def main(args):
with fitsio.FITS(args.catalogue) as infile:
hdu = infile[1]
ra1 = hdu['RA_1'][:]
dec1 = hdu['DEC_1'][:]
ra2 = hdu['ra_2'][:]
dec2 = hdu['dec_2'][:]
coords1 = ICRS(ra=ra1, dec=dec1, unit=(u.radian, u.radian))
coords2 = ICRS(ra=ra2, dec=dec2, unit=(u.degree, u.degree))
separations = coords1.separation(coords2).degree * 3600.
fig, axes = plt.subplots(figsize=(11, 8))
axes.hist(separations, 30, histtype='step')
axes.set_xlabel(r'Separation / arcseconds')
axes.grid(True)
fig.tight_layout()
if args.output is not None:
fig.savefig(args.output, bbox_inches='tight')
else:
plt.show()
def main(args):
with fitsio.FITS(args.catalogue) as infile:
hdu = infile[1]
ra1 = hdu['RA_1'][:]
dec1 = hdu['DEC_1'][:]
ra2 = hdu['ra_2'][:]
dec2 = hdu['dec_2'][:]
x = hdu['X_coordinate'][:]
y = hdu['Y_coordinate'][:]
coords1 = ICRS(ra=ra1, dec=dec1, unit=(u.radian, u.radian))
coords2 = ICRS(ra=ra2, dec=dec2, unit=(u.degree, u.degree))
separations = coords1.separation(coords2).degree * 3600.
fig, axes = plt.subplots(2, 2, sharex=True, figsize=(11, 8))
[(x_axis, y_axis), (x_zoomed, y_zoomed)] = axes
nsigma = 5
nbins = 2048 / 128
print('Using {} bins'.format(nbins))
x_axis.plot(x, separations, 'k.', color='0.4')
x_axis.set_ylabel(r'X')
ledges, x_binned = compute_binned(x, separations, nbins)
_, x_binned_error = compute_binned_errors(x, separations, ledges)
bin_centres = compute_bin_centres(ledges)
for ax in [x_axis, x_zoomed]:
ax.errorbar(bin_centres[:-1], x_binned[:-1], x_binned_error[:-1],
color='r', ls='None')
ax.plot(ledges, x_binned, color='r', drawstyle='steps-post')
y_axis.plot(y, separations, 'k.', color='0.4')
y_axis.set_ylabel(r'y')
ledges, y_binned = compute_binned(y, separations, nbins)
_, y_binned_error = compute_binned_errors(y, separations, ledges)
for ax in [y_axis, y_zoomed]:
ax.errorbar(bin_centres[:-1], y_binned[:-1], x_binned_error[:-1],
color='r', ls='None')
ax.plot(ledges, y_binned, color='r', drawstyle='steps-post')
link_y_limits(x_zoomed, y_zoomed)
for ax in axes.flatten():
ax.grid(True)
fig.tight_layout()
if args.output is not None:
fig.savefig(args.output, bbox_inches='tight')
else:
plt.show()
def ra_dec_distance(ra1, dec1, ra2, dec2, use_icrs=False, arcsec=False):
# conversion between degree and radians
pi = 3.1415926536
d2r = pi/180.00
if use_icrs:
coord1 = ICRS(ra=ra1, dec=dec1, unit=(u.degree,u.degree))
coord2 = ICRS(ra=ra2, dec=dec2, unit=(u.degree,u.degree))
else:
coord1 = FK5(ra=ra1, dec=dec1, unit=(u.degree,u.degree))
coord2 = FK5(ra=ra2, dec=dec2, unit=(u.degree,u.degree))
# The separation is in unit of arcsecond or degree
if arcsec:
sep = coord1.separation(coord2).arcsecond
else:
sep = (coord1.separation(coord2).radian / d2r )
return sep
class SkyCircle(object):
"""A circle on the sky.
Parameters
----------
center : `~astropy.coordinates.coordsystems.SphericalCoordinatesBase`
Circle center coordinate
radius : `~astropy.coordinates.angles.Angle`
Circle radius
"""
def __init__(self, center, radius):
from astropy.coordinates import ICRS, Angle
self.center = ICRS(center)
self.radius = Angle(radius)
def contains(self, coordinate):
"""Checks if the coordinate lies inside the circle.
Parameters
----------
coordinate : `~astropy.coordinates.coordsystems.SphericalCoordinatesBase`
Coordinate to check for containment.
Returns
-------
contains : bool
Does this region contain the coordinate?
"""
return self.center.separation(coordinate) <= self.radius
def intersects(self, other):
"""Checks if two sky circles overlap.
Parameters
----------
other : `~SkyCircle`
Other region.
"""
return self.center.separation(other.center) <= self.radius + other.radius
def test_moon_radec(self):
"""Verify moon (ra,dec) for first week of 2020"""
ephem = get_ephem()
for i, jd in enumerate(self.table['jd']):
t = Time(jd, format='jd')
night = ephem.get_night(t)
f_moon = get_object_interpolator(night, 'moon', altaz=False)
dec, ra = f_moon(t.mjd)
truth = ICRS(ra=self.table['ra'][i] * u.deg,
dec=self.table['dec'][i] * u.deg)
calc = ICRS(ra=ra * u.deg, dec=dec * u.deg)
sep = truth.separation(calc)
self.assertTrue(abs(sep.to(u.deg).value) < 0.3)
def test_array_separation():
c1 = ICRS([0, 0]*u.deg, [0, 0]*u.deg)
c2 = ICRS([1, 2]*u.deg, [0, 0]*u.deg)
npt.assert_array_almost_equal(c1.separation(c2).degree, [1, 2])
c3 = ICRS([0, 3.]*u.deg, [0., 0]*u.deg, distance=[1, 1.] * u.kpc)
c4 = ICRS([1, 1.]*u.deg, [0., 0]*u.deg, distance=[1, 1.] * u.kpc)
# the 3-1 separation should be twice the 0-1 separation, but not *exactly* the same
sep = c3.separation_3d(c4)
sepdiff = sep[1] - (2 * sep[0])
assert abs(sepdiff.value) < 1e-5
assert sepdiff != 0
def test_array_separation():
c1 = ICRS([0, 0] * u.deg, [0, 0] * u.deg)
c2 = ICRS([1, 2] * u.deg, [0, 0] * u.deg)
npt.assert_array_almost_equal(c1.separation(c2).degree, [1, 2])
c3 = ICRS([0, 3.] * u.deg, [0., 0] * u.deg, distance=[1, 1.] * u.kpc)
c4 = ICRS([1, 1.] * u.deg, [0., 0] * u.deg, distance=[1, 1.] * u.kpc)
# the 3-1 separation should be twice the 0-1 separation, but not *exactly* the same
sep = c3.separation_3d(c4)
sepdiff = sep[1] - (2 * sep[0])
assert abs(sepdiff.value) < 1e-5
assert sepdiff != 0
def test_table_can_be_read_and_coords_good():
objs = Table.read(TABLE_NAME, format='ascii', delimiter=',')
columns = ['object', 'ra', 'dec']
for col in columns:
assert col in objs.colnames
for row in objs:
try:
simbad_pos = ICRS.from_name(row['object'])
except name_resolve.NameResolveError:
continue
table_pos = ICRS(row['ra'], row['dec'], unit=(u.hour, u.degree))
# CHANGE ASSERT TO IF/THEN, print name then assert 0
sep = table_pos.separation(simbad_pos).arcsec
warn = ''
if sep > MAX_SEP:
warn = ('Bad RA/Dec for object {}, '
'separation is {} arcsec'.format(row['object'], sep))
print (warn)
assert len(warn) == 0
def main(args):
with fitsio.FITS(args.catalogue) as infile:
hdu = infile[1]
ra1 = hdu['RA_1'][:]
dec1 = hdu['DEC_1'][:]
ra2 = hdu['ra_2'][:]
dec2 = hdu['dec_2'][:]
jmag = hdu['jmag'][:]
coords1 = ICRS(ra=ra1, dec=dec1, unit=(u.radian, u.radian))
coords2 = ICRS(ra=ra2, dec=dec2, unit=(u.degree, u.degree))
separations = coords1.separation(coords2).degree * 3600.
nbins = 30
height, xedges, yedges = np.histogram2d(jmag, separations, nbins)
fig, axis = plt.subplots(figsize=(11, 8))
mappable = axis.pcolormesh(xedges[:-1], yedges[:-1], np.log10(height.T + 1),
cmap=plt.cm.binary)
axis.plot(jmag, separations, 'k.', alpha=0.2)
stat, ledges, _ = stats.binned_statistic(jmag, separations, statistic='median',
bins=nbins)
axis.plot(ledges[:-1], stat, drawstyle='steps-post', color='r')
axis.set_xlabel(r'2MASS J Magnitude')
axis.set_ylabel(r'Separation / arcseconds')
axis.grid(True)
fig.tight_layout()
if args.output is not None:
fig.savefig(args.output, bbox_inches='tight')
else:
plt.show()
class ObjCat(Table):
"""
The __init__ method has been changed to return something like a record
array, which has the same number of rows as the old 2D float array, but
which stores each row as a single tuple. It is thus a 1D array, sort of
like a structure array in C. The columns can be accessed by field name,
which for now is just 'f0', 'f1', etc., unless the input catalog is in
SExtractor's FITS LDAC format, in which case the field names actually
correspond to the SExtractor variable names.
The code used to expect the old 2D float array format. It should have
all been updated, but there may still be some issues.
"""
def __init__(self,
incat,
catformat='ldac',
verbose=True,
namecol=None,
racol=None,
deccol=None,
rafield=None,
decfield=None,
usecols=False):
"""
This method gets called when the user types something like
cat = ObjCat(infile)
Inputs:
incat - input table data. This can be in one of two forms:
1. a file containing the catalog (most common)
2. a Table instance containing the catalog data
catformat - format of the input file, if incat is a filename.
