def main(*args, **kwargs):
""" Runs the XSpecGui on an input file
"""
import argparse
parser = argparse.ArgumentParser(description='Parse for XSpec')
parser.add_argument("file", type=str, help="Spectral file")
parser.add_argument("-zsys", type=float, help="System Redshift")
parser.add_argument("--un_norm", help="Spectrum is NOT normalized",
action="store_true")
parser.add_argument("-exten", type=int, help="FITS extension")
pargs = parser.parse_args()
from PyQt4 import QtGui
from linetools.guis.xspecgui import XSpecGui
# Normalized?
norm = True
if pargs.un_norm:
norm = False
# Extension
exten = (pargs.exten if hasattr(pargs, 'exten') else 0)
# Second spectral file?
zsys = (pargs.zsys if hasattr(pargs, 'zsys') else None)
app = QtGui.QApplication(sys.argv)
gui = XSpecGui(pargs.file, zsys=zsys, norm=norm, exten=exten)
gui.show()
app.exec_()
def main(args, unit_test=False):
""" Runs the XSpecGui on an input file
"""
import sys
import pdb
# List only?
if args.list:
from astropy.io import fits
print("Showing object names for input file...")
hdu = fits.open(args.file)
for ii in range(1,len(hdu)):
name = hdu[ii].name
print("EXT{:07d} = {}".format(ii, name))
sys.exit()
from linetools.guis.xspecgui import XSpecGui
from pypit import arload
# Load spectrum
spec = arload.load_1dspec(args.file, exten=args.exten, extract=args.extract,
objname=args.obj, flux=args.flux)
if unit_test is False:
from PyQt5.QtWidgets import QApplication
app = QApplication(sys.argv)
# Screen dimensions
width = app.desktop().screenGeometry().width()
scale = 2. * (width/3200.)
gui = XSpecGui(spec, unit_test=unit_test, screen_scale=scale)
if unit_test is False:
gui.show()
app.exec_()
def main(args):
""" Runs the XSpecGui on an input file
"""
import sys
import numpy as np
from qtpy.QtWidgets import QApplication
from linetools.guis.xspecgui import XSpecGui
from pypeit import specobjs
from pypeit import msgs
sobjs = specobjs.SpecObjs.from_fitsfile(args.file, chk_version=False)
# List only?
if args.list:
print("Showing object names for input file...")
for ii in range(len(sobjs)):
line = "EXT{:07d} = {}".format(ii + 1, sobjs[ii].NAME)
if sobjs[ii].RA is not None:
line += " {:0.5f} {:0.5f} {:s}".format(
sobjs[ii].RA, sobjs[ii].DEC, sobjs[ii].MASKDEF_OBJNAME)
if sobjs[ii].MASKDEF_EXTRACT is not None and sobjs[
ii].MASKDEF_EXTRACT is True:
line += " maskdef_extract"
if sobjs[ii].hand_extract_flag is True:
line += " manual_extract"
#
print(line)
return
if args.obj is not None:
exten = np.where(sobjs.NAME == args.obj)[0][0]
if exten < 0:
msgs.error("Bad input object name: {:s}".format(args.obj))
else:
exten = args.exten - 1 # 1-index in FITS file
# Check Extraction
if args.extract == 'OPT':
if sobjs[exten][
'OPT_WAVE'] is None: #not in sobjs[exten]._data.keys():
msgs.error(
"Spectrum not extracted with OPT. Try --extract BOX")
spec = sobjs[exten].to_xspec1d(extraction=args.extract,
fluxed=args.flux)
# Setup
app = QApplication(sys.argv)
# Screen dimensions
width = app.screens()[0].geometry().width()
scale = 2. * (width / 3200.)
