Mailman 3 November 2014 - yt-dev

yt Community Survey
by Cameron Hummels 08 Dec '14

08 Dec '14

Fellow yt users: We at the yt development team want to make yt better for you, the user. We have prepared a short survey to gain your valuable feedback to help us understand what is working in yt and what is not. Could you please spare 2 minutes to fill out our survey below? We plan to collect responses and make available a selection of results by December 10, so please let us know what you think at the following URL: http://goo.gl/forms/hRNryOWTPO On behalf of the yt development team, Cameron -- Cameron Hummels Postdoctoral Researcher Steward Observatory University of Arizona http://chummels.org

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Issue #946: Covering grid doesn't set "center" field parameter (yt_analysis/yt)
by Kacper Kowalik 30 Nov '14

30 Nov '14

New issue 946: Covering grid doesn't set "center" field parameter https://bitbucket.org/yt_analysis/yt/issue/946/covering-grid-doesnt-set-cen… Kacper Kowalik: This simple script: ``` #!python import yt ds = yt.load("Sedov_3d/sedov_hdf5_chk_0003") data = ds.covering_grid(1, left_edge=ds.domain_left_edge, dims=[32,32,32]) data["radial_velocity"] ``` yields rather confusing traceback: ``` #!text Traceback (most recent call last): File "bug.py", line 4, in <module> data["radial_velocity"] File "yt/src/yt-my/yt/data_objects/data_containers.py", line 249, in __getitem__ self.get_data(f) File "yt/src/yt-my/yt/data_objects/construction_data_containers.py", line 531, in get_data if len(gen) > 0: self._generate_fields(gen) File "yt/src/yt-my/yt/data_objects/data_containers.py", line 719, in _generate_fields fd = self._generate_field(field) File "yt/src/yt-my/yt/data_objects/data_containers.py", line 286, in _generate_field tr = self._generate_fluid_field(field) File "yt/src/yt-my/yt/data_objects/data_containers.py", line 306, in _generate_fluid_field rv = finfo(gen_obj) File "yt/src/yt-my/yt/fields/derived_field.py", line 184, in __call__ dd = self._function(self, data) File "yt/src/yt-my/yt/fields/vector_operations.py", line 109, in _radial theta = data['index', 'spherical_theta'] File "yt/src/yt-my/yt/data_objects/data_containers.py", line 249, in __getitem__ self.get_data(f) File "yt/src/yt-my/yt/data_objects/construction_data_containers.py", line 531, in get_data if len(gen) > 0: self._generate_fields(gen) File "yt/src/yt-my/yt/data_objects/data_containers.py", line 719, in _generate_fields fd = self._generate_field(field) File "yt/src/yt-my/yt/data_objects/data_containers.py", line 286, in _generate_field tr = self._generate_fluid_field(field) File "yt/src/yt-my/yt/data_objects/data_containers.py", line 306, in _generate_fluid_field rv = finfo(gen_obj) File "yt/src/yt-my/yt/fields/derived_field.py", line 184, in __call__ dd = self._function(self, data) File "yt/src/yt-my/yt/fields/geometric_fields.py", line 104, in _spherical_theta coords = get_periodic_rvec(data) File "yt/src/yt-my/yt/fields/field_functions.py", line 51, in get_periodic_rvec coords = obtain_rvec(data) File "yt/utilities/lib/geometry_utils.pyx", line 89, in yt.utilities.lib.geometry_utils.obtain_rvec (yt/utilities/lib/geometry_utils.c:2228) TypeError: 'NoneType' object has no attribute '__getitem__' ``` `covering_grid` should either set sane default for *center* or fields using `ValidateParameter()` should catch this earlier and more gracefully.

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Issue #945: Adding multiple sets of annotations to a slice is slow (yt_analysis/yt)
by Daniel Fenn 29 Nov '14

29 Nov '14

New issue 945: Adding multiple sets of annotations to a slice is slow https://bitbucket.org/yt_analysis/yt/issue/945/adding-multiple-sets-of-anno… Daniel Fenn: If I open a large dataset and create a slice, then add density contours, followed by text annotations, the text annotations take a very long time to add. If I add the text annotations before adding the contours, it's much faster. If I add multiple sets of density contours, each set takes progressively longer. Nathan Goldbaum has suggested that implementing caching would alleviate the issue. Responsible: yt_analysis

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Issue #944: Slices of fields that need ghost zones are slow for patch AMR data (yt_analysis/yt)
by Nathan Goldbaum 27 Nov '14

27 Nov '14

New issue 944: Slices of fields that need ghost zones are slow for patch AMR data https://bitbucket.org/yt_analysis/yt/issue/944/slices-of-fields-that-need-g… Nathan Goldbaum: On my laptop, the following script: ``` #!python import yt import time def test(field): slc = yt.SlicePlot(ds, 2, field) if __name__ == "__main__": ds = yt.load("GasSloshing/sloshing_nomag2_hdf5_plt_cnt_0150") ds.periodicity = (True, True, True) setup = "from __main__ import test" t0 = time.time() test('density') tden = time.time() - t0 t0 = time.time() test('velocity_divergence') tdiv = time.time() - t0 print tden, tdiv ``` shows that it takes about 3.5 seconds to do the density slice and 63 seconds to do the velocity_divergence slice.