The options are:
ascii -
asciitab -
ldac -
csv -
sdssfits -
secat -
NOTE: this parameter is not used if incat is a Table
rather than the name of an input file
"""
""" Set a flag showing whether the file has been modified """
self.modified = False
""" Set other default values """
self.radec = None
self.rafield = None
self.decfield = None
self.centpos = None
self.galmask = None
self.starmask = None
"""
Start by loading the catalog information
"""
incattype = (str(type(incat))).split('.')[-1]
if incattype[0:3] == 'Tab' or incattype[0:4] == 'FITS':
self.data = incat.copy()
if rafield:
self.rafield = rafield
if decfield:
self.decfield = decfield
self.nrows = len(incat)
self.ncols = len(incat.columns)
self.catformat = 'Table'
elif isinstance(incat, str):
self.load_from_file(incat,
catformat=catformat,
verbose=verbose,
namecol=namecol,
racol=racol,
deccol=deccol,
rafield=rafield,
decfield=decfield,
usecols=usecols)
else:
print('')
print('ERROR: input catalog must either be a filename or a Table')
print(' Input catalog type is' + str(type(incat)))
print('')
return None
#-----------------------------------------------------------------------
def load_from_file(self,
incat,
catformat='ldac',
verbose=True,
namecol=None,
racol=None,
deccol=None,
rafield=None,
decfield=None,
usecols=False):
if verbose:
print('')
print("Loading data from catalog file %s" % incat)
print("-----------------------------------------------")
print("Expected catalog format: %s" % catformat)
print('')
"""
Define a flag for successful reading of input catalog
"""
read_success = True
""" Read in catalog in a manner appropriate to the catformat """
if catformat == 'secat':
try:
self.data = ascii.read(incat)
ncols = len(self.data.colnames)
nrows = len(self.data)
""" Set the field names """
self.rafield = 'ALPHA_J2000'
self.decfield = 'DELTA_J2000'
except:
print(" ERROR. Problem in loading file %s" % incat)
print(
" Check to make sure filename matches an existing file.")
print('')
print(
" This also may have failed if the input file is in the")
print(" SExtractor FITS LDAC format. Checking that...")
print('')
read_success = False
elif catformat == 'asciitab':
f = open(incat)
foo = f.readline()
f.close()
if foo[0] == '#':
try:
self.data = ascii.read(incat,
guess=False,
format='commented_header')
except:
print('')
print('ERROR: Could not read data from %s' % incat)
print(' Tried using "commented_header" format but failed')
print(' Please check input file.')
print('')
raise IOError
else:
try:
self.data = ascii.read(incat)
except:
print('')
print('ERROR: Could not properly read data from %s' %
incat)
print('Tried using the automatic formatting but failed')
print(' Please check input file.')
print('')
raise IOError
ncols = len(self.data.colnames)
nrows = len(self.data)
""" Set the field names """
if rafield:
self.rafield = rafield
if decfield:
self.decfield = decfield
elif catformat == 'ascii':
""" ASCII format """
try:
""" Set up the data format in the catalog """
foo = np.loadtxt(incat, dtype='S30')
ncols = foo.shape[1]
del foo
coltypes = np.ones(ncols, dtype='S3')
coltypes[:] = 'f8'
if namecol is not None:
print("Object name column: %d" % namecol)
coltypes[namecol] = 'S30'
colstr = ''
for i in range(ncols):
colstr = '%s,%s' % (colstr, coltypes[i])
colstr = colstr[1:]
dt = np.dtype(colstr)
""" Actually read in the data """
self.informat = 'ascii'
self.data = np.loadtxt(incat, dtype=dt)
nrows = self.data.shape[0]
""" Set the field names """
if racol is not None:
self.rafield = 'f%d' % racol
else:
self.rafield = None
if deccol is not None:
self.decfield = 'f%d' % deccol
else:
self.decfield = None
if namecol is not None:
self.namefield = 'f%d' % namecol
else:
self.namefield = None
except:
print(" ERROR. Problem in loading file %s" % incat)
print(
" Check to make sure filename matches an existing file.")
print(" ")
print(" This may have failed if there is a string column in")
print(" the input catalog (e.g., for an object name). ")
print(
" If this is the case, use the namecol to indicate which "
)
print(
" column contains the string values (column numbers are "
)
print(" zero-indexed)")
print('')
print(
" This also may have failed if the input file is in the")
print(" SExtractor FITS LDAC format. Checking that...")
print('')
read_success = False
elif catformat.lower() == 'ldac' or read_success == False:
try:
self.data = Table.read(incat, format='fits', hdu=2)
except:
print(" ERROR. Problem in loading file %s" % incat)
print(
" Check to make sure filename matches an existing file.")
print('')
return
self.informat = 'ldac'
nrows = len(self.data)
ncols = len(self.data.columns)
""" Set the field names """
self.rafield = 'ALPHA_J2000'
self.decfield = 'DELTA_J2000'
elif catformat.lower() == 'csv' or read_success == False:
try:
self.data = Table.read(incat)
except:
print(" ERROR. Problem in loading file %s" % incat)
print(
" Check to make sure filename matches an existing file.")
print('')
return
self.informat = 'csv'
nrows = len(self.data)
ncols = len(self.data.columns)
""" Set the field names """
self.rafield = 'raStack'
self.decfield = 'decStack'
elif catformat.lower() == 'sdssfits' or read_success == False:
try:
self.data = Table.read(incat, format='fits', hdu=1)
except:
print(" ERROR. Problem in loading file %s" % incat)
print(
" Check to make sure filename matches an existing file.")
print('')
return
self.informat = 'sdss'
nrows = len(self.data)
ncols = len(self.data.columns)
""" Set the field names """
self.rafield = 'ra'
self.decfield = 'dec'
"""
Split the stars from the galaxies, according to the SDSS
classification.
In the SDSS scheme, type=3 is a galaxy and type=6 is a star
"""
if 'type' in self.data.colnames:
objclass = self.data['type']
elif 'type_r' in self.data.colnames:
objclass = self.data['type_r']
else:
objclass = None
if objclass is not None:
self.galmask = objclass == 3
self.starmask = objclass == 6
else:
self.galmask = np.ones(dtype=bool)
self.starmask = None
print('Read SDSS catalog from %s' % incat)
print('Number of galaxies: %5d' % self.galmask.sum())
if self.starmask is not None:
print('Number of stars: %5d' % self.starmask.sum())
else:
print('')
print('Unrecognized format. Must be one of:')
print(' ascii, secat, ldac, sdssfits')
sys.exit()
if verbose:
print("Number of rows: %d" % nrows)
print("Number of columns: %d" % ncols)
if self.rafield is not None:
print('RA field name: %s' % self.rafield)
if self.decfield is not None:
print('Dec field name: %s' % self.decfield)
self.infile = incat
self.catformat = catformat
self.nrows = nrows
self.ncols = ncols
#-----------------------------------------------------------------------
def close_ldac(self):
"""
Closes the catalog. If the catalog is in fits format and it has
been modified (as shown by the modified parameter in this ObjCat class)
then use flush rather than close.
"""
""" Close the file if it is in the expected format """
if self.informat == 'ldac':
if self.modified:
self.hdu.flush()
print('Updating input fits LDAC file: %s' % self.infile)
else:
self.hdu.close()
else:
print('')
print('WARNING. Calling close_ldac but file is not in ldac format')
print('')
#----------------------------------------------------------------------
def make_magmask(self, magname, mfaint=None, mbright=None):
"""
Makes a mask that is True for magnitudes brighter than mfaint and
fainter than mbright.
Note that one of these two could have the value None, in which case
it would be ignored. For example, if mbright is None, then the mask
will be True for all galaxies brighter than mfaint
Inputs:
magname - the name in the catalog for the column that represents the
object magnitudes. This could be something like, e.g., 'r'
or 'MAG_AUTO'
"""
mag = self.data[magname].astype(float)
if mfaint is None and mbright is None:
self.magmask = np.ones(self.nrows, dtype=bool)
elif mfaint is None:
self.magmask = mag >= mbright
elif mbright is None:
self.magmask = mag <= mfaint
else:
self.magmask = (mag >= mbright) & (mag <= mfaint)
#-----------------------------------------------------------------------
def get_radec(self):
"""
Extracts the RA and Dec information from the data container. This
is not necessary, and some of the data containers may not even have
WCS info, but extracting the coordinates if it does simplifies some
later tasks.
"""
""" Extract the information into the new containers """
self.ra = None
self.dec = None
if self.rafield is not None:
try:
self.ra = self.data[self.rafield].copy()
except:
try:
self.ra = self.data['x_world'].copy()
except:
self.ra = None
if self.decfield is not None:
try:
self.dec = self.data[self.decfield].copy()
except:
try:
self.dec = self.data['y_world'].copy()
except:
self.dec = None
""" Make sure that values are in the correct range """
self.ra = self.ra.astype(float)
self.dec = self.dec.astype(float)
print(self.ra)
print(type(self.ra))
ramask = (self.ra >= 0.) & (self.ra < 360.)
decmask = (self.dec >= -90.) & (self.dec <= 90.)
mask = (ramask) & (decmask)
self.ra = self.ra[mask]
self.dec = self.dec[mask]
self.data = self.data[mask]
"""
Put data into a SkyCoords container for easy coordinate-based calculations
"""
if (self.ra is not None) and (self.dec is not None):
"""
Determine whether the RA coordinate is in hours or in degrees
For now this test is made simple: if the format of the RA data is
a string, then the data is expected to be in hms format, otherwise
expect decimal degrees.
"""
if type(self.ra[0]) is str or type(self.ra[0]) is np.string_:
raunit = u.hourangle
else:
raunit = u.deg
self.radec = SkyCoord(self.ra, self.dec, unit=(raunit, u.deg))
"""
If radec has not been set, report this information
(consider raising an exception in future versions of the code)
"""
if self.radec is None:
print('')
print(
'WARNING: get_radec was called but RA and Dec information was')
print(
' not found. Please check the format of your catalog.'
)
print('')
#----------------------------------------------------------------------
def read_centpos(self, posfile, verbose=False):
"""
Reads a position in from a file and converts it to an astropy SkyCoord
format.
NOTE: right now this is hard-wired to just read in a file in the
standard Keck starlist format:
label rahr ramin rasec decdeg decamin decasec equinox
which matches the *.pos in CDF's Lenses/Data/* directories
Inputs:
posfile - file containing the RA and dec
"""
""" Read the data from the file """
posinfo = ascii.read(posfile,
names=[
'object', 'rahr', 'ramin', 'rasec', 'decdeg',
'decamin', 'decasec', 'equinox'
])
""" Convert to SkyCoord format """
i = posinfo[0]
ra = '%d:%d:%f' % (i['rahr'], i['ramin'], i['rasec'])
dec = '%d:%d:%f' % (i['decdeg'], i['decamin'], i['decasec'])
radec = SkyCoord(ra, dec, unit=(u.hourangle, u.deg))
""" Print out information if requested """
if verbose:
print('')
print('Object: %s' % i['object'])
print('Coordinates: %s %s' % \
(radec.ra.to_string(unit=u.hourangle, decimal=False,
sep=':', precision=3, pad=True),
radec.dec.to_string(decimal=False, sep=':', precision=3,
alwayssign=True, pad=True)))
""" Save the output within the class """
self.centpos = radec
#----------------------------------------------------------------------
def sort_by_pos(self, centpos):
"""
Sorts the catalog in terms of distance from some central position, which
is passed as a SkyCoord variable (from astropy.coordinates)
"""
""" First check to see that we actual have WCS information """
if self.radec is None:
print('')
print('ERROR: sort_by_pos. No WCS information in catalog')
print('')
return
""" Otherwise, use the SkyCoords functionality to easily sort """
sep = self.radec.separation(centpos)
try:
offsets = centpos.spherical_offsets_to(self.radec)
except:
offsets = None
ind = np.argsort(sep.arcsec)
if self.catformat == 'ascii':
self.data = self.data[ind, :]
else:
print(self.catformat)
self.data = self.data[ind]
""" Also sort things that are outside the data table """
self.radec = self.radec[ind]
self.ra = self.ra[ind]
self.dec = self.dec[ind]
self.sep = sep[ind]
if offsets is None:
self.dx = None
self.dy = None
else:
self.dx = (offsets[0].arcsecond)[ind]
self.dy = (offsets[1].arcsecond)[ind]
self.sortind = ind
#-----------------------------------------------------------------------
def make_reg_file(self,
outfile,
rcirc,
color='green',
fluxcol=None,
fluxerrcol=None,
labcol=None,
labdx=0.0012,
labdy=0.0012,
plot_high_snr=False,
mask=None,
snrgood=10.):
"""
Uses the RA and Dec info in the catalog to make a region file that
can be used with ds9.
