def getOverscanInfo():
if 'INSTRUMENT' not in os.environ:
raise NoInstrumentException
instrumentFile = '%s.ini' % os.environ['INSTRUMENT']
return OverscanInfo(bashreader.parseFile(instrumentFile))
def calcNearestNeighborCut(options, cat, psfsize, ldaclensing):
curdir = os.getcwd()
os.chdir(ldaclensing)
progs = bashreader.parseFile('progs.ini')
temp_inputcatfile = utilities.getTempFile(dir=progs.tempdir, suffix='.cat')
temp_outputcatfile = utilities.getTempFile(dir=progs.tempdir, suffix='.cat')
print cat.sourcefile
hdulist = pyfits.open(cat.sourcefile)
newhdus = [pyfits.PrimaryHDU()]
for hdu in hdulist[1:]:
if hdu.header['EXTNAME'] == 'OBJECTS':
newhdus.append(cat.hdu)
elif hdu.header['EXTNAME'] == 'FIELDS':
fieldstable = ldac.LDACCat(hdu)
fieldstable['OBJECT_COUNT'][:] = np.array([len(cat)])
newhdus.append(fieldstable.hdu)
hdulist = pyfits.HDUList(newhdus)
hdulist.writeto(temp_inputcatfile, clobber=True)
stringvals = copy.copy(options)
stringvals.inputcatfile = temp_inputcatfile
stringvals.outputcatfile = temp_outputcatfile
#BASH script hardcodes what the comparison catalog is. Bewarned!
command = './cut_nearest_neighbours_cc.sh %(cluster)s %(filter)s %(image)s %(inputcatfile)s %(outputcatfile)s %(psfsize)2.4f' % stringvals
try:
subprocess.check_call(command.split())
outputcat = ldac.openObjectFile(temp_outputcatfile)
ids = {}
for id in cat['SeqNr']:
ids[id] = False
for id in outputcat['SeqNr']:
ids[id] = True
nearest_neighbor_cut = np.array([ids[id] for id in cat['SeqNr']])
finally:
# if os.path.exists(temp_inputcatfile):
# os.remove(temp_inputcatfile)
# if os.path.exists(temp_outputcatfile):
# os.remove(temp_outputcatfile)
os.chdir(curdir)
return nearest_neighbor_cut
def sextract(filter):
from config_bonn import appendix, cluster, tag, arc, filter_root
import utilities
import os, re, bashreader, sys, string
from glob import glob
from copy import copy
dict = bashreader.parseFile('progs.ini')
for key in dict.keys():
os.environ[key] = str(dict[key])
TEMPDIR = '/tmp/'
PHOTCONF = './photconf/'
path = '/nfs/slac/g/ki/ki05/anja/SUBARU/%(cluster)s/' % {
'cluster': cluster
}
search_params = {
'path': path,
'cluster': cluster,
'filter': filter,
'appendix': appendix,
'PHOTCONF': PHOTCONF,
'tag': tag,
'DATACONF': os.environ['DATACONF'],
'TEMPDIR': TEMPDIR,
'fwhm': 1.00
}
searchstr = "/%(path)s/*%(filter)s*/SCIENCE/*1*fits" % search_params
print searchstr
files = glob(searchstr)
files.sort()
print files
exposures = {}
# first 30 files
print files[0:30]
for file in files: #[0:30]:
if string.find(file, 'wcs') == -1 and string.find(file,
'.sub.fits') == -1:
res = re.split('_', re.split('/', file)[-1])
print res
if not exposures.has_key(res[0]): exposures[res[0]] = {}
if not exposures[res[0]].has_key('images'):
exposures[res[0]]['images'] = []
if not exposures[res[0]].has_key('keywords'):
exposures[res[0]]['keywords'] = {}
exposures[res[0]]['images'].append(
file) # res[0] is the root of the image name
print 'hey', file
reload(utilities)
if not exposures[res[0]]['keywords'].has_key(
'ROTATION'
): #if exposure does not have keywords yet, then get them
exposures[res[0]]['keywords']['filter'] = filter
res2 = re.split('/', file)
for r in res2:
if string.find(r, filter) != -1:
print r
exposures[res[0]]['keywords']['date'] = r.replace(
filter + '_', '')
exposures[res[0]]['keywords']['fil_directory'] = r
search_params['fil_directory'] = r
kws = utilities.get_header_kw(
file, ['ROTATION']) # return KEY/NA if not SUBARU
for kw in kws.keys():
exposures[res[0]]['keywords'][kw] = kws[kw]
print 'hey2!!!!!!'
print exposures
#raw_input()
#first = exposures[exposures.keys()[0]]
#first['images'] = [first['images'][0]]
#exposures = {exposures.keys()[0]: first}
exposures = {exposures.keys()[0]: exposures[exposures.keys()[0]]}
print exposures
print 'stop1'
#temporary method
for kw in exposures.keys(): # now go through exposure by exposure
exposure = exposures[kw]
print kw, exposure['images']
children = []
print exposure['images']
print 'hey!!!!!!'
for image in exposure['images']:
child = os.fork()
if child:
children.append(child)
else:
params = copy(search_params)
params['GAIN'] = 1.000 #float(exposure['keywords']['GAIN'])
params['PIXSCALE'] = float(exposure['keywords']['PIXSCALE'])
ROOT = re.split('\.', re.split('\/', image)[-1])[0]
params['ROOT'] = ROOT
NUM = re.split('O', re.split('\_', ROOT)[1])[0]
params['NUM'] = NUM
print ROOT
weightim = "/%(path)s/%(fil_directory)s/WEIGHTS/%(ROOT)s.weight.fits" % params
#flagim = "/%(path)s/%(fil_directory)s/WEIGHTS/globalflag_%(NUM)s.fits" % params
#finalflagim = TEMPDIR + "flag_%(ROOT)s.fits" % params
params['finalflagim'] = weightim
#os.system('rm ' + finalflagim)
#command = "ic -p 16 '1 %2 %1 0 == ?' " + weightim + " " + flagim + " > " + finalflagim
#print command
#raw_input()
#utilities.run(command)
command = "sex /%(path)s/%(fil_directory)s/SCIENCE/%(ROOT)s.fits -c %(PHOTCONF)s/singleastrom.conf.sex \
-FLAG_IMAGE ''\
-FLAG_TYPE MAX\
-CATALOG_NAME %(TEMPDIR)s/seeing_%(ROOT)s.cat \
-FILTER_NAME %(PHOTCONF)s/default.conv\
-CATALOG_TYPE 'ASCII' \
-DETECT_MINAREA 5 -DETECT_THRESH 5.\
-ANALYSIS_THRESH 5 \
-WEIGHT_IMAGE /%(path)s/%(fil_directory)s/WEIGHTS/%(ROOT)s.weight.fits\
-WEIGHT_TYPE MAP_WEIGHT\
-PARAMETERS_NAME %(PHOTCONF)s/singleastrom.ascii.flag.sex" % params
print command
os.system(command)
sys.exit(0)
for child in children:
os.waitpid(child, 0)
command = 'cat ' + TEMPDIR + 'seeing_' + kw + '*cat > ' + TEMPDIR + 'paste_seeing_' + kw + '.cat'
utilities.run(command)
file_seeing = TEMPDIR + '/paste_seeing_' + kw + '.cat'
PIXSCALE = float(exposure['keywords']['PIXSCALE'])
reload(utilities)
print file_seeing, kw, PIXSCALE, exposure['keywords']['PIXSCALE']
fwhm = utilities.calc_seeing(file_seeing, 10, PIXSCALE)
