Field extraction from arbitrary grids
Dear yt-users, I am trying to extract a unigrid data cube within a specific region and specified dimensions, thus I am using arbitrary_grid(), however, beyond the example given in the docs <http://yt-project.org/doc/analyzing/objects.html#arbitrary-grid>, my field extractions all fail. I would like to extract temperature, HI_Density and HII_Density. Here is a snippet from my code: obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256]) print(obj["deposit", "all_density"]) print(obj["temperature"]) print(obj["HI_Density"]) The line print(obj["deposit", "all_density"]) works, but the two lines after both fail. Here is the traceback from the temperature <https://pastebin.com/BusfAeKh>, and I even tried out deposited temperature <https://pastebin.com/me9uKMHP> and deposited HI_Density <https://pastebin.com/BxPJj7B0>. Am I formatting this incorrectly, or is there a different way to extract the fields? Kind regards, Carla Bernhardt PhD Student ZAH Institut für Theoretische Astrophysik Universität Heidelberg
Hi Carla, Interesting. It's possible, for the call to "temperature" (which raises NotImplementedError) that the version of yt you're on doesn't yet support mesh fields in arbitrary grids; that was added reasonably recently. For the others, I'm not totally sure why it's breaking -- which version of yt are you using, and what type of data? It may just be that they aren't deposit fields. In that case, try explicitly stating obj["gas","temperature"] or obj["gas","HI_Density"]. It may also be that the aliasing is getting in the way, in which case instead of "HI_Density" you might need to try "Hp0_density". On Tue, Jul 11, 2017 at 5:42 AM, Carla Bernhardt <carla.j.bernhardt@gmail.com> wrote:
Dear yt-users,
I am trying to extract a unigrid data cube within a specific region and specified dimensions, thus I am using arbitrary_grid(), however, beyond the example given in the docs, my field extractions all fail. I would like to extract temperature, HI_Density and HII_Density. Here is a snippet from my code:
obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256]) print(obj["deposit", "all_density"]) print(obj["temperature"]) print(obj["HI_Density"])
The line print(obj["deposit", "all_density"]) works, but the two lines after both fail. Here is the traceback from the temperature, and I even tried out deposited temperature and deposited HI_Density. Am I formatting this incorrectly, or is there a different way to extract the fields?
Kind regards, Carla Bernhardt PhD Student ZAH Institut für Theoretische Astrophysik Universität Heidelberg
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Hi Matthew, Thank you for your reply. I was using yt Version 3.2.3 and am working out some installation issues on our server with version 3.3.5. As for the type of data, I have an enzo simulation with static nested grids as well as up to 6 levels AMR grids. I will have to get back to you once I get past the issues with the newest installation of yt.... Thanks for the initial pointers. Cheers, Carla 2017-07-11 14:15 GMT+02:00 Matthew Turk <matthewturk@gmail.com>:
Hi Carla,
Interesting. It's possible, for the call to "temperature" (which raises NotImplementedError) that the version of yt you're on doesn't yet support mesh fields in arbitrary grids; that was added reasonably recently. For the others, I'm not totally sure why it's breaking -- which version of yt are you using, and what type of data? It may just be that they aren't deposit fields. In that case, try explicitly stating obj["gas","temperature"] or obj["gas","HI_Density"]. It may also be that the aliasing is getting in the way, in which case instead of "HI_Density" you might need to try "Hp0_density".
Dear yt-users,
I am trying to extract a unigrid data cube within a specific region and specified dimensions, thus I am using arbitrary_grid(), however, beyond
On Tue, Jul 11, 2017 at 5:42 AM, Carla Bernhardt <carla.j.bernhardt@gmail.com> wrote: the
example given in the docs, my field extractions all fail. I would like to extract temperature, HI_Density and HII_Density. Here is a snippet from my code:
obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256]) print(obj["deposit", "all_density"]) print(obj["temperature"]) print(obj["HI_Density"])
The line print(obj["deposit", "all_density"]) works, but the two lines after both fail. Here is the traceback from the temperature, and I even tried out deposited temperature and deposited HI_Density. Am I formatting this incorrectly, or is there a different way to extract the fields?
