def makeFlat(self, combine='median', flatlist=[], output='flatima.fits'):
'''
Combines the flat field frames to a single flat frame.
:note: this does not do any sigma clipping at the moment
'''
self.combinedFlat = output
if len(flatlist) == 0:
flatlist = self.flatFiles
if self.dataWeird:
filedata = [pf.getdata(x, ignore_missing_end=True)[0] for x in flatlist]
else:
filedata = [pf.getdata(x, ignore_missing_end=True) for x in flatlist]
if len(set(x.shape for x in filedata)) > 1:
self.log.info('FLAT images are not of same size! Program will exit..')
sys.exit('FLAT images are not of same size! Program will exit..')
#combine the files
cmd = 'np.' + combine + '(filedata, axis=0)'
self.flat = eval(cmd)
self.log.info('FLAT frames combined with {0:>s}'.format(cmd))
#write the output
hdu = pf.PrimaryHDU(self.flat)
hdulist = pf.HDUList([hdu])
hdulist.writeto(self.combinedFlat)
self.log.info('Combined flat saved to {0:>s}'.format(self.combinedFlat))
return self.flat
def do_trace_align(im,fibers2,params):
imdat, imhead = pf.getdata(im), pf.getheader(im)
outname = im[:-5]+'_t.fits'
#outer = pl.array( [ pl.arange(len(dat[0]))*0 for i in range(params.FIBER_WIDTH*len(fibers2)) ] )
outer = pf.getdata(im)*0
# DONT DO IT IF THE FILE EXISTS
globber = gl.glob(outname)
if len(globber)==1: return outname
for fib in fibers2:
fib_cnt = 1
for f in range(len(fib.xy)):
xy = fib.xy[f]
rescale = fib.rescale[f]
#rescaled_vals = dat[ xy[1] , xy[0] ] * rescale
# print 'xy = ',xy
# print 'rescale = ',rescale
# print 'rescaled = ',rescaled_vals
for y in range( len(rescale) ):
rescaled_val = imdat[ xy[1][y] ][ xy[0] ] ###* rescale[y]
outer[(len(rescale)+1)*fib.id+y][xy[0]] = rescaled_val
fib_cnt += 1
pf.writeto( outname, outer, header=imhead )
return outname
def bfixpix(image_file, mask_file, outsuffix='_f', msksuffix='_s'):
"""
Inputs
---------
image_file : string
input image file to fix bad pixels on
mask_file : string
mask file (0 == good pixels, >0 == bad pixels
outsuffix : string
suffix for fixed image. default = '_f'
msksuffix : string
suffix for bad pixels significance mask. default = '_s'
"""
outf = image_file.replace('.fits', outsuffix + '.fits')
outm = image_file.replace('.fits', msksuffix + '.fits')
util.rmall([outf, outm])
print("bfixpix: {0} -> {1}".format(image_file, outf))
# fetch the image, fetch the mask
img, hdr = pyfits.getdata(image_file, header=True)
msk = pyfits.getdata(mask_file)
# median the image
medimg = ndimage.median_filter(img, 3, mode='nearest')
# generate the pixel files
outf_img = np.where(msk == 0, img, medimg)
outm_img = np.where(msk == 1, (img - medimg), 0)
pyfits.writeto(outf, outf_img, hdr)
pyfits.writeto(outm, outm_img, hdr)
def whole_image(X,Y,imagefile,PARAMS,preset):
centroids = zip(X,Y);
if len(centroids) == 0:
logging.warning("No objects in given (X,Y lists). Finishing.");
return False;
# Run Sextractor over the whole image:
_Dsex = sextractor.run_segobj(imagefile,PARAMS,preset=preset);
segimg = pyfits.getdata(_Dsex['SEGMENTATION']);
objimg = pyfits.getdata(_Dsex['OBJECTS']);
objIDs = [ segimg[o_o[1],o_o[0]] for o_o in centroids ];
objIDs = list(set(objIDs)-set([0]));
# Take only the objects of interest...
# from image:
selobjimg = imcp.copy_objects(objimg,segimg,objIDs);
del segimg,objimg;
# and catalog:
cathdu = pyfits.open(_Dsex['CATALOG'])[1];
selobjhdu = fts.select_entries(cathdu,'NUMBER',*objIDs);
del cathdu;
# Re-identify each object:
for i in range(len(objIDs)):
selobjhdu.data.field('NUMBER')[i] = i;
return (selobjimg,selobjhdu);
def get_1d_2d_spectra(IDtuple):
""" Given a tuple of mask id, quadrant number, slit_id and object
number, return the 1d extracted flux, error, the 2d image of the
slit in which the object falls, and the y-coordinate of the objet
in the slit.
Note each slit can have several objects (up to 9?), each one has a
different object number. The object y centres and edges are in
object_?, start_? and end_?, where '?' is the object number in
the slit.
Returns
-------
wa, fl, er, sky, image, (ystart, yobj, yend)
"""
quad, iext, slit_id, obj = IDtuple
image = pyfits.getdata('mos_science_flux_extracted.fits', iext)
fluxes = pyfits.getdata('mos_science_flux_reduced.fits', iext)
skies = pyfits.getdata('mos_sci_sky_reduced.fits', iext)
errors = pyfits.getdata('mos_sci_error_flux_reduced.fits', iext)
hd = pyfits.getheader('mos_science_flux_extracted.fits', iext)
wa = hd['CRVAL1'] + np.arange(hd['NAXIS1']) * hd['CD1_1']
i0, i1, pos, ind = get_pos_ind(IDtuple)
fl = fluxes[ind]
er = errors[ind]
sky = skies[ind]
return wa, fl, er, sky, image[i0:i1, :], pos-i0
def SavePreviewRGC(config,filename_rgc,n_gals_preview=10):
"""
Function for eyeballing the contents of the created mock RGC catalogs.
