Merge branch 'master' of github.com:drphilmarshall/Pangloss

doc/references.bib

@@ -3280,3 +3280,92 @@ @ARTICLE{Jasche+Wandelt2013
              galaxy density. Poisson likelihood for counts in cells, model is density in
              voxels. Made possible by HMC sampling. Resolution ~ 6Mpc or so.}
 }
+
+@ARTICLE{KarpenkaEtal2013,
+   author = {{Karpenka}, N.~V. and {March}, M.~C. and {Feroz}, F. and {Hobson}, M.~P.
+	},
+    title = "{Bayesian constraints on dark matter halo properties using gravitationally lensed supernovae}",
+  journal = {\mnras},
+archivePrefix = "arXiv",
+   eprint = {1207.3708},
+ keywords = {gravitational lensing: weak, methods: data analysis, methods: statistical, supernovae: general, galaxies: haloes},
+     year = 2013,
+    month = aug,
+   volume = 433,
+    pages = {2693-2705},
+      doi = {10.1093/mnras/sts700},
+   adsurl = {http://adsabs.harvard.edu/abs/2013MNRAS.433.2693K},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System},
+     note = {Weak lensing of SN, modeled hierarchically with halos.
+            Halos are SIS, with velocity dispersion scaled with galaxy
+            luminosity according to Faber-Jackson relation. Relation
+            parameters are fitted, but zero scatter is assumed - so
+            model only has 4 parameters, not 4+many. The hierarachical
+            part refers to the SN analysis, not the halo modeling.
+            They carry out evidence testing of models with and without
+            lensing, finding that the evidence for lensing is driven
+            by the few most strongly lensed systems. In real (SNLS)
+            data they see only very marginal lensing signal in this
+            way. NFW models are discussed, shear data is not. Paper is
+            a response to claims by Jonsson et al and others that the
+            SNIa sample contains weak lensing signal.}
+}
+
+@ARTICLE{SmithEtal2014,
+   author = {{Smith}, M. and {Bacon}, D.~J. and {Nichol}, R.~C. and {Campbell}, H. and
+	{Clarkson}, C. and {Maartens}, R. and {D'Andrea}, C.~B. and
+	{Bassett}, B.~A. and {Cinabro}, D. and {Finley}, D.~A. and {Frieman}, J.~A. and
+	{Galbany}, L. and {Garnavich}, P.~M. and {Olmstead}, M.~D. and
+	{Schneider}, D.~P. and {Shapiro}, C. and {Sollerman}, J.},
+    title = "{The Effect of Weak Lensing on Distance Estimates from Supernovae}",
+  journal = {\apj},
+archivePrefix = "arXiv",
+   eprint = {1307.2566},
+ primaryClass = "astro-ph.CO",
+ keywords = {cosmology: observations, distance scale, supernovae: general, surveys },
+     year = 2014,
+    month = jan,
+   volume = 780,
+      eid = {24},
+    pages = {24},
+      doi = {10.1088/0004-637X/780/1/24},
+   adsurl = {http://adsabs.harvard.edu/abs/2014ApJ...780...24S},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System},
+     note = {Marginal detection of weak lensing in SDSS II and BOSS
+             SNe sample, via Hubble residual analysis. New parameter
+             gamma controls linear dependence of Hubble residuals on
+             kappa_gal, the convergence estimated from the number
+             counts of galaxies in bins.}
+}
+
+@ARTICLE{Schneider2014,
+   author = {{Schneider}, P.},
+    title = "{Generalized multi-plane gravitational lensing: time delays, recursive lens equation, and the mass-sheet transformation}",
+  journal = {ArXiv e-prints},
+archivePrefix = "arXiv",
+   eprint = {1409.0015},
+ keywords = {Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Astrophysics of Galaxies},
+     year = 2014,
+    month = aug,
+   adsurl = {http://adsabs.harvard.edu/abs/2014arXiv1409.0015S},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System},
+     note = {Intense theoretical paper laying out teh formalism for
+             general multi-plane lens time delays. A generalized
+             mass sheet transformation exists, but seems like it may
+             not be important in practice, due to its "curious"
+             nature. Peter writes: "This curious behavior of the MST 
+             in multi-plane lensing may indeed offer a way to break
+             the corresponding degeneracy, at least in a statistical
+             way. As we discussed before, in the case of vanishing
+             perturbations between the main lens planes, the MST
+             corresponds to mass sheets of alternating sign from plane
+             to plane. Since such a mass sheet changes the slope of
+             the to-tal mass distribution, it means that this slope
+             change also alternates. If one now makes the perhaps
+             plausible assumption that the shape of the mean mass
+             profiles of lenses is the same, this alternating slope
+             change would violate the universality of the mean mass
+             profile. Thus, in multi-plane lensing, the mass-sheet
+             generacy may be more easily lifted than in the case of a
+             single lens plane only."}
+}

example/example.config

@@ -6,8 +6,8 @@
 # Name : Value pair to be read into the parameters dictionary.
 #
 # This file is part of the Pangloss project, distributed under the
-# GPL v2, by Tom Collett (IoA) and  Phil Marshall (Oxford). 
-# Please cite: Collett et al 2013, arxiv/###
+# GPL v2, by Tom Collett (IoA) and  Phil Marshall (Oxford).
+# Please cite: Collett et al 2013, http://arxiv.org/abs/1303.6564
 #
 # ======================================================================
 
