def __init__(self, savedir, code, **kwargs):
keyword_options.process(self, kwargs)
self.savedir = expandvars(savedir)
self.code = code
print 'Putting jobs in %s' % self.savedir
def __init__(self, savedir, keys, **kwargs):
keyword_options.process(self, kwargs)
self.savedir = expandvars(savedir)
self.keys = keys
self._merge()
def __init__(self, roi_dir, ps_manager, ds_manager, spectral_analysis,
**kwargs):
""" roi_dir -- the center of the ROI
ps_manager -- an instance of ROIPointSourceManager
ds_manager -- an instance of ROIDiffuseManager
"""
keyword_options.process(self, kwargs)
self.__dict__.update(**kwargs)
self.roi_dir = roi_dir
self.psm = ps_manager
self.dsm = ds_manager
self.bgm = self.dsm ### bgm is deprecated, set here for convenience of interactive access
self.sa = spectral_analysis
self.logl = None
self.prev_logl = None
self.__setup_bands__()
self.__warn_about_binning__()
self.bin_centers = np.sort(list(set([b.e for b in self.bands])))
self.bin_edges = np.sort(
list(
set([b.emin
for b in self.bands] + [b.emax for b in self.bands])))
self.param_state, self.param_vals = None, None
if self.skip_setup:
if not self.quiet:
print 'No likelihood setup done: skip_setup is set'
return
self.__pre_fit__()
self.logl = self.prev_logl = -self.logLikelihood(
self.get_parameters()) # make sure everything initialized
def __init__(self, band, sources, free, roi, **kwargs):
"""
band : bands.EnergyBand object
sources : list of sources.Source objects
free : [array of bool | None]
to select models with variable parameters
If None, select all
roi reference to the ROI
"""
keyword_options.process(self, kwargs)
# make a list of the Response objects
self.bandsources = np.array(
map(lambda s: s.response(band, quiet=self.quiet, roi=roi),
sources))
self.band = band
self.event_type_name = config.event_type_name(band.event_type)
self.exposure_factor = band.exposure.correction
self.data = band.pix_counts if band.has_pixels else [
] # data from the band
self.pixels = len(self.data)
self.initialize(free)
self.update()
# special code to unweight if galactic diffuse too large
self.unweight = self.make_unweight()
def __init__(self, ft1_file, **kwargs):
"""
"""
keyword_options.process(self, kwargs)
self.ft1_hdus=ft1 = fits.open(ft1_file)
self.tstart = ft1[1].header['TSTART'] # changed from 0 (redundant?) due to new Ballet FT1-generation
# extract arrays for values of interest
data =ft1['EVENTS'].data
self.glon, self.glat, self.energy, self.et, self.z, self.theta =\
[data[x] for x in 'L B ENERGY EVENT_TYPE ZENITH_ANGLE THETA'.split()]
#self.front = np.array([x[-1] for x in self.et],bool) # et is arrray of array of bool, last one true if Front
# generate event_type masks
self.et_mask={}
for et in self.etypes:
self.et_mask[et]= self.et[:,-1-et]
self.data_cut = np.logical_and(self.theta<self.theta_cut, self.z<self.z_cut)
if self.verbose>0:
print 'Found {} events. Removed: {:.2f} %'.format(len(data), 100.- 100*sum(self.data_cut)/float(len(data)));
# DataFrame with component values for energy and event type, nside
t = {}
band=0
for ie in range(len(self.ebins)-1):
for et in self.etypes:
order = self.orders[et if et<2 else 0][ie] # use max if PSF
nside = 2**order
t[band]= dict(ie=ie, event_type=et, nside=nside)
band+=1
self.df = pd.DataFrame(t).T
def __init__(self, like, name, *args, **kwargs):
keyword_options.process(self, kwargs)
self.like = like
self.name = name
if self.ul_algorithm not in BaseGtlikeSED.ul_choices:
raise Exception("Upper Limit Algorithm %s not in %s" % (self.ul_algorithm,str(BaseGtlikeSED.ul_choices)))
if self.bin_edges is not None:
if not BaseGtlikeSED.good_binning(like, self.bin_edges):
raise Exception("bin_edges is not commensurate with the underlying energy binning of pyLikelihood.")
