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desHostMatch.py
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desHostMatch.py
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#!/usr/bin/env python
"""
Ravi Gupta, Chris D'Andrea - adapted for GW candidates by Antonella Palmese Jan 2017
10 Dec 2013
This script queries the NCSA Oracle DB table SNCAND to obtain transient coordinates
which are then matched to potential host galaxies, whose information is given in
Rachel Cane's merged source catalogs. For each transient, the script searches within
a 15 arcsec radius and ranks all sources according to their separation from the transient
in units of directional light radius (DLR).
The results are output to a text file and written to DB.
DEPENDENCIES: Python, cx_Oracle package, atc-tools
INPUTS:
-- NCSA Oracle DB
-- 10 catalog files (one for each SN field)
OUTPUTS:
-- outfile = "DES_hostmatch_sep_ABT.txt" (All objects w/in 15 arcsec ordered by ang. sep.)
-- outfile2 = "DES_hostmatch_DLR_ABT.txt" (This contains the actual hosts you want)
-- outfile3 = "DES_host_discrepancy_ABT.txt" (List of objects for which host!=nearest object)
v1.0 GW: Jan 2017 -- Searches for hosts in a catalog containing Y1Q2 with Le Phare photozs,
2MASS and SDSS galaxies. The search is done in the healpix pixel containing the
candidate and all the 8 adjacent pixels.
v2.1: August 2014 -- Updates the searched catalog to be a mix of the SVA1-GOLD catalog
(where defined) and the SVA1 catalog.
v2.2: Sep 17 2014 -- With update to ATC2, use atc-tools to ingest the closest host galaxy as a
target and add a tag on the transient pointing to the host.
v2.3: Oct 14 2014 -- Fix bug where all magnitudes written to SNGALS table due to comparison
being made on value of array (which is type STRING) instead of float(STRING)
v2.4: Oct 22 2014 -- Change injestion into ATC2 from the nearest galaxy to the three nearest
galaxies.
v2.5: Oct 31 2014 -- Bug fix introduced in last update: was tagging in ATC incorrect galaxies
as the host. Added the requirement on hostinfo['rank'][k] == 1
v3.0: Jul 16 2015 -- Make code command-line runnable
-- Edited text for readability (100 char width) & enhanced comments
-- Changed names, locations of output files
-- Added ability to read in input file in case there is a failure in an
earlier running of the script.
-- Split off algorithms that compute the DLR into a separate script.
v3.1 Jun 15 2016 -- Add call to function that computes HOST_CONFUSION
-- Input HOST_CONFUSION into SNCAND table
v3.2 Sep 12 2016 -- Update SNGALS for all *good* candidates with numepochs_ml>=1 instead of
just those with a transient_name
-- Only insert into ATC hosts for candidates with a transient_name
-- Select field location for host match from FIELD column in SNCAND table
-- Instead of entering nothing into SNGALS for hostless candidates,
write SNGALID=-1, DLR_RANK=0 for those candidates. Are thus excluded
from matching from there onwards.
-- improved the logfile output readability
-- Change order in which HOST CATALOG files are read in; if there is nothing
to match in a field, the file is skipped.
"""
import cx_Oracle
import shutil
import sys
import os
import math
import numpy as np
import time
import argparse
import healpy
#from healpy.pixelfunc import ang2pix
#from healpy.pixelfunc import get_all_neighbours
from astropy.io import fits
from math import pi
#from atc_tools.ext import helpers as atcfuncs
import HostMatchAlgorithms_Ravi as hma # RRG
import ConfigParser
#config = ConfigParser.ConfigParser()
#if os.path.isfile('./postproc_'+str(season)+'.ini'):
# inifile = config.read('./postproc_'+str(season)+'.ini')[0]
################### Input Parsing #################################################################
#parser2 = argparse.ArgumentParser( description = "Assignment of DES transient "
# "names to SN candidates (SNIDs) based on the current set of naming "
# "criteria. Subsequently ingests targets into the ATC if the relevant"
# " flag is set. Required arguments is SEASON." )
#parser.add_argument( "--input", help = "File containing list of named "
# "transients to ingest to ATC." )
#parser2.add_argument( "--dbname", "-db", help = "Name of Database at NCSA in "
# "which we are looking for new transients. Default is desoper.",
# default="destest")
my_dbname = "destest"
#parser2.add_argument( "--username", "-u", help = "Username for NCSA access. "
# "Default is read-only generic username. CANNOT ACCESS Y2 DB.",
# default="testtest") # testing (Paulo_12-14-18)
#parser2.add_argument( "--password", "-p", help = "Password for NCSA access. "
# "Default is read-only generic password. CANNOT ACCESS Y2 DB.",
# default="testtest") # testing (Paulo_12-14-18)
#parser2.add_argument( "--verbose", "-v", help = "Print helpful statements to "
# "check progress of code. Default is false.", action = "count", default=False)
my_verbose=False
#parser2.add_argument( "--season", type=int, help = "Season number for transient. Default is 70. ",
# default=70)
my_season=70
#parser.add_argument( "--atc", help = "Ingest all targets into the ATC. "
# "Default is false. In either case, transients info is "
# "written to a log file.", action = "store_true" )
#parser2.add_argument( "--test", "-t" , help = "Test mode: No writing to "
# "database is done. Rather, only an output file is written to "
# "scratch with the transient names and host names, along with "
# "information about the test ATC ingestion.", action = "store_true" )
#parser2.add_argument( "--testdb", "-tdb" , help = "Test mode: No writing to "
# "database SNGAL is done. It writes to SNGAL_TEST instead. ", action = "store_true" )
#args2 = parser2.parse_args()
#config = ConfigParser.ConfigParser()
#if os.path.isfile('./postproc_'+str(season)+'.ini'):
# inifile = config.read('./postproc_'+str(season)+'.ini')[0]
##################### DEFINE GLOBAL VARIABLES #################################################
rad = np.pi/180 # convert deg to rad
search = 15.0 # search radius (arcsec)
farc = search/3600 # search radius (degree)
isNearest = 0 # number of cases for which smallest DLR galaxy is also
#the nearest
DLR_cut = 4.0 #keep as potential hosts only galaxies with d_DLR
#less than this
#Catalog = 'SVA1' #SVA1-GOLD catalog in fact. Variable is prefix for name.
