[yt-users] halo finding on gadget snapshots

Hilary Egan hilaryye at gmail.com
Tue Jun 24 11:05:16 PDT 2014


Hi Desika,

This is almost certainly a problem with the old halo finders (anything that
you import from analysis_modules.halo_finding) not being completely
compatible with yt-3.0 at the moment. The best way to access their
functionality now is to go through the new HaloCatalog api. I have only
gone through the old halo catalog methods to fix them enough to work with
the new HaloCatalog api, and didn't test them in general with the idea that
they will be phased out as stand alone tools.

Here is an example script for finding the halos using a halo catalog:
http://paste.yt-project.org/show/4826/

If you'd like more information about how the halo catalog works, its mostly
documented here:
http://yt-project.org/docs/dev-3.0/analyzing/analysis_modules/halo_catalogs.html

Hopefully that works for you!
-Hilary


On Tue, Jun 24, 2014 at 11:39 AM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

>
>
>
> On Tue, Jun 24, 2014 at 8:57 AM, Desika Narayanan <dnarayan at haverford.edu>
> wrote:
>
>> Hi All,
>>
>> I'm having some issues with really basic halo finding on gadget snapshots
>> in the bleeding edge version.  What I want to do is ID halos in a volume,
>> save a list of the halos, and plot a projection plot with circles over the
>> halos (all of which I think should be possible).
>>
>> The principle script is:  http://paste.yt-project.org/show/4824/
>>
>> The error I get when trying to save the halos is:
>>
>> http://paste.yt-project.org/show/4822/
>>
>
> I don't think I can speak to this beyond that this error indicates that
> something is going wrong with field detection.  It might be helpful to
> rerun the script with yt's log level threshold decreased to 10, which will
> show debug messages.  See this page:
> http://yt-project.org/docs/dev-3.0/reference/configuration.html
>
> Running with debug logs will allow us to see if any fields are raising
> exceptions during field detection.
>
>
>>
>>
>> and in trying to annotate the halos on the projection plot is:
>>
>> http://paste.yt-project.org/show/4823/
>>
>> Am I either doing something wrong in my commands?  (hopefully as simple
>> as that...) or are these not supported yet in the bleeding edge yt?
>>
>
> This looks like a straight up typo in the HaloCatalogCallback.  You could
> try commenting out the line it's failing on.
>
> It looks like Hillary Egan was the last one to touch this in May.
>
>
>>
>> thanks
>> desika
>>
>> ps. On another (related) note, is it possible to manually draw circles on
>> a projection plot?  Or arrows, or tick marks, or anything that I could use
>> to visually show off individual halos?
>>
>
>>
>
> You can access the underlying matplotlib primitives like so:
>
> slc = SlicePlot(pf, 0, 'density')
> plot = slc.plots['density']
> fig = plot.figure  # matplotlib figure object
> ax = plot.axes   # matplotlib axes object
> cax = plot.cax   # matplotlib colorbar axes object
> cb = plot.cb      # matplotlib colorbar object
> image = plot.image  # matplotlib AxesImage object
>
> Using these objects you should be able to customize the plot however you'd
> like.
>
> -Nathan
>
>
>
>
>>
>>
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20140624/2d7fcb17/attachment.html>


More information about the yt-users mailing list