Mailman 3 Camera Options - yt-users

15 Apr 2016

      Dear yt:
I would like to change/customize/rotate my camera angle for my slice plots
without rotating the axis.
What options do I have using yt if I want to move my camera angle by say 45
degrees?
Can I use the following link or can you suggest me something else
http://yt-project.org/doc/visualizing/volume_rendering.html
Thanks in advance
On Thu, Mar 31, 2016 at 10:11 PM, yt-users-request@lists.spacepope.org
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Today's Topics:

Inclination problem (Sushilkumar)

Message: 1
Date: Thu, 31 Mar 2016 22:11:09 -0500
From: Sushilkumar sushil.sush19us@gmail.com
To: Discussion of the yt analysis package
        yt-users@lists.spacepope.org
Subject: [yt-users] Inclination problem
Message-ID:
        <
CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear Nathan:
Thank you very much, implementing now
On Thu, Mar 31, 2016 at 9:50 AM, yt-users-request@lists.spacepope.org
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Today's Topics:

Re: Inclination problem (Nathan Goldbaum)

Message: 1
Date: Thu, 31 Mar 2016 09:50:31 -0500
From: Nathan Goldbaum nathan12343@gmail.com
To: Discussion of the yt analysis package
        yt-users@lists.spacepope.org
Subject: Re: [yt-users] Inclination problem
Message-ID:
        <CAJXewOnvXjZ+shfKG4SPubn_TYTAbLUu8y9ZRvovzBu=
DcFZtQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi SK,
I'm going to reference this example:
http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines
...
specifically this snippet:
for stream in streamlines.streamlines:
    stream = stream[np.all(stream != 0.0, axis=1)]
    ax.plot3D(stream[:,0], stream[:,1], stream[:,2], alpha=0.1)
Here, the 'stream' object is just a Nx3 numpy array, where N is the
number
...
of points sampled along the streamline. So each row of the numpy array is
just the coordinates of the streamline along one direction.
To answer your question, no, there's nothing in yt that will rotate the
streamlines into a new coordinate system. Fortunately you should be able
to
...
do it yourself using e.g. an Euler angle rotation matrix. You will need
to
...
identify the new coordinate system you would like to transform to,
calculate a 3D rotation matrix, then apply it using matrix multiplication
(e.g. np.dot, which supports broadcasting) to each coordinate along the
streamline.
Hope that helps,
Nathan
On Thu, Mar 31, 2016 at 8:56 AM, Sushilkumar sushil.sush19us@gmail.com
wrote:
...
Dear Matt:
Pleas correct me if I am wrong but "off axis slices" takes slices of
the
...
...
plot that is already plotted.
However, I would like to plot my data in a new coordinate frame
(x`,y`,z`)
...
which is inclined at an angle of say alpha from the default (x,y,z)
frame.
...
Or I would like to plot my data in a rotated frame (x`,y`,z`), which is
rotated at an angle of alpha from (x,y,z).
On Wed, Mar 30, 2016 at 5:01 PM, <yt-users-request@lists.spacepope.org
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Today's Topics:

Re: load spherical polar coordinate data with mesh refinement
in HDF5 (Jiang, Yanfei)
Re: load spherical polar coordinate data with mesh refinement
in HDF5 (Matthew Turk)
Re: Inclination problem (Matthew Turk)
Re: load spherical polar coordinate data with mesh refinement
in HDF5 (Jonah Miller)