# Launch
gui = XSpecGui(spec) #, screen_scale=scale)
gui.show()
app.exec_()
def main(*args, **kwargs):
""" Runs the XSpecGui on an input file
"""
import argparse
parser = argparse.ArgumentParser(description='Parse for XSpec')
parser.add_argument("file", type=str, help="Spectral file")
parser.add_argument("--zsys", type=float, help="System Redshift")
parser.add_argument("--norm", help="Show spectrum continuum normalized (if continuum is provided)",
action="store_true")
parser.add_argument("--exten", type=int, help="FITS extension")
parser.add_argument("--wave_tag", type=str, help="Tag for wave in Table")
parser.add_argument("--flux_tag", type=str, help="Tag for flux in Table")
parser.add_argument("--sig_tag", type=str, help="Tag for sig in Table")
parser.add_argument("--var_tag", type=str, help="Tag for var in Table")
parser.add_argument("--ivar_tag", type=str, help="Tag for ivar in Table")
pargs = parser.parse_args()
from PyQt4 import QtGui
from linetools.guis.xspecgui import XSpecGui
# Normalized?
if pargs.norm is True:
norm = True
else:
norm = False
# Extension
exten = (pargs.exten if hasattr(pargs, 'exten') else 0)
# Second spectral file?
zsys = (pargs.zsys if hasattr(pargs, 'zsys') else None)
# Read spec keywords
rsp_kwargs = {}
if pargs.wave_tag is not None:
rsp_kwargs['wave_tag'] = pargs.wave_tag
if pargs.flux_tag is not None:
rsp_kwargs['flux_tag'] = pargs.flux_tag
if pargs.sig_tag is not None:
rsp_kwargs['sig_tag'] = pargs.sig_tag
if pargs.var_tag is not None:
rsp_kwargs['var_tag'] = pargs.var_tag
if pargs.ivar_tag is not None:
rsp_kwargs['ivar_tag'] = pargs.ivar_tag
app = QtGui.QApplication(sys.argv)
gui = XSpecGui(pargs.file, zsys=zsys, norm=norm, exten=exten,
rsp_kwargs=rsp_kwargs)
gui.show()
app.exec_()
def main(args, unit_test=False):
""" Runs the XSpecGui on an input file
"""
import sys
import pdb
from astropy.io import fits
from PyQt5.QtWidgets import QApplication
from linetools.guis.xspecgui import XSpecGui
from pypeit import specobjs
from pypeit import msgs
from IPython import embed
sobjs = specobjs.SpecObjs.from_fitsfile(args.file)
# List only?
if args.list:
print("Showing object names for input file...")
for ii in range(len(sobjs)):
name = sobjs[ii].name
print("EXT{:07d} = {}".format(ii + 1, name))
return
# Load spectrum
if args.obj is not None:
exten = sobjs.name.index(args.obj)
if exten < 0:
msgs.error("Bad input object name: {:s}".format(args.obj))
else:
exten = args.exten - 1 # 1-index in FITS file
# Check Extraction
if args.extract == 'OPT':
if 'OPT_WAVE' not in sobjs[exten]._data.keys():
msgs.error("Spectrum not extracted with OPT. Try --extract=BOX")
# XSpectrum1D
spec = sobjs[exten].to_xspec1d(extraction=args.extract, fluxed=args.flux)
if unit_test is False:
app = QApplication(sys.argv)
# Screen dimensions
width = app.desktop().screenGeometry().width()
scale = 2. * (width / 3200.)
gui = XSpecGui(spec, unit_test=unit_test, screen_scale=scale)
if unit_test is False:
gui.show()
app.exec_()
def main(args):
""" Runs the XSpecGui on an input file
"""
try:
sobjs = specobjs.SpecObjs.from_fitsfile(args.file)
except:
# place holder until coadd data model is sorted out
wave, flux, flux_ivar, flux_mask, meta_spec, head = general_spec_reader(
args.file)
spec = XSpectrum1D.from_tuple(
(wave * u.AA, flux, np.sqrt(utils.inverse(flux_ivar))),
masking='none')
else:
# List only?
if args.list:
print("Showing object names for input file...")
