Merge branch 'main' of github.com:aymgal/COOLEST

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)

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,