def test_simple():
query = {}
query["-source"] = "VII/258/vv10"
query["-out"] = ["Name", "Sp", "Vmag"]
query["Vmag"] = "5.0..11.0"
table1 = vizier.vizquery(query)
#Find sources in 2MASS matching the AGNs positions to within 2 arcsec
query = {}
query["-source"] = "II/246/out"
query["-out"] = ["RAJ2000", "DEJ2000", "2MASS", "Kmag"]
query["-c.rs"] = "2"
query["-c"] = table1
table2 = vizier.vizquery(query)
print(table1)
print(table2)
def align_to_reference(ROOT_DIRECT,
ALIGN_IMAGE,
fitgeometry="shift",
clean=True,
verbose=False,
ALIGN_EXTENSION=0,
toler=3,
skip_swarp=False,
align_sdss_ds9=False,
catalog=None):
"""
xshift, yshift, rot, scale, xrms, yrms = align_to_reference()
"""
import os
import glob
import shutil
from pyraf import iraf
from iraf import stsdas, dither
import threedhst
from threedhst import catIO
no = iraf.no
yes = iraf.yes
INDEF = iraf.INDEF
#### Clean slate
rmfiles = [
'SCI.fits', 'WHT.fits', 'align.cat', 'direct.cat'
'align.map', 'align.match', 'align.reg', 'align.xy', 'direct.reg',
'direct.xy', 'ds9_align.tsv'
]
for file in rmfiles:
try:
os.remove(file)
except:
pass
if catalog is not None:
align_sdss_ds9 = True
#### Get only images that overlap from the ALIGN_IMAGE list
if not align_sdss_ds9:
align_img_list = find_align_images_that_overlap(
ROOT_DIRECT + '_drz.fits',
ALIGN_IMAGE,
ALIGN_EXTENSION=ALIGN_EXTENSION)
if not align_img_list:
print 'threedhst.shifts.align_to_reference: no alignment images overlap.'
return 0, 0
#### Use swarp to combine the alignment images to the same image
#### dimensions as the direct mosaic
if (not skip_swarp) & (not align_sdss_ds9):
try:
os.remove(ROOT_DIRECT + '_align.fits')
except:
pass
matchImagePixels(input=align_img_list,
matchImage=ROOT_DIRECT + '_drz.fits',
output=ROOT_DIRECT + '_align.fits',
match_extension=1,
input_extension=ALIGN_EXTENSION)
#### Run SExtractor on the direct image, with the WHT
#### extension as a weight image
se = threedhst.sex.SExtractor()
se.aXeParams()
se.copyConvFile()
se.overwrite = True
se.options['CHECKIMAGE_TYPE'] = 'NONE'
se.options['WEIGHT_TYPE'] = 'MAP_WEIGHT'
se.options['WEIGHT_IMAGE'] = 'WHT.fits'
se.options['FILTER'] = 'Y'
## Detect thresholds (default = 1.5)
THRESH = 10
if align_sdss_ds9:
if 'Vizier' not in REFERENCE_CATALOG:
THRESH = 20
se.options['DETECT_THRESH'] = '%d' % (THRESH)
se.options['ANALYSIS_THRESH'] = '%d' % (THRESH)
se.options['MAG_ZEROPOINT'] = str(threedhst.options['MAG_ZEROPOINT'])
#### Run SExtractor on direct and alignment images
## direct image
se.options['CATALOG_NAME'] = 'direct.cat'
iraf.imcopy(ROOT_DIRECT + '_drz.fits[1]', "SCI.fits")
iraf.imcopy(ROOT_DIRECT + '_drz.fits[2]', "WHT.fits")
status = se.sextractImage('SCI.fits')
## Read the catalog
directCat = threedhst.sex.mySexCat('direct.cat')
if align_sdss_ds9:
### Use ds9 SDSS catalog to refine alignment
import threedhst.dq
import pywcs
import threedhst.catIO as catIO
wcs = pywcs.WCS(pyfits.getheader('SCI.fits', 0))
#wcs = pywcs.WCS(pyfits.getheader('Q0821+3107-F140W_drz.fits', 1))
if 'Vizier' in REFERENCE_CATALOG:
#### Use (unstable) astroquery Vizier search
#### CFHTLS-Deep: 'Vizier.II/317'
VIZIER_CAT = REFERENCE_CATALOG.split('Vizier.')[1]
print 'Align to Vizier catalog: http://vizier.u-strasbg.fr/viz-bin/VizieR?-source=%s' % (
VIZIER_CAT)
import astroquery
if astroquery.__version__ < '0.0.dev1078':
from astroquery import vizier
query = {}
query["-source"] = VIZIER_CAT
#query["-out"] = ["_r", "CFHTLS", "rmag"]
query["-out"] = ["_RAJ2000", "_DEJ2000"] ### Just RA/Dec.
