Mailman 3 May 2022 - yt-users

enzo-mrp-music/get_halo_initial_extent.py not working with yt 4.0.1
by C Bernhardt 02 Jun '23

02 Jun '23

Dear yt users, I just updated yt to 4.0.1 and now I get this error message when trying to run enzo-mrp-music.py from John Wise on https://github.com/jwise77/enzo-mrp-music. Traceback (most recent call last): File "enzo-mrp-music/enzo-mrp-music.py", line 264, in <module> params = find_lagrangian_region(params) File "enzo-mrp-music/enzo-mrp-music.py", line 177, in find_lagrangian_region get_center_and_extent(params["halo_info"], File "enzo-mrp-music/get_halo_initial_extent.py", line 147, in get_center_and_extent halo_indices, halo_com, shifted = get_halo_indices(my_halo, final_dataset, File "enzo-mrp-music/get_halo_initial_extent.py", line 119, in get_halo_indices get_halo_sphere_particles(my_halo, dataset, radius_factor=radius_factor) File "enzo-mrp-music/get_halo_initial_extent.py", line 73, in get_halo_sphere_particles my_sphere = pf.h.sphere(my_halo_data['center'], radius_factor * r_200) AttributeError: 'EnzoDataset' object has no attribute 'h' I am honestly not sure what the attribute 'h' does in this case, so I didn't know what to try to adjust. Any suggestions for getting around this? Or how can I go back to yt 3? Kind regards, -- Carla Bernhardt PhD Student Universität Heidelberg ZAH Institut für Theoretische Astrophysik

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Porting .ply files to Blender with colors?
by Jill P. Naiman 14 Aug '22

14 Aug '22

Hi All, I was curious if anyone has had any luck porting .ply files generated with yt into Blender with colors? It seems to port in the surfaces just fine, but they are a uniform color. From what I can gather, Blender imports .ply files with face color instead of vertex so I tried the surf.export_ply routine with "face" instead of "vertex" for sample_type, but no luck ("vertex" doesn't work either). Let me know if I can provide any more useful info. Thanks for any help, -J

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ANN: yt 4.0.4 is now available
by Clément Robert 27 May '22

27 May '22

yt 4.0.4 is out ! This is a bugfix release. Most notably it fixes (future) compatibility with matplotlib 3.6, as well as a couple minor bugs. It is available on PyPI and conda-forge. See the release notes for how to upgrade https://github.com/yt-project/yt/releases/tag/yt-4.0.4 Happy data crunching Clément

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Axis symmetry for cylindrical (r-z) mesh
by benbayer.kouider＠gmail.com 25 May '22

25 May '22

Hi all. I want ti do a simulation with FLASH data in 2D cylindrical (r-z) In FLASH code the r axis it's always greater than zero in 2D cylindrical mesh (0<r<500) um i want to do simulation for (-500<r<500 um) using symmetry of axis. How can do that with yt My best regards.

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Runtime error when plot derived field
by hyf＠stu.pku.edu.cn 12 May '22

12 May '22

Hi everyone: I met trouble when I tried to plot derived vorticity field in yt. The dataset is written in AMRex form (multiple layers). However, it will call Runtimeerror raised by "in _fill_fields" in construction_data_containers.py. I will be appreciate if anyone can give me some suggestions! -------------------------------------------------------------------------------------------------------------------------------------------- Here is python command in brief (ds is dataset, u,v are velocity component in x, y direction, vor_z is Vorticity in z direction): for ds in ts.piter(): ds.periodicity=(False,False,False) u_gradient = ds.add_gradient_fields(("boxlib","u_mixt")) v_gradient = ds.add_gradient_fields(("boxlib","v_mixt")) derived_fields = [ # field name, units, displayname ('vort_z', '1 / cm', 'Vorticity in z direction'), ] for name, unitstr, dispname in derived_fields: ds.add_field( ('boxlib', name), units = unitstr, function = eval(name + '_func'), sampling_type = 'cell', display_name = dispname ) chang =0.112 kuan =0.056 slc = yt.SlicePlot(ds, 'z', 'vort_z', width=((chang,'cm'),(kuan,'cm')),center=([0.48,0.028,0.01],'cm')) slc.save() ------------------------------------------------------------------------------------------------------------------------ Here is the error info: yt : [ERROR ] RuntimeError: 1005 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 1006 File "vorfield.py", line 90, in <module> 1007 slc = yt.SlicePlot(ds, 'z', 'vort_z', width=((chang,'cm'),(kuan,'cm')),center=([0.46,0.028,0.01],'cm')) 1008 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/visualization/plot_window.py", line 1986, in SlicePlot 1009 return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs) 1010 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/visualization/plot_window.py", line 1282, in __init__ 1011 slc.get_data(fields) 1012 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 1583, in get_data 1013 self._generate_fields(fields_to_generate) 1014 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 1603, in _generate_fields 1015 fd = self._generate_field(field) 1016 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 293, in _generate_field 1017 tr = self._generate_fluid_field(field) 1018 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 311, in _generate_fluid_field 1019 rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) 1020 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 341, in _generate_spatial_fluid 1021 gz[field][ngz:-ngz, ngz:-ngz, ngz:-ngz], 1022 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 256, in __getitem__ 1023 self.get_data(f) 1024 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/construction_data_containers.py", line 691, in get_data 1025 if len(fill) > 0: self._fill_fields(fill) 1026 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/construction_data_containers.py", line 1060, in _fill_fields 1027 raise RuntimeError best wishes, He Yifeng