Message: 1
Date: Wed, 30 Mar 2016 15:49:26 -0400
From: "Jiang, Yanfei" yanfei.jiang@cfa.harvard.edu
To: Discussion of the yt analysis package
        yt-users@lists.spacepope.org
Subject: Re: [yt-users] load spherical polar coordinate data with mesh
        refinement in HDF5
Message-ID:
        <
CANixPav-VmbXfhNvmA5wb5gj19mF+-Ryq5YD-LrYrByDe3Ne7A@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi Jonah,
I am able to load the data to yt now using load_amr_grids(). I
notice
...
...
...
that it can also set geometry to spherical. This is great. But to make
life
more complicate. Is it possible to let yt know that the grid is
logarithmic? Currently, load_amr_grids() just take left and right
edges
...
of
...
...
each block. I guess yt assumes the grid is uniform between left and
right
...
...
edges. Is it possible to provide arrays of coordinate values for each
cell
...
...
in each block?
Thanks.
On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller <
jonah.maxwell.miller@gmail.com> wrote:
...
Hi Yan-Feng,
I haven't tried it, but I think there is functionality for this. You
can
...
...
...
use the load_amr_grids() function which can load amr data in
Cartesian,
...
...
...
spherical, or polar coordinates. Here's the documentation:
http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar...
...
...
...
...
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
...
...
...
...
Best,
Jonah
On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <
yanfei.jiang@cfa.harvard.edu>
...
wrote:
...
Hi,
         I have some data from a new version of Athena simulations.
It
...
...
is
...
...
in spherical polar coordinate with mesh refinement written in HDF5.
The
...
...
...
...
data structure is similar to flash data but not the same. Does
anyone
...
...
...
have
...
...
suggestions to load such data to yt directly?
Thank you.
Yan-Fei Jiang
Einstein Fellow
Harvard-Smithsonian Center for Astrophysics
60 Garden Street, Cambridge MA USA 02138
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--
Yan-Fei Jiang
Einstein Fellow
Harvard-Smithsonian Center for Astrophysics
60 Garden Street, Cambridge MA USA 02138
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Message: 2
Date: Wed, 30 Mar 2016 16:15:30 -0500
From: Matthew Turk matthewturk@gmail.com
To: Discussion of the yt analysis package
        yt-users@lists.spacepope.org
Subject: Re: [yt-users] load spherical polar coordinate data with mesh
        refinement in HDF5
Message-ID:
        <CALO3=
5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi Yanfei,
This is possible -- but it will also slow some things down.  You can
use the load_hexahedral_mesh function, and there're examples of this.
This takes away some of the optimizations that regular grids can do,
but we're hoping to add them back in shortly.  Like the other
functions it too takes a geometry argument.
-Matt
On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei
yanfei.jiang@cfa.harvard.edu wrote:
...
Hi Jonah,
I am able to load the data to yt now using load_amr_grids(). I
notice
...
...
...
that it can also set geometry to spherical. This is great. But to
make
...
...
...
life
...
more complicate. Is it possible to let yt know that the grid is
logarithmic?
...
Currently, load_amr_grids() just take left and right edges of each
block. I
...
guess yt assumes the grid is uniform between left and right edges.
Is
...
it
...
...
...
possible to provide arrays of coordinate values for each cell in
each
...
...
...
block?
...
Thanks.
On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller
jonah.maxwell.miller@gmail.com wrote:
...
Hi Yan-Feng,
I haven't tried it, but I think there is functionality for this.
You
...
...
...
can
...
...
use the load_amr_grids() function which can load amr data in
Cartesian,
...
...
...
...
spherical, or polar coordinates. Here's the documentation:
http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar...
...
...
...
...
...
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
...
...
...
...
...
Best,
Jonah
On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <
yanfei.jiang@cfa.harvard.edu>
...
...
wrote:
>
> Hi,
>          I have some data from a new version of Athena
simulations.
...
...
...
It is
...
...
> in spherical polar coordinate with mesh refinement written in
HDF5.
...
...
...
The data
...
...
> structure is similar to flash data but not the same. Does anyone
have
...
...
...
...
> suggestions to load such data to yt directly?
>
> Thank you.
> --
> Yan-Fei Jiang
>
> Einstein Fellow
> Harvard-Smithsonian Center for Astrophysics
> 60 Garden Street, Cambridge MA USA 02138
> _______________________________________________
> yt-users mailing list
> yt-users@lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

yt-users mailing list
yt-users@lists.spacepope.org
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--
Yan-Fei Jiang
Einstein Fellow
Harvard-Smithsonian Center for Astrophysics
60 Garden Street, Cambridge MA USA 02138

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Message: 3
Date: Wed, 30 Mar 2016 16:16:22 -0500
From: Matthew Turk matthewturk@gmail.com
To: Discussion of the yt analysis package
        yt-users@lists.spacepope.org
Subject: Re: [yt-users] Inclination problem
Message-ID:
        <CALO3=5HMB=
joejr6BBh+zdxkwGzJS2NPrkK9tvMJnbch5-7BgQ@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi SK,
I'm not sure I totally understand, but if you have an inclination
angle you can use this directly in yt in the off axis slices and so
on.  They typically take a vector, but you should be able to convert
one to the other.
-Matt
On Tue, Mar 29, 2016 at 1:37 PM, Sushilkumar <
sushil.sush19us@gmail.com
...
...
...
wrote:
...
Dear yt:
I am trying to numerically solve the region around a pulsar. Now
since
...
...
...
...
pulsar is an inclined rotator with inclination angle between
rotation
...
...
...
axis
...
and dipole axis I would like to include in my yt script.
My original code written in FORTRAN incorporated this inclination
but
...
...
...
how
...
would I incorporate it into my visualization using yt without
changing
...
...
...
my
...
data.
Could you suggest ways for the same?
The google drive link to my script (streamline.py) and streamline
plot
...
...
...
...
(streamline_t000.png) is included
https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc
Thanks in advance
On Tue, Mar 29, 2016 at 12:54 PM, <
yt-users-request@lists.spacepope.org
...
...
...
wrote:
...
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...
...
...
...
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Today's Topics:

Re: gadget onto unigrid (Carla Bernhardt)
Re: gadget onto unigrid (Matthew Turk)

...
...
...
...
Message: 1
Date: Tue, 29 Mar 2016 15:55:27 +0200
From: Carla Bernhardt carla.j.bernhardt@gmail.com
To: Discussion of the yt analysis package
        yt-users@lists.spacepope.org
Subject: Re: [yt-users] gadget onto unigrid
Message-ID:
<CAFK0O=2vH24ViqeZ5QS3DY3uido0kEaF=
UhyGS_beuiUMbw7Ag@mail.gmail.com>
...
...
...
...
...
Content-Type: text/plain; charset="utf-8"
Hi All,
A follow-up question: In using arbitrary_grid (but with enzo data),
how
...
...
...
...
does one then extract a field of an arbitrary_grid? I tried
arbgrid["density"] as I have done with a smoothed_covering_grid
object,
...
...
...
...
but
it does not work (here is the traceback <
http://pastebin.com/afgcgpp0%3E
...
...
I
...
...
got).
Thanks,
Carla
2016-02-23 17:21 GMT+01:00 Matthew Turk matthewturk@gmail.com:
> Hi Desika,
>
> Yup, this can be done reasonably easily using either the
> .arbitrary_grid object (which was designed for this) or the
interface
...
...
...
...
> to the arbitrary grid that's in the development version, which is
> ds.r[ ... ] where the ... is some combination of bounds and
steps.
...
...
...
...
...
>
>
http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid
...
...
...
...
>
>
>
http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-sel...
...
...
...
...
...
>
> On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan
> desika.narayanan@gmail.com wrote:
> > Hi All,
> >
> > Is it possible to deposit the particles from a gadget data set
onto a
...
...
> > uniform grid in yt?  Or, could it be possible to trick the
octree
...
...
...
...
...
> deposition
> > into doing it by forcing no refinements, but some sort of
native
...
...
...
grid
...
...
> > resolution?
> >
> > thanks,
> > desika
> >
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users@lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
> _______________________________________________
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> yt-users@lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
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Message: 2
Date: Tue, 29 Mar 2016 08:57:08 -0500
From: Matthew Turk matthewturk@gmail.com
To: Discussion of the yt analysis package
        yt-users@lists.spacepope.org
Subject: Re: [yt-users] gadget onto unigrid
Message-ID:
<CALO3=5HR=zLHujWKgLpqwei_98vBOjpYvQ4m8nnUFR=
P098utA@mail.gmail.com>
...
...
...
...
...
Content-Type: text/plain; charset=UTF-8
Hi Carla,
This functionality was recently implemented and is in the
development
...
...
...
...
...
version, but not yet in the stable.  We're hoping for a release
very
...
...
...
...
...
shortly, but you can also try the dev version if you'd like!
-Matt
On Tue, Mar 29, 2016 at 8:55 AM, Carla Bernhardt
carla.j.bernhardt@gmail.com wrote:
> Hi All,
>
> A follow-up question: In using arbitrary_grid (but with enzo
data),
...
...
...
how
...
...
> does
> one then extract a field of an arbitrary_grid? I tried
> arbgrid["density"] as
> I have done with a smoothed_covering_grid object, but it does not
work
...
...
> (here
> is the traceback I got).
>
> Thanks,
> Carla
>
> 2016-02-23 17:21 GMT+01:00 Matthew Turk matthewturk@gmail.com:
>>
>> Hi Desika,
>>
>> Yup, this can be done reasonably easily using either the
>> .arbitrary_grid object (which was designed for this) or the
interface
...
...
>> to the arbitrary grid that's in the development version, which
is
...
...
...
...
...
>> ds.r[ ... ] where the ... is some combination of bounds and
steps.
...
...
...
...
...
>>
>>
http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid
...
...
>>
>>
>>
http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-sel...
...
...
...
...
...
>>
>> On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan
>> desika.narayanan@gmail.com wrote:
>> > Hi All,
>> >
>> > Is it possible to deposit the particles from a gadget data set
onto a
...
...
>> > uniform grid in yt?  Or, could it be possible to trick the
octree
...
...
...
...
>> > deposition
>> > into doing it by forcing no refinements, but some sort of
native
...
...
...
grid
...
...
>> > resolution?
>> >
>> > thanks,
>> > desika
>> >
>> >
>> > _______________________________________________
>> > yt-users mailing list
>> > yt-users@lists.spacepope.org
>> >
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
...
...
...
...
...
>> >
>> _______________________________________________
>> yt-users mailing list
>> yt-users@lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
>
> _______________________________________________
> yt-users mailing list
> yt-users@lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>

