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- 11 participants
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Hi all,
> If you grep the source for KDTree, you should find a couple examples of its
> use. It may be a bit slower than the fortran kdtree, but it is at least
> readily available.
(Chiming in from the great beyond)
Britton makes a good suggestion, but I think that people should be
aware of two things:
- cKDTree will be much faster than KDTree. The latter is pure-python
- Looking at the source below, it looks like I never added periodicity
to KDTree operations
https://bitbucket.org/yt_analysis/yt/src/tip/yt/utilities/spatial/?at=yt
It wouldn't be difficult to add periodicity to KDTree, but I just didn't do it.
--
Stephen Skory
s(a)skory.us
http://stephenskory.com/
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Hi Suoqing,
Thanks, that worked.
Sandy
On Tue, Mar 24, 2015 at 4:10 PM, <yt-users-request(a)lists.spacepope.org>
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> Today's Topics:
>
> 1. Re: Line-of-sight velocity dispersion? (Suoqing JI)
> 2. Periodic enzo volume? (Kalina Borkiewicz)
> 3. Re: Particle Size in Projection Plots (Yuan Li)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 24 Mar 2015 12:30:32 -0700
> From: Suoqing JI <suoqing(a)physics.ucsb.edu>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] Line-of-sight velocity dispersion?
> Message-ID: <67698C33-B4FE-4E93-B9FD-01ABB2D755CC(a)physics.ucsb.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Sandy,
>
> The easiest way occurring to me is, since the standard deviation can be
> expressed as:
>
> sqrt( E(X^2) - E(X)^2 )
>
> so you could defined the ?z-velocity squared? as a new field, and
> calculate its average for each column (that is E(X^2) ). Then you have both
> E(X)^2 and E(X^2), thus the standard deviation can be computed.
>
> Best wishes,
> --
> Suoqing JI
> Ph.D Student
> Department of Physics
> University of California, Santa Barbara
> http://web.physics.ucsb.edu/~suoqing
>
> > On Mar 24, 2015, at 12:04 PM, Sandy Yuan <sihany(a)princeton.edu> wrote:
> >
> > Hi all,
> > I have created a box object containing the data field "z-velocity".
> Right now, I can project "z-velocity" along the z axis to get the average
> "z-velocity" for each column, but is there a way to calculate the standard
> deviation of "z-velocity" along each column as well? What is the best way
> to do this in yt 2.6? Any suggestion would be greatly appreciated.
> > Best,
> > --
> > Sandy
> > _______________________________________________
> > yt-users mailing list
> > yt-users(a)lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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> ------------------------------
>
> Message: 2
> Date: Tue, 24 Mar 2015 14:56:02 -0500
> From: Kalina Borkiewicz <kalina(a)illinois.edu>
> To: <yt-users(a)lists.spacepope.org>
> Subject: [yt-users] Periodic enzo volume?
> Message-ID: <5511C152.3070205(a)illinois.edu>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> Hi! Yt newbie here, sorry if my question is stupid or simple or both.
> I'm trying to render a periodic enzo volume. I figured I could just set
> ds.periodicity = (True, True True) , but that didn't seem to do anything.
> Searching the docs for "periodicity" doesn't have any results relating
> to EnzoDataset, so I'm wondering, can I make this periodic? How?
>
> Thanks,
> Kalina
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> ------------------------------
>
> Message: 3
> Date: Tue, 24 Mar 2015 16:10:05 -0400
> From: Yuan Li <bear0980(a)gmail.com>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] Particle Size in Projection Plots
> Message-ID:
> <CANx7jWiGbzZ=
> P9euh9HGa-pw-H4hzosp00N3HfeWgubtzf8icw(a)mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Cameron,
>
> I tired that, and this is the error message I get:
>
> *** YTDataSelectorNotImplemented: Data selector 'arbitrary_grid' not
> implemented.
>
>
> I looks like I will have to do it with matplotlib as Britton suggested
> after all :).
