[yt-users] Radial velocity Projections

John Regan johnanthonyregan at gmail.com
Thu Dec 19 00:07:40 PST 2013


Hi Matt,

I think I rooted out the issue. It seems the "RadialVelocity" field is set
to be a log field (or rather not set to be not log). This caused it to fall
over. I updated the field in universal_fields.py and it all seems to work
now.

Thanks for pointing me in the right direction with the grid updates.
Without setting the center for each grid, what does it default to? Center
of the box?

Cheers,
John


On Tue, Dec 17, 2013 at 2:25 PM, John Regan <johnanthonyregan at gmail.com>wrote:

> Hi Matt,
>
> Thanks for having a look.  It seemed to sample the field OK but then fell
> over.
>
> Traceback (most recent call last):
>   File "OffAxisProjection_RadialVelocity_TimeSeries.py", line 46, in
> <module>
>     depth=depth, weight_field="Density")
>   File
> "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py",
> line 1149, in __init__
>     self.set_axes_unit(axes_unit)
>   File
> "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py",
> line 56, in newfunc
>     args[0]._setup_plots()
>   File
> "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py",
> line 665, in _setup_plots
>     cax)
>   File
> "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py",
> line 1416, in __init__
>     self._init_image(data, cbname, cmap, extent, aspect)
>   File
> "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/visualization/base_plot_types.py",
> line 109, in _init_image
>     self.cb = self.figure.colorbar(self.image, self.cax)
>   File
> "/homeappl/home/regan/appl_taito/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/figure.py",
> line 1451, in colorbar
>     cb = cbar.colorbar_factory(cax, mappable, **kw)
>   File
> "/homeappl/home/regan/appl_taito/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/colorbar.py",
> line 1274, in colorbar_factory
>     cb = Colorbar(cax, mappable, **kwargs)
>   File
> "/homeappl/home/regan/appl_taito/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/colorbar.py",
> line 877, in __init__
>     ColorbarBase.__init__(self, ax, **kw)
>   File
> "/homeappl/home/regan/appl_taito/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/colorbar.py",
> line 317, in __init__
>     self.draw_all()
>   File
> "/homeappl/home/regan/appl_taito/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/colorbar.py",
> line 338, in draw_all
>     self._process_values()
>   File
> "/homeappl/home/regan/appl_taito/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/colorbar.py",
> line 652, in _process_values
>     b = self.norm.inverse(self._uniform_y(self.cmap.N + 1))
>   File
> "/homeappl/home/regan/appl_taito/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/colors.py",
> line 1003, in inverse
>     return vmin * ma.power((vmax / vmin), val)
>   File
> "/homeappl/home/regan/appl_taito/YT/yt-x86_64/lib/python2.7/site-packages/numpy/ma/core.py",
> line 3648, in __mul__
>     return multiply(self, other)
>   File
> "/homeappl/home/regan/appl_taito/YT/yt-x86_64/lib/python2.7/site-packages/numpy/ma/core.py",
> line 941, in __call__
>     if m:
> ValueError: The truth value of an array with more than one element is
> ambiguous. Use a.any() or a.all()
>
>
> The snippet of code that I run is
>
>  for grid in pf.h.grids:
>             grid.set_field_parameter("center", c)
>             grid.set_field_parameter("normal", L)
>         proj = OffAxisProjectionPlot(pf, L, "RadialVelocity",
> center='max', width=(width, 'pc'),
>                                      depth=depth, weight_field="Density")
>
> Cheers,
> John
>
>
>
> On Mon, Dec 16, 2013 at 5:30 PM, Matthew Turk <matthewturk at gmail.com>wrote:
>
>> Hi John,
>>
>> Yup, you can.  I'm looking at the code right now and I think the issue
>> is going to be tricky to maneuver through the code base in a reliable
>> way the field parameters.  Here's what I'd suggest doing --
>>
>> for grid in pf.h.grids:
>>     grid.set_field_parameter("center", c)
>>
>> just before you call OffAxisProjection.  This is something that the
>> grid machinery is a bit annoying about the way that things work in
>> 2.x, but we're fixing in 3.0.  You'll also have to set the "normal"
>> field parameter.
>>
>> Let me know if that works,
>>
>> -Matt
>>
>>
>> On Mon, Dec 16, 2013 at 9:55 AM, John Regan <johnanthonyregan at gmail.com>
>> wrote:
>> > Hi Matt,
>> >
>> > Yes it is the OAP I am interested in. I had originally weighted the
>> > projection using the density field.
>> >
>> > The projected velocity may look funny and it would be interesting to
>> try to
>> > compare that to the planar. Could I also pass cyl_RadialVelocity to the
>> OAP
>> > API?
>> >
>> > Cheers,
>> > John
>> >
>> > On 16 Dec 2013 16:09, "Matthew Turk" <matthewturk at gmail.com> wrote:
>> >>
>> >> Hi John,
>> >>
>> >> Sorry for the delay in replying.
>> >>
>> >> On Fri, Dec 13, 2013 at 8:59 AM, John Regan <
>> johnanthonyregan at gmail.com>
>> >> wrote:
>> >> > Hi All,
>> >> >
>> >> > I was trying to make an OffAxis radial projection. Naively using
>> >> >
>> >> >  proj = OffAxisProjectionPlot(pf, L, "RadialVelocityKMS",
>> center='max',
>> >> > width=(width, 'pc'),
>> >> >                                      depth=depth)
>> >> >
>> >> > fails with a message of type
>> >> >
>> >> > yt.data_objects.field_info_container.NeedsParameter: (['center'])
>> >> >
>> >> >
>> >> > The RadialVelocity probably isn't the field to use here and requires
>> >> > some
>> >> > manipulation to be a quantity suitable for plotting.
>> >> >
>> >> > Any suggestions on the best way forward would be much appreciated.
>> >> >
>> >>
>> >> So, a few questions.  Do you want to show the way that the radial
>> >> velocity is distributed, with respect to an image plane that isn't
>> >> axis aligned?  If you so, you might have more luck using the
>> >> OffAxisSlicePlot, which will take a slice through the domain.  The OAP
>> >> plot will integrate along the line of sight; you will probably want to
>> >> take an average if this is what you want, by supplying the weight
>> >> parameter here, as otherwise it'll just sum up the RV values at all
>> >> points.  I think the issue with it not having the parameter center is
>> >> fixable, but we should probably make sure that's what you're looking
>> >> for first.  It's also going to be doing the full 3D radial velocity,
>> >> not the planar velocity, so if your velocity is roughly spherical it
>> >> might have odd morphology in the resultant plot.
>> >>
>> >> If a slice will do what you're looking for, I'd recommend the
>> >> OffAxisSlicePlot -- if you indeed do want a radial average, then I'll
>> >> take a look at passing the parameter in.  (This will also help by
>> >> enabling you to pass in the bulk velocity.)  And if you want to find
>> >> the planar RV, you'll have to use a field like cyl_RadialVelocity.
>> >>
>> >> -Matt
>> >>
>> >> > Cheers,
>> >> > John
>> >> >
>> >> > _______________________________________________
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