def choose_model(parfile,
category_order=None,
name=None,
check_for_missing_parameters=False):
"""Determine which model components are appropriate for parfile."""
if name is None:
if isinstance(parfile, str):
name = os.path.basename(parfile)
else:
name = ""
if category_order is None:
category_order = DEFAULT_ORDER
models_by_category = defaultdict(list)
for k, c_type in Component.component_types.items():
models_by_category[c_type.category].append(c_type)
par_dict = {}
par_lines = []
multi_tags = set([
"JUMP",
"ECORR",
"T2EFAC",
"T2EQUAD",
"EQUAD",
"EFAC",
"DMJUMP",
"DMEFAC",
"DMEQUAD",
])
multi_line = Counter()
for l in interesting_lines(lines_of(parfile), comments=("#", "C ")):
ll = l.split()
k = ll[0]
if k in multi_tags:
multi_line[k] += 1
k = k + str(multi_line[k])
if k in par_dict:
# FIXME: what happens with JUMPs?
log.info("Lines with duplicate keys in par file: {} and {}".format(
[k] + par_dict[k], ll))
par_dict[k] = ll[1:]
par_lines.append(l)
models_to_use = {}
for category, models in models_by_category.items():
acceptable = []
for m_type in models:
m = m_type()
if m.is_in_parfile(par_dict):
acceptable.append(m)
if len(acceptable) > 1:
raise ValueError(
"Multiple models are compatible with this par file: {}".format(
acceptable))
if acceptable:
models_to_use[category] = acceptable[0]
if "BINARY" in par_dict:
vals = par_dict["BINARY"]
if len(vals) != 1:
raise ValueError("Mal-formed binary model selection: {}".format(
repr(" ".join(["BINARY"] + vals))))
(bm, ) = vals
if "pulsar_system" not in models_to_use:
# Either we're missing parameters or the model is bogus
# FIXME: distinguish
raise UnknownBinaryModel(
"Unknown binary model requested in par file: {}".format(bm))
# FIXME: consistency check - the componens actually chosen should know the name bm
models_in_order = []
for category in category_order:
try:
models_in_order.append(models_to_use.pop(category))
except KeyError:
pass
models_in_order.extend(v for k, v in sorted(models_to_use.items()))
tm = TimingModel(name, models_in_order)
# FIXME: this should go in TimingModel for when you try to
# add conflicting components
alias_map = {}
for prefix_type in ["prefixParameter", "maskParameter"]:
for pn in tm.get_params_of_type_top(prefix_type):
par = getattr(tm, pn)
for a in [par.prefix] + par.prefix_aliases:
if a in alias_map:
raise ValueError(
"Two prefix/mask parameters have the same "
"alias {}: {} and {}".format(a, alias_map[a], par))
alias_map[a] = par
leftover_params = par_dict.copy()
for k in tm.get_params_mapping():
leftover_params.pop(k, None)
for a in getattr(tm, k).aliases:
leftover_params.pop(a, None)
for p in leftover_params:
try:
pre, idxstr, idxV = split_prefixed_name(p)
try:
par = alias_map[pre]
except KeyError:
if pre in ignore_prefix:
# log.warning("Ignoring unhandled prefix {}".format(pre))
continue
else:
raise ValueError(
"Mystery parameter {}, prefix {} with number {}".
format(p, pre, idxV))
component = tm.get_params_mapping()[par.name]
new_parameter = par.new_param(idxV)
if hasattr(tm, new_parameter.name):
raise ValueError("Received duplicate parameter {}".format(
new_parameter.name))
tm.add_param_from_top(new_parameter, component)
# print("added", new_parameter)
except PrefixError:
pass
return tm
class ModelBuilder:
"""A class for model construction interface.
Parameters
----------
name : str
Name for the model.
parfile : str optional
The .par file input for select components. If the parfile is
provided the self.model_instance will be put model instance
with .par file read in. If it is not provided, self.model_instance
will return as None.
