def mass_stat(args):
files = os.listdir(args.im_folder)
with open(args.data_file_name, 'a') as data_file:
for filename in files:
if filename.startswith(args.stem) and (filename.endswith(".fit") or filename.endswith(".fits")):
im_path = args.im_folder + filename
image = fits.open(im_path)
date = image[0].header['DATE-OBS']
dt = sidereal.parseDatetime(date)
st = SidTime(sidereal.SiderealTime.fromDatetime(dt).lst(-2.05393104))
data_file.write(date + ' ' + str(st) + imutil.imstat(im_path, Stdout=1)[1] + '\n')
amplifiers = 6
exposure = fits[0].header['EXPTIME']
elif instrument.count('SALTICAM') > 0:
amplifiers = 4
exposure = fits[0].header['EXPTIME']
else:
amplifiers = 1
exposure = fits[0].header['KCT']
instrument = 'SHOC'
if i == 0:
start = (fits[0].header['FRAME']).split('T')[1]
if i == len(fitslist)-1:
frames = (fits[0].header['NUMKIN'])
if ext in ('0',''):
extensions = 1
imagestatistics = imutil.imstat(images = fitslist[i]+'[0]'+'[]', mode = "h", fields = 'image,mean',Stdout=1)
image = imagestatistics[1].split()[0]
mean = imagestatistics[1].split()[-1]
print 'Image:', image, 'Mean: ', mean
means.append(float(mean))
exposures.append(float(exposure))
utc = imutil.hselect(images = fitslist[i]+'[0]', fields = '$I,UTC-OBS', expr = 'yes',Stdout=1)[0]
print >> pulsetiming, image, mean
print >> pulsetiming, utc
else:
ext = int(ext)
extensions = int(fits[0].header['NEXTEND'])
print >> pulsetiming, '# Extentions per cube: ', extensions
for j in range(extensions/amplifiers):
imagestatistics = imutil.imstat(images = fitslist[i]+'['+str(j*amplifiers+ext)+']'+'[]', mode = "h", fields = 'image,mean',Stdout=1)
image = imagestatistics[1].split()[0]
# TRANSFORM science files
#Alexei wiki: transform input=stdstar.fits output=stdstarw.fits fitnames=refspec interptype=linear flux=yes blank=INDEF x1=INDEF x2=INDEF dx=INDEF y1=INDEF y2=INDEF dy=INDEF
print >> reduction, "longslit.transform(input='spectra"+str(targetcount+1)+".fits', output='f.spectra"+str(targetcount+1)+".fits', fitnames='cr.Arc1', interptype='linear')"
# TRIM science files to appropriate portion only (relevant line and surrounds)
print >> reduction, "imutil.imcopy(input='f.spectra"+str(targetcount+1)+".fits[*,"+trimbox+"]', output='tf.spectra"+str(targetcount+1)+".fits', verbose='yes')"
print >> targetlist, 'Reduced/spectra'+str(targetcount+1)+'.fits'
#print >> targetlist, '# Original filename:', filenames[i], utcdate, utctime
#print >> targetlist, '#', gratingvalues
targetcount = targetcount + 1
targetfiles.append(filenames[i])
# FLAT file: CCDTYPE = 'FLAT '
if obstype.count('FLAT') > 0:
# Strip multi header:
flatfield = 'Reduced/flat'+str(flatcount+1)+'.fits'
imutil.imcopy(input=filenames[i]+'[SCI,inherit]', output=flatfield,verbose='yes')
averageflux = imutil.imstat(images=flatfield, mode="h", fields='image,mean,stddev',Stdout=1)[1].split()[-2]
imutil.imarith(operand1=flatfield, op="/", operand2=str(averageflux), result=flatfield, title="Normalized FLAT", mode="h")
print filenames[i]+' is a FLAT'
print >> flatlist, flatfield
#print >> flatlist, '# Original filename:', filenames[i], gratingvalues
flatcount = flatcount + 1
if flatcount > 0:
# Make MASTER flat
flatlist.close()
immatch.imcombine.input = '@flatlist'
immatch.imcombine.output = 'MasterFlat.fits'
immatch.imcombine.combine = "median"
immatch.imcombine.reject = "none"
immatch.imcombine.mode = "h"
immatch.imcombine()
print "# (x1,y2)_________________(x2,y2) #"
print "# | | #"
print "# (x1,y1)_________________(x2,y1) #"
print "# #"
print "# It will help you to determine the standard deviation of the background #"
print "# which are required inputs for the IRAF tasks 'daofind' and 'phot' #"
print "###########################################################################"
if dumpdata in ('N','n'):
os.system("ds9 "+fitslist[0]+"&")