for ii in range(len(sobjs)):
name = sobjs[ii].NAME
print("EXT{:07d} = {}".format(ii + 1, name))
return
if args.obj is not None:
exten = sobjs.name.index(args.obj)
if exten < 0:
msgs.error("Bad input object name: {:s}".format(args.obj))
else:
exten = args.exten - 1 # 1-index in FITS file
# Check Extraction
if args.extract == 'OPT':
if 'OPT_WAVE' not in sobjs[exten]._data.keys():
msgs.error(
"Spectrum not extracted with OPT. Try --extract=BOX")
spec = sobjs[exten].to_xspec1d(extraction=args.extract,
fluxed=args.flux)
# Setup
app = QApplication(sys.argv)
# Screen dimensions
width = app.desktop().screenGeometry().width()
scale = 2. * (width / 3200.)
# Launch
gui = XSpecGui(spec, screen_scale=scale)
gui.show()
app.exec_()
def main(*args, **kwargs):
""" Runs the XSpecGui on an input file
"""
import argparse
parser = argparse.ArgumentParser(description='Parse')
parser.add_argument("file", type=str, help="Spectral file")
parser.add_argument("--list", default=False, help="List the extensions only?", action="store_true")
parser.add_argument("--exten", type=int, help="FITS extension")
parser.add_argument("--optimal", default=False,
help="Show Optimal? Default is boxcar", action="store_true")
pargs = parser.parse_args()
# List?
if pargs.list:
from astropy.io import fits
hdu = fits.open(pargs.file)
print(hdu.info())
return
from PyQt4 import QtGui
from linetools.guis.xspecgui import XSpecGui
# Extension
exten = (pargs.exten if hasattr(pargs, 'exten') else 0)
# Read spec keywords
rsp_kwargs = {}
if pargs.optimal:
rsp_kwargs['wave_tag'] = 'opt_wave'
rsp_kwargs['flux_tag'] = 'opt_counts'
rsp_kwargs['var_tag'] = 'opt_var'
else:
rsp_kwargs['wave_tag'] = 'box_wave'
rsp_kwargs['flux_tag'] = 'box_counts'
rsp_kwargs['var_tag'] = 'box_var'
app = QtGui.QApplication(sys.argv)
gui = XSpecGui(pargs.file, exten=exten, rsp_kwargs=rsp_kwargs)
gui.show()
app.exec_()
def main(args):
""" Runs the XSpecGui on an input file
"""
sobjs = specobjs.SpecObjs.from_fitsfile(args.file)
# List only?
if args.list:
print("Showing object names for input file...")
for ii in range(len(sobjs)):
name = sobjs[ii].NAME
print("EXT{:07d} = {}".format(ii + 1, name))
return
if args.obj is not None:
exten = np.where(sobjs.NAME == args.obj)[0][0]
if exten < 0:
msgs.error("Bad input object name: {:s}".format(args.obj))
else:
exten = args.exten - 1 # 1-index in FITS file
# Check Extraction
if args.extract == 'OPT':
if sobjs[exten]['OPT_WAVE'] is None: #not in sobjs[exten]._data.keys():
msgs.error("Spectrum not extracted with OPT. Try --extract=BOX")
spec = sobjs[exten].to_xspec1d(extraction=args.extract, fluxed=args.flux)
# Setup
app = QApplication(sys.argv)
# Screen dimensions
width = app.desktop().screenGeometry().width()
scale = 2. * (width / 3200.)
