def test_name_from_coord():
coord = SkyCoord(ra=15.4, dec=-23.1, unit='deg')
name = ltu.name_from_coord(coord)
assert name == 'J010136.00-230600.0'
# Name 2
name2 = ltu.name_from_coord(coord, precision=(0, 0))
assert name2 == 'J010136-230600'
def test_name_from_coord():
coord = SkyCoord(ra=15.4, dec=-23.1, unit='deg')
name = ltu.name_from_coord(coord)
assert name == 'J010136.00-230600.0'
# Name 2
name2 = ltu.name_from_coord(coord, precision=(0, 0))
assert name2 == 'J010136-230600'
def main(pargs):
""" Run
"""
import json
from linetools import utils as ltu
from frb import frb
# Load
frb_name = pargs.frb_name if pargs.frb_name[:3].upper() == 'FRB' else 'FRB'+pargs.frb_name
try:
FRB = frb.FRB.by_name(frb_name.upper())
except FileNotFoundError:
print("Your desired FRB is not in this Repo. Sorry..")
return
def pjson(obj):
return json.dumps(obj, sort_keys=True, indent=4,
separators=(',', ': '))
# Coords
print("=========================================================\n")
print(frb_name)
print(ltu.name_from_coord(FRB.coord, precision=(4,4)), '\n ra,dec = {:0.7f},{:0.7f} deg'.format(FRB.coord.ra.value,
FRB.coord.dec.value))
print('sig_a = {:0.3f} arcsec'.format(FRB.sig_a))
print('sig_b = {:0.3f} arcsec'.format(FRB.sig_b))
print('PA = {:0.1f} deg'.format(FRB.eellipse['theta']))
print('')
print('DM={}'.format(FRB.DM))
print('Repeater={}'.format(FRB.repeater))
if pargs.verbose:
print('ee={}'.format(pjson(FRB.eellipse)))
print('DM_ISM(ne2001)={:0.1f}'.format(FRB.DMISM))
# Host
hg = FRB.grab_host()
if hg is not None:
print("")
print("=========================================================\n")
print("Host\n")
print(ltu.name_from_coord(hg.coord))
print('z: \n {}'.format(pjson(hg.redshift)))
if pargs.verbose:
# photometry
print('photom: \n {}'.format(pjson(hg.photom)))
print('derived: \n {}'.format(pjson(hg.derived)))
print('morphology: \n {}'.format(pjson(hg.morphology)))
print('neb_lines: \n {}'.format(pjson(hg.neb_lines)))
def __init__(self, radec, sl_type=None, em_type=None, comment=None, name=None, **kwargs):
""" Initiator
Parameters
----------
radec : tuple or SkyCoord
(RA,DEC) in deg or astropy.coordinate.SkyCoord
sl_type : str, optional
Sightline type, e.g. IGM
em_type : str, optional
Type of emission source for absorption sightline, e.g. QSO
comment : str, optional
A comment, default is ``
name : str, optional
Name of the sightline, e.g. '3C273'
"""
# Required
self.coord = ltu.radec_to_coord(radec)
# Lists
self._components = []
# Name
if name is None:
self.name = ltu.name_from_coord(self.coord)
else:
self.name = name
# Others
self.em_type = em_type
self.sl_type = sl_type
self._abssystems = None # Saving the namespace for future usage
def __init__(self, radec, sl_type='', em_type='', comment=None, name=None, **kwargs):
""" Initiator
Parameters
----------
radec : tuple or SkyCoord
(RA,DEC) in deg or astropy.coordinate.SkyCoord
sl_type : str, optional
Sightline type, e.g. IGM
em_type : str, optional
Type of emission source for absorption sightline, e.g. QSO
comment : str, optional
A comment, default is ``
name : str, optional
Name of the sightline, e.g. '3C273'
"""
# Required
self.coord = ltu.radec_to_coord(radec)
# Lists
self._components = []
# Name
if name is None:
self.name = ltu.name_from_coord(self.coord)
else:
self.name = name
# Others
self.em_type = em_type
self.sl_type = sl_type
self._abssystems = [] # Saving the namespace for future usage
def plot_spec(specDB, meta, frb=None):
import numpy as np
from astropy.coordinates import SkyCoord
from linetools import utils as ltu
""" Plot galaxy spectra """
# Grab spectra
spec = specDB.spectra_from_meta(meta)
# Add labels
lbls = ['None'] * len(meta)
ugroups = np.unique(meta['GROUP'])
for ugroup in ugroups:
rows = np.where(meta['GROUP'] == ugroup)[0]
coords = SkyCoord(ra=meta['RA_GROUP'][rows],
dec=meta['DEC_GROUP'][rows],
unit='deg')
if frb is None:
for kk, row, imeta in zip(range(len(rows)), rows, meta):
# JNAME
jname = ltu.name_from_coord(coords[kk])
lbls[row] = '{:s}_{:s}'.format(jname, meta['INSTR'][row])
else:
seps = frb.coord.separation(coords).to('arcsec')
pas = frb.coord.position_angle(coords).to('deg')
for row, sep, pa, imeta in zip(rows, seps, pas, meta):
# Separation and PA
lbls[row] = '{:s}_{:s}_{:d}_{:d}'.format(
frb.frb_name, meta['INSTR'][row], int(pa.value),
int(sep.value))
spec.labels = lbls
# Add object type
spec.stypes = ['Galaxy'] * len(lbls)
# Add redshift
spec.z = meta['zem_GROUP']
# Plot
spec.plot(xspec=True) #, scale=1.5)
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 plot_spec(specDB, meta, frb, dust_correct=False):
import numpy as np
from astropy.coordinates import SkyCoord
from linetools import utils as ltu
from frb.galaxies import nebular
""" Plot galaxy spectra """
# Grab spectra
spec = specDB.spectra_from_meta(meta)
# Dust?
if dust_correct:
import extinction
EBV = nebular.get_ebv(frb.coord)['meanValue'] #
AV = EBV * 3.1 # RV
for kk in range(spec.nspec):
spec.select = kk
Al = extinction.fm07(spec.wavelength.value, AV)#, 3.1)
spec.flux = spec.flux * 10 ** (Al / 2.5)
spec.sig = spec.sig * 10 ** (Al / 2.5)
# Add labels
lbls = ['None']*len(meta)
ugroups = np.unique(meta['GROUP'])
for ugroup in ugroups:
rows = np.where(meta['GROUP'] == ugroup)[0]
coords = SkyCoord(ra=meta['RA_GROUP'][rows], dec=meta['DEC_GROUP'][rows], unit='deg')
if frb is None:
for kk, row, imeta in zip(range(len(rows)), rows, meta):
# JNAME
jname = ltu.name_from_coord(coords[kk])
lbls[row]='{:s}_{:s}'.format(jname, meta['INSTR'][row])
else:
seps = frb.coord.separation(coords).to('arcsec')
pas = frb.coord.position_angle(coords).to('deg')
for row, sep, pa, imeta in zip(rows, seps, pas, meta):
# Separation and PA
lbls[row]='{:s}_{:s}_{:d}_{:d}'.format(frb.frb_name, meta['INSTR'][row],
int(pa.value), int(sep.value))
spec.labels = lbls
# Add object type
spec.stypes = ['Galaxy']*len(lbls)
# Add redshift
spec.z = meta['zem_GROUP']
# Plot
spec.plot(xspec=True)#, scale=1.5)
def generate(image,
wcs,
title,
flip_ra=False,
flip_dec=False,
log_stretch=False,
cutout=None,
primary_coord=None,
secondary_coord=None,
third_coord=None,
slit=None,
vmnx=None,
extra_text=None,
outfile=None):
"""
Basic method to generate a Finder chart figure
Args:
image (np.ndarray):
Image for the finder
wcs (astropy.wcs.WCS):
WCS solution
title (str):
Title; typically the name of the primary source
flip_ra (bool, default False):
Flip the RA (x-axis). Useful for southern hemisphere finders.
