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funcs2run_bat_tools.py
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import os
import subprocess
import sys
sys.path.append('/storage/work/jjd330/local/bat_data/BatML/HeasoftTools')
from gen_tools import run_ftool
from bat_tool_funcs import ev2dpi, mk_pc_img, mk_sky_img, run_batcelldetect
import time
import numpy as np
import multiprocessing as mp
import pandas as pd
from astropy.table import Table
from astropy.io import fits
from astropy.wcs import WCS
from sqlite_funcs import get_conn, write_cats2db, write_sigimg_line
import logging, traceback
def do_bkg(bkg_tstart, bkg_tstop, ev_fname, dmask, savedir, e0=14.0, e1=194.9):
# bkg_tstart = args.bkgt0
# bkg_tstop = args.bkgt0 + args.bkgdt
dpif = 'dpi_%.1f_%.1f_%.3f_%.3f_.dpi' %(e0, e1, bkg_tstart, bkg_tstop)
dpi_bkg_fname = os.path.join(savedir, dpif)
ev2dpi(ev_fname, dpi_bkg_fname, bkg_tstart, bkg_tstop, e0, e1, dmask)
return dpi_bkg_fname
def do_pc(dmask, att_fname, work_dir, ovrsmp=4, detapp=False):
pc_fname = os.path.join(work_dir, 'pc_%d.img' %(ovrsmp))
if not os.path.exists(pc_fname):
mk_pc_img(dmask, pc_fname, dmask, att_fname,\
ovrsmp=ovrsmp, detapp=detapp)
return pc_fname
def mk_sig_imgs_pix(tstarts, dts, evf, dpi_bkg_fname, pc_fname,\
attfile, dmask, savedir, work_dir, trig_time, conn, db_fname,\
e0=14.0, e1=194.9,\
oversamp=4, snr_cuts=None):
arg_dict_keys = ['tstart', 'dt', 'ev_fname',
'bkg_dpi',
'pc_fname', 'att_fname', 'dmask',
'savedir', 'pc_fname', 'e0', 'e1',
'oversamp']
args_dict_list = []
for i in range(len(tstarts)):
arg_dict = {'tstart':tstarts[i], 'dt':dts[i], 'ev_fname':evf,
'bkg_dpi':dpi_bkg_fname,
'att_fname':attfile, 'pc_fname':pc_fname,
'dmask':dmask, 'savedir':savedir, 'e0':e0,
'e1':e1, 'oversamp':oversamp}
args_dict_list.append(arg_dict)
t0 = time.time()
logging.info("%d images to make" %(len(args_dict_list)))
PC = fits.open(pc_fname)[0]
w_t = WCS(PC.header, key='T')
pc = PC.data
pc_bl = (pc>=0.1)
dtp = [('snr', np.float), ('imx', np.float), ('imy', np.float)]
Nimgs = len(args_dict_list)
for i in range(Nimgs):
img_fname, sig_img_fname = mk_sky_sig_img4mp(args_dict_list[i])
logging.debug("Made img %s" %(sig_img_fname))
sig_img = fits.open(sig_img_fname)[0].data
logging.debug("Opened fits file")
if snr_cuts is None:
snr_cut = 3.0
else:
snr_cut = snr_cuts[i]
snr_bl = (sig_img>=snr_cut)
img_bl = (pc_bl&snr_bl)
sig_arr = np.empty(np.sum(img_bl), dtype=dtp)
sig_arr['snr'] = sig_img[img_bl]
logging.info("%d pix pass cut" %(np.sum(img_bl)))
inds = np.where(img_bl)
imxys = w_t.all_pix2world(inds[1], inds[0], 0)
sig_arr['imx'] = imxys[0]
sig_arr['imy'] = imxys[1]
sig_pix_fname = os.path.join(work_dir, os.path.basename(sig_img_fname)[:-4])
np.save(sig_pix_fname, sig_arr)
logging.info("saved to %s" %(sig_pix_fname+'.npy'))
try:
write_sigimg_line(conn, args_dict_list[i]['tstart'],\
args_dict_list[i]['dt'], trig_time,\
sig_pix_fname+'.npy', np.sum(img_bl))
logging.info("written to DB")
except:
conn.close()
conn = get_conn(db_fname)
try:
write_sigimg_line(conn, args_dict_list[i]['tstart'],\
args_dict_list[i]['dt'], trig_time,\
sig_pix_fname+'.npy', np.sum(img_bl))
logging.info("written to DB")
except Exception as E:
logging.error(str(E))
logging.warn("Failed to write to DB")
try:
os.remove(sig_img_fname)
os.remove(img_fname)
logging.info("Deleted img files")
except:
logging.info("Failed to delete a file")
pass
logging.info("Done with all images")
logging.info("Took %.2f seconds, %.2f minutes"\
%(time.time()-t0,(time.time()-t0)/60.))
