#!/usr/bin/env python
""" Compute the intrinsic colors and the off-axis covariance matrix value
for JHKs colors.
This program requires an input file in the format:
ra dec j_mag j_mag_sigma h_mag h_mag_sigma k_mag k_mag_sigma
"""
from readcmd import ReadCmd
spec = """# Compute intrinsic colors on an input data file
in = ??? # Input (table) file name"""
arg = ReadCmd(spec)
infile = arg.getstr("in",exist=True)
from numpy import loadtxt,sum,sqrt,average,cov
data = loadtxt(infile,usecols=[2,3,4,5,6,7])
wJH = 1./(data[:,1]**2 + data[:,3]**2)
wHK = 1./(data[:,3]**2 + data[:,5]**2)
wJHHK = sqrt(wJH*wHK)
sumJH = sum(wJH*(data[:,0] - data[:,2]))
sumHK = sum(wHK*(data[:,2] - data[:,4]))
sumJH2 = sum(wJH*(data[:,0] - data[:,2])**2)
sumHK2 = sum(wHK*(data[:,2] - data[:,4])**2)
sumJHHK = sum(wJHHK*(data[:,0] - data[:,2])*(data[:,2] - data[:,4]))
sumwJH = sum(wJH)
sumwHK = sum(wHK)
sumwJHHK = sum(wJHHK)
#!/usr/bin/env python
"""Simple script to do subimages of a larger FITS"""
from readcmd import ReadCmd
import sys
spec = """in = ??? # Input filename
region = ??? # Region to clip, as xmin:xmax,ymin:ymax
out = ??? # Output filename
wcs = True # Compute new WCS for output image?"""
arg = ReadCmd(spec,head=__doc__)
inFile = arg.getstr('in',exist=True)
region = arg.getliststr('region',length=2)
outFile = arg.getstr('out',exist=False)
wcsFlag = arg.getbool('wcs')
keys = arg.getkeys(comment='IMSUB.PY:',format=80,time=True).strip().split('\n')
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(':')
elif intrinsic['method'] == 'hk':
Av = ((magh - magks) - intrinsic['hk'][0])/intrinsic['k2']
dAv = sqrt((sigmah**2 + sigmaks**2 + intrinsic['hk'][1]**2))/intrinsic['k2']
else:
Av = None
dAv = None
return Av,dAv
def rjce(intrinsic, magj, sigmaj, magh, sigmah, magks, sigmaks):
"""Compute extinction using RJCE (Majewski TODO)"""
return None,None
if __name__ == "__main__":
arg = ReadCmd(spec)
infile = arg.getstr("in",exist=True)
outfile = arg.getstr("out",exist=False)
intrinsic = {}
intrinsic['k1'] = 1./arg.getfloat("avaj")
intrinsic['k2'] = 1./arg.getfloat("avah")
intrinsic['jh'] = arg.getlistfloat("jh")
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])
import nlclib
from readcmd import ReadCmd
spec = """# Grid a data set
in = ??? # Input file
xrange = ??? # Range in x (min,max)
yrange = ??? # Range in y (min,max)
bins = 10 # Number of bins (can be x,y)
xcol = 1 # Column with x values
ycol = 2 # Column with y values
out = ??? # Output fits image
norm = None # Normalize by sum, max, or none (no normalization)"""
spec = ReadCmd(spec)
inFile = spec.getstr('in')
rangex = spec.getlistfloat('xrange',length=2)
rangey = spec.getlistfloat('yrange',length=2)
nbins = spec.getlistint('bins',length=[1,2])
xcol = spec.getint('xcol',min=1) - 1
ycol = spec.getint('ycol',min=1) - 1
outFile = spec.getstr('out',exist=False)
norm = spec.getstr('norm',option=['sum','none','max'],ignorecase=True)
if norm is None:
norm = 'none'
if len(nbins) == 1: #by default make x and y the same size
nbins.append(nbins[0])
import pyfits
#!/usr/bin/env python
"""change zeros in the FITS file to NaNs"""
from readcmd import ReadCmd
spec = """in = ??? # Input FITS file
tol = 3 # Round to this many decimal places before NaN conversion"""
arg = ReadCmd(spec,__doc__)
fitsfile = arg.getstr('in',exist=True)
tol = arg.getint('tol')
import pyfits,numpy
import nlclib
fimg = pyfits.open(fitsfile,mode='update')
data = fimg[0].data
hdr = fimg[0].header
if hdr['bitpix'] != -32:
fimg.close()
nlclib.error("Bitpix is not -32, NaNs will not work!")
