def output_tidas(args, comm, data, totalname, common_flag_name, flag_name):
if args.tidas is None:
return
autotimer = timing.auto_timer()
from toast.tod.tidas import OpTidasExport, TODTidas
tidas_path = os.path.abspath(args.tidas)
comm.comm_world.Barrier()
if comm.comm_world.rank == 0:
print('Exporting TOD to a TIDAS volume at {}'.format(tidas_path),
flush=args.flush)
start = MPI.Wtime()
export = OpTidasExport(tidas_path, TODTidas, backend="hdf5",
use_todchunks=True,
ctor_opts={"group_dets":"sim"},
cache_name=totalname)
export.exec(data)
comm.comm_world.Barrier()
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print('Wrote simulated TOD to {}:{} in {:.2f} s'
''.format(tidas_path, totalname,
stop-start), flush=args.flush)
return
def simulate_sky_signal(args, comm, data, mem_counter, focalplanes, subnpix,
localsm, signalname):
""" Use PySM to simulate smoothed sky signal.
"""
# Convolve a signal TOD from PySM
start = MPI.Wtime()
op_sim_pysm = ttm.OpSimPySM(
comm=comm.comm_rank,
out=signalname,
pysm_model=args.input_pysm_model,
pysm_precomputed_cmb_K_CMB=args.input_pysm_precomputed_cmb_K_CMB,
focalplanes=focalplanes,
nside=args.nside,
subnpix=subnpix,
localsm=localsm,
apply_beam=args.apply_beam,
debug=args.debug,
coord=args.coord)
op_sim_pysm.exec(data)
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print('PySM took {:.2f} seconds'.format(stop - start),
flush=args.flush)
tod = data.obs[0]['tod']
for det in tod.local_dets:
ref = tod.cache.reference(signalname + "_" + det)
print('PySM signal first observation min max', det, ref.min(),
ref.max())
del ref
del op_sim_pysm
mem_counter.exec(data)
def scan_signal(args, comm, data, localsm, subnpix):
""" Scan time-ordered signal from a map.
"""
signalname = None
if args.input_map:
if comm.comm_world.rank == 0:
print('Scanning input map', flush=args.flush)
start = MPI.Wtime()
autotimer = timing.auto_timer()
npix = 12*args.nside**2
# Scan the sky signal
if comm.comm_world.rank == 0 and not os.path.isfile(args.input_map):
raise RuntimeError(
'Input map does not exist: {}'.format(args.input_map))
distmap = tm.DistPixels(
comm=comm.comm_world, size=npix, nnz=3,
dtype=np.float32, submap=subnpix, local=localsm)
distmap.read_healpix_fits(args.input_map)
scansim = tt.OpSimScan(distmap=distmap, out='signal')
scansim.exec(data)
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print('Read and sampled input map: {:.2f} seconds'
''.format(stop-start), flush=args.flush)
signalname = 'signal'
return signalname
def output_tidas(args, comm, data, totalname, common_flag_name, flag_name):
if args.tidas is None:
return
autotimer = timing.auto_timer()
from toast.tod.tidas import OpTidasExport
tidas_path = os.path.abspath(args.tidas)
comm.comm_world.Barrier()
if comm.comm_world.rank == 0:
print('Exporting TOD to a TIDAS volume at {}'.format(tidas_path),
flush=args.flush)
start = MPI.Wtime()
export = OpTidasExport(tidas_path,
name=totalname,
common_flag_name=common_flag_name,
flag_name=flag_name,
usedist=True)
export.exec(data)
comm.comm_world.Barrier()
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print('Wrote simulated TOD to {}:{} in {:.2f} s'
''.format(tidas_path, totalname, stop - start),
flush=args.flush)
return
def apply_madam(args, comm, data, madampars, outpath, detweights,
totalname_madam, flag_name, common_flag_name):
if args.madam:
if comm.comm_world.rank == 0:
print('Destriping signal', flush=args.flush)
start = MPI.Wtime()
autotimer = timing.auto_timer()
# create output directory for this realization
madampars['path_output'] = outpath
madam = tm.OpMadam(params=madampars,
detweights=detweights,
name=totalname_madam,
common_flag_name=common_flag_name,
flag_name=flag_name,
common_flag_mask=args.common_flag_mask,
purge_tod=True)
madam.exec(data)
comm.comm_world.barrier()
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print('Madam took {:.3f} s'.format(stop - start), flush=args.flush)
return
def get_submaps(args, comm, data):
""" Get a list of locally hit pixels and submaps on every process.
"""
autotimer = timing.auto_timer()
if comm.comm_world.rank == 0:
print('Scanning local pixels', flush=args.flush)
start = MPI.Wtime()
# Prepare for using distpixels objects
nside = args.nside
subnside = 16
if subnside > nside:
subnside = nside
subnpix = 12 * subnside * subnside
# get locally hit pixels
lc = tm.OpLocalPixels()
localpix = lc.exec(data)
if localpix is None:
raise RuntimeError(
'Process {} has no hit pixels. Perhaps there are fewer '
'detectors than processes in the group?'.format(
comm.comm_world.rank))
# find the locally hit submaps.
localsm = np.unique(np.floor_divide(localpix, subnpix))
comm.comm_world.barrier()
stop = MPI.Wtime()
elapsed = stop - start
if comm.comm_world.rank == 0:
print('Local submaps identified in {:.3f} s'.format(elapsed),
flush=args.flush)
return localpix, localsm, subnpix
def load_schedule(args, comm):
start = MPI.Wtime()
autotimer = timing.auto_timer()
if comm.comm_world.rank == 0:
fn = args.schedule
if not os.path.isfile(fn):
raise RuntimeError('No such schedule file: {}'.format(fn))
start = MPI.Wtime()
f = open(fn, 'r')
while True:
line = f.readline()
if line.startswith('#'):
continue
(site_name, telescope, site_lat, site_lon, site_alt) = line.split()
site_alt = float(site_alt)
site = [site_name, site_lat, site_lon, site_alt]
break
all_ces = []
for line in f:
if line.startswith('#'):
continue
start_date, start_time, stop_date, stop_time, mjdstart, mjdstop, \
name, azmin, azmax, el, rs, \
sun_el1, sun_az1, sun_el2, sun_az2, \
moon_el1, moon_az1, moon_el2, moon_az2, moon_phase, \
scan, subscan = line.split()
start_time = start_date + ' ' + start_time
stop_time = stop_date + ' ' + stop_time
try:
start_time = dateutil.parser.parse(start_time + ' +0000')
stop_time = dateutil.parser.parse(stop_time + ' +0000')
except:
start_time = dateutil.parser.parse(start_time)
stop_time = dateutil.parser.parse(stop_time)
start_timestamp = start_time.timestamp()
stop_timestamp = stop_time.timestamp()
all_ces.append([
start_timestamp, stop_timestamp, name, float(mjdstart),
int(scan), int(subscan), float(azmin), float(azmax), float(el)])
f.close()
stop = MPI.Wtime()
elapsed = stop - start
print('Load schedule: {:.2f} seconds'.format(stop-start),
flush=args.flush)
else:
site = None
all_ces = None
site = comm.comm_world.bcast(site)
all_ces = comm.comm_world.bcast(all_ces)
comm.comm_world.barrier()
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print('Loading schedule {:.3f} s'.format(stop-start), flush=args.flush)
return site, all_ces
def subtract_signal(self, tod, cworld, rank, masksampler, mapsampler,
local_intervals):
""" Subtract a signal estimate from the TOD and update the
flags for noise estimation.
"""
start_signal_subtract = MPI.Wtime()
for det in tod.local_dets:
if rank == 0:
print('Subtracting signal for {}'.format(det), flush=True)
tod.cache.report()
fsample = self._rimo[det].fsample
epsilon = self._rimo[det].epsilon
eta = (1 - epsilon) / (1 + epsilon)
signal = tod.local_signal(det, name=self._signal)
flags = tod.local_flags(det, name=self._flags)
flags &= self._detmask
for ival in local_intervals:
ind = slice(ival.first, ival.last + 1)
sig = signal[ind]
flg = flags[ind]
quat = tod.local_pointing(det)[ind]
if self._pol:
theta, phi, psi = qa.to_angles(quat)
iw = np.ones_like(theta)
qw = eta * np.cos(2 * psi)
uw = eta * np.sin(2 * psi)
iquw = np.column_stack([iw, qw, uw])
else:
theta, phi = qa.to_position(quat)
if masksampler is not None:
maskflg = masksampler.at(theta, phi) < 0.5
flg[maskflg] |= 255
if mapsampler is not None:
if self._pol:
bg = mapsampler.atpol(theta, phi, iquw)
else:
bg = mapsampler.at(theta, phi)
if self._calibrate_signal_estimate:
good = flg == 0
ngood = np.sum(good)
if ngood > 1:
templates = np.vstack([np.ones(ngood), bg[good]])
invcov = np.dot(templates, templates.T)
cov = np.linalg.inv(invcov)
proj = np.dot(templates, sig[good])
coeff = np.dot(cov, proj)
bg = coeff[0] + coeff[1] * bg
sig -= bg
cworld.barrier()
stop_signal_subtract = MPI.Wtime()
if rank == 0:
print('TOD signal-subtracted in {:.2f} s'.format(
stop_signal_subtract - start_signal_subtract),
flush=True)
return fsample
def elapsed(mcomm, start, msg):
mcomm.barrier()
stop = MPI.Wtime()
dur = stop - start
if mcomm.rank == 0:
print("{}: {:.3f} s".format(msg, dur), flush=True)
return stop
def simulate_sky_signal(args, comm, data, mem_counter, focalplanes, subnpix, localsm, signalname):
""" Use PySM to simulate smoothed sky signal.
"""
# Convolve a signal TOD from PySM
start = MPI.Wtime()
op_sim_pysm = ttm.OpSimPySM(comm=comm.comm_rank,
out=signalname,
pysm_model=args.input_pysm_model,
focalplanes=focalplanes,
nside=args.nside,
subnpix=subnpix, localsm=localsm,
apply_beam=args.apply_beam)
op_sim_pysm.exec(data)
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print('PySM took {:.2f} seconds'.format(stop-start),
flush=args.flush)
mem_counter.exec(data)
def expand_pointing(args, comm, data):
""" Expand the bore sight pointing to every detector.
"""
start = MPI.Wtime()
autotimer = timing.auto_timer()
hwprpm = args.hwprpm
hwpstep = None
if args.hwpstep is not None:
hwpstep = float(args.hwpstep)
hwpsteptime = args.hwpsteptime
npix = 12 * args.nside**2
if comm.comm_world.rank == 0:
print('Expanding pointing', flush=args.flush)
pointing = tt.OpPointingHpix(nside=args.nside,
nest=True,
mode='IQU',
hwprpm=hwprpm,
hwpstep=hwpstep,
hwpsteptime=hwpsteptime)
pointing.exec(data)
# Only purge the pointing if we are NOT going to export the
# data to a TIDAS volume
if args.tidas is None:
for ob in data.obs:
tod = ob['tod']
tod.free_radec_quats()
comm.comm_world.barrier()
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print('Pointing generation took {:.3f} s'.format(stop - start),
flush=args.flush)
return
def apply_polyfilter(args, comm, data, totalname_freq):
if args.polyorder:
if comm.comm_world.rank == 0:
print('Polyfiltering signal', flush=args.flush)
start = MPI.Wtime()
autotimer = timing.auto_timer()
common_flag_name = 'common_flags'
flag_name = 'flags'
polyfilter = tt.OpPolyFilter(order=args.polyorder,
name=totalname_freq,
common_flag_name=common_flag_name,
common_flag_mask=args.common_flag_mask,
flag_name=flag_name)
polyfilter.exec(data)
comm.comm_world.barrier()
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print('Polynomial filtering took {:.3f} s'.format(stop - start),
flush=args.flush)
return
def apply_groundfilter(args, comm, data, totalname_freq):
if args.wbin_ground:
if comm.comm_world.rank == 0:
print('Ground filtering signal', flush=args.flush)
start = MPI.Wtime()
autotimer = timing.auto_timer()
common_flag_name = 'common_flags'
flag_name = 'flags'
groundfilter = tt.OpGroundFilter(
wbin=args.wbin_ground, name=totalname_freq,
common_flag_name=common_flag_name,
common_flag_mask=args.common_flag_mask,
flag_name=flag_name)
groundfilter.exec(data)
comm.comm_world.barrier()
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print('Ground filtering took {:.3f} s'.format(stop-start),
flush=args.flush)
return
def create_observations(args, comm, fp, all_ces, site):
""" Simulate constant elevation scans.
Simulate constant elevation scans at "site" matching entries in
"all_ces". Each operational day is assigned to a different
process group to allow making day maps.
