def __init__(self,
ispec,
parent=None,
lls_fit_file=None,
outfil=None,
smooth=3.,
zqso=None):
QtGui.QMainWindow.__init__(self, parent)
'''
ispec = Spectrum1D or specfil
lls_fit_file: str, optional
Name of the LLS fit file to input
smooth: float, optional
Number of pixels to smooth on (FWHM)
zqso: float, optional
Redshift of the quasar. If input, a Telfer continuum is used
'''
# Build a widget combining several others
self.main_widget = QtGui.QWidget()
# Status bar
self.create_status_bar()
# Initialize
if outfil is None:
self.outfil = 'LLS_fit.json'
else:
self.outfil = outfil
self.count_lls = 0
self.lls_model = None
self.all_forest = []
self.flag_write = False
# Spectrum
spec, spec_fil = xxgu.read_spec(ispec)
# Continuum
self.conti_dict = xspc.init_conti_dict(
Norm=float(np.median(spec.flux.value)),
piv_wv=np.median(spec.dispersion.value),
igm='True')
if zqso is not None:
self.zqso = zqso
# Read Telfer and apply IGM
tspec = xspc.get_telfer_spec(
zqso=zqso, igm=(self.conti_dict['igm'] == 'True'))
# Rebin
self.continuum = tspec.rebin(spec.dispersion)
# Reset pivot wave
self.conti_dict['piv_wv'] = 1025. * (1 + zqso)
else:
self.zqso = None
self.continuum = XSpectrum1D.from_tuple(
(spec.dispersion, np.ones(len(spec.dispersion))))
self.base_continuum = self.continuum.flux
self.update_conti()
# Full Model (LLS+continuum)
self.full_model = XSpectrum1D.from_tuple(
(spec.dispersion, np.ones(len(spec.dispersion))))
self.smooth = smooth
# LineList
self.llist = xxgu.set_llist('Strong')
self.llist['z'] = 0.
self.plt_wv = zip(
np.array([911.7, 972.5367, 1025.7222, 1215.6700]) * u.AA,
['LL', 'Lyg', 'Lyb', 'Lya'])
# z and N boxes
self.zwidget = xxgu.EditBox(-1., 'z_LLS=', '{:0.5f}')
self.Nwidget = xxgu.EditBox(-1., 'NHI=', '{:0.2f}')
self.bwidget = xxgu.EditBox(-1., 'b=', '{:0.1f}')
self.Cwidget = xxgu.EditBox('None', 'Comment=', '{:s}')
# Grab the pieces and tie together
self.abssys_widg = xspw.AbsSysWidget(
[],
only_one=True,
no_buttons=True,
linelist=self.llist[self.llist['List']])
self.spec_widg = xspw.ExamineSpecWidget(
spec,
status=self.statusBar,
llist=self.llist,
key_events=False,
abs_sys=self.abssys_widg.abs_sys)
self.spec_widg.continuum = self.continuum
#if other_spec is not None:
# ospec, ospec_fil = xxgu.read_spec(other_spec)
# self.spec_widg.other_spec = ospec
# Initial file
if lls_fit_file is not None:
self.init_LLS(lls_fit_file)
# Outfil
wbtn = QtGui.QPushButton('Write', self)
wbtn.setAutoDefault(False)
wbtn.clicked.connect(self.write_out)
#self.out_box = QtGui.QLineEdit()
#self.out_box.setText(self.outfil)
#self.connect(self.out_box, QtCore.SIGNAL('editingFinished ()'), self.set_outfil)
# Quit
buttons = QtGui.QWidget()
wqbtn = QtGui.QPushButton('Write\n Quit', self)
wqbtn.setAutoDefault(False)
wqbtn.clicked.connect(self.write_quit)
qbtn = QtGui.QPushButton('Quit', self)
qbtn.setAutoDefault(False)
qbtn.clicked.connect(self.quit)
# Connections (buttons are above)
self.spec_widg.canvas.mpl_connect('key_press_event', self.on_key)
self.abssys_widg.abslist_widget.itemSelectionChanged.connect(
self.on_list_change)
self.connect(self.Nwidget.box, QtCore.SIGNAL('editingFinished ()'),
self.setbzN)
self.connect(self.zwidget.box, QtCore.SIGNAL('editingFinished ()'),
self.setbzN)
self.connect(self.bwidget.box, QtCore.SIGNAL('editingFinished ()'),
self.setbzN)
self.connect(self.Cwidget.box, QtCore.SIGNAL('editingFinished ()'),
self.setbzN)
# Layout
anly_widg = QtGui.QWidget()
anly_widg.setMaximumWidth(400)
anly_widg.setMinimumWidth(250)
# Write/Quit buttons
hbox1 = QtGui.QHBoxLayout()
hbox1.addWidget(wbtn)
hbox1.addWidget(wqbtn)
hbox1.addWidget(qbtn)
buttons.setLayout(hbox1)
# z,N
zNwidg = QtGui.QWidget()
hbox2 = QtGui.QHBoxLayout()
hbox2.addWidget(self.zwidget)
hbox2.addWidget(self.Nwidget)
hbox2.addWidget(self.bwidget)
zNwidg.setLayout(hbox2)
#vbox.addWidget(self.pltline_widg)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(zNwidg)
vbox.addWidget(self.Cwidget)
vbox.addWidget(self.abssys_widg)
vbox.addWidget(buttons)
anly_widg.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.spec_widg)
hbox.addWidget(anly_widg)
self.main_widget.setLayout(hbox)
# Point MainWindow
self.setCentralWidget(self.main_widget)
def __init__(self, ispec, parent=None, lls_fit_file=None,
srch_id=True, outfil=None, fwhm=3., zqso=None,plot_residuals=True):
QtGui.QMainWindow.__init__(self, parent)
'''
spec = Spectrum1D
lls_fit_file: str, optional
Name of the LLS fit file to input
smooth: float, optional
Number of pixels to smooth on
zqso: float, optional
Redshift of the quasar. If input, a Telfer continuum is used
plot_residuals : bool, optional
Whether to plot residuals
'''
# TODO
# 1. Fix convolve window size
# 2. Avoid sorting of wavelengths
# 3. Remove astropy.relativity
# 4. Display self.z
# 5. Recenter on 'z'
# 6. Add COS LSF
# 7. Refit component key 'F'
# 8. Plot only selected components [DEPRECATED]
# 9. Avoid shifting z of component outside its velocity range
# 10. Write Component vlim to JSON
# 11. Key to set line as some other transition (e.g. RMB in XSpec)
# 12. Mask array with points
# 13. Toggle line ID names
# 14. Add error + residual arrays [NT]
# 15. Adjust component redshift by keystroke
# 16. Input redshift value via Widget
# 17. Use Component list to jump between components (like 'S')
# Build a widget combining several others
self.main_widget = QtGui.QWidget()
