def dla_stat(DLAs, qsos, vprox=None, buff=3000.*u.km/u.s,
zem_min=0., flg_zsrch=0, vmin=0.*u.km/u.s,
LLS_CUT=None, partial=False, prox=False):
""" Identify the statistical DLA in a survey
Parameters
----------
vmin : Quantity
vprox
maxdz
zem_min
buff : Quantity
Buffer velocity in Proximate analysis [not ready for this]
NHI_cut
flg_zsrch
dz_toler
partial : bool, optional
Analyze partial LLS? [pLLS]
prox : bool, optional
Proximate LLS? [PLLS]
Returns
-------
msk_smpl : bool array
True = statistical
"""
from linetools.utils import z_from_v
from astropy.coordinates import SkyCoord
# DLA
msk_smpl = DLAs.zem != DLAs.zem
#zmax = z_from_v(qsos['ZEM'], vprox)
zmin = z_from_v(qsos['Z_START'], vmin)
# Make some lists
qsos_coord = SkyCoord(ra=qsos['RA'], dec=qsos['DEC'])
for qq, idla in enumerate(DLAs._abs_sys):
# In stat?
small_sep = idla.coord.separation(qsos_coord) < 3.6*u.arcsec
close_zem = np.abs(idla.zem-qsos['ZEM']) < 0.03
idx = np.where(small_sep & close_zem)[0]
if len(idx) == 0:
continue
elif len(idx) == 1:
#pdb.set_trace()
if ((idla.zabs >= zmin[idx]) &
(idla.zabs <= qsos[idx]['Z_END']) &
(qsos[idx]['FLG_BAL'] != 2)):
msk_smpl[qq] = True
else:
pdb.set_trace()
raise ValueError("Should not be here")
# Return
return msk_smpl
def on_key(self,event):
# Init
rescale = True
fig_clear = False
wrest = None
flg = 0
sv_idx = self.idx_line
## Change rows/columns
if event.key == 'k':
self.sub_xy[0] = max(0, self.sub_xy[0]-1)
if event.key == 'K':
self.sub_xy[0] = self.sub_xy[0]+1
if event.key == 'c':
self.sub_xy[1] = max(0, self.sub_xy[1]-1)
if event.key == 'C':
self.sub_xy[1] = max(0, self.sub_xy[1]+1)
## NAVIGATING
if event.key in self.psdict['nav']:
flg = ltgu.navigate(self.psdict,event)
if event.key == '-':
self.idx_line = max(0, self.idx_line-self.sub_xy[0]*self.sub_xy[1]) # Min=0
if self.idx_line == sv_idx:
print('Edge of list')
if event.key == '=':
self.idx_line = min(len(self.llist['show_line'])-self.sub_xy[0]*self.sub_xy[1],
self.idx_line + self.sub_xy[0]*self.sub_xy[1])
if self.idx_line == sv_idx:
print('Edge of list')
## Reset z
if event.key == 'z':
newz = ltu.z_from_v(self.z, event.xdata)
self.z = newz
# Drawing
self.psdict['x_minmax'] = self.vmnx.value
# Single line command
if event.key in ['1','2','B','U','L','N','V','A', 'x', 'X',
'^', '&']:
try:
wrest = event.inaxes.get_gid()
except AttributeError:
return
else:
absline = self.grab_line(wrest)
## Velocity limits
unit = u.km/u.s
if event.key == '1':
absline.limits.set((event.xdata, absline.limits.vlim[1].value)*unit)
if event.key == '2':
absline.limits.set((absline.limits.vlim[0].value, event.xdata)*unit)
if event.key == '!': # Set all lines to this value
for iline in self.abs_lines:
iline.limits.set((event.xdata, iline.limits.vlim[1].value)*unit)
if event.key == '@':
for iline in self.abs_lines:
iline.limits.set((iline.limits.vlim[0].value, event.xdata)*unit)
## Line type
if event.key == 'A': # Add to lines
self.generate_line((self.z,wrest))
if event.key == 'x': # Remove line
if self.remove_line(wrest):
print('VelPlot: Removed line {:g}'.format(wrest))
if event.key == 'X': # Remove all lines
# Double check
gui = simple_widgets.WarningWidg('About to remove all lines. \n Continue??')
gui.exec_()
if gui.ans is False:
return
#
self.abs_lines = [] # Flush??
