def make_mosaic(struct, gap, xshift, yshift, rotation, interp_type='linear',
boundary='constant', constant=0, geotran=True, fill=False,
cleanup=True, log=None, verbose=False):
"""Given a SALT image struct, combine each of the individual amplifiers and
apply the geometric CCD transformations to the image
"""
# get the name of the file
infile = saltkey.getimagename(struct[0], base=True)
outpath = './'
# identify instrument
instrume, keyprep, keygain, keybias, keyxtalk, keyslot = \
saltkey.instrumid(struct)
# how many amplifiers?
nsciext = saltkey.get('NSCIEXT', struct[0])
nextend = saltkey.get('NEXTEND', struct[0])
nccds = saltkey.get('NCCDS', struct[0])
amplifiers = nccds * 2
if nextend > nsciext:
varframe = True
else:
varframe = False
# CCD geometry coefficients
if (instrume == 'RSS' or instrume == 'PFIS'):
xsh = [0., xshift[0], 0., xshift[1]]
ysh = [0., yshift[0], 0., yshift[1]]
rot = [0., rotation[0], 0., rotation[1]]
elif instrume == 'SALTICAM':
xsh = [0., xshift[0], 0.]
ysh = [0., yshift[0], 0.]
rot = [0., rotation[0], 0]
# how many extensions?
nextend = saltkey.get('NEXTEND', struct[0])
# CCD on-chip binning
xbin, ybin = saltkey.ccdbin(struct[0])
# create temporary primary extension
outstruct = []
outstruct.append(struct[0])
# define temporary FITS file store tiled CCDs
tilefile = saltio.tmpfile(outpath)
tilefile += 'tile.fits'
if varframe:
tilehdu = [None] * (3 * int(nsciext / 2) + 1)
else:
tilehdu = [None] * int(nsciext / 2 + 1)
tilehdu[0] = fits.PrimaryHDU()
#tilehdu[0].header = struct[0].header
if log:
log.message('', with_stdout=verbose)
# iterate over amplifiers, stich them to produce file of CCD images
for i in range(int(nsciext / 2)):
hdu = i * 2 + 1
# amplifier = hdu%amplifiers
# if (amplifier == 0): amplifier = amplifiers
# read DATASEC keywords
datasec1 = saltkey.get('DATASEC', struct[hdu])
datasec2 = saltkey.get('DATASEC', struct[hdu + 1])
xdsec1, ydsec1 = saltstring.secsplit(datasec1)
xdsec2, ydsec2 = saltstring.secsplit(datasec2)
# read images
imdata1 = saltio.readimage(struct, hdu)
imdata2 = saltio.readimage(struct, hdu + 1)
# tile 2n amplifiers to yield n CCD images
outdata = numpy.zeros((ydsec1[1] +
abs(ysh[i +
1] /
ybin), xdsec1[1] +
xdsec2[1] +
abs(xsh[i +
1] /
xbin)), numpy.float32)
# set up the variance frame
if varframe:
vardata = outdata.copy()
vdata1 = saltio.readimage(struct, struct[hdu].header['VAREXT'])
vdata2 = saltio.readimage(struct, struct[hdu + 1].header['VAREXT'])
bpmdata = outdata.copy()
bdata1 = saltio.readimage(struct, struct[hdu].header['BPMEXT'])
bdata2 = saltio.readimage(struct, struct[hdu + 1].header['BPMEXT'])
x1 = xdsec1[0] - 1
if x1 != 0:
msg = 'The data in %s have not been trimmed prior to mosaicking.' \
% infile
log.error(msg)
if xsh[i + 1] < 0:
x1 += abs(xsh[i + 1] / xbin)
x2 = x1 + xdsec1[1]
y1 = ydsec1[0] - 1
if ysh[i + 1] < 0:
y1 += abs(ysh[i + 1] / ybin)
y2 = y1 + ydsec1[1]
outdata[y1:y2, x1:x2] =\
imdata1[ydsec1[0] - 1:ydsec1[1], xdsec1[0] - 1:xdsec1[1]]
if varframe:
vardata[y1:y2, x1:x2] =\
vdata1[ydsec1[0] - 1:ydsec1[1], xdsec1[0] - 1:xdsec1[1]]
bpmdata[y1:y2, x1:x2] =\
bdata1[ydsec1[0] - 1:ydsec1[1], xdsec1[0] - 1:xdsec1[1]]
x1 = x2
x2 = x1 + xdsec2[1]
y1 = ydsec2[0] - 1
if ysh[i + 1] < 0:
y1 += abs(ysh[i + 1] / ybin)
y2 = y1 + ydsec2[1]
outdata[y1:y2, x1:x2] =\
imdata2[ydsec1[0] - 1:ydsec1[1], xdsec1[0] - 1:xdsec1[1]]
if varframe:
vardata[y1:y2, x1:x2] =\
vdata2[ydsec1[0] - 1:ydsec1[1], xdsec1[0] - 1:xdsec1[1]]
bpmdata[y1:y2, x1:x2] =\
bdata2[ydsec1[0] - 1:ydsec1[1], xdsec1[0] - 1:xdsec1[1]]
# size of new image
naxis1 = str(xdsec1[1] + xdsec2[1])
naxis2 = str(ydsec1[1])
# add image and keywords to HDU list
tilehdu[i + 1] = fits.ImageHDU(outdata)
tilehdu[i + 1].header = struct[hdu].header
#tilehdu[
# i + 1].header['DATASEC'] = '[1:' + naxis1 + ',1:' + naxis2 + ']'
if varframe:
vext = i + 1 + int(nsciext / 2.)
tilehdu[vext] = fits.ImageHDU(vardata)
#tilehdu[vext].header = struct[struct[hdu].header['VAREXT']].header
#tilehdu[vext].header[
# 'DATASEC'] = '[1:' + naxis1 + ',1:' + naxis2 + ']'
bext = i + 1 + 2 * int(nsciext / 2.)
