def separation(ra1, dec1, ra2, dec2, pa, incl, D_gal, wcsheader):
logfile = "rhodump.log"
logdump(logfile, "{0} {1} {2} {3}\n".format(ra1, dec1, ra2, dec2))
#Assuming ra & dec come in as strings as "hh mm ss.sss"
#1. calculate separation angle between the two coordinates, giving us r_raw
#Strip: can't have leading or trailing whitespaces
r1, d1 = astCoords.hms2decimal(strip(ra1), " "), astCoords.dms2decimal(strip(dec1), " ")
r2, d2 = astCoords.hms2decimal(strip(ra2), " "), astCoords.dms2decimal(strip(dec2), " ")
angle = astCoords.calcAngSepDeg(r1, d1, r2, d2)
r_raw = D_gal * m.radians(angle)
#print r_raw, "r_raw"
#2. correct for pa, i by deprojecting radius
#For this we need x and y coordinates through the wcs header
x1, y1 = wcsheader.wcs2pix(r1, d1)
x2, y2 = wcsheader.wcs2pix(r2, d2)
e_a = e_angle_rad(x1, y1, x2, y2, pa) #get the angle
esqd = 1 - (m.cos(m.radians(incl)))**2. #deproject
sqrtf = m.sqrt((1-esqd)/(1-esqd*m.cos(e_a)**2.))
#print esqd, m.cos(e_a), sqrtf, "esqd cos(angle) sqrtf"
#calculate separation in parsec from angle and ellipse deprojection
logdump(logfile, "{0} {1} {2}\n".format(r_raw, sqrtf, r_raw/sqrtf))
#Append to a ds9-style file - replace our ' ' with ':'
r1s = ra1.strip().replace(' ', ':')
d1s = dec1.strip().replace(' ', ':')
r2s = ra2.strip().replace(' ', ':')
d2s = dec2.strip().replace(' ', ':')
logdump("rholog.reg", "circle({0},{1},{2}\")\n".format(r1s, d1s, r_raw/sqrtf/D_gal*3600))
logdump("rholog.reg", "point({0},{1})\n".format(r2s,d2s))
return r_raw / sqrtf #in units of D_gal (e.g. kpc)
def create_lobos_ms (infile='',ra='',dec='',nP=3,radius=2.5):
infile='L401323_SB349_uv.dppp.MS'
ra,dec,radius,nP='13:40:00','55:00:00',2.5,3
try: # ra, dec input can either be decimal or hh:mm:ss, dd:mm:ss
ra, dec = 1.0*ra, 1.0*dec
hexra = astCoords.decimal2hms(ra,':')
hexdec = astCoords.decimal2dms(dec,':')
except:
hexra, hexdec = ra, dec
ra = astCoords.hms2decimal(ra,':')
dec = astCoords.dms2decimal(dec,':')
if not os.path.isfile ('lobos_stats.sum'):
os.system ('wget http://www.jb.man.ac.uk/~njj/lobos_stats.sum')
lobos = np.loadtxt('lobos_stats.sum',dtype='S')
for l in lobos:
new = np.array([astCoords.hms2decimal(l[1],':'),\
astCoords.dms2decimal(l[2],':')])
try:
lobos_coord = np.vstack((lobos_coord,new))
except:
lobos_coord = np.copy(new)
a = correlate(np.array([[ra,dec]]),0,1,lobos_coord,0,1,radius)
nlobos = 0
os.system('rm lshift_*')
for i in np.asarray(a[:,1],dtype='int'):
if lobos[i][5].count('P')>=nP:
oroot = infile.replace('uv.dppp.MS','')
namera = lobos[i,1].replace(':','').split('.')[0]
namedec = lobos[i,2].replace(':','').split('.')[0]
dpppra = lobos[i,1].replace(':','h',1).replace(':','m',1)+'s'
dpppdec = lobos[i,2].replace(':','d',1).replace(':','m',1)+'s'
hemisphere = '-' if '-' in hexdec else '+'
f = open('lshift_%03d'%nlobos, 'w')
f.write('msin = '+infile+'\n')
f.write('msout = '+oroot+namera+hemisphere+namedec+'.ms\n')
f.write('msin.datacolumn = DATA\n')
f.write('steps = [shift,adder,filter,avg]\n')
f.write('shift.type = \'phaseshift\'\n')
f.write('shift.phasecenter = [\''+dpppra+'\',\''+dpppdec+'\']\n')
f.write('adder.type = \'stationadder\'\n')
f.write('adder.stations = {TS001:\'CS*\'}\n')
f.write('filter.type = \'filter\'\n')
f.write('filter.baseline = \'!CS*&*\'\n')
f.write('avg.type = average\n')
f.write('avg.freqstep = 16\n')
f.write('avg.timestep = 20\n')
f.close()
nlobos+=1
lshift_thread.parallel = parallel_function(lshift_thread)
k = range(nlobos)
parallel_result = lshift_thread.parallel(k)
def get_filenames(self):
''' This script will get called if we choose not to swarp the images.
This makes sure that all of the variables are defined.
