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SEProcPool.py
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SEProcPool.py
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#!/usr/bin/env python
#
# A test of `multiprocessing.Pool` class
#
# Copyright (c) 2006-2008, R Oudkerk
# All rights reserved.
#
import multiprocessing
import time
import random
import sys
#!/usr/bin/env python
import logging
import numpy as np
import pyfits
import os
import ConfigParser
import argparse
from despyfits.DESImage import DESImage
import subprocess
from scipy import stats
import getopt
import glob
from matplotlib.rcsetup import ValidateInStrings
#import multiprocessing
import pathos
from pathos.multiprocessing import ProcessingPool as Pool
from scipy.weave.catalog import os_dependent_catalog_name
def runL1P(args):
SEproc, x = args # unpack args
return SEproc.l1p(x)
def runL2P(args):
SEproc, x = args # unpack args
return SEproc.l2p(x)
def runL3P(args):
SEproc, x = args # unpack args
return SEproc.l3p(x)
class SEProcPool():
def __init__(self,confFile):
self.parser = argparse.ArgumentParser()
self.parser.add_argument(confFile,help="Need a configuration file.")
self.args = self.parser.parse_args()
self.inargs = {}
########### Configuration ############
self.Config = ConfigParser.ConfigParser()
self.configFile = self.args.confFile
self.Config.read(self.configFile)
self.template_file = self.ConfigSectionMap("General")['template']
self.exp_template_file = self.ConfigSectionMap("General")['exp_template']
self.chiplist = self.ConfigSectionMap("General")['chiplist']
self.data_dir = self.ConfigSectionMap("General")['data_dir']
self.data_file = self.ConfigSectionMap("General")['data_file']
self.data_conf = self.ConfigSectionMap("General")['conf_dir']
self.correc_dir = self.ConfigSectionMap("General")['corr_dir']
self.year = self.ConfigSectionMap("General")['year']
self.yearb = self.ConfigSectionMap("General")['yearb']
self.epoch = self.ConfigSectionMap("General")['epoch']
self.epochb = self.ConfigSectionMap("General")['epochb']
self.FILTER = self.ConfigSectionMap("General")['filter']
#--------------------------------------------------------#
# crosstalk #
#--------------------------------------------------------#
self.xtalk_file = self.ConfigSectionMap("crosstalk")['xtalk']
self.xtalk_template = self.ConfigSectionMap("crosstalk")['template']
self.replace_file = self.ConfigSectionMap("crosstalk")['replace']
#-----------------------------------------------------------#
# pixcorrect #
#-----------------------------------------------------------#
self.bias = self.ConfigSectionMap("pixcorrect")['bias']
self.bpm = self.ConfigSectionMap("pixcorrect")['bpm']
self.linearity = self.ConfigSectionMap("pixcorrect")['linearity']
self.bf = self.ConfigSectionMap("pixcorrect")['bf']
self.flat =self.ConfigSectionMap("pixcorrect")['flat']
self.copy_from_Dcache(self.correc_dir+'lin_'+str(self.yearb)+'/'+self.linearity)
self.copy_from_Dcache(self.correc_dir+'bf_'+str(self.yearb)+'/'+self.bf)
#---------------------------------------#
# skyCombine #
#---------------------------------------#
self.PCFILENAMEPREFIX = self.ConfigSectionMap("skyCombineFit")['pcafileprefix']
self.PCFILENAME = self.PCFILENAMEPREFIX
# starflat #
self.starflat = self.ConfigSectionMap("starflat")['starflat']
# skySubtract
self.pc_filename = self.ConfigSectionMap("skysubtract")['pcfilename']
self.weight = self.ConfigSectionMap("skysubtract")['weight']
#------------------------------------------#
# scamp #
#------------------------------------------#
self.imagflags = self.ConfigSectionMap("scamp")['imagflags']
self.flag_mask = self.ConfigSectionMap("scamp")['flag_mask']
self.flag_astr = self.ConfigSectionMap("scamp")['flag_astr']
self.catalog_ref = self.ConfigSectionMap("scamp")['catalog_ref']