atc_flag = 0 #Set to non-zero for each failure at ATC target ingestion
db_flag = 0 #Set to non-zero for each failure at DB update
#################### Location and names of the catalog files ######################################
from time import strftime
thisTime = strftime("%Y%m%d.%H%M%S")
#DIR = "/data/des60.b/data/palmese/GW_reject_cat/"
#INPUT_DIR = DIR + '/v1.0.1/'
#OUTPUT_DIR = DIR + '/hostmatching/RUNLOGS/' + thisTime + '/'
#Test an environmental change to employ new hostgal catalog
#TopHost='/data/des60.b/data/palmese/GW_reject_cat/GW_DES_Y3A2'
TopHost='/data/des60.b/data/palmese/GW_reject_cat/v1.0.2'
os.environ['TOPDIR_HOSTMATCH']=TopHost
INPUT_DIR = os.environ.get('TOPDIR_HOSTMATCH') + '/'
OUTPUT_DIR = str(os.environ.get('OUTDIR_HOSTMATCH')) #+ '/hostmatch/'
print('TOPDIR_HOSTMATCH='+INPUT_DIR)
print('OUTDIR_HOSTMATCH='+OUTPUT_DIR)
#sys.exit('Nora made me exit. Blame her. But really, this was just a test to ensure I crash anyway due to there being no TOPDIR_HOSTMATCH (as least probably)')
#OUTPUT_DIR = OUTPUT_DIR + thisTime + '/'
if not os.path.isdir(OUTPUT_DIR):
os.makedirs(OUTPUT_DIR,0755)
#try:
# os.mkdir(OUTPUT_DIR, 0755)
#except:
# sys.exit("Could not create output directory for RUNLOGS ... " + OUTPUT_DIR)
outfile_sep = OUTPUT_DIR + "byAngularSeparation.ABT.txt"
outfile_dlr = OUTPUT_DIR + "byDLR.ABT.txt"
outfile_mismatch = OUTPUT_DIR + "mismatchhost.ABT.txt"
file_sep = open(outfile_sep, 'a' )
file_dlr = open(outfile_dlr, 'a' )
file_mismatch = open(outfile_mismatch, 'a' )
# header
h = ('#trans_name SNID COADD_OBJ_ID RA DEC sep '
'DLR A B rPHI rank\n' )
h2 = ('#trans_name SNID COADD_OBJ_ID RA DEC sep '
'DLR A B rPHI rank host\n')
file_sep.write(h)
file_dlr.write(h2)
file_mismatch.write(h)
logfile_name_atc = OUTPUT_DIR + "hostmatch.atc.log"
logfile_name_db = OUTPUT_DIR + "hostmatch.db.log"
logfile_atc = open(logfile_name_atc,'w')
logfile_db = open(logfile_name_db,'w')
logfile_db.write('#DB\n')
logfile_db.write('#List of new host galaxies assigned\n')
logfile_db.write('#Status=0 --> Successful update to database\n')
logfile_db.write('#Status=1 --> Failed update\n')
logfile_db.write('# A new run of desHostMatch should be done\n')
logfile_db.write('# if there are any failures in desHostMatch\n')
logfile_db.write('# Input file NOT REQUIRED.\n')
logfile_db.write('{0:<16}{1:<16}{2:<16}{3:<12}{4:<12}{5:>10}{6:>7}\n'.format(
'#SNID','TransientName','HostObjectID','RA','DEC','DLR_RANK','Status'))
logfile_atc.write('#ATC\n')
logfile_atc.write('#List of new host galaxies assigned\n')
logfile_atc.write('#Status=0 --> Successful ingestion to ATC\n')
logfile_atc.write('#Status=1 --> Failed ingestion; remains to be uploaded\n')
logfile_atc.write('#Status=2 --> Failed tagging; remains to be associated with SN\n')
logfile_atc.write('#Status=4 --> ATC tagging skipped. remains to be associated with SN\n')
logfile_atc.write('# Any Status > 0 requires a new run of desHostMatch\n')
logfile_atc.write('# with this file given to the --input flag\n')
logfile_atc.write('{0:<16}{1:<25}{2:<16}{3:<16}{4:<7}{5:<7}\n'.format(
'#TransientName','HostName','RA','DEC','DLR_RANK','Status'))
#replace args.season with environment variable if it was set for compatibility with postproc.py
season_number = os.environ.get('SEASON')
if season_number:
#args2.season = season_number
my_season=season_number
############################### MAIN ##########################################################
def main(season):
global isNearest
global maxgalid
global db_flag
global atc_flag
print("test")
#if args2.verbose > 0:
# print 'verbose = ',args2.verbose
#if args2.testdb >0:
#sngals_file = 'SNGALS_TEST'
