[YT-USERS] Incoherence when ploting a slice - from FLASH simulation
by Gabriel RIGON
Dear all,
I recently start to work with yt to analyze my FLASH simulation. The output of those simulation is an hdf5 file.
When I try to plot a slice of my simulation, some weird lines appear on it. Here is an example of the python script and the results it leads to.
"""
import yt
ds = yt.load("lasslab_hdf5_plt_cnt_0000.hdf5")
yt.SlicePlot(ds, 'z', "dens").show()
[cid:972219b9-edbb-4265-81cf-9a07e61cf360]
"""
Actually they also appear went plotting the results of a frb of a slice (even when I try to plot the x or y coordinate in 2d).
Do you have any idea of the reason for such lines, or a solution for my problem?
Best regards,
Gabriel Rigon
1 year, 8 months
yt for analyzing Millennium simulation data
by Ankit Singh
Hi all,
For some work, I had to use Millenium Simulation data. I have a catalog of
halos with their positions, and I wanted to get the halos in voids. Can yt
be of any use for such an analysis? The thing that makes it difficult is
periodic boundary conditions it doesn't allow you to use KDtree straight
away.
Please help,
Thanks,
With Regards,
Ankit
1 year, 9 months
Covering GIZMO data to uniform grid
by 梁家豪
Hello yt-commuinty,
I was trying to use yt to analyse GIZMO data.
Is there a function which can translate GIZMO gas data,particle0, to
uniform grid with neutral hydrogen,velocity,temperature.etc?
I know the "deposit " field and covering_grid in yt, but "deposit" isn't
uniform and covering_grid is designed for grid-like data..
Thank you!
Edward
1 year, 9 months
reading the fields correctly (ramses-rt)
by sacielo
Hi all,
I'm experiencing a little trouble in reading some RAMSES files which
include radiative transfer.
In this (broadly used) implementation some of the fields do not follow the
order they have classical RAMSES files; e.g. the pressure field is later in
the fields list. Indeed when I read the files those fields do not have the
correct content.
Can someone please suggest a possible workaround? For instance a plugin for
this kind of files, if it exists, or suggest how I could swap the fields,
or rename them with the correct name?
I do not want simply to create new fields, without correcting the default
ones, as all derived fields (and possibly other valuable yt features) would
not work properly.
Thank you very much!
Best,
Salvatore
1 year, 9 months
2-D radial profile plotting
by Joshua Wall
Hello Dear Users,
I'm recently trying to recreate some of the interesting 2-D radial
plots of stellar and gas surface density the ALMA folks are making (see
https://arxiv.org/abs/1703.07029 for instance) using my simulations. I've
been experimenting with using an FRB to do this, but I'm having trouble
resolving the innermost cells even though the FRB resolution matches my
grid's highest resolution.
I see that there was some discussion of including this in the code a
couple of years ago (as well as where I got the idea to try FRBs for this):
http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2015-June/006...
Did this ever make it in? I'd love to be able to use it if so.
Cordially,
Josh
--
Joshua Wall
Doctoral Candidate
Department of Physics
Drexel University
3141 Chestnut Street
Philadelphia, PA 19104
1 year, 9 months
producing smooth sliceplots instead of pixelated sliceplot images
by tazkera haque
Hi People,
I was wondering if yt can produce smooth images of zoomed-in sliceplots,
where the pixelated AMR grids are not clearly visible. I was interested to
see the colors get mixed in smoothly (something like tetrahedralization),
is that possible anyway in yt?
Best
Tazkera
1 year, 10 months
transparency and color from two arrays (cont.)
by Matěj Týč
Hello guys,
our research group would like to visualize volume data, where the
transfer function is bivariate (see
http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2017-April/00...
). We have been struggling with this task, so I would like you to help
me understand some of the basic concepts I have come across and that I
find confusing.
1. I think that I somehow understand the concept of transfer functions
with multiple fields, but I have difficulties of creating a volume
source with multiple fields. I have somehow examined the source code,
and it seems to me that only the first field is used (judging by
https://github.com/yt-project/yt/blob/master/yt/visualization/volume_rend...
). If I am wrong and it is meaningful and possible to construct a source
with multiple fields, could you please provide an example?
2. I have no doubts that transfer functions work, but I was unable to
find out how are they involved in the integration process. What I came
across were the integration routines and they have mentioned that the
transfer function is not used:
https://github.com/yt-project/yt/blob/master/yt/utilities/lib/ray_integra...
