def test_build_components_from_lines():
# Lines
abscomp,HIlines = mk_comp('HI')
abscomp,SiIIlines = mk_comp('SiII', vlim=[-250,80.]*u.km/u.s, add_spec=True)
# Components
comps = ltiu.build_components_from_abslines([HIlines[0],HIlines[1],SiIIlines[0],SiIIlines[1]])
assert len(comps) == 2
def test_build_components_from_lines():
# Lines
abscomp, HIlines = mk_comp('HI')
abscomp, SiIIlines = mk_comp('SiII',
vlim=[-250, 80.] * u.km / u.s,
add_spec=True)
# Components
comps = ltiu.build_components_from_abslines(
[HIlines[0], HIlines[1], SiIIlines[0], SiIIlines[1]])
assert len(comps) == 2
def write_out(self):
# Add components
comps = ltiu.build_components_from_abslines(self.vplt_widg.abs_lines)
self.vplt_widg.abs_sys._components = comps
# Dict
adict = self.vplt_widg.abs_sys.to_dict()
with io.open(self.outfil, 'w', encoding='utf-8') as f:
f.write(unicode(json.dumps(adict, sort_keys=True, indent=4,
separators=(',', ': '))))
def from_abslines(cls, abslines, vlim=None, **kwargs):
"""Instantiate from a list of AbsLines
Parameters
----------
components : list
List of AbsComponent objects
"""
# Generate components
components = ltiu.build_components_from_abslines(abslines, **kwargs)
# Instantiate
slf = cls.from_components(components, vlim=vlim)
# Return
return slf
def set_new_comps(self):
""" Generate new components and fill into abs_sys
Ignores velocity limits when building
"""
# Add spectrum filename, coord
abs_lines = self.vplt_widg.abs_lines
for line in abs_lines:
line.analy['datafile'] = self.vplt_widg.spec_fil
line.attrib['coord'] = self.abs_sys.coord
# Components
comps = ltiu.build_components_from_abslines(abs_lines, chk_vel=False)
self.abs_sys._components = comps
# Return
return
def from_abslines(cls, abslines, vlim=None, **kwargs):
"""Instantiate from a list of AbsLines
Parameters
----------
components : list
List of AbsComponent objects
"""
# Generate components
components = ltiu.build_components_from_abslines(abslines, **kwargs)
# Instantiate
slf = cls.from_components(components, vlim=vlim)
# Return
return slf
def write_out(self):
# Generate components
comps = ltiu.build_components_from_abslines(self.vplt_widg.abs_lines, chk_vel=False)
self.vplt_widg.abs_sys._components = comps
# Dict
adict = self.vplt_widg.abs_sys.to_dict()
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
print("Wrote abs_sys to {:s}".format(self.outfil))
with io.open(self.outfil, 'w', encoding='utf-8') as f:
f.write(json.dumps(adict, sort_keys=True, indent=4,
separators=(',', ': ')))
def set_new_comps(self):
""" Generate new components and fill into abs_sys
Ignores velocity limits when building
"""
# Add spectrum filename, coord
abs_lines = self.vplt_widg.abs_lines
for line in abs_lines:
line.analy['datafile'] = self.vplt_widg.spec_fil
line.attrib['coord'] = self.abs_sys.coord
# Components
comps = ltiu.build_components_from_abslines(abs_lines, chk_vel=False)
self.abs_sys._components = comps
# Return
return
def write_out(self):
# Generate components
comps = ltiu.build_components_from_abslines(self.vplt_widg.abs_lines,
chk_vel=False)
self.vplt_widg.abs_sys._components = comps
# Dict
adict = self.vplt_widg.abs_sys.to_dict()
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
print("Wrote abs_sys to {:s}".format(self.outfil))
with io.open(self.outfil, 'w', encoding='utf-8') as f:
f.write(
json.dumps(adict,
sort_keys=True,
indent=4,
separators=(',', ': ')))
def add_DLA(self,
z,
NHI=20.3,
bval=30. * u.km / u.s,
comment='None',
model=True):
"""Generate a new DLA
"""
# Lya, Lyb
dla_lines = [] # For convenience
for trans in ['HI 1025', 'HI 1215']:
iline = AbsLine(trans, z=z)
iline.attrib['flag_N'] = 1
iline.attrib['N'] = 10**NHI / u.cm**2