# Status bar
self.create_status_bar()
# Initialize
if outfil is None:
self.outfil = 'IGM_model.json'
else:
self.outfil = outfil
self.fwhm = fwhm
self.plot_residuals = plot_residuals
# Spectrum
spec, spec_fil = xxgu.read_spec(ispec)
spec.mask = np.zeros(len(spec.dispersion),dtype=int)
# Full Model
self.model = XSpectrum1D.from_tuple((
spec.dispersion,np.ones(len(spec.dispersion))))
# LineList (Grab ISM and HI as defaults)
self.llist = xxgu.set_llist('ISM')
# Load others
self.llist['HI'] = LineList('HI')
self.llist['Strong'] = LineList('Strong')
self.llist['Lists'].append('HI')
self.llist['HI']._data = self.llist['HI']._data[::-1] #invert order of Lyman series
#self.llist['show_line'] = np.arange(10) #maximum 10 to show for Lyman series
#define initial redshift
z=0.0
self.llist['z'] = z
# Grab the pieces and tie together
self.slines_widg = xspw.SelectedLinesWidget(
self.llist[self.llist['List']], parent=self,
init_select='All')
self.fiddle_widg = FiddleComponentWidget(parent=self)
self.comps_widg = ComponentListWidget([], parent=self)
self.velplot_widg = IGGVelPlotWidget(spec, z,
parent=self, llist=self.llist, fwhm=self.fwhm,plot_residuals=self.plot_residuals)
self.wq_widg = xxgu.WriteQuitWidget(parent=self)
# Setup strongest LineList
self.llist['strongest'] = LineList('ISM')
self.llist['Lists'].append('strongest')
self.update_strongest_lines()
self.slines_widg.selected = self.llist['show_line']
self.slines_widg.on_list_change(
self.llist[self.llist['List']])
# Connections (buttons are above)
#self.spec_widg.canvas.mpl_connect('key_press_event', self.on_key)
#self.abssys_widg.abslist_widget.itemSelectionChanged.connect(
# self.on_list_change)
# Layout
anly_widg = QtGui.QWidget()
anly_widg.setMaximumWidth(400)
anly_widg.setMinimumWidth(250)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.fiddle_widg)
vbox.addWidget(self.comps_widg)
vbox.addWidget(self.slines_widg)
vbox.addWidget(self.wq_widg)
anly_widg.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.velplot_widg)
hbox.addWidget(anly_widg)
self.main_widget.setLayout(hbox)
# Point MainWindow
self.setCentralWidget(self.main_widget)
def __init__(self, ispec, parent=None, lls_fit_file=None,
outfil=None, smooth=3., zqso=None):
QtGui.QMainWindow.__init__(self, parent)
'''
ispec = Spectrum1D or specfil
lls_fit_file: str, optional
Name of the LLS fit file to input
smooth: float, optional
Number of pixels to smooth on (FWHM)
zqso: float, optional
Redshift of the quasar. If input, a Telfer continuum is used
'''
# Build a widget combining several others
self.main_widget = QtGui.QWidget()
# Status bar
self.create_status_bar()
# Initialize
if outfil is None:
self.outfil = 'LLS_fit.json'
else:
self.outfil = outfil
self.count_lls = 0
self.lls_model = None
self.all_forest = []
self.flag_write = False
# Spectrum
spec, spec_fil = xxgu.read_spec(ispec)
# Continuum
self.conti_dict = xspc.init_conti_dict(
Norm=float(np.median(spec.flux.value)),
piv_wv=np.median(spec.dispersion.value),
igm='True')
if zqso is not None:
self.zqso = zqso
# Read Telfer and apply IGM
tspec = xspc.get_telfer_spec(zqso=zqso,
igm=(self.conti_dict['igm']=='True'))
# Rebin
self.continuum = tspec.rebin(spec.dispersion)
# Reset pivot wave
self.conti_dict['piv_wv'] = 1025.*(1+zqso)
else:
self.zqso = None
self.continuum = XSpectrum1D.from_tuple((
spec.dispersion,np.ones(len(spec.dispersion))))
self.base_continuum = self.continuum.flux
self.update_conti()
# Full Model (LLS+continuum)
self.full_model = XSpectrum1D.from_tuple((
spec.dispersion,np.ones(len(spec.dispersion))))
self.smooth = smooth
# LineList
self.llist = xxgu.set_llist('Strong')
self.llist['z'] = 0.
self.plt_wv = zip(np.array([911.7,972.5367,1025.7222,1215.6700])*u.AA,
['LL','Lyg','Lyb','Lya'])
# z and N boxes
self.zwidget = xxgu.EditBox(-1., 'z_LLS=', '{:0.5f}')
self.Nwidget = xxgu.EditBox(-1., 'NHI=', '{:0.2f}')
self.bwidget = xxgu.EditBox(-1., 'b=', '{:0.1f}')
self.Cwidget = xxgu.EditBox('None', 'Comment=', '{:s}')
# Grab the pieces and tie together
self.abssys_widg = xspw.AbsSysWidget([],only_one=True,
no_buttons=True, linelist=self.llist[self.llist['List']])
self.spec_widg = xspw.ExamineSpecWidget(spec,status=self.statusBar,
llist=self.llist, key_events=False,
abs_sys=self.abssys_widg.abs_sys)
self.spec_widg.continuum = self.continuum
#if other_spec is not None:
# ospec, ospec_fil = xxgu.read_spec(other_spec)
# self.spec_widg.other_spec = ospec
# Initial file
if lls_fit_file is not None:
self.init_LLS(lls_fit_file)
# Outfil
wbtn = QtGui.QPushButton('Write', self)
wbtn.setAutoDefault(False)
wbtn.clicked.connect(self.write_out)
#self.out_box = QtGui.QLineEdit()
#self.out_box.setText(self.outfil)
#self.connect(self.out_box, QtCore.SIGNAL('editingFinished ()'), self.set_outfil)
# Quit
buttons = QtGui.QWidget()
wqbtn = QtGui.QPushButton('Write\n Quit', self)
wqbtn.setAutoDefault(False)
wqbtn.clicked.connect(self.write_quit)
qbtn = QtGui.QPushButton('Quit', self)
qbtn.setAutoDefault(False)