#### Center position and query radius
r0, d0 = wcs.wcs_pix2sky([[wcs.naxis1 / 2., wcs.naxis2 / 2.]],
1)[0]
rll, dll = wcs.wcs_pix2sky([[0, 0]], 1)[0]
corner_radius = np.sqrt(
(r0 - rll)**2 * np.cos(d0 / 360. * 2 * np.pi)**2 +
(d0 - dll)**2) * 60. * 1.5
h = query["-c"] = "%.6f %.6f" % (r0, d0)
query["-c.rm"] = "%.3f" % (corner_radius
) ### xxx check image size
#### Run the query
vt = vizier.vizquery(query)
else:
#### Newer astroquery
from astroquery.vizier import Vizier
import astropy.coordinates as coord
import astropy.units as u
Vizier.ROW_LIMIT = -1
r0, d0 = wcs.wcs_pix2sky([[wcs.naxis1 / 2., wcs.naxis2 / 2.]],
1)[0]
rll, dll = wcs.wcs_pix2sky([[0, 0]], 1)[0]
corner_radius = np.sqrt(
(r0 - rll)**2 * np.cos(d0 / 360. * 2 * np.pi)**2 +
(d0 - dll)**2) * 60. * 1.5
#
c = coord.ICRSCoordinates(ra=r0, dec=d0, unit=(u.deg, u.deg))
#### something with astropy.coordinates
# c.icrs.ra.degree = c.icrs.ra.degrees
# c.icrs.dec.degree = c.icrs.dec.degrees
#
vt = Vizier.query_region(c,
width=u.Quantity(
corner_radius, u.arcminute),
catalog=[VIZIER_CAT])[0]
#### Make a region file
ra_list, dec_list = vt['RAJ2000'], vt['DEJ2000']
print 'Vizier, found %d objects.' % (len(ra_list))
fp = open('%s.vizier.reg' % (ROOT_DIRECT), 'w')
fp.write('# %s, r=%.1f\'\nfk5\n' % (VIZIER_CAT, corner_radius))
for ra, dec in zip(ra_list, dec_list):
fp.write('circle(%.6f, %.6f, 0.5")\n' % (ra, dec))
#
fp.close()
else:
#### Use DS9 catalog
ds9 = threedhst.dq.myDS9()
ds9.set('file SCI.fits')
#ds9.set('file Q0821+3107-F140W_drz.fits')
ds9.set('catalog %s' % (REFERENCE_CATALOG))
### Can't find XPA access point for "copy to regions"
ds9.set('catalog export tsv ds9_align.tsv')
lines = open('ds9_align.tsv').readlines()
ra_list, dec_list = [], []
for line in lines[1:]:
spl = line.split()
ra, dec = float(spl[0]), float(spl[1])
ra_list.append(ra)
dec_list.append(dec)
#
del (ds9)
x_image, y_image = [], []
for ra, dec in zip(ra_list, dec_list):
x, y = wcs.wcs_sky2pix([[ra, dec]], 1)[0]
x_image.append(x)
y_image.append(y)
alignCat = catIO.EmptyCat()
alignCat['X_IMAGE'] = np.array(x_image)
alignCat['Y_IMAGE'] = np.array(y_image)
else:
## alignment image
se.options['CATALOG_NAME'] = 'align.cat'
status = se.sextractImage(ROOT_DIRECT + '_align.fits')
alignCat = threedhst.sex.mySexCat('align.cat')
xshift = 0
yshift = 0
rot = 0
scale = 1.
xrms = 2
yrms = 2
NITER = 5
IT = 0
while (IT < NITER):
IT = IT + 1
#### Get x,y coordinates of detected objects
## direct image
fp = open('direct.xy', 'w')
for i in range(len(directCat.X_IMAGE)):
fp.write('%s %s\n' % (directCat.X_IMAGE[i], directCat.Y_IMAGE[i]))
fp.close()
## alignment image
fp = open('align.xy', 'w')
for i in range(len(alignCat.X_IMAGE)):
fp.write('%s %s\n' % (np.float(alignCat.X_IMAGE[i]) + xshift,
np.float(alignCat.Y_IMAGE[i]) + yshift))
fp.close()
iraf.flpr()
iraf.flpr()
iraf.flpr()
#### iraf.xyxymatch to find matches between the two catalogs
pow = toler * 1.