# get the CRPIX values for
#image = exposure['images'][0]
start = 1
for image in exposure['images']:
print image
res = re.split('\_\d+', re.split('\/', image)[-1])
#print res
imroot = "/%(path)s/%(fil_directory)s/SCIENCE/" % search_params
im = imroot + res[0] + '_1' + res[1]
#print im
crpix = utilities.get_header_kw(
image, ['CRPIX1', 'CRPIX2', 'NAXIS1', 'NAXIS2'])
if start == 1:
crpixzero = copy(crpix)
crpixhigh = copy(crpix)
start = 0
from copy import copy
if float(crpix['CRPIX1']) > float(crpixzero['CRPIX1']) and float(
crpix['CRPIX2']) > float(crpixzero['CRPIX2']):
crpixzero = copy(crpix)
if float(crpix['CRPIX1']) < float(crpixhigh['CRPIX1']) and float(
crpix['CRPIX2']) < float(crpixhigh['CRPIX2']):
crpixhigh = copy(crpix)
print crpix, crpixzero, crpixhigh
LENGTH1 = abs(float(crpixhigh['CRPIX1']) -
float(crpixzero['CRPIX1'])) + float(crpix['NAXIS1'])
LENGTH2 = abs(float(crpixhigh['CRPIX2']) -
float(crpixzero['CRPIX2'])) + float(crpix['NAXIS2'])
print crpixhigh['CRPIX1'], crpixzero['CRPIX1'], crpix['NAXIS1'], crpix[
'NAXIS2']
children = []
for image in exposure['images']:
child = os.fork()
if child:
children.append(child)
else:
params = copy(search_params)
params['fwhm'] = fwhm
params['GAIN'] = 1.000 #float(exposure['keywords']['GAIN'])
params['PIXSCALE'] = float(exposure['keywords']['PIXSCALE'])
ROOT = re.split('\.', re.split('\/', image)[-1])[0]
params['ROOT'] = ROOT
NUM = re.split('O', re.split('\_', ROOT)[1])[0]
params['NUM'] = NUM
print ROOT
finalflagim = TEMPDIR + "flag_%(ROOT)s.fits" % params
weightim = "/%(path)s/%(fil_directory)s/WEIGHTS/%(ROOT)s.weight.fits" % params
#flagim = "/%(path)s/%(fil_directory)s/WEIGHTS/globalflag_%(NUM)s.fits" % params
#finalflagim = TEMPDIR + "flag_%(ROOT)s.fits" % params
params['finalflagim'] = weightim
im = "/%(path)s/%(fil_directory)s/SCIENCE/%(ROOT)s.fits" % params
crpix = utilities.get_header_kw(im, ['CRPIX1', 'CRPIX2'])
command = "sex /%(path)s/%(fil_directory)s/SCIENCE/%(ROOT)s.fits -c %(PHOTCONF)s/phot.conf.sex \
-PARAMETERS_NAME %(PHOTCONF)s/phot.param.sex \
-CATALOG_NAME %(TEMPDIR)s/%(ROOT)s.cat \
-FILTER_NAME %(DATACONF)s/default.conv\
-FILTER Y \
-FLAG_TYPE MAX\
-FLAG_IMAGE ''\
-SEEING_FWHM %(fwhm).3f \
-DETECT_MINAREA 5 -DETECT_THRESH 5 -ANALYSIS_THRESH 5 \
-MAG_ZEROPOINT 27.0 \
-GAIN %(GAIN).3f \
-WEIGHT_IMAGE /%(path)s/%(fil_directory)s/WEIGHTS/%(ROOT)s.weight.fits\
-WEIGHT_TYPE MAP_WEIGHT" % params
#-CHECKIMAGE_TYPE BACKGROUND,APERTURES,SEGMENTATION\
#-CHECKIMAGE_NAME /%(path)s/%(fil_directory)s/PHOTOMETRY/coadd.background.fits,/%(path)s/%(fil_directory)s/PHOTOMETRY/coadd.apertures.fits,/%(path)s/%(fil_directory)s/PHOTOMETRY/coadd.segmentation.fits\
catname = "%(TEMPDIR)s/%(ROOT)s.cat" % params
print command
utilities.run(command, [catname])
import commands
lines = commands.getoutput('ldactoasc -s -b -i ' + catname +
' -t LDAC_OBJECTS | wc -l')
import re
res = re.split('\n', lines)
print lines
if int(res[-1]) == 0:
print 'NO OBJECTS, exiting...'
sys.exit(0)
poscatname = "%(TEMPDIR)s/%(ROOT)s.pos.cat" % params
command = 'ldaccalc -i ' + catname + ' -o ' + TEMPDIR + params[
'ROOT'] + '.scamp.cata -t LDAC_OBJECTS -c "(XWIN_IMAGE + ' + str(
float(crpixzero['CRPIX1']) - float(crpix['CRPIX1'])
) + ');" -k FLOAT -n XWIN_IMAGE_TEMP "" -c "(YWIN_IMAGE + ' + str(
float(crpixzero['CRPIX2']) - float(crpix['CRPIX2'])
) + ');" -k FLOAT -n YWIN_IMAGE_TEMP "" -c "(YWIN_IMAGE*0 + ' + str(
params['NUM']) + ');" -k FLOAT -n CHIP "" '
print command
utilities.run(command)
command = 'ldacdelkey -i ' + TEMPDIR + params[
'ROOT'] + '.scamp.cata -t LDAC_OBJECTS -o ' + TEMPDIR + params[
'ROOT'] + '.scamp.catb -k XWIN_IMAGE YWIN_IMAGE'
utilities.run(command)
command = 'ldacrenkey -i ' + TEMPDIR + params[
'ROOT'] + '.scamp.catb -t LDAC_OBJECTS -o ' + TEMPDIR + params[
'ROOT'] + '.scamp.catc -k XWIN_IMAGE_TEMP XWIN_IMAGE YWIN_IMAGE_TEMP YWIN_IMAGE'
utilities.run(command)
#command = 'ldacrenkey
sys.exit(0)
for child in children:
#print 'waiting for' child
os.waitpid(child, 0)
''' run SCAMP on entire image '''
newposlist = glob(TEMPDIR + kw + '*scamp.catc')
outcatscamp = TEMPDIR + 'tmppaste_' + kw + '.scampall.cat'
outheadscamp = TEMPDIR + 'tmppaste_' + kw + '.scampall.head'
print newposlist
if len(newposlist) > 1:
command = 'ldacpaste -i ' + TEMPDIR + kw + '*scamp.cat -o ' + outcatscamp
print command
else:
command = 'cp ' + newposlist[0] + ' ' + outcatscamp
utilities.run(command)
command = 'scamp ' + outcatscamp + " -SOLVE_PHOTOM N -ASTREF_CATALOG SDSS-R6 -CHECKPLOT_TYPE NONE -WRITE_XML N "
print command
utilities.run(command)
headfile = outheadscamp
print headfile
#raw_input()
children = []
for image in exposure['images']:
child = os.fork()
if child:
children.append(child)
else:
params = copy(search_params)
params['fwhm'] = fwhm
params['GAIN'] = 1.000 #float(exposure['keywords']['GAIN'])
params['PIXSCALE'] = float(exposure['keywords']['PIXSCALE'])
ROOT = re.split('\.', re.split('\/', image)[-1])[0]
params['ROOT'] = ROOT
NUM = re.split('O', re.split('\_', ROOT)[1])[0]
params['NUM'] = NUM
print ROOT
finalflagim = TEMPDIR + "flag_%(ROOT)s.fits" % params
weightim = "/%(path)s/%(fil_directory)s/WEIGHTS/%(ROOT)s.weight.fits" % params
#flagim = "/%(path)s/%(fil_directory)s/WEIGHTS/globalflag_%(NUM)s.fits" % params
#finalflagim = TEMPDIR + "flag_%(ROOT)s.fits" % params
params['finalflagim'] = weightim
im = "/%(path)s/%(fil_directory)s/SCIENCE/%(ROOT)s.fits" % params
crpix = utilities.get_header_kw(im, ['CRPIX1', 'CRPIX2'])
hf = open(headfile, 'r').readlines()
hdict = {}
for line in hf:
import re
if string.find(line, '=') != -1:
res = re.split('=', line)
name = res[0].replace(' ', '')
res = re.split('/', res[1])
value = res[0].replace(' ', '')
print name, value
hdict[name] = value
imfix = "/tmp/%(ROOT)s.fixwcs.fits" % params
command = "cp " + im + " " + imfix
