def test_lsf_COS():
gratings = ['G130M', 'G160M', 'G140L', 'G230L', 'G185M', 'G225M', 'G285M']
life_positions = ['1', '2', '3']
cen_waves_G160M = ['1577', '1589', '1600', '1611', '1623']
cen_waves_G130M = ['1291', '1300', '1309', '1318', '1327']
for grating in gratings:
for lp in life_positions:
instr_config = dict(name='COS', grating=grating, life_position=lp)
if lp in ['2', '3']:
if grating not in ['G130M', 'G160M']:
continue
if grating == 'G130M':
cen_waves_aux = cen_waves_G130M
elif grating == 'G160M':
cen_waves_aux = cen_waves_G160M
for cen_wave in cen_waves_aux:
instr_config['cen_wave'] = cen_wave
lsf = LSF(instr_config)
print(lp, grating, cen_wave)
elif lp == '1':
lsf = LSF(instr_config)
print(lp, grating)
def test_interpolate_to_wv0_wv0shortlong(plot=False):
err_msg = 'Something is wrong with short wavelength handling in LSF.interpolate_to_wv0()'
wv0 = 1105.0 * u.AA
cos_dict = dict(name='COS', grating='G130M', life_position='1')
lsf_cos = LSF(cos_dict)
lsf_tab = lsf_cos.interpolate_to_wv0(wv0)
assert lsf_tab[len(lsf_tab) // 2]['wv'] == wv0.value, err_msg
assert lsf_tab[len(lsf_tab) // 2]['kernel'] == np.max(
lsf_tab['kernel']), err_msg
if plot:
import matplotlib.pyplot as plt
lsf_tab = lsf_cos.interpolate_to_wv0(wv0)
plt.plot(lsf_tab['wv'] - wv0.value, lsf_tab['kernel'], '-')
plt.show()
err_msg = 'Something is wrong with long wavelength handling in LSF.interpolate_to_wv0()'
wv0 = 1796.0 * u.AA
cos_dict = dict(name='COS', grating='G160M', life_position='1')
lsf_cos = LSF(cos_dict)
lsf_tab = lsf_cos.interpolate_to_wv0(wv0)
assert lsf_tab[len(lsf_tab) // 2]['wv'] == wv0.value, err_msg
assert lsf_tab[len(lsf_tab) // 2]['kernel'] == np.max(
lsf_tab['kernel']), err_msg
if plot:
import matplotlib.pyplot as plt
lsf_tab = lsf_cos.interpolate_to_wv0(wv0)
plt.plot(lsf_tab['wv'] - wv0.value, lsf_tab['kernel'], '-')
plt.show()
# test error outside range
wv0 = 1300.0 * u.AA
with pytest.raises(ValueError):
lsf_tab = lsf_cos.interpolate_to_wv0(wv0)
wv0 = 1900.0 * u.AA
with pytest.raises(ValueError):
lsf_tab = lsf_cos.interpolate_to_wv0(wv0)
def test_interpolate_to_wv0(plot=False, lp='2'):
err_msg = 'Something is wrong with LSF.interpolate_to_wv0()'
wv0 = 1160 * u.AA
cos_dict = dict(name='COS', grating='G130M', life_position=lp, cen_wave='1309')
stis_dict = dict(name='STIS', grating='G140L', slit='52x0.2')
lsf_cos = LSF(cos_dict)
lsf_stis = LSF(stis_dict)
for lsf in [lsf_cos, lsf_stis]:
lsf_tab = lsf.interpolate_to_wv0(wv0)
assert lsf_tab[len(lsf_tab) // 2]['wv'] == wv0.value, err_msg
assert lsf_tab[len(lsf_tab) // 2]['kernel'] == np.max(lsf_tab['kernel']), err_msg
if plot:
import matplotlib.pyplot as plt
if lp == '3':
wv_array = np.linspace(1200, 1400, 10) * u.AA
else:
wv_array = np.arange(1200, 1400, 10) * u.AA
for wv in wv_array:
lsf_tab = lsf_cos.interpolate_to_wv0(wv)
plt.plot(lsf_tab['wv'] - wv.value, lsf_tab['kernel'], '-')
plt.suptitle(lsf.name)
# import pdb; pdb.set_trace()
plt.show()
# test last column interpolation
lsf = LSF(dict(name='COS', grating='G130M', life_position='1'))