if hdr['naxis'] == 3:
mask = numpy.where(data[0,:,:].round(tol) == 0)
data[mask] = numpy.nan
elif hdr['naxis'] == 2:
mask = numpy.where(data.round(tol) == 0)
data[mask] = numpy.nan
else:
fimg.close()
nlclib.error("NAXIS is not 2 or 3. I don't know what to do!")
#!/usr/bin/env python
from readcmd import ReadCmd
import os
import tempfile
spec = """# Take a ds9 contour file and make it usable by WIP
in = ??? # DS9 contour file
out = ??? # Output WIP file
dir = ??? # Output directory with WIP contours
units = wcs # Units of contour file, other option is linear"""
if __name__ == "__main__":
arg = ReadCmd(spec)
infile = arg.getstr('in', exist=True)
outfile = arg.getstr('out', exist=False)
units = arg.getstr('units', option=['wcs', 'linear'])
contdir = arg.getstr('dir', exist=False)
os.mkdir(contdir)
fp0 = open(infile, 'r')
fp1 = open(outfile, 'w')
fp1.write("symbol -1\n")
written = 0
fp2 = tempfile.NamedTemporaryFile(mode='w', dir=contdir, delete=False)
for line in fp0:
if len(line) == 0: # blank line starts/ends a contour
fp2.close()
if written:
fp1.write("data %s\n" % fp2.name)
#!/usr/bin/env python
from readcmd import ReadCmd
import os
import tempfile
spec = """# Take a ds9 contour file and make it usable by WIP
in = ??? # DS9 contour file
out = ??? # Output WIP file
dir = ??? # Output directory with WIP contours
units = wcs # Units of contour file, other option is linear"""
if __name__ == "__main__":
arg = ReadCmd(spec)
infile = arg.getstr('in',exist=True)
outfile = arg.getstr('out',exist=False)
units = arg.getstr('units',option=['wcs','linear'])
contdir = arg.getstr('dir',exist=False)
os.mkdir(contdir)
fp0 = open(infile,'r')
fp1 = open(outfile,'w')
fp1.write("symbol -1\n")
written = 0
fp2 = tempfile.NamedTemporaryFile(mode='w',dir=contdir,delete=False)
for line in fp0:
if len(line) == 0: # blank line starts/ends a contour
fp2.close()
if written:
fp1.write("data %s\n" %fp2.name)
title = None # Title for plot
width = 1 # line thickness
xcol = 1 # X column number(s)
dxcol = None # X error column number(s)
xlabel = None # X-axis label
ycol = 2 # Y column number(s)
dycol = None # Y error column number(s)
ylabel = None # Y-axis label"""
def error(text):
"""Write out error message and quit"""
sys.stderr.write("### Fatal Error! %s\n" %text)
sys.exit()
arg = ReadCmd(spec)
infile = arg.getstr('in',exist=True)
xcol = arg.getlistint('xcol',min=1)
ycol = arg.getlistint('ycol',min=1)
dxcol = arg.getlistint('dxcol',min=1)
dycol = arg.getlistint('dycol',min=1)
style = arg.getliststr('style')
color = arg.getliststr('color')
limits = arg.getlistfloat('limits',length=4)
out = arg.getstr('out')
xlab = arg.getstr('xlabel')
ylab = arg.getstr('ylabel')
mytext = arg.getliststr('text')
mytitle = arg.getstr('title')
mywidth = arg.getliststr('width')
legloc = arg.getlistfloat('legend',length=2)
#!/usr/bin/env python
"""Parse extension(s) from one or more files and combine into a cube"""
from readcmd import ReadCmd
import sys
spec = """in = ??? # Input file(s) to process
ext = ??? # Extension(s) to extract (start at 1)
out = ??? # Output filename"""
arg = ReadCmd(spec,head=__doc__)
infiles = arg.getliststr('in',exist=True)
ext = arg.getliststr('ext')
outfile = arg.getstr('out',exist=False)
