Hi yt-users! I have what I think should be a relatively simple question. I am trying to make a 3D image of a region of a cosmological simulation, and plot points in the image. I define my region with box(left_edge,right_edge) where left_edge and right_edge are in code units. However, the points that I read in from an earlier file are in cgs units. Since the file was written using yt output, I would like to just let yt do the conversions, but nothing has units attached. I want the 3d image to get everything into the same units. I feel like there are a few ways I could fix this problem--1) tell yt that my points are in cgs units, 2) force the create_scene to be in cgs units, 3) get yt to tell me the conversion factor from code units to cgs units. Unfortunately, I don't know how to do any of these things! Can someone give me some advice on what to do here? Thanks! Stephanie -- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com
Hi Stephanie, If you have a loaded dataset, you can convert an ndarray that you know is in centimeters to a YTArray in code_length units like so: arr_in_code_length = ds.arr(ndarray_in_centimeters, 'cm').to('code_length') In addition, I don't think you actually need to convert to code_length units if you are passing this array to yt, since yt will internally do the conversion if you hand it a YTArray with units, so just creating an array like this is sufficient: from yt.units import cm arr_in_cm = ndarray_in_centimeters * cm And then pass arr_in_cm to some yt function. If all you want is the conversion factor from CGS to code length units, then you can inspect ds.length_unit. For example, the conversion from code length units to CGS is ds.length_unit.in_cgs(). There are a number of unit attributes that are attached to datasets (ds.mass_unit, ds.velocity_unit, ds.pressure_unit) that are useful for this sort of thing. Hope that helps! -Nathan On Mon, Jun 19, 2017 at 7:38 PM, Stephanie Tonnesen <stonnes@gmail.com> wrote:
Hi yt-users!
I have what I think should be a relatively simple question. I am trying to make a 3D image of a region of a cosmological simulation, and plot points in the image. I define my region with box(left_edge,right_edge) where left_edge and right_edge are in code units. However, the points that I read in from an earlier file are in cgs units. Since the file was written using yt output, I would like to just let yt do the conversions, but nothing has units attached. I want the 3d image to get everything into the same units. I feel like there are a few ways I could fix this problem--1) tell yt that my points are in cgs units, 2) force the create_scene to be in cgs units, 3) get yt to tell me the conversion factor from code units to cgs units.
Unfortunately, I don't know how to do any of these things!
Can someone give me some advice on what to do here?
Thanks!
Stephanie
-- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Nathan (and yt-users), Thanks! Yes, arr_in_cm = ndarray_in_centimeters * cm got yt to see that I was talking about cm. The problem is that I still don't see the points. Is there any example of putting points on a volume rendering? I am trying to mix the "Volume Rendering with Lines" cookbook recipe with the PointSource api description, but am not sure what I am hoping my result will look like--for example, how big can I expect my points to be? Is that something I can set? Thanks, Stephanie -- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com On Mon, Jun 19, 2017 at 5:48 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Stephanie,
If you have a loaded dataset, you can convert an ndarray that you know is in centimeters to a YTArray in code_length units like so:
arr_in_code_length = ds.arr(ndarray_in_centimeters, 'cm').to('code_length')
In addition, I don't think you actually need to convert to code_length units if you are passing this array to yt, since yt will internally do the conversion if you hand it a YTArray with units, so just creating an array like this is sufficient:
from yt.units import cm
arr_in_cm = ndarray_in_centimeters * cm
And then pass arr_in_cm to some yt function.
If all you want is the conversion factor from CGS to code length units, then you can inspect ds.length_unit. For example, the conversion from code length units to CGS is ds.length_unit.in_cgs(). There are a number of unit attributes that are attached to datasets (ds.mass_unit, ds.velocity_unit, ds.pressure_unit) that are useful for this sort of thing.
Hope that helps!
-Nathan
On Mon, Jun 19, 2017 at 7:38 PM, Stephanie Tonnesen <stonnes@gmail.com> wrote:
Hi yt-users!
I have what I think should be a relatively simple question. I am trying to make a 3D image of a region of a cosmological simulation, and plot points in the image. I define my region with box(left_edge,right_edge) where left_edge and right_edge are in code units. However, the points that I read in from an earlier file are in cgs units. Since the file was written using yt output, I would like to just let yt do the conversions, but nothing has units attached. I want the 3d image to get everything into the same units. I feel like there are a few ways I could fix this problem--1) tell yt that my points are in cgs units, 2) force the create_scene to be in cgs units, 3) get yt to tell me the conversion factor from code units to cgs units.