#sngals_file_id = 'COADD_OBJECTS_ID'#'OBJECTS_ID'
#else:
sngals_file = 'SNGALS'
sngals_file_id = 'OBJECTS_ID'# 'COADD_OBJECTS_ID'
start_time = time.time()
hostname = 'desdb-sci.ncsa.illinois.edu'
port = 1521
# dbname = args.dbname
dbname = os.environ.get('DBNAME')
# username = args.username
username = os.environ.get('DB_USERNAME')
# password = args.password
password = os.environ.get('DB_PASSWD')
dsn = cx_Oracle.makedsn(hostname, port, service_name = dbname)
print(dsn)
connection = cx_Oracle.Connection(username, password, dsn)
cursor = connection.cursor()
#----------------------------------------------------------------------------------------------
#----------- Query all transients that have no entry in the SNGALS table. ---------------------
# ---------- These are the galaxies we are to host-match --------------------------------------
#----------------------------------------------------------------------------------------------
print("test1")
query = ( "SELECT c.transient_name, c.SNID, c.ra, c.dec, "
#"substr(c.transient_name,6,2), FIELD "
"from SNCAND c LEFT JOIN SNGALS g on c.SNID=g.SNID "
"where c.transient_name is not NULL "
"and c.transient_status >= 0 and c.snfake_id = 0 "
"and g.SNGALID is NULL " )
query_new = ( "SELECT c.transient_name, c.SNID, c.ra, c.dec "
#"c.FIELD as field "
"from SNCAND c LEFT JOIN "+sngals_file+" g on c.SNID=g.SNID "
#TO BE PUT BACK LATER! "where c.numepochs_ml>=1 and c.numobs_ml>=2 "
"where (c.transient_status is NULL or c.transient_status >=0) "
"and c.snfake_id=0 and c.cand_type >=0 "
"and g.SNGALID is NULL "
#"and g.SNGALID is NULL and c.FIELD is not NULL ")
#"and c.season="+str(args2.season)+" ")
"and c.season="+str(my_season)+" ")
print("test 2")
print query_new
cursor.execute(query_new)
data=cursor.fetchall()
#if args2.verbose > 0:
# print "Number of DES Candidates to match = ",len(data)
#Sort by field to lessen memory issues on loading large files
if len(data) > 0:
#data.sort(key=lambda x:x[4])
data = np.array(data)
else:
status='0'
hostms=open('hostmatchstatus.txt','w')
hostms.write(status)
hostms.close()
print
print "WARNING:"
print "The list of galaxies to host match is empty."
print "The query below has failed:"
print
print query_new
print
print "This could be due to a previous successful run."
print "If you wish to rerun, please clear the database using the following command:"
print
#print "delete from SNGALS where season="+str(args.season)+';'
print
print('update SNGALS SET sngalid=NULL where season=416;')
print('(Maybe)')
return
print("test 3")
#----------------------------------------------------------------------------------------------
#------------ Query the maximum SNGALID to start counting with --------------------------------
#----------------------------------------------------------------------------------------------
query = "SELECT max(SNGALID) from "+sngals_file
cursor.execute(query)
galmax=cursor.fetchall()
if galmax[0][0] is None:
maxgalid = 0
else:
maxgalid = galmax[0][0]
#if args2.verbose > 0:
# print "Max GALID = ",maxgalid
#----------------------------------------------------------------------------------------------
#------------- Select all field names where a transient is ------------------------------------
#------------- lacking an identified host and requires matching -------------------------------
#----------------------------------------------------------------------------------------------
ra_cand = np.array(data[:,2],dtype=float)
dec_cand = np.array(data[:,3],dtype=float)
idx = [ra_cand<0.0]
ra_cand[idx] = ra_cand[idx]+360.
ra_cand = ra_cand*pi/180.
dec_cand = (90.-dec_cand)*pi/180.
