def test_add_component():
radec = SkyCoord(ra=123.1143 * u.deg, dec=-12.4321 * u.deg)
# HI Lya, Lyb
lya = AbsLine(1215.670 * u.AA)
lya.analy['vlim'] = [-300., 300.] * u.km / u.s
lya.attrib['z'] = 2.92939
lya.attrib['N'] = 1e17 / u.cm**2
lyb = AbsLine(1025.7222 * u.AA)
lyb.analy['vlim'] = [-300., 300.] * u.km / u.s
lyb.attrib['z'] = lya.attrib['z']
abscomp = AbsComponent.from_abslines([lya, lyb])
abscomp.coord = radec
# Instantiate
abssys = GenericAbsSystem.from_components([abscomp])
# New component
oi = AbsLine('OI 1302')
oi.analy['vlim'] = [-300., 300.] * u.km / u.s
oi.attrib['z'] = lya.attrib['z']
abscomp2 = AbsComponent.from_abslines([oi])
abscomp2.coord = radec
# Standard
assert abssys.add_component(abscomp2)
# Fail
abssys = GenericAbsSystem.from_components([abscomp])
abscomp2.vlim = [-400., 300.] * u.km / u.s
assert not abssys.add_component(abscomp2)
# Overlap
assert abssys.add_component(abscomp2, overlap_only=True)
def test_add_component():
radec = SkyCoord(ra=123.1143*u.deg, dec=-12.4321*u.deg)
# HI Lya, Lyb
lya = AbsLine(1215.670*u.AA)
lya.analy['vlim'] = [-300.,300.]*u.km/u.s
lya.attrib['z'] = 2.92939
lya.attrib['N'] = 1e17 / u.cm**2
lyb = AbsLine(1025.7222*u.AA)
lyb.analy['vlim'] = [-300.,300.]*u.km/u.s
lyb.attrib['z'] = lya.attrib['z']
abscomp = AbsComponent.from_abslines([lya,lyb])
abscomp.coord = radec
# Instantiate
abssys = GenericAbsSystem.from_components([abscomp])
# New component
oi = AbsLine('OI 1302')
oi.analy['vlim'] = [-300.,300.]*u.km/u.s
oi.attrib['z'] = lya.attrib['z']
abscomp2 = AbsComponent.from_abslines([oi])
abscomp2.coord = radec
# Standard
assert abssys.add_component(abscomp2)
# Fail
abssys = GenericAbsSystem.from_components([abscomp])
abscomp2.vlim = [-400.,300.]*u.km/u.s
assert not abssys.add_component(abscomp2)
# Overlap
assert abssys.add_component(abscomp2, overlap_only=True)
def abssys_from_json(filename):
"""
Parameters
----------
filename
Returns
-------
abs_sys : AbsSystem
"""
# Load JSON file to determine type
adict = ltu.loadjson(filename)
if 'class' in adict.keys():
if adict['class'] == 'MgIISystem':
from pyigm.abssys.igmsys import MgIISystem
abs_sys = MgIISystem.from_dict(adict)
else:
warnings.warn(
"Unknown or uncoded class: {:s}.\nMaking a Generic one".format(
adict['class']))
abs_sys = GenericAbsSystem.from_dict(adict)
else:
abs_sys = GenericAbsSystem.from_dict(adict)
# Return
return abs_sys
def test_init_strradec():
# Simple properties
gensys = GenericAbsSystem(('01:32:21', '+22:15:53.3'),
1.244, [-500, 500] * u.km / u.s,
NHI=16.)
# Test
assert gensys.abs_type == 'Generic'
np.testing.assert_allclose(gensys.coord.ra.value, 23.087499999999995)
#
gensys = GenericAbsSystem('013221+221553.3',
1.244, [-500, 500] * u.km / u.s,
NHI=16.)
np.testing.assert_allclose(gensys.coord.ra.value, 23.087499999999995)
def test_add_component():
abscomp = lyman_comp(radec)
# Instantiate
abssys = GenericAbsSystem.from_components([abscomp])
# New component
oicomp = oi_comp(radec, vlim=[-300., 300.] * u.km / u.s, z=abscomp.zcomp)
# Standard
assert abssys.add_component(oicomp)
# Fail
abssys = GenericAbsSystem.from_components([abscomp])
oicomp2 = oi_comp(radec, vlim=[-400., 300.] * u.km / u.s, z=abscomp.zcomp)
assert not abssys.add_component(oicomp2)
# Overlap
assert abssys.add_component(oicomp2, overlap_only=True)
def test_from_systems():
radec = SkyCoord(ra=123.1143 * u.deg, dec=-12.4321 * u.deg)
# HI
lyacomp1 = lyman_comp(radec, z=0.45)
lyacomp2 = lyman_comp(radec, z=0.25)
# SiII
SiII_comp1 = si2_comp(radec, z=0.45)
SiII_comp2 = si2_comp(radec, z=0.25)
# Instantiate systems
sys1 = GenericAbsSystem.from_components([lyacomp1, SiII_comp1])
sys2 = GenericAbsSystem.from_components([lyacomp2, SiII_comp2])
# Instantiate sightline
sl = GenericAbsSightline.from_systems([sys1, sys2])
# Test
assert len(sl._abssystems) == 2
def test_from_systems():
radec = SkyCoord(ra=123.1143*u.deg, dec=-12.4321*u.deg)
# HI
lyacomp1 = lyman_comp(radec, z=0.45)
lyacomp2 = lyman_comp(radec, z=0.25)
# SiII
SiII_comp1 = si2_comp(radec, z=0.45)
SiII_comp2 = si2_comp(radec, z=0.25)
# Instantiate systems
sys1 = GenericAbsSystem.from_components([lyacomp1,SiII_comp1])
sys2 = GenericAbsSystem.from_components([lyacomp2, SiII_comp2])
# Instantiate sightline
sl = GenericAbsSightline.from_systems([sys1,sys2])
# Test
assert len(sl._abssystems) == 2
def test_add_component():
abscomp = lyman_comp(radec)
# Instantiate
abssys = GenericAbsSystem.from_components([abscomp])
# New component
oicomp = oi_comp(radec, vlim=[-300.,300.]*u.km/u.s, z=abscomp.zcomp)
# Standard
assert abssys.add_component(oicomp)
# Fail
abssys = GenericAbsSystem.from_components([abscomp])
oicomp2 = oi_comp(radec, vlim=[-400.,300.]*u.km/u.s, z=abscomp.zcomp)
warnings.filterwarnings("ignore")
assert not abssys.add_component(oicomp2)
# Overlap
assert abssys.add_component(oicomp2, overlap_only=True)
def test_from_json():
# Tests from_dict too
HIsys = LymanAbsSystem.from_json(data_path('HILya_abssys.json'))
np.testing.assert_allclose(HIsys.zabs, 2.92939)
# Tests ordering
gensys = GenericAbsSystem.from_json(data_path('generic_abssys.json'))
np.testing.assert_allclose(gensys._components[0].zcomp, 2.92939)
def test_init():
# Simple properties
radec = SkyCoord(ra=123.1143 * u.deg, dec=-12.4321 * u.deg)
gensys = GenericAbsSystem(radec, 1.244, [-500, 500] * u.km / u.s, NHI=16.)
