Mailman 3 August 2016 - yt-dev

Registration open for the Learn yt Workshop: Oct 10-12, 2016
by Nathan Goldbaum Sept. 20, 2016

Sept. 20, 2016

Hi all, Registration is now open for the Learn yt Workshop at the University of Illinois Urbana-Champaign, October 10-12, 2016. This workshop will introduce attendees to the yt project (yt-project.org), a python toolkit for the analysis and visualization of volumetric data. We have create a website for the workshop with more information: http://yt-project.org/workshop2016/ In addition, if you wold like to register for the workshop, please fill out this online form: https://goo.gl/forms/c6oIzNQywU1YWgOe2 The workshop will cover basic usage of yt, including the yt data model, yt's field system, low-level data inspection, basic visualization workflows, and data analysis and reduction tasks. We will also cover more advanced usages like generating simulated observations, halo finding and halo analysis, volume rendering, advanced 3D visualizations, and advanced data analysis and reduction tasks. Finally, we will cover how to modify and extend yt, as well as the development and contribution process. In addition, there will be time set aside for exploring data you bring to the workshop, along with opportunities to work directly with yt developers to load and explore your data. The workshop will take place at the National Center for Supercomputing Applications building on the north end of the UIUC campus. The NCSA building is about a block away from the conference hotel and is next door to a parking structure that offers metered all-day parking. There are a number of food trucks nearby, a university-run cafeteria about 2 blocks away, and a university business district with many good lunch restaurants about a half a mile away. We are planning to offer funding for hotel and travel for those requesting support. If you request funding, you will be notified of available funds by September 15. Travel awards will be made in the form of arranged lodging and airfare, with reservations being made by the conference organizers. We hope to see you there. On behalf of the organizing committee, Matt Turk Nathan Goldbaum Jill Naiman John ZuHone Kandace Turner

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Issue #1269: Add an interface for setting the background color of yt plots (yt_analysis/yt)
by Nathan Goldbaum Aug. 31, 2016

Aug. 31, 2016

New issue 1269: Add an interface for setting the background color of yt plots https://bitbucket.org/yt_analysis/yt/issues/1269/add-an-interface-for-setti… Nathan Goldbaum: This has come up several times on the mailing list recently. We should have a nicer, more obvious, documented interface for this. Some example solutions that work right now: https://gist.github.com/dcea5b6ede57b701f00df6089fc68b23 https://gist.github.com/98bd8fcca8da5331f056e0a8ee53fb97 http://stackoverflow.com/questions/38753964/sliceplot-for-bound-material-in…

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Issue #1268: enzo embedded parallel python/yt problem with gradient field (yt_analysis/yt)
by Bodo Schwabe Aug. 31, 2016

Aug. 31, 2016

New issue 1268: enzo embedded parallel python/yt problem with gradient field https://bitbucket.org/yt_analysis/yt/issues/1268/enzo-embedded-parallel-pyt… Bodo Schwabe: I currently try to run enzo with embedded parallelized python/yt (Version = 3.4-dev Changeset = c941aa457bc3 (yt) tip) with the following user_script.py < http://paste.yt-project.org/show/6794/ > . It works fine on a single processor (mpirun -n 1 ...) but gives me the following error message for multiple processors <http://paste.yt-project.org/show/6795/ > . Regular derived_fields are working well, but gradient_fields aren't. Thank you very much for any suggestions.

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Issue #1267: Profile datasets don't save profile.field_info dict data (yt_analysis/yt)
by Nathan Goldbaum Aug. 29, 2016

Aug. 29, 2016

New issue 1267: Profile datasets don't save profile.field_info dict data https://bitbucket.org/yt_analysis/yt/issues/1267/profile-datasets-dont-save Nathan Goldbaum: This is illustrated by the following script: ``` import yt ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030') ad = ds.all_data() prof = yt.create_profile(ad, [('gas', 'H_number_density'), ('gas', 'temperature')\ ], fields='cell_mass') print (prof.field_info) prof.save_as_dataset() prof_ds = yt.load('galaxy0030_Profile2D.h5') print (prof_ds.profile.field_info) plot = yt.PhasePlot(prof_ds.data, "H_number_density", "temperature", "cell_mass",\ weight_field=None) ``` On my machine this prints: ``` {('gas', 'temperature'): Alias Field for "('enzo', 'Temperature')" (gas, temperature): (units: K), ('gas', 'H_number_density'): Derived Field (gas, H_number_density): (units: cm**(-3)), ('gas', 'cell_mass'): Derived Field (gas, cell_mass): (units: g)} {} ``` And then crashes with the following traceback: ``` Traceback (most recent call last): File "test.py", line 11, in <module> weight_field=None) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/profile_plotter.py", line 745, in __init__ if isinstance(data_source.ds, YTProfileDataset): File "/Users/goldbaum/Documents/yt-hg/yt/visualization/profile_plotter.py", line 775, in _initialize_instance obj._setup_plots() File "/Users/goldbaum/Documents/yt-hg/yt/visualization/profile_plotter.py", line 856, in _setup_plots x_scale, y_scale, z_scale = self._get_field_log(f, self.profile) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/profile_plotter.py", line 815, in _get_field_log zfi = profile.field_info[field_z] KeyError: ('data', 'cell_mass') ``` @brittonsmith any chance you can take a look at this?

