def __init__(self, polar_root_file, reference_time=0., rsp_file=None):
"""
container class that converts raw POLAR root data into useful python
variables
:param polar_root_file: path to polar event file
:param reference_time: reference time of the events (tunix?)
:param rsp_file: path to rsp file
"""
# open the event file
with open_ROOT_file(polar_root_file) as f:
tmp = tree_to_ndarray(f.Get('polar_out'))
# extract the pedestal corrected ADC channels
# which are non-integer and possibly
# less than zero
pha = tmp['Energy']
# non-zero ADC channels are invalid
idx = pha >= 0
pha = pha[idx]
# get the dead time fraction
self._dead_time_fraction = tmp['dead_ratio'][idx]
# get the arrival time, in tunix of the events
self._time = tmp['tunix'][idx] - reference_time
# digitize the ADC channels into bins
# these bins are preliminary
with open_ROOT_file(rsp_file) as f:
matrix = th2_to_arrays(f.Get('rsp'))[-1]
ebounds = th2_to_arrays(f.Get('EM_bounds'))[-1]
mc_low = th2_to_arrays(f.Get('ER_low'))[-1]
mc_high = th2_to_arrays(f.Get('ER_high'))[-1]
mc_energies = np.append(mc_low, mc_high[-1])
# build the POLAR response
self._rsp = InstrumentResponse(matrix=matrix,
ebounds=ebounds,
monte_carlo_energies=mc_energies)
# bin the ADC channels
self._binned_pha = np.digitize(pha, ebounds)
def __init__(self, polar_root_file, reference_time=0., rsp_file=None):
"""
container class that converts raw POLAR root data into useful python
variables
:param polar_root_file: path to polar event file
:param reference_time: reference time of the events (tunix?)
:param rsp_file: path to rsp file
"""
# open the event file
with open_ROOT_file(polar_root_file) as f:
tmp = tree_to_ndarray(f.Get('polar_out'))
# extract the pedestal corrected ADC channels
# which are non-integer and possibly
# less than zero
pha = tmp['Energy']
# non-zero ADC channels are invalid
idx = pha >= 0
pha = pha[idx]
# get the dead time fraction
self._dead_time_fraction = tmp['dead_ratio'][idx]
# get the arrival time, in tunix of the events
self._time = tmp['tunix'][idx] - reference_time
# digitize the ADC channels into bins
# these bins are preliminary
with open_ROOT_file(rsp_file) as f:
matrix = th2_to_arrays(f.Get('rsp'))[-1]
ebounds = th2_to_arrays(f.Get('EM_bounds'))[-1]
mc_low = th2_to_arrays(f.Get('ER_low'))[-1]
mc_high = th2_to_arrays(f.Get('ER_high'))[-1]
mc_energies = np.append(mc_low, mc_high[-1])
# build the POLAR response
self._rsp = InstrumentResponse(matrix=matrix,
ebounds=ebounds,
monte_carlo_energies=mc_energies)
# bin the ADC channels
self._binned_pha = np.digitize(pha, ebounds)
def __init__(self, root_file, run_name):
self._run_name = run_name
# Read the data from the ROOT file
with open_ROOT_file(root_file) as f:
# Read first the TTrees as pandas DataFrame
self._data_on = tree_to_ndarray(
f.Get(run_name + '/data_on')) # type: np.ndarray
self._data_off = tree_to_ndarray(
f.Get(run_name + '/data_off')) # type: np.ndarray
self._tRunSummary = np.squeeze(
tree_to_ndarray(f.Get(run_name +
'/tRunSummary'))) # type: np.ndarray
# Now read the histogram
self._log_recon_energies, \
self._log_mc_energies, \
self._hMigration = th2_to_arrays(f.Get(run_name + "/hMigration"))
# Transform energies to keV (they are in TeV)
self._log_recon_energies += 9
self._log_mc_energies += 9
# Compute bin centers and bin width of the Monte Carlo energy bins
self._dE = (10**self._log_mc_energies[1:] -
10**self._log_mc_energies[:-1])
self._mc_energies_c = (10**self._log_mc_energies[1:] +
