def test_doublet():
o = type(str('Dummy'), (object,), {})
o.xdata = 5000.
i = type(str('Dummy2'), (object,), {})
for key in ['C','M','4','X','8','B']:
o.key = key
_ = ltgu.set_doublet(i, o)
def test_doublet():
o = type(str('Dummy'), (object, ), {})
o.xdata = 5000.
i = type(str('Dummy2'), (object, ), {})
for key in ['C', 'M', '4', 'X', '8', 'B']:
o.key = key
_ = ltgu.set_doublet(i, o)
def test_doublet():
o = type(str("Dummy"), (object,), {})
o.xdata = 5000.0
i = type(str("Dummy2"), (object,), {})
for key in ["C", "M", "4", "X", "8", "B"]:
o.key = key
_ = ltgu.set_doublet(i, o)
def on_key(self, event):
""" Deals with key events
Parameters
----------
event : event object
"""
# Flag to control re-draw
flg = -1
# NAVIGATING
if event.key in self.psdict['nav']:
flg = ltgu.navigate(self.psdict, event)
# DOUBLETS
if event.key in ['C', 'M', 'X', '4', '8', 'B']:
wave = ltgu.set_doublet(self, event)
#print('wave = {:g},{:g}'.format(wave[0], wave[1]))
self.ax.plot([wave[0], wave[0]], self.psdict['y_minmax'], '--', color='red')
self.ax.plot([wave[1], wave[1]], self.psdict['y_minmax'], '--', color='red')
flg = 2 # Layer
## SMOOTH
if event.key == 'S':
self.spec = self.spec.box_smooth(2)
flg = 1
if event.key == 'U':
self.spec = self.orig_spec
flg = 1
## Lya Profiles
if event.key in ['D', 'R']:
# Set NHI
if event.key == 'D':
NHI = 10**20.3 * u.cm**-2
elif event.key == 'R':
NHI = 10**19.0 * u.cm**-2
zlya = event.xdata/1215.6701 - 1.
self.llist['z'] = zlya
# Generate Lya profile
lya_line = AbsLine(1215.6701*u.AA)
lya_line.attrib['z'] = zlya
lya_line.attrib['N'] = NHI
lya_line.attrib['b'] = 30. * u.km/u.s
self.lya_line = ltv.voigt_from_abslines(self.spec.dispersion,
lya_line, fwhm=3.)
self.adict['flg'] = 4
# QtCore.pyqtRemoveInputHook()
# import pdb; pdb.set_trace()
# QtCore.pyqtRestoreInputHook()
flg = 1
# ANALYSIS: AODM, EW, Stats, Gaussian
if event.key in ['N', 'E', '$', 'G']:
# If column check for line list
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
if (event.key in ['N', 'E']) & (self.llist['List'] == 'None'):
print('xspec: Choose a Line list first!')
try:
self.statusBar().showMessage('Choose a Line list first!')
