def cutout(filename='', hdu=None, center=[None, None],im_size=0.1,pix=False,
writepdf=False, writefits=False, silent=False):
'''
>> sub_hdu = cutout(filename='file.fits', center=[12,-1.], im_size=0.1,
writepdf=False, writefits=False)
>> sub_hdu = cutout(hdu=hdu, center=[12,-1.], im_size=0.1,
writepdf=False, writefits=False
returns:
pyfits.core.PrimaryHDU
input:
- hdu (pyfits.core.HDUList or pyfits.core.PrimaryHDU ) or filename of fits image
- center=[ra,dec] (deg)
- im_size=0.1 (deg)
optional input:
- pix input center and im_size are in pixel units
- writepdf='name.pdf' or True (write filename_sub.pdf)
- writefits='name.fits' or True (fileanme+sub.fits
the creation of new WCS header doesnt seem to work for all cases...
'''
if (filename=='') and not(hdu):
print 'please give filename= or hdu='
return
if not(hdu) and not(os.path.isfile(filename)):
print 'file :'+ filename+ '\n not found'
return
if not np.isscalar(center[0]):
print 'please give center=[ra, dec]'
return
center = np.array(center)
# read or index to PrimaryHDU
if not(hdu):
hdu = pyfits.open(filename)[0]
elif type(hdu) == pyfits.core.HDUList:
hdu = hdu[0]
elif type(hdu) != pyfits.core.PrimaryHDU:
print 'type(hdu:)', type(hdu)
print 'ERROR: type(hdu) needs to be <pyfits.core.HDUList> or pyfits.core.PrimaryHDU'
return
# get image
im = hdu.data
# get WCS,
if not(pix):
wcs = pywcs.WCS(header=hdu.header, naxis=2) #fobj=hdulist,
if not silent: print 'image shape', im.shape
if (len(im.shape) == 3):
if not silent: print 'using first layer of image'
im = im[0,:,:]
print 'new image shape', im.shape
if (len(im.shape) == 4):
if not silent: print 'using first layer of image'
im = im[0,0,:,:]
if not silent: print 'new image shape', im.shape
# conver center en overplot coordinates
#pcenter = (wcs.wcs_sky2pix([center], 1))[0] # if pywcs
pcenter = (wcs.wcs_world2pix([center],0))[0] # if astropy.wcs
else:
pcenter = center
# slice the image
if not silent: print 'center in pixel coordinates', pcenter
# use true sky location (creates non-square images)
#delta_ax1 = (np.abs(wcs.wcs_sky2pix([ [center[0]-im_size, center[1]] ], 1) - pcenter)/2.)[0][0]
#delta_ax2 = (np.abs(wcs.wcs_sky2pix([ [center[0], center[1]-im_size] ], 1) - pcenter)/2.)[0][1]
#delta = [delta_ax1, delta_ax2]
#delta= np.abs(wcs.wcs_sky2pix( [center-im_size], 1)[0] - pcenter)/2.
# use pixel scale to define boundaries
if not(pix):
delta = np.abs(0.5*im_size / np.array([hdu.header['CDELT1'], hdu.header['CDELT2']]))
else:
delta = (im_size/2., im_size/2.)
ax1l = pcenter[0]-delta[0]
ax1u=pcenter[0]+delta[0]
ax2l = pcenter[1]-delta[1]
ax2u=pcenter[1]+delta[1]
# check limits
if (ax1l < 0): ax1l = 0
if (ax1u > im.shape[1]): ax1u = im.shape[1]
if (ax2l < 0): ax2l = 0
if (ax2u > im.shape[0]): ax2u = im.shape[0]
if not silent: print 'ax2l,ax2u, ax1l,ax1u', ax2l,ax2u,ax1l,ax1u
subim = im[ax2l:ax2u,ax1l:ax1u ]
if not silent: print 'subim shape:',subim.shape
if min(subim.shape) == 0:
print 'ERROR. something is wrong with the cutout (center+/-im_size out of bounds?) '
return None
# set the base of the output file
if (writepdf==True) or (writefits==True):
srem = ['.FITS', '.FIT', '.fit', '.fits']
outname = filename
for srm in srem: outname=outname.split(srm)[0]
if filename =='':
print 'warning, not filename given pdf or fits file, using IAU name'
outname = iau_name(center[0], center[1])
if not silent: print 'base for output file:', outname
if writepdf:
# determine color range, we use arcsinh scaling
scaled_subim = np.arcsinh(subim)
vals = scaled_subim.reshape(subim.shape[0]*subim.shape[1])
#nbins=50
#h_vals = np.histogram(np.log10(vals), new=False, bins=nbins)
svals = np.sort(vals)
slen = len(svals)
vmin = svals[0.01*slen]
vmax = svals[0.99*slen] #np.power(10, h_vals[1][nbins-10])
plt.imshow(scaled_subim, vmin=vmin, vmax=vmax,
cmap='hot', interpolation='bilinear')
# set filename (if not given)
if not(type(writepdf) is str):
outfile = outname+'_sub.pdf'
else: outfile = writepdf
if not silent: print 'writing', outfile
plt.savefig(outfile, format='pdf')
#make new WCS and save fits
sub_hdr = hdu.header.copy() #sub_hdu.header
## this wrong: slightly rotates the image
#sub_hdr['CRVAL1'] = center[0]
#sub_hdr['CRVAL2'] = center[1]
#sub_hdr['CRPIX1'] = pcenter[0]-ax1l
#sub_hdr['CRPIX2'] = pcenter[1]-ax2l