Unfortunately, I don't know how to do any of these things!
Can someone give me some advice on what to do here?
Thanks!
Stephanie
-- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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On Tue, Jun 20, 2017 at 12:42 AM, Stephanie Tonnesen <stonnes@gmail.com> wrote:
Hi Nathan (and yt-users),
Thanks! Yes, arr_in_cm = ndarray_in_centimeters * cm
got yt to see that I was talking about cm.
The problem is that I still don't see the points. Is there any example of putting points on a volume rendering? I am trying to mix the "Volume Rendering with Lines" cookbook recipe with the PointSource api description, but am not sure what I am hoping my result will look like--for example, how big can I expect my points to be? Is that something I can set?
Yup: http://yt-project.org/docs/dev/cookbook/complex_plots.html#volume-rendering-... It looks like PontSource optionally takes either a scalar or ndarray of radii (one radius value for each point): http://yt-project.org/docs/dev/reference/api/yt.visualization.volume_renderi...
Thanks,
Stephanie
-- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com
On Mon, Jun 19, 2017 at 5:48 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Stephanie,
If you have a loaded dataset, you can convert an ndarray that you know is in centimeters to a YTArray in code_length units like so:
arr_in_code_length = ds.arr(ndarray_in_centimeters, 'cm').to('code_length')
In addition, I don't think you actually need to convert to code_length units if you are passing this array to yt, since yt will internally do the conversion if you hand it a YTArray with units, so just creating an array like this is sufficient:
from yt.units import cm
arr_in_cm = ndarray_in_centimeters * cm
And then pass arr_in_cm to some yt function.
If all you want is the conversion factor from CGS to code length units, then you can inspect ds.length_unit. For example, the conversion from code length units to CGS is ds.length_unit.in_cgs(). There are a number of unit attributes that are attached to datasets (ds.mass_unit, ds.velocity_unit, ds.pressure_unit) that are useful for this sort of thing.
Hope that helps!
-Nathan
On Mon, Jun 19, 2017 at 7:38 PM, Stephanie Tonnesen <stonnes@gmail.com> wrote:
Hi yt-users!
I have what I think should be a relatively simple question. I am trying to make a 3D image of a region of a cosmological simulation, and plot points in the image. I define my region with box(left_edge,right_edge) where left_edge and right_edge are in code units. However, the points that I read in from an earlier file are in cgs units. Since the file was written using yt output, I would like to just let yt do the conversions, but nothing has units attached. I want the 3d image to get everything into the same units. I feel like there are a few ways I could fix this problem--1) tell yt that my points are in cgs units, 2) force the create_scene to be in cgs units, 3) get yt to tell me the conversion factor from code units to cgs units.
Unfortunately, I don't know how to do any of these things!
Can someone give me some advice on what to do here?
Thanks!
Stephanie
-- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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On Tue, Jun 20, 2017 at 1:00 AM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Tue, Jun 20, 2017 at 12:42 AM, Stephanie Tonnesen <stonnes@gmail.com> wrote:
Hi Nathan (and yt-users),
Thanks! Yes, arr_in_cm = ndarray_in_centimeters * cm
got yt to see that I was talking about cm.
The problem is that I still don't see the points. Is there any example of putting points on a volume rendering? I am trying to mix the "Volume Rendering with Lines" cookbook recipe with the PointSource api description, but am not sure what I am hoping my result will look like--for example, how big can I expect my points to be? Is that something I can set?
Yup:
http://yt-project.org/docs/dev/cookbook/complex_plots. html#volume-rendering-with-points
It looks like PontSource optionally takes either a scalar or ndarray of radii (one radius value for each point):
http://yt-project.org/docs/dev/reference/api/yt.visualization.volume_ rendering.render_source.html#yt.visualization.volume_ rendering.render_source.PointSource
And the radii must be given in pixels. I guess we should probably improve this API to handle units better.
Thanks,
Stephanie
-- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com
On Mon, Jun 19, 2017 at 5:48 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Stephanie,
If you have a loaded dataset, you can convert an ndarray that you know is in centimeters to a YTArray in code_length units like so:
arr_in_code_length = ds.arr(ndarray_in_centimeters, 'cm').to('code_length')
In addition, I don't think you actually need to convert to code_length units if you are passing this array to yt, since yt will internally do the conversion if you hand it a YTArray with units, so just creating an array like this is sufficient:
from yt.units import cm
arr_in_cm = ndarray_in_centimeters * cm
And then pass arr_in_cm to some yt function.