self.bin_edges = np.asarray(self.bin_edges)
energy = np.sqrt(self.bin_edges[1:]*self.bin_edges[:-1])
else:
# These energies are always in MeV
self.bin_edges = like.energies
energy = like.e_vals
self.lower=self.bin_edges[:-1]
self.upper=self.bin_edges[1:]
source=self.like.logLike.getSource(name)
self.init_spectrum=source.spectrum()
self.init_model=build_pointlike_model(self.init_spectrum)
self.results = dict(
Name=name,
spectrum=name_to_spectral_dict(like,name, errors=True, covariance_matrix=True),
)
self._calculate(like)
super(GtlikeSED,self).__init__(self.results, **keyword_options.defaults_to_kwargs(self, SED))
def __init__(self, roi, which, **kwargs):
""" Compute an upper limit on the source extension, by the "PDG Method". """
keyword_options.process(self, kwargs)
self.roi = roi
self.which = which
self.init_ts = roi.TS(which, quick=False)
if self.init_ts < 4:
# Bunt on extension upper limits for completely insignificant sources
print 'Unable to compute extension upper limit for point-like source with too-small TS'
self.extension_limit = None
else:
if not isinstance(self.spatial_model,type):
raise Exception("The spatial model bust be a type, like Gaussian, not an instance, like Gaussian()")
# Note, since the input is the class, not the instance, the
# position parmaeters have not yet been added on.
n = self.spatial_model.param_names
assert len(n) == 1 and n[0] == 'Sigma'
self.saved_state = PointlikeState(roi)
self.spatial_low_lim, self.spatial_hi_lim = self.spatial_model.default_limits[0]
results = self._compute()
self.saved_state.restore()
def __init__(self,roi,which,**kwargs):
""" Object for calculating TS as a function of sigma. """
self.roi = roi
self.which = which
keyword_options.process(self, kwargs)
self.source = roi.get_source(which)
if not hasattr(self.source,'spatial_model'):
raise Exception("An extension profile can only be calculated for extended sources")
self.spatial_model=self.source.spatial_model
if not len(self.spatial_model.p)==3:
raise Exception("An extension profile can only be calculated for extended sources with 3 parameters (position + one extension)")
self.fit_kwargs = dict(estimate_errors=False)
if self.use_gradient is not None: self.fit_kwargs['use_gradient']=self.use_gradient
self.ts_kwargs = dict(which=self.which)
if self.quick is not None: self.ts_kwargs['quick']=self.quick
self.fill()
def __init__(self, config, roi_spec, **kwargs):
"""config : configuration.Configuration object
used to find model info
roi_spec : integer or string or ...
ROI specification, passed to load_sources in a subclass
"""
keyword_options.process(self, kwargs)
self.config = config
self.config.diffuse = config.diffuse.copy(
) # since something changes??
if self.ecat is None: #speed up if already loaded
self.ecat = extended.ExtendedCatalog(self.config.extended,
quiet=self.quiet)
# clear if called again
while len(self) > 0:
self.pop()
# sources loaded by a subclass that must implement this function
self.load_sources(roi_spec, **self.load_kw)
if config.auxcat is not None:
self.add_sources(config.auxcat)
self.initialize()
if len(self.parameters) == 0:
print 'WARNING: there are no free parameters'
print self.summary()
self.selected_source = None
def __init__(self, like, name, bin_edges, **kwargs):
""" Parameters:
* like - pyLikelihood object
* name - source to make an SED for
* bin_edges - if specified, calculate the SED in these bins.
"""
keyword_options.process(self, kwargs)
self.like = like
self.name = name
if not BaseGtlikeSED.good_binning(self.like, bin_edges):
raise Exception("bin_edges is not commensurate with the underlying energy binning of pyLikelihood.")
source=self.like.logLike.getSource(name)
self.init_spectrum=source.spectrum()
self.init_model=build_pointlike_model(self.init_spectrum)
self.init_energes = self.like.energies[[0,-1]]
bin_edges = np.asarray(bin_edges)
self.lower_energy=bin_edges[:-1]
self.upper_energy=bin_edges[1:]
self.middle_energy=np.sqrt(self.lower_energy*self.upper_energy)
if self.ul_algorithm not in self.ul_choices:
raise Exception("Upper Limit Algorithm %s not in %s" % (self.ul_algorithm,str(self.ul_choices)))
empty = lambda: np.empty_like(self.middle_energy)
self._calculate()
def __init__(self, data_specification, **kwargs):
"""
Create a new spectral analysis object.
data_specification: an instance of DataSpec with links to the
FT1/FT2, and/or binned data / livetime cube needed
for analysis (see docstring for that class).
Instance may be given as a pickle file.
