science/2014_dc_aas/H68_SE4_3936_combined_img_loc606.fits'
ccd2 = '/Users/bostroem/science/2014_dc_aas/H68_SE4_4194_combined_img_loc435.fits'
ccd3 = '/Users/bostroem/science/2014_dc_aas/H68_SE4_4451_combined_img_loc608.fits'
ccd4 = '/Users/bostroem/science/2014_dc_aas/H68_SE4_4706_combined_img_loc604.fits'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 1.8], [0.6, 1.6], 'H68', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2014_dc_aas/H68_cr_remove_spec.pdf') )
def make_H71_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0041_G140L.fits')
ccd1 = '/Users/bostroem/science/2014_dc_aas/H71_SE9_3936_combined_img_loc502.fits'
ccd2 = '/Users/bostroem/science/2014_dc_aas/H71_SE9_4194_combined_img_loc539.fits'
ccd3 = '/Users/bostroem/science/2014_dc_aas/H71_SE9_4451_combined_img_loc502.fits'
ccd4 = '/Users/bostroem/science/2014_dc_aas/H71_SE9_4706_combined_img_loc499.fits'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 1.8], [0.6, 1.6], 'H71', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2014_dc_aas/H71_cr_remove_spec.pdf') )
def make_H75_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0031_G140L.fits')
ccd1 = '/Users/bostroem/science/2014_dc_aas/H75_NW8_3936_combined_img_loc531.fits'
ccd2 = '/Users/bostroem/science/2014_dc_aas/H75_NW8_4194_combined_img_loc512.fits'
ccd3 = '/Users/bostroem/science/2014_dc_aas/H75_NW8_4451_combined_img_loc531.fits'
ccd4 = '/Users/bostroem/science/2014_dc_aas/H75_NW8_4706_combined_img_loc529.fits'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 1.8], [0.6, 1.5], 'H75', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2014_dc_aas/H75_cr_remove_spec.pdf') )
def make_H77_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0039_G140L.fits')
ccd1 = '/Users/bostroem/science/2014_dc_aas/H77_SE6_3936_combined_img_loc517.fits'
ccd2 = '/Users/bostroem/science/2014_dc_aas/H77_SE6_4194_combined_img_loc523.fits'
ccd3 = '/Users/bostroem/science/2014_dc_aas/H77_SE6_4451_combined_img_loc518.fits'
ccd4 = '/Users/bostroem/science/2014_dc_aas/H77_SE6_4706_combined_img_loc515.fits'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 1.8], [0.6, 1.5], 'H77', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2014_dc_aas/H77_cr_remove_spec.pdf') )
def make_H78_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0038_G140L.fits')
ccd1 = '/Users/bostroem/science/2014_dc_aas/H78_NW2_3936_combined_img_loc539.fits'
ccd2 = '/Users/bostroem/science/2014_dc_aas/H78_NW3_4194_combined_img_loc503.fits'
ccd3 = '/Users/bostroem/science/2014_dc_aas/H78_NW2_4451_combined_img_loc540.fits'
ccd4 = '/Users/bostroem/science/2014_dc_aas/H78_NW2_4706_combined_img_loc538.fits'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 1.8], [0.6, 1.7], 'H78', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2014_dc_aas/H78_cr_remove_spec.pdf') )
def make_H90_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0044_G140L.fits')
ccd1 = '/Users/bostroem/science/2014_dc_aas/H90_NW3_3936_combined_img_loc534.fits'
ccd2 = '/Users/bostroem/science/2014_dc_aas/H90_NW3_4194_combined_img_loc508.fits'
ccd3 = '/Users/bostroem/science/2014_dc_aas/H90_NW3_4451_combined_img_loc534.fits'
ccd4 = '/Users/bostroem/science/2014_dc_aas/H90_NW3_4706_combined_img_loc532.fits'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 1.8], [0.6, 1.7], 'H90', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2014_dc_aas/H90_cr_remove_spec.pdf') )
def make_H92_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0046_G140L.fits')
ccd1 = '/Users/bostroem/science/2014_dc_aas/H92_NW6_3936_combined_img_loc526.fits'