flip_dec (bool, default False):
Flip the Dec (y-axis). Useful for southern hemisphere finders.
log_stretch (bool, optional):
Use a log stretch for the image display
cutout (tuple, optional):
SkyCoord (center coordinate) and Quantity (image angular size)
for a cutout from the input image.
primary_coord (astropy.coordinates.SkyCoord, optional):
If provided, place a mark in red at this coordinate
secondary_coord (astropy.coordinates.SkyCoord, optional):
If provided, place a mark in cyan at this coordinate
Assume it is an offset star (i.e. calculate offsets)
third_coord (astropy.coordinates.SkyCoord, optional):
If provided, place a mark in yellow at this coordinate
slit (tuple, optional):
If provided, places a rectangular slit with specified
coordinates, width, length, and position angle on image (from North to East)
[SkyCoords('21h44m25.255s',-40d54m00.1s', frame='icrs'), 1*u.arcsec, 10*u.arcsec, 20*u.deg]
vmnx (tuple, optional):
Used for scaling the image. Otherwise, the image
is analyzed for these values.
extra_text : str
Extra text to be added at the bottom of the Figure.
e.g. `DSS r-filter`
outfile (str, optional):
Filename for the figure. File type will be according
to the extension
Returns:
matplotlib.pyplot.figure, matplotlib.pyplot.Axis
"""
utils.set_mplrc()
plt.clf()
fig = plt.figure(figsize=(7, 8.5))
# fig.set_size_inches(7.5,10.5)
# Cutout?
if cutout is not None:
cutout_img = Cutout2D(image, cutout[0], cutout[1], wcs=wcs)
# Overwrite
wcs = cutout_img.wcs
image = cutout_img.data
# Axis
ax = fig.add_axes([0.10, 0.20, 0.75, 0.5], projection=wcs)
# Show
if log_stretch:
norm = mplnorm.ImageNormalize(stretch=LogStretch())
else:
norm = None
cimg = ax.imshow(image, cmap='Greys', norm=norm)
# Flip so RA increases to the left
if flip_ra is True:
ax.invert_xaxis()
if flip_dec is True:
ax.invert_yaxis()
# N/E
overlay = ax.get_coords_overlay('icrs')
overlay['ra'].set_ticks(color='white')
overlay['dec'].set_ticks(color='white')
overlay['ra'].set_axislabel('Right Ascension')
overlay['dec'].set_axislabel('Declination')
overlay.grid(color='green', linestyle='solid', alpha=0.5)
# Contrast
if vmnx is None:
mean, median, stddev = sigma_clipped_stats(
image
) # Also set clipping level and number of iterations here if necessary
#
vmnx = (median - stddev, median + 2 * stddev
) # sky level - 1 sigma and +2 sigma above sky level
print("Using vmnx = {} based on the image stats".format(vmnx))
cimg.set_clim(vmnx[0], vmnx[1])
# Add Primary
if primary_coord is not None:
c = SphericalCircle((primary_coord.ra, primary_coord.dec),
2 * units.arcsec,
transform=ax.get_transform('icrs'),
edgecolor='red',
facecolor='none')
ax.add_patch(c)
# Text
jname = ltu.name_from_coord(primary_coord)
ax.text(0.5,
1.34,
jname,
fontsize=28,
horizontalalignment='center',
transform=ax.transAxes)
# Secondary
if secondary_coord is not None:
c_S1 = SphericalCircle((secondary_coord.ra, secondary_coord.dec),
2 * units.arcsec,
transform=ax.get_transform('icrs'),
edgecolor='cyan',
facecolor='none')
ax.add_patch(c_S1)
# Text
jname = ltu.name_from_coord(secondary_coord)