# Test
assert gensys.abs_type == 'Generic'
np.testing.assert_allclose(gensys.zabs, 1.244)
def test_from_json():
# Tests from_dict too
HIsys = LymanAbsSystem.from_json(data_path('HILya_abssys.json'))
np.testing.assert_allclose(HIsys.zabs, 2.92939)
# Tests ordering
gensys = GenericAbsSystem.from_json(data_path('generic_abssys.json'))
np.testing.assert_allclose(gensys._components[0].zcomp, 2.92939)
def test_multi_components():
radec = SkyCoord(ra=123.1143*u.deg, dec=-12.4321*u.deg)
# HI Lya, Lyb
lya = AbsLine(1215.670*u.AA)
lya.analy['vlim'] = [-300.,300.]*u.km/u.s
lya.attrib['z'] = 2.92939
lyb = AbsLine(1025.7222*u.AA)
lyb.analy['vlim'] = [-300.,300.]*u.km/u.s
lyb.attrib['z'] = lya.attrib['z']
abscomp = AbsComponent.from_abslines([lya,lyb])
abscomp.coord = radec
# SiII
SiIItrans = ['SiII 1260', 'SiII 1304', 'SiII 1526', 'SiII 1808']
abslines = []
for trans in SiIItrans:
iline = AbsLine(trans)
iline.attrib['z'] = 2.92939
iline.analy['vlim'] = [-250.,80.]*u.km/u.s
abslines.append(iline)
#
SiII_comp = AbsComponent.from_abslines(abslines)
SiII_comp.coord = radec
# Instantiate
LLSsys = GenericAbsSystem.from_components([abscomp,SiII_comp])
# Test
assert len(LLSsys._components) == 2
def test_list_of_abslines():
radec = SkyCoord(ra=123.1143*u.deg, dec=-12.4321*u.deg)
# HI Lya, Lyb
lya = AbsLine(1215.670*u.AA)
lya.analy['vlim'] = [-300.,300.]*u.km/u.s
lya.attrib['z'] = 2.92939
lyb = AbsLine(1025.7222*u.AA)
lyb.analy['vlim'] = [-300.,300.]*u.km/u.s
lyb.attrib['z'] = lya.attrib['z']
abscomp = AbsComponent.from_abslines([lya,lyb])
abscomp.coord = radec
# SiII
SiIItrans = ['SiII 1260', 'SiII 1304', 'SiII 1526', 'SiII 1808']
abslines = []
for trans in SiIItrans:
iline = AbsLine(trans)
iline.attrib['z'] = 2.92939
iline.analy['vlim'] = [-250.,80.]*u.km/u.s
abslines.append(iline)
#
SiII_comp = AbsComponent.from_abslines(abslines)
SiII_comp.coord = radec
# Instantiate
gensys = GenericAbsSystem.from_components([abscomp,SiII_comp])
# Now the list
abslines = gensys.list_of_abslines()
# Test
assert len(abslines) == 6
# Grab one line
lyb = gensys.get_absline('HI 1025')
np.testing.assert_allclose(lyb.wrest.value, 1025.7222)
lyb = gensys.get_absline(1025.72*u.AA)
np.testing.assert_allclose(lyb.wrest.value, 1025.7222)
def reload(self):
print('AbsSysWidget: Reloading systems..')
self.all_abssys = []
for abssys_fil in self.abssys_list:
self.all_abssys.append(GenericAbsSystem.from_json(abssys_fil,
linelist=self.linelist))
#self.add_item(abssys_fil)
self.on_list_change()
def test_init():
# Simple properties
gensys = GenericAbsSystem(radec, 1.244, [-500, 500] * u.km / u.s, NHI=16.)
# Test
assert gensys.abs_type == 'Generic'
assert gensys.flag_NHI == 1
np.testing.assert_allclose(gensys.zabs, 1.244)
np.testing.assert_allclose(gensys.vlim.value, [-500, 500])
def main(*args, **kwargs):
""" Runs the AbsKinGui
Command line
or from Python
Examples:
1. python ~/xastropy/xastropy/xguis/abskingui.py
2. abskingui.main(filename)
3. abskingui.main(spec1d)
"""
import sys
import argparse
parser = argparse.ArgumentParser(description='Parse for AbsKinGui')
parser.add_argument("file", type=str, help="Spectral file")
parser.add_argument("-sysfile", type=str, help="System JSON file")
parser.add_argument("-zsys", type=float, help="System Redshift")
parser.add_argument("-outfil", type=str, help="Output filename")
parser.add_argument("--un_norm", help="Spectrum is NOT normalized",
action="store_true")
if len(args) == 0:
pargs = parser.parse_args()
else: # better know what you are doing!
if isinstance(args[0],(Spectrum1D, tuple)):
if not kwargs['rerun']:
app = QtGui.QApplication(sys.argv)
xdb.set_trace()
gui = AbsKinGui(args[0], **kwargs)
gui.exec_()
#gui.show()
#app.exec_()
return gui, app
else: # String parsing
largs = [iargs for iargs in args]
pargs = parser.parse_args(largs)