self.default_scamp = self.ConfigSectionMap("scamp")['default_scamp']
self.head_file = self.ConfigSectionMap("scamp")['head']
self.farg = {'filter':self.FILTER}
self.head_FILE = self.head_file.format(**self.farg)
#
self.copy_from_Dcache(self.data_conf+self.default_scamp)
self.copy_from_Dcache(self.data_conf+self.head_FILE)
#-----------------------------------------#
# sextractor #
#-----------------------------------------#
self.sexnnwFile = self.ConfigSectionMap("sextractor")['starnnw_name']
self.sexconvFile = self.ConfigSectionMap("sextractor")['filter_name']
self.sexparamFile = self.ConfigSectionMap("sextractor")['parameters_name']
self.sexparamPSFEXFile = self.ConfigSectionMap("sextractor")['parameters_name_psfex']
self.configFile = self.ConfigSectionMap("sextractor")['configfile']
self.confPSF = self.ConfigSectionMap("sextractor")['sexforpsfexconfigfile']
self.copy_from_Dcache(self.data_conf+self.sexnnwFile)
self.copy_from_Dcache(self.data_conf+self.sexconvFile)
self.copy_from_Dcache(self.data_conf+self.sexparamFile)
self.copy_from_Dcache(self.data_conf+self.sexparamPSFEXFile)
self.copy_from_Dcache(self.data_conf+self.configFile)
self.copy_from_Dcache(self.data_conf+'default.psf')
self.copy_from_Dcache(self.data_conf+self.confPSF)
self.copy_from_Dcache(self.data_conf+'sex.param_bkg')
self.sexbkgparamFile='sex.param_bkg'
#----------------------------------------#
# psfex #
#----------------------------------------#
self.config_filePSF = self.ConfigSectionMap("psfex")['configfile']
self.copy_from_Dcache(self.data_conf+self.config_filePSF)
#-----------------------------------------#
# sextractor with psf #
#-----------------------------------------#
self.sexparamFile_2 = self.ConfigSectionMap("sextractor")['parameters_name2']
self.configFile2 = self.ConfigSectionMap("sextractor")['configfile2']
self.sexconvFile2 = self.ConfigSectionMap("sextractor")['filter_name2']
self.copy_from_Dcache(self.data_conf+self.sexconvFile2)
self.copy_from_Dcache(self.data_conf+self.sexparamFile_2)
self.copy_from_Dcache(self.data_conf+self.configFile2)
self.copy_from_Dcache(self.data_conf+'default.psf')
def ConfigSectionMap(self,section):
dict1 = {}
options = self.Config.options(section)
for option in options:
try:
dict1[option] = self.Config.get(section, option)
if dict1[option] == -1:
# DebugPrint("skip: %s" % option)
print "skip: %s" % option
except:
print("exception on %s!" % option)
dict1[option] = None
return dict1
#---------------------------#
# copy functions #
#---------------------------#
def copy_from_Dcache(self,fileN):
cmd = 'ifdh cp -D ' + fileN + ' . '
retval = subprocess.call(cmd.split(),stderr=subprocess.STDOUT)
if retval != 0:
sys.exit(1)
return
def copy_to_Dcache(self, fileN, dirN):
cmd = 'ifdh cp -D ' + fileN + ' ' + dirN
retval = subprocess.call(cmd.split(),stderr=subprocess.STDOUT)
if retval != 0:
sys.exit(1)
return
#----------------------------------------------------------#
# this function runs crosstalk trough a flat-field #
#----------------------------------------------------------#
def crosstalk(self,EXPFILE,NITE,**args):
self.copy_from_Dcache(self.data_conf+self.xtalk_file) #copy xtalk file
self.copy_from_Dcache(self.data_dir + NITE + '/' + EXPFILE) #copy data
self.copy_from_Dcache(self.data_conf+self.replace_file)
cmd = 'DECam_crosstalk ' + EXPFILE + \
' ' + self.xtalk_template.format(**args) +\
' -crosstalk ' + self.xtalk_file + \
' -ccdlist ' + self.chiplist +\
' -overscanfunction 0 -overscansample 1 -overscantrim 5 ' + \
' -photflag 1 -verbose 0' +\
' -replace '+ self.replace_file
retval = subprocess.call(cmd.split(),stderr=subprocess.STDOUT)
if retval != 0:
sys.exit(1)
os.remove(EXPFILE)
return
#---------------------------------------------------------------#