qbtn.clicked.connect(self.quit)
# Connections (buttons are above)
self.spec_widg.canvas.mpl_connect('key_press_event', self.on_key)
self.abssys_widg.abslist_widget.itemSelectionChanged.connect(
self.on_list_change)
self.connect(self.Nwidget.box,
QtCore.SIGNAL('editingFinished ()'), self.setbzN)
self.connect(self.zwidget.box,
QtCore.SIGNAL('editingFinished ()'), self.setbzN)
self.connect(self.bwidget.box,
QtCore.SIGNAL('editingFinished ()'), self.setbzN)
self.connect(self.Cwidget.box,
QtCore.SIGNAL('editingFinished ()'), self.setbzN)
# Layout
anly_widg = QtGui.QWidget()
anly_widg.setMaximumWidth(400)
anly_widg.setMinimumWidth(250)
# Write/Quit buttons
hbox1 = QtGui.QHBoxLayout()
hbox1.addWidget(wbtn)
hbox1.addWidget(wqbtn)
hbox1.addWidget(qbtn)
buttons.setLayout(hbox1)
# z,N
zNwidg = QtGui.QWidget()
hbox2 = QtGui.QHBoxLayout()
hbox2.addWidget(self.zwidget)
hbox2.addWidget(self.Nwidget)
hbox2.addWidget(self.bwidget)
zNwidg.setLayout(hbox2)
#vbox.addWidget(self.pltline_widg)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(zNwidg)
vbox.addWidget(self.Cwidget)
vbox.addWidget(self.abssys_widg)
vbox.addWidget(buttons)
anly_widg.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.spec_widg)
hbox.addWidget(anly_widg)
self.main_widget.setLayout(hbox)
# Point MainWindow
self.setCentralWidget(self.main_widget)
def __init__(self,
ispec,
parent=None,
lls_fit_file=None,
outfil=None,
smooth=3.,
zqso=None,
fN_gamma=None,
template=None,
dw=0.1,
skip_wveval=False):
QtGui.QMainWindow.__init__(self, parent)
'''
ispec : Spectrum1D or specfil
lls_fit_file: str, optional
Name of the LLS fit file to input
smooth : float, optional
Number of pixels to smooth on (FWHM)
zqso : float, optional
Redshift of the quasar. If input, a Telfer continuum is used
fN_gamma : float, optional
Redshift evolution of f(N) or IGM fiddled continuum
template : str, optional
Filename of a QSO template to use instead of the Telfer
continuum. Only used if zqso is also given.
dw : float, optional
Pixel width in Angstroms for the wavelength array used to
generate optical depths. Default is 0.1.
skip_wveval : bool, optional
Skip rebinning of wavelengths in the Voigt profile generation.
This can speed up the code considerably, but use it wisely.
'''
# Build a widget combining several others
self.main_widget = QtGui.QWidget()
# Status bar
self.create_status_bar()
# Initialize
if outfil is None:
self.outfil = 'LLS_fit.json'
else:
self.outfil = outfil
self.count_lls = 0
self.lls_model = None
self.smooth = None
self.base_continuum = None
self.all_forest = []
self.flag_write = False
self.dw = float(dw)
self.skip_wveval = skip_wveval
if skip_wveval:
warnings.warn("Skipping wavelength rebinning in Voigt.")
warnings.warn("Make sure you know what you are doing!")
# Spectrum
spec, spec_fil = xxgu.read_spec(ispec)
# LineList
self.llist = xxgu.set_llist('Strong')
self.llist['z'] = 0.
self.plt_wv = zip(
np.array([911.7, 949.743, 972.5367, 1025.7222, 1215.6700]) * u.AA,
['LL', 'Lyd', 'Lyg', 'Lyb', 'Lya'])
# z and N boxes
self.zwidget = xxgu.EditBox(-1., 'z_LLS=', '{:0.5f}')
self.Nwidget = xxgu.EditBox(-1., 'NHI=', '{:0.2f}')
self.bwidget = xxgu.EditBox(-1., 'b=', '{:0.1f}')
self.Cwidget = xxgu.EditBox('None', 'Comment=', '{:s}')
# Grab the pieces and tie together
self.abssys_widg = xspw.AbsSysWidget(
[],
only_one=True,
no_buttons=True,
linelist=self.llist[self.llist['List']])
vlines = [(912 * (1 + zqso) if zqso is not None else None)]
self.spec_widg = xspw.ExamineSpecWidget(
spec,
status=self.statusBar,
llist=self.llist,
key_events=False,
abs_sys=self.abssys_widg.abs_sys,
vlines=vlines,
plotzero=1)
# Initialize continuum (and LLS if from a file)
if lls_fit_file is not None:
self.init_LLS(lls_fit_file, spec)
else:
self.conti_dict = xspc.init_conti_dict(
Norm=float(np.median(spec.flux.value)),
piv_wv=1215. * (1 + zqso),
#piv_wv2=915.*(1+zqso),
igm='True')
if self.base_continuum is None:
if zqso is not None:
self.zqso = zqso
# Read Telfer and apply IGM
if template is not None:
tspec = lsi.readspec(template)
# assume wavelengths
tspec = XSpectrum1D.from_tuple(
(tspec.dispersion.value * (1 + zqso),
tspec.flux.value))
else:
tspec = xspc.get_telfer_spec(
zqso=zqso, igm=(self.conti_dict['igm'] == 'True'))
# Rebin
self.continuum = tspec.rebin(spec.dispersion)
# Reset pivot wave
self.conti_dict['piv_wv'] = 915. * (1 + zqso)
#self.conti_dict['piv_wv'] = 1215.*(1+zqso)
#self.conti_dict['piv_wv2'] = 915.*(1+zqso)
else:
self.zqso = None
self.continuum = XSpectrum1D.from_tuple(
(spec.dispersion, np.ones(len(spec.dispersion))))
self.base_continuum = self.continuum.flux
self.update_conti()
self.spec_widg.continuum = self.continuum
# Full Model (LLS+continuum)
self.full_model = XSpectrum1D.from_tuple(
(spec.dispersion, np.ones(len(spec.dispersion))))
if self.smooth is None:
self.smooth = smooth
# Initialize as needed
if lls_fit_file is not None:
self.update_boxes()
self.update_model()
# Outfil
wbtn = QtGui.QPushButton('Write', self)
wbtn.setAutoDefault(False)
wbtn.clicked.connect(self.write_out)
#self.out_box = QtGui.QLineEdit()
#self.out_box.setText(self.outfil)
#self.connect(self.out_box, QtCore.SIGNAL('editingFinished ()'), self.set_outfil)
