intrinsic['hk'] = arg.getlistfloat("hk")
intrinsic['cov'] = arg.getfloat("cov")
intrinsic['method'] = arg.getstr("method",option=['jh','hk','nicer','rjce'])
from numpy import loadtxt,savetxt,sqrt
data = loadtxt(infile,dtype=str)
d = data[:,2:8].astype(float)
if intrinsic['method'] == 'jh' or intrinsic['method'] == 'hk':
Av,dAv = nice(intrinsic, d[:,0],d[:,1],d[:,2],d[:,3],d[:,4],d[:,5])
elif intrinsic['method'] == 'nicer':
Av,dAv = nicer(intrinsic,d[:,0],d[:,1],d[:,2],d[:,3],d[:,4],d[:,5])
elif intrinsic['method'] == 'rjce':
Av,dAv = rjce(intrinsic, d[:,0],d[:,1],d[:,2],d[:,3],d[:,4],d[:,5])
else:
arg.error('Invalid extinction method: %s' %intrinsic['method'])
fp = open(outfile,'w')
fp.write("# ra dec J dJ H dH Ks ")
fp.write("dKs Av dAv\n")
for i in xrange(data.shape[0]):
fp.write("%10s " %data[i,0])
fp.write("%10s " %data[i,1])
fp.write("%6s " %data[i,2])
fp.write("%5s " %data[i,3])
fp.write("%6s " %data[i,4])
fp.write("%5s " %data[i,5])
fp.write("%6s " %data[i,6])
fp.write("%5s " %data[i,7])
fp.write("%11.4e" %Av[i])
fp.write("%11.4e\n" %dAv[i])
expand = arg.getbool('expand')
tmpext = arg.getstr('ext')
rot = arg.getstr('rot')
hist = arg.getkeys(comment='IMROTATE.PY:',format=72,time=True).strip().split('\n')
import nlcastro
import pyfits
import scipy.interpolate
from numpy import nan,isnan,pi,arctan2,cos,sin,meshgrid,arange,ceil,floor
from numpy import amin,amax,where,isfinite,zeros,around
ext = nlcastro.findExt(inFile,tmpext)
header = pyfits.getheader(inFile,ext=ext)
if header['naxis'] != 2:
arg.error('Can only rotate 2-d images!')
data = pyfits.getdata(inFile,ext=ext)
angle = getAngle(rot,header)
data2 = doRotate(data,angle,expand)
if expand is True: # fix header so center is still at center of map
naxis2,naxis1 = data2.shape
header['naxis1'] = naxis1
header['naxis2'] = naxis2
header['crpix1'] = naxis1/2. + 0.5
header['crpix2'] = naxis2/2. + 0.5
# add history
for h in hist:
header.add_history(h)
import pyfits,pywcs
from numpy import where,nan
# open FITS image and read header
if inFile == '-':
fp = sys.stdin
else:
fp = pyfits.open(inFile)
header = fp[0].header
# read and interpret region keyword
tmp1 = region[0].split(':')
tmp2 = region[1].split(':')
if len(tmp1) != 2 or len(tmp2) != 2:
arg.error('Specify region keyword as xmin:xmax,ymin:ymax')
try:
xmin = int(tmp1[0])
except ValueError:
if tmp1[0] == 'xmin':
xmin = 1
try:
xmax = int(tmp1[1])
except ValueError:
if tmp1[1] == 'xmax':
xmax = int(header['naxis1'])
else:
arg.error('Specify region keyword as xmin:xmax,ymin:ymax')
try:
ymin = int(tmp2[0])
xmin = None # Min value for bins (defaults to data min)
xmax = None # Max value for bins (defaults to data max)
nbin = 10 # Number of bins"""
arg = ReadCmd(spec)
infile = arg.getstr("in",exist=True)
xcol = arg.getint("xcol",min=1)
ycol = arg.getint("ycol",min=1)
dxcol = arg.getint("dxcol",min=1)
dycol = arg.getint("dycol",min=1)
xmin = arg.getfloat("xmin")
xmax = arg.getfloat("xmax")
nbin = arg.getint("nbin",min=1)
if xcol is None:
arg.error("You must specify a column number for x!")
cols = []
for i in [xcol,ycol,dxcol,dycol]:
if i is not None:
cols.append(i-1)
errxFlag = True # set to false if no x errors
erryFlag = True # set to false if no y errors
# load data
data = loadtxt(infile,usecols=cols)
xcol = data[:,0]
n = data.shape[0]
if dycol is None or ycol is None:
dycol = ones(n)
import nlcastro
import pyfits
keylist = [a.lower() for a in junk]
img = pyfits.open(inFile)
idx = nlcastro.findExt(img,inext)
head1 = img[idx].header
img.close()
junk = [a.lower() for a in head1.keys()]
if keylist[0] != 'all':
for key in keylist:
if key not in junk:
arg.error("Keyword '%s' not in '%s'" %(key,inFile))
img = pyfits.open(outFile,'update')
# make sure all output extensions exist first
outidx = [nlcastro.findExt(img,out) for out in outext]
for idx in outidx:
head2 = img[idx].header
if keylist[0] != 'all':
for key in keylist:
head2.update(key,head1[key])
else:
for key in junk:
head2.update(key,head1[key])
if i == 0:
s1 = d.shape
if nfiles == 1: # one file, so no cube
data.append(d)
else: # if multiple files, make a cube. Each plane of cube is 1 file
tmp = zeros(tuple([nfiles] + list(s1)))
tmp[0] = d
data.append(tmp)
for i in xrange(1,nfiles):
idx = nlcastro.findExt(infiles[i],ext)
for j in xrange(next): # loop over extension indexes
d2 = pyfits.getdata(infiles[i],idx[j])
s2 = d2.shape
if s1 != s2:
arg.error('shape mis-match among input arrays!')
data[j][i] = d2
tmphdu = []
tmphdu.append(pyfits.PrimaryHDU(data[0]))
tmphdu[0].header.extend(header[0].cards,update=True)
for i in xrange(1,next):
tmphdu.append(pyfits.ImageHDU(data[i]))
tmphdu[i].header.extend(header[i].cards,update=True)
if next == 1:
hdu = tmphdu[0]
if 'EXTEND' in hdu.header.keys():
hdu.header.update('EXTEND',False)
if 'XTENSION' in hdu.header.keys():
cdFlag = arg.getstr('cd')
import nlclib
blah = nlclib.createtempname() # new file made by rotatevector.py
# get path of this script so we can call rotatevector.py in the same dir
path,junk = os.path.split(os.path.abspath(sys.argv[0]))
os.system('%s/rotatevector.py in=%s fits=%s out=%s ext=%d cd=%s' %(path,
infile,fits,blah,ext,cdFlag))
data1 = nlclib.readdata(infile)
data2 = nlclib.readdata(blah,dtype=float)
if len(data1) != len(data2):
arg.error('Problem rotating vectors!')
fp = open(outfile,'w')
fp.write('# x y Pol dPol Angle dAngle H dH Filename\n')
fp.write('# (pix) (pix) (%) (%) (deg) (deg) (mag) (mag) (string)\n')
for l1,l2 in zip(data1,data2):
fp.write('%8.3f %8.3f ' %(l2[0],l2[1])) # x,y from data2
fp.write('%6s %6s ' %(l1[2],l1[3])) # pol,dpol from data1
try:
fp.write('%7.3f %7s ' %(l2[3],l1[5])) # angle from data2,dangle from data1
except IndexError:
fp.close()
arg.error('Missing angle or delta angle for input file')
try:
fp.write('%7s %7s ' %(l1[6],l1[7])) # Hmag,dHmag from data1