iline.attrib['sig_N'] = 1 / u.cm**2 # Avoid nan
iline.attrib['b'] = bval
iline.attrib['coord'] = SkyCoord(ra=0 * u.deg, dec=0 * u.deg)
dla_lines.append(iline)
# Generate system
HIcomponent = ltiu.build_components_from_abslines(dla_lines)[0]
HIcomponent.synthesize_colm()
new_sys = DLASystem.from_components([HIcomponent
]) #(0*u.deg,0*u.deg),z,None,NHI)
#QtCore.pyqtRemoveInputHook()
#import pdb; pdb.set_trace()
#QtCore.pyqtRestoreInputHook()
new_sys.bval = bval # This is not standard, but for convenience
new_sys.comment = comment
new_sys.dla_lines = dla_lines # Also for convenience
# Name
self.count_dla += 1
new_sys.label = 'DLA_Sys_{:d}'.format(self.count_dla)
# Add
self.abssys_widg.add_fil(new_sys.label)
self.abssys_widg.all_abssys.append(new_sys)
self.abssys_widg.abslist_widget.item(len(
self.abssys_widg.all_abssys)).setSelected(True)
# Update
self.llist['Plot'] = False # Turn off metal-lines
if model: # For dealing with initialization
self.update_model()
def load_coolgas(self):
""" Load data on cool gas (CII, CIV, SiII, SiIII)
Richter+17
"""
llist = LineList('ISM')
# Ricther+17
print('Loading Richter+17 for CII, CIV, SiII, SiIII')
r17_a1_file = resource_filename('pyigm',
'/data/CGM/Galaxy/richter17_A1.fits')
r17_a1 = Table.read(r17_a1_file)
r17_a2_file = resource_filename('pyigm',
'/data/CGM/Galaxy/richter17_A2.fits')
r17_a2 = Table.read(r17_a2_file)
# Coords
coords = SkyCoord(ra=r17_a1['_RAJ2000'],
dec=r17_a1['_DEJ2000'],
unit='deg')
gc = coords.transform_to('galactic')
ra = np.zeros((len(r17_a2)))
dec = np.zeros((len(r17_a2)))
# Loop on Sightlines
for kk, row in enumerate(r17_a1):
if self.debug and (kk == 5):
break
a2_idx = np.where(r17_a2['Name'] == row['Name'])[0]
if len(a2_idx) == 0:
continue
ra[a2_idx] = row['_RAJ2000']
dec[a2_idx] = row['_DEJ2000']
# Generate the components
icoord = gc[kk]
alines = []
for jj, idx in enumerate(a2_idx):
# Transition
trans = '{:s} {:d}'.format(r17_a2['Ion'][idx].strip(),
int(r17_a2['lambda0'][idx]))
try:
aline = AbsLine(trans, linelist=llist)
except ValueError:
pdb.set_trace()
aline.attrib['coord'] = icoord
# Skip EW=0 lines
if r17_a2['e_W'][idx] == 0:
continue
# Velocity
z = 0.
aline.setz(z)
vlim = np.array([r17_a2['vmin'][idx], r17_a2['vmax'][idx]
]) * u.km / u.s
aline.limits.set(vlim) # These are v_LSR
# EW
aline.attrib['flag_EW'] = 1
aline.attrib['EW'] = r17_a2['W'][idx] / 1e3 * u.AA
aline.attrib['sig_EW'] = r17_a2['e_W'][idx] / 1e3 * u.AA
# Column
if np.isnan(
r17_a2['logN']
[idx]): # Odd that some lines had an error but no value
aline.attrib['flag_N'] = 0
elif r17_a2['l_logN'][idx] == '>':
aline.attrib['flag_N'] = 2
aline.attrib['sig_logN'] = 99.99
else:
aline.attrib['flag_N'] = 1
aline.attrib['sig_logN'] = r17_a2['e_logN'][idx]
aline.attrib['logN'] = r17_a2['logN'][idx]
# Fill linear
_, _ = linear_clm(aline.attrib)
alines.append(aline)
# Generate components from abslines
comps = ltiu.build_components_from_abslines(alines,
chk_sep=False,
chk_vel=False)
# Limits
vmin = np.min([icomp.limits.vmin.value for icomp in comps])
vmax = np.max([icomp.limits.vmax.value for icomp in comps])
# Instantiate
s_kwargs = dict(name=row['Name'] + '_z0')
c_kwargs = dict(chk_sep=False, chk_z=False)
abssys = IGMSystem.from_components(comps,
vlim=[vmin, vmax] * u.km / u.s,
s_kwargs=s_kwargs,
c_kwargs=c_kwargs)
# CGM Abs
rho, ang_sep = calc_Galactic_rho(abssys.coord)
cgmabs = CGMAbsSys(self.galaxy,
abssys,
rho=rho,
ang_sep=ang_sep,
cosmo=self.cosmo)
# Add to cgm_abs
self.abs.cgm_abs.append(cgmabs)
# Finish
r17_a2['RA'] = ra
r17_a2['DEC'] = dec
self.richter17 = r17_a2
# Reference
if len(self.refs) > 0:
self.refs += ','
self.refs += 'Richter+17'