# Quit
buttons = QtGui.QWidget()
wqbtn = QtGui.QPushButton('Write\n Quit', self)
wqbtn.setAutoDefault(False)
wqbtn.clicked.connect(self.write_quit)
qbtn = QtGui.QPushButton('Quit', self)
qbtn.setAutoDefault(False)
qbtn.clicked.connect(self.quit)
# Connections (buttons are above)
self.spec_widg.canvas.mpl_connect('key_press_event', self.on_key)
self.abssys_widg.abslist_widget.itemSelectionChanged.connect(
self.on_list_change)
self.connect(self.Nwidget.box, QtCore.SIGNAL('editingFinished ()'),
self.setbzN)
self.connect(self.zwidget.box, QtCore.SIGNAL('editingFinished ()'),
self.setbzN)
self.connect(self.bwidget.box, QtCore.SIGNAL('editingFinished ()'),
self.setbzN)
self.connect(self.Cwidget.box, QtCore.SIGNAL('editingFinished ()'),
self.setbzN)
# Layout
anly_widg = QtGui.QWidget()
anly_widg.setMaximumWidth(400)
anly_widg.setMinimumWidth(250)
# Write/Quit buttons
hbox1 = QtGui.QHBoxLayout()
hbox1.addWidget(wbtn)
hbox1.addWidget(wqbtn)
hbox1.addWidget(qbtn)
buttons.setLayout(hbox1)
# z,N
zNwidg = QtGui.QWidget()
hbox2 = QtGui.QHBoxLayout()
hbox2.addWidget(self.zwidget)
hbox2.addWidget(self.Nwidget)
hbox2.addWidget(self.bwidget)
zNwidg.setLayout(hbox2)
#vbox.addWidget(self.pltline_widg)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(zNwidg)
vbox.addWidget(self.Cwidget)
vbox.addWidget(self.abssys_widg)
vbox.addWidget(buttons)
anly_widg.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.spec_widg)
hbox.addWidget(anly_widg)
self.main_widget.setLayout(hbox)
# Point MainWindow
self.setCentralWidget(self.main_widget)
#self.spec_widg.setFixedWidth(900)
self.spec_widg.setMinimumWidth(900)
def __init__(self, ispec, z, parent=None, llist=None, norm=True,
vmnx=[-500., 500.]*u.km/u.s, fwhm=0.,plot_residuals=True):
'''
spec = Spectrum1D
Norm: Bool (False)
Normalized spectrum?
abs_sys: AbsSystem
Absorption system class
'''
super(IGGVelPlotWidget, self).__init__(parent)
# Initialize
self.parent = parent
spec, spec_fil = xxgu.read_spec(ispec)
self.spec = spec
self.spec_fil = spec_fil
self.fwhm = fwhm
self.z = z
self.vmnx = vmnx
self.norm = norm
# Init
self.flag_add = False
self.flag_idlbl = False
self.flag_mask = False
self.wrest = 0.
self.avmnx = np.array([0.,0.])*u.km/u.s
self.model = XSpectrum1D.from_tuple((
spec.dispersion,np.ones(len(spec.dispersion))))
self.plot_residuals = plot_residuals
#Define arrays for plotting residuals
if self.plot_residuals:
self.residual_normalization_factor = 0.02/np.median(self.spec.sig)
self.residual_limit = self.spec.sig * self.residual_normalization_factor
self.residual = (self.spec.flux - self.model.flux) * self.residual_normalization_factor
self.psdict = {} # Dict for spectra plotting
self.psdict['xmnx'] = self.vmnx.value # Too much pain to use units with this
self.psdict['ymnx'] = [-0.1, 1.1]
self.psdict['nav'] = xxgu.navigate(0,0,init=True)
# Status Bar?
#if not status is None:
# self.statusBar = status
# Line List
if llist is None:
self.llist = xxgu.set_llist(['HI 1215', 'HI 1025'])
else:
self.llist = llist
self.llist['z'] = self.z
# Indexing for line plotting
self.idx_line = 0
self.init_lines()
# Create the mpl Figure and FigCanvas objects.
#
self.dpi = 150
self.fig = Figure((8.0, 4.0), dpi=self.dpi)
self.canvas = FigureCanvas(self.fig)
self.canvas.setParent(self)
self.canvas.setFocusPolicy( QtCore.Qt.ClickFocus )
self.canvas.setFocus()
self.canvas.mpl_connect('key_press_event', self.on_key)
self.canvas.mpl_connect('button_press_event', self.on_click)
# Sub_plots
self.sub_xy = [5,3]
self.subxy_state = 'Out'
self.fig.subplots_adjust(hspace=0.0, wspace=0.1,left=0.04,right=0.975)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.canvas)
self.setLayout(vbox)
# Draw on init
self.on_draw()
def __init__(self, ispec, parent=None, lls_fit_file=None,
outfil=None, smooth=3., zqso=None, fN_gamma=None, template=None,
dw=0.1, skip_wveval=False):
QtGui.QMainWindow.__init__(self, parent)
'''
ispec : Spectrum1D or specfil
lls_fit_file: str, optional
Name of the LLS fit file to input
smooth : float, optional
Number of pixels to smooth on (FWHM)
zqso : float, optional
Redshift of the quasar. If input, a Telfer continuum is used
fN_gamma : float, optional
Redshift evolution of f(N) or IGM fiddled continuum
template : str, optional
Filename of a QSO template to use instead of the Telfer
continuum. Only used if zqso is also given.
dw : float, optional
Pixel width in Angstroms for the wavelength array used to
generate optical depths. Default is 0.1.
skip_wveval : bool, optional
Skip rebinning of wavelengths in the Voigt profile generation.
This can speed up the code considerably, but use it wisely.
'''
# Build a widget combining several others
self.main_widget = QtGui.QWidget()
# Status bar
self.create_status_bar()
# Initialize
if outfil is None:
self.outfil = 'LLS_fit.json'
else:
self.outfil = outfil
self.count_lls = 0
self.lls_model = None
self.smooth = None
self.base_continuum = None
self.all_forest = []
self.flag_write = False
self.dw = float(dw)
self.skip_wveval = skip_wveval
if skip_wveval:
warnings.warn("Skipping wavelength rebinning in Voigt.")
warnings.warn("Make sure you know what you are doing!")
