def main():
usage = "usage: %(prog)s [config file]"
description = "Run fermipy analysis chain."
parser = argparse.ArgumentParser(usage=usage,description=description)
parser.add_argument('--config', default = 'sample_config.yaml')
parser.add_argument('--source', default = None)
args = parser.parse_args()
gta = GTAnalysis(args.config,logging={'verbosity' : 3},
fileio={'workdir_regex' : ['\.xml$|\.npy$']})
logfile = os.path.join(gta.outdir,'run-region-analysis.log')
if not check_log(logfile)=='Successful':
print('Region analysis incomplete. Exiting.')
sys.exit(1)
gta.setup()
halo_width = np.logspace(-1.25,0.25,13)
halo_index = np.array([1.5,1.75,2.0,2.25,2.5,2.75,3.0,3.25,3.5])
src_name = gta.roi.sources[0].name
for i in range(1,6):
npy_file = os.path.join(gta.workdir,'fit%i.npy'%i)
if not os.path.isfile(npy_file):
continue
gta.load_roi('fit%i'%i,reload_sources=True)
fit_halo_scan(gta,'fit%i'%i,src_name,
halo_width,halo_index,optimizer='NEWTON')
def run_analysis(self, argv):
"""Run this analysis"""
args = self._parser.parse_args(argv)
if not HAVE_ST:
raise RuntimeError("Trying to run fermipy analysis, but don't have ST")
gta = GTAnalysis(args.config,
logging={'verbosity': 3},
fileio={'workdir_regex': '\.xml$|\.npy$'})
gta.setup(overwrite=False)
gta.load_roi('fit_baseline')
gta.print_roi()
basedir = os.path.dirname(args.config)
# This should be a no-op, b/c it was done in the baseline analysis
gta.free_sources(skydir=gta.roi.skydir, distance=1.0, pars='norm')
for profile in args.profiles:
pkey, pdict = SEDAnalysis._build_profile_dict(basedir, profile)
# test_case need to be a dict with spectrum and morphology
gta.add_source(pkey, pdict)
# refit the ROI
gta.fit()
# build the SED
gta.sed(pkey, outfile="sed_%s.fits" % pkey)
# remove the source
gta.delete_source(pkey)
# put the ROI back to how it was
gta.load_xml('fit_baseline')
return gta
def run_analysis(self, argv):
"""Run this analysis"""
args = self._parser.parse_args(argv)
if not HAVE_ST:
raise RuntimeError(
"Trying to run fermipy analysis, but don't have ST")
workdir = os.path.dirname(args.config)
_config_file = self._clone_config_and_srcmaps(args.config, args.seed)
gta = GTAnalysis(_config_file,
logging={'verbosity': 3},
fileio={'workdir_regex': '\.xml$|\.npy$'})
gta.load_roi(args.roi_baseline)
simfile = os.path.join(workdir,
'sim_%s_%s.yaml' % (args.sim, args.sim_profile))
mcube_file = "%s_%s_%06i" % (args.sim, args.sim_profile, args.seed)
sim_config = utils.load_yaml(simfile)
injected_source = sim_config.get('injected_source', None)
if injected_source is not None:
src_dict = injected_source['source_model']
src_dict['ra'] = gta.config['selection']['ra']
src_dict['dec'] = gta.config['selection']['dec']
injected_name = injected_source['name']
gta.add_source(injected_name, src_dict)
gta.write_model_map(mcube_file)
mc_spec_dict = dict(
true_counts=gta.model_counts_spectrum(injected_name),
energies=gta.energies,
model=src_dict)
mcspec_file = os.path.join(
workdir, "mcspec_%s_%06i.yaml" % (mcube_file, args.seed))
utils.write_yaml(mc_spec_dict, mcspec_file)
else:
injected_name = None
gta.write_roi('sim_baseline_%06i' % args.seed)
test_sources = {}
for profile in args.profiles:
profile_path = os.path.join(workdir, 'profile_%s.yaml' % profile)
test_source = load_yaml(profile_path)
test_sources[profile] = test_source
first = args.seed
last = first + args.nsims
for seed in range(first, last):
self._run_simulation(gta,
args.roi_baseline,
injected_name,
test_sources,
first,
seed,
non_null_src=args.non_null_src,
do_find_src=args.do_find_src)
def run_analysis(self, argv):
"""Run this analysis"""
args = self._parser.parse_args(argv)
if not HAVE_ST:
raise RuntimeError(
"Trying to run fermipy analysis, but don't have ST")
workdir = os.path.dirname(args.config)
_config_file = self._clone_config_and_srcmaps(args.config, args.seed)
gta = GTAnalysis(_config_file, logging={'verbosity': 3},
fileio={'workdir_regex': '\.xml$|\.npy$'})
gta.load_roi(args.roi_baseline)
simfile = os.path.join(workdir, 'sim_%s_%s.yaml' %
(args.sim, args.sim_profile))
mcube_file = "%s_%s_%06i" % (args.sim, args.sim_profile, args.seed)
sim_config = utils.load_yaml(simfile)
injected_source = sim_config.get('injected_source', None)
if injected_source is not None:
src_dict = injected_source['source_model']
src_dict['ra'] = gta.config['selection']['ra']
src_dict['dec'] = gta.config['selection']['dec']
injected_name = injected_source['name']
gta.add_source(injected_name, src_dict)
gta.write_model_map(mcube_file)
mc_spec_dict = dict(true_counts=gta.model_counts_spectrum(injected_name),
energies=gta.energies,
model=src_dict)
mcspec_file = os.path.join(workdir,
"mcspec_%s_%06i.yaml" % (mcube_file, args.seed))
utils.write_yaml(mc_spec_dict, mcspec_file)
else:
injected_name = None
gta.write_roi('sim_baseline_%06i' % args.seed)
test_sources = []
for profile in args.profiles:
profile_path = os.path.join(workdir, 'profile_%s.yaml' % profile)
test_source = load_yaml(profile_path)
test_sources.append(test_source)
first = args.seed
last = first + args.nsims
for seed in range(first, last):
self._run_simulation(gta, args.roi_baseline,
injected_name, test_sources, first, seed,
non_null_src=args.non_null_src)
def run_analysis(self, argv):
"""Run this analysis"""
args = self._parser.parse_args(argv)
if not HAVE_ST:
raise RuntimeError(
"Trying to run fermipy analysis, but don't have ST")