'''
# this is to convert the hms/dms coordinates back into decimal degrees.
# I don't really want to use this, but I am not rewriting things.
from astLib import astCoords
self.combima = {}
self.combcat = {}
self.weightima = {}
self.outdir = os.path.join(self.outpath, self.tilename)
self.center_dither(dryrun=True)
self.xo = astCoords.hms2decimal(self.xo, ':')
self.yo = astCoords.dms2decimal(self.yo, ':')
for filter in self.filters:
# Store the names
self.combima[filter] = "%s%s" % (self.tilename, filter)
self.weightima[filter] = "%s%s_weight.fits" % (self.tilename,
filter)
# make the combined catalog filenames
if os.path.isfile('{}{}.cat'.format(self.tilename, filter)):
self.combcat[filter] = '{}{}.cat'.format(self.tilename, filter)
elif os.path.isfile('{}{}_cal.cat'.format(self.tilename, filter)):
self.combcat[filter] = '{}{}_cal.cat'.format(self.tilename,
filter)
# The default output names
self.colorCat = self.tilename + ".color"
self.columnsFile = self.tilename + ".columns"
return
def __init__(self,name,RA,DEC):
self.name = name
if type(RA) == str:
self.RA = astCoords.hms2decimal(RA,":")
else:
self.RA = RA
if type(DEC) == str:
self.DEC = astCoords.dms2decimal(DEC,":")
else:
self.DEC = DEC
self.observations = []
def _getDistance(self, threshold=3.0):
"""
looking for nearby fibres. The unit of distance is arcmin (')
"""
fibrelist = self.FEList.translate.keys()
fibdis = {}
for fibre in fibrelist:
fRA = ac.hms2decimal(self._get_coord(fibre)[0], ':')
fDEC = ac.dms2decimal(self._get_coord(fibre)[1], ':')
temp_neigbhour = []
for key, value in self.FEList.translate.iteritems():
if key == fibre: # if the two fibres are actually the same, do nothing
pass
else:
dRA = ac.hms2decimal(self._get_coord(key)[0], ':')
dDEC = ac.dms2decimal(self._get_coord(key)[1], ':')
distance = np.sqrt((dRA - fRA)**2 + (dDEC - fDEC)**2)*60.0
if distance <= threshold:
temp_neigbhour.append(int(key))
fibdis[int(fibre)] = temp_neigbhour
return fibdis
def parseForm(self,cd):
coordstr = cd['coords'].replace(',',' ').strip()
try:
radius = cd['radius_arcmin']
units = 'arcminutes'
except KeyError:
radius = cd['radius_arcsec']
units = 'arcseconds'
# User input data validation
if ':' in coordstr:
# Remember to add sanity checks!
try:
c = coordstr.split()
ra = astCoords.hms2decimal(c[0],':')
dec = astCoords.dms2decimal(c[1],':')
except:
raise CoordinateParseError
else:
try:
c = coordstr.split()
ra,dec = map(float,c)
except:
raise CoordinateParseError
try:
radius = min(float(radius),300)
radius = max(radius,1)
except:
raise AreaParseError
try:
n_bands = float(cd['n_bands'])
except:
n_bands = None
try:
forcedetect = cd['forcedetect']
except:
forcedetect = None
formdata = {
'radius':radius,
'ra':ra,
'dec':dec,
'units':units,
'n_bands':n_bands,
'forcedetect':forcedetect,
}
return formdata
def _getDistance(self, threshold=3.0):
"""
looking for nearby fibres. The unit of distance is arcmin (')
"""
fibrelist = self.fibreExtDic.keys()
fibdis = {}
for fibre in fibrelist:
fRA = ac.hms2decimal(self.getCoordinate(fibre)[0], ':')
fDEC = ac.dms2decimal(self.getCoordinate(fibre)[1], ':')
temp_neigbhour = []
for key, value in self.fibreExtDic.iteritems():
if key == fibre: # if the two fibres are actually the same, do nothing
pass
else:
dRA = ac.hms2decimal(self.getCoordinate(key)[0], ':')
dDEC = ac.dms2decimal(self.getCoordinate(key)[1], ':')
distance = np.sqrt((dRA - fRA)**2 +
(dDEC - fDEC)**2) * 60.0
if distance <= threshold:
temp_neigbhour.append(int(key))
fibdis[int(fibre)] = temp_neigbhour
return fibdis
def load_coords(fibers, fiberPositions):