# this function runs pixcorrect trough crosstalk output #
#---------------------------------------------------------------#
def pixcorrect(self,outname, CCD, **args):
args['ccd']=CCD
# copy_from_Dcache(correc_dir+'superflat_'+str(year)+'_'+str(epoch)+'/biascor/'+bias.format(**args))
self.copy_from_Dcache(self.correc_dir+'/biascor/'+str(self.year)+str(self.epoch)+'/'+self.bias.format(**args))
# copy_from_Dcache(correc_dir+'superflat_'+str(year)+'_'+str(epoch)+'/norm-dflatcor/'+flat.format(**args) )
self.copy_from_Dcache(self.correc_dir+'/norm_dflatcor/'+str(self.year)+str(self.epoch)+'/'+self.flat.format(**args) )
# copy_from_Dcache(correc_dir+'bpm_'+str(yearb)+'_'+str(epochb)+'/'+bpm.format(**args))
self.copy_from_Dcache(self.correc_dir+'bpm/'+str(self.year)+str(self.epoch)+'/'+self.bpm.format(**args))
cmd = 'pixcorrect_im --verbose --in ' + self.template_file.format(**args)+'_xtalk.fits' + \
' -o ' +self.template_file.format(**args)+'_'+outname+'.fits' \
' --bias ' + self.bias.format(**args) + \
' --bpm ' + self.bpm.format(**args) + \
' --lincor ' + self.linearity + \
' --bf ' + self.bf + \
' --gain ' + \
' --flat ' + self.flat.format(**args) + \
' --resaturate --fixcols --addweight'
print '\n',cmd,'\n'
retval = subprocess.call(cmd.split(),stderr=subprocess.STDOUT)
if retval != 0:
sys.exit(1)
return
#----------------------------------------#
# this function runs mkbleedmask #
#----------------------------------------#
#adding -L 30
def bleedmask(self,CCD,inname,outname,**args):
args['ccd']=CCD
cmd = 'mkbleedmask ' + self.template_file.format(**args)+'_'+inname+'.fits' + \
' ' + self.template_file.format(**args)+'_'+outname+'.fits' + \
' -m -b 5 -f 1.0 -l 7 -n 7 -r 5 -t 20 -v 3 -w 2.0 -y 1.0 -s 100 -v 3 -E 6 -L 30' + \
' -x ' +self.template_file.format(**args)+'_trailbox.fits -o ' +self.template_file.format(**args)+'_satstars.fits'
print '\n',cmd,'\n'
retval = subprocess.call(cmd.split(),stderr=subprocess.STDOUT)
if retval != 0:
sys.exit(1)
os.remove(self.template_file.format(**args)+'_'+inname+'.fits')
return
#------------------------------#
# skycompress mkbleedmask #
#------------------------------#
def skycompress(self,CCD,inname,outname,**args):
args['ccd']=CCD
cmd = 'sky_compress --in ' + self.template_file.format(**args)+'_'+inname+'.fits' + \
' --skyfilename ' + self.template_file.format(**args)+'_'+outname+'.fits' + \
' --blocksize 128'
print '\n',cmd,'\n'
retval = subprocess.call(cmd.split(),stderr=subprocess.STDOUT)
if retval != 0:
sys.exit(1)
return
#----------------------------------------#
# this function runs immask #
#----------------------------------------#
def immask(self,CCD, inname,bkgname, outname, **args):
args['ccd']=CCD
cmd = 'immask all ' + self.template_file.format(**args)+'_'+inname+'.fits' +\
' ' + self.template_file.format(**args)+'_'+outname+'.fits' +\
' --minSigma 6.0 --max_angle 75 --max_width 300 --nsig_detect 18 --nsig_mask 12 --nsig_merge 12'+\
' --nsig_sky 1.5 --min_fill 0.33 --min_DN 600 --nGrowCR 1 '+\
' --bkgfile '+self.template_file.format(**args)+'_'+bkgname+'.fits'+\
' --draw --write_streaks --streaksfile ' + self.template_file.format(**args)+'_streaksfile.fits'
print '\n',cmd,'\n'
retval = subprocess.call(cmd.split(),stderr=subprocess.STDOUT)
if retval != 0:
sys.exit(1)
os.remove(self.template_file.format(**args)+'_'+inname+'.fits')
return
#---------------------------------------#
# skyCombine #
#---------------------------------------#
#PCFILENAME = PCFILENAMEPREFIX+'_'+str(year)+'_e1_'+FILTER+'_n04.fits'
#PCFILENAME = PCFILENAMEPREFIX+'_'+str(year)+'_'+str(epoch)+'_'+FILTER+'_n04.fits'
#copy_from_Dcache(correc_dir+'skytemp_'+str(year)+'_e1/'+PCFILENAME)
#copy_from_Dcache(correc_dir+'skytemp_'+str(year)+'_'+str(epoch)+'/'+PCFILENAME)
def skyCombineFit(self,inputFile,skycombineFile,skyfitinfoFile,**args):
