def __init__(self,
ispec,
zqso,
parent=None,
lls_fit_file=None,
outfil=None,
smooth=3.,
fN_gamma=None,
template=None,
dw=0.1,
skip_wveval=False,
coord=None,
**kwargs):
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 = QWidget()
# Status bar
self.create_status_bar()
# Initialize
self.update = True
if outfil is None:
self.outfil = 'LLS_fit.json'
else:
self.outfil = outfil
self.zqso = zqso
self.count_lls = 0
self.model_spec = -1
self.lls_model = None
self.template = template
self.coord = coord
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
if isinstance(ispec, XSpectrum1D):
spec = ispec
spec_fil = spec.filename
else:
# this is broken
spec, spec_fil = ltgu.read_spec(ispec, **kwargs)
# LineList
self.llist = ltgu.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 = ltgsm.EditBox(-1., 'z_LLS=', '{:0.5f}')
self.Nwidget = ltgsm.EditBox(-1., 'NHI=', '{:0.2f}')
self.bwidget = ltgsm.EditBox(-1., 'b=', '{:0.1f}')
self.Cwidget = ltgsm.EditBox('None', 'Comment=', '{:s}')
# Grab the pieces and tie together
self.abssys_widg = ltgsp.AbsSysWidget(
[],
only_one=True,
no_buttons=True,
linelist=self.llist[self.llist['List']])
vlines = [912 * (1 + zqso)]
self.spec_widg = ltgsp.ExamineSpecWidget(
spec,
status=self.statusBar,
llist=self.llist,
key_events=False,
abs_sys=self.abssys_widg.abs_sys,
vlines=vlines,
plotzero=1,
norm=False)
#QtCore.pyqtRemoveInputHook()
#pdb.set_trace()
#QtCore.pyqtRestoreInputHook()
#self.spec_widg.canvas.mpl_connect('button_press_event', self.on_click)
# Multi spec
self.mspec_widg = ltgsp.MultiSpecWidget(self.spec_widg)
# Initialize continuum (and LLS if from a file)
if lls_fit_file is not None:
self.init_LLS(lls_fit_file, spec)
#QtCore.pyqtRemoveInputHook()
#pdb.set_trace()
#QtCore.pyqtRestoreInputHook()
self.update_conti()
self.spec_widg.continuum = self.continuum
if self.model_spec < 0:
print(
"NOTE: You must specify the spectrum for fitting the LLS with # before modeling will begin"
)
if self.smooth is None:
self.smooth = smooth
self.llist['Plot'] = False
# Initialize as needed
if lls_fit_file is not None:
if len(self.abssys_widg.all_abssys) > 0:
self.update_boxes()
self.update_model()
# Outfil
wbtn = 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 = QWidget()
wqbtn = QPushButton('Write\n Quit', self)
wqbtn.setAutoDefault(False)
wqbtn.clicked.connect(self.write_quit)
qbtn = 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.Nwidget.box.textChanged[str].connect(self.setbzN)
self.zwidget.box.textChanged[str].connect(self.setbzN)
self.bwidget.box.textChanged[str].connect(self.setbzN)
self.Cwidget.box.textChanged[str].connect(self.setbzN)
# Layout
anly_widg = QWidget()
anly_widg.setMaximumWidth(400)
anly_widg.setMinimumWidth(250)
# Write/Quit buttons
hbox1 = QHBoxLayout()
hbox1.addWidget(wbtn)
hbox1.addWidget(wqbtn)
hbox1.addWidget(qbtn)
buttons.setLayout(hbox1)
# z,N
zNwidg = QWidget()
hbox2 = QHBoxLayout()
hbox2.addWidget(self.zwidget)
hbox2.addWidget(self.Nwidget)
hbox2.addWidget(self.bwidget)
zNwidg.setLayout(hbox2)
#vbox.addWidget(self.pltline_widg)
vbox = QVBoxLayout()
vbox.addWidget(zNwidg)
vbox.addWidget(self.Cwidget)
vbox.addWidget(self.abssys_widg)
vbox.addWidget(buttons)
vbox.addWidget(self.mspec_widg)
anly_widg.setLayout(vbox)
hbox = 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,
dla_fit_file=None,
zqso=None,
outfil=None,
smooth=3.,
dw=0.1,
skip_wveval=False,
norm=True):
QtGui.QMainWindow.__init__(self, parent)
"""
ispec : Spectrum1D or specfil
dla_fit_file: str, optional
Name of the LLS fit file to input
smooth : float, optional
Number of pixels to smooth on (FWHM)
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.
norm : bool, optional
Whether to normalize the spectrum by dividing by the
continuum (default True).
