def MEFarithOLD(MEF, image, out, op, result):
if os.path.exists(out + '.fits'):
os.remove(out + '.fits')
for i in range(1, 88):
header = pyfits.open(MEF + '.fits')
extname = header[i].header['EXTNAME']
if extname == 'DQ' or extname == 'VAR':
iraf.imarith(operand1=MEF + '[' + str(i) + ']',
op='*',
operand2='1',
result=out)
if extname == 'SCI':
iraf.imarith(operand1=MEF + '[' + str(i) + ']',
op=op,
operand2=image,
result=out,
divzero=0.0)
iraf.fxcopy(input=MEF + '[0],' + out, output=result)
iraf.hedit(result + '[1]',
field='EXTNAME',
value='SCI',
add='yes',
verify='no')
iraf.hedit(result + '[1]',
field='EXTVER',
value='1',
add='yes',
verify='no')
def MEFarith(MEF, image, op, result):
if os.path.exists(result):
os.remove(result)
iraf.fxcopy(input=MEF+'[0]', output=result)
for i in range(1,88):
iraf.fxinsert(input=MEF+'['+str(i)+']', output=result+'['+str(i)+']', groups='', verbose = 'no')
for i in range(1,88):
header = astropy.io.fits.open(result)
extname = header[i].header['EXTNAME']
if extname == 'SCI':
iraf.imarith(operand1=result+'['+str(i)+']', op=op, operand2 = image, result = result+'['+str(i)+', overwrite]', divzero = 0.0)
def finalMergeCubes(mergeType, over):
"""
Merge final merged cubes from all observations.
"""
# Load data from the previous step.
path = os.getcwd()
with open('mergedInfo.txt') as data_file:
mergedData = json.load(data_file)
mergedCubes = mergedData['mergedCubes']
Merged = mergedData['Merged']
if len(mergedCubes)>1:
os.chdir(Merged)
iraffunctions.chdir(Merged)
gratlist = []
for i in range(len(mergedCubes)):
cubeheader = astropy.io.fits.open(mergedCubes[i])
grat = cubeheader[0].header['GRATING']
gratlist.append(grat)
print "gratlist is: ", gratlist
# TODO(nat): right now we do more final merges here than we have to. Eg, if there are three H
# grating directories in gratlist, we will do a final merge three times. We should only be doing this once!
# Right now it is only a problem when overwrite is turned on but it should still be fixed.
for n in range(len(gratlist)): # For each unique grating
# Grab the indices of the cubes associated with that grating.
indices = [k for k, x in enumerate(gratlist) if x==gratlist[n]]
newcubelist = []
for ind in indices:
newcubelist.append(mergedCubes[ind])
print newcubelist
# Do some housekeeping before the final cube merging.
resizeAndCenterCubes(newcubelist, over)
makeWavelengthOffsets(newcubelist, grat)
for i in range(len(newcubelist)):
# Build an input string containing all the cubes to combine.
if i==0:
inputstring = newcubelist[i]+'[1]'
else:
inputstring += ','+newcubelist[i]+'[1]'
if os.path.exists('temp_merged'+gratlist[n][0]+'.fits'):
if over:
iraf.delete('temp_merged'+gratlist[n][0]+'.fits')
iraf.imcombine(inputstring, output = 'temp_merged'+gratlist[n][0]+'.fits', combine = mergeType, offsets = 'waveoffsets'+grat[0]+'.txt')
iraf.fxcopy(input=newcubelist[0]+'[0], temp_merged'+gratlist[n][0]+'.fits', output = 'TOTAL_merged'+gratlist[0][0]+'.fits')
else:
logging.info('Output exists and -over- not set - skipping final cube merge')
else:
iraf.imcombine(inputstring, output = 'temp_merged'+gratlist[n][0]+'.fits', combine = mergeType, offsets = 'waveoffsets'+grat[0]+'.txt')
iraf.fxcopy(input=newcubelist[0]+'[0], temp_merged'+gratlist[n][0]+'.fits', output = 'TOTAL_merged'+gratlist[n][0]+'.fits')
os.chdir(path)
def mergeCubes(obsDirList, cubeType, mergeType, use_pq_offsets, im3dtran, over=""):
"""MERGE
This module contains all the functions needed to merge
the final data cubes.