# Kinematics
if event.key == '^': # Low-Ion
try:
fkin = absline.analy['flag_kin']
except KeyError:
fkin = 0
fkin += (-1)**(fkin % 2**1 >= 2**0) * 2**0
absline.analy['flag_kin'] = fkin
if event.key == '&': # High-Ion
try:
fkin = absline.analy['flag_kin']
except KeyError:
fkin = 0
fkin += (-1)**(fkin % 2**2 >= 2**1) * 2**1
absline.analy['flag_kin'] = fkin
# Toggle blend
if event.key == 'B':
try:
feye = absline.analy['flg_eye']
except KeyError:
feye = 0
feye = (feye + 1) % 2
absline.analy['flg_eye'] = feye
# Toggle NG
if event.key == 'N':
try:
fanly = absline.analy['do_analysis']
except KeyError:
fanly = 1
if fanly == 0:
fanly = 1
else:
fanly = 0
absline.analy['do_analysis'] = fanly
if event.key == 'V': # Normal
absline.analy['flg_limit'] = 1
if event.key == 'L': # Lower limit
absline.analy['flg_limit'] = 2
if event.key == 'U': # Upper limit
absline.analy['flg_limit'] = 3
'''
# AODM plot
if event.key == ':': #
# Grab good lines
from xastropy.xguis import spec_guis as xsgui
gdl = [iline.wrest for iline in self.abs_sys.lines
if iline.analy['do_analysis'] > 0]
# Launch AODM
if len(gdl) > 0:
gui = xsgui.XAODMGui(self.spec, self.z, gdl, vmnx=self.vmnx, norm=self.norm)
gui.exec_()
else:
print('VelPlot.AODM: No good lines to plot')
'''
if wrest is not None: # Single window
flg = 3
if event.key in ['c','C','k','K','W','!', '@', '=', '-', 'X', 'z','R']: # Redraw all
flg = 1
if event.key in ['Y']:
rescale = False
if event.key in ['k','c','C','K', 'R']:
fig_clear = True
# Print help message
if event.key == '?':
print(self.help_message)
if flg == 1: # Default is not to redraw
self.on_draw(rescale=rescale, fig_clear=fig_clear)
elif flg == 2: # Layer (no clear)
self.on_draw(replot=False, rescale=rescale)
elif flg == 3: # Layer (no clear)
self.on_draw(in_wrest=wrest, rescale=rescale)
def get_zpeak(self):
""" Measure zpeak from an ionic transition
"""
if self.ions is None:
print('get_zpeak: Need to fill ions with get_ions first.')
return
# Ions for analysis
low_ions = [ (14,2), (6,2), (13,2), (26,2), (13,3)] # SiII,CII,AlII,FeII,AlIII
high_ions= [(14,4), (6,4)] # SiIV, CIV
for tt in range(4):
if tt == 0:
ions = low_ions
iflg = 1 # Standard
elif tt == 1:
ions = low_ions
iflg = 2 # Saturated
elif tt == 2:
ions = high_ions
iflg = 1 # Standard
elif tt == 3:
ions = high_ions
iflg = 2 # Standard
else:
raise ValueError('Bad value')
# Search
for ion in ions:
try:
t = self.ions[ion]
except KeyError:
continue
# Measurement?
if t['flag_N'] == iflg:
# Identify the transition
gdi = np.where( (self.ions.trans['Z'] == ion[0]) &
(self.ions.trans['ion'] == ion[1]) &
(self.ions.trans['flag_N'] <= iflg) )[0]
# Take the first one
gdt = self.ions.trans[gdi[0]]
wrest = gdt['wrest']
flgs = self.clm_analy.clm_lines[wrest].analy['FLAGS']
spec_file = self.clm_analy.fits_files[flgs[1] % 64]
# Generate an Abs_Line with spectrum
line = AbsLine(wrest, z=self.clm_analy.zsys, spec_file=spec_file)
# vpeak
from linetools import utils as ltu
vpeak = line.vpeak()
self.zpeak = ltu.z_from_v(self.clm_analy.zsys, vpeak)
if tt == 3:
print('zpeak WARNING: Using saturated high-ions!!')
break
else:
continue
break
# Error catching
if self.zpeak is None:
# Skip primordial LLS
print('lls.zpeak: No transition in {:s}'.format(self.clm_analy.clm_fil))
return (0,0), 0.