tab = lsf.interpolate_to_wv0(1450 * u.AA)
def use_custom_lsf(self,FWHM='6.5',grating='G130M',life_position='1',cen_wave='1300A'):
if FWHM=='COS':
instr_config=dict(name='COS',grating=grating,life_position=life_position,cen_wave=cen_wave)
coslsf=LSF(instr_config)
s,data=coslsf.load_COS_data()
#if 1150A 1200A 1250A 1300A 1350A 1400A 1450A
kernel = CustomKernel(data[cen_wave].data)
else:
COS_kernel=np.double(FWHM)/2.355 #6.5 pixels
#window_size_number_of_points=np.round(FWHM /(2.355*np.abs(velgrid[2]-velgrid[1])))
# Create kernel
kernel = Gaussian1DKernel(stddev=COS_kernel)
self.kernel=kernel
def test_interpolate_to_wv0(plot=False, lp='2'):
err_msg = 'Something is wrong with LSF.interpolate_to_wv0()'
wv0 = 1160 * u.AA
cos_dict = dict(name='COS',
grating='G130M',
life_position=lp,
cen_wave='1309')
stis_dict = dict(name='STIS', grating='G140L', slit='52x0.2')
stis_echelle_dict = dict(name='STIS', grating='E140M', slit='0.2x0.06')
lsf_cos = LSF(cos_dict)
lsf_stis = LSF(stis_dict)
lsf_stis_echelle = LSF(stis_echelle_dict)
for lsf in [lsf_cos, lsf_stis, lsf_stis_echelle]:
lsf_tab = lsf.interpolate_to_wv0(wv0)
assert lsf_tab[len(lsf_tab) // 2]['wv'] == wv0.value, err_msg
assert lsf_tab[len(lsf_tab) // 2]['kernel'] == np.max(
lsf_tab['kernel']), err_msg
if plot:
import matplotlib.pyplot as plt
if lp == '3':
wv_array = np.linspace(1200, 1400, 10) * u.AA
else:
wv_array = np.arange(1200, 1400, 10) * u.AA
for wv in wv_array:
lsf_tab = lsf_cos.interpolate_to_wv0(wv)
plt.plot(lsf_tab['wv'] - wv.value, lsf_tab['kernel'], '-')
plt.suptitle(lsf.name)
# import pdb; pdb.set_trace()
plt.show()
# test last column interpolation
lsf = LSF(dict(name='COS', grating='G130M', life_position='1'))
tab = lsf.interpolate_to_wv0(1450 * u.AA)
def test_interpolate_to_wv_array(plot=False, lp='2'):
err_msg = 'Something is wrong with LSF.interpolate_to_wv_array()'
wv_array = np.arange(1600, 1601, 0.001) * u.AA
wv_array = np.arange(1600, 1650, 0.001) * u.AA
cen_waves = ['1577', '1589A', '1600', '1611', '1623']
colors = ['k', 'b', 'g', 'r', 'orange']
lsf_dict = dict()
for i, cen_wave in enumerate(cen_waves):
cos_dict_aux = dict(name='COS', grating='G160M', life_position=lp, cen_wave=cen_wave)
lsf_dict[cen_wave] = LSF(cos_dict_aux)
lsf_tab = lsf_dict[cen_wave].interpolate_to_wv_array(wv_array)
assert isinstance(lsf_tab, Table), err_msg
if plot:
import matplotlib.pyplot as plt
plt.plot(wv_array, lsf_tab['kernel'], '-', color=colors[i])
if plot:
plt.show()
# other tests
lsf = LSF(dict(name='COS', grating='G130M', life_position='1'))
wv_array = np.linspace(1210, 1211, 100) * u.AA
# cubic
tab = lsf.interpolate_to_wv_array(wv_array, kind='cubic', debug=True)
# errors
with pytest.raises(SyntaxError):
tbl = lsf.interpolate_to_wv_array('bad_input')
with pytest.raises(SyntaxError):
x = np.array([[1, 2, 3], [4, 5, 6]])
tbl = lsf.interpolate_to_wv_array(x) # bad shape
with pytest.raises(ValueError):
tbl = lsf.interpolate_to_wv_array(np.array([1, 2]) * u.AA, kind='wrong_kind')