Arguments
---------
config config dict
filename_rgc filename of the newly created real galaxy catalog fits
n_gals_preview how many plots to produce (default=10)
"""
# open the RGC
table = pyfits.open(filename_rgc)[1].data
# get the image and PSF filenames
fits_gal = table[0]['GAL_FILENAME']
fits_psf = table[0]['PSF_FILENAME']
import pylab
# loop over galaxies and save plots
for n in range(n_gals_preview):
img_gal = pyfits.getdata(fits_gal,ext=n)
img_psf = pyfits.getdata(fits_psf,ext=n)
pylab.subplot(1,2,1)
pylab.imshow(img_gal,interpolation='nearest')
pylab.title('galaxy')
pylab.subplot(1,2,2)
pylab.imshow(img_psf,interpolation='nearest')
pylab.title('PSF')
filename_fig = 'fig.previewRGC.%s.%d.png' % (config['args'].filename_config,n)
pylab.savefig(filename_fig)
def combine_bins(targetSN, bins=None, outfile="a.fits"):
""" Combine spectra of given bins. """
data = pf.getdata("binned_sn{0}.fits".format(targetSN), 0)
error = pf.getdata("binned_sn{0}.fits".format(targetSN), 1)
binimg = pf.getdata("voronoi_sn{0}.fits".format(targetSN)).flatten()
for i,bin in enumerate(bins):
N = np.where(binimg==bin)[0].size
spec = data[bin-1,:]
specerr = error[bin-1,:]
if i == 0:
combined = N * spec
comberr = N * specerr
Ntot = N
else:
combined += N * spec
Ntot += N * spec
comberr += N * specerr
h = pf.getheader("binned_sn{0}.fits".format(targetSN))
h["NAXIS"] = 1
del h["NAXIS2"]
hdu0 = pf.PrimaryHDU(combined, h)
hdu1 = pf.ImageHDU(comberr, h)
hdulist = pf.HDUList([hdu0, hdu1])
hdulist.writeto(outfile, clobber=True)
return
def main():
'''Input a set of R G B images and return a color image'''
# Setup command line options
parser = argparse.ArgumentParser(description='Coadd R,G,B fits images and return color png')
parser.add_argument("rFile", help='Input R image', default='r.fits')
parser.add_argument("gFile", help='Input G image', default='g.fits')
parser.add_argument("bFile", help='Input B image', default='b.fits')
parser.add_argument('--addNoise', dest="noise", nargs='+', type=float, help='Gaussian noise to add to each image', default=[0,0,0])
parser.add_argument('--outputFile', dest="outputFile", help='Output PNG file name', default='rgb.png')
args = parser.parse_args()
images = []
images.append(pyfits.getdata(args.rFile,0))
images.append(pyfits.getdata(args.gFile,0))
images.append(pyfits.getdata(args.bFile,0))
# add noise
if (args.noise != [0,0,0]):
addNoise(images,args.noise)
# scale image
scaledImages = scaleAsinh(images, scales =[1.,1.,1.])
# create RGB
mode='RGB'
pngImage = Image.new(mode, scaledImages[0].shape)
pngImage.paste(createRGB(scaledImages),(0,0))
pngImage.save(args.outputFile)
def spt_mapping_images_to_jpeg():
spti = pyfits.getdata("swarp.SPT-CLJ0307-5042.2x2.i.fits")
sptv = pyfits.getdata("swarp.SPT-CLJ0307-5042.2x2.r.fits")
sptb = pyfits.getdata("swarp.SPT-CLJ0307-5042.2x2.g.fits")
# sptb=sptb[5066-587:5066+587,5262-587:5262+587]
##sptv=sptv[5441-587:5441+587,5372-587:5372+587]
# sptv=sptv[5066-587:5066+587,5262-587:5262+587]
# spti=spti[5066-587:5066+587,5262-587:5262+587]
spti = spti[5262 - 587 : 5262 + 587, 5066 - 587 : 5066 + 587]
sptv = sptv[5372 - 587 : 5372 + 587, 5441 - 587 : 5441 + 587]
sptb = sptb[5262 - 587 : 5262 + 587, 5066 - 587 : 5066 + 587]
skypi, sigpi = plotim(spti)
skypv, sigpv = plotim(sptv)
skypb, sigpb = plotim(sptb)
print skypi, sigpi, skypv, sigpv, skypb, sigpb
sptii = spti - skypi
sptii = sptii / sigpi
sptiv = sptv - skypv
sptiv = sptiv / sigpv
sptib = sptb - skypb
sptib = sptib / sigpb
acut = 0.3
icut = 50.0 * acut
vcut = 60.0 * acut
bcut = 30.0 * acut
sptii = cut_out_tails(sptii, 0, icut)
sptiv = cut_out_tails(sptiv, 0, vcut)
sptib = cut_out_tails(sptib, 0, bcut)
sptii = (sptii * 255 / icut).astype(int)
sptiv = (sptiv * 255 / vcut).astype(int)
sptib = (sptib * 255 / bcut).astype(int)
im = np.zeros((3, 1174, 1174), dtype=np.uint8)
im[0, :, :] = sptii
im[1, :, :] = sptiv
im[2, :, :] = sptib
# figure()
# contour(sptii)
# figure()
# contour(sptiv)
# figure()
# contour(sptib)
# show()
im = np.uint8(im)
scipy.misc.imsave("spt_comp.jpg", im)
return 0
def twilightFlatMaker(flatImagesPath,flatDarkImagesPath,masterFlatSavePath,plots=False):
'''
Make a master flat using a series of images taken at twilight
by fitting the individual pixel intensities over time using least-squares
and use the intercept as the normalizing factor in the master flat.
INPUTS: flatImagesPath - Path to the flat field exposures
flatDarkImagesPath - Path to the flat field darks
masterFlatSavePath - Where to save the master flat that is created
plots - Plot the master flat on completion when plots=True
'''
## Create zero array with the dimensions of the first image for the flat field
[dim1, dim2] = np.shape(pyfits.getdata(flatImagesPath[0]))
flatSum = np.zeros([dim1, dim2])
## Create N-dimensional array for N dark frames, where the first
## two dimensions are the dimensions of the first image
darks = np.zeros([len(flatDarkImagesPath),dim1,dim2])
## Take mean of all darks
for i in range(0,len(flatDarkImagesPath)):
darks[i,:,:] = pyfits.getdata(flatDarkImagesPath[i])
dark = np.mean(darks,axis=0)
## Create N-dimensional array for N flat frames, where the first
## two dimensions are the dimensions of the first image
flats = np.zeros([len(flatImagesPath),dim1,dim2])
## Assemble data cube of flats
for i in range(0,len(flatImagesPath)):
flats[i,:,:] = pyfits.getdata(flatImagesPath[i]) - dark
def linearFitIntercept(x,y):
'''Use least-squares to find the best-fit y-intercept '''
return np.linalg.lstsq(np.vstack([x,np.ones(len(x))]).T,y)[0][1] ## Returns intercept
flat = np.zeros([dim1,dim2])
for i in range(0,dim1):
print 'Master flat computing step:',i+1,'of',dim1
for j in range(0,dim2):
flat[i,j] = linearFitIntercept(range(len(flats[:,i,j])),flats[:,i,j])
masterFlat = flat/np.mean(flat)
if plots:
## If plots == True, plot the resulting master flat
fig = plt.figure()
a = plt.imshow(masterFlat,interpolation='nearest')
a.set_cmap('gray')
plt.title('Normalized Master Flat Field')
fig.colorbar(a)
fig.canvas.set_window_title('oscaar2.0 - Master Flat')
plt.show()
## Write out both a Numpy pickle (.NPY) and a FITS file
np.save(masterFlatSavePath+'.npy',masterFlat)
pyfits.writeto(masterFlatSavePath+'.fits',masterFlat)
def __init__(self, nfiles, mode='obs'):
if mode=='obs': self.files = glob.glob("Buzzard*.fit")
self.nfil = nfiles
self.cat = pyfits.getdata(self.files[0])
for i in range(1,nfiles): self.cat = np.concatenate((self.cat,pyfits.getdata(self.files[i])))
self.ngal = len(self.cat)
print 'Got %2.2f M galaxies.' %(self.ngal/1.0e6)
def shiftRGB(redF,greenF,blueF,blueshiftr=0,blueshiftc=0,greenshiftr=0,greenshiftc=0,redshiftr=0,redshiftc=0,ext=None):
"""
this code shift the pixels of three r, g, b images. Using g image as reference and shift the other two images. It will return the shifted r,g,b images.
