Mailman 3 - yt-users

Off-Axis SlicePlot Error with TNG data in yt
by 缘边 15 Mar '24

15 Mar '24

Hi I've recently started using yt for visualizing the gas density of TNG galaxies with an OffAxisSlicePlot. I want the top of the image to align with the galaxy's velocity direction [0.9196489, 0.15788311, -0.35960928], so I set north_vector = [0.9196489, 0.15788311, -0.35960928]. The projection direction is the normal vector perpendicular to the galaxy's velocity direction. Here's my code snippet: c = ds.arr([Subhalo["SubhaloPos"][0], Subhalo["SubhaloPos"][1], Subhalo["SubhaloPos"][2]], "code_length") a = np.array([0.9196489, 0.15788311, -0.35960928]) # Choose a simple vector that is not collinear with 'a' b = np.array([0, 0, 1]) # For example, the unit vector along the z-axis # Calculate the cross product to get the perpendicular vector v_perpendicular = np.cross(a, b) slc = yt.SlicePlot(ds, v_perpendicular, ("gas","density"), width=(300, "kpc"), center=c, north_vector=a) However, I keep encountering this error: YTNonIndexedDataContainer: The data container type (ParticleContainer) is an unindexed type. Operations such as ires, icoords, fcoords, and fwidth will not work on it. Did you just attempt to perform an off-axis operation? Be sure to consult the latest documentation to see whether the operation you tried is actually supported for your data type. Has anyone faced a similar issue or can suggest a workaround? Is there a specific approach to making off-axis plots for particle data in yt?

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Spherical harmonic decomposition of sphere surface
by Samuel Patrick 15 Mar '24

15 Mar '24

Hi all, I would like to perform a spherical harmonic decomposition of the density within a spherical shell, essentially a Fourier transform of the density (or any scalar quantity) on the surface of a sphere object . I'm aware of python libraries like Healpy which have functions such as map2alm which take a healpix map and return the corresponding Alm coefficients; are there any utilities within yt that can either do this directly or return a healpix map from a sphere object? Thanks and best, Sam Patrick The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

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Change the center position while using plot_2d function.
by vashishthanitin5＠gmail.com 04 Mar '24

04 Mar '24

Hi yt Team, I am not able to change the centre position of the selection while plotting the density from a simulation output file using yt.plot_2d function. It is taking the domain centre as the centre value, even if I change it. I am also not able to change the origin of the output plot as well. Following is the code, please look into it. The output file is from amrvac code. It is the output of a 2.5 MHD code in spherical geometry. My domain centre values are [5.5 1.5707963267948966 0.5] code_length. Basically, r goes from 1 to 10 and theta from 0 to pi. path = "path" file = "filepath" ds = yt.load(file, geometry_override="Spherical_2.5D",parfiles= path + "amrvac.par", units_override = units_override, unit_system="mks") p = yt.plot_2d(ds,("gas","density"),center= [2.0,1.5707963267948966,0],width = (2.0,2.0)) after applying this, my plot range from 4.0 to 6.0 in x direction and from -1.0 to 1.0 in y direction. Please help. Thanks.

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FLIP IN A MULTI PLOT
by FERNANDO ILLACANCHI GUERRA 27 Feb '24

27 Feb '24

Hi Everyone, I have a simulation with an axis symmetry so i want to plor full simulation using the flip function. However, both plots are flipped in te resulting imagen. Is there a way to flip just one of them? Thanks in advance. for i in range(0,2): print(i) # Load the data and create a single plot ds = yt.load(fn) # load data p = yt.plot_2d(ds, ("Temp")) p.set_width((4,1)) if i == 1: p.flip_vertical() print("vertical") # This forces the ProjectionPlot to redraw itself on the AxesGrid axes. plot = p.plots[("Temp")] plot.figure = fig plot.axes = grid[i].axes plot.cax = grid.cbar_axes[i] # Finally, this actually redraws the plot. p.render() plt.savefig("multiplot_2x2_time_series.png")

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yt notebook
by Daniel Ruvalcaba 27 Feb '24

