# -*- coding: utf-8 -*-
import copy
import pathlib
import numpy as np
import pandas as pd
from ..fit_manager import FitManager
from ..log import logging
from .chi2_utils import Chi2tableCalculator
from .coefficients_utils import CoefficientsPlotter, compute_confidence_level
from .correlations import plot_correlations
from .fisher import FisherCalculator
from .html_utils import html_link, write_html_container
from .latex_tools import compile_tex
from .pca import PcaCalculator
from .summary import SummaryWriter
_logger = logging.getLogger(__name__)
[docs]
class Report:
r"""Report class manager.
If :math:`\chi^2`, Fisher or Data vs Theory plots are produced it computes the
best fit theory predictions.
Attributes
----------
report: str
path to report folder
fits: numpy.ndarray
array with fits (instances of `smefit.fit_manager.FitManger`) included in the report
data_info: pandas.DataFrame
datasets information (references and data groups)
coeff_info: pandas.DataFrame
coefficients information (group and latex name)
Parameters
----------
report_path: pathlib.Path, str
path to base folder, where the reports will be stored.
result_path: pathlib.Path, str
path to base folder, where the results are stored.
report_config: dict
dictionary with report configuration, see `/run_cards/analyze/report_runcard.yaml`
for an example
"""
def __init__(self, report_path, result_path, report_config):
self.report = pathlib.Path(f"{report_path}/{report_config['name']}").absolute()
self.fits = []
# build the fits labels if needed
if "fit_labels" not in report_config:
fit_labels = [
f"${{\\rm {fit}}}$".replace("_", r"\ ")
for fit in report_config["result_IDs"]
]
else:
fit_labels = report_config["fit_labels"]
# Loads fits
for name, label in zip(report_config["result_IDs"], fit_labels):
fit = FitManager(result_path, name, label)
fit.load_results()
if any(k in report_config for k in ["chi2_plots", "PCA", "fisher"]):
fit.load_datasets()
self.fits.append(fit)
self.fits = np.array(self.fits)
# Loads useful information about data
self.data_info = self._load_grouped_info(report_config["data_info"], "datasets")
# Loads coefficients grouped with latex name
self.coeff_info = self._load_grouped_info(
report_config["coeff_info"], "coefficients"
)
self.html_index = ""
self.html_content = ""
def _load_grouped_info(self, raw_dict, key):
"""Load grouped info of coefficients and datasets.
Only elements appearing at least once in the fit configs are kept.
Parameters
----------
raw_dict: dict
raw dictionary with relevant information
key: "datasets" or "coefficients"
key to check
Returns
_______
grouped_config: pandas.DataFrame
table with information by group
"""
out_dict = {}
for group, entries in raw_dict.items():
out_dict[group] = {}
for val in entries:
if np.any([val[0] in fit.config[key] for fit in self.fits]):
out_dict[group][val[0]] = val[1]
if len(out_dict[group]) == 0:
out_dict.pop(group)
return pd.DataFrame(out_dict).stack().swaplevel()
def _append_section(self, title, links=None, figs=None, tables=None):
self.html_index += html_link(f"#{title}", title, add_meta=False)
self.html_content += write_html_container(
title, links=links, figs=figs, dataFrame=tables
)
[docs]
def summary(self):
"""Summary Table runner."""
summary = SummaryWriter(self.fits, self.data_info, self.coeff_info)
section_title = "Summary"
coeff_tab = "coefficient_summary"
data_tab = "dataset_summary"
# write summary tables
compile_tex(self.report, summary.write_coefficients_table(), coeff_tab)
compile_tex(self.report, summary.write_dataset_table(), data_tab)
self._append_section(
section_title,
links=[(data_tab, "Dataset summary"), (coeff_tab, "Coefficient summary")],
tables=summary.fit_settings(),
)
[docs]
def chi2(self, table=True, plot_experiment=None, plot_distribution=None):
r""":math:`\chi^2` table and plots runner.