each row goes along ra direction
each col goes along dec direction
CRVAL1 ; ra direction
CRVAL2: dec direction
"""
blueHdr = pf.getheader(blueF,ext)
greenHdr = pf.getheader(greenF,ext)
redHdr = pf.getheader(redF,ext)
bluerow = blueHdr['crval1']*3600./0.27
bluecol = blueHdr['crval2']*3600./0.27
greenrow = greenHdr['crval1']*3600./0.27
greencol = greenHdr['crval2']*3600./0.27
redrow = redHdr['crval1']*3600./0.27
redcol = redHdr['crval2']*3600./0.27
"""
col0=int(blueHdr['datasec'].split('[')[1].split(']')[0].split(',')[0].split(':')[0])-1
col1=int(blueHdr['datasec'].split('[')[1].split(']')[0].split(',')[0].split(':')[1])
row0=int(blueHdr['datasec'].split('[')[1].split(']')[0].split(',')[1].split(':')[0])-1
row1=int(blueHdr['datasec'].split('[')[1].split(']')[0].split(',')[1].split(':')[1])
"""
blue = pf.getdata(blueF,ext)
green = pf.getdata(greenF,ext)
red = pf.getdata(redF,ext)
ctgreenrow = (bluerow+greenrow+redrow)/3.
ctgreencol = (bluecol+greencol+redcol)/3.
blue = nd.shift(blue,[bluerow - ctgreenrow+blueshiftr,bluecol-ctgreencol+blueshiftc],mode='nearest',order=1)
green = nd.shift(green,[greenrow - ctgreenrow+greenshiftr,greencol-ctgreencol+greenshiftc],mode='nearest',order=1)
red = nd.shift(red,[redrow - ctgreenrow+redshiftr, redcol-ctgreencol+redshiftc],mode='nearest',order=1)
return red,green,blue
def calc_sky_from_seg(infile,segfile):
"""
Description: Calculates the sky level in an image using only
those regions in which SExtractor's segmentation file has
a value of 0.
Inputs:
infile: input fits file
segfile: SExtractor segmentation file associated with infile.
"""
""" Load data """
indat = pf.getdata(infile)
segdat = pf.getdata(segfile)
""" Set mask region and select associated regions of indat """
mask = segdat == 0
sky = indat[mask]
# NB: These preceding 2 lines could have been combined as
# sky = indat[segdat==0]
""" Calculate statistics """
print "Statistics of sky outside masked regions"
print "----------------------------------------"
print " N_pix = %d" % sky.size
print " Median = %f" % n.median(sky)
print " Mean = %f" % n.mean(sky)
return
def flatfield(flatF,dataF,outdir=None):
flat = pyfits.getdata(flatF)
data = pyfits.getdata(dataF)
if get_HWP(flatF) != get_HWP(dataF):
exit('HWP positions of flat and data do not match!')
newData = data / flat
hdr = pyfits.getheader(dataF)
hdr['FLATFILE'] = (flatF,'Flat applied')
hdr['FLATPROC'] = (True, 'Flat-fielded')
HWP = get_HWP(dataF)
hdr['FILTER'] = HWP
hdr['HWP'] = HWP
if outdir is None:
newName = dataF
else:
newName = os.path.join(outdir,os.path.basename(dataF))
print 'Writing to %s' % newName
pyfits.writeto(newName,newData,header=hdr,clobber=True)
return newName
def collapse_cube(w1, w2):
""" Collapse a MUSE data cube.
Arguments
cube : MUSE data cube name containing both data and stat extensions.
iext : Initial extension to be used. Default is one for combined cubes.
"""
fits = "slice_w{0}_{1}.fits".format(w1, w2)
outfits = "collapsed_w{0}_{1}.fits".format(w1, w2)
data = pf.getdata(fits, 0)
error = pf.getdata(fits, 1)
h = pf.getheader(fits, 0)
h2 = pf.getheader(fits, 1)
h["NAXIS"] = 2
del h["NAXIS3"]
h2["NAXIS"] = 2
del h2["NAXIS3"]
print "Starting collapsing process..."
start = time.time()
w = wavelength_array(fits)
# newdata = np.trapz(data, dx=np.diff(w)[0], axis=0)
# newdata = np.nansum(data, axis=0) * np.diff(w)[0]
newdata = np.nanmedian(data, axis=0)
noise = 1.482602 / np.sqrt(6.) * np.nanmedian(np.abs(2.* data - \
np.roll(data, 2, axis=0) - np.roll(data, -2, axis=0)), \
axis=0)
end = time.time()
print "Collapsing lasted {0} minutes.".format((end - start)/60.)
hdu = pf.PrimaryHDU(newdata, h)
hdu2 = pf.ImageHDU(noise, h2)
hdulist = pf.HDUList([hdu, hdu2])
hdulist.writeto(outfits, clobber=True)
return
def do_nods(filelist):
"""
"""
headers = [pyfits.getheader(fn) for fn in filelist]
for ii,fn in (enumerate(filelist)):
if ii==len(filelist)-1:
break
try:
if headers[ii]['BOREOFFX'] == 0 and headers[ii+1]['BOREOFFX'] == -5.9220000000000E-03:
fitsfile = pyfits.open(fn)
fitsfile[0].data -= pyfits.getdata(filelist[ii+1])
matches = difflib.SequenceMatcher(None,fn,filelist[ii+1]).get_matching_blocks()
outfilename = fn[matches[0].a:matches[0].size] + fn[matches[0].size:matches[1].a] + "-" + filelist[ii+1][matches[0].size:matches[1].b] + fn[matches[1].a:matches[1].size+matches[1].a]
fitsfile.writeto(outfilename)
print matches, outfilename
elif headers[ii+1]['BOREOFFX'] == 0 and headers[ii]['BOREOFFX'] == -5.9220000000000E-03:
fitsfile = pyfits.open(fn)
fitsfile[0].data = pyfits.getdata(filelist[ii+1]) - fitsfile[0].data
matches = difflib.SequenceMatcher(None,fn,filelist[ii+1]).get_matching_blocks()
outfilename = fn[matches[0].a:matches[0].size] + filelist[ii+1][matches[0].size:matches[1].b] + "-" + fn[matches[0].size:matches[1].a] + fn[matches[1].a:matches[1].size+matches[1].a]
fitsfile.writeto(outfilename)
print matches, outfilename
except IOError:
pass
def imWeightedAve( image1, image2, weight1, weight2, outfile, clobber=False, verbose=False):
"""
construct a weighted average of image1 and image2:
(weight1*image1 + weight2*image2) / (weight1+weight2)
Mean image is written to outfile.