Kind regards, Carla Bernhardt PhD Student ZAH Institut für Theoretische Astrophysik Universität Heidelberg
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Hi yt-users, I was able to get the arbitrary grid working by updating yt to the newest version. I am quite confused, however, by the output. If I extract my arbitrary grid: obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256]) and extract the desired fields: temp = obj["temperature"] HIdens = obj["HI_Density"] (which all works successfully), I then want to write this to a file and would expect that such a file would have 256^3 = 16777216 lines, but I not only don't get this number of lines for my outputs, I even get different number of lines for different fields. Here is the part of my code <https://pastebin.com/REcRd2u0> that writes the file. Ideas? Thanks in advance. Cheers, Carla 2017-07-12 12:35 GMT+02:00 Carla Bernhardt <carla.j.bernhardt@gmail.com>:
Hi Matthew,
Thank you for your reply. I was using yt Version 3.2.3 and am working out some installation issues on our server with version 3.3.5. As for the type of data, I have an enzo simulation with static nested grids as well as up to 6 levels AMR grids. I will have to get back to you once I get past the issues with the newest installation of yt.... Thanks for the initial pointers.
Cheers, Carla
2017-07-11 14:15 GMT+02:00 Matthew Turk <matthewturk@gmail.com>:
Hi Carla,
Interesting. It's possible, for the call to "temperature" (which raises NotImplementedError) that the version of yt you're on doesn't yet support mesh fields in arbitrary grids; that was added reasonably recently. For the others, I'm not totally sure why it's breaking -- which version of yt are you using, and what type of data? It may just be that they aren't deposit fields. In that case, try explicitly stating obj["gas","temperature"] or obj["gas","HI_Density"]. It may also be that the aliasing is getting in the way, in which case instead of "HI_Density" you might need to try "Hp0_density".
Dear yt-users,
I am trying to extract a unigrid data cube within a specific region and specified dimensions, thus I am using arbitrary_grid(), however, beyond
On Tue, Jul 11, 2017 at 5:42 AM, Carla Bernhardt <carla.j.bernhardt@gmail.com> wrote: the
example given in the docs, my field extractions all fail. I would like to extract temperature, HI_Density and HII_Density. Here is a snippet from my code:
obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256]) print(obj["deposit", "all_density"]) print(obj["temperature"]) print(obj["HI_Density"])
The line print(obj["deposit", "all_density"]) works, but the two lines after both fail. Here is the traceback from the temperature, and I even tried out deposited temperature and deposited HI_Density. Am I formatting this incorrectly, or is there a different way to extract the fields?
Kind regards, Carla Bernhardt PhD Student ZAH Institut für Theoretische Astrophysik Universität Heidelberg
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Hi Carla, It's possible that it's writing out the particle values. If you explicitly ask for ["gas", "temperature"] it may write that value out. You can control how the values are deposited on the grid by specifying smoothed, deposited, etc fields. On Thu, Jul 20, 2017 at 5:03 AM, Carla Bernhardt <carla.j.bernhardt@gmail.com> wrote:
Hi yt-users,
I was able to get the arbitrary grid working by updating yt to the newest version. I am quite confused, however, by the output. If I extract my arbitrary grid:
obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256])
and extract the desired fields:
temp = obj["temperature"] HIdens = obj["HI_Density"]
(which all works successfully), I then want to write this to a file and would expect that such a file would have 256^3 = 16777216 lines, but I not only don't get this number of lines for my outputs, I even get different number of lines for different fields. Here is the part of my code that writes the file. Ideas? Thanks in advance.
Cheers, Carla
2017-07-12 12:35 GMT+02:00 Carla Bernhardt <carla.j.bernhardt@gmail.com>:
Hi Matthew,
Thank you for your reply. I was using yt Version 3.2.3 and am working out some installation issues on our server with version 3.3.5. As for the type of data, I have an enzo simulation with static nested grids as well as up to 6 levels AMR grids. I will have to get back to you once I get past the issues with the newest installation of yt.... Thanks for the initial pointers.
Cheers, Carla
2017-07-11 14:15 GMT+02:00 Matthew Turk <matthewturk@gmail.com>:
Hi Carla,
Interesting. It's possible, for the call to "temperature" (which raises NotImplementedError) that the version of yt you're on doesn't yet support mesh fields in arbitrary grids; that was added reasonably recently. For the others, I'm not totally sure why it's breaking -- which version of yt are you using, and what type of data? It may just be that they aren't deposit fields. In that case, try explicitly stating obj["gas","temperature"] or obj["gas","HI_Density"]. It may also be that the aliasing is getting in the way, in which case instead of "HI_Density" you might need to try "Hp0_density".
