def get_fisher_matrices(template_settings, grid_settings, IMH=True, NMH=False, dump_all_stages=False,
save_templates=False, outdir=None):
'''
Main function that runs the Fisher analysis for the chosen hierarchy(ies) (inverted by default).
Returns a dictionary of Fisher matrices, in the format:
{'IMH': {'cscd': [...],
'trck': [...],
'comb': [...],
},
'NMH': {'cscd': [...],
'trck': [...],
'comb': [...],
}
}
If save_templates=True and no hierarchy is given, only fiducial templates will be written out;
if one is given, then the templates used to obtain the gradients will be written out in
addition.
'''
if outdir is None and (save_templates or dump_all_stages):
logging.info("No output directory specified. Will save templates to current working directory.")
outdir = os.getcwd()
profile.info("start initializing")
# Get the parameters
params = template_settings['params']
bins = template_settings['binning']
# Artifically add the hierarchy parameter to the list of parameters
# The method get_hierarchy_gradients below will know how to deal with it
params['hierarchy_nh'] = { "value": 1., "range": [0.,1.],
"fixed": False, "prior": None}
params['hierarchy_ih'] = { "value": 0., "range": [0.,1.],
"fixed": False, "prior": None}
chosen_data = []
if IMH:
chosen_data.append(('IMH',False))
logging.info("Fisher matrix will be built for IMH.")
if NMH:
chosen_data.append(('NMH',True))
logging.info("Fisher matrix will be built for NMH.")
if chosen_data == []:
# In this case, only the fiducial maps (for both hierarchies) will be written
logging.info("No Fisher matrices will be built.")
# There is no sense in performing any of the following steps if no Fisher matrices are to be built
# and no templates are to be saved.
if chosen_data!=[] or dump_all_stages or save_templates:
# Initialise return dict to hold Fisher matrices
fisher = { data_tag:{'cscd':[],'trck':[],'comb':[]} for data_tag, data_normal in chosen_data }
# Get a template maker with the settings used to initialize
template_maker = TemplateMaker(get_values(params),**bins)
profile.info("stop initializing\n")
# Generate fiducial templates for both hierarchies (needed for partial derivatives
# w.r.t. hierarchy parameter)
fiducial_maps = {}
for hierarchy in ['NMH','IMH']:
logging.info("Generating fiducial templates for %s."%hierarchy)
# Get the fiducial parameter values corresponding to this hierarchy
fiducial_params = select_hierarchy(params,normal_hierarchy=(hierarchy=='NMH'))
# Generate fiducial maps, either all of them or only the ultimate one
profile.info("start template calculation")
with Timer() as t:
fid_maps = template_maker.get_template(get_values(fiducial_params),
return_stages=dump_all_stages)
profile.info("==> elapsed time for template: %s sec"%t.secs)
fiducial_maps[hierarchy] = fid_maps[4] if dump_all_stages else fid_maps
# save fiducial map(s)
# all stages
if dump_all_stages:
stage_names = ("0_unoscillated_flux","1_oscillated_flux","2_oscillated_counts","3_reco","4_pid")
stage_maps = {}
for stage in xrange(0,len(fid_maps)):
stage_maps[stage_names[stage]] = fid_maps[stage]
logging.info("Writing fiducial maps (all stages) for %s to %s."%(hierarchy,outdir))
to_json(stage_maps,os.path.join(outdir,"fid_map_"+hierarchy+".json"))
# only the final stage
elif save_templates:
logging.info("Writing fiducial map (final stage) for %s to %s."%(hierarchy,outdir))
to_json(fiducial_maps[hierarchy],os.path.join(outdir,"fid_map_"+hierarchy+".json"))
# Get_gradients and get_hierarchy_gradients will both (temporarily)
# store the templates used to generate the gradient maps
store_dir = outdir if save_templates else tempfile.gettempdir()
# Calculate Fisher matrices for the user-defined cases (NHM true and/or IMH true)
for data_tag, data_normal in chosen_data:
logging.info("Running Fisher analysis for %s."%(data_tag))
# The fiducial params are selected from the hierarchy case that does NOT match
# the data, as we are varying from this model to find the 'best fit'
fiducial_params = select_hierarchy(params,not data_normal)
# Get the free parameters (i.e. those for which the gradients should be calculated)
free_params = select_hierarchy(get_free_params(params),not data_normal)
gradient_maps = {}
for param in free_params.keys():
# Special treatment for the hierarchy parameter
if param=='hierarchy':
gradient_maps[param] = get_hierarchy_gradients(data_tag,
fiducial_maps,
fiducial_params,
grid_settings,
store_dir,
)
else:
gradient_maps[param] = get_gradients(data_tag,
param,
template_maker,
fiducial_params,
grid_settings,
store_dir
)
logging.info("Building Fisher matrix for %s."%(data_tag))
# Build Fisher matrices for the given hierarchy
fisher[data_tag] = build_fisher_matrix(gradient_maps,fiducial_maps['IMH'] if data_normal else fiducial_maps['NMH'],fiducial_params)
