def make_mean_rmf(energy_true,
energy_reco,
center,
ObsList,
outdir,
source_name=""):
"""
Compute the mean psf for a set of observation and a given energy band
Parameters
----------
energy_true: Tuple for the energy true bin: (Emin,Emax,nbins)
energy_reco: Tuple for the energy reco bin: (Emin,Emax,nbins)
center: SkyCoord of the source
ObsList: ObservationList to use to compute the psf (could be different that the data_store for G0p9 for the GC for example)
outdir: directory where the fits image will go
source_name: name of the source for which you want to compute the mean RMF
Returns
-------
"""
# Here all the observations have a center at less than 2 degrees from the Crab so it will be ok to estimate the mean psf on the Crab source postion (the area is define for offset equal to 2 degrees...)
emin_true, emax_true, nbin_true = energy_true
emin_reco, emax_reco, nbin_reco = energy_reco
energy_true_bins = EnergyBounds.equal_log_spacing(emin_true, emax_true,
nbin_true, 'TeV')
energy_reco_bins = EnergyBounds.equal_log_spacing(emin_reco, emax_reco,
nbin_reco, 'TeV')
rmf = ObsList.make_mean_edisp(position=center,
e_true=energy_true_bins,
e_reco=energy_reco_bins)
rmf.write(outdir + "/mean_rmf" + source_name + ".fits", clobber=True)
def make_mean_rmf(energy_true, energy_reco, center, ObsList):
"""
Compute the mean psf for a set of observation and a given energy band
Parameters
----------
energy_true: Tuple for the energy axis: (Emin,Emax,nbins)
for the true energy array
energy_reco: Tuple for the energy axis: (Emin,Emax,nbins)
for the reco energy array
source_name: name of the source you want to compute the image
center: SkyCoord of the source
ObsList: ObservationList to use to compute the psf (could be different that the data_store for G0p9 for the GC for example)
Returns
-------
rmf: `~gammapy.irf.EnergyDispersion`
Stacked EDISP for a set of observation
"""
# Here all the observations have a center at less than 2 degrees from the Crab so it will be ok to estimate the mean psf on the Crab source postion (the area is define for offset equal to 2 degrees...)
emin_true, emax_true, nbin_true = energy_true
emin_reco, emax_reco, nbin_reco = energy_reco
energy_true_bins = EnergyBounds.equal_log_spacing(emin_true, emax_true,
nbin_true, 'TeV')
energy_reco_bins = EnergyBounds.equal_log_spacing(emin_reco, emax_reco,
nbin_reco, 'TeV')
rmf = ObsList.make_mean_edisp(position=center,
e_true=energy_true_bins,
e_reco=energy_reco_bins)
return rmf
def read(cls, filename, offset='0.5 deg'):
"""Read from a FITS file.
Compute RMF at 0.5 deg offset on fly.
Parameters
----------
filename : `str`
File containing the IRFs
"""
filename = str(make_path(filename))
with fits.open(filename, memmap=False) as hdulist:
aeff = EffectiveAreaTable.from_hdulist(hdulist=hdulist)
edisp = EnergyDispersion2D.read(filename, hdu='ENERGY DISPERSION')
bkg = BgRateTable.from_hdulist(hdulist=hdulist)
psf = Psf68Table.from_hdulist(hdulist=hdulist)
sens = SensitivityTable.from_hdulist(hdulist=hdulist)
# Create rmf with appropriate dimensions (e_reco->bkg, e_true->area)
e_reco_min = bkg.energy.lo[0]
e_reco_max = bkg.energy.hi[-1]
e_reco_bin = bkg.energy.nbins
e_reco_axis = EnergyBounds.equal_log_spacing(
e_reco_min,
e_reco_max,
e_reco_bin,
'TeV',
)
e_true_min = aeff.energy.lo[0]
e_true_max = aeff.energy.hi[-1]
e_true_bin = aeff.energy.nbins
e_true_axis = EnergyBounds.equal_log_spacing(
e_true_min,
e_true_max,
e_true_bin,
'TeV',
)
rmf = edisp.to_energy_dispersion(
offset=offset,
e_reco=e_reco_axis,
e_true=e_true_axis,
)
return cls(aeff=aeff,
bkg=bkg,
edisp=edisp,
psf=psf,
sens=sens,
rmf=rmf)
def get_psf_table(psf, emin, emax, bins):
"""Returns a table of energy and containment radius
from an EnergyDependentTablePSF object."""
# Container for data
data = []
# Loop over energies and determine PSF containment radius
ebounds = EnergyBounds.equal_log_spacing(emin, emax, bins, 'MeV')
for energy in ebounds:
energy_psf = psf.table_psf_at_energy(energy)
containment_68 = energy_psf.containment_radius(0.68)
containment_95 = energy_psf.containment_radius(0.95)
row = dict(ENERGY=energy.value,
CONT_68=containment_68.value,
CONT_95=containment_95.value)
data.append(row)
# Construct table and add correct units to columns
table = Table(data)
table['ENERGY'].units = energy.unit
table['CONT_68'].units = containment_68.unit
table['CONT_95'].units = containment_95.unit
return table
def get_psf_table(psf, emin, emax, bins):
"""Returns a table of energy and containment radius
from an EnergyDependentTablePSF object."""