Parameters
----------
table: bool, optional
write the latex :math:`\chi^2` table per dataset
plot_experiment: bool, optional
plot the :math:`\chi^2` per dataset
plot_distribution: bool, optional
plot the :math:`\chi^2` distribution per each replica
"""
links_list = None
figs_list = []
chi2_cal = Chi2tableCalculator(self.data_info)
# here we store the info for each fit
chi2_dict = {}
chi2_dict_group = {}
chi2_replica = {}
for fit in self.fits:
# This computes the chi2 by taking the mean of the replicas
_, chi2_total_rep = chi2_cal.compute(
fit.datasets,
fit.smeft_predictions,
)
chi2_df_best, _ = chi2_cal.compute(
fit.datasets, fit.smeft_predictions_best_fit
)
chi2_replica[fit.label] = chi2_total_rep
chi2_dict[fit.label] = chi2_cal.add_normalized_chi2(chi2_df_best)
chi2_dict_group[fit.label] = chi2_cal.group_chi2_df(chi2_df_best)
if table:
lines = chi2_cal.write(chi2_dict, chi2_dict_group)
compile_tex(self.report, lines, "chi2_tables")
links_list = [("chi2_tables", "Tables")]
if plot_experiment is not None:
_logger.info("Plotting : chi^2 for each dataset")
chi2_cal.plot_exp(chi2_dict, f"{self.report}/chi2_bar", **plot_experiment)
figs_list.append("chi2_bar")
if plot_distribution is not None:
_logger.info("Plotting : chi^2 distribution for each replica")
chi2_cal.plot_dist(
chi2_replica, f"{self.report}/chi2_histo", **plot_distribution
)
figs_list.append("chi2_histo")
self._append_section("Chi2", links=links_list, figs=figs_list)
[docs]
def coefficients(
self,
scatter_plot=None,
confidence_level_bar=None,
pull_bar=None,
spider_plot=None,
posterior_histograms=True,
contours_2d=None,
hide_dofs=None,
show_only=None,
logo=True,
table=None,
double_solution=None,
):
"""Coefficients plots and table runner.
Parameters
----------
hide_dofs: list
list of operator not to display
show_only: list
list of all the operator to display, if None all the free dof are presented
logo: bool
if True add logo to the plots
scatter_plot: None, dict
kwarg confidence level bar plot or None
confidence_level_bar: None, dict
kwarg scatter plot or None
posterior_histograms: bool
if True plot the posterior distribution for each coefficient
table: None, dict
kwarg the latex confidence level table per coefficient or None
double_solution: dict
operator with double solution per fit
"""
links_list = None
figs_list = []
coeff_config = self.coeff_info
if show_only is not None:
coeff_config = coeff_config.loc[:, show_only]
if hide_dofs is not None:
coeff_config = coeff_config.drop(hide_dofs, level=1)
coeff_plt = CoefficientsPlotter(
self.report,
coeff_config,
logo=logo,
)
# compute confidence level bounds
bounds_dict = {}
for fit in self.fits:
bounds_dict[fit.label] = compute_confidence_level(
fit.results["samples"],
coeff_plt.coeff_info,
fit.has_posterior,
(
double_solution.get(fit.name, None)
if double_solution is not None
else None
),
)
if scatter_plot is not None:
_logger.info("Plotting : Central values and Confidence Level bounds")
coeff_plt.plot_coeffs(bounds_dict, **scatter_plot)
figs_list.append("coefficient_central")
# when we plot the 95% CL we show the 95% CL for null solutions.
# the error coming from a degenerate solution is not taken into account.
if confidence_level_bar is not None:
_logger.info("Plotting : Confidence Level error bars")
bar_cl = confidence_level_bar["confidence_level"]
confidence_level_bar.pop("confidence_level")
zero_sol = 0
coeff_plt.plot_coeffs_bar(
{
name: -bound_df.loc[zero_sol, f"low{bar_cl}"]
+ bound_df.loc[zero_sol, f"high{bar_cl}"]
for name, bound_df in bounds_dict.items()
},
**confidence_level_bar,
)
figs_list.append("coefficient_bar")