"""
if not isinstance(data_specification,dataman.DataSpec):
if os.path.exists(data_specification):
from cPickle import load
try:
data_specification = load(file(data_specification))
except UnpicklingError:
print 'Invalid pickle file for DataSpecification.'
raise Exception
self.ae = self.dataspec = data_specification
keyword_options.process(self, kwargs)
#pixeldata name for backward compatibility
self.dataman=self.pixeldata = self.dataspec()
self.CALDBManager = pycaldb.CALDBManager(irf=self.irf,psf_irf=self.psf_irf,
CALDB=self.CALDB,custom_irf_dir=self.custom_irf_dir)
self.exposure = ExposureManager(self.dataman,self.CALDBManager,verbose=self.verbose)
self.psf = pypsf.CALDBPsf(self.CALDBManager)
def __init__(self, savedir, code, **kwargs):
keyword_options.process(self, kwargs)
self.savedir = expandvars(savedir)
self.code = code
print 'Putting jobs in %s' % self.savedir
def __init__(self, savedir, keys, **kwargs):
keyword_options.process(self, kwargs)
self.savedir = expandvars(savedir)
self.keys = keys
self._merge()
def __init__(self,roi,**kwargs):
keyword_options.process(self, kwargs)
if self.npix is None:
self.npix = float(self.size)/self.pixelsize
self.roi = roi
self.selected_bands = tuple(self.roi.bands if self.conv_type < 0 else \
[ band for band in self.roi.bands if band.ct == self.conv_type ])
# by default, use get energy range and image center from roi.
if self.center is None: self.center=self.roi.roi_dir
# bins in theta^2
self.bin_edges_deg = np.linspace(0.0,self.size**2,self.npix+1)
self.bin_centers_deg = (self.bin_edges_deg[1:] + self.bin_edges_deg[:-1])/2.0
# two factors of radians b/c theta^2
self.bin_edges_rad = np.radians(np.radians(self.bin_edges_deg))
self.bin_centers_rad = np.radians(np.radians(self.bin_centers_deg))
# the lower and upper agle for each bin.
self.theta_pairs_rad = zip(np.sqrt(self.bin_edges_rad[:-1]),
np.sqrt(self.bin_edges_rad[1:]))
self.fill()
def __init__(self, lcf, **kwargs):
keyword_options.process(self, kwargs)
self.lcf = lcf # uw.pulsar.lcfitters.LCFitter
self.lct = lcf.template # uw.pulsar.lcfitters.LCTemplate
self._fit()
def __init__(self, index, **kwargs):
""" index : int
HEALpix index for the ROI (RING)
"""
keyword_options.process(self, kwargs)
assert type(index) == types.IntType, 'Expect int type'
self.myindex = index
self.mskydir = self.skydir(index)
def __init__(self, **kwargs):
keyword_options.process(self, kwargs)
#ct0_file,ct1_file = get_irf_file(self.irf,CALDB=self.CALDB)
cdbm = pycaldb.CALDBManager(self.irf)
ct0_file, ct1_file = cdbm.get_aeff()
self._read_aeff(ct0_file, ct1_file)
if self.use_phidep:
self._read_phi(ct0_file, ct1_file)
def __init__(self, results, **kwargs):
keyword_options.process(self, kwargs)
if isinstance(results,dict):
self.results = results
elif isinstance(results, str):
self.results = loaddict(results)
else:
raise Exception("Unrecognized results %s" % results)
def __init__(self, output=None, **kwargs):
""" **NB -- if ft1 is None, binfile MUST be set to a real file
**NB -- if ft2 is None, either ltcube must be set to a real file or $FERMI/ft2.fits must exist
"""
keyword_options.process(self, kwargs)
self._set_bins()
self.dss = None # initialize
self.gti = None
def init_data():
self.ft1files = self._parse_filename(self.ft1)
if self.ft1files is not None:
# Register FT1 DSS keywords
self._get_ft1_dss()
self._make_cuts()
# Get GTI from FT1 if not already set
if self.gti is None:
self.gti = self._get_GTI()
if not self._check_binfile():
if self.nocreate:
raise DataManException('need to create %s' %
self.binfile)
self._make_binfile()
elif not self._check_binfile():
raise ValueError(
'No FT1 files or valid binned data found. (Looking for %s)'
% self.binfile)
init_data()
def init_exposure():
self.ft2files = self._parse_filename(self.ft2)
if self.exposure_cube is not None:
print 'using exposure cube files: ignore FT2'
full = [
os.path.join(os.path.expandvars('$FERMI/data'), f)
for f in self.exposure_cube
]
assert np.all(
map(os.path.exists,
full)), 'Exposure cube file(s) #s not found' % full
self.exposure_cube = full #replace with full path
return
if self.ft2files is not None:
if not self._check_ltcube():
if self.nocreate:
raise DataManException('need to create %s' %
self.ltcube)
self._make_ltcube()
elif not self._check_ltcube():
raise ValueError('No FT2 files or valid livetime found.')