"""
start = MPI.Wtime()
autotimer = timing.auto_timer()
data = toast.Data(comm)
site_name, site_lat, site_lon, site_alt = site
detectors = sorted(fp.keys())
detquats = {}
for d in detectors:
detquats[d] = fp[d]['quat']
nces = len(all_ces)
breaks = []
do_break = False
for i in range(nces - 1):
# If current and next CES are on different days, insert a break
tz = args.timezone / 24.
start1 = all_ces[i][3] # MJD start
start2 = all_ces[i + 1][3] # MJD start
scan1 = all_ces[i][4]
scan2 = all_ces[i + 1][4]
if scan1 != scan2 and do_break:
breaks.append(i + 1)
do_break = False
continue
day1 = int(start1 + tz)
day2 = int(start2 + tz)
if day1 != day2:
if scan1 == scan2:
# We want an entire CES, even if it crosses the day bound.
# Wait until the scan number changes.
do_break = True
else:
breaks.append(i + 1)
nbreak = len(breaks)
if nbreak != comm.ngroups - 1:
raise RuntimeError(
'Number of observing days ({}) does not match number of process '
'groups ({}).'.format(nbreak + 1, comm.ngroups))
groupdist = toast.distribute_uniform(nces, comm.ngroups, breaks=breaks)
group_firstobs = groupdist[comm.group][0]
group_numobs = groupdist[comm.group][1]
# Create the noise model used by all observations
fmin = {}
fknee = {}
alpha = {}
NET = {}
rates = {}
for d in detectors:
rates[d] = args.samplerate
fmin[d] = fp[d]['fmin']
fknee[d] = fp[d]['fknee']
alpha[d] = fp[d]['alpha']
NET[d] = fp[d]['NET']
noise = tt.AnalyticNoise(rate=rates,
fmin=fmin,
detectors=detectors,
fknee=fknee,
alpha=alpha,
NET=NET)
for ices in range(group_firstobs, group_firstobs + group_numobs):
ces = all_ces[ices]
CES_start, CES_stop, name, mjdstart, scan, subscan, azmin, azmax, \
el = ces
totsamples = int((CES_stop - CES_start) * args.samplerate)
# create the single TOD for this observation
try:
tod = tt.TODGround(comm.comm_group,
detquats,
totsamples,
detranks=comm.comm_group.size,
firsttime=CES_start,
rate=args.samplerate,
site_lon=site_lon,
site_lat=site_lat,
site_alt=site_alt,
azmin=azmin,
azmax=azmax,
el=el,
scanrate=args.scanrate,
scan_accel=args.scan_accel,
CES_start=None,
CES_stop=None,
sun_angle_min=args.sun_angle_min,
coord=args.coord,
sampsizes=None)
except RuntimeError as e:
print('Failed to create the CES scan: {}'.format(e),
flush=args.flush)
return
# Create the (single) observation
ob = {}
ob['name'] = 'CES-{}-{}-{}'.format(name, scan, subscan)
ob['tod'] = tod
if len(tod.subscans) > 0:
ob['intervals'] = tod.subscans
else:
raise RuntimeError('{} has no valid intervals'.format(ob['name']))
ob['baselines'] = None
ob['noise'] = noise
ob['id'] = int(mjdstart * 10000)
data.obs.append(ob)
for ob in data.obs:
tod = ob['tod']
tod.free_azel_quats()
if comm.comm_group.rank == 0:
print('Group # {:4} has {} observations.'.format(
comm.group, len(data.obs)),
flush=args.flush)
if len(data.obs) == 0:
raise RuntimeError('Too many tasks. Every MPI task must '
'be assigned to at least one observation.')
comm.comm_world.barrier()
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print('Simulated scans in {:.2f} seconds'
''.format(stop - start),
flush=args.flush)
return data
def load_fp(args, comm):
start = MPI.Wtime()
autotimer = timing.auto_timer()
fp = None
# Load focalplane information
nullquat = np.array([0, 0, 0, 1], dtype=np.float64)
if comm.comm_world.rank == 0:
if args.fp is None:
# in this case, create a fake detector at the boresight
# with a pure white noise spectrum.
fake = {}
fake['quat'] = nullquat
fake['fwhm'] = 30.0
fake['fknee'] = 0.0
fake['fmin'] = 1e-9
fake['alpha'] = 1.0
fake['NET'] = 1.0
fake['color'] = 'r'
fp = {}
# Second detector at 22.5 degree polarization angle
fp['bore1'] = fake
fake2 = {}
zrot = qa.rotation(ZAXIS, 22.5 * degree)
fake2['quat'] = qa.mult(fake['quat'], zrot)
fake2['fwhm'] = 30.0
fake2['fknee'] = 0.0
fake2['fmin'] = 1e-9
fake2['alpha'] = 1.0
fake2['NET'] = 1.0
fake2['color'] = 'r'
fp['bore2'] = fake2
# Third detector at 45 degree polarization angle
fake3 = {}
zrot = qa.rotation(ZAXIS, 45 * degree)
fake3['quat'] = qa.mult(fake['quat'], zrot)
fake3['fwhm'] = 30.0
fake3['fknee'] = 0.0
fake3['fmin'] = 1e-9
fake3['alpha'] = 1.0
fake3['NET'] = 1.0
fake3['color'] = 'r'
fp['bore3'] = fake3
# Fourth detector at 67.5 degree polarization angle
fake4 = {}
zrot = qa.rotation(ZAXIS, 67.5 * degree)
fake4['quat'] = qa.mult(fake['quat'], zrot)
fake4['fwhm'] = 30.0
fake4['fknee'] = 0.0
fake4['fmin'] = 1e-9
fake4['alpha'] = 1.0
fake4['NET'] = 1.0
fake4['color'] = 'r'
fp['bore4'] = fake4
else:
with open(args.fp, 'rb') as p:
fp = pickle.load(p)
fp = comm.comm_world.bcast(fp, root=0)
stop = MPI.Wtime()
elapsed = stop - start
if comm.comm_world.rank == 0:
print('Create focalplane: {:.2f} seconds'.format(stop - start),
flush=args.flush)
start = stop
if args.debug:
if comm.comm_world.rank == 0:
outfile = '{}/focalplane.png'.format(args.outdir)
tt.plot_focalplane(fp, 6, 6, outfile)
detectors = sorted(fp.keys())
detweights = {}
for d in detectors:
net = fp[d]['NET']
detweights[d] = 1.0 / (args.samplerate * net * net)
return fp, detweights
def exec(self, data):
"""
Generate atmosphere timestreams.
This iterates over all observations and detectors and generates
the atmosphere timestreams.
Args:
data (toast.Data): The distributed data.
"""
autotimer = timing.auto_timer(type(self).__name__)
group = data.comm.group
for obs in data.obs:
try:
obsname = obs["name"]
except Exception:
obsname = "observation"
prefix = "{} : {} : ".format(group, obsname)
tod = self._get_from_obs("tod", obs)
comm = tod.mpicomm
site = self._get_from_obs("site_id", obs)
weather = self._get_from_obs("weather", obs)
# Get the observation time span and initialize the weather
# object if one is provided.
times = tod.local_times()
tmin = times[0]
tmax = times[-1]
tmin_tot = comm.allreduce(tmin, op=MPI.MIN)
tmax_tot = comm.allreduce(tmax, op=MPI.MAX)
weather.set(site, self._realization, tmin_tot)
key1, key2, counter1, counter2 = self._get_rng_keys(obs)
absorption = self._get_absorption_and_loading(obs)
cachedir = self._get_cache_dir(obs, comm)
comm.Barrier()
if comm.rank == 0:
print(prefix + "Setting up atmosphere simulation", flush=self._flush)
comm.Barrier()
# Cache the output common flags
common_ref = tod.local_common_flags(self._common_flag_name)
scan_range = self._get_scan_range(obs, comm)
# Loop over the time span in "wind_time"-sized chunks.
# wind_time is intended to reflect the correlation length
# in the atmospheric noise.
if self._report_timing:
comm.Barrier()
tstart = MPI.Wtime()
tmin = tmin_tot
istart = 0
counter1start = counter1
while tmin < tmax_tot:
if self._report_timing:
comm.Barrier()
tstart = MPI.Wtime()
comm.Barrier()
if comm.rank == 0:
print(
prefix + "Instantiating the atmosphere for t = {}"
"".format(tmin - tmin_tot),
flush=self._flush,
)
istart, istop, tmax = self._get_time_range(
tmin, istart, times, tmax_tot, common_ref, tod, weather
)
ind = slice(istart, istop)
nind = istop - istart
comm.Barrier()
rmin = 0
rmax = 100
scale = 10
counter2start = counter2
counter1 = counter1start
xstart, ystart, zstart = self._xstep, self._ystep, self._zstep
while rmax < 100000:
sim, counter2 = self._simulate_atmosphere(
weather,
scan_range,
tmin,
tmax,
comm,
key1,
key2,
counter1,
counter2start,
cachedir,
prefix,
tmin_tot,
tmax_tot,
rmin,
rmax,
)
if self._verbosity > 15:
self._plot_snapshots(
sim,
prefix,
obsname,
scan_range,
tmin,
tmax,
comm,
rmin,
rmax,
)
self._observe_atmosphere(
sim,
tod,
comm,
prefix,
common_ref,
istart,
nind,
ind,
scan_range,
times,
absorption,
)
rmin = rmax
rmax *= scale
self._xstep *= np.sqrt(scale)
self._ystep *= np.sqrt(scale)
self._zstep *= np.sqrt(scale)
counter1 += 1
if self._verbosity > 5:
self._save_tod(
obsname, tod, times, istart, nind, ind, comm, common_ref
)
self._xstep, self._ystep, self._zstep = xstart, ystart, zstart
tmin = tmax
if self._report_timing:
comm.Barrier()
tstop = MPI.Wtime()
if comm.rank == 0:
print(
prefix
+ "Simulated and observed atmosphere in {:.2f} s".format(
tstop - tstart
),
flush=self._flush,
)
return
def _simulate_atmosphere(
self,
weather,
scan_range,
tmin,
tmax,
comm,
key1,
key2,
counter1,
counter2,
cachedir,
prefix,
tmin_tot,
tmax_tot,
rmin,
rmax,
):
if self._report_timing:
comm.Barrier()
tstart = MPI.Wtime()
T0_center = weather.air_temperature
wx = weather.west_wind
wy = weather.south_wind
w_center = np.sqrt(wx ** 2 + wy ** 2)
wdir_center = np.arctan2(wy, wx)
azmin, azmax, elmin, elmax = scan_range
sim = atm_sim_alloc(
azmin,
azmax,
elmin,
elmax,
tmin,
tmax,
self._lmin_center,
self._lmin_sigma,
self._lmax_center,
self._lmax_sigma,
w_center,
0,
wdir_center,
0,
self._z0_center,
self._z0_sigma,
T0_center,
0,
self._zatm,
self._zmax,
self._xstep,
self._ystep,
self._zstep,
self._nelem_sim_max,
self._verbosity,
comm,
key1,
key2,
counter1,
counter2,
cachedir,
rmin,
rmax,
)
if sim == 0:
raise RuntimeError(prefix + "Failed to allocate simulation")
if self._report_timing:
comm.Barrier()
tstop = MPI.Wtime()
if comm.rank == 0 and tstop - tstart > 1:
print(
prefix + "OpSimAtmosphere: Initialized "
"atmosphere in {:.2f} s".format(tstop - tstart),
flush=self._flush,
)
tstart = tstop
comm.Barrier()
use_cache = cachedir is not None
if comm.rank == 0:
fname = os.path.join(
cachedir,
"{}_{}_{}_{}_metadata.txt".format(key1, key2, counter1, counter2),
)
if use_cache and os.path.isfile(fname):
print(
prefix + "Loading the atmosphere for t = {} "
"from {}".format(tmin - tmin_tot, fname),
flush=self._flush,
)
cached = True
else:
print(
prefix + "Simulating the atmosphere for t = {}"
"".format(tmin - tmin_tot),
flush=self._flush,
)
cached = False
err = atm_sim_simulate(sim, use_cache)
if err != 0:
raise RuntimeError(prefix + "Simulation failed.")
# Advance the sample counter in case wind_time broke the
# observation in parts
counter2 += 100000000
if self._report_timing:
comm.Barrier()
tstop = MPI.Wtime()
if comm.rank == 0 and tstop - tstart > 1:
if cached:
op = "Loaded"
else:
op = "Simulated"
print(
prefix + "OpSimAtmosphere: {} atmosphere in "
"{:.2f} s".format(op, tstop - tstart),
flush=self._flush,
)
tstart = tstop
return sim, counter2
def bin_maps(args, comm, data, rootname, zmap, invnpp, zmap_group,
invnpp_group, detweights, totalname_freq, flag_name,
common_flag_name, outpath):
""" Use TOAST facilities to bin stored signal.
"""
if not args.skip_bin:
if comm.comm_world.rank == 0:
print('Binning unfiltered maps', flush=args.flush)
start0 = MPI.Wtime()
start = start0
autotimer = timing.auto_timer()
# Bin a map using the toast facilities
zmap.data.fill(0.0)
build_zmap = tm.OpAccumDiag(detweights=detweights,
zmap=zmap,
name=totalname_freq,
flag_name=flag_name,
common_flag_name=common_flag_name,
common_flag_mask=args.common_flag_mask)
build_zmap.exec(data)
zmap.allreduce()
comm.comm_world.barrier()
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print(' - Building noise weighted map took {:.3f} s'
''.format(stop - start),
flush=args.flush)
start = stop
tm.covariance_apply(invnpp, zmap)
comm.comm_world.barrier()
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print(' - Computing {} map took {:.3f} s'
''.format(rootname, stop - start),
flush=args.flush)
start = stop
fn = os.path.join(outpath, rootname + '.fits')
if args.zip:
fn += '.gz'
zmap.write_healpix_fits(fn)
comm.comm_world.barrier()
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print(' - Writing {} map to {} took {:.3f} s'
''.format(rootname, fn, stop - start),
flush=args.flush)
if zmap_group is not None:
zmap_group.data.fill(0.0)
build_zmap_group = tm.OpAccumDiag(
detweights=detweights,
zmap=zmap_group,
name=totalname_freq,
flag_name=flag_name,
common_flag_name=common_flag_name,
common_flag_mask=args.common_flag_mask)
build_zmap_group.exec(data)
zmap_group.allreduce()
comm.comm_group.barrier()
stop = MPI.Wtime()
if comm.comm_group.rank == 0:
print(' - Building group noise weighted map took '
'{:.3f} s'.format(stop - start),
flush=args.flush)
start = stop
tm.covariance_apply(invnpp_group, zmap_group)
comm.comm_group.barrier()
stop = MPI.Wtime()
elapsed = stop - start
if comm.comm_group.rank == 0:
print(' - Computing {} map took {:.3f} s'
''.format(rootname, stop - start),
flush=args.flush)
start = stop
fn = os.path.join(
outpath, '{}_group_{:04}.fits'
''.format(rootname, comm.group))
if args.zip:
fn += '.gz'
zmap_group.write_healpix_fits(fn)
comm.comm_group.barrier()
stop = MPI.Wtime()
if comm.comm_group.rank == 0:
print(' - Writing group {} map to {} took '
'{:.3f} s'.format(rootname, fn, stop - start),
flush=args.flush)
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print('Mapmaking took {:.3f} s'
''.format(stop - start0),
flush=args.flush)
return
def main():
comm = MPI.COMM_WORLD
if comm.rank == 0:
print("Running with {} processes".format(comm.size))
global_start = MPI.Wtime()
parser = argparse.ArgumentParser( description='Read a toast covariance matrix and write the inverse condition number map' )
parser.add_argument( '--input', required=True, default=None, help='The input covariance FITS file' )
parser.add_argument( '--output', required=False, default=None, help='The output inverse condition map FITS file.' )
args = timing.add_arguments_and_parse(parser, timing.FILE(noquotes=True))
autotimer = timing.auto_timer(timing.FILE())
# get options
infile = args.input
outfile = None
if args.output is not None:
outfile = args.output
else:
inmat = re.match(r'(.*)\.fits', infile)
if inmat is None:
print("input file should have .fits extension")
sys.exit(0)
inroot = inmat.group(1)
outfile = "{}_rcond.fits".format(inroot)