## keep CRVAL1 the same, but swift its pixel coodindates
sub_hdr['CRPIX1'] = np.floor(hdu.header['CRPIX1'] - ax1l ) +1
sub_hdr['CRPIX2'] = np.floor(hdu.header['CRPIX2'] - ax2l ) +1
if not silent: print 'orgininal CRVAL (', hdu.header['CRVAL1'], hdu.header['CRVAL2'],\
') in sub image pixel coordindates:', sub_hdr['CRPIX1'] , sub_hdr['CRPIX2']
# note, after this call sub_hdu.header is differnt the input than sub_hdr
# (eg, NAXIS, NAXIS1, are updated)
sub_hdu = pyfits.PrimaryHDU(data=subim, header=sub_hdr)
# write files
if writefits:
if not(type(writefits) is str):
outfile = outname+'_sub.fits'
else: outfile = writefits
if not silent: print 'writing:', outfile
sub_hdu.writeto(outfile,clobber=True)
return sub_hdu
def get_dss(ra, dec, size=1/60., name=None, sdir=None, color='red',
debug=False, noclobber=False):
'''
wrapper to get the DSS image, requires that dss2 application is installed
(see http://archive.eso.org/cms/tools-documentation/the-eso-st-ecf-digitized-sky-survey-application)
>> fitsim = get_dss(ra, dec, size=1/60., name=None, sdir=None, color='red')
input:
ra, dec, size in degree
sdir: location to save image, default is sjoert.catdir/DSS/fits/
name: image name default is name dss+pl_Id (pl_Id=dss plate naming convention)
color: blue, red, IR
'''
change_name = True
if name is None:
name = 'dss'
change_name = False
name = name
if sdir is None:
sdir = dirs.catdir+'DSS/fits/'
indir = dirs.catdir+'DSS/infiles/' #keep log somewhere else
else:
indir=sdir
new_name = sdir+name+'.fits'
if noclobber and os.path.isfile(new_name):
print 'not rerunning, reading:', new_name
hdu = pyfits.open(new_name)
return hdu
infile_name = indir+name+'.in'
logfile_name = indir+name+'.log'
errfile_name = indir+name+'.err'
infile = file(infile_name,'w')
sradec = string2radec.radec2string(ra, dec)
sra = sradec[0:11]
sdec = sradec[11:]
long_sra = sra[0:2]+' '+sra[3:5]+' '+sra[6:]
long_sdec = sdec[0:3]+' '+sdec[4:6]+' '+sdec[7:]
long_ssize = str(size*60)+' '+str(size*60)
line =name+' '+long_sra+' '+long_sdec+ ' '+long_ssize
infile.writelines(line+ ' \n')
infile.close()
command_line = 'cd '+sdir+' ; dss2 '+color+' -i '+infile_name +' > '+logfile_name #+' 2> '+ errfile_name
command_line = 'dss2 '+color+' -i '+infile_name #+' > '+logfile_name #+' 2> '+ errfile_name
if debug:
print sradec
print line
print command_line
#p = subprocess.Popen(command_line, shell=True)
#t = os.popen(command_line)
#p = subprocess.call(command_line, shell=True)
os.system('touch '+logfile_name)
logfile = open(logfile_name, 'r')
args = shlex.split(command_line)
if debug: print args
#p3 = subprocess.call('dss2 red -i /Users/sjoertvanvelzen/Documents/project/catalogs/DSS/fits/sjoert.in', shell=True)
proc = subprocess.Popen(args, cwd=sdir, stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
sleep_time = (size*60)
if sleep_time <10: sleep_time = 10
print 'sleeping for (s):', sleep_time
time.sleep(sleep_time )
# at this point we either have an image, or we give up
proc.terminate()
if proc.wait() < 0:
print 'problem with dss call'
print 'id:', proc.pid
#proc.kill()
#os.kill(proc.pid, signal.SIGHUP) # doesn't work ?
return None
#time.sleep(1)
#proc.kill()
#stdout_value = proc.communicate()[0]
stderr_value = proc.stderr.read()
print 'stderr:', stderr_value
stdout_value = proc.stdout.read()
if debug:
print '\n stdout: ', stdout_value
lines = (stdout_value).split('\n')
if not(len(lines)):
print 'empty log file', logfile_name
return None
i=0
while not re.search("Field", lines[i]) and (i < (len(lines)-1)):
i+=1
if i == (len(lines)-3):
print 'no info from log file:',logfile_name
return None
info_line = lines[i+2].split()
if len(info_line) < 7:
print 'no info on plate id:', info_line
return None
Pl_Id = lines[i+2].split()[8].swapcase()
if debug: print 'Pl_Id:', Pl_Id
force_name = sdir+name[0:20]+Pl_Id+'.fits' # max 20 characters...
if debug: print 'dss image name:', force_name
if change_name:
os.system('mv '+force_name+' '+new_name)
if debug: print 'new name:', new_name
try:
hdu = pyfits.open(new_name)
print 'created:', new_name
except IOError:
print 'file not created:', new_name
return None
else:
try:
hdu = pyfits.open(force_name)
print 'created:', force_name
except IOError:
print 'file not created:', force_name
return None
return hdu
