def calculateac05(self, input, column, operation, outputfmt): ''' Can be used to calculate the ac05 (from 3 pix to 10pix) aperture correction. Uses IRAF task tcalc, and adds the calculated values as a new column at the end of the table. ''' I.tcalc(input, column, operation, colfmt=outputfmt)
def calculateac05(self, input, column, operation, outputfmt):
'''
Can be used to calculate the ac05 (from 3 pix to 10pix) aperture correction.
Uses IRAF task tcalc, and adds the calculated values as a new column at the
end of the table.
'''
I.tcalc(input, column, operation, colfmt=outputfmt)
def post_correction_check(config, sky, sky_nofits, total_sci_ext, fits_number):
for i in range(1,total_sci_ext+1):
galaxy.instres(sky,linelist='igaldir$GMOSsky_instres.dat', sci_ext='sci,%d' % i)
iraf.rename('%s_instres.tab' % sky_nofits, '%s_instres_slit%d_post.tab' % (sky_nofits, i))
iraf.tcalc('%s_instres_slit%d_post.tab' % (sky_nofits, i), 'dlambda', 'LAMBDAIN-lambdaout', colfmt='f6.3')
iraf.tstat('%s_instres_slit%d_post.tab' % (sky_nofits, i), 'dlambda', outtable='%s_lambdaoffall_post.tab' % config)
iraf.tstat('%s_instres_slit%d_post.tab' % (sky_nofits, i), 'dlambda', outtable='%s_lambdaoff_post.tab' % config, lowlim=(iraf.tstat.median-3*iraf.tstat.stddev), highlim=(iraf.tstat.median+3*iraf.tstat.stddev))
end_row = total_sci_ext * fits_number #the mdf is minus 1 bc the offset between MDF index # and actual number
beg_row = (total_sci_ext * fits_number) - (total_sci_ext-1) #the mdf is -2; -1 to account for offset and another -1
print 'Taking the median of rows: %s - %s in the %s file for file #%d of the file list' % (beg_row, end_row, '*_lambdaoff.tab', fits_number)
iraf.tstat('%s_lambdaoff_post.tab' % config,'median',outtable='%s_lambdaoffmed_post.tab' % config,row='%s - %s' % (beg_row, end_row), Stdout=0)
def checkMDF(self, rawMDF, flatList, **kwargs):
# copy raw MDF to local directory
mdf = rawMDF
if not os.path.exists(mdf):
print "\nFETCHING RAW MDF"
mdfPath = "/Users/roedigerj/anaconda/envs/astroconda/iraf_extern/gemini/gmos/data/"
rawMDF = mdfPath + rawMDF
shutil.copy(rawMDF, "./")
# TODO: check that flatList is not empty
# grab the name of a single flat to reduce
im = utils.getImPaths(flatList)[0]
print "\nCHECKING MDF WITH " + im
# repeat the following steps until the MDF deemed correct
while True:
# do basic reduction of selected exposure
_ = self.reduceIm(im, fl_inter="no", fl_gscrrej="no", \
fl_extract="no", fl_wavtran="no", fl_skysub="no", \
fl_fluxcal="no", mdffile=mdf, mdfdir="./", verbose="no", \
**kwargs)
# extract spectrum to check match between MDF and IFU flat
logFile = ""
if "logfile" in kwargs.keys():
logFile = kwargs["logfile"]
iraf.delete("database/aperg" + im[:im.find(".")] + "*",
verify="yes")
self.extractSpec("rg" + im, fl_inter="yes", logfile=logFile, \
verbose="no")
# TODO: remove any extracted files
# call tcalc to fix MDF (if necessary)
fixMDF = bool(input("\nDoes MDF need fixing? (True/False): "))
if fixMDF:
fiber = input("Fiber to fix: ")
flag = input("Flag value: ")
iraf.tcalc(
mdf, "BEAM", "if NO == " + str(fiber) + "then " +
str(flag) + " else BEAM")
else:
break
return
def slit_offset(config, sky, sky_nofits, total_sci_ext):
#the range matches up the index with the MDF science extensions; instres only works on science extensions
for i in range(1,total_sci_ext+1):
#this creates an STsci table (which can be read, edited, etc from the ttools package)
line_list='igaldir$GMOSsky_instres.dat'
galaxy.instres(sky, linelist=line_list, output='%s_instres_slit%d.tab' % (sky_nofits, i), sci_ext='sci,%d' % i)