# Spectrum
spec, spec_fil = xxgu.read_spec(ispec)
# LineList
self.llist = xxgu.set_llist('Strong')
self.llist['z'] = 0.
self.plt_wv = zip(np.array([911.7, 949.743, 972.5367,1025.7222,1215.6700])*u.AA,
['LL','Lyd', 'Lyg','Lyb','Lya'])
# z and N boxes
self.zwidget = xxgu.EditBox(-1., 'z_LLS=', '{:0.5f}')
self.Nwidget = xxgu.EditBox(-1., 'NHI=', '{:0.2f}')
self.bwidget = xxgu.EditBox(-1., 'b=', '{:0.1f}')
self.Cwidget = xxgu.EditBox('None', 'Comment=', '{:s}')
# Grab the pieces and tie together
self.abssys_widg = xspw.AbsSysWidget([],only_one=True,
no_buttons=True, linelist=self.llist[self.llist['List']])
vlines = [(912 * (1 + zqso) if zqso is not None else None)]
self.spec_widg = xspw.ExamineSpecWidget(spec,status=self.statusBar,
llist=self.llist, key_events=False,
abs_sys=self.abssys_widg.abs_sys,
vlines=vlines, plotzero=1)
# Initialize continuum (and LLS if from a file)
if lls_fit_file is not None:
self.init_LLS(lls_fit_file,spec)
else:
self.conti_dict = xspc.init_conti_dict(
Norm=float(np.median(spec.flux.value)),
piv_wv=1215.*(1+zqso),
#piv_wv2=915.*(1+zqso),
igm='True')
if self.base_continuum is None:
if zqso is not None:
self.zqso = zqso
# Read Telfer and apply IGM
if template is not None:
tspec = lsi.readspec(template)
# assume wavelengths
tspec = XSpectrum1D.from_tuple(
(tspec.dispersion.value * (1 + zqso),
tspec.flux.value))
else:
tspec = xspc.get_telfer_spec(zqso=zqso,
igm=(self.conti_dict['igm']=='True'))
# Rebin
self.continuum = tspec.rebin(spec.dispersion)
# Reset pivot wave
self.conti_dict['piv_wv'] = 915.*(1+zqso)
#self.conti_dict['piv_wv'] = 1215.*(1+zqso)
#self.conti_dict['piv_wv2'] = 915.*(1+zqso)
else:
self.zqso = None
self.continuum = XSpectrum1D.from_tuple((
spec.dispersion,np.ones(len(spec.dispersion))))
self.base_continuum = self.continuum.flux
self.update_conti()
self.spec_widg.continuum = self.continuum
# Full Model (LLS+continuum)
self.full_model = XSpectrum1D.from_tuple((
spec.dispersion,np.ones(len(spec.dispersion))))
if self.smooth is None:
self.smooth = smooth
# Initialize as needed
if lls_fit_file is not None:
self.update_boxes()
self.update_model()
# Outfil
wbtn = QtGui.QPushButton('Write', self)
wbtn.setAutoDefault(False)
wbtn.clicked.connect(self.write_out)
#self.out_box = QtGui.QLineEdit()
#self.out_box.setText(self.outfil)
#self.connect(self.out_box, QtCore.SIGNAL('editingFinished ()'), self.set_outfil)
# Quit
buttons = QtGui.QWidget()
wqbtn = QtGui.QPushButton('Write\n Quit', self)
wqbtn.setAutoDefault(False)
wqbtn.clicked.connect(self.write_quit)
qbtn = QtGui.QPushButton('Quit', self)
qbtn.setAutoDefault(False)
qbtn.clicked.connect(self.quit)
# Connections (buttons are above)
self.spec_widg.canvas.mpl_connect('key_press_event', self.on_key)
self.abssys_widg.abslist_widget.itemSelectionChanged.connect(
self.on_list_change)
self.connect(self.Nwidget.box,
QtCore.SIGNAL('editingFinished ()'), self.setbzN)
self.connect(self.zwidget.box,
QtCore.SIGNAL('editingFinished ()'), self.setbzN)
self.connect(self.bwidget.box,
QtCore.SIGNAL('editingFinished ()'), self.setbzN)
self.connect(self.Cwidget.box,
QtCore.SIGNAL('editingFinished ()'), self.setbzN)
# Layout
anly_widg = QtGui.QWidget()
anly_widg.setMaximumWidth(400)
anly_widg.setMinimumWidth(250)
# Write/Quit buttons
hbox1 = QtGui.QHBoxLayout()
hbox1.addWidget(wbtn)
hbox1.addWidget(wqbtn)
hbox1.addWidget(qbtn)
buttons.setLayout(hbox1)
# z,N
zNwidg = QtGui.QWidget()
hbox2 = QtGui.QHBoxLayout()
hbox2.addWidget(self.zwidget)
hbox2.addWidget(self.Nwidget)
hbox2.addWidget(self.bwidget)
zNwidg.setLayout(hbox2)
#vbox.addWidget(self.pltline_widg)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(zNwidg)
vbox.addWidget(self.Cwidget)
vbox.addWidget(self.abssys_widg)
vbox.addWidget(buttons)
anly_widg.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.spec_widg)
hbox.addWidget(anly_widg)
self.main_widget.setLayout(hbox)
# Point MainWindow
self.setCentralWidget(self.main_widget)
#self.spec_widg.setFixedWidth(900)
self.spec_widg.setMinimumWidth(900)
def __init__(self, ispec, parent=None, lls_fit_file=None,
srch_id=True, outfil=None, fwhm=3., zqso=None):
QtGui.QMainWindow.__init__(self, parent)
'''
spec = Spectrum1D
lls_fit_file: str, optional
Name of the LLS fit file to input
smooth: float, optional
Number of pixels to smooth on
zqso: float, optional
Redshift of the quasar. If input, a Telfer continuum is used
'''
# TODO
# 1. Fix convolve window size
# 2. Avoid sorting of wavelengths
# 3. Remove astropy.relativity
# 4. Display self.z
# 5. Recenter on 'z'
# 6. Add COS LSF
# 7. Refit component key 'F'
# 8. Plot only selected components
# 9. Avoid shifting z of component outside its velocity range
# 10. Write Component vlim to JSON
# 11. Key to set line as some other transition (e.g. RMB in XSpec)
# 12. Mask array with points
# 13. Toggle line ID names
# 14. Add error + residual arrays [NT]
# 15. Adjust component redshift by keystroke
# Build a widget combining several others
self.main_widget = QtGui.QWidget()
# Status bar
self.create_status_bar()
# Initialize
if outfil is None:
self.outfil = 'IGM_model.json'
else:
self.outfil = outfil
self.fwhm = fwhm
# Spectrum
spec, spec_fil = xxgu.read_spec(ispec)
spec.mask = np.zeros(len(spec.dispersion),dtype=int)
# Full Model
self.model = XSpectrum1D.from_tuple((
spec.dispersion,np.ones(len(spec.dispersion))))
