def saltfpeprofile(plottype, infile, logfile, verbose):
"""Line profile fitting and display"""
plottype = str(plottype)
plottype = plottype.strip()
if plottype == 'xwindow':
plottype = '/xw'
else:
plottype = '/ps'
# getting paths for filenames
pathin = os.path.dirname(infile)
basein = os.path.basename(infile)
pathlog = os.path.dirname(logfile)
baselog = os.path.basename(logfile)
print pathin, basein
# start log now that all parameters are set up
with logging(logfile, debug) as log:
# Some basic checks, some tests are done in the FORTRAN code itself
# is the input file specified?
saltsafeio.filedefined('Input', infile)
# if the input file is a file, does it exist?
if basein[0] != '@':
saltsafeio.fileexists(infile)
# if a list is input throw an error
if basein[0] == '@':
raise SaltIOError(basein + ' list input instead of a file')
# The file contains a list of images, check they exist
# format is 4x dummy lines, then a line/lines containing: x,y,wave0,sn,norm,dnorm,filename
testfile = open(infile)
print testfile
for i in range(1, 5):
line = testfile.readline()
line = 'dummy'
infiles = []
while (len(line.strip()) != 0):
line = testfile.readline()
if (len(line.strip()) > 0):
linearray = line.split()
infiles.append(linearray[6])
# check input files exist
saltsafeio.filesexist(infiles, '', 'r')
# If all looks OK, run the FORTRAN code
print 'input filename = ', infile
eprofile_wrapper.eprofile(plottype, infile)
def saltfpevelocity(infile, existfit, xc, yc, rmax, logfile, verbose):
"""XXX"""
# getting paths for filenames
pathin = os.path.dirname(infile)
basein = os.path.basename(infile)
pathlog = os.path.dirname(logfile)
baselog = os.path.basename(logfile)
print pathin, basein
# start log now that all parameters are set up
with logging(logfile, debug) as log:
# Some basic checks, some tests are done in the FORTRAN code itself
# is the input file specified?
saltsafeio.filedefined('Input', infile)
# if the input file is a file, does it exist?
if basein[0] != '@':
saltsafeio.fileexists(infile)
# if a list is input throw an error
if basein[0] == '@':
raise SaltIOError(basein + ' list input instead of a file')
# The file contains a list of images, check they exist
# format is 4x dummy lines, then a line/lines containing: x,y,wave0,sn,norm,dnorm,filename
testfile = open(infile)
print testfile
for i in range(1, 5):
line = testfile.readline()
line = 'dummy'
infiles = []
while (len(line.strip()) != 0):
line = testfile.readline()
if (len(line.strip()) > 0):
linearray = line.split()
infiles.append(linearray[6])
# check input files exist
saltsafeio.filesexist(infiles, '', 'r')
# convert existfile to a one letter string
if existfit == 'yes':
existfit == 'y'
else:
existfit == 'n'
# If all looks OK, run the FORTRAN code
print infile, 'input filename'
print existfit, xc, yc, rmax
evelocity_wrapper2.evelocity2(infile, existfit, xc, yc, rmax)
def slotpreview(images,outfile,ampperccd=2,ignorexp=6,recenter_radius=5,
tgt_col='b',cmp_col='g', tgt_lw=2,cmp_lw=2,cmap='gray',
scale='zscale',contrast=0.1,clobber=True,logfile='salt.log',
verbose=True):
with logging(logfile,debug) as log:
# is the input file specified?
saltsafeio.filedefined('Input',images)
# if the input file is a list, does it exist?
if images[0] == '@':
saltsafeio.listexists('Input',images)
# parse list of input files
imlist=saltsafeio.listparse('Raw image',images,'','','')
# check input files exist
saltsafeio.filesexist(imlist,'','r')
# is the output file specified?
saltsafeio.filedefined('Output',outfile)
# check output file does not exist, optionally remove it if it does exist
if os.path.exists(outfile) and clobber:
os.remove(outfile)
elif os.path.exists(outfile) and not clobber:
raise SaltIOError('File '+outfile+' already exists, use clobber=y')
# Get the number of ccds to calculate the number of frames to skip
try:
nccds=pyfits.getheader(imlist[0])['NCCDS']
except:
raise SaltIOError('Could not read NCCDS parameter from header of first fits file.')
# Create GUI
App = QtGui.QApplication(sys.argv)
aw = ApplicationWindow(imlist=imlist,
number=ignorexp*ampperccd*nccds+1,
config=outfile, target_line_color=tgt_col,
comparison_line_color=cmp_col, target_line_width=tgt_lw,
comparison_line_width=cmp_lw, distance=recenter_radius,
cmap=cmap, scale=scale, contrast=contrast)
aw.show()
# Start application event loop
exit=App.exec_()
# Check if GUI was executed succesfully
if exit!=0:
log.warning('Slotpreview GUI has unexpected exit status'+str(exit))
def slotutcfix(images,update,outfile,ampperccd,ignorexp,droplimit,inter,plotdata,logfile,verbose,debug):
with logging(logfile,debug) as log:
# set up the variables
utc_list = []
# is the input file specified?
saltsafeio.filedefined('Input',images)
# if the input file is a list, does it exist?
if images[0] == '@':
saltsafeio.listexists('Input',images)
# parse list of input files and place them in order
infiles=saltsafeio.listparse('Raw image',images,'','','')
infiles.sort()
# check input files exist
saltsafeio.filesexist(infiles,'','r')
# check to see if the output file exists and if so, clobber it
if os.path.isfile(outfile):
try:
os.remove(outfile)
except:
raise SaltIOError('File ' + outfile + ' can not be removed')
# open the outfile
if outfile:
try:
fout=open(outfile,'w')
except:
raise SaltIOError('File ' + outfile + ' can not be opened')
# get time of first exposure and basic information about the observations
infile=infiles[0]
struct=saltsafeio.openfits(infile)
# check to make sure slotmode data
detmode=saltsafekey.get('DETMODE',struct[0], infile)
if detmode != 'Slot Mode':
raise SaltIOError('Data are not Slot Mode Observations')
# Check to see if SLOTUTCFIX has already been run
# and print a warning if they have
if saltsafekey.found('SLOTUTC', struct[0]):
message='Data have already been processed by SLOTUTCFIX'
log.warning(message)
# check to make sure that it is the right version of the software
scamver=saltsafekey.get('DETSWV', struct[0], infile)
try:
scamver=float(scamver.split('-')[-1])
if 4.42 <= scamver <= 5.00:
pass
else:
raise SaltError('cannot currently correct this version of the SCAM software.')