tilehdu[bext] = fits.ImageHDU(bpmdata)
#tilehdu[bext].header = struct[struct[hdu].header['BPMEXT']].header
#tilehdu[bext].header[
# 'DATASEC'] = '[1:' + naxis1 + ',1:' + naxis2 + ']'
# image tile log message #1
if log:
message = os.path.basename(infile) + '[' + str(hdu) + ']['
message += str(xdsec1[0]) + ':' + str(xdsec1[1]) + ','
message += str(ydsec1[0]) + ':' + str(ydsec1[1]) + '] --> '
message += os.path.basename(tilefile) + '[' + str(i + 1) + ']['
message += str(xdsec1[0]) + ':' + str(xdsec1[1]) + ','
message += str(ydsec1[0]) + ':' + str(ydsec1[1]) + ']'
log.message(message, with_stdout=verbose, with_header=False)
message = os.path.basename(infile) + '[' + str(hdu + 1) + ']['
message += str(xdsec1[0]) + ':' + str(xdsec1[1]) + ','
message += str(ydsec1[0]) + ':' + str(ydsec1[1]) + '] --> '
message += os.path.basename(tilefile) + '[' + str(i + 1) + ']['
message += str(xdsec1[1] + 1) + ':' + \
str(xdsec1[1] + xdsec2[1]) + ','
message += str(ydsec2[0]) + ':' + str(ydsec2[1]) + ']'
log.message(message, with_stdout=verbose, with_header=False)
# write temporary file of tiled CCDs
hdulist = fits.HDUList(tilehdu)
hdulist.writeto(tilefile)
# iterate over CCDs, transform and rotate images
yrot = [None] * 4
xrot = [None] * 4
tranfile = [' ']
tranhdu = [0]
if varframe:
tranfile = [''] * (3 * int(nsciext / 2) + 1)
tranhdu = [0] * (3 * int(nsciext / 2) + 1)
else:
tranfile = [''] * int(nsciext / 2 + 1)
tranhdu = [0] * int(nsciext / 2 + 1)
# this is hardwired for SALT where the second CCD is considered the
# fiducial
for hdu in range(1, int(nsciext / 2 + 1)):
tranfile[hdu] = saltio.tmpfile(outpath)
tranfile[hdu] += 'tran.fits'
if varframe:
tranfile[hdu + nccds] = saltio.tmpfile(outpath) + 'tran.fits'
tranfile[hdu + 2 * nccds] = saltio.tmpfile(outpath) + 'tran.fits'
ccd = hdu % nccds
if (ccd == 0):
ccd = nccds
# correct rotation for CCD binning
yrot[ccd] = rot[ccd] * ybin / xbin
xrot[ccd] = rot[ccd] * xbin / ybin
dxshift = xbin * int(float(int(gap) / xbin) + 0.5) - gap
# transformation using geotran IRAF task
# if (ccd == 1):
if (ccd != 2):
if geotran:
message = '\nSALTMOSAIC -- geotran ' + tilefile + \
'[' + str(ccd) + '] ' + tranfile[hdu]
message += ' \"\" \"\" xshift=' + \
str((xsh[ccd] + (2 - ccd) * dxshift) / xbin) + ' '
message += 'yshift=' + \
str(ysh[ccd] / ybin) + ' xrotation=' + str(xrot[ccd]) + ' '
message += 'yrotation=' + \
str(yrot[ccd]) + ' xmag=1 ymag=1 xmin=\'INDEF\''
message += 'xmax=\'INDEF\' ymin=\'INDEF\' ymax=\'INDEF\' '
message += 'ncols=\'INDEF\' '
message += 'nlines=\'INDEF\' verbose=\'no\' '
message += 'fluxconserve=\'yes\' nxblock=2048 '
message += 'nyblock=2048 interpolant=\'' + \
interp_type + '\' boundary=\'constant\' constant=0'
log.message(message, with_stdout=verbose)
yd, xd = tilehdu[ccd].data.shape
ncols = 'INDEF' # ncols=xd+abs(xsh[ccd]/xbin)
nlines = 'INDEF' # nlines=yd+abs(ysh[ccd]/ybin)
geo_xshift = xsh[ccd] + (2 - ccd) * dxshift / xbin
geo_yshift = ysh[ccd] / ybin
iraf.images.immatch.geotran(tilefile + "[" + str(ccd) + "]",
tranfile[hdu],
"",
"",
xshift=geo_xshift,
yshift=geo_yshift,
xrotation=xrot[ccd],
yrotation=yrot[ccd],
xmag=1, ymag=1, xmin='INDEF',
xmax='INDEF', ymin='INDEF',
ymax='INDEF', ncols=ncols,
nlines=nlines, verbose='no',
fluxconserve='yes', nxblock=2048,
nyblock=2048, interpolant="linear",
boundary="constant", constant=0)
if varframe:
var_infile = tilefile + "[" + str(ccd + nccds) + "]"
iraf.images.immatch.geotran(var_infile,
tranfile[hdu + nccds],
"",
"",
xshift=geo_xshift,
yshift=geo_yshift,
xrotation=xrot[ccd],
yrotation=yrot[ccd],
xmag=1, ymag=1, xmin='INDEF',
xmax='INDEF', ymin='INDEF',
ymax='INDEF', ncols=ncols,
nlines=nlines, verbose='no',
fluxconserve='yes',
nxblock=2048, nyblock=2048,
interpolant="linear",
boundary="constant",
constant=0)
var2_infile = tilefile + "[" + str(ccd + 2 * nccds) + "]"
iraf.images.immatch.geotran(var2_infile,
tranfile[hdu + 2 * nccds],
"",
"",
xshift=geo_xshift,
yshift=geo_yshift,
xrotation=xrot[ccd],
yrotation=yrot[ccd],
xmag=1, ymag=1, xmin='INDEF',
xmax='INDEF', ymin='INDEF',
ymax='INDEF', ncols=ncols,
nlines=nlines, verbose='no',
fluxconserve='yes',
nxblock=2048, nyblock=2048,
interpolant="linear",
boundary="constant",
constant=0)
# open the file and copy the data to tranhdu
tstruct = fits.open(tranfile[hdu])
tranhdu[hdu] = tstruct[0].data
tstruct.close()
if varframe:
tranhdu[
hdu +
nccds] = fits.open(
tranfile[
hdu +
nccds])[0].data
tranhdu[
hdu +
2 *
nccds] = fits.open(
tranfile[
hdu +
2 *
nccds])[0].data
else:
log.message(
"Transform CCD #%i using dx=%s, dy=%s, rot=%s" %
(ccd,
xsh[ccd] /
2.0,
ysh[ccd] /
2.0,
xrot[ccd]),
with_stdout=verbose,
with_header=False)
tranhdu[hdu] = geometric_transform(
tilehdu[ccd].data,
tran_func,
prefilter=False,
order=1,
extra_arguments=(
xsh[ccd] / 2,
ysh[ccd] / 2,
1,
1,
xrot[ccd],
yrot[ccd]))
tstruct = fits.PrimaryHDU(tranhdu[hdu])
tstruct.writeto(tranfile[hdu])
if varframe:
tranhdu[hdu + nccds] = geometric_transform(
tilehdu[hdu + 3].data,
tran_func,
prefilter=False,
order=1,
extra_arguments=(
xsh[ccd] / 2, ysh[ccd] / 2,
1, 1,
xrot[ccd], yrot[ccd]))
tranhdu[hdu + 2 * nccds] = geometric_transform(
tilehdu[hdu + 6].data,
tran_func,
prefilter=False,
order=1,
extra_arguments=(
xsh[ccd] / 2, ysh[ccd] / 2,
1, 1,
xrot[ccd], yrot[ccd]))
else:
log.message(
"Transform CCD #%i using dx=%s, dy=%s, rot=%s" %
(ccd, 0, 0, 0), with_stdout=verbose, with_header=False)
tranhdu[hdu] = tilehdu[ccd].data
if varframe:
tranhdu[hdu + nccds] = tilehdu[ccd + nccds].data
tranhdu[hdu + 2 * nccds] = tilehdu[ccd + 2 * nccds].data