utilities.run(command)
for name in [
'CRVAL1', 'CRVAL2', 'CD1_1', 'CD1_2', 'CD2_1', 'CD2_2'
]: #,'CRPIX1','CRPIX1']:
command = 'sethead ' + imfix + ' ' + name + '=' + hdict[
name]
print command
os.system(command)
crpix = utilities.get_header_kw(im, ['CRPIX1', 'CRPIX2'])
command = "sex /tmp/%(ROOT)s.fixwcs.fits -c %(PHOTCONF)s/phot.conf.sex \
-PARAMETERS_NAME %(PHOTCONF)s/phot.param.sex \
-CATALOG_NAME %(TEMPDIR)s/%(ROOT)s.fixwcs.cat \
-FILTER_NAME %(DATACONF)s/default.conv\
-FILTER Y \
-FLAG_TYPE MAX\
-FLAG_IMAGE ''\
-SEEING_FWHM %(fwhm).3f \
-DETECT_MINAREA 5 -DETECT_THRESH 5 -ANALYSIS_THRESH 5 \
-MAG_ZEROPOINT 27.0 \
-GAIN %(GAIN).3f \
-WEIGHT_IMAGE /%(path)s/%(fil_directory)s/WEIGHTS/%(ROOT)s.weight.fits\
-WEIGHT_TYPE MAP_WEIGHT" % params
#-CHECKIMAGE_TYPE BACKGROUND,APERTURES,SEGMENTATION\
#-CHECKIMAGE_NAME /%(path)s/%(fil_directory)s/PHOTOMETRY/coadd.background.fits,/%(path)s/%(fil_directory)s/PHOTOMETRY/coadd.apertures.fits,/%(path)s/%(fil_directory)s/PHOTOMETRY/coadd.segmentation.fits\
catname = "%(TEMPDIR)s/%(ROOT)s.cat" % params
print command
utilities.run(command, [catname])
catname = "%(TEMPDIR)s/%(ROOT)s.cat" % params
print command
utilities.run(command, [catname])
import commands
lines = commands.getoutput('ldactoasc -s -b -i ' + catname +
' -t LDAC_OBJECTS | wc -l')
import re
res = re.split('\n', lines)
print lines
if int(res[-1]) == 0: sys.exit(0)
command = 'scamp ' + catname + " -SOLVE_PHOTOM N -ASTREF_CATALOG SDSS-R6 -CHECKPLOT_TYPE NONE -WRITE_XML N "
print command
utilities.run(command)
headfile = "%(TEMPDIR)s/%(ROOT)s.head" % params
hf = open(headfile, 'r').readlines()
hdict = {}
for line in hf:
import re
if string.find(line, '=') != -1:
res = re.split('=', line)
name = res[0].replace(' ', '')
res = re.split('/', res[1])
value = res[0].replace(' ', '')
print name, value
hdict[name] = value
imfix = "/tmp/%(ROOT)s.fixwcs.fits" % params
command = "cp " + im + " " + imfix
utilities.run(command)
for name in [
'CRVAL1', 'CRVAL2', 'CD1_1', 'CD1_2', 'CD2_1', 'CD2_2',
'CRPIX1', 'CRPIX1'
]:
command = 'sethead ' + imfix + ' ' + name + '=' + hdict[
name]
print command
os.system(command)
command = "sex /tmp/%(ROOT)s.fixwcs.fits -c %(PHOTCONF)s/phot.conf.sex \
-PARAMETERS_NAME %(PHOTCONF)s/phot.param.sex \
-CATALOG_NAME %(TEMPDIR)s/%(ROOT)s.fixwcs.cat \
-FILTER_NAME %(DATACONF)s/default.conv\
-FILTER Y \
-FLAG_TYPE MAX\
-FLAG_IMAGE ''\
-SEEING_FWHM %(fwhm).3f \
-DETECT_MINAREA 5 -DETECT_THRESH 5 -ANALYSIS_THRESH 5 \
-MAG_ZEROPOINT 27.0 \
-GAIN %(GAIN).3f \
-WEIGHT_IMAGE /%(path)s/%(fil_directory)s/WEIGHTS/%(ROOT)s.weight.fits\
-WEIGHT_TYPE MAP_WEIGHT" % params
#-CHECKIMAGE_TYPE BACKGROUND,APERTURES,SEGMENTATION\
#-CHECKIMAGE_NAME /%(path)s/%(fil_directory)s/PHOTOMETRY/coadd.background.fits,/%(path)s/%(fil_directory)s/PHOTOMETRY/coadd.apertures.fits,/%(path)s/%(fil_directory)s/PHOTOMETRY/coadd.segmentation.fits\
catname = "%(TEMPDIR)s/%(ROOT)s.cat" % params
print command
utilities.run(command, [catname])
command = 'ldacconv -b 1 -c R -i ' + TEMPDIR + params[
'ROOT'] + '.fixwcs.cat -o ' + TEMPDIR + params[
'ROOT'] + '.conv'
print command
utilities.run(command)
# Xpos_ABS is difference of CRPIX and zero CRPIX
command = 'ldaccalc -i ' + TEMPDIR + params[
'ROOT'] + '.conv -o ' + TEMPDIR + params[
'ROOT'] + '.newpos -t OBJECTS -c "(Xpos + ' + str(
float(crpixzero['CRPIX1']) - float(crpix['CRPIX1'])
) + ');" -k FLOAT -n Xpos_ABS "" -c "(Ypos + ' + str(
float(crpixzero['CRPIX2']) - float(crpix['CRPIX2'])
) + ');" -k FLOAT -n Ypos_ABS "" -c "(Ypos*0 + ' + str(
params['NUM']) + ');" -k FLOAT -n CHIP "" '
#command = 'ldaccalc -i ' + TEMPDIR + params['ROOT'] + '.conv -o ' + TEMPDIR + params['ROOT'] + '.newpos -t OBJECTS -c "(' + str(crpix['CRPIX1']) + ' - Xpos);" -k FLOAT -n Xpos_ABS "" -c "(' + str(crpix['CRPIX2']) + ' - Ypos);" -k FLOAT -n Ypos_ABS "" -c "(Ypos*0 + ' + str(params['NUM']) + ');" -k FLOAT -n CHIP "" '
print command
utilities.run(command)
sys.exit(0)
for child in children:
#print 'waiting for' child
os.waitpid(child, 0)
from glob import glob
outcat = TEMPDIR + 'tmppaste_' + kw + '.cat'
newposlist = glob(TEMPDIR + kw + '*newpos')
if len(newposlist) > 1:
command = 'ldacpaste -i ' + TEMPDIR + kw + '*newpos -o ' + outcat
print command
else:
command = 'cp ' + newposlist[0] + ' ' + outcat
utilities.run(command)
os.system('ldactoasc -i ' + outcat +
' -b -s -k MAG_APER MAGERR_APER -t OBJECTS > /tmp/' + kw +
'aper')
os.system('asctoldac -i /tmp/' + kw + 'aper -o /tmp/' + kw +
'cat1 -t OBJECTS -c ./photconf/MAG_APER.conf')
outfinal = TEMPDIR + 'paste_' + kw + '.cat'
os.system('ldacjoinkey -i ' + outcat + ' -p /tmp/' + kw + 'cat1 -o ' +
outfinal +
' -k MAG_APER1 MAG_APER2 MAGERR_APER1 MAGERR_APER2')
exposures[kw]['pasted_cat'] = outfinal
return exposures, LENGTH1, LENGTH2
max = 0
k = 0
for i in range(nbins):
if bin[i] > max:
k = i
max = bin[i]
fwhm = 0.3 + k * binsize
print 'fwhm', fwhm
return fwhm
import os, sys, bashreader, commands
from utilities import *
dict = bashreader.parseFile('progs.ini')
for key in dict.keys():
os.environ[key] = str(dict[key])
cluster = 'MACS2243-09'
appendix = '_all' #_good'
TEMPDIR = '/tmp/'
PHOTCONF = './photconf/'
tag = 'local50'
path = '/nfs/slac/g/ki/ki05/anja/SUBARU/%(cluster)s/' % {'cluster': cluster}
type = 'all'
filters = ['B', 'W-J-V', 'W-C-RC', 'W-C-IC', 'W-S-Z+']
filter_root = 'W-J-V'
def doit():
usage = '''
get_seeing.py
gets the seeing for all exposures
usage:
get_seeing.py [maindir] [cluster] [ending] [list of filters:optional]
example:
./get_seeing.py ${SUBARUDIR} MACS1427+44
./get_seeing.py ${SUBARUDIR} MACS1427+44 "_t1"
./get_seeing.py ${SUBARUDIR} MACS1427+44 "" W-J-V W-J-B
If no filters given, all filters will be included, otherwinse only the listed filters will be considered.