try:
os.remove('align.match')
except:
pass
status1 = iraf.xyxymatch(input="direct.xy",
reference="align.xy",
output="align.match",
tolerance=2**pow,
separation=0,
verbose=yes,
Stdout=1)
nmatch = 0
while status1[-1].startswith('0') | (nmatch < 10):
pow += 1
os.remove('align.match')
status1 = iraf.xyxymatch(input="direct.xy",
reference="align.xy",
output="align.match",
tolerance=2**pow,
separation=0,
verbose=yes,
Stdout=1)
#
nmatch = 0
for line in open('align.match').xreadlines():
nmatch += 1
if verbose:
for line in status1:
print line
#### Compute shifts with iraf.geomap
iraf.flpr()
iraf.flpr()
iraf.flpr()
try:
os.remove("align.map")
except:
pass
status2 = iraf.geomap(input="align.match",
database="align.map",
fitgeometry=fitgeometry,
interactive=no,
xmin=INDEF,
xmax=INDEF,
ymin=INDEF,
ymax=INDEF,
maxiter=10,
reject=2.0,
Stdout=1)
if verbose:
for line in status2:
print line
#fp = open(root+'.iraf.log','a')
#fp.writelines(status1)
#fp.writelines(status2)
#fp.close()
#### Parse geomap.output
fp = open("align.map", "r")
for line in fp.readlines():
spl = line.split()
if spl[0].startswith('xshift'):
xshift += float(spl[1])
if spl[0].startswith('yshift'):
yshift += float(spl[1])
if spl[0].startswith('xrotation'):
rot = float(spl[1])
if spl[0].startswith('xmag'):
scale = float(spl[1])
if spl[0].startswith('xrms'):
xrms = float(spl[1])
if spl[0].startswith('yrms'):
yrms = float(spl[1])
fp.close()
#os.system('wc align.match')
print 'Shift iteration #%d, xshift=%f, yshift=%f, rot=%f, scl=%f (rms: %5.2f,%5.2f)' % (
IT, xshift, yshift, rot, scale, xrms, yrms)
im = pyfits.open('SCI.fits')
shutil.copy('align.map', ROOT_DIRECT + '_align.map')
shutil.copy('align.match', ROOT_DIRECT + '_align.match')
#### Cleanup
if clean:
rmfiles = [
'SCI.fits', 'WHT.fits', 'align.cat', 'align.map', 'align.match',
'align.reg', 'align.xy', 'direct.cat', 'direct.reg', 'direct.xy',
'drz_sci.fits', 'drz_wht.fits', 'bg.fits'
]
for file in rmfiles:
try:
os.remove(file)
except:
pass
return xshift, yshift, rot, scale, xrms, yrms
def align_to_reference(
ROOT_DIRECT,
ALIGN_IMAGE,
fitgeometry="shift",
clean=True,
verbose=False,
ALIGN_EXTENSION=0,
toler=3,
skip_swarp=False,
align_sdss_ds9=False,
catalog=None,
):
"""
xshift, yshift, rot, scale, xrms, yrms = align_to_reference()
"""
import os
import glob
import shutil
from pyraf import iraf
from iraf import stsdas, dither
import threedhst
from threedhst import catIO
no = iraf.no
yes = iraf.yes
INDEF = iraf.INDEF
#### Clean slate
rmfiles = [
"SCI.fits",
"WHT.fits",
"align.cat",
"direct.cat" "align.map",
"align.match",
"align.reg",
"align.xy",
"direct.reg",
"direct.xy",
"ds9_align.tsv",
]
for file in rmfiles:
try:
os.remove(file)
except:
pass
if catalog is not None:
align_sdss_ds9 = True
#### Get only images that overlap from the ALIGN_IMAGE list
if not align_sdss_ds9:
align_img_list = find_align_images_that_overlap(
ROOT_DIRECT + "_drz.fits", ALIGN_IMAGE, ALIGN_EXTENSION=ALIGN_EXTENSION
)
if not align_img_list:
print "threedhst.shifts.align_to_reference: no alignment images overlap."
