[yt-users] updated examples for 3.0 volume rendering

Fri Mar 28 16:52:15 PDT 2014

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()

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 (including some out-of-date information that we need to update) are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
>>>>
>>>> _______________________________________________
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>>>>
>>>>
>>>
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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
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