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, z=None, parent=None, llist=None, norm=True,
vmnx=[-300., 300.]*u.km/u.s, abs_sys=None, outfil='dum_kin.json',
sel_wv=None):
"""
spec : Filename or Spectrum1D
Norm : Bool (False)
Normalized spectrum?
abs_sys : AbsSystem
Absorption system class
sel_wv : Selected wavelength. Used to inspect a single, unknown line
"""
super(AbsKinGui, self).__init__(parent)
# Initialize
self.abs_sys = abs_sys
if self.abs_sys is not None:
self.z = self.abs_sys.zabs
else:
if z is None:
raise ValueError('AbsKin: Need to set abs_sys or z!')
self.z = z
self.vmnx = vmnx
self.outfil = outfil
self.norm = norm
self.sel_wv = sel_wv
# Grab the pieces and tie together
self.vplt_widg = xspw.VelPlotWidget(ispec, abs_sys=self.abs_sys, llist=llist,
vmnx=self.vmnx, z=self.z, norm=self.norm)
self.pltline_widg = ltgl.PlotLinesWidget(init_llist=self.vplt_widg.llist,
init_z=self.z)
#self.pltline_widg.spec_widg = self.vplt_widg
self.slines = ltgl.SelectedLinesWidget(self.vplt_widg.llist[self.vplt_widg.llist['List']],
init_select=self.vplt_widg.llist['show_line'],
plot_widget=self.vplt_widg)
# Connections
self.pltline_widg.llist_widget.currentItemChanged.connect(self.on_llist_change)
self.connect(self.pltline_widg.zbox, QtCore.SIGNAL('editingFinished ()'), self.setz)
self.vplt_widg.canvas.mpl_connect('key_press_event', self.on_key)
# 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)
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
# Quit
buttons = QtGui.QWidget()
wqbtn = QtGui.QPushButton('Write+Quit', self)
wqbtn.setAutoDefault(False)
wqbtn.clicked.connect(self.write_quit)
qbtn = QtGui.QPushButton('Quit', self)
qbtn.setAutoDefault(False)
qbtn.clicked.connect(self.quit)
# Sizes
lines_widg = QtGui.QWidget()
lines_widg.setMaximumWidth(300)
lines_widg.setMinimumWidth(200)
# Layout
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.pltline_widg)
vbox.addWidget(self.slines)
vbox.addWidget(wbtn)
vbox.addWidget(self.out_box)
# Write/Quit buttons
hbox1 = QtGui.QHBoxLayout()
hbox1.addWidget(wqbtn)
hbox1.addWidget(qbtn)
buttons.setLayout(hbox1)
#
vbox.addWidget(buttons)
lines_widg.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.vplt_widg)
hbox.addWidget(lines_widg)
self.setLayout(hbox)
# Initial draw
self.vplt_widg.on_draw()
def __init__(self,
ispec,
abs_sys,
parent=None,
llist=None,
norm=True,
vmnx=[-300., 300.] * u.km / u.s,
outfil=None):
"""
spec : Filename or Spectrum1D
abs_sys : AbsSystem
Absorption system class
Norm : bool, optional
Normalized spectrum?
"""
from linetools.guis import spec_widgets as ltgs
super(XAbsSysGui, self).__init__(parent)
# Initialize
self.abs_sys = abs_sys
self.z = self.abs_sys.zabs
abs_lines = abs_sys.list_of_abslines()
self.vmnx = vmnx
if outfil is None:
self.outfil = 'tmp_abskin.json'
warnings.warn(
"Outfil not specified. Using {:s} as the default".format(
self.outfil))
else:
self.outfil = outfil
self.norm = norm
# Grab the pieces and tie together
newfont = QtGui.QFont("Times", 10, QtGui.QFont.Bold)
sys_label = QtGui.QLabel('Name: \n {:s}'.format(abs_sys.name))
sys_label.setFont(newfont)
self.vplt_widg = ltgs.VelPlotWidget(ispec,
self.z,
abs_lines=abs_lines,
llist=llist,
vmnx=self.vmnx,
norm=self.norm)
self.pltline_widg = ltgl.PlotLinesWidget(
init_llist=self.vplt_widg.llist, init_z=self.z, edit_z=False)
#self.pltline_widg.spec_widg = self.vplt_widg
self.slines = ltgl.SelectedLinesWidget(
self.vplt_widg.llist[self.vplt_widg.llist['List']],
init_select=self.vplt_widg.llist['show_line'],
plot_widget=self.vplt_widg)
# Connections
self.pltline_widg.llist_widget.currentItemChanged.connect(
self.on_llist_change)
#self.connect(self.pltline_widg.zbox, QtCore.SIGNAL('editingFinished ()'), self.setz)
self.vplt_widg.canvas.mpl_connect('key_press_event', self.on_key)
# 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)
#QtCore.pyqtRemoveInputHook()
#pdb.set_trace()
#QtCore.pyqtRestoreInputHook()
# Quit
buttons = QtGui.QWidget()
wqbtn = QtGui.QPushButton('Write+Quit', self)
wqbtn.setAutoDefault(False)
wqbtn.clicked.connect(self.write_quit)
qbtn = QtGui.QPushButton('Quit', self)
qbtn.setAutoDefault(False)
qbtn.clicked.connect(self.quit)
# Sizes
lines_widg = QtGui.QWidget()
lines_widg.setMaximumWidth(300)
lines_widg.setMinimumWidth(200)
# Layout
vbox = QtGui.QVBoxLayout()
vbox.addWidget(sys_label)
vbox.addWidget(self.pltline_widg)
vbox.addWidget(self.slines)
vbox.addWidget(wbtn)
vbox.addWidget(self.out_box)
# Write/Quit buttons
hbox1 = QtGui.QHBoxLayout()
hbox1.addWidget(wqbtn)
hbox1.addWidget(qbtn)
buttons.setLayout(hbox1)
#
vbox.addWidget(buttons)
lines_widg.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.vplt_widg)
hbox.addWidget(lines_widg)
self.setLayout(hbox)
# Initial draw
self.vplt_widg.on_draw()
def __init__(self, ispec, 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)
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)
# Hook the spec widget to Plot Line
self.spec_widg = ltgsp.ExamineSpecWidget(ispec,status=self.statusBar,
parent=self, llist=self.pltline_widg.llist,
zsys=zsys, norm=norm, exten=exten,
screen_scale=self.scale,
rsp_kwargs=rsp_kwargs, **kwargs)
self.pltline_widg.spec_widg = self.spec_widg
self.spec_widg.canvas.mpl_connect('button_press_event', self.on_click)
extras = QWidget()
extras.setMaximumWidth(130*self.scale)
vbox = QVBoxLayout()
qbtn = QPushButton(self)
qbtn.setText('Quit')
qbtn.clicked.connect(self.quit)
vbox.addWidget(self.pltline_widg)
vbox.addWidget(qbtn)
extras.setLayout(vbox)
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,
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)