# when we plot the 95% CL we show the 95% CL for null solutions.
# the error coming from a degenerate solution is not taken into account.
if pull_bar is not None:
_logger.info("Plotting : Pull ")
zero_sol = 0
coeff_plt.plot_pull(
{
name: bound_df.loc[zero_sol, "pull"]
for name, bound_df in bounds_dict.items()
},
**pull_bar,
)
figs_list.append("pull_bar")
if spider_plot is not None:
_logger.info("Plotting : spider plot")
spider_cl = spider_plot["confidence_level"]
spider_plot.pop("confidence_level")
spider_bounds = {}
for name, bound_df in bounds_dict.items():
dbl_solution = bound_df.index.get_level_values(0)
# if dbl solution requested, add the confidence intervals, otherwise just
# use the sum of the hdi intervals
if 1 in dbl_solution:
dbl_op = double_solution.get(fit.name, None)
idx = [
np.argwhere(
self.coeff_info.index.get_level_values(1) == op
).flatten()[0]
for op in dbl_op
]
bound_df_dbl = bound_df.iloc[:, idx]
width_0 = bound_df_dbl.loc[0, f"hdi_{spider_cl}"]
width_1 = bound_df_dbl.loc[1, f"hdi_{spider_cl}"]
width_tot = width_0 + width_1
# update bound df
bound_df.loc[0, f"hdi_{spider_cl}"].iloc[idx] = width_tot
spider_bounds[name] = bound_df.loc[0, f"hdi_{spider_cl}"]
else:
spider_bounds[name] = bound_df.loc[0, f"hdi_{spider_cl}"]
coeff_plt.plot_spider(
spider_bounds,
labels=[fit.label for fit in self.fits],
**spider_plot,
)
figs_list.append("spider_plot")
if posterior_histograms:
_logger.info("Plotting : Posterior histograms")
disjointed_lists = [
(
double_solution.get(fit.name, None)
if double_solution is not None
else None
)
for fit in self.fits
]
coeff_plt.plot_posteriors(
[fit.results["samples"] for fit in self.fits],
labels=[fit.label for fit in self.fits],
disjointed_lists=disjointed_lists,
)
figs_list.append("coefficient_histo")
if table is not None:
_logger.info("Writing : Confidence level table")
lines = coeff_plt.write_cl_table(bounds_dict, **table)
compile_tex(self.report, lines, "coefficients_table")
links_list = [("coefficients_table", "CL table")]
if contours_2d:
_logger.info("Plotting : 2D confidence level projections")
coeff_plt.plot_contours_2d(
[
(
fit.results["samples"][fit.coefficients.free_parameters.index],
fit.config["use_quad"],
)
for fit in self.fits
],
labels=[fit.label for fit in self.fits],
confidence_level=contours_2d["confidence_level"],
dofs_show=contours_2d["dofs_show"],
double_solution=double_solution,
)
figs_list.append("contours_2d")
self._append_section("Coefficients", links=links_list, figs=figs_list)
[docs]
def correlations(
self, hide_dofs=None, thr_show=0.1, title=True, fit_list=None, figsize=(10, 10)
):
"""Plot coefficients correlation matrix.
Parameters
----------
hide_dofs: list
list of operator not to display.
thr_show: float, None
minimum threshold value to show.
If None the full correlation matrix is displayed.
title: bool
if True display fit label name as title
fit_list: list, optional
list of fit names for which the correlation is computed.
By default all the fits included in the report
"""
figs_list = []
if fit_list is not None:
fit_list = [fit for fit in self.fits if fit in fit_list]
else:
fit_list = self.fits
for fit in fit_list:
_logger.info(f"Plotting correlations for: {fit.name}")
coeff_to_keep = fit.coefficients.free_parameters.index
plot_correlations(
fit.results["samples"][coeff_to_keep],
latex_names=self.coeff_info.droplevel(0),
fig_name=f"{self.report}/correlations_{fit.name}",
title=fit.label if title else None,
hide_dofs=hide_dofs,
thr_show=thr_show,
figsize=figsize,
)
figs_list.append(f"correlations_{fit.name}")
self._append_section("Correlations", figs=figs_list)
[docs]
def pca(
self,
table=True,
plot=None,
thr_show=1e-2,
fit_list=None,
):
"""Principal Components Analysis runner.