"""
import os
import pyfits
from numpy import ndarray, nan_to_num
import exceptions
if os.path.isfile(outfile) :
if clobber :
os.unlink( outfile )
else :
print( "%s exists. Not clobbering."%outfile )
return( outfile )
# read in the sci and wht images
im1hdr = pyfits.getheader( image1 )
im1 = pyfits.getdata( image1 )
im2 = pyfits.getdata( image2 )
wht1 = pyfits.getdata( weight1 )
wht2 = pyfits.getdata( weight2 )
meanim = nan_to_num( (wht1*im1 + wht2*im2)/(wht1+wht2) )
# TODO : make a useful header
outdir = os.path.dirname( outfile )
if not os.path.isdir(outdir):
os.makedirs( outdir )
pyfits.writeto( outfile, meanim, header=im1hdr )
return( outfile )
def irstack(myfiles):
data = []
tempfiles = glob("templist")+glob("*b.fits")+glob("*r.fits")+glob("flat.fits")
for myfile in tempfiles:
os.remove(myfile)
for myfile in myfiles:
data.append(pyfits.getdata(myfile))
#sky subtract and replace with median
mediansky = mean([median(data[i]) for i in range(len(data))])
for i in range(len(myfiles)):
fred = pyfits.open(myfiles[i])
im = fred[0].data
im2 = (im.transpose() - median(im,axis=0)).transpose() + mediansky
fred[0].data = im2
fred.writeto("%ibb.fits"%i,'ignore',True)
iraf.imcomb("*bb.fits","flat",combine="median",reject="sigclip",lsigma=3,hsigma=2)
flat = pyfits.getdata('flat.fits')
flat /= median(flat)
fred.writeto('flat.fits','ignore',True)
for i in range(len(myfiles)):
fred = pyfits.open(myfiles[i])
im = fred[0].data
im2 = ((im/flat).transpose() - median(im,axis=0)).transpose()
fred[0].data = im2
fred.writeto("%irb.fits"%i,'ignore',True)
iraf.files("*rb.fits",Stdout="templist")
iraf.stack("templist","output",1,'none')
def make_color_ao_image():
h_img = pyfits.getdata(workdir + 'mag05jullgs_h_rot.fits')
h_imgScl = img_scale.sqrt(h_img, scale_min=50, scale_max=5500)
kp_img = pyfits.getdata(workdir + 'mag05jullgs_kp_rot.fits')
kp_imgScl = img_scale.sqrt(kp_img, scale_min=10, scale_max=17000)
lp_img = pyfits.getdata(workdir + 'mag05jullgs_lp_rot.fits')
lp_imgScl = img_scale.sqrt(lp_img, scale_min=-100, scale_max=60000)
sgra = np.array([540, 410])
scale = 0.00995
h_xextent = np.array([0, h_img.shape[0]])
h_yextent = np.array([0, h_img.shape[0]])
h_xextent = (h_xextent - sgra[0]) * -scale
h_yextent = (h_yextent - sgra[1]) * scale
h_extent = [h_xextent[0], h_xextent[-1], h_yextent[0], h_yextent[-1]]
img = np.zeros((h_img.shape[0], h_img.shape[1], 3), dtype=float)
img[:,:,0] = lp_imgScl
img[:,:,1] = kp_imgScl
img[:,:,2] = h_imgScl
py.figure(4, figsize=(10, 10))
py.clf()
py.subplots_adjust(left=0, right=1, bottom=0, top=1)
py.imshow(img, extent=h_extent)
ax = py.gca()
py.setp(ax.get_xticklabels(), visible=False)
py.setp(ax.get_yticklabels(), visible=False)
py.xlim(5, -5)
py.ylim(-4, 6)
py.savefig(workdir + 'img_lgsao_color.png')
def reduceData(data):
for filter in data:
for file in data[filter]:
fh = pyfits.open(file)
images = []
for ext in [1,2,3,4]:
bias = pyfits.getdata('BIAS%i.fits' % ext, ext=0)
flat = pyfits.getdata('FLAT_%s_%i.fits' % (filter, ext), ext=0)
image = fh[ext].data
hdr = fh[ext].header
biassec = hdr['BIASSEC'].strip().replace('[', '').replace(']','').replace(',',':').split(':')
overscan = numpy.median(image[int(biassec[2])+1:int(biassec[3])-1,
int(biassec[0])+1:int(biassec[1])-1].copy().ravel())
print 'subtracting bias of about ', numpy.mean(bias)
if overscan > 5000:
img = (1.*image) - bias
else:
img = (1.*image) - (bias/overscan) - overscan
img /= flat
images.append(img)
fh.close()
fh = pyfits.open(file)
for ext in [1,2,3,4]:
fh[ext].data = images[ext-1]
fh.writeto('RED%s' % (file))
def plot_image(fits,ax, rms=np.nan, F=np.nan, cont=None, contcol='r', stretch='sqrt'):
ax.set_frame_color('k')
ax.set_tick_color('k')
ax.tick_labels.set_font(size='xx-small')
ax.tick_labels.set_xformat('ddd.dd')
ax.tick_labels.set_yformat('ddd.dd')
head = pf.getheader(fits)
try:
image = pf.getdata(fits)
except:
print 'problem with image: ',fits
return
ximgsize = head.get('NAXIS1')
yimgsize = head.get('NAXIS2')
pixscale = head.get('CDELT1')
if np.isnan(rms):
rms = np.std(image)
av = np.median(image)
n_one = np.ones(image.shape)
for i in range(5):
#print rms, av
within1sigma = np.where((image - av*n_one) < 3.*rms*n_one)
av = np.median(image[within1sigma])
rms = np.std(image[within1sigma])
if np.isnan(F):
F = image.max()
dat = pf.getdata(fits)
mean = np.median(dat)
sig = np.std(dat)
for i in range(10):
dat = np.ma.masked_where(abs(dat - mean) > 5.*sig,dat).compressed()
mean = np.median(dat)
sig = np.std(dat)
#, vmid = mean+20*sig
ax.show_grayscale(vmin = mean-0.5*sig, vmax = mean+15*sig, stretch=stretch, invert=True)
if cont!=None:
image = pf.getdata(cont)
rms = np.std(image)
av = np.median(image)
n_one = np.ones(image.shape)
for i in range(5):
within1sigma = np.where((image - av*n_one) < 3.*rms*n_one)
av = np.median(image[within1sigma])
rms = np.std(image[within1sigma])