init_exposure()
# save version to allow custom processing for backwards compat.
self.version = dataman_version
if output is not None: self.dump(output)
def __init__(self, config_dir, roi_spec=None, xml_file=None, **kwargs):
"""Start pointlike v2 (like2) in the specified ROI
parameters
----------
config_dir : string
file path to a folder containing a file config.txt
see configuration.Configuration
roi_spec : [None |integer | (ra,dec) tuple ]
If None, require that the input_model dict has a key 'xml_file'
if an integer, it must be <1728, the ROI number
if a string, assume a source name and load the ROI containing it
"""
keyword_options.process(self, kwargs)
self.config = config = configuration.Configuration(
config_dir, quiet=self.quiet, postpone=self.postpone)
ecat = extended.ExtendedCatalog(config.extended)
if isinstance(roi_spec, str):
# try:
# roi_sources =from_xml.ROImodelFromXML(config, roi_spec)
# roi_index = roi_sources.index
# except:
# print 'No ROI specification (an index) or presence of an xml file'
# raise
# Change to just expecting the name of a source
sourcelist = glob.glob('sources_*.csv')[0]
df = pd.read_csv(sourcelist,
index_col=3 if roi_spec[0] == 'J' else 0)
if roi_spec not in df.index:
print 'Source name "{}" not found '.format(roi_spec)
raise Exception
roi_index = int(df.loc[roi_spec]['roiname'][-4:])
print 'Loading ROI #{}, containing source "{}"'.format(
roi_index, roi_spec)
elif isinstance(roi_spec, int):
roi_index = roi_spec
elif type(roi_spec) == tuple and len(roi_spec) == 2:
roi_index = Band(12).index(SkyDir(*roi_spec))
else:
raise Exception('Did not recoginze roi_spec: %s' % (roi_spec))
roi_sources = from_healpix.ROImodelFromHealpix(
config,
roi_index,
ecat=ecat,
)
config.roi_spec = configuration.ROIspec(healpix_index=roi_index)
self.name = config.roi_spec.name if config.roi_spec is not None else roi_spec
roi_bands = bands.BandSet(config, roi_index)
roi_bands.load_data()
super(ROI, self).__init__(roi_bands, roi_sources)
def __init__(self, code, results, hypothesis, **kwargs):
keyword_options.process(self, kwargs)
self.code = code
self.results = results
self.hypothesis = hypothesis
assert self.code in ['gtlike','pointlike']
self._load_results()
def __init__(self, center, **kwargs):
""" center -- a SkyDir giving the center of the grid on which to convolve bg
kwargs are passed to Grid.
"""
keyword_options.process(self, kwargs)
defaults=dict(bounds_error=False)
defaults.update(kwargs)
# note do not use code in superclass needing psf, diffuse function
super(ConvolvableGrid, self).__init__(center, None, None, **defaults)
self.center = center
def __init__(self, code, results, hypothesis, **kwargs):
keyword_options.process(self, kwargs)
self.code = code
self.results = results
self.hypothesis = hypothesis
assert self.code in ['gtlike', 'pointlike']
self._load_results()
def __init__(self, roi, which, **kwargs):
""" Required arguments:
roi - ROIAnalysis boject
which - source for which to compute upper limit.
"""
keyword_options.process(self, kwargs)
self.roi = roi
self.which = which
self._compute()
def __init__(self, roi, name, **kwargs):
keyword_options.process(self, kwargs)
self.roi = roi
self.name = name
bf = BandFlux(self.roi, which=self.name, merge=self.merge, scale_factor=1)
results = PointlikeSED.pointlike_sed_to_dict(bf, flux_units=self.flux_units, energy_units=self.energy_units)
results['spectrum'] = name_to_spectral_dict(roi, name, errors=True, covariance_matrix=True)
super(PointlikeSED,self).__init__(results, **keyword_options.defaults_to_kwargs(self, SED))
def __init__(self, roi, name, param_name, param_min, param_max, **kwargs):
self.roi = roi
self.name = name
self.param_name = param_name
self.param_min = param_min
self.param_max = param_max
keyword_options.process(self, kwargs)
self._calculate()
def __init__(self, roi, name, param_name, param_min, param_max, **kwargs):
self.roi = roi
self.name = name
self.param_name = param_name
self.param_min = param_min
self.param_max = param_max
keyword_options.process(self, kwargs)
self._calculate()
def __init__(self, input_model, emin, emax, **kwargs):
""" Create an approximate power law spectrum. """
raise Exception("This code doesn't work yet. I think you need the exposure to do the fit correctly.")