ccd2 = '/Users/bostroem/science/2014_dc_aas/H92_NW6_4194_combined_img_loc516.fits'
ccd3 = '/Users/bostroem/science/2014_dc_aas/H92_NW6_4451_combined_img_loc526.fits'
ccd4 = '/Users/bostroem/science/2014_dc_aas/H92_NW6_4706_combined_img_loc524.fits'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 1.8], [0.6, 1.7], 'H92', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2014_dc_aas/H92_cr_remove_spec.pdf') )
def make_H94_spec(options, base_dir):
fuv = os.path.join(base_dir, 'multispec/R136_G140L/star0048_G140L.fits')
ccd1 = '/Users/bostroem/science/2014_dc_aas/H94_SE6_3936_combined_img_loc525.fits'
ccd2 = '/Users/bostroem/science/2014_dc_aas/H94_SE6_4194_combined_img_loc516.fits'
ccd3 = '/Users/bostroem/science/2014_dc_aas/H94_SE6_4451_combined_img_loc525.fits'
ccd4 = '/Users/bostroem/science/2014_dc_aas/H94_SE6_4706_combined_img_loc522.fits'
ax1, ax2, ax3, fig = make_plots(fuv, ccd1, ccd2, ccd3, ccd4, options.reject_cr_flag, options.norm_spec_flag, [-0.1, 1.8], [0.6, 1.6], 'H94', base_dir, bin_flag = options.bin_flag)
ax1, ax2, ax3 = label_spectrum(ax1, ax2, ax3)
pyplot.draw()
pdb.set_trace()
pyplot.savefig(os.path.join(base_dir, '2014_dc_aas/H94_cr_remove_spec.pdf') )
if __name__ == "__main__":
#If --norm is not supllied norm_spec_flag is set to True = user wants to normalize the spectrum
parser = OptionParser()
parser.add_option('--crrej', dest = 'reject_cr_flag', action = 'store_false', help = 'Use previously produce CR rejected file', default = True)
parser.add_option('--norm', dest = 'norm_spec_flag', action = 'store_false', help = 'Use previously normalized spectrum file', default = True)
parser.add_option('--bin', dest = 'bin_flag', action = 'store_true', help = 'Bin data', default = False)
(options, args) = parser.parse_args()
#----------------RHODES---------------#
############## H9/R136 b################
#make_r136b_spec(options, base_dir)
############## H36################
#make_H36_spec(options, base_dir)
############## R136/a6################
#make_r136a6_spec(options, base_dir)
############## H62 ################
#make_H62_spec(options, base_dir)
############## H50 ################
#make_H50_spec(options, base_dir)
############## H48 ################
#make_H48_spec(options, base_dir)
############## H55 ################
#make_H55_spec(options, base_dir)
############## H47 ################
#make_H47_spec(options, base_dir)
############## H40 ################
#make_H40_spec(options, base_dir)
############## H35 ################
#make_H35_spec(options, base_dir)
############## R136/a7################
#make_r136a7_spec(options, base_dir)
############## H58 ################
#make_H58_spec(options, base_dir)
#-----------DC AAS-------------------#
############## H42 ################
#make_H42_spec(options, base_dir)
############## H45 ################
#make_H45_spec(options, base_dir)
############## H52 ################
#make_H52_spec(options, base_dir)
############## H64 ################
#make_H64_spec(options, base_dir)
############## H68 ################
#make_H68_spec(options, base_dir)
############## H71 ################
#make_H71_spec(options, base_dir)
############## H75 ################
#make_H75_spec(options, base_dir)
############## H77 ################
#make_H77_spec(options, base_dir)
############## H78 ################
make_H78_spec(options, base_dir)
############## H90 ################
#make_H90_spec(options, base_dir)
############## H92 ################
#make_H92_spec(options, base_dir)
############## H94 ################
#make_H94_spec(options, base_dir)