# determines which fibers should be included and returns the fiber number
# along with the position (RA,DEC) of each.
coords = np.genfromtxt(fiberPositions, dtype=str)
temp = []
for f in fibers:
ra = coords[f-1, 1]
dec = coords[f-1,2]
ra_deg = astCoords.hms2decimal(ra, ':')
dec_deg = astCoords.dms2decimal(dec, ':')
#temp.append({'fiber':f, 'ra':ra_deg, 'dec':dec_deg})
temp.append((ra_deg, dec_deg))
return temp
def map():
#p: [[RA,DEC],[center_RA,center_DEC], [header, image, solar, err_img], [pa, incl, D_gal(kpc), Rgal], astWCS header]
#Returns the pixel value at a given RA, DEC
#p: [[RA, DEC], astWCS header, numpy image array]
#print "Converting to d/d0 with solar 12+log(O/H)={0}".format(p[2][2])
r, d = astCoords.hms2decimal(strip(p[0][0]), " "), astCoords.dms2decimal(strip(p[0][1]), " ")
oh = soh = 0
if p[2][0].coordsAreInImage(r, d):
x, y = np.round(p[2][0].wcs2pix(r, d))
#astLib returns indices for the image array; 1 lower in value than DS9 x, y
#Assume the image is the first entry in the hdulist
#PyFits Handbook p. 16: slow axis first, last axis last,
#!At this time we assume a 12+log(O/H) map so the conversion is hardcoded and should be parameters!!:
oh = p[2][1][y,x]
if (m.isnan(oh) or oh==0):
#Even if p[2][0] is in image, this box might not be
try:
#If there is no value at this location we will take the highest value within a small box and warn about it (ignore NaNs)
oh = np.nanmax(p[2][1][y-2:y+3,x-2:x+3])
except:
print "Tried to scan outside image; setting oh to 0"
if (m.isnan(oh) or oh==0):
print "Warning: no value found"
else:
soh = p[2][3][y-2:y+3,x-2:x+3].ravel()[np.nanargmax(p[2][1][y-2:y+3,x-2:x+3])]
#Note that the proper index applies to a subselection of both images ^
print "Read 12+log(O/H) = {} +/- {} -- maximum value nearby".format(oh, soh)
else:
soh = p[2][3][y,x]
print "Read 12+log(O/H) = {} +/- {}".format(oh, soh)
else: #coordinate is not on the map
print "Warning: coordinate outside map; setting 0"
#R = separation(p[0][0], p[0][1], p[1][0], p[1][1], p[3][0], p[3][1], p[3][2], p[4])
if (oh > 9.5):
print "Warning: OH > 9.5 rejected, set to 0"
oh = 0
dd0 = 10**(oh - p[2][2])
sdd0 = dd0 * p[2][2] * soh / 10. #absolute error; all errors absolute to avoid confusion
#sdd0 = p[2][2] * soh / 10. #relative error
#a value of oh = 0 will result in artificially high n
return dd0, sdd0
def make_images(cd,radius=10):
bands = cd['bands']
coordstr = cd['coords'].replace(',',' ').strip()
area = cd['area']
unit_area = cd['unit_area']
#-------------------------------------
# User input data validation
if ':' in coordstr:
# Remember to add sanity checks!
try:
c = coordstr.split()
ra = astCoords.hms2decimal(c[0],':')
dec = astCoords.dms2decimal(c[1],':')
except:
raise CoordinateParseError
else:
try:
c = coordstr.split()
ra,dec = map(float,c)
except:
raise CoordinateParseError
try:
float(area)
except:
raise AreaParseError
#-------------------------------------
results = ImageHeader.objects.filter(FILTER__in=bands).imagePositionFilter(ra,dec,radius=radius,units='degrees')
if not results:
raise NoCoverageError(radius=radius)
images = []
for i in results:
image = i.__dict__
image['DATE_OBS'] = image['DATE_OBS'].replace('T',' ')
d = pyfits.open(i.PATH)[0].data
unique_filename = uuid.uuid4()
fname = '%s.png' % unique_filename
image['PATH_PNG'] = fname
image['PATH_RAW'] = i.PATH
astImages.saveBitmap(os.path.join(MEDIA_ROOT,fname),d,cutLevels=["smart", 99.5],size=300,colorMapName='gray')
images.append(image)
print image
return images
def _calculatePosition(self):
"""
This method can be used to calculate the WCS values.
Uses the pywcs to calculate the pixel to RA and DEC transformations.
Uses astLib.astCoords to transform RA and DEC to decimal degrees.
"""
#get RA and DEC from the header
ra = self.slits[self.centralFile]['header0']['RA']
dec = self.slits[self.centralFile]['header0']['DEC']
ra = astCoords.hms2decimal(ra, ':')
dec = astCoords.dms2decimal(dec, ':')
pix = self.direct['WCS'].wcs_sky2pix(np.array([[ra, dec], ]), 1)
self.direct['xposition'] = int(pix[0, 0])
self.direct['yposition'] = int(pix[0, 1])
self.result['RAinit'] = ra
self.result['DECinit'] = dec
if self.debug:
print self.direct['xposition'], self.direct['yposition']
def SetUpFramecoords(self):
""" Set up the boundary and center coordinates of the grid.
Keep in mind that in RA/DEC space the frame is rectangular.
As such the "left" RA_low coordinate is not equal to the
"left" RA_high coordinate.
"""
centercoords = self.obRun.obFrameCoords[self.gridnr]
RA_c = centercoords[0]
DEC_c = centercoords[1]
self.RA_c = astCoords.hms2decimal(RA_c, ":")
self.DEC_c = astCoords.dms2decimal(DEC_c, ":")
DEC_lo = self.DEC_c - 0.5 * self.obRun.aperture_DEC
DEC_hi = self.DEC_c + 0.5 * self.obRun.aperture_DEC
if DEC_hi < DEC_lo:
DEC_lo, DEC_hi = DEC_hi, DEC_lo
RA_lo_l = self.RA_c - (0.5 * self.obRun.aperture_RA /
np.cos(DEC_lo * (np.pi / 180.)))
RA_lo_r = self.RA_c + (0.5 * self.obRun.aperture_RA /
np.cos(DEC_lo * (np.pi / 180.)))
RA_hi_l = self.RA_c - (0.5 * self.obRun.aperture_RA /
np.cos(DEC_hi * (np.pi / 180.)))