# Container for data
data = []
# Loop over energies and determine PSF containment radius
ebounds = EnergyBounds.equal_log_spacing(emin, emax, bins, 'MeV')
for energy in ebounds:
energy_psf = psf.table_psf_at_energy(energy)
containment_68 = energy_psf.containment_radius(0.68)
containment_95 = energy_psf.containment_radius(0.95)
row = dict(ENERGY=energy.value,
CONT_68=containment_68.value,
CONT_95=containment_95.value)
data.append(row)
# Construct table and add correct units to columns
table = Table(data)
table['ENERGY'].units = energy.unit
table['CONT_68'].units = containment_68.unit
table['CONT_95'].units = containment_95.unit
return table
def load_irf(self):
filename = os.path.join(self.outdir, "irf.fits.gz")
with fits.open(filename, memmap=False) as hdulist:
aeff = EffectiveAreaTable2D.from_hdulist(hdulist=hdulist)
edisp = EnergyDispersion2D.read(filename, hdu="ENERGY DISPERSION")
bkg_fits_table = hdulist["BACKGROUND"]
bkg_table = Table.read(bkg_fits_table)
energy_lo = bkg_table["ENERG_LO"].quantity
energy_hi = bkg_table["ENERG_HI"].quantity
bkg = bkg_table["BGD"].quantity
axes = [
BinnedDataAxis(energy_lo,
energy_hi,
interpolation_mode="log",
name="energy")
]
bkg = BkgData(data=NDDataArray(axes=axes, data=bkg))
# Create rmf with appropriate dimensions (e_reco->bkg, e_true->area)
e_reco_min = bkg.energy.lo[0]
e_reco_max = bkg.energy.hi[-1]
e_reco_bin = bkg.energy.nbins
e_reco_axis = EnergyBounds.equal_log_spacing(e_reco_min, e_reco_max,
e_reco_bin, "TeV")
e_true_min = aeff.data.axes[0].lo[0]
e_true_max = aeff.data.axes[0].hi[-1]
e_true_bin = len(aeff.data.axes[0].bins) - 1
e_true_axis = EnergyBounds.equal_log_spacing(e_true_min, e_true_max,
e_true_bin, "TeV")
# Fake offset...
rmf = edisp.to_energy_dispersion(offset=0.5 * u.deg,
e_reco=e_reco_axis,
e_true=e_true_axis)
# This is required because in gammapy v0.8
# gammapy.spectrum.utils.integrate_model
# calls the attribute aeff.energy which is an attribute of
# EffectiveAreaTable and not of EffectiveAreaTable2D
# WARNING the angle is not important, but only because we started with
# on-axis data! TO UPDATE
aeff = aeff.to_effective_area_table(Angle("1d"))
self.irf = Irf(bkg=bkg, aeff=aeff, rmf=rmf)
def read(cls, filename, offset='0.5 deg'):
"""Read from a FITS file.
Compute RMF at 0.5 deg offset on fly.
Parameters
----------
filename : `str`
File containing the IRFs
"""
filename = str(make_path(filename))
with fits.open(filename, memmap=False) as hdulist:
aeff = EffectiveAreaTable.from_hdulist(hdulist=hdulist)
edisp = EnergyDispersion2D.read(filename, hdu='ENERGY DISPERSION')
bkg = BgRateTable.from_hdulist(hdulist=hdulist)
psf = Psf68Table.from_hdulist(hdulist=hdulist)
sens = SensitivityTable.from_hdulist(hdulist=hdulist)
# Create rmf with appropriate dimensions (e_reco->bkg, e_true->area)
e_reco_min = bkg.energy.lo[0]
e_reco_max = bkg.energy.hi[-1]
e_reco_bin = bkg.energy.nbins
e_reco_axis = EnergyBounds.equal_log_spacing(
e_reco_min, e_reco_max, e_reco_bin, 'TeV',
)
e_true_min = aeff.energy.lo[0]
e_true_max = aeff.energy.hi[-1]
e_true_bin = aeff.energy.nbins
e_true_axis = EnergyBounds.equal_log_spacing(
e_true_min, e_true_max, e_true_bin, 'TeV',
)
rmf = edisp.to_energy_dispersion(
offset=offset, e_reco=e_reco_axis, e_true=e_true_axis,
)
return cls(
aeff=aeff,
bkg=bkg,
edisp=edisp,
psf=psf,
sens=sens,
rmf=rmf
)
def make_counts_array():
"""Make an example counts array with energy and offset axes."""
data_store = DataStore.from_dir(gammapy_extra.dir / 'datasets/hess-crab4')
event_lists = data_store.load_all('events')
ebounds = EnergyBounds.equal_log_spacing(0.1, 100, 100, 'TeV')
offset = np.linspace(0, 2.5, 100)
array = EnergyOffsetArray(ebounds, offset)
array.fill_events(event_lists)
return array
def table_model():
energy_edges = EnergyBounds.equal_log_spacing(0.1 * u.TeV, 100 * u.TeV, 1000)
energy = energy_edges.log_centers
index = 2.3 * u.Unit('')
amplitude = 4 / u.cm ** 2 / u.s / u.TeV
reference = 1 * u.TeV
pl = PowerLaw(index, amplitude, reference)
flux = pl(energy)
return TableModel(energy, flux, 1 * u.Unit(''))
def table_model():
energy_edges = EnergyBounds.equal_log_spacing(0.1 * u.TeV, 100 * u.TeV, 1000)
energy = energy_edges.log_centers
index = 2.3 * u.Unit('')
amplitude = 4 / u.cm ** 2 / u.s / u.TeV
reference = 1 * u.TeV
pl = PowerLaw(index, amplitude, reference)
flux = pl(energy)
return TableModel(energy, flux, 1 * u.Unit(''))
def make_counts_array():
"""Make an example counts array with energy and offset axes."""
