def test_rdspec():
spec, spec_fil = ltgu.read_spec(data_path('UM184_nF.fits'))
#
ispec = lsio.readspec(data_path('UM184_nF.fits'))
spec, spec_fil = ltgu.read_spec(ispec)
# as tuple without units
ispec = (np.ones(10), np.ones(10), np.ones(10))
spec, spec_fil = ltgu.read_spec(ispec)
assert spec_fil == 'none'
# as list of files
ispec = [data_path('UM184_nF.fits')]*2
spec, spec_fil = ltgu.read_spec(ispec)
spec, spec_fil = ltgu.read_spec(ispec, exten=[1,1]) # is iterable exten
# wrong format
with pytest.raises(ValueError):
spec, spec_fil = ltgu.read_spec(dict(a='dummy')) # input is a dict
# normalize
spec, spec_fil = ltgu.read_spec(data_path('UM184_nF.fits'))
spec.co = spec.flux
spec, spec_fil = ltgu.read_spec(spec)
assert spec.normed
def test_rdspec():
spec, spec_fil = ltgu.read_spec(data_path('UM184_nF.fits'))
#
ispec = lsio.readspec(data_path('UM184_nF.fits'))
spec, spec_fil = ltgu.read_spec(ispec)
# as tuple without units
ispec = (np.ones(10), np.ones(10), np.ones(10))
spec, spec_fil = ltgu.read_spec(ispec)
assert spec_fil == 'none'
# as list of files
ispec = [data_path('UM184_nF.fits')] * 2
spec, spec_fil = ltgu.read_spec(ispec)
spec, spec_fil = ltgu.read_spec(ispec, exten=[1, 1]) # is iterable exten
# wrong format
with pytest.raises(ValueError):
spec, spec_fil = ltgu.read_spec(dict(a='dummy')) # input is a dict
# normalize
spec, spec_fil = ltgu.read_spec(data_path('UM184_nF.fits'))
spec.co = spec.flux
spec, spec_fil = ltgu.read_spec(spec)
assert spec.normed
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
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)
# 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.dispersion.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.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, status=None, llist=None,
abs_sys=None, norm=True, second_file=None, zsys=None,
key_events=True, vlines=None, plotzero=False, exten=None,
xlim=None, ylim=None):
"""
Parameters
----------
ispec : Spectrum1D or tuple of arrays
exten : int, optional
extension for the spectrum in multi-extension FITS file
parent : Widget parent, optional
status : Point to status bar, optional
llist : dict, optional
Used to guide the line lists
abs_sys : list, optional
AbsSystem's
zsys : float, optional
intial redshift
key_events : bool, optional
Use key events? [True]
Useful when coupling to other widgets
xlim : tuple of two floats
Initial x plotting limits
ylim : tuple of two floats
Initial y plotting limits
"""
super(ExamineSpecWidget, self).__init__(parent)
# Spectrum
spec, spec_fil = ltgu.read_spec(ispec, exten=exten, norm=norm)
self.orig_spec = spec # For smoothing
self.spec = self.orig_spec
self.vlines = []
if vlines is not None:
self.vlines.extend(vlines)
self.plotzero = plotzero
# Other bits (modified by other widgets)
self.continuum = None
self.model = None
self.bad_model = None # Discrepant pixels in model
self.use_event = 1
# Abs Systems
if abs_sys is None:
self.abs_sys = []
else:
self.abs_sys = abs_sys
self.norm = norm
self.psdict = {} # Dict for spectra plotting
self.adict = {} # Dict for analysis
self.init_spec(xlim=xlim, ylim=ylim)
self.xval = None # Used with velplt
# Status Bar?
if not status is None:
self.statusBar = status
# Line List?
if llist is None:
self.llist = {'Plot': False, 'List': 'None', 'z': 0., 'Lists': []}
else:
self.llist = llist
# zsys
if zsys is not None:
self.llist['z'] = zsys
# Create the mpl Figure and FigCanvas objects.
# 5x4 inches, 100 dots-per-inch
#
self.dpi = 150 # 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()
if key_events:
self.canvas.mpl_connect('key_press_event', self.on_key)
self.canvas.mpl_connect('button_press_event', self.on_click)
# Make two plots
self.ax = self.fig.add_subplot(1, 1, 1)
self.fig.subplots_adjust(hspace=0.1, wspace=0.1)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.canvas)
self.setLayout(vbox)
# Draw on init
self.on_draw()
def __init__(self, ispec, z, abs_lines=None, parent=None, llist=None, norm=True,
vmnx=[-300., 300.]*u.km/u.s):
'''
spec : XSpectrum1D
z : float
abs_lines: list, optional
List of AbsLines
llist : LineList, optional
Input line list. Defaults to 'Strong'
norm : bool, optional
Normalized spectrum?