# Launch
gui = XSpecGui(spec, screen_scale=scale)
gui.show()
app.exec_()
def main(args, unit_test=False):
""" Runs the XSpecGui on an input file
"""
import sys
# List only?
if args.list:
from astropy.io import fits
hdu = fits.open(args.file)
print(hdu.info())
return
from linetools.guis.xspecgui import XSpecGui
# Extension
exten = (args.exten if hasattr(args, 'exten') else 0)
# Read spec keywords
rsp_kwargs = {}
if args.optimal:
rsp_kwargs['wave_tag'] = 'opt_wave'
rsp_kwargs['flux_tag'] = 'opt_counts'
rsp_kwargs['var_tag'] = 'opt_var'
else:
rsp_kwargs['wave_tag'] = 'box_wave'
rsp_kwargs['flux_tag'] = 'box_counts'
rsp_kwargs['var_tag'] = 'box_var'
if unit_test is False:
from PyQt4 import QtGui
app = QtGui.QApplication(sys.argv)
gui = XSpecGui(args.file, exten=exten, rsp_kwargs=rsp_kwargs, unit_test=unit_test)
if unit_test is False:
gui.show()
app.exec_()
def main(*args, **kwargs):
""" Runs the XSpecGui on an input file
"""
import argparse
parser = argparse.ArgumentParser(description='Parser for lt_xspec v1.2; \n Note: Extra arguments are passed to read_spec (e.g. --flux_tag=FX)')
parser.add_argument("file", type=str, help="Spectral file; specify extension by appending #exten#")
parser.add_argument("-guessfile", "--guessfile", type=str, help="Igmguesses file, see https://github.com/pyigm/pyigm/blob/master/docs/igmguesses.rst ")
parser.add_argument("-z", "--zsys", type=float, help="System Redshift")
parser.add_argument("--norm", help="Show spectrum continuum normalized (if continuum is provided)",
action="store_true")
parser.add_argument("--air", default=False, help="Convert input spectrum wavelengths from air to vacuum", action="store_true")
parser.add_argument("--exten", type=int, help="FITS extension")
parser.add_argument("--splice", type=str, help="Splice with the input file; extension convention applies")
parser.add_argument("--scale", type=float, help="Scale factor for GUI size [1. is default]")
#parser.add_argument("--wave_tag", type=str, help="Tag for wave in Table")
#parser.add_argument("--flux_tag", type=str, help="Tag for flux in Table")
#parser.add_argument("--sig_tag", type=str, help="Tag for sig in Table")
#parser.add_argument("--var_tag", type=str, help="Tag for var in Table")
#parser.add_argument("--ivar_tag", type=str, help="Tag for ivar in Table")
#pargs = parser.parse_args()
pargs, unknown = parser.parse_known_args()
from PyQt5.QtWidgets import QApplication
from linetools.guis.xspecgui import XSpecGui
# Normalized?
if pargs.norm is True:
norm = True
else:
norm = False
# Extension
file = pargs.file
if pargs.file[-1] == '#':
prs = pargs.file.split('#')
exten = int(prs[1])
file = prs[0]
else:
exten = (pargs.exten if hasattr(pargs, 'exten') else 0)
# zsys
zsys = (pargs.zsys if hasattr(pargs, 'zsys') else None)
# guesses
guessfile = (pargs.guessfile if hasattr(pargs, 'guessfile') else None)
# Splice?
if pargs.splice is not None:
pdb.set_trace()
if pargs.splice[-1] == '#':
prs = pargs.splice.split('#')
exten = [exten, int(prs[1])]
file = [file, prs[0]]
else:
exten = [exten, None]
file = [file, pargs.splice]
# Read spec keywords
rsp_kwargs = {}
for arg in unknown:
spl = arg.split('=')
rsp_kwargs[spl[0][2:]] = spl[1]
# GUI
app = QApplication(sys.argv)
# Scale
if pargs.scale is None:
# Screen dimensions
width = app.desktop().screenGeometry().width()
scale = 2. * (width/3200.)