>
>
> By the way, in the examples given on Filtering Particle Fields here
> http://yt-project.org/doc/analyzing/filtering.html, sometimes "Stars" is
> used
> and sometimes it is the lowercase "stars". Is that a typo?
>
>
> Yuan
>
>
> On Tue, Mar 24, 2015 at 12:26 PM, Cameron Hummels <chummels(a)gmail.com>
> wrote:
>
> > I think you may be able to do the ProjectionPlot() by specifying the
> > keyword "data_source=obj":
> >
> >
> >
> http://yt-project.org/docs/dev/reference/api/generated/yt.visualization.plo…
> >
> > On Tue, Mar 24, 2015 at 9:03 AM, Yuan Li <bear0980(a)gmail.com> wrote:
> >
> >> Hi all,
> >>
> >> I was thinking about doing what Britton suggested or making a 2d
> >> histogram in matplotlib, but Cameron's suggestion sounds like what I was
> >> looking for. How do I project this obj after it is created? When I
> tried to
> >> do yt.ProjectionPlot(obj.....) I got the error message saying this
> object
> >> has no attribute 'coordinates'.
> >>
> >> Yuan
> >>
> >> On Tue, Mar 24, 2015 at 11:03 AM, Britton Smith <brittonsmith(a)gmail.com
> >
> >> wrote:
> >>
> >>> In this situation, you might just want to plot the particles themselves
> >>> using a scatter plot in matplotlib. The matplotlib.scatter function
> allows
> >>> you to specify both the color and/or size of the points with arrays, so
> >>> those properties can vary for the individual particles.
> >>>
> >>> Britton
> >>>
> >>> On Tue, Mar 24, 2015 at 2:58 PM, Cameron Hummels <chummels(a)gmail.com>
> >>> wrote:
> >>>
> >>>> Hi Yuan,
> >>>>
> >>>> I think the issue here is that you're taking a particle
> >>>> quantity--stellar ages--and trying to deposit that quantity on to the
> grid,
> >>>> which is primarily defined in enzo by the distribution of gas. Thus,
> young
> >>>> stars tend to occur in locations of star formation, which is to say,
> where
> >>>> there is cold dense gas, the grid is more refined there (assuming
> you're
> >>>> using density-based AMR). This means that you'll tend to get smaller
> >>>> "pixels" for young stars than for old stars where the stars may have
> >>>> drifted into regions of coarser spatial resolution and get larger
> "pixels".
> >>>>
> >>>> One solution for this would be to define your own underlying grid on
> to
> >>>> which you should deposit your particle quantities. That way you can
> make a
> >>>> fixed resolution grid (so all the pixels are the same size) and
> deposit
> >>>> your particle quantities like Stellar Age, and it should solve your
> >>>> problem. To find out more about doing this, check out this section
> of the
> >>>> docs:
> >>>>
> >>>>
> >>>>
> http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grids-objec…
> >>>>
> >>>> Good luck, and let us know how it goes!
> >>>>
> >>>> Cameron
> >>>>
> >>>> On Sun, Mar 22, 2015 at 9:40 PM, Yuan Li <yuan(a)astro.columbia.edu>
> >>>> wrote:
> >>>>
> >>>>> Hi all,
> >>>>>
> >>>>> I have a basic question related to the sizes of particles in a
> >>>>> projection plot (in yt2). I am trying to make a plot that shows the
> average
> >>>>> line of sight star particle ages.
> >>>>>
> >>>>> Right now I am plotting the stellar-density-weighted star ages, and a
> >>>>> lot of the young stars look very small (see figure attached). I
> would like
> >>>>> to show that the stars far away from the center are younger. Is
> there a way
> >>>>> to make the small dots bigger? Other suggestions are also welcome!
> >>>>>
> >>>>>
> >>>>> Thank you!
