Coverage for pesummary/gw/file/formats/default.py: 87.8%
82 statements
« prev ^ index » next coverage.py v7.4.4, created at 2024-05-02 08:42 +0000
1# Licensed under an MIT style license -- see LICENSE.md
3import numpy as np
4from pesummary.gw.file.formats.base_read import (
5 GWRead, GWSingleAnalysisRead, GWMultiAnalysisRead
6)
7from pesummary.core.file.formats.default import Default as CoreDefault
9__author__ = ["Charlie Hoy <charlie.hoy@ligo.org>"]
12class SingleAnalysisDefault(GWSingleAnalysisRead):
13 """Class to handle result files which only contain a single analysis
15 Parameters
16 ----------
17 path_to_results_file: str
18 path to the results file you wish to load
19 remove_nan_likelihood_samples: Bool, optional
20 if True, remove samples which have log_likelihood='nan'. Default True
22 Attributes
23 ----------
24 parameters: list
25 list of parameters stored in the result file
26 converted_parameters: list
27 list of parameters that have been derived from the sampled distributions
28 samples: 2d list
29 list of samples stored in the result file
30 samples_dict: dict
31 dictionary of samples stored in the result file keyed by parameters
32 input_version: str
33 version of the result file passed.
34 extra_kwargs: dict
35 dictionary of kwargs that were extracted from the result file
36 converted_parameters: list
37 list of parameters that have been added
38 pe_algorithm: str
39 name of the algorithm used to generate the posterior samples
41 Methods
42 -------
43 to_dat:
44 save the posterior samples to a .dat file
45 to_latex_table:
46 convert the posterior samples to a latex table
47 generate_latex_macros:
48 generate a set of latex macros for the stored posterior samples
49 to_lalinference:
50 convert the posterior samples to a lalinference result file
51 generate_all_posterior_samples:
52 generate all posterior distributions that may be derived from
53 sampled distributions
54 """
55 def __init__(self, *args, _data=None, **kwargs):
56 super(SingleAnalysisDefault, self).__init__(*args, **kwargs)
57 if _data is not None:
58 self.load(None, _data=_data, **kwargs)
61class MultiAnalysisDefault(GWMultiAnalysisRead):
62 """Class to handle result files which contain multiple analyses
64 Parameters
65 ----------
66 path_to_results_file: str
67 path to the results file you wish to load
68 remove_nan_likelihood_samples: Bool, optional
69 if True, remove samples which have log_likelihood='nan'. Default True
71 Attributes
72 ----------
73 parameters: 2d list
74 list of parameters stored in the result file for each analysis
75 converted_parameters: 2d list
76 list of parameters that have been derived from the sampled distributions
77 samples: 3d list
78 list of samples stored in the result file for each analysis
79 samples_dict: dict
80 dictionary of samples stored in the result file keyed by analysis label
81 input_version: str
82 version of the result file passed.
83 extra_kwargs: dict
84 dictionary of kwargs that were extracted from the result file
86 Methods
87 -------
88 samples_dict_for_label: dict
89 dictionary of samples for a specific analysis
90 reduced_samples_dict: dict
91 dictionary of samples for one or more analyses
92 to_dat:
93 save the posterior samples to a .dat file
94 to_latex_table:
95 convert the posterior samples to a latex table
96 generate_latex_macros:
97 generate a set of latex macros for the stored posterior samples
98 to_lalinference:
99 convert the posterior samples to a lalinference result file
100 generate_all_posterior_samples:
101 generate all posterior distributions that may be derived from
102 sampled distributions
103 """
104 def __init__(self, *args, _data=None, **kwargs):
105 super(MultiAnalysisDefault, self).__init__(*args, **kwargs)
106 if _data is not None:
107 self.load(None, _data=_data, **kwargs)
110class Default(CoreDefault):
111 """Class to handle the default loading options.
113 Parameters
114 ----------
115 path_to_results_file: str
116 path to the results file you wish to load
117 remove_nan_likelihood_samples: Bool, optional
118 if True, remove samples which have log_likelihood='nan'. Default True
120 Attributes
121 ----------
122 parameters: list
123 list of parameters stored in the result file
124 converted_parameters: list
125 list of parameters that have been derived from the sampled distributions
126 samples: 2d list
127 list of samples stored in the result file
128 samples_dict: dict
129 dictionary of samples stored in the result file keyed by parameters
130 input_version: str
131 version of the result file passed.