"""
"""
Start by putting the RA and Dec info into a somewhat more convenient
format
"""
self.get_radec()
if self.radec is None:
print('')
print(
"ERROR: Could not read RA and Dec information from input file")
return
"""
If the flux information is given, then report on high SNR detections
"""
ngood = 0
snrmask = None
if fluxcol is not None and fluxerrcol is not None:
if self.informat == 'ldac':
if type(fluxcol) is int:
flux = self.data.field(fluxcol)
fluxerr = self.data.field(fluxerrcol)
else:
flux = self.data[fluxcol]
fluxerr = self.data[fluxerrcol]
else:
flux = self.data['f%d' % fluxcol]
fluxerr = self.data['f%d' % fluxerrcol]
snr = flux / fluxerr
snrmask = snr > snrgood
""" Mask the input data if requested """
print('Total objects in catalog: %d' % len(self.radec))
if mask is not None:
radec = self.radec[mask]
selmask = mask
print('Objects selected by mask: %d' % len(radec))
else:
radec = self.radec
selmask = np.ones(len(radec), dtype=bool)
ntot = len(radec)
radeg = radec.ra.degree
decdeg = radec.dec.degree
""" Select the high SNR objects, if requested """
if snrmask is not None:
selsnrmask = (selmask) & (snrmask)
radecgood = self.radec[selsnrmask]
ngood = len(radecgood)
print('Of those, objects with SNR>%.1f: %d' % (snrgood, ngood))
gradeg = radecgood.ra.degree
gdecdeg = radecgood.dec.degree
""" Write the output region file """
f = open(outfile, 'w')
f.write('global color=%s\n' % color)
for i in range(ntot):
f.write('fk5;circle(%10.6f,%+10.6f,%.1f")\n' %
(radeg[i], decdeg[i], rcirc))
if plot_high_snr and ngood > 0:
f.write('global color=red\n')
for i in range(ngood):
f.write('fk5;circle(%10.6f,%+10.6f,0.0011)\n' \
%(gradeg[i],gdecdeg[i]))
""" Add labels if requested """
if labcol is not None:
lab = self.data[labcol][selmask]
cosdec = np.cos(pi * self.dec[selmask] / 180.)
xx = self.ra[selmask] + labdx * cosdec
yy = self.dec[selmask] + labdy
f.write('global color=%s\n' % color)
for i in range(ntot):
f.write('fk5;text(%10.6f,%+10.6f) # text={%s}\n'% \
(xx[i],yy[i],str(lab[i])))
""" Wrap up """
print("Wrote region file %s" % outfile)
f.close()
#-----------------------------------------------------------------------
def _print_autoslit_infile(self,
filename,
galmask,
starmask,
maskcent,
magcol,
smagcol,
objroot=None,
add_lens=False,
ndigits=4):
"""
This method is called by lrismask_prep. It prints out a file that
is used as input for the autoslit3 code.
"""
""" Set up the object name column """
ind = np.arange(len(self.data)) + 1
objname = np.zeros(len(self.data), dtype='U16')
if objroot is not None:
for i, obj in enumerate(ind):
objname[i] = '%s_%04d' % (objroot, obj)
else:
for i, obj in enumerate(ind):
objname[i] = '%04d' % obj
""" Set up the output table """
outnames = [
'name', 'priority', 'mag', 'rahr', 'ramin', 'rasec', 'decdeg',
'decamin', 'decasec', 'epoch', 'equinox', 'pm_ra', 'pm_dec'
]
tmpgal = self.data[galmask]
radec = self.radec[galmask]
pri = np.ones(len(tmpgal)) * 100
tmpgal[magcol][tmpgal[magcol] < 0.] = 99.
epoch = np.ones(len(tmpgal)) * 2000.
pm = np.zeros(len(tmpgal))
galtab = Table([
objname[galmask], pri, tmpgal[magcol], radec.ra.hms.h,
radec.ra.hms.m, radec.ra.hms.s, radec.dec.dms.d,
np.fabs(radec.dec.dms.m),
np.fabs(radec.dec.dms.s), epoch, epoch, pm, pm
],
names=outnames)
""" Set up the guidestar table """
tmpstar = self.data[starmask]
radec = self.radec[starmask]
pri = np.ones(len(tmpstar)) * -1
epoch = np.ones(len(tmpstar)) * 2000.
pm = np.zeros(len(tmpstar))
starname = np.zeros(len(tmpstar), dtype='U16')
starind = ind[starmask]
for i, si in enumerate(starind):
starname[i] = 'S%04d' % si
startab = Table([
starname, pri, tmpstar[smagcol], radec.ra.hms.h, radec.ra.hms.m,
radec.ra.hms.s, radec.dec.dms.d,
np.fabs(radec.dec.dms.m),
np.fabs(radec.dec.dms.s), epoch, epoch, pm, pm
],
names=outnames)
"""
Make a mini-table containing the mask center and, optionally, the lens.
These one or two lines will be at the top of the output file
"""
if add_lens:
hdrrows = 2
else:
hdrrows = 1
hdrtab = Table(np.zeros((hdrrows, (len(outnames) - 1))),
names=outnames[1:])
hdrtab.add_column(galtab['name'][:hdrrows], index=0)
ra = maskcent.ra
dec = maskcent.dec
hdrtab[0] = [
'CENTER', 9999, 0., ra.hms.h, ra.hms.m, ra.hms.s, dec.dms.d,
fabs(dec.dms.m),
fabs(dec.dms.s), 2000., 2000., 0., 0.
]
if add_lens:
cra = self.centpos.ra.hms
cdec = self.centpos.dec.dms
hdrtab[1] = [
'Lens', 900, 20., cra.h, cra.m, cra.s, cdec.d,
fabs(cdec.m),
fabs(cdec.s), 2000., 2000., 0., 0.
]
""" Combine the two tables """
outtab = vstack([hdrtab, galtab, startab])
""" Set up the formatting """
outtab['priority'].format = '%4d'
outtab['mag'].format = '%5.2f'
outtab['rahr'].format = '%02d'
outtab['ramin'].format = '%02d'
outtab['rasec'].format = '%06.3f'
outtab['decdeg'].format = '%+03d'
outtab['decamin'].format = '%02d'
outtab['decasec'].format = '%05.2f'
outtab['epoch'].format = '%6.1f'
outtab['equinox'].format = '%6.1f'
outtab['pm_ra'].format = '%3.1f'
outtab['pm_dec'].format = '%3.1f'
print('')
print(outtab)
""" Save the table to the output file """
print('')
print('Writing selected objects to %s' % filename)
outtab.write(filename, format='ascii.no_header', overwrite=True)
#-----------------------------------------------------------------------
def lrismask_prep(self,
maskcent,
PA,
mask_w=3.,
mask_h=7.,
galmagcol='r',
galmagrange=None,
galmask='default',
starmask='default',
smagcol='g',
smaglim=[17., 19.],
galreg='maskobj.reg',
objcolor='green',
rcirc=1.,
starreg='maskstar.reg',
add_lens=True,
outfile=None,
objroot=None):
"""
Code to select objects for a LRIS slitmask
"""
"""
Make sure that the catalog has been sorted, since this code needs to
use the self.dx and self.dy arrays
"""
if self.dx is None:
print('')
print(
'Position offsets are missing. You must run sort_by_pos first'
)
print('')
return
""" Get the offset of the mask center from the origin of (dx,dy) """
maskcoord = SkyCoord(maskcent[0], maskcent[1], unit=(u.deg, u.deg))
maskxy = self.centpos.spherical_offsets_to(maskcoord)
print('Requested mask center has (dx,dy) = (%+7.2f, %+7.2f)' %
(maskxy[0].arcsec, maskxy[1].arcsec))
"""
Translate and rotate the object (dx,dy) to a masked-centered frame in
which the mask is rectilinear. That is, first make the mask center
the origin and then rotate by the NEGATIVE of the mask PA.
"""
rot_ang = -1. * PA * pi / 180.
xtmp = (self.dx - maskxy[0].arcsec)
ytmp = (self.dy - maskxy[1].arcsec)
xx = xtmp * np.cos(rot_ang) + ytmp * np.sin(rot_ang)
yy = -xtmp * np.sin(rot_ang) + ytmp * np.cos(rot_ang)
""" Select only the objects that lie within the mask """
star_extra = 75.
xbound = 0.5 * mask_w * 60.
ybound = 0.5 * mask_h * 60.
objmask = (xx >= -xbound) & (xx <= xbound) & (yy >= -ybound) \
& (yy <= ybound)
starsonmask = (xx >= -xbound-star_extra) & (xx <= xbound+star_extra) & \
(yy >= -ybound) & (yy <= ybound)
""" Choose the galaxies and stars that fall within the mask """
if galmask == 'default':
if self.galmask is not None:
totgalmask = np.logical_and(self.galmask, objmask)
else:
totgalmask = objmask
elif galmask is not None:
totgalmask = np.logical_and(galmask, objmask)
else:
totgalmask = objmask
if starmask == 'default':
if self.starmask is not None:
totstarmask = np.logical_and(self.starmask, starsonmask)
else:
totstarmask = starsonmask
elif starmask is not None:
totstarmask = np.logical_and(starmask, starsonmask)
else:
totstarmask = starsonmask
stardata = self.data[smagcol].astype(float)
guidestarmask = totstarmask & (stardata >= smaglim[0]) & \
(stardata <= smaglim[1])
""" Make ds9 region files for diagnostic checks """
print('')
print('Making ds9 region file for possible targets for slitmask')
self.make_reg_file(galreg, rcirc, color=objcolor, mask=totgalmask)
print('')
print('Making ds9 region file for possible guide stars for slitmask')
self.make_reg_file(starreg,
rcirc * 1.5,
color='red',
mask=guidestarmask)
""" Write out the autoslit3 input file """
if outfile is not None:
self._print_autoslit_infile(outfile,
totgalmask,
guidestarmask,
maskcoord,
galmagcol,
smagcol,
objroot=objroot,
add_lens=add_lens)
#-----------------------------------------------------------------------
#def plot_radec(self, symb='bo'):
#-----------------------------------------------------------------------
def plot_fwhm(self,
fwhmcol='FWHM_IMAGE',
magcol='MAG_AUTO',
xlim=(0, 15),
ylim=(28, 16)):
"""
Plots FWHM vs. magnitude. This can be used to find the stellar locus
and, thus, determine the seeing.