@@ -20,7 +20,7 @@ ExperimentName: example
 # Simulated data for calibration. One halo catalog per kappa map,
 # environment variables and wildcards will be expanded:
 CalibrationCatalogs: $PANGLOSS_DIR/calib/Millennium/catalog_example*.*
-CalibrationKappamaps: $PANGLOSS_DIR/calib/Millennium/kappa*.fits 
+CalibrationKappamaps: $PANGLOSS_DIR/calib/Millennium/kappa*.fits
 
 # Observed data:
 ObservedCatalog: $PANGLOSS_DIR/example/example_catalog.txt
@@ -62,7 +62,7 @@ LightconeDepthBand: i
 NCalibrationLightcones: 1000
 
 # Destination directory for the calibration lightcones. This should be
-# in your local workspace, because the lightcones will be specific to 
+# in your local workspace, because the lightcones will be specific to
 # this experiment
 CalibrationFolder: calib
 
@@ -80,12 +80,12 @@ MakeNewCalibrations : True
 
 # We want the PDF Pr(kappah|D), in the form of a list of samples - or
 # equivalently, realisations of the lightcone mass distribution:
-NRealisations: 100 
+NRealisations: 100
 
 # Reconstructing the calibration lines of sight is expensive. If we have already# done this for an !*!identical!*! experiment setup we needen't do it again.
 ReconstructCalibrations : True
 
-StellarMass2HaloMassRelation: Behroozi 
+StellarMass2HaloMassRelation: Behroozi
 # No other options encoded so far...
 
 # Halo mass function catalog for empirical Pr(Mh):
@@ -95,19 +95,19 @@ HMFfile: $PANGLOSS_DIR/calib/SHMR/HaloMassRedshiftCatalog.pickle
 PhotozError: 0.1
 
 # Assumed Mstar uncertainty:
-PhotometricMstarError: 0.45 # dex 
+PhotometricMstarError: 0.45 # dex
 SpectroscopicMstarError: 0.15 # dex
 
 
 RayTracingScheme: sum
-# The default ray-traced kappamap from Hilbert et al 2008 was made by 
+# The default ray-traced kappamap from Hilbert et al 2008 was made by
 # simply summing the convergences on each lens plane. If you want a more
 # complicated scheme for kappa_ext or mu_ext, you will need to change
 # this. This is the correct scheme for weak lensing, but may need some
 # modification if the system contains a strong lens
 
-# How does the quality of data vary with radius and magnitude, for the 
-# real line of sight? This will allow the creation of an accurate 
+# How does the quality of data vary with radius and magnitude, for the
+# real line of sight? This will allow the creation of an accurate
 # calibration dataset:
 PhotometricRadius: [1,2] # arcmin
 PhotometricDepth: [26,26] # must pair with PhotometricRadius
@@ -122,7 +122,7 @@ SpectroscopicDepth: [24,23] # must pair with SpectroscopicRadius
 # Calibrating
 # --------------
 
-# For a robust transformation between Pr(kappah|D) and Pr(kappa|D), we 
+# For a robust transformation between Pr(kappah|D) and Pr(kappa|D), we
 # found we needed to go through a compression step, to reduce the
 # influence of the poorly estimated high kappa halos. Pr(kappa|<kappah>)
 # (where <> denotes the median) seems to work well.

pangloss/io.py

@@ -14,22 +14,22 @@
         Useful general functions to streamline file input and output.
 
     COMMENTS
-            
+
     FUNCTIONS
         writePickle(contents,filename):
-        
+
         readPickle(filename): returns contents of pickle
-        
+
         readCatalog(filename,config): returns table, given column names
                                       in configuration config
-    
+
         rm(filename): silent file removal
-        
+
     BUGS
 
     AUTHORS
       This file is part of the Pangloss project, distributed under the
-      GPL v2, by Tom Collett (IoA) and  Phil Marshall (Oxford). 
+      GPL v2, by Tom Collett (IoA) and  Phil Marshall (Oxford).
       Please cite: Collett et al 2013, http://arxiv.org/abs/1303.6564
 
     HISTORY
@@ -54,6 +54,37 @@ def readPickle(filename):
 
 def readCatalog(filename,config):
 
+# PJM: we need to switch to astropy tables...
+# Here's how Richard McMahon uses them, admittedly when reading in FITS:
+
+"""
+here is an example; I like to write out the version number to help with debugging.
+
+import astropy
+print('astropy: ', astropy.version)
+from astropy.table import Table
+from astropy.io import fits
+
+infile_OM10="/home/rgm/soft/OM10/OM10/data/qso_mock.fits"
+print 'Read in with Astropy FITS table reader'
+table=Table.read(infile_OM10)
+table.pprint()
+print 'Numer of rows: ', len(table)
+print 'columns: ', table.columns
+
+print 'colnames: ', table.colnames
+print 'meta: ', table.meta
+
+# see http://astropy.readthedocs.org/en/latest/table/modify_table.html
+# to see how to add a column, e.g.
+# to insert before the first table column, do:
+
+table.add_column(aa, index=0)
+
+table.write('new.fits')
+
+"""
+
     table = atpy.Table(filename, type='ascii')
 
     try: table.rename_column(config.parameters['nRAName'],'nRA')
@@ -72,10 +103,10 @@ def readCatalog(filename,config):
     except: pass
     try: table.rename_column(config.parameters['ObsRedshiftName'],'z_obs')
     except: pass
-    try: 
+    try:
         mag = table[config.parameters['MagName']]
         table.add_column('mag',mag)
-    except: 
+    except:
         raise "Error in io.readCatalog: no mag column called "+config.parameters['MagName']
 
     return table
@@ -89,5 +120,5 @@ def rm(filename):
     except OSError:
         pass
     return
-    
+
 # ======================================================================