with pytest.raises(ValueError):
tbl = lsf.interpolate_to_wv_array(np.array([1, 2]) * u.AA, kind='cubic') # bad input wv_array
def test_interpolate_to_wv0_wv0shortlong(plot=False):
err_msg = 'Something is wrong with short wavelength handling in LSF.interpolate_to_wv0()'
wv0 = 1105.0 * u.AA
cos_dict = dict(name='COS', grating='G130M', life_position='1')
lsf_cos = LSF(cos_dict)
lsf_tab = lsf_cos.interpolate_to_wv0(wv0)
assert lsf_tab[len(lsf_tab) // 2]['wv'] == wv0.value, err_msg
assert lsf_tab[len(lsf_tab) // 2]['kernel'] == np.max(lsf_tab['kernel']), err_msg
if plot:
import matplotlib.pyplot as plt
lsf_tab = lsf_cos.interpolate_to_wv0(wv0)
plt.plot(lsf_tab['wv'] - wv0.value, lsf_tab['kernel'], '-')
plt.show()
err_msg = 'Something is wrong with long wavelength handling in LSF.interpolate_to_wv0()'
wv0 = 1796.0 * u.AA
cos_dict = dict(name='COS', grating='G160M', life_position='1')
lsf_cos = LSF(cos_dict)
lsf_tab = lsf_cos.interpolate_to_wv0(wv0)
assert lsf_tab[len(lsf_tab) // 2]['wv'] == wv0.value, err_msg
assert lsf_tab[len(lsf_tab) // 2]['kernel'] == np.max(lsf_tab['kernel']), err_msg
if plot:
import matplotlib.pyplot as plt
lsf_tab = lsf_cos.interpolate_to_wv0(wv0)
plt.plot(lsf_tab['wv'] - wv0.value, lsf_tab['kernel'], '-')
plt.show()
# test error outside range
wv0 = 1300.0 * u.AA
with pytest.raises(ValueError):
lsf_tab = lsf_cos.interpolate_to_wv0(wv0)
wv0 = 1900.0 * u.AA
with pytest.raises(ValueError):
lsf_tab = lsf_cos.interpolate_to_wv0(wv0)
def test_interpolate_to_wv0(plot=False):
err_msg = 'Something is wrong with LSF.interpolate_to_wv0()'
wv0 = 1160*u.AA
cos_dict = dict(name='COS',grating='G130M',life_position='2',cen_wave='1309')
lsf_cos = LSF(cos_dict)
lsf_tab = lsf_cos.interpolate_to_wv0(wv0)
assert lsf_tab[len(lsf_tab)/2]['wv'] == wv0.value, err_msg
assert lsf_tab[len(lsf_tab)/2]['kernel'] == np.max(lsf_tab['kernel']), err_msg
if plot:
import matplotlib.pyplot as plt
wv_array = np.arange(1200,1400,10)*u.AA
for wv in wv_array:
lsf_tab = lsf_cos.interpolate_to_wv0(wv)
plt.plot(lsf_tab['wv']-wv.value,lsf_tab['kernel'],'-')
plt.show()
def get_lsfs():
lsfobjs=[]
for i,inst in enumerate(cfg.instr):
if inst in ['COS','STIS']:
lsfobjs.append(LSF(dict(name=inst, grating=cfg.gratings[i],
life_position=cfg.lps[i], cen_wave=cfg.cen_wave[i],
slit=cfg.slits[i])))
elif inst in ['Gaussian','gaussian']:
lsfobjs.append(LSF(dict(name=inst, pixel_scale=cfg.pixel_scales[i],
FWHM=cfg.fwhms[i])))
cfg.lsfs=[]
for fg in cfg.fgs:
if isinstance(fg,int):
lamobs=cfg.wave[fg]
lsfmatch = jbg.wherebetween(lamobs, cfg.lsfranges[:, 0], cfg.lsfranges[:, 1])
lsf = lsfobjs[lsfmatch[0]].interpolate_to_wv_array(cfg.wave[cfg.fgs] * u.AA, kind='cubic')
cfg.lsfs.append(lsf['kernel'])
break
else:
lamobs=np.median(cfg.wave[fg])
lsfmatch = jbg.wherebetween(lamobs, cfg.lsfranges[:, 0], cfg.lsfranges[:, 1])
if len(fg) < 10:
print("Line at {:.2f} AA is undersampling the LSF. Will increase number of pixels at either side to"
" include at least 10.".format(lamobs))
if np.isnan(lamobs):
import pdb;pdb.set_trace()
