obsutils.py
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# ==========================================================================
# CTA observation handling support functions
#
# Copyright (C) 2011-2016 Juergen Knoedlseder
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# ==========================================================================
import gammalib
import ctools
# ===================== #
# Simulate observations #
# ===================== #
def sim(obs, log=False, debug=False, chatter=2, edisp=False, seed=0,
emin=None, emax=None, nbins=0,
binsz=0.05, npix=200, proj='TAN', coord='GAL'):
"""
Simulate events for all observations in the container
Simulate events for all observations using ctobssim. If the number of
energy bins is positive, the events are then binned in a counts cube
using ctbin. If multiple observations are simulated, the counts cube is
a stacked cube and the corresponding response cubes are computed using
ctexpcube, ctpsfcube, ctbkgcube and optionally ctedispcube. The response
cubes are attached to the first observation in the container, which
normally is the observation with the counts cube.
Parameters
----------
obs : `~gammalib.GObservations`
Observation container without events
log : bool, optional
Create log file(s)
debug : bool, optional
Create console dump?
chatter : int, optional
Chatter level
edisp : bool, optional
Apply energy dispersion?
seed : int, optional
Seed value for simulations
emin : float, optional
Minimum energy of counts cube for binned (TeV)
emax : float, optional
Maximum energy of counts cube for binned (TeV)
nbins : int, optional
Number of energy bins (0=unbinned)
binsz : float, optional
Pixel size for binned simulation (deg/pixel)
npix : int, optional
Number of pixels in X and Y for binned simulation
proj : str, optional
Projection for binned simulation
coord : str, optional
Coordinate system for binned simulation
Returns
-------
obs : `~gammalib.GObservations`
Observation container filled with simulated events
"""
# Allocate ctobssim application and set parameters
sim = ctools.ctobssim(obs)
sim['seed'] = seed
sim['edisp'] = edisp
sim['chatter'] = chatter
sim['debug'] = debug
# Optionally open the log file
if log:
sim.logFileOpen()
# Run ctobssim application. This will loop over all observations in the
# container and simulation the events for each observation. Note that
# events are not added together, they still apply to each observation
# separately.
sim.run()
# Binned option?
if nbins > 0:
# If energy boundaries are not given then determine common energy
# boundaries for all observations
if emin == None or emax == None:
emin = None
emax = None
for run in sim.obs():
run_emin = run.events().ebounds().emin().TeV()
run_emax = run.events().ebounds().emax().TeV()
if emin == None:
emin = run_emin
elif run_emin > emin:
emin = run_emin
if emax == None:
emax = run_emax
elif run_emax > emax:
emax = run_emax
# Allocate ctbin application and set parameters
bin = ctools.ctbin(sim.obs())
bin['ebinalg'] = 'LOG'
bin['emin'] = emin
bin['emax'] = emax
bin['enumbins'] = nbins
bin['usepnt'] = True # Use pointing for map centre
bin['nxpix'] = npix
bin['nypix'] = npix
bin['binsz'] = binsz
bin['coordsys'] = coord
bin['proj'] = proj
bin['chatter'] = chatter
bin['debug'] = debug
# Optionally open the log file
if log:
bin.logFileOpen()
# Run ctbin application. This will loop over all observations in
# the container and bin the events in counts maps
bin.run()
# If we have multiple input observations then create stacked response
# cubes and append them to the observation
if len(sim.obs()) > 1:
# First get the cube. We need this because ctbin builds a cube on
# the fly. We should avoid this and make the cube part of ctbin
cube = bin.cube()
# Get xref, yref, coordsys and proj from counts cube
_xref = cube.counts().projection().crval(0)
_yref = cube.counts().projection().crval(1)
_coordsys = cube.counts().projection().coordsys()
_proj = cube.counts().projection().code()