if args.load_baseline:
gta = GTAnalysis.create(args.roi_baseline, args.config)
else:
gta = GTAnalysis(args.config,
logging={'verbosity': 3},
fileio={'workdir_regex': '\.xml$|\.npy$'})
gta.setup()
if is_not_null(args.input_pars):
gta.load_parameters_from_yaml(args.input_pars)
gta.write_roi(args.roi_baseline,
save_model_map=True,
save_weight_map=True,
make_plots=args.make_plots)
src_list = get_src_names(gta)
plotter = plotting.AnalysisPlotter(gta.config['plotting'],
fileio=gta.config['fileio'],
logging=gta.config['logging'])
if is_null(args.fit_strategy):
return
fit_strategy = load_yaml(args.fit_strategy)
npred_current = None
npred_prev = None
plots_only = False
for fit_stage in fit_strategy:
mask = fit_stage.get('mask', None)
npred_threshold = fit_stage.get('npred_threshold', 1.0e4)
frac_threshold = fit_stage.get('frac_threshold', 0.5)
npred_frac = fit_stage.get('npred_frac', 0.9999)
if plots_only:
gta.load_roi("%s.npy" % fit_stage['key'])
npred_current = set_wts_get_npred_wt(gta, mask)
skip_list_region = get_unchanged(src_list,
npred_current,
npred_prev,
frac_threshold=frac_threshold)
else:
npred_current = set_wts_get_npred_wt(gta, mask)
skip_list_region = get_unchanged(src_list,
npred_current,
npred_prev,
frac_threshold=frac_threshold)
gta.optimize(npred_frac=npred_frac,
npred_threshold=npred_threshold,
skip=skip_list_region)
snapshot(gta,
plotter,
fit_stage['key'],
make_plots=args.make_plots)
npred_prev = npred_current
npred_current = build_srcdict(gta, 'npred_wt')
class ExtensionFit:
def __init__(self, configFile):
self.gta = GTAnalysis(configFile, logging={'verbosity': 3})
self.target = None
self.targetRadius = None
self.distance = None
self.catalog = fits.getdata('/users-data/mfalxa/code/gll_psch_v13.fit',
1)
def setSourceName(self, sourceObject, newName):
self.gta.delete_source(sourceObject['name'])
self.gta.add_source(newName, sourceObject)
''' INITIALIZE '''
def initialize(self, sizeROI, rInner, addToROI, TSMin, debug):
self.gta.setup()
if self.gta.config['selection']['emin'] >= 10000:
self.gta.set_parameter('galdiff', 'Scale', 30000)
if debug == True:
self.gta.make_plots('startAll')
self.gta.residmap(prefix='startAll', make_plots=True)
# Get model source names
sourceList = self.gta.get_sources(exclude=['isodiff', 'galdiff'])
# Delete sources unassociated with TS < 50
for i in range(len(sourceList)):
if sourceList[i]['catalog']['TS_value'] < TSMin and self.catalog[
'CLASS'][self.catalog['Source_Name'] == sourceList[i]
['name']][0] == '':
self.gta.delete_source(sourceList[i]['name'])
closests = self.gta.get_sources(distance=rInner,
exclude=['isodiff', 'galdiff'])
# Delete all unidentified sources
for i in range(len(closests)):
if self.catalog['CLASS'][self.catalog['Source_Name'] == closests[i]
['name']][0].isupper() == False:
self.gta.delete_source(closests[i]['name'])
if self.catalog['CLASS'][self.catalog['Source_Name'] == closests[i]
['name']][0] == 'SFR':
self.target = closests[i]
self.setSourceName(self.target, 'TESTSOURCE')
# If debug, save ROI and make plots
if debug == True:
self.gta.write_roi('startModel')
self.gta.residmap(prefix='start', make_plots=True)
self.gta.make_plots('start')
# Optmize spectral parameters for sources with npred > 1
self.gta.optimize(npred_threshold=1, skip=['isodiff'])
# Get model source names
sourceList = self.gta.get_sources(distance=sizeROI + addToROI,
square=True,
exclude=['isodiff', 'galdiff'])
# Iterate source localizing on source list
for i in range(len(sourceList)):
if sourceList[i].extended == False:
self.gta.localize(sourceList[i]['name'],
write_fits=False,
write_npy=False,
update=True)
# Free sources within ROI size + extra distance from center
self.gta.free_sources(distance=sizeROI + addToROI, square=True)
# Re-optimize ROI
self.gta.optimize(skip=['isodiff'])
# Save and make plots if debug
if debug == True:
self.gta.write_roi('modelInitialized')
self.gta.residmap(prefix='initialized', make_plots=True)
self.gta.make_plots('initialized')
# Lock sources
self.gta.free_sources(free=False)
''' OUTER REGION '''
def outerRegionAnalysis(self, sizeROI, rInner, sqrtTsThreshold,
minSeparation, debug):
self.gta.free_sources(distance=sizeROI,
pars='norm',
square=True,
free=True)
self.gta.free_sources(distance=rInner, free=False)
self.gta.free_source('galdiff', free=True)
self.gta.free_source('isodiff', free=False)
# Seek new sources until none are found
sourceModel = {
'SpectrumType': 'PowerLaw',
'Index': 2.0,
'Scale': 30000,
'Prefactor': 1.e-15,
'SpatialModel': 'PointSource'
}
newSources = self.gta.find_sources(sqrt_ts_threshold=sqrtTsThreshold,
min_separation=minSeparation,
model=sourceModel,
**{
'search_skydir':
self.gta.roi.skydir,
'search_minmax_radius':
[rInner, sizeROI]
})
if len(newSources) > 0:
for i in range(len(newSources)):
if newSources['sources'][i]['ts'] > 100.:
self.gta.set_source_spectrum(
newSources['sources'][i]['name'],
spectrum_type='LogParabola')
self.gta.free_source(newSources['sources'][i]['name'])
self.gta.fit()
self.gta.free_source(newSources['sources'][i]['name'],
free=False)
# Optimize all ROI
self.gta.optimize(skip=['isodiff'])
# Save sources found
if debug == True:
self.gta.residmap(prefix='outer', make_plots=True)
self.gta.write_roi('outerAnalysisROI')
self.gta.make_plots('outer')
''' INNER REGION '''
def innerRegionAnalysis(self, sizeROI, rInner, maxIter, sqrtTsThreshold,