except:
raise SaltError('Not able to read software version')
# requested exposure time
req_texp=saltsafekey.get('EXPTIME',struct[0],infile)
# how many extensions?
nextend=saltsafekey.get('NEXTEND',struct[0],infile)
# how many amplifiers
amplifiers=saltsafekey.get('NCCDS',struct[0],infile)
amplifiers = int(ampperccd*float(amplifiers))
if ampperccd>0:
nframes = nextend/amplifiers
nstep=amplifiers
else:
nframes = nextend
nstep=1
# how many total frame and unique times
ntotal=nextend*len(infiles)
nunique=len(infiles)*nframes-ignorexp+1
# Create arrays necessary for analysis
id_arr=np.arange(nunique)
utc_arr=np.zeros(nunique,dtype=float)
# Read in each file and make a list of the UTC values
if verbose:
log.message('Reading in files to create list of UTC values.')
j=0
for n,infile in enumerate(infiles):
# Show progress
if verbose:
percent=100.*float(n)/float(len(infiles))
ctext='Percentage Complete: %.2f\r' % percent
sys.stdout.write(ctext)
sys.stdout.flush()
struct=saltsafeio.openfits(infile)
if not len(struct)-1==nextend:
raise SaltIOError(infile,' has a different number of extensions from the first file')
# Skip through the frames and read in the utc
istart=1
if infile==infiles[0]:
istart=ignorexp*amplifiers+1
for i in range(istart,len(struct), amplifiers):
try:
utc_list.append(saltsafekey.get('UTC-OBS', struct[i], infile))
utc_arr[j]=slottool.getobstime(struct[i], infile)
j += 1
except Exception, e:
raise SaltIOError('Unable to create array of UTC times. Please check the number of extensions in the files')
# close FITS file
saltsafeio.closefits(struct)
# set up the other important arrays
try:
diff_arr=utc_arr.copy()
diff_arr[1:]=diff_arr[1:]-utc_arr[:-1]
diff_arr[0]=-1
dsec_arr=utc_arr-utc_arr.astype(int)
except:
raise SaltIOError('Unable to create timing arrays')
# calculate the real exposure time
if verbose:
log.message('Calculating real exposure time.')
real_expt, med_expt, t_start, t_arr, ysum_arr=calculate_realexptime(id_arr, utc_arr, dsec_arr, diff_arr, req_texp, utc_list)
# plot the results
if plotdata:
if verbose:
log.message('Plotting data.')
plt.ion()
plt.plot(t_arr,ysum_arr,linewidth=0.5,linestyle='-',marker='',color='b')
plt.xlabel('Time (s)')
plt.ylabel('Fit')
# Calculate the corrrect values
if verbose:
log.message('Calculating correct values')
i_start = abs(utc_arr-t_start).argmin()
t_diff=utc_arr*0.0+real_expt
nd=utc_arr*0.0
ndrop=0
for i in range(len(utc_arr)):
if utc_arr[i] >= t_start:
t_new=t_start+real_expt*(i-i_start+ndrop)
t_diff[i]=utc_arr[i]-t_new
while (t_diff[i]>real_expt and nd[i] < droplimit):
nd[i]+= 1
t_new=t_start+real_expt*(i-i_start+ndrop+nd[i])
t_diff[i]=utc_arr[i]-t_new
if (nd[i]<droplimit):
ndrop += nd[i]
else:
t_new=t_start+real_expt*(i-i_start)
t_diff[i]=utc_arr[i]-t_new
while (t_diff[i]>real_expt and nd[i] < droplimit):
nd[i]+= 1
t_new=t_start+real_expt*(i-i_start-nd[i])
t_diff[i]=utc_arr[i]-t_new
# calculate the corrected timestamp by counting 6 record files forward and
# 8 recored + unrecorded files back--or just 8*t_exp forward.
# if the object is near the end of the run, then just replace it with
# the correct value assuming no dropped exposures.
# first make the array of new times
new_arr=utc_arr-t_diff
# Next loop through them to find the corrected time
corr_arr=utc_arr*0.0
for i in range(len(new_arr)):
if i+6 < len(new_arr)-1:
corr_arr[i]=new_arr[i+6]-8*real_expt
else:
corr_arr[i]=new_arr[i]-2*real_expt
t_diff=utc_arr-corr_arr
# write out the first results
msg="Dwell Time=%5.3f Requested Exposure Time=%5.3f Nobs = %i Dropped = %i" % (real_expt, req_texp, nunique, ndrop)
if verbose:
log.message(msg)
if outfile:
fout.write('#'+msg+'\n')
fout.write('#%23s %2s %12s %12s %10s %8s %4s \n' % ('File', 'N', 'UTC_old', 'UTC_new', 'UTC_new(s)', 'Diff', 'drop' ))
# Give the user a chance to update the value
if inter:
message='Update headers with a dwell time of %5.3f s [y/n]? ' % real_expt
update=saltsafeio.yn_ask(message)
if not update:
message='Set Dwell Time manually [y/n]? '
update=saltsafeio.yn_ask(message)
if update:
message='New Dwell Time: '
real_expt=saltsafeio.ask(message)
try:
real_expt=float(real_expt)
except Exception, e:
msg='Could not set user dwell time because %s' % e
raise SaltError(msg)
def saltfpcalprofile(axc,ayc,arad,rxc,ryc,filter, filterfreq,filterwidth,plottype,itmax,conv, fitwidth,rlo,rhi,rfixed,cenfixed,images,outfile,comment,cala, calb, calc, cald, calf,calprofilelogfile,logfile,useconfig,configfile,verbose):
"""Fits a Voigt profile to a ring in one or more Fabry-Perot calibration ring images"""
# default parameter values are set up in the pyraf .par file. The values used are then changed if a FORTRAN config file exists and the user elects to override the pyraf .par file.
