[yt-users] updated examples for 3.0 volume rendering
Michael Zingale
michael.zingale at stonybrook.edu
Fri Mar 28 16:59:19 PDT 2014
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?
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 (including some out-of-date information that we need to update) are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
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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
>>>>
>>>
>>>
>>>
>>> --
>>> 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
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