def test_cgmsurvey_from_fields_sightlines():
# Instantiate fields and add galaxies
field1 = ('PG1407+265', 212.349634 * u.deg, 26.3058650 * u.deg)
fieldobj1 = IgmGalaxyField((field1[1], field1[2]),
name=field1[0],
verbose=False)
field2 = ('PG1148+549', 177.83526042 * u.deg, 54.625855 * u.deg)
fieldobj2 = IgmGalaxyField((field2[1], field2[2]),
name=field2[0],
verbose=False)
f1ras = [212.33310891, 212.329875] * u.deg
f1decs = [26.3722716934, 26.3084391667] * u.deg
f1zs = [0.974413514137, 0.22016787529]
f1gals = Table([f1ras, f1decs, f1zs], names=['RA', 'DEC', 'Z'])
f2ras = [177.835229336, 178.536958333] * u.deg
f2decs = [54.625851084, 54.6176108333] * u.deg
f2zs = [0.0595485754311, 0.00385531364009]
f2gals = Table([f2ras, f2decs, f2zs], names=['RA', 'DEC', 'Z'])
fieldobj1.galaxies = f1gals
fieldobj2.galaxies = f2gals
fields = [fieldobj1, fieldobj2]
# Instantiate sightlines
sl1coord = SkyCoord(field1[1], field1[2], unit='deg')
sl2coord = SkyCoord(field2[1], field2[2], unit='deg')
comp11 = AbsComponent(sl1coord, (8, 6), 0.9743, [-200, 200] * u.km / u.s)
comp12 = AbsComponent(sl1coord, (1, 1), 0.9743, [-200, 200] * u.km / u.s)
al11 = AbsLine('OVI 1031')
al11.attrib['coord'] = sl1coord
al11.analy['spec'] = 'files/J0042-1037.358_9.fits.gz'
al12 = AbsLine('HI 1215')
al12.attrib['coord'] = sl1coord
al12.analy['spec'] = 'files/J0042-1037.358_9.fits.gz'
comp11.add_absline(al11, chk_sep=False, chk_vel=False)
comp12.add_absline(al12, chk_sep=False, chk_vel=False)
sys1 = IGMSystem.from_components([comp11, comp12])
sl1 = IGMSightline.from_systems([sys1])
comp21 = AbsComponent(sl2coord, (6, 4), 0.0037, [-200, 200] * u.km / u.s)
comp22 = AbsComponent(sl2coord, (1, 1), 0.0037, [-200, 200] * u.km / u.s)
al21 = AbsLine('CIV 1548')
al21.attrib['coord'] = sl1coord
al21.analy['spec'] = 'files/J0042-1037.358_9.fits.gz'
al22 = AbsLine('HI 1215')
al22.attrib['coord'] = sl1coord
al22.analy['spec'] = 'files/J0042-1037.358_9.fits.gz'
comp21.add_absline(al21, chk_sep=False, chk_vel=False)
comp22.add_absline(al22, chk_sep=False, chk_vel=False)
sys2 = IGMSystem.from_components([comp21, comp22])
sl2 = IGMSightline.from_systems([sys2])
sightlines = [sl1, sl2]
# Run function
csurvey = cgmsurvey_from_sightlines_fields(fields, sightlines)
assert isinstance(csurvey, CGMAbsSurvey)
def cgm_from_galaxy_igmsystems(galaxy,
igmsystems,
rho_max=300 * u.kpc,
dv_max=400 * u.km / u.s,
cosmo=None,
dummysys=False,
dummyspec=None,
verbose=True,
**kwargs):
""" Generate a list of CGMAbsSys objects given an input galaxy and a list of IGMSystems
Parameters
----------
galaxy : Galaxy
igmsystems : list
list of IGMSystems
rho_max : Quantity
Maximum projected separation from sightline to galaxy
dv_max
Maximum velocity offset between system and galaxy
dummysys: bool, optional
If True, instantiate CGMAbsSys even if no match is found in igmsystems
dummyspec : XSpectrum1D, optional
Spectrum object to attach to dummy AbsLine/AbsComponent objects when
adding IGMSystems if dummysys is True.
Returns
-------
cgm_list : list
list of CGM objects generated
"""
from pyigm.cgm.cgm import CGMAbsSys
# Cosmology
if cosmo is None:
cosmo = cosmology.Planck15
if dummysys is True:
if dummyspec is None:
dummyspec = igmsystems[0]._components[0]._abslines[0].analy['spec']
dummycoords = igmsystems[0].coord
# R -- speed things up
rho, angles = calc_cgm_rho(galaxy, igmsystems, cosmo, **kwargs)
if len(igmsystems) == 1: # Kludge
rho = u.Quantity([rho])
angles = u.Quantity([angles])
# dv
igm_z = np.array([igmsystem.zabs for igmsystem in igmsystems])
dv = ltu.dv_from_z(igm_z, galaxy.z)
# Rules
match = np.where((rho < rho_max) & (np.abs(dv) < dv_max))[0]
### If none, see if some system has a component that's actually within dv_max
if (len(match) == 0) & (rho[0] < rho_max):
zcomps = []
sysidxs = []
for i, csys in enumerate(igmsystems):
thesezs = [comp.zcomp for comp in csys._components]
sysidxs.extend([i] * len(thesezs))
zcomps.extend(thesezs)
zcomps = np.array(zcomps)
sysidxs = np.array(sysidxs)
dv_comps = ltu.dv_from_z(zcomps, galaxy.z)
match = np.unique(sysidxs[np.where(np.abs(dv_comps) < dv_max)[0]])
if len(match) == 0:
if dummysys is False:
print(
"No IGMSystem paired to this galaxy. CGM object not created.")
return []
else:
if verbose:
print("No IGMSystem match found. Attaching dummy IGMSystem.")
dummysystem = IGMSystem(dummycoords, galaxy.z, vlim=None)
dummycomp = AbsComponent(dummycoords, (1, 1), galaxy.z,
[-100., 100.] * u.km / u.s)
dummycomp.flag_N = 3
dummyline = AbsLine(
'HI 1215',
**kwargs) # Need an actual transition for comp check
dummyline.analy['spec'] = dummyspec
dummyline.attrib['coord'] = dummycoords
dummycomp.add_absline(dummyline, chk_vel=False, chk_sep=False)
dummysystem.add_component(dummycomp, chk_vel=False, chk_sep=False)
cgm = CGMAbsSys(galaxy, dummysystem, cosmo=cosmo, **kwargs)
cgm_list = [cgm]
else:
# Loop to generate
cgm_list = []
for imatch in match:
# Instantiate new IGMSystem
# Otherwise, updates to the IGMSystem cross-pollinate other CGMs
sysmatch = igmsystems[imatch]
newisys = sysmatch.copy()
# Handle z limits
zlim = ltu.z_from_dv((-dv_max.value, dv_max.value) * u.km / u.s,
galaxy.z)
newlims = zLimits(galaxy.z, zlim.tolist())
newisys.limits = newlims
# Allow for components extending beyond dv_max
newisys.update_vlim()
newisys.update_component_vel()
# Finish
cgm = CGMAbsSys(galaxy,
newisys,
cosmo=cosmo,
rho=rho[imatch],
ang_sep=angles[imatch],
**kwargs)
cgm_list.append(cgm)
# Return
return cgm_list