# Return
return ion, vpeak
def on_key(self, event):
# Init
rescale = True
fig_clear = False
wrest = None
flg = 0
sv_idx = self.idx_line
## Change rows/columns
if event.key == 'k':
self.sub_xy[0] = max(0, self.sub_xy[0] - 1)
if event.key == 'K':
self.sub_xy[0] = self.sub_xy[0] + 1
if event.key == 'c':
self.sub_xy[1] = max(0, self.sub_xy[1] - 1)
if event.key == 'C':
self.sub_xy[1] = max(0, self.sub_xy[1] + 1)
## NAVIGATING
if event.key in self.psdict['nav']:
flg = ltgu.navigate(self.psdict, event)
if event.key == '-':
self.idx_line = max(0, self.idx_line -
self.sub_xy[0] * self.sub_xy[1]) # Min=0
if self.idx_line == sv_idx:
print('Edge of list')
if event.key == '=':
self.idx_line = min(
len(self.llist['show_line']) - self.sub_xy[0] * self.sub_xy[1],
self.idx_line + self.sub_xy[0] * self.sub_xy[1])
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
if self.idx_line == sv_idx:
print('Edge of list')
## Reset z
if event.key == 'z':
newz = ltu.z_from_v(self.z, event.xdata)
self.z = newz
self.abs_sys.zabs = newz
# Drawing
self.psdict['xmnx'] = self.vmnx.value
# Single line command
if event.key in [
'1', '2', 'B', 'U', 'L', 'N', 'V', 'A', 'x', 'X', '^', '&'
]:
try:
wrest = event.inaxes.get_gid()
except AttributeError:
return
else:
absline = self.grab_line(wrest)
kwrest = wrest.value
## Velocity limits
unit = u.km / u.s
if event.key == '1':
absline.analy['vlim'][0] = event.xdata * unit
if event.key == '2':
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
absline.analy['vlim'][1] = event.xdata * unit
if event.key == '!':
for iline in self.abs_sys.lines:
iline.analy['vlim'][0] = event.xdata * unit
if event.key == '@':
for iline in self.abs_sys.lines:
iline.analy['vlim'][1] = event.xdata * unit
## Line type
if event.key == 'A': # Add to lines
self.generate_line((self.z, wrest))
if event.key == 'x': # Remove line
if self.remove_line(wrest):
print('VelPlot: Removed line {:g}'.format(wrest))
if event.key == 'X': # Remove all lines
# Double check
gui = xguiu.WarningWidg(
'About to remove all lines. \n Continue??')
gui.exec_()
if gui.ans is False:
return
#
self.abs_lines = [] # Flush??
# Kinematics
if event.key == '^': # Low-Ion
try:
fkin = absline.analy['flag_kin']
except KeyError:
fkin = 0
fkin += (-1)**(fkin % 2**1 >= 2**0) * 2**0
absline.analy['flag_kin'] = fkin
if event.key == '&': # High-Ion
try:
fkin = absline.analy['flag_kin']
except KeyError:
fkin = 0
fkin += (-1)**(fkin % 2**2 >= 2**1) * 2**1
absline.analy['flag_kin'] = fkin
# Toggle blend
if event.key == 'B':
try:
feye = absline.analy['flg_eye']
except KeyError:
feye = 0
feye = (feye + 1) % 2
absline.analy['flg_eye'] = feye
# Toggle NG
if event.key == 'N':
try:
fanly = absline.analy['do_analysis']
except KeyError:
fanly = 1
if fanly == 0:
fanly = 1
else:
fanly = 0
absline.analy['do_analysis'] = fanly
if event.key == 'V': # Normal
absline.analy['flg_limit'] = 1
if event.key == 'L': # Lower limit
absline.analy['flg_limit'] = 2
if event.key == 'U': # Upper limit
absline.analy['flg_limit'] = 3
# AODM plot
if event.key == ':': #
# Grab good lines
from xastropy.xguis import spec_guis as xsgui
gdl = [
iline.wrest for iline in self.abs_sys.lines
if iline.analy['do_analysis'] > 0
]
# Launch AODM
if len(gdl) > 0:
gui = xsgui.XAODMGui(self.spec,
self.z,
gdl,
vmnx=self.vmnx,
norm=self.norm)
gui.exec_()
else:
print('VelPlot.AODM: No good lines to plot')
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
if not wrest is None: # Single window
flg = 3
if event.key in [
'c', 'C', 'k', 'K', 'W', '!', '@', '=', '-', 'X', 'z', 'R'
]: # Redraw all
flg = 1
if event.key in ['Y']:
rescale = False
if event.key in ['k', 'c', 'C', 'K', 'R']:
fig_clear = True
if flg == 1: # Default is not to redraw
self.on_draw(rescale=rescale, fig_clear=fig_clear)
elif flg == 2: # Layer (no clear)
self.on_draw(replot=False, rescale=rescale)
elif flg == 3: # Layer (no clear)
self.on_draw(in_wrest=wrest, rescale=rescale)
def lls_stat(LLSs, qsos, vprox=3000.*u.km/u.s, maxdz=99.99,
zem_min=0., NHI_cut=17.5, flg_zsrch=0, dz_toler=0.04,
LLS_CUT=None, partial=False, prox=False):
""" Identify the statistical LLS in a survey
Parameters
----------
vprox
maxdz
zem_min
NHI_cut
flg_zsrch
dz_toler
partial : bool, optional
Analyze partial LLS? [pLLS]
prox : bool, optional
Proximate LLS? [PLLS]
Returns
-------
msk_smpl : bool array
True = statistical
"""
from linetools.utils import z_from_v
# Search redshift
if flg_zsrch == 0:
zsrch = qsos['ZT2']
elif flg_zsrch == 1:
zsrch = qsos['ZT1']
elif flg_zsrch == 2:
zsrch = qsos['ZT0']
# Modify by LLS along QSO sightline as required
if LLS_CUT is not None:
pdb.set_trace()
#zsrch = zsrch > qsos.zlls[LLS_CUT]
# LLS
msk_smpl = LLSs.zem != LLSs.zem
zmax = z_from_v(qsos['ZEM'], vprox)
# Make some lists
lls_coord = LLSs.coord
lls_zem = LLSs.zem
lls_zabs = LLSs.zabs
qsos_coord = SkyCoord(ra=qsos['RA']*u.deg, dec=qsos['DEC']*u.deg)
for qq, ills in enumerate(LLSs._abs_sys):