RA_hi_r = self.RA_c + (0.5 * self.obRun.aperture_RA /
np.cos(DEC_hi * (np.pi / 180.)))
if RA_lo_r < RA_lo_l:
RA_lo_r, RA_lo_l = RA_lo_l, RA_lo_r
if RA_hi_r < RA_hi_l:
RA_hi_r, RA_hi_l = RA_hi_l, RA_hi_r
if RA_hi_l < RA_lo_l:
RA_lo_r, RA_hi_r, RA_lo_l, RA_hi_l = \
RA_hi_r, RA_lo_r, RA_hi_l, RA_lo_l
self.DEC_lo = DEC_lo
self.DEC_hi = DEC_hi
self.RA_lo_l = RA_lo_l
self.RA_lo_r = RA_lo_r
self.RA_hi_l = RA_hi_l
self.RA_hi_r = RA_hi_r
def wcslabels(wcs, xlim, ylim, xsep='00:00:01', ysep='00:00:15',
ax=None, label_color='k', rotate_x=0, rotate_y=90):
"""
Get WCS ticklabels
Parameters
----------
wcs : astWCS.WCS instance
the wcs of the image to be shown
xlim : sequence of length 2
the minimum and maximum values of the x axis
ylim : sequence of length 2
the minimum and maximum values of the y axis
xsep : string
separation of right ascension ticks in the x axis,
in colon-separated hms format
xsep : string
separation of declination ticks in the y axis, in
colon-separated dms format
ax : matplotlib.Axes instance (optional)
if provided, the ticks will be displayed on it
label_color : string or matplotlib color
color with which the tick labels will be displayed,
if ax is provided
rotate_x : float
by how much to rotate the x tick labels if ax is
provided
rotate_y : float
by how much to rotate the y tick labels if ax is
provided
Returns
-------
[xticks, xticklabels] : lists containing the positions and
labels for right ascension hms labels
[yticks, yticklabels] : lists containing the positions and
labels for declination dms labels
"""
def format_wcs(x):
"""
replace the 60's for 0's and change other values consistently,
and add 0's at the beginning of single-digit values
"""
x = x.split(':')
x[2] = round(float(x[2]), 0)
x[2] = '{0:.0f}'.format(x[2]) if x[2] >= 10 \
else '0{0:.0f}'.format(x[2])
for i in (1, 0):
if x[i+1] == '60':
if x[0][0] == '-':
if i == 0:
x[i] = '-{0}'.format(str(int(x[i]) - 1))
else:
x[i] = str(int(x[i]) - 1)
else:
x[i] = str(int(x[i]) + 1)
x[i+1] = '00'
for i in xrange(len(x)):
if 0 <= int(x[i]) < 10:
x[i] = '0{:.0f}'.format(int(x[i]))
elif -10 < int(x[i]) < 0:
x[i] = '-0{:.0f}'.format(-int(x[i]))
return ':'.join(x)
left, right = xlim
bottom, top = ylim
wcslim = [wcs.pix2wcs(left, bottom), wcs.pix2wcs(right, top)]
ralim, declim = numpy.transpose(wcslim)
rasep = astCoords.hms2decimal(xsep, ':')
decsep = astCoords.dms2decimal(ysep, ':')
raticks = numpy.arange(0, max(ralim), rasep)
raticks = raticks[raticks > min(ralim)]
decticks = numpy.arange(-90, max(declim), decsep)
decticks = decticks[decticks > min(declim)]
# this assumes that the rotation angle of the image is 0/90/180/270
# degrees
xticks = [wcs.wcs2pix(x, declim[0])[0] for x in raticks]
yticks = [wcs.wcs2pix(ralim[0], y)[0] for y in decticks]
xticklabels = [astCoords.decimal2hms(t, ':') for t in raticks]
yticklabels = [astCoords.decimal2dms(t, ':').replace('+', '')
for t in decticks]
# format properly (remove 60's and add 0's)
xticklabels = [format_wcs(xt) for xt in xticklabels]
yticklabels = [format_wcs(yt) for yt in yticklabels]
# get tick positions for rounded labels
raticks = [astCoords.hms2decimal(xt, ':') for xt in xticklabels]
decticks = [astCoords.dms2decimal(yt, ':') for yt in yticklabels]
xticks = [wcs.wcs2pix(x, declim[0])[0] for x in raticks]
yticks = [wcs.wcs2pix(ralim[0], y)[1] for y in decticks]
