def deg2sex(value,coord):
'''Convert degrees to sexagesimal, unless it is already in sexagesimal'''
try:
tmp = map(float,str(value).split(':'))
except ValueError:
nlclib.error('Invalid string given for conversion to sexagesimal: %s' %value)
n = len(tmp)
if n == 1: # assume it was in degrees
junk = tmp[0]
if coord == 'ra':
junk = junk/15.0
hours = int(junk)
junk = 60*(abs(junk) - abs(hours))
minutes = int(junk)
if abs(minutes - 60) < 1e-7:
minutes = 0
hours += 1
junk = 60*(junk - minutes)
seconds = float(junk)
if abs(seconds - 60) < 1e-7:
seconds = 0
minutes += 1
if abs(minutes - 60) < 1e-7:
minutes = 0
hours += 1
tmp[0] = hours
tmp.append(minutes)
tmp.append(seconds)
elif n == 2: # assume it was already sexagesimal, but no seconds given
tmp.append(0.0)
return tmp
def makeout(outroot,diridx):
"""Make output directory with error checking for pre-existing files"""
outdir = '%s%d' %(outroot,diridx)
if os.path.exists(outdir):
nlclib.error('Fatal Error! Output directory %s already exists!' %outdir)
os.mkdir(outdir)
return outdir
def getstepoffset(offset,coord):
"""Get stepdec and declabel given the range in declination plotted"""
# label steps in arcseconds
offlabel = array([1 ,5,10,15,20,30,60,300,600,900,1200,1800,3600,18000,36000])
offstep = array([0.5,1, 5, 5, 5,10,20, 60,300,300, 300, 600,1200, 3600,18000])
tmp = abs(offset[1] - offset[0])
if coord == 'so': # arcsecond offset
tmp = 3600*tmp
elif coord == 'mo': # arcminute offset
offlabel = offlabel/60.
offstep = offsetep/60.
tmp = 60*tmp
elif coord == 'do': # degree offset
offlabel = offlabel/3600.
offstep = offstep/3600.
else:
nlclib.error("getstepoffset(): coord keyword must be one of: so, mo, do!")
guess = tmp/6. # aim for about 6 labels
diff = [abs(guess-a) for a in offlabel]
idx = diff.index(min(diff))
return offstep[idx],offlabel[idx]
def deg2sex(value, coord):
'''Convert degrees to sexagesimal, unless it is already in sexagesimal'''
try:
tmp = map(float, str(value).split(':'))
except ValueError:
nlclib.error('Invalid string given for conversion to sexagesimal: %s' %
value)
n = len(tmp)
if n == 1: # assume it was in degrees
junk = tmp[0]
if coord == 'ra':
junk = junk / 15.0
hours = int(junk)
junk = 60 * (abs(junk) - abs(hours))
minutes = int(junk)
if abs(minutes - 60) < 1e-7:
minutes = 0
hours += 1
junk = 60 * (junk - minutes)
seconds = float(junk)
if abs(seconds - 60) < 1e-7:
seconds = 0
minutes += 1
if abs(minutes - 60) < 1e-7:
minutes = 0
hours += 1
tmp[0] = hours
tmp.append(minutes)
tmp.append(seconds)
elif n == 2: # assume it was already sexagesimal, but no seconds given
tmp.append(0.0)
return tmp
def deg2sex(value, coord):
'''Convert degrees to sexagesimal, unless it is already in sexagesimal
Returns a tuple of HMS or DMS, depending on if coord is 'ra' or not.'''
try:
tmp = map(float, str(value).split(':'))
except ValueError:
nlclib.error('Invalid string given for conversion to sexagesimal: %s' %
value)
n = len(tmp)
if n == 1: # assume it was in degrees
junk = tmp[0]
if coord == 'ra':
junk = junk / 15.0
hours = int(junk)
junk = 60 * (numpy.abs(junk) - numpy.abs(hours))
minutes = int(junk)
junk = 60 * (junk - minutes)
seconds = float(junk)
tmp[0] = hours
tmp.append(minutes)
tmp.append(seconds)
elif n == 2: # assume it was already sexagesimal, but no seconds given
tmp.append(0.0)
return tmp
def deg2sex(value,coord):
'''Convert degrees to sexagesimal, unless it is already in sexagesimal
Returns a tuple of HMS or DMS, depending on if coord is 'ra' or not.'''