return
def mk_sig_imgs_mp(nproc, tstarts, dts, evf, dpi_bkg_fname, pc_fname,\
attfile, dmask, savedir, e0=14.0, e1=194.9,\
oversamp=4, detapp=False, rebal=True):
arg_dict_keys = ['tstart', 'dt', 'ev_fname',
'bkg_dpi',
'pc_fname', 'att_fname', 'dmask',
'savedir', 'pc_fname', 'e0', 'e1',
'oversamp']
args_dict_list = []
for i in xrange(len(tstarts)):
arg_dict = {'tstart':tstarts[i], 'dt':dts[i], 'ev_fname':evf,
'bkg_dpi':dpi_bkg_fname,
'att_fname':attfile, 'pc_fname':pc_fname,
'dmask':dmask, 'savedir':savedir, 'e0':e0,
'e1':e1, 'oversamp':oversamp, 'detapp':detapp,
'rebal':rebal}
args_dict_list.append(arg_dict)
t0 = time.time()
logging.info("%d images to make" %(len(args_dict_list)))
if nproc > 1:
p = mp.Pool(nproc)
logging.info("Starting %d procs" %(nproc))
sig_img_fnames = p.map(mk_sky_sig_img4mp, args_dict_list)
p.close()
p.join()
else:
sig_img_fnames = map(mk_sky_sig_img4mp, args_dict_list)
logging.info("Done with all images")
logging.info("Took %.2f seconds, %.2f minutes"\
%(time.time()-t0,(time.time()-t0)/60.))
return
def mk_sky_sig_img4mp(arg_dict):
img_fname, sig_img_fname = mk_sky_sig_img(arg_dict['tstart'],\
arg_dict['dt'], arg_dict['ev_fname'], arg_dict['bkg_dpi'],\
arg_dict['att_fname'], arg_dict['dmask'],\
arg_dict['savedir'], e0=arg_dict['e0'],\
e1=arg_dict['e1'], oversamp=arg_dict['oversamp'],\
detapp=arg_dict['detapp'], rebal=arg_dict['rebal'])
return img_fname, sig_img_fname
def get_sig_pix_mp(nproc, tstarts, dts, evf, dpi_bkg_fname, pc_fname,\
attfile, dmask, savedir, e0=14.0, e1=194.9,\
oversamp=4, db_fname=None, timeIDs=None, RateTSs=None):
arg_dict_keys = ['tstart', 'dt', 'ev_fname',
'bkg_dpi',
'pc_fname', 'att_fname', 'dmask',
'savedir', 'pc_fname', 'e0', 'e1',
'oversamp', 'db_fname']
args_dict_list = []
exp_bins = [.2, .3, .6, 2]
TS_cuts = [2.25, 2.0, 1.8, 1.7, 1.65]
exp_bins = np.digitize(dts, bins=exp_bins)
for i in xrange(len(tstarts)):
if RateTSs is not None:
if RateTSs[i] < TS_cuts[exp_bins[i]]:
continue
arg_dict = {'tstart':tstarts[i], 'dt':dts[i], 'ev_fname':evf,
'bkg_dpi':dpi_bkg_fname,
'att_fname':attfile, 'pc_fname':pc_fname,
'dmask':dmask, 'savedir':savedir, 'e0':e0,
'e1':e1, 'oversamp':oversamp, 'db_fname':db_fname}
if timeIDs is not None:
arg_dict['timeID'] = timeIDs[i]
arg_dict['RateTS'] = RateTSs[i]
args_dict_list.append(arg_dict)
t0 = time.time()
p = mp.Pool(nproc)
logging.info("%d images to make" %(len(args_dict_list)))
logging.info("Starting %d procs" %(nproc))
sig_img_fnames = p.map(get_sig_pix, args_dict_list)
p.close()
p.join()
logging.info("Done with all images")
logging.info("Took %.2f seconds, %.2f minutes"\
%(time.time()-t0,(time.time()-t0)/60.))