# If Fisher matrices exist for both channels, add the matrices to obtain the combined one.
if len(fisher[data_tag].keys()) > 1:
fisher[data_tag]['comb'] = FisherMatrix(matrix=np.array([f.matrix for f in fisher[data_tag].itervalues()]).sum(axis=0),
parameters=gradient_maps.keys(), #order is important here!
best_fits=[fiducial_params[par]['value'] for par in gradient_maps.keys()],
priors=[fiducial_params[par]['prior'] for par in gradient_maps.keys()],
)
return fisher
else:
logging.info("Nothing to be done.")
return {}
'--outdir',
metavar='DIR',
default="",
help="Directory to save the output figures.")
parser.add_argument('-v',
'--verbose',
action='count',
default=0,
help='set verbosity level')
args = parser.parse_args()
set_verbosity(args.verbose)
template_settings = from_json(args.template_settings)
with Timer() as t:
template_maker = TemplateMaker(get_values(template_settings['params']),
**template_settings['binning'])
tprofile.info("==> elapsed time to initialize templates: %s sec" % t.secs)
# Make nmh template:
nmh_params = select_hierarchy(template_settings['params'],
normal_hierarchy=True)
imh_params = select_hierarchy(template_settings['params'],
normal_hierarchy=False)
with Timer(verbose=False) as t:
nmh = template_maker.get_template(get_values(nmh_params),
return_stages=args.all)
tprofile.info("==> elapsed time to get NMH template: %s sec" % t.secs)
with Timer(verbose=False) as t:
imh = template_maker.get_template(get_values(imh_params),
return_stages=args.all)
tprofile.info("==> elapsed time to get IMH template: %s sec" % t.secs)
# make sure that both pseudo data and template are using the same
# channel. Raise Exception and quit otherwise
channel = template_settings['params']['channel']['value']
if channel != pseudo_data_settings['params']['channel']['value']:
error_msg = "Both template and pseudo data must have same channel!\n"
error_msg += " pseudo_data_settings chan: '%s', template chan: '%s' " % (
pseudo_data_settings['params']['channel']['value'], channel)
raise ValueError(error_msg)
if args.gpu_id is not None:
template_settings['params']['gpu_id'] = {}
template_settings['params']['gpu_id']['value'] = args.gpu_id
template_settings['params']['gpu_id']['fixed'] = True
template_maker = TemplateMaker(get_values(template_settings['params']),
**template_settings['binning'])
if args.pseudo_data_settings:
pseudo_data_template_maker = TemplateMaker(
get_values(pseudo_data_settings['params']),
**pseudo_data_settings['binning'])
else:
pseudo_data_template_maker = template_maker
# Put in try/except block?
#store results from all the trials
trials = []
try:
for itrial in xrange(1, args.ntrials + 1):
profile.info("start trial %d" % itrial)
def get_fisher_matrices(template_settings,
grid_settings,
IMH=True,
NMH=False,
dump_all_stages=False,
save_templates=False,
outdir=None):
'''
Main function that runs the Fisher analysis for the chosen hierarchy(ies) (inverted by default).