except AttributeError:
pass
self.adict['flg'] = 0
return
flg = 1
if self.adict['flg'] == 0:
self.adict['wv_1'] = event.xdata # wavelength
self.adict['C_1'] = event.ydata # continuum
self.adict['flg'] = 1 # Plot dot
else:
self.adict['wv_2'] = event.xdata # wavelength
self.adict['C_2'] = event.ydata # continuum
self.adict['flg'] = 2 # Ready to plot + print
# Sort em + make arrays
iwv = np.array(sorted([self.adict['wv_1'],
self.adict['wv_2']])) * self.spec.wcs.unit
ic = np.array(sorted([self.adict['C_1'],
self.adict['C_2']]))
# Calculate the continuum (linear fit)
param = np.polyfit(iwv, ic, 1)
cfunc = np.poly1d(param)
self.spec.conti = cfunc(self.spec.dispersion)
if event.key == '$': # Simple stats
pix = self.spec.pix_minmax(iwv)[0]
mean = np.mean(self.spec.flux[pix])
median = np.median(self.spec.flux[pix])
stdv = np.std(self.spec.flux[pix]-self.spec.conti[pix])
S2N = median / stdv
mssg = 'Mean={:g}, Median={:g}, S/N={:g}'.format(
mean,median,S2N)
elif event.key == 'G': # Fit a Gaussian
# Good pixels
pix = self.spec.pix_minmax(iwv)[0]
# EW
EW = np.sum(self.spec.conti[pix]-self.spec.flux[pix])
if EW > 0.: # Absorption line
sign=-1
else: # Emission
sign=1
# Amplitude
Aguess = np.max(self.spec.flux[pix]-self.spec.conti[pix])
Cguess = np.mean(self.spec.dispersion[pix])
sguess = 0.1*np.abs(self.adict['wv_1']-self.adict['wv_2'])
#QtCore.pyqtRemoveInputHook()
#pdb.set_trace()
#QtCore.pyqtRestoreInputHook()
g_init = models.Gaussian1D(amplitude=Aguess, mean=Cguess, stddev=sguess)
fitter = fitting.LevMarLSQFitter()
parm = fitter(g_init, self.spec.wavelength[pix].value,
sign*(self.spec.flux[pix]-self.spec.conti[pix]))
g_final = models.Gaussian1D(amplitude=parm.amplitude.value, mean=parm.mean.value, stddev=parm.stddev.value)
# Plot
model_Gauss = g_final(self.spec.dispersion.value)
self.model = XSpectrum1D.from_tuple((self.spec.wavelength, self.spec.conti + sign*model_Gauss))
# Message
mssg = 'Gaussian Fit: '
mssg = mssg+' :: Mean={:g}, Amplitude={:g}, sigma={:g}, flux={:g}'.format(
parm.mean.value, parm.amplitude.value, parm.stddev.value,
parm.stddev.value*(parm.amplitude.value-np.median(self.spec.conti[pix]))*np.sqrt(2*np.pi))
else:
# Find the spectral line (or request it!)
rng_wrest = iwv / (self.llist['z']+1)
gdl = np.where( (self.llist[self.llist['List']].wrest-rng_wrest[0]) *
(self.llist[self.llist['List']].wrest-rng_wrest[1]) < 0.)[0]
if len(gdl) == 1:
wrest = self.llist[self.llist['List']].wrest[gdl[0]]
else:
if len(gdl) == 0: # Search through them all
gdl = np.arange(len(self.llist[self.llist['List']]))
sel_widg = ltgl.SelectLineWidget(self.llist[self.llist['List']]._data[gdl])
sel_widg.exec_()
line = sel_widg.line
#wrest = float(line.split('::')[1].lstrip())
quant = line.split('::')[1].lstrip()
spltw = quant.split(' ')
wrest = Quantity(float(spltw[0]), unit=spltw[1])
# Units
if not hasattr(wrest,'unit'):
# Assume Ang
wrest = wrest * u.AA
# Generate the Spectral Line
aline = AbsLine(wrest,linelist=self.llist[self.llist['List']])
aline.attrib['z'] = self.llist['z']
aline.analy['spec'] = self.spec
# AODM
if event.key == 'N':
# Calculate the velocity limits and load-up
aline.analy['vlim'] = const.c.to('km/s') * (
( iwv/(1+self.llist['z']) - wrest) / wrest )
# AODM
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
aline.measure_aodm()
mssg = 'Using '+ aline.__repr__()
mssg = mssg + ' :: logN = {:g} +/- {:g}'.format(
aline.attrib['logN'], aline.attrib['sig_logN'])
elif event.key == 'E': #EW
aline.analy['wvlim'] = iwv
aline.measure_restew()
mssg = 'Using '+ aline.__repr__()
mssg = mssg + ' :: Rest EW = {:g} +/- {:g}'.format(
aline.attrib['EW'].to(mAA), aline.attrib['sig_EW'].to(mAA))
# Display values
try:
self.statusBar().showMessage(mssg)
except AttributeError:
pass
print(mssg)
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
"""
## Velocity plot
if event.key == 'v':
z=self.llist['z']
# Check for a match in existing list and use it if so
if len(self.abs_sys) > 0:
zabs = np.array([abs_sys.zabs for abs_sys in self.abs_sys])
mt = np.where( np.abs(zabs-z) < 1e-4)[0]
else:
mt = []
if len(mt) == 1:
ini_abs_sys = self.abs_sys[mt[0]]
outfil = ini_abs_sys.absid_file
self.vplt_flg = 0 # Old one
print('Using existing ID file {:s}'.format(outfil))
else:
ini_abs_sys = None
outfil = None
if self.llist['List'] == 'None':
print('Need to set a line list first!!')