pix = healpy.pixelfunc.ang2pix(32,dec_cand,ra_cand)
fields_cands = np.array(pix)
fields = np.unique(pix)
#----------------------------------------------------------------------------------------------
#------------- Select all the host galaxies that have already been assigned -------------------
#------------- to a transient; this way we reassign the same SNGALID if one -------------------
#------------- has previously been used -------------------------------------------------------
#----------------------------------------------------------------------------------------------
query = ( "select SNID, "+sngals_file_id+" , SNGALID from "+sngals_file+
" where "+sngals_file_id+" is not NULL" )
cursor.execute(query)
temp = cursor.fetchall()
temp = np.array(temp)
current_host = np.zeros(np.sum(max(len(temp),1)), \
dtype={'names':['SNID','SNGALID','COADD_ID'], \
'formats':['S8','S8','S12']})
#if args2.verbose > 0:
# print 'Number of objects currently in SNGALS: ',len(temp)
if len(temp):
current_host['SNID'] = temp[:,0]
current_host['COADD_ID'] = temp[:,1]
current_host['SNGALID'] = temp[:,2]
else:
current_host['SNID'] = -1
current_host['COADD_ID'] = -1
current_host['SNGALID'] = -1
#----------------------------------------------------------------------------------------------
#------------- Loop through the data, querying for nearby galaxies ----------------------------
#------------- and writing results to the database --------------------------------------------
#----------------------------------------------------------------------------------------------
for thisField in fields:
#if args2.verbose > 0:
# print "Starting field = ",thisField
# Find all candidates in this field ...
NCands = 0
if len(data) > 0:
index = np.where(pix == thisField)
index = [s for s in data[index]]
NCands = len(index)
pix_edges = healpy.pixelfunc.get_all_neighbours(32,thisField)
# if args2.verbose > 0 :
# print "\t",NCands," entries to match in this field"
if NCands > 0:
# Read in field catalog using 'loadtxt' and store relevant data to an array
if thisField < 10000:
filename = INPUT_DIR + "GW_cat_hpx_0" + str(thisField) + ".fits"
else:
filename = INPUT_DIR + "GW_cat_hpx_" + str(thisField) + ".fits"
#if args2.verbose > 0:
# print "\tReading in catalog from file . . . . \n"
# print filename+'\n'
h = fits.open(filename)
cat = h[1].data
for pix_edge in pix_edges:
if pix_edge < 10000:
filename = INPUT_DIR + "GW_cat_hpx_0" + str(pix_edge) + ".fits"
else:
filename = INPUT_DIR + "GW_cat_hpx_" + str(pix_edge) + ".fits"
h = fits.open(filename)
cat_edge = h[1].data
cat = np.concatenate((cat,cat_edge))
# cat = np.loadtxt(filename, \
# dtype={'names': ('COADD_OBJECTS_ID','RA','DEC','PHOTOZ','PHOTOZ_ERR', \
# 'MAG_AUTO_G','MAG_AUTO_R','MAG_AUTO_I','MAG_AUTO_Z', \
# 'MAGERR_AUTO_G','MAGERR_AUTO_R','MAGERR_AUTO_I', \
# 'MAGERR_AUTO_Z','MAG_APER_4_G','MAG_APER_4_R', \
# 'MAG_APER_4_I','MAG_APER_4_Z','MAGERR_APER_4_G', \
# 'MAGERR_APER_4_R','MAGERR_APER_4_I','MAGERR_APER_4_Z', \
# 'MAG_DETMODEL_G','MAG_DETMODEL_R','MAG_DETMODEL_I', \
# 'MAG_DETMODEL_Z','MAGERR_DETMODEL_G', \
# 'MAGERR_DETMODEL_R','MAGERR_DETMODEL_I',\
# 'MAGERR_DETMODEL_Z','THETA_IMAGE','A_IMAGE','B_IMAGE', \
# 'GALFLAG','CATALOG'), 'formats': \
# ('S12','f8','f8','f8','f8','S10','S10','S10','S10','S10','S10', \
# 'S10','S10','S10','S10','S10','S10','S10','S10','S10','S10', \
# 'S10','S10','S10','S10','S10','S10','S10','S10',\
# 'f8','f8','f8','f4','S12')}, \
# skiprows=1, usecols=[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,\
# 20,21,22,23,24,25,26,27,28,29,30,31,32,33])
#if args2.verbose > 0 :
# print "\tCatalog contains",cat.shape[0],"rows\n"
#Begin Loop...
for i,entry in enumerate(index): #this will not work
transient_name = entry[0]
if transient_name is None:
transient_name = 'NULL'
SNID = entry[1]
ra = float(entry[2])
dec = float(entry[3])
#field = entry[4]
if os.path.isfile(OUTPUT_DIR+'/SNIDList'):
yo=open(OUTPUT_DIR+'/SNIDList','a')
#yo=open(OUTPUT_DIR+'/outputs/hostmatch/SNIDList','a')
else:
yo=open(OUTPUT_DIR+'/SNIDList','w')
yo.write(str(SNID)+"\n")
yo.close()
##Debugging
#if args2.verbose > 0:
# print '\ni=',i, entry[0], entry[1], '(RA, dec) = (',ra,',',dec,')'
# First pass search over a box
jndex = (cat['RA'] > ra - farc/math.cos(dec*rad) ) & \
(cat['RA'] < ra + farc/math.cos(dec*rad) ) & \
(cat['DEC'] > dec - farc) & (cat['DEC'] < dec + farc)
# store all catalog objects within tolerance in a temporary array
array = cat[jndex]
#Keep track of whether a host has been assigned for this object.