# Kluge: map "EQU" to "CEL" coordinate system (not sure why the
# GSkyProjection::coordsys returns "EQU" instead of "CEL"
if _coordsys == 'EQU':
_coordsys = 'CEL'
# Get stacked response
response = get_stacked_response(sim.obs(), _xref, _yref,
binsz=binsz, nxpix=npix, nypix=npix,
emin=emin, emax=emax, enumbins=nbins,
edisp=edisp,
coordsys=_coordsys, proj=_proj,
log=log, debug=debug,
chatter=chatter)
# Set stacked response
if edisp:
bin.obs()[0].response(response['expcube'],
response['psfcube'],
response['edispcube'],
response['bkgcube'])
else:
bin.obs()[0].response(response['expcube'],
response['psfcube'],
response['bkgcube'])
# Set new models
bin.obs().models(response['models'])
# Make a deep copy of the observation that will be returned
# (the ctbin object will go out of scope one the function is
# left)
obs = bin.obs().copy()
else:
# Make a deep copy of the observation that will be returned
# (the ctobssim object will go out of scope one the function is
# left)
obs = sim.obs().copy()
# Delete the simulation
del sim
# Return observation container
return obs
# ================ #
# Fit observations #
# ================ #
def fit(obs, log=False, debug=False, chatter=2, edisp=False):
"""
Perform maximum likelihood fitting of observations in the container
Parameters
----------
obs : `~gammalib.GObservations`
Observation container
log : bool, optional
Create log file(s)
debug : bool, optional
Create console dump?
chatter : int, optional
Chatter level
edisp : bool, optional
Apply energy dispersion?
Returns
-------
like : `~ctools.ctlike`
ctlike application
"""
# Allocate ctlike application and set parameters
like = ctools.ctlike(obs)
like['debug'] = debug
like['chatter'] = chatter
like['edisp'] = edisp
# Optionally open the log file
if log:
like.logFileOpen()
# Run ctlike application.
like.run()
# Return observations
return like
# ============================================================== #
# Fit observations and determine errors using likelihood profile #
# ============================================================== #
def cterror(obs, srcname, log=False, debug=False, chatter=2):
"""
Fit observations and determine errors using likelihood profile
Parameters
----------
obs : `~gammalib.GObservations`
Observation container
srcname : str
Source name
log : bool, optional
Create log file(s)
debug : bool, optional
Create console dump?
chatter : int, optional
Chatter level
Returns
-------
error : `~ctools.cterror`
cterror application
"""
# Allocate cterror application and set parameters
error = ctools.cterror(obs)
error['srcname'] = srcname
error['debug'] = debug
error['chatter'] = chatter
# Optionally open the log file
if log:
error.logFileOpen()
# Run cterror application.
error.run()
# Return observations
return error
# ================= #
# Create counts map #
# ================= #
def cntmap(obs, proj='TAN', coord='GAL', xval=0.0, yval=0.0, \
binsz=0.05, nxpix=200, nypix=200, \
outname='cntmap.fits'):
"""
Creates a counts map by combining the events of all observations
The counts map will be a summed map over all energies
Parameters
----------
obs : `~gammalib.GObservations`
Observation container without events
proj : str, optional
Projection for binned simulation
coord : str, optional
Coordinate system for binned simulation
xval : float, optional
Counts map centre of X direction (deg)
yval : float, optional
Counts map centre of Y direction (deg)
binsz : float, optional
Pixel size for binned simulation (deg/pixel)
nxpix : int, optional
Number of pixels in X direction
nypix : int, optional
Number of pixels in Y direction
outname : str, optional
Counts map file name
Returns
-------
map : `~gammalib.GSkyMap`
Counts map
"""
# Allocate counts map
map = gammalib.GSkyMap(proj, coord, xval, yval, -binsz, binsz, nxpix, nypix, 1)
# Set maximum pixel number
maxpixel = nxpix * nypix
# Fill all observations
for run in obs:
# Loop over all events
for event in run.events():
# Determine sky pixel
skydir = event.dir().dir()
pixel = map.dir2inx(skydir)
# Set pixel
if pixel < maxpixel:
map[pixel] += event.counts()