> >>>>> Yuan
> >>>>> [image: Inline image 1]
> >>>>>
> >>>>> _______________________________________________
> >>>>> yt-users mailing list
> >>>>> yt-users(a)lists.spacepope.org
> >>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>> --
> >>>> Cameron Hummels
> >>>> Postdoctoral Researcher
> >>>> Steward Observatory
> >>>> University of Arizona
> >>>> http://chummels.org
> >>>>
> >>>> _______________________________________________
> >>>> yt-users mailing list
> >>>> yt-users(a)lists.spacepope.org
> >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>>
> >>>>
> >>>
> >>> _______________________________________________
> >>> yt-users mailing list
> >>> yt-users(a)lists.spacepope.org
> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>
> >>>
> >>
> >> _______________________________________________
> >> yt-users mailing list
> >> yt-users(a)lists.spacepope.org
> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>
> >>
> >
> >
> > --
> > Cameron Hummels
> > Postdoctoral Researcher
> > Steward Observatory
> > University of Arizona
> > http://chummels.org
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users(a)lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
> >
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> End of yt-users Digest, Vol 85, Issue 77
> ****************************************
>
--
Sandy
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Hi,
Thank you both. Nathan, is there a way to change the resolution of the
frb using your approach?
Thanks again,
Sandy
On Mon, Mar 16, 2015 at 10:21 AM, <yt-users-request(a)lists.spacepope.org>
wrote:
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> Today's Topics:
>
> 1. Re: What's the best way to project volume density to surface
> density? (Suoqing JI)
> 2. Re: What's the best way to project volume density to surface
> density? (Nathan Goldbaum)
> 3. Re: twinkle while rotate during volume rendering (Michael Zingale)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 15 Mar 2015 19:43:18 -0700
> From: Suoqing JI <suoqing(a)physics.ucsb.edu>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] What's the best way to project volume density
> to surface density?
> Message-ID: <F495764F-5CA0-4E90-B98B-29D02176F900(a)physics.ucsb.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Sandy,
>
> I think you mean by this:
> http://yt-project.org/docs/2.6/reference/api/generated/yt.data_objects.data…
> <
> http://yt-project.org/docs/2.6/reference/api/generated/yt.data_objects.data…
> >
>
> where frb[?Density?] is just the data you want.
>
> Best wishes,
> --
> Suoqing JI
> Ph.D Student
> Department of Physics
> University of California, Santa Barbara
> http://web.physics.ucsb.edu/~suoqing
>
> > On Mar 15, 2015, at 7:07 PM, Sandy Yuan <sihany(a)princeton.edu> wrote:
> >
> > Hi all,
> > I have created a box object centered on a galaxy in an enzo
> cosmological simulation. What is the best way to project the volume density
> field of the object along the x,y,z axes to obtain the surface densities in
> yt 2.6? I can visualize the projection by using ProjectionPlot, but I don't
> know how to get the actual surface density data in this way. There is also
> the proj command, but I am not sure how to use it. Any help would be
> greatly appreciated.
> > Thanks a lot in advance,
> > --
> > Sandy
> > _______________________________________________
> > yt-users mailing list
> > yt-users(a)lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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> ------------------------------
>
> Message: 2
> Date: Sun, 15 Mar 2015 20:08:26 -0700
> From: Nathan Goldbaum <nathan12343(a)gmail.com>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] What's the best way to project volume density
> to surface density?
> Message-ID:
> <
> CAJXewOn1ghu0-pyzgW9-Y8ZOKjzeUAgJcYVsQygWJAPhjuGuDg(a)mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Alternatively, if you already have a ProjectionPlot, you can get its
> associated FRB object like so:
>
> plot = ProjectionPlot(...)
>
> frb = plot._frb
>
> dens_image = frb['density']
>
> You can also access the frb via plot.frb in yt 3.0 or newer.
>
> To use suoqing's method you will need to create a custom projection data
> object. This is the "proj" function you were confused about.
>
> I'd encourage you to look at these pages in th docs to learn more about
> data objects and how to use them:
>
> http://yt-project.org/docs/3.1/analyzing/objects.html
>
> Note these are the docs for yt 3.1 but the concepts are the same for 2.6,
> just somewhat different syntax.