self.copy_from_Dcache(self.correc_dir+'/skypca/'+str(self.year)+str(self.epoch)+'/'+self.PCFILENAME.format(**args))
#-----------------------
cmd = 'ls *'+inputFile+'.fits > listpcain'
print'\n', cmd,'\n'
retval = subprocess.call(cmd, shell=True)
if retval != 0:
sys.exit(1)
del cmd, retval
#------------------------
cmd = 'sky_combine --miniskylist listpcain -o ' + self.exp_template_file.format(**args)+'_'+skycombineFile+'.fits --ccdnums 1,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,62 --invalid S30,N30'
print cmd
retval = subprocess.call(cmd.split(),stderr=subprocess.STDOUT)
if retval != 0:
sys.exit(1)
del cmd, retval
#----------------------
cmd = 'sky_fit --infilename ' + self.exp_template_file.format(**args)+'_'+ skycombineFile+'.fits'
cmd += ' --outfilename '+ self.exp_template_file.format(**args)+'_'+skyfitinfoFile+'.fits --pcfilename '
cmd += (self.PCFILENAME[self.PCFILENAME.rfind("/")+1:]).format(**args)
print cmd
retval = subprocess.call(cmd.split(),stderr=subprocess.STDOUT)
if retval != 0:
sys.exit(1)
#----------------------------------------#
# starflat #
#----------------------------------------#
def pixcorr_starflat(self,inname, outname, CCD,**args):
args['ccd']=CCD
self.copy_from_Dcache(self.correc_dir+'/starflat/'+str(self.year)+str(self.epoch)+'/'+self.starflat.format(**args))
cmd = 'pixcorrect_im --verbose --in ' +self.template_file.format(**args)+'_'+inname+'.fits' +\
' --starflat '+ self.starflat.format(**args) +\
' --out '+self.template_file.format(**args)+'_'+outname+'.fits'
print '\n',cmd,'\n'
retval = subprocess.call(cmd.split(),stderr=subprocess.STDOUT)
if retval != 0:
sys.exit(1)
os.remove(self.template_file.format(**args)+'_'+inname+'.fits')
#--------------------------------------------#
# skysubtract #
#----------------------------------------- -#
# pc_filename = ConfigSectionMap("skysubtract")['pcfilename']
# weight = ConfigSectionMap("skysubtract")['weight']
def skysubtract(self,CCD, inname, outname, skyfitinfoFile,**args ):
args['ccd']=CCD
#
self.copy_from_Dcache(self.correc_dir+'/skypca/'+str(self.year)+str(self.epoch)+'/skytemp/'+self.pc_filename.format(**args))
# copy_from_Dcache(correc_dir+'skytemp_'+str(year)+'_'+str(epoch)+'/'+pc_filename.format(**args))
cmd = 'sky_subtract -i ' +self.template_file.format(**args)+'_'+inname+'.fits'+\
' -o ' + self.template_file.format(**args)+'_'+outname+'.fits' +\
' --fitfilename '+ self.exp_template_file.format(**args)+'_'+skyfitinfoFile+'.fits ' +\
' --pcfilename ' +self.pc_filename.format(**args) +\
' --domefilename ' +self.flat.format(**args) +\
' --weight ' +self.weight
print '\n',cmd,'\n'
retval = subprocess.call(cmd.split(),stderr=subprocess.STDOUT)
if retval != 0:
sys.exit(1)
# clean used files
os.remove(self.template_file.format(**args)+'_'+inname+'.fits' )
os.remove(self.pc_filename.format(**args))
os.remove(self.flat.format(**args))
return
#------------------------------------------#
# scamp #
#------------------------------------------#
def scamp(self,inputFile):
cmd = 'scamp ' + inputFile +\
' ' + '-AHEADER_GLOBAL ' + self.head_FILE +\
' -ASTRINSTRU_KEY DUMMY -AHEADER_SUFFIX .aheadnoexist -ASTREFMAG_LIMITS -99,17 ' +\
' -ASTREF_CATALOG ' +self.catalog_ref +' -c ' +self.default_scamp +\
' -WRITE_XML Y -XML_NAME scamp.xml -MOSAIC_TYPE SAME_CRVAL -ASTREF_BAND DEFAULT -POSITION_MAXERR 10.0 -NTHREADS 1 '
print '\n',cmd,'\n'
retval = subprocess.call(cmd.split(),stderr=subprocess.STDOUT)
if retval != 0:
sys.exit(1)
return
#-----------------------------------------#
# combineFiles
#----------------------------------------#-
def combineFiles(self,inputFile, outputFile):
cmd = ['fitscombine']
file_list = glob.glob(inputFile)
sort_list = sorted(file_list)
for fileN in sort_list:
cmd.append(fileN)
cmd.append(outputFile)
retval = subprocess.call(cmd)
if retval != 0:
sys.exit(1)
return
#------------------------------------------#
# clean files of given extension #
#------------------------------------------#
def fileclean(self,patt,ext):
templ='*'+patt+ext
file_list = glob.glob(templ)
for fileN in file_list:
os.remove(fileN)
#------------------------------------------#
# sextractor #
#------------------------------------------#
def sextractor(self, inname, outname, CCD, **args):
args['ccd']=CCD
cmd = 'sex ' + self.template_file.format(**args)+'_'+inname+'.fits[0]'+\
' -c ' + self.configFile + ' -FILTER_NAME ' + self.sexconvFile + ' -STARNNW_NAME ' +self.sexnnwFile + ' -CATALOG_NAME ' + self.template_file.format(**args)+'_'+outname+'.fits'+\
' -FLAG_IMAGE ' + self.template_file.format(**args)+'_'+inname+'.fits[1] -PARAMETERS_NAME ' + self.sexparamFile +\
' -DETECT_THRESH 10.0 -SATUR_KEY SATURATE -CATALOG_TYPE FITS_LDAC -WEIGHT_IMAGE ' + self.template_file.format(**args)+'_'+inname+'.fits[2]'+\
' -WEIGHT_TYPE MAP_WEIGHT '
print '\n',cmd,'\n'
retval = subprocess.call(cmd.split(),stderr=subprocess.STDOUT)
if retval != 0:
sys.exit(1)
return
#------------------------------------------#
# sextractor for PSFEX #
#------------------------------------------#
def sextractorPSFEX(self, inname, outname, CCD, **args):
args['ccd']=CCD
cmd = 'sex ' + self.template_file.format(**args)+'_'+inname+'.fits[0]'+\
' -c ' + self.confPSF + ' -FILTER_NAME ' + self.sexconvFile + ' -STARNNW_NAME ' +self.sexnnwFile + ' -CATALOG_NAME ' + self.template_file.format(**args)+'_'+outname+'.fits'+\
' -FLAG_IMAGE ' + self.template_file.format(**args)+'_'+inname+'.fits[1] -PARAMETERS_NAME ' +self.sexparamPSFEXFile +\
' -SATUR_KEY SATURATE -CATALOG_TYPE FITS_LDAC -WEIGHT_IMAGE ' + self.template_file.format(**args)+'_'+inname+'.fits[2]'+\
' -WEIGHT_TYPE MAP_WEIGHT '
print '\n',cmd,'\n'
retval = subprocess.call(cmd.split(),stderr=subprocess.STDOUT)
if retval != 0:
sys.exit(1)
return
#-----------------------------------#
# nulling weights for sky ccd31 #
#-----------------------------------#
def nullweightbkg(self, inname, outname,CCD,**args):
args['ccd']=CCD
# Preprocess the image for SExtractor by nulling weights in bad regions
cmd = 'null_weights -i ' + self.template_file.format(**args)+'_'+inname+'.fits' \
' -o ' + self.template_file.format(**args)+'_'+outname+'.fits' + \
' --null_mask BADAMP,EDGEBLEED,EDGE,STAR,TRAIL'
retval = subprocess.call(cmd.split(),stderr=subprocess.STDOUT)
if retval != 0:
sys.exit(1)
#---------------------------------------------
# sextractorsky bkg calculator
#---------------------------------------------
def sextractorsky(self, inname, outname, CCD, **args):
args['ccd']=CCD
cmd = 'sex ' + self.template_file.format(**args)+'_'+inname+'.fits[0]'+\
' -c ' + self.configFile +' -CHECKIMAGE_TYPE BACKGROUND ' +\
' -DETECT_THRESH 1000 -FILTER N ' +\
' -CHECKIMAGE_NAME ' + self.template_file.format(**args)+'_'+outname+'.fits'+\
' -WEIGHT_TYPE MAP_WEIGHT -WEIGHT_IMAGE '+self.template_file.format(**args)+'_'+inname+'.fits[2],'+self.template_file.format(**args)+'_'+inname+'.fits[2]' +\
' -PARAMETERS_NAME ' + self.sexbkgparamFile +\
' -CATALOG_TYPE NONE -INTERP_TYPE ALL -INTERP_MAXXLAG 16 -INTERP_MAXYLAG 16 '
print '\n',cmd,'\n'
retval = subprocess.call(cmd.split(),stderr=subprocess.STDOUT)
if retval != 0:
sys.exit(1)
return
#--------------------------------------------#
# psfex #
#--------------------------------------------#
def psfex(self, name,CCD, **args):
args['ccd']=CCD
cmd = 'psfex ' + self.template_file.format(**args)+'_'+name+'.fits -c ' +self.config_filePSF +\
' -OUTCAT_NAME '+ self.template_file.format(**args)+'_psflist.fits -OUTCAT_TYPE FITS_LDAC'
print '\n',cmd,'\n'
retval = subprocess.call(cmd.split(),stderr=subprocess.STDOUT)
if retval != 0:
sys.exit(1)
return
#---------------------------------------------#