minSeparation, dmMin, TSm1Min, TSextMin, debug):
self.gta.free_sources(distance=sizeROI, square=True, free=False)
self.gta.free_sources(distance=rInner, free=True, exclude=['isodiff'])
# Keep closest source if identified with star forming region in catalog or look for new source closest to center within Rinner
if self.target != None:
print('Closest source identified with star forming region : ',
self.target['name'])
self.gta.set_source_morphology('TESTSOURCE',
**{'spatial_model': 'PointSource'})
else:
closeSources = self.gta.find_sources(sqrt_ts_threshold=2.,
min_separation=minSeparation,
max_iter=1,
**{
'search_skydir':
self.gta.roi.skydir,
'search_minmax_radius':
[0., rInner]
})
dCenter = np.array([])
for i in range(len(closeSources['sources'])):
dCenter = np.append(
dCenter,
self.gta.roi.skydir.separation(
closeSources['sources'][i].skydir).value)
self.target = closeSources['sources'][np.argmin(dCenter)]
print('Target name : ', self.target['name'])
self.setSourceName(self.target, 'TESTSOURCE')
for i in [
x for x in range(len(closeSources['sources']))
if x != (np.argmin(dCenter))
]:
self.gta.delete_source(closeSources['sources'][i]['name'])
self.gta.optimize(skip=['isodiff'])
# Initialize n sources array
nSources = []
# Save ROI without extension fit
self.gta.write_roi('nSourcesFit')
if debug == True:
self.gta.make_plots('innerInit')
self.gta.residmap(prefix='innerInit', make_plots=True)
# Test for extension
extensionTest = self.gta.extension('TESTSOURCE',
make_plots=True,
write_npy=debug,
write_fits=debug,
spatial_model='RadialDisk',
update=True,
free_background=True,
fit_position=True)
extLike = extensionTest['loglike_ext']
TSext = extensionTest['ts_ext']
print('TSext : ', TSext)
extAIC = 2 * (len(self.gta.get_free_param_vector()) -
self.gta._roi_data['loglike'])
self.gta.write_roi('extFit')
if debug == True:
self.gta.residmap(prefix='ext0', make_plots=True)
self.gta.make_plots('ext0')
self.gta.load_roi('nSourcesFit', reload_sources=True)
for i in range(1, maxIter + 1):
# Test for n point sources
nSourcesTest = self.gta.find_sources(
sources_per_iter=1,
sqrt_ts_threshold=sqrtTsThreshold,
min_separation=minSeparation,
max_iter=1,
**{
'search_skydir': self.gta.roi.skydir,
'search_minmax_radius': [0., rInner]
})
if len(nSourcesTest['sources']) > 0:
if nSourcesTest['sources'][0]['ts'] > 100.:
self.gta.set_source_spectrum(
nSourcesTest['sources'][0]['name'],
spectrum_type='LogParabola')
self.gta.free_source(nSourcesTest['sources'][0]['name'])
self.gta.fit()
self.gta.free_source(nSourcesTest['sources'][0]['name'],
free=False)
if debug == True:
self.gta.make_plots('nSources' + str(i))
nSources.append(nSourcesTest['sources'])
self.gta.localize(nSourcesTest['sources'][0]['name'],
write_npy=debug,
write_fits=debug,
update=True)
nAIC = 2 * (len(self.gta.get_free_param_vector()) -
self.gta._roi_data['loglike'])
self.gta.free_source(nSourcesTest['sources'][0]['name'],
free=True)
self.gta.residmap(prefix='nSources' + str(i), make_plots=True)
self.gta.write_roi('n1SourcesFit')
# Estimate Akaike Information Criterion difference between both models
dm = extAIC - nAIC
print('AIC difference between both models = ', dm)
# Estimate TS_m+1
extensionTestPlus = self.gta.extension(
'TESTSOURCE',
make_plots=True,
write_npy=debug,
write_fits=debug,
spatial_model='RadialDisk',
update=True,
free_background=True,
fit_position=True)
TSm1 = 2 * (extensionTestPlus['loglike_ext'] - extLike)
print('TSm+1 = ', TSm1)
if debug == True:
self.gta.residmap(prefix='ext' + str(i), make_plots=True)
self.gta.make_plots('ext' + str(i))
if dm < dmMin and TSm1 < TSm1Min:
self.gta.load_roi('extFit', reload_sources=True)
break
else:
# Set extension test to current state and save current extension fit ROI and load previous nSources fit ROI
extensionTest = extensionTestPlus
extLike = extensionTestPlus['loglike_ext']
TSext = extensionTestPlus['ts_ext']
print('TSext : ', TSext)
extAIC = 2 * (len(self.gta.get_free_param_vector()) -
self.gta._roi_data['loglike'])
self.gta.write_roi('extFit')
self.gta.load_roi('n1SourcesFit', reload_sources=True)
self.gta.write_roi('nSourcesFit')
else:
if TSext > TSextMin:
self.gta.load_roi('extFit', reload_sources=True)
break
else:
self.gta.load_roi('nSourcesFit', reload_sources=True)
break
self.gta.fit()
# Get source radius depending on spatial model
endSources = self.gta.get_sources()
for i in range(len(endSources)):
if endSources[i]['name'] == 'TESTSOURCE':
self.target = endSources[i]
self.distance = self.gta.roi.skydir.separation(
endSources[i].skydir).value
if endSources[i].extended == True:
self.targetRadius = endSources[i]['SpatialWidth']
else:
self.targetRadius = endSources[i]['pos_r95']
''' CHECK OVERLAP '''
def overlapDisk(self, rInner, radiusCatalog):
print('Target radius : ', self.targetRadius)
# Check radius sizes
if radiusCatalog < self.targetRadius:
r = float(radiusCatalog)
R = float(self.targetRadius)
else:
r = float(self.targetRadius)
R = float(radiusCatalog)
# Estimating overlapping area
d = self.distance
print('Distance from center : ', d)
if d < (r + R):
if R < (r + d):
area = r**2 * np.arccos(
(d**2 + r**2 - R**2) / (2 * d * r)) + R**2 * np.arccos(
(d**2 + R**2 - r**2) / (2 * d * R)) - 0.5 * np.sqrt(
(-d + r + R) * (d + r - R) * (d - r + R) *
(d + r + R))
overlap = round((area / (np.pi * r**2)) * 100, 2)
else:
area = np.pi * r**2
overlap = 100.0
else:
area = 0.