try:
tmp = map(float,str(value).split(':'))
except ValueError:
nlclib.error('Invalid string given for conversion to sexagesimal: %s' %value)
n = len(tmp)
if n == 1: # assume it was in degrees
junk = tmp[0]
if coord == 'ra':
junk = junk/15.0
hours = int(junk)
junk = 60*(numpy.abs(junk) - numpy.abs(hours))
minutes = int(junk)
junk = 60*(junk - minutes)
seconds = float(junk)
tmp[0] = hours
tmp.append(minutes)
tmp.append(seconds)
elif n == 2: # assume it was already sexagesimal, but no seconds given
tmp.append(0.0)
return tmp
def getTickLocs(pixels,coords,stepsize,wcsrange=(0,360)):
"""Get tickmark locations in pixel coordinates."""
if not all(diff(coords) > 0):
nlclib.error("coords passed to getTickLocs() must be monotonically increasing!")
minval = amin(coords)
maxval = amax(coords)
tickmark = arange(wcsrange[0],wcsrange[1]+stepsize,stepsize)
mask = where((tickmark >= minval) & (tickmark <= maxval))
tickmark = tickmark[mask]
tickpix = interp(tickmark,coords,pixels)
return tickpix,tickmark
def _initialTemp(flux1,flux2,wave1,wave2,beta):
"""Estimate of initial temp based on where changes sign"""
start = 1000
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))
def apply(self):
"""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!')
def findExt(fname, extname):
"""Try to match extname, which is a either an integer or string, with
the extension in fname (the filename as a string)
returns the extension number as an integer (starting from zero)"""
if isinstance(fname, str): # string with filename, so open
img = pyfits.open(fname)
elif isinstance(fname, pyfits.HDUList):
img = fname
else:
nlclib.error("findExt(): fname must be a string or pyfits.HDUList")
n = len(img) # number of HDUs
# first check if string of a integer, e.g. '1'
try:
ext = int(extname)
except:
ext = extname
if isinstance(ext, int):
if 1 <= ext <= n:
tmp = ext - 1
else:
img.close()
nlclib.error("Extension number must be in range %d-%d for %s!" %
(1, n, img.filename()))
elif isinstance(ext, str):
ext = ext.lower()
junk = [img[i].header['extname'].strip().lower() for i in xrange(1, n)]
if 'EXTNAME' in img[0].header.keys():
junk.insert(0, img[0].header['extname'].strip().lower())
else:
junk.insert(0, 'primary')
if ext in junk:
tmp = junk.index(ext)
else:
img.close()
nlclib.error("Extension name '%s' not found in %s!" %
(ext, img.filename()))
elif isinstance(ext, (list, tuple)):
tmp = []
for tmpext in ext:
blah = findExt(img, tmpext)
tmp.append(blah)
else:
img.close()
nlclib.error("Extension must be an integer or string!")
if isinstance(fname, str): # string with filename, so close
img.close()
return tmp
def findExt(fname,extname):
"""Try to match extname, which is a either an integer or string, with
the extension in fname (the filename as a string)
returns the extension number as an integer (starting from zero)"""
if isinstance(fname,str): # string with filename, so open
img = pyfits.open(fname)
elif isinstance(fname,pyfits.HDUList):
img = fname
else:
nlclib.error("findExt(): fname must be a string or pyfits.HDUList")
n = len(img) # number of HDUs
# first check if string of a integer, e.g. '1'
try:
ext = int(extname)
except:
ext = extname
if isinstance(ext,int):
if 1 <= ext <= n:
tmp = ext - 1
else:
img.close()
nlclib.error("Extension number must be in range %d-%d for %s!" %(1,n,img.filename()))
elif isinstance(ext,str):
ext = ext.lower()
junk = [img[i].header['extname'].strip().lower() for i in xrange(1,n)]
if 'EXTNAME' in img[0].header.keys():
junk.insert(0,img[0].header['extname'].strip().lower())
else:
junk.insert(0,'primary')
if ext in junk:
tmp = junk.index(ext)
else:
img.close()
nlclib.error("Extension name '%s' not found in %s!" %(ext,img.filename()))
elif isinstance(ext,(list,tuple)):
tmp = []
for tmpext in ext:
blah = findExt(img,tmpext)
tmp.append(blah)
else:
img.close()
nlclib.error("Extension must be an integer or string!")
