[yt-users] updated examples for 3.0 volume rendering

Matthew Turk matthewturk at gmail.com
Fri Mar 28 17:00:13 PDT 2014 

On Fri, Mar 28, 2014 at 7:59 PM, Michael Zingale
<michael.zingale at stonybrook.edu> wrote:
> Thanks.  I see in there
>
> def _temperature(field,data):
>     mu = data.get_field_parameter("mu")
>     return ( (data.pf.gamma-1.0) * mu * mh *
>              data["thermal_energy"] / (kboltz * data["density"]) )
>
> is it the case that yt will assume a gamma-law gas?

Only if temperature isn't defined -- the field system is set up now to
be able to dynamically swap these in and out, so we definitely should.

-Matt

>
>
> On Fri, Mar 28, 2014 at 7:53 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>>
>>
>>
>> On Fri, Mar 28, 2014 at 4:52 PM, Michael Zingale
>> <michael.zingale at stonybrook.edu> wrote:
>>>
>>> ok, final update -- I am able to do a basic volume rendering, but I need
>>> to set
>>>
>>> no_ghost=True
>>>
>>> if this is False, then there is a units error in sanitize_units_add.
>>> Perhaps when the ghost-cells are added, that is done as a normal ndarray and
>>> not a YTarray?
>>>
>>> Similar issues arise if I try to draw_coordinate_vectors()
>>>
>>>
>>
>> Can you report these issues on our bug tracker?  A test script that fails
>> for you would be especially helpful.
>>
>>>
>>>
>>> On Fri, Mar 28, 2014 at 7:26 PM, Michael Zingale
>>> <michael.zingale at stonybrook.edu> wrote:
>>>>
>>>> I made a bit more progress here, but I get an error in
>>>>
>>>> amr_kdtree/amr_kdtree.py
>>>>
>>>> in line 257, it does
>>>>
>>>>         dds = grid.dds.ndarray_view()
>>>>
>>>> but grid.dds is already an ndarray, so this should be
>>>>
>>>>         dds = grid.dds
>>>>
>>>> still not through the cam.snapshot() part of my script, but I got
>>>> everything up to there working.
>>>>
>>>>
>>>>
>>>> On Fri, Mar 28, 2014 at 4:23 PM, Michael Zingale
>>>> <michael.zingale at stonybrook.edu> wrote:
>>>>>
>>>>> On Fri, Mar 28, 2014 at 3:37 PM, Nathan Goldbaum
>>>>> <nathan12343 at gmail.com> wrote:
>>>>>>
>>>>>> Hi Mike,
>>>>>>
>>>>>> You've hit a bunch of big changes we've been making recently.  If you
>>>>>> want to get back to the version of yt before we merged these big changes in,
>>>>>> you'll need to update to the 'development' bookmark.  Right now you're on
>>>>>> the 'experimental' bookmark.
>>>>>>
>>>>>
>>>>> Oh... lucky me.
>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri, Mar 28, 2014 at 12:10 PM, Michael Zingale
>>>>>> <michael.zingale at stonybrook.edu> wrote:
>>>>>>>
>>>>>>> Is there any updated examples for using the yt 3.0 volume rendering?
>>>>>>>
>>>>>>> For instance, looking at this:
>>>>>>>
>>>>>>>
>>>>>>> http://yt-project.org/docs/dev/cookbook/simple_plots.html#simple-volume-rendering
>>>>>>
>>>>>>
>>>>>> We haven't finished updating the docs yet.  In-development docs
>>>>>> (including some out-of-date information that we need to update) are
>>>>>> available here: http://yt-project.org/docs/dev-3.0/
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> The field name is no longer simply "Density", but now, for my data, I
>>>>>>> need to use a tuple like:
>>>>>>>
>>>>>>> field =  ('boxlib', 'magvel')
>>>>>>
>>>>>>
>>>>>> We no longer have a 'Density' field, since this introduces ambiguities
>>>>>> for Enzo data and to create a consistent naming scheme for fields.  The new
>>>>>> name is 'density'. See:
>>>>>> http://ytep.readthedocs.org/en/latest/YTEPs/YTEP-0003.html
>>>>>
>>>>>
>>>>> thanks for the list.  Maestro has it's own fun with variables (two
>>>>> definitions for temperature, several pressures, etc., magvel above is not
>>>>> simply the vector magnitude of x_vel, y_vel, z_vel, etc), so I'll pay
>>>>> attention to these definitions.
>>>>>
>>>>>
>>>>>
>>>>>>>
>>>>>>>
>>>>>>> And then when I look at the extrema, I no longer take the [0] index,
>>>>>>> as that just gives the min, but instead if I look at:
>>>>>>>
>>>>>>
>>>>>> That true, we've simplified the derived quantity API somewhat.  This
>>>>>> fixes a long-standing issue at the cost of breaking some old user scripts.
>>>>>> As you can see we are planning to break backward compatibility somewhat for
>>>>>> the final yt 3.0 release.