# sextractor with PSF #
#---------------------------------------------#
def sextractorPSF(self, name, name1, outname, filepsf, CCD, **args):
args['ccd']=CCD
h=DESImage.load(self.template_file.format(**args)+'_'+str(name)+'.fits')
fwhm = 0.263*float(h.header['FWHM'])
cmd = 'sex ' + self.template_file.format(**args)+'_'+name+'.fits[0]'+\
' -PSF_NAME ' + self.template_file.format(**args)+'_'+filepsf+\
' -c ' + self.configFile2 + ' -FILTER_NAME ' + self.sexconvFile2 + ' -STARNNW_NAME ' +self.sexnnwFile + ' -CATALOG_NAME ' + self.template_file.format(**args)+'_'+outname+'.fits'+\
' -FLAG_IMAGE ' + self.template_file.format(**args)+'_'+name+'.fits[1] -PARAMETERS_NAME ' + self.sexparamFile_2 +\
' -INTERP_TYPE VAR_ONLY -INTERP_MAXXLAG 4 -INTERP_MAXYLAG 4 -SEEING_FWHM ' + str(fwhm) +\
' -DETECT_THRESH 1.5 -SATUR_KEY SATURATE -CATALOG_TYPE FITS_LDAC '+\
' -WEIGHT_IMAGE '+self.template_file.format(**args)+'_'+name1+'.fits[2],'+self.template_file.format(**args)+'_'+name1+'.fits[2]'+ \
' -WEIGHT_TYPE MAP_WEIGHT -CHECKIMAGE_NAME ' + self.template_file.format(**args)+'_segmap.fits -CHECKIMAGE_TYPE SEGMENTATION '
print ' sextractorPSF \n',cmd,'\n'
# ' -INTERP_TYPE NONE -SEEING_FWHM ' + str(fwhm) +\
retval = subprocess.call(cmd.split(),stderr=subprocess.STDOUT)
if retval != 0:
sys.exit(1)
os.remove(self.template_file.format(**args)+'_'+name+'.fits')
return
#--------------------------------------#
# fwhm routine from Wrappers #
#--------------------------------------#
debug = 0
def fwhm(self, incat ,debug):
debug = 0
"""
Get the median FWHM and ELLIPTICITY from the scamp catalog (incat)
"""
CLASSLIM = 0.75 # class threshold to define star
MAGERRLIMIT = 0.1 # mag error threshold for stars
if debug: print "!!!! WUTL_STS: (fwhm): Opening scamp_cat to calculate median FWHM & ELLIPTICITY.\n"
hdu = pyfits.open(incat,"readonly")
if debug: print "!!!! WUTL_STS: (fwhm): Checking to see that hdu2 in scamp_cat is a binary table.\n"
if 'XTENSION' in hdu[2].header:
if hdu[2].header['XTENSION'] != 'BINTABLE':
print "!!!! WUTL_ERR: (fwhm): this HDU is not a binary table"
exit(1)
else:
print "!!!! WUTL_ERR: (fwhm): XTENSION keyword not found"
exit(1)
if 'NAXIS2' in hdu[2].header:
nrows = hdu[2].header['NAXIS2']
print "!!!! WUTL_INF: (fwhm): Found %s rows in table" % nrows
else:
print "!!!! WUTL_ERR: (fwhm): NAXIS2 keyword not found"
exit(1)
tbldct = {}
for colname in ['FWHM_IMAGE','ELLIPTICITY','FLAGS','MAGERR_AUTO','CLASS_STAR']:
if colname in hdu[2].columns.names:
tbldct[colname] = hdu[2].data.field(colname)
else:
print "!!!! WUTL_ERR: (fwhm): No %s column in binary table" % colname
exit(1)
hdu.close()
flags = tbldct['FLAGS']
cstar = tbldct['CLASS_STAR']
mgerr = tbldct['MAGERR_AUTO']
fwhm = tbldct['FWHM_IMAGE']
ellp = tbldct['ELLIPTICITY']
fwhm_sel = []
ellp_sel = []
count = 0
for i in range(nrows):
if flags[i] < 1 and cstar[i] > CLASSLIM and mgerr[i] < MAGERRLIMIT and fwhm[i]>0.5 and ellp[i]>=0.0:
fwhm_sel.append(fwhm[i])
ellp_sel.append(ellp[i])
count+=1
fwhm_sel.sort()
ellp_sel.sort()
# allow the no-stars case count = 0 to proceed without crashing
if count <= 0:
fwhm_med = 4.0
ellp_med = 0.0
else:
if count%2:
# Odd number of elements
fwhm_med = fwhm_sel[count/2]
ellp_med = ellp_sel[count/2]
else:
# Even number of elements
fwhm_med = 0.5 * (fwhm_sel[count/2]+fwhm_sel[count/2-1])
ellp_med = 0.5 * (ellp_sel[count/2]+ellp_sel[count/2-1])
if debug:
print "FWHM=%.4f" % fwhm_med
print "ELLIPTIC=%.4f" % ellp_med
print "NFWHMCNT=%s" % count
return (fwhm_med,ellp_med,count)
#------------------------------------#
# changing head #
#------------------------------------#
def change_head(self, FileN, catalog, image, outname, CCD, **args):
ccdLen = len(CCD)
#Getting the data and saving into an array
o = open(FileN,'r').read().splitlines()
info_array = ['CRVAL1','CRVAL2','CRPIX1','CRPIX2','CD1_1','CD1_2','CD2_1','CD2_2',\