self.input_model = input_model
self.emin = emin
self.emax = emax
keyword_options.process(self, kwargs)
self._calculate()
def __init__(self, roi, name, **kwargs):
keyword_options.process(self, kwargs)
self.roi = roi
self.name = name
if self.emin is None and self.emax is None:
self.emin, self.emax = get_full_energy_range(roi)
self._compute()
def __init__(self, like, name, **kwargs):
keyword_options.process(self, kwargs)
self.like = like
self.name = name
if self.emin is None and self.emax is None:
self.emin, self.emax = get_full_energy_range(like)
self.e = np.sqrt(self.emin*self.emax)
self._compute()
def __init__(self, roi, which, model0, model1, **kwargs):
keyword_options.process(self, kwargs)
state = PointlikeState(roi)
self.roi=roi
self.which=which
self.model0=model0.copy()
self.model1=model1.copy()
self.compute()
state.restore()
def __init__(self, ft2files, ft1files, **kwargs):
keyword_options.process(self, kwargs)
self.prev_vals = self.prev_ra = self.prev_dec = None # initialize caching
self.fields = [
'START', 'STOP', 'LIVETIME', 'RA_SCZ', 'DEC_SCZ', 'RA_ZENITH',
'DEC_ZENITH', 'RA_SCX', 'DEC_SCX'
]
self._setup_gti(ft1files)
self._setup_ft2(ft2files)
self._update_gti()
self._process_ft2()
self._finish()
def __init__(self, roi, which, model0, model1, **kwargs):
keyword_options.process(self, kwargs)
state = PointlikeState(roi)
self.roi = roi
self.which = which
self.model0 = model0.copy()
self.model1 = model1.copy()
self.compute()
state.restore()
def __init__(self, roi, **kwargs):
self.roi = roi
keyword_options.process(self, kwargs)
self.pf = self.create_pyfits()
self.data = self.pf[0].data
self.header = self.pf[0].header
if self.fitsfile is not None:
self.pf.writeto(self.fitsfile, clobber=True)
def __init__(self, roi, **kwargs):
keyword_options.process(self, kwargs)
roi.setup_energy_bands()
self.emin = np.asarray([eb.emin for eb in roi.energy_bands])
self.emax = np.asarray([eb.emax for eb in roi.energy_bands])
which = self.which
old_roi_p = roi.get_parameters().copy()
# extended hypothesis
source=roi.get_source(which='IC443')
sm = source.spatial_model
manager,index=roi.mapper(which)
roi.fit(estimate_errors=False)
self.ll_ext,self.ll_pt = [],[]
for eb in roi.energy_bands:
self.ll_ext.append(
-sum(band.logLikelihood() for band in eb.bands)
)
sm.shrink()
manager.bgmodels[index].initialize_counts(roi.bands)
roi.__update_state__()
roi.fit(estimate_errors=False)
# point hypothesis
manager,index=roi.mapper('IC443')
for eb in roi.energy_bands:
self.ll_pt.append(
-sum(band.logLikelihood() for band in eb.bands)
)
sm.unshrink()
manager.bgmodels[index].initialize_counts(roi.bands)
roi.set_parameters(old_roi_p)
roi.__update_state__()
self.ll_ext = np.asarray(self.ll_ext)
self.ll_pt = np.asarray(self.ll_pt)
self.ts_ext=2*(self.ll_ext-self.ll_pt)
self.ts_ext[self.ts_ext<0]=0
def __init__(self,roi,which=0,**kwargs):
keyword_options.process(self, kwargs)
self.roi,self.which = roi, which
self.quiet = roi.quiet
# we need a reference both to the center of the ROI, for use in calculating overlap,
# and to the original position of the point source, which may or may not be the same
self.rd = roi.roi_dir
self.set_source_info()
if self.bandfits: self.do_bandfits()
self.tsref=0
self.tsref = self.TSmap(self.sd) # source position not necessarily ROI center
def __init__(self, roi, name, param_name, **kwargs):
self.roi = roi
self.name = name
self.param_name = param_name
keyword_options.process(self, kwargs)
if self.param_vals is not None:
assert self.param_min is None and self.param_max is None and self.nparams is None
else:
assert self.param_min is not None and self.param_max is not None and self.nparams is not None
self.param_vals = np.linspace(self.param_min, self.param_max, self.nparams)
self._calculate()
def __init__(self, roi, name, param_name, **kwargs):
self.roi = roi
self.name = name
self.param_name = param_name
keyword_options.process(self, kwargs)
if self.param_vals is not None:
assert self.param_min is None and self.param_max is None and self.nparams is None
else:
assert self.param_min is not None and self.param_max is not None and self.nparams is not None
self.param_vals = np.linspace(self.param_min, self.param_max,
self.nparams)
self._calculate()
def __init__(self,
spectral_analysis,
diffuse_source,
roi_dir,
name=None,
**kwargs):
self.sa = spectral_analysis
self.roi_dir = roi_dir
self.diffuse_source = diffuse_source
self.dmodel = diffuse_source.dmodel
self.smodel = diffuse_source.smodel
self.name = diffuse_source.name
keyword_options.process(self, kwargs)
self.setup()
def __init__(self, irf, **kwargs):
keyword_options.process(self, kwargs)
self.irf = irf
if self.CALDB is None:
try:
self.CALDB = os.environ['CALDB']
except:
try:
from facilities import py_facilities
os_environ = py_facilities.commonUtilities_getEnvironment
self.CALDB = os_environ('CALDB')
except:
raise Exception(
'Environment variable CALDB must be set, or findable by py_facilities package'
)
if self.custom_irf_dir is not None:
if not os.path.exists(self.custom_irf_dir):
raise Exception("custom_irf_dir %s does not exist" %
self.custom_irf_dir)
else:
self.custom_irf_dir = os.environ.get('CUSTOM_IRF_DIR', None)
if self.custom_irf_dir is not None and self.custom_irf_dir != '':
if not self.quiet:
print 'CALDBManager: using custom irf: "%s"' % self.custom_irf_dir
self.bcf = join(self.CALDB, 'bcf')
if not os.path.exists(self.bcf):
self.CALDB = join(self.CALDB, 'data', 'glast', 'lat')
self.bcf = join(self.CALDB, 'bcf')
if not os.path.exists(self.bcf):
raise Exception('Invalid CALDB directory %s.' % self.bcf)
self.CALDB_index = os.path.join(self.CALDB, 'caldb.indx')
if not os.path.exists(self.CALDB_index):
raise Exception("caldb.indx file %s does not exist." %
self.CALDB_index)
self.load_caldb_indx()
self.construct_psf()
if not self.quiet: print 'PSF: %s' % self.psf_files
self.construct_aeff()
def __init__(self, roi, name, *args, **kwargs):
self.roi = roi
keyword_options.process(self, kwargs)
self.pointlike_fit_kwargs = dict(use_gradient=False)
self.name = name
self._setup_savedir()
self._setup_time_bins()
saved_state = PointlikeState(roi)
self._test_variability()
saved_state.restore()
def __init__(self, roi, name, *args, **kwargs):
self.roi = roi
keyword_options.process(self, kwargs)
self.pointlike_fit_kwargs = dict(use_gradient=False)
self.name = name
self._setup_savedir()
self._setup_time_bins()
saved_state = PointlikeState(roi)
self._test_variability()
saved_state.restore()
def __init__(self,**kwargs):
keyword_options.process(self, kwargs)
if self.point_sources == [] and self.diffuse_sources == []:
self.point_sources, self.diffuse_sources = self.get_default_sources()
ltcube = join(self.tempdir,'ltcube.fits')
ds = DataSpecification(
ft1files = join(self.tempdir,'ft1.fits'),
ft2files = join(self.tempdir,'ft2.fits'),
ltcube = ltcube,
binfile = join(self.tempdir,'binfile.fits')
)
sa = SpectralAnalysisMC(ds,
seed=self.seed,
emin=self.emin,
emax=self.emax,
binsperdec=self.binsperdec,
event_class=self.event_class,
conv_type=self.conv_type,
roi_dir=self.roi_dir,
minROI=self.maxROI,
maxROI=self.maxROI,
irf=self.irf,
use_weighted_livetime=True,
savedir=self.tempdir,
tstart=0,
tstop=self.simtime,
ltfrac=0.9,
)
roi = sa.roi(roi_dir=self.roi_dir,
point_sources = self.point_sources,
diffuse_sources = self.diffuse_sources)
self.roi = roi
fix_pointlike_ltcube(ltcube)
def __init__(self,roi,bin_edges,nrows=1,grid_kwargs=dict(),**kwargs):
default_grid_kwargs = dict(axes_pad=0.1,
cbar_location="top",
cbar_mode="each",
cbar_size="7%",
cbar_pad="2%")
self.grid_kwargs = default_grid_kwargs.copy()
self.grid_kwargs.update(grid_kwargs)
self.roi = roi
keyword_options.process(self, kwargs)
self.nrows=nrows
self.bin_edges = bin_edges
self.nplots = len(self.bin_edges)-1
self.ncols= int(math.ceil(float(self.nplots)/self.nrows))
for e in bin_edges:
if not np.any(np.abs(e-roi.bin_edges) < 0.5):
raise Exception("Energy %.1f inconsistent with ROI energy binning." % e)
self.lower_energies = bin_edges[:-1]
self.upper_energies = bin_edges[1:]
state = PointlikeState(roi)