overlap = 0.
print('Overlapping surface : ', area)
print('Overlap : ', overlap)
if overlap > 68. and self.distance < rInner:
associated = True
else:
associated = False
return associated
''' CHECK UPPER LIMIT '''
def upperLimit(self, name, radius):
sourceModel = {
'SpectrumType': 'PowerLaw',
'Index': 2.0,
'Scale': 30000,
'Prefactor': 1.e-15,
'SpatialModel': 'RadialDisk',
'SpatialWidth': radius,
'glon': self.gta.config['selection']['glon'],
'glat': self.gta.config['selection']['glat']
}
self.gta.add_source(name, sourceModel, free=True)
self.gta.fit()
self.gta.residmap(prefix='upperLimit', make_plots=True)
print('Upper limit : ', self.gta.get_sources()[0]['flux_ul95'])
def run_analysis(self, argv):
"""Run this analysis"""
args = self._parser.parse_args(argv)
if not HAVE_ST:
raise RuntimeError(
"Trying to run fermipy analysis, but don't have ST")
if is_null(args.skydirs):
skydir_dict = None
else:
skydir_dict = load_yaml(args.skydirs)
gta = GTAnalysis(args.config,
logging={'verbosity': 3},
fileio={'workdir_regex': '\.xml$|\.npy$'})
#gta.setup(overwrite=False)
gta.load_roi(args.roi_baseline)
gta.print_roi()
basedir = os.path.dirname(args.config)
# This should be a no-op, b/c it was done in the baseline analysis
for profile in args.profiles:
if skydir_dict is None:
skydir_keys = [None]
else:
skydir_keys = sorted(skydir_dict.keys())
for skydir_key in skydir_keys:
if skydir_key is None:
pkey, pdict = AnalyzeSED._build_profile_dict(
basedir, profile)
else:
skydir_val = skydir_dict[skydir_key]
pkey, pdict = AnalyzeSED._build_profile_dict(
basedir, profile)
pdict['ra'] = skydir_val['ra']
pdict['dec'] = skydir_val['dec']
pkey += "_%06i" % skydir_key
outfile = "sed_%s.fits" % pkey
# Add the source and get the list of correlated soruces
correl_dict = add_source_get_correlated(gta,
pkey,
pdict,
correl_thresh=0.25)
# Write the list of correlated sources
correl_yaml = os.path.join(basedir, "correl_%s.yaml" % pkey)
write_yaml(correl_dict, correl_yaml)
gta.free_sources(False)
for src_name in correl_dict.keys():
gta.free_source(src_name, pars='norm')
# build the SED
gta.sed(pkey, outfile=outfile, make_plots=args.make_plots)
# remove the source
gta.delete_source(pkey)
# put the ROI back to how it was
gta.load_xml(args.roi_baseline)
return gta
def run_analysis(self, argv):
"""Run this analysis"""
args = self._parser.parse_args(argv)
if not HAVE_ST:
raise RuntimeError(
"Trying to run fermipy analysis, but don't have ST")
if args.load_baseline:
gta = GTAnalysis.create(args.roi_baseline,
args.config)
else:
gta = GTAnalysis(args.config,
logging={'verbosity': 3},
fileio={'workdir_regex': '\.xml$|\.npy$'})
gta.setup()
if is_not_null(args.input_pars):
gta.load_parameters_from_yaml(args.input_pars)
gta.write_roi(args.roi_baseline,
save_model_map=True,
save_weight_map=True,
make_plots=args.make_plots)
src_list = get_src_names(gta)
plotter = plotting.AnalysisPlotter(gta.config['plotting'],
fileio=gta.config['fileio'],
logging=gta.config['logging'])
if is_null(args.fit_strategy):
return
fit_strategy = load_yaml(args.fit_strategy)
npred_current = None
npred_prev = None
plots_only = False
for fit_stage in fit_strategy:
mask = fit_stage.get('mask', None)
npred_threshold = fit_stage.get('npred_threshold', 1.0e4)
frac_threshold = fit_stage.get('frac_threshold', 0.5)
npred_frac = fit_stage.get('npred_frac', 0.9999)
if plots_only:
gta.load_roi("%s.npy" % fit_stage['key'])
npred_current = set_wts_get_npred_wt(gta, mask)
skip_list_region = get_unchanged(src_list,
npred_current,
npred_prev,
frac_threshold=frac_threshold)
else:
npred_current = set_wts_get_npred_wt(gta, mask)
skip_list_region = get_unchanged(src_list,
npred_current,
npred_prev,
frac_threshold=frac_threshold)
gta.optimize(npred_frac=npred_frac,
npred_threshold=npred_threshold,
skip=skip_list_region)
snapshot(gta, plotter, fit_stage['key'], make_plots=args.make_plots)
npred_prev = npred_current
npred_current = build_srcdict(gta, 'npred_wt')
def main():
usage = "usage: %(prog)s -c config.yaml"
description = "Run the lc analysis"
parser = argparse.ArgumentParser(usage=usage, description=description)
parser.add_argument('-c', '--conf', required=True)
parser.add_argument('-i',
required=False,
default=0,
help='Set local or scratch calculation',
type=int)
parser.add_argument('--state',
help='analysis state',
choices=['avgspec', 'setup'],
default='avgspec')
parser.add_argument('--forcepl',
default=0,
help='Force the target source to have power-law shape',
type=int)
parser.add_argument('--createsed',
default=0,
help='Create SED from best fit model',
type=int)
parser.add_argument(
'--adaptive',
default=0,
help='Use adaptive binning for minute scale light curves',
type=int)
parser.add_argument('--srcprob', default = 0,
help='Calculate the source probability for the photons,' \
' only works when no sub orbit time scales are used',
type=int)
parser.add_argument(
'--mincounts',
default=2,
help='Minimum number of counts within LC bin to run analysis',
type=int)
parser.add_argument('--simulate', default = None,
