def test_fromtodict():
SiIIcomp1,_ = mk_comp('SiII',vlim=[-300.,50.]*u.km/u.s, add_spec=True)
cdict = SiIIcomp1.to_dict()
#
assert isinstance(cdict, dict)
assert cdict['Zion'] == (14, 2)
# And instantiate
newcomp = AbsComponent.from_dict(cdict)
assert isinstance(newcomp, AbsComponent)
newcomp = AbsComponent.from_dict(cdict, coord=SkyCoord(0,0, unit='deg'))
def test_fromtodict():
SiIIcomp1, _ = mk_comp('SiII',
vlim=[-300., 50.] * u.km / u.s,
add_spec=True)
cdict = SiIIcomp1.to_dict()
#
assert isinstance(cdict, dict)
assert cdict['Zion'] == (14, 2)
# And instantiate
newcomp = AbsComponent.from_dict(cdict)
assert isinstance(newcomp, AbsComponent)
newcomp = AbsComponent.from_dict(cdict, coord=SkyCoord(0, 0, unit='deg'))
def complist_from_igmgjson(igmguesses_json):
"""Creates a list of AbsComponenbts from a igmguesses_json file
Parameters
----------
igmguesses_json : str
Name of the json file genereted by IGMGUESSES
Returns
-------
comp_list : list of AbsComponents
A list of AbsComponents
"""
return ltiio.read_igmg_to_components(igmguesses_json, linelist='ISM')
# Read the JSON file
with open(igmguesses_json) as data_file:
igmg_dict = json.load(data_file)
# Components
comp_list = []
for ii, key in enumerate(igmg_dict['cmps'].keys()):
comp_dict = igmg_dict['cmps'][key]
comp_dict['flag_N'] = 1
comp_dict['logN'] = comp_dict['Nfit']
comp_dict['sig_logN'] = -1
# import pdb; pdb.set_trace()
try:
comp = AbsComponent.from_dict(comp_dict,
chk_sep=False,
chk_data=False,
chk_vel=False,
linelist="ISM")
except:
comp = AbsComponent.from_dict(comp_dict,
chk_sep=False,
chk_data=False,
chk_vel=False,
linelist='H2')
# add extra attributes manually
comp.attrib['b'] = comp_dict['bfit']
comp.attrib['sig_b'] = -1
comp.attrib['reliability'] = comp_dict['Reliability']
comp_list += [comp]
return comp_list
def json_eqw(json_file, fits_file, outfile, overwrite=False):
ion_name = []
restwave = []
col = []
col_err = []
flag = []
zcomp = []
if not os.path.isfile(json_file):
return np.array(ion_name), np.array(restwave), np.array(col), \
np.array(col_err), np.array(flag), np.array(zcomp)
if not os.path.isfile(outfile) or overwrite == True:
out = open(outfile, 'w')
out.write('#ion_name, restwave, logN, logN_err, flag_N, zcomp\n')
with open(json_file) as data_file:
igmg_dict = json.load(data_file)
comp_list = []
for ii, key in enumerate(igmg_dict['cmps'].keys()):
comp = AbsComponent.from_dict(igmg_dict['cmps'][key],
chk_sep=False,
chk_data=False,
chk_vel=False)
comp_list += [comp]
spec = readspec(fits_file)
for i, cc in enumerate(comp_list):
for j, al in enumerate(cc._abslines):
al.analy['spec'] = spec
al.measure_ew()
al.measure_aodm()
ion_name.append(al.ion_name)
restwave.append(al.wrest.value)
col.append(al.attrib['logN'])
sig_logN = al.attrib['sig_logN']
if np.isnan(sig_logN):
sig_logN = 0.0
col_err.append(sig_logN)
flag.append(al.attrib['flag_N'])
zcomp.append(al.z)
out.write('%s\t%f\t%e\t%e\t%d\t%0.6f\n'%(al.ion_name, al.wrest.value, \
al.attrib['logN'], sig_logN, al.attrib['flag_N'], al.z))
out.close()
if os.path.isfile(outfile) and len(open(outfile).readlines()) > 1:
ion_name = np.loadtxt(outfile,
unpack=True,
skiprows=1,
usecols=0,
dtype='str')
restwave, col, col_err, flag, zcomp = \
np.loadtxt(outfile, unpack = True, skiprows = 1, usecols = (1, 2, 3, 4, 5))
return np.array(ion_name), np.array(restwave), np.array(col), np.array(
col_err), np.array(flag), np.array(zcomp)
def complist_from_igmgjson(igmguesses_json):
"""Creates a list of AbsComponenbts from a igmguesses_json file
Parameters
----------
igmguesses_json : str
Name of the json file genereted by IGMGUESSES
Returns
-------
comp_list : list of AbsComponents
A list of AbsComponents
"""
return ltiio.read_igmg_to_components(igmguesses_json, linelist='ISM')
# Read the JSON file
with open(igmguesses_json) as data_file:
igmg_dict = json.load(data_file)
# Components
comp_list = []
for ii, key in enumerate(igmg_dict['cmps'].keys()):
comp_dict = igmg_dict['cmps'][key]
comp_dict['flag_N'] = 1
comp_dict['logN'] = comp_dict['Nfit']
comp_dict['sig_logN'] = -1
# import pdb; pdb.set_trace()
try:
comp = AbsComponent.from_dict(comp_dict, chk_sep=False, chk_data=False, chk_vel=False, linelist="ISM")
except:
comp = AbsComponent.from_dict(comp_dict, chk_sep=False, chk_data=False, chk_vel=False, linelist='H2')
# add extra attributes manually
comp.attrib['b'] = comp_dict['bfit']
comp.attrib['sig_b'] = -1
comp.attrib['reliability'] = comp_dict['Reliability']
comp_list += [comp]
return comp_list
def build_components_from_dict(idict, coord=None, **kwargs):
""" Generate a list of components from an input dict
Parameters
----------
idict : dict
Must contain either components or lines as a key
coord : SkyCoord, optional
Returns
-------
components :
list of AbsComponent objects
Sorted by zcomp
"""
from linetools.spectralline import AbsLine
components = []
if 'components' in idict.keys():