# open outfile
if varframe:
outlist = 4 * [None]
else:
outlist = 2 * [None]
#outlist[0] = struct[0].copy()
outlist[0] = fits.PrimaryHDU()
outlist[0].header = struct[0].header
naxis1 = int(gap / xbin * (nccds - 1))
naxis2 = 0
for i in range(1, nccds + 1):
yw, xw = tranhdu[i].shape
naxis1 += xw + int(abs(xsh[ccd] / xbin)) + 1
naxis2 = max(naxis2, yw)
outdata = numpy.zeros((naxis2, naxis1), numpy.float32)
outdata.shape = naxis2, naxis1
if varframe:
vardata = outdata * 0
bpmdata = outdata * 0 + 1
# iterate over CCDs, stich them to produce a full image
hdu = 0
totxshift = 0
for hdu in range(1, nccds + 1):
# read DATASEC keywords
ydsec, xdsec = tranhdu[hdu].shape
# define size and shape of final image
# tile CCDs to yield mosaiced image
x1 = int((hdu - 1) * (xdsec + gap / xbin)) + int(totxshift)
x2 = xdsec + x1
y1 = int(0)
y2 = int(ydsec)
outdata[y1:y2, x1:x2] = tranhdu[hdu]
totxshift += int(abs(xsh[hdu] / xbin)) + 1
if varframe:
vardata[y1:y2, x1:x2] = tranhdu[hdu + nccds]
bpmdata[y1:y2, x1:x2] = tranhdu[hdu + 2 * nccds]
# make sure to cover up all the gaps include bad areas
if varframe:
baddata = (outdata == 0)
baddata = nd.maximum_filter(baddata, size=3)
bpmdata[baddata] = 1
# fill in the gaps if requested
if fill:
if varframe:
outdata = fill_gaps(outdata, 0)
else:
outdata = fill_gaps(outdata, 0)
# add to the file
outlist[1] = fits.ImageHDU(outdata)
if varframe:
outlist[2] = fits.ImageHDU(vardata,name='VAR')
outlist[3] = fits.ImageHDU(bpmdata,name='BPM')
# create the image structure
outstruct = fits.HDUList(outlist)
# update the head informaation
# housekeeping keywords
saltkey.put('NEXTEND', 2, outstruct[0])
saltkey.new('EXTNAME', 'SCI', 'Extension name', outstruct[1])
saltkey.new('EXTVER', 1, 'Extension number', outstruct[1])
if varframe:
saltkey.new('VAREXT', 2, 'Variance frame extension', outstruct[1])
saltkey.new('BPMEXT', 3, 'BPM Extension', outstruct[1])
try:
saltkey.copy(struct[1], outstruct[1], 'CCDSUM')
except:
pass
# Add keywords associated with geometry
saltkey.new('SGEOMGAP', gap, 'SALT Chip Gap', outstruct[0])
c1str = '{:3.2f} {:3.2f} {:3.4f}'.format(xshift[0],
yshift[0],
rotation[0])
saltkey.new('SGEOM1', c1str, 'SALT Chip 1 Transform', outstruct[0])
c2str = '{:3.2f} {:3.2f} {:3.4f}'.format(xshift[1],
yshift[1],
rotation[1])
saltkey.new('SGEOM2', c2str, 'SALT Chip 2 Transform', outstruct[0])
# WCS keywords
saltkey.new('CRPIX1', 0, 'WCS: X reference pixel', outstruct[1])
saltkey.new('CRPIX2', 0, 'WCS: Y reference pixel', outstruct[1])
saltkey.new(
'CRVAL1',
float(xbin),
'WCS: X reference coordinate value',
outstruct[1])
saltkey.new(
'CRVAL2',
float(ybin),
'WCS: Y reference coordinate value',
outstruct[1])
saltkey.new('CDELT1', float(xbin), 'WCS: X pixel size', outstruct[1])
saltkey.new('CDELT2', float(ybin), 'WCS: Y pixel size', outstruct[1])
saltkey.new('CTYPE1', 'pixel', 'X type', outstruct[1])
saltkey.new('CTYPE2', 'pixel', 'Y type', outstruct[1])
# cleanup temporary files
if cleanup:
for tfile in tranfile:
if os.path.isfile(tfile):
saltio.delete(tfile)
if os.path.isfile(tilefile):
status = saltio.delete(tilefile)
# return the file
return outstruct
def slot(struct,infile,dbspeed,dbrate,dbgain,dbnoise,dbbias,dbamp,xcoeff,gaindb,xtalkfile,
logfile,verbose):
import saltprint, saltkey, saltio, saltstat, time
# identify instrument
instrume,keyprep,keygain,keybias,keyxtalk,keyslot,status = saltkey.instrumid(struct,infile,logfile)
# number of image HDU
nextend = 0
while (status == 0):
try:
struct[nextend+1].header['XTENSION']
nextend += 1
except:
break
nccds,status = saltkey.get('NCCDS',struct[0],infile,logfile)
amplifiers = nccds * 2
if (nextend%(amplifiers) != 0):
message = '\nERROR -- SALTSLOT: Number of image extensions and'
message += 'number of amplifiers are not consistent'
status = saltprint.err(saltlog,message)
status = saltkey.new('NSCIEXT',nextend,'Number of science extensions',struct[0],infile,logfile)
status = saltkey.new('NEXTEND',nextend,'Number of data extensions',struct[0],infile,logfile)
# check image file and gain database are compatible
if (status == 0):
ngains = len(dbgain)
if (int(max(dbamp)) != amplifiers):
message = '\nERROR -- SALTGSLOT: ' + infile + ' contains ' + str(amplifiers) + ' amplifiers'
message += ', the gaindb file ' + gaindb + ' contains ' + str(max(dbamp)) + ' amplifiers'
status = saltprint.err(logfile,message)
# check image file and cross talk database are compatible
if (status == 0):
if (len(xcoeff)-1 != amplifiers):
message = '\nERROR -- SALTSLOT: ' + infile + ' contains ' + str(amplifiers) + ' amplifiers'
message += ', the cross talk file ' + xtalkfile + ' contains ' + str(len(xcoeff)-1) + ' amplifiers'
status = saltprint.err(logfile,message)
# housekeeping keywords
if (status == 0):
status = saltkey.put('SAL-TLM',time.asctime(time.localtime()),struct[0],infile,logfile)
status = saltkey.new(keyslot,time.asctime(time.localtime()),
'Data have been cleaned by SALTSLOT',struct[0],infile,logfile)
# keywords for image extensions
for i in range(nextend):
hdu = i + 1
status = saltkey.new('EXTNAME','SCI','Extension name',struct[hdu],infile,logfile)
status = saltkey.new('EXTVER',hdu,'Extension number',struct[hdu],infile,logfile)
# log coefficent table
if (status == 0):
message = '%30s %5s %4s %8s' % ('HDU','Gain','Bias','Xtalk')
saltprint.log(logfile,'\n ---------------------------------------------',verbose)
saltprint.log(logfile,message,verbose)
saltprint.log(logfile,' ---------------------------------------------',verbose)
