Thanks Matthew for your reply, the general problem of doing that is that the 'data' structure can point to arrays of 1, 2 or 3 dimensions, so it's difficult to loop over it. I ended up solving the problem in a better way: I switched to a scipy RectBivariateSpline interpolator, rather than a simpler interp2d object. Now I no more need to loop on the single elements, and can pass the full arrays. To get the numerical array, now I could simply use data['mydata'].value (I had to reshape it to a 1D array, but that was easy). Thank you anyway! Best, On Wed, Jul 12, 2017 at 6:14 PM, wrote:

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Today's Topics:

1. Re: accessing single elements of data when defining a new field (Matthew Turk) 2. Re: IO error (Britton Smith) 3. Re: Field extraction from arbitrary grids (Carla Bernhardt) 4. 3-D Mass power spectra (???) 5. Re: 3-D Mass power spectra (Nathan Goldbaum)

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Message: 1 Date: Tue, 11 Jul 2017 07:16:20 -0500 From: Matthew Turk To: Discussion of the yt analysis package Subject: Re: [yt-users] accessing single elements of data when defining a new field Message-ID: Content-Type: text/plain; charset="UTF-8"

Hi Salvatore,

This is odd -- I believe that it should work as you have written it. Can you describe how it fails? And, what happens if instead of doing

for ii in range(0, len(t)):

you did something like:

for val in t:

and then operated on val?

On Tue, Jul 11, 2017 at 4:59 AM, sacielo wrote:

...

Hello

I am trying to define a new field for a grid simulation (using ramses, if it matters), basically an estimate of radiative cooling in a simulation that does not include that.

I find myself to perform a 2D interpolation in a table (cooling rate given temperature and metal content), then I wish to save this as a new field. I am using a scipy 2D interpolator in order to do so. The problem is that for the interpolation I need to access the single elements in the temperature and metal fields, within the function I use to define a new dataset (unfortunately, I am forced to loop on the fields).

Now, I can't understand how to do that from the "data" and "field" arguments of the functions.

Something like t = data['temperature'] for ii in range(0, len(t)): print t[ii]

fails (t[ii] is a complex array itself)

t.base() and t.item() or t[ii].item()

fail as well....

Any idea?

Thank you!

-- Salvatore

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Message: 2 Date: Tue, 11 Jul 2017 11:09:12 -0700 From: Britton Smith To: Discussion of the yt analysis package Subject: Re: [yt-users] IO error Message-ID: Content-Type: text/plain; charset="utf-8"

Hi everyone,

I just wanted to provide some resolution to this issue. The issue had to do with some problems that have cropped up when trying to read hdf5 string attributes in Python 3. You wouldn't see this if you were still using Python 2. This has been resolved with the following pull request, which has already been accepted: https://github.com/yt-project/yt/pull/1487

Britton

On Mon, Jul 10, 2017 at 1:13 PM, Britton Smith wrote:

...

Hi Nick,

This is a bit puzzling since I think there have been relatively few changes to the halo catalog frontend responsible for loading that data. That said, I would be more than happy to take a look as I am responsible for much of this code. Would you be able to share either 1) this dataset that is failing to load or 2) a script that uses example data that I can run to reproduce this?

Britton

On Mon, Jul 10, 2017 at 8:53 AM, Nick Gnedin wrote:

...

Folks,

I have encountered a bizarre IO error. I am reading a file previously created by yt HOP halo finder on two separate machines. The file reads correctly on the machine it was created on, but on another machine with

the

...

most recent anaconda install (yt 3.3.5) the format is not recognized. Both machines are little endian. Is there any way to get more info on what yt does not like about that file?

yt : [ERROR ] 2017-07-10 10:46:00,454 Couldn't figure out output type for hop.0.h5 Traceback (most recent call last): File "hmf.py", line 14, in <module> Plot("hop.0.h5",color="b") File "hmf.py", line 8, in Plot my_halos = load(file) File "/ext/anaconda3/lib/python3.6/site-packages/yt/convenience.py", line 98, in load raise YTOutputNotIdentified(args, kwargs) yt.utilities.exceptions.YTOutputNotIdentified: Supplied ('hop.0.h5',) {}, but could not load!

Here is the script (taken form your examples):

import yt from yt.mods import * from yt.analysis_modules.halo_mass_function.api import * import matplotlib.pyplot as plt

def Plot(file,color="r"): my_halos = load(file) hmf = HaloMassFcn(halos_ds=my_halos) plt.loglog(hmf.masses_analytic, hmf.n_cumulative_analytic,colo r="orange",linewidth=3) plt.loglog(hmf.masses_sim, hmf.n_cumulative_sim,color=col or,linewidth=3)

Plot("hop.0.h5",color="b")

Thank you for your advice,

Nick Gnedin _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Message: 3 Date: Wed, 12 Jul 2017 12:35:14 +0200 From: Carla Bernhardt To: Discussion of the yt analysis package Subject: Re: [yt-users] Field extraction from arbitrary grids Message-ID: Content-Type: text/plain; charset="utf-8"

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 :

...

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 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 f?r Theoretische Astrophysik Universit?t Heidelberg

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Message: 4 Date: Thu, 13 Jul 2017 00:10:02 +0800 From: ??? To: Discussion of the yt analysis package Subject: [yt-users] 3-D Mass power spectra Message-ID: Content-Type: text/plain; charset="utf-8"

Dear yt

Can current yt calculate 3-D Mass power spectra? I checked the website but I didn't find any information. I think calculating 3-D Mass power spectra is a very useful for cosmological simulations. So I guess maybe yt supports this function now....?

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Message: 5 Date: Wed, 12 Jul 2017 11:13:50 -0500 From: Nathan Goldbaum To: Discussion of the yt analysis package Subject: Re: [yt-users] 3-D Mass power spectra Message-ID: Content-Type: text/plain; charset="utf-8"

We have an example in our docs that shows how to create a kinetic energy power spectrum with the numpy FFT:

http://yt-project.org/doc/cookbook/calculating_information.html#making-a- turbulent-kinetic-energy-power-spectrum

I think this could be adapted for your needs.

Right now there isn't an analysis routine explicitly for computing power spectra in yt. If someone wanted to add it (or just wanted to add more examples to the docs of how to compute power spectra using e.g. pyfftw) I think that would be a very welcome contribution.

-Nathan

On Wed, Jul 12, 2017 at 11:10 AM, ??? wrote:

...

Dear yt

Can current yt calculate 3-D Mass power spectra? I checked the website but I didn't find any information. I think calculating 3-D Mass power spectra is a very useful for cosmological simulations. So I guess maybe yt supports this function now....?

Thanks in advance

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End of yt-users Digest, Vol 113, Issue 17 *****************************************

-- Salvatore