ax.text(0.5,
1.24,
jname,
fontsize=22,
color='blue',
horizontalalignment='center',
transform=ax.transAxes)
# Print offsets
if primary_coord is not None:
sep = primary_coord.separation(secondary_coord).to('arcsec')
PA = primary_coord.position_angle(secondary_coord)
# RA/DEC
dec_off = np.cos(PA) * sep # arcsec
ra_off = np.sin(PA) * sep # arcsec (East is *higher* RA)
ax.text(
0.5,
1.22,
'Offset from Ref. Star (cyan) to Target (red):\nRA(to targ) = {:.2f} DEC(to targ) = {:.2f}'
.format(-1 * ra_off.to('arcsec'), -1 * dec_off.to('arcsec')),
fontsize=15,
horizontalalignment='center',
transform=ax.transAxes,
color='blue',
va='top')
# Add tertiary
if third_coord is not None:
c = SphericalCircle((third_coord.ra, third_coord.dec),
2 * units.arcsec,
transform=ax.get_transform('icrs'),
edgecolor='yellow',
facecolor='none')
ax.add_patch(c)
# Slit
if ((slit is not None) and (flag_photu is True)):
# List of values - [coodinates, width, length, PA],
# e.g. [SkyCoords('21h44m25.255s',-40d54m00.1s', frame='icrs'), 1*u.arcsec, 10*u.arcsec, 20*u.deg]
slit_coords, width, length, pa = slit
pa_deg = pa.to('deg').value
aper = SkyRectangularAperture(
positions=slit_coords, w=length, h=width, theta=pa
) # For theta=0, width goes North-South, which is slit length
apermap = aper.to_pixel(wcs)
apermap.plot(color='purple', lw=1)
plt.text(0.5,
-0.1,
'Slit PA={} deg'.format(pa_deg),
color='purple',
fontsize=15,
ha='center',
va='top',
transform=ax.transAxes)
if ((slit is not None) and (flag_photu is False)):
raise IOError('Slit cannot be placed without photutils package')
# Title
ax.text(0.5,
1.44,
title,
fontsize=32,
horizontalalignment='center',
transform=ax.transAxes)
# Extra text
if extra_text is not None:
ax.text(-0.1,
-0.25,
extra_text,
fontsize=20,
horizontalalignment='left',
transform=ax.transAxes)
# Sources
# Labels
#ax.set_xlabel(r'\textbf{DEC (EAST direction)}')
#ax.set_ylabel(r'\textbf{RA (SOUTH direction)}')
if outfile is not None:
plt.savefig(outfile)
plt.close()
else:
plt.show()
# Return
return fig, ax
def generate(image,
wcs,
title,
log_stretch=False,
cutout=None,
primary_coord=None,
secondary_coord=None,
third_coord=None,
vmnx=None,
outfile=None):
"""
Basic method to generate a Finder chart figure
Args:
image (np.ndarray):
Image for the finder
wcs (astropy.wcs.WCS):
WCS solution
title (str):
TItle; typically the name of the primry source
log_stretch (bool, optional):
Use a log stretch for the image display
cutout (tuple, optional):
SkyCoord (center coordinate) and Quantity (image angular size)
for a cutout from the input image.
primary_coord (astropy.coordinates.SkyCoord, optional):
If provided, place a mark in red at this coordinate
secondary_coord (astropy.coordinates.SkyCoord, optional):
If provided, place a mark in cyan at this coordinate
Assume it is an offset star (i.e. calculate offsets)
third_coord (astropy.coordinates.SkyCoord, optional):
If provided, place a mark in yellow at this coordinate
vmnx (tuple, optional):
Used for scaling the image. Otherwise, the image
is analyzed for these values.