data_store = DataStore.from_dir('$GAMMAPY_EXTRA/datasets/hess-crab4-hd-hap-prod2')
event_lists = data_store.load_all('events')
ebounds = EnergyBounds.equal_log_spacing(0.1, 100, 100, 'TeV')
offset = Angle(np.linspace(0, 2.5, 100), "deg")
array = EnergyOffsetArray(ebounds, offset)
array.fill_events(event_lists)
return array
def load_irf(self):
filename = os.path.join(self.outdir, 'irf.fits.gz')
with fits.open(filename, memmap=False) as hdulist:
aeff = EffectiveAreaTable.from_hdulist(hdulist=hdulist)
edisp = EnergyDispersion2D.read(filename, hdu="ENERGY DISPERSION")
bkg_fits_table = hdulist["BACKGROUND"]
bkg_table = Table.read(bkg_fits_table)
energy_lo = bkg_table["ENERG_LO"].quantity
energy_hi = bkg_table["ENERG_HI"].quantity
bkg = bkg_table["BGD"].quantity
axes = [
BinnedDataAxis(
energy_lo, energy_hi, interpolation_mode="log", name="energy"
)
]
bkg = BkgData(data=NDDataArray(axes=axes, data=bkg))
# Create rmf with appropriate dimensions (e_reco->bkg, e_true->area)
e_reco_min = bkg.energy.lo[0]
e_reco_max = bkg.energy.hi[-1]
e_reco_bin = bkg.energy.nbins
e_reco_axis = EnergyBounds.equal_log_spacing(
e_reco_min, e_reco_max, e_reco_bin, "TeV"
)
e_true_min = aeff.energy.lo[0]
e_true_max = aeff.energy.hi[-1]
e_true_bin = aeff.energy.nbins
e_true_axis = EnergyBounds.equal_log_spacing(
e_true_min, e_true_max, e_true_bin, "TeV"
)
# Fake offset...
rmf = edisp.to_energy_dispersion(
offset=0.5 * u.deg, e_reco=e_reco_axis, e_true=e_true_axis
)
self.irf = Irf(bkg=bkg, aeff=aeff, rmf=rmf)
def make_psf_cube(image_size,
energy_cube,
source_name,
center_maps,
center,
ObsList,
outdir,
spectral_index=2.3):
"""
Compute the mean psf for a set of observation for different energy bands
Parameters
----------
image_size:int, Total number of pixel of the 2D map
energy: Tuple for the energy axis: (Emin,Emax,nbins)
source_name: name of the source you want to compute the image
center_maps: SkyCoord
center of the images
center: SkyCoord
position where we want to compute the psf
ObsList: ObservationList to use to compute the psf (could be different that the data_store for G0p9 for the GC for example)
outdir: directory where the fits image will go
spectral_index: assumed spectral index to compute the psf
Returns
-------
"""
ref_cube = make_empty_cube(image_size, energy_cube, center_maps)
header = ref_cube.sky_image_ref.to_image_hdu().header
energy_bins = ref_cube.energies(mode="edges")
for i_E, E in enumerate(energy_bins[0:-1]):
energy_band = Energy(
[energy_bins[i_E].value, energy_bins[i_E + 1].value],
energy_bins.unit)
energy = EnergyBounds.equal_log_spacing(energy_band[0].value,
energy_band[1].value, 100,
energy_band.unit)
# Here all the observations have a center at less than 2 degrees from the Crab so it will be ok to estimate the mean psf on the Crab source postion (the area is define for offset equal to 2 degrees...)
psf_energydependent = ObsList.make_mean_psf(center, energy, theta=None)
try:
psf_table = psf_energydependent.table_psf_in_energy_band(
energy_band, spectral_index=spectral_index)
except:
psf_table = TablePSF(
psf_energydependent.offset,
Quantity(np.zeros(len(psf_energydependent.offset)), u.sr**-1))
ref_cube.data[i_E, :, :] = fill_acceptance_image(
header, center_maps, psf_table._offset.to("deg"),
psf_table._dp_domega,
psf_table._offset.to("deg")[-1]).data
ref_cube.write(outdir + "/mean_psf_cube_" + source_name + ".fits",
format="fermi-counts")
def make_mean_psf_cube(image_size,
energy_cube,
center_maps,
center,
ObsList,
spectral_index=2.3):
"""
Compute the mean psf for a set of observation for different energy bands
Parameters
----------
image_size:int, Total number of pixel of the 2D map
energy: Tuple for the energy axis: (Emin,Emax,nbins)
center_maps: SkyCoord
center of the images
center: SkyCoord
position where we want to compute the psf
ObsList: ObservationList to use to compute the psf (could be different that the data_store for G0p9 for the GC for example)
spectral_index: assumed spectral index to compute the psf
Returns
-------
ref_cube : `~gammapy.cube.SkyCube`
PSF mean cube
"""
ref_cube = make_empty_cube(image_size, energy_cube, center_maps)
header = ref_cube.sky_image_ref.to_image_hdu().header
energy_bins = ref_cube.energies()
for i_E, E in enumerate(energy_bins[0:-1]):
energy_band = Energy(
[energy_bins[i_E].value, energy_bins[i_E + 1].value],
energy_bins.unit)
energy = EnergyBounds.equal_log_spacing(energy_band[0].value,
energy_band[1].value, 100,
energy_band.unit)
psf_energydependent = ObsList.make_psf(center, energy, theta=None)
try:
psf_table = psf_energydependent.table_psf_in_energy_band(
energy_band, spectral_index=spectral_index)
except:
psf_table = TablePSF(
psf_energydependent.offset,
Quantity(np.zeros(len(psf_energydependent.offset)), u.sr**-1))
ref_cube.data[i_E, :, :] = fill_acceptance_image(
header, center_maps, psf_table._offset.to("deg"),
psf_table._dp_domega,
psf_table._offset.to("deg")[-1]).data
return ref_cube
def plot_energy_hist(self, ax=None, ebounds=None, **kwargs):
"""
A plot showing counts as a function of energy.