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--
SK2
"Claiming that something can move faster than light is a good
conversation-stopper in physics. People edge away from you in
cocktail
...
...
...
...
parties; friends never return phone calls. You just don?t mess with
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Message: 4
Date: Wed, 30 Mar 2016 18:01:04 -0400
From: Jonah Miller jonah.maxwell.miller@gmail.com
To: yt-users@lists.spacepope.org
Subject: Re: [yt-users] load spherical polar coordinate data with mesh
        refinement in HDF5
Message-ID: 56FC4CA0.4030403@gmail.com
Content-Type: text/plain; charset=windows-1252; format=flowed
Hi Yanfei,
To add to Matt's comment. Here is the documentation for using
load_hexahedral_mesh.
http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-d...
...
...
...
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
...
...
...
Best,
Jonah
On 16-03-30 05:15 PM, Matthew Turk wrote:
...
Hi Yanfei,
This is possible -- but it will also slow some things down.  You can
use the load_hexahedral_mesh function, and there're examples of
this.
...
...
...
...
This takes away some of the optimizations that regular grids can do,
but we're hoping to add them back in shortly.  Like the other
functions it too takes a geometry argument.
-Matt
On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei
yanfei.jiang@cfa.harvard.edu wrote:
...
Hi Jonah,
I am able to load the data to yt now using load_amr_grids(). I

notice
...
...
that it can also set geometry to spherical. This is great. But to
make
...
...
life
...
...
more complicate. Is it possible to let yt know that the grid is
logarithmic?
...
...
Currently, load_amr_grids() just take left and right edges of each
block. I
...
...
guess yt assumes the grid is uniform between left and right edges.
Is
...
...
...
it
...
...
possible to provide arrays of coordinate values for each cell in
each
...
...
...
block?
...
...
Thanks.
On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller
jonah.maxwell.miller@gmail.com wrote:
> Hi Yan-Feng,
>
> I haven't tried it, but I think there is functionality for this.
You
...
...
...
can
...
...
> use the load_amr_grids() function which can load amr data in
Cartesian,
...
...
> spherical, or polar coordinates. Here's the documentation:
>
>
>
http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar...
...
...
...
...
...
>
>
>
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
...
...
...
...
...
>
> Best,
> Jonah
>
> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <
yanfei.jiang@cfa.harvard.edu>
...
...
> wrote:
>> Hi,
>>           I have some data from a new version of Athena
simulations.
...
...
It is
...
...
>> in spherical polar coordinate with mesh refinement written in
HDF5.
...
...
...
The data
...
...
>> structure is similar to flash data but not the same. Does anyone
have
...
...
...
...
>> suggestions to load such data to yt directly?
>>
>> Thank you.
>> --
>> Yan-Fei Jiang
>>
>> Einstein Fellow
>> Harvard-Smithsonian Center for Astrophysics
>> 60 Garden Street, Cambridge MA USA 02138
>> _______________________________________________
>> yt-users mailing list
>> yt-users@lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
> _______________________________________________
> yt-users mailing list
> yt-users@lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
--
Yan-Fei Jiang
Einstein Fellow
Harvard-Smithsonian Center for Astrophysics
60 Garden Street, Cambridge MA USA 02138

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End of yt-users Digest, Vol 97, Issue 37

--
*SK2*
*"**Claiming that something can move faster than light is a good
conversation-stopper in physics. People edge away from you in cocktail
parties; friends never return phone calls. You just don?t mess with
Albert
...
Einstein.**"*

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End of yt-users Digest, Vol 97, Issue 39

--
*SK2*
*"**Claiming that something can move faster than light is a good
conversation-stopper in physics. People edge away from you in cocktail
parties; friends never return phone calls. You just don?t mess with Albert
Einstein.**"*
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End of yt-users Digest, Vol 97, Issue 41

-- 
*SK2*

*"**Claiming that something can move faster than light is a good
conversation-stopper in physics. People edge away from you in cocktail
parties; friends never return phone calls. You just don’t mess with Albert
Einstein.**"*