help='None or full path to yaml file which contains src name' \
'and spec to be simulated',
)
parser.add_argument(
'--make_plots',
default=0,
type=int,
help='Create sed plot',
)
parser.add_argument(
'--randomize',
default=1,
help=
'If you simulate, use Poisson realization. If false, use Asimov data set',
type=int)
args = parser.parse_args()
utils.init_logging('DEBUG')
config = yaml.load(open(args.conf))
tmpdir, job_id = lsf.init_lsf()
if not job_id:
job_id = args.i
logging.info('tmpdir: {0:s}, job_id: {1:n}'.format(tmpdir, job_id))
os.chdir(tmpdir) # go to tmp directory
logging.info('Entering directory {0:s}'.format(tmpdir))
logging.info('PWD is {0:s}'.format(os.environ["PWD"]))
# copy the ft1,ft2 and ltcube files
#for k in ['evfile','scfile','ltcube']:
# don't stage them, done automatically by fermipy if needed
# config[k] = utils.copy2scratch(config[k], tmpdir)
# set the scratch directories
logging.debug(config['data'])
config['fileio']['scratchdir'] = tmpdir
# set the log file
logdir = copy.deepcopy(config['fileio']['logfile'])
config['fileio']['logfile'] = path.join(tmpdir, 'fermipy.log')
# debugging: all files will be saved (default is False)
#config['fileio']['savefits'] = True
# if simulating an orbit, save fits files
if args.simulate is not None:
config['fileio']['savefits'] = True
# copy all fits files already present in outdir
# run the analysis
lc_config = copy.deepcopy(config['lightcurve'])
fit_config = copy.deepcopy(config['fit_pars'])
# remove parameters from config file not accepted by fermipy
for k in ['configname', 'tmp', 'log', 'fit_pars']:
config.pop(k, None)
if 'adaptive' in config['lightcurve'].keys():
config['lightcurve'].pop('adaptive', None)
# set the correct time bin
config['selection']['tmin'], config['selection']['tmax'], nj = set_lc_bin(
config['selection']['tmin'],
config['selection']['tmax'],
config['lightcurve']['binsz'],
job_id - 1 if job_id > 0 else 0,
ft1=config['data']['evfile'])
logging.debug('setting light curve bin' + \
'{0:n}, between {1[tmin]:.0f} and {1[tmax]:.0f}'.format(job_id, config['selection']))
if args.adaptive:
config['fileio']['outdir'] = utils.mkdir(
path.join(config['fileio']['outdir'],
'adaptive{0:.0f}/'.format(lc_config['adaptive'])))
if args.state == 'setup':
config['fileio']['outdir'] = utils.mkdir(
path.join(config['fileio']['outdir'],
'setup{0:05n}/'.format(job_id if job_id > 0 else 1)))
else:
config['fileio']['outdir'] = utils.mkdir(
path.join(config['fileio']['outdir'],
'{0:05n}/'.format(job_id if job_id > 0 else 1)))
logging.info('Starting with fermipy analysis')
logging.info('using fermipy version {0:s}'.format(fermipy.__version__))
logging.info('located at {0:s}'.format(fermipy.__file__))
if config['data']['ltcube'] == '':
config['data'].pop('ltcube', None)
compute_sub_gti_lc = False
if type(config['lightcurve']['binsz']) == str:
if len(config['lightcurve']['binsz'].strip('gti')):
compute_sub_gti_lc = True
if config['lightcurve']['binsz'].find('min') > 0:
config['lightcurve']['binsz'] = float(
config['lightcurve']['binsz'].strip('gti').strip(
'min')) * 60.
logging.info("set time bin length to {0:.2f}s".format(
config['lightcurve']['binsz']))
else:
config['lightcurve']['binsz'] = 3. * 3600.
try:
gta = GTAnalysis(config, logging={'verbosity': 3})
except Exception as e:
logging.error("{0}".format(e))
config['selection']['target'] = None
gta = GTAnalysis(config, logging={'verbosity': 3})
sep = gta.roi.sources[0]['offset']
logging.warning(
"Source closets to ROI center is {0:.3f} degree away".format(sep))
if sep < 0.1:
config['selection']['target'] = gta.roi.sources[0]['name']
gta.config['selection']['target'] = config['selection']['target']
logging.info("Set target to {0:s}".format(
config['selection']['target']))
# stage the full time array analysis results to the tmp dir
# do not copy png images
files = [
fn for fn in glob(fit_config['avgspec'])
if fn.find('.xml') > 0 or fn.find('.npy') > 0
]
files += [config['data']['evfile']]
utils.copy2scratch(files, gta.workdir)
# we're using actual data
if args.simulate is None:
# check before the analysis start if there are any events in the master file
# in the specified time range
logging.info('Checking for events in initial ft1 file')
t = Table.read(path.join(gta.workdir,
path.basename(config['data']['evfile'])),
hdu='EVENTS')
logging.info("times in base ft1: {0} {1} {2}".format(
t["TIME"].max(), t["TIME"].min(),
t["TIME"].max() - t["TIME"].min()))
m = (t["TIME"] >= config['selection']['tmin']) & (
t["TIME"] <= config['selection']['tmax'])
if np.sum(m) < args.mincounts + 1:
logging.error(
"*** Only {0:n} events between tmin and tmax! Exiting".format(
np.sum(m)))
assert np.sum(m) > args.mincounts
else:
logging.info("{0:n} events between tmin and tmax".format(
np.sum(m)))
# check how many bins are in each potential light curve bin
if compute_sub_gti_lc:
# select time of first and last
# photon instead of GTI time
m = (t["TIME"] >= config['selection']['tmin']) & \
(t["TIME"] <= config['selection']['tmax'])
tmin = t["TIME"][m].min() - 1.