# display?
if ax:
ax.set_xticks(xticks)
ax.set_yticks(yticks)
ax.set_xticklabels(xticklabels, color=label_color, rotation=rotate_x)
ax.set_yticklabels(yticklabels, color=label_color, rotation=rotate_y)
return [xticks, xticklabels], [yticks, yticklabels]
import os
from astLib import astCoords
import glob
import numpy as np
for files in glob.glob('*.txt'):
fbits = files.split('_')
if not os.path.isfile(fbits[0] + '_combined_tiles.txt'):
tiles = glob.glob(fbits[0] + '*')
with open(fbits[0] + '_combined_tiles.txt', 'wt') as newf:
newf.writelines('# tile dither fiber fiber_ra fiber_dec\n')
for f in tiles:
tile = f.split('_')[1]
dither = f.split('_')[2]
print(fbits[0], tile, dither)
data = np.genfromtxt(f, dtype='str')
for fiber, ra, dec in zip(
range(1, len(data[:, 0]) + 1), data[:, 1], data[:, 2]):
ra_deg = astCoords.hms2decimal(ra, ':')
dec_deg = astCoords.dms2decimal(dec, ':')
newf.writelines('%s %s %s %s %s\n' %
(tile, dither, fiber, ra_deg, dec_deg))
line = result.readline()
if line.startswith("ERROR".encode()):
print('ERROR')
ofp = sys.stderr
else:
with open(outfile, 'wt') as ofp:
cnt = 0
while line:
ofp.write(line.rstrip().decode() + os.linesep)
line = result.readline()
cnt += 1
if cnt < 3:
os.remove(outfile)
# get file data
data = np.genfromtxt('../catalogs/PSZ2_unconfirmed_catalog - Master.csv',
delimiter=',',
names=True,
dtype=None)
for i, (ra, dec, name) in enumerate(zip(data['RA'], data['DEC'],
data['Name'])):
print(data['Name'][i])
ra = astCoords.hms2decimal(ra, ':')
dec = astCoords.dms2decimal(dec, ':')
work(ra, dec, './SDSS/%s_SDSS_catalog.csv' % (name.decode()))
sleep(1)
cwd = os.getcwd()
for f in filelist:
data = np.loadtxt(f, dtype='str')
fBits = f.split('_')
print fBits[0]
if not os.path.isdir(fBits[0]):
os.mkdir(fBits[0])
os.chdir(fBits[0])
if not os.path.isdir(fBits[1]):
os.mkdir(fBits[1])
os.chdir(fBits[1])
if not os.path.isdir(fBits[2]):
os.mkdir(fBits[2])
os.chdir(fBits[2])
for fiber, ra, dec in zip(data[:,0], data[:,1], data[:,2]):
if not os.path.isfile(fiber.zfill(3)+'.txt'):
ra = astCoords.hms2decimal(ra, ':')
dec = astCoords.dms2decimal(dec, ':')
work(ra, dec, fiber.zfill(3)+'.txt')
#print fiber, ra, dec
time.sleep(2)
else:
pass
os.chdir(cwd)
def dms(self):
dms_orig = '12:34:56.78'
decimal = astCoords.dms2decimal(dms_orig, ':')
dms_new = astCoords.decimal2dms(decimal, ':')
self.assertEqual(dms_new, dms_orig)
def testdms2decimal(self):
for dms, result in self.dms2decimal:
answer = astCoords.dms2decimal(dms, ':')
self.assertEqual(result, answer)
downloads = []
for field in fields:
f_ra_h = field[1:3]
f_ra_m = field[3:5]
f_dec_sign_str = field[5]
if f_dec_sign_str == 'M':
f_dec_sign = '-'
else:
f_dec_sign = ''
f_dec_d = field[6:8]
f_ra_hms = f_ra_h + ':' + f_ra_m + ':00'
f_dec_dms = f_dec_sign + f_dec_d + ':00:00'
f_ra = ac.hms2decimal(f_ra_hms, delimiter=':')
f_dec = ac.dms2decimal(f_dec_dms, delimiter=':')
if in_area(f_ra, f_dec, ra_min, ra_max, dec_min, dec_max):
downloads.append(field)
for dl in downloads:
get_nvss(dl)
os.system('gunzip ' + dl + '.gz')
os.system('mv ' + dl + ' ' + dl + '.fits')
os.system('mSubimage -p ' + dl + '.fits ' + dl +
'_crop.fits 0 0 1024 1024')
os.system('rm ' + dl + '.fits')
os.system('mv ' + dl + '_crop.fits ' + tempdir)
os.chdir(tempdir)
os.system('mImgtbl . images.tbl')
os.system('mMakeHdr images.tbl template.hdr')
def query(ra, dec, radius=2., unit='arcmin', z=0., cosmo=None,
catalogs=None, return_single=True, squeeze=False,
return_values=('name','ra','dec','z','index','dist','dz')):
"""
Query different catalogs for clusters close to a given set of coordinates.
To-do's:
-possibility to return survey observables
Parameters
----------
ra : (array of) float or str
if float, should be the RA in decimal degrees; if str,
should be in hms format ('hh:mm:ss', requires astLib)
dec : (array of) float or str
if float, should be the Dec in decimal degrees; if str,
should be in dms format ('dd:mm:ss', requires astLib)
radius : float (default 2)
the search radius, in units given by argumetn "unit"
unit : {'arcmin', 'Mpc'}
the units of argument "radius". If Mpc, then argument "z"
must be larger than zero.
z : (array of) float (optional)
redshift(s) of the cluster(s). Must be >0 if unit=='Mpc'.
cosmo : module astro.cosmology (optional)
if the matching is done in physical distance then pass
this module to make sure all cosmological parameters are
used consistently with the parent code!
catalogs : str (optional)
list or comma-separated names of catalogs to be searched.
If not given, all available catalogs are searched. Allowed
values are:
* 'maxbcg' (Koester et al. 2007)
* 'gmbcg' (Hao et al. 2010)
* 'hecs2013' (Rines et al. 2013)
* 'hecs2016' (Rines et al. 2016) NOT YET
* 'orca' (Geach, Murphy & Bower 2011)
* 'psz1' (Planck Collaboration XXIX 2014)
* 'psz2' (Planck Collaboration XXVII 2016)
* 'redmapper' (Rykoff et al. 2014, v5.10)
* 'whl' (Wen, Han & Liu 2012, Wen & Han 2015)
return_single : bool
whether to return the single closest matching cluster (if
within the search radius) or all those falling within the
search radius
return_values : any subset of ('name','ra','dec','z','index','dist','dz')
what elements to return. 'index', 'dist' and 'dz' refer to
the index in the catalog and the distances of the matching
cluster(s) in arcmin and redshift space, respectively.