10**self._log_mc_energies[:-1]) / 2.0
self._recon_energies_c = (10**self._log_recon_energies[1:] +
10**self._log_recon_energies[:-1]) / 2.0
self._n_chan = self._log_recon_energies.shape[0] - 1
# Remove all nans by substituting them with 0.0
idx = np.isfinite(self._hMigration)
self._hMigration[~idx] = 0.0
# Read the TGraph
tgraph = f.Get(run_name + "/gMeanEffectiveArea")
self._log_eff_area_energies, self._eff_area = tgraph_to_arrays(
tgraph)
# Transform the effective area to cm2 (it is in m2 in the file)
self._eff_area *= 1e8 #This value is for VEGAS, because VEGAS effective area is in cm2
# Transform energies to keV
self._log_eff_area_energies += 9
# Now use the effective area provided in the file to renormalize the migration matrix appropriately
self._renorm_hMigration()
# Exposure is tOn*(1-tDeadtimeFrac)
self._exposure = float(1 -
self._tRunSummary['DeadTimeFracOn']) * float(
self._tRunSummary['tOn'])
# Members for generating OGIP equivalents
self._mission = "VERITAS"
self._instrument = "VERITAS"
# Now bin the counts
self._counts, _ = self._bin_counts_log(self._data_on['Erec'] * 1e9,
self._log_recon_energies)
# Now bin the background counts
self._bkg_counts, _ = self._bin_counts_log(
self._data_off['Erec'] * 1e9, self._log_recon_energies)
print(
"Read a %s x %s matrix, spectrum has %s bins, eff. area has %s elements"
% (self._hMigration.shape[0], self._hMigration.shape[1],
self._counts.shape[0], self._eff_area.shape[0]))
# Read in the background renormalization (ratio between source and background region)
self._bkg_renorm = float(self._tRunSummary['OffNorm'])
self._start_energy = np.log10(175E6) #175 GeV in keV
self._end_energy = np.log10(18E9) #18 TeV in keV
self._first_chan = (
np.abs(self._log_recon_energies -
self._start_energy)).argmin() #Values used by Giacomo 61
self._last_chan = (
np.abs(self._log_recon_energies -
self._end_energy)).argmin() #Values used by Giacomo 110
def __init__(self, root_file, run_name):
self._run_name = run_name
# Read the data from the ROOT file
with open_ROOT_file(root_file) as f:
# Read first the TTrees as pandas DataFrame
self._data_on = tree_to_ndarray(f.Get(run_name+'/data_on')) # type: np.ndarray
self._data_off = tree_to_ndarray(f.Get(run_name+'/data_off')) # type: np.ndarray
self._tRunSummary = np.squeeze(tree_to_ndarray(f.Get(run_name+'/tRunSummary'))) # type: np.ndarray
# Now read the histogram
self._log_recon_energies, \
self._log_mc_energies, \
self._hMigration = th2_to_arrays(f.Get(run_name + "/hMigration"))
# Transform energies to keV (they are in TeV)
self._log_recon_energies += 9
self._log_mc_energies += 9
# Compute bin centers and bin width of the Monte Carlo energy bins
self._dE = (10 ** self._log_mc_energies[1:] - 10 ** self._log_mc_energies[:-1])
self._mc_energies_c = (10 ** self._log_mc_energies[1:] + 10 ** self._log_mc_energies[:-1]) / 2.0
self._recon_energies_c = (10 ** self._log_recon_energies[1:] + 10 ** self._log_recon_energies[:-1]) / 2.0
self._n_chan = self._log_recon_energies.shape[0] - 1
# Remove all nans by substituting them with 0.0
idx = np.isfinite(self._hMigration)
self._hMigration[~idx] = 0.0
# Read the TGraph
tgraph = f.Get(run_name + "/gMeanEffectiveArea")
self._log_eff_area_energies, self._eff_area = tgraph_to_arrays(tgraph)
# Transform the effective area to cm2 (it is in m2 in the file)
self._eff_area *= 1e8 #This value is for VEGAS, because VEGAS effective area is in cm2