xdb.set_trace() # Not setup for command line yet
# Normalized?
norm = True
if pargs.un_norm:
norm = False
# Read AbsSystem
from linetools.isgm.abssystem import GenericAbsSystem
if pargs.sysfile is not None:
abs_sys = GenericAbsSystem.from_json(pargs.sysfile, chk_vel=False)
else:
abs_sys = None
app = QtGui.QApplication(sys.argv)
gui = AbsKinGui(pargs.file, z=pargs.zsys, norm=norm, abs_sys=abs_sys, outfil=pargs.outfil)
gui.show()
app.exec_()
return gui, app
def test_multi_components():
# HI
abscomp = lyman_comp(radec)
# SiII
SiII_comp = si2_comp(radec)
# Instantiate
LLSsys = GenericAbsSystem.from_components([abscomp,SiII_comp])
# Test
np.testing.assert_allclose(LLSsys.NHI, 17.0)
assert len(LLSsys._components) == 2
def write_comps_to_sys():
from linetools.isgm.abssystem import GenericAbsSystem
radec = SkyCoord(ra=123.1143*u.deg, dec=-12.4321*u.deg)
# HI
abscomp = lyman_comp(radec, z=2.92940)
# SiII
SiII_comp = si2_comp(radec)
gensl = GenericAbsSystem.from_components([abscomp, SiII_comp])
# Write
gensl.write_json()
def write_comps_to_sys():
from linetools.isgm.abssystem import GenericAbsSystem
radec = SkyCoord(ra=123.1143 * u.deg, dec=-12.4321 * u.deg)
# HI
abscomp = lyman_comp(radec, z=2.92940)
# SiII
SiII_comp = si2_comp(radec)
gensl = GenericAbsSystem.from_components([abscomp, SiII_comp])
# Write
gensl.write_json()
def test_multi_components():
# HI
abscomp = lyman_comp(radec)
# SiII
SiII_comp = si2_comp(radec)
# Instantiate
LLSsys = GenericAbsSystem.from_components([abscomp, SiII_comp])
# Test
np.testing.assert_allclose(LLSsys.NHI, 17.0)
assert len(LLSsys._components) == 2
def make_gensl():
radec = SkyCoord(ra=123.1143*u.deg, dec=-12.4321*u.deg)
# HI
abscomp = lyman_comp(radec)
# SiII
SiII_comp = si2_comp(radec)
gensl = GenericAbsSightline.from_components([abscomp, SiII_comp])
# Add a system
sys = GenericAbsSystem.from_components([abscomp, SiII_comp])
gensl._abssystems = [sys]
return gensl
def test_multi_components():
radec = SkyCoord(ra=123.1143 * u.deg, dec=-12.4321 * u.deg)
# HI
abscomp = lyman_comp(radec)
# SiII
SiII_comp = si2_comp(radec)
# Instantiate
LLSsys = GenericAbsSystem.from_components([abscomp, SiII_comp])
# Test
np.testing.assert_allclose(LLSsys.NHI, 17.0)
assert len(LLSsys._components) == 2
def add_forest(self, inp, z):
'''Add a Lya/Lyb forest line
'''
from linetools.isgm.abssystem import GenericAbsSystem
forest = GenericAbsSystem((0. * u.deg, 0. * u.deg), z,
[-300., 300.] * u.km / u.s)
# NHI
NHI_dict = {'6': 12., '7': 13., '8': 14., '9': 15.}
forest.NHI = NHI_dict[inp]
# Lines
for name in ['HI 1215', 'HI 1025', 'HI 972']:
aline = AbsLine(name, linelist=self.llist[self.llist['List']])
# Attributes
aline.attrib['N'] = 10**forest.NHI * u.cm**-2
aline.attrib['b'] = 20. * u.km / u.s
aline.setz(forest.zabs)
# Append
forest.lines.append(aline)
# Append to forest lines
self.all_forest.append(forest)
def make_gensl():
radec = SkyCoord(ra=123.1143 * u.deg, dec=-12.4321 * u.deg)
# HI
abscomp = lyman_comp(radec)
# SiII
SiII_comp = si2_comp(radec)
gensl = GenericAbsSightline.from_components([abscomp, SiII_comp])
# Add a system
sys = GenericAbsSystem.from_components([abscomp, SiII_comp])
gensl._abssystems = [sys]
return gensl
def test_multi_components():
radec = SkyCoord(ra=123.1143*u.deg, dec=-12.4321*u.deg)
# HI
abscomp = lyman_comp(radec)
# SiII
SiII_comp = si2_comp(radec)
# Instantiate
LLSsys = GenericAbsSystem.from_components([abscomp,SiII_comp])
# Test
np.testing.assert_allclose(LLSsys.NHI, 17.0)
assert len(LLSsys._components) == 2
def main(*args, **kwargs):
""" Runs the XAbsSysGui on input files
"""
import argparse
parser = argparse.ArgumentParser(description='Parse for XAbsSys')
parser.add_argument("spec_file", type=str, help="Spectral file")
parser.add_argument("abssys_file", type=str, help="AbsSys file (JSON)")
parser.add_argument("-outfile", type=str, help="Output filename")
parser.add_argument("-llist", type=str, help="Name of LineList")
#parser.add_argument("-exten", type=int, help="FITS extension")
parser.add_argument("--un_norm",
help="Spectrum is NOT normalized",
action="store_true")
pargs = parser.parse_args()
from PyQt5.QtWidgets import QApplication
from linetools.guis.xabssysgui import XAbsSysGui
# Normalized?
norm = True
if pargs.un_norm:
norm = False
# Extension
#exten = (pargs.exten if hasattr(pargs, 'exten') else 0)
# Read spec keywords
rsp_kwargs = {}
# Line list
if pargs.llist is not None:
from linetools.lists.linelist import LineList
llist = LineList(pargs.llist)
else:
llist = None
# Read AbsSystem
from linetools.isgm.abssystem import GenericAbsSystem
abs_sys = GenericAbsSystem.from_json(pargs.abssys_file) #, chk_vel=False)
app = QApplication(sys.argv)
gui = XAbsSysGui(pargs.spec_file,
abs_sys,
norm=norm,
llist=llist,
outfil=pargs.outfile)
gui.show()
app.exec_()
def main(*args, **kwargs):
""" Runs the XAbsSysGui on input files
"""
import argparse
parser = argparse.ArgumentParser(description='Parse for XAbsSys')
parser.add_argument("spec_file", type=str, help="Spectral file")
parser.add_argument("abssys_file", type=str, help="AbsSys file (JSON)")
parser.add_argument("-outfile", type=str, help="Output filename")
parser.add_argument("-llist", type=str, help="Name of LineList")
#parser.add_argument("-exten", type=int, help="FITS extension")
parser.add_argument("--un_norm", help="Spectrum is NOT normalized",
action="store_true")
pargs = parser.parse_args()