cont_levels = 3.*rms*np.array([-2.**(1 * j ) for j in range(0, 2 )] + [ 2.**(1. * j ) for j in range(0, 10 ) ] )
ax.show_contour(cont, hdu=0, layer='contour', levels=cont_levels, filled=False, cmap=None, colors=contcol, returnlevels=False, convention=None, slices=[0,1], smooth=None, kernel='gauss')
#else:
#cont_levels = 3.*rms*np.array([-2.**(1 * j ) for j in range(0, 2 )] + [ 2.**(1. * j ) for j in range(0, 10 ) ] )
#ax.show_contour(fits, hdu=0, layer='contour', levels=cont_levels, filled=False, cmap=None, colors=contcol, returnlevels=False, convention=None, slices=[0,1], smooth=None, kernel='gauss')
return
def run(fields, targetSN, bins=None, Nsim=30, run_parallel=False):
""" Interface to calculate the errors of the Lick indices. """
for field in fields:
os.chdir(os.path.join(data_dir, "combined_{0}".format(field)))
specs = "binned_sn{0}.fits".format(targetSN)
data = pf.getdata(specs)
w = wavelength_array(specs, axis=1, extension=0)
ssps_file = os.path.join(templates_dir, 'miles_FWHM_2.51.fits')
ssps = pf.getdata(ssps_file, 0)
wssps = np.power(np.e, pf.getdata(ssps_file, 1))
databins = wavelength_array(specs, axis=2, extension=0)
os.chdir(os.path.join(data_dir, "combined_{0}".format(field),
"logs_sn{0}".format(targetSN)))
######################################################################
# If bins are not specified, then look for all available bins
if bins == None:
bins = databins
######################################################################
if run_parallel:
pool = mp.Pool()
for bin in bins:
spec = data[bin - 1]
pool.apply_async(run_mc,
args=(field, bin, w, spec, wssps, ssps, Nsim))
pool.close()
pool.join()
else:
for bin in bins:
spec = data[bin - 1]
run_mc(field, bin, w, spec, wssps, ssps, Nsim)
def unionmask( imfile1, imfile2, outfile, clobber=False, verbose=False):
"""
construct the union of image1 and image2 badpix masks
Returns the name of the output union bad pixel mask file.
"""
import os
import pyfits
import exceptions
from numpy import array, uint8
# read in the images
im1head = pyfits.getheader( imfile1 )
imdat1 = pyfits.getdata( imfile1 )
imdat2 = pyfits.getdata( imfile2 )
if os.path.exists( outfile ) :
if not clobber :
print( "%s exists. Not clobbering."%outfile)
return( outfile )
else :
os.remove( outfile )
uniondat = array(imdat1,dtype=uint8) | array(imdat2,dtype=uint8)
# TODO : make a useful header
im1head.update("SRCIM1",imfile1,"First source image for badpixunion")
im1head.update("SRCIM2",imfile2,"Second source image for badpixunion")
outdir = os.path.split( outfile )[0]
if outdir :
if not os.path.isdir(outdir):
os.makedirs( outdir )
pyfits.writeto( outfile, uniondat, header=im1head,clobber=clobber,
output_verify='fix')
return( outfile )
def OpenLight():
#Open if they are the light frames
global lightimages
lightimages = askopenfilenames()
#This next part is to display the choices made to alow for checking
lightbox = Frame(master)
lightbox.grid(row=2, rowspan=3)
scrolllight = Scrollbar(lightbox, orient=HORIZONTAL)
fileslist = Listbox(lightbox, xscrollcommand=scrolllight.set)
scrolllight.config(command=fileslist.xview)
for item in lightimages:
fileslist.insert(END, item)
fileslist.pack()
scrolllight.pack(fill=X)
numlight = len(lightimages)
tempfile = PF.getdata(lightimages[0], header=False)
ny, nx = tempfile.shape
global lightframes
lightframes = N.zeros((numlight, ny, nx), dtype=float)
#Lets actualy read in the lights now
for i in N.arange(numlight):
lightframes[i] = PF.getdata(lightimages[i], header=False)
def make_voronoi_intens(targetSN, w1, w2):
""" Make image"""
image = "collapsed_w{0}_{1}.fits".format(w1, w2)
intens = pf.getdata(image)
extent = calc_extent(image)
vordata = pf.getdata("voronoi_sn{0}_w{1}_{2}.fits".format(targetSN, w1,
w2))
vordata = np.ma.array(vordata, mask=np.isnan(vordata))
bins = np.unique(vordata)[:-1]
combined = np.zeros_like(intens)
combined[:] = np.nan
for j, bin in enumerate(bins):
idx, idy = np.where(vordata == bin)
flux = intens[idx,idy]
combined[idx,idy] = np.nanmean(flux)
vmax = np.nanmedian(intens) + 4 * np.nanstd(intens)
fig = plt.figure(1)
plt.minorticks_on()
make_contours()
plt.imshow(combined, cmap="cubehelix_r", origin="bottom", vmax=vmax,
extent=extent, vmin=0)
plt.xlabel("X [kpc]")
plt.ylabel("Y [kpc]")
cbar = plt.colorbar()
cbar.set_label("Flux [$10^{-20}$ erg s$^{-1}$ cm$^{-2}$]")
plt.savefig("figs/intens_sn{0}.png".format(targetSN), dpi=300)
pf.writeto("figs/intens_sn{0}.fits".format(targetSN), combined,
clobber=True)
return
def __init__(self):
'''
Run oscaar.parseRegionsFile() to get the inital guesses for the
initial centroids of the stars from the DS9 regions file, create
dictionaries in which to store all of the data collected
for each star. Allocate the memory for these arrays wherever possible.
Parse the init.par file to grab the paths and initial parameters for
the run.
INPUTS: None.