vmnx : Quantity array, optional
Starting velocity range for the widget
'''
super(VelPlotWidget, self).__init__(parent)
self.help_message = """
Click on any white region within the velocity plots
for the following keystroke commands to work:
i,o : zoom in/out x limits
I,O : zoom in/out x limits (larger re-scale)
y : zoom out y limits
t,b : set y top/bottom limit
l,r : set left/right x limit
[,] : pan left/right
C,c : add/remove column
K,k : add/remove row
=,- : move to next/previous page
1,2 : Modify velocity region of the single line (left, right sides)
!,@ : Modify velocity region of all lines (left, right)
A,x : Add/remove select line from analysis list
X : Remove all lines from analysis list
^,& : Flag line to be analyzed for low/high-ion kinematics
B : Toggle as blend/no-blend (orange color = blend)
N : Toggle as do/do-not include for analysis (red color = exclude)
V : Indicate as a normal value
L : Indicate as a lower limit
U : Indicate as a upper limit
? : Print this
"""
# Initialize
spec, spec_fil = ltgu.read_spec(ispec)
self.spec = spec
self.spec_fil = spec_fil
self.z = z
self.vmnx = vmnx
self.norm = norm
# Abs Lines
if abs_lines is None:
self.abs_lines = []
else:
self.abs_lines = abs_lines
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
self.psdict = {} # Dict for spectra plotting
self.psdict['x_minmax'] = self.vmnx.value # Too much pain to use units with this
self.psdict['y_minmax'] = [-0.1, 1.1]
self.psdict['nav'] = ltgu.navigate(0,0,init=True)
# Line List
if llist is None:
self.llist = ltgu.set_llist('Strong')
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 (Initial)
self.sub_xy = [3,4]
self.fig.subplots_adjust(hspace=0.0, wspace=0.1)
# Layout
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.canvas)
self.setLayout(vbox)
# Print help message
print(self.help_message)
# Draw on init
self.on_draw()
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, z=None, parent=None, llist=None, norm=True,
vmnx=[-300., 300.]*u.km/u.s, abs_sys=None):
'''
spec = Spectrum1D
Norm: Bool (False)
Normalized spectrum?
abs_sys: AbsSystem
Absorption system class
'''
super(VelPlotWidget, self).__init__(parent)
# Initialize
spec, spec_fil = ltgu.read_spec(ispec)
self.spec = spec
self.spec_fil = spec_fil
self.z = z
self.vmnx = vmnx
self.norm = norm
# Abs_System
self.abs_sys = abs_sys
if self.abs_sys is None:
self.abs_sys = GenericAbsSystem((0.*u.deg,0.*u.deg), self.z, self.vmnx)
self.abs_lines = []
else:
self.z = self.abs_sys.zabs
# Line list
if llist is None:
self.abs_lines = self.abs_sys.list_of_abslines()
if len(self.abs_lines)>0:
lwrest = [iline.wrest for iline in self.abs_lines]
else:
lwrest = None
if lwrest is not None:
llist = ltgu.set_llist(lwrest) # Not sure this is working..
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
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'] = ltgu.navigate(0,0,init=True)