. This is really interesting, how is it in reality?
3. You have mentioned the PlanckTransferFunction as a good example of
multivariate transfer function.
However, doing a Google search, hoping that we will find a code snippet
featuring a non-trivial example did not yield any results. Would you be
so kind and provide one?
Best regards,
Matej
https://github.com/matejak
1 year, 10 months
Re: [yt-users] yt-users Digest, Vol 111, Issue 44
by Alexander Hamilton
Hi Matt,
Cheers for the info, I’ll take a look at your Unity code, I’m betting it’ll be better than my stab at it a few months back, I used someone else’s ray-marching code:
https://github.com/brianasu/unity-ray-marching/tree/volumetric-textures
Is it a mercurial repository? (I’ve just never used that before)
Hi Nathan,
My skillset doesn’t cover Open GL or general graphics either (yet, maybe in time), but I’m more than happy to help where I can and I have enough people here interested to get their data in VR that there’s a good amount of support. :)
I assume yt’s OpenGL volume rendering uses ray-marching?
Hi Suoqing,
Cheers, that’s cool, I’ll have to give that a try too, I’ll have to see if the data will look good on that.
Hi Jill,
That’s a good idea, I’d never heard of sketchfab, most of our datasets are more volume then surface, but it’s worth a try for some of my solar stuff.
Thanks guys, I’m getting loads of cool ideas from here.
Regards
Alex
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Today's Topics:
1. Re: YT VR Visualisation (Naiman, Jill)
2. Re: YT VR Visualisation (Suoqing Ji)
3. Ramses MHD visualization (Daniel William Murray)
----------------------------------------------------------------------
Message: 1
Date: Tue, 23 May 2017 10:00:31 +1000
From: "Naiman, Jill" <jill.naiman(a)cfa.harvard.edu>
To: Discussion of the yt analysis package
<yt-users(a)lists.spacepope.org>
Subject: Re: [yt-users] YT VR Visualisation
Message-ID:
<CAFwWoV-K5rWnL_9LZVQ4ZVhvaH8znbMo0Vi1yrg0MeApeSxuXw(a)mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi All,
Just FYI - one can also generate points/surfaces with yt and upload them
somewhere like Sketchfab and use their VR mechanisms.
Looking forward to what comes of it!
Cheers,
-Jill
On Tue, May 23, 2017 at 2:14 AM, Nathan Goldbaum <nathan12343(a)gmail.com>
wrote:
>
>
> On Mon, May 22, 2017 at 11:07 AM, Matthew Turk <matthewturk(a)gmail.com>
> wrote:
>
>> Hi Alex,
>>
>> Yup, we have been, and with the vive and oculus specifically. Right
>> now though, it never got past much of a tech demo phase -- there's
>> code on my group's bitbucket account (bitbucket.org/data-exp-lab/ )
>> that runs in Unity, and Nathan Goldbaum got some of the stuff that's
>> in yt (the volume rendering) to work with the OpenVR python bindings
>> directly (not srue where that code is) but it's all still pretty early
>> on.
>
>
> This code isn't really usable yet. In order for this to actually work,
> we'll need a big overhaul of the OpenGL volume rendering in yt to use
> multiple passes.
>
> In addition there were significant performance issues that I never tracked
> down. Unfortunately I'm no expert on graphics programming and that's
> probably what's needed here.
>
>
>> Not sure it's quite shovel ready. There're some students coming
>> on soon that will take another look, but July might be a bit
>> optimistic... That being said, it'd be an awesome hack or
>> collaboration and if you are interested in trying to push it at all,
>> that'd be pretty rad.
>>
>> -Matt
>>
>> On Mon, May 22, 2017 at 10:10 AM, Alexander Hamilton
>> <A.Hamilton(a)2016.hull.ac.uk> wrote:
>> > Hi guys, I?m Alex from Hull University.
>> > We?re hosting the UK?s National Astronomy Meeting in July and I?ve been
>> > asked to run the hack day.
>> >
>> > I?ve managed to procure some VR headsets (HTC Vive, Oculus Rift and MS
>> > Hololens) and want to try and see if we could use them for visualising
>> some
>> > of our simulation data.
>> > I hear you guys may have been playing with VR, is that true? Is there
>> > anything that we could use/play-with at this point?