result:
file seeing_[clustername].cat in local directory with list of exposures and seeing.
options:
-h this
'''
# if -h called, or not enough args, show usage and quit
if ('-h' in sys.argv) or len(sys.argv) <3:
print usage
exit(0)
# set up directory structure:
maindir=sys.argv[1] # this should be ${SUBARUDIR}
cluster=sys.argv[2] # full cluster name
if (len(sys.argv) == 3):
filterlist=['all']
else:
filterlist = sys.argv[3:]
# get the progs from prog.ini
dict = bashreader.parseFile('progs.ini')
# definitions...
path=maindir+'/'+cluster
TEMPDIR = tempfile.mkdtemp(dir='/tmp')
PHOTCONF = './photconf/'
# different filters...
subarufilters=['W-J-B','W-J-V','W-C-RC','W-C-IC','W-S-I+','W-S-Z+']
cfhtfilters=['u','g','r','i','z']
# for the case of all filters
if filterlist[0]=='all':
list_of_images = glob.glob(path+'/W-?-??/SCIENCE/coadd_'+cluster+'_SUPA*/coadd.fits')
list_of_images.extend(glob.glob(path+'/W-?-??/SCIENCE/coadd_'+cluster+'_all/coadd.fits'))
list_of_images.extend(glob.glob(path+'/W-?-?/SCIENCE/coadd_'+cluster+'_SUPA*/coadd.fits'))
list_of_images.extend(glob.glob(path+'/W-?-?/SCIENCE/coadd_'+cluster+'_all/coadd.fits'))
list_of_images.extend(glob.glob(path+'/?/SCIENCE/coadd_'+cluster+'_*p/coadd.fits'))
list_of_images.extend(glob.glob(path+'/?/SCIENCE/coadd_'+cluster+'_all/coadd.fits'))
list_of_images.extend(glob.glob(path+'/W-?-?_*_CALIB/SCIENCE/coadd_'+cluster+'_all/coadd.fits'))
list_of_images.extend(glob.glob(path+'/W-?-??_*_CALIB/SCIENCE/coadd_'+cluster+'_all/coadd.fits'))
else : # for specific filters
list_of_images=[]
for f in filterlist:
thislist = glob.glob(path+'/'+f+'/SCIENCE/coadd_'+cluster+'_SUPA*/coadd.fits')
thislist.append(path+'/'+f+'/SCIENCE/coadd_'+cluster+'_all/coadd.fits')
thislist.extend(glob.glob(path+'/'+f+'/SCIENCE/coadd_'+cluster+'_*p/coadd.fits'))
list_of_images = list_of_images + thislist
print "Measuring the seeing of ..."
for image in list_of_images:
print image
# if no images, quit
if len(list_of_images)==0:
print 'no images '
exit(1)
children = [] # this is supposed to make it faster
# its the parallel mechanism
for image in list_of_images:
child = os.fork() # forking!
if child:
children.append(child) # children processes.
else:
flagimage=image[:-4]+'flag.fits' # assumes the flag file is coadd.flag.fits
if len(flagimage) == 0: # if we can't find it
print 'Can not find '+flagimage
exit(1)
tag = findImageTag(image)
params = {'path':path,
'cluster':cluster,
'PHOTCONF':PHOTCONF,
'TEMPDIR': TEMPDIR,
'image':image,
'flagimage':flagimage,
'tag':tag}
# now run sextractor to determine the seeing:
command = 'sex %(image)s \
-c %(PHOTCONF)s/singleastrom.conf.sex \
-FLAG_IMAGE %(flagimage)s \
-FLAG_TYPE MAX \
-CATALOG_NAME %(TEMPDIR)s/seeing_%(tag)s.cat \
-FILTER_NAME %(PHOTCONF)s/default.conv \
-CATALOG_TYPE "ASCII" \
-DETECT_MINAREA 10 -DETECT_THRESH 10. \
-ANALYSIS_THRESH 5 \
-PARAMETERS_NAME %(PHOTCONF)s/singleastrom.ascii.param.sex' % params
print command
sys.stderr.write(command + '\n')
os.system(command)
sys.exit(0)
for child in children:
os.waitpid(child,0)
# Got seeing
############################################
# Now we are just going to organize it a bit
#
############################################
openfile = open('seeing_'+cluster+'.cat','w')