"""
# Build a widget combining several others
self.main_widget = QtGui.QWidget()
# Status bar
self.create_status_bar()
# Initialize
if outfil is None:
self.outfil = 'DLA_fit.json'
else:
self.outfil = outfil
self.count_dla = 0
self.dla_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
self.zqso = zqso
if skip_wveval:
warnings.warn("Skipping wavelength rebinning in Voigt.")
warnings.warn("Make sure you know what you are doing!")
# Spectrum
if isinstance(ispec, XSpectrum1D):
spec = ispec
spec_fil = spec.filename
else:
spec, spec_fil = ltgu.read_spec(ispec)
self.spec = spec
# LineList
self.llist = ltgu.set_llist('Strong')
self.llist['z'] = 0.
self.plt_wv = zip(
np.array([972.5367, 1025.7222, 1215.6700]) * u.AA,
['Lyg', 'Lyb', 'Lya'])
# z and N boxes
self.zwidget = ltgsm.EditBox(-1., 'z_DLA=', '{:0.5f}')
self.Nwidget = ltgsm.EditBox(-1., 'NHI=', '{:0.2f}')
self.bwidget = ltgsm.EditBox(-1., 'b=', '{:0.1f}')
self.Cwidget = ltgsm.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 = ltgsp.ExamineSpecWidget(
spec,
status=self.statusBar,
llist=self.llist,
key_events=False,
abs_sys=self.abssys_widg.abs_sys,
plotzero=1,
norm=norm)
# Initialize continuum (and LLS if from a file)
if dla_fit_file is not None:
self.init_DLA(dla_fit_file, spec)
else:
if zqso is not None:
co, knots = laco.find_continuum(spec, redshift=self.zqso)
else:
co, knots = laco.find_continuum(spec, kind='default')
self.conti_dict = dict(co=co, knots=knots)
self.update_conti()
#self.spec_widg.continuum = self.continuum
# Full Model (LLS+continuum)
self.full_model = XSpectrum1D.from_tuple(
(spec.wavelength, np.ones(len(spec.wavelength))))
if self.smooth is None:
self.smooth = smooth
# Initialize as needed
if dla_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, dla_fit_file=None,
zqso=None, outfil=None, smooth=None, dw=0.1, zdla=None,
NHI=None,
skip_wveval=False, norm=True, conti_file=None):
QMainWindow.__init__(self, parent)
"""
ispec : Spectrum1D or specfil
dla_fit_file: str, optional
Name of the LLS fit file to input
smooth : float, optional
Number of pixels to smooth on (FWHM). Will not smooth if 0.
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.
norm : bool, optional
Whether to normalize the spectrum by dividing by the
continuum (default True).
conti_file : str, optional
ASCII file containing the continuum knots (wave, flux)
zdla : float, optional
Create a DLA at the input redshift
"""
self.help_message = """
Begin by left-clicking in the plot window!
