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notes.md

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TODO:

(Some of these are already done???)

  • Allow "ancillary" derived parameters/calculations in addition to the MCMC model params (e.g., the ML amplitudes in a marginalized gaussian model -- could store alongside or even as part of MCMC.samples)

  • problem when a window is always 0 (or ~0) in a bin for a single experiment? seems to want very large bandpowers? [[iS THIS THE low-ell PROBLEM???]]

  • translate/wrap wmap3 likelihood

  • polarization in ClData/ and binnedCl/ modules

  • allow linear combinations of params

  • which methods should take the linear combination and which the real parameters?

    • how about package/unpackage?

  • For sequences, (strings, lists, tuples), use the fact that empty sequences are false, so if not seq or if seq is preferable to if len(seq) or if not len(seq). [ but doesn't work for arrays ]

  • just make window fns win[nbin, ncl, lmax]

  • change mixedCase names to lower_with_underscores as per pep?

  • get rid of map in favor of list comprehension? (a la python regret)

  • get rid of static methods in favor of module-level functions?

  • may need to modify __init__ = blabla to def __init__(self, stuff) = self.blabla(stuff)

  • rename Likelihood -> beamLikelihood?

  • data.get_quadratic_form method which does A^T N^-1 B or A^T N^-1 A without full inverse if uncorrelated? (Otherwise likelihood needs to know which is appropriate)

  • allow MCMC to take a sequence of likelihoods?

  • or allow likelihood to take a sequence of data?

    • need to wrap lnLike, lnNorm in something like [for dat in self.data]
    • (latter enforces the requirement that they all have the same model, which is crucial, but may be harder to deal with, and requires that every likelihood class do this. or could do with a lnLike1, lnNorm1 which are then wrapped only in the superclass?

  • reorganize package/modules

DONE:

  • allow priors from the data? (e.g., reasonable limits on parameter values?)

    • or could subclass the model for specific cases?

  • need to make Likelihood take an instance of the model class?

    • can't do that -- need to make the xy ranges into static class variables.

    • need to link the data, model, likelihood classes more strongly?

    • [done with classmethod]

  • how to determine if an object is a vector or an array? len(asarray(obj))?

    • or:

            try: l=len(obj)
      except: TypeError: l=1

    • [use asarray(object).size() -- is there a better way?]

  • generic gaussian data (d, sigma/sig2/noise_matrix) subclassed for extra info (x, y for beams, bins for C_l , etc)

svn2git notes

Created using svn2git (installed with sudo gem install svn2git):

svn2git svn+ssh://mekon.ph.imperial.ac.uk/Library/Subversion/Repository/MCMC --no-minimize-url --exclude TOIbeams.pickle --authors ../MCMC/authors-transform.txt
  • Need --no-minimize since this repo has several projects at the top level.
  • Need --exclude TOIbeams.pickle since that file is too big for github.
  • Need --authors ../MCMC/authors-transform.txt to get full git-style author names
    • authors-transform.txt has been added to root of the project.

Push to github at the end (should I use --all -u below?):

git remote add origin https://github.com/defjaf/MCMC.git
git push -u origin master
git push --all 
git push --tags

(Also tried git push --mirror https://github.com/defjaf/MCMC.git but this seems to be the official way...)

Note also that git svn show-ignore seems to fail, alas.

I previously tried to follow these instructions, but the branch structure seems weird. Could be due to the same structure that required --no-minimize above.

git svn clone svn+ssh://mekon.ph.imperial.ac.uk/Library/Subversion/Repository/MCMC --no-metadata -A authors-transform.txt --stdlayout ~/temp

with the following additions:

  • remove large file: git filter-branch --force --index-filter 'git rm --cached --ignore-unmatch ./TOIbeams.pickle' --prune-empty --tag-name-filter cat -- --all
  • See https://help.github.com/articles/removing-sensitive-data-from-a-repository/
  • For some reason, the master branch is called origin/trunk, so needed git branch -m origin/trunk master
  • Push to github at the end: git push --mirror https://github.com/defjaf/MCMC.git