tmax = t["TIME"][m].max() + 1.
logging.info("There will be up to {0:n} time bins".format(np.ceil(
(tmax - tmin) / \
config['lightcurve']['binsz'])))
bins = np.arange(tmin, tmax, config['lightcurve']['binsz'])
bins = np.concatenate([bins, [config['selection']['tmax']]])
counts = calc_counts(t, bins)
# remove the starting times of the bins with zero counts
# and rebin the data
logging.info("Counts before rebinning: {0}".format(counts))
mincounts = 10.
mc = counts < mincounts
if np.sum(mc):
# remove trailing zeros
if np.any(counts == 0.):
mcounts_post, mcounts_pre = rm_trailing_zeros(counts)
counts = counts[mcounts_post & mcounts_pre]
bins = np.concatenate([
bins[:-1][mcounts_post & mcounts_pre],
[bins[1:][mcounts_post & mcounts_pre].max()]
])
bins = rebin(counts, bins)
logging.info("Bin lengths after rebinning: {0}".format(
np.diff(bins)))
logging.info("Bin times after rebinning: {0}".format(bins))
counts = calc_counts(t, bins)
logging.info("Counts after rebinning: {0}".format(counts))
else:
logging.info("Regular time binning will be used")
bins = list(bins)
logging.info('Running fermipy setup')
try:
gta.setup()
except (RuntimeError, IndexError) as e:
logging.error(
'Caught Runtime/Index Error while initializing analysis object')
logging.error('Printing error:')
logging.error(e)
if e.message.find("File not found") >= 0 and e.message.find(
'srcmap') >= 0:
logging.error("*** Srcmap calculation failed ***")
if e.message.find("NDSKEYS") >= 0 and e.message.find('srcmap') >= 0:
logging.error(
"*** Srcmap calculation failed with NDSKEYS keyword not found in header ***"
)
logging.info("Checking if there are events in ft1 file")
ft1 = path.join(gta.workdir, 'ft1_00.fits')
f = glob(ft1)
if not len(f):
logging.error(
"*** no ft1 file found at location {0:s}".format(ft1))
raise
t = Table.read(f[0], hdu='EVENTS')
if not len(t):
logging.error("*** The ft1 file contains no events!! ***".format(
len(t)))
else:
logging.info("The ft1 file contains {0:n} event(s)".format(len(t)))
return
# end here if you only want to calulate
# intermediate fits files
if args.state == 'setup':
return gta
logging.info('Loading the fit for the average spectrum')
gta.load_roi('avgspec') # reload the average spectral fit
logging.info('Running fermipy optimize and fit')
# we're using actual data
if args.simulate is None:
if args.forcepl:
gta = set_src_spec_pl(
gta, gta.get_source_name(config['selection']['target']))
# to do add EBL absorption at some stage ...
# gta = add_ebl_atten(gta, gta.get_source_name(config['selection']['target']), fit_config['z'])
# make sure you are fitting data
gta.simulate_roi(restore=True)
if compute_sub_gti_lc:
if args.adaptive:
# do import only here since root must be compiled
from fermiAnalysis import adaptivebinning as ab
# compute the exposure
energy = 1000.
texp, front, back = ab.comp_exposure_phi(gta, energy=1000.)
# compute the bins
result = ab.time_bins(
gta,
texp,
0.5 * (front + back),
#critval = 20., # bins with ~20% unc
critval=lc_config['adaptive'],
Epivot=None, # compute on the fly
# tstart = config['selection']['tmin'],
# tstop = config['selection']['tmax']
)
# cut the bins to this GTI
mask = result['tstop'] > config['selection']['tmin']
mask = mask & (result['tstart'] < config['selection']['tmax'])
# try again with catalog values
if not np.sum(mask):
logging.error(
"Adaptive bins outside time window, trying catalog values for flux"
)
result = ab.time_bins(
gta,
texp,
0.5 * (front + back),
critval=lc_config['adaptive'], # bins with ~20% unc
Epivot=None, # compute on the fly
forcecatalog=True,
# tstart = config['selection']['tmin'],
# tstop = config['selection']['tmax']
)
# cut the bins to this GTI
mask = result['tstop'] > config['selection']['tmin']
mask = mask & (result['tstart'] <
config['selection']['tmax'])
if not np.sum(mask):
logging.error(
"Adaptive bins do not cover selected time interval!"
)
logging.error("Using original bins")
else:
bins = np.concatenate((result['tstart'][mask],
[result['tstop'][mask][-1]]))
bins[0] = np.max(
[config['selection']['tmin'], bins[0]])
bins[-1] = np.min(
[config['selection']['tmax'], bins[-1]])
bins = list(bins)
# removing trailing zeros
counts = calc_counts(t, bins)
mcounts_post, mcounts_pre = rm_trailing_zeros(counts)
logging.info(
"count masks: {0} {1}, bins: {2}, counts: {3}".
