[yt-users] yt-users Digest, Vol 85, Issue 53

Sandy Yuan sihany at princeton.edu
Tue Mar 17 11:35:50 PDT 2015 

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 at 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 at physics.ucsb.edu>
> To: Discussion of the yt analysis package
>         <yt-users at 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 at 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_containers.AMRSliceBase.to_frb.html?highlight=to_frb
> <
> http://yt-project.org/docs/2.6/reference/api/generated/yt.data_objects.data_containers.AMRSliceBase.to_frb.html?highlight=to_frb
> >
>
> 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 at 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 at 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 at gmail.com>
> To: Discussion of the yt analysis package
>         <yt-users at lists.spacepope.org>
> Subject: Re: [yt-users] What's the best way to project volume density
>         to surface density?
> Message-ID:
>         <
> CAJXewOn1ghu0-pyzgW9-Y8ZOKjzeUAgJcYVsQygWJAPhjuGuDg at 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 at 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_containers.AMRSliceBase.to_frb.html?highlight=to_frb
> >
> > 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 at princeton.edu
> > <javascript:_e(%7B%7D,'cvml','sihany at 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 at lists.spacepope.org
> > <javascript:_e(%7B%7D,'cvml','yt-users at 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 at stonybrook.edu>
> To: Discussion of the yt analysis package
>         <yt-users at lists.spacepope.org>
> Subject: Re: [yt-users] twinkle while rotate during volume rendering
> Message-ID:
>         <
> CAGO1_wr9hx_Fejqk6Wk6qR2osM9LDKe13ewUeChJn80HYUxUFg at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 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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> >>>>>
> >>>> _______________________________________________
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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
> >>  _______________________________________________
> >> 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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> >
> >
> >
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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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> ****************************************
>



-- 
Sandy
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