[Yt-dev] HaloProfiler overhaul

[Britton Smith]

Greetings,

I have just finished an extensive overhaul of the HaloProfiler that includes
a bunch of new features, as well as completely changes the running syntax.
Other than the addition of various new features, the main goals of this
overhaul were:
1) to make the tool more general (mostly by removing hard-coded filtering by
virial quantities), essentially allowing someone to profile a random list of
points that may or may not be actual halos
Easy filtering of halos by virial quantities remains an option, but is now
simply a specific instance of something more general and far more powerful:
a halo filtering device that allow the user to create their own filter
functions to comb through radial profile data and decide whether a halo
meets certain criteria.

2) to remove the dependence on an additional parameter file for the various
options.
The parameter file is now gone.  Most of the HaloProfiler parameters have
been turned into instantiation keyword args.  The keyword list is now
considerably longer, but the benefit is that the number of files needed to
run this thing has been reduced from 2 (running script and par file) to just
1 (running script).  There are a large number of keywords options that are
specific to either the profile or projection routines that are taken in at
instantiation and stored as attributes.  This was done to keep those
function calls simple.  I'm curious to know peoples' thoughts on whether
these keyword args should stay put or move to the individual function
calls.  Adding fields for profiling and projections have been moved to
functions addProfile and addProjection.

Here is a brief list of the new features that I can remember:
 - the halo list read routine can be easily customized to read in columned
ascii data of varying formats through the use of a dictionary (see attribute
self.halo_list_format)
 - ability to change the function call, args, and kwargs for the halo finder
Profiles:
 - filter halo list with user-written filter functions (see new file
HaloFilters.py for an example of a function to filter based on virial
quantities)
 - extract and output scalar quantities from halos using the filter
functions
 - pre-filter halos based on values in the initial halo list (skipping the
profiling altogether and saving a load of time)
Projections:
 - choose the axes to be projected (instead of hard-coded to all three)
 - easily select the list of halos to be projected (the total list, filtered
list, a new file, or an actual list)

Before I commit all this, I'd like a little feedback, mostly on the
migration of the par file parameters to keyword args.  I put three files in
the pastebin for people to download.  I chose not to submit a diff since the
changes were so sweeping.
The new HaloProfiler.py: http://paste.enzotools.org/show/178/
HaloFilters.py (should go in yt/extensions with HaloProfiler.py)
http://paste.enzotools.org/show/179/
runHaloProfiler.py (an example script to run the new HaloProfiler)
http://paste.enzotools.org/show/180/

I will try my best to write up full documentation for this as soon as
possible, perhaps even today.

Please let me know what you think.

Britton
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