from PyQt4 import QtGui
from linetools.guis.xabssysgui import XAbsSysGui
# Normalized?
norm = True
if pargs.un_norm:
norm = False
# Extension
#exten = (pargs.exten if hasattr(pargs, 'exten') else 0)
# Read spec keywords
rsp_kwargs = {}
# Line list
if pargs.llist is not None:
from linetools.lists.linelist import LineList
llist = LineList(pargs.llist)
else:
llist = None
# Read AbsSystem
from linetools.isgm.abssystem import GenericAbsSystem
abs_sys = GenericAbsSystem.from_json(pargs.abssys_file, chk_vel=False)
app = QtGui.QApplication(sys.argv)
gui = XAbsSysGui(pargs.spec_file, abs_sys, norm=norm, llist=llist,
outfil=pargs.outfile)
gui.show()
app.exec_()
def init_system():
radec = SkyCoord(ra=123.1143*u.deg, dec=-12.4321*u.deg)
# HI Lya, Lyb
lya = AbsLine(1215.670*u.AA, z=2.92939)
lya.limits.set([-300.,300.]*u.km/u.s)
lya.attrib['coord'] = radec
lyb = AbsLine(1025.7222*u.AA, z=lya.z)
lyb.limits.set([-300.,300.]*u.km/u.s)
lyb.attrib['coord'] = radec
abscomp = AbsComponent.from_abslines([lya,lyb])
# SiII
SiIItrans = ['SiII 1260', 'SiII 1304', 'SiII 1526', 'SiII 1808']
abslines = []
for trans in SiIItrans:
iline = AbsLine(trans, z=2.92939)
iline.attrib['coord'] = radec
iline.limits.set([-250.,80.]*u.km/u.s)
abslines.append(iline)
#
SiII_comp = AbsComponent.from_abslines(abslines)
# Instantiate
gensys = GenericAbsSystem.from_components([abscomp,SiII_comp])
return gensys
def init_system():
radec = SkyCoord(ra=123.1143 * u.deg, dec=-12.4321 * u.deg)
# HI Lya, Lyb
lya = AbsLine(1215.670 * u.AA, z=2.92939)
lya.limits.set([-300., 300.] * u.km / u.s)
lya.attrib['coord'] = radec
lyb = AbsLine(1025.7222 * u.AA, z=lya.z)
lyb.limits.set([-300., 300.] * u.km / u.s)
lyb.attrib['coord'] = radec
abscomp = AbsComponent.from_abslines([lya, lyb])
# SiII
SiIItrans = ['SiII 1260', 'SiII 1304', 'SiII 1526', 'SiII 1808']
abslines = []
for trans in SiIItrans:
iline = AbsLine(trans, z=2.92939)
iline.attrib['coord'] = radec
iline.limits.set([-250., 80.] * u.km / u.s)
abslines.append(iline)
#
SiII_comp = AbsComponent.from_abslines(abslines)
# Instantiate
gensys = GenericAbsSystem.from_components([abscomp, SiII_comp])
return gensys
def build_systems_from_components(comps, **kwargs):
""" Build a list of AbsSystems from a list of AbsComponents
Current default implementation allows for overlapping components, i.e.
only_overalp=True in add_component
Parameters
----------
comps : list
Returns
-------
abs_systems : list
"""
from linetools.isgm.abssystem import GenericAbsSystem
if 'overlap_only' not in kwargs.keys():
kwargs['overlap_only'] = True
# Add
abs_systems = []
cpy_comps = [comp.copy() for comp in comps]
# Loop until all components assigned
while len(cpy_comps) > 0:
# Use the first one
comp = cpy_comps.pop(0)
abssys = GenericAbsSystem.from_components([comp])
abs_systems.append(abssys)
# Try the rest
comps_left = []
for icomp in cpy_comps:
if abssys.add_component(icomp, **kwargs):
pass
else:
comps_left.append(icomp)
cpy_comps = comps_left
# Return
return abs_systems
def main(*args, **kwargs):
""" Runs the AbsKinGui
Command line
or from Python
Examples:
1. python ~/xastropy/xastropy/xguis/abskingui.py
2. abskingui.main(filename)
3. abskingui.main(spec1d)
"""
import sys
import argparse
parser = argparse.ArgumentParser(description='Parse for AbsKinGui')
parser.add_argument("file", type=str, help="Spectral file")
parser.add_argument("-sysfile", type=str, help="System JSON file")
parser.add_argument("-zsys", type=float, help="System Redshift")
parser.add_argument("-outfil", type=str, help="Output filename")
parser.add_argument("--un_norm",
help="Spectrum is NOT normalized",
action="store_true")
if len(args) == 0:
pargs = parser.parse_args()
else: # better know what you are doing!
if isinstance(args[0], (Spectrum1D, tuple)):
if not kwargs['rerun']:
app = QtGui.QApplication(sys.argv)
xdb.set_trace()
gui = AbsKinGui(args[0], **kwargs)
gui.exec_()
#gui.show()
#app.exec_()
return gui, app
else: # String parsing
largs = [iargs for iargs in args]
pargs = parser.parse_args(largs)
xdb.set_trace() # Not setup for command line yet
# Normalized?
norm = True
if pargs.un_norm:
norm = False
# Read AbsSystem
from linetools.isgm.abssystem import GenericAbsSystem
if pargs.sysfile is not None:
abs_sys = GenericAbsSystem.from_json(pargs.sysfile, chk_vel=False)
else:
abs_sys = None
app = QtGui.QApplication(sys.argv)
gui = AbsKinGui(pargs.file,
z=pargs.zsys,
norm=norm,
abs_sys=abs_sys,
outfil=pargs.outfil)
gui.show()
app.exec_()
return gui, app
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()
class VelPlotWidget(QtGui.QWidget):
''' Widget for a velocity plot with interaction.
19-Dec-2014 by JXP
'''
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()
# Load them up for display
def init_lines(self):
wvmin = np.min(self.spec.dispersion)
wvmax = np.max(self.spec.dispersion)
#
wrest = self.llist[self.llist['List']].wrest
wvobs = (1+self.z) * wrest
gdlin = np.where( (wvobs > wvmin) & (wvobs < wvmax) )[0]
self.llist['show_line'] = gdlin
# Update/generate lines [will not update]
for idx in gdlin:
self.generate_line((self.z,wrest[idx]))
def grab_line(self, wrest):
""" Grab a line from the list
Parameters
----------
wrest
Returns
-------
iline : AbsLine object
"""
awrest = [iline.wrest for iline in self.abs_lines]
try:
idx = awrest.index(wrest)
except ValueError:
return None
else:
return self.abs_lines[idx]
def generate_line(self, inp):
''' Generate a new line, if it doesn't exist
Parameters:
----------
inp: tuple
(z,wrest)
'''
# Generate?
if self.grab_line(inp[1]) is None:
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
newline = AbsLine(inp[1],linelist=self.llist[self.llist['List']])
print('VelPlot: Generating line {:g}'.format(inp[1]))
newline.analy['vlim'] = self.vmnx/2.