#showing a graph that plots the gaussian fit to the sky lines in the image
#iraf.gkimos('tmp.gki')
#os.system('rm tmp.gki')
#this is determining the change in wavelength (delta lambda) of the line-list from the measured lines
#LAMDAIN is the rest wavelength line and lambdaout is the skyline from our frame (colfmt gives the type of unit)
iraf.tcalc('%s_instres_slit%d.tab' % (sky_nofits, i), 'dlambda', 'LAMBDAIN-lambdaout', colfmt='f6.3')
#this is extracting the dlambda column of the file and putting it into a new table
#the new table will be populated with the mean, stddev, median, min, and max values for the loaded table column (dlambda)
iraf.tstat('%s_instres_slit%d.tab' % (sky_nofits, i), 'dlambda', outtable='%s_lambdaoffall.tab' % config)
#this is extracting the dlambda column of the loaded file and putting it into another table if it's within certain limits
#the new table will be populated with the mean, stddev, median, min, and max values for the restricted dlambda values
iraf.tstat('%s_instres_slit%d.tab' % (sky_nofits, i), 'dlambda', outtable='%s_lambdaoff.tab' % config, lowlim=(iraf.tstat.median-3*iraf.tstat.stddev), highlim=(iraf.tstat.median+3*iraf.tstat.stddev))
def correctMagnitude(self, input, column, operation, outputfmt):
'''
Essentially the same as calculateac05 function.
'''
I.tcalc(input, column, operation, colfmt=outputfmt)
for i in mask2:
root = i[0:13]
#this is copying the primary header unit to the new MEF
iraf.imcopy('corrected_cmgs%s[%d]' % (i, 0), 'corrected_cmgs%s_ext25.fits' % root)
#this is copying the MDF extension to the new MEF (using iraf's table select function to create a new table from rows of an old one)
#the MDF index number is different than the MEF extension # - the MDF counts acquisition stars, the MEF index doesn't;
#I'm copying the MDF information about ext 25 to the MDF of the new MEF we're making
iraf.tselect('corrected_cmgs%s.fits[MDF]' % root,'corrected_cmgs%s_ext25.fits[1]' % root, 'extver==24')
#this is allowing us to rename extension 1's name to 'MDF' in the newly created MEF (can check it worked with pyfits.info(filename))
iraf.parkey("MDF",'corrected_cmgs%s_ext25.fits[1]' % root,"EXTNAME",add='yes')
#we are re-writing the 'extver' value (written two steps before) in the MDF to 1 in this step.
iraf.tcalc('corrected_cmgs%s_ext25.fits[MDF]' % root, 'extver','1')
#here we are inserting the 25th extension (the double object slit) into extension 2 of our newly-created MEF
iraf.fxinsert('corrected_cmgs%s.fits[25]' % root, 'corrected_cmgs%s_ext25.fits[2]' % root)
#hedit allows us to change header values; here I'm adjusting some of the values so they reflect the position in the new MEF
#these are values changed in the actual data part of the image (how is that possible? no keywords are there?)
iraf.hedit('corrected_cmgs%s_ext25.fits[2]' % root, 'EXTVER', 1, upd='yes', ver='no')
iraf.hedit('corrected_cmgs%s_ext25.fits[2]' % root, "MDFROW", 1, upd='yes', ver='no') # used by gsskysub
#these are values changed in the header of the image
iraf.hedit('corrected_cmgs%s_ext25.fits[0]' % root, "NSCIEXT", 1, upd='yes', ver='no') #number of science extensions
iraf.hedit('corrected_cmgs%s_ext25.fits[0]' % root, "NEXTEND", 2, upd='yes', ver='no') #number of extensions in file
#running those extracted slits through gsskysub manually;
def correctMagnitude(self, input, column, operation, outputfmt): ''' Essentially the same as calculateac05 function. ''' I.tcalc(input, column, operation, colfmt=outputfmt)