>
> On Sunday, March 15, 2015, Suoqing JI <suoqing(a)physics.ucsb.edu> wrote:
>
> > Hi Sandy,
> >
> > I think you mean by this:
> >
> http://yt-project.org/docs/2.6/reference/api/generated/yt.data_objects.data…
> >
> > where frb[?Density?] is just the data you want.
> >
> > Best wishes,
> > --
> > Suoqing JI
> > Ph.D Student
> > Department of Physics
> > University of California, Santa Barbara
> > http://web.physics.ucsb.edu/~suoqing
> >
> > On Mar 15, 2015, at 7:07 PM, Sandy Yuan <sihany(a)princeton.edu
> > <javascript:_e(%7B%7D,'cvml','sihany(a)princeton.edu');>> wrote:
> >
> > Hi all,
> > I have created a box object centered on a galaxy in an enzo
> cosmological
> > simulation. What is the best way to project the volume density field of
> the
> > object along the x,y,z axes to obtain the surface densities in yt 2.6? I
> > can visualize the projection by using ProjectionPlot, but I don't know
> how
> > to get the actual surface density data in this way. There is also the
> proj
> > command, but I am not sure how to use it. Any help would be greatly
> > appreciated.
> > Thanks a lot in advance,
> > --
> > Sandy
> > _______________________________________________
> > yt-users mailing list
> > yt-users(a)lists.spacepope.org
> > <javascript:_e(%7B%7D,'cvml','yt-users(a)lists.spacepope.org');>
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
> >
> >
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> Message: 3
> Date: Mon, 16 Mar 2015 10:21:22 -0400
> From: Michael Zingale <michael.zingale(a)stonybrook.edu>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] twinkle while rotate during volume rendering
> Message-ID:
> <
> CAGO1_wr9hx_Fejqk6Wk6qR2osM9LDKe13ewUeChJn80HYUxUFg(a)mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> My thought was that clip_ratio operates on each render independently, so it
> will adjust the scale of one frame of your movie without knowing about the
> other frames. Instead, you want a constant normalization throughout the
> entire sequence. This may mean computing the normalization once and then
> manually normalizing each frame by the same amount. That's the approach I
> usually do.
>
> On Sun, Mar 15, 2015 at 9:13 PM, Yuxiang Qin <
> yuxiangq(a)student.unimelb.edu.au> wrote:
>
> > Hi Matthew,
> >
> > I think I misunderstood you and Michael. Are you saying clip_ratio limits
> > the data according to std()? If so, what?s the difference between using
> > clip_ratio and restricting data by std() manually? Btw, I actually used
> > clip_ratio every time when I rotate the camera.
> >
> > Cheers,
> > Yuxiang
> >
> > On 13 Mar 2015, at 10:43, Matthew Turk <matthewturk(a)gmail.com> wrote:
> >
> > I think that's a likely possibility! I do the same. This can be mitigated
> > by supplying a clip ratio because that is with respect to the std(), not
> > max(), which is often slower varying.
> >
> > On Thu, Mar 12, 2015, 6:40 PM Michael Zingale <
> > michael.zingale(a)stonybrook.edu> wrote:
> >
> >> I'm not 100% sure, but when you feed the clip_ratio to the camera, it
> >> will renomalize each image indepedently using the max value for that
> >> particular image, so the overall scaling is not preserved from one
> image to
> >> the next. I've done this instead by defining the amount I want to
> rescale
> >> based on the first image and then manually rescaling all the other
> images
> >> with the same factor.
> >>
> >> On Thu, Mar 12, 2015 at 7:32 PM, Yuxiang Qin <
> >> yuxiangq(a)student.unimelb.edu.au> wrote:
> >>
> >>> yes, it?s a gadget data. I would try it now.
> >>>
> >>>
> >>> On 13 Mar 2015, at 10:30, Sam Skillman <samskillman(a)gmail.com> wrote:
> >>>
> >>> Just a quick thought, can you remove try removing the .transpose()
> after
> >>> block['gas','density']? Is this gadget data?