# Two LLS on one sightline?
small_sep = ills.coord.separation(lls_coord) < 3.6*u.arcsec
close_zem = np.abs(ills.zem-lls_zem) < 0.03
close_zabs = np.abs(ills.zabs-lls_zabs) < dz_toler
if np.sum(small_sep & close_zem & close_zabs) != 1:
raise ValueError("LLS are probably too close in z")
# Cut on NHI
if partial & (ills.NHI > NHI_cut):
continue
if ~partial & (ills.NHI <= NHI_cut):
continue
# Match to QSO RA, DEC
idx = np.where( (ills.coord.separation(qsos_coord) < 3.6*u.arcsec) &
(np.abs(qsos['ZEM']-ills.zem) < 0.03))[0]
if len(idx) != 1:
raise ValueError("Problem with matches")
# Query redshift
if ((zsrch[idx] > 0.) &
(ills.zabs > max(zsrch[idx], qsos['ZEM'][idx] - maxdz) - 1e-4) &
(qsos['ZEM'][idx] > zem_min)):
if (~prox) & (ills.zabs < zmax[idx]): # Intervening
msk_smpl[qq] = True
if prox & (ills.zabs >= zmax[idx]): # Proximate
msk_smpl[qq] = True
# Return
return msk_smpl
def get_zpeak(self):
""" Measure zpeak from an ionic transition
"""
if self.ions is None:
print('get_zpeak: Need to fill ions with get_ions first.')
return
# Ions for analysis
low_ions = [(14, 2), (6, 2), (13, 2), (26, 2),
(13, 3)] # SiII,CII,AlII,FeII,AlIII
high_ions = [(14, 4), (6, 4)] # SiIV, CIV
for tt in range(4):
if tt == 0:
ions = low_ions
iflg = 1 # Standard
elif tt == 1:
ions = low_ions
iflg = 2 # Saturated
elif tt == 2:
ions = high_ions
iflg = 1 # Standard
elif tt == 3:
ions = high_ions
iflg = 2 # Standard
else:
raise ValueError('Bad value')
# Search
for ion in ions:
try:
t = self.ions[ion]
except KeyError:
continue
# Measurement?
if t['flag_N'] == iflg:
# Identify the transition
gdi = np.where((self.ions.trans['Z'] == ion[0])
& (self.ions.trans['ion'] == ion[1])
& (self.ions.trans['flag_N'] <= iflg))[0]
# Take the first one
gdt = self.ions.trans[gdi[0]]
wrest = gdt['wrest']
flgs = self.clm_analy.clm_lines[wrest].analy['FLAGS']
spec_file = self.clm_analy.fits_files[flgs[1] % 64]
# Generate an Abs_Line with spectrum
line = AbsLine(wrest,
z=self.clm_analy.zsys,
spec_file=spec_file)
# vpeak
from linetools import utils as ltu
vpeak = line.vpeak()
self.zpeak = ltu.z_from_v(self.clm_analy.zsys, vpeak)
if tt == 3:
print('zpeak WARNING: Using saturated high-ions!!')
break
else:
continue
break
# Error catching
if self.zpeak is None:
# Skip primordial LLS
print('lls.zpeak: No transition in {:s}'.format(
self.clm_analy.clm_fil))
return (0, 0), 0.
# Return
return ion, vpeak
