def test_clean_duplicates():
field = ('PG1407+265', 212.349634 * u.deg, 26.3058650 * u.deg)
lfield = IgmGalaxyField((field[1], field[2]), name=field[0], verbose=False)
targets = create_fake_target_table()
new_target = lfield.clean_duplicates(targets)
np.testing.assert_allclose(new_target['TARG_RA'], np.arange(0, 10, 1))
def test_clean_duplicates():
field = ('PG1407+265', 212.349634*u.deg, 26.3058650*u.deg)
lfield = IgmGalaxyField((field[1],field[2]), name=field[0], verbose=False)
targets = create_fake_target_table()
new_target = lfield.clean_duplicates(targets)
np.testing.assert_allclose(new_target['TARG_RA'], np.arange(0,10,1))
def __init__(self, radec, igal_rand=10, iabs_rand=100, proper=False, field_name='',
wrapped=True, cosmo=None, **kwargs):
IgmGalaxyField.__init__(self, radec, **kwargs)
self.igal_rand = igal_rand
self.iabs_rand = iabs_rand
self.absreal = None # absreal # np rec array with absorber properties (single ion)
self.absrand = None
# Cosmology
if cosmo is None:
cosmo = Planck15
self.cosmo = cosmo
# Central coordiantes
self.CRA = self.coord.ra.value #np.mean(self.absreal.RA)
self.CDEC = self.coord.dec.value # np.mean(self.absreal.DEC)
if len(field_name) == 0:
self.name = ltu.name_from_coord(self.coord)
else:
self.name = field_name
self.proper = proper
self.wrapped = wrapped
self.galreal = None # Filled with addGal
self.absreal = None # Filled with addAbs
self.ion = None
def test_calc_rho():
field = ('PG1407+265', 212.349634 * u.deg, 26.3058650 * u.deg)
lfield = IgmGalaxyField((field[1], field[2]), name=field[0], verbose=False)
# Objects
obj = dict(RA=np.array([212.349634] * 3),
DEC=np.array([26.3057] * 3),
Z=np.array([0.1, 0.2, 0.3]))
rho = lfield.calc_rhoimpact(obj)
np.isclose(rho[0].value, 1.244429196296971)
def load_field(field):
''' Load up CASBAH data for a given field
Parameters:
-----------
field: tuple
(Name, ra, dec)
Returns:
--------
lfield:
Loaded IgmGalaxyField class
'''
reload(xcasbahu)
lfield = IgmGalaxyField((field[1],field[2]), name=field[0])
# Load targets
targ_file = xcasbahu.get_filename(field,'TARGETS')
lfield.targets = Table.read(targ_file,delimiter='|',
format='ascii.fixed_width',
fill_values=[('--','0','MASK_NAME')])
# Load observing details for multi-object follow-up
obs_file = xcasbahu.get_filename(field,'MULTI_OBJ')
lfield.observing = Table.read(obs_file,delimiter='|',
format='ascii.fixed_width',
fill_values=[('--','0','DATE_OBS','TEXP')])
lfield.observing = Table(lfield.observing,masked=True) # Insist on Masked
# Load galaxies
sdss_file = xcasbahu.get_filename(field,'SDSS')
sdss_tab = Table.read(sdss_file)
# VSTACK
hectospec_file = xcasbahu.get_filename(field,'HECTOSPEC')
lfield.galaxies = sdss_tab
# Return
return lfield
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 load_field(field):
''' Load up CASBAH data for a given field
Parameters:
-----------
field: tuple
(Name, ra, dec)
Returns:
--------
lfield:
Loaded IgmGalaxyField class
'''
reload(xcasbahu)
lfield = IgmGalaxyField((field[1], field[2]), name=field[0])
# Load targets
targ_file = xcasbahu.get_filename(field, 'TARGETS')
lfield.targets = Table.read(targ_file,
delimiter='|',
format='ascii.fixed_width',
fill_values=[('--', '0', 'MASK_NAME')])
# Load observing details for multi-object follow-up
obs_file = xcasbahu.get_filename(field, 'MULTI_OBJ')
lfield.observing = Table.read(obs_file,
delimiter='|',
format='ascii.fixed_width',
fill_values=[('--', '0', 'DATE_OBS', 'TEXP')
])
lfield.observing = Table(lfield.observing, masked=True) # Insist on Masked
# Load galaxies
sdss_file = xcasbahu.get_filename(field, 'SDSS')
sdss_tab = Table.read(sdss_file)
# VSTACK
hectospec_file = xcasbahu.get_filename(field, 'HECTOSPEC')
lfield.galaxies = sdss_tab
# Return
return lfield
def test_init():
field = ('PG1407+265', 212.349634 * u.deg, 26.3058650 * u.deg)
lfield = IgmGalaxyField((field[1], field[2]), name=field[0], verbose=True)
print(lfield)