# Save sky map. The clobber flag is set to True, so any existing FITS
# file will be overwritten.
map.save(outname, True)
# Return counts map
return map
# ================ #
# Create model map #
# ================ #
def modmap(obs, eref=0.1, proj='TAN', coord='GAL', xval=0.0, yval=0.0, \
binsz=0.05, nxpix=200, nypix=200, \
outname='modmap.fits'):
"""
Make model map for a given reference energy by combining all observations
The model map will be evaluated for a given reference energy 'eref' and will
be given in units of [counts/(sr MeV s)].
Parameters
----------
obs : `~gammalib.GObservations`
Observation container without events
eref : float, optional
Reference energy for which model is created (TeV)
proj : str, optional
Projection for binned simulation
coord : str, optional
Coordinate system for binned simulation
xval : float, optional
Counts map centre of X direction (deg)
yval : float, optional
Counts map centre of Y direction (deg)
binsz : float, optional
Pixel size for binned simulation (deg/pixel)
nxpix : int, optional
Number of pixels in X direction
nypix : int, optional
Number of pixels in Y direction
outname : str, optional
Model map file name
Returns
-------
map : `~gammalib.GSkyMap`
Model map
"""
# Allocate model map
map = gammalib.GSkyMap(proj, coord, xval, yval, -binsz, binsz, nxpix, nypix, 1)
# Set reference energy, time and direction. The time is not initialised and is
# in fact not used (as the IRF is assumed to be time independent for now).
# The sky direction is set later using the pixel values.
energy = gammalib.GEnergy()
time = gammalib.GTime()
instdir = gammalib.GCTAInstDir()
energy.TeV(eref)
# Loop over all map pixels
for pixel in range(map.npix()):
# Get sky direction
skydir = map.inx2dir(pixel)
instdir.dir(skydir)
# Create event atom for map pixel
atom = gammalib.GCTAEventAtom()
atom.dir(instdir)
atom.energy(energy)
atom.time(time)
# Initialise model value
value = 0.0
# Loop over all observations
for run in obs:
value += obs.models().eval(atom, run)
# Set map value
map[pixel] = value
# Save sky map
map.save(outname, True)
# Return model map
return map
# ======================= #
# Set one CTA observation #
# ======================= #
def set_obs(pntdir, tstart=0.0, duration=1800.0, deadc=0.95, \
emin=0.1, emax=100.0, rad=5.0, \
irf='South_50h', caldb='prod2', id='000000'):
"""
Set a single CTA observation
The function sets a single CTA observation containing an empty CTA
event list. By looping over this function you can add CTA observations
to the observation container.