# Is the input FORTRAN config file specified?
# If it is blank, then it will be ignored.
if useconfig:
configfile = configfile.strip()
if len(configfile) > 0:
#check exists
saltsafeio.fileexists(configfile)
# read updated parameters from the file
array=getpfp(configfile,"axc")
s=len(array)
flag = array[s-1]
if flag == 1:
axc=float(array[0])
array=getpfp(configfile,"ayc")
s=len(array)
flag = array[s-1]
if flag == 1:
ayc=float(array[0])
array=getpfp(configfile,"arad")
s=len(array)
flag = array[s-1]
if flag == 1:
arad=float(array[0])
array=getpfp(configfile,"rxc")
s=len(array)
flag = array[s-1]
if flag == 1:
rxc=float(array[0])
array=getpfp(configfile,"ryc")
s=len(array)
flag = array[s-1]
if flag == 1:
ryc=float(array[0])
array=getpfp(configfile,"calring_filter")
s=len(array)
flag = array[s-1]
if flag == 1:
filter=str(array[0])
array=getpfp(configfile,"calring_filter_width")
s=len(array)
flag = array[s-1]
if flag == 1:
filterwidth=int(array[0])
array=getpfp(configfile,"calring_filter_freq")
s=len(array)
flag = array[s-1]
if flag == 1:
filterfreq=int(array[0])
array=getpfp(configfile,"calring_itmax")
s=len(array)
flag = array[s-1]
if flag == 1:
itmax=int(array[0])
array=getpfp(configfile,"calring_conv")
s=len(array)
flag = array[s-1]
if flag == 1:
conv=float(array[0])
array=getpfp(configfile,"calring_fitwidth")
s=len(array)
flag = array[s-1]
if flag == 1:
fitwidth=float(array[0])
array=getpfp(configfile,"calring_rlo")
s=len(array)
flag = array[s-1]
if flag == 1:
rlo=float(array[0])
array=getpfp(configfile,"calring_rhi")
s=len(array)
flag = array[s-1]
if flag == 1:
rhi=float(array[0])
array=getpfp(configfile,"calring_fixed")
s=len(array)
flag = array[s-1]
if flag == 1:
cenfixed=str(array[0])
array=getpfp(configfile,"calibration_a")
s=len(array)
flag = array[s-1]
if flag == 1:
cala=float(array[0])
array=getpfp(configfile,"calibration_b")
s=len(array)
flag = array[s-1]
if flag == 1:
calb=float(array[0])
array=getpfp(configfile,"calibration_c")
s=len(array)
flag = array[s-1]
if flag == 1:
calc=float(array[0])
array=getpfp(configfile,"calibration_d")
s=len(array)
flag = array[s-1]
if flag == 1:
cald=float(array[0])
array=getpfp(configfile,"calibration_f")
s=len(array)
flag = array[s-1]
if flag == 1:
calf=float(array[0])
cenfixed=str(cenfixed)
if cenfixed[0] == 'y' or cenfixed[0] == 'Y':
cenfixed = 1
else:
cenfixed = 0
cenfixed = bool(cenfixed)
filter = str(filter)
if filter[0] == 'y' or filter[0] == 'Y':
filter = 1
else:
filter = 0
filter = bool(filter)
plottype = str(plottype)
plottype = plottype.strip()
if plottype == 'xwindow':
plottype = '/xw'
else:
plottype = '/ps'
# getting paths for filenames
pathin = os.path.dirname(images)
basein = os.path.basename(images)
pathout = os.path.dirname(outfile)
baseout = os.path.basename(outfile)
pathlog = os.path.dirname(logfile)
baselog = os.path.basename(logfile)
pathcalprofilelog = os.path.dirname(calprofilelogfile)
basecalprofilelog = os.path.basename(calprofilelogfile)
# forcing logfiles to be created in the same directory as the input data
# (we change to this directory once starting the fortran code)
if len(pathin) > 0:
logfile = baselog
calprofilelogfile = basecalprofilelog
# start log now that all parameter are set up
with logging(logfile, debug) as log:
# Some basic checks, many tests are done in the FORTRAN code itself
# is the input file specified?
saltsafeio.filedefined('Input',images)
# if the input file is a file, does it exist?
if basein[0] != '@':
saltsafeio.fileexists(images)
infile = images
# if the input file is a list, does it exist?
if basein[0] == '@':
infile2 = basein.lstrip('@')
if (len(pathin) > 0):
infile = pathin + '/' + infile2
else:
infile = infile2
saltsafeio.listexists('Input',infile)
# parse list of input files
infiles=fpsafeio.fplistparse('Raw image',images,'','','')
# check input files exist
saltsafeio.filesexist(infiles,'','r')
# is the proposed output file specified?
saltsafeio.filedefined('Output',outfile)
# check whether the proposed output file exists
path = os.path.dirname(images)
if len(path) > 0:
dir = path + '/'
else:
dir = './'
# print dir, ' directory with data'
outfile = outfile.strip()
if os.path.isfile(outfile):
print 'output file exists, appending'
# saltsafeio.delete(outfile)
# optionally update the FORTRAN config file with new values - not implemented currently
# If all looks OK, run the FORTRAN code
infile = basein
if len(pathout) > 0 :
if (pathin == pathout):
outfile = baseout
# absolute path then leave alone
elif pathout[0] == '/':
outfile = outfile
else:
# as will move to directory of input data, need to strip this off if its in the path
a = pathout.lstrip(pathin)
b = a.lstrip('/')
outfile = b + '/' + baseout
print dir, infile, outfile, 'input directory, input and output files'
if basein[0] == '@':
print infiles,'infiles'
# Get current working directory as the Fortran code changes dir
startdir = os.getcwd()
calprofile_wrapper.calprofile(dir,calprofilelogfile,outfile,comment, axc, ayc,arad, rxc,ryc,filter,filterfreq,filterwidth,plottype,itmax,conv,fitwidth,rlo,rhi,rfixed, cenfixed,infile, cala, calb, calc, cald, calf)
# go back to starting directory
os.chdir(startdir)
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 slotpreview(images,
outfile,
ampperccd=2,
ignorexp=6,
recenter_radius=5,
tgt_col='b',
cmp_col='g',
tgt_lw=2,
cmp_lw=2,
cmap='gray',
scale='zscale',
contrast=0.1,
clobber=True,
logfile='salt.log',
verbose=True):
with logging(logfile, debug) as log:
# is the input file specified?
saltsafeio.filedefined('Input', images)
# if the input file is a list, does it exist?
if images[0] == '@':
saltsafeio.listexists('Input', images)
# parse list of input files
imlist = saltsafeio.listparse('Raw image', images, '', '', '')
# check input files exist
saltsafeio.filesexist(imlist, '', 'r')
# is the output file specified?
saltsafeio.filedefined('Output', outfile)
# check output file does not exist, optionally remove it if it does exist
if os.path.exists(outfile) and clobber:
os.remove(outfile)
elif os.path.exists(outfile) and not clobber:
raise SaltIOError('File ' + outfile +
' already exists, use clobber=y')
# Get the number of ccds to calculate the number of frames to skip
try:
nccds = pyfits.getheader(imlist[0])['NCCDS']
except:
raise SaltIOError(
'Could not read NCCDS parameter from header of first fits file.'
)
# Create GUI
App = QtGui.QApplication(sys.argv)
aw = ApplicationWindow(imlist=imlist,
number=ignorexp * ampperccd * nccds + 1,
config=outfile,
target_line_color=tgt_col,
comparison_line_color=cmp_col,
target_line_width=tgt_lw,
comparison_line_width=cmp_lw,
distance=recenter_radius,
cmap=cmap,
scale=scale,
contrast=contrast)
aw.show()
# Start application event loop
exit = App.exec_()
# Check if GUI was executed succesfully
if exit != 0:
log.warning('Slotpreview GUI has unexpected exit status' +
str(exit))
def saltheadtime(images,timetype,writetoheader,clobber,logfile,verbose,debug):
# Start log.
with logging(logfile,debug) as log:
# is the input file specified?
saltsafeio.filedefined('Input',images)
# 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')
# Loop over the input files.
for file in infiles:
print '---------------------------------------------------------\n\
'
print 'Reading file ', file
openfile= saltsafeio.openfits(file)
#Get information from header, display it, and close file.