'''
self.parseInit() ## parse init.par using the parseInit() method
self.parseObservatory()
assert len(self.imagesPaths) > 1, 'Must have at least one data image'
if self.flatPath != 'None':
self.masterFlat = pyfits.getdata(self.flatPath)
self.masterFlatPath = self.flatPath
elif self.flatPath == 'None':
print 'Using an isotropic ("placebo") master-flat (array of ones)'
dim1,dim2 = np.shape(pyfits.getdata(self.imagesPaths[0]))
self.masterFlat = np.ones([dim1,dim2])
self.allStarsDict = {}
init_x_list,init_y_list = parseRegionsFile(self.regsPath)
zeroArray = np.zeros_like(self.imagesPaths,dtype=np.float32)
self.times = np.zeros_like(self.imagesPaths,dtype=np.float64)
self.keys = []
self.targetKey = '000'
for i in range(0,len(init_x_list)):
self.allStarsDict[paddedStr(i,3)] = {'x-pos':np.copy(zeroArray), 'y-pos':np.copy(zeroArray),\
'rawFlux':np.copy(zeroArray), 'rawError':np.copy(zeroArray),'flag':False,\
'scaledFlux':np.copy(zeroArray), 'scaledError':np.copy(zeroArray), 'chisq':0}
self.allStarsDict[paddedStr(i,3)]['x-pos'][0] = init_x_list[i]
self.allStarsDict[paddedStr(i,3)]['y-pos'][0] = init_y_list[i]
self.keys.append(paddedStr(i,3))
def plot_fits_reg_vs_out(fits_dir, regular, outliers, objids2name):
reg_fits = [os.path.join(fits_dir, objids2name[p]) for p in regular]
outl_fits = [os.path.join(fits_dir, objids2name[p]) for p in outliers]
reg_fits_data = [pyfits.getdata(fit) for fit in reg_fits]
outl_fits_data = [pyfits.getdata(fit) for fit in outl_fits]
plot_fits_by_size(reg_fits_data, name='-reg')
plot_fits_by_size(outl_fits_data, name='-outl')
def get_model(t,g,z): if os.access(get_oriname(t,g,z),os.F_OK): if library == 'P': mf = pyfits.getdata(get_oriname(t,g,z))[Iwav] mhd = pyfits.getheader(get_oriname(t,g,z)) if 'PHXXI_L' in mhd.keys(): mict = float(mhd['PHXXI_L']) else: mict = 2.0 elif library == 'C': mf = pyfits.getdata(get_oriname(t,g,z))[0][Iwav] if g>=2.75: mict = 1. elif g >=1.25 and g<=2.75: mict = 1.8 elif g < 1.25: mict = 2.5 elif library == 'R': mf = pyfits.getdata(get_oriname(t,g,z))[Iwav] if g>=2.75: mict = 1. elif g >=1.25 and g<=2.75: mict = 1.8 elif g < 1.25: mict = 2.5 else: if linear_interpolation: mf,mict = get_linear_interpol(t,g,z) else: mf,mict = get_interpolated(t,g,z) return mf,mict
def mk_image(galaxy):
base = './../../images_v5/GS_2.5as_matched/gs_all_'
i_img = pyf.getdata(base+str(galaxy)+'_I.fits')
j_img = pyf.getdata(base+str(galaxy)+'_J.fits')
h_img = pyf.getdata(base+str(galaxy)+'_H.fits')
#include 90% of pixels
x = pyl.hstack(i_img)
i_lim = scoreatpercentile(x,99)
x = pyl.hstack(j_img)
j_lim = scoreatpercentile(x,99)
x = pyl.hstack(h_img)
h_lim = scoreatpercentile(x,99)
print galaxy, i_lim, j_lim, h_lim
img = pyl.zeros((h_img.shape[0], h_img.shape[1], 3), dtype=float)
img[:,:,0] = img_scale.asinh(h_img, scale_min=-0.1*h_lim, scale_max=h_lim,
non_linear=0.5)
img[:,:,1] = img_scale.asinh(j_img, scale_min=-0.1*j_lim, scale_max=j_lim,
non_linear=0.5)
img[:,:,2] = img_scale.asinh(i_img, scale_min=-0.1*i_lim, scale_max=i_lim,
non_linear=0.5)
return img
def fitsread(imgname, header = False):
"""
Read CSUSB telescope FITS image cube.
Parameters
----------
image : string
FITS image name
header : boolean
Return FITS image header?
Returns
-------
img_data : numpy array
2D or 3D numpy array
"""
try:
if header:
img_data, header = pyfits.getdata(imgname, ignore_missing_end = True, header = True)
return img_data, header
else:
img_data = pyfits.getdata(imgname, ignore_missing_end = True)
return img_data
except IOError:
print "FITSREAD: Unable to open FITS image %s" %imgname
return
def mk_galaxy_struc():
from mk_galaxy_struc_fortable import galaxy
galaxies = []
# Add Sample
data = pyf.getdata('../samples/sample_1.5_3.5_gs_all.fits')
for i in range(len(data)):
galaxies.append(
galaxy(data['ID'][i], data['RA'][i], data['DEC'][i],
data['Imag'][i], data['Zmag'][i], data['Jmag'][i],
data['Hmag'][i], data['z'][i]))
# Add ICD info
data = pyf.getdata('../results/icd_IH.fits')
#data = pyf.getdata('../results/IH_icd_20140806.fits')
for i in range(len(data)):
look = data['ID'][i]
for galaxy in galaxies:
if look == galaxy.ID:
galaxy.ICD_IH = data['ICD_IH'][i]
galaxy.ICD_IH_ERR = data['ICD_IH_ERR'][i]
galaxy.ston_I = data['ston_I'][i]
data = pyf.getdata('../results/icd_JH.fits')
#data = pyf.getdata('../results/JH_icd_20140806.fits')
for i in range(len(data)):
look = data['ID'][i]
for galaxy in galaxies:
if look == galaxy.ID:
galaxy.ICD_JH = data['ICD_JH'][i]
galaxy.ICD_JH_ERR = data['ICD_JH_ERR'][i]
galaxy.ston_J = data['ston_J'][i]
data = pyf.getdata('../results/icd_VJ.fits')
#data = pyf.getdata('../results/VJ_icd_20140806.fits')
for i in range(len(data)):
look = data['ID'][i]
for galaxy in galaxies:
if look == galaxy.ID:
galaxy.ICD_VJ = data['ICD_VJ'][i]
galaxy.ICD_VJ_ERR = data['ICD_VJ_ERR'][i]
galaxy.ston_V = data['ston_V'][i]
# Add FAST results
data = pyf.getdata('./data/FAST_result_GS_1.5_3.5.fits')
for i in range(len(data)):
look = data['id'][i] # note the difference
for galaxy in galaxies:
if look == galaxy.ID:
galaxy.Mass = data['lmass'][i]
galaxy.AV = data['Av'][i]
galaxy.lsfr = data['lsfr'][i]
galaxy.lssfr = data['lssfr'][i]
# Add EAZY results
u = np.loadtxt('./data/photz.153.rf')
v = np.loadtxt('./data/photz.155.rf')
j = np.loadtxt('./data/photz.161.rf')
for ID, u1, v1, j1 in zip(u[:, 0], u[:, 5], v[:, 5], j[:, 5]):
look = int(ID)
for galaxy in galaxies:
if look == galaxy.ID:
galaxy.Uflux_rest = u1
galaxy.Vflux_rest = v1
galaxy.Jflux_rest = j1
# Add GalFit data
data = pyf.getdata('./data/gs_all_candels_ers_udf_f160w_v0.5_galfit.fits')
for i in range(len(data)):
look = data['id'][i]
for galaxy in galaxies:
if look == galaxy.ID:
galaxy.sersic = data['n'][i]
galaxy.axis_ratio = data['q'][i]
galaxy.halflight = data['re'][i]
# Add Color Gradient for GSD
hdulist =\
pyf.open('./data/GOODS-S_May2013_colourGradients_diff_all_no-pegs_2013-06-20.fits')
tbdata = hdulist[1].data
for i in range(len(tbdata.field('ID'))):
look = tbdata.field('ID')[i]
for galaxy in galaxies:
if look == galaxy.ID:
galaxy.Color_grad = tbdata.field('grad_i-H_obs')[i]
#galaxy.Color_grad = tbdata.field('grad_z-H_obs')[i]
# MIPS
hdulist =\
pyf.open('./data/Sample_MIPS_matched.fits')
tbdata = hdulist[1].data
for i in range(len(tbdata.field('ID_GSD'))):
look = tbdata.field('ID_GSD')[i]
for galaxy in galaxies:
if look == galaxy.ID:
galaxy.Mips = tbdata.field('F24')[i]