# LineList
self.llist = xxgu.set_llist(['HI 1215', 'HI 1025', 'CIV 1548'],sort=False)
z=0.112
self.llist['z'] = z
# Grab the pieces and tie together
self.fiddle_widg = FiddleComponentWidget(parent=self)
self.comps_widg = ComponentListWidget([], parent=self,
linelist=self.llist[self.llist['List']])
self.velplot_widg = IGGVelPlotWidget(spec, z,
parent=self, llist=self.llist, fwhm=self.fwhm)
self.wq_widg = xxgu.WriteQuitWidget(parent=self)
self.slines_widg = xspw.SelectedLinesWidget(
self.llist[self.llist['List']], parent=self, init_select='All')
# Connections (buttons are above)
#self.spec_widg.canvas.mpl_connect('key_press_event', self.on_key)
#self.abssys_widg.abslist_widget.itemSelectionChanged.connect(
# self.on_list_change)
# Layout
anly_widg = QtGui.QWidget()
anly_widg.setMaximumWidth(400)
anly_widg.setMinimumWidth(250)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.fiddle_widg)
vbox.addWidget(self.comps_widg)
vbox.addWidget(self.slines_widg)
vbox.addWidget(self.wq_widg)
anly_widg.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.velplot_widg)
hbox.addWidget(anly_widg)
self.main_widget.setLayout(hbox)
# Point MainWindow
self.setCentralWidget(self.main_widget)
def __init__(self, ispec, parent=None, lls_fit_file=None, outfil=None, smooth=3.0, zqso=None):
QtGui.QMainWindow.__init__(self, parent)
"""
ispec = Spectrum1D or specfil
lls_fit_file: str, optional
Name of the LLS fit file to input
smooth: float, optional
Number of pixels to smooth on
zqso: float, optional
Redshift of the quasar. If input, a Telfer continuum is used
"""
# Build a widget combining several others
self.main_widget = QtGui.QWidget()
# Status bar
self.create_status_bar()
# Initialize
if outfil is None:
self.outfil = "LLS_fit.json"
else:
self.outfil = outfil
self.count_lls = 0
self.lls_model = None
self.all_forest = []
# Spectrum
spec, spec_fil = xxgu.read_spec(ispec)
# Continuum
self.conti_dict = {
"Norm": float(np.median(spec.flux.value)),
"tilt": 0.0,
"piv_wv": np.median(spec.dispersion.value),
}
if zqso is not None:
# Read Telfer
telfer = ascii.read(xa_path + "/data/quasar/telfer_hst_comp01_rq.ascii", comment="#")
scale = telfer["flux"][(telfer["wrest"] == 1450.0)]
tspec = XSpectrum1D.from_tuple((telfer["wrest"] * (1 + zqso), telfer["flux"] / scale[0])) # Observer frame
# Rebin
self.continuum = tspec.rebin(spec.dispersion)
else:
self.continuum = XSpectrum1D.from_tuple((spec.dispersion, np.ones(len(spec.dispersion))))
self.base_continuum = self.continuum.flux
self.update_conti()
# Full Model (LLS+continuum)
self.full_model = XSpectrum1D.from_tuple((spec.dispersion, np.ones(len(spec.dispersion))))
self.smooth = smooth
# LineList
self.llist = xxgu.set_llist("Strong")
self.llist["z"] = 0.0
# z and N boxes
self.zwidget = xxgu.EditBox(-1.0, "z_LLS=", "{:0.5f}")
self.Nwidget = xxgu.EditBox(-1.0, "NHI=", "{:0.2f}")
self.bwidget = xxgu.EditBox(-1.0, "b=", "{:0.1f}")
self.Cwidget = xxgu.EditBox("None", "Comment=", "{:s}")
# Grab the pieces and tie together
self.abssys_widg = xspw.AbsSysWidget(
[], only_one=True, no_buttons=True, linelist=self.llist[self.llist["List"]]
)
self.spec_widg = xspw.ExamineSpecWidget(
spec, status=self.statusBar, llist=self.llist, key_events=False, abs_sys=self.abssys_widg.abs_sys
)
self.spec_widg.continuum = self.continuum
# if other_spec is not None:
# ospec, ospec_fil = xxgu.read_spec(other_spec)
# self.spec_widg.other_spec = ospec
# Initial file
if lls_fit_file is not None:
self.init_LLS(lls_fit_file)
# Outfil
wbtn = QtGui.QPushButton("Write", self)
wbtn.setAutoDefault(False)
wbtn.clicked.connect(self.write_out)
# self.out_box = QtGui.QLineEdit()
# self.out_box.setText(self.outfil)
# self.connect(self.out_box, QtCore.SIGNAL('editingFinished ()'), self.set_outfil)
# Quit
buttons = QtGui.QWidget()
wqbtn = QtGui.QPushButton("Write\n Quit", self)
wqbtn.setAutoDefault(False)
wqbtn.clicked.connect(self.write_quit)
qbtn = QtGui.QPushButton("Quit", self)
qbtn.setAutoDefault(False)
qbtn.clicked.connect(self.quit)
# Connections (buttons are above)
self.spec_widg.canvas.mpl_connect("key_press_event", self.on_key)
self.abssys_widg.abslist_widget.itemSelectionChanged.connect(self.on_list_change)
self.connect(self.Nwidget.box, QtCore.SIGNAL("editingFinished ()"), self.setbzN)
self.connect(self.zwidget.box, QtCore.SIGNAL("editingFinished ()"), self.setbzN)
self.connect(self.bwidget.box, QtCore.SIGNAL("editingFinished ()"), self.setbzN)
self.connect(self.Cwidget.box, QtCore.SIGNAL("editingFinished ()"), self.setbzN)
# Layout
anly_widg = QtGui.QWidget()
anly_widg.setMaximumWidth(400)
anly_widg.setMinimumWidth(250)
# Write/Quit buttons
hbox1 = QtGui.QHBoxLayout()
hbox1.addWidget(wbtn)
hbox1.addWidget(wqbtn)
hbox1.addWidget(qbtn)
buttons.setLayout(hbox1)
# z,N
zNwidg = QtGui.QWidget()
hbox2 = QtGui.QHBoxLayout()
hbox2.addWidget(self.zwidget)
hbox2.addWidget(self.Nwidget)
hbox2.addWidget(self.bwidget)
zNwidg.setLayout(hbox2)
# vbox.addWidget(self.pltline_widg)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(zNwidg)
vbox.addWidget(self.Cwidget)
vbox.addWidget(self.abssys_widg)
vbox.addWidget(buttons)
anly_widg.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.spec_widg)
hbox.addWidget(anly_widg)
self.main_widget.setLayout(hbox)
# Point MainWindow
self.setCentralWidget(self.main_widget)
