[yt-users] Profile plot of a 2d projection FRB object

Tue Jun 2 14:28:02 PDT 2015

On Tue, Jun 2, 2015 at 2:25 PM, John Zuhone <jzuhone at gmail.com> wrote:

> I recall we’ve batted around the idea of using slice and projection
> objects directly as datasets—I suspect there probably is some way to load
> them as in-memory AMR datasets, but I’m not sure how easy that is. Anyone
> else care to comment?
>

Probably doable as a 2D dataset, loading the quadtree in-memory. Would take
some work.

>
> In general, when I make FRBs for anything other than imaging, I make sure
> that the resolution matches the finest cell size, and that it matches the
> layout of the underlying AMR grids (e.g., no partial overlaps between FRB
> resolution elements and AMR cells). Something tells me we ought to have a
> short-hand of some kind for creating an FRB in this way.
>

This is basically a reduced dimensionality covering grid.  I don't think we
have such a thing yet but I think it would be a worthwhile addition, I
could see it being useful to not need to think about aligning a FRB with
cell boundaries.

>
> On Jun 2, 2015, at 5:14 PM, Cameron Hummels <chummels at gmail.com> wrote:
>
> My script basically did this:
>
> 1) Make a projection (of a galaxy)
> 2) Identify a central point (ie the center of the galaxy i cared about)
> 3) Measure the projected distance from the central point to each pixel in
> the projection.
> 4) Bin these projected pixels into radial bins
> 5) Take the median value of different projected fields for each radial bin
> (e.g. column density, density-weighted temperature, etc.)
> 6) Plot up each of these fields as they vary for projected radius
>
> If I were to do it again, I'd probably rely on the new FRB interface as it
> seems cleaner.  And, it looks like it would better address what you're
> trying to do right now.
>
> Cameron
>
> On Tue, Jun 2, 2015 at 1:57 PM, David Collins <dcollins4096 at gmail.com>
> wrote:
>
>>
>>
>>
>>> Just to clarify, you want to make a phase plot of a projected object?
>>> So you want something like how column density varies with density-weighted
>>> temperature in a 2D plot?  Or something like this?  I only ever did a
>>> radial
>>>
>>
>> That's exactly right.  I'll give the FRB a shot first.  Since the
>> ultimate goal is comparison to the sky, FRB is probably just fine.
>>
>> How different was your code?
>>
>>
>>
>>> profile of projected fields (column density, or metal column density,
>>> etc.), but I could try to help you put something together.  The FRB idea
>>> suggested by John might be the easiest approach depending on what you want.
>>>
>>> On Tue, Jun 2, 2015 at 8:21 AM, David Collins <dcollins4096 at gmail.com>
>>> wrote:
>>>
>>>> Hi, Everybody--
>>>>
>>>> This was discussed a while back, but I wanted to further clarify, and
>>>> possibly mooch a script or two off y'all.
>>>>
>>>> I'd like a PhasePlot from a projected region.  Earlier FRBs were
>>>> discussed; has anyone successfully done the same on a YTQuadTreeProj?  I'd
>>>> like to retain all the high resolution data, if possible.
>>>>
>>>> Cameron, back in Jan you mentioned you had a script.  Did you manage to
>>>> track it down, and/or would you be willing to send it my way?
>>>>
>>>> Thanks!
>>>> d.
>>>>
>>>>
>>>>
>>>> On Fri, Jan 16, 2015 at 10:31 PM, John ZuHone <jzuhone at gmail.com>
>>>> wrote:
>>>>
>>>>> This is a bit of a long way around, but you could write the FRB to a
>>>>> FITS file and read it in as a dataset. You would get the coordinate system,
>>>>> units, etc., and the whole YT machinery.
>>>>>
>>>>> Use the export_fits method:
>>>>>
>>>>> my_frb.export_fits("myfile.fits", fields)
>>>>>
>>>>> Then:
>>>>>
>>>>> ds = yt.load("my_file.fits")
>>>>>
>>>>> I'm not at a computer so I don't remember the exact signature, but it
>>>>> should be in the code and you can check using help(my_frb.export_fits). If
>>>>> you're interested I can write back with more info later.
>>>>>
>>>>> The other advantage of this is that you can store the data to disk.
>>>>> You'll have to install the AstroPy package.
>>>>>
>>>>> Kavli Center for Astrophysics and Space Research
>>>>> Massachusetts Institute of Technology
>>>>> 77 Massachusetts Ave., 37-582G
>>>>> Cambridge, MA 02139
>>>>> (w) 617-253-2354
>>>>> (m) 781-708-5004
>>>>> jzuhone at space.mit.edu
>>>>> jzuhone at gmail.com
>>>>> http://www.jzuhone.com
>>>>>
>>>>> On Jan 16, 2015, at 8:34 PM, Ben Thompson <bthompson2090 at gmail.com>
