Re: [yt-users] Inclination problem

31 Mar 2016

      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 
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, 
wrote:
...
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Today's Topics:
1. Re: load spherical polar coordinate data with mesh refinement
      in HDF5 (Jiang, Yanfei)
   2. Re: load spherical polar coordinate data with mesh refinement
      in HDF5 (Matthew Turk)
   3. Re: Inclination problem (Matthew Turk)
   4. 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" 
To: Discussion of the yt analysis package

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
_______________________________________________
yt-users mailing list
yt-users@lists.spacepope.org
http://lists.spacepope.org/listinfo.cgi/yt-users-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: 2
Date: Wed, 30 Mar 2016 16:15:30 -0500
From: Matthew Turk 
To: Discussion of the yt analysis package

Subject: Re: [yt-users] load spherical polar coordinate data with mesh
        refinement in HDF5
Message-ID:

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
...
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
On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei
 wrote:
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
 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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------------------------------
Message: 3
Date: Wed, 30 Mar 2016 16:16:22 -0500
From: Matthew Turk 
To: Discussion of the yt analysis package

Subject: Re: [yt-users] Inclination problem
Message-ID:

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 
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, 
wrote:
...
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Today's Topics:
1. Re: gadget onto unigrid (Carla Bernhardt)
   2. Re: gadget onto unigrid (Matthew Turk)
----------------------------------------------------------------------
Message: 1
Date: Tue, 29 Mar 2016 15:55:27 +0200
From: Carla Bernhardt 
To: Discussion of the yt analysis package

Subject: Re: [yt-users] gadget onto unigrid
Message-ID:

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
I
...
got).
Thanks,
Carla
2016-02-23 17:21 GMT+01:00 Matthew Turk :
...
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
 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
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Message: 2
Date: Tue, 29 Mar 2016 08:57:08 -0500
From: Matthew Turk 
To: Discussion of the yt analysis package

Subject: Re: [yt-users] gadget onto unigrid
Message-ID:

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
 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 :
...
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
 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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"Claiming that something can move faster than light is a good
conversation-stopper in physics. People edge away from you in cocktail
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Message: 4
Date: Wed, 30 Mar 2016 18:01:04 -0400
From: Jonah Miller 
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
...
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
 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
On 16-03-30 05:15 PM, Matthew Turk wrote:
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
 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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****************************************
--
*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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Re: [yt-users] Inclination problem

Nathan Goldbaum