# loop over image extensions
if (status == 0):
for i in range(nextend/2):
hdu = i * 2 + 1
amplifier = hdu%amplifiers
if (amplifier == 0): amplifier = amplifiers
if (status == 0):
value,status = saltkey.get('NAXIS1',struct[hdu],infile,logfile)
naxis1 = int(value)
if (status == 0):
value,status = saltkey.get('NAXIS1',struct[hdu+1],infile,logfile)
naxis2 = int(value)
if (status == 0 and hdu == 1): biassec, status = saltkey.get('BIASSEC',struct[hdu],infile,logfile)
if (status == 0 and hdu == 1):
ranges = biassec.lstrip('[').rstrip(']').split(',')
x1_1 = int(ranges[0].split(':')[0]) - 1
x2_1 = int(ranges[0].split(':')[1]) - 1
y1_1 = int(ranges[1].split(':')[0]) - 1
y2_1 = int(ranges[1].split(':')[1]) - 1
if (status == 0 and hdu == 1): biassec, status = saltkey.get('BIASSEC',struct[hdu+1],infile,logfile)
if (status == 0 and hdu == 1):
ranges = biassec.lstrip('[').rstrip(']').split(',')
x1_2 = int(ranges[0].split(':')[0]) - 1
x2_2 = int(ranges[0].split(':')[1]) - 1
y1_2 = int(ranges[1].split(':')[0]) - 1
y2_2 = int(ranges[1].split(':')[1]) - 1
if (status == 0 and hdu == 1): datasec,status = saltkey.get('DATASEC',struct[hdu],infile,logfile)
if (status == 0 and hdu == 1):
ranges = datasec.lstrip('[').rstrip(']').split(',')
dx1_1 = int(ranges[0].split(':')[0]) - 1
dx2_1 = int(ranges[0].split(':')[1])
dy1_1 = int(ranges[1].split(':')[0]) - 1
dy2_1 = int(ranges[1].split(':')[1])
if (status == 0 and hdu == 1): datasec,status = saltkey.get('DATASEC',struct[hdu+1],infile,logfile)
if (status == 0 and hdu == 1):
ranges = datasec.lstrip('[').rstrip(']').split(',')
dx1_2 = int(ranges[0].split(':')[0]) - 1
dx2_2 = int(ranges[0].split(':')[1])
dy1_2 = int(ranges[1].split(':')[0]) - 1
dy2_2 = int(ranges[1].split(':')[1])
if (status == 0 and dx2_1 - dx1_1 != dx2_2 - dx1_2):
message = 'ERROR -- SALTSLOT: HDUs '+infile
message += '['+str(hdu)+'] and '+infile+'['+str(hdu+1)+']'
message += ' have different dimensions'
status = saltprint.err(logfile,message)
# read speed and gain of each exposure
if (status == 0 and hdu == 1):
gainset,status = saltkey.get('GAINSET',struct[0],infile,logfile)
rospeed,status = saltkey.get('ROSPEED',struct[0],infile,logfile)
if (rospeed == 'NONE'):
saltprint.log(logfile," ",verbose)
message = "ERROR -- SALTSLOT: Readout speed is 'NONE' in "
message += "primary keywords of " + infile
status = saltprint.err(logfile,message)
# read raw images
if (status == 0):
imagedata1,status = saltio.readimage(struct,hdu,logfile)
imagedata2,status = saltio.readimage(struct,hdu+1,logfile)
# gain correction
if (status == 0):
for j in range(len(dbgain)):
if (gainset == dbrate[j] and rospeed == dbspeed[j] and amplifier == int(dbamp[j])):
try:
gain1 = float(dbgain[j])
imagedata1 *= gain1
except:
mesage = 'ERROR -- SALTSLOT: Cannot perform gain correction on image '
message += infile+'['+str(hdu)+']'
status = saltprint.err(logfile,message)
elif (gainset == dbrate[j] and rospeed == dbspeed[j] and amplifier + 1 == int(dbamp[j])):
try:
gain2 = float(dbgain[j])
imagedata2 *= gain2
except:
mesage = 'ERROR -- SALTSLOT: Cannot perform gain correction on image '
message += infile+'['+str(hdu+1)+']'
status = saltprint.err(logfile,message)
# crosstalk correction
if (status == 0):
revimage1 = imagedata1 * float(xcoeff[amplifier])
revimage2 = imagedata2 * float(xcoeff[amplifier+1])
for j in range(dx2_1-dx1_1+1):
imagedata1[:,j] -= revimage2[:,dx2_2-j-1]
imagedata2[:,j] -= revimage1[:,dx2_1-j-1]
# bias subtraction
if (status == 0):
overx_val_1 = []
overx_val_2 = []
for x in range(x1_1,x2_1+1):
list_1 = imagedata1[y1_1:y2_1,x] * 1.0
overx_val_1.append(saltstat.median(list_1,logfile))
overlevel_1 = saltstat.median(overx_val_1,logfile)
for x in range(x1_2,x2_2+1):
list_2 = imagedata2[y1_2:y2_2,x] * 1.0
overx_val_2.append(saltstat.median(list_2,logfile))
overlevel_2 = saltstat.median(overx_val_2,logfile)
imagedata1 -= overlevel_1
imagedata2 -= overlevel_2
# trim overscan
if (status == 0):
imagedata1 = imagedata1[dy1_1:dy2_1,dx1_1:dx2_1]
imagedata2 = imagedata2[dy1_2:dy2_2,dx1_2:dx2_2]
datasec = '[1:'+str(dx2_1-dx1_1)+',1:'+str(dy2_1-dy1_1)+']'
status = saltkey.put('DATASEC',datasec,struct[hdu],infile,logfile)
status = saltkey.rem('BIASSEC',struct[hdu],infile,logfile)
datasec = '[1:'+str(dx2_2-dx1_2)+',1:'+str(dy2_2-dy1_2)+']'
status = saltkey.put('DATASEC',datasec,struct[hdu+1],infile,logfile)
status = saltkey.rem('BIASSEC',struct[hdu+1],infile,logfile)
# log coefficient table
if (status == 0):
infilename = infile.split('/')
infilename = infilename[len(infilename)-1]
message = '%25s[%3d] %5.2f %4d %8.6f' % \
(infilename, hdu, gain1, overlevel_1, float(xcoeff[amplifier+1]))
saltprint.log(logfile,message,verbose)
message = '%25s[%3d] %5.2f %4d %8.6f' % \
(infilename, hdu+1, gain2, overlevel_2,float(xcoeff[amplifier]))
saltprint.log(logfile,message,verbose)
# update image in HDU structure
if (status == 0):
struct,status = saltio.writeimage(struct,hdu,imagedata1,logfile)
struct,status = saltio.writeimage(struct,hdu+1,imagedata2,logfile)
return struct, status
def make_mosaic(struct,
gap,
xshift,
yshift,
rotation,
interp_type='linear',
boundary='constant',
constant=0,
geotran=True,
fill=False,
cleanup=True,
log=None,
verbose=False):
"""Given a SALT image struct, combine each of the individual amplifiers and
apply the geometric CCD transformations to the image
"""
# get the name of the file
infile = saltkey.getimagename(struct[0], base=True)
outpath = './'
# identify instrument
instrume, keyprep, keygain, keybias, keyxtalk, keyslot = \
saltkey.instrumid(struct)