self.vplt_flg = -1 # Nothing to do here
return
self.vplt_flg = 1 # New one
# Outfil
if outfil is None:
i0 = self.spec.filename.rfind('/')
i1 = self.spec.filename.rfind('.')
if i0 < 0:
path = './ID_LINES/'
else:
path = self.spec.filename[0:i0]+'/ID_LINES/'
outfil = path + self.spec.filename[i0+1:i1]+'_z'+'{:.4f}'.format(z)+'_id.fits'
d = os.path.dirname(outfil)
if not os.path.exists(d):
os.mkdir(d)
self.outfil = outfil
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
# Launch
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
gui = xsgui.XVelPltGui(self.spec, z=z, outfil=outfil, llist=self.llist,
abs_sys=ini_abs_sys, norm=self.norm,
sel_wv=self.xval*self.spec.wcs.unit)
gui.exec_()
if gui.flg_quit == 0: # Quit without saving (i.e. discarded)
self.vplt_flg = 0
else:
# Push to Abs_Sys
if len(mt) == 1:
self.abs_sys[mt[0]] = gui.abs_sys
else:
self.abs_sys.append(gui.abs_sys)
print('Adding new abs system')
# Redraw
flg=1
"""
# Dummy keys
if event.key in ['shift', 'control', 'shift+super', 'super+shift']:
flg = 0
# Draw
if flg==1: # Default is not to redraw
self.on_draw()
elif flg==2: # Layer (no clear)
self.on_draw(replot=False)
elif flg==-1: # Layer (no clear)
try:
self.statusBar().showMessage('Not a valid key! {:s}'.format(event.key))
except AttributeError:
pass
def on_key(self, event):
""" Deals with key events
Parameters
----------
event : event object
"""
# Flag to control re-draw
flg = -1
# Quit
if event.key == 'q':
self.parent.quit()
return
# NAVIGATING
if event.key in self.psdict['nav']:
flg = ltgu.navigate(self.psdict, event,
flux=self.spec.flux.value,
wave=self.spec.wavelength.value)
# DOUBLETS
if event.key in ['C', 'M', 'X', '4', '8', 'B']:
wave, name = ltgu.set_doublet(self, event)
# Lines
self.ax.plot([wave[0]]*2, self.psdict['y_minmax'], '--', color='red')
self.ax.plot([wave[1]]*2, self.psdict['y_minmax'], '--', color='red')
# Name
for wv in wave:
self.ax.text(wv, self.psdict['y_minmax'][0]+0.8*(
self.psdict['y_minmax'][1]-self.psdict['y_minmax'][0]), name, color='red')
flg = 2 # Layer
## SMOOTH
if event.key == 'S':
self.spec = self.spec.box_smooth(2)
flg = 1
if event.key == 'U':
self.spec = self.orig_spec
flg = 1
## Lya Profiles
if event.key in ['D', 'R']:
# Set NHI
if event.key == 'D':
NHI = 10**20.3 * u.cm**-2
elif event.key == 'R':
NHI = 10**19.0 * u.cm**-2
zlya = event.xdata/1215.6701 - 1.
self.llist['z'] = zlya
# Generate Lya profile
lya_line = AbsLine(1215.6701*u.AA)
lya_line.attrib['z'] = zlya
lya_line.attrib['N'] = NHI
lya_line.attrib['b'] = 30. * u.km/u.s
lya_spec = ltv.voigt_from_abslines(self.spec.wavelength, lya_line, fwhm=3.)