132 extra_kwargs: dict
133 dictionary of kwargs that were extracted from the result file
134 converted_parameters: list
135 list of parameters that have been added
137 Methods
138 -------
139 to_dat:
140 save the posterior samples to a .dat file
141 to_latex_table:
142 convert the posterior samples to a latex table
143 generate_latex_macros:
144 generate a set of latex macros for the stored posterior samples
145 to_lalinference:
146 convert the posterior samples to a lalinference result file
147 generate_all_posterior_samples:
148 generate all posterior distributions that may be derived from
149 sampled distributions
150 """
151 def load_map(self):
152 _load_map = super(Default, self).load_map(self)
153 _load_map.update({
154 "xml": self._grab_data_from_xml_file
155 })
156 return _load_map
158 def __new__(self, path_to_results_file, **kwargs):
159 data = super(Default, self).__new__(
160 self, path_to_results_file, _single_default=SingleAnalysisDefault,
161 _multi_default=MultiAnalysisDefault, **kwargs
162 )
163 self.module = "gw"
164 return data
166 @staticmethod
167 def grab_extra_kwargs(parameters, samples):
168 """Grab any additional information stored in the file
169 """
170 def find_parameter_given_alternatives(parameters, options):
171 if any(i in options for i in parameters):
172 parameter = [i for i in parameters if i in options]
173 ind = parameters.index(parameter[0])
174 return ind
175 return None
177 kwargs = {"sampler": {}, "meta_data": {}}
178 possible_f_ref = ["f_ref", "fRef", "fref", "fref_template"]
179 ind = find_parameter_given_alternatives(parameters, possible_f_ref)
180 if ind is not None:
181 kwargs["meta_data"]["f_ref"] = samples[0][ind]
182 possible_f_low = ["flow", "f_low", "fLow", "flow_template"]
183 ind = find_parameter_given_alternatives(parameters, possible_f_low)
184 if ind is not None:
185 kwargs["meta_data"]["f_low"] = samples[0][ind]
186 return kwargs
188 @staticmethod
189 def _grab_data_from_dat_file(path, **kwargs):
190 """Grab the data stored in a .dat file
191 """
192 data = CoreDefault._grab_data_from_dat_file(path)
193 parameters, samples = data["parameters"], data["samples"]
194 parameters = GWRead._check_definition_of_inclination(parameters)
195 condition1 = "luminosity_distance" not in parameters
196 condition2 = "logdistance" in parameters
197 if condition1 and condition2:
198 parameters.append("luminosity_distance")
199 for num, i in enumerate(samples):
200 samples[num].append(
201 np.exp(i[parameters.index("logdistance")]))
202 try:
203 extra_kwargs = Default.grab_extra_kwargs(parameters, samples)
204 except Exception:
205 extra_kwargs = {"sampler": {}, "meta_data": {}}
206 extra_kwargs["sampler"]["nsamples"] = len(samples)
207 return {
208 "parameters": parameters, "samples": samples,
209 "injection": Default._default_injection(parameters),
210 "kwargs": extra_kwargs
211 }
213 @staticmethod
214 def _grab_data_from_hdf5_file(path, path_to_samples=None, **kwargs):
215 """Grab the data stored in an hdf5 file
216 """
217 return CoreDefault._grab_data_from_hdf5_file(
218 path, remove_params=["waveform_approximant"],
219 path_to_samples=path_to_samples, **kwargs
220 )
222 @staticmethod
223 def _grab_data_from_numpy_file(path, file_format=None, **kwargs):
224 """Grab the data stored in a .npy file
225 """
226 if file_format is not None:
227 try:
228 import importlib
229 module = importlib.import_module(
230 "pesummary.gw.file.formats.{}".format(file_format)
231 )
232 data = getattr(module, "read_{}".format(file_format))(path, **kwargs)
233 return {
234 "parameters": data[0], "samples": data[1],
235 "injection": Default._default_injection(data[0])
236 }
237 except ModuleNotFoundError:
238 from pesummary.utils.utils import logger
239 logger.warning(
240 "Failed to find the module '{}'. Therefore ignoring "
241 "file_format={} and using default load".format(
242 "pesummary.gw.file.formats.{}".format(file_format),
243 file_format
244 )
245 )
246 return CoreDefault._grab_data_from_numpy_file(path, **kwargs)
248 @staticmethod
249 def _grab_data_from_prior_file(path, **kwargs):
250 """Grab the data stored in a .prior file
251 """
252 return CoreDefault._grab_data_from_prior_file(
253 path, module="gw", **kwargs
254 )
256 @staticmethod
257 def _grab_data_from_xml_file(path, **kwargs):
258 """Grab the data stored in an xml file
259 """
260 from pesummary.gw.file.formats.xml import read_xml
262 parameters, samples = read_xml(path, **kwargs)
263 extra_kwargs = {"sampler": {"nsamples": len(samples)}, "meta_data": {}}
264 return {
265 "parameters": parameters, "samples": samples,
266 "injection": Default._default_injection(parameters),
267 "kwargs": extra_kwargs
268 }