headers=openfile[0].header
dateTimeString=[]
ra=headers['RA']
dec=headers['DEC']
objEpoch=headers['EPOCH']
obsEquinox=headers['EQUINOX']
if headers['DETMODE']=='SLOT':
numExtensions=headers['NEXTEND']
print 'Detector mode is slot. Number of extensions in this file is '+str(numExtensions)+'.'
for num in range(numExtensions+1):
extheader=openfile[num].header
dateTimeString.append(extheader['DATE-OBS']+extheader['TIME-OBS'])
else:
dateTimeString.append(headers['DATE-OBS']+headers['TIME-OBS'])
openfile.close()
#Convert times. All equations are in library, salttime.py.
newTime=[]
if timetype=="JD(UTC)":
for num in range(len(dateTimeString)):
newTime.append(convertUTtoJDUTC(dateTimeString[num]))
keyword='JDUT-OBS'
comment='Julian Date ref. to UTC.'
print 'The date and time from header extension '+ str(num) +' are:', dateTimeString[num], "UTC"
print 'Converted time ('+ timetype +') ='+str(newTime[num])+'\n\
'
elif timetype=="JD(TT)":
for num in range(len(dateTimeString)):
newTime.append(convertUTtoJD(dateTimeString[num]))
keyword='JD-OBS'
comment='Julian Date ref. to TT (Terrestrial timescale)'
print 'The date and time from header extension '+ str(num) +' are:', dateTimeString[num], "UTC"
print 'Converted time ('+ timetype +') ='+str(newTime[num])+'\n\
'
elif timetype=="MJD(TT)":
for num in range(len(dateTimeString)):
newTime.append(convertUTtoMJD(dateTimeString[num]))
keyword='MJD-OBS'
comment='Modified JD ref. to TT (Terrestrial timescale)'
print 'The date and time from header extension '+ str(num) +' are:', dateTimeString[num], "UTC"
print 'Converted time ('+ timetype +') ='+str(newTime[num])+'\n\
'
elif timetype=="HJD(TT)":
for num in range(len(dateTimeString)):
newTime.append(convertUTtoHJD(dateTimeString[num],ra,dec))
keyword='HJD-OBS'
comment='Heliocentric JD ref. to TT (Terrestrial timescale)'
print 'The date and time from header extension '+ str(num) +' are:', dateTimeString[num], "UTC"
print 'Converted time ('+ timetype +') ='+str(newTime[num])+'\n\
'
elif timetype=="BJD(TDB)":
for num in range(len(dateTimeString)):
newTime.append(convertUTtoBJD(dateTimeString[num],ra,dec))
keyword='BJD-OBS'
comment='Barycentric JD ref. to TDB (Barycentric Dynamical Time)'
print 'The date and time from header extension '+ str(num) +' are:', dateTimeString[num], "UTC"
print 'Converted time ('+ timetype +') ='+str(newTime[num])+'\n\
'
#Open file to write new time to header, if desired.
if writetoheader:
try:
filetowrite=fits.open(file,mode='update')
except Exception, e:
print e
for num in range(len(dateTimeString)):
hdr=filetowrite[num].header
if hdr.has_key(keyword)==1:
if clobber:
hdr.update(keyword,newTime[num],comment)
print 'Keyword ' +keyword +' has been updated in header extension '+str(num)+' to the following value: '+ str(newTime[num])
else:
print 'Keyword '+keyword+' has not been updated.'
else:
hdr.update(keyword,newTime[num],comment,after='TIME-OBS')
print 'Keyword ' + keyword +' has been added to header extension '+str(num)+' as the following value: '+ str(newTime[num])
filetowrite.flush()
filetowrite.close()
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 saltfpevelocity(infile,existfit,xc,yc,rmax,logfile, verbose):
"""XXX"""
# getting paths for filenames
pathin = os.path.dirname(infile)
basein = os.path.basename(infile)
pathlog = os.path.dirname(logfile)
baselog = os.path.basename(logfile)
print(pathin, basein)
# start log now that all parameters are set up
with logging(logfile, debug) as log:
# Some basic checks, some tests are done in the FORTRAN code itself
# is the input file specified?
saltsafeio.filedefined('Input',infile)
# if the input file is a file, does it exist?
if basein[0] != '@':
saltsafeio.fileexists(infile)
# if a list is input throw an error
if basein[0] == '@':
raise SaltIOError(basein + ' list input instead of a file' )
# The file contains a list of images, check they exist
# format is 4x dummy lines, then a line/lines containing: x,y,wave0,sn,norm,dnorm,filename
testfile= open(infile)
print(testfile)
for i in range(1, 5):
line = testfile.readline()
line = 'dummy'
infiles=[]
while (len(line.strip()) != 0):
line = testfile.readline()
if (len(line.strip()) > 0):
linearray = line.split()
infiles.append(linearray[6])
# check input files exist
saltsafeio.filesexist(infiles,'','r')
# convert existfile to a one letter string
if existfit == 'yes':
existfit == 'y'
else:
existfit =='n'
# If all looks OK, run the FORTRAN code
print(infile, 'input filename')
print(existfit, xc, yc, rmax)
evelocity_wrapper2.evelocity2(infile,existfit,xc,yc,rmax)
def saltfpnightring(axc, ayc, arad, rxc, ryc, filter, filterfreq, filterwidth,
plot, plottype, itmax, conv, fitwidth, images, outfile,
comment, cala, calb, calc, cald, calf, nightringlogfile,
logfile, useconfig, configfile, verbose):
"""Measures the centre coordinates and radius of one or more
night-time calibration rings """
# default parameter values are set up in the pyraf .par file. The values used are then changed if a FORTRAN config file exists and the user elects to override the pyraf .par file.