Inputs:
fwhmcol - column name for the FWHM data. Default = 'fwhm_image'
magcol - column name for the magnitude data. Default = 'mag_auto'
xlim - initial limits for FWHM axis on plot. Default = (0,15)
ylim - initial limits for mag axis on plot. Default = (28,16)
"""
try:
fwhm = self.data[fwhmcol]
except KeyError:
print('')
print('Catalog does not contain a %d column' % fwhmcol)
print('')
return
try:
mag = self.data[magcol]
except KeyError:
print('')
print('Catalog does not contain a %d column' % magcol)
print('')
return
plt.plot(fwhm, mag, 'bo')
plt.xlim(xlim)
plt.ylim(ylim)
plt.xlabel('FWHM (pixels)')
plt.ylabel('Magnitude')
plt.show()
#-----------------------------------------------------------------------
def plot_nhist(self,
magcol='MAG_AUTO',
usestarmask=False,
magmin=15,
magmax=28,
color='b',
alpha=1.):
"""
Plots a histogram of galaxy magnitudes (similar to a log N-log S plot)
that can be used to determine the magnitude to which the catalog is
complete. A minimum FWHM can be set in order to select objects that
are likely to be galaxies, but this is not required.
Inputs:
magcol - column containing the magnitudes. Default = 'mag_auto'
usestarmask - when this parameter is set to True, then use the
starmask mask to select the galaxies.
NOTE: this means that the set_starmask method has to
have been run for each of the input catalogs, or
else all objects will be plotted
Default=False
magmin - minimum magnitude to use for the plot. Default=15
magmax - maximum magnitude to use for the plot. Default=28
"""
""" Get the magnitudes to be plotted """
if usestarmask:
if self.starmask is None:
print('')
print('WARNING: you have set usestarmask=True but there are')
print(' no stars selected by the starmask')
print('Please make sure that set_starmask has been run BEFORE'
'runing plot_nhist')
print(' if you want to use this mask')
print('')
return
else:
mag = (self.data[self.starmask == False][magcol]).copy()
else:
mag = self.data[magcol].copy()
mag = mag[np.isfinite(mag)]
""" Plot the histogram """
nbins = int(2 * (magmax - magmin))
plt.hist(mag,
range=(magmin, magmax),
bins=nbins,
color=color,
alpha=alpha)
del (mag)
#-----------------------------------------------------------------------
def match_radec(self, ra2, dec2, rmatch, dra2=0., ddec2=0., doplot=True):
"""
*** UNDER CONSTRUCTION! DO NOT USE YET. ***
Given a list of ra,dec coordinates (ra2, dec2), possibly from a second
catalog, and a match tolerance, find the matches to the catalog
contained in self.data
Inputs:
ra2 - RA (decimal degrees) for catalog
dec2 - Dec (decimal degrees) for second catalog
rmatch - max distance for a valid match (arcsec)
dra2 - optional offset in ARCSEC to apply to ra2, if there is a known
offset between the catalogs (default=0.0)
ddec2 - optional offset in ARCSEC to apply to dec2, if there is a
known offset between the catalogs (default=0.0)
"""
print('')
print("Matching catalogs: basic info")
print("--------------------------------------------")
print(" Catalog 1: %d coordinates" % self.ra.size)
print(" Catalog 2: %d coordinates" % ra2.size)
""" Initialize containers for output information """
ramatch = np.zeros(self.ra.size)
decmatch = np.zeros(self.ra.size)
self.nmatch = np.zeros(self.ra.size, dtype=int)
self.matchdx = np.zeros(self.ra.size)
self.matchdy = np.zeros(self.ra.size)
self.indmatch = np.ones(self.ra.size, dtype=int) * -1
""" Correct for known shifts """
ra2 = ra2.copy() + dra2 / (3600. * np.cos(dec2))
dec2 = dec2.copy() + ddec2 / 3600.
""" Loop over catalog """
print('')
print("Searching for matches...")
print("------------------------------")
for i in range(self.ra.size):
dx, dy = coords.sky_to_darcsec(self.ra[i], self.dec[i], ra2, dec2)
dpos = np.sqrt(dx**2 + dy**2)
isort = np.argsort(dpos)
if dpos[isort[0]] <= rmatch:
ramatch[i] = self.ra[i]
decmatch[i] = self.dec[i]
self.matchdx[i] = dx[isort[0]]
self.matchdy[i] = dy[isort[0]]
self.nmatch[i] = dpos[dpos <= rmatch].size
self.indmatch[i] = isort[0]
del dx, dy, dpos
print(" Number of matches between the catalogs: %d" %
(self.nmatch > 0).sum())
mra = ramatch[self.nmatch > 0]
mdec = decmatch[self.nmatch > 0]
mdx = self.matchdx[self.nmatch > 0]
mdy = self.matchdy[self.nmatch > 0]
mdx0 = np.median(mdx)
mdy0 = np.median(mdy)
print(" Median offset for matches (RA): %+6.2f arcsec" % mdx0)
print(" Median offset for matches (Dec): %+6.2f arcsec" % mdy0)
""" Plot up some offsets, if desired """
if doplot:
plt.figure(1)
plt.scatter(mdx, mdy)
plt.axis('scaled')
plt.xlabel(r'$\Delta \alpha$ (arcsec)')
plt.ylabel(r'$\Delta \delta$ (arcsec)')
plt.title('Offsets between matched sources (rmatch = %5.2f)' %
rmatch)
plt.axvline(0.0, color='r')
plt.axhline(0.0, color='r')
plt.plot(np.array([mdx0]), np.array([mdy0]), 'r*', ms=20)
plt.xlim(-1.1 * rmatch, 1.1 * rmatch)
plt.ylim(-1.1 * rmatch, 1.1 * rmatch)
plt.figure(2)
#
ax1 = plt.subplot(221)
plt.scatter(mra, mdy)
plt.setp(ax1.get_xticklabels(), visible=False)
plt.ylabel(r'$\Delta \delta$ (arcsec)')
plt.axhline(0.0, color='r')
#
ax2 = plt.subplot(223, sharex=ax1)
plt.scatter(mra, mdx)
plt.xlabel(r'$\alpha$')
plt.ylabel(r'$\Delta \alpha$ (arcsec)')
plt.axhline(0.0, color='r')
#
ax3 = plt.subplot(222, sharey=ax1)
plt.scatter(mdec, mdy)
plt.axhline(0.0, color='r')
plt.setp(ax3.get_xticklabels(), visible=False)
plt.setp(ax3.get_yticklabels(), visible=False)
#
ax4 = plt.subplot(224)
plt.scatter(mdec, mdx)
plt.xlabel(r'$\delta$')
plt.axhline(0.0, color='r')
plt.setp(ax4.get_yticklabels(), visible=False)
plt.show()
""" Clean up """
del ramatch, decmatch
del mdx, mdy, mra, mdec
#-----------------------------------------------------------------------
def print_ccmap(self, outfile, verbose=True):
"""
Prints out a file that can be used as the input for the pyraf ccmap
task. This file has 4 columns: x y RA Dec
Inputs:
outfile - output file to be used as input for ccmap
verbose - print task info
"""
if verbose:
print('')
print("Printing to file for use in ccmap: %s" % outfile)
print('')
f = open(outfile, 'w')
f.write('# (x,y) catalog: %s\n' % self.infile)
f.write('# Astrometric catalog: %s\n' % self.matchcat)
f.write('# Columns are x y RA Dec\n')
for i in range(self.nmatch):
f.write('%8.2f %8.2f %11.7f %+11.7f\n' % \
(self.matchx[i],self.matchy[i],self.matchra[i],
self.matchdec[i]))
f.close()
#-----------------------------------------------------------------------
def find_closest_xy(self, xast, yast, xcol, ycol):
"""
Finds the closest match, in (x,y) space to each member of the astrometric
catalog (represented by xast,yast).
"""
self.matchind = np.zeros(xast.size, dtype=int)
xfield = 'f%d' % xcol
yfield = 'f%d' % ycol
for i in range(xast.size):
dx = xast[i] - self.data[xfield]
dy = yast[i] - self.data[yfield]
dpos = dx**2 + dy**2
sindex = np.argsort(dpos)
self.matchind[i] = sindex[0]
self.matchdx = xast - self.data[xfield][self.matchind]
self.matchdy = yast - self.data[yfield][self.matchind]
#-----------------------------------------------------------------------
def match_xy(self, xa, ya, max_offset=None, xcol=8, ycol=9, verbose=True):
"""
Find the closest match to each astrometric catalog object and calculate the
offsets.
Do two loops, to deal with possible confusion of sources on first pass
through
"""
dxmed = 0
dymed = 0
for i in range(2):
if verbose:
print('')
print('Pass %d' % (i + 1))
print('------------------------')
xa0 = xa - dxmed
ya0 = ya - dymed
self.find_closest_xy(xa0, ya0, xcol, ycol)
dxmed = np.median(self.matchdx)
dymed = np.median(self.matchdy)
if max_offset is not None:
dpos = np.sqrt(self.matchdx**2 + self.matchdy**2)
goodmask = dpos < max_offset
if verbose:
print("Applying a maximum offset cut of %7.1f pixels" %
max_offset)
print("Median shifts before clipping: %7.2f %7.2f" %
(dxmed, dymed))
else:
goodmask = np.ones(xa.size, dtype=bool)
dxm = self.matchdx[goodmask]
dym = self.matchdy[goodmask]
dxmed = np.median(dxm)
dymed = np.median(dym)
if verbose:
print("Median shifts after pass: %7.2f %7.2f" %
(dxmed, dymed))
"""
Transfer information into object and clean up
"""
if verbose:
print('')
print('Found %d astrometric objects within FOV of image' % xa.size)
print('Matched %d objects to astrometric catalog.' % dxm.size)
self.nmatch = dxm.size
self.goodmask = goodmask.copy()
self.matchind = self.matchind[goodmask]
del xa0, ya0, goodmask
#-----------------------------------------------------------------------
def match_fits_to_ast(self,
fitsfile,
astcat,
outfile=None,
max_offset=None,
racol=1,
deccol=2,
xcol=8,
ycol=9,
doplot=True,
edgedist=50.,
imhdu=0,
verbose=True):
"""
Given the fits file from which this object (self) was defined
and an astrometric catalog, find the closest matches of the
astrometric objects to those contained in this object, using the WCS
information in the fits header.
"""
if (verbose):
print("Running match_fits_to_ast with:")
print(" fitsfile = %s" % fitsfile)
print(" astcat = %s" % astcat)
self.infits = fitsfile
self.matchcat = astcat
"""
Start by opening the fits file and reading the appropriate columns from
the catalogs
"""
hdulist = imf.open_fits(fitsfile)
hdr = hdulist[imhdu].header
if verbose:
print('')
hdulist.info()
"""
Select the astrometric catalog objects that fall within the fits file FOV
(at least with its current WCS)
"""
# raa,deca,xa,ya,astmask = select_good_ast(astcat,hdr,racol,deccol,edgedist)
if verbose:
print('Found %d astrometric objects within FOV of image' %
raa.size)
"""
Find the closest match to each astrometric catalog object
"""
self.match_xy(xa, ya, max_offset, xcol, ycol, verbose)
""" Transfer info about matches into the object """
xfield = 'f%d' % xcol
yfield = 'f%d' % ycol
self.astmask = astmask.copy()
self.matchx = self.data[xfield][self.matchind].copy()
self.matchy = self.data[yfield][self.matchind].copy()
self.matchra = raa[self.goodmask].copy()
self.matchdec = deca[self.goodmask].copy()
self.matchdx = self.matchdx[self.goodmask]
self.matchdy = self.matchdy[self.goodmask]
""" Plot the offsets if desired """
if doplot:
dxmed = np.median(self.matchdx)
dymed = np.median(self.matchdx)
plt.figure()
plt.scatter(self.matchdx, self.matchdy)
plt.xlabel('x offset (pix)')
plt.ylabel('y offset (pix)')
plt.axhline(color='k')
plt.axvline(color='k')
plt.axvline(dxmed, color='r')
plt.axhline(dymed, color='r')
print('')
print("Black lines represent x=0 and y=0 axes")
print("Red lines show median offsets of dx_med=%7.2f and "
"dy_med=%7.2f" % (dxmed, dymed))
#plt.show()
""" Write the output file, in a format appropriate for input to ccmap """
if outfile is not None:
self.print_ccmap(outfile, verbose)
""" Clean up """
hdulist.close()
del hdr, raa, deca, xa, ya, astmask
# -----------------------------------------------------------------------
def set_starmask(self, mask):
"""
Takes the input mask and assigns it to an internal mask associated
with this instance of the ObjCat class.