newline.attrib['z'] = self.abs_sys.zabs
newline.analy['do_analysis'] = 1 # Init to ok
# Spec file
if self.spec_fil is not None:
newline.analy['datafile'] = self.spec_fil
# Append
self.abs_lines.append(newline)
def remove_line(self, wrest):
""" Remove a line, if it exists
Parameters
----------
wrest : Quantity
"""
awrest = [iline.wrest for iline in self.abs_lines]
try:
idx = awrest.index(wrest)
except ValueError:
return None
else:
_ = self.abs_lines.pop(idx)
# Key stroke
def on_key(self,event):
# Init
rescale = True
fig_clear = False
wrest = None
flg = 0
sv_idx = self.idx_line
## Change rows/columns
if event.key == 'k':
self.sub_xy[0] = max(0, self.sub_xy[0]-1)
if event.key == 'K':
self.sub_xy[0] = self.sub_xy[0]+1
if event.key == 'c':
self.sub_xy[1] = max(0, self.sub_xy[1]-1)
if event.key == 'C':
self.sub_xy[1] = max(0, self.sub_xy[1]+1)
## NAVIGATING
if event.key in self.psdict['nav']:
flg = ltgu.navigate(self.psdict,event)
if event.key == '-':
self.idx_line = max(0, self.idx_line-self.sub_xy[0]*self.sub_xy[1]) # Min=0
if self.idx_line == sv_idx:
print('Edge of list')
if event.key == '=':
self.idx_line = min(len(self.llist['show_line'])-self.sub_xy[0]*self.sub_xy[1],
self.idx_line + self.sub_xy[0]*self.sub_xy[1])
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
if self.idx_line == sv_idx:
print('Edge of list')
## Reset z
if event.key == 'z':
newz = ltu.z_from_v(self.z, event.xdata)
self.z = newz
self.abs_sys.zabs = newz
# Drawing
self.psdict['xmnx'] = self.vmnx.value
# Single line command
if event.key in ['1','2','B','U','L','N','V','A', 'x', 'X',
'^', '&']:
try:
wrest = event.inaxes.get_gid()
except AttributeError:
return
else:
absline = self.grab_line(wrest)
kwrest = wrest.value
## Velocity limits
unit = u.km/u.s
if event.key == '1':
absline.analy['vlim'][0] = event.xdata*unit
if event.key == '2':
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
absline.analy['vlim'][1] = event.xdata*unit
if event.key == '!':
for iline in self.abs_sys.lines:
iline.analy['vlim'][0] = event.xdata*unit
if event.key == '@':
for iline in self.abs_sys.lines:
iline.analy['vlim'][1] = event.xdata*unit
## Line type
if event.key == 'A': # Add to lines
self.generate_line((self.z,wrest))
if event.key == 'x': # Remove line
if self.remove_line(wrest):
print('VelPlot: Removed line {:g}'.format(wrest))
if event.key == 'X': # Remove all lines
# Double check
gui = xguiu.WarningWidg('About to remove all lines. \n Continue??')
gui.exec_()
if gui.ans is False:
return
#
self.abs_lines = [] # Flush??
# Kinematics
if event.key == '^': # Low-Ion
try:
fkin = absline.analy['flag_kin']
except KeyError:
fkin = 0
fkin += (-1)**(fkin % 2**1 >= 2**0) * 2**0
absline.analy['flag_kin'] = fkin
if event.key == '&': # High-Ion
try:
fkin = absline.analy['flag_kin']
except KeyError:
fkin = 0
fkin += (-1)**(fkin % 2**2 >= 2**1) * 2**1
absline.analy['flag_kin'] = fkin
# Toggle blend
if event.key == 'B':
try:
feye = absline.analy['flg_eye']
except KeyError:
feye = 0
feye = (feye + 1) % 2
absline.analy['flg_eye'] = feye
# Toggle NG
if event.key == 'N':
try:
fanly = absline.analy['do_analysis']
except KeyError:
fanly = 1
if fanly == 0:
fanly = 1
else:
fanly = 0
absline.analy['do_analysis'] = fanly
if event.key == 'V': # Normal
absline.analy['flg_limit'] = 1
if event.key == 'L': # Lower limit
absline.analy['flg_limit'] = 2
if event.key == 'U': # Upper limit
absline.analy['flg_limit'] = 3
# AODM plot
if event.key == ':': #
# Grab good lines
from xastropy.xguis import spec_guis as xsgui
gdl = [iline.wrest for iline in self.abs_sys.lines
if iline.analy['do_analysis'] > 0]
# Launch AODM
if len(gdl) > 0:
gui = xsgui.XAODMGui(self.spec, self.z, gdl, vmnx=self.vmnx, norm=self.norm)
gui.exec_()
else:
print('VelPlot.AODM: No good lines to plot')
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
if not wrest is None: # Single window
flg = 3
if event.key in ['c','C','k','K','W','!', '@', '=', '-', 'X', 'z','R']: # Redraw all
flg = 1
if event.key in ['Y']:
rescale = False
if event.key in ['k','c','C','K', 'R']:
fig_clear = True
if flg==1: # Default is not to redraw
self.on_draw(rescale=rescale, fig_clear=fig_clear)
elif flg==2: # Layer (no clear)
self.on_draw(replot=False, rescale=rescale)
elif flg==3: # Layer (no clear)
self.on_draw(in_wrest=wrest, rescale=rescale)
# Click of main mouse button
def on_click(self,event):
try:
print('button={:d}, x={:f}, y={:f}, xdata={:f}, ydata={:f}'.format(
event.button, event.x, event.y, event.xdata, event.ydata))
except ValueError:
return
if event.button == 1: # Draw line
self.ax.plot( [event.xdata,event.xdata], self.psdict['ymnx'], ':', color='green')
self.on_draw(replot=False)
# Print values
try:
self.statusBar().showMessage('x,y = {:f}, {:f}'.format(event.xdata,event.ydata))
except AttributeError:
return
def on_draw(self, replot=True, in_wrest=None, rescale=True, fig_clear=False):
""" Redraws the figure
"""
#
if replot is True:
if fig_clear:
self.fig.clf()
# Loop on windows
all_idx = self.llist['show_line']
nplt = self.sub_xy[0]*self.sub_xy[1]
if len(all_idx) <= nplt:
self.idx_line = 0
subp = np.arange(nplt) + 1
subp_idx = np.hstack(subp.reshape(self.sub_xy[0],self.sub_xy[1]).T)
#print('idx_l={:d}, nplt={:d}, lall={:d}'.format(self.idx_line,nplt,len(all_idx)))
for jj in range(min(nplt, len(all_idx))):
try:
idx = all_idx[jj+self.idx_line]
except IndexError:
continue # Likely too few lines
#print('jj={:d}, idx={:d}'.format(jj,idx))
# Grab line
wrest = self.llist[self.llist['List']].wrest[idx]