# Transform energies to keV
self._log_eff_area_energies += 9
# Now use the effective area provided in the file to renormalize the migration matrix appropriately
self._renorm_hMigration()
# Exposure is tOn*(1-tDeadtimeFrac)
self._exposure = float(1 - self._tRunSummary['DeadTimeFracOn']) * float(self._tRunSummary['tOn'])
# Members for generating OGIP equivalents
self._mission = "VERITAS"
self._instrument = "VERITAS"
# Now bin the counts
self._counts, _ = self._bin_counts_log(self._data_on['Erec'] * 1e9, self._log_recon_energies)
# Now bin the background counts
self._bkg_counts, _ = self._bin_counts_log(self._data_off['Erec'] * 1e9, self._log_recon_energies)
print("Read a %s x %s matrix, spectrum has %s bins, eff. area has %s elements" %
(self._hMigration.shape[0], self._hMigration.shape[1], self._counts.shape[0], self._eff_area.shape[0]))
# Read in the background renormalization (ratio between source and background region)
self._bkg_renorm = float(self._tRunSummary['OffNorm'])
self._start_energy = np.log10(175E6)#175 GeV in keV
self._end_energy = np.log10(18E9)#18 TeV in keV
self._first_chan = (np.abs(self._log_recon_energies-self._start_energy)).argmin()
self._last_chan = (np.abs(self._log_recon_energies-self._end_energy)).argmin()
def from_root_file(cls, map_tree_file, roi):
"""
Create a MapTree object from a ROOT file and a ROI. Do not use this directly, use map_tree_factory instead.
:param map_tree_file:
:param roi:
:return:
"""
map_tree_file = sanitize_filename(map_tree_file)
# Check that they exists and can be read
if not file_existing_and_readable(map_tree_file):
raise IOError("MapTree %s does not exist or is not readable" %
map_tree_file)
# Make sure we have a proper ROI (or None)
assert isinstance(roi, HealpixROIBase) or roi is None, "You have to provide an ROI choosing from the " \
"available ROIs in the region_of_interest module"
if roi is None:
custom_warnings.warn(
"You have set roi=None, so you are reading the entire sky")
# Read map tree
with open_ROOT_file(map_tree_file) as f:
data_bins_labels = list(
root_numpy.tree2array(f.Get("BinInfo"), "name"))
# A transit is defined as 1 day, and totalDuration is in hours
# Get the number of transit from bin 0 (as LiFF does)
n_transits = root_numpy.tree2array(f.Get("BinInfo"),
"totalDuration") / 24.0
n_bins = len(data_bins_labels)
# These are going to be Healpix maps, one for each data analysis bin_name
data_analysis_bins = []
for i in range(n_bins):
name = data_bins_labels[i]
bin_label = "nHit0%s/%s" % (name, "data")
bkg_label = "nHit0%s/%s" % (name, "bkg")
# Get ordering scheme
nside = f.Get(bin_label).GetUserInfo().FindObject(
"Nside").GetVal()
nside_bkg = f.Get(bkg_label).GetUserInfo().FindObject(
"Nside").GetVal()
assert nside == nside_bkg
scheme = f.Get(bin_label).GetUserInfo().FindObject(
"Scheme").GetVal()
scheme_bkg = f.Get(bkg_label).GetUserInfo().FindObject(
"Scheme").GetVal()
assert scheme == scheme_bkg
assert scheme == 0, "NESTED scheme is not supported yet"
if roi is not None:
# Only read the elements in the ROI
active_pixels = roi.active_pixels(nside,
system='equatorial',
ordering='RING')
counts = cls._read_partial_tree(nside, f.Get(bin_label),
active_pixels)
bkg = cls._read_partial_tree(nside, f.Get(bkg_label),
active_pixels)
this_data_analysis_bin = DataAnalysisBin(
name,
SparseHealpix(counts, active_pixels, nside),
SparseHealpix(bkg, active_pixels, nside),
active_pixels_ids=active_pixels,
n_transits=n_transits[i],
scheme='RING')
else:
# Read the entire sky.
counts = tree_to_ndarray(f.Get(bin_label),
"count").astype(np.float64)
bkg = tree_to_ndarray(f.Get(bkg_label),
"count").astype(np.float64)
this_data_analysis_bin = DataAnalysisBin(
name,
DenseHealpix(counts),
DenseHealpix(bkg),
active_pixels_ids=None,
n_transits=n_transits[i],
scheme='RING')
data_analysis_bins.append(this_data_analysis_bin)
return cls(data_bins_labels, data_analysis_bins, roi)
def __init__(self, response_file_name):
# Make sure file is readable
response_file_name = sanitize_filename(response_file_name)
# Check that they exists and can be read
if not file_existing_and_readable(response_file_name):
raise IOError("Response %s does not exist or is not readable" % response_file_name)
self._response_file_name = response_file_name
# Read response
with open_ROOT_file(response_file_name) as f:
# Get the name of the trees
object_names = get_list_of_keys(f)
# Make sure we have all the things we need
assert 'LogLogSpectrum' in object_names
assert 'DecBins' in object_names
assert 'AnalysisBins' in object_names
# Read spectrum used during the simulation
self._log_log_spectrum = TF1Wrapper(f.Get("LogLogSpectrum"))
# Get the analysis bins definition
dec_bins = tree_to_ndarray(f.Get("DecBins"))
dec_bins_lower_edge = dec_bins['lowerEdge'] # type: np.ndarray
dec_bins_upper_edge = dec_bins['upperEdge'] # type: np.ndarray
dec_bins_center = dec_bins['simdec'] # type: np.ndarray
self._dec_bins = zip(dec_bins_lower_edge, dec_bins_center, dec_bins_upper_edge)
# Read in the ids of the response bins ("analysis bins" in LiFF jargon)
response_bins_ids = tree_to_ndarray(f.Get("AnalysisBins"), "id") # type: np.ndarray
# Now we create a list of ResponseBin instances for each dec bin_name
self._response_bins = collections.OrderedDict()
for dec_id in range(len(self._dec_bins)):
this_response_bins = []
min_dec, dec_center, max_dec = self._dec_bins[dec_id]
for response_bin_id in response_bins_ids:
this_response_bin = ResponseBin(f, dec_id, response_bin_id, self._log_log_spectrum,
min_dec, dec_center, max_dec)
this_response_bins.append(this_response_bin)
self._response_bins[self._dec_bins[dec_id][1]] = this_response_bins
del f
def from_root_file(cls, response_file_name):
# Make sure file is readable
response_file_name = sanitize_filename(response_file_name)
# Check that they exists and can be read
if not file_existing_and_readable(
response_file_name): # pragma: no cover
raise IOError("Response %s does not exist or is not readable" %
response_file_name)
# Read response
with open_ROOT_file(response_file_name) as f:
# Get the name of the trees
object_names = get_list_of_keys(f)
# Make sure we have all the things we need
assert 'LogLogSpectrum' in object_names
assert 'DecBins' in object_names
assert 'AnalysisBins' in object_names
# Read spectrum used during the simulation
log_log_spectrum = f.Get("LogLogSpectrum")
# Get the analysis bins definition
dec_bins_ = tree_to_ndarray(f.Get("DecBins"))
dec_bins_lower_edge = dec_bins_['lowerEdge'] # type: np.ndarray
dec_bins_upper_edge = dec_bins_['upperEdge'] # type: np.ndarray
dec_bins_center = dec_bins_['simdec'] # type: np.ndarray
dec_bins = zip(dec_bins_lower_edge, dec_bins_center,
dec_bins_upper_edge)
# Read in the ids of the response bins ("analysis bins" in LiFF jargon)
response_bins_ids = tree_to_ndarray(f.Get("AnalysisBins"),
"id") # type: np.ndarray
# Now we create a list of ResponseBin instances for each dec bin_name
response_bins = {}
for dec_id in range(len(dec_bins)):
this_response_bins = []
min_dec, dec_center, max_dec = dec_bins[dec_id]
for response_bin_id in response_bins_ids:
this_response_bin = ResponseBin.from_ttree(
f, dec_id, response_bin_id, log_log_spectrum, min_dec,
dec_center, max_dec)
this_response_bins.append(this_response_bin)
response_bins[dec_bins[dec_id][1]] = this_response_bins
# Now the file is closed. Let's explicitly remove f so we are sure it is freed
del f
# Instance the class and return it
instance = cls(response_file_name, dec_bins, response_bins)
return instance