Mailman 3 April 2018 - yt-users

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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Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

Hi all, Thanks for all your help over the last couple of days. One more question: - Can I plot particles on a volume rendered image? I have stars and I want to show where they are! Thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

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Variance in phase/profiles
by david collins 11 Apr '20

11 Apr '20

Hi, Everybody! Does anyone out there have a technique for getting the variance out of a profile object? A profile object is good at getting <X> vs. B, I'd then like to get < (X - <X>)^2 > vs B. Matt and I had spittballed the possibility some time ago, but I was wondering if anyone out there had successfully done it. Thanks, d. -- Sent from my computer.

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3-D Mass power spectra
by 梁家豪 03 Jun '19

03 Jun '19

Dear yt Can current yt calculate 3-D Mass power spectra? I checked the website but I didn't find any information. I think calculating 3-D Mass power spectra is a very useful for cosmological simulations. So I guess maybe yt supports this function now....? Thanks in advance

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TypeError: only length-1 arrays can be converted to Python scalars
by Guido granda muñoz 02 May '18

02 May '18

Hello yt-users, I'm trying to read 2D flash data using a disk data object. The code is the following: import yt import numpy as np import matplotlib.pyplot as plt def angular_velocity(x,y,vx,vy): r=np.sqrt(x**2+y**2) theta=np.arctan2(y/x) w=(-vx*np.sin(theta)+vy*np.cos(theta))/r return w data_f="/home/guido/FLASH4.5/object/qsub/" data_name="rotator_mhd_2d_hdf5_chk_0015" property="density" field="dynamical_time" ds=yt.load(data_f+data_name) disk=ds.disk(ds.domain_center,[0.0,0.0,1.0],(ds.domain_ center/2.0,'cm'),(1,'cm')) time=ds.current_time.in_units("yr") print("field list \n:",ds.field_list) rp1=yt.create_profile(disk,'radius','temp') And the error I got is: yt : [INFO ] 2018-04-25 19:30:40,053 Particle file found: rotator_mhd_2d_hdf5_chk_0015 yt : [INFO ] 2018-04-25 19:30:40,079 Parameters: current_time = 0.75008895406 yt : [INFO ] 2018-04-25 19:30:40,079 Parameters: domain_dimensions = [8 8 1] yt : [INFO ] 2018-04-25 19:30:40,080 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2018-04-25 19:30:40,080 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2018-04-25 19:30:40,080 Parameters: cosmological_simulation = 0.0 Traceback (most recent call last): File "plot_ang.py", line 28, in <module> rp1=yt.create_profile(disk,'radius','temp') File "/home/guido/.conda/envs/kuro/lib/python3.5/site-packages/yt/data_objects/profiles.py", line 1034, in create_profile for f, l in zip(bin_fields, logs)] File "/home/guido/.conda/envs/kuro/lib/python3.5/site-packages/yt/data_objects/profiles.py", line 1034, in <listcomp> for f, l in zip(bin_fields, logs)] File "/home/guido/.conda/envs/kuro/lib/python3.5/site-packages/yt/data_objects/derived_quantities.py", line 511, in __call__ rv = super(Extrema, self).__call__(fields, non_zero) File "/home/guido/.conda/envs/kuro/lib/python3.5/site-packages/yt/data_objects/derived_quantities.py", line 66, in __call__ for sto, ds in parallel_objects(chunks, -1, storage = storage): File "/home/guido/.conda/envs/kuro/lib/python3.5/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 507, in parallel_objects for result_id, obj in oiter: File "/home/guido/.conda/envs/kuro/lib/python3.5/site-packages/yt/data_objects/data_containers.py", line 1223, in chunks self.get_data() # Ensure we have built ourselves File "/home/guido/.conda/envs/kuro/lib/python3.5/site-packages/yt/data_objects/data_containers.py", line 1266, in get_data self.index._identify_base_chunk(self) File "/home/guido/.conda/envs/kuro/lib/python3.5/site-packages/yt/geometry/grid_geometry_handler.py", line 293, in _identify_base_chunk gi = dobj.selector.select_grids(self.grid_left_edge, File "/home/guido/.conda/envs/kuro/lib/python3.5/site-packages/yt/data_objects/data_containers.py", line 1218, in selector self._selector = sclass(self) File "yt/geometry/selection_routines.pyx", line 1006, in yt.geometry.selection_routines.DiskSelector.__init__ TypeError: only length-1 arrays can be converted to Python scalars I am using : yt ,3.4.1 ,py35_0 And the output of the statistics of the input file used is: $ yt stats ~/FLASH4.5/wind_tunnel/qsub_folder/windtunnel_4lev_hdf5_chk_0000 yt : [INFO ] 2018-04-25 19:33:56,124 Particle file found: windtunnel_4lev_hdf5_chk_0000 yt : [INFO ] 2018-04-25 19:33:56,149 Parameters: current_time = 0.0 yt : [INFO ] 2018-04-25 19:33:56,150 Parameters: domain_dimensions = [120 40 1] yt : [INFO ] 2018-04-25 19:33:56,150 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2018-04-25 19:33:56,150 Parameters: domain_right_edge = [ 3. 1. 1.] yt : [INFO ] 2018-04-25 19:33:56,150 Parameters: cosmological_simulation = 0.0 level # grids # cells # cells^3 ---------------------------------------------- 0 63 4032 16 ---------------------------------------------- 63 4032 t = 0.00000000e+00 = 0.00000000e+00 s = 0.00000000e+00 years Smallest Cell: Width: 8.102e-27 Mpc Width: 8.102e-21 pc Width: 1.671e-15 AU Width: 2.500e-02 cm Could you please help me to find out what I am doing wrong, I'm new to this yt version. Kind Regards, -- Guido

