From 0eefb794292dd12dc02b224c7ad7c700ebd8c57b Mon Sep 17 00:00:00 2001 From: Dan F-M Date: Thu, 3 Aug 2023 07:42:37 -0400 Subject: [PATCH 1/2] Fixing journal name macros --- joss/paper.bib | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/joss/paper.bib b/joss/paper.bib index c6711a5..2ba4cd4 100644 --- a/joss/paper.bib +++ b/joss/paper.bib @@ -20,7 +20,7 @@ @ARTICLE{lenstronomy2021 @ARTICLE{herculens2022, author = {{Galan}, A. and {Vernardos}, G. and {Peel}, A. and {Courbin}, F. and {Starck}, J. -L.}, title = "{Using wavelets to capture deviations from smoothness in galaxy-scale strong lenses}", - journal = {\aap}, + journal = {Astronomy and Astrophysics}, keywords = {galaxies: structure, dark matter, methods: data analysis, gravitation, gravitational lensing: strong, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Astrophysics of Galaxies}, year = 2022, month = dec, @@ -38,7 +38,7 @@ @ARTICLE{herculens2022 @ARTICLE{vkl2022, author = {{Vernardos}, G. and {Koopmans}, L.~V.~E.}, title = "{The very knotty lenser: Exploring the role of regularization in source and potential reconstructions using Gaussian process regression}", - journal = {\mnras}, + journal = {Monthly Notices of the RAS}, keywords = {gravitational lensing: strong, Astrophysics - Astrophysics of Galaxies}, year = 2022, month = oct, @@ -56,7 +56,7 @@ @ARTICLE{vkl2022 @ARTICLE{molet2022, author = {{Vernardos}, G.}, title = "{Simulating time-varying strong lenses}", - journal = {\mnras}, + journal = {Monthly Notices of the RAS}, keywords = {gravitational lensing: strong, gravitational lensing: micro, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics}, year = 2022, month = apr, @@ -87,7 +87,7 @@ @article{pyautolens2021 @ARTICLE{gigalens2022, author = {{Gu}, A. and {Huang}, X. and {Sheu}, W. and {Aldering}, G. and {Bolton}, A.~S. and {Boone}, K. and {Dey}, A. and {Filipp}, A. and {Jullo}, E. and {Perlmutter}, S. and {Rubin}, D. and {Schlafly}, E.~F. and {Schlegel}, D.~J. and {Shu}, Y. and {Suyu}, S.~H.}, title = "{GIGA-Lens: Fast Bayesian Inference for Strong Gravitational Lens Modeling}", - journal = {\apj}, + journal = {Astrophysical Journal}, keywords = {GPU computing, Markov chain Monte Carlo, Strong gravitational lensing, Einstein rings, Bayesian statistics, Cosmology, 1969, 1889, 1643, 451, 1900, 343, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics, Statistics - Applications}, year = 2022, month = aug, @@ -106,7 +106,7 @@ @ARTICLE{gigalens2022 @ARTICLE{glee2010, author = {{Suyu}, S.~H. and {Halkola}, A.}, title = "{The halos of satellite galaxies: the companion of the massive elliptical lens SL2S J08544-0121}", - journal = {\aap}, + journal = {Astronomy and Astrophysics}, keywords = {galaxies: halos, galaxies: groups: individual: SL2S J08544-0121, gravitational lensing: strong, methods: data analysis, Astrophysics - Cosmology and Extragalactic Astrophysics}, year = 2010, month = dec, @@ -124,7 +124,7 @@ @ARTICLE{glee2010 @ARTICLE{glass2020, author = {{Denzel}, Philipp and {Mukherjee}, Sampath and {Coles}, Jonathan P. and {Saha}, Prasenjit}, title = "{Lessons from a