def __init__(self,
ispec,
parent=None,
lls_fit_file=None,
srch_id=True,
outfil=None,
fwhm=3.,
zqso=None):
QtGui.QMainWindow.__init__(self, parent)
'''
spec = Spectrum1D
lls_fit_file: str, optional
Name of the LLS fit file to input
smooth: float, optional
Number of pixels to smooth on
zqso: float, optional
Redshift of the quasar. If input, a Telfer continuum is used
'''
# TODO
# 1. Fix convolve window size
# 2. Avoid sorting of wavelengths
# 3. Remove astropy.relativity
# 4. Display self.z
# 5. Recenter on 'z'
# 6. Add COS LSF
# 7. Refit component key 'F'
# 8. Plot only selected components
# 9. Avoid shifting z of component outside its velocity range
# 10. Write Component vlim to JSON
# 11. Key to set line as some other transition (e.g. RMB in XSpec)
# 12. Mask array with points
# 13. Toggle line ID names
# 14. Add error + residual arrays [NT]
# 15. Adjust component redshift by keystroke
# Build a widget combining several others
self.main_widget = QtGui.QWidget()
# Status bar
self.create_status_bar()
# Initialize
if outfil is None:
self.outfil = 'IGM_model.json'
else:
self.outfil = outfil
self.fwhm = fwhm
# Spectrum
spec, spec_fil = xxgu.read_spec(ispec)
spec.mask = np.zeros(len(spec.dispersion), dtype=int)
# Full Model
self.model = XSpectrum1D.from_tuple(
(spec.dispersion, np.ones(len(spec.dispersion))))
# LineList
self.llist = xxgu.set_llist(['HI 1215', 'HI 1025', 'CIV 1548'],
sort=False)
z = 0.112
self.llist['z'] = z
# Grab the pieces and tie together
self.fiddle_widg = FiddleComponentWidget(parent=self)
self.comps_widg = ComponentListWidget(
[], parent=self, linelist=self.llist[self.llist['List']])
self.velplot_widg = IGGVelPlotWidget(spec,
z,
parent=self,
llist=self.llist,
fwhm=self.fwhm)
self.wq_widg = xxgu.WriteQuitWidget(parent=self)
self.slines_widg = xspw.SelectedLinesWidget(
self.llist[self.llist['List']], parent=self, init_select='All')
# Connections (buttons are above)
#self.spec_widg.canvas.mpl_connect('key_press_event', self.on_key)
#self.abssys_widg.abslist_widget.itemSelectionChanged.connect(
# self.on_list_change)
# Layout
anly_widg = QtGui.QWidget()
anly_widg.setMaximumWidth(400)
anly_widg.setMinimumWidth(250)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.fiddle_widg)
vbox.addWidget(self.comps_widg)
vbox.addWidget(self.slines_widg)
vbox.addWidget(self.wq_widg)
anly_widg.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.velplot_widg)
hbox.addWidget(anly_widg)
self.main_widget.setLayout(hbox)
# Point MainWindow
self.setCentralWidget(self.main_widget)
def __init__(self,
ispec,
z,
parent=None,
llist=None,
norm=True,
vmnx=[-300., 300.] * u.km / u.s,
fwhm=0.):
'''
spec = Spectrum1D
Norm: Bool (False)
Normalized spectrum?
abs_sys: AbsSystem
Absorption system class
'''
super(IGGVelPlotWidget, self).__init__(parent)
# Initialize
self.parent = parent
spec, spec_fil = xxgu.read_spec(ispec)
self.spec = spec
self.spec_fil = spec_fil
self.fwhm = fwhm
self.z = z
self.vmnx = vmnx
self.norm = norm
# Init
self.flag_add = False
self.flag_idlbl = False
self.flag_mask = False
self.wrest = 0.
self.avmnx = np.array([0., 0.]) * u.km / u.s
self.model = XSpectrum1D.from_tuple(
(spec.dispersion, np.ones(len(spec.dispersion))))
self.psdict = {} # Dict for spectra plotting
self.psdict[
'xmnx'] = self.vmnx.value # Too much pain to use units with this
self.psdict['ymnx'] = [-0.1, 1.1]
self.psdict['nav'] = xxgu.navigate(0, 0, init=True)
# Status Bar?
#if not status is None:
# self.statusBar = status
# Line List
if llist is None:
self.llist = xxgu.set_llist(['HI 1215', 'HI 1025'])
else:
self.llist = llist
self.llist['z'] = self.z
# Indexing for line plotting
self.idx_line = 0
self.init_lines()
# Create the mpl Figure and FigCanvas objects.
#
self.dpi = 150
self.fig = Figure((8.0, 4.0), dpi=self.dpi)
self.canvas = FigureCanvas(self.fig)
self.canvas.setParent(self)
self.canvas.setFocusPolicy(QtCore.Qt.ClickFocus)
self.canvas.setFocus()
self.canvas.mpl_connect('key_press_event', self.on_key)
self.canvas.mpl_connect('button_press_event', self.on_click)
# Sub_plots
self.sub_xy = [3, 4]
self.fig.subplots_adjust(hspace=0.0, wspace=0.1)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.canvas)
self.setLayout(vbox)
# Draw on init
self.on_draw()
def __init__(self,
ispec,
parent=None,
lls_fit_file=None,
srch_id=True,
outfil=None,
smooth=3.):
QtGui.QMainWindow.__init__(self, parent)
'''
spec = Spectrum1D
lls_fit_file: str, optional
Name of the LLS fit file to input
smooth: float, optional
Number of pixels to smooth on
'''
# Build a widget combining several others
self.main_widget = QtGui.QWidget()
# Status bar
self.create_status_bar()
# Initialize
if outfil is None:
self.outfil = 'LLS_fit.json'
else:
self.outfil = outfil
self.count_lls = 0
self.lls_model = None
self.all_forest = []
# Spectrum
spec, spec_fil = xxgu.read_spec(ispec)
# Continuum
self.conti_dict = {
'Norm': np.median(spec.flux),
'tilt': 0.,
'piv_wv': np.median(spec.dispersion.value)
}
self.continuum = XSpectrum1D.from_tuple(
(spec.dispersion, np.ones(len(spec.dispersion))))
self.base_continuum = self.continuum.flux
self.update_conti()
# Full Model (LLS+continuum)
self.full_model = XSpectrum1D.from_tuple(
(spec.dispersion, np.ones(len(spec.dispersion))))
self.smooth = smooth
# LineList
self.llist = xxgu.set_llist('Strong')
self.llist['z'] = 0.