>> >
>> >
>> >
>> > Thanks
>> >
>> > Alex
>> >
>> > **************************************************
>> > To view the terms under which this email is
>> > distributed, please go to
>> > http://www2.hull.ac.uk/legal/disclaimer.aspx
>> > **************************************************
>> > _______________________________________________
>> > 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
>>
>
>
> _______________________________________________
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Message: 2
Date: Mon, 22 May 2017 17:18:20 -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] YT VR Visualisation
Message-ID: <ca3136c6-5fe9-4aac-92df-09d17d82bffc@Spark>
Content-Type: text/plain; charset="utf-8"
Hi Alex,
Just to add up one more point: yt is always able to generate pre-rendered virtual reality movies with stereo-spherical lens, which works perfectly with Google Cardboard.
To generate the movie, you could refer to this page: http://yt-project.org/docs/dev/visualizing/volume_rendering.html#spherica...
An example move is at:?https://www.youtube.com/watch?v=ZYWY53X7UQE . You could also put your smartphone into Google Cardboard to watch the video with Youtube App.
Best wishes,
?
Suoqing Ji
Ph.D Candidate
Department of Physics
University of California, Santa Barbara
http://physics.ucsb.edu/~suoqing
On May 22, 2017, 5:00 PM -0700, Naiman, Jill <jill.naiman(a)cfa.harvard.edu>, wrote:
> Hi All,
>
> Just FYI - one can also generate points/surfaces with yt and upload them somewhere like Sketchfab and use their VR mechanisms.
>
> Looking forward to what comes of it!
>
> Cheers,
> -Jill
>
> > On Tue, May 23, 2017 at 2:14 AM, Nathan Goldbaum <nathan12343(a)gmail.com> wrote:
> > >
> > >
> > > > On Mon, May 22, 2017 at 11:07 AM, Matthew Turk <matthewturk(a)gmail.com> wrote:
> > > > > Hi Alex,
> > > > >
> > > > > Yup, we have been, and with the vive and oculus specifically.? Right
> > > > > now though, it never got past much of a tech demo phase -- there's
> > > > > code on my group's bitbucket account (bitbucket.org/data-exp-lab/ )
> > > > > that runs in Unity, and Nathan Goldbaum got some of the stuff that's
> > > > > in yt (the volume rendering) to work with the OpenVR python bindings
> > > > > directly (not srue where that code is) but it's all still pretty early
> > > > > on.
> > > >
> > > > This code isn't really usable yet. In order for this to actually work, we'll need a big overhaul of the OpenGL volume rendering in yt to use multiple passes.
> > > >
> > > > In addition there were significant performance issues that I never tracked down. Unfortunately I'm no expert on graphics programming and that's probably what's needed here.
> > > >
> > > > > Not sure it's quite shovel ready.? There're some students coming
> > > > > on soon that will take another look, but July might be a bit
> > > > > optimistic...? That being said, it'd be an awesome hack or
> > > > > collaboration and if you are interested in trying to push it at all,
> > > > > that'd be pretty rad.
> > > > >
> > > > > -Matt
> > > > >
> > > > > On Mon, May 22, 2017 at 10:10 AM, Alexander Hamilton
> > > > > <A.Hamilton(a)2016.hull.ac.uk> wrote:
> > > > > > Hi guys, I?m Alex from Hull University.
> > > > > > We?re hosting the UK?s National Astronomy Meeting in July and I?ve been
> > > > > > asked to run the hack day.
> > > > > >
> > > > > > I?ve managed to procure some VR headsets (HTC Vive, Oculus Rift and MS
> > > > > > Hololens) and want to try and see if we could use them for visualising some
> > > > > > of our simulation data.
> > > > > > I hear you guys may have been playing with VR, is that true? Is there
> > > > > > anything that we could use/play-with at this point?