blind study of simulated lenses: image reconstructions do not always reproduce true convergence}", - journal = {\mnras}, + journal = {Monthly Notices of the RAS}, keywords = {gravitational lensing: strong, methods: numerical, Galaxy: fundamental parameters, Galaxy: structure, Astrophysics - Astrophysics of Galaxies}, year = 2020, month = mar, @@ -160,7 +160,7 @@ @ARTICLE{lenstool2007 @ARTICLE{Meneghetti2017, author = {{Meneghetti}, M. and {Natarajan}, P. and {Coe}, D. and {Contini}, E. and {De Lucia}, G. and {Giocoli}, C. and {Acebron}, A. and {Borgani}, S. and {Bradac}, M. and {Diego}, J.~M. and {Hoag}, A. and {Ishigaki}, M. and {Johnson}, T.~L. and {Jullo}, E. and {Kawamata}, R. and {Lam}, D. and {Limousin}, M. and {Liesenborgs}, J. and {Oguri}, M. and {Sebesta}, K. and {Sharon}, K. and {Williams}, L.~L.~R. and {Zitrin}, A.}, title = "{The Frontier Fields lens modelling comparison project}", - journal = {\mnras}, + journal = {Monthly Notices of the RAS}, keywords = {gravitational lensing: strong, gravitational lensing: weak, galaxies: clusters: general, galaxies: high-redshift, Astrophysics - Cosmology and Nongalactic Astrophysics}, year = 2017, month = dec, @@ -178,7 +178,7 @@ @ARTICLE{Meneghetti2017 @ARTICLE{glafic201O, author = {{Oguri}, Masamune}, title = "{The Mass Distribution of SDSS J1004+4112 Revisited}", - journal = {\pasj}, + journal = {Publications of the ASJ}, keywords = {dark matter, galaxies: clusters: general, galaxies: quasars: individual (SDSS J1004+4112), gravitational lensing, Astrophysics - Cosmology and Nongalactic Astrophysics}, year = 2010, month = aug, @@ -195,7 +195,7 @@ @ARTICLE{glafic201O @ARTICLE{tdlmc2021, author = {{Ding}, X. and {Treu}, T. and {Birrer}, S. and {Chen}, G.~C. -F. and {Coles}, J. and {Denzel}, P. and {Frigo}, M. and {Galan}, A. and {Marshall}, P.~J. and {Millon}, M. and {More}, A. and {Shajib}, A.~J. and {Sluse}, D. and {Tak}, H. and {Xu}, D. and {Auger}, M.~W. and {Bonvin}, V. and {Chand}, H. and {Courbin}, F. and {Despali}, G. and {Fassnacht}, C.~D. and {Gilman}, D. and {Hilbert}, S. and {Kumar}, S.~R. and {Lin}, J.~Y. -Y. and {Park}, J.~W. and {Saha}, P. and {Vegetti}, S. and {Van de Vyvere}, L. and {Williams}, L.~L.~R.}, title = "{Time delay lens modelling challenge}", - journal = {\mnras}, + journal = {Monthly Notices of the RAS}, keywords = {gravitational lensing: strong, methods: data analysis, cosmology: observations, Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Astrophysics of Galaxies, Astrophysics - Instrumentation and Methods for Astrophysics}, year = 2021, month = may, @@ -213,7 +213,7 @@ @ARTICLE{tdlmc2021 @ARTICLE{tdcosmo2022, author = {{Shajib}, A.~J. and {Wong}, K.~C. and {Birrer}, S. and {Suyu}, S.~H. and {Treu}, T. and {Buckley-Geer}, E.~J. and {Lin}, H. and {Rusu}, C.~E. and {Poh}, J. and {Palmese}, A. and {Agnello}, A. and {Auger-Williams}, M.~W. and {Galan}, A. and {Schuldt}, S. and {Sluse}, D. and {Courbin}, F. and {Frieman}, J. and {Millon}, M.