# Is the input FORTRAN config file specified?
# If it is blank, then it will be ignored.
if useconfig:
configfile = configfile.strip()
if len(configfile) > 0:
#check exists
saltsafeio.fileexists(configfile)
# read updated parameters from the file
array = getpfp(configfile, "axc")
s = len(array)
flag = array[s - 1]
if flag == 1:
axc = float(array[0])
array = getpfp(configfile, "ayc")
s = len(array)
flag = array[s - 1]
if flag == 1:
ayc = float(array[0])
array = getpfp(configfile, "arad")
s = len(array)
flag = array[s - 1]
if flag == 1:
arad = float(array[0])
array = getpfp(configfile, "rxc")
s = len(array)
flag = array[s - 1]
if flag == 1:
rxc = float(array[0])
array = getpfp(configfile, "ryc")
s = len(array)
flag = array[s - 1]
if flag == 1:
ryc = float(array[0])
array = getpfp(configfile, "calring_filter")
s = len(array)
flag = array[s - 1]
if flag == 1:
filter = str(array[0])
array = getpfp(configfile, "calring_filter_width")
s = len(array)
flag = array[s - 1]
if flag == 1:
filterwidth = int(array[0])
array = getpfp(configfile, "calring_filter_freq")
s = len(array)
flag = array[s - 1]
if flag == 1:
filterfreq = int(array[0])
array = getpfp(configfile, "calring_itmax")
s = len(array)
flag = array[s - 1]
if flag == 1:
itmax = int(array[0])
array = getpfp(configfile, "calring_conv")
s = len(array)
flag = array[s - 1]
if flag == 1:
conv = float(array[0])
array = getpfp(configfile, "calring_fitwidth")
s = len(array)
flag = array[s - 1]
if flag == 1:
fitwidth = float(array[0])
array = getpfp(configfile, "calibration_a")
s = len(array)
flag = array[s - 1]
if flag == 1:
cala = float(array[0])
array = getpfp(configfile, "calibration_b")
s = len(array)
flag = array[s - 1]
if flag == 1:
calb = float(array[0])
array = getpfp(configfile, "calibration_c")
s = len(array)
flag = array[s - 1]
if flag == 1:
calc = float(array[0])
array = getpfp(configfile, "calibration_d")
s = len(array)
flag = array[s - 1]
if flag == 1:
cald = float(array[0])
array = getpfp(configfile, "calibration_f")
s = len(array)
flag = array[s - 1]
if flag == 1:
calf = float(array[0])
filter = str(filter)
if filter[0] == 'y' or filter[0] == 'Y':
filter = 1
else:
filter = 0
filter = bool(filter)
plot = str(plot)
if plot[0] == 'y' or plot[0] == 'Y':
plot = 1
else:
plot = 0
plot = bool(plot)
plottype = str(plottype)
plottype = plottype.strip()
if plottype == 'xwindow':
plottype = '/xw'
else:
plottype = '/ps'
# additional verbose command as required in the fortran code too. Set this to whatever is input in the epar file.
verb = str(verbose)
if verb[0] == 'y' or verb[0] == 'Y':
verb = 1
else:
verb = 0
verb = bool(verb)
# getting paths for filenames
pathin = os.path.dirname(images)
basein = os.path.basename(images)
pathout = os.path.dirname(outfile)
baseout = os.path.basename(outfile)
pathlog = os.path.dirname(logfile)
baselog = os.path.basename(logfile)
pathnightringlog = os.path.dirname(nightringlogfile)
basenightringlog = os.path.basename(nightringlogfile)
# forcing logfiles to be created in the same directory as the input data
# (we change to this directory once starting the fortran code)
if len(pathin) > 0:
logfile = baselog
nightringlogfile = basenightringlog
# start log now that all parameter are set up
with logging(logfile, debug) as log:
# Some basic checks, many tests are done in the FORTRAN code itself
# is the input file specified?
saltsafeio.filedefined('Input', images)
# if the input file is a file, does it exist?
if basein[0] != '@':
saltsafeio.fileexists(images)
infile = images
# if the input file is a list, does it exist?
if basein[0] == '@':
infile2 = basein.lstrip('@')
if (len(pathin) > 0):
infile = pathin + '/' + infile2
else:
infile = infile2
saltsafeio.listexists('Input', infile)
# parse list of input files
infiles = fpsafeio.fplistparse('Raw image', images, '', '', '')
# check input files exist
saltsafeio.filesexist(infiles, '', 'r')
# is the proposed output file specified?
saltsafeio.filedefined('Output', outfile)
# check whether the proposed output file exists
path = os.path.dirname(images)
if len(path) > 0:
dir = path + '/'
else:
dir = './'
# print dir, ' directory with data'
outfile = outfile.strip()
if os.path.isfile(outfile):
print 'output file exists, appending'
# saltsafeio.delete(outfile)
# optionally update the FORTRAN config file with new values - not implemented currently
# If all looks OK, run the FORTRAN code
infile = basein
if len(pathout) > 0:
if (pathin == pathout):
outfile = baseout
# absolute path then leave alone
elif pathout[0] == '/':
outfile = outfile
else:
# as will move to directory of input data, need to strip this off if its in the path
a = pathout.lstrip(pathin)
b = a.lstrip('/')
outfile = b + '/' + baseout
print dir, infile, outfile, 'input directory, input and output files'
if basein[0] == '@':
print infiles, 'infiles'
# Get current working directory as the Fortran code changes dir
startdir = os.getcwd()
nightring_wrapper.nightring(dir, nightringlogfile, outfile, comment,
axc, ayc, arad, rxc, ryc, filter,
filterfreq, filterwidth, plot, plottype,
itmax, conv, fitwidth, infile, cala, calb,
calc, cald, calf, verb)
# go back to starting directory
os.chdir(startdir)
def saltfpeprofile(plottype,infile,logfile, verbose):
"""Line profile fitting and display"""
plottype = str(plottype)
plottype = plottype.strip()
if plottype == 'xwindow':
plottype = '/xw'
else:
plottype = '/ps'
# getting paths for filenames
pathin = os.path.dirname(infile)
basein = os.path.basename(infile)
pathlog = os.path.dirname(logfile)
baselog = os.path.basename(logfile)
print pathin, basein
# start log now that all parameters are set up
with logging(logfile, debug) as log:
# Some basic checks, some tests are done in the FORTRAN code itself
# is the input file specified?
saltsafeio.filedefined('Input',infile)
# if the input file is a file, does it exist?
if basein[0] != '@':
saltsafeio.fileexists(infile)
# if a list is input throw an error
if basein[0] == '@':
raise SaltIOError(basein + ' list input instead of a file' )
# The file contains a list of images, check they exist
# format is 4x dummy lines, then a line/lines containing: x,y,wave0,sn,norm,dnorm,filename
testfile= open(infile)
print testfile
for i in range(1, 5):
line = testfile.readline()
line = 'dummy'
infiles=[]
while (len(line.strip()) != 0):
line = testfile.readline()
if (len(line.strip()) > 0):
linearray = line.split()
infiles.append(linearray[6])
# check input files exist
saltsafeio.filesexist(infiles,'','r')
# If all looks OK, run the FORTRAN code
print 'input filename = ', infile
eprofile_wrapper.eprofile(plottype,infile)
def saltheadtime(images, timetype, writetoheader, clobber, logfile, verbose,
debug):
# Start log.
with logging(logfile, debug) as log:
# is the input file specified?
saltsafeio.filedefined('Input', images)
# 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')
# Loop over the input files.
for file in infiles:
print '---------------------------------------------------------\n\
'
print 'Reading file ', file
openfile = saltsafeio.openfits(file)
#Get information from header, display it, and close file.
headers = openfile[0].header
dateTimeString = []
ra = headers['RA']
dec = headers['DEC']
objEpoch = headers['EPOCH']
obsEquinox = headers['EQUINOX']
if headers['DETMODE'] == 'SLOT':
numExtensions = headers['NEXTEND']
print 'Detector mode is slot. Number of extensions in this file is ' + str(
numExtensions) + '.'