On Tue, Jul 11, 2017 at 5:42 AM, Carla Bernhardt <carla.j.bernhardt@gmail.com> wrote:
Dear yt-users,
I am trying to extract a unigrid data cube within a specific region and specified dimensions, thus I am using arbitrary_grid(), however, beyond the example given in the docs, my field extractions all fail. I would like to extract temperature, HI_Density and HII_Density. Here is a snippet from my code:
obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256]) print(obj["deposit", "all_density"]) print(obj["temperature"]) print(obj["HI_Density"])
The line print(obj["deposit", "all_density"]) works, but the two lines after both fail. Here is the traceback from the temperature, and I even tried out deposited temperature and deposited HI_Density. Am I formatting this incorrectly, or is there a different way to extract the fields?
Kind regards, Carla Bernhardt PhD Student ZAH Institut für Theoretische Astrophysik Universität Heidelberg
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Hi Matthew, Thank you for the suggestion. That works much better for the temperature field. I also need, however, HI_Density and HII_Density and these do not seem to be within the "gas" (here is the Traceback <https://pastebin.com/CKHsXDd5> from when I try that). This is the field list <https://pastebin.com/44ZtK8JU> from my data, do you have any suggestions for how I could also extract the HI_Density and HII_Density successfully? Thanks, Carla 2017-07-20 16:38 GMT+02:00 Matthew Turk <matthewturk@gmail.com>:
Hi Carla,
It's possible that it's writing out the particle values. If you explicitly ask for ["gas", "temperature"] it may write that value out. You can control how the values are deposited on the grid by specifying smoothed, deposited, etc fields.
Hi yt-users,
I was able to get the arbitrary grid working by updating yt to the newest version. I am quite confused, however, by the output. If I extract my arbitrary grid:
obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256])
and extract the desired fields:
temp = obj["temperature"] HIdens = obj["HI_Density"]
(which all works successfully), I then want to write this to a file and would expect that such a file would have 256^3 = 16777216 lines, but I not only don't get this number of lines for my outputs, I even get different number of lines for different fields. Here is the part of my code that writes the file. Ideas? Thanks in advance.
Cheers, Carla
2017-07-12 12:35 GMT+02:00 Carla Bernhardt <carla.j.bernhardt@gmail.com :
Hi Matthew,
Thank you for your reply. I was using yt Version 3.2.3 and am working
out
some installation issues on our server with version 3.3.5. As for the type of data, I have an enzo simulation with static nested grids as well as up to 6 levels AMR grids. I will have to get back to you once I get past the issues with the newest installation of yt.... Thanks for the initial pointers.
Cheers, Carla
2017-07-11 14:15 GMT+02:00 Matthew Turk <matthewturk@gmail.com>:
Hi Carla,
Interesting. It's possible, for the call to "temperature" (which raises NotImplementedError) that the version of yt you're on doesn't yet support mesh fields in arbitrary grids; that was added reasonably recently. For the others, I'm not totally sure why it's breaking -- which version of yt are you using, and what type of data? It may just be that they aren't deposit fields. In that case, try explicitly stating obj["gas","temperature"] or obj["gas","HI_Density"]. It may also be that the aliasing is getting in the way, in which case instead of "HI_Density" you might need to try "Hp0_density".
On Tue, Jul 11, 2017 at 5:42 AM, Carla Bernhardt <carla.j.bernhardt@gmail.com> wrote:
Dear yt-users,
I am trying to extract a unigrid data cube within a specific region
and
specified dimensions, thus I am using arbitrary_grid(), however, beyond the example given in the docs, my field extractions all fail. I would
to extract temperature, HI_Density and HII_Density. Here is a snippet from my code:
obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256]) print(obj["deposit", "all_density"]) print(obj["temperature"]) print(obj["HI_Density"])
The line print(obj["deposit", "all_density"]) works, but the two
after both fail. Here is the traceback from the temperature, and I even
On Thu, Jul 20, 2017 at 5:03 AM, Carla Bernhardt <carla.j.bernhardt@gmail.com> wrote: like lines tried
out deposited temperature and deposited HI_Density. Am I formatting this incorrectly, or is there a different way to extract the fields?
