Mailman 3 March 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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YTUnidentifiedDataType: Could not determine input format
by yurinakazato0207＠g.ecc.u-tokyo.ac.jp 08 Apr '22

08 Apr '22

Hi, I try to make a projection figure by yt. My output data is from ART simulation. I tried the following command , ds = yt.load("../FirstLight/test/FL633_G016.a0.115.dat") but there is an error. YTUnidentifiedDataType: Could not determine input format from `'../FirstLight/test/FL633_G016.a0.115.dat'`. I googled this error and tried ds = yt.load_amr_grids() but still doesn't work. Are there any solutions?

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added field in sphere regions
by HyeonYong Kim 29 Mar '22

29 Mar '22

Hi, everyone I want to utilize data using ds.region function. I have used the CHANGA code-Tipsy dataset, which has 3 particle types - Gas, Stars, Darkmatter. Because there is no particle index, so I added a field this way. ``` ds=yt.load("My data~~") gas_num=np.shape(ds.all_data()['Gas','Mass'])[0] #number of gas particle star_num=np.shape(ds.all_data()['Stars','Mass'])[0] #number of star particle dm_num=np.shape(ds.all_data()['DarkMatter','Mass'])[0] #number of darkmatter particle gas_index=range(gas_num) #gas index star_index=range(gas_num,gas_num+star_num) #star index dm_index=range(gas_num+star_num,gas_num+star_num+dm_num) #darkmatter index all_index=range(gas_num+star_num+dm_num) def _gas_index(field,data): #define index field return (ds.arr(gas_index)) def _star_index(field,data): return (ds.arr(star_index)) def _dm_index(field,data): return (ds.arr(dm_index)) def _all_index(field,data): return (ds.arr(all_index)) yt.add_field( name=("Gas", "particle_index"), function=_gas_index, sampling_type="particle", units="(dimensionless)", ) ds.add_field( name=("Gas", "particle_index"), function=_gas_index, sampling_type="particle", units="(dimensionless)", ) yt.add_field( name=("Stars", "particle_index"), function=_star_index, sampling_type="particle", units="(dimensionless)", ) ds.add_field( name=("Stars", "particle_index"), function=_star_index, sampling_type="particle", units="(dimensionless)", ) yt.add_field( name=("DarkMatter", "particle_index"), function=_dm_index, sampling_type="particle", units="(dimensionless)", ) ds.add_field( name=("DarkMatter", "particle_index"), function=_dm_index, sampling_type="particle", units="(dimensionless)", ) yt.add_field( name=("all", "particle_index"), function=_all_index, sampling_type="particle", units="(dimensionless)", ) ds.add_field( name=("all", "particle_index"), function=_all_index, sampling_type="particle", units="(dimensionless)", ) ``` and then, I made a sphere region to select data in this region. However, the problem is although I made the regions, particle_index returns all datasets. ``` sp=ds.sphere(center,(radius,"kpc")) len(ds.all_data()["DarkMatter","particle_mass"]) -->19584552 len(sp["DarkMatter","particle_mass"]) -->1287749 ``` this is what I expected, but ``` len(ds.all_data()["DarkMatter","particle_index"]) -->19584552 len(sp["DarkMatter","particle_index"]) -->19584552 ``` the particle_index field returns the same value. It seems that this is because I just used array when I define the field function, but I don't have an idea. I would appreciate it if anyone can give me some favors. Thank you for reading! Sincerely, HyeonYong

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How to plot one kind of field value over another field value
by hyf＠stu.pku.edu.cn 26 Mar '22

26 Mar '22

Hi everyone: I want to plot two kinds of field values in one figure and I have searched information about OVERPLOT of YT. It seems that there is no function can do this. I will be appreciated if anyone can give me some suggestions, thank you all! Best wishes, He Yifeng

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Two slices overlaid
by Nick Gnedin 04 Mar '22

04 Mar '22

I wonder if I can plot slices of two fields overlaid, with the top field being partially translucent, so that the bottom field is also visible. Specifically, I would like to show gas density in greyscale, overlaid with the neutral fraction with low opacity and a sequential cmap like "Oranges", then the relation between the gas density and ionized regions will be very visible.

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gcc failure compiling yt
by Michael Zingale 03 Mar '22

03 Mar '22

Hi all, when I try to install the latest yt from source, I get a gcc compilation failure: yt/utilities/lib/image_samplers.cpp: In function ‘PyObject* __Pyx_Coroutine_Send(PyObject*, PyObject*)’: yt/utilities/lib/image_samplers.cpp:36240:19: error: ‘_PyGen_Send’ was not declared in this scope; did you mean ‘_PyGen_yf’? 36240 | ret = _PyGen_Send((PyGenObject*)yf, value == Py_None ? NULL : value); | ^~~~~~~~~~~ | _PyGen_yf yt/utilities/lib/image_samplers.cpp:36245:19: error: ‘_PyGen_Send’ was not declared in this scope; did you mean ‘_PyGen_yf’? 36245 | ret = _PyGen_Send((PyGenObject*)yf, value == Py_None ? NULL : value); | ^~~~~~~~~~~ | _PyGen_yf yt/utilities/lib/image_samplers.cpp: In function ‘PyObject* __Pyx_Generator_Next(PyObject*)’: yt/utilities/lib/image_samplers.cpp:36329:19: error: ‘_PyGen_Send’ was not declared in this scope; did you mean ‘_PyGen_yf’? 36329 | ret = _PyGen_Send((PyGenObject*)yf, NULL); | ^~~~~~~~~~~ | _PyGen_yf Has anyone seen this? I'm using GCC 11.2 and python 3.10. Mike -- Michael Zingale Professor of Physics and Astronomy Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: michael.zingale(a)stonybrook.edu *web*: https://zingale.github.io github: https://github.com/zingale <http://github.com/zingale>

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yt dies/hangs with latest python/conda
by romeeld＠gmail.com 03 Mar '22

03 Mar '22

Hi, I seem to be unable to import yt after I had to upgrade my Anaconda to the latest version. First there was the dreaded cubehelix import error: % python Python 3.9.7 (default, Sep 16 2021, 13:09:58) [GCC 7.5.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information. >>> import yt Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/rad/anaconda3/lib/python3.9/site-packages/yt/__init__.py", line 63, in <module> from yt.fields.api import \ File "/home/rad/anaconda3/lib/python3.9/site-packages/yt/fields/api.py", line 19, in <module> from . import angular_momentum File "/home/rad/anaconda3/lib/python3.9/site-packages/yt/fields/angular_momentum.py", line 26, in <module> from .vector_operations import \ File "/home/rad/anaconda3/lib/python3.9/site-packages/yt/fields/vector_operations.py", line 32, in <module> from yt.geometry.geometry_handler import \ File "/home/rad/anaconda3/lib/python3.9/site-packages/yt/geometry/geometry_handler.py", line 29, in <module> from yt.utilities.parallel_tools.parallel_analysis_interface import \ File "/home/rad/anaconda3/lib/python3.9/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 30, in <module> from yt.data_objects.image_array import ImageArray File "/home/rad/anaconda3/lib/python3.9/site-packages/yt/data_objects/image_array.py", line 18, in <module> from yt.visualization.image_writer import write_bitmap, write_image File "/home/rad/anaconda3/lib/python3.9/site-packages/yt/visualization/image_writer.py", line 26, in <module> from .color_maps import mcm File "/home/rad/anaconda3/lib/python3.9/site-packages/yt/visualization/color_maps.py", line 164, in <module> add_colormap("cubehelix", _cubehelix_data) File "/home/rad/anaconda3/lib/python3.9/site-packages/yt/visualization/color_maps.py", line 52, in add_colormap mcm.register_cmap(name, yt_colormaps[name]) File "/home/rad/anaconda3/lib/python3.9/site-packages/matplotlib/cm.py", line 245, in register_cmap raise ValueError(msg) ValueError: Trying to re-register the builtin cmap 'cubehelix'. >>> I tried a conda update yt, also installing from pip, same result. So I pulled the latest development version and installed it. This doesn't give the cubehelix error, but it simply hangs with no output whenever I try to import (or run) yt. Any suggestions would be appreciated, thanks.

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yt-users March 2022