Mailman 3 April 2014 - yt-dev

Issue #831: 'kamae' colormap raises IndexError in matplotlib (yt_analysis/yt)
by Kacper Kowalik April 22, 2014

April 22, 2014

New issue 831: 'kamae' colormap raises IndexError in matplotlib https://bitbucket.org/yt_analysis/yt/issue/831/kamae-colormap-raises-indexe… Kacper Kowalik: Following script: ``` #!python from yt.mods import load, SlicePlot pf = load("IsolatedGalaxy/galaxy0030/galaxy0030") slc = SlicePlot(pf, 2, "density") slc.set_cmap("density", "kamae") slc.save() ``` yields: ``` #!text Traceback (most recent call last): File "ala.py", line 8, in <module> slc.save() File "/home/xarth/… [View More]codes/yt-my/yt/visualization/plot_container.py", line 443, in save names.append(v.save(n, mpl_kwargs)) File "/home/xarth/codes/yt-my/yt/visualization/base_plot_types.py", line 84, in save canvas.print_figure(name, **mpl_kwargs) File "/usr/lib64/python2.7/site-packages/matplotlib/backend_bases.py", line 2220, in print_figure **kwargs) File "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py", line 505, in print_png FigureCanvasAgg.draw(self) File "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py", line 451, in draw self.figure.draw(self.renderer) File "/usr/lib64/python2.7/site-packages/matplotlib/artist.py", line 54, in draw_wrapper draw(artist, renderer, *args, **kwargs) File "/usr/lib64/python2.7/site-packages/matplotlib/figure.py", line 1034, in draw func(*args) File "/usr/lib64/python2.7/site-packages/matplotlib/artist.py", line 54, in draw_wrapper draw(artist, renderer, *args, **kwargs) File "/usr/lib64/python2.7/site-packages/matplotlib/axes.py", line 2086, in draw a.draw(renderer) File "/usr/lib64/python2.7/site-packages/matplotlib/artist.py", line 54, in draw_wrapper draw(artist, renderer, *args, **kwargs) File "/usr/lib64/python2.7/site-packages/matplotlib/image.py", line 364, in draw im = self.make_image(renderer.get_image_magnification()) File "/usr/lib64/python2.7/site-packages/matplotlib/image.py", line 588, in make_image transformed_viewLim) File "/usr/lib64/python2.7/site-packages/matplotlib/image.py", line 204, in _get_unsampled_image x = self.to_rgba(self._A, bytes=False) File "/usr/lib64/python2.7/site-packages/matplotlib/cm.py", line 261, in to_rgba x = self.cmap(x, alpha=alpha, bytes=bytes) File "/usr/lib64/python2.7/site-packages/matplotlib/colors.py", line 542, in __call__ self._init() File "/usr/lib64/python2.7/site-packages/matplotlib/colors.py", line 724, in _init self.N, self._segmentdata['red'], self._gamma) File "/usr/lib64/python2.7/site-packages/matplotlib/colors.py", line 449, in makeMappingArray if len(shape) != 2 and shape[1] != 3: IndexError: tuple index out of range ``` with ``` #!text $ yt instinfo yt module located at: /home/xarth/codes/yt-my The current version and changeset for the code is: --- Version = 3.0-dev Changeset = 71196d4289bf --- This installation CAN be automatically updated. Could not determine when yt stack was last updated. $ python -c 'import matplotlib; print matplotlib.__version__' 1.3.0 ``` [View Less]

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Issue #830: Number density is only defined for multispecies datasets (yt_analysis/yt)
by Nathan Goldbaum April 21, 2014

April 21, 2014

New issue 830: Number density is only defined for multispecies datasets https://bitbucket.org/yt_analysis/yt/issue/830/number-density-is-only-defin… Nathan Goldbaum: Right now querying the `number_density` field raises an IndexError in the field definition for a single fluid/color dataset. The following diff fixes the issue for me and my enzo datasets, but clearly isn't the correct solution for all supported codes: ``` #!diff diff -r 71196d4289bf yt/fields/fluid_fields.py --- a/yt/fields/… [View More]