outfile (str, optional):
Filename for the figure. File type will be according
to the extension
Returns:
matplotlib.pyplot.figure, matplotlib.pyplot.Axis
"""
utils.set_mplrc()
plt.clf()
fig = plt.figure(dpi=600)
fig.set_size_inches(7.5, 10.5)
# Cutout?
if cutout is not None:
cutout_img = Cutout2D(image, cutout[0], cutout[1], wcs=wcs)
# Overwrite
wcs = cutout_img.wcs
image = cutout_img.data
# Axis
ax = fig.add_axes([0.10, 0.20, 0.80, 0.5], projection=wcs)
# Show
if log_stretch:
norm = mplnorm.ImageNormalize(stretch=LogStretch())
else:
norm = None
cimg = ax.imshow(image, cmap='Greys', norm=norm)
# Flip so RA increases to the left
ax.invert_xaxis()
# N/E
overlay = ax.get_coords_overlay('icrs')
overlay['ra'].set_ticks(color='white')
overlay['dec'].set_ticks(color='white')
overlay['ra'].set_axislabel('Right Ascension')
overlay['dec'].set_axislabel('Declination')
overlay.grid(color='green', linestyle='solid', alpha=0.5)
# Contrast
if vmnx is None:
mean, median, stddev = sigma_clipped_stats(
image
) # Also set clipping level and number of iterations here if necessary
#
vmnx = (median - stddev, median + 2 * stddev
) # sky level - 1 sigma and +2 sigma above sky level
print("Using vmnx = {} based on the image stats".format(vmnx))
cimg.set_clim(vmnx[0], vmnx[1])
# Add Primary
if primary_coord is not None:
c = SphericalCircle((primary_coord.ra, primary_coord.dec),
2 * units.arcsec,
transform=ax.get_transform('icrs'),
edgecolor='red',
facecolor='none')
ax.add_patch(c)
# Text
jname = ltu.name_from_coord(primary_coord)
ax.text(0.5,
1.34,
jname,
fontsize=28,
horizontalalignment='center',
transform=ax.transAxes)
# Secondary
if secondary_coord is not None:
c_S1 = SphericalCircle((secondary_coord.ra, secondary_coord.dec),
2 * units.arcsec,
transform=ax.get_transform('icrs'),
edgecolor='cyan',
facecolor='none')
ax.add_patch(c_S1)
# Text
jname = ltu.name_from_coord(secondary_coord)
ax.text(0.5,
1.24,
jname,
fontsize=22,
color='blue',
horizontalalignment='center',
transform=ax.transAxes)
# Print offsets
if primary_coord is not None:
sep = primary_coord.separation(secondary_coord).to('arcsec')
PA = primary_coord.position_angle(secondary_coord)
# RA/DEC
dec_off = np.cos(PA) * sep # arcsec
ra_off = np.sin(PA) * sep # arcsec (East is *higher* RA)
ax.text(0.5,
1.14,
'RA(to targ) = {:.2f} DEC(to targ) = {:.2f}'.format(
-1 * ra_off.to('arcsec'), -1 * dec_off.to('arcsec')),
fontsize=18,
horizontalalignment='center',
transform=ax.transAxes)
# Add tertiary
if third_coord is not None:
c = SphericalCircle((third_coord.ra, third_coord.dec),
2 * units.arcsec,
transform=ax.get_transform('icrs'),
edgecolor='yellow',
facecolor='none')
ax.add_patch(c)
# Slit?
'''
if slit is not None:
r = Rectangle((primary_coord.ra.value, primary_coord.dec.value),
slit[0]/3600., slit[1]/3600., angle=360-slit[2],
transform=ax.get_transform('icrs'),
facecolor='none', edgecolor='red')
ax.add_patch(r)
'''
# Title
ax.text(0.5,
1.44,
title,
fontsize=32,
horizontalalignment='center',
transform=ax.transAxes)
# Sources
# Labels
#ax.set_xlabel(r'\textbf{DEC (EAST direction)}')
#ax.set_ylabel(r'\textbf{RA (SOUTH direction)}')
if outfile is not None:
plt.savefig(outfile)
plt.close()
else:
plt.show()
# Return
return fig, ax
def write_to_igmguesses(self,
outfile,
fwhm=3.,
specfilename=None,
creator=None,
instrument='unknown',
altname='unknown',
date=None,
overwrite=False):
import json
"""
Writes an IGMGuesses formatted JSON file
Parameters
----------
outfile : str
Name of the IGMGuesses JSON file to write to.