>>>>>>
>>>>>>>
>>>>>>> dd.quantities["Extrema"](field)
>>>>>>>
>>>>>>> I get:
>>>>>>>
>>>>>>> (124.858613718 dimensionless, 18061918.0546 dimensionless)
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> (not sure why they are dimensionless, but that's a different
>>>>>>> problem).
>>>>>>>
>>>>>>
>>>>>> If you do
>>>>>>
>>>>>> type(dd.quantities["Extrema"](field)[0])
>>>>>>
>>>>>> you will see that it is a new type, YTQuantity, which is a new class
>>>>>> we've defined to handle units for scalar data.  YTArray does the same thing
>>>>>> for array data.  More detail here:
>>>>>> http://yt-project.org/docs/dev-3.0/analyzing/units/index.html
>>>>>>
>>>>>> These are 'dimensionless' because the boxlib frontend does not know
>>>>>> what the appropriate units are for the 'magvel' field.  It may be the case
>>>>>> that we could modify the frontend to detect the units
>>>>>>
>>>>>>>
>>>>>>> Finally, if I try to make a transfer function, like:
>>>>>>>
>>>>>>> tf = ColorTransferFunction((mi, ma))
>>>>>>>
>>>>>>> I get:
>>>>>>>
>>>>>>> NameError: name 'ColorTransferFunction' is not defined
>>>>>>
>>>>>>
>>>>>> I think this was an oversight on Matt's part.  Thanks for the report!
>>>>>> For now you should be able to import ColorTransferFunction from
>>>>>> yt.visualization.volume_rendering.api, but this should be fixed soon.
>>>>>>
>>>>>> The reason this happened is that we've changed the way imports work in
>>>>>> the top-level yt namespace in the interest of yt behaving more like a
>>>>>> 'normal' scientific python package.  More detail is available here:
>>>>>>
>>>>>> http://ytep.readthedocs.org/en/latest/YTEPs/YTEP-0019.html
>>>>>>
>>>>>> as well as in the following pull request:
>>>>>>
>>>>>> https://bitbucket.org/yt_analysis/yt/pull-request/729/ytep-0019/diff
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> I just synced up with the development version today.
>>>>>>>
>>>>>>> Mike
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> We're working hard to update the docs and get the code into shape to
>>>>>> release.  If you're ok with dealing with not having fully up-to-date docs,
>>>>>> we'd really appreciate you trying out the changes to the code, letting us
>>>>>> know what you think, and reporting any bugs you find.
>>>>>>
>>>>>
>>>>> yeah, I'm happy to keep playing with this version if it helps.  The
>>>>> reason I updated today is because Matt told me that he had incorporated the
>>>>> Maestro field info that I sent him.
>>>>>
>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Michael Zingale
>>>>>>> Associate Professor
>>>>>>>
>>>>>>> Dept. of Physics & Astronomy * Stony Brook University * Stony Brook,
>>>>>>> NY 11794-3800
>>>>>>> phone:  631-632-8225
>>>>>>> e-mail: Michael.Zingale at stonybrook.edu
>>>>>>> web: http://www.astro.sunysb.edu/mzingale
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Michael Zingale
>>>>> Associate Professor
>>>>>
>>>>> Dept. of Physics & Astronomy * Stony Brook University * Stony Brook, NY
>>>>> 11794-3800
>>>>> phone:  631-632-8225
>>>>> e-mail: Michael.Zingale at stonybrook.edu
>>>>> web: http://www.astro.sunysb.edu/mzingale
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Michael Zingale
>>>> Associate Professor
>>>>
>>>> Dept. of Physics & Astronomy * Stony Brook University * Stony Brook, NY
>>>> 11794-3800
>>>> phone:  631-632-8225
>>>> e-mail: Michael.Zingale at stonybrook.edu
>>>> web: http://www.astro.sunysb.edu/mzingale
>>>
>>>
>>>
>>>
>>> --
>>> Michael Zingale
>>> Associate Professor
>>>
>>> Dept. of Physics & Astronomy * Stony Brook University * Stony Brook, NY
>>> 11794-3800
>>> phone:  631-632-8225
>>> e-mail: Michael.Zingale at stonybrook.edu
>>> web: http://www.astro.sunysb.edu/mzingale
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>
>>
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>>
>
>
>
> --
> Michael Zingale
> Associate Professor
>
> Dept. of Physics & Astronomy * Stony Brook University * Stony Brook, NY
> 11794-3800
> phone:  631-632-8225
> e-mail: Michael.Zingale at stonybrook.edu
> web: http://www.astro.sunysb.edu/mzingale
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>

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