for num in range(numExtensions + 1):
extheader = openfile[num].header
dateTimeString.append(extheader['DATE-OBS'] +
extheader['TIME-OBS'])
else:
dateTimeString.append(headers['DATE-OBS'] +
headers['TIME-OBS'])
openfile.close()
#Convert times. All equations are in library, salttime.py.
newTime = []
if timetype == "JD(UTC)":
for num in range(len(dateTimeString)):
newTime.append(convertUTtoJDUTC(dateTimeString[num]))
keyword = 'JDUT-OBS'
comment = 'Julian Date ref. to UTC.'
print 'The date and time from header extension ' + str(
num) + ' are:', dateTimeString[num], "UTC"
print 'Converted time (' + timetype + ') =' + str(
newTime[num]) + '\n\
'
elif timetype == "JD(TT)":
for num in range(len(dateTimeString)):
newTime.append(convertUTtoJD(dateTimeString[num]))
keyword = 'JD-OBS'
comment = 'Julian Date ref. to TT (Terrestrial timescale)'
print 'The date and time from header extension ' + str(
num) + ' are:', dateTimeString[num], "UTC"
print 'Converted time (' + timetype + ') =' + str(
newTime[num]) + '\n\
'
elif timetype == "MJD(TT)":
for num in range(len(dateTimeString)):
newTime.append(convertUTtoMJD(dateTimeString[num]))
keyword = 'MJD-OBS'
comment = 'Modified JD ref. to TT (Terrestrial timescale)'
print 'The date and time from header extension ' + str(
num) + ' are:', dateTimeString[num], "UTC"
print 'Converted time (' + timetype + ') =' + str(
newTime[num]) + '\n\
'
elif timetype == "HJD(TT)":
for num in range(len(dateTimeString)):
newTime.append(convertUTtoHJD(dateTimeString[num], ra,
dec))
keyword = 'HJD-OBS'
comment = 'Heliocentric JD ref. to TT (Terrestrial timescale)'
print 'The date and time from header extension ' + str(
num) + ' are:', dateTimeString[num], "UTC"
print 'Converted time (' + timetype + ') =' + str(
newTime[num]) + '\n\
'
elif timetype == "BJD(TDB)":
for num in range(len(dateTimeString)):
newTime.append(convertUTtoBJD(dateTimeString[num], ra,
dec))
keyword = 'BJD-OBS'
comment = 'Barycentric JD ref. to TDB (Barycentric Dynamical Time)'
print 'The date and time from header extension ' + str(
num) + ' are:', dateTimeString[num], "UTC"
print 'Converted time (' + timetype + ') =' + str(
newTime[num]) + '\n\
'
#Open file to write new time to header, if desired.
if writetoheader:
try:
filetowrite = fits.open(file, mode='update')
except Exception, e:
print e
for num in range(len(dateTimeString)):
hdr = filetowrite[num].header
if hdr.has_key(keyword) == 1:
if clobber:
hdr.update(keyword, newTime[num], comment)
print 'Keyword ' + keyword + ' has been updated in header extension ' + str(
num) + ' to the following value: ' + str(
newTime[num])
else:
print 'Keyword ' + keyword + ' has not been updated.'
else:
hdr.update(keyword,
newTime[num],
comment,
after='TIME-OBS')
print 'Keyword ' + keyword + ' has been added to header extension ' + str(
num) + ' as the following value: ' + str(
newTime[num])
filetowrite.flush()
filetowrite.close()
def slotutcfix(images, update, outfile, ampperccd, ignorexp, droplimit, inter,
plotdata, logfile, verbose, debug):
with logging(logfile, debug) as log:
# set up the variables
utc_list = []
# is the input file specified?
saltsafeio.filedefined('Input', images)
# if the input file is a list, does it exist?
if images[0] == '@':
saltsafeio.listexists('Input', images)
# parse list of input files and place them in order
infiles = saltsafeio.listparse('Raw image', images, '', '', '')
infiles.sort()
# check input files exist
saltsafeio.filesexist(infiles, '', 'r')
# check to see if the output file exists and if so, clobber it
if os.path.isfile(outfile):
try:
os.remove(outfile)
except:
raise SaltIOError('File ' + outfile + ' can not be removed')
# open the outfile
if outfile:
try:
fout = open(outfile, 'w')
except:
raise SaltIOError('File ' + outfile + ' can not be opened')
# get time of first exposure and basic information about the observations
infile = infiles[0]
struct = saltsafeio.openfits(infile)
# check to make sure slotmode data
detmode = saltsafekey.get('DETMODE', struct[0], infile)
if detmode != 'Slot Mode':
raise SaltIOError('Data are not Slot Mode Observations')
# Check to see if SLOTUTCFIX has already been run
# and print a warning if they have
if saltsafekey.found('SLOTUTC', struct[0]):
message = 'Data have already been processed by SLOTUTCFIX'
log.warning(message)
# check to make sure that it is the right version of the software
scamver = saltsafekey.get('DETSWV', struct[0], infile)
try:
scamver = float(scamver.split('-')[-1])
if 4.42 <= scamver <= 5.00:
pass
else:
raise SaltError(
'cannot currently correct this version of the SCAM software.'
)
except:
raise SaltError('Not able to read software version')
# requested exposure time
req_texp = saltsafekey.get('EXPTIME', struct[0], infile)
# how many extensions?
nextend = saltsafekey.get('NEXTEND', struct[0], infile)
# how many amplifiers
amplifiers = saltsafekey.get('NCCDS', struct[0], infile)
amplifiers = int(ampperccd * float(amplifiers))
if ampperccd > 0:
nframes = nextend / amplifiers
nstep = amplifiers
else:
nframes = nextend
nstep = 1
# how many total frame and unique times
ntotal = nextend * len(infiles)
nunique = len(infiles) * nframes - ignorexp + 1
# Create arrays necessary for analysis
id_arr = np.arange(nunique)
utc_arr = np.zeros(nunique, dtype=float)
# Read in each file and make a list of the UTC values
if verbose:
log.message('Reading in files to create list of UTC values.')
j = 0
for n, infile in enumerate(infiles):
# Show progress
if verbose:
percent = 100. * float(n) / float(len(infiles))
ctext = 'Percentage Complete: %.2f\r' % percent
sys.stdout.write(ctext)
sys.stdout.flush()
struct = saltsafeio.openfits(infile)
if not len(struct) - 1 == nextend:
raise SaltIOError(
infile,
' has a different number of extensions from the first file'
)
# Skip through the frames and read in the utc
istart = 1
if infile == infiles[0]:
istart = ignorexp * amplifiers + 1
for i in range(istart, len(struct), amplifiers):
try:
utc_list.append(
saltsafekey.get('UTC-OBS', struct[i], infile))
utc_arr[j] = slottool.getobstime(struct[i], infile)
j += 1
except Exception, e:
raise SaltIOError(
'Unable to create array of UTC times. Please check the number of extensions in the files'
)
# close FITS file
saltsafeio.closefits(struct)
# set up the other important arrays
try:
diff_arr = utc_arr.copy()
diff_arr[1:] = diff_arr[1:] - utc_arr[:-1]
diff_arr[0] = -1
dsec_arr = utc_arr - utc_arr.astype(int)
except:
raise SaltIOError('Unable to create timing arrays')
# calculate the real exposure time
if verbose:
log.message('Calculating real exposure time.')