>>>>> wrote:
>>>>>
>>>>> Hey guys.
>>>>>
>>>>> I have a solution together for myself involving the new
>>>>> particle_position_relative_[xyz] fields and multiple instances of
>>>>> np.histogram and np.linspace which seems to do the trick.
>>>>>
>>>>> Although I would not complain if a piece of code that would be more
>>>>> native to the inner workings of YT existed that made use of the FRB data
>>>>> objects :). So that would be very nice Cameron. Don't feel the need to rush
>>>>> with it though, as I made a numpy solution for myself. But I would be
>>>>> interested to see that code.
>>>>>
>>>>> Ben
>>>>> On 17 Jan 2015 01:27, "Britton Smith" <brittonsmith at gmail.com> wrote:
>>>>>
>>>>>> Hi Ben,
>>>>>>
>>>>>> I seem to recall people on this list doing similar things in the past
>>>>>> with their own external code.  Does anyone still have their 2D radial
>>>>>> profile code around anymore?
>>>>>>
>>>>>> Would it perhaps work to create a uniform grid dataset from an FRB
>>>>>> array?
>>>>>>
>>>>>> Britton
>>>>>>
>>>>>> On Tue, Jan 13, 2015 at 12:49 PM, Ben Thompson <
>>>>>> bthompson2090 at gmail.com> wrote:
>>>>>>
>>>>>>> Hello everyone.
>>>>>>>
>>>>>>> I was wondering if anyone has had experience with producing a
>>>>>>> profile plot from a 2d projection object (FRB object).
>>>>>>>
>>>>>>> Essentially, what I am trying to do is plot the stellar surface
>>>>>>> density of a galaxy as a function of radius.
>>>>>>>
>>>>>>> This is achieved by doing the following from a disk YT object called
>>>>>>> cylinder (in which the origional simulation object is called shot)
>>>>>>>
>>>>>>> center = cylinder.get_field_parameter("center")
>>>>>>> normal = cylinder.get_field_parameter("normal")
>>>>>>> image_width = (100,"kpc")
>>>>>>> three_image_width = YTArray((image_width[0], image_width[0],
>>>>>>> image_width[0]),image_width[1])
>>>>>>> left = center - image_width
>>>>>>> right = center + image_width
>>>>>>> region = shot.region(center, left, right)
>>>>>>>
>>>>>>> proj =
>>>>>>> yt.ProjectionPlot(cylinder.ds,"z",[("deposit","stars_density")],center=center,width=image_width,data_source=region,axes_unit="kpc")
>>>>>>>
>>>>>>> the error arrises here
>>>>>>>
>>>>>>> prof =
>>>>>>> yt.create_profile(proj,bin_fields="cylindrical_r",fields=[("deposit","stars_density")],n_bins=128,weight_field=None
>>>>>>> )
>>>>>>>
>>>>>>> where I get the error
>>>>>>>
>>>>>>>
>>>>>>> /gpfs/home/........./profiles.pyc in create_profile(data_source,
>>>>>>> bin_fields, fields, n_bins, extrema, logs, units, weight_field,
>>>>>>> accumulation, fractional)
>>>>>>>    1304     else:
>>>>>>>    1305         raise NotImplementedError
>>>>>>> -> 1306     bin_fields = data_source._determine_fields(bin_fields)
>>>>>>>    1307     fields = data_source._determine_fields(fields)
>>>>>>>    1308     if units is not None:
>>>>>>>
>>>>>>> AttributeError: 'FixedResolutionBuffer' object has no attribute
>>>>>>> '_determine_fields'
>>>>>>>
>>>>>>> Any ideas how to get around this error?
>>>>>>>
>>>>>>>
>>>>>>> Also some other things to add as a postscript. Since how the
>>>>>>> projection works, if I provide weights=None as a keyword argument within
>>>>>>> the ProjectionPlot object, I get a surface density (g/cm^2). But also a
>>>>>>> "cylindrical_r" in cm^2 as well. I *think* the way to get around this is to
>>>>>>> do another projection where weights="ones", get the radius values out of
>>>>>>> that profile.. and then in matplotlib, useing the surface density array
>>>>>>> from the former profile, and the radius bin array from the latter...
>>>>>>> Produce a plot of the surface density as a function of radius from those
>>>>>>> two arrays (I might check by hand afterwards to see if this does the
>>>>>>> trick). This seems kinda convoluted so I am wondering if there is an easier
>>>>>>> way than this.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>>
>>>>>>>
>>>>>>
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>>>>
>>>>
>>>> --
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>>>
>>>
>>> --
>>> Cameron Hummels
>>> Postdoctoral Researcher
>>> Steward Observatory
>>> University of Arizona
>>> http://chummels.org
>>>
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>
>
> --
> Cameron Hummels
> Postdoctoral Researcher
> Steward Observatory
> University of Arizona
> http://chummels.org
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