Convert to a `~gammapy.spectrum.CountsSpectrum` internally
"""
if ebounds is None:
emin = np.min(self['ENERGY'].quantity)
emax = np.max(self['ENERGY'].quantity)
ebounds = EnergyBounds.equal_log_spacing(emin, emax, 100)
from gammapy.spectrum import CountsSpectrum
spec = CountsSpectrum.from_eventlist(self, ebounds)
spec.plot(ax=ax, **kwargs)
return ax
def plot_energy_hist(self, ax=None, ebounds=None, **kwargs):
"""
A plot showing counts as a function of energy.
Convert to a `~gammapy.spectrum.CountsSpectrum` internally
"""
if ebounds is None:
emin = np.min(self['ENERGY'].quantity)
emax = np.max(self['ENERGY'].quantity)
ebounds = EnergyBounds.equal_log_spacing(emin, emax, 100)
from gammapy.spectrum import CountsSpectrum
spec = CountsSpectrum.from_eventlist(self, ebounds)
spec.plot(ax=ax, **kwargs)
return ax
def make_1d_expected_counts(self,
spectral_index=2.3,
for_integral_flux=False,
eref=None):
"""Compute the 1D exposure table for one observation for an offset table.
Parameters
----------
spectral_index : float
Assumed power-law spectral index
for_integral_flux : bool
True if you want that the total excess / exposure gives the integrated flux
eref: `~gammapy.utils.energy.Energy`
Reference energy at which you want to compute the exposure. Default is the log center of the energy band of
the image.
Returns
-------
table : `astropy.table.Table`
Two columns: offset in the FOV "theta" and expected counts "npred"
"""
energy = EnergyBounds.equal_log_spacing(self.energy_band[0].value,
self.energy_band[1].value, 100,
self.energy_band.unit)
energy_band = energy.bands
energy_bin = energy.log_centers
if not eref:
eref = EnergyBounds(self.energy_band).log_centers
spectrum = (energy_bin / eref)**(-spectral_index)
offset = Angle(
np.linspace(self.offset_band[0].value, self.offset_band[1].value,
10), self.offset_band.unit)
arf = self.aeff.data.evaluate(offset=offset, energy=energy_bin).T
npred = np.sum(arf * spectrum * energy_band, axis=1)
npred *= self.livetime
if for_integral_flux:
norm = np.sum(spectrum * energy_band)
npred /= norm
table = Table()
table['theta'] = offset
table['npred'] = npred
return table
def make_psf(energy_band,
source_name,
center,
ObsList,
outdir,
spectral_index=2.3):
"""
Compute the mean psf for a set of observation and a given energy band
Parameters
----------
energy_band: energy band on which you want to compute the map
source_name: name of the source you want to compute the image
center: SkyCoord of the source
ObsList: ObservationList to use to compute the psf (could be different that the data_store for G0p9 for the GC for example)
outdir: directory where the fits image will go
spectral_index: assumed spectral index to compute the psf
Returns
-------
"""
energy = EnergyBounds.equal_log_spacing(energy_band[0].value,
energy_band[1].value, 100,
energy_band.unit)
# Here all the observations have a center at less than 2 degrees from the Crab so it will be ok to estimate the mean psf on the Crab source postion (the area is define for offset equal to 2 degrees...)
psf_energydependent = ObsList.make_mean_psf(center, energy, theta=None)
#import IPython; IPython.embed()
try:
psf_table = psf_energydependent.table_psf_in_energy_band(
energy_band, spectral_index=spectral_index)
except:
psf_table = TablePSF(
psf_energydependent.offset,
Quantity(np.zeros(len(psf_energydependent.offset)), u.sr**-1))
Table_psf = Table()
c1 = Column(psf_table._dp_domega,
name='psf_value',
unit=psf_table._dp_domega.unit)
c2 = Column(psf_table._offset, name='theta', unit=psf_table._offset.unit)
Table_psf.add_column(c1)
Table_psf.add_column(c2)
filename_psf = outdir + "/psf_table_" + source_name + "_" + str(
energy_band[0].value) + '_' + str(energy_band[1].value) + ".fits"
Table_psf.write(filename_psf, overwrite=True)
def make_model():
dir = str(gammapy_extra.dir) + '/datasets/hess-crab4-hd-hap-prod2'
data_store = DataStore.from_dir(dir)
obs_table = data_store.obs_table
ebounds = EnergyBounds.equal_log_spacing(0.1, 100, 100, 'TeV')
offset = sqrt_space(start=0, stop=2.5, num=100) * u.deg
excluded_sources = make_excluded_sources()
multi_array = EnergyOffsetBackgroundModel(ebounds, offset)
multi_array.fill_obs(obs_table, data_store, excluded_sources)
#multi_array.fill_obs(obs_table, data_store)
multi_array.compute_rate()
bgarray = multi_array.bg_rate
energy_range = Energy([1, 10], 'TeV')
table = bgarray.acceptance_curve_in_energy_band(energy_range, energy_bins=10)
multi_array.write('energy_offset_array.fits', overwrite=True)
table.write('acceptance_curve.fits', overwrite=True)
def make_model():
dir = str(gammapy_extra.dir) + '/datasets/hess-crab4-hd-hap-prod2'
data_store = DataStore.from_dir(dir)
obs_table = data_store.obs_table
ebounds = EnergyBounds.equal_log_spacing(0.1, 100, 100, 'TeV')
offset = sqrt_space(start=0, stop=2.5, num=100) * u.deg
excluded_sources = make_excluded_sources()
multi_array = EnergyOffsetBackgroundModel(ebounds, offset)
multi_array.fill_obs(obs_table, data_store, excluded_sources)