hist = arg.getkeys(comment='IMEXTRACT.PY:',format=72,time=True).strip().split('\n')
next = len(ext)
nfiles = len(infiles)
import pyfits
import nlcastro
from numpy import zeros
# do first file, need outside loop in case there is only one file in total
idx = nlcastro.findExt(infiles[0],ext)
header = [pyfits.getheader(infiles[0],idx[i]) for i in xrange(next)]
# compile list with names of extensions. Read from first file
img = pyfits.open(infiles[0])
extname = [img[idx[i]].name for i in xrange(next)]
img.close()
#!/usr/bin/env python
from readcmd import ReadCmd
spec = """# recenter an image so crpix1,2 and crval1,2 are at the center of the map
in = ??? # Input FITS image
out = ??? # Output FITS image
"""
arg = ReadCmd(spec)
infile = arg.getstr("in",exist=True,type="file")
outfile = arg.getstr("out",exist=False)
hist = arg.getkeys(comment='RECENTER.PY:',format=72,time=True).strip().split('\n')
import pyfits
import pywcs
fp = pyfits.open(infile)
wcs = pywcs.WCS(fp[0].header)
crpix1 = fp[0].header['naxis1']/2. + 0.5
crpix2 = fp[0].header['naxis2']/2. + 0.5
ra,dec = wcs.wcs_pix2sky(crpix1,crpix2,1)
fp[0].header['crpix1'] = crpix1
fp[0].header['crpix2'] = crpix2
fp[0].header['crval1'] = ra[0]
fp[0].header['crval2'] = dec[0]
# add history
for h in hist:
fp[0].header.add_history(h)
from readcmd import ReadCmd
import math
spec = """# Make a ds9 region file from vectors
in = ??? # Input file
cols = 1,2,3,5 # Columns for x,y,polarization,angle
out = ??? # Output region file
scale = 5 # length of 1% polarization (in pixels or arcsec)
color = green # Color for region file
width = 1 # Line width
coord = fk5 # coordinates of vectors [fk5,physical]
mag = p # Make vector lengths (p)roportional or (u)niform?"""
arg = ReadCmd(spec)
infile = arg.getstr('in',exist=True)
cols = arg.getlistint('cols',length=4,min=1)
outfile = arg.getstr('out',exist=False)
scale = arg.getfloat('scale')
color = arg.getstr('color')
width = arg.getint('width')
coord = arg.getstr('coord',option=['fk5','physical'])
mag = arg.getstr('mag',option=['p','u'])
from numpy import loadtxt,pi,sin,cos
cols = [a - 1 for a in cols] # make zero-based
data = loadtxt(infile,usecols=cols)
if coord == 'fk5':
arg.warning("fk5 doesn't work correctly yet!")
# wgtavg will compute weighted average
from readcmd import ReadCmd
import nlclib
spec = """# Combine FITS images into one
in = ??? # Input images
err = None # Optional error images for input images
oper = avg # Can compute sum, avg, or wgtavg (weighted average)
out = ??? # Output image
outerr = None # Optional output error image (coverage map if no err)"""
arg = ReadCmd(spec)
inFiles = arg.getliststr('in',exist=True)
errFiles = arg.getliststr('err',exist=True,length=[1,len(inFiles)])
oper = arg.getstr('oper',option=['avg','sum','wgtavg'])
outFile = arg.getstr('out',exist=False)
outErr = arg.getstr('outerr',exist=False)
nimages = len(inFiles)
errFlag = False
if len(errFiles) > 0:
errFlag = True
if len(errFiles) == 1:
errFiles = nimages*errFiles
import pyfits
from numpy import zeros,isfinite,where,sqrt
for i in range(nimages):
img = pyfits.open(inFiles[i])
#!/usr/bin/env python
"""Convert the WCS coordinates in a polarization file to pixels.