# Add the morphology data.
data1 = np.genfromtxt('./gini_m20/gdss-match.txt', names=True)
for i in range(len(data1)):
look = data1[i]['ID_1'] # ID
for galaxy in galaxies:
if look == galaxy.ID:
G = galaxy.Gini = data1[i]['G']
M = galaxy.M20 = data1[i]['M20']
if G <= (-0.14 * M + 0.33) and G > (0.14 * M +
0.80): # E/S0/Sa
galaxy.Elliptical = True
elif G <= (-0.14 * M + 0.33) and G <= (0.14 * M +
0.80): #Sb-Ir
galaxy.Spiral = True
elif G > (-0.14 * M + 0.33): # Mergers
galaxy.Merger = True
# Add extra stuff
data = pyf.getdata('./data/gs_all_tf_h_130511b_multi.fits')
for galaxy in galaxies:
galaxy.stellarity = data['CLASS_STAR'][galaxy.ID - 1]
galaxy.halflight = data['FLUX_RADIUS_2'][galaxy.ID - 1]
data = np.genfromtxt('./data/centers_removed.dat', names=True)
for i in range(len(data)):
look = data['ID'][i]
for galaxy in galaxies:
if look == galaxy.ID:
galaxy.ICD_IH_cored = data['ICD'][i]
data = np.genfromtxt('./data/clumpylist_4steven.dat')
for i in range(len(data)):
look = data[i][0]
for galaxy in galaxies:
if look == galaxy.ID:
# Number of blobs with UV Luminosity L_blob/L_galaxy>0.08
#galaxy.clumps = data[i][5]
# Number of blobs with UV Luminosity L_blob/L_galaxy>0.05
galaxy.clumps = data[i][4]
# Number of blobs with UV Luminosity L_blob/L_galaxy>0.01
galaxy.clumps = data[i][3]
data = np.genfromtxt('./data/sfrs.txt', names=True)
for i in data:
look = i['UserID']
for galaxy in galaxies:
if look == galaxy.ID:
if i['SFR_Wuyts'] < 0.0:
a2800 = 1.79289 * i['FAST_ma05_Av']
#a2800 = 1.79289 * galaxy.AV
correction = 10.0**(a2800 / 2.5)
galaxy.sfr2800 = i['SFR_2800']
galaxy.sfrtotal = i['SFR_2800'] * correction
else:
a2800 = 1.79289 * i['FAST_ma05_Av']
#a2800 = 1.79289 * galaxy.AV
correction = 10.0**(a2800 / 2.5)
galaxy.sfr2800 = i['SFR_2800']
galaxy.sfrir = (i['SFR_Wuyts'] +
i['SFR_2800']) / 10**0.2178
galaxy.sfrtotal = (i['SFR_Wuyts'] +
i['SFR_2800']) / 10**0.2178
#galaxy.Mass = i['FAST_ma05_lmass']
galaxy.ssfr = galaxy.sfrtotal / 10**galaxy.Mass
galaxy.mips24 = i['mips24_cryo']
data = np.genfromtxt('./data/masses_from_CANDELS.txt', names=True)
for i in data:
look = i['UserID']
for galaxy in galaxies:
if look == galaxy.ID:
galaxy.mass_candels = i['FAST_ma05_lmass']
x = [galaxy.ID for galaxy in galaxies if galaxy.stellarity > 0.78]
# Bad galaxy removal
bad = [
1073.0, 3736.0, 8030.0, 10832.0, 15769.0, 949.0, 1961.0, 3608.0,
4956.0, 10426.0, 18801.0
] + x
galaxies = filter(lambda galaxy: galaxy.ID not in bad, galaxies)
pickle.dump(galaxies, open('galaxies_fortable.pickle', 'wb'))
'''
def compareLabelLists(labelFile1, labelFile2, magCut=18):
t = 2006.580
## Read in star labels
tab1 = asciidata.open(labelFile1)
name1 = [tab1[0][ss].strip() for ss in range(tab1.nrows)]
mag1 = tab1[1].tonumpy()
x01 = tab1[2].tonumpy()
y01 = tab1[3].tonumpy()
vx1 = tab1[6].tonumpy()
vy1 = tab1[7].tonumpy()
t01 = tab1[10].tonumpy()
x1 = x01 + vx1 * (t - t01) / 10**3
y1 = y01 + vy1 * (t - t01) / 10**3
tab2 = asciidata.open(labelFile2)
name2 = [tab2[0][ss].strip() for ss in range(tab2.nrows)]
mag2 = tab2[1].tonumpy()
x02 = tab2[2].tonumpy()
y02 = tab2[3].tonumpy()
vx2 = tab2[6].tonumpy()
vy2 = tab2[7].tonumpy()
t02 = tab2[10].tonumpy()
x2 = x02 + vx2 * (t - t02) / 10**3
y2 = y02 + vy2 * (t - t02) / 10**3
# Image
im = pyfits.getdata(
'/u/ghezgroup/data/gc/06maylgs1/combo/mag06maylgs1_dp_msc_kp.fits')
imgsize = (im.shape)[0]
# pixel position (0,0) is at upper left
xpix = np.arange(0, im.shape[0], dtype=float)
ypix = np.arange(0, im.shape[1], dtype=float)
sgra = [1422.6, 1543.8]
scale_jpg = 0.00995
xim = (xpix - sgra[0]) * scale_jpg * -1.0
yim = (ypix - sgra[1]) * scale_jpg
py.clf()
py.grid(True)
py.subplots_adjust(left=0.05, right=0.95, bottom=0.05, top=0.95)
py.imshow(np.log10(im),
extent=[xim[0], xim[-1], yim[0], yim[-1]],
aspect='equal',
vmin=1.9,
vmax=6.0,
cmap=py.cm.gray)
py.xlabel('X Offset from Sgr A* (arcsec)')
py.ylabel('Y Offset from Sgr A* (arcsec)')
py.title('UCLA/Keck Galactic Center Group', fontsize=20, fontweight='bold')
thePlot = py.gca()
py.axis([15, -15, -15, 15])
idx2 = np.where(mag2 < magCut)[0]
py.plot(x2[idx2], y2[idx2], 'ro', color='cyan', mfc='none', mec='cyan')
for ii in idx2:
py.text(x2[ii], y2[ii], name2[ii], color='cyan', fontsize=10)
idx1 = np.where(mag1 < magCut)[0]
py.plot(x1[idx1], y1[idx1], 'ro', color='orange', mfc='none', mec='orange')
for ii in idx1:
py.text(x1[ii], y1[ii], name1[ii], color='orange', fontsize=10)
def plotStarfinderList(
starList,
hasErrors=True,
magCut=18,
cooStarList='16C',
cooStarLabels='irs16C',
scaleList=0.00995,
scaleImg=0.00995,
image='/u/ghezgroup/data/gc/06maylgs1/combo/mag06maylgs1_dp_msc_kp.fits'
):
"""
Plot the specified image and overlay the photo_calib.dat sources on top.