def get_sig_pix(arg_dict):
img_fname, sig_img_fname = mk_sky_sig_img(arg_dict['tstart'],\
arg_dict['dt'], arg_dict['ev_fname'], arg_dict['bkg_dpi'],\
arg_dict['att_fname'], arg_dict['dmask'],\
arg_dict['savedir'], e0=arg_dict['e0'],\
e1=arg_dict['e1'], oversamp=arg_dict['oversamp'])
PC = fits.open(arg_dict['pc_fname'])[0]
sig_img = fits.open(sig_img_fname)[0]
w_t = WCS(sig_img.header, key='T')
exp_bins = [.2, .3, .6, 2]
TSaims = [5.25, 5.0, 4.8, 4.6, 4.5]
exp_bin = np.digitize(arg_dict['dt'], bins=exp_bins)
snr_cut = max(2.*(TSaims[exp_bin] - arg_dict['RateTS']), 2.0)
bl = (PC.data>=.1)
bl_snr = (sig_img.data>snr_cut)&bl
if np.sum(bl_snr) < 1:
return
bl_snr_inds = np.where(bl_snr)
imxys = w_t.all_pix2world(bl_snr_inds[1], bl_snr_inds[0], 0)
SNRs = sig_img.data[bl_snr]
bins = [np.linspace(-2,2,10*4+1),
np.linspace(-1,1,10*2+1)]
imx_inds = np.digitize(imxys[0], bins=bins[0]) - 1
imy_inds = np.digitize(imxys[1], bins=bins[1]) - 1
job_inds = np.arange(19)
job_ids = -1*np.ones(len(imx_inds), dtype=np.int)
imx_bins0 = [-1.2, -1.2, -0.8, -0.8, -0.4,
-0.4, 0.0, 0.0, 0.4, 0.4, 0.8,
0.8, -1.5, 0.0, -1.5, 0.0, -2.0,
1.2, -2.0]
imx_bins1 = [-0.8, -0.8, -0.4, -0.4, 0.0,
0.0, 0.4, 0.4, 0.8, 0.8, 1.2,
1.2, 0.0, 1.5, 0.0, 1.5, 2.0,
2.0, -1.2]
imy_bins0 = [-0.3, 0.2, -0.3, 0.2, -0.3,
0.2, -0.3, 0.2, -0.3, 0.2,
-0.3, 0.2, -0.5, -0.5, -1.0,
-1.0, 0.7, -0.3, -0.3]
imy_bins1 = [0.2, 0.7, 0.2, 0.7, 0.2, 0.7,
0.2, 0.7, 0.2, 0.7, 0.2, 0.7,
-0.3, -0.3, -0.5, -0.5, 1,
0.7, 0.7]
for i in job_inds:
bl_bin = (imxys[0]>=imx_bins0[i])&(imxys[0]<imx_bins1[i])&\
(imxys[1]>=imy_bins0[i])&(imxys[1]<imy_bins1[i])
job_ids[bl_bin] = i
if arg_dict['db_fname'] is not None:
df_dict = {}
df_dict['timeID'] = arg_dict['timeID']
df_dict['imx_ind'] = imx_inds
df_dict['imy_ind'] = imy_inds
df_dict['imx'] = imxys[0]
df_dict['imy'] = imxys[1]
df_dict['snr'] = SNRs
df_dict['proc_group'] = job_ids
df_dict['done'] = 0
df = pd.DataFrame(df_dict)
conn = get_conn(arg_dict['db_fname'])
df.to_sql('ImageSigs', conn, if_exists='append', index=False)
return sig_img_fname
def mk_sky_sig_img(tstart, dt, evf, dpi_bkg_fname, attfile,\
dmask, savedir, e0=14.0, e1=194.9, oversamp=4,\
detapp=False, rebal=True):
tstop = tstart + dt
dpif = 'dpi_%.1f_%.1f_%.3f_%.3f_.dpi' %(e0, e1, tstart, tstop)
dpi_fname = os.path.join(savedir, dpif)
if not os.path.exists(dpi_fname):
ev2dpi(evf, dpi_fname, tstart, tstop, e0, e1, dmask)
img_fname = os.path.join(savedir, 'sky_%.1f_%.1f_%.3f_%.3f_os%d_.img'\
%(e0, e1, tstart, tstop, oversamp))
sig_img_fname = os.path.join(savedir, 'sig_%.1f_%.1f_%.3f_%.3f_os%d_.img'\
