[yt-users] halo finding on gadget snapshots

[Desika Narayanan]

Hi Hilary and Nathan,

Thanks a lot for the info on the new 3.0 halo modules.

I tried running your script, Hilary, and got the following errors:
http://paste.yt-project.org/show/4831/

Any thoughts/help would be greatly appreciated!  I can re-run with
increased log level like Nathan mentioned if that's useful.

thanks,
desika





On Tue, Jun 24, 2014 at 2:05 PM, Hilary Egan <hilaryye at gmail.com> wrote:

> 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
>>
>>
>>
>>
>>>
>>>
>>>
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>>>
>>
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