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prettying up the field list
by Michael Zingale 26 Nov '14

26 Nov '14

I've been looking over the field list: http://yt-project.org/docs/dev/reference/field_list.html#field-list At the bottom of that page, we list the fields specific to each frontend/code. I'd like to make the presentation for each frontend a table, with columns for the name, units, what its aliases to, and whether it is a particle -- these are what we currently list, and perhaps show the display name. Showing it as a table for each frontend would be more compact than the list, and I think it would be clearer for people to read. Before I hack the script that writes that page, I wanted to see if there are any objections. Also, a minor point, there is a _dynamical_time() field which I assume is the free-fall timescale assuming uniform density throughout the collapse. I've always seen a '32' not '16' in the denominator (see, e.g. Carroll & Ostlie, Eq. 12.26 or Kippenhahn & Weigert Eq. 27.10). -- Michael Zingale Associate Professor Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale(a)stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale

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PlotWindow show() outside of notebook
by John ZuHone 25 Nov '14

25 Nov '14

Hi gang, I got an inquiry about using the PlotWindow plot show() method outside of the notebook. How hard would it be to extend this to other matplotlib backends, so that a window pops up on the screen when you want to see a plot, but aren't in the notebook? Obviously matplotlib does this already, so it's a matter of figuring out how to get it hooked up. Best, John Z Sent from John ZuHone's iPad

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Issue #943: Derived fields not properly recognized in create profile (yt_analysis/yt)
by Hilary Egan 24 Nov '14

24 Nov '14

New issue 943: Derived fields not properly recognized in create profile https://bitbucket.org/yt_analysis/yt/issue/943/derived-fields-not-properly-… Hilary Egan: When creating a profile plot of a derived field, you can't access the derived field unless you originally defined it as ('gas', 'my_field') or ('index', 'my_field'). This is confusing, and I don't think it's supposed to work this way. Example script that does not work: http://paste.yt-project.org/show/5226/ Traceback: http://paste.yt-project.org/show/5227/ Script that fixes the problem: http://paste.yt-project.org/show/5228/

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Doc build timeouts//failures
by Nathan Goldbaum 23 Nov '14

23 Nov '14

Hi all, If anyone has some time this week, it would be great if you could take a look at the latest docs builds: http://tests.yt-project.org/job/yt-docs-3.0/395/console Some of the recipes seem to be triggering tracebacks and the total docs build time now regularly exceeds the 200 min timeout. It would be great if we could bring the total docs build time down - I bet there are a few recipes that are dominating the build time. Thanks for your help getting yt 3.1 out the door. -Nathan

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A plea for failing tests
by Matthew Turk 23 Nov '14

23 Nov '14

Hi all, Cameron and I were chatting, and it looks like only 5/19 of the analysis modules have tests. I think it would be really valuable to have tests -- even failing ones -- so that we can start finishing the job of porting to yt-3.0 all of the analysis modules. So what do you think -- should we start writing some tests designed to fail? -Matt

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Issue #941: CutRegionSelector doesn't work with some data types (yt_analysis/yt)
by Nathan Goldbaum 21 Nov '14

21 Nov '14

New issue 941: CutRegionSelector doesn't work with some data types https://bitbucket.org/yt_analysis/yt/issue/941/cutregionselector-doesnt-wor… Nathan Goldbaum: It turns out the `CutRegionSelector` I recently added doesn't work so well for FLASH data: ``` #!python import yt ds = yt.load("GasSloshing/sloshing_nomag2_hdf5_plt_cnt_0150") dd = ds.all_data() dd = dd.cut_region("obj['density'] > 1e-27") slc = yt.SlicePlot(ds, 2, 'density', data_source=dd) slc.set_zlim('density', 1e-30, 1e-25) slc.set_figure_size(5) slc.save() ``` ![sloshing_nomag2_hdf5_plt_cnt_0150_Slice_z_density.png](https://bitbucket.org/repo/BXbAb/images/3572484347-sloshing_nomag2_hdf5_plt_cnt_0150_Slice_z_density.png) This is happening because `CutRegionSelector` is using a fragile exact comparison between floats. It does this to take advantage of an efficient hashing algorithm, but it looks like this comes at the cost of maintaining bitwise identicality between two different ways of calculating cell positions. The fix is either: 1. Figure out why the FLASH cell position fields are not bitwise identical to the cell positions calculated inside `SelectorObject.fill_mask`. It seems Enzo data is unaffected by the round-off artifacts we see with FLASH data, so we know that means it is possible to rely on the cell positions matching exactly at some level. 2. Use a more forgiving data structure to retrieve matching cell positions. A KD-tree seems like a natural choice, but I'm unsure if there's a ready-to-use KD-tree library available. Responsible: ngoldbaum

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