Returns
-------
A class contains the result model instance if parfile is provided and
method to build the model.
"""
def __init__(self, parfile=None, name=""):
self.timing_model = None
self.name = name
self.param_inparF = None
self.param_unrecognized = {}
self.param_inModel = []
self.param_prefix = {}
self.select_comp = {}
self.control_params = ["EPHEM", "CLK"]
if parfile is not None:
self.parfile = parfile
self.build_model(self.parfile, self.name)
def __str__(self):
result = "Model name : " + self.name + "\n"
result += "Components in the model : \n"
for c in self.select_comp:
result += " " + str(c) + "\n"
if self.model_instance is not None:
result += "Read parameters from : " + self.parfile + "\n"
result += "The model instance is :\n" + str(self.model_instance)
return result
def preprocess_parfile(self, parfile):
"""Preprocess the par file.
Return
------
A dictionary with all the parfile parameters with values in string
"""
param = {}
repeat_par = {}
pfile = open(parfile, "r")
for l in [pl.strip() for pl in pfile.readlines()]:
# Skip blank lines
if not l:
continue
# Skip commented lines
if l.startswith("#") or l[:2] == "C ":
continue
k = l.split()
if (k[0] in param.keys()
): # repeat parameter TODO: add JUMP1 even there is only one
if k[0] in repeat_par.keys():
repeat_par[k[0]] += 1
else:
repeat_par[k[0]] = 2
param[k[0] + str(repeat_par[k[0]])] = k[1:]
else:
param[k[0]] = k[1:]
self.param_inparF = param
for key in repeat_par.keys():
self.param_inparF[key + str(1)] = self.param_inparF.pop(key)
pfile.close()
return self.param_inparF
def get_all_categories(self, ):
"""Obtain a dictionary from category to a list of instances."""
comp_category = defaultdict(list)
for k, cp in Component.component_types.items():
comp_category[cp.category].append(cp())
return dict(comp_category)
def get_comp_from_parfile(self, parfile):
"""Right now we only have one component on each category."""
params_inpar = self.preprocess_parfile(parfile)
for cat, cmps in self.get_all_categories().items():
selected_c = None
for cpi in cmps:
if cpi.component_special_params:
if any(par in params_inpar
for par in cpi.component_special_params):
selected_c = cpi
# Once have match, stop searching
break
else:
continue
else:
if cpi.is_in_parfile(params_inpar):
selected_c = cpi
if selected_c is not None:
self.select_comp[cat] = selected_c
def sort_components(self, category_order=DEFAULT_ORDER):
"""Sort the components into order.
Parameters
----------
category_order: list, optional
The order for the order sensitive component categories.
Note
----
If a category is not listed in the category_order, it will be treated
as order non-sensitive category and put in the end of sorted order list.
"""
sorted_components = []
for cat in self.get_all_categories():
# FIXME, I am not sure adding orders here is a good idea.
if cat not in category_order:
category_order.append(cat)
for co in category_order:
if co not in self.select_comp:
continue
cp = self.select_comp[co]
sorted_components.append(cp)
return sorted_components
def search_prefix_param(self, paramList, model, prefix_type):
"""Check if the Unrecognized parameter has prefix parameter"""
prefixs = {}
prefix_inModel = model.get_params_of_type_top(prefix_type)
for pn in prefix_inModel:
par = getattr(model, pn)
prefixs[par.prefix] = []
for p in paramList:
try:
pre, idxstr, idxV = split_prefixed_name(p)
if pre in [par.prefix] + par.prefix_aliases:
prefixs[par.prefix].append(p)
except ValueError: # FIXME: is this meant to catch KeyErrors?
continue
return prefixs
def build_model(self, parfile=None, name=""):
"""Read parfile using the model_instance attribute. Throws error if
mismatched coordinate systems detected.
