[yt-users] updated examples for 3.0 volume rendering

Nathan Goldbaum nathan12343 at gmail.com
Fri Mar 28 16:53:45 PDT 2014


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 (including some out-of-date information that we need to update) are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