# We need to read the header to get the size of the matrix.
# This would be a trivial function call in astropy.fits or
# fitsio, but we don't want to bring in a whole new dependency
# just for that. Instead, we open the file with healpy in memmap
# mode so that nothing is actually read except the header.
nside = 0
nnz = 0
if comm.rank == 0:
fake, head = hp.read_map(infile, h=True, memmap=True)
for key, val in head:
if key == 'NSIDE':
nside = int(val)
if key == 'TFIELDS':
nnz = int(val)
nside = comm.bcast(nside, root=0)
nnz = comm.bcast(nnz, root=0)
npix = 12 * nside**2
subnside = int(nside / 16)
if subnside == 0:
subnside = 1
subnpix = 12 * subnside**2
nsubmap = int( npix / subnpix )
# divide the submaps as evenly as possible among processes
dist = toast.distribute_uniform(nsubmap, comm.size)
local = np.arange(dist[comm.rank][0], dist[comm.rank][0] + dist[comm.rank][1])
if comm.rank == 0:
if os.path.isfile(outfile):
os.remove(outfile)
comm.barrier()
# create the covariance and inverse condition number map
cov = tm.DistPixels(comm=comm, dtype=np.float64, size=npix, nnz=nnz, submap=subnpix, local=local)
# read the covariance
cov.read_healpix_fits(infile)
# every process computes its local piece
rcond = tm.covariance_rcond(cov)
# write the map
rcond.write_healpix_fits(outfile)
def __init__(self, bolo_id, IMO, filterlen=2 ** 20, fsample=180.3737,
lfer='LFER8', overlap=10000, extra_global_offset=None,
filterfile=None, tabulated_tf=None, fnorm=0.016, comm=None,
normalize_filter=True):
"""
Instantiate the deconvolution object
bolo_id -- Bolometer ID (e.g. 00_100_1a)
IMO -- Either an IMO object or a path to IMO XML dump
filterlen -- Fourier transform length, actual length will be a
power of 2 AT LEAST as long as this
fsample -- fixed sampling frequency
lfer -- Transfer function to seek from the IMO and deconvolve
overlap -- number of samples read for boundary effects. These
are not written into the filtered TOI
notch -- vector of line frequencies to notch out
wnotch -- relative width of the notch
extra_global_offset -- add another phase shift by hand; in same
units as global_offset in IMO.
tabulated_tf(None) -- When set, overrides LFER and IMO and
filterfile. A 3-element tuple containing frequency, real,
imaginary
filterfile(None) -- When set, overrides LFER and IMO. A 3 column
ASCII file containing the transfer function to convolve with
fnorm -- the frequency at which the transfer function is
normalized to 1.0. default is the dipole frequency.
"""
self.bolo_id = bolo_id
self.IMO = IMO
self.filterlen = 2
while self.filterlen < filterlen or self.filterlen < 3 * overlap:
self.filterlen *= 2
self.overlap = overlap
self.comm = comm
if self.comm is None:
self.ntask = 1
self.rank = 0
else:
self.ntask = self.comm.size
self.rank = self.comm.rank
self.normalize_filter = normalize_filter
# DEBUG begin
if self.rank == 0:
print("Initializing TauDeconvolver. bolo_id = {}, IMO = {}, filterlen = {}, fsample = {}, lfer = {}, filterfile = {}".format(bolo_id, IMO, filterlen, fsample, lfer, filterfile), flush=True)
# DEBUG end
freq = np.fft.rfftfreq(self.filterlen, 1. / fsample)
self.freq = freq
if tabulated_tf is not None:
self.tf = np.interp(
self.freq, tabulated_tf[0],
tabulated_tf[1]) + 1j * np.interp(self.freq, tabulated_tf[0],
tabulated_tf[2])
if self.normalize_filter:
norm = np.abs(
np.interp(fnorm, tabulated_tf[0], tabulated_tf[1]) +
1j * np.interp(fnorm, tabulated_tf[0], tabulated_tf[2]))
self.tf = self.tf / norm
self.tfinv = 1. / self.tf
self.tfinv[np.abs(self.tf) < 1e-4] = 0
self.lowpass = time_response_tools.filter_function(freq)
self.filter = self.lowpass * self.tfinv
self.fsample = fsample
if extra_global_offset is not None:
if extra_global_offset != 0.0:
phase = -2. * np.pi * extra_global_offset * freq / fsample
shift_tf = np.cos(phase) + 1j * np.sin(phase)
self.filter /= shift_tf
self.tf *= shift_tf
else:
self.filterfile = filterfile
if self.filterfile is not None:
if self.rank == 0:
try:
filt = np.genfromtxt(filterfile).T
except Exception as e:
raise Exception('Failed to load filter function from '
'{}: {}'.format(filterfile, e))
else:
filt = None
if self.comm is not None:
filt = self.comm.bcast(filt)
self.filter = np.interp(self.freq, filt[0], filt[1]) + \
1j * np.interp(self.freq, filt[0], filt[2])
if self.normalize_filter:
norm = np.abs(np.interp(fnorm, filt[0], filt[1]) +
1j * np.interp(fnorm, filt[0], filt[2]))
self.filter = self.filter / norm
# Invert the filter to allow convolving
self.tf = self.filter.copy()
good = self.filter != 0
self.tf[good] = 1. / self.filter[good]
self.tf[np.abs(self.filter) < 1e-4] = 0
else:
self.global_offset = self.IMO.get(
'IMO:HFI:DET:Phot_Pixel Name="{}":NoiseAndSyst:TimeResp:'
'LFER8:global_offset'.format(bolo_id), np.float64)
if extra_global_offset is not None:
self.global_offset += extra_global_offset
self.pars = {}
npole = 0
if lfer == 'LFER8':
prefix = 'IMO:HFI:DET:Phot_Pixel Name="{}":NoiseAndSyst:' \
'TimeResp:LFER8:'.format(bolo_id)
self.pars['a1'] = self.IMO.get(prefix + 'par1', np.float64)
self.pars['a2'] = self.IMO.get(prefix + 'par2', np.float64)
self.pars['a3'] = self.IMO.get(prefix + 'par3', np.float64)
self.pars['a4'] = self.IMO.get(prefix + 'par9', np.float64)
self.pars['a5'] = self.IMO.get(prefix + 'par11', np.float64)
self.pars['a6'] = self.IMO.get(prefix + 'par13', np.float64)
self.pars['a7'] = self.IMO.get(prefix + 'par15', np.float64)
self.pars['a8'] = self.IMO.get(prefix + 'par17', np.float64)
self.pars['tau1'] = self.IMO.get(prefix + 'par4',
np.float64)
self.pars['tau2'] = self.IMO.get(prefix + 'par5',
np.float64)
self.pars['tau3'] = self.IMO.get(prefix + 'par6',
np.float64)
self.pars['tau4'] = self.IMO.get(prefix + 'par10',
np.float64)
self.pars['tau5'] = self.IMO.get(prefix + 'par12',
np.float64)
self.pars['tau6'] = self.IMO.get(prefix + 'par14',
np.float64)
self.pars['tau7'] = self.IMO.get(prefix + 'par16',
np.float64)
self.pars['tau8'] = self.IMO.get(prefix + 'par18',
np.float64)
self.pars['tau_stray'] = self.IMO.get(prefix + 'par7',
np.float64)
self.pars['Sphase'] = self.IMO.get(prefix + 'par8',
np.float64)
prefix = 'IMO:HFI:DET:Phot_Pixel Name="{}":NoiseAndSyst:' \
'TimeResp:SallenKeyHPF:'.format(bolo_id)
self.pars['tauhp1'] = self.IMO.get(prefix + 'tauhp1',
np.float64)
self.pars['tauhp2'] = self.IMO.get(prefix + 'tauhp2',
np.float64)
npole = 8
for i in range(8, 0, -1):
if self.pars['tau' + str(i)] != 0:
break
npole -= 1
if self.pars['tauhp1'] != self.pars['tauhp2']:
raise Exception(
'Don\'t know how to handle the case where tauhp1 '
'({}) is not equal to tauhp2 ({})'.format(
self.pars['tauhp1'], self.pars['tauhp2']))
elif lfer == 'LFER1':
npole = 1
self.pars['a1'] = 1.0
self.pars['tau1'] = 0.01
self.pars['tau_stray'] = 2.095108e-03
self.pars['Sphase'] = 0.0
else:
raise Exception(
'Don\'t know how to parse {} transfer function '
'parameters from IMO'.format(lfer))
norm_f = np.array([0.0, fnorm])
norm_tf = time_response_tools.LFERn(norm_f, npole, self.pars)
phase = -2. * np.pi * self.global_offset * norm_f / fsample
shift_tf = np.cos(phase) + 1j * np.sin(phase)
norm_tf = norm_tf * (np.cos(phase) + 1j * np.sin(phase))
norm = np.abs(norm_tf[1])
tstart = MPI.Wtime()
if self.ntask == 1:
self.tf = time_response_tools.LFERn(freq, npole, self.pars) \
/ norm
else:
nfreq = len(freq)
nfreq_task = np.int(np.ceil(nfreq / self.ntask))
# First frequency must be zero for normalization
my_freq = np.hstack(
[[0.0],
freq[nfreq_task * self.rank:
nfreq_task * (self.rank + 1)]])
# Discard the extra frequency bin here
my_tf = time_response_tools.LFERn(
my_freq, npole, self.pars)[1:] / norm
self.tf = np.hstack(self.comm.allgather(my_tf))
tstop = MPI.Wtime()
if self.rank == 0:
print('Computed the LFER transfer function in {:.2f} s.'
''.format(tstop - tstart), flush=True)
self.tfinv = 1. / self.tf
self.tfinv[np.abs(self.tf) < 1e-4] = 0
self.lowpass = time_response_tools.filter_function(freq)
self.filter = self.lowpass * self.tfinv
self.fsample = fsample
phase = -2. * np.pi * self.global_offset * freq / fsample
shift_tf = np.cos(phase) + 1j * np.sin(phase)
self.filter /= shift_tf
self.tf *= shift_tf
self.init_flag_kernels()
return
def main():
if MPI.COMM_WORLD.rank == 0:
print("Running with {} processes".format(MPI.COMM_WORLD.size),
flush=True)
global_start = MPI.Wtime()
parser = argparse.ArgumentParser( description="Simulate satellite "
"boresight pointing and make a noise map.", fromfile_prefix_chars="@" )
parser.add_argument( "--groupsize", required=False, type=int, default=0,
help="size of processor groups used to distribute observations" )
parser.add_argument( "--samplerate", required=False, type=float,
default=40.0, help="Detector sample rate (Hz)" )
parser.add_argument( "--starttime", required=False, type=float,
default=0.0, help="The overall start time of the simulation" )
parser.add_argument( "--spinperiod", required=False, type=float,
default=10.0, help="The period (in minutes) of the rotation about the "
"spin axis" )
parser.add_argument( "--spinangle", required=False, type=float,
default=30.0, help="The opening angle (in degrees) of the boresight "
"from the spin axis" )
parser.add_argument( "--precperiod", required=False, type=float,
default=50.0, help="The period (in minutes) of the rotation about the "
"precession axis" )
parser.add_argument( "--precangle", required=False, type=float,
default=65.0, help="The opening angle (in degrees) of the spin axis "
"from the precession axis" )
parser.add_argument( "--hwprpm", required=False, type=float,
default=0.0, help="The rate (in RPM) of the HWP rotation" )
parser.add_argument( "--hwpstep", required=False, default=None,
help="For stepped HWP, the angle in degrees of each step" )
parser.add_argument( "--hwpsteptime", required=False, type=float,
default=0.0, help="For stepped HWP, the the time in seconds between "
"steps" )
parser.add_argument( "--obs", required=False, type=float, default=1.0,
help="Number of hours in one science observation" )
parser.add_argument( "--gap", required=False, type=float, default=0.0,
help="Cooler cycle time in hours between science obs" )
parser.add_argument( "--numobs", required=False, type=int, default=1,
help="Number of complete observations" )
parser.add_argument( "--outdir", required=False, default="out",
help="Output directory" )
parser.add_argument( "--debug", required=False, default=False,
action="store_true", help="Write diagnostics" )
parser.add_argument( "--nside", required=False, type=int, default=64,
help="Healpix NSIDE" )
parser.add_argument( "--subnside", required=False, type=int, default=4,
help="Distributed pixel sub-map NSIDE" )
parser.add_argument( "--baseline", required=False, type=float,
default=60.0, help="Destriping baseline length (seconds)" )
parser.add_argument( "--noisefilter", required=False, default=False,
action="store_true", help="Destripe with the noise filter enabled" )
parser.add_argument( "--madam", required=False, default=False,
action="store_true", help="If specified, use libmadam for map-making" )
parser.add_argument( "--madampar", required=False, default=None,
help="Madam parameter file" )
parser.add_argument('--flush',
required=False, default=False, action='store_true',
help='Flush every print statement.')
parser.add_argument( "--MC_start", required=False, type=int, default=0,
help="First Monte Carlo noise realization" )
parser.add_argument( "--MC_count", required=False, type=int, default=1,
help="Number of Monte Carlo noise realizations" )
parser.add_argument( "--fp", required=False, default=None,
help="Pickle file containing a dictionary of detector properties. "
"The keys of this dict are the detector names, and each value is also "
"a dictionary with keys \"quat\" (4 element ndarray), \"fwhm\" "
"(float, arcmin), \"fknee\" (float, Hz), \"alpha\" (float), and \"NET\" "
"(float). For optional plotting, the key \"color\" can specify a "
"valid matplotlib color string." )
parser.add_argument('--tidas',
required=False, default=None,
help='Output TIDAS export path')
parser.add_argument('--input_map', required=False,
help='Input map for signal')
parser.add_argument('--input_pysm_model', required=False,
help='Comma separated models for on-the-fly PySM '
'simulation, e.g. s3,d6,f1,a2"')
parser.add_argument('--apply_beam', required=False, action='store_true',
help='Apply beam convolution to input map with gaussian '
'beam parameters defined in focalplane')
parser.add_argument('--input_dipole', required=False,
help='Simulate dipole, possible values are '
'total, orbital, solar')
parser.add_argument('--input_dipole_solar_speed_kms', required=False,
help='Solar system speed [km/s]', type=float,
default=369.0)
parser.add_argument('--input_dipole_solar_gal_lat_deg', required=False,
help='Solar system speed galactic latitude [degrees]',
type=float, default=48.26)
parser.add_argument('--input_dipole_solar_gal_lon_deg', required=False,
help='Solar system speed galactic longitude[degrees]',
type=float, default=263.99)
args = timing.add_arguments_and_parse(parser, timing.FILE(noquotes=True))
autotimer = timing.auto_timer("@{}".format(timing.FILE()))
if args.tidas is not None:
if not tt.tidas_available:
raise RuntimeError("TIDAS not found- cannot export")
groupsize = args.groupsize
if groupsize == 0:
groupsize = MPI.COMM_WORLD.size
# This is the 2-level toast communicator.
if MPI.COMM_WORLD.size % groupsize != 0:
if MPI.COMM_WORLD.rank == 0:
print("WARNING: process groupsize does not evenly divide into "
"total number of processes", flush=True)
comm = toast.Comm(world=MPI.COMM_WORLD, groupsize=groupsize)
# get options
hwpstep = None
if args.hwpstep is not None:
hwpstep = float(args.hwpstep)
npix = 12 * args.nside * args.nside
subnside = args.subnside
if subnside > args.nside:
subnside = args.nside
subnpix = 12 * subnside * subnside
start = MPI.Wtime()
fp = None
# Load focalplane information
if comm.comm_world.rank == 0:
if args.fp is None:
# in this case, create a fake detector at the boresight
# with a pure white noise spectrum.
fake = {}
fake["quat"] = np.array([0.0, 0.0, 1.0, 0.0])
fake["fwhm"] = 30.0
fake["fknee"] = 0.0
fake["alpha"] = 1.0
fake["NET"] = 1.0
fake["color"] = "r"
fp = {}
fp["bore"] = fake
else:
with open(args.fp, "rb") as p:
fp = pickle.load(p)
fp = comm.comm_world.bcast(fp, root=0)
stop = MPI.Wtime()
elapsed = stop - start
if comm.comm_world.rank == 0:
print("Create focalplane: {:.2f} seconds".format(stop-start),
flush=True)
start = stop
if args.debug:
if comm.comm_world.rank == 0:
outfile = "{}_focalplane.png".format(args.outdir)
set_backend()
tt.plot_focalplane(fp, 10.0, 10.0, outfile)
# Since we are simulating noise timestreams, we want
# them to be contiguous and reproducible over the whole
# observation. We distribute data by detector within an
# observation, so ensure that our group size is not larger
# than the number of detectors we have.
if groupsize > len(fp.keys()):
if comm.comm_world.rank == 0:
print("process group is too large for the number of detectors",
flush=True)
comm.comm_world.Abort()
# Detector information from the focalplane
detectors = sorted(fp.keys())
detquats = {}
detindx = None
if "index" in fp[detectors[0]]:
detindx = {}
for d in detectors:
detquats[d] = fp[d]["quat"]
if detindx is not None:
detindx[d] = fp[d]["index"]
# Distribute the observations uniformly
groupdist = toast.distribute_uniform(args.numobs, comm.ngroups)
# Compute global time and sample ranges of all observations
obsrange = tt.regular_intervals(args.numobs, args.starttime, 0,
args.samplerate, 3600*args.obs, 3600*args.gap)
# Create the noise model used for all observations
fmin = {}
fknee = {}
alpha = {}
NET = {}
rates = {}
for d in detectors:
rates[d] = args.samplerate
fmin[d] = fp[d]["fmin"]
fknee[d] = fp[d]["fknee"]
alpha[d] = fp[d]["alpha"]
NET[d] = fp[d]["NET"]
noise = tt.AnalyticNoise(rate=rates, fmin=fmin, detectors=detectors,
fknee=fknee, alpha=alpha, NET=NET)
mem_counter = tt.OpMemoryCounter()
# The distributed timestream data
data = toast.Data(comm)
# Every process group creates its observations
group_firstobs = groupdist[comm.group][0]
group_numobs = groupdist[comm.group][1]
for ob in range(group_firstobs, group_firstobs + group_numobs):
tod = tt.TODSatellite(
comm.comm_group,
detquats,
obsrange[ob].samples,
firsttime=obsrange[ob].start,
rate=args.samplerate,
spinperiod=args.spinperiod,
spinangle=args.spinangle,
precperiod=args.precperiod,
precangle=args.precangle,
detindx=detindx,
detranks=comm.group_size
)
obs = {}
obs["name"] = "science_{:05d}".format(ob)
obs["tod"] = tod
obs["intervals"] = None
obs["baselines"] = None
obs["noise"] = noise
obs["id"] = ob
data.obs.append(obs)
stop = MPI.Wtime()
elapsed = stop - start
if comm.comm_world.rank == 0:
print("Read parameters, compute data distribution: "
"{:.2f} seconds".format(stop-start), flush=True)
start = stop
# we set the precession axis now, which will trigger calculation
# of the boresight pointing.
for ob in range(group_numobs):
curobs = data.obs[ob]
tod = curobs["tod"]
# Get the global sample offset from the original distribution of
# intervals
obsoffset = obsrange[group_firstobs + ob].first
# Constantly slewing precession axis
degday = 360.0 / 365.25
precquat = tt.slew_precession_axis(nsim=tod.local_samples[1],
firstsamp=obsoffset, samplerate=args.samplerate,
degday=degday)
tod.set_prec_axis(qprec=precquat)
stop = MPI.Wtime()
elapsed = stop - start
if comm.comm_world.rank == 0:
print("Construct boresight pointing: "
"{:.2f} seconds".format(stop-start), flush=True)
start = stop
# make a Healpix pointing matrix.
pointing = tt.OpPointingHpix(nside=args.nside, nest=True, mode="IQU",
hwprpm=args.hwprpm, hwpstep=hwpstep, hwpsteptime=args.hwpsteptime)
pointing.exec(data)
comm.comm_world.barrier()
stop = MPI.Wtime()
elapsed = stop - start
if comm.comm_world.rank == 0:
print("Pointing generation took {:.3f} s".format(elapsed), flush=True)
start = stop
localpix, localsm, subnpix = get_submaps(args, comm, data)
signalname = "signal"
if args.input_pysm_model:
simulate_sky_signal(args, comm, data, mem_counter,
[fp], subnpix, localsm, signalname=signalname)
if args.input_dipole:
print("Simulating dipole")
op_sim_dipole = tt.OpSimDipole(mode=args.input_dipole,
solar_speed=args.input_dipole_solar_speed_kms,
solar_gal_lat=args.input_dipole_solar_gal_lat_deg,
solar_gal_lon=args.input_dipole_solar_gal_lon_deg,
out=signalname,
keep_quats=True,
keep_vel=False,
subtract=False,
coord="G",
freq=0, # we could use frequency for quadrupole correction
flag_mask=255, common_flag_mask=255)
op_sim_dipole.exec(data)
# Mapmaking. For purposes of this simulation, we use detector noise
# weights based on the NET (white noise level). If the destriping
# baseline is too long, this will not be the best choice.
detweights = {}
for d in detectors:
net = fp[d]["NET"]
detweights[d] = 1.0 / (args.samplerate * net * net)
if not args.madam:
if comm.comm_world.rank == 0:
print("Not using Madam, will only make a binned map!", flush=True)
# get locally hit pixels
lc = tm.OpLocalPixels()
localpix = lc.exec(data)
# find the locally hit submaps.
localsm = np.unique(np.floor_divide(localpix, subnpix))
# construct distributed maps to store the covariance,
# noise weighted map, and hits
invnpp = tm.DistPixels(comm=comm.comm_world, size=npix, nnz=6,
dtype=np.float64, submap=subnpix, local=localsm)
hits = tm.DistPixels(comm=comm.comm_world, size=npix, nnz=1,
dtype=np.int64, submap=subnpix, local=localsm)
zmap = tm.DistPixels(comm=comm.comm_world, size=npix, nnz=3,
dtype=np.float64, submap=subnpix, local=localsm)
# compute the hits and covariance once, since the pointing and noise
# weights are fixed.
invnpp.data.fill(0.0)
hits.data.fill(0)
build_invnpp = tm.OpAccumDiag(detweights=detweights, invnpp=invnpp,
hits=hits)
build_invnpp.exec(data)
invnpp.allreduce()
hits.allreduce()
comm.comm_world.barrier()
stop = MPI.Wtime()
elapsed = stop - start
if comm.comm_world.rank == 0:
print("Building hits and N_pp^-1 took {:.3f} s".format(elapsed),
flush=True)
start = stop
hits.write_healpix_fits("{}_hits.fits".format(args.outdir))
invnpp.write_healpix_fits("{}_invnpp.fits".format(args.outdir))
comm.comm_world.barrier()
stop = MPI.Wtime()
elapsed = stop - start
if comm.comm_world.rank == 0:
print("Writing hits and N_pp^-1 took {:.3f} s".format(elapsed),
flush=True)
start = stop
# invert it
tm.covariance_invert(invnpp, 1.0e-3)
comm.comm_world.barrier()
stop = MPI.Wtime()
elapsed = stop - start
if comm.comm_world.rank == 0:
print("Inverting N_pp^-1 took {:.3f} s".format(elapsed),
flush=True)
start = stop
invnpp.write_healpix_fits("{}_npp.fits".format(args.outdir))
comm.comm_world.barrier()
stop = MPI.Wtime()
elapsed = stop - start
if comm.comm_world.rank == 0:
print("Writing N_pp took {:.3f} s".format(elapsed),
flush=True)
start = stop
# in debug mode, print out data distribution information
if args.debug:
handle = None
if comm.comm_world.rank == 0:
handle = open("{}_distdata.txt".format(args.outdir), "w")
data.info(handle)
if comm.comm_world.rank == 0:
handle.close()
comm.comm_world.barrier()
stop = MPI.Wtime()
elapsed = stop - start
if comm.comm_world.rank == 0:
print("Dumping debug data distribution took "
"{:.3f} s".format(elapsed), flush=True)
start = stop
mcstart = start
# Loop over Monte Carlos
firstmc = int(args.MC_start)
nmc = int(args.MC_count)
for mc in range(firstmc, firstmc+nmc):
# create output directory for this realization
outpath = "{}_{:03d}".format(args.outdir, mc)
if comm.comm_world.rank == 0:
if not os.path.isdir(outpath):
os.makedirs(outpath)
comm.comm_world.barrier()
stop = MPI.Wtime()
elapsed = stop - start
if comm.comm_world.rank == 0:
print("Creating output dir {:04d} took {:.3f} s".format(mc,
elapsed), flush=True)
start = stop
# clear all signal data from the cache, so that we can generate
# new noise timestreams.
tod.cache.clear("tot_signal_.*")
# simulate noise
nse = tt.OpSimNoise(out="tot_signal", realization=mc)
nse.exec(data)
# add sky signal
add_sky_signal(args, comm, data, totalname="tot_signal", signalname=signalname)
if mc == firstmc:
# For the first realization, optionally export the
# timestream data to a TIDAS volume.
if args.tidas is not None:
from toast.tod.tidas import OpTidasExport
tidas_path = os.path.abspath(args.tidas)
export = OpTidasExport(tidas_path, name="tot_signal")
export.exec(data)
comm.comm_world.barrier()
stop = MPI.Wtime()
elapsed = stop - start
if comm.comm_world.rank == 0:
print(" Noise simulation {:04d} took {:.3f} s".format(mc,
elapsed), flush=True)
start = stop
zmap.data.fill(0.0)
build_zmap = tm.OpAccumDiag(zmap=zmap, name="tot_signal",
detweights=detweights)
build_zmap.exec(data)
zmap.allreduce()
comm.comm_world.barrier()
stop = MPI.Wtime()
elapsed = stop - start
if comm.comm_world.rank == 0:
print(" Building noise weighted map {:04d} took {:.3f} s".format(
mc, elapsed), flush=True)
start = stop
tm.covariance_apply(invnpp, zmap)
comm.comm_world.barrier()
stop = MPI.Wtime()
elapsed = stop - start
if comm.comm_world.rank == 0:
print(" Computing binned map {:04d} took {:.3f} s".format(mc,
elapsed), flush=True)
start = stop
zmap.write_healpix_fits(os.path.join(outpath, "binned.fits"))
comm.comm_world.barrier()
stop = MPI.Wtime()
elapsed = stop - start
if comm.comm_world.rank == 0:
print(" Writing binned map {:04d} took {:.3f} s".format(mc,
elapsed), flush=True)
elapsed = stop - mcstart
if comm.comm_world.rank == 0:
print(" Mapmaking {:04d} took {:.3f} s".format(mc, elapsed),
flush=True)
start = stop
else:
# Set up MADAM map making.
pars = {}
cross = args.nside // 2
pars[ "temperature_only" ] = "F"
pars[ "force_pol" ] = "T"
pars[ "kfirst" ] = "T"
pars[ "concatenate_messages" ] = "T"
pars[ "write_map" ] = "T"
pars[ "write_binmap" ] = "T"
pars[ "write_matrix" ] = "T"
pars[ "write_wcov" ] = "T"
pars[ "write_hits" ] = "T"
pars[ "nside_cross" ] = cross
pars[ "nside_submap" ] = subnside
if args.madampar is not None:
pat = re.compile(r"\s*(\S+)\s*=\s*(\S+(\s+\S+)*)\s*")
comment = re.compile(r"^#.*")
with open(args.madampar, "r") as f:
for line in f:
if comment.match(line) is None:
result = pat.match(line)
if result is not None:
key, value = result.group(1), result.group(2)
pars[key] = value
pars[ "base_first" ] = args.baseline
pars[ "nside_map" ] = args.nside
if args.noisefilter:
pars[ "kfilter" ] = "T"
else:
pars[ "kfilter" ] = "F"
pars[ "fsample" ] = args.samplerate
# Loop over Monte Carlos
firstmc = int(args.MC_start)
nmc = int(args.MC_count)
for mc in range(firstmc, firstmc+nmc):
# clear all total signal data from the cache, so that we can generate
# new noise timestreams.
tod.cache.clear("tot_signal_.*")
# simulate noise
nse = tt.OpSimNoise(out="tot_signal", realization=mc)
nse.exec(data)
# add sky signal
add_sky_signal(args, comm, data, totalname="tot_signal", signalname=signalname)
comm.comm_world.barrier()
stop = MPI.Wtime()
elapsed = stop - start
if comm.comm_world.rank == 0:
print("Noise simulation took {:.3f} s".format(elapsed),
flush=True)
start = stop
# create output directory for this realization
pars[ "path_output" ] = "{}_{:03d}".format(args.outdir, mc)
if comm.comm_world.rank == 0:
if not os.path.isdir(pars["path_output"]):
os.makedirs(pars["path_output"])
# in debug mode, print out data distribution information
if args.debug:
handle = None
if comm.comm_world.rank == 0:
handle = open(os.path.join(pars["path_output"],
"distdata.txt"), "w")
data.info(handle)
if comm.comm_world.rank == 0:
handle.close()
madam = tm.OpMadam(params=pars, detweights=detweights,
name="tot_signal")
madam.exec(data)
comm.comm_world.barrier()
stop = MPI.Wtime()
elapsed = stop - start
if comm.comm_world.rank == 0:
print("Mapmaking took {:.3f} s".format(elapsed), flush=True)
comm.comm_world.barrier()
stop = MPI.Wtime()
elapsed = stop - global_start
if comm.comm_world.rank == 0:
print("Total Time: {:.2f} seconds".format(elapsed), flush=True)
def process_noise_estimate(self, signal1, signal2, flags, gapflags,
gapflags_nsum, timestamps, fsample, cworld,
rank, fileroot, det1, det2, local_intervals):
# High pass filter the signal to avoid aliasing
# self.highpass(signal1, noise_flags)
# self.highpass(signal2, noise_flags)
# Compute the autocovariance function and the matching
# PSD for each stationary interval
start = MPI.Wtime()
if signal2 is None:
my_psds1 = tf.autocov_psd(timestamps,
signal1,
flags + gapflags,
self._lagmax,
self._stationary_period,
fsample,
comm=cworld)
else:
my_psds1 = tf.crosscov_psd(timestamps,
signal1,
signal2,
flags + gapflags,
self._lagmax,
self._stationary_period,
fsample,
comm=cworld)
# Get another PSD for a down-sampled TOD to measure the
# low frequency power
timestamps_decim = timestamps[::self._nsum]
# decimate() will smooth and downsample the signal in
# each valid interval separately
signal1_decim, flags_decim = self.decimate(signal1, flags,
gapflags_nsum,
local_intervals)
if signal2 is not None:
signal2_decim, flags_decim = self.decimate(signal2, flags,
gapflags_nsum,
local_intervals)
if signal2 is None:
my_psds2 = tf.autocov_psd(timestamps_decim,
signal1_decim,
flags_decim,
min(self._lagmax, timestamps_decim.size),
self._stationary_period,
fsample / self._nsum,
comm=cworld)
else:
my_psds2 = tf.crosscov_psd(timestamps_decim,
signal1_decim,
signal2_decim,
flags_decim,
min(self._lagmax,
timestamps_decim.size),
self._stationary_period,
fsample / self._nsum,
comm=cworld)
# Ensure the two sets of PSDs are of equal length
my_new_psds1 = []
my_new_psds2 = []
i = 0
while i < min(len(my_psds1), len(my_psds2)):
t1 = my_psds1[i][0]
t2 = my_psds2[i][0]
if np.isclose(t1, t2):
my_new_psds1.append(my_psds1[i])
my_new_psds2.append(my_psds2[i])
i += 1
else:
if t1 < t2:
del my_psds1[i]
else:
del my_psds2[i]
my_psds1 = my_new_psds1
my_psds2 = my_new_psds2
if len(my_psds1) != len(my_psds2):
while my_psds1[-1][0] > my_psds2[-1][0]:
del my_psds1[-1]
while my_psds1[-1][0] < my_psds2[-1][0]:
del my_psds2[-1]
# frequencies that are usable in the down-sampled PSD
fcut = fsample / 2 / self._naverage / 100
stop = MPI.Wtime()
if rank == 0:
print('Correlators and PSDs computed in {:.2f} s'
''.format(stop - start),
flush=True)
# Now bin the PSDs
fmin = 1 / self._stationary_period
fmax = fsample / 2
start = MPI.Wtime()
my_binned_psds1, my_times1, binfreq10 = self.bin_psds(
my_psds1, fmin, fmax)
my_binned_psds2, _, binfreq20 = self.bin_psds(my_psds2, fmin, fmax)
stop = MPI.Wtime()
"""
# DEBUG begin
import pdb
import matplotlib.pyplot as plt
plt.figure()
plt.loglog(my_psds2[0][2], my_psds2[0][3], 'r.')
plt.loglog(my_psds1[0][2], my_psds1[0][3], 'b.')
plt.loglog(binfreq20, my_binned_psds2[0], 'r-')
plt.loglog(binfreq10, my_binned_psds1[0], 'b-')
plt.gca().axvline(fcut, color='k')
plt.draw()
plt.show()
pdb.set_trace()
# DEBUG end
"""
# concatenate
if binfreq10 is None or binfreq20 is None:
my_times = []
my_binned_psds = []
binfreq0 = None
else:
my_times = my_times1
ind1 = binfreq10 > fcut
ind2 = binfreq20 <= fcut
binfreq0 = np.hstack([binfreq20[ind2], binfreq10[ind1]])
my_binned_psds = []
for psd1, psd2 in zip(my_binned_psds1, my_binned_psds2):
my_binned_psds.append(np.hstack([psd2[ind2], psd1[ind1]]))
# Collect and write the PSDs. Start by determining the first
# process to have a valid PSD to determine binning
start = MPI.Wtime()
have_bins = binfreq0 is not None
have_bins_all = cworld.allgather(have_bins)
root = 0
if np.any(have_bins_all):
while not have_bins_all[root]:
root += 1
else:
raise RuntimeError('None of the processes have valid PSDs')
binfreq = cworld.bcast(binfreq0, root=root)
if binfreq0 is not None and np.any(binfreq != binfreq0):
raise Exception(
'{:4} : Binned PSD frequencies change. len(binfreq0)={}'
', len(binfreq)={}, binfreq0={}, binfreq={}. '
'len(my_psds)={}'.format(rank, binfreq0.size, binfreq.size,
binfreq0, binfreq, len(my_psds1)))
if len(my_times) != len(my_binned_psds):
raise Exception(
'ERROR: Process {} has len(my_times) = {}, len(my_binned_psds)'
' = {}'.format(rank, len(my_times), len(my_binned_psds)))
all_times = cworld.gather(my_times, root=0)
all_psds = cworld.gather(my_binned_psds, root=0)
stop = MPI.Wtime()
if rank == 0:
if len(all_times) != len(all_psds):
raise Exception(
'ERROR: Process {} has len(all_times) = {}, len(all_psds)'
' = {} before deglitch'.format(rank, len(all_times),
len(all_psds)))
# De-glitch the binned PSDs and write them to file
i = 0
while i < len(all_times):
if len(all_times[i]) == 0:
del all_times[i]
del all_psds[i]
else:
i += 1
all_times = np.hstack(all_times)
all_psds = np.vstack(all_psds)
if len(all_times) != len(all_psds):
raise Exception(
'ERROR: Process {} has len(all_times) = {}, len(all_psds)'
' = {} AFTER deglitch'.format(rank, len(all_times),
len(all_psds)))
# if self._no_spin_harmonics:
# binfreq, all_psds = self.discard_spin_harmonics(binfreq, all_psds)
good_psds, good_times = self.discard_outliers(
binfreq, all_psds, all_times)
self.save_psds(binfreq, all_psds, all_times, det1, det2, fsample,
fileroot)
self.save_psds(binfreq, good_psds, good_times, det1, det2, fsample,
fileroot + '_good')
return
def binned_map(data, npix, subnpix, out="."):
"""Make a binned map
This function should exist in toast, but all the pieces do. If we are
doing MCs we break these operations into two pieces and only generate
the noise weighted map each realization.
"""
# The global MPI communicator
cworld = data.comm.comm_world
# construct distributed maps to store the covariance,
# noise weighted map, and hits
invnpp = tm.DistPixels(data, nnz=6, dtype=np.float64)
hits = tm.DistPixels(data, nnz=1, dtype=np.int64)
zmap = tm.DistPixels(data, nnz=3, dtype=np.float64)
invnpp.data.fill(0.0)
hits.data.fill(0)
zmap.data.fill(0.0)
start = MPI.Wtime()
if cworld.rank == 0:
print("Accumulating hits and N_pp'^-1 ...", flush=True)
# Setting detweights to None gives uniform weighting.
build_invnpp = tm.OpAccumDiag(detweights=None,
invnpp=invnpp,
hits=hits,
zmap=zmap,
name="signal",
pixels="pixels",
weights="weights",
common_flag_name="flags_common",
common_flag_mask=1)
build_invnpp.exec(data)
invnpp.allreduce()
hits.allreduce()
zmap.allreduce()
cworld.barrier()
stop = MPI.Wtime()
elapsed = stop - start
if cworld.rank == 0:
print("Building hits and N_pp^-1 took {:.3f} s".format(elapsed),
flush=True)
if cworld.rank == 0:
print("Writing hits and N_pp'^-1 ...", flush=True)
hits.write_healpix_fits(os.path.join(out, "hits.fits"))
invnpp.write_healpix_fits(os.path.join(out, "invnpp.fits"))
start = stop
if cworld.rank == 0:
print("Inverting N_pp'^-1 ...", flush=True)
# invert it
tm.covariance_invert(invnpp, 1.0e-3)
cworld.barrier()
stop = MPI.Wtime()
elapsed = stop - start
if cworld.rank == 0:
print("Inverting N_pp^-1 took {:.3f} s".format(elapsed), flush=True)
if cworld.rank == 0:
print("Writing N_pp' ...", flush=True)
invnpp.write_healpix_fits(os.path.join(out, "npp.fits"))
start = stop
if cworld.rank == 0:
print("Computing binned map ...", flush=True)
tm.covariance_apply(invnpp, zmap)
cworld.barrier()
stop = MPI.Wtime()
elapsed = stop - start
if cworld.rank == 0:
print("Computing binned map took {:.3f} s".format(elapsed), flush=True)
start = stop
if cworld.rank == 0:
print("Writing binned map ...", flush=True)
zmap.write_healpix_fits(os.path.join(out, "binned.fits"))
if cworld.rank == 0:
print("Binned map done", flush=True)
return
def measure_correction(self, fn=None, gain=None):
"""
Estimate the ADC correction per bin for each 4K phase
"""
self.corrections = []
if fn is not None and self.rank == 0:
fn_out = os.path.join(self._out, fn)
hdulist = [pf.PrimaryHDU()]
else:
fn_out = None
hdulist = None
if gain is not None and gain != 0:
for phase in self.signal_estimate:
for estimate in phase:
mean_before = np.mean(estimate)
estimate[:] = (estimate - mean_before) / gain + mean_before
for phase in range(self._nphase4k):
tstart_phase = MPI.Wtime()
if self.rank == 0:
print('Estimating ADC correction for phase {}'.format(phase),
flush=True)
signal_ADU = self.signal_ADU[phase]
signal_estimate = self.signal_estimate[phase]
signal_offset = self.signal_offset[phase]
nl = [] # Additive offset between input and output signal
for sig_ADU, estimate in zip(signal_ADU, signal_estimate):
nl.append(sig_ADU - estimate)
bins = []
for sig in signal_estimate:
bins.append(np.floor(sig / self._wbin).astype(np.int32))
my_binmin = 99999999
my_binmax = -99999999
for binvec in bins:
my_binmin = min(my_binmin, np.amin(binvec))
my_binmax = max(my_binmax, np.amax(binvec))
binmin = self.comm.allreduce(my_binmin, MPI.MIN)
binmax = self.comm.allreduce(my_binmax, MPI.MAX)
bin_offset = binmin
nbin = binmax - binmin + 1
if nbin < 1:
raise RuntimeError(
'{} : ERROR in measure_correction: No valid bins '
'for phase = {} / {}. binmin, binmax = {}, {}, '
'my_binmin, my_binmax = {}, {}, nbin = {}'.format(
self.rank, phase + 1, self._nphase4k, binmin, binmax,
my_binmin, my_binmax, nbin))
for binvec in bins:
binvec -= bin_offset
my_rings = []
for binvec, sampvec, offset in zip(bins, nl, signal_offset):
hitmap = np.zeros(nbin, dtype=np.int32)
sigmap = np.zeros(nbin, dtype=np.float64)
destripe_tools.fast_hit_binning(binvec, hitmap)
destripe_tools.fast_binning(sampvec, binvec, sigmap)
bin_centers = (0.5 + np.arange(nbin) + bin_offset) * self._wbin
hit = hitmap != 0
hitmap = hitmap[hit].copy()
bin_centers = bin_centers[hit].copy()
sigmap = sigmap[hit].copy()
sigmap /= hitmap
# Fit a line to the ring measurement of NL
coeff, cov = self.fit_line(bin_centers, sigmap, hitmap)
slope = coeff[1]
slope_err = np.sqrt(cov[1, 1])
my_rings.append(
(bin_centers, sigmap, hitmap, offset, slope, slope_err))
# The ring offset optimization is done serially until we can
# find a nonlinear parallel solver
rings = self.comm.gather(my_rings, root=0)
if self.rank == 0:
# Flatten the ring list
rings = [ring for ringlist in rings for ring in ringlist]
if fn_out.endswith('.fits'):
fn = fn_out.replace(
'.fits', '_ring_data_phase{:02}.pck'.format(phase))
else:
fn = fn_out + '_ring_data_phase{:02}.pck'.format(phase)
pickle.dump(rings, open(fn, 'wb'), protocol=2)
print('ADC ring data saved in {}'.format(fn), flush=True)
polyorder = 10
ring_rms = []
for ring in rings:
ring_rms.append(np.std(ring[1]))
ring_rms = np.array(ring_rms)
outliers = np.isnan(ring_rms)
if ring_rms.size > 100:
for i in range(10):
good = np.logical_not(outliers)
mn = np.mean(ring_rms[good])
rms = np.std(ring_rms[good])
bad = np.abs(ring_rms - mn) > 4 * rms
bad[outliers] = False
nbad = np.sum(bad)
if nbad == 0:
break
outliers[bad] = True
nout = np.sum(outliers)
print(
'iter = {}: Discarding {} outlier RMS out of {}. '
'Total outliers: {}.'.format(
i, nbad, ring_rms.size, nout))
ring_len = []
for ring in rings:
ring_len.append(ring[0].size)
ring_len = np.array(ring_len)
if ring_len.size > 100:
for i in range(10):
good = np.logical_not(outliers)
smooth = flagged_running_average(
ring_len, outliers, 100)
rms = np.std((ring_len - smooth)[good])
bad = np.abs(ring_len - smooth) > 4 * rms
bad[outliers] = False
nbad = np.sum(bad)
if nbad == 0:
break
outliers[bad] = True
nout = np.sum(outliers)
print(
'iter = {}: Discarding {} outlier lengths out of '
'{}. Total outliers: {}.'.format(
i, nbad, ring_len.size, nout))
# Build an initial correction by integrating the
# ring-by-ring derivatives (slopes)
offset = []
deriv = []
err = []
for ring in rings:
offset_ring, deriv_ring, deriv_err = ring[3:6]
offset.append(offset_ring)
deriv.append(deriv_ring)
err.append(deriv_err)
offset = np.hstack(offset)
deriv = np.hstack(deriv)
err = np.hstack(err)
if offset.size > 100:
for i in range(10):
good = np.logical_not(outliers)
smooth = flagged_running_average(deriv, outliers, 100)
rms = np.std((deriv - smooth)[good])
bad = np.abs(deriv - smooth) > 4 * rms
bad[outliers] = False
nbad = np.sum(bad)
if nbad == 0:
break
outliers[bad] = True
nout = np.sum(outliers)
print('iter = {}: Discarding {} outlier slopes out of '
'{}. Total outliers: {}.'.format(
i, nbad, offset.size, nout))
good = np.logical_not(outliers)
offset = offset[good]
deriv = deriv[good]
ind = np.argsort(offset)
offset = offset[ind]
deriv = deriv[ind]
total_offset = np.zeros(offset.size, dtype=np.float64)
for i in range(offset.size - 1):
total_offset[i + 1] = total_offset[i] + deriv[i] * (
offset[i + 1] - offset[i])
w = offset[-1] - offset[0]
# Domain will shift with the offset correction
domain = [offset[0] - w / 10, offset[-1] + w / 10]
polyorder = min(polyorder, offset.size - 1)
# Omit the offset term
x0 = np.polynomial.legendre.Legendre.fit(
offset, total_offset, polyorder, domain=domain).coef[1:]
# Collapse pointing periods that have the same offset
collapsed_ring_lists = {}
wbin_offset = (domain[1] - domain[0]) / 1000
for (ring, outlier) in zip(rings, outliers):
if outlier:
continue
bin_centers, sigmap, hitmap, offset = ring[:4]
offset_bin = np.int(np.floor(offset / wbin_offset))
if offset_bin not in collapsed_ring_lists:
collapsed_ring_lists[offset_bin] = []
collapsed_ring_lists[offset_bin].append(ring)
collapsed_rings = []
for offset_bin, offset_rings in collapsed_ring_lists.items():
# co-add the rings that have the same offset
center_min = offset_rings[0][0][0]
center_max = offset_rings[0][0][-1]
for ring in offset_rings[1:]:
bin_centers = ring[0]
center_min = min(center_min, bin_centers[0])
center_max = max(center_max, bin_centers[-1])
nbin = np.int(
np.rint((center_max - center_min) / self._wbin)) + 1
all_bin_centers = center_min + np.arange(nbin) * self._wbin
all_sigmap = np.zeros(nbin, dtype=np.float64)
all_hitmap = np.zeros(nbin, dtype=np.float64)
for ring in offset_rings:
bin_centers, sigmap, hitmap, offset = ring[:4]
ind = np.searchsorted(all_bin_centers,
bin_centers,
side='left')
all_hitmap[ind] += hitmap
all_sigmap[ind] += sigmap * hitmap
good = all_hitmap != 0
all_bin_centers = all_bin_centers[good]
all_sigmap = all_sigmap[good]
all_hitmap = all_hitmap[good]
all_sigmap /= all_hitmap
collapsed_rings.append(
(all_bin_centers, all_sigmap, all_hitmap,
(offset_bin + .5) * wbin_offset))
# Collect the ring-by-ring vectors into single vectors
all_bin_centers = []
all_sigmaps = []
all_hitmaps = []
all_offsets = []
all_ranges = []
istart = 0
for ring in collapsed_rings:
bin_centers, sigmap, hitmap, offset = ring
all_bin_centers.append(bin_centers)
all_sigmaps.append(sigmap)
all_hitmaps.append(hitmap)
all_offsets.append(offset)
all_ranges.append(slice(istart, istart + sigmap.size))
istart += sigmap.size
all_bin_centers = np.hstack(all_bin_centers).astype(np.float64)
all_sigmaps = np.hstack(all_sigmaps).astype(np.float64)
all_hitmaps = np.hstack(all_hitmaps).astype(np.float64)
all_offsets = np.hstack(all_offsets).astype(np.float64)
def get_nl(param, all_bin_centers, all_sigmaps, all_hitmaps,
all_offsets, domain):
# Add zeroth term, this is not a free parameter
pfull = np.append([0], param)
get_offset_nl = np.polynomial.legendre.Legendre(
pfull, domain=domain)
# Adjust the zeroth term to minimize offset
x = np.linspace(domain[0], domain[1], 100)
get_offset_nl.coef[0] = -np.median(get_offset_nl(x))
all_bins = all_bin_centers.copy()
all_nl = all_sigmaps.copy()
for ind, off in zip(all_ranges, all_offsets):
delta = get_offset_nl(off)
all_bins[ind] -= delta
all_nl[ind] += delta
all_bins = np.floor(all_bins / self._wbin).astype(np.int64)
all_hits = all_hitmaps
binmin = np.amin(all_bins)
binmax = np.amax(all_bins)
nbin = binmax - binmin + 1
all_bins -= binmin
hitmap = np.zeros(nbin, dtype=np.float64)
nlmap = np.zeros(nbin, dtype=np.float64)
destripe_tools.fast_binning(all_hits,
all_bins.astype(np.int32),
hitmap)
destripe_tools.fast_binning(all_nl * all_hits,
all_bins.astype(np.int32),
nlmap)
hit = hitmap != 0
nlmap[hit] /= hitmap[hit]
bin_centers = (0.5 + np.arange(nlmap.size) +
binmin) * self._wbin
nlmap_offset = get_offset_nl(bin_centers)
return (nlmap, nlmap_offset, hitmap, all_nl, all_hits,
all_bins, binmin)
def get_nl_resid(param, all_bin_centers, all_sigmaps,
all_hitmaps, all_offsets, domain):
# Measure the residual between signal/estimate
# difference and a binned+unrolled version of the
# difference
(nlmap, nlmap_offset, hitmap, nl, hits, bins,
binmin) = get_nl(param, all_bin_centers, all_sigmaps,
all_hitmaps, all_offsets, domain)
nl_from_map = nlmap[bins]
nl_from_offset_map = nlmap_offset[bins]
return np.hstack([(nl - nl_from_map) * np.log(hits),
(nl - nl_from_offset_map) * np.log(hits)
])
start = MPI.Wtime()
try:
xopt, _, infodict, mesg, ierr = scipy.optimize.leastsq(
get_nl_resid,
x0,
args=(all_bin_centers, all_sigmaps, all_hitmaps,
all_offsets, domain),
full_output=True,
Dfun=None,
maxfev=1000)
except Exception as e:
print('leastsq failed with {}'.format(e))
raise
if ierr not in [1, 2, 3, 4]:
raise RuntimeError('leastsq failed with {}'.format(mesg))
stop = MPI.Wtime()
print('Nonlinear optimization finished in {:.2f} s after {} '
'evaluations.'.format(stop - start, infodict['nfev']),
flush=True)
print('Uncorrected residual: {}'.format(
np.std(
get_nl_resid(x0 * 0, all_bin_centers, all_sigmaps,
all_hitmaps, all_offsets, domain))))
print('First guess residual: {}'.format(
np.std(
get_nl_resid(x0, all_bin_centers, all_sigmaps,
all_hitmaps, all_offsets, domain))))
print(' Optimized residual: {}'.format(
np.std(
get_nl_resid(xopt, all_bin_centers, all_sigmaps,
all_hitmaps, all_offsets, domain))),
flush=True)
nlmap, _, hitmap, nl, _, bins, binmin = get_nl(
xopt, all_bin_centers, all_sigmaps, all_hitmaps,
all_offsets, domain)
bin_centers = (0.5 + np.arange(nlmap.size) + binmin) \
* self._wbin
good = hitmap > 100
nlmap = nlmap[good].copy()
hitmap = hitmap[good].copy()
bin_centers = bin_centers[good].copy()
# Apply a median filter to remove bin-to-bin variation
# and make the poorly sampled end points usable
nwin = min(101, (nlmap.size // 8) * 4 + 1)
good = np.ones(bin_centers.size, dtype=np.bool)
good[:nwin] = False
good[-nwin:] = False
steps = np.diff(bin_centers)
step = np.median(steps)
for i in np.argwhere(steps > nwin * step / 10).ravel():
good[i - nwin // 2:i + nwin // 2] = False
bin_centers = scipy.signal.medfilt(bin_centers, nwin)[good]
nlmap = scipy.signal.medfilt(nlmap, nwin)[good]
else:
bin_centers = None
hitmap = None
nlmap = None
bin_centers = self.comm.bcast(bin_centers, root=0)
hitmap = self.comm.bcast(hitmap, root=0)
sigmap = self.comm.bcast(nlmap)
V_in, V_delta = bin_centers, sigmap
V_out = V_in + V_delta
# Stretch the last two bins to get a rough extrapolation
V_out[0] = 0
V_out[-1] = 1e7
self.corrections.append([V_out, -V_delta])
if hdulist is not None:
phasename = 'phase{:02}'.format(phase)
cols = []
cols.append(pf.Column(name='V_out', format='D', array=V_out))
cols.append(
pf.Column(name='V_corr', format='D', array=-V_delta))
hdu = pf.BinTableHDU.from_columns(pf.ColDefs(cols))
hdu.header['extname'] = phasename
hdulist.append(hdu)
tstop_phase = MPI.Wtime()
if self.rank == 0:
print('ADC correction for phase {} done in {:.2f} s'.format(
phase, tstop_phase - tstart_phase),
flush=True)
if hdulist is not None:
if os.path.isfile(fn_out):
os.remove(fn_out)
pf.HDUList(hdulist).writeto(fn_out)
print('ADC correction saved in {}'.format(fn_out), flush=True)
return
nside = 256
file_sync = '/Users/reijo/data/PR2/foregroundmaps/' \
'COM_CompMap_Synchrotron-commander_0256_R2.00.fits'
file_sync_pol = '/Users/reijo/data/PR2/foregroundmaps/' \
'COM_CompMap_SynchrotronPol-commander_0256_R2.00.fits'
file_freefree = '/Users/reijo/data/PR2/foregroundmaps/' \
'COM_CompMap_freefree-commander_0256_R2.00.fits'
file_ame = '/Users/reijo/data/PR2/foregroundmaps/' \
'COM_CompMap_AME-commander_0256_R2.00.fits'
file_dust = '/Users/reijo/data/PR2/foregroundmaps/' \
'COM_CompMap_dust-commander_0256_R2.00.fits'
file_dust_pol = '/Users/reijo/data/PR2/foregroundmaps/' \
'COM_CompMap_DustPol-commander_1024_R2.00.fits'
t1 = MPI.Wtime()
skymodel = SkyModel(nside, file_sync, file_sync_pol, file_freefree,
file_ame, file_dust, file_dust_pol, MPI.COMM_WORLD)
t2 = MPI.Wtime()
print('{:4} : Initialized sky model in {:.2f} s'.format(
skymodel.rank, t2 - t1),
flush=True)
skymodel.cache.report()
norm = 1e6
amp = 3e2
pol_amp = 5e1
deriv_amp = 10
pol_deriv_amp = 1
freqs = [30, 44, 70, 100, 143, 217, 353]
def build_npp(args, comm, data, localsm, subnpix, detweights, flag_name,
common_flag_name):
""" Build pixel-pixel noise covariance matrices.
"""
if not args.skip_bin:
if comm.comm_world.rank == 0:
print('Preparing distributed map', flush=args.flush)
start0 = MPI.Wtime()
start = start0
autotimer = timing.auto_timer()
npix = 12 * args.nside**2
# construct distributed maps to store the covariance,
# noise weighted map, and hits
invnpp = tm.DistPixels(comm=comm.comm_world,
size=npix,
nnz=6,
dtype=np.float64,
submap=subnpix,
local=localsm)
invnpp.data.fill(0.0)
hits = tm.DistPixels(comm=comm.comm_world,
size=npix,
nnz=1,
dtype=np.int64,
submap=subnpix,
local=localsm)
hits.data.fill(0)
zmap = tm.DistPixels(comm=comm.comm_world,
size=npix,
nnz=3,
dtype=np.float64,
submap=subnpix,
local=localsm)
comm.comm_world.barrier()
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print(' - distobjects initialized in {:.3f} s'
''.format(stop - start),
flush=args.flush)
start = stop
invnpp_group = None
hits_group = None
zmap_group = None
if comm.comm_group.size < comm.comm_world.size:
invnpp_group = tm.DistPixels(comm=comm.comm_group,
size=npix,
nnz=6,
dtype=np.float64,
submap=subnpix,
local=localsm)
invnpp_group.data.fill(0.0)
hits_group = tm.DistPixels(comm=comm.comm_group,
size=npix,
nnz=1,
dtype=np.int64,
submap=subnpix,
local=localsm)
hits_group.data.fill(0)
zmap_group = tm.DistPixels(comm=comm.comm_group,
size=npix,
nnz=3,
dtype=np.float64,
submap=subnpix,
local=localsm)
comm.comm_group.barrier()
stop = MPI.Wtime()
if comm.comm_group.rank == 0:
print(' - group distobjects initialized in {:.3f} s'
''.format(stop - start),
flush=args.flush)
start = stop
# compute the hits and covariance once, since the pointing and noise
# weights are fixed.
build_invnpp = tm.OpAccumDiag(detweights=detweights,
invnpp=invnpp,
hits=hits,
flag_name=flag_name,
common_flag_name=common_flag_name,
common_flag_mask=args.common_flag_mask)
build_invnpp.exec(data)
comm.comm_world.barrier()
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print(' - distobjects accumulated in {:.3f} s'
''.format(stop - start),
flush=args.flush)
start = stop
invnpp.allreduce()
if not args.skip_hits:
hits.allreduce()
comm.comm_world.barrier()
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print(' - distobjects reduced in {:.3f} s'.format(stop - start),
flush=args.flush)
start = stop
if invnpp_group is not None:
build_invnpp_group = tm.OpAccumDiag(
detweights=detweights,
invnpp=invnpp_group,
hits=hits_group,
flag_name=flag_name,
common_flag_name=common_flag_name,
common_flag_mask=args.common_flag_mask)
build_invnpp_group.exec(data)
comm.comm_group.barrier()
stop = MPI.Wtime()
if comm.comm_group.rank == 0:
print(' - group distobjects accumulated in {:.3f} s'
''.format(stop - start),
flush=args.flush)
start = stop
invnpp_group.allreduce()
if not args.skip_hits:
hits_group.allreduce()
comm.comm_group.barrier()
stop = MPI.Wtime()
if comm.comm_group.rank == 0:
print(' - group distobjects reduced in {:.3f} s'
''.format(stop - start),
flush=args.flush)
start = stop
if not args.skip_hits:
fn = '{}/hits.fits'.format(args.outdir)
if args.zip:
fn += '.gz'
hits.write_healpix_fits(fn)
comm.comm_world.barrier()
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print(' - Writing hit map to {} took {:.3f} s'
''.format(fn, stop - start),
flush=args.flush)
start = stop
del hits
if hits_group is not None:
if not args.skip_hits:
fn = '{}/hits_group_{:04}.fits'.format(args.outdir, comm.group)
if args.zip:
fn += '.gz'
hits_group.write_healpix_fits(fn)
comm.comm_group.barrier()
stop = MPI.Wtime()
if comm.comm_group.rank == 0:
print(' - Writing group hit map to {} took {:.3f} s'
''.format(fn, stop - start),
flush=args.flush)
start = stop
del hits_group
if not args.skip_hits:
fn = '{}/invnpp.fits'.format(args.outdir)
if args.zip:
fn += '.gz'
invnpp.write_healpix_fits(fn)
comm.comm_world.barrier()
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print(' - Writing N_pp^-1 to {} took {:.3f} s'
''.format(fn, stop - start),
flush=args.flush)
start = stop
if not args.skip_hits:
if invnpp_group is not None:
fn = '{}/invnpp_group_{:04}.fits'.format(
args.outdir, comm.group)
if args.zip:
fn += '.gz'
invnpp_group.write_healpix_fits(fn)
comm.comm_group.barrier()
stop = MPI.Wtime()
if comm.comm_group.rank == 0:
print(' - Writing group N_pp^-1 to {} took {:.3f} s'
''.format(fn, stop - start),
flush=args.flush)
start = stop
# invert it
tm.covariance_invert(invnpp, 1.0e-3)
comm.comm_world.barrier()
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print(' - Inverting N_pp^-1 took {:.3f} s'.format(stop - start),
flush=args.flush)
start = stop
if not args.skip_hits:
fn = '{}/npp.fits'.format(args.outdir)
if args.zip:
fn += '.gz'
invnpp.write_healpix_fits(fn)
comm.comm_world.barrier()
stop = MPI.Wtime()
if comm.comm_world.rank == 0:
print(' - Writing N_pp to {} took {:.3f} s'
''.format(fn, stop - start),
flush=args.flush)
start = stop
if invnpp_group is not None:
tm.covariance_invert(invnpp_group, 1.0e-3)
comm.comm_group.barrier()
stop = MPI.Wtime()
if comm.comm_group.rank == 0:
print(' - Inverting group N_pp^-1 took {:.3f} s'
''.format(stop - start),
flush=args.flush)
start = stop
if not args.skip_hits:
fn = '{}/npp_group_{:04}.fits'.format(args.outdir, comm.group)
if args.zip:
fn += '.gz'
invnpp_group.write_healpix_fits(fn)
comm.comm_group.barrier()
stop = MPI.Wtime()
if comm.comm_group.rank == 0:
print(' - Writing group N_pp to {} took {:.3f} s'.format(
fn, stop - start),
flush=args.flush)
start = stop
stop = MPI.Wtime()
if comm.comm_group.rank == 0:
print('Building Npp took {:.3f} s'.format(stop - start0),
flush=args.flush)
return invnpp, zmap, invnpp_group, zmap_group, flag_name, common_flag_name
def _observe_atmosphere(
self,
sim,
tod,
comm,
prefix,
common_ref,
istart,
nind,
ind,
scan_range,
times,
absorption,
):
azmin, azmax, elmin, elmax = scan_range
nsamp = tod.local_samples[1]
if self._report_timing:
comm.Barrier()
tstart = MPI.Wtime()
if comm.rank == 0:
print(prefix + "Observing the atmosphere", flush=self._flush)
for det in tod.local_dets:
# Cache the output signal
cachename = "{}_{}".format(self._out, det)
if tod.cache.exists(cachename):
ref = tod.cache.reference(cachename)
else:
ref = tod.cache.create(cachename, np.float64, (nsamp,))
# Cache the output flags
flag_ref = tod.local_flags(det, self._flag_name)
if self._apply_flags:
good = np.logical_and(
common_ref[ind] & self._common_flag_mask == 0,
flag_ref[ind] & self._flag_mask == 0,
)
ngood = np.sum(good)
else:
try:
good = common_ref[ind] & tod.UNSTABLE == 0
ngood = np.sum(good)
except:
good = slice(0, nind)
ngood = nind
if ngood == 0:
continue
try:
# Some TOD classes provide a shortcut to Az/El
az, el = tod.read_azel(detector=det, local_start=istart, n=nind)
az = az[good]
el = el[good]
except Exception as e:
azelquat = tod.read_pntg(
detector=det, local_start=istart, n=nind, azel=True
)[good]
# Convert Az/El quaternion of the detector back into
# angles for the simulation.
theta, phi = qa.to_position(azelquat)
# Azimuth is measured in the opposite direction
# than longitude
az = 2 * np.pi - phi
el = np.pi / 2 - theta
atmdata = np.zeros(ngood, dtype=np.float64)
if np.ptp(az) < np.pi:
azmin_det = np.amin(az)
azmax_det = np.amax(az)
else:
# Scanning across the zero azimuth.
azmin_det = np.amin(az[az > np.pi]) - 2 * np.pi
azmax_det = np.amax(az[az < np.pi])
elmin_det = np.amin(el)
elmax_det = np.amax(el)
if (
not (azmin <= azmin_det and azmax_det <= azmax)
and not (
azmin <= azmin_det - 2 * np.pi and azmax_det - 2 * np.pi <= azmax
)
) or not (elmin <= elmin_det and elmin_det <= elmax):
raise RuntimeError(
prefix + "Detector Az/El: [{:.5f}, {:.5f}], "
"[{:.5f}, {:.5f}] is not contained in "
"[{:.5f}, {:.5f}], [{:.5f} {:.5f}]"
"".format(
azmin_det,
azmax_det,
elmin_det,
elmax_det,
azmin,
azmax,
elmin,
elmax,
)
)
# Integrate detector signal
err = atm_sim_observe(sim, times[ind], az, el, atmdata, ngood, 0)
if err != 0:
# Observing failed
print(
prefix + "OpSimAtmosphere: Observing FAILED. "
"det = {}, rank = {}".format(det, comm.rank),
flush=self._flush,
)
atmdata[:] = 0
flag_ref[ind] = 255
if self._gain:
atmdata *= self._gain
if absorption is not None:
# Apply the frequency-dependent absorption-coefficient
atmdata *= absorption
ref[ind][good] += atmdata
del ref
err = atm_sim_free(sim)
if err != 0:
raise RuntimeError(prefix + "Failed to free simulation.")
if self._report_timing:
comm.Barrier()
tstop = MPI.Wtime()
if comm.rank == 0 and tstop - tstart > 1:
print(
prefix + "OpSimAtmosphere: Observed atmosphere "
"in {:.2f} s".format(tstop - tstart),
flush=self._flush,
)
return
def exec(self, data):
"""
Generate atmosphere timestreams.
This iterates over all observations and detectors and generates
the atmosphere timestreams.
Args:
data (toast.Data): The distributed data.
"""
autotimer = timing.auto_timer(type(self).__name__)
group = data.comm.group
for obs in data.obs:
try:
obsname = obs['name']
except Exception:
obsname = 'observation'
prefix = '{} : {} : '.format(group, obsname)
tod = self._get_from_obs('tod', obs)
comm = tod.mpicomm
obsindx = self._get_from_obs('id', obs)
telescope = self._get_from_obs('telescope_id', obs)
site = self._get_from_obs('site_id', obs)
altitude = self._get_from_obs('altitude', obs)
weather = self._get_from_obs('weather', obs)
fp_radius = np.radians(self._get_from_obs('fpradius', obs))
# Get the observation time span and initialize the weather
# object if one is provided.
times = tod.local_times()
tmin = times[0]
tmax = times[-1]
tmin_tot = comm.allreduce(tmin, op=MPI.MIN)
tmax_tot = comm.allreduce(tmax, op=MPI.MAX)
weather.set(site, self._realization, tmin_tot)
"""
The random number generator accepts a key and a counter,
each made of two 64bit integers.
Following tod_math.py we set
key1 = realization * 2^32 + telescope * 2^16 + component
key2 = obsindx * 2^32
counter1 = currently unused (0)
counter2 = sample in stream (incremented internally in the atm code)
"""
key1 = self._realization * 2 ** 32 + telescope * 2 ** 16 \
+ self._component
key2 = site * 2**16 + obsindx
counter1 = 0
counter2 = 0
if self._freq is not None:
absorption = atm_get_absorption_coefficient(
altitude, weather.air_temperature,
weather.surface_pressure, weather.pwv, self._freq)
loading = atm_get_atmospheric_loading(altitude,
weather.air_temperature,
weather.surface_pressure,
weather.pwv, self._freq)
tod.meta['loading'] = loading
else:
absorption = None
if self._cachedir is None:
cachedir = None
else:
# The number of atmospheric realizations can be large. Use
# sub-directories under cachedir.
subdir = str(int((obsindx % 1000) // 100))
subsubdir = str(int((obsindx % 100) // 10))
subsubsubdir = str(obsindx % 10)
cachedir = os.path.join(self._cachedir, subdir, subsubdir,
subsubsubdir)
if comm.rank == 0:
try:
os.makedirs(cachedir)
except FileExistsError:
pass
comm.Barrier()
if comm.rank == 0:
print(prefix + 'Setting up atmosphere simulation',
flush=self._flush)
comm.Barrier()
# Cache the output common flags
common_ref = tod.local_common_flags(self._common_flag_name)
# Read the extent of the AZ/EL boresight pointing, and use that
# to compute the range of angles needed for simulating the slab.
(min_az_bore, max_az_bore, min_el_bore,
max_el_bore) = tod.scan_range
# print("boresight scan range = {}, {}, {}, {}".format(
# min_az_bore, max_az_bore, min_el_bore, max_el_bore))
# Use a fixed focal plane radius so that changing the actual
# set of detectors will not affect the simulated atmosphere.
elfac = 1 / np.cos(max_el_bore + fp_radius)
azmin = min_az_bore - fp_radius * elfac
azmax = max_az_bore + fp_radius * elfac
if azmin < -2 * np.pi:
azmin += 2 * np.pi
azmax += 2 * np.pi
elif azmax > 2 * np.pi:
azmin -= 2 * np.pi
azmax -= 2 * np.pi
elmin = min_el_bore - fp_radius
elmax = max_el_bore + fp_radius
azmin = comm.allreduce(azmin, op=MPI.MIN)
azmax = comm.allreduce(azmax, op=MPI.MAX)
elmin = comm.allreduce(elmin, op=MPI.MIN)
elmax = comm.allreduce(elmax, op=MPI.MAX)
if elmin < 0 or elmax > np.pi / 2:
raise RuntimeError(
'Error in CES elevation: elmin = {:.2f}, elmax = {:.2f}'
''.format(elmin, elmax))
comm.Barrier()
# Loop over the time span in "wind_time"-sized chunks.
# wind_time is intended to reflect the correlation length
# in the atmospheric noise.
tmin = tmin_tot
istart = 0
while tmin < tmax_tot:
while times[istart] < tmin:
istart += 1
tmax = tmin + self._wind_time
if tmax < tmax_tot:
# Extend the scan to the next turnaround
istop = istart
while istop < times.size and times[istop] < tmax:
istop += 1
while istop < times.size and (common_ref[istop]
| tod.TURNAROUND == 0):
istop += 1
if istop < times.size:
tmax = times[istop]
else:
tmax = tmax_tot
else:
tmax = tmax_tot
istop = times.size
ind = slice(istart, istop)
nind = istop - istart
if self._report_timing:
comm.Barrier()
tstart = MPI.Wtime()
comm.Barrier()
if comm.rank == 0:
print(prefix + 'Instantiating the atmosphere for t = {}'
''.format(tmin - tmin_tot),
flush=self._flush)
comm.Barrier()
T0_center = weather.air_temperature
wx = weather.west_wind
wy = weather.south_wind
w_center = np.sqrt(wx**2 + wy**2)
wdir_center = np.arctan2(wy, wx)
sim = atm_sim_alloc(
azmin, azmax, elmin, elmax, tmin, tmax, self._lmin_center,
self._lmin_sigma, self._lmax_center, self._lmax_sigma,
w_center, 0, wdir_center, 0, self._z0_center,
self._z0_sigma, T0_center, 0, self._zatm, self._zmax,
self._xstep, self._ystep, self._zstep, self._nelem_sim_max,
self._verbosity, comm, self._gangsize, key1, key2,
counter1, counter2, cachedir)
if sim == 0:
raise RuntimeError(prefix +
'Failed to allocate simulation')
if self._report_timing:
comm.Barrier()
tstop = MPI.Wtime()
if comm.rank == 0 and tstop - tstart > 1:
print(prefix + 'OpSimAtmosphere: Initialized '
'atmosphere in {:.2f} s'.format(tstop - tstart),
flush=self._flush)
tstart = tstop
comm.Barrier()
use_cache = cachedir is not None
if comm.rank == 0:
fname = os.path.join(
cachedir, '{}_{}_{}_{}_metadata.txt'.format(
key1, key2, counter1, counter2))
if use_cache and os.path.isfile(fname):
print(prefix + 'Loading the atmosphere for t = {} '
'from {}'.format(tmin - tmin_tot, fname),
flush=self._flush)
cached = True
else:
print(prefix + 'Simulating the atmosphere for t = {}'
''.format(tmin - tmin_tot),
flush=self._flush)
cached = False
err = atm_sim_simulate(sim, use_cache)
if err != 0:
raise RuntimeError(prefix + 'Simulation failed.')
# Advance the sample counter in case wind_time broke the
# observation in parts
counter2 += 100000000
if self._report_timing:
comm.Barrier()
tstop = MPI.Wtime()
if comm.rank == 0 and tstop - tstart > 1:
if cached:
op = 'Loaded'
else:
op = 'Simulated'
print(prefix + 'OpSimAtmosphere: {} atmosphere in '
'{:.2f} s'.format(op, tstop - tstart),
flush=self._flush)
tstart = tstop
if self._verbosity > 0:
self._plot_snapshots(sim, prefix, obsname, azmin, azmax,
elmin, elmax, tmin, tmax, comm)
nsamp = tod.local_samples[1]
if self._report_timing:
comm.Barrier()
tstart = MPI.Wtime()
if comm.rank == 0:
print(prefix + 'Observing the atmosphere',
flush=self._flush)
for det in tod.local_dets:
# Cache the output signal
cachename = '{}_{}'.format(self._out, det)
if tod.cache.exists(cachename):
ref = tod.cache.reference(cachename)
else:
ref = tod.cache.create(cachename, np.float64,
(nsamp, ))
# Cache the output flags
flag_ref = tod.local_flags(det, self._flag_name)
if self._apply_flags:
good = np.logical_and(
common_ref[ind] & self._common_flag_mask == 0,
flag_ref[ind] & self._flag_mask == 0)
ngood = np.sum(good)
if ngood == 0:
continue
azelquat = tod.read_pntg(detector=det,
local_start=istart,
n=nind,
azel=True)[good]
atmdata = np.zeros(ngood, dtype=np.float64)
else:
ngood = nind
azelquat = tod.read_pntg(detector=det,
local_start=istart,
n=nind,
azel=True)
atmdata = np.zeros(nind, dtype=np.float64)
# Convert Az/El quaternion of the detector back into
# angles for the simulation.
theta, phi, _ = qa.to_angles(azelquat)
# Azimuth is measured in the opposite direction
# than longitude
az = 2 * np.pi - phi
el = np.pi / 2 - theta
if np.ptp(az) < np.pi:
azmin_det = np.amin(az)
azmax_det = np.amax(az)
else:
# Scanning across the zero azimuth.
azmin_det = np.amin(az[az > np.pi]) - 2 * np.pi
azmax_det = np.amax(az[az < np.pi])
elmin_det = np.amin(el)
elmax_det = np.amax(el)
if ((not (azmin <= azmin_det and azmax_det <= azmax)
and not (azmin <= azmin_det - 2 * np.pi
and azmax_det - 2 * np.pi <= azmax)) or
not (elmin <= elmin_det and elmin_det <= elmax)):
raise RuntimeError(
prefix + 'Detector Az/El: [{:.5f}, {:.5f}], '
'[{:.5f}, {:.5f}] is not contained in '
'[{:.5f}, {:.5f}], [{:.5f} {:.5f}]'
''.format(azmin_det, azmax_det, elmin_det,
elmax_det, azmin, azmax, elmin, elmax))
# Integrate detector signal
err = atm_sim_observe(sim, times[ind], az, el, atmdata,
ngood, 0)
if err != 0:
# Observing failed
print(prefix + 'OpSimAtmosphere: Observing FAILED. '
'det = {}, rank = {}'.format(det, comm.rank),
flush=self._flush)
atmdata[:] = 0
flag_ref[ind] = 255
if self._gain:
atmdata *= self._gain
if absorption is not None:
# Apply the frequency-dependent absorption-coefficient
atmdata *= absorption
if self._apply_flags:
ref[ind][good] += atmdata
else:
ref[ind] += atmdata
del ref
err = atm_sim_free(sim)
if err != 0:
raise RuntimeError(prefix + 'Failed to free simulation.')
if self._report_timing:
comm.Barrier()
tstop = MPI.Wtime()
if comm.rank == 0 and tstop - tstart > 1:
print(prefix + 'OpSimAtmosphere: Observed atmosphere '
'in {:.2f} s'.format(tstop - tstart),
flush=self._flush)
tmin = tmax
return
def main():
if MPI.COMM_WORLD.rank == 0:
print("Running with {} processes".format(MPI.COMM_WORLD.size),
flush=True)
global_start = MPI.Wtime()
parser = argparse.ArgumentParser(
description="Read existing data and make a simple map.",
fromfile_prefix_chars="@",
)
parser.add_argument(
"--groupsize",
required=False,
type=int,
default=0,
help="size of processor groups used to distribute "
"observations",
)
parser.add_argument(
"--hwprpm",
required=False,
type=float,
default=0.0,
help="The rate (in RPM) of the HWP rotation",
)
parser.add_argument(
"--samplerate",
required=False,
default=100.0,
type=np.float,
help="Detector sample rate (Hz)",
)
parser.add_argument("--outdir",
required=False,
default="out",
help="Output directory")
parser.add_argument("--nside",
required=False,
type=int,
default=64,
help="Healpix NSIDE")
parser.add_argument(
"--subnside",
required=False,
type=int,
default=8,
help="Distributed pixel sub-map NSIDE",
)
parser.add_argument("--coord",
required=False,
default="E",
help="Sky coordinate system [C,E,G]")
parser.add_argument(
"--baseline",
required=False,
type=float,
default=60.0,
help="Destriping baseline length (seconds)",
)
parser.add_argument(
"--noisefilter",
required=False,
default=False,
action="store_true",
help="Destripe with the noise filter enabled",
)
parser.add_argument(
"--madam",
required=False,
default=False,
action="store_true",
help="If specified, use libmadam for map-making",
)
parser.add_argument("--madampar",
required=False,
default=None,
help="Madam parameter file")
parser.add_argument(
"--polyorder",
required=False,
type=int,
help="Polynomial order for the polyfilter",
)
parser.add_argument(
"--wbin_ground",
required=False,
type=float,
help="Ground template bin width [degrees]",
)
parser.add_argument(
"--flush",
required=False,
default=False,
action="store_true",
help="Flush every print statement.",
)
parser.add_argument("--tidas",
required=False,
default=None,
help="Input TIDAS volume")
parser.add_argument("--tidas_detgroup",
required=False,
default=None,
help="TIDAS detector group")
parser.add_argument("--spt3g",
required=False,
default=None,
help="Input SPT3G data directory")
parser.add_argument(
"--spt3g_prefix",
required=False,
default=None,
help="SPT3G data frame file prefix",
)
parser.add_argument(
"--common_flag_mask",
required=False,
default=0,
type=np.uint8,
help="Common flag mask",
)
parser.add_argument(
"--debug",
required=False,
default=False,
action="store_true",
help="Write data distribution info and focalplane plot",
)
args = timing.add_arguments_and_parse(parser, timing.FILE(noquotes=True))
# args = parser.parse_args(sys.argv)
autotimer = timing.auto_timer("@{}".format(timing.FILE()))
if (args.tidas is not None) and (args.spt3g is not None):
raise RuntimeError("Cannot read two datasets!")
if (args.tidas is None) and (args.spt3g is None):
raise RuntimeError("No dataset specified!")
if args.tidas is not None:
if not tt.tidas_available:
raise RuntimeError("TIDAS not found- cannot load")
if args.spt3g is not None:
if not tt.spt3g_available:
raise RuntimeError("SPT3G not found- cannot load")
groupsize = args.groupsize
if groupsize == 0:
groupsize = MPI.COMM_WORLD.size
# Pixelization
nside = args.nside
npix = 12 * args.nside * args.nside
subnside = args.subnside
if subnside > nside:
subnside = nside
subnpix = 12 * subnside * subnside
# This is the 2-level toast communicator.
if MPI.COMM_WORLD.size % groupsize != 0:
if MPI.COMM_WORLD.rank == 0:
print(
"WARNING: process groupsize does not evenly divide into "
"total number of processes",
flush=True,
)
comm = toast.Comm(world=MPI.COMM_WORLD, groupsize=groupsize)
# Create output directory
mtime = MPI.Wtime()
if comm.comm_world.rank == 0:
if not os.path.isdir(args.outdir):
os.makedirs(args.outdir)
mtime = elapsed(comm.comm_world, mtime, "Creating output directory")
# The distributed timestream data
data = None
if args.tidas is not None:
if args.tidas_detgroup is None:
raise RuntimeError("you must specify the detector group")
data = tds.load_tidas(
comm,
comm.group_size,
args.tidas,
"r",
args.tidas_detgroup,
tds.TODTidas,
group_dets=args.tidas_detgroup,
distintervals="chunks",
)
if args.spt3g is not None:
if args.spt3g_prefix is None:
raise RuntimeError("you must specify the frame file prefix")
data = s3g.load_spt3g(
comm,
comm.group_size,
args.spt3g,
args.spt3g_prefix,
s3g.obsweight_spt3g,
s3g.TOD3G,
)
mtime = elapsed(comm.comm_world, mtime, "Distribute data")
# In debug mode, print out data distribution information
if args.debug:
handle = None
if comm.comm_world.rank == 0:
handle = open("{}_distdata.txt".format(args.outdir), "w")
data.info(handle)
if comm.comm_world.rank == 0:
handle.close()
mtime = elapsed(comm.comm_world, mtime,
"Dumping debug data distribution")
if comm.comm_world.rank == 0:
outfile = "{}_focalplane.png".format(args.outdir)
set_backend()
# Just plot the dets from the first TOD
temptod = data.obs[0]["tod"]
# FIXME: change this once we store det info in the metadata.
dfwhm = {x: 10.0 for x in temptod.detectors}
tt.plot_focalplane(temptod.detoffset(),
10.0,
10.0,
outfile,
fwhm=dfwhm)
comm.comm_world.barrier()
mtime = elapsed(comm.comm_world, mtime, "Plotting debug focalplane")
# Compute pointing matrix
pointing = tt.OpPointingHpix(nside=args.nside,
nest=True,
mode="IQU",
hwprpm=args.hwprpm)
pointing.exec(data)
mtime = elapsed(comm.comm_world, mtime, "Expand pointing")
# Mapmaking.
# FIXME: We potentially have a different noise model for every
# observation. We need to have both spt3g and tidas format Noise
# classes which read the information from disk. Then the mapmaking
# operators need to get these noise weights from each observation.
detweights = {d: 1.0 for d in data.obs[0]["tod"].detectors}
if not args.madam:
if comm.comm_world.rank == 0:
print("Not using Madam, will only make a binned map!", flush=True)
# Filter data if desired
if args.polyorder:
polyfilter = tt.OpPolyFilter(
order=args.polyorder, common_flag_mask=args.common_flag_mask)
polyfilter.exec(data)
mtime = elapsed(comm.comm_world, mtime, "Polynomial filtering")
if args.wbin_ground:
groundfilter = tt.OpGroundFilter(
wbin=args.wbin_ground, common_flag_mask=args.common_flag_mask)
groundfilter.exec(data)
mtime = elapsed(comm.comm_world, mtime,
"Ground template filtering")
# Compute pixel space distribution
lc = tm.OpLocalPixels()
localpix = lc.exec(data)
if localpix is None:
raise RuntimeError(
"Process {} has no hit pixels. Perhaps there are fewer "
"detectors than processes in the group?".format(
comm.comm_world.rank))
localsm = np.unique(np.floor_divide(localpix, subnpix))
mtime = elapsed(comm.comm_world, mtime, "Compute local submaps")
# construct distributed maps to store the covariance,
# noise weighted map, and hits
mtime = MPI.Wtime()
invnpp = tm.DistPixels(
comm=comm.comm_world,
size=npix,
nnz=6,
dtype=np.float64,
submap=subnpix,
local=localsm,
)
hits = tm.DistPixels(
comm=comm.comm_world,
size=npix,
nnz=1,
dtype=np.int64,
submap=subnpix,
local=localsm,
)
zmap = tm.DistPixels(
comm=comm.comm_world,
size=npix,
nnz=3,
dtype=np.float64,
submap=subnpix,
local=localsm,
)
# compute the hits and covariance.
invnpp.data.fill(0.0)
hits.data.fill(0)
build_invnpp = tm.OpAccumDiag(
detweights=detweights,
invnpp=invnpp,
hits=hits,
common_flag_mask=args.common_flag_mask,
)
build_invnpp.exec(data)
invnpp.allreduce()
hits.allreduce()
mtime = elapsed(comm.comm_world, mtime, "Building hits and N_pp^-1")
hits.write_healpix_fits("{}_hits.fits".format(args.outdir))
invnpp.write_healpix_fits("{}_invnpp.fits".format(args.outdir))
mtime = elapsed(comm.comm_world, mtime, "Writing hits and N_pp^-1")
# invert it
tm.covariance_invert(invnpp, 1.0e-3)
mtime = elapsed(comm.comm_world, mtime, "Inverting N_pp^-1")
invnpp.write_healpix_fits("{}_npp.fits".format(args.outdir))
mtime = elapsed(comm.comm_world, mtime, "Writing N_pp")
zmap.data.fill(0.0)
build_zmap = tm.OpAccumDiag(zmap=zmap,
detweights=detweights,
common_flag_mask=args.common_flag_mask)
build_zmap.exec(data)
zmap.allreduce()
mtime = elapsed(comm.comm_world, mtime, "Building noise weighted map")
tm.covariance_apply(invnpp, zmap)
mtime = elapsed(comm.comm_world, mtime, "Computing binned map")
zmap.write_healpix_fits(os.path.join(args.outdir, "binned.fits"))
mtime = elapsed(comm.comm_world, mtime, "Writing binned map")
else:
# Set up MADAM map making.
pars = {}
pars["temperature_only"] = "F"
pars["force_pol"] = "T"
pars["kfirst"] = "T"
pars["concatenate_messages"] = "T"
pars["write_map"] = "T"
pars["write_binmap"] = "T"
pars["write_matrix"] = "T"
pars["write_wcov"] = "T"
pars["write_hits"] = "T"
pars["nside_cross"] = nside // 2
pars["nside_submap"] = subnside
if args.madampar is not None:
pat = re.compile(r"\s*(\S+)\s*=\s*(\S+(\s+\S+)*)\s*")
comment = re.compile(r"^#.*")
with open(args.madampar, "r") as f:
for line in f:
if comment.match(line) is None:
result = pat.match(line)
if result is not None:
key, value = result.group(1), result.group(2)
pars[key] = value
pars["base_first"] = args.baseline
pars["nside_map"] = nside
if args.noisefilter:
pars["kfilter"] = "T"
else:
pars["kfilter"] = "F"
pars["fsample"] = args.samplerate
madam = tm.OpMadam(params=pars,
detweights=detweights,
common_flag_mask=args.common_flag_mask)
madam.exec(data)
mtime = elapsed(comm.comm_world, mtime, "Madam mapmaking")
comm.comm_world.barrier()
stop = MPI.Wtime()
dur = stop - global_start
if comm.comm_world.rank == 0:
print("Total Time: {:.2f} seconds".format(dur), flush=True)
return
