def slotmerge(images, outimages, outpref, geomfile, clobber, logfile, verbose):
with logging(logfile, debug) as log:
# are the arguments defined
saltsafeio.argdefined('images', images)
saltsafeio.argdefined('geomfile', geomfile)
saltsafeio.argdefined('logfile', logfile)
# if the input file is a list, does it exist?
if images[0] == '@':
saltsafeio.listexists('Input', images)
# parse list of input files
infiles = saltsafeio.listparse('Raw image', images, '', '', '')
# check input files exist
saltsafeio.filesexist(infiles, '', 'r')
# load output name list: @list, * and comma separated
outimages = outimages.strip()
outpref = outpref.strip()
if len(outpref) == 0 and len(outimages) == 0:
raise SaltIOError('Output file(s) not specified')
# test output @filelist exists
if len(outimages) > 0 and outimages[0] == '@':
saltsafeio.listexists('Output', outimages)
# parse list of output files
outfiles = saltsafeio.listparse('Output image', outimages, outpref,
infiles, '')
# are input and output lists the same length?
saltsafeio.comparelists(infiles, outfiles, 'Input', 'output')
# do the output files already exist?
if not clobber:
saltsafeio.filesexist(outfiles, '', 'w')
# does CCD geometry definition file exist
geomfilefile = geomfile.strip()
saltsafeio.fileexists(geomfile)
# read geometry definition file
gap = 0
xshift = [0, 0]
yshift = [0, 0]
rotation = [0, 0]
gap, xshift, yshift, rotation = saltsafeio.readccdgeom(geomfile)
for ro in rotation:
if ro != 0:
log.warning('SLOTMERGE currently ignores CCD rotation')
# Begin processes each file
for infile, outfile in zip(infiles, outfiles):
# determine the name for the output file
outpath = outfile.rstrip(os.path.basename(outfile))
if (len(outpath) == 0):
outpath = '.'
# open each raw image
struct = saltsafeio.openfits(infile)
# identify instrument
instrume, keyprep, keygain, keybias, keyxtalk, keyslot = saltsafekey.instrumid(
struct, infile)
# how many amplifiers?
nccds = saltsafekey.get('NCCDS', struct[0], infile)
amplifiers = nccds * 2
#if (nccds != 2):
# raise SaltError('Can not currently handle more than two CCDs')
# CCD geometry coefficients
if instrume == 'RSS' or instrume == 'PFIS':
xsh = [xshift[0], 0., xshift[1]]
ysh = [yshift[0], 0., yshift[1]]
rot = [rotation[0], 0., rotation[1]]
refid = 1
if instrume == 'SALTICAM':
xsh = [xshift[0], 0.]
ysh = [yshift[0], 0.]
rot = [rotation[0], 0]
refid = 1
# how many extensions?
nextend = saltsafekey.get('NEXTEND', struct[0], infile)
# how many exposures
exposures = nextend / amplifiers
# CCD on-chip binning
xbin, ybin = saltsafekey.ccdbin(struct[0], infile)
gp = int(gap / xbin)
# create output hdu structure
outstruct = [None] * int(exposures + 1)
outstruct[0] = struct[0]
# iterate over exposures, stitch them to produce file of CCD images
for i in range(exposures):
# Determine the total size of the image
xsize = 0
ysize = 0
for j in range(amplifiers):
hdu = i * amplifiers + j + 1
try:
xsize += len(struct[hdu].data[0])
if ysize < len(struct[hdu].data):
ysize = len(struct[hdu].data)
except:
msg = 'Unable to access extension %i ' % hdu
raise SaltIOError(msg)
xsize += gp * (nccds - 1)
maxxsh, minxsh = determineshifts(xsh)
maxysh, minysh = determineshifts(ysh)
xsize += (maxxsh - minxsh)
ysize += (maxysh - minysh)
# Determine the x and y origins for each frame
xdist = 0
ydist = 0
shid = 0
x0 = np.zeros(amplifiers)
y0 = np.zeros(amplifiers)
for j in range(amplifiers):