kwrest = wrest.value # For the Dict
# Single window?
if in_wrest is not None:
if np.abs(wrest-in_wrest) > (1e-3*u.AA):
continue
# Abs_Sys: Color the lines
if self.abs_sys is not None:
absline = self.grab_line(wrest)
# Generate plot
self.ax = self.fig.add_subplot(self.sub_xy[0],self.sub_xy[1], subp_idx[jj])
self.ax.clear()
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
# Zero line
self.ax.plot( [0., 0.], [-1e9, 1e9], ':', color='gray')
# Velocity
wvobs = (1+self.z) * wrest
velo = (self.spec.dispersion/wvobs - 1.)*const.c.to('km/s')
# Plot
self.ax.plot(velo, self.spec.flux, 'k-',drawstyle='steps-mid')
# GID for referencing
self.ax.set_gid(wrest)
# Labels
#if jj >= (self.sub_xy[0]-1)*(self.sub_xy[1]):
if (((jj+1) % self.sub_xy[0]) == 0) or ((jj+1) == len(all_idx)):
self.ax.set_xlabel('Relative Velocity (km/s)')
else:
self.ax.get_xaxis().set_ticks([])
lbl = self.llist[self.llist['List']].name[idx]
# Kinematics
kinl = ''
if absline is not None:
if (absline.analy['flag_kin'] % 2) >= 1:
kinl = kinl + 'L'
if (absline.analy['flag_kin'] % 4) >= 2:
kinl = kinl + 'H'
self.ax.text(0.1, 0.05, lbl+kinl, color='blue', transform=self.ax.transAxes,
size='x-small', ha='left')
# Reset window limits
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
self.ax.set_xlim(self.psdict['xmnx'])
# Rescale?
if (rescale is True) & (self.norm is False):
gdp = np.where( (velo.value > self.psdict['xmnx'][0]) &
(velo.value < self.psdict['xmnx'][1]))[0]
if len(gdp) > 5:
per = xstats.basic.perc(self.spec.flux[gdp])
self.ax.set_ylim((0., 1.1*per[1]))
else:
self.ax.set_ylim(self.psdict['ymnx'])
else:
self.ax.set_ylim(self.psdict['ymnx'])
# Fonts
xputils.set_fontsize(self.ax,6.)
clr='black'
if absline is not None:
try:
vlim = absline.analy['vlim']
except KeyError:
pass
# Color coding
try: # .clm style
flag = absline.analy['FLAGS'][0]
except KeyError:
flag = None
else:
if flag <= 1: # Standard detection
clr = 'green'
elif flag in [2,3]:
clr = 'blue'
elif flag in [4,5]:
clr = 'purple'
# ABS ID
try: # NG?
flagA = absline.analy['do_analysis']
except KeyError:
flagA = None
else:
if (flagA>0) & (clr == 'black'):
clr = 'green'
try: # Limit?
flagL = absline.analy['flg_limit']
except KeyError:
flagL = None
else:
if flagL == 2:
clr = 'blue'
if flagL == 3:
clr = 'purple'
try: # Blends?
flagE = absline.analy['flg_eye']
except KeyError:
flagE = None
else:
if flagE == 1:
clr = 'orange'
if flagA == 0:
clr = 'red'
pix = np.where( (velo > vlim[0]) & (velo < vlim[1]))[0]
self.ax.plot(velo[pix], self.spec.flux[pix], '-',
drawstyle='steps-mid', color=clr)
# Draw
self.canvas.draw()
def __init__(self, abssys_list, parent=None,
only_one=False, linelist=None, no_buttons=False):
"""
only_one: bool, optional
Restrict to one selection at a time? [False]
no_buttons: bool, optional
Eliminate Refine/Reload buttons?
"""
super(AbsSysWidget, self).__init__(parent)
#if not status is None:
# self.statusBar = status
self.abssys_list = abssys_list
# Speeds things up
if linelist is None:
self.linelist = LineList('ISM')
else:
self.linelist = linelist
# Create the line list
list_label = QLabel('Abs Systems:')
self.abslist_widget = QListWidget(self)
if not only_one:
self.abslist_widget.setSelectionMode(QAbstractItemView.ExtendedSelection)
self.abslist_widget.addItem('None')
#self.abslist_widget.addItem('Test')
# Lists
self.abs_sys = []
self.items = []
self.all_items = []
self.all_abssys = []
for abssys_fil in self.abssys_list:
self.all_abssys.append(GenericAbsSystem.from_json(abssys_fil,
linelist=self.linelist))
self.add_item(abssys_fil)
self.abslist_widget.setCurrentRow(0)
self.abslist_widget.itemSelectionChanged.connect(self.on_list_change)
# Layout
vbox = QVBoxLayout()
vbox.addWidget(list_label)
# Buttons
if not no_buttons:
buttons = QWidget()
self.refine_button = QPushButton(self)
self.refine_button.setText('Refine')
#self.refine_button.clicked.connect(self.refine) # CONNECTS TO A PARENT
reload_btn = QPushButton(self)
reload_btn.setText('Reload')
reload_btn.clicked.connect(self.reload)
hbox1 = QHBoxLayout()
hbox1.addWidget(self.refine_button)
hbox1.addWidget(reload_btn)
buttons.setLayout(hbox1)
vbox.addWidget(buttons)
vbox.addWidget(self.abslist_widget)
self.setLayout(vbox)
def test_xabsgui():
# Init
spec_fil = data_path('UM184_nF.fits')
abs_sys = GenericAbsSystem((0., 0.), 3., [-500, 500] * u.km / u.s)
xabsgui = xabssysgui.XAbsSysGui(spec_fil, abs_sys)
class VelPlotWidget(QtGui.QWidget):
''' Widget for a velocity plot with interaction.
19-Dec-2014 by JXP
'''
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()
# Load them up for display
def init_lines(self):
wvmin = np.min(self.spec.dispersion)
wvmax = np.max(self.spec.dispersion)
#
wrest = self.llist[self.llist['List']].wrest
wvobs = (1 + self.z) * wrest
gdlin = np.where((wvobs > wvmin) & (wvobs < wvmax))[0]
self.llist['show_line'] = gdlin
# Update/generate lines [will not update]
for idx in gdlin:
self.generate_line((self.z, wrest[idx]))
def grab_line(self, wrest):
""" Grab a line from the list
Parameters
----------
wrest
Returns
-------
iline : AbsLine object
"""
awrest = [iline.wrest for iline in self.abs_lines]
try:
idx = awrest.index(wrest)
except ValueError:
return None
else:
return self.abs_lines[idx]
def generate_line(self, inp):
''' Generate a new line, if it doesn't exist
Parameters:
----------
inp: tuple
(z,wrest)
'''
# Generate?
if self.grab_line(inp[1]) is None:
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
newline = AbsLine(inp[1], linelist=self.llist[self.llist['List']])
print('VelPlot: Generating line {:g}'.format(inp[1]))
newline.analy['vlim'] = self.vmnx / 2.