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Issue #1266: ds.add_gradient_fields not working properly on 2D data (yt_analysis/yt)
by Dominik Derigs Aug. 29, 2016

Aug. 29, 2016

New issue 1266: ds.add_gradient_fields not working properly on 2D data https://bitbucket.org/yt_analysis/yt/issues/1266/dsadd_gradient_fields-not-… Dominik Derigs: I want to plot the divergence of the magnetic field. For this, I think, the right approach is to use the function add_gradient_field. However, I have been unable to successfully generate any gradient field on my data (2D, FLASH). There is no suitable public dataset available that could be used to show my problem (2D, periodic, magnetic fields), so I uploaded an exemplary data file [here](https://hera.ph1.uni-koeln.de/~derigs/rotor_mhd_2d_hdf5_chk_0003_cleaning). MWE: ``` #!python import yt ds = yt.load("rotor_mhd_2d_hdf5_chk_0003_cleaning") slc = yt.SlicePlot(ds, 'z', ["pressure", "pressure_gradient_x", "pressure_gradient_y"]) slc.save() ``` **While the pressure plot is correct, the gradient plots are just empty.** pressure: ![rotor_mhd_2d_hdf5_chk_0003_cleaning_Slice_z_pressure.png](https://bitbucket.org/repo/BXbAb/images/2652892335-rotor_mhd_2d_hdf5_chk_0003_cleaning_Slice_z_pressure.png) pressure_gradient_x: ![rotor_mhd_2d_hdf5_chk_0003_cleaning_Slice_z_pressure_gradient_x.png](https://bitbucket.org/repo/BXbAb/images/4076349652-rotor_mhd_2d_hdf5_chk_0003_cleaning_Slice_z_pressure_gradient_x.png) pressure_gradient_y: ![rotor_mhd_2d_hdf5_chk_0003_cleaning_Slice_z_pressure_gradient_y.png](https://bitbucket.org/repo/BXbAb/images/1628325399-rotor_mhd_2d_hdf5_chk_0003_cleaning_Slice_z_pressure_gradient_y.png)

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Issue #1265: Helper functions for profiles need narrative docs (yt_analysis/yt)
by Kacper Kowalik Aug. 25, 2016

Aug. 25, 2016

New issue 1265: Helper functions for profiles need narrative docs https://bitbucket.org/yt_analysis/yt/issues/1265/helper-functions-for-profi… Kacper Kowalik: as per [comment](https://bitbucket.org/yt_analysis/yt/pull-requests/2332/implement-… Responsible: MatthewTurk

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Issue #1264: Ambiguity when converting between code units of two datasets (yt_analysis/yt)
by Nathan Goldbaum Aug. 24, 2016

Aug. 24, 2016

New issue 1264: Ambiguity when converting between code units of two datasets https://bitbucket.org/yt_analysis/yt/issues/1264/ambiguity-when-converting-… Nathan Goldbaum: This is illustrated by the following test script: ``` from yt.testing import fake_random_ds ds1 = fake_random_ds(32, length_unit=1) ds2 = fake_random_ds(32, length_unit=3) l1 = ds1.quan(0.3, 'unitary') l2 = ds2.quan(l1, 'unitary') print l1.in_cgs() print l2.in_cgs() print ds1.quan(0.3, 'unitary').in_cgs() print ds2.quan(0.3, 'unitary').in_cgs() ``` Right now this prints: ``` 0.9 cm 0.9 cm 0.3 cm 0.9 cm ``` I would expect it to print: ``` 0.3 cm 0.9 cm 0.3 cm 0.9 cm ``` I noticed @brittonsmith was working around this, but I don't think it should be necessary to do that. Responsible: ngoldbaum

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Website
by Matthew Turk Aug. 22, 2016

Aug. 22, 2016

Hi folks, A while ago, yt-project.org was converted to a "generated" site. Templates are used to generate each page, so it's much easier to modify. I've also moved the calculation of contributors into a function, and the gallery and the members list are in .yaml files, so they can be updated without writing raw HTML. I took some time this week to experiment a bit with the website. My fork is here: https://bitbucket.org/MatthewTurk/yt.website and a build is here: http://matt-website.hub.yt/ The big changes: * Light instead of dark background ("cyborg" theme to "flatly") * Made the text more normal-sized most places * Changed the masthead on the front page to *not* be a carousel and have the new logo, along with a more punchy intro * Added a set of "examples", which come from a .yaml file. I've been experimenting with the examples and the theme in particular, and I personally like it a lot more. If you fork my repo and make changes (especially if you want to add examples, which can take *either* text output *or* images) as soon as the changes go in, it auto-builds on matt-website.hub.yt . Feedback here or on slack would be very much appreciated, and if folks like it, I'd like to deploy it. A few other things it would need before it's ready: * Add an extensions page, with extension information drawn from .yaml file * Make the blog look like this thing, and maybe figure out if the blog could be part of the repo * Update the text and images wherever appropriate (i.e., update references to the hub) * Streamline navigation a little bit * Fill out the examples, maybe even have them link to the hub -Matt

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Favorite couple-line script?
by Matthew Turk Aug. 22, 2016

Aug. 22, 2016

Hi folks, I'm updating the website with examples (see the thread from last week about this) and I wanted to publicly ask for your favorite examples of doing or making something cool in yt with just a few lines. Especially if it's something pretty cool or special, it'd be great to include. Reply to me off list and I'll add them to the examples! Thanks, Matt

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PR review hangout
by Nathan Goldbaum Aug. 22, 2016

Aug. 22, 2016

Hi all, Let's have a PR review hangout this week. I've scheduled it for Wednesday at 1:00 PM CDT: https://plus.google.com/b/107728486871834552760/events/c3npc7tguf2ar4ve6rr5… -Nathan

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