# Components
for key in idict['components']:
components.append(
AbsComponent.from_dict(idict['components'][key],
coord=coord,
**kwargs))
elif 'lines' in idict.keys(): # to be deprecated
lines = []
for key in idict['lines']:
if isinstance(idict['lines'][key], AbsLine):
line = idict['lines'][key]
elif isinstance(idict['lines'][key], dict):
line = AbsLine.from_dict(idict['lines'][key],
coord=coord,
**kwargs)
else:
raise IOError("Need those lines")
if coord is not None:
line.attrib['coord'] = coord
lines.append(line)
components = build_components_from_abslines(lines, **kwargs)
else:
warnings.warn("No components in this dict")
# Sort by z -- Deals with dict keys being random
z = [comp.zcomp for comp in components]
isrt = np.argsort(np.array(z))
srt_comps = list(np.array(components)[isrt])
# Return
return srt_comps
def build_components_from_dict(idict, coord=None, **kwargs):
""" Generate a list of components from an input dict
Parameters
----------
idict : dict
Must contain either components or lines as a key
coord : SkyCoord, optional
Returns
-------
components :
list of AbsComponent objects
Sorted by zcomp
"""
from linetools.spectralline import AbsLine
components = []
if 'components' in idict.keys():
# Components
for key in idict['components']:
components.append(AbsComponent.from_dict(idict['components'][key], coord=coord, **kwargs))
elif 'lines' in idict.keys(): # to be deprecated
lines = []
for key in idict['lines']:
if isinstance(idict['lines'][key], AbsLine):
line = idict['lines'][key]
elif isinstance(idict['lines'][key], dict):
line = AbsLine.from_dict(idict['lines'][key], coord=coord)
else:
raise IOError("Need those lines")
if coord is not None:
line.attrib['coord'] = coord
lines.append(line)
components = build_components_from_abslines(lines, **kwargs)
else:
warnings.warn("No components in this dict")
# Sort by z -- Deals with dict keys being random
z = [comp.zcomp for comp in components]
isrt = np.argsort(np.array(z))
srt_comps = []
for idx in isrt:
srt_comps.append(components[idx])
# Return
return srt_comps
def from_igmguesses_to_complist(infile):
"""Reads .json file generated by IGMGuesses and return a list of AbsComponent objects
Parameters
----------
infile : str
Name of the .json file from IGMGuesses
Returns:
complist : list of AbsComponent
"""
import json
# Read the JSON file
with open(infile) as data_file:
igmg_dict = json.load(data_file)
# Components
comp_list = []
for ii, key in enumerate(igmg_dict['cmps'].keys()):
# QtCore.pyqtRemoveInputHook()
# pdb.set_trace()
# QtCore.pyqtRestoreInputHook()
# import pdb; pdb.set_trace()
idict = igmg_dict['cmps'][key]
idict['logN'] = idict['attrib']['logN']
try:
idict['flag_N'] = idict['attrib']['flag_N']
except:
idict['flag_N'] = 0.
try:
idict['sig_logN'] = idict['attrib']['sig_logN']
except:
idict['sig_logN'] = 0.
comp = AbsComponent.from_dict(idict,
skip_abslines=False,
chk_sep=False,
chk_data=False,
chk_vel=False)
comp_list += [comp]
return comp_list
def build_components_from_dict(idict, coord=None, **kwargs):
""" Generate a list of components from an input dict
Parameters
----------
idict : dict
Must contain either components or lines as a key
coord : SkyCoord, optional
Returns
-------
components :
list of AbsComponent objects
"""
from linetools.spectralline import AbsLine
components = []
if 'components' in idict.keys():
# Components
for key in idict['components']:
components.append(AbsComponent.from_dict(idict['components'][key]))
elif 'lines' in idict.keys(): # to be deprecated
lines = []
for key in idict['lines']:
if isinstance(idict['lines'][key], AbsLine):
line = idict['lines'][key]
elif isinstance(idict['lines'][key], dict):
line = AbsLine.from_dict(idict['lines'][key])
else:
raise IOError("Need those lines")
if coord is not None:
line.attrib['coord'] = coord
lines.append(line)
components = build_components_from_abslines(lines, **kwargs)
else:
warnings.warn("No components in this dict")
# Return
return components
def from_igmguesses_to_complist(infile):
"""Reads .json file generated by IGMGuesses and return a list of AbsComponent objects
Parameters
----------
infile : str
Name of the .json file from IGMGuesses
Returns:
complist : list of AbsComponent
"""
import json
# Read the JSON file
with open(infile) as data_file:
igmg_dict = json.load(data_file)
# Components
comp_list = []
for ii, key in enumerate(igmg_dict['cmps'].keys()):
# QtCore.pyqtRemoveInputHook()
# pdb.set_trace()
# QtCore.pyqtRestoreInputHook()
# import pdb; pdb.set_trace()
idict = igmg_dict['cmps'][key]
idict['logN'] = idict['attrib']['logN']
try:
idict['flag_N'] = idict['attrib']['flag_N']
except:
idict['flag_N'] = 0.
try:
idict['sig_logN'] = idict['attrib']['sig_logN']
except:
idict['sig_logN'] = 0.
comp = AbsComponent.from_dict(idict, skip_abslines=False, chk_sep=False, chk_data=False, chk_vel=False)
comp_list += [comp]
return comp_list
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()