NOTE: altering the order of the elements in return_values
will have no effect in the order in which they are returned!
squeeze : bool
whether to return a list instead of a dictionary if only
one catalog is provided
Returns
-------
matches : dict
matching elements per catalog. Each requested catalog is
a key of this dictionary if more than one catalog was
searched or if squeeze==False. If only one catalog was
provided and squeeze==True, then return a list with
matching entry/ies.
withmatch : dict
for each searched catalog, contains hte indices of the
provided clusters for which at least one match was found.
The same formatting as for "matches" applies.
"""
available = ('maxbcg', 'gmbcg', 'hecs2013', 'orca', 'psz1', 'psz2',
'redmapper', 'whl')
# some formatting for convenience
if not hasattr(ra, '__iter__'):
ra = [ra]
dec = [dec]
if not hasattr(z, '__iter__'):
z = array([z])
# in the case of matching by physical radius, demand z > 0
if unit == 'Mpc' and npany(z <= 0):
msg = "ERROR: in catalogs.query:"
msg += " if unit=='Mpc' then z must be larger than 0"
print msg
exit()
if unit == 'Mpc':
if cosmo is None:
cosmo = cosmology
dproj = cosmo.dProj
# will this fail for numpy.string_?
if isinstance(ra[0], basestring):
ra = array([hms2decimal(x, ':') for x in ra])
dec = array([dms2decimal(y, ':') for y in dec])
if unit == 'arcmin':
radius = ones(ra.size) * radius# / 60
else:
radius = array([dproj(zi, radius, input_unit='Mpc', unit='arcmin')
for zi in z])
if catalogs is None:
catalogs = available
else:
try:
catalogs = catalogs.split(',')
# if this happens then we assume catalogs is already a list
except ValueError:
pass
for name in catalogs:
if name not in available:
msg = 'WARNING: catalog {0} not available'.format(name)
print msg
labels = {'maxbcg': 'maxBCG', 'gmbcg': 'GMBCG', 'hecs2013': 'HeCS',
'hecs2016': 'HeCS-SZ', 'orca': 'ORCA', 'psz1': 'PSZ1',
'psz2': 'PSZ2', 'redmapper': 'redMaPPer', 'whl': 'WHL'}
filenames = {'maxbcg': 'maxbcg/maxBCG.fits',
'gmbcg': 'gmbcg/GMBCG_SDSS_DR7_PUB.fit',
'hecs2013': 'hecs/2013/data.fits',
'orca': 'orca/fullstripe82.fits',
'psz1': osjoin('planck', 'PSZ-2013', 'PLCK-DR1-SZ',
'COM_PCCS_SZ-union_R1.11.fits'),
'psz2': osjoin('planck', 'PSZ-2015',
'HFI_PCCS_SZ-union_R2.08.fits'),
'redmapper': 'redmapper/redmapper_dr8_public' + \
'_v5.10_catalog.fits',
'whl': 'whl/whl2015.fits'}
columns = {'maxbcg': 'none,RAJ2000,DEJ2000,zph',
'gmbcg': 'OBJID,RA,DEC,PHOTOZ',
'hecs2013': 'Name,RAJ2000,DEJ2000,z',
'orca': 'ID,ra_bcg,dec_bcg,redshift',
'psz1': 'NAME,RA,DEC,REDSHIFT',
'psz2': 'NAME,RA,DEC,REDSHIFT',
'redmapper': 'NAME,RA,DEC,Z_LAMBDA',
'whl': 'WHL,RAJ2000,DEJ2000,zph'}
for cat in catalogs:
filenames[cat] = osjoin(path, filenames[cat])
columns[cat] = columns[cat].split(',')
matches = {}
withmatch = {}
for cat in available:
if cat not in catalogs:
continue
data = getdata(filenames[cat], ext=1)
aux = {}
for name in data.names:
aux[name] = data[name]
data = aux
# if the catalog doesn't give a name
if columns[cat][0] == 'none':
columns[cat][0] = 'Name'
data['Name'] = chararray(data[columns[cat][1]].size, itemsize=4)
data['Name'][:] = 'none'
data = [data[v] for v in columns[cat]]
name, xcat, ycat, zcat = data
colnames = 'name,ra,dec,z'.split(',')
close = [(abs(xcat - x) < 2*r/60.) & (abs(ycat - y) < 2*r/60.)
