def call_specrectify(file, i, object, calfile, file_out, verbose=0):
if (verbose > 0):
print "\n ** Calling SPECRECTIFY(" + file + ")\n\n"
s = iraf.specrectify(images=file,
solfile=calfile,
outimages=file_out,
caltype='line',
function='polynomial',
order=3,
inttype='interp',
outpref='',
w1='None',
w2='None',
dw='None',
nw='None',
blank=0.0,
clobber=1,
logfile='salt_specrectify.log',
verbose=(verbose > 1))
rcParams['figure.figsize'] = 20, 30
hdulist = fits.open(file_out)
image = hdulist['SCI'].data
dy_spect_plot = 400 # How many rows vertically is the spectrum? ** Changes 2014 vs. 2015
ny = image.shape[
0] # Look up the central row of the spectrum, and take +- dy/2 rows from that
plt.imshow(log(image))
plt.ylim((ny / 2 - dy_spect_plot / 2, ny / 2 + dy_spect_plot / 2))
plt.title(file + ", " + object + ", " + ' RECT')
plt.show()
hdulist.close()
def rectify(ids=None, fs=None):
iraf.cd('work')
if ids is None:
ids = np.array(glob('id2/arc*id2*.db'))
if fs is None:
fs = glob('srt/*mos*.fits')
if len(ids) == 0:
print "WARNING: No wavelength solutions for rectification."
iraf.cd('..')
return
if len(fs) == 0:
print "WARNING: No images for rectification."
iraf.cd('..')
return
# Get the grating angles of the solution files
idgas = []
for i, thisid in enumerate(ids):
f = open(thisid)
idlines = np.array(f.readlines(), dtype=str)
f.close()
idgaline = idlines[np.char.startswith(idlines, '#graang')][0]
idgas.append(float(idgaline.split('=')[1]))
ims, gas = get_scis_and_arcs(fs)
if not os.path.exists('rec'):
os.mkdir('rec')
for i, f in enumerate(ims):
fname = f.split('/')[1]
typestr = fname[:3]
ga, imgnum = gas[i], fname[-9:-5]
outfile = 'rec/' + typestr + '%05.2frec' % (ga) + imgnum + '.fits'
iraf.unlearn(iraf.specrectify)
iraf.flpr()
print('_____idgas_____')
print (np.array(idgas))
print('_____ga_____')
print (ga)
idfile = ids[np.array(idgas) == ga][0]
iraf.specrectify(images=f, outimages=outfile, solfile=idfile,
outpref='', function='legendre', order=3,
inttype='interp', conserve='yes', clobber='yes',
verbose='yes')
# Update the BPM to mask any blank regions
h = pyfits.open(outfile, 'update')
# Cover the chip gaps. The background task etc do better if the chip
# gaps are straight
# To deal with this we just throw away the min and max of each side of
# the curved chip gap
chipgaps = get_chipgaps(h)
print(" -- chipgaps --")
print(chipgaps)
# Chip 1
h[2].data[:, chipgaps[0][0]:chipgaps[0][1]] = 1
# Chip 2
h[2].data[:, chipgaps[1][0]:chipgaps[1][1]] = 1
# edge of chip 3
h[2].data[:, chipgaps[2][0]:chipgaps[2][1]] = 1
# Cover the other blank regions
h[2].data[[h[1].data == 0]] = 1
# Set all of the data to zero in the BPM
h[1].data[h[2].data == 1] = 0.0
h.flush()
h.close()
iraf.cd('..')
##########
if (object[i] in ["Pluto", "HD 146233", "ARC"]) & (DO_SPECRECTIFY):
e = os.path.exists(files_cr_rect[i])
print "SPECRECTIFY: File " + files_cr_rect[i] + " exists: " + repr(e)
if (not e) | (DO_FORCE_CAL_SINGLE):
print "\n ** Calling SPECRECTIFY(" + files[i] + "), i = " + repr(
i) + ", object = " + object[i] + "\n\n"
s = iraf.specrectify(images=files_cr[i],
solfile=calfile,
outimages=files_cr_rect[i],
caltype='line',
function='polynomial',
order=3,
inttype='interp',
outpref='',
w1='None',
w2='None',
dw='None',
nw='None',
blank=0.0,
clobber=1,
logfile='salt_specrectify.log',
verbose=1)
rcParams['figure.figsize'] = 20, 30
hdulist = fits.open(files_cr_rect[i])
image = hdulist['SCI'].data
dy_spect_plot = 400 # How many rows vertically is the spectrum?
ny = image.shape[
0] # Look up the central row of the spectrum, and take +- dy/2 rows from that
plt.imshow(log(image))
def rectify(ids=None, fs=None):
iraf.cd('work')
if ids is None:
ids = np.array(glob('id2/arc*id2*.db'))
if fs is None:
fs = glob('mos/*mos*.fits')
if len(ids) == 0:
print "WARNING: No wavelength solutions for rectification."
iraf.cd('..')
return
if len(fs) == 0:
print "WARNING: No images for rectification."
iraf.cd('..')
return
# Get the grating angles of the solution files
idgas = []
for i, thisid in enumerate(ids):
f = open(thisid)
idlines = np.array(f.readlines(), dtype=str)
f.close()
idgaline = idlines[np.char.startswith(idlines, '#graang')][0]
idgas.append(float(idgaline.split('=')[1]))
ims, gas = get_scis_and_arcs(fs)
if not os.path.exists('rec'):
os.mkdir('rec')
for i, f in enumerate(ims):
fname = f.split('/')[1]
typestr = fname[:3]
ga, imgnum = gas[i], fname[-9:-5]
outfile = 'rec/' + typestr + '%05.2frec' % (ga) + imgnum + '.fits'
iraf.unlearn(iraf.specrectify)
iraf.flpr()
idfile = ids[np.array(idgas) == ga][0]
iraf.specrectify(images=f, outimages=outfile, solfile=idfile,
outpref='', function='legendre', order=3,
inttype='interp', conserve='yes', clobber='yes',
verbose='yes')
# Update the BPM to mask any blank regions
h = pyfits.open(outfile, 'update')
# Cover the chip gaps. The background task etc do better if the chip
# gaps are straight
# To deal with this we just throw away the min and max of each side of
# the curved chip gap
chipgaps = get_chipgaps(h)
# Chip 1
h[2].data[:, chipgaps[0][0]:chipgaps[0][1]] = 1
# Chip 2
h[2].data[:, chipgaps[1][0]:chipgaps[1][1]] = 1
# edge of chip 3
h[2].data[:, chipgaps[2][0]:chipgaps[2][1]] = 1
# Cover the other blank regions
h[2].data[[h[1].data == 0]] = 1
# Set all of the data to zero in the BPM
h[1].data[h[2].data == 1] = 0.0
h.flush()
h.close()
iraf.cd('..')