The internal mask is called starmask and has values of True for objects
that have been identified as stars by the provided external mask.
The external mask will be based on some characteristics in the catalog.
Examples could be objects with a SExtractor CLASS_STAR value greater
than 0.7, or a FWHM_IMAGE less than a certain value, or ...
"""
self.starmask = mask
# -----------------------------------------------------------------------
def set_galmask(self, mask):
self.galmask = mask
def proc_sa104(file_path=None,outdir=None, bias_fil=None):
from astropy.coordinates import ICRS
from astropy.io import ascii
from astropy import units as u
from astropy.io.fits import getdata
import xastropy.PH136.experiments.hrdiagram as hrd
# Defaults
if file_path == None:
file_path = 'Raw/'
if outdir == None:
outdir = 'Std/'
# Bias frame
if bias_fil == None:
bias_fil = 'Bias.fits'
bias_img,bias_head = getdata(bias_fil,0,header=True)
# Read Log
data = ascii.read('simple.log',delimiter='|')
nfil = len(data)
all_coord = ICRS(ra=data['RA'], dec=data['DEC'], unit=(u.hour,u.degree))
# M67 coords
sa104_rac = '12:43:44.3'
sa104_decc = '-00:29:40.0'
sa104_c = ICRS(sa104_rac, sa104_decc, unit=(u.hour,u.degree))
# Find all SA 104
sep = (sa104_c.separation(all_coord)).degree
isa104, = np.where( sep < 1. ) # 1 degree
sa104 = data[isa104]
# Filters
all_filt=np.array(sa104['Filter'])
filters,ifilt = np.unique(all_filt,return_index=True)
# Loop on Filterse
all_fil = []
for ff in filters:
# Load Sky frame
skyfil = 'Sky_'+ff+'.fits'
sky_img,head = getdata(skyfil,0,header=True)
# Images
idx = np.where(sa104['Filter'] == ff)
# Loop on images
for kk in np.concatenate(idx,axis=0):
# Read
img,head = getdata(sa104[kk]['File'],0,header=True)
# Bias subtract
img = img - bias_img
# Trim
timg = hrd.trimflip_img(img)
# Flat field
timg = timg / sky_img
# Normalize by exposure
timg = timg / sa104[kk]['Exp']
# Filename
outfil = outdir+'SA104_t'+str(int(sa104[kk]['Exp']))+'_'+ff+'.fits'
# Check for duplicate
flg_skip = 0
mt = [i for i in range(len(all_fil)) if all_fil[i] == outfil]
if len(mt) > 0:
print 'Duplicate image', outfil
print 'Skipping...'
continue
all_fil.append(outfil)
# Write
print 'Writing ', outfil
fits.writeto(outfil, timg, head, clobber=True)
return
def proc_m67(file_path=None,outdir=None, bias_fil=None):
from astropy.coordinates import ICRS
from astropy.io import ascii
from astropy import units as u
from astropy.io.fits import getdata
import xastropy.PH136.experiments.hrdiagram as hrd
# Defaults
if file_path == None:
file_path = 'Raw/'
if outdir == None:
outdir = 'Science/'
# Bias frame
if bias_fil == None:
bias_fil = 'Bias.fits'
bias_img,bias_head = getdata(bias_fil,0,header=True)
# Read Log
data = ascii.read('simple.log',delimiter='|')
nfil = len(data)
all_coord = ICRS(ra=data['RA'], dec=data['DEC'], unit=(u.hour,u.degree))
# M67 coords
m67_rac = '08:54:24'
m67_decc = '+11:49:00'
m67_c = ICRS(m67_rac, m67_decc, unit=(u.hour,u.degree))
# Find all M67
sep = (m67_c.separation(all_coord)).degree
im67, = np.where( sep < 1. ) # 1 degree
m67 = data[im67]
# 5 positions
m67_ra = ['08:52:02.2', '08:52:15.3', '08:51:49.9', '08:51:50.0', '08:52:16.2']
m67_dec = ['+11:52:41.0', '+11:55:51.0', '+11:55:53.0', '+11:49:38.0', '+11:49:40.0']
m67_pointings = ICRS(ra=m67_ra, dec=m67_dec, unit=(u.hour, u.degree))
# Filters
all_filt=np.array(m67['Filter'])
filters,ifilt = np.unique(all_filt,return_index=True)
# Loop on Filterse
all_fil = []
for ff in filters:
# Load Sky frame
skyfil = 'Sky_'+ff+'.fits'
sky_img,head = getdata(skyfil,0,header=True)
# Images
idx = np.where(m67['Filter'] == ff)
# Loop on images
for kk in np.concatenate(idx,axis=0):
# Read
img,head = getdata(m67[kk]['File'],0,header=True)
# Bias subtract
img = img - bias_img
# Trim
timg = hrd.trimflip_img(img)
# Flat field
timg = timg / sky_img
# Normalize by exposure
timg = timg / m67[kk]['Exp']
# Filename
coord = ICRS(head['RA'], head['DEC'], unit=(u.hour,u.degree))
sep = (coord.separation(m67_pointings)).degree
ipos = np.argmin(sep)
outfil = outdir+'M67_C'+str(ipos)+'_t'+str(int(m67[kk]['Exp']))+'_'+ff+'.fits'
# Check for duplicate
flg_skip = 0
mt = [i for i in range(len(all_fil)) if all_fil[i] == outfil]
if len(mt) > 0:
print 'Duplicate image', outfil
print 'Skipping...'
continue
all_fil.append(outfil)
# Write
print 'Writing ', outfil
fits.writeto(outfil, timg, clobber=True)
return
def PulsarVis(sourcename, times):
if sourcename in {'PSRJ0030+0451', 'PSRJ0437-4715'}:
SunAvoidance = 55.0 * u.deg
else:
SunAvoidance = 45.0 * u.deg
print("Sun Avoidance: {0:.3f}".format(SunAvoidance))
MoonAvoidance = 15.0 * u.deg
# Each pulsar's feasible observation range based on ISS hardware data
if sourcename in 'PSRB1821-24': #Analysis ticket 890
HardwareUpperAvoidance = 120 * u.deg #360*u.deg
HardwareLowerAvoidance = 88 * u.deg #0*u.deg
elif sourcename in 'PSRB1937+21':
HardwareUpperAvoidance = 142.0 * u.deg #360*u.deg
HardwareLowerAvoidance = 91.0 * u.deg #0*u.deg
elif sourcename in 'PSRJ0218+4232':
HardwareUpperAvoidance = 156.0 * u.deg #360*u.deg
HardwareLowerAvoidance = 88.0 * u.deg #0*u.deg
elif sourcename in 'PSRJ0030+0451':
HardwareUpperAvoidance = 148.0 * u.deg #360*u.deg
HardwareLowerAvoidance = 95.0 * u.deg #0*u.deg
elif sourcename in 'PSRJ0437-4715':
HardwareUpperAvoidance = 95.0 * u.deg #360*u.deg
HardwareLowerAvoidance = 35.0 * u.deg #0*u.deg
else:
HardwareUpperAvoidance = 360.0 * u.deg #360*u.deg
HardwareLowerAvoidance = 0.0 * u.deg #0*u.deg
print("ISS Upper:", HardwareUpperAvoidance, "Lower:",
HardwareLowerAvoidance, "\n".format(HardwareLowerAvoidance,
HardwareUpperAvoidance))
tle160lines = [
'1 25544U 98067A 17160.91338884 +.00001442 +00000-0 +29152-4 0 9993',
'2 25544 051.6425 074.5823 0004493 253.3640 193.9362 15.54003243060621'
]
tle167lines = [
'1 25544U 98067A 17167.53403196 +.00002711 +00000-0 +48329-4 0 9994',
'2 25544 051.6431 041.5846 0004445 283.0899 147.8207 15.54043876061656'
]
platform = 'ISS (ZARYA)'
# Set up two TLEs so we can compute the precession rate from the
# change of RA of ascending node with time
tle1 = tlefile.read(platform, line1=tle160lines[0], line2=tle160lines[1])
tle2 = tlefile.read(platform, line1=tle167lines[0], line2=tle167lines[1])
# print(platform)
ISSInclination = tle2.inclination * u.deg
# print("Inclination = {0:.3f}".format(ISSInclination))
StarboardPoleDec0 = -1 * (90.0 * u.deg - ISSInclination)
PortPoleDec0 = -1 * StarboardPoleDec0
#print("Starboard Orbit Pole Declination {0:.2f}".format(StarboardPoleDec0))
# print("Port Orbit Pole Declination {0:.2f}".format(PortPoleDec0))
# Compute ISS precession rate in degrees per day
ISSPrecessionRate = (tle2.right_ascension - tle1.right_ascension) / (
tle2.epoch_day - tle1.epoch_day) * u.deg / u.d
# print("ISS Precession Rate {0:.3f} ({1:.3f} period)".format(ISSPrecessionRate,
# np.abs(360.0*u.deg/ISSPrecessionRate)))
ttle2 = Time("{0:4d}-01-01T00:00:00".format(int(tle2.epoch_year) + 2000),
format='isot',
scale='utc') + tle2.epoch_day * u.d
# print("ttle2 = ",ttle2.isot)
StarboardPoleRA0 = np.fmod(tle2.right_ascension + 90.0, 360.0) * u.deg
PortPoleRA0 = np.fmod(StarboardPoleRA0 + 180.0 * u.deg, 360.0 * u.deg)
# print("Starboard Pole RA @ ttle2 = {0:.3f}".format(StarboardPoleRA0))
# print("Port Pole RA @ ttle2 = {0:.3f}".format(PortPoleRA0))
def StarboardPoleDec(t):
return np.ones_like(t) * StarboardPoleDec0
def PortPoleDec(t):
return np.ones_like(t) * StarboardPoleDec0
def StarboardPoleRA(t):
return np.fmod(
StarboardPoleRA0 + (t - ttle2).to(u.d) * ISSPrecessionRate,
360.0 * u.deg)
def PortPoleRA(t):
return np.fmod(StarboardPoleRA(t) + 180.0 * u.deg, 360.0 * u.deg)
def StarboardPoleCoord(t):
return SkyCoord(StarboardPoleRA(t).value,
StarboardPoleDec(t).value,
unit=u.deg,
frame="icrs")
def PortPoleCoord(t):
return SkyCoord(PortPoleRA(t).value,
PortPoleDec(t).value,
unit=u.deg,
frame="icrs")
now = Time.now()
doy_now = np.float(now.yday.split(':')[1])
# print("Current DOY = {0}".format(np.int(doy_now)))
#print("StarboardPoleRA (now) = {0:.3f}".format(StarboardPoleRA(now)))
#print("PortPoleRA (now) = {0:.3f}".format(PortPoleRA(now)))
if sourcename[0:2] != 'PSR':
SourcePos = get_icrs_coordinates(sourcename)
else:
splitstr = sourcename.split(',')
SourcePos = ICRS(ra=Angle(double(splitstr[0])),
dec=Angle(double(splitstr[1])))
#print("\nSource: {0} at {1}, {2}".format(sourcename,SourcePos.ra, SourcePos.dec))
#print("Separation from Starboard Pole = {0:.3f}".format(SourcePos.separation(StarboardPoleCoord(now))))
#print("Separation from Port Pole = {0:.3f}".format(SourcePos.separation(PortPoleCoord(now))))
#Calculate terms and references to do check
#doy2XXX = np.arange(365.0)
#times = doy2XXX*u.d + startepoch
issseps = SourcePos.separation(StarboardPoleCoord(times)).to(u.deg)