# step 1, test consistentcy of each energy with binning in pointlike
kwargs['title'] = '' # dont title the subplots
self.maps = []
for i,(lower,upper) in enumerate(zip(self.lower_energies, self.upper_energies)):
roi.change_binning(fit_emin=lower,fit_emax=upper)
self.maps.append(self.object(roi,**kwargs))
state.restore()
def __init__(self, roi, diffuse_kwargs, **kwargs):
""" diffuse_kwargs passed into get_gulli_diffuse
"""
keyword_options.process(self, kwargs)
self.roi = roi
self.diffuse_kwargs = diffuse_kwargs
def __init__(self, roi, name, *args, **kwargs):
keyword_options.process(self, kwargs)
self.roi = roi
self.name = name
self._calculate()
def __init__(self, like, name, *args, **kwargs):
keyword_options.process(self, kwargs)
self.like = like
self.name = name
self._calculate()
def __init__(self, roi, **kwargs):
""" Build a gtlike pyLikelihood object
which is consistent with a pointlike roi. """
keyword_options.process(self, kwargs)
self.roi = roi
if not roi.quiet: print 'Running a gtlike followup'
self.old_dir=os.getcwd()
if self.savedir is not None:
self.savedata = True
if not os.path.exists(self.savedir):
os.makedirs(self.savedir)
else:
self.savedata = False
self.savedir=mkdtemp(prefix=self.savedir_prefix)
# put pfiles into savedir
os.environ['PFILES']=self.savedir+';'+os.environ['PFILES'].split(';')[-1]
if not roi.quiet: print 'Saving files to ',self.savedir
cut_ft1=join(self.savedir,"ft1_cut.fits")
input_srcmdl_file=join(self.savedir,'srcmdl.xml')
expmap = join(self.savedir,"expmap.fits")
ltcube=roi.sa.pixeldata.ltcube
ft2=Gtlike.get_ft2(roi)
irfs=Gtlike.get_gtlike_irfs(roi)
ct = roi.sa.pixeldata.conv_type
radius = roi.sa.maxROI
ra = roi.roi_dir.ra()
dec = roi.roi_dir.dec()
emin,emax=roi.bin_edges[0],roi.bin_edges[-1]
Gtlike.save_xml(roi, input_srcmdl_file)
evfile=Gtlike.make_evfile(roi,self.savedir)
if not os.path.exists(cut_ft1):
if not roi.quiet: print 'Running gtselect'
gtselect=GtApp('gtselect','dataSubselector')
gtselect.run(infile=evfile,
outfile=cut_ft1,
ra=ra, dec=dec, rad=radius,
tmin=0, tmax=0,
emin=emin, emax=emax,
zmax=180, convtype=ct,
chatter=self.chatter)
else:
if not roi.quiet: print '... Skiping gtselect'
if not os.path.exists(expmap):
# Run gtexpmap following suggestions from tutorial
# pad 10deg on radius to account for nearby sources,
# nlat has half degree pixels
if not roi.quiet: print 'Running gtexpmap'
gtexpmap=GtApp('gtexpmap')
gtexpmap.run(evfile=cut_ft1,
scfile=ft2,
expcube=ltcube,
outfile=expmap,
irfs=irfs,
srcrad=radius+10,
nlong=int(np.ceil(0.5*(radius+10)*2)),
nlat=int(np.ceil(0.5*(radius+10)*2)),
nenergies=int(np.ceil(np.log10(emax)-np.log10(emin)))*4,
chatter=self.chatter,
)
else:
if not roi.quiet: print '... Skiping gtexpmap'
gtdiffrsp = GtApp('gtdiffrsp')
if not roi.quiet: print 'Running gtdiffrsp'
gtdiffrsp.run(evfile=cut_ft1,
scfile=ft2,
srcmdl=input_srcmdl_file,
irfs=irfs,
chatter=self.chatter,
)
if not roi.quiet: print 'Creating Unbinned LIKE'
obs = UnbinnedObs(eventFile=cut_ft1, scFile=ft2, expMap=expmap, expCube=ltcube, irfs=irfs)
self.like = UnbinnedAnalysis(observation=obs,srcModel=input_srcmdl_file,optimizer=self.optimizer)
if not roi.quiet: print 'Unbinned LIKE Created!'
def __init__(self, roi, **kwargs):
""" Build a gtlike pyLikelihood object
which is consistent with a pointlike roi. """
keyword_options.process(self, kwargs)
self.roi = roi
if not roi.quiet: print 'Running a gtlike followup'
self.old_dir=os.getcwd()
if self.savedir is not None:
self.savedata = True
if not os.path.exists(self.savedir):
os.makedirs(self.savedir)
else:
self.savedata = False
self.savedir=mkdtemp(prefix=self.savedir_prefix)
# put pfiles into savedir
os.environ['PFILES']=self.savedir+';'+os.environ['PFILES'].split(';')[-1]
if not roi.quiet: print 'Saving files to ',self.savedir
if self.emin==None and self.emax==None and self.enumbins==None:
self.emin,self.emax=roi.bin_edges[0],roi.bin_edges[-1]
self.enumbins=len(roi.bin_edges)-1
elif self.emin is not None and \
self.emax is not None and \
self.enumbins is not None:
# all set
pass
else:
raise Exception("emin, emax, and enumbins must all be set.")
