Profile plot of a 2d projection FRB object
by Ben Thompson
Hello everyone.
I was wondering if anyone has had experience with producing a profile plot
from a 2d projection object (FRB object).
Essentially, what I am trying to do is plot the stellar surface density of
a galaxy as a function of radius.
This is achieved by doing the following from a disk YT object called
cylinder (in which the origional simulation object is called shot)
center = cylinder.get_field_parameter("center")
normal = cylinder.get_field_parameter("normal")
image_width = (100,"kpc")
three_image_width = YTArray((image_width[0], image_width[0],
image_width[0]),image_width[1])
left = center - image_width
right = center + image_width
region = shot.region(center, left, right)
proj =
yt.ProjectionPlot(cylinder.ds,"z",[("deposit","stars_density")],center=center,width=image_width,data_source=region,axes_unit="kpc")
the error arrises here
prof =
yt.create_profile(proj,bin_fields="cylindrical_r",fields=[("deposit","stars_density")],n_bins=128,weight_field=None
)
where I get the error
/gpfs/home/........./profiles.pyc in create_profile(data_source,
bin_fields, fields, n_bins, extrema, logs, units, weight_field,
accumulation, fractional)
1304 else:
1305 raise NotImplementedError
-> 1306 bin_fields = data_source._determine_fields(bin_fields)
1307 fields = data_source._determine_fields(fields)
1308 if units is not None:
AttributeError: 'FixedResolutionBuffer' object has no attribute
'_determine_fields'
Any ideas how to get around this error?
Also some other things to add as a postscript. Since how the projection
works, if I provide weights=None as a keyword argument within the
ProjectionPlot object, I get a surface density (g/cm^2). But also a
"cylindrical_r" in cm^2 as well. I *think* the way to get around this is to
do another projection where weights="ones", get the radius values out of
that profile.. and then in matplotlib, useing the surface density array
from the former profile, and the radius bin array from the latter...
Produce a plot of the surface density as a function of radius from those
two arrays (I might check by hand afterwards to see if this does the
trick). This seems kinda convoluted so I am wondering if there is an easier
way than this.
_______________________________________________
yt-users mailing list
yt-users(a)lists.spacepope.org
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
3 years, 7 months
Recenter Halo
by Chen Jingjing
Dear yt-users,
I am having a little problem on finding the exact center of a halo. I used
to do
"hc = HaloCatalog(data_ds=data_ds, finder_method='hop')"
to create a halo catalog. But I think the position in the catalog is a
little bit off the exact center judging from the plots I made. I need the
exact center to compute the angular momentum so the off-center result could
cause some problem. I tried to recenter at the maximum gas density by
adding this line
"hc.sphere_field_max_recenter('density')"
But I got an error, AttributeError: 'HaloCatalog' object has no attribute
'sphere_field_max_recenter'.
Can anyone tell me what is the right way to find the center as the location
of maximum gas density?
Thanks,
Jingjing
--
Jingjing Chen [ chenjj235(a)gmail.com ]
Department of Astronomy
Columbia University
550 West 120th Street
New York, New York 10027
Cell Phone: +1(347)5746709
_______________________________________________
yt-users mailing list
yt-users(a)lists.spacepope.org
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
3 years, 9 months
Re: [yt-users] ImageArray.write_png() always rescales ...
by Matthew Turk
Hi Stuart,
On Mon, Mar 30, 2015 at 3:59 PM, Stuart Levy <salevy(a)illinois.edu> wrote:
> I'm trying to use the notebook interface to render, view image result, tweak
> parameters, etc. within a single yt session.
>
> I want to disable auto-brightness-scaling of images, so am calling
>
> ImageArray.write_png()
>
> Although write_png() takes a rescale= parameter, it effectively always
> rescales.
> It passes its array to write_bitmap(), which does rescaling unless the image
> datatype is already numpy.uint8.
You're right. It does look like write_bitmap accepts a max_val, which
will be used in lieu of computing the max, before converting to uint8.
Would that work for your purposes?
>
> But if you try to do that yourself, then write_png() crashes inside
> matplotlib, because write_bitmap "must be an rgba buffer". It's using a
> Python C-level routine to do this check, but I think the problem is that the
> array is not C-contiguous,
> since write_bitmap() has called swapaxes(0,1) on it and not copy()ied it
> afterward.
>
> Demo program at:
>
> http://paste.yt-project.org/show/5502/
>
>
>
> and here:
>
> import yt
> from yt.data_objects.image_array import ImageArray
> import numpy
>
> # 3x4x4 array, ranging from 0 to about 0.5
> v = (numpy.arange(12)/24.) .reshape(3,4,1) * numpy.ones((1,1,4))
> # Write
> ImageArray(v).write_png('grays_rescaled.png', rescale=True)
> # Write, but asking not to rescale. It rescales anyway since
> yt.data_objects.image_array() calls write_bitmap()
> ImageArray(v).write_png('grays_unscaled.png', rescale=False)
>
> # write_bitmap rescales internally unless the image's datatype is exactly
> "numpy.uint8".