If all you want is the conversion factor from CGS to code length units, then you can inspect ds.length_unit. For example, the conversion from code length units to CGS is ds.length_unit.in_cgs(). There are a number of unit attributes that are attached to datasets (ds.mass_unit, ds.velocity_unit, ds.pressure_unit) that are useful for this sort of thing.
Hope that helps!
-Nathan
On Mon, Jun 19, 2017 at 7:38 PM, Stephanie Tonnesen <stonnes@gmail.com> wrote:
Hi yt-users!
I have what I think should be a relatively simple question. I am trying to make a 3D image of a region of a cosmological simulation, and plot points in the image. I define my region with box(left_edge,right_edge) where left_edge and right_edge are in code units. However, the points that I read in from an earlier file are in cgs units. Since the file was written using yt output, I would like to just let yt do the conversions, but nothing has units attached. I want the 3d image to get everything into the same units. I feel like there are a few ways I could fix this problem--1) tell yt that my points are in cgs units, 2) force the create_scene to be in cgs units, 3) get yt to tell me the conversion factor from code units to cgs units.
Unfortunately, I don't know how to do any of these things!
Can someone give me some advice on what to do here?
Thanks!
Stephanie
-- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Thanks for pointing all this out--I have no idea how I passed the points example straight to the lines example! I need to fiddle for a little while and see if I can get this to give me what I want. Thanks again! Stephanie -- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com On Mon, Jun 19, 2017 at 11:00 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Tue, Jun 20, 2017 at 1:00 AM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Tue, Jun 20, 2017 at 12:42 AM, Stephanie Tonnesen <stonnes@gmail.com> wrote:
Hi Nathan (and yt-users),
Thanks! Yes, arr_in_cm = ndarray_in_centimeters * cm
got yt to see that I was talking about cm.
The problem is that I still don't see the points. Is there any example of putting points on a volume rendering? I am trying to mix the "Volume Rendering with Lines" cookbook recipe with the PointSource api description, but am not sure what I am hoping my result will look like--for example, how big can I expect my points to be? Is that something I can set?
Yup:
http://yt-project.org/docs/dev/cookbook/complex_plots.html# volume-rendering-with-points
It looks like PontSource optionally takes either a scalar or ndarray of radii (one radius value for each point):
http://yt-project.org/docs/dev/reference/api/yt.visualizatio n.volume_rendering.render_source.html#yt.visualization. volume_rendering.render_source.PointSource
And the radii must be given in pixels. I guess we should probably improve this API to handle units better.
Thanks,
Stephanie
-- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com
On Mon, Jun 19, 2017 at 5:48 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Stephanie,
If you have a loaded dataset, you can convert an ndarray that you know is in centimeters to a YTArray in code_length units like so:
arr_in_code_length = ds.arr(ndarray_in_centimeters, 'cm').to('code_length')
In addition, I don't think you actually need to convert to code_length units if you are passing this array to yt, since yt will internally do the conversion if you hand it a YTArray with units, so just creating an array like this is sufficient:
from yt.units import cm
arr_in_cm = ndarray_in_centimeters * cm
And then pass arr_in_cm to some yt function.
If all you want is the conversion factor from CGS to code length units, then you can inspect ds.length_unit. For example, the conversion from code length units to CGS is ds.length_unit.in_cgs(). There are a number of unit attributes that are attached to datasets (ds.mass_unit, ds.velocity_unit, ds.pressure_unit) that are useful for this sort of thing.
Hope that helps!
-Nathan
On Mon, Jun 19, 2017 at 7:38 PM, Stephanie Tonnesen <stonnes@gmail.com> wrote:
Hi yt-users!
I have what I think should be a relatively simple question. I am trying to make a 3D image of a region of a cosmological simulation, and plot points in the image. I define my region with box(left_edge,right_edge) where left_edge and right_edge are in code units. However, the points that I read in from an earlier file are in cgs units. Since the file was written using yt output, I would like to just let yt do the conversions, but nothing has units attached. I want the 3d image to get everything into the same units. I feel like there are a few ways I could fix this problem--1) tell yt that my points are in cgs units, 2) force the create_scene to be in cgs units, 3) get yt to tell me the conversion factor from code units to cgs units.
Unfortunately, I don't know how to do any of these things!
Can someone give me some advice on what to do here?
Thanks!
Stephanie
-- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com
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participants (2)
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Nathan Goldbaum -
Stephanie Tonnesen