real_expt, med_expt, t_start, t_arr, ysum_arr = calculate_realexptime(
id_arr, utc_arr, dsec_arr, diff_arr, req_texp, utc_list)
# plot the results
if plotdata:
if verbose:
log.message('Plotting data.')
plt.ion()
plt.plot(t_arr,
ysum_arr,
linewidth=0.5,
linestyle='-',
marker='',
color='b')
plt.xlabel('Time (s)')
plt.ylabel('Fit')
# Calculate the corrrect values
if verbose:
log.message('Calculating correct values')
i_start = abs(utc_arr - t_start).argmin()
t_diff = utc_arr * 0.0 + real_expt
nd = utc_arr * 0.0
ndrop = 0
for i in range(len(utc_arr)):
if utc_arr[i] >= t_start:
t_new = t_start + real_expt * (i - i_start + ndrop)
t_diff[i] = utc_arr[i] - t_new
while (t_diff[i] > real_expt and nd[i] < droplimit):
nd[i] += 1
t_new = t_start + real_expt * (i - i_start + ndrop + nd[i])
t_diff[i] = utc_arr[i] - t_new
if (nd[i] < droplimit):
ndrop += nd[i]
else:
t_new = t_start + real_expt * (i - i_start)
t_diff[i] = utc_arr[i] - t_new
while (t_diff[i] > real_expt and nd[i] < droplimit):
nd[i] += 1
t_new = t_start + real_expt * (i - i_start - nd[i])
t_diff[i] = utc_arr[i] - t_new
# calculate the corrected timestamp by counting 6 record files forward and
# 8 recored + unrecorded files back--or just 8*t_exp forward.
# if the object is near the end of the run, then just replace it with
# the correct value assuming no dropped exposures.
# first make the array of new times
new_arr = utc_arr - t_diff
# Next loop through them to find the corrected time
corr_arr = utc_arr * 0.0
for i in range(len(new_arr)):
if i + 6 < len(new_arr) - 1:
corr_arr[i] = new_arr[i + 6] - 8 * real_expt
else:
corr_arr[i] = new_arr[i] - 2 * real_expt
t_diff = utc_arr - corr_arr
# write out the first results
msg = "Dwell Time=%5.3f Requested Exposure Time=%5.3f Nobs = %i Dropped = %i" % (
real_expt, req_texp, nunique, ndrop)
if verbose:
log.message(msg)
if outfile:
fout.write('#' + msg + '\n')
fout.write('#%23s %2s %12s %12s %10s %8s %4s \n' %
('File', 'N', 'UTC_old', 'UTC_new', 'UTC_new(s)',
'Diff', 'drop'))
# Give the user a chance to update the value
if inter:
message = 'Update headers with a dwell time of %5.3f s [y/n]? ' % real_expt
update = saltsafeio.yn_ask(message)
if not update:
message = 'Set Dwell Time manually [y/n]? '
update = saltsafeio.yn_ask(message)
if update:
message = 'New Dwell Time: '
real_expt = saltsafeio.ask(message)
try:
real_expt = float(real_expt)
except Exception, e:
msg = 'Could not set user dwell time because %s' % e
raise SaltError(msg)
def slotphot(images,outfile,srcfile,newfits=None,phottype='square',
subbacktype='median',sigback=3,mbin=7,sorder=3,niter=5,sigdet=5,
contpix=10,ampperccd=2,ignorexp=6,driftlimit=10.,finddrift=True,
outtype='ascii',reltime=True,clobber=True,logfile='salt.log',
verbose=True):
"""Perform photometry on listed SALT slotmode *images*."""
with logging(logfile,debug) as log:
# set up the variables
entries = []
vig_lo = {}
vig_hi = {}
amp = {}
x = {}
y = {}
x_o = {}
y_o = {}
r = {}
br1 = {}
br2 = {}
hour = 0
min = 0
sec = 0.
time0 = 0.
nframes = 0
bin=mbin
order=sorder
# is the input file specified?
saltsafeio.filedefined('Input',images)
# 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')
# is the output file specified?
saltsafeio.filedefined('Output',outfile)
# check output file does not exist, optionally remove it if it does exist
if os.path.exists(outfile) and clobber:
os.remove(outfile)
elif os.path.exists(outfile) and not clobber:
raise SaltIOError('File '+outfile+' already exists, use clobber=y')
# open output ascii file
if outtype=='ascii':
try:
lc = open(outfile,'a')
except:
raise SaltIOError('Cannot open ouput file '+outfile)
# is the extraction region defintion file specified?
saltsafeio.filedefined('Extraction region defintion',srcfile)
# check extraction region defintion file exists
srcfile = srcfile.strip()
saltsafeio.fileexists(srcfile)
# read extraction region defintion file
amp, x, y, x_o, y_o, r, br1, br2=slottool.readsrcfile(srcfile)
# set the writenewfits parameter
if not newfits or newfits=='none':
writenewfits=False
else:
writenewfits=newfits
# get time of first exposure and basic information about the observations
infile=infiles[0]
struct=saltsafeio.openfits(infile)
# identify instrument
instrume,keyprep,keygain,keybias,keyxtalk,keyslot=saltsafekey.instrumid(struct,infile)
# how many extensions?
nextend=saltsafekey.get('NEXTEND',struct[0],infile)
if nextend < amp['comparison']:
msg='Insufficient number of extensions in %s' % (infile)
raise SaltIOError(msg)
# how many amplifiers?
amplifiers=saltsafekey.get('NCCDS',struct[0],infile)
amplifiers = int(ampperccd*float(amplifiers))
if ampperccd>0:
nframes = int(nextend/amplifiers)
nstep=amplifiers
else:
nframes = nextend
nstep=1
ntotal=nframes*len(infiles)
# image size
naxis1=saltsafekey.get('NAXIS1',struct[amp['comparison']],infile)
naxis2=saltsafekey.get('NAXIS2',struct[amp['comparison']],infile)
# CCD binning
ccdsum=saltsafekey.get('CCDSUM',struct[0],infile)
binx=int(ccdsum.split(' ')[0])
biny=int(ccdsum.split(' ')[1])
# Identify the time of the observations
ext = 1
try:
time0=slottool.getobstime(struct[ext], infile+'['+str(ext)+']')
dateobs=saltsafekey.get('DATE-OBS',struct[ext],infile)
dateobs=dateobs.replace('-','/')
except:
raise SaltIOError('No time or obsdate in first image')
# If a total file is to be written out, create it and update it
if writenewfits:
if os.path.isfile(writenewfits):
if clobber:
saltsafeio.delete(writenewfits)
else:
raise SaltIOError('Newfits file exists, use clobber')
try:
hdu=pyfits.PrimaryHDU()
hdu.header=struct[0].header
hdu.header['NCCDS']=1
hdu.header['NSCIEXT']=ntotal-ignorexp
hdu.header['NEXTEND']=ntotal-ignorexp
hduList=pyfits.HDUList(hdu)
hduList.verify()
hduList.writeto(writenewfits)
except:
raise SaltIOError('Could not create newfits file, '+writenewfits)
# Close image file
saltsafeio.closefits(struct)
# Read newfits file back in for updating
if writenewfits:
try:
hduList=pyfits.open(writenewfits,mode='update')
except:
raise SaltIOError('Cannot open newfits file '+writenewfits+' for updating.')
# set up the arrays
j=0
time=np.zeros(ntotal ,dtype='float')-1.0
dx=np.zeros(ntotal ,dtype='float')
dy=np.zeros(ntotal ,dtype='float')
tflux=np.zeros(ntotal ,dtype='float')
terr =np.zeros(ntotal ,dtype='float')
cflux=np.zeros(ntotal ,dtype='float')
cerr =np.zeros(ntotal ,dtype='float')
ratio=np.zeros(ntotal ,dtype='float')
rerr =np.zeros(ntotal ,dtype='float')
tgt_x=np.zeros(ntotal ,dtype='float')
tgt_y=np.zeros(ntotal ,dtype='float')
cmp_x=np.zeros(ntotal ,dtype='float')
cmp_y=np.zeros(ntotal ,dtype='float')
p_one=100./ntotal # One percent
p_old=-1 # Previous completed percentage
p_new=0 # New completed percentage
p_n=1 # Counter number
for infile in infiles:
# Log
if verbose:
log.message('Starting photometry on file '+infile, with_stdout=False)
struct=pyfits.open(infile)
# Skip through the frames and process each frame individually
for i in range(nframes):
# Show progress
if verbose:
p_new=int(p_n*p_one)
p_n+=1
if p_new!=p_old:
ctext='Percentage Complete: %d\r' % p_new
sys.stdout.write(ctext)
sys.stdout.flush()
p_old=p_new
if not (infile==infiles[0] and i < ignorexp):
ext=amp['comparison']+i*nstep
try:
header=struct[ext].header
array=struct[ext].data
array=array*1.0
except:
msg='Unable to open extension %i in image %s' % (ext, infile)
raise SaltIOError(msg)
# starti the analysis of each frame
# get the time
time[j]=slottool.getobstime(struct[ext],infile+'['+str(ext)+']')
# gain and readout noise
try:
gain=float(header['GAIN'])
except:
gain=1
raise SaltIOError('Gain not specified in image header')
try:
rdnoise=float(header['RDNOISE'])
except:
rdnoise=0
raise SaltIOError('RDNOISE not specified in image header')
# background subtraction
if not subbacktype=='none':
try:
array=subbackground(array, sigback, bin, order, niter, subbacktype)
except SaltError:
log.warning('Image '+infile+' extention '+str(ext)+' is blank, skipping')
continue
# x-y fit to the comparison star and update the x,y values
if finddrift:
carray, fx,fy=slottool.finddrift(array, x['comparison'], y['comparison'], r['comparison'], naxis1, naxis2, sigdet, contpix, sigback, driftlimit, niter)
if fx > -1 and fy > -1:
if fx < naxis1 and fy < naxis2:
dx[j]=x['comparison']-fx
dy[j]=y['comparison']-fy
x['comparison']=fx
y['comparison']=fy
x['target']=x['target']-dx[j]
y['target']=y['target']-dy[j]
else:
dx[j]=0
dy[j]=0
x['comparison']=x_o['comparison']
y['comparison']=y_o['comparison']
x['target']=x_o['target']
y['target']=y_o['target']
else:
msg='No comparison object found in image file ' + infile+' on extension %i skipping.' % ext
log.warning(msg)
pass
# do photometry
try:
tflux[j],terr[j],cflux[j],cerr[j],ratio[j],rerr[j]=slottool.dophot(phottype, array, x, y, r, br1, br2, gain, rdnoise, naxis1, naxis2)
except SaltError, e:
msg='Could not do photometry on extension %i in image %s because %s skipping.' % (ext, infile, e)
log.warning(msg)
tgt_x[j]=x['target']
tgt_y[j]=y['target']
cmp_x[j]=x['comparison']
cmp_y[j]=y['comparison']
# record results
# TODO! This should be removed in favor of the write all to disk in the end
if outtype=='ascii':
slottool.writedataout(lc, j+1, time[j], x, y, tflux[j], terr[j], cflux[j],cerr[j],ratio[j],rerr[j],time0, reltime)
# write newfits file
if writenewfits:
# add original name and extension number to header
try:
hdue=pyfits.ImageHDU(array)
hdue.header=header
hdue.header.update('ONAME',infile,'Original image name')
hdue.header.update('OEXT',ext,'Original extension number')
hduList.append(hdue)
except:
log.warning('Could not update image in newfits '+infile+' '+str(ext))
# increment counter
j+=1
# close FITS file
saltsafeio.closefits(struct)
# close newfits file
if writenewfits:
try:
hduList.flush()
hduList.close()
except:
raise SaltIOError('Cannot close newfits file.')
# write to output
if outtype=='ascii':
# close output ascii file
try:
lc.close()
except:
raise SaltIOError('Cannot close ouput file ' + outfile)
elif outtype=='fits':
print 'writing fits'
try:
c1=pyfits.Column(name='index',format='D',array=np.arange(ntotal))
if reltime:
c2=pyfits.Column(name='time',format='D',array=time-time0)
else:
c2=pyfits.Column(name='time',format='D',array=time)
c3=pyfits.Column(name='tgt_x',format='D',array=tgt_x)
c4=pyfits.Column(name='tgt_y',format='D',array=tgt_y)
c5=pyfits.Column(name='tgt_flux',format='D',array=tflux)
c6=pyfits.Column(name='tgt_err',format='D',array=terr)
c7=pyfits.Column(name='cmp_x',format='D',array=cmp_x)
c8=pyfits.Column(name='cmp_y',format='D',array=cmp_y)
c9=pyfits.Column(name='cmp_flux',format='D',array=cflux)
c10=pyfits.Column(name='cmp_err',format='D',array=cerr)
c11=pyfits.Column(name='flux_ratio',format='D',array=ratio)
c12=pyfits.Column(name='flux_ratio_err',format='D',array=rerr)
tbhdu=pyfits.new_table([c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12])
# Add header information
tbhdu.header.update('RELTIME',str(reltime),'Time relative to first datapoint or absolute.')
tbhdu.writeto(outfile)
print 'fits written to ',outfile
except:
raise SaltIOError('Could not write to fits table.')