Returns a dictionary of Fisher matrices, in the format:
{'IMH': {'cscd': [...],
'trck': [...],
'comb': [...],
},
'NMH': {'cscd': [...],
'trck': [...],
'comb': [...],
}
}
If save_templates=True and no hierarchy is given, only fiducial templates will be written out;
if one is given, then the templates used to obtain the gradients will be written out in
addition.
'''
if outdir is None and (save_templates or dump_all_stages):
logging.info(
"No output directory specified. Will save templates to current working directory."
)
outdir = os.getcwd()
tprofile.info("start initializing")
# Get the parameters
params = template_settings['params']
bins = template_settings['binning']
# Artifically add the hierarchy parameter to the list of parameters
# The method get_hierarchy_gradients below will know how to deal with it
params['hierarchy_nh'] = {
"value": 1.,
"range": [0., 1.],
"fixed": False,
"prior": None
}
params['hierarchy_ih'] = {
"value": 0.,
"range": [0., 1.],
"fixed": False,
"prior": None
}
chosen_data = []
if IMH:
chosen_data.append(('IMH', False))
logging.info("Fisher matrix will be built for IMH.")
if NMH:
chosen_data.append(('NMH', True))
logging.info("Fisher matrix will be built for NMH.")
if chosen_data == []:
# In this case, only the fiducial maps (for both hierarchies) will be written
logging.info("No Fisher matrices will be built.")
# There is no sense in performing any of the following steps if no Fisher matrices are to be built
# and no templates are to be saved.
if chosen_data != [] or dump_all_stages or save_templates:
# Initialise return dict to hold Fisher matrices
fisher = {
data_tag: {
'cscd': [],
'trck': [],
'comb': []
}
for data_tag, data_normal in chosen_data
}
# Get a template maker with the settings used to initialize
template_maker = TemplateMaker(get_values(params), **bins)
tprofile.info("stop initializing\n")
# Generate fiducial templates for both hierarchies (needed for partial derivatives
# w.r.t. hierarchy parameter)
fiducial_maps = {}
for hierarchy in ['NMH', 'IMH']:
logging.info("Generating fiducial templates for %s." % hierarchy)
# Get the fiducial parameter values corresponding to this hierarchy
fiducial_params = select_hierarchy(
params, normal_hierarchy=(hierarchy == 'NMH'))
# Generate fiducial maps, either all of them or only the ultimate one
tprofile.info("start template calculation")
with Timer() as t:
fid_maps = template_maker.get_template(
get_values(fiducial_params), return_stages=dump_all_stages)
tprofile.info("==> elapsed time for template: %s sec" % t.secs)
fiducial_maps[
hierarchy] = fid_maps[4] if dump_all_stages else fid_maps
# save fiducial map(s)
# all stages
if dump_all_stages:
stage_names = ("0_unoscillated_flux", "1_oscillated_flux",
"2_oscillated_counts", "3_reco", "4_pid")
stage_maps = {}
for stage in xrange(0, len(fid_maps)):
stage_maps[stage_names[stage]] = fid_maps[stage]
logging.info(
"Writing fiducial maps (all stages) for %s to %s." %
(hierarchy, outdir))
to_json(stage_maps,
os.path.join(outdir, "fid_map_" + hierarchy + ".json"))
# only the final stage
elif save_templates:
logging.info(
"Writing fiducial map (final stage) for %s to %s." %
(hierarchy, outdir))
to_json(fiducial_maps[hierarchy],
os.path.join(outdir, "fid_map_" + hierarchy + ".json"))
# Get_gradients and get_hierarchy_gradients will both (temporarily)
# store the templates used to generate the gradient maps
store_dir = outdir if save_templates else tempfile.gettempdir()
# Calculate Fisher matrices for the user-defined cases (NHM true and/or IMH true)
for data_tag, data_normal in chosen_data:
logging.info("Running Fisher analysis for %s." % (data_tag))
# The fiducial params are selected from the hierarchy case that does NOT match
# the data, as we are varying from this model to find the 'best fit'
fiducial_params = select_hierarchy(params, not data_normal)
# Get the free parameters (i.e. those for which the gradients should be calculated)
free_params = select_hierarchy(get_free_params(params),
not data_normal)
gradient_maps = {}
for param in free_params.keys():
# Special treatment for the hierarchy parameter
if param == 'hierarchy':
gradient_maps[param] = get_hierarchy_gradients(
data_tag=data_tag,
fiducial_maps=fiducial_maps,
fiducial_params=fiducial_params,
grid_settings=grid_settings,
store_dir=store_dir)
else:
gradient_maps[param] = get_gradients(
data_tag=data_tag,
param=param,
template_maker=template_maker,
fiducial_params=fiducial_params,
grid_settings=grid_settings,
store_dir=store_dir)
logging.info("Building Fisher matrix for %s." % (data_tag))
# Build Fisher matrices for the given hierarchy
fisher[data_tag] = build_fisher_matrix(
gradient_maps=gradient_maps,
fiducial_map=fiducial_maps['IMH']
if data_normal else fiducial_maps['NMH'],
template_settings=fiducial_params)