}, title = "{TDCOSMO. IX. Systematic comparison between lens modelling software programs: Time-delay prediction for WGD 2038{\ensuremath{-}}4008}", - journal = {\aap}, + journal = {Astronomy and Astrophysics}, keywords = {gravitational lensing: strong, methods: data analysis, galaxies: elliptical and lenticular, cD, distance scale, Astrophysics - Cosmology and Nongalactic Astrophysics}, year = 2022, month = nov, @@ -231,7 +231,7 @@ @ARTICLE{tdcosmo2022 @ARTICLE{refsdal2016, author = {{Treu}, T. and {Brammer}, G. and {Diego}, J.~M. and {Grillo}, C. and {Kelly}, P.~L. and {Oguri}, M. and {Rodney}, S.~A. and {Rosati}, P. and {Sharon}, K. and {Zitrin}, A. and {Balestra}, I. and {Brada{\v{c}}}, M. and {Broadhurst}, T. and {Caminha}, G.~B. and {Halkola}, A. and {Hoag}, A. and {Ishigaki}, M. and {Johnson}, T.~L. and {Karman}, W. and {Kawamata}, R. and {Mercurio}, A. and {Schmidt}, K.~B. and {Strolger}, L. -G. and {Suyu}, S.~H. and {Filippenko}, A.~V. and {Foley}, R.~J. and {Jha}, S.~W. and {Patel}, B.}, title = "{``Refsdal'' Meets Popper: Comparing Predictions of the Re-appearance of the Multiply Imaged Supernova Behind MACSJ1149.5+2223}", - journal = {\apj}, + journal = {Astrophysical Journal}, keywords = {gravitational lensing: strong, Astrophysics - Cosmology and Nongalactic Astrophysics}, year = 2016, month = jan, @@ -250,7 +250,7 @@ @ARTICLE{refsdal2016 @ARTICLE{glad2020, author = {{Chiriv{\`\i}}, G. and {Y{\i}ld{\i}r{\i}m}, A. and {Suyu}, S.~H. and {Halkola}, A.}, title = "{Gravitational Lensing and Dynamics (GLaD): combined analysis to unveil properties of high-redshift galaxies}", - journal = {\aap}, + journal = {Astronomy and Astrophysics}, keywords = {gravitational lensing: strong, galaxies: kinematics and dynamics, galaxies: high-redshift, galaxies: individual: RX J1131-1231}, year = 2020, month = nov, From 14dadf20531c4e5337e17c3611b2aeb4bb1e230e Mon Sep 17 00:00:00 2001 From: gvernard Date: Thu, 3 Aug 2023 18:40:53 -0400 Subject: [PATCH 2/2] Added option for plotting filled contours (or not). --- coolest/api/plotting.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/coolest/api/plotting.py b/coolest/api/plotting.py index d3f5bc4..c90a55f 100644 --- a/coolest/api/plotting.py +++ b/coolest/api/plotting.py @@ -463,7 +463,7 @@ def plot_lens(self,idx_file=0): -def plot_corner(parameter_id_list,chain_objs,chain_dirs,chain_names=None,point_estimate_objs=None,point_estimate_dirs=None,point_estimate_names=None,colors=None,labels=None,subplot_size=1,mc_samples_kwargs=None): +def plot_corner(parameter_id_list,chain_objs,chain_dirs,chain_names=None,point_estimate_objs=None,point_estimate_dirs=None,point_estimate_names=None,colors=None,labels=None,subplot_size=1,mc_samples_kwargs=None,filled_contours=True): """ Adding this as just a function for the moment. Takes a list of COOLEST files as input, which must have a chain file associated to them, and returns a corner plot. @@ -574,7 +574,7 @@ def plot_corner(parameter_id_list,chain_objs,chain_dirs,chain_names=None,point_e image.triangle_plot(mcsamples, params=parameter_id_list, legend_labels=chain_names, - filled=True, + filled=filled_contours, colors=colors, line_args=[{'ls':'-', 'lw': 2, 'color': c} for c in colors], contour_colors=colors)