else:
scale = pargs.scale
#
gui = XSpecGui(file, guessfile=guessfile, zsys=zsys, norm=norm, exten=exten,
rsp_kwargs=rsp_kwargs, air=pargs.air,
screen_scale=scale)
gui.show()
app.exec_()
def main(*args, **kwargs):
""" Runs the XSpecGui on an input file
"""
import argparse
parser = argparse.ArgumentParser(description='Parser for lt_xspec; \n Note: Extra arguments are passed to read_spec (e.g. --flux_tag=FX)')
parser.add_argument("file", type=str, help="Spectral file; specify extension by appending #exten#")
parser.add_argument("-z", "--zsys", type=float, help="System Redshift")
parser.add_argument("--norm", help="Show spectrum continuum normalized (if continuum is provided)",
action="store_true")
parser.add_argument("--air", default=False, help="Convert input spectrum wavelengths from air to vacuum", action="store_true")
parser.add_argument("--exten", type=int, help="FITS extension")
parser.add_argument("--splice", type=str, help="Splice with the input file; extension convention applies")
#parser.add_argument("--wave_tag", type=str, help="Tag for wave in Table")
#parser.add_argument("--flux_tag", type=str, help="Tag for flux in Table")
#parser.add_argument("--sig_tag", type=str, help="Tag for sig in Table")
#parser.add_argument("--var_tag", type=str, help="Tag for var in Table")
#parser.add_argument("--ivar_tag", type=str, help="Tag for ivar in Table")
#pargs = parser.parse_args()
pargs, unknown = parser.parse_known_args()
from PyQt5 import QtGui
from PyQt5.QtWidgets import QApplication
from linetools.guis.xspecgui import XSpecGui
# Normalized?
if pargs.norm is True:
norm = True
else:
norm = False
# Extension
file = pargs.file
if pargs.file[-1] == '#':
prs = pargs.file.split('#')
exten = int(prs[1])
file = prs[0]
else:
exten = (pargs.exten if hasattr(pargs, 'exten') else 0)
# zsys
zsys = (pargs.zsys if hasattr(pargs, 'zsys') else None)
# Splice?
if pargs.splice is not None:
pdb.set_trace()
if pargs.splice[-1] == '#':
prs = pargs.splice.split('#')
exten = [exten, int(prs[1])]
file = [file, prs[0]]
else:
exten = [exten, None]
file = [file, pargs.splice]
# Read spec keywords
rsp_kwargs = {}
for arg in unknown:
spl = arg.split('=')
rsp_kwargs[spl[0][2:]] = spl[1]
# GUI
app = QApplication(sys.argv)
gui = XSpecGui(file, zsys=zsys, norm=norm, exten=exten,
rsp_kwargs=rsp_kwargs, air=pargs.air)
gui.show()
app.exec_()
def plot(self, **kwargs):
""" Plot the spectrum
Parameters
----------
show : bool
If True (the default), then run the matplotlib.pyplot show
command to display the plot. Disable this if you are running
from a script and wish to delay showing the plot.
xlim : tuple of two floats
The initial x plotting limits (xmin, xmax)
inline : bool
Recommended to use if displaying inline in a Notebook
plot_two : XSpectrum1D
Plot another spectrum
xspec : bool
Launch XSpecGUI instead
Other keyword arguments are passed to the matplotlib plot
command.
"""
# Launch XSpectrum1D??
if 'xspec' in kwargs:
import sys
from PyQt4 import QtGui
from linetools.guis.xspecgui import XSpecGui
app = QtGui.QApplication(sys.argv)
gui = XSpecGui(self)
gui.show()
app.exec_()
return
import matplotlib.pyplot as plt
from ..analysis.interactive_plot import PlotWrapNav
plt.rcParams['axes.formatter.useoffset'] = False # avoid scientific notation in axes tick labels
# Keywords
nocolor = (False if 'color' in kwargs else True)
xlim = kwargs.pop('xlim', None)
inline = kwargs.pop('inline', False)
xspec2 = kwargs.pop('plot_two', None)
if inline:
fig = plt.figure(figsize=(12,8))
else:
fig = plt.gcf()
ax = plt.gca()
artists = {}
ax.axhline(0, color='k', lw=0.5)
show = kwargs.pop('show', True)
if nocolor:
kwargs.update(color='0.5')
artists['fl'] = ax.plot(self.wavelength, self.flux,
drawstyle='steps-mid', **kwargs)[0]
# Error
if nocolor:
kwargs.update(color='g')
if self.sig_is_set:
ax.plot(self.wavelength, self.sig, **kwargs)
# Continuum
if (not np.isnan(self.data['co'][self.select][0])) and (not self.normed):
if nocolor:
kwargs.update(color='r')
ax.plot(self.wavelength, self.co, **kwargs)
# Second spectrum
if xspec2 is not None:
ax.plot(xspec2.wavelength, xspec2.flux, color='blue')
ax.set_ylim(*get_flux_plotrange(self.flux))
if xlim is not None:
xmin, xmax = xlim
else:
xmin, xmax = self.wavelength.value[0], self.wavelength.value[-1]
ax.set_xlim(xmin, xmax)
# Labels
ax.set_xlabel('Wavelength ({:s})'.format(self.units['wave'].name), size=16)
ax.set_ylabel('Flux', size=16)
if plt.get_backend() == 'MacOSX':
warnings.warn("""\
Looks like you're using the MacOSX matplotlib backend. Switch to the TkAgg
or QtAgg backends to enable all interactive plotting commands.