format(mcounts_post, mcounts_pre, bins, counts))
counts = counts[mcounts_post & mcounts_pre]
bins = np.concatenate([
np.array(bins)[:-1][mcounts_post & mcounts_pre],
[
np.array(bins)[1:][mcounts_post
& mcounts_pre].max()
]
])
logging.info(
"Using bins {0}, total n={1:n} bins".format(
bins,
len(bins) - 1))
logging.info("bins widths : {0}".format(np.diff(bins)))
logging.info("counts per bin: {0} ".format(
calc_counts(t, bins)))
bins = list(bins)
# TODO: test that this is working also with GTIs that have little or no counts
lc = gta.lightcurve(
config['selection']['target'],
binsz=config['lightcurve']['binsz'],
free_background=config['lightcurve']['free_background'],
free_params=config['lightcurve']['free_params'],
free_radius=config['lightcurve']['free_radius'],
make_plots=False,
multithread=True,
nthread=4,
#multithread = False,
#nthread = 1,
save_bin_data=True,
shape_ts_threshold=16.,
use_scaled_srcmap=True,
use_local_ltcube=True,
write_fits=True,
write_npy=True,
time_bins=bins,
outdir='{0:.0f}s'.format(config['lightcurve']['binsz']))
else:
# run the fitting of the entire time and energy range
try:
o = gta.optimize() # perform an initial fit
logging.debug(o)
except RuntimeError as e:
logging.error("Error in optimize: {0}".format(e))
logging.info("Trying to continue ...")
gta = set_free_pars_lc(gta, config, fit_config)
f = gta.fit()
if 'fix_sources' in fit_config.keys():
skip = fit_config['fix_sources'].keys()
else:
skip = []
gta, f = refit(gta,
config['selection']['target'],
f,
fit_config['ts_fixed'],
skip=skip)
gta.print_roi()
gta.write_roi('lc')
if args.createsed:
if args.make_plots:
init_matplotlib_backend()
gta.load_roi('lc') # reload the average spectral fit
logging.info('Running sed for {0[target]:s}'.format(
config['selection']))
sed = gta.sed(config['selection']['target'],
prefix = 'lc_sed',
free_radius = None if config['sed']['free_radius'] == 0. \
else config['sed']['free_radius'],
free_background= config['sed']['free_background'],
free_pars = fa.allnorm,
make_plots = args.make_plots,
cov_scale = config['sed']['cov_scale'],
use_local_index = config['sed']['use_local_index'],
bin_index = config['sed']['bin_index']
)
# debugging: calculate sed and resid maps for each light curve bin
#logging.info('Running sed for {0[target]:s}'.format(config['selection']))
#sed = gta.sed(config['selection']['target'], prefix = 'lc')
#model = {'Scale': 1000., 'Index' : fit_config['new_src_pl_index'], 'SpatialModel' : 'PointSource'}
#resid_maps = gta.residmap('lc',model=model, make_plots=True, write_fits = True, write_npy = True)
if args.srcprob:
logging.info("Running srcprob with srcmdl {0:s}".format('lc'))
gta.compute_srcprob(xmlfile='lc', overwrite=True)
# we are simulating a source
else:
# TODO: I probably have to run the setup here. Do on weekly files, i.e., no time cut? Only do that later?
with open(args.simulate) as f:
simsource = np.load(f, allow_pickle=True).flat[0]
# set the source to the simulation value
gta.set_source_spectrum(
simsource['target'],
spectrum_type=simsource['spectrum_type'],
spectrum_pars=simsource['spectrum_pars'][job_id - 1])
logging.info("changed spectral parameters to {0}".format(
gta.roi.get_source_by_name(simsource['target']).spectral_pars))
# simulate the ROI
gta.simulate_roi(randomize=bool(args.randomize))
gta = set_free_pars_lc(gta, config, fit_config)
# fit the simulation
f = gta.fit()
gta, f = refit(gta, config['selection']['target'], f,
fit_config['ts_fixed'])
gta.print_roi()
gta.write_roi('lc_simulate_{0:s}'.format(simsource['suffix']))
return gta
#first optimization run with output
fit_res = gta.optimize()
gta.write_roi('fit_optimize')
#free parameters for full likelihood fit
gta.free_sources(pars='norm')
gta.free_sources(distance = 3.0)
gta.free_source('galdiff')
gta.free_source('isodiff')
#do the likelihood fit
fit_results = gta.fit()
if fit_results['fit_success']!=True:
gta.load_roi('fit_optimize.npy')
gta.free_sources(free=False)
gta.free_sources(pars='norm', distance = 3.0)
gta.free_sources(distance = 1.)
gta.free_source('galdiff')
gta.free_source('isodiff')
fit_res2 = gta.fit()
if fit_results['fit_success']!=True:
gta.load_roi('fit_optimize.npy')
gta.free_sources(free=False)
gta.free_sources(pars='norm', distance = 1.5)
gta.free_sources(distance = 0.5)
gta.free_source('galdiff')
gta.free_source('isodiff')
fit_res2 = gta.fit()
def main():
usage = "usage: %(prog)s [config file]"
description = "Run fermipy analysis chain."
