def womrebindriver(hop, mode):
"""input info to call womrebin functions"""
import matplotlib.pyplot as plt
import numpy as np
from tmath.wombat.inputter import inputter
from tmath.wombat.waveparse import waveparse
from tmath.wombat.yesno import yesno
from tmath.wombat.womashrebin import womashrebin
from tmath.wombat.womscipyrebin import womscipyrebin
print('Current A/pix is {}'.format(hop[0].wave[1] - hop[0].wave[0]))
print('Wavelength rage: {} to {}'.format(hop[0].wave[0], hop[0].wave[-1]))
plt.cla()
plt.plot(hop[0].wave, hop[0].flux, drawstyle='steps-mid')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
plt.title(hop[0].obname)
done = False
while (not done):
newdelt=inputter('Rebin to how many Angstroms per pixel? ', \
'float',False)
waveb, waver = waveparse()
if (waveb > waver):
waveb, waver = waver, waveb
if (newdelt > 0):
newbin = (waver - waveb) / newdelt + 1.0
frac, whole = np.modf(newbin)
if (frac > 0.000001):
print('NON-INTEGER number of bins')
testwave = newdelt * whole + waveb
print('Closest match is: {} to {}'.format(waveb, testwave))
print('Would you like this wavelength range?')
answer = yesno('y')
if (answer == 'y'):
waver = testwave
done = True
else:
print('Rebinning to {} A/pix, {} to {}'.format(newdelt,waveb,\
waver))
print('Is this OK?')
answer = yesno('y')
if (answer == 'y'):
done = True
nwave = np.arange(0, whole) * newdelt + waveb
if (mode == 'ash'):
nflux = womashrebin(hop[0].wave, hop[0].flux, nwave)
nvar = womashrebin(hop[0].wave, hop[0].var, nwave)
else:
nflux = womscipyrebin(hop[0].wave, hop[0].flux, nwave)
nvar = womscipyrebin(hop[0].wave, hop[0].var, nwave)
print('Overplotting rebinned spectrum')
plt.cla()
plt.plot(hop[0].wave, hop[0].flux, drawstyle='steps-mid')
plt.plot(nwave, nflux, drawstyle='steps-mid')
#FIX header
hop[0].wave = nwave.copy()
hop[0].flux = nflux.copy()
hop[0].var = nvar.copy()
return hop
def womwaverange(wave, flux, mode):
import matplotlib.pyplot as plt
from tmath.wombat.waveparse import waveparse
from tmath.wombat.womget_element import womget_element
from tmath.wombat.inputter_single import inputter_single
from tmath.wombat.yesno import yesno
from tmath.wombat.wshow import wshow
if (mode == 'none'):
print('Enter method to select wavelength range')
mode = inputter_single(
'Enter (w)avelengths or mark with the (m)ouse? (w/m) ', 'wm')
print(mode)
print('Spectrum runs from {} to {}.'.format(wave[0], wave[-1]))
plt.cla()
plt.plot(wave, flux, drawstyle='steps-mid')
plt.ylabel('Flux')
plt.xlabel('Wavelength')
wshow()
done = False
while (not done):
if (mode == 'w'):
waveb, waver = waveparse()
else:
pickpoints = plt.ginput(2, timeout=-1)
waveb = pickpoints[0][0]
waver = pickpoints[1][0]
if (waveb > waver):
waveb, waver = waver, waveb
indexblue = womget_element(wave, waveb)
indexred = womget_element(wave, waver)
print('Range selected: {} to {}'.format(wave[indexblue],
wave[indexred]))
plt.plot(wave[indexblue:indexred+1],flux[indexblue:indexred+1], \
drawstyle='steps-mid',color='r')
plt.pause(0.01)
print('Is this range correct?')
answer = yesno('y')
if (answer == 'n'):
plt.cla()
plt.plot(wave, flux, drawstyle='steps-mid')
plt.ylabel('Flux')
plt.xlabel('Wavelength')
wshow()
else:
done = True
return wave[indexblue:indexred + 1], flux[indexblue:indexred + 1], mode
def wommkbb(hop):
import numpy as np
import matplotlib.pyplot as plt
from tmath.wombat.waveparse import waveparse
from tmath.wombat.inputter import inputter
from tmath.wombat.inputter_single import inputter_single
light_speed = 2.99792458e10
h_planck = 6.6260755e-27
k_boltzmann = 1.380658e-16
print('This routine will create a blackbody curve for a given temperature')
print('with 1 Angstrom bins')
print('\n')
temp = inputter('Enter temperature in degrees Kelvin: ', 'float', False)
if (temp <= 0):
temp = 1.0
waveb, waver = waveparse()
if (waver < waveb):
waveb, waver = waver, waveb
if (waver == waveb):
waver = waver + 1.