%(e0, e1, tstart, tstop, oversamp))
mk_sky_img(dpi_fname, img_fname, dmask, attfile,\
bkg_file=dpi_bkg_fname, ovrsmp=oversamp,\
sig_map=sig_img_fname, detapp=detapp,\
rebal=rebal)
return img_fname, sig_img_fname
def do_bkg_ebins(args, ebins):
bkg_tstart = args.bkgt0
bkg_tstop = args.bkgt0 + args.bkgdt
dpif = 'dpi_bkg_ebins_%.3f_%.3f_.dpi' %(bkg_tstart, bkg_tstop)
dpi_bkg_fname = os.path.join(args.savedir, args.obsid, dpif)
ev2dpi_ebins(args.evf, dpi_bkg_fname, bkg_tstart, bkg_tstop, ebins, args.dmask)
return dpi_bkg_fname
def std_grb(tstart, dt, evf, dpi_bkg_fnames, attfile,\
dmask, savedir,\
pc="NONE", e0=14.0, e1=194.9, oversamp=4,\
sigmap=False, bkgvar=False, detapp=False):
# 1 make dpi e0-e1 for sig and bkg times
# 2 make bkg subtracted sky image
# 3 run batcelldetect
tstop = tstart + dt
# 1
# obsid_dir = args.obsid
# aux_dir = os.path.join(obsid_dir, 'auxil')
# attfile = os.path.join(aux_dir, [fname for fname in os.listdir(aux_dir) if 'pat' in fname][0])
if np.isscalar(e0):
e0 = [e0]
e1 = [e1]
cat_fnames = []
for i in xrange(len(e0)):
dpif = 'dpi_%.1f_%.1f_%.3f_%.3f_.dpi' %(e0[i], e1[i], tstart, tstop)
dpi_fname = os.path.join(savedir, dpif)
ev2dpi(evf, dpi_fname, tstart, tstop, e0[i], e1[i], dmask)
# 2
img_fname = os.path.join(savedir, 'sky_%.1f_%.1f_%.3f_%.3f_os%d_.img' %(e0[i], e1[i], tstart,\
tstop, oversamp))
mk_sky_img(dpi_fname, img_fname, dmask, attfile,\
bkg_file=dpi_bkg_fnames[i], ovrsmp=oversamp,\
detapp=detapp)
# 3
cat_fname = os.path.join(savedir, 'cat_%.1f_%.1f_%.3f_%.3f_os%d_.fits' %(e0[i], e1[i], tstart,\
tstop, oversamp))
cat_fnames.append(cat_fname)
if sigmap:
sig_fname = os.path.join(savedir, 'sig_%.1f_%.1f_%.3f_%.3f_os%d_.img' %(e0[i], e1[i], tstart,\
tstop, oversamp))
else:
sig_fname = None
if bkgvar:
bkgvar_fname = os.path.join(savedir, 'bkgvar_%.1f_%.1f_%.3f_%.3f_os%d_.img' %(e0[i], e1[i], tstart,\
tstop, oversamp))
else:
bkgvar_fname = None
run_batcelldetect(img_fname, cat_fname,\
ovrsmp=oversamp, pcode=pc,\
sigmap=sig_fname, bkgvar=bkgvar_fname)
return cat_fnames
def mk_sky_imgs4time_list(tstarts, dts, evf, attfile,\
dmask, savedir, e0=14.0, e1=194.9, oversamp=4,\
sigmap=False, bkgvar=False, detapp=False,\
bkg_dpi="None"):
if np.isscalar(tstarts):
tstarts = [tstarts]
dts = [dts]
Ntimes = len(tstarts)
for i in range(Ntimes):
tstart = tstarts[i]
tstop = tstart + dts[i]
dpif = 'dpi_%.1f_%.1f_%.3f_%.3f_.dpi' %(e0, e1, tstart, tstop)
dpi_fname = os.path.join(savedir, dpif)
ev2dpi(evf, dpi_fname, tstart, tstop, e0, e1, dmask)
# 2
img_fname = os.path.join(savedir, 'sky_%.1f_%.1f_%.3f_%.3f_os%d_.img' %(e0, e1, tstart,\