newline.attrib['z'] = self.abs_sys.zabs
newline.analy['do_analysis'] = 1 # Init to ok
# Spec file
if self.spec_fil is not None:
newline.analy['datafile'] = self.spec_fil
# Append
self.abs_lines.append(newline)
def remove_line(self, wrest):
""" Remove a line, if it exists
Parameters
----------
wrest : Quantity
"""
awrest = [iline.wrest for iline in self.abs_lines]
try:
idx = awrest.index(wrest)
except ValueError:
return None
else:
_ = self.abs_lines.pop(idx)
# Key stroke
def on_key(self, event):
# Init
rescale = True
fig_clear = False
wrest = None
flg = 0
sv_idx = self.idx_line
## Change rows/columns
if event.key == 'k':
self.sub_xy[0] = max(0, self.sub_xy[0] - 1)
if event.key == 'K':
self.sub_xy[0] = self.sub_xy[0] + 1
if event.key == 'c':
self.sub_xy[1] = max(0, self.sub_xy[1] - 1)
if event.key == 'C':
self.sub_xy[1] = max(0, self.sub_xy[1] + 1)
## NAVIGATING
if event.key in self.psdict['nav']:
flg = ltgu.navigate(self.psdict, event)
if event.key == '-':
self.idx_line = max(0, self.idx_line -
self.sub_xy[0] * self.sub_xy[1]) # Min=0
if self.idx_line == sv_idx:
print('Edge of list')
if event.key == '=':
self.idx_line = min(
len(self.llist['show_line']) - self.sub_xy[0] * self.sub_xy[1],
self.idx_line + self.sub_xy[0] * self.sub_xy[1])
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
if self.idx_line == sv_idx:
print('Edge of list')
## Reset z
if event.key == 'z':
newz = ltu.z_from_v(self.z, event.xdata)
self.z = newz
self.abs_sys.zabs = newz
# Drawing
self.psdict['xmnx'] = self.vmnx.value
# Single line command
if event.key in [
'1', '2', 'B', 'U', 'L', 'N', 'V', 'A', 'x', 'X', '^', '&'
]:
try:
wrest = event.inaxes.get_gid()
except AttributeError:
return
else:
absline = self.grab_line(wrest)
kwrest = wrest.value
## Velocity limits
unit = u.km / u.s
if event.key == '1':
absline.analy['vlim'][0] = event.xdata * unit
if event.key == '2':
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
absline.analy['vlim'][1] = event.xdata * unit
if event.key == '!':
for iline in self.abs_sys.lines:
iline.analy['vlim'][0] = event.xdata * unit
if event.key == '@':
for iline in self.abs_sys.lines:
iline.analy['vlim'][1] = event.xdata * unit
## Line type
if event.key == 'A': # Add to lines
self.generate_line((self.z, wrest))
if event.key == 'x': # Remove line
if self.remove_line(wrest):
print('VelPlot: Removed line {:g}'.format(wrest))
if event.key == 'X': # Remove all lines
# Double check
gui = xguiu.WarningWidg(
'About to remove all lines. \n Continue??')
gui.exec_()
if gui.ans is False:
return
#
self.abs_lines = [] # Flush??
# Kinematics
if event.key == '^': # Low-Ion
try:
fkin = absline.analy['flag_kin']
except KeyError:
fkin = 0
fkin += (-1)**(fkin % 2**1 >= 2**0) * 2**0
absline.analy['flag_kin'] = fkin
if event.key == '&': # High-Ion
try:
fkin = absline.analy['flag_kin']
except KeyError:
fkin = 0
fkin += (-1)**(fkin % 2**2 >= 2**1) * 2**1
absline.analy['flag_kin'] = fkin
# Toggle blend
if event.key == 'B':
try:
feye = absline.analy['flg_eye']
except KeyError:
feye = 0
feye = (feye + 1) % 2
absline.analy['flg_eye'] = feye
# Toggle NG
if event.key == 'N':
try:
fanly = absline.analy['do_analysis']
except KeyError:
fanly = 1
if fanly == 0:
fanly = 1
else:
fanly = 0
absline.analy['do_analysis'] = fanly
if event.key == 'V': # Normal
absline.analy['flg_limit'] = 1
if event.key == 'L': # Lower limit
absline.analy['flg_limit'] = 2
if event.key == 'U': # Upper limit
absline.analy['flg_limit'] = 3
# AODM plot
if event.key == ':': #
# Grab good lines
from xastropy.xguis import spec_guis as xsgui
gdl = [
iline.wrest for iline in self.abs_sys.lines
if iline.analy['do_analysis'] > 0
]
# Launch AODM
if len(gdl) > 0:
gui = xsgui.XAODMGui(self.spec,
self.z,
gdl,
vmnx=self.vmnx,
norm=self.norm)
gui.exec_()
else:
print('VelPlot.AODM: No good lines to plot')
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
if not wrest is None: # Single window
flg = 3
if event.key in [
'c', 'C', 'k', 'K', 'W', '!', '@', '=', '-', 'X', 'z', 'R'
]: # Redraw all
flg = 1
if event.key in ['Y']:
rescale = False
if event.key in ['k', 'c', 'C', 'K', 'R']:
fig_clear = True
if flg == 1: # Default is not to redraw
self.on_draw(rescale=rescale, fig_clear=fig_clear)
elif flg == 2: # Layer (no clear)
self.on_draw(replot=False, rescale=rescale)
elif flg == 3: # Layer (no clear)
self.on_draw(in_wrest=wrest, rescale=rescale)
# Click of main mouse button
def on_click(self, event):
try:
print('button={:d}, x={:f}, y={:f}, xdata={:f}, ydata={:f}'.format(
event.button, event.x, event.y, event.xdata, event.ydata))
except ValueError:
return
if event.button == 1: # Draw line
self.ax.plot([event.xdata, event.xdata],
self.psdict['ymnx'],
':',
color='green')
self.on_draw(replot=False)
# Print values
try:
self.statusBar().showMessage('x,y = {:f}, {:f}'.format(
event.xdata, event.ydata))
except AttributeError:
return
def on_draw(self,
replot=True,
in_wrest=None,
rescale=True,
fig_clear=False):
""" Redraws the figure
"""
#
if replot is True:
if fig_clear:
self.fig.clf()
# Loop on windows
all_idx = self.llist['show_line']
nplt = self.sub_xy[0] * self.sub_xy[1]
if len(all_idx) <= nplt:
self.idx_line = 0
subp = np.arange(nplt) + 1
subp_idx = np.hstack(
subp.reshape(self.sub_xy[0], self.sub_xy[1]).T)
#print('idx_l={:d}, nplt={:d}, lall={:d}'.format(self.idx_line,nplt,len(all_idx)))
for jj in range(min(nplt, len(all_idx))):
try:
idx = all_idx[jj + self.idx_line]
except IndexError:
continue # Likely too few lines
#print('jj={:d}, idx={:d}'.format(jj,idx))
# Grab line
wrest = self.llist[self.llist['List']].wrest[idx]