Uses rotatevector.py to do the heavy lifting."""
from readcmd import ReadCmd
import os,sys
spec = """in = ??? # Input polarization file
fits = ??? # FITS image
out = ??? # Output file
ext = 0 # Extension number
cd = False # Set to True to use cd_matrix instead of cdelt"""
arg = ReadCmd(spec,__doc__)
infile = arg.getstr('in',exist=True)
fits = arg.getstr('fits',exist=True)
outfile= arg.getstr('out',exist=False)
ext = arg.getint('ext')
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)
#!/usr/bin/env python
from readcmd import ReadCmd
import nlclib
spec = """# Convert image to table of pixels or wcs
in = ??? # Input image
ext = 1 # Extension name/number
wcs = False # Set to true to output RA/DEC instead of pixels
out = ??? # Output file (can be - for stdout)"""
arg = ReadCmd(spec)
infile = arg.getstr("in",exist=True)
ext = arg.getstr("ext")
wcsFlag = arg.getbool("wcs")
outFile = arg.getstr("out",exist=False)
# try to convert extension to an integer
try:
blah = int(ext) - 1
ext = blah
except ValueError:
pass
import pyfits,pywcs
from numpy import arange,meshgrid,savetxt,column_stack
fp = pyfits.open(infile) #,ignore_missing_end=True)
data = fp[ext].data
header = fp[ext].header
fp.close()
#!/usr/bin/env python
"""This program will read the output of extmap and make a FITS image"""
from readcmd import ReadCmd
spec = """in = ??? # Input file from extmap
out = ??? # Output FITS file"""
arg = ReadCmd(spec,head=__doc__)
inFile = arg.getstr("in",exist=True)
outFile = arg.getstr("out",exist=False)
import pyfits
from numpy import loadtxt
# read header
head = {'comment' : [], 'history' : []}
fp = open(inFile,'r')
for line in fp:
if line[0] == '#':
tmp = line.split()
key = tmp[1].lower()
if key == 'comment':
head['comment'].append(' '.join(tmp[2:]))
elif key == 'history':
head['history'].append(' '.join(tmp[2:]))
elif key in ('naxis1','naxis2'):
head[key] = int(tmp[3])
elif key in ('cdelt1','cdelt2','crval1','crval2','crpix1','crpix2'):
head[key] = float(tmp[3])
elif key in ('ctype1','ctype2'):
#!/usr/bin/env python
from readcmd import ReadCmd
spec = """# compute statistics on an image or subregion of an image
in = ??? # Input image
ext = 1 # Extension number to read from in file
reg = None # subregion given as xmin:xmax,ymin:ymax (pixels)"""
arg = ReadCmd(spec)
infile = arg.getstr("in",exist=True,type='file')
reg = arg.getliststr('reg',length=[0,2])
ext = arg.getstr("ext")
import nlclib
import pyfits
from numpy import isfinite,where,nanmin,nanmax,median,average,std
ext = nlclib.findExt(infile,ext)
reg = nlclib.readRegion(reg)
header = pyfits.getheader(infile,ext=ext)
data = pyfits.getdata(infile,ext=ext)
if reg is None:
minval = nanmin(data)
maxval = nanmax(data)
mask = where(isfinite(data))
medval = median(data[mask])
avgval = average(data[mask])
stdval = std(data[mask],ddof=1)