# now we order the seeings, find which is the worst.
fwhms = {}
for image in list_of_images:
# get some info
try:
GAIN, PIXSCALE, EXPTIME = utilities.get_header_info(image)
except Exception:
sys.stderr.write('Skipping %s!' % image)
continue
tag = findImageTag(image)
# get all the info together in one array
fwhms[tag] = {'IMAGE':image,'GAIN':GAIN,'PIXSCALE':PIXSCALE, 'EXPTIME': EXPTIME}
# the output cat from above
file_seeing = '%(TEMPDIR)s/seeing_%(tag)s.cat' % {'TEMPDIR': TEMPDIR,'tag':tag}
# gets seeing
fwhms[tag]['SEEING'] = utilities.calc_seeing(file_seeing,PIXSCALE)
print 'image', tag, fwhms[tag]['SEEING']
openfile.write(tag+' '+ str(fwhms[tag]['SEEING']) + ' \n')
fwhms_comp=[fwhms[x] for x in fwhms.keys()] # list of fwhm's
fwhms_comp.sort(utilities.compare) # sort
seeing_worst = fwhms_comp[0]['SEEING'] # worst
image_worst = fwhms_comp[0]['IMAGE'] # worst image
print ' worst SEEING', image_worst, seeing_worst
[ os.remove('%s/%s' % (TEMPDIR,file)) for file in os.listdir(TEMPDIR) ]
os.rmdir(TEMPDIR)
#!/usr/bin/env python
import sys, pyfits, bashreader, ldac, math, os, re, numpy
inputfile = sys.argv[1]
outputfile = sys.argv[2]
image = sys.argv[3]
config = bashreader.parseFile('./progs.ini')
npara =int(config.npara)
inputcat = pyfits.open(inputfile)
if inputcat is None:
print 'Cannot open %s' % inputfile
sys.exit(1)
root, ext = os.path.splitext(inputfile)
objects = None
hfindpeaks = None
fields = None
for hdu in inputcat:
try:
if 'OBJECTS' == hdu.header['EXTNAME']:
objects = ldac.LDACCat(hdu)
elif 'HFINDPEAKS' == hdu.header['EXTNAME']:
hfindpeaks = hdu
elif 'FIELDS' == hdu.header['EXTNAME']:
fields = hdu
except KeyError:
def sextract(self,exposures):
#from config_bonn import appendix, cluster, tag, arc, filter_root
import utilities
import os, re, bashreader, sys, string
from glob import glob
from copy import copy
dict = bashreader.parseFile('progs.ini')
for key in dict.keys():
os.environ[key] = str(dict[key])
TEMPDIR = '/tmp/'
PHOTCONF = './photconf/'
path='/nfs/slac/g/ki/ki05/anja/SUBARU/%(cluster)s/' % {'cluster':cluster}
print exposures.keys()
print exposures_zero.keys()
print exposures_one.keys()
print 'hey2!!!!!!'
print exposures
first = exposures[exposures.keys()[0]]
first['images'] = first['images']
exposures = {exposures.keys()[0]: first}
#exp_tmp = {}
#for exposure in exposures.keys()[2:4]:
# exp_tmp[exposure] = exposures[exposure]
#exposures = exp_tmp
#exposures = {exposures.keys()[0]: exposures[exposures.keys()[0:4]]}
print exposures
print 'stop1'
#temporary method
measure_fwhm = 1
for kw in exposures.keys(): # now go through exposure by exposure
exposure = exposures[kw]
print kw, exposure['images']
print exposure['images']
''' get the CRPIX values '''
start = 1
for image in exposure['images']:
print image
res = re.split('\_\d+',re.split('\/',image)[-1])
#print res
imroot = "/%(path)s/%(fil_directory)s/SCIENCE/" % search_params
im = imroot + res[0] + '_1' + res[1]
#print im
crpix = utilities.get_header_kw(image,['CRPIX1','CRPIX2','NAXIS1','NAXIS2'])
if start == 1:
crpixzero = copy(crpix)
crpixhigh = copy(crpix)
start = 0
from copy import copy
if float(crpix['CRPIX1']) > float(crpixzero['CRPIX1']) and float(crpix['CRPIX2']) > float(crpixzero['CRPIX2']):
crpixzero = copy(crpix)
if float(crpix['CRPIX1']) < float(crpixhigh['CRPIX1']) and float(crpix['CRPIX2']) < float(crpixhigh['CRPIX2']):
crpixhigh = copy(crpix)
print crpix, crpixzero, crpixhigh
LENGTH1 = abs(float(crpixhigh['CRPIX1']) - float(crpixzero['CRPIX1'])) + float(crpix['NAXIS1'])
LENGTH2 = abs(float(crpixhigh['CRPIX2']) - float(crpixzero['CRPIX2'])) + float(crpix['NAXIS2'])
print crpixhigh['CRPIX1'], crpixzero['CRPIX1'], crpix['NAXIS1'], crpix['NAXIS2']
print exposure['images']
'exposures'
children = []
for image in exposure['images']:
child = os.fork()
if child:
children.append(child)
else:
print fwhm
params = copy(search_params)
finalflagim = TEMPDIR + "flag_%(ROOT)s.fits" % params
weightim = "/%(path)s/%(fil_directory)s/WEIGHTS/%(ROOT)s.weight.fits" % params
#flagim = "/%(path)s/%(fil_directory)s/WEIGHTS/globalflag_%(NUM)s.fits" % params
#finalflagim = TEMPDIR + "flag_%(ROOT)s.fits" % params
params['finalflagim'] = weightim
im = "/%(path)s/%(fil_directory)s/SCIENCE/%(ROOT)s.fits" % params
crpix = utilities.get_header_kw(im,['CRPIX1','CRPIX2'])
command = "sex /%(path)s/%(fil_directory)s/SCIENCE/%(ROOT)s.fits -c %(PHOTCONF)s/phot.conf.sex \
-PARAMETERS_NAME %(PHOTCONF)s/phot.param.sex \
-CATALOG_NAME %(TEMPDIR)s/%(ROOT)s.cat \
-FILTER_NAME %(DATACONF)s/default.conv\
-FILTER Y \
-FLAG_TYPE MAX\
-FLAG_IMAGE ''\
-SEEING_FWHM %(fwhm).3f \
-DETECT_MINAREA 10 -DETECT_THRESH 10 -ANALYSIS_THRESH 10 \
-MAG_ZEROPOINT 27.0 \
-GAIN %(GAIN).3f \
-WEIGHT_IMAGE /%(path)s/%(fil_directory)s/WEIGHTS/%(ROOT)s.weight.fits\
-WEIGHT_TYPE MAP_WEIGHT" % params
#-CHECKIMAGE_TYPE BACKGROUND,APERTURES,SEGMENTATION\
#-CHECKIMAGE_NAME /%(path)s/%(fil_directory)s/PHOTOMETRY/coadd.background.fits,/%(path)s/%(fil_directory)s/PHOTOMETRY/coadd.apertures.fits,/%(path)s/%(fil_directory)s/PHOTOMETRY/coadd.segmentation.fits\
catname = "%(TEMPDIR)s/%(ROOT)s.cat" % params
filtcatname = "%(TEMPDIR)s/%(ROOT)s.filt.cat" % params
print command
utilities.run(command,[catname])
utilities.run('ldacfilter -i ' + catname + ' -o ' + filtcatname + ' -t LDAC_OBJECTS\
-c "(CLASS_STAR > 0.5);"',[filtcatname])
import commands
lines = commands.getoutput('ldactoasc -s -b -i ' + filtcatname + ' -t LDAC_OBJECTS | wc -l')
import re
res = re.split('\n',lines)
print lines
if int(res[-1]) == 0: sys.exit(0)
command = 'scamp ' + filtcatname + " -SOLVE_PHOTOM N -ASTREF_CATALOG SDSS-R6 -CHECKPLOT_TYPE NONE -WRITE_XML N "
print command
utilities.run(command)
#headfile = "%(TEMPDIR)s/%(ROOT)s.head" % params
headfile = "%(TEMPDIR)s/%(ROOT)s.filt.head" % params
hf = open(headfile,'r').readlines()
hdict = {}
for line in hf:
import re
if string.find(line,'=') != -1:
res = re.split('=',line)
name = res[0].replace(' ','')
res = re.split('/',res[1])
value = res[0].replace(' ','')
print name, value
hdict[name] = value
imfix = "/tmp/%(ROOT)s.fixwcs.fits" % params
command = "cp " + im + " " + imfix
utilities.run(command)
for name in ['CRVAL1','CRVAL2','CD1_1','CD1_2','CD2_1','CD2_2','CRPIX1','CRPIX1']:
command = 'sethead ' + imfix + ' ' + name + '=' + hdict[name]
print command
os.system(command)
command = "sex /tmp/%(ROOT)s.fixwcs.fits -c %(PHOTCONF)s/phot.conf.sex \
-PARAMETERS_NAME %(PHOTCONF)s/phot.param.sex \
-CATALOG_NAME %(TEMPDIR)s/%(ROOT)s.fixwcs.cat \
-FILTER_NAME %(DATACONF)s/default.conv\
-FILTER Y \
-FLAG_TYPE MAX\
-FLAG_IMAGE ''\
-SEEING_FWHM %(fwhm).3f \
-DETECT_MINAREA 5 -DETECT_THRESH 5 -ANALYSIS_THRESH 5 \
-MAG_ZEROPOINT 27.0 \
-GAIN %(GAIN).3f \
-WEIGHT_IMAGE /%(path)s/%(fil_directory)s/WEIGHTS/%(ROOT)s.weight.fits\
-WEIGHT_TYPE MAP_WEIGHT" % params
#-CHECKIMAGE_TYPE BACKGROUND,APERTURES,SEGMENTATION\
#-CHECKIMAGE_NAME /%(path)s/%(fil_directory)s/PHOTOMETRY/coadd.background.fits,/%(path)s/%(fil_directory)s/PHOTOMETRY/coadd.apertures.fits,/%(path)s/%(fil_directory)s/PHOTOMETRY/coadd.segmentation.fits\
catname = "%(TEMPDIR)s/%(ROOT)s.cat" % params
print command
utilities.run(command,[catname])
command = 'ldacconv -b 1 -c R -i ' + TEMPDIR + params['ROOT'] + '.fixwcs.cat -o ' + TEMPDIR + params['ROOT'] + '.conv'
print command
utilities.run(command)
# Xpos_ABS is difference of CRPIX and zero CRPIX
command = 'ldaccalc -i ' + TEMPDIR + params['ROOT'] + '.conv -o ' + TEMPDIR + params['ROOT'] + '.newpos -t OBJECTS -c "(Xpos + ' + str(float(crpixzero['CRPIX1']) - float(crpix['CRPIX1'])) + ');" -k FLOAT -n Xpos_ABS "" -c "(Ypos + ' + str(float(crpixzero['CRPIX2']) - float(crpix['CRPIX2'])) + ');" -k FLOAT -n Ypos_ABS "" -c "(Ypos*0 + ' + str(params['NUM']) + ');" -k FLOAT -n CHIP "" '
#command = 'ldaccalc -i ' + TEMPDIR + params['ROOT'] + '.conv -o ' + TEMPDIR + params['ROOT'] + '.newpos -t OBJECTS -c "(' + str(crpix['CRPIX1']) + ' - Xpos);" -k FLOAT -n Xpos_ABS "" -c "(' + str(crpix['CRPIX2']) + ' - Ypos);" -k FLOAT -n Ypos_ABS "" -c "(Ypos*0 + ' + str(params['NUM']) + ');" -k FLOAT -n CHIP "" '
print command
utilities.run(command)
sys.exit(0)
for child in children:
#print 'waiting for' child
os.waitpid(child,0)
from glob import glob
outcat = TEMPDIR + 'tmppaste_' + kw + '.cat'
newposlist = glob(TEMPDIR + kw + '*newpos')
if len(newposlist) > 1:
command = 'ldacpaste -i ' + TEMPDIR + kw + '*newpos -o ' + outcat
print command
else:
command = 'cp ' + newposlist[0] + ' ' + outcat
utilities.run(command)
os.system('ldactoasc -i ' + outcat + ' -b -s -k MAG_APER MAGERR_APER -t OBJECTS > /tmp/' + kw + 'aper')
os.system('asctoldac -i /tmp/' + kw + 'aper -o /tmp/' + kw + 'cat1 -t OBJECTS -c ./photconf/MAG_APER.conf')
outfinal = TEMPDIR + 'paste_' + kw + '.cat'
os.system('ldacjoinkey -i ' + outcat + ' -p /tmp/' + kw + 'cat1 -o ' + outfinal + ' -k MAG_APER1 MAG_APER2 MAGERR_APER1 MAGERR_APER2')
exposures[kw]['pasted_cat'] = outfinal
return exposures, LENGTH1, LENGTH2
import numpy as np
import pyfits
import pywcs
import sys
import os
import multiprocessing
import bashreader as bash
dir = sys.argv[1]
filter = sys.argv[2]
coaddvers = sys.argv[3]
fsources = sys.argv[4]
pixscale = float(sys.argv[5])
survey = sys.argv[6]
outdir = sys.argv[7]
usedcpus = bash.parseFile('progs.ini')['npara']
sources = np.genfromtxt(fsources, dtype='str')
fzero = open(outdir + '/' + survey + '_pointings_available_sum_zero.txt', 'w')
fnotzero = open(outdir + '/' + survey + '_pointings_available_sum_not_zero.txt', 'w')
allpointings = sources[:,0]
unique = []
[unique.append(item) for item in allpointings if item not in unique]
def check_coords(pointing):
sumzerolist = []
sumnotzerolist = []
usage = \
'''createExclusion.py FILE
FILE a txt file with IMAGE 1,2,5,7-9
'''
if len(sys.argv) != 2:
print usage
# BonnLogger.updateStatus(__bonn_logger_id__, 1)
sys.exit(1)
if 'INSTRUMENT' not in os.environ:
print "INSTRUMENT not set!"
sys.exit(1)
config = bashreader.parseFile('%s.ini' % os.environ['INSTRUMENT'])
if config is None:
print "Cannot read %s.ini!" % os.environ['INSTRUMENT']
sys.exit(1)
filePrefix = config.prefix
nchips = int(config.nchips)
####################
def parseChipList(chipList):
chips = []
for entry in filter(lambda x: x != '',
def do_multiple(OBJNAME):
#!/usr/bin/env python
import os, sys, bashreader, commands
from utilities import *
from config_bonn import appendix, cluster, tag, arc, filters, filter_root, appendix_root
dict = bashreader.parseFile('progs.ini')
for key in dict.keys():
os.environ[key] = str(dict[key])
TEMPDIR = '/tmp/'
PHOTCONF = './photconf/'
path = '/nfs/slac/g/ki/ki05/anja/SUBARU/%s/' % cluster
#type='each'
type = 'all'
filecommand = open('record.analysis', 'w')
BASE = "coadd"
image = BASE + '.fits'
print 'Finished Loading Config, utils'
if type == 'all' or type == 'each':
children = []
for filter in filters:
child = os.fork()
if child:
children.append(child)
else:
params = {
'path': path,
'filter_root': filter_root,
'cluster': cluster,
'filter': filter,
'appendix': appendix,
'PHOTCONF': PHOTCONF,
'TEMPDIR': TEMPDIR
}
print params
# now run sextractor to determine the seeing:
command = 'sex %(path)s/%(filter)s/SCIENCE/coadd_%(cluster)s%(appendix)s/coadd.fits -c %(PHOTCONF)s/singleastrom.conf.sex \
-FLAG_IMAGE /%(path)s/%(filter)s/SCIENCE/coadd_%(cluster)s%(appendix)s/coadd.flag.fits \
-FLAG_TYPE MAX\
-CATALOG_NAME %(TEMPDIR)s/seeing_%(filter)s.cat \
-FILTER_NAME %(PHOTCONF)s/default.conv\
-CATALOG_TYPE "ASCII" \
-DETECT_MINAREA 10 -DETECT_THRESH 10.\
-ANALYSIS_THRESH 5 \
-PARAMETERS_NAME %(PHOTCONF)s/singleastrom.ascii.param.sex' % params
print command
os.system(command)
sys.exit(0)
for child in children:
os.waitpid(child, 0)
print 'DONE W/ SEEING'
fwhms = {}
for filter in filters:
file_header = '/%(path)s/%(filter)s/SCIENCE/coadd_%(cluster)s%(appendix)s/coadd.fits' % {
'TEMPDIR': TEMPDIR,
'filter': filter,
'path': path,
'cluster': cluster,
'appendix': appendix
}
GAIN, PIXSCALE, EXPTIME = get_header_info(file_header)
print GAIN, PIXSCALE
fwhms[filter] = {
'FILTER': filter,
'GAIN': GAIN,
'PIXSCALE': PIXSCALE,
'EXPTIME': EXPTIME
}
if type == 'all' or type == 'each':
file_seeing = '%(TEMPDIR)s/seeing_%(filter)s.cat' % {
'TEMPDIR': TEMPDIR,
'filter': filter
}
NLINES = 50
print 'filter', filter
fwhms[filter]['SEEING'] = calc_seeing(file_seeing, NLINES,
PIXSCALE)
if type == 'all' or type == 'each':
fwhms_comp = [fwhms[x] for x in fwhms.keys()]
fwhms_comp.sort(compare)
seeing_worst = fwhms_comp[0]['SEEING']
filter_worst = fwhms_comp[0]['FILTER']
print fwhms
print 'SEEING', filter_worst, seeing_worst
for x in fwhms.keys():
print x, fwhms[x]
import commands
for filter in filters:
print filter
params = {
'seeing_orig': float(fwhms[filter]['SEEING']),
'seeing_new': float(seeing_worst),
'PIXSCALE': float(PIXSCALE),
'path': path,
'cluster': cluster,
'appendix': appendix,
'filter': filter,
'path': path,
'DATACONF': os.environ['DATACONF']
}
command = 'mkdir %(DATACONF)s/default.conv %(path)s/%(filter)s/PHOTOMETRY/' % params
os.system(command)
if filter != filter_worst:
print params
command = 'python create_gausssmoothing_kernel.py %(seeing_orig).3f %(seeing_new).3f %(PIXSCALE).3f %(path)s/%(filter)s/PHOTOMETRY/' % params
print command
os.system(command)
else:
command = 'cp %(DATACONF)s/default.conv %(path)s/%(filter)s/PHOTOMETRY/gauss.conv' % params
os.system(command)
children = []
for filter in filters:
os.system("mkdir /" + path + "/" + filter + "/PHOTOMETRY/")
os.system("rm /" + path + "/" + filter + "/PHOTOMETRY/" + BASE +
".all" + tag + ".cat")
child = os.fork()
if child:
children.append(child)
else:
command = "rm /%(path)s/%(filter)s/PHOTOMETRY/%(filter)s.all.cat" % {
'path': path,
'filter': filter
}
print command
os.system(command)
if type == 'all':
params = {
'path': path,
'filter_root': filter_root,
'appendix_root': appendix_root,
'cluster': cluster,
'filter': filter,
'appendix': appendix,
'PHOTCONF': PHOTCONF,
'fwhm': seeing_worst,
'BASE': BASE,
'GAIN': float(fwhms[filter]['GAIN']),
'DATACONF': os.environ['DATACONF'],
'tag': tag
}
if filter != filter_worst:
''' convolve image -- no background subtraction -- high detection threshold -- no dual detection '''
command = "sex /%(path)s/%(filter)s/SCIENCE/coadd_%(cluster)s%(appendix)s/coadd.fits -c %(PHOTCONF)s/phot.conf.sex \
-PARAMETERS_NAME %(PHOTCONF)s/phot.param.short.sex \
-CATALOG_NAME /%(path)s/%(filter)s/PHOTOMETRY/%(filter)s.all%(tag)s.cat \
-FILTER_NAME /%(path)s/%(filter)s/PHOTOMETRY/gauss.conv \
-FILTER Y \
-SEEING_FWHM %(fwhm).3f \
-DETECT_MINAREA 3 -DETECT_THRESH 10000 -ANALYSIS_THRESH 10000 \
-MAG_ZEROPOINT 27.0 \
-FLAG_TYPE OR\
-FLAG_IMAGE /%(path)s/%(filter)s/SCIENCE/coadd_%(cluster)s%(appendix)s/coadd.flag.fits \
-GAIN %(GAIN).3f \
-CHECKIMAGE_NAME /%(path)s/%(filter)s/PHOTOMETRY/coadd.filtered.fits\
-CHECKIMAGE_TYPE FILTERED\
-BACK_TYPE MANUAL\
-BACK_VALUE 0.0\
-WEIGHT_IMAGE /%(path)s/%(filter)s/SCIENCE/coadd_%(cluster)s%(appendix)s/coadd.weight.fits \
-WEIGHT_TYPE MAP_WEIGHT" % params
else:
command = 'cp /%(path)s/%(filter)s/SCIENCE/coadd_%(cluster)s%(appendix)s/coadd.fits /%(path)s/%(filter)s/PHOTOMETRY/coadd.filtered.fits' % params
print command
print 'making filtered image'
os.system(command)
''' detection images -- one flag image --- one filter -- detect on lensing band '''
command = "sex /%(path)s/%(filter_root)s/SCIENCE/coadd_%(cluster)s%(appendix_root)s/coadd.fits,/%(path)s/%(filter)s/PHOTOMETRY/coadd.filtered.fits -c %(PHOTCONF)s/phot.conf.sex \
-PARAMETERS_NAME %(PHOTCONF)s/phot.param.short.sex \
-CATALOG_NAME /%(path)s/%(filter)s/PHOTOMETRY/%(filter)s.all%(tag)s.cat \
-FILTER_NAME %(DATACONF)s/default.conv \
-FILTER Y \
-SEEING_FWHM %(fwhm).3f \
-DETECT_MINAREA 3 -DETECT_THRESH 1.5 -ANALYSIS_THRESH 1.5 \
-MAG_ZEROPOINT 27.0 \
-FLAG_TYPE OR\
-FLAG_IMAGE /%(path)s/%(filter)s/SCIENCE/coadd_%(cluster)s%(appendix)s/coadd.flag.fits \
-GAIN %(GAIN).3f \
-CHECKIMAGE_NAME /%(path)s/%(filter)s/PHOTOMETRY/coadd.background.fits,/%(path)s/%(filter)s/PHOTOMETRY/coadd.apertures.fits,/%(path)s/%(filter)s/PHOTOMETRY/coadd.segmentation.fits\
-CHECKIMAGE_TYPE BACKGROUND,APERTURES,SEGMENTATION\
-WEIGHT_IMAGE /%(path)s/%(filter_root)s/SCIENCE/coadd_%(cluster)s%(appendix_root)s/coadd.weight.fits,/%(path)s/%(filter)s/SCIENCE/coadd_%(cluster)s%(appendix)s/coadd.weight.fits \
