def __init__(self,
inspec,
parent=None,
abssys_dir=None,
absid_list=None,
norm=True,
srch_id=True,
id_dir='ID_LINES/'):
QtGui.QMainWindow.__init__(self, parent)
'''
spec = Spectrum1D
second_file = Second spectrum file (e.g. COS + STIS)
'''
# Build a widget combining several others
self.main_widget = QtGui.QWidget()
# Status bar
self.create_status_bar()
# Initialize
if absid_list is None:
# Automatically search for ID files
if srch_id:
absid_list = glob.glob(id_dir + '*id.fits')
else:
absid_list = []
# Grab the pieces and tie together
self.abssys_widg = xspw.AbsSysWidget(absid_list)
self.pltline_widg = xspw.PlotLinesWidget(status=self.statusBar)
self.spec_widg = xspw.ExamineSpecWidget(
inspec,
status=self.statusBar,
llist=self.pltline_widg.llist,
norm=norm,
abs_sys=self.abssys_widg.abs_sys)
self.pltline_widg.spec_widg = self.spec_widg
# Connections
self.spec_widg.canvas.mpl_connect('button_press_event', self.on_click)
self.spec_widg.canvas.mpl_connect('key_press_event', self.on_key)
self.abssys_widg.refine_button.clicked.connect(self.refine_abssys)
# Layout
anly_widg = QtGui.QWidget()
anly_widg.setMaximumWidth(300)
anly_widg.setMinimumWidth(150)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.pltline_widg)
vbox.addWidget(self.abssys_widg)
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, zsys=None, norm=None):
QtGui.QMainWindow.__init__(self, parent)
'''
Parameters
--------------
spec = Spectrum1D or tuple of arrays
Input spectrum. If tuple then (wave,fx) or (wave,fx,sig)
'''
from linetools.lists.linelist import LineList
#reload(xxgu)
#reload(xspw)
# INIT
spec, _ = xxgu.read_spec(ispec)
#xdb.set_trace()
#
mpl.rcParams[
'agg.path.chunksize'] = 20000 # Needed to avoid carsh in large spectral files
# Build a widget combining several others
self.main_widget = QtGui.QWidget()
# Status bar
self.create_status_bar()
# Grab the pieces and tie together
self.pltline_widg = xspw.PlotLinesWidget(status=self.statusBar,
init_z=zsys)
self.pltline_widg.setMaximumWidth(300)
# Hook the spec widget to Plot Line
self.spec_widg = xspw.ExamineSpecWidget(spec,
status=self.statusBar,
llist=self.pltline_widg.llist,
zsys=zsys,
norm=norm)
self.pltline_widg.spec_widg = self.spec_widg
self.spec_widg.canvas.mpl_connect('button_press_event', self.on_click)
extras = QtGui.QWidget()
extras.setMaximumWidth(130)
vbox = QtGui.QVBoxLayout()
qbtn = QtGui.QPushButton('Quit', self)
qbtn.clicked.connect(self.quit)
vbox.addWidget(self.pltline_widg)
vbox.addWidget(qbtn)
extras.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.spec_widg)
hbox.addWidget(extras)
self.main_widget.setLayout(hbox)
# Point MainWindow
self.setCentralWidget(self.main_widget)
def __init__(self, spec, parent=None, zsys=None, norm=None):
QtGui.QMainWindow.__init__(self, parent)
'''
spec = Spectrum1D
'''
mpl.rcParams['agg.path.chunksize'] = 20000 # Needed to avoid carsh in large spectral files
# Build a widget combining several others
self.main_widget = QtGui.QWidget()
# Status bar
self.create_status_bar()
# Grab the pieces and tie together
self.pltline_widg = xspw.PlotLinesWidget(status=self.statusBar, init_z=zsys)
self.pltline_widg.setMaximumWidth(300)
# Hook the spec widget to Plot Line
self.spec_widg = xspw.ExamineSpecWidget(spec,status=self.statusBar,
llist=self.pltline_widg.llist,
zsys=zsys, norm=norm)
self.pltline_widg.spec_widg = self.spec_widg
self.spec_widg.canvas.mpl_connect('button_press_event', self.on_click)
extras = QtGui.QWidget()
extras.setMaximumWidth(130)
vbox = QtGui.QVBoxLayout()
qbtn = QtGui.QPushButton('Quit', self)
qbtn.clicked.connect(self.quit)
vbox.addWidget(self.pltline_widg)
vbox.addWidget(qbtn)
extras.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.spec_widg)
hbox.addWidget(extras)
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,
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)