Parameters
----------
table: bool, optional
if True writes the PC directions in a latex list
plot: bool, optional
if True produces a PC heatmap
thr_show: float
minimum threshold value to show
fit_list: list, optional
list of fit names for which the PCA is computed.
By default all the fits included in the report
"""
figs_list, links_list = [], []
if fit_list is not None:
fit_list = [fit for fit in self.fits if fit in fit_list]
else:
fit_list = self.fits
for fit in fit_list:
_logger.info(f"Computing PCA for fit {fit.name}")
pca_cal = PcaCalculator(
fit.datasets,
fit.coefficients,
self.coeff_info.droplevel(0),
)
pca_cal.compute()
if table:
compile_tex(
self.report,
pca_cal.write(fit.label, thr_show),
f"pca_table_{fit.name}",
)
links_list.append((f"pca_table_{fit.name}", f"Table {fit.label}"))
if plot is not None:
title = fit.name
# TODO: check why **fit_plot got removed (see PR)
pca_cal.plot_heatmap(
f"{self.report}/pca_heatmap_{fit.name}", title=title
)
figs_list.append(f"pca_heatmap_{fit.name}")
self._append_section("PCA", figs=figs_list, links=links_list)
[docs]
def fisher(
self,
norm="coeff",
summary_only=True,
plot=None,
fit_list=None,
log=False,
):
"""Fisher information table and plots runner.
Summary table and plots are the default
Parameters
----------
norm: "coeff", "dataset"
fisher information normalization: per coefficient, or per dataset
summary_only: bool, optional
if False writes the fine grained fisher tables per dataset and group
if True only the summary table with grouped a datsets is written
plot: None, dict
plot options
fit_list: list, optional
list of fit names for which the fisher information is computed.
By default all the fits included in the report
log: bool, optional
if True shows the log of the Fisher informaltion
"""
figs_list, links_list = [], []
if fit_list is not None:
fit_list = [fit for fit in self.fits if fit in fit_list]
else:
fit_list = self.fits
for fit in fit_list:
compute_quad = fit.config["use_quad"]
fisher_cal = FisherCalculator(fit.coefficients, fit.datasets, compute_quad)
fisher_cal.compute_linear()
fisher_cal.lin_fisher = fisher_cal.normalize(
fisher_cal.lin_fisher, norm=norm, log=log
)
fisher_cal.summary_table = fisher_cal.groupby_data(
fisher_cal.lin_fisher, self.data_info, norm, log
)
# if necessary compute the quadratic Fisher
if compute_quad:
fisher_cal.compute_quadratic(
fit.results["samples"], fit.smeft_predictions
)
fisher_cal.quad_fisher = fisher_cal.normalize(
fisher_cal.quad_fisher, norm=norm, log=log
)
fisher_cal.summary_HOtable = fisher_cal.groupby_data(
fisher_cal.quad_fisher, self.data_info, norm, log
)
# Write down the table in latex
free_coeff_config = self.coeff_info.loc[
:, fit.coefficients.free_parameters.index
]
compile_tex(
self.report,
fisher_cal.write_grouped(
free_coeff_config, self.data_info, summary_only
),
f"fisher_{fit.name}",
)
links_list.append((f"fisher_{fit.name}", f"Table {fit.label}"))
if plot is not None:
fit_plot = copy.deepcopy(plot)
title = fit.label if fit_plot.pop("title") else None
fisher_cal.plot(
free_coeff_config,
f"{self.report}/fisher_heatmap_{fit.name}",
title=title,
**fit_plot,
)
figs_list.append(f"fisher_heatmap_{fit.name}")
self._append_section("Fisher", figs=figs_list, links=links_list)