# NT: this could happen when pixels with S/N<0 exist, i.e. pixels where flux is <0 (e.g. black lines).
# For this reason, is better to remove the option to eliminate pixels based on S/N.
n_more_side = int(np.ceil((10 - len(fg))/2 + 1))
inds_right = [np.max(fg) + ii + 1 for ii in range(n_more_side)]
inds_left = [np.min(fg) - ii - 1 for ii in range(n_more_side)]
inds_left.sort()
fg = inds_left + fg.tolist() + inds_right
fg = np.array(fg)
print("New fg is: {}".format(fg))
try:
lsf = lsfobjs[lsfmatch[0]].interpolate_to_wv_array(cfg.wave[fg] * u.AA, kind='cubic')
except:
import pdb; pdb.set_trace()
# except:
# QtCore.pyqtRemoveInputHook()
# import pdb; pdb.set_trace()
# QtCore.pyqtRestoreInputHook()
cfg.lsfs.append(lsf['kernel'])
def test_lsf_STIS():
gratings = [
'G750L', 'G140M', 'G140L', 'G230M', 'G230L', 'E140H', 'E140M', 'E230H',
'E230M'
]
# G750M, G430M, G430L, G230LB G230MB still not fully implemented.
#todo : implement G430M, G430L, G230LB, G230MB
available_slits = {
'G140L': ['52x0.1', '52x0.2', '52x0.5', '52x2.0'],
'G140M': ['52x0.1', '52x0.2', '52x0.5', '52x2.0'],
'G230L': ['52x0.1', '52x0.2', '52x0.5', '52x2.0'],
'G230M': ['52x0.1', '52x0.2', '52x0.5', '52x2.0'],
'E140H': ['0.1x0.03', '0.2x0.09', '0.2x0.2', '6x0.2'],
'E140M': ['0.1x0.03', '0.2x0.06', '0.2x0.2', '6x0.2'],
'E230H': ['0.1x0.03', '0.1x0.09', '0.1x0.2', '6x0.2'],
'E230M': ['0.1x0.03', '0.2x0.06', '0.2x0.2', '6x0.2'],
'G430L': ['52x0.1', '52x0.2', '52x0.5', '52x2.0'],
'G750L': ['52x0.1', '52x0.2', '52x0.5', '52x2.0']
}
for grating in gratings:
# slits
for slit in available_slits[grating]:
instr_config = dict(name='STIS', grating=grating, slit=slit)
lsf = LSF(instr_config)
def test_lsf_Gaussian():
fwhms = [0.4, 1.2, 1.6]
pix_scales = [0.225, 0.01, 1.75]
for ff in fwhms:
# slits
for ps in pix_scales:
instr_config = dict(name='Gaussian', pixel_scale=ps, FWHM=ff)
lsf = LSF(instr_config)
def test_lsf_COS():
gratings = ['G130M', 'G160M', 'G140L', 'G230L', 'G185M', 'G225M', 'G285M']
life_positions = ['1', '2', '3', '4']
cen_waves_G160M = ['1577', '1589', '1600', '1611', '1623']
cen_waves_G130M = ['1291', '1300', '1309', '1318', '1327']
cen_waves_G140L = ['1105', '1230', '1280']
for grating in gratings:
for lp in life_positions:
instr_config = dict(name='COS', grating=grating, life_position=lp)
if lp in ['2', '3', '4']:
if grating not in ['G130M', 'G160M', 'G140L']:
continue
if grating == 'G130M':
cen_waves_aux = cen_waves_G130M
if lp in ['3', '4']:
# add the extra Cen Wave
cen_waves_aux += ['1222']
elif grating == 'G160M':
cen_waves_aux = cen_waves_G160M
if lp == '4':
# add the extra Cen Wave
cen_waves_aux += ['1533']
elif grating == 'G140L':
cen_waves_aux = cen_waves_G140L
if (lp == '4'):