> > > > > >
> > > > > >
> > > > > >
> > > > > > Thanks
> > > > > >
> > > > > >? ? ?Alex
> > > > > >
> > > > > > **************************************************
> > > > > > To view the terms under which this email is
> > > > > > distributed, please go to
> > > > > > http://www2.hull.ac.uk/legal/disclaimer.aspx
> > > > > > **************************************************
> > > > > > _______________________________________________
> > > > > > 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
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Message: 3
Date: Tue, 23 May 2017 17:59:15 +0000
From: Daniel William Murray <dwmurray(a)uwm.edu>
To: "yt-users(a)lists.spacepope.org" <yt-users(a)lists.spacepope.org>
Subject: [yt-users] Ramses MHD visualization
Message-ID:
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Dear yt folks,
I am trying to visualize some RAMSES MHD simulation data. The simulation is for gravitationally collapsing gas looking at star formation. I'm looking to obtain projection and slice plots and then annotate the magnetic fields onto the resulting image.
I'm on Mac OS X 10.9.5
I'm using conda 4.3.18
My version of yt is: 3.3.5-py27_0
and python 2.7.12
All of what I believe is the relevant code:
pf = yt.load('output_00284/info_00284.txt')
sp = pf.h.sphere(part_center, (zoom_width + 0.5, "pc"))
L = sp.quantities.angular_momentum_vector()
p = yt.OffAxisSlicePlot(pf, L, 'density', center=part_center, width =(zoom_width, "pc"))
p.annotate_magnetic_field()
p.save('test.png')
The error:
yt.utilities.exceptions.YTPlotCallbackError: annotate_magnetic_field callback failed with the following error: Could not find field '('all', 'magnetic_field_x')' in info_00284.
If I load the field list for the data set, I can see that the B field data is there, but under 'ramses', not 'all'
('ramses', 'x-Bfield-left'),
('ramses', 'x-Bfield-right'),
('ramses', 'x-velocity'),
('ramses', 'y-Bfield-left'),
('ramses', 'y-Bfield-right'),
('ramses', 'y-velocity'),
('ramses', 'z-Bfield-left'),
('ramses', 'z-Bfield-right'),
Is there a way to pass these fields to annotate_magnetic_field? Or a manner in which I can have this information load in the field ('all', 'magnetic_field_')
I should also note that I can create and save the plots with no issues, so long as I do not try to annotate the magnetic fields.
Cheers,
Daniel Murray
Graduate student at University of Wisconsin Milwaukee
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1 year, 10 months
Ramses MHD visualization
by Daniel William Murray
Dear yt folks,
I am trying to visualize some RAMSES MHD simulation data. The simulation is for gravitationally collapsing gas looking at star formation. I'm looking to obtain projection and slice plots and then annotate the magnetic fields onto the resulting image.
I'm on Mac OS X 10.9.5
I'm using conda 4.3.18
My version of yt is: 3.3.5-py27_0
and python 2.7.12
All of what I believe is the relevant code:
pf = yt.load('output_00284/info_00284.txt')
sp = pf.h.sphere(part_center, (zoom_width + 0.5, "pc"))
L = sp.quantities.angular_momentum_vector()
p = yt.OffAxisSlicePlot(pf, L, 'density', center=part_center, width =(zoom_width, "pc"))
p.annotate_magnetic_field()
p.save('test.png')
The error:
yt.utilities.exceptions.YTPlotCallbackError: annotate_magnetic_field callback failed with the following error: Could not find field '('all', 'magnetic_field_x')' in info_00284.
If I load the field list for the data set, I can see that the B field data is there, but under 'ramses', not 'all'
('ramses', 'x-Bfield-left'),
('ramses', 'x-Bfield-right'),
('ramses', 'x-velocity'),
('ramses', 'y-Bfield-left'),
('ramses', 'y-Bfield-right'),
('ramses', 'y-velocity'),
('ramses', 'z-Bfield-left'),
('ramses', 'z-Bfield-right'),
Is there a way to pass these fields to annotate_magnetic_field? Or a manner in which I can have this information load in the field ('all', 'magnetic_field_')
I should also note that I can create and save the plots with no issues, so long as I do not try to annotate the magnetic fields.
Cheers,
Daniel Murray
Graduate student at University of Wisconsin Milwaukee
1 year, 10 months
YT VR Visualisation
by Alexander Hamilton
Hi guys, I’m Alex from Hull University.
We’re hosting the UK’s National Astronomy Meeting in July and I’ve been asked to run the hack day.
I’ve managed to procure some VR headsets (HTC Vive, Oculus Rift and MS Hololens) and want to try and see if we could use them for visualising some of our simulation data.
I hear you guys may have been playing with VR, is that true? Is there anything that we could use/play-with at this point?
Thanks
Alex
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1 year, 10 months