# Status Bar?
#if not status is None:
# self.statusBar = status
# Line List
if llist is None:
self.llist = ltgu.set_llist('Strong')
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,
guessfile=None,
parent=None,
zsys=None,
norm=None,
exten=None,
rsp_kwargs={},
unit_test=False,
screen_scale=1.,
**kwargs):
QMainWindow.__init__(self, parent)
"""
ispec = str, XSpectrum1D or tuple of arrays
Input spectrum or spectrum filename. If tuple then (wave,
fx), (wave, fx, sig) or (wave, fx, sig, co)
guessfile : str, optional
name of the .json file generated with igmguesses GUI in Pyigm (see https://github.com/pyigm/pyigm/blob/master/docs/igmguesses.rst)
if not None - overplot fitted line profiles from igmguesses
parent : Widget parent, optional
zsys : float, optional
intial redshift
exten : int, optional
extension for the spectrum in multi-extension FITS file
norm : bool, optional
True if the spectrum is normalized
screen_scale : float, optional
Scale the default sizes for the gui size
"""
#reload(ltgl)
#reload(ltgsp)
# INIT
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
self.scale = screen_scale
# Needed to avoid crash in large spectral files
rcParams['agg.path.chunksize'] = 20000
rcParams[
'axes.formatter.useoffset'] = False # avoid scientific notation in axes tick labels
# Build a widget combining several others
self.main_widget = QWidget()
# Status bar
self.create_status_bar()
# Grab the pieces and tie together
self.pltline_widg = ltgl.PlotLinesWidget(status=self.statusBar,
init_z=zsys,
screen_scale=self.scale)
self.pltline_widg.setMaximumWidth(300 * self.scale)
## Abs sys
abs_sys = None
voigtsfit = None
if guessfile is not None:
# Load
ism = LineList('ISM')
igm_guess = ltu.loadjson(guessfile)
comps = []
for key in igm_guess['cmps'].keys():
comp = AbsComponent.from_dict(igm_guess['cmps'][key],
chk_vel=False,
linelist=ism)
comps.append(comp)
abs_sys = ltiu.build_systems_from_components(
comps, vsys=500. * u.km /
u.s) # ,chk_z=False) ### 100000.*u.km/u.s ok
### voigt fit - added
# Spectrum
spec, spec_fil = ltgu.read_spec(ispec,
exten=exten,
norm=norm,
rsp_kwargs=rsp_kwargs)
voigtsfit = np.asarray([0] * len(spec.wavelength))
alllines = []
for iabs_sys in abs_sys:
lines = iabs_sys.list_of_abslines()
alllines = alllines + lines
if len(alllines) > 0:
voigtsfit = lav.voigt_from_abslines(spec.wavelength,
alllines,
fwhm=3.).flux.value
if not norm:
voigtsfit = voigtsfit * spec.co
# Hook the spec widget to Plot Line
self.spec_widg = ltgsp.ExamineSpecWidget(ispec,
guessfile=guessfile,
voigtsfit=voigtsfit,
status=self.statusBar,
parent=self,
llist=self.pltline_widg.llist,
zsys=zsys,
norm=norm,
exten=exten,
abs_sys=abs_sys,
screen_scale=self.scale,
rsp_kwargs=rsp_kwargs,
**kwargs)
# Reset redshift from spec
if zsys is None:
if hasattr(self.spec_widg.spec, 'z'):
self.pltline_widg.setz(
str(self.spec_widg.spec.z[self.spec_widg.select]))
# 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)
self.spec_widg.canvas.mpl_connect('button_press_event', self.on_click)
# Layout
# 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.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()
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,
z=None,
parent=None,
llist=None,
norm=True,
vmnx=[-300., 300.] * u.km / u.s,
abs_sys=None):
'''
spec = Spectrum1D
Norm: Bool (False)
Normalized spectrum?
abs_sys: AbsSystem
Absorption system class
'''
super(VelPlotWidget, self).__init__(parent)
# Initialize
spec, spec_fil = ltgu.read_spec(ispec)
self.spec = spec
self.spec_fil = spec_fil
self.z = z
self.vmnx = vmnx
self.norm = norm
# Abs_System
self.abs_sys = abs_sys
if self.abs_sys is None:
self.abs_sys = GenericAbsSystem((0. * u.deg, 0. * u.deg), self.z,
self.vmnx)
self.abs_lines = []
else:
self.z = self.abs_sys.zabs
# Line list
if llist is None:
self.abs_lines = self.abs_sys.list_of_abslines()
if len(self.abs_lines) > 0:
lwrest = [iline.wrest for iline in self.abs_lines]
else:
lwrest = None
if lwrest is not None:
llist = ltgu.set_llist(
lwrest) # Not sure this is working..
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
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'] = ltgu.navigate(0, 0, init=True)
# Status Bar?
#if not status is None:
# self.statusBar = status
# Line List
if llist is None:
self.llist = ltgu.set_llist('Strong')
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, 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 test_rdspec():
spec, spec_fil = ltgu.read_spec(data_path('UM184_nF.fits'))
#
ispec = lsio.readspec(data_path('UM184_nF.fits'))
spec, spec_fil = ltgu.read_spec(ispec)
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, 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)