wave = np.arange(waveb, waver + 1)
wavecm = wave / 1.e8
answer = inputter_single('Calculate B_nu(n) or B_lambda(l) ', 'nl')
if (answer.lower()[0] == 'l'):
flux=(2.0*h_planck*light_speed*light_speed/wavecm**5)/ \
(np.exp((h_planck*light_speed)/(wavecm*k_boltzmann*temp))-1.0)
flux = np.pi * flux / (1.e8)
ext = 'flm'
else:
nu = light_speed / wavecm
flux=(2.0*h_planck*nu**3/light_speed/light_speed)/ \
(np.exp((h_planck*nu)/(k_boltzmann*temp))-1.0)
flux = np.pi * flux * 1.e11
ext = 'fnu'
spectxt = 'bb{}.{}'.format(temp, ext)
plt.cla()
plt.plot(wave, flux, drawstyle='steps-mid')
plt.title(spectxt)
hop[0].wave = wave.copy()
hop[0].flux = flux.copy()
hop[0].obname = spectxt
hop[0].var = np.ones(wave.shape)
hop[0].header = ''
return hop
def womblo(hop, fig):
"""blotch out bad data"""
import logging
import numpy as np
import matplotlib.pyplot as plt
from scipy.interpolate import splrep, splev
from tmath.wombat.inputter_single import inputter_single
from tmath.wombat.waveparse import waveparse
from tmath.wombat.womwaverange import womwaverange
from tmath.wombat.womget_element import womget_element
from tmath.wombat.yesno import yesno
global nsplinepoints, tmpsplptsx, tmpsplptsy, pflag
print('Select regions to blotch')
wave = hop[0].wave.copy()
flux = hop[0].flux.copy()
done = False
while (not done):
plt.cla()
plt.plot(wave, flux, drawstyle='steps-mid')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
plt.title(hop[0].obname)
wavesub, fluxsub, mode = womwaverange(wave, flux, 'none')
wavebind = womget_element(wave, wavesub[0])
waverind = womget_element(wave, wavesub[-1])
plt.cla()
plt.plot(wave[wavebind:waverind+1],flux[wavebind:waverind+1], \
drawstyle='steps-mid')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
plt.title(hop[0].obname)
plt.pause(0.01)
print('Do you want to enter blotch wavelengths by hand (w),')
print('mark points (m), fit a spline (s), or quit (q)?')
choice = inputter_single('(w/m/s/q): ', 'wmsq')
if (choice == 'w') or (choice == 'm'):
blotchgood = False
while (not blotchgood):
wavechoicedone = False
while (not wavechoicedone):
if (choice == 'w'):
waveselb, waveselr = waveparse()
else:
print('Mark the two endpoints of the blotch region')
endpoints = plt.ginput(2, timeout=-1)
waveselb = endpoints[0][0]
waveselr = endpoints[1][0]
if (waveselb > waveselr):
waveselb, waveselr = waveselr, waveselb
waveselbind = womget_element(wave, waveselb)
waveselrind = womget_element(wave, waveselr)
print(waveselb, waveselr, waveselbind, waveselrind)
if (waveselbind == 0) or (waveselrind == (len(wave) - 1)):
print('Wavelengths incorrect--too close to endpoints')
else:
wavechoicedone = True
contblue = flux[waveselbind - 1]
contred = flux[waveselrind + 1]
delta = (contred - contblue) / (waveselrind - waveselbind + 1)
fluxcor = flux.copy()
for i in range(waveselbind, waveselrind + 1):
fluxcor[i] = contblue + (i - waveselbind + 1) * delta
plt.plot(wave[wavebind:waverind+1],fluxcor[wavebind:waverind+1], \
drawstyle='steps-mid')
plt.pause(0.01)
print('Is this acceptable')
answer = yesno('y')
if (answer == 'y'):
flux = fluxcor.copy()
blotchgood = True
logging.info('File {} blotched from {} to {}'.format(
hop[0].obname, wave[waveselbind], wave[waveselrind]))
elif (choice == 's'):
xmin, xmax = plt.xlim()
ymin, ymax = plt.ylim()
plt.xlim([xmin, xmax])
plt.ylim([ymin, ymax])
nsplinepoints = 0
tmpsplptsx = []
tmpsplptsy = []
spldone = False
while (not spldone):
plt.cla()
plt.plot(wave[wavebind:waverind+1],flux[wavebind:waverind+1], \
drawstyle='steps-mid')
if (len(tmpsplptsx) > 0):
plt.plot(tmpsplptsx, tmpsplptsy, 'ro')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
plt.title(hop[0].obname)
plt.xlim([xmin, xmax])
plt.ylim([ymin, ymax])
cid = fig.canvas.mpl_connect('button_press_event', onclick)
print('\nClick on continuum points for spline fit.')