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get_topmost_subplotspec error while customizing plot
by Guido Granda Muñoz 11 May '22

11 May '22

Hello, I'm trying to change the appearance of a multiplot created with yt for publication. I'm using the example https://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=panel… and I just added two lines at the beginning. These are : import os import matplotlib.pyplot as plt dirFile='/fs/posgrado04/other0/guido/python_tools/plot_styles' plt.style.use(os.path.join(dirFile,'paper_fig.mplstyle')) The content of the style file is the following: xtick.labelsize:16 ytick.labelsize:16 font.size:15 figure.autolayout: True figure.figsize: 7.2,4.45 axes.titlesize : 16 axes.labelsize : 17 lines.linewidth : 2 lines.markersize : 6 legend.fontsize: 13 mathtext.fontset: stix font.family: STIXGeneral After running the code, I get the following error:: Traceback (most recent call last): File "multiplot_2x2_time_series.py", line 54, in <module> plt.savefig("multiplot_2x2_time_series_style.png") File "/fs/posgrado04/other0/guido/yt-conda/lib/python3.8/site-packages/matplotlib/pyplot.py", line 859, in savefig res = fig.savefig(*args, **kwargs) File "/fs/posgrado04/other0/guido/yt-conda/lib/python3.8/site-packages/matplotlib/figure.py", line 2311, in savefig self.canvas.print_figure(fname, **kwargs) File "/fs/posgrado04/other0/guido/yt-conda/lib/python3.8/site-packages/matplotlib/backend_bases.py", line 2210, in print_figure result = print_method( File "/fs/posgrado04/other0/guido/yt-conda/lib/python3.8/site-packages/matplotlib/backend_bases.py", line 1639, in wrapper return func(*args, **kwargs) File "/fs/posgrado04/other0/guido/yt-conda/lib/python3.8/site-packages/matplotlib/backends/backend_agg.py", line 509, in print_png FigureCanvasAgg.draw(self) File "/fs/posgrado04/other0/guido/yt-conda/lib/python3.8/site-packages/matplotlib/backends/backend_agg.py", line 407, in draw self.figure.draw(self.renderer) File "/fs/posgrado04/other0/guido/yt-conda/lib/python3.8/site-packages/matplotlib/artist.py", line 41, in draw_wrapper return draw(artist, renderer, *args, **kwargs) File "/fs/posgrado04/other0/guido/yt-conda/lib/python3.8/site-packages/matplotlib/figure.py", line 1857, in draw self.tight_layout(**self._tight_parameters) File "/fs/posgrado04/other0/guido/yt-conda/lib/python3.8/site-packages/matplotlib/cbook/deprecation.py", line 411, in wrapper return func(*inner_args, **inner_kwargs) File "/fs/posgrado04/other0/guido/yt-conda/lib/python3.8/site-packages/matplotlib/figure.py", line 2601, in tight_layout subplotspec_list = get_subplotspec_list(self.axes) File "/fs/posgrado04/other0/guido/yt-conda/lib/python3.8/site-packages/matplotlib/tight_layout.py", line 197, in get_subplotspec_list subplotspec = subplotspec.get_topmost_subplotspec() AttributeError: 'NoneType' object has no attribute 'get_topmost_subplotspec' This kind of error only appears when using AxisGrid, have you seen sth similar ? Regards,

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yt-napari follow up poll!
by Chris Havlin 06 May '22

06 May '22

Hello! If you've had a chance to try out yt-napari, or even if you're interested but haven't gotten around to it, I'd love to hear what you think (link to yt-napari in case you missed it: https://github.com/data-exp-lab/yt-napari ) Do you have ideas for analyses you might want to do from within napari? Suggestions for improvements? Ways we might help you get started with using it? I'd love to hear your thoughts! Feel free to email back or find me on slack, but I also created a poll : https://pollunit.com/polls/plijx3w15wnjwvriilr1ca You can upvote any number of the listed ideas there, comment on ideas or add your own ideas (which others can see and vote on). So head on over if you have a moment and are interested in yt-napari! Much appreciated, Chris Havlin

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yt-napari is released!
by Chris Havlin 03 May '22

03 May '22

Hello yt-users! I wanted to draw your attention to the newly released yt-napari plugin! The yt-napari plugin facilitates loading selections from yt datasets into napari (https://napari.org/), giving yt users a new way to interactively explore their data! The current release includes methods for loading data into napari from a Jupyter notebook, from the napari GUI and from a schema-based json file. If you'd like to take it for a spin, you can checkout the examples and installation instructions at the github repository ( https://github.com/data-exp-lab/yt-napari) or full documentation site ( https://yt-napari.readthedocs.io/en/latest/). If you do try it out, please let us know what you think! Feel free to report issues via github or reach out directly via email or the yt-slack. And while you’re testing it out, keep in mind that while this release focuses on reading and loading data, there is ample opportunity for additional yt-napari plugins that focus more on analysis once data is loaded. So if you have ideas or if you’re interested in writing your own napari plugins for yt and want a hand getting started, please reach out! Finally, a big thank you to the Chan Zuckerberg Initiative for supporting development of the yt-napari plugin through the napari Plugin Accelerator Grants program! Best, Chris Havlin

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