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parallel_objects not freeing communicators?
by Josh Moloney April 18, 2014

April 18, 2014

I have a script that I'm using to perform various analysis functions on halos from an Enzo simulation. In this script I'm using parallel_objects to split the halos up among multiple processors. for sto, halo in parallel_objects(halos, num_procs, storage=halo_props): sto.result_id = halo.id sto.result = analyze_halo(pf, halo, radius, old_time, current_time, f_ej) within analyze_halo I use WeightedAverageQuantity on a region containing each halo, which from what I understand … [View More]

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covering_grid and BCs
by Michael Zingale April 18, 2014

April 18, 2014

If I create a covering_grid for a full domain that is not triply-periodic, the code will abort when I try to access the data in the covering grid with an error generated by selection_routines.pyx that is looking to make sure that the boundary conditions are supported. I understand that this support is not yet in place, but I don't think that it should be an issue for a covering_grid. The covering grid procedure itself should not ever need boundary conditions, if I understand what it intends … [View More]

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power spectra in yt
by Michael Zingale April 17, 2014

April 17, 2014

Dear yters, I am interested in using yt to do power spectra for analyzing turbulence in our simulations. I quickly coded up a script to do this (warning: I haven't verified this, so some of the normalization may be wrong, but it doesn't assume a cubic domain, and it looked ok by eye): http://paste.yt-project.org/show/4528/ The caveat is that we need to put this onto a uniform grid to do the FFT, but then we can use the numpy FFT routines. I think that it would be nice to have some sort of … [View More]

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TipsyDataset Will Not Load, and Requires Parameter File
by Cameron Hummels April 16, 2014

April 16, 2014

Hi everyone, I was trying to use yt 3.0 with the Gasoline sample dataset that we have available on http://yt-project.org/data , and it fails in two ways: 1) yt cannot figure out what the dataset is using the simple "load" command as in: from yt.mods import * ds = load(filename) ... yt.utilities.exceptions.YTOutputNotIdentified: Supplied ('agora_1e11.0040',) {}, but could not load! 2) When I manually ask it to see the file as a TipsyDataset, it also fails, as it expects parameters to be … [View More]

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Python 3 PR part 1
by Matthew Turk April 16, 2014

April 16, 2014

Hi all, Here's part one of getting yt to run on Python 3. Reviews welcome! https://bitbucket.org/yt_analysis/yt/pull-request/828/python-3-compatibilit… Once this is accepted, we should also pull in a no-op merge. I started my efforts on yt-2.x, but then moved to yt-3.0 today. -Matt

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Cheatsheet link 404s
by B.W. Keller April 16, 2014

April 16, 2014

Hey all, The link to the yt cheatsheet on the main webpage is dead. Is a new one being made or something? Ben

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Orientation, coordinate systems
by Matthew Turk April 15, 2014

April 15, 2014

Hi all, I'd like to open up the discussion of "fixing" the yt coordinate systems, as we move nearer and nearer on 3.0. Jeff, Nathan and Britton have brought this up a couple times, that the x/y/z ordering is not consistent with what they expect, and I'd like to figure out if we can fix that now -- it's as good a time as any for bandaid ripping. It may just be a matter of the transposition of buffers and the x_dict and y_dict, or it might be more complex, although I suspect it won't be much … [View More]

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problem with non-periodic domain and rendering
by Michael Zingale April 15, 2014

April 15, 2014

Recently I made the Maestro BoxLib frontend set the correct boundary periodicity for a data set, and I can confirm this when I load the data in yt and look at periodicity. However, when I try to volume render, with no_ghost=False, I get an error in the non-periodic direction (we are periodic in x and y, and non-periodic in z). The error is: Error: bad Region in non-periodic domain: -24.0 code_length 0.0 code_length 408.0 code_length 4608.0 code_length for reference, the domain size is: … [View More]

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