#If not, mark as hostless in SNGALS to prevent repeated searches
#for this candidate on subsequent runs.
hostlessFlag = 1
if len(array) > 0:
# distance to SN in arcsec
dist = 3600. * np.sqrt( ( np.cos( dec*rad ) * ( array['RA'] - ra ) )**2 + \
( array['DEC'] - dec )**2 )
# Check if galaxies are within search radius
circle = dist < search
if np.sum(circle) > 0:
# define structured array containing potential host info
#hostinfo = np.zeros(np.sum(circle), \
# dtype={'names':['transient_name','SNID','SNGALID', \
# 'COADD_ID','RA','DEC','sep','DLR', \
# 'rank','host', 'X2','Y2','XY','A','B', \
# 'rPHI','A_IMAGE','B_IMAGE','THETA_IMAGE','ZPHOTO'],\
# 'formats':['S12','S8','S8','S20','f8','f8','f8', \
# 'f8','i4','i4','f8','f8','f8','f8','f8',\
# 'f8','f8','f8','f8','f4']})
hostinfo = np.zeros(np.sum(circle), \
dtype={'names':['transient_name','SNID','SNGALID', \
'COADD_ID','RA','DEC','sep','DLR', \
'rank','host', 'X2','Y2','XY','A','B', \
'rPHI','A_IMAGE','B_IMAGE','THETA_IMAGE','ZPHOTO'],\
'formats':['S12','S8','S8','S20','f8','f8','f8', \
'f8','i4','i4','f8','f8','f8','f8','f8',\
'f8','f8','f8','f8','f4']})
hostinfo['transient_name'][:] = transient_name
hostinfo['SNID'][:] = SNID
hostinfo['sep'] = dist[circle] # SN-galaxy separation
hostinfo['COADD_ID'] = array['ID'][circle]
hostinfo['RA'] = array['RA'][circle]
hostinfo['DEC'] = array['DEC'][circle]
hostinfo['A_IMAGE'] = array['A'][circle]
hostinfo['B_IMAGE'] = array['B'][circle]
hostinfo['THETA_IMAGE'] = array['THETA'][circle]
hostinfo['ZPHOTO'] = array['ZPHOTO'][circle]
#print array.shape,hostinfo['COADD_ID']
#Deprecated until these parameters are included in DESDM catalogs
#hostinfo['X2'] = array['X2WIN_IMAGE'][circle]
#hostinfo['Y2'] = array['Y2WIN_IMAGE'][circle]
#hostinfo['XY'] = array['XYWIN_IMAGE'][circle]
# Compute d_DLR for all potential hosts
retval = hma.get_DLR_ABT( ra, dec, hostinfo['RA'], hostinfo['DEC'],\
hostinfo['A_IMAGE'], hostinfo['B_IMAGE'], \
hostinfo['THETA_IMAGE'], hostinfo['sep'] )
hostinfo['DLR'] = retval[0]
hostinfo['A'] = retval[1]
hostinfo['B'] = retval[2]
hostinfo['rPHI'] = retval[3]
# Compute HOST_CONFUSION parameter and insert into SNCAND # RRG
#HC = hma.compute_HC(hostinfo['DLR'])
#if args.verbose > 0:
# print "\tHOST_CONFUSION = ", HC
#query_HC = ("UPDATE SNCAND SET HOST_CONFUSION = {0} "
# "WHERE SNID={1}").format(HC, SNID)
#if not args.test:
# cursor.execute(query_HC)
# connection.commit()
# continue # RRG -- skip the host matching part
#------------------------------------------------------------------------------
#-------------- Order by Angular Separation -----------------------------------
#-------------- Results are output to file, and compared to -------------------
#---------------DLR, but are not written to database --------------------------
#------------------------------------------------------------------------------
hostinfo.sort(order='sep')
for k in range(0, len(hostinfo)):
# rank ordered galaxies
hostinfo['rank'][k] = k+1
s = ( "{:10s} {:7s} {:30s} {:10.5f} {:10.5f} {:10.5f} "
"{:10.5f} {:8.4f} {:8.4f} {:8.4f} {:d} {:8.4f}\n" )
s = s.format(hostinfo['transient_name'][k], hostinfo['SNID'][k], \
hostinfo['COADD_ID'][k], hostinfo['RA'][k], \
hostinfo['DEC'][k], hostinfo['sep'][k], hostinfo['DLR'][k], \
hostinfo['A'][k], hostinfo['B'][k], \
hostinfo['rPHI'][k], hostinfo['rank'][k],hostinfo['ZPHOTO'][k])