return 0, 0
#### Use swarp to combine the alignment images to the same image
#### dimensions as the direct mosaic
if (not skip_swarp) & (not align_sdss_ds9):
try:
os.remove(ROOT_DIRECT + "_align.fits")
except:
pass
matchImagePixels(
input=align_img_list,
matchImage=ROOT_DIRECT + "_drz.fits",
output=ROOT_DIRECT + "_align.fits",
match_extension=1,
input_extension=ALIGN_EXTENSION,
)
#### Run SExtractor on the direct image, with the WHT
#### extension as a weight image
se = threedhst.sex.SExtractor()
se.aXeParams()
se.copyConvFile()
se.overwrite = True
se.options["CHECKIMAGE_TYPE"] = "NONE"
se.options["WEIGHT_TYPE"] = "MAP_WEIGHT"
se.options["WEIGHT_IMAGE"] = "WHT.fits"
se.options["FILTER"] = "Y"
## Detect thresholds (default = 1.5)
THRESH = 10
if align_sdss_ds9:
if "Vizier" not in REFERENCE_CATALOG:
THRESH = 20
se.options["DETECT_THRESH"] = "%d" % (THRESH)
se.options["ANALYSIS_THRESH"] = "%d" % (THRESH)
se.options["MAG_ZEROPOINT"] = str(threedhst.options["MAG_ZEROPOINT"])
#### Run SExtractor on direct and alignment images
## direct image
se.options["CATALOG_NAME"] = "direct.cat"
iraf.imcopy(ROOT_DIRECT + "_drz.fits[1]", "SCI.fits")
iraf.imcopy(ROOT_DIRECT + "_drz.fits[2]", "WHT.fits")
status = se.sextractImage("SCI.fits")
## Read the catalog
directCat = threedhst.sex.mySexCat("direct.cat")
if align_sdss_ds9:
### Use ds9 SDSS catalog to refine alignment
import threedhst.dq
import pywcs
import threedhst.catIO as catIO
wcs = pywcs.WCS(pyfits.getheader("SCI.fits", 0))
# wcs = pywcs.WCS(pyfits.getheader('Q0821+3107-F140W_drz.fits', 1))
if "Vizier" in REFERENCE_CATALOG:
#### Use (unstable) astroquery Vizier search
#### CFHTLS-Deep: 'Vizier.II/317'
VIZIER_CAT = REFERENCE_CATALOG.split("Vizier.")[1]
print "Align to Vizier catalog: http://vizier.u-strasbg.fr/viz-bin/VizieR?-source=%s" % (VIZIER_CAT)
import astroquery
if astroquery.__version__ < "0.0.dev1078":
from astroquery import vizier
query = {}
query["-source"] = VIZIER_CAT
# query["-out"] = ["_r", "CFHTLS", "rmag"]
query["-out"] = ["_RAJ2000", "_DEJ2000"] ### Just RA/Dec.
#### Center position and query radius
r0, d0 = wcs.wcs_pix2sky([[wcs.naxis1 / 2.0, wcs.naxis2 / 2.0]], 1)[0]
rll, dll = wcs.wcs_pix2sky([[0, 0]], 1)[0]
corner_radius = (
np.sqrt((r0 - rll) ** 2 * np.cos(d0 / 360.0 * 2 * np.pi) ** 2 + (d0 - dll) ** 2) * 60.0 * 1.5
)
h = query["-c"] = "%.6f %.6f" % (r0, d0)
query["-c.rm"] = "%.3f" % (corner_radius) ### xxx check image size
#### Run the query
vt = vizier.vizquery(query)
else:
#### Newer astroquery
from astroquery.vizier import Vizier
import astropy.coordinates as coord
import astropy.units as u
Vizier.ROW_LIMIT = -1
r0, d0 = wcs.wcs_pix2sky([[wcs.naxis1 / 2.0, wcs.naxis2 / 2.0]], 1)[0]
rll, dll = wcs.wcs_pix2sky([[0, 0]], 1)[0]
corner_radius = (
np.sqrt((r0 - rll) ** 2 * np.cos(d0 / 360.0 * 2 * np.pi) ** 2 + (d0 - dll) ** 2) * 60.0 * 1.5
)
#
c = coord.ICRSCoordinates(ra=r0, dec=d0, unit=(u.deg, u.deg))
#### something with astropy.coordinates
# c.icrs.ra.degree = c.icrs.ra.degrees
# c.icrs.dec.degree = c.icrs.dec.degrees
#
vt = Vizier.query_region(c, width=u.Quantity(corner_radius, u.arcminute), catalog=[VIZIER_CAT])[0]
#### Make a region file
ra_list, dec_list = vt["RAJ2000"], vt["DEJ2000"]
print "Vizier, found %d objects." % (len(ra_list))
fp = open("%s.vizier.reg" % (ROOT_DIRECT), "w")
fp.write("# %s, r=%.1f'\nfk5\n" % (VIZIER_CAT, corner_radius))
for ra, dec in zip(ra_list, dec_list):
fp.write('circle(%.6f, %.6f, 0.5")\n' % (ra, dec))
#
fp.close()
else:
#### Use DS9 catalog
ds9 = threedhst.dq.myDS9()
ds9.set("file SCI.fits")
# ds9.set('file Q0821+3107-F140W_drz.fits')
ds9.set("catalog %s" % (REFERENCE_CATALOG))
### Can't find XPA access point for "copy to regions"
ds9.set("catalog export tsv ds9_align.tsv")
lines = open("ds9_align.tsv").readlines()
ra_list, dec_list = [], []
for line in lines[1:]:
spl = line.split()
ra, dec = float(spl[0]), float(spl[1])
ra_list.append(ra)
dec_list.append(dec)
#
del (ds9)
x_image, y_image = [], []
for ra, dec in zip(ra_list, dec_list):
x, y = wcs.wcs_sky2pix([[ra, dec]], 1)[0]
x_image.append(x)
y_image.append(y)
alignCat = catIO.EmptyCat()
alignCat["X_IMAGE"] = np.array(x_image)
alignCat["Y_IMAGE"] = np.array(y_image)
else:
## alignment image
se.options["CATALOG_NAME"] = "align.cat"
status = se.sextractImage(ROOT_DIRECT + "_align.fits")
alignCat = threedhst.sex.mySexCat("align.cat")
xshift = 0
yshift = 0
rot = 0
scale = 1.0
xrms = 2
yrms = 2
NITER = 5
IT = 0
while IT < NITER:
IT = IT + 1
#### Get x,y coordinates of detected objects
## direct image
fp = open("direct.xy", "w")
for i in range(len(directCat.X_IMAGE)):
fp.write("%s %s\n" % (directCat.X_IMAGE[i], directCat.Y_IMAGE[i]))
fp.close()
## alignment image
fp = open("align.xy", "w")
for i in range(len(alignCat.X_IMAGE)):
fp.write("%s %s\n" % (np.float(alignCat.X_IMAGE[i]) + xshift, np.float(alignCat.Y_IMAGE[i]) + yshift))
fp.close()
iraf.flpr()
iraf.flpr()
iraf.flpr()
#### iraf.xyxymatch to find matches between the two catalogs
pow = toler * 1.0
try:
os.remove("align.match")
except:
pass
status1 = iraf.xyxymatch(
input="direct.xy",
reference="align.xy",
output="align.match",
tolerance=2 ** pow,
separation=0,
verbose=yes,
Stdout=1,
)
nmatch = 0
while status1[-1].startswith("0") | (nmatch < 10):
pow += 1
os.remove("align.match")
status1 = iraf.xyxymatch(
input="direct.xy",
reference="align.xy",
output="align.match",
tolerance=2 ** pow,
separation=0,
verbose=yes,
Stdout=1,
)
#
nmatch = 0
for line in open("align.match").xreadlines():
nmatch += 1
if verbose:
for line in status1:
print line
#### Compute shifts with iraf.geomap
iraf.flpr()
iraf.flpr()
iraf.flpr()
try:
os.remove("align.map")
except:
pass
status2 = iraf.geomap(
input="align.match",
database="align.map",
fitgeometry=fitgeometry,
interactive=no,
xmin=INDEF,
xmax=INDEF,
ymin=INDEF,
ymax=INDEF,
maxiter=10,
reject=2.0,
Stdout=1,
)
if verbose:
for line in status2:
print line
# fp = open(root+'.iraf.log','a')
# fp.writelines(status1)
# fp.writelines(status2)
# fp.close()
#### Parse geomap.output
fp = open("align.map", "r")
for line in fp.readlines():
spl = line.split()
if spl[0].startswith("xshift"):
xshift += float(spl[1])
if spl[0].startswith("yshift"):
yshift += float(spl[1])
if spl[0].startswith("xrotation"):
rot = float(spl[1])
if spl[0].startswith("xmag"):
scale = float(spl[1])
if spl[0].startswith("xrms"):
xrms = float(spl[1])
if spl[0].startswith("yrms"):
yrms = float(spl[1])
fp.close()
# os.system('wc align.match')
print "Shift iteration #%d, xshift=%f, yshift=%f, rot=%f, scl=%f (rms: %5.2f,%5.2f)" % (
IT,
xshift,
yshift,
rot,
scale,
xrms,
yrms,
)
im = pyfits.open("SCI.fits")
shutil.copy("align.map", ROOT_DIRECT + "_align.map")
shutil.copy("align.match", ROOT_DIRECT + "_align.match")
#### Cleanup
if clean:
rmfiles = [
"SCI.fits",
"WHT.fits",
"align.cat",
"align.map",
"align.match",
"align.reg",
"align.xy",
"direct.cat",
"direct.reg",
"direct.xy",
"drz_sci.fits",
"drz_wht.fits",
"bg.fits",
]
for file in rmfiles:
try:
os.remove(file)
except:
pass
return xshift, yshift, rot, scale, xrms, yrms