lconti = event.ydata
self.lya_line = XSpectrum1D.from_tuple((lya_spec.wavelength, lya_spec.flux*lconti))
self.adict['flg'] = 4
# QtCore.pyqtRemoveInputHook()
# import pdb; pdb.set_trace()
# QtCore.pyqtRestoreInputHook()
flg = 1
# ANALYSIS: AODM, EW, Stats, Gaussian
if event.key in ['N', 'E', '$', 'G']:
# If column check for line list
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
if (event.key in ['N', 'E']) & (self.llist['List'] == 'None'):
print('xspec: Choose a Line list first!')
try:
self.statusBar().showMessage('Choose a Line list first!')
except AttributeError:
pass
self.adict['flg'] = 0
return
flg = 1
if (self.adict['flg'] == 0) or (self.adict['flg'] > 2):
self.adict['wv_1'] = event.xdata # wavelength
self.adict['C_1'] = event.ydata # local continuum
self.adict['flg'] = 1 # Plot dot
print("Dot at x={:g}, y={:g}".format(event.xdata, event.ydata))
else:
self.adict['wv_2'] = event.xdata # wavelength
self.adict['C_2'] = event.ydata # local continuum
self.adict['flg'] = 2 # Ready to plot + print
print("Dot at x={:g}, y={:g}".format(event.xdata, event.ydata))
# Sort em + make arrays
iwv = np.array(sorted([self.adict['wv_1'],
self.adict['wv_2']])) * self.spec.units['wave']
ic = np.array(sorted([self.adict['C_1'],
self.adict['C_2']]))
# Calculate the continuum (linear fit)
param = np.polyfit(iwv, ic, 1)
cfunc = np.poly1d(param)
lconti = cfunc(self.spec.wavelength.value) # Local continuum
if event.key == '$': # Simple stats
pix = self.spec.pix_minmax(iwv)[0]
mean = np.mean(self.spec.flux[pix])
median = np.median(self.spec.flux[pix])
stdv = np.std(self.spec.flux[pix]-lconti[pix])
S2N = median / stdv
mssg = 'Mean={:g}, Median={:g}, S/N={:g}'.format(
mean,median,S2N)
elif event.key == 'G': # Fit a Gaussian
# Good pixels
pix = self.spec.pix_minmax(iwv)[0]
# EW
EW = np.sum(lconti[pix]-self.spec.flux[pix])
if EW > 0.: # Absorption line
sign=-1
else: # Emission
sign=1
# Amplitude
Aguess = np.max(self.spec.flux[pix]-lconti[pix])
Cguess = np.mean(self.spec.wavelength[pix])
sguess = 0.1*np.abs(self.adict['wv_1']-self.adict['wv_2'])
# Fit
g_init = models.Gaussian1D(amplitude=Aguess, mean=Cguess, stddev=sguess)
fitter = fitting.LevMarLSQFitter()
parm = fitter(g_init, self.spec.wavelength[pix].value,
sign*(self.spec.flux[pix]-lconti[pix]))
# Error
var = [fitter.fit_info['param_cov'][ii,ii] for ii in range(3)]
sig = np.sqrt(var) # amplitude, mean, stddev
sig_dict = {g_init.param_names[0]:sig[0],
g_init.param_names[1]:sig[1],
g_init.param_names[2]:sig[2], }
# Plot
g_final = models.Gaussian1D(amplitude=parm.amplitude.value,
mean=parm.mean.value, stddev=parm.stddev.value)
model_Gauss = g_final(self.spec.wavelength.value)
self.model = XSpectrum1D.from_tuple((self.spec.wavelength, lconti + sign*model_Gauss))
# Flux
flux = parm.stddev.value*parm.amplitude.value*np.sqrt(2*np.pi)
#flux = parm.stddev.value*(parm.amplitude.value-np.median(lconti[pix]))*np.sqrt(2*np.pi)
sig_flux1 = np.sqrt( (sig_dict['stddev']*parm.amplitude.value*np.sqrt(2*np.pi))**2 + (parm.stddev.value*sig_dict['amplitude']*np.sqrt(2*np.pi))**2)
if self.spec.sig_is_set:
sig_flux2 = np.sqrt(np.sum(self.spec.sig[pix].value**2))
else:
sig_flux2 = 9e9
#QtCore.pyqtRemoveInputHook()
#pdb.set_trace()
#QtCore.pyqtRestoreInputHook()
# Message
mssg = 'Gaussian Fit: '
mssg = mssg+' :: Mean={:g}, Amplitude={:g}, sigma={:g}, flux={:g}'.format(
parm.mean.value, parm.amplitude.value, parm.stddev.value, flux)
mssg = mssg+' :: sig(Mean)={:g}, sig(Amplitude)={:g}, sig(sigma)={:g}, sig(flux)={:g}'.format(
sig_dict['mean'], sig_dict['amplitude'], sig_dict['stddev'], min(sig_flux1,sig_flux2))
else:
# Find the spectral line (or request it!)
rng_wrest = iwv / (self.llist['z']+1)
gdl = np.where( (self.llist[self.llist['List']].wrest-rng_wrest[0]) *
(self.llist[self.llist['List']].wrest-rng_wrest[1]) < 0.)[0]
if len(gdl) == 1:
wrest = self.llist[self.llist['List']].wrest[gdl[0]]
closest = False
else:
if len(gdl) == 0: # Search through them all
gdl = np.arange(len(self.llist[self.llist['List']]))
sel_widg = ltgl.SelectLineWidget(self.llist[self.llist['List']]._data[gdl])
sel_widg.exec_()
line = sel_widg.line
#wrest = float(line.split('::')[1].lstrip())
quant = line.split('::')[1].lstrip()
spltw = quant.split(' ')
wrest = Quantity(float(spltw[0]), unit=spltw[1])
closest = True
# Units
if not hasattr(wrest,'unit'):
# Assume Ang
wrest = wrest * u.AA
# Generate the Spectral Line
aline = AbsLine(wrest,linelist=self.llist[self.llist['List']],
z=self.llist['z'], closest=closest)
# Generate a temporary spectrum for analysis and apply the local continuum
tspec = XSpectrum1D.from_tuple((self.spec.wavelength,
self.spec.flux, self.spec.sig))
tspec.normalize(lconti)
aline.analy['spec'] = tspec
# AODM
if event.key == 'N':
# Calculate the velocity limits and load-up
aline.limits.set(const.c.to('km/s') * (
(iwv/(1+self.llist['z']) - wrest) / wrest ))
# AODM
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
aline.measure_aodm()
mssg = 'Using '+ aline.__repr__()
mssg = mssg + ' :: logN = {:g} +/- {:g}'.format(
aline.attrib['logN'], aline.attrib['sig_logN'])
elif event.key == 'E': #EW
aline.limits.set(iwv)
aline.measure_restew()
mssg = 'Using '+ aline.__repr__()
mssg = mssg + ' :: Rest EW = {:g} +/- {:g}'.format(
aline.attrib['EW'].to(mAA), aline.attrib['sig_EW'].to(mAA))
# Display values
try:
self.statusBar().showMessage(mssg)
except AttributeError:
pass
print(mssg)
## Velocity plot
if event.key == 'v':
z=self.llist['z']
# Launch
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
abs_sys = GenericAbsSystem((0.,0.), z, (-300,300)*u.km/u.s)
gui = XAbsSysGui(self.spec, abs_sys, norm=self.norm, llist=self.llist)
gui.exec_()
# Redraw
flg=1
# Dummy keys
if event.key in ['shift', 'control', 'shift+super', 'super+shift']:
flg = 0
if event.key == '?': # open the XSpecGUI help page
import webbrowser
webbrowser.open("http://linetools.readthedocs.org/en/latest/xspecgui.html#navigating-these-key-strokes-help-you-explore-the-spectrum-be-sure-to-click-in-the-spectrum-panel-first")
# Draw
if flg==1: # Default is not to redraw
self.on_draw()
elif flg==2: # Layer (no clear)
self.on_draw(replot=False)
elif flg==-1: # Layer (no clear)
try:
self.statusBar().showMessage('Not a valid key! {:s}'.format(event.key))
except AttributeError:
pass