for x, y, r in izip(ra, dec, radius)]
withmatch[cat] = [j for j, c in enumerate(close) if name[c].size]
dist = [60 * calcAngSepDeg(xcat[j], ycat[j], x, y)
for j, x, y in izip(close, ra, dec)]
match = [(d <= r) for d, r in izip(dist, radius)]
withmatch[cat] = array([w for w, m in izip(count(), match)
if w in withmatch[cat] and name[m].size])
if return_single:
match = [argmin(d) if d.size else None for d in dist]
matches[cat] = {}
# keeping them all now because they may be needed for other properties
for name, x in izip(colnames, data):
matches[cat][name] = array([x[j][mj] for w, j, mj
in izip(count(), close, match)
if w in withmatch[cat]])
if 'index' in return_values:
matches[cat]['index'] = array([arange(xcat.size)[j][m]
for w, j, m in izip(count(),
close, match)
if w in withmatch[cat]])
if 'dist' in return_values:
matches[cat]['dist'] = array([d[m] for w, d, m
in izip(count(), dist, match)
if w in withmatch[cat]])
if unit == 'Mpc':
matches[cat]['dist'] *= array([dproj(zi, 1, unit='Mpc',
input_unit='arcmin')
for zi in matches[cat]['z']])
if 'dz' in return_values:
matches[cat]['dz'] = array([zcat[j][m] - zj for w, j, m, zj
in izip(count(), close, match, z)
if w in withmatch[cat]])
for key in matches[cat].keys():
if key not in return_values:
matches[cat].pop(key)
if not return_single and name[j][match].size == 1:
for key in matches[cat].keys():
matches[cat][key] = matches[cat][key][0]
if len(catalogs) == 1 and squeeze:
return matches[catalogs[0]], withmatch[catalogs[0]]
return matches, withmatch
"""
Various coordinates utilities
Variables
---------
epoch : Epoch. Right now only 'J2000' is implemented
aNGP : Right Ascension of the North Galactic Pole, for the chosen epoch
dNGP : Declination of the North Galactic Pole, for the chosen epoch
"""
epoch = 'J2000'
if epoch == 'J2000':
aNGP = astCoords.hms2decimal('12:51:26.28', ':')
dNGP = astCoords.dms2decimal('+27:07:42.0', ':')
def torad(x):
"""
Input: coordinate in degrees
Returns : coordinate in radians
"""
return numpy.pi * x / 180
def todeg(x):
"""
Input: coordinate in radians
Returns: coordinate in degrees
"""
def _processDirectImage(self, ext=0):
"""
Processes the given Direct Image file.
This method performs several tasks:
1. trims the image (optional, depends on self.cutout)
2. supersamples the original image by a given factor
3. rotates the image by -POSANGLE degrees, note the minus sign
4. gets the plate scale from the rotated header
:param ext: FITS extension, change this if the SDSS data changes or if other data are used.
:type ext: int
"""
#load images
fh = pf.open(self.dirfile)
self.direct['originalHeader0'] = fh[ext].header
img = fh[ext].data
fh.close()
self.direct['originalImage'] = img
#cut out a region
if self.cutout:
ra = self.slits[self.centralFile]['header0']['RA']
dec = self.slits[self.centralFile]['header0']['DEC']
ra = astCoords.hms2decimal(ra, ':')
dec = astCoords.dms2decimal(dec, ':')
wcs = pywcs.WCS(self.direct['originalHeader0'])
pix = wcs.wcs_sky2pix(np.array([[ra, dec], ]), 1)
xmid = pix[0, 0]
ymid = pix[0, 1]
xstart = int(xmid - self.direct['xsize'] / 2.)
xstop = int(xmid + self.direct['xsize'] / 2.)
ystart = int(ymid - self.direct['ysize'] / 2.)
ystop = int(ymid + self.direct['ysize'] / 2.)
imgT, hdrT = modify.hextract(self.dirfile, xstart, xstop, ystart, ystop)
shape = imgT.shape
file = 'resized.fits'
else:
shape = img.shape
file = self.dirfile
#super sample
if self.direct['factor'] != 1:
xnew = int(shape[1] * self.direct['factor'])
ynew = int(shape[0] * self.direct['factor'])
imgS, hdrS = modify.hrebin(file, xnew, ynew, total=True)
self.direct['xnew'] = xnew
self.direct['ynew'] = ynew
self.direct['supersampledImage'] = imgS
self.direct['supersampledHeader'] = hdrS
self.direct['supersampledFile'] = 'rebinned.fits'
else:
self.direct['xnew'] = int(shape[1])
self.direct['ynew'] = int(shape[0])
self.direct['supersampledImage'] = img
self.direct['supersampledHeader'] = self.direct['originalHeader0']
self.direct['supersampledFile'] = self.dirfile
#set rotation, note that the rotation is in minus direction
#instead of using SPA one could also calculate this from WCS CD matrix
self.direct['rotation'] = -self.slits[self.centralFile]['POSANGLE'] + self.direct['originalHeader0']['SPA']
#make a rotation
imgR, hdrR = modify.hrot(self.direct['supersampledFile'],
self.direct['rotation'],
xc=None,
yc=None)
self.direct['rotatedImage'] = imgR
self.direct['rotatedHeader'] = hdrR
self.direct['rotatedFile'] = 'rotated.fits'
#convert the images from nanomaggies to micro Janskys
self.direct['originalImage'] = convert.nanomaggiesToJansky(self.direct['originalImage']) * 1e6
self.direct['supersampledImage'] = convert.nanomaggiesToJansky(self.direct['supersampledImage']) * 1e6
self.direct['rotatedImage'] = convert.nanomaggiesToJansky(self.direct['rotatedImage']) * 1e6
#WCS info
self.direct['WCS'] = pywcs.WCS(hdrR)
#self.direct['WCS'] = wcs.Projection(hdrR)
if self.debug:
print '\ndirect:'
print self.direct
else:
print("\n\tHalting setup process!\n")
quit()
os.chdir(working_dir + "/redux/")
for raw_dir in raw_dirs: os.mkdir(raw_dir.name)
### THIS IS WHERE OBJECTS ARE FOUND FROM TARGETS.list
### ... THEY MUST BE WITHIN 0.04deg (2.4") OF THE TARGETS.list VALUE
for raw_dir in raw_dirs:
targetstxt = open("targets.txt", "w")
for target in targets:
made_dir = False
target_ra = astCoords.hms2decimal(target[1], ":")
target_dec = astCoords.dms2decimal(target[2], ":")
for im in raw_dir.obj:
obj_ra = astCoords.hms2decimal(pf.getval(working_dir + "/raw/"
+ raw_dir.name + "/"
+ im, "RA"), ":")
obj_dec = astCoords.dms2decimal(pf.getval(working_dir + "/raw/"
+ raw_dir.name + "/"
+ im, "DEC"), ":")
if astCoords.calcAngSepDeg(target_ra, target_dec,
obj_ra, obj_dec) < 0.04:
if not made_dir:
os.mkdir(raw_dir.name+"/"+target[0])
made_dir = True
targetstxt.write(target[0]+"\n")
os.chdir(raw_dir.name + "/" + target[0])
ln_cmd = "ln -s " + working_dir + "/raw/" \
def get_astrometry(self, newfirm=False):
''' This calls the pp script to astrometrically correct the images. I'm
breaking it appart from the rest of the script so I can control when
things happen. It is mostly for testing.
