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Commit 47f33669 authored by BURGARELLA Denis's avatar BURGARELLA Denis
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Merge branch 'develop' of gitlab.oamp.dev:yannick/pcigale into develop

parents ae31073e c33eb557
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pcigale/analysis_modules/pdf_analysis/workers.py
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......@@ -11,6 +11,7 @@ import time
import numpy as np
from scipy import optimize
from scipy.special import erf
import scipy.stats as st
from .utils import (save_best_sed, save_pdf, save_chi2, dchi2_over_ds2)
from ...warehouse import SedWarehouse
......@@ -255,16 +256,14 @@ def analysis(idx, obs):
)
if lim_flag is True:
norm_init = norm_facts
for imod in range(len(model_fluxes)):
norm_facts[imod] = optimize.newton(dchi2_over_ds2, norm_init[imod],
norm_facts[imod] = optimize.newton(dchi2_over_ds2, norm_facts[imod],
tol=1e-16,
args=(obs_fluxes, obs_errors,
model_fluxes[mod, :]))
model_fluxes[imod, :]))
model_fluxes *= norm_facts[:, np.newaxis]
# χ² of the comparison of each model to each observation.
mask_data = np.logical_and(obs_fluxes > tolerance, obs_errors > tolerance)
if lim_flag is True:
# This mask selects the filter(s) for which measured fluxes are given
# i.e., when (obs_flux is >=0. and obs_errors>=0.) and lim_flag=True
......@@ -273,53 +272,47 @@ def analysis(idx, obs):
# i.e., when (obs_flux is >=0. (and obs_errors>=-9990., obs_errors<0.))
# and lim_flag=True
mask_lim = np.logical_and(obs_errors >= -9990., obs_errors < tolerance)
chi2_data = np.sum(np.square(
chi2_ = np.sum(np.square(
(obs_fluxes[mask_data]-model_fluxes[:, mask_data]) /
obs_errors[mask_data]), axis=1)
chi2_lim = -2. * np.sum(
chi2_ += -2. * np.sum(
np.log(
np.sqrt(np.pi/2.)*(-obs_errors[mask_lim])*(
1.+erf(
(obs_fluxes[mask_lim]-model_fluxes[:, mask_lim]) /
(np.sqrt(2)*(-obs_errors[mask_lim]))))), axis=1)
chi2_ = chi2_data + chi2_lim
else:
mask_data = np.logical_and(obs_fluxes > tolerance,
obs_errors > tolerance)
chi2_ = np.sum(np.square(
(obs_fluxes[mask_data] - model_fluxes[:, mask_data]) /
obs_errors[mask_data]), axis=1)
# We use the exponential probability associated with the χ² as
# likelihood function.
likelihood = np.exp(-chi2_/2)
# For the analysis, we consider that the computed models explain
# each observation. We normalise the likelihood function to have a
# total likelihood of 1 for each observation.
likelihood /= np.sum(likelihood)
# We don't want to take into account the models with a probability
# less that the threshold.
wlikely = np.where(likelihood >= MIN_PROBABILITY)
likelihood = likelihood[wlikely]
# We re-normalise the likelihood.
likelihood /= np.sum(likelihood)
##################################################################
# Variable analysis #
##################################################################
# We define the best fitting model for each observation as the one
# with the least χ².
if len(chi2_)==0:
# It sometimes happen because models are older than the Universe's age
print("--------------------------------------------------------------")
print("No suitable model selected for the object #", idx, "we skip it")
print("One possible origin is that models are older than the Universe")
print("--------------------------------------------------------------")
if chi2_.size == 0:
# It sometimes happen because models are older than the Universe's age
print("No suitable model found for the object {}. One possible origin "
"is that models are older than the Universe.".format(obs['id']))
else:
# We select only models that have at least 0.1% of the probability of the
# best model to reproduce the observations. It helps eliminating very bad
# models.
maxchi2 = st.chi2.isf(st.chi2.sf(np.min(chi2_), obs_fluxes.size-1)*1e-3,
obs_fluxes.size-1)
wlikely = np.where(chi2_ < maxchi2)
# We use the exponential probability associated with the χ² as
# likelihood function.
likelihood = np.exp(-chi2_[wlikely]/2)
best_index = chi2_.argmin()
# We compute once again the best sed to obtain its info
# We compute once again the best sed to obtain its info
global gbl_previous_idx
if gbl_previous_idx > -1:
gbl_warehouse.partial_clear_cache(
......@@ -330,24 +323,23 @@ def analysis(idx, obs):
sed = gbl_warehouse.get_sed(gbl_params.modules,
gbl_params.from_index([wz[0][wvalid[0][best_index]]]))
# We correct the mass-dependent parameters
# We correct the mass-dependent parameters
for key in sed.mass_proportional_info:
sed.info[key] *= norm_facts[best_index]
for index, variable in enumerate(gbl_analysed_variables):
if variable in sed.mass_proportional_info:
model_variables[:, index] *= norm_facts
# We compute the weighted average and standard deviation using the
# likelihood as weight.
# We compute the weighted average and standard deviation using the
# likelihood as weight.
analysed_averages = np.empty(len(gbl_analysed_variables))
analysed_std = np.empty_like(analysed_averages)
# We check how many unique parameter values are analysed and if less than
# Npdf (= 100), the PDF is initally built assuming a number of bins equal
# to the number of unique values for a given parameter (e.g., average_sfr,
# age, attenuation.uv_bump_amplitude, dust.luminosity, attenuation.FUV,
# etc.).
# We check how many unique parameter values are analysed and if less
# than Npdf (= 100), the PDF is initally built assuming a number of
# bins equal to the number of unique values for a given parameter
# (e.g., average_sfr, age, attenuation.uv_bump_amplitude,
# dust.luminosity, attenuation.FUV, etc.).
Npdf = 100
var = np.empty((Npdf, len(analysed_averages)))
pdf = np.empty((Npdf, len(analysed_averages)))
......@@ -382,7 +374,7 @@ def analysis(idx, obs):
pdf[:, i] = np.interp(var[:, i], pdf_x, pdf_prob)
# TODO Merge with above computation after checking it is fine with a MA.
# TODO Merge with above computation after checking it is fine with a MA
gbl_analysed_averages[idx, :] = analysed_averages
gbl_analysed_std[idx, :] = analysed_std
......@@ -392,7 +384,7 @@ def analysis(idx, obs):
gbl_best_chi2[idx] = chi2_[best_index]
gbl_best_chi2_red[idx] = chi2_[best_index] / obs_fluxes.size
# If observed SED analysis
# If observed SED analysis
if gbl_phase == 1:
if gbl_save['best_sed']:
save_best_sed(obs['id'], sed, norm_facts[best_index])
......
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