#if args2.verbose > 1:
# print '\tSep: ',k, hostinfo['sep'][k], hostinfo['DLR'][k], \
# hostinfo['rank'][k], hostinfo['X2'][k], hostinfo['Y2'][k], \
# hostinfo['XY'][k], hostinfo['ZPHOTO'][k]
file_sep.write(s)
hostinfo.sort(order='DLR')
if hostinfo['DLR'][0] == 99.99:
hostinfo.sort(order='sep')
# if nearest ordered DLR host has DLR = 99.99,
# default to nearest separation
# Write to file_mismatch if host by angular separation and DLR are different
# Write both galaxies
if hostinfo['rank'][0] == 1: # smallest DLR is already nearest galaxy
isNearest += 1 # increment counter for this case
else:
# write smallest angular separation object
r = np.where(hostinfo['rank'] == 1)
s = ( "{:10s} {:7s} {:30s} {:10.5f} {:10.5f} {:10.5f} {:10.5f} "
"{:8.4f} {:8.4f} {:8.4f} {:d} {:8.4f}\n" )
s = s.format( hostinfo['transient_name'][r[0][0]], \
hostinfo['SNID'][r[0][0]], hostinfo['COADD_ID'][r[0][0]], \
hostinfo['RA'][r[0][0]], hostinfo['DEC'][r[0][0]], \
hostinfo['sep'][r[0][0]], hostinfo['DLR'][r[0][0]], \
hostinfo['A'][r[0][0]], hostinfo['B'][r[0][0]], \
hostinfo['rPHI'][r[0][0]], hostinfo['rank'][r[0][0]], hostinfo['ZPHOTO'][r[0][0]] )
file_mismatch.write(s)
hostinfo['rank'][:] = 0 # reset all to 0 to clear the nearest galaxy
hostinfo['rank'][0] = 1 # set smallest DLR to have host=1
# write smallest DLR object
r = np.where(hostinfo['rank'] == 1)
s = ( "{:10s} {:7s} {:30s} {:10.5f} {:10.5f} {:10.5f} {:10.5f} "
"{:8.4f} {:8.4f} {:8.4f} {:d} {:8.4f}\n" )
s = s.format(hostinfo['transient_name'][r[0][0]], \
hostinfo['SNID'][r[0][0]], hostinfo['COADD_ID'][r[0][0]], \
hostinfo['RA'][r[0][0]], hostinfo['DEC'][r[0][0]], \
hostinfo['sep'][r[0][0]], hostinfo['DLR'][r[0][0]], \
hostinfo['A'][r[0][0]], hostinfo['B'][r[0][0]], \
hostinfo['rPHI'][r[0][0]], hostinfo['rank'][r[0][0]],hostinfo['ZPHOTO'][r[0][0]] )
file_mismatch.write(s)
#------------------------------------------------------------------------------
#------------------ Now go through each galaxy by DLR -------------------------
#------------------ (already sorted above) and write to file, -----------------
#------------------ write to DB, ngest into ATC, and tag there ----------------
#------------------------------------------------------------------------------
### KRH debug 2019-03-14
for k in range(0,len(hostinfo)):
# rank ordered galaxies
if hostinfo['DLR'][k] < DLR_cut:
hostinfo['rank'][k] = k+1
else:
# assign negative rank if fails DLR cut
hostinfo['rank'][k] = (k+1)*-1
if hostinfo['rank'][k] == 1:
# assign 'host'=1 only if 'rank'=1, else 'host'=0
hostinfo['host'][k] = 1
else:
hostinfo['host'][k] = 0
s = ( "{:10s} {:7s} {:30s} {:10.5f} {:10.5f} {:10.5f} {:10.5f} "
"{:8.4f} {:8.4f} {:8.4f} {:3d} {:d} {:8.4f}\n" )
s = s.format(hostinfo['transient_name'][k], hostinfo['SNID'][k], \
hostinfo['COADD_ID'][k], hostinfo['RA'][k], \
hostinfo['DEC'][k], hostinfo['sep'][k], hostinfo['DLR'][k], \
hostinfo['A'][k], hostinfo['B'][k], hostinfo['rPHI'][k], \
hostinfo['rank'][k], hostinfo['host'][k], hostinfo['ZPHOTO'][k] )
#if args2.verbose > 1:
# print '\tDLR: ',k, hostinfo['sep'][k], hostinfo['DLR'][k], \
# hostinfo['host'][k],hostinfo['X2'][k], hostinfo['Y2'][k], \
# hostinfo['XY'][k]
# Only write top 3 ranked galaxies to file/DB
if k < 3:
# ---------------- Write to File --------------------------------------
file_dlr.write(s)