# This is a python replacement for overlap.c, which chokes when pixels are
# too far from image. This works, but does have a 180 degree bug in pywcs.
# (e.g. ra,dec = 230,-30 will return a valid pixel even though it is exactly
# 180 degrees away from actual valid coordinates of ra,dec = 50,+30
from readcmd import ReadCmd
spec = """# Overlap coordinates in a file with a FITS image
in = ??? # Input file
col = 1,2 # Column numbers to read for RA,DEC
fits = ??? # Input FITS image(s)
out = ??? # Output file(s) of sources inside(,outside) image(s)
logic = and # 'and' = in all image(s), 'or' = in any image(s)"""
# null = NaN # Pixels with this value are considered outside"""
arg = ReadCmd(spec)
infile = arg.getstr("in",exist=True)
col = arg.getlistint("col",length=2,min=1)
fits = arg.getliststr("fits",exist=True)
out = arg.getliststr("out",length=[1,2],exist=False)
logic = arg.getstr("logic",option=['and','or'])
#null = arg.getstr("null")
import pyfits,pywcs
from numpy import loadtxt,transpose,ones,zeros,array,where,isnan
# read in ra/dec only
data = loadtxt(infile,usecols=[col[0]-1,col[1]-1])
mask = zeros(data.shape[0])
for f in fits:
header = pyfits.getheader(f)
#!/usr/bin/env python
from readcmd import ReadCmd
spec = """# Copy header keywords from input file to output file
in = ??? # Input file (from file)
inext = 1 # Extension name/number of input file
key = ??? # Header key(s) to copy (all for all keywords)
out = ??? # Output file (to file, must exist)
outext = 1 # Output extension(s) to modify"""
arg = ReadCmd(spec)
inFile = arg.getstr('in',exist=True)
inext = arg.getstr('inext')
junk = arg.getliststr('key')
outFile = arg.getstr('out',exist=True)
outext = arg.getliststr('outext')
hist = arg.getkeys(comment='CPHEAD.PY:',format=72,time=True).strip().split('\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()]
header['CD1_2'] = 0.0
header['CD2_1'] = 0.0
header['CD2_2'] = scale
angle = 180./pi*angle
else:
try:
angle = float(header[rot]) # try to extract value from FITS header
del(header[rot])
except KeyError:
arg.error("No header keyword '%s' found for rotation angle!" %rot)
except ValueError:
arg.error("Cannot read rotation angle '%s'!" %header[rot])
return angle
arg = ReadCmd(spec)
inFile = arg.getstr('in',exist=True,type='file')
outFile = arg.getstr('out',exist=False)
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)
"""Action to take when user clicks on 'Show' button"""
global _circsize,_circlecolor
_circsize = self.size.get()
_circlecolor = self.color.get()
os.system('xpaset -p %s regions format ds9' %self.window)
blah = nlclib.createtempname()
try:
fp = open(blah,'w')
ds9.makeRegion(fp,_all.ra,_all.dec,self.color.get(),float(self.size.get()),
self.number.get())
fp.close()
except IOError, value:
if "Permission denied" in value:
nlclib.error('You do not have write permissions for %s' %os.getcwd())
else:
nlclib.error('Unknown problem with opening temp. region file!')