if isinstance(fname,str): # string with filename, so close
img.close()
return tmp
def dobin(image,offset,bin,unit):
"""Combine all steps for reading a fits image and binning radially"""
junk = nlclib.createtempname() # list of pixel values with distances in arcsecs
outdata = nlclib.createtempname() # binned data
# read fits header to get crpix and cdelt
crpix1 = crpix2 = -1
cdelt1 = cdelt2 = -1
header = iraf.imheader(image,Stdout=1)
for line in header:
if re.match(r'^CRPIX1',line):
crpix1 = float(line.split()[2])
elif re.match(r'^CRPIX2',line):
crpix2 = float(line.split()[2])
elif re.match(r'^CDELT1',line):
cdelt1 = float(line.split()[2])
elif re.match(r'^CDELT2',line):
cdelt2 = float(line.split()[2])
if crpix1 == -1 or crpix2 == -1:
nlclib.error("Couldn't read crpix values!")
if cdelt1 == -1 or cdelt2 == -1:
nlclib.error("Couldn't read cdelt values!")
# Add in offsets
fac = abs(cdelt1)*3600 # convert pixel distances to arcsecs
crpix1 = crpix1 - offset[0]/fac
crpix2 = crpix2 + offset[1]/fac
# figure out binning
if unit == 'step':
count = int((bin[1] - bin[0])/bin[2])
elif unit == 'nbin':
count = bin[2]
if count < 0:
nlclib.error('Number of bins is negative!')
# get pixel values
fp = open(junk,'w')
x = iraf.listpixels(image,Stdout=1)
for line in x:
t = map(float,line.split())
dist = fac*math.sqrt((t[0] - crpix1)**2 + (t[1] - crpix2)**2)
fp.write('%f %f\n' %(dist,t[3]))
fp.close()
# bin data
cmd = 'dobin in=%s bin=%f:%f:%d > %s' %(junk,bin[0],bin[1],count,outdata)
os.system(cmd)
nlclib.remove(junk)
return outdata
def _convert(value,coord,precision=0):
"""Convert a single value in deg to sexagesimal. Use in conjunction with
deg2sex() below.
Returns sexagesimal value as a string
value = sexagesimal or degrees as a string
coord = either 'ra' or 'dec' to specify coordinate type
precision = number of decimal places for rounding seconds"""
negFlag = False # set to true if value is negative
try:
tmp = map(float,value.split(':'))
if tmp[0] < 0:
negFlag = True
tmp[0] = abs(tmp[0])
except ValueError:
nlclib.error('Invalid string given for conversion to sexagesimal: %s' %value)
n = len(tmp)
if n == 1: # assume it was in degrees
junk = tmp[0]
if coord == 'ra':
junk = junk/15.0
hours = int(junk)
try:
junk = 60*(junk%hours)
minutes = int(junk)
except ZeroDivisionError:
minutes = int(60*junk)
try:
seconds = 60*(junk%minutes)
except ZeroDivisionError:
seconds = 60*junk
while seconds >= 60:
seconds = seconds - 60
minutes += 1
while minutes >= 60:
minutes = minutes - 60
hours += 1
tmp = [hours,minutes,seconds]
elif n == 2: # assume it was already sexagesimal, but no seconds given
tmp.append(0.0)
# now convert to a string
seconds = round(tmp[2],precision)
if precision == 0:
seconds = int(seconds)
while seconds >= 60:
seconds -= 60
tmp[1] += 1
minutes = tmp[1]
while minutes >= 60:
minutes -= 60
tmp[0] += 1
if seconds < 10:
tmp = "%d:%02d:0%s" %(tmp[0],minutes,str(seconds))
else:
tmp = "%d:%02d:%s" %(tmp[0],minutes,str(seconds))
if negFlag: # catch cases where deg. is neg
tmp = '-' + tmp
return tmp
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
data = loadtxt(infile)
wave = data[:,0]*1e-4 # wavelengths in cm
ncol = data.shape[1]
nsources = (ncol - 1)/2
if ncol%2 == 0: # even number of columns
nlclib.error('You must have an odd number of columns: wave f1 df1...')