# ---------------- Write to Database ----------------------------------
temp_galid = 0
db_status = 0
# Does this galaxy already exist in the DB?
kndex = np.where(current_host['COADD_ID'] == hostinfo['COADD_ID'][k])
if len(kndex[0]) > 0:
temp_galid = current_host['SNGALID'][kndex[0][0]]
else:
maxgalid += 1
temp_galid = maxgalid
#print array
kndex = np.where(array['ID'][:] == int(hostinfo['COADD_ID'][k]))
tt = kndex[0][0]
# hostname = hostinfo['SURVEY'][k] + "_ID-" + str(array['ID'][tt])
query = ( "INSERT INTO "+sngals_file+
" ( "+sngals_file_id+", RA, DEC, PHOTOZ, "
"PHOTOZ_ERR, MAG_AUTO_I, "
"THETA_IMAGE, A_IMAGE, B_IMAGE, "
"SNID, TRANSIENT_NAME, SNGALID, SEPARATION, "
"DLR_RANK, HOST, SEASON, SURVEY,MAG_APER_4_I ) " #Add DLR again once the a b issues are fixed
"VALUES ("
"{0},{1},{2},{3},{4},{5},{6},{7},{8},{9},{10},{11},{12},"
"{13},{14},{15},{16},{17} )" )
# The Galaxy Catalogs use 99.999 for mag uncertainties.
# We have an upper limit of 9.999.
# Here's a very stupid fix to that.
#if float(array['MAGERR_AUTO_G'][tt]) >= 10:
# array['MAGERR_AUTO_G'][tt] = 9.000
#if float(array['MAGERR_AUTO_R'][tt]) >= 10:
# array['MAGERR_AUTO_R'][tt] = 9.000
#if float(array['MAGERR_AUTO_I'][tt]) >= 10:
# array['MAGERR_AUTO_I'][tt] = 9.000
#if float(array['MAGERR_AUTO_Z'][tt]) >= 10:
# array['MAGERR_AUTO_Z'][tt] = 9.000
#if float(array['MAGERR_APER_4_G'][tt]) >= 10:
# array['MAGERR_APER_4_G'][tt] = 9.000
#if float(array['MAGERR_APER_4_R'][tt]) >= 10:
# array['MAGERR_APER_4_R'][tt] = 9.000
#if float(array['MAGERR_APER_4_I'][tt]) >= 10:
# array['MAGERR_APER_4_I'][tt] = 9.000
#if float(array['MAGERR_APER_4_Z'][tt]) >= 10:
# array['MAGERR_APER_4_Z'][tt] = 9.000
#if float(array['MAGERR_DETMODEL_G'][tt]) >= 10:
# array['MAGERR_DETMODEL_G'][tt] = 9.000
#if float(array['MAGERR_DETMODEL_R'][tt]) >= 10:
# array['MAGERR_DETMODEL_R'][tt] = 9.000
#if float(array['MAGERR_DETMODEL_I'][tt]) >= 10:
# array['MAGERR_DETMODEL_I'][tt] = 9.000
#if float(array['MAGERR_DETMODEL_Z'][tt]) >= 10:
# array['MAGERR_DETMODEL_Z'][tt] = 9.000
# Now execute query
query = query.format(array['ID'][tt],array['RA'][tt],\
array['DEC'][tt],array['ZPHOTO'][tt],\
array['ZPHOTO_ERR'][tt],array['MAG_I'][tt],\
array['THETA'][tt],array['A'][tt],\
array['B'][tt],\
hostinfo['SNID'][k],\
hostinfo['transient_name'][k],temp_galid,\
hostinfo['sep'][k],\
#hostinfo['rank'][k],hostinfo['host'][k],args2.season,'\''+array['CATALOG'][tt]+'\'',array['MAG_I'][tt])
hostinfo['rank'][k],hostinfo['host'][k],my_season,'\''+array['CATALOG'][tt]+'\'',array['MAG_I'][tt])
#if args2.verbose > 0:
# print hostinfo['SNID'][k],hostinfo['transient_name'][k],\
# array['ID'][tt],\
# array['THETA'][tt],array['A'][tt],\
# array['B'][tt]
dbstring = 'SN: {0:<12}{1:<16}{2:<16}{3:<12}{4:<12}{5:>10}{6:>7}\n'
hostlessFlag = 0
print(query)
try:
# if not args2.test:
cursor.execute(query)
connection.commit()
db_status = 0
except:
db_status = 1
db_flag += 1
#print hostlessFlag
logfile_db.write( dbstring.format(hostinfo['SNID'][k],
hostinfo['transient_name'][k],
array['ID'][tt],
array['RA'][tt],array['DEC'][tt],
hostinfo['rank'][k],hostinfo['ZPHOTO'][k],db_status) )
#-------------------- Ingest to ATC (if not star ) --------------------
#if int(array['GALFLAG'][tt]) == 1:
# atcstring = 'SN: {0:<12}{1:<25}{2:<16.8f}{3:<16.8f}{4:<7d}\n'
# atc_status = 0
#Only ingest the host galaxies if a) we set the ingest flag, and
# b) the object the galaxies are associated with have a name.
# While this latter step is not strictly necessary, it saves time
# by avoiding ingesting lots of unneccesary entries.
#if args.atc and transient_name != 'NULL':