# how many amplifiers?
nsciext = saltkey.get('NSCIEXT', struct[0])
nextend = saltkey.get('NEXTEND', struct[0])
nccds = saltkey.get('NCCDS', struct[0])
amplifiers = nccds * 2
if nextend > nsciext:
varframe = True
else:
varframe = False
# CCD geometry coefficients
if (instrume == 'RSS' or instrume == 'PFIS'):
xsh = [0., xshift[0], 0., xshift[1]]
ysh = [0., yshift[0], 0., yshift[1]]
rot = [0., rotation[0], 0., rotation[1]]
elif instrume == 'SALTICAM':
xsh = [0., xshift[0], 0.]
ysh = [0., yshift[0], 0.]
rot = [0., rotation[0], 0]
# how many extensions?
nextend = saltkey.get('NEXTEND', struct[0])
# CCD on-chip binning
xbin, ybin = saltkey.ccdbin(struct[0])
# create temporary primary extension
outstruct = []
outstruct.append(struct[0])
# define temporary FITS file store tiled CCDs
tilefile = saltio.tmpfile(outpath)
tilefile += 'tile.fits'
if varframe:
tilehdu = [None] * (3 * int(nsciext / 2) + 1)
else:
tilehdu = [None] * int(nsciext / 2 + 1)
tilehdu[0] = fits.PrimaryHDU()
#tilehdu[0].header = struct[0].header
if log:
log.message('', with_stdout=verbose)
# iterate over amplifiers, stich them to produce file of CCD images
for i in range(int(nsciext / 2)):
hdu = i * 2 + 1
# amplifier = hdu%amplifiers
# if (amplifier == 0): amplifier = amplifiers
# read DATASEC keywords
datasec1 = saltkey.get('DATASEC', struct[hdu])
datasec2 = saltkey.get('DATASEC', struct[hdu + 1])
xdsec1, ydsec1 = saltstring.secsplit(datasec1)
xdsec2, ydsec2 = saltstring.secsplit(datasec2)
# read images
imdata1 = saltio.readimage(struct, hdu)
imdata2 = saltio.readimage(struct, hdu + 1)
# tile 2n amplifiers to yield n CCD images
outdata = numpy.zeros(
(int(ydsec1[1] + abs(ysh[i + 1] / ybin)),
int(xdsec1[1] + xdsec2[1] + abs(xsh[i + 1] / xbin))),
numpy.float32)
# set up the variance frame
if varframe:
vardata = outdata.copy()
vdata1 = saltio.readimage(struct, struct[hdu].header['VAREXT'])
vdata2 = saltio.readimage(struct, struct[hdu + 1].header['VAREXT'])
bpmdata = outdata.copy()
bdata1 = saltio.readimage(struct, struct[hdu].header['BPMEXT'])
bdata2 = saltio.readimage(struct, struct[hdu + 1].header['BPMEXT'])
x1 = xdsec1[0] - 1
if x1 != 0:
msg = 'The data in %s have not been trimmed prior to mosaicking.' \
% infile
log.error(msg)
if xsh[i + 1] < 0:
x1 += int(abs(xsh[i + 1] / xbin))
x2 = x1 + xdsec1[1]
y1 = ydsec1[0] - 1
if ysh[i + 1] < 0:
y1 += int(abs(ysh[i + 1] / ybin))
y2 = y1 + ydsec1[1]
outdata[y1:y2, x1:x2] =\
imdata1[ydsec1[0] - 1:ydsec1[1], xdsec1[0] - 1:xdsec1[1]]
if varframe:
vardata[y1:y2, x1:x2] =\
vdata1[ydsec1[0] - 1:ydsec1[1], xdsec1[0] - 1:xdsec1[1]]
bpmdata[y1:y2, x1:x2] =\
bdata1[ydsec1[0] - 1:ydsec1[1], xdsec1[0] - 1:xdsec1[1]]
x1 = x2
x2 = x1 + xdsec2[1]
y1 = ydsec2[0] - 1
if ysh[i + 1] < 0:
y1 += abs(ysh[i + 1] / ybin)
y2 = y1 + ydsec2[1]
outdata[y1:y2, x1:x2] =\
imdata2[ydsec1[0] - 1:ydsec1[1], xdsec1[0] - 1:xdsec1[1]]
if varframe:
vardata[y1:y2, x1:x2] =\
vdata2[ydsec1[0] - 1:ydsec1[1], xdsec1[0] - 1:xdsec1[1]]
bpmdata[y1:y2, x1:x2] =\
bdata2[ydsec1[0] - 1:ydsec1[1], xdsec1[0] - 1:xdsec1[1]]
# size of new image
naxis1 = str(xdsec1[1] + xdsec2[1])
naxis2 = str(ydsec1[1])
# add image and keywords to HDU list
tilehdu[i + 1] = fits.ImageHDU(outdata)
tilehdu[i + 1].header = struct[hdu].header
#tilehdu[
# i + 1].header['DATASEC'] = '[1:' + naxis1 + ',1:' + naxis2 + ']'
if varframe:
vext = i + 1 + int(nsciext / 2.)
tilehdu[vext] = fits.ImageHDU(vardata)
#tilehdu[vext].header = struct[struct[hdu].header['VAREXT']].header
#tilehdu[vext].header[
# 'DATASEC'] = '[1:' + naxis1 + ',1:' + naxis2 + ']'
bext = i + 1 + 2 * int(nsciext / 2.)