""")
else:
# Enable xspecplot-style navigation (i/o for zooming, etc).
# Need to save this as an attribute so it doesn't get
# garbage-collected.
self._plotter = PlotWrapNav(
fig, ax, self.wavelength, self.flux, artists, printhelp=False,
xlim=(xmin, xmax))
if show:
plt.show()
def main(*args, **kwargs):
""" Runs the XSpecGui on an input file
"""
import argparse
parser = argparse.ArgumentParser(
description=
'Parser for lt_xspec; \n Note: Extra arguments are passed to read_spec (e.g. --flux_tag=FX)'
)
parser.add_argument(
"file",
type=str,
help="Spectral file; specify extension by appending #exten#")
parser.add_argument("-z", "--zsys", type=float, help="System Redshift")
parser.add_argument(
"--norm",
help="Show spectrum continuum normalized (if continuum is provided)",
action="store_true")
parser.add_argument(
"--air",
default=False,
help="Convert input spectrum wavelengths from air to vacuum",
action="store_true")
parser.add_argument("--exten", type=int, help="FITS extension")
parser.add_argument(
"--splice",
type=str,
help="Splice with the input file; extension convention applies")
#parser.add_argument("--wave_tag", type=str, help="Tag for wave in Table")
#parser.add_argument("--flux_tag", type=str, help="Tag for flux in Table")
#parser.add_argument("--sig_tag", type=str, help="Tag for sig in Table")
#parser.add_argument("--var_tag", type=str, help="Tag for var in Table")
#parser.add_argument("--ivar_tag", type=str, help="Tag for ivar in Table")
#pargs = parser.parse_args()
pargs, unknown = parser.parse_known_args()
from PyQt4 import QtGui
from linetools.guis.xspecgui import XSpecGui
# Normalized?
if pargs.norm is True:
norm = True
else:
norm = False
# Extension
file = pargs.file
if pargs.file[-1] == '#':
prs = pargs.file.split('#')
exten = int(prs[1])
file = prs[0]
else:
exten = (pargs.exten if hasattr(pargs, 'exten') else 0)
# zsys
zsys = (pargs.zsys if hasattr(pargs, 'zsys') else None)
# Splice?
if pargs.splice is not None:
pdb.set_trace()
if pargs.splice[-1] == '#':
prs = pargs.splice.split('#')
exten = [exten, int(prs[1])]
file = [file, prs[0]]
else:
exten = [exten, None]
file = [file, pargs.splice]
# Read spec keywords
rsp_kwargs = {}
for arg in unknown:
spl = arg.split('=')
rsp_kwargs[spl[0][2:]] = spl[1]
# GUI
app = QtGui.QApplication(sys.argv)
gui = XSpecGui(file,
zsys=zsys,
norm=norm,
exten=exten,
rsp_kwargs=rsp_kwargs,
air=pargs.air)
gui.show()
app.exec_()