tstop, oversamp))
if bkgvar:
bkgvar_fname = os.path.join(savedir, 'bkgvar_%.1f_%.1f_%.3f_%.3f_os%d_.img' %(e0, e1, tstart,\
tstop, oversamp))
else:
bkgvar_fname = "NONE"
mk_sky_img(dpi_fname, img_fname, dmask, attfile,\
bkg_file=bkg_dpi, ovrsmp=oversamp,\
detapp=detapp, bkgvar_map=bkgvar_fname)
def do_search(arg_dict):
cat_fnames = std_grb(arg_dict['tstart'], arg_dict['dt'], arg_dict['ev_fname'],\
arg_dict['bkg_dpis'],\
arg_dict['att_fname'], arg_dict['dmask'], arg_dict['savedir'],\
pc=arg_dict['pc_fname'], e0=arg_dict['e0'], e1=arg_dict['e1'],\
oversamp=arg_dict['oversamp'])
if arg_dict['db_fname'] is not None:
conn = get_conn(arg_dict['db_fname'], timeout=30.0)
try:
write_cats2db(conn, cat_fnames, arg_dict['timeID'])
logging.info("Wrote results from timeID " +\
str(arg_dict['timeID']) + " into DB")
except Exception as E:
logging.error(str(E))
logging.error(traceback.format_exc())
logging.warning("Failed to write results from timeID " +\
str(arg_dict['timeID']) + " into DB")
logging.info("Trying again")
conn.close()
time.sleep(1.0)
conn = get_conn(arg_dict['db_fname'], timeout=60.0)
try:
write_cats2db(conn, cat_fnames, arg_dict['timeID'])
logging.info("Wrote results from timeID " +\
str(arg_dict['timeID']) + " into DB")
except Exception as E:
logging.error(E)
logging.error(traceback.format_exc())
logging.error("Failed to write results from timeID "\
+ str(arg_dict['timeID']) + " into DB")
logging.error("And not trying again")
conn.close()
return cat_fnames
def do_search_mp(nproc, tstarts, dts, ev_fname, bkg_dpis, pc_fname, att_fname,\
dmask, savedir, e0=14.0, e1=194.9, oversamp=4,\
db_fname=None, timeIDs=None):
arg_dict_keys = ['tstart', 'dt', 'ev_fname',
'bkg_dpis',
'pc_fname', 'att_fname', 'dmask',
'savedir', 'pc_fname', 'e0', 'e1',
'oversamp', 'db_fname']
args_dict_list = []
for i in xrange(len(tstarts)):
arg_dict = {'tstart':tstarts[i], 'dt':dts[i], 'ev_fname':ev_fname,
'bkg_dpis':bkg_dpis,
'pc_fname':pc_fname, 'att_fname':att_fname,
'dmask':dmask, 'savedir':savedir, 'e0':e0,
'e1':e1, 'oversamp':oversamp, 'db_fname':db_fname}
if timeIDs is not None:
arg_dict['timeID'] = timeIDs[i]
args_dict_list.append(arg_dict)
t0 = time.time()
if nproc == 1:
for i in xrange(len(args_dict_list)):
do_search(args_dict_list[i])
else:
p = mp.Pool(nproc)
logging.info("Starting %d procs" %(nproc))
cat_fnames = p.map_async(do_search, args_dict_list).get()
p.close()
p.join()
logging.info("Done with all searches")
logging.info("Took %.2f seconds, %.2f minutes"\
%(time.time()-t0,(time.time()-t0)/60.))