Coordinates are converted from pixels to arcsec using the coo star and
assuming that the angle of the image is 0.
This code assumes coordinates are NIRC2 narrow pixels coordaintes. You can modify this by
changing the scale. But +x must be to the west in the starlist.
"""
# Load up the photometric calibraters table.
lis = starTables.StarfinderList(starList, hasErrors=hasErrors)
labels = starTables.Labels()
# Find the coo star in the starlist and in the labels
ii1 = np.where(lis.name == cooStarList)[0]
ii2 = np.where(labels.name == cooStarLabels)[0]
dt = lis.epoch[0] - labels.t0
labels.x += (labels.vx / 10**3) * dt
labels.y += (labels.vy / 10**3) * dt
# Convert the pixels in the starlist into arcsec
x = ((lis.x - lis.x[ii1]) * -scaleList) + labels.x[ii2]
y = ((lis.y - lis.y[ii1]) * scaleList) + labels.y[ii2]
im = pyfits.getdata(image)
imgsize = (im.shape)[0]
# pixel position (0,0) is at upper left
xpix = np.arange(0, im.shape[0], dtype=float)
ypix = np.arange(0, im.shape[1], dtype=float)
# Read in the image coo file
# Coo star pixel coordinates
_coo = open(image.replace('.fits', '.coo'), 'r')
coordsTmp = _coo.readline().split()
coords = [float(coo) for coo in coordsTmp]
print 'Coordinates for %s:' % cooStarLabels
print ' [%10.4f, %10.4f] pixels' % (coords[0], coords[1])
print ' [%10.4f, %10.4f] arcsec' % (labels.x[ii2], labels.y[ii2])
sgrax = coords[0] - (labels.x[ii2] / -scaleImg)
sgray = coords[1] - (labels.y[ii2] / scaleImg)
sgra = [sgrax, sgray]
# Image coordinates (in arcsec)
xim = (xpix - sgra[0]) * -scaleImg
yim = (ypix - sgra[1]) * scaleImg
py.clf()
py.close(2)
py.figure(2, figsize=(6, 4.5))
py.grid(True)
py.subplots_adjust(left=0.05, right=0.95, bottom=0.05, top=0.95)
py.imshow(np.log10(im),
extent=[xim[0], xim[-1], yim[0], yim[-1]],
aspect='equal',
vmin=1.9,
vmax=6.0,
cmap=py.cm.gray)
py.xlabel('X Offset from Sgr A* (arcsec)')
py.ylabel('Y Offset from Sgr A* (arcsec)')
py.title('UCLA/Keck Galactic Center Group', fontsize=20, fontweight='bold')
thePlot = py.gca()
py.axis([15, -15, -15, 15])
idx = (np.where((lis.mag < magCut) & (x > xim.min()) & (x < xim.max())
& (y > yim.min()) & (y < yim.max())))[0]
py.plot(x[idx], y[idx], 'r+', color='orange')
for ii in idx:
py.text(x[ii], y[ii], lis.name[ii], color='orange', fontsize=10)
def plotPhotoCalib(
image,
cooStar,
photoCalib='/u/ghezgroup/data/gc/source_list/photo_calib.dat'):
"""
Plot the specified image and overlay the photo_calib.dat sources on top.
Coordinates are converted from pixels to arcsec using the coo star and
assuming that the angle of the image is 0.
"""
# Load up the photometric calibraters table.
_tab = asciidata.open(photoCalib)
name = _tab[0].tonumpy()
x = _tab[1].tonumpy()
y = _tab[2].tonumpy()
# Load up the image
imageRoot = image.replace('.fits', '')
im = pyfits.getdata(imageRoot + '.fits')
# Coo star pixel coordinates
_coo = open(imageRoot + '.coo', 'r')
tmp = _coo.readline().split()
cooPixel = [float(tmp[0]), float(tmp[1])]
imgsize = (im.shape)[0]
xpix = np.arange(0, im.shape[0], dtype=float)
ypix = np.arange(0, im.shape[1], dtype=float)
cooIdx = np.where(name == cooStar)[0]
if len(cooIdx) == 0:
print 'Failed to find the coo star %s in %s' % (cooStar, photoCalib)
cooArcsec = [x[cooIdx[0]], y[cooIdx[0]]]
scale = 0.00994
xim = ((xpix - cooPixel[0]) * scale * -1.0) + cooArcsec[0]
yim = ((ypix - cooPixel[1]) * scale) + cooArcsec[1]
py.figure(1)
py.clf()
py.grid(True)
py.subplots_adjust(left=0.05, right=0.95, bottom=0.05, top=0.95)
py.imshow(np.log10(im),
extent=[xim[0], xim[-1], yim[0], yim[-1]],
aspect='equal',
vmin=1.9,
vmax=6.0,
cmap=py.cm.gray)
py.xlabel('X Offset from Sgr A* (arcsec)')
py.ylabel('Y Offset from Sgr A* (arcsec)')
py.title(imageRoot)
thePlot = py.gca()
idx = (np.where((x > xim.min()) & (x < xim.max()) & (y > yim.min())
& (y < yim.max())))[0]
py.plot(x[idx], y[idx], 'r+', color='orange')
for ii in idx:
py.text(x[ii], y[ii], name[ii], color='orange', fontsize=12)