# multi_array.fill_obs(obs_table, data_store)
multi_array.compute_rate()
bgarray = multi_array.bg_rate
energy_range = Energy([1, 10], 'TeV')
table = bgarray.acceptance_curve_in_energy_band(energy_range,
energy_bins=10)
multi_array.write('energy_offset_array.fits', overwrite=True)
table.write('acceptance_curve.fits', overwrite=True)
obs_summary = ObservationSummary(stats)
fig = plt.figure(figsize=(10, 6))
ax1 = fig.add_subplot(121)
obs_summary.plot_excess_vs_livetime(ax=ax1)
ax2 = fig.add_subplot(122)
obs_summary.plot_significance_vs_livetime(ax=ax2)
# ## Extract spectrum
#
# Now, we're going to extract a spectrum using the [SpectrumExtraction](https://docs.gammapy.org/0.10/api/gammapy.spectrum.SpectrumExtraction.html) class. We provide the reconstructed energy binning we want to use. It is expected to be a Quantity with unit energy, i.e. an array with an energy unit. We use a utility function to create it. We also provide the true energy binning to use.
# In[ ]:
e_reco = EnergyBounds.equal_log_spacing(0.1, 40, 40, unit="TeV")
e_true = EnergyBounds.equal_log_spacing(0.05, 100.0, 200, unit="TeV")
# Instantiate a [SpectrumExtraction](https://docs.gammapy.org/0.10/api/gammapy.spectrum.SpectrumExtraction.html) object that will do the extraction. The containment_correction parameter is there to allow for PSF leakage correction if one is working with full enclosure IRFs. We also compute a threshold energy and store the result in OGIP compliant files (pha, rmf, arf). This last step might be omitted though.
# In[ ]:
ANALYSIS_DIR = "crab_analysis"
extraction = SpectrumExtraction(
observations=observations,
bkg_estimate=background_estimator.result,
containment_correction=False,
)
extraction.run()
# ### Spectral points
#
# Finally, let's compute spectral points. The method used is to first choose an energy binning, and then to do a 1-dim likelihood fit / profile to compute the flux and flux error.
# In[ ]:
# Flux points are computed on stacked observation
stacked_obs = extract.observations.stack()
print(stacked_obs)
# In[ ]:
ebounds = EnergyBounds.equal_log_spacing(1, 40, 4, unit=u.TeV)
seg = SpectrumEnergyGroupMaker(obs=stacked_obs)
seg.compute_groups_fixed(ebounds=ebounds)
fpe = FluxPointEstimator(
obs=stacked_obs, groups=seg.groups, model=fit.result[0].model
)
fpe.compute_points()
fpe.flux_points.table
# ### Plot
#
# Let's plot the spectral model and points. You could do it directly, but there is a helper class.
# Note that a spectral uncertainty band, a "butterfly" is drawn, but it is very thin, i.e. barely visible.
)
# In[5]:
# Estimation of the background
bkg_estimator = ReflectedRegionsBackgroundEstimator(
on_region=on_region,
obs_list=obs_list,
exclusion_mask=exclusion_mask,
)
bkg_estimator.run()
# In[6]:
# Extract the spectral data
e_reco = EnergyBounds.equal_log_spacing(0.7, 100, 50,
unit='TeV') # fine binning
e_true = EnergyBounds.equal_log_spacing(0.05, 100, 200, unit='TeV')
extraction = SpectrumExtraction(
obs_list=obs_list,
bkg_estimate=bkg_estimator.result,
containment_correction=False,
e_reco=e_reco,
e_true=e_true,
)
extraction.run()
extraction.compute_energy_threshold(
method_lo='area_max',
area_percent_lo=10.0,
)
# ## Light curve estimation
"""
from astropy.coordinates import SkyCoord, Angle
from gammapy.datasets import gammapy_extra
from gammapy.image import ExclusionMask
from gammapy.data import DataStore
from gammapy.region import SkyCircleRegion
from gammapy.spectrum import SpectrumAnalysis
from gammapy.utils.energy import EnergyBounds
center = SkyCoord(83.63, 22.01, unit='deg', frame='icrs')
radius = Angle('0.3 deg')
on_region = SkyCircleRegion(pos=center, radius=radius)
bkg_method = dict(type='reflected', n_min=3)
exclusion_file = gammapy_extra.filename("datasets/exclusion_masks/"
"tevcat_exclusion.fits")
excl = ExclusionMask.from_fits(exclusion_file)
bounds = EnergyBounds.equal_log_spacing(1, 10, 40, unit='TeV')
store = gammapy_extra.filename("datasets/hess-crab4")
ds = DataStore.from_dir(store)
obs = [23523, 23559]
ana = SpectrumAnalysis(datastore=ds, obs=obs, on_region=on_region,
bkg_method=bkg_method, exclusion=excl, ebounds=bounds)
ana.write_ogip_data(outdir='ogip_data')
modymin = 413
modymax = 573
#E1=0.50
#E2=1.44
#E1=1.44
#E2=4.16
#E1=4.16
#E2=12.01
config_name = input_param["general"]["config_name"]
energy_reco = [
Energy(input_param["energy binning"]["Emin"], "TeV"),
Energy(input_param["energy binning"]["Emax"], "TeV"),
input_param["energy binning"]["nbin"]
]
energy_bins = EnergyBounds.equal_log_spacing(0.5, 100, 1, "TeV")
for i_E, E in enumerate(energy_bins):
E1 = energy_bins[i_E].value
E2 = energy_bins[i_E + 1].value
visible_grid = True
delta_grid = 1.0
minor_tick = 5
palette = VariableColormap('../b.lut', name='b')
#palette.set_scale('SQRT')
directory = make_outdir_filesresult(source_name,
name_method_fond,
config_name,
image_size,
for_integral_flux=False,
ereco=energy_reco)
fileb = directory + '/residual_morpho_et_flux_step_'