parser = argparse.ArgumentParser(usage=usage,description=description)
parser.add_argument('--config', default = 'sample_config.yaml')
parser.add_argument('--source', default = None)
args = parser.parse_args()
gta = GTAnalysis(args.config,logging={'verbosity' : 3},
fileio={'workdir_regex' : '\.xml$|\.npy$'})
gta.setup()
names = [s.name for s in gta.roi.sources if not s.diffuse]
gta.reload_sources(names)
sqrt_ts_threshold=3
model0 = { 'SpatialModel' : 'PointSource', 'Index' : 1.5 }
model1 = { 'SpatialModel' : 'PointSource', 'Index' : 2.0 }
model2 = { 'SpatialModel' : 'PointSource', 'Index' : 2.5 }
#src_name = gta.roi.sources[0].name
if args.source is None:
src_name = gta.config['selection']['target']
else:
src_name = args.source
# -----------------------------------
# Fit the Baseline Model
# -----------------------------------
# Get a reasonable starting point for the spectral model
gta.free_source(src_name)
gta.fit()
gta.free_source(src_name,False)
gta.optimize()
# Localize 3FGL sources
for s in gta.roi.sources:
if not s['SpatialModel'] == 'PointSource':
continue
if s['offset'] < 0.5 or s['ts'] < 25.:
continue
if s['offset_roi_edge'] > -0.1:
continue
gta.localize(s.name,nstep=5,dtheta_max=0.5,update=True,
prefix='base')
gta.free_source(s.name,False)
gta.tsmap('base',model=model1)
# Look for new point sources outside the inner 1.0 deg
gta.find_sources('base',model=model1,
search_skydir=gta.roi.skydir,
max_iter=5,min_separation=0.5,
sqrt_ts_threshold=sqrt_ts_threshold,
search_minmax_radius=[1.0,None])
gta.optimize()
gta.print_roi()
gta.write_roi('base')
# -----------------------------------
# Pass 0 - Source at Nominal Position
# -----------------------------------
fit_region(gta,'fit0',src_name)
# -------------------------------------
# Pass 1 - Source at Localized Position
# -------------------------------------
gta.localize(src_name,nstep=5,dtheta_max=0.5,update=True,
prefix='fit1')
fit_region(gta,'fit1',src_name)
fit_halo(gta,'fit1',src_name)
gta.load_roi('fit1')
# -------------------------------------
# Pass 2 - 2+ Point Sources
# -------------------------------------
srcs = []
# Fit up to 4 sources
for i in range(2,6):
srcs_fit = gta.find_sources('fit%i'%i,
search_skydir=gta.roi.skydir,
max_iter=1,
sources_per_iter=1,
sqrt_ts_threshold=3,
min_separation=0.5,
search_minmax_radius=[None,1.0])
if len(srcs_fit['sources']) == 0:
break
srcs += srcs_fit['sources']
best_fit_idx = i
gta.localize(src_name,nstep=5,dtheta_max=0.4,
update=True,prefix='fit%i'%i)
# Relocalize new sources
for s in sorted(srcs, key=lambda t: t['ts'],reverse=True):
gta.localize(s.name,nstep=5,dtheta_max=0.4,
update=True,prefix='fit%i'%i)
fit_region(gta,'fit%i'%i,src_name)
fit_halo(gta,'fit%i'%i,src_name)
gta.load_roi('fit%i'%i)
new_source_data = []
for s in srcs:
src_data = gta.roi[s.name].data
new_source_data.append(copy.deepcopy(src_data))
np.save(os.path.join(gta.workdir,'new_source_data.npy'),
new_source_data)
sqrt_ts_threshold=sqrt_ts_threshold,
search_minmax_radius=[1.0,None])
gta.optimize()
gta.print_roi()
gta.write_roi('base')
# -----------------------------------
# Pass 0 - Source at Nominal Position
# -----------------------------------
fit_region(gta,'fit0',src_name)
#fit_region(gta,'fit0_emin40',src_name,erange=[4.0,5.5])
gta.load_roi('fit0')
# -------------------------------------
# Pass 1 - Source at Localized Position
# -------------------------------------
gta.localize(src_name,nstep=5,dtheta_max=0.5,update=True,
prefix='fit1')
fit_region(gta,'fit1',src_name)
fit_halo(gta,'fit1',src_name,halo_width,halo_index)
#fit_region(gta,'fit1_emin40',src_name,erange=[4.0,5.5])
#fit_halo(gta,'fit1_emin40',src_name,halo_width,halo_index,erange=[4.0,5.5])
gta.load_roi('fit1')
def run_analysis(self, argv):
"""Run this analysis"""
args = self._parser.parse_args(argv)
if not HAVE_ST:
raise RuntimeError(
"Trying to run fermipy analysis, but don't have ST")
if is_null(args.skydirs):
skydir_dict = None
else:
skydir_dict = load_yaml(args.skydirs)
gta = GTAnalysis(args.config,
logging={'verbosity': 3},
fileio={'workdir_regex': '\.xml$|\.npy$'})
#gta.setup(overwrite=False)
gta.load_roi(args.roi_baseline)
gta.print_roi()
basedir = os.path.dirname(args.config)
# This should be a no-op, b/c it was done in the baseline analysis
for profile in args.profiles:
if skydir_dict is None:
skydir_keys = [None]
else:
skydir_keys = sorted(skydir_dict.keys())
for skydir_key in skydir_keys:
if skydir_key is None:
pkey, psrc_name, pdict = build_profile_dict(basedir, profile)
else:
skydir_val = skydir_dict[skydir_key]
pkey, psrc_name, pdict = build_profile_dict(basedir, profile)
pdict['ra'] = skydir_val['ra']
pdict['dec'] = skydir_val['dec']
pkey += "_%06i" % skydir_key
outfile = "sed_%s.fits" % pkey
# Add the source and get the list of correlated soruces
correl_dict, test_src_name = add_source_get_correlated(gta, psrc_name,
pdict, correl_thresh=0.25,
non_null_src=args.non_null_src)
# Write the list of correlated sources
correl_yaml = os.path.join(basedir, "correl_%s.yaml" % pkey)
write_yaml(correl_dict, correl_yaml)
gta.free_sources(False)
for src_name in correl_dict.keys():
gta.free_source(src_name, pars='norm')
# build the SED
if args.non_null_src:
gta.update_source(test_src_name, reoptimize=True)
gta.write_roi("base_%s"% pkey, make_plots=False)
gta.sed(test_src_name, prefix=pkey, outfile=outfile, make_plots=args.make_plots)
# remove the source
gta.delete_source(test_src_name)
# put the ROI back to how it was
gta.load_xml(args.roi_baseline)
return gta
if not check_log(logfile) == "Successful":
sys.exit(1)
gta.setup()
sqrt_ts_threshold = 3
halo_width = np.logspace(-1, 0, 9)
halo_index = np.array([1.5, 1.75, 2.0, 2.25, 2.5, 2.75, 3.0])
model0 = {"SpatialModel": "PointSource", "Index": 1.5}
model1 = {"SpatialModel": "PointSource", "Index": 2.0}
model2 = {"SpatialModel": "PointSource", "Index": 2.5}
src_name = gta.roi.sources[0].name
gta.load_roi("base", reload_sources=True)
# gta.tsmap('base',model=model1)
gta.tsmap("base_emin40", model=model1, erange=[4.0, 5.5])
gta.print_roi()
# -----------------------------------
# Pass 0 - Source at Nominal Position
# -----------------------------------
gta.load_roi("fit0", reload_sources=True)
# fit_region(gta,'fit0',src_name)
fit_region(gta, "fit0_emin40", src_name, erange=[4.0, 5.5])
# -------------------------------------