'PV1_0','PV1_1 ','PV1_2','PV1_4','PV1_5','PV1_6','PV1_7','PV1_8','PV1_9','PV1_10',\
'PV2_0','PV2_1 ','PV2_2','PV2_4','PV2_5','PV2_6','PV2_7','PV2_8','PV2_9','PV2_10']
n = len(info_array)
matrix = []
for ii in o:
for oo in info_array:
if oo in ii.split('=')[0] :
#print ii.split('=')[0], ii.split('=')[1].split('/')[0]
matrix.append(ii.split('=')[1].split('/')[0])
matrix = np.array(matrix)
#changing the header
cont = 0
for i in range(ccdLen):
ccdstring="%02d"%int(CCD[i])
args['ccd']=ccdstring
catalog1 = self.template_file.format(**args)+'_'+catalog+'.fits'
image1 = self.template_file.format(**args)+'_'+image+'.fits'
(fwhm_, ellip, count) = self.fwhm(catalog1,0)
h=DESImage.load(image1)
h.header['FWHM'] = fwhm_
h.header['ELLIPTIC'] = ellip
h.header['SCAMPFLG'] = 0
im=h.data
iterate1=stats.sigmaclip(im,5,5)[0]
iterate2=stats.sigmaclip(iterate1,5,5)[0]
iterate3=stats.sigmaclip(iterate2,3,3)[0]
skybrite=np.median(iterate3)
skysigma=np.std(iterate3)
h.header['SKYBRITE'] = skybrite
h.header['SKYSIGMA'] = skysigma
h.header['CAMSYM'] = 'D'
h.header['SCAMPCHI'] = 0.0
h.header['SCAMPNUM'] = 0
for j in range(n):
h.header[info_array[j]] = float(matrix[cont])
cont = cont + 1
h.save(self.template_file.format(**args)+'_'+outname+'.fits')
#-----------------------------------#
# nulling weights in bad regions #
#-----------------------------------#
def rowinterp_nullweight(self, inname, outname,CCD,**args):
args['ccd']=CCD
# Preprocess the image for SExtractor by interpolating (temporarily) across bleedtrails
cmd = 'rowinterp_nullweight -i ' + self.template_file.format(**args)+'_'+inname+'.fits' \
' -o ' + self.template_file.format(**args)+'_'+outname+'.fits' + \
' -l ' + self.template_file.format(**args)+'_'+outname+'.log' + \
' --interp_mask TRAIL --invalid_mask EDGE --max_cols 50 -vv --null_mask ' + \
' BADAMP,EDGEBLEED,EDGE,CRAY'
retval = subprocess.call(cmd.split(),stderr=subprocess.STDOUT)
if retval != 0:
sys.exit(1)
#-----------------------------------#
# nulling weights in bad regions #
#-----------------------------------#
def nullweight(self, inname, outname,CCD,**args):
args['ccd']=CCD
# Preprocess the image for SExtractor by nulling weights in bad regions
cmd = 'null_weights -i ' + self.template_file.format(**args)+'_'+inname+'.fits' \
' -o ' + self.template_file.format(**args)+'_'+outname+'.fits' + \
' -l ' + self.template_file.format(**args)+'_'+outname+'.log' + \
' --null_mask BADAMP,EDGEBLEED,EDGE' + \
' --resaturate'
retval = subprocess.call(cmd.split(),stderr=subprocess.STDOUT)
if retval != 0:
sys.exit(1)
#--------------------------------#
# creating regions #
#--------------------------------#
def read_geometry(self, inname, outname, CCD, **args):
args['ccd']=CCD
fileN = self.template_file.format(**args)+'_'+inname+'.fits'
cat = pyfits.open(fileN)
XWIN_IMAGE = cat[2].data.field('XWIN_IMAGE').copy()
YWIN_IMAGE = cat[2].data.field('YWIN_IMAGE').copy()
A_IMAGE = cat[2].data.field('A_IMAGE').copy()
B_IMAGE = cat[2].data.field('B_IMAGE').copy()
THETA_IMAGE = cat[2].data.field('THETA_IMAGE').copy()
SPREAD_MODEL = cat[2].data.field('SPREAD_MODEL').copy()
FLAGS = cat[2].data.field('FLAGS').copy()
IMAFLAGS_ISO = cat[2].data.field('IMAFLAGS_ISO').copy()
del cat
c = 5
A_IMAGE = c*A_IMAGE
B_IMAGE = c*B_IMAGE
color = []
ellipse = []
widht = []
N = len(SPREAD_MODEL)
for i in range(N):
ellipse.append("ellipse")
if FLAGS[i]<4:
if IMAFLAGS_ISO[i] == 0:
if SPREAD_MODEL[i] < 0.003 and SPREAD_MODEL[i] > -0.003:
color.append("#color=red") #stars
widht.append('width = 4')
elif SPREAD_MODEL[i] >= 0.003:
color.append("#color=yellow") #galaxies
widht.append('width = 4')
else:
color.append("#color=green") #garbage
widht.append('width = 2')
elif IMAFLAGS_ISO[i] & 32 !=0:
color.append("#color=blue") #detection near a bright stars.