# try:
# host_incept = atcfuncs.create_incept_post(hostname,
# array['RA'][tt],
# array['DEC'][tt])
# except:
# atc_status += 1
# try:
# out = atcfuncs.send_posts(host_incept,
# test_mode = args.test)
# if args.verbose > 0:
# print ('Successfully ingested host of ' +
# hostinfo['transient_name'][k] +
# ' as galaxy ' + hostname )
# except:
# # Assumes that all ATC post errors are due to the
# # host galaxy already existing in the DB.
# print ('WARNING: ' + hostinfo['transient_name'][k] +
# ' host ' + hostname + ' already exists in ATC.')
#
# if int(hostinfo['rank'][k]) == 1:
# host_tag = atcfuncs.create_host_post(
# hostinfo['transient_name'][k],hostname
# )
# try:
# out = atcfuncs.send_posts(host_tag,
# test_mode = args.test)
# except:
# print ('WARNING: unable to tag transient ' +
# hostinfo['transient_name'][k] +
# ' with host ' + hostname )
# atc_status += 2
#
#else:
# # If there is no attempt to write to the ATC, then candidates
# # by definition remain to be uploaded
# atc_status += 4
#
#if atc_status > 0 and transient_name != 'NULL':
# atc_flag += 1
#If the atc_status flag is set, we print a failure warning
#UNLESS the SN candidate the host is matched to has no name,
# in which case there is nowhere to upload to.
# Write to logfile for potential later ingestion
#logfile_atc.write( atcstring.format( transient_name,
# hostname, array['RA'][tt],
# array['DEC'][tt], atc_status ) )
#At this point we know whether the hostlessFlag has been updated, or if the SNID
# has no matching host galaxy. If there is none, update with -1 values
if hostlessFlag:
nohost_GALID = -1
nohost_RANK = 0
query = ( "INSERT INTO "+sngals_file+" (SNID, TRANSIENT_NAME, SNGALID, DLR_RANK) VALUES "
" ({0}, '{1}', {2}, {3}) " )
query = query.format(SNID, transient_name, nohost_GALID, nohost_RANK)
#if args.verbose > 0:
# print SNID, transient_name,' NO HOST'
dbstring = 'SN: {0:<12}{1:<16}{2:<16}{3:<12}{4:<12}{5:>10}{6:>7}\n'
#try:
# if not args2.test:
# cursor.execute(query)
# connection.commit()
# db_status = 0
#except:
# db_status = 1
#db_flag += 1
#### I have added this line as it was giving error (didn't know what to put as db_status in logfile_db.write)
##if args2.test:
db_status = 1
logfile_db.write( dbstring.format(SNID, transient_name,'N/A',
'N/A','N/A',0,db_status) )
#------------------------------------------------------------------------------
#------------------- Summarize and close log files; Post to ATC ---------------
#------------------------------------------------------------------------------
print 'db_flag ',db_flag
if db_flag == 0:
logfile_db.write('#HostMatch Database Update: SUCCESS\n')
print 'HostMatch Database Update: SUCCESS'
else:
logfile_db.write('#HostMatch Database Update: FAILURE '
'on {} uploads\n'.format(db_flag))
logfile_db.write('#Re-run HostMatch. No input files needed.\n')
print 'HostMatch Database Update: FAILURE '
#if (args.atc and atc_flag == 0):
# logfile_atc.write('#HostMatch ATC Posting & Tagging: SUCCESS\n')
#else:
# if args.atc:
# logfile_atc.write('#HostMatch ATC Posting & Tagging: FAILURE '
# 'on {} posts\n'.format(atc_flag))
# print 'HostMatch ATC Posting & Tagging: FAILURE'
# else:
logfile_atc.write('#HostMatchATC Posting & Tagging: SKIPPED '
'on ALL posts\n')
print 'HostMatch ATC Posting & Tagging: SKIPPED'
logfile_atc.write('#Re-run with --input flag set and input file:\n')
logfile_atc.write('#{0}'.format(logfile_name_atc))
print 'Run with desHostMatchFix with input file set as {0}'.format(logfile_name_atc)
#if args2.test:
logfile_atc.write('#...Except this was only a TEST, so nothing has REALLY happened!\n')
print '...Except this was only a TEST, so nothing has REALLY happened!'
file_dlr.close()
file_sep.close()
file_mismatch.close()
logfile_atc.close()
logfile_db.close()
connection.close()
#status='1'
hostms=open('hostmatchstatus.txt','w')
hostms.write(str(db_flag))
hostms.close()
thisisnottheDroidyouarelookingfor=OUTPUT_DIR+'hostmatch.db.log'
#thisistheDroidyouarelookingfor='./'+season+'/outputs/hostmatch/hostmatch.db.log'
###Unhardcode this file location, plz
###database log file containing all the information necessary to build snid dictionary for html documentation
#shutil.copy2(thisisnottheDroidyouarelookingfor,thisistheDroidyouarelookingfor)
#irksome=open('./'+season+'/outputs/hostmatch/databaseLocation.txt','w+')
irksome=open(OUTPUT_DIR+'databaseLocation.txt','w+')
#irksome.write(thisistheDroidyouarelookingfor)
irksome.write(thisisnottheDroidyouarelookingfor)
irksome.close()
############################### Call main script ##################################################
if __name__ == "__main__":
main()