# z and N boxes
self.zwidget = xxgu.EditBox(-1., 'z_LLS=', '{:0.5f}')
self.Nwidget = xxgu.EditBox(-1., 'NHI=', '{:0.2f}')
# Grab the pieces and tie together
self.abssys_widg = xspw.AbsSysWidget(
[],
only_one=True,
no_buttons=True,
linelist=self.llist[self.llist['List']])
self.spec_widg = xspw.ExamineSpecWidget(
spec,
status=self.statusBar,
llist=self.llist,
key_events=False,
abs_sys=self.abssys_widg.abs_sys)
self.spec_widg.continuum = self.continuum
# Initial file
if lls_fit_file is not None:
self.init_LLS(lls_fit_file)
# Outfil
wbtn = QtGui.QPushButton('Write', self)
wbtn.setAutoDefault(False)
wbtn.clicked.connect(self.write_out)
#self.out_box = QtGui.QLineEdit()
#self.out_box.setText(self.outfil)
#self.connect(self.out_box, QtCore.SIGNAL('editingFinished ()'), self.set_outfil)
# Quit
buttons = QtGui.QWidget()
wqbtn = QtGui.QPushButton('Write\n Quit', self)
wqbtn.setAutoDefault(False)
wqbtn.clicked.connect(self.write_quit)
qbtn = QtGui.QPushButton('Quit', self)
qbtn.setAutoDefault(False)
qbtn.clicked.connect(self.quit)
# Connections (buttons are above)
self.spec_widg.canvas.mpl_connect('key_press_event', self.on_key)
self.abssys_widg.abslist_widget.itemSelectionChanged.connect(
self.on_list_change)
self.connect(self.Nwidget.box, QtCore.SIGNAL('editingFinished ()'),
self.setzN)
self.connect(self.zwidget.box, QtCore.SIGNAL('editingFinished ()'),
self.setzN)
# Layout
anly_widg = QtGui.QWidget()
anly_widg.setMaximumWidth(400)
anly_widg.setMinimumWidth(200)
# Write/Quit buttons
hbox1 = QtGui.QHBoxLayout()
hbox1.addWidget(wbtn)
hbox1.addWidget(wqbtn)
hbox1.addWidget(qbtn)
buttons.setLayout(hbox1)
# z,N
zNwidg = QtGui.QWidget()
hbox2 = QtGui.QHBoxLayout()
hbox2.addWidget(self.zwidget)
hbox2.addWidget(self.Nwidget)
zNwidg.setLayout(hbox2)
#vbox.addWidget(self.pltline_widg)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(zNwidg)
vbox.addWidget(self.abssys_widg)
vbox.addWidget(buttons)
anly_widg.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.spec_widg)
hbox.addWidget(anly_widg)
self.main_widget.setLayout(hbox)
# Point MainWindow
self.setCentralWidget(self.main_widget)
def __init__(self, ispec, parent=None, lls_fit_file=None,
srch_id=True, outfil=None, smooth=3.):
QtGui.QMainWindow.__init__(self, parent)
'''
spec = Spectrum1D
lls_fit_file: str, optional
Name of the LLS fit file to input
smooth: float, optional
Number of pixels to smooth on
'''
# Build a widget combining several others
self.main_widget = QtGui.QWidget()
# Status bar
self.create_status_bar()
# Initialize
if outfil is None:
self.outfil = 'LLS_fit.json'
else:
self.outfil = outfil
self.count_lls = 0
self.lls_model = None
self.all_forest = []
# Spectrum
spec, spec_fil = xxgu.read_spec(ispec)
# Continuum
self.conti_dict = {'Norm': np.median(spec.flux), 'tilt': 0.,
'piv_wv': np.median(spec.dispersion.value)}
self.continuum = XSpectrum1D.from_tuple((
spec.dispersion,np.ones(len(spec.dispersion))))
self.base_continuum = self.continuum.flux
self.update_conti()
# Full Model (LLS+continuum)
self.full_model = XSpectrum1D.from_tuple((
spec.dispersion,np.ones(len(spec.dispersion))))
self.smooth = smooth
# LineList
self.llist = xxgu.set_llist('Strong')
self.llist['z'] = 0.
# z and N boxes
self.zwidget = xxgu.EditBox(-1., 'z_LLS=', '{:0.5f}')
self.Nwidget = xxgu.EditBox(-1., 'NHI=', '{:0.2f}')
# Grab the pieces and tie together
self.abssys_widg = xspw.AbsSysWidget([],only_one=True,
no_buttons=True, linelist=self.llist[self.llist['List']])
self.spec_widg = xspw.ExamineSpecWidget(spec,status=self.statusBar,
llist=self.llist, key_events=False,
abs_sys=self.abssys_widg.abs_sys)
self.spec_widg.continuum = self.continuum
# Initial file
if lls_fit_file is not None:
self.init_LLS(lls_fit_file)
# Outfil
wbtn = QtGui.QPushButton('Write', self)
wbtn.setAutoDefault(False)
wbtn.clicked.connect(self.write_out)
#self.out_box = QtGui.QLineEdit()
#self.out_box.setText(self.outfil)
#self.connect(self.out_box, QtCore.SIGNAL('editingFinished ()'), self.set_outfil)
# Quit
buttons = QtGui.QWidget()
wqbtn = QtGui.QPushButton('Write\n Quit', self)
wqbtn.setAutoDefault(False)
wqbtn.clicked.connect(self.write_quit)
qbtn = QtGui.QPushButton('Quit', self)
qbtn.setAutoDefault(False)
qbtn.clicked.connect(self.quit)
# Connections (buttons are above)
self.spec_widg.canvas.mpl_connect('key_press_event', self.on_key)
self.abssys_widg.abslist_widget.itemSelectionChanged.connect(
self.on_list_change)
self.connect(self.Nwidget.box,
QtCore.SIGNAL('editingFinished ()'), self.setzN)
self.connect(self.zwidget.box,
QtCore.SIGNAL('editingFinished ()'), self.setzN)
# Layout
anly_widg = QtGui.QWidget()
anly_widg.setMaximumWidth(400)
anly_widg.setMinimumWidth(200)
# Write/Quit buttons
hbox1 = QtGui.QHBoxLayout()
hbox1.addWidget(wbtn)
hbox1.addWidget(wqbtn)
hbox1.addWidget(qbtn)
buttons.setLayout(hbox1)
# z,N
zNwidg = QtGui.QWidget()
hbox2 = QtGui.QHBoxLayout()
hbox2.addWidget(self.zwidget)
hbox2.addWidget(self.Nwidget)
zNwidg.setLayout(hbox2)
#vbox.addWidget(self.pltline_widg)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(zNwidg)
vbox.addWidget(self.abssys_widg)
vbox.addWidget(buttons)
anly_widg.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.spec_widg)
hbox.addWidget(anly_widg)
self.main_widget.setLayout(hbox)
# Point MainWindow
self.setCentralWidget(self.main_widget)