def alignClean(self):
try:
os.chdir(self.dirClean)
# Get the align data type
fitsFile = self.cleanFiles[0] + '.fits'
alignType = nirc2_util.get_align_type(fitsFile, errors=False)
alignCombo = alignType + 1
# Make the align*.list file
os.chdir(self.dirCleanAln)
alnList = 'align_%s%s_%3.1f.list' % (self.imgSuffix, self.filt, self.corrClean)
_list = open(alnList, 'w')
# copy main map into it
_list.write('%smag%s%s_%s_rms.lis %d ref\n' %
(self.dirComboStf, self.epoch, self.imgSuffix, self.filt, alignCombo))
# Add each clean file
for ff in self.cleanFiles:
_list.write('../%s_%3.1f_stf_cal.lis %d\n' %
(ff, self.corrClean, alignType))
_list.close()
# Run align
cmd = 'java -Xmx1024m align %s ' % (self.alignFlags)
cmd += '-N %s ' % self.labellist
if (self.orbitlist != None) and (self.orbitlist != ''):
cmd += '-o %s ' % self.orbitlist
cmd += '-r align_%s%s_%3.1f_named ' % (self.imgSuffix, self.filt, self.corrClean)
cmd += alnList
#os.system(cmd)
subp = subprocess.Popen(cmd, shell=True, executable="/bin/tcsh")
tmp = subp.communicate()
# Copy over the label.dat file that was used.
shutil.copyfile(self.labellist,
'align_%s%s_%3.1f_named_label_list.txt' %
(self.imgSuffix, self.filt, self.corrClean))
if (self.orbitlist != None) and (self.orbitlist != ''):
shutil.copyfile(self.orbitlist,
'align_%s%s_%3.1f_named_orbit_list.txt' %
(self.imgSuffix, self.filt, self.corrClean))
os.chdir(self.dirStart)
except:
os.chdir(self.dirStart)
raise
def alignCombo(self):
print 'ALIGN_RMS combo'
if self.type == 'ao':
file_ext = '_' + self.filt
else:
file_ext = self.filt
try:
os.chdir(self.dirCombo)
# Get the align data type
if self.type == 'ao':
fitsFile = 'mag%s%s_%s.fits' % (self.epoch, self.imgSuffix, self.filt)
elif self.type == 'speckle':
fitsFile = 'mag%s.fits' % self.epoch
alignType = nirc2_util.get_align_type(fitsFile, errors=False)
os.chdir(self.dirComboAln)
# Put the files in to the align*.list file
alnList1 = 'align%s%s_%3.1f.list' % (self.imgSuffix, file_ext, self.corrMain)
alnList2 = 'align%s%s_%3.1f_named.list' % (self.imgSuffix, file_ext, self.corrMain)
_list = open(alnList1, 'w')
if self.deblend == 1:
_list.write('../mag%s%s%s_%3.1fd_stf_cal.lis %d ref\n' %
(self.epoch, self.imgSuffix, file_ext, self.corrMain, alignType))
else:
_list.write('../mag%s%s%s_%3.1f_stf_cal.lis %d ref\n' %
(self.epoch, self.imgSuffix, file_ext, self.corrMain, alignType))
for ss in range(self.numSubMaps):
if self.deblend == 1:
_list.write('../m%s%s%s_%d_%3.1fd_stf_cal.lis %d\n' %
(self.epoch, self.imgSuffix, file_ext, ss+1, self.corrSub, alignType))
else:
_list.write('../m%s%s%s_%d_%3.1f_stf_cal.lis %d\n' %
(self.epoch, self.imgSuffix, file_ext, ss+1, self.corrSub, alignType))
_list.close()
shutil.copyfile(alnList1, alnList2)
# Make an unlabeled version
cmd = 'java -Xmx1024m align %s ' % (self.alignFlags)
cmd += '-r align%s%s_%3.1f ' % (self.imgSuffix, file_ext, self.corrMain)
cmd += alnList1
print cmd
#os.system(cmd)
subp = subprocess.Popen(cmd, shell=True, executable="/bin/tcsh")
tmp = subp.communicate()
# Make a named/labeled version
cmd = 'java -Xmx1024m align %s ' % (self.alignFlags)
cmd += '-N %s ' % self.labellist
if (self.orbitlist != None) and (self.orbitlist != ''):
cmd += '-o %s ' % self.orbitlist
cmd += '-r align%s%s_%3.1f_named ' % (self.imgSuffix, file_ext, self.corrMain)
cmd += alnList2
print cmd
subp = subprocess.Popen(cmd, shell=True, executable="/bin/tcsh")
tmp = subp.communicate()
align_options = 'align%s%s_%3.1f %d -e' % \
(self.imgSuffix, file_ext, self.corrMain, self.minSubMaps)
align_rms.run(align_options.split())
align_options = 'align%s%s_%3.1f_named %d -e' % \
(self.imgSuffix, file_ext, self.corrMain, self.minSubMaps)
align_rms.run(align_options.split())
# Move the resulting files to their final resting place
os.rename('align%s%s_%3.1f_rms.lis' %
(self.imgSuffix, file_ext, self.corrMain),
'../mag%s%s%s_rms.lis' %
(self.epoch, self.imgSuffix, file_ext))
os.rename('align%s%s_%3.1f_named_rms.lis' %
(self.imgSuffix, file_ext, self.corrMain),
'../mag%s%s%s_rms_named.lis' %
(self.epoch, self.imgSuffix, file_ext))
# Copy over the label.dat and orbit.dat file that was used.
shutil.copyfile(self.labellist,
'align%s%s_%3.1f_named_label_list.txt' %
(self.imgSuffix, file_ext, self.corrMain))
if (self.orbitlist != None) and (self.orbitlist != ''):
shutil.copyfile(self.orbitlist,
'align%s%s_%3.1f_named_orbit_list.txt' %
(self.imgSuffix, file_ext, self.corrMain))
# Now plot up the results
plotSuffix = self.imgSuffix + file_ext
os.chdir(self.dirComboStf)
plotPosError('mag%s%s%s_rms.lis' % (self.epoch, self.imgSuffix, file_ext),
raw=True, suffix=plotSuffix, magCutOff=self.plotPosMagCut)
os.chdir(self.dirStart)
except:
os.chdir(self.dirStart)
raise