x0[j] = xdist + xsh[shid] - minxsh
y0[j] = ysh[shid] - minysh
hdu = i * amplifiers + j + 1
darr = struct[hdu].data
xdist += len(darr[0])
if j % 2 == 1:
xdist += gp
shid += 1
# make the out image
outarr = np.zeros((ysize, xsize), np.float64)
# Embed each frame into the output array
for j in range(amplifiers):
hdu = i * amplifiers + j + 1
darr = struct[hdu].data
outarr = salttran.embed(darr, x0[j], y0[j], outarr)
# Add the outimage to the output structure
hdu = i * amplifiers + 1
outhdu = i + 1
outstruct[outhdu] = pyfits.ImageHDU(outarr)
outstruct[outhdu].header = struct[hdu].header
# Fix the headers in each extension
datasec = '[1:%4i,1:%4i]' % (xsize, ysize)
saltsafekey.put('DATASEC', datasec, outstruct[outhdu], outfile)
saltsafekey.rem('DETSIZE', outstruct[outhdu], outfile)
saltsafekey.rem('DETSEC', outstruct[outhdu], outfile)
saltsafekey.rem('CCDSEC', outstruct[outhdu], outfile)
saltsafekey.rem('AMPSEC', outstruct[outhdu], outfile)
# add housekeeping key words
outstruct[outhdu] = addhousekeeping(outstruct[outhdu], outhdu,
outfile)
# close input FITS file
saltsafeio.closefits(struct)
# housekeeping keywords
keymosaic = 'SLOTMERG'
fname, hist = history(level=1, wrap=False)
saltsafekey.housekeeping(struct[0], keymosaic,
'Amplifiers have been mosaiced', hist)
#saltsafekey.history(outstruct[0],hist)
# this is added for later use by
saltsafekey.put('NCCDS', 0.5, outstruct[0])
saltsafekey.put('NSCIEXT', exposures, outstruct[0])
saltsafekey.put('NEXTEND', exposures, outstruct[0])
# write FITS file of mosaiced image
outstruct = pyfits.HDUList(outstruct)
saltsafeio.writefits(outstruct, outfile, clobber=clobber)
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 slotmerge(images,outimages,outpref,geomfile,clobber,logfile,verbose):
with logging(logfile,debug) as log:
# are the arguments defined
saltsafeio.argdefined('images',images)
saltsafeio.argdefined('geomfile',geomfile)
saltsafeio.argdefined('logfile',logfile)
# if the input file is a list, does it exist?
if images[0] == '@':
saltsafeio.listexists('Input',images)
# parse list of input files
infiles=saltsafeio.listparse('Raw image',images,'','','')
# check input files exist
saltsafeio.filesexist(infiles,'','r')
# load output name list: @list, * and comma separated
outimages = outimages.strip()
outpref = outpref.strip()
if len(outpref) == 0 and len(outimages) == 0:
raise SaltIOError('Output file(s) not specified')
# test output @filelist exists
if len(outimages) > 0 and outimages[0] == '@':
saltsafeio.listexists('Output',outimages)
# parse list of output files
outfiles=saltsafeio.listparse('Output image',outimages,outpref,infiles,'')
# are input and output lists the same length?
saltsafeio.comparelists(infiles,outfiles,'Input','output')
# do the output files already exist?
if not clobber:
saltsafeio.filesexist(outfiles,'','w')
# does CCD geometry definition file exist
geomfilefile = geomfile.strip()
saltsafeio.fileexists(geomfile)
# read geometry definition file
gap = 0
xshift = [0, 0]
yshift = [0, 0]
rotation = [0, 0]
gap, xshift, yshift, rotation=saltsafeio.readccdgeom(geomfile)
for ro in rotation:
if ro!=0:
log.warning('SLOTMERGE currently ignores CCD rotation')
# Begin processes each file
for infile, outfile in zip(infiles, outfiles):
# determine the name for the output file
outpath = outfile.rstrip(os.path.basename(outfile))
if (len(outpath) == 0):
outpath = '.'