Parameters
---------
name: str, optional
The name for the timing model
parfile : str optional
The parfile name
"""
if parfile is not None:
self.get_comp_from_parfile(parfile)
# ensure coordinate systems match for POS and PM
if "RAJ" in self.preprocess_parfile(parfile).keys():
if "PMELONG" in self.preprocess_parfile(parfile):
raise AttributeError(
"Cannot have Ecliptic proper motion parameters (PMELONG/PMELAT) with Equatorial position parameters (RAJ/DECJ) in par file."
)
elif "PMELAT" in self.preprocess_parfile(parfile):
raise AttributeError(
"Cannot have Ecliptic proper motion parameters (PMELONG/PMELAT) with Equatorial position parameters (RAJ/DECJ) in par file."
)
elif "ELONG" in self.preprocess_parfile(parfile).keys():
if "PMRA" in self.preprocess_parfile(parfile):
raise AttributeError(
"Cannot have Equatorial proper motion parameters (PMRA/PMDEC) with Ecliptic position parameters (ELONG/ELAT) in par file."
)
elif "PMDEC" in self.preprocess_parfile(parfile):
raise AttributeError(
"Cannot have Equatorial proper motion parameters (PMRA/PMDEC) with Ecliptic position parameters (ELONG/ELAT) in par file."
)
sorted_comps = self.sort_components()
self.timing_model = TimingModel(name, sorted_comps)
param_inModel = self.timing_model.get_params_mapping()
# Find unrecognised parameters in par file.
if self.param_inparF is not None:
parName = []
# add aliases
for p in list(param_inModel.keys()):
parName += getattr(self.timing_model, p).aliases
parName += param_inModel.keys()
for pp in self.param_inparF.keys():
if pp not in parName:
self.param_unrecognized[pp] = self.param_inparF[pp]
for ptype in ["prefixParameter", "maskParameter"]:
prefix_param = self.search_prefix_param(
self.param_unrecognized, self.timing_model, ptype)
prefix_in_model = self.timing_model.get_params_of_type_top(
ptype)
for key in prefix_param:
ppnames = [x for x in prefix_in_model if x.startswith(key)]
for ppn in ppnames:
pfx, idxs, idxv = split_prefixed_name(ppn)
if pfx == key:
exm_par = getattr(self.timing_model, ppn)
else:
continue
exm_par_comp = param_inModel[exm_par.name]
for parname in prefix_param[key]:
pre, idstr, idx = split_prefixed_name(parname)
if idx == exm_par.index:
continue
if hasattr(exm_par, "new_param"):
new_par = exm_par.new_param(idx)
self.timing_model.add_param_from_top(
new_par, exm_par_comp)
if "BINARY" in self.param_inparF:
vals = self.param_inparF["BINARY"]
if len(vals) != 1:
raise ValueError(
"Mal-formed binary model selection: {}".format(
repr(" ".join(["BINARY"] + vals))))
(bm, ) = vals
cats = self.timing_model.get_components_by_category()
if "pulsar_system" not in cats:
raise UnknownBinaryModel(
"Unknown binary model requested in par file: {}".
format(bm))
# FIXME: consistency check - the componens actually chosen should know the name bm
for p in self.timing_model.params:
if isinstance(self.timing_model[p], maskParameter):
# maskParameters need a bogus alias for parfile parsing
# remove this bogus alias
try:
ix = self.timing_model[p].aliases.index(
self.timing_model[p].prefix)
except ValueError:
pass
else:
del self.timing_model[p].aliases[ix]
if parfile is not None:
self.timing_model.read_parfile(parfile)
def get_control_info(self):
info = {}
if not self.param_unrecognized == {}:
for ctrlp in self.control_params:
if ctrlp in self.param_unrecognized:
info[ctrlp] = self.param_unrecognized[ctrlp]
else:
# Check if the prefix match
for p in self.control_params.keys():
if p.startswith(ctrlp):
info[ctrlp] = self.param_unrecognized[ctrlp]
return info