# The Sun and Moon positions are returned in the GCRS frame
# Convert them to ICRS so .separation doesn't go insane when
# comparing different frames with different obstimes.
SunPos = get_sun(times)
SunPos = SkyCoord(SunPos.ra, SunPos.dec, frame='icrs')
MoonPos = get_moon(times)
MoonPos = SkyCoord(MoonPos.ra, MoonPos.dec, frame='icrs')
# Hold indicies when Sun and Moon cause constraint violation
sunseps = SourcePos.separation(SunPos).to(u.deg)
idxsun = sunseps < SunAvoidance
moonseps = SourcePos.separation(MoonPos).to(u.deg)
idxmoon = moonseps < MoonAvoidance
# Hold indicies when sep is outside of 91 to 142 deg due to hardware violation (KWood analysis 10/27/2017)
idxang = ~((issseps > HardwareLowerAvoidance) &
(issseps < HardwareUpperAvoidance))
# Apply all vis constraints
indxall = idxsun | idxmoon | idxang #true when constraint is violated
# Generate and populate signal output
vis = np.ones(len(doy2XXX))
vis[indxall] = float('NaN')
#Return result
return vis
class Secat:
"""
The __init__ method has been changed to return something like a record
array, which has the same number of rows as the old 2D float array, but
which stores each row as a single tuple. It is thus a 1D array, sort of
like a structure array in C. The columns can be accessed by field name,
which for now is just 'f0', 'f1', etc., unless the input catalog is in
SExtractor's FITS LDAC format, in which case the field names actually
correspond to the SExtractor variable names.
The code used to expect the old 2D float array format. It should have
all been updated, but there may still be some issues.
"""
def __init__(self, incat, catformat='ldac', verbose=True, namecol=None,
racol=None, deccol=None, rafield=None, decfield=None,
usecols=False):
"""
This method gets called when the user types something like
secat = Secat(infile)
Inputs:
incat - input table data. This can be in one of two forms:
1. a file containing the catalog (most common)
2. a Table instance containing the catalog data
catformat - format of the input file, if incat is a filename.
The options are:
ascii -
asciitab -
ldac -
sdssfits -
secat -
NOTE: this parameter is not used if incat is a Table
rather than the name of an input file
"""
""" Set a flag showing whether the file has been modified """
self.modified = False
""" Set other default values """
self.radec = None
self.rafield = None
self.decfield = None
self.centpos = None
self.galmask = None
self.starmask = None
"""
Start by loading the catalog information
"""
incattype = (str(type(incat))).split('.')[-1]
if incattype[0:3] == 'Tab' or incattype[0:4] == 'FITS':
self.data = incat.copy()
if rafield:
self.rafield = rafield
if decfield:
self.decfield = decfield
self.nrows = len(incat)
self.ncols = len(incat.columns)
self.catformat = 'Table'
elif isinstance(incat, str):
self.load_from_file(incat, catformat=catformat, verbose=verbose,
namecol=namecol, racol=racol, deccol=deccol,
rafield=rafield, decfield=decfield,
usecols=usecols)
else:
print('')
print('ERROR: input catalog must either be a filename or a Table')
print(' Input catalog type is' + str(type(incat)))
print('')
return None
#-----------------------------------------------------------------------
def load_from_file(self, incat, catformat='ldac', verbose=True, namecol=None,
racol=None, deccol=None, rafield=None, decfield=None,
usecols=False):
if verbose:
print ""
print "Loading data from catalog file %s" % incat
print "-----------------------------------------------"
print "Expected catalog format: %s" % catformat
print ""
"""
Define a flag for successful reading of input catalog
"""
read_success = True
""" Read in catalog in a manner appropriate to the catformat """
if catformat == 'secat':
try:
self.data = ascii.read(incat)
ncols = len(self.data.colnames)
nrows = len(self.data)
""" Set the field names """
self.rafield = 'ALPHA_J2000'
self.decfield = 'DELTA_J2000'
except:
print " ERROR. Problem in loading file %s" % incat
print " Check to make sure filename matches an existing file."
print ""
print " This also may have failed if the input file is in the"
print " SExtractor FITS LDAC format. Checking that..."
print ""
read_success = False
elif catformat == 'asciitab':
f = open(incat)
foo = f.readline()
f.close()
if foo[0] == '#':
try:
self.data = ascii.read(incat, guess=False,
format='commented_header')
except:
print('')
print('ERROR: Could not read data from %s' % incat)
print(' Tried using "commented_header" format but failed')
print(' Please check input file.')
print('')
raise IOError
else:
try:
self.data = ascii.read(incat)
except:
print ''
print 'ERROR: Could not properly read data from %s' % incat
print 'Tried using the automatic formatting but failed'
print ' Please check input file.'
print ''
raise IOError
ncols = len(self.data.colnames)
nrows = len(self.data)
""" Set the field names """
if rafield:
self.rafield = rafield
if decfield:
self.decfield = decfield
elif catformat=='ascii':
""" ASCII format """
try:
""" Set up the data format in the catalog """
foo = np.loadtxt(incat,dtype='S30')
ncols = foo.shape[1]
del foo
coltypes = np.ones(ncols,dtype='S3')
coltypes[:] = 'f8'
if namecol is not None:
print "Object name column: %d" % namecol
coltypes[namecol] = 'S30'
colstr = ''
for i in range(ncols):
colstr = '%s,%s' % (colstr,coltypes[i])
colstr = colstr[1:]
dt = np.dtype(colstr)
""" Actually read in the data """
self.informat = 'ascii'
self.data = np.loadtxt(incat,dtype=dt)
nrows = self.data.shape[0]
""" Set the field names """
if racol is not None:
self.rafield = 'f%d' % racol
else:
self.rafield = None
if deccol is not None:
self.decfield = 'f%d' % deccol
else:
self.decfield = None
if namecol is not None:
self.namefield = 'f%d' % namecol
else:
self.namefield = None
except:
print " ERROR. Problem in loading file %s" % incat
print " Check to make sure filename matches an existing file."
print " "
print " This may have failed if there is a string column in"
print " the input catalog (e.g., for an object name). "
print " If this is the case, use the namecol to indicate which "
print " column contains the string values (column numbers are "
print " zero-indexed)"
print ""
print " This also may have failed if the input file is in the"
print " SExtractor FITS LDAC format. Checking that..."
print ""
read_success = False
elif catformat.lower()=='ldac' or read_success==False:
try:
self.data = Table.read(incat, format='fits', hdu=2)
except:
print " ERROR. Problem in loading file %s" % incat
print " Check to make sure filename matches an existing file."
print " "
return
self.informat = 'ldac'
nrows = len(self.data)
ncols = len(self.data.columns)
""" Set the field names """
self.rafield = 'ALPHA_J2000'
self.decfield = 'DELTA_J2000'
elif catformat.lower()=='sdssfits' or read_success==False:
try:
self.data = Table.read(incat, format='fits', hdu=1)
except:
print " ERROR. Problem in loading file %s" % incat
print " Check to make sure filename matches an existing file."
print " "
return
self.informat = 'sdss'
nrows = len(self.data)
ncols = len(self.data.columns)
""" Set the field names """
self.rafield = 'ra'
self.decfield = 'dec'
"""
Split the stars from the galaxies, according to the SDSS
classification.
In the SDSS scheme, type=3 is a galaxy and type=6 is a star
"""
if 'type' in self.data.colnames:
oclass = self.data['type']
elif 'type_r' in self.data.colnames:
oclass = self.data['type_r']
else:
oclass = None
if oclass is not None:
self.galmask = oclass == 3
self.starmask = oclass == 6
else:
self.galmask = np.ones(dtype=bool)
self.starmask = None
print('Read SDSS catalog from %s' % incat)
print('Number of galaxies: %5d' % self.galmask.sum())
if self.starmask is not None:
print('Number of stars: %5d' % self.starmask.sum())
else:
print ''
print 'Unrecognized format. Must be one of:'
print ' ascii, secat, ldac, sdssfits'
sys.exit()
if verbose:
print "Number of rows: %d" % nrows
print "Number of columns: %d" % ncols
if self.rafield is not None:
print 'RA field name: %s' % self.rafield
if self.decfield is not None:
print 'Dec field name: %s' % self.decfield
self.infile = incat
self.catformat = catformat
self.nrows = nrows
self.ncols = ncols
#-----------------------------------------------------------------------
def close_ldac(self):
"""
Closes the catalog. If the catalog is in fits format and it has
been modified (as shown by the modified parameter in this Secat class)
then use flush rather than close.
"""
""" Close the file if it is in the expected format """
if self.informat == 'ldac':
if self.modified:
self.hdu.flush()
print 'Updating input fits LDAC file: %s' % self.infile
else:
self.hdu.close()
else:
print ''
print 'WARNING. Calling close_ldac but file is not in ldac format'
print ''
#----------------------------------------------------------------------
def make_magmask(self, magname, mfaint=None, mbright=None):
"""
Makes a mask that is True for magnitudes brighter than mfaint and
fainter than mbright.
Note that one of these two could have the value None, in which case
it would be ignored. For example, if mbright is None, then the mask
will be True for all galaxies brighter than mfaint
Inputs:
magname - the name in the catalog for the column that represents the
object magnitudes. This could be something like, e.g., 'r'
or 'MAG_AUTO'
"""
mag = self.data[magname]
if mfaint is None and mbright is None:
self.magmask = np.ones(self.nrows,dtype=bool)
elif mfaint is None:
self.magmask = mag >= mbright
elif mbright is None:
self.magmask = mag <= mfaint
else:
self.magmask = (mag >= mbright) & (mag <= mfaint)
#-----------------------------------------------------------------------
def get_radec(self):
"""
Extracts the RA and Dec information from the data container. This
is not necessary, and some of the data containers may not even have
WCS info, but extracting the coordinates if it does simplifies some
later tasks.
"""
""" Extract the information into the new containers """
self.ra = None
self.dec = None
if self.rafield is not None:
try:
self.ra = self.data[self.rafield].copy()
except:
try:
self.ra = self.data['x_world'].copy()
except:
self.ra = None
if self.decfield is not None:
try:
self.dec = self.data[self.decfield].copy()
except:
try:
self.dec = self.data['y_world'].copy()
except:
self.dec = None
"""
Put data into a SkyCoords container for easy coordinate-based calculations
"""
if (self.ra is not None) and (self.dec is not None):
"""
Determine whether the RA coordinate is in hours or in degrees
For now this test is made simple: if the format of the RA data is
a string, then the data is expected to be in hms format, otherwise
expect decimal degrees.
"""
if type(self.ra[0]) is str or type(self.ra[0]) is np.string_:
raunit = u.hourangle
else:
raunit = u.deg
self.radec = SkyCoord(self.ra,self.dec,unit=(raunit,u.deg))
"""
If radec has not been set, report this information
(consider raising an exception in future versions of the code)
"""
if self.radec is None:
print ''
print 'WARNING: get_radec was called but RA and Dec information was'
print ' not found. Please check the format of your catalog.'
print ''
#----------------------------------------------------------------------
def read_centpos(self, posfile, verbose=False):
"""
Reads a position in from a file and converts it to an astropy SkyCoord
format.
NOTE: right now this is hard-wired to just read in a file in the
standard Keck starlist format:
label rahr ramin rasec decdeg decamin decasec equinox
which matches the *.pos in CDF's Lenses/Data/* directories
Inputs:
posfile - file containing the RA and dec
"""
""" Read the data from the file """
posinfo = ascii.read(posfile,
names=['object', 'rahr', 'ramin', 'rasec',
'decdeg', 'decamin', 'decasec', 'equinox'])
""" Convert to SkyCoord format """
i = posinfo[0]
ra = '%d:%d:%f' % (i['rahr'], i['ramin'], i['rasec'])
dec = '%d:%d:%f' % (i['decdeg'], i['decamin'], i['decasec'])
radec = SkyCoord(ra, dec, unit=(u.hourangle, u.deg))
""" Print out information if requested """
if verbose:
print('')
print('Object: %s' % i['object'])
print('Coordinates: %s %s' % \
(radec.ra.to_string(unit=u.hourangle, decimal=False,
sep=':', precision=3, pad=True),
radec.dec.to_string(decimal=False, sep=':', precision=3,
alwayssign=True, pad=True)))
""" Save the output within the class """
self.centpos = radec
#----------------------------------------------------------------------
def sort_by_pos(self, centpos):
"""
Sorts the catalog in terms of distance from some central position, which
is passed as a SkyCoord variable (from astropy.coordinates)
"""
""" First check to see that we actual have WCS information """
if self.radec is None:
print ''
print 'ERROR: sort_by_pos. No WCS information in catalog'
print ''
return
""" Otherwise, use the SkyCoords functionality to easily sort """
sep = self.radec.separation(centpos)
try:
offsets = self.radec.spherical_offsets_to(centpos)
except:
offsets = None
ind = np.argsort(sep.arcsec)
if self.catformat == 'ascii':
self.data = self.data[ind,:]
else:
print self.catformat
self.data = self.data[ind]
""" Also sort things that are outside the data table """
self.radec = self.radec[ind]
self.ra = self.ra[ind]
self.dec = self.ra[ind]
self.sep = sep[ind]
if offsets is None:
self.dx = None
self.dy = None
else:
self.dx = (offsets[0].arcsecond)[ind]
self.dy = (offsets[1].arcsecond)[ind]
self.sortind = ind
#-----------------------------------------------------------------------
def make_reg_file(self, outfile, rcirc, color='green', fluxcol=None,
fluxerrcol=None, labcol=None, labdx=0.0012, labdy=0.0012,
plot_high_snr=False, mask=None, snrgood=10.):
"""
Uses the RA and Dec info in the catalog to make a region file that
can be used with ds9.
"""
"""
Start by putting the RA and Dec info into a somewhat more convenient
format
"""
self.get_radec()
if self.radec is None:
print ""
print "ERROR: Could not read RA and Dec information from input file"
return
"""
If the flux information is given, then report on high SNR detections
"""
ngood = 0
snrmask = None
if fluxcol is not None and fluxerrcol is not None:
if self.informat == 'ldac':
if type(fluxcol) is int:
flux = self.data.field(fluxcol)
fluxerr = self.data.field(fluxerrcol)
else:
flux = self.data[fluxcol]
fluxerr = self.data[fluxerrcol]
else:
flux = self.data['f%d' %fluxcol]
fluxerr = self.data['f%d' % fluxerrcol]
snr = flux / fluxerr
snrmask = snr>snrgood
""" Mask the input data if requested """
print('Total objects in catalog: %d' % len(self.radec))
if mask is not None:
radec = self.radec[mask]
selmask = mask
print('Objects selected by mask: %d' % len(radec))
else:
radec = self.radec
selmask = np.ones(len(radec), dtype=bool)
ntot = len(radec)
radeg = radec.ra.degree
decdeg = radec.dec.degree
""" Select the high SNR objects, if requested """
if snrmask is not None:
selsnrmask = (selmask) & (snrmask)
radecgood = self.radec[selsnrmask]
ngood = len(radecgood)
print 'Of those, objects with SNR>%.1f: %d' % (snrgood,ngood)
gradeg = radecgood.ra.degree
gdecdeg = radecgood.dec.degree
""" Write the output region file """
f = open(outfile,'w')
f.write('global color=%s\n' % color)
for i in range(ntot):
f.write('fk5;circle(%10.6f,%+10.6f,%.1f")\n' %
(radeg[i],decdeg[i],rcirc))
if plot_high_snr and ngood>0:
f.write('global color=red\n')
for i in range(ngood):
f.write('fk5;circle(%10.6f,%+10.6f,0.0011)\n' \
%(gradeg[i],gdecdeg[i]))
""" Add labels if requested """
if labcol is not None:
lab = self.data[labcol][selmask]
cosdec = np.cos(pi * self.dec[selmask] / 180.)
xx = self.ra[selmask] + labdx * cosdec
yy = self.dec[selmask] + labdy
f.write('global color=%s\n' % color)
for i in range(ntot):
f.write('fk5;text(%10.6f,%+10.6f) # text={%s}\n'% \
(xx[i],yy[i],str(lab[i])))
""" Wrap up """
print "Wrote region file %s" % outfile
f.close()
#-----------------------------------------------------------------------
#def plot_radec(self, symb='bo'):
#-----------------------------------------------------------------------
def plot_fwhm(self, fwhmcol='FWHM_IMAGE', magcol='MAG_AUTO',
xlim=(0,15), ylim=(28,16)):
"""
Plots FWHM vs. magnitude. This can be used to find the stellar locus
and, thus, determine the seeing.
Inputs:
fwhmcol - column name for the FWHM data. Default = 'fwhm_image'
magcol - column name for the magnitude data. Default = 'mag_auto'
xlim - initial limits for FWHM axis on plot. Default = (0,15)
ylim - initial limits for mag axis on plot. Default = (28,16)
"""
try:
fwhm = self.data[fwhmcol]
except KeyError:
print ''
print 'Catalog does not contain a %d column' % fwhmcol
print ''
return
try:
mag = self.data[magcol]
except KeyError:
print ''
print 'Catalog does not contain a %d column' % magcol
print ''
return
plt.plot(fwhm,mag,'bo')
plt.xlim(xlim)
plt.ylim(ylim)
plt.xlabel('FWHM (pixels)')
plt.ylabel('Magnitude')
plt.show()
#-----------------------------------------------------------------------
def plot_nhist(self, magcol='MAG_AUTO', usestarmask=False,
magmin=15, magmax=28, color='b', alpha=1.):
"""
Plots a histogram of galaxy magnitudes (similar to a log N-log S plot)
that can be used to determine the magnitude to which the catalog is
complete. A minimum FWHM can be set in order to select objects that
are likely to be galaxies, but this is not required.
Inputs:
magcol - column containing the magnitudes. Default = 'mag_auto'
usestarmask - when this parameter is set to True, then use the
starmask mask to select the galaxies.
NOTE: this means that the set_starmask method has to
have been run for each of the input catalogs, or
else all objects will be plotted
Default=False
magmin - minimum magnitude to use for the plot. Default=15
magmax - maximum magnitude to use for the plot. Default=28
"""
""" Get the magnitudes to be plotted """
if usestarmask:
if self.starmask is None:
print('')
print('WARNING: you have set usestarmask=True but there are')
print(' no stars selected by the starmask')
print('Please make sure that set_starmask has been run BEFORE'
'runing plot_nhist')
print(' if you want to use this mask')
print('')
return
else:
mag = (self.data[self.starmask==False][magcol]).copy()
else:
mag = self.data[magcol].copy()
mag = mag[np.isfinite(mag)]
""" Plot the histogram """
nbins = int(2 * (magmax - magmin))
plt.hist(mag,range=(magmin, magmax), bins=nbins, color=color,
alpha=alpha)
del(mag)
#-----------------------------------------------------------------------
def match_radec(self, ra2, dec2, rmatch, dra2=0., ddec2=0., doplot=True):
"""
*** UNDER CONSTRUCTION! DO NOT USE YET. ***
Given a list of ra,dec coordinates (ra2, dec2), possibly from a second
catalog, and a match tolerance, find the matches to the catalog
contained in self.data
Inputs:
ra2 - RA (decimal degrees) for catalog
dec2 - Dec (decimal degrees) for second catalog
rmatch - max distance for a valid match (arcsec)
dra2 - optional offset in ARCSEC to apply to ra2, if there is a known
offset between the catalogs (default=0.0)
ddec2 - optional offset in ARCSEC to apply to dec2, if there is a
known offset between the catalogs (default=0.0)
"""
print ""
print "Matching catalogs: basic info"
print "--------------------------------------------"
print " Catalog 1: %d coordinates" % self.ra.size
print " Catalog 2: %d coordinates" % ra2.size
""" Initialize containers for output information """
ramatch = np.zeros(self.ra.size)
decmatch = np.zeros(self.ra.size)
self.nmatch = np.zeros(self.ra.size,dtype=int)
self.matchdx = np.zeros(self.ra.size)
self.matchdy = np.zeros(self.ra.size)
self.indmatch = np.ones(self.ra.size,dtype=int) * -1
""" Correct for known shifts """
ra2 = ra2.copy() + dra2/(3600.*np.cos(dec2))
dec2 = dec2.copy() + ddec2/3600.
""" Loop over catalog """
print ""
print "Searching for matches..."
print "------------------------------"
for i in range(self.ra.size):
dx,dy = coords.sky_to_darcsec(self.ra[i],self.dec[i],ra2,dec2)
dpos = np.sqrt(dx**2 + dy**2)
isort = np.argsort(dpos)
if dpos[isort[0]]<=rmatch:
ramatch[i] = self.ra[i]
decmatch[i] = self.dec[i]
self.matchdx[i] = dx[isort[0]]
self.matchdy[i] = dy[isort[0]]
self.nmatch[i] = dpos[dpos<=rmatch].size
self.indmatch[i] = isort[0]
del dx,dy,dpos
print " Number of matches between the catalogs: %d" % \
(self.nmatch>0).sum()
mra = ramatch[self.nmatch>0]
mdec = decmatch[self.nmatch>0]
mdx = self.matchdx[self.nmatch>0]
mdy = self.matchdy[self.nmatch>0]
mdx0 = np.median(mdx)
mdy0 = np.median(mdy)
print " Median offset for matches (RA): %+6.2f arcsec" % mdx0
print " Median offset for matches (Dec): %+6.2f arcsec" % mdy0
""" Plot up some offsets, if desired """
if doplot:
plt.figure(1)
plt.scatter(mdx,mdy)
plt.axis('scaled')
plt.xlabel(r'$\Delta \alpha$ (arcsec)')
plt.ylabel(r'$\Delta \delta$ (arcsec)')
plt.title('Offsets between matched sources (rmatch = %5.2f)' % rmatch)
plt.axvline(0.0,color='r')
plt.axhline(0.0,color='r')
plt.plot(np.array([mdx0]),np.array([mdy0]),'r*',ms=20)
plt.xlim(-1.1*rmatch,1.1*rmatch)
plt.ylim(-1.1*rmatch,1.1*rmatch)
plt.figure(2)
#
ax1 = plt.subplot(221)
plt.scatter(mra,mdy)
plt.setp(ax1.get_xticklabels(), visible=False)
plt.ylabel(r'$\Delta \delta$ (arcsec)')
plt.axhline(0.0,color='r')
#
ax2 = plt.subplot(223, sharex=ax1)
plt.scatter(mra,mdx)
plt.xlabel(r'$\alpha$')
plt.ylabel(r'$\Delta \alpha$ (arcsec)')
plt.axhline(0.0,color='r')
#
ax3 = plt.subplot(222, sharey=ax1)
plt.scatter(mdec,mdy)
plt.axhline(0.0,color='r')
plt.setp(ax3.get_xticklabels(), visible=False)
plt.setp(ax3.get_yticklabels(), visible=False)
#
ax4 = plt.subplot(224)
plt.scatter(mdec,mdx)
plt.xlabel(r'$\delta$')
plt.axhline(0.0,color='r')
plt.setp(ax4.get_yticklabels(), visible=False)
plt.show()
""" Clean up """
del ramatch,decmatch
del mdx,mdy,mra,mdec
#-----------------------------------------------------------------------
def print_ccmap(self, outfile, verbose=True):
"""
Prints out a file that can be used as the input for the pyraf ccmap
task. This file has 4 columns: x y RA Dec
Inputs:
outfile - output file to be used as input for ccmap
verbose - print task info
"""
if verbose:
print ""
print "Printing to file for use in ccmap: %s" % outfile
print ""
f = open(outfile,'w')
f.write('# (x,y) catalog: %s\n' % self.infile)
f.write('# Astrometric catalog: %s\n' % self.matchcat)
f.write('# Columns are x y RA Dec\n')
for i in range(self.nmatch):
f.write('%8.2f %8.2f %11.7f %+11.7f\n' % \
(self.matchx[i],self.matchy[i],self.matchra[i],
self.matchdec[i]))
f.close()
#-----------------------------------------------------------------------
def find_closest_xy(self, xast, yast, xcol, ycol):
"""
Finds the closest match, in (x,y) space to each member of the astrometric
catalog (represented by xast,yast).
"""
self.matchind = np.zeros(xast.size, dtype=int)
xfield = 'f%d' % xcol
yfield = 'f%d' % ycol
for i in range(xast.size):
dx = xast[i] - self.data[xfield]
dy = yast[i] - self.data[yfield]
dpos = dx**2 + dy**2
sindex = np.argsort(dpos)
self.matchind[i] = sindex[0]
self.matchdx = xast - self.data[xfield][self.matchind]
self.matchdy = yast - self.data[yfield][self.matchind]
#-----------------------------------------------------------------------
def match_xy(self, xa, ya, max_offset=None, xcol=8, ycol=9, verbose=True):
"""
Find the closest match to each astrometric catalog object and calculate the
offsets.
Do two loops, to deal with possible confusion of sources on first pass
through
"""
dxmed = 0
dymed = 0
for i in range(2):
if verbose:
print ''
print 'Pass %d' % (i+1)
print '------------------------'
xa0 = xa - dxmed
ya0 = ya - dymed
self.find_closest_xy(xa0,ya0,xcol,ycol)
dxmed = np.median(self.matchdx)
dymed = np.median(self.matchdy)
if max_offset is not None:
dpos = np.sqrt(self.matchdx**2 + self.matchdy**2)
goodmask = dpos<max_offset
if verbose:
print "Applying a maximum offset cut of %7.1f pixels" % max_offset
print "Median shifts before clipping: %7.2f %7.2f" % (dxmed,dymed)
else:
goodmask = np.ones(xa.size,dtype=bool)
dxm = self.matchdx[goodmask]
dym = self.matchdy[goodmask]
dxmed = np.median(dxm)
dymed = np.median(dym)
if verbose:
print "Median shifts after pass: %7.2f %7.2f" % (dxmed,dymed)
"""
Transfer information into object and clean up
"""
if verbose:
print ''
print 'Found %d astrometric objects within FOV of image' % xa.size
print 'Matched %d objects to astrometric catalog.' % dxm.size
self.nmatch = dxm.size
self.goodmask = goodmask.copy()
self.matchind = self.matchind[goodmask]
del xa0,ya0,goodmask
#-----------------------------------------------------------------------
def match_fits_to_ast(self, fitsfile, astcat, outfile=None, max_offset=None,
racol=1, deccol=2, xcol=8, ycol=9,
doplot=True, edgedist=50., imhdu=0, verbose=True):
"""
Given the fits file from which this object (self) was defined
and an astrometric catalog, find the closest matches of the
astrometric objects to those contained in this object, using the WCS
information in the fits header.
"""
if(verbose):
print "Running match_fits_to_ast with:"
print " fitsfile = %s" % fitsfile
print " astcat = %s" % astcat
self.infits = fitsfile
self.matchcat = astcat
"""
Start by opening the fits file and reading the appropriate columns from
the catalogs
"""
hdulist = imf.open_fits(fitsfile)
hdr = hdulist[imhdu].header
if verbose:
print ""
hdulist.info()
"""
Select the astrometric catalog objects that fall within the fits file FOV
(at least with its current WCS)
"""
raa,deca,xa,ya,astmask = select_good_ast(astcat,hdr,racol,deccol,edgedist)
if verbose:
print 'Found %d astrometric objects within FOV of image' % raa.size
"""
Find the closest match to each astrometric catalog object
"""
self.match_xy(xa,ya,max_offset,xcol,ycol,verbose)
""" Transfer info about matches into the object """
xfield = 'f%d' % xcol
yfield = 'f%d' % ycol
self.astmask = astmask.copy()
self.matchx = self.data[xfield][self.matchind].copy()
self.matchy = self.data[yfield][self.matchind].copy()
self.matchra = raa[self.goodmask].copy()
self.matchdec = deca[self.goodmask].copy()
self.matchdx = self.matchdx[self.goodmask]
self.matchdy = self.matchdy[self.goodmask]
""" Plot the offsets if desired """
if doplot:
dxmed = np.median(self.matchdx)
dymed = np.median(self.matchdx)
plt.figure()
plt.scatter(self.matchdx,self.matchdy)
plt.xlabel('x offset (pix)')
plt.ylabel('y offset (pix)')
plt.axhline(color='k')
plt.axvline(color='k')
plt.axvline(dxmed,color='r')
plt.axhline(dymed,color='r')
print ""
print "Black lines represent x=0 and y=0 axes"
print "Red lines show median offsets of dx_med=%7.2f and dy_med=%7.2f" \
% (dxmed,dymed)
#plt.show()
""" Write the output file, in a format appropriate for input to ccmap """
if outfile is not None:
self.print_ccmap(outfile,verbose)
""" Clean up """
hdulist.close()
del hdr,raa,deca,xa,ya,astmask
# -----------------------------------------------------------------------
def set_starmask(self, mask):
"""
Takes the input mask and assigns it to an internal mask associated
with this instance of the Secat class.
The internal mask is called starmask and has values of True for objects
that have been identified as stars by the provided external mask.
The external mask will be based on some characteristics in the catalog.
Examples could be objects with a SExtractor CLASS_STAR value greater
than 0.7, or a FWHM_IMAGE less than a certain value, or ...
"""
self.starmask = mask
r = (rX + rY)
# and for the pointing center
# first go from altitude to zenith angle
theta0 = numpy.radians((90 - obs.elevation))
phi0 = numpy.radians(obs.azimuth)
# this is the response for XX and YY
try:
respX, respY = primary_beam.MWA_Tile_analytic(theta0,
phi0,
freq=obs.center_channel *
1.28e6,
delays=obs.delays)
except:
logger.error('Error creating primary beams\n')
sys.exit(1)
rX = numpy.real(numpy.conj(respX) * respX)
rY = numpy.real(numpy.conj(respY) * respY)
# make a pseudo-I beam
r0 = (rX + rY)
coord_pointing = ICRS(ra=obs.RA, dec=obs.Dec, unit=(u.degree, u.degree))
separation = coord.separation(coord_pointing).degree
logger.info('Observation at gpstime=%d, %d MHz, delays=%s' %
(obs.observation_number, obs.center_channel * 1.28, obs.delays))
logger.info('Calculating for RA,Dec=%s' %
(coord.to_string(precision=1, sep=':')))
print 'Separation: %.2f deg' % separation
print 'Power: %.2f' % (r / r0)
now = Time.now()
doy_now = np.float(now.yday.split(':')[1])
print("Current DOY = {0}".format(np.int(doy_now)))
print("StarboardPoleRA (now) = {0:.3f}".format(StarboardPoleRA(now)))
print("PortPoleRA (now) = {0:.3f}".format(PortPoleRA(now)))
if args.ra is None or args.dec is None:
SourcePos = get_icrs_coordinates(args.sourcename)
else:
SourcePos = ICRS(ra=Angle(args.ra), dec=Angle(args.dec))
print("\nSource: {0} at {1}, {2}".format(args.sourcename, SourcePos.ra,
SourcePos.dec))
print("Separation from Starboard Pole = {0:.3f}".format(
SourcePos.separation(StarboardPoleCoord(now))))
print("Separation from Port Pole = {0:.3f}".format(
SourcePos.separation(PortPoleCoord(now))))
# Plot separation from orbit pole for all of 2017 and beyond
doy2017 = np.arange(600.0)
times = doy2017 * u.d + Time("2017-01-01T00:00:00", format='isot', scale='utc')
fig, ax = plt.subplots()
seps = SourcePos.separation(StarboardPoleCoord(times))
ax.plot(doy2017, seps.to(u.deg))
# The Sun and Moon positions are returned in the GCRS frame
# Convert them to ICRS so .separation doesn't go insane when
# comparing different frames with different obstimes.
SunPos = get_sun(times)