tilehdu[bext] = fits.ImageHDU(bpmdata)
#tilehdu[bext].header = struct[struct[hdu].header['BPMEXT']].header
#tilehdu[bext].header[
# 'DATASEC'] = '[1:' + naxis1 + ',1:' + naxis2 + ']'
# image tile log message #1
if log:
message = os.path.basename(infile) + '[' + str(hdu) + ']['
message += str(xdsec1[0]) + ':' + str(xdsec1[1]) + ','
message += str(ydsec1[0]) + ':' + str(ydsec1[1]) + '] --> '
message += os.path.basename(tilefile) + '[' + str(i + 1) + ']['
message += str(xdsec1[0]) + ':' + str(xdsec1[1]) + ','
message += str(ydsec1[0]) + ':' + str(ydsec1[1]) + ']'
log.message(message, with_stdout=verbose, with_header=False)
message = os.path.basename(infile) + '[' + str(hdu + 1) + ']['
message += str(xdsec1[0]) + ':' + str(xdsec1[1]) + ','
message += str(ydsec1[0]) + ':' + str(ydsec1[1]) + '] --> '
message += os.path.basename(tilefile) + '[' + str(i + 1) + ']['
message += str(xdsec1[1] + 1) + ':' + \
str(xdsec1[1] + xdsec2[1]) + ','
message += str(ydsec2[0]) + ':' + str(ydsec2[1]) + ']'
log.message(message, with_stdout=verbose, with_header=False)
# write temporary file of tiled CCDs
hdulist = fits.HDUList(tilehdu)
hdulist.writeto(tilefile)
# iterate over CCDs, transform and rotate images
yrot = [None] * 4
xrot = [None] * 4
tranfile = [' ']
tranhdu = [0]
if varframe:
tranfile = [''] * (3 * int(nsciext / 2) + 1)
tranhdu = [0] * (3 * int(nsciext / 2) + 1)
else:
tranfile = [''] * int(nsciext / 2 + 1)
tranhdu = [0] * int(nsciext / 2 + 1)
# this is hardwired for SALT where the second CCD is considered the
# fiducial
for hdu in range(1, int(nsciext / 2 + 1)):
tranfile[hdu] = saltio.tmpfile(outpath)
tranfile[hdu] += 'tran.fits'
if varframe:
tranfile[hdu + nccds] = saltio.tmpfile(outpath) + 'tran.fits'
tranfile[hdu + 2 * nccds] = saltio.tmpfile(outpath) + 'tran.fits'
ccd = hdu % nccds
if (ccd == 0):
ccd = nccds
# correct rotation for CCD binning
yrot[ccd] = rot[ccd] * ybin / xbin
xrot[ccd] = rot[ccd] * xbin / ybin
dxshift = xbin * int(float(int(gap) / xbin) + 0.5) - gap
# transformation using geotran IRAF task
# if (ccd == 1):
if (ccd != 2):
if geotran:
message = '\nSALTMOSAIC -- geotran ' + tilefile + \
'[' + str(ccd) + '] ' + tranfile[hdu]
message += ' \"\" \"\" xshift=' + \
str((xsh[ccd] + (2 - ccd) * dxshift) / xbin) + ' '
message += 'yshift=' + \
str(ysh[ccd] / ybin) + ' xrotation=' + str(xrot[ccd]) + ' '
message += 'yrotation=' + \
str(yrot[ccd]) + ' xmag=1 ymag=1 xmin=\'INDEF\''
message += 'xmax=\'INDEF\' ymin=\'INDEF\' ymax=\'INDEF\' '
message += 'ncols=\'INDEF\' '
message += 'nlines=\'INDEF\' verbose=\'no\' '
message += 'fluxconserve=\'yes\' nxblock=2048 '
message += 'nyblock=2048 interpolant=\'' + \
interp_type + '\' boundary=\'constant\' constant=0'
log.message(message, with_stdout=verbose)
yd, xd = tilehdu[ccd].data.shape
ncols = 'INDEF' # ncols=xd+abs(xsh[ccd]/xbin)
nlines = 'INDEF' # nlines=yd+abs(ysh[ccd]/ybin)
geo_xshift = xsh[ccd] + (2 - ccd) * dxshift / xbin
geo_yshift = ysh[ccd] / ybin
iraf.images.immatch.geotran(tilefile + "[" + str(ccd) + "]",
tranfile[hdu],
"",
"",
xshift=geo_xshift,
yshift=geo_yshift,
xrotation=xrot[ccd],
yrotation=yrot[ccd],
xmag=1,
ymag=1,
xmin='INDEF',
xmax='INDEF',
ymin='INDEF',
ymax='INDEF',
ncols=ncols,
nlines=nlines,
verbose='no',
fluxconserve='yes',
nxblock=2048,
nyblock=2048,
interpolant="linear",
boundary="constant",
constant=0)
if varframe:
var_infile = tilefile + "[" + str(ccd + nccds) + "]"
iraf.images.immatch.geotran(var_infile,
tranfile[hdu + nccds],
"",
"",
xshift=geo_xshift,
yshift=geo_yshift,
xrotation=xrot[ccd],
yrotation=yrot[ccd],
xmag=1,
ymag=1,
xmin='INDEF',
xmax='INDEF',
ymin='INDEF',
ymax='INDEF',
ncols=ncols,
nlines=nlines,
verbose='no',
fluxconserve='yes',
nxblock=2048,
nyblock=2048,
interpolant="linear",
boundary="constant",
constant=0)
var2_infile = tilefile + "[" + str(ccd + 2 * nccds) + "]"
iraf.images.immatch.geotran(var2_infile,
tranfile[hdu + 2 * nccds],
"",
"",
xshift=geo_xshift,
yshift=geo_yshift,
xrotation=xrot[ccd],
yrotation=yrot[ccd],
xmag=1,
ymag=1,
xmin='INDEF',
xmax='INDEF',
ymin='INDEF',
ymax='INDEF',
ncols=ncols,
nlines=nlines,
verbose='no',
fluxconserve='yes',
nxblock=2048,
nyblock=2048,
interpolant="linear",
boundary="constant",
constant=0)
# open the file and copy the data to tranhdu
tstruct = fits.open(tranfile[hdu])
tranhdu[hdu] = tstruct[0].data
tstruct.close()
if varframe:
tranhdu[hdu + nccds] = fits.open(tranfile[hdu +
nccds])[0].data
tranhdu[hdu + 2 * nccds] = fits.open(
tranfile[hdu + 2 * nccds])[0].data
else:
log.message("Transform CCD #%i using dx=%s, dy=%s, rot=%s" %
(ccd, xsh[ccd] / 2.0, ysh[ccd] / 2.0, xrot[ccd]),
with_stdout=verbose,
with_header=False)
tranhdu[hdu] = geometric_transform(
tilehdu[ccd].data,
tran_func,
prefilter=False,
order=1,
extra_arguments=(xsh[ccd] / 2, ysh[ccd] / 2, 1, 1,
xrot[ccd], yrot[ccd]))
tstruct = fits.PrimaryHDU(tranhdu[hdu])
tstruct.writeto(tranfile[hdu])
if varframe:
tranhdu[hdu + nccds] = geometric_transform(
tilehdu[hdu + 3].data,
tran_func,
prefilter=False,
order=1,
extra_arguments=(xsh[ccd] / 2, ysh[ccd] / 2, 1, 1,
xrot[ccd], yrot[ccd]))
tranhdu[hdu + 2 * nccds] = geometric_transform(
tilehdu[hdu + 6].data,
tran_func,
prefilter=False,
order=1,
extra_arguments=(xsh[ccd] / 2, ysh[ccd] / 2, 1, 1,
xrot[ccd], yrot[ccd]))
else:
log.message("Transform CCD #%i using dx=%s, dy=%s, rot=%s" %
(ccd, 0, 0, 0),
with_stdout=verbose,
with_header=False)
tranhdu[hdu] = tilehdu[ccd].data
if varframe:
tranhdu[hdu + nccds] = tilehdu[ccd + nccds].data
tranhdu[hdu + 2 * nccds] = tilehdu[ccd + 2 * nccds].data
# open outfile
if varframe:
outlist = 4 * [None]
else:
outlist = 2 * [None]
#outlist[0] = struct[0].copy()
outlist[0] = fits.PrimaryHDU()
outlist[0].header = struct[0].header
naxis1 = int(gap / xbin * (nccds - 1))
naxis2 = 0
for i in range(1, nccds + 1):
yw, xw = tranhdu[i].shape
naxis1 += xw + int(abs(xsh[ccd] / xbin)) + 1
naxis2 = max(naxis2, yw)
outdata = numpy.zeros((naxis2, naxis1), numpy.float32)
outdata.shape = naxis2, naxis1
if varframe:
vardata = outdata * 0
bpmdata = outdata * 0 + 1
# iterate over CCDs, stich them to produce a full image
hdu = 0
totxshift = 0
for hdu in range(1, nccds + 1):
# read DATASEC keywords
ydsec, xdsec = tranhdu[hdu].shape
# define size and shape of final image
# tile CCDs to yield mosaiced image
x1 = int((hdu - 1) * (xdsec + gap / xbin)) + int(totxshift)
x2 = xdsec + x1
y1 = int(0)
y2 = int(ydsec)
outdata[y1:y2, x1:x2] = tranhdu[hdu]
totxshift += int(abs(xsh[hdu] / xbin)) + 1
if varframe:
vardata[y1:y2, x1:x2] = tranhdu[hdu + nccds]
bpmdata[y1:y2, x1:x2] = tranhdu[hdu + 2 * nccds]
# make sure to cover up all the gaps include bad areas
if varframe:
baddata = (outdata == 0)
baddata = nd.maximum_filter(baddata, size=3)
bpmdata[baddata] = 1
# fill in the gaps if requested
if fill:
if varframe:
outdata = fill_gaps(outdata, 0)
else:
outdata = fill_gaps(outdata, 0)
# add to the file
outlist[1] = fits.ImageHDU(outdata)
if varframe:
outlist[2] = fits.ImageHDU(vardata, name='VAR')
outlist[3] = fits.ImageHDU(bpmdata, name='BPM')
# create the image structure
outstruct = fits.HDUList(outlist)
# update the head informaation
# housekeeping keywords
saltkey.put('NEXTEND', 2, outstruct[0])
saltkey.new('EXTNAME', 'SCI', 'Extension name', outstruct[1])
saltkey.new('EXTVER', 1, 'Extension number', outstruct[1])
if varframe:
saltkey.new('VAREXT', 2, 'Variance frame extension', outstruct[1])
saltkey.new('BPMEXT', 3, 'BPM Extension', outstruct[1])
try:
saltkey.copy(struct[1], outstruct[1], 'CCDSUM')
except:
pass
# Add keywords associated with geometry
saltkey.new('SGEOMGAP', gap, 'SALT Chip Gap', outstruct[0])
c1str = '{:3.2f} {:3.2f} {:3.4f}'.format(xshift[0], yshift[0], rotation[0])
saltkey.new('SGEOM1', c1str, 'SALT Chip 1 Transform', outstruct[0])
c2str = '{:3.2f} {:3.2f} {:3.4f}'.format(xshift[1], yshift[1], rotation[1])
saltkey.new('SGEOM2', c2str, 'SALT Chip 2 Transform', outstruct[0])
# WCS keywords
saltkey.new('CRPIX1', 0, 'WCS: X reference pixel', outstruct[1])
saltkey.new('CRPIX2', 0, 'WCS: Y reference pixel', outstruct[1])
saltkey.new('CRVAL1', float(xbin), 'WCS: X reference coordinate value',
outstruct[1])
saltkey.new('CRVAL2', float(ybin), 'WCS: Y reference coordinate value',
outstruct[1])
saltkey.new('CDELT1', float(xbin), 'WCS: X pixel size', outstruct[1])
saltkey.new('CDELT2', float(ybin), 'WCS: Y pixel size', outstruct[1])
saltkey.new('CTYPE1', 'pixel', 'X type', outstruct[1])
saltkey.new('CTYPE2', 'pixel', 'Y type', outstruct[1])
# cleanup temporary files
if cleanup:
for tfile in tranfile:
if os.path.isfile(tfile):
saltio.delete(tfile)
if os.path.isfile(tilefile):
status = saltio.delete(tilefile)
# return the file
return outstruct
def slot(struct, infile, dbspeed, dbrate, dbgain, dbnoise, dbbias, dbamp,
xcoeff, gaindb, xtalkfile, logfile, verbose):
import saltprint, saltkey, saltio, saltstat, time
# identify instrument
instrume, keyprep, keygain, keybias, keyxtalk, keyslot, status = saltkey.instrumid(
struct, infile, logfile)
# number of image HDU
nextend = 0
while (status == 0):
try:
struct[nextend + 1].header['XTENSION']
nextend += 1
except:
break
nccds, status = saltkey.get('NCCDS', struct[0], infile, logfile)
amplifiers = nccds * 2
if (nextend % (amplifiers) != 0):
message = '\nERROR -- SALTSLOT: Number of image extensions and'
message += 'number of amplifiers are not consistent'
status = saltprint.err(saltlog, message)
status = saltkey.new('NSCIEXT', nextend, 'Number of science extensions',
struct[0], infile, logfile)
status = saltkey.new('NEXTEND', nextend, 'Number of data extensions',
struct[0], infile, logfile)
# check image file and gain database are compatible
if (status == 0):
ngains = len(dbgain)
if (int(max(dbamp)) != amplifiers):
message = '\nERROR -- SALTGSLOT: ' + infile + ' contains ' + str(
amplifiers) + ' amplifiers'
message += ', the gaindb file ' + gaindb + ' contains ' + str(
max(dbamp)) + ' amplifiers'
status = saltprint.err(logfile, message)
# check image file and cross talk database are compatible
if (status == 0):
if (len(xcoeff) - 1 != amplifiers):
message = '\nERROR -- SALTSLOT: ' + infile + ' contains ' + str(
amplifiers) + ' amplifiers'
message += ', the cross talk file ' + xtalkfile + ' contains ' + str(
len(xcoeff) - 1) + ' amplifiers'
status = saltprint.err(logfile, message)
# housekeeping keywords
if (status == 0):
status = saltkey.put('SAL-TLM', time.asctime(time.localtime()),
struct[0], infile, logfile)
status = saltkey.new(keyslot, time.asctime(time.localtime()),
'Data have been cleaned by SALTSLOT', struct[0],
infile, logfile)
# keywords for image extensions
for i in range(nextend):
hdu = i + 1
status = saltkey.new('EXTNAME', 'SCI', 'Extension name', struct[hdu],
infile, logfile)
status = saltkey.new('EXTVER', hdu, 'Extension number', struct[hdu],
infile, logfile)
# log coefficent table
if (status == 0):
message = '%30s %5s %4s %8s' % ('HDU', 'Gain', 'Bias', 'Xtalk')