> # Let's try doing that ourselves.
> vv = (v*255).astype(numpy.uint8)
> print vv.flags
> ImageArray(vv).write_png('grays8.png', background=None, rescale=False)
>
> # Crashes! inside matplotlib/src/_png.cpp.
>
> # Why? yt/visualization/image_writer.py's write_bitmap(), if it doesn't
> rescale the image,
> # simply calls swapaxes(0,1) on it and passes the result to matplotlib.
> # But the resulting array is no longer C-contiguous (write_bitmap.flags
> shows False).
>
> # When rescaling *does* happen, write_bitmap() is constructed by
> np.concatenate() which makes a new contiguous array.
>
>
>
> _______________________________________________
> 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
3 years, 9 months
data_source SlicePlot Error
by Andrew James Emerick
Hello everyone,
I just ran into an error in using "data_source" kwarg with the SlicePlot
function (error message copied below):
slice = yt.SlicePlot(ds, axis, field, data_source=region)
File
"/home/emerick/.local/lib/python2.7/site-packages/yt-3.1dev-py2.7-linux-x86_64.egg/yt/visualization/plot_window.py",
line 1816, in SlicePlot
return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs)
TypeError: __init__() got an unexpected keyword argument 'data_source'
I have no problem doing the above with ProjectionPlot. If anyone knows what
could be causing this I'd appreciate the help. Otherwise I can do some
digging into the code myself.
Thanks,
Andrew E.
--
Graduate Student
Columbia University
Department of Astronomy
_______________________________________________
yt-users mailing list
yt-users(a)lists.spacepope.org
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
3 years, 9 months
cStringIO error
by Daniel Fenn
Hi everyone,
I've been working here and there on making the two point functions
compatible with yt 3. I've run into an issue with the file i/o that's got
me puzzled.
There's a call to write_on_root() that's failing with the error
*AttributeError: 'builtin_function_or_method' object has no attribute
'StringIO'*
Looking at the definition for write_on_root()
in parallel_analysis_interface.py, I see that the offending line is:
*return cStringIO.StringIO()*
So apparently there's no function called StringIO(), even though the
documentation for cStringIO says there should be.
I think the issue is how cStringIO is being imported:
*from yt.extern.six.moves import cStringIO*
Looking through yt/extern/six.py, it looks like it's modifying how the
modules are imported, or something like that, but I can't really figure out
what's going on in that file.
Does anyone have any thoughts on this?
Thanks,
Daniel
_______________________________________________
yt-users mailing list
yt-users(a)lists.spacepope.org
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
3 years, 10 months
Re: [yt-users] yt-users Digest, Vol 85, Issue 77
by Sandy Yuan
Hi Suoqing,
Thanks, that worked.
Sandy
On Tue, Mar 24, 2015 at 4:10 PM, <yt-users-request(a)lists.spacepope.org>
wrote:
> Send yt-users mailing list submissions to
> yt-users(a)lists.spacepope.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> or, via email, send a message with subject or body 'help' to
> yt-users-request(a)lists.spacepope.org
>
> You can reach the person managing the list at
> yt-users-owner(a)lists.spacepope.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of yt-users digest..."
>
>
> 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
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2...
> >
>
> ------------------------------
>
> 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
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2...
> >
>
> ------------------------------
>
> 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.p...
> >
> > 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-obj...
> >>>>
> >>>> 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
> >
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2...
> >
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: stest_0063_Projection_x_StarAgeYears_young_star_density.png
> Type: image/png
> Size: 27500 bytes
> Desc: not available
> URL: <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2...
> >
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> yt-users mailing list
> yt-users(a)lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
> ------------------------------
>
> End of yt-users Digest, Vol 85, Issue 77
> ****************************************
>
--
Sandy
_______________________________________________
yt-users mailing list
yt-users(a)lists.spacepope.org
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
3 years, 10 months
Re: [yt-users] yt-users Digest, Vol 85, Issue 53
by Sandy Yuan
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:
> Send yt-users mailing list submissions to
> yt-users(a)lists.spacepope.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> or, via email, send a message with subject or body 'help' to
> yt-users-request(a)lists.spacepope.org
>
> You can reach the person managing the list at
> yt-users-owner(a)lists.spacepope.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of yt-users digest..."
>
>
> 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.da...
> <
> http://yt-project.org/docs/2.6/reference/api/generated/yt.data_objects.da...
> >
>
> 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
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2...
> >
>
> ------------------------------
>
> 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.da...
> >
> > 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
> >
> >
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2...
> >
>
> ------------------------------
>
> 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
> >>>>> 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
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> 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
> >>>
> >>>
> >>
> >>
> >> --
> >> 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
> > 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
> >
> >
>
>
> --
> 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
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2...
> >
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> yt-users mailing list
> yt-users(a)lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
> ------------------------------
>
> End of yt-users Digest, Vol 85, Issue 53
> ****************************************
>
--
Sandy
_______________________________________________
yt-users mailing list
yt-users(a)lists.spacepope.org
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
3 years, 10 months