NOTE: If you wish to shift the cubes manually in QFits View
you can combine them in this script by making sure that you
attach the prefix "shif" to each shifted image and save them
in the observation directory (ie. obs108). This is necessary
for very faint objects.
TODO(nat): I think what we want as a final product is one cube per grating,
per object. I need to finish generalizing this so it really works with multiple
gratings, observations and objects.
We should loop like this: For each object, for each grating, for each observation.
Merge all cubes in an observation. Then Merge all cubes of the same grating. Then
do that for every object in the program.
INPUT:
- Reference data cubes
- A list of paths where final data cubes are located
- Transformed integral field spectra
OUTPUT:
- Merged cubes for each observation (ie. DATE_obs##(#).fits)
- One final merged cube from entire observation program
"""
# Store the current working directory so we can find our way back later on.
path = os.getcwd()
iraffunctions.chdir(path)
# Set the default logfile for iraf tasks.
# TODO: Set the logfile for all iraf tasks! Right now it is not logging their output because of im3dtran...
# It seems im3dtran doesn't have a "log" parameter.
log = "Nifty.log"
# Set appropriate suffix for cube type.
if cubeType == "uncorrected":
suffix = "_uncorrected"
unmergedDirectory = 'products_uncorrected'
elif cubeType == "telluricCorrected":
suffix = "_telluricCorrected"
unmergedDirectory = 'products_telluric_corrected'
elif cubeType == "telCorAndFluxCalibrated":
suffix = "_telCorAndFluxCalibrated"
unmergedDirectory = 'products_fluxcal_AND_telluric_corrected'
else:
logging.info("No suffix found!")
return
# Create some lists here.
listsOfCubes = [] # List of lists of cubes (one list for each science observation directory).
mergedCubes = [] # List of Merged cubes (one merged cube for each science observation directory).
obsidlist = [] # List of science observation id s.
# Store the merged directory
targetDirectory = None
# Pixel scale in arcseconds/pixel.
pixScale = 0.05
# TODO(nat): implement a way to read and save cubelists to textfiles. It would be nice for users to
# be able to edit the list of cubes to merge by hand.
# If no Merged directory exists that contains a textfile list of cubes:
# Go to each science directory and copy cubes from there to a new directory called Merged.
# TODO(nat): This code seems to work really well, but it could use some polishing. Feel free to refactor nicely!
for obsDir in obsDirList:
# Get date, obsid and obsPath by splitting each science directory name.
# Eg: directory name is ""/Users/ncomeau/research/newer-nifty/hd165459/20160705/H/obs13", then:
# temp1 == ('/Users/ncomeau/research/newer-nifty/hd165459/20160705/H', 'obs13')
# temp2 == ('/Users/ncomeau/research/newer-nifty/hd165459/20160705', 'H')
# temp3 == ('/Users/ncomeau/research/newer-nifty/hd165459', '20160705')
# temp4 == ('/Users/ncomeau/research/newer-nifty', 'hd165459')
if not obsDir:
raise ValueError("nifsMerge: There was a problem with the science directory list.")