# If Fisher matrices exist for both channels, add the matrices to obtain
# the combined one.
if len(fisher[data_tag].keys()) > 1:
fisher[data_tag]['comb'] = FisherMatrix(
matrix=np.array([
f.matrix for f in fisher[data_tag].itervalues()
]).sum(axis=0),
parameters=gradient_maps.keys(), #order is important here!
best_fits=[
fiducial_params[par]['value']
for par in gradient_maps.keys()
],
priors=[
Prior.from_param(fiducial_params[par])
for par in gradient_maps.keys()
],
)
return fisher
else:
logging.info("Nothing to be done.")
return {}
args = parser.parse_args()
set_verbosity(args.verbose)
#Read in the settings
template_settings = from_json(args.template_settings)
minimizer_settings = from_json(args.minimizer_settings)
grid_settings = from_json(args.grid_settings)
if args.gpu_id is not None:
template_settings['params']['gpu_id'] = {}
template_settings['params']['gpu_id']['value'] = args.gpu_id
template_settings['params']['gpu_id']['fixed'] = True
with Timer() as t:
template_maker = TemplateMaker(get_values(template_settings['params']),
**template_settings['binning'])
profile.info("==> elapsed time to initialize templates: %s sec" % t.secs)
#Get the parameters
params = template_settings['params']
mctrue_types = [('true_NMH', True), ('true_IMH', False)]
results = {}
# Store for future checking:
results['template_settings'] = template_settings
results['minimizer_settings'] = minimizer_settings
results['grid_settings'] = grid_settings
for true_tag, true_normal in mctrue_types:
results[true_tag] = {}
help="Plot all stages 1-5 of templates and Asymmetry")
parser.add_argument('--title',metavar="str",default='',
help="Title of the geometry or test in plots")
parser.add_argument('--save',action='store_true',default=False,
help="Save plots in cwd")
parser.add_argument('-o','--outdir',metavar='DIR',default="",
help="Directory to save the output figures.")
parser.add_argument('-v', '--verbose', action='count', default=0,
help='set verbosity level')
args = parser.parse_args()
set_verbosity(args.verbose)
template_settings = from_json(args.template_settings)
with Timer() as t:
template_maker = TemplateMaker(get_values(template_settings['params']),
**template_settings['binning'])
profile.info("==> elapsed time to initialize templates: %s sec"%t.secs)
# Make nmh template:
nmh_params = select_hierarchy(template_settings['params'],
normal_hierarchy=True)
imh_params = select_hierarchy(template_settings['params'],
normal_hierarchy=False)
with Timer(verbose=False) as t:
nmh = template_maker.get_template(get_values(nmh_params), return_stages=args.all)
profile.info("==> elapsed time to get NMH template: %s sec"%t.secs)
with Timer(verbose=False) as t:
imh = template_maker.get_template(get_values(imh_params), return_stages=args.all)
profile.info("==> elapsed time to get IMH template: %s sec"%t.secs)
# Or equivalently, if args.all:
