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 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 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 saltfpcalibrate(plottype, infile, outfile, calibratelogfile, logfile,
verbose):
"""Determines the wavelength calibration of the Fabry-Perot
interactively, using the ring measurements from the CALRING program."""
plottype = str(plottype)
plottype = plottype.strip()
if plottype == 'xwindow':
plottype = '/xw'
else:
plottype = '/ps'
# 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', infile)
# The input file in this case is a file, does it exist?
if infile[0] != '@':
saltsafeio.fileexists(infile)
# is the proposed output file specified?
saltsafeio.filedefined('Output', outfile)
# check whether the proposed output file exists
path = os.path.dirname(infile)
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)
# check whether the calibrate logfile is defined
saltsafeio.filedefined('Log', calibratelogfile)
# Get current working directory as the Fortran code changes dir
startdir = os.getcwd()
# If all looks OK, run the FORTRAN code
calibrate_wrapper.calibrate(plottype, infile, outfile,
calibratelogfile)
# go back to starting directory
os.chdir(startdir)
def saltfpcalibrate(plottype,infile,outfile,calibratelogfile,logfile,verbose):
"""Determines the wavelength calibration of the Fabry-Perot
interactively, using the ring measurements from the CALRING program."""
plottype = str(plottype)
plottype = plottype.strip()
if plottype == 'xwindow':
plottype = '/xw'
else:
plottype = '/ps'
# 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',infile)
# The input file in this case is a file, does it exist?
if infile[0] != '@':
saltsafeio.fileexists(infile)
# is the proposed output file specified?
saltsafeio.filedefined('Output',outfile)
# check whether the proposed output file exists
path = os.path.dirname(infile)
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)
# check whether the calibrate logfile is defined
saltsafeio.filedefined('Log',calibratelogfile)
# Get current working directory as the Fortran code changes dir
startdir = os.getcwd()
# If all looks OK, run the FORTRAN code
calibrate_wrapper.calibrate(plottype,infile, outfile, calibratelogfile)
# go back to starting directory
os.chdir(startdir)
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 saltfpringfilter(axc,ayc,arad,rxc,ryc,filterfreq,filterwidth,itmax,conv, fitwidth,image,logfile,useconfig,configfile,verbose):
""" Determines the center coordinates of a ring, bins the ring radially and computes its power spectrum, and allows the user to select a smoothing filter for the ring. """
# 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_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])
# getting paths for filenames
pathin = os.path.dirname(image)
basein = os.path.basename(image)
pathlog = os.path.dirname(logfile)
baselog = os.path.basename(logfile)
# 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
# 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',image)
# if the input file is a file, does it exist?
if basein[0] != '@':
saltsafeio.fileexists(image)
infile = image
# if the input file is a list, throw an error
if basein[0] == '@':
raise SaltIOError(basein + ' list input instead of a file' )
# optionally update the FORTRAN config file with new values - not implemented currently
# If all looks OK, run the FORTRAN code
if len(pathin) > 0:
dir = pathin
else:
dir = './'
infile = basein
print(dir, infile, 'input directory and input file')
# Get current working directory as the Fortran code changes dir
startdir = os.getcwd()
ringfilter_wrapper.ringfilter(dir,axc, ayc,arad, rxc,ryc,filterfreq,filterwidth,itmax,conv,fitwidth,infile)
# go back to starting directory
os.chdir(startdir)
def saltfpringfilter(axc, ayc, arad, rxc, ryc, filterfreq, filterwidth, itmax,
conv, fitwidth, image, logfile, useconfig, configfile,
verbose):
""" Determines the center coordinates of a ring, bins the ring radially and computes its power spectrum, and allows the user to select a smoothing filter for the ring. """
# 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_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])
# getting paths for filenames
pathin = os.path.dirname(image)
basein = os.path.basename(image)
pathlog = os.path.dirname(logfile)
baselog = os.path.basename(logfile)
# 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
# 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', image)
# if the input file is a file, does it exist?
if basein[0] != '@':
saltsafeio.fileexists(image)
infile = image
# if the input file is a list, throw an error
if basein[0] == '@':
raise SaltIOError(basein + ' list input instead of a file')
# optionally update the FORTRAN config file with new values - not implemented currently
# If all looks OK, run the FORTRAN code
if len(pathin) > 0:
dir = pathin
else:
dir = './'
infile = basein
print dir, infile, 'input directory and input file'
# Get current working directory as the Fortran code changes dir
startdir = os.getcwd()
ringfilter_wrapper.ringfilter(dir, axc, ayc, arad, rxc, ryc,
filterfreq, filterwidth, itmax, conv,
fitwidth, infile)
# go back to starting directory
os.chdir(startdir)
def slotback(images,
outfits,
extension,
imgtype='image',
subbacktype='median',
sigback=3,
mbin=7,
sorder=3,
niter=5,
ampperccd=2,
ignorexp=6,
clobber=False,
logfile='salt.log',
verbose=True):
with logging(logfile, debug) as log:
# set up the variables
order = sorder
plotfreq = 0.01
ftime = plotfreq
# is the input file specified?
infiles = saltio.argunpack('Input', images)
# is the output file specified?
saltio.filedefined('Output', outfits)
#open the first file and check its charactistics
struct = saltio.openfits(infiles[0])
# how many extensions?
nextend = saltkey.get('NEXTEND', struct[0])
if nextend < extension:
msg = 'Insufficient number of extensions in %s' % (infile)
raise SaltIOError(msg)
# how many amplifiers?
amplifiers = saltkey.get('NCCDS', struct[0])
amplifiers = int(ampperccd * float(amplifiers))
if ampperccd > 0:
nframes = nextend / amplifiers
nstep = amplifiers
else:
nframes = nextend
nstep = 1
ntotal = nframes * len(infiles)
# image size
naxis1 = saltkey.get('NAXIS1', struct[extension])
naxis2 = saltkey.get('NAXIS2', struct[extension])
# CCD binning
ccdsum = saltkey.get('CCDSUM', struct[0])
binx = int(ccdsum.split(' ')[0])
biny = int(ccdsum.split(' ')[1])
# If a total file is to written out, create it and update it
hdu = 1
# delete the file if clobber is on and the file exists
if os.path.isfile(outfits):
if clobber:
saltio.delete(outfits)
else:
raise SaltIOError(
'Output fits file ' + writenewfits +
'already exists. Use Clobber=yes to overwrite file')
# create the output file
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(outfits)
except:
raise SaltIOError('Could not create new fits file named ' +
writenewfits)
# read it back in for updating
hduList = saltio.openfits(outfits, mode='update')
# set up the completeness tracker
if verbose:
j = 0
x2 = float(j) / float(ntotal)
ctext = 'Percentage Complete: %3.2f' % x2
sys.stdout.write(ctext)
sys.stdout.flush()
for infile in infiles:
struct = saltio.openfits(infile)
# Skip through the frames and process each frame individually
for i in range(nframes):
if not (infile == infiles[0] and i < ignorexp):
hdu = extension + i * nstep
try:
header = struct[hdu].header
array = struct[hdu].data
array = array * 1.0
except Exception, e:
msg = 'Unable to open extension %i in image %s because %s' % (
hdu, infile, e)
raise SaltIOError(msg)
# start the analysis of each frame
# gain and readout noise
try:
gain = float(header['GAIN'])
except:
gain = 1
log.warning('Gain not specified in image header')
try:
rdnoise = float(header['RDNOISE'])
except:
rdnoise = 0
log.warning('RDNOISE not specified in image header')
# background subtraction
if not subbacktype == 'none':
try:
narray = subbackground(array, sigback, mbin, order,
niter, subbacktype)
except:
log.warning('Image ' + infile + ' extention ' +
str(i) + ' is blank, skipping')
continue
# create output array
try:
if imgtype == 'background':
oarray = narray - array
else:
oarray = narray
except:
oarray = array
# print progress
if verbose:
x2 = float(j) / float(ntotal)
if x2 > ftime:
ctext = '\b\b\b\b\b %3.2f' % x2
sys.stdout.write(ctext)
sys.stdout.flush()
ftime += plotfreq
# update the header values with the image name and extension number
try:
hdue = pyfits.ImageHDU(oarray)
hdue.header = header
hdue.header.update('ONAME', infile,
'Original image name')
hdue.header.update('OEXT', hdu,
'Original extension number')
except Exception, e:
msg='SALTPHOT--WARNING: Could not update image in newfits file for %s ext %i because %s' \
% (infile, hdu, e)
raise SaltIOError(msg)
hduList.append(hdue)
j += 1
# close FITS file
saltio.closefits(struct)
def slotback(images,outfits,extension,imgtype='image',subbacktype='median',
sigback=3,mbin=7,sorder=3,niter=5,ampperccd=2,ignorexp=6,
clobber=False,logfile='salt.log',verbose=True):
with logging(logfile,debug) as log:
# set up the variables
order=sorder
plotfreq=0.01
ftime=plotfreq
# is the input file specified?
infiles = saltio.argunpack ('Input',images)
# is the output file specified?
saltio.filedefined('Output',outfits)
#open the first file and check its charactistics
struct=saltio.openfits(infiles[0])
# how many extensions?
nextend=saltkey.get('NEXTEND',struct[0])
if nextend < extension:
msg='Insufficient number of extensions in %s' % (infile)
raise SaltIOError(msg)
# how many amplifiers?
amplifiers=saltkey.get('NCCDS',struct[0])
amplifiers = int(ampperccd*float(amplifiers))
if ampperccd>0:
nframes = nextend/amplifiers
nstep=amplifiers
else:
nframes = nextend
nstep=1
ntotal=nframes*len(infiles)
# image size
naxis1=saltkey.get('NAXIS1',struct[extension])
naxis2=saltkey.get('NAXIS2',struct[extension])
# CCD binning
ccdsum=saltkey.get('CCDSUM',struct[0])
binx=int(ccdsum.split(' ')[0])
biny=int(ccdsum.split(' ')[1])
# If a total file is to written out, create it and update it
hdu = 1
# delete the file if clobber is on and the file exists
if os.path.isfile(outfits):
if clobber:
saltio.delete(outfits)
else:
raise SaltIOError('Output fits file '+writenewfits+'already exists. Use Clobber=yes to overwrite file')
# create the output file
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(outfits)
except:
raise SaltIOError('Could not create new fits file named '+writenewfits)
# read it back in for updating
hduList = saltio.openfits(outfits,mode='update')
# set up the completeness tracker
if verbose:
j=0
x2=float(j)/float(ntotal)
ctext='Percentage Complete: %3.2f' % x2
sys.stdout.write(ctext)
sys.stdout.flush()
for infile in infiles:
struct=saltio.openfits(infile)
# Skip through the frames and process each frame individually
for i in range(nframes):
if not (infile==infiles[0] and i < ignorexp):
hdu=extension+i*nstep
try:
header=struct[hdu].header
array=struct[hdu].data
array=array*1.0
except Exception as e:
msg='Unable to open extension %i in image %s because %s' % (hdu, infile, e)
raise SaltIOError(msg)
# start the analysis of each frame
# gain and readout noise
try:
gain=float(header['GAIN'])
except:
gain=1
log.warning('Gain not specified in image header')
try:
rdnoise=float(header['RDNOISE'])
except:
rdnoise=0
log.warning('RDNOISE not specified in image header')
# background subtraction
if not subbacktype=='none':
try:
narray=subbackground(array, sigback, mbin, order, niter, subbacktype)
except:
log.warning('Image '+infile+' extention '+str(i)+' is blank, skipping')
continue
# create output array
try:
if imgtype=='background':
oarray=narray-array
else:
oarray=narray
except:
oarray=array
# print progress
if verbose:
x2=float(j)/float(ntotal)
if x2 > ftime:
ctext='\b\b\b\b\b %3.2f' % x2
sys.stdout.write(ctext)
sys.stdout.flush()
ftime += plotfreq
# update the header values with the image name and extension number
try:
hdue = pyfits.ImageHDU(oarray)
hdue.header=header
hdue.header.update('ONAME',infile,'Original image name')
hdue.header.update('OEXT',hdu,'Original extension number')
except Exception as e:
msg='SALTPHOT--WARNING: Could not update image in newfits file for %s ext %i because %s' \
% (infile, hdu, e)
raise SaltIOError(msg)
hduList.append(hdue)
j +=1
# close FITS file
saltio.closefits(struct)
# close the output fits file:
try:
# write out the file
hduList.flush()
hduList.close()
except Exception as e:
raise SaltIOError('Failed to write %s because %s' % (outfits, e))
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 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 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 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 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.')