Parameters
----------
pntdir : `~gammalib.GSkyDir`
Pointing direction
tstart : float, optional
Start time (seconds)
duration : float, optional
Duration of observation (seconds)
deadc : float, optional
Deadtime correction factor
emin : float, optional
Minimum event energy (TeV)
emax : float, optional
Maximum event energy (TeV)
rad : float, optional
ROI radius used for analysis (deg)
irf : str, optional
Instrument response function
caldb : str, optional
Calibration database path
id : str, optional
Observation identifier
Returns
-------
obs : `~gammalib.GCTAObservation`
CTA observation
"""
# Allocate CTA observation
obs_cta = gammalib.GCTAObservation()
# Set calibration database
db = gammalib.GCaldb()
if (gammalib.dir_exists(caldb)):
db.rootdir(caldb)
else:
db.open('cta', caldb)
# Set pointing direction
pnt = gammalib.GCTAPointing()
pnt.dir(pntdir)
obs_cta.pointing(pnt)
# Set ROI
roi = gammalib.GCTARoi()
instdir = gammalib.GCTAInstDir()
instdir.dir(pntdir)
roi.centre(instdir)
roi.radius(rad)
# Set GTI
gti = gammalib.GGti()
gti.append(gammalib.GTime(tstart), gammalib.GTime(tstart+duration))
# Set energy boundaries
ebounds = gammalib.GEbounds(gammalib.GEnergy(emin, 'TeV'),
gammalib.GEnergy(emax, 'TeV'))
# Allocate event list
events = gammalib.GCTAEventList()
events.roi(roi)
events.gti(gti)
events.ebounds(ebounds)
obs_cta.events(events)
# Set instrument response
obs_cta.response(irf, db)
# Set ontime, livetime, and deadtime correction factor
obs_cta.ontime(duration)
obs_cta.livetime(duration*deadc)
obs_cta.deadc(deadc)
obs_cta.id(id)
# Return CTA observation
return obs_cta
# ============================ #
# Set list of CTA observations #
# ============================ #
def set_obs_list(obsdeflist, tstart=0.0, duration=1800.0, deadc=0.95, \
emin=0.1, emax=100.0, rad=5.0, \
irf='South_50h', caldb='prod2'):
"""
Returns an observation container filled with a list of CTA observations
The list is defined by the obsdeflist parameter which is a dictionnary
containing the mandatory keywords 'ra' and 'dec' that specify the
pointing direction for a given observation. Optional keyword give control
over other observation proposerties, such as duration, deadtime correction,
energy range, etc. If an optional keyword is not specified, the function
keyword is used instead.
Parameters
----------
obsdeflist : list of dict
Observation definition list
tstart : float, optional
Start time (seconds)
duration : float, optional
Duration of observation (seconds)
deadc : float, optional
Deadtime correction factor
emin : float, optional
Minimum event energy (TeV)
emax : float, optional
Maximum event energy (TeV)
rad : float, optional
ROI radius used for analysis (deg)
irf : str, optional
Instrument response function
caldb : str, optional
Calibration database path
Returns
-------
obs : `~gammalib.GObservations`
Observation container filled with CTA observation
"""
# Initialise empty observation container
obs = gammalib.GObservations()
# Initialise first time and identifier
obs_start = tstart
obs_id = 1
# Loop over observation definition list
for obsdef in obsdeflist:
# Set pointing direction
pntdir = gammalib.GSkyDir()
pntdir.radec_deg(obsdef['ra'], obsdef['dec'])
# Set duration (use default if not found in definition list)
if 'duration' in obsdef:
obs_duration = obsdef['duration']
else:
obs_duration = duration
# Set emin (use default if not found in definition list)
if 'emin' in obsdef:
obs_emin = obsdef['emin']
else:
obs_emin = emin
# Set emax (use default if not found in definition list)
if 'emax' in obsdef:
obs_emax = obsdef['emax']
else:
obs_emax = emax
# Set radius (use default if not found in definition list)
if 'rad' in obsdef:
obs_rad = obsdef['rad']
else:
obs_rad = rad
# Set deadc (use default if not found in definition list)
if 'deadc' in obsdef:
obs_deadc = obsdef['deadc']
else:
obs_deadc = deadc
# Set caldb (use default if not found in definition list)
if 'caldb' in obsdef:
obs_caldb = obsdef['caldb']
else:
obs_caldb = caldb
# Set irf (use default if not found in definition list)
if 'irf' in obsdef:
obs_irf = obsdef['irf']
else:
obs_irf = irf
# Generate identifier string
id = '%6.6d' % obs_id
# Set CTA observation
obs_cta = set_obs(pntdir, tstart=obs_start, duration=obs_duration, \
deadc=obs_deadc, emin=obs_emin, emax=obs_emax, \