# shouldn't matter, but must contain sufficient number of digits,
# so that CDELT1 and CDELT2 are not truncated, when wcs.to_header() is called
# seems to be a bug...
refheader['CDELT3'] = 2.02
refheader['CTYPE1'] = 'RA---CAR'
refheader['CTYPE2'] = 'DEC--CAR'
refheader['CTYPE3'] = 'log_Energy' # shouldn't matter
refheader['CUNIT1'] = 'deg'
refheader['CUNIT2'] = 'deg'
refheader['CRVAL1'] = events.meta['RA_OBJ']
refheader['CRVAL2'] = events.meta['DEC_OBJ']
refheader['CRVAL3'] = 10.0 # shouldn't matter
energies = EnergyBounds.equal_log_spacing(0.5, 80, 8, 'TeV')
data = Quantity(np.zeros((len(energies), 200, 200)))
wcs = WCS(refheader)
refcube = SpectralCube(data, wcs, energy=energies)
# Counts cube
log.info('Bin events into cube.')
counts_hdu = bin_events_in_cube(events, refcube, energies)
counts = SpectralCube(Quantity(counts_hdu.data, 'count'), wcs, energies)
log.info('Counts cube shape: {}'.format(counts_hdu.shape))
log.info('Number of events in cube: {}'.format(counts_hdu.data.sum()))
counts.writeto('counts.fits', clobber=True)
# Exposure cube
pointing = SkyCoord(events.meta['RA_PNT'], events.meta['DEC_PNT'], "icrs", unit="deg")
livetime = Quantity(events.meta['LIVETIME'], 's')
"--",
label="Interpolated values",
)
plt.xlabel("{} [{}]".format(nddata.axes[0].name, nddata.axes[0].unit))
plt.ylabel("{} [{}]".format("Exposure", nddata.data.unit))
plt.legend();
# ## 2D example
#
# Another common use case is to store a Quantity as a function of field of view offset and energy. The following shows how to use the NDDataArray to slice the data array at any values of offset and energy
# In[ ]:
energy_data = EnergyBounds.equal_log_spacing(1, 10, 50, unit=u.TeV)
energy_axis = BinnedDataAxis(
lo=energy_data.lower_bounds,
hi=energy_data.upper_bounds,
name="energy",
interpolation_mode="log",
)
offset_data = np.linspace(0, 2, 4) * u.deg
offset_axis = DataAxis(offset_data, name="offset")
data_temp = 10 * np.exp(-energy_data.log_centers.value / 10)
data = np.outer(data_temp, (offset_data.value + 1))
nddata2d = NDDataArray(
axes=[energy_axis, offset_axis], data=data * u.Unit("cm-2 s-1 TeV-1")
)
if freeze_bkg:
name += "_bkg_fix"
else:
name += "_bkg_free"
for_integral_flux = input_param["exposure"]["for_integral_flux"]
fwhm_frozen = input_param["param_fit"]["gauss_configuration"]["fwhm_frozen"]
name += "_fwhm_gauss" + str(fwhm_frozen)
if fwhm_frozen:
name += "_value" + str(
input_param["param_fit"]["gauss_configuration"]["fwhm_init"] * 2.35)
if input_param["param_fit"]["use_EM_model"]:
name += "_emission_galactic_True"
#Energy binning
energy_bins = EnergyBounds.equal_log_spacing(
input_param["energy binning"]["Emin"],
input_param["energy binning"]["Emax"],
input_param["energy binning"]["nbin"], 'TeV')
energy_centers = energy_bins.log_centers
#outdir result and plot
config_name = input_param["general"]["config_name"]
outdir_result = make_outdir_filesresult(source_name, name_method_fond,
len(energy_bins), config_name,
image_size, for_integral_flux)
outdir_plot = make_outdir_plot(source_name, name_method_fond, len(energy_bins),
config_name, image_size, for_integral_flux)
#store the fit result for the model of the source
filename_table_result = outdir_result + "/flux_fit_result" + name + ".txt"
filename_covar_result = outdir_result + "/flux_covar_result" + name + ".txt"
table_models = Table.read(filename_table_result, format="ascii")
# load catalogs
fermi_3fgl = SourceCatalog3FGL()
fermi_2fhl = SourceCatalog2FHL()
# access crab data by corresponding identifier
crab_3fgl = fermi_3fgl['3FGL J0534.5+2201']
crab_2fhl = fermi_2fhl['2FHL J0534.5+2201']
ax = crab_3fgl.spectral_model.plot(crab_3fgl.energy_range, energy_power=2,
label='Fermi 3FGL', color='r',
flux_unit='erg-1 cm-2 s-1')
ax.set_ylim(1e-12, 1E-9)
# set up an energy array to evaluate the butterfly
emin, emax = crab_3fgl.energy_range
energy = EnergyBounds.equal_log_spacing(emin, emax, 100)
butterfly_3fg = crab_3fgl.spectrum.butterfly(energy)
butterfly_3fg.plot(crab_3fgl.energy_range, ax=ax, energy_power=2, color='r',
flux_unit='erg-1 cm-2 s-1')
crab_3fgl.flux_points.plot(ax=ax, sed_type='eflux', color='r',
y_unit='erg cm-2 s-1')
crab_2fhl.spectral_model.plot(crab_2fhl.energy_range, ax=ax, energy_power=2,
c='g', label='Fermi 2FHL', flux_unit='erg-1 cm-2 s-1')
# set up an energy array to evaluate the butterfly using the 2FHL energy range
emin, emax = crab_2fhl.energy_range
energy = EnergyBounds.equal_log_spacing(emin, emax, 100)
butterfly_2fhl = crab_2fhl.spectrum.butterfly(energy)