# Note that this formulation makes the gtlike slightly smaller than
# the pointlike ROI (so the gtlike ROI is inside the pointlike ROI)
roi_radius=np.degrees(max(_.radius_in_rad for _ in roi.bands))
if self.bigger_roi:
npix=int(math.ceil(2.0*roi_radius/self.binsz))
else:
npix=int(math.ceil(np.sqrt(2.0)*roi_radius/self.binsz))
ct = roi.sa.pixeldata.conv_type
cmap_file=join(self.savedir,'ccube.fits')
srcmap_file=join(self.savedir,'srcmap.fits')
bexpmap_file=join(self.savedir,'bexpmap.fits')
input_srcmdl_file=join(self.savedir,'srcmdl.xml')
cut_ft1=join(self.savedir,"ft1_cut.fits")
ft2=Gtlike.get_ft2(roi)
ltcube=roi.sa.pixeldata.ltcube
if self.fix_pointlike_ltcube:
print 'Fixing pointlike ltcube %s' % ltcube
livetime.fix_pointlike_ltcube(ltcube)
irfs=Gtlike.get_gtlike_irfs(roi)
if self.galactic:
x,y,coordsys_str=roi.roi_dir.l(),roi.roi_dir.b(),'GAL'
else:
x,y,coordsys_str=roi.roi_dir.ra(),roi.roi_dir.dec(),'CEL'
Gtlike.save_xml(roi, input_srcmdl_file, extended_dir_name=self.extended_dir_name)
evfile=Gtlike.make_evfile(roi,self.savedir)
if not os.path.exists(cut_ft1):
if not roi.quiet: print 'Running gtselect'
gtselect=GtApp('gtselect','dataSubselector')
gtselect.run(infile=evfile,
outfile=cut_ft1,
ra=0, dec=0, rad=180,
tmin=0, tmax=0,
emin=self.emin, emax=self.emax,
zmax=180, convtype=ct,
chatter=self.chatter)
else:
if not roi.quiet: print '... Skiping gtselect'
if not os.path.exists(cmap_file):
if not roi.quiet: print 'Running gtbin (ccube)'
gtbin=GtApp('gtbin','evtbin')
gtbin.run(algorithm='ccube',
nxpix=npix, nypix=npix, binsz=self.binsz,
evfile=cut_ft1,
outfile=cmap_file,
scfile=ft2,
xref=x, yref=y, axisrot=0, proj=self.proj,
ebinalg='LOG', emin=self.emin, emax=self.emax, enumbins=self.enumbins,
coordsys=coordsys_str,
chatter=self.chatter)
else:
if not roi.quiet: print '... Skiping gtbin (ccube)'
if not os.path.exists(bexpmap_file):
# Use the default binning all sky, 1deg/pixel
if not roi.quiet: print 'Running gtexpcube'
gtexpcube=GtApp('gtexpcube2','Likelihood')
gtexpcube.run(infile=ltcube,
cmap='none',
ebinalg='LOG', emin=self.emin, emax=self.emax, enumbins=self.enumbins,
outfile=bexpmap_file, proj='CAR',
nxpix=360, nypix=180, binsz=1,
irfs=irfs,
coordsys=coordsys_str,
chatter=self.chatter)
else:
if not roi.quiet: print '... Skiping gtexpcube'
if not os.path.exists(srcmap_file):
if not roi.quiet: print 'Running gtsrcmaps'
gtsrcmaps=GtApp('gtsrcmaps','Likelihood')
gtsrcmaps.run(scfile=ft2,
expcube=ltcube,
cmap=cmap_file,
srcmdl=input_srcmdl_file,
bexpmap=bexpmap_file,
outfile=srcmap_file,
irfs=irfs,
rfactor=self.rfactor,
resample=self.resample,
minbinsz=self.minbinsz,
chatter=self.chatter)
else:
if not roi.quiet: print '... Skiping gtsrcmaps'
if not roi.quiet: print 'Creating Binned LIKE'
obs=BinnedObs(srcMaps=srcmap_file,expCube=ltcube,binnedExpMap=bexpmap_file,irfs=irfs)
self.like = BinnedAnalysis(binnedData=obs,srcModel=input_srcmdl_file,optimizer=self.optimizer)
if self.enable_edisp:
if not roi.quiet: print 'Enabeling energy dispersion'
self.like.logLike.set_edisp_flag(True)
if not roi.quiet: print 'Binned LIKE Created!'