diff --git a/doc/litter/KarpenkaEtal2013.pdf b/doc/litter/KarpenkaEtal2013.pdf new file mode 100644 index 0000000..b720d72 Binary files /dev/null and b/doc/litter/KarpenkaEtal2013.pdf differ diff --git a/doc/references.bib b/doc/references.bib index 8d60812..df90b11 100644 --- a/doc/references.bib +++ b/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."} +} diff --git a/example/example.config b/example/example.config index 6b380d9..210a94c 100644 --- a/example/example.config +++ b/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|) # (where <> denotes the median) seems to work well. diff --git a/pangloss/io.py b/pangloss/io.py index 44c57ef..945b942 100644 --- a/pangloss/io.py +++ b/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 - + # ======================================================================