# We will also produce a debug plot in order to show how the global fit matches one of the individual observations.
# In[46]:
fit.result[0].plot()
# we can compute flux points by fitting the norm of the global model in energy bands. We’ll use a fixed energy binning for now.
# In[47]:
from gammapy.utils.energy import EnergyBounds
# Flux points are computed on stacked observation
stacked_obs = extract.observations.stack()
print(stacked_obs)
ebounds = EnergyBounds.equal_log_spacing(0.1, 40, 15, unit=u.TeV)
seg = SpectrumEnergyGroupMaker(obs=stacked_obs)
seg.compute_range_safe()
seg.compute_groups_fixed(ebounds=ebounds)
print(seg.groups)
# In[48]:
fpe = FluxPointEstimator(
obs=stacked_obs,
groups=seg.groups,
model=fit.result[0].model,
)
fpe.compute_points()
radius[np.isnan(radius)] = 0.3
exclusion_table['Radius'] = radius * u.deg
exclusion_table = Table(exclusion_table)
#now run the bgmaker
bgmaker = OffDataBackgroundMaker(
data_store=datastore,
outdir=outdir,
run_list=None,
obs_table=obs_table_with_group_id,
ntot_group=obs_groups.n_groups,
excluded_sources=exclusion_table,
)
# Define the energy and offset binning to use
ebounds = EnergyBounds.equal_log_spacing(0.1, 100, 15, 'TeV')
#offset = sqrt_space(start=0, stop=2.5, num=20) * u.deg
offset=np.linspace(0,2.5,20) * u.deg
# Make the model (i.e. stack counts and livetime)
bgmaker.make_model("2D", ebounds=ebounds, offset=offset)
# Smooth the model
bgmaker.smooth_models("2D")
# Write the model to disk
bgmaker.save_models("2D")
bgmaker.save_models(modeltype="2D", smooth=True)
#now copy the background files as bkg into the source runs
data_dir="data_new"
shutil.move(outdir, data_dir)
plt.plot(x, y)
plt.show()
time = (datastore.obs_table["TSTART"]> 55562.0) & (datastore.obs_table["TSTOP"] < 56927)
sel=(time) & (sep<2.0*u.deg)
sel
np.where(sel)
crabrun=(datastore.obs_table[sel])
on_region=CircleSkyRegion(crab,0.15 * u.deg)
model = models.LogParabola(
alpha = 2.3,
beta = 0,
amplitude = 1e-11 * u.Unit('cm-2 s-1 TeV-1'),
reference = 1 * u.TeV,
)
flux_point_binning = EnergyBounds.equal_log_spacing(0.7, 30, 5, u.TeV)
exclusion_mask = SkyImage.read('$GAMMAPY_EXTRA/datasets/exclusion_masks/tevcat_exclusion.fits')
import gammapy
import numpy as np
import astropy
import regions
import sherpa
import matplotlib.pyplot as plt
import astropy.units as u
from astropy.coordinates import SkyCoord, Angle
from astropy.table import vstack as vstack_table
from regions import CircleSkyRegion
from gammapy.data import DataStore, ObservationList
from gammapy.data import ObservationStats, ObservationSummary
from gammapy.background.reflected import ReflectedRegionsBackgroundEstimator
bkg_estimator = PhaseBackgroundEstimator(
observations=obs_list_vela,
on_region=on_region,
on_phase=on_phase_range,
off_phase=off_phase_range,
)
bkg_estimator.run()
bkg_estimate = bkg_estimator.result
# The rest of the analysis is the same as for a standard spectral analysis with Gammapy. All the specificity of a phase-resolved analysis is contained in the PhaseBackgroundEstimator, where the background is estimated in the ON-region OFF-phase rather than in an OFF-region.
#
# We can now extract a spectrum with the SpectrumExtraction class. It takes the reconstructed and the true energy binning. Both are expected to be a Quantity with unit energy, i.e. an array with an energy unit. EnergyBounds is a dedicated class to do it.