# TODO: make this clearer.
temp1 = os.path.split(obsDir)
temp2 = os.path.split(temp1[0])
temp3 = os.path.split(temp2[0])
temp4 = os.path.split(temp3[0])
objname = temp3[1]
date = temp3[1]
obsid = temp1[1]
obsPath = temp3[0]
targetDirectory = temp4[0]
try:
os.chdir(obsDir + '/'+unmergedDirectory)
except OSError:
raise OSError("nifsMerge: a science directory didn't exist.")
obsidlist.append(obsPath+'/Merged'+suffix+'/'+date+'_'+obsid)
# Create a directory called Merged and copy all the data cubes to this directory.
if not os.path.exists(obsPath+'/Merged'+suffix+'/'):
os.mkdir(obsPath+'/Merged'+suffix+'/')
logging.info('\nI am creating a directory called Merged'+str(suffix))
Merged = obsPath+'/Merged'+suffix
if not os.path.exists(Merged+'/'+date+'_'+obsid):
os.mkdir(Merged+'/'+date+'_'+obsid)
logging.info('\nI am creating a directory with date and abs ID inside Merged.')
# If a list called shiftedcubes already exists then just merge those shifted cubes and continue.
if glob.glob("./shift*.fits"):
if over:
if os.path.exists('./'+obsid+'_merged.fits'):
os.remove('./'+obsid+'_merged.fits')
iraf.gemcube(input="shif*.fits[SCI]", output=obsid+'_merged', logfile = log)
elif not os.path.exists('./'+obsid+'_merged.fits'):
iraf.gemcube(input="shif*.fits[SCI]", output=obsid+'_merged', logfile = log)
else:
logging.info("Output exists and -over- not set - shifted cubes are not being merged")
shutil.copy('./'+obsid+'_merged.fits', Merged)
if obsDir==obsDirList[-1]:
return
else:
continue
# Create a list called cubes, which stores all the cubes from a particular night.
# Store all the cubes lists in a list of lists called listsOfCubes.
# TODO: syntax is fairly ugly; there may be a better way to do this.
if cubeType == "uncorrected":
cubes = glob.glob('ctfbrsnN*.fits') # Cubes order at this point is arbitrary so we need to sort.
if cubes:
cubes.sort(key=lambda x: x[-8:-5]) # Sort cubes in increasing order by last three digits.
listsOfCubes.append(cubes)
else:
logging.info("Warning: no uncorrected cubes found in " + str(os.getcwd()))
logging.info("Skipping cube merging in this directory.")
return
elif cubeType == "telluricCorrected":
cubes = glob.glob('actfbrsnN*.fits')
if cubes:
cubes.sort(key=lambda x: x[-8:-5]) # Sort cubes in increasing order by last three digits.
listsOfCubes.append(cubes)
else:
logging.info("Warning: no telluric corrected cubes found in " + str(os.getcwd()))
logging.info("Skipping cube merging in this directory.")
return
elif cubeType == "telCorAndFluxCalibrated":
cubes = glob.glob('factfbrsnN*.fits')
if cubes:
cubes.sort(key=lambda x: x[-8:-5]) # Sort cubes in increasing order by last three digits.
listsOfCubes.append(cubes)
else:
logging.info("Warning: no flux calibrated and telluric corrected cubes found in " + str(os.getcwd()))
logging.info("Skipping cube merging in this directory.")
return
else:
logging.info("Invalid cube type; skipping cube merge for " + str(os.getcwd()))
return
# Copy cubes to their respective data_obsid directory within Merged.
for cube in cubes:
shutil.copy(cube, Merged+'/'+date+'_'+obsid)
os.chdir(Merged)
n=0
for cubes in listsOfCubes:
shiftlist = []
os.chdir(obsidlist[n])
iraffunctions.chdir(obsidlist[n])
if use_pq_offsets:
# Set the zero point p and q offsets to the p and q offsets of the first cube in each list of cubes.
header = astropy.io.fits.open(cubes[0])
p0 = header[0].header['POFFSET']
q0 = header[0].header['QOFFSET']
foff = open('offsets.txt', 'w')
foff.write('%d %d %d\n' % (0, 0, 0))
foff.close()
suffix = cubes[0][-8:-5]
if im3dtran:
if os.path.exists('transcube'+suffix+'.fits'):
if not over:
logging.info('Output already exists and -over- not set - skipping im3dtran')
if over:
os.remove('transcube'+suffix+'.fits')
iraf.im3dtran(input = cubes[0]+'[SCI][*,*,-*]', new_x=1, new_y=3, new_z=2, output = 'transcube'+suffix)
else:
iraf.im3dtran(input = cubes[0]+'[SCI][*,*,-*]', new_x=1, new_y=3, new_z=2, output = 'transcube'+suffix)
else:
iraf.imcopy(cubes[0]+'[SCI][*,*,*]', 'NONtranscube'+suffix+'.fits')
shiftlist.append('cube'+suffix+'.fits')
iraffunctions.chdir(os.getcwd())
for i in range(len(cubes)):
# Skip the first cube!
if i == 0:
continue
header2 = astropy.io.fits.open(cubes[i])
# Check to see if we are using ALTAIR. If we are, later we will invert the x offset
# because of the different light path.
ALTAIR = header2[0].header['AOFOLD'].strip() == 'IN'
suffix = cubes[i][-8:-5]
# If user wants to merge using p and q offsets, grab those from .fits headers.
if use_pq_offsets:
# find the p and q offsets of the other cubes in the sequence.
xoff = header2[0].header['POFFSET']
yoff = header2[0].header['QOFFSET']
# calculate the difference between the zero point offsets and the offsets of the other cubes and convert that to pixels
if ALTAIR:
xShift = round(-1*(xoff - p0)/pixScale)
else:
xShift = round((xoff - p0)/pixScale)
yShift = round((yoff - q0)/pixScale)
# write all offsets to a text file (keep in mind that the x and y offsets use different pixel scales)
foff = open('offsets.txt', 'a')
if im3dtran:
# If we swap the y and lambda axis we must also write the offsets in x, lambda, y.
foff.write('%d %d %d\n' % (int(xShift), 0, int(yShift)))
else:
# Write offsets in regular x, y, lambda.
foff.write('%d\t%d\t%d\n' % (xShift, yShift, 0.))
foff.close()
if im3dtran:
prefix = 'transcube'
if os.path.exists('transcube'+suffix+'.fits'):
if not over:
logging.info('Output already exists and -over- not set - skipping im3dtran')
if over:
os.remove('transcube'+suffix+'.fits')
iraf.im3dtran(input = cubes[i]+'[SCI][*,*,-*]', new_x=1, new_y=3, new_z=2, output = 'transcube'+suffix)
else:
iraf.im3dtran(input = cubes[i]+'[SCI][*,*,-*]', new_x=1, new_y=3, new_z=2, output = 'transcube'+suffix)
else:
prefix = 'NONtranscube'
iraf.imcopy(cubes[i]+'[SCI][*,*,*]', prefix+suffix+'.fits')
shiftlist.append('cube'+suffix+'.fits')
if not use_pq_offsets:
# Before we combine make sure a suitable offsets.txt file exists.
a = raw_input("\nPaused. Please provide a suitable offsets.txt file in ", obsidlist[n])
while not os.path.exists('offsets.txt'):
a = raw_input("No offsets.txt file found. Please try again.")
logging.info('offsets.txt found successfully for', obsidlist[n])
if os.path.exists('cube_merged.fits'):
if over:
os.remove('cube_merged.fits')
iraf.imcombine(prefix+'*', output = 'cube_merged.fits', combine = mergeType, offsets = 'offsets.txt')
else:
logging.info('Output already exists and -over- not set - skipping imcombine')
else:
iraf.imcombine(prefix+'*', output = 'cube_merged.fits', combine = mergeType, offsets = 'offsets.txt')
# TODO(nat): barf. This is pretty nasty... We should fix the overwrite statements here and
# find a way to use less nesting
if im3dtran:
# Transpose the cube back to x, y, lambda.
if os.path.exists('out.fits'):
if over:
os.remove('out.fits')
iraf.im3dtran(input='cube_merged[*,-*,*]', new_x=1, new_y=3, new_z=2, output = 'out.fits')
else:
logging.info('Output already exists and -over- not set - skipping final im3dtran')
else:
iraf.im3dtran(input='cube_merged[*,-*,*]', new_x=1, new_y=3, new_z=2, output = 'out.fits')
iraf.fxcopy(input=cubes[0]+'[0], out.fits', output = obsidlist[n]+'_merged.fits')
else:
iraf.fxcopy(input=cubes[0]+'[0], cube_merged.fits', output = obsidlist[n]+'_merged.fits')
mergedCubes.append(obsidlist[n]+'_merged.fits')
n+=1
os.chdir(Merged)
os.chdir(path)
# Save the data with JSON so we can grab it in the next step.
mergedData = {}
mergedData['mergedCubes'] = mergedCubes
mergedData['Merged'] = Merged
with open(targetDirectory+"/mergedInfo.txt", "w") as outfile:
json.dump(mergedData, outfile)
def start(obsDirList, use_pq_offsets, im3dtran, over=""):
"""MERGE
This module contains all the functions needed to merge
the final data cubes.
NOTE: If you wish to shift the cubes manually in QFits View
you can combine them in this script by making sure that you
attach the prefix "shif" to each shifted image and save them
in the observation directory (ie. obs108). This is necessary
for very faint objects.
INPUT:
- Reference data cubes
- A list of paths where final data cubes are located
- Transformed integral field spectra
OUTPUT:
- Merged cubes for each observation (ie. DATE_obs##(#).fits)
- One final merged cube from entire observation program
"""
# Store the current working directory so we can find our way back later on.
path = os.getcwd()
iraf.gemini()
iraf.nifs()
iraf.gnirs()
iraf.gemtools()
# Unlearn the used tasks.
iraf.unlearn(iraf.gemini, iraf.gemtools, iraf.gnirs, iraf.nifs)
# Prepare the package for NIFS
iraf.nsheaders("nifs", logfile="Nifty.log")
iraf.set(stdimage='imt2048')
user_clobber = iraf.envget("clobber")
iraf.reset(clobber='yes')
# Set the default logfile for iraf tasks.
# TODO: Set the logfile for all iraf tasks! Right now it is not logging their output because of im3dtran...
# It seems im3dtran doesn't have a "log" parameter.
log = "Nifty.log"
# Change to the directory in iraf.
iraffunctions.chdir(path)
# Create some lists here.
listsOfCubes = [
] # List of lists of cubes (one list for each science observation directory).
mergedCubes = [
] # List of Merged cubes (one merged cube for each science observation directory).
obsidlist = [] # List of science observation id s.
# Pixel scale in arcseconds/pixel.
pixScale = 0.05
# TODO(ncomeau[*AT*]uvic.ca): implement a way to read and save cubelists to textfiles. It would be nice for users to
# be able to edit the list of cubes to merge by hand.
# If no Merged directory exists that contains a textfile list of cubes:
# Go to each science directory and copy cubes from there to a new directory called Merged.
for obsDir in obsDirList:
# Get date, obsid and obsPath by splitting each science directory name.
# Eg: directory name is ""/Users/ncomeau/research/newer-nifty/hd165459/20160705/H/obs13", then:
# temp1 == ('/Users/ncomeau/research/newer-nifty/hd165459/20160705/H', 'obs13')
# temp2 == ('/Users/ncomeau/research/newer-nifty/hd165459/20160705', 'H')
# temp3 == ('/Users/ncomeau/research/newer-nifty/hd165459', '20160705')
# temp4 == ('/Users/ncomeau/research/newer-nifty', 'hd165459')
# TODO: make this clearer.
temp1 = os.path.split(obsDir)
temp2 = os.path.split(temp1[0])
temp3 = os.path.split(temp2[0])
temp4 = os.path.split(temp3[0])
objname = temp4[1]
date = temp3[1]
obsid = temp1[1]
obsPath = temp3[0]
os.chdir(obsDir)
obsidlist.append(date + '_' + obsid)