'''
# we have to prepare the images first.
print()
check_exe('pp_prepare')
check_exe('pp_register')
# little patch to keep it from crashing
try:
os.mkdir('.diagnostics')
except FileExistsError:
pass
# make the diagnostics file too
open('diagnostics.html', 'a').close()
try:
if ':' in self.xo or ':' in self.yo:
from astLib import astCoords
self.xo = astCoords.hms2decimal(self.xo, ':')
self.yo = astCoords.dms2decimal(self.yo, ':')
except TypeError:
pass
subprocs = []
for filter in self.filters:
if not newfirm and filter == 'K':
continue
mosaic = '{}.fits'.format(self.combima[filter])
if self.pixscale == 0.25:
cmd = 'pp_prepare -ra {} -dec {} -telescope {} {}'.format(
self.xo, self.yo, 'KPNO4MOS3', mosaic)
elif self.pixscale == 0.2666:
cmd = 'pp_prepare -ra {} -dec {} -telescope {} {}'.format(
self.xo, self.yo, 'KPNO4MOS1', mosaic)
else:
cmd = 'pp_prepare -ra {} -dec {} {}'.format(
self.xo, self.yo, mosaic)
if not self.dryrun:
print(cmd)
subprocs.append(subprocess.Popen(shlex.split(cmd)))
[p.wait(timeout=600) for p in subprocs]
[i.kill() for i in subprocs]
for filter in self.filters:
if not newfirm and filter == 'K':
continue
mosaic = '{}.fits'.format(self.combima[filter])
cmd = 'pp_register -snr 10 -minarea 12 {}'.format(mosaic)
if not self.dryrun:
subprocs.append(subprocess.Popen(shlex.split(cmd)))
[p.wait(timeout=600) for p in subprocs]
[i.kill() for i in subprocs]
for filter in self.filters:
if not newfirm and filter == 'K':
continue
mosaic = '{}.fits'.format(self.combima[filter])
# correct the header information to make sure floats are floats and
# not strings
with fits.open(mosaic, mode='update') as f:
header = f[0].header
for key, val in list(header.items()):
if 'CD1_' in key or 'CD2_' in key or \
'CRVAL' in key or 'CRPIX' in key or \
'EQUINOX' in key:
f[0].header[key] = float(val)
if 'PV' in key:
f[0].header[key] = str(val)
return
if wayOk == False:
print("<way>: either \"to_decimal\" or \"to_hmsdms\"")
sys.exit()
reader = open(inFile, "r")
lines = reader.readlines()
reader.close()
writer = open(outFile, "w")
for row in lines:
if len(row)>1:
if "#" not in row[:1]:
rowBits = row.split("\t")
if way == "to_decimal":
RADeg = astCoords.hms2decimal(rowBits[RACol], delimiter)
decDeg = astCoords.dms2decimal(rowBits[decCol], delimiter)
if way == "to_hmsdms":
RADeg = astCoords.decimal2hms(float(rowBits[RACol]),
delimiter)
decDeg = astCoords.decimal2dms(float(rowBits[decCol]),
delimiter)
writeString = ""
for i in range(len(rowBits)):
if i == RACol:
writeString = writeString+str(RADeg)+"\t"
elif i == decCol:
writeString = writeString+str(decDeg)+"\t"
elif rowBits[i].find("\n") != -1:
writeString = writeString+str(rowBits[i])
else:
writeString = writeString+str(rowBits[i])+"\t"
print('Obtaining useful sources from catalogue...')
#Get relevant data from the catalogue:
cat = np.loadtxt(catFile, usecols=[0,1,2,3,4,5,7],skiprows=2)
#Get the R.A. in degrees for each source
h,m,s=cat[:,0],cat[:,1],cat[:,2]
RAdeg=[]
for i in range(len(h)):
RAdeg.append( hms2decimal("%s"%(h[i])+" "+"%s"%(m[i])+" "+"%s"%(s[i]),' ' ))
#Get the Dec. in degrees for each source
d,m,s=cat[:,3],cat[:,4],cat[:,5]
DECdeg=[]
for i in range(len(h)):
DECdeg.append( dms2decimal("%s"%(d[i])+" "+"%s"%(m[i])+" "+"%s"%(s[i]),' ' ))
#Get the the peak and coordinates for each source as np arrays
Fpeak = cat[:,6]
RAdeg = np.array(RAdeg)
DECdeg = np.array(DECdeg)
#Get initial list of possible filenames
print('Getting initial list of possible associated filenames...')
#The below process should be handled more elegantly, as above.
#Might rewrite this.
filenames = []
f = open(catFile,'r')
for line in f:
if (line[0] == '#'): continue