widht.append('width = 3')
else:
color.append("#color=cyan") #object with questionable flags Flags >=4
widht.append('width = 3')
else:
color.append("#color=magenta") #object with questionable flags Flags >=4
widht.append('width = 2')
DAT = np.column_stack((ellipse, XWIN_IMAGE, YWIN_IMAGE, A_IMAGE, B_IMAGE, THETA_IMAGE, color, widht))
np.savetxt(self.template_file.format(**args)+'_'+outname+'.reg', DAT, delimiter=" ", fmt="%s")
def sanityCheck(self,fName):
f = pyfits.open(fName)
nstar = f[2].header['NAXIS2']
f.close()
if nstar < 5:
raise ValueError('A very low number of stars')
return nstar
def setArgs(self,**args):
self.inargs = args
def l1p(self,ccdstring):
args = self.inargs.copy()
self.pixcorrect('detrend',ccdstring,**args)
self.nullweight('detrend', 'nullweight', ccdstring,**args)
self.sextractor('nullweight', 'sextractor', ccdstring,**args )
def l2p(self,ccdstring):
self.bleedmask(ccdstring,'wcs','bleedmasked',**self.inargs)
self.skycompress(ccdstring,'bleedmasked','bleedmask-mini',**self.inargs)
def l3p(self,ccdstring):
self.skysubtract(ccdstring,'bleedmasked','skysub','skyfit-binned-fp',**self.inargs )
self.pixcorr_starflat('skysub', 'starflat', ccdstring,**self.inargs)
self.nullweightbkg('starflat','nullwtbkg',ccdstring,**self.inargs)
self.sextractorsky('nullwtbkg','bkg',ccdstring,**self.inargs)
self.immask(ccdstring,'starflat','bkg','immask',**self.inargs)
self.rowinterp_nullweight('immask', 'nullweightimmask', ccdstring,**self.inargs)
self.sextractorPSFEX('nullweightimmask', 'sextractorPSFEX', ccdstring,**self.inargs )
# se.immask(ccdstring,'starflat','immask',**args)
self.psfex( 'sextractorPSFEX', ccdstring,**self.inargs)
self.sextractorPSF('nullweightimmask', 'nullweightimmask', 'fullcat', 'sextractorPSFEX.psf', ccdstring,**self.inargs)
#
if __name__ == '__main__':
nbpar = len(sys.argv)
print sys.argv
conF = "confFile"
conF = sys.argv[1]
multiprocessing.freeze_support()
print " Start SEProc.py with conf File %s\n" % conF
se = SEProcPool(conF)
print "instance created \n"
EXPNUM = se.ConfigSectionMap("General")['expnum']
FILTER = se.ConfigSectionMap("General")['filter']
NITE = se.ConfigSectionMap("General")['nite']
data_dir = se.ConfigSectionMap("General")['data_dir']
data_file = se.ConfigSectionMap("General")['data_file']
CCD = (se.ConfigSectionMap("General")['chiplist']).split( ',')
rRun = str(se.ConfigSectionMap("General")['r'])
pRun = str(se.ConfigSectionMap("General")['p'])
YEAR = se.ConfigSectionMap("General")['year']
EPOCH = se.ConfigSectionMap("General")['epoch']
ncpu = int(se.ConfigSectionMap("General")['ncpu'])
print "ncpu=%d \n" % ncpu
#EXPFILE = 'DECam_00'+str(EXPNUM)+'.fits.fz'
EXPFILE = data_file
print "Start working with file %s \n" % EXPFILE
args = {'expnum': EXPNUM, 'filter': FILTER, 'ccd':'0', 'r':rRun, 'p':pRun, 'year': YEAR, 'epoch': EPOCH}
se.setArgs(**args)
#running crosstalk
# parameters are crosstalk(EXPFILE,NITE,**args)
# I have to replace NITE with empty string to avoid modification of the file path
# as it add to the path NITE and we have different data model
#
print " Start crosstalk \n"
se.crosstalk(EXPFILE,'',**args)
nccd = len(CCD)
xfiles_list = glob.glob('*_xtalk.fits')
if len(xfiles_list) < nccd:
print " Possibly corrupted file expect %d extensions but got only %d \n" % (nccd,len(xfiles_list))
sys.exit(-1)
#running pixelcorrect and bleedmask
se.copy_from_Dcache(se.data_conf+'default.psf')
instrings = []
for ccd in CCD:
ccdstring= "%02d"%int(ccd)
instrings.append(ccdstring)
pool = Pool(ncpu)
pars = [(se, ccdstring) for ccdstring in instrings ]
pool.map(runL1P, pars)
se.fileclean('xtalk','.fits')
se.fileclean('nullweight','.fits')
se.combineFiles('D'+("%08d" % int(EXPNUM))+'**sextractor.fits', 'Scamp_allCCD_r'+rRun+'p'+pRun+'.fits')
try:
se.sanityCheck('D'+("%08d" % int(EXPNUM))+'_'+FILTER+'_01'+'_r'+rRun+'p'+pRun+'_sextractor.fits')
except ValueError as err:
print(err.args)
sys.exit(-1)
se.fileclean('bpm','.fits')
se.fileclean('biascor','.fits')
se.scamp('Scamp_allCCD_r'+rRun+'p'+pRun+'.fits')
se.change_head('Scamp_allCCD_r'+rRun+'p'+pRun+'.head', 'sextractor', 'detrend', 'wcs', CCD, **args)
#
print "SECOND LOOP \n"
pool.map(runL2P, pars)
se.fileclean('detrend','.fits')
se.skyCombineFit('bleedmask-mini','bleedmask-mini-fp','skyfit-binned-fp',**args)
#
print "THIRD LOOP \n"
pool.map(runL3P, pars)
se.fileclean('nullwtbkg','.fits')
pool.close()
pool.join()
# print res
print " End run on exposure \n"