# Create a directory called Merged and copy all the data cubes to this directory.
if not os.path.exists(obsPath + '/Merged/'):
os.mkdir(obsPath + '/Merged/')
logging.info('I am creating a directory called Merged')
Merged = obsPath + '/Merged'
if not os.path.exists(Merged + '/' + date + '_' + obsid):
os.mkdir(Merged + '/' + date + '_' + obsid)
logging.info(
'I am creating a directory with date and abs ID inside Merged '
)
# If a list called shiftedcubes already exists then just merge those shifted cubes and continue.
if glob.glob("./shift*.fits"):
if over:
if os.path.exists('./' + obsid + '_merged.fits'):
os.remove('./' + obsid + '_merged.fits')
iraf.gemcube(input="shif*.fits[SCI]",
output=obsid + '_merged',
logfile=log)
elif not os.path.exists('./' + obsid + '_merged.fits'):
iraf.gemcube(input="shif*.fits[SCI]",
output=obsid + '_merged',
logfile=log)
else:
logging.info(
"Output exists and -over- not set - shifted cubes are not being merged"
)
shutil.copy('./' + obsid + '_merged.fits', Merged)
if obsDir == obsDirList[-1]:
return
else:
continue
# Create a list called cubes, which stores all the cubes from a particular night.
# Store all the cubes lists in a list of lists called listsOfCubes.
# TODO: syntax is fairly ugly; there may be a better way to do this.
cubes = glob.glob(
'catfbrsnN*.fits'
) # Cubes order at this point is arbitrary so we need to sort.
cubes.sort(key=lambda x: x[-8:-5]
) # Sort cubes in increasing order by last three digits.
if cubes:
listsOfCubes.append(cubes)
else:
cubes = glob.glob('cptfbrsnN*.fits')
if cubes:
cubes.sort(
key=lambda x: x[-8:-5]
) # Sort cubes in increasing order by last three digits.
listsOfCubes.append(cubes)
else:
cubes = glob.glob('ctfbrsnN*.fits')
if cubes:
cubes.sort(
key=lambda x: x[-8:-5]
) # Sort cubes in increasing order by last three digits.
listsOfCubes.append(cubes)
else:
logging.info(
"\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
)
logging.info(
"+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
)
logging.info("")
logging.info(" ERROR in merge: no cubes found!")
logging.info("")
logging.info(
"+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
)
logging.info(
"+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n"
)
raise SystemExit
# Copy cubes to their respective data_obsid directory within Merged.
for cube in cubes:
shutil.copy(cube, Merged + '/' + date + '_' + obsid)
os.chdir(Merged)
n = 0
for cubes in listsOfCubes:
shiftlist = []
os.chdir(Merged + '/' + obsidlist[n])
iraffunctions.chdir(Merged + '/' + obsidlist[n])
if use_pq_offsets:
# Set the zero point p and q offsets to the p and q offsets of the first cube in each list of cubes.
header = astropy.io.fits.open(cubes[0])
p0 = header[0].header['POFFSET']
q0 = header[0].header['QOFFSET']
foff = open('offsets.txt', 'w')
foff.write('%d %d %d\n' % (0, 0, 0))
foff.close()
suffix = cubes[0][-8:-5]
if im3dtran:
if os.path.exists('transcube' + suffix + '.fits'):
if not over:
logging.info(
'Output already exists and -over- not set - skipping im3dtran'
)
if over:
os.remove('transcube' + suffix + '.fits')
iraf.im3dtran(input=cubes[0] + '[SCI][*,*,-*]',
new_x=1,
new_y=3,
new_z=2,
output='transcube' + suffix)
else:
iraf.im3dtran(input=cubes[0] + '[SCI][*,*,-*]',
new_x=1,
new_y=3,
new_z=2,
output='transcube' + suffix)
else:
iraf.imcopy(cubes[0] + '[SCI][*,*,*]',
'NONtranscube' + suffix + '.fits')
shiftlist.append('cube' + suffix + '.fits')
iraffunctions.chdir(os.getcwd())
for i in range(len(cubes)):