Then any of the following keystroke commands will work:
i,o : zoom in/out x limits
I,O : zoom in/out x limits (larger re-scale)
Y : zoom out y limits
y : guess y limits
W : Show original zooom
t,b : set y top/bottom limit
l,r : set left/right x limit
a,m,d : Add/modify/delete continuum knot
A : Add a new DLA
g : Move nearest Lyman line to cursor and reset z
N/n : Increase/decrease NHI
V/v : Increase/decrease bvalue
Z/z : Increase/decrease zabs
U/u : Increase/decrease sig_NHI [Default is 0.1 dex]
D : Delete DLA
$ : Toggle displaying metal lines
6,7,8,9 : Add forest lines
? : Print these help notes
P : Save current screen in dla_plot.pdf
Q : Quit the GUI
"""
# Build a widget combining several others
self.main_widget = QWidget()
# Status bar
self.create_status_bar()
# Initialize
self.update = True
self.sig_NHI = 0.1
if outfil is None:
self.outfil = 'DLA_fit.json'
else:
self.outfil = outfil
self.count_dla = 0
self.dla_model = None
if smooth is None:
self.smooth = 3. # Pixels to smooth model by
else:
self.smooth = smooth
self.base_continuum = None
self.all_forest = []
self.flag_write = False
self.dw = float(dw)
self.skip_wveval = skip_wveval
self.zqso = zqso
if skip_wveval:
warnings.warn("Skipping wavelength rebinning in Voigt.")
warnings.warn("Make sure you know what you are doing!")
# Spectrum
if isinstance(ispec, XSpectrum1D):
spec = ispec
spec_fil = spec.filename
else:
kwargs = {}
kwargs['rsp_kwargs'] = {}
kwargs['rsp_kwargs']['masking'] = 'edges'
spec, spec_fil = ltgu.read_spec(ispec, norm=norm, **kwargs)
self.spec = spec
# LineList
self.llist = ltgu.set_llist('Strong')
self.llist['z'] = 0.
self.plt_wv = zip(np.array([972.5367,1025.7222,1215.6700])*u.AA,
['Lyg','Lyb','Lya'])
# z and N boxes
self.zwidget = ltgsm.EditBox(-1., 'z_DLA=', '{:0.5f}')
self.Nwidget = ltgsm.EditBox(-1., 'NHI=', '{:0.2f}')
self.bwidget = ltgsm.EditBox(-1., 'b=', '{:0.1f}')
self.Cwidget = ltgsm.EditBox('None', 'Comment=', '{:s}')
# Grab the pieces and tie together
self.abssys_widg = ltgsp.AbsSysWidget([],only_one=True,
no_buttons=True, linelist=self.llist[self.llist['List']])
self.spec_widg = ltgsp.ExamineSpecWidget(spec,status=self.statusBar,
llist=self.llist, key_events=False,
abs_sys=self.abssys_widg.abs_sys,
plotzero=1, norm=norm)
# Create a DLA?
if zdla is not None:
self.add_DLA(zdla, NHI=NHI, model=False)
# Initialize continuum (and DLA if from a file)
if dla_fit_file is not None:
self.init_DLA(dla_fit_file,spec)
else:
if conti_file is not None:
# Read continuum
cspec = lsi.readspec(conti_file)
if not cspec.sig_is_set:
cspec.sig = 0.1*np.median(cspec.flux)
else:
cspec = spec
if zqso is not None:
co, knots = laco.find_continuum(cspec, redshift=self.zqso)
else:
co, knots = laco.find_continuum(cspec, kind='default')
self.conti_dict = dict(co=co, knots=knots)
self.update_conti()
#self.spec_widg.continuum = self.continuum
# Full Model (LLS+continuum)
self.full_model = XSpectrum1D.from_tuple((
spec.wavelength,np.ones(len(spec.wavelength))))
# Initialize as needed
if (dla_fit_file is not None) or (zdla is not None):
self.update_boxes()
self.update_model()
# Outfil
wbtn = QPushButton(self)
wbtn.setText('Write')
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 = QWidget()
wqbtn = QPushButton(self)
wqbtn.setText('Write\n Quit')
wqbtn.setAutoDefault(False)
wqbtn.clicked.connect(self.write_quit)
qbtn = QPushButton(self)
qbtn.setText('Quit')
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.Nwidget.box.textChanged[str].connect(self.setbzN)
self.zwidget.box.textChanged[str].connect(self.setbzN)
self.bwidget.box.textChanged[str].connect(self.setbzN)
self.Cwidget.box.textChanged[str].connect(self.setbzN)
# Layout
anly_widg = QWidget()
anly_widg.setMaximumWidth(400)
anly_widg.setMinimumWidth(250)
# Write/Quit buttons
hbox1 = QHBoxLayout()
hbox1.addWidget(wbtn)
hbox1.addWidget(wqbtn)
hbox1.addWidget(qbtn)
buttons.setLayout(hbox1)
# z,N
zNwidg = QWidget()
hbox2 = QHBoxLayout()
hbox2.addWidget(self.zwidget)
hbox2.addWidget(self.Nwidget)
hbox2.addWidget(self.bwidget)
zNwidg.setLayout(hbox2)
#vbox.addWidget(self.pltline_widg)
vbox = QVBoxLayout()
vbox.addWidget(zNwidg)
vbox.addWidget(self.Cwidget)
vbox.addWidget(self.abssys_widg)
vbox.addWidget(buttons)
anly_widg.setLayout(vbox)
hbox = 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)
# Print help message
print(self.help_message)
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,
norm=True):
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.