print(
'Spline will replace values between first and last point')
print('Left button = add point')
print('Middle button = delete point')
print('Right button = done\n')
pflag = ''
while (pflag != 'done'):
plt.pause(0.01)
fig.canvas.mpl_disconnect(cid)
splptsy = [z for _, z in sorted(zip(tmpsplptsx, tmpsplptsy))]
splptsx = sorted(tmpsplptsx)
spline = splrep(splptsx, splptsy, k=3)
splblueindex = womget_element(wave, splptsx[0])
splredindex = womget_element(wave, splptsx[-1])
splwave = wave[splblueindex:splredindex + 1].copy()
splineresult = splev(splwave, spline)
fluxcor = flux.copy()
fluxcor[splblueindex:splredindex + 1] = splineresult.copy()
plt.plot(splwave, splineresult, drawstyle='steps-mid')
print('Is this acceptable')
answer = yesno('y')
if (answer == 'y'):
flux = fluxcor.copy()
spldone = True
logging.info(
'File {} blotched with spline from {} to {}'.format(
hop[0].obname, wave[splblueindex],
wave[splredindex]))
else:
done = True
print('Do another region?')
another = yesno('n')
if (another == 'n'):
done = True
hop[0].flux = flux.copy()
return hop
def wommkatmdisp(hop):
import numpy as np
import matplotlib.pyplot as plt
from tmath.wombat.waveparse import waveparse
from tmath.wombat.inputter import inputter
from tmath.wombat.airtovac import airtovac
light_speed = 2.99792458e10
h_planck = 6.6260755e-27
k_boltzmann = 1.380658e-16
print('This routine will create a curve of the dispersion of light')
print('by the atmosphere in arc seconds per 1 Angstrom bin')
print('\n')
print('Enter airmass for the calculation: ')
airmass = inputter('(default = 1.5): ', 'float', True, 1.5)
if (airmass < 1.0) or (airmass > 7.0):
airmass = 1.5
print('Enter temperature at telescope in degrees Celsius: ')
temp = inputter('(default = 7C [45F]): ', 'float', True, 7.0)
if (temp <= -100) or (temp >= 100):
temp = 7.0
print('Enter barometric pressure at telescope in mm of Hg: ')
press = inputter('(default = 600 mm Hg): ', 'float', True, 600.0)
if (press <= 0):
press = 600.0
print('Enter water vapor pressure at telescope in mm of Hg: ')
water = inputter('(default = 8 mm Hg): ', 'float', True, 8.0)
if (water <= 0):
water = 8.0
waveb, waver = waveparse()
if (waver < waveb):
waveb, waver = waver, waveb
if (waver == waveb):
waver = waver + 1.
print('\nOK, calculating dispersion of light in arc seconds over the')
print('range {}A to {}A at temperature {}C, pressure {} mm Hg,'.format(
waveb, waver, temp, press))
print('and water vapor pressure {} mm Hg at airmass {}.'.format(
water, airmass))
print('Zero is set at 5000A.')
wave = np.arange(waveb, waver + 1.)
vacuum = airtovac(wave)
lfactor = (1.e4 / vacuum)**2
waterfactor = water * ((0.0624 - 0.000680 * lfactor) /
(1.0 + 0.003661 * temp))
nstp = 1E-6 * (64.328 + (29498.1 / (146.0 - lfactor)) + (255.4 /
(41 - lfactor)))
n = (nstp)*((press*(1.0+(1.049-0.0157*temp)*1E-6*press))/ \
(720.883*(1.0+0.003661*temp)))-waterfactor*1.0E-6
n = n + 1.0
five = airtovac(np.array([5000.0]))
fivefact = (1.e4 / five)**2
wfive = water * ((0.0624 - 0.000680 * fivefact) / (1.0 + 0.003661 * temp))
nstpfive = 1E-6 * (64.328 + (29498.1 / (146.0 - fivefact)) +
(255.4 / (41 - fivefact)))
nfive = (nstpfive)*((press*(1.0+(1.049-0.0157*temp)*1E-6*press))/ \
(720.883*(1.0+0.003661*temp)))-wfive*1.0E-6
nfive = nfive + 1.0
cosz = 1. / airmass
tanz = (np.sqrt(1 - cosz**2)) / cosz
flux = 206265. * (n - nfive) * tanz
spectxt = 'Atmospheric dispersion curve at z = {}'.format(airmass)
plt.cla()
plt.plot(wave, flux, drawstyle='steps-mid')
plt.title(spectxt)
hop[0].wave = wave.copy()
hop[0].flux = flux.copy()
hop[0].obname = spectxt
hop[0].var = np.ones(wave.shape)
hop[0].header = ''
return hop