-WEIGHT_TYPE MAP_WEIGHT" % params
print command
print 'measuring filtered image'
os.system(command)
#command = "sex /%(path)s/%(filter_root)s/SCIENCE/coadd_%(cluster)s%(appendix)s/coadd.fits,/%(path)s/%(filter)s/SCIENCE/coadd_%(cluster)s%(appendix)s/coadd.fits -c %(PHOTCONF)s/phot.conf.sex \
#-PARAMETERS_NAME %(PHOTCONF)s/phot.param.sex \
#-CATALOG_NAME /%(path)s/%(filter)s/PHOTOMETRY/%(filter)s.all%(tag)s.cat \
#-DETECT_MINAREA 10 -DETECT_THRESH 10 -ANALYSIS_THRESH 10 \
#-MAG_ZEROPOINT 27.0 \
#-FLAG_TYPE MAX\
#-FLAG_IMAGE '' \
#-GAIN %(GAIN).3f \
#-WEIGHT_IMAGE /%(path)s/%(filter_root)s/SCIENCE/coadd_%(cluster)s%(appendix)s/coadd.weight.fits,'' \
#-WEIGHT_TYPE MAP_WEIGHT" % params
elif type == 'each':
params = {
'path': path,
'filter_root': filter_root,
'cluster': cluster,
'filter': filter,
'appendix': appendix,
'PHOTCONF': PHOTCONF,
'fwhm': seeing_worst,
'BASE': BASE,
'GAIN': float(fwhms[filter]['GAIN']),
'DATACONF': os.environ['DATACONF'],
'tag': tag
}
command = "sex /%(path)s/%(filter)s/SCIENCE/coadd_%(cluster)s%(appendix)s/coadd.fits -c %(PHOTCONF)s/phot.conf.sex \
-PARAMETERS_NAME %(PHOTCONF)s/phot.param.sex \
-CATALOG_NAME /%(path)s/%(filter)s/PHOTOMETRY/%(filter)s.each%(tag)s.cat \
-FILTER_NAME %(DATACONF)s/default.conv \
-FILTER Y \
-SEEING_FWHM %(fwhm).3f \
-DETECT_MINAREA 3 -DETECT_THRESH 3 -ANALYSIS_THRESH 3 \
-MAG_ZEROPOINT 27.0 \
-FLAG_TYPE OR\
-FLAG_IMAGE /%(path)s/%(filter)s/SCIENCE/coadd_%(cluster)s%(appendix)s/coadd.flag.fits \
-GAIN %(GAIN).3f \
-WEIGHT_IMAGE /%(path)s/%(filter)s/SCIENCE/coadd_%(cluster)s%(appendix)s/coadd.weight.fits \
-WEIGHT_TYPE MAP_WEIGHT" % params
elif type == 'arc':
params = {
'path': path,
'filter_root': filter_root,
'cluster': cluster,
'filter': filter,
'appendix': appendix,
'PHOTCONF': PHOTCONF,
'BASE': BASE,
'GAIN': float(fwhms[filter]['GAIN']),
'DATACONF': os.environ['DATACONF'],
'tag': tag
}
#command = "sex /%(path)s/%(filter_root)s/SCIENCE/coadd_%(cluster)s%(appendix)s/coadd.fits,/%(path)s/%(filter)s/SCIENCE/coadd_%(cluster)s%(appendix)s/coadd.fits -c %(PHOTCONF)s/phot.conf.sex \
commandA = "sex /%(path)s/%(filter_root)s/PHOTOMETRY/coadd.small.fits,/%(path)s/%(filter)s/PHOTOMETRY/coadd.small.fits -c %(PHOTCONF)s/phot.conf.sex \
-PHOT_APERTURES 70,100 \
-BACK_SIZE 10 \
-BACK_FILTERSIZE 2 \
-BACKPHOTO_TYPE GLOBAL \
-BACK_TYPE AUTO \
-PARAMETERS_NAME %(PHOTCONF)s/phot.param.sex \
-CATALOG_NAME /%(path)s/%(filter)s/PHOTOMETRY/%(filter)s.arc.all%(tag)s.cat \
-FILTER_NAME %(DATACONF)s/default.conv,%(DATACONF)s/default.conv\
-FILTER Y \
-DETECT_MINAREA 3 -DETECT_THRESH 0.5 -ANALYSIS_THRESH 0.5 \
-MAG_ZEROPOINT 27.0 \
-INTERP-TYPE NONE\
-FLAG_TYPE MAX\
-FLAG_IMAGE \"\"\
-SATUR_LEVEL 30000.0 \
-MAG_ZEROPOINT 27.0 \
-GAIN %(GAIN).3f \
-CHECKIMAGE_NAME /%(path)s/%(filter)s/PHOTOMETRY/coadd.arc.background.fits,/%(path)s/%(filter)s/PHOTOMETRY/coadd.arc.apertures.fits,/%(path)s/%(filter)s/PHOTOMETRY/coadd.arc.segmentation.fits\
-CHECKIMAGE_TYPE BACKGROUND,APERTURES,SEGMENTATION\
-WEIGHT_IMAGE /%(path)s/%(filter_root)s/PHOTOMETRY/coadd.weight.arc.small.fits,%(path)s/%(filter)s/PHOTOMETRY/coadd.weight.arc.small.fits\
-WEIGHT_TYPE NONE" % params
params['BACK_VALUE'] = 0
if filter == 'W-J-V':
params['BACK_VALUE'] = -0.02
commandB = "sex /%(path)s/%(filter_root)s/PHOTOMETRY/coadd_small.sub.fits,/%(path)s/%(filter)s/PHOTOMETRY/coadd_small.sub.fits -c %(PHOTCONF)s/phot.conf.sex \
-PHOT_APERTURES 70,100 \
-BACK_SIZE 64 \
-BACK_FILTERSIZE 3 \
-BACKPHOTO_TYPE GLOBAL \
-BACK_TYPE MANUAL \
-BACK_VALUE -0.02 \
-PARAMETERS_NAME %(PHOTCONF)s/phot.param.sex \
-CATALOG_NAME /%(path)s/%(filter)s/PHOTOMETRY/%(filter)s.arc.all%(tag)s.cat \
-FILTER_NAME %(DATACONF)s/default.conv,%(DATACONF)s/default.conv\
-FILTER Y \
-DETECT_MINAREA 3 -DETECT_THRESH 0.5 -ANALYSIS_THRESH 0.5 \
-MAG_ZEROPOINT 27.0 \
-INTERP-TYPE NONE\
-FLAG_TYPE MAX\
-FLAG_IMAGE \"\"\
-SATUR_LEVEL 30000.0 \
-MAG_ZEROPOINT 27.0 \
-GAIN %(GAIN).3f \
-CHECKIMAGE_NAME /%(path)s/%(filter)s/PHOTOMETRY/coadd.arc.apertures.fits,/%(path)s/%(filter)s/PHOTOMETRY/coadd.arc.segmentation.fits\
-CHECKIMAGE_TYPE APERTURES,SEGMENTATION\
-WEIGHT_IMAGE /%(path)s/%(filter_root)s/PHOTOMETRY/coadd.weight.arc.small.fits,%(path)s/%(filter)s/PHOTOMETRY/coadd.weight.arc.small.fits\
-WEIGHT_TYPE MAP_WEIGHT" % params
command = commandB
#-WEIGHT_IMAGE /%(path)s/%(filter_root)s/SCIENCE/coadd_%(cluster)s%(appendix)s/coadd.weight.fits,%(path)s/%(filter)s/SCIENCE/coadd_%(cluster)s%(appendix)s/coadd.weight.fits\
print command
filecommand.write(command + '\n')
sys.exit(0)
for child in children:
os.waitpid(child, 0)
print 'DONE!!!!'
def setUp(self):
progs = bashreader.parseFile('progs.ini')
self.sex_command = progs['p_sex']
'''
######################
import sys, unittest, os, subprocess, glob, shutil, optparse, difflib
import numpy, astropy, astropy.io.fits as pyfits
import ldac, bashreader
#######################
__cvs_id__ = "$Id: extract_object_cats.py,v 1.10 2010-11-12 20:33:56 dapple Exp $"
#######################
# GLOBAL CONSTANTS
#######################
PROGS = bashreader.parseFile('progs.ini')
PHOTCONF = './photconf'
DATACONF = PROGS['dataconf']
DETECT_OBJS_CONFIG = './photconf/detect.objs.conf.sex'
SMOOTH_IMAGE_CONFIG = './photconf/smooth.image.conf.sex'
DEFAULT_CONV = '%s/default.conv' % DATACONF
os.environ['DATACONF'] = DATACONF
#######################
# USER FUNCTIONS
#######################
def sextractor(image,
detect=None,