# In[ ]:
etrue = EnergyBounds.equal_log_spacing(0.005, 10.0, 100, unit="TeV")
ereco = EnergyBounds.equal_log_spacing(0.01, 10, 30, unit="TeV")
extraction = SpectrumExtraction(
observations=obs_list_vela,
bkg_estimate=bkg_estimate,
containment_correction=True,
e_true=etrue,
e_reco=ereco,
)
extraction.run()
extraction.compute_energy_threshold(method_lo="energy_bias",
bias_percent_lo=20)
# Now let's a look at the files we just created with spectrum_observation.
large_gaus = Gauss2D("g2")
source_center_SgrA = SkyCoord.from_name("SgrA*")
large_gaus.xpos,large_gaus.ypos=skycoord_to_pixel(source_center_SgrA, excess.wcs)
CS_map=SkyMap.read("CStot.fits")
cs_reproj=CS_map.reproject(excess)
cs_reproj.data[np.where(np.isnan(cs_reproj.data))]=0
#cs_reproj.data[np.where(cs_reproj.data<50)]=0
cs_reproj.write("cs_map_reproj.fits", clobber=True)
load_table_model("CS","cs_map_reproj.fits")
set_full_model(psf_SgrA(large_gaus*CS))
#large_gaus.fwhm=150
#freeze(large_gaus.fwhm)
fit()
"""
pt.ion()
energy_bins = EnergyBounds.equal_log_spacing(0.5, 100, 5, 'TeV')
#E1=energy_bins[1].value
# E2=energy_bins[2].value
#for i_E, E in enumerate(energy_bins[0:-3]):
for i_E, E in enumerate(energy_bins[0:-5]):
#E1 = energy_bins[i_E].value
#E2 = energy_bins[i_E+1].value
E1 = energy_bins[0].value
E2 = energy_bins[3].value
print "Energy band= E1=" + str(E1) + "et E2=" + str(E2)
# on = SkyMapCollection.read("fov_bg_maps"+str(E1)+"_"+str(E2)+"_TeV.fits")["excess"]
on = SkyMapCollection.read("fov_bg_maps" + str(E1) + "_" + str(E2) + "_TeV.fits")["counts"]
bkgmap = SkyMapCollection.read("fov_bg_maps" + str(E1) + "_" + str(E2) + "_TeV.fits")["bkg"]
exp = SkyMapCollection.read("fov_bg_maps" + str(E1) + "_" + str(E2) + "_TeV.fits")["exposure"]
# source_J1745_303 = SkyCoord(358.76,-0.51, unit='deg',frame="galactic")
# Now we'll define the input for the spectrum analysis. It will be done the python way, i.e. by creating a config dict containing python objects. We plan to add also the convenience to configure the analysis using a plain text config file.
# In[3]:
crab_pos = SkyCoord.from_name('crab')
on_region = CircleSkyRegion(crab_pos, 0.15 * u.deg)
model = models.LogParabola(
alpha = 2.3,
beta = 0,
amplitude = 1e-11 * u.Unit('cm-2 s-1 TeV-1'),
reference = 1 * u.TeV,
)
flux_point_binning = EnergyBounds.equal_log_spacing(0.7, 30, 5, u.TeV)
exclusion_mask = SkyImage.read('$GAMMAPY_EXTRA/datasets/exclusion_masks/tevcat_exclusion.fits')
# In[4]:
config = dict(
outdir = None,
background = dict(
on_region=on_region,
exclusion_mask=exclusion_mask,
min_distance = 0.1 * u.rad,
),
extraction = dict(containment_correction=False),
input_param = yaml.load(open(sys.argv[1]))
image_size = input_param["general"]["image_size"]
# Input param fit and source configuration
# Sur quelle taille de la carte on fait le fit
freeze_bkg = input_param["param_fit_morpho"]["freeze_bkg"]
source_name = input_param["general"]["source_name"]
name_method_fond = input_param["general"]["name_method_fond"]
if freeze_bkg:
name = "_bkg_fix"
else:
name = "_bkg_free"
for_integral_flux = input_param["exposure"]["for_integral_flux"]
# Energy binning
energy_bins = EnergyBounds.equal_log_spacing(
input_param["energy binning"]["Emin"],
input_param["energy binning"]["Emax"],
input_param["energy binning"]["nbin"], 'TeV')
energy_centers = energy_bins.log_centers
energy_reco = [
Energy(input_param["energy binning"]["Emin"], "TeV"),
Energy(input_param["energy binning"]["Emax"], "TeV"),
input_param["energy binning"]["nbin"]
]
# outdir data and result
config_name = input_param["general"]["config_name"]
outdir_data = make_outdir_data(source_name,
name_method_fond,
config_name,
image_size,
for_integral_flux=False,
fermi_2fhl = SourceCatalog2FHL()
# access crab data by corresponding identifier
crab_3fgl = fermi_3fgl['3FGL J0534.5+2201']
crab_2fhl = fermi_2fhl['2FHL J0534.5+2201']
ax = crab_3fgl.spectral_model.plot(crab_3fgl.energy_range,
energy_power=2,
label='Fermi 3FGL',
color='r',
flux_unit='erg-1 cm-2 s-1')
ax.set_ylim(1e-12, 1E-9)
# set up an energy array to evaluate the butterfly
emin, emax = crab_3fgl.energy_range
energy = EnergyBounds.equal_log_spacing(emin, emax, 100)
butterfly_3fg = crab_3fgl.spectrum.butterfly(energy)
butterfly_3fg.plot(crab_3fgl.energy_range,
ax=ax,
energy_power=2,
color='r',
flux_unit='erg-1 cm-2 s-1')
crab_3fgl.flux_points.plot(ax=ax,
sed_type='eflux',
color='r',
flux_unit='erg cm-2 s-1')
crab_2fhl.spectral_model.plot(crab_2fhl.energy_range,
ax=ax,