norm : bool, optional
Whether to normalize the spectrum by dividing by the
continuum (default True).
'''
# 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
if isinstance(ispec, XSpectrum1D):
spec = ispec
spec_fil = spec.filename
else:
# this is broken
spec, spec_fil = ltgu.read_spec(ispec)
# LineList
self.llist = ltgu.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 = ltgsm.EditBox(-1., 'z_LLS=', '{:0.5f}')
self.Nwidget = ltgsm.EditBox(-1., 'NHI=', '{:0.2f}')
self.bwidget = ltgsm.EditBox(-1., 'b=', '{:0.1f}')
self.Cwidget = ltgsm.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 = ltgsp.ExamineSpecWidget(
spec,
status=self.statusBar,
llist=self.llist,
key_events=False,
abs_sys=self.abssys_widg.abs_sys,
vlines=vlines,
plotzero=1,
norm=norm)
# 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 = pycc.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.wavelength.value * (1 + zqso),
tspec.flux.value))
else:
tspec = pycq.get_telfer_spec(
zqso=zqso, igm=(self.conti_dict['igm'] == 'True'))
# Rebin
self.continuum = tspec.rebin(spec.wavelength)
# 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.wavelength, np.ones(len(spec.wavelength))))
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.wavelength, np.ones(len(spec.wavelength))))
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,
redrock_file,
parent=None,
zdict=None,
coadd_dict=None,
outfile='tmp.json',
unit_test=False,
screen_scale=1.,
**kwargs):
QMainWindow.__init__(self, parent)
"""
redrock_file = str
Input RedRock output FITS file from our redrock script
parent : Widget parent, optional
zsys : float, optional
intial redshift either from a previous vet_rr json or the original
rr guesses
screen_scale : float, optional
Scale the default sizes for the gui size
"""
# Load up
self.outfile = outfile
self.rr_hdul = fits.open(redrock_file)
if coadd_dict is not None:
self.slit_info = {}
for key in coadd_dict.keys():
if isinstance(coadd_dict[key], dict):
if '2D_xval' in coadd_dict[key].keys():
name = coadd_dict[key]['outfile'].replace('.fits', '')
self.slit_info[name] = {}
self.slit_info[name]['xval'] = coadd_dict[key][
'2D_xval']
self.slit_info[name]['Gslit'] = coadd_dict[key][
'Gemini_slit']
else:
self.slit_info = None
# names, spectra, zs = [], [], []
names, spectra = [], []
if zdict is None:
self.zdict = OrderedDict()
load_z = True
else:
self.zdict = OrderedDict()
load_z = False
for hdu in self.rr_hdul[1:]:
# Grab the spectrum
spec_file = hdu.name
# tmp = XSpectrum1D.from_file(spec_file.replace('FITS','fits'))
spectra.append(
XSpectrum1D.from_file(spec_file.replace('FITS', 'fits'),
masking='edges'))
names.append(spec_file.replace('.FITS', ''))
# RedRock
data = hdu.data
# Init the dict
if load_z:
self.zdict[names[-1]] = {}
self.zdict[names[-1]]['zRR'] = data['z']
self.zdict[names[-1]]['ZQ'] = -99
self.zdict[names[-1]]['Comment'] = ''
self.zdict[names[-1]]['z'] = data['z'][0]
else:
self.zdict[names[-1]] = zdict[names[-1]]
# Collate
ispec = lspu.collate(spectra, masking='edges')
