[Yt-dev] HaloProfiler overhaul

[Matthew Turk]

Hi Britton,

This is awesome!  I just have a couple comments.

* You can't include {} in a function dec -- it is instantiated at
parse-time, so it persists and any modifications made are kept.
Usually what's done is to default to None, and do an if something is
None: something = {}
* lists in function declaration must be copied with [:] ; in fact, I'd
say avoid DeepCopy unless you know for a fact it will be something
other than strings (which I don't think is the case for these objects)
* addProfile and addProjection should be add_profile and
add_projection; I'd prefer *all* code follow PEP-8 (
http://www.python.org/dev/peps/pep-0008/ ) but I'd definitely like to
keep a consistent lowercase-underscore mechanism for methods on
objects.  (I also think we should try to follow the function
declaration guidelines with respect to spaces and commas.)
* na.array(range(something)) can just be na.arange(something)
* if type(something) is list should be isinstance(something,
types.ListType) (I think)
* I'm inclined to think we don't want a second verbosity check, and
instead put stuff into mylog.debug, but I'll leave that up to you...

All in all, this looks like a great addition, and a great set of
extensions.  Thanks so much for doing all this!

-Matt

On Mon, Aug 24, 2009 at 12:51 PM, Britton Smith<brittonsmith at gmail.com> wrote:
> 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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