elif ncol < 3:
nlclib.error('You must have at least 3 columns!')
print '#id Luminosity (L_solar)'
for i in range(nsources):
flux = data[:,2*i+1]
dflux = data[:,2*i+2]
wtemp = wave
mask = where(flux != 0)
flux = flux[mask]
dflux = dflux[mask]
wtemp = wtemp[mask]
flux1 = flux[:-1]
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!")
fimg.close()
fp = pyfits.open(infile) #,ignore_missing_end=True)
data = fp[ext].data
header = fp[ext].header
fp.close()
shape = data.shape
if len(shape) == 3:
nrows = shape[1]
ncols = shape[2]
data = data[0,:,:].flatten() # only read first plane of cube
elif len(shape) == 2:
nrows = shape[0]
ncols = shape[1]
data = data.flatten()
else:
nlclib.error("Input file must have 2-D or 3-D data!")
points = meshgrid(arange(ncols),arange(nrows))
x,y = (points[0].flatten() + 1, points[1].flatten() + 1)
fp = nlclib.nlcopen(outFile,'w')
if wcsFlag:
wcs = pywcs.WCS(header)
ra,dec = wcs.wcs_pix2sky(x,y,1)
fp.write("# RA DEC data\n")
savetxt(fp,column_stack((ra,dec,data)),fmt='%lf %lf %lf')
else:
fp.write("#x y data\n")
savetxt(fp,column_stack((x,y,data)),fmt='%d %d %lf')
fp.close()
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])
data = img[0].data
if i == 0: # take shape and header from first file
header1 = img[0].header
shape = data.shape
elif data.shape != shape:
img.close()
nlclib.error("Shape mismatch between %s and %s" %(inFiles[0],inFiles[i]))
img.close()
if oper == 'avg':
if errFlag:
img = pyfits.open(errFiles[i])
junk = img[0].data**2
if i == 0:
header2 = img[0].header
img.close()
else:
junk = zeros(shape)
mask = where(isfinite(data))
junk[mask] = 1
if i == 0:
total = data
outroot = arg.getstr('out')
pad = arg.getint('pad')
fileidx = 1 # filenumber index
diridx = 1 # output directory index
count = 0 # number of files moved to outdir
f,r = makefiles(inroot,fileidx,pad)
outdir = makeout(outroot,diridx)
while os.path.exists(f):
try:
os.rename(f,'%s/%s' %(outdir,f))
os.rename(r,'%s/%s' %(outdir,r))
except OSError:
nlclib.error('Problem moving %s and %s to %s' %(f,r,outdir))
count += 1
fileidx += 1
f,r = makefiles(inroot,fileidx,pad)
if count == 720:
print "moved %d files to %s..." %(count,outdir)
diridx += 1
outdir = makeout(outroot,diridx)
count = 0 # number of files moved to outdir
if count == 0: # empty final directory
os.system('rm -r %s' %outdir)
else:
print "moved %d files to %s..." %(count,outdir)
# all the drag-and-drop code since I didn't need it. Also greatly
# simplified the readin module to make it easier to add arbitrary file
# formats
spec = """# View a source file using DS9
in = None # Input data file
window = ds9 # Name of DS9 window
nframes = 1 # Number of frames in DS9 window"""
from readcmd import ReadCmd
import os,ds9
import readin,nlclib
try:
from Tkinter import *
except ImportError:
nlclib.error('You need Tkinter installed in python to use p6_ds9.py')
try:
from pywip import *
_plotFlag = True
except ImportError:
nlclib.warning('Cannot find module pywip. Plotting is disabled.')
_plotFlag = False
from tkMessageBox import showwarning
from tkMessageBox import askokcancel
from tkSimpleDialog import askinteger
from mytkinter import genericDialog
from mytkinter import inputFile
from mytkinter import myOptionMenu
from mytkinter import _HIGHLIGHT_COLOR
from mytkinter import _THEME_COLOR