Kind regards, Carla Bernhardt PhD Student ZAH Institut für Theoretische Astrophysik Universität Heidelberg
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Hi Carla, You could use the ('enzo', 'HI_Density') and ('enzo', 'HII_Density') fields. The reasons there aren't 'gas' fields for those field names is that yt has a different internal naming convention for species fields. If you take a look at ds.derived_field_list, I bet you have ('gas', 'H_p0_density') and ('gas', 'H_p1_density') fields. These are the "universal" alias fields for the Enzo fields you are looking for. -Nathan On Fri, Jul 21, 2017 at 6:13 AM Carla Bernhardt <carla.j.bernhardt@gmail.com> wrote:
Hi Matthew,
Thank you for the suggestion. That works much better for the temperature field. I also need, however, HI_Density and HII_Density and these do not seem to be within the "gas" (here is the Traceback <https://pastebin.com/CKHsXDd5> from when I try that). This is the field list <https://pastebin.com/44ZtK8JU> from my data, do you have any suggestions for how I could also extract the HI_Density and HII_Density successfully?
Thanks, Carla
2017-07-20 16:38 GMT+02:00 Matthew Turk <matthewturk@gmail.com>:
Hi Carla,
It's possible that it's writing out the particle values. If you explicitly ask for ["gas", "temperature"] it may write that value out. You can control how the values are deposited on the grid by specifying smoothed, deposited, etc fields.
Hi yt-users,
I was able to get the arbitrary grid working by updating yt to the newest version. I am quite confused, however, by the output. If I extract my arbitrary grid:
obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256])
and extract the desired fields:
temp = obj["temperature"] HIdens = obj["HI_Density"]
(which all works successfully), I then want to write this to a file and would expect that such a file would have 256^3 = 16777216 lines, but I not only don't get this number of lines for my outputs, I even get different number of lines for different fields. Here is the part of my code that writes the file. Ideas? Thanks in advance.
Cheers, Carla
2017-07-12 12:35 GMT+02:00 Carla Bernhardt <carla.j.bernhardt@gmail.com :
Hi Matthew,
Thank you for your reply. I was using yt Version 3.2.3 and am working
out
some installation issues on our server with version 3.3.5. As for the type of data, I have an enzo simulation with static nested grids as well as up to 6 levels AMR grids. I will have to get back to you once I get past the issues with the newest installation of yt.... Thanks for the initial pointers.
Cheers, Carla
2017-07-11 14:15 GMT+02:00 Matthew Turk <matthewturk@gmail.com>:
Hi Carla,
Interesting. It's possible, for the call to "temperature" (which raises NotImplementedError) that the version of yt you're on doesn't yet support mesh fields in arbitrary grids; that was added reasonably recently. For the others, I'm not totally sure why it's breaking -- which version of yt are you using, and what type of data? It may just be that they aren't deposit fields. In that case, try explicitly stating obj["gas","temperature"] or obj["gas","HI_Density"]. It may also be that the aliasing is getting in the way, in which case instead of "HI_Density" you might need to try "Hp0_density".
On Tue, Jul 11, 2017 at 5:42 AM, Carla Bernhardt <carla.j.bernhardt@gmail.com> wrote:
Dear yt-users,
I am trying to extract a unigrid data cube within a specific region
and
specified dimensions, thus I am using arbitrary_grid(), however, beyond the example given in the docs, my field extractions all fail. I would
to extract temperature, HI_Density and HII_Density. Here is a snippet from my code:
obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256]) print(obj["deposit", "all_density"]) print(obj["temperature"]) print(obj["HI_Density"])
The line print(obj["deposit", "all_density"]) works, but the two
after both fail. Here is the traceback from the temperature, and I even
On Thu, Jul 20, 2017 at 5:03 AM, Carla Bernhardt <carla.j.bernhardt@gmail.com> wrote: like lines tried
out deposited temperature and deposited HI_Density. Am I formatting this incorrectly, or is there a different way to extract the fields?
Kind regards, Carla Bernhardt PhD Student ZAH Institut für Theoretische Astrophysik Universität Heidelberg
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Hi Nathan, Now that you mention it, it seems so obvious! Thank you for helping me out. That seems to work just fine. Cheers, Carla 2017-07-21 16:13 GMT+02:00 Nathan Goldbaum <nathan12343@gmail.com>:
Hi Carla,
You could use the ('enzo', 'HI_Density') and ('enzo', 'HII_Density') fields.
The reasons there aren't 'gas' fields for those field names is that yt has a different internal naming convention for species fields. If you take a look at ds.derived_field_list, I bet you have ('gas', 'H_p0_density') and ('gas', 'H_p1_density') fields. These are the "universal" alias fields for the Enzo fields you are looking for.
-Nathan
On Fri, Jul 21, 2017 at 6:13 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Hi Matthew,
Thank you for the suggestion. That works much better for the temperature field. I also need, however, HI_Density and HII_Density and these do not seem to be within the "gas" (here is the Traceback <https://pastebin.com/CKHsXDd5> from when I try that). This is the field list <https://pastebin.com/44ZtK8JU> from my data, do you have any suggestions for how I could also extract the HI_Density and HII_Density successfully?
Thanks, Carla
2017-07-20 16:38 GMT+02:00 Matthew Turk <matthewturk@gmail.com>:
Hi Carla,
It's possible that it's writing out the particle values. If you explicitly ask for ["gas", "temperature"] it may write that value out. You can control how the values are deposited on the grid by specifying smoothed, deposited, etc fields.
Hi yt-users,
I was able to get the arbitrary grid working by updating yt to the newest version. I am quite confused, however, by the output. If I extract my arbitrary grid:
obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256])
and extract the desired fields:
temp = obj["temperature"] HIdens = obj["HI_Density"]
(which all works successfully), I then want to write this to a file and would expect that such a file would have 256^3 = 16777216 lines, but I not only don't get this number of lines for my outputs, I even get different number of lines for different fields. Here is the part of my code that writes the file. Ideas? Thanks in advance.
Cheers, Carla
2017-07-12 12:35 GMT+02:00 Carla Bernhardt < carla.j.bernhardt@gmail.com>:
Hi Matthew,
Thank you for your reply. I was using yt Version 3.2.3 and am working
out
some installation issues on our server with version 3.3.5. As for the type of data, I have an enzo simulation with static nested grids as well as up to 6 levels AMR grids. I will have to get back to you once I get past the issues with the newest installation of yt.... Thanks for the initial pointers.
Cheers, Carla
2017-07-11 14:15 GMT+02:00 Matthew Turk <matthewturk@gmail.com>:
Hi Carla,
Interesting. It's possible, for the call to "temperature" (which raises NotImplementedError) that the version of yt you're on doesn't yet support mesh fields in arbitrary grids; that was added reasonably recently. For the others, I'm not totally sure why it's breaking -- which version of yt are you using, and what type of data? It may
just
be that they aren't deposit fields. In that case, try explicitly stating obj["gas","temperature"] or obj["gas","HI_Density"]. It may also be that the aliasing is getting in the way, in which case instead of "HI_Density" you might need to try "Hp0_density".
On Tue, Jul 11, 2017 at 5:42 AM, Carla Bernhardt <carla.j.bernhardt@gmail.com> wrote: > Dear yt-users, > > I am trying to extract a unigrid data cube within a specific region and > specified dimensions, thus I am using arbitrary_grid(), however, beyond > the > example given in the docs, my field extractions all fail. I would
> to > extract temperature, HI_Density and HII_Density. Here is a snippet from > my > code: > > obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256]) > print(obj["deposit", "all_density"]) > print(obj["temperature"]) > print(obj["HI_Density"]) > > The line print(obj["deposit", "all_density"]) works, but the two
> after > both fail. Here is the traceback from the temperature, and I even
> out > deposited temperature and deposited HI_Density. Am I formatting
On Thu, Jul 20, 2017 at 5:03 AM, Carla Bernhardt <carla.j.bernhardt@gmail.com> wrote: like lines tried this
> incorrectly, or is there a different way to extract the fields? > > Kind regards, > Carla Bernhardt > PhD Student > ZAH Institut für Theoretische Astrophysik > Universität Heidelberg > > _______________________________________________ > 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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participants (3)
-
Carla Bernhardt -
Matthew Turk -
Nathan Goldbaum