27 Feb '24

Hello I am currently trying to install and setup yt on my laptop using the miniconda/anaconda/pip/whatever will work and I keep running into the issue of not being able to open my yt notebook. For pip/git it does not accept the command and for miniconda/anaconda it keeps giving me this error: Traceback (most recent call last): File "C:\ProgramData\miniconda3\Scripts\yt-script.py", line 10, in <module> sys.exit(run_main()) ^^^^^^^^^^ File "C:\Users\.\AppData\Roaming\Python\Python311\site-packages\yt\utilities\command_line.py", line 1613, in run_main args.func(args) File "C:\Users\.\AppData\Roaming\Python\Python311\site-packages\yt\utilities\command_line.py", line 223, in run self(args) File "C:\Users\.\AppData\Roaming\Python\Python311\site-packages\yt\utilities\command_line.py", line 1071, in __call__ from notebook.notebookapp import NotebookApp ModuleNotFoundError: No module named 'notebook.notebookapp' I have tried downloading various notebook software both onto this computer and from the conda install to no luck. I am stuck and would really appreciate help so I can resolve this issue. Thank you, Daniel

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updating list of yt extensions and external frontends
by Chris Havlin 21 Feb '24

21 Feb '24

Hi there! Do you use or maintain a yt extension or externally packaged frontend that is not part of the main yt package? I'm working on updating the docs to include a more current list so if you're aware of any not yet listed in https://github.com/yt-project/yt/issues/4824 I'd appreciate a note! Best, Chris

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Error in Loading vtk Files
by A. Lam 13 Feb '24

13 Feb '24

Dear yt Dev Team, Hope this email finds you well! I am writing to seek assistance regarding an issue I encountered while attempting to load vtk files. Specifically, I am trying to extract data from vtk files generated by athena simulations using the ds.load function. However, the code returned the following error message, Traceback (most recent call last): File "/home/wkal2/rds/hpc-work/project/code/plot.py", line 13, in <module> ds = yt.load(vtk_filename,parameters=parameters) File "/home/wkal2/ENTER/envs/ml/lib/python3.9/site-packages/yt/_maintenance/deprecation.py", line 69, in inner return func(*args, **kwargs) File "/home/wkal2/ENTER/envs/ml/lib/python3.9/site-packages/yt/loaders.py", line 144, in load return cls(fn, *args, **kwargs) File "/home/wkal2/ENTER/envs/ml/lib/python3.9/site-packages/yt/frontends/athena/data_structures.py", line 488, in __init__ Dataset.__init__( File "/home/wkal2/ENTER/envs/ml/lib/python3.9/site-packages/yt/data_objects/static_output.py", line 293, in __init__ self._parse_parameter_file() File "/home/wkal2/ENTER/envs/ml/lib/python3.9/site-packages/yt/frontends/athena/data_structures.py", line 572, in _parse_parameter_file self.domain_dimensions[2] = np.int32(1) ValueError: assignment destination is read-only I would greatly appreciate any insights you can provide on what might be causing this issue with the code. For your reference, I am using yt version 4.3.0. Thank you for your attention and I look forward to hearing from you! Best regards, Amelie Lam

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Follow-Up: Error in Loading vtk Files - Urgent Response Needed
by A. Lam 13 Feb '24

13 Feb '24

Dear yt Dev Team, Hope this email finds you well! I am reaching out to follow up on my previous email with the subject "Error in Loading vtk Files." Unfortunately, I have not received any response thus far, except for an automated message stating that my email is pending approval from the list moderator. Given the urgency of the matter at hand, I kindly request your prompt attention to this issue. Your assistance in addressing this matter would be greatly appreciated. If there are any additional details or information needed from my end to expedite the process, please do not hesitate to let me know. Thank you for your understanding and I look forward to hearing from you soon! Best regards, Amelie Lam

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Loading a SWIFT .hdf5 snapshot using latest version of yt
by hannah.obrennan.2021＠mumail.ie 30 Jan '24