for i in range(0,self.numframes):
print "starting frame %d" %(i+1)
ds9.region(self.window,i+1,blah,self.delete.get())
ds9.view(self.window)
nlclib.remove(blah)
if self.reset.get():
os.system('xpaset -p %s frame center' %self.window)
os.system('xpaset -p %s zoom 1' %self.window)
if __name__ == '__main__':
arg = ReadCmd(spec)
start(arg.getstr('in',exist=True),arg.getstr('window'),arg.getint('nframes'))
#!/usr/bin/env python
from readcmd import ReadCmd
spec = """# Rotate vectors to account for WCS curvature
in = ??? # Input file
cols = 1,2,3,5 # Columns for ra,dec,polarization percent,angle
out = ??? # Output file of x,y,polarization percent, new angle
fits = ??? # FITS image
ext = 0 # Extension number for fits file"""
arg = ReadCmd(spec)
image = arg.getstr('fits',exist=True)
infile = arg.getstr('in',exist=True)
cols = arg.getlistint('cols',length=4)
outfile= arg.getstr('out',exist=False)
ext = arg.getint('ext')
cols = map(lambda a: a-1,cols) # convert cols to a zero-based column numbers
import worldpos
from numpy import loadtxt,savetxt,sin,cos,pi,arctan,column_stack
import pyfits
# read CDELT from FITS header to pick an appropriate distance for scaling
fp = pyfits.open(image,mode='readonly')
cdelt = abs(float(fp[ext].header['cdelt2'])) # cdelt in degrees
scale = 5*cdelt
fp.close()
]
ralabel = map(lambda a: a / 3600., tmplabel) # convert to hours
stepra = map(lambda a: a / 3600., tmpstep) # convert to hours
tmp = abs(maxra - minra)
guess = tmp / 6. # aim for about 6 labels
diff = [abs(guess - a) for a in ralabel]
idx = diff.index(min(diff))
return stepra[idx], ralabel[idx]
if __name__ == "__main__":
arg = ReadCmd(spec)
image = arg.getstr('in', exist=True)
rangex = arg.getlistfloat('xrange', length=2)
rangey = arg.getlistfloat('yrange', length=2)
tmplength = arg.getfloat('length')
tmpra = arg.getlistfloat('ra', length=2)
tmpdec = arg.getlistfloat('dec', length=2)
outfile = arg.getstr('out', exist=False)
import worldpos
wcs = worldpos.wcs(image)
if wcs.header['rot'] != 0:
error('WIP cannot handle rotations!')
if len(rangex) == 0:
xmin = 0.5
xmax = naxis1 + 0.5
if data[2][i] <= 0:
del(data[0][i])
del(data[1][i])
del(data[2][i])
del[data[3][i]]
else:
data[2][i] = data[2][i]/maxy
data[3][i] = data[3][i]/(maxy*math.sqrt(data[1][i])) #std.dev. mean
return data
### Start Program ###
arg = ReadCmd(spec)
image = arg.getliststr('in',exist=True)
bin = arg.getlistfloat('bin',length=3)
unit = arg.getstr('unit',option=['nbin','step'])
offset = arg.getlistfloat('offset',length=2)
outplot = arg.getstr('out')
junk = arg.getlistfloat('range',length=2)
xmin = junk[0]
xmax = junk[1]
step = arg.getstr('step',option=['b','p'])
if 'b' in step: # do binning
outdata = []
from pyraf import iraf
for i in image:
outdata.append(dobin(i,offset,bin,unit))
for t in range(1,1000):
f = _func(t,flux1,flux2,wave1,wave2,beta)
if isfinite(f):
sign = f/abs(f)
start = t
break
for t in range(start,10000):
f = _func(t,flux1,flux2,wave1,wave2,beta)
s = f/abs(f)
if sign*s == -1:
return t
nlclib.error('Could not estimate initial temperature for wavelengths %f,%f!' %(wave1,wave2))
if __name__ == "__main__":
arg = ReadCmd(spec,__doc__)
infile = arg.getstr('in',exist=True)
dist = arg.getfloat('dist')
beta = arg.getfloat('beta')
sumMethod = arg.getstr('sum',option=['midpoint','simpson','trapezoid'])
from numpy import loadtxt,where,exp,zeros,pi,log,seterr,arange,linspace,isnan,isfinite
seterr(over='ignore')
# some constants
sun_lum = 3.826e33 # solar luminosity in ergs/s
parsec = 3.08567802e18 # 1 parsec in cm
planck = 6.62618e-27 # Planck's constant in erg s
light = 2.99792458e10 # speed of light in cm/s
boltz = 1.38066e-16 # Boltzmann's constant in K^-1
hck = planck*light/boltz