# open each raw image
struct=saltsafeio.openfits(infile)
# identify instrument
instrume,keyprep,keygain,keybias,keyxtalk,keyslot=saltsafekey.instrumid(struct,infile)
# how many amplifiers?
nccds=saltsafekey.get('NCCDS',struct[0],infile)
amplifiers = nccds * 2
#if (nccds != 2):
# raise SaltError('Can not currently handle more than two CCDs')
# CCD geometry coefficients
if instrume == 'RSS' or instrume == 'PFIS':
xsh = [xshift[0], 0., xshift[1]]
ysh = [yshift[0], 0., yshift[1]]
rot = [rotation[0], 0., rotation[1]]
refid = 1
if instrume == 'SALTICAM':
xsh = [xshift[0], 0.]
ysh = [yshift[0], 0.]
rot = [rotation[0], 0]
refid = 1
# how many extensions?
nextend=saltsafekey.get('NEXTEND',struct[0],infile)
# how many exposures
exposures = nextend/amplifiers
# CCD on-chip binning
xbin, ybin=saltsafekey.ccdbin(struct[0],infile)
gp = int(gap / xbin)
# create output hdu structure
outstruct = [None] * int(exposures+1)
outstruct[0]=struct[0]
# iterate over exposures, stitch them to produce file of CCD images
for i in range(exposures):
# Determine the total size of the image
xsize=0
ysize=0
for j in range(amplifiers):
hdu=i*amplifiers+j+1
try:
xsize += len(struct[hdu].data[0])
if ysize < len(struct[hdu].data):
ysize=len(struct[hdu].data)
except:
msg='Unable to access extension %i ' % hdu
raise SaltIOError(msg)
xsize += gp* (nccds-1)
maxxsh, minxsh = determineshifts(xsh)
maxysh, minysh = determineshifts(ysh)
xsize += (maxxsh-minxsh)
ysize += (maxysh-minysh)
# Determine the x and y origins for each frame
xdist=0
ydist=0
shid=0
x0=np.zeros(amplifiers)
y0=np.zeros(amplifiers)
for j in range(amplifiers):
x0[j]=xdist+xsh[shid]-minxsh
y0[j]=ysh[shid]-minysh
hdu=i*amplifiers+j+1
darr=struct[hdu].data
xdist += len(darr[0])
if j%2==1:
xdist += gp
shid += 1
# make the out image
outarr=np.zeros((ysize, xsize), np.float64)
# Embed each frame into the output array
for j in range(amplifiers):
hdu=i*amplifiers+j+1
darr=struct[hdu].data
outarr=salttran.embed(darr, x0[j], y0[j], outarr)
# Add the outimage to the output structure
hdu=i*amplifiers+1
outhdu=i+1
outstruct[outhdu] = pyfits.ImageHDU(outarr)
outstruct[outhdu].header=struct[hdu].header
# Fix the headers in each extension
datasec='[1:%4i,1:%4i]' % (xsize, ysize)
saltsafekey.put('DATASEC',datasec, outstruct[outhdu], outfile)
saltsafekey.rem('DETSIZE',outstruct[outhdu],outfile)
saltsafekey.rem('DETSEC',outstruct[outhdu],outfile)
saltsafekey.rem('CCDSEC',outstruct[outhdu],outfile)
saltsafekey.rem('AMPSEC',outstruct[outhdu],outfile)
# add housekeeping key words
outstruct[outhdu]=addhousekeeping(outstruct[outhdu], outhdu, outfile)
# close input FITS file
saltsafeio.closefits(struct)
# housekeeping keywords
keymosaic='SLOTMERG'
fname, hist=history(level=1, wrap=False)
saltsafekey.housekeeping(struct[0],keymosaic,'Amplifiers have been mosaiced', hist)
#saltsafekey.history(outstruct[0],hist)
# this is added for later use by
saltsafekey.put('NCCDS', 0.5, outstruct[0])
saltsafekey.put('NSCIEXT', exposures, outstruct[0])
saltsafekey.put('NEXTEND', exposures, outstruct[0])
# write FITS file of mosaiced image
outstruct=pyfits.HDUList(outstruct)
saltsafeio.writefits(outstruct, outfile, clobber=clobber)
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