kwrest = wrest.value # For the Dict
# Single window?
if in_wrest is not None:
if np.abs(wrest - in_wrest) > (1e-3 * u.AA):
continue
# Abs_Sys: Color the lines
if self.abs_sys is not None:
absline = self.grab_line(wrest)
# Generate plot
self.ax = self.fig.add_subplot(self.sub_xy[0], self.sub_xy[1],
subp_idx[jj])
self.ax.clear()
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
# Zero line
self.ax.plot([0., 0.], [-1e9, 1e9], ':', color='gray')
# Velocity
wvobs = (1 + self.z) * wrest
velo = (self.spec.dispersion / wvobs - 1.) * const.c.to('km/s')
# Plot
self.ax.plot(velo, self.spec.flux, 'k-', drawstyle='steps-mid')
# GID for referencing
self.ax.set_gid(wrest)
# Labels
#if jj >= (self.sub_xy[0]-1)*(self.sub_xy[1]):
if (((jj + 1) % self.sub_xy[0]) == 0) or ((jj + 1)
== len(all_idx)):
self.ax.set_xlabel('Relative Velocity (km/s)')
else:
self.ax.get_xaxis().set_ticks([])
lbl = self.llist[self.llist['List']].name[idx]
# Kinematics
kinl = ''
if absline is not None:
if (absline.analy['flag_kin'] % 2) >= 1:
kinl = kinl + 'L'
if (absline.analy['flag_kin'] % 4) >= 2:
kinl = kinl + 'H'
self.ax.text(0.1,
0.05,
lbl + kinl,
color='blue',
transform=self.ax.transAxes,
size='x-small',
ha='left')
# Reset window limits
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
self.ax.set_xlim(self.psdict['xmnx'])
# Rescale?
if (rescale is True) & (self.norm is False):
gdp = np.where((velo.value > self.psdict['xmnx'][0])
& (velo.value < self.psdict['xmnx'][1]))[0]
if len(gdp) > 5:
per = xstats.basic.perc(self.spec.flux[gdp])
self.ax.set_ylim((0., 1.1 * per[1]))
else:
self.ax.set_ylim(self.psdict['ymnx'])
else:
self.ax.set_ylim(self.psdict['ymnx'])
# Fonts
xputils.set_fontsize(self.ax, 6.)
clr = 'black'
if absline is not None:
try:
vlim = absline.analy['vlim']
except KeyError:
pass
# Color coding
try: # .clm style
flag = absline.analy['FLAGS'][0]
except KeyError:
flag = None
else:
if flag <= 1: # Standard detection
clr = 'green'
elif flag in [2, 3]:
clr = 'blue'
elif flag in [4, 5]:
clr = 'purple'
# ABS ID
try: # NG?
flagA = absline.analy['do_analysis']
except KeyError:
flagA = None
else:
if (flagA > 0) & (clr == 'black'):
clr = 'green'
try: # Limit?
flagL = absline.analy['flg_limit']
except KeyError:
flagL = None
else:
if flagL == 2:
clr = 'blue'
if flagL == 3:
clr = 'purple'
try: # Blends?
flagE = absline.analy['flg_eye']
except KeyError:
flagE = None
else:
if flagE == 1:
clr = 'orange'
if flagA == 0:
clr = 'red'
pix = np.where((velo > vlim[0]) & (velo < vlim[1]))[0]
self.ax.plot(velo[pix],
self.spec.flux[pix],
'-',
drawstyle='steps-mid',
color=clr)
# Draw
self.canvas.draw()
def main(*args, **kwargs):
""" Runs the XAbsSysGui on input files
"""
import argparse
parser = argparse.ArgumentParser(description='Parse for XAbsSys')
parser.add_argument("spec_file", type=str, help="Spectral file")
parser.add_argument("abssys_file", type=str, help="AbsSys file (JSON)")
parser.add_argument("-outfile", type=str, help="Output filename")
parser.add_argument("-llist", type=str, help="Name of LineList")
#parser.add_argument("-exten", type=int, help="FITS extension")
parser.add_argument("--specdb",
help="Spectral file is a SPECDB database",
action="store_true")
parser.add_argument("--group", type=str, help="SPECDB group name")
parser.add_argument("--un_norm",
help="Spectrum is NOT normalized",
action="store_true")
parser.add_argument(
"--chk_z",
help="Check the z limits of your components? [default=False]",
action="store_true")
pargs = parser.parse_args()
from PyQt5.QtWidgets import QApplication
from linetools.guis.xabssysgui import XAbsSysGui
from linetools.isgm.io import abssys_from_json
from IPython import embed
# Normalized?
norm = True
if pargs.un_norm:
norm = False
# Extension
#exten = (pargs.exten if hasattr(pargs, 'exten') else 0)
# Read spec keywords
rsp_kwargs = {}
# Line list
if pargs.llist is not None:
from linetools.lists.linelist import LineList
llist = LineList(pargs.llist)
else:
llist = None
# Read AbsSystem
from linetools.isgm.abssystem import GenericAbsSystem
abs_sys = GenericAbsSystem.from_json(pargs.abssys_file) #, chk_vel=False)
if not pargs.chk_z:
warnings.warn(
"Not checking your system's velocity limits. This is the Default but be so warned."
)
abs_sys = GenericAbsSystem.from_json(pargs.abssys_file, chk_z=pargs.chk_z)
if len(abs_sys.list_of_abslines()) == 0:
warnings.warn(
"No absorption lines given. I hope you intended that to be the case!"
)
app = QApplication(sys.argv)
# Load spectrum using specdb?
if pargs.specdb:
# Instantiate
from specdb.specdb import SpecDB
from specdb import group_utils
sdb = SpecDB(db_file=pargs.spec_file)
# Grab spectrum
if pargs.group is not None:
groups = [pargs.group]
else:
groups = None
spec, meta = sdb.spectra_from_coord(abs_sys.coord, groups=groups)
if spec.nspec > 1:
group_utils.show_group_meta(meta,
idkey=sdb.idkey,
show_all_keys=False)
raise ValueError(
"Retreived more than 1 spectrum. Choose your GROUP with --group="
)
spec_file = pargs.spec_file + '_{:s}'.format(meta['GROUP'][0])
else:
spec = pargs.spec_file
spec_file = pargs.spec_file
# Save spectrum filename to AbsSystem
abs_sys.spec_file = spec_file
# Run
gui = XAbsSysGui(spec,
abs_sys,
norm=norm,
llist=llist,
outfil=pargs.outfile)
gui.show()
app.exec_()
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()