> >>>
> >>> On Thu, Mar 12, 2015 at 4:22 PM Yuxiang Qin <yuxiang.l.qin(a)gmail.com>
> >>> wrote:
> >>>
> >>>> Hi Sam,
> >>>>
> >>>> Here are the scripts (I use the parallel script to render on different
> >>>> snapshot and use the normal script to do the rotation and zoom) :
> >>>>
> >>>>
> >>>> and result:
> >>>>
> >>>> https://www.dropbox.com/s/50yrzjj3rg3pdo0/rendering.gif?dl=0
> >>>>
> >>>> Thanks for your help!
> >>>>
> >>>> Cheers,
> >>>> Yuxiang
> >>>>
> >>>> On 13 Mar 2015, at 07:45, Sam Skillman <samskillman(a)gmail.com> wrote:
> >>>>
> >>>> Hi Yuxiang,
> >>>> Can you attach the script you used, or perhaps paste it on
> >>>> http://paste.yt-project.org/ and send the resulting link?
> >>>> Thanks,
> >>>> Sam
> >>>>
> >>>> On Wed, Mar 11, 2015 at 7:46 PM Yuxiang Qin <
> >>>> yuxiangq(a)student.unimelb.edu.au> wrote:
> >>>>
> >>>>> Hi Professor Zingale,
> >>>>>
> >>>>> I did use no_ghost = False, when I created my camera.The grids are
> >>>>> still there?
> >>>>>
> >>>>> Cheers,
> >>>>> Yuxiang
> >>>>>
> >>>>> On 12 Mar 2015, at 03:42, Michael Zingale <
> >>>>> michael.zingale(a)stonybrook.edu> wrote:
> >>>>>
> >>>>> Not sure if anyone answered this yet. For the artificial grids,
> >>>>> perhaps this is because you are not using using ghost cells? Make
> sure you
> >>>>> have "no_ghost=False" in the Camera creation.
> >>>>>
> >>>>> On Tue, Mar 10, 2015 at 12:55 AM, Yuxiang Qin <
> yuxiang.l.qin(a)gmail.com
> >>>>> > wrote:
> >>>>>
> >>>>> Dear yt users,
> >>>>>>
> >>>>>> I just saw someone talks about artificial things appearing on volume
> >>>>>> rendering. Actually I also have this kind of problem.
> >>>>>>
> >>>>>> 1. When I try to rotate on my volume rendering plots, It suddenly
> >>>>>> goes dark then kind of twinkles during rotating. What I have done
> is making
> >>>>>> the grid by myself then reading it back again and volume rendering
> it. I
> >>>>>> fixed the clip_ratio. But I still got this twinkling problems.
> >>>>>>
> >>>>>> 2. The other problem is the artificial grids as you can see on my
> >>>>>> plots. I changed my resolution, over_refine_factor and other
> parameters.
> >>>>>> It?s also still there?
> >>>>>>
> >>>>>> I really appreciate your help :)
> >>>>>>
> >>>>>> Cheers,
> >>>>>> Yuxiang
> >>>>>>
> >>>>>> Here are two example. One is before rotation and the second one is
> >>>>>> rotated by 0.5 degree.
> >>>>>>
> >>>>>
> >>>>>> <103 copy 3.jpg><rotate_000 copy.jpg>
> >>>>>>
> >>>>>
> >>>>>> _______________________________________________
> >>>>>> yt-users mailing list
> >>>>>> yt-users(a)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(a)stonybrook.edu
> >>>>> *web*: http://www.astro.sunysb.edu/mzingale
> >>>>>
> >>>>> _______________________________________________
> >>>>> yt-users mailing list
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> >>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>>>
> >>>>> _______________________________________________
> >>>>> yt-users mailing list
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> >>>>>
> >>>> _______________________________________________
> >>>> 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(a)stonybrook.edu
> >> *web*: http://www.astro.sunysb.edu/mzingale
> >> _______________________________________________
> >> yt-users mailing list
> >> yt-users(a)lists.spacepope.org
> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>
> > _______________________________________________
> > yt-users mailing list
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> > 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(a)stonybrook.edu
> *web*: http://www.astro.sunysb.edu/mzingale
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--
Sandy
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