skybox = raw_input("Enter coordinates of a box without stars in the format [x1:x2,y1:y2] : ")
if skybox != '':
while skybox.count('[')<1 or skybox.count(']')<1 or skybox.count(':')<2 or skybox.count(',')<1:
skybox = raw_input("The correct format is [x1:x2,y1:y2] , with all the brackets and punctuation included. Please try again: ")
print >> inputs, skybox
# Determine the standard deviation in the backgound
stddev = imutil.imstat(images = fitslist[0]+skybox , mode = "h", fields = 'image,mean,stddev',Stdout=1)[1].split()[-1]
print 'STDDEV in the background is :', stddev
# Allow the user to accept the values of the parameter file, revert to default or exit to adjust the file before runnning PHOTscript
print "###########################################################################"
print "CONTENTS OF THE 'parameters' FILE IN THIS DIRECTORY IS:"
print "###########################################################################"
print " "
os.system('cat parameters')
print "###########################################################################"
print " "
promtpar = raw_input("Do you wish to continue with the photometry using the parameters listed above (Y/N)? ")
promtpar = checkYNinput(promtpar)
print >> inputs, promtpar
if promtpar not in ('Y','y',''):
print "###########################################################################"
1) + ".fits[*," + trimbox + "]', output='tf.spectra" + str(
targetcount + 1) + ".fits', verbose='yes')"
print >> targetlist, 'Reduced/spectra' + str(targetcount + 1) + '.fits'
#print >> targetlist, '# Original filename:', filenames[i], utcdate, utctime
#print >> targetlist, '#', gratingvalues
targetcount = targetcount + 1
targetfiles.append(filenames[i])
# FLAT file: CCDTYPE = 'FLAT '
if obstype.count('FLAT') > 0:
# Strip multi header:
flatfield = 'Reduced/flat' + str(flatcount + 1) + '.fits'
imutil.imcopy(input=filenames[i] + '[SCI,inherit]',
output=flatfield,
verbose='yes')
averageflux = imutil.imstat(images=flatfield,
mode="h",
fields='image,mean,stddev',
Stdout=1)[1].split()[-2]
imutil.imarith(operand1=flatfield,
op="/",
operand2=str(averageflux),
result=flatfield,
title="Normalized FLAT",
mode="h")
print filenames[i] + ' is a FLAT'
print >> flatlist, flatfield
#print >> flatlist, '# Original filename:', filenames[i], gratingvalues
flatcount = flatcount + 1
if flatcount > 0:
# Make MASTER flat
flatlist.close()
print "# which are required inputs for the IRAF tasks 'daofind' and 'phot' #"
print "###########################################################################"
skybox = raw_input(
"Enter coordinates of a box without stars in the format [x1:x2,y1:y2] : "
)
if skybox != '':
while skybox.count('[') < 1 or skybox.count(
']') < 1 or skybox.count(':') < 2 or skybox.count(',') < 1:
skybox = raw_input(
"The correct format is [x1:x2,y1:y2] , with all the brackets and punctuation included. Please try again: "
)
print >> inputs, skybox
# Determine the standard deviation in the backgound
stddev = imutil.imstat(images=fitslist[0] + skybox,
mode="h",
fields='image,mean,stddev',
Stdout=1)[1].split()[-1]
print 'STDDEV in the background is :', stddev
# Allow the user to accept the values of the parameter file, revert to default or exit to adjust the file before runnning PHOTscript
print "###########################################################################"
print "CONTENTS OF THE 'parameters' FILE IN THIS DIRECTORY IS:"
print "###########################################################################"
print " "
os.system('cat parameters')
print "###########################################################################"
print " "
promtpar = raw_input(
"Do you wish to continue with the photometry using the parameters listed above (Y/N)? "
)
promtpar = checkYNinput(promtpar)