# Skip the first cube!
if i == 0:
continue
header2 = astropy.io.fits.open(cubes[i])
suffix = cubes[i][-8:-5]
# If user wants to merge using p and q offsets, grab those from .fits headers.
if use_pq_offsets:
# find the p and q offsets of the other cubes in the sequence.
xoff = header2[0].header['POFFSET']
yoff = header2[0].header['QOFFSET']
# calculate the difference between the zero point offsets and the offsets of the other cubes and convert that to pixels
xShift = round((xoff - p0) / pixScale)
yShift = round((yoff - q0) / pixScale)
# write all offsets to a text file (keep in mind that the x and y offsets use different pixel scales)
foff = open('offsets.txt', 'a')
if im3dtran:
# If we swap the y and lambda axis we must also write the offsets in x, lambda, y.
foff.write('%d %d %d\n' % (int(xShift), 0, int(yShift)))
else:
# Write offsets in regular x, y, lambda.
foff.write('%d\t%d\t%d\n' % (xShift, yShift, 0.))
foff.close()
if im3dtran:
prefix = 'transcube'
if os.path.exists('transcube' + suffix + '.fits'):
if not over:
logging.info(
'Output already exists and -over- not set - skipping im3dtran'
)
if over:
os.remove('transcube' + suffix + '.fits')
iraf.im3dtran(input=cubes[i] + '[SCI][*,*,-*]',
new_x=1,
new_y=3,
new_z=2,
output='transcube' + suffix)
else:
iraf.im3dtran(input=cubes[i] + '[SCI][*,*,-*]',
new_x=1,
new_y=3,
new_z=2,
output='transcube' + suffix)
else:
prefix = 'NONtranscube'
iraf.imcopy(cubes[i] + '[SCI][*,*,*]',
prefix + suffix + '.fits')
shiftlist.append('cube' + suffix + '.fits')
if not use_pq_offsets:
# Before we combine make sure a suitable offsets.txt file exists.
a = raw_input(
"\nPaused. Please provide a suitable offsets.txt file in ",
Merged + '/' + obsidlist[n])
while not os.path.exists('offsets.txt'):
a = raw_input("No offsets.txt file found. Please try again.")
logging.info('offsets.txt found successfully for', obsidlist[n])
if os.path.exists('cube_merged.fits'):
if over:
os.remove('cube_merged.fits')
iraf.imcombine(prefix + '*',
output='cube_merged.fits',
combine='median',
offsets='offsets.txt')
else:
logging.info(
'Output already exists and -over- not set - skipping imcombine'
)
else:
iraf.imcombine(prefix + '*',
output='cube_merged.fits',
combine='median',
offsets='offsets.txt')
if im3dtran:
# Transpose the cube back to x, y, lambda.
if os.path.exists('out.fits'):
if over:
os.remove('out.fits')
iraf.im3dtran(input='cube_merged[*,-*,*]',
new_x=1,
new_y=3,
new_z=2,
output='out.fits')
else:
logging.info(
'Output already exists and -over- not set - skipping final im3dtran'
)
else:
iraf.im3dtran(input='cube_merged[*,-*,*]',
new_x=1,
new_y=3,
new_z=2,
output='out.fits')
iraf.fxcopy(input=cubes[0] + '[0], out.fits',
output=obsidlist[n] + '_merged.fits')
else:
iraf.fxcopy(input=cubes[0] + '[0], cube_merged.fits',
output=obsidlist[n] + '_merged.fits')
mergedCubes.append(obsidlist[n] + '_merged.fits')
n += 1
os.chdir(Merged)
# Copy the merged observation sequence data cubes to the Merged directory.
for i in range(len(mergedCubes)):
shutil.copy(Merged + '/' + obsidlist[i] + '/' + mergedCubes[i], './')
# Merge all the individual merged observation sequence data cubes.
# TODO: test. Still untested.
"""
import getopt