cen_waves_aux = ['1105',
'1280'] # 1230 not available for LP4
for cen_wave in cen_waves_aux:
instr_config['cen_wave'] = cen_wave
lsf = LSF(instr_config)
print(lp, grating, cen_wave)
elif lp == '1':
lsf = LSF(instr_config)
print(lp, grating)
def test_get_lsf(plot=False, lp='2'):
err_msg = 'Something is wrong with LSF.get_lsf()'
wv_array = np.arange(1250, 1251, 0.0001) * u.AA
cen_waves = ['1291', '1300', '1309', '1318A', '1327A']
colors = ['k', 'b', 'g', 'r', 'orange']
lsf_dict = dict()
for i, cen_wave in enumerate(cen_waves):
cos_dict_aux = dict(name='COS',
grating='G130M',
life_position=lp,
cen_wave=cen_wave)
lsf_dict[cen_wave] = LSF(cos_dict_aux)
lsf_kernel = lsf_dict[cen_wave].get_lsf(wv_array)
assert isinstance(lsf_kernel, np.ndarray), err_msg
if plot:
import matplotlib.pyplot as plt
plt.plot(wv_array, lsf_kernel, '-', color=colors[i])
# test for G140L grating
wv_array = np.arange(1200, 1400, 0.1) * u.AA
cen_waves = ['1105', '1280']
colors = ['k', 'b', 'g', 'r', 'orange']
lsf_dict = dict()
for i, cen_wave in enumerate(cen_waves):
cos_dict_aux = dict(name='COS',
grating='G140L',
life_position=lp,
cen_wave=cen_wave)
lsf_dict[cen_wave] = LSF(cos_dict_aux)
lsf_kernel = lsf_dict[cen_wave].get_lsf(wv_array)
assert isinstance(lsf_kernel, np.ndarray), err_msg
if plot:
import matplotlib.pyplot as plt
plt.plot(wv_array, lsf_kernel, '-', color=colors[i])
if plot:
plt.show()
def test_shift_to_wv0(plot=False):
instr_dict1 = {'name': 'Gaussian', 'pixel_scale': 0.225, 'FWHM': 0.7}
glsf1 = LSF(instr_config=instr_dict1)
thislsf1 = glsf1.shift_to_wv0(3600. * u.AA)
# should not work for multiple tabulated kernels
cos_dict = dict(name='COS', grating='G130M', life_position='1')
lsf_cos = LSF(cos_dict)
with pytest.raises(ValueError):
thislsfX = lsf_cos.interpolate_to_wv0(3600. * u.AA)
def test_lsf_init_errors():
with pytest.raises(TypeError):
lsf = LSF('not_a_dict')
with pytest.raises(SyntaxError):
lsf = LSF(dict(wrong_key='xx'))
with pytest.raises(NotImplementedError):
lsf = LSF(dict(name='bad_instrument'))
# for COS
with pytest.raises(SyntaxError):
lsf = LSF(dict(name='COS', not_grating_given='xx'))
with pytest.raises(NotImplementedError):
lsf = LSF(dict(name='COS', grating='not_implemented_grating'))
with pytest.raises(SyntaxError):
lsf = LSF(dict(name='COS', grating='G130M', not_life_pos_given='xx'))
with pytest.raises(ValueError):
lsf = LSF(dict(name='COS', grating='G130M', life_position='-1'))
with pytest.raises(SyntaxError):
lsf = LSF(
dict(name='COS',
grating='G130M',
life_position='2',
no_cen_wave_given='xx'))
# for STIS
with pytest.raises(SyntaxError):
lsf = LSF(dict(name='STIS', not_grating_given='xx'))
with pytest.raises(NotImplementedError):
