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, 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, **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 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_()
