def alignToMaster(self):
refList = 'master.lis'
for ii in range(len(self.images)):
alignRoot = self.alignDir + 'master_' + str(ii)
alignRoot += '_' + self.fields[ii]
alignRootBoot = self.alignDir + 'master_boot_' + str(ii)
alignRootBoot += '_' + self.fields[ii]
starList = self.images[ii] + '_rms_dist.lis'
print '*** Aligning to master:'
print '*** Working on %s ***' % starList
print
# ==========
# Re-order refList to shift common source to the top.
# ==========
newRefList = self.lisDir + 'master_%d_%s' % (ii, refList) # Always the same ref list, but with
# different stars at the top
newStarList = self.lisDir + 'nirc2_%d_%s' % (ii, starList)
# Ref List
shiftToTopOfList(self.lisDir + refList, newRefList,
self.refStars[self.fields[ii]])
# Star List
shiftToTopOfList(self.lisDir + starList, newStarList,
self.refStars[self.fields[ii]])
# Get the align data type
fitsFile = self.dataDir + '../%s.fits' % (self.images[ii])
alignType = dataUtil.get_align_type(fitsFile, errors=True)
# Get the angle
posAngle = dataUtil.get_pos_angle(fitsFile)
if posAngle != 0 and self.alignOrder == 0:
print 'You must allow for rotation with alignOrder > 0'
# ==========
# Align
# ==========
_list = open(alignRoot + '.list', 'w')
_list.write('%s %d ref\n' % (newRefList, alignType))
_list.write('%s %d\n' % (newStarList, alignType))
_list.close()
print '\n*** Aligning %s ***' % starList
cmd = 'java align -v -p -a %d -r %s %s.list' % (self.alignOrder, alignRoot, alignRoot)
os.system(cmd)
# Bootstrap
print '\n*** Aligning %s (bootstrap) ***' % starList
ntrials = 100
cmd = 'java align -v -p -a %d -n %d -r %s %s.list' % \
(self.alignOrder, ntrials, alignRootBoot, alignRoot)
os.system(cmd)
def makeNamedStarlist(self):
"""
We would like to make a named starlist. We do this with a trick...
just align a dummy starlist to our *rms.lis and pass in
label.dat to align.
"""
mosaicRoot = 'mag' + self.epoch +'_'+ self.mosaic +'_'+ self.filter
starlist = self.tableDir + mosaicRoot + '_rms_dist.lis'
dumblist = self.lisDir + self.images[0] + '_rms_dist.lis' # This is shorter
newList1 = self.lisDir + mosaicRoot + '_align_label.lis'
newList2 = self.lisDir + self.images[0] + '_align_label.lis'
# Match sources at the top
shiftToTopOfList(starlist, newList1, self.refStars[self.fields[0]])
shiftToTopOfList(dumblist, newList2, self.refStars[self.fields[0]])
# Get the align data type
fitsFile = self.dataDir + '../%s.fits' % (self.images[0])
alignType = dataUtil.get_align_type(fitsFile, errors=True)
alignRoot = self.alignDir + 'align_label'
_list = open(alignRoot + '.list', 'w')
_list.write('%s %d ref\n' % (newList1, alignType))
_list.write('%s %d\n' % (newList2, alignType))
_list.close()
cmd = 'java align -v -p -a 2 -R 1 '
cmd += '-N /g/lu/data/orion/source_list/label.dat '
cmd += '-r %s %s.list' % (alignRoot, alignRoot)
print cmd
os.system(cmd)
# This will be our new starlist
list = starTables.StarfinderList(None, hasErrors=True)
# Make a new starlist out of the resulting align output
s = starset.StarSet(alignRoot)
# Trim out all stars only detected in the dummy epoch.
mag = s.getArrayFromEpoch(0, 'mag')
idx = np.where(mag != 0)[0]
newStars = []
for ii in idx:
newStars.append(s.stars[ii])
s.stars = newStars
# Pull the data from the aligned epoch
list.name = np.array(s.getArray('name'))
list.epoch = np.zeros(len(s.stars), dtype=float) + s.years[0]
list.mag = s.getArrayFromEpoch(0, 'mag')
list.x = s.getArrayFromEpoch(0, 'xpix')
list.y = s.getArrayFromEpoch(0, 'ypix')
list.xerr = s.getArrayFromEpoch(0, 'xpixerr_p')
list.yerr = s.getArrayFromEpoch(0, 'ypixerr_p')
list.snr = s.getArrayFromEpoch(0, 'snr')
list.corr = s.getArrayFromEpoch(0, 'corr')
list.nframes = s.getArrayFromEpoch(0, 'nframes')
list.counts = s.getArrayFromEpoch(0, 'fwhm')
list.saveToFile(starlist.replace('rms_dist', 'rms_named'))
shutil.copyfile(self.tableDir + mosaicRoot + '_rms_named.lis',
self.dataDir + mosaicRoot + '_rms_named.lis')
def alignToMakeMaster(self):
"""
Loop through and align the images to the master list that
is slowly being built up.
Include the alignment of central to central field in order to
include the distortion error in that image and to include those
positions when computing the average
"""
# Define a running variable that contains the refList. This
# will be updated after each loop.
refList = self.firstRefList
for ii in range(0, len(self.images)):
alignRoot = self.alignDir + 'align_'
alignRoot += str(ii) + '_' + self.fields[ii]
alignRootBoot = self.alignDir + 'align_boot_'
alignRootBoot += str(ii) + '_' + self.fields[ii]
starList = self.images[ii] + '_rms_dist.lis'
# ==========
# Re-order refList to shift common source to the top.
# ==========
newRefList = self.lisDir + 'ref_%d_%s' % (ii, refList)
newStarList = self.lisDir + 'nirc2_%d_%s' % (ii, starList)
# Ref List
shiftToTopOfList(self.lisDir + refList, newRefList,
self.refStars[self.fields[ii]])
# Star List
shiftToTopOfList(self.lisDir + starList, newStarList,
self.refStars[self.fields[ii]])
# Get the align data type
fitsFile = self.dataDir + '../%s.fits' % (self.images[ii])
alignType = dataUtil.get_align_type(fitsFile, errors=True)
# Get the angle
posAngle = dataUtil.get_pos_angle(fitsFile)
if posAngle != 0 and self.alignOrder == 0:
print 'You must allow for rotation with alignOrder > 0'
# ==========
# Align
# ==========
_list = open(alignRoot + '.list', 'w')
_list.write('%s %s ref\n' % (newRefList, alignType))
_list.write('%s %d\n' % (newStarList, alignType))
_list.close()
print '\n*** Aligning %s ***' % starList
cmd = 'java align -v -p -a %d -r %s %s.list' % (self.alignOrder, alignRoot, alignRoot)
os.system(cmd)
# Bootstrap
print '\n*** Aligning %s (bootstrap) ***' % starList
ntrials = 100
cmd = 'java align -v -p -a %d -n %d -r %s %s.list' % \
(self.alignOrder, ntrials, alignRootBoot, alignRoot)
os.system(cmd)
# ==========
# Make a new reference list out of the previous align results
# This builds up a list after each alignment
# ==========
refList = 'aligned_%d_%s' % (ii, starList)
starPrefix = 'ep%d' % ii
makeNewRefList(alignRootBoot, self.lisDir + refList,
starPrefix=starPrefix)
shutil.copyfile(self.lisDir + refList, self.lisDir + 'master.lis')