lsf = LSF(dict(name='STIS', grating='not_implemented_grating'))
with pytest.raises(SyntaxError):
lsf = LSF(dict(name='STIS', grating='G140L', not_slit_given='xx'))
with pytest.raises(NotImplementedError):
lsf = LSF(dict(name='STIS', grating='G140L', slit='bad_slit'))
# for Gaussian
with pytest.raises(KeyError):
lsf = LSF(dict(name='Gaussian', not_ps_given=0.225, FWHM=0.4))
with pytest.raises(KeyError):
lsf = LSF(dict(name='Gaussian', pixel_scale=0.225, not_fwhm_given=0.4))
def get_lsfs():
lsfobjs = []
for i, inst in enumerate(cfg.instr):
if inst in ['COS', 'STIS']:
lsfobjs.append(
LSF(
dict(name=inst,
grating=cfg.gratings[i],
life_position=cfg.lps[i],
cen_wave=cfg.cen_wave[i],
slit=cfg.slits[i])))
elif inst in ['Gaussian', 'gaussian']:
lsfobjs.append(
LSF(
dict(name=inst,
pixel_scale=cfg.pixel_scales[i],
FWHM=cfg.fwhms[i])))
cfg.lsfs = []
fg_drop_list = []
for fg_e, fg in enumerate(cfg.fgs):
if isinstance(fg, int):
lamobs = cfg.wave[fg]
lsfmatch = jbg.wherebetween(lamobs, cfg.lsfranges[:, 0],
cfg.lsfranges[:, 1])
lsf = lsfobjs[lsfmatch[0]].interpolate_to_wv_array(
cfg.wave[cfg.fgs] * u.AA, kind='cubic')
cfg.lsfs.append(lsf['kernel'])
break
else:
if multiple_gratings(cfg.wave[fg]):
#Wave region straddles gratings, LSF solution unclear
#not giving it an lsf, so also need to remove the wave region
#from the wave region list
fg_drop_list.append(fg_e)
else:
lamobs = np.median(cfg.wave[fg])
lsfmatch = jbg.wherebetween(lamobs, cfg.lsfranges[:, 0],
cfg.lsfranges[:, 1])
if len(fg) < 10:
print(
"Line at {:.2f} AA is undersampling the LSF. Will increase number of pixels at either side to"
" include at least 10.".format(lamobs))
if np.isnan(lamobs):
import pdb
pdb.set_trace()
# NT: this could happen when pixels with S/N<0 exist, i.e. pixels where flux is <0 (e.g. black lines).
# For this reason, is better to remove the option to eliminate pixels based on S/N.
n_more_side = int(np.ceil((10 - len(fg)) / 2 + 1))
inds_right = [
np.max(fg) + ii + 1 for ii in range(n_more_side)
]
inds_left = [
np.min(fg) - ii - 1 for ii in range(n_more_side)
]
inds_left.sort()
fg = inds_left + fg.tolist() + inds_right
fg = np.array(fg)
print("New fg is: {}".format(fg))
try:
lsf = lsfobjs[lsfmatch[0]].interpolate_to_wv_array(
cfg.wave[fg] * u.AA, kind='cubic')
except:
# import pdb; pdb.set_trace()
print(
"Generally when this happens, the line spans the two gratings."
)
from IPython import embed
embed()
# except:
# QtCore.pyqtRemoveInputHook()
# import pdb; pdb.set_trace()
# QtCore.pyqtRestoreInputHook()
cfg.lsfs.append(lsf['kernel'])
#remove wave regions that don't have an LSF solution
#go backwards so that indices remain valid
for drop_idx in fg_drop_list[::-1]:
cfg.fgs.pop(drop_idx)