saltprint.log(logfile,
'\n ---------------------------------------------',
verbose)
saltprint.log(logfile, message, verbose)
saltprint.log(logfile,
' ---------------------------------------------',
verbose)
# loop over image extensions
if (status == 0):
for i in range(nextend / 2):
hdu = i * 2 + 1
amplifier = hdu % amplifiers
if (amplifier == 0): amplifier = amplifiers
if (status == 0):
value, status = saltkey.get('NAXIS1', struct[hdu], infile,
logfile)
naxis1 = int(value)
if (status == 0):
value, status = saltkey.get('NAXIS1', struct[hdu + 1], infile,
logfile)
naxis2 = int(value)
if (status == 0 and hdu == 1):
biassec, status = saltkey.get('BIASSEC', struct[hdu], infile,
logfile)
if (status == 0 and hdu == 1):
ranges = biassec.lstrip('[').rstrip(']').split(',')
x1_1 = int(ranges[0].split(':')[0]) - 1
x2_1 = int(ranges[0].split(':')[1]) - 1
y1_1 = int(ranges[1].split(':')[0]) - 1
y2_1 = int(ranges[1].split(':')[1]) - 1
if (status == 0 and hdu == 1):
biassec, status = saltkey.get('BIASSEC', struct[hdu + 1],
infile, logfile)
if (status == 0 and hdu == 1):
ranges = biassec.lstrip('[').rstrip(']').split(',')
x1_2 = int(ranges[0].split(':')[0]) - 1
x2_2 = int(ranges[0].split(':')[1]) - 1
y1_2 = int(ranges[1].split(':')[0]) - 1
y2_2 = int(ranges[1].split(':')[1]) - 1
if (status == 0 and hdu == 1):
datasec, status = saltkey.get('DATASEC', struct[hdu], infile,
logfile)
if (status == 0 and hdu == 1):
ranges = datasec.lstrip('[').rstrip(']').split(',')
dx1_1 = int(ranges[0].split(':')[0]) - 1
dx2_1 = int(ranges[0].split(':')[1])
dy1_1 = int(ranges[1].split(':')[0]) - 1
dy2_1 = int(ranges[1].split(':')[1])
if (status == 0 and hdu == 1):
datasec, status = saltkey.get('DATASEC', struct[hdu + 1],
infile, logfile)
if (status == 0 and hdu == 1):
ranges = datasec.lstrip('[').rstrip(']').split(',')
dx1_2 = int(ranges[0].split(':')[0]) - 1
dx2_2 = int(ranges[0].split(':')[1])
dy1_2 = int(ranges[1].split(':')[0]) - 1
dy2_2 = int(ranges[1].split(':')[1])
if (status == 0 and dx2_1 - dx1_1 != dx2_2 - dx1_2):
message = 'ERROR -- SALTSLOT: HDUs ' + infile
message += '[' + str(hdu) + '] and ' + infile + '[' + str(
hdu + 1) + ']'
message += ' have different dimensions'
status = saltprint.err(logfile, message)
# read speed and gain of each exposure
if (status == 0 and hdu == 1):
gainset, status = saltkey.get('GAINSET', struct[0], infile,
logfile)
rospeed, status = saltkey.get('ROSPEED', struct[0], infile,
logfile)
if (rospeed == 'NONE'):
saltprint.log(logfile, " ", verbose)
message = "ERROR -- SALTSLOT: Readout speed is 'NONE' in "
message += "primary keywords of " + infile
status = saltprint.err(logfile, message)
# read raw images
if (status == 0):
imagedata1, status = saltio.readimage(struct, hdu, logfile)
imagedata2, status = saltio.readimage(struct, hdu + 1, logfile)
# gain correction
if (status == 0):
for j in range(len(dbgain)):
if (gainset == dbrate[j] and rospeed == dbspeed[j]
and amplifier == int(dbamp[j])):
try:
gain1 = float(dbgain[j])
imagedata1 *= gain1
except:
mesage = 'ERROR -- SALTSLOT: Cannot perform gain correction on image '
message += infile + '[' + str(hdu) + ']'
status = saltprint.err(logfile, message)
elif (gainset == dbrate[j] and rospeed == dbspeed[j]
and amplifier + 1 == int(dbamp[j])):
try:
gain2 = float(dbgain[j])
imagedata2 *= gain2
except:
mesage = 'ERROR -- SALTSLOT: Cannot perform gain correction on image '
message += infile + '[' + str(hdu + 1) + ']'
status = saltprint.err(logfile, message)
# crosstalk correction
if (status == 0):
revimage1 = imagedata1 * float(xcoeff[amplifier])
revimage2 = imagedata2 * float(xcoeff[amplifier + 1])
for j in range(dx2_1 - dx1_1 + 1):
imagedata1[:, j] -= revimage2[:, dx2_2 - j - 1]
imagedata2[:, j] -= revimage1[:, dx2_1 - j - 1]
# bias subtraction
if (status == 0):
overx_val_1 = []
overx_val_2 = []
for x in range(x1_1, x2_1 + 1):
list_1 = imagedata1[y1_1:y2_1, x] * 1.0
overx_val_1.append(saltstat.median(list_1, logfile))
overlevel_1 = saltstat.median(overx_val_1, logfile)
for x in range(x1_2, x2_2 + 1):
list_2 = imagedata2[y1_2:y2_2, x] * 1.0
overx_val_2.append(saltstat.median(list_2, logfile))
overlevel_2 = saltstat.median(overx_val_2, logfile)
imagedata1 -= overlevel_1
imagedata2 -= overlevel_2
# trim overscan
if (status == 0):
imagedata1 = imagedata1[dy1_1:dy2_1, dx1_1:dx2_1]
imagedata2 = imagedata2[dy1_2:dy2_2, dx1_2:dx2_2]
datasec = '[1:' + str(dx2_1 - dx1_1) + ',1:' + str(dy2_1 -
dy1_1) + ']'
status = saltkey.put('DATASEC', datasec, struct[hdu], infile,
logfile)
status = saltkey.rem('BIASSEC', struct[hdu], infile, logfile)
datasec = '[1:' + str(dx2_2 - dx1_2) + ',1:' + str(dy2_2 -
dy1_2) + ']'
status = saltkey.put('DATASEC', datasec, struct[hdu + 1],
infile, logfile)
status = saltkey.rem('BIASSEC', struct[hdu + 1], infile,
logfile)
# log coefficient table
if (status == 0):
infilename = infile.split('/')
infilename = infilename[len(infilename) - 1]
message = '%25s[%3d] %5.2f %4d %8.6f' % \
(infilename, hdu, gain1, overlevel_1, float(xcoeff[amplifier+1]))
saltprint.log(logfile, message, verbose)
message = '%25s[%3d] %5.2f %4d %8.6f' % \
(infilename, hdu+1, gain2, overlevel_2,float(xcoeff[amplifier]))
saltprint.log(logfile, message, verbose)
# update image in HDU structure
if (status == 0):
struct, status = saltio.writeimage(struct, hdu, imagedata1,
logfile)
struct, status = saltio.writeimage(struct, hdu + 1, imagedata2,
logfile)
return struct, status