# Fill
ispec.labels = names
ispec.stypes = ['galaxy'] * ispec.nspec
# ispec.z = zs # DO NOT SET THE REDSHIFT HERE
self.RRi = 0
self.scale = screen_scale
# Needed to avoid crash in large spectral files
rcParams['agg.path.chunksize'] = 20000
# avoid scientific notation in axes tick labels
rcParams['axes.formatter.useoffset'] = False
# Build a widget combining several others
self.main_widget = QWidget()
# Status bar
self.create_status_bar()
# ZQ window
self.ZQ_widg = ltgsm.EditBox(-99, 'ZQ', '{:d}')
self.ZQ_values = [-99, -1, 0, 1, 3, 4]
# Comment window
self.comment_widg = ltgsm.EditBox('', 'Comment', '{:s}')
# Grab the pieces and tie together
self.pltline_widg = ltgl.PlotLinesWidget(status=self.statusBar,
screen_scale=self.scale)
self.pltline_widg.setMaximumWidth(300 * self.scale)
# Hook the spec widget to Plot Line
self.spec_widg = ltgsp.ExamineSpecWidget(ispec,
status=self.statusBar,
parent=self,
llist=self.pltline_widg.llist,
screen_scale=self.scale,
**kwargs)
# Reset redshift from spec
# Auto set line list if spec has proper object type
if hasattr(self.spec_widg.spec, 'stypes'):
if self.spec_widg.spec.stypes[
self.spec_widg.select].lower() == 'galaxy':
self.pltline_widg.llist = ltgu.set_llist(
'Galaxy', in_dict=self.pltline_widg.llist)
elif self.spec_widg.spec.stypes[
self.spec_widg.select].lower() == 'absorber':
self.pltline_widg.llist = ltgu.set_llist(
'Strong', in_dict=self.pltline_widg.llist)
self.pltline_widg.llist['Plot'] = True
idx = self.pltline_widg.lists.index(
self.pltline_widg.llist['List'])
self.pltline_widg.llist_widget.setCurrentRow(idx)
#
self.pltline_widg.spec_widg = self.spec_widg
# Multi spec
self.mspec_widg = ltgsp.MultiSpecWidget(self.spec_widg,
extra_method=self)
self.spec_widg.canvas.mpl_connect('key_press_event', self.on_key)
self.spec_widg.canvas.mpl_connect('button_press_event', self.on_click)
self.prev_select = 0 # Index of previous spectrum; starts at 0
# Legend -- specific to this GUI
self.legend = {}
self.wv_dict = {'*': 3727., '(': 3950., ')': 4940., '_': 6564.}
self.legend['zoom'] = self.wv_dict
self.legend['&'] = 'Toggle through ZQ'
self.legend[
'#'] = 'Toggle through zRR (WARNING: will not necessary start at the first one)'
self.legend['%'] = 'Set z=0 (for stars)'
self.legend['9'] = 'Skip to next spectrum with ZQ=-99'
self.legend['x'] = 'Next spectrum'
for key, value in self.legend.items():
print(key, value)
# Extras
extras = QWidget()
extras.setMinimumWidth(180 * self.scale)
extras.setMaximumWidth(280 * self.scale)
vbox = QVBoxLayout()
qbtn = QPushButton(self)
qbtn.setText('Quit')
qbtn.clicked.connect(self.quit)
vbox.addWidget(self.pltline_widg)
vbox.addWidget(self.ZQ_widg)
vbox.addWidget(self.comment_widg)
vbox.addWidget(self.mspec_widg)
vbox.addWidget(qbtn)
extras.setLayout(vbox)
# Main window
hbox = QHBoxLayout()
hbox.addWidget(self.spec_widg)
hbox.addWidget(extras)
self.main_widget.setLayout(hbox)
# Point MainWindow
self.setCentralWidget(self.main_widget)
if unit_test:
self.quit()
# Giddy up
self.run_with_select(save=False)