30 Jan '24

Has anyone recently been able to load a SWIFT snapshot using yt.load? I created a conda env using python=3. I installed the latest version of yt using: conda install -c conda-forge yt I installed h5py using: conda install h5py I also installed yt_astro_analysis (to use HaloCatalog later) using: git clone https://github.com/yt-project/yt_astro_analysis; cd yt_astro_analysis; python -m pip install -e . I attempted to create a Dataset using yt.load("SWIFT_filename.hdf5") and found the following error: Traceback (most recent call last): File "/data/regan_data/Hannah_WS/Halo_mass_function_project/2023-10_11_12/FOF_Rockstar_comparison/hc_creation.py", line 62, in <module> data_ds = yt.load(dir_name) ^^^^^^^^^^^^^^^^^ File "/home/hannah/anaconda3/envs/yt-10_01_2024/lib/python3.12/site-packages/yt/_maintenance/deprecation.py", line 69, in inner return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/hannah/anaconda3/envs/yt-10_01_2024/lib/python3.12/site-packages/yt/loaders.py", line 144, in load return cls(fn, *args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/hannah/anaconda3/envs/yt-10_01_2024/lib/python3.12/site-packages/yt/frontends/swift/data_structures.py", line 36, in __init__ super().__init__( File "/home/hannah/anaconda3/envs/yt-10_01_2024/lib/python3.12/site-packages/yt/frontends/sph/data_structures.py", line 34, in __init__ super().__init__( File "/home/hannah/anaconda3/envs/yt-10_01_2024/lib/python3.12/site-packages/yt/data_objects/static_output.py", line 2123, in __init__ super().__init__( File "/home/hannah/anaconda3/envs/yt-10_01_2024/lib/python3.12/site-packages/yt/data_objects/static_output.py", line 293, in __init__ self._parse_parameter_file() File "/home/hannah/anaconda3/envs/yt-10_01_2024/lib/python3.12/site-packages/yt/frontends/swift/data_structures.py", line 100, in _parse_parameter_file runtime_parameters = self._get_info_attributes("RuntimePars") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/hannah/anaconda3/envs/yt-10_01_2024/lib/python3.12/site-packages/yt/frontends/swift/data_structures.py", line 84, in _get_info_attributes header = dict(handle[dataset].attrs) ~~~~~~^^^^^^^^^ File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "/home/hannah/anaconda3/envs/yt-10_01_2024/lib/python3.12/site-packages/h5py/_hl/group.py", line 357, in __getitem__ oid = h5o.open(self.id, self._e(name), lapl=self._lapl) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5o.pyx", line 190, in h5py.h5o.open KeyError: "Unable to open object (object 'RuntimePars' doesn't exist)" When I examine the keys from the .hdf5 file in python, I find: >>> import h5py >>> f = h5py.File('../SWIFT__0.5_cMpc_h/N_512/RedshiftOutput0002.hdf5') >>> list(f.keys()) ['Cells', 'Code', 'Cosmology', 'DMParticles', 'GravityScheme', 'Header', 'InternalCodeUnits', 'Parameters', 'PartType1', 'PhysicalConstants', 'Policy', 'SubgridScheme', 'Units', 'UnusedParameters'] 'RuntimePars' is not one of the keys listed. Strangely, I was able to load the snapshot successfully on 12/12/2023 but cannot now, nor can I load any others. This is the same error found by Romeel Davé (January 2022) in https://mail.python.org/archives/list/yt-users@python.org/message/NUKRAWV7J… Any help with would be much appreciated, thank you! - Hannah

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help
by 张小霞 13 Dec '23

13 Dec '23

Hi, I have a problem when using yt to obtain the X-ray luminosity of a simulated region. I found that yt 4.3 and yt 4.4 give very different results, i.e., about 5 vs. 10 (* 1e39 erg/s). Do you know what causes this difference? Here is the code. Thanks! import yt ds = yt.load('snapshot_155.hdf5') xray_fields = yt.add_xray_emissivity_field(ds, 0.5, 2.0, table_type='apec', metallicity=1.0) sp = ds.sphere("c", (100.0, "kpc")) shpere= sp.quantities.total_quantity("xray_luminosity_0.5_2.0_keV") print(shpere) Best, Dr. Xiaoxia Zhang (张小霞) Department of Astronomy Xiamen University

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