fwhm : int
FWHM for IGMguesses
specfilename : str
Name of the spectrum file these guesses are associated to.
altname : str
Alternative name for the sightline. e.g. 3C273
creator : str
Name of the person who is creating the file. Important for tracking.
instrument : str
String indicating the instrument and its configuration associated to the specfilename.
e.g. HST/COS/G130M+G160M/LP2
overwrite : bool
Wthether to overwrite output
Returns
-------
"""
import datetime
# Slurp IGMGuesses component attributes
from pyigm.guis.igmguesses import comp_init_attrib
from linetools.isgm.abscomponent import AbsComponent
tmp = AbsComponent((10.0 * u.deg, 45 * u.deg), (14, 2), 1.0,
[-300, 300] * u.km / u.s)
comp_init_attrib(tmp)
igmg_akeys = list(tmp.attrib.keys())
# components
comp_list = self._components
coord_ref = comp_list[0].coord
if date is None:
date = str(datetime.date.today().strftime('%Y-%b-%d'))
# spec_file, meta
if hasattr(self, 'igmg_dict'):
spec_file = self.igmg_dict['spec_file']
meta = self.igmg_dict['meta']
# Updates
meta['Date'] = date
if creator is not None:
meta['Creator'] = creator
#
fwhm = self.igmg_dict['fwhm']
else:
spec_file = specfilename
# coordinates and meta
RA = coord_ref.ra.to('deg').value
DEC = coord_ref.dec.to('deg').value
jname = ltu.name_from_coord(coord_ref, precision=(2, 1))
if self.zem is None:
zem = 0. # IGMGuesses rules
else:
zem = self.zem
if creator is None:
creator = 'unknown'
meta = {
'RA': RA,
'DEC': DEC,
'ALTNAME': altname,
'zem': zem,
'Creator': creator,
'Instrument': instrument,
'Date': date,
'JNAME': jname
}
# Create dict of the components
out_dict = dict(cmps={},
spec_file=spec_file,
fwhm=fwhm,
bad_pixels=[],
meta=meta)
for comp in comp_list:
key = comp.name
out_dict['cmps'][key] = comp.to_dict()
# import pdb; pdb.set_trace()
# check coordinate
if comp.coord != coord_ref:
raise ValueError(
"All AbsComponent objects must have the same coordinates!")
out_dict['cmps'][key]['zcomp'] = comp.zcomp
# IGMGuesses specific component attr
for igm_key in [
'zfit', 'Nfit', 'bfit', 'wrest', 'mask_abslines', 'vlim'
]:
out_dict['cmps'][key][igm_key] = comp.igmg_attrib['top_level'][
igm_key]
# IGMGuesses attribute dict
out_dict['cmps'][key]['attrib'] = {}
for igm_key in igmg_akeys:
try:
out_dict['cmps'][key]['attrib'][
igm_key] = comp.igmg_attrib[igm_key]
except KeyError:
out_dict['cmps'][key]['attrib'][igm_key] = comp.attrib[
igm_key]
#out_dict['cmps'][key]['vlim'] = list(comp.vlim.value)
out_dict['cmps'][key]['reliability'] = str(comp.reliability)
out_dict['cmps'][key]['comment'] = str(comp.comment)
# Compatability on sig_logN
out_dict['cmps'][key]['attrib']['sig_logN'] = comp.attrib[
'sig_logN'][0]
# JSONify
gd_dict = ltu.jsonify(out_dict)
# Write file
ltu.savejson(outfile,
gd_dict,
overwrite=overwrite,
sort_keys=True,
indent=4,
separators=(',', ': '))
print('Wrote: {:s}'.format(outfile))