rad=obs_rad, irf=obs_irf, caldb=obs_caldb, id=id)
# Append to container
obs.append(obs_cta)
# Update start time and identifier
obs_start += obs_duration
obs_id += 1
# Return observation container
return obs
# ============================ #
# Set CTA observation patterns #
# ============================ #
def set_obs_patterns(pattern, ra=83.6331, dec=22.0145, offset=1.5):
"""
Sets a number of standard patterns
Parameters
----------
pattern : str
Observation pattern ("single", "four")
ra : float, optional
Right Ascension of pattern centre (deg)
dec : float, optional
Declination of pattern centre (deg)
offset : float, optional
Offset from pattern centre (deg)
Returns
-------
obsdeflist : list
Observation definition list
"""
# Initialise observation definition list
obsdeflist = []
# If the pattern is a single observation then append the Right Ascension
# and Declination to the observation definition list
if pattern == 'single':
obsdef = {'ra': ra, 'dec': dec}
obsdeflist.append(obsdef)
# ... otherwise, if the pattern is four observations then append four
# observations offset by a certain amount from the pattern centre to the
# observation definition list
elif pattern == 'four':
# Set pattern centre
centre = gammalib.GSkyDir()
centre.radec_deg(ra, dec)
# Append pointings
for phi in [0.0, 90.0, 180.0, 270.0]:
pntdir = centre.copy()
pntdir.rotate_deg(phi, offset)
obsdeflist.append({'ra': pntdir.ra_deg(), 'dec': pntdir.dec_deg()})
# ... otherwise we have an unknown pattern
else:
print('Warning: Observation pattern "'+str(pattern)+'" not recognized.')
# Return observation definition list
return obsdeflist
# ======================== #
# Set model for TS fitting #
# ======================== #
def set_ts_model(models, srcname, ra=None, dec=None, fitspat=False, fitspec=False):
"""
Set model for TS fitting
Parameters
----------
models : `~gammalib.GModels`
Input model container
srcname : str
Test source name
ra : float, optional
Right Ascension of test source (deg)
dec : float, optional
Declination of test source (deg)
fitspat : bool, optional
Fit spatial parameter?
fitspec : bool, optional
Fit spectral parameters?
Returns
-------
model : `~gammalib.GModels`
Model container for TS fitting
"""
# Create a clone of the input model
outmodels = models.copy()
# Disable TS computation for all model components (will enable the
# test source later)
for model in outmodels:
model.tscalc(False)
# Get source model and enable TS computation
model = outmodels[srcname]
model.tscalc(True)
# If source model has no "Prefactor" parameter then raise an exception
if not model.has_par('Prefactor'):
msg = ('Model "%s" has no parameter "Prefactor". Only spectral '
'models with a "Prefactor" parameter are supported.' %
srcname)
raise RuntimeError(msg)
# Set position of test source
if ra != None and dec != None:
if model.has_par('RA') and model.has_par('DEC'):
model['RA'].value(ra)
model['DEC'].value(dec)
# Set possible spatial and spectral parameters
spatial = ['RA', 'DEC', 'Sigma', 'Radius', 'Width', 'PA',
'MinorRadius', 'MajorRadius']
spectral = ['Index', 'Index1', 'Index2', 'BreakEnergy', 'CutoffEnergy',
'InverseCutoffEnergy']
# Fit or fix spatial parameters
for par in spatial:
if model.has_par(par):
if fitspat:
model[par].free()
else:
model[par].fix()
# Fit or fix spectral parameters
for par in spectral:
if model.has_par(par):
if fitspec:
model[par].free()
else:
model[par].fix()
# Return model container
return outmodels
# ==================== #
# Get stacked response #
# ==================== #
def get_stacked_response(obs, xref, yref, binsz=0.05, nxpix=200, nypix=200,
emin=0.1, emax=100.0, enumbins=20, edisp=False,
coordsys='GAL', proj='TAN',
log=False, debug=False, chatter=2):
"""
Get stacked response cubes
Parameters
----------
obs : `~gammalib.GObservations`
Observation container
xref : float
Right Ascension or Galactic longitude of response centre (deg)
yref : float
Declination or Galactic latitude of response centre (deg)
binsz : float, optional
Pixel size (deg/pixel)
nxpix : int, optional
Number of pixels in X direction
nypix : int, optional
Number of pixels in Y direction
emin : float, optional
Minimum energy (TeV)
emax : float, optional
Maximum energy (TeV)
enumbins : int, optional
Number of energy bins
edisp : bool, optional
Apply energy dispersion?