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Tracking current memory usage
by Nick Gnedin 27 Apr '18

27 Apr '18

A newbie question: is there a way to track the current memory usage by yt? I tried searching the docs, but failed to find any info on memory usage. It would be helpful to know it when running yt in the batch mode on clusters, to determine what the minimum possible number of nodes to ask for. Without it, it has to be done by trial and error, and can take a while. Thank you, Nick Gnedin

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Particle Projection Plot: Increase Marker size
by Stephanie Ho 25 Apr '18

25 Apr '18

Hi, For particle projection plots, is there a way to increase the marker size? I am sorry if I overlooked, but I don't seem to see a relevant keyword for marker size under ParticleProjectionPlot (documentation: http://yt-project.org/doc/reference/api/yt.visualization.particle_plots.htm…) Thanks, Stephanie

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Fwd: [numfocus] 2018 John Hunter Excellence in Plotting Contest
by Nathan Goldbaum 25 Apr '18

25 Apr '18

---------- Forwarded message --------- From: Michael Droettboom <mdboom(a)gmail.com> Date: Wed, Apr 25, 2018 at 8:15 AM Subject: [numfocus] 2018 John Hunter Excellence in Plotting Contest To: NumFOCUS <numfocus(a)googlegroups.com> In memory of John Hunter, we are pleased to be reviving the SciPy John Hunter Excellence in Plotting Competition for 2018. This open competition aims to highlight the importance of data visualization to scientific progress and showcase the capabilities of open source software. Participants are invited to submit scientific plots to be judged by a panel. The winning entries will be announced and displayed at the conference. John Hunter’s family and NumFocus are graciously sponsoring cash prizes for the winners in the following amounts: - 1st prize: $1000 - 2nd prize: $750 - 3rd prize: $500 - Entries must be submitted by June, 8th to the form at https://goo.gl/forms/7q86zgu5OYUOjODH3. - Winners will be announced at Scipy 2018 in Austin, TX. - Participants do not need to attend the Scipy conference. - Entries may take the definition of “visualization” rather broadly. Entries may be, for example, a traditional printed plot, an interactive visualization for the web, or an animation. - Source code for the plot must be provided, in the form of Python code and/or a Jupyter notebook, along with a rendering of the plot in a widely used format. This may be, for example, PDF for print, standalone HTML and Javascript for an interactive plot, or MPEG-4 for a video. If the original data can not be shared for reasons of size or licensing, "fake" data may be substituted, along with an image of the plot using real data. - Each entry must include a 300-500 word abstract describing the plot and its importance for a general scientific audience. - Entries will be judged on their clarity, innovation and aesthetics, but most importantly for their effectiveness in communicating a real-world problem. Entrants are encouraged to submit plots that were used during the course of research or work, rather than merely being hypothetical. - SciPy reserves the right to display any and all entries, whether prize-winning or not, at the conference, use in any materials or on its website, with attribution to the original author(s). SciPy John Hunter Excellence in Plotting Competition Co-Chairs Thomas Caswell Michael Droettboom Nelle Varoquaux -- You received this message because you are subscribed to the Google Groups "NumFOCUS" group. To unsubscribe from this group and stop receiving emails from it, send an email to numfocus+unsubscribe(a)googlegroups.com. For more options, visit https://groups.google.com/d/optout.

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ANN: ytree 2.1 released
by Britton Smith 20 Apr '18

20 Apr '18

Hello! I am very happy to announce the release of version 2.1 of ytree! ytree <https://github.com/brittonsmith/ytree> is an extension of yt <http://yt-project.org/> for working with merger-tree data from multiple sources. For a brief example of using ytree, see this notebook <https://github.com/brittonsmith/ytree/blob/master/doc/source/notebooks/Intr…> . This release of ytree adds two new supported formats: - *LHaloTree* (thanks to Meagan Lang) - *Amiga Halo Finder* In addition to the new formats, i/o and field access in the native ytree format has been significantly optimized. ytree can be installed with pip: pip install ytree or from source, by going to https://github.com/brittonsmith/ytree git clone https://github.com/brittonsmith/ytree cd ytree pip install -e . Full documentation can be found at http://ytree.readthedocs.io/. The following people contributed to this release (new in bold): *Meagan Lang* *Bili Dong* Britton Smith Many thanks to the amazing yt project, whose community and code have made this possible.

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Enquire about the lightcore
by lianxiaoli87 19 Apr '18

19 Apr '18

Dear all: When I use the command Lightcore like: lc = LightCone('data/enzo_tiny_cosmology/32Mpc_32.enzo', 'Enzo', 0., 0.1, observer_redshift=0.0, time_data=False) I want to make a lightcore for Gadget simulation, so I change it as: lc = LightCone('multiphys.params', 'Gadget', 0., 0.1, observer_redshift=0.0, time_data=False) The command with Enzo can works well, while after changing to Gadget, it received a error report like: AttributeError: 'GadgetSimulation' object has no attribute 'all_redshift_outputs' May I know the reason for this, and does tihs command (Lightcore) apply only to the simulation with Enzo? Best Regards Xiaoli Lian

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