coordsys : str, optional
Coordinate system
proj : str, optional
Projection
log : bool, optional
Create log file(s)
debug : bool, optional
Create console dump?
chatter : int, optional
Chatter level
Returns
-------
result : dict
Dictionary of response cubes
"""
# Compute spatial binning for point spread function and
# energy dispersion cubes
psf_binsz = 10.0 * binsz
psf_nxpix = min(nxpix // 10, 2) # Make sure result is int
psf_nypix = min(nypix // 10, 2) # Make sure result is int
# Create exposure cube
expcube = ctools.ctexpcube(obs)
expcube['incube'] = 'NONE'
expcube['usepnt'] = False
expcube['ebinalg'] = 'LOG'
expcube['xref'] = xref
expcube['yref'] = yref
expcube['binsz'] = binsz
expcube['nxpix'] = nxpix
expcube['nypix'] = nypix
expcube['enumbins'] = enumbins
expcube['emin'] = emin
expcube['emax'] = emax
expcube['coordsys'] = coordsys
expcube['proj'] = proj
if log:
expcube.logFileOpen()
expcube.run()
# Create point spread function cube
psfcube = ctools.ctpsfcube(obs)
psfcube['incube'] = 'NONE'
psfcube['usepnt'] = False
psfcube['ebinalg'] = 'LOG'
psfcube['xref'] = xref
psfcube['yref'] = yref
psfcube['binsz'] = psf_binsz
psfcube['nxpix'] = psf_nxpix
psfcube['nypix'] = psf_nypix
psfcube['enumbins'] = enumbins
psfcube['emin'] = emin
psfcube['emax'] = emax
psfcube['coordsys'] = coordsys
psfcube['proj'] = proj
if log:
psfcube.logFileOpen()
psfcube.run()
# Create background cube
bkgcube = ctools.ctbkgcube(obs)
bkgcube['incube'] = 'NONE'
bkgcube['usepnt'] = False
bkgcube['ebinalg'] = 'LOG'
bkgcube['xref'] = xref
bkgcube['yref'] = yref
bkgcube['binsz'] = binsz
bkgcube['nxpix'] = nxpix
bkgcube['nypix'] = nypix
bkgcube['enumbins'] = enumbins
bkgcube['emin'] = emin
bkgcube['emax'] = emax
bkgcube['coordsys'] = coordsys
bkgcube['proj'] = proj
if log:
bkgcube.logFileOpen()
bkgcube.run()
# If energy dispersion is requested then create energy dispersion cube
if edisp:
edispcube = ctools.ctedispcube(obs)
edispcube['incube'] = 'NONE'
edispcube['usepnt'] = False
edispcube['ebinalg'] = 'LOG'
edispcube['xref'] = xref
edispcube['yref'] = yref
edispcube['binsz'] = psf_binsz
edispcube['nxpix'] = psf_nxpix
edispcube['nypix'] = psf_nypix
edispcube['enumbins'] = enumbins
edispcube['emin'] = emin
edispcube['emax'] = emax
edispcube['coordsys'] = coordsys
edispcube['proj'] = proj
if log:
edispcube.logFileOpen()
edispcube.run()
# Build response dictionary
response = {}
response['expcube'] = expcube.expcube().copy()
response['psfcube'] = psfcube.psfcube().copy()
response['bkgcube'] = bkgcube.bkgcube().copy()
response['